title: Mouse_116_homo_dim (E6_Guang_GL9989-2)

description: E6_Guang_GL9989-2-ACTGAGCG-TATGCAGT_S160


title: Mouse_116_homo_bright (G2_Guang_GL9989-2)

status: Public on Apr 13 2021

type: SRA

city: Pittsburgh

first: guang

last: li

state: PA

address: 530 45th St. 8116 Rangos Research Center

country: USA

institute: university of pittsburgh

description: G2_Guang_GL9989-2-CGTACTAG-TCTTACGC_S171

library_source: transcriptomic

data_processing:
The data were demultiplexed based on barcode sequences using Illumina sorfware  bcl2fastq
The fastq files were aligned to the reference sequences consisting of mouse genome, eGFP, and human Bag3 transcript sequences using STAR2.7.0f with the default parameters, and gene expression counts were calculated using STAR “–quantMode GeneCounts” parameter.
Supplementary_files_format_and_content: Gene_expression_counts_matrix.csv

molecule: total RNA

organism: Mus musculus

source_name: mouse cardiomyocyte

growth_protocol: The transgenic PGKcre:BAG3P209L mice were generated through overxpression of a mutated BAG3.

extract_protocol:
Cardiomyocytes (CMs) were isolated from hearts using Langendorff system and picked up using hand pippete.
The mRNA in single CMs were isolatedy following the SMART-seq2 protocol.
The single cell libraries were made by following the SMART-seq 2 protocol. The cells with low amount of cDNA were excluded for library preparations. Different barcodes were used to label each single cell for multiplexing purpose when generating the libraries and demultiplexing during analysis.

tag: strain

tag: genotype

tag: cell type

value: cardiomyocyte (CM)


title: Mouse_116_homo_bright (E4_Guang_GL9989-2)

description: E4_Guang_GL9989-2-TAGCGCTC-TATGCAGT_S158


title: Mouse_116_homo_bright (E1_Guang_GL9989-2)

description: E1_Guang_GL9989-2-TAGGCATG-TATGCAGT_S155


title: Mouse_116_homo_bright (E2_Guang_GL9989-2)

description: E2_Guang_GL9989-2-ATGCGCAG-TATGCAGT_S156


title: Mouse_116_homo_bright (E3_Guang_GL9989-2)

description: E3_Guang_GL9989-2-CTCTCTAC-TATGCAGT_S157


title: Mouse_116_homo_dim (D7_Guang_GL9989-2)

description: D7_Guang_GL9989-2-GGACTCCT-TATGCAGT_S153


title: Mouse_116_homo_dim (D6_Guang_GL9989-2)

description: D6_Guang_GL9989-2-CGGAGCCT-TATGCAGT_S152


title: Mouse_116_homo_bright (D4_Guang_GL9989-2)

description: D4_Guang_GL9989-2-GCGTAGTA-TATGCAGT_S150


title: Mouse_116_homo_dim (F6_Guang_GL9989-2)

description: F6_Guang_GL9989-2-TCGACGTC-TATGCAGT_S168


title: Mouse_116_homo_bright (D2_Guang_GL9989-2)

description: D2_Guang_GL9989-2-GGAGCTAC-TATGCAGT_S148


title: Mouse_116_homo_bright (D3_Guang_GL9989-2)

description: D3_Guang_GL9989-2-AGGCAGAA-TATGCAGT_S149


title: Mouse_116_homo_dim (C5_Guang_GL9989-2)

description: C5_Guang_GL9989-2-TAAGGCGA-TATGCAGT_S145


title: Mouse_116_homo_dim (C8_Guang_GL9989-2)

description: C8_Guang_GL9989-2-ACTCGCTA-TATGCAGT_S146


title: Mouse_116_homo_bright (D1_Guang_GL9989-2)

description: D1_Guang_GL9989-2-CGTACTAG-TATGCAGT_S147


title: Mouse_116_homo_bright (C4_Guang_GL9989-2)

description: C4_Guang_GL9989-2-TCGACGTC-ACTCTAGG_S144


title: Mouse_116_homo_bright (C3_Guang_GL9989-2)

description: C3_Guang_GL9989-2-ATCTCAGG-ACTCTAGG_S143


title: Mouse_116_homo_bright (C1_Guang_GL9989-2)

description: C1_Guang_GL9989-2-GCTCATGA-ACTCTAGG_S141


title: Mouse_116_homo_bright (C2_Guang_GL9989-2)

description: C2_Guang_GL9989-2-TGCAGCTA-ACTCTAGG_S142


title: Mouse_116_homo_dim (B8_Guang_GL9989-2)

description: B8_Guang_GL9989-2-CGATCAGT-ACTCTAGG_S140


title: Mouse_116_homo_dim (B7_Guang_GL9989-2)

description: B7_Guang_GL9989-2-GTAGAGGA-ACTCTAGG_S139


title: Mouse_116_homo_dim (E5_Guang_GL9989-2)

description: E5_Guang_GL9989-2-CGAGGCTG-TATGCAGT_S159


title: Mouse_116_homo_dim (B6_Guang_GL9989-2)

description: B6_Guang_GL9989-2-CCTAAGAC-ACTCTAGG_S138


title: Mouse_116_homo_dim (B5_Guang_GL9989-2)

description: B5_Guang_GL9989-2-AAGAGGCA-ACTCTAGG_S137


title: Mouse_116_homo_bright (B4_Guang_GL9989-2)

description: B4_Guang_GL9989-2-ACTGAGCG-ACTCTAGG_S136


title: Mouse_116_homo_bright (B2_Guang_GL9989-2)

description: B2_Guang_GL9989-2-TAGCGCTC-ACTCTAGG_S134


title: Mouse_116_homo_dim (D5_Guang_GL9989-2)

description: D5_Guang_GL9989-2-TCCTGAGC-TATGCAGT_S151


title: Mouse_116_homo_bright (B1_Guang_GL9989-2)

description: B1_Guang_GL9989-2-CTCTCTAC-ACTCTAGG_S133


title: Mouse_116_homo_dim (A7_Guang_GL9989-2)

description: A7_Guang_GL9989-2-ATGCGCAG-ACTCTAGG_S132


title: Mouse_116_homo_dim (A6_Guang_GL9989-2)

description: A6_Guang_GL9989-2-TAGGCATG-ACTCTAGG_S131


title: Mouse_116_homo_dim (D8_Guang_GL9989-2)

description: D8_Guang_GL9989-2-TACGCTGC-TATGCAGT_S154


title: Mouse_116_homo_bright (A1_Guang_GL9989-2)

description: A1_Guang_GL9989-2-GCGTAGTA-ACTCTAGG_S126


title: Mouse_73_wt (H9_Guang_GL9989-1)

description: H9_Guang_GL9989-1-AGGCAGAA-ACTCTAGG_S125

value: control


title: Mouse_72_het_dim (H6_Guang_GL9989-1)

description: H6_Guang_GL9989-1-CGTACTAG-ACTCTAGG_S123


title: Mouse_72_het_bright (H4_Guang_GL9989-1)

description: H4_Guang_GL9989-1-ACTCGCTA-ACTCTAGG_S122


title: Mouse_72_het_dim (H8_Guang_GL9989-1)

description: H8_Guang_GL9989-1-GGAGCTAC-ACTCTAGG_S124


title: Mouse_116_homo_bright (A3_Guang_GL9989-2)

description: A3_Guang_GL9989-2-CGGAGCCT-ACTCTAGG_S128


title: Mouse_116_homo_bright (A4_Guang_GL9989-2)

description: A4_Guang_GL9989-2-GGACTCCT-ACTCTAGG_S129


title: Mouse_72_het_bright (H3_Guang_GL9989-1)

description: H3_Guang_GL9989-1-TAAGGCGA-ACTCTAGG_S121


title: Mouse_72_het_bright (H2_Guang_GL9989-1)

description: H2_Guang_GL9989-1-TCGACGTC-CTCCTTAC_S120


title: Mouse_72_het_bright (H1_Guang_GL9989-1)

description: H1_Guang_GL9989-1-ATCTCAGG-CTCCTTAC_S119


title: LAT

city: Kyoto

first: Satoshi

last: Okubo

address: Yamashina-ku

country: Japan

institute: Nippon Shinyaku Co., Ltd.

data_processing:
cDNA libraries were sequenced by using Illumina HiSeq 2500.
Adapter sequences were removed by using cutadapt1.1.
Low quality sequences were removed by using trimmomatic0.32. Low quality sequences (read with ambiguous bases ‘N’), reads with Q-value < 20 bases, and sequences smaller than 50 were eliminated.
The high quality reads were assembled into contigs using Trinity2.11.
Transcript levels were quantified by using align_and_estimate_abundance.pl command in Trinity. Expression values were calculated by Bowtie1.12 and RSEM included in Trinity package.
CD-Hit (cd-hit-est) was used for clustering with the option of threshold (-c) 0.9 in order to obtain unigenes.
Using unigene sequence, we researched common genes which had highly similarities with the fruits of C. latifolia and C. capitulata each other. The BLASTn search were performed with E-values 1e-5 for transcripts of the fruits each other followed by selecting by tophit.
All assembled data by Trinity were annotaed by NCBI nr, RefSeq, Uni-prot, and COG databases by using blastx with -max_target_seqs 1,  -evalue 1e-05, and -outfmt "6 qseqid sseqid stitle pident length mismatch gapopen qstart qend sstart send evalue bitscore sseq" options.
Functions of assembled transcripts were classified using Gene Ontology (GO). We analyzed BLASTx with transcripts against Nr database and performed with Blast2GO.
Genome_build: reference sequence used for read alignment
Supplementary_files_format_and_content: excel file include pident, length, mismatch, gapopen, qstart, qend, sstart, send, evalue, and bitscore.

organism: Molineria latifolia

source_name: fruit

growth_protocol: C. latifolia and C. capitulata were cultivated in the greenhouse of the Yamashina Botanical Research Institute. Greenhouse were mainteined over 19 °C by electric heater.

extract_protocol:
Fruits were stored in -80 ºC until used. The samples were broken into powder in liquid nitrogen prior to extract the RNA. Total RNA was extracted from the frozen powder by the phenol-SDS method, and the poly(A)+mRNA was purified using an mRNA Purification Kit (Amersham Biosciences).
cDNA library was generated by TruSeq RNA Sample Prep Kit v2 (Illumina, Inc.).

treatment_protocol: Flowers of C. latifolia were pollinated by hands at the morning of flowering day. Those of C. capitulata were taken 50 ppm of 1-naphthylacetic acid (NAA) at the morning of both the first and the second flowering day. After about 60 days after flowering, mature fruits were harvested and immediately soaked in RNA laterTM solution (Thermo Fischer Scientific).

tag: developmental stage

value: mature fruit


title: Mouse_73_wt (G11_Guang_GL9989-1)

description: G11_Guang_GL9989-1-TGCAGCTA-CTCCTTAC_S118


title: Mouse_72_het_dim (G7_Guang_GL9989-1)

description: G7_Guang_GL9989-1-CGATCAGT-CTCCTTAC_S116


title: CAP

organism: Molineria capitulata


title: Mouse_116_homo_bright (B3_Guang_GL9989-2)

description: B3_Guang_GL9989-2-CGAGGCTG-ACTCTAGG_S135


title: Mouse_72_het_bright (G4_Guang_GL9989-1)

description: G4_Guang_GL9989-1-AAGAGGCA-CTCCTTAC_S113


title: Mouse_116_homo_dim (A5_Guang_GL9989-2)

description: A5_Guang_GL9989-2-TACGCTGC-ACTCTAGG_S130


title: Mouse_72_het_dim (G6_Guang_GL9989-1)

description: G6_Guang_GL9989-1-GTAGAGGA-CTCCTTAC_S115


title: Mouse_72_het_bright (G2_Guang_GL9989-1)

description: G2_Guang_GL9989-1-CGAGGCTG-CTCCTTAC_S111


title: Mouse_116_homo_bright (A2_Guang_GL9989-2)

description: A2_Guang_GL9989-2-TCCTGAGC-ACTCTAGG_S127


title: Cd_Rob1_hom-1

city: Irapuato

first: Eugenio

last: Mancera

state: Guanajuato

address: Km. 9.6 Libramiento Norte Carretera Irapuato-Leon

department: Ingenieria Genetica

country: Mexico

institute: Cinvestav

description:
ChIPspglu-I-CEM343
samples for processed file: ChIPspglu-I-CEM343 - ChIPspglu_I_CEM091

library_source: genomic

data_processing:
Quality analysis performed with FastQC
ChIP-seq reads were mapped to their corresponding genome using Bowtie 2 with default parameters
SAMtools package was used to convert, sort and index the sequenced reads to BAM format
Adjusted the number of reads in the different treatment-control dataset pairs using SAMtools view -s function prior to peak calling
Peak calling was performed using MACS2 with a q-value cutoff of 0.01; the shiftsize parameter was determined using the SPP package in R
Genome_build: http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly21/archive/C_albicans_SC5314_version_A21-s02-m09-r02_chromosomes.fasta.gz; http://www.candidagenome.org/download/sequence/C_dubliniensis_CD36/archive/C_dubliniensis_CD36_version_s01-m02-r08_chromosomes.fasta.gz; http://www.candidagenome.org/download/sequence/C_tropicalis_MYA-3404/current/C_tropicalis_MYA-3404_chromosomes.fasta.gz; www.candidagenome.org/download/sequence/C_parapsilosis_CDC317/archive/C_parapsilosis_CDC317_version_s01-m03-r13_chromosomes.fasta.gz
Supplementary_files_format_and_content: peaks.txt files were generated for each experiment with tagged proteins using untagged strains as a control in MACS2.

