title: 8.1 (RNA-Seq)


title: 8.2 (RNA-Seq)

status: Public on Sep 21 2017

type: SRA

city: London

first: Kathy

last: Niakan

address: Mill Hill

country: United Kingdom

institute: The Francis Crick Institute

library_source: transcriptomic

data_processing:
TopHat2
Samtools
Htseq-count
Genome_build: GRCh38
Supplementary_files_format_and_content: RPKM values in csv document

molecule: polyA RNA

organism: Homo sapiens

source_name: Human Embryo

extract_protocol:
Single cells were isolated from blastocyst stage embryos (6-7 days post fertilisation) for subsequent analysis by micromanipulation, with a duration of less than 20 minutes. Embryos were placed in drops of G-MOPS solution (Vitrolife) on a petri dish overlaid with mineral oil. The plate was placed on a microscope stage (Olympus IX70) and the embryos were held with an opposing holding pipette and blastomere biopsy pipette (Research Instruments) using Narishige micromanipulators (Narishige, Japan). The biopsy mode of a Saturn 5 laser (Research Instruments) was used to separate the majority of the mural TE from the ICM and polar TE. The ICM and polar TE were washed quickly in PBS without Ca2+ and Mg2+ (Invitrogen) then placed in 0.05% trypsin/EDTA (Invitrogen) for 5 minutes at room temperature. Trypsin was quenched using Global Media supplemented with 5 mg/mL LifeGlobal Protein Supplement. After quenching, the cell clump was placed back on the stage in a drop of G-MOPS solution and pipetted up and down several times using the blastomere biopsy pipette.Single cells were picked using 100 μm inner diameter Stripper pipette (Origio) and transferred to individual low bind RNAse-free tubes containing 2.5 µl RLP plus buffer.
Samples were processed using a previously published protocol that was adapted where indicated (Macaulay et al. 2016).To separate RNA from gDNA 50 µl of Dynabeads were washed and incubated with 100 uM biotinylated poly-dT oligonucleotide (IDT). 10 µl of oligo-dT beads were added to each tube containing the single cell. Samples were incubated in a thermomixer for 20 min at room temperature at 2000 rpm. Tubes were put on a magnet until the beads collected into a pellet and the supernatant went clear. The supernatant containing the gDNA was transferred to a new collection tube. Beads were washed three times to collect any residual gDNA.cDNA was generated from the RNA captured on the bead using the SMARTer v4 Ultra Low Input kit. First strand cDNA was synthesised by adding 2 µl 5X Ultra low First strand buffer, 0.5 ul SMART-Seq v4 Oligo, 0.25 µl RNase Inhibitor, 6.25 µl Nuclease free water and 1 µl SMARTScribe Reverse Transcriptase to each sample. Reverse transcription was performed on the thermomixer using the settings 2 min at 42oC at 2000 rpm,  60 min at 42oC at 1500 rpm, 30 min at 50oCat 1500 rpm and 10 min at 60oCat 1500 rpm. cDNA was amplified by adding 12.5 μl 2X SeqAmp PCR buffer, 0.5 μl  PCR Primer II A (12µM), 0.5 µl SeqAmp DNA polymerase, 1.5 μl Nuclease free water. Beads were mixed on thermomixer for 60 sec at room temperature at 2000 rpm and then were incubated on a PCR machine using the following settings: 95oC for 1 min, 24 cycles of 98oC for 10 sec, 65oC for 30 sec and 68oC for 3 min, before a final extension for 10 min at 72oC. Amplified cDNA was purified by adding 25 μl SPRI Ampure XP beads, mixing well and incubating at room temperature for 8 min to allow amplified cDNA to bind to the beads. Sample tubes were placed on the magnet and allowed to stand until all beads had been immobilised. Supernatant was removed and discarded and beads were washed twice by adding 200 µl freshly prepared 80% ethanol and leaving for 30 sec before discarding the supernatant. Tubes were spun briefly to collect residual liquid. The bead pellet was allowed to air dry. 12 µl of purification buffer was added to rehydrate the pellet and incubated for 2 min at room temperature. cDNA was eluted by pipetting up and down 10 times before returning the tube to the magnet. The clear supernatant containing the cDNA was removed from the immobilised beads and transferred to a new low-bind tube. cDNA was stored at -80°C until library preparation. cDNA quality was assessed by High Sensitivity DNA assay on an Agilent 2100 Bioanalyser with good quality cDNA showing a broad peak from 300 to 9000 bp. cDNA concentration was measured using QuBit dsDNA HS kit (Life Technologies UK Ltd.).Libraries with a molar concentration greater than 2nM were submitted for 100-bp paired-end sequencing on Illumina HiSeq 2000.

treatment_protocol: Human embryo microinjections were performed in Global Total media with HEPES under mineral oil on a heated stage with a holding pipet (Research Instruments) and a Femtojet 4i microinjection manipulator set at approximately 40 injection pressure and 20 constant pressure. Embryos were microinjected with a mixture of Cas9  protein plus sgRNA back-filled into microfilament glass capillary injection needles (World Precision Instruments #TW100F-6) pulled using a pipet puller (Suter P-97 micropipette puller). Control embryos were injected with Cas9 protein. Human embryos were cultured in drops of pre-equilibrated Global media (LifeGlobal # LGGG-20) supplemented with 5 mg/mL protein supplement (LifeGlobal # LGPS-605) and overlaid with mineral oil (Origio #ART-4008-5P). Pre-implantation embryos were incubated at 37oC and 5.5% CO2 in an EmbryoScope+ (Vitrolife) time-lapse incubator for  5-6 days (human).

tag: developmental stage

value: Blastocyst

tag: embryo number

value: Cas9 Injected control 8

tag: sample type

value: Single cell


title: 5.8 (RNA-Seq)

value: Cas9 Injected control 5


title: 5.7 (RNA-Seq)


title: 8.3 (RNA-Seq)


title: C12.11b (RNA-Seq)

value: CRISPR 12


title: 2.3 (RNA-Seq)

value: Cas9 Injected control 2


title: 2.9 (RNA-Seq)


title: 2.4 (RNA-Seq)


title: 2.5 (RNA-Seq)


title: 7TE.3 (RNA-Seq)

value: Cas9 Injected control 7

value: Trophectoderm biopsy


title: 2.2 (RNA-Seq)


title: 2.14 (RNA-Seq)


title: 2.1 (RNA-Seq)


title: 7.2 (RNA-Seq)


title: T190conCB

city: Worcester

first: Neil

last: Aronin

state: MA

address: 368 Plantation St.

country: USA

institute: University of Massachusetts Medical School

description:
CB_combindisos.tsv
HumCB_all_gene_coverage.tsv
CB_analyzed_isos.tsv
CB_analyzed_DE.tsv

