title: C11_LTLB2


title: B2_LTLB2

status: Public on Jun 21 2017

type: SRA

city: Leipzig

first: Gray

last: Camp

address: Deutscher Pl. 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

description:
Single cell transcriptome from late time point liver buds
data.lb.late.csv

library_source: transcriptomic

data_processing:
"freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.)
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.)
Reads were aligned against the human genome (build GRCh38.77 from ENSEMBLE) or mouse genome (mm10 from UCSC) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.6
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1
Genome_build: GRCh38, mm10
Supplementary_files_format_and_content: Master data frame including sample name, gene ID, and FPKM values for each single cell.

molecule: total RNA

organism: Homo sapiens

source_name: iPSC line TkDA3-4

growth_protocol: see information for each individual sample

extract_protocol:
Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions at a dilution of 1:40,000.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.
mRNA-seq

tag: strain

tag: cell type


title: A4_LTLB2

treatment_protocol: see information for each individual sample

value: Single cell transcriptome from late time point liver buds


title: A6_LTLB2


title: A5_LTLB2


title: A12_LTLB2


title: H9_LTLB1


title: A1_LTLB2


title: A2_LTLB2


title: A3_LTLB2


title: A11_LTLB2


title: H6B_LTLB1


title: H9B_LTLB1


title: B1_LTLB2


title: H5B_LTLB1


title: H5_LTLB1


title: H2_LTLB1


title: G9_LTLB1


title: H3B_LTLB1


title: H1_LTLB1


title: H1B_LTLB1


title: H10_LTLB1


title: G6B_LTLB1


title: G3B_LTLB1


title: G4_LTLB1


title: G4B_LTLB1


title: G8_LTLB1


title: G3_LTLB1


title: G2_LTLB1


title: H11_LTLB1


title: H2B_LTLB1


title: H12B_LTLB1


title: G7_LTLB1


title: G1B_LTLB1


title: G12_LTLB1


title: G6_LTLB1


title: G2B_LTLB1


title: G10_LTLB1


title: F9B_LTLB1


title: F8B_LTLB1


title: F7B_LTLB1


title: F4_LTLB1


title: G9B_LTLB1


title: G12B_LTLB1


title: F12_LTLB1


title: F3_LTLB1


title: F3B_LTLB1


title: F4B_LTLB1


title: F11_LTLB1


title: F1B_LTLB1


title: F2B_LTLB1


title: F12B_LTLB1


title: H12_LTLB1


title: E9B_LTLB1


title: E7_LTLB1


title: E7B_LTLB1


title: E4B_LTLB1


title: E4_LTLB1


title: E6B_LTLB1


title: E3B_LTLB1


title: E1B_LTLB1


title: E8B_LTLB1


title: E5_LTLB1


title: F11B_LTLB1


title: E5B_LTLB1


title: E11_LTLB1


title: F9_LTLB1


title: E10_LTLB1


title: E11B_LTLB1


title: E10B_LTLB1


title: F10B_LTLB1


title: E2_LTLB1


title: D9_LTLB1


title: E12_LTLB1


title: D8_LTLB1


title: D8B_LTLB1


title: D7B_LTLB1


title: D6_LTLB1


title: D5B_LTLB1


title: D6B_LTLB1


title: D1B_LTLB1


title: D10_LTLB1


title: D5_LTLB1


title: D3B_LTLB1


title: C6B_LTLB1


title: C5B_LTLB1


title: D12_LTLB1


title: C9_LTLB1


title: D10B_LTLB1


title: C5_LTLB1


title: C7_LTLB1


title: C3B_LTLB1


title: C2B_LTLB1


title: C2_LTLB1


title: C12B_LTLB1


title: C1B_LTLB1


title: C11_LTLB1


title: C11B_LTLB1


title: B8B_LTLB1


title: B9_LTLB1


title: D3_LTLB1


title: B7B_LTLB1


title: C6_LTLB1


title: C9B_LTLB1


title: B6B_LTLB1


title: C8B_LTLB1


title: B3B_LTLB1


title: B3_LTLB1


title: B2_LTLB1


title: B5_LTLB1


title: B2B_LTLB1


title: B12_LTLB1


title: B12B_LTLB1


title: A7B_LTLB1


title: A6B_LTLB1


title: A9B_LTLB1


title: A5B_LTLB1


title: A9_LTLB1


title: A2B_LTLB1


title: A2_LTLB1


title: A1B_LTLB1


title: A3B_LTLB1


title: B7_LTLB1


title: A11B_LTLB1


title: A10_LTLB1


title: H1A_fetalHep2_fetal17

description:
Single cell transcriptome from fetal liver
data.human.liver.csv


title: H4A_fetalHep2_fetal17

value: Single cell transcriptome from fetal liver


title: G10A_fetalHep2_fetal17


title: F8A_fetalHep2_fetal17


title: B10B_LTLB1


title: F6A_fetalHep2_fetal17


title: B11_LTLB1


title: F1A_fetalHep2_fetal17


title: F3A_fetalHep2_fetal17


title: E8A_fetalHep2_fetal17


title: A6_LTLB1


title: E5A_fetalHep2_fetal17


title: E2A_fetalHep2_fetal17


title: E12A_fetalHep2_fetal17


title: E11A_fetalHep2_fetal17


title: E10A_fetalHep2_fetal17


title: D8A_fetalHep2_fetal17


title: D9A_fetalHep2_fetal17


title: D7A_fetalHep2_fetal17


title: D6A_fetalHep2_fetal17


title: D5A_fetalHep2_fetal17


title: D4A_fetalHep2_fetal17


title: G2A_fetalHep2_fetal17


title: F7A_fetalHep2_fetal17


title: F4A_fetalHep2_fetal17


title: F2A_fetalHep2_fetal17


title: D12A_fetalHep2_fetal17


title: D11A_fetalHep2_fetal17


title: C8A_fetalHep2_fetal17


title: D10A_fetalHep2_fetal17


title: C7A_fetalHep2_fetal17


title: C9A_fetalHep2_fetal17


title: E3A_fetalHep2_fetal17


title: C12A_fetalHep2_fetal17


title: C11A_fetalHep2_fetal17


title: E1A_fetalHep2_fetal17


title: C1A_fetalHep2_fetal17


title: C2A_fetalHep2_fetal17


title: C6A_fetalHep2_fetal17


title: C5A_fetalHep2_fetal17


title: B7A_fetalHep2_fetal17


title: B8A_fetalHep2_fetal17


title: A11_LTLB1


title: B4A_fetalHep2_fetal17


title: B5A_fetalHep2_fetal17


title: A7A_fetalHep2_fetal17


title: A8A_fetalHep2_fetal17


title: B3A_fetalHep2_fetal17


title: B6A_fetalHep2_fetal17


title: B1A_fetalHep2_fetal17


title: B11A_fetalHep2_fetal17


title: A9A_fetalHep2_fetal17


title: A6A_fetalHep2_fetal17


title: A2A_fetalHep2_fetal17


title: B10A_fetalHep2_fetal17


title: A12A_fetalHep2_fetal17


title: A3A_fetalHep2_fetal17


title: A4A_fetalHep2_fetal17


title: A11A_fetalHep2_fetal17


title: H7B_fetalHep2_fetal10


title: D7B_fetalHep2_fetal10


title: F5B_fetalHep2_fetal10


title: F7B_fetalHep2_fetal10


title: H4B_fetalHep2_fetal10


title: E5B_fetalHep2_fetal10


title: H9B_fetalHep2_fetal10


title: D8B_fetalHep2_fetal10


title: G8B_fetalHep2_fetal10


title: D1B_fetalHep2_fetal10


title: D2B_fetalHep2_fetal10


title: F12B_fetalHep2_fetal10


title: C9B_fetalHep2_fetal10


title: C6B_fetalHep2_fetal10


title: D12B_fetalHep2_fetal10


title: C3B_fetalHep2_fetal10


title: Fes WT – repl 4

city: Leuven

first: Sara

last: Aibar

address: Herestraat 49

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

data_processing:
Samples sequenced on Illumina NextSeq 500 High 75 generating on average 19.8 million reads per sample.
FastQC was used to assess the quality of the sequenced data
Raw reads mapped to the mouse reference genome (mm10) using STAR (version 2.51b)
Reads assigned to Ensembl genes (GRCm38.84) and counted using Subread (version 1.4.6)
Genome_build: mm10
Supplementary_files_format_and_content: [RNAseq_counts.txt] Tab-delimited text file including mapped counts.
Supplementary_files_format_and_content: [RNAseq_SFnorm_log2_counts.txt] Tab-delimited text file including log2 size-factor normalized counts.

organism: Mus musculus

source_name: Fes WT, melanoma

extract_protocol:
RNA extracted using RNeasy Mini kit (Qiagen) following manufacturer’s instructions. The RNA quality was assessed using Bioanalyzer’s RNA nanochip (Agilent) and RNA with RIN values >7 were used for library preparation.
RNA libraries prepared using Illumina’s NextSeq library prep kit (Illumina) and library quality confirmed on Bioanalyzer.

treatment_protocol: Topical treatment on the back skin with 5 mM 4OH-Tamoxifen

tag: tissue

value: Melanoma

tag: genotype/variation

value: Fes WT


title: C2B_fetalHep2_fetal10


title: Fes WT – repl 5


title: C7B_fetalHep2_fetal10


title: Fes WT – repl 3


title: C10B_fetalHep2_fetal10


title: Fes KO – repl 5

source_name: Fes KO, melanoma

value: Fes KO


title: B9B_fetalHep2_fetal10


title: Fes KO – repl 4


title: Fes KO – repl 3


title: B7B_fetalHep2_fetal10


title: B6B_fetalHep2_fetal10


title: Fes WT – repl 1


title: Fes KO – repl 2


title: B2B_fetalHep2_fetal10


title: B4B_fetalHep2_fetal10


title: B3B_fetalHep2_fetal10


title: B1B_fetalHep2_fetal10


title: Fes KO – repl 1


title: A3B_fetalHep2_fetal10


title: A10A_fetalHep2_fetal17


title: H7A_fetalHep1_fetal17


title: A10B_fetalHep2_fetal10


title: H5A_fetalHep1_fetal17


title: H6A_fetalHep1_fetal17


title: H1A_fetalHep1_fetal17


title: H12A_fetalHep1_fetal17


title: H10A_fetalHep1_fetal17


title: H2A_fetalHep1_fetal17


title: G9A_fetalHep1_fetal17


title: G8A_fetalHep1_fetal17


title: A9B_fetalHep2_fetal10


title: G1A_fetalHep1_fetal17


title: G4A_fetalHep1_fetal17


title: A4B_fetalHep2_fetal10


title: G5A_fetalHep1_fetal17


title: G10A_fetalHep1_fetal17


title: A2B_fetalHep2_fetal10


title: F4A_fetalHep1_fetal17


title: F5A_fetalHep1_fetal17


title: Fes WT – repl 2


title: A12B_fetalHep2_fetal10


title: G2A_fetalHep1_fetal17


title: F8A_fetalHep1_fetal17


title: G6A_fetalHep1_fetal17


title: G11A_fetalHep1_fetal17


title: F6A_fetalHep1_fetal17


title: F10A_fetalHep1_fetal17


title: F12A_fetalHep1_fetal17


title: F1A_fetalHep1_fetal17


title: E5A_fetalHep1_fetal17


title: E12A_fetalHep1_fetal17


title: E2A_fetalHep1_fetal17


title: E3A_fetalHep1_fetal17


title: E1A_fetalHep1_fetal17


title: E6A_fetalHep1_fetal17


title: E11A_fetalHep1_fetal17


title: F3A_fetalHep1_fetal17


title: D4A_fetalHep1_fetal17


title: D7A_fetalHep1_fetal17


title: D1A_fetalHep1_fetal17


title: F2A_fetalHep1_fetal17


title: D8A_fetalHep1_fetal17


title: D12A_fetalHep1_fetal17


title: C8A_fetalHep1_fetal17


title: C1A_fetalHep1_fetal17


title: C12A_fetalHep1_fetal17


title: D3A_fetalHep1_fetal17


title: C3A_fetalHep1_fetal17


title: C10A_fetalHep1_fetal17


title: C7A_fetalHep1_fetal17


title: D9A_fetalHep1_fetal17


title: C11A_fetalHep1_fetal17


title: D2A_fetalHep1_fetal17


title: E9A_fetalHep1_fetal17


title: D11A_fetalHep1_fetal17


title: B8A_fetalHep1_fetal17


title: B5A_fetalHep1_fetal17


title: B6A_fetalHep1_fetal17


title: B3A_fetalHep1_fetal17


title: B11A_fetalHep1_fetal17


title: B1A_fetalHep1_fetal17


title: B10A_fetalHep1_fetal17


title: A9A_fetalHep1_fetal17


title: A8A_fetalHep1_fetal17


title: A7A_fetalHep1_fetal17


title: A6A_fetalHep1_fetal17


title: A5A_fetalHep1_fetal17


title: A4A_fetalHep1_fetal17


title: A2A_fetalHep1_fetal17


title: A3A_fetalHep1_fetal17


title: A11A_fetalHep1_fetal17


title: A1A_fetalHep1_fetal17


title: H6A_e16.5

description:
Single cell transcriptome from e16.5 mouse liver
data.mouse.liver.csv


