title: DU-145 cells, shSLC4A4

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Using software from Illumina (bcl2fastq), sequencing reads were assigned into individual samples.
Sequencing reads were filtered for adapter sequence and low quality sequence. Low quality is defined as reads with more than 5% unknown bases (“N”) and reads having more than 50% of bases with quality value <= 11.
Filtered reads were mapped to reference genome (GRCh38) using STAR 2.5.2, followed by quantification of expression by RSEM 1.2.31.
Differentially expressed genes were identified by EBSeq 1.18.0.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: Prostate Cancer

growth_protocol: DU 145 Epithelial cells were maintained in EMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using PureLink® RNA Mini Kit according to the manufacturer's protocol.
cDNA libraries were prepared by KAPA mRNA HyperPrep Kit according to the manufacturer's protocol.

treatment_protocol: DU 145 Epithelial cells were knockdown with SLC4A4 shRNA

value: Prostate Cancer

value: Epithelial

value: Kockdown ShCL4A4 plasmid


title: 4501B SAM24395512

status: Public on Dec 05 2024

type: SRA

city: South San Francisco

first: Brad

middle: A

last: Friedman

state: CA

address: 1 DNA Way

department: Bioinformatics

country: USA

institute: Genentech, Inc.

library_source: transcriptomic

data_processing:
Reads were aligned to the genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package.
Assembly: Macaca_fascicularis_5.0
Supplementary files format and content: Each sample has a TSV data file with counts

molecule: total RNA

organism: Macaca fascicularis

source_name: Brain Frontal Cortex

extract_protocol:
RNA was extracted using the RNeasy Lipid Tissue extraction kit with on-column DNase digestion (Qiagen). Quality and quantity of total RNA samples were determined using ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent), respectively.
NGS Lab

tag: tissue

value: Brain Frontal Cortex

tag: animalsample

value: B

tag: treatment

tag: animalid


title: 4503B SAM24395514


title: DU-145 cells, shControl

organism: Homo sapiens

tag: cell line

tag: cell type

value: Kockdown Ctl plasmid


title: HL+187-5days-R-2 [M_19_2053_20_AD021_L003]

city: Jeddah

first: Sabiha

last: Parween

address: Thuwal

department: Hirt lab

country: Saudi Arabia

institute: KAUST

data_processing:
Illumina next generation sequencing platform
The reads were aligned to the reference genomes with Tophat v2.0.13. The obtained bam files were further converted in to gff files to analyse the data further. The number of reads in the alignments that overlap with gene features were counted with feature Counts 1.4.6.
Gene expression levels were normalized using log2 transform count Normalization
Arabidopsis thaliana
Assembly: Arabidopsis thaliana
Supplementary files format and content: Excel, log2 transform count based Normalization

organism: Arabidopsis thaliana

source_name: plant seedling

growth_protocol: Arabidopsis thaliana plants were grown at 22⁰C under 16 h light and 8 h dark period

extract_protocol:
Total RNA was extracted using Nucleospin RNA plant kit (Macherey-Nagel), we further followed with DNaseI treatment to remove gemomic DNA as per manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Ribo-zero Illumina protocol

treatment_protocol: Two different light stress regimes (normal light 130 μmol m-2 s-1 and high light 1050 μmol m-2 s-1 ) were implemented on SA187 colonized plants

value: plant seedling


title: LUHMES D115, D15, Rep2

city: Edinburgh

first: Aleksandra

last: Helwak

address: Max Born Crescent

department: Wellcome Centre for Cell Biology

country: United Kingdom

institute: The University of Edinburgh

data_processing:
Flexbar (version 3.4.0) - adapter trimming and quality fitering (quality threshold 30)
Reads were mapped to the genome (GRCh38 downloaded from Ensembl) using STAR (version 2.7.3a, --outMultimapperOrder Random)
Reads were aligned to the genomic features from annotation from GENECODE (gencode.v34.annotation.gtf; evidence-based annotation of the human genome (GRCh38), version 34 (Ensembl 100) from 2020-03-24) using featureCounts (version: 2.0.0, parameters: -p -t exon -g gene_id -Q 10 -s 2).
Assembly: hg38
Supplementary files format and content: tab-delimited output files from featureCounts with raw counts for each genomic feature; one processed file per sample

source_name: Brain; Mesencephalon

growth_protocol: Proliferating cells were grown on poly-L-ornithine and fibronectin coated dishes in Advanced DMEM/F12 with addition of L-Glutamine, N2 supplement and βFGF at 37C and 5% CO2.

extract_protocol:
Cells were lysed in Trizol and after the phase separation, aqueous phase was further purified using Zymo Direct-Zol Plus kit. Total RNA was treated with DNase RQ1 and the integrity was tested on Bioanalyzer.
Ribosomal RNA was depleted with NEBNext rRNA Depletion kit. RNAseq libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturers protocol and sequenced by BGI Genomics.

treatment_protocol: Cells were differentiated in two steps: for pre-differentiation proliferating cells were seeded in proliferation medium. The next day proliferation medium was exchanged for differentiation medium:  advanced DMEM/F12 with addition of L-Glutamine, N2, GDNF, cAMP and doxycycline for two days. On day 2 of differentiation cells were trypsinized, counted and seeded on 10 cm dish, starting second step of differentiation.  During the subsequent differentiation process, half of the medium was changed every second day. Cells were taken for analysis, 6 (D06), 10 (D10) and 15 (D15) days after the initial exchange to differentiation medium.

value: Brain; Mesencephalon

value: LUHMES

value: immortalized embryonic neuronal progenitor

tag: genotype

value: homozygous deletion of SNORD115 cluster

tag: clone

value: differentiation

tag: time


title: 1504C SAM24395507

value: C


title: 4502B SAM24395513


title: HL+187-5days-R-1 [M_19_2052_19_AD020_L003]


title: LUHMES H115, D10, Rep2

value: heterozygous deletion of SNORD115 cluster


title: WT replicate 4 experiment 2

city: La Jolla

first: Wolfgang

last: Busch

address: 10010 N Torrey Pines Rd

department: Plant Biology

institute: Salk Institute for Biological Studies

description:
14 day old A. thaliana Col-0 primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
myb67A_WT_r4_S4

data_processing:
Read quality was judged to be acceptable using FASTQC and FastqScreen. Low quality and adapter sequences were removed using Trimmomatic v0.39. The parameters used were ILLUMINACLIP:TruSeq.fasta:2:30:10 and SLIDINGWINDOW:4:15, with adapter sequences for paired-end reads provided with the Trimmomatic release. Trimmed reads were aligned using STAR v2.7.10a to a suffix array representation of the Arabidopsis thaliana TAIR10 assembly created using STAR --runMode genomeGenerate with default parameters and --genomeSAindexNbases 12 STAR --runMode alignReads was executed using default parameters and --outFilterMultimapNmax 1 to report only alignments from uniquely mapping reads, --outFilterMismatchNmax, 2, --alignIntronMax, 6000, --alignMatesGapMax, 7500, and --alignEndsType, EndToEnd. Visualizations of alignment coverage were generated using Integrative Genomics Viewer. First, SAM-format alignment data were converted to BedGraph format using makeUCSCfile from the HOMER collection 5  then converted to TDF format using igvtools 38 and loaded into IGV. Expression was quantified based on transcripts from the TAIR10 genome annotation using analyzeRepeats.pl from the HOMER suite. DEGs were determined using DESeq2 v1.40.1 48 with the design formula ~ batch + group where libraries from respective experiment were classified as batch and myb67 mutant and WT libraries were classified as group. False discovery rates (FDRs) were estimated using the Benjamini-Hochberg method and genes with a fold change magnitude of at least 1.5 and FDR less than 0.05 were reported. Periderm-specific DEG were determined to be those with expression in at least 5% of the nuclei in clusters 9 or 15 and less than 5% mean percentage of expression across all other clusters.
Assembly: TAIR10
Supplementary files format and content: myb67_mutant_mRNAseq_counts.tsv: estimated transcript counts from aligned reads
Supplementary files format and content: myb67_mutant_vs_WT.DEG.tsv: genes differentially expressed in myb67 mutant relative to WT Col-0

source_name: upper primary root day14

growth_protocol: Col-0 and myb67-1 mutant seeds were sown together on 1% agarose [Phytotech] media containing 2.22g/1L Murashige & Skoog Basal Salts [Phytotech] (pH5.7-5.8) in square (120 x 120 x 15mm) growth-plates [Greiner] for 14 days.

extract_protocol:
Starting at the base of the hypocotyl, 1.5cm of mature primary root tissue, with lateral roots removed, was collected in 1.5ml microcentrifuge tubes [Eppendorf] (~40 seedlings per biological replicate) and flash frozen in liquid nitrogen. Frozen tissue was ground by hand into a fine powder using plastic pestles and RNA was isolated using RNeasy Plant Mini Kit [Qiagen] following the manufacturer’s instructions.
RNeasy Plant Mini Kit [Qiagen]

value: upper primary root day14

value: plant root


title: LUHMES H115, D10, Rep1


title: 1504B SAM24395506


title: NL+187-R-3 [M_19_2051_18_AD019_L003]


title: 1504A SAM24395505

value: A


title: NL+187-R-2 [M_19_2050_17_AD018_L003]


title: LUHMES D115, D06, Rep2


title: WT replicate 2 experiment 2

description:
14 day old A. thaliana Col-0 primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
myb67A_WT_r2_S2


title: NL+187-R-1 [M_19_2049_16_AD016_L003]


title: 1503B SAM24395504


title: WT replicate 1 experiment 2

description:
14 day old A. thaliana Col-0 primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
myb67A_WT_r1_S1


title: LUHMES D115, D06, Rep1


title: WT replicate 5 experiment 2

description:
14 day old A. thaliana Col-0 primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
myb67A_WT_r5_S5


title: 1502B SAM24395503


title: myb67 replicate 5 experiment 2

description:
14 day old A. thaliana myb67 mutant in Col-0 background primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
myb67A_r5_S10

value: myb67 mutant


title: LUHMES D115, D10, Rep1


title: myb67 replicate 4 experiment 2

description:
14 day old A. thaliana myb67 mutant in Col-0 background primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
myb67A_r4_S9


title: LUHMES H115, D06, Rep2


title: LUHMES H115, D06, Rep1


title: 1501B SAM24395502


title: NL-1h-R2 [M_19_2047_14_AD014_L002]


title: NL-1h-R3 [M_19_2048_15_AD015_L002]


title: Chipseq_Lig4mm_Rad21_Auxin_rep2

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

library_source: genomic

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

growth_protocol: Cells were cultured using McCoy’s 5A media with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100ug/ml streptomycin. Cells were grown at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
Chipseq: Cultured cells were fixed with 1% formaldehyde for 10 min at room temperature and the reaction was quenched with 125 mM glycine. Twenty million fixed cells were washed with PBS, snap-frozen and stored at -80°C until further processing. Before use, the cells were resuspended in 1 ml of RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100 and freshly added Complete Mini EDTA free proteinase inhibitor. Sonication was performed using Branson sonicator at amplitude 35%, 12 cycles of 20 sec sonication followed by 30 sec of pause or using Covaris ME220 sonicator at duty factor 20%, peak incident power 75, cycle/burst 1000 for 6 min at 4°C. The antibody-protein solution was then incubated with 40 ml of Dynabeads Protein A for 40 min at room temperature under agitation. Antibody-bound beads were washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with LiCl buffer (0.25M LiCl, 0.5% NP-40, 0.5% NaDOC), once with TE pH 8.0 containing 0.2% Triton X-100, and once with TE pH 8.0. Crosslinks were reversed by incubating the beads at 65°C for 4 hours in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by ChIP DNA clean and concentrator column.
Chipseq: Ovation Ultralow Library System V2 kit , Hi-C library were amplified directly from of the beads with 4-6 cycles of PCR, using Illumina primers (Bioo Scientific) and Q5 Hi-Fidelity DNA polymerase

treatment_protocol: HCT116-Rad21-mAID-clover cells were grown for 3 days before addition of media containing 750uM indole-3-acetic acid (IAA). For AsiSI induction, HCT-116 cells containing the nAsiSI-T2A-BFP construct show efficient induction of breaks 4-8 hours following treatment with 1M 4OHT. In experiments where DNA damage was induced for 72h, fresh 4OHT was added every 24h. Inhibition of ATM was achieved by incubating cells with 1M KU-55933 for 1 hour prior to induction of DSBs

tag: chip antibody

value: Rad21 (abcam, Ab992)

value: Human colorectal carcinoma cell

value: Rad21_AIDdegron, Lig4-/-

value: IAA


title: LUHMES D115, D00, Rep2


title: HL-1hr-R3 [M_19_2043_9_AD009_L002]


title: myb67 replicate 3 experiment 2

description:
14 day old A. thaliana myb67 mutant in Col-0 background primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
myb67A_r3_S8


title: LUHMES D115, D00, Rep1


title: myb67 replicate 2 experiment 2

description:
14 day old A. thaliana myb67 mutant in Col-0 background primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
myb67A_r2_S7


title: Chipseq_Lig4mm_Rad21_Auxin


title: HL-1hr-R2 [M_19_2042_8_AD008_L002]


title: WT replicate 3 experiment 2

description:
14 day old A. thaliana Col-0 primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
myb67A_WT_r3_S3


title: LUHMES H115, D00, Rep2


title: myb67 replicate 1 experiment 2

description:
14 day old A. thaliana myb67 mutant in Col-0 background primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
myb67A_r1_S6


title: Chipseq_WT_Rad21_Auxin


title: HL-1hr-R1 [M_19_2041_7_AD007_L001]


title: WT replicate 6 experiment 1

description:
14 day old A. thaliana Col-0 primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
WT_r6_S6


title: LUHMES H115, D00, Rep1


title: Chipseq_WT_Mre11_ATMi_rep2

value: Mre11 (Novus Biologicals NB100-142)

value: DSB(4OHT), ATMi


title: WT replicate 5 experiment 1

description:
14 day old A. thaliana Col-0 primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
WT_r5_S5


title: LUHMES WT, D15, Rep2

value: Brain; Mesencephalon

value: WT

value: no clonal selection


title: RbpB (BT_1887) XL-minus, R2

city: Würzburg

first: Alexander

middle: J.

