title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C10_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B9_AD012_indexed

status: Public on Aug 26 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: AI

tag: Sex

value: male

tag: age

tag: strain


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C10_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B8_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B9_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C10_AD008_indexed


title: MG52D

city: Grugliasco

first: Eugenio

last: Martignani

state: TO

address: Largo Braccini 2

department: Veterinary Science

country: Italy

institute: University of Torino

library_source: transcriptomic

data_processing:
Basecalling was performed with software bcl2fastq v1.8
Sequenced reads were mapped to bosTau8 whole genome using STAR v2.5
Aligned reads were counted at the gene level with Rsubread's featureCounts (with options useMetaFeatures = T,  GTF.featureType = 'exon', countMultiMappingReads = F, countChimericFragments=F, allowMultiOverlap = F, strandSpecific = 0, isPairedEnd = Y) using ENSEMBL annotation v85.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were obtained using R package edgeR's rpkm function.
Genome_build: bosTau8 UMD3.1, genome-build-accession NCBI:GCA_000003055.3
Supplementary_files_format_and_content: RPKM normalized counts

molecule: total RNA

organism: Bos taurus

growth_protocol: Cell were isolated from bovine udders

extract_protocol:
Cells were sorted in tubes containing 0,1% volume of FBS, centrifuged and lised with Trizol. RNA was then extracted and quantified.
Truseq mRNA non stranded (Illumina)

treatment_protocol: Cells were directly sorted with a FACSAria III

tag: breed

value: Piedmontese

tag: animal id

tag: cell type

value: Primary mammary epithelial cells

tag: cell fraction


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B9_AD006_indexed


title: seq-n9rk6j

city: San Diego

first: Samuel

last: Levy

state: California

address: 10578 Science Center Drive, Suite 210

institute: Bluestar Genomics

data_processing:
Library strategy: 5hmC
Basecalls were converted using bcl2fastq2.
Sequencing reads were aligned to the hg19 reference genome using BWA-MEM with default parameters
Gene-based counting of 5hmC reads were determine by defining genes bodies from transcription start to transcription stop, coordinates obtained from the genome annotation version XXXX
Prior to identifying chromatin states, BAM files containing the locations of aligned reads were filtered for poorly mapped (MAPQ < 30) and not properly paired reads. Chromatin states were determined using ChromHMM.
Genome_build: hg19
Supplementary_files_format_and_content: txt files (gene counts per gene for 5hmC) and bed files (chromatin state coordinates) : Format for gene counts file (chrID, begin, end, gene symbol, length, strand, number reads) and format for chromatin state coordinates (chrID, begin, end, state)

organism: Homo sapiens

extract_protocol:
Peripheral blood was collected in Streck Blood Collection Tubes and processed within 24 hours of collection. This involve two centriguations to isolated the plasma. Cell free DNA was extracted from plasma using the Qiasymphony cell free DNA extraction automation.
10 ng of cell free DNA was used as input to a click chemistry enrichment protocol to identify DNA fragments bearing a 5-hydromethylcytosine (5hmC) residue. The biotinylation of DNA fragments contain 5hmC residue was enriched using strepavidin coated magnetic beads.

tag: cohort

value: Discovery


title: MG52B


title: seq-rd9y43


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B8_AD006_indexed


title: seq-a8wm3k


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B9_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C10_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B9_AD001_indexed


title: siRNA HAND2_rep3b

city: Buffalo

first: Vincent

middle: J.

last: Lynch

state: NY

address: 551 Cooke Hall

department: Department of Biological Sciences

institute: University at Buffalo, SUNY

description:
rRNA depleted total RNA
HAND2_KD_DeSeq2_Outfile.tabular.txt

data_processing:
All sequencing data were uploaded and analyzed on the Galaxy platform (https://usegalaxy.org/; Version 20.01). Individual reads for particular samples ("_rep1a" and "_rep1b") were concatenated using the “Concatenate datasets” tool (version 1.0.0). We used HISAT2 (version 2.1.0+galaxy5) (Kim, Langmead and Salzberg, 2015) to align reads to the Human hg38 reference genome using “Single-end” option, and reporting alignments tailored for transcript assemblers including StringTie. Transcripts were assembled and quantified using StringTie (v1.3.6) (Pertea et al., 2015, 2016), with reference file to guide assembly and the “reference transcripts only” option, and output count files for differential expression with DESeq2/edgeR/limma-voom. Differentially expressed genes were identified using DESeq2 (version 2.11.40.6+galaxy1) (Anders and Huber, 2010; Love, Huber and Anders, 2014). The reference file for StringTie guided assembly was wgEncodeGencodeBasicV33. The volcano plot was generated using Blighe K., Rana S., and Lewis M. (2018): EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling (available at https://github.com/kevinblighe/EnhancedVolcano).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: HAND2_KD_DeSeq2_Outfile.tabular.txt: Unmodified DESeq2 output; gene count file.

source_name: Endometrial Stromal Fibroblasts

growth_protocol: Human hTERT-immortalized endometrial stromal fibroblasts (T-HESC; CRL-4003, ATCC) were grown in maintenance medium, consisting of Phenol Red-free DMEM (31053-028, Thermo Fisher Scientific), supplemented with 10% charcoal-stripped fetal bovine serum (CS-FBS; 12676029, Thermo Fisher Scientific), 1% L-glutamine (25030-081, Thermo Fisher Scientific), 1% sodium pyruvate (11360070, Thermo Fisher Scientific), and 1x insulin-transferrin-selenium (ITS; 41400045, Thermo Fisher Scientific).

extract_protocol:
RNA from knockdown and control samples were DNase treated with TURBO DNA-free Kit (AM1907, Thermo Fisher Scientific).
RNA-Seq libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human (RS-122-2201, Illumina Inc.) following manufacturer’s protocol. Library quality and quantity were checked on 2100 Bioanalyzer and the pool of libraries was sequenced on Illumina HiSEQ4000 (single-end 50bp) using manufacturer’s reagents and protocols. Quality control, Ribo-Zero library preparation and Illumina sequencing were performed at the Genomics Facility at The University of Chicago.

