title: 45_1 single_cell_mrna_seq


title: D21_42

status: Public on Jul 31 2020

type: SRA

city: Guangzhou

first: Jinyong

last: Wang

state: GuangDong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

country: China

institute: Guangzhou Institutes of Biomedicine and Health (GIBH)

library_source: transcriptomic

data_processing:
Bcl2fastq (verison 2.16.0.10) convert .bcl files into fastq files
Fastq files were aligned to mm10 genome.*.ht2 files to generate *.sam file by HISAT2 (version 2.1.0). And the used samtools (version 0.1.19) to convert and sort the sam file to bam file. StringTie (version 1.3.4) were used to calculated genes expression level in TPM.
Gene expression levels in TPM of different samples were normalized by Stringtie.
Genome_build: mm10
Supplementary_files_format_and_content: TPM table was a csv file

molecule: polyA RNA

organism: Mus musculus

source_name: Day10 induced hematopoietic progenitor cells

growth_protocol: Expression of defined factors Hoxa9 and Runx1 in ESC/iPSC led to the production of an hematopoietic cell type

extract_protocol:
The procedure of RNA extraction and reverse transcription into double-stranded DNA were prepared using Discover-sc WTA Kit V2(Vazyme, N711)
Libraries were prepared according to instruction of TruePrepTM  DNA Library Prep Kit V2 (Vazyme,TD503).

treatment_protocol: The single iHECs and iHPCs were sorted for RNAseq analysis.

tag: cell type

tag: strain


title: D21_37

value: Day10 induced hematopoietic progenitor cells


title: 42_3 single_cell_mrna_seq

city: Groningen

first: Bart

last: Eggen

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

country: Netherlands

institute: UMCG Groningen

data_processing:
RNA-Seq
Reads without cell barcode or UMIs were removed and remaining raw reads were aligned to the human genome using HiSat2 (v.2.1.0) in single-end mode.
Genome_build: Homo.sapiens.GrCh38
Supplementary_files_format_and_content: A tab-delimited text file containing gene counts of ~84 single cells, resulting in 12 processed data files for each sample.
ATAC-seq
Raw reads were aligned to the human genome using bowtie2 (v.2.3.4.3) in paired-end mode.
Samtools (v.1.9) was used to remove duplicated reads (rmdup), filter reads that mapped to mitochondrial genome or blacklisted regions, and sort the reads.
Reads longer than 100 bp were removed, and reads were normalized and scaled to the effective genome size using reads per genomic content (RPGC) with deeptools (v.3.3.0).
Peak calling was performed using JetBrains SPAN peak analyzer (v.0.11.0.4882) with an FDR threshold of 1E-6 and a gap of 2.
Genome_build: Homo.sapiens.GrCh38
Supplementary_files_format_and_content: A tab-delimited text file containing called peaks per sample.

molecule: total RNA

organism: Homo sapiens

source_name: microglia

extract_protocol: Microglia were isolated by mechanical tissue dissociation and Percoll gradient centrifugation at 4°C followed by flow cytometry of single, viable (DAPI-, DRAQ5+), CD45+, CD11B+ cells. From two samples, the  CD45-, CD11B- population was collected as well. After cell lysis and barcoded poly-dT primer annealing, RNA was reverse-transcribed with a biotinylated barcoded template switching oligo (BC-TSO). Primer-dimers and small fragments were removed by exonuclease treatment. cDNA libraries were amplified and multiplexed. When cDNA libraries showed an average size of 1.5-2 kb, libraries were tagmented and indexed according to the Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1024) with an input of 500 pg cDNA. Samples were sequence on an Ilumina NextSeq 500. using 75 bp paired-end reads. Read 1 comprises the poolbarcode and read 2 the cDNA.

tag: donor/fetus

tag: gestational week+day


title: 39_4 single_cell_mrna_seq


title: D21_36


title: D21_38


title: D21_35


title: D21_34


title: 37_1 single_cell_mrna_seq


title: 31_3 single_cell_mrna_seq


title: D21_32


title: D21_31


title: D21_30


title: D21_29


title: RNA-seq of F1-C mice liver1

city: Shanghai

first: Dong

last: Zhang

address: dongchuan road

institute: shanghaijiaotong university

description: whose father were treated with saline1

data_processing:
The “OLB” and “CASAVA” software programs allowed the retrieval of the original fastq sequence data.
Using the fastx package, clean reads were attained.
“TOPHAT” was used after the reads and junction reads were mapped to the reference sequence.
The gene expression data estimated from the RPKM values were obtained using “Cuffinks”.
Genome_build: mm8
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample ...

source_name: liver

extract_protocol:
RNA was extracted using Trizol reagent. TruSeqTM DNA Sample Prep Kit-Set A  was used with 20 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After an adult male mouse (approximately 8 weeks of age) was sacrificed, the liver was carefully isolated.

tag: developmental stage

value: adult

tag: age

value: 8 weeks

tag: tissue

value: liver

tag: paternal treatment

value: saline


title: RNA-seq of F1-C mice liver3

description: whose father were treated with saline3


title: RNA-seq of F1-N mice liver3

description: whose father were treated with nicotine3

value: nicotine


title: RNA-seq of F1-C mice liver2

description: whose father were treated with saline2


title: RNA-seq of F1-N mice liver2

description: whose father were treated with nicotine2


title: KO Fat replicate 4

city: Washington

first: Rong

last: Li

state: DC

address: 2300 I Street

department: Biochemistry and Molecular Medicine

country: USA

institute: The George Washington University

data_processing:
Basecalls performed using Illuminal CASAVA software.
Reads were aligned to mm10 genome assembly using Tophat.
Differentially expressed genes were detected by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each Sample

source_name: Visceral fat tissue

extract_protocol:
RNA was harvested using Trizol reagent. About 500 ng RNA was used for the construction of sequencing libraries.
RNA libraries were prepared following the Illumina TruSeq stranded mRNA-seq sample preparation guide.

value: Visceral Fat

tag: treatment

value: Visceral fat after HFD feeding


title: RNA-seq of F1-N mice liver1

description: whose father were treated with nicotine1


title: D21_28


title: 26_1 single_cell_mrna_seq


title: KO Fat replicate 3


title: 28_4 single_cell_mrna_seq


title: KO Fat replicate 2


title: KO Fat replicate 1


title: 20_3 single_cell_mrna_seq


title: 34_2 single_cell_mrna_seq


title: D21_33


title: D21_26


title: ApoE3_rep1

city: Boise

first: Troy

last: Rohn

state: ID

address: 1910 W University Dr

department: Department of Biology

institute: Boise State University

data_processing:
Adapter sequences were trimmed using Trim Galore v0.5.0
Read quality was assessed using FastQC v0.11.8
Trimmed reads were mapped the mouse genome using Hisat2 v2.1.0
Gene counts were determined using HTSeq v0.11.0
Genome_build: version GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene

source_name: Microglial Cells

growth_protocol: BV2 microglial cells were maintained in a humidified chamber at 37°C and 6% carbon dioxide. Cells were cultured in T25 flasks with 50mL of RPMI 1640 media supplemented with 10% standard fetal bovine serum, 10% Cellgro MEM nonessential amino acid and penicillin streptomycin.

extract_protocol:
Total RNA was extracted from cells using a Direct-zol™ RNA MicroPrep kit following manufacturer's protocol.
Standard Illumina protocols were used to prepare RNA libraries for sequencing

treatment_protocol: Cells were treated with 25 µg/mL of amino-terminal (residues 1-151) ApoE3 fragments, amino-terminal (residues 1-151) Apoe4 fragments or PBS vehicle for five hours.

value: Treated with amino-terminal fragmented ApoE3 (residues 1-151)

tag: cell line

value: Microglial Cells

tag: brenda tissue ontology (bto)


title: ControlB_rep3

value: Untreated (Control for ApoE3)


title: ApoE3_rep2


title: ControlB_rep1


title: ApoE4_rep3

value: Treated with amino-terminal fragmented ApoE4 (residues 1-151)


title: WT Fat replicate 3


title: D21_25


title: 23_2 single_cell_mrna_seq


title: ApoE4_rep2


title: 14_4 single_cell_mrna_seq


title: ApoE4_rep1


title: 39_3 single_cell_mrna_seq


title: D21_27


title: D21_22


title: ControlA_rep3

value: Untreated (Control for ApoE4)


title: 36_4 single_cell_mrna_seq


title: 42_2 single_cell_mrna_seq


title: ControlB_rep2


title: Tumor in KO2

description: allSamples_Genes_ReadCount_E0771alone.txt

source_name: E0771 mammary tumor

value: Tumor

value: Transplanted tumor


title: ControlA_rep2


title: D21_24


title: 34_1 single_cell_mrna_seq


title: D21_21


title: ControlA_rep1


title: Tumor in KO1


title: 31_2 single_cell_mrna_seq


title: D21_20


title: Tumor in WT3


title: 28_3 single_cell_mrna_seq


title: rna.ko2

city: Okazaki

first: Kaori

last: Nakazawa

address: Nishigonaka 38, Myodaiji

country: Japan

institute: National Institute for Basic Biology

description: mRNA-seq

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.3.4.2
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
Genome_build: mm10
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

source_name: P.0.5 mouse eye

extract_protocol:
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling) or TruSeq (illumina) (for mRNA-seq)
Ribosome profiling and RNA-seq

tag: genetic background

tag: extracted molecule

value: total RNA

value: Truseq stranded mRNA library prep


title: D21_19

value: Day10 induced hematopoietic progenitor cells


title: rna.ko3

description: mRNA-seq


title: 25_4 single_cell_mrna_seq


title: Tumor in WT2


title: WT Fat replicate 1


title: Tumor in KO3


title: WT Fat replicate 2


title: D21_18


title: D21_23


title: rna.ko1

description: mRNA-seq


title: Tumor in WT1


title: rna.wt3

description: mRNA-seq

value: WT


title: 23_1 single_cell_mrna_seq


title: D21_15


title: rna.wt2

description: mRNA-seq


title: 14_3 single_cell_mrna_seq


title: D21_14


title: D21_17


title: ribo.ko3

description: Ribosome Profiling

value: Rnase I footprinting, ribosome pelleting, RNA extraction


title: BAT in Old mouse, room temp (24°c) smp5

city: Los Angeles

first: Claudio

last: Villanueva

state: CA

address: 610 Charles E. Young Drive East Box 957239

department: Integrative Biology and Physiology

institute: UCLA

data_processing:
Library quality control assays were performed by using Invitrogen Qubit dsDNA High Sensitivity Assay and Agilent ScreenTape Assay to qualify individual libraries and normalize the library pool.
We used the Rsubread package (version v1.20.2; Liao et al., 2014) to align the reads to Mus musculus reference genome (Release-76, http://useast.ensembl.org/info/data/ftp/index.html) and to produce gene-level summarized values based on the corresponding gene annotation format file (ftp://ftp.ensembl.org/pub/release-97/gtf/mus_musculus).
we used the limma (version 3.20.9; Smyth, 2004) and edgeR (version v3.6.8; Nikolayeva and Robinson, 2014; Robinson et al., 2010) packages to calculate FPKM values (Li and Dewey, 2011), and used a custom script to convert FPKM to TPM values (Li and Dewey, 2011; Wagner et al., 2012). We removed genes of TPM values that have < 0.01 variance across 6 samples and kept only 6,461 genes.
We used R version 3.2.2 and Bioconductor version 3.2 (Gentleman et al., 2004; R Core Team, 2014; http://www.R-project. org/).
The selection of differentially expressed genes (DEGs) among samples was performed based on the TPM values of transcripts,
Genome_build: Mus musculus reference genome (Release-76, http://useast.ensembl.org/info/data/ftp/index.html)
Supplementary_files_format_and_content: tab-delimited text file includes the expression level of 20,554 genes in TPM values (log2) for 19 samples.

