title: L284: 3C-seq of WT cells after 48 h growth in MP5 liquid medium at 30°C - replicate 2

data_processing:
Library strategy: 3C-seq
STAR software was used for mapping RNA-seq to the reference genome (genome-build-accession NCBI_Assembly: GCF_001267885.1) containing only one terminal inverted repeat (TIR), to avoid any biases associated to multiple mapping within the duplicated extremities of the genome (since the two TIR sequences are indiscernible).
FeatureCounts program was used to quantify reads in sense and antisense orientation generated from RNA-sequencing technology in terms of “Gene” feature according to S. ambofaciens ATCC 23877 most recent annotation (GCF_001267885.1_ASM126788v1_genomic.gff – released on the 06/15/2020).
3C-seq libraries were proccessed using the 3C-seq pipeline available at (https://github.com/koszullab/).
Removal of PCR duplicates based on the 20 first bp of the read containing a 6 nt random tag (home made script).
mapping against Streptomyces ambofaciens chromosome (without considering the Terminal Inverted Repeats):  bowtie2 --very-sensitive local
Filtering, Mapping quality=30, no ambiguous reads
Assignment to restriction fragment
Binning at  10kb.
Genome_build: Streptomyces ambofaciens ATCC 23877
Supplementary_files_format_and_content: RNA-seq data in txt format. 791x791 normalized contact matrix in txt format for the 3C-seq data.

extract_protocol:
Spores of S. ambofaciens ATCC 23877 (≈ 4.107) were inoculated in 200 ml of MP5 or YEME liquid medium. In these media, bacterial growth was monitored by opacimetry. At the indicated time point, cells were harvested from 100 ml samples of culture, adjusted to an OD600 nm of about 0.15 (with the appropriate fresh medium) and fixed by adding formaldehyde solution (3 % final concentration). Cells were then incubated under moderate agitation for 30 min at room temperature and 30 min more at 4°C. Glycine (250 mM final concentration) was added, and the bacteria incubated 30 min at 4°C with moderate agitation. Cells were then harvested by centrifugation for 10 min at 4,000 g at 4°C. The cells were gently suspended in 50 ml of PBS 1X and then again harvested by centrifugation for 10 min at 4,000 g at 4°C. This washing step was repeated once before suspending the cells in 1 ml of PBS before final harvesting by 10 min at 4,000 g at 4°C. The dry pellets were stored at -80°C until use.
Frozen pellets of exponentially grown cells were thawed, suspended in 600 µl Tris 10 mM EDTA 0.5 mM (TE) (pH 8) with 4 µl of lysozyme (35 U/µl; Tebu Bio) and incubated at RT for 20 min. For the samples collected after 48h, the pellets were thawed, suspended in TE (pH 8) with 4 µl of lysozyme (35 U/µl; Tebu Bio) for 45 min and then homogenized with a Bioruptor sonication device (3 cycles of 30 seconds, with a pause of 30 second pause for each). Then, for both 24 h and 48 h samples, SDS was added to the mix (final concentration 0.5%) of cells and incubated for 10 minutes at RT. 500 µl of lysed cells were transferred to a tube containing 4.5 ml of digestion mix (1X NEB 3 buffer, 1% triton X-100) and 100 µl of the lysed cells were transferred to a tube containing 0.9 ml of digestion mix. 800 units of SalI were added to the 5 ml digestion mix. Both tubes were then incubated for 2 h at 37°C and 250 units of SalI were added to the 5 ml tube and further incubated, 2 h at 37°C. To stop the digestion reaction, 4 ml of the digestion mix were immediately centrifuged for 20 min at 20,000 g, and pellets suspended in 4 ml of sterile water. The digested DNA (4 ml in total) was split into 4 aliquots and diluted in 8 ml ligation buffer (1X ligation buffer NEB 3 (without ATP), 1 mM ATP, 0.1 mg/ml BSA, 125 Units of T4 DNA ligase 5 U/µl). Ligation was performed at 16°C for 4 h, followed by incubation overnight at 65°C with 100 µl of proteinase K (20 mg/ml) and 100µl EDTA 500 mM. DNA was then precipitated with an equal volume of 3 M Na-Acetate (pH 5.2) and two volumes of iso-propanol. After one hour at -80°C, DNA was pelleted and suspended in 500 µl 1X TE buffer. The remaining 1ml digestion mix with or without SalI were directly incubated with 100 µl of proteinase K (20 mg/ml) overnight at 65°C. Finally, all the tubes were transferred into 2 ml centrifuge tubes (8 tubes), extracted once with 400 µl phenol-chloroform pH 8.0, precipitated, washed with 1 ml cold ethanol 70% and diluted in 30 µl 1X TE buffer in the presence of RNAse A (1 g/ml). Tubes containing the ligated DNA (3C libraries) were pooled. The efficiency of the 3C preparation was assayed by running aliquots of the 3C-librairies, the digested DNA or the non-digested DNA on 1% agarose gel. Finally the 3C libraries were quantified on the gel using QuantityOne software (BioRad).
Approximately 5 µg of a 3C library was suspended in water (final volume 130 µL) and sheared using a Covaris S220 instrument (Duty cycle 5, Intensity 5, cycles/burst 200, time 60 sec for 4 cycles). The DNA was purified using Qiaquick® PCR purification kit, DNA ends were prepared for adapter ligation following standard protocols (see Cournac 2016).  Custom-made adapters (Marbouty 2015) were ligated overnight at 4°C. Ligase was inactivated by incubating the tubes at 65°C for 20 minutes. To purify DNA fragments ranging in size from 400 to 900 pb, a PippinPrep apparatus (SAGE Science) was used. For each library, one PCR reaction of 12 cycles was performed (using 2 µL of 3C library, 0.2 µM Illumina primers PE1.0 and PE2.0 and xx units of Taq Phusion [Finnzymes]). The PCR product was purified on Qiagen MinElute columns and primers dimers were removed from the 3C library by using AMPure XP beads following manufacturer’s protocol (Beckman Coulter). Finally, libraries were subject to paired-end sequencing on an Illumina sequencer (NextSeq).


title: LBM5: 3C-seq of WT cells after 48 h growth in MP5 liquid medium at 30°C - replicate 1

status: Public on Jul 01 2021

type: SRA

city: Gif-sur-Yvette

first: Stéphanie

middle: Germaine

last: Bury-Moné

address: 1 Avenue de la Terrasse

country: France

institute: Institute for Integrative Biology of the Cell

library_source: genomic

molecule: genomic DNA

organism: Streptomyces ambofaciens ATCC 23877

growth_protocol: Twenty million spores of S. ambofaciens ATCC 23877 were inoculated in 100 ml of media before growth at 30°C in a shaking agitator (220 rpm, INFORS HT multitron standard). Media composition: MP5 medium (7 g/l yeast extract, 20.9 g/l MOPS, 5 g/l NaCl, 1 g/l NaNO3, 36 ml/l glycerol – pH 7.5) , or YEME medium 10.3 % saccharose (3 g/l yeast extract, 5 g/l bactotryptone, 3 g/l malt extract, 10 g/l glucose, 103 g/l saccharose; pH 7.0-7.2)

treatment_protocol: 25 ml (for samples harvested after 24 h growth) or 10 ml of cultures (for other time points) were added to an equal volume of cold ethanol. Cells were then harvested through centrifugation for 15 min at 4,000 g at 4°C, and stored at -20°C.

tag: strain

tag: genotype

value: WT


title: Pooled sera_51130

city: Sydney

first: Antibiotic Resistant Sepsis Pathogens Framework Initiative

last: Bioplatforms Australia

state: NSW

address: Level 4, Building 4WW, Research Park Drive, Macquarie University

country: Australia

institute: Bioplatforms Australia

description: Additional information about the bacterial cultures is available from the Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Initiative website. https://data.bioplatforms.com/organization/about/bpa-sepsis

library_source: transcriptomic

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900622685.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2
Supplementary_files_format_and_content: genome annotations

molecule: total RNA

organism: Streptococcus pyogenes

source_name: Bacteria in growth media

growth_protocol: Complete information about the bacterial cultures is available from the Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Initiative website. https://data.bioplatforms.com/organization/about/bpa-sepsis

extract_protocol: Bacterial rRNA depletion with Illumina Ribo-Zero rRNA Removal Kit (Bacteria) followed by strand RNAseq sample preparation with Illumina TruSeq Stranded mRNA Library Prep Kit

tag: growth media

value: Pooled sera

tag: growth time

value: 2 hrs exposure to sera

tag: growth phase

tag: od600 reading

tag: temperature

tag: bpa identifier

tag: serovar

value: M1T1 clone


title: RPMI_51126

value: RPMI

value: 1.5 hrs

value: Mid log phase


title: L233: 3C-seq of WT cells after 24 h growth in MP5 liquid medium at 30°C - replicate 2


title: Pooled sera_51129


title: RPMI_51125


title: PBS 1 [BH181212-sample-1]

city: Los Angeles

first: Benjamin

middle: Pierre

last: Hurrell

state: CA

address: 1450 Biggy Street

department: MMI

country: USA

institute: University of Southern California

data_processing:
Image analysis and base calling was carried out using RTA 1.13.48.0.  Final file formatting, demultiplexing and fastq generation were carried out using CASAVA v 1.8.2.
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25 nt were excluded from downstream analyses)
Trimmed reads were then mapped to the mouse genome mm10 using STAR (v3.5.3) with default parameter settings
Gencode M20 annotation was used to quantify the aligned reads to genes/transcripts using Partek E/M method.
read counts per gene/transcript in all samples were normalized using Upper Quartile normalization and analyzed for differential expression using Partek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
Genome_build: mm10
Supplementary_files_format_and_content: .txt file with normalized gene counts

organism: Mus musculus

source_name: PBS_sorted ILC2s

extract_protocol:
Total RNA was isolated using MicroRNAeasy (Qiagen, Valencia, California). 10ng of input RNA was used to produce cDNA for downstream library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly isolated ILC2s after 3 i.p. injections of 1µg rm-IL33 were stimulated with rm-IL-2 (10ng/mL) and rm-IL-7 (10ng/mL) at 37°C with rmTNFa (40ng/mL) or PBS control for 48 hours.

value: BALB/c

tag: age

value: 6 weeks

tag: treatment

value: PBS

tag: tissue

value: lung

tag: cell type

value: sorted ILC2s


title: RPMI_51123


title: genomic DNA from bone metastasis sample 55 [Met.55]

type: genomic

city: UMEÅ

first: Pernilla

last: Wikström

address: Department of Medical biosciences, Buildning 6M, 2nd floor

department: Medical biosciences, Pathology

country: Sweden

institute: Umeå University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation EPIC arrays using standard Illumina protocol