treatment_protocol: 2x10e5 cells were plated per well of a 6-well plate and 18 hours later cells in 1750μl of Opti-MEM (31985070, Thermo Fisher Scientific) were transfected with 50nM of siRNA targeting HAND2 (s18133; Silencer Select Pre-Designed siRNA; cat#4392420, Thermo Fisher Scientific) and 9μl of Lipofectamine RNAiMAX (133778-150, Invitrogen) in 250μl Opti-MEM. BlockIT Fluorescent Oligo (44-2926, Thermo Fisher Scientific) was used as a scrambled non-targeting RNA control. Cells were incubated in the transfection mixture for 6 hours. Then, cells were washed with PBS and incubated in the maintenance medium overnight. Cells in the control wells were checked under the microscope for fluorescence the next day. 48 hours post treatment cells were washed with PBS, trypsinized (0.05% Trypsin-EDTA; 15400-054, Thermo Fisher Scientific) and total RNA was extracted using RNeasy Plus Mini Kit (74134, QIAGEN) following the manufacturer’s protocol. The knockdown experiment was done in 3 biological replicates. To test for the efficiency of the knockdown, cDNA was synthesized from 100-200ng RNA using Maxima H Minus First Strand cDNA Synthesis Kit (K1652, Thermo Fisher Scientific) following the manufacturer’s protocol. qRT-PCR was performed using QuantiTect SYBR Green PCR (204143, QIAGEN). HAND2 primers: fwd CACCAGCTACATCGCCTACC, rev ATTTCGTTCAGCTCCTTCTTCC. GAPDH housekeeping gene was used for normalization; primers fwd AATCCCATCACCATCTTCCA, rev TGGACTCCACGACGTACTCA. Samples that showed >70% KD efficiency were used for RNA-Seq.

tag: cell line

value: T HESCs (ATCC CRL-4003)

value: Endometrial Stromal Fibroblasts

tag: sirna

tag: treatment

value: Non-hormone treated


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B8_AD001_indexed


title: seq-nek4vf


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B7_AD008_indexed


title: siRNA HAND2_rep3a


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B7_AD010_indexed


title: siRNA HAND2_rep2b


title: seq-vwbrah


title: siRNA HAND2_rep2a


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B6_AD007_indexed


title: seq-abp8j7


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B6_AD010_indexed


title: MG52A


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B8_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B6_AD012_indexed


title: seq000748


title: seq-yu98mh


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B7_AD001_indexed


title: siRNA HAND2_rep1b


title: seq000750


title: siRNA HAND2_rep1a


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B5_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B7_AD006_indexed


title: seq000739


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B6_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B9_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B7_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B4_AD006_indexed


title: siRNA Ctrl_rep3b

value: Control


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B8_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B5_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D4_AD001_indexed


title: seq000744


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B8_AD004_indexed


title: seq000736


title: siRNA Ctrl_rep3a


title: seq000735


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B7_AD007_indexed


title: seq000730


title: siRNA Ctrl_rep2a


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B5_AD007_indexed


title: siRNA Ctrl_rep1b


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B5_AD002_indexed


title: seq000729


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B4_AD012_indexed


title: siRNA Ctrl_rep1a


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B4_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B6_AD006_indexed


title: seq000728


title: siRNA Ctrl_rep2b


title: seq-xmw4nb


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B5_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B5_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B4_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B6_AD002_indexed


title: seq000870


title: N2.input

city: Nantong

first: Peng fei

last: li

state: Jiangsu

address: Eye Institute, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, Jiangsu, China.

department: Eye Institute

country: China

data_processing:
m6A: Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
m6A: First, clean reads of input libraries were aligned to reference genome (UCSC HG19) by STAR software. Then circRNAs were identified by DCC software using the STAR alignment results. After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps.
input: Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs
input: The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.
Genome_build: hg19
Supplementary_files_format_and_content: excel format

source_name: Lens Epithelium Cells from control patient

extract_protocol:
Total RNA was isolated using trizol.Total RNA (1 μg) was used for removing the rRNAs using NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA)  following the manufacturer's instructions
m6A RIP: m6A RNA immunoprecipitation was performed with the GenSeqTM m6A-MeRIP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input samples without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA).
Input: RNA high throughput sequencing was performed by Cloud-Seq Biotech (Shanghai, China). Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions.
The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.

tag: diagnosis

value: healthy control

tag: tissue

value: Anterior capsular tissue of lens


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B4_AD002_indexed


title: N2.IP

institute: Affiliated Hospital of Nantong University


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B5_AD008_indexed


title: seq000869


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B4_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B3_AD010_indexed


title: N3.IP

value: female


title: N1.input


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B3_AD012_indexed


title: N3.input


title: seq000868


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B4_AD008_indexed


title: seq000867


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B3_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B1_AD006_indexed


title: N1.IP


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B3_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B3_AD006_indexed


title: seq000863


title: ARC3.input

source_name: Lens Epithelium Cells from ARC patient

value: Age-related Cataract (ARC)


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B3_AD008_indexed


title: ARC3.IP


title: ARC2.input


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B2_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B1_AD008_indexed


title: seq000861


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B2_AD012_indexed


title: seq000858


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B1_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B1_AD004_indexed


title: ARC2.IP


title: ARC1.input


title: seq000855


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B1_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B1_AD001_indexed


title: seq000854


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B1_AD012_indexed


title: seq000853


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B12_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B12_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B12_AD004_indexed


title: Sample 24_Tob2_induced_6

city: Houston

first: Ann-Bin

last: Shyu

state: Texas

address: 6431 Fannin Street, Rm 6.200

institute: The University of Texas Health Science Center at Houston

data_processing:
Adapters were trimmed with trim_galore with default parameter
Bowtie2 was used fo the mapping of the trimmed reads to the hg19 transcripts set and RSEM v1.3.0 was used for the gene counting
TPM method was used for the gene expression normalization
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file contains transcripts per million for each sample.

growth_protocol: Human U2OS cell line was purchased from ATCC and cultured following the manufacturer's protocol.

extract_protocol:
RNeasy Mini Kit (QIAGEN) was used to extract total cytoplasmic RNA from uninduced or induced cells following the manufacturer's protocols.  Bromouridine (BrU)-labeled RNAs were then immunoprecipitated from total cyctoplasmic RNA sample using anti-BrU antibody.
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells from a custom madeTet-off double stable line were uninduced or induced for wild-type Tob2 expression by adding or skipping doxycycline in culture medium.