source_name: Brown Adipose Tissue

growth_protocol: All procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of University of Utah. Mice were housedat 22°C–24°C using a 12 hr light/12 hr dark cycle. Animals were maintained on a Teklad global soy protein-free diet (2920x-030917M). Animals had ad libitum access to water at all times, and food was only withdrawn if required for an experiment. Male mice C57BL6J at 3 months or 24 months of age, unless otherwise stated. Mice were purchased from Jackson Laboratories.

extract_protocol:
Total RNA was isolated using TRIzol from the brown adipose tissue of C57BL6J mice in sterile condition.
Total RNA integrity was checked using 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) with an RNA integrity number (RIN) value greater than 7. For RNA-Seq, RNA libraries were prepared using the TruSeq RNA library preparation kit (Illumina, San Diego, CA, USA) with a modified protocol.
Illumina TruSeq Stranded Total RNA Library Prep Kit was used for library prepartion. rRNA was removed by Ribo-Zero, a reagent consisting of biotinylated oligonucleotides that are complimentary to rRNA. The purified mRNA was cleaved and reverse-transcribed into first-strand cDNA using reverse transcriptase and random primers. The RNA template was removed, followed by second-strand cDNA synthesis. End repair, 3’ adenylation and adapter ligation were performed. The purified cDNA templates were then enriched using PCR. The constructed libraries were 50 bp single-end sequenced using an Illumina HiSeq 2000 sequencer.

treatment_protocol: 10 of young (3 months) and 9 of old (24 month) male mice were assigned to cold room or room temperature. Mice are all wild type and were singly housed with no food, no bedding, but ready access to water. Starting at T0, mice were placed at the specified tem-perature of either 24°C (room temperature), or 4°C (cold exposure) for 5 hours. Body temperatureswere taken every hour with a physitemp A590 rectal probe using an Oaklon Thermocouple digital thermomete

value: Brown Adipose Tissue

value: 24 months

tag: genotype

value: wild type


title: 42_1 single_cell_mrna_seq


title: BAT in Young mouse, room temp (24°c) smp5

value: 3 months


title: BAT in Young mouse, cold room (4°c) smp5


title: 39_2 single_cell_mrna_seq


title: ribo.ko2

description: Ribosome Profiling


title: 36_3 single_cell_mrna_seq


title: ribo.ko1

description: Ribosome Profiling


title: BAT in Old mouse, room temp (24°c) smp4


title: D21_11


title: D21_16


title: ribo.wt3

description: Ribosome Profiling


title: BAT in Old mouse, room temp (24°c) smp3


title: ribo.wt2

description: Ribosome Profiling


title: 20_2 single_cell_mrna_seq


title: BAT in Old mouse, cold room (4°c) smp4


title: D21_10


title: rna.wt1

description: mRNA-seq


title: 31_1 single_cell_mrna_seq


title: 33_4 single_cell_mrna_seq


title: 28_2 single_cell_mrna_seq


title: D21_9


title: D21_8


title: 25_3 single_cell_mrna_seq


title: SW620 lim2 - untreated sample

type: RNA

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

description: SW620 lim2 - untreated sample

hyb_protocol: Hybridization of the samples to HG1.0ST gene expression chip (Affymetrix) were performed by Functional Genomics Core Facility of IRB, Barcelona using standard methodology

scan_protocol: Gene chips were scanned using GeneChip Scanner 3000 from affymetrix

data_processing: RMA normalization method as implemented in oligo Bioconductor R package

label: biotin

source_name: SW620 lim2 - untreated sample

label_protocol: Labeling of the samples to HG1.0ST gene expression chip (Affymetrix) were performed by Functional Genomics Core Facility of IRB, Barcelona using standard methodology

growth_protocol: Cell lines were maintained in 5% CO2 at 37ºC in DMEM medium supplemented with glutamine (0.29 mg/ml), penicillin (100 U/ml), streptomycin (0.1 mg/ml), and  5% fetal bovine serum (FBS)

extract_protocol: RNA was extracted using RNeasy Mini Kit

treatment_protocol: Cells were treated for 24 h with 10 μM U0126 MEK1/2 inhibitor

tag: sample id

value: Untreated

tag: group


title: SW620 lim2 - mek1/2 inhibitor treated sample

value: MEK1/2 inhibitor treated


title: D21_13


title: D21_12


title: BAT in Young mouse, room temp (24°c) smp4


title: BAT in Old mouse, cold room (4°c) smp3


title: 22_4 single_cell_mrna_seq


title: D21_7


title: BAT in Young mouse, room temp (24°c) smp3


title: 6mo-10ppm-male-rep2.WGBS

city: RTP

first: Janine

last: Santos

state: NC

address: 111 TW Alexander drive

department: GISBL

institute: NIEHS

description: WGBS

library_source: genomic

data_processing:
For consistency and quality reasons, only read1 was used in WGBS analysis. Reads were filtered to retain only those with average base quality score >20. Adapter trimming was performed with Cutadapt v1.2 (parameters -a AGATCGGAAGAG -O 5 -q 0 -f fastq); only reads at least 30nt after trimming were retained.
Filtered and trimmed WGBS reads were mapped to the mm10 reference genome via Bismark v0.18.1 at default parameters using Bowtie2 v2.3.0. Reads not mapped as full-length queries were re-submitted after clipping at the 3' end in an attempt to salvage additional alignments.
Mapped hits were deduplicated within libraries. Additional post-mapping processing included discarding reads with 3 or more methylated cytosines in non-CpG context and clipping alignments to remove regions with positional methylation bias as determined by the tool bismark_methylation_extractor. Mapped hits from multiple libraries of the same animal were aggregated after all quality filters and clipping were applied.
RNA-seq reads were filtered to retain only those with average base quality score >20. Read pairs were mapped to the mm10 reference genome via TopHat with the following parameters: --b2-sensitive --library-type fr-unstranded -g 1 --mate-inner-dist -40 --mate-std-dev 50. Resulting hits were coordinate-sorted and deduplicated with Picard tool suite v1.96.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Counts of methylated and unmethylated counts at CpG sites in tab-delimited text format (WGBS); percent methylation at CpG sites in bigWig format (WGBS).
Supplementary_files_format_and_content: RPKM per gene per sample in tab-delimited text format (RNAseq).

molecule: genomic DNA

source_name: mouse liver

extract_protocol:
Livers were surgically retrieved, frozen in dry ice, and stored at -80°C. Pelleted minced tissue was homogenized further with sterile disposable pestles using a hand-held motor (Kimble) in the presence of 1 mL of Trizol reagent (Invitrogen) and fractionated according to the manufacturer's instructions to obtain total RNA, genomic DNA, and protein fractions.
WGBS libraries were constructed from starting 1ug genomic DNA and 50ng phage lambda, sheared via BioRuptor, subjected to bisulfite conversion (EZ DNA methylation kit; Zymo research), ligated and amplified with methylated adapters (TruSeq RNA v2; Illumina) and low-input DNA ligation chemistry (HyperPrep; KAPA Biosystems).
RNAseq libraries were constructed starting with poly-A-selected RNA from 1 µg of DNaseI-treated total RNA input using a magnetic poly-dT bead hybridization capture (Illumina), eluted in 10µL of nuclease-free H2O, transferred as magnetically isolated supernatant to RNase-free wells of a 96-well reaction plate, and used directly for rRNA-free library assembly using a KAPA Stranded RNA-Seq with RiboErase commercial kit (KAPA Biosystems).

treatment_protocol: Rotenone was administered through the diet at 10 ppm for 8 weeks; control diet did not contain rotenone.

value: liver

tag: Sex

value: male

value: 6 months

tag: dam treatment

value: 10ppm rotenone


title: 20_1 single_cell_mrna_seq


title: D21_6

tag: cell type

tag: strain


title: 14_2 single_cell_mrna_seq

tag: donor/fetus

tag: gestational week+day


title: BAT in Young mouse, cold room (4°c) smp4

tag: age


title: 9_4 single_cell_mrna_seq


title: D21_5


title: 6mo-10ppm-male-rep1.WGBS

description: WGBS

tag: tissue


title: 6mo-0ppm-male-rep3.WGBS

description: WGBS

value: control


title: ribo.wt1

description: Ribosome Profiling


title: D21_4


title: BAT in Old mouse, room temp (24°c) smp2


title: D21_3


title: BAT in Old mouse, room temp (24°c) smp1


title: 6mo-0ppm-male-rep1.WGBS

description: WGBS


title: 39_1 single_cell_mrna_seq


title: D21_2


title: BAT in Old mouse, cold room (4°c) smp2


title: 6mo-10ppm-male-rep3.WGBS

description: WGBS


title: D22-10ppm-male-rep3.WGBS

description: WGBS


title: 33_3 single_cell_mrna_seq


title: D21_1


title: 36_1 single_cell_mrna_seq


title: BAT in Old mouse, cold room (4°c) smp1


title: D22-10ppm-male-rep2.WGBS

description: WGBS


title: 30_4 single_cell_mrna_seq


title: BAT in Young mouse, cold room (4°c) smp3


title: D22-10ppm-male-rep1.WGBS

description: WGBS


title: D17_18

source_name: Day6 induced hematopoietic progenitor cells


title: 28_1 single_cell_mrna_seq


title: D17_17

value: Day6 induced hematopoietic progenitor cells


title: 6mo-0ppm-male-rep2.WGBS

description: WGBS


title: D22-0ppm-male-rep2.WGBS

description: WGBS


title: BAT in Young mouse, cold room (4°c) smp2


title: D22-0ppm-male-rep3.WGBS

description: WGBS


title: BAT in Young mouse, room temp (24°c) smp2

extract_protocol:
Total RNA was isolated using TRIzol from the brown adipose tissue of C57BL6J mice in sterile condition.
Total RNA integrity was checked using 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) with an RNA integrity number (RIN) value greater than 7. For RNA-Seq, RNA libraries were prepared using the TruSeq RNA library preparation kit (Illumina, San Diego, CA, USA) with a modified protocol.
Illumina TruSeq Stranded Total RNA Library Prep Kit was used for library prepartion. rRNA was removed by Ribo-Zero, a reagent consisting of biotinylated oligonucleotides that are complimentary to rRNA. The purified mRNA was cleaved and reverse-transcribed into first-strand cDNA using reverse transcriptase and random primers. The RNA template was removed, followed by second-strand cDNA synthesis. End repair, 3’ adenylation and adapter ligation were performed. The purified cDNA templates were then enriched using PCR. The constructed libraries were 50 bp paired-end sequenced using an Illumina HiSeq 2000 sequencer.