data_processing:
software used for basecalling was Illumina CASAVA version 1.8.2.
We sorted indexed reads into samples and removed the barcode and randomer with cutadapt version 1.9 (parameter -u 12). Cutadapt trimmed the 3′ polyA tail (parameter -a AAAAAAA) and low quality bases (phred<25), excluding reads less than 15 nucleotides (parameter -q 25 -m 15). We mapped remaining reads to the hg19 or mm10 genome with Bowtie version 1.0.0. Samtools version 0.0.19 converted sam files to bam files, and Bedtools version 2.25.0 converted the bam files to bed files and computed the read 3′ end coverage of each coordinate (parameters -bg -3 -i).
Because the site of cleavage and polyA is heterogeneous, we wrote a peak-calling program to combine reads within 24 nucleotides of the coordinate with the most 3′ end coverage for each polyA site.
We mapped peaks with more than 5 reads to gene ORF or 3′UTRs using intersectBed (BedTools), excluding peaks with non-unique mapping. For each gene, we defined the 3′UTR as the terminal (most 3′) coordinates from the UCSC table browser.
We used CleanUpdTSeq to remove genomically-primed peaks.
We identified alternatively polyadenylated genes as genes with more than one 3′UTR peak. For differential expression analysis, we combined all reads mapping to a gene, either the ORF or the 3′UTR.
Our peak-calling program generated slightly different coordinates between samples for the same isoform due to small inter-sample variations in isoform 3′ end coverage. We considered isoform peaks between samples to be the same if they were within 40 nucleotides of each other. We normalized the expression of each isoform in APA genes by dividing the isoform abundance by the total reads mapping to the gene 3′UTR.
We compared the normalized isoform abundance between HD and control samples using t-tests with or without multiple-hypothesis testing correction using the Benjamini-Hochburg procedure. We considered an adjusted p-value <0.1 to be significant unless otherwise stated (false discovery rate<10%). We did not place a fold or percent change cutoff because small changes in isoform abundances of some genes may affect cellular functions. Only isoforms represented in at least five disease and control samples were considered.
The total reads mapping to each gene were compared between patients and controls using the DESeq2 differential expression package. We considered genes with a fold change greater than 50% and false discovery rate <10% (Benjamini Hochburg correction) significantly expressed differently.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: For human brain sequencing, TSV files were obtained by combining the raw number of reads corresponding to each gene for each sample, or the isoform abundance (normalized to total 3′UTR reads) corresponding to each isoform for each sample.  For mouse brain sequencing,  isoform peaks mappint to huntingtin were extracted from total peaks for each sample.
Supplementary_files_format_and_content: Gr1MCx_combinedisos.tsv: raw read counts for each isoform peak for all samples
Supplementary_files_format_and_content: Gr2MCx_combinedisos.tsv: raw read counts for each isoform peak for all samples
Supplementary_files_format_and_content: HumMCx_all_gene_coverageGr1.tsv: raw read counts for each gene for all samples
Supplementary_files_format_and_content: HumMCx_all_gene_coverageGr2.tsv: raw read counts for each gene for all samples
Supplementary_files_format_and_content: MCxgr1_analyzed_isos.tsv: analyzed isoform expression (HD vs control)
Supplementary_files_format_and_content: MCxgr2_analyzed_isos.tsv: analyzed isoform expression (HD vs control)
Supplementary_files_format_and_content: MCxgr1_analyzed_DE.tsv: analyzed gene expression (HD vs control)
Supplementary_files_format_and_content: MCxgr2_analyzed_DE.tsv: analyzed gene expression (HD vs control)
Supplementary_files_format_and_content: CB_combinedisos.tsv: raw read counts for each isoform peak for all samples
Supplementary_files_format_and_content: HumCB_all_gene_coverage.tsv: raw read counts for each gene for all samples
Supplementary_files_format_and_content: CB_analyzed_isos.tsv: analyzed isoform expression (HD vs control)
Supplementary_files_format_and_content: CB_analyzed_DE.tsv: analyzed gene expression (HD vs control)
Supplementary_files_format_and_content: Mouse_combinedHTTpeaks.tsv: raw read counts for each HTT isoform peak for all mouse samples

molecule: total RNA

source_name: cerebellum tissue

extract_protocol:
5-10μg total RNA was collected from homogenized tissue using Trizol (Ambion), and RNA quality was assessed by Bioanalyzer (Agilent). RNA was treated with TurboDNAse (Ambion) and cleaned with Clean and Concentrator columns (Zymo).
Cleaned RNA was fragmented in 1x SuperScript III first strand buffer (Invitrogen) at 94°C for 5 minutes 30 seconds and immediately placed on ice. SuperScript III (Invitrogen) reverse transcribed fragmented RNA from the custom Passeq oligo d(T) primer, and 20 minute incubation with RNAse I hydrolyzed remaining RNA (Life Technologies). Samples were run on a denaturing 8M urea, 10% acrylamide gel, and 160-200 nucleotide cDNA fragments were eluted overnight in elution buffer (300mM NaCl, 10mM EDTA). Spin-X columns (Corning) removed remaining gel pieces, and eluted cDNA was precipitated by incubation with 50% isopropanol at -20°C for 30 minutes followed by centrifugation at maximum speed for 45 minutes at 4°C. The pellet was washed with 70% ethanol and collected by spinning at maximum speed for 10 minutes 4°C. Dried pellets were resuspended in water. cDNA was circularized by incubation with CircLigase II (Epicentre) at 60°C for 4 hours. Phusion polymerase (NEB) amplified the insert and adaptors with PE 1.0 and PE 2.0 primers by incubation at 98°C for 30 seconds; 14 cycles of 98°C for 5 seconds, 62°C for 10 seconds, and 72°C for 10 seconds; and a final extension of 72°C for 2 minutes. The PCR products were run on a non-denaturing 10% polyacrylamide gel. The 215-254 nucleotide library was extracted and eluted and precipitated as above. Libraries were Bioanalyzed (Agilent) for quality control and sequenced with single-end 100 base-pair sequencing on the HiSeq 2000 machine (Illumina).
Passeq

tag: diagnosis

value: control


title: 2.13 (RNA-Seq)


title: T164conCB


title: 5.6 (RNA-Seq)


title: T144conCB

value: control, ALS


title: T2010conCB


title: T551conCB


title: T461HDCB

value: Huntington's disease grade 2


title: T309HDCB


title: T1488conCB


title: T550HDCB


title: T273HDCB


title: T289HDCB


title: T1482HDCB


title: T128HDCB

value: Huntington's disease grade 4


title: T3049HDCB


title: T551conMCx

description:
Gr1MCx_combinedisos.tsv
Gr2MCx_combinedisos.tsv
HumMCx_all_gene_coverageGr1.tsv
HumMCx_all_gene_coverageGr2.tsv
MCxgr1_analyzed_isos.tsv
MCxgr1_analyzed_DE.tsv
MCxgr2_analyzed_isos.tsv
MCxgr2_analyzed_DE.tsv

source_name: motor cortex tissue


title: T343conMCx


title: T144conMCx


title: T145conMCx


title: T139conMCx


title: HC86HDMCx

description:
Gr1MCx_combinedisos.tsv
HumMCx_all_gene_coverageGr1.tsv
MCxgr1_analyzed_isos.tsv
MCxgr1_analyzed_DE.tsv

value: Huntington's disease grade 1


title: 2.11 (RNA-Seq)


title: HC74HDMCx


title: HC137HDMCx


title: HC132HDMCx


title: T310HDCB


title: HC105HDMCx


title: HC103HDMCx


title: Afum-2hr-1

city: Farmington

first: Reinhard

last: Laubenbacher

state: CT

address: 263 Farmington Avenue

department: Center for Quantitative Medicine MC 6029

institute: University of Connecticut Health Center

description: Sample 7

data_processing:
reads aligned using Bowtie 2 2.0.0 and Tophat 2.0.8 to hg19
transcripts were assembled using Cufflinks 2.0.1
we compared assmbled transcripts using Cufflinks 2.0.1
used Cuffmerge (found in Cufflinks 2.0.1) to merge transcripts
Cuffdiff (found in Cufflinks 2.0.1) was used to find differentially expressed genes
Genome_build: hg19
Supplementary_files_format_and_content: 2hr.txt: CuffDiff output of comparison of 2 hr samples control  with A. fumigatus treated.
Supplementary_files_format_and_content: 6hr.txt: CuffDiff output of comparison of 6 hr samples control  with A. fumigatus treated.
Supplementary_files_format_and_content: 12hr.txt: CuffDiff output of comparison of 12 hr samples control  with A. fumigatus treated.
Supplementary_files_format_and_content: 2hr_sig.txt: Statistical signifcant values (described as yes in the signficance columnn of 2 hr file).
Supplementary_files_format_and_content: 6hr_sig.txt: Statistical signifcant values (described as yes in the signficance columnn of 6 hr file).
Supplementary_files_format_and_content: 12hr_sig.txt: Statistical signifcant values (described as yes in the signficance columnn of 12 hr file).
Supplementary_files_format_and_content: 2hr_sig_final.txt: selection of only those genes found to be statistically significant in (2 hr sig) but removal of the genes meeting the  condition q-value=p-value=0.
Supplementary_files_format_and_content: 6hr_sig_final.txt: selection of only those genes found to be statistically significant in (6 hr sig) but removal of the genes meeting the  condition q-value=p-value=0.
Supplementary_files_format_and_content: 12hr_sig_final.txt: selection of only those genes found to be statistically significant in (12 hr sig) but removal of the genes meeting the  condition q-value=p-value=0.

source_name: NHBE cells, A. fumigatus treated, 2 hr

growth_protocol: Normal human bronchial epithelial (NHBE) cells were grown in bronchial epithelial growth media (BEGM) with SingleQuot (Lonza) supplements and growth factors (bovine pituitary Extract [BPE], hydrocortisone, human epidermal growth factor [hEGF], epinephrine, transferrin, insulin, retinoic acid, triiodothyronine, and bovine serum albumin – fatty acid free [BSA-FAF]) as recommended by the manufacturer. Cells were cultured in 75 cm2 tissue culture flasks at 37°C and 5% CO2 until reaching 80% confluence.

