title: 4C_St3gal6.TSS_Dox_Treated_rep1 [763]

data_processing:
library strategy: 4C-seq
Fastq files have been demultiplexed by Cutadapt.
4C-seq reads were mapped on Mm10/GRCm38 genome assembly and signal normalized by pipe4C (v1.1) R-package (Krijger PHL, et al., Methods, 2019) in “cis” mode and with default parameters.
Normalization between density files of different conditions (bigWig) was performed by using pipe4C (v1.1) R-package (Krijger PHL, et al., Methods, 2019).
Assembly: mm10
Supplementary files format and content: Normalized bigWig files were generated using pipe4C (v1.1) R-package (Krijger PHL, et al., Methods, 2019).

extract_protocol:
4C-seq experiments were performed as previously described (Krijger PHL, et al., Methods, 2019). For Alas2_enhancer the enzymes used were DpnII>EcoRI while for St3gal6_TSS DpnII>Csp6I.
For library preparation purified circular fragments were amplified by PCR with View-Point specific primers. Resulting amplicons were purified with AMPure XP beads (0.8×) and amplified using standard indexed Illumina primers as previously described (Krijger PHL, et al., Methods, 2019). Second-round PCR products were purified with PCR purification columns (Qiagen) and quantified by 2100 Bioanalyzer (Agilent, DNA 7500 kit). 4C library was prepared by equimolar mix of the samples. The library was cleaned-up by AMPure XP beads (0.8x) to remove PCR dimers before sequencing through Illumina MiSeq with a 75bp Single-End reads setup.

treatment_protocol: Cells were treated or not with doxycycline for 48h to induce the expression of an shRNA against Spi1. One biological replicate was generated for all conditions.

value: Leukemic erythroid cells


title: KO MOZ-TIF2 AML, Input (H3K23ac)

status: Public on Jul 24 2022

type: SRA

city: Tokyo

first: Takuo

last: Katsumoto

address: 5-1-1 Tsukiji, Chuo-ku

department: Research Institute

country: Japan

institute: National Cancer Center

library_source: genomic

data_processing:
All data analysis were performed in Galaxy Europe website (https://usegalaxy.eu).
To trim adaptor sequences, sequence reads were processed with the Trimmomatic tool (Garaxy Ver. 0.38.1) for defalt setting.
Sequence reads were mapped on UCSC mm10 of the mouse genome using the Bowtie2 tool (Galaxy Ver. 2.4.5) for defalt setting.
Aligned sequences were removed PCR duplicates using RmDup samtools (Galaxy Ver. 1.3.1) and sorted into chromosomes using Samtools sort (Galaxy Ver. 1.13) for defalt setting.
To visualize the ChIP-Seq results, modified aligned sequences were converted to BigWig files using deeptools (Galaxy Ver. 3.51) for defalt setting.
Assembly: mm10
Supplementary files format and content: BigWig

molecule: genomic DNA

organism: Mus musculus

source_name: MOZ-TIF2 AML cells

growth_protocol: Methocult 3234 methylcellulose media, murine IL-3 20 ng/ml, CSF 50 ng/ml, GM-CSF 10ng/ml, and 100 U/ml Penicillin/Streptmycin. Cells were cultured at 37C, at 5 % CO2.

extract_protocol:
MOZ-TIF2 AML cells were fixed with 1% formaldehyde for 7 minutes. After quenching and cell lysis, chromatin was sonicated using a S220 focused-ultrasonicator (Covaris).
ChIP-Seq libralies were prepared with VAHTS Universal Pro DNA Library Prep Kit (Vazyme) for Illumina.

tag: strain

tag: cell type

value: MOZ-TIF2 AML cells

tag: genotype

value: Moz-/-

tag: chip antibody


title: WT MOZ-TIF2 AML, H3K23ac, Merck

value: Moz+/+


title: 4C_Alas2.enhancer_Dox_Treated_rep1 [763]

city: VILLEJUIF

first: Christel

last: GUILLOUF

address: 114 rue Edouard vaillant

country: France

institute: Gustave Roussy

source_name: Bone marrow leukemic cells

growth_protocol: Cells were maintained in culture with EPO, in exponential growth before treatment with Dox

tag: treatment


title: 4C_Alas2.enhancer_Dox_Untreated_rep1 [763]


title: WT MOZ-TIF2 AML, Input (H3K23ac)


title: KO MOZ-TIF2 AML, H3K23ac, Merck


title: YL-RAD21mAC-0IAA-G1-R2-T1

city: Worcester

first: Yu

last: Liu

state: MA

address: 368 Plantation Street

department: Program in Systems Biology

country: USA

institute: University of Massachusetts Medical School

description: Human colon carcinoma cell line; established from the primary colon carcinoma of an adult man.

data_processing:
Fastq files of Hi-C were mapped and parsed to generate cooler files using Distiller
Cooler files were directly processed for compartment and insulation pileup analysis using cooltools
Cooler files were transfer to cWord matrix files to generate contact heatmaps and analyze insulation and loop pileup
Fastq files of ChIPseq were mapped using Bowtie to generate sam files
HOMER (PMID 20513432) was used to generate tag and bigwig files and call peaks from sam files
DeepTools was used for ChIP signal stacking up
Genome_build: hg19
Supplementary_files_format_and_content: cooler for Hi-C and BigWig files for ChIPseq

organism: Homo sapiens

source_name: HCT116-RAD21-mAC cells

growth_protocol:
HAP1-RAD21-TEV are grown in IMDM medium, with GlutaMAX, 10% FBS and 1% penicillin-streptomycin at 37C in 5% CO2
HCT116-RAD21-mAC cells are grown in McCoy's 5A medium, with GlutaMAX, 10% FBS and 1% penicillin-streptomycin at 37C in 5% CO2.

extract_protocol:
Nuclei were purified using hytonic buffer and after treatments, nuclei were fixed for Hi-C protocol
Hi-C 2.0 (PMID28435001)
After cells were fixed, cells or G1 sorted cells were used for Hi-C protocol
Hi-C 2.0 (PMID28435001)

treatment_protocol:
TEV protease treatment: 15U/ml at 4C for overnight; NB contains 10mM PIPES pH 7.4, 2mM MgCl2 and 10mM KCl; NBS1 and NBS2 buffers are NB with 132mM and 200mM NaCl, respectively. NBS1 is physical conditional buffer.
500mM 3-indole acetic acid in DMSO was added to culture to obtain final concentration of 500uM

tag: protocol

tag: enzyme

value: HindIII

tag: cell line

value: HCT116-RAD21-mAC cells


title: CTRL1_R3

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

library_source: transcriptomic

data_processing:
The raw RNA-seq fastq files were quality-checked using the FastQC software and the data was pre-processed using the software package Rsubread
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes count values derived from Rsubread processing for each sample

molecule: total RNA

growth_protocol: Smits et al., npj Parkinson's Disease, 2019

extract_protocol:
RNA was extracted using Allprep DNA/RNA mini kit (QIAGEN #80204). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420L).

value: Midbrain organoids

value: wt/wt

tag: Sex

value: Female

tag: age

tag: disease

value: Healthy


title: KO MOZ-TIF2 AML, Input (H3K9ac)


title: YL-RAD21mAC-0IAA-syn-R1-T1


title: 4C_St3gal6.TSS_Dox_Untreated_rep1 [763]


title: KO MOZ-TIF2 AML, H3K9ac, Activemotif

value: H3K9ac (Activemotif, 39317)


title: PD2_R1

value: PD


title: 4C_St3gal6.TSS_Dox_Treated_rep1 [722]


title: YL-RAD21mAC-6hrIAA-ns-R1-T1


title: YL-RAD21mAC-6hrIAA-syn-R1-T1


title: WT MOZ-TIF2 AML, Input (H3K9ac)


title: YL-RAD21mAC-2hrIAA-syn-R1-T1


title: YL-RAD21mAC-2hrIAA-ns-R1-T1


title: YL-RAD21mAC-0IAA-ns-R1-T1


title: 4C_St3gal6.TSS_Dox_Untreated_rep1 [722]


title: WT MOZ-TIF2 AML, H3K9ac, Activemotif


title: 4C_Alas2.enhancer_Dox_Treated_rep1 [722]


title: 4C_Alas2.enhancer_Dox_Untreated_rep1 [722]


title: HDAC1_CUTandTag

data_processing:
library strategy: CUT&Tag
reads were onto mm10 genome assembly using bowtie2 with the following parameters: --end-to-end --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files generated using bamCoverage from deepTools

source_name: Bone marrow Leukemic cells

growth_protocol: Cells were maintained in culture with EPO, in exponential growth  before processing

extract_protocol: The CUT&Tag assay was performed using CUT&Tag-IT Assay Kit (Active Motif) following the manufacturer’s protocol on 0.5×10^6 leukemic cells.

value: Untreated

tag: molecule subtype

value: tagmented DNA


title: m1Aseq-Alkb-KO2 CD4 T cell-6h

status: Public on Jul 23 2022

city: Hangzhou

first: Xiaoyu

last: Li

state: Zhejiang

address: 866 Yuhangtang Road

department: SCHOOL OF BASIC MEDICAL SCIENCES

country: China

institute: Zhejiang University

description: tRNA

data_processing:
Reads adapters were removed by Trim_galore ( v0.6.6)
For RNA-seq, Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the mm10 genome using Hisat2 (v2.0.5) ,and then featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. For Ribo-seq, the rRNA removed reads of each sample were mapped to the reference genome by Bowtie2(V 2.4.1) allowing no mismatches. For m1A-seq, clean reads were mapped to mm10 tRNA genome by bowtie2.
Genome_build: mm10 genome;mm10 tRNA reference

source_name: Primary CD4 T cells

growth_protocol: Primary T cells were isolated from the spleens of age-matched WT and conditional knockout mice (8 weeks old). Naive CD4 T cells were purified by using EasySep Mouse Naïve CD4+ T Cell Isolation Kit (STEMCELL Technologies) according to the instructions, respectively. The purified T cells were cultured with X-VIVO mediums.

extract_protocol:
RNAseq: total RNA was extracted based on the manufacturer’s protocol by using TRIzol reagent (Invitrogen). Riboseq: we performed the ribosome profiling by strictly following the manual for the Illumina TruSeq Ribo Profile (Mammalian) Kit. m1Aseq: 200 ng small RNA fraction (<200 nt; mainly composed of mature tRNA) was purified from total RNA using MEGAclear Kit (Thermo Fisher Scientific).
RNAseq:RNA libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB) based on the manufacturer’s instructions. RiboTagseq: libraries were constructed using NEBNext® Multiple Small RNA Library Prep Set for Illumina® (no. E7300S, E7300L). m1Aseq: Purified small RNA was deacylated by incubating in 0.1 M Tris-HCl, pH 9 at 37°C for 45 min. Half of the deacylated small RNA fraction was subjected to demethylation treatment by using AlkB in vivo reaction. RNA samples were dephosphorylated with PNK (NEB) and ligated to 3’ RNA linker using T4 RNA ligase2, truncated KQ (NEB). Reverse transcription was carried using different reverse transcriptase for different samples. 5’ adaptor was ligated to cDNA and then amplified by PCR. PCR products were purified by 8% TBE gel.

treatment_protocol: The purified T cells were stimulated with plate-bound anti-CD3 (5 μg/ml) and anti-CD28 (2 μg/ml) in replicate wells of 96-well plates.