last: Westermann

address: Josef-Schneider-Straße 2/D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI),

data_processing:
CLIP libraries were filtered and trimmed with BBDuk (paired-end mode, phred score cutoff: 20, minimal length of reads: 12 nt)
Reads were deduplicated with FastUniq 1.1
Mapping was done with READemption 1.0.5 pipeline using segemehl 0.3.4 as mapping algorithm
Peak calling was performed with PEAKachu pipeline version 0.2.0
Assembly: B. thetaiotaomicron VPI-5482 reference genome (NC_004663.1) and plasmid (NC_004703.1)
Supplementary files format and content: Coverage files as wiggle format

organism: Bacteroides thetaiotaomicron

source_name: Bacteria

growth_protocol: For CLIP-assays, cultures were grown in TYG medium to an OD of 2

extract_protocol:
Co-immunoprecipitated RNA was isolated using Phenol/Chloroform/Isoamylalcohol
For CLIP-seq, libraries were prepared with the TruSeq Library Prep kit for Illumina

tag: strain

value: Bacteria

tag: condition

value: non-cross-linked control, 3xflag tagged RbpB, immunoprecipitated


title: WT replicate 4 experiment 1

description:
14 day old A. thaliana Col-0 primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
WT_r4_S4


title: RbpB (BT_1887) XL-plus, R2

value: UV cross-linked, 3xflag tagged RbpB, immunoprecipitated


title: Chipseq_WT_Mre11_ATMi


title: RbpB (BT_1887) XL-plus, R1


title: Chipseq_WT_Rad21_DSB_rep2


title: RbpB (BT_1887)XL-minus, R1


title: Chipseq_WT_Rad21_UTR_rep2


title: LUHMES WT, D10, Rep4

value: LUHMES

value: immortalized embryonic neuronal progenitor

value: differentiation


title: WT replicate 2 experiment 1

description:
14 day old A. thaliana Col-0 primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
WT_r2_S2

value: upper primary root day14

value: plant root


title: striatum TAAR5-WT mice, 10 months, animal 6

city: Saint-Petersburg

first: Nataliia

middle: Victorovna

last: Katolikova

address: Universitetskaya emb. 7-9-11

department: Institute of Translational Biomedicine

country: Russia

institute: Saint-Petersburg State University

data_processing:
The sequenced reads were checked for quality using the FastQC tool
Sequenced reads were trimmed using Cutadapt v4.1  with default parameters for single strand reads
Transcript expression, pre-processed reads were aligned with the reference genome M35 (GRCm39) with STAR (version 2.7.11b)
Gene expression was calculated with featureCounts v2.0.6
Assembly: genome M35 (GRCm39)
Supplementary files format and content: tab-determinated file with counts for each sample, non-normalised

molecule: polyA RNA

organism: Mus musculus

source_name: striatum

growth_protocol: The mice were housed three to four per cage and maintained under standard lab conditions (12 h light/dark cycle, 21 ± 1◦C, and 40–70% humidity) with food and water provided ad libitum. 10-months old C57Bl/6 littermate wild type (WT) and TAAR5-KO (KO) mice (Espinoza et al., 2020) were used in experiments.

extract_protocol:
Brains were dissected using Rodent brain matrices (1 mm coronal section, cat. # 69808-C, Electron Microscopy Sciences). The slice between AP 2 mm and Bregma was isolated. The cortex was removed from the slice and the remaining striatum was used for RNA isolation. Total RNA was isolated using ExtractRNA (cat. # BC032, Evrogen).
RNA quality was checked by capillary electrophoresis using the QIAxcel Advanced program (QIAGEN, Germany). rRNA was removed from total RNA using MGIEasy rRNA Depletion Kit MGIEasy rRNA Depletion Kit according to the manufacturer's recommendations, then RNA was quantified on a Quntus fluorimeter (Promega, USA) and used for preparation of directional libraries using MGIEasy RNA Directional Library Prep Set according to the manufacturer's recommendations. The quality of libraries was checked by capillary electrophoresis using QIAxcel Advanced program (QIAGEN, Germany).

value: striatum


title: Chipseq_WT_Rad21_Auxin_rep2

value: Rad21 (abcam, Ab992)

value: Human colorectal carcinoma cell


title: Chipseq_WT_Rad21_DSB_ATMi_rep2


title: LUHMES WT, D10, Rep3


title: striatum TAAR5-WT mice, 10 months, animal 5


title: WT replicate 1 experiment 1

description:
14 day old A. thaliana Col-0 primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
WT_r1_S1


title: LUHMES WT, D10, Rep2


title: myb67 replicate 6 experiment 1

description:
14 day old A. thaliana myb67 mutant in Col-0 background primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
myb67_r6_S17

value: myb67 mutant


title: striatum TAAR5-WT mice, 10 months, animal 4


title: LUHMES WT, D15, Rep3


title: Chipseq_Lig4mm_Mre11

value: Mre11 (Novus Biologicals NB100-142)

value: Rad21_AIDdegron, Lig4-/-


title: myb67 replicate 5 experiment 1

description:
14 day old A. thaliana myb67 mutant in Col-0 background primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
myb67_r5_S16


title: striatum TAAR5-WT mice, 10 months, animal 3


title: LUHMES WT, D10, Rep1

value: Brain; Mesencephalon


title: WT replicate 3 experiment 1

description:
14 day old A. thaliana Col-0 primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
WT_r3_S3


title: myb67 replicate 4 experiment 1

description:
14 day old A. thaliana myb67 mutant in Col-0 background primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
myb67_r4_S15


title: LUHMES WT, D06, Rep4

value: WT


title: Chipseq_WT_Mre11_rep2


title: Chipseq_Lig4mm_Rad21_UTR_rep2


title: LUHMES WT, D06, Rep3

value: no clonal selection


title: striatum TAAR5-WT mice, 10 months, animal 1


title: LUHMES WT, D06, Rep2


title: Chipseq_Lig4mm_Rad21_DSB_rep2


title: myb67 replicate 2 experiment 1

description:
14 day old A. thaliana myb67 mutant in Col-0 background primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
myb67_r2_S13


title: Chipseq_Lig4mm_Mre11_rep2


title: myb67 replicate 1 experiment 1

description:
14 day old A. thaliana myb67 mutant in Col-0 background primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
myb67_r1_S12


title: LUHMES WT, D06, Rep1


title: striatum TAAR5-KO mice, 10 months, animal 6


title: Chipseq_WT_Rad21_UTR

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
HiC-Seq: alignment: bwa-sw with default parameter (map each read separately)
HiC-Seq: filter: remove duplicates and near duplicates, removes reads that map to the same fragemnt and low quality reads (MAPQ <30)
HiC-Seq: generate contact matrix: juicer runnning with default parameter
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: hic

extract_protocol:
Chipseq: Cultured cells were fixed with 1% formaldehyde for 10 min at room temperature and the reaction was quenched with 125 mM glycine. Twenty million fixed cells were washed with PBS, snap-frozen and stored at -80°C until further processing. Before use, the cells were resuspended in 1 ml of RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100 and freshly added Complete Mini EDTA free proteinase inhibitor. Sonication was performed using Branson sonicator at amplitude 35%, 12 cycles of 20 sec sonication followed by 30 sec of pause or using Covaris ME220 sonicator at duty factor 20%, peak incident power 75, cycle/burst 1000 for 6 min at 4°C. The antibody-protein solution was then incubated with 40 ml of Dynabeads Protein A for 40 min at room temperature under agitation. Antibody-bound beads were washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with LiCl buffer (0.25M LiCl, 0.5% NP-40, 0.5% NaDOC), once with TE pH 8.0 containing 0.2% Triton X-100, and once with TE pH 8.0. Crosslinks were reversed by incubating the beads at 65°C for 4 hours in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by ChIP DNA clean and concentrator column.
HiC: Cultured cells were fixed with 1% formaldehyde and the reaction was quenched with 200 mM glycine. Cells were then lysed and digested with the MboI restriction enzyme. DNA ends were then marked with biotin-14-dATP and ligated by proximity. After reverse crosslinking, DNA was sheered to an average size of 200-400 bp. This DNA was then pulled down using MyOne Streptavidin T1 beads and washed.
Chipseq: Ovation Ultralow Library System V2 kit , Hi-C library were amplified directly from of the beads with 4-6 cycles of PCR, using Illumina primers (Bioo Scientific) and Q5 Hi-Fidelity DNA polymerase


title: striatum TAAR5-KO mice, 10 months, animal 4


title: empty vector replicate 2

description:
A. thaliana root empty vector DAP-seq library
AtMYB67_binding_motif1.homer
AtMYB67_binding_motif1_coords.fimo_qval_0.05.bed
AtMYB67_peaks.narrowPeak
AtMYB67_peaks_genes_motifs.fimo_qval_0.05.tsv

data_processing:
Read quality was judged to be acceptable using FASTQC and FastqScreen. Low quality and adapter sequences were removed using Trimmomatic v0.39. The parameters used were ILLUMINACLIP:TruSeq-PE.fasta:2:30:10 and SLIDINGWINDOW:4:15, with adapter sequences for paired-end reads provided with the Trimmomatic release. Trimmed reads were aligned to the Arabidopsis thaliana TAIR10 assembly using STAR v2.7.10a. The STAR index was created using default parameters and --genomeSAindexNbases 12, and STAR was run with default parameters and --outFilterMultimapNmax 1 to report only alignments from uniquely mapping reads. Duplicate alignments were removed using the Picard Tools v2.27.1 program MarkDuplicates (Broad Institute, https://broadinstitute.github.io/picard/). Visualizations of alignment coverage were generated using Integrative Genomics Viewer. First, SAM-format alignment data were converted to BedGraph format using makeUCSCfile from the HOMER collection using the parameter -fragLength 150 to smooth the peaks by extending alignment tags to 150bp, then converted to TDF format using igvtools and loaded into IGV. Regions with enriched read alignments (peaks) were identified using macs3 v3.0.0a7 (q value = <0.05) with replicate libraries for both the MYB67 and the empty vector samples used as inputs. Genes from the Araport11 gene annotation were associated with peaks using UROPA v4.0.2 following the rule: if a peak falls within 2000bp upstream or 500bp downstream of the TSS or within the gene body, then the gene is considered to be a putative target of the MYB67, with ties going to the closest gene. De novo motif discovery was carried out using findMotifsGenome.pl of the HOMER package. Peak sequences were searched for overrepresented 5-13 bp sub-sequences. The null distribution consisted of GC-normalized random draws from the entire genome sequence, enrichment was determined using the binomial test, and enriched motifs were compared to remove redundancy. One motif was highly prevalent among peaks and was visualized using the R universalmotif package. The positions of this motif within the peak loci were determined using fimo 8as follows. Peak loci sequences were obtained using BedTools the HOMER-style motif position weight matrix was converted to meme format using chen2meme from the MEME suite and a log-likelihood ratio score was computed by fimo for each peak subsequence, determining a p-value based on a null model of randomly generated sequences using the background base frequencies calculated from the entire genome using pyfastx. Bootstrapping was used to estimate false discovery rates (FDR, q-value) and motifs with an FDR of less than 0.05 were retained.
Assembly: TAIR10
Supplementary files format and content: *.tdf: alignment tracks for Integrative Genomics Viewer (IGV)
Supplementary files format and content: *.homer: Position Weight Matrix (PWM) in HOMER format
Supplementary files format and content: *.bed: genomic coordinates of motif occurrences in BED format
Supplementary files format and content: *.narrowPeak: genomic coordinateas of DAP-seq peaks in narrowPeak format
Supplementary files format and content: *.tsv: data associated with DAP-seq peaks including associated genes and motifs
Library strategy: DAP-seq