extract_protocol:
Total RNA was collected by addition of 1mL TRIzol (Invitrogen Carlsbad, CA) directly to the cell culture plate and gentle agitation using a cell lifter. RNA extraction was carried out per manufacturer’s instructions followed by clean-up using the Qiagen RNeasy Kit (Qiagen, Valencia, CA) with on-column DNase digestion to remove residual genomic DNA. RNA was eluted in 50μl of RNase-free water and integrity (A260/A280) and concentration were assessed using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).  For each time point, equal amounts of RNA from three treatment replicates were pooled to one sample for a total of three samples per time point in duplicates. A control replicate pool was also generated from each of the three time points (2, 6, and 12 hrs.) in the same manner. RNA samples were then stored at -80°C until further analysis.
library was constructuted at Iowa State University prior to data processing as described at http://www.dna.iastate.edu/nextgensequencing.html

treatment_protocol: Cells were sub-cultured into six-well tissue culture dishes at a concentration of 1 x 106 cells per well and allowed to adhere overnight. The cells were washed twice with DPBS and cultured in a final volume of 1.5mL BEGM media without addition of the provided gentamicin/amphotericin-B component to avoid antifungal effects. Nine individual samples were prepared for each treatment by addition of 0.5 x 106 A. fumigatus spores or left untreated (control). Cells were incubated at 37°C and 5% CO2. Samples were collected at 2, 6, and 12 hrs., following initial stimulation. Culture supernatant was collected and debris was removed by centrifugation before storing at -80°C. The cells were washed twice with DPBS before RNA extraction.

tag: tissue

value: lung

tag: cell type

value: NHBE

tag: infection

value: Afum

tag: time


title: Afum-12hr-1

description: Sample 11

source_name: NHBE cells, A. fumigatus treated, 12 hr


title: Afum-2hr-2

description: Sample 8


title: NF Mi12 mBlast ex2b genomiphi ON (MiSeq, Sample 243)

library_source: genomic

data_processing: Processed data not appropriate as we use the raw Fastq files to just collapse reads of similar types using the on-line program (CRISPR Genome Analyser: http://54.80.152.219).

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryo

extract_protocol:
phenolchloroform DNA extraction
MiSeq

value: embryo


title: NF Mi13 mBlast ex2b genomiphi ON (MiSeq, Sample 244)


title: Afum-6hr-2

description: Sample 10

source_name: NHBE cells, A. fumigatus treated, 6 hr


title: Control- 6hr-2

description: Sample 4

source_name: NHBE cells, negative control, 6 hr

value: Control


title: Exon2b_sgRNA_mouse blastocyst 30 (MiSeq, Sample 241)


title: Control- 12hr-2

description: Sample 6

source_name: NHBE cells, negative control, 12 hr


title: Exon2b_sgRNA_mouse blastocyst 27 (MiSeq, Sample 238)


title: Afum-12hr-2

description: Sample 12


title: Control- 6hr-1

description: Sample 3


title: Exon2b_sgRNA_mouse blastocyst 28 (MiSeq, Sample 239)


title: Control- 2hr-1

description: Sample 1

source_name: NHBE cells, negative control, 2 hr


title: Control- 12hr-1

description: Sample 5


title: Exon2b_sgRNA_mouse blastocyst 26 (MiSeq, Sample 237)


title: Exon2b_sgRNA_mouse blastocyst 29 (MiSeq, Sample 240)


title: Exon2b_sgRNA_mouse blastocyst 24 (MiSeq, Sample 235)


title: Exon2b_sgRNA_mouse blastocyst 23 (MiSeq, Sample 234)


title: Exon2b_sgRNA_mouse blastocyst 22 (MiSeq, Sample 233)


title: Afum-6hr-1

description: Sample 9


title: Exon2b_sgRNA_mouse blastocyst 19 (MiSeq, Sample 231)


title: Control- 2hr-2

description: Sample 2


title: Exon2b_sgRNA_mouse blastocyst 15 (MiSeq, Sample 230)


title: NF Mi11 mBlast ex2b genomiphi ON (MiSeq, Sample 242)


title: Exon2b_sgRNA_mouse blastocyst 14 (MiSeq, Sample 229)


title: M9_NF (MiSeq, Sample 227)


title: M10_NF (MiSeq, Sample 228)


title: Exon2b_sgRNA_blastocyst_19 (MiSeq, Sample 215)


title: M3_NF (MiSeq, Sample 221)


title: Exon2b_sgRNA_blastocyst_17 (MiSeq, Sample 214)


title: Exon2b_sgRNA_blastocyst_20 (MiSeq, Sample 216)


title: M5_NF (MiSeq, Sample 223)


title: M6_NF (MiSeq, Sample 224)


title: Exon2b_sgRNA_blastocyst_27 (MiSeq, Sample 218)


title: M4_NF (MiSeq, Sample 222)


title: Exon2b_sgRNA_blastocyst_16 (MiSeq, Sample 213)


title: Exon2b_sgRNA_blastocyst_15 (MiSeq, Sample 217)


title: M7_NF (MiSeq, Sample 225)


title: Exon2b_sgRNA_blastocyst_25 (MiSeq, Sample 220)


title: Exon2b_sgRNA_blastocyst_11 (MiSeq, Sample 210)


title: Exon2b_sgRNA_blastocyst_12 (MiSeq, Sample 211)


title: Exon2b_sgRNA_mouse blastocyst 21 (MiSeq, Sample 232)


title: Exon2b_sgRNA_blastocyst_10 (MiSeq, Sample 209)


title: Exon2b_sgRNA_blastocyst_9 (MiSeq, Sample 208)


title: Exon2b_sgRNA_blastocyst_7 (MiSeq, Sample 207)


title: Exon2b_sgRNA_blastocyst_5 (MiSeq, Sample 205)


title: Exon2b_sgRNA_blastocyst_6 (MiSeq, Sample 206)


title: Exon2b_sgRNA_blastocyst_4 (MiSeq, Sample 204)


title: M8_NF (MiSeq, Sample 226)


title: Exon2b_sgRNA_blastocyst_26 (MiSeq, Sample 219)


title: Exon2b_sgRNA_blastocyst_1 (MiSeq, Sample 202)


title: Exon2b_sgRNA_blastocyst_14 (MiSeq, Sample 212)


title: PU.1 SpiB DKO rep1 naive

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
RNA sequencing reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped reads were retained. Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included.
Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in at least two libraries. Counts were converted to log2 counts per million, quantile normalized and precision weighted with the ‘voom’ function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.15 or less.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including normalized log2-RPKM expression values of genes in each sample

source_name: lymph node

extract_protocol:
RNA was isolated from activated (48 hours in CD40L+IL-4) lymph node derived B cells using the RNeasy kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer's instructions.

tag: strain

value: naive B cells

tag: genotype

value: Spi1fl/fl Cd23T/+ Spib-/-


title: PU.1 cKO rep1 LPS + IL-4

value: Activated B cells LPS + IL-4

value: Spi1fl/fl Cd23T/+


title: PU.1 cKO rep2 LPS + IL-4


title: Control rep2 LPS + IL-4


title: PU.1 SpiB DKO rep2 naive


title: SpiB KO rep1 naive

value: Spi1fl/fl Cd23+/+ Spib-/-


title: Control rep2 naive


title: SpiB KO rep1 LPS + IL-4


title: PU.1 cKO rep1 naive


title: PU.1 cKO rep2 naive


title: PU.1 SpiB DKO rep1 LPS + IL-4


title: PU.1 SpiB DKO rep2 LPS + IL-4


title: Control rep1 naive


title: LU_CD44pos_CD62Lneg_CD45IVneg_S4_exp6

city: Chicago

first: Nicolas

last: Chevrier

state: Illinois

address: 5640 South Ellis Avenue

department: Pritzker School of Molecular Engineering

institute: The University of Chicago

description:
Sorted CD44+CD62L-CD45IV- CD8+ T cells
raw_counts_exp6_IVstaining_sortedCD8.txt

data_processing:
Fastq files were demultiplexed with custom scripts and quality checked with FastQC.
Read mapping using STAR aligner with mm10 genome.
FeatureCounts was used to count mapped reads for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each sample. Rows = genes, and columns = whole-tissue or sorted CD8+ cell samples.

