title: Breast cancer BRC122


title: Breast cancer BRC123

status: Public on Mar 18 2020

type: RNA

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

hyb_protocol: Labeled, amplified material (1,500 ng per array) was hybridized to a ver.3 of the Illumina HT-12 expression BeadChip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual.

scan_protocol: Arrays were scanned with an Illumina BeadArray Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions.

data_processing: Array data were obtained from Illumina GenomeStudio software. We normalized gene expression data using Quantile normalization and log2 transformation.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Primary breast cancer

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina’s recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina® TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using RiboGreen were measured (Quant-iTTM RiboGreen® RNA assay kit; Invitrogen-Molecular Probes, ON, Canada) by the Victor3 spectrophotometer (PerkinElmer, CT) and cRNA quality was checked on a 1% agarose gel.

extract_protocol: Total RNA was isolated from tissues with TRIzol (Life Technologies, NY) reagent according to the manufacturer’s protocol. RNA quality and integrity were confirmed by electrophoresis on agarose gel stained with ethidium bromide and examined under ultraviolet light.

tag: disease status

value: Breast cancer

tag: tissue

value: Primary breast cancer tumor

tag: age

tag: ajcc stage

tag: vital status

value: Alive

tag: follow-up time (month)


title: 04504700T_RNA-seq

type: SRA

library_source: transcriptomic

data_processing:
Base calling was performed by Illumina Genome Studio(V2010.1).
Reference genome sequence data from Homo sapiens were obtained from the University of California Santa Cruz Genome Browser Gateway (assembly ID: hg38). The reference genome index and reads mapping of tissue samples were performed using the STAR software (ver. 2.5.3a).
The read counts per
million fragments mapped (CPM) of each sample was used to estimate the expression level of each gene. The CPM data were normalized by the quantile method and log2-transformed.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text format with log2 transformed CPM values of transcripts

source_name: diffuse type gastric cancer

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.

value: gastric cancer

tag: cancer type

value: diffuse type

tag: gender

value: F

tag: histologic type

value: poorly cohesive carcinoma


title: 04504407T_RNA-seq


title: 04504140T_RNA-seq

value: M

value: poorly differentiated


title: 04503493T_RNA-seq


title: 04505498T_RNA-seq

source_name: intestinal type gastric cancer

value: intestinal type


title: 04503847T_RNA-seq


title: 04503290T_RNA-seq


title: 04505176T_RNA-seq


title: Breast cancer BRC121


title: Breast cancer BRC117


title: Breast cancer BRC115


title: Breast cancer BRC124

value: Dead


title: Breast cancer BRC114


title: Breast cancer BRC135


title: Breast cancer BRC112


title: 04504530T_RNA-seq

value: mucinous adenocarcinoma


title: 04502817T_RNA-seq


title: Breast cancer BRC109


title: Breast cancer BRC120


title: Breast cancer BRC113


title: 04502455T_RNA-seq


title: 04501923T_RNA-seq

value: adenocarcinoma


title: 04501978T_RNA-seq


title: 04502067T_RNA-seq


title: 04501923N_RNA-seq

source_name: Normal mucosae

value: normal intestinal mucosae


title: 04501327T_RNA-seq


title: 04502227T_RNA-seq


title: Breast cancer BRC102


title: 04500663T_RNA-seq


title: 04500652T_RNA-seq


title: 04501325T_RNA-seq


title: Breast cancer BRC118


title: Breast cancer BRC096


title: Breast cancer BRC099


title: Breast cancer BRC098


title: Breast cancer BRC101


title: 04426537T_RNA-seq

value: Medullary carcinoma


title: 04351995T_RNA-seq


title: Breast cancer BRC089


title: 04418901T_RNA-seq


title: 04346050T_RNA-seq


title: 04459904T_RNA-seq


title: Breast cancer BRC100


title: Breast cancer BRC090


title: Breast cancer BRC095


title: Breast cancer BRC091


title: Breast cancer BRC084


title: Breast cancer BRC082


title: Breast cancer BRC080


title: Breast cancer BRC086


title: Breast cancer BRC081


title: 04389901T_RNA-seq

value: papillary adenocarcinoma


title: 04321069T_RNA-seq


title: 04321069N_RNA-seq


title: 04306216T_RNA-seq


title: 04270213T_RNA-seq


title: 04264114T_RNA-seq


title: 04234126T_RNA-seq


title: 04234041N_RNA-seq


title: Breast cancer BRC076


title: 04173490T_RNA-seq


title: 04173490N_RNA-seq


title: 04142974N_RNA-seq


title: 04103025T_RNA-seq


title: Breast cancer BRC105


title: 04100321T_RNA-seq


title: Breast cancer BRC074


title: Breast cancer BRC072


title: 04234041T_RNA-seq


title: Breast cancer BRC073


title: 04096615T_RNA-seq


title: Breast cancer BRC069


title: Breast cancer BRC079


title: Breast cancer BRC071


title: Breast cancer BRC065


title: Breast cancer BRC070


title: Breast cancer BRC061


title: Breast cancer BRC056


title: Breast cancer BRC064


title: Breast cancer BRC066


title: 04107642T_RNA-seq


title: 04142974T_RNA-seq

value: papillary


title: 04046478T_RNA-seq


title: Breast cancer BRC053

value: Breast cancer


title: Breast cancer BRC062

value: Primary breast cancer tumor


title: Breast cancer BRC054

value: Alive


title: Breast cancer BRC059


title: Breast cancer BRC055


title: Breast cancer BRC051


title: EHF_NMPs_H8

city: Oeiras

first: Moises

last: Mallo

address: Rua da Quinta Grande 6

country: Portugal

institute: Instituto Gulbenkian de Ciencia

data_processing:
Raw sequences were aligned to the GRCm38 (mm10) reference genome using Hisat2 (Kim et al., 2013).
The “featureCounts” R function was used to count reads mapping to annotated genes.
Genome_build: mm10
Supplementary_files_format_and_content: R software

organism: Mus musculus

source_name: neuromesodermal progenitor cells and mesoderm cells

extract_protocol:
A region immediately lateral to the posterior edge of the node and lateral to the primitive streak, extending to about half the length of the primitive streak was microdissected in M2 medium using hand-pulled solid glass needles. Single-cells were sorted by Fluorescence-activated cell sorting with a FACS Aria II (BD Biosciences) into individual wells of a 96-well PCR plate containing the ERCC RNA spike-in Mix (Ambion,#4456740) diluted (1:100.000)
Libraries from a total of 91 single cells were prepared using a Nextera XT index kit (Illumina)

tag: strain

tag: developmental stage

value: early headfold stage (around E8.0)

value: caudal lateral epiblast


title: EHF_NMPs_H9


title: 04027022T_RNA-seq

value: gastric cancer

value: diffuse type


title: EHF_NMPs_H7


title: EHF_NMPs_H5


title: EHF_NMPs_H11


title: EHF_NMPs_H6


title: EHF_NMPs_H4


title: EHF_NMPs_H3


title: Breast cancer BRC092


title: Breast cancer BRC048


title: EHF_NMPs_H1


title: EHF_NMPs_H2


title: Breast cancer BRC047


title: Breast cancer BRC043


title: Breast cancer BRC052


title: Breast cancer BRC141


title: Breast cancer BRC045


title: 04002179T_RNA-seq

value: F


title: EHF_NMPs_G11


title: Breast cancer BRC046


title: EHF_NMPs_G12


title: Breast cancer BRC034


title: EHF_NMPs_G10


title: EHF_NMPs_G8


title: EHF_NMPs_G9


title: Breast cancer BRC033


title: Breast cancer BRC035


title: Breast cancer BRC031


title: Breast cancer BRC041


title: Breast cancer BRC030


title: EHF_NMPs_G6


title: EHF_NMPs_G7


title: Breast cancer BRC028


title: Breast cancer BRC027


title: EHF_NMPs_G3


title: EHF_NMPs_G2


title: EHF_NMPs_G4


title: Breast cancer BRC025


title: EHF_NMPs_G5


title: EHF_NMPs_G1


title: EHF_NMPs_F12


title: EHF_NMPs_F10


title: EHF_NMPs_F11


title: EHF_NMPs_F9


title: EHF_NMPs_F8


title: EHF_NMPs_F7


title: EHF_NMPs_F4


title: EHF_NMPs_F3


title: EHF_NMPs_F6


title: EHF_NMPs_F5


title: EHF_NMPs_F2


title: EHF_NMPs_F1


title: Breast cancer BRC005


title: Breast cancer BRC004


title: Breast cancer BRC003


title: Breast cancer BRC011


title: Breast cancer BRC016E


title: Breast cancer BRC026


title: Breast cancer BRC024


title: EHF_NMPs_E12


title: EHF_NMPs_E11


title: Breast cancer BRC006


title: Breast cancer BRC002


title: EHF_NMPs_E8


title: EHF_NMPs_E9


title: EHF_NMPs_E10


title: Breast cancer BRC008


title: Breast cancer BRC012


title: Breast cancer BRC015


title: Breast cancer BRC007


title: Breast cancer BRC009


title: EHF_NMPs_E5


title: EHF_NMPs_E3


title: EHF_NMPs_E4


title: EHF_NMPs_E2


title: EHF_NMPs_E1


title: EHF_NMPs_D12


title: EHF_NMPs_D11


title: EHF_NMPs_D10


title: EHF_NMPs_D8


title: EHF_NMPs_D9


title: EHF_NMPs_D5


title: EHF_NMPs_D7


title: EHF_NMPs_D6


title: EHF_NMPs_E6


title: EHF_NMPs_D4


title: ATAC_E2_M2-5

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

country: USA

institute: University of Utah

library_source: genomic

data_processing:
Reads were aligned to hg19 using bowtie (Langmead et al., 2009) and the following parameters: -m 1 -t–best -q -S -l 32 -e 80 -n 2.
SAM files were converted to BAM files for peak calling using samtools (Li et al., 2009).
MACS2 (Zhang et al., 2008) was used to call peaks without an input using the following command: macs2 callpeak --nomodel --shift -100 --extsize 200 –B –SPMR.
Peaks were overlapped with ER binding sites and reads were counted using bedtools (Quinlan and Hall, 2010).
ATAC-seq signals of an enhancer deletion was compared to clones that were wildtype for that locus but harbored enhancer deletions nearby the other gene. For example, MMP17-1 enhancer deletions were compared to CISH-1 and CISH-2 deletions as controls.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files
Supplementary_files_format_and_content: narrowPeak files (from MACS2)

molecule: genomic DNA

source_name: Ishikawa (Endometrioid adenocarcinoma)

growth_protocol: Ishikawa cell lines containing deletions of individual ER binding sites were generated as described previously (Carleton et al., 2017). Ishikawa cells were maintained in RPMI 1640 (Gibco) supplemented with 10% FBS (Gibco) and 1% pencillin/streptomycin (Gibco). Cells were placed in hormone-depleted RPMI (phenol red-free RPMI-1640 supplemented with 10% Charcoal/Dextran treated fetal bovine serum (HyClone) and 1% penicillin-streptomycin) for at least 6 days prior to estradiol treatment. The input control used in peak-calling was derived from the parental Ishikawa line.

extract_protocol:
For each of the clones, approximately 250,000 cells were lysed and nuclei were harvested for transposition as described previously (Buenrostro et al., 2013). Tn5 transposase with Illumina adapters was assembled as previously described (Picelli et al., 2014).
ATAC-seq libraries were prepared as previously described (Buenrostro et al., 2013)

treatment_protocol: A 1 h 10 nM E2 induction or a 1 h DMSO (vehicle) treatment was performed prior to harvest.