tag: tissue

value: spleen

value: 8 weeks

value: Trmt61a cKO

value: primary CD4 T cells


title: m1Aseq-Alkb-KO1 CD4 T cell-6h

description: tRNA


title: RL-95-2 transfected with tRF-20-S998LO9D mimics

city: Nanjing

first: Shanliang

last: Zhong

address: Baiziting 42

institute: The Affiliated Cancer Hospital of Nanjing Medical University

data_processing:
Basecalls performed using CASAVA.
RNA-seq reads were aligned to the GRCh38 genome assembly using Hisat2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: endometrium

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on DNBSEQ-T7 platform at Tsingke Biotechnology Co., Ltd..

value: Endometrial cancer cell line

tag: transfection


title: HEC-1-A transfected with tRF-20-S998LO9D mimics


title: HEC-1-A transfected with negative control of mimics

value: negative control


title: RL-95-2 transfected with negative control of mimics


title: m1Aseq-Alkb-WT2 CD4 T cell-6h

description: tRNA

value: wild type


title: m1Aseq-KO2 CD4 T cell-6h

description: tRNA


title: m1Aseq-Alkb-WT1 CD4 T cell-6h

description: tRNA


title: m1Aseq-WT1 CD4 T cell-6h

description:
tRNA
m1Aseq-tRNA-WT-CKO.csv


title: m1Aseq-KO1 CD4 T cell-6h

description: tRNA


title: Input_MCF7rescue_E2

city: Basel

first: Charly

last: Jehanno

address: HebelStrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University of basel

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Assembly: hg19
Supplementary files format and content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

growth_protocol: MCF7 cells were grown in 2D monolayer, starved for 72h in DMEM 2% charcoal strip FBS and treated for 50 minutes with 10nM of E2 or EtOH to induce ER alpha dimerization and binding to chromatin.

extract_protocol:
Cells were fixed for 10 min 1.5% formaldehyde. Reaction was stopped using 1.5M glycine. Cell lysates (triton and SDS based) were clarified after sonication and subjected to immunoprecipitation with ER antibody.
Libarary construction was performed by : https://www.france-genomique.org/

tag: experimental conditions

value: 2D monolayer, DMEM 2percent charcoal strip FBS

tag: antibody


title: CHIP_MCF7rescue_E2

value: ER alpha antibody, HC-20 Santa Cruz :sc-543


title: Input_MCF7rescue_EtOH


title: CHIP_MCF7control_EtOH


title: CHIP_MCF7Hypoxia_EtOH

tag: agent

value: Cobalt Chloride 200uM


title: CHIP_MCF7control_E2


title: m1Aseq-WT2 CD4 T cell-6h

description: tRNA

tag: strain


title: CHIP_MCF7Hypoxia_E2


title: Input_MCF7hypoxia_E2


title: Input_MCF7hypoxia_EtOH


title: Input_MCF7control_E2


title: Input_MCF7control_EtOH


title: CHIP_MCF7rescue_EtOH


title: S13-30612-A11

type: RNA

city: Philadelphia

first: Mariana

last: Franco Fragoso

state: PA

address: 333 Cottman Avenue

department: Cancer Prevention and Control

institute: Fox Chase Cancer Center

description: Epithelial cells from FFPE were microdissected from inflamed areas

hyb_protocol: Samples were diluted 1:10, and 5ul each miRNA-tag sample (equivalent to 10ng total RNA) were added to hybridizations with 10 ul or reporter code set, 10 ul hybridization buffer and 5 ul of capture probe set.

scan_protocol: Scans were completed with GEN2 Digital Analyzer.

data_processing: NanoString raw counts were normalized by quantile normalization, and transformed to log2-scale

label: miR-taq, Reporter Code Set and Capture Probe Set

source_name: colon biopsies

label_protocol: ~100ng (or 3ul) of each RNA sample was added to the miRNA-tag ligation reaction for annealing, followed by ligation and purification.

growth_protocol: Colon biopsies from Penn State Health Milton S. Hershey Medical Center were obtained from patients with Ulcerative Colitis (UC) and reviewed by a pathologist. Epithelial cells of confirmed areas of non-dysplastic inflamed colon, flat and polypoid dysplasia were used for total RNA extraction followed by NanoString Human miRNA platform profiling.

extract_protocol: RNA was extracted from pure populations of colonic epithelial cells using the RecoverAll™ Isolation kit (Life Technologies). All RNAs were subjected to DNAse treatment. Quality was assessed on RNA 6000 Pico LabChip and evaluated on Agilent Bioanalyzer 2100 using Eukaryote Total RNA Pico Assay.

treatment_protocol: Patients were not treated.

tag: lesion

value: dysplasia


title: S12-37069-B2


title: S12-14404A5


title: S12-14404A4


title: S11-5381C5

value: inflammation


title: C11_03

city: Durham

first: Sudarshan

last: Rajagopal

state: NC

address: Box 102147, Duke University Medical Center

department: Biochemistry

institute: Duke University School of Medicine

description: gene.description.xls

data_processing:
Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and our wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
To allow for log adjustment, genes with 0 FPKM are assigned a value of 0.001. Correlation were determined using the cor.test function in R with options set alternative =”greater” and method = “Spearman”.
Genome_build:  NCBI/UCSC/Ensembl
Supplementary_files_format_and_content: gene.description.xls: The description of genes, including gene structure, differential results and annotation results.
Supplementary_files_format_and_content: Description of each column:
Supplementary_files_format_and_content: The location description of genes: columns 1~6
Supplementary_files_format_and_content: geneID: The gene id.
Supplementary_files_format_and_content: GeneName: The gene name
Supplementary_files_format_and_content: Chrom: The chromosome (contig/scaffold) number.
Supplementary_files_format_and_content: Strand: The strand information.
Supplementary_files_format_and_content: Start: The start position of that gene.
Supplementary_files_format_and_content: End: The end position of that gene.
Supplementary_files_format_and_content: GeneLength: The length of that gene.
Supplementary_files_format_and_content: Expression Quantification:
Supplementary_files_format_and_content: sample_readcount: gene expression quantification, calculated all genes'readcount.
Supplementary_files_format_and_content: sample_fpkm: gene expression quantification table, calculated all genes' FPKM.
Supplementary_files_format_and_content: group_group_fpkm: FPKM of each group(bio-replicate group name in Information table).
Supplementary_files_format_and_content: The differential analysis results of all genes:
Supplementary_files_format_and_content: sample_readcount(compare): the readcount values of each sample after normalized.
Supplementary_files_format_and_content: log2FoldChange(compare): log2(Group1/Group2)
Supplementary_files_format_and_content: pvalue(compare): the pvalue;
Supplementary_files_format_and_content: padj(compare): pvalue after normalization.The smaller the qvalue is, the more significant the difference is.
Supplementary_files_format_and_content: significant(compare): whether this gene is a DEG or not.
Supplementary_files_format_and_content: GeneType: gene type
Supplementary_files_format_and_content: GeneDescription: gene function description

source_name: CD8+ T cell

growth_protocol: Frozen donor CD8+ T cells were thawed and cultured at 37ºC in 5% CO2 in RPMI 1640 with 10% fetal bovine serum and 1% penicillin/streptomycin for 24 hours. CD3/CD28 activation beads at a 1:1 ratio were added and cells were cultured for 72 hours. Beads were then removed and cells were placed in new RPMI 1640 with 10% fetal bovine serum and 1% penicillin/streptomycin for 72 hours.

extract_protocol:
Cells were collected and total RNA was isolated using the Qiagen RNeasy Plus Kit (Catalog #74134)
RNA libraries were prepared for sequencing using standard Novogene protocols

treatment_protocol: Cells were serum starved for four hours and then stimulated with the listed treatment for 2 hours – chemokines were added a final concentration of 100nM.

tag: cell type

value: Donor primary CD8+ T cell


title: C11_02

description: gene.description.xls


title: C11_01

description: gene.description.xls


title: C10_03

description: gene.description.xls


title: S11-2296A17


title: S11-25805A8


title: C10_02

description: gene.description.xls


title: S11-2296-A12


title: S09-5602B3


title: S09-5602B4


title: S09-17685A5


title: C9_01

description: gene.description.xls


title: S09-24067-A7


title: S11-29541B4


title: Veh_03

description: gene.description.xls

value: Vehicle


title: S09-17686A8


title: Veh_02

description: gene.description.xls


title: S09-12003-A13


title: C9_03

description: gene.description.xls


title: DS3-iPSC

city: Shanghai

first: Jiajun

last: Qiu

address: West BeiJing Road

institute: Shanghai Children’s Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University School of Medicine

description:
D_I_filtered_barcodes.tsv.gz
D_I_filtered_features.tsv.gz
D_I_filtered_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
The raw reads were first processed to remove any reads that contained adapter sequences and those containing poly-N and low-quality reads. After filtering of the reads, the index of the reference genome was built using Hisat2 v2.0.5, and paired-end clean reads were aligned to the reference genome.
FeatureCounts v1.5.0 p3 was used to count the read numbers mapped to each gene. Subsequently, the fragments per kilobase of transcript per million mapped reads of each gene were calculated based on the length of the gene in question and the reads count mapped to this gene.
Differential expression analysis of each group was performed using the R package DESeq2 (version 1.16.1). The resulting P-values were adjusted using Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-value<0.05 identified by DESeq2 were assigned as differentially expressed genes (DEGs).
Cell Ranger Single Cell Software Suite 3.0 (10x Genomics) was used to process the sequencing data into transcript count tables. The ‘Cellranger mkfastq’ pipeline demultiplexed raw base call files generated by Illumina sequencers into sample-specific FASTQ files. Subsequently, ‘Cellranger count’ used FASTQ files as input and aligned the reads onto the hg38 human reference using Spliced Transcripts Alignment to a Reference. After filtering, barcode counting and the unique molecular identifiers (UMI) counting process, the ‘cellranger aggr’ pipeline was used to combine data from multiple samples into an experiment-wide feature-barcode matrix for downstream analysis.

extract_protocol:
Total RNA was extracted using TRIzol™ (Tiangen Biotech Co., Ltd.) reagent, and RNA purity was checked using an Implen NanoPhotometer® spectrophotometer (Implen USA, Inc.). RNA integrity was assessed using the RNA Nano6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, Inc.).
A total of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep kit for Illumina® (New England BioLabs, Inc.) following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample. The library preparations were sequenced on a NovaSeq 6000 platform (Illumina, Inc.), and 125 bp/150 bp paired-end reads were generated. Single-cell RNA sequencing was performed by Novogene Co., Ltd. using a 10x Genomics Chromium system and the Illumina Hiseq PE150 protocol.

value: iPS cell

tag: genotype

value: trisomy of chromosome 21


title: S08-6890-A5


title: Veh_01

description: gene.description.xls

tag: treatment


title: DS2-iPSC


title: S09-11592-A10


title: DS1-iPSC


title: C10_01

description: gene.description.xls


title: S08-31423-A8


title: S08-5313-B10


title: S08-39439A2


title: S07-22207-B3


title: NC2-iPSC

description:
N_I_filtered_barcodes.tsv.gz
N_I_filtered_features.tsv.gz
N_I_filtered_matrix.mtx.gz

value: Control


title: DS3-NSC

description:
D_N_filtered_barcodes.tsv.gz
D_N_filtered_features.tsv.gz
D_N_filtered_matrix.mtx.gz

value: neural stem cell


title: CFA5

city: ZHENGZHOU

first: Qian

last: Bai

address: NO2 JINGBA ROAD

institute: Second Affiliated Hospital of Zhengzhou Uni

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Supplementary files format and content: FPKM

source_name: trigeminal ganglia

extract_protocol:
trigeminal ganglia 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 experimental group of mice received intra-TMJ injection of CFA (10 μl, 5 mg/ml, Chondrex, Inc.), while the control group received saline (10 μl) under isoflurane anesthesia.