source_name: Lung

extract_protocol:
For whole organs, samples were lysed in Trizol and total RNA was extracted by phenol-chloroform extraction followed by purification with Dynabeads MyOne Silane beads (Thermoscientific). For sorted cell populations, CD8+ T cell populations (5,000-10,000 cells per sample) were lysed in RLT buffer (Qiagen) containing 1% beta-mercaptoethanol and total RNA was extracted with Dynabeads MyOne Silane beads. After bead-based enrichment, total RNA samples were purified by on-bead DNase I treatment followed by cleanup with 80% ethanol. RNA concentration was normalized across samples prior to library construction.
Total RNA was heat-fragmented to an average size of ~500 bp fragments and reverse transcribed with barcoded oligo(dT) primers containing an Illumina-compatible adapter sequence. After RNA degradation, barcoded, single-stranded cDNA samples were pooled and flanked by an Illumina-compatible adapter sequence in their 3’ end using DNA Pol I. cDNA pools flanked on both ends with illumina sequences were then amplified by PCR and sequenced on Illumina sequencers.

tag: cohort

tag: days post infection

tag: mouse id

tag: experiment id

tag: sequencing batch


title: SpiB KO rep2 LPS + IL-4


title: SpiB KO rep2 naive


title: Exon2b_sgRNA_blastocyst_3 (MiSeq, Sample 203)


title: LU_CD44pos_CD62Lneg_CD45IVpos_S4_exp6

description:
Sorted CD44+CD62L-CD45IV+ CD8+ T cells
raw_counts_exp6_IVstaining_sortedCD8.txt


title: LU_CD44neg_CD62Lpos_S4_exp6

description:
Sorted CD44-CD62L+ CD8+ T cells
raw_counts_exp6_IVstaining_sortedCD8.txt


title: LU_CD44pos_CD62Lpos_S4_exp6

description:
Sorted CD44+CD62L+ CD8+ T cells
raw_counts_exp6_IVstaining_sortedCD8.txt


title: LU_CD44pos_CD62Lneg_CD45IVpos_S3_exp6


title: LU_CD44pos_CD62Lneg_CD45IVneg_S3_exp6


title: LU_CD44pos_CD62Lpos_S3_exp6


title: LU_CD44pos_CD62Lneg_CD45IVpos_S2_exp6


title: LU_CD44neg_CD62Lpos_S3_exp6


title: Control rep1 LPS + IL-4


title: Exon2b_sgRNA_mouse blastocyst 25 (MiSeq, Sample 236)


title: LU_CD44pos_CD62Lneg_CD45IVneg_S2_exp6


title: LU_CD44pos_CD62Lpos_S2_exp6


title: LU_CD44neg_CD62Lpos_S2_exp6


title: LU_CD44pos_CD62Lneg_CD45IVpos_S1_exp6


title: LU_CD44pos_CD62Lpos_S1_exp6


title: LU_CD44pos_CD62Lneg_CD45IVneg_S1_exp6


title: LU_CD44neg_CD62Lpos_S1_exp6


title: MnPO-132-cells-TGCAGCTA-TATGCAGT

city: Stanford

first: Liqun

last: Luo

state: CA

address: Herrin Labs, Rooms 152 and 154

institute: Stanford University

data_processing:
Illumina RTAv2 was used for base calling and quality determination
RSEM (Li et al., Bioinformatics, 2011) and STAR software (Dobin et al., Bioinformatics, 2012) were used for alignment directly to the ENSEMBL transcriptome, and to calculate TPM scores for each cell. FASTQ files containing few reads (<1 MB in size for first paired-end read) were not mapped or subsequently analyzed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files of cell x gene for each sample.

source_name: brain

extract_protocol:
Acute brain slices were cute from juvenile Fos-p2A-CreER;Ai14 mice that had previously had thirst-associated neurons in the median preoptic hypothalamus labeled after 48 hr water deprivation. The preoptic hypothalamus was microdissected out, and processed into a single cell suspension following established protocols (Hempel et al., 2007). Live tdTomato+ cells were sorted on a BD FACSAria II into 96 well plates containing lysis buffer, frozen at -80oC, then had their transcriptomes individually converted into cDNA and amplified following the SmartSeq2 (Picelli et al., 2014) protocol. Finally, the Illumina Nextera XT kit was used to prepare the libraries for sequencing, following the manufacturer's instructions, which were then sequencing on an Illumina NextSeq 500. Several mice were pooled for each replicate, and there were two replicates.
Multiplexed libraries were constructed with the Illumina Nextera XT kit using standard protocols.

value: preoptic hypothalamus


title: MnPO-132-cells-TGCAGCTA-TACTCCTT


title: MnPO-132-cells-TGCAGCTA-CGGAGAGA


title: MnPO-132-cells-TGCAGCTA-CTCCTTAC


title: MnPO-132-cells-TGCAGCTA-ATTAGACG


title: MnPO-132-cells-TGCAGCTA-AGGCTTAG


title: MnPO-132-cells-TGCAGCTA-ATAGAGAG


title: MnPO-132-cells-TCCTGAGC-TATGCAGT


title: MnPO-132-cells-TCCTGAGC-AGGCTTAG


title: MnPO-132-cells-TGCAGCTA-AGAGGATA


title: MnPO-132-cells-TCCTGAGC-ATAGAGAG


title: MnPO-132-cells-TCCTGAGC-ATTAGACG


title: MnPO-132-cells-TCCTGAGC-CGGAGAGA


title: MnPO-132-cells-TCCTGAGC-TACTCCTT


title: MnPO-132-cells-TCCTGAGC-AGAGGATA


title: MnPO-132-cells-TAGGCATG-TATGCAGT


title: MnPO-132-cells-TCCTGAGC-CTCCTTAC


title: MnPO-132-cells-TAGGCATG-CGGAGAGA


title: MnPO-132-cells-TAGGCATG-CTCCTTAC


title: MnPO-132-cells-TAGGCATG-TACTCCTT


title: MnPO-132-cells-TAGGCATG-ATAGAGAG


title: MnPO-132-cells-TAGGCATG-ATTAGACG


title: MnPO-132-cells-TAGCGCTC-TATGCAGT


title: MnPO-132-cells-TAGCGCTC-CTCCTTAC


title: MnPO-132-cells-TAGGCATG-AGGCTTAG


title: MnPO-132-cells-TAGGCATG-AGAGGATA


title: MnPO-132-cells-TAGCGCTC-ATAGAGAG


title: MnPO-132-cells-TAGCGCTC-ATTAGACG


title: MnPO-132-cells-TAGCGCTC-AGAGGATA


title: MnPO-132-cells-TAAGGCGA-ATTAGACG


title: MnPO-132-cells-TAGCGCTC-TACTCCTT


title: MnPO-132-cells-TAAGGCGA-ATAGAGAG


title: MnPO-132-cells-TACGCTGC-TATGCAGT


title: MnPO-132-cells-TACGCTGC-AGAGGATA


title: MnPO-132-cells-TACGCTGC-ATTAGACG


title: MnPO-132-cells-TAAGGCGA-CGGAGAGA


title: MnPO-132-cells-TACGCTGC-TACTCCTT


title: MnPO-132-cells-TAAGGCGA-TACTCCTT


title: MnPO-132-cells-TAAGGCGA-TATGCAGT


title: MnPO-132-cells-TAAGGCGA-AGGCTTAG


title: MnPO-132-cells-GTAGAGGA-TATGCAGT


title: MnPO-132-cells-TAAGGCGA-AGAGGATA


title: MnPO-132-cells-GTAGAGGA-TACTCCTT


title: MnPO-132-cells-TAGCGCTC-CGGAGAGA


title: MnPO-132-cells-GTAGAGGA-CGGAGAGA


title: MnPO-132-cells-TAGCGCTC-AGGCTTAG


title: MnPO-132-cells-TACGCTGC-CTCCTTAC


title: MnPO-132-cells-GTAGAGGA-ATTAGACG


title: MnPO-132-cells-GTAGAGGA-ATAGAGAG


title: MnPO-132-cells-GGAGCTAC-TACTCCTT


title: MnPO-132-cells-TACGCTGC-CGGAGAGA


title: MnPO-132-cells-GTAGAGGA-AGAGGATA


title: MnPO-132-cells-GGAGCTAC-TATGCAGT


title: MnPO-132-cells-GTAGAGGA-AGGCTTAG


title: MnPO-132-cells-GGAGCTAC-CGGAGAGA


title: MnPO-132-cells-GGACTCCT-CTCCTTAC


title: MnPO-132-cells-GGACTCCT-ATTAGACG


title: MnPO-132-cells-GGACTCCT-TACTCCTT


title: MnPO-132-cells-GGAGCTAC-ATAGAGAG


title: MnPO-132-cells-GGACTCCT-ATAGAGAG


title: MnPO-132-cells-GGACTCCT-CGGAGAGA


title: MnPO-132-cells-GGACTCCT-TATGCAGT


title: MnPO-132-cells-GTAGAGGA-CTCCTTAC


title: MnPO-132-cells-GGACTCCT-AGAGGATA


title: MnPO-132-cells-GGAGCTAC-AGAGGATA


title: MnPO-132-cells-GCTCATGA-TATGCAGT


title: MnPO-132-cells-GCTCATGA-CTCCTTAC


title: MnPO-132-cells-GCTCATGA-CGGAGAGA


title: MnPO-132-cells-GGACTCCT-AGGCTTAG


title: MnPO-132-cells-GCTCATGA-TACTCCTT


title: MnPO-132-cells-GCTCATGA-ATTAGACG


title: C12.8 (RNA-Seq)