title: BAT in Young mouse, room temp (24°c) smp1


title: D17_15


title: 25_2 single_cell_mrna_seq


title: D22-0ppm-male-rep1.WGBS

description: WGBS


title: 22_3 single_cell_mrna_seq


title: D17_16


title: 8_4 single_cell_mrna_seq

source_name: doubleneg


title: BAT in Young mouse, cold room (4°c) smp1


title: 6mo-10ppm-female-rep5.WGBS

description: WGBS

value: female


title: D17_13


title: 6mo-10ppm-female-rep4.WGBS

description: WGBS


title: Adult_whole_DTAmut_d5

city: Minato-ku

first: Hideto

last: Koso

state: Tokyo

address: 4-6-1 Shirokanedai

institute: Institute of Medical Science, The University of Tokyo

data_processing:
CASAVA-1.8.2 (for d5 samples) and bcl2fastq-1.8.4 (for d1 samples) used for basecalling with default parameters
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mouse mm9 reference genome assembly with the option (--coverage-search --max-multihits 50).
FPKM (Fragments Per Kilobase of transcript per Million mapped reads) with Cufflinks ver. 2.1.1 with the default option.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Retina

extract_protocol:
RNA was harvested retinas using Sepazol reagent. The RNA-seq library was constructed using the mRNA-seq sample preparation kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain background

value: C57BL/6；129 mixed

value: ~8 weeks of age

tag: genotype/variation

value: Msi1-CreERT2/+; R26R-DTA/+

value: retina

tag: time point

value: day 5 post-injury


title: D17_12


title: Adult_whole_DTAwt_d5


title: 9-3 single_cell_mrna_seq


title: 6mo-10ppm-female-rep3.WGBS

description: WGBS


title: D17_11


title: 68-4 single_cell_mrna_seq


title: 6mo-0ppm-female-rep5.WGBS

description: WGBS


title: D17_10


title: 6mo-0ppm-female-rep2.WGBS

description: WGBS


title: 33-2 single_cell_mrna_seq


title: D17_14


title: 6mo-0ppm-female-rep1.WGBS

description: WGBS


title: 27-4 single_cell_mrna_seq


title: D22-10ppm-female-rep3.WGBS

description: WGBS


title: 14_1 single_cell_mrna_seq


title: D17_8


title: D17_9


title: D17_7


title: D22-10ppm-female-rep2.WGBS

description: WGBS


title: 25-1 single_cell_mrna_seq


title: D17_6


title: D17_5


title: D22-10ppm-female-rep1.WGBS

description: WGBS


title: 22-2 single_cell_mrna_seq


title: 36-1 single_cell_mrna_seq


title: 8-3 single_cell_mrna_seq


title: D22-0ppm-female-rep4.WGBS

description: WGBS


title: D17_4


title: D22-0ppm-female-rep3.WGBS

description: WGBS


title: 30-3 single_cell_mrna_seq


title: D17_3


title: D22-0ppm-female-rep2.WGBS

description: WGBS


title: D17_2


title: 68_3 single_cell_mrna_seq


title: 9_2 single_cell_mrna_seq


title: 13-4 single_cell_mrna_seq


title: D17_1


title: Prostate, PTEN KO LXR KO, Castrated_47

city: AUBIERE

first: silvere

last: BARON

address: 10 avenue Blaise Pascal

department: Endocrine, Signaling and Cancer

country: France

institute: Université Clermont Auvergne

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Genome_build: mm10
Supplementary_files_format_and_content: raw and normalized counts

source_name: prostatic samples

extract_protocol: RNA-Seq libraries were generated from --- ng of total RNA using TruSeq Stranded mRNA Sample Preparation Kit (Illumina, Part Number RS-122-2101). Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman Coulter) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: PTEN KO LXR KO

tag: treatment

value: Castrated

value: prostate


title: Prostate, PTEN KO LXR KO, Castrated_44


title: D14_20

source_name: Day3 induced hematopoietic progenitor cells


title: Prostate, PTEN KO LXR KO, Castrated_46


title: 33_1 single_cell_mrna_seq


title: 30_2 single_cell_mrna_seq


title: D14_19

value: Day3 induced hematopoietic progenitor cells


title: 27_3 single_cell_mrna_seq


title: D14_18


title: Prostate, PTEN KO LXR KO, Sham_40

value: Sham


title: 24_4 single_cell_mrna_seq


title: Prostate, PTEN KO LXR KO, Sham_41


title: D14_17


title: Prostate, PTEN KO LXR KO, Sham_39


title: D14_16


title: 65_4 single_cell_mrna_seq


title: D14_15


title: Prostate, PTEN KO LXR KO, Sham_38


title: D14_21


title: 22_1 single_cell_mrna_seq


title: PB_donor2_γδT_TCR

city: Hamburg

first: Immo

last: Prinz

address: Falkenried 94

department: Institute of Systems Immunology

country: Germany

institute: University medical center Hamburg Eppendorf

description: TCR  γδ

data_processing:
Data processing of single-cell RNA sequencing libraries:   To generate the cell (barcode)-gene matrices, raw sequencing data were demultiplexed to individual fastq files, then aligned and quantified by Cell Ranger v3.1 (10xGenomics) under default setting. Human genome GRCh38 (UCUS) was adopted as reference. Ambient RNA in raw cell-gene matrices were cleaned based on the nUMI-barcode saturation curves.
Cell clustering and differentially expressed gene profile:   The R package Seurat v3.1 was used under R v3.6 for scRNA-seq data trimming, analyzing, and visualization (Butler et al., 2018; Stuart et al., 2019). Briefly, cell-gene matrices were exported to R as Seurat projects. Cells contain less than 1,500 unique molecular identifiers (UMIs) or more than 6,000 UMIs, or greater than 11% mitochondrial RNA content were trimmed from analysis. Cell cycling score and cell phases were assigned by the function ‘CellCycleScoring’ according to a gene list of cell cycle markers (Kowalczyk et al., 2015). Raw data matrices were then normalized and scaled by regularized negative binomial regression by ‘SCTransform’ function (Hafemeister and Satija, 2019); contents of mitochondrial genes and ribosomal genes, donor batch effects, and cycling scores were regressed out as unwanted heterogeneity during normalization. Datasets from different donor groups (adult versus newborns) were integrated by Seurat data integration pipeline (Stuart et al., 2019), 3,000 genes represent the correspondences between cells in two groups were used as ‘anchors’ to harmonize and integrate the datasets. Integrated data were subject to a principal component analysis (PCA), 100 components were calculated. The significance of each component was evaluated by Jackstraw score. The significant components were then selected for K-nearest neighbor (KNN) based unsupervised clustering with resolution = 0.8, and Uniform Manifold Approximation and Projection (UMAP) visualization. After clustering, clusters with no CD3 expression (CD3D, CD3E) were trimmed as contamination.   Differentially expressed genes (DEGs) were identified by bimod method as average log2-fold change (logFC) ≥ 0.25, expressed in minimal percentage cells in at least 1 test group (min.pct) ≥ 15%, and adjust p-value ≤ 0.01.   Clusters defined by unsupervised-clustering were further adjusted according to the DEGs:  We calculated the DEGs between neighboring clusters and set the cutoff of DEG as logFC ≥ 0.5. Two neighboring clusters which have less than 30 non-mitochondrial/ribosomal DEGs were merged as one cluster. Therefore, we reduced the cluster number from 16 to 12.  The integrated neonatal and adult single-cell transcriptome dataset was export as Human_gdt_seurat_proj.rds
Single-cell TCR sequencing analysis: Cell Ranger VDJ pipeline (10xGenomics) under default parameters was performed to generate scTCR annotations on the assembled contigs and on the clonotype consensus sequences. Human genome GRCh38 was used as reference for alignment. The two scTCR annotation tables from two rounds of sequencing of a same sample were merged together after removing duplicates. The merged annotation tables were exported as processed data. Further, by matching the cellular barcodes, scTCR data was joined into the metadata of scRNA Seurat project (Human_gdt_seurat_proj.rds) we created above.
Genome_build: GRCh38

source_name: γδ T cells, adult

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) and cord blood mononuclear cells (CBMCs) were isolated from fresh blood samples stored in EDTA using a density gradient media (Pancoll, PAN-Biotech). After isolation, mononuclear cells were washed twice in PBS 10% FBS (Sigma-Aldrich) and cryopreserved at -80°C in freezing medium (50% FBS (Sigma-Aldrich), 40% RPMI 1640 (Gibco), 10% DMSO (Roth)). Cells were cultured overnight in X-Vivo 15 medium (Lonza) before antibody staining and cell sorting and treated with 5% FcR block in buffer (PBS with 3% FCS, 4 mM EDTA) right before staining. Cells were stained with hCD3 FITC (1:100; clone BW264/56; Miltenyi), hTCR γδ PE (1:50; clone 11F2; Miltenyi), and DAPI (0.1 μg/ml) to determine living cells. For sequencing experiments, DAPI−, CD3+, γδ+ T cells were sorted on a FACS Aria Fusion cytometer (BD) and subsequently used for the preparation of single-cell libraries using the single-cell immune profiling platform of 10x Genomics.
scRNA-seq and single-cell TCR libraries were prepared using the Chromium Single Cell V(D)J Reagent Kit (10x Genomics). For each sample, 3*104 γδ T cells mixed with a master mix for cDNA generation were used in a droplet-based approach for the generation of Gel Bead-in-emulsion (GEMs). 5’ Gel beads contain adapters and oligonucleotides for amplification and barcoding of sequences (Illumina R1 sequence (read 1 sequencing primer), 10x barcode, unique molecular identifier (UMI) and template switch oligo (TSO)). Subsequently, pooled GEMs of each sample were used for the construction of two libraries, the scRNA library containing the 5’ gene expression profile and the single-cell TCR library comprising single-cell TRG and TRD sequences. Downstream processing and library construction, including clean-up steps, were performed according to the protocol provided by 10x Genomics. Agilent Bioanalyzer High Sensitivity chips were applied for quality control. To amplify γδ TCR chains, the primers were used for the enrichment of γδ TCR chains instead of primers for αβ TCR profiling (10x Genomics User Guide CG000086, Step 4, Target Enrichment from cDNA).    The scRNA-seq libraries were sequenced on the Illumina NextSeq 5500 platform using read lengths of 26 base pairs (bp) read1 and 100 bp read2. The single-cell TCR libraries were sequenced by Illumina MiSeq.  For each scRNA-seq , two rounds of sequencing were performed. For each scRNA-seq , three rounds of sequencing were performed.

value: gamma delta T cells

value: peripheral blood

value: adult


title: PB_donor1_γδT_TCR

description: TCR  γδ


title: 13_3 single_cell_mrna_seq


title: CB_donor2_γδT_TCR

description: TCR  γδ

source_name: γδ T cells, neonate

value: cord blood

value: neonate


title: Prostate, PTEN KO, Castrated_35

value: PTEN KO


title: CB_donor1_γδT_TCR

description: TCR  γδ


title: D14_13


title: Prostate, PTEN KO, Castrated_34


title: D14_12


title: D14_14


title: 68_2 single_cell_mrna_seq


title: 9_1 single_cell_mrna_seq


title: Prostate, PTEN KO, Castrated_31


title: Ioc3△cHLB△Yaf9_2

city: Smithville

first: Blaine

last: Bartholomew

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

data_processing:
Fragments were mapped to the yeast  reference genome sacCer3 using TopHat V2.0.10, Bowtie V2.0 and R V3.1.0. Differential gene expression analysis was performed using edgeR 3.6.2, limma 3.20.4 and htseq-  count V0.6.0.
Supplementary_files_format_and_content: Excel file containing edgeR Count Per Million (cpm) data

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown in YPD to an OD 600 of approximately 0.7-0.9 in three independent biological replicates.