source_name: root

extract_protocol:
Genomic DNA(gDNA)libraries for Arabidopsis were created following protocols in Bartlett et al. andO’Malleyet al. with minor modifications.
10µg of Arabidopsis gDNA extracted from leaf tissue was fragmented to∼200bp ina CovarisS2sonicator. The fragmented gDNA was end-repaired using the End-It DNA End-Repair Kit (Biosearch Technologies, ER81050), A-tailed usingKlenow Fragment (3–5′exo) (NEB, M0212L), and the adaptor was ligatedusingthe truncatedIllumina TruSeq Y-adaptor.The adapter-ligatedlibrary was confirmed withRTqPCRas described in Bartlett et al. The MYB67 cDNA was TOPO cloned into a pIX-Halo plasmid (ABRC, stock # CD3-1742) per manufacturer’s instructions (ThermoFisher, 450218). This construct, along with an empty plasmid containing only the Halo tag, were incubated with the TNT SP6 Coupled Wheat Germ Extract System to produce Halo-MYB67 or Halo only proteins, respectively (Promega, PRL4130). 40µl of the resulting protein extracts were mixed with 10µl Magne HaloTag Beads (Promega, G7281) and 30ul of wash buffer (WB1; PBS + 0.005% NP40) on a rotator for 1h at room temperature. The beads with protein were then washed with WB1 as described in Bartlett et al. and then incubated with 100ng of the adapter-ligated gDNA library and also washed with WB1 for 1hr. The beads were then washed with WB1 as described in Bartlett et al. to remove unbound DNA fragments and then incubated at 98°C for 10min to denature the protein and release the bound DNA fragments. To amplify the released DNA, PCR reactions were prepared using Phusion DNA Polymerase (NEB, M0530S), a universal primer, and a unique Illumina index primer, to allow multiple samples to be pooled in one sequencing run. PCR products were then size-selected using Sera-Mag beads (Sigma-Aldrich, GE65152105050250) at a 1.0x ratio. The purified DNA libraries were measured by the Qubit HS ds DNA Assay Kit (ThermoFisher, Q32854) and sequenced on the Nextseq2000 with 100 cycles and 50bp sequence length.

value: root

tag: vector

value: empty


title: LUHMES WT, D00, Rep4


title: striatum TAAR5-KO mice, 10 months, animal 5


title: Chipseq_WT_Rad21_DSB_ATMi

value: DSB(4OHT), ATMi


title: empty vector replicate 1


title: striatum TAAR5-KO mice, 10 months, animal 3


title: striatum TAAR5-KO mice, 10 months, animal 2


title: MYB67 replicate 2

description:
A. thaliana root MYB67 DAP-seq library
AtMYB67_binding_motif1.homer
AtMYB67_binding_motif1_coords.fimo_qval_0.05.bed
AtMYB67_peaks.narrowPeak
AtMYB67_peaks_genes_motifs.fimo_qval_0.05.tsv


title: striatum TAAR5-WT mice, 10 months, animal 2


title: LUHMES WT, D15, Rep1

value: LUHMES


title: LUHMES WT, D00, Rep1

value: immortalized embryonic neuronal progenitor


title: Chipseq_Lig4mm_Rad21_UTR


title: myb67 replicate 3 experiment 1

description:
14 day old A. thaliana myb67 mutant in Col-0 background primary root
myb67_mutant_mRNAseq_counts.tsv
myb67_mutant_vs_WT.DEG.tsv
myb67_r3_S14


title: striatum TAAR5-KO mice, 10 months, animal 1


title: MYB67 replicate 1


title: Chipseq_Lig4mm_Rad21_DSB


title: Chipseq_WT_Rad21_DSB


title: Caco-2 cells, Air-Liquid, VIP treatment, replicate 1

status: Public on Dec 04 2024

city: Utrecht

first: Karin

last: Strijbis

state: Utrecht

address: Yalelaan 1

department: Biomolecular Health Sciences

country: Netherlands

institute: Utrecht University

description: Library name: EX43_2_ALI_VIP

data_processing:
all samples were subjected and passed quality control using FastQC (version 0.11.9). Subsequently, sequencing reads were mapped to the human genome (assembly GRCh38.109) using STAR RNA aligner (version 2.7.10b) 45. In addition, raw and processed sequencing files were evaluated by MultiQC (version 1.13 (8dd46e3). FeatureCounts was used to count the mapped reads (version 2.0.3). For DEG analysis, the mapped reads were analyzed using R (RStudio 2023.03.1+446) package DEseq2 (version 1.34.0) for differential expression genes and FDR-corrected values of p < 0.05 were considered statistically significant.
Assembly: human genome (assembly GRCh38.109)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: Caco-2 cells were medium in low glucose Dulbecco’s modified Eagle’s medium (DMEM) (Sigma) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 UI/ml penicillin, and 100 µg/ml streptomycin (lab A) or DMEM with pyruvate and glutamax (Thermo Fisher) with 10% FBS (lab B).

extract_protocol:
Total RNA was extracted from Caco-2 cultures using the RNAeasy isolation kit (Qiagen) or NucleoSpin RNA isolation kit (MACHEREY-NAGEL)
RNA was used for mRNA library preparation using the TruSeq Stranded mRNA kit (Illumina)

treatment_protocol: Cells were seeded in rat-tail-collagen-I coated polyester Transwell inserts with 0.4 µm pores (Corning) (lab A) or polyethylene therephthalate (PET) tissue culture inserts with 0.4 µm pores from Sarstedt (lab B) and grown to confluency for 3 days followed by differentiation for 14 days (lab A) or 11 days with supplementation of 100 UI/ml penicillin and 100 ug/ml streptomycin (lab B) under 4 different culture conditions. In liquid-liquid interface non treated conditions (LLI-NT), medium was refreshed in both apical and basolateral compartment without additional stimuli. In liquid-liquid interface VIP conditions (LLI-VIP), medium was refreshed in the apical compartment and medium with 330 ng/ml vasoactive intestinal peptide (VIP) (#AS-22872; AnaSpec) was added to the basolateral compartment. In air-liquid interface non treated conditions (ALI-NT), medium was removed from the apical compartment at day 3 and medium without any additional stimuli was added to the basolateral compartment. In air-liquid interface VIP conditions (ALI-VIP), medium was removed from the apical compartment at day 3 and medium containing 330 ng/ml VIP was added to the basolateral compartment. For all culture conditions, the compartments with medium with and without VIP were refreshed every 1-3 days depending on experimental design.

value: epithelial colorectal adenocarcinoma cells

value: ALI-VIP


title: Caco-2 cells, Air-Liquid, VIP treatment, replicate 3

description: Library name: EX43_4_ALI_VIP


title: Caco-2 cells, Air-Liquid, VIP treatment, replicate 2

description: Library name: EX43_3_ALI_VIP


title: Caco-2 cells, Air-Liquid, no treatment, replicate 2

description: Library name: EX43_3_ALI_NT

value: ALI-NT


title: LUHMES WT, D00, Rep3

value: differentiation


title: Caco-2 cells, Liquid-Liquid, VIP treatment, replicate 5

description: Library name: EX35_1_LLI_VIP

value: LLI-VIP


title: Caco-2 cells, Liquid-Liquid, VIP treatment, replicate 2

description: Library name: EX43_2_LLI_VIP


title: Caco-2 cells, Air-Liquid, no treatment, replicate 4

description: Library name: EX35_1_ALI_NT


title: Caco-2 cells, Air-Liquid, no treatment, replicate 3

description: Library name: EX43_4_ALI_NT


title: Caco-2 cells, Air-Liquid, VIP treatment, replicate 4

description: Library name: EX35_1_ALI_VIP


title: Caco-2 cells, Liquid-Liquid, VIP treatment, replicate 1

description: Library name: EX43_1_LLI_VIP


title: Caco-2 cells, Liquid-Liquid, VIP treatment, replicate 4

description: Library name: EX43_4_LLI_VIP


title: Caco-2 cells, Liquid-Liquid, no treatment, replicate 4

description: Library name: EX35_1_LLI_NT

value: LLI-NT


title: Caco-2 cells, Liquid-Liquid, VIP treatment, replicate 3

description: Library name: EX43_3_LLI_VIP


title: Caco-2 cells, Air-Liquid, no treatment, replicate 1

description: Library name: EX43_1_ALI_NT


title: Chipseq_WT_Mre11

value: Human colorectal carcinoma cell


title: Caco-2 cells, Liquid-Liquid, no treatment, replicate 3

description: Library name: EX43_4_LLI_NT


title: LUHMES WT, D00, Rep2


title: Caco-2 cells, Liquid-Liquid, no treatment, replicate 2

description: Library name: EX43_3_LLI_NT


title: 71668_GTGGCC_S80_L007

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

data_processing:
STAR alignment
HTSeq for gene quantification
Assembly: hg19
Supplementary files format and content: read counts

source_name: skin

extract_protocol:
RNA was isolated using Qiagen RNeasy Plus kit
RNA sequencing was performed by the U-M Advanced Genomics Core on the Novaseq 6000 platform