title: H8B_fetalHep1_fetal10


title: H3A_e16.5

value: Single cell transcriptome from e16.5 mouse liver


title: H4A_e16.5


title: G6B_fetalHep1_fetal10


title: G5A_e16.5


title: G2A_e16.5


title: H7B_fetalHep1_fetal10


title: F6A_e16.5


title: G4B_fetalHep1_fetal10


title: H12B_fetalHep1_fetal10


title: G3B_fetalHep1_fetal10


title: B12A_fetalHep1_fetal17


title: F5A_e16.5


title: G1B_fetalHep1_fetal10


title: F3A_e16.5


title: F6B_fetalHep1_fetal10


title: C11B_fetalHep2_fetal10


title: H5A_e16.5


title: E5A_e16.5


title: E6A_e16.5


title: E4A_e16.5


title: F5B_fetalHep1_fetal10


title: H5B_fetalHep1_fetal10


title: D6A_e16.5


title: F1B_fetalHep1_fetal10


title: F10B_fetalHep1_fetal10


title: D2A_e16.5


title: G10B_fetalHep1_fetal10


title: C5A_e16.5


title: E9B_fetalHep1_fetal10


title: E8B_fetalHep1_fetal10


title: E6B_fetalHep1_fetal10


title: C3A_e16.5


title: E5B_fetalHep1_fetal10


title: C4A_e16.5


title: G2B_fetalHep1_fetal10


title: F1A_e16.5


title: B7A_e16.5


title: C2A_e16.5


title: E1B_fetalHep1_fetal10


title: C1A_e16.5


title: E2B_fetalHep1_fetal10


title: E11B_fetalHep1_fetal10


title: B3A_e16.5


title: E12B_fetalHep1_fetal10


title: E10B_fetalHep1_fetal10


title: B2A_e16.5


title: B5A_e16.5


title: D9B_fetalHep1_fetal10


title: A5A_e16.5


title: D8B_fetalHep1_fetal10


title: D7B_fetalHep1_fetal10


title: D4B_fetalHep1_fetal10


title: A1A_e16.5


title: H8B_e15.5

description:
Single cell transcriptome from e15.5 mouse liver
data.mouse.liver.csv


title: D3B_fetalHep1_fetal10


title: H7B_e15.5

value: Single cell transcriptome from e15.5 mouse liver


title: B6A_e16.5


title: D1B_fetalHep1_fetal10


title: H1B_e15.5


title: D2B_fetalHep1_fetal10


title: G3B_e15.5


title: G2B_e15.5


title: D10B_fetalHep1_fetal10


title: F3B_e15.5


title: C3B_fetalHep1_fetal10


title: F8B_e15.5


title: C12B_fetalHep1_fetal10


title: F1B_e15.5


title: C6B_fetalHep1_fetal10


title: E9B_e15.5


title: B8B_fetalHep1_fetal10


title: E8B_e15.5


title: B5B_fetalHep1_fetal10


title: B4B_fetalHep1_fetal10


title: E7B_e15.5


title: E4B_e15.5


title: B3B_fetalHep1_fetal10


title: E3B_e15.5


title: B1B_fetalHep1_fetal10


title: E2B_e15.5


title: B12B_fetalHep1_fetal10


title: B11B_fetalHep1_fetal10


title: A9B_fetalHep1_fetal10


title: E1B_e15.5


title: F2B_e15.5


title: A8B_fetalHep1_fetal10


title: A3B_fetalHep1_fetal10


title: D8B_e15.5


title: A6B_fetalHep1_fetal10


title: C5B_e15.5


title: D2B_e15.5


title: B6B_fetalHep1_fetal10


title: A12B_fetalHep1_fetal10


title: A11B_fetalHep1_fetal10


title: A10B_fetalHep1_fetal10


title: C3B_e15.5


title: H3_hLivEC

description:
Single cell transcriptome from adult liver
data.human.liver.csv


title: D9B_e15.5


title: C1B_e15.5


title: D3B_e15.5


title: D10B_e15.5


title: C12B_e15.5


title: G12_hLivEC

value: Single cell transcriptome from adult liver


title: B8B_e15.5


title: B9B_e15.5


title: G10_hLivEC


title: D11B_e15.5


title: B5B_e15.5


title: F8_hLivEC


title: B4B_e15.5


title: F7_hLivEC


title: F6_hLivEC


title: B2B_e15.5


title: F1_hLivEC


title: B1B_e15.5


title: F12_hLivEC


title: A8B_e15.5


title: G8_hLivEC


title: A4B_e15.5


title: A2B_e15.5


title: D12_hLivEC


title: E12_hLivEC


title: H7A_e14.5

description:
Single cell transcriptome from e14.5 mouse liver
data.mouse.liver.csv


title: D10_hLivEC


title: H2A_e14.5

value: Single cell transcriptome from e14.5 mouse liver


title: G11_hLivEC


title: H1A_e14.5


title: G4A_hep3_hHep


title: H12A_e14.5


title: H10A_e14.5


title: G3A_hep3_hHep


title: G7A_e14.5


title: G9A_e14.5


title: E11_hLivEC


title: D11_hLivEC


title: A1B_e15.5


title: F3B_fetalHep1_fetal10


title: A10B_e15.5


title: G12A_hep3_hHep


title: G10A_hep3_hHep


title: F9A_hep3_hHep


title: G4A_e14.5


title: F6A_hep3_hHep


title: G3A_e14.5


title: F5A_hep3_hHep


title: G10A_e14.5


title: H11A_hep3_hHep


title: F4A_hep3_hHep


title: H10A_hep3_hHep


title: NSF_LT_ATAC-seq

city: Shanghai

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

country: China

institute: Institutes of Biomedical Sciences Fudan University

library_source: genomic

data_processing:
Library strategy: ATAC-seq
Mouse
Basecalls performed using CASAVA version 1.4
ATAC-seq reads were aligned to the mm9 genome assembly using bowtie with with the parameters –m 1 -best-strata –X 2000, with two mismatches permitted in the seed (default value).
Duplicated reads and reads mapped to mitochondrial were removed with samtools and grep, which were used for further analysis.
ATAC-seq peaks were called by MACS1.4. Peaks were annotated to promoter regions (TSS-/+2 kb) based on mm9 Refseq annotation.
Heterocephalus glaber
Basecalls performed using CASAVA version 1.4
ATAC-seq reads were aligned to the hetGla2 genome assembly using bowtie with with the parameters –m 1 -best-strata –X 2000, with two mismatches permitted in the seed (default value).
Duplicated reads and reads mapped to mitochondrial were removed with samtools and grep, which were used for further analysis.
ATAC-seq peaks were called by MACS1.4. Peaks were annotated to promoter regions (TSS-/+2 kb) based on hetGla2 Refseq annotation.
Genome_build: mm9; hetGla2
Supplementary_files_format_and_content: bedgraph files was generated using bedtools, peaks bed files was generated using macs1.4.

molecule: genomic DNA

organism: Heterocephalus glaber

source_name: Naked mole rate fibroblast

growth_protocol: The adult skin fibroblasts from NMR or mouse were cultured using EMEM medium (ATCC) plus 15% FBS (Gibco) and 1% P/S (Gibco). The culture conditions were 32oC for NMR and 37oC for mouse at 5%CO2 and 3%O2.

extract_protocol:
The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition the sample was purified using a Qiagen MinElute kit.
The eluate was then amplified for a total of 10–12 cycles and the PCR products were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ~30 nM in 20 μL

treatment_protocol: For ATAC-seq 50,000 cells were used. After washing with PBS, cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) for 5min at 4C. Nuclei pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water).

tag: protocol

value: Introduce SV40 Large T antigen

tag: passages

value: Passage 16


title: NSF_ATAC-seq

value: Control


title: F8A_e14.5


title: G1A_hep3_hHep


title: G6A_e14.5


title: F7A_e14.5


title: F4A_e14.5


title: F10A_hep3_hHep


title: E9A_e14.5


title: E8A_hep3_hHep


title: E8A_e14.5


title: E3A_e14.5


title: G1A_e14.5


title: E10A_hep3_hHep


title: E1A_hep3_hHep


title: E1A_e14.5


title: E2A_hep3_hHep


title: D9A_hep3_hHep


title: E11A_e14.5


title: D12A_hep3_hHep


title: D5A_e14.5


title: D4A_e14.5


title: D11A_hep3_hHep


title: C2A_hep3_hHep


title: D3A_e14.5


title: F3A_hep3_hHep


title: C4A_hep3_hHep


title: E7A_hep3_hHep


title: D10A_e14.5


title: F2A_hep3_hHep


title: C11A_hep3_hHep


title: C10A_hep3_hHep


title: C7A_e14.5


title: D1A_e14.5


title: C8A_e14.5


title: E2A_e14.5


title: B9A_hep3_hHep


title: C6A_e14.5


title: C1A_hep3_hHep


title: D8A_e14.5


title: B8A_hep3_hHep


title: B6A_hep3_hHep


title: B8A_e14.5


title: B9A_e14.5


title: A8A_hep3_hHep


title: B4A_e14.5


title: B1A_e14.5


title: B10A_hep3_hHep


title: A7A_hep3_hHep


title: B11A_e14.5


title: B10A_e14.5


title: A9A_e14.5


title: A10A_hep3_hHep


title: A5A_hep3_hHep


title: A7A_e14.5


title: Contact_Crab_2nd

city: Seoul

first: Han Young

last: Chung

address: 1 Gwanak-ro, Gwanak-gu, Seoul 151-742

country: South Korea

institute: Seoul National University

data_processing:
The Ribo-Zero rRNA removal kit (Epicentre, USA) was used for ribosomal RNA depletion according to manufacturer instructions.
Libraries for Illumina sequencing were made with the TruSeq Stranded mRNA sample prep kit (Illumina, USA) following the manufacturer’s protocol.
The quality of cDNA libraries was determined by Agilent 2100 Bioanalyzer (Agilent Technologies). Strand-specific paired-ended 100 nucleotide reads from each cDNA library were obtained using HiSeq2500 (Illumina).
For biological replication, two libraries were separately constructed and sequenced from RNAs isolated from two independent filtered culture supernatants of FORC_022.
The reads obtained from RNA-sequencing were mapped to the FORC_022 reference genome using CLC Genomics Workbench ver. 7.5.1 (CLC bio, Aarhus, Denmark). The whole genome sequence of V. parahaemolyticus FORC_022 was deposited in the GenBank of NCBI (http://www.ncbi.nlm.nih.gov/) under accession numbers CP013248, CP013249 and CP013250 for chromosome I, II, and a plasmid, respectively
Supplementary_files_format_and_content: Count and RPKM calculation by Cuffquant and Cuffdiff -> BAM file generation

organism: Vibrio parahaemolyticus

source_name: Crab

growth_protocol: FORC_022 was grown to mid-log phase (A600 of 0.8) in VFMG (Vibrio fisheri minimal medium containing glycerol) medium

extract_protocol: Total RNAs were isolated using miRNeasy Mini Kit (Qiagen) according to the manufacturer's procedure. The DNA contaminations were removed by TURBO DNase (AMbion, Austin, TX), and then extracted RNAs were cleaned up using RNeasy MinElute Cleanup kit (Qiagen). The extracted RNA was verified by Agilent 2100 Bioanalyzer with Agilent RNA 6000 Nano reagens (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: We artificially contact the FORC_022 strain to crab, and contact to crab for 4 h. Non-contact strain to crab in VFGM medium also prepared as negative control.