extract_protocol:
Total RNA was extracted using the hot acid phenol method (Collart and  Oliviero, 2001) . Samples were extracted with phenol/chloroform, precipitated with ethanol and  resuspended in 50 µl of diethylpyrocarbonate-treated water.
Libraries were prepared using standard Illumina protocols

tag: epitop tag

value: FLAG


title: Prostate, PTEN KO, Sham_29


title: 62_4 single_cell_mrna_seq


title: Ioc3△cHLB△Yaf9_1


title: D14_11


title: Prostate, PTEN KO LXR KO, Castrated_43


title: D14_10


title: HCT116_LIG1cpp

type: genomic

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Ave NE

department: Center for Epigenetics

institute: Van Andel Research Institute

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: openSesame from SeSAMe R package

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol

growth_protocol: 37ºC, 5% CO2, McCoy's 5A (HCT116) or DMEM (HeLa) media with 10% FBS and no antibiotics

extract_protocol: Qiagen Dneasy kit

tag: cell line

tag: compound


title: Prostate, PTEN KO, Sham_28

tag: genotype


title: △Ioc3△Yaf9_3


title: 30_1 single_cell_mrna_seq


title: D14_8


title: HeLa_LIG1cpp

source_name: HeLa

value: HeLa


title: D14_9


title: D14_7


title: △Ioc3△Yaf9_2


title: HeLa_water

value: water


title: HCT116_unc0638


title: 24_3 single_cell_mrna_seq

source_name: microglia


title: Prostate, LXR KO, Castrated_23

value: LXR KO


title: △Ioc3△Yaf9_1


title: WT ISW1a△Yaf9_3

source_name: WT ISW1a△Yaf9

value: WT ISW1a{delta}Yaf9


title: HCA 4

city: Philadelphia

first: Zubair

middle: H

last: Aghai

state: PA

address: 833 Chestnut Street, Suite 1201

department: Pediatrics/ Neonatology

institute: Thomas Jefferson University/ Nemours

description: Cord Blood Mononuclear Leukocyte

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged with Illumina iScan Reader using standard recommended Illumina scanner setting

data_processing: Illumina GenomeStudio

label: Cy5 and Cy3

source_name: CBML from HCA exposed neonate

extract_protocol:
Human cord blood was collected in sterile EDTA tubes and Mononuclear Leucocytes were isolated by Ficoll-Paque Plus density gradient
Genomic DNA was isolated using QIAamp DNA Mini kit from 2 million cells according to manufacturer's instruction

treatment_protocol: No treatment. Compared disease condition (HCA) with control group (healthy neonates)

tag: disease

value: Histological chorioamnionitis


title: 21_4 single_cell_mrna_seq


title: Prostate, PTEN KO, Castrated_36


title: Prostate, PTEN KO, Sham_26


title: HCA 5

description: Cord Blood Mononuclear Leukocyte


title: Prostate, LXR KO, Castrated_22


title: D14_6


title: HCT116_dmso

value: DMSO


title: HCA 1

description: Cord Blood Mononuclear Leukocyte


title: Control 5

description: Cord Blood Mononuclear Leukocyte

source_name: CBML from Healthy Neonate

value: Control


title: 27_2 single_cell_mrna_seq


title: Ioc3△cHLB△Yaf9_3


title: WT ISW1a△Yaf9_2


title: 8_1 single_cell_mrna_seq


title: Prostate, PTEN KO, Sham_27

value: prostate


title: WT ISW1a△Yaf9_1


title: D14_4

value: Day3 induced hematopoietic progenitor cells


title: Prostate, LXR KO, Castrated_19

value: Castrated


title: HCA 3

description: Cord Blood Mononuclear Leukocyte


title: 7-4 single_cell_mrna_seq


title: Ioc3△cHLB_3


title: D14_3


title: HCA 2

description: Cord Blood Mononuclear Leukocyte


title: 68-1 single_cell_mrna_seq


title: 13_2 single_cell_mrna_seq


title: 8_2 single_cell_mrna_seq


title: D14_2


title: Ioc3△cHLB_1


title: Control 2

description: Cord Blood Mononuclear Leukocyte


title: D14_5


title: Control 1

description: Cord Blood Mononuclear Leukocyte


title: HCT116_water_2


title: Prostate, LXR KO, Sham_16

value: Sham


title: 65-2 single_cell_mrna_seq


title: D14_1


title: Prostate, LXR KO, Sham_17


title: Prostate, LXR KO, Sham_13


title: Control 4

description: Cord Blood Mononuclear Leukocyte


title: Control 3

description: Cord Blood Mononuclear Leukocyte


title: △Ioc3_2


title: iHEC_65

source_name: induced hematopoietic endothelia cells

value: induced hematopoietic endothelia cells


title: Prostate, LXR KO, Sham_12


title: 62-3 single_cell_mrna_seq


title: Prostate, LXR KO, Castrated_21


title: iHEC_64


title: △Ioc3_1


title: 27-1 single_cell_mrna_seq


title: Prostate, CW, Castrated_10

value: CW


title: iHEC_63


title: WT ISW1a_3

source_name: WT ISW1a

value: WT ISW1a


title: iHEC_62


title: WT ISW1a_2


title: 24-2 single_cell_mrna_seq


title: WT ISW1a_1


title: Prostate, CW, Castrated_8


title: Prostate, CW, Castrated_11


title: 21-3 single_cell_mrna_seq


title: 18-4 single_cell_mrna_seq


title: iHEC_61


title: Ioc3△cHLB_2


title: Prostate, CW, Sham_5


title: 13-1 single_cell_mrna_seq


title: Prostate, CW, Castrated_7


title: Ioc3△cHLB_2_IP

description: processed data file: Merged_dcHLB.bw

data_processing:
Files were mapped using CASAVA 1.8.2 (Illumina) and sacCer3 was used as the reference genome. Peaks were called using MACS2 and the peak centers were plotted using deepTools2.
Genome_build: sacCer3
Supplementary_files_format_and_content: Bigwig files with peak data

growth_protocol: Yeast strains having a 13xMYC tag at the C-terminus of IOC3 were grown in YPD to an OD 600 of ~0.8  and formaldehyde crosslinked

extract_protocol:
The cells were lysed using glass beads (zirconia/silica beads, 0.5 mm, BioSpec) after shaking for 1 hour at 4˚C. Lysed cells were sonicated for 22 min (Bioruptor, high setting, 30” on and 30” off). Chromatin was incubated overnight at 4˚C with 10 ug anti-myc antibody (Abcam) after preclearing for 6 hrs using magnetic beads.
Libraries were prepared using standard Illumina protocols

tag: epitope

tag: chip antibody

value: Anti-Myc tag  [9E10] - ChIP Grade- Abcam


title: iHEC_59

extract_protocol:
The procedure of RNA extraction and reverse transcription into double-stranded DNA were prepared using Discover-sc WTA Kit V2(Vazyme, N711)
Libraries were prepared according to instruction of TruePrepTM  DNA Library Prep Kit V2 (Vazyme,TD503).

tag: cell type


title: Ioc3△cHLB_1_IP

description: processed data file: Merged_dcHLB.bw


title: 59-4 single_cell_mrna_seq

extract_protocol: Microglia were isolated by mechanical tissue dissociation and Percoll gradient centrifugation at 4°C followed by flow cytometry of single, viable (DAPI-, DRAQ5+), CD45+, CD11B+ cells. From two samples, the  CD45-, CD11B- population was collected as well. After cell lysis and barcoded poly-dT primer annealing, RNA was reverse-transcribed with a biotinylated barcoded template switching oligo (BC-TSO). Primer-dimers and small fragments were removed by exonuclease treatment. cDNA libraries were amplified and multiplexed. When cDNA libraries showed an average size of 1.5-2 kb, libraries were tagmented and indexed according to the Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1024) with an input of 500 pg cDNA. Samples were sequence on an Ilumina NextSeq 500. using 75 bp paired-end reads. Read 1 comprises the poolbarcode and read 2 the cDNA.


title: Prostate, CW, Sham_4


title: Prostate, CW, Sham_3


title: iHEC_58

tag: strain


title: Ioc3△cHLB_2_Input

description: processed data file: Merged_dcHLB.bw


title: 7_3 single_cell_mrna_seq

tag: donor/fetus


title: iHEC_57


title: Prostate, CW, Sham_2


title: 67_4 single_cell_mrna_seq

tag: gestational week+day


title: 65_1 single_cell_mrna_seq


title: Ioc3△cHLB_1_Input

description: processed data file: Merged_dcHLB.bw


title: iHEC_60


title: iHEC_56


title: 62_2 single_cell_mrna_seq


title: WT_ISW1a_2_IP

description: processed data file: Merged_WT_ISW1a.bw


title: SML treated

city: Mysore

first: Ram

last: Rajasekharan

state: Karnataka

address: Cheluvamba Mansion

country: India

institute: Central Food Technological Research Institute (CSIR-CFTRI)

data_processing:
Base calls were performed using Illumina Casava version 1.8
RNA seq reads were aligned to the mm10 Mus musculus genome assembly
Data were filtered using NGSQC toolkit
gtf files were generated using Cufflinks and diffrential was performed using Cufdiff from Tuxedo pipeline
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file with FPKM values for each sample.

source_name: Brown adipose tissue

growth_protocol: Standard animal house conditions.

extract_protocol:
1 μg total RNA with an RNA integrity number (RIN) of 8.0 was used for mRNA purification using oligo-dT beads (TruSeq RNA Sample Preparation Kit, Illumina). The purified mRNA was fragmented and reverse transcribed using Superscript II Reverse Transcriptase (Life Technologies). Second strand cDNA was synthesized on the first strand template using RNaseH and DNA polymerase I. The cDNAs were cleaned using Beckman Coulter Agencourt Ampure XP SPRI beads.
The sequencing library was prepared by random fragmentation of the cDNA sample, followed by 5' and 3' adapter ligation, after end-repair and the addition of an ‘A’ base and SPRI cleanup. Adapter-ligated fragments were enriched by PCR. The individual libraries were quantified using a NanoDrop spectrophotometer (Thermo Scientific) and validated for quality with a Bioanalyzer (Agilent Technologies). Adapter-ligated fragments are then PCR amplified and gel purified

treatment_protocol: 8-12 week old male C57BL6/J mice were challenged with a 60% kcal high fat diet with or without SML (5mg/ kg BW, intraperitoneal) for 10 days

tag: developmental stage

value: 8-12 weeks old male


title: WT_ISW1a_1_IP

description: processed data file: Merged_WT_ISW1a.bw


title: iHEC_55

data_processing:
Bcl2fastq (verison 2.16.0.10) convert .bcl files into fastq files
Fastq files were aligned to mm10 genome.*.ht2 files to generate *.sam file by HISAT2 (version 2.1.0). And the used samtools (version 0.1.19) to convert and sort the sam file to bam file. StringTie (version 1.3.4) were used to calculated genes expression level in TPM.
Gene expression levels in TPM of different samples were normalized by Stringtie.
Genome_build: mm10
Supplementary_files_format_and_content: TPM table was a csv file


title: iHEC_54


title: iHEC_53


title: 59_3 single_cell_mrna_seq

data_processing:
RNA-Seq
Reads without cell barcode or UMIs were removed and remaining raw reads were aligned to the human genome using HiSat2 (v.2.1.0) in single-end mode.
Genome_build: Homo.sapiens.GrCh38
Supplementary_files_format_and_content: A tab-delimited text file containing gene counts of ~84 single cells, resulting in 12 processed data files for each sample.
ATAC-seq
Raw reads were aligned to the human genome using bowtie2 (v.2.3.4.3) in paired-end mode.
Samtools (v.1.9) was used to remove duplicated reads (rmdup), filter reads that mapped to mitochondrial genome or blacklisted regions, and sort the reads.
Reads longer than 100 bp were removed, and reads were normalized and scaled to the effective genome size using reads per genomic content (RPGC) with deeptools (v.3.3.0).
Peak calling was performed using JetBrains SPAN peak analyzer (v.0.11.0.4882) with an FDR threshold of 1E-6 and a gap of 2.
Genome_build: Homo.sapiens.GrCh38
Supplementary_files_format_and_content: A tab-delimited text file containing called peaks per sample.


