title: tomato:pepper heterograft - 5 DAG - Replicate 3

status: Public on Sep 30 2021

type: SRA

city: Raleigh

first: Lisa

last: Van den Broeck

state: NORTH CAROLINA

address: 112 Derieux Place

department: Plant and Microbial Biology

country: USA

institute: North Carolina State University

description:
Named TP_5d in processed file
Supplemental_Table5
TP_5d_R3

library_source: transcriptomic

data_processing:
Gene expression analysis of raw RNA-seq data was performed using the TuxNet interface (Spurney et al, 2019).
TuxNet uses ea-utils fastq-mcf (Aronesty, 2011, Aronesty, 2013) for preprocessing, hisat2 (Kim et al, 2015) for genome alignment, and Cufflinks (Trapnell et al, 2012) for differential expression analysis.

molecule: total RNA

organism:
Capsicum annuum
Solanum lycopersicum

source_name: Graft junction

extract_protocol:
RNA was extracted using TRIzol reagent. The purified RNA was treated with DNAseI.
RNA-seq libraries were constructed using 2.5 µg of total RNA per sample, isolated with the NEBNext® Poly(A) mRNA Magnetic Isolation Module, followed by the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® using NEBNext® Multiplex Oligos for Illumina®.

tag: treatment

value: tomato:pepper heterograft - 5 DAG


title: tomato:pepper heterograft - 3 DAG - Replicate 3

description:
Named TP_3d in processed file
Supplemental_Table5
TP_3d_R3

value: tomato:pepper heterograft - 3 DAG


title: tomato:pepper heterograft - 1 DAG - Replicate 3

description:
Named TP_1d in processed file
Supplemental_Table5
TP_1d_R3

value: tomato:pepper heterograft - 1 DAG


title: pepper:tomato heterograft - 5 DAG - Replicate 3

description:
Named PT_5d in processed file
Supplemental_Table5
PT_5d_R3

value: pepper:tomato heterograft - 5 DAG


title: pepper:tomato heterograft - 3 DAG - Replicate 4

description:
Named PT_3d in processed file
Supplemental_Table5
PT_3d_R4

value: pepper:tomato heterograft - 3 DAG


title: tomato:pepper heterograft - 5 DAG - Replicate 1

description:
Named TP_5d in processed file
Supplemental_Table5
TP_5d_R1


title: pepper:tomato heterograft - 3 DAG - Replicate 3

description:
Named PT_3d in processed file
Supplemental_Table5
PT_3d_R3


title: tomato:pepper heterograft - 5 DAG - Replicate 2

description:
Named TP_5d in processed file
Supplemental_Table5
TP_5d_R2


title: tomato:pepper heterograft - 1 DAG - Replicate 2

description:
Named TP_1d in processed file
Supplemental_Table5
TP_1d_R2


title: pepper:tomato heterograft - 1 DAG - Replicate 3

description:
Named PT_1d in processed file
Supplemental_Table5
PT_1d_R3

value: pepper:tomato heterograft - 1 DAG


title: pepper:tomato heterograft - 5 DAG - Replicate 2

description:
Named PT_5d in processed file
Supplemental_Table5
PT_5d_R2


title: pepper:tomato heterograft - 5 DAG - Replicate 4

description:
Named PT_5d in processed file
Supplemental_Table5
PT_5d_R4


title: tomato:pepper heterograft - 1 DAG - Replicate 1

description:
Named TP_1d in processed file
Supplemental_Table5
TP_1d_R1


title: tomato:pepper heterograft - 3 DAG - Replicate 2

description:
Named TP_3d in processed file
Supplemental_Table5
TP_3d_R2


title: tomato:pepper heterograft - 3 DAG - Replicate 4

description:
Named TP_3d in processed file
Supplemental_Table5
TP_3d_R4


title: tomato:pepper heterograft - 1 DAG - Replicate 4

description:
Named TP_1d in processed file
Supplemental_Table5
TP_1d_R4


title: pepper:tomato heterograft - 3 DAG - Replicate 2

description:
Named PT_3d in processed file
Supplemental_Table5
PT_3d_R2


title: pepper:tomato heterograft - 5 DAG - Replicate 1

description:
Named PT_5d in processed file
Supplemental_Table5
PT_5d_R1


title: tomato:pepper heterograft - 5 DAG - Replicate 4

description:
Named TP_5d in processed file
Supplemental_Table5
TP_5d_R4


title: pepper:tomato heterograft - 3 DAG - Replicate 1

description:
Named PT_3d in processed file
Supplemental_Table5
PT_3d_R1


title: tomato:pepper heterograft - 3 DAG - Replicate 1

description:
Named TP_3d in processed file
Supplemental_Table5
TP_3d_R1


title: pepper:tomato heterograft - 1 DAG - Replicate 4

description:
Named PT_1d in processed file
Supplemental_Table5
PT_1d_R4


title: pepper:tomato heterograft - 1 DAG - Replicate 2

description:
Named PT_1d in processed file
Supplemental_Table5
PT_1d_R2


title: FR04: 21 dpi SARS-CoV-2

city: Covington

first: Joseph

middle: C

last: Mudd

state: LA

address: 18703 Three Rivers rd

institute: Tulane University

data_processing:
Sequencing reads were demultiplexed and adapter-trimmed with Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).  The –hardtrim  option was used to clip the first 6 basepairs of mate R2 that exhibited low quality scores.  Because reads were derived from 2 separate species with different genomes and different genome annotations, these were treated as different datasets from alignment to gene correlation steps.  In brief, lanes were concatenated and mapped with STAR aligner to their respective species genomes, Mmul_10 (GCF_003339764.) for RM and ChlSabl.1 (GCF_000409795.2) for AGM (49).  Parameters were modified from the default run option that gave the highest percentage of uniquely mapped reads:  --outFilterScoreMinOverLread 0   --outFilterMatchNmin 0   --outFilterMatchNminOverLread 0   --outFilterMismatchNmax 2.  Counts were generated by the STAR option –quantMode geneCounts and an n  n matrix was prepared as input for the R package DESeq2 (50).  Data was fitted to a generalized linear model in accordance with the DEseqdataset function.  Samples that received an RNA concentration step during the isolation process were found to strongly influence fitted values of the model.  Thus a revised analysis was performed incorporating the effect of RNA clean-up into the generalized linear model.  Hidden variables were further incorporated with the R package SVA and the object was post-filtered to remove genes with at least 4 samples having normalized counts < 10.
Genome_build: Mmul_8.0.1 (for rhesus samples), ChlSabl.1 (for AGM samples
Supplementary_files_format_and_content: tab delimited text files correspond to transcript read counts calculated by Htseq-count

organism: Macaca mulatta

source_name: PAXgene

extract_protocol:
collection protocol: Whole venous blood was collected from nonhuman primates using a BD Vacutainer Safety-Lok Blood Collection Set (BD catg#367281) and BD Vacutainer one use needle holder (BD catg# 364815). Blood was added to the PAXgene Blood RNA reagent tube (PreAnalytiX catg#762165) in the same ratio as the manufacturer’s guidelines. Post collection, PAXgene blood tubes were stored upright for a minimum of two hours and then placed into the -20C freezer until further processing.
Samples were processed in accordance with the PreAnalytiX PAXgene Blood RNA Kit (PreAnalytiX catg#762165). The RNA Clean & Concentrator-5 kit (Zymo, Catg#R1015) was used to purify and increase RNA samples with low yields. Procedures were followed per manufacturer’s guidelines. For AGM NC33, Paxgene tubes were not collected at 1 and 3 dpi due to blood being prioritized for other assays.
Total RNA samples were quantitated using Qubit RNA HS Assay kit (Invitrogen Q32855). A RIN for each sample was determined by running 1ul on an Agilent 4150 TapeStation using RNA Screen Tapes (Agilent 5067-5576). 1-2 ug of each sample were treated with Baseline Zero DNase (Epicentre, DB0711K) for 30 minutes at 37°C. DNase was inactivated by adding 2ul 10X Stop solution and following a 10 minute incubation at 65°C. The Total RNAs were then purified using Agencourt RNAClean XP magnetic beads by following the manufactory recommendation (Beckman Coulter Life Sciences). 10 ng of each sample were used to make SMART-Seq libraries following the SMART-Seq Stranded Kit User Manual (Takara Bio). Briefly, cDNAs were first generated from all total RNA fragments after RNA fragmentation. Addition of Illumina adapters and indexes and then library purification were followed. Final library amplification and purification were performed after enzymatically removing ribosomal fragments originating from rRNA molecules by using probes specific to mammalian rRNA.
Libraries were quantitated using Qubit DNA HS Assay kit (Molecular Probes Life Technologies, Q32854). Average size of each library was determined by running each sample on Agilent 4150 TapeStation using D1000 Screen Tapes. (Agilent 5067-5582). Each library was diluted to 4nM in DNase RNase free ultrapure water (Invitrogen 10977-015). All libraries were pooled at a concentration of 4nM before denaturing with 0.2 N NaOH for 5 min at RT. The libraries were neutralized using 0.2 N Tris-HCl, pH 7 before being diluted to 20pM in HT1 buffer (Illumina).
Finally, denatured libraries were loaded into an Illumina NextSeq 550 v2 High-Output reagent cartridge at a final concentration of 1.2pM in HT1 buffer. Denatured PhiX control library was also included at 1% concentration. Dual indexes and paired end 75bp sequencing was performed on a High-Output flow cell yielding about 18M read pairs per sample.

tag: tissue

value: Blood

tag: time


title: HD09: 7 dpi SARS-CoV-2


title: HD09: 21 dpi SARS-CoV-2


title: FR04: 14 dpi SARS-CoV-2


title: pepper:tomato heterograft - 1 DAG - Replicate 1

description:
Named PT_1d in processed file
Supplemental_Table5
PT_1d_R1


title: HB37: 21 dpi SARS-CoV-2


title: Vestibular flat epithelium, biological rep4

type: RNA

city: Beijing

first: Lu

last: He

address: No.95 Yongan Road

country: China

institute: Bejing Friendship Hospital, Capital Medical University

description:
severe lesion
Gene expression data from vestibular flat epithelium

hyb_protocol: cRNA was fragmented, and then hybridised to Affymetrix Mouse Clariom® S Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: All arrays were scanned by using Affymetrix® GeneChip Command Console (AGCC) which was installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analysed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as a normalisation method.

label: biotin

organism: Mus musculus

source_name: utriclular epithelium at 2 weeks after severe lesion

label_protocol: cDNA was synthesized with One-Cycle Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA, USA), and cRNA was created using GeneChip IVT Labeling Kit (Affymetrix)

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

treatment_protocol: When mice were 6 weeks old, 400 µg of streptomycin dissolved in normal saline (400 g/L, 1 µL), was inoculated into the inner ear through the posterior semicircular canal to induce a severe lesion in the mouse utricle.  After 2 weeks of damage, normal utricle and vestibular flat epithelium samples were collected for RNA extraction.

value: Vestibular flat epithelium


title: Normal utricle, biological rep1

description:
control
Gene expression data from normal utricle

source_name: normal utriclular sensory epithelium

value: Normal utricle


title: Vestibular flat epithelium, biological rep2


title: Normal utricle, biological rep4


title: Vestibular flat epithelium, biological rep5


title: Vestibular flat epithelium, biological rep3


title: Normal utricle, biological rep2


title: FR04: 3 dpi SARS-CoV-2


title: HB37: 3 dpi SARS-CoV-2


title: Normal utricle, biological rep5


title: HB37: 1 dpi SARS-CoV-2


title: GH99: 14 dpi SARS-CoV-2


title: HD09: 4 dpi SARS-CoV-2


title: GH99: 21 dpi SARS-CoV-2


title: HB37: 7 dpi SARS-CoV-2


title: Vestibular flat epithelium, biological rep1


title: GH99: pre-infection

value: uninfected

value: PRE


title: FR04: pre-infection


title: FR04: 7 dpi SARS-CoV-2


title: HB37: pre-infection


title: FR04: 1dpi SARS-CoV-2


title: B2: dibutyl phthalate (DBP)

city: Zhenjiang

first: Hui

last: Chen

address: Xuefu Road

institute: jiangsu university

data_processing:
Data filtering was performed on Raw Data, the linker sequences and low-quality reads were removed to obtain high-quality Clean Data.
HISAT2 was used to sequence alignment.
The reads numbers mapped to each gene were counted by HTSeq v0.6.1.
The number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) was used to estimate the gene expression levels of each gene which was calculated based on the length of the gene and reads count mapped to this gene
Genome_build: ftp://ftp.ensembl.org/pub/release-91/fasta/danio_rerio/dna/Danio_rerio.GRCz10.dna.toplevel.fa
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Danio rerio

source_name: testis

extract_protocol:
Testis were removed and snap frozen in liquid nitrogen, and total RNA was extracted through an RNeasy Mini Kit (Qiagen, USA). 3 μg RNA per sample was used to establish the sequencing libraries. The NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) was applied to construct the cDNA library.
RNA libraries were sequenced by the Illumina HiSeq X Ten with the pair-end mode (Genepioneer Biotechnologies Company)

tag: strain

value: AB

tag: Sex

value: male

tag: age

value: 5 months old

value: testis

tag: genotype

value: wild type


title: HUVEC ctrl rep2

city: Stanford

first: Ashby

middle: J

last: Morrison

state: CA

address: 371 Serra Mall Gilbert Bldg, Room 326

department: Biology

institute: Stanford University

data_processing:
Sequenced reads were aligned using STARv2.6.0a with paramaters --outFilterMultimapNmax 1 --outFilterMatchNmin 35
Raw counts were then used as input of DESeq2. Only genes with 40 reads total in all 4 replicates are included in the analysis. p=0.01 is used as the cut off to identify significantly differentially expressed genes
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: Human umbilical vein endothelial cells (HUVECs)

growth_protocol: Cells were seeded and grown in Endothelial Cell Growth Medium (EGM-2, Lonza). Cells were grown in humidified 37C chamber with 5% CO2.