tag: cell line

value: Ishikawa

tag: enhancer deleted

tag: treatment

value: 10nM E2 1 hr


title: ATAC_E2_M1-66


title: ATAC_E2_M2-3


title: ATAC_E2_C2-14


title: ATAC_E2_M1-91


title: ATAC_E2_C2-3


title: EHF_NMPs_C11


title: EHF_NMPs_C12


title: EHF_NMPs_C10


title: ATAC_DMSO_M2-5

value: DMSO 1hr


title: EHF_NMPs_C9


title: EHF_NMPs_C6


title: ATAC_DMSO_M2-3


title: EHF_NMPs_C8


title: ATAC_E2_C1-8


title: ATAC_DMSO_M1-91


title: ATAC_DMSO_M1-66


title: EHF_NMPs_C2


title: ATAC_DMSO_C2-3


title: ATAC_DMSO_C2-14


title: EHF_NMPs_D3


title: ATAC_DMSO_C1-8


title: ATAC_E2_C1-5


title: EHF_NMPs_D1


title: EHF_NMPs_C3


title: EHF_NMPs_B12


title: EHF_NMPs_B11


title: EHF_NMPs_C4


title: sample_74_T_cells

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

description: SureSelect  XT  Methyl-Seq Target   Enrichment System

data_processing:
Basecalls was performed using CASAVA
After trimming for low-quality bases (Phred score<30) and reads with a length <40 bp with TrimGalore, the reads were aligned to the human genome (GRCh37) using Bismark with paired end mode and default setting. Unpaired reads after trimming were aligned separately using single end-mode and the same settings.
Duplicate reads were removed using Picard tools.
SNP calling was performed with BisSNP [47] using default settings, except for the maximum coverage filter set at 200. C>T SNPs on negative strand were filtered out as well as heterozygous SNPs with less than 5 reads per allele. In addition, SNP with multiple mapping positions were filtered out, as well as SNPs with more than one minor allele with allele frequency>0.05. or deviating significantly from Hardy-Weinberg equilibrium based on exact tests corrected for multiple tests
ASM calling was performed after separating the SNP-containing reads by allele using R. After Bismark methylation extractor is applied, CpG methylation calls by allele are retrieved using allele tagged read IDs. Paired reads with ambiguous SNP calling (i.e., called as REF allele on one paired end and ALT allele on the other) were discarded.
Genome_build: GRCh37
Supplementary_files_format_and_content: Processed files per sample contain difference in methylation percentage at the CpG level between the alternate and reference alleles for each SNPs associated with high confidence ASM (observed in >2 biological samples) if the given sample was informative. The columns include chromosome, start and end of the CpG (reported on positive strand), difference in methylayion percentage and SNP ID. The unique identifier in these files is the CpG coordinate AND SNP ID.

source_name: T cells

extract_protocol:
DNA extracted using phenol-chloroform protocol after RNAse treatment. DNA was bisulfite converted with the EZ DNA methylation kit (Zymo).
Agilent SureSelect methyl-seq DNA hybrid capture kit was used according to the manufacturer’s instructions.

tag: subject id

tag: cancer status

value: non-cancer

tag: organ

value: blood


title: ATAC_DMSO_C1-5


title: sample_70_T_cells


title: sample_73_T_cells


title: EHF_NMPs_B10


title: EHF_NMPs_B8


title: EHF_NMPs_B9


title: EHF_NMPs_C5


title: sample_67_T_cells


title: EHF_NMPs_B7


title: sample_57_PBL

source_name: PBL


title: EHF_NMPs_B5


title: EHF_NMPs_B6


title: sample_55_PBL


title: sample_35_GM12878_LCL

source_name: GM12878 LCL

value: lymphoblastoid


title: EHF_NMPs_B4


title: sample_56_PBL


title: EHF_NMPs_C1


title: sample_30_brain

source_name: brain

value: brain


title: EHF_NMPs_B1


title: sample_29_brain


title: EHF_NMPs_B2


title: EHF_NMPs_A12


title: sample_27_brain


title: sample_28_brain


title: EHF_NMPs_B3


title: EHF_NMPs_A11


title: sample_26_brain


title: EHF_NMPs_A8


title: EHF_NMPs_A10


title: EHF_NMPs_A7


title: sample_18_brain


title: Ctrl_2

city: New York

first: Deli

last: Liu

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

description: RNA-seq

data_processing:
Reads were mapped to the human reference genome sequence (hg19) using STAR v2.4.0j.  Then the resulting BAM files were subsequently converted into mapped-read format (MRF) using RSEQtools.
The read count of each gene was calculated via HTSeq using GENCODE as reference gene annotation set.  Quantification of gene expression was performed via RSEQtools v0.6, and expression levels (RPKM) were estimated by counting all nucleotides mapped to each gene and were normalized by the total number of mapped nucleotides (per million) and the gene length (per kb).  Combat v3.20.0 was used to remove the batch effect of different RNA-seq libraries for the downstream gene expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: First column represents the gene name, and second represents the expression level (RPKM) for each gene.

source_name: prostate transitional zone

extract_protocol:
Fresh tissue samples were collected and processed using Weill Cornell Medicine standard operating procedure
RNA-seq library for BPH and control samples from patients without BPH symptoms were generated using Poly-A and Ribo-Zero kits. Poly-A: BPH_1, BPH_2, BPH_3, BPH_7, BPH_10, BPH_11, BPH_12, BPH_14, BPH_15, Ctrl_1, Ctrl_2, Ctrl_3, Ctlr_4; Ribo-Zero: BPH_4, BPH_5, BPH_6, BPH_8, BPH_9, BPH_13, BPH_16, BPH_17, BPH_18

treatment_protocol: No treatments were applied prior to cDNA extraction

tag: condition

value: control


title: EHF_NMPs_A9

tag: tissue


title: Ctrl_3

description: RNA-seq


title: EHF_NMPs_A6


title: Ctrl_1

description: RNA-seq


title: EHF_NMPs_A5


title: EHF_NMPs_A4


title: Ctrl_4

description: RNA-seq


title: BPH_17

description: RNA-seq

value: BPH


title: EHF_NMPs_A3


title: BPH_18

description: RNA-seq


title: BPH_16

description: RNA-seq


title: EHF_NMPs_A2


title: Nfya_2

first: Zhaoning

last: Wang

address: 701 West 168th Street Hammer 14 - 1410

department: Genetics and Development

institute: Columbia University

description:
NRVM_RawCountTable.txt
NRVM_RPKMTable.txt
NfyavsGFP_edgeR.txt

data_processing:
Quality control of RNA-Seq data was performed using FastQC Tool (Version 0.11.4).
Sequencing reads were aligned to mouse GRCm38 (mm10) reference genome using HiSTAT2 (Version 2.0.4) with default settings and --rna-strandness F.
Aligned reads were counted using featurecount (Version 1.6.0) per gene ID.
Differential gene expression analysis was performed with the R package edgeR (Version 3.20.5) using the GLM approach. For each comparison, genes with more than 1 CPM (Count Per Million) in at least three samples were considered as expressed and were used for calculating normalization factor. Cutoff values of absolute fold change greater than 2.0 and false discovery rate less than 0.01 were used to select differentially expressed genes between sample group comparisons. Normalized gene CPM values were used to calculate RPKM (Reads Per Kilobase per Million mapped reads) values, which were then used for heatmap plotting.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files including raw count values and RPKM values for each sample, and differential expression analysis results from edgeR.

organism: Rattus norvegicus

source_name: Neonatal rat ventricular cardiomyocytes (NRVMs)

growth_protocol: Neonatal rat ventricular myocytes (NRVMs) were isolated from 1- or 2-day-old Sprague-Dawley rats with the Isolation System for Neonatal Rat/Mouse Cardiomyocytes (Cellutron, nc-6031) according to the manufacturer’s instructions. NRVMs were plated at a density of 1.5x10^5 cells/well to gelatin-coated 12-well plates and were maintained in Dulbecco’s modified Eagle’s medium (DMEM/199 medium (3:1) with 3% fetal bovine serum (FBS), and penicillin-streptomycin for 48 h before adenoviral infection.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN, 74104) according to the manufacturer’s protocol.
Stranded mRNA-Seq libraries were generated using the KAPA mRNA HyperPrep Kit (Roche, KK8581) following manufacturer’s protocol.

treatment_protocol: NRVMs were treated with 8 µL adenovirus in 1 mL serum-free medium (DMEM/199 medium) per each well in a 12-well plate for 48 h before collecting RNA.

value: Sprague Dawley

tag: adenovirus infected

value: Nfya


title: Nfya_1


title: BPH_15

description: RNA-seq


title: EHF_NMPs_A1


title: Nfe2l1_3

description:
NRVM_RawCountTable.txt
NRVM_RPKMTable.txt
Nfe2l1vsGFP_edgeR.txt


title: Nfe2l1_2


title: Nfe2l1_1


title: GFP_2

description:
NRVM_RawCountTable.txt
NRVM_RPKMTable.txt
Nfe2l1vsGFP_edgeR.txt
NfyavsGFP_edgeR.txt

value: GFP


title: GFP_3


title: GFP_1


title: Tumor_mouse5Plate1

city: Amsterdam

first: Lennart

last: Kester

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description: single cell mRNA

data_processing:
Read1 contains the the Unique Molecule Identifier (nt 1-6) and the cell barcode (nt 7-14), read2 was mapped to the mm10 RefSeq transcriptome using Burrows-Wheeler Aligner with standard parameters. Seurat (R package Seurat (Stuart et al., 2019) was used for analyzing the single cell data. Single cell transcriptomes were filtered for cells that had at least 1,000 unique transcripts and subsequently log-normalized to 10,000 transcripts per cell. Clustering was performed on the first 13 principal components and clusters were identified with a resolution of 1. Differential gene expression analysis was performed with the roc test. Cell type identification was performed based on the differentially expressed genes between the clusters.
Genome_build: mm10 RefSeq transcriptome
Supplementary_files_format_and_content: the csv file contains the transcript counts per single cell

source_name: Murine colorectal cancer tumor cells

growth_protocol: Orthotopic transplantation of colorectal cancer organoids was performed as previously described (Fumagalli et al., 2017; Fumagalli et al., 2018). In brief, the day before transplantation organoids were collected and dissociated into small cell clumps. About 250,000 cells were plated in 15 μl drops neutralized Rat Tail High Concentrated Type I Collagen (Corning, cat. no. 354249) and let to recover overnight at 37°C, 5% CO2 in CRC medium containing 100 μM Y-27632 (Abmole Bioscience, cat. no. M1817). At the day of transplantation, acceptor mice were sedated using isoflurane inhalation anesthesia (~2% isoflurane/O2 mixture). Before surgery, the mice were treated subcutaneously with a single dose of buprenorphine (Buprecare, Multidosis-Astfarma, 3μg per mouse). The cecum was exposed through a midline abdominal incision and a collagen drop containing tumor cells was surgically transplanted in the caecal submucosa. The tumor growth was monitored weekly by abdominal palpation.

extract_protocol:
Orthotopic colorectal cancer tumors were collected and minced on ice using sterile scalpels. The tumor mass was digested at 37 ⁰C for about 1 hour in 5mg/ml Collagenase II brown powder (Thermo Fisher Scientific, cat. no. 17101015) dissolved in advanced DMEM/F12 medium (adDMEM/F12; Thermo Fisher Scientific, cat. no. 12634-010) containing 100 μM Y-27632 (Abmole Bioscience, cat. no. M1817), 4μg/ml DNAse I (Sigma-Aldrich, cat. no. 10104159001), 20 μg/ml hyaluronidase (Sigma-Aldrich, cat. no. 37326-33-3). Digested cell clumps were incubated in TryplE (Thermo Fisher Scientific, cat. no. 12605-010) mix containing 100 μM Y-27632 (Abmole Bioscience, cat. no. M1817), 4μg/ml DNAse I (Sigma-Aldrich, cat. no. 10104159001) for 15 minutes at 37 ⁰C and spun down. The cell pellet was resuspended in FACS buffer (composition described above) and filtered through a 35 μm strainer (BD Falcon). DAPI 1ng/ml was added right before sorting.
Single-cell mRNA sequencing was performed using Sort-seq as described in Muraro et al. (Muraro et al., 2016). Single-cell libraries were sequenced on Illumina NextSeq500 with 75bp paired end reads.
Final illumina libraries were generated using the illumina small RNA adapters

tag: genotype

tag: replicate

value: Not Applicable


title: BPH_14

description: RNA-seq


title: BPH_13

description: RNA-seq


title: BPH_12

description: RNA-seq


title: Nfya_3


title: Tumor_mouse4Plate1

description: single cell mRNA


title: TAPBPR library sorted for rescue of surface HLA-A2 expression in tapasin-KO cells (Replicate 2)

