title: OM_mock_1

value: Olfactory Mucosa

value: mock


title: S5KO_AKT_RV_RNAseq_set1_rep1 (set3)

status: Public on Oct 03 2022

type: SRA

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

country: USA

institute: NIAMS

library_source: transcriptomic

data_processing:
RNAseq FASTQ alignment with Tophat 2, ChIPseq FASTQ alignment with FASTQ alignment with Bowtie 2
Gene expression read count data were generated using htseq-count
ChIPseq peak calling with MACS2 (default p-value threshold of 1E-5)
ChIPseq BigWig tracks genarted with bedtools and UCSC tools (bedGraphToBigWig)
Assembly: mm9
Supplementary files format and content: BigWig (ChIPseq), peak.bed (ChIPseq)
Supplementary files format and content: Excel file for RNA-seq gene expression count data

molecule: total RNA

organism: Mus musculus

source_name: in vitro cultured CD4+ T cells

growth_protocol: CD4+ T cells were enriched by negative selection (Miltenyi), purified to naïve population by high speed cell sorting  (CD4+CD44-CD25-), then stimulated with with plate-bound anti-CD3 and soluble anti-CD28 under the indicated conditions

extract_protocol:
Total RNA  isolated with TRIzol and  phenol/chloroform, then mRNA enriched with NEBNext Poly(A) mRNA Magnetic Isolation Module
NEBNext Ultra Library Prep Kit for Illumina (E7530L, NEB)

tag: strain

tag: tissue

value: pooled spleen and peripheral lymph nodes

tag: cell type

value: Effector CD4+ T cell

tag: treatment

value: Retroviral transduction > hIL-2 (18h)

tag: genotype

value: Stat5a/b flox/flox Cd4-Cre+/-

tag: growth protocol

value: 4 day in vitro culture


title: S5KO_STAT5_RV_RNAseq_set1_rep2 (set3)


title: SK-UT-1 UNTREATED, rep 1

city: udine

first: raffaella

last: picco

address: piazzale kolbe 4

department: department of medical and biological sciences

country: Italy

institute: university of Udine

description: UNTREATED, round 1

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were clipped from their adapter sequences using the Trimmomatic software (v0.35). Reads with an average Phred quality lower than 28 were discarded.
Transcripts were quantified from raw reads with STAR (v2.5.0) on the human transcriptome GRCh38 (Ensembl 104). Quantifications were summarized to gene level with StringTie (v2.1.5).
Differential expression analysis was performed with DESeq2 package (v1.32.0)). Genes were considered differentially expressed if FDR <0.05 and abs(log2(FoldChange)) >1.
Assembly: GRCh38 (Ensembl 104)
Supplementary files format and content: tab-delimited text file includes TPM values for each sample and quantified gene
Supplementary files format and content: tab-delimited text file with raw gene counts for every gene and every sample

organism: Homo sapiens

extract_protocol:
Cells were lysed using Tri-Reagent (Molecular Research Center). RNA was extracted with Quick-RNA MagBead kit (Zymo Research) following the manufacturer’s instructions in the presence of DNAse I.
cDNA libraries were prepared from poly(A) selected RNA following Illumina specifications

tag: cell line

value: leiomyosarcomas cell lines

value: UNTREATED

tag: time

value: 0 h

tag: replicate

value: round 1


title: AAV-15

city: beijing

first: Yuejiao

last: Ma

address: No. 10.wai xi tou tiao, you an men street.

country: China

description: integrin α5 KD

data_processing:
Image processing and base recognition were performed using Solexa pipeline version 1.8.
The RNA sequencing reads were aligned to the mice reference genome mm10 using HISAT2 (version 2.1.0) with default parameters.
The normalized expression value, fragments per kilobase of transcript per million mapped reads (FPKM), was calculated for each gene using StringTie (version 1.3.1c).
FPKM at the gene level and transcript level were calculated using Ballgown (version 2.8.4). Differentially expressed genes with a fold change≥1.5, p-value ≤ 0.05 and FPKM≤0.5 were screened and retained in groups.
Genome_build: mm10
Supplementary_files_format_and_content: The Express file format is xlsx, which analyses the expression of gene and transcript; the Diff_express file format is xlsx, which analyses all differentially expressed genes /transcripts and differentially expressed genes /transcripts.

source_name: Liver tissues

extract_protocol:
RNA was harvested using Trizol reagent and the KAPA Stranded RNA-Seq Library Prep Kit (Illumina) was used with 1-2 ug of total RNA for the construction of sequencing libraries.
Approximately 1-2 µg of total RNA isolated from each independent biological sample was processed with a Ribo-Zero Magnetic Gold kit (Epicentre Biotechnologies) to reduce ribosomal RNA abundance. Sequencing libraries were then constructed using the KAPA Stranded RNA-Seq Library Prep kit (Illumina). The quality of the constructed sequencing libraries was analysed using an Agilent 2100 Bioanalyzer. Quantitative real-time PCR was performed to quantify the sequencing libraries, and the mixed different sample libraries were sequenced using an Illumina HiSeq 4000 platform.

treatment_protocol: The Itgα5 KD groups (n=3) were obtained by the injection of AAV8 vectors packaged with crisp-case9 target liver-specific Itgα5 sgRNA plasmids with LP1 promotor. Control KD groups (n=3) were obtained by the injection of equal dose of control AAV8 vectors. Mice were sacrificed at 4 weeks after tail vein injection.

value: BALB/c

value: liver

tag: group

value: Test


title: hutsmc treated with 2C for 3h, rep 1

description: 2C, 3h, round 1

source_name: HUtSMC

value: HUtSMC

value: human uterine smooth muscle cells

value: 3 h


title: SK-UT-1 UNTREATED, rep 2

description: UNTREATED, round 2

value: round 2


title: hutsmc treated with 2C for 12h, rep 1

description: 2C, 12h, round 1


title: S5KO_CTL_RV_RNAseq_set1_rep1 (set3)


title: AAV-17

description: integrin α5 KD


title: SK-UT-1 treated with 2C for 12h, rep 1

description: 2C, 12h, round 1


title: MW2c phi13kan, - Mitomycin C, Rep 3 [12-MW2c-phi-13Kana-delta-rep_PSS]

city: Tübingen

first: Christiane

last: Wolz

address: Elfriede-Aulhorn-Strasse 6

country: Germany

institute: University Tübingen

description: 5´P Íllumina TruSeq sequencing tag CTGAAGCT to enrich PSS before TEX-treatment

data_processing:
library strategy: tagRNA-seq
CLC Genomics Workbench 20.0.3
Sequence reads were trimmed for adaptor sequence list using CLC genomic benchwork (parameter- Quality trim = yes / Quality limit: 0.05 / PolyA-tail <10)
Trimmed sequence reads were mapped 8325-4phi13Kana or MW2cphi13Kana genomic sequence using CLC genomic benchwork (mismath cost: 2; insertion cost: 3; deletion cost: 3; length fraction: 0.8; similarity fraction: 0.8)
Read count extraction and normalization (of  unassigned (trimmed)-files) resulting in RPKM values were performed using CLC genomic benchwork
Transcriptional start site prediction was performed with TSS.fastq.gz-files as the enriched libraries and PSS.fastq.gz-files as control normal libraries using TSSpredator. A detailed description of TSSpredator parameters, TSS classes and output files can be taken from the UserManual available at:  http://it.inf.uni-tuebingen.de/?page_id=190.
Assembly: NCBI ID: S. aureus NCTC 8325: NC_007795.1; S. aureus MW2: NC_003923.1, both strains were manually phagecured and phi13 prophage sequence inserted manually into hlb gene
Supplementary files format and content: txt format files (GE): RPKM values calculated from unassigned (trimmed)-data

organism: Staphylococcus aureus

growth_protocol: Samples of 8325-4phi13kana and MW2cphi13kana were grown to OD600 = 0.7 (late exponential growth phase) at 37°C,200 rpm in TSB.

extract_protocol:
Bacterial pellets were resuspended in TRIzol (Thermo Fisher Scientific) and mechanically lysed using zirconia/silica beads in a high speed homogenizer. RNA was further purified using the ExpressArt® RNA ready Add-on Kit for TRIzol extraction (AmpTec) with the following modifications. After loading the sample on an RNAready column, RNA was washed additionally with inhibitor removal buffer (5 M guanidine-HCl, 20 mM Tris-HCl pH 6.6, 37 % (v/v) EtOH). DNase digest of the sample was directly performed on the column.
Library preparation on rRNA depleted RNA samples was performed as follows: first Illumina TruSeq sequencing adapter (CTGAAGCT) was ligated to RNAs containing a 5´monophosphate end (resulting from processing events and thereby represent PSS) followed by treatment with TEX (Terminator Exonuclease, Lucigen) to remove unligated 5´P-ends. Next, RNA 5´Polyphosphatase (5´PP, Lucigen) was used to convert triphosphate groups at 5´-RNA ends to monophosphate 5´-RNA ends. Formed monophosphate ends were then tagged by ligation of a second Illumina TruSeq sequencing adapter (TAATGCGC) (representing TSS).
After fragmentation, an oligonucleotide adapter was ligated to the 3´ end of RNA fragments and cDNA synthesis performed using M-MLV reverse transcriptase. cDNA was PCR amplified within 16 cycles using high fidelity DNA polymerase. cDNA was purified using Agencourt AMPure XP Kit (Beckman Coulter Genomics)

treatment_protocol: Samples were treated by induction with mitomycin C (300 ng/ml) or without treatment of mitomycin C as a control for 1 h. Each strain and condition was performed in biological triplicates

tag: variant

value: single-lysogen

tag: prophage

value: control


title: S5KO_STAT5_RV_RNAseq_set1_rep1 (set3)

value: pooled spleen and peripheral lymph nodes

value: Effector CD4+ T cell


title: S5KO_CTL_RV_RNAseq_set1_rep2 (set3)

value: Retroviral transduction > hIL-2 (18h)

value: Stat5a/b flox/flox Cd4-Cre+/-


title: hutsmc UNTREATED, rep 1

description: UNTREATED, round 1


title: MW2c phi13kan, - Mitomycin C, Rep 2 [11-MW2c-phi-13Kana-delta-rep_PSS]


title: MW2c phi13kan, - Mitomycin C, Rep 1 [10-MW2c-phi-13Kana-delta-rep_PSS]


title: WT_CD25_RV_RNAseq_set1_rep2 (set3)

value: Wild type

value: 4 day in vitro culture


title: WT_CD25_RV_RNAseq_set1_rep1 (set3)


title: medn [GEX]

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

data_processing:
align with cellranger
Assembly: hg38/GRCh38
Supplementary files format and content: h5, matrix.mtx

source_name: Normal responder health worker

extract_protocol:
10x genomics chromium 5' Next GEM  single cell RNAseq kit
follow 10x genomics instruction

value: PBMC

value: normal responder


title: WT_AKT_RV_RNAseq_set1_rep2 (set3)


title: MW2c phi13kan, + Mitomycin C, Rep 3 [9-MW2c-phi-13Kana-delta-rep_PSS]

value: mitomycin C treated


title: medn-HTO


title: WT_AKT_RV_RNAseq_set1_rep1 (set3)


title: lown [GEX]

source_name: low responder health worker

value: low responder


title: MW2c phi13kan, + Mitomycin C, Rep 2 [8-MW2c-phi-13Kana-delta-rep_PSS]


title: MW2c phi13kan, + Mitomycin C, Rep 1 [7-MW2c-phi-13Kana-delta-rep_PSS]


title: WT_STAT5_RV_RNAseq_set1_rep2 (set3)


title: 8325-4phi13kan, + Mitomycin C, Rep 3 [6-8325-4DF-phi-13Kana-delta-rep_PSS]


title: WT_STAT5_RV_RNAseq_set1_rep1 (set3)


title: 8325-4phi13kan, + Mitomycin C, Rep 2 [5-8325-4DF-phi-13Kana-delta-rep_PSS]


title: BmGCs, siNC, hCG, 12h, 05_06_2021

city: Lexington

first: Thomas

middle: E.

last: Curry Jr.

state: KY

address: 800 Rose St, Room MS331

department: OB/GYN

institute: University of Kentucky

data_processing:
The Mus musculus transcriptome file “GCF_000001635.27_GRCm39_rna.fna.gz” from Annotation Release 109 from NCBI was used for quasi-mapping and count generation. This transcriptome is derived from genome GRCm39; Since the quasi-mapping step only uses transcript sequences, the gene model file “GCF_000001635.27_GRCm39_genomic.gff.gz” was solely used to generate a transcript-gene mapping table (“trx_EGids_GRCm39_annot109.txt”) for obtaining gene-level counts.
Quality check report was sent by the sequencing center that performed FASTQC1 (version 0.11.8) on individual samples then was summarized into a single html report by using MultiQC2 version 1.9. Average per-base read quality scores are over 30 in all samples and no adapter sequences were found indicating those reads are high in quality. Thus, the trimming step was skipped and directly proceed to transcripts mapping and quantification.
Salmon version 1.4.0 was used to quasi-map reads to the transcriptome and quantify the abundance of each transcript. The transcriptome was first indexed using the decoy-aware method in Salmon with the entire genome file “GCF_000001635.27_GRCm39_genomic.fna.gz” as the decoy sequence. Then quasi-mapping was performed to map reads to transcriptome with additional arguments --seqBias and --gcBias to correct sequence-specific and GC content biases, --numBootstraps=30 to compute bootstrap transcript abundance estimates and --validateMappings to help improve the accuracy of mappings. Gene-level counts were then estimated based on transcript-level counts using the “bias corrected counts without an offset” method from the tximport package. This method provides more accurate gene-level counts estimates and keeps multi-mapped reads in the analysis compared to traditional alignment-based method.
RNA sequencing data were analyzed in R (version 4.1.0) using packages as described. Briefly, the number of reads per genes was normalized using the trimmed mean of M-values (TMM values) normalization method in the edgeR package (version 4.1.0).
Multidimensional scaling in the limma package was used as a sample QC step to check for outliers or batch effects. Differential gene expression (DE) analysis was performed using the limma-trend method using a model of Group + Date
Assembly: NCBI GRCm39
Supplementary files format and content: For Curry_rawCounts_2021-06-23.xlsx, gene-level counts summed from length-normalized transcript counts.
Supplementary files format and content: For glimmaTablesiNC_hCG_4h.vs.siNC_Ctrl_4h_05.xlsx, genes that were significantly different after hCG treatment were sorted on the basis of P<0.05.
Supplementary files format and content: For glimmaTablesiNTS_hCG_4h.vs.siNC_hCG_4h_05.xlxs, genes that were significantly different after silencing neurotensin were sorted on the basis of P<0.05.
Supplementary files format and content: For glimmaTablesiNC_hCG_12h.vs.siNC_Ctrl_12h_05.xlsx, genes that were significantally different after hCG treatment were sorted on the basis of P<0.05.
Supplementary files format and content: For glimmaTablesiNTS_hCG_12h.vs.siNC_hCG_12h_05.xlsx, genes that were significantly different after silencing neurotensin were sorted on the basis of P<0.05.