molecule: genomic DNA

organism: Candida dubliniensis

source_name: a/alpha cell

growth_protocol: Experiments were performed under biofilm growth conditions in 6-well polystyrene plates as previously described (Nobile et al., Cell, 2012). After 48 hours of biofilm growth in Spider 1% glucose at 37°C and 200 rpm

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. Cell disruption and immunoprecipitation were performed as previously described (Hernday et al., Methods Enzymol 470: 737-758, 2010) using a c-Myc tag monoclonal antibody (RRID: AB_2536303).
Performed using an NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina sequencing

tag: dna-binding gene

tag: epitope

value: c-myc

tag: growth

value: biofilm

tag: media

value: Spider 1% glucose

tag: chip antibody

value: c-Myc tag monoclonal antibody (RRID:AB_2536303)


title: Mouse_72_het_dim (F7_Guang_GL9989-1)

description: F7_Guang_GL9989-1-ATGCGCAG-CTCCTTAC_S108


title: Cd_Rob1_hom-2

description:
ChIIPspglu-II-CEM343
samples for processed file: ChIIPspglu-II-CEM343 - ChIPspglu_II_CEM091


title: Cd_Tec1_hom-1

description:
ChIPspglu-I-CEM344
samples for processed file: ChIPspglu-I-CEM344 - ChIPspglu_I_CEM091


title: Cd_Tec1_hom-2

description:
ChIIPspglu-II-CEM344
samples for processed file: ChIIPspglu-II-CEM344 - ChIPspglu_II_CEM091


title: Mouse_72_het_bright (G3_Guang_GL9989-1)

description: G3_Guang_GL9989-1-ACTGAGCG-CTCCTTAC_S112


title: Mouse_72_het_dim (G8_Guang_GL9989-1)

description: G8_Guang_GL9989-1-GCTCATGA-CTCCTTAC_S117


title: Mouse_72_het_dim (G5_Guang_GL9989-1)

description: G5_Guang_GL9989-1-CCTAAGAC-CTCCTTAC_S114


title: Mouse_72_het_dim (F6_Guang_GL9989-1)

description: F6_Guang_GL9989-1-TAGGCATG-CTCCTTAC_S107


title: Cd_Ndt80_hom-1

description:
ChIPspglu-I-CEM342
samples for processed file: ChIPspglu-I-CEM342 - ChIPspglu_I_CEM091


title: Genomic DNA from pancretatic tissue_PK04-29N

status: Public on Apr 14 2021

type: genomic

city: Shinjyuku-ku

first: Yae

last: Kanai

state: Tokyo

address: 35, Shinano-machi

institute: Keio University School of Medicine

description: Non-cancerous pancreatic tissue

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450K Beadchip using standard Illumina protocol.

scan_protocol: Hybridization fluorescence signals were read by the iScan reader  using standard recommended Illumina scanner setting.

data_processing: GenomeStudio methylation software

label: Cy5 and Cy3

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: High-molecular-weight DNA was extracted from fresh frozen tissue samples using phenol–chloroform, followed by dialysis.

tag: gender

value: Female

tag: age


title: Mouse_72_het_dim (F5_Guang_GL9989-1)

description: F5_Guang_GL9989-1-TACGCTGC-CTCCTTAC_S106


title: C. dubliniensis CEM002 Planktonic Growth in Spider Glucose Replicate 1

type: RNA

hyb_protocol: Equal amounts of the Cy3 and Cy5 labeled cDNA hybridized to the array overnight, as described in the Agilent protocol. Following hybridization, the arrays were washed as specified by Agilent.

scan_protocol: Arrays were scanned at 5 μm, averaging 2 lines, with an Axon GenePix 4000A scanner.

data_processing: Arrays were gridded using GenePix Pro version 5.1. Global Lowess normalization analysis was performed for each array using a Goulphar script (The R Foundation for Statistical Computing). Normalized data was collapsed first by averaging the result for all duplicate probes and finally by taking the median of the probes for each ORF. Data was transformed as described for each experiment. Note that comparisons between arrays can only be made if they share a pooled reference (Ch2)

source_name: CEM002 spider glucose planktonic

label_protocol: cDNA was dried and resuspended in 5 μL 0.1 M sodium bicarbonate. An equivalent volume of Cy3 (pool) or Cy5 (individual) dye (Amersham) was added (dyes were resuspended in 60 μL of DMSO) and the reaction incubated at 65° for 20 minutes in the dark. Labeled cDNAs were purified using a Clean and Concentrator -5 kit (Zymo Research).

growth_protocol: Cultures for the extraction of total RNA under biofilm growth conditions were performed on biofilms grown on the bottom of 6-well polystyrene plates for 48 hours at 37°C and 200 rpm as previously described (Nobile et al. 2012). The media used was Spider 1% glucose and Spider. Planktonic cultures for total RNA were grown in the same media by inoculating with cells from an overnight 30°C YPD culture to an OD600 of 0.05. Cultures were then grown in flasks at 37°C with shaking at 225 rpm until they reached an OD600 of 1.0.

extract_protocol: RNA was isolated and reverse transcribed as previously described (Nobile et al. 2012). Additionally, reverse transcription reactions were performed on either individual samples or on RNA in which an equivalent amount of each RNA sample was pooled.

treatment_protocol: Nobile et al. Cell 2012

value: Spider glucose

value: planktonic

source_name: pooled reference

tag: sample type

value: pooled reference


title: C. dubliniensis CEM002 Planktonic Growth in Spider Replicate 1

source_name: CEM002 spider planktonic

value: Spider


title: C. dubliniensis CEM002 Planktonic Growth in Spider Replicate 2


title: C. dubliniensis CEM002 Biofilm Growth in Spider Replicate 1

source_name: CEM002 spider biofilm


title: C. dubliniensis CEM002 Biofilm Growth in Spider Replicate 2


title: C. dubliniensis CEM002 Biofilm Growth in Spider Glucose Replicate 1

source_name: CEM002 spider glucose biofilm


title: Cd_Efg1_hom-2

description:
ChIIPspglu-II-CEM341
samples for processed file: ChIIPspglu-II-CEM341 - ChIPspglu_II_CEM091


title: Cd_Efg1_hom-1

description:
ChIPspglu-I-CEM341
samples for processed file: ChIPspglu-I-CEM341 - ChIPspglu_I_CEM091


title: Mouse_72_het_bright (G1_Guang_GL9989-1)

description: G1_Guang_GL9989-1-TAGCGCTC-CTCCTTAC_S110


title: C. dubliniensis CEM002 Planktonic Growth in Spider Glucose Replicate 2


title: Mouse_72_het_bright (F4_Guang_GL9989-1)

description: F4_Guang_GL9989-1-GGACTCCT-CTCCTTAC_S105


title: Mouse_72_het_dim (F8_Guang_GL9989-1)

description: F8_Guang_GL9989-1-CTCTCTAC-CTCCTTAC_S109


title: Mouse_72_het_bright (F2_Guang_GL9989-1)

description: F2_Guang_GL9989-1-CGGAGCCT-CTCCTTAC_S104


title: Mouse_73_wt (E10_Guang_GL9989-1)

description: E10_Guang_GL9989-1-GCGTAGTA-CTCCTTAC_S102


title: Mouse_72_het_bright (F1_Guang_GL9989-1)

description: F1_Guang_GL9989-1-TCCTGAGC-CTCCTTAC_S103


title: Cd_Brg1_hom-1

description:
ChIPspglu-I-CEM340
samples for processed file: ChIPspglu-I-CEM340 - ChIPspglu_I_CEM091


title: Cd_Brg1_hom-2

description:
ChIIPspglu-II-CEM340
samples for processed file: ChIIPspglu-II-CEM340 - ChIPspglu_II_CEM091


title: Mouse_73_wt (E9_Guang_GL9989-1)

description: E9_Guang_GL9989-1-AGGCAGAA-CTCCTTAC_S101


title: Cd_Ndt80_hom-2

description:
ChIIPspglu-II-CEM342
samples for processed file: ChIIPspglu-II-CEM342 - ChIPspglu_II_CEM091


title: Cd_Bcr1_hom-1

description:
ChIPspglu-I-CEM339
samples for processed file: ChIPspglu-I-CEM339 - ChIPspglu_I_CEM091


title: Mouse_72_het_dim (E8_Guang_GL9989-1)

description: E8_Guang_GL9989-1-GGAGCTAC-CTCCTTAC_S100


title: Mouse_72_het_dim (E7_Guang_GL9989-1)


title: Mouse_72_het_dim (E5_Guang_GL9989-1)


title: Mouse_72_het_dim (E6_Guang_GL9989-1)


title: P2MCBwt2_1

city: Xiamen

first: shaoxuan

last: chen

state: Fujian Province

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District

country: China

institute: xiamen university

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute using BGISEQ-500 sequencer
Clean reads were mapped onto the mouse genome (GRCm38/mm10) using hisat2 to obtain the aligned bam files.
Genome_build: mm10

source_name: cerebellum

extract_protocol:
Total RNA was extracted from sorted BG using TRIzol Reagent
RNA was subsequently used for cDNA library construction with RNA integrity numbers (RIN) up to 7, and then sequencing was performed by the BGI Genomics Co.,Ltd. using BGISEQ-500 platform

treatment_protocol: For activation of CreERT2 mediated recombination,a month or two months Mash1-iTom mice were gavaged at a dosage of 200 μg/g for three consecutive days

tag: tissue

value: cerebellum

value: post natal day 60

value: Mash1 cre-ERT2, R26-LSL-tdTomato


title: P2MCBwt1_1


title: Mouse_72_het_bright (E1_Guang_GL9989-1)


title: P10BGmt2_1

value: Bergmann glia

value: post natal day 10


title: P7CBwt2_1

value: post natal day 7

value: Nestin-<delta>TK-IRES-GFP


title: P10BGmt1_1


title: P7CBwt1_1


title: Mouse_72_het_bright (E2_Guang_GL9989-1)

value: cardiomyocyte (CM)


title: Mouse_73_wt (D10_Guang_GL9989-1)

description: D10_Guang_GL9989-1-CGATCAGT-AGCTAGAA_S92

value: control


title: P10BGct4_1

value: Setdb1fl/fl; Nestin-<delta>TK-IRES-GFP


title: 2MBGwt4_1


title: Mouse_72_het_dim (D7_Guang_GL9989-1)


title: C. dubliniensis CEM002 Biofilm Growth in Spider Glucose Replicate 2

value: biofilm


title: 2MBGwt3_1


title: Mouse_72_het_dim (D6_Guang_GL9989-1)


title: Cd_Bcr1_hom-2

description:
ChIIPspglu-II-CEM339
samples for processed file: ChIIPspglu-II-CEM339 - ChIPspglu_II_CEM091

value: c-myc

value: Spider 1% glucose

value: c-Myc tag monoclonal antibody (RRID:AB_2536303)


title: Mouse_72_het_bright (D4_Guang_GL9989-1)


title: 1MBGwt2_1

value: post natal day 30


title: 2MBGwt2_1


title: 1MBGwt1_1


title: Mouse_72_het_bright (E4_Guang_GL9989-1)


title: P16BGwt3_1

value: post natal day 16


title: Mouse_73_wt (D11_Guang_GL9989-1)