extract_protocol:
Zymo research Quick-RNA™ Miniprep Plus Kit (R1057)
RNA libraries were prepared using NEB Next Ultra RNA library prep kit

treatment_protocol: Cells were transfected with either siRNA targeting Ino80 (Sigma-Aldrich, cat. No. EHU069661) or negative control siRNA (Ambion, cat. No. AM4636) with a final concentration of 13.8 uM.

tag: cell type

tag: knockdown

value: negative control siRNA


title: HUVEC ctrl rep1

value: Human umbilical vein endothelial cells (HUVECs)


title: I2: Diisobutyl phthalate (DiBP)


title: HUVEC siINO80 rep2


title: HUVEC siINO80 rep1


title: GH99: 1 dpi SARS-CoV-2


title: GH99: 7 dpi SARS-CoV-2


title: GH99: 4 dpi SARS-CoV-2


title: Normal utricle, biological rep3


title: HD09: pre-infection


title: HB37: 14 dpi SARS-CoV-2


title: Ex_vivo_erythroid_Donor1_Day10 DNaseI-seq

city: Seattle

first: Grigorios

last: Georgolopoulos

state: WA

address: 2211 Elliott Ave #400

institute: Altius Institute

library_source: genomic

data_processing:
Library strategy: DNaseI-seq
Basecalling, RTA v3.4.4
Alignments to GRCh38, BWA v0.7.12
Read processing, Samtools v1.3
Read density, Bedops v2.4.15
Peak calling, Hotspot2 v2.1.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalized density tracks, DHS peak calls as a .bed file

molecule: genomic DNA

growth_protocol: We used a 2-step differentiation protocol as described in Giarratana et al., 2011, Blood. Briefly, frozen CD34+ HSPCs are conditioned overnight in serum-free media in the presence of FLT3, TPO and IL3. Cells were then transferred in Step 1, serum-free media supplemented with BSA, Insulin, human-holotransferrin, heparin, hydrocortisone, human recombinant IL-3, hrEPO, and hrSCF and maintained for 7 days. On day 8, cells were transferred to Step 2 media where we withdraw hydrocortisone and IL-3 and maintain the rest of the components. Cells are maintained in Step 2 media until culture termination on day 12.

extract_protocol:
Approximately 100,000 nuclei were extracted and DNaseI digested according to John, S. et al., 2013, Curr Protoc Mol Biol
Genomic library was constructed using ThruPLEX DNA-seq kit, Rubicon Genomics (now TAKARA) according to manufacturer's instructions

tag: differentiation day

tag: dnase u/ml


title: Ex_vivo_erythroid_Donor3_Day11 DNaseI-seq


title: Ex_vivo_erythroid_Donor1_Day12 DNaseI-seq


title: Ex_vivo_erythroid_Donor1_Day11 DNaseI-seq


title: HD09: 14 dpi SARS-CoV-2


title: Ex_vivo_erythroid_Donor1_Day9 DNaseI-seq


title: HD09: 1 dpi SARS-CoV-2


title: Ex_vivo_erythroid_Donor2_Day10 DNaseI-seq


title: Ex_vivo_erythroid_Donor2_Day11 DNaseI-seq


title: Ex_vivo_erythroid_Donor3_Day12 DNaseI-seq


title: Ex_vivo_erythroid_Donor3_Day8 DNaseI-seq


title: Comb2: both DBP and DiBP


title: CK2: control


title: Ex_vivo_erythroid_Donor2_Day12 DNaseI-seq


title: Ex_vivo_erythroid_Donor3_Day9 DNaseI-seq


title: Ex_vivo_erythroid_Donor3_Day10 DNaseI-seq


title: Ex_vivo_erythroid_Donor2_Day6 DNaseI-seq


title: Ex_vivo_erythroid_Donor3_Day7 DNaseI-seq


title: Ex_vivo_erythroid_Donor3_Day5 DNaseI-seq


title: Ex_vivo_erythroid_Donor2_Day9 DNaseI-seq


title: Ex_vivo_erythroid_Donor1_Day7 DNaseI-seq


title: Ex_vivo_erythroid_Donor1_Day5 DNaseI-seq


title: Ex_vivo_erythroid_Donor3_Day6 DNaseI-seq


title: Ex_vivo_erythroid_Donor2_Day8 DNaseI-seq


title: Ex_vivo_erythroid_Donor2_Day5 DNaseI-seq


title: Ex_vivo_erythroid_Donor2_Day7 DNaseI-seq


title: Ex_vivo_erythroid_Donor1_Day8 DNaseI-seq


title: Ex_vivo_erythroid_Donor2_Day1 DNaseI-seq


title: Ex_vivo_erythroid_Donor1_Day6 DNaseI-seq


title: Ex_vivo_erythroid_Donor3_Day1 DNaseI-seq


title: Ex_vivo_erythroid_Donor3_Day3 DNaseI-seq


title: Ex_vivo_erythroid_Donor1_Day0 DNaseI-seq


title: Ex_vivo_erythroid_Donor2_Day3 DNaseI-seq


title: S1785_00026_S7_R

city: Belfast

first: Stuart

last: McIntosh

address: 97 Lisburn Road

country: United Kingdom

institute: Queen's University Belfast

description: Breast cancer post-treatment sample

data_processing:
Base calling was carried out using the Illumina bcl2fastq tool
Read alignment was performed using StarAlign
BWA and samtools flagstat were used to determine read alignment to a ribosomal RNA sequence database
Cufflinks was used to generate gene expression data, represented as Fragments per Kilobase per Million fragments mapped for each gene present in the human ENSEMBL annotation file.
HTSeq was used to count the number of reads aligning to each gene present in the human ENSEMBL annotation file
Genome_build: GRCH37
Supplementary_files_format_and_content: Tab delimited text file with normalised expression counts for every gene and every sample

source_name: Breast cancer

extract_protocol:
Core biopsies were taken under image guidance from breast tumours before, during and after chemotherapy treatment. Pathology review was conducted to identify tumour areas within each core, which were subsequently macrodissected under RNAse-free conditions. Following RNA extraction, total RNA was amplified using the NuGEN WT-Ovation FFPE RNA amplification System V2.
Libraries were prepared for sequencing using the Illumina Tru-Seq RNA Exome library preparation kit and standard Illumina protocols

tag: timepoint

value: Post-chemotherapy


title: Ex_vivo_erythroid_Donor1_Day1 DNaseI-seq


title: Ex_vivo_erythroid_Donor2_Day4 DNaseI-seq


title: S1785_00018_S7_R

description: Breast cancer mid-treatment sample

value: Mid-chemotherapy


title: S1785_00032_S1_R

description: Breast cancer post-treatment sample


title: Ex_vivo_erythroid_Donor1_Day3 DNaseI-seq


title: S1785_00030_S10_R

description: Breast cancer post-treatment sample


title: S1785_00031_S1_R

description: Breast cancer post-treatment sample


title: S1785_00022_S6_R

description: Breast cancer mid-treatment sample


title: S1785_00005_S5_R

description: Breast cancer mid-treatment sample


title: S1785_00021_S3_R

description: Breast cancer mid-treatment sample


title: Ex_vivo_erythroid_Donor2_Day0 DNaseI-seq


title: Ex_vivo_erythroid_Donor1_Day4 DNaseI-seq


title: S1785_00004_S9_R

description: Breast cancer mid-treatment sample


title: S1785_00016_S3_R

description: Breast cancer mid-treatment sample


title: Ex_vivo_erythroid_Donor3_Day4 DNaseI-seq


title: S1785_00011_S6_R

description: Breast cancer mid-treatment sample


title: S1785_00017_S10_R

description: Breast cancer mid-treatment sample


title: Ex_vivo_erythroid_Donor3_Day0 DNaseI-seq


title: S1785_00029_S9_R

description: Breast cancer post-treatment sample


title: S1785_00001_S6_R

description: Breast cancer mid-treatment sample


title: S1785_00003_S11_R

description: Breast cancer mid-treatment sample


title: S1630_00047_S5_R

description: Breast cancer baseline sample

value: Pre-chemotherapy


title: S1785_00027_S5_R

description: Breast cancer post-treatment sample


title: S1785_00023_S6_R

description: Breast cancer mid-treatment sample


title: S1785_00043_S8_R

description: Breast cancer baseline sample


title: S1785_00044_S4_R

description: Breast cancer baseline sample


title: S1785_00025_S2_R

description: Breast cancer mid-treatment sample


title: S1785_00041_S2_R

description: Breast cancer baseline sample


title: S1785_00040_S2_R

description: Breast cancer baseline sample


title: S1785_00028_S5_R

description: Breast cancer post-treatment sample


title: S1785_00006_S4_R

description: Breast cancer mid-treatment sample


title: S1785_00014_S11_R

description: Breast cancer mid-treatment sample


title: S1785_00020_S8_R

description: Breast cancer mid-treatment sample


title: S1630_00046_S18_R

description: Breast cancer baseline sample


title: S1785_00007_S4_R

description: Breast cancer mid-treatment sample


title: S1630_00038_S19_R

description: Breast cancer baseline sample


title: S1785_00024_S3_R

description: Breast cancer mid-treatment sample


title: S1785_00042_S7_R

description: Breast cancer baseline sample


title: S1630_00039_S1_R

description: Breast cancer baseline sample


title: S1785_00009_S1_R

description: Breast cancer mid-treatment sample


title: S1630_00044_S18_R

description: Breast cancer baseline sample


title: S1630_00031_S16_R

description: Breast cancer baseline sample


title: S1785_00037_S8_R

description: Breast cancer baseline sample


title: S1785_00008_S2_R

description: Breast cancer mid-treatment sample


title: S1630_00028_S2_R

description: Breast cancer baseline sample


title: S1630_00043_S7_R

description: Breast cancer baseline sample


title: S1630_00027_S14_R

description: Breast cancer baseline sample


title: S1630_00045_S4_R

description: Breast cancer baseline sample


title: S1630_00021_S15_R

description: Breast cancer baseline sample


title: S1785_00036_S11_R

description: Breast cancer baseline sample


title: S1785_00010_S3_R

description: Breast cancer mid-treatment sample


title: S1630_00037_S22_R

description: Breast cancer baseline sample


title: S1630_00042_S6_R

description: Breast cancer baseline sample


title: S1630_00033_S10_R

description: Breast cancer baseline sample


title: S1785_00034_S9_R

description: Breast cancer baseline sample


title: S1630_00050_S20_R

description: Breast cancer baseline sample


title: S1785_00039_S5_R

description: Breast cancer baseline sample


title: S1785_00035_S1_R

description: Breast cancer baseline sample


title: cord blood CD34+ cell Group0-4

city: Indianapolis

first: Bin

last: Guo

state: Indiana

address: 950 W. Walnut Street

department: Microbiology & Immunology

institute: Indiana University

description: Sample 4

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NextSeq500
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to hg38 genes using featureCounts (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 4 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.20.8).
Genome_build: hg38
Supplementary_files_format_and_content: raw count (excel)

molecule: polyA RNA

source_name: cord blood

growth_protocol: CB CD34+ cells were cultured in Stemline II Hematopoietic Stem Cell Expansion Medium (Sigma, S0912) with 100 ng/mL stem cell factor (SCF) (R&D Systems, #7466-SC-010/CF), 100 ng/mL thrombopoietin (TPO) (R&D Systems, #288-TP-200/CF), and 50 ng/mL Fms-like tyrosine kinase 3 ligand (Ftl3L) (BioLegend, # 710802) in the presence of with 50 IU/mL penicillin and 50 μg/mL streptomycin. All CD34+ cell cultures were incubated in a 5% O2 and 5% CO2 humidified cell incubator.