source_name: primary mouse granulosa cells

growth_protocol: 23 days old immature mice were administered with PMSG to stimulate follicular growth. 48h post PMSG administration, mice were euthanized, and ovaries were isolated. Then, granulosa cells were isolated from the ovaries and pooled from 2 mice. Cells were counted with hemocytometer and then plated in 12 well dish.

extract_protocol:
Total RNA was isolated from the cultured granulosa cells using a Rneasy Plus mini kit (Qiagen) and eluted in 30 ul of nuclease-free water.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand. The libraries were pooled; quantitated by qPCR and sequenced on two SP lanes for 151 cycles from both ends of the fragments on a NovaSeq 6000. Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina) and adaptors were trimmed by the sequencing center.

treatment_protocol: granulosa cells were plated and immediately these cells were transfected with either siNegative control or siRNA specific to mouse Nts for 3h. After 3 h, treatment of hCG or plain media (as control) was given for additional 4h and 12h after which cells were harvested for RNA isolation.

value: ovary

value: primary granulosa cells

tag: transfection

value: siNC

value: hCG


title: BmGCs, siNTS, hCG, 12h, 05_06_2021

value: siNTS


title: ATAC-R5_2

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

library_source: genomic

data_processing:
Quality control was performed using FastQC software and if needed adapater trimming was done with Trimomatic
Genome mapping against Medicago reference genome MtrunA17r5.0-20161119-ANR.fasta was perfomed using STAR mapper
Duplicated reads were identified using picard MarkDuplicates and filtrered using Samtools flagstat
Bigwig files were generated using bamCoverage and normalised using bamScale
Assembly: MtrunA17r5.0-20161119-ANR.fasta
Supplementary files format and content: bigwig files representing the chromatin accessibility (more reads = more accessible)

molecule: genomic DNA

organism: Medicago truncatula

source_name: DNA from radicles germinated 20°C dark_R5

growth_protocol: Seeds were scarified using sand paper and germinated under dark conditions in petri dishes containing a imbibed wathaman paper at 20°C

extract_protocol:
extraction of nuclei was performed based on Kaester lab protocol.
Library construction by Active motif protocol. Samples were sent to BGI, Hong Kong, for sequencing.

treatment_protocol: desiccation treatment or PEG then desiccation treatment (P) and radicles were collected at 1mm (R1) or 5mm (R5)

tag: cultivar

value: 5mm radicle+desiccation

tag: age

value: seeds from 2017 and 2018

value: dried radicles


title: ATAC-R1_3

source_name: DNA from radicles germinated 20°C dark_R1

value: 1mm radicle+desiccation


title: ATAC-R1P_3

source_name: DNA from radicles germinated 20°C dark_R1P

value: 1mm radicle+PEG treat.+desiccation


title: WT_CTL_RV_RNAseq_set1_rep2 (set3)

value: pooled spleen and peripheral lymph nodes

value: Effector CD4+ T cell

value: Retroviral transduction > hIL-2 (18h)


title: 8325-4phi13kan, + Mitomycin C, Rep 1 [4-8325-4DF-phi-13Kana-delta-rep_PSS]

value: single-lysogen


title: WT_CTL_RV_RNAseq_set1_rep1 (set3)

value: Wild type

value: 4 day in vitro culture


title: 8325-4phi13kan, - Mitomycin C, Rep 3 [3-8325-4DF-phi-13Kana-delta-rep_PSS]

value: control


title: ATAC-R1P_2


title: S5KO_MYC_RV_RNAseq_set2_rep2 (set2)

value: Stat5a/b flox/flox Cd4-Cre+/-


title: BmGCs, siNC, hCG, 12h, 04_29_2021

value: ovary

value: primary granulosa cells


title: 8325-4phi13kan, - Mitomycin C, Rep 2 [2-8325-4DF-phi-13Kana-delta-rep_PSS]


title: lown-HTO

value: PBMC

value: low responder


title: S5KO_MYC_RV_RNAseq_set2_rep1 (set2)


title: 8325-4phi13kan, - Mitomycin C, Rep 1 [1-8325-4DF-phi-13Kana-delta-rep_PSS]


title: ATAC-R5_1

value: 5mm radicle+desiccation


title: BmGCs, siNC, Notreatment, 12h, 04_29_2021

value: siNC

value: No treatment


title: S5KO_STAT5_RV_RNAseq_set2_rep2 (set2)


title: BmGCs, siNTS, hCG, 12h, 04_29_2021

value: siNTS

value: hCG


title: MW2c phi13kan, - Mitomycin C, Rep 3 [12-MW2c-phi-13Kana-delta-rep_TSS]

description: 5´P Íllumina TruSeq sequencing tag TAATGCGC to enrich TSS after TEX-treatment


title: ATAC-R1P_1

value: 1mm radicle+PEG treat.+desiccation

value: seeds from 2017 and 2018

value: dried radicles


title: BmGCs, siNC, Notreatment, 12h, 05_06_2021


title: MW2c phi13kan, - Mitomycin C, Rep 2 [11-MW2c-phi-13Kana-delta-rep_TSS]

value: single-lysogen


title: ATAC-R1_1

value: 1mm radicle+desiccation


title: AmGCs, siNC, Notreatment, 12h, 04_29_2021


title: MW2c phi13kan, - Mitomycin C, Rep 1 [10-MW2c-phi-13Kana-delta-rep_TSS]


title: MW2c phi13kan, + Mitomycin C, Rep 3 [9-MW2c-phi-13Kana-delta-rep_TSS]

value: mitomycin C treated


title: INR5.1

data_processing:
TrimGalore to trim short reads (remove adapters)
Fastqc to check sequencing quality control
STAR mapper to map reads against the genome: STAR --readFilesIn read1.fq.gz read2.fq.gz --genomeDir genome index --outFileNamePrefix results_file --runThreadN 20 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 1 --outSAMtype BAM SortedByCoordinate --readFilesCommand 'gunzip -c'
Read deduplication using Picard Markduplicates algorithm
BAMcoverage to transform raw data in bigwig
Peak calling using macs2 callpeak function to statistically identify binding sites using INPUT and IP files. Broad peak calling setting for H3K27me3 and narrow peak calling setting for H3ac according to ENCODe recommendations.
Assembly: MtrunA17r5.0-20161119-ANR.fasta
Supplementary files format and content: bigwig files representing the chromatin accessibility (more reads = chromatin regions bound with h3K27me3)

growth_protocol: Plants were grown in a culture room in trays containing a sterile soil at 20°C/18°C, with a 16 h light photoperiod at 200 μmol photons m -²s-².

extract_protocol:
Extraction protocol as explained in Cortijo et al, 2018 (https://doi.org/10.1007/978-1-4939-7747-5_18)
Library construction by Microplex diagenodef protocol. Samples were sent to BGI, Hong Kong, for sequencing. https://www.diagenode.com/en/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns

treatment_protocol: desiccation or PEG and desiccation

tag: harvest

tag: chip antibody


title: S5KO_CTL_RV_RNAseq_set2_rep2 (set2)

tag: strain

value: pooled spleen and peripheral lymph nodes

value: Effector CD4+ T cell

value: Retroviral transduction > hIL-2 (18h)

value: 4 day in vitro culture


title: S5KO_CTL_RV_RNAseq_set2_rep1 (set2)

tag: tissue

value: Stat5a/b flox/flox Cd4-Cre+/-


title: ATAC-R1_2


title: MW2c phi13kan, + Mitomycin C, Rep 2 [8-MW2c-phi-13Kana-delta-rep_TSS]


title: AmGCs, siNC, hCG, 12h, 03_25_2021

value: ovary

tag: cell type

value: primary granulosa cells


title: INR1P.2

tag: treatment


title: WT_MYC_RV_RNAseq_set2_rep1 (set2)

tag: genotype

value: Wild type


title: INR1P.1


title: AmGCs, siNC, Notreatment, 12h, 03_25_2021

value: siNC

value: No treatment


title: BmGCs, siNTS, hCG, 4h, 05_06_2021

value: siNTS

value: hCG


title: WT_STAT5_RV_RNAseq_set2_rep2 (set2)

tag: growth protocol


title: INR1.2

value: seeds from 2017 and 2018


title: AmGCs, siNC, hCG, 12h, 04_29_2021


title: BmGCs, siNC, hCG, 4h, 05_06_2021


title: S5KO_STAT5_RV_RNAseq_set2_rep1 (set2)


title: INR1.1

value: dried radicles


title: WT_STAT5_RV_RNAseq_set2_rep1 (set2)


title: INR5.2

value: 5mm radicle+desiccation


title: AmGCs, siNTS, hCG, 12h, 03_25_2021


title: 8325-4phi13kan, + Mitomycin C, Rep 2 [5-8325-4DF-phi-13Kana-delta-rep_TSS]

value: single-lysogen


title: WT_CTL_RV_RNAseq_set2_rep2 (set2)


title: WT_CTL_RV_RNAseq_set2_rep1 (set2)


title: H3K27me3_IP_R5.2


title: 8325-4phi13kan, - Mitomycin C, Rep 3 [3-8325-4DF-phi-13Kana-delta-rep_TSS]

value: control


title: WT_IL2_RNAseq_rep3 (set1)

value: pooled spleen and peripheral lymph nodes

value: Overnight Rest > hIL-2 (18h)


title: WT_MYC_RV_RNAseq_set2_rep2 (set2)

value: Effector CD4+ T cell

value: Retroviral transduction > hIL-2 (18h)


title: BmGCs, siNC, hCG, 4h, 04_29_2021


title: H3K27me3_IP_R5.1


title: BmGCs, siNTS, hCG, 4h, 04_29_2021


title: H3K27me3_IP_R1P.2

value: 1mm radicle+PEG treat.+desiccation


title: MW2c phi13kan, + Mitomycin C, Rep 1 [7-MW2c-phi-13Kana-delta-rep_TSS]

value: mitomycin C treated


title: WT_IL2_RNAseq_rep2 (set1)

value: 4 day in vitro culture


title: BmGCs, siNC, Notreatment, 4h, 04_29_2021

value: ovary

value: primary granulosa cells


title: H3K27me3_IP_R1P.1


title: 8325-4phi13kan, + Mitomycin C, Rep 3 [6-8325-4DF-phi-13Kana-delta-rep_TSS]


title: 8325-4phi13kan, - Mitomycin C, Rep 2 [2-8325-4DF-phi-13Kana-delta-rep_TSS]


title: AmGCs, siNTS, hCG, 4h, 04_29_2021


title: WT_IL2_RNAseq_rep1 (set1)

value: Wild type


title: H3K27me3_IP_R1.2

value: 1mm radicle+desiccation


title: AmGCs, siNC, hCG, 4h, 04_29_2021

value: siNC

value: hCG


title: MW2c phi13kan, - Mitomycin C, Rep 3 [12-MW2c-phi-13Kana-delta-rep_unassigned]

description: unassigned fastq sequence file


title: WT_Rest_RNAseq_rep3 (set1)

value: Overnight Rest

value: 3 day in vitro culture


title: BmGCs, siNC, Notreatment, 4h, 05_06_2021

value: No treatment


title: H3K27me3_IP_R1.1

value: seeds from 2017 and 2018

value: dried radicles


title: AmGCs, siNC, Notreatment, 4h, 04_29_2021


title: AmGCs, siNTS, hCG, 12h, 04_29_2021

value: siNTS


title: 8325-4phi13kan, + Mitomycin C, Rep 1 [4-8325-4DF-phi-13Kana-delta-rep_TSS]

value: single-lysogen


title: MW2c phi13kan, - Mitomycin C, Rep 2 [11-MW2c-phi-13Kana-delta-rep_unassigned]

description: unassigned fastq sequence file

value: control


title: WT_Rest_RNAseq_rep2 (set1)

value: pooled spleen and peripheral lymph nodes

value: Effector CD4+ T cell


title: INPUT_R5.2

description:
Rep2
sorted_R5_2_H2ak119ub_qpois.bw

data_processing:
TrimGalore to trim short reads (remove adapters)
Fastqc to check sequencing quality control
STAR mapper to map reads against the genome: STAR --readFilesIn read1.fq.gz read2.fq.gz --genomeDir genome index --outFileNamePrefix results_file --runThreadN 20 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 1 --outSAMtype BAM SortedByCoordinate --readFilesCommand 'gunzip -c'
Read deduplication using Picard Markduplicates algorithm
BAMcoverage to transform raw data in bigwig
Assembly: Peak calling using macs2 callpeak function to statistically identify binding sites using INPUT and IP files. Broad peak calling setting for H3K27me3 and narrow peak calling setting for H3ac according to ENCODe recommendations.