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

data_processing:
Beta values were obtained using GenomeStudio (Illumina). Beta values were normalized using BMIQ. Multimapping CpGs, CpGs close to SNPs, meQTLs, CpGs with Detection P-values > 0.05 in any sample, CpGs with standard deviation < 0.05 and CpGs outside promoter region (TSS1500, TSS200, 5’UTR), were filtered.
matrix processed value definition: BMIQ normalized and filtered Average Beta
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

organism: Homo sapiens

source_name: bone metastasis sample

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from frozen tissue using the AllPrep DNA/RNA/Protein method (Qiagen, Hilden, Germany), according to standard instructions.

tag: disease stage

value: Castration-resistant prostate cancer

tag: epithelial fraction

tag: meta-c class

value: MetB

tag: ar gene amplification

value: No

tag: ar activity score

tag: proliferation score

tag: mca class

value: Negative


title: Exp2 72h UL87HF Flavo 6h dTAG Pro-seq

city: Iowa City

first: Jeffery

middle: L

last: Meier

state: IA

address: SW34 GH, Department of Internal Medicine, University of Iowa. 200 Hawkins Drive

department: Departments of Internal Medicine and Epidemiology

institute: University of Iowa and Iowa City Veterans Affairs Health Care System

data_processing:
Adapter trimming using trim_galore 0.4.4.
Alignment of trimmed reads to concatenated hg38 (human), FJ616285.1 or KF297339.1 (Towne and TB40, respectively), and, for samples that included moth spike-in cells, JQCY02.1 (spodoptera) genome assemblies.
Deduplication of mapped reads according to unique molecular identifiers using dedup (https://github.com/P-TEFb/dedup).
Reads were parsed out based on the genome to which they aligned.
Bedgraphs were generated using bedTools genomecov 2.26 and Data were normalized by library size and spike-in reads accorind to Ball et. al. (2019, PMID: 30743000).
Bigwigs were generated using kentUtils.
Custom UCSC track hubs were set up for Towne and TB40/E data.
For analysis of host transcription effects upon depletion of UL87LTF or UL79LTF and annotation of gene 5' ends based on PRO-Seq data, we applied a new truQuant algorithm that utilizes our previously published tsrfinder tool. Our application of these tools is described in the manuscript. Source code is avaliable on GitHub at https://github.com/meierjl/truQuant.
Genome_build: hg38 (human), FJ616285.1 (HCMV Towne), KF297339.1 (HCMV TB40/E), JQCY02.1 (Spodoptera).
Supplementary_files_format_and_content: bigwigs contain PRO-Seq pileups, bigwigs for ChIP-Seq samples

source_name: HCMV-infected primary human foreskin fibroblast

growth_protocol: HFF were isolated and cultured as described in the manuscript. Cells were maintained in Minimum Essential Medium and grown to confluence for at least one week before infection. All HFF used for these studies were at passage number ≤ 6.

extract_protocol:
Nuclei isolation was carried out as described in Parida et. al. (2019, PMID: 30755505) and Li et. al. (2020, PMID: 32251483) .
PRO-Seq library preparation to extract and sequence nascent RNAs and ChIP-seq library preparation to extract and sequence is carefully detailed in the manuscript and was carried out as previously described by  Li et. al. (2020, PMID: 32251483), with noted modifications.

treatment_protocol:
Cells were treated with the indicated drugs (dTAG 6h and Flavo 1h) during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

value: HFF

tag: infection

value: HCMV strain Towne BAC

tag: infection duration

value: 72 hours

tag: ltf depletion

value: dTAG 6h and Flavo 1h

tag: fraction

value: nascent RNA


title: RPMI_51127

tag: growth media

value: RPMI

tag: strain

tag: growth time

tag: growth phase

tag: od600 reading

tag: temperature

tag: bpa identifier

value: M1T1 clone


title: Exp2 72h UL87HF Flavo Pro-seq

treatment_protocol:
Cells were treated with Flavo 1h and DMSO 6h during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

tag: cell type

tag: treatment

value: Flavo 1h and DMSO 6h


title: genomic DNA from bone metastasis sample 49 [Met.49]

tag: disease stage

tag: epithelial fraction

tag: meta-c class

tag: ar gene amplification

value: Yes


title: PBS 2 [BH181212-sample-2-repeat]

value: BALB/c

tag: age

value: 6 weeks

tag: tissue


title: Exp2 72h UL87HF Flavo 6h PFA Pro-seq

treatment_protocol:
Cells were treated with the indicated drugs (PFA 6h and Flavo 1h) during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

tag: infection

tag: infection duration

tag: ltf depletion

value: PFA 6h and Flavo 1h


title: C7-c: RNA-seq of WT cells after 48 h growth in YEME liquid medium at 30°C - replicate 3

description: Remark : Librairy prepared with Total RNA Stranded (reversely stranded) kit => The R1 file corresponds to antisense orientation, and R2 to the sense orientation.

data_processing:
STAR software was used for mapping RNA-seq to the reference genome (genome-build-accession NCBI_Assembly: GCF_001267885.1) containing only one terminal inverted repeat (TIR), to avoid any biases associated to multiple mapping within the duplicated extremities of the genome (since the two TIR sequences are indiscernible).
FeatureCounts program was used to quantify reads in sense and antisense orientation generated from RNA-sequencing technology in terms of “Gene” feature according to S. ambofaciens ATCC 23877 most recent annotation (GCF_001267885.1_ASM126788v1_genomic.gff – released on the 06/15/2020).
3C-seq libraries were proccessed using the 3C-seq pipeline available at (https://github.com/koszullab/).
Removal of PCR duplicates based on the 20 first bp of the read containing a 6 nt random tag (home made script).
mapping against Streptomyces ambofaciens chromosome (without considering the Terminal Inverted Repeats):  bowtie2 --very-sensitive local
Filtering, Mapping quality=30, no ambiguous reads
Assignment to restriction fragment
Binning at  10kb.
Genome_build: Streptomyces ambofaciens ATCC 23877
Supplementary_files_format_and_content: RNA-seq data in txt format. 791x791 normalized contact matrix in txt format for the 3C-seq data.

extract_protocol:
Pellets were washed with 1 ml of DEPC water, centrifuged for 5 min at 16,000 g at 4°C, and homogenized with glass beads (≤ 106 µm; G4649, SIGMA) in 350 µl of lysis buffer (RNeasy Plus Mini Kit, QIAGEN) supplemented with 10 µl/ml β-mercaptoethanol. Samples were processed 3 times for 45 sec each in FastPrep-24TM 5G instrument (MP Biomedicals) at setting 6 with 1 min cooling between the stages. After centrifugation for 10 min at 16,000 g at 4°C, total RNAs were isolated from the supernatants using RNeasy Plus Mini Kit (QIAGEN) and gDNA Eliminator columns, following manufacturer’s recommendations. To remove genomic DNA, RNA samples were incubated from 30 min at 37°C with 20 U of RNase-free DNase I (Roche) in a final reaction volume of 30 µl. RNA were then cleaned up using the RNeasy Mini Kit (QIAGEN), following manufacturer’s recommendations. The absence of DNA in the preparations was checked by PCR on an aliquot. RNA samples were quantified using QubitTM RNA HS Assay kit (ThermoFischer Scientific), following manufacturer’s recommendations.  Total RNA quality was assessed on an Agilent Bioanalyzer 2100, using RNA 6000 pico kit (Agilent Technologies). 500 ng of total RNA were treated with DNAse (Baseline Zero DNAse, Epicentre) prior to ribosomal RNA depletion using the RiboZero bacteria magnetic Kit from Illumina according to the manufacturer recommendations. After the Ribo-Zero step, the samples were checked on the Agilent Bioanalyzer for proper rRNA depletion.
Libraries were pooled in equimolar proportions and sequenced (Paired-end 2x43 bp) on an Illumina NextSeq500 instrument, using a NextSeq 500 High Output 75 cycles kit. Demultiplexing has been done (bcl2fastq.gz2 V2.2.18.12) and adapters (adapter_3p_R1: AGATCGGAAGAGCACACGTCTGAACT; adapter_3p_R2: AGATCGGAAGAGCGTCGTGTAGGGA) were trimmed with Cutadapt1.15, only reads longer than 10 bp were kept.

tag: strain

tag: genotype

value: WT


title: Pooled sera_51157

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900619605.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2
Supplementary_files_format_and_content: genome annotations

tag: growth media

value: Pooled sera

tag: growth time

value: 2 hrs exposure to sera

tag: growth phase

tag: serovar


title: genomic DNA from bone metastasis sample 48 [Met.48]

value: Castration-resistant prostate cancer

value: MetA

tag: ar activity score

tag: proliferation score

tag: mca class


title: C7-b: RNA-seq of WT cells after 48 h growth in YEME liquid medium at 30°C - replicate 2


title: Pooled sera_51156

tag: od600 reading

tag: temperature

tag: bpa identifier


title: genomic DNA from bone metastasis sample 54 [Met.54]

tag: disease stage

tag: epithelial fraction

tag: meta-c class

tag: ar gene amplification

value: Positive


title: Exp2 72h UL87HF Pro-seq

treatment_protocol:
Cells were treated with DMSO 6h during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

tag: cell type

value: HFF

tag: infection

value: HCMV strain Towne BAC

tag: infection duration

tag: ltf depletion

tag: treatment

value: DMSO 6h

tag: fraction


title: genomic DNA from bone metastasis sample 51 [Met.51]

value: MetB

value: Negative


title: genomic DNA from bone metastasis sample 53 [Met.53]


title: Pooled sera_51155

tag: growth media

tag: strain

tag: growth time

tag: growth phase

tag: serovar

value: M1T1 clone


title: C7-a: RNA-seq of WT cells after 48 h growth in YEME liquid medium at 30°C - replicate 1

tag: genotype


title: LBM1: 3C-seq of WT cells after 24 h growth in YEME liquid medium at 30°C - replicate 2


title: L216: 3C-seq of WT cells after 24 h growth in YEME liquid medium at 30°C - replicate 1


title: genomic DNA from bone metastasis sample 46 [Met.46]

tag: ar activity score

tag: proliferation score

tag: mca class


title: genomic DNA from bone metastasis sample 50 [Met.50]

tag: disease stage

tag: epithelial fraction

tag: meta-c class


title: Exp2 72h UL87HF Flavo 6h dTAG 6h PFA Pro-seq

treatment_protocol:
Cells were treated with the indicated drugs (dTAG 6h, Flavo 1h, and PFA 6h) during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

tag: cell type

tag: infection

value: 72 hours

value: dTAG 6h, Flavo 1h, and PFA 6h

value: nascent RNA


title: Pooled sera_51153

tag: od600 reading

tag: temperature

tag: bpa identifier


title: L263: 3C-seq of WT cells after 24 h growth in MP5 liquid medium at 30°C - replicate 1


title: 3C-seq of WT cells after 24 h growth in YEME liquid medium at 30°C in the presence of congocidine 1µg/ml