value: trigeminal ganglia

value: male

value: WT

value: CFA-TMJ injection

tag: time

value: Day 6


title: DS2-NSC


title: NC3-iPSC


title: NC1-iPSC


title: CFA6


title: C9_02

description: gene.description.xls


title: CFA4


title: (SMA, scRNAseq

city: nantong

first: junjie

last: sun

state: jiangsu province

address: 19 Qixiu Road

institute: nantong university

description: 10x Genomics

data_processing:
The Cell Ranger Single-Cell toolkit (version 3.0.0) provided by 10× genomics was applied to align reads and generate the gene-cell unique molecular identifier (UMI) matrix for each sample (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest). The read data were mapped using the corresponding Mus musculus reference genome. Different samples were merged using the cellranger aggr function. The obtained raw_feature_bc_matrix was loaded, and Seurat R package (v 3.2.2) was further used for downstream analyses .
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spinal cord

extract_protocol:
Whole spinal cords were obtained from transgenic mice, and the spinal cords were stripped according to established methods and placed in ice-cold phosphate-buffered saline (PBS). The tissue was minced and dissociated with 0.25% trypsin in a centrifuge tube for 30 min at 28 °C, followed by 1 mg/mL collagenase II for 20 min, with gentle mixing every 10 min. The enzymatic reaction was terminated through the addition of 10% fetal bovine serum (FBS). The sample was filtered using a 70 µm strainer to obtain a single-cell suspension.
Using single-cell 3 ‘Library and Gel Bead Kit V3 (10× Genomics, 1000075) and Chromium Single Cell B Chip Kit (10× Genomics, 1000074), the cell suspension (300–600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10× Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% bovine serum albumin (BSA). Approximately 6000 cells were added to each channel, and the target cell recovered was estimated to be approximately 3000 cells. Captured cells were lysed, and the released RNAs were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on an S1000TM Touch Thermal Cycler (Bio Rad) at 53 °C for 45 min followed by 85 °C for 5 min, and incubated at 4 °C. The complementary DNA (cDNA) was generated and then amplified, and the quality was assessed using an Agilent 4200. According to the manufacturer’s instruction, scRNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with a pair-end 150 bp reading strategy.

value: Spinal cord

value: (mSmn-/-, hSMN22tg/0)

value: postnatal day 4

value: FVB


title: CFA3

value: Day 3


title: NC3-NSC

description:
N_N_filtered_barcodes.tsv.gz
N_N_filtered_features.tsv.gz
N_N_filtered_matrix.mtx.gz


title: NC2-NSC


title: DS1-NSC


title: CFA2


title: CFA1


title: Yak10

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

institute: Chinese Academy of Agricultural Sciences

description: 4-year-old yak

data_processing:
Raw reads in FASTQ format were first processed using Trimomatic, including: (1) de-linker; (2) removal of low-quality reads; (3) different removal from 3' and 5' ends Low-quality bases; (4) Count the original sequencing quantity, effective sequencing quantity, Q30, GC content, and conduct a comprehensive evaluation.
Clean reads were mapped to the genome (version: LU_Bosgru_v3.0) using HISAT2, FPKM for each gene was calculated using Cufflinks and read counts for each gene were obtained by HTSeqcount.
Differential expression analysis was performed using the DESeq (2012) R package.
Assembly: LU_Bosgru_v3.0
Supplementary files format and content: FPKM_anno.txt: Tab-delimited text file includes FPKM values for each Sample.

organism: Bos grunniens

source_name: testis

growth_protocol: Three male Gannan yaks in Linxia County, Linxia Hui Autonomous Prefecture. Three male cattleyaks were F1 generations from the crossbred offspring between Jersey cattle (♂) and Gannan yak (♀), in Xiahe County, Gannan Tibetan Autonomous Prefecture. Here, all the animals were 4 years old.

extract_protocol:
Total RNA was extracted with TRIzol reagent. RNA purity and quantification were evaluated using the NanoDrop 2000 Spectrophotometer. RNA integrity was assessed using the Agilent 2100 Bioanalyzer.
We constructed the library using the TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer's instructions. Libraries were sequenced on the Illumina HiSeqTM 2500 platform and 150 bp paired-end reads were generated.

treatment_protocol: The testicular tissue is immediately stored in liquid nitrogen for RNA isolation. Testicular samples were obtained by castration.

value: testis

value: 4 years

tag: breed

value: Gannan


title: S06-34900-A4

value: inflammation


title: Saline-2

value: Saline-TMJ injection


title: Yak9

description: 4-year-old yak


title: NC1-NSC

tag: cell line

value: Control


title: Yak8

description: 4-year-old yak

tag: Sex


title: Saline-3


title: Saline-1


title: RNAseq-KO2 CD4 T cell-48h

description: total RNA

value: spleen

tag: age

value: 8 weeks

value: Trmt61a cKO

value: primary CD4 T cells


title: RNAseq-KO2 CD4 T cell-6h

description: total RNA


title: RNAseq-KO2 CD4 T cell-3h

description: total RNA


title: RNAseq-KO1 CD4 T cell-48h

description: total RNA


title: RNAseq-KO1 CD4 T cell-3h

description: total RNA


title: RNAseq-KO2 CD4 T cell-0h

description: total RNA


title: RNAseq-KO1 CD4 T cell-6h

description: total RNA


title: Micorwell-seq datasets of Drosophila_D36_COL35

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

data_processing:
Base call files were performed with Illumina bcl2fastq.
Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode: in read1, the bases 1-6, 22-27, 43-48 are merged (18bp); UMI: in read1, the bases 49-54 (6bp).
scRNA-seq reads were aligned to the Drosophila melanogaster BDGP6.28 genome assembly using STAR (version 2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix (DGE) based on UMI counts. The cell barcode is tagged with XC, the UMI is tagged with XM, and the gene is tagged with GE.
Assembly: Drosophila melanogaster BDGP6.28
Supplementary files format and content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMI counts, with genes as rows and cells as columns.

molecule: polyA RNA

organism: Drosophila melanogaster

extract_protocol:
Whole-body single-cell dissociation and lysate
Library preparations were performed with the Microwell-seq protocol

value: 36 day after laying eggs

value: whole organism

tag: gender

value: Female


title: Micorwell-seq datasets of Drosophila_D36_COL37


title: RNAseq-KO1 CD4 T cell-0h

description: total RNA


title: Micorwell-seq datasets of Drosophila_D41_COL46

value: 41 day after laying eggs


title: Micorwell-seq datasets of Drosophila_D41_COL47


title: Micorwell-seq datasets of Drosophila_D41_COL45


title: Micorwell-seq datasets of Drosophila_D31_COL32

value: 31 day after laying eggs


title: Micorwell-seq datasets of Drosophila_D31_COL34


title: RNAseq-WT1 CD4 T cell-48h

description:
total RNA
RNA-cKO_48hvsWT_48h_deg_all.xls

value: wild type


title: Micorwell-seq datasets of Drosophila_D31_COL33


title: Micorwell-seq datasets of Drosophila_D41_COL15


title: RNAseq-WT2 CD4 T cell-48h

description: total RNA


title: Micorwell-seq datasets of Drosophila_D26_COL29

value: 26 day after laying eggs


title: Micorwell-seq datasets of Drosophila_D31_COL31


title: RNAseq-WT1 CD4 T cell-6h

description:
total RNA
RNA-cKO_6hvsWT_6h_deg_all.xls


title: RNAseq-WT1 CD4 T cell-18h

description: total RNA


title: Micorwell-seq datasets of Drosophila_D26_COL28


title: RNAseq-WT2 CD4 T cell-6h

description: total RNA


title: RNAseq-WT2 CD4 T cell-3h

description: total RNA


title: Micorwell-seq datasets of Drosophila_D36_COL36


title: RNAseq-WT2 CD4 T cell-0h

description: total RNA


title: Micorwell-seq datasets of Drosophila_D26_COL26


title: RNAseq-WT1 CD4 T cell-3h

description:
total RNA
RNA-cKO_3hvsWT_3h_deg_all.xls


title: Micorwell-seq datasets of Drosophila_D21_COL24

value: 21 day after laying eggs


title: Micorwell-seq datasets of Drosophila_D26_COL27


title: (Con, scRNAseq

description: 10x Genomics

value: Spinal cord

value: (mSmn+/-, hSMN22tg/0)

value: postnatal day 4

value: FVB


title: RNAseq-WT2 CD4 T cell-18h

description:
total RNA
RNAseq-time-point-merge.xlsx


title: Micorwell-seq datasets of Drosophila_D21_COL23


title: Micorwell-seq datasets of Drosophila_D26_COL25


title: Micorwell-seq datasets of EighteenMonthsUterus_1

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp)； UMI:In read1, the　bases　49-54 (6bp)
ScRNA-seq reads were aligned to the Mus_musculus.GRCm38.88 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cell barcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: Mus_musculus.GRCm38.88 genome
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq protocol

value: Uterus


title: Micorwell-seq datasets of TwoYearsUterus_2


title: Micorwell-seq datasets of Drosophila_D26_COL30


title: Micorwell-seq datasets of Drosophila_D21_COL22


title: Micorwell-seq datasets of OneYearUterus_2


title: RNAseq-WT1 CD4 T cell-0h

description:
total RNA
RNA-cKO_UNvsWT_UN_deg_all.xls

value: spleen


title: Micorwell-seq datasets of Drosophila_D21_COL21


title: Micorwell-seq datasets of OneYearUterus_1


title: Micorwell-seq datasets of Drosophila_D21_COL19


title: Micorwell-seq datasets of AdultThymus_2

value: Thymus


title: Micorwell-seq datasets of Drosophila_D21_COL20


title: Micorwell-seq datasets of OneYearThymus_1


title: Micorwell-seq datasets of Drosophila_D21_COL17


title: Micorwell-seq datasets of AdultThymus_1


title: Micorwell-seq datasets of TwoYearsTestis_3

value: Testis

value: Male


title: Micorwell-seq datasets of TwoYearsUterus_1


title: RNA-seq of NLP7andKIN10_3

city: Qingdao

first: Honglei

last: Wang

state: Shandong

address: BinHai Street

department: School of Life Sciences

institute: Shandong University

description:
biological replicate 3
NLP7andKIN10_3

data_processing:
The sequence reads were mapped to the Arabidopsis genome using HISAT and Bowtie2 software, and differential gene expression was analyzed using Noiseq software.
Assembly: tair 10
Supplementary files format and content: XLS file for two sample comparison testing if a gene is differentially expressed

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana Landsberg erecta seedling

growth_protocol:
Seedling of wild-type Col-0 were grown on the soil for 4 weeks under 8 h light/16 h dark. The Arabidopsis mesophyll protoplast of Col-0 plants were transiently expressed NLP7-GFP and KIN10-Myc. The total RNA were extracted from the protoplasts expressed with NLP7-GFP and KIN10-Myc to perform transcriptomic analysis.
Wild type Ler and p35S:KIN10-HA were grown on MGRL medium containing 5 mM nitrate for 7 days, subjected to nitrogen-free medium for 2 days, and then treated with 5 mM KCl or 5 mM KNO3 for 1 h.///Wild type Columbia were grown in the soil for 4 weeks and then the protoplasts were dissociated for plasmid transformation.

extract_protocol:
Total RNA was extracted with Trizaol RNA extraction kit (Transgene)
the mRNA sequencing libraries construction and sequencing on the BGISEQ-500 platform were performed at Beijing Geonomics institute(BGI)

treatment_protocol: 5 mM nitrate in MGRL medium.///The plasmid GFP, NLP-GFP and KIN10-Myc were transformed into protoplasts.

