title: B10500-A8_BS_single

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

library_source: genomic

data_processing:
Read pairs were merged with PEAR. Assembled reads were mapped to the reference fasta file using Bismark with the --non_directional flag. Methylation status per CpG per read was extracted using bismark_methylation_extractor, and then summarized to a total count, methylated count, and % methylation per CpG for all reads in the sample.
Genome_build: Custom: HBV genomic sequence derived from subtype ayw (ACCESSION No: V01460 J02203). Mouse amplicon sequences derived from mm10.
Supplementary_files_format_and_content: Content: contains total read counts, methylated read counts, and % methylation for each CpG in each sample.
Supplementary_files_format_and_content: Content: reference genomic sequences for HBV and mouse sequences.

molecule: genomic DNA

organism:
Mus musculus
Hepatitis B virus

source_name: Mouse liver protein-free genomic DNA

growth_protocol: Standard mouse breeding

extract_protocol:
Protein-free mouse genomic DNA was isolated from liver tissue as described (McFadden, V.C., Shalaby, R.E., Iram, S., Oropeza, C.E., Landolfi, J.A., Lyubimov, A.V., Maienschein-Cline, M., Green, S.J., Kaestner, K.H., and McLachlan, A. (2017). PLOS Pathogens 13, e1006239).
BS only: Genomic DNA for methylation analysis was performed using the EZ DNA Methylation-Lightning™ Kit (D5030; Zymo Research, Inc., Irvine, CA, USA)
OxBS + BS: Genomic DNA for separate methylation analysis of 5hmC and 5mC levels was performed using TrueMethyl oxBS module kit (0414-32; NuGEN Technologies, Inc., Redwood City, CA, USA).
amplification and sequencing: The CpG sequences in the HBV DNA genome were targeted using PCR amplification of the bisulfite- and oxidative-bisulfite treated DNA, followed by sequencing of the amplicons on an Illumina MiSeq instrument.  Preparation of DNA for high-throughput amplicon sequencing was performed in two PCR steps as described previously (McFadden et al. 2017).  Twelve HBV primer pairs targeting 94 of the 99 CpG sites were used.   The primer pairs targeting the bisulfite converted HBV DNA were (i) 5’-ACACTGACGACATGGTTCTACACAATACCTAAACCTTTACCC-3’ (oligo CS1FP1; HBV nucleotide coordinates 1131-1150) and 5’-TACGGTAGCAGAGACTTGGTCTGTTTTAGTTAGTGGGGGT-3’ (oligo CS2RP1; HBV coordinates 1214-1197), (ii) 5’-ACACTGACGACATGGTTCTACACAAACTTTCACTTTCTC-3’ (oligo CS1FP1a; HBV coordinates 1086-1102) and 5’-TACGGTAGCAGAGACTTGGTCTGTTGATGGTTTATGATTAA (oligo CS2RP1a; HBV coordinates 1233-1215), (iii) 5’-ACACTGACGACATGGTTCTACACCCCCACTAACTAAAAC-3’ (oligo CS1FP2; HBV nucleotide coordinates 1198-1214) and 5’-TACGGTAGCAGAGACTTGGTCTGGGTAATATTTGGTGG-3’ (oligo CS2RP2; HBV nucleotide coordinates 1645-1630), (iv)                                                   5’-  ACACTGACGACATGGTTCTACATTAAACTCTCAACAATATCA-3’ (oligo CS1FP3; HBV nucleotide coordinates 1668-1687) and 5’-TACGGTAGCAGAGACTTGGTCTAAGTTATTTAAGGTATAGTTTG-3’                                                             (oligoCS2RP3; HBV nucleotide coordinates 1896-1875), (v) 5’-ACACTGACGACATGGTTCTACAGTGGTTTTGGGGTATGG-3’ (oligo CS1FP4; HBV nucleotide coordinates 1890-1906) and 5’-TACGGTAGCAGAGACTTGGTCTCAAATTAACACCCACCC-3’ (oligo CS2RP4; HBV nucleotide coordinates 2130-2114), (vi) 5’-ACACTGACGACATGGTTCTACAAGTTATAGAGTATTTGGTGT-3’ (oligo CS1FP5a; HBV nucleotide coordinates 2244-2263) and 5’-TACGGTAGCAGAGACTTGGTCTCCCAATAAAATTCCCCA-3’ (oligo CS2RP5a; HBV nucleotide coordinates 2491-2475), (vii) 5’- ACACTGACGACATGGTTCTACAGATTGTAATTGATTATGTTTG -3’ (oligo CS1FP6; HBV nucleotide coordinates 2625-2645) and 5’- TACGGTAGCAGAGACTTGGTCTCCATACTATAAATCTTATTCCC-3’ (oligo CS2RP6; HBV nucleotide coordinates 2832-2853), (viii)                      5’-  ACACTGACGACATGGTTCTACAGGGAATAAGATTTATAGTATGG (oligo CS1FP7; HBV  nucleotide coordinates 2832-2853) and 5’-TACGGTAGCAGAGACTTGGTCTTAAACCTAAAAACTCCACC-3’ (oligo CS2RP7; HBV nucleotide coordinates 3061-3043, (ix) 5’-ACACTGACGACATGGTTCTACAAATCAAAAAAACAACCTACC-3’ (oligo CS1FP8; HBV  nucleotide coordinates 3115-3134) and 5’-TACGGTAGCAGAGACTTGGTCTGTGAGTGATTGGAGGT-3’ (oligo CS2RP8; HBV  nucleotide coordinates 340-325), (x) 5’-ACACTGACGACATGGTTCTACAACCTCCAATCACTCAC-3’ (oligo CS1FP9; HBV nucleotide coordinates 325-340) and 5’-TACGGTAGCAGAGACTTGGTCTGTTAAATAGTGGGGGAAAG-3’ (oligo CS2RP9; HBV nucleotide coordinates 730-712), (xi) 5’-ACACTGACGACATGGTTCTACAGGATGATGTGGTATTGG-3’ (oligo CS1FP10; HBV nucleotide coordinates 743-759) and 5’-TACGGTAGCAGAGACTTGGTCTCAAAACCCAAAAAACCCAC-3’ (oligo CS2RP10; HBV nucleotide coordinates 1020-1002), and (xii) 5’-  ACACTGACGACATGGTTCTACATTGATGTTTTTGTATGTA-3’ (oligo     CS1FP11; HBV nucleotide coordinates 1053-1070) and 5’-TACGGTAGCAGAGACTTGGTCTATAACCAAACCCCAACC-3’ (oligo CS2RP11; HBV nucleotide coordinates 1222-1206).  These primers contained linker sequences (underlined) at the 5’ ends of the oligonucleotides, termed common sequences (CS1 and CS2). These PCR reactions were performed using ZymoTaq PreMix according to the manufacturer’s instructions (Zymo Research).  PCR amplification involved 10 minutes denaturation at 95°C, followed by 40 cycles of 95°C for 30 s, 50°C for 40 s (ramp rate 95-50 was set to 0.3C/s), 72°C for 60 s.  Finally, a 7 minute incubation at 72°C was performed.  The HBV amplicons were subsequently subjected to a second stage PCR reaction (MyTaq HS Mix, 2X, Bioline USA Inc., Taunton, MA, USA), used to incorporate unique barcodes and sequencing adapters. The PCR primers used were 5’-  AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA-3’ (oligo PE1CS1) and 5’-CAAGCAGAAGACGGCATACGAGATNNNNNNNNNNTACGGTAGCAGAGACTTGGTCT-3’ (oligo PE2BCCS2).  The 10-base sample-specific barcodes are indicated with bold Ns and represent barcode sequences from a set of 384 unique primer pairs (Fluidigm Access Array Barcode Library for Illumina Sequencers).  PCR amplification involved 5 minutes denaturation at 95°C, followed by 8 cycles of 95°C for 30 s, 60°C for 30 s, 72°C for 30 s.  Finally, a 7 minute incubation at 72°C was performed.  The resulting final PCR products (libraries) contain Illumina sequencing adapters and a sample-specific barcode.
Pooled libraries were sequenced using an Illumina MiSeq instrument and data were analyzed using the Casava1.8 pipeline. Sequencing was performed using MiSeq V3 chemistry, with paired-end 2x300 base reads, employing Access Array custom sequencing primers.