value: human bone osteosarcoma epithelial cells

value: Tob2 induced

tag: time (hours)

tag: rip antibody

value: anti-BrU antibody

tag: molecule subtype

value: Bromouridine-IP RNA


title: Sample 22_Tob2_induced_2


title: Sample 23_Tob2_induced_4


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B12_AD010_indexed

tag: brain region

value: AI


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B12_AD006_indexed

tag: Sex

value: male


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B12_AD002_indexed

tag: age


title: seq000848


title: seq000746


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B12_AD001_indexed

tag: strain


title: Sample 21_Tob2_induced_1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B2_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B11_AD008_indexed


title: ARC1.IP


title: seq-jctmd6


title: seq-7y9nvk


title: Sample 20_Tob2_induced_0.5


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B10_AD008_indexed


title: seq-3rfvx7


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B11_AD004_indexed


title: seq000852


title: seq-mkn8df


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B11_AD007_indexed


title: Sample 19_Tob2_induced_0


title: Sample 17_Tob2_uninduced_4

value: uninduced


title: Sample 18_Tob2_uninduced_6


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B11_AD006_indexed


title: seq000847


title: seq000862


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B11_AD002_indexed


title: Sample 16_Tob2_uninduced_2


title: Sample 15_Tob2_uninduced_1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B11_AD012_indexed


title: Sample 14_Tob2_uninduced_0.5


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B11_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A9_AD002_indexed


title: seq-f6pry9


title: Sample 13_Tob2_uninduced_0


title: seq-7fdbma


title: Sample 12_Vector_induced_6

value: Vector-induced


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A9_AD004_indexed


title: seq000859

value: Discovery


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A9_AD006_indexed


title: seq000749


title: Sample 10_Vector_induced_2


title: Sample 11_Vector_induced_4


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A9_AD007_indexed


title: Sample 9_Vector_induced_1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B10_AD010_indexed


title: Sample 8_Vector_induced_0.5


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B10_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A8_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F3_AD010_indexed


title: Sample 6_Vector_uninduced_6


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B10_AD001_indexed


title: Sample 7_Vector_induced_0


title: Sample 4_Vector_uninduced_2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A9_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A8_AD002_indexed


title: Sample 3_Vector_uninduced_1


title: seq-863te7


title: Sample 2_Vector_uninduced_0.5


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A8_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A8_AD007_indexed


title: Sample 1_Vector_uninduced_0


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A8_AD006_indexed


title: Sample 24: Rep2_induced_6

source_name: human bone osteosarcoma epithelial cells

treatment_protocol: Cells from a custom madeTet-off double stable line were uninduced or induced for Tob2-S254D expression by adding or skipping doxycycline in culture medium.

value: Tob2-S254D induced


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A8_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A8_AD001_indexed


title: Sample 22: Rep2_induced_2


title: Sample 23: Rep2_induced_4


title: Sample 21: Rep2_induced_1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A7_AD012_indexed


title: Sample 20: Rep2_induced_0.5


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A7_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A7_AD008_indexed


title: Sample 17: Rep2_uninduced_4


title: Sample 19: Rep2_induced_0


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A6_AD012_indexed


title: Sample 5_Vector_uninduced_4


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A7_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B10_AD004_indexed


title: Sample 15: Rep2_uninduced_1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A7_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A6_AD004_indexed


title: Sample 14: Rep2_uninduced_0.5


title: Sample 12: Rep1_induced_6


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A6_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A7_AD006_indexed


title: Sample 13: Rep2_uninduced_0


title: Sample 11: Rep1_induced_4


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A6_AD010_indexed


title: Sample 10: Rep1_induced_2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A5_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A6_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A5_AD008_indexed


title: Sample 18: Rep2_uninduced_6


title: K2KO1

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to mouse genome release mm10 using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: TSV text file containing FPKM for all samples and genes

source_name: BMDMs

growth_protocol: Bone marrow was isolated from mice from the femur and tibia bilaterally. Flushed marrow was plated in DMEM  supplmented with L929 conditioned media for 6 days. On the sixth day, cells were replated at appropriate densities.

extract_protocol:
Cell lysates were isolated using the Roche HighPure RNA isolation kit. 1ug of RNA was used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: LysM Cre/Cre KLF2 flox/flox (K2KO)

value: 3 months

value: BMDMs


title: K2KO2


title: Sample 8: Rep1_induced_0.5


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A5_AD010_indexed


title: K2KO3


title: LysM4

value: LysM Cre/Cre


title: Sample 9: Rep1_induced_1


title: LysM3


title: Sample 7: Rep1_induced_0


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A3_AD006_indexed


title: LysM2


title: Sample 16: Rep2_uninduced_2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A3_AD010_indexed


title: Sample 6: Rep1_uninduced_6


title: K2KO4


title: Sample 4: Rep1_uninduced_2


title: LysM1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A6_AD008_indexed


title: Sample 5: Rep1_uninduced_4


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A3_AD008_indexed


title: Sample 3: Rep1_uninduced_1


title: IWP2-d8-Input

city: Stanford

first: Zhuoqing

last: Fang

address: 300 Pasteur Drive

institute: Stanford

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to hg19 genome assembly by bowtie2 (v2.3.2) by defalut prameters
Peaks were called using MACS2 (v2.1.0) with setting: fdr-q (0.01)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated by MACS2

source_name: Neural progenitors

extract_protocol:
Neural progenitor cell lysates were clarified from sonicated nuclei and SOX1 complexes were immunoprecipitated with SOX1 antibody (R&D AF3369, respectively. Protein A and G Magenetic Dynabeads were used to capture antibody bound protein-DNA complexes.
The ChIP-enriched DNA samples were treated with end-repair of the DNA, adding “A” bases to the DNA, ligating sequencing adapters to DNA fragments, amplifying adapter-modified DNA by PCR and gel purification for ChIPseq using NEBNext Ultra DNA Library Prep Kit for Illumina. Purified libraries were sequenced on Illumina HiSeq X-ten platforms.

value: Human ES-derived neural progenitors

tag: chip antibody

value: wild type


title: IWP2-d8-SOX1

tag: cell type


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A5_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A7_AD004_indexed


title: Sample 2: Rep1_uninduced_0.5


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A4_AD004_indexed


title: CT1.0-d8-Input


title: Sample 1: Rep1_uninduced_0


title: CT1.0-d8-SOX1


title: CT1.0-d4-Input


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A4_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A4_AD008_indexed


title: CT1.0-d4-SOX1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A4_AD002_indexed


title: 22690: WT YPD 3

city: Iowa City

first: Damian

middle: J

last: Krysan

state: IA

address: 25 South Grand, 2040 ML

department: Division of Pediatrics & Infectious Disease

institute: University of Iowa Hospitals and Clinics

data_processing:
Read files were mapped to C. albicans reference genome SC5314 using HISAT2.
Gene transcript expression was quantified using Stringtie.
Differential expression fold change, Wald test p values and Benjamini-Hochberg adjustment for multiple comparisons were determined using DESeq2.
Genome_build: FungiDB-46_CalbicansSC5314_Genome
Supplementary_files_format_and_content: tab delimited text files contain expression levels relative to wild-type controls
Supplementary_files_format_and_content: matrix table with gene counts for each gene and sample