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

description:
A2_rescue_2_AGTCAA
processed data file: TAPBPR_deep_mutagenesis.xlsx

data_processing:
Data was analyzed using python scripts in the Enrich package: http://depts.washington.edu/sfields/software/enrich/
Fuser command (Fragment A):
python Paired_read_fuser.py --path directory_A/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq --read2 sample_R2.fastq --wtseq gaggtgacctgtgagatctcccgctactttctccagatgacagagaccactgttaagacagcagcttggttcatggccaacgtgcaggtctctggagggggacctagcatctccttggtgatgaagactcccagggtcgccaag --read1_overlap_start 26 --read1_overlap_end 170 --read2_overlap_start 67 --read2_overlap_end 211 --mode B
Fuser command (Fragment B):
python Paired_read_fuser.py --path directory_B/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq --read2 sample_R2.fastq --wtseq gtggagttccaggtgatgacacagacccaatccctgagcttcctgctggggtcctcagcctccttggactgtggcttctccatggcaccgggcttggacctcatcagtgtggagtggcgactgcagcacaagggcaggggt --read1_overlap_start 45 --read1_overlap_end 186 --read2_overlap_start 89 --read2_overlap_end 230 --mode B
Fuser command (Fragment C):
python Paired_read_fuser.py --path directory_C/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq --read2 sample_R2.fastq --wtseq gagcctgcacaactgggcatggccagggatgcctccctcaccctgcccggcctcactatacaggacgaggggacctacatttgccagatcaccacctctctgtaccgagctcagcagatcatccagctcaacatccaagcttcccctaaagtacga --read1_overlap_start 63 --read1_overlap_end 219 --read2_overlap_start 41 --read2_overlap_end 197 --mode B
Fuser command (Fragment D):
python Paired_read_fuser.py --path directory_D/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq --read2 sample_R2.fastq --wtseq ctcatctgcgacattgctggctattaccctctggatgtggtggtgacgtggacccgagaggagctgggtggatccccagcccaagtctctggtgcctccttctccagcctcaggcaaagcgtggcaggcacctacagcatctcctcctctctcaccgcagaacctggctctgcaggtgccacttacacctgccaggtcacacacatctctctggag --read1_overlap_start 25 --read1_overlap_end 241 --read2_overlap_start 2 --read2_overlap_end 218 --mode B
Aligner command (Fragment A):
python2.7 Fused_read_aligner.py --path directory_A/ --infile sample_R1.fast_B_qc1 --referenceDNA GAGGTGACCTGTGAGATCTCCCGCTACTTTCTCCAGATGACAGAGACCACTGTTAAGACAGCAGCTTGGTTCATGGCCAACGTGCAGGTCTCTGGAGGGGGACCTAGCATCTCCTTGGTGATGAAGACTCCCAGGGTCGCCAAG --referenceAA EVTCEISRYFLQMTETTVKTAAWFMANVQVSGGGPSISLVMKTPRVAK --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment B):
python2.7 Fused_read_aligner.py --path directory_B/ --infile sample_R1.fast_B_qc1 --referenceDNA gtggagttccaggtgatgacacagacccaatccctgagcttcctgctggggtcctcagcctccttggactgtggcttctccatggcaccgggcttggacctcatcagtgtggagtggcgactgcagcacaagggcaggggt --referenceAA VEFQVMTQTQSLSFLLGSSASLDCGFSMAPGLDLISVEWRLQHKGRG --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment C):
python2.7 Fused_read_aligner.py --path directory_C/ --infile sample_R1.fast_B_qc1 --referenceDNA gagcctgcacaactgggcatggccagggatgcctccctcaccctgcccggcctcactatacaggacgaggggacctacatttgccagatcaccacctctctgtaccgagctcagcagatcatccagctcaacatccaagcttcccctaaagtacga --referenceAA EPAQLGMARDASLTLPGLTIQDEGTYICQITTSLYRAQQIIQLNIQASPKVR --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment D):
python2.7 Fused_read_aligner.py --path directory_D/ --infile sample_R1.fast_B_qc1 --referenceDNA ctcatctgcgacattgctggctattaccctctggatgtggtggtgacgtggacccgagaggagctgggtggatccccagcccaagtctctggtgcctccttctccagcctcaggcaaagcgtggcaggcacctacagcatctcctcctctctcaccgcagaacctggctctgcaggtgccacttacacctgccaggtcacacacatctctctggag --referenceAA LICDIAGYYPLDVVVTWTREELGGSPAQVSGASFSSLRQSVAGTYSISSSLTAEPGSAGATYTCQVTHISLE --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
MapCounts command: python mapCounts.py --path directory/ --infile sample_R1.fast_B_qc1_PRO_qc2
MapRatios command Example: python mapRatios.py --path directory/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts command: python mapParts.py --path directory/ --infile mapratios_sorted_library --mode mutations:1
Unlink script: python mapUnlink.py --path directory/ --infile mapratios_sorted_library.m1 --type protein --mode ratios --size number_of_residues_in_fragment
In Excel, the log(base2) enrichment ratio of the wildtype sequence was subtracted from the log(2) enrichment ratios for all single mutations.
Genome_build: Not applicable
Supplementary_files_format_and_content: Excel spreadsheet of log(base2) enrichment ratios for each single amino acid substitution. Also includes the frequency of each mutation in the naïve plasmid library.

source_name: Synthetic coding sequences

extract_protocol:
Total RNA was extracted from FACS sorted cells using a GeneJet kit (Thermo Scientific), and cDNA was synthesized using high fidelity Accuscript (Agilent) primed from a gene-specific primer. The TAPBPR cDNA was PCR amplified as four overlapping fragments for full coverage by Illumina sequencing. In a first round of PCR, primer overhangs added sequences for annealing to the Illumina sequencing primers. In a second round of PCR, primer overhangs added unique barcodes and Illumina adaptors. To determine the frequencies of mutations in the naive library, the library plasmid DNA was used as the template for PCR amplification and Illumina sequencing.
Primer pair for 1st round of PCR (Fragment A):
Illumina_TAPBPR_273_for (TCTTTCCCTACACGACGCTCTTCCGATcttgctccatgctgactgca) and Illumina_TAPBPR_483_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCAGTGGCAAGTTCAGCGTTG)
Primer pair for 1st round of PCR (Fragment B):
Illumina_TAPBPR_466_for (TCTTTCCCTACACGACGCTCTTCCGATCTacgctgaacttgccactgag) and Illumina_TAPBPR_671_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGTCCAGCTGTACACCAACTG)
Primer pair for 1st round of PCR (Fragment C):
Illumina_TAPBPR_649_for (TCTTTCCCTACACGACGCTCTTCCGATCTggtcagttggtgtacagctg) and Illumina_TAPBPR_920_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCCAGCAATGTCGCAGATGAG)
Primer pair for 1st round of PCR (Fragment D):
Illumina_TAPBPR_875_for (TCTTTCCCTACACGACGCTCTTCCGATCtggcaaacgaagctctgctg) and Illumina_TAPBPR_1148_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGGACAACCTGGGTGCTG)
Primer pair for 2nd round of PCR (added I5 and I7 Illumina adaptors):
MiSeq_Start_Adaptamer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and MiSeq_Index_Adaptamer (CAAGCAGAAGACGGCATACGAGAT-6nt-barcode-GTGACTGGAGTTCAGACGTGTGCTCTTC)
Amplicons were deep sequenced on a NovaSeq 6000 using a 2x250 nt paired end protocol.

treatment_protocol: Tapasin-KO Expi293F cells were transfected with a plasmid library encoding variants of chimeric TAPBPR-CT, where the TAPBPR C-terminus is replaced with the equivalent residues of tapasin. Library DNA was diluted with a large excess of carrier DNA to ensure that cells typically acquired no more than one TAPBPR variant, maintaining a tight genotype-to-phenotype link. 24 h post-transfection, cells with the highest surface HLA-A2 (the top 0.5% of fluorescent cells after staining with PE-conjugated anti-HLA-A2) were collected by FACS.

tag: cell type

value: Tapasin-KO Expi293F

tag: protein

value: TAPBPR

tag: sort gate

value: Top 0.5% of cells for surface HLA-A2 expression


title: BPH_11

description: RNA-seq


title: TAPBPR library sorted for rescue of surface HLA-A2 expression in tapasin-KO cells (Replicate 1)

description:
A2_rescue_1_CACCGG
processed data file: TAPBPR_deep_mutagenesis.xlsx


title: HMSCs

city: Shanghai

first: Mingjian

last: Huang

address: 768 Shuangliao Road

country: China

institute: Xin Hua Hospital Affliated to Shanghai Jiao Tong University School of Medicien (SJTUSM)

description: Untreated HMSCs sample

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-045997 Arraystar human lncRNA microarray V3 for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Raw lncRNA data normalization and low intensity filtering: Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5, and low intensity lncRNAs were filtered (lncRNAs that at least 3 out of 5 samples have flags in Present or Marginal were chosen for further analysis).

source_name: hMSCs untreated

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: hMSCs untreated and hMSCs treated with chondrogenic medium (DMEM high-glucose medium supplemented with ITS1Premix: 6.25 mg/mL insulin, 6.25 mg/mL transferrin, 5.33 mg/mL linoleic acid, 1.25 mg/mL bovine serum albumin, 100nM dexamethasone, 50 mg/mL ascorbate-2 phosphate, 1mM sodium pyruvate, 100 mg/mL penicillin, and 10 mg/mL streptomycin, 10 ng/mL TGF-b1). We replaced the chondrogenic induced medium every three days maintaining 21 days.