value: protoplasts

value: wild-type Col-0 protopladts


title: RNA-seq of NLP7andKIN10_2

description:
biological replicate 2
NLP7andKIN10_2


title: Micorwell-seq datasets of TwoYearsTestis_1


title: Micorwell-seq datasets of EighteenMonthsThymus_1

value: Female


title: RNA-seq of NLP7andKIN10_1

description:
biological replicate 1
NLP7andKIN10_1


title: RNA-seq of NLP7_2

description:
biological replicate 2
NLP7_2

growth_protocol:
Seedling of wild-type Col-0 were grown on the soil for 4 weeks under 8 h light/16 h dark. The Arabidopsis mesophyll protoplast of Col-0 plants were transiently expressed NLP7-GFP. The total RNA were extracted from the protoplasts expressed with NLP7-GFP to perform transcriptomic analysis.
Wild type Ler and p35S:KIN10-HA were grown on MGRL medium containing 5 mM nitrate for 7 days, subjected to nitrogen-free medium for 2 days, and then treated with 5 mM KCl or 5 mM KNO3 for 1 h.///Wild type Columbia were grown in the soil for 4 weeks and then the protoplasts were dissociated for plasmid transformation.


title: RNA-seq of NLP7_3

description:
biological replicate 3
NLP7_3


title: Micorwell-seq datasets of EighteenMonthsTestis_1


title: Micorwell-seq datasets of TwoYearsStomach_3

value: Stomach


title: RNA-seq of GFP_2

description:
biological replicate 2
GFP_2

growth_protocol:
Seedling of wild-type Col-0 were grown on the soil for 4 weeks under 8 h light/16 h dark. The Arabidopsis mesophyll protoplast of Col-0 plants were transiently expressed GFP. The total RNA were extracted from the protoplasts expressed with GFP to perform transcriptomic analysis.
Wild type Ler and p35S:KIN10-HA were grown on MGRL medium containing 5 mM nitrate for 7 days, subjected to nitrogen-free medium for 2 days, and then treated with 5 mM KCl or 5 mM KNO3 for 1 h.///Wild type Columbia were grown in the soil for 4 weeks and then the protoplasts were dissociated for plasmid transformation.


title: RNA-seq of NLP7_1

description:
biological replicate 1
NLP7_1


title: Micorwell-seq datasets of OneYearTestis_1


title: Micorwell-seq datasets of OneYearStomach_2


title: RNA-seq of GFP_1

description:
biological replicate 1
GFP_1


title: Micorwell-seq datasets of OneYearStomach_1


title: RNA-seq of Ler_5N_3

description:
biological replicate 3
Ler_5N_3

growth_protocol:
Seedling of wild-type Ler  transgenic plants were grown on MGRL medium containing 5 mM nitrate for 7 days, subjected to nitrate starvation 2 days, and then treated with 5 mM KNO3 for 1 hour. The roots of wild type were harvested to perform transcriptomic analysis.
Wild type Ler and p35S:KIN10-HA were grown on MGRL medium containing 5 mM nitrate for 7 days, subjected to nitrogen-free medium for 2 days, and then treated with 5 mM KCl or 5 mM KNO3 for 1 h.///Wild type Columbia were grown in the soil for 4 weeks and then the protoplasts were dissociated for plasmid transformation.

value: root

value: wild-type Ler


title: RNA-seq of Ler_0N_3

description:
biological replicate 3
Ler_0N_3

growth_protocol:
Seedling of wild-type Ler  transgenic plants were grown on MGRL medium containing 5 mM nitrate for 7 days, subjected to nitrate starvation 2 days, and then treated with 5 mM KCl for 1 hour. The roots of wild type were harvested to perform transcriptomic analysis.
Wild type Ler and p35S:KIN10-HA were grown on MGRL medium containing 5 mM nitrate for 7 days, subjected to nitrogen-free medium for 2 days, and then treated with 5 mM KCl or 5 mM KNO3 for 1 h.///Wild type Columbia were grown in the soil for 4 weeks and then the protoplasts were dissociated for plasmid transformation.


title: RNA-seq of GFP_3

description:
biological replicate 3
GFP_3


title: Micorwell-seq datasets of TwoYearsStomach_1


title: Micorwell-seq datasets of EighteenMonthsStomach_1


title: RNA-seq of Ler_5N_2

description:
biological replicate 2
Ler_5N_2


title: Micorwell-seq datasets of TwoYearsSpleen_3

value: Spleen


title: Micorwell-seq datasets of TwoYearsSpleen_2


title: Micorwell-seq datasets of TwoYearsTestis_2


title: RNA-seq of Ler_0N_2

description:
biological replicate 2
Ler_0N_2


title: RNA-seq of KIN10_5N_3

description:
biological replicate 3
KIN10_5N_3

growth_protocol:
Seedling of p35S:KIN10-HA transgenic plants were grown on MGRL medium containing 5 mM nitrate for 7 days, subjected to nitrate starvation 2 days, and then treated with 5 mM KNO3 for 1 hour. The roots of wild type were harvested to perform transcriptomic analysis.
Wild type Ler and p35S:KIN10-HA were grown on MGRL medium containing 5 mM nitrate for 7 days, subjected to nitrogen-free medium for 2 days, and then treated with 5 mM KCl or 5 mM KNO3 for 1 h.///Wild type Columbia were grown in the soil for 4 weeks and then the protoplasts were dissociated for plasmid transformation.

value: p35S:KIN10-HA transgenic plants


title: Micorwell-seq datasets of TwoYearsSpleen_1


title: RNA-seq of KIN10_5N_2

description:
biological replicate 2
KIN10_5N_2


title: Micorwell-seq datasets of TwoYearsStomach_2


title: Micorwell-seq datasets of EighteenMonthsSpleen_1


title: RNA-seq of KIN10_0N_2

description:
biological replicate 2
KIN10_0N_2

growth_protocol:
Seedling of p35S:KIN10-HA transgenic plants were grown on MGRL medium containing 5 mM nitrate for 7 days, subjected to nitrate starvation 2 days, and then treated with 5 mM KCl for 1 hour. The roots of wild type were harvested to perform transcriptomic analysis.
Wild type Ler and p35S:KIN10-HA were grown on MGRL medium containing 5 mM nitrate for 7 days, subjected to nitrogen-free medium for 2 days, and then treated with 5 mM KCl or 5 mM KNO3 for 1 h.///Wild type Columbia were grown in the soil for 4 weeks and then the protoplasts were dissociated for plasmid transformation.


title: Micorwell-seq datasets of TwoYearsProstate_3A

value: Prostate


title: RNA-seq of KIN10_0N_3

description:
biological replicate 3
KIN10_0N_3


title: RNA-seq of KIN10_5N_1

description:
biological replicate 1
KIN10_5N_1


title: RNA-seq of Ler_5N_1

description:
biological replicate 1
Ler_5N_1


title: Micorwell-seq datasets of Drosophila_D21_COL18

value: 21 day after laying eggs

value: whole organism


title: Micorwell-seq datasets of TwoYearsProstate_1P


title: Micorwell-seq datasets of AdultSpleen_1


title: Micorwell-seq datasets of Zebrafish_21d_COL81

data_processing:
Base call files were performed with Illumina bcl2fastq.
Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. For raw file 1 in each COL, cellbarcode: in read1, the bases 1-6, 22-27, 43-48 are merged (18bp); UMI: in read1, the bases 49-54 (6bp). For raw file 2-5 in each COL, cellbarcode: in read1, the bases 1-6, 7-12, 13-18 are merged (18bp); UMI: in read1, the bases 19-24 (6bp).
scRNA-seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR (version 2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix (DGE) based on UMI counts. The cell barcode is tagged with XC, the UMI is tagged with XM, and the gene is tagged with GE.
Assembly: Danio rerio GRCz11
Supplementary files format and content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMI counts, with genes as rows and cells as columns.

organism: Danio rerio

value: AB

value: 21 day


title: Micorwell-seq datasets of TwoYearsProstate_2A


title: Micorwell-seq datasets of Zebrafish_21d_COL80


title: Micorwell-seq datasets of Zebrafish_21d_COL79


title: RNA-seq of Ler_0N_1

description:
biological replicate 1
Ler_0N_1

growth_protocol:
Seedling of wild-type Ler  transgenic plantswere grown on MGRL medium containing 5 mM nitrate for 7 days, subjected to nitrate starvation 2 days, and then treated with 5 mM KCl for 1 hour. The roots of wild type were harvested to perform transcriptomic analysis.
Wild type Ler and p35S:KIN10-HA were grown on MGRL medium containing 5 mM nitrate for 7 days, subjected to nitrogen-free medium for 2 days, and then treated with 5 mM KCl or 5 mM KNO3 for 1 h.///Wild type Columbia were grown in the soil for 4 weeks and then the protoplasts were dissociated for plasmid transformation.