tag: age

value: 28.5 days

tag: library type

value: Bisulfite (BS)

tag: library protocol

value: BS only

tag: paired sample for oxbs + bs

tag: biological specimen id


title: B10500-A7_OxBS_combined

status: Public on Dec 10 2020

type: SRA

country: USA

value: 24.5 days

value: Oxidatitive bisulfite (OxBS)

value: OxBS + BS


title: B10500-A8_BS_combined


title: RAL-321_fatBody_T=ZT15_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_fatbody_norm.csv.gz
BRB1_FB_ZT15_29655

library_source: transcriptomic

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

molecule: total RNA

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

tag: strain

tag: tissue

value: whole fat body

tag: time of harvesting

tag: replicate

tag: library

tag: bloomington

tag: time series type

value: Time-series for RAL-321


title: RAL-321_fatBody_T=ZT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_ZT1_29655


title: RAL-321_brain_T=ZT21_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_ZT21_29655

value: whole brain


title: RAL-321_brain_T=ZT23_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_ZT23_29655


title: G37-1

type: RNA

city: Tokyo

first: Hidehiro

last: Irie

address: 35 Shinanomachi Shinjuku-ku

country: Japan

institute: Keio University

description: Gene expression of air exposure

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45°C on GeneChip Clariom S Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Scanned output files were analyzed using the Transcriptome Analysis Console (Affymetrix/Thermo Fisher Scientific).

label: biotin

organism: Mus musculus

source_name: Gene expression of air exposure

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip WT PLUS Reagent Kit User Manual ,  Affymetrix).Biotinylated ss-cDNA yield were checked with the NanoDrop ND-2000c Spectrophotometer.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified using a NanoDrop-2000c spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: lung

tag: cell type

value: SPC/GFP+ EpCAM+ cells


title: G37-3

description: Gene expression after 3 week intermittent smoke exposure


title: B10500-A6_OxBS_combined

value: 20.5 days


title: B10500-A7_BS_single


title: B10500-A7_BS_combined


title: B10500-A6_BS_combined


title: B10500-A8_OxBS_combined


title: B10500-A6_BS_single


title: RAL-321_brain_T=ZT19_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_ZT19_29655


title: RAL-321_brain_T=ZT17_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_ZT17_29655


title: B10500-A5_OxBS_combined

value: 16.5 days


title: B10500-A5_BS_combined


title: G37-2

description: Gene expression after 3 week continuous smoke exposure


title: B10500-A4_OxBS_combined

value: 13.5 days


title: RAL-321_brain_T=ZT15_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_ZT15_29655


title: RAL-321_brain_T=ZT13_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_ZT13_29655


title: RAL-321_brain_T=ZT11_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_ZT11_29655


title: RAL-321_brain_T=ZT5_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_ZT5_29655


title: RAL-321_brain_T=ZT3_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_ZT3_29655


title: RAL-321_brain_T=ZT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB8_Brain_ZT1_29655


title: RAL-321_brain_T=ZT7_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_ZT7_29655


title: RAL-208_gut_T=CT21_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_CT21_25174

value: whole gut

value: Time-series for RAL-208


title: B10500-A2_OxBS_combined

value: 6.5 days


title: RAL-208_gut_T=CT9_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_CT9_25174


title: RAL-208_gut_T=CT17_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_CT17_25174


title: B10500-A4_BS_single


title: B10500-A1_BS_single

value: 2.5 days


title: RAL-208_gut_T=CT13_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_CT13_25174


title: B10500-A2_BS_combined

value: Bisulfite (BS)


title: B10499-B6_OxBS_combined

value: 29.5 days


title: B10499-B6_BS_single

value: BS only


title: B10500-A2_BS_single


title: B10499-B5_OxBS_combined

value: 5.5 days

value: Oxidatitive bisulfite (OxBS)


title: B10499-B6_BS_combined

value: OxBS + BS


title: RAL-208_gut_T=CT5_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_CT5_25174


title: B10500-A5_BS_single


title: RAL-208_gut_T=CT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_CT1_25174


title: RAL-321_brain_T=ZT9_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_ZT9_29655

value: Time-series for RAL-321


title: B10499-B5_BS_combined


title: B10500-A4_BS_combined


title: RAL-208_fatBody_T=CT21_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB3_FB_CT21_25174

value: whole fat body


title: B10499-B5_BS_single


title: RAL-208_fatBody_T=CT17_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_CT17_25174


title: RAL-208_fatBody_T=CT13_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_CT13_25174


title: B10500-A3_BS_single

value: 8.5 days


title: B10499-B4_BS_combined

value: 3.5 days


title: B10499-B4_BS_single


title: B10499-B3_BS_single


title: B10499-B2_BS_single

value: 1.5 days


title: RAL-208_fatBody_T=CT9_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_CT9_25174


title: RAL-208_brain_T=CT21_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_CT21_25174

value: whole brain


title: RAL-208_fatBody_T=CT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_CT1_25174


title: B10499-B1_BS_single

value: 0.5 days


title: B10499-A5_OxBS_combined

value: 28.5 days


title: RAL-208_brain_T=CT13_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_CT13_25174

value: Time-series for RAL-208


title: RAL-208_brain_T=CT17_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_CT17_25174


title: RAL-208_brain_T=CT5_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_CT5_25174


title: B10499-A5_BS_single


title: B10499-A4_OxBS_combined

value: 18.5 days


title: w1118_malpighianTubules_T=CT23_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT48_Aug_2

value: whole malpighian tubules

value: Time-series for w1118


title: RAL-208_brain_T=CT9_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_CT9_25174


title: B10499-A4_BS_combined

value: Bisulfite (BS)


title: w1118_malpighianTubules_T=CT23_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT36_Aug_2


title: B10499-B4_OxBS_combined


title: B10499-A4_BS_single

value: BS only


title: w1118_malpighianTubules_T=CT21_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT35_Aug_2


title: B10499-A3_OxBS_combined

value: 10.5 days


title: w1118_malpighianTubules_T=CT19_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT46_Aug_2


title: B10499-A3_BS_combined


title: w1118_malpighianTubules_T=CT19_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT34_Aug_2


title: RAL-208_fatBody_T=CT5_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
BRB2_FB_CT5_25174


title: B10499-A3_BS_single


title: B10499-A2_OxBS_combined

value: Oxidatitive bisulfite (OxBS)


title: B10499-A5_BS_combined

value: OxBS + BS


title: B10499-A2_BS_combined


title: B10499-A2_BS_single


title: w1118_malpighianTubules_T=CT15_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT44_Aug_2


title: w1118_malpighianTubules_T=CT17_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT33_Aug_2


title: RAL-208_brain_T=CT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB7_Brain_CT1_25174


title: B10499-A1_OxBS_combined

value: 4.5 days


title: w1118_malpighianTubules_T=CT17_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT33_Jan_11


title: B10499-A1_BS_combined


title: B10499-A1_BS_single


title: w1118_malpighianTubules_T=CT15_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT32_Aug_2


title: w1118_malpighianTubules_T=CT21_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT47_Aug_2


title: w1118_malpighianTubules_T=CT13_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT43_Aug_2


title: w1118_malpighianTubules_T=CT11_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT42_Aug_2


title: w1118_malpighianTubules_T=CT11_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT30_Aug_2


title: B10498-B6_OxBS_combined


title: w1118_malpighianTubules_T=CT13_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT31_Aug_2


title: B10498-B6_BS_single


title: w1118_malpighianTubules_T=CT9_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT41_Aug_2


title: B10498-B6_BS_combined


title: B10498-B5_OxBS_combined


title: w1118_malpighianTubules_T=CT9_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT29_Aug_2


title: w1118_malpighianTubules_T=CT17_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT45_Aug_2


title: B10498-B5_BS_single


title: B10498-B5_BS_combined


title: w1118_malpighianTubules_T=CT9_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT29_Jan_11


title: w1118_malpighianTubules_T=CT7_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT40_Aug_2


title: B10498-B4_BS_combined


title: B10498-B4_OxBS_combined


title: w1118_malpighianTubules_T=CT7_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT28_Aug_2


title: B10498-B4_BS_single


title: w1118_malpighianTubules_T=CT3_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT26_Aug_2


title: w1118_malpighianTubules_T=CT5_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT39_Aug_2


title: B10498-B3_BS_combined

value: 2.5 days


title: w1118_malpighianTubules_T=CT5_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT27_Aug_2


title: B10498-B3_OxBS_combined


title: w1118_malpighianTubules_T=CT1_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT37_Aug_2