value: undifferentiated mesenchymal stem cells

tag: passage

value: passage 4

tag: tissue source

value: bone marrow


title: Library of TAPBPR variants

description:
TAPBPR_library_ATGTCA
Plasmid DNA
processed data file: TAPBPR_deep_mutagenesis.xlsx


title: Chondrogenesis

description: HMSCs differentiation sample

source_name: hMSCs chondrogenic differentiation

value: mesenchymal stem cells during chondrogenesis


title: MCF7-empty_18hr

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description: Gene expression

hyb_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip Expression Wash, Stain and Scan protocol.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G scanner according to the instruction manual

data_processing: RNA normalization, summarization by mean, all were done by Partek Genomics suite (version 6.6))

source_name: human MCF7 cells transfected with plasmid containing a non-coding shRNA sequence (control shRNA) time 18hr

label_protocol: Samples were prepared according to manufacturer’s instruction manual

growth_protocol: MCF7 cells were seeded in 10-cm Petri dishes until reaching 100% confluence. The cells were washed with phosphate-buffered saline (PBS)

extract_protocol: Total RNA was isolated using the TRIzol reagent (InVitrogen, Waltham, MA, USA), according to the RNA extraction guidelines for Affimetrix GeneChip Assays

treatment_protocol: Transfecion with plasmid containing a non-coding shRNA sequence (control shRNA) for various times


title: Tumor_mouse3Plate2

description: single cell mRNA


title: MCF7-empty_24hr

description: Gene expression

source_name: human MCF7 cells transfected with plasmid containing a non-coding shRNA sequence (control shRNA) time 24hr


title: BPH_10

description: RNA-seq


title: MCF7-empty_4hr

description: Gene expression

source_name: human MCF7 cells transfected with plasmid containing a non-coding shRNA sequence (control shRNA) time 4hr


title: MCF7-empty_96hr

description: Gene expression

source_name: human MCF7 cells transfected with plasmid containing a non-coding shRNA sequence (control shRNA) time 96hr


title: MCF7-empty_1W

description: Gene expression

source_name: human MCF7 cells transfected with plasmid containing a non-coding shRNA sequence (control shRNA) time 1 week


title: sample_108_monocytes

description: Bisulfite-converted DNA

data_processing:
Basecalls was performed using CASAVA
After trimming for low-quality bases (Phred score<30) and reads with a length <40 bp with TrimGalore, the reads were aligned to the human genome (GRCh37) using Bismark with paired end mode and default setting . For ACCEL-NGS Methyl-Seq DNA Library, as recommended by the manufacturer, 15 bp were trimmed on 5' and 3' of both reads.
Duplicate reads were removed using Picard tools and reads with more than 10% unconverted CHG or CHH cytosines were filtered out
SNP calling was performed with BisSNP using default settings, except for the maximum coverage filter set at 200. Heterozygous SNPs with less than 5 reads per allele were filtered out. In addition, SNP with multiple mapping positions were filtered out, as well as SNPs with more than one minor allele with allele frequency>0.05. or deviating significantly from Hardy-Weinberg equilibrium based on exact tests corrected for multiple tests. C/T and G/A SNPs were assessed after filtering out reads mapping to the C/T strand.
ASM calling was performed after separating the SNP-containing reads by allele using R. After Bismark methylation extractor is applied, CpG methylation calls by allele are retrieved using allele tagged read IDs. Paired reads with ambiguous SNP calling (i.e., called as REF allele on one paired end and ALT allele on the other) were discarded.
Genome_build: GRCh37
Supplementary_files_format_and_content: Processed files per sample contain difference in methylation percentage at the CpG level between the alternate and reference alleles for each SNPs associated with high confidence ASM (observed in >2 biological samples) if the given sample was informative. The columns include chromosome, start and end of the CpG (reported on positive strand), difference in methylayion percentage and SNP ID. The unique identifier in these files is the CpG coordinate AND SNP ID.

source_name: monocytes

extract_protocol:
DNA extracted using phenol-chloroform protocol after RNAse treatment. DNA was bisulfite converted with the EZ DNA methylation kit (Zymo).
For Nextera transposase-based library approach, genomic DNA was first tagmented using Nextera XT transposome and end repair was performed using 5mC. After bisulfite conversion, Illumina adapters and custom bisulfite converted adapters are attached by limited cycle PCR. Illumina TruSeq DNA Methylation Kit and ACCEL-NGS Methyl-Seq DNA Library kit were used according to the manufacturer’s instructions.

value: non-cancer

tag: library

value: ACCEL-NGS Methyl-Seq DNA Library


title: sample_110_extravillous_trophoblast_mat

description: Bisulfite-converted DNA

source_name: extravillous trophoblast

value: placenta, maternal

value: TruSeq DNA Methylation Kit


title: sample_109_cytotrophoblast_mat

description: Bisulfite-converted DNA

source_name: cytotrophoblast


title: sample_107_monocytes

description: Bisulfite-converted DNA

value: blood


title: sample_106_GBM

description: Bisulfite-converted DNA

source_name: GBM

value: cancer


title: Tumor_mouse2Plate2

description: single cell mRNA


title: BPH_7

description: RNA-seq

value: BPH


title: sample_105_B_cells

description: Bisulfite-converted DNA

source_name: B cells

value: brain


title: Tumor_mouse1Plate2

description: single cell mRNA


title: BPH_6

description: RNA-seq


title: Tumor_mouse4Plate2

description: single cell mRNA


title: Tumor_mouse1Plate1

description: single cell mRNA


title: Tumor_mouse3Plate1

description: single cell mRNA


title: BPH_4

description: RNA-seq


title: BPH_5

description: RNA-seq


title: sample_104_myeloma

description: Bisulfite-converted DNA

source_name: myeloma


title: sample_103_monocytes

description: Bisulfite-converted DNA


title: BPH_9

description: RNA-seq

source_name: prostate transitional zone


title: CRC_organoidsPlate6

description: single cell mRNA

source_name: Murine colorectal cancer organoids

growth_protocol: Murine colorectal cancer organoids were cultured in BME (R&D Systems, cat. no.3433-005-01). Minimal colorectal cancer organoid culture medium (minimal CRC medium) contained advanced DMEM/F12 medium (adDMEM/F12; Thermo Fisher Scientific, cat. no. 12634-010), B27 2% (Thermo Fisher Scientific, cat. no. 17504-044), N-acetylcysteine 1.25 mM (Sigma-Aldrich, cat. no. A9165) and Noggin 1% (PeproTech, cat. no. 120-10C).

extract_protocol:
Colorectal cancer organoids were collected and mechanically dissociated with a fire-pointed glass pipet. Subsequently cells were incubated in in TryplE (Thermo Fisher Scientific, cat. no. 12605-010) mix containing 100 μM Y-27632 (Abmole Bioscience, cat. no. M1817), 4μg/ml DNAse I (Sigma-Aldrich, cat. no. 10104159001) for 10 minutes at 37 ⁰C and spun down. Cells were resuspended in FACS buffer containing 2% B27 (Thermo Fisher Scientific, cat. no. 17504-044), 1.25 mM N-acetylcysteine (Sigma-Aldrich, cat. no. A9165), 1% Noggin (PeproTech, cat. no. 120-10C), 100 μM Y-27632 (Abmole Bioscience, cat. no. M1817), 4μg/ml DNAse I (Sigma-Aldrich, cat. no. 10104159001), 0.01% FCS (Sigma-Aldrich, cat. no. F7524) in PBS and filtered through a 100 μm and 35 μm strainers (BD Falcon). DAPI 1ng/ml was added right before sorting.
Single-cell mRNA sequencing was performed using Sort-seq as described in Muraro et al. (Muraro et al., 2016). Single-cell libraries were sequenced on Illumina NextSeq500 with 75bp paired end reads.
Final illumina libraries were generated using the illumina small RNA adapters

value: replicate 2


title: BPH_3

description: RNA-seq


title: CRC_organoidsPlate5

description: single cell mRNA


title: CA46_RNA-seq_shMyc+DMS

city: He Fei

first: Shi-Ting

last: Li

state: An Hui

address: No.443, Huangshan Road

department: Innovation Center for Cell Biology

institute: University of Science and Technology of China

description: sample treatment: CA46 cells were infected with viruses expressing Myc shRNA. Before harvesting, CA46 cells were exposed to 10mM dimethyl succinate (DMS, sigma) for 20h

data_processing:
As to ChIP-seq data, raw data (raw reads) of fastq format were firstly processed through BCL2FASTQ programs.
Data filtering parameters：Clean Parameter: fastp  -g 5 –q 5 -u 50 –n 15 -l 150
Sequenced reads were separately aligned to either the human genome hg19 or the D. melanogaster genome (dm6) using Bowtie2 software (version 2.2.6). Aligned reads were used for subsequent generation of binding profiles, peak callings, motif analyses and traveling ratio analyses. MACS (version 1.4.2) was used for peak callings from the aligned reads. The method of ChIP-seq normalization referred to the manufacturer’s instruction (Active Motif).
As to RNA-seq data, raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Clean reads were aligned to the reference genome using TopHat2 v2.1.0.
Cuffdiff v2.2.1 was used to count the reads numbers mapped to each gene.
Genome_build: hg19 and dm6
Supplementary_files_format_and_content: Excel for RNA-seq data and bw for ChIP-seq data

source_name: Human B lymphocyte CA46 cells

growth_protocol: Human B lymphocyte CA46 cells were cultured in RPMI 1640 (GIBCO) with 20%FBS. Cells were maintained in a water-jacketed incubator with 5% CO2 in 37 °C.

extract_protocol:
The CA46 cells’ ChIP-seq experiments with spike-in control was referred to the manufacturer’s instruction (Active Motif). In this experiment, the DNA fragments were sonicated between 200bp to 500bp. For H3K4me3 ChIP and a Drosophila-specific antibody (Active Motif 61686), 1.5 X 107 CA46 cells were used.
As to RNA-seq, total RNA was extracted using TRIZOL Reagent (Life technologies) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100.Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample
ChIP-sequencing libraries were prepared according to generated using NEBNext® Ultra™ IIDNA Library Prep Kit (#E7645).
RNA-sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: CA46 cells were infected with viruses expressing non-targeting control (NTC) or Myc shRNA. Before harvesting, CA46 cell were exposed to 10mM dimethyl succinate (DMS, sigma) or not for 20h, followed by H3K4me3 ChIP-seq and RNA-seq.

value: Human B lymphocyte cell line

tag: cell line

tag: genotype/variation

value: Myc shRNA


title: Tumor_mouse2Plate1

description: single cell mRNA

source_name: Murine colorectal cancer tumor cells

value: Not Applicable


title: CRC_organoidsPlate4

description: single cell mRNA


title: CA46_RNA-seq_shMyc-DMS

description: sample treatment: CA46 cells were infected with viruses expressing Myc shRNA. Before harvesting, CA46 cells were exposed to PBS for 20h

tag: treatment

value: exposed to PBS for 20h


title: BPH_2

description: RNA-seq


title: CA46_RNA-seq_NTC+DMS

description: sample treatment: CA46 cells were infected with viruses expressing non-targeting control (NTC). Before harvesting, CA46 cells were exposed to 10mM dimethyl succinate (DMS, sigma) for 20h

value: non-targeting control


title: CRC_organoidsPlate3

description: single cell mRNA

value: replicate 1


title: BPH_1

description: RNA-seq


title: CA46_RNA-seq_NTC-DMS

description: sample treatment: CA46 cells were infected with viruses expressing non-targeting control (NTC). Before harvesting, CA46 cells were exposed to PBS for 20h


title: BPH_8

description: RNA-seq


title: spike-in_Input_NTC-DMS

source_name: cell line: Human B lymphocyte CA46 cells; spike-in reference organism:  Drosophila melanogaster; spike-in cell line: S2

tag: chip antibody


title: Input

data_processing:
As to ChIP-seq data, raw data (raw reads) of fastq format were firstly processed through BGI programs.
Data filtering parameters：Clean Parameter: SOAPnuke filter -l 5 -q 0.5 -n 0.1 -i -c 10 -Q 2 -51 -c12
Sequenced reads were mapped to the UCSC human genome hg19 using software Bowtie2 (version 2.2.6). Aligned reads were used for subsequent generation of bindingprofiles, peak callings, motif analyses and traveling ratio analyses. MACS (version 1.4.2) was used for peak callings from the aligned reads
As to RNA-seq data, raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reads were alligned to the human genome hg19 with BOWTIE2 v2.2.6 and clean reads were aligned to the reference genome using TopHat2 v2.1.0.
Cuffdiff v2.2.1 was used to count the reads numbers mapped to each gene.
Genome_build: hg19
Supplementary_files_format_and_content: fastq for RNA-seq data and bed for ChIP-seq data

source_name: Human B lymphocyte P493-6 cells

growth_protocol: Human B lymphocyte P493-6 cells were cultured in RPMI 1640 (GIBCO) with 10%FBS. Cells were maintained in a water-jacketed incubator with 5% CO2 in 37 °C.