description: D11_Guang_GL9989-1-GCTCATGA-AGCTAGAA_S93


title: Mouse_72_het_bright (D2_Guang_GL9989-1)


title: Mouse_72_het_bright (D1_Guang_GL9989-1)


title: P16BGwt2_1


title: P10BGct5_1


title: Mouse_72_het_dim (C8_Guang_GL9989-1)


title: P13BGwt5_1

value: post natal day 13


title: Mouse_72_het_dim (C7_Guang_GL9989-1)


title: Mouse_72_het_dim (C6_Guang_GL9989-1)


title: Mouse_73_wt (D9_Guang_GL9989-1)


title: P13BGwt4_1


title: P10BGwt2_1


title: Mouse_72_het_bright (C4_Guang_GL9989-1)


title: Mouse_72_het_dim (C5_Guang_GL9989-1)


title: P10BGwt1_1


title: P7BGwt3_1


title: Mouse_72_het_bright (C3_Guang_GL9989-1)


title: P7BGwt4_1


title: P7BGwt2_1


title: Mouse_72_het_bright (C2_Guang_GL9989-1)


title: Mouse_72_het_bright (D3_Guang_GL9989-1)


title: P7BGwt1_1


title: P4BGwt2_1

value: post natal day 4


title: Mouse_72_het_dim (B6_Guang_GL9989-1)


title: Mouse_72_het_bright (B4_Guang_GL9989-1)


title: Mouse_72_het_bright (C1_Guang_GL9989-1)


title: Mouse_72_het_dim (B8_Guang_GL9989-1)


title: P4BGwt1_1


title: P1BGwt2_1

value: post natal day 1


title: Mouse_73_wt (A12_Guang_GL9989-1)

description: A12_Guang_GL9989-1-ATCTCAGG-AGAGGATA_S71


title: Mouse_72_het_bright (B1_Guang_GL9989-1)


title: P1BGwt1_1


title: Mouse_73_wt (A10_Guang_GL9989-1)

description: A10_Guang_GL9989-1-TGCAGCTA-AGAGGATA_S70


title: Mouse_72_het_dim (A8_Guang_GL9989-1)


title: Mouse_72_het_bright (A2_Guang_GL9989-1)


title: Mouse_72_het_dim (A6_Guang_GL9989-1)


title: Mouse_72_het_dim (A5_Guang_GL9989-1)


title: Mouse_72_het_dim (A7_Guang_GL9989-1)


title: Mouse_72_het_bright (A3_Guang_GL9989-1)


title: Mouse_72_het_bright (B2_Guang_GL9989-1)


title: Mouse_26_wt (H11_Guang_GL-9122b)

description: H11_Guang_GL-9122b-CGAGGCTG-AGAGGATA_S63


title: Mouse_25_homo_dim (H6_Guang_GL-9122b)


title: Mouse_25_homo_dim (H5_Guang_GL-9122b)


title: Mouse_25_homo_dim (H4_Guang_GL-9122b)


title: C. albicans SN250 Biofilm Growth in RPMI Replicate 2

organism: Candida albicans

source_name: SN250 rpmi biofilm

growth_protocol: Cultures for the extraction of total RNA under biofilm growth conditions were performed on biofilms grown on the bottom of 6-well polystyrene plates for 48 hours at 37°C and 200 rpm as previously described (Nobile et al. 2012). The media used was Spider 1% glucose, Spider and RPMI 1% glucose. Planktonic cultures for total RNA were grown in the same media by inoculating with cells from an overnight 30°C YPD culture to an OD600 of 0.05. Cultures were then grown in flasks at 37°C with shaking at 225 rpm until they reached an OD600 of 1.0.

treatment_protocol: See Nobile et al. Cell 2012

value: RPMI

tag: tag

value: pooled reference


title: C. albicans SN250 Biofilm Growth in Spider Glucose Replicate 1

source_name: SN250 spider glucose biofilm

value: Spider glucose


title: C. albicans SN250 Biofilm Growth in Spider Replicate 2

source_name: SN250 spider biofilm

value: Spider


title: C. albicans SN250 Planktonic Growth in RPMI Replicate 2

source_name: SN250 rpmi planktonic

value: planktonic


title: C. albicans SN250 Biofilm Growth in Spider Glucose Replicate 2


title: C. albicans SN250 Biofilm Growth in Spider Replicate 1


title: Liver_APS treatment_rep1

city: Shanghai

first: Xuyun

last: He

address: Cailun Road 1200

institute: Shanghai University of Traditional Chinese Medicine

description:
S37_33_NS
Gene expression after 12 week high-fat-diet with APS treatment in mice liver.

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent Technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent Technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent Technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent Technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US).
Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: Liver, APS treatment, 12 week

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent Technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: 24 male C57bl/6J mice were randomly divided into 3 groups including control group (Con), HFD group and APS groups. All animals were fed with corresponding diet for consecutive 12 weeks during which their body weight was measured weekly.

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Control group was fed with chow food, HFD group was fed with high-fat-diet (60 kcal% Fat, Research Diets, D12492), APS group was fed with HFD mixed with APS (40 g APS/kg HFD).

tag: strain/background

value: male

value: 16 weeks

value: Liver

tag: treatment

value: high-fat diet with APS


title: Mouse_25_homo_bright (G8_Guang_GL-9122b)

value: cardiomyocyte (CM)


title: Mouse_26_wt (G9_Guang_GL-9122b)

value: control


title: Mouse_26_wt (G12_Guang_GL-9122b)

description: G12_Guang_GL-9122b-CGGAGCCT-AGAGGATA_S56


title: Liver_high-fat-diet_rep2

description:
S37_25_NS
Gene expression after 12 week high-fat-diet in mice liver.

source_name: Liver, high-fat-diet, 12 week

value: high-fat diet


title: Liver_APS treatment_rep3

description:
S37_35_NS
Gene expression after 12 week high-fat-diet with APS treatment in mice liver.


title: Mouse_26_wt (G11_Guang_GL-9122b)

description: G11_Guang_GL-9122b-TCCTGAGC-AGAGGATA_S55


title: Mouse_25_homo_bright (H3_Guang_GL-9122b)


title: Liver_high-fat-diet_rep1

description:
S37_24_NS
Gene expression after 12 week high-fat-diet in mice liver.


title: Liver_APS treatment_rep2

description:
S37_34_NS
Gene expression after 12 week high-fat-diet with APS treatment in mice liver.


title: Liver_Control_rep2

description:
S33_104_NS
Gene expression after 12 week chow food in mice liver.

source_name: Liver, control, 12 week

value: control chow


title: Liver_Control_rep1

description:
S33_101_NS
Gene expression after 12 week chow food in mice liver.


title: C. albicans SN250 Biofilm Growth in RPMI Replicate 1

value: biofilm


title: C. albicans SN250 Planktonic Growth in Spider Replicate 2

source_name: SN250 spider planktonic


title: Liver_Control_rep3

description:
S33_109_NS
Gene expression after 12 week chow food in mice liver.


title: Mouse_25_homo_bright (H1_Guang_GL-9122b)

source_name: mouse cardiomyocyte


title: Liver_high-fat-diet_rep3

description:
S37_27_NS
Gene expression after 12 week high-fat-diet in mice liver.


title: Mouse_25_homo_bright (H2_Guang_GL-9122b)


title: Mouse_26_wt (F12_Guang_GL-9122b)

description: F12_Guang_GL-9122b-TAAGGCGA-AGAGGATA_S49


title: FlatCoatedRetriever11

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

description: FCR11 from Bioproject PRJNA685036

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on an Illumina iScan.

data_processing:
Image data was analyzed using GenomeStudio with GT module (Illumina).
genotypes AA, AB, BB, NC=no call

organism: Canis lupus familiaris

source_name: whole blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.

tag: breed

value: Flatcoated Retriever


title: Mouse_25_homo_bright (G2_Guang_GL-9122b)

tag: strain


title: FlatCoatedRetriever10

description: FCR10 from Bioproject PRJNA685036


title: Mouse_25_homo_dim (G6_Guang_GL-9122b)

tag: genotype


title: Mouse_25_homo_dim (G5_Guang_GL-9122b)

tag: cell type


title: C. albicans SN250 Planktonic Growth in Spider Glucose Replicate 2

source_name: SN250 spider glucose planktonic


title: Mouse_26_wt (F10_Guang_GL-9122b)

description: F10_Guang_GL-9122b-TCGACGTC-CTAGTCGA_S48


title: Mouse_25_homo_dim (F6_Guang_GL-9122b)


title: Mouse_25_homo_dim (F7_Guang_GL-9122b)


title: Mouse_26_wt (F9_Guang_GL-9122b)


title: Mouse_25_homo_bright (F8_Guang_GL-9122b)


title: FlatCoatedRetriever09

description: FCR09 from Bioproject PRJNA685036


title: FlatCoatedRetriever311


title: FlatCoatedRetriever08

description: FCR08 from Bioproject PRJNA685036


title: Mouse_25_homo_bright (F3_Guang_GL-9122b)


title: FlatCoatedRetriever02

description: FCR02 from Bioproject PRJNA685036


title: C. albicans SN250 Planktonic Growth in Spider Replicate 1


title: FlatCoatedRetriever07

description: FCR07 from Bioproject PRJNA685036


title: C. albicans SN250 Planktonic Growth in RPMI Replicate 1


title: FlatCoatedRetriever312


title: C. albicans SN250 Planktonic Growth in Spider Glucose Replicate 1


title: FlatCoatedRetriever309


title: Mouse_25_homo_dim (F5_Guang_GL-9122b)


title: FlatCoatedRetriever01

description: FCR01 from Bioproject PRJNA685036


title: Mouse_25_homo_bright (F1_Guang_GL-9122b)


title: FlatCoatedRetriever308


title: Mouse_25_homo_bright (F2_Guang_GL-9122b)


title: Mouse_26_wt (E9_Guang_GL-9122b)


title: FlatCoatedRetriever310


title: FlatCoatedRetriever03

description: FCR03 from Bioproject PRJNA685036


title: FlatCoatedRetriever05

description: FCR05 from Bioproject PRJNA685036


title: Mouse_26_wt (E11_Guang_GL-9122b)

description: E11_Guang_GL-9122b-TAGCGCTC-CTAGTCGA_S38


title: FlatCoatedRetriever06

description: FCR06 from Bioproject PRJNA685036


title: Mouse_25_homo_bright (E8_Guang_GL-9122b)


title: FlatCoatedRetriever307


title: FlatCoatedRetriever304


title: FlatCoatedRetriever306


title: FlatCoatedRetriever302


title: Mouse_25_homo_bright (E2_Guang_GL-9122b)


title: Mouse_25_homo_dim (E4_Guang_GL-9122b)


title: Mouse_26_wt (E12_Guang_GL-9122b)

description: E12_Guang_GL-9122b-CGAGGCTG-CTAGTCGA_S39


title: FlatCoatedRetriever305


title: FlatCoatedRetriever303


title: Mouse_26_wt (D11_Guang_GL-9122b)

description: D11_Guang_GL-9122b-AGGCAGAA-CTAGTCGA_S29


title: FlatCoatedRetriever298


title: Mouse_26_wt (D10_Guang_GL-9122b)

description: D10_Guang_GL-9122b-GGAGCTAC-CTAGTCGA_S28


title: Mouse_26_wt (D12_Guang_GL-9122b)

description: D12_Guang_GL-9122b-GCGTAGTA-CTAGTCGA_S30


title: FlatCoatedRetriever299


title: FlatCoatedRetriever300


title: Mouse_25_homo_dim (E5_Guang_GL-9122b)


title: FlatCoatedRetriever301


title: Mouse_25_homo_dim (D5_Guang_GL-9122b)


title: Mouse_25_homo_dim (D6_Guang_GL-9122b)


title: Mouse_26_wt (D9_Guang_GL-9122b)


title: FlatCoatedRetriever297


title: FlatCoatedRetriever296


title: Mouse_25_homo_dim (D4_Guang_GL-9122b)


title: Mouse_25_homo_bright (D3_Guang_GL-9122b)


title: FlatCoatedRetriever293


title: FlatCoatedRetriever295


title: FlatCoatedRetriever294


title: Mouse_25_homo_bright (D1_Guang_GL-9122b)


title: Mouse_25_homo_bright (E3_Guang_GL-9122b)


title: Mouse_26_wt (C12_Guang_GL-9122b)