value: FORC_022 strain

tag: treatment

value: Contact


title: A6A_e14.5


title: G8B_hep25_hHep


title: G9B_hep25_hHep


title: G4B_hep25_hHep


title: Control_Crab_2nd

source_name: Vibrio fischeri minimal medium  containing 32.6 mM glycerol (VFMG) media (Non crab)

value: Control (Non-contact)


title: G5B_hep25_hHep


title: A3A_e14.5


title: Contact_Crab_1st


title: G2B_hep25_hHep


title: A4A_e14.5


title: A2A_e14.5


title: G1B_hep25_hHep


title: A10A_e14.5


title: Control_Crab_1st


title: F8B_hep25_hHep


title: F6B_hep25_hHep


title: MSF_ATAC-seq

source_name: Mouse fibroblast


title: F3B_hep25_hHep


title: RNA-seq_Het.e12.5

city: Davis

first: Alex

last: Nord

state: CA

address: 1544 Newton Court

department: Neurobiology, Physiology, and Behavior

country: USA

institute: University of California Davis

description:
Het e12.5
Gompers_logRPKM_Matrix.txt

data_processing:
Base calls were performed with bcl2fastq2.
RNA-seq: FASTQ files were aligned to the mouse genome (mm9) using STAR (2.4.2a).
ChIP-seq: Reads were filtered and mapped to the mouse genome mm9 via BWA (v0.7.13) and peak-calling was performed using MACS (v2.10) with a p-value cutoff of 1E-4.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files containing coverage, and txt containing MACS2 peak-calls.

molecule: polyA RNA

source_name: Bulk forebrain

extract_protocol:
Bulk forebrain was microdissected from Chd8+/del5 and matched WT littermates at e12.5,e14.5, e17.5, P0, and from adults (>P56). Total RNA was isolated using Ambion RNAqueous and assayed using an AgilentBioAnalyzer instrument.
Stranded mRNA sequencing libraries were prepared using TruSeqStranded mRNA kits and 6-12 samples per lane were pooled and sequenced on the IlluminaHiSeq platform using a single end 50 bp (e14.5, e17.5, P0, adult) or paired end 100 bp (e12.5) strategy.

tag: Stage

tag: genotype

value: Het


title: F11B_hep25_hHep


title: GcgR KO rep3

city: DALLAS

first: WEN-HONG

last: LI

state: Texas

address: 6000 Harry Hines Blvd.

department: Department of Cell Biology

institute: UT Southwestern Medical Center

data_processing:
Raw sequence reads were decoded based on their barcodes and read quality was evaluated with FastQC. Sequence reads were processed with Cutadapt (version 1.3) to trim off 3’ adaptor sequence if any. After trimming, reads shorter 20 bp were discarded. Reads were mapped to the mouse genome version 10 (mm10) with TopHat2 (Version 2.0.10) using the default setting. To identify differentially expressed genes, the statistical significance (p-value) of the differential expressions was assessed with DESeq package (version 2.0).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files include RPKM values for each samples.

source_name: FACS-purified non-beta cells

growth_protocol: Mice were injected with Ex4-SRB or Ex4-Cy5 0.2 µmol/kg throught tile vein 2 hours before islet isolation. Islets were isolated by collagnease injection through the common bile duct. Isolated islets were cultured in RPMI 1640 medium supplemented with 11 mM glucose and 10% FBS and pen/strep and 2 mM glutamine. Islets were dispersed by Enzyme Free Cell Dissociation Solution for FACS purification. FACS purified cells were collected in Trizol LS.

extract_protocol:
Total RNA was isolated with Trizol (Invitrogen, 15596-018) by a chloroform extraction, and was precipitated by isopropanol and redissolved in 20 µL of RNase free water. After digesting the sample with TURBOTM DNase (Ambion, AM2239), we extracted RNA (in 100 µL water) with chloroform/phenol and precipitated RNA with 250 µL of 100% ethanol and 10 µL of 3M NaOAc at -80 °C overnight. Ribosome RNA was removed by using Ribo-ZeroTM rRNA removal kit (Epicenter, MRZH116).
The purified RNA was used for the cDNA library preparation using the TruSeq Stranded mRNA Library Prep Kit.
The library was sequenced using the Illumina HiSeq 2000 platform through 50-cycle single-end runs.

value: islets

value: non-beta cells

value: GcgR-/-

tag: gender

value: male


title: 5U

city: Bar Harbor

first: Michael

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
FASTQ files were generated with Casava v. 1.8.2
Sequence files were aligned to the Amel_4.5 genome (OGSv3.2 annotation build) using Tophat2 v. 2.0.10. with Bowtie2 v. 2.1.0 and Samtools v. 0.1.19.
Contamination by deformed wing virus (DWV) was calculated by aligning to the Pennsylvania variant of the DWV genome (GenBank accession: AY292384) using Bowtie 2 v. 2.1.0. Though there was some DWV contamination, the levels were an order of magnitude lower than experiments where DWV has been problematic.
Reads inside of gene features were counted using htseq-count in the HTSeq Python framework v. 0.6.1
Genome_build: Amel_4.5 (OGSv3.2 annotation) with Pennsylvania build of DWV (GenBank accession: AY292384)
Supplementary_files_format_and_content: Tab-delimited text files containing gene IDs and counts of reads mapped inside each gene feature.

organism: Apis mellifera

source_name: mushroom bodies

growth_protocol: One-day-old adult bees were obtained by removing frames of honeycomb containing pupae from colonies, placing them in an incubator (34°C, 50 ± 5% relative humidity), and then monitoring their emergence every 24 h. One-day-old bees were individually marked on their thoraces with a spot of paint (Testor’s PLA) and placed in groups. Bees were kept in the laboratory in vertically oriented Petri dishes (100 X 20 mm) with a beeswax foundation sheet placed on the “wall” of the dish to mimic in-hive conditions. Dishes were supplied with one tube of honey (~1.4 mL), 30% sucrose solution (2 mL) and a mixture of fresh frozen pollen and 30% sugar solution (~10 mm diameter ball).

extract_protocol:
The groups included in the gene expression study included well distinguished bees of each the three behavioural types: nurses, guards, and unresponsive bees. The bees were collected by flash freezing in liquid nitrogen and were placed in marked 1.5 mL microcentrifuge tube in a dry ice bucket. The bees were kept at -80° C until tissue collection. Six groups of bees from each of two SDI colonies were included in the gene expression analysis. Bees’ heads were separated from bodies on dry ice and placed in a dissection dish with 200 proof ethanol and dry ice to prevent RNA degradation during dissection. The cuticle of the head capsule was removed and each head was placed in RNAlaterICE (Life Technologies) at -20ºC for 14 h to 18 h. The heads were then opened, the hypopharyngeal glands removed, and the whole brain removed. Using a fine scalpel, the optic lobes were removed and a horizontal incision was made across the midbrain through the posterior protocerebral lobe. The lower part of the midbrain containing the antennal lobes and the subesophageal ganglion were removed. The upper part of the midbrain containing mostly the mushroom bodies (MB) and the central brain was used for gene expression analysis. MB were placed in a new 1.5 mL microcentrifuge tube and kept frozen at -80° C until RNA extraction. RNA extraction was performed with a PicoPure RNA Isolation Kit (Applied Biosystems; Lot #1210063) according to the manufacturer’s specifications, including a DNase treatment (QIAGEN) to remove genomic DNA contamination. 550 ng RNA from each sample were used for whole mRNA expression analysis.
The RNA-Seq libraries were constructed with the TruSeq® Stranded mRNA HT (Illumina) using an ePMotion 5075 robot (Eppendorf) according to manufacturer's specifications. The libraries were pooled in equimolar concentration as instructed and each pool was quantitated by qPCR and sequenced  for 101 cycles on a HiSeq2500 using a HiSeq SBS sequencing kit v. 4.

treatment_protocol: Groups of 10 individually marked seven-day-old adult bees were held in Petri dishes inside an incubator room (34° C ± 1° C, 50% ± 10% RH). The bees were held in the dish from adult emergence with ad libitum food supply and were not exposed to outside stimuli until the beginning of the experiment. All behavioural observations were performed in the incubator room, which mimics the hive environment. Observations were performed in white light. For defining bees’ behavioural types within a group, we developed a new assay using two behavioural subassays: the well-established resident-intruder assay8 and a the nursing assay 10. Briefly, the resident-intruder assay is a five minute survey of all aggressive interactions with an unrelated bee following its introduction to the groups; typically, about 3 bees will react with highly aggressive behaviours, attacking the intruder with biting and stinging. The nursing assay is a five minute survey of all nurturing interactions with a four-days-old queen larva in queen cup that is introduced to the groups; bees in the groups respond to the queen cell by entering the cell for inspection (short visits of less than 10 sec) or larval nursing (long visits of 11 sec or more). Typically, 2-3 bees will conduct nursing behaviour for more than 30s during the assay. Both subassays were done on the same group one after the other in random order according to a coin flip, then both subassays were repeated in random order an hour after the completion of the first set of subassays. Bees conducting highly aggressive behaviour including biting and stinging in both intruder assay were consider guard (G) bees; bees conducting larval nursing twice were consider nurses (N). Bees that didn’t respond with any overt social behaviour were defined as unresponsive (U) bees. The rest of the bees in the group were defined by their behaviour, which included “low responders”, bees that showed weak responses to a social stimulus, and animals that showed hybrid responses. Only the well-defined bees of the three behavioural types were used for further analysis. Individual observers conducted each of the four behavioural subassays in the social responsivity assay blind to any former observation while tracking the bees. The behavioural experiment was repeated with seven different colonies and the average of the percentage of bees in each behavioural type was calculated.

value: brain

tag: colony

value: Unresponsive


title: 5N

value: Nurse


title: 5G

value: Guard


title: F10B_hep25_hHep

value: Single cell transcriptome from adult liver


title: E7B_hep25_hHep


title: E9B_hep25_hHep


title: GcgR KO rep1


title: GcgR KO rep2


title: 40U


title: 40N


title: 40G


title: H5A_hep3_hHep


title: E11B_hep25_hHep


title: WT rep1

value: GcgR+/+


title: E10B_hep25_hHep


title: MSF_LT_ATAC-seq

value: Introduce SV40 Large T antigen


title: F5B_hep25_hHep


title: WT rep2


title: D11B_hep25_hHep


title: B11B_hep25_hHep


title: 36N


title: 36U


title: 36G


title: A4B_hep25_hHep


title: 35U


title: A1B_hep25_hHep


title: WT rep3


title: 35N


title: CAGE_MWCNT_15

city: Hørsholm

first: Yun

last: Chen

address: Bøge Alle 10

department: Health & Nutrition

country: Denmark

institute: Chr Hansen A/S

description: barcode: CTTCAGCAG

data_processing:
CAGE: basecalling by CASAVA version 1.8.2.
The first 11 nt from 5'-end and the last 13nt from 3'-end are trimmed off (check sample description)
All the reads are then filtered by fastq_quality_filter (fastx_toolkit) using -q 30 -p 50
Reads are mapped to mm9 by Bowtie version 0.12.7 using --strata --best -k 10 -v 2
Only the 5'-end of single mapped reads are used in the analysis and mitochondrial reads are filtered away.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files are TPM-normalized stranded signals of mapped CAGE reads using above mapping steps.

source_name: Lung cell_MWCNT

growth_protocol: Female C57BL/6 mice aged 5-7 weeks were obtained from Taconic (Ry, Denmark). The mice were allowed to acclimatize for 1-3 weeks before the experiment

extract_protocol:
Lungs was removed and snap frozen in liquid nitrogen immediatly after the sacrifice of the mice. Isolated lungs were stored at -80 C until purification with Trizol and Purelink RNA mini kit (Ambion) with on-column purification as recommend by manufacturer. RNA concentration was measured on a Nanodrop 1000 spectrophotometer and the RNA intergrity was checked on a Bioanalyzer and had a RIN score above 8.7.
CAGE libraries was constructed using 3000 ng of total RNA as input for the protocol published by Takahashi et al 2012 (PMID: 21938627)

treatment_protocol: C57BL/6 mice was exposed to vehicle or multi walled carbon nanotubes (MWCNT) by intratracheal installation. 5 mice was exposed to 162 ug of MWCNTs ( XNRI-7;  lot05072001K28, Hadoga Chemical industry (formerly known as Mitsui) disolved in 0.9% NaCl  and 10% v/v cellfree cellular broncho alveolar lavage (BAL) fluid collected from C57BL/6 mice. 6 mice was exposed to the previously decribed saline/BAL solution but without carbon nanotubes. The mice was sacrified 24 hr after exposure.