title: Micorwell-seq datasets of TwoYearsSpleen_4


title: Micorwell-seq datasets of Zebrafish_21d_COL77


title: Micorwell-seq datasets of OneYearProstate_P3


title: Micorwell-seq datasets of Zebrafish_21d_COL76


title: Micorwell-seq datasets of OneYearProstate_P1


title: Micorwell-seq datasets of OneYearSpleen_1


title: Micorwell-seq datasets of Zebrafish_21d_COL75


title: Micorwell-seq datasets of EighteenMonthsProstate_2


title: Micorwell-seq datasets of OneYearProstate_A2


title: Micorwell-seq datasets of OneYearProstate_P2


title: Micorwell-seq datasets of Zebrafish_21d_COL72


title: Micorwell-seq datasets of AdultProstate_P


title: Micorwell-seq datasets of Zebrafish_21d_COL71


title: Micorwell-seq datasets of Zebrafish_21d_COL78


title: Micorwell-seq datasets of AdultProstate_A1


title: Micorwell-seq datasets of AdultProstate_A3


title: Micorwell-seq datasets of Zebrafish_21d_COL70


title: Micorwell-seq datasets of Zebrafish_21d_COL73


title: Micorwell-seq datasets of mouse_AdultPleura_2

value: Pleura


title: Micorwell-seq datasets of AdultProstate_1


title: Micorwell-seq datasets of Zebrafish_21d_COL68


title: Micorwell-seq datasets of Zebrafish_21d_COL69


title: Micorwell-seq datasets of EighteenMonthsProstate_1


title: Micorwell-seq datasets of mouse_AdultPleura_1


title: Micorwell-seq datasets of AdultProstate_2


title: RNA-seq of KIN10_0N_1

description:
biological replicate 1
KIN10_0N_1


title: Micorwell-seq datasets of Zebrafish_21d_COL66


title: Micorwell-seq datasets of Zebrafish_21d_COL74


title: Micorwell-seq datasets of Zebrafish_21d_COL65


title: Micorwell-seq datasets of TwoYearsPancreas_3

value: Pancreas


title: Micorwell-seq datasets of TwoYearsPancreas_4


title: Micorwell-seq datasets of OneYearProstate_A1


title: Micorwell-seq datasets of EighteenMonthsPancreas_2


title: Micorwell-seq datasets of Zebrafish_21d_COL62


title: Micorwell-seq datasets of Zebrafish_21d_COL63


title: Micorwell-seq datasets of Zebrafish_21d_COL64


title: Micorwell-seq datasets of TwoYearsPancreas_2


title: Micorwell-seq datasets of Zebrafish_21d_COL61


title: Micorwell-seq datasets of OneYearPancreas_3


title: Micorwell-seq datasets of Zebrafish_21d_COL67


title: Micorwell-seq datasets of OneYearPancreas_2


title: Micorwell-seq datasets of EighteenMonthsPancreas_1


title: Micorwell-seq datasets of Zebrafish_22m_COL128

value: 22 month


title: Micorwell-seq datasets of mouse_AdultOmentum_2

value: Omentum


title: Micorwell-seq datasets of OneYearPancreas_1


title: Micorwell-seq datasets of Zebrafish_22m_COL126


title: Micorwell-seq datasets of Zebrafish_22m_COL125


title: Micorwell-seq datasets of Zebrafish_22m_COL124


title: Micorwell-seq datasets of Zebrafish_22m_COL127


title: Micorwell-seq datasets of mouse_AdultOmentum_3


title: Micorwell-seq datasets of mouse_AdultOmentum_4


title: Micorwell-seq datasets of Zebrafish_22m_COL123


title: Micorwell-seq datasets of TwoYearsLung_2

value: Lung


title: Micorwell-seq datasets of Zebrafish_22m_COL122


title: Micorwell-seq datasets of mouse_AdultOmentum_1


title: Micorwell-seq datasets of Zebrafish_22m_COL121


title: Micorwell-seq datasets of Zebrafish_22m_COL99


title: Micorwell-seq datasets of EighteenMonthsLung_2


title: Micorwell-seq datasets of Zebrafish_22m_COL98


title: Micorwell-seq datasets of Zebrafish_22m_COL100


title: Micorwell-seq datasets of TwoYearsPancreas_1

value: Male


title: Micorwell-seq datasets of EighteenMonthsLung_1

value: Female


title: Micorwell-seq datasets of OneYearLung_2


title: Micorwell-seq datasets of Zebrafish_22m_COL28


title: Micorwell-seq datasets of OneYearLung_1


title: Micorwell-seq datasets of Zebrafish_22m_COL26


title: Micorwell-seq datasets of TwoYearsLiver_4

value: Liver


title: Micorwell-seq datasets of TwoYearsLung_1


title: Micorwell-seq datasets of Zebrafish_22m_COL29


title: Micorwell-seq datasets of Zebrafish_22m_COL14


title: Micorwell-seq datasets of Zebrafish_22m_COL13


title: Micorwell-seq datasets of Zebrafish_22m_COL25


title: Micorwell-seq datasets of TwoYearsKidney_4

value: Kidney


title: Micorwell-seq datasets of TwoYearsLiver_2


title: Micorwell-seq datasets of Zebrafish_22m_COL95


title: Micorwell-seq datasets of EighteenMonthsLiver_1


title: Micorwell-seq datasets of OneYearLiver_1


title: Micorwell-seq datasets of Zebrafish_22m_COL93


title: Micorwell-seq datasets of TwoYearsLiver_3


title: Micorwell-seq datasets of OneYearLiver_2


title: Micorwell-seq datasets of TwoYearsKidney_3


title: Micorwell-seq datasets of Zebrafish_22m_COL90


title: Micorwell-seq datasets of Zebrafish_22m_COL97


title: Micorwell-seq datasets of TwoYearsLiver_1


title: Micorwell-seq datasets of Zebrafish_22m_COL16


title: Micorwell-seq datasets of Zebrafish_22m_COL15


title: Micorwell-seq datasets of EighteenMonthsKidney_1


title: Micorwell-seq datasets of Zebrafish_22m_COL94


title: Micorwell-seq datasets of Zebrafish_22m_COL91


title: Micorwell-seq datasets of OneYearKidney_1


title: Micorwell-seq datasets of Zebrafish_22m_COL92


title: Micorwell-seq datasets of TwoYearsIntestine_1

value: Intestine


title: Micorwell-seq datasets of Zebrafish_22m_COL96


title: Micorwell-seq datasets of Zebrafish_22m_COL85


title: Micorwell-seq datasets of Zebrafish_22m_COL86


title: Micorwell-seq datasets of OneYearKidney_2


title: Micorwell-seq datasets of Zebrafish_22m_COL83


title: H1975-TAZS89AOE_siMESH1-01_72h-rep3

first: Jen-Tsan

last: Chi

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450

scan_protocol: scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

data_processing: The data were analyzed with Agilent 2100 Bioanalyzer G2939A

label: biotin

source_name: H1975 cells

label_protocol: Standard Affymetrix protocol

growth_protocol: All H1975 cells were cultured in the DMEM media supplement with 10% FBS and Penicillin/Streptomycin

extract_protocol: RNA was extracted by RNAeasy kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: H1975 cells were reverse transfected with the corresponding siRNA together with the Lipofectamine RNAiMAX reagent (ThermoFisher) and Opti-MEM according to the manufacture's instructions.

value: TAZS89A and reverse transfected with the siRNA targeting MESH1 CDS (siMESH1) for 72h


title: Micorwell-seq datasets of Zebrafish_22m_COL87


title: Micorwell-seq datasets of TwoYearsIntestine_2


title: Micorwell-seq datasets of Zebrafish_22m_COL89


title: Micorwell-seq datasets of Zebrafish_22m_COL81


title: Micorwell-seq datasets of Zebrafish_22m_COL88


title: Micorwell-seq datasets of Zebrafish_22m_COL84


title: Micorwell-seq datasets of OneYearIntestine_1


title: Micorwell-seq datasets of Zebrafish_22m_COL82


title: H1975-TAZS89AOE_siMESH1-01_72h-rep2


title: H1975-TAZS89AOE_siNT_72h-rep1

value: TAZS89A and reverse transfected with the non-tagteing siRNA (siNT) for 72h


title: Micorwell-seq datasets of Zebrafish_22m_COL78


title: Micorwell-seq datasets of Zebrafish_22m_COL80


title: H1975-TAZS89AOE_siMESH1-01_72h-rep1


title: Micorwell-seq datasets of Zebrafish_22m_COL77


title: Micorwell-seq datasets of Zebrafish_22m_COL74


title: Micorwell-seq datasets of Zebrafish_22m_COL76


title: Micorwell-seq datasets of EighteenMonthsIntestine_1


title: Micorwell-seq datasets of Zebrafish_22m_COL75


title: H1975-TAZS89AOE_siNT_72h-rep2


title: Micorwell-seq datasets of TwoYearsHeart_3

value: Heart


title: Micorwell-seq datasets of TwoYearsHeart_4


title: H1975-TAZS89AOE_siNT_72h-rep3


title: H1975-plx304_siMESH1-01_72h-rep1

value: plx304 vector and reverse transfected with the siRNA targeting MESH1 CDS (siMESH1) for 72h


title: Micorwell-seq datasets of TwoYearsHeart_5


title: H1975-plx304_siMESH1-01_72h-rep3


title: H1975-plx304_siNT_72h-rep3

value: plx304 vector and reverse transfected with the non-tagteing siRNA (siNT) for 72h


title: Micorwell-seq datasets of Zebrafish_22m_COL72

value: AB

value: whole organism


title: Micorwell-seq datasets of TwoYearsHeart_1


title: Micorwell-seq datasets of Zebrafish_22m_COL79


title: Micorwell-seq datasets of EighteenMonthsHeart_2


title: Micorwell-seq datasets of Zebrafish_22m_COL73


title: Micorwell-seq datasets of TwoYearsHeart_2


title: Micorwell-seq datasets of Zebrafish_22m_COL67


title: Micorwell-seq datasets of Zebrafish_22m_COL71


title: Micorwell-seq datasets of Zebrafish_22m_COL69


title: H1975-plx304_siMESH1-01_72h-rep2


title: Micorwell-seq datasets of Zebrafish_22m_COL66


title: Cas9.REDD1_KO.FA, Experiment 2

city: Tempe

first: Ben

last: Readhead

state: AZ

address: 797 E. Tyler Street

institute: ASU-Banner Neurodegenerative Disease Research Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: We used the R software package, Limma, and the neqc function to perform background subtraction using the negative control probes, and quantile normalization using both positive and negative control probes.

label: Biotin

source_name: Keratinocytes

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays (Thermo Fisher Scientific)

growth_protocol: HaCaT human keratinocytes were grown in DMEM supplemented with 10 % Fetal Bovine Serum and 1 X Pen/Strep

extract_protocol: RNA was extracted using EZNA Total RNA Kit I  (Omega Bio-tek, GA, USA)  exactly according to the manufacturer's  instructions . The RNA quality and concentration was analyzed using Nanodrop  spectrophotometer.

treatment_protocol: At 70% confluency, REDD1 KO and Cas9 HaCaT cells were switched to DMEM with Charcoal stripped Fetal Bovine Serumovernight, and then  were treated with vechicle (0.1% acetone, control)  or  1 μM of glucocorticoid fluocinolone acetonide ( FA ) for  24 h.

value: HaCaT

value: Keratinocytes

value: REDD1 KO

value: FA

tag: batch


title: Micorwell-seq datasets of Zebrafish_22m_COL70

value: 22 month

tag: tissue


title: Micorwell-seq datasets of Zebrafish_22m_COL68


title: H1975-plx304_siNT_72h-rep2

tag: transfection


title: Micorwell-seq datasets of Zebrafish_22m_COL65


title: Micorwell-seq datasets of Zebrafish_22m_COL63


title: Micorwell-seq datasets of OneYearHeart_3


title: Micorwell-seq datasets of EighteenMonthsHeart_1


title: Micorwell-seq datasets of Zebrafish_22m_COL64


title: Micorwell-seq datasets of Zebrafish_22m_COL61


title: Cas9.Control.FA, Experiment 2

value: control


title: Micorwell-seq datasets of OneYearHeart_2

value: Female


title: Micorwell-seq datasets of OneYearHeart_1


title: Cas9.REDD1_KO, Experiment 2

value: vehicle


title: Micorwell-seq datasets of Zebrafish_22m_COL44


title: Micorwell-seq datasets of E9.5DayPlusPlacenta_1

value: EmbryoPlusPlacenta


title: Micorwell-seq datasets of Zebrafish_22m_COL43


title: Cas9.Control, Experiment 2


title: Micorwell-seq datasets of Zebrafish_22m_COL41


title: Micorwell-seq datasets of Zebrafish_22m_COL42


title: Micorwell-seq datasets of Zebrafish_22m_COL62


title: H1975-plx304_siNT_72h-rep1


title: Micorwell-seq datasets of E9.5DayEmbryo_3

value: Embryo


title: Micorwell-seq datasets of Zebrafish_22m_COL38


title: Micorwell-seq datasets of Zebrafish_22m_COL45


title: ME49EW cyst, 30 days replicate1

city: TAMPA

first: David

middle: Dongpyo

last: Hong

state: FL

address: 3720 SPECTRUM BLVD. #325

department: Internal Medicine

institute: UNIVERSITY OF SOUTH FLORIDA

data_processing:
Reads were filtered by Sanger quality score using FASTQ Groomer v. 1.0.4 and paired end reads were aligned against the genomes of T. gondii (TGME49 version 46; ToxoDB.org) references uploaded into Galaxy using HISAT2
The DESeq2 module was used for normalization, differential gene expression and statistical analysis of uniquely mapped paired-end reads using the default parameters
Assembly: TGME49 version 46; ToxoDB.org
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Toxoplasma gondii

source_name: Mouse brain

growth_protocol: Tacyzoite and bradyzoite were grown in T175 flasks in human foreskin fibroblasts for 48hrs. ME49EW cysts were from mouse brain (30 days)

extract_protocol:
Qiagen RNA easy, double DNAse digestion
NuGen Universal RNA-Seq System

treatment_protocol: in vitro growth  at different pHs (pH7.0, pH8.2) in vitro, 48hrs