source_name: WT cells

extract_protocol:
Spores of S. ambofaciens ATCC 23877 (≈ 4.107) were inoculated in 200 ml of MP5 or YEME liquid medium. In these media, bacterial growth was monitored by opacimetry. At the indicated time point, cells were harvested from 100 ml samples of culture, adjusted to an OD600 nm of about 0.15 (with the appropriate fresh medium) and fixed by adding formaldehyde solution (3 % final concentration). Cells were then incubated under moderate agitation for 30 min at room temperature and 30 min more at 4°C. Glycine (250 mM final concentration) was added, and the bacteria incubated 30 min at 4°C with moderate agitation. Cells were then harvested by centrifugation for 10 min at 4,000 g at 4°C. The cells were gently suspended in 50 ml of PBS 1X and then again harvested by centrifugation for 10 min at 4,000 g at 4°C. This washing step was repeated once before suspending the cells in 1 ml of PBS before final harvesting by 10 min at 4,000 g at 4°C. The dry pellets were stored at -80°C until use.   Frozen pellets of exponentially grown cells were thawed, suspended in 600 µl Tris 10 mM EDTA 0.5 mM (TE) (pH 8) with 4 µl of lysozyme (35 U/µl; Tebu Bio) and incubated at RT for 20 min. For the samples collected after 48h, the pellets were thawed, suspended in TE (pH 8) with 4 µl of lysozyme (35 U/µl; Tebu Bio) for 45 min and then homogenized with a Bioruptor sonication device (3 cycles of 30 seconds, with a pause of 30 second pause for each). Then, for both 24 h and 48 h samples, SDS was added to the mix (final concentration 0.5%) of cells and incubated for 10 minutes at RT. 500 µl of lysed cells were transferred to a tube containing 4.5 ml of digestion mix (1X NEB 3 buffer, 1% triton X-100) and 100 µl of the lysed cells were transferred to a tube containing 0.9 ml of digestion mix. 800 units of SalI were added to the 5 ml digestion mix. Both tubes were then incubated for 2 h at 37°C and 250 units of SalI were added to the 5 ml tube and further incubated, 2 h at 37°C. To stop the digestion reaction, 4 ml of the digestion mix were immediately centrifuged for 20 min at 20,000 g, and pellets suspended in 4 ml of sterile water. The digested DNA (4 ml in total) was split into 4 aliquots and diluted in 8 ml ligation buffer (1X ligation buffer NEB 3 (without ATP), 1 mM ATP, 0.1 mg/ml BSA, 125 Units of T4 DNA ligase 5 U/µl). Ligation was performed at 16°C for 4 h, followed by incubation overnight at 65°C with 100 µl of proteinase K (20 mg/ml) and 100µl EDTA 500 mM. DNA was then precipitated with an equal volume of 3 M Na-Acetate (pH 5.2) and two volumes of iso-propanol. After one hour at -80°C, DNA was pelleted and suspended in 500 µl 1X TE buffer. The remaining 1ml digestion mix with or without SalI were directly incubated with 100 µl of proteinase K (20 mg/ml) overnight at 65°C. Finally, all the tubes were transferred into 2 ml centrifuge tubes (8 tubes), extracted once with 400 µl phenol-chloroform pH 8.0, precipitated, washed with 1 ml cold ethanol 70% and diluted in 30 µl 1X TE buffer in the presence of RNAse A (1 g/ml). Tubes containing the ligated DNA (3C libraries) were pooled. The efficiency of the 3C preparation was assayed by running aliquots of the 3C-librairies, the digested DNA or the non-digested DNA on 1% agarose gel. Finally the 3C libraries were quantified on the gel using QuantityOne software (BioRad).
Approximately 5 µg of a 3C library was suspended in water (final volume 130 µL) and sheared using a Covaris S220 instrument (Duty cycle 5, Intensity 5, cycles/burst 200, time 60 sec for 4 cycles). The DNA was purified using Qiaquick® PCR purification kit, DNA ends were prepared for adapter ligation following standard protocols (see Cournac 2016).  Custom-made adapters (Marbouty 2015) were ligated overnight at 4°C. Ligase was inactivated by incubating the tubes at 65°C for 20 minutes. To purify DNA fragments ranging in size from 400 to 900 pb, a PippinPrep apparatus (SAGE Science) was used. For each library, one PCR reaction of 12 cycles was performed (using 2 µL of 3C library, 0.2 µM Illumina primers PE1.0 and PE2.0 and xx units of Taq Phusion [Finnzymes]). The PCR product was purified on Qiagen MinElute columns and primers dimers were removed from the 3C library by using AMPure XP beads following manufacturer’s protocol (Beckman Coulter). Finally, libraries were subject to paired-end sequencing on an Illumina sequencer (NextSeq).


title: genomic DNA from bone metastasis sample 45 [Met.45]

tag: ar gene amplification

value: No


title: Pooled sera_51154

tag: growth media

tag: strain


title: genomic DNA from bone metastasis sample 52 [Met.52]

value: Yes


title: RPMI_51122

value: RPMI

tag: growth time

value: 1.5 hrs

tag: growth phase

value: Mid log phase


title: RPMI_51124

tag: serovar


title: Exp2 72h UL87HF 6h dTAG Pro-seq

treatment_protocol:
Cells were treated with dTAG 6h during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

tag: infection duration

tag: ltf depletion

tag: treatment

value: dTAG 6h

tag: fraction


title: Micorwell-seq datasets of papillary thyroid carcinoma with Hashimoto's thyroiditis_8

city: Hangzhou

first: Fang

last: Ye

state: Zhejiang

address: 866 Yuhangtang Rd

country: China

institute: Zhejiang University

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp)； UMI:In read1, the　bases　49-54 (6bp)
ScRNA-seq reads were aligned to the  Homo_sapiens.GRCh38 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cell barcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: Homo_sapiens.GRCh38 genome
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

molecule: polyA RNA

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

tag: tissue

value: Thyroid

tag: disease state

value: papillary thyroid carcinoma

tag: Sex

value: Female


title: Micorwell-seq datasets of papillary thyroid carcinoma without Hashimoto's thyroiditis_7

value: Male


title: Micorwell-seq datasets of papillary thyroid carcinoma with Hashimoto's thyroiditis_6


title: Micorwell-seq datasets of normal adjacent tissue from papillary thyroid carcinoma with Hashimoto's thyroiditis_8

value: normal adjacent tissue


title: RPMI_51151


title: C6-a: RNA-seq of WT cells after 24 h growth in YEME liquid medium at 30°C - replicate 1

tag: genotype

value: WT


title: genomic DNA from bone metastasis sample 43 [Met.43]

tag: disease stage

value: Castration-resistant prostate cancer

tag: epithelial fraction

tag: meta-c class

value: MetA

tag: ar activity score

tag: proliferation score

tag: mca class

value: Positive


title: C6-c: RNA-seq of WT cells after 24 h growth in YEME liquid medium at 30°C - replicate 3

tag: strain


title: RPMI_51150

tag: growth media

tag: growth time

tag: growth phase

tag: od600 reading

tag: temperature

tag: bpa identifier

value: M1T1 clone


title: C6-b: RNA-seq of WT cells after 24 h growth in YEME liquid medium at 30°C - replicate 2


title: C5-c: RNA-seq of WT cells after 72 h growth in MP5 liquid medium at 30°C - replicate 3

description: Remark : Librairy prepared with Script-Seq (stranded) kit => The R1 file corresponds to sense orientation, and R2 to the antisense orientation.


title: Pooled sera_51152

value: Pooled sera

value: 2 hrs exposure to sera

tag: serovar


title: genomic DNA from bone metastasis sample 47 [Met.47]

value: MetB

tag: ar gene amplification

value: Yes


title: genomic DNA from bone metastasis sample 42 [Met.42]

value: Negative


title: genomic DNA from bone metastasis sample 44 [Met.44]


title: Micorwell-seq datasets of normal adjacent tissue from papillary thyroid carcinoma with Hashimoto's thyroiditis_6

tag: tissue

tag: disease state

tag: Sex


title: OSC - Nxf2-KD - HiC_rep2

city: Tokyo

first: Yuka

middle: W.

last: Iwasaki

address: 35 Shinanomachi, Shinjuku-ku,

department: Department of Molecular Biology

country: Japan

institute: Keio University School of Medicine

description: NXF2merge_40kb.ICEcor.Norm.ginteractions.tsv

data_processing:
Hi-C: HiCExplorer v3.3 software (Ramirez et al., 2018) was used for the calculation of HiC matrix, and GENOVA v1.0 was used for visualizing the results. Two replicates were performed per knockdown, and hicCorrelate was used to calculate correlation between replicate samples. Due to the high correlation between replicates, samples were combined by using hicSumMatrices for the further analysis. Bins of too low or high coverage were removed and the HiC matrix was iteratively corrected by ICE using hicCorrectMatrix. HiC matrix was further normalized between different knockdown samples using hicNormalize. TADs were defined using hicFindTADs function and matrixes were converted into ginteractions file using hicConvertFormat.
DamID-seq: Adapters were removed using cutadapt, and reads shorter than 50nt after adapter removal was discarded. damidseq_pipeline (Marshall and Brand, 2015) was used to map the reads to Drosophila melanogaster (dm3) genome, followed by normalization and background reduction. We used q-value cutoff 0 (to include multi-mapped reads), and fragment size of 300. Due to the high correlation of replicate samples, two replicate reads were merged for the further analysis. After mapping of DamID-seq reads to the genome, log2 ratio of LamDam/Dam was calculated and bedgraph file was generated using damidseq_pipeline.
ChIP-seq: For ChIP-seq analysis, adapters were removed from the reads using Cutadapt, and subsequent reads shorter than 50 nt were discarded. ChIP-seq reads were mapped to the Drosophila genome (dm3) using Bowtie 2.2.9 (Langmead and Salzberg, 2012) with the default parameters. MACS 1.4.2 (Zhang et al., 2008) was used for peak calling and generation of wig files.
Genome_build: dm3
Supplementary_files_format_and_content: Hi-C: ginteractions file (tsv format) generated using HiCExplorer v3.3 (Ramirez et al., 2018)
Supplementary_files_format_and_content: DamID-seq: bedgraph file generated using damidseq_pipeline v1.4.5 (Marshall and Brand, 2015)
Supplementary_files_format_and_content: ChIP-seq: wig file generated using MACS v1.4.2 (Zhang, 2008)

organism: Drosophila melanogaster

source_name: Ovarian Somatic Cells

growth_protocol: Ovarian somatic cells (OSCs) was established in the previous studies (Niki et al., 2006; Saito et al., 2009). OSCs were cultured in Shield and Sang M3 Insect Medium (Caisson Laboratories) supplemented with 10% fly extract, 10% fetal bovine serum, 0.6 mg/ml glutathione, and 10 μg/ml insulin.