value: female

value: lung


title: CAGE_MWCNT_18

description: barcode: ATCCAGACG


title: CAGE_MWCNT_17

description: barcode: ACGCAGCAG


title: CAGE_MWCNT_16

description: barcode: GATCAGCAG


title: 35G


title: A12B_hep25_hHep


title: H9A_hep4_hHep


title: CAGE_MWCNT_14

description: barcode: CTTCAGCAG


title: CAGE_MWCNT_13

description: barcode: CTTCAGCAG


title: H7A_hep4_hHep


title: CAGE_CONTROL_560

description: barcode: ACGCAGCAG

source_name: Lung cell_control


title: H5A_hep4_hHep


title: CAGE_CONTROL_559

description: barcode: GATCAGCAG


title: CAGE_CONTROL_548

description: barcode: CTTCAGCAG


title: H2A_hep4_hHep


title: 32N


title: 32U


title: H4A_hep4_hHep


title: CAGE_CONTROL_549

description: barcode: CTTCAGCAG


title: H1A_hep4_hHep


title: 32G


title: 237U


title: 237G


title: 237N


title: 230U


title: G2A_hep4_hHep


title: CAGE_CONTROL_547

description: barcode: CTTCAGCAG


title: G10A_hep4_hHep


title: ITD_MNC_rep4

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

description: polyA mRNA

data_processing:
Reads were aligned using Bowtie (Langmead et al., 2009) against the murine transcriptome (mouse NCBI build38 (mm10) UCSC transcripts).
Non-uniquely mapped reads were discarded.
Expression levels of all genes were quantified using RSEM with default parameters (Li and Dewey, 2011).
Genome_build: mm10
Supplementary_files_format_and_content: Read counts and RPKM values from RNA sequencing

source_name: Bone marrow MNCs

extract_protocol:
cDNA was generated as described in the manual for "SMARTer Ultra Low RNA Kit for Illumina sequencing" marketed by Clontech. Then, a sequencing library was generated as described in Illumina's "Ultra Low Input mRNA-Seq Guide".
For RNA-Seq NEBNext® DNA Library Prep Reagent Set for Illumina®

treatment_protocol: Cell populations isolated by FACS sorting from mouse bone marrow

value: Bone Lining Cells

value: C57 BL6, Flt3-ITD knock-in

tag: phenotype

value: Bone marrow MNCs


title: 230G


title: ITD_MNC_rep3

description: polyA mRNA


title: ITD_MNC_rep2

description: polyA mRNA


title: F3A_hep4_hHep


title: ITD_MNC_rep1

description: polyA mRNA


title: 222N


title: 222U


title: F10A_hep4_hHep


title: WT_MNC_rep4

description: polyA mRNA

value: C57 BL6


title: 222G


title: E7A_hep4_hHep


title: WT_MNC_rep2

description: polyA mRNA


title: WT_MNC_rep3

description: polyA mRNA


title: D9A_hep4_hHep


title: WT_MNC_rep1

description: polyA mRNA


title: 213U


title: ITD_MSCs_rep5

description: polyA mRNA

source_name: Bone Lining Cells


title: 213N


title: 213G


title: D3A_hep4_hHep


title: D2A_hep4_hHep


title: 210U


title: 230N


title: F4A_hep4_hHep


title: 210N


title: C4A_hep4_hHep


title: ITD_MSCs_rep3

description: polyA mRNA


title: ITD_MSCs_rep2

description: polyA mRNA


title: 210G


title: D10A_hep4_hHep


title: ITD_MSCs_rep1

description: polyA mRNA


title: C1A_hep4_hHep


title: B7B_e15.5

value: Single cell transcriptome from e15.5 mouse liver


title: 205U


title: E12A_hep4_hHep


title: 205N


title: B9A_hep4_hHep


title: WT_MSCs_rep5

description: polyA mRNA


title: ITD_MSCs_rep4

description: polyA mRNA


title: B3A_hep4_hHep


title: 205G


title: B2A_hep4_hHep


title: WT_MSCs_rep3

description: polyA mRNA


title: WT_MSCs_rep2

description: polyA mRNA


title: WT_MSCs_rep1

description: polyA mRNA


title: B12A_hep4_hHep


title: B10A_hep4_hHep


title: 19N


title: delta_hfq-rep3

city: West Haven

first: Irnov

last: Irnov

state: Connecticut

address: 840 West Campus Drive

department: Molecular, Cellular, and Developmental Biology

institute: Yale University

data_processing:
Default Illumina pipeline sofware packwage was used to generate sequencing reads
Sequencing reads were trimmed using Cutadapt and mapped into the C. crescentus CB15N reference genome (NC_011916.1) using Bowtie2
Differential expression analysis was carried out using DeSeq2
The expression level for each gene was calculated as the number of reads mapped per kilobase of gene (‘gene count’) normalized by the 75th-percentile of all gene counts in the sample (Bullard et al., 2010, BMC Bioinformatics)
Genome_build: NC_011916.1
Supplementary_files_format_and_content: tab-delimited text files include gene name, expression level for each replicates of WT (1-3), expression level for each replicate of delta_hfq (1-3), mean expression for WT, standard deviation for WT, mean expression for delta_hfq, standard deviation for delta_hfq, fold change between delta_hfq and WT (in log2, generated from DESeq2), adjusted p_value (from DESeq2)

organism: Caulobacter vibrioides

source_name: bacterial culture

growth_protocol: Exponential phase, PYE medium, 30 C

extract_protocol:
Total RNA was extracted using Trizol. Ribo-zero kit for Gram-Negative bacteria was used to deplete ribosomal RNA.
RNA-Seq library was generated using Illumina ScriptSeqv2

value: CB15N hfq::tet


title: 19G


title: A8A_hep4_hHep


title: delta_hfq-rep2


title: ITD_ECs_rep5

description: polyA mRNA


title: ITD_ECs_rep4

description: polyA mRNA


title: delta_hfq-rep1


title: ITD_ECs_rep2

description: polyA mRNA


title: 2D_stage 3 day 3

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

data_processing:
All sequence reads were extracted in FASTQ format using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
Calculation of gene expression value and normalization were performed by RPKMforgenes (10th, Dec, 2012).
Genome_build: The sequence reads were mapped to hg19 reference genes, downloaded on 25th April 2014
Supplementary_files_format_and_content: The processed data file contains Genename, Refseq, RPKM, and Rawcount columns (from left to right), and the expression level was represented by RPKM.

source_name: Human ES cell-derived pancreatic progenitor cell

growth_protocol: The human ES cell (hESC) line, KhES-3 was grown on feeder layers of mitomycin C-treated SNL 76/7 in media containing Primate ES medium (ReproCELL) supplemented with 500 U/ml penicillin/streptomycin and 4 ng/ml recombinant human basic fibroblast growth factor (bFGF) at 37 ºC in a humidified incubator with 5% CO2. The hESC-derived pancreatic progenitor cells were cultured in Improved MEM Zinc Option with 1% of B27, 100 ng/ml keratinocyte growth factor (KGF), 100 ng/ml NOGGIN, 50 ng/ml epidermal growth factor (EGF).

extract_protocol:
RNA was extracted with QIAGEN RNeasy mini kit, followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. RNA was quantified using a NanoDrop-1000 spectrophotometer.
We generated sequencing libraries using TruSeqStranded Total RNA with Ribo-Zero Gold from 100ng of total RNA.

treatment_protocol: The hESC-derived pancreatic progenitor cells were re-seeded on Matrigel-coated plates at a density of 1.2 × 10^5 cells/cm^2 (2D) or formed cellular aggregates (Agg).

tag: cell line

tag: differentiation status

value: pancreatic bud cells

tag: culture protocol

value: low density (2D)


title: ITD_ECs_rep3

description: polyA mRNA


title: WT-rep2


title: WT-rep3


title: 2D_stage 3 day 2

value: male


title: 2D_stage 3 day 1


title: WT-rep1


title: ITD_ECs_rep1

description: polyA mRNA


title: WT_MSCs_rep4

description: polyA mRNA


title: WT_ECs_rep5

description: polyA mRNA


title: Agg_stage 3 day 3

value: aggregates


title: 19U

value: brain

value: Unresponsive


title: Agg_stage 3 day 1


title: WT_ECs_rep4

description: polyA mRNA


title: wild type RNA-seq repeat2

city: Wuhan

first: shaoli

last: zhou

state: Hubei

address: shizishan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

data_processing:
For RNA-seq, Tophat (version 2.0.13) was used to align the clean tags filtered by Trimmomatic (version 0.32) to the reference genome of Niponbarre (version 7.0). Cufflinks (version 2.2.1) was used for identification of differentially expressed genes.
Genome_build: RGAP version 7.0
Supplementary_files_format_and_content: tab-delimited text file of output of Cufflink and Cuffdiff software. Files with suffix "fpkm_tracking" represent RPKM value of all genes in each sequencing data. File with suffix "diff" represents wheter genes in genome are different expressed or not in wox11 mutant compared with wild type.

organism: Oryza sativa Japonica Group

source_name: wild type_root tips

growth_protocol: The germinated rice seedlings were grown in field of Wuhan area from May and seeds were harvested in the end of September. For RNA-seq material harvest, wox11 mutant and wild type HY were surface-sterilized by 0.15% HgCl2, and washed by sterilized dH2O for 8 times, clean seeds were germinated in 1/2 MS media containing 0.8% agar and 3% sucrose at 28 °C (in light) and 24 °C (in dark) with 14-h-light/10-h-dark cycle. 3-5mm root tips of 7 day (after germination) seedling were harvest for RNA extraction.

extract_protocol:
The total RNA samples of 3-5mm root tip were isolated using TRIzol reagent (Invitrogen) from wox11 mutant and corresponding wild type Hwayoung, which were 5 days after germination. The total RNA was used to generate Illumina sequencing libraries following the manufacturer's protocol.
RNA libraries were prepared according to the Illumina RNA-seq library construction protocol strictly.  Briefly, 4 μg of total RNAs was used for mRNA purification, first strand cDNA systhesis, second strand cDNA systhesis, 3' end of blunt double strand cDNA ligated with "A" nuleotide, index primers ligation, low cycle PCR amplyfication, and double-strand DNA purification.

tag: background

value: Hwayoung

value: wild type

value: 3-7 mm root tip from 7 day seedling


title: WT_ECs_rep3

description: polyA mRNA


title: Agg_stage 3 day 2


title: WT_ECs_rep1

description: polyA mRNA


title: wild type RNA-seq repeat1


title: stage 3 day 0


title: WT_ECs_rep2

description: polyA mRNA


title: wox11 mutant RNA-seq repeat1

source_name: wox11 mutant_root tips

value: wox11 mutant

value: 3-5 mm root tip from 7 day seedling


title: wox11 mutant RNA-seq repeat2


title: 2D_stage 3 day 4


title: z_5d_pci_1

status: Public on Jun 20 2017

city: Bad Nauheim

first: Shih-Lei

middle: Ben

last: Lai

state: Hessen

address: Ludwigstraße 43

department: Developmental Genetics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Read quality trimming with Trimmomatic version 0.33 (java -jar trimmomatic-0.33.jar PE ... LEADING:3 TRAILING:3 SLIDINGWINDOW:5:15 CROP:500 MINLEN:30)
Mapping of reads versus zebrafish genome assembly 10 (Danio rerio GRCz10) and medaka assembly 1 (Oryzias latipes MEDAKA1) using STAR 2.4.0a (--outFilterMismatchNoverLmax 0.1)
Read counting per gene with featureCounts 1.4.5-p1 from the Subread package using default parameters
Raw gene counts for both organisms were joined to a common matrix based on gene homology (BioMart) resulting in 15292 genes
The common matrix of gene counts was normalized with DESeq
Genome_build: Danio rerio GRCz10, Oryzias latipes MEDAKA1
Supplementary_files_format_and_content: The tab-delimited text file (matrix.txt) contains DESeq normalized counts for all homologous genes

organism: Danio rerio

source_name: Ventricle

growth_protocol: Zebrafish were raised and handled in compliance with local animal welfare legislation and maintained according to standard protocols (zfin.org). All animals were maintained at 28 °C in a re-circulating system and fish at >6 months of age were used in the experiment.

extract_protocol:
For RNA-seq, RNA was isolated from medaka and zebrafish ventricles using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.  RNA and library preparation integrity were verified with a BioAnalyzer 2100 (Agilent) or LabChip Gx Touch 24 (Perkin Elmer).
500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina).

treatment_protocol: WT zebrafish (AB strain) and medaka (Cab strain) from 6-9 month old with similar body size were anethesized and operated (untouched, sham operation, or cryoinjurd) as previously described (Gonzalez-Rosa et al., 2011, Chablais et al., 2011, Schnabel et al., 2011).  Fish were recovered after operation, and lived until specified time points of sample collection.