organism: Candida albicans

source_name: wild-type exponential phase growth yeast cells

growth_protocol: Growth in YPD to exponential phase

extract_protocol:
Cells were collected via centrifugation from growth medium and RNA harvested according to manufacturer protocol for MasterPure Yeast RNA Purification Kit
Total RNA libraries (1ug) were prepared according to the TruSeq Stranded mRNA sample preparation guide (Rev. E) using the Illumina TruSeq Stranded mRNA Sample Preparation Kit

value: exponential phase growth yeast cells


title: 22693: cbk1∆∆ YPD 3

source_name: cbk1∆∆ exponential phase growth yeast cells


title: 22691: cbk1∆∆ YPD 1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A3_AD002_indexed


title: 22692: cbk1∆∆ YPD 2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A5_AD002_indexed


title: 22689: WT YPD 2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A5_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A3_AD012_indexed


title: PY02H2: ace2∆∆ SM 2

source_name: ace2∆∆ spider-induced hyphal cells

growth_protocol: Growth in spider medium for 4 hours at 37C

value: spider-induced hyphal cells


title: PNG_OrNV_infected_4

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

country: Australia

institute: The University of Queensland

description: host: Oryctes rhinoceros

data_processing:
The CLC Genomics Workbench version 12.0.1 was used for bioinformatics analyses. All libraries were trimmed from any vector or adapter sequences remaining.  Low quality reads (quality score below 0.05) and reads with more than two ambiguous nucleotides were discarded. For identification of the virus consensus from each sample, clean reads mapped to a recently reported Oryctes rhinoceros nudivirus complete genome sequence (MN623374). We implemented strict mapping criteria (mismatch, insertion and deletion costs: 2: 3: 3 respectively). The minimum similarity and length fraction of 0.9 between a mapped segment, and the reference was allowed in mapping criteria. We also permitted minimum 5 reads as low coverage threshold and inserted N as ambiguity symbols for handling the low coverage region. The quality score for each nucleotide has been used to resolve any conflict. For production of multiple sequence alignments, we used MUltiple Sequence Comparison by Log-Expectation (MUSCLE v3.8.425) to compare OrNV whole-genome consensus sequence from different libraries.
To detect structural modifications among different OrNV infected O. rhinoceros populations, CLC Genomic Workbench low-frequency variant detection tool, which is based on a neighbourhood quality standard (NQS) algorithm was used. Variants such as single nucleotide variant (SNV) multiple nucleotide variant (MNV), insertion, deletion and amino acid modification were then called based on neighbourhood radius (5), a maximum number of gaps and mismatches (2), the minimum average quality of surrounding bases (15), and minimum quality of the central base (20). We also used a minimum coverage filter of 10 and a minimum variant frequency of 35% to exclude sequencing artefacts. The final alignments for downstream analysis were OrNV 11x126,183nt and for the partial CoxI 11x621nt. For the construction of the maximum-likelihood phylogenetic tree of both host mitochondrial DNA and OrNV, we selected a nucleotide substitution model based on the consensus outcome of hierarchical likelihood ratio test (hLRT), Bayesian information criterion (BIC), Akaike information criterion (AIC). For the OrNV phylogenetic inference the General Time Reversible (GTR) +G rate variation (4 categories), +T topology variation was selected from all tests. For the mitochondrial CoxI the Hasegawa-Kishino-Yano (HKY) substitution model with +T topology variation was selected. The maximum-likelihood phylogeny was then constructed using CLC Genomics Workbench with a Neighbour Joining starting tree construction method under the nucleotide-substitution models mentioned above with 1000 bootstraps. Resultant trees were exported and visualised using FigTree version 1.4 (A. Rambaut; http://tree.bio.ed.ac.uk/software/figtree/).
For examination of OrNV gene expression profiles in different O. rhinoceros populations, clean reads were mapped to the OrNV genome using the RNA Sequencing Tool on CLC genomics workbench.  Expression values for all OrNV genes were calculated as total mapped read count and then normalised to reads per kilobase of transcript per million mapped viral reads (RPKM). The most highly expressed OrNV genes in O. rhinoceros gut tissue in different populations were identified and ranked. The viral gene expression profile was created based on calculated RPKM values. For comparison of viral gene expression analysis among different OrNV infected O. rhinoceros populations, hierarchical clustering analysis with Euclidean distance metric on the log2-transformed RPKM value (normalised expression value) were performed. Differential expression profiles between the four different populations were modelled using a separate Generalised Linear Model (GLM). The use of the GLM formalism allows the fitting of curves to expression values without assuming that the error on the values is normally distributed. The Wald test was also used to compare each sample against its control group to test whether a given coefficient is non-zero. We considered genes with more than 2-fold changes and a false discovery rate (FDR) of less than 0.05 as significantly modulated viral genes.
For further functional annotation of OrNV hypothetical proteins, we search for a conserved domain through IntrProScan database. We also used EggNOG version 4.5 to run pairwise orthology prediction on Cluster of Orthologous Groups
NA
Genome_build: Oryctes rhinoceros nudivirus complete genome sequence (MN623374)
Supplementary_files_format_and_content: Excel (Gene expression and Variants)

organism: Oryctes rhinoceros

source_name: Oryctes rhinoceros nudivirus

extract_protocol:
Individual female insects were disinfected by soaking in 75% Ethanol for 30s and then rinsing in phosphate-buffered saline (PBS) before their gut tissues were dissected, removed and preserved in an RNA stabilisation reagent (RNAlater®, QIAGEN). The gut from OrNV positive individuals was further dissected and transferred to Qiazol lysis reagent for RNA extraction according to manufacturer’s instructions (QIAGEN; Cat No.: 79306). The RNA samples were treated with DNase I for 1hr at 37°C and then their concentrations were measured using a spectrophotometer and integrity was ensured through analysis of RNA on a 1% (w/v) agarose gel.
After checking the RNA quality, total RNA samples were submitted to the Novogene Genomics Singapore Pte Ltd for RNA sequencing (RNA-seq). The PCR-based cDNA libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit and were sequenced using Novaseq6000 (PE150) technology with the insert size between 250-300 bp.