title: B10498-B3_BS_single


title: w1118_malpighianTubules_T=CT3_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT38_Aug_2


title: B10498-B2_OxBS_combined


title: w1118_malpighianTubules_T=CT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT25_Aug_2


title: w1118_malpighianTubules_T=ZT23_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT24_Aug_2


title: B10498-B2_BS_single


title: B10498-B1_OxBS_combined


title: w1118_malpighianTubules_T=ZT23_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT12_Aug_2


title: w1118_malpighianTubules_T=ZT21_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT23_Aug_2


title: B10498-B1_BS_combined


title: B10498-B2_BS_combined


title: B10498-B1_BS_single


title: B10498-A5_BS_single


title: B10498-A4_BS_single

value: 19.5 days


title: B10498-A3_OxBS_combined

value: 11.5 days


title: w1118_malpighianTubules_T=ZT19_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT22_Aug_2


title: w1118_malpighianTubules_T=ZT21_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT11_Aug_2


title: w1118_malpighianTubules_T=ZT21_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT11_Jan_11


title: B10498-A3_BS_combined


title: B10498-A3_BS_single


title: w1118_malpighianTubules_T=ZT17_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT21_Aug_2


title: B10498-A2_OxBS_combined

value: 9.5 days


title: w1118_malpighianTubules_T=ZT15_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT8_Aug_2


title: w1118_malpighianTubules_T=ZT15_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT20_Aug_2


title: w1118_malpighianTubules_T=ZT13_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT7_Aug_2


title: w1118_malpighianTubules_T=ZT13_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT19_Aug_2


title: B10498-A2_BS_combined


title: B10498-A2_BS_single


title: B10498-A1_OxBS_combined

value: 5.5 days


title: B10498-A1_BS_combined


title: B10498-A1_BS_single


title: w1118_malpighianTubules_T=ZT11_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT6_Aug_2


title: w1118_malpighianTubules_T=ZT11_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT18_Aug_2


title: w1118_malpighianTubules_T=ZT19_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT10_Aug_2


title: w1118_malpighianTubules_T=ZT11_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT6_Jan_11


title: w1118_malpighianTubules_T=ZT9_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT17_Aug_2


title: w1118_malpighianTubules_T=ZT9_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT5_Aug_2


title: B10496-A4_OxBS_combined

value: 3.5 days


title: B10496-A4_BS_combined


title: B10496-A4_BS_single


title: w1118_malpighianTubules_T=ZT5_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT3_Aug_2


title: w1118_malpighianTubules_T=ZT7_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT16_Aug_2


title: w1118_malpighianTubules_T=ZT17_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT9_Aug_2


title: B10496-A3_OxBS_combined


title: B10496-A3_BS_combined


title: B10496-A3_BS_single


title: B10496-A2_OxBS_combined

value: 1.5 days


title: w1118_malpighianTubules_T=ZT7_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT4_Aug_2


title: B10496-A2_BS_combined


title: w1118_malpighianTubules_T=ZT5_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT15_Aug_2


title: B10496-A2_BS_single


title: w1118_malpighianTubules_T=ZT17_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT9_Jan_11


title: w1118_malpighianTubules_T=ZT3_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT2_Aug_2


title: B10496-A1_BS_combined

value: 0.5 days


title: w1118_malpighianTubules_T=ZT1_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT1_Aug_2


title: B10290-A7_BS_single


title: w1118_malpighianTubules_T=ZT3_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT14_Aug_2


title: w1118_gut_T=CT23_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT48_Aug_2

value: whole gut


title: w1118_gut_T=CT23_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT36_Aug_2


title: w1118_gut_T=CT21_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT35_Jan_6


title: w1118_malpighianTubules_T=ZT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_malpighiantubules_norm.csv.gz
MT13_Aug_2

value: whole malpighian tubules


title: B10290-A5_BS_single


title: w1118_gut_T=CT21_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT47_Aug_2

value: Time-series for w1118


title: B10290-A3_BS_single

value: Bisulfite (BS)


title: B10290-A2_OxBS_combined


title: B10290-A4_BS_single

value: BS only


title: B10290-A2_BS_combined


title: B10290-A2_BS_single


title: w1118_gut_T=CT19_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT34_Aug_2


title: w1118_gut_T=CT17_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT45_Aug_2


title: w1118_gut_T=CT17_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT33_Jan_4


title: w1118_gut_T=CT19_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT46_Aug_2


title: w1118_gut_T=CT17_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT33_Aug_2


title: B10290-A1_BS_single


title: B10286-F3_BS_single


title: B10496-A1_OxBS_combined


title: B10286-F2_BS_single


title: w1118_gut_T=CT15_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT44_Aug_2


title: B10286-F1_BS_single


title: w1118_gut_T=CT15_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT32_Aug_2


title: B10496-A1_BS_single


title: B10286-E2_BS_single


title: B10290-A6_BS_single


title: w1118_gut_T=CT13_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT31_Jan_6


title: B10286-E1_BS_single


title: w1118_gut_T=CT13_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT43_Aug_2


title: B10286-C2_BS_single


title: w1118_gut_T=CT21_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT35_Aug_2


title: w1118_gut_T=CT13_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT31_Aug_2


title: B10286-B6_BS_single


title: B10286-C1_BS_single


title: w1118_gut_T=CT9_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT41_Aug_2


title: B10286-B3_OxBS_combined


title: w1118_gut_T=CT9_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT29_Aug_2


title: w1118_gut_T=CT7_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT40_Aug_2


title: w1118_gut_T=CT7_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT28_Aug_2


title: B10286-B3_BS_combined


title: B10286-B2_BS_single


title: w1118_gut_T=CT5_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT39_Aug_2


title: B10286-B1_BS_single


title: B10286-B3_BS_single


title: w1118_gut_T=CT5_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT27_Aug_2


title: w1118_gut_T=CT3_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT26_Aug_2


title: w1118_gut_T=CT1_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT37_Aug_2


title: B10286-A3_OxBS_combined


title: B10286-A4_BS_single


title: B10286-A3_BS_combined


title: B10286-A3_BS_single


title: w1118_gut_T=CT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT25_Aug_2


title: w1118_gut_T=ZT23_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT24_Aug_2


title: B10286-A2_BS_single


title: w1118_gut_T=ZT23_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT12_Aug_2


title: B10286-A1_BS_single


title: w1118_gut_T=CT11_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT30_Aug_2


title: B10082-Liver_OxBS_combined

value: 109 days; Female


title: B10082-Liver_BS_combined


title: w1118_gut_T=ZT21_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT23_Aug_2


title: w1118_gut_T=ZT21_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT11_Jan_4


title: B10035-Liver_OxBS_combined

value: 139 days; Male

value: Oxidatitive bisulfite (OxBS)


title: w1118_gut_T=ZT21_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT11_Aug_2


title: B10035-Liver_BS_combined

value: OxBS + BS


title: w1118_gut_T=ZT19_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT22_Aug_2


title: shCTRL_rep3_Ribo_seq

city: Boston

first: Yanqiang

last: Li

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

data_processing:
Library strategy: Ribo-seq
In brief, we first used the software PEAR(2) to merge and integrate the reads and quality information of pair-end reads. The adapters were removed after merging of the paired-end reads. The barcodes were removed using cutadapt and the reads were split into different samples based on their barcode sequences. Then the reads mapped to the human rRNA were removed by the bowtie methods, 40~60% of the reads are from rRNA were removed. We used the UMI information combined with the seqkit rmdup method to remove PCR duplication. After that, we mapped the clean reads from all biological RNA-seq and Ribo-seq replicates to the human hg19 genome and assigned to the exons of genes using TopHat. Only the unique mapped reads were used for the further analysis. Read counts for each gene were calculated by the htseq-count function of the tool HTSeq and subsequently, Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated and normalized using quantile normalization procedures in R (https://www.r-project.org/).
An Ribo-seq pipeline deltaTE  was used to detect the translationally regulated genes by integrative analysis of our Ribo-seq and RNA-seq data. Translation efficiency was calculated by the ratio of Ribo-seq counts over RNA-seq counts within a within a gene’s coding sequence (CDS). The FDR less than 0.05 and fold change more than 1.5 were used as the difference cutoffs of translation efficiency, Ribo-seq and RNA-seq. The wiq function of DANPOS (Chen et al., 2013)  was used to perform the quantile normalization between different samples. The normalized wig files were transformed into bigwig file using wigToBigWig. Genomic track files bigwigs from the ribo-seq and RNA-seq were visualized by the washU genome browser(http://epigenomegateway.wustl.edu/).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include raw reads count of RNA-seq and Ribo-seq seprately.