extract_protocol:
The ChIP was performed with an EZ-ChIP kit (Millipuro) following the manufacture’s instruction. In this experiment, the DNA fragments were sonicated between 100bp to 500bp. For H3K4me3 ChIP, 2 X 107 cells were used.
As to RNA-seq, total RNA was extracted using TRIZOL Reagent (Life technologies) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100.Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample
ChIP-sequencing libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).
RNA-sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: P493-6 cells were treated with tetracycline (tet) or without for 48h. Before harvesting, P493-6 cell were exposed to 10mM dimethyl succinate (DMS, sigma) or not for 20h, followed by H3K4me3 ChIP-seq and RNA-seq. Furthermore, we also treated P493-6 cell with tet or without for 48h, which were exposed to 500 μM 3-NPA (SDH enzyme inhibitor, sigma) for 20h before harvesting and followed by RNA-seq.

value: Input

value: B lymphocyte cells


title: CRC_organoidsPlate1

description: single cell mRNA


title: spike-in_ChIP-seq_shMyc+DMS

value: exposed to 10mM dimethyl succinate (DMS, sigma) for 20h

value: ChIP antibody:H3K4me3 antibody (Millipore, 07-473) ;spike-in ChIP antibody:H2Av (Active Motif, 61686)


title: ChIP-seq+tet+DMS

value: +tet+DMS

value: H3K4me3 antibody (Millipore, 07-473)


title: ChIP-seq+tet-DMS

value: +tet-DMS


title: P1D3MI

data_processing:
The CellRanger ATAC v1.1.0 was used for primary analysis of the scATAC-seq data.
Raw base call (BCL) files were converted to FASTQ files and filtered reads were aligned to the mouse mm10 reference genome.
Transposase cut sites in each cell were quantified using barcoded UMIs and 10x cell barcode sequences.
Count matrix for accessible chromatin peaks was generated for downstream analysis using the R package Signac (v0.1.6).
Genome_build: mm10
Supplementary_files_format_and_content: csv file documenting single cell barcodes and QC information, tsv file documenting accessible chromatin fragments, h5 file documenting open chromatin peak x cell matrix, tsv file for cell barcodes, mtx file for peak x cell matrix, and bed file for open chromatin peak regions generated from CellRanger-atac primary analysis of the raw sequencing data.

source_name: Cardiomyocyte nuclei isolated from ventricle tissue below left anterior descending artery ligation plane

growth_protocol: Animals were housed in a 12 h light/dark cycle in a temperature-controlled room in the Animal Research Center of UT Southwestern, with ad libitum access to water and food.

extract_protocol:
Mice were euthanized at 3d post injury. Ventricle tissues below LAD ligation plane from MI hearts were collected for nuclei extraction. Extracted nuclei were stained with cardiac nuclear membrane marker PCM1 antibody and PCM1+ cardiomyocyte nuclei were sorted by FACS.
Sorted cardiomyocyte nuclei were subjected to single nucleus RNA-sequencing using 10xGenomics platform. Library preparation was performed using Chromium Single Cell ATAC library & Gel Bead Kit V1.0 (10xGenomics) according to the manufacturer’s protocol.
single cell ATAC-seq

treatment_protocol: Neonatal P1 mice were subjected to myocardial infarction, induced by permanent ligation of LAD coronary artery.

tag: strain


title: spike-in_ChIP-seq_shMyc-DMS


title: Sample 15_RvD6-isomer

city: San Diego

first: Thang

middle: Luong

last: Pham

state: California

address: 4445 Eastgate Mall, Suite 200

institute: BioTuring

data_processing:
Raw data was downloaded from Illumina basespace hub with four separated files corresponding for 4 lanes in the Nextseq run for each sample. Files from a same sample were concatenated using Terminal on Ubuntu LTS 16.4 operating system.
The Rsubread v1.34.6 software was installed on the R 3.6.1 version. The primary genenome assembly of the mouse GRCm38 (Release M22, gencodegenes.org/mouse/) was indexed as reference sequence.
The merged fastq.gz files were aligned to the mouse genome using subjunc function of Rsubread. The results were eported as BAM files.
All BAM files were subjected to the Subread v1.6.5. Then, the featureCounts function was used to quantify the aligned reads with the compatible annotation (Comprehensive gene annotation). The outputs were summerized into the counts.txt file.
The counts.txt file was subjected into differential gene expression analysis using DESeq2 package for R. The normalized counts were exported into csv file to provide data for box plot charts. There were two comparisons: RvD6_isomer_vs_vehicle and RvD6_standard_vs_vehicle in the study. The adjusted p-values was regarded as false discover rate (FDR).
Significantly changed genes (FDR < 0.05) were subjected to the enrichment analysis using Enrichr and pathway analysis using the IPA.
Genome_build: GRCm38
Supplementary_files_format_and_content: counts

source_name: RvD6-isomer_Trigeminal ganglia

extract_protocol:
Trigeminal ganglia were homogenized in the RLT buffer using a Dounce homogenizer. Then, total mRNA was extracted using a RNeasy mini kit (Qiagen, Germantown, MD, USA).
RNA sequencing was performed using the adapted Smart-seq2 protocol. Briefly, one ng of total RNA was reverse transcribed with the Oligo-dT30VN and template-switching oligo (TSO) primers. The total cDNAs were amplified using ISPCR primers and the library was made using the Nextera XT DNA library preparation kit (Illumina, San Diego, CA, USA).

treatment_protocol: The center of the right cornea was demarcated with a 2-mm trephine, and the epithelium and the anterior stroma were gently removed under a surgical microscope using a corneal rust ring remover. Then, mice were treated with RvD6-isomer and RvD6-standard three times per day for 12 days. The right trigeminal ganglia was harvested.

value: Trigeminal ganglia


title: ChIP-seq-tet-DMS

value: -tet-DMS


title: Sample 14_RvD6-isomer


title: spike-in_ChIP-seq_NTC+DMS


title: spike-in_ChIP-seq_NTC-DMS


title: CRC_organoidsPlate2

description: single cell mRNA


title: Sample 13_RvD6-isomer


title: ERRBS_Ctrl_5

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Raw reads alignment and CpG methylation call were formed by using an in-house pipeline described in Akalin et al., PLoSGenetics, 2012.
Genome_build: hg19
Supplementary_files_format_and_content: methylcall files are in .txt format

extract_protocol:
For RRBS genomic DNA was isolated from BPH and control samples.
ERRBS libraries were prepared according to a previously published protocol (Akalin et al., PLoSGenetics, 2012).

treatment_protocol: No treatments were applied prior to genomic DNA extraction

value: prostate transitional zone

tag: sample type

value: Control


title: ERRBS_Ctrl_4


title: Sample 11_RvD6-isomer


title: ChIP-seq-tet+DMS

value: -tet+DMS


title: sample_9b_B_cells

description:
Bisulfite-converted DNA
Sample 9a and 9b were bioinformatically pooled for downstream analysis
see sample_9_B_cells_diff_cpg_level.txt

data_processing:
Basecalls was performed using CASAVA
After trimming for low-quality bases (Phred score<30) and reads with a length <40 bp with TrimGalore, the reads were aligned to the human genome (GRCh37) using Bismark with paired end mode and default setting . For ACCEL-NGS Methyl-Seq DNA Library, as recommended by the manufacturer, 15 bp were trimmed on 5' and 3' of both reads.
Duplicate reads were removed using Picard tools and reads with more than 10% unconverted CHG or CHH cytosines were filtered out
SNP calling was performed with BisSNP using default settings, except for the maximum coverage filter set at 200. Heterozygous SNPs with less than 5 reads per allele were filtered out. In addition, SNP with multiple mapping positions were filtered out, as well as SNPs with more than one minor allele with allele frequency>0.05. or deviating significantly from Hardy-Weinberg equilibrium based on exact tests corrected for multiple tests. C/T and G/A SNPs were assessed after filtering out reads mapping to the C/T strand.
ASM calling was performed after separating the SNP-containing reads by allele using R. After Bismark methylation extractor is applied, CpG methylation calls by allele are retrieved using allele tagged read IDs. Paired reads with ambiguous SNP calling (i.e., called as REF allele on one paired end and ALT allele on the other) were discarded.
genome build: GRCh37
processed data files format and content: Processed files per sample contain difference in methylation percentage at the CpG level between the alternate and reference alleles for each SNPs associated with high confidence ASM (observed in >2 biological samples) if the given sample was informative. The columns include chromosome, start and end of the CpG (reported on positive strand), difference in methylayion percentage and SNP ID. The unique identifier in these files is the CpG coordinate AND SNP ID.

tag: subject id

tag: cancer status

value: non-cancer

tag: organ

value: blood

value: TruSeq DNA Methylation Kit


title: sample_9a_B_cells

description:
Bisulfite-converted DNA
Sample 9a and 9b were bioinformatically pooled for downstream analysis

value: ACCEL-NGS Methyl-Seq DNA Library


title: sample_99_myeloma

description: Bisulfite-converted DNA

value: cancer

value: bone marrow


title: sample_98_myeloma

description: Bisulfite-converted DNA


title: Sample 12_RvD6-isomer

tag: tissue


title: Sample 9_RvD6-standard

source_name: RvD6-standard_Trigeminal ganglia


title: ERRBS_Ctrl_3


title: Sample 10_RvD6-standard


title: Sample 8_RvD6-standard


title: sample_97_myeloma

description: Bisulfite-converted DNA


title: ERRBS_Ctrl_2


title: ERRBS_BPH_18

value: Benign prostatic hyperplasia (BPH)


title: sample_96_GBM

description: Bisulfite-converted DNA

value: brain


title: Sample 7_RvD6-standard


title: ERRBS_BPH_17


title: sample_95_GBM

description: Bisulfite-converted DNA


title: Sample 6_RvD6-standard


title: ERRBS_BPH_16


title: sample_94_GBM

description: Bisulfite-converted DNA


title: ERRBS_Ctrl_1


title: ERRBS_BPH_15


title: sample_92_GBM

description: Bisulfite-converted DNA


title: Sample 4_vehicle

source_name: vehicle_Trigeminal ganglia

value: vehicle


title: sample_91_GBM

description: Bisulfite-converted DNA


title: Sample 3_vehicle


title: ERRBS_BPH_14


title: ERRBS_BPH_13


title: Sample 5_vehicle


title: sample_90_FL

description: Bisulfite-converted DNA

source_name: FL

value: lymph node


title: Sample 2_vehicle


title: ERRBS_BPH_12


title: Sample 1_vehicle


title: sample_89_DLBCL

description: Bisulfite-converted DNA

source_name: DLBCL


title: ERRBS_BPH_11


title: sample_88_DLBCL

description: Bisulfite-converted DNA


title: BPH-18 [prostate transitional zone]

type: genomic

description: BPH

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: not provided

data_processing: Quality control, segmentation and copy number analysis were performed as previously described in TCGA prostate cancer study

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA from BPH and patient matched control samples from blood were analyzed by Affymetrix SNP 6.0 arrays to detect the regions of somatic copy number alteration.

tag: patient diagnosis

value: Benign Prostatic Hyperplasia


title: BPH-18 [blood]

description: control

source_name: blood


title: BPH-16 [prostate transitional zone]

description: BPH

label: BPH


title: BPH-17 [prostate transitional zone]

description: BPH


title: sample_87_T_cells_CD8

description: Bisulfite-converted DNA

source_name: T cells CD8


title: ERRBS_BPH_10


title: BPH-16 [blood]

description: control


title: P8MID3

data_processing:
The Cell Ranger Single-Cell Software Suit (10xGenomics) was used to perform sample demultiplexing, barcode processing and single-cell 3′ gene counting.
The cDNA reads were aligned to the mm10/GRCm38 premRNA reference genome to generated gene-barcode matrix.
R package Seurat was used for downstream quality filtering and data analysis. Potential cell doublets and low quality cells were removed from the data.
Data were normalized and scaled, taken number of genes (nGene) and unique molecular/ identifiers (nUMI) into consideration.
Normalized expression matrix was output from Seurat R object.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text (txt) files of normalized gene expression value for nuclei analyzed; Tab separated value (tsv) files and matrix (mtx) files for filtered gene barcode matrices generated from CellRanger primary analysis from raw sequencing data.