extract_protocol:
Hi-C: Hi-C using OSCs were performed as described previously (Ulianov et al., 2016) with some minor modifications. OSCs were fixed with 1% formaldehyde for 10min, and stored at -80 degrees before usage. 5 x 10^5 cells were lysed and chromatin digested using 30G needle. Chromatin digestion was performed using HindIII restriction enzyme. Ends were filled with biotin-14-dCTP followed by blunt-end ligation. Proteins were reverse crosslinked form the cells, and DNA purification was performed. Biotin was removed from un-ligated ends and DNA was sonicated using covaris S220 (covaris). Sonicated DNA was used for biotin pull down by streptavidin conjugated to Dynabeads Streptavidin C1 beads (Invitrogen). Pulled-down DNA was used as the template to construct DNA library.
DamID-seq: Dam-ID-seq was performed as described previously (Pickersgill et al., 2006) with some modifications to analyze methylated sequences using deep-sequencing rather than microarray. DamID vectors were transfected into OSCs using Nucleofector, one day before cell harvest. pNDamMyc plasmid (van Steensel and Henikoff, 2000) was a kind gift from Dr. Bas van Steensel. Lamin was cloned into pNDamMyc vector as described previously (Pickersgill et al., 2006). Genome DNA precipitation, DpnI digestion, adapter ligation, DpnII digestion, PCR, and PCR cleanup was performed as described within “Van Steensel Lab version 28/08/2006” protocol. Obtained DNA was used as the template to prepare deep sequencing library.
ChIP-seq: ChIP was performed as described previously (Iwasaki et al., 2016). Briefly, OSCs (3×107) were fixed, lysed, and their nuclei were isolated using truChIP Chromatin Shearing Kits (Covaris), in accordance with the manufacturer’s instructions. DNA was sonicated to ~300 bases using Bioruptor (Cosmobio), and then diluted with ChIP buffer. DNA–protein complexes were incubated with antibody on Dynabeads-Protein G for 4 h, at 4 degrees. Beads were washed with ChIP buffer, high-salt lysis buffer, and wash buffer followed by TE. After reversing cross-linking for 12–16 h at 65 degrees, samples were treated with RNase for 30 min at 37 degrees and Proteinase K for 60 min at 55 degrees. DNA was then recovered.
DNA library was constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), in accordance with the manufacturer’s instructions.

treatment_protocol: For the transfection of siRNAs into OSCs, 200 pmol siRNA duplex was nucleofected into 3.0 × 10^6 cells using the Cell Line 96-well Nucleofector Kit SF (Lonza) and program DG150 of the 96-well Shuttle Device (Lonza). The siRNAs were transfected twice for 4-day KD, and once for 2-day KD. Co-transfection of siRNA and plasmid DNA was performed using the Cell Line Nucleofector Kit V (Lonza) and program T-029 of the Nucleofector II Device (Lonza).

tag: cell line

value: Ovarian Somatic Cells

tag: treatment


title: C5-b: RNA-seq of WT cells after 72 h growth in MP5 liquid medium at 30°C - replicate 2

tag: genotype


title: genomic DNA from bone metastasis sample 41 [Met.41]

tag: disease stage

tag: epithelial fraction

tag: meta-c class

value: MetC

tag: ar activity score

tag: proliferation score


title: RPMI_51149

tag: growth media

value: RPMI

tag: strain

tag: growth time

value: 1.5 hrs

tag: growth phase

value: Mid log phase


title: Micorwell-seq datasets of papillary thyroid carcinoma without Hashimoto's thyroiditis_5

value: Thyroid

value: papillary thyroid carcinoma

value: Female


title: RPMI_51148

tag: od600 reading

tag: temperature

tag: bpa identifier

tag: serovar


title: Micorwell-seq datasets of papillary thyroid carcinoma without Hashimoto's thyroiditis_4

tag: tissue

tag: disease state

tag: Sex

value: Male


title: genomic DNA from bone metastasis sample 40 [Met.40]

value: Castration-resistant prostate cancer

tag: ar gene amplification

tag: mca class


title: Micorwell-seq datasets of papillary thyroid carcinoma without Hashimoto's thyroiditis_3


title: C4-c: RNA-seq of WT cells after 48 h growth in MP5 liquid medium at 30°C - replicate 3

tag: genotype

value: WT


title: C5-a: RNA-seq of WT cells after 72 h growth in MP5 liquid medium at 30°C - replicate 1


title: genomic DNA from bone metastasis sample 39 [Met.39]

tag: disease stage

tag: epithelial fraction

tag: meta-c class

value: MetA

value: Positive


title: Micorwell-seq datasets of papillary thyroid carcinoma without Hashimoto's thyroiditis_2


title: C4-b: RNA-seq of WT cells after 48 h growth in MP5 liquid medium at 30°C - replicate 2


title: RPMI_51146

tag: growth media

value: M1T1 clone


title: Pooled sera_51169

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900619615.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2
Supplementary_files_format_and_content: genome annotations

value: Pooled sera

tag: strain

value: 2 hrs exposure to sera

value: M77, unusual M type associated with peurperal sepsis


title: C4-a: RNA-seq of WT cells after 48 h growth in MP5 liquid medium at 30°C - replicate 1


title: C5-d: RNA-seq of WT cells after 72 h growth in MP5 liquid medium at 30°C - replicate 4


title: U1-GA variant treated HEK293 cells, replicate 2, RNAseq

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

description: U1v-GA_RNAseq_Junction.ReadCounts.txt.gz

data_processing:
RNA sequencing reads were mapped to human genome (hg19) using STAR (version 2.5), only uniquely mapped reads (with MAPQ>10) with <5nt/100nt mismatches and properly paired reads were used.
For gene expression analysis, the number of read in the coding sequence (CDS) region of protein-coding genes and exonic region of non-coding genes were counted and analysed using DESeq2 (Bioconductor).
For splicing analysis, reads were counted for different exons or exonic regions. For each exon, a Percent-Spliced-In (PSI) value was calculated using the percent of average read number supporting the inclusion of the exon (include both the upstream and downstream junctions) among all reads supporting either the inclusion or the exclusion of an exon. A minimal of 20 for the denominator of PSI calculation was required. Otherwise a “NA” value would be generated. PSI values for biological replicates were averaged and the PSI difference between two treatment groups was calculated. For statistical test, a 2x2 read counts table was made for each exon with rows for reads supporting inclusion or exclusion and columns for the two comparing sample groups (biological replicates were combined). Fisher’s Exact Test was used for statistical test. PSI change of >20% (or < -20%) and P-value <0.001 was used to select exons being regulated by the treatment.
Genome_build: hg19
Supplementary_files_format_and_content: The "Junction.ReadCounts.txt" files are tab-delimited text files with rows representing splice junctions (from a 5'ss to a 3'ss) and columns read counts in different RNAseq samples. "HTT-C2_RNAseq-Gene_counts.txt" is a tab-delimited text file with rows representing genes and columns representing read counts in RNAseq of HTT-C2 or DMSO-treated SHSY5Y cells.

source_name: HEK293 cells

growth_protocol: SHY5Y cells (ATCC) derived from a bone marrow biopsy of a female patient with neuroblastoma were plated at 600,000 cells/well in 2 mL DMEM with 10% FBS in 6-well plates, and incubated for 4 hours in a cell culture incubator (37 ºC, 5% CO2, 100% relative humidity).

extract_protocol:
Total RNA was extracted using the RNeasy plus mini kit.
Library construction and sequencing were performed at Novogene. Briefly, mRNA was enriched from about 3 µg of total RNA using oligo(dT) beads (Supplier). The mRNA was fragmented randomly using fragmentation buffer followed by cDNA synthesis using mRNA template and random hexamers primer. Second-strand synthesis buffer (Illumina), deoxynucleotides, ribonuclease H and DNA polymerase I were added to initiate second-strand synthesis. After a series of terminal repair, A-ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment. RNA libraries were sequenced in a HiSeq sequencer (Illumina).

treatment_protocol: Cells were then treated with two biological replicates of HTT-C2 at 24nM or 100nM (in 0.1% DMSO), or four biological replicates of vehicle control (DMSO) for 24 hours. For the U1-GA variant RNA-seq study, U1 wildtype and U1-GA minigenes were designed at PTC and synthesized at GenScript. For the transient transfection, 5e6 HEK293 cells were transfected with 2 µg plasmid or mock control in 6-well plates, using 6 µl Fugene6® (Promega) according to the protocol provided by the manufacturer.

tag: cell type

tag: treatment

value: U1-GA variant

tag: replicate


title: Micorwell-seq datasets of papillary thyroid carcinoma with Hashimoto's thyroiditis_1


title: genomic DNA from bone metastasis sample 38 [Met.38]

value: Yes

tag: ar activity score

tag: proliferation score


title: Pooled sera_51168

tag: growth time

tag: growth phase

tag: od600 reading

tag: temperature

tag: bpa identifier

tag: serovar


title: C3-a: RNA-seq of WT cells after 36 h growth in MP5 liquid medium at 30°C - replicate 1

tag: genotype


title: genomic DNA from bone metastasis sample 36 [Met.36]

tag: disease stage

tag: ar gene amplification

value: No

tag: mca class

value: Negative


title: genomic DNA from bone metastasis sample 34 [Met.34]

tag: epithelial fraction

tag: meta-c class


title: mock treated HEK293 cells, replicate 1, RNAseq

tag: cell type

value: mock


title: genomic DNA from bone metastasis sample 33 [Met.33]


title: C3-b: RNA-seq of WT cells after 36 h growth in MP5 liquid medium at 30°C - replicate 2

tag: strain


title: Pooled sera_51165

tag: growth media


title: mock treated HEK293 cells, replicate 2, RNAseq

tag: treatment

tag: replicate


title: Pooled sera_51166

tag: growth time


title: genomic DNA from bone metastasis sample 37 [Met.37]

tag: ar activity score

tag: proliferation score


title: C2-b: RNA-seq of WT cells after 30 h growth in MP5 liquid medium at 30°C - replicate 2


title: RPMI_51147

value: RPMI

value: 1.5 hrs

tag: growth phase

value: Mid log phase

tag: od600 reading

tag: temperature


title: RPMI_51163

tag: bpa identifier

tag: serovar


title: genomic DNA from bone metastasis sample 32 [Met.32]

tag: disease stage

tag: ar gene amplification


title: genomic DNA from bone metastasis sample 31 [Met.31]

tag: epithelial fraction

tag: mca class


title: C2-a: RNA-seq of WT cells after 30 h growth in MP5 liquid medium at 30°C - replicate 1

tag: genotype


title: C2-c: RNA-seq of WT cells after 30 h growth in MP5 liquid medium at 30°C - replicate 3

tag: strain


title: 100nM HTT-C2 treated SHSY5Y cells, replicate 2, RNAseq

description:
HTT-C2_RNAseq_Junction.ReadCounts.txt.gz
HTT-C2_RNAseq-Gene_counts.txt.gz

source_name: SHSY5Y cells

tag: cell type

value: 100nM HTT-C2


title: U1-GA variant treated HEK293 cells, replicate 1, RNAseq

tag: treatment


title: genomic DNA from bone metastasis sample 30 [Met.30]