extract_protocol:
CB CD34+ cells were lysed and RNA was extracted using RNeasy Mini Kit (QIAGEN, Valencia, CA, USA).
RNA sequencing analysis was performed at SeqWright Genomic Services (GE Healthcare). RNA samples were subjected to poly-A selection TruSeq RNA Sample Prep, library construction, and cluster generation. RNA libraries were sequenced on an Illumina HiSeq 2500 machine with 2×100 bp read lengths for a total of 2×20 M reads per sample.

treatment_protocol: Freshly isolated CD34+ cells without any treatment are defined as Group 0 cells, and CD34+ cells which were cultured with 100ng/mL SCF, TPO and Flt3L in Stemline II medium are defined as Group 4 cells.

value: CD34+ cell

value: no treatment


title: S1630_00014_S23_R

description: Breast cancer baseline sample


title: cord blood CD34+ cell Group4-1

description: Sample 41

value: Stemline II medium with SCF/TPO/Flt3L


title: cord blood CD34+ cell Group0-2

description: Sample 2


title: cord blood CD34+ cell Group4-3

description: Sample 43


title: S1630_00023_S1_R

description: Breast cancer baseline sample


title: cord blood CD34+ cell Group4-4

description: Sample 44


title: S1630_00022_S6_R

description: Breast cancer baseline sample


title: cord blood CD34+ cell Group0-3

description: Sample 3


title: S1785_00038_S7_R

description: Breast cancer baseline sample


title: S1630_00019_S24_R

description: Breast cancer baseline sample


title: siEA2_pH_rep2

city: Glasgow

first: Holly

last: Hall

address: Garscube Estate, Switchback Road, Bearsden

institute: Cancer Research UK Scotland Institute

data_processing:
quality checks on the raw RNASeq data files were performed using fastqc version 0.11.7 and fastq screen version 0.12.0
RNAseq paired-end reads were aligned to the GRCm38 version of the human genome and annotation using HiSat2 version 2.1.0
Expression levels were determined and statistically analysed using a combination of HTSeq version 0.9.1, the R environment version 3.4.4, utilizing packages from the Bioconductor data analysis suite
differential gene expression analysis was performed using voom pipeline from the limma package in R
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalised counts

source_name: H1299 cells

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 1% pen/step and 2 mM L-glutamine (hereafter called complete medium). All cell lines were incubated at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Cells were lysed directly in Trizol followed by chloroform extraction
Quality of the purified RNA was tested on a 2200 Tapestation using RNA screentape (Agilent). Libraries for cluster generation and DNA sequencing were prepared using the TruSeq Stranded mRNA LT Kit (Illuma). Quality and quantity of the DNA libraries was assessed on the 2200 Tapestation (D1000 screentape) and Qubit (Thermo Fisher Scientific) respectively. The libraries were run on the Next Seq 500 (Illumina) using the High Output 75 cycles kit (2x36cycles, paired end reads, single index).

treatment_protocol:
For siRNA treatment cells were nucleoporated either by using a non-targeting siRNA or a siRNA targeting human EphA2. Cells were cultured for further 48h after transfection.
For the HGF treatment, 48h after siRNA transfection cells were treated with 10ng/ml human HGF for 20min and then lysed.

tag: cell line

value: EphA2 siRNA

value: 20 minutes HGF


title: siEA2_pH_rep1


title: cord blood CD34+ cell Group0-1

description: Sample 1


title: cord blood CD34+ cell Group4-2

description: Sample 42


title: siEA2_pH_rep3


title: nt_H_rep3

value: non targeting siRNA

value: 20 minutes vehicle


title: nt_H_rep1


title: siEA2_H_rep2


title: nt_pH_rep3


title: nt_pH_rep1


title: PANC-1-SiRNA 1

city: Dublin

first: Bruce

last: Moran

address: Nutley Lane, Dublin 4

department: Dept. of Pathology

country: Ireland

institute: St. Vincent's University Hospital

description:
Pansi1
pancreas/duct; epithelial cell; carcinoma
cytoplasmic RNA

data_processing:
Data were trimmed of sequencing adaptors and low quality base calls using BBDuk tool in the BBMap package. Alignment to the human hg19/GRCh37 genome reference was done using STAR version 2.5.2a23. Duplicate reads were marked using Picard MarkDuplicates. Read counts were produced by the featureCounts tool from the SubRead package24.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: markdup.featco.2.counts.txt: Raw count matrix.

source_name: Pancreas

growth_protocol: Human pancreatic cancer cell lines PANC-1 and MIAPaCa-2 were maintained in RPMI1640 or DMEM medium supplemented with 10% FBS and antibiotics (100 U/ml penicillin and 100 μg/ml streptomycin) in a humified 5% CO2 atmosphere at 37oC.

extract_protocol:
RNA purification was performed using Trizol with phasemaker tubes according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using Illumina TruSeq v2 kits.
Paired-end 75bp

treatment_protocol: For siRNA transfection, pancreatic cancer cells were seeded in T-25 flasks (4-7x10^5 cells) and incubated 72h in 37oC. The cells were then washed twice with phosphate buffered saline (PBS) and received growth medium without FBS, together with lipofectamine 2000 and negative control or anti-RBM3 (s11858+s11860) siRNA in OptiMEM to a final siRNA concentration of 25 nM. The transfection was stopped after 4.5h, medium changed to full growth medium and the cells were left to recover overnight. The following day, cells were harvested and spun down to pellets. The pellets were either fixated, dehydrated and embedded in paraffin for immunohistochemistry or resuspended in Trizol and stored in -20oC for qPCR.

value: pancreatic cancer cell line

tag: sirna


title: siEA2_H_rep3


title: nt_H_rep2


title: PANC-1- control 4

description:
Panctrl4
pancreas/duct; epithelial cell; carcinoma
cytoplasmic RNA

value: control


title: PANC-1-SiRNA 3

description:
Pansi3
pancreas/duct; epithelial cell; carcinoma
cytoplasmic RNA


title: nt_pH_rep2


title: PANC-1- control 2

description:
Panctrl2
pancreas/duct; epithelial cell; carcinoma
cytoplasmic RNA


title: MIAPaCa2- control 1

description:
Micctrl1
pancreas; epithelial cell; carcinoma
cytoplasmic RNA


title: MIAPaCa2- control 4

description:
Micctrl4
pancreas; epithelial cell; carcinoma
cytoplasmic RNA


title: MIAPaCa2- SiRNA 2

description:
Micsi2
pancreas; epithelial cell; carcinoma
cytoplasmic RNA


title: MIAPaCa2- SiRNA 1

description:
MIcsi1
pancreas; epithelial cell; carcinoma
cytoplasmic RNA


title: MIAPaCa2- control 2

description:
Micctrl2
pancreas; epithelial cell; carcinoma
cytoplasmic RNA


title: PANC-1-SiRNA 2

description:
Pansi2
pancreas/duct; epithelial cell; carcinoma
cytoplasmic RNA


title: siEA2_H_rep1


title: kidney, sample 1, scATAC-seq

city: Nanjing

first: Jingping

last: Yang

state: Jiangsu

address: 22 Hankou Road

department: Medical School

institute: Nanjing University

description:
peaks_and_bigwigs.tar
master_peak.bed
scATAC_SparseMatrix.rds
scATAC_barcodes.csv

data_processing:
For each read, we first appended the barcode which was in the whitelist to the read name. Then adapter sequences were trimmed  using trimmomatic (0.32). Bowtie2 (2.3.0) was used to align reads to the hg38 reference genome with ‘-X 2000 -3 1’ as options. Read pairs that did not map uniquely to autosomes or sex chromosomes with a mapping quality of at least 30 were filtered out using samtools (1.3.1).
High quality cells were identified as log10(unique fragments) > 3.4, ratio of fragments in TSS region > 0.15 and a log-transformed nucleosomal periodicity score > -1.75.
Harmony was used for batch correction and Louvain was used for clustering by SnapATAC package.
MACS2 was used for peak calling for each cluster with the following parameters:’ --nomodel --keep-dup all --extsize 200 --shift 100 –nolambda -q 0.001’.  Peaks overlapping ENCODE blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists) were removed for each cluster to generate clean peaks and  a master peak list  was generated by taking clean peaks identified in any cluster and merged them with the bedtools.
Genome_build: hg38
Supplementary_files_format_and_content: bed file represents master peak list
Supplementary_files_format_and_content: csv file represents information of barcodes
Supplementary_files_format_and_content: tar file includes narrowpeaks and bigwig files for each cluster
Supplementary_files_format_and_content: rds Matrix table with raw counts for each peak in each cell

source_name: kidney paracancerous tissue

extract_protocol:
Kidney paracancerous tissues was stored in PBS on ice and then cut into 1mm3 segments for nuclei isolation. Samples were homogenized using a Dounce homogenizer  in 1ml chilled Lysis Buffer on ice. Following lysis, 9 ml chilled Wash Buffer was added and the resulting solution was filtered through a 30-µm cell strainer. Nuclei were centrifuged (500g for 5 min at 4 °C) and the supernatant removed without disrupting the nuclei pellet. Nuclei were resuspended in chilled Diluted Nuclei Buffer at approximately 3,000–4,000 nuclei per µl.
10X Chromium libraries were prepared according to manufacturer protocol.

value: kidney

value: male


title: MIAPaCa2- SiRNA 5

description:
Micsi5
pancreas; epithelial cell; carcinoma
cytoplasmic RNA


title: K108003 MeCap

first: Natascia

last: Marino

state: IN

address: 980 W. Walnut St, R3-C238

department: Hematology/Oncology Division

institute: Indiana University School of Medicine

description: whole methylome (Methyl Capture)

data_processing:
The raw methyl-capture reads were cleaned using Trimmomatic version 0.36 (Bolger et al. 2014) setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded. (parameters: LEADING:20 TRAILING:20 SLIDINGWINDOW:3:20 MINLEN:20)
The cleaned reads were aligned to the human genome reference, GRCh38.p12 using bwa (version 0.7.17-r1188) (Li and Durbin, 2010).
Potential PCR duplicates were marked using Picard tools version 2.20.3 (http://broadinstitute.github.io/picard/).
Deduplicated insert alignments were inferred from the deduplicated, concordantly mapped read pair alignments using Samtools version 1.9 (Li et al. 2009).
The deduplicated insert coverage was estimated by counting the number of deduplicated inserts spanning over each base position on the reference genome and saved to the wiggle files.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Wiggle files containing deduplicated insert coverage

source_name: breast

growth_protocol: The breast tissue cores are collected by using a needle biopsy needle (Hologic, Marlborough, MA). The skin is cleaned, then numbed with lidocaine. The physician nicks the skin with a scalpel, usually in the upper-outer quadrant of the breast, and the needle is inserted into this incision. From this single incision, five sample cores are removed from the breast (approximately 200mg). A nurse/surgeon’s assistant holds pressure on the incision for 10 full minutes, then applies a pressure bandage. An ice pack is immediately placed on the breast. Within 10 min from collection the tissue cores are fresh frozen in liquid nitrogen

extract_protocol:
Total DNA was extracted using the Allprep DNA/RNA/miRNA Universal Kit (QIAGEN, Germantown, MD).
The concentration and quality of total DNA samples was first assessed using Agilent 2100 Bioanalyzer. For the DNA methylation analysis: Library was generated using MethylCap Library Kit (Diagenode, Denville NJ, US) according to the manufacturer′s protocols followed by single-end 75-bp sequencing on Illumina Nextseq 500.