value: Blastocyst

value: CRISPR 12

value: SIngle cell


title: MnPO-132-cells-GCTCATGA-ATAGAGAG


title: MnPO-132-cells-GCTCATGA-AGGCTTAG


title: MnPO-132-cells-CTCTCTAC-CTCCTTAC


title: MnPO-132-cells-CTCTCTAC-TATGCAGT


title: MnPO-132-cells-GGAGCTAC-CTCCTTAC


title: MnPO-132-cells-CTCTCTAC-ATTAGACG


title: MnPO-132-cells-CTCTCTAC-TACTCCTT


title: MnPO-132-cells-CTCTCTAC-ATAGAGAG


title: MnPO-132-cells-CTCTCTAC-AGGCTTAG


title: MnPO-132-cells-CTCTCTAC-CGGAGAGA


title: MnPO-132-cells-CTCTCTAC-AGAGGATA


title: MnPO-132-cells-GGAGCTAC-ATTAGACG


title: MnPO-132-cells-GCTCATGA-AGAGGATA


title: MnPO-132-cells-CGTACTAG-TACTCCTT


title: MnPO-132-cells-CGTACTAG-CTCCTTAC


title: MnPO-132-cells-CGTACTAG-CGGAGAGA


title: MnPO-132-cells-CGAGGCTG-TATGCAGT


title: MnPO-132-cells-CGTACTAG-ATAGAGAG


title: MnPO-132-cells-CGAGGCTG-TACTCCTT


title: MnPO-132-cells-CGTACTAG-ATTAGACG


title: MnPO-132-cells-CGTACTAG-AGGCTTAG


title: MnPO-132-cells-CGAGGCTG-AGAGGATA


title: MnPO-132-cells-CGTACTAG-AGAGGATA


title: MnPO-132-cells-CGAGGCTG-CTCCTTAC


title: MnPO-132-cells-CGAGGCTG-ATTAGACG


title: MnPO-132-cells-CGAGGCTG-ATAGAGAG


title: MnPO-132-cells-ATGCGCAG-TATGCAGT


title: MnPO-132-cells-ATGCGCAG-CGGAGAGA


title: MnPO-132-cells-ATGCGCAG-AGAGGATA


title: MnPO-132-cells-ATGCGCAG-ATTAGACG


title: MnPO-132-cells-ATGCGCAG-TACTCCTT


title: MnPO-132-cells-ATGCGCAG-CTCCTTAC


title: MnPO-132-cells-CGAGGCTG-CGGAGAGA


title: MnPO-132-cells-ATGCGCAG-AGGCTTAG


title: MnPO-132-cells-ATCTCAGG-TACTCCTT


title: MnPO-132-cells-ATCTCAGG-ATTAGACG


title: MnPO-132-cells-ATCTCAGG-CTCCTTAC


title: MnPO-132-cells-ATCTCAGG-ATAGAGAG


title: MnPO-132-cells-ATCTCAGG-CGGAGAGA


title: MnPO-132-cells-CGAGGCTG-AGGCTTAG


title: MnPO-132-cells-ATCTCAGG-TATGCAGT


title: MnPO-132-cells-ATCTCAGG-AGAGGATA


title: MnPO-132-cells-AGGCAGAA-CGGAGAGA


title: MnPO-132-cells-AGGCAGAA-TACTCCTT


title: MnPO-132-cells-ATCTCAGG-AGGCTTAG


title: MnPO-132-cells-AGGCAGAA-ATTAGACG


title: MnPO-132-cells-AGGCAGAA-ATAGAGAG


title: MnPO-132-cells-AAGAGGCA-TACTCCTT


title: MnPO-132-cells-AGGCAGAA-CTCCTTAC


title: MnPO-132-cells-AAGAGGCA-TATGCAGT


title: MnPO-132-cells-AGGCAGAA-AGGCTTAG


title: MnPO-132-cells-AGGCAGAA-AGAGGATA


title: MnPO-132-cells-AAGAGGCA-CTCCTTAC


title: MnPO-132-cells-AAGAGGCA-CGGAGAGA


title: MnPO-132-cells-AAGAGGCA-ATTAGACG


title: MnPO-132-cells-ATGCGCAG-ATAGAGAG


title: MnPO-132-cells-AAGAGGCA-ATAGAGAG


title: Mn-PO-r3-Sat-99-GCGTAGTA-ATAGAGAG


title: MnPO-132-cells-AAGAGGCA-AGGCTTAG


title: MnPO-132-cells-AAGAGGCA-AGAGGATA


title: MnPO-132-cells-AGGCAGAA-TATGCAGT


title: T139conCB

value: control


title: Mn-PO-r3-Sat-91-CTCTCTAC-CGGAGAGA


title: Mn-PO-r3-Sat-94-GTAGAGGA-CGGAGAGA


title: Mn-PO-r3-Sat-93-AAGAGGCA-CGGAGAGA


title: Mn-PO-r3-Sat-95-GCTCATGA-CGGAGAGA


title: Mn-PO-r3-Sat-96-ATCTCAGG-CGGAGAGA


title: Mn-PO-r3-Sat-92-CGAGGCTG-CGGAGAGA


title: Mn-PO-r3-Sat-9-AAGAGGCA-ATAGAGAG


title: Mn-PO-r3-Sat-88-TCCTGAGC-CGGAGAGA


title: Mn-PO-r3-Sat-89-GGACTCCT-CGGAGAGA


title: Mn-PO-r3-Sat-87-AGGCAGAA-CGGAGAGA


title: Mn-PO-r3-Sat-98-GGAGCTAC-ATAGAGAG


title: Mn-PO-r3-Sat-86-CGTACTAG-CGGAGAGA


title: Mn-PO-r3-Sat-84-ATCTCAGG-ATTAGACG


title: Mn-PO-r3-Sat-82-GTAGAGGA-ATTAGACG


title: Mn-PO-r3-Sat-80-CGAGGCTG-ATTAGACG


title: Mn-PO-r3-Sat-81-AAGAGGCA-ATTAGACG


title: Mn-PO-r3-Sat-78-TAGGCATG-ATTAGACG


title: Mn-PO-r3-Sat-77-GGACTCCT-ATTAGACG


title: Mn-PO-r3-Sat-8-CGAGGCTG-ATAGAGAG


title: Mn-PO-r3-Sat-97-ACTCGCTA-ATAGAGAG


title: Mn-PO-r3-Sat-79-CTCTCTAC-ATTAGACG


title: Mn-PO-r3-Sat-76-TCCTGAGC-ATTAGACG


title: Mn-PO-r3-Sat-75-AGGCAGAA-ATTAGACG


title: Mn-PO-r3-Sat-73-TAAGGCGA-ATTAGACG


title: Mn-PO-r3-Sat-71-GCTCATGA-AGGCTTAG


title: Mn-PO-r3-Sat-70-GTAGAGGA-AGGCTTAG


title: Mn-PO-r3-Sat-69-AAGAGGCA-AGGCTTAG


title: Mn-PO-r3-Sat-85-TAAGGCGA-CGGAGAGA


title: Mn-PO-r3-Sat-90-TAGGCATG-CGGAGAGA


title: Mn-PO-r3-Sat-72-ATCTCAGG-AGGCTTAG


title: Mn-PO-r3-Sat-60-ATCTCAGG-TACTCCTT