value: skin

value: Keratinocytes


title: Caco-2 cells, Liquid-Liquid, no treatment, replicate 1

description: Library name: EX43_2_LLI_NT


title: 71667_TAGCTT_S79_L008

value: TNFa


title: 71666_ATCACG_S78_L008


title: 71667_TAGCTT_S79_L007


title: 71666_ATCACG_S78_L007


title: 71665_GAGTGG_S77_L008


title: 71668_GTGGCC_S80_L008


title: 71665_GAGTGG_S77_L007


title: 71664_TGACCA_S76_L008


title: 71664_TGACCA_S76_L007


title: 71663_GTGAAA_S75_L008

value: IFNg


title: 71660_GTTTCG_S72_L008


title: 71659_AGTTCC_S71_L008


title: 71658_CGTACG_S70_L007


title: 71662_CAGATC_S74_L008

value: IFNa


title: 71656_GGCTAC_S68_L008


title: 71661_CGATGT_S73_L008

value: Control


title: 71657_ACTTGA_S69_L007


title: 71656_GGCTAC_S68_L007


title: 71662_CAGATC_S74_L007


title: 71658_CGTACG_S70_L008


title: 71663_GTGAAA_S75_L007


title: 71653_GATCAG_S65_L008


title: 71661_CGATGT_S73_L007


title: 71653_GATCAG_S65_L007


title: 71655_ATTCCT_S67_L008


title: 71655_ATTCCT_S67_L007


title: 71652_TTAGGC_S64_L008


title: 71660_GTTTCG_S72_L007


title: 71652_TTAGGC_S64_L007


title: 71651_CCGTCC_S63_L008


title: 71654_ACTGAT_S66_L008


title: 71650_CTTGTA_S62_L008


title: 71650_CTTGTA_S62_L007


title: 71649_ATGTCA_S61_L008


title: 71651_CCGTCC_S63_L007


title: 71654_ACTGAT_S66_L007


title: 71649_ATGTCA_S61_L007


title: 71659_AGTTCC_S71_L007


title: 71657_ACTTGA_S69_L008


title: 71648_GCCAAT_S60_L005


title: 71647_ACAGTG_S59_L005


title: 71647_ACAGTG_S59_L006


title: 71645_AGTCAA_S57_L006


title: 71646_GTCCGC_S58_L005


title: 71646_GTCCGC_S58_L006


title: 71644_GTGGCC_S56_L006


title: 71643_TAGCTT_S55_L006


title: 71644_GTGGCC_S56_L005


title: 71643_TAGCTT_S55_L005


title: 71642_ATCACG_S54_L006


title: 71641_GAGTGG_S53_L005


title: 71648_GCCAAT_S60_L006


title: 71640_TGACCA_S52_L006


title: 71641_GAGTGG_S53_L006


title: 71642_ATCACG_S54_L005


title: 71638_CAGATC_S50_L006


title: 71639_GTGAAA_S51_L006


title: 71640_TGACCA_S52_L005


title: 71645_AGTCAA_S57_L005


title: 71636_GTTTCG_S48_L006


title: 71636_GTTTCG_S48_L005


title: 71637_CGATGT_S49_L006


title: 71635_AGTTCC_S47_L005


title: 71637_CGATGT_S49_L005


title: 71635_AGTTCC_S47_L006


title: 71634_CGTACG_S46_L005


title: 71633_ACTTGA_S45_L006


title: 71634_CGTACG_S46_L006


title: 71633_ACTTGA_S45_L005


title: 71630_ACTGAT_S42_L006


title: 71631_ATTCCT_S43_L006


title: 71631_ATTCCT_S43_L005


title: 71630_ACTGAT_S42_L005


title: 71632_GGCTAC_S44_L006


title: 71632_GGCTAC_S44_L005


title: 71638_CAGATC_S50_L005


title: 71628_TTAGGC_S40_L004


title: 71628_TTAGGC_S20_L001


title: 71627_CCGTCC_S19_L001


title: 71627_CCGTCC_S39_L004


title: 71639_GTGAAA_S51_L005


title: 71626_CTTGTA_S18_L001


title: 71625_ATGTCA_S37_L004


title: 71624_GCCAAT_S16_L001


title: 71629_GATCAG_S41_L005


title: 71624_GCCAAT_S36_L004


title: 71626_CTTGTA_S38_L004


title: 71622_GTCCGC_S34_L004


title: 71621_AGTCAA_S13_L001


title: 71623_ACAGTG_S35_L004


title: 71621_AGTCAA_S33_L004


title: 71622_GTCCGC_S14_L001


title: 71625_ATGTCA_S17_L001


title: 71623_ACAGTG_S15_L001


title: 71620_GTGGCC_S12_L001


title: 71629_GATCAG_S41_L006


title: 71620_GTGGCC_S32_L004


title: 71619_TAGCTT_S31_L004


title: 71619_TAGCTT_S11_L001


title: 71618_ATCACG_S10_L001


title: 71617_GAGTGG_S9_L001


title: 71616_TGACCA_S28_L004


title: 71615_GTGAAA_S27_L004


title: 71616_TGACCA_S8_L001


title: 71614_CAGATC_S26_L004


title: 71618_ATCACG_S30_L004


title: 71617_GAGTGG_S29_L004


title: 71615_GTGAAA_S7_L001


title: 71613_CGATGT_S5_L001


title: 71614_CAGATC_S6_L001


title: 71610_CGTACG_S2_L001


title: 71613_CGATGT_S25_L004


title: 71610_CGTACG_S22_L004


title: 71611_AGTTCC_S3_L001


title: 71609_ACTTGA_S1_L001


title: 71612_GTTTCG_S24_L004


title: 71608_GGCTAC_S20_L002


title: 71607_ATTCCT_S19_L003


title: 71608_GGCTAC_S20_L003


title: 71607_ATTCCT_S19_L002


title: 71606_ACTGAT_S18_L002


title: 71606_ACTGAT_S18_L003


title: 71605_GATCAG_S17_L002


title: 71604_TTAGGC_S16_L003


title: 71605_GATCAG_S17_L003


title: 71604_TTAGGC_S16_L002


title: 71602_CTTGTA_S14_L002


title: 71603_CCGTCC_S15_L003


title: 71601_ATGTCA_S13_L003


title: 71603_CCGTCC_S15_L002


title: 71599_ACAGTG_S11_L002


title: 71609_ACTTGA_S21_L004


title: 71601_ATGTCA_S13_L002


title: 71612_GTTTCG_S4_L001


title: 71602_CTTGTA_S14_L003


title: 71600_GCCAAT_S12_L002


title: 71598_GTCCGC_S10_L002


title: 71596_GTGGCC_S8_L003


title: 71598_GTCCGC_S10_L003


title: 71600_GCCAAT_S12_L003


title: 71599_ACAGTG_S11_L003


title: 71597_AGTCAA_S9_L003


title: 71595_TAGCTT_S7_L003


title: 71593_GAGTGG_S5_L003


title: 71594_ATCACG_S6_L002


title: 71593_GAGTGG_S5_L002


title: 71611_AGTTCC_S23_L004


title: 71594_ATCACG_S6_L003


title: 71592_TGACCA_S4_L002


title: 71592_TGACCA_S4_L003


title: 71591_GTGAAA_S3_L002


title: 71590_CAGATC_S2_L003


title: 71589_CGATGT_S1_L003


title: 71590_CAGATC_S2_L002


title: 71492_GTGGCC_S40_L003


title: 71491_TAGCTT_S39_L004


title: 71597_AGTCAA_S9_L002


title: 71596_GTGGCC_S8_L002


title: 71489_GAGTGG_S37_L003


title: 71595_TAGCTT_S7_L002


title: 71487_GTGAAA_S35_L004


title: 71488_TGACCA_S36_L004


title: 71490_ATCACG_S38_L003


title: 71489_GAGTGG_S37_L004


title: 71490_ATCACG_S38_L004


title: 71491_TAGCTT_S39_L003


title: 71487_GTGAAA_S35_L003


title: 71485_CGATGT_S33_L003


title: 71485_CGATGT_S33_L004


title: 71486_CAGATC_S34_L003


title: 71484_GTTTCG_S32_L003


title: 71591_GTGAAA_S3_L003


title: 71484_GTTTCG_S32_L004


title: 71483_AGTTCC_S31_L004


title: 71483_AGTTCC_S31_L003


title: 71482_CGTACG_S30_L003


title: 71589_CGATGT_S1_L002


title: 71482_CGTACG_S30_L004


title: 71492_GTGGCC_S40_L004


title: 71481_ACTTGA_S29_L004


title: 71479_ATTCCT_S27_L003


title: 71479_ATTCCT_S27_L004


title: 71488_TGACCA_S36_L003


title: 71481_ACTTGA_S29_L003


title: 71477_GATCAG_S25_L004


title: 71480_GGCTAC_S28_L003


title: 71480_GGCTAC_S28_L004


title: 71477_GATCAG_S25_L003


title: 71476_TTAGGC_S24_L004


title: 71478_ACTGAT_S26_L004


title: 71476_TTAGGC_S24_L003


title: 71486_CAGATC_S34_L004


title: 71478_ACTGAT_S26_L003


title: 71470_GTCCGC_S58_L005


title: 71471_ACAGTG_S39_L004


title: 71474_CTTGTA_S22_L003


title: 71473_ATGTCA_S21_L003


title: 71474_CTTGTA_S22_L004


title: 71473_ATGTCA_S21_L004


title: 71472_GCCAAT_S40_L004


title: 71469_AGTCAA_S57_L005


title: 71475_CCGTCC_S23_L003


title: 71468_GTGGCC_S56_L005


title: 71469_AGTCAA_S37_L004


title: 71472_GCCAAT_S60_L005


title: 71470_GTCCGC_S38_L004


title: 71468_GTGGCC_S36_L004


title: 71467_TAGCTT_S55_L005


title: 71464_TGACCA_S32_L004


title: 71466_ATCACG_S54_L005


title: 71464_TGACCA_S52_L005


title: 71463_GTGAAA_S31_L004


title: 71466_ATCACG_S34_L004


title: 71465_GAGTGG_S33_L004


title: 71462_CAGATC_S30_L004


title: 71462_CAGATC_S50_L005


title: 71465_GAGTGG_S53_L005


title: 71461_CGATGT_S29_L004


title: 71461_CGATGT_S49_L005


title: 71475_CCGTCC_S23_L004


title: 71471_ACAGTG_S59_L005


title: 71460_GTTTCG_S28_L004


title: 71459_AGTTCC_S27_L004


title: 71458_CGTACG_S26_L004


title: 71460_GTTTCG_S48_L005


title: 71456_GGCTAC_S24_L004


title: 71455_ATTCCT_S43_L005


title: 71457_ACTTGA_S45_L005


title: 71454_ACTGAT_S42_L005


title: 71454_ACTGAT_S22_L004


title: 71456_GGCTAC_S44_L005


title: 71459_AGTTCC_S47_L005


title: 71458_CGTACG_S46_L005


title: 71467_TAGCTT_S35_L004


title: 71455_ATTCCT_S23_L004


title: 71457_ACTTGA_S25_L004


title: 71453_GATCAG_S21_L004


title: 71452_TTAGGC_S80_L006


title: 71452_TTAGGC_S80_L007


title: 71463_GTGAAA_S51_L005


title: 71451_CCGTCC_S79_L007


title: 71449_ATGTCA_S77_L006


title: 71450_CTTGTA_S78_L007


title: 71451_CCGTCC_S79_L006


title: 71448_GCCAAT_S76_L007


title: 71449_ATGTCA_S77_L007


title: 71447_ACAGTG_S75_L006


title: 71448_GCCAAT_S76_L006


title: 71447_ACAGTG_S75_L007


title: 71446_GTCCGC_S74_L007


title: 71446_GTCCGC_S74_L006


title: 71445_AGTCAA_S73_L006


title: 71443_TAGCTT_S71_L007


title: 71444_GTGGCC_S72_L006


title: 71443_TAGCTT_S71_L006


title: 71453_GATCAG_S41_L005


title: 71442_ATCACG_S70_L006


title: 71441_GAGTGG_S69_L006


title: 71440_TGACCA_S68_L007


title: 71440_TGACCA_S68_L006


title: 71439_GTGAAA_S67_L006


title: 71450_CTTGTA_S78_L006


title: 71442_ATCACG_S70_L007


title: 71441_GAGTGG_S69_L007


title: 71436_GTTTCG_S64_L007


title: 71438_CAGATC_S66_L006


title: 71437_CGATGT_S65_L006


title: 71435_AGTTCC_S63_L006


title: 71435_AGTTCC_S63_L007


title: 71437_CGATGT_S65_L007


title: 71439_GTGAAA_S67_L007


title: 71438_CAGATC_S66_L007


title: 71434_CGTACG_S62_L006


title: 71433_ACTTGA_S61_L006


title: 71436_GTTTCG_S64_L006


title: 71433_ACTTGA_S61_L007


title: 71434_CGTACG_S62_L007


title: 71445_AGTCAA_S73_L007


title: 71432_GGCTAC_S20_L003


title: 71431_ATTCCT_S99_L008


title: 71431_ATTCCT_S19_L003


title: 71429_GATCAG_S17_L003


title: 71430_ACTGAT_S98_L008


title: 71428_TTAGGC_S96_L008


title: 71427_CCGTCC_S15_L003


title: 71426_CTTGTA_S94_L008


title: 71426_CTTGTA_S14_L003


title: 71427_CCGTCC_S95_L008


title: 71425_ATGTCA_S13_L003


title: 71425_ATGTCA_S93_L008


title: 71421_AGTCAA_S9_L003


title: 71444_GTGGCC_S72_L007


title: 71422_GTCCGC_S90_L008


title: 71423_ACAGTG_S91_L008


title: 71424_GCCAAT_S12_L003


title: 71423_ACAGTG_S11_L003


title: 71421_AGTCAA_S89_L008


title: 71419_TAGCTT_S7_L003


title: 71419_TAGCTT_S87_L008


title: 71418_ATCACG_S6_L003


title: 71432_GGCTAC_S100_L008


title: 71417_GAGTGG_S85_L008


title: 71417_GAGTGG_S5_L003


title: 71418_ATCACG_S86_L008


title: 71428_TTAGGC_S16_L003


title: 71429_GATCAG_S97_L008


title: 71430_ACTGAT_S18_L003


title: 71416_TGACCA_S84_L008


title: 71415_GTGAAA_S3_L003


title: 71416_TGACCA_S4_L003


title: 71414_CAGATC_S82_L008


title: 71414_CAGATC_S2_L003


title: 71415_GTGAAA_S83_L008


title: 71424_GCCAAT_S92_L008


title: 71413_CGATGT_S81_L008


title: 71413_CGATGT_S1_L003


title: 71420_GTGGCC_S8_L003


title: 71420_GTGGCC_S88_L008


title: 70067_GTGGCC_S80_L005


title: 70064_GAGTGG_S77_L005


title: 70065_ATCACG_S58_L008


title: 70067_GTGGCC_S60_L008


title: 70064_GAGTGG_S57_L008


title: 70065_ATCACG_S78_L005


title: 70066_TAGCTT_S79_L005


title: 70066_TAGCTT_S59_L008


title: 70063_TGACCA_S76_L005


title: 70063_TGACCA_S56_L008


title: 70062_GTGAAA_S75_L005


title: 70062_GTGAAA_S55_L008


title: 70061_CAGATC_S74_L005


title: 70061_CAGATC_S54_L008


title: 70060_CGATGT_S73_L005


title: 70059_GTTTCG_S52_L008


title: 70058_AGTTCC_S71_L005


title: 70057_CGTACG_S70_L005


title: 70058_AGTTCC_S51_L008


title: 70059_GTTTCG_S72_L005


title: 70057_CGTACG_S50_L008


title: 70056_ACTTGA_S49_L008


title: 70055_GGCTAC_S48_L008


title: 70055_GGCTAC_S68_L005


title: 70054_ATTCCT_S47_L008


title: 70053_ACTGAT_S66_L005


title: 70054_ATTCCT_S67_L005


title: 70053_ACTGAT_S46_L008


title: 70052_GATCAG_S45_L008