tag: study cohort

value: Healthy Control

tag: racial background

value: Caucasian

tag: body mass index


title: K108052 MeCap

description: whole methylome (Methyl Capture)


title: K108157 MeCap

description: whole methylome (Methyl Capture)


title: K107548 MeCap

description: whole methylome (Methyl Capture)


title: K107235 MeCap

description: whole methylome (Methyl Capture)

value: Caucasian/Hispanic


title: K107598 MeCap

description: whole methylome (Methyl Capture)


title: K107013 MeCap

description: whole methylome (Methyl Capture)


title: K107069 MeCap

description: whole methylome (Methyl Capture)


title: K106939 MeCap

description: whole methylome (Methyl Capture)

value: Caucasian/ Pacific Islander


title: K107296 MeCap

description: whole methylome (Methyl Capture)


title: K107036 MeCap

description: whole methylome (Methyl Capture)

value: African American


title: PANC-1- control 1

description:
Panctrl1
pancreas/duct; epithelial cell; carcinoma
cytoplasmic RNA


title: K107977 MeCap

description: whole methylome (Methyl Capture)

value: Susceptible


title: K107913 MeCap

description: whole methylome (Methyl Capture)


title: K108429 MeCap

description: whole methylome (Methyl Capture)


title: K108358 MeCap

description: whole methylome (Methyl Capture)


title: K107912 MeCap

description: whole methylome (Methyl Capture)


title: K106839 MeCap

description: whole methylome (Methyl Capture)


title: K107273 MeCap

description: whole methylome (Methyl Capture)


title: K107280 MeCap

description: whole methylome (Methyl Capture)


title: K107616 MeCap

description: whole methylome (Methyl Capture)


title: K107138 MeCap

description: whole methylome (Methyl Capture)


title: K107237 MeCap

description: whole methylome (Methyl Capture)


title: K106859 MeCap

description: whole methylome (Methyl Capture)


title: K105316 MeCap

description: whole methylome (Methyl Capture)


title: K104653 MeCap

description: whole methylome (Methyl Capture)


title: K105140 MeCap

description: whole methylome (Methyl Capture)


title: K104589 MeCap

description: whole methylome (Methyl Capture)


title: K106357 MeCap

description: whole methylome (Methyl Capture)


title: K104728 MeCap

description: whole methylome (Methyl Capture)


title: K104430 MeCap

description: whole methylome (Methyl Capture)


title: K108429 RNASeq

description: transcriptome profile

data_processing:
The raw RNA-seq reads were cleaned using Trimmomatic version 0.36 (Bolger et al. 2014) setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded. (parameters: LEADING:20 TRAILING:20 SLIDINGWINDOW:3:20 MINLEN:20)
The cleaned reads were aligned to the human genome reference, GRCh38.p12 using STAR (version STAR_2.5.2b) (Dobin et al. 2013).
Individual gene expression was quantified by counting the number reads mapping to the exon regions of each of the annotated genes from gencode v.28 using featureCounts tool of subread package (version 2.0.0) (Liao et al. 2014). Those reads that mapped to antisense strand, or mapped to multiple regions on the genome or those reads that overlapped with multiple genes were excluded. (parameters: -s 2 -p -B -C)
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tab deliminted text files containing counts of reads overlapping with exon regions of the genes.

source_name: Breast

extract_protocol:
Total RNA was extracted using the Allprep DNA/RNA/miRNA Universal Kit (QIAGEN, Germantown, MD).
The concentration and quality of total RNA samples was first assessed using Agilent 2100 Bioanalyzer. For the RNAsequencing: cDNA library was prepared using the TruSeq Stranded Total RNA Kit (Illumina) and sequenced.


title: K108157 RNASeq

description: transcriptome profile


title: K108052 RNASeq

description: transcriptome profile


title: K107598 RNASeq

description: transcriptome profile


title: K107913 RNASeq

description: transcriptome profile


title: K107069 RNASeq

description: transcriptome profile


title: K107013 RNASeq

description: transcriptome profile


title: K107036 RNASeq

description: transcriptome profile


title: K108003 RNASeq

description: transcriptome profile


title: K107235 RNASeq

description: transcriptome profile


title: K107296 RNASeq

description: transcriptome profile


title: K107280 RNASeq

description: transcriptome profile


title: K107548 RNASeq

description: transcriptome profile


title: K106939 RNASeq

description: transcriptome profile


title: K107273 RNASeq

description: transcriptome profile


title: K107616 RNASeq

description: transcriptome profile


title: K107237 RNASeq

description: transcriptome profile


title: K107977 RNASeq

description: transcriptome profile


title: K107912 RNASeq

description: transcriptome profile


title: K106859 RNASeq

description: transcriptome profile


title: K107138 RNASeq

description: transcriptome profile


title: K106357 RNASeq

description: transcriptome profile


title: K104589 RNASeq

description: transcriptome profile


title: K104728 RNASeq

description: transcriptome profile


title: K105140 RNASeq

description: transcriptome profile


title: K104653 RNASeq

description: transcriptome profile


title: K104430 RNASeq

description: transcriptome profile


title: K105316 RNASeq

description: transcriptome profile


title: K108358 RNASeq

description: transcriptome profile


title: K106839 RNASeq

description: transcriptome profile


title: input - replicate 1

city: Parkville

first: Waruni

last: Abeysekera

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the human genome by Rsubread version 2.0.1
Read counts were summarized by genomic regions - Gene bodies, TSS - 2 kb to TSS + 2 kb regions, TES - 2 kb to TES + 2 kb regions, TSS - 2 kb to TSS regions, TES to TES + 2 kb regions, TSS to TSS + 1 kb regions, and Intergenic regions defined as ≥10 kb away from any gene excluding blacklisted regions - using the Rsubread's featureCounts function and hg38 NCBI annotation.
Genome_build: hg38 (NCBI build 38.1)
Supplementary_files_format_and_content: Tab-delimited text files for gene body counts; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene. Tab-delimited text files for other region counts around TSS and TES of genes; columns represent Entrez Gene ID, and the number of reads mapping to that region. Tab-delimited text files for intergenic region counts; columns represent region ID, and the number of reads mapping to that region.

growth_protocol: HUVEC were grown in EGM-2 media (Lonza, #CC-3162) under hypoxic (3%) conditions.

extract_protocol:
Lysates were isolated from formaldehyde cross-linked HUVECs and chromatin was fragmented with micrococcal nuclease, then immunoprecipitated with antibody.
Sequencing libraries were generated using an Illumina TruSeq DNA library prep kit

treatment_protocol: 90-100% confluent HUVEC were stimulated with 25 ng/ml VEGF165 (Peprotech, #100-20) for 2 hours prior to harvesting.

value: HUVECs

value: Endothelial cells

value: Human umbelical vein endothelial cells

tag: experiment

value: B

tag: treatment

value: VEGFA

tag: chip antibody

value: input (none)


title: DOPPA-2 (Drug182-2)

description: Sample 5

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NextSeq500
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to hg38 genes using featureCounts (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 4 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.20.8).
Genome_build: hg38
Supplementary_files_format_and_content: analysis with raw count (excel) from edgeR

source_name: human cord blood

growth_protocol: DMSO or DOPPA-treated CD34+ cells were cultured in Stemline® II Hematopoietic Stem Cell Expansion Medium (S0192) in 6-well cell culture plate for 4 days. The following cytokines were added into the expansion medium: 100 ng/mL stem cell factor (SCF) (R&D Systems, #7466-SC-010/CF), thrombopoietin (TPO) (R&D Systems, #288-TP-200/CF), Fms-like tyrosine kinase 3 ligand (FL) (BioLegend, # 710802).

extract_protocol: CB CD34+ cells were expanded by vehicle control or DOPPA for 4 days. RNA was extracted using the RNeasy Mini Kit following manufacturer’s protocol (QIAGEN, #74106).

treatment_protocol: 100 nM DOPPA was used to treat cord blood CD34+ cells for 4 days. 0.1% DMSO was used as the vehicle control.

tag: tissue

value: cord blood

value: CD34+ cell

value: 100 nM DOPPA Stemline HSC expansion medium, ex vivo culture for 4-day


title: panH3 - replicate 2

value: C

value: pan H3 (abcam, ab10799)


title: H3K14ac - replicate 3

value: H3K14ac (abcam, ab52946)


title: panH3 - replicate 1


title: H3K14ac - replicate 1

value: A


title: DOPPA-3 (Drug182-3)

description: Sample 6


title: H3K14ac - replicate 2


title: Vehicle-1 (DMSO-1)

description: Sample 1

value: DMSO Stemline HSC expansion medium, ex vivo culture for 4-day


title: Vehicle-2 (DMSO-2)

description: Sample 2


title: input - replicate 2


title: DOPPA-1 (Drug182-1)

description: Sample 4


title: RNA-seq_HID-3

city: Hangzhou

first: Li

last: Jiang

state: Zhejiang porvince

address: Number 866, Yuhangtang Road

institute: Zhejiang University School of Medicine

data_processing:
Both enzymes target the same CCGG sequence, and sequencing read counts mapped to HpaII and MspI cutting sites provide a quantitative digital measure of CpG methylation within genomic CCGG sites.RNA-seq reads were mapped to the mouse reference genome using TopHat.
For sequencing read alignment, a set of possible 17- and 18-bp tags was created from all CCGG sites in the Mus musculus genome assembly; Only uniquely aligned reads were used for gene and exon quantification.
methylation percentage=100%*count inverse library/(ratio*count HpaII library+ count inverse library)
ratio=count inverse standard/count HpaII standard where HpaII-library: HpaII digested, inverse-library: Mspl digested (Guo et al., 2011).
If the read count of a particular CCGG site less than 30, this site will not be used in further analysis. Also, if a site has zero reads in the HpaII library, it will not be used in further analysis.
The locations of the CCGG sites were annotated as the gene promoter (-2000 to -1 bp), coding sequence (CDS), exon, intron, 5'UTR, 3'UTR, or intergenic region.
The Cufflinks (v2.2.1) tool was used to quantify isoform expression. Differentially methylated sites were analyzed using a one-way ANOVA (R package) and mapped to signaling pathways using the KEGG pathway mapping tool.
Genome_build: mm9

source_name: mice tissue

extract_protocol:
For DNA methylation sequencing, genomic DNA from the livers of C57B/6J mice was extracted and purified using the Qiagen DNeasy Kit; For RNA sequencing, mice livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
CpG methylation status across the genome was characterized using methylation-sensitive HpaII and the methylation-insensitive isoschizomer MspI; RNA-seq libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina).

treatment_protocol: Where indicated, 6-weeks-old male mice were fed a high-iron diet (HID) or standard-iron diet (SID) containing 8.3 g or 50 mg carbonyl iron/kg, or 3-weeks-old male mice were fed a low-iron diet (LID) containing 0.9 mg carbonyl iron/kg, respectively (Research Diets, Inc.).

value: liver

value: High Iron Diet

tag: strain

tag: Sex

value: male

tag: restriction enzyme


title: RNA-seq_LID-2

value: Low Iron Diet


title: RNA-seq_LID-3


title: Bisulfite-seq_LID-2M

value: Mspl digested inverse library


title: Bisulfite-seq_HID-3H

value: HpaII digested library


title: Bisulfite-seq_LID-1H


title: RNA-seq_HID-2


title: Bisulfite-seq_LID-1M


title: Bisulfite-seq_LID-3M


title: Bisulfite-seq_HID-2M


title: Bisulfite-seq_HID-1H


title: Bisulfite-seq_LID-2H


title: RNA-seq_SID-3

value: Normal Diet


title: RNA-seq_SID-2


title: RNA-seq_SID-1


title: RNA-seq_HID-1


title: RNA-seq_LID-1


title: Vehicle-3 (DMSO-3)

description: Sample 3

tag: cell type


title: Bisulfite-seq_SID-3M


title: Bisulfite-seq_HID-3M


title: Bisulfite-seq_SID-3H


title: Bisulfite-seq_HID-2H


title: Bisulfite-seq_SID-1H


title: Bisulfite-seq_SID-2H


title: Bisulfite-seq_SID-1M


title: Bisulfite-seq_SID-2M


title: Bisulfite-seq_LID-3H


title: 2015_S18

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

data_processing:
Data processing was performed using partek Flow build version 9.0.20.0804
Bases were trimmied on quality score=20. Adaptors were also trimmed.
Filter BAM files with minimal mapping quality=20.
Alignment usign STAR - 2.6.1d.
Quantification to transcriptome performed using Partek E/M algorithm.
Genome_build: mm10

source_name: spleen

growth_protocol: Mice were housed in a 12-h light/12-h dark cycle facility, and free access to rodent chow and water was available.

extract_protocol:
Total RNA was extracted from 14-week-old mouse spleens and sequenced using standard methods on NextSeq500 system (Illumina)(RNA was extracted using TRI Reagent (T9242, Sigma-Aldrich, MO,USA) kit followed by mRNA libraries construction)
Customary Illumina TruSeq™ RNA Sample Prep Kit v2 protocol (catalog No. RS-122-2001)

treatment_protocol: Mouse pups were subcutaneously administrated with NAP (25 μg NAP/1 ml saline). At 21 days of age mice were administered daily intranasal NAP in vehicle solution.