treatment_protocol: All samples are wild type and field collected OrNV infected insects

tag: host population

value: Papua New Guinea

tag: host tissue

value: gut


title: PNG_OrNV_infected_3

description: host: Oryctes rhinoceros


title: PY02H3: ace2∆∆ SM 3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A2_AD004_indexed


title: PNG_OrNV_infected_1

description: host: Oryctes rhinoceros


title: PNG_OrNV_infected_2

description: host: Oryctes rhinoceros


title: SI_OrNV_infected_1

description: host: Oryctes rhinoceros

value: Solomon Islands


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A11_AD006_indexed

value: AI


title: PY02H1: ace2∆∆ SM 1


title: WTH3: WT SM 3

source_name: wild-type spider-induced hyphal cells


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A2_AD006_indexed

value: male


title: PHI_OrNV_infected_3

description: host: Oryctes rhinoceros

value: Philippines


title: PHI_OrNV_infected_2

description: host: Oryctes rhinoceros


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A2_AD010_indexed


title: WTH2: WT SM 2


title: PHI_OrNV_infected_1

description: host: Oryctes rhinoceros


title: SI_OrNV_infected_2

description: host: Oryctes rhinoceros


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A2_AD001_indexed


title: WTH1: WT SM 1


title: 22688: WT YPD 1


title: Fiji_OrNV_infected_2

description: host: Oryctes rhinoceros

value: Fiji


title: PY02Y2: ace2∆∆ YPD 2

source_name: ace2∆∆ exponential phase growth yeast cells


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A1_AD012_indexed


title: PY02Y3: ace2∆∆ YPD 3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A1_AD010_indexed


title: Fiji_OrNV_infected_1

description: host: Oryctes rhinoceros


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A3_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A1_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A3_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A1_AD007_indexed


title: Jejunum_10

city: Cambridge

first: Alexander

last: Sheh

state: ma

address: 77 Massachusetts ave 16-828

department: Biological Engineering

institute: MIT

description: total RNA with rRNA depletion

data_processing:
Basecalls performed by Illumina HiSeq4000 software
Alignment performed using align function in Rsubread v2.0.1 using an index based on the calJac3.fa marmoset genome. GappedIndex=TRUE and alignment to the index was performed with minFragLength=50 and maxFragLength=600. Annotations were based on exons based on calJac3.ncbiRefSeq.gtf and matched to gene_id. Lowly expressed exons were trimmed based on counts per million being greater than 2 per million and found in at least 2 samples. TMM normalization was used
Genome_build: calJac3
Supplementary_files_format_and_content: Individual tables with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Individual tables with TMM normalized gene counts after trimming for every sample

organism: Callithrix jacchus

source_name: Jejunum - tissue cross-section

extract_protocol:
Necropsy samples were flash frozen in liquid nitrogen and stored at -80C. Tissue was homogenized with a pestle and extracted using TRIzol.
Total RNA was shipped to Arraystar. Total RNA was depleted of rRNA. Illumina kits were used for the RNA-seq library preparation including RNA fragmentation, random hexamer primed first strand cDNA synthesis, dUTP based second strand cDNA synthesis, end-repairing, A-tailing, adaptor ligation and library PCR amplification.

value: Jejunum

tag: disease state

value: Non-IBD control (stricture)


title: Jejunum_6

description: total RNA with rRNA depletion

value: IBD


title: Jejunum_15

description: total RNA with rRNA depletion


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A3_AD004_indexed


title: Jejunum_8

description: total RNA with rRNA depletion


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A11_AD007_indexed


title: Duodenum_post_21

description: total RNA with rRNA depletion

source_name: Duodenum - tissue cross-section

value: Duodenum

value: Duodenal stricture/ulcer


title: Jejunum_2

description: total RNA with rRNA depletion


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A12_AD004_indexed


title: Duodenum_post_14

description: total RNA with rRNA depletion


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A2_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A12_AD008_indexed


title: R256C_3

city: Smithville

first: Bin

last: Liu

state: TX

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

data_processing:
read aligment with Tophat
sorting with samtool
read count with HT-seq count
DE Analysis with DESeq
Genome_build: R64
Supplementary_files_format_and_content: Raw counts for each gene, text file

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: For RNA sample preparation from yeast strains, three biological replicates for each strain were inoculated overnight and diluted back to OD660 0.3 to grow in rich medium YPD at 30°C. 1.5X107 cells were collected by centrifugation when the culture reached early phase of exponential growth OD660 0.9.

extract_protocol:
RNA was extracted using Qiagen RNeasy plus Mini kit with extra enzymatic lysis step of the yeast cell wall using zymolyase 100T (100U per 107 cells).
cDNA Libraries were prepared using the Illumina TruSeq Stranded mRNA (Cat. # RS-122-2101) kit according to the manufacturer’s protocol starting with 1μg total RNA. Briefly, mRNAs were purified with oligo(dT) beads to capture polyA tails, then fragmented and converted to cDNA with reverse transcriptase. The resulting cDNAs were converted to double stranded cDNAs and subjected to end-repair, A-tailing, and adapter ligation.

treatment_protocol: No treatment


title: R256C_2


title: R256C_1


title: PY02Y1: ace2∆∆ YPD 1


title: Duodenum_post_5

description: total RNA with rRNA depletion


title: Duodenum_9

description: total RNA with rRNA depletion

value: Non-stricture control (IBD)


title: WT_3

value: WT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A12_AD012_indexed


title: WTY3: WT YPD 3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A12_AD007_indexed


title: WTY2: WT YPD 2


title: Duodenum_7

description: total RNA with rRNA depletion


title: GFI1-ChIP-seq

city: Shanghai

first: Yun

last: Tan

state: Shanghai

address: Room 1109, Building 11, 197 Ruijin Er Rd

department: Shanghai Institute of Hematology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Sequencing reads were aligned to hg38 by Bowtie2 (version 2.2.9). The uniquely mapped and non-redundant reads were left to conduct peak calling.
ChIP-seq peak regions were called using MACS (version 1.4.2) at a p-value cut off of 10e-8.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: peak.bed files were generated by MACS software

source_name: Acute promyelocytic leukemia cells

growth_protocol: NB4 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Cells were washed once with PBS buffer and 3 times with lysis buffer (10 mM Tris-HCl, PH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40, 1 mM PMSF). The pellets were then re-suspended in ChIP buffer (Active motif) containing 1 mM PMSF and proteinase inhibitor cocktail (Sigma). Chromatin shearing was performed using a Biorupter Pico ultrasonicator device (Diagenode) with 30s ON then 30s OFF for 30 cycles. Solubilized chromatin was used for immunoprecipitation by incubating overnight at 4 °C with 5 μg antibodies against PML/RARα fusion protein. The immunoprecipitation reaction was transferred to the Protein G agarose Column (53039, Active Motif) and incubated for 2 hours at 4 °C, then each column was washed 4 times with 900 μL Wash Buffer AM1 (Active motif). The ChIPed sample was eluted using 100 μL 37 °C Elution Buffer AM4 (Active Motif). Cross-linking was reversed by adding 5 μL Proteinase K and the sample was incubated overnight at 65 °C. Input and ChIPed DNA were purified using a DNA purification column (Active Motif).
DNA libraries were prepared with the MicroPlex Library Preparation Kit (Diagenode) according to the manufacturer’s instructions.