tag: hours/days after injury

tag: operation

value: cryoinjury


title: z_3d_pci_1


title: z_1d_pci_1


title: z_5d_ps_1

value: sham operation


title: z_2d_pci_1


title: z_3d_ps_1


title: z_0h_1

value: 0h = untreated


title: z_1d_ps_1


title: z_6h_ps_1


title: z_2d_ps_1


title: Agg_stage 3 day 4


title: TRAP_Chat_2

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

data_processing:
Aligned to genome using STAR
Used HTSeq to obtain gene-level counts
(Processing of sequence data performed by Genome Technology Access Center at Washington University in St. Louis)
Genome_build: Mus_musculus reference build Ensembl_R76
Supplementary_files_format_and_content: CSV file containing gene counts for each sample

source_name: TRAP sample from Chat mouse

extract_protocol:
TRAP on spinal cord from Snap25 and Chat bacTRAP mice. TRAP samples underwent immunopurification for four hours at 4°C. Both TRAP and pre-immunopurification control RNA samples were extracted through TRIzol purification, DNase treatment, and Qiagen RNeasy Mini columns (74104).
Sequencing libraries were amplified using Nugen Amplification Kit Ovation® RNA‐Seq System V2 (7102). Genome Technology Access Center at Washington University in St. Louis performed adapter ligation and sequencing of the libraries on the Illumina Hiseq2500

tag: strain

tag: age

value: post natal day 21

value: spinal cord


title: TRAP_Snap25_3

source_name: TRAP sample from Snap25 mouse

tag: tissue


title: TRAP_Chat_1


title: TRAP_Snap25_2


title: TRAP_Snap25_1


title: PreIP_Chat_1

source_name: PreIP control from Chat mouse


title: PreIP_Chat_3


title: PreIP_Snap25_3

source_name: PreIP control from Snap25 mouse


title: PreIP_Snap25_1


title: mKO2lo-aIL9-2-2

city: Beijing

first: Hai

last: Qi

state: Beijing

address: Tsinghuayuan Street

department: School of Medicine

institute: Tsinghua University

description:
mKO2hi_mKO2lo_PBS_IL9_aIL9_fpkm.txt
mKO2hi_mKO2lo_PBS_IL9_aIL9_counts.txt

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to mm9 whole genome using TopHat2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by Cufflinks and raw counts were summarized by htseq-count for DESeq2 input
Gene differential expression was analyzed by DESeq2 according to its mannual
Genome_build: NCBI build37.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and tab-delimited text files include raw reads counts for each Sample

source_name: spleen

growth_protocol: 5-6 weeks UBP-2A-FucciTg C57BL/6 mice were routinely immunized with NP-KLH in Alum (or SRBC) i.p. Splenocytes were collected on day 13 (or day 8) and pre-enriched by biotin-GL7 or biotin-NIP plus streptavidin-Microbeads. Cell subsets of interest were sorted directly into the lysis buffer by AriaIII.

extract_protocol:
Cells were directly sorted into the lysis buffer and follow the modified the protocol initially developed for single-cell RNA-seq (Tang, 2011) to accommodate 100-200 sorted cells by doubling reaction volumes with extra buffers until the step for second strand DNA synthesis
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PBS/IL-9/anti-IL-9 were administrated 24 hours before sacrificing the mice. IL-9, 1.33ug/mice. Anti-IL-9, 200ug/mice.

tag: cell type

value: mKO2loCD38-GL7+FAS+ B cells

value: UBP-2A-FucciTg C57BL/6

tag: immunization

value: SRBC 8dpi


title: mKO2lo-IL9-2-3

tag: treatment


title: mKO2lo-aIL9-2-1


title: PreIP_Snap25_2


title: mKO2lo-IL9-2-2


title: z_6h_pci_1


title: TRAP_Chat_3


title: mKO2lo-IL9-2-1


title: mKO2lo-PBS-2-1

value: PBS


title: mKO2hi-IL9-2-2

value: mKO2hiCD38+GL7+FAS+ B cells


title: mKO2hi-aIL9-2-2


title: mKO2hi-PBS-2-2


title: mKO2lo-PBS-2-2


title: mKO2hi-aIL9-2-1


title: mKO2hi-IL9-2-3


title: mKO2lo-PBS-2-3


title: mKO2hi-PBS-2-3


title: mKO2hi-PBS-2-1


title: mKO2lo-aIL9-1-1


title: mKO2lo-IL9-1-3


title: mKO2hi-aIL9-2-3


title: PreIP_Chat_2


title: mKO2lo-aIL9-1-2


title: mKO2lo-aIL9-2-3


title: mKO2lo-IL9-1-1


title: mKO2lo-aIL9-1-3


title: mKO2lo-PBS-1-1


title: mKO2lo-PBS-1-2


title: mKO2lo-IL9-1-2


title: mKO2lo-PBS-1-3


title: mKO2hi-aIL9-1-3


title: mKO2hi-aIL9-1-1


title: mKO2hi-IL9-1-3


title: mKO2hi-IL9-2-1


title: mKO2hi-IL9-1-1


title: mKO2hi-IL9-1-2


title: BMPC-4-2

description:
mKO2hi_mKO2lo_memory_PC_fpkm.txt
mKO2hi_mKO2lo_memory_PC_counts.txt

source_name: bone marrow

value: NP-KLH/LPS/Alum 13dpi


title: BMPC-4-1


title: mKO2hi-PBS-1-1


title: mKO2hi-PBS-1-3


title: BMPC-4-3


title: SPPC-4-2


title: memory-4-2

value: NIP+CD19+CD38+GL7-FAS-IgM-IgD- memory B cells


title: BMPC-3-2


title: SPPC-4-3


title: BMPC-3-1


title: SPPC-4-1


title: mKO2hi-3-2

value: NIP+mKO2hiCD38+GL7+FAS+ B cells


title: BMPC-3-3


title: mKO2hi-aIL9-1-2


title: mKO2lo-2-3


title: mKO2lo-3-1

value: NIP+mKO2loCD38-GL7+FAS+ B cells


title: mKO2lo-3-2


title: mKO2lo-2-1


title: mKO2hi-3-1


title: mKO2hi-2-2


title: mKO2hi-2-3


title: mKO2lo-1-3


title: mKO2lo-1-2


title: memory-3-1


title: SPPC-3-1


title: mKO2hi-PBS-1-2


title: memory-3-2


title: memory-4-1


title: mKO2lo-1-1


title: mKO2hi-2-1


title: mKO2hi-1-2


title: K5-2_LNEP

city: PHILADELPHIA

first: Andrew

last: Vaughan

state: United States

address: 3800 Spruce Street

institute: University of Pennsylvania

data_processing:
bcl2fastq 1.8.4 was used to separate out the data for each sample using unique barcode combinations from the Nextera XT preparation and to generate *.fastq files.
fastq groomer and fastq trimmer
paired reads were aligned against mm10 using bowtie2-2.2.3 and tophat-2.0.13
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: K5, LNEP

growth_protocol: Mice were housed in filtered cages and all experiments were performed in accordance with approved IACUC protocols.

extract_protocol:
Cells were flow sorted and lysed using RNA using ReliaPrep™ RNA Tissue Miniprep kit (Promega). Reverse-transcription of mRNA into cDNA as well as preamplification of cDNA was performed using SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

treatment_protocol: Uninjured Foxj1-Cre / CC10-Cre / mTmG mice were administered 5 doses of  0.25 mg / g body weight tamoxifen in 50 ul corn oil, with each dose seperated by 48 hours, and animals were housed 1 week prior to sacrifice.  Influenza-infected Krt5-CreERT2 / mTmG mice were given a single dose (0.125 mg / g body weight) between days 7 to 9 post-infection.  Lungs were exposed via standard procedures and perfused with PBS.  After installation with agarose and subsequent hardening by a brief incubation on ice, each lobe was cut away from the mainstem bronchi. The proximal-most ¼ of each lobe surrounding the bronchi was then cut away to minimize the inclusion of basal cells in the cell preparation.  Cells were incubated for 30 min at room temperature with anti-integrin B4, anti-EpCam-PE, and sytox blue, washed, and sorted.

tag: infection

value: influenza

value: lung

value: activated LNEPs


title: mKO2hi-1-3


title: K5-1_LNEP


title: Ptbp2-deficient (cKO) 2 RNA-Seq

city: Cleveland

first: Donny

last: Licatalosi

state: Ohio

address: 10900 Euclid Avenue

department: Center for RNA Molecular Biology

institute: Case Western Reserve University

data_processing:
For each sample,raw file 1 was concatenated with raw file 3, and raw file 2 was concatenated with raw file 4 to generate input files for paired-end mapping.
Reads were aligned to the mm10 genome with OLego (Wu J. et al, 2013).
Transcript structure, alternative splicing, and gene expression were calculated using the Quantas pipeline (Yan, Q. et al, 2015).
Genomic coordinates in the output files were converted to mm9 with LiftOver (Kent, W.J. et al, 2002).
Overlapping coordinates reported in the alternative splicing output files were collapsed to single events.
For gene expression analyses, replicate RPKM values were averaged together for WT and cKO samples. Outputs were then statistically filtered for events where p.adj<0.01 and FC≥2 in genes that have an Avg RPKM>1 in both WT and cKO samples.
Genome_build: mm9
Supplementary_files_format_and_content: xlsx files include collapsed alternative splicing events and statistically filtered RPKM values for each sample

source_name: Conditional knockout, replicate 2

extract_protocol:
Testes were collected from mice at postnatal day 25 (p25) and selected for poly(A)+ RNA.
Paired-end RNA-Seq libraries were prepared from the testes of two wild type (WT) and two Ptbp2-deficient (cKO) mice at postnatal day 25 (p25) using Illumina ScriptSeq™ v2 RNA-Seq library preparation kits. RNA-Seq libraries were generated from 0.5 to 50 nanograms of rRNA-depleted RNA.

tag: Sex

value: Male

value: Testis

value: Postnatal day 25 (p25)

tag: genotype/variation

value: Ptbp2-deficient (cKO)


title: Ctr-1_LNEP

source_name: Ctr, LNEP

value: control

value: quiescent LNEPs


title: mKO2hi-1-1

value: UBP-2A-FucciTg C57BL/6


title: Ptbp2-deficient (cKO) 1 RNA-Seq

source_name: Conditional knockout, replicate 1


title: mKO2lo-2-2

value: mKO2loCD38-GL7+FAS+ B cells


title: WT 2 RNA-Seq

source_name: Wild type, replicate 2

value: wild type (WT)


title: WT 1 RNA-Seq

source_name: Wild type, replicate 1


title: Testis HITS-CLIP 1

data_processing:
Library strategy: HITS-CLIP
Reads were mapped to the mouse genome (mm9) with Bowtie and collapsed to identify unique CLIP tags.
Genome_build: mm9
Supplementary_files_format_and_content: BED file contains processed reads from individual samples are color coded (column 9). [Sample 1 = 255,0,0; Sample 2 = 0,255,0; Sample 3 = 0,0,255]

source_name: Testes

extract_protocol: Libraries were generated following HITS-CLIP protocol (Licatalosi et al., 2008).  The 5' linker has NNNNG at the 3'end.  These are the first bases sequenced for each read. 79 base sequencing performed on Illumina Genome Analyzer IIx.

value: 8 weeks


title: Testis HITS-CLIP 2


title: Teratoma (G-Z-14-T-R-1)

city: Sheffield

first: Paul

last: Gokhale

address: Western Bank

department: Biomedical Science

institute: University of Sheffield

description:
RHT376
Barcode: CAGATC

data_processing:
Illumina Casava1.7 software used for basecalling.
Transcripts were counted using Tophat and Cufflinks
Genome_build: Hg 19
Supplementary_files_format_and_content: File includes FPKM values for each Sample

source_name: ESC

growth_protocol: DMEM/F-12 + 20% KOSR, 10ng/ml FGF2, MEF feeders

extract_protocol:
RNA was exacted using PicoPure RNA isolation kit (Arcturus Bioscience) and QCed using a 2100 Bioanalyzer (Agilent Technologies)
RNA libraries were prepared for sequencing using  RNA sample preparation kit v2 (Illumina) according to the manufacturers standard protocol.  polyadenylated RNA was first purified from total RNA was first purified through oligo-dT attached magnetic beads using two rounds of purification. Poly(A) RNA was subsequently fragmented and primed with random hexamers for cDNA synthesis. First strand cDNA synthesis was for 50 min at 42oC using SuperScript II reverse transcriptase. After second strand cDNA synthesis, multiple indexing adapters were ligated, and libraries QCed with 2100 Bioanalyzer (Agilent Technologies), normalized and pooled prior to sequencing.   Libraries were subjected to 101 base pair-end multiplex sequencing on an Illumina HiSeq 2000 in high output mode.  Samples were multiplexed (7 to 8 samples per lane) resulting in an average depth of 58 million reads per sample

tag: laboratory

value: WCELL

value: H9 (WCELL)

value: Female

tag: teratoma, number of cells injected (x10^6)

tag: teratoma, injection volume

tag: teratoma injection site

value: center of upper back

tag: teratoma, mouse strain

value: SCID-Beige

tag: teratoma, mouse age

tag: teratoma, mouse sex

tag: teratoma, replicate


title: Teratoma (G-Z-195-T-R-3)