description: C12_Guang_GL-9122b-GCTCATGA-ATAGAGAG_S21


title: Mouse_25_homo_bright (E1_Guang_GL-9122b)


title: Mouse_26_wt (C10_Guang_GL-9122b)

description: C10_Guang_GL-9122b-GTAGAGGA-ATAGAGAG_S19


title: FlatCoatedRetriever291


title: FlatCoatedRetriever290


title: FlatCoatedRetriever286


title: FlatCoatedRetriever289


title: Mouse_26_wt (C11_Guang_GL-9122b)

description: C11_Guang_GL-9122b-CGATCAGT-ATAGAGAG_S20


title: FlatCoatedRetriever288


title: FlatCoatedRetriever292


title: FlatCoatedRetriever287


title: Mouse_26_wt (B12_Guang_GL-9122b)

description: B12_Guang_GL-9122b-ACTGAGCG-ATAGAGAG_S16


title: Mouse_26_wt (B11_Guang_GL-9122b)

description: B11_Guang_GL-9122b-CGAGGCTG-ATAGAGAG_S15


title: Mouse_25_homo_dim (C6_Guang_GL-9122b)


title: Mouse_25_homo_bright (C8_Guang_GL-9122b)


title: FlatCoatedRetriever285


title: FlatCoatedRetriever284


title: Mouse_25_homo_bright (B8_Guang_GL-9122b)


title: Mouse_26_wt (B9_Guang_GL-9122b)


title: FlatCoatedRetriever283


title: Mouse_25_homo_dim (B7_Guang_GL-9122b)


title: FlatCoatedRetriever282


title: Mouse_25_homo_dim (B5_Guang_GL-9122b)


title: FlatCoatedRetriever281


title: Mouse_25_homo_bright (B3_Guang_GL-9122b)


title: Mouse_25_homo_bright (B2_Guang_GL-9122b)


title: FlatCoatedRetriever280


title: FlatCoatedRetriever279


title: FlatCoatedRetriever278


title: Mouse_26_wt (A12_Guang_GL-9122b)


title: Mouse_25_homo_bright (B1_Guang_GL-9122b)


title: Mouse_26_wt (B10_Guang_GL-9122b)

description: B10_Guang_GL-9122b-TAGCGCTC-ATAGAGAG_S14


title: FlatCoatedRetriever277


title: FlatCoatedRetriever276


title: Mouse_26_wt (A11_Guang_GL-9122b)


title: Mouse_26_wt (A9_Guang_GL-9122b)


title: FlatCoatedRetriever275


title: FlatCoatedRetriever272


title: FlatCoatedRetriever273


title: Mouse_25_homo_dim (A6_Guang_GL-9122b)


title: FlatCoatedRetriever271


title: tet_pos_RNA

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

description: 5' gene expression library (10X Genomics)

data_processing:
Processed with cellranger pipeline, version 3.1.0
Genome_build: mm10

molecule: polyA RNA

source_name: Spenocytes from 21 dpi with LCMV-c13

extract_protocol: 10X Genomics Single Cell 5' Library & Gel Bead Kit

value: gp-33 specific CD8 T cells


title: FlatCoatedRetriever270


title: Mouse_25_homo_bright (A3_Guang_GL-9122b)


title: Ca_untagged_spglu-1

data_processing:
Quality analysis performed with FastQC
ChIP-seq reads were mapped to their corresponding genome using Bowtie 2 with default parameters
SAMtools package was used to convert, sort and index the sequenced reads to BAM format
Peak calling was performed using MACS2 with a q-value cutoff of 0.01; the shiftsize parameter was determined using the SPP package in R
Genome_build: http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly21/archive/C_albicans_SC5314_version_A21-s02-m09-r02_chromosomes.fasta.gz; http://www.candidagenome.org/download/sequence/C_dubliniensis_CD36/archive/C_dubliniensis_CD36_version_s01-m02-r08_chromosomes.fasta.gz; http://www.candidagenome.org/download/sequence/C_tropicalis_MYA-3404/current/C_tropicalis_MYA-3404_chromosomes.fasta.gz
Supplementary_files_format_and_content: enrich.txt files have the maximum fold enrichment between tagged and untagged control experiment for each upstream intergenic region in the genome.

source_name: a/alpha cell

growth_protocol: Experiments were performed under biofilm growth conditions in 6-well polystyrene plates as previously described (Nobile et al., Cell, 2012). After 48 hours of biofilm growth in Spider and Spider 1% glucose for C. albicans and C. dubliniensis, and in RPMI 1% glucose and Spider 1% for C. tropicalis, samples were harvested.  Biofilm growth was done at 37°C and 200 rpm.

value: untagged

value: Spider 1% glucose

value: c-Myc tag monoclonal antibody (RRID:AB_2536303)


title: Ca_untagged_spglu-2


title: Ca_untagged_spider-1


title: Ca_untagged_spider-2


title: FlatCoatedRetriever269


title: FlatCoatedRetriever268


title: FlatCoatedRetriever267


title: FlatCoatedRetriever265


title: Ca_Ndt80_spglu-2

description:
ChIPspglu_II_CEM272
samples for processed file: ChIPspglu_II_CEM272 - ChIPspglu_II_CEM093
calb_bothmedia.enrich.txt

value: c-myc


title: FlatCoatedRetriever264


title: Ca_Ndt80_spider-2

description:
ChIP_II_CEM272
samples for processed file: ChIP_II_CEM272 - ChIP_II_CEM093
calb_bothmedia.enrich.txt

value: Spider


title: Ca_Ndt80_spglu-1

description:
ChIPspglu_I_CEM272
samples for processed file: ChIPspglu_I_CEM272 - ChIPspglu_I_CEM093
calb_bothmedia.enrich.txt


title: Ca_Ndt80_spider-1

description:
ChIP_I_CEM272
samples for processed file: ChIP_I_CEM272 - ChIP_I_CEM093
calb_bothmedia.enrich.txt


title: FlatCoatedRetriever274


title: Ca_untagged_hom-6


title: FlatCoatedRetriever263


title: Mouse_25_homo_dim (A5_Guang_GL-9122b)


title: FlatCoatedRetriever262


title: Ca_untagged_hom-5


title: FlatCoatedRetriever261


title: FlatCoatedRetriever259


title: Ca_untagged_hom-2


title: Ca_untagged_hom-4


title: FlatCoatedRetriever260


title: FlatCoatedRetriever258


title: Ca_untagged_hom-1


title: Ca_Tec1_hom-2

description:
ChIPspglu_II_CEM332
samples for processed file: ChIPspglu_II_CEM332 - ChIPspglu_II_CEM093


title: Ca_Tec1_hom-1

description:
ChIPspglu_I_CEM332
samples for processed file: ChIPspglu_I_CEM332 - ChIPspglu_I_CEM093


title: FlatCoatedRetriever266


title: FlatCoatedRetriever255


title: FlatCoatedRetriever254


title: Ca_Rob1_hom-1

description:
ChIPspglu_I_CEM273
samples for processed file: ChIPspglu_I_CEM273 - ChIPspglu_V_CEM093


title: FlatCoatedRetriever253


title: Ca_Ndt80_hom-2

description:
ChIPspglu_II_CEM272
samples for processed file: ChIPspglu_II_CEM272 - ChIPspglu_VI_CEM093


title: FlatCoatedRetriever252


title: Ca_Ndt80_hom-1

description:
ChIPspglu_I_CEM272
samples for processed file: ChIPspglu_I_CEM272 - ChIPspglu_V_CEM093


title: FlatCoatedRetriever256


title: Ca_Efg1_hom-2

description:
ChIPspglu_II_CEM271
samples for processed file: ChIPspglu_II_CEM271 - ChIPspglu_II_CEM093


title: Ca_Brg1_hom-4

description:
ChIPspglu_IV_CEM270
samples for processed file: ChIPspglu_IV_CEM270 - ChIPspglu_IV_CEM093


title: FlatCoatedRetriever250


title: Ca_Brg1_hom-2

description:
ChIPspglu_II_CEM270
samples for processed file: ChIPspglu_II_CEM270 - ChIPspglu_IV_CEM093


title: FlatCoatedRetriever249


title: FlatCoatedRetriever248


title: Ca_Bcr1_hom-2

description:
ChIPspglu_II_CEM269
samples for processed file: ChIPspglu_II_CEM269 - ChIPspglu_II_CEM093


title: FlatCoatedRetriever257


title: FlatCoatedRetriever247


title: FlatCoatedRetriever244


title: FlatCoatedRetriever245


title: Ca_Efg1_hom-1

description:
ChIPspglu_I_CEM271
samples for processed file: ChIPspglu_I_CEM271 - ChIPspglu_I_CEM093


title: FlatCoatedRetriever246


title: Ca_Rob1_hom-2

description:
ChIPspglu_II_CEM273
samples for processed file: ChIPspglu_II_CEM273 - ChIPspglu_VI_CEM093


title: FlatCoatedRetriever242


title: FlatCoatedRetriever243


title: FlatCoatedRetriever241


title: FlatCoatedRetriever240


title: FlatCoatedRetriever251


title: FlatCoatedRetriever239


title: FlatCoatedRetriever238


title: NHP_CIRCLE-off-target-site3_invivo_control_Rep3

city: Zurich

first: Tanja

last: Rothgangl

address: Winterthurerstrasse, 190

department: Pharmacology and Toxicology

country: Switzerland

institute: UZH Zurich

data_processing:
Library strategy: targeted amplicon sequencing
CIRCLE-seq pipeline (https://github.com/tsailabSJ/circleseq)
CHANGE-seq pipeline (https://github.com/tsailabSJ/changeseq)
iGUIDE pipeline (https://github.com/cnobles/iGUIDE)
For all targeted amplicon sequencing files, we used CRISPRESSO2 for the analysis: https://crispresso.pinellolab.partners.org/submission . This platform directly reads in a fastq.gz file and provides a summary about editing rates and allele frequency.
Genome_build: Hg38, mm10
Supplementary_files_format_and_content: for CIRCLE, CHANGE-seq and iGUIDE: text files containing identified off-target sites; html report file containing identified off-target sites; fastq-index output file generated by Miseq

organism: Macaca fascicularis

source_name: gDNA

growth_protocol: DMEM growth medium supplemented with 10% FBS and 1% P/S for HEK293T and Hepa1-6 cells; EMEM with same supplements for HepG2 cells

extract_protocol:
Detachment with TryplE, wash with PBS, lysis and DNA isolation for cell lines and whole tissue or primary hepatocyte isolation for in vivo samples.
targeted amplicon sequencing; CIRCLE-seq, CHANGE-seq or iGUIDE library preparation

treatment_protocol: per 48 well plate: 1 ug total DNA with 1.5 ul Lipofectamine2000, cells were treated with the respective base-editor targeting the indicated locus. For HepG2 cells, the base editor and sgRNA was inroduced by NEON electroporation. In vivo treatment was delivery by AAV or LNP mediated delivery via tail vein injection.