title: WT_ISW1a_2_Input

description: processed data file: Merged_WT_ISW1a.bw


title: 56_4 single_cell_mrna_seq


title: iHEC_52


title: 24_1 single_cell_mrna_seq


title: 21_2 single_cell_mrna_seq


title: iHEC_51


title: siZIP7-3-3

city: Durham

first: Wei

last: Chen

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

data_processing:
HiSeq Control Software (Application Version: HD 3.4.0.38, RTA Version: 2.7.7)
Illumina HiSeq 4000 reads were processed using the TrimGalore toolkit v0.4.1 to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads.  Only reads that were 20nt or longer after trimming were kept for further analysis. Read quality was checked for each sample using FastQC v0.11.2.
Reads were mapped to the GRCh38v93 version of the human genome and transcriptome using the STAR RNA-seq alignment tool v2.5.0c.  Reads were kept for subsequent analysis if they mapped to a single genomic location.
Gene counts were compiled using the HTSeq tool v0.6.1.  Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression was carried out using the DESeq2 Bioconductor package v1.16.1 with the R statistical programming environment v3.4.1_3.
Genome_build: GRCh38v93
Supplementary_files_format_and_content: htseq read count text file

source_name: triple negative breast cancer

growth_protocol: Cells were cultured at 37'C with 5%CO2 in DMEM (with FBS and penicillin/streptomycin)

extract_protocol:
RNeasy mini kit and DNase I treatment
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA for 96 h by reverse transfection

tag: tissue

value: breast

value: triple negative breast cancer

value: ZIP7 siRNA_1


title: 18_3 single_cell_mrna_seq


title: siZIP7-3-2


title: 65_3 single_cell_mrna_seq


title: iHEC_50

city: Guangzhou

first: Jinyong

last: Wang

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health (GIBH)


title: HFD Control


title: iHEC_49


title: 12_4 single_cell_mrna_seq

city: Groningen

first: Bart

last: Eggen

address: Antonius Deusinglaan 1

institute: UMCG Groningen


title: 7_2 single_cell_mrna_seq


title: iHEC_48


title: 67_3 single_cell_mrna_seq


title: siNC-3

value: nontargeting control siRNA


title: 64_4 single_cell_mrna_seq


title: WT_ISW1a_1_Input

description: processed data file: Merged_WT_ISW1a.bw

tag: strain background


title: iHEC_47


title: iHEC_46


title: siNC-2


title: siZIP7-6-2

value: ZIP7 siRNA_2


title: siZIP7-6-3


title: iHEC_45


title: siZIP7-3-1


title: 59_2 single_cell_mrna_seq


title: 62_1 single_cell_mrna_seq


title: iHEC_44


title: 56_3 single_cell_mrna_seq


title: iHEC_43


title: KRAS_2_1_AB

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

description: Cancer cell line obtained from ATCC

data_processing:
A 100 nt singled-end sequencing was performed using an Illumina HiSeq 4000 platform, and ~20 million reads per sample were obtained.
The short-sequenced reads were mapped to the human reference genome (hg19) with the RNA-Seq unified mapper (RUM) V2.0.5. 06 (http://cbil.upenn.edu/RUM/).
The R/Bioconductor packages were employed to accurately calculate the gene expression abundance using the aligned BAM files.
To identify differentially expressed genes between various treatment groups and vehicle samples we employed the edgeR Bioconductor package based on the normalized log2 based count per million values.
Genome_build: hg19
Supplementary_files_format_and_content: CSV tab delimited format containing log2 Count per millon values

source_name: H2009 cells subject to KRAS K3RNAi duplex

growth_protocol: Authenticated H2009 lung adenocarcinoma cell lines were obtained from ATCC, and cultured in RPMI medium supplemented with 10% FBS, 2 mM glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol:
Total RNA was isolated from subconfluent plates using the RNeasy kit (Qiagen, Valencia, CA).
RNA concentration and integrity were determined on an Agilent 2100 Bioanalyzer (Agilent Technologies). Samples were processed for directional RNA-Seq library construction and sequencing at the NGS Core facility of the Perelman School of Medicine, University of Pennsylvania.

treatment_protocol: Cells were transfected with RNAi duplexes for either PKCe or KRAS from Dharmacon (Lafayette, CO) using Lipofectamine RNAi Max (Invitrogen, Carlsbad, CA).

value: subject to KRAS K3RNAi duplex

value: H2009 lung cancer cell line

value: Lung adenocarcinoma


title: iHEC_42


title: KRAS_2_2_AB

description: Cancer cell line obtained from ATCC


title: 53_4 single_cell_mrna_seq


title: pme36_1 24H post-stratification seeds, biological rep4

city: AMIENS

first: Laurent

last: Gutierrez

address: 33 rue Saint Leu

institute: CRRBM-UPJV

description: Gene expression data from Arabidopsis knockout pme36 line, 24H post-stratification seeds. This is the fourth of the four biological replicates used in this study.

hyb_protocol: Hybridization was performed on Gene Atlas array strips (Arabidopsis Gene 1,1 ST Array strip) at 48°C for 18 hours on the Affymetrix GeneAtlas Hybridization Station.

scan_protocol: Strips were scanned using the Gene Atlas imaging station.

data_processing:
Data were analyzed using TAC 4.0 software (Affymetrix) to process .CELL files with default settings.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = AraGene-1_1-st
program-name = Expression Console
program-version = 1.4.0.38

organism: Arabidopsis thaliana

source_name: mutant 24H post-stratification seeds

label_protocol: Labeling was performed according to the GeneChip WTPLUS Reagent kit protocol

growth_protocol: Stratified Arabidopsis seeds were grown in Pétri dishes containing Duchefa liquid medium and incubated at 21°C in the dark during 16H or 24H

extract_protocol: Seeds were frozen and ground at -80°C. Total RNA was extracted using the phenol/chloroform protocol.

treatment_protocol: Arabidopsis wild-type Col0 or pme36-1mutant were used

tag: ecotype background

tag: genotype/variation

value: pme36-1 mutant

value: 24H post-stratification

value: Arabidopsis seeds


title: KRAS_2_3_AB

description: Cancer cell line obtained from ATCC

tag: treatment


title: Col0 24H post-stratification seeds, biological rep4

description: Gene expression data from Arabidopsis Col0 24H post-stratification seeds. This is the fourth of the four biological replicates used in this study.

source_name: WT 24H post-stratification seeds

value: wild type

tag: time point


title: Col0 24H post-stratification seeds, biological rep3

description: Gene expression data from Arabidopsis Col0 24H post-stratification seeds. This is the third of the four biological replicates used in this study.


title: KRAS_1_3_AB

description: Cancer cell line obtained from ATCC

source_name: H2009 cells subject to KRAS K1RNAi duplex

value: subject to KRAS K1RNAi duplex

tag: cell line


title: iHEC_41

value: induced hematopoietic endothelia cells


title: KRAS_1_2_AB

description: Cancer cell line obtained from ATCC


title: pme36_1 24H post-stratification seeds, biological rep1

description: Gene expression data from Arabidopsis knockout pme36 line, 24H post-stratification seeds. This is the first of the four biological replicates used in this study.


title: pme36_1 24H post-stratification seeds, biological rep2

description: Gene expression data from Arabidopsis knockout pme36 line, 24H post-stratification seeds. This is the second of the four biological replicates used in this study.


title: pme36_1 24H post-stratification seeds, biological rep3

description: Gene expression data from Arabidopsis knockout pme36 line, 24H post-stratification seeds. This is the third of the four biological replicates used in this study.


title: 21_1 single_cell_mrna_seq


title: siNC-1


title: 18_2 single_cell_mrna_seq


title: Col0 24H post-stratification seeds, biological rep2

description: Gene expression data from Arabidopsis Col0 24H post-stratification seeds. This is the second of the four biological replicates used in this study.


title: iHEC_40


title: pme36_1 16H post-stratification seeds, biological rep3

description: Gene expression data from Arabidopsis knockout pme36 line, 16H post-stratification seeds. This is the third of the four biological replicates used in this study.

source_name: mutant 16H post-stratification seeds

value: 16H post-stratification


title: pme36_1 16H post-stratification seeds, biological rep4

description: Gene expression data from Arabidopsis knockout pme36 line, 16H post-stratification seeds. This is the fourth of the four biological replicates used in this study.


title: Col0 24H post-stratification seeds, biological rep1

description: Gene expression data from Arabidopsis Col0 24H post-stratification seeds. This is the first of the four biological replicates used in this study.


title: iHEC_38


title: KRAS_1_1_AB

description: Cancer cell line obtained from ATCC


title: pme36_1 16H post-stratification seeds, biological rep1

description: Gene expression data from Arabidopsis knockout pme36 line, 16H post-stratification seeds. This is the first of the four biological replicates used in this study.


title: PKCe_2_1_AB

description: Cancer cell line obtained from ATCC

source_name: H2009 cells subject to PKCe e3RNAi duplex

value: subject to PKCe e3RNAi duplex


title: PKCe_2_2_AB

description: Cancer cell line obtained from ATCC


title: Col0 16H post-stratification seeds, biological rep4

description: Gene expression data from Arabidopsis Col0 16H post-stratification seeds. This is the fourth of the four biological replicates used in this study.

source_name: WT 16H post-stratification seeds


title: 12_3 single_cell_mrna_seq


title: iHEC_36


title: 64-3 single_cell_mrna_seq


title: PKCe_2_3_AB

description: Cancer cell line obtained from ATCC


title: 67-2 single_cell_mrna_seq


title: iHEC_37


title: 7-1 single_cell_mrna_seq


title: iHEC_35


title: PKCe_1_2_AB

description: Cancer cell line obtained from ATCC

source_name: H2009 cells subject to PKCe e1RNAi duplex

value: subject to PKCe e1RNAi duplex


title: PKCe_1_3_AB

description: Cancer cell line obtained from ATCC


title: Col0 16H post-stratification seeds, biological rep3

description: Gene expression data from Arabidopsis Col0 16H post-stratification seeds. This is the third of the four biological replicates used in this study.


title: 59-1 single_cell_mrna_seq


title: iHEC_39


title: PKCe_1_1_AB

description: Cancer cell line obtained from ATCC


title: 61-4 single_cell_mrna_seq


title: iHEC_34


title: pme36_1 16H post-stratification seeds, biological rep2

description: Gene expression data from Arabidopsis knockout pme36 line, 16H post-stratification seeds. This is the second of the four biological replicates used in this study.