value: Mouse brain

value: Type II

value: Tissue cyst

value: 30 days in mice


title: Cas9.REDD1_KO.FA, Experiment 1


title: Cas9.Control.FA, Experiment 1


title: Micorwell-seq datasets of E9.5DayEmbryo_1


title: Cas9.REDD1_KO, Experiment 1


title: ME49EW cyst, 30 days replicate2


title: Micorwell-seq datasets of Zebrafish_22m_COL36


title: Micorwell-seq datasets of Zebrafish_22m_COL35


title: Micorwell-seq datasets of Zebrafish_22m_COL39


title: Micorwell-seq datasets of E9.5DayEmbryo_2


title: ME49_Tir1 strain, pH8.2, 48hrs

source_name: HFF cell

value: HFF cell

value: Bradyzoite


title: Cas9.Control, Experiment 1


title: Micorwell-seq datasets of Zebrafish_22m_COL33

value: AB

value: whole organism


title: Micorwell-seq datasets of Zebrafish_22m_COL32


title: Micorwell-seq datasets of Zebrafish_22m_COL34


title: Micorwell-seq datasets of Zebrafish_22m_COL37


title: Micorwell-seq datasets of TwoYearsBrain_3

value: Brain

value: Male


title: Micorwell-seq datasets of Zebrafish_22m_COL30


title: Micorwell-seq datasets of EighteenMonthsBrain_1


title: Micorwell-seq datasets of Zebrafish_22m_COL3


title: Micorwell-seq datasets of Zebrafish_22m_COL4


title: Walnut LF rep3 [miRNA-seq]

city: Alar

first: Qiang

last: Jin

email: jqzky@163.com, qiangjin@taru.edu.cn

address: Alar 843300, China

institute: College of Horticulture and Forestry，Tarim University

data_processing:
After removing the adapter and primer sequences, low quality reads with more than 20% low quality bases (quality < 20) were filtered out using FastQC packages (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Clean reads were mapped to M. viride genome using Hisat2 v2.1.051. Gene expression levels (FPKM) were calculated using Cufflinks with default parameters. Differentially expressed genes (DEGs) were identified by DEseq2 package, and only transcripts with fold change ≥ 2 and FDR ≤ 0.01 were considered as DEGs.
Genome_build: JrSerr_v1.0 [PMID  32432329]
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Juglans regia

source_name: late fruiting walnut (WS)

growth_protocol: Walnut plant materials were planted and collected in a field in Aksu city, Xingjiang Province.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Life Technologies). Samples were then subjected to poly(A) purification using oligo-dT beads (Life Technologies) followed by rRNA removal using Ribo-Zero Kit (Epicenter) according to the manufacturer’s instructions. RNA integrity was measured using 2100 RNA Nano 6000 Assay Kit (Agilent Technologies).
Library construction were done using TruSeq® Stranded mRNA Library Prep Kit following the manufacturer’s instructions (Illumina). 16 paired-end libraries were constructed and sequenced according to the Illumina HiSeqTM platform sequencing protocols.

tag: developmental stage

value: Late flower

value: Flower buds


title: Micorwell-seq datasets of TwoYearsBrain_2


title: Micorwell-seq datasets of TwoYearsBrain_1


title: ME49_Tir1 strain, pH7.0, 48hrs

value: Tacyzoite


title: Walnut LF rep2 [miRNA-seq]


title: Walnut LF rep1 [miRNA-seq]


title: Micorwell-seq datasets of OneYearBrain_3

value: Female


title: Walnut EF rep3 [miRNA-seq]

source_name: precocious walnut (ZS)

value: Early flower


title: Walnut EF rep1 [miRNA-seq]


title: Micorwell-seq datasets of OneYearBrain_2


title: SNU-878 cells, EV

city: Hong Kong

first: Jie

last: Luo

address: 21 Sassoon Road, Pokfulam, Hong Kong

department: Clinical Oncology

country: Hong Kong

institute: Li Ka Shing Faculty of Medicine, The University of Hong Kong

data_processing:
Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 40bp. Low Quality is defined as:
i. Reads with more than 5% unknown bases (“N”)
ii. Reads having more than 50% of bases with quality value <= 11
Subsequently, sequencing reads were filtered for rRNA sequence and remaining reads were used for downstream analysis
Reads were mapped to the reference genome using STAR (Version 2.5.2, default parameters) with the following exception: i. twopassMode: Basic
Differentially expression analysis was done using EBSeq (Version 1.18.0). Differentially expressed genes/transcripts were defined as FDR < 0.05
RSEM (Version 1.2.31) was used for Quantify expression
Assembly: Human Genome GRCh38
Supplementary files format and content: Excel files (.xlsx format) for differentially expressed gene and transcript analyses of each cell group, respectively.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit (KR1352-v5.17)  following manufacturer's protocols.

value: HCC cells

value: WT


title: SNU-878 cells, ADAR1p110

value: ADAR1p110 overexpression


title: Walnut LF rep3 [RNA-seq]


title: SNU-449 cells, EV


title: Walnut EF rep2 [miRNA-seq]


title: SNU-449 cells, ADAR1p110


title: Micorwell-seq datasets of OneYearBrain_1


title: SNU-878 cells, sh2ADAR1

value: ADAR1 knockdown


title: Walnut LF rep2 [RNA-seq]


title: PLC8024 cells, sh2ADAR1


title: PLC8024 cells, shNC


title: Walnut LF rep1 [RNA-seq]


title: Micorwell-seq datasets of TwoYearsBladder_1

value: Bladder


title: Walnut EF rep3 [RNA-seq]


title: Micorwell-seq datasets of AdultBladder_1


title: SNU-878 cells, shNC


title: Micorwell-seq datasets of TwoYearsBladder_2


title: Micorwell-seq datasets of mouse_AdultArenalGland_1

value: ArenalGland


title: Walnut EF rep2 [RNA-seq]


title: Walnut EF rep1 [RNA-seq]


title: dexamethasone-treated  condition,bio rep3

city: Tokyo

first: Sihui

last: Ma

address: Yayoi 1-1-1

institute: The university of Tokyo

description: Gene expression data of muscle tissue, dexamethasone-treated

hyb_protocol: Synthesis of double-stranded cDNA and complementary RNA (cRNA) was performed following the manufacturer’s instructions. The synthesized cRNA was hybridized onto the array chip at 45℃ for 16 h and stained with streptavidin-phycoerythrin using GeneChip™ Fluidics Station 450 (Applied Biosystems™, CA, USA).

scan_protocol: Images were obtained using GeneChip™ Scanner 3000 (Affymetrix, CA, USA).

data_processing: The obtained CEL file data was normalized using mas5-Signal. Comparison between the two groups was performed via Rank Product analysis. Gene probes wi+B23th a signal intensity of less than 50 were removed. The cut-off conditions were FDR < 0.05 and |log ratio| ≥ 0.6.

label: bitoin

source_name: dexamethasone

label_protocol: For global expression profiling, total RNA (250ng) was labeled using streptavidin-phycoerythrin.

growth_protocol: Fifteen-week-old male C57BL/6J mice were fed an AIN93-based diet or 2% TE supplemented AIN93-based diet. Five days later, 0.9% of saline or 5 mg/kg body weight of dexamethasone (DEX) was intraperitoneally administered every day for a week. The mice were individually housed in cages in a temperature-controlled (22 ± 1 ◦C), 12 h light-dark cycle environment and provided ad libitum access to drinking water and diet.

extract_protocol: Qiagen Rneasy Kit lysis buffer extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The skeletal muscle sample was homogenized with 600 µL of lysis buffer. Total RNA was then isolated from half of the lysate (300 µL) using RNeasy Tissue Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.

value: male

value: Tibialis anterior muscle

value: dexamethasone


title: TES5

description: 4-year-old cattle-yak

organism: Bos grunniens x Bos taurus

value: testis

value: 4 years

value: Gannan x Jersey


title: Turmeric extract treated after dexamethasone-treated, bio rep2

description: Gene expression data of muscle tissue, turmeric extract treated after dexamethasone-treated

source_name: Turmeric extract

value: dexamethasone and turmeric


title: Micorwell-seq datasets of EighteenMonthsBladder_1


title: Turmeric extract treated after dexamethasone-treated, bio rep1


title: Micorwell-seq datasets of mouse_AdultArenalGland_3


title: Micorwell-seq datasets of mouse_AdultArenalGland_2


title: C57BL/6J Blood Old, GEX

status: Public on Jul 22 2022

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

data_processing:
The initial demultiplexing, barcode processing, GEX counting, V(D)J counting and cell surface marker barcode identification was performed using Cell Ranger v5.0.0. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/5.0/what-is-cell-ranger).
The data were demultiplexed using cell surface protein marker counts, on which an in-house R script was applied to determine cells (and cellular barcodes corrected by Cellranger) belonging to this experiment and separate them from another, unrelated one.
The mapping and counting of separated experiment was performed using Cell Ranger v5.0.0.
Analysis, integration of data from young and old mice, integration of V(D)J data, count normalization, variable feature detection, dimensional reduction and clustering was performed using Seurat package v4.0.3 on R  v4.0.4.
Assembly: GRCm38 (Ensembl release 102)
Supplementary files format and content: rds file of analyzed data-set obtained by integration of all samples, in form of SeuratObject containing log-normalized counts, detected variable features, UMAP and PCA dimensional reductions, clustering, mice-relevant annotation and V(D)J information.

source_name: blood

growth_protocol: Mice were bred in SPF Facility (Institute of Molecular Genetics of the Czech Academy of Sciences, IMG) in accordance with the laws of the Czech Republic and  were kept in the animal facility with 12 hours of light and dark cycle with food and water ad libitum. A group of young (n = 3, age = 8 weeks) and old (n = 3, age = 88 week) was used for this experiment.

extract_protocol:
Mice were anesthetized using an i.p. injection of Ketamine-Xylazine. Carotid artery blood was collected to individual EDTA-coated tubes supplemented with 100 μL of 3.5mM EDTA, blood from each mice age group was pooled, spinned down (4 °C, 400 g, 5 min) and the supernatant was removed. Cells were lysed in 5 mL of ACK buffer for 3 minutes in room temperature, and the reaction was stopped by adding 10mL of PBS. The lysis step was repeated once more. Cells were stained on ice in darkness in 200 µL of PBS supplemented with 2% FBS and 400× diluted feature barcoding antibody markers to distinguish cells from this experiment from another, unrelated one. After 10 min of staining, 200× diluted mouse anti-CD5  and anti-CD8α were added for additional 20 min. CD8α+ CD5+ cells were sorted on an Influx.
The gene expression and cell surface protein libraries were constructed following Feature Barcode technology for Cell Surface Protein protocol (#CG000186 Rev D) with the Chromium Single Cell 5’ Library & Gel Bead and Chromium Single Cell 5' Feature Barcode Library kits (10x Genomics, #PN-1000014, #PN-1000020, #PN-1000080, #PN-1000009, #PN-1000084). The V(D)J library was built following the same protocol with Chromium Single Cell V(D)J Enrichment Kit, Mouse T Cell kit (10X Genomics, #PN-1000071).
scRNAseq (10x Genomics Single Cell Immune Profiling with Feature Barcoding)

value: Old

value: 88 weeks

value: blood

value: PBMC

tag: cell subset

value: CD8+ T cells


title: C57BL/6J Blood Old, CSP

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

description:
cell surface markers
b6_blood_integrated.rds

library_source: other

molecule: protein

value: WT


title: C57BL/6J Blood Young, GEX

value: Young

value: 8 weeks


title: C57BL/6J Blood Young, VDJ

description:
VDJ gene transcripts
b6_blood_integrated.rds


title: TES7

description: 4-year-old cattle-yak


title: MEF_Control_5D_3

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
Reads were aligned to the mouse genome by Rsubread version 1.30.5
Fragment (read-pair) counts were summarized by RefSeq Gene ID using the Rsubread featureCounts function
Genes were identified using Rsubreads inbuilt mm10 annotation
Assembly: mm10
Supplementary files format and content: tab-delimited text files wre written from the R prompt; columns represent RefSeq Gene ID, total gene length (total base count of all exons) and the number of fragments mapping to that gene

source_name: Murine embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts (MEFs) isolated from E13.5 embryos were cultured in MEF medium (DMEM, 10% FBS, and 2mM GlutaMAXTM) at 37 °C, in 5% CO2, and 3% O2 (near-physiological tissue oxygen concentration).