value: off-target

value: Untreated

value: targeted amplicon sequencing


title: NHP_CIRCLE-off-target-site2_invivo_control_Rep3


title: NHP_CIRCLE-off-target-site4_invivo_control_Rep3


title: NHP_CIRCLE-off-target-site5_invivo_control_Rep3


title: NHP_CIRCLE-off-target-site8_invivo_control_Rep3


title: NHP_CIRCLE-off-target-site6_invivo_control_Rep3


title: NHP_CIRCLE-off-target-site7_invivo_control_Rep3


title: FlatCoatedRetriever237


title: NHP_CIRCLE-off-target-site7_invivo_control_Rep2


title: Ca_Bcr1_hom-1

description:
ChIPspglu_I_CEM269
samples for processed file: ChIPspglu_I_CEM269 - ChIPspglu_I_CEM093


title: FlatCoatedRetriever236


title: NHP_CIRCLE-off-target-site6_invivo_control_Rep2


title: FlatCoatedRetriever235


title: FlatCoatedRetriever233


title: FlatCoatedRetriever234


title: FlatCoatedRetriever232


title: NHP_CIRCLE-off-target-site3_invivo_control_Rep2


title: NHP_CIRCLE-off-target-site2_invivo_control_Rep2


title: NHP_CIRCLE-off-target-site1_invivo_control_Rep2


title: FlatCoatedRetriever230


title: FlatCoatedRetriever231


title: FlatCoatedRetriever229


title: NHP_CIRCLE-off-target-site8_invivo_control_Rep1


title: NHP_CIRCLE-off-target-site7_invivo_control_Rep1


title: NHP_CIRCLE-off-target-site8_invivo_control_Rep2


title: FlatCoatedRetriever228


title: NHP_CIRCLE-off-target-site5_invivo_control_Rep2


title: FlatCoatedRetriever227


title: NHP_CIRCLE-off-target-site5_invivo_control_Rep1


title: NHP_CIRCLE-off-target-site3_invivo_control_Rep1


title: NHP_CIRCLE-off-target-site6_invivo_control_Rep1


title: NHP_CIRCLE-off-target-site4_invivo_control_Rep1


title: FlatCoatedRetriever222


title: NHP_CIRCLE-off-target-site8_invitro_control_Rep3

value: Lipofection/Untreated


title: FlatCoatedRetriever223


title: NHP_CIRCLE-off-target-site2_invivo_control_Rep1


title: NHP_CIRCLE-off-target-site1_invivo_control_Rep1


title: FlatCoatedRetriever220


title: FlatCoatedRetriever221


title: NHP_CIRCLE-off-target-site7_invitro_control_Rep3


title: NHP_CIRCLE-off-target-site4_invivo_control_Rep2


title: NHP_CIRCLE-off-target-site6_invitro_control_Rep3


title: FlatCoatedRetriever219


title: FlatCoatedRetriever218


title: FlatCoatedRetriever217


title: FlatCoatedRetriever224


title: FlatCoatedRetriever215


title: FlatCoatedRetriever216


title: NHP_CIRCLE-off-target-site2_invitro_control_Rep3


title: NHP_CIRCLE-off-target-site3_invitro_control_Rep3


title: FlatCoatedRetriever226


title: FlatCoatedRetriever225


title: FlatCoatedRetriever214


title: NHP_CIRCLE-off-target-site7_invitro_control_Rep2


title: NHP_CIRCLE-off-target-site8_invitro_control_Rep2


title: FlatCoatedRetriever213


title: FlatCoatedRetriever211


title: FlatCoatedRetriever212


title: NHP_CIRCLE-off-target-site6_invitro_control_Rep2


title: NHP_CIRCLE-off-target-site5_invitro_control_Rep2


title: NHP_CIRCLE-off-target-site3_invitro_control_Rep2


title: FlatCoatedRetriever207


title: FlatCoatedRetriever210


title: FlatCoatedRetriever209


title: NHP_CIRCLE-off-target-site4_invitro_control_Rep2


title: NHP_CIRCLE-off-target-site2_invitro_control_Rep2


title: NHP_CIRCLE-off-target-site8_invitro_control_Rep1


title: NHP_CIRCLE-off-target-site7_invitro_control_Rep1


title: FlatCoatedRetriever208


title: FlatCoatedRetriever206


title: NHP_CIRCLE-off-target-site4_invitro_control_Rep3


title: NHP_CIRCLE-off-target-site5_invitro_control_Rep3


title: NHP_CIRCLE-off-target-site1_invitro_control_Rep2


title: FlatCoatedRetriever205


title: FlatCoatedRetriever203


title: FlatCoatedRetriever204


title: NHP_CIRCLE-off-target-site5_invitro_control_Rep1


title: NHP_CIRCLE-off-target-site1_invitro_control_Rep3


title: FlatCoatedRetriever202


title: NHP_CIRCLE-off-target-site4_invitro_control_Rep1


title: FlatCoatedRetriever201


title: NHP_CIRCLE-off-target-site3_invitro_control_Rep1


title: FlatCoatedRetriever200


title: FlatCoatedRetriever199


title: NHP_CIRCLE-off-target-site2_invitro_control_Rep1


title: NHP_CIRCLE-off-target-site8_invitro_Rep3

value: Lipofection

value: base-edited PCSK9


title: FlatCoatedRetriever197


title: NHP_CIRCLE-off-target-site8_invitro_Rep2


title: FlatCoatedRetriever196


title: FlatCoatedRetriever195


title: NHP_CIRCLE-off-target-site8_invitro_Rep1


title: NHP_CIRCLE-off-target-site6_invitro_Rep3


title: NHP_CIRCLE-off-target-site6_invitro_control_Rep1


title: FlatCoatedRetriever193


title: NHP_CIRCLE-off-target-site6_invitro_Rep2


title: FlatCoatedRetriever194


title: NHP_CIRCLE-off-target-site6_invitro_Rep1


title: FlatCoatedRetriever192


title: NHP_CIRCLE-off-target-site5_invitro_Rep3


title: FlatCoatedRetriever189


title: NHP_CIRCLE-off-target-site5_invitro_Rep2


title: FlatCoatedRetriever190


title: NHP_CIRCLE-off-target-site5_invitro_Rep1


title: NHP_CIRCLE-off-target-site4_invitro_Rep3


title: FlatCoatedRetriever188


title: NHP_CIRCLE-off-target-site4_invitro_Rep2


title: FlatCoatedRetriever187


title: NHP_CIRCLE-off-target-site1_invitro_control_Rep1


title: NHP_CIRCLE-off-target-site4_invitro_Rep1


title: FlatCoatedRetriever198


title: FlatCoatedRetriever185


title: NHP_CIRCLE-off-target-site3_invitro_Rep3


title: FlatCoatedRetriever184


title: FlatCoatedRetriever183


title: FlatCoatedRetriever182


title: NHP_CIRCLE-off-target-site3_invitro_Rep1


title: NHP_CIRCLE-off-target-site2_invitro_Rep3


title: NHP_CIRCLE-off-target-site3_invitro_Rep2


title: FlatCoatedRetriever191


title: NHP_CIRCLE-off-target-site2_invitro_Rep2


title: NHP_CIRCLE-off-target-site2_invitro_Rep1


title: FlatCoatedRetriever181


title: NHP_CIRCLE-off-target-site8_Group4_403

value: intravenous


title: FlatCoatedRetriever177


title: FlatCoatedRetriever175


title: FlatCoatedRetriever178


title: NHP_CIRCLE-off-target-site8_Group3_302


title: NHP_CIRCLE-off-target-site8_Group4_402


title: NHP_CIRCLE-off-target-site8_Group3_303


title: NHP_CIRCLE-off-target-site8_Group3_301


title: NHP_CIRCLE-off-target-site8_Group4_401


title: FlatCoatedRetriever176


title: FlatCoatedRetriever186


title: NHP_CIRCLE-off-target-site7_invitro_Rep3


title: FlatCoatedRetriever174


title: NHP_CIRCLE-off-target-site7_invitro_Rep2


title: NHP_CIRCLE-off-target-site7_invitro_Rep1


title: FlatCoatedRetriever170


title: FlatCoatedRetriever171


title: FlatCoatedRetriever180


title: NHP_CIRCLE-off-target-site7_Group4_402


title: NHP_CIRCLE-off-target-site7_Group4_403


title: FlatCoatedRetriever168


title: FlatCoatedRetriever169


title: NHP_CIRCLE-off-target-site7_Group3_303


title: NHP_CIRCLE-off-target-site7_Group4_401


title: FlatCoatedRetriever179


title: FlatCoatedRetriever167


title: NHP_CIRCLE-off-target-site7_Group3_302


title: FlatCoatedRetriever166


title: FlatCoatedRetriever165


title: FlatCoatedRetriever173


title: FlatCoatedRetriever164


title: NHP_CIRCLE-off-target-site6_Group4_403


title: NHP_CIRCLE-off-target-site6_Group4_402


title: FlatCoatedRetriever163


title: FlatCoatedRetriever172


title: FlatCoatedRetriever161


title: NHP_CIRCLE-off-target-site7_Group3_301


title: FlatCoatedRetriever160


title: NHP_CIRCLE-off-target-site6_Group3_303


title: NHP_CIRCLE-off-target-site6_Group3_302


title: NHP_CIRCLE-off-target-site6_Group4_401


title: NHP_CIRCLE-off-target-site6_Group3_301


title: FlatCoatedRetriever159


title: FlatCoatedRetriever158


title: FlatCoatedRetriever157


title: NHP_CIRCLE-off-target-site5_Group4_403


title: NHP_CIRCLE-off-target-site5_Group4_402


title: NHP_CIRCLE-off-target-site5_Group4_401


title: FlatCoatedRetriever156


title: NHP_CIRCLE-off-target-site5_Group3_303


title: NHP_CIRCLE-off-target-site5_Group3_302


title: FlatCoatedRetriever154


title: FlatCoatedRetriever153


title: NHP_CIRCLE-off-target-site4_Group4_403


title: FlatCoatedRetriever162


title: FlatCoatedRetriever152


title: FlatCoatedRetriever151


title: FlatCoatedRetriever150


title: NHP_CIRCLE-off-target-site5_Group3_301


title: NHP_CIRCLE-off-target-site4_Group3_302


title: NHP_CIRCLE-off-target-site4_Group4_401


title: NHP_CIRCLE-off-target-site4_Group3_303


title: NHP_CIRCLE-off-target-site4_Group3_301


title: FlatCoatedRetriever148


title: FlatCoatedRetriever149


title: FlatCoatedRetriever147


title: NHP_CIRCLE-off-target-site3_Group4_403


title: FlatCoatedRetriever146


title: NHP_CIRCLE-off-target-site4_Group4_402


title: NHP_CIRCLE-off-target-site3_Group4_402


title: NHP_CIRCLE-off-target-site3_Group4_401


title: FlatCoatedRetriever144


title: FlatCoatedRetriever155


title: NHP_CIRCLE-off-target-site3_Group3_303


title: FlatCoatedRetriever143


title: NHP_CIRCLE-off-target-site3_Group3_301


title: FlatCoatedRetriever141


title: FlatCoatedRetriever142


title: NHP_CIRCLE-off-target-site2_Group4_402


title: NHP_CIRCLE-off-target-site2_Group4_403


title: FlatCoatedRetriever140


title: FlatCoatedRetriever139


title: FlatCoatedRetriever138


title: FlatCoatedRetriever137


title: FlatCoatedRetriever136


title: NHP_CIRCLE-off-target-site1_invitro_Rep3


title: NHP_CIRCLE-off-target-site2_Group3_302


title: NHP_CIRCLE-off-target-site2_Group4_401


title: NHP_CIRCLE-off-target-site2_Group3_301


title: NHP_CIRCLE-off-target-site2_Group3_303


title: FlatCoatedRetriever145


title: NHP_CIRCLE-off-target-site1_invitro_Rep1


title: FlatCoatedRetriever133


title: NHP_CIRCLE-off-target-site1_Group4_403


title: FlatCoatedRetriever134


title: NHP_CIRCLE-off-target-site1_invitro_Rep2


title: FlatCoatedRetriever132


title: FlatCoatedRetriever135


title: FlatCoatedRetriever131


title: FlatCoatedRetriever129


title: FlatCoatedRetriever130


title: NHP_CIRCLE-off-target-site1_Group4_401


title: NHP_CIRCLE-off-target-site3_Group3_302


title: NHP_CIRCLE-off-target-site1_Group4_402


title: NHP_CIRCLE-off-target-site1_Group3_303


title: NHP_CIRCLE-off-target-site1_Group3_302


title: FlatCoatedRetriever127


title: FlatCoatedRetriever126


title: NHP_CIRCLE-off-target-site1_Group3_301


title: FlatCoatedRetriever125


title: Group4_403_testes

source_name: whole tissue lysate


title: Group4_403_spleen


title: FlatCoatedRetriever122


title: FlatCoatedRetriever124


title: FlatCoatedRetriever123


title: Group4_403_pancreas


title: Group4_403_skeletal_muscle


title: Group4_403_lung


title: Group4_403_kidney


title: FlatCoatedRetriever121


title: FlatCoatedRetriever120


title: TNF+VAL sample 3

city: Kannapolis

first: Dragan

last: Milenkovic

state: NC

address: 600 Laureate Way

department: Department of Food Bioprocessing & Nutrition Sciences

institute: North Carolina State University

description: Gene expression data from cells exposed to valerolactone metabolites

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix chips

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

data_processing:
data analysis were performed using Thermo Fisher Scientific Transcriptome Analysis Console software version 4.0.2
RMA

label: biotin

source_name: human brain microvascular endothelial cells with TNF treatement + Mixture of valerolactone metabolites

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

growth_protocol: Cells, at passage 2 were grown until passage 5 when they received the treatement

extract_protocol: Total RNA, including short RNAs as miRNAs, were extracted using Monarch® Total RNA Miniprep Kit (New England BioLabs, USA) following manufacture’s instruction.