title: NovoVA_RppH_Minus_Rep3

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

description: Novosphingobium aromaticivorans Transcription Start Site sequencing sample grown in glucose plus vanillic acid media. RppH Minus. Biological repliate 3

data_processing:
The resulting FASTQ files are split using the index barcode sequences to separate the sequences for the RppH- and RppH+ samples using fastx_barcode_splitter.pl version 0.0.13.2 (www.hannonlab.cshl.edu/fastx_toolkit).
The sequences are then trimmed to remove any remaining adapter-derived bases using Trimmomatic version 0.3 (HEADCROP of 6, MINLEN of 25).
The trimmed sequence reads are aligned to the N. aromaticivorans genome (GCF_000013325.1, Assembly ASM1332v1) using Bowtie2 version 2.3.5.1, allowing for one mismatch. The aligned Bowtie2 file is then further processed with Picard tools version 2.10.0 (https://broadinstitute.github.io/picard/) and samtools.
The bedtools version 2.27.0 genomeCov command (https://bedtools.readthedocs.io/en/latest/) is used to map genomic locations that corresponds to the position of the first base in each aligned read, which is defined as the transcription start site. A pseudocount of 1 was added to all TSS read values to prevent dividing by zero and edgeR version 3.10 was used to identify locations with a statistically significant increase in read abundance in the RppH+ strain compared to the RppH- strain.
Locations with a significant increase in read count in the RppH+ sample (FDR ≤ 0.05) were retained and TSSs were associated with genes downstream within 350 bp of the translation start site.
Genome_build: GCF_000013325.1, Assembly ASM1332v1
Supplementary_files_format_and_content: Bedtools GenomeCov mapped read value to each location in the genome; TSS locations

organism: Novosphingobium aromaticivorans

growth_protocol: Three replicates each of N. aromaticivorans cultures grown on glucose and vanillic acid or glucose alone were inoculated from an overnight culture containing glucose and grown at 30°C. Cultures were grown overnight, then fresh media was added, and cells were harvested in exponential phase during aerobic conditions at 30°C.

extract_protocol:
RNA was isolated using a hot phenol method
The isolated RNA was split into two equal groups and one group was treated with the enzyme RppH (NEB, M0356S) at 37°C for 2 hours to remove the outer two phosphate groups from the 5ʹ end of the non-processed RNA species (RppH+ sample). The other group is untreated (no incubation with RppH) and thus the non-processed RNA species retain a tri-phosphate at the 5ʹ end of these molecules (RppH- sample). Both groups are treated with NaIO4 for 1.5 hours at 4°C in the dark to inactivate the 3ʹ end of the RNA transcripts and reduce the production of side products during the subsequent ligation of amplification primers. The sequencing adapter with desired index barcode sequence is ligated to the 5ʹ end of RNA species with a single phosphate group. Note that RNA species with tri-phosphate groups at the 5ʹ end of the RNA are not substrates for ligation and thus will form a product with this sequencing adapter. The ligated RNA is purified using SPRI beads (Beckman, B23317), eluted in water, and quantitated using a NanoDrop 2000. Both the RppH+ and RppH- samples are subjected to rRNA depletion using the RiboZero kit (Epicentre, MRZB12424) following standard protocols and then reverse transcribed using a random primer attached to the second Illumina sequencing adapter following manufacturer’s recommendations. PCR is used to amplify cDNA species in both the RppH- and RppH+ samples that contain both Illumina sequencing adapters using a KAPA Hi-Fi PCR-read mix (KAPA Biosystems KK2601) following manufacturer’s protocol. The PCR products are cleaned using SPRI beads twice and resuspended in a final volume of 20 µL. The TSS-seq library is quantified using a 2100 Bioanalyzer (Agilent) and identifying fragments ~130 bp.

value: RppH-

tag: growth condition

value: glucose plus vanillic acid

tag: growth phase

value: exponential


title: iHEC_33


title: 56-2 single_cell_mrna_seq


title: Col0 16H post-stratification seeds, biological rep2

description: Gene expression data from Arabidopsis Col0 16H post-stratification seeds. This is the second of the four biological replicates used in this study.


title: Col0 16H post-stratification seeds, biological rep1

description: Gene expression data from Arabidopsis Col0 16H post-stratification seeds. This is the first of the four biological replicates used in this study.


title: NovoVA_RppH_Minus_Rep2

description: Novosphingobium aromaticivorans Transcription Start Site sequencing sample grown in glucose plus vanillic acid media. RppH Minus. Biological repliate 2


title: iHEC_31


title: SCR Cat+

city: Kahoku

first: Eri

last: Kubo

state: Ishikawa

address: 1-1 Daigaku, Uchinada

department: Ophthalmology

institute: Kanazawa Medical University

description: Gene expression data from 5-week-old cataractous (Cat+) SCR with Lss mutation

hyb_protocol: Following fragmentation, 10.0 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Rat gene 2.0 ST array . GeneChips were washed and stained in theGene Chip® Fluidics Station 450.

scan_protocol: Air-dried slides were scanned with a GeneChip® Scanner 3000 7G.

data_processing: Scanned images were analyzed with Ausing GeneSpring software package version 14.9 (Agilent)..

organism: Rattus norvegicus

source_name: Rat LEC

label_protocol: Biotinylated cRNA were prepared using GeneChip™ WT Pico Reagent Kit according to the manufactured protocol

growth_protocol: Lens epithelial cells from 5 weeks-old SCR Cat- and Cat+

extract_protocol: Lens capsules with LECs were removed from all eyes. Total RNA from each LEC sample obtained from SCR was extracted using the miRNeasy Micro Kit (Qiagen, Valencia, CA) following the manufacturer's protocol.

treatment_protocol: All rats were provided ad libitum access to regular or experimental chow. The rats were divided into two groups, i.e., control (Cat-) and cataractous (Cat+). Cat+ and Cat- SCRs were distinguished via PCR using genomic DNA isolated from the tails of 4-week-old rats.

tag: sample type

value: with cataract at 5W

value: LECs

tag: age


title: 53-3 single_cell_mrna_seq

source_name: microglia


title: iHEC_32


title: Parental_2_AB

description: Cancer cell line obtained from ATCC

source_name: H2009 parental cells

value: parental cells


title: iHEC_30


title: 50-4 single_cell_mrna_seq


title: NovoVA_RppH_Plus_Rep3

description: Novosphingobium aromaticivorans Transcription Start Site sequencing sample grown in glucose plus vanillic acid media. RppH Plus. Biological repliate 3

value: RppH+


title: NovoVA_RppH_Plus_Rep2

description: Novosphingobium aromaticivorans Transcription Start Site sequencing sample grown in glucose plus vanillic acid media. RppH Plus. Biological repliate 2


title: 18-1 single_cell_mrna_seq


title: iHEC_29


title: NovoVA_RppH_Plus_Rep1

description: Novosphingobium aromaticivorans Transcription Start Site sequencing sample grown in glucose plus vanillic acid media. RppH Plus. Biological repliate 1


title: NTC_2_AB

description: Cancer cell line obtained from ATCC

source_name: H2009 non-target control (NTC) RNAi duplex

value: non-target control (NTC) RNAi duplex

value: H2009 lung cancer cell line

value: Lung adenocarcinoma


title: 2-4 single_cell_mrna_seq

source_name: doubleneg


title: 12-2 single_cell_mrna_seq


title: NTC_3_AB

description: Cancer cell line obtained from ATCC


title: NTC_1_AB

description: Cancer cell line obtained from ATCC


title: SCR Cat-

description: Gene expression data from f5-week-old  non-cataractous (Cat-) SCRs without Lss mutation as control

value: without cataract at 5W


title: NovoGlu_RppH_Minus_Rep3

description: Novosphingobium aromaticivorans Transcription Start Site sequencing sample grown in glucose media. RppH Minus. Biological repliate 3

value: glucose


title: NovoVA_RppH_Minus_Rep1

description: Novosphingobium aromaticivorans Transcription Start Site sequencing sample grown in glucose plus vanillic acid media. RppH Minus. Biological repliate 1


title: iHEC_27

source_name: induced hematopoietic endothelia cells


title: Parental_1_AB

description: Cancer cell line obtained from ATCC


title: NovoGlu_RppH_Minus_Rep2

description: Novosphingobium aromaticivorans Transcription Start Site sequencing sample grown in glucose media. RppH Minus. Biological repliate 2


title: EPN_909

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

data_processing:
UMI count matrices were generated using the 10X Genomics Cell Ranger (3.0.1) pipeline with default parameters.
The Seurat package in R was then used to aggregate the matrices, which were further filtered to exclude cells not passing the following QC measures: at least 200 genes detected (UMI > 0), fewer than 30% of UMIs derived from mitochondia, and fewer than 70,000 UMIs (to exclude putative doublets). . Genes were also excluded if they were not expressed in at least 5 cells (UMI count > 0).
Next, we applied Harmony alignment to correct for inter-sample variation due to experimental or sequencing batch effects.
After alignment, the harmony reduction used for UMAP projection and graph based clustering.
Genome_build: GRCh38
Supplementary_files_format_and_content: Count matrix with UMI counts per gene per cell. Cell_metadata.tsv contains information about each cell in the count matrix.

source_name: Ependymoma

extract_protocol:
Surgical material was collected at our institution at the time of surgery with consent (COMIRB 95-500) and processed identically. Samples were rapidly dissociated into single cells using a mechanical process as described previously, viably cryopreserved and banked at <80C for later use. Samples were thawed in 2 batches and flow sorted (Astrios EQ) to obtain viable single cells based on propidium iodide (PI) exclusion. Cells were processed using the 10x chromium platform to generate single cell RNA-Seq libraries, which were sequenced on the Illumina HiSeq or NovaSeq.
10x Genomics 3' end library kit (v2)

value: Ependymoma

tag: subtype

value: ST-RELA


title: EPN_870


title: NovoGlu_RppH_Minus_Rep1

description: Novosphingobium aromaticivorans Transcription Start Site sequencing sample grown in glucose media. RppH Minus. Biological repliate 1


title: 61-3 single_cell_mrna_seq


title: 64-2 single_cell_mrna_seq


title: EPN_1101


title: NovoGlu_RppH_Plus_Rep3

description: Novosphingobium aromaticivorans Transcription Start Site sequencing sample grown in glucose media. RppH Plus. Biological repliate 3


title: iHEC_24

tag: cell type

value: induced hematopoietic endothelia cells


title: iHEC_25

tag: strain


title: 58-4 single_cell_mrna_seq

tag: donor/fetus


title: EPN_930


title: iHEC_28


title: iHEC_23


title: NovoGlu_RppH_Plus_Rep1

description: Novosphingobium aromaticivorans Transcription Start Site sequencing sample grown in glucose media. RppH Plus. Biological repliate 1


title: iHEC_22


title: 56-1 single_cell_mrna_seq

tag: gestational week+day


title: 53-2 single_cell_mrna_seq


title: 67-1 single_cell_mrna_seq


title: EPN_928


title: iHEC_21


title: 50-3 single_cell_mrna_seq


title: iHEC_26


title: EPN_911


title: EPN_897


title: iHEC_20


title: EPN_871


title: 47-4 single_cell_mrna_seq


title: NovoGlu_RppH_Plus_Rep2

description: Novosphingobium aromaticivorans Transcription Start Site sequencing sample grown in glucose media. RppH Plus. Biological repliate 2


title: EPN_859


title: 12-1 single_cell_mrna_seq


title: iHEC_18


title: iHEC_17


title: 5-3 single_cell_mrna_seq


title: 5-4 single_cell_mrna_seq


title: EPN_848


title: 5-2 single_cell_mrna_seq


title: iHEC_16


title: EPN_839


title: EPN_1239


title: 5-1 single_cell_mrna_seq


title: iHEC_15


title: iHEC_14


title: 3-2 single_cell_mrna_seq


title: iHEC_13


title: 6-3 single_cell_mrna_seq


title: 6-2 single_cell_mrna_seq


title: iHEC_12


title: bovine endometrial main population (MP) cells_rep 2

city: Nagoya

first: Ryoki

last: Tatebayashi

state: Aichi

address: Furo-cho, Chikusa

department: Graduate school of Bioagricultual Sciences

institute: Nagoya University

data_processing:
DNBSEQ-G400 was used to sequence the libraries.
Sequenced raw reads were processed through Cutadapt ver 2.5 to remove adapter and trim low-quality reads.
Clean reads were aligned to the Bos taurus reference genome (ARS-UCD1.2) using HISAT  v2.1.0.
FPKM (Fragment Per Kilobase of transcript per Million mapped reads) were calculated from the mapping results.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: FPKM value for each sample

organism: Bos taurus

source_name: Endometrial main population cells

extract_protocol:
Total RNA of side and main population cells were extracted by using QIAGEN RNeasy Plus micro kit, according to manifactuar's instruction.
TruSeq Stranded mRNA Library Prep  and MGI Easy Universal Library Conversion Kit  were used to prepare sequencing libraries from extracted total RNA following the manufacturer’s recommendations.