value: Castration-resistant prostate cancer

tag: meta-c class


title: Pooled sera_51167

tag: growth media

tag: growth time


title: Pooled sera_51164


title: C1-c: RNA-seq of WT cells after 24 h growth in MP5 liquid medium at 30°C - replicate 3

value: WT


title: 100nM HTT-C2 treated SHSY5Y cells, replicate 1, RNAseq

tag: replicate


title: RPMI_51161

tag: growth phase


title: 24nM HTT-C2 treated SHSY5Y cells, replicate 2, RNAseq

value: 24nM HTT-C2


title: RPMI_51162

tag: od600 reading


title: genomic DNA from bone metastasis sample 29 [Met.29]

value: MetA

tag: ar activity score

tag: proliferation score

value: Positive


title: RPMI_51160

tag: temperature

tag: bpa identifier

tag: serovar


title: genomic DNA from bone metastasis sample 35 [Met.35]

tag: disease stage

tag: epithelial fraction

tag: ar gene amplification


title: genomic DNA from bone metastasis sample 26 [Met.26]

value: MetC

tag: mca class


title: genomic DNA from bone metastasis sample 27 [Met.27]


title: genomic DNA from bone metastasis sample 28 [Met.28]


title: genomic DNA from bone metastasis sample 25 [Met.25]


title: C1-a: RNA-seq of WT cells after 24 h growth in MP5 liquid medium at 30°C - replicate 1

tag: strain

tag: genotype


title: DMSO treated SHSY5Y cells, replicate 2, RNAseq

tag: cell type

tag: treatment

value: DMSO


title: Dahl Salt Sensitive 2

city: Toledo

first: Sivarajan

last: Kumarasamy

state: OH

address: 3000 Arlington Ave

department: Physiology Pharmacology

institute: University of Toledo College of Medicine and Life Sciences

data_processing:
Base Quality and Phred score relationship with the Illumina CASAVA v1.8 software:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter,  reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30  and GC content the clean data were calculated. All the downstream analyses were based on  the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using hisat2 2.1.0 and paired-  end clean reads were aligned to the reference genome using HISAT2.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM  of each gene was calculated based on the length of the gene and reads count mapped to this  gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per  Millions base pairs sequenced, considers the effect of sequencing depth and gene length  for the reads count at the same time, and is currently the most commonly used method for  estimating gene expression levels (Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5.).
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: fpkm.stat: gene count table of different expression levels, calculation of gene numbers in different expression levels and the expression levels of each single gene.
Supplementary_files_format_and_content: fpkm, expression quantification table, calculation of all genes' RPKM.
Supplementary_files_format_and_content: readcount: gene expression quantification table, calculation of all genes' readcount.

organism: Rattus norvegicus

source_name: Dahl Salt Sensitive

extract_protocol:
At the age of 6 weeks, both control and Resp18mutant rats diet was switched to det containing 2% high salt diet. Rats were euthanized after one week exposure to 2% high salt diet and kidneys were removed, flash frozen on liquid nitrogen, and total RNA was isolated using PureLink RNA Mini Kit. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina protocols

tag: genotype/variation

value: Dahl Salt Sensitive

tag: tissue

value: Kidney

tag: gender

value: Male

tag: age

value: 7 Weeks


title: DMSO treated SHSY5Y cells, replicate 3, RNAseq

tag: replicate


title: 24nM HTT-C2 treated SHSY5Y cells, replicate 1, RNAseq


title: Pooled sera_51181

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900619625.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements

tag: growth media

value: Pooled sera

tag: growth time

value: 2 hrs exposure to sera

tag: growth phase

tag: od600 reading


title: C1-b: RNA-seq of WT cells after 24 h growth in MP5 liquid medium at 30°C - replicate 2


title: genomic DNA from bone metastasis sample 24 [Met.24]

tag: disease stage

tag: meta-c class

value: MetB

value: Yes

tag: ar activity score

tag: proliferation score


title: DMSO treated SHSY5Y cells, replicate 1, RNAseq


title: genomic DNA from bone metastasis sample 22 [Met.22]

tag: epithelial fraction

tag: ar gene amplification

tag: mca class


title: RPMI_51159

value: RPMI

tag: strain

value: 1.5 hrs

value: Mid log phase

tag: temperature

tag: bpa identifier

tag: serovar

value: M77, unusual M type associated with peurperal sepsis


title: Pooled sera_51178


title: genomic DNA from bone metastasis sample 23 [Met.23]

value: Castration-resistant prostate cancer

value: Negative


title: Dahl Salt Sensitive 1

tag: genotype/variation

tag: tissue

tag: gender

tag: age


title: Pooled sera_51180

tag: growth media

tag: growth time

tag: growth phase


title: DHT+A4B17_rep3

city: Boston

first: Irene

last: Lee

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
RNA-seq analysis was conducted using VIPER software (Cornwell et al. BMC Bioinformatics (2018) 19:135).
Genome_build: hg19
Supplementary_files_format_and_content: Expression matrix

source_name: LNCaP

growth_protocol: 3.75 x105 LNCaP cells/well in 6-well plate were serum starved for 72 h in phenol red-free RPMI medium, supplemented with 3% CCS.

extract_protocol:
RNA was extracted using innuPREP RNA mini Kit 2.0 (Analytic Jena, Berlin, Germany). 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: Cells were treated with vehicle, 10 nM dihydrotestosterone (DHT), the BAG1L inhibitor (A4B17) (10-5 M) and a combination of DHT and A4B17 for 16 h.

tag: cell type

value: prostate cancer cells

tag: treatment


title: A4B17_rep3


title: Brazil Ae. aegypti midguts nonfed triplicates

city: Fort Collins

first: Ken

middle: E

last: Olson

state: CO

address: 3185 Rampart Road

department: Microbiology, Immunology, Pathology

institute: Colorado State University

description:
AeAeg_BRARe_NFmgut_r123
siRNA

data_processing:
Illumina Nextseq 500 on instrument base calling.
FastX initial quality score trimming and filtering of reads against structural RNAs, microRNAs, viral RNAs.
Mapped to the Aedes aegypt reference genome with Bowtie allowing up to 2 mismatches.
SAM file of reads counted against RefSeq database of all transcripts, counts per locus region and both strands measured.
Genome_build: Aedes aegypti: AaegL5
Supplementary_files_format_and_content: *txt: Tab-delimited tables of read counts mapped to RefSeq transcripts.

organism: Aedes aegypti

source_name: Brazil Ae. aegypti midguts nonfed

growth_protocol: Ae. aegypti were maintained at 28°C with 75-80% relative humidity and a 12h light/12h dark cycle. Eggs were hatched in sterile water, and larva were fed ground TetraMin fish food.

extract_protocol:
15 midguts or abdomens per library were flash frozen on dry ice, and small RNAs were isolated using the mirVana miRNA isolation kit.
Small RNA libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina following manufacturer's instructions. Libraries were run on a 2% agarose gel, and small RNAs were isolated by gel excision.
NextSeq 1x75 cycle.

treatment_protocol: Mated females were either maintained on a sucrose diet (nonfed) or were fed artificial bloodmeals consisting of defibrinated sheep blood approximately 4 days post emergence, and tissues were collected 48h later.

tag: origin

value: Recife, Brazil

value: midgut

tag: bloodfeed status

value: nonfed


title: DHT+A4B17_rep2


title: DMSO treated SHSY5Y cells, replicate 4, RNAseq

value: DMSO

tag: replicate


title: Resp18 mutant 3

source_name: Resp18 mutant 3

value: Resp18 mutant

value: Kidney

value: Male


title: DHT+A4B17_rep1


title: Resp18 mutant 2

source_name: Resp18 mutant 2

value: 7 Weeks


title: genomic DNA from bone metastasis sample 20 [Met.20]

tag: disease stage

tag: epithelial fraction

tag: meta-c class

value: MetB

tag: ar gene amplification

tag: ar activity score

tag: proliferation score

tag: mca class

value: Positive


title: Dahl Salt Sensitive 3

tag: genotype/variation

value: Dahl Salt Sensitive

tag: tissue

tag: gender


title: Brazil Ae. aegypti abdomens nonfed triplicates

description:
AeAeg_BRARe_NFabdm_r123
siRNA

source_name: Brazil Ae. aegypti abdomens nonfed

value: abdomen


title: A4B17_rep2


title: Pooled sera_51179

tag: strain

tag: growth media

value: Pooled sera

tag: growth time

value: 2 hrs exposure to sera

tag: od600 reading

tag: temperature

tag: bpa identifier

tag: serovar


title: DHT_rep3

tag: cell type

tag: treatment

value: DHT


title: genomic DNA from bone metastasis sample 21 [Met.21]

tag: disease stage

value: Castration-resistant prostate cancer

tag: epithelial fraction

tag: meta-c class

value: MetA

value: Yes

value: Negative


title: Resp18 mutant 1

source_name: Resp18 mutant 1

tag: age


title: genomic DNA from bone metastasis sample 18 [Met.18]

value: Untreated

tag: ar gene amplification

value: No


title: Brazil Ae. aegypti midguts 48h pBF triplicates

description:
AeAeg_BRARe_48mgut_r123
siRNA

source_name: Brazil Ae. aegypti midguts 48h pBF

tag: origin

value: Recife, Brazil

value: midgut

tag: bloodfeed status

value: 48h pBF


title: RPMI_51173

value: RPMI

value: 1.5 hrs

tag: growth phase

value: Mid log phase


title: Pooled sera_51176

tag: strain


title: RPMI_51158

tag: growth media

value: M77, unusual M type associated with peurperal sepsis


title: Pooled sera_51177

tag: growth time


title: DHT_rep1

value: prostate cancer cells


title: genomic DNA from bone metastasis sample 16 [Met.16]

tag: ar activity score

tag: proliferation score

tag: mca class

value: Positive


title: A4B17_rep1


title: RPMI_51172

tag: od600 reading

tag: temperature

tag: bpa identifier

tag: serovar


title: Mexico Ae. aegypti abdomens nonfed triplicates

description:
AeAeg_MEXPR_NFabdm_r123
siRNA

source_name: Mexico Ae. aegypti abdomens nonfed

value: Poza Rica, Mexico

tag: tissue

value: abdomen

value: nonfed


title: Brazil Ae. aegypti abdomens 48h pBF triplicates

description:
AeAeg_BRARe_48abdm_r123
siRNA

source_name: Brazil Ae. aegypti abdomens 48h pBF


title: RPMI_51174

source_name: Bacteria in growth media


title: Mexico Ae. aegypti midguts nonfed triplicates

description:
AeAeg_MEXPR_NFmgut_r123
siRNA

source_name: Mexico Ae. aegypti midguts nonfed


title: RPMI_51175


title: RPMI_51170


title: Jc1-E2FLAGv_34

city: Strasbourg

first: Thomas

middle: F

last: Baumert

address: 3, rue Koeberlé

department: University of Strasbourg

institute: Inserm U1110

description:
Single-cell RNA-Seq
HCV-infected

data_processing:
Reads were aligned to the human (hg19 UCSC) and HCV (Jc1) reference genomes using TopHat with default setttings.
Human gene expression levels were quantified using Cuffquant (Cufflinks 2.2.1 suite) with default settings.
Human gene expression levels were normalized across all samples using Cuffnorm (Cufflinks2.2.1 suite) with default settings.
HCV copy number was calculated as the percentage of viral read pairs mapped relative to all human and viral read pairs mapped.
Genome_build: hg19 UCSC and HCV Jc1
Supplementary_files_format_and_content: [.txt] Tab-delimited text files with human gene expression levels (FPKM) and HCV copy number for each sample.