tag: gender

value: NAP

tag: genotype

value: WT

value: spleen


title: 6992-2nd_S11

value: saline


title: 6724-2nd_S6

value: female

value: HTR


title: 6967-2nd_S24


title: 6725_S5


title: 6734_S15


title: 6982_S23


title: 6743_S13


title: 6729_S17


title: 6985_S8


title: 6970_S12


title: 2008-2nd_S20


title: 2007-2nd_S19


title: 2012_S9


title: Bisulfite-seq_HID-1M


title: 6801-6757_S4


title: 6728_S2


title: 6957_S3


title: SpenKO_Day7_Dox_Rep2

city: Rotterdam

first: Beatrice

last: Tan

address: Dr. Molewaterplein 40

department: Developmental Biology

country: Netherlands

institute: Erasmus MC

data_processing:
The SNPs in the 129/Sv and Cast/Ei lines were downloaded from the Sanger institute (v.5 SNP142). These were used as input for SNPsplit v0.3.4, to construct an N-masked reference genome based on mm10 in which all SNPs between 129/Sv and Cast/Ei were masked. The 50 bp single-end RNA-seq reads were mapped to this N-masked reference genome using the default settings of hisat2 v2.2.1. SNPsplit was then used to assign the reads to either the 129/Sv or Cast/Ei bam file based on the best alignment or to a common bam file if mapping to a region without allele-specific SNPs. The allele-specific and unassigned bam files were sorted using samtools v1.10.
The number of mapped reads per gene were counted for both alleles separately and for the unassigned reads using HTSeq v0.12.4 (--nonunique=none -m intersection-nonempty) based on the gene annotation from ensembl v98. For each sample, the gene counts for 129/Sv, Cast/Ei and unassigned reads were merged into a tab-delimited text file.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each gene based on the 129/Sv, Cast/Ei and unassigned reads

source_name: mESC

growth_protocol: Mouse ESCs were grown on male feeder cells and medium containing DMEM (Gibco), 15% Foetal Calf Serum (FCS), 0.1 mM non-essential amino acids (NEAA), 100 U mL-1 penicillin, 100 ug mL-1 streptomycin, 0.1 mM 2-mercaptoethanol (Gibco) and 1000 U mL-1 LIF. Previous to monolayer differentiation, cells were plated in non-gelatinized plates to eliminate feeder cells. Then, plated at specific densities per time point in differentiation medium composed of IMDM-glutamax (Gibco), 15% FCS, 0.1 mM NEAA, 100 U mL-1 penicillin, 100 ug mL-1 streptomycin, 37.8 uL L-1 monothioglicerol and 50 mg mL-1 ascorbic acid.

extract_protocol:
RNA was isolated using the ReliaPrep RNA Cell Miniprep System.
Libraries were created according to the Smart-seq2 protocol, using the Nextera DNA Flex library prep kit (Illumina) to create a library from full-length cDNA. Samples were sequenced on a HiSeq2500 sequencer (50 bp single-end reads).

treatment_protocol: When appropriate, medium was supplemented with 2 μg mL-1 doxycycline for 4 days previous to differentiation and during differentiaton. Doxycycline treated cells were sorted to isolate dsRed positive cells upregulating Xist from the desired allele.

value: 129/Sv x Cast/Ei

value: mESC

value: Spen KO

tag: time

value: Day 7

value: Doxycycline


title: WT_Day7_Dox_Rep1

value: Wild type


title: 6963-2nd_S10


title: 6742_S7

value: male


title: WT_Day7_Dox_Rep2


title: 6756_S1


title: SpenKO_Day7_Dox_Rep1


title: SpenKO_Day3_NoDox_Rep2

value: Day 3

value: Untreated


title: 6959-2nd_S16


title: 6723_S14


title: 2011_S21


title: 6727_S22


title: SpenKO_Day3_NoDox_Rep1


title: SpenKO_Day0_NoDox_Rep2

value: Day 0


title: WT_Day0_Dox_Rep1


title: WT_Day0_NoDox_Rep1


title: SpenKO_Day0_Dox_Rep1


title: WT_Day0_Dox_Rep2


title: WT_Day3_H3K27me3_Rep2

data_processing:
The SNPs in the 129/Sv and Cast/Ei lines were downloaded from the Sanger institute (v.5 SNP142). These were used as input for SNPsplit v0.3.4, to construct an N-masked reference genome based on mm10 in which all SNPs between 129/Sv and Cast/Ei were masked. The 50 bp paired-end ChIP-seq reads reads were mapped to this N-masked reference genome using the default settings of bowtie2 v2.4.1. SNPsplit (with --paired) was then used to assign the reads to either the 129/Sv or Cast/Ei bam file based on the best alignment or to a common bam file if mapping to a region without allele-specific SNPs. The allele-specific and unassigned bam files were sorted using samtools v1.10.
The allele-specific ChIP-seq bam files were normalized using the ‘callpeak’ and ‘bdgcmp’ functions of MACS2 v2.2.7.1. We called broad peaks (-f BAMPE --broad --bdg) and used the Poisson P-value as method for normalizing the tracks.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files with normalized ChIP-seq tracks for both alleles seperately

extract_protocol:
50.10^6 cells were trypsinised, resuspended and fixed in 50 mL warm medium and 1% PFA for 10 min at 37oC. 2.5 mL Glycine 2.5 M were added to the cells (final concentration 0.125 M) to quench the PFA, 5 min RT on rotator. All buffers from now on contain protease inhibitors (Roche, 4693132001). Cells were washed twice with cold PBS. Then 1x in 10 mL Buffer 1 (10 mM Hepes pH 7.5, 10 mM EDTA, 0.5 mM EGTA, 0.75% Triton X-100) and 1x in Buffer 2 (10 mM Hepes pH 7.5, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), 10 min rotating in at 4oC. Nuclei were then resuspended in Lysis/Sonication Buffer (150 mM NaCl, 25 mM Tris pH 7.5, 5 mM EDTA, 1% Triton, 0.1% SDS, 0.5% Deoxycholate) and left 30 min on ice. Nuclei were then sonicated 2x 15 min (30’’ ON/OFF, max input, ice cold water) in a Bioruptor. A small fraction of the lysate was run on a gel to confirm size population of 100-500 bp. 1 µg of antibody (Cell Signaling, 9733S) was conjugated with 25 µL magnetic beads (Life Technologies, 10004D) for 3h rotating at 4oC. 25 ug of chromatin was IP’d with the Ab-beads overnight rotating at 4oC. Beads were washed 2x in standard RIPA buffer (140 mM NaCl, 10 mM Tris-HCl pH 7.5150 mM NaCl, 1 mM EDTA pH8.0, 0.5 mM EGTA pH 8.0, 1% Triton, 0.1% SDS, 0.5% Deoxycholate), 1x in High Salt RIPA (same as standard RIPA but with 500 mM NaCl), 1x LiCl RIPA (same as standard RIPA but with 250 mM LiCl instead of NaCl) and rinsed once with TE, 10 min 4oC each wash. Chromatin was eluted with 450 µL of Elution Buffer (1% SDS; 0.1M NaHCO3 in Water) with 22 ul protease K (10 mg mL-1) and 5 ul RNAse A (10 mg mL-1) and shaken at 1000 rpm for 2hrs at 37oC first and then 65oC overnight. DNA was then Phenol-Chloroform extracted and resuspended in 20 µL H20. 0.25 µL was used per PCR to confirm the ChIP’s success. The concentration was then measured.
The ChIP-seq library was prepared following the manufacturer’s instructions (ThruPLEX DNA, Takara Bio) and sequenced on an Illumina HiSeq 2500 sequencer (50 bp paired-end reads).

value: H3K27me3 antibody (Cell Signaling, 9733S)


title: WT_Day3_input


title: SpenKO_Day0_H3K27me3_Rep2


title: WT_Day0_H3K27me3_Rep1


title: SpenKO_Day0_Dox_Rep2


title: WT_Day3_H3K27me3_Rep1


title: SpenKO_Day0_H3K27me3_Rep1


title: SpenKO_Day0_NoDox_Rep1


title: WT_Day0_input


title: H2A.Z_ChIPSeq rep 3

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

description:
H2AZ PS5
Three biological replicates H2AZ PS2, H2AZ PS3 and H2AZ PS5 were merged for downstream analysis. More details please see the Data processing section.
H2AZ_CPM.bw

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Raw reads were aligned to UCSC mm9 mouse genome obtained from iGenome with BWA (0.7.5a) for single-end reads and bowtie2 (2.3.4) with arguments -p 8 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 for paired-end reads.
Aligned reads were sorted and converted to bam by samtools (1.6).
Duplicated reads were removed by Picard MarkDuplicates tool (1.9).
Merged bam files from biological replicates were produced by samtools.
Duplicated reads were removed from merged bam files by Picard MarkDuplicates tool (1.9).
bigWig files were generated from merged duplicated reads removed bam files by bedtools genomeCoverageBed (normalized to Reads Per Million; RPM) and bedGraphToBigWig obtained from UCSC.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigWig files

source_name: resting B cells isolated from spleen

extract_protocol:
Spleens were isolated from 6- to 10-week-old C57B6 mice and homogenized through a sieve in B cell culture medium (RPMI-1640 (Lonza), 10% fetal calf serum (FCS) (Sigma), 0.1 U/ml penicillin (Lonza), 0.1 μg/ml streptomycin (Lonza), 2mM L-Glutamine (Lonza), 50μM beta-mercaptoethanol (Gibco)). The cell suspension was centrifuged on a Ficoll-Paque (GE Healthcare) cushion and the buffy coat layer was resuspended at a concentration of 1x 10e8 cells/ml in PBS + 2% FCS/ 1mM EDTA. Resting B cells were isolated using an EasySep Negative Selection- Mouse B Cell Isolation Kit (STEMCELL Technologies), which depletes for non-B cell markers and activated CD43+ B cells.
5ng of ChIP/Input DNA was used to prepare libraries using the NEBNext® Ultra™ II DNA LibraryPrep Kit for Illumina following the manufacturer recommendations. Library quality and quantity were assessed on a Bioanalyser and Qubit, respectively. Libraries were sequenced on an Illumina Hiseq 2500 (v4 chemistry), and single-end 50bp reads or paired-end 100bp reads per sample were generated.

value: Resting B cells


title: SpenKO_Day0_input


title: SpenKO_Day3_H3K27me3_Rep2


title: WT_Day3_NoDox_Rep2


title: input DNA for PS5

description:
INPUT PS5
Three biological replicates INPUT PS2, INPUT PS3 and INPUT PS5 were merged for downstream analysis as INPUT_2. More details please see the Data processing section.
INPUT_2_CPM.bw

value: WT


title: SpenKO_Day3_H3K27me3_Rep1


title: WT_Day0_NoDox_Rep2


title: WT_Day0_H3K27me3_Rep2


title: H3K4me3_ChIPSeq rep 3

description:
H3K4me3 PS12
Three biological replicates H3K4me3 PS10, H3K4me3 PS11 and H3K4me3 PS12 were merged for downstream analysis. More details please see the Data processing section.
H3K4me3_CPM.bw

value: H3K4me3 (Merck Millipore- 07-473)


title: SpenKO_Day3_input


title: H3K4me3_ChIPSeq rep 2

description:
H3K4me3 PS11
Three biological replicates H3K4me3 PS10, H3K4me3 PS11 and H3K4me3 PS12 were merged for downstream analysis. More details please see the Data processing section.
H3K4me3_CPM.bw


title: WT_Day3_NoDox_Rep1


title: H3K4me3_ChIPSeq rep 1

description:
H3K4me3 PS10
Three biological replicates H3K4me3 PS10, H3K4me3 PS11 and H3K4me3 PS12 were merged for downstream analysis. More details please see the Data processing section.
H3K4me3_CPM.bw


title: input DNA for PS11

description:
INPUT PS11
Three biological replicates INPUT PS10, INPUT PS11 and INPUT PS12 were merged for downstream analysis as INPUT_3. More details please see the Data processing section.
INPUT_3_CPM.bw


title: input DNA for PS12

description:
INPUT PS12
Three biological replicates INPUT PS10, INPUT PS11 and INPUT PS12 were merged for downstream analysis as INPUT_3. More details please see the Data processing section.
INPUT_3_CPM.bw


title: input DNA for PS10

description:
INPUT PS10
Three biological replicates INPUT PS10, INPUT PS11 and INPUT PS12 were merged for downstream analysis as INPUT_3. More details please see the Data processing section.
INPUT_3_CPM.bw


title: H2A.Z_ChIPSeq rep 1

description:
H2AZ PS2
Three biological replicates H2AZ PS2, H2AZ PS3 and H2AZ PS5 were merged for downstream analysis. More details please see the Data processing section.
H2AZ_CPM.bw


title: RUNX1_ChIPSeq rep 2

description:
Runx1 PS2
Three biological replicates Runx1 PS1, Runx1 PS2 and Runx1 PS3 were merged for downstream analysis. More details please see the Data processing section.
RUNX1_CPM.bw

value: RUNX1 (Abcam- ab23980)


title: RING1B_ChIPSeq rep 3

description:
Ring1B PS3
Three biological replicates Ring1B PS1, Ring1B PS2 and Ring1B PS3 were merged for downstream analysis. More details please see the Data processing section.
RING1B_CPM.bw

value: RING1B (MBL - D139-3)


title: RING1B_ChIPSeq rep 1

description:
Ring1B PS1
Three biological replicates Ring1B PS1, Ring1B PS2 and Ring1B PS3 were merged for downstream analysis. More details please see the Data processing section.
RING1B_CPM.bw


title: RUNX1_ChIPSeq rep 3

description:
Runx1 PS3
Three biological replicates Runx1 PS1, Runx1 PS2 and Runx1 PS3 were merged for downstream analysis. More details please see the Data processing section.
RUNX1_CPM.bw


title: H2A.Z_ChIPSeq rep 2

description:
H2AZ PS3
Three biological replicates H2AZ PS2, H2AZ PS3 and H2AZ PS5 were merged for downstream analysis. More details please see the Data processing section.
H2AZ_CPM.bw


title: Runx1-KO rep2 - 3hrs activated B cells

description:
Runx1-KO_3hrs_2
Genecounts.csv

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using tophat2 (2.0.11) with default settings.
Gene annotations were obtained from Ensembl Mouse genome (NCBIM37). Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Genecounts.csv: Comma-separated text file includes gene counts for each Sample; raw counts of sequencing reads for genes.