title: Mn-PO-r3-Sat-68-CGAGGCTG-AGGCTTAG


title: Mn-PO-r3-Sat-63-AGGCAGAA-AGGCTTAG


title: Mn-PO-r3-Sat-61-TAAGGCGA-AGGCTTAG


title: Mn-PO-r3-Sat-62-CGTACTAG-AGGCTTAG


title: Mn-PO-r3-Sat-67-CTCTCTAC-AGGCTTAG


title: Mn-PO-r3-Sat-66-TAGGCATG-AGGCTTAG


title: Mn-PO-r3-Sat-64-TCCTGAGC-AGGCTTAG


title: Mn-PO-r3-Sat-83-GCTCATGA-ATTAGACG


title: Mn-PO-r3-Sat-59-GCTCATGA-TACTCCTT


title: Mn-PO-r3-Sat-58-GTAGAGGA-TACTCCTT


title: Mn-PO-r3-Sat-56-CGAGGCTG-TACTCCTT


title: Mn-PO-r3-Sat-57-AAGAGGCA-TACTCCTT


title: Mn-PO-r3-Sat-74-CGTACTAG-ATTAGACG


title: Mn-PO-r3-Sat-55-CTCTCTAC-TACTCCTT


title: Mn-PO-r3-Sat-54-TAGGCATG-TACTCCTT


title: Mn-PO-r3-Sat-52-TCCTGAGC-TACTCCTT


title: Mn-PO-r3-Sat-53-GGACTCCT-TACTCCTT


title: Mn-PO-r3-Sat-49-TAAGGCGA-TACTCCTT


title: Mn-PO-r3-Sat-5-GGACTCCT-ATAGAGAG


title: Mn-PO-r3-Sat-47-GCTCATGA-TATGCAGT


title: Mn-PO-r3-Sat-51-AGGCAGAA-TACTCCTT


title: Mn-PO-r3-Sat-48-ATCTCAGG-TATGCAGT


title: Mn-PO-r3-Sat-46-GTAGAGGA-TATGCAGT


title: Mn-PO-r3-Sat-7-CTCTCTAC-ATAGAGAG


title: Mn-PO-r3-Sat-45-AAGAGGCA-TATGCAGT


title: Mn-PO-r3-Sat-42-TAGGCATG-TATGCAGT


title: Mn-PO-r3-Sat-6-TAGGCATG-ATAGAGAG


title: Mn-PO-r3-Sat-44-CGAGGCTG-TATGCAGT


title: Mn-PO-r3-Sat-41-GGACTCCT-TATGCAGT


title: Mn-PO-r3-Sat-4-TCCTGAGC-ATAGAGAG


title: Mn-PO-r3-Sat-40-TCCTGAGC-TATGCAGT


title: Mn-PO-r3-Sat-39-AGGCAGAA-TATGCAGT


title: Mn-PO-r3-Sat-381-CCTAAGAC-TCGCATAA


title: Mn-PO-r3-Sat-384-TCGACGTC-TCGCATAA


title: Mn-PO-r3-Sat-382-CGATCAGT-TCGCATAA


title: Mn-PO-r3-Sat-380-ACTGAGCG-TCGCATAA


title: Mn-PO-r3-Sat-38-CGTACTAG-TATGCAGT


title: Mn-PO-r3-Sat-379-TAGCGCTC-TCGCATAA


title: Mn-PO-r3-Sat-378-ATGCGCAG-TCGCATAA


title: Mn-PO-r3-Sat-376-CGGAGCCT-TCGCATAA


title: Mn-PO-r3-Sat-377-TACGCTGC-TCGCATAA


title: Mn-PO-r3-Sat-374-GGAGCTAC-TCGCATAA


title: Mn-PO-r3-Sat-373-ACTCGCTA-TCGCATAA


title: Mn-PO-r3-Sat-375-GCGTAGTA-TCGCATAA


title: Mn-PO-r3-Sat-50-CGTACTAG-TACTCCTT


title: Mn-PO-r3-Sat-368-ACTGAGCG-TAAGGCTC


title: Mn-PO-r3-Sat-370-CGATCAGT-TAAGGCTC


title: Mn-PO-r3-Sat-367-TAGCGCTC-TAAGGCTC


title: Mn-PO-r3-Sat-366-ATGCGCAG-TAAGGCTC


title: Mn-PO-r3-Sat-37-TAAGGCGA-TATGCAGT


title: Mn-PO-r3-Sat-369-CCTAAGAC-TAAGGCTC


title: Mn-PO-r3-Sat-383-TGCAGCTA-TCGCATAA


title: Mn-PO-r3-Sat-371-TGCAGCTA-TAAGGCTC


title: Mn-PO-r3-Sat-362-GGAGCTAC-TAAGGCTC


title: Mn-PO-r3-Sat-361-ACTCGCTA-TAAGGCTC


title: Mn-PO-r3-Sat-36-ATCTCAGG-CTCCTTAC


title: Mn-PO-r3-Sat-359-TGCAGCTA-ATAGCCTT


title: Mn-PO-r3-Sat-364-CGGAGCCT-TAAGGCTC


title: Mn-PO-r3-Sat-360-TCGACGTC-ATAGCCTT


title: Mn-PO-r3-Sat-358-CGATCAGT-ATAGCCTT


title: Mn-PO-r3-Sat-352-CGGAGCCT-ATAGCCTT


title: Mn-PO-r3-Sat-351-GCGTAGTA-ATAGCCTT


title: Mn-PO-r3-Sat-372-TCGACGTC-TAAGGCTC


title: Mn-PO-r3-Sat-350-GGAGCTAC-ATAGCCTT


title: Mn-PO-r3-Sat-353-TACGCTGC-ATAGCCTT


title: Mn-PO-r3-Sat-354-ATGCGCAG-ATAGCCTT


title: Mn-PO-r3-Sat-348-TCGACGTC-CTTAATAG


title: Mn-PO-r3-Sat-349-ACTCGCTA-ATAGCCTT


title: Mn-PO-r3-Sat-346-CGATCAGT-CTTAATAG


title: Mn-PO-r3-Sat-345-CCTAAGAC-CTTAATAG


title: Mn-PO-r3-Sat-35-GCTCATGA-CTCCTTAC


title: Mn-PO-r3-Sat-347-TGCAGCTA-CTTAATAG


title: Mn-PO-r3-Sat-344-ACTGAGCG-CTTAATAG


title: Mn-PO-r3-Sat-338-GGAGCTAC-CTTAATAG


title: Mn-PO-r3-Sat-342-ATGCGCAG-CTTAATAG


title: Mn-PO-r3-Sat-34-GTAGAGGA-CTCCTTAC


title: Mn-PO-r3-Sat-341-TACGCTGC-CTTAATAG


title: Mn-PO-r3-Sat-339-GCGTAGTA-CTTAATAG


title: Mn-PO-r3-Sat-357-CCTAAGAC-ATAGCCTT


title: Mn-PO-r3-Sat-340-CGGAGCCT-CTTAATAG


title: Mn-PO-r3-Sat-356-ACTGAGCG-ATAGCCTT


title: Mn-PO-r3-Sat-337-ACTCGCTA-CTTAATAG


title: Mn-PO-r3-Sat-335-TGCAGCTA-TCTTACGC


title: Mn-PO-r3-Sat-333-CCTAAGAC-TCTTACGC


title: Mn-PO-r3-Sat-334-CGATCAGT-TCTTACGC


title: Mn-PO-r3-Sat-355-TAGCGCTC-ATAGCCTT


title: Mn-PO-r3-Sat-331-TAGCGCTC-TCTTACGC


title: Mn-PO-r3-Sat-33-AAGAGGCA-CTCCTTAC


title: Mn-PO-r3-Sat-329-TACGCTGC-TCTTACGC


title: rdrp13 PolyA_a

city: New York

first: Jaspreet

last: Khurana

state: NY

address: 701 West 168th St.