treatment_protocol: Cells were stressed with TNF for 4 hours, or without TNF for negative control. Following the TNF traitement, the cells were exposed to the mixture of gut metabolites for 20h. The metabolites were 5-(4′-Hydroxyphenyl)-γ-valerolactone-3′-sulfate (γVL3′G) and 5-(4′-Hydroxyphenyl)-γ-valerolactone-3′-O-glucuronide (γVL3′S)

value: primary brain microvascular endothelial cells


title: Group4_403_brain


title: FlatCoatedRetriever128


title: FlatCoatedRetriever116


title: FlatCoatedRetriever117


title: Group4_403_heart


title: FlatCoatedRetriever118


title: FlatCoatedRetriever115


title: FlatCoatedRetriever119


title: TNF+VAL sample 2


title: Group4_403_adrenal_Gland


title: TNF+VAL sample 1


title: TNF sample 3

source_name: human brain microvascular endothelial cells with TNF treatement


title: Group4_402_testes


title: FlatCoatedRetriever111


title: FlatCoatedRetriever110


title: FlatCoatedRetriever109


title: Group4_402_spleen


title: TNF sample 1


title: FlatCoatedRetriever112


title: FlatCoatedRetriever108


title: FlatCoatedRetriever107


title: FlatCoatedRetriever105


title: Negative control 3

source_name: human brain microvascular endothelial cells without treatement


title: FlatCoatedRetriever114


title: FlatCoatedRetriever106


title: Negative control 2


title: Group4_402_skeletal_muscle


title: Group4_402_heart


title: FlatCoatedRetriever103


title: Group4_402_lung


title: FlatCoatedRetriever104


title: Negative control 1


title: JN_9

city: Changchun City

first: Dan

last: Yao

address: No.2888 Xincheng street, Changchun City, Jilin Province

institute: country College of Life Sciences, Jilin Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
First, 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.
Then, we aligned reads of samples to the reference genome using TopHat2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
CPC and CNCI were used  to predict coding potential of novel lncRNAs longer than 200nt.
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: Glycine max

source_name: soybean

growth_protocol: the fourth-generation low-linolenic acid mutant ‘MT72’

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA removal kit (Illumina, San Diego, USA).Then the left RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the Truseq Stranded Total RNA HT Sample Prep Kit (Illumina, San Diego, USA).

treatment_protocol: wild type‘JN18’

tag: genotype/variation

value: JN18 wild type

value: 30d after flowering

value: young pods


title: Group4_402_pancreas


title: FlatCoatedRetriever102

value: Flatcoated Retriever


title: FlatCoatedRetriever101


title: FlatCoatedRetriever100


title: FlatCoatedRetriever113


title: Group4_402_brain


title: FlatCoatedRetriever99


title: TNF sample 2


title: JN_8


title: NHP_CIRCLE-off-target-site1_invivo_control_Rep3


title: Group4_402_adrenal_Gland


title: FlatCoatedRetriever96


title: JN_7


title: FlatCoatedRetriever97


title: FlatCoatedRetriever95


title: Group4_402_kidney


title: FlatCoatedRetriever93


title: JN_6

value: 40d after flowering


title: FlatCoatedRetriever92


title: FlatCoatedRetriever94


title: Wild-type 2

city: St. Louis

first: Muhammad Farooq

last: Rai

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 7 top-level assembly with STAR version 2.0.4b. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Isoform expression of known Ensembl transcripts were estimated with Sailfish version 0.6.13. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.3.
All gene counts were then imported into the R/Bioconductor package EdgeR5 and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis. The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights function and coefficients for conditions, sex, age, and BMI were fitted using a Limma generalized linear model with additional unknown latent effects as determined by surrogate variable analysis (SVA). The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
For each contrast extracted with Limma, global perturbations in known Gene Ontology (GO) terms, MSigDb, and KEGG pathways were detected using the R/Bioconductor package GAGE to test for changes in expression of the reported log 2 fold-changes reported by Limma in each term versus the background log 2 fold-changes of all genes found outside the respective term. The R/Bioconductor package heatmap3 was used to display heatmaps across groups of samples for each GO or MSigDb term with a Benjamini-Hochberg false-discovery rate adjusted p-value less than or equal to 0.05. Perturbed KEGG pathways where the observed log 2 fold-changes of genes within the term were significantly perturbed in a single-direction versus background or in any direction compared to other genes within a given term with p-values less than or equal to 0.05 were rendered as annotated KEGG graphs with the R/Bioconductor package Pathview.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.gene_counts.txt: Tab-delimited text files include CPM and RPKM.

source_name: Wild-type

growth_protocol: Chondrocytes were isolated from femoral head cartilage. Total RNA was extracted from chondrocytes after 2 days of culture.

extract_protocol:
RNA isolation was performed using RNeasy Spin Column method (Qiagen). RNA quality and concentrations were measured by Agilent Bioanalyzer.
ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol.
cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina HiSeq 3000 using single-end reads extending 50 bases.

treatment_protocol: No treatment. Only the differences between wild-type and Postn-null mice were determined at baseline.

value: WT

tag: Sex

value: Male

value: 21 days

value: Joint chondrocytes


title: Wild-type 3


title: Group4_401_skeletal_muscle

value: off-target


title: FlatCoatedRetriever90


title: Group4_401_lung


title: Group4_401_pancreas


title: MT_9

value: low-linolenic acid mutant MT72


title: MT_8


title: Group4_401_spleen

value: targeted amplicon sequencing


title: Periostin knockout 3

source_name: Periostin knockout

value: Periostin knockout


title: JN_4


title: JN_5


title: Wild-type 1


title: Group4_401_kidney


title: FlatCoatedRetriever98


title: FlatCoatedRetriever89


title: Periostin knockout 2


title: MT_7


title: FlatCoatedRetriever88


title: Group4_401_heart


title: Group4_401_testes


title: Periostin knockout 1


title: Group4_401_brain


title: MT_6


title: FlatCoatedRetriever91


title: MT_5


title: FlatCoatedRetriever86


title: FlatCoatedRetriever87


title: Group4_401_adrenal_Gland


title: MT_4


title: FlatCoatedRetriever84


title: Group3_303_testes


title: Group3_303_spleen


title: LP_ovary6

city: Hangzhou

first: Haiguang

last: Mao

state: Zhejiang

address: Yuhangtang Road 866

institute: Zhejiang University

description: ovary with  low egg  production performance

data_processing:
Firstly, cutadapt-1.9 (cutadapt.readthedocs.io/en/stable/) was used to remove the reads that contained adapter contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC v0.10.1 (www.bioinformatics.babraham.ac.uk/projects/fastqc/).
We used hisat2-2.0.4 (ccb.jhu.edu/software/hisat2/)to map reads to the genome of Homo sapiens, Ensembl v96 (command line: hisat2 -1 R1.fastq.gz -2 R2.fastq.gz -S mapped.sam). The mapped reads of each sample were assembled using stringtie-1.3.4 (ccb.jhu.edu/software/stringtie/) with default parameters (command line: stringtie -p 2 -G genome.gtf -o output.gtf -l mapped.bam). Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using gffcompare (github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kb)]).
LncRNA identification:First of all, transcripts that overlapped with known mRNAs and transcripts shorter than 200 bp were discarded. Then we utilized CPC0.9-r2 (cpc2.cbi.pku.edu.cn/) with default parameters(cpc2 -i novel.fa -o cpc2.out) and CNCI2.0 (wwww.bioinfo.org/software/cnci) with default parameters (CNCI.py -f novel.fa -o CNCI.result -p 1 -m ve -g novel.gtf -d genome.fa) to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 were removed and remained transcripts were considered as lncRNAs.
Different expression analysis of mRNAs and lncRNAs:StringTie was used to perform expression level for mRNAs and lncRNAs by calculating FPKM. The differentially expressed mRNAs and lncRNAs were selected with log2 (fold change) >= 1 or log2 (fold change) <= -1 and with statistical significance p value < 0.05 by R package edgeR (bioconductor.org/packages/release/bioc/html/edgeR.html/) .
Target gene prediction and functional analysis of lncRNAs:To explore the function of lncRNAs, we predicted the cis-target genes of lncRNAs. lncRNAs may play a cis role acting on neighboring target genes. In this study, coding genes in 100,000 upstream and downstream were selected by python script. Then, we showed functional analysis of the target genes for lncRNAs with GO and KEGG enrichment analysis.
Genome_build: Columba livia (assembly Cliv_1.0)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Columba livia

extract_protocol:
Total RNA was isolated and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, USA). After the enriched circRNAs were fragmented into small pieces using divalent cations under high temperature. After removing ribosomal RNAs, the left RNAs were reverse-transcribed to create the cDNA,which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single-or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs.The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

tag: tisssue

value: ovary

value: 2 years old

tag: development satge

value: sexual maturity


title: FlatCoatedRetriever83


title: LP_ovary5

source_name: ovary with  low egg  production performance


title: LP_ovary4


title: FlatCoatedRetriever82


title: Group3_303_pancreas

value: intravenous

value: base-edited PCSK9


title: Group3_303_lung


title: FlatCoatedRetriever81


title: HP_ovary3

description: ovary with  high egg  production performance


title: HP_ovary2

source_name: ovary with  high egg  production performance


title: HP_ovary1


title: FlatCoatedRetriever85


title: Group3_303_heart


title: FlatCoatedRetriever78


title: Group3_303_skeletal_muscle


title: FlatCoatedRetriever79


title: FlatCoatedRetriever77


title: Input-CzcR

first: Ke

last: Fan

address: No.646, Songtao Road

institute: Shanghai Institute of Materia Medica

data_processing:
Basecalls performed using Bcl2fastq (v2.17.1.14)
Data were filtered using Cutadapt（version 1.9.1）with the following specification:In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt[1]（version 1.9.1）to be high quality clean data.
ChIP-seq reads were aligned to the PAO1 genome assembly using bowtie2(Version: 2.2.6) with the following configuration:Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, bowtie-build was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Bowtie2.
peaks were called using MACS2 version 2 with the following setting: p-value (≤1e-5), Enrichment Fold (1)
Genome_build: p.aeruginosa PAO1(ASM676v1)
Supplementary_files_format_and_content: peak text files

organism: Pseudomonas aeruginosa

source_name: pseudomonas aeruginosa

growth_protocol: the strain was cultured in LB for three hours at 37°C in a roller

extract_protocol:
Protein-DNA complexes were cross-linked by addition of formaldehyde (final concentration 1%) and incubated at 37°C for ten minutes in a roller. Cross-linking was quenched by addition of glycine (final concentration 125 mM). The final OD600 was recorded and cells were collected from 30 OD600 of culture via centrifugation and washed twice with Tris-buffered saline (20 mM Tris-HCl pH 8.0, 150 mM NaCl). Pellets were re-suspended in 1.5 ml Immunoprecipitation buffer (IP buffer) (50 mM Hepes-KOH pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, protease inhibitor cocktail) and sonicated to shear DNA to an average size of 200–700 bp, Samples were sonicated on Scientz (JY92-IIDN) with the following conditions: total output 10%, 1-second on, 2-second off, for 39 min on ice. Insoluble cellular debris was removed by centrifugation (14,000 rpm, 25 minutes, and 4°C) and the supernatant used as input sample in IP experiments. The protein A beads (Yue-ke Biotechnology CO.,LTD, Lot#YK-2009-33) were blocked at 4°C in IP buffer for four hours with 10μL anti-Flag monoclonal antibody (Cat#: AGM12165, Aogma), approximately 1.0 ml of the input sample was incubated overnight at 4°C on a rotating wheel with 10 µl anti-Flag antibodies. The protein A beads were then collected and washed once with immunoprecipitation buffer, once with immunoprecipitation buffer plus 500 mM NaCl, once with immunoprecipitation buffer plus 500 mM LiCl, and once with Tris-EDTA buffer (pH 8.0). 100 μl Elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) was added to the beads and incubated at 65°C for 20 minutes. The supernatants were saved after spin. 150 μl elution buffer 2 (0.67% Tris-EDTA buffer) was then added into the remaining beads. The elution buffer 1 and elution buffer 2 were combined for each sample, and then incubated for overnight at 65 °C to reverse crosslinking. Samples were then treated with RNase A by incubation for 1h at 37°C and 2h at 65°C in elution buffer plus 100 µg proteinase K. DNA was extracted twice with phenolchloroform, precipitated and re-suspended in 20 µl of water.
DNA fragments (150 to 300 bp) were selected for library construction, and sequencing libraries prepared using the NEBNext Ultra II DNA Library Prep kit. The final DNA libraries were validated with Agilent 2100 Bioanalyzer using Agilent High Sensitivity DNA Kit, then the libraries were sequenced using the HiSeq X ten system (Illumina).