extract_protocol:
B cells (30x10e6) were lysed in 1ml of Trizol and 30μl of 1:100 diluted ERCC RNA Spike-In Mix (Ambion) was added to each lysate. RNA was isolated and eluted in a final volume of 20μl. 1μl of each sample was used for quality and concentration analysis on a 2100 Bioanalyzer using the RNA 6000 Nano kit (Agilent).
500ng of RNA was used to prepare each mRNA library. PolyA+ RNA selected RNA libraries were generated by the LMS Core Genomics Facility using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: CD23iCre/Runx1 ck/o

tag: age

value: 8 weeks

value: B cells

tag: condition

value: Activated with anti-IgM+IL4

tag: timepoint


title: H3K7me3_ChIPSeq rep 2

description:
H3K27me3 PS2
Three biological replicates H3K27me3 PS1, H3K27me3 PS2 and H3K27me3 PS3 were merged for downstream analysis. More details please see the Data processing section.
H3K27me3_CPM.bw


title: SRCAP_ChIPSeq rep 2

description:
SRCAP PS3
Two biological replicates SRCAP PS2 and SRCAP PS3 were merged for downstream analysis. More details please see the Data processing section.
SRCAP_CPM.bw

value: SRCAP (Novus Biologicals- NBP145244)


title: Runx1-KO rep3 - restingB (0hrs)

description:
Runx1-KO_0hrs_3
Genecounts.csv

value: Resting


title: CD23-iCre rep2 - 3hrs activated B cells

description:
CD23-iCre_3hrs_2
Genecounts.csv


title: Runx1-KO rep1 - 3hrs activated B cells

description:
Runx1-KO_3hrs_1
Genecounts.csv


title: Runx1-KO rep3 - 3hrs activated B cells

description:
Runx1-KO_3hrs_3
Genecounts.csv


title: input DNA for PS3

description:
INPUT PS3
Three biological replicates INPUT PS1, INPUT PS2 and INPUT PS3 were merged for downstream analysis as INPUT_1. Three biological replicates INPUT PS2, INPUT PS3 and INPUT PS5 were merged for downstream analysis as INPUT_2. More details please see the Data processing section.
INPUT_1_CPM.bw
INPUT_2_CPM.bw


title: SRCAP_ChIPSeq rep 1

description:
SRCAP PS2
Two biological replicates SRCAP PS2 and SRCAP PS3 were merged for downstream analysis. More details please see the Data processing section.
SRCAP_CPM.bw


title: input DNA for PS1

description:
INPUT PS1
Three biological replicates INPUT PS1, INPUT PS2 and INPUT PS3 were merged for downstream analysis as INPUT_1. More details please see the Data processing section.
INPUT_1_CPM.bw


title: H3K7me3_ChIPSeq rep 1

description:
H3K27me3 PS1
Three biological replicates H3K27me3 PS1, H3K27me3 PS2 and H3K27me3 PS3 were merged for downstream analysis. More details please see the Data processing section.
H3K27me3_CPM.bw


title: Runx1-KO rep2 - restingB (0hrs)

description:
Runx1-KO_0hrs_2
Genecounts.csv


title: RUNX1_ChIPSeq rep 1

description:
Runx1 PS1
Three biological replicates Runx1 PS1, Runx1 PS2 and Runx1 PS3 were merged for downstream analysis. More details please see the Data processing section.
RUNX1_CPM.bw


title: Runx1-KO rep1 - restingB (0hrs)

description:
Runx1-KO_0hrs_1
Genecounts.csv


title: CD23-iCre rep3 - 3hrs activated B cells

description:
CD23-iCre_3hrs_3
Genecounts.csv


title: H3K7me3_ChIPSeq rep 3

description:
H3K27me3 PS3
Three biological replicates H3K27me3 PS1, H3K27me3 PS2 and H3K27me3 PS3 were merged for downstream analysis. More details please see the Data processing section.
H3K27me3_CPM.bw


title: RING1B_ChIPSeq rep 2

description:
Ring1B PS2
Three biological replicates Ring1B PS1, Ring1B PS2 and Ring1B PS3 were merged for downstream analysis. More details please see the Data processing section.
RING1B_CPM.bw


title: CD23-iCre rep1 - 3hrs activated B cells

description:
CD23-iCre_3hrs_1
Genecounts.csv


title: CD23-iCre rep3 - restingB (0hrs)

description:
CD23-iCre_0hrs_3
Genecounts.csv


title: CD23-iCre rep1 - restingB (0hrs)

description:
CD23-iCre_0hrs_1
Genecounts.csv


title: CD23-iCre rep2 - restingB (0hrs)

description:
CD23-iCre_0hrs_2
Genecounts.csv


title: F-H-L rep2

city: Wuhan

first: Yu

last: Sun

address: Luojiashan Street

institute: Wuhan University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.1.0 with default parameters. The number of reads mapped to each gene was calculated by Htseq.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and counts for each Sample

source_name: epididymal WAT

growth_protocol: C57BL/6 breeding pairs were housed at a controlled temperature with a 12 hr/12 hr light/dark cycle, with free access to water and food. Animals were handled according to the Guidelines of the China Animal Welfare Legislation and approved by the Committee on Ethics in the Care and Use of Laboratory Animals of College of Life Sciences, Wuhan University.

extract_protocol:
Total RNA from each sample was extracted using Trizol reagent (Life Technologies), and concentration was measured using an ND-1000 NanoDrop (Thermo Scientific, Wilmington, DE). RNA integrity was evaluated using the Agilent 2200 Tape Station (Agilent Technologies, Santa Cruz Biotechnology), and samples with an RNA integrity value above 7.0 were used. RNA-Seq was performed at RiboBio Co., Ltd. (Guangzhou, China) using the HiSeq 2500 platform (Illumina, San Diego, CA). Prior to sequencing, raw data were filtered to produce high-quality clean data, and all subsequent analyses were performed using clean data.
Briefly, mRNAs were isolated from total RNA, fragmented to approximately 200 bp, and subjected to first strand and second strand cDNA synthesis followed by adaptor ligation and low-cycle enrichment according to the instructions of the TruSeq RNA LT/HT Sample Prep Kit (Illumina, San Diego, CA, USA). Purified library products were evaluated using the Agilent 2200 Tape Station and Qubit 2.0 software (Life Technologies)

treatment_protocol: C57BL/6 mice were fed with high fat diet (HF) (60% kcal fat; Research Diets Inc., New Brunswick, NJ) or low fat diet (LF) (10% kcal fat; Research Diets Inc.) at 6-week-old. Nine weeks after in HF, a part of mice was switched to LF for one week followed by one week HF as one cycle, and the mice under this one week diet switch protocol for 10 cycles were named HF-LF cycled mice, while the left part of mice under continuously HF-feeding were named HF mice. The mice kept in the continuously LF-feeding were named LF mice

value: epididymal WAT

value: wild type


title: input DNA for PS2

description:
INPUT PS2
Three biological replicates INPUT PS1, INPUT PS2 and INPUT PS3 were merged for downstream analysis as INPUT_1. Three biological replicates INPUT PS2, INPUT PS3 and INPUT PS5 were merged for downstream analysis as INPUT_2. More details please see the Data processing section.
INPUT_1_CPM.bw
INPUT_2_CPM.bw


title: F-H rep2


title: F-H rep1


title: F-L rep2


title: F-L rep1


title: E11_E14

city: San Francisco

first: Corey

last: Harwell

address: 35 Medical Center way

department: Neurology

institute: University of California, San Francisco

description: E11 + E14

data_processing:
The raw fastq files uploaded here were prepared from Illumina bcl files in a format compatible with the inDrops.py pipeline. In brief, each NextSeq run results in 16 fastq files (4 lanes x 4 reads per lane). The read files have the following content, also as described in the documentation for inDrops.py (github/indrops):   *_R1_001.fastq.gz   : contains the 3' UTR cDNA read  *_R2_001.fastq.gz   : contains the first half of the cell barcode  *_R3_001.fastq.gz   : contains the library index for demultiplexing libraries  *_R4_001.fastq.gz   : contains the second half of the barcode and the UMI.
All  subsequent processing steps from fastq files to count matrices were performed using a custom pipeline for inDrops data analysis (github.com/indrops).  The following steps are provided as an overview on the internal workings of inDrops.py.
inDrops.py first filters reads based on information present in read files 2, 3 and 4, for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index. inDrops.py demultiplexes by Illumina library index (read 3).  For read 3, the library indices provided to the inDrops.py custom pipeline are given in the yaml files.
inDrops.py then trims Read 1 using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
inDrops.py then matches cell barcodes (revealed by Read 2 and 4) against a list of the pre-determined barcodes. The reads were then split into barcode-specific files for mapping and UMI filtering.
inDrops.py then aligns the reads using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 70 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.88) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes). The reference index is assembled using inDrops.py as described in the manual.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene.
Genome_build: GRCm38.88
Supplementary_files_format_and_content: cd_norm: Gene Expression Matrix of count data normalized by total counts in each cell; matrix.tsv:  Raw cell/counts tables each sample;  seurat_metadata.csv: Metadata for individual cells: cell barcode, assigned cell type and other metadata for establishing clusters.

source_name: septum + medial ganglionic eminence / preoptic area from embryonic brains at E11 and E14

extract_protocol:
RNA was isolated within the droplets according to the inDrops protocol (Klein et al. Cell 2015, Zilionis et al. Nature Protocols 2017).
polyA RNA captured via inDrops platform
2 libraries of approximately 3000 cells were collected from each biological replicate: pools from animals from the same litter for embryonic and early postnatal stages (E11 - 3 litters, 35 embryos total; E14 - 3 litters, 33 embryos total; E17 - 2 litters, 8 embryos total; P3 - 2 litters, 4 pups total), or individual animals for later postnatal stages (P10 - one male and one female pup from the same litter; P30 - two male and two female animals from the same litter). inDrops library preparation was performed as previously described (Klein et al. Cell 2015, Zilionis et al. Nature Protocols 2017) Libraries were sequenced on the Illumina NextSeq system.
custom inDrops single-cell RNA-Seq

value: CD-1 (strain code 022, Charles River)

value: not determined

value: mixed sample representing E11, E14

value: mixed sample representing septum, MGE/PoA


title: E17_P3_P10

description: E17 + P3 + P10

source_name: septum + medial ganglionic eminence / preoptic area from embryonic (E17) and septum from postnatal (P3 and P10) brains

value: mixed sample representing E17, P3, P10

value: mixed sample representing Septum, MGE/PoA (E17) / septum (P3/P10)