tag: condition

value: desiccation sensitive

value: 5mm radicle+desiccation

value: none (input)


title: MW2c phi13kan, - Mitomycin C, Rep 1 [10-MW2c-phi-13Kana-delta-rep_unassigned]

description: unassigned fastq sequence file


title: AmGCs, siNTS, hCG, 4h, 03_25_2021

value: ovary

value: primary granulosa cells

tag: time


title: WT_Rest_RNAseq_rep1 (set1)

value: Wild type


title: AmGCs, siNC, hCG, 4h, 03_25_2021

value: siNC

value: hCG


title: MW2c phi13kan, + Mitomycin C, Rep 3 [9-MW2c-phi-13Kana-delta-rep_unassigned]

description: unassigned fastq sequence file

value: mitomycin C treated


title: 8325-4phi13kan, - Mitomycin C, Rep 1 [1-8325-4DF-phi-13Kana-delta-rep_TSS]


title: Input_CTL_ChIPseq_rep2

extract_protocol:
Whole cell lysates were clarified and used for 'input' control
Purified DNA fragments (10ng) were blunt-end ligated to illumina adaptors, amplified and made into a library

value: 5 day in vitro culture

value: None (input control)


title: AAV-5

description: integrin α5 KD

value: BALB/c

value: liver

value: Test


title: MW2c phi13kan, + Mitomycin C, Rep 2 [8-MW2c-phi-13Kana-delta-rep_unassigned]

description: unassigned fastq sequence file

value: single-lysogen


title: INPUT_R1P.1

description:
Rep1
sorted_R1P_1_H2ak119ub_qpois.bw

value: desiccation resistant

value: 1mm radicle+PEG treat.+desiccation

value: seeds from 2017 and 2018

value: dried radicles


title: Input_CTL_ChIPseq_rep1

value: pooled spleen and peripheral lymph nodes

value: Effector CD4+ T cell


title: AmGCs, siNC, Notreatment, 4h, 03_25_2021

value: ovary

value: primary granulosa cells

value: No treatment


title: CD43-ckit-_rep3

city: Shanghai

first: Mengxi

last: Wang

address: 197# Rui Jin Road II, Shanghai 200025 CHINA.

institute: Shanghai Institute of Hematology

data_processing:
Basecalls performed using CASAVA version 1.8
Adapter sequences were removed by using SeqPrep, and then poor quality reads filtered by sickle(version 1.200) for quality control
Quality filtered reads were then mapped to GRCh38 using TopHat (v2.0.4)
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FPKM) . RSEM was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
GO functional enrichment and KEGG pathway analysis were carried out by Goatools  and KOBAS
Genome_build: GRCh38
Supplementary_files_format_and_content: All.HTSeq.counts.txt

source_name: bone marrow cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 6-8 weeks

tag: disease model

value: AML1-ETO9a murine model of leukemia

value: bone marrow

value: bone marrow cell

tag: cell subtype


title: MW2c phi13kan, + Mitomycin C, Rep 1 [7-MW2c-phi-13Kana-delta-rep_unassigned]

description: unassigned fastq sequence file

tag: variant

value: mitomycin C treated


title: H3K4me1_ChIPseq_rep2

extract_protocol:
Whole cell lysates were clarified and histone-DNA complexes were isolated with antibody
Purified DNA fragments (10ng) were blunt-end ligated to illumina adaptors, amplified and made into a library

value: Wild type

value: 5 day in vitro culture

value: anti-H3K4m1(Abcam, ab8895)


title: INPUT_R1.2

description:
Rep2
sorted_R1_2_H2ak119ub_qpois.bw

value: desiccation sensitive

value: 1mm radicle+desiccation

value: none (input)


title: 8325-4phi13kan, + Mitomycin C, Rep 3 [6-8325-4DF-phi-13Kana-delta-rep_unassigned]

description: unassigned fastq sequence file

value: single-lysogen

tag: prophage


title: H3K4me1_ChIPseq_rep1

value: pooled spleen and peripheral lymph nodes


title: 8325-4phi13kan, + Mitomycin C, Rep 2 [5-8325-4DF-phi-13Kana-delta-rep_unassigned]

description: unassigned fastq sequence file


title: INPUT_R1.1

description:
Rep1
sorted_R1_1_H2ak119ub_qpois.bw

value: seeds from 2017 and 2018

value: dried radicles


title: CD43-ckit-_rep1


title: H2AK119Ub_IP_R5.2

description:
Rep2
sorted_R5_2_H2ak119ub_qpois.bw

value: 5mm radicle+desiccation


title: CD43-ckit-_rep2


title: H3K27ac_ChIPseq_rep2

value: Effector CD4+ T cell

value: anti-H3K27ac (Abcam, ab4729)


title: H3K27ac_ChIPseq_rep1


title: 8325-4phi13kan, + Mitomycin C, Rep 1 [4-8325-4DF-phi-13Kana-delta-rep_unassigned]

description: unassigned fastq sequence file


title: CD43+ckit-_rep3

value: 6-8 weeks

value: AML1-ETO9a murine model of leukemia


title: CD43+ckit-_rep2

value: bone marrow

value: bone marrow cell


title: 8325-4phi13kan, - Mitomycin C, Rep 3 [3-8325-4DF-phi-13Kana-delta-rep_unassigned]

description: unassigned fastq sequence file

value: control


title: INPUT_R1P.2

description:
Rep2
sorted_R1P_2_H2ak119ub_qpois.bw

value: desiccation resistant

value: 1mm radicle+PEG treat.+desiccation


title: H2AK119Ub_IP_R1P.2

description:
Rep2
sorted_R1P_2_H2ak119ub_qpois.bw


title: 8325-4phi13kan, - Mitomycin C, Rep 2 [2-8325-4DF-phi-13Kana-delta-rep_unassigned]

description: unassigned fastq sequence file


title: CD43+ckit-_rep1


title: P300_ChIPseq_rep1

extract_protocol:
Whole cell lysates were clarified and TF-DNA complexes were isolated with antibody
Purified DNA fragments (10ng) were blunt-end ligated to illumina adaptors, amplified and made into a library

value: Wild type

value: 5 day in vitro culture

value: anti-p300 (Santa Cruz, sc-585)


title: 8325-4phi13kan, - Mitomycin C, Rep 1 [1-8325-4DF-phi-13Kana-delta-rep_unassigned]

description: unassigned fastq sequence file

value: single-lysogen


title: H2AK119Ub_IP_R1P.1

description:
Rep1
sorted_R1P_1_H2ak119ub_qpois.bw


title: INPUT_R5.1

description:
Rep1
sorted_R5_1_H2ak119ub_qpois.bw

value: desiccation sensitive

value: none (input)


title: CD43++ckit+_rep3


title: STAT5_ChIPseq_rep2

value: pooled spleen and peripheral lymph nodes

value: anti-STAT5A + anti-STAT5B (R&D Systems, PA-ST5A and PA-ST5A)


title: H2AK119Ub_IP_R1.2

description:
Rep2
sorted_R1_2_H2ak119ub_qpois.bw

value: 1mm radicle+desiccation

value: seeds from 2017 and 2018

value: dried radicles


title: CD43++ckit+_rep2

value: 6-8 weeks

value: AML1-ETO9a murine model of leukemia


title: H2AK119Ub_IP_R1.1

description:
Rep1
sorted_R1_1_H2ak119ub_qpois.bw


title: STAT5_ChIPseq_rep1

value: Effector CD4+ T cell


title: CD43++ckit+_rep1

value: bone marrow

value: bone marrow cell


title: E22_3805_Lib_MKD261_PCAT14_KD_HUVEC_3

status: Public on Oct 02 2022

city: Bad Nauheim

first: Sweta

last: Talyan

address: Ludwigstraße 43

institute: MPI

description: HUVEC cells, Passage 2, GapmeR Targeting PCAT14

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmonatics with a quality drop threshold below a mean of Q20 in a window of 5 nucleotides.
Trimmed sequence reads were mapped to hg38 (Ensembl release 104) using STAR 2.7.9a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% .
Read count was performed using featureCounts 2.0.2 tool from the Subread package and differntial gene expression were identified using DESeq2 version 1.30.0  with log fold change of +-1,pvalue of 0.05 and mean of 5 reads.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Deseq2 Normalized counts for each Sample

source_name: HUVEC

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq processed with the RNeasy Mini Kit (Qiagen, Hilden, Germany).

tag: cell line

value: HUVEC

value: Human Umbilical Vein Endothelial cells

value: Passage 2

value: GapmerR targeting PCAT14


title: E22_3805_Lib_MKD261_PCAT14_KD_HUVEC_1


title: E22_3805_Lib_MKD261_CTL_HUVEC_3

description: HUVEC cells, Passage 2, GapmeR Negative CTL

value: GapmeR Negative CTL


title: E22_3805_Lib_MKD261_CTL_HUVEC_2


title: E22_3805_Lib_MKD261_CTL_HUVEC_1


title: H2AK119Ub_IP_R5.1

description:
Rep1
sorted_R5_1_H2ak119ub_qpois.bw

tag: cultivar

value: desiccation sensitive

value: 5mm radicle+desiccation


title: E21_3042_Lib_SI745_Aged_6

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmonatics with a quality drop threshold below a mean of Q20 in a window of 5 nucleotides.
Trimmed sequence reads were mapped to hg38 (Ensembl release 104) using STAR 2.7.9a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% .
Read count was performed using featureCounts 2.0.2 tool from the Subread package and differntial gene expression were identified using DESeq2 version 1.30.0  with log fold change of +-1,pvalue of 0.05 and mean of 5 reads.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include deseq2 normalized counts for each Sample

source_name: endothelial cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen, Hilden, Germany). 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq processed with the RNeasy Mini Kit (Qiagen, Hilden, Germany).

value: endothelial cells

value: Aged


title: E21_3042_Lib_SI745_Aged_3


title: E21_3042_Lib_SI745_Aged_4


title: E21_3042_Lib_SI745_Aged_1


title: P300_ChIPseq_rep2

value: pooled spleen and peripheral lymph nodes

value: Wild type

value: 5 day in vitro culture

value: anti-p300 (Santa Cruz, sc-585)


title: PSL_CD8T

type: RNA

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

country: Japan

institute: Ehime University

description: gene expression in Prednisolone (PSL)-treated CD8T cells

hyb_protocol: Hybridization and washing were done according to Agilent One-Color Gene Expression protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan microarray scanner (G2600D) using one color scan setting

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software (Agilent; 12.0.3.1) using default parameters to obtain bakground subtracted and spatially detrended processed signal intensities

source_name: splenic naïve CD8 T cell

label_protocol: 100 ng of total RNA was amplifies and labeled using Low Input Quick Amp Labeling Kit, One-Color

growth_protocol: Naïve CD8 T (CD44lowCD62Lhigh) cells were prepared using a CD8+ T cell Isolation kit (cat#480035; BioLegend) with biotin anti-CD44 antibody (cat#103044; BioLegend).  Naïve CD8 T cells (0.75 × 10^6) were stimulated with immobilized anti-TCR-β mAb (3 μg/ml, H57-597; BioLegend) and anti-CD28 mAb (1 μg/ml, 37.5; BioLegend) for two days in the presence of IL-2 (10 ng/ml, Pepro Tech) with or without predonisolone (1 uM, cat#P0637; TGI).  Next, the cells were transferred to a new plate and further cultured in the presence of IL-2 (10 ng/ml) for three days.

extract_protocol: Total RNA was isolated with RNeasy Mini Kit (QIAGEN) according to the manufacture's protocol

value: spleen

value: prednisolone 1uM


title: E21_3042_Lib_SI745_Young_5

value: Young


title: E21_3042_Lib_SI745_Young_4


title: E21_3042_Lib_SI745_Young_1


title: E21_3042_Lib_SI745_Aged_2


title: E21_3042_Lib_SI745_Aged_5


title: E21_3042_Lib_SI745_Young_2


title: E22_3805_Lib_MKD261_PCAT14_KD_HUVEC_2

tag: age


title: Umod R186S/+, 4 months [R186S_4.1]

city: Zurich

first: Olivier

last: Devuyst

address: Winterthurerstrasse 190

department: Institute of Physiology

country: Switzerland

institute: University of Zurich

data_processing:
A PhiX library was added before sequencing to estimate the sequencing quality.
BWA-MEM (version 0.7.12-r1039) was used for mapping reads to GRCm38/mm10.
featureCounts (version 1.5.1) was used to generate raw read counts.
Assembly: mm10
Supplementary files format and content: RNA-seq_raw_counts.txt: Tab-delimited text file with raw read counts for each sample.

source_name: Kidney

extract_protocol:
Total RNA was extracted using the Aurum Total RNA Fatty and Fibrous Tissue Kit from Bio-Rad. 1 µg of Total RNA was used for library construction.
RNA libraries were prepared using the Illumina stranded mRNA prep kit.