treatment_protocol: untreated

tag: growth protocol

value: LB for 3 hrs


title: Y, biological rep 1

city: Ankara

first: Ceren

last: Sucularli

address: Sihhiye

country: Turkey

institute: Hacettepe University

description: Y, rep1

hyb_protocol: Following fragmentation, 3.5 μg of cRNA were hybridized for 16 hr at 45oC on GeneChip Cartridge Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Command Console (P/N 702569)

data_processing: RMA normalized using Affymetrix Expression Console Software 1.4.1.46

source_name: HeLa cells

label_protocol: Biotinylated cRNA were prepared according to the standard GeneChip WT PLUS Reagent Kit protocol from 5.5 μg total RNA (GeneChip WT PLUS Reagent Kit user manual, P/N 703174).

growth_protocol: 5x106 HeLa cells were plated in T75 flask and placed in a 5% CO2 37oC incubator for 16 h

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.

treatment_protocol: Different treatment was applied to each experimental group. K group: HeLa cells were incubated for 6 days without treatment. D group: HeLa cells were treated with 300 nM doxorubicin for 72 h and then incubated for 72 hours without treatment.  D+Ys group: HeLa cells were treated with 300 nM doxorubicin for 72 h and then treated with 10μM Y27632 ( a Rho kinase inhibitor) for 72 h. D+Y group: HeLa cells were pretreated with 10μM Y27632 (30 min) and treated with 300 nM doxorubicin for 72 h. and then incubated for 72 hours without treatment.  Y group:  HeLa cells were incubated for 72 h without treatment and then treated with 10μM Y27632 ( a Rho kinase inhibitor) for 72h.

tag: cell line

value: HeLa

tag: agent

value: incubated for 72 h without treatment and then treated with 10μM Y27632 ( a Rho kinase inhibitor) for 72 h


title: Y, biological rep 3

description: Y, rep3


title: Control, biological rep 1

description: K, rep1

value: incubated for 6 days without treatment


title: Control, biological rep 3

description: K ,rep3


title: Control, biological rep 2

description: K, rep2


title: FlatCoatedRetriever80

value: Flatcoated Retriever


title: Group3_303_kidney


title: D, biological rep 2

description: D, rep2

value: treated with 300 nM doxorubicin for 72 h and then incubated for 72 hours without treatment


title: D, biological rep 1

description: D, rep1


title: ChIP-CzcR-3

tag: chip antibody

value: anti-Flag monoclonal antibody (Cat#:AGM12165, Aogma)


title: D, biological rep 3

description: D, rep3


title: Y, biological rep 2

description: Y, rep2


title: ChIP-CzcR-2


title: FlatCoatedRetriever75


title: Group3_302_testes


title: Group3_303_brain


title: Group3_303_adrenal_Gland


title: FlatCoatedRetriever76


title: ChIP-CzcR-1


title: Group3_302_spleen


title: Group3_302_skeletal_muscle


title: Input-DK2-PB6h

data_processing:
Basecalls performed using Bcl2fastq (v2.17.1.14)
Data were filtered using Cutadapt（version 1.9.1）with the following specification:In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt[1]（version 1.9.1）to be high quality clean data.
ChIP-seq reads were aligned to the PAO1 or DK2 genome assembly using bowtie2(Version: 2.2.6) with the following configuration:Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, bowtie-build was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Bowtie2.
peaks were called using MACS2 version 2 with the following setting: p-value (<1e-5), Enrichment Fold (1)
Genome_build: p.aeruginosa PAO1 (ASM676v1), DK2 (ASM27136v1)
Supplementary_files_format_and_content: peak text files

growth_protocol: the strain was cultured in low Pi medium (LPM) for six hours at 37°C in a roller

value: PB (medium for Cultivation of pseudomonas aeruginosa) for 6 hrs


title: FlatCoatedRetriever74


title: FlatCoatedRetriever72


title: FlatCoatedRetriever73


title: Group3_302_pancreas

value: off-target


title: D+YS, biological rep 3

description: D+YS, rep3

value: treated with 300 nM doxorubicin for 72 h and then treated with 10μM Y27632 ( a Rho kinase inhibitor) for 72h


title: Group3_302_kidney

value: targeted amplicon sequencing


title: D+YS, biological rep 2

description: D+YS, rep2


title: D+YS, biological rep 1

description: D+YS, rep1


title: ChIP-DK2-PB6h-1


title: ChIP-DK2-PB6h-2


title: Group3_302_lung


title: Group3_302_brain


title: FlatCoatedRetriever69


title: Input-PB6h


title: D+Y, biological rep 1

description: D+Y, rep1

value: pretreated with 10μM Y27632 ( a Rho kinase inhibitor, 30 min) and treated with 300 nM doxorubicin for 72 h, and then incubated for 72 hours without treatment


title: ChIP-PB6h-1


title: D+Y, biological rep 2

description: D+Y, rep2


title: ChIP-LPM24h-2

value: low Pi medium (LPM) for 24 hrs


title: D+Y, biological rep 3

description: D+Y, rep3


title: FlatCoatedRetriever71


title: FlatCoatedRetriever68


title: S10601: ETA sheet-3

city: Yokohama-shi

first: Jafar

last: Sharif

state: Kanagawa-ken

address: 1-7-22 Suehiuro-cho, Tsurumi-ku

department: IMS

institute: RIKEN

data_processing:
Transcripts Per Kilobase Million (TPM) values were calculated with Salmon.
Raw reads were mapped to the mouse (mm9) genome using Bowtie2.
Genome_build: mm9
Supplementary_files_format_and_content: TPMs for each sample

source_name: Ear skin

extract_protocol:
Mouse ear was dissected and separate the dorsal and ventral side of skin. Ear was incubated with dispase solution or exofoliative toxin A solution at 37 °C. Epidermal sheet and ETA sheet were removed and subjected to isolation of total RNA. Total RNA was prepared using the RNeasy mini kit (QIAGEN). ど
RNA-seq library was prepared by the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA). Libraries were quantified using the KAPA Library Quantification Kit (Illumina GA). Samples were multiplexed, adjusted to 2 nM, and sequenced on an Illumina HiSeq 2000 instrument. Reads were generated via 25 bp paired-end sequencing.

value: Ear

tag: age

value: 8 week old

tag: gender

value: female


title: Group3_302_adrenal_Gland

value: intravenous

value: base-edited PCSK9


title: FlatCoatedRetriever70

source_name: whole blood


title: FlatCoatedRetriever67


title: Group3_301_testes


title: Input-LPM

value: low Pi medium (LPM)


title: ChIP-LPM24h-1


title: FlatCoatedRetriever66


title: Group3_302_heart


title: ChIP-LPM6h-3

value: low Pi medium (LPM) for 6 hrs


title: Group3_301_spleen


title: Group3_301_skeletal_muscle


title: ChIP-LPM6h-2


title: FlatCoatedRetriever64


title: Group3_301_pancreas


title: Nkx3.1 -/- Prostate - Paraquat (CAD59)

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

description: processed data file: matrix for mouse_ENS.txt

data_processing:
RNA-seq pipeline description:
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.
We use RTA (Illumina) for base calling and CASAVA (version 1.8.2) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat [1] (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.  We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [2] (version 2.0.2) with default settings. We test for differentially expressed genes under various conditions using DEseq [3]. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Raw RNAseq counts were normalized (variance stabilization) using DESeq package in R-studio Version 0.99.484
Genome_build: Ensembl/GRCm38.p2
Supplementary_files_format_and_content: Tab-delimited text file includes DESeq normalized values for each Sample

source_name: Prostate tissue

extract_protocol:
RNA was extracted using the MagMAX-96 RNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyser 2100
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.

value: hybrid 129/SvImJ and C57Bl/6J strain

tag: tissue

value: prostate

value: 4 months

value: paraquat


title: FlatCoatedRetriever63

value: Flatcoated Retriever


title: Group3_301_lung

value: off-target


title: Nkx3.1 -/- Prostate - Paraquat (CAD58)


title: Group3_301_kidney


title: FlatCoatedRetriever62


title: FlatCoatedRetriever61


title: Nkx3.1 -/- Prostate - Paraquat (CAD56)


title: BM_PP_2

city: Beijing

first: Yan

state: Beijing

address: 2 Yuanmingyuan West Road

department: Plant Genetics and Breeding

institute: China Agricultural University

data_processing:
Library strategy: Polysome profiling
Base calling was performed following the standard Illumina protocol.
Raw paired-end reads of m6A-Seq, RNA-Seq and polysome profiling were filtered and adapter sequences were trimmed out by Trimmomatic (v0.35) with parameters ILLUMINACLIP TruSeq3-PE-2.fa MINLEN 30.
Cleaned reads from B73 and F1 hybrid B73×Mo17 were mapped to the maize B73 reference genome (AGPv4.38) and clean reads from Mo17 were mapped to the maize Mo17 pseudogenome constructed by substituting maize B73 reference genome (AGPv4.38) with single nucleotide polymorphisms from Mo17 (CAU-1.0) using Hisat2 (v2.1.0).
Reads matching to less than five places were retained for further analysis.
m6A peaks were identified using the MACS2 peak calling algorithm with the input as background and the parameter of effective genome size was adjusted to the transcriptome size (417272442) and q value was set to 0.01.
Genome_build: Zea mays B73 RefGen_v4, Zm-Mo17-REFERENCE-CAU-1.0
Supplementary_files_format_and_content: Tab-delimited text files include m6A peaks locus for each sample.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of genes for each sample.

organism: Zea mays

source_name: seedlings

growth_protocol: Plants were grown under normal condition with a photoperiod of 16 h light at 28°C and 8 h dark at 25°C.

extract_protocol:
Total RNA was extracted using Trizol reagent (Ambion life technologies) according to manufacturer’s protocol. Polysome-bound RNA was extracted as described in Zhang et al., 2017.
Libraries of RNA-seq, m6A-seq, and polysome profiling for F1 hybrid were constructed using the NEBNext Ultra II RNA Library Prep Kit (E7770S, NEB) following the manufacturer’s protocol.

tag: ecotype

value: Seedlings

value: 14 days


title: Nkx3.1 -/- Prostate - Paraquat (CAD57)

tag: treatment


title: Group3_301_heart

value: targeted amplicon sequencing


title: Group3_301_brain


title: FlatCoatedRetriever60

tag: breed


title: Nkx3.1 -/- Prostate - Paraquat (CAD60)

tag: strain


title: A549_siPLANE_4

city: Zhengzhou

first: liu

last: Teng

address: No 7,Weiwu Road,Jinshui  District

department: Translational Research Institute

institute: Henan Provincial People’s Hospital and People’s Hospital of Zhengzhou University

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Trimmomatic (v0.30) to be high quality clean data.
Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq Bioconductor package, a model based on the negative binomial distribution. After adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate, P-value of genes were setted <0.05 to detect differential expressed ones.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, log2foldchange, pvalue, qvalue

source_name: Lung adinocarcinoma cell  line

growth_protocol: cells were maintained in DMEM (Biological Industries, #01-052-1ACS; Beit Haemek, Israel) supplemented with 10% fetal bovine serum (FBS, Biological Industries, #04-001-1A; Beit Haemek, Israel) and 1% penicillin-streptomycin (Biological Industries, #03-031-1BCS，Beit Haemek, Israel).  Cells were cultured in a humidified incubator at 37 °C and 5% CO2.