description:
RHT377
Barcode: CTTGTA

tag: cell line


title: Teratoma (G-01-201-T-R-2)

description:
RHT370
Barcode: AGTCAA

source_name: iPSC


title: Teratoma (G-01-202-T-R-3)

description:
RHT371
Barcode: AGTTCC


title: Teratoma (G-01-200-T-R-1)

description:
RHT369
Barcode: CTTGTA


title: Teratoma (UK-I9-1-T-R-3)

description:
RHT366
Barcode: ACAGTG

growth_protocol: mTeSR1, Matrigel

value: UKSCB

value: NIBSC 5

value: in-between shoulder blades

value: NOD.CB17-Prkdcscid/ J


title: Teratoma (UK-I9-3-T-R-1)

description:
RHT368
Barcode: CAGATC


title: Teratoma (UK-I9-2-T-R-1)

description:
RHT367
Barcode: GCCAAT


title: Teratoma (G-02-162-T-R-2)

description:
RHT373
Barcode: TGACCA

value: Male


title: Ctr-2_LNEP

value: lung


title: Teratoma (UK-I9-1-T-R-2)

description:
RHT365
Barcode: TGACCA


title: Teratoma (UK-S3-3-T-R-1)

description:
RHT363
Barcode: AGTTCC


title: Teratoma (UK-I9-1-T-R-1)

description:
RHT364
Barcode: CGATGT


title: Teratoma (UK-S3-2-T-R-2)

description:
RHT362
Barcode: AGTCAA


title: Teratoma (UK-Z-2-T-R-1)

description:
RHT358
Barcode: ACAGTG

value: H9 (UKSCB)


title: Teratoma (UK-OX2-1-T-R-1)

description:
RHT359
Barcode: GCCAAT


title: Teratoma (MC-Z-1-T-R-1)

description:
RHT355
Barcode: AGTTCC

growth_protocol: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders

value: MCRI

value: H9 (MCRI)

value: back of the neck or caudal flank near the hip


title: Teratoma (G-03-127-T-R-1)

description:
RHT374
Barcode: ACAGTG


title: Teratoma (MC-03-3-T-R-3)

description:
RHT354
Barcode: AGTCAA

value: iPSC RM3.5


title: Testis HITS-CLIP 3

value: Testis

tag: strain

tag: age

value: 8 weeks


title: Teratoma (MC-Z-3-T-R-3)

description:
RHT356
Barcode: CGATGT


title: Teratoma (MC-03-2-T-R-2)

description:
RHT353
Barcode: CTTGTA


title: Teratoma (G-02-160-T-R-1)

description:
RHT372
Barcode: CGATGT

value: WCELL


title: Teratoma (UK-OX2-2-T-R-1)

description:
RHT360
Barcode: CAGATC

value: Female


title: Teratoma (MC-01-2-T-R-2)

description:
RHT347
Barcode: AGTTCC

value: HES3/MIXL1 GFP/w


title: Teratoma (MC-02-1-T-R-1)

description:
RHT349
Barcode: TGACCA

value: MEL1/INS GFP/w


title: Teratoma (MC-01-3-T-R-3)

description:
RHT348
Barcode: CGATGT


title: Teratoma (B-03-113-T-R-1)

description:
RHT344
Barcode: CAGATC

growth_protocol: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, SNL feeders.

value: KYOU

value: subcutaneous

value: FOX CHASE SCID C.B-17/lcr-scid/scidJcl


title: Teratoma (B-01-105-T-R-3)

description:
RHT342
Barcode: ACAGTG


title: Teratoma (B-01-103-T-R-2)

description:
RHT341
Barcode: TGACCA


title: Teratoma (B-03-115-T-R-2)

description:
RHT345
Barcode: CTTGTA


title: Teratoma (MC-01-1-T-R-1)

description:
RHT346
Barcode: AGTCAA


title: Teratoma (B-02-107-T-R-1)

description:
RHT343
Barcode: GCCAAT


title: Teratoma (UK-S3-1-T-R-1)

description:
RHT361
Barcode: CTTGTA

value: UKSCB

value: in-between shoulder blades

value: NOD.CB17-Prkdcscid/ J


title: Teratoma (B-01-101-T-R-1)

description:
RHT340
Barcode: CGATGT

value: Male


title: Teratoma (UK-Z-1-T-R-1)

description:
RHT357
Barcode: TGACCA

value: H9 (UKSCB)


title: Sample241

city: Atlanta

first: Urko M.

last: Marigorta

state: Georgia

address: 950 Atlantic Drive

department: School of Biosciences

institute: Georgia Institute of Technology

data_processing:
Reads were mapped to the human genome (hg19) with TopHat 2.0.13 using default parameters,
aligned reads were transformed with SAMtools to quantify number of reads at the gene level with HTSeq-0.6.1 using default “union” mode.
counts were transformed to RPKM to follow GTEx QC guidelines, retaining 13,769 genes with RPKM>1 and >6 read counts in at least 10 individuals
finally, original raw counts of the retained genes were normalized using TMM normalization with edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts at the gene level for each sample

source_name: Crohn's disease_Ileal biopsy

extract_protocol:
RNA was isolated using the Qiagen AllPrep RNA/DNA Mini Kit from ileal biopsies stored at -80C.
RNA sequencing (RNA-seq) libraries were prepared using the Illumina TruSeq RNA preparation kit and sequenced on the Illumina HiSeq 2000 with single-end 50-bp reads (Illumina, San Diego, CA).

tag: diagnosis

value: Crohn's disease

tag: gender

tag: age at diagnosis

tag: paris age

tag: ancestry

value: Other/Mixed

tag: progression to complication

value: yes

tag: tissue

value: Ileal biopsy


title: Sample243

value: European


title: Sample244


title: Sample245


title: Sample242


title: Sample240


title: Teratoma (MC-02-3-T-R-3)

description:
RHT351
Barcode: GCCAAT

tag: laboratory

value: MCRI

tag: Sex

tag: teratoma, number of cells injected (x10^6)

value: back of the neck or caudal flank near the hip


title: Teratoma (MC-02-2-T-R-2)

description:
RHT350
Barcode: ACAGTG

tag: teratoma, injection volume

tag: teratoma injection site

tag: teratoma, mouse strain

value: Female


title: Sample238


title: Sample239


title: Sample237


title: Sample232


title: Sample235


title: Teratoma (MC-03-1-T-R-1)

description:
RHT352
Barcode: CAGATC

value: iPSC RM3.5

tag: teratoma, mouse age

tag: teratoma, mouse sex

tag: teratoma, replicate


title: Sample233


title: Sample236


title: Sample230


title: Sample229

source_name: Non-IBD control_Ileal biopsy

value: Non-IBD control


title: Sample234


title: Sample228


title: Sample231


title: Sample227


title: Sample226


title: Sample225


title: Sample223


title: Sample221


title: Sample224


title: Sample219


title: Sample218


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title: Sample216


title: Sample215


title: Sample213


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title: Sample198


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title: Sample195


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title: Sample161


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title: Sample157

value: African


title: Sample183


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title: Sample76


title: Sample53


title: Sample54


title: Sample71


title: Sample50


title: Sample49


title: Sample47


title: Sample46


title: Sample48


title: Sample44


title: Sample43


title: Sample42


title: Sample45


title: Sample60


title: Sample37


title: Sample38


title: Sample39


title: Sample40


title: Sample41


title: Sample32


title: Sample33


title: Sample30


title: Sample34


title: Sample27


title: Sample35


title: Sample31


title: Sample25


title: Sample29


title: Sample51


title: Sample36


title: Sample24


title: Sample23


title: Sample21


title: Sample18


title: Sample14


title: Sample19


title: Sample16


title: Sample20


title: Sample17


title: Sample13


title: Sample12


title: Sample9


title: Sample11


title: Sample28


title: Sample7


title: Sample8


title: Sample26


title: Sample6


title: Sample5


title: Sample10


title: Sample4


title: Sample3


title: Sample2


title: Sample1


title: Aneuploid arrested cells replicate 3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
Sequencing run with HiSeq Control Software (HCS) version 2.2.58 and Real Time Analysis (RTA) version 1.18.64
Fastq sequences prepared with bcl2fastq version 2.15.0
Sequence alignment and preparation of expected_count and FPKM abundance measurements done using bowtie version 1.0.1, RSEM version 1.2.15 and samtools/0.1.19 with the UCSC known genes annotation file from the hg19 assembly
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] tab delimited file with RSEM expected counts and FPKM data for each UCSC transcript or transcripts.

source_name: Aneuploid arrested cells

growth_protocol: RPE-1 cells were synchronized at the G1/S border by Thymidine treatment. Six hours after Thymidine release treatment procedure was initiated.

extract_protocol:
The RNA were extracted by the RNeasy Micro kit (Qiagen).
50 ng RNA processed with NEOprep followed by cDNA processing on SPRIworks
RNA-Seq 50 nucleotide single-ended reads with two 6 nucleotide indicies

treatment_protocol: Six hours after Thymidine release, cells were treated with control vehicle or 0.5uM Reversine for 12 hours. After wash-out, cells have been placed in fresh medium and either harvested 66 hours later (euploid and aneuploid cycling cells) or exposed to Nocodazole. 12 hours later, mitotic cells have been removed by shake-off and the remainders of the cells have been placed in fresh medium containing Nocodazole. This procedure has been repeated three times in order to remove all cycling cells and to enrich for aneuploid arrested cells.

tag: cell line

value: RPE-1 cells

tag: treatment

value: 0.5 μM Reversine for 12 hours followed by 330 nM Nocodazole

tag: cell state

value: aneuploid arrested cells


title: Aneuploid arrested cells replicate 1


title: Aneuploid arrested cells replicate 2


title: Aneuploid cycling cells replicate 3

source_name: Aneuploid cycling cells

value: 0.5 μM Reversine for 12 hours

value: aneuploid cycling cells


title: Sample15

tag: diagnosis

tag: gender

value: Male

tag: age at diagnosis


title: Aneuploid cycling cells replicate 2


title: Sample22

value: Crohn's disease

tag: paris age

tag: ancestry

tag: progression to complication


title: Aneuploid cycling cells replicate 1


title: Euploid control replicate 2

source_name: Euploid control

value: vehicle

value: control


title: Euploid control replicate 1


title: nascent RNA-Seq shcontrol replicate 1

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

data_processing:
The resulting reads were trimmed for adaptor sequence, mapped against the hg19 reference using the aligner STAR with annotation (transcriptome annotation) from the gencode project (version 18).
Cufflinks/Cuffdiff was used to detect differentially transcribed transcripts.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Kasumi-1 cells

growth_protocol: Kasumi-1 cells stably expressing control shRNA or shRNA targeting AES were cultured in RPMI-1640 medium with 20% FBS.

extract_protocol:
Total RNA was isolated by RNeasy spin column (Qiagen) purification according to manufacturer’s instructions. 100 µg of total RNA were biotinylated with 200 µg/ml EZ-Link HPDP Biotin (Thermo Scientific) in 1 ml labeling buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA). Biotinylated RNA was bound to streptavidin magnetic beads (Thermo Scientific), washed as recommended by the manufacturer and separated by applying RNA-beads to µMACS columns and magnetic stand (Miltenyi Biotec). The retained material was eluted with 100mM DTT. After a final purification on RNeasy columns nascent RNA was subjected to library preparation and next generation sequencing.
Paired-end library was made from the isolated nascent RNA with TruSeq Stranded Total RNA Sample Prep Kit (Illumina) according to the instructions of manufacturer with the exclusion of poly-A purification step.

treatment_protocol: Newly transcribed RNA (nascent RNA) was labeled by direct administration of 4-thiouridine (Sigma) to cell culture medium to a final concentration of 100 µM for 1 hour.

tag: shRNA

value: control shRNA


title: nascent RNA-Seq shAES replicate 2

value: shRNA targeting AES


title: nascent RNA-Seq shcontrol replicate 2


title: cgas_tp4.1

city: Lausanne

first: Selene

last: Glück

address: Station 19

department: SV-GHI

country: Switzerland

institute: EPFL

description: cGAS KO MEFs d42 rep1

data_processing:
Mapping: software Bowtie2 v.2.2.1, assembly: mm10
web-based HTSstation was used to process the data (David, et al. 2014)
RNA counter: HTSstation
Differential expression analysis: Bioconductor limma (v. 3.18.13)
Supplementary_files_format_and_content: tab-delimited text files include counts and RPKM values for each sample.

source_name: cGAS KO MEFs d42

extract_protocol:
Total RNA from bulk MEF populations was extracted using the RNeasy mini kit (Qiagen). 1.5 and 3 ug of total RNA was used for the preparation of the library using the TruSeq mRNA stranded LT (Illumina kit)
TruSeq mRNA stranded LT (Illumina kit), with qubit quantification and QC with  tapestation 4200 and Fragment analyzer.