institute: Columbia University

description:
Biological replicate A
wt_dcl1_rdrp_PolyA2teloRPKM.txt

data_processing:
All sequencing data were quality trimmed (Q > 20). Genomic DNA and Poly(A) RNAseq were selected for length above 40bp using cutadapt program in Galaxy. Reads were mapped to the Oxytricha trifallax JRB310 and JRB510 macronuclear reference genomes using Bowtie 2 with end-to-end and very-sensitive paramters.
For RNA-seq and DNA-seq data, Coverage was calculated using SAMtools based on the sequencing depth of the individual samples. For RNAseq datasets, a value of 0.0001 was added to all the samples to avoid computing log of 0. The DNAseq datasets were further normalized by the number of reads mapping to the mitochondrial genome in each sample to account for the differences in cell number. Mitochondrial DNA copy number in all the samples was validated by qPCR to confirm the validity of this approach. In addition, small RNA datasets were processed as follows. Reads of length 17-25nt or 30-50nt (for sRNA and pre-sRNA, respectively) were filtered prior to mapping.
Genome_build: Oxytricha trifallax JRB310 macronuclear genome (August 2013 build) and Oxytricha trifallax JRB510 macronuclear genome (September 2015 build)

organism: Oxytricha trifallax

source_name: Poly(A) selected RNA

growth_protocol: Vegetative Oxytricha trifallax cells cultured in Pringsheim media (0.11 mM Na2HPO4, 0.08 mM MgSO4, 0.85 mM Ca(NO3)2, 0.35 mM KCl, pH 7.0) and fed daily with Chlamydomonas reinhardtii and supplemented with Klebsiella sp. Cells were filtered through cheesecloth to remove leftover food.

extract_protocol:
Poly-A RNA enrichment was performed using polyA Spin mRNA Isolation Kit (NEB). Enriched RNA was reverse transcribed using Superscript III (ThermoFisher) and strand-specific libraries were constructed using published methods (Zhang et al. 2012).
polyA+ RNAseq (Single-read sequencing)

value: Vegetative


title: rdrp13 PolyA_b

description:
Biological replicate B
wt_dcl1_rdrp_PolyA2teloRPKM.txt


title: Mn-PO-r3-Sat-343-TAGCGCTC-CTTAATAG


title: WT_JRB310_PolyA_b


title: dcl-141 PolyA_a


title: Mn-PO-r3-Sat-328-CGGAGCCT-TCTTACGC


title: Mn-PO-r3-Sat-326-GGAGCTAC-TCTTACGC


title: WT_JRB310_PolyA_a


title: Mn-PO-r3-Sat-327-GCGTAGTA-TCTTACGC


title: rdrp13_DNA

source_name: Whole cells

extract_protocol:
For genomic DNA isolation,  Nucleospin Tissue kit (Macherey-Nagel) was used.  Genomic DNA was sheared into 300 bp fragments using a Covaris LE220 ultra-sonicator (Covaris).
Standard TruSeq Illumina DNA library construction protocol

value: Oxytricha trifallax rdrp13


title: Mn-PO-r3-Sat-336-TCGACGTC-TCTTACGC


title: Mn-PO-r3-Sat-321-CCTAAGAC-ACTCTAGG


title: Mn-PO-r3-Sat-323-TGCAGCTA-ACTCTAGG


title: Mn-PO-r3-Sat-325-ACTCGCTA-TCTTACGC


title: dcl-141_PolyA_b


title: dcl-123_sRNAs

extract_protocol:
For RNA isolation, cells were centrifuged at 200g in 50mL conical tubes. Media was decanted and cells were resuspended in 1.5mL polypropylene tubes and centrifuged again. Cells were resuspended in TriZol reagent (Thermo Fisher) and stored in -80 C until further use.
Standard TruSeq Illumina sRNA library construction protocol

value: Oxytricha trifallax dcl-123


title: WT_JRB310_DNA

value: Oxytricha trifallax strain JRB310


title: Mn-PO-r3-Sat-324-TCGACGTC-ACTCTAGG


title: dcl-141_DNA

value: Oxytricha trifallax dcl-141


title: Mn-PO-r3-Sat-322-CGATCAGT-ACTCTAGG


title: rdrp13_sRNAs


title: Mn-PO-r3-Sat-330-ATGCGCAG-TCTTACGC


title: Mn-PO-r3-Sat-32-CGAGGCTG-CTCCTTAC


title: Mn-PO-r3-Sat-332-ACTGAGCG-TCTTACGC


title: WT_exconjugant_DNA

value: Oxytricha trifallax (F1 between JRB310 and JRB510)


title: WT_sRNAs


title: H9_clone2-3_Day4+Dox_Offtarget 7B (MiSeq, Sample 201)

description: Offtarget POU5F1P5

source_name: hESC

value: hESC


title: Mn-PO-r3-Sat-319-TAGCGCTC-ACTCTAGG


title: Mn-PO-r3-Sat-318-ATGCGCAG-ACTCTAGG


title: Mn-PO-r3-Sat-317-TACGCTGC-ACTCTAGG


title: Mn-PO-r3-Sat-316-CGGAGCCT-ACTCTAGG


title: H9_clone2-1_Day4+Dox_Offtarget 7B (MiSeq, Sample 199)

description: Offtarget POU5F1P5


title: H9_clone2-3_Day4_Offtarget 7B (MiSeq, Sample 198)

description: Offtarget POU5F1P5


title: H9_clone2-2_Day4+Dox_Offtarget 7B (MiSeq, Sample 200)

description: Offtarget POU5F1P5


title: Mn-PO-r3-Sat-320-ACTGAGCG-ACTCTAGG


title: Mn-PO-r3-Sat-315-GCGTAGTA-ACTCTAGG


title: Mn-PO-r3-Sat-314-GGAGCTAC-ACTCTAGG


title: H9_clone2-2_Day4_Offtarget 7B (MiSeq, Sample 197)

description: Offtarget POU5F1P5


title: H9_clone2-3_Day4+Dox (MiSeq, Sample 195)


title: H9_clone2-1_Day4_Offtarget 7B (MiSeq, Sample 196)

description: Offtarget POU5F1P5


title: H9_clone2-2_Day4+Dox (MiSeq, Sample 194)


title: Mn-PO-r3-Sat-311-TGCAGCTA-AGCTAGAA


title: H9_clone2-1_Day4+Dox (MiSeq, Sample 193)


title: Mn-PO-r3-Sat-313-ACTCGCTA-ACTCTAGG


title: H9_clone2-3_Day4 (MiSeq, Sample 192)


title: Mn-PO-r3-Sat-308-ACTGAGCG-AGCTAGAA


title: H9_clone2-2_Day4 (MiSeq, Sample 191)


title: Mn-PO-r3-Sat-312-TCGACGTC-AGCTAGAA


title: H9_clone2-1_Day4 (MiSeq, Sample 190)


title: Mn-PO-r3-Sat-307-TAGCGCTC-AGCTAGAA


title: Mn-PO-r3-Sat-310-CGATCAGT-AGCTAGAA


title: dcl-141_sRNAs


title: Mn-PO-r3-Sat-306-ATGCGCAG-AGCTAGAA


title: H9_clone2-3_Day3+Dox (MiSeq, Sample 189)


title: Mn-PO-r3-Sat-305-TACGCTGC-AGCTAGAA


title: H9_clone2-2_Day3+Dox (MiSeq, Sample 188)


title: Mn-PO-r3-Sat-304-CGGAGCCT-AGCTAGAA


title: Mn-PO-r3-Sat-363-GCGTAGTA-TAAGGCTC


title: Mn-PO-r3-Sat-303-GCGTAGTA-AGCTAGAA


title: H9_clone2-2_Day3 (MiSeq, Sample 185)


title: Mn-PO-r3-Sat-302-GGAGCTAC-AGCTAGAA


title: Mn-PO-r3-Sat-301-ACTCGCTA-AGCTAGAA


title: H9_clone2-3_Day3 (MiSeq, Sample 186)


title: H9_clone2-1_Day3+Dox (MiSeq, Sample 187)


title: Mn-PO-r3-Sat-309-CCTAAGAC-AGCTAGAA


title: H9_clone2-1_Day3 (MiSeq, Sample 184)


title: H9_clone2-3_Day2+Dox (MiSeq, Sample 183)


title: Mn-PO-r3-Sat-300-TCGACGTC-CTAGTCGA


title: H9_clone2-1_Day2+Dox (MiSeq, Sample 181)


title: Mn-PO-r3-Sat-30-TAGGCATG-CTCCTTAC


title: Mn-PO-r3-Sat-3-AGGCAGAA-ATAGAGAG


title: H9_clone2-2_Day2 (MiSeq, Sample 179)