value: Kidney

tag: Sex

value: male

value: Umod R186S/+

value: 4 months


title: Umod C171Y/+, 4 months [C171Y_4.3]

value: Umod C171Y/+


title: Umod R186S/+, 4 months [R186S_4.2]


title: Umod R186S/+, 1 month [R186S_1.3]

value: 1 month


title: Umod +/+, 4 months [WT_4.1]

value: WT


title: Umod C171Y/+, 4 months [C171Y_4.2]


title: Umod R186S/+, 1 month [R186S_1.2]


title: Umod R186S/+, 4 months [R186S_4.3]


title: Umod C171Y/+, 4 months [C171Y_4.1]


title: Umod +/+, 4 months [WT_4.2]


title: Umod C171Y/+, 1 month [C171Y_1.2]


title: Umod C171Y/+, 1 month [C171Y_1.3]


title: Umod R186S/+, 1 month [R186S_1.1]


title: Umod C171Y/+, 1 month [C171Y_1.1]


title: E21_3042_Lib_SI745_Young_6


title: Umod +/+, 1 month [WT_1.3]


title: Umod +/+, 1 month [WT_1.2]


title: Umod +/+, 1 month [WT_1.1]


title: Ctrl_CD8T

description: gene expression in vehicle control (Ctrl)-treated CD8T cells

value: vehicle control


title: E21_3042_Lib_SI745_Young_3

value: endothelial cells


title: α-Syn_AKG1

city: Guangzhou

first: Wenlong

last: Zhang

address: Yuexiu

institute: The First Affiliated Hospital of Guangzhou Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: RPKM values for each Sample

source_name: brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: brain

tag: tissue type

value: substantia nigra

value: AAV-α-synuclein+AKG


title: α-Syn_AKG2

tag: strain


title: AKG2

tag: tissue

value: AKG


title: WT2

value: control


title: α-Syn2

value: AAV-α-synuclein


title: Umod +/+, 4 months [WT_4.3]


title: α-Syn1


title: AKG1


title: WT1


title: Motor Neurons, Plxnd1-KO, Batch1

city: Milano

first: Stefano

last: de Pretis

address: Via Olgettina, 58

department: Center for Omics Sciences

institute: IRCCS San Raffaele Institute

data_processing:
Sequence reads were trimmed for adaptor sequence using Trimmomatic (version 0.39)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR aligner (STAR_2.5.3a)
Read count extraction was performed using featureCounts (v1.6.4) on the Gencode release vM22
Read count normalization and differential expression analysis were performed using the R/Bioconductor package DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

molecule: polyA RNA

source_name: Spinal Cord

extract_protocol:
The spinal cord and surrounding meninges were dissected, pooled according to genotype, and dissociated with Papain Dissociation System (Worthington Biochemical). GFP+ motor neurons and Cherry+ endothelial cells were isolated on a BD Influx Cell Sorter and collected in RLT lysis buffer (Qiagen) containing β-mercaptoethanol. RNA was extracted with RNeasy Mini Kit and on-column DNase digestion (Qiagen).
Stranded mRNA libraries prepared with Illumina TruSeq RNA Library Preparation Kit (v2)

value: Spinal Cord

tag: cell type

value: Motor Neurons

value: Plxnd1 knockout

value: FACS-sorted

tag: cell sorting

value: ISL1-fGFP+ sorted motor neurons


title: Motor Neurons, WT, Batch1

tag: genotype

tag: treatment


title: Motor Neurons, WT, Batch2


title: Endothelial cells, Plxnd1-KO, Batch1

value: Endothelial cells

value: Kdr-Cherry+ sorted endothelial cells


title: Endothelial cells, WT, Batch3


title: Motor Neurons, WT, Batch3


title: Endothelial cells, WT, Batch2


title: Endothelial cells, Plxnd1-KO, Batch2


title: Endothelial cells, WT, Batch1


title: Endothelial cells, Plxnd1-KO, Batch3


title: Motor Neurons, Plxnd1-KO, Batch2


title: LFHT1_ROW40_20

city: Geneva

first: Ivan

last: Rodriguez

address: 30 quai Ernest Anrsermet

department: Genetics and Evolution

institute: University of Geneva

data_processing:
Two rounds of demultiplexing were performed on the raw Illumina data. The first round consisted in demultiplexing the Illumina indices using bcl2fastq2 Conversion Software version 2.20.0 (Illumina), which generated fastq files for each pool of 40 cells. The second round consisted in demultiplexing Fluidigm’s C1 HT IFC indices using the C1 mRNA Seq HT Demultiplexing Script version 1.0.2 (a Perl script from Fluidigm), which generated a pair of fastq files per cell (i.e. reads 1 and 2).
Digital gene expression matrices (i.e. matrices where genes are in rows, cells are in columns, and the corresponding gene counts are matrix entries) were generated following the single-cell analysis pipeline of UMI-tools version 0.5.3. First, unique molecular identifier (UMI) sequences were retrieved from read 1 and appended to the read names using the extract function from UMI-tools. The reads in read 2 (i.e. biological reads) were then mapped to the Ensembl release 86 of the Mus musculus genome reference 38 (GRCm38) using STAR version 2.5.4b. An updated version of the Ensembl release 86 GTF file of the mouse genome GRCm38 (mm10) was used. This custom gene annotation file included the manual re-annotation of the 3’ UTRs of the transcripts of vomeronasal receptor genes (V1rs, V2rs and Fprs), as well as the transcript annotations of de novo identified V1r pseudogenes. Multi-mapping of reads was allowed and the maximum number of hits was set to 4 (--outFilterMultimapNmax 4). For a detailed description, please refer to the methods section of the manuscript. Reads were then assigned to genes using featureCounts version 1.6.1 of the Subread package, and BAM files were sorted and indexed using SAMtools version 1.5. Deduplicated UMIs were then counted using the count function from UMI-tools. For each gene, UMIs that differed by 1 hamming distance were collapsed using the directional adjacency method (--method=directional --edit-distance-threshold=1 --per-gene --gene-tag=XT).
Genome_build: GRCm38
Supplementary_files_format_and_content: The vno_scRNAseq-e20170403_umi_tools_5bpUMI_pseudogenes_multimapping_fractional_LFJT20200404.txt file is a space-separated text file corresponding to the digital gene expression matrix of the single-cell RNA sequencing dataset. Rows are genes, columns are cells, and the corresponding gene counts (UMIs) are matrix entries. Column IDs correspond to sample titles and row IDs correspond to Ensembl mouse gene names.

source_name: vomeronasal sensory neuron

extract_protocol:
3' end single-cell RNA sequencing using Fluidigm's C1 HT IFC with 5bp UMIs and 800 capture chambers
OMP(GFP/wt) males aged of 66 days were used (n=7). Mice were anesthetized using isoflurane and euthanized by decapitation. VNOs were dissected and their cartilaginous envelope were discarded. The tissues were immediately placed in ice-cold oxygenated artificial cerebro-spinal fluid (ACSF) with an osmolarity of 300 mOsm and pH at 7.4. After microdissection, the tissues extracted from the 7 mice were pooled into two tubes (i.e. 3 and 4 mice, respectively). Tissue dissociations were performed using the Papain Dissociation System (cat #LK003150, lot #35S16330; Worthington® Biochemical Corporation, New Jersey, USA) following the manufacturer’s protocol, with slight modifications; the EBSS solutions and the medium solution with serum were adapted from Saxena et al. (DOI: 10.2144/0000113878). To ensure the exclusive isolation of live nucleated cells, cell suspensions were incubated with 2 μg/ml of Hoechst 33342 (a UV fluorescent adenine-thymine binding dye; #H1399, Life Technologies) at 37°C for 15 min. In order to exclude dead cells, 1 μM of DRAQ7 (a far-red fluorescent DNA intercalating dye; #DR71000, BioStatus) was added to the cell suspensions before fluorescence activated cell sorting (FACS). Approximately 6000 GFP+/Hoechst+/DRAQ7- cells were collected from each single-cell suspension pool, each in a final volume of 15 μl. After FACS sorting, 4 μl of C1 Suspension Reagent (Fluidigm) was added to the 10 μl of cell suspensions, yielding mixes of 300 cells/μl. Cells were captured using the C1 Single-Cell mRNA Seq high-throughput (HT) integrated fluidic circuit (IFC) designed for 10-17 μm cells (cat #100-5760, Fluidigm). Each 14 μl mix was loaded on one side of the chip which was processed on the C1 System (cat #100-7000, Fluidigm) following the manufacturer’s protocol. Cell lysis, barcoding, reverse transcription and PCR amplification were performed directly on the C1 chip using Fluidigm’s C1 Single-Cell mRNA Seq HT Reagent Kit v2 (cat #101-3473, Fluidigm) following the manufacturer’s protocol. For a detailed description of the protocol, please refer to the methods section of Fodoulian et al. (2020) bioRxiv (https://doi.org/10.1101/2020.10.14.339259).
The cDNA content of each column on the chip (formed of 40 cells) was pooled before harvesting. Twenty cDNA libraries were generated using the Nextera XT DNA Library Preparation Kit (cat #FC-131-1024, Illumina) and Nextera XT Index Kit (cat #FC-131-1002, Illumina) following Fluidigm’s protocol. Before the final purification step, all 20 cDNA libraries were pooled. The library pool molarity and quality were assessed with the Qubit 2.0 using the Qubit dsDNA HS Assay Kit (cat #Q32854; Thermo Fisher Scientific) and the TapeStation using the Agilent High Sensitivity DNA Chip (cat #5067-5584; Agilent Technologies). The pool was then loaded at 7 pM on 4 lanes for clustering on a rapid paired-end Illumina Flow Cell (cat #PE-402-4002; Illumina) and sequenced on an Illumina HiSeq 2500 sequencer using the HiSeq Rapid SBS Kit v2 (cat #FC-402-4021; Illumina) chemistry. Read 1 consisted of 11 bases (6 bases for the cell barcode, and 5 bases for the unique molecular identifier), while read 2 was formed of 80 bases.

value: OMP(GFP/wt)