organism: Homo sapiens

growth_protocol: Human PCa cell lines C4-2, was purchased from ATCC. The C4-2, shCTRL, shEZH2 and shFBL cells were grown in RPMI 1640 medium supplemented with 10% FBS, while VCaP cells were grown in DMEM medium supplemented with 10% FBS and used within 20 passages after receipt. The cells were cultured in a 37°C incubator and a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was isolated from cells using the RNA MiniPrep kit (Direct-zol, R2052, ZYMO Research) with the procedure provided by the manufacturer.  RNA libraries were prepared for sequencing using standard Illumina protocols
Ribosome profiling experiment is performed following the method described in Methods. 2017 Aug 15;126:112-129.  Briefly, 4 million cells are rapidly harvested and lysed under conditions that maintain in vivo ribosome positions on mRNAs. These cell lysates are then subjected to nuclease footprinting with RNase I, and ribosomes are recovered by ultracentrifugation. Ribosome footprints are purified and ligated to a single-stranded linker. The RNA-DNA hybrid molecules are used as templates for reverse transcription, and following gel-based purification of full-length products. The first-strand reverse transcription products are then circularized. Finally, a double-stranded DNA library for Illumina sequencing is constructed from the single-stranded cDNA circles by means of a PCR amplification.

tag: genotype

value: shCTRL

tag: cell line


title: shEZH2_rep3_Ribo_seq


title: w1118_gut_T=ZT17_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT21_Aug_2


title: w1118_gut_T=ZT17_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT9_Aug_2


title: w1118_gut_T=ZT19_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT10_Aug_2


title: shFBL_rep3_Ribo_seq

value: shFBL


title: w1118_gut_T=ZT15_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT8_Aug_2


title: shFBL_rep1_Ribo_seq

description: ribosome-protected mRNA

data_processing:
Library strategy: Ribo-seq
In brief, we first used the software PEAR(2) to merge and integrate the reads and quality information of pair-end reads. The adapters were removed after merging of the paired-end reads. The barcodes were removed using cutadapt and the reads were split into different samples based on their barcode sequences. Then the reads mapped to the human rRNA were removed by the bowtie methods, 40~60% of the reads are from rRNA were removed. We used the UMI information combined with the seqkit rmdup method to remove PCR duplication. After that, we mapped the clean reads from all biological RNA-seq and Ribo-seq replicates to the human hg19 genome and assigned to the exons of genes using TopHat. Only the unique mapped reads were used for the further analysis. Read counts for each gene were calculated by the htseq-count function of the tool HTSeq and subsequently, Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated and normalized using quantile normalization procedures in R (https://www.r-project.org/).
An Ribo-seq pipeline deltaTE  was used to detect the translationally regulated genes by integrative analysis of our Ribo-seq and RNA-seq data. Translation efficiency was calculated by the ratio of Ribo-seq counts over RNA-seq counts within a within a gene’s coding sequence (CDS). The FDR less than 0.05 and fold change more than 1.5 were used as the difference cutoffs of translation efficiency, Ribo-seq and RNA-seq. The wiq function of DANPOS (Chen et al., 2013)  was used to perform the quantile normalization between different samples. The normalized wig files were transformed into bigwig file using wigToBigWig. Genomic track files bigwigs from the ribo-seq and RNA-seq were visualized by the washU genome browser(http://epigenomegateway.wustl.edu/).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include quantile normalized reads for 12 Samples.

molecule: polyA RNA

treatment_protocol: no

value: Human PCa cell line C4-2


title: shFBL_rep2_Ribo_seq

description: ribosome-protected mRNA


title: shEZH2_rep2_Ribo_seq

description: ribosome-protected mRNA


title: w1118_gut_T=ZT15_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT8_Jan_4


title: w1118_gut_T=ZT13_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT7_Jan_4


title: shEZH2_rep1_Ribo_seq

description: ribosome-protected mRNA


title: w1118_gut_T=ZT15_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT20_Aug_2


title: w1118_gut_T=ZT13_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT7_Aug_2


title: shCTRL_rep2_Ribo_seq

description: ribosome-protected mRNA


title: w1118_gut_T=CT3_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT38_Aug_2


title: shCTRL_rep1_Ribo_seq

description: ribosome-protected mRNA


title: w1118_gut_T=ZT11_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT6_Aug_2


title: w1118_gut_T=ZT9_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT5_Jan_6


title: w1118_gut_T=ZT11_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT18_Aug_2


title: 4-3_S7

city: Callaghan

first: Jessie

middle: M

last: Sutherland

state: New South Wales

address: Life Sciences Building, Ring Road

department: School of Biomedical Science and Pharmacy

country: Australia

institute: University of Newcastle

data_processing:
quality of data visualised via FastqQC, TrimGalore was used to check and remove adapters from the sequences (Phred score <30 were trimmed), reads shorter than 25 bas pairs were discarded
hisat2 was used to map the cleaned reads to the mouse transcriptome (grcm38) with --dta option
mapped reads assmebled into transcripts using StringTies and Ensembl reference annotation (Mus_musculus.GRCm38.93.gtf)
Abundances estimated using -e parameter and differential expression analysis performed using Ballgown (R software)
low abundance genes with a transcript vairance less than one across the samples were removed
differential gene expression between postnatal day 1 and postnatal day 4 samples were calculated using the stattest() function with FPKM values. Data was then sorted by their adjusted p-value (q-value) and absolute log2fold change values
Genome_build: grcm38
Supplementary_files_format_and_content: Abundance, differential expression between the two groups with fold change and p-values (after filtering low abundance transcripts)
Supplementary_files_format_and_content: Raw counts including the FPKM values for each of the samples after filtering low abundance transcripts

source_name: postnatal day 4

extract_protocol:
After isolating granulosa cells, cells were placed on ice for immediate RNA extraction using the RNeasy Plus Micro Kit (Qiagen, cat no. 74034)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: granulosa cells

value: postnatal day 4


title: 4-1_S5


title: w1118_gut_T=ZT9_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT5_Aug_2


title: 4-4_S8


title: 4-2_S6


title: 1-3_S3

source_name: postnatal day 1

value: postnatal day 1


title: w1118_gut_T=ZT9_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT17_Aug_2


title: RNA-seq_MCF-7_HA-3A-MTA1_R2

city: panjin

first: bo

middle: yu

last: liu

state: liaoning

address: Dagong Road 2

country: China

institute: Dalian University of Technology

data_processing:
base-calling: in-house BGISEQ-500 software
Bowtie2 (version: v2.2.5) was used to map clean reads to reference gene
peak-calling: MACS2 for ChIP-Seq; FPKM method was used in calculated RNA-seq expression level.
Deeptools was used for generating bigwig files. ChIPseeker for the annotation of peaks.
Genome_build: Genome_build: ChIP-Seq: hg19; RNA-Seq: hg19;
Supplementary_files_format_and_content: Supplementary files format and content: bigwig: The signal intensity of binding.

source_name: human breast cancer cell MCF-7

extract_protocol:
HA-WT-MTA1 and HA-3A-MTA1 cells were maintained in RPMI-1640 medium with 10% fetal calf serum. Approximately 2 x 10e7 cells were used for ChIP-seq assay.  For MTA1, HA-WT(wild type)-MTA1, or HA-3A(Ser237/Ser241/Ser246 → Ala)-MTA1 ChIP-seq, crosslinked chromatin complexes were immunoprecipitated with anti-HA-magnetic beads. For RNA-seq, total RNA was extracted from the WT-MTA1 and 3A-MTA1 cells using Trizol reagent (Invitrogen). RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, USA). RNA libraries were prepared for sequencing using standard BGI protocols.
DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptor. PCR amplification and size selection (usually 100-300bp, including adaptor sequence. Qualified library for sequencing. RNA-seq libraries were constructed using SMARTer cDNA library construction kit.

treatment_protocol: MCF-7  cells were cultured in RPMI-1640 medium with 10% fetal calf serum.  HA-tagged full-length wild type (WT) human MTA1 and O-GlcNAc amino acid sites mutant (human MTA1, Ser237/Ser241/Ser246 → Ala) MTA1 were subcloned into LvCGP04-Puro. Transfection of the MCF-7 cells was performed with Lentivirus according to the manufacturer’s instructions. The stably transfected cells were then selected by the addition of puromycin to the medium. ~2x10e7 cells were used as a unit of cells for each experiment.