organism:
Homo sapiens
Hepacivirus hominis

source_name: Huh7.5.1 cell_HCV-infected

growth_protocol: For proliferation arrest and differentiation, Huh7.5.1 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) containing 1% DMSO for 10 days, followed by additional 7 days after HCV infection.

extract_protocol:
RNA was isolated using the RNeasy kit (Qiagen) according to manufacturer 's protocol.
Refer to Trombetta et al, 2014

treatment_protocol: DMSO-differentiated Huh7.5.1 cells were infected or not using HCV cell-culture derived particles (HCVcc Jc1E2FLAG). On day 7 post-infection, single-cells were sorted into 96-well plates using a well-established limiting dilution assay. Single-cells were lysed in 5 µl TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol. Cellular mRNA was isolated using the RNeasy mini kit (Qiagen) and sequenced using the SMART-Seq 2 procedure described by Trombetta et a, 2014 on one NextSeq500. HCV RNA was co-amplified with cellular mRNA using a SMART-compatible primer (sequence: 5'-Biotin-AAGCAGTGGTATCAACGCAGAGTACTCTGCGGAACCGGTGAGTA-3')). The modulation of specific gene signatures in association with the normalized HCV copy number in single cell RNA-Seq data was determined using the pre-ranked GSEA module implemented in GenePattern with Pearson correlation as the rank metric.

tag: cell line

tag: cell type

value: DMSO-differentiated Huh7.5.1 cell

tag: treatment

value: Jc1E2FLAG HCV


title: Pooled sera_51144

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900619595.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2
Supplementary_files_format_and_content: genome annotations

value: Pooled sera

value: 2 hrs exposure to sera


title: genomic DNA from bone metastasis sample 17 [Met.17]

source_name: bone metastasis sample

tag: disease stage

value: Untreated

tag: epithelial fraction

tag: meta-c class

value: MetA

tag: ar gene amplification

value: No


title: DHT_rep2

value: DHT


title: Vehicle_rep3

value: Vehicle Control


title: genomic DNA from bone metastasis sample 14 [Met.14]


title: genomic DNA from bone metastasis sample 15 [Met.15]

value: MetC

value: Negative


title: genomic DNA from bone metastasis sample 19 [Met.19]

value: Castration-resistant prostate cancer

value: Yes


title: Pooled sera_51143

tag: strain

tag: growth media

tag: growth phase


title: RPMI_51171

value: RPMI

tag: growth time

value: 1.5 hrs

value: Mid log phase


title: Vehicle_rep2

value: prostate cancer cells


title: Pooled sera_51142


title: genomic DNA from bone metastasis sample 13 [Met.13]

tag: ar activity score

tag: proliferation score

tag: mca class

value: Positive


title: Mexico Ae. aegypti abdomens 48h pBF triplicates

description:
AeAeg_MEXPR_48abdm_r123
siRNA

source_name: Mexico Ae. aegypti abdomens 48h pBF

tag: origin

value: Poza Rica, Mexico

value: abdomen

tag: bloodfeed status

value: 48h pBF


title: Mexico Ae. aegypti midguts 48h pBF triplicates

description:
AeAeg_MEXPR_48mgut_r123
siRNA

source_name: Mexico Ae. aegypti midguts 48h pBF

tag: tissue

value: midgut


title: Vehicle_rep1


title: genomic DNA from bone metastasis sample 10 [Met.10]

value: short-term treated


title: Pooled sera_51145

value: Pooled sera

value: 2 hrs exposure to sera

tag: od600 reading

tag: temperature

tag: bpa identifier

tag: serovar


title: genomic DNA from bone metastasis sample 12 [Met.12]

tag: disease stage

value: Untreated

tag: epithelial fraction

value: No


title: Jc1-E2FLAGv_31

description:
Single-cell RNA-Seq
HCV-infected

tag: cell line

tag: cell type

value: DMSO-differentiated Huh7.5.1 cell

tag: treatment

value: Jc1E2FLAG HCV


title: CSDE1_IP_control_eDRG 2

city: Dalseonggun, Daegu

first: Yongcheol

last: Cho

state: Daegu

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Department of Brain Sciences

country: South Korea

institute: DGIST

description:
Control
CSDE1-associated RNA

data_processing:
The flow cells were used with more than 800 active pores from the initial pore check. MinION and MinKNOW (Oxford Nanopore Technologies, ver. 20.10.3) was used for sequencing with the integrated basecaller guppy for real-time fast-basecalling. Sequencing process was setup with duration of 72 hours, Q-score of 7, and fast-basecalling of Guppy (ver. 4.2.2). After basecalling and de-multiplexing from MinKNOW, the sequencing reads were subjected to NanoStat and NanoPlot to check quality of reads with scores and lengths 95, and mapped using Minimap2 (option, -ax splice:hq -uf) 96 with a reference Mus musculus (GRCm38.p6, GCA_000001635.8). Samtools were used for sorting and indexing the mapped reads 97 and edgeR was used for statistical analysis of differential levels between uninjured and injured DRG samples 36,37. To screen the target genes for downstream analysis, total 12,967 identified protein-coding genes were selected and plotted as x-y plot, with the x-axis of bulk-seq result indicating differential expression levels after sciatic nerve injury and the y-axis of the relative levels of ribosome-association efficiency after injury. To visualize the statistical significance from the edgeR analysis result, the relative level of -log10 P-value was indicated as the relative size of the circle.
Nanopore sequencing was performed as per manufacturer's guidelines using R9.4 SpotON flow cells (FLO-MIN106, ONT) with MinION sequencer winth MinKNOW software by setting duration 72 hours. Basecalled reads was mapped to the Mus musculus reference (GRCm38.p6, GCA_000001635.8) using MiniMap2 (option, -ax splice -uf -k14). Indexing and statistical analysis was done using Samtools and edgeR. Total three biological replicates were subjected to edgeR analysis for testing statistical significance of injury-responsive differential expression.   To analyze CSDE1-associated RNA, mouse embryonic DRG spot-culture was used. Spot-culture DRG neurons were infected with control or 5’UTRm lentivirus at DIV2 and then lysed in TRAP lysis buffer at DIV5. The quantified total extracts were incubated with anti-CSDE1 antibody and the immunopricipitants were subjected to RNA extraction and library preparation same as described in RiboTag-seq. analysis. Two biological replicates were subjected to edgeR analysis to test statistical significance.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Excel file, Differential expression list

source_name: E13.5 eDRG DIV5 CSDE1_IP

growth_protocol: Embryonic DRG cultures were generated as previously described. Embryonic DRG collected from embryonic day 13.5 mice were dissociated in 0.05% trypsin-EDTA and plated on poly-D-lysine/laminin-coated dishes in Neurobasal medium (Gibco) supplemented with 2% B-27 (Gibco), 1% Glutamax, 1 μM 5-fluoro-2'-deoxyuridine (Sigma), 1 μM uridine (Sigma), 1% penicillin-streptomycin, and 50 ng/ml 2.5S nerve growth factor (Envigo, BT-5017).

extract_protocol:
RNA extraction and analysis procedures were performed with RNAqueous Total RNA isolation kit (Thermo, AM1931), RevertAid Reverse Transcriptase (Thermo, EP0441), and PowerUP SYBR green master mix (Thermo, A25918) from L4-5 DRG tissues or cultured embryonic neurons (E13, DIV 5), following the manufacturer’s instructions. The transcript levels were compared between conditions by the ΔΔCt method, using Gapdh transcript levels as an internal control.
RNA samples were prepared using RNAqueous Total RNA isolation kit (Thermo Fisher Scientific, AM1931). To analyze ribosome-associated RNA, Nanopore PCR-cDNA barcoding sequencing kit (Oxford Nanopore Technologies, SQK-PCB109) was used for library preparation. The quantified RNA samples (50ng) were subjected to reverse transcription reaction followed by strand-switching reaction as the manufacturer’s guide. The VN primer was annealed to the RNA to target poly A tail, and first-strand cDNA was synthesized by Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific, EP0752). The RNA-cDNA hybrid was purified using Agencourt AMPure XP magnetic beads (Beckman Coulter, A63880). The library from the Cre- negative control, Cre+ DRG without injury and Cre+ DRG with injury was subjected to barcoding process using barcode primers (Oxford Nanopore Technologies, BP01-BP12). PCR was performed using 2x LongAmp Taq Master Mix (New England Biolabs, M0287S) to select full-length transcripts followed by a second purification step using Agencourt beads (as described above). The barcoded libraries from the triplicates of the uninjured DRG tissue (labeled as u1, u2, u3) and from the triplicates of the injured DRG tissues (labeled as x1, x2, x3) were multiplexed with concentration normalization and loaded onto Flow Cell (Oxford Nanopore Technologies, FLO-MIN106D) as the manufacturer’s guide. The flow cells were used with more than 800 active pores from the initial pore check. MinION and MinKNOW (Oxford Nanopore Technologies, ver. 20.10.3) was used for sequencing with the integrated basecaller guppy for real-time fast-basecalling. Sequencing process was setup with duration of 72 hours, Q-score of 7, and fast-basecalling of Guppy (ver. 4.2.2). After basecalling and de-multiplexing from MinKNOW, the sequencing reads were subjected to NanoStat and NanoPlot to check quality of reads with scores and lengths 95, and mapped using Minimap2 (option, -ax splice:hq -uf) 96 with a reference Mus musculus (GRCm38.p6, GCA_000001635.8). Samtools were used for sorting and indexing the mapped reads 97 and edgeR was used for statistical analysis of differential levels between uninjured and injured DRG samples 36,37. To screen the target genes for downstream analysis, total 12,967 identified protein-coding genes were selected and plotted as x-y plot, with the x-axis of bulk-seq result indicating differential expression levels after sciatic nerve injury and the y-axis of the relative levels of ribosome-association efficiency after injury. To visualize the statistical significance from the edgeR analysis result, the relative level of -log10 P-value was indicated as the relative size of the circle.   To analyze total DEGs of bulk-seq. from adult DRG tissues after sciatic nerve crush injury, three C57/BL6 mice were used as a set of a biological replicate. Right side sciatic nerves were crushed and L4,5 DRGs were dissected at 24 hours after injury. Left side L4,5 DRGs were subjected to uninjured DRG samples. Total RNA was extracted from DRG tissues using RNAqueous Total RNA isolation kit (Thermo Fisher Scientific, AM1931). Nanopore libraries were prepared from total RNA by using Nanopore Direct RNA sequencing Kit (Oxford Nanopore Technologies, SQK-RNA002) according to the manufacturer’s instructions. The RT adapter was annealed to the RNA for reverse transcription and reverse-transcribed RNA was then purified using Agencourt RNAClean XP magnetic beads (Beckman Coulter, A63880). The purified RNA was eluted by adding 21μl Elution Buffer and resuspending the beads, incubating at room temperature for 10 min, pelleting the beads again, and transferring the supernatant (pre-sequencing mix) to a new tube. Then the sequencing adapter was ligated to the library. Nanopore sequencing was performed as per manufacturer's guidelines using R9.4 SpotON flow cells (FLO-MIN106, ONT) with MinION sequencer winth MinKNOW software by setting duration 72 hours. Basecalled reads was mapped to the Mus musculus reference (GRCm38.p6, GCA_000001635.8) using MiniMap2 (option, -ax splice -uf -k14). Indexing and statistical analysis was done using Samtools and edgeR. Total three biological replicates were subjected to edgeR analysis for testing statistical significance of injury-responsive differential expression.   To analyze CSDE1-associated RNA, mouse embryonic DRG spot-culture was used. Spot-culture DRG neurons were infected with control or 5’UTRm lentivirus at DIV2 and then lysed in TRAP lysis buffer at DIV5. The quantified total extracts were incubated with anti-CSDE1 antibody and the immunopricipitants were subjected to RNA extraction and library preparation same as described in RiboTag-seq. analysis. Two biological replicates were subjected to edgeR analysis to test statistical significance.
Nanopore direct RNA-Seq, PCR-cDNA seq