treatment_protocol: Bovine side and main population cells were isolated from endometrial stromal cells by using cell sorters. Bovine uteri were collected from local slaughterhouses and healthy uteri in luteal phase were used for isolation of endometrial cells. The stages of the estrous cycle of the tissues were estimated by the ovarian morphology. Intracarrancular endometrium removed luminal epithelium was minced and incubated with 0.2% collagenase-Dulbecco`s modified eagle’s medium supplemented with 4 mM NaHCO3, 100 U/mL penicillin and 100 μg/mL streptomycin for 1 h at 37℃ with gentle shaking to isolate endometrial stromal cells. Collected cells were stained with 10 µg/mL Hoechst 33342 for 90 min at 37℃ either alone or in combination with 50 µM verapamil, an inhibitor of ABCG2. Propidium Iodide (2 µg/ml, Sigma-Aldrich) was simultaneously added to Hoechst-stained cells in order to exclude dead cells prior to the flow cytometric analysis and sorting. Flow cytometric analysis and cell sorting were performed on a FACS SORP Aria2. Hoechst 33342 was excited at 355 nm, and the fluorescence emission was detected using a 450/50 and 670/LP nm band-pass filters for Hoechst blue and Hoechst red, respectively. After collecting 5× 10e4 events, the SP cells and main population (MP) cells were defined by the ability to pump out Hoechst 33342. SP and MP cells were sorted and stored at -80℃ until RNA extraction.

value: Endometrium

value: main population cells

tag: estrous cycles

value: luteal phase


title: bovine endometrial main population (MP) cells_rep 1

tag: tissue


title: iHEC_11


title: 6-1 single_cell_mrna_seq


title: bovine endometrial side population (SP) cells_rep 3

source_name: Endometrial side population cells

value: side population cells


title: bovine endometrial main population (MP) cells_rep 3


title: bovine endometrial side population (SP) cells_rep 2


title: iHEC_19


title: bovine endometrial side population (SP) cells_rep 1


title: iHEC_10


title: rna.1402

city: Okazaki

first: Kaori

last: Nakazawa

address: Nishigonaka 38, Myodaiji

institute: National Institute for Basic Biology

description: mRNA-seq

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
Genome_build: CriGri_1.0
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

organism: Cricetulus griseus

extract_protocol:
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling) or TruSeq (illumina) (for mRNA-seq)
Ribosome profiling and RNA-seq

tag: genetic background

value: CHO

tag: extracted molecule

value: total RNA

value: Truseq stranded mRNA library prep


title: iHEC_9


title: 1-4 single_cell_mrna_seq


title: 1-2 single_cell_mrna_seq


title: 1-1 single_cell_mrna_seq


title: iHEC_7


title: rna.1401

description: mRNA-seq


title: rna.cont2

description: mRNA-seq

value: WT


title: 2018-44_atac

extract_protocol: After cell lysis, ATAC-sequencing libraries were generated according to the manufacturer’s protocol of the Nextera DNA Sample Preparation Kit (Illumina, FC-121-1030). Per 80,000 cells, 50 µl tagmentation mix was added. Samples were sequenced on an Illumina NextSeq 500 using 75 bp paired-end reads..


title: iHEC_8


title: iHEC_6


title: rna.cont1

description: mRNA-seq


title: ribo.1402

description: Ribosome Profiling

value: Rnase I footprinting, ribosome pelleting, RNA extraction


title: iHEC_4


title: 2018-43_atac


title: ribo.1401

description: Ribosome Profiling


title: iHEC_5


title: 2018-37_atac


title: siZIP7-6-1

source_name: triple negative breast cancer

value: breast

value: triple negative breast cancer

value: ZIP7 siRNA_2


title: 2018-42_atac


title: 1-3 single_cell_mrna_seq


title: ribo.cont2

description: Ribosome Profiling


title: ribo.cont1

description: Ribosome Profiling


title: iHEC_2


title: iHEC_3


title: iHEC_1


title: iR-iHEC-4-8

source_name: induced endothelia hematopoietic cells

growth_protocol: Expression of defined factors in ESC/iPSC led to the production of an hematopoietic cell type

treatment_protocol: The single HCs were sorted for RNAseq analysis.

value: induced endothelia hematopoietic cells


title: 2018-36_atac


title: TM5_2_24_2_SynAnt49_4_µg _ml-1

city: Dresden

first: Thorsten

last: Mascher

address: Zellescherweg 20b

institute: TU Dresden

data_processing:
reverse complement of fastq files with fastx_reverse_complement (version: FASTX Toolkit 0.0.14)
mapping with bowtie2 (cmd: bowtie2 --mm --very-sensitive; version: 2.3.4.1)
filter for mapped reads and convert to sorted bam (cmd: samtools view -F 4 -Shb {input} | samtools sort -o {output.bam}; Version: 1.8)
counting features with FeatureCounts (cmd: featureCounts -s 1 -t 'gene' -g 'ID' -a annotation.gff; version: subread=1.6.1)
DESeq2 normalized counts and differential gene expression (version: bioconductor-deseq2=1.18.1, R version 3.4)
read counts and normalized read counts were pooled for this analysis; consiting of TM5_2_05_1-3 (non-induced), TM5_2_23_1-3 (AmpB treatnent), TM5_2_24_1-3 (BDTL049 treatment) and TM5_2_25_1-3 (Streptomyces supernatatns); AmpB RNA seq data can be retrieved under the GEO accession: GSE148903
Genome_build: Assembly ASM904v1 (RefSeq: GCF_000009045.1); Annotation based on Nicolas P et al., 2012 (https://www.ncbi.nlm.nih.gov/pubmed/22383849) supplementary table S5

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: whole cells_SynAnt49_4_µg _ml-1

growth_protocol: Overnight cultures of B. subtilis W168 (Nicolas et al., 2012) were prepared in LB (Sigma L3522) and incubated at 37°C, 220rpm. On the next day, 10 ml day culture of LB (Sigma L3522) was inoculated 1:100 and grown till OD600 = 0.4. Subsequently, a second day culture of 200 ml LB (Sigma L3522) was started to an OD600 = 0.1. Once this second day culture reached OD600 = 0.5, cells were split into 25 ml aliquots and either exposed to SynAnt49 (4  µg ml-1, final concertation) or remained untreated for 10 min. After that, cells were directly placed onto ice and centrifuged at 4° C and 8000 rpm for 3 min. The falcons containing the cell pellets were then frozen in liquid nitrogen and kept at -80 °C.

extract_protocol:
B. subtilis cells were disrupted using a micro-dismembrator. Total RNA isolation was performed with a phenol-chloroform isoamyl-alcohol (25:24:1, pH 5.5) extraction method.
rRNA was subtracted from the samples with the Illumina Ribo-Zero rRNA removal Kit (Bacteria) according to manufacturer instructions. The cDNA library was prepared using the NEB Ultra directional RNA library prep kit for Illumina according to instructions and sequencing was performed on an Illumina HiSeq3000 system.

treatment_protocol: Triplicates of non-induced (TM5_2_05_1 - TM5_2_05_3) and triplicates of SynAnt49 (4 µg ml-1) induced (TM5_2_24_1 - TM5_2_24_3) samples

tag: genotype

value: trp+

value: logaritmic phase

value: SynAnt49 (4 µg ml-1) induced


title: 2018-33_atac


title: TM5_2_24_1_SynAnt49_4_µg _ml-1

tag: treatment


title: iR-iHEC-4-7


title: iR-iHEC-4-6


title: 2018-32_atac


title: TM5_2_05_3_no_treatment [re-analysis]

description:
3549_BW_run508_TACGCAGG_S131_L005
3549_BW_run513_TACGCAGG_S42_L007

source_name: whole cells_no treatment


title: TM5_2_05_2_no_treatment [re-analysis]

description:
3549_BV_run508_TTCTCCGA_S130_L005
3549_BV_run513_TTCTCCGA_S41_L007


title: iR-iHEC-4-1


title: iR-iHEC-4-3


title: iR-iHEC-4-2


title: TM5_2_24_3_SynAnt49_4_µg _ml-1


title: iR-iHEC-4-13


title: 2018-34_atac


title: iR-iHEC-4-14


title: iR-iHEC-4-11


title: iR-iHEC-4-4


title: iR-iHEC-3-9


title: iR-iHEC-4-12


title: iR-iHEC-4-10


title: lin-40(yth27) EV replicate 1

city: Beijing

first: Ye

last: Tian

address: No.1 West Beichen Road,Chaoyang District

institute: Institute of genetics and developmental biology

data_processing:
Illumina HiSeq xten reads were trimmed of adapter sequences and filtered for read that passed quality filtering
Then clean reads were separately aligned to reference genome with orientation mode using TopHat (http://tophat.cbcb.umd.edu/, version2.0.0) software
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/)  was used to quantify gene abundances.
Genome_build: Wormbase WS273
Supplementary_files_format_and_content: tab-delimited .txt file includes raw counts associated with each transcript

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Worms were grown at 20ºC

extract_protocol:
Total RNA was extracted from the worms using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using RQ1 RNase-Free DNase (Promega). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >2μg) was used to construct sequencing library.
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina).  Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 200–300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten (2 × 150bp read length).

treatment_protocol: N2 and lin-40(yth27) animals were grown from hatch at 20ºC on either empty vector (EV) or EV+cco-1 RNAi bacteria and collected by washing with M9 at the L4 stage, followed by snap frozen in liquid nitrogen.