extract_protocol:
Mice were euthanized at 1d or 3d post injury. Ventricle tissues below LAD ligation plane from MI hearts, and ventricle tissues at similar region from sham hearts, were collected for nuclei extraction. Extracted nuclei were stained with cardiac nuclear membrane marker PCM1 antibody and PCM1+ cardiomyocyte nuclei were sorted by FACS.
Sorted cardiomyocyte nuclei were subjected to single nucleus RNA-sequencing using 10xGenomics platform. Library preparation was performed using Single Cell 3’ Reagent Kits v2 (10xGenomics) according to the manufacturer’s protocol.
Single Cell RNA-Seq (Single Nucleus RNA-Seq)

treatment_protocol: Neonatal P1 or P8 mice were subjected to myocardial infarction, induced by permanent ligation of LAD coronary artery, or sham surgery.

tag: surgery performed at developmental age

tag: sample collected at post-surgical day

value: day 3

tag: surgery type

value: MI

tag: cell type

value: cardiomyocytes


title: BPH-15 [blood]

description: control


title: BPH-12 [blood]

description: control


title: ERRBS_BPH_9

value: prostate transitional zone


title: sample_86_T_cells_CD8

description: Bisulfite-converted DNA


title: P8ShamD3

description:
P1_8_ShamCM.txt
P1_8_AllCM.txt

source_name: Cardiomyocyte nuclei isolated from ventricle tissue approximate to below left anterior descending artery ligation plane in age-matched MI samples

value: Sham


title: BPH-11 [blood]

description: control


title: P8ShamD1

description:
P1_8_ShamCM.txt
P1_8_AllCM.txt

value: day 1


title: ERRBS_BPH_8


title: BPH-12 [prostate transitional zone]

description: BPH


title: BPH-17 [blood]

description: control


title: BPH-14 [prostate transitional zone]

description: BPH


title: sample_85_T_cells_CD4

description: Bisulfite-converted DNA

source_name: T cells CD4

value: non-cancer


title: sample_84_T_cells_CD4

description: Bisulfite-converted DNA

value: blood


title: ERRBS_BPH_7


title: P1ShamD3

description:
P1_8_ShamCM.txt
P1_8_AllCM.txt


title: P8MID1


title: sample_83_T_cells_CD4

description: Bisulfite-converted DNA


title: BPH-13 [blood]

description: control


title: P1MID3


title: ERRBS_BPH_5


title: BPH-8 [blood]

description: control


title: BPH-15 [prostate transitional zone]

description: BPH


title: P1ShamD1

description:
P1_8_ShamCM.txt
P1_8_AllCM.txt


title: BPH-10 [blood]

description: control


title: BPH-10 [prostate transitional zone]

description: BPH


title: ERRBS_BPH_4


title: sample_81_T_cells

description: Bisulfite-converted DNA

source_name: T cells


title: BPH-7 [prostate transitional zone]

description: BPH

source_name: prostate transitional zone


title: P1MID1


title: sample_80_T_cells

description: Bisulfite-converted DNA

value: TruSeq DNA Methylation Kit


title: BPH-8 [prostate transitional zone]

description: BPH


title: BPH-9 [blood]

description: control


title: ERRBS_BPH_2


title: sample_8_B_cells

description: Bisulfite-converted DNA

source_name: B cells


title: ERRBS_BPH_3


title: BPH-13 [prostate transitional zone]

description: BPH


title: ERRBS_BPH_1


title: ERRBS_BPH_6


title: sample_7b_B_cells

description:
Bisulfite-converted DNA
Sample 7a and 7b were bioinformatically pooled for downstream analysis
see sample_7_B_cells_diff_cpg_level.txt


title: Patient 53

city: Munich

first: Oliver

last: Weigert

address: Max-Lebsche-Platz 30

country: Germany

institute: Experimental Leukemia and Lymphoma Research

hyb_protocol: See manufacturer's website http://www.nanostring.com

scan_protocol: maschine: NanoString nCounter MAX system; scan protocol: 555 fields of view (FOV)

data_processing: The normalization was performed under default settings in nSolver 4.0 software.

source_name: lymph node_diagnostic_biopsy

label_protocol: NanoString nCounter technology

growth_protocol: formalin-fixed paraffin-embedded tissue

extract_protocol: ExpressArt FFPE Clear RNAready kit (AmpTec) or the AllPrep FFPE (Qiagen)

tag: gender

tag: age

tag: ffs

tag: protein exchange

tag: copy number gain


title: Patient 54


title: HBEC_DBC_4 [miRNA-seq]

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

description: lane4-s027-indexRPI48-TCGGCA-SCT-4H_S27_L004

data_processing:
Cutadapt (version 1.8.1) to trim adapter sequences from single-end reads
The human genome assembly GRCh38.p8 was indexed using bowtie-build (version 0.12.9) for use with Bowtie.
The trimmed reads were aligned to the indexed reference genome using Bowtie (version 0.12.9) using a seed length of 22 nucleotides with no more than two mismatches in the seed and reporting the best alignment to the output.
The aligned reads were then run in featureCounts (version 1.6.0) along with the gff3 annotation file from mirbase.org (Release 22).
The count table produced by featureCounts was used in DESeq2 (version 1.18.1) to calculate differential expression (q<0.05).
Genome_build: GRCh38.p8
Supplementary_files_format_and_content: abundance measurements

growth_protocol: Primary HBEC differentiated on transwell inserts (EpiAirway™ 100, Mattek, Ashland, MA) were transferred to 6-well plates each well containing 1 ml of assay medium and equilibrated for 24 hours at 37°C, 5% CO2 followed by a change of fresh medium before treatment.

extract_protocol:
Total RNA was isolated from HBEC (n=4) using TRizol® reagent and was quantified on a Synergy HTX plate reader equipped with a Take3 module (BioTek).  RNA quality was evaluated based on 260/280 ratio (acceptable range 2.0-2.1) and by examining 18S and 28S peaks (Bioanalyzer 2100, Agilent, Santa Clara, CA). Acceptable RNA quality was based on RIN ≥ 8.5.
TrueSeq Small RNA Library Prep

treatment_protocol: Inserts were washed with phosphate buffered saline (PBS, pH 7.4) and then treated with PAHs in acetone vehicle on apical surface for up to 48 hrs, BAP (500 ug/ml), DBC (10 ug/ml) .

value: primary human 3D bronchial epithelial cells (HBEC)

tag: Stage

value: differentiated at air-liquid interface

tag: treatment

value: Dibenzo[def,p]chrysene


title: sample_7a_B_cells

description:
Bisulfite-converted DNA
Sample 7a and 7b were bioinformatically pooled for downstream analysis

tag: library

value: ACCEL-NGS Methyl-Seq DNA Library


title: BPH-7 [blood]

description: control

tag: subject id


title: Patient 52


title: CYC9-co

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

institute: Institute of hydrobiology, CAS

data_processing:
Adaptors of raw reads were trimmed by Trim-Galore (version 0.4.0)
mRNA-Seq data processing: Trimmed-reads were mapped to the Tetrahymena themophila MAC genome (version 2014: http://ciliate.org/index.php/home/downloads) using TopHat (version 2.0.9).Genes expression values were quantify to the number of fragments per kilobase of exon per million fragments mapped (FPKM) using Cuffdiff (version 2.1.1).
Genome_build: Tetrahymena themophila MAC genome (version 2014: http://ciliate.org/index.php/home/downloads)
Supplementary_files_format_and_content: Reads counts table matrix

organism: Tetrahymena thermophila

source_name: costimulation cells

growth_protocol: Tetrahymena thermophila cells were grown in SPP medium at 30 oC.  For conjugation, log-phase growing cells (~200k cells/ml) of two different mating types were washed, starved (~16 hrs) and mixed in 10 mM Tris buffer (pH 7.4) at 30°C.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols. First strand specific libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kit (RS-122-2101). The Poly-A tailed mRNA as purified using the Sera‐Mag Magnetic Oligo(dT) Beads. The mRNA fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, A tailing, adaptor ligation and PCR amplification were performed according to the stranded mRNA sample preparation guide of the kit.  Sequencing (Single-end (52X1) for C3 and C6, Paired-end (101x2) FOR C10) was performed using an Illumina HiSeq 4000 sequencer (DNA Sequencing Core of University of Michigan).

tag: strain

value: CU427 stimulated by CU428

tag: genotype

value: CYC9 Knock out

value: costimulation


title: BPH-14 [blood]

description: control

value: Benign Prostatic Hyperplasia

tag: tissue


title: HBEC_DBC_3 [miRNA-seq]

description: lane4-s024-indexRPI45-TCATTC-SCT-4G_S24_L004


title: CYC9-S

source_name: Starvation cells

value: Starvation


title: BPH-6 [prostate transitional zone]

description: BPH

tag: patient diagnosis


title: sample_79_T_cells

description: Bisulfite-converted DNA

tag: cancer status

tag: organ


title: Patient 51

value: female


title: sample_82_T_cells_CD4

description: Bisulfite-converted DNA


title: BPH-6 [blood]

description: control


title: sample_77_T_cells

description: Bisulfite-converted DNA


title: HBEC_DBC_2 [miRNA-seq]

description: lane4-s021-indexRPI42-TAATCG-SCT-4F_S21_L004


title: HBEC_DBC_1 [miRNA-seq]

description: lane4-s018-indexRPI39-CTATAC-SCT-4E_S18_L004


title: CDK19-co

value: CDK19 Knock out


title: sample_75_T_cells

description: Bisulfite-converted DNA


title: sample_72_T_cells

description: Bisulfite-converted DNA


title: Patient 48


title: HBEC_BAP_4 [miRNA-seq]

description: lane4-s026-indexRPI47-TCGAAG-SCT-3H_S26_L004

value: Benzo[a]pyrene


title: HBEC_BAP_2 [miRNA-seq]

description: lane4-s020-indexRPI41-GACGAC-SCT-3F_S20_L004


title: HBEC_BAP_3 [miRNA-seq]

description: lane4-s023-indexRPI44-TATAAT-SCT-3G_S23_L004


title: WT-S

value: WT


title: Patient 46


title: BPH-11 [prostate transitional zone]

description: BPH

value: prostate transitional zone


title: Patient 47

value: male


title: sample_71_T_cells

description: Bisulfite-converted DNA

value: non-cancer

value: blood


title: HBEC_BAP_1 [miRNA-seq]

description: lane4-s017-indexRPI38-CTAGCT-SCT-3E_S17_L004

value: primary human 3D bronchial epithelial cells (HBEC)


title: Patient 50


title: EdU+_WT

city: Zürich

first: Baptiste

middle: N

last: Jaeger

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zürich

description: animals were i.p. injected with EdU (100mg/kg) twice daily for 3 days. On day 4, hippocampal nuclei were isolated, stained using Click-it plus EdU-A647 Flow Cytometry Assay kit (Invitrogen Cat#C10635), and sorted by flow cytometry.

data_processing:
Reads were trimmed with Trimmomatic version 0.36 (2 bases were hard-trimmed from the start; adapter trimming was done at the end).
Trimmed reads were aligned to the Mus musculus reference genome and transcriptome (GRCm38.p5 Ensembl release 89) with STAR version 2.5.3a.
Read quantification was done using the R/Bioconductor package Rsubread version 1.28.1.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Tab-delimited text files showing raw read counts for each cell (columns) and each gene (rows). Each file corresponds to individual sample.