title: 70051_TTAGGC_S44_L008


title: 70050_CCGTCC_S63_L005


title: 70052_GATCAG_S65_L005


title: 70050_CCGTCC_S43_L008


title: 70051_TTAGGC_S64_L005


title: 70049_CTTGTA_S62_L005


title: 70049_CTTGTA_S42_L008


title: 70048_ATGTCA_S61_L005


title: 70060_CGATGT_S53_L008


title: 70048_ATGTCA_S41_L008


title: 70047_GCCAAT_S40_L007


title: 70046_ACAGTG_S39_L007


title: 70047_GCCAAT_S60_L004


title: 70046_ACAGTG_S59_L004


title: 70045_GTCCGC_S58_L004


title: 70044_AGTCAA_S37_L007


title: 70043_GTGGCC_S56_L004


title: 70043_GTGGCC_S36_L007


title: 70045_GTCCGC_S38_L007


title: 70056_ACTTGA_S69_L005


title: 70044_AGTCAA_S57_L004


title: 70042_TAGCTT_S35_L007


title: 70042_TAGCTT_S55_L004


title: 71422_GTCCGC_S10_L003


title: 70040_GAGTGG_S53_L004


title: 70041_ATCACG_S54_L004


title: 70040_GAGTGG_S33_L007


title: 70039_TGACCA_S52_L004


title: 70038_GTGAAA_S51_L004


title: 70039_TGACCA_S32_L007


title: 70037_CAGATC_S50_L004


title: 70036_CGATGT_S49_L004


title: 70035_GTTTCG_S48_L004


title: 70036_CGATGT_S29_L007


title: 70034_AGTTCC_S27_L007


title: 70034_AGTTCC_S47_L004


title: 70033_CGTACG_S26_L007


title: 70035_GTTTCG_S28_L007


title: 70032_ACTTGA_S25_L007


title: 70032_ACTTGA_S45_L004


title: 70037_CAGATC_S30_L007


title: 70030_ATTCCT_S43_L004


title: 70031_GGCTAC_S44_L004


title: 70029_ACTGAT_S42_L004


title: 70028_GATCAG_S21_L007


title: 70028_GATCAG_S41_L004


title: 70041_ATCACG_S34_L007


title: 70029_ACTGAT_S22_L007


title: 70030_ATTCCT_S23_L007


title: 70031_GGCTAC_S24_L007


title: 70027_TTAGGC_S40_L002


title: 70026_CCGTCC_S39_L002


title: 70026_CCGTCC_S39_L003


title: 70038_GTGAAA_S31_L007


title: 70027_TTAGGC_S40_L003


title: 70025_CTTGTA_S38_L002


title: 70024_ATGTCA_S37_L002


title: 70023_GCCAAT_S36_L003


title: 70024_ATGTCA_S37_L003


title: 70023_GCCAAT_S36_L002


title: 70022_ACAGTG_S35_L003


title: 70022_ACAGTG_S35_L002


title: 70033_CGTACG_S46_L004


title: 70021_GTCCGC_S34_L003


title: 70021_GTCCGC_S34_L002


title: 70020_AGTCAA_S33_L003


title: 70020_AGTCAA_S33_L002


title: 70019_GTGGCC_S32_L002


title: 70019_GTGGCC_S32_L003


title: 70018_TAGCTT_S31_L002


title: 70018_TAGCTT_S31_L003


title: 70014_GTGAAA_S27_L002


title: 70016_GAGTGG_S29_L002


title: 70015_TGACCA_S28_L003


title: 70014_GTGAAA_S27_L003


title: 70017_ATCACG_S30_L002


title: 70016_GAGTGG_S29_L003


title: 70025_CTTGTA_S38_L003


title: 70015_TGACCA_S28_L002


title: 70017_ATCACG_S30_L003


title: 70011_GTTTCG_S24_L002


title: 70011_GTTTCG_S24_L003


title: 70012_CGATGT_S25_L002


title: 70013_CAGATC_S26_L003


title: 70013_CAGATC_S26_L002


title: 70010_AGTTCC_S23_L002


title: 70012_CGATGT_S25_L003


title: 70010_AGTTCC_S23_L003


title: 70008_ACTTGA_S21_L003


title: 70009_CGTACG_S22_L003


title: 70008_ACTTGA_S21_L002


title: 70007_GGCTAC_S20_L006


title: 70006_ATTCCT_S19_L001


title: 70006_ATTCCT_S19_L006


title: 70005_ACTGAT_S18_L001


title: 70007_GGCTAC_S20_L001


title: 70005_ACTGAT_S18_L006


title: 70004_GATCAG_S17_L001


title: 70002_CCGTCC_S15_L006


title: 70001_CTTGTA_S14_L001


title: 70000_ATGTCA_S13_L006


title: 70002_CCGTCC_S15_L001


title: 70003_TTAGGC_S16_L006


title: 70000_ATGTCA_S13_L001


title: 69999_GCCAAT_S12_L001


title: 69999_GCCAAT_S12_L006


title: 70009_CGTACG_S22_L002


title: 69997_GTCCGC_S10_L001


title: 69995_GTGGCC_S8_L001


title: 69997_GTCCGC_S10_L006


title: 69995_GTGGCC_S8_L006


title: 70001_CTTGTA_S14_L006


title: 69994_TAGCTT_S7_L001


title: 69993_ATCACG_S6_L006


title: 69992_GAGTGG_S5_L001


title: 69998_ACAGTG_S11_L006


title: 69992_GAGTGG_S5_L006


title: 69994_TAGCTT_S7_L006


title: 69996_AGTCAA_S9_L001


title: 69996_AGTCAA_S9_L006


title: 69991_TGACCA_S4_L001


title: 69990_GTGAAA_S3_L001


title: 69990_GTGAAA_S3_L006


title: 69988_CGATGT_S1_L001


title: 70003_TTAGGC_S16_L001


title: 69988_CGATGT_S1_L006


title: 69998_ACAGTG_S11_L001


title: 70004_GATCAG_S17_L006


title: 68687_GTGGCC_S80_L004


title: 68687_GTGGCC_S80_L008


title: 68686_TAGCTT_S79_L008


title: 69993_ATCACG_S6_L001


title: 68685_ATCACG_S78_L004


title: 68683_TGACCA_S76_L004


title: 68685_ATCACG_S78_L008


title: 68684_GAGTGG_S77_L008


title: 68681_CAGATC_S74_L004


title: 68681_CAGATC_S74_L008


title: 68682_GTGAAA_S75_L008


title: 68683_TGACCA_S76_L008


title: 68682_GTGAAA_S75_L004


title: 68679_GTTTCG_S72_L008


title: 68678_AGTTCC_S71_L004


title: 69989_CAGATC_S2_L001


title: 69989_CAGATC_S2_L006


title: 69991_TGACCA_S4_L006


title: 68680_CGATGT_S73_L004


title: 68678_AGTTCC_S71_L008


title: 68677_CGTACG_S70_L004


title: 68686_TAGCTT_S79_L004


title: 68676_ACTTGA_S69_L004


title: 68676_ACTTGA_S69_L008


title: 68677_CGTACG_S70_L008


title: 68684_GAGTGG_S77_L004


title: 68673_ACTGAT_S66_L008


title: 68672_GATCAG_S65_L004


title: 68674_ATTCCT_S67_L004


title: 68675_GGCTAC_S68_L004


title: 68680_CGATGT_S73_L008


title: 68672_GATCAG_S65_L008


title: 68673_ACTGAT_S66_L004


title: 68671_TTAGGC_S64_L008


title: 68671_TTAGGC_S64_L004


title: 68674_ATTCCT_S67_L008


title: 68679_GTTTCG_S72_L004


title: 68670_CCGTCC_S63_L008


title: 68669_CTTGTA_S62_L004


title: 68669_CTTGTA_S62_L008


title: 68670_CCGTCC_S63_L004


title: 68668_ATGTCA_S61_L008


title: 68667_GCCAAT_S60_L007


title: 68666_ACAGTG_S59_L003


title: 68667_GCCAAT_S60_L003


title: 68665_GTCCGC_S58_L007


title: 68665_GTCCGC_S58_L003


title: 68666_ACAGTG_S59_L007


title: 68664_AGTCAA_S57_L003


title: 68675_GGCTAC_S68_L008


title: 68664_AGTCAA_S57_L007


title: 68662_TAGCTT_S55_L003


title: 68663_GTGGCC_S56_L003


title: 68663_GTGGCC_S56_L007


title: 68662_TAGCTT_S55_L007


title: 68661_ATCACG_S54_L007


title: 68659_TGACCA_S52_L003


title: 68661_ATCACG_S54_L003


title: 68660_GAGTGG_S53_L007


title: 68658_GTGAAA_S51_L003


title: 68658_GTGAAA_S51_L007


title: 68668_ATGTCA_S61_L004


title: 68656_CGATGT_S49_L007


title: 68656_CGATGT_S49_L003


title: 68655_GTTTCG_S48_L003


title: 68659_TGACCA_S52_L007


title: 68657_CAGATC_S50_L003


title: 68654_AGTTCC_S47_L003


title: 68654_AGTTCC_S47_L007


title: 68653_CGTACG_S46_L003


title: 68655_GTTTCG_S48_L007


title: 68653_CGTACG_S46_L007


title: 68657_CAGATC_S50_L007


title: 68652_ACTTGA_S45_L007


title: 68651_GGCTAC_S44_L003


title: 68652_ACTTGA_S45_L003


title: 68651_GGCTAC_S44_L007


title: 68649_ACTGAT_S42_L003


title: 68650_ATTCCT_S43_L007


title: 68650_ATTCCT_S43_L003


title: 68647_TTAGGC_S40_L006


title: 68660_GAGTGG_S53_L003


title: 68647_TTAGGC_S40_L002


title: 68646_CCGTCC_S39_L002


title: 68645_CTTGTA_S38_L002


title: 68645_CTTGTA_S38_L006


title: 68644_ATGTCA_S37_L006


title: 68644_ATGTCA_S37_L002


title: 68643_GCCAAT_S36_L002


title: 68642_ACAGTG_S35_L002


title: 68641_GTCCGC_S34_L002


title: 68643_GCCAAT_S36_L006


title: 68642_ACAGTG_S35_L006


title: 68640_AGTCAA_S33_L006


title: 68638_TAGCTT_S31_L002


title: 68639_GTGGCC_S32_L006


title: 68639_GTGGCC_S32_L002


title: 68640_AGTCAA_S33_L002


title: 68637_ATCACG_S30_L002


title: 68638_TAGCTT_S31_L006


title: 68637_ATCACG_S30_L006


title: 68636_GAGTGG_S29_L002


title: 68649_ACTGAT_S42_L007


title: 68648_GATCAG_S41_L007


title: 68648_GATCAG_S41_L003


title: 68636_GAGTGG_S29_L006


title: 68635_TGACCA_S28_L002


title: 68635_TGACCA_S28_L006


title: 68634_GTGAAA_S27_L006


title: 68634_GTGAAA_S27_L002


title: 68633_CAGATC_S26_L002


title: 68633_CAGATC_S26_L006


title: 68632_CGATGT_S25_L002


title: 68632_CGATGT_S25_L006


title: 68631_GTTTCG_S24_L002


title: 68641_GTCCGC_S34_L006


title: 68631_GTTTCG_S24_L006


title: 68630_AGTTCC_S23_L002


title: 68630_AGTTCC_S23_L006


title: 68629_CGTACG_S22_L002


title: 68628_ACTTGA_S21_L002


title: 68627_GGCTAC_S20_L001


title: 68626_ATTCCT_S19_L005


title: 68627_GGCTAC_S20_L005


title: 68628_ACTTGA_S21_L006


title: 68629_CGTACG_S22_L006


title: 68626_ATTCCT_S19_L001


title: 68646_CCGTCC_S39_L006


title: 68623_TTAGGC_S16_L001


title: 68622_CCGTCC_S15_L001


title: 68624_GATCAG_S17_L005


title: 68623_TTAGGC_S16_L005


title: 68624_GATCAG_S17_L001


title: 68622_CCGTCC_S15_L005


title: 68621_CTTGTA_S14_L005


title: 68620_ATGTCA_S13_L001


title: 68620_ATGTCA_S13_L005


title: 68619_GCCAAT_S12_L001


title: 68619_GCCAAT_S12_L005


title: 68617_GTCCGC_S10_L001


title: 68617_GTCCGC_S10_L005


title: 68618_ACAGTG_S11_L001


title: 68625_ACTGAT_S18_L001


title: 68625_ACTGAT_S18_L005


title: 68615_GTGGCC_S8_L001


title: 68613_ATCACG_S6_L005


title: 68615_GTGGCC_S8_L005


title: 68614_TAGCTT_S7_L005


title: 68612_GAGTGG_S5_L005


title: 68612_GAGTGG_S5_L001


title: 68611_TGACCA_S4_L001


title: 68610_GTGAAA_S3_L001


title: 68611_TGACCA_S4_L005


title: 68609_CAGATC_S2_L001


title: 68610_GTGAAA_S3_L005


title: 68621_CTTGTA_S14_L001


title: 68609_CAGATC_S2_L005


title: 68608_CGATGT_S1_L001


title: 64667_GTGGCC_S20_L001


title: 68608_CGATGT_S1_L005


title: 68618_ACAGTG_S11_L005


title: 64667_GTGGCC_S20_L008


title: 64666_TAGCTT_S19_L001


title: 68616_AGTCAA_S9_L001


title: 68616_AGTCAA_S9_L005


title: 64665_ATCACG_S18_L001


title: 64666_TAGCTT_S19_L008


title: 64665_ATCACG_S18_L008


title: 64664_GAGTGG_S17_L001


title: 68614_TAGCTT_S7_L001


title: 64664_GAGTGG_S17_L008


title: 64663_TGACCA_S16_L008


title: 68613_ATCACG_S6_L001


title: 64660_CGATGT_S13_L001


title: 64661_CAGATC_S14_L008


title: 64659_GTTTCG_S12_L008


title: 64662_GTGAAA_S15_L008


title: 64663_TGACCA_S16_L001


title: 64660_CGATGT_S13_L008


title: 64661_CAGATC_S14_L001


title: 64656_ACTTGA_S9_L008


title: 64657_CGTACG_S10_L001


title: 64658_AGTTCC_S11_L008


title: 64656_ACTTGA_S9_L001


title: 64657_CGTACG_S10_L008


title: 64655_GGCTAC_S8_L008


title: 64655_GGCTAC_S8_L001


title: 64658_AGTTCC_S11_L001


title: 64659_GTTTCG_S12_L001


title: 64654_ATTCCT_S7_L008


title: 64654_ATTCCT_S7_L001


title: 64651_TTAGGC_S4_L008


title: 64652_GATCAG_S5_L001


title: 64653_ACTGAT_S6_L001


title: 64652_GATCAG_S5_L008


title: 64653_ACTGAT_S6_L008


title: 64651_TTAGGC_S4_L001


title: 64662_GTGAAA_S15_L001


title: 64650_CCGTCC_S3_L001


title: 64649_CTTGTA_S2_L001


title: 64649_CTTGTA_S2_L008


title: 64650_CCGTCC_S3_L008


title: 64648_ATGTCA_S1_L001


title: 64648_ATGTCA_S1_L008


title: 64647_GCCAAT_S60_L008


title: 64647_GCCAAT_S60_L007


title: 64646_ACAGTG_S59_L008


title: 64646_ACAGTG_S59_L007


title: 64645_GTCCGC_S58_L007


title: 64644_AGTCAA_S57_L008


title: 64645_GTCCGC_S58_L008


title: 64644_AGTCAA_S57_L007


title: 64643_GTGGCC_S56_L008


title: 64643_GTGGCC_S56_L007


title: 64642_TAGCTT_S55_L008


title: 64642_TAGCTT_S55_L007


title: 64641_ATCACG_S54_L007


title: 64640_GAGTGG_S53_L008


title: hypoxia1

city: 武汉

first: li

last: jun

state: 湖北

address: 湖北省武汉市东湖南路7号

country: China

institute: 中国科学院水生生物研究所

description: Library name: Hyp_1

data_processing:
data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Tophat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant proteinNt (NCBI non-redundant nucleotide Pfam (Protein KOG/COG (Clusters of Orthologous Groups of Swiss-Prot (A manually annotated and reviewed protein sequence KO (KEGG Ortholog GO (Gene Ontology).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
For the samples with biological replicates:Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.10.1). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.05 found by DESeq were assigned as differentially expressed.For the samples without biological replicates:Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two samples was performed using the DEGseq (2010) R package. Pvalue was adjusted using q value (Storey et al,2003). qvalue < 0.005 & |log2 foldchange））| ≥1 was set as the threshold for significantly differential expression.Gene Ontology (GO) enrichment analysis of the differentially expressed genes (DEGs) was implemented by the GOseq R packages based Wallenius non-central hyper-geometric distribution Young et al, 2010 which can adjust for gene length bias in DEGs.KEGG (Kanehisa et al., 2008) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS (Mao et al., 2005) software to test the statistical enrichment of differential expression genes in KEGG pathways.The sequences of the DEGs was blast (blastx) to the genome of a related species (the protein protein interaction of which exists in the STRING database: http://string-db.org/) to get the predicted PPI of these DEGs. Then the PPI of these DEGs were visualized in Cytoscape (Shannon et al, 2005).
Assembly: ASM1881202v1
Supplementary files format and content: include RPKM values for each sample

organism: Megalobrama amblycephala

source_name: brain

growth_protocol: M. amblycephala  were reared in 120 × 100 × 45 cm3 tanks with continuous freshwater aeration under fluorescent lamps light from 8:00 am to 8:00 pm.

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system(Agilent Technologies, CA, USA).
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X））. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase RNase H））. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 200-250 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: M. amblycephala (2 mpf) of similar weight were selected for hypoxia experiments. The flask was filled with 200 ml of water. Three M. amblycephala were placed in a flask under normoxia (21% O2) or hypoxia (5% O2) for 2 hours. These above sampled fish were euthanized by a concentration of 0.3 mg/L MS-222, and the brain was dissected and immediately stored in liquid nitrogen for total RNA extraction.

value: brain

value: WT

value: Hypoxia treatment


title: hypoxia5

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: Hyp_5


title: normoxia5

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: Nor_5

value: normoxia


title: hypoxia2

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: Hyp_2


title: 64640_GAGTGG_S53_L007


title: hypoxia4

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: Hyp_4


title: normoxia4

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: Nor_4


title: normoxia3

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: Nor_3


title: hypoxia3

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: Hyp_3


title: 64639_TGACCA_S52_L008


title: 64641_ATCACG_S54_L008


title: normoxia2

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: Nor_2


title: 64639_TGACCA_S52_L007


title: HEK_ORF10_Dox_Yes_S2_3

city: Philadelphia

first: Jeffrey

middle: Allen

last: Haltom

state: PA

address: 3501 Civic Center Blvd

department: Center for Mitochondrial and Epigenomic Medicine

institute: Children's Hospital of Philadelphia

data_processing:
Using pyrpipe, samples were trimmed for quality and adapters, and mapped using salmon to the human transcriptome (GencodeV36) , SARS-CoV-2 transcriptome (ASM985889v3) , and the human evidence based (EB) gene transcripts, which includes non-canonical alt-spliced, intronic, and intergenic genes, following the pipeline in https://github.com/jahaltom/COVID-19-Quantification. To increase mapping accuracy, the human genome along with viral decoys and spike-ins from the Genomic Data Commons (GRCh38.d1.vd1) were used as decoys for Salmon.
DE was calculated by tximport and  DESeq2.
ToppGene functional enrichment analysis for DE genes was based on the 200 genes with the greatest L2FC in A549 and 293T cells.
Assembly: GencodeV36, ASM985889v3, EB
Supplementary files format and content: TSV of TPM for all smaples. Transcript level.
Supplementary files format and content: TSV of Salmon counts for all smaples. Transcript level.

source_name: HEK

extract_protocol:
Qiagen RNAeasy kit
NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina

value: HEK


title: 64637_CAGATC_S50_L007


title: 64636_CGATGT_S49_L008


title: HEK_ORF10_Dox_Yes_S2_4


title: 64637_CAGATC_S50_L008


title: 64636_CGATGT_S49_L007


title: HEK_ORF10_Dox_No_S1_4


title: HEK_ORF10_Dox_Yes_S2_1


title: HEK_ORF10_Dox_No_S1_3


title: 64638_GTGAAA_S51_L008


title: HEK_ORF10_Dox_Yes_S2_2


title: 64634_AGTTCC_S47_L007


title: 64635_GTTTCG_S48_L007


title: HEK_GFP_Dox_Yes_S3_4


title: HEK_ORF10_Dox_No_S1_2


title: 64633_CGTACG_S46_L007


title: 64638_GTGAAA_S51_L007


title: HEK_GFP_Dox_Yes_S3_3


title: HEK_GFP_Dox_Yes_S3_2


title: 64632_ACTTGA_S45_L008


title: 64632_ACTTGA_S45_L007


title: HEK_Dox_Yes_S4_4

value: Dox


title: HEK_ORF10_Dox_No_S1_1


title: 64633_CGTACG_S46_L008


title: HEK_Dox_Yes_S4_3


title: normoxia1

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: Nor_1


title: 64631_GGCTAC_S44_L008


title: 64635_GTTTCG_S48_L008


title: HEK_Dox_Yes_S4_1


title: HEK_GFP_Dox_Yes_S3_1


title: 64631_GGCTAC_S44_L007


title: A549_ORF10_Dox_Yes_S6_4


title: 64630_ATTCCT_S43_L008


title: 64630_ATTCCT_S43_L007


title: 64634_AGTTCC_S47_L008


title: A549_ORF10_Dox_Yes_S6_3


title: 64629_ACTGAT_S42_L007


title: 64629_ACTGAT_S42_L008


title: A549_ORF10_Dox_Yes_S6_1


title: 64628_GATCAG_S41_L008


title: A549_ORF10_Dox_Yes_S6_2


title: A549_ORF10_Dox_No_S5_4


title: 64628_GATCAG_S41_L007


title: A549_ORF10_Dox_No_S5_3


title: 64627_TTAGGC_S25_L006


title: A549_ORF10_Dox_No_S5_2


title: 64627_TTAGGC_S25_L002


title: A549_ORF10_Dox_No_S5_1


title: 64626_CCGTCC_S24_L002


title: A549_GFP_Dox_Yes_S7_4


title: 64626_CCGTCC_S24_L006


title: A549_GFP_Dox_Yes_S7_3


title: 64625_CTTGTA_S23_L002


title: A549_GFP_Dox_Yes_S7_2


title: A549_GFP_Dox_Yes_S7_1


title: 64624_ATGTCA_S22_L006


title: A549_Dox_Yes_S8_4


title: A549_Dox_Yes_S8_3


title: CD103+CD56+ ILCs sorted from sample OV744

city: Toronto

first: Pamela

last: Ohashi

state: Ontario

address: 610 University Ave

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
RNA-seq FASTQ file were mapped using STAR v2.5.2b aligner with human transcript coordinates from Human Release 29 GENCODE (GRCh37). Reads were summarized per gene using RSEM v1.3.0.
Assembly: GRCh37
Supplementary files format and content: .txt tab-delimited text file containing a per-gene counts matrix

source_name: Ovarian

extract_protocol:
RNA was extracted from sorted patient-matched CD103+CD56+ ILCs and CD103-CD56+ ILCs (N=4) using RNeasy Mini Kit (catalog no. 74104, Qiagen) according to the manufacturer’s instructions. Quantity and quality was assessed using Agilent Bioanalyzer RNA Nano 6000 Kit (catalog no. 5067-1511, Agilent) and KAPA ZYBRR FAST qPCR kit (catalog no. KK44602, Roche).
RNA libraries were prepared and ribosomal RNA were removed using SMARTer Stranded Total RNA-seq Kit V3 – Pico Input Mammalian (catalog no. 634485, Takara Bio USA Inc.). Libraries were normalized, pooled, and loaded onto Illumina Novaseq V1.5 catridge for cluster generation and sequencing on an Illumina Novaseq 6000 instrument (Illumina).

value: Ovarian

value: Sorted CD103+CD56+ ILC Cells


title: 64622_ACAGTG_S40_L006


title: NOK cells, SA3

type: genomic

city: LYON

first: Samrat

last: Das

address: 25 avenue Tony Garnier

country: France

institute: International Agency for Research on Cancer (IARC)

hyb_protocol: 500ng DNA were bisulfite converted to enable quantitative assessment of methylation level over 850K CpG sites.

scan_protocol: Arrays were imaged with standard recommended Illumina scanner settings

data_processing: We employed version 3.14 of the minfi R package to preprocess the raw data, which involved normalization using the 'funnorm' method, probe filtering, and imputation of missing values. Beta values were converted to M values for subsequent statistical analysis and batch correction was performed using the sva package. Identification of differentially methylated positions (DMPs) was conducted using the limma package. The entire workflow is integrated in the methylkey pipeline (https://github.com/IARCbioinfo/methylkey).

label: Cy3 and Cy5

source_name: htert-Normal oral keratinocytes

label_protocol: Standard Illumina protocol

extract_protocol: genomic DNA from the cells was extracted using the NucleoSpin Tissue kit (Macherey-Nagel).

value: htert-Normal oral keratinocytes

value: Sodium arsenite treated htert-Normal oral keratinocytes


title: NOK cells, SLT3

value: smokeless tobacco aqueous extract treated htert-Normal oral keratinocytes


title: CD103-CD56+ ILCs sorted from sample OV744

value: Sorted CD103-CD56+ ILC Cells


title: NOK cells, SA+SLT_2

value: Co-exposure of sodium arsenite and smokeless tobacco aqueous extract htert-Normal oral keratinocytes


title: 64621_GTCCGC_S39_L002

value: skin

value: Keratinocytes


title: 64625_CTTGTA_S23_L006


title: HEK_Dox_Yes_S4_2


title: NOK cells, Parental 2

value: Parental htert-Normal oral keratinocytes


title: NOK cells, SA+SLT_3


title: cardiac fibroblasts,Pw1 CKO,MI 3d,rep5

city: shanghai

first: Shan

last: Kou

address: No.393 Middle Huaxia Road

department: Life Science and Technology

institute: ShanghaiTech University

data_processing:
Bowtie2 was applied to align the clean reads to the mouse reference genome (Mus musculus GRCm38), a database built by BGI (Beijing Genomic Institute in ShenZhen).
Expression level of genes were calculated by RSEM
The DESeq2 was used for differential expression analysis with Q value ≤ 0.05
Differentially expressed genes were functionally classified according to gene ontology (GO) and KEGG annotation results and classification in DAVID for KEGG enrichment analysis and GO enrichment analysis
Assembly: GRCm38
Supplementary files format and content: genes expression of FPKM, TPM and read counts

source_name: heart

extract_protocol:
Total RNA was extracted using the Magzol reagent (Magen, R480102) and 1μg of RNA was used for the construction of sequencing libraries.
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.The PCR reaction system and program are configured and set up to amplify the product.