tag: developmental stage

tag: RNAi treatment

value: empty vector(EV)

value: whole worm lysate


title: lin-40(yth27) EV replicate 3


title: lin-40(yth27) cco-1 replicate 2

value: cco-1 RNAi


title: lin-40(yth27) cco-1 replicate 3


title: N2 cco-1 replicate 3

value: control (N2)


title: lin-40(yth27) cco-1 replicate 1


title: lin-40(yth27) EV replicate 2


title: N2 cco-1 replicate 2


title: TM5_2_05_1_no_treatment [re-analysis]

description:
3549_BU_run508_ACGTAGCG_S129_L005
3549_BU_run513_ACGTAGCG_S40_L007


title: N2 EV replicate 3


title: △Ioc3_3

data_processing:
Fragments were mapped to the yeast  reference genome sacCer3 using TopHat V2.0.10, Bowtie V2.0 and R V3.1.0. Differential gene expression analysis was performed using edgeR 3.6.2, limma 3.20.4 and htseq-  count V0.6.0.
Supplementary_files_format_and_content: Excel file containing edgeR Count Per Million (cpm) data

extract_protocol:
Total RNA was extracted using the hot acid phenol method (Collart and  Oliviero, 2001) . Samples were extracted with phenol/chloroform, precipitated with ethanol and  resuspended in 50 µl of diethylpyrocarbonate-treated water.
Libraries were prepared using standard Illumina protocols

tag: strain background

tag: genotype/variation

tag: epitop tag

value: FLAG


title: iR-iHEC-3-5


title: iR-iHEC-3-8


title: iR-iHEC-3-6


title: N2 EV replicate 2


title: 48 hours post fertilization embryos

city: Providence

first: nathalie

last: oulhen

state: RI

address: 185 meeting street

institute: Brown university

description: single cell mRNA

data_processing:
The Cell Ranger Single Cell Software Suite 3.0.2 was used to perform single cells demultiplexing and UMI counting.The custom transcriptome reference was generated from assembly Spur_4.2 using CellRanger. Cells that have at least 400 or at most 2,500 genes detected were included in the downstream analysis using Seurat 3.1.4. The union of the top 2,000 highest dispersion genes from the compared datasets were selected for the alignment. T‐SNE projection and clustering analysis (dims = 1:15 and resolution = 0.5) were performed using Seurat. Markers were found using FindConservedMarkers and FindMarkers functions.
Genome_build: Spur_4.2
Supplementary_files_format_and_content: Seurat Object (RDS), Cell Ranger output files

organism: Strongylocentrotus purpuratus

source_name: 48 hours post fertilization

extract_protocol: The single‐cell RNA‐seq protocol was performed using the ChromiumTM Single Cell 3′ reagent kit v3 chemistry and cells were loaded on a 10x Chromium Controller (10× Genomics, Pleasanton, CA). Libraries were sequenced on Illumina HiSeq with the  configuration of 2x150 bp paired-end runs.

tag: time

value: 48 hours post fertilization

value: embryos


title: Time 56_PyrkII CLD_Rep 4

city: Baltimore

first: Anne

middle: E.

last: Jedlicka

state: MD

address: 615 N. Wolfe street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins University, School of Public Health

description: Gene Expression Data

hyb_protocol: The eight time course samples were hybridized (along with the manufacturer’s RNA spike-in controls) according to standard protocol to the 8 sectors of an Agilent 8x15K platform microarray (AMADID 037237) with separate microarray slides used for each biological replicate (in triplicate for each treatment condition).

scan_protocol: Arrays were scanned with the Agilent G2600D SureScan microarray scanner using scan protocol AgilentHD_GX_1color. Agilent’s Feature Extraction Software was used to assign grids, provide raw image files per array, and generate QC metric reports from the microarray scan data.

data_processing: Txt files from the Feature Extraction software were imported into the Partek Genomics Suite (v7.0; Partek) for detailed analyses of gene expression. Within Partek, the gProcessedSignal was imported, and the intensity values were normalized to the 75th percentile, lower expressed genes were filtered out using a max cutoff of <=0.5, and log transformation base 2.0 was performed.

organism: Plasmodium falciparum

source_name: PyrkII CLD Nf54 attB parasites,Time 56, Rep 4

label_protocol: From 100 ng of total RNA, Cyanine-3 labeled cRNA was prepared using the Low Input Quick Amp Labeling Kit One-Color (Agilent).

growth_protocol: Blood-stage P. falciparum parasites were cultured in human erythrocytes at 2% hematocrit in CMA (Complete Medium with Albumax) containing RPMI 1640 medium with L-glutamine (USBiological Life Sciences), supplemented with 20mM HEPES, 0.2% sodium bicarbonate, 12.5μg/ml hypoxanthine, 0.5μM R-lipoic acid, 5g/L Albumax II (Life Technologies) and 25μg/mL gentamicin. Cultures were maintained in 25cm2 gassed flasks (94% N2, 3% O2, 3% CO2) and incubated at 37°C.

extract_protocol: For each data point, RNA was extracted from 100 µL of packed RBC culture with Trizol Reagent and the PureLink Mini Kit (Invitrogen/Thermo Fisher Scientific). 1ml Trizol was added to each sample, followed by high-speed disruption in tubes containing Lysing Matrix D (MP Biomedical) in a FastPrep 120 Instrument at speed 6 for 20 seconds. Homogenates were subsequently processed according to the PureLink Mini Kit manufacturer’s (Invitrogen/Thermo Fisher Scientific) protocol, including on-column DNase treatment.

treatment_protocol: The CLD-PyrKII parasite line was synchronized via magnetic purification and used to seed a 50mL culture flask at 1% parasitemia and 2% hematocrit. Six hours post synchronization (mid-schizogeny) 500nM Shield1 was added, representing time 0. Media containing 500nM Shield1 was replaced at 16 hours and every 24 hours thereafter.

value: Blood-stage PyrkII CLD Nf54 attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit in media containing 500nM Shield1

value: Time 56

value: PyrkII CLD

tag: slide id (array batch)

tag: replicate

value: Rep 4


title: 72 hours post fertilization embryos

description: single cell mRNA

source_name: 72 hours post fertilization

value: 72 hours post fertilization


title: 48 hours post fertilization embryos, control MO injected

description: single cell mRNA

source_name: 48 hours post fertilization control MO injected

value: control MO injected


title: 48 hours post fertilization embryos, gcm MO injected

description: single cell mRNA

source_name: 48 hours post fertilization gcm MO injected

value: gcm MO injected


title: Time 48_PyrkII CLD_Rep 4

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 48, Rep 4

value: Time 48


title: iR-iHEC-3-2

state: GuangDong

extract_protocol:
The procedure of RNA extraction and reverse transcription into double-stranded DNA were prepared using Discover-sc WTA Kit V2(Vazyme, N711)
Libraries were prepared according to instruction of TruePrepTM  DNA Library Prep Kit V2 (Vazyme,TD503).

tag: cell type

value: induced endothelia hematopoietic cells

tag: strain


title: Time 32_PyrkII CLD_Rep 4

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 32, Rep 4

value: Time 32


title: delta-pdeL+ctrl rep3

city: Cologne

first: Karin

last: Schnetz

address: Zuelpicher Str. 47a

department: Institute for Genetics

institute: University of Cologne

data_processing:
Galaxy platform was used for all data processing steps (https://usegalaxy.org/)
Sequences were aligned with Bowtie2 (Galaxy version 2.3.4.2) and default settings
Reads mapping to genes were counted with Htseq (Galaxy version 0.9.1) in union mode and a minimum alignment quality of 10 in addition to default settings
Differential expression of genes was tested using DESeq2 (Galaxy version 2.11.40.2) and default settings.
Genome_build: GCA_000005845.2_ASM584v2
Supplementary_files_format_and_content: tab-delimited text files includes measured gene abundance for each sample.

organism: Escherichia coli K-12

source_name: bacterial cells

growth_protocol: For RNA extraction 10 ml of LB medium supplemented with 25 µg/ml kanamycin were inoculated to an OD600 of 0.08 using fresh overnight cultures grown. Cultures were grown at 37°C whilst shaking. At OD600=0.35 (after approximately one hour of growth) isopropyl-β-D-thiogalactopyranosid (IPTG) to 1 mM final concentration for induction. The cultures were grown for additional 15 minutes and 2 ml samples were harvested.

extract_protocol:
Total RNA was extracted from 2 ml of culture using RNAprotect Bacteria Reagent (Qiagen, cat. No 76506) and RNeasy Mini Kit (Qiagen, cat. No 74134) with on column DNase I digestion (Qiagen, cat. No 79254), according to the manufacturer’s instructions (Qiagen, Germany). Enrichment of primary transcripts and depletion of ribosomal RNA was performed by TEX treatment, as described (Borries et. al, 2012 https://doi.org/10.1002/9783527644582.ch7)
Illumina TruSeq RNA Library Kit (without Poly-A selection)

value: BW30270  delta_pdeL


title: Time 24_PyrkII CLD_Rep 4

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 24, Rep 4

value: Time 24


title: Time 40_PyrkII CLD_Rep 4

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 40, Rep 4

value: Time 40


title: Parental_3_AB

description: Cancer cell line obtained from ATCC

source_name: H2009 parental cells

value: parental cells

tag: cell line

value: H2009 lung cancer cell line

value: Lung adenocarcinoma


title: delta-pdeL+PdeL rep3


title: Time 48_PyrkII CLD_Rep 3

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 48, Rep 3

value: Rep 3


title: Time 0_PyrkII CLD_Rep 4

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 0, Rep 4

value: Blood-stage PyrkII CLD Nf54 attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit in media containing 500nM Shield1

value: Time 0


title: iR-iHEC-3-3

source_name: induced endothelia hematopoietic cells


title: N2 cco-1 replicate 1

value: control (N2)

value: cco-1 RNAi

value: whole worm lysate


title: iR-iHEC-3-1


title: N2 EV replicate 1

value: empty vector(EV)


title: Time 08_PyrkII CLD_Rep 4

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 08, Rep 4

value: Time 08

value: PyrkII CLD

value: Rep 4


title: delta-pdeL+PdeLDBD_cIc rep3


title: iR-iHEC-3-4

value: induced endothelia hematopoietic cells


title: delta-pdeL+PdeL rep2

value: BW30270  delta_pdeL


title: iR-iHEC-3-15


title: Time 56_PyrkII CLD_Rep 3

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 56, Rep 3

value: Time 56


title: iR-iHEC-3-13


title: iR-iHEC-3-14


title: wt+ctrl rep3

value: MG1655 rph+


title: wt+ctrl rep2


title: delta-pdeL+PdeLDBD_cIc rep2


title: delta-pdeL+PdeL rep1


title: iR-iHEC-3-12


title: delta-pdeL+ctrl rep2


title: iR-iHEC-2-9


title: iR-iHEC-3-11


title: Time 16_PyrkII CLD_Rep 4

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 16, Rep 4

value: Time 16


title: Time 32_PyrkII CLD_Rep 3

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 32, Rep 3

value: Time 32


title: iR-iHEC-2-8


title: delta-pdeL+PdeLDBD_cIc rep1


title: Time 40_PyrkII CLD_Rep 3

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 40, Rep 3

value: Time 40


title: iR-iHEC-2-6


title: delta-pdeL+ctrl rep1


title: iR-iHEC-2-7


title: wt+ctrl rep1


title: Time 16_PyrkII CLD_Rep 3

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 16, Rep 3

value: Rep 3


title: CU-5

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

description: Nasal

data_processing:
cutadapt
STAR alignment
featureCount, gene-level extraction
Genome_build: hg38
Supplementary_files_format_and_content: tab delimeted format Normalized-log2CPM.csv

source_name: Nasal brush biopsy

extract_protocol:
Invitrogen Purelink RNA Minikit, supplemented with the Proteinase K and Rnase-Free Dnaset (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: nasal epithelial cells

tag: growth conditions

value: cultured epithelia


title: Time 08_PyrkII CLD_Rep 3

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 08, Rep 3

tag: tissue

value: Blood-stage PyrkII CLD Nf54 attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit in media containing 500nM Shield1


title: Time 24_PyrkII CLD_Rep 3

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 24, Rep 3

value: Time 24


title: Time 56_PyrkII CLD_Rep 2

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 56, Rep 2

value: Rep 2


title: Time 48_PyrkII CLD_Rep 2

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 48, Rep 2

value: Time 48


title: Time 40_PyrkII CLD_Rep 2

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 40, Rep 2


title: Time 0_PyrkII CLD_Rep 3

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 0, Rep 3

value: Time 0


title: CU-4

description: Nasal