tag: gender

value: male

value: vomeronasal epithelium

value: vomeronasal sensory neuron

tag: c1 capture chamber state

value: single cell in capture chamber


title: LFHT1_ROW40_19


title: LFHT1_ROW40_17

value: empty capture chamber


title: LFHT1_ROW40_14

value: multiple cells in capture chamber


title: LFHT1_ROW40_16


title: LFHT1_ROW40_13


title: LFHT1_ROW40_12


title: LFHT1_ROW40_11


title: LFHT1_ROW40_18


title: LFHT1_ROW40_15


title: LFHT1_ROW40_10


title: LFHT1_ROW40_9


title: LFHT1_ROW40_7


title: LFHT1_ROW40_8


title: LFHT1_ROW40_6


title: LFHT1_ROW40_4


title: LFHT1_ROW40_5


title: Motor Neurons, Plxnd1-KO, Batch3


title: LFHT1_ROW40_3


title: LFHT1_ROW39_19


title: LFHT1_ROW39_14


title: LFHT1_ROW40_1


title: LFHT1_ROW40_2


title: LFHT1_ROW39_11


title: LFHT1_ROW39_10


title: LFHT1_ROW39_13


title: LFHT1_ROW39_16


title: LFHT1_ROW39_8


title: LFHT1_ROW39_9


title: LFHT1_ROW39_20


title: LFHT1_ROW39_7


title: LFHT1_ROW39_15


title: LFHT1_ROW39_4


title: LFHT1_ROW39_5


title: LFHT1_ROW39_17


title: LFHT1_ROW39_2


title: LFHT1_ROW39_1


title: LFHT1_ROW38_17


title: LFHT1_ROW39_18


title: LFHT1_ROW38_18


title: LFHT1_ROW38_16


title: LFHT1_ROW38_15


title: LFHT1_ROW38_13


title: LFHT1_ROW38_14


title: LFHT1_ROW39_6

value: putative single cell in capture chamber


title: LFHT1_ROW39_12


title: LFHT1_ROW39_3


title: LFHT1_ROW38_6


title: LFHT1_ROW38_11


title: LFHT1_ROW38_19


title: LFHT1_ROW38_5


title: LFHT1_ROW38_4


title: LFHT1_ROW38_9


title: LFHT1_ROW38_12


title: LFHT1_ROW38_1


title: LFHT1_ROW38_8


title: LFHT1_ROW37_20


title: LFHT1_ROW37_18


title: LFHT1_ROW38_2


title: LFHT1_ROW37_17


title: LFHT1_ROW38_10


title: LFHT1_ROW38_20


title: LFHT1_ROW37_14


title: LFHT1_ROW38_3


title: LFHT1_ROW37_15


title: LFHT1_ROW37_9


title: LFHT1_ROW38_7


title: LFHT1_ROW37_19


title: LFHT1_ROW37_13


title: LFHT1_ROW37_8


title: LFHT1_ROW37_12


title: LFHT1_ROW37_7


title: LFHT1_ROW37_11


title: LFHT1_ROW37_16


title: LFHT1_ROW37_6


title: LFHT1_ROW37_5


title: LFHT1_ROW37_4


title: LFHT1_ROW36_19


title: LFHT1_ROW36_18


title: LFHT1_ROW36_17


title: LFHT1_ROW37_2


title: LFHT1_ROW36_14


title: LFHT1_ROW36_20


title: LFHT1_ROW36_10


title: LFHT1_ROW37_1


title: LFHT1_ROW37_3


title: LFHT1_ROW37_10


title: LFHT1_ROW36_13


title: LFHT1_ROW36_6


title: LFHT1_ROW36_12


title: LFHT1_ROW36_4


title: LFHT1_ROW35_20


title: LFHT1_ROW36_3


title: LFHT1_ROW36_8


title: LFHT1_ROW36_9


title: LFHT1_ROW35_18


title: LFHT1_ROW36_7


title: LFHT1_ROW36_5


title: LFHT1_ROW36_2


title: LFHT1_ROW35_19


title: LFHT1_ROW36_1


title: LFHT1_ROW35_17


title: LFHT1_ROW35_16


title: LFHT1_ROW36_15


title: LFHT1_ROW36_11


title: LFHT1_ROW36_16


title: LFHT1_ROW35_14


title: LFHT1_ROW35_15


title: LFHT1_ROW35_10


title: LFHT1_ROW35_12


title: LFHT1_ROW35_11


title: LFHT1_ROW35_6


title: LFHT1_ROW35_9


title: LFHT1_ROW35_7


title: LFHT1_ROW35_13


title: LFHT1_ROW35_2


title: LFHT1_ROW34_16


title: LFHT1_ROW35_4


title: LFHT1_ROW35_8


title: LFHT1_ROW34_20


title: LFHT1_ROW35_1


title: LFHT1_ROW34_17


title: LFHT1_ROW35_5


title: LFHT1_ROW34_19


title: LFHT1_ROW35_3


title: LFHT1_ROW34_14


title: LFHT1_ROW34_13


title: LFHT1_ROW34_18


title: LFHT1_ROW34_15


title: LFHT1_ROW34_11


title: LFHT1_ROW34_12


title: LFHT1_ROW34_9


title: LFHT1_ROW34_10


title: LFHT1_ROW34_8


title: LFHT1_ROW34_6


title: LFHT1_ROW34_7


title: LFHT1_ROW34_4


title: LFHT1_ROW34_5


title: LFHT1_ROW34_3


title: LFHT1_ROW34_1


title: LFHT1_ROW33_19


title: LFHT1_ROW33_20


title: LFHT1_ROW33_16


title: LFHT1_ROW33_18


title: LFHT1_ROW33_13


title: LFHT1_ROW33_8


title: LFHT1_ROW33_9


title: LFHT1_ROW33_7


title: LFHT1_ROW33_4


title: LFHT1_ROW33_14


title: LFHT1_ROW33_1


title: LFHT1_ROW33_3


title: LFHT1_ROW33_5


title: LFHT1_ROW33_12


title: LFHT1_ROW32_19


title: LFHT1_ROW33_2


title: LFHT1_ROW32_18


title: LFHT1_ROW32_17


title: LFHT1_ROW33_15


title: LFHT1_ROW32_16


title: LFHT1_ROW32_20


title: LFHT1_ROW33_17


title: LFHT1_ROW32_15


title: LFHT1_ROW34_2


title: LFHT1_ROW32_14


title: LFHT1_ROW33_10


title: LFHT1_ROW32_13


title: LFHT1_ROW33_6


title: LFHT1_ROW32_12


title: LFHT1_ROW33_11


title: LFHT1_ROW32_11


title: LFHT1_ROW32_9


title: LFHT1_ROW32_7


title: LFHT1_ROW32_6


title: LFHT1_ROW32_5


title: LFHT1_ROW32_3


title: LFHT1_ROW32_1


title: LFHT1_ROW31_20


title: LFHT1_ROW31_19


title: LFHT1_ROW31_18


title: LFHT1_ROW31_17


title: LFHT1_ROW31_15


title: LFHT1_ROW31_14


title: LFHT1_ROW31_12


title: LFHT1_ROW31_16


title: LFHT1_ROW31_10


title: LFHT1_ROW31_11


title: LFHT1_ROW31_9


title: LFHT1_ROW31_8


title: LFHT1_ROW31_7


title: LFHT1_ROW31_6


title: LFHT1_ROW31_5


title: LFHT1_ROW32_10


title: LFHT1_ROW32_8


title: LFHT1_ROW31_4


title: LFHT1_ROW31_2


title: LFHT1_ROW31_3


title: LFHT1_ROW31_1


title: LFHT1_ROW32_4


title: LFHT1_ROW30_16


title: LFHT1_ROW32_2


title: LFHT1_ROW31_13


title: LFHT1_ROW30_14


title: LFHT1_ROW30_13


title: LFHT1_ROW30_12


title: LFHT1_ROW30_11


title: LFHT1_ROW30_17


title: LFHT1_ROW30_10


title: LFHT1_ROW30_9


title: LFHT1_ROW30_18


title: LFHT1_ROW30_5


title: LFHT1_ROW30_3


title: LFHT1_ROW30_2


title: LFHT1_ROW29_20


title: LFHT1_ROW30_1


title: LFHT1_ROW30_20


title: LFHT1_ROW29_19


title: LFHT1_ROW29_16


title: LFHT1_ROW29_18


title: LFHT1_ROW29_15


title: LFHT1_ROW30_8


title: LFHT1_ROW29_17


title: LFHT1_ROW29_13


title: LFHT1_ROW30_15


title: LFHT1_ROW29_11


title: LFHT1_ROW29_12


title: LFHT1_ROW30_7


title: LFHT1_ROW29_8


title: LFHT1_ROW29_6


title: LFHT1_ROW29_7


title: LFHT1_ROW29_9


title: LFHT1_ROW29_10


title: LFHT1_ROW30_6


title: LFHT1_ROW29_5


title: LFHT1_ROW29_2


title: LFHT1_ROW29_4


title: LFHT1_ROW30_4


title: LFHT1_ROW29_3


title: LFHT1_ROW29_1


title: LFHT1_ROW28_18


title: LFHT1_ROW28_19


title: LFHT1_ROW28_17


title: LFHT1_ROW28_16


title: LFHT1_ROW28_15


title: LFHT1_ROW28_11


title: LFHT1_ROW28_13


title: LFHT1_ROW28_10


title: LFHT1_ROW28_9


title: LFHT1_ROW28_12


title: LFHT1_ROW29_14


title: LFHT1_ROW28_8


title: LFHT1_ROW28_20


title: LFHT1_ROW28_7


title: LFHT1_ROW28_6


title: LFHT1_ROW28_2


title: LFHT1_ROW28_4


title: LFHT1_ROW27_20


title: LFHT1_ROW28_3


title: LFHT1_ROW28_14


title: LFHT1_ROW28_5


title: LFHT1_ROW27_18


title: LFHT1_ROW27_16


title: LFHT1_ROW27_19


title: LFHT1_ROW30_19


title: LFHT1_ROW27_15


title: LFHT1_ROW27_13


title: LFHT1_ROW27_14


title: LFHT1_ROW27_10


title: LFHT1_ROW27_9


title: LFHT1_ROW27_8


title: LFHT1_ROW27_7


title: LFHT1_ROW27_4


title: LFHT1_ROW27_5


title: LFHT1_ROW27_3


title: LFHT1_ROW27_1


title: LFHT1_ROW27_6


title: LFHT1_ROW26_19


title: LFHT1_ROW26_20


title: LFHT1_ROW27_2


title: LFHT1_ROW27_17


title: LFHT1_ROW26_16


title: LFHT1_ROW28_1


title: LFHT1_ROW26_12


title: LFHT1_ROW26_15


title: LFHT1_ROW26_13


title: LFHT1_ROW26_10


title: LFHT1_ROW26_7


title: LFHT1_ROW27_11


title: LFHT1_ROW26_6


title: LFHT1_ROW26_11


title: LFHT1_ROW26_14


title: LFHT1_ROW26_9


title: LFHT1_ROW27_12


title: LFHT1_ROW26_5


title: LFHT1_ROW26_8


title: LFHT1_ROW26_3


title: LFHT1_ROW26_2


title: LFHT1_ROW26_18


title: LFHT1_ROW25_20


title: LFHT1_ROW25_19


title: LFHT1_ROW25_18


title: LFHT1_ROW25_17


title: LFHT1_ROW26_1


title: LFHT1_ROW25_13


title: LFHT1_ROW25_15


title: LFHT1_ROW25_14


title: LFHT1_ROW26_17


title: LFHT1_ROW25_16


title: LFHT1_ROW25_12


title: LFHT1_ROW25_10


title: LFHT1_ROW25_9


title: LFHT1_ROW25_8


title: LFHT1_ROW25_7


title: LFHT1_ROW25_6


title: LFHT1_ROW25_5


title: LFHT1_ROW25_2


title: LFHT1_ROW25_1


title: LFHT1_ROW25_4


title: LFHT1_ROW24_20


title: LFHT1_ROW26_4


title: LFHT1_ROW24_18


title: LFHT1_ROW24_19


title: LFHT1_ROW24_16


title: LFHT1_ROW24_17


title: LFHT1_ROW24_15


title: LFHT1_ROW24_13


title: LFHT1_ROW24_14


title: LFHT1_ROW25_3


title: LFHT1_ROW24_6


title: LFHT1_ROW24_8


title: LFHT1_ROW24_10


title: LFHT1_ROW25_11


title: LFHT1_ROW24_9


title: LFHT1_ROW24_11


title: LFHT1_ROW24_12


title: LFHT1_ROW24_7


title: LFHT1_ROW23_20


title: LFHT1_ROW24_3


title: LFHT1_ROW24_1


title: LFHT1_ROW23_19


title: LFHT1_ROW24_5


title: LFHT1_ROW24_2


title: LFHT1_ROW24_4


title: LFHT1_ROW23_17


title: LFHT1_ROW23_16


title: LFHT1_ROW23_18


title: LFHT1_ROW23_13


title: LFHT1_ROW23_12


title: LFHT1_ROW23_11


title: LFHT1_ROW23_9


title: LFHT1_ROW23_8


title: LFHT1_ROW23_7


title: LFHT1_ROW23_14


title: LFHT1_ROW23_10


title: LFHT1_ROW23_5


title: LFHT1_ROW22_20


title: LFHT1_ROW23_2


title: LFHT1_ROW23_3


title: LFHT1_ROW22_17


title: LFHT1_ROW23_1


title: LFHT1_ROW22_16


title: LFHT1_ROW22_15


title: LFHT1_ROW23_15


title: LFHT1_ROW22_13


title: LFHT1_ROW23_6


title: LFHT1_ROW22_12


title: LFHT1_ROW22_10


title: LFHT1_ROW22_11


title: LFHT1_ROW22_14


title: LFHT1_ROW22_9


title: LFHT1_ROW22_19


title: LFHT1_ROW22_8


title: LFHT1_ROW22_7


title: LFHT1_ROW22_6


title: LFHT1_ROW22_4


title: LFHT1_ROW22_5


title: LFHT1_ROW22_3


title: LFHT1_ROW22_2


title: LFHT1_ROW22_1


title: LFHT1_ROW21_20


title: LFHT1_ROW22_18


title: LFHT1_ROW21_17


title: LFHT1_ROW21_15


title: LFHT1_ROW21_19


title: LFHT1_ROW23_4


title: LFHT1_ROW21_16


title: LFHT1_ROW21_18


title: LFHT1_ROW21_14


title: LFHT1_ROW21_13


title: LFHT1_ROW21_11


title: LFHT1_ROW21_12


title: LFHT1_ROW21_10


title: LFHT1_ROW21_8


title: LFHT1_ROW21_6


title: LFHT1_ROW21_5


title: LFHT1_ROW21_4


title: LFHT1_ROW21_7


title: LFHT1_ROW21_3


title: LFHT1_ROW21_1


title: LFHT1_ROW21_9


title: LFHT1_ROW21_2


title: LFHT1_ROW20_17


title: LFHT1_ROW20_16


title: LFHT1_ROW20_14


title: LFHT1_ROW20_20


title: LFHT1_ROW20_13


title: LFHT1_ROW20_12


title: LFHT1_ROW20_10


title: LFHT1_ROW20_11


title: LFHT1_ROW20_8


title: LFHT1_ROW20_7


title: LFHT1_ROW20_6


title: LFHT1_ROW20_9


title: LFHT1_ROW20_5


title: LFHT1_ROW20_4


title: LFHT1_ROW20_2


title: LFHT1_ROW20_1


title: LFHT1_ROW20_19


title: LFHT1_ROW19_19


title: LFHT1_ROW19_18


title: LFHT1_ROW20_3


title: LFHT1_ROW20_15


title: LFHT1_ROW19_15


title: LFHT1_ROW19_17


title: LFHT1_ROW19_14


title: LFHT1_ROW19_12


title: LFHT1_ROW19_20


title: LFHT1_ROW20_18


title: LFHT1_ROW19_16


title: LFHT1_ROW19_11


title: LFHT1_ROW19_10


title: LFHT1_ROW19_7


title: LFHT1_ROW19_8


title: LFHT1_ROW19_9


title: LFHT1_ROW19_5


title: LFHT1_ROW19_4


title: LFHT1_ROW19_2


title: LFHT1_ROW19_3


title: LFHT1_ROW18_20


title: LFHT1_ROW18_18


title: LFHT1_ROW18_19


title: LFHT1_ROW19_1


title: LFHT1_ROW18_17


title: LFHT1_ROW18_16