extract_protocol:
RNA was isolated using RNeasy Kit (Qiagen, 74106).
The Stranded TruSeq mRNA Library Kit (Illumina, 20020594) was used to generate barcoded cDNA libraries. The indexed libraries were pooled and diluted to 1.5 pM for paired end sequencing (2x 81 cycles) on a NextSeq 500 instrument using the v2 150 cycle High Output kit (Illumina) as per manufacturer’s instructions, generating 80 bp paired-end reads.

treatment_protocol: Tip60 gene deletion was induced by treatment with 250 nM 4-OHT for 3 and 5 days.

value: Murine embryonic fibroblasts

tag: litter

value: Female

tag: time point

value: 5 days

tag: cell id

tag: replicate

value: E13.5 embryo


title: normal condition,bio rep2

description: Gene expression data of muscle tissue, normal condition

source_name: normal condition

tag: strain

value: male

value: Tibialis anterior muscle

value: normal control


title: Turmeric extract treated after dexamethasone-treated, bio rep3

tag: treatment


title: normal condition,bio rep3


title: dexamethasone-treated  condition,bio rep1

value: dexamethasone


title: MEF_Control_5D_1

tag: genotype


title: normal condition,bio rep1


title: TES6

description: 4-year-old cattle-yak

value: testis

value: 4 years

tag: breed

value: Gannan x Jersey


title: MEF_Tip60_KO_5D_4

value: Male


title: Skin biopsies

city: Ann Arbor

first: Jun Hee

last: Lee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

description: Processed in Seq-Scope procedure

data_processing:
Library strategy: Seq-scope
1st-Seq and 2nd-Seq data were processed as previously described (PMID: 34115981).
Sequencing by Illumina HiSeq2500 (1st-Seq) and HiSeq-X (2nd-Seq) platforms.
Alignment: From 1st-Seq data, HDMI sequences of clusters located on the bottom tile were extracted and used as a “whitelist” for the cell (HDMI) barcode. First 9 basepairs of 2nd-Seq data Read 2 were copied to Read 1 and used as the unique molecular identifier (UMI). Read 2 was trimmed at the 3’end to remove polyA tails of length 10 or greater, then aligned to human genome (GRCh38) using GeneFull option with no length threshold and no cell filtering using Star/StarSolo 2.7.5c.
Data Binning and Collapsing: The digital expression matrix generated by STARsolo with GeneFull option were combined with spatial information, and further the imaging space were divided into into 100 μm2 (10 μm-sided) square grids and collapsing all HDMI-UMI information into one barcode per grid. We then further refined the spatial resolution of the dataset by transferring the annotations obtained under 10 um grids to the sliding-grid datasets with 5 um, 2 um and 1 um intervals between grids. These processed data are not accepted by GEO, so will be made available in a separate deposit.
Genome_build: human genome (GRCh38)

source_name: Frozen OCT section

extract_protocol:
A 6 mm punch skin biopsy was frozen in OCT medium and stored at -80°C until sectioning.
Seq-scope: 1st-Seq was performed using synthetic HDMI-oligo library. 2nd-Seq was constructed from the tissue as previously described (PMID: 34115981)

value: Control and Acne skin biopsies


title: Micorwell-seq datasets of OneYearBladder_1

value: Bladder


title: C57BL/6J Blood Young, CSP

value: blood

tag: cell type

value: PBMC

value: CD8+ T cells

value: WT


title: C57BL/6J Blood Old, VDJ

value: Old

value: 88 weeks


title: MEF_Tip60_KO_3D_4

value: Murine embryonic fibroblasts

value: 3 days

value: E13.5 embryo


title: MEF_Tip60_KO_5D_1

value: 5 days


title: dexamethasone-treated  condition,bio rep2

tag: Sex

value: male

value: Tibialis anterior muscle

value: dexamethasone


title: MEF_Control_5D_4


title: MEF_Control_3D_3

value: Female


title: e4.TMAO

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: experiment 4, single cell, TMAO

data_processing:
The scRNA-seq data was preprocessed using Cell Ranger Suite (v3.1.0, https://support.10xgenomics.com) with refdata-cellranger-mm10-3.0.0 transcriptome as a reference

Assembly: mm10
Supplementary files format and content: standard cellranger output

extract_protocol:
The scRNA-seq was performed on fluorescence-activated cell sorting (FACS) enriched live CD45+ cells from tumors of orthotopic PDAC bearing mice. Single cell droplets were generated using the Chromium next gem single cell 3' kit v3.1 (10x Genomics)
cDNA synthesis and amplification, library preparation and indexing were done using the 10x Genomics Library Preparation kit (10x Genomics)

tag: group

tag: source

value: TMAO


title: MEF_Control_3D_1

tag: gender


title: MEF_Tip60_KO_5D_3

tag: tissue

value: Male


title: MEF_Control_5D_2


title: e4.ctrl

description: experiment 4, single cell, control

value: control


title: MEF_Tip60_KO_3D_3


title: MEF_Control_3D_2


title: MEF_Tip60_KO_5D_2


title: CUT&RUN, follicular, B, cell, IL4, treated, H3.3, rep1

city: Boston

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

data_processing:
Fastq data were adaptor trimmed using Trim Galore v0.6.6.
Reads were aligned to mm10 reference genome using bowtie2 v.2.3.4.3 with parameters -X 700 -I 10.
Non-unique, duplicated and ChrM reads were removed using SAMTools view and Picard MarkDuplicates.
BEDTools with the option intersect -v was used to filter reads that did not overlap with ENCODE blacklist. Reads that overlapped with gene bodies were identified and quantified using bedtools intersect from BEDTools and GRCm38.06 gene body annotations from Ensembl release 67.
Peaks were called using SEACR with the option ‘norm’ and ‘relaxed’ for H3K4me3 and H3K27ac while ‘norm’ and ‘stringent’ were used for H3.3, H3K27me3, H3K36me3 and H3K4me1. Genome coverage tracks were generated using deeptools2 with parameters bamCoverage --binSize 50 --normalizeUsing CPM --ignoreDuplicates –extendReads and visualized using IGV v2.10.2.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: Spleen

extract_protocol:
CUT&RUN protocol was followed for genomic DNA extraction.
CUTANA CUT&RUN Library Prep Kit was used.

value: Spleen

value: Follicular B cells

tag: antibody


title: CUT&RUN, follicular, B, cell, IL4, treated, H3K27ac, rep1


title: CUT&RUN, follicular, B, cell, IL4, treated, H3K36me3, rep1


title: CUT&RUN, follicular, B, cell, IL4, treated, H3K4me3, rep1


title: CUT&RUN, follicular, B, cell, IL4, treated, H3K27ac, rep2


title: CUT&RUN, follicular, B, cell, IL4, treated, H3.3, rep2


title: CUT&RUN, follicular, B, cell, IL4, treated, H3K27me3, rep1


title: CUT&RUN, follicular, B, cell, IL4, treated, H3K4me1, rep2


title: CUT&RUN, follicular, B, cell, IL4, treated, H3K4me3, rep2


title: CUT&RUN, follicular, B, cell, IL4, treated, H3K27me3, rep2


title: CUT&RUN, follicular, B, cell, control, H3K27ac, rep2

value: PBS


title: CUT&RUN, follicular, B, cell, IL4, treated, H3K36me3, rep2


title: CUT&RUN, follicular, B, cell, control, H3K36me3, rep1


title: CUT&RUN, follicular, B, cell, IL4, treated, IgG, rep2

value: IgG


title: CUT&RUN, follicular, B, cell, control, H3.3, rep1


title: MEF_Tip60_KO_3D_2

tag: developmental stage


title: CUT&RUN, follicular, B, cell, control, H3K36me3, rep2


title: CUT&RUN, follicular, B, cell, control, H3K27me3, rep2


title: CUT&RUN, follicular, B, cell, control, H3K4me3, rep2


title: CUT&RUN, follicular, B, cell, IL4, treated, IgG, rep1


title: CUT&RUN, follicular, B, cell, IL4, treated, H3K4me1, rep1


title: CUT&RUN, follicular, B, cell, control, H3K27ac, rep1


title: CUT&RUN, follicular, B, cell, control, H3.3, rep2


title: CUT&RUN, follicular, B, cell, control, IgG, rep2


title: CUT&RUN, follicular, B, cell, control, IgG, rep1


title: CUT&RUN, follicular, B, cell, control, H3K27me3, rep1


title: L7spheres

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

institute: East Carolina University

data_processing:
Kallisto for pseudo-alignment to transcriptome of hg38
DESeq2 for differential gene expression
Genome_build: hg38
Supplementary_files_format_and_content: A .csv file including TPM of each gene for all 16 samples

source_name: healthy_not-migrated interneurons

growth_protocol: Interneurons were generated from iPSCs according to previously published protocols (Kim, T.G., et al. Efficient specification of interneurons from human pluripotent stem cells by dorsoventral and rostrocaudal modulation. Stem cells 32, 1789-1804, 2014).

extract_protocol:
Samples were harvested using Trizol reagent (Invitrogen).
NEBNext Ultra II Directional RNA library Prep Kit for Illumina

treatment_protocol: Interneurons were embedded in Geltrex to isolate migrated interneurons, and harvested for RNAseq preparation 2 weeks after embedding.

value: iPSC-derived interneurons

tag: subject status

value: healthy

tag: sample group

value: not migrated


title: 67spheres

source_name: schizophrenia_not-migrated interneurons

value: schizophrenia


title: 292spheres


title: 212migrated

source_name: schizophrenia_migrated interneurons

value: migrated interneurons


title: 755migrated


title: 292migrated

source_name: healthy_migrated interneurons


title: 689spheres


title: CUT&RUN, follicular, B, cell, control, H3K4me1, rep1


title: CUT&RUN, follicular, B, cell, control, H3K4me1, rep2


title: CUT&RUN, follicular, B, cell, control, H3K4me3, rep1


title: 67migrated


title: L5migrated


title: 190migrated


title: 212spheres


title: 689migrated


title: 483migrated


title: No insomina disorder [930c24864]

city: Los Angeles

first: Donald

middle: M.

last: Lamkin

state: CA

address: 300 UCLA Medical Plaza, Room 3160

department: Semel Institute for Neuroscience

institute: UCLA

description: Illumina HumanHT-12 v4.0 expression beadchip

hyb_protocol: Standard Illumina hybridization protocol (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  Data were then log2 transformed before analysis

source_name: PBMCs

label_protocol: Biotinylated cRNA were prepared with Ambion TotalPrep for Illumina arrays (carried out by UCLA Neuroscience Genomics Core).

extract_protocol: Total RNA was extracted from PMBC samples lysed in RLT buffer following the protocol from a QIAGEN RNeasy mini kit on a QIACube instrument and included DNase I treatment.