tag: morphology type

value: epithelial type of breast cancer cell


title: RNA-seq_MCF-7_HA-WT-MTA1_R2

growth_protocol: RPMI-1640 medium with 10% fetal calf serum.


title: 1-2_S2


title: RNA-seq_MCF-7_HA-WT-MTA1_R1


title: ChIP-seq_MCF-7_HA-WT-MTA1_R2

tag: chip antibody/selection

value: HA


title: ChIP-seq_MCF-7_HA-3A-MTA1_R1


title: 1-1_S1

tag: age


title: w1118_gut_T=ZT13_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT19_Aug_2

value: whole gut


title: w1118_gut_T=ZT11_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT6_Jan_4


title: ChIP-seq_MCF-7_HA-WT-MTA1_R1


title: ChIP-seq_MCF-7_input_MTA1_R2


title: w1118_gut_T=ZT7_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT4_Aug_2


title: w1118_gut_T=ZT7_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT16_Aug_2


title: w1118_gut_T=ZT7_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT4_Jan_6


title: siEZH2_RiboMeth_rep2_2

data_processing:
Library strategy: RiboMeth-seq
In brief, the adapter of each read was trimmed by cutadapt. The reads were then mapped to the rRNA with bowtie2 in End-to-End module. Only uniquely mapped reads were used to do the further analysis. The bam files were converted into bed files using the function bamtobed in the package bedtools.
Bedtools was also used to calculate the number of 5′ and 3′ reads in the bed files. R scripts  were used to compute the MethScore for each site of 18S and 28S rRNA from the coverage of 5′ -end reads. Twelve neighboring nucleotides (+/−6 nt window) were taken into account to calculate the 2′-O-Me scores. For the 5.8S rRNA, to avoid the negative value for MethScore, an optimized method with 4 neighboring nucleotides (+/-2 nt window) from the 5′ -end reads and 3′-end reads were used to calculate the MethScore. The Unix and R scripts were downloaded from https://github.com/FlorianPichot/RiboMethSeqPipeline.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include the 2'-O-Methylation score of 7 samples.

growth_protocol: Human PCa cell lines C4-2, was purchased from ATCC. The siCTRL, siEZH2 of C4-2 cells were grown in RPMI 1640 medium supplemented with 10% FBS and used within 20 passages after receipt. The cells were cultured in a 37°C incubator and a humidified atmosphere with 5% CO2.

extract_protocol:
RiboMeth-seq analyses were performed in control and siEZH2 C4-2 cells based on a previously described protocol32. Biological triplicates were used for control cells while a total of 4 replicates (2 for siEZH2-1 and 2 for siEZH2-2) were used for siEZH2 cells. In brief, the total RNA was extracted using RNeasy Plus Mini Kit (Qiagen), followed by alkaline hydrolysis into short fragments. After fragmentation, size of RNA fragments (30–200 nt) generated was assessed by capillary electrophoresis using a PicoRNA chip on Bioanalyzer 2100 (Agilent). Fragmented RNA was 3′-end dephosphorylated directly using 5 U of Antarctic Phosphatase (NEB) After inactivation of the phosphatase, RNA fragments were phosphorylated at the 5′-end using T4 PNK (NEB) and 1 mM ATP. End-repaired RNA fragments were then purified using RNeasy MinElute Cleanup kit (QIAGEN) according to the manufacturer’s recommendations. The eluted RNA was subjected to BGI for library preparation and sequencing using the DNBseq platform with a 50 bp single-end read mode.
Briefly, 4 million cells are rapidly harvested and lysed under conditions that maintain in vivo ribosome positions on mRNAs. These cell lysates are then subjected to nuclease footprinting with RNase I, and ribosomes are recovered by ultracentrifugation. Ribosome footprints are purified and ligated to a single-stranded linker. The RNA-DNA hybrid molecules are used as templates for reverse transcription, and following gel-based purification of full-length products. The first-strand reverse transcription products are then circularized. Finally, a double-stranded DNA library for Illumina sequencing is constructed from the single-stranded cDNA circles by means of a PCR amplification.

tag: sirna


title: AB9834

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
read 1 contains the biological sequence
read2 used to read cell and molecule barcodes only. The first 7N is the cell barcode the next  8N is the UMI for the read.
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

growth_protocol: mSOD1 mice were at different ages (92 , 106, 136 and 161 days old) were used in the study.

extract_protocol:
Mice were euthanized and spinal cord meninges and cervical LNs were disected. cLN were digested in IMDM (Sigma-Aldrich) media supplemented with Liberase-TL (100μg/ml, Roche) and DNase-I (100μg/ml, Roche), and spinal cord meninges were digested in RPMI (Sigma-Aldrich) media supplemented with collagenase IV (40U/ml, Roche) and DNase-I (100μg/ml, Roche). Both tissues were incubated with frequent agitation at 37oC for 20 min. After the dissociation procedures, cells were washed with sorting buffer, filtered through 100μm, 70μm and 40μm cell strainers, and centrifuged at 380g, 5min, 4oC.
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

tag: organ

value: meninges

value: B cells

tag: selection marker

tag: infection

tag: time point

tag: mouse age


title: 1-4_S4

tag: strain


title: siEZH2_RiboMeth_rep2_1


title: ChIP-seq_MCF-7_HA-3A-MTA1_R2


title: siEZH2_RiboMeth_rep1_2


title: w1118_gut_T=ZT5_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT15_Aug_2

tag: tissue

tag: time of harvesting

tag: replicate

value: Time-series for w1118


title: RNA-seq_MCF-7_HA-3A-MTA1_R1


title: AB9833


title: AB7322

value: B and T cells


title: siCTRL_RiboMeth_rep2

value: siCTRL


title: AB9832


title: w1118_gut_T=ZT3_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT2_Jan_5

tag: library

tag: bloomington

tag: time series type


title: siCTRL_RiboMeth_rep3

tag: cell line


title: shFBL_rep2_RNA_seq

data_processing:
In brief, we first used the software PEAR(2) to merge and integrate the reads and quality information of pair-end reads. The adapters were removed after merging of the paired-end reads. The barcodes were removed using cutadapt and the reads were split into different samples based on their barcode sequences. Then the reads mapped to the human rRNA were removed by the bowtie methods, 40~60% of the reads are from rRNA were removed. We used the UMI information combined with the seqkit rmdup method to remove PCR duplication. After that, we mapped the clean reads from all biological RNA-seq and Ribo-seq replicates to the human hg19 genome and assigned to the exons of genes using TopHat. Only the unique mapped reads were used for the further analysis. Read counts for each gene were calculated by the htseq-count function of the tool HTSeq and subsequently, Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated and normalized using quantile normalization procedures in R (https://www.r-project.org/).
An Ribo-seq pipeline deltaTE  was used to detect the translationally regulated genes by integrative analysis of our Ribo-seq and RNA-seq data. Translation efficiency was calculated by the ratio of Ribo-seq counts over RNA-seq counts within a within a gene’s coding sequence (CDS). The FDR less than 0.05 and fold change more than 1.5 were used as the difference cutoffs of translation efficiency, Ribo-seq and RNA-seq. The wiq function of DANPOS (Chen et al., 2013)  was used to perform the quantile normalization between different samples. The normalized wig files were transformed into bigwig file using wigToBigWig. Genomic track files bigwigs from the ribo-seq and RNA-seq were visualized by the washU genome browser(http://epigenomegateway.wustl.edu/).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include quantile normalized reads for 12 Samples.