treatment_protocol: cardiac fibroblasts isolated from the injured left ventricles of Pw1 control or CKO mice at 3 days post-MI

value: heart

value: cardiac fibriblasts

value: PDGFRa Cre+;Pw1 fl/fl

value: 3d post-MI


title: NOK cells, SLT2


title: NOK cells, NT_2

value: Non-treated, time matched control htert-Normal oral keratinocytes


title: CD103+CD56+ ILCs sorted from sample OV738


title: NOK cells, SA2


title: 64620_AGTCAA_S38_L002

value: Control


title: 64622_ACAGTG_S40_L002

value: IFNg


title: NOK cells, SA1


title: cardiac fibroblasts,Pw1 CKO,MI 3d,rep4


title: 64620_AGTCAA_S38_L006


title: 64623_GCCAAT_S21_L006

value: IFNa


title: 64621_GTCCGC_S39_L006


title: A549_Dox_Yes_S8_1

value: Dox


title: CD103-CD56+ ILCs sorted from sample OV738

value: Ovarian


title: NOK cells, NT_1

value: htert-Normal oral keratinocytes


title: NOK cells, Parental 3


title: 64619_GTGGCC_S37_L002


title: NOK cells, SLT1

value: smokeless tobacco aqueous extract treated htert-Normal oral keratinocytes


title: 64618_TAGCTT_S36_L002


title: 64618_TAGCTT_S36_L006


title: cardiac fibroblasts,control,MI 3d,rep5

value: Pw1 fl/fl


title: 64619_GTGGCC_S37_L006


title: NOK cells, SA+SLT_1

value: Co-exposure of sodium arsenite and smokeless tobacco aqueous extract htert-Normal oral keratinocytes


title: CD103-CD56+ ILCs sorted from sample OV332

value: Sorted CD103-CD56+ ILC Cells


title: 64617_ATCACG_S35_L002

value: skin

value: Keratinocytes


title: NOK cells, NT_3


title: cardiac fibroblasts,control,MI 3d,rep6

value: heart


title: 64624_ATGTCA_S22_L002

value: TNFa


title: CD103+CD56+ ILCs sorted from sample OV332

value: Sorted CD103+CD56+ ILC Cells


title: NOK cells, Parental_1

value: Parental htert-Normal oral keratinocytes


title: cardiac fibroblasts,control,MI 3d,rep4

value: cardiac fibriblasts

value: 3d post-MI


title: 64623_GCCAAT_S21_L002


title: 64617_ATCACG_S35_L006


title: 64616_GAGTGG_S34_L002


title: 64616_GAGTGG_S34_L006


title: CD103-CD56+ ILCs sorted from sample OV225


title: heart left ventrical,MI,rep6

treatment_protocol: sham and MI 7d

value: wild type

value: MI 7d


title: 64615_TGACCA_S33_L006

value: IFNa


title: 64615_TGACCA_S33_L002


title: A549_Dox_Yes_S8_2

value: Dox


title: 64614_GTGAAA_S32_L006

value: IFNg


title: 64614_GTGAAA_S32_L002


title: Localized prostate cancer biopsy sample 44 scRNAseq

city: San Francisco

first: Aram

last: Lyu

address: 513 Parnassus Avenue, HSE 301

institute: University of California San Francisco

description: The processed data includes only scRNAseq

library_source: transcriptomic single cell

data_processing:
CellRanger v5 count was run on mouse scRNAseq and CITEseq libraries from the same sample to generate a single set of barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz. CellRanger v3 count was run on patient scRNAseq to generate a single set of barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.
Assembly: GRCm38, GRCh38, mouse_reference_CITEseq.csv
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: prostate

extract_protocol:
For patients, viably cryopreserved tumor tissue samples were digested in RPMI containing Collagenase I & II (0.1 mg/ml, Thermo Fisher Scientific) and DNase I (Thermo Fisher Scientific), minced, and then subjected to 1-hour digestion using the gentleMACS system (Miltenyi Biotec). Live cell isolation was performed using MACS LS columns (Miltenyi Biotec). The 10x Genomics Chromium Controller was utilized to generate GEM bead emulsions using the Single Cell 5′ Library & Gel Bead Kit (10x Genomics). For mice, a cohort of FVB/NJ mice bearing MyC-CaP were injected s.c. with either degarelix (n = 3) or PBS (n = 3), as described above. HSPC or CRPC tissues were harvested upon reaching a tumor volume > 350 mm3. Tumors were sequentially digested 3 times with 12 ml of a cocktail of 2 mg/ml (w/v) Collagenase Type IV and 100 Kunitz U/ml DNase I (both from Sigma-Aldrich) for 12 minutes per digest. All single-cell suspensions were filtered using 70 μm filters (Fisher Scientific) and subjected to red blood cell lysis using ACK Lysing Buffer (Quality Biological). For the cell surface protein staining, cells were incubated with CD45.1-Brilliant Violet 510 (A20) for 30 minutes at 4°C. After immunostaining, cells were washed twice in FWB and resuspended in FWB containing 1 μg/ml propidium iodide for viability assessment. Cells were then sorted into CD45+ and CD45- populations using BD FACSAria (BD Biosciences). Each population was transferred into separate 75 mm flow cytometry tubes, centrifuged for 5 minutes at 250 g at 4˚C, and the supernatant was discarded. After staining with the hashtag (2, 4, and 6 (M1/42, 30-F11)) and TotalSeq-C surface (CD11c (N418), CD163 (S15049I), F4/80 (BM8), and Ly-6G (1A8)) antibodies, cell viability and count were reassessed. The 10x Genomics Chromium Controller was utilized to generate GEM bead emulsions using the Single Cell 5′ Library & Gel Bead Kit (10x Genomics) according to the manufacturer's protocol.
After generating GEM bead emulsions, we performed the synthesis and amplification of cDNA, followed by library preparation steps using 10x Genomics kits according to the manufacturer's protocol.

value: prostate

value: tumor biopsy including immune and non-immune cells

tag: library type

value: mRNA


title: 64613_CAGATC_S31_L002


title: Localized prostate cancer biopsy sample 43 scRNAseq


title: heart left ventrical,sham,rep6

value: sham


title: heart left ventrical,MI,rep5


title: Localized prostate cancer biopsy sample 42 scRNAseq


title: heart left ventrical,MI,rep3


title: 64613_CAGATC_S31_L006

value: skin


title: 64612_CGATGT_S30_L002

value: Keratinocytes

value: Control


title: 64611_GTTTCG_S29_L002


title: 64612_CGATGT_S30_L006


title: Localized prostate cancer biopsy sample 41 scRNAseq


title: heart left ventrical,sham,rep5

value: heart


title: NOK cells, Parental_2

value: htert-Normal oral keratinocytes


title: CD103+CD56+ ILCs sorted from sample OV225

value: Ovarian

value: Sorted CD103+CD56+ ILC Cells


title: 64611_GTTTCG_S29_L006


title: heart left ventrical,sham,rep4


title: Localized prostate cancer biopsy sample 40 scRNAseq


title: heart left ventrical,MI,rep4


title: 64610_AGTTCC_S28_L006


title: Localized prostate cancer biopsy sample 39 scRNAseq


title: 64609_CGTACG_S27_L002


title: 64608_ACTTGA_S26_L002

value: TNFa


title: heart left ventrical,sham,rep3

value: wild type


title: 64609_CGTACG_S27_L006


title: 64607_GGCTAC_S20_L005


title: 64608_ACTTGA_S26_L006


title: Localized prostate cancer biopsy sample 37 scRNAseq


title: 64607_GGCTAC_S20_L001


title: Localized prostate cancer biopsy sample 38 scRNAseq


title: fibroblasts of left ventrical,Pfas CKO,MI 3d,rep5

treatment_protocol: Cardiac fibroblasts were isolated from the Pfas control and CKO mice after MI 3d.Pfas CKO mice were injected Tamoxifen at 7d,3d before MI and 1d post-MI.

value: cardiac fibriblasts

value: PDGFRa CreER/+;Pfas fl/fl

value: 3d post-MI


title: Localized prostate cancer biopsy sample 36 scRNAseq


title: 64606_ATTCCT_S19_L005

value: IFNg


title: 64606_ATTCCT_S19_L001


title: fibroblasts of left ventrical,Pfas CKO,MI 3d,rep4


title: fibroblasts of left ventrical,Pfas CKO,MI 3d,rep3


title: 64605_ACTGAT_S18_L001


title: Localized prostate cancer biopsy sample 35 scRNAseq

value: prostate


title: 64604_GATCAG_S17_L001


title: 64604_GATCAG_S17_L005


title: fibroblasts of left ventrical,Pfas CKO,MI 3d,rep2


title: 64610_AGTTCC_S28_L002


title: Localized prostate cancer biopsy sample 34 scRNAseq

value: tumor biopsy including immune and non-immune cells


title: Localized prostate cancer biopsy sample 33 scRNAseq

value: mRNA


title: 64603_TTAGGC_S16_L001


title: fibroblasts of left ventrical,Pfas CKO,MI 3d,rep1


title: fibroblasts of left ventrical,Pfas CKO,MI 3d,rep6


title: 64603_TTAGGC_S16_L005


title: 64602_CCGTCC_S15_L001


title: Localized prostate cancer biopsy sample 32 scRNAseq


title: 64602_CCGTCC_S15_L005


title: fibroblasts of left ventrical,control,MI 3d,rep6

value: PDGFRa CreER/+;Pfas fl/+


title: 64601_CTTGTA_S14_L005

value: skin


title: 64601_CTTGTA_S14_L001

value: Keratinocytes


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 30 scRNAseq


title: fibroblasts of left ventrical,control,MI 3d,rep5


title: fibroblasts of left ventrical,control,MI 3d,rep4


title: 64600_ATGTCA_S13_L005


title: 64599_GCCAAT_S12_L001

value: IFNa


title: 64605_ACTGAT_S18_L005


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 29 scRNAseq


title: 64599_GCCAAT_S12_L005


title: cardiac fibroblasts,Pw1 CKO,MI 3d,rep3

data_processing:
Bowtie2 was applied to align the clean reads to the mouse reference genome (Mus musculus GRCm38), a database built by BGI (Beijing Genomic Institute in ShenZhen).
Expression level of genes were calculated by RSEM
The DESeq2 was used for differential expression analysis with Q value ≤ 0.05
Differentially expressed genes were functionally classified according to gene ontology (GO) and KEGG annotation results and classification in DAVID for KEGG enrichment analysis and GO enrichment analysis
Assembly: GRCm38

value: heart


title: cardiac fibroblasts,Pw1 CKO,MI 3d,rep2


title: 64597_GTCCGC_S10_L001


title: 64597_GTCCGC_S10_L005


title: cardiac fibroblasts,Pw1 CKO,MI 3d,rep1


title: 64598_ACAGTG_S11_L001


title: 64596_AGTCAA_S9_L001

value: Control


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 26 scRNAseq


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 27 scRNAseq


title: 64598_ACAGTG_S11_L005


title: 64596_AGTCAA_S9_L005


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 25 scRNAseq


title: cardiac fibroblasts,control,MI 3d,rep2

value: wild type, Pw1fl/+ or Pw1fl/fl


title: 64595_GTGGCC_S8_L001


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 31 scRNAseq


title: cardiac fibroblasts,control,MI 3d,rep3


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 24 scRNAseq


title: 64600_ATGTCA_S13_L001


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 28 scRNAseq


title: 64593_ATCACG_S6_L005


title: cardiac fibroblasts,control,MI 3d,rep1


title: 64592_GAGTGG_S5_L001


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 22 scRNAseq


title: 64593_ATCACG_S6_L001


title: heart left ventrical,MI,rep2

data_processing:
Bowtie23 was applied to align the clean reads to the mouse reference genome (Mus musculus GRCm38), a database built by BGI (Beijing Genomic Institute in ShenZhen).
Expression level of genes were calculated by RSEM4
The DESeq25 was used for differential expression analysis with Q value ≤ 0.05
Differentially expressed genes were functionally classified according to gene ontology (GO) and KEGG annotation results and classification in DAVID for KEGG enrichment analysis and GO enrichment analysis
Assembly: GRCm38
Supplementary files format and content: GeneExpression.FPKM