treatment_protocol: NB4 cells were cross-linked with 1% formaldehyde in Phosphate Buffered Saline (PBS) buffer for 10min at room temperature, and the fixation reactions were quenched by adding glycine to a final concentration of 0.125 M.

tag: antibodies

value: anti-GFI1 (Catalog No.sc-376949, Santa Cruz)


title: WTY1: WT YPD 1

value: exponential phase growth yeast cells


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A10_AD012_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: Jejunum_4

description: total RNA with rRNA depletion


title: WT_2


title: Duodenum_3

description: total RNA with rRNA depletion


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A10_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A12_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A10_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_A11_AD002_indexed


title: 24-month-C3

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

institute: 6/5000 Shandong Agricultural University

data_processing:
The sequence containing the adaptor was removed . Reads less than 50 nt after cleaving the adaptor sequences were discarded. Reads that were all A bases were removed. Reads with an N ratio greater than 10% were removed. Low-quality reads were removed (number of bases with a quality score (Q value) greater than 50% of the total reads).
The alignment tool Bowtie2 (2.2.8) was used to map the high-quality clean reads to a ribosomal RNA (rRNA) database (mismatch number: 0). rRNA reads were removed, and then the comparison software Tophat2 (2.1.1) was used to align the remaining reads to the goat reference genome
The tophat2-based alignment results were used to reconstruct transcripts using Cufflinks.
Genome_build: Capra hircus ARS1
Supplementary_files_format_and_content: Excel table file with raw counts of each sample

organism: Capra hircus

source_name: submandibular gland

extract_protocol:
After slaughter and exsanguination, the submandibular gland was collected, placed in liquid nitrogen immediately and then stored at −80 °C for long-term storage. Total RNA was extracted from 9 submandibular gland samples using TRIzol (Invitrogen, Carlsbad, CA, USA) reagent. The integrity and quality of the extracted RNA was determined by measuring the absorbance at 260/280 nm (A260/A280) using an Agilent BioAnalyzer 2100 (Agilent, Shanghai, China).
Ribosomal RNA was removed, and all other RNA was retained. Total RNA was randomly cleaved into short fragments, and to synthesize first-strand cDNA, the fragmented RNA was used as the template, with random hexamers, buffered dNTPs (dUTP instead of dTTP) and RnaseH. Second-strand cDNA was synthesized using DNA polymerase I. cDNAs were purified using a QiaQuick PCR kit (QIAGEN) and eluted with EB buffer (10 mM Tris-HCl, pH 8.0). The cohesive end was repaired, and an adaptor sequence was ligated to base “A” at the 3’end of the cDNA; the second strand was subsequently degraded with uracil-N-glycosylase (UNG). The ligated product was reverse transcribed by PCR amplification, and the product was purified to generate a cDNA library. To generate the library, the cDNA was sequenced using an Illumina HiSeqTM 4000 from Gene Denovo Biotechnology Co. (Guangzhou, China).


title: 24-month-C2


title: LP-1 BR-SI2-rep2

city: Tianjin

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

institute: Tianjin Medical University

data_processing:
Basecalls performed using BGISEQ-500
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using BWA.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample

growth_protocol: LP-1 wild-type cell and bortezomib-resistant cell were cultured in RPMI-1640 medium with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using BGI protocols

treatment_protocol: Cell was 25nM SI-2 treated for 24 hours.

value: B lymphoblast

tag: tumor type

value: mutiple myeloma

tag: cell line

tag: phenotype

value: bortezomib-resistant

tag: treatment

value: cultured with bortezomib for 2 months, and treated with SI2 for 24 hours before harvest


title: 24pbm_1: HWE_15mgt_sirna_24hbf

city: Fort Collins

first: Ken

middle: E

last: Olson

state: CO

address: 3185 Rampart Road

department: Microbiology, Immunology, Pathology

institute: Colorado State University

data_processing:
Clipped illumina adapters via fastx toolkit
Ran size select perl script
Created ebwt files & ran bowtie for alignment
Genome_build: prvabc59.fasta
Supplementary_files_format_and_content: bowtie results (.fastq) after alignment to prvabc59 (ZIKV) genome
Supplementary_files_format_and_content: reads grouped by nucleotide size (.fastq)
Supplementary_files_format_and_content: histogram of aligned reads grouped by nucleotide size (.txt)

organism: Aedes aegypti

source_name: 15 pooled midguts

growth_protocol: Ae. aegypti were maintained at 28°C with 75-80% relative humidity and a 12h light/12h dark cycle. Eggs were hatched in sterile water, and larva were fed ground TetraMin fish food.

extract_protocol:
15 midguts per library were flash frozen on dry ice and total RNA was extracted using TRIzol
Libraries were constructed by the University of Missouri DNA Core using Illumina TruSeq small RNA library prep kits following manufacturer's instructions

treatment_protocol: Mated females were fed artificial bloodmeals consisting of defibrinated sheep blood approximately 4 days post emergence, and tissues were collected 24h later.

value: Higgs White Eye

tag: bloodfeed status

value: 24 hours post-BF

tag: tissue

value: midguts


title: 24pbm_2: anti_ZIKV_15mgt_sirna_24hbf

value: anti-NS3/4A-ZIKV (Higgs White Eye genetic background)


title: LP-1 BR-SI2-rep1


title: LP-1 BR-DMSO-rep2

value: cultured with bortezomib for 2 months


title: LP-1 BR-DMSO-rep1


title: 12-month-B2


title: 12-month-B3


title: LP-1 WT-SI2-rep2

value: treated with SI2 for 24 hours


title: LP-1 WT-SI2-rep1


title: 12-month-B1


title: WT_1


title: 1-month-A2


title: 24-month-C1


title: LP-1 WT-DMSO_rep1

value: untreated


title: 1-month-A1


title: ParenC14

status: Public on Aug 25 2020

city: Raleigh

first: Yogesh

last: Saini

state: NC

address: 1060 William Moore Dr

department: Biomedical Sciences

institute: North Carolina State University

description: Parenchyma from filtered air exposed females

data_processing:
Illumina Novaseq 6000 used for sequencing
Sequenced reads were trimmed for adaptor sequence by fastp, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR V2.6.1
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from mapped read by HTSeq
Differeantial expression analysis with DEseq2
Genome_build: Mus Musculus mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample, and differential expressed gene for each comparasion

source_name: Parenchyma

growth_protocol: Adult mice were used to harvest tissues

extract_protocol:
RNA-Seq was performed on airway epithelium-enriched airways, parenchyma, and purified airspace macrophages.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We chronically exposed adult males and females to 0.8ppm ozone or filtered air.