tag: genotype


title: siCTRL_RiboMeth_rep1


title: shEZH2_rep2_RNA_seq


title: w1118_gut_T=ZT3_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT2_Aug_2


title: AB7306

value: lymph node

tag: cell type


title: w1118_gut_T=ZT3_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT14_Aug_2


title: ChIP-seq_MCF-7_input_MTA1_R1

tag: morphology type

tag: chip antibody/selection


title: AB7305

tag: organ


title: shEZH2_rep1_RNA_seq


title: w1118_gut_T=ZT1_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT1_Jan_4


title: shCTRL_rep1_RNA_seq


title: w1118_gut_T=ZT5_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT3_Aug_2


title: AB7304

tag: selection marker


title: ATAC-seq WT - rep4

city: San Francisco

first: Hannes

last: Braberg

state: CA

institute: UCSF

description: norm.wildtype.bdg

data_processing:
RNA-Seq: Reads were filtered for quality and aligned to the yeast genome using tophat.
RNA-Seq: Non-unique reads and reads mapping to ribosomal RNA were removed prior to analysis.
RNA-Seq: Transcript counts were extracted using htseq-count
RNA-Seq: Differential expression was measured using the Dseq2 package in R
ATAC-Seq: Sequence reads were trimmed and aligned to the genome of S.cerevisiae
ATAC-Seq: Reads with a length <100bp were removed
ATAC-Seq: Replicates belonging to an allele (wt, H3K36A, H3K122A, set2∆) were merged and normalized to the smallest read number.
ATAC-Seq: Count files were generated with “featureCounts v1.5.3”
Genome_build: SacCer3 from http://hgdownload.cse.ucsc.edu/downloads.html
Supplementary_files_format_and_content: RNA-seq: Gene-Expression-Data.xlsx contains two tabs in matrix format: 1) Raw counts separately for each mutant and replicate. 2) log2 fold-change over wt for each histone mutant, with replicates averaged.
Supplementary_files_format_and_content: ATAC-seq: One BedGraph (.bdg, http://genome.ucsc.edu/goldenPath/help/bedgraph.html) file for each mutant and wt. The chromosomes are labeled by their NCBI accession numbers, and the last ("dataValue") column contains the read counts.

organism: Saccharomyces cerevisiae

source_name: Budding yeast cells

extract_protocol:
RNA-Seq: RNA was extracted with hot acidic phenol  as described in "M. A. Collart, S. Oliviero, Preparation of yeast RNA. Curr Protoc Mol Biol Chapter 13, Unit13 12 (2001)". ATAC-Seq: DNA was purified (Qiagen MinElute DNA Purification Kit), amplified and barcoded by PCR.
RNA-Seq: RNA-seq libraries were generated using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen). ATAC-Seq: See treatment and extract protocols. Purified PCR-products were then sequenced.

treatment_protocol: ATAC-Seq:  Yeast cells (2.5x106) were grown to mid-log phase, pelleted, washed with SB-buffer (1.4 M Sorbitol, 40 mM HEPES-KOH pH 7.5, 0.5 mM MgCl2), resuspended in 200 μl SB buffer + 10 mM DTT with 10 μl of 10 mg/ml 100T zymolyase (MP Biomedicals) solution and incubated for 5min at 30 °C. Spheroblasted cells were washed with SB-buffer and incubated for 15 min at 37 °C in 25 μl transposase solution (12.5 μl 2x TD buffer, 1.25 μl Nextera enzyme, 11.25 μl water).

tag: strain background

value: MSY196 (based on S288C)

value: WT


title: ATAC-seq WT - rep3

description: norm.wildtype.bdg


title: w1118_gut_T=ZT1_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT1_Aug_2


title: w1118_gut_T=ZT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_gut_norm.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT13_Aug_2


title: ATAC-seq WT - rep2

description: norm.wildtype.bdg


title: ATAC-seq WT - rep1

description: norm.wildtype.bdg


title: AB7321

tag: infection

tag: time point


title: ATAC-seq set2 deletion - rep3

value: set2 deletion


title: AB7303

tag: strain

tag: mouse age


title: AB7301


title: ATAC-seq set2 deletion - rep2


title: w1118_fatBody_T=CT23_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB36_Oct_2

tag: tissue

value: whole fat body

tag: time of harvesting


title: shCTRL_rep2_RNA_seq

value: shCTRL

value: Human PCa cell line C4-2


title: ATAC-seq H3K36A - rep3

tag: replicate


title: ATAC-seq set2 deletion - rep1


title: w1118_fatBody_T=CT21_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB47_Oct_2

tag: library

tag: bloomington


title: ATAC-seq H3K36A - rep4


title: RM-Lib-6_Aged SW (Batch 2)

city: Stanford

last: Blau

address: Stanford University School of Medicine, 269 Campus Drive, CCSR 3210

institute: Baxter Laboratory for Stem Cell Biology,

description: Treated with SW i.p for 4 weeks

data_processing:
Illumina Casava1.7 software used for basecalling.
STAR read mapping
RSEM
Differential expression was analysed in R using DESeq2 library
Genome_build: mm9
Supplementary_files_format_and_content: TPM and count values, and DESeq output contining LFC and p-values.

source_name: Whole muscle lysates

extract_protocol:
Trizol RNA extraction with Qiagen RNAeasy Mini Kit
TruSEQ RNA Library Preparation Kit v2 (Illumina)

treatment_protocol: Mice were treated with daily i.p. injections of vehicle (10% ethanol, 5% Cremophor EL, 85% D5W (Dextrose 5% Water)) or 5mg/kg SW033291. Muscles were harvested and processed after 4 weeks of treatment.

value: Quadriceps muscle

tag: age

tag: treatment


title: AB7300

tag: cell type


title: ATAC-seq H3K36A - rep1

tag: genotype


title: ATAC-seq H3K36A - rep2


title: w1118_fatBody_T=CT21_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB35_Oct_2

tag: time series type


title: RM-Lib-4_Aged SW (Batch 2)

description: Treated with SW i.p for 4 weeks


title: ATAC-seq H3K122A - rep2


title: ATAC-seq H3K122A - rep3


title: w1118_fatBody_T=CT19_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB46_Oct_2


title: ATAC-seq H3K122A - rep1


title: RM-Lib-1_Aged SW (Batch 2)

description: Treated with SW i.p for 4 weeks


title: AB7302

tag: organ


title: WT - rep4

description: RNA-Seq.xlsx


title: RM-Lib-8_Aged Veh (Batch 2)

description: Treated with Veh i.p for 4 weeks

value: vehicle


title: WT - rep3

description: RNA-Seq.xlsx


title: w1118_fatBody_T=CT23_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB48_Oct_2


title: WT - rep2

description: RNA-Seq.xlsx


title: siEZH2_RiboMeth_rep1_1

tag: sirna

tag: cell line


title: WT - rep1

description: RNA-Seq.xlsx

tag: strain background


title: H4Y88F - rep3

description: RNA-Seq.xlsx


title: w1118_fatBody_T=CT17_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB45_Oct_2


title: w1118_fatBody_T=CT19_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB34_Oct_2


title: H4Y88F - rep2

description: RNA-Seq.xlsx


title: RM-Lib-2_Aged Veh (Batch 2)

description: Treated with Veh i.p for 4 weeks


title: H4Y88F - rep1

description: RNA-Seq.xlsx


title: w1118_fatBody_T=CT17_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB33_Oct_2


title: AV3_Aged Veh (Batch 1)

description: Treated with Veh i.p for 4 weeks


title: H4Y88A - rep3

description: RNA-Seq.xlsx


title: H4Y88A - rep4

description: RNA-Seq.xlsx


title: w1118_fatBody_T=CT15_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB44_Oct_2


title: H4Y88A - rep1

description: RNA-Seq.xlsx


title: AV2_Aged Veh (Batch 1)

description: Treated with Veh i.p for 4 weeks


title: w1118_fatBody_T=CT15_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB32_Oct_2


title: H4Y88A - rep2

description: RNA-Seq.xlsx


title: H4R55A - rep3

description: RNA-Seq.xlsx


title: H4R55A - rep2

description: RNA-Seq.xlsx


title: Aged4_Aged Veh (Batch 1)

description: Treated with Veh i.p for 4 weeks


title: H4R55A - rep1

description: RNA-Seq.xlsx


title: w1118_fatBody_T=CT13_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB43_Oct_2


title: H4K91R - rep3

description: RNA-Seq.xlsx


title: YV5_Young Veh (Batch 1)

description: Treated with Veh i.p for 4 weeks

value: 3 mo.


title: w1118_fatBody_T=CT13_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB31_Oct_2


title: H4K91R - rep2

description: RNA-Seq.xlsx


title: YV4_Young Veh (Batch 1)

description: Treated with Veh i.p for 4 weeks


title: RM-Lib-3_Aged Veh (Batch 2)

description: Treated with Veh i.p for 4 weeks


title: H4K91R - rep1

description: RNA-Seq.xlsx


title: H4K91Q - rep3

description: RNA-Seq.xlsx


title: w1118_fatBody_T=CT11_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB30_Oct_2


title: H4K91Q - rep2

description: RNA-Seq.xlsx


title: w1118_fatBody_T=CT9_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB41_Oct_2


title: H4K91Q - rep1

description: RNA-Seq.xlsx


title: w1118_fatBody_T=CT17_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB33_Jan_1


title: YV3_Young Veh (Batch 1)

description: Treated with Veh i.p for 4 weeks


title: H4K44R - rep2

description: RNA-Seq.xlsx


title: w1118_fatBody_T=CT9_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB29_Oct_2


title: YV1_Young Veh (Batch 1)

description: Treated with Veh i.p for 4 weeks


title: disome-seq_negative_control

city: Beijing

first: Yan-Ming

last: Chen

address: Beichen West Rd.