value: MI 7d


title: 64594_TAGCTT_S7_L005


title: heart left ventrical,MI,rep1


title: 64591_TGACCA_S4_L001


title: 64591_TGACCA_S4_L005


title: heart left ventrical,sham,rep2

value: sham


title: 64592_GAGTGG_S5_L005

value: TNFa


title: 64590_GTGAAA_S3_L001


title: heart left ventrical,sham,rep1

value: wild type


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 21 scRNAseq


title: 64590_GTGAAA_S3_L005


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 19 scRNAseq


title: 64595_GTGGCC_S8_L005


title: 64589_CAGATC_S2_L001


title: fibroblasts of left ventrical,control,MI 3d,rep3

data_processing:
Bowtie23 was applied to align the clean reads to the mouse reference genome (Mus musculus GRCm38), a database built by BGI (Beijing Genomic Institute in ShenZhen).
Expression level of genes were calculated by RSEM4
The DESeq25 was used for differential expression analysis with Q value ≤ 0.05
Differentially expressed genes were functionally classified according to gene ontology (GO) and KEGG annotation results and classification in DAVID for KEGG enrichment analysis and GO enrichment analysis
Assembly: GRCm38

value: cardiac fibriblasts


title: 64588_CGATGT_S1_L005


title: 64594_TAGCTT_S7_L001


title: fibroblasts of left ventrical,control,MI 3d,rep2

value: 3d post-MI


title: 64588_CGATGT_S1_L001


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 18 scRNAseq


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 17 scRNAseq


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 23 scRNAseq


title: fibroblasts of left ventrical,control,MI 3d,rep1


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 16 scRNAseq


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 20 scRNAseq


title: C1_46_BL

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

data_processing:
Raw demultiplexed fastq paired end read files were trimmed of adapters and filtered using the program skewer to throw out any with an average phred quality score of less than 30 or a length of less than 10.
Trimmed reads were then aligned using the HISAT2 aligner to the Homo sapiens NCBI reference genome assembly version GRCh38 and sorted using SAMtools
Aligned reads were counted and assigned to gene meta-features using the program featureCounts as part of the Subread package.
Count files were imported into the R programming language and were assessed for quality control, normalized and analyzed utilizing the limma trend method.
Assembly: GRCh38
Supplementary files format and content: CSV file contains raw counts for each sample.
Supplementary files format and content: CSV file contains log2(n+3) TMM normalized counts per million for each sample.

source_name: PBMC

growth_protocol: in vivo

extract_protocol:
PBMC samples were thawed, pelleted, and lysed in 350 uL of RLT with beta-mercaptoethanol. RNA was isolated using the RNeasy Mini kit (Qiagen). RNA quality was assessed with the Fragment Analyzer (Agilent) and its Standard Sensitivity RNA kit.
Total RNA was normalized to 100 ng prior to random hexamer priming and libraries generated by the TruSeq Stranded Total RNA – Globin kit (Illumina). The resulting libraries were assessed on the Fragment Analyzer (Agilent) with the High Sense Large Fragment kit and quantified using a Qubit 3.0 fluorometer (Life Technologies)

value: PBMC

tag: Sex

value: F

tag: batch

tag: donor

tag: timepoint

value: BL

tag: vaccine response

value: R

tag: response status

value: LR


title: C2_139_BL

value: M

value: NR


title: C2_135_BL


title: C2_210_BL


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 14 scRNAseq

tag: tissue

value: prostate

value: tumor biopsy including immune and non-immune cells

value: mRNA


title: C2_100_BL


title: C2_130_BL


title: C2_196_BL


title: C2_121_BL


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 15 scRNAseq


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 13 scRNAseq


title: C1_27_BL


title: C1_32_BL


title: C2_201_BL


title: 64589_CAGATC_S2_L005

value: skin

value: Keratinocytes

tag: treatment


title: C1_44_BL

tag: cell type


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 11 scRNAseq


title: C2_166_BL


title: C2_173_BL


title: C2_190_BL


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 10 scRNAseq


title: C2_154_BL


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 9 scRNAseq


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 8 scRNAseq


title: C2_150_BL

value: HR


title: C2_149_BL


title: C2_148_BL


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 7 scRNAseq


title: C2_140_BL


title: Metastatic hormone-sensitve prostate cancer (mHSPC) biopsy sample 12 scRNAseq


title: C2_108_BL


title: Metastatic castration-resistant prostate cancer (mCRPC) biopsy sample 6 scRNAseq

source_name: lymph node metastasis

value: lymph node metastasis


title: Metastatic castration-resistant prostate cancer (mCRPC) biopsy sample 4 scRNAseq

source_name: bladder metastasis

value: bladder metastasis


title: C2_164_BL


title: C2_114_BL


title: C2_93_BL


title: C2_137_BL


title: C2_87_BL


title: P25 Nogo-A KO tgg #4

city: Zürich

first: Laurence

last: Pirenne

address: Weststrasse 133

country: Switzerland

institute: University of Zürich

description: Library name: P25_KO_5R

data_processing:
Adapter and quality trimming of the raw reads were performed using fastp (v0.20.0) considering a minimum read length of 18 nts and a quality cut-off of 20.
Gene-level expression quantification was carried out using Kallisto (Version 0.46)
The DESeq2 package (v1.32.0) was used to obtain differentially expressed genes between WT and KO samples.
Assembly: GRCm39 /Release_M26-2021-04-20
Supplementary files format and content: for each sample, tab-delimited text files including the raw counts

source_name: Trigeminal ganglion

extract_protocol:
Total RNA was extracted from E14 and P25 WT and Nogo-A KO tgg, using TRIzol reagent (Thermofischer, #15596026). Briefly, tissues were broken down using a motor pestle. Prior incubation with phenol/chloroform/iso-amyl alcohol (Sigma, #P1944), 2M sodium acetate at pH4 was added for 10 minutes at room temperature. After centrifugation, the aqueous phase was transferred and further cleaned with chloroform. RNA was then precipitated using isopropanol and resuspended in RNase free H2O (Sigma, #W4502).
Libraries were prepared using the TruSeq stranded mRNA library (Illumina, Zürich, Switzerland, #20020595) assay

value: Trigeminal ganglion

tag: genotype

value: Nogo-A KO

tag: age


title: P25 Nogo-A KO tgg #1

description: Library name: P25_KO_1R


title: P25 Nogo-A KO tgg #3

description: Library name: P25_KO_3R


title: C2_115_BL

value: PBMC


title: C2_83_BL

value: F


title: Metastatic castration-resistant prostate cancer (mCRPC) biopsy sample 3 scRNAseq

source_name: liver metastasis

value: liver metastasis


title: C2_68_BL

value: BL


title: Metastatic castration-resistant prostate cancer (mCRPC) biopsy sample 2 scRNAseq


title: P25 WT tgg #4

description: Library name: P25_WT_4R

value: Wild-type


title: P25 WT tgg #3

description: Library name: P25_WT_3R


title: C1_42_BL

value: R


title: C1_41_BL


title: P25 WT tgg #2

description: Library name: P25_WT_2R


title: C2_37_BL

value: M

value: NR


title: Metastatic castration-resistant prostate cancer (mCRPC) biopsy sample1 scRNAseq

source_name: bone metastasis

value: bone metastasis

value: tumor biopsy including immune and non-immune cells


title: C2_107_BL


title: Metastatic castration-resistant prostate cancer (mCRPC) biopsy sample 5 scRNAseq

value: mRNA


title: P25 Nogo-A KO tgg #2

description: Library name: P25_KO_2R


title: MUT_Rep3_RNA

city: Saint Louis

first: Sofia

last: Origanti

state: MO

address: 3507 laclede avenue

institute: Saint Louis University

data_processing:
FastQC (v0.12.1) was used to performed QC
Perform STAR(v2.5.2b) mapping aligned to hg38/GRCh38(NCBI GCA_000001405.15)
RSEM(v1.2.28) was used to perform gene/transcript quantification
DESeq2 (v1.42.0) was used to performed DE analysis
Assembly: DESeq2 (v1.42.0) was used to performed DE analysis
Supplementary files format and content: RNA_summary_gene_count_table.txt
Supplementary files format and content: summary_RNA_TPM_table.txt, summary_RNA_FPKM_table.txt

growth_protocol: The human colorectal carcinoma line (HCT116) was maintained in McCoy's 5A (modified) medium with 10% fetal bovine serum (FBS) and 100 units/mL penicillin and 100 mg/mL streptomycin (Gibco) (Penn/Strep). The generation of eIF6N106S/N106S homozygous mutant clones by CRISPR/Cas9 editing was as described in our previous study.

extract_protocol:
HCT116 cells of the indicated genotype were cultured to 60 to 70% cell density and were washed and scraped gently with ice cold PBS and snap frozen. Cells were resuspended in lysis buffer and mechanically syringed lysed, RNA was isolated by phenol-chloroform extraction.
NEB Next ultra II RNAseq kit

tag: cell line

value: MUT


title: P25 WT tgg #1

description: Library name: P25_WT_1R


title: C2_28_BL


title: E14 Nogo-A KO tgg #4

description: Library name: E14_KO_10R


title: MUT_Rep2_RNA


title: C1_30_BL

value: HR


title: C2_36_BL


title: MUT_Rep1_RNA


title: C1_25_BL


title: C2_25_BL


title: E14 Nogo-A KO tgg #2

description: Library name: E14_KO_11R


title: WT_Rep3_RNA

value: Wt


title: C1_24_BL


title: C1_15_BL


title: C1_23_BL

value: LR


title: E14 Nogo-A KO tgg #3

description: Library name: E14_KO_9L

value: Trigeminal ganglion


title: E14 Nogo-A KO tgg #1

description: Library name: E14_KO_9R

value: Nogo-A KO


title: C1_16_BL

value: PBMC


title: WT_Rep1_RNA


title: WT_Rep2_RNA


title: C2_59_BL


title: E14 WT tgg #4

description: Library name: E14_WT_4L


title: C1_6_BL


title: MUT_Rep3_RPF

description:
rS06
Ribosome Profiling

library_source: other

data_processing:
FastQC (v0.12.1) was used to performed QC; fastq_quality_filter and fastx_collapser (FASTQX Toolkit 0.0.14) was used to perform seq collapse and the reads where less than 70% of bases with an accuracy for at least 99% were eleminated; Cutadapt (v4.6) was used to cut univerasl illumina Truseq adaptor; Perform STAR(v2.5.2b) mapping aligned to HG38(NCBI GCA_000001405.15); RibosomeProfilingqc (v1.12.0) was performed to obtain teh trascript tables; DESeq2 (v1.42.0) was used to performed DE analysis.
fastq_quality_filter and fastx_collapser (FASTQX Toolkit 0.0.14) was used to perform seq collapse and the reads where less than 70% of bases with an accuracy for at least 99% were eliminated
Cutadapt (v4.6) was used to cut universal illumina Truseq adaptor
Perform STAR(v2.5.2b) mapping aligned to HG38(NCBI GCA_000001405.15)
RibosomeProfilingqc (v1.12.0) was performed to obtain the transcript tables; DESeq2 (v1.42.0) was used to perform DE analysis.
Assembly: HG38(NCBI GCA_000001405.15)
Supplementary files format and content: RPFs_table_geneLevel.txt
Library strategy: Ribo-Seq

molecule: other

extract_protocol:
HCT116 cells of the indicated genotype were cultured to 60 to 70% cell density and were washed and scraped gently with ice cold PBS and snap frozen. Cells were then processed for Ribo-seq analysis at the RNA core at Case Western University. The appropriate volume of cell extract containing equal OD was treated with MNase, CaCl2 (5mM final concentration), and Turbo DNAse I and incubated at 25°C for 30 min; the digestion was stopped with SUPERase-inhibitor and placing on ice. The cell extract was then loaded onto a 15%-45% sucrose gradient to separate the polysomes by ultra-centrifugation at 41,000 RPM for 2 hours and 26 min at 4°C. The relevant fractions corresponding to the 80S monosome were collected and precipitated using ethanol and the RNA was isolated by phenol-chloroform extraction. The ribosome-protected fragments were then subjected to denaturing polyacrylamide-mediated gel electrophoresis and were gel-extracted based on size 25nt to 35nt. The RNA was precipitated and subjected to the RiboMinus Ribosomal RNA depletion kit (Ambion). The rRNA-depleted RNA footprints were then subjected to dephosphorylation.
Adapter ligation, reverse transcription and subsequent cDNA amplification was performed using the NEXT-Flex smRNA-Seq Kit v3 (Perkin Elmer)


title: C2_196_Wk2


title: MUT_Rep2_RPF

description:
rS05
Ribosome Profiling


title: C1_31_BL


title: E14 WT tgg #3

description: Library name: E14_WT_3R


title: E14 WT tgg #2

description: Library name: E14_WT_4R


title: C2_127_Wk2

value: F


title: C2_150_Wk2


title: C2_116_Wk2


title: C2_107_Wk2


title: MUT_Rep1_RPF

description:
rS04
Ribosome Profiling


title: C2_87_Wk2


title: WT_Rep2_RPF

description:
rS02
Ribosome Profiling


title: E14 WT tgg #1

description: Library name: E14_WT_2R


title: C2_72_Wk2