source_name: hippocampus

extract_protocol:
Flow cytometry sorting of single nuclei isolated from the mouse hippocampus (Lacar et al., Nat. Comm., 2016, PMID:27090946)
SmartSeq2 protocol (Picelli et al., Nat. Protoc., 2014, PMID:24385147)

tag: marker

value: EdU+

value: 8.5 month old

tag: genotype/variation


title: sample_69_T_cells

description: Bisulfite-converted DNA

value: ACCEL-NGS Methyl-Seq DNA Library


title: Patient 45

tag: gender


title: HBEC_VehCon_4 [miRNA-seq]

description: lane4-s025-indexRPI46-TCCCGA-SCT-1H_S25_L004

tag: cell type

value: differentiated at air-liquid interface

value: Acetone


title: Patient 44

tag: age

tag: ffs


title: sample_64_lymph_node

description: Bisulfite-converted DNA

source_name: lymph node

value: lymph node


title: BPH-5 [blood]

description: control

value: Benign Prostatic Hyperplasia


title: NeuN+_Fasn-R1812W

description: single hippocampal nuclei were stained with anti-NeuN-A488 antibodies (EMD Millipore, MAB377X) and sorted by flow cytometry.

value: NeuN+


title: HBEC_VehCon_3 [miRNA-seq]

description: lane4-s022-indexRPI43-TACAGC-SCT-1G_S22_L004


title: sample_59_PBL

description: Bisulfite-converted DNA

source_name: PBL


title: BPH-4 [prostate transitional zone]

description: BPH


title: BPH-3 [blood]

description: control


title: HBEC_VehCon_1 [miRNA-seq]

description: lane4-s016-indexRPI37-CGGAAT-SCT-1E_S16_L004


title: sample_63_cytotrophoblast

description: Bisulfite-converted DNA

source_name: cytotrophoblast

value: placenta


title: NeuN+_WT


title: HBEC_VehCon_2 [miRNA-seq]

description: lane4-s019-indexRPI40-CTCAGA-SCT-1F_S19_L004


title: sample_58_PBL

description: Bisulfite-converted DNA


title: sample_51a_neurons

description:
Bisulfite-converted DNA
Sample 51a and 51b were bioinformatically pooled for downstream analysis

source_name: neurons

value: brain


title: Patient 41

value: female

tag: protein exchange

tag: copy number gain


title: BPH-1 [prostate transitional zone]

description: BPH


title: sre1∆_pH8, 4

city: Durham

first: J

middle: Andrew

last: Alspaugh

state: NC

address: 337 Sands Research Building, 303 Research Drive, DUMC 102359

department: Molecular Genetics and Microbiology

institute: Duke University

description:
sre1∆
22_2019_P_M1_S22_sort_dedup

data_processing:
Quality control was assessed by FastQC.
RNA-Seq reads were trimmed for adaptor sequences and filtered using "fastq-mcf" with the following parameters: -q 20 , -x 0.5.  Trimmed and filtered reads were aligned to the C. neoformans H99 genome using "STAR" with the following parameters: --quantMode GeneCounts, --alignIntronMax 5000, --outSJfilterIntronMaxVsReadN 500 1000 2000.
Bam files were sorted, indexed, and merged using "Samtools". Duplicate reads were removed from bam files using "picard".
Differential expression analyses were performed in R using an RNA‐Seq Bioconductor (Love 2015, F1000Research) workflow followed by the DESeq2 package with a false discovery rate (FDR) of 5% (Love 2014, Genome Biol).
Genome_build: CNA3.44
Supplementary_files_format_and_content: raw counts

organism: Cryptococcus neoformans

source_name: Vegetative fungal cells

growth_protocol: H99 and sre1∆ cells were incubated at 30°C with 150 rpm shaking in YPD media to mid-logarithmic growth phase.

extract_protocol:
All cells were pelleted, flash frozen on dry ice, and lyophilized overnight. RNA was isolated using the Qiagen RNeasy Plant Minikit with  optional  on  column DNase  digestion  (Qiagen, Valencia, CA). RNA concentration and quality were measured using the Agilent 2100 Bioanalyzer.
The NEBNext Poly(A) mRNA Magnetic Isolation Module was used to enrich for mRNA and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to prepare libraries (New England Biolabs, Ipswich, MA). Libraries were sequenced on the Illumina NextSeq 500 with 75 base pair, single-end reads.

treatment_protocol: Approximately 1x10^9 cells from each strain were pelleted and resuspended in YPD media buffered to pH4 or pH8 and incubated at 30°C for 90 minutes with 150 rpm shaking.

tag: condition

tag: replicate


title: BPH-2 [prostate transitional zone]

description: BPH

tag: subject id


title: HBEC_DBC_3

description: lane1-s015-indexRPI15-ATGTCA-SCT-4C_S15_L001

data_processing:
Cutadapt (version 1.8.1) to trim adapter sequences from the paired-end reads
The human genome assembly GRCh38.84 was indexed using bowtie2-build (version 2.2.3)
TopHat (version 2.1.1.) was used to index the transcriptome and to align the trimmed reads to indexed transcriptome and genome.
Differential expression (q<0.05) was determined in CuffDiff (version 2.2.1) compared to vehicle control.
Genome_build: GRCh38.84
Supplementary_files_format_and_content: abudance measurements

extract_protocol:
Total RNA was isolated from HBEC (n=4) using TRizol® reagent and was quantified on a Synergy HTX plate reader equipped with a Take3 module (BioTek).  RNA quality was evaluated based on 260/280 ratio (acceptable range 2.0-2.1) and by examining 18S and 28S peaks (Bioanalyzer 2100, Agilent, Santa Clara, CA). Acceptable RNA quality was based on RIN ≥ 8.5.
mRNA was poly-A selected, and libraries were prepared with the PrepXTM mRNA and Illumina sequencing workflow (Wafergen Biosystems, Fremont, CA).

tag: Stage

tag: treatment

value: Dibenzo[def,p]chrysene


title: BPH-4 [blood]

description: control

tag: tissue


title: sre1∆_pH8, 5

description:
sre1∆
23_2019_P_M1_S23_sort_dedup

tag: genotype


title: HBEC_DBC_4

description: lane1-s016-indexRPI16-CCGTCC-SCT-4D_S16_L001


title: WT-co

tag: strain

value: CU427 stimulated by CU428

value: WT

value: costimulation


title: Patient 39

value: male


title: HBEC_DBC_2

description: lane1-s014-indexRPI14-AGTTCC-SCT-4B_S14_L001

value: primary human 3D bronchial epithelial cells (HBEC)


title: Patient 38


title: EdU+_Fasn-R1812W

value: EdU+


title: sre1∆_pH8, 2

description:
sre1∆
20_2019_P_M1_S20_sort_dedup


title: sample_50a_neurons

description:
Bisulfite-converted DNA
Sample 50a and 50b were bioinformatically pooled for downstream analysis

tag: cancer status

value: non-cancer

tag: organ

tag: library


title: BPH-3 [prostate transitional zone]

description: BPH

tag: patient diagnosis

value: prostate transitional zone


title: BPH-1 [blood]

description: control

value: blood


title: sre1∆_pH8, 3

description:
sre1∆
21_2019_P_M1_S21_sort_dedup


title: BPH-5 [prostate transitional zone]

description: BPH


title: sre1∆_pH8, 1

description:
sre1∆
19_2019_P_M1_S19_sort_dedup


title: Patient 43

tag: gender


title: HBEC_DBC_1

description: lane1-s013-indexRPI13-AGTCAA-SCT-4A_S13_L001

tag: cell type

value: differentiated at air-liquid interface


title: sample_5_liver

description: Bisulfite-converted DNA

source_name: liver

value: liver

value: ACCEL-NGS Methyl-Seq DNA Library


title: Patient 37

tag: age

tag: ffs


title: sample_50b_neurons

description:
Bisulfite-converted DNA
Sample 50a and 50b were bioinformatically pooled for downstream analysis
see sample_50_neurons_diff_cpg_level.txt

value: TruSeq DNA Methylation Kit


title: Patient 36

tag: protein exchange

tag: copy number gain


title: H99_pH8, 6

tag: condition

tag: replicate


title: HBEC_BAP_3

description: lane1-s011-indexRPI11-GGCTAC-SCT-3C_S11_L001

tag: Stage

value: Benzo[a]pyrene


title: HBEC_BAP_4

description: lane1-s012-indexRPI12-CTTGTA-SCT-3D_S12_L001

tag: treatment


title: HBEC_BAP_1

description: lane1-s009-indexRPI9-GATCAG-SCT-3A_S9_L001


title: sample_46_glial_cells

description: Bisulfite-converted DNA

source_name: glial cells

tag: subject id

value: brain


title: H99_pH8, 3

tag: genotype


title: H99_pH8, 4


title: H99_pH8, 5


title: Patient 35

value: female


title: sample_44_monocytes

description: Bisulfite-converted DNA

source_name: monocytes


title: sample_45_monocytes

description: Bisulfite-converted DNA


title: H99_pH8, 2


title: sample_49_glial_cells

description: Bisulfite-converted DNA


title: HBEC_VehCon_4

description: lane1-s004-indexRPI4-TGACCA-SCT-1D_S4_L001

value: Acetone


title: sample_43_monocytes

description: Bisulfite-converted DNA


title: Patient 49


title: HBEC_BAP_2

description: lane1-s010-indexRPI10-TAGCTT-SCT-3B_S10_L001


title: Patient 31


title: H99_pH8, 1


title: Patient 34


title: Patient 33


title: HBEC_VehCon_2

description: lane1-s002-indexRPI2-CGATGT-SCT-1B_S2_L001


title: sre1∆_pH4, 6

description:
sre1∆
12_2019_P_M1_S12_sort_dedup


title: sample_41_mammary_epith_cells

description: Bisulfite-converted DNA

source_name: mammary epith cells

value: breast cell line


title: sre1∆_pH4, 4

description:
sre1∆
10_2019_P_M1_S10_sort_dedup


title: HBEC_VehCon_1

description: lane1-s001-indexRPI1-ATCACG-SCT-1A_S1_L001


title: BPH-9 [prostate transitional zone]

description: BPH

value: Benign Prostatic Hyperplasia

tag: tissue


title: sre1∆_pH4, 5

description:
sre1∆
11_2019_P_M1_S11_sort_dedup


title: Patient 29


title: sample_40_mammary_epith_cells

description: Bisulfite-converted DNA

tag: cancer status


title: sample_39_mammary_epith_cells

description: Bisulfite-converted DNA

tag: organ


title: Patient 32


title: HBEC_VehCon_3

description: lane1-s003-indexRPI3-TTAGGC-SCT-1C_S3_L001


title: BPH-2 [blood]

description: control

source_name: blood


title: Patient 27


title: sre1∆_pH4, 3

description:
sre1∆
9_2019_P_M1_S9_sort_dedup


title: sample_42_monocytes

description: Bisulfite-converted DNA

tag: library


title: Patient 30


title: PooledAnimals_Treated_14d_rep3

city: Beijing

first: Qianqian

last: Zhang

state: (Click to Select US State)

address: Shuangqing Road

institute: Research Center for Eco-Environmental Sciences

description: Gene expression after 14d in F. candida exposed to BDE209

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat. No. 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat. No. G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat. No. 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat. No. 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat. No. G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

organism: Folsomia candida

source_name: Pooled animals, treated, 14d, replicate 3

label_protocol: Total RNA was amplified and labeled using Low Input Quick Amp Labeling Kit (One color, Cat. No. 5190-2305, Agilent technologies, USA) following the manufacturer’s instructions.

growth_protocol: The springtail Folsomia candida was cultured in Petri dishes on a moistened substrate consisting of plaster of Paris and activated carbon (9:1 weight ratio) under controlled conditions (20±1℃, 70±5% relative humidity and constant darkness).

extract_protocol: Total RNA of each replicate (30 animals) was extracted using RNAiso Plus (Cat. No. 9109, TAKARA, Japan). RNA integrity was inspected by Agilent Bioanalyzer 2100 (Agilent technologies, USA).