title: LFHT1_ROW18_15


title: LFHT1_ROW18_13


title: LFHT1_ROW18_14


title: LFHT1_ROW18_8


title: LFHT1_ROW19_13


title: LFHT1_ROW18_10


title: LFHT1_ROW18_7


title: LFHT1_ROW18_9


title: LFHT1_ROW19_6


title: LFHT1_ROW18_4


title: LFHT1_ROW18_12


title: LFHT1_ROW18_6


title: LFHT1_ROW18_3


title: LFHT1_ROW18_2


title: LFHT1_ROW18_1


title: LFHT1_ROW18_11


title: LFHT1_ROW17_19


title: LFHT1_ROW18_5


title: LFHT1_ROW17_20


title: LFHT1_ROW17_18


title: LFHT1_ROW17_17


title: LFHT1_ROW17_16


title: LFHT1_ROW17_14


title: LFHT1_ROW17_15


title: LFHT1_ROW17_12


title: LFHT1_ROW17_11


title: LFHT1_ROW17_10


title: LFHT1_ROW17_13


title: LFHT1_ROW17_7


title: LFHT1_ROW17_6


title: LFHT1_ROW17_8


title: LFHT1_ROW17_5


title: LFHT1_ROW17_4


title: LFHT1_ROW16_20


title: LFHT1_ROW16_19


title: LFHT1_ROW17_3


title: LFHT1_ROW16_11


title: LFHT1_ROW16_13


title: LFHT1_ROW16_18


title: LFHT1_ROW16_10


title: LFHT1_ROW16_15


title: LFHT1_ROW16_16


title: LFHT1_ROW16_9


title: LFHT1_ROW16_14


title: LFHT1_ROW17_1


title: LFHT1_ROW16_8


title: LFHT1_ROW17_2


title: LFHT1_ROW16_5


title: LFHT1_ROW17_9


title: LFHT1_ROW16_6


title: LFHT1_ROW16_4


title: LFHT1_ROW16_2


title: LFHT1_ROW16_3


title: LFHT1_ROW16_1


title: LFHT1_ROW15_20


title: LFHT1_ROW15_19


title: LFHT1_ROW16_17


title: LFHT1_ROW15_18


title: LFHT1_ROW16_12


title: LFHT1_ROW15_16


title: LFHT1_ROW15_15


title: LFHT1_ROW16_7


title: LFHT1_ROW15_10


title: LFHT1_ROW15_5


title: LFHT1_ROW15_6


title: LFHT1_ROW15_13


title: LFHT1_ROW15_7


title: LFHT1_ROW15_9


title: LFHT1_ROW15_12


title: LFHT1_ROW15_3


title: LFHT1_ROW15_1


title: LFHT1_ROW15_2


title: LFHT1_ROW14_19


title: LFHT1_ROW14_20


title: LFHT1_ROW14_17


title: LFHT1_ROW14_16


title: LFHT1_ROW14_18


title: LFHT1_ROW14_13


title: LFHT1_ROW15_17


title: LFHT1_ROW14_15


title: LFHT1_ROW14_14


title: LFHT1_ROW14_11


title: LFHT1_ROW15_14


title: LFHT1_ROW15_11


title: LFHT1_ROW14_8


title: LFHT1_ROW14_9


title: LFHT1_ROW15_8


title: LFHT1_ROW15_4


title: LFHT1_ROW14_7


title: LFHT1_ROW14_6


title: LFHT1_ROW14_5


title: LFHT1_ROW14_1


title: LFHT1_ROW14_3


title: LFHT1_ROW13_18


title: LFHT1_ROW14_2


title: LFHT1_ROW13_20


title: LFHT1_ROW13_19


title: LFHT1_ROW13_15


title: LFHT1_ROW13_13


title: LFHT1_ROW13_11


title: LFHT1_ROW13_17


title: LFHT1_ROW14_12


title: LFHT1_ROW13_14


title: LFHT1_ROW13_9


title: LFHT1_ROW13_7


title: LFHT1_ROW14_10


title: LFHT1_ROW13_10


title: LFHT1_ROW13_6


title: LFHT1_ROW13_8


title: LFHT1_ROW13_4


title: LFHT1_ROW13_5


title: LFHT1_ROW13_3


title: LFHT1_ROW13_2


title: LFHT1_ROW13_1


title: LFHT1_ROW12_20


title: LFHT1_ROW14_4


title: LFHT1_ROW12_19


title: LFHT1_ROW12_18


title: LFHT1_ROW13_16


title: LFHT1_ROW12_14


title: LFHT1_ROW12_15


title: LFHT1_ROW12_16


title: LFHT1_ROW12_17


title: LFHT1_ROW12_12


title: LFHT1_ROW12_13


title: LFHT1_ROW13_12


title: LFHT1_ROW12_8


title: LFHT1_ROW12_5


title: LFHT1_ROW12_7


title: LFHT1_ROW12_6


title: LFHT1_ROW12_11


title: LFHT1_ROW12_10


title: LFHT1_ROW12_4


title: LFHT1_ROW12_9


title: LFHT1_ROW11_20


title: LFHT1_ROW11_18


title: LFHT1_ROW11_16


title: LFHT1_ROW11_17


title: LFHT1_ROW12_2


title: LFHT1_ROW12_1


title: LFHT1_ROW11_15


title: LFHT1_ROW11_19


title: LFHT1_ROW11_14


title: LFHT1_ROW11_12


title: LFHT1_ROW11_13


title: LFHT1_ROW12_3


title: LFHT1_ROW11_10


title: LFHT1_ROW11_7


title: LFHT1_ROW11_3


title: LFHT1_ROW11_6


title: LFHT1_ROW11_9


title: LFHT1_ROW11_2


title: LFHT1_ROW11_5


title: LFHT1_ROW11_4


title: LFHT1_ROW10_20


title: LFHT1_ROW10_19


title: LFHT1_ROW10_17


title: LFHT1_ROW10_16


title: LFHT1_ROW10_15


title: LFHT1_ROW10_18


title: LFHT1_ROW10_13


title: LFHT1_ROW10_12


title: LFHT1_ROW10_11


title: LFHT1_ROW10_10


title: LFHT1_ROW10_9


title: LFHT1_ROW10_8


title: LFHT1_ROW10_7


title: LFHT1_ROW11_11


title: LFHT1_ROW10_5


title: LFHT1_ROW10_4


title: LFHT1_ROW10_3


title: LFHT1_ROW10_2


title: LFHT1_ROW11_8


title: LFHT1_ROW10_1


title: LFHT1_ROW09_19


title: LFHT1_ROW09_20


title: LFHT1_ROW11_1


title: LFHT1_ROW09_17


title: LFHT1_ROW09_14


title: LFHT1_ROW09_16


title: LFHT1_ROW09_13


title: LFHT1_ROW09_12


title: LFHT1_ROW10_14


title: LFHT1_ROW09_10


title: LFHT1_ROW10_6


title: LFHT1_ROW09_6


title: LFHT1_ROW09_3


title: LFHT1_ROW09_4


title: LFHT1_ROW09_9


title: LFHT1_ROW09_5


title: LFHT1_ROW09_7


title: LFHT1_ROW09_8


title: LFHT1_ROW09_11


title: LFHT1_ROW08_18


title: LFHT1_ROW09_1


title: LFHT1_ROW08_20


title: LFHT1_ROW08_15


title: LFHT1_ROW08_19


title: LFHT1_ROW08_17


title: LFHT1_ROW08_16


title: LFHT1_ROW08_12


title: LFHT1_ROW08_10


title: LFHT1_ROW09_15


title: LFHT1_ROW09_18


title: LFHT1_ROW08_14


title: LFHT1_ROW08_11


title: LFHT1_ROW08_13


title: LFHT1_ROW08_8


title: LFHT1_ROW08_7


title: LFHT1_ROW08_6


title: LFHT1_ROW08_9


title: LFHT1_ROW09_2


title: LFHT1_ROW08_5


title: LFHT1_ROW08_4


title: LFHT1_ROW08_3


title: LFHT1_ROW08_1


title: LFHT1_ROW07_20


title: LFHT1_ROW07_17


title: LFHT1_ROW07_19


title: LFHT1_ROW07_16


title: LFHT1_ROW08_2


title: LFHT1_ROW07_15


title: LFHT1_ROW07_18


title: LFHT1_ROW07_14


title: LFHT1_ROW07_13


title: LFHT1_ROW07_12


title: LFHT1_ROW07_11


title: LFHT1_ROW07_10


title: LFHT1_ROW07_9


title: LFHT1_ROW07_8


title: LFHT1_ROW07_6


title: LFHT1_ROW07_5


title: LFHT1_ROW07_2


title: LFHT1_ROW07_4


title: LFHT1_ROW07_3


title: LFHT1_ROW07_1


title: LFHT1_ROW06_20


title: LFHT1_ROW06_18


title: LFHT1_ROW06_16


title: LFHT1_ROW06_14


title: LFHT1_ROW06_11


title: LFHT1_ROW06_17


title: LFHT1_ROW06_9


title: LFHT1_ROW06_6


title: LFHT1_ROW06_4


title: LFHT1_ROW06_3


title: LFHT1_ROW06_7


title: LFHT1_ROW06_15


title: LFHT1_ROW06_12


title: LFHT1_ROW06_13


title: LFHT1_ROW06_8


title: LFHT1_ROW06_1


title: LFHT1_ROW05_20


title: LFHT1_ROW07_7


title: LFHT1_ROW05_18


title: LFHT1_ROW05_17


title: 2019_Rn_4

description: Whole tissue RNA sequencing; 1 rat; flushed VNO.

data_processing:
RNA-seq reads were mapped with STAR (Dobin et al., 2013) version 2.7.1a, setting the parameter --outFilterMultimapNmax at 4.
An updated version of the Ensembl release 67 GTF file of the rat genome RGSC3.4 was used. This custom gene annotation file included the transcript annotations of de novo identified V1r pseudogenes. For a detailed description, please refer to the methods section of the manuscript.
Gene expression quantification of the bulk RNA-seq data was carried using featureCounts (Liao et al., 2014) version 1.6.5 and our custom gene annotation file, considering reversely stranded reads.
Genome_build: RGSC3.4
Supplementary_files_format_and_content: *featureCounts_pseudogenes_multimapping_fractional_LFJT20210219_counts.txt files are featureCounts output files.

organism: Rattus norvegicus

source_name: vomeronasal epithelium

extract_protocol:
8-week-old Lewis rats were flushed of blood with a heparin solution under anesthesia. Vomeronasal epithelia were isolated and transferred to a tube containing 500–600 μL of ice-cold lysis buffer, 5–6 μL β-mercaptoethanol and a 0.5-cm diameter steel ball, and then put on ice, following the manufacturer's protocol (Qiagen). Samples were then homogenized using a FastPrep-24 instrument (MP Biomedicals) at 6 ms−1 for 30 s and kept on ice. RNA was extracted using the Qiagen RNeasy Mini kit SII following the manufacturers' instructions. Two DNase treatments were performed on all samples: first using the Qiagen RNase-Free DNase Set and then using the Life Technologies Ambion DNase I kit. RNA samples were then aliquoted and stored at −80 °C.
cDNA libraries were generated with the TruSeq RNA and DNA sample preparation kits after selection of polyA-containing mRNAs. Adapters for RNA-seq multiplexing were added to the cDNAs. The cDNA libraries were sequenced with a HiSeq2500 Sequencing system to generate stranded single-end 100 reads of 100 nucleotides length.

value: LEW/Crl

value: 8 weeks


title: LFHT1_ROW06_5


title: 2019_Rn_6


title: LFHT1_ROW05_19


title: LFHT1_ROW06_19


title: LFHT1_ROW05_16


title: LFHT1_ROW05_15


title: 2019_Rn_5


title: 2019_Rn_3


title: LFHT1_ROW05_14


title: 2019_Rn_1


title: 2019_Rn_2


title: LFHT1_ROW05_13


title: LFHT1_ROW05_9


title: LFHT1_ROW05_12


title: LFHT1_ROW05_10


title: LFHT1_ROW05_6


title: LFHT1_ROW05_11


title: LFHT1_ROW05_5


title: LFHT1_ROW05_7


title: LFHT1_ROW05_8


title: 2019_Rn_7


title: LFHT1_ROW05_4


title: LFHT1_ROW05_3


title: LFHT1_ROW05_2


title: LFHT1_ROW05_1


title: LFHT1_ROW04_20


title: LFHT1_ROW04_19


title: LFHT1_ROW04_16


title: LFHT1_ROW04_14


title: LFHT1_ROW04_12


title: LFHT1_ROW04_15


title: LFHT1_ROW04_13


title: LFHT1_ROW04_11


title: SC 13-24_Na_ve sc microglia_02

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

institute: Cleveland Clinic

hyb_protocol: 100ng total RNA was hybridised to fluorescent barcode labelled probes from the nCounter Myeloid Innate Immunity panel, as per manufacturer's instructions

scan_protocol: All samples were read on nCounter Analysis System (NanoString Technologies).

data_processing: The NanoString nCounter system directly captures and counts individual mRNA transcripts using a multiplexed measurement system thereby omitting cDNA based amplification. Analysis was performed using nSolver Analysis Software v3.0 and Ingenuity pathway analysis (Qiagen, Hilden, Germany).

source_name: Macrophage

label_protocol: manufacturer's protocol

extract_protocol: RNA was prepared by extraction with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and Direct-zol RNA mini prep (Zymo Research, Irvine, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: For cell purification, spinal cords from PBS-perfused CX3CR1GFP/+CCR2RFP/+ mice were finely minced with a razor blade. Minced tissues were enzymatically digested in RPMI 1640 medium containing 10% fetal calf serum, 0.5% collagenase D (100 mg/ml) Roche, Basel, Switzerland and 1% DNase I (1 mg/ml) (Sigma Aldrich, St. Louis, MO, USA) for 40 min at 37°C. Collagenase was then inactivated by addition of 1% 0.1 M EDTA for 5 min at 37°C prior centrifugation at 400 g for 7 min at 4°C. Spinal cord-derived cells from seven mice were pooled and isolated using percoll gradients 30/70% to recover CNS mononuclear cells

value: SC Microglia

tag: time point


title: LFHT1_ROW04_17


title: colon mucosa-replicate 7

city: Bronx

first: Elena

last: Tosti

address: 1301 Morris park avenue

institute: Albert Einstein College of Medicine

description: gene expression data from CRC model with  Msh2 and Tgfbr2inactivaton