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

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

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)

value: rich medium


title: H4K44Q - rep2

description: RNA-Seq.xlsx


title: H4K44R - rep1

description: RNA-Seq.xlsx


title: w1118_fatBody_T=CT7_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB40_Oct_2


title: mRNA-seq-3AT_rep1

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


title: mRNA-seq-3AT_rep2


title: H4K44Q - rep1

description: RNA-Seq.xlsx


title: H3T3D - rep2

description: RNA-Seq.xlsx


title: w1118_fatBody_T=CT7_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB28_Oct_2


title: H3T3D - rep1

description: RNA-Seq.xlsx


title: H3T3A - rep2

description: RNA-Seq.xlsx


title: H3T3A - rep1

description: RNA-Seq.xlsx


title: w1118_fatBody_T=CT5_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB39_Oct_2


title: monosome-seq-3AT_rep1


title: H4K44R - rep3

description: RNA-Seq.xlsx


title: H3S86A - rep3

description: RNA-Seq.xlsx


title: H3S86A - rep2

description: RNA-Seq.xlsx


title: monosome-seq-3AT_rep2


title: w1118_fatBody_T=CT9_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB29_Jan_1


title: w1118_fatBody_T=CT3_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB26_Oct_2


title: w1118_fatBody_T=CT3_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB38_Oct_2


title: H3S86A - rep1

description: RNA-Seq.xlsx


title: disome-seq_rep2


title: H3S86D - rep2

description: RNA-Seq.xlsx


title: H3S31D - rep3

description: RNA-Seq.xlsx


title: w1118_fatBody_T=CT1_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB37_Oct_2


title: H3S31D - rep2

description: RNA-Seq.xlsx


title: H3S86D - rep1

description: RNA-Seq.xlsx


title: w1118_fatBody_T=CT1_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB25_Oct_2


title: disome-seq_rep1


title: H3S86D - rep3

description: RNA-Seq.xlsx


title: H3R40K - rep3

description: RNA-Seq.xlsx


title: H4K44Q - rep3

description: RNA-Seq.xlsx


title: w1118_fatBody_T=CT5_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB27_Oct_2


title: Gastric cancer cell line SNU1750 (Long-read Iso-seq)

city: Singapore

first: Kie Kyon

last: Huang

state: Select State/Province

address: 8 College Road

country: Singapore

institute: Duke-NUS Graduate Medical School

description:
Long-read Iso-seq
PacBio Sequel System

data_processing:
We used CCS module of IsoSeq3 program (https://github.com/PacificBiosciences/IsoSeq3) to generate circular consensus sequence (CCS) reads from the sub-reads generated from the sequencing run.
Reads that were identified as full length were considered for de-novo clustering of reads using cluster module of IsoSeq3 to identify unique isoforms.
Isoforms were mapped to human genome (version hg38) using GMAP and only high-quality isoforms (supported by at least two FLNC reads) were considered for further analysis.
Isoforms identified across all cell lines were merged into a single non-redundant transcriptome using gffcompare (https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) and annotated using SQANTI2.
Transcript-level expression in the unit of transcript per million (tpm) were estimated for each identified isoform using Kallisto applied on short-read sequencing data and reference transcriptome defined using Iso-seq.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: gtf file containing the merged, non-redundant gastric cancer transcriptome.
Supplementary_files_format_and_content: Matrix table with tpm value for every isoform and every sample.

source_name: Gastric cancer cell line

extract_protocol:
Total RNA was extracted from 10 gastric cell-lines using RNeasy Mini Kit (QIAGEN) according to manufacturer’s instructions.
For long-read Iso-seq, amplified cDNA products were made into SMRTbell template libraries according to the Iso-Seq protocol by Pacific Biosciences.
For short-read RNA-seq, two micrograms of total RNA was used to create libraries with Illumina TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, California, USA) according to manufacturer’s instructions.

value: Gastric cancer cell line


title: w1118_fatBody_T=CT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB25_Jan_2


title: H3R40K - rep1

description: RNA-Seq.xlsx


title: Gastric cancer cell line SNU1967 (Long-read RNA-seq)

description:
Long-read Iso-seq
PacBio Sequel System


title: H3S31D - rep1

description: RNA-Seq.xlsx


title: H3R40K - rep2

description: RNA-Seq.xlsx


title: w1118_fatBody_T=ZT23_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB24_Oct_2


title: disome-seq-3AT_rep2


title: disome-seq-3AT_rep1


title: H3K4R - rep3

description: RNA-Seq.xlsx


title: Gastric cancer cell line SNU719 (Long-read Iso-seq)

description:
Long-read Iso-seq
PacBio Sequel System


title: w1118_fatBody_T=ZT23_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB12_Oct_2


title: H3K4Q - rep2

description: RNA-Seq.xlsx


title: H3K4Q - rep3

description: RNA-Seq.xlsx


title: Gastric cancer cell line SNU484 (Long-read Iso-seq)

description:
Long-read Iso-seq
PacBio Sequel System


title: H3K4R - rep1

description: RNA-Seq.xlsx


title: w1118_fatBody_T=ZT23_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB12_Jan_2


title: Gastric cancer cell line NCC59 (Long-read Iso-seq)

description:
Long-read Iso-seq
PacBio Sequel System


title: H3K4Q - rep1

description: RNA-Seq.xlsx


title: H3K37R - rep3

description: RNA-Seq.xlsx


title: w1118_fatBody_T=ZT21_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB11_Jan_3


title: Gastric cancer cell line NCC24 (Long-read Iso-seq)

description:
Long-read Iso-seq
PacBio Sequel System


title: H3K37R - rep2

description: RNA-Seq.xlsx


title: H3K4R - rep2

description: RNA-Seq.xlsx


title: H3K37R - rep1

description: RNA-Seq.xlsx


title: shFBL_rep1_RNA_seq

value: shFBL


title: Gastric cancer cell line NCC19 (Long-read Iso-seq)

description:
Long-read Iso-seq
PacBio Sequel System


title: H3K37Q - rep2

description: RNA-Seq.xlsx


title: H3K37Q - rep3

description: RNA-Seq.xlsx


title: w1118_fatBody_T=ZT21_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB11_Oct_2


title: Gastric cancer cell line OCUM1 (Long-read Iso-seq)

description:
Long-read Iso-seq
PacBio Sequel System


title: w1118_fatBody_T=ZT21_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB23_Oct_2


title: H3K37Q - rep1

description: RNA-Seq.xlsx


title: H3K36R - rep2

description: RNA-Seq.xlsx


title: w1118_fatBody_T=ZT19_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB10_Oct_2


title: H3K36Q - rep3

description: RNA-Seq.xlsx


title: H3K36R - rep1

description: RNA-Seq.xlsx


title: w1118_fatBody_T=ZT19_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB22_Oct_2


title: Gastric cancer cell line MKN1 (Long-read Iso-seq)

description:
Long-read Iso-seq
PacBio Sequel System


title: Gastric cancer cell line IM95 (Long-read Iso-seq)

description:
Long-read Iso-seq
PacBio Sequel System


title: w1118_fatBody_T=ZT19_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB10_Jan_1


title: H3K36Q - rep2

description: RNA-Seq.xlsx


title: H3K36Q - rep1

description: RNA-Seq.xlsx


title: H3K36A - rep2

description: RNA-Seq.xlsx


title: H3K36A - rep3

description: RNA-Seq.xlsx


title: H3K36A - rep1

description: RNA-Seq.xlsx


title: H3K18A - rep2

description: RNA-Seq.xlsx


title: w1118_fatBody_T=ZT17_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB21_Oct_2


title: H3K18A - rep3

description: RNA-Seq.xlsx


title: H3K36R - rep3

description: RNA-Seq.xlsx


title: H3K18A - rep1

description: RNA-Seq.xlsx


title: H3K122Q - rep1

description: RNA-Seq.xlsx


title: H3K122Q - rep2

description: RNA-Seq.xlsx


title: H3K122Q - rep3

description: RNA-Seq.xlsx


title: H3K122A - rep3

description: RNA-Seq.xlsx


title: w1118_fatBody_T=ZT17_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB9_Jan_1