tag: strain

tag: genotype

value: cGAS KO

tag: cell type

value: primary mouse embryonic fibroblast

tag: passages


title: nascent RNA-Seq shAES replicate 1


title: cgas_tp4.4

description: cGAS KO MEFs d42 rep4


title: cgas_tp3.1

description: cGAS KO MEFs d36 rep1

source_name: cGAS KO MEFs d36


title: cgas_tp4.3

description: cGAS KO MEFs d42 rep3


title: cgas_tp3.4

description: cGAS KO MEFs d36 rep4


title: cgas_tp3.2

description: cGAS KO MEFs d36 rep2


title: cgas_tp4.2

description: cGAS KO MEFs d42 rep2


title: cgas_tp1.4

description: cGAS KO MEFs d33 rep4

source_name: cGAS KO MEFs d33


title: wt_tp4.3

description: WT MEFs d42 rep3

source_name: WT MEFs d42

value: WT


title: wt_tp4.4

description: WT MEFs d42 rep4


title: cgas_tp1.2

description: cGAS KO MEFs d33 rep2


title: cgas_tp1.1

description: cGAS KO MEFs d33 rep1


title: wt_tp4.1

description: WT MEFs d42 rep1


title: wt_tp3.3

description: WT MEFs d36 rep3

source_name: WT MEFs d36


title: wt_tp3.4

description: WT MEFs d36 rep4


title: wt_tp3.2

description: WT MEFs d36 rep2


title: wt_tp1.3

description: WT MEFs d33 rep3

source_name: WT MEFs d33


title: wt_tp3.1

description: WT MEFs d36 rep1


title: wt_tp1.2

description: WT MEFs d33 rep2


title: wt_tp1.1

description: WT MEFs d33 rep1


title: Dicer_P0_2

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

description:
Steady state
Figure 6E Dicer P0

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7
FastQ files were indexed and mapped for Mm9 genome assembly using HISAT 0.1.5
SAM files were converted to BAM using SAMtools
Gene count and normalization was done using Homer for Fig3 (analyzeRepeats.pl rna mm9 -d <List of tag dir> -count 3utr -condenseGenes -strand + -norm 1e7 ) and DESEQ2 (single factor) for all other tables
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Freshly isolated brain microglia

tag: tissue

value: brain

tag: age (weeks)

value: P0 (NewBorn)

tag: transfer


title: Dicer_P0_1

description:
Steady state
Figure 6E Dicer P0


title: cgas_tp3.3

description: cGAS KO MEFs d36 rep3


title: WT_Adult_5

description:
Steady state
Figure 6A WT Adult

value: Dicerfl/fl (Control)

value: 6-8 weeks


title: WT_Adult_3

description:
Steady state
Figure 6A WT Adult


title: WT_P0_4

description:
Steady state
Figure 6A WT P0


title: WT_P0_3

description:
Steady state
Figure 6A and Figure 6E WT P0


title: WT_P0_1


title: WT_P0_2


title: WT_E14_4

description:
Steady state
Figure 6A WT E14

value: E14 (Embryo)


title: cgas_tp1.3

description: cGAS KO MEFs d33 rep3


title: wt_tp4.2

description: WT MEFs d42 rep2


title: WT_Adult_2

description:
Steady state
Figure 6A WT Adult


title: wt_tp1.4

description: WT MEFs d33 rep4


title: Hippocampal_MG_WT_2

description:
Steady state
Figure S4 (also related to Figure 5A) Hippocampal_WT steady state

source_name: Freshly isolated brain (hippocampal) microglia

value: 10-12 weeks


title: Hippocampal_MG_WT_1


title: Hippocampal_MG_Dicer_6

description:
Steady state
Figure S4 (also related to Figure 5A) Hippocampal_Dicer steady state


title: WT_Adult_1

description:
Steady state
Figure 6A WT Adult


title: Hippocampal_MG_LPS_WT_16

description:
6hr post LPS 1mg/Kg i.p
Figure S4 (also related to Figure 5A) Hippocampal_WT LPS


title: Hippocampal_MG_Dicer_4


title: Hippocampal_MG_LPS_Dicer_20

description:
6hr post LPS 1mg/Kg i.p
Figure S4 (also related to Figure 5A) Hippocampal_Dicer LPS


title: Hippocampal_MG_LPS_WT_15


title: WT_Adult_4

description:
Steady state
Figure 6A WT Adult


title: WT_P0_5

description:
Steady state
Figure 6A WT P0


title: Total_brain_MG_WT_9

description:
Steady state
Figure 4 WT PBS


title: Total_brain_MG_WT_7

description:
Steady state
Figure 4 WT PBS


title: Total_brain_MG_WT_8

description:
Steady state
Figure 4 WT PBS


title: WT_E14_2

description:
Steady state
Figure 6A WT E14


title: WT_E14_3

description:
Steady state
Figure 6A WT E14


title: Total_brain_MG_Dicer_11b

description:
Steady state
Figure 4 Dicer PBS


title: Total_brain_MG_Dicer_5

description:
Steady state
Figure 4 Dicer PBS


title: Total_brain_MG_LPS_WT_33

description:
6hr post LPS 1mg/Kg i.p
Figure 4 WT LPS 6hr


title: WT_E14_1

description:
Steady state
Figure 6A WT E14


title: Total_brain_MG_LPS_WT_31


title: Total_brain_MG_LPS_WT_17


title: Total_brain_MG_LPS_Dicer_38

description:
6hr post LPS 1mg/Kg i.p
Figure 4 Dicer LPS 6hr


title: Total_brain_MG_LPS_WT_32


title: WT_4

description:
Steady state
Figure 3 WT steady state


title: Total_brain_MG_LPS_Dicer_35


title: WT_2

description:
Steady state
Figure 3 WT steady state


title: Total_brain_MG_LPS_Dicer_37


title: Total_brain_MG_LPS_Dicer_36


title: Hippocampal_MG_Dicer_5


title: Dicer_3

description:
Steady state
Figure 3 Dicer steady state


title: Dicer_2


title: WT_3

description:
Steady state
Figure 3 WT steady state


title: Dicer_1


title: Hippocampal_MG_LPS_Dicer_18


title: MYC_AES_WT

description: small RNA sequencing

data_processing:
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina HiScan-SQ
CASAVA BclToFastq was used to export fastq files
Illumina adapter sequences were removed using Cutadapt
Reads were mapped using Bowtie2 and further processed to BAM format using samtools
Regions with coverage were called from mapped reads using the bedtools genomeCoverageBed algorithm
Sequences from the extracted regions were compiled to a consensus sequence which was subject to BLAST against a custom small RNA database. Regions with a BLAST hit were further aggregated calculating the mean of the average coverages and further normalized to the total number of mapped reads by the identified hit name.
Genome_build: hg19 for human samples and mm10 for mouse samples
Supplementary_files_format_and_content: Each processed file contains a column for the identified small nucleolar RNA (snoRNA) elements and the normalized average coverage for the respective sample.

extract_protocol: Total RNA was extracted with the Qiagen miRNeasy kit and 500 ng was subject to library preparation using the Illumina Truseq small RNA kit. Molecules with the size of 40-200 nt were purified from a gel before sequencing.

value: primary mouse lineage negative bone marrow cells retrovirally transduced with myc


title: AF9_AES_KO

description: small RNA sequencing

value: primary mouse lineage negative bone marrow cells retrovirally transduced with MLL-AF9


title: MYC_AES_KO

description: small RNA sequencing

source_name: mouse lineage negative bone marrow cells


title: primary mouse lineage negative bone marrow cells retrovirally transduced with empty vector MIG_rep1

tag: sample type


title: primary mouse lineage negative bone marrow cells retrovirally transduced with AML-ETO9a MIG_AML_ETO9a


title: primary mouse lineage negative bone marrow cells retrovirally transduced with myc MIG_MYC


title: AF9_AES_WT

description: small RNA sequencing


title: primary mouse lineage negative bone marrow cells retrovirally transduced with empty vector MIG_rep2


title: Total_brain_MG_Dicer_12

description:
Steady state
Figure 4 Dicer PBS


title: K_11 scNOMe-seq Sample

city: Chicago

first: Sebastian

last: Pott

state: Il

address: 920 58th Street

department: Human Genetics

institute: University of Chicago

description: bisulfite converted DNA

data_processing:
reads were trimmed to remove low quality bases and 6 bp were clipped from the 5prime end of each read to avoid mismatches introduced by amplification, in the case of GM12878 cells 6 bp were clipped from either end. Only reads that remained longer than 20 bp were kept for further analyses. these processing steps were performed using trim_galore version 0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the following settings: trim_galore --quality 30 --phred33 --illumina --stringency 1 -e 0.1 --clip_R1 6 --gzip --length 20 --output_dir outdir Sample.fastq.gz
sequencing data was aligned to the in silico bisulfite converted human genome assembly hg38 using Bismark aligner v0.15 (Krueger, F., Kreck, B., Franke, A. & Andrews, S. R. DNA methylome analysis using short bisulfite sequencing data. Nat Meth 9, 145–151 (2012).) with default settings (bismark --fastq --prefix SamplePrefix --output_dir output_dir --non_directional --phred33-quals --score_min L,0,-0.2 --bowtie2 genome.index trimmed.fastq.gz). Reads were aligned in single end modus with each read of a paired-end read aligned separately
Coverage and methylation status of all cytosines was extracted using bismarkmethyl extract (bismark_methylation_extractor -s --ignore 6 --output outdir --cytosine_report --CX --genome_folder path_to_genome SampleAligned.bam).
Coverage files were used to extract the methylation status of cytosines specifically in GpC and CpG di-nucleotides using the coverage2cytosine script in Bismark. The resulting files contained the coverage and methylation information at individual GpC and CpG di-nucleotides. Cytosines in ambiguous GCG positions were removed from the coverage files. Regions covered by a read with more than 3 unconverted cytosines in non-CpG and non-GpC context were removed from further analyses as well.
Genome_build: hg38
Supplementary_files_format_and_content: GpC and CpG coverage files <chr><start><stop><%methylation><count methylated><total count> counts above 1 are a reflection of redundant reads that were not removed due to sequencing error or different length (after clipping)

source_name: lymphoblast cell line

growth_protocol: GM12878 and K562 cells were obtained from Coriell and ATCC, respectively. GM12878 were grown in RPMI medium 1640 (Gibco), supplemented with 2mM L-Glutamine (Gibco), and Penicilin and Streptavidin (Pen Strep, Gibco), and 15% fetal bovine serum (FBS, Gibco). K562 were grown in RPMI medium 1640 of the same composition but with 10% FBS.

extract_protocol:
Between 2 M and 5 M cells were collected by centrifuging the cell suspension for 5 min at 500x g. Cells were washed once with 1x PBS, resuspended in 1 ml lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2) and incubated for 10 min on ice. IGEPAL CA-630 (Sigma) was added to a final concentration of 0.025% and cell suspension was transferred to a 2 ml Dounce homogenizer. Nuclei were released by 15 strokes with the pestle. Success of lysis was confirmed by inspection under a light microscope. Nuclei were pelleted at at 4C and washed twice with cold lysis buffer without detergent. One million nuclei were resupended in reaction buffer to yield 100 ul with a final concentration of 1x GpC MTase buffer (NEB), 0.32 mM S-Adenosylmethionine (SAM) (NEB). 50 ul of GpC methyltransferase (4U/ul)) from M.CviPl (NEB)were added. The suspension was carefully mixed before incubation for 8 min at 37C after which another 25 ul of enzyme and 0.7 ul of 32mM SAM were added for an additional 8 min incubation at 37C. To avoid disruption of nuclei incubation was stopped by adding 750 ul of 1x PBS and pelleting the nuclei at 800 xg. Supernatant was removed and nuclei were resuspended in 500 ul 1x PBS containing Hoechst 33342 DNA dye (NucBlue Live reagent, Hoechst). Nuclei were kept on ice until sorting. Nuclei were sorted at the Flow Cytometry core at the University of Chicago on a BD FACSAria or BD FACSAria Fusio equipped with a 96-well-plate holder. To obtain individual and intact nuclei gates were set to exclude aggregates and debris, and to include cells with DNA content corresponding to cells in G1 phase of the cell cycle to maintain similar DNA content per cell and to remove potential heterogeneity attributable to cell cycle. Cells were sorted into individual wells pre-filled wth 19 ul of 1x M-Digestion buffer (EZ DNA Methylation Direct Kit, Zymo Research) containing 1mg/ml Proteinase K. Following collection, the plates were briefly spun to collect droplets that might formed during handling. Nuclei were lysed by incubating the samples at 50C for 20 min in a PCR cycler. DNA was subjected to bisulfite conversion by adding 130 ul of freshly prepared CT Conversion reagent (EZ DNA Methylation Direct Kit, Zymo) to the lysed nuclei. Conversion was performed by denaturing the DNA at 98C for 8 min followed by 3.5 hrs incubation at 65C. DNA isolation was performed using the EZ DNA Methylation Direct Kit (Zymo Research) following the manufacturer’s instruction with the modification that the DNA was eluted in only 8 ul of elution buffer.
Libraries were prepared using the Pico Methyl-seq Library prep Kit (Zymo Research) following the manufacturer’s instruction for low input samples. Specifically, the random primers were diluted 1:2 before the initial pre-amplification step and the first amplification extended to a total of 10 amplification cycles. Libraries were amplified with barcoded primers allowing for multiplexing. The sequences can be found in supplementary material, primers were ordered from IDT. The purification of amplified libraries was performed using Ampure beads, using a 1:1 ratio of bedas and libraries. Concentration and size distribution of the final libraries was assessed on an Bioanalyzer (Agilent). Libraries with average fragment size above 150bp were pooled and sequenced.