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized by the Genomics Core at Einstein, according to manufacturer’s instructions, for 16 hr at 45C on GeneChip Mouse Gene Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned by the Genomics Core at Einstein using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Microarray data were pre-processed and analyzed using R-Bioconductor software.Raw data were background-corrected and RMA-normalized, expression values calculated (oligo package) followed by annotation with the pd.mogene.1.0.st.v1 package

label: biotin

source_name: matched colon mucosa  from Mus musculus model

label_protocol: biotinaltion labeling was performed by the Genomics core at Einstein according to the standard Affymetrix protocol from 100 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: tissue was collected from sacrfied mice

extract_protocol: RNA was isolated from tumor and adjacent tumor-free colon mucosa using the RNA easy mini-Kit (Qiagen).RNA quantity was determined using a 2100 Bioanalyzer (Agilent

treatment_protocol: intestinal tissues collected from Msh2 and Tgfbr2 intestinal epithelium inactivated mouse model

value: colon cancer free mucosa


title: colon mucosa-replicate 5


title: colon mucosa-replicate 2


title: CRC-replicate 6

source_name: colon cancer from Mus musculus model

value: colon cancer


title: SC 13-24_Na_ve blood monocyte_01

source_name: blood monocyte

value: SC blood monocyte


title: colon mucosa-replicate 4


title: CRC-replicate 5


title: colon mucosa-replicate 6


title: CRC-replicate 1


title: CRC-replicate 2


title: LFHT1_ROW04_18


title: LFHT1_ROW04_9


title: colon mucosa-replicate 1


title: colon mucosa-replicate 3


title: SC 13-24_d7 sc macs_05

value: SC Macrophage


title: SC 13-24_d7 sc microglia_06

source_name: Microglia


title: LFHT1_ROW04_7


title: CRC-replicate 4


title: CRC-replicate 7


title: CRC-replicate 3


title: LFHT1_ROW04_8


title: LFHT1_ROW04_10


title: LFHT1_ROW04_6


title: SC 13-24_d5 sc microglia_04


title: SC 13-24_d5 sc macs_03


title: LFHT1_ROW04_5


title: LFHT1_ROW04_4


title: LFHT1_ROW04_3


title: SC 13-24_d14 sc2 microglia_12


title: LFHT1_ROW04_2


title: LFHT1_ROW04_1


title: LFHT1_ROW03_19


title: SC 13-24_d14 sc2 macs_11


title: SC 13-24_d14 sc1 microglia_10


title: LFHT1_ROW03_20


title: LFHT1_ROW03_18


title: LFHT1_ROW03_17


title: SC 13-24_d14  sc1 macs_09


title: SC 13-24_d10 sc microglia_08


title: SC 13-24_d10 sc macs_07


title: LFHT1_ROW03_16


title: Brain 1-12_Na_ve blood monocyte_01

value: Brain blood monocyte NA


title: LFHT1_ROW03_15


title: Brain 1-12_d7 brain microglia_06

value: Brain microglia


title: Brain 1-12_d5 brain microglia_04


title: LFHT1_ROW03_13

value: OMP(GFP/wt)


title: Brain 1-12_d7 brain macs_05

value: Brain Macrophage


title: LFHT1_ROW03_14

value: male

value: vomeronasal epithelium


title: LFHT1_ROW03_12

value: vomeronasal sensory neuron

value: single cell in capture chamber


title: Brain 1-12_d5 brain macs_03


title: LFHT1_ROW03_11

value: empty capture chamber


title: Brain 1-12_d14 brain2 macs_11


title: LFHT1_ROW03_10


title: Brain 1-12_Na_ve Brain microglia_02

value: Brain Microglia NA


title: Brain 1-12_d14 brain2 microglia_12


title: Brain 1-12_d14  brain1 macs_09


title: LFHT1_ROW03_8


title: Brain 1-12_d10 brain macs_07


title: Brain 1-12_d14 brain1 microglia_10


title: LFHT1_ROW03_7


title: LFHT1_ROW03_6


title: LFHT1_ROW03_5


title: Brain 1-12_d10 brain microglia_08


title: LFHT1_ROW03_3

value: multiple cells in capture chamber


title: Uveal melanoma cell_MUM2B-1

first: AI

last: ZHUANG

address: 639 Zhizaoju Road

department: Ophthalmology

institute: Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine

description:
M2B_1_H3K27ac
Uveal melanoma patient

data_processing:
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
We calculate the fragment sizes for read pairs given a BAM file from paired-end sequencing. Several regions are sampled depending on the size of the genome and number of processors to estimate the summary statistics on the fragment lengths. Properly paired reads are used for computation.
Reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
The HOMER's findMotifsGenome.pl tool was used for Motif analysis. The input file is the peak file and the genome fasta file. The DNA sequence is extracted according to the peak file, and the sequence is compared with the Motif database to obtain the Motif.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig and narrowPeak files.
Library strategy: CUT&Tag

growth_protocol: The Mum2B cells were cultured in DMEM supplemented with 10% FBS. The PIG1 cells were cultured in f-12k with 10% FBS.

extract_protocol:
RNA was extracted using TRIzol according to the manufacturer's protocol.
For library construction, 21μl DNA was mixed with 2μl of a universal i5 and a uniquely barcoded i7 primer, and then 25μl NEB Next HiFi 2× PCR Master mix was added and mixed. A total volume of 50μl sample was placed in a PCR thermal cycler with a heated lid via the following program: 72°C for 5min; 98°C for 30s; 16 cycles of 98°C for 10s and 63°C for 30s; final extension at 72°C for 1 min and hold at 4°C. To purify PCR products, 1.5 × volumes of AMPure XP beads (Beckman Coulter) were added and incubated for 15 min at RT. Next, the libraries were washed twice gently in 80% ethanol, and eluted in 30μl 10mM Tris pH 8.0. The size distribution of libraries was determined by Agilent 2100 TapeStation analysis.

treatment_protocol: The cells were digested by trypsin and resuspended with culture medium.

value: uveal melanoma cells

tag: antibody


title: Uveal melanoma cell_MUM2B-3

description:
M2B_3_H3K27ac
Uveal melanoma patient


title: Normal melanocyte_PIG1-1

description:
PIG1_1_H3K27ac
Nevus

value: normal melanocytes


title: Uveal melanoma cell_MUM2B-2

description:
M2B_2_H3K27ac
Uveal melanoma patient


title: Normal melanocyte_PIG1-3

description:
PIG1_3_H3K27ac
Nevus


title: Normal melanocyte_PIG1-2

description:
PIG1_2_H3K27ac
Nevus


title: LFHT1_ROW02_19


title: LFHT1_ROW03_9


title: P-1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.

growth_protocol: Uveal melanoma cells 92.1 were cultured with 1640 supplemented with 10% fetus bovine serum.

extract_protocol:
Uveal melanoma cells samples were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The uveal melanoma cells 92.1 were treated with 0.1μM LBH589 for 24 hours before RNA extraction. The control 92.1 cells were treated with the same dose of DMSO for 24 hours.

value: Uveal melanoma cell

value: 24 hour


title: P-3


title: NC-3

value: DMSO


title: NC-2


title: LFHT1_ROW02_17


title: NC-1


title: LFHT1_ROW02_16


title: LFHT1_ROW03_4


title: S314_Post_CD4_Me RNAseq

city: Seoul

first: Sojeong

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Blood Cancer Research Institute

country: South Korea

institute: Yonsei University College of Medicine

description:
RNAseq
RNAseq

data_processing:
Raw reads were assembled and low-quality reads were filtered using Cutadapt (version 2.8).
Filtered reads were aligned on a reference genome downloaded from Ensembl (GRCh38.p13, Accession number: GCA_000001405.28) using STAR (version 2.7.1a).
Assembly: Ensembl (GRCh38.p13, Accession number: GCA_000001405.28) for RNAseq, human reference V, D, J and C genes of TCRs for IR-Seq
Supplementary files format and content: gene expression files of RNAseq contains raw gene counts IR-Seq processed data consists of raw read counts of each CDR3

source_name: blood PBMCs

extract_protocol:
TRIzol reagent (Invitrogen) and QIAgen_RLT_buffer were used for isolation of total RNA for RNAseq, and IR-seq, respectively
Extracted RNAs were processed using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer‟s instructions.
RNA-seq/ IR-seq

value: blood PBMCs

value: T-cells

tag: il-7 administration

value: Post

value: Male


title: LFHT1_ROW02_14

value: OMP(GFP/wt)


title: S303_Post_CD4_Me RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW02_15

value: male


title: S301_Post_CD4_Me RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW02_13

value: vomeronasal epithelium


title: LFHT1_ROW06_2

value: vomeronasal sensory neuron


title: P-2


title: LFHT1_ROW02_20


title: LFHT1_ROW03_2


title: S216_Post_CD4_Me RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW02_10

value: single cell in capture chamber


title: LFHT1_ROW02_12


title: S207_Post_CD4_Me RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW02_11

value: empty capture chamber


title: LFHT1_ROW02_18


title: S301_Post_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW02_9


title: S303_Post_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW02_8


title: S207_Post_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW02_6


title: LFHT1_ROW02_5


title: LFHT1_ROW02_4


title: S314_D7_CD4_Me RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW02_3


title: S301_D7_CD4_Me RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW02_2


title: LFHT1_ROW02_1


title: S314_Post_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW01_20


title: S207_D7_CD4_Me RNAseq

description:
RNAseq
RNAseq


title: S203_D7_CD4_Me RNAseq

description:
RNAseq
RNAseq

value: Female


title: LFHT1_ROW01_19


title: S303_D7_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: S301_D7_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW02_7

value: multiple cells in capture chamber


title: LFHT1_ROW01_18


title: S314_D7_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: IL3D6

city: shanghai

first: ruoyu

last: tang

address: si ping road

institute: tongji university

description: rRNA-free RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 software 2.2.1
bam2wig.py converts all types of RNA-seq data from BAM format into wiggle format
Wiggle file format was applied to detect and analyze regions of signal on each strand. Data visualization was aided by IGV based on information of reads depth
Assembly: mm10
Supplementary files format and content: wiggle

source_name: bone marrow

extract_protocol:
Bone marrow (BM) cells were flushed from femurs and tibiae of 6-10 weeks age of mice of wild type, and RNA was harvested using Trizol reagent.Ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre). Sequencing libraries were subsequently generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bone marrow cells were cultured in RPMI 1640 medium (GIBCO, Invitrogen) containing 10% heat-inactivated FBS (GIBCO, Invitrogen), 50 uM 2-mercaptoethanol (GIBCO) at 1x106 /ml. 10 ng/ml IL-3 was added for induction of FcεRIα-expressing cells

value: bone marrow

value: IL-3-treated for 6 days


title: MC/9

description: rRNA-free RNA

source_name: mast cell line

value: liver

value: untreated


title: S203_Post_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: S216_D7_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW01_17


title: S216_Post_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: S203_D7_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: lnNC30D12

city: Xuzhou

first: Zuobin

last: Zhu

state: Jiangsu

address: Tongshan road 209

department: Department of Genetics

institute: Xuzhou Medical University

data_processing:
The raw reads with rRNA, low quality, joint contamination, and unknown base N content too high were filtered out
Clean reads were matched to the reference genome using HISAT and then assembled using StringTie
After obtaining the new transcript, the mRNA and lncRNA were distinguished by using the three software CPC, txCdsPredict, CNCI and the database is Pfam
The score exceeded the threshold score(CPC_threshold = 0, CNCI_threshold = 0, txCdsPredict_threshold = 500) and if the transcript can be compared to the pfam database were conserved to be mRNA, otherwise were conserved to be lncRNA.
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Caenorhabditis elegans

source_name: Whole cell tissue

growth_protocol: C. elegans were fed E. coli OP50 at 20 °C on normal growth medium (NGM).