extract_protocol:
RNA was extracted using TRIzol™ Reagent(Catalog number:  15596026,ThermoFisher Scientific) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549 cells were seeded in 6-well plate (1.5X10^5/well). Transfections were performed after 24h by using Lipofectamine™ 3000 Transfection Reagent (Thermo Fisher, L3000-015) according to the manufacturer’s instructions.In this study,we used two different PLANE siRNAs, A549_siPLANE_1 & A549_siPLANE_2  were transfacted with siRNA1, and  A549_siPLANE_3 & A549_siPLANE_4  were transfacted with siRNA2, NC was used for siRNA control

value: transfected with  PLANE siRNA(siRNA2)


title: FlatCoatedRetriever59


title: FlatCoatedRetriever65


title: BM_PP_1


title: A549_siPLANE_3


title: BM_CK_2

description: PolyA RNA

data_processing:
Base calling was performed following the standard Illumina protocol.
Raw paired-end reads of m6A-Seq, RNA-Seq and polysome profiling were filtered and adapter sequences were trimmed out by Trimmomatic (v0.35) with parameters ILLUMINACLIP TruSeq3-PE-2.fa MINLEN 30.
Cleaned reads from B73 and F1 hybrid B73×Mo17 were mapped to the maize B73 reference genome (AGPv4.38) and clean reads from Mo17 were mapped to the maize Mo17 pseudogenome constructed by substituting maize B73 reference genome (AGPv4.38) with single nucleotide polymorphisms from Mo17 (CAU-1.0) using Hisat2 (v2.1.0).
Reads matching to less than five places were retained for further analysis.
m6A peaks were identified using the MACS2 peak calling algorithm with the input as background and the parameter of effective genome size was adjusted to the transcriptome size (417272442) and q value was set to 0.01.
Genome_build: Zea mays B73 RefGen_v4, Zm-Mo17-REFERENCE-CAU-1.0
Supplementary_files_format_and_content: Tab-delimited text files include m6A peaks locus for each sample.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of genes for each sample.


title: ChIP-LPM6h-1

value: anti-Flag monoclonal antibody (Cat#:AGM12165, Aogma)


title: BM_CK_1

description: PolyA RNA


title: Nkx3.1 +/+ Prostate- Paraquat (CAD46)

tag: genotype


title: NHP_Untreated_3

source_name: whole liver lysate

value: on-target

value: Untreated


title: Nkx3.1 +/+ Prostate- Paraquat (CAD47)


title: FlatCoatedRetriever57


title: FlatCoatedRetriever58


title: BM_IP_2

data_processing:
Library strategy: MeRIP-seq
Base calling was performed following the standard Illumina protocol.
Raw paired-end reads of m6A-Seq, RNA-Seq and polysome profiling were filtered and adapter sequences were trimmed out by Trimmomatic (v0.35) with parameters ILLUMINACLIP TruSeq3-PE-2.fa MINLEN 30.
Cleaned reads from B73 and F1 hybrid B73×Mo17 were mapped to the maize B73 reference genome (AGPv4.38) and clean reads from Mo17 were mapped to the maize Mo17 pseudogenome constructed by substituting maize B73 reference genome (AGPv4.38) with single nucleotide polymorphisms from Mo17 (CAU-1.0) using Hisat2 (v2.1.0).
Reads matching to less than five places were retained for further analysis.
m6A peaks were identified using the MACS2 peak calling algorithm with the input as background and the parameter of effective genome size was adjusted to the transcriptome size (417272442) and q value was set to 0.01.
Genome_build: Zea mays B73 RefGen_v4, Zm-Mo17-REFERENCE-CAU-1.0
Supplementary_files_format_and_content: Tab-delimited text files include m6A peaks locus for each sample.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of genes for each sample.


title: NHP_Untreated_2

value: intravenous


title: Nkx3.1 +/+ Prostate- Paraquat (CAD45)


title: FlatCoatedRetriever56

data_processing:
Image data was analyzed using GenomeStudio with GT module (Illumina).
genotypes AA, AB, BB, NC=no call


title: BM_IP_1


title: Nkx3.1 +/+ Prostate- Paraquat (CAD44)


title: Nkx3.1 -/- Prostate - Paraquat (CAD55)


title: NHP_Untreated_1


title: NHP_Group4_403_6

value: base-edited PCSK9


title: FlatCoatedRetriever55


title: Nkx3.1 +/+ Prostate- Paraquat (CAD48)


title: NHP_Group4_402_6


title: FlatCoatedRetriever54


title: Group3_301_adrenal_Gland

source_name: whole tissue lysate


title: HIGM2 unswitched memory B cells replicate 1

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

data_processing:
Raw sequence reads were initially processed using FastQC (Babraham Institute, Cambridge, UK)
Adapter sequences and poor quality reads were removed using TrimGalore that uses Cutadapt for trimming
Quality-filtered reads were then mapped to the human genome (hg19) using STAR and uniquely mapped reads were retained
Read counts were calculated using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: dds_matrix.txt (DESeq2 count matrix)

source_name: Blood / PBMCs

extract_protocol:
Total RNA was extracted using Maxwell SimplyRNA kit
RNA-sequencing libraries from total mRNA were prepared and purified using Illumina Stranded mRNA Prep, Ligation kit (Illumina)

value: AICDA-/-

tag: cell type

value: unswitched memory B cells


title: FlatCoatedRetriever53


title: NHP_Group4_401_6


title: HIGM2 naive B cells replicate 2

value: naive B cells


title: NHP_Group3_303_6


title: FlatCoatedRetriever52


title: NHP_Group3_302_6


title: FlatCoatedRetriever51


title: HIGM2 naive B cells replicate 1


title: Control unswitched memory B cells replicate 2

value: WT


title: NHP_Group3_301_6


title: FlatCoatedRetriever50


title: HIGM2 unswitched memory B cells replicate 2


title: Control unswitched memory B cells replicate 1


title: FlatCoatedRetriever49


title: Control naive B cells replicate 2


title: NHP_Group2_203_6


title: FlatCoatedRetriever48


title: Nkx3.1 +/+ Prostate- Paraquat (CAD43)

value: hybrid 129/SvImJ and C57Bl/6J strain

value: prostate

value: 4 months


title: K09_12H_3 (2)

city: Nanjing

first: wang

last: yinying

state: Jiangsu

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

department: College of Agriculture

institute: Nanjing Agricultural University

description: count.csv

data_processing:
alignment: Hisat2 software version 2.1.0
assemble: stringtie software version 1.3.5
Genome_build: B73 AGPv4.59 reference genome
Supplementary_files_format_and_content: format: csv, content: genes reads count

source_name: seedling stalk

growth_protocol: K09 (resistant) and A08 (susceptible) seedling  are planted at a temperature at 26 ± 2 °C during a 14/10 h light/dark cycle, with the light density of 600 LUX, a  humidity approximately 75%.

extract_protocol:
RNA was extracted from the seedling stems at different time points inoculated with F. graminearum using TRIzol reagent (Invitrogen), then purified with the RNeasy
RNA samples were subject to quality control prior to the library construction using Illumina TruSeq RNA library prep kit v2

treatment_protocol: 20 μl of 1.0ⅹ10 6 /ml Fusarium graminearum  spore suspensions  in 0.001% Tween-20 were inoculated to the K09 (resistant) and A08 (susceptible)， seedling stem，and the seedling stalk of K09 and A08 were  harvested at 6h，12h，24h，48h and 72h. with non-infected materials at 6h as control.

value: stem

tag: developmental stage

value: seeding

tag: hours post inoculated

value: wild type


title: A08_12H_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: A08_24H_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: K09_24H_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: K09_CT_7

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv

value: MOCK


title: NHP_Group2_202_6

data_processing:
Library strategy: targeted amplicon sequencing
CIRCLE-seq pipeline (https://github.com/tsailabSJ/circleseq)
CHANGE-seq pipeline (https://github.com/tsailabSJ/changeseq)
iGUIDE pipeline (https://github.com/cnobles/iGUIDE)
For all targeted amplicon sequencing files, we used CRISPRESSO2 for the analysis: https://crispresso.pinellolab.partners.org/submission . This platform directly reads in a fastq.gz file and provides a summary about editing rates and allele frequency.
Genome_build: Hg38, mm10
Supplementary_files_format_and_content: for CIRCLE, CHANGE-seq and iGUIDE: text files containing identified off-target sites; html report file containing identified off-target sites; fastq-index output file generated by Miseq

value: targeted amplicon sequencing


title: Control naive B cells replicate 1


title: NHP_Group2_201_6


title: A08_CT_6

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: FlatCoatedRetriever47

value: Flatcoated Retriever


title: K09_48H_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: NHP_Group1_103_6

value: on-target


title: FlatCoatedRetriever46


title: K09_12H_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: single cell RNAseq SHF

city: Los Angeles

first: Reza

last: Ardehali

state: CA

address: 675 Charles E Young dr

department: Cardiology

institute: UCLA

data_processing:
RNA-seq data was mapped with OLego (v.1.1.5) and normalized by using TPM (transcripts per millions) analysis
Total number of reads mapped to a known transcript annotation was estimated using featureCounts version v1.5.0-p2
Expression levels for each transcript were determined by normalizing the counts returned by featureCounts using a custom Perl script
Genome_build: GRCH38/hg38
Supplementary_files_format_and_content: Raw feature counts for each sample

source_name: hESC-derived CMs-SHF

extract_protocol:
as described in paper
as described in paper
single cell RNA-seq

value: embryonic stem cell


title: single cell RNAseq FHF

source_name: hESC-derived CMs-FHF


title: K09_12H_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: NHP_Group1_102_6

value: intravenous


title: FlatCoatedRetriever45


title: K09_CT_6

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: FlatCoatedRetriever44


title: NHP_Group1_101_6

value: base-edited PCSK9


title: K09_48H_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: K09_24H_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: FlatCoatedRetriever42


title: FlatCoatedRetriever41


title: NHP_Group4_401_5


title: CPPS-rep3

city: Harbin

first: Guangyue

last: Li

state: heilongjang

address: No.26 Hexing Road Xiangfang District

department: College of Life Science

institute: Northeast Forestry University

data_processing:
ChIP-seq reads were quality and adapter trimmed with Cutadapt (version 1.14), before being aligned to the human hg38 genome with bowtie2 (version 2.3.5) using default parameters.
Resulting BAM files were sorted and indexed with samtools and PCR duplicates were filtered with picard tools MarkDuplicates (version 2.18.26) and MultiBamSummary and PlotCorrelation programs in DeepTools were used to complete correlation analysis of repeated samples.
Peaks were called on filtered input and control BAM files with MAC2 set to broadPeak with the following command line parameters: macs2 callpeak -t Input.bam -c Control.bam -f BAMPE -g hs -n CPP2 --broad --broad-cutoff 0.05 -q 0.05 --outdir . --keep-dup all
High confidence peak screening between samples was performed using Bedtools (v2.29.2) and BigWig coverage files were generated using bedGraphToBigWig (version 4) from MACS2 resulting bedgraphs.
Peaks were annotated by ChipSeeker package and the differences of each group on the Peaks were analyzed by DiffBind package in R
Genome_build: GRCh38
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: Bigwig files of histone marks

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells were cultured in RPMI-1640, supplemented with 10% fetal bovine serum (FBS) (Biological Industries USA, Inc.), and maintained at 37°C in an atmosphere of 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (cat# E7645S) from New England Biolabs Inc. (Ipswich, MA). The following steps were followed for library preparation: end repair, 5’ phosphorylation, dA-tailing, adapter ligation, U excision, cleanup of adaptor-ligated DNA without size selection, and library amplification for 12 to 13 cycles followed by clean-up with Agencourt AMPure XP. The quality of the libraries was assessed using the Agilent High Sensitivity DNA kit (cat# 5067-4626) on the Agilent 2100 Bioanalyzer (Agilent Technologies) and quantified using the NEBNext Library Quant kit for Illumina (cat# E7630S) from New England Biolabs Inc

treatment_protocol: Cells were individually treated with 30 μM of YPB, OPB and a control peptide for 48 h

value: triple negative breast cancer (TNBC) cell lines

value: control peptides


title: NHP_Group4_403_5


title: CPPS-rep2


title: CPPS-rep1


title: OPB-rep3

value: OPB


title: NHP_Group4_402_5


title: K09_CT_5

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: NHP_Group3_303_5


title: NHP_Group3_302_5


title: OPB-rep2


title: OPB-rep1


title: NHP_Group3_301_5


title: FlatCoatedRetriever38

first: Alexander

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.


title: FlatCoatedRetriever39


title: OPB-Input

value: untreated


title: A08_48H_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: CPPS-Input


title: FlatCoatedRetriever43


title: K09_CT_4

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: ChIP-PB6h-2

city: Shanghai

value: anti-Flag monoclonal antibody (Cat#:AGM12165, Aogma)

value: PB (medium for Cultivation of pseudomonas aeruginosa) for 6 hrs


title: K09_48H_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: NHP_Group2_203_5


title: K09_12H_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv


title: FlatCoatedRetriever37

city: Bethesda


title: YPB-rep3

value: YPB


title: A08_24H_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

description: count.csv

value: stem


title: YPB-rep2


title: NHP_Group2_201_5