treatment_protocol: For lentiviral transduction, lentivirus was added to the culture at DIV 2. For re-plating assay using the embryonic DRG cultures, neurons were re-plated at DIV 5. Briefly, cultures were incubated in DMEM/0.05% Trypsin-EDTA mixture (1:1) for 5 min at 37°C, 5% CO2 and rinsed with culture medium described above. Cells were then dissociated by gentle pipetting and transferred to new culture plates coated with poly-D-lysine/laminin. Re-plated Neurons were incubated over night at 37°C with 5% CO2.

tag: genotype

value: control

tag: developmental stage

value: Embryonic E13.5

tag: injury

value: DRG


title: Jc1-E2FLAGv_30

description:
Single-cell RNA-Seq
HCV-infected


title: genomic DNA from bone metastasis sample 11 [Met.11]

tag: meta-c class

value: MetA

tag: ar gene amplification

tag: ar activity score

tag: proliferation score


title: genomic DNA from bone metastasis sample 9 [Met.9]

tag: mca class


title: Jc1-E2FLAGv_28

description:
Single-cell RNA-Seq
HCV-infected


title: CSDE1_IP_5'UTRm_eDRG 2

description:
5'UTRm
CSDE1-associated RNA

value: 5'UTRm overexpression

tag: tissue


title: Jc1-E2FLAGv_32

description:
Single-cell RNA-Seq
HCV-infected


title: CSDE1_IP_5'UTRm_eDRG 1

description:
5'UTRm
CSDE1-associated RNA


title: OE_REP2_stably transfected U-2 OS cell line

city: guangzhou

first: xu

middle: man

last: hao

state: China

address: 132 East Waihuan Rd, Rm 438 Higher Education Mega

department: School of Life Sciences

institute: sun yet-sen university

data_processing:
Illumina CASAVA 1.8 software used for basecalling.
Qualified reads were obtained after removing raw reads with adapters or of low quality and then aligned to the Neurospora crassa genome by HISAT with default parameters.
RSeQC was used to measured gene expression abundance as reads per kilobase per million mapped reads (RPKM).
Differential expression analysis of two samples was performed using the previous statistics model. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate and adjusted P-value <0.05 were assigned as differentially expressed gene.
Supplementary_files_format_and_content: RPKM

source_name: bone

growth_protocol: To make the complete growth medium, add the following components to the base medium: fetal bovine serum to a final concentration of 10%. Culture Conditions :Temperature: 37°,CO2 5%,Humidity 95%C

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and treated with DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: OE_REP2 and OE_NC stably transfected U-2 OScells were cultured in Dulbecco modified Eagle medium (DMEM) supplemented with 10% fetal serum and antibiotics (100 U of penicillin and 0.1mg of Streptomycin/ml) in 48h for synchronization.

value: U-2 OS cell


title: Pooled sera_51140

tag: strain

tag: growth media

tag: growth time

tag: growth phase

tag: od600 reading

tag: temperature


title: OE_NC stably transfected U-2 OS cell line

tag: cell line


title: RPMI_51138

value: RPMI

value: 1.5 hrs

value: Mid log phase

tag: bpa identifier

tag: serovar


title: CSDE1_IP_control_eDRG 1

description:
Control
CSDE1-associated RNA

tag: genotype

tag: developmental stage


title: Jc1-E2FLAGv_18

description:
Single-cell RNA-Seq
HCV-infected

tag: cell type

tag: treatment


title: Jc1-E2FLAGv_26

description:
Single-cell RNA-Seq
HCV-infected


title: genomic DNA from bone metastasis sample 5 [Met.5]

tag: disease stage

tag: epithelial fraction

tag: meta-c class

tag: ar gene amplification

tag: ar activity score

value: Positive


title: RPMI_51375

tag: strain

tag: growth media


title: x3

description:
Injury
Rpl22HA-immunoprecipitated RNA

source_name: Adult RiboTag x Adv-Cre mouse L4,5 DRG tissues

value: RiboTag x Adv-Cre

value: Adult

tag: injury

value: sciatic nerve injury_24hours

tag: tissue


title: Jc1-E2FLAGv_15

description:
Single-cell RNA-Seq
HCV-infected


title: genomic DNA from bone metastasis sample 8 [Met.8]

value: short-term treated

tag: proliferation score

tag: mca class


title: Pooled sera_51141

value: Pooled sera

tag: growth time

value: 2 hrs exposure to sera

tag: growth phase

tag: od600 reading

tag: temperature

tag: bpa identifier


title: genomic DNA from bone metastasis sample 7 [Met.7]

value: Untreated

value: No


title: Jc1-E2FLAGv_24

description:
Single-cell RNA-Seq
HCV-infected

tag: cell line

tag: cell type

value: DMSO-differentiated Huh7.5.1 cell

tag: treatment

value: Jc1E2FLAG HCV


title: IgG_eDRG

description:
Control
IgG-associated RNA

source_name: E13.5 eDRG DIV5 IgG_IP

tag: genotype

value: control

tag: developmental stage

value: Embryonic E13.5

value: DRG


title: RPMI_51376

value: RPMI

tag: serovar


title: genomic DNA from bone metastasis sample 2 [Met.2]

tag: disease stage

tag: epithelial fraction

tag: meta-c class

value: MetB

tag: ar gene amplification

tag: ar activity score


title: x2

description:
Injury
Rpl22HA-immunoprecipitated RNA

tag: injury

tag: tissue


title: RPMI_51134

tag: strain

tag: growth media

tag: growth time

value: 1.5 hrs

tag: growth phase

value: Mid log phase


title: genomic DNA from bone metastasis sample 4 [Met.4]

value: MetA

tag: proliferation score

tag: mca class

value: Positive


title: scRNAseq_ThrbNeg_rep2

city: BOSTON

first: CHANGHEE

last: LEE

address: 77 AVENUE LOUIS PASTEUR

department: Genetics

institute: Harvard Medical School

data_processing:
For 10X Chromium libraries, sequencing output was demultiplexed by Cell Ranger (version 3.0.0), then mapped with dropEst (Petukhov et al, Genome Biology 2018) pipeline
Quality score above 0.9 were filtered and then any cells more than 4,000 features filtered out for doublet removal and cells above 15% mitochondrial content removed
Genome_build: galGal5 (Ensembl, release 94, only protein coding and lincRNA with two additional transgenes MCHERRY and EGFP)
Supplementary_files_format_and_content: Seurat (v3.1.5) object with meta information; equivalent text file in market matrix format (MTX) with rownames (features) and colnames (barcodes)

organism: Gallus gallus

growth_protocol: Retina progenitor cells were cultured in DMEM with 10% FBS

extract_protocol:
Total RNA is extracted using Direct-zol RNA Kits (Zymo Research)
1ug of RNA is used to make the library using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

tag: cell type

value: Retina Progentor Cell

tag: treatment/condition

value: ThrbNeg


title: Jc1-E2FLAGv_17

description:
Single-cell RNA-Seq
HCV-infected

tag: cell line

tag: treatment


title: RPMI_51139

tag: od600 reading

tag: temperature

tag: bpa identifier

tag: serovar


title: genomic DNA from bone metastasis sample 3 [Met.3]

data_processing:
Beta values were obtained using GenomeStudio (Illumina). Beta values were normalized using BMIQ. Multimapping CpGs, CpGs close to SNPs, meQTLs, CpGs with Detection P-values > 0.05 in any sample, CpGs with standard deviation < 0.05 and CpGs outside promoter region (TSS1500, TSS200, 5’UTR), were filtered.
matrix processed value definition: BMIQ normalized and filtered Average Beta
matrix signal intensities value definition: Unmethylated and methylated signal intensities

tag: disease stage

value: short-term treated

tag: epithelial fraction

tag: meta-c class

tag: ar gene amplification

tag: ar activity score


title: RPMI_51374

tag: strain

tag: growth media

tag: growth time


title: x1

description:
Injury
Rpl22HA-immunoprecipitated RNA

tag: genotype

value: RiboTag x Adv-Cre

tag: developmental stage

value: Adult

tag: injury

value: sciatic nerve injury_24hours

tag: tissue


title: Jc1-E2FLAGv_14

description:
Single-cell RNA-Seq
HCV-infected

tag: cell line

tag: cell type

value: DMSO-differentiated Huh7.5.1 cell

tag: treatment


title: Jc1-E2FLAGv_13

description:
Single-cell RNA-Seq
HCV-infected

value: Jc1E2FLAG HCV


title: Jc1-E2FLAGv_11

description:
Single-cell RNA-Seq
HCV-infected


title: u2

description:
Control
Rpl22HA-immunoprecipitated RNA

value: no injury


title: Leg Disc Control rep3

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

institute: igred

data_processing:
Quality score trimming and filtering were performed with Trimmomatic (v0.32).
Trimmed reads were aligned to Drosophila melanogaster  using Bowtie2 (v2.1.0)
RPKM (Reads Per Kilobase of exon per Megabase of library size)  were caclulated using Cufflinks (2.2.1)
Differential gene expression was analyzed using the R package DESeq2 (v1.2.8)
Genome_build: BDGP dm6
Supplementary_files_format_and_content: tab-delimited text files include FBGN number and RPKM values for each sample.