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. Subsequently, total RNA was qualified and quantified using a NanoDrop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: trans-nuclear

value: day 12


title: lnNC30D9

value: day 9


title: S216_D7_CD4_Me RNAseq

description:
RNAseq
RNAseq

value: blood PBMCs

value: T-cells


title: S303_D7_CD4_Me RNAseq

description:
RNAseq
RNAseq

value: Male


title: LFHT1_ROW01_16

value: OMP(GFP/wt)

value: male


title: S216_D0_CD4_Me RNAseq

description:
RNAseq
RNAseq


title: S314_D0_CD4_Me RNAseq

description:
RNAseq
RNAseq


title: S303_D0_CD4_Me RNAseq

description:
RNAseq
RNAseq


title: S301_D0_CD4_Me RNAseq

description:
RNAseq
RNAseq


title: lnNC30D6

value: day 6


title: lnNC30D0A3

value: day 0


title: LFHT1_ROW01_15

value: vomeronasal epithelium

value: vomeronasal sensory neuron

value: empty capture chamber


title: S203_D0_CD4_Me RNAseq

description:
RNAseq
RNAseq

value: Female


title: S207_D0_CD4_Me RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW01_14

value: single cell in capture chamber


title: S301_D0_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW01_12


title: lnNC30D0A2


title: LFHT1_ROW01_11


title: S207_D0_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: S314_D0_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: S203_D0_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: lnN2D12

value: wild type


title: LFHT1_ROW03_1


title: lnN2D9


title: S207_D7_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: S303_D0_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW01_13


title: S216_D0_CD4_Na RNAseq

description:
RNAseq
RNAseq


title: lnN2D6


title: S313_D7_CD8_ME RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW01_10


title: LFHT1_ROW01_9


title: S313_D7_CD8_NA RNAseq

description:
RNAseq
RNAseq


title: S313_Post_CD8_ME RNAseq

description:
RNAseq
RNAseq

value: Post


title: lnN2D0A2


title: S313_Post_CD8_NA RNAseq

description:
RNAseq
RNAseq


title: lnNC30D0A1

value: trans-nuclear


title: LFHT1_ROW01_8


title: S313_D0_CD8_ME RNAseq

description:
RNAseq
RNAseq

value: Before


title: lnN2D0A3


title: S313_D0_CD8_NA RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW01_7


title: S306_D7_CD8_ME RNAseq

description:
RNAseq
RNAseq


title: S306_D7_CD8_NA RNAseq

description:
RNAseq
RNAseq


title: lnN2D0A1


title: LFHT1_ROW01_5


title: S306_D0_CD8_ME RNAseq

description:
RNAseq
RNAseq


title: S306_Post_CD8_NA RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW01_6


title: S306_D0_CD8_NA RNAseq

description:
RNAseq
RNAseq


title: S302_D7_CD8_ME RNAseq

description:
RNAseq
RNAseq


title: S302_D7_CD8_NA RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW01_4


title: Primary Schwann cells,CLL-Rat-input

city: Nantong

first: Qianqian

last: Chen

state: Please Select

address: 19 Qixiu Road, Chongchuan District

institute: Nantong University

data_processing:
trimfastq.py  https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/master/src/trimfastq.py
Bowtie2 version 2.2.6
SAMtools 1.7
SAMstats (version 0.2.1)
MACSv2  https://github.com/taoliu/MACS/
Assembly: deeptools (v3.3.0)
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: Sciatic nerve

growth_protocol: 4.5 g/L DMEM, 10% fetal bovine serum,  1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB catalogue number E6240L) and then run on the Illumina sequencer HiSeq 2500. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Cultured cells were transfected with pRlenti-SFH-EGFP-P2A-Puro-CMV-FOSL1-3Flag-2.

value: Sciatic nerve

value: Primary cultured Schwann cells

value: Schwann cells

value: WT

tag: chip antibody


title: S306_Post_CD8_ME RNAseq

description:
RNAseq
RNAseq

value: blood PBMCs

value: T-cells


title: Primary Schwann cells,CLL-Rat-FOSL1

tag: cell line


title: Naïve CD8 T cells_S313_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta

value: Male


title: S302_Post_CD8_NA RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW01_3

value: OMP(GFP/wt)

value: male


title: S302_Post_CD8_ME RNAseq

description:
RNAseq
RNAseq


title: Memory CD8 T cells_S313_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: S302_D0_CD8_NA RNAseq

description:
RNAseq
RNAseq


title: S302_D0_CD8_ME RNAseq

description:
RNAseq
RNAseq


title: Naïve CD4 T cells_S313_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: S216_D7_CD8_NA RNAseq

description:
RNAseq
RNAseq


title: S216_D7_CD8_ME RNAseq

description:
RNAseq
RNAseq


title: S216_Post_CD8_NA RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW01_1

value: vomeronasal epithelium

value: vomeronasal sensory neuron


title: S216_Post_CD8_ME RNAseq

description:
RNAseq
RNAseq


title: m3VNO

description: Whole tissue RNA sequencing; 1 mouse; flushed VNO.

data_processing:
RNA-seq reads were mapped with STAR (Dobin et al., 2013) version 2.7.1a, setting the parameter --outFilterMultimapNmax at 4.
An updated version of the Ensembl release 86 GTF file of the mouse genome GRCm38 (mm10) was used. This custom gene annotation file included the manual re-annotation of the 3’ UTRs of the transcripts of vomeronasal receptor genes (V1rs, V2rs and Fprs), as well as the transcript annotations of de novo identified V1r pseudogenes. For a detailed description, please refer to the methods section of the manuscript.
Gene expression quantification of the bulk RNA-seq data was carried using featureCounts (Liao et al., 2014) version 1.6.5 and our custom gene annotation file, considering reversely stranded reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: *featureCounts_pseudogenes_multimapping_fractional_LFJT20200404_counts.txt files are featureCounts output files.

extract_protocol:
8-week-old C57BL/6J mice were flushed of blood with a heparin solution under anesthesia. Vomeronasal epithelia were isolated and transferred to a tube containing 500–600 μL of ice-cold lysis buffer, 5–6 μL β-mercaptoethanol and a 0.5-cm diameter steel ball, and then put on ice, following the manufacturer's protocol (Qiagen). Samples were then homogenized using a FastPrep-24 instrument (MP Biomedicals) at 6 ms−1 for 30 s and kept on ice. RNA was extracted using the Qiagen RNeasy Mini kit SII following the manufacturers' instructions. Two DNase treatments were performed on all samples: first using the Qiagen RNase-Free DNase Set and then using the Life Technologies Ambion DNase I kit. RNA samples were then aliquoted and stored at −80 °C.
cDNA libraries were generated with the TruSeq RNA and DNA sample preparation kits after selection of polyA-containing mRNAs. Adapters for RNA-seq multiplexing were added to the cDNAs. The cDNA libraries were sequenced with a HiSeq2500 Sequencing system to generate stranded single-end 100 reads of 100 nucleotides length.

value: 8 weeks


title: Naïve CD8 T cells_S313_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Memory CD8 T cells_S313_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: S216_D0_CD8_NA RNAseq

description:
RNAseq
RNAseq


title: S216_D0_CD8_ME RNAseq

description:
RNAseq
RNAseq


title: f3VNO

value: female


title: S214_D7_CD8_NA RNAseq

description:
RNAseq
RNAseq

value: Female


title: S214_D7_CD8_ME RNAseq

description:
RNAseq
RNAseq


title: S214_Post_CD8_ME RNAseq

description:
RNAseq
RNAseq

value: Post


title: Naïve CD4 T cells_S313_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: f2VNO


title: S214_Post_CD8_NA RNAseq

description:
RNAseq
RNAseq


title: S214_D0_CD8_NA RNAseq

description:
RNAseq
RNAseq


title: Memory CD4 T cells_S313_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: D_F3F4

description: Whole tissue RNA sequencing; pool of 2 mice; non-flushed VNO.


title: S214_D0_CD8_ME RNAseq

description:
RNAseq
RNAseq


title: LFHT1_ROW01_2

value: single cell in capture chamber


title: LFHT1_ROW06_10

value: empty capture chamber


title: C_F1F2


title: Naïve CD8 T cells_S308_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: S203_D7_CD8_NA RNAseq

description:
RNAseq
RNAseq


title: Memory CD4 T cells_S313_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: Memory CD8 T cells_S308_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: m1VNO


title: S203_D0_CD8_NA RNAseq

description:
RNAseq
RNAseq

value: Before


title: Naïve CD4 T cells_S308_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: B_M3M4


title: A_M1M2


title: S203_D0_CD8_ME RNAseq

description:
RNAseq
RNAseq


title: Naïve CD8 T cells_S308_D0 IR-Seq

description:
IR-Seq
iReperoire human TCR beta


title: RNA-seq_K562_cas9-ZNF234-promoter

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

data_processing:
Hi-TrAC data raw paired-end reads in FASTQ files were first trimmed of linker sequence CTGTCTCTTATACACATCT for both ends. Only PETs with both ends length >=10bp were kept. Trimmed PETs were mapped to hg38 using Bowtie2 with key parameters of --end-to-end --very-sensitive. Mapped PETs with MAPQ >=10 were converted to BEDPE files. Mapped PETs with distance shorter than 1kb without linker sequence in any end were further filtered. PCR replicates of PETs were filtered if both ends locations were identical.  Unique intra-chromosomal PETs (cis PETs) as BEDPE files were mainly used for downstream analysis. All described processing steps were summarized as tracPre2.py in the cLoops2 package. Raw RNA-seq data reads were mapped to human reference genome hg38 by STAR (v2.7.3a). Gene annotation file (v30) downloaded from GENCODE 89 were used to quantify gene expression level by Cufflinks (v2.2.1). Raw ChIP-seq and ATAC-seq data reads were mapped to human reference genome hg38 by Bowtie2 with key parameters of --local --very-sensitive --no-unal --no-mixed --no-discordant. Mapped PETs with MAPQ >=10 were converted to normalized signals (reads per million) as bigWig files by deepTools for visualization.  Raw Hi-C data reads were processed to human reference genome hg38 by HiC-Pro (v2.11.1). Only intra-chromosomal PETs from the files with a suffix of allValidPairs output by HiC-Pro were used for all following analysis.
Assembly: hg38
Supplementary files format and content: BEDPE files contain the high quality and unique processed interaction paired-end tags.

growth_protocol: GM12878 cells were cultured in RPMI 1640 medium supplied with 15% fetal bovine serum and 2mM L-glutamine. K562 cells were cultured in RPMI 1640 mudium supplied with 10% fetal bovine serum  and antibiotics ( 100 units/mL Penicillin, 100 µg/mL Streptomycin). Mouse ES cells were cultured with PMEF as feeder cells on gelatin coated plates in ES medium ( MEM, 15% FBS, 2 mM GlutaMAX, 1 mM Sodium Pyruvate, 100 µM Non-essential amino acids, 0.1 mM 2-mercaptoethanol, 10 ng/mL LIF, Penicillin-Streptomycin).

extract_protocol:
For Hi-TrAC and Hi-C, genomic DNA was purified by Phenol-Chloroform extraction. RNA was extracted with QIAzol lysis reagent (QIAGEN) and RNeasy mini kit (QIAGEN). For ChIP-seq and ATAC-seq, genomic DNA was purified with QIAGEN MinElute Reaction Cleanup Kit.
For Hi-TrAC, repair DNA gaps with T4 DNA polymerase. Remove free bridging linker by AMPure XP beads. Then, Digest purified DNA with restriction enzymes MluCI/NlaIII, and enrich biotin-labeled DNA fragments with streptavidin beads. Perform adapter ligation on beads. After washing the beads, run PCR with illumina multiplexing indexed primers. For RNA-seq, libraries were constructed following Smart-seq2 protocol (Picelli et al., 2014). For ChIP-seq, DNA was purified, then end-repaired using End-It DNA End-Repair kit (Epicentre). A-tailing was performed with Klenow Fragment (3'->5' exo-) with the presence of dATP. Universal adapters were then ligated. The libraries were then amplified by PCR using indexed primers. For ATAC-seq, purified genomic DNA was amplified by PCR with indexed primers to construct the libraries. For Hi-C, purified genomic DNA was treated with T4 DNA polymerase to remove biotin labels at DNA ends. Fragment the DNA by sonication to 300-500 bp. Fragmentated DNA was end-repaired, followed with A-tailing. Biotin labeled DNA was enriched with MyOne Streptavidin C1 beads (Invitrogen). PCR adapters were then ligated to the enriched DNA on beads. Perform PCR with indexed primers to amplify the libraries.

treatment_protocol: Cells for Hi-TrAC were fixed with 1% Formaldehyde in culture medium at room temperature for 10 minutes. Wash cells with ice-cold PBS twice, then resuspend cells  with 100 µL reaction buffer (50mM Tris-acetate, pH 7.5, 150mM potassium acetate, 10mM magnesium acetate, 4mM spermidine, 0.5% NP-40). Incubate at 37 ℃ for 4 hours. To extract RNA for RNA-seq, add 700 µL QIAzol to 5,000 cells. Cells for ChIP-seq were fixed with 1% Formaldehyde in culture medium at room temperature for 10 minutes. Wash cells with ice-cold PBS twice. Then perform sonication to break chromatins. Sheared chromatin was immunoprecipitated with anti-CTCF, anti-RAD21, anti-HCFC1, anti-ZNF143 antibodies. After washing, perform Portease K digestion and reverse cross-linking at 65 ℃ overnight. For ATAC-seq, cells were lysed in 100 µL lysis buffer (10 mM Tris-HCl, 10 mM sodium chloride, 3 mM manesium chloride, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin) on ice for 3 minutes. Add 1 mL wash buffer (10 mM Tris-HCl, 10 mM sodium chloride, 3 mM manesium chloride, 0.1% Tween-20), then collect the nuclei by spinning at 500 xg for 10 minutes. Resuspend the nuclei in transposition reaction buffer, and add Tnp complex to perform transposition at 37 ℃ for 30 minutes.  For Hi-C, 1% Formaldehyde fixed cells were permeabilized with lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40, 1 X protease inhibitor). Chromatin was decondensed with the presence of 0.1% SDS in 1 x restriction enzyme digestion buffer at 65 ℃ for 10 minutes. Add 1% Triton X-100, and incubate at 37 ℃ for 1 hour to quench SDS. Digest the chromatin with restriction enzymes CviQ I, CviA II and BfaI. Wash cells twice with wash buffer (1 x PBS, 1 mM EDTA, 0.1% Triton X-100). The DNA ends of digested chromatin were blunted and labeled with biotin by Klenow enzyme with the presence of dCTP, dGTP, dTTP and biotin-14-dATP, followed by ligation using T4 DNA ligase. Reverse cross-linking at 65 ℃ overnight.

tag: genotype/variation

value: ZNF234 gene promoter deletion


title: Memory CD4 T cells_S308_Post IR-Seq

description:
IR-Seq
iReperoire human TCR beta

tag: age


title: RNA-seq_K562_cas9-CEMIP2-E3

value: CEMIP2 gene enhancer E3 deleiton


title: RNA-seq_K562_cas9-CEMIP2-E2

value: CEMIP2 gene enhancer E2 deleiton


title: RNA-seq_K562_cas9-CEMIP2-E5

value: CEMIP2 gene enhancer E5 deleiton