tag: sample type


title: ParenC15

value: Parenchyma from filtered air exposed females


title: ParenC16


title: Primordia intemediate stage; biological repetition 3

type: RNA

city: Montpellier

first: Pascal

last: Gantet

address: Avenue Agropolis

department: IRD

country: France

institute: Université Montpellier 2

description: Gene expression data from intermediate stage crown root primordia tissue

hyb_protocol: Following fragmentation and biotin end labeling, 4 ug of cDNA were hybridized for 20 hr at 48°C on the Affymetrix® Rice Gene 1.1ST Jp Array. Strip arrays were washed and stained on the fluidic station of the Affymetrix GeneAtlas system using Hybridization Wash & Stain kit.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas Scanner.

data_processing:
Data were generated with Affymetrix Epression Console v 1.4.1 and GCRMA algorithm.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = RJpGene-1_1-st
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

organism: Oryza sativa Japonica Group

source_name: Rice stem base_intermediate stage crown root primordia

label_protocol: Biotinylated double strand cDNA were prepared according to the Affymetrix GeneAtlas WT PICO protocol from 1 or 2 ng total RNA (GeneAtlas WT PICO Technical Manual, 2015, P/N703262 Rev1 Affymetrix).

growth_protocol: Oryza sativa L. ssp. Japonica cv. Taichung 65 seeds were disinfected (3 min in ethanol 70%, 90 min in sodium hypochlorite 9,6%:Milli-Q water, 2:3 v:v plus 500 µL of Tween® 80 (ref. 822187, Merck, Germany), quadruple rinsed in sterile Milli-Q water) and inoculated under axenic conditions in round Petri dishes (ref. 82.1473.001, Starstedt, Germany) containing a filter pad (ref. 1001-090, Whatman paper, GE Healthcare, UK) and 15 mL half strength Murashige and Skoog (MS/2) medium (ref. M0231, Duchefa Biochemie, The Netherlands). Culture chambers were set at 27°C, 70% relative humidity, and 14 hour daylight. After 5 days, the plantlets were transferred into 250 mL wide-collar Erlenmeyer flasks containing 30 mL MS/2 medium, and let to grow during 3 days before sampling.

extract_protocol: Samples from two stem bases were pooled to perform  RNA extractions from the three primordia developmental stages and cortex, that correspond to one independent repetition of the experiment. In total 3 x 2 stem bases were processed that corespond to three intependant repetition of the experiment. RNA was isolated using the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific).

treatment_protocol: Stem bases were harvested in 2 mL ice-cold ethanol:acetic acid 3:1, v:v ﬁxative solution, inﬁltrated thrice under a mild vacuum for 15 min and stored for 20 h in fresh ﬁxative solution at 4°C. Embedding for dissection was performed as described by Mantegazza et al. 2014. A total of six stem base were cut into 15 µm sections on a Jung RM2055 (Leica Biosystems, Germany) or Microm HM355S (Thermo Fisher Scientific, Waltham, MA, USA) microtome. Sample ribbons were mounted on Leica LMD slides (ref. 11505190), deparaffinized by a 10 sec xylene bath at 4°C and dissected on a LMD 7000 laser dissector (Leica Biosystems). CR primordia belonging to the three successive rings present in stem bases at this stage were separately collected. Stem cortex tissues were sampled from the same sections where the CR primordia were collected from.