source_name: leg disc

extract_protocol:
RNA extraction was performed with Zymo Quick-RNA microprep kit
Library preparation was performed using NEB RNA Ultra kit and dToligos probe were used to target mRNA for cDNA synthesis. Single-end multiplex was performed.

treatment_protocol: white pupae (0h APF) were dissected on ice to collect 250–300 leg imaginal discs in M3 (S3652 Sigma Aldrich) complemented medium. Leg disc cells were dissociated in collagenase (P4762-Sigma Aldrich) and papain (C267-Sigma Aldrich) solution for 1h at 30°C, 300 rpm. After filtering, cells were sorted were using FACSAriaTM device (4°C, 20 psi, nozzle  100 μm) and collected in Trizol before RNA extraction

value: whole leg disc cells

tag: age

value: 0h APF


title: u1

description:
Control
Rpl22HA-immunoprecipitated RNA

value: DRG


title: genomic DNA from bone metastasis sample 6 [Met.6]

value: Untreated

value: MetC

value: Yes

tag: proliferation score

tag: mca class

value: Negative


title: n3dx

description: Injury

source_name: Adult C57/BL6 wild type mouse L4,5 DRG tissues

value: C57/BL6 wild type


title: Jc1-E2FLAGv_9

description:
Single-cell RNA-Seq
HCV-infected


title: Jc1-E2FLAGv_12

description:
Single-cell RNA-Seq
HCV-infected


title: u3

description:
Control
Rpl22HA-immunoprecipitated RNA


title: Jc1-E2FLAGv_7

description:
Single-cell RNA-Seq
HCV-infected


title: Leg Disc Control rep2


title: Jc1-E2FLAGv_5

description:
Single-cell RNA-Seq
HCV-infected


title: Jc1-E2FLAGv_3

description:
Single-cell RNA-Seq
HCV-infected


title: n1dx

description: Injury


title: n1du

description: Control


title: genomic DNA from bone metastasis sample 1 [Met.1]

tag: disease stage

tag: epithelial fraction

value: MetA

value: No

value: Positive


title: Jc1-E2FLAGv_4

description:
Single-cell RNA-Seq
HCV-infected


title: Leg Disc Control rep1


title: n3du

description: Control


title: n2dx

description: Injury


title: n2du

description: Control


title: Jc1-E2FLAGv_6

description:
Single-cell RNA-Seq
HCV-infected


title: 100B

city: Palavas

first: Mélanie

last: Blanc

address: Route de Maguelone

department: UMR MARBEC

institute: INRAE

data_processing:
Base calling and prefiltering (adaptor removal) was performed by BGI
STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters
Counts of reads per gene were obtained with HTSeq v0.11.2 (gtf annotation file GRCz11.97)
Use of DESeq2 v1.24.0 for differential gene expression analysis
Genome_build: DanRer11
Supplementary_files_format_and_content: csv file including raw counts obtained from htseq (unnormalized).

organism: Danio rerio

extract_protocol:
Fish were euthanized, brains were dissected and flash frozen in liquid nitrogen, and RNA was extracted using TriPrep extraction kit (Macherey-Nagel). One microg of total RNA was sent to BGI Europe A/S for pair-ended transcriptome sequencing on BGI-Seq500
according to BGI standard protocol

value: whole brain

value: adult

value: AB line

tag: generation

tag: Sex

value: M


title: Pooled sera_50900

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900622665.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2

organism: Escherichia coli

extract_protocol: Bacterial rRNA depletion with Illumina Ribo-Zero rRNA Removal Kit (Bacteria) followed by strand RNAseq sample preparation with Illumina TruSeq Stranded mRNA Library Prep Kit

tag: strain

value: Pooled sera

value: 2 hrs exposure to sera

tag: growth phase

tag: od600 reading

tag: temperature

tag: bpa identifier

tag: serovar


title: Leg Disc GFP positive rep1

tag: genotype

tag: tissue

value: leg disc tendon cells


title: Zmroot_sc_read1/2_rep1

city: New York

first: Kenneth

middle: David

last: Birnbaum

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

description:
H5CHJBGX7
barcode read single cell run1 (4 primers combined)
transcript read single cell run1 (4 primers combined)

data_processing:
Raw base calls were demultiplexed using Illumina's bcl2fastq.
Alignment, barcode and UMI quantification were performed with Chromium 10x Cell Ranger software package. Samples were normalized, and cell clusters determined using Seurat.
Differential gene expression analyses between cell clusters was perfomed using the ROC algorithm from Seurat.
Genome_build: Zea mays ssp mays B73 v4
Supplementary_files_format_and_content: Matrix table with raw counts for every cell (column) and gene (rows). The three replicates were combined.

organism: Zea mays

source_name: Maize root meristem

growth_protocol: Growth chamber: 26 oC, 12h light/12 h dark. Plantlets were grown on germination paper to avoid the presence of substrate.

extract_protocol:
Root tips from maize seminal and principal roots were cut and collected (3-4 mm lenght). Root tip were incubated in a enzymatic solution to digest cell walls and produce protoplasts. Protoplasts were filtered using a cell strainer and used as input for the 10x Chromium Single Cell 3' V2 pipeline.
Libraries were prepared using Chromium Single Cell 3' Reagent Kit V2

tag: cultivar

value: wild type

value: 7 DAG

value: Maize root meristem


title: Leg Disc GFP positive rep2

value: 0h APF


title: Jc1-E2FLAGv_20

description:
Single-cell RNA-Seq
HCV-infected

tag: cell line

tag: cell type

value: DMSO-differentiated Huh7.5.1 cell

tag: treatment

value: Jc1E2FLAG HCV


title: Jc1-E2FLAGv_2

description:
Single-cell RNA-Seq
HCV-infected


title: Pooled sera_50899

city: Sydney

first: Antibiotic Resistant Sepsis Pathogens Framework Initiative

last: Bioplatforms Australia

institute: Bioplatforms Australia

tag: growth media

tag: growth time


title: Jc1-E2FLAGv_1

description:
Single-cell RNA-Seq
HCV-infected


title: 99B

tag: age


title: 80B

tag: generation

value: F


title: Pooled sera_51063


title: Mock_FLAGp23

description:
Single-cell RNA-Seq
Control

source_name: Huh7.5.1 cell_control

value: FLAG-peptide


title: Mock_FLAGp22

description:
Single-cell RNA-Seq
Control


title: Pooled sera_51062


title: 97B

tag: Sex


title: 121B

tag: strain


title: Neonatal Blood Spot, 202784980040_R02C01

city: Atlanta

first: Anna

middle: K

last: Knight

state: Georgia

address: 101 Woodruff Circle NE

institute: Emory University

description: Illumina Infinium MethylationEPIC array- standard protocol

hyb_protocol: MethylationEPIC

scan_protocol: BeadStudio

data_processing: noob, remove SNPs and cross-reactive probes, combat

label: biotin

source_name: Neonatal Blood Spot

label_protocol: MethylationEPIC

extract_protocol: QIAamp DNA Mini

tag: sex (male= 1, female=2)

tag: race

value: African American

tag: gestational age


title: RPMI_50894

address: Level 4, Building 4WW, Research Park Drive, Macquarie University

value: RPMI

value: 1 hr

tag: growth phase

value: Mid log phase

tag: od600 reading

tag: temperature

tag: bpa identifier


title: Mock_FLAGp25

description:
Single-cell RNA-Seq
Control


title: Pooled sera_51064

tag: serovar


title: Leg Disc GFP positive rep3

tag: genotype

tag: tissue


title: Pooled sera_51061


title: RPMI_50893


title: 95B

value: whole brain

value: adult

value: AB line


title: Mock_FLAGp24

description:
Single-cell RNA-Seq
Control

tag: cell line

tag: cell type

tag: treatment


title: 79B

tag: age


title: RPMI_51059

tag: growth media

tag: growth time


title: Neonatal Blood Spot, 202784980040_R01C01


title: 77B

tag: strain

tag: generation

tag: Sex


title: Mock_FLAGp15

description:
Single-cell RNA-Seq
Control


title: Mock_FLAGp16

description:
Single-cell RNA-Seq
Control


title: 78B


title: 94B

value: M


title: RPMI_51060


title: Neonatal Blood Spot, 202784980014_R07C01

tag: sex (male= 1, female=2)

tag: race

tag: gestational age


title: Mock_FLAGp17

description:
Single-cell RNA-Seq
Control


title: RPMI_51058

tag: growth phase

tag: od600 reading

tag: temperature


title: Mock_FLAGp13

description:
Single-cell RNA-Seq
Control


title: 92B


title: RPMI_51057

tag: bpa identifier

tag: serovar


title: Mock_FLAGp14

description:
Single-cell RNA-Seq
Control

tag: cell line


title: Mock_FLAGp12

description:
Single-cell RNA-Seq
Control

tag: cell type


title: 75B

tag: tissue


title: Pooled sera_50912

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900622685.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2

value: Pooled sera

value: 2 hrs exposure to sera


title: Mock_FLAGp11

description:
Single-cell RNA-Seq
Control

tag: treatment


title: Mock_FLAGp9

description:
Single-cell RNA-Seq
Control


title: 74B

tag: age


title: Neonatal Blood Spot, 202784980014_R05C01


title: Pooled sera_50911

tag: growth media

tag: growth time


title: Pooled sera_51072

tag: strain


title: Neonatal Blood Spot, 202784980014_R08C01


title: 72B

tag: generation

tag: Sex


title: Neonatal Blood Spot, 202784980014_R01C01

tag: sex (male= 1, female=2)

tag: race


title: Neonatal Blood Spot, 202784980014_R02C01

tag: gestational age


title: Mock_FLAGp8

description:
Single-cell RNA-Seq
Control


title: Pooled sera_51070

tag: growth phase

tag: od600 reading


title: 71B


title: Mock_FLAGp7

description:
Single-cell RNA-Seq
Control


title: Neonatal Blood Spot, 202128330122_R08C01


title: 172B


title: Neonatal Blood Spot, 202784980014_R06C01


title: Neonatal Blood Spot, 202128330122_R06C01


title: Neonatal Blood Spot, 202784980014_R03C01


title: 93B


title: Pooled sera_51069

tag: temperature

tag: bpa identifier


title: Mock_FLAGp5

description:
Single-cell RNA-Seq
Control

tag: cell line


title: 170B


title: Neonatal Blood Spot, 202128330122_R07C01


title: RPMI_50905

tag: serovar


title: Mock_FLAGp6

description:
Single-cell RNA-Seq
Control

tag: cell type


title: 173B

tag: tissue


title: Neonatal Blood Spot, 202784980014_R04C01


title: 171B

tag: age