treatment_protocol: Thirty adult springtails (23-day old) were exposed to BDE209-polluted soil (0.81 mg/kg dry soil) or solvent control soil for 2, 7 or 14 days.

tag: life stage

value: adult

tag: time point


title: sre1∆_pH8, 6

description:
sre1∆
24_2019_P_M1_S24_sort_dedup


title: PooledAnimals_Treated_14d_rep2

source_name: Pooled animals, treated, 14d, replicate 2

value: BDE209-polluted soil (0.81 mg/kg dry soil)


title: sample_38_macrophages_type_2

description: Bisulfite-converted DNA

source_name: macrophages type 2


title: sre1∆_pH4, 2

description:
sre1∆
8_2019_P_M1_S8_sort_dedup


title: Patient 26

source_name: lymph node_diagnostic_biopsy

tag: gender

value: male


title: sample_37_macrophages_type_1

description: Bisulfite-converted DNA

source_name: macrophages type 1


title: sre1∆_pH4, 1

description:
sre1∆
7_2019_P_M1_S7_sort_dedup


title: PooledAnimals_Treated_14d_rep1

source_name: Pooled animals, treated, 14d, replicate 1

tag: age


title: Patient 42

tag: ffs


title: Patient 28

tag: protein exchange


title: Patient 25

tag: copy number gain


title: sample_31_breast

description: Bisulfite-converted DNA

source_name: breast

value: breast (primary tissue)


title: PooledAnimals_Treated_7d_rep3

description: Gene expression after 7d in F. candida exposed to BDE209

source_name: Pooled animals, treated, 7d, replicate 3


title: sample_36_GM12878_LCL

description: Bisulfite-converted DNA

source_name: GM12878 LCL

value: lymphoblastoid

value: cell line


title: Patient 24


title: H99_pH4, 5

tag: condition


title: PooledAnimals_Treated_7d_rep2

source_name: Pooled animals, treated, 7d, replicate 2


title: sample_3_liver

description: Bisulfite-converted DNA

value: non-cancer


title: Patient 23


title: sample_23_brain

description: Bisulfite-converted DNA

source_name: brain


title: PooledAnimals_Treated_7d_rep1

source_name: Pooled animals, treated, 7d, replicate 1


title: H99_pH4, 4

source_name: Vegetative fungal cells

tag: replicate


title: H99_pH4, 2


title: H99_pH4, 3


title: Patient 22


title: sample_20_brain

description: Bisulfite-converted DNA


title: Patient 20


title: PooledAnimals_Treated_2d_rep3

description: Gene expression after 2d in F. candida exposed to BDE209

source_name: Pooled animals, treated, 2d, replicate 3


title: sample_62_placenta

description: Bisulfite-converted DNA

source_name: placenta

value: placenta


title: H99_pH4, 1


title: H99_pH4, 6


title: PooledAnimals_Treated_2d_rep2

source_name: Pooled animals, treated, 2d, replicate 2


title: PooledAnimals_Treated_2d_rep1

source_name: Pooled animals, treated, 2d, replicate 1


title: Patient 19


title: sample_17_bladder_epith_cells

description: Bisulfite-converted DNA

source_name: bladder epith cells

value: bladder cell line


title: sample_2_liver

description: Bisulfite-converted DNA

source_name: liver

value: liver

value: ACCEL-NGS Methyl-Seq DNA Library


title: PooledAnimals_Control_14d_rep3

description: Gene expression after 14d in F. candida in control group

source_name: Pooled animals, control, 14d, replicate 3

value: solvent control soil


title: sample_22_brain

description: Bisulfite-converted DNA

value: brain

value: TruSeq DNA Methylation Kit


title: sample_16_bladder_epith_cells

description: Bisulfite-converted DNA


title: PooledAnimals_Control_14d_rep2

source_name: Pooled animals, control, 14d, replicate 2


title: Patient 21

source_name: lymph node_diagnostic_biopsy

value: female


title: Patient 16


title: Patient 40


title: PooledAnimals_Control_14d_rep1

source_name: Pooled animals, control, 14d, replicate 1


title: F26_72_1

city: Taian

first: shan

last: feng

address: Daizong Avenue

department: Forestry College

institute: Shandong Agricultural University

data_processing:
FASTQC (v 0.11.5) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). was used to assess the quality of raw sequence data and Trimmomatic was used to filter low-quality reads
The previously published genome database the J. regia genome sequence (https://www.ncbi.nlm.nih.gov/genome/?term=Juglans%20regia) was used as reference genome to map the high-quality reads by using HISAT (version 0.11.5) with default parameters
Stringtie (v 1.3.1) was used to assemble the aligned reads for all sample into transcripts
StringTie-Merge to combine the StringTie assembly results of each sample and the gene expression (FPKM) was calculated using StringTie's own script prepDE.py
The differently expressed genes (DEGs) were identified by using DESeq2 (version 1.22.1)
Genome_build: https://www.ncbi.nlm.nih.gov/genome/?term=Juglans%20regia

organism: Juglans regia

source_name: The anthracnose-resistant F26 fruits samples at 72 hour during infection proces

growth_protocol: Walnut trees (Juglans regia L.) of the anthracnose-resistant clone B26 and the clone 4-23 were grown at the Forestry Experimental Station of Shandong Agricultural University, Tai’an, Shandong Province, China (N36°10′ 19.2″, E117°09′ 1.3″). The fruits of 4-23 clone (i.e., F423 fruits) and B26 clone (i.e., F26 fruits) were used as experimental materials. Colletotrichum gloeosporioides m9 isolates (GenBank ID: GU597322) used in this study were maintained by our group.

extract_protocol:
Total RNA was extracted from F423 and F26 samples with the Thermo Gene JET Plant RNA Purification Mini Kit (Thermo Fisher Scientific Inc., USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: tissues at 0 hpi, pathological tissues at 24 hpi, 48 hpi, 72 hpi, and distal uninoculated tissues at 120 hpi of F26 and F423  fruit bracts

tag: strain

value: Juglans regia clone B26

value: fruit sample


title: F26_120_2

source_name: The anthracnose-resistant F26 fruits samples at 120 hour during infection proces


title: F26_72_2


title: Patient 15


title: sample_15_B_cells

description: Bisulfite-converted DNA

source_name: B cells

extract_protocol:
DNA extracted using phenol-chloroform protocol after RNAse treatment. DNA was bisulfite converted with the EZ DNA methylation kit (Zymo).
For Nextera transposase-based library approach, genomic DNA was first tagmented using Nextera XT transposome and end repair was performed using 5mC. After bisulfite conversion, Illumina adapters and custom bisulfite converted adapters are attached by limited cycle PCR. Illumina TruSeq DNA Methylation Kit and ACCEL-NGS Methyl-Seq DNA Library kit were used according to the manufacturer’s instructions.

value: blood


title: F26_120_1


title: Patient 14


title: sample_14_B_cells

description: Bisulfite-converted DNA


title: F26_48_2

source_name: The anthracnose-resistant F26 fruits samples at 48 hour during infection proces


title: PooledAnimals_Control_7d_rep2

description: Gene expression after 7d in F. candida in control group

source_name: Pooled animals, control, 7d, replicate 2

value: adult

tag: treatment


title: F26_48_1


title: sample_13_B_cells

description: Bisulfite-converted DNA

tag: subject id


title: PooledAnimals_Control_7d_rep3

source_name: Pooled animals, control, 7d, replicate 3


title: Patient 17

value: male


title: sample_12_B_cells

description: Bisulfite-converted DNA


title: Patient 13


title: Patient 18


title: PooledAnimals_Control_7d_rep1

source_name: Pooled animals, control, 7d, replicate 1


title: F26_24_2

source_name: The anthracnose-resistant F26 fruits samples at 24 hour during infection proces


title: PooledAnimals_Control_2d_rep3

description: Gene expression after 2d in F. candida in control group

source_name: Pooled animals, control, 2d, replicate 3


title: Patient 12


title: sample_11_B_cells

description: Bisulfite-converted DNA


title: F26_24_1


title: sample_102_myeloma

description: Bisulfite-converted DNA

source_name: myeloma

value: cancer

value: bone marrow


title: CDK19-S

source_name: Starvation cells

tag: genotype

value: CDK19 Knock out

value: Starvation


title: PooledAnimals_Control_2d_rep2

source_name: Pooled animals, control, 2d, replicate 2


title: sample_101_myeloma

description: Bisulfite-converted DNA


title: F26_0_1

source_name: The anthracnose-resistant F26 fruits samples at 0 hour during infection proces

tag: tissue


title: S_7_2

city: Changchun

first: Lei

address: 4888 Shengbei Street

institute: Northeast Institute of Geography and Agroecology, CAS

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) 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.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Beta vulgaris

source_name: roots_treated_7 days

extract_protocol:
Total RNA was extracted using Total RNA Purification Kit, TRK1001 (LC Science, Houston, TX) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.Approximately 10 ug of total RNArepresenting a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature.
Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeqsample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-endlibraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (LC Sceiences, USA) following the vendor’s recommended protocol.

tag: developmental stage

value: Seedling stage

tag: treatment group

value: treated 7 days

value: fresh roots


title: PooledAnimals_Control_2d_rep1

source_name: Pooled animals, control, 2d, replicate 1


title: F26_0_2


title: F423_120_2

source_name: the anthracnose-susceptible F423 fruits samples at 120 hour during infection proces

value: Juglans regia clone 4-23


title: F423_120_1


title: S_7_1


title: CK_7_3

source_name: roots_control_7 days

value: control for 7 days


title: S_7_3


title: sample_100_myeloma

first: Benjamin

address: 40 prospect avenue

institute: HUMC

description: Bisulfite-converted DNA

tag: cancer status

tag: organ

tag: library

value: ACCEL-NGS Methyl-Seq DNA Library


title: Patient 8

source_name: lymph node_diagnostic_biopsy

tag: gender


title: Patient 9

tag: age


title: F423_72_2

source_name: the anthracnose-susceptible F423 fruits samples at 72 hour during infection proces


title: Patient 10

tag: ffs


title: Patient 11

tag: protein exchange


title: CK_7_2


title: RNA-seq+tet+3-NPA

source_name: Human B lymphocyte P493-6 cells

tag: cell type

value: B lymphocyte cells

tag: cell line


title: sample_1_breast

description: Bisulfite-converted DNA

source_name: breast

value: non-cancer

value: breast (primary tissue)


title: Patient 6

value: female

tag: copy number gain


title: CK_7_1


title: Patient 5


title: RNA-seq+tet+PBS

value: +tet+PBS


title: F423_72_1

tag: strain

value: fruit sample


title: F423_48_2

source_name: the anthracnose-susceptible F423 fruits samples at 48 hour during infection proces


title: S_1_3

source_name: roots_treated_1 day

value: treated 1 day


title: RNA-seq-tet+3-NPA

tag: treatment


title: S_1_2


title: RNA-seq-tet+PBS

value: -tet+PBS


title: S_1_1


title: F423_48_1


title: Patient 4

value: male


title: RNA-seq+tet+DMS

value: +tet+DMS


title: F423_24_2

source_name: the anthracnose-susceptible F423 fruits samples at 24 hour during infection proces


title: CK_1_3

source_name: roots_control_1 day

value: control for 1 day


title: Patient 7


title: Patient 2


title: F423_24_1


title: Patient 1


title: CK_1_2

value: Seedling stage


title: F423_0_2

source_name: the anthracnose-susceptible F423 fruits samples at 0 hour during infection proces


title: RNA-seq+tet-DMS

value: +tet-DMS


title: RNA-seq-tet+DMS

value: -tet+DMS


title: F423_0_1

value: Juglans regia clone 4-23


title: CK_1_1

value: fresh roots


title: RNA-seq-tet-DMS

value: -tet-DMS