title: eCLIP-seq IP, rep 2

first: Gun Woo

last: Byeon

address: 279 Campus Dr., Beckman Center B309

description:
Replicate 2
CGATGT

data_processing:
Read alignment: For removal of adapter sequences, low quality bases, and short reads, we use cutadapt (Martin, 2011) to trim Illumina adapter sequences and <Q20 bases (parameters -m 18 -a CTGTAGGCACCATCAAT --overlap=5 --trimmed-only --quality-cutoff=20). For splice-aware alignment using STAR (Dobin et al., 2013), we used STAR to align the reads to a reference genome/transcriptome. STAR reference is built using a combination of mouse genome (mm10), mouse rDNA sequence (GenBank GU372691), and mouse transcript annotations (GENCODE vM18). Only uniquely mapped reads were retained (Parameters --outFilterMultimapNmax 1 --alignEndsType EndToEnd --alignIntronMax 1000000 --alignIntronMin 20 --outFilterMismatchNmax 999 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8). For deduplication using UMI, we used umi_tools to deduplicate the alignments. Deduplicated alignments are re-aligned using STAR and the same parameters as before. For read quantification, we used bedtools (Quinlan and Hall, 2010) to count alignments over 10nt sliding windows with step size of 5nt across the mouse genome.
Genome_build: STAR reference is built using a combination of mouse genome (mm10), mouse rDNA sequence (GenBank GU372691), and mouse transcript annotations (GENCODE vM18).
Supplementary_files_format_and_content: Text file includes read counts across the genome in 10nt sliding windows

source_name: Mouse

extract_protocol:
For CLIP-Seq, dissected neural tube and somites from 1 litter of E11.5 embryos (20-23 somite number from tail to hind limb) were used for CLIP-seq. The cell pellet was re-suspended in 0.5 ml of cold lysis buffer (50 mM Tris pH 7.4, 100 mM NaCl, 1 % NP-40, 0.5 % SDS, 0.5 % Sodium deoxycholate, 1x cOmplete, EDTA-free Protease Inhibitor Cocktail (Sigma, 11873580001)) and incubated for 30 min at 4 °C with occasional vortexing. The lysate was clarified by sequential centrifugation for 5 min at 1,800 g and 10,000 g at 4 °C to remove nuclei and mitochondria. The lysate was then treated with RNase I (Ambion, AM2294) for 5 min at 37 ºC (1 Unit of RNase1 for 45 µg of RNA in the lysate). The digestion was stopped by adding 16 µl of SUPERaseIn RNase Inhibitor (20 U/µl, Ambion AM2696). 5 % of lysate was taken for input sample. Lysate was then mixed with magnetic beads (Invitrogen, 10002D) 1hr at 4 ºC for pre-clear then mixed with 40 µl of beads conjugated with eIF3c antibody (Novus, NB100-511) and incubated for 2 hr at 4 ºC. Beads were washed three times by High wash buffer (50 mM Tris pH 7.4, 1 M NaCl, 1 mM EDTA, 1 % NP-40, 0.5 % SDS, 0.5 % Sodium deoxycholate) and twice by low wash buffer (20 mM Tris pH 7.4, 10 mM MgCl2, 0.2 % Tween-20). RNA on the beads was treated with Fast AP (LifeTech, EF0652) and T4 PNK (NEB, M0201L) for dephosphorylation, ligated with 3’ adaptor (NEB, S1315S, Sequence: 5’ rAppCTGTAGGCACCATCAAT-NH2 3’) by T4 RNA ligase 2 truncated (NEB, M0242S), and then radiolabeled by gamma 32P-ATP Kination treating with OptiKinase (Affymetrix, 78334X). After radioactive labeling of RNA, CLIP and Input samples were denatured and run on NuPAGE and transferred to nitrocellulose membrane for the size selection. The strong radioactive band at the size of eIF3c (105 kDa) was cut out from membrane as well as from the size matched input lane. RNA on the membrane was recovered by protease K treatment followed by Phenol/chloroform and Zymo column (Zymo, R1015) RNA purification. Input RNA was processed for dephosphorylation and 3’ linker ligation. To take out the remaining free linker, Input RNA was run on the 10 % Urea Gel and recovered ligated input RNA.
The cDNA for eCLIP sample and Input was produced by Super Script III (Invitrogen, 18080093) and RNA was digested by 1 N NaOH. Cleaned cDNAs were circulized by CircLigase (Epicentre, CL4111K) at 60 ºC overnight. Library was produced by 2 times of PCR reactions by Phusion polymerase (NEB, M0530S).

value: FVB

value: neural tube and somites

tag: rip antibody

value: eIF3c antibody


title: neural tube, Mutant RNA-seq (run2_TC6_mut_RNA_S12_L001)

description: Replicate 3

data_processing:
Read alignment: For removal of adapter sequences, low quality bases, and short reads, we use cutadapt (Martin, 2011) to trim Illumina adapter sequences and <Q20 bases (parameters -m 18 -a CTGTAGGCACCATCAAT --quality-cutoff=20). For splice-aware alignment using STAR (Dobin et al., 2013), we used STAR to align the reads to a reference genome/transcriptome. STAR reference is built using a combination of mouse genome (mm10), mouse rDNA sequence (GenBank GU372691), and mouse transcript annotations (GENCODE vM18). Only uniquely mapped reads were retained (Parameters --outFilterMultimapNmax 1 --alignEndsType EndToEnd --alignIntronMax 1000000 --alignIntronMin 20 --outFilterMismatchNmax 999 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8). For read quantification, we used bedtools (Quinlan and Hall, 2010) to count alignments over annotated coding regions excluding the first 45 bases from the start codon and last 15 bases from the stop codon.
Genome_build: STAR reference is built using a combination of mouse genome (mm10), mouse rDNA sequence (GenBank GU372691), and mouse transcript annotations (GENCODE vM18).
Supplementary_files_format_and_content: Text file includes read counts across the different regions of each annotated transcript

source_name: neural tube

extract_protocol:
Ribosome profiling was performed following the procedures described before (Fujii et al., 2017). For Ribo-Seq, neural tubes from 1 litter of E11.5 embryos (20-23 somite number from tail to hind limb) were used. The Papain dissociated cells were split into two tubes. One was dissolved by Trizol (Invitrogen, 15596) for RNA seq. Another cell pellet was re-suspended in 0.5 ml of cold lysis buffer (20 mM Tris pH 7.5, 150 mM NaCl, 15 mM MgCl2, 1 % Triton X-100, 1 mM DTT, 8 % Glycerol, 20 Unit/ml TURBO DNase, 100µg/ml Cycloheximide) and incubated for 30 min at 4 °C with occasional vortexing. The lysate was clarified by sequential centrifugation for 5 min at 1,800 g and 10,000 g at 4 °C to remove nuclei and mitochondria. The lysate was then treated with RNase I (Ambion, AM2294) for 30 min at RT to digest mRNAs not protected by the ribosome. The digestion was stopped by adding 4.5 µl of SUPERaseIn RNase Inhibitor (20 U/µl, Ambion AM2696). Lysate was then loaded onto a 1 M sucrose cushion. Ribosomes and ribosome protected fragments (RPFs) were pelleted by ultracentrifugation at 70,000 rpm for 4 hr at 4 ºC by TLA120.2 rotor. The pellet was re-suspended in Trizol (Invitrogen, 15596) and RNAs were extracted by following manufacturer’s protocol. RNA-seq: RNA was extracted from Trizol (Invitrogen, 15596) following manufactuer’s protocol and polyA mRNA was isolated using Oligotex mRNA Mini Kit (Qiagen, 70022) following manufacturer’s protocol. Purified mRNAs were fragmented in alkaline fragmentation buffer (100 mM NaCO3 pH 9.2, 2 mM EDTA).
Ribo-seq/RNA-seq Library production: RPFs and fragmented RNAs were loaded onto a 15% urea gel. 28–31 nt RPFs and 30–50 nt fragmented RNAs were excised from the gel for Ribo-Seq and RNA-Seq respectively. RNAs were eluted, dephosphorylated by PNK (NEB, M0201S), and ligated to the miRNA Cloning linker (NEB, S1315S) by T4 RNA Ligase2 truncated K227Q (NEB, M0242S). Ligated RNA was gel purified and reverse transcribed by Superscript III (Invitrogen, 18080). Gel purified cDNAs were circularized by Circligase (Epicentra, CL4111K) and rRNA sequence were subtracted using biotinylated oligos. Amplification was done using Phusion High Fidelity DNA Polymerase (NEB, M0530S). PCR amplification was performed for 6–7 cycles and products were loaded onto non-denaturing 8 % PAGE gel. DNA fragment were purified for Illumina sequencing.

value: neural tube


title: neural tube, Wild-type RNA-seq (run1_TC5_WT_RNA_S8_L004)

description: Replicate 2


title: neural tube, Mutant Ribo-seq (run2_TC5_mut_Ribo_S5_L001)

description: Replicate 2

data_processing:
Library strategy: Ribo-seq
Read alignment: For removal of adapter sequences, low quality bases, and short reads, we use cutadapt (Martin, 2011) to trim Illumina adapter sequences and <Q20 bases (parameters -m 18 -a CTGTAGGCACCATCAAT --quality-cutoff=20). For splice-aware alignment using STAR (Dobin et al., 2013), we used STAR to align the reads to a reference genome/transcriptome. STAR reference is built using a combination of mouse genome (mm10), mouse rDNA sequence (GenBank GU372691), and mouse transcript annotations (GENCODE vM18). Only uniquely mapped reads were retained (Parameters --outFilterMultimapNmax 1 --alignEndsType EndToEnd --alignIntronMax 1000000 --alignIntronMin 20 --outFilterMismatchNmax 999 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8). For read quantification, we used bedtools (Quinlan and Hall, 2010) to count alignments over annotated coding regions excluding the first 45 bases from the start codon and last 15 bases from the stop codon.
Genome_build: STAR reference is built using a combination of mouse genome (mm10), mouse rDNA sequence (GenBank GU372691), and mouse transcript annotations (GENCODE vM18).
Supplementary_files_format_and_content: Text file includes read counts across the different regions of each annotated transcript


title: neural tube, Mutant RNA-seq (run1_TC1_mut_RNA_S10_L002)

description: Replicate 1


title: neural tube, Mutant RNA-seq (run2_TC5_mut_RNA_S11_L001)

description: Replicate 2


title: eCLIP-seq input, rep 2

description:
Replicate 2
TCTGAC


title: neural tube, Mutant RNA-seq (run1_TC6_mut_RNA_S12_L002)

description: Replicate 3


title: eCLIP-seq input, rep 1

description:
Replicate 1
GAGCTA


title: neural tube, Mutant RNA-seq (run1_TC5_mut_RNA_S11_L003)

description: Replicate 2


title: neural tube, Wild-type Ribo-seq (run1_TC5_WT_Ribo_S2_L001)

description: Replicate 2


title: neural tube, Wild-type RNA-seq (run2_TC6_WT_RNA_S9_L003)

description: Replicate 3


title: neural tube, Mutant Ribo-seq (run2_TC6_mut_Ribo_S6_L004)

description: Replicate 3


title: neural tube, Wild-type Ribo-seq (run1_TC6_WT_Ribo_S3_L004)

description: Replicate 3


title: neural tube, Wild-type Ribo-seq (run1_TC1_WT_Ribo_S1_L004)

description: Replicate 1


title: neural tube, Mutant RNA-seq (run1_TC1_mut_RNA_S10_L001)

description: Replicate 1


title: neural tube, Mutant Ribo-seq (run2_TC5_mut_Ribo_S5_L003)

description: Replicate 2


title: neural tube, Wild-type RNA-seq (run1_TC5_WT_RNA_S8_L003)

description: Replicate 2


title: F-H-L rep1


title: neural tube, Wild-type RNA-seq (run1_TC1_WT_RNA_S7_L004)

description: Replicate 1


title: neural tube, Mutant Ribo-seq (run2_TC6_mut_Ribo_S6_L002)

description: Replicate 3


title: neural tube, Wild-type Ribo-seq (run1_TC5_WT_Ribo_S2_L004)

description: Replicate 2


title: eCLIP-seq IP, rep 1

description:
Replicate 1
ATCACG


title: neural tube, Mutant RNA-seq (run1_TC6_mut_RNA_S12_L004)

description: Replicate 3


title: neural tube, Wild-type RNA-seq (run1_TC6_WT_RNA_S9_L004)

description: Replicate 3


title: neural tube, Mutant RNA-seq (run1_TC5_mut_RNA_S11_L001)

description: Replicate 2


title: neural tube, Wild-type Ribo-seq (run1_TC6_WT_Ribo_S3_L002)

description: Replicate 3


title: neural tube, Wild-type Ribo-seq (run1_TC1_WT_Ribo_S1_L002)

description: Replicate 1


title: neural tube, Mutant RNA-seq (run1_TC6_mut_RNA_S12_L001)

description: Replicate 3


title: neural tube, Wild-type RNA-seq (run1_TC6_WT_RNA_S9_L002)

description: Replicate 3


title: neural tube, Wild-type Ribo-seq (run1_TC1_WT_Ribo_S1_L003)