tag: insomnia

value: no

tag: age

value: female

tag: race

value: white

tag: education (years)

tag: bmi

tag: comorbidity

tag: bdi

tag: bdins

tag: history of depression


title: No insomina disorder [930c19426]

value: male


title: No insomina disorder [930c19097]


title: No insomina disorder [930c17787]

value: yes


title: No insomina disorder [930c25759]


title: No insomina disorder [930c13504]


title: No insomina disorder [930c12645]


title: No insomina disorder [930c12728]


title: 190spheres

tag: cell type


title: L7migrated


title: No insomina disorder [930c12795]

value: non-white


title: 99migrated


title: No insomina disorder [930c08672]


title: No insomina disorder [930c11316]


title: No insomina disorder [930c22458]


title: No insomina disorder [930c13017]


title: No insomina disorder [930c12581]


title: No insomina disorder [930c14402]


title: No insomina disorder [930c14509]


title: No insomina disorder [930c16909]


title: No insomina disorder [930c01334]


title: No insomina disorder [930c08217]


title: No insomina disorder [930c00610]


title: No insomina disorder [930c06134]


title: Insomnia Disorder [1400c289]


title: No insomina disorder [930c10095]


title: No insomina disorder [930c03209]


title: No insomina disorder [930c01434]


title: Insomnia Disorder [1400c288]


title: No insomina disorder [930c02526]


title: EA.hy926, LPS-induced sepsis HUVECs, LPS2, 12h

city: Beijing

first: Haiyan

last: Liao

state: Beijing

address: 168 Litang Road Changping District, Beijing, China

institute: Tsinghua University

data_processing:
Illumina PE150
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts.
Clean reads for each sample were first mapped to a reference genome with the software HISAT2. Reads alignment results were transferred to the program StringTie for transcript assembly.
Quantification of the transcripts and genes was performed using StringTie software and fragments per kilobase of exon per million mapped fragments (FPKM) was obtained.
analysis
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: HUVECs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using total RNA kit (TAKARA, Japan)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sepsis was induced by treatment of 12h with 1000ng/ml LPS (Sigma),

tag: cell line

value: endothelial cells

tag: genotype

value: LPS-induced

tag: treatment

value: Sepsis

tag: time

value: Human umbilical vein endothelial


title: EA.hy926, LPS-induced sepsis HUVECs, LPS1, 12h


title: Insomnia Disorder [1400c204]

tag: gender


title: Insomnia Disorder [1400c240]


title: EA.hy926, Human umbilical vein endothelial cells (HUVECs), Control3, 12h

value: WT


title: Insomnia Disorder [1400c287]


title: Control ChIP-seq from K562 (ENCLB457NMG)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR828WYU/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq matched with ChIP-seq on human K562 eGFP-tagged transcription factors. The White lab used goat anti-GFP antibody to perform ChIP in untagged K562 cells as a background control.
experiment encode accession: ENCSR828WYU
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2011-06-03
lab: Kevin White, UChicago
library encode accession: ENCLB457NMG
fragmentation methods: see document

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens K562 cell line

tag: line

value: cell line

tag: description

value: K562 cell line used as an untransfected matched control to one stably transfected with a construct containing an eGFP-tagged transcription factor.

tag: biosample encode accession

value: 53 year

tag: Sex

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

tag: link

value: ENCBS209TSR at ENCODE; https://www.encodeproject.org/ENCBS209TSR/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Insomnia Disorder [1400c279]

tag: insomnia

tag: age

value: female

tag: race

value: white

tag: education (years)

tag: bmi

tag: comorbidity

tag: bdi

tag: bdins


title: Insomnia Disorder [1400c271]

value: yes

tag: gender

tag: history of depression

value: no


title: in_HD6

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

data_processing:
Mapping - RNAseq (STAR aligner (2.6.0))
Bam to bigwig - RNAseq (bamCompare; deeptools)
Quantification of reads mapping to genes - RNAseq (featureCounts from Subread (1.6.3))
Genome_build: GRCh38 v30
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: featureCounts

growth_protocol: All cell culture work on fibroblasts cells and direct neuronal conversion was perfomed as described before (Drouin-Ouellet J, Lau S, Brattås PL, Rylander Ottosson D, Pircs K, Grassi DA, et al. REST suppression mediates neural conversion of adult human fibroblasts via microRNA-dependent and -independent pathways. EMBO Mol Med. 2017;9(8):1117-31.)

extract_protocol:
Total RNA was extracted from 10,000 cells/ sample with RNeasy micro kit (Qiagen) according to manufacturer’s protocol
cDNA was synthesized with the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara/Clontech) and assessed with the Bioanalyzer high sensitivity DNA kit, followed by library preparation using Nextera XT (Illumina). The quality and concentration of the libraries was assessed with the Bioanalyzer high sensitivity DNA kit and Qubit dsDNA BR DNA assay kit, respectively.

treatment_protocol: 10,000 induced neurons were FACS sorted based on NCAM+ staining after 28 days as described before (Shrigley S, Pircs K, Barker RA, Parmar M, Drouin-Ouellet J. Simple Generation of a High Yield Culture of Induced Neurons from Human Adult Skin Fibroblasts. J Vis Exp. 2018(132).)

tag: cell type

value: Induced neurons

tag: condition

value: Huntington


title: Insomnia Disorder [1400c130]

value: male


title: Insomnia Disorder [1400c133]


title: Insomnia Disorder [1400c173]


title: Insomnia Disorder [1400c255]


title: Insomnia Disorder [1400c200]


title: EA.hy926, LPS-induced sepsis HUVECs, LPS3, 12h

tag: cell line

value: endothelial cells

tag: genotype

value: LPS-induced

tag: treatment

value: Sepsis

tag: time

value: Human umbilical vein endothelial


title: in_HD2


title: Insomnia Disorder [1400c154]

value: non-white


title: Insomnia Disorder [1400c122]


title: in_HD1


title: Insomnia Disorder [1400c198]


title: Insomnia Disorder [1400c169]


title: Insomnia Disorder [1400c195]


title: in_HD7


title: in_C2

value: Control


title: EA.hy926, Human umbilical vein endothelial cells (HUVECs), Control1, 12h

value: WT


title: in_C6


title: in_C7


title: EA.hy926, Human umbilical vein endothelial cells (HUVECs), Control2, 12h


title: in_HD10


title: in_C5


title: in_HD5


title: fb_C2

value: Fibroblasts


title: fb_HD10


title: fb_HD1


title: fb_HD2


title: in_C3


title: fb_HD7


title: fb_HD9


title: in_HD9


title: Emerged haustoria-PARE/Degradome bioreplicate 1

city: Uppsala

first: German

last: Martinez

state: Uppsala

address: Almas Allé 8

department: Plant Biology

institute: Swedish University of Agricultural Sciences

data_processing:
Library strategy: Degradome-seq
sRNA libraries were trimmed using Trim Galore (https://github.com/FelixKrueger/TrimGalore)
Reads were aligned using bowtie (Langmead, et al. 2009) with the command “–v2” that allows two mismatches. The r0.32 version of the C. campestris genome (Vogel et al., 2018) and the miRbase version 21 (https://www.mirbase.org/) were used in this analysis. TE annotation for the r0.32 version of the C. campestris genome was retrieved from e!DAL (https://edal.ipk-gatersleben.de/)
Conserved miRNAs were identified using miRProf with only genome-matching sRNAs. New miRNAs were identified using miRCat and only considering new miRNAs with the following characteristics: 21-22 nt in length, detection of miRNA* complement, at least 10 reads in total and identification in multiple bioreplicates.
miRNA accumulation raw and normalized (in reads per million) values are shown in the miRNA_accumulation_values tabular file.
Genome_build: Cuscuta campestris r0.32; FASTA file with miRNA transcript sequences is available on the series record.

organism: Cuscuta campestris

source_name: Emerged haustoria

growth_protocol: Seeds from C. campestris were harvested from a culture of the parasite that was grown in a glasshouse at the phytotron of the University of Tromsø, Norway, in 24 h of light at 21 °C on Pelargonium zonale L. as host. To increase germination percentage, the seeds were scarified with concentrated sulfuric acid (96% v/v) for 20 minutes before being rinsed with water and placed on moist sterile filter paper. Young seedlings were harvested when they were 3 to 6 cm long. For the non-infective parts of mature C. campestris vines, the top 3 cm measured from the growing tip were harvested directly from the C. campestris culture on P. zonale. Shoot segments with developing haustoria (prehaustorial stage and emerged haustoria, respectively) were harvested after induction by far-red light and a tactile stimulus as described by Olsen et al. (2016)

extract_protocol:
Total RNA was isolated using TRIzol reagent (Life Technologies, Carlsbad, CA, USA). Small RNAs were gel purified in a 15% acrylamide/8M urea gel. Purified sRNAs were used as input to generate sRNA libraries using the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA, USA) following the manufacturer instructions. This procedure is identical to the one described in Martinez et al. (2016). PARE libraries were constructed following the protocol described in Zhai et al. (2014).
sRNA libraries were generated using the standard NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA, USA) protocol. PARE libraries were constructed following the protocol described in Zhai et al. (2014) which, briefly, is based on the enrichment of 5'P-mRNA molecules that are ligated to an RNA adapter. After reverse transcription the adapter is used to generate 20 nt fragments using a restriction enzyme. These fragments are then ligated again to adapters that are compatible with standard sRNA Illumina primers and indexes.

tag: tissue

value: Emerged haustoria

tag: sample type

value: Degradome

tag: molecule subtype

value: 5'P RNA


title: fb_HD6


title: in_C4


title: Prehaustoria-PARE/Degradome bioreplicate 1

source_name: Prehaustoria

value: Prehaustoria


title: fb_C7


title: ChrS-Ala245fs_vs_WT_3

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

hyb_protocol: Purified cDNA samples to be compared were pooled and the prepared two-color samples were hybridized at 65°C while rotating for 16 hours using Agilent’s Gene Expression Hybridization Kit, hybridization oven and hybridization chamber. After hybridization the arrays were washed using Agilent’s Wash Buffer Kit according to the manufacturer’s instructions.

scan_protocol: Fluorescence of hybridized DNA microarrays was determined at 532 nm (Cy3) and 635 nm (Cy5) at 5 μm resolution with a GenePix 4000B laser scanner and GenePix Pro 7 software (Molecular Devices, Sunnyvale, CA, USA). Fluorescence images were saved to raw data files in TIFF format (GenePix Pro 7). Quantitative TIFF image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 7).

data_processing: For ratio calculation and ratio normalization, GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

organism: Corynebacterium glutamicum

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532 and in Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott. 2004. Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol. Microbiol. 54: 420-438.

growth_protocol: pre-culture 1: in reaction tubes, 5 ml BHI, triplicates (3x WT, 3x ChrS-Ala245fs mutant), inoculated from a fresh agar plate, 30 C, 170 rpm, ~ 8 h; pre-culture 2: in 100 ml flasks, 2 ml of pre-culture 1 was transferred to 20 ml CGXII + 2% glucose + PCA + trace elements without any iron, 30 C, 120 rpm, over night;  main culture: 500 ml flasks, cells were pelleted so that they were inoculated at an OD of 1 in 50 ml CGXII + 2% glucose + PCA + trace elements without iron + 4 µM hemin;

extract_protocol: Harvesting: after 6 h of cultivation, mutant strains reached ~ OD 5 and WT ~ OD 2.5 were harvested in 25 ml ice falcons for later RNA Isolation. The preparation of total RNA was performed as described previously with the RNeasy Kit from Qiagen (Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott, (2004) Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol Microbiol 54: 420-438.)

treatment_protocol: see growth protocol


title: ChrS-Ala245fs_vs_WT_1