value: C.V. Taichung 65

value: stem base

tag: tissue subtype

value: intermediate stage crown root primordia


title: Primordia late stage; biological repetition 3

description: Gene expression data from late stage crown root primordia tissue

source_name: Rice stem base_late stage crown root primordia

value: late stage crown root primordia


title: Primordia early stage; biological repetition 1

description: Gene expression data from early stage crown root primordia tissue

source_name: Rice stem base_early stage crown root primordia

value: early stage crown root primordia


title: ParenC13


title: ParenC11

description: Parenchyma from ozone exposed females

value: Parenchyma from ozone exposed females


title: ParenC12

description: Parenchyma from ozone exposed females


title: Primordia late stage; biological repetition 2


title: Primordia early stage; biological repetition 3


title: 1-month-A3

tag: age


title: ParenC9

description: Parenchyma from ozone exposed females


title: Stem cortex; biological repetition 3

description: Gene expression data from cortex tissue of stem base

source_name: Rice stem base_cortex

value: cortex


title: ParenC7

description: Parenchyma from filtered air exposed males


title: ParenC10

description: Parenchyma from ozone exposed females


title: ParenC8

value: Parenchyma from filtered air exposed males


title: ParenC6


title: Primordia intemediate stage; biological repetition 1


title: LP-1 WT-DMSO_rep2

value: B lymphoblast

value: mutiple myeloma

value: WT


title: Primordia late stage; biological repetition 1


title: Stem cortex; biological repetition 1


title: Primordia intemediate stage; biological repetition 2


title: ParenC5


title: Stem cortex; biological repetition 2


title: ParenC2

description: Parenchyma from ozone exposed males

value: Parenchyma from ozone exposed males


title: Primordia early stage; biological repetition 2


title: ParenC3

description: Parenchyma from ozone exposed males


title: ParenC1

description: Parenchyma from ozone exposed males


title: EPAC11

description: Airways from ozone exposed females

source_name: Extrapulmonary Airways

value: Airways from ozone exposed females


title: EPAC16

description: Airways from filtered air exposed females


title: EPAC13

value: Airways from filtered air exposed females


title: EPAC12

description: Airways from ozone exposed females


title: EPAC8

description: Airways from filtered air exposed males

value: Airways from filtered air exposed males


title: EPAC5

description: Airways from filtered air exposed males


title: EPAC4

description: Airways from ozone exposed males

value: Airways from ozone exposed males


title: EPAC6

description: Airways from filtered air exposed males


title: EPAC10

description: Airways from ozone exposed females


title: EPAC1

description: Airways from ozone exposed males


title: MacC13

description: Macrophages from ozone exposed females

source_name: CD11b-negative Alveolar Macrophages

value: Macrophages from ozone exposed females


title: MacC16

description: Macrophages from ozone exposed females


title: EPAC15


title: EPAC3

description: Airways from ozone exposed males


title: EPAC2

description: Airways from ozone exposed males


title: MacC15

description: Macrophages from ozone exposed females


title: MacC14

description: Macrophages from ozone exposed females


title: EPAC14


title: ParenC4

description: Parenchyma from ozone exposed males


title: MacC12

description: Macrophages from filtered air exposed females


title: MacC9

value: Macrophages from filtered air exposed females


title: MacC8

description: Macrophages from filtered air exposed males


title: MacC7

value: Macrophages from filtered air exposed males


title: MacC11


title: MacC10


title: MacC4

description: Macrophages from ozone exposed males

value: Macrophages from ozone exposed males


title: MacC3

description: Macrophages from ozone exposed males


title: MacC2

description: Macrophages from ozone exposed males


title: MacC5


title: EPAC7

description: Airways from filtered air exposed males


title: EPAC9

description: Airways from ozone exposed females


title: DDCrhCY2-WT934

city: Osaka

first: Le

middle: Thi Thanh

last: Thuy

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku, Osaka 545-8585, Japan

department: Department of Hepatology

country: Japan

institute: Osaka City University, Graduate School of Medicine

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated using FastQC v0.11.7
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed
Trimmed reads are mapped to reference genome with HISAT2 version 2.1.0, splice-aware aligner
Transcript is assembled by StringTie version 1.3.4d with aligned reads
Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage. The FPKM value or the RPKM is used as a normalization value.
In groups with different conditions, genes or transcripts that express differentially are filtered out through statistical hypothesis testing
In case of known gene annotation, functional annotation and gene-set enrichment analysis are performed using GO and KEGG database on differentially expressed genes
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Liver

extract_protocol:
1 μg of total RNA was subjected to library synthesis using TruSeq Stranded mRNA LT Sample Prep Kit. The resulting mRNA was fragmented, reverse transcribed using random primers into cDNA, and ligated adapters onto both ends of the cDNA fragments. After amplifying fragments using PCR, select fragments with insert sizes between 200-400 bp. For paired-end sequencing, both ends of the cDNA is sequenced by the read length
TruSeq Stranded mRNA Sample Preparation Guide.

treatment_protocol: Two groups of WT mice were received 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)-supplemented diet for 4 weeks. In the last 2 weeks of DDC, mice were injected either rhCYGB (2 mg/kg/time, twice a week) or its vehicle (normal saline). Mice were sacrificed 2 days after the last dose of rhCYGB.

tag: strain

value: Liver

value: wild-type

value: DDC and rhCYGB


title: DDC4w-WT852

tag: genotype

value: DDC


title: DDCrhCY2-WT933


title: DDC4w-WT924


title: TAArhCY5-WT27

treatment_protocol: Three groups of WT mice were given an intraperitoneal (i.p.) injection of an escalating dose of Thioacetamide (TAA) twice a week for totally 10 weeks. During the last 5 weeks or 2 weeks of TAA injection, mice have treated with rhCYGB 2 mg/kg body weight (BW), tail vein (i.v.) injection, twice a week as treatment groups. The control group was injected with normal saline. Mice were sacrificed 2 days after the last dose of rhCYGB

value: TAA 10 weeks and treated with rhCYGB (2 mg/kg) for the last 5 weeks of TAA treatment


title: TAArhCY2-WT18

value: TAA 10 weeks and treated with rhCYGB (2 mg/kg) for the last 2 weeks of TAA treatment


title: DDC4w-WT925


title: TAArhCY5-WT23


title: TAArhCY2-WT19


title: DDCrhCY2-WT931


title: TAArhCY2-WT17


title: TAA10w-WT12

value: TAA 10 weeks


title: TAA10w-WT14


title: TAArhCY5-WT28


title: MacC6


title: Liver non-parenchymal cells, CCl4 2w A

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Demultiplexing, alignment and counting of the samples were performed by application of the Cell Ranger 2.1.0 pipeline.
To perform the abovementioned steps the features mkfastq and count were run.
Genome_build: mm10
Supplementary_files_format_and_content: The raw count matrix is provided as an mtx.gz file along with gene and barcode names as tsv.gz files

source_name: Liver non-parenchymal cells

extract_protocol:
Cells were isolated based on enzymatic digestion followed by fluorescent antibody labeling. Fluorescently labeled cells were purified by FACS.
10x Genomics Chromium Single Cell 3' V2 solution

value: CCl4 2w

tag: disease status

value: fibrosis induction

value: liver

value: mixed sample (non-demultiplexed) of non-parenchymal cell types (hepatic stellate cells, liver endothelial cells, macrophages)


title: Liver non-parenchymal cells, CCl4 4w B

value: CCl4 4w

tag: cell type


title: Liver non-parenchymal cells, CCl4 4w A


title: MacC1

description: Macrophages from ozone exposed males


title: Liver non-parenchymal cells, CCl4 4w C


title: Liver non-parenchymal cells, CCl4 2w C


title: Liver non-parenchymal cells, Ctrl B

value: Ctrl


title: Liver non-parenchymal cells, Ctrl C


title: Liver non-parenchymal cells, Ctrl A


title: TAA10w-WT13


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_C8_AD007_indexed

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: MOp

tag: Sex

value: male


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_E3_AD004_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_G3_AD010_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H7_AD010_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_B7_AD012_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_1_CEMBA180410_2C_2_H8_AD008_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_A5_AD006_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_1_CEMBA180410_2C_2_C8_AD007_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_1_CEMBA180410_2C_2_H3_AD012_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_1_CEMBA180410_2C_2_C1_AD006_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_1_CEMBA180410_2C_2_C1_AD004_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_1_CEMBA180410_2C_2_C7_AD006_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_1_CEMBA180410_2C_2_C7_AD012_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_1_CEMBA180410_2C_2_C7_AD008_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_1_CEMBA180410_2C_2_A11_AD008_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_1_CEMBA180410_2C_2_A5_AD001_indexed


title: Liver non-parenchymal cells, CCl4 2w B


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title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_1_CEMBA180410_2C_2_A3_AD004_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_1_CEMBA180410_2C_2_A2_AD006_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H8_AD010_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H7_AD008_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H5_AD012_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H7_AD012_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H8_AD012_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H7_AD007_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H5_AD010_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H6_AD010_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H4_AD010_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H5_AD007_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H2_AD012_indexed


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title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H4_AD012_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H9_AD008_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H2_AD010_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H3_AD012_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H3_AD008_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H12_AD007_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H2_AD008_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H3_AD007_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H3_AD010_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H1_AD010_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H1_AD008_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H1_AD012_indexed


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title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_H10_AD010_indexed


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title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_G4_AD012_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_G10_AD012_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_G3_AD007_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_G2_AD008_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_G3_AD008_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_G2_AD012_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_G9_AD012_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_G12_AD012_indexed


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title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_G12_AD007_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_G2_AD007_indexed


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title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_F9_AD012_indexed


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title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_F9_AD007_indexed


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title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_F8_AD008_indexed


title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_F5_AD008_indexed


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title: 180508_CEMBA_mm_P56_P63_2C_CEMBA180410_2C_3_CEMBA180410_2C_4_G3_AD012_indexed


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