title: w1118_fatBody_T=ZT15_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB8_Oct_2


title: w1118_fatBody_T=ZT15_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB8_Jan_2


title: H3K122A - rep2

description: RNA-Seq.xlsx


title: H3K122A - rep1

description: RNA-Seq.xlsx


title: H3K121R - rep3

description: RNA-Seq.xlsx


title: w1118_fatBody_T=ZT15_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB20_Oct_2


title: w1118_fatBody_T=ZT17_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB9_Oct_2


title: H3K121R - rep1

description: RNA-Seq.xlsx


title: H3K121R - rep2

description: RNA-Seq.xlsx


title: w1118_fatBody_T=ZT13_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB7_Oct_2


title: RNA-seq_Case11_A

city: Chongqing

first: Guanghui

state: Chongqing

address: Xinqiao Street No. 2r

department: Xinqiao Hospital

institute: Army Medical University

data_processing:
RNA-seq were performed in the Illumina Novaseq System. All libraries were sequenced on the Novaseq using 2×150 bp paired-end sequencing.
Adaptor sequences were trimmed, and reads were processed into clean reads. Each RNA-seq data required approxiimately 10 G.
A novel network flow algorithm used in StringTie (version 2.2.1)  was applied to perform transcript assembly and quantify gene expression in fragments per kilobase of transcript per million fragment mapped units for RNA-seq.
DESeq (version 1.24.0)  was used to identify differentially expressed genes (DEGs)
Genome_build: genome GRCh37.75
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted from tumor tissues using TRIzol™ Reagent (Life Technologies) for transcriptome analyses. RNA integrity, purity, and concentration were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies). Nanodrop and Qubit 3.0. RNA-seq libraries were constructed using KAPA mRNA HyperPrep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Computed tomography-guided puncture biopsy of the lung deposit was performed a week before SBRT, and were then placed in the refrigerator (-80°C) to preserve sample integrity.

value: non-small-cell lung cancer

tag: diagnosis

tag: histology

value: Adenocarcinoma

value: Fraction of radiotherapy:60Gy/19F


title: RNA-seq_Case11_B

source_name: Computed tomography-guided puncture biopsy of the lung deposit

value: NO


title: RNA-seq_Case10_B

value: colorectal cancer

value: Metastasis


title: H3K121Q - rep2

description: RNA-Seq.xlsx

value: MSY196 (based on S288C)


title: w1118_fatBody_T=ZT13_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB19_Oct_2

tag: strain

value: Time-series for w1118


title: experimental group 5

first: Yan

last: PAN

address: 38 Xueyuan Rd, Haidian District

department: Pharmacology

institute: Peking University

hyb_protocol: cDNA of PC-3M-adhered HUVECs (TC-EC), or from HUVECs controls (EC) was hybridized to Human Gene 2.0 ST GeneChip® arrays (Affymetrix, America) according to the User Manuals.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: Raw data (CEL files) were normalized at transcript level using robust multiaverage method (RMA workflow). Median summarization of transcript expressions was calculated. Gene-level data was then filtered to include only those probe sets that are in the ‘core’ metaprobe list, which represent RefSeq genes.

source_name: Human umbilical vein endothelial cells + PC-3M

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

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were isolated by collagenase І digestion of umbilical veins from undamaged sections of fresh umbilical cords. HUVECs were cultured in M199 supplemented with 20% heat-inactivated fetal bovine serum (FBS), 20 µg/ml endothelial cell growth supplement, 100 U/ml penicillin, 100 µg/ml streptomycin and 2 mM L-glutamine. PC-3M cells were cultured in RPMI 1640 medium containing 10% heat-inactivated FBS, 100 U/ml penicillin and 100 µg/ml streptomycin in a humidified incubator with 5 % CO2 in air at 37°C.

extract_protocol: Total RNA was isolated with TRIzol reagent and purified using RNeasy Mini Kit, including a DNase digestion treatment.

treatment_protocol: HUVECs were cultured in 96-well dishes coated with 1 % gelatin. When HUVECs reached an approximate confluence of 100 %, PC-3M cells were washed and resuspended in culture medium (105 cells/ml). One hundred microliters of the tumor cell suspension were added to HUVECs monolayers in 96-well dishes and co-cultured with HUVECs for 30 min at 37°C. At the end of the incubation, wells were washed three times with PBS to try to remove adherent and non-adherent PC-3M cells.

value: Human umbilical vein endothelial cells

tag: condition

value: co-cultured with PC-3M(removed after co-culturing)


title: experimental group 4


title: control group 2

source_name: Human umbilical vein endothelial cells

value: cultured alone


title: H3K121Q - rep1

description: RNA-Seq.xlsx


title: control group 3


title: control group 1


title: experimental group 6


title: H3K121A - rep2

description: RNA-Seq.xlsx


title: H3K121A - rep3

description: RNA-Seq.xlsx


title: RNA-seq_Case9_B

tag: tissue


title: w1118_fatBody_T=ZT11_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB18_Oct_2

value: whole fat body

tag: time of harvesting

tag: replicate


title: w1118_fatBody_T=ZT9_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB5_Jan_3

tag: library

tag: bloomington


title: H3K115R - rep3

description: RNA-Seq.xlsx


title: H3K115R - rep2

description: RNA-Seq.xlsx


title: w1118_fatBody_T=ZT9_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB5_Oct_2


title: RNA-seq_Case8_B

tag: treatment


title: RNA-seq_Case9_A

value: Fraction of radiotherapy:60Gy/17F


title: H3K121Q - rep3

description: RNA-Seq.xlsx


title: H3K115R - rep1

description: RNA-Seq.xlsx


title: w1118_fatBody_T=ZT9_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB17_Oct_2


title: H3K115Q - rep1

description: RNA-Seq.xlsx


title: RNA-seq_Case8_A

value: Fraction of radiotherapy:60Gy/16F


title: H3K115Q - rep3

description: RNA-Seq.xlsx


title: w1118_fatBody_T=ZT11_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB6_Oct_2


title: w1118_fatBody_T=ZT7_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB4_Jan_3


title: H3K115A - rep3

description: RNA-Seq.xlsx


title: RNA-seq_Case7_B


title: RNA-seq_Case10_A

value: Fraction of radiotherapy:60Gy/18F


title: H3K115A - rep2

description: RNA-Seq.xlsx


title: w1118_fatBody_T=ZT7_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB4_Oct_2


title: H3K121A - rep1

description: RNA-Seq.xlsx


title: H3K115A - rep1

description: RNA-Seq.xlsx


title: RNA-seq_Case7_A

value: Fraction of radiotherapy:60Gy/15F


title: w1118_fatBody_T=ZT7_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB16_Oct_2


title: LPS 4 hours 3

city: Charlestown

first: Mahesh Chandra

last: Kodali

department: Neurology

institute: Massachusetts General Hospital / Harvard Medical School

description:
one male and one female pooled together
DESeq2_normalized_counts.txt

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

source_name: Cerebral Vessels

extract_protocol:
RNA was extracted from mouse cerebral vessels after trizol homogenization, and then using QIAGEN miRNeasy micro Kit. Samples were later DNAse treated and cleaned up using RNEasy minelute clean up kit, finally eluted in RNAse free water from Qiagen.
Isolated RNA sample quality was determined using High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and concentration was measured using Qubit 2.0 RNA High Sensitivity assay (ThermoFisher, Massachusetts, USA). Libraries were then constructed following manufacturer’s instructions for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio USA Inc., California, USA) followed by Nextera® XT DNA Library Prep Kit (Illumina, California, USA). Final library quantities were measured by KAPA SYBR® FAST qPCR and quality was assessed using TapeStation D1000 ScreenTape (Agilent Technologies, CA, USA). Resulting final library size was about 430bp with an insert size of about 200bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed basing on QC values and sequencing was performed on an Illumina® NovaSeq 6000 (Illumina, California, USA). The read length configuration was 150 PE for 20M PE reads per sample (10M in each direction).

value: wild type

value: 10mg/kg LPS for 4 hours

tag: Sex

value: pooled male and female


title: LPS 4 hours 2

tag: genotype


title: LPS 4 hours 1


title: RNA-seq_Case6_B

value: Adenocarcinoma