tag: cell line

tag: enzyme

value: GpC Methyltransferase M.CviPl (NEB)


title: K_8 scNOMe-seq Sample

description: bisulfite converted DNA


title: K_7 scNOMe-seq Sample

description: bisulfite converted DNA


title: K_6 scNOMe-seq Sample

description: bisulfite converted DNA


title: K_10 scNOMe-seq Sample

description: bisulfite converted DNA


title: primary mouse lineage negative bone marrow cells retrovirally transduced with MLL-AF9 MIG_MLL_AF9


title: K_5 scNOMe-seq Sample

description: bisulfite converted DNA


title: WT_1

description:
Steady state
Figure 3 WT steady state


title: K_4 scNOMe-seq Sample

description: bisulfite converted DNA


title: K_9 scNOMe-seq Sample

description: bisulfite converted DNA


title: K_3 scNOMe-seq Sample

description: bisulfite converted DNA


title: K_2 scNOMe-seq Sample

description: bisulfite converted DNA


title: Sample80

tag: diagnosis

value: Crohn's disease

value: Male

value: European

value: yes

value: Ileal biopsy


title: scler_ht280_H6

data_processing:
bcl2fastq 1.8.4 was used to separate out the data for each single cell using unique barcode combinations from the Nextera XT preparation and to generate *.fastq files.
paired reads were aligned against hg19 using bowtie2-2.2.3 and tophat-2.0.13
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: scleroderma patient

extract_protocol:
Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

treatment_protocol: Tissue was mechanically and enzymatically disaggregated using dispase.  Single cells were then stained with antibodies and flow sorted.

value: lung epithelial cells

tag: facs purification

value: live, CD45-, Epcam+, HTII-280+


title: scler_ht280_H5


title: MIA L1 3

city: Los Angeles

first: David

last: Dawson

state: California

address: 650 Charles E Young Dr South

department: Pathology

institute: UCLA

data_processing:
Raw reads were aligned to the UCSC Human Genome hg19 using Bowtie2 aligner (version 2.29) with the following parameters: -sensitive, -dpad 0, -gbar 99999999, -mp 1,1, -np 1, -score min L,0, -0.1
Read count was performbed by RSEM (version 1.2.25)
Differential expression analysis was performed with the edgeR Bioconductor package
Genome_build: UCSC Genome hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM, generated using RSEM

source_name: pancreatic adenocarcinoma cells

growth_protocol: cells are grown in DMEM with 10% FBS + 1X pen strep.

extract_protocol:
RNA was extracted from cell pellets using Zymo Quick-RNA MiniPrep Kit Catalog: 11-327
Constructed using the KAPA stranded mRNA kit

treatment_protocol: Cells are transfected with 20 nM siRNA in Opti-MEM for 6 hours. Cells are collected 48 hours post transfection

tag: sirna

value: ambion silencer select s37905


title: K_1 scNOMe-seq Sample

description: bisulfite converted DNA


title: PANC1 CTRL LC 2

value: ambion silencer select CAT 4390844


title: PANC1 CTRL LC 1


title: scler_ht280_H4


title: PANC1 siL1 LC 1


title: PANC1 CTRL LC 3


title: PANC1 siL1 LC 2


title: PANC1 siL1 LC 3


title: MIA L1 1


title: scler_ht280_H7


title: scler_ht280_H1


title: scler_ht280_G9


title: scler_ht280_H3


title: Bb2860_H2O2_1h

city: Tianjin

first: Liu

last: Qian

address: Xi 7 Dao No.32 Airport Economic Area

institute: TIB CAS

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
The clean reads were mapped against predicted transcripts from the Beauveriabassiana genome (version 3) with less than 3-base mismatching, using BWA (version 0.6.2)
The counts of reads that uniquely mapped to only one gene were calculated for each gene express abundanceusing SAM files as input
The normalized expression values for each gene were calculated by the number of uniquely mapped reads per kilobase of exon region per million mapped reads (RPKM) and differentially expressed (DE) genes wascarried out using the using the edgeR package (v3.4.2)
Genome_build: Beauveria bassiana Bb2860
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each sample.

organism: Beauveria bassiana

source_name: BbWT

growth_protocol: Conidia suspension (106 conidia) of WT and ΔBmh1/2 were inoculated into 50ml minimal broth (MB) at 25 °C for 2-day with shaking (120 r.p.m) growth to exponential phase.

extract_protocol:
Total RNA was isolated from frozen mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA) and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Resultant mycelia of each strain were harvested and washed in sterile water twice. For osmotic stress, mycelia of each sample were transferred to fresh MB exposed to 0.5 M NaCl with shaking for 1-h response. For oxidative stress, mycelia transferred to fresh MB containing 40 mM H2O2 for 1-h.

tag: genotype/variation

value: BbWT

tag: culture time

value: 2 days

value: mycelia


title: [delta]Bmh2_H2O2_1h


title: [delta]Bmh1_NaCl_1h


title: [delta]Bmh1_H2O2_1h


title: MIA L1 2


title: scler_ht280_G4


title: [delta]Bmh2_NaCl_1h


title: MIA CTRL 2


title: MIA CTRL 1


title: Bb2860_NaCl_1h


title: scler_ht280_F6


title: scler_ht280_G7


title: scler_ht280_G12


title: scler_ht280_G8


title: scler_ht280_F12


title: rna_rct1rrm_1

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

data_processing:
Sequencing adapters were trimmed from reads using Trimmomatic 0.30 (Bolger et al., 2014), and surviving read pairs with both mates longer than 25 bp were retained. Reads were then mapped to isolated rDNA annotations with Bowtie 2 2.1.0 with default options (Langmead and Salzberg, 2012). Only read pairs that failed to map concordantly to rDNA were retained. Subsequently, reads were aligned to the Ensembl 21 S. pombe genome release with STAR 2.3.1z (Dobin et al., 2013). Genome index construction was performed with the option --sjdbOverhang 100 and the Ensembl 21 annotations supplied to --sjdbGTFfile. Alignment was performed with the following options: --outFilterMultimapNmax 100 --outFilterMismatchNmax 5. Non-primary and non-concordant alignments were removed with samtools 0.1.19 (Li et al., 2009). One random placement was chosen for multi-mapping reads. Coverage tracks were prepared from STAR alignments with Bedtools 2.19.0-7 and UCSC BigWig utilities (Quinlan and Hall, 2010). BAM alignments were converted to BED format, and the strand of the second read in each aligned pair inverted so base coverage for both mates would be counted on the origin strand. Base coverage was tallied with Bedtools genomecov for each strand and normalized by millions of reads mapped.
Genome_build: ASM294v2
Supplementary_files_format_and_content: Genome coverage per strand normalized by mapped RPM in bigWig format.

organism: Schizosaccharomyces pombe

growth_protocol: All yeast strains were cultured in YES (yeast exact with supplements) media at 30 °C.

extract_protocol: ScriptSeq V2 kit (Epicentre) was used to prepare barcoded RNA-Seq libraries. 50 ng ribosomal RNA (rRNA)-depleted RNA samples were used as starting material following manufacturer's protocol. Ribo-Zero Gold kit (Epicentre) was used to remove rRNA from total RNA (DNA free) samples. Barcoded libraries were pooled and sequenced on Illumina HiSeq platform.


title: rna_rct1_2


title: rna_wt_1


title: rna_rct1rrm_2


title: rna_wt_2


title: MIA CTRL 3


title: scler_ht280_F9


title: scler_ht280_G1


title: scler_ht280_F5


title: rna_rct1_1


title: scler_ht280_F10


title: scler_ht280_E8


title: chip2_wce_wt

data_processing:
Obtained reads were quality filtered using Trimmomatic and aligned to the S. pombe genome assembly ASM294v2.21 using Bowtie v2.1.0 and local alignment, with multi-mappers randomly distributed. All read counts were normalized to reads per million (RPM) using total library size. ChIP enrichment was calculated as the log2 of the ratio of normalized IP reads to normalized input (whole cell extract) reads. Quantification at individual features was performed by intersecting reads with the feature of interest.
Genome_build: ASM294v2
Supplementary_files_format_and_content: Coverage of ChIP enrichment calculated as the log2 of the ratio of normalized IP reads to normalized input (whole cell extract) reads in bigWig format.

extract_protocol: Cells were spheroplasted by zymolyase at 37°C and then sonicated using a bioruptor for 8 cycles (30s ON 60s OFF). For each IP, 500-750 ug of chromatin were used with 3 to 5 ul antibody. 1 ng of DNA purified from ChIP experiments was made into libraries by using NEB enzymes. In brief, DNA was end-repaired by T4 DNA polymerase, Klenow fragment and T4 DNA PNK. “A” bases were added to the 3’ end of end-repaired DNA fragment with Klenow 3’ to 5’ exo minus and dATP. Barcoded Truseq adaptors (Illumina) were ligated to DNA fragments using quick ligase at 25°C. Five PCR cycles were performed prior to size selection. After size selection, purified DNA was PCR amplified with 6 to 12 cycles (Kapa HiFi HotStart ready mix). Barcoded libraries were pooled and sequenced on Illumina HiSeq platform.

treatment_protocol: Yeast cells were grown to a concentration of ~1 X 10^7 cells/ml, then fixed in 1% formaldehyde at 25°C for 20 min. Fixation was stopped by adding glysine to a final concentration of 0.125 M, and cells were washed twice in 1XPBS then stored in -80°C until all strains were harvested.

tag: chip antibody

value: whole cell extract


title: rna_ago1_1


title: rna_clr3_1


title: scler_ht280_E7


title: rna_clr3_2


title: chip2_wce_rct1rrm


title: scler_ht280_G2


title: scler_ht280_E4


title: scler_ht280_E5


title: chip2_wce_dcr1


title: chip2_wce_rct1_1


title: chip2_wce_ago1


title: scler_ht280_E3


title: rna_rct1_clr3_2


title: chip2_s2p_wt

value: RNAPII phospho S2 (Abcam ab5095)


title: rna_dcr1_1


title: rna_rct1_clr3_1


title: chip2_s2p_rct1_1


title: chip2_s2p_rct1rrm


title: chip2_wce_rct1_2


title: chip2_s2p_rct1_2


title: scler_ht280_E11


title: chip2_s5p_wt

value: RNAPII phospho S5 (Abcam ab5131)


title: chip2_s2p_ago1


title: chip2_s2p_dcr1


title: chip2_s5p_rct1_2


title: chip2_s5p_rct1_1


title: scler_ht280_E12


title: scler_ht280_D8


title: chip2_s5p_rct1rrm


title: scler_ht280_E10


title: scler_ht280_D2


title: chip2_h3k9me3_rct1rrm

value: H3K9me3 (Abcam ab8898)


title: chip2_s5p_dcr1


title: chip2_s5p_ago1


title: chip2_h3k9me3_wt


title: scler_ht280_C8


title: chip2_h3k9me3_rct1_1


title: scler_ht280_C6


title: chip2_h3k9me3_ago1


title: chip2_8wg16_wt

value: RNAPII 8WG16 (Abcam ab817)


title: chip2_h3k9me3_dcr1


title: chip2_h3k9me3_rct1_2


title: scler_ht280_C5


title: scler_ht280_C4


title: scler_ht280_C3


title: chip2_8wg16_rct1_2


title: chip2_8wg16_rct1rrm


title: chip2_8wg16_rct1_1


title: chip2_8wg16_ago1


title: scler_ht280_C12


title: scler_ht280_D7


title: chip1_wce_wt


title: chip2_8wg16_dcr1


title: chip1_wce_rct1rrm