description: Replicate 1


title: neural tube, Wild-type RNA-seq (run2_TC1_WT_RNA_S7_L001)

description: Replicate 1


title: neural tube, Wild-type RNA-seq (run1_TC6_WT_RNA_S9_L001)

description: Replicate 3


title: neural tube, Mutant RNA-seq (run1_TC5_mut_RNA_S11_L002)

description: Replicate 2


title: neural tube, Mutant Ribo-seq (run1_TC1_mut_Ribo_S4_L004)

description: Replicate 1


title: neural tube, Mutant Ribo-seq (run2_TC5_mut_Ribo_S5_L004)

description: Replicate 2


title: neural tube, Mutant Ribo-seq (run1_TC6_mut_Ribo_S6_L002)

description: Replicate 3


title: neural tube, Mutant Ribo-seq (run1_TC5_mut_Ribo_S5_L001)

description: Replicate 2


title: neural tube, Mutant Ribo-seq (run1_TC1_mut_Ribo_S4_L001)

description: Replicate 1


title: neural tube, Mutant RNA-seq (run1_TC1_mut_RNA_S10_L003)

description: Replicate 1


title: neural tube, Mutant Ribo-seq (run1_TC1_mut_Ribo_S4_L003)

description: Replicate 1


title: neural tube, Mutant Ribo-seq (run1_TC1_mut_Ribo_S4_L002)

description: Replicate 1


title: neural tube, Wild-type RNA-seq (run1_TC5_WT_RNA_S8_L002)

description: Replicate 2


title: neural tube, Wild-type Ribo-seq (run1_TC5_WT_Ribo_S2_L003)

description: Replicate 2


title: neural tube, Wild-type RNA-seq (run1_TC1_WT_RNA_S7_L003)

description: Replicate 1


title: neural tube, Wild-type Ribo-seq (run1_TC6_WT_Ribo_S3_L003)

description: Replicate 3


title: neural tube, Wild-type RNA-seq (run1_TC1_WT_RNA_S7_L002)

description: Replicate 1


title: neural tube, Mutant Ribo-seq (run2_TC6_mut_Ribo_S6_L001)

description: Replicate 3


title: neural tube, Mutant RNA-seq (run2_TC1_mut_RNA_S10_L002)

description: Replicate 1


title: neural tube, Wild-type Ribo-seq (run1_TC6_WT_Ribo_S3_L001)

description: Replicate 3


title: neural tube, Wild-type Ribo-seq (run2_TC5_WT_Ribo_S2_L001)

description: Replicate 2


title: neural tube, Wild-type Ribo-seq (run1_TC1_WT_Ribo_S1_L001)

description: Replicate 1


title: neural tube, Mutant RNA-seq (run2_TC5_mut_RNA_S11_L004)

description: Replicate 2


title: neural tube, Mutant RNA-seq (run2_TC6_mut_RNA_S12_L004)

description: Replicate 3


title: neural tube, Wild-type RNA-seq (run1_TC5_WT_RNA_S8_L001)

description: Replicate 2


title: neural tube, Wild-type RNA-seq (run2_TC6_WT_RNA_S9_L004)

description: Replicate 3


title: neural tube, Mutant Ribo-seq (run2_TC6_mut_Ribo_S6_L003)

description: Replicate 3


title: neural tube, Wild-type RNA-seq (run2_TC5_WT_RNA_S8_L004)

description: Replicate 2


title: neural tube, Wild-type RNA-seq (run2_TC1_WT_RNA_S7_L004)

description: Replicate 1


title: neural tube, Wild-type Ribo-seq (run2_TC5_WT_Ribo_S2_L004)

description: Replicate 2


title: neural tube, Mutant Ribo-seq (run2_TC1_mut_Ribo_S4_L004)

description: Replicate 1


title: neural tube, Wild-type Ribo-seq (run2_TC1_WT_Ribo_S1_L003)

description: Replicate 1


title: neural tube, Wild-type Ribo-seq (run2_TC6_WT_Ribo_S3_L004)

description: Replicate 3


title: neural tube, Mutant RNA-seq (run2_TC6_mut_RNA_S12_L003)

description: Replicate 3


title: neural tube, Mutant RNA-seq (run2_TC5_mut_RNA_S11_L003)

description: Replicate 2


title: neural tube, Wild-type RNA-seq (run2_TC1_WT_RNA_S7_L003)

description: Replicate 1


title: neural tube, Mutant Ribo-seq (run1_TC5_mut_Ribo_S5_L004)

description: Replicate 2


title: neural tube, Mutant RNA-seq (run2_TC1_mut_RNA_S10_L004)

description: Replicate 1


title: neural tube, Mutant Ribo-seq (run2_TC1_mut_Ribo_S4_L003)

description: Replicate 1


title: neural tube, Mutant RNA-seq (run2_TC6_mut_RNA_S12_L002)

description: Replicate 3


title: neural tube, Wild-type Ribo-seq (run2_TC5_WT_Ribo_S2_L002)

description: Replicate 2


title: neural tube, Mutant RNA-seq (run2_TC1_mut_RNA_S10_L001)

description: Replicate 1


title: neural tube, Mutant Ribo-seq (run1_TC6_mut_Ribo_S6_L003)

description: Replicate 3


title: neural tube, Mutant RNA-seq (run1_TC1_mut_RNA_S10_L004)

description: Replicate 1


title: neural tube, Wild-type RNA-seq (run2_TC1_WT_RNA_S7_L002)

description: Replicate 1


title: neural tube, Wild-type RNA-seq (run1_TC6_WT_RNA_S9_L003)

description: Replicate 3


title: neural tube, Wild-type RNA-seq (run2_TC5_WT_RNA_S8_L003)

description: Replicate 2


title: neural tube, Mutant Ribo-seq (run1_TC5_mut_Ribo_S5_L003)

description: Replicate 2


title: neural tube, Wild-type Ribo-seq (run2_TC1_WT_Ribo_S1_L002)

description: Replicate 1


title: neural tube, Wild-type RNA-seq (run2_TC5_WT_RNA_S8_L001)

description: Replicate 2


title: neural tube, Mutant Ribo-seq (run2_TC5_mut_Ribo_S5_L002)

description: Replicate 2


title: neural tube, Mutant RNA-seq (run2_TC5_mut_RNA_S11_L002)

description: Replicate 2


title: neural tube, Wild-type Ribo-seq (run2_TC6_WT_Ribo_S3_L001)

description: Replicate 3


title: neural tube, Mutant Ribo-seq (run2_TC1_mut_Ribo_S4_L001)

description: Replicate 1


title: neural tube, Wild-type Ribo-seq (run2_TC1_WT_Ribo_S1_L001)

description: Replicate 1


title: Untreated Control_2

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

data_processing:
Raw reads were aligned to the reference genome
Aligned reads varied between 90-95 % in each sample.
The DESeq algorithm (StrandNGS software) was used to obtain normalized gene expression values.
Gene expression differences between treated and control groups were compared by a moderated t test; the Benjamini-Hochberg false discovery rate was used for multiple-testing correction, and a corrected p value of <0.05 was considered significant (differentially expressed genes).
Genome_build: Genome: „http://fungi.ensembl.org/candida_auris_gca_002759435/Info/Index”; features:”http://www.candidagenome.org/download/gff/C_auris_B8441/archive/C_auris_B8441_version_s01-m01-r11_features_with_chromosome_sequences.gff.gz”
Supplementary_files_format_and_content: Exel file includes corrected p values, fold change values, normalized and  raw data.

organism: Candidozyma auris

source_name: fungal cells

growth_protocol: The strain was maintained on YPDA (1% yeast extract, 2% mycological peptone, 2% glucose, 2% agar, pH 5.6). The pre-cultures were grown in YPD medium at 30ºC with 2.3 Hz shaking frequency for 18 hours then diluted to OD640 0.1 value in 20 mL of YPD and incubated at 37ºC with 2.3 Hz shaking frequency.

extract_protocol:
Freeze- lyophilized cells were processed using TRISOL reagent (Invitrogen, Austria) reagent and glass beads. RNA concentration and purity were determined using NanoDrop (ThermoFisher Scientific, Waltham, MA USA) and capillary electrophoresis.
The quality of RNA was determined with the Eukaryotic Total RNA Nano kit (Agilent, USA) using Agilent Bioanalyzer. RNA-Seq libraries were prepared from total RNA using NEBNext Ultra II RNA Sample Preparation kit (NEB, USA) according to the manufacturer’s protocol. The single read 75 bp long sequencing reads were generated on Illumina NextSeq500 instrument. Approximately 18-22 million reads per samples were generated.

treatment_protocol: Following 4 hours incubation time YPD medium was supplemented with a final concentration of 75 μM farnesol and fungal cells were collected 2 hours following farnesol exposure by centrifugation (5 min, RCF=4000×g, 4°C). The cells were washed three times with phosphate-buffered saline and stored at -70°C until use.

value: isolate 12

tag: agent


title: Farnesol_2

value: Farnesol


title: Farnesol_3


title: neural tube, Mutant Ribo-seq (run1_TC6_mut_Ribo_S6_L004)

description: Replicate 3


title: Untreated Control_3


title: neural tube, Mutant RNA-seq (run1_TC6_mut_RNA_S12_L003)

description: Replicate 3


title: Farnesol_1


title: neural tube, Wild-type Ribo-seq (run1_TC5_WT_Ribo_S2_L002)

description: Replicate 2


title: Untreated Control_1


title: neural tube, Wild-type RNA-seq (run2_TC6_WT_RNA_S9_L001)

description: Replicate 3


title: neural tube, Wild-type Ribo-seq (run2_TC6_WT_Ribo_S3_L003)

description: Replicate 3


title: neural tube, Wild-type RNA-seq (run2_TC5_WT_RNA_S8_L002)

description: Replicate 2


title: neural tube, Wild-type RNA-seq (run1_TC1_WT_RNA_S7_L001)

description: Replicate 1


title: neural tube, Mutant Ribo-seq (run1_TC6_mut_Ribo_S6_L001)

description: Replicate 3


title: neural tube, Mutant RNA-seq (run2_TC1_mut_RNA_S10_L003)

description: Replicate 1


title: neural tube, Mutant Ribo-seq (run2_TC1_mut_Ribo_S4_L002)

description: Replicate 1


title: neural tube, Wild-type Ribo-seq (run2_TC6_WT_Ribo_S3_L002)

description: Replicate 3


title: neural tube, Mutant RNA-seq (run1_TC5_mut_RNA_S11_L004)

description: Replicate 2


title: neural tube, Wild-type Ribo-seq (run2_TC5_WT_Ribo_S2_L003)

description: Replicate 2


title: neural tube, Mutant Ribo-seq (run1_TC5_mut_Ribo_S5_L002)

description: Replicate 2


title: Donor5_5aru

city: Wellington

first: Ellie-May

last: Jarvis

address: Malaghan Institute of Medical Research, PO Box 7060

country: New Zealand

institute: Malaghan Institute of Medical Reseatch

hyb_protocol: Briefly, RNA was hybridised with the Reporter CodeSet for 18 hours at 65 ºC and then incubated with the Capture ProbeSet at 65 ºC  for a further 12 hours.

scan_protocol: Following this, samples were loaded into cartridges via the NanoString PrepStation and RNA quantified via a Digital Analyser.

data_processing: The raw data was imported into nSolver (v3.0, NanoString Technologies, Inc.) and RNA counts normalised to housekeeping genes. Data was then log2-transformed and trimmed to exclude counts greater than 1.5 mean absolute deviations from the median value  using RStudio (RStudio, Inc.).

source_name: PBMC

label_protocol: PanCancer Immune nCounter Assay (NanoString Technologies, Inc.) was utilised to label, hybridise and quantify RNA expression according to the manufacturer’s instructions.

growth_protocol: Healthy donor PBMCs isolated using lymphoprep. They were seeded at 3 x 10^5 cells/well and stimuli or media control added.

extract_protocol: RNA was extracted using the Qiagen RNA mini kit according to manufacurer's instructions

treatment_protocol: Innate-like T-cell stimuli used were 200 nM agc for NKT-cell activation, 1 µM 5-A-RU/MG for MAIT-cell activations or 1 µM BrHPP for V[gama]9V[delta]2 T-cell stimulation

tag: disease state

value: healthy

tag: culture


title: Donor5_BrHPP

value: BrHPP


title: Donor3_BrHPP


title: Donor1_BrHPP


title: Donor4_BrHPP


title: Donor6_BrHPP


title: Donor4_5aru


title: neural tube, Wild-type Ribo-seq (run2_TC1_WT_Ribo_S1_L004)

institute: Stanford University

description: Replicate 1


title: Donor2_5aru


title: Donor2_BrHPP