title: H9_clone2-3_Day2 (MiSeq, Sample 180)


title: Mn-PO-r3-Sat-299-TGCAGCTA-CTAGTCGA


title: H9_clone2-2_Day2+Dox (MiSeq, Sample 182)


title: H9_clone2-1_Day2 (MiSeq, Sample 178)


title: H9_clone2-3_Day1+Dox (MiSeq, Sample 177)


title: Mn-PO-r3-Sat-297-CCTAAGAC-CTAGTCGA


title: H9_clone2-2_Day1+Dox (MiSeq, Sample 176)


title: Mn-PO-r3-Sat-295-TAGCGCTC-CTAGTCGA


title: Mn-PO-r3-Sat-294-ATGCGCAG-CTAGTCGA


title: H9_clone2-1_Day1+Dox (MiSeq, Sample 175)


title: Mn-PO-r3-Sat-293-TACGCTGC-CTAGTCGA


title: Mn-PO-r3-Sat-296-ACTGAGCG-CTAGTCGA


title: H9_clone2-3_Day1 (MiSeq, Sample 174)


title: Mn-PO-r3-Sat-291-GCGTAGTA-CTAGTCGA


title: H9_clone2-2_Day1 (MiSeq, Sample 173)


title: H9_Control (MiSeq, Sample 171)


title: Mn-PO-r3-Sat-29-GGACTCCT-CTCCTTAC


title: H9_clone2-3_Day4+Dox (MiSeq, Sample 170)


title: H9_clone2-1_Day1 (MiSeq, Sample 172)


title: Mn-PO-r3-Sat-288-ATCTCAGG-TCGCATAA


title: Mn-PO-r3-Sat-289-ACTCGCTA-CTAGTCGA


title: H9_clone2-1_Day4+Dox (MiSeq, Sample 168)


title: Mn-PO-r3-Sat-287-GCTCATGA-TCGCATAA


title: H9_clone2-3_Day4 (MiSeq, Sample 167)


title: H9_clone2-2_Day4 (MiSeq, Sample 166)


title: Mn-PO-r3-Sat-298-CGATCAGT-CTAGTCGA


title: Mn-PO-r3-Sat-286-GTAGAGGA-TCGCATAA


title: Mn-PO-r3-Sat-284-CGAGGCTG-TCGCATAA


title: H9_clone2-1_Day4 (MiSeq, Sample 165)


title: H9_clone2-2_Day3+Dox (MiSeq, Sample 163)


title: Mn-PO-r3-Sat-282-TAGGCATG-TCGCATAA


title: H9_clone2-1_Day3+Dox (MiSeq, Sample 162)


title: Mn-PO-r3-Sat-283-CTCTCTAC-TCGCATAA


title: Mn-PO-r3-Sat-281-GGACTCCT-TCGCATAA


title: Mn-PO-r3-Sat-292-CGGAGCCT-CTAGTCGA


title: H9_clone2-3_Day3 (MiSeq, Sample 161)


title: Mn-PO-r3-Sat-285-AAGAGGCA-TCGCATAA


title: Mn-PO-r3-Sat-280-TCCTGAGC-TCGCATAA


title: Mn-PO-r3-Sat-28-TCCTGAGC-CTCCTTAC


title: H9_clone2-2_Day3 (MiSeq, Sample 160)


title: H9_clone2-1_Day3 (MiSeq, Sample 159)


title: Mn-PO-r3-Sat-290-GGAGCTAC-CTAGTCGA


title: Mn-PO-r3-Sat-279-AGGCAGAA-TCGCATAA


title: Mn-PO-r3-Sat-278-CGTACTAG-TCGCATAA


title: H9_clone2-2_Day4+Dox (MiSeq, Sample 169)


title: Mn-PO-r3-Sat-276-ATCTCAGG-TAAGGCTC


title: H9_clone2-1_Day2+Dox (MiSeq, Sample 156)


title: H9_clone2-3_Day2 (MiSeq, Sample 155)


title: H9_clone2-2_Day2+Dox (MiSeq, Sample 157)


title: Mn-PO-r3-Sat-275-GCTCATGA-TAAGGCTC


title: H9_clone2-3_Day3+Dox (MiSeq, Sample 164)


title: H9_clone2-3_Day1+Dox (MiSeq, Sample 152)


title: H9_clone2-3_Day2+Dox (MiSeq, Sample 158)


title: H9_clone2-1_Day2 (MiSeq, Sample 153)


title: Mn-PO-r3-Sat-273-AAGAGGCA-TAAGGCTC


title: H9_clone2-2_Day2 (MiSeq, Sample 154)


title: Mn-PO-r3-Sat-272-CGAGGCTG-TAAGGCTC


title: Mn-PO-r3-Sat-271-CTCTCTAC-TAAGGCTC


title: H9_clone2-2_Day1+Dox (MiSeq, Sample 151)


title: Mn-PO-r3-Sat-270-TAGGCATG-TAAGGCTC


title: Mn-PO-r3-Sat-27-AGGCAGAA-CTCCTTAC


title: H9_clone2-1_Day1+Dox (MiSeq, Sample 150)


title: H9_clone2-2_Day1 (MiSeq, Sample 148)


title: Mn-PO-r3-Sat-269-GGACTCCT-TAAGGCTC


title: H9_clone2-3_Day1 (MiSeq, Sample 149)


title: H9_clone2-1_Day1 (MiSeq, Sample 147)


title: Mn-PO-r3-Sat-268-TCCTGAGC-TAAGGCTC


title: Mn-PO-r3-Sat-277-TAAGGCGA-TCGCATAA


title: H9_Control (MiSeq, Sample 146)


title: H9_clone2-1_Day4+Dox_Offtarget 6B (MiSeq, Sample 145)


title: Mn-PO-r3-Sat-266-CGTACTAG-TAAGGCTC


title: Mn-PO-r3-Sat-267-AGGCAGAA-TAAGGCTC


title: Mn-PO-r3-Sat-265-TAAGGCGA-TAAGGCTC


title: H9_clone2-1_Day4+Dox_Offtarget 6B (MiSeq, Sample 143)


title: Mn-PO-r3-Sat-264-ATCTCAGG-ATAGCCTT


title: Mn-PO-r3-Sat-274-GTAGAGGA-TAAGGCTC


title: H9_clone2-1_Day4_Offtarget 6B (MiSeq, Sample 142)


title: Mn-PO-r3-Sat-263-GCTCATGA-ATAGCCTT


title: H9_clone2-1_Day4_Offtarget 6B (MiSeq, Sample 141)


title: Mn-PO-r3-Sat-262-GTAGAGGA-ATAGCCTT


title: H9_clone2-1_Day4_Offtarget 6B (MiSeq, Sample 140)


title: Mn-PO-r3-Sat-261-AAGAGGCA-ATAGCCTT


title: H9_clone2-3_Day4_Dox (MiSeq, Sample 139)


title: H9_wt (MiSeq, Sample 138)


title: H9_clone2-1_Day4_Dox (MiSeq, Sample 136)


title: Mn-PO-r3-Sat-259-CTCTCTAC-ATAGCCTT


title: H9_clone2-2_Day4_Dox (MiSeq, Sample 137)


title: Mn-PO-r3-Sat-26-CGTACTAG-CTCCTTAC


title: Mn-PO-r3-Sat-258-TAGGCATG-ATAGCCTT


title: Mn-PO-r3-Sat-260-CGAGGCTG-ATAGCCTT


title: Mn-PO-r3-Sat-256-TCCTGAGC-ATAGCCTT


title: H9_clone2-2_Day4 (MiSeq, Sample 134)


title: Mn-PO-r3-Sat-255-AGGCAGAA-ATAGCCTT


title: H9_clone2-1_Day4 (MiSeq, Sample 133)


title: H9_clone2-3_Day4 (MiSeq, Sample 135)


title: H9_clone2-1_Day4+Dox_Offtarget 6B (MiSeq, Sample 144)


title: Mn-PO-r3-Sat-254-CGTACTAG-ATAGCCTT


title: H9_clone2-3_Day3_Dox (MiSeq, Sample 132)


title: H9_clone2-1_Day3_Dox (MiSeq, Sample 130)


title: H9_clone2-2_Day3_Dox (MiSeq, Sample 131)


title: Mn-PO-r3-Sat-251-GCTCATGA-CTTAATAG


title: Mn-PO-r3-Sat-253-TAAGGCGA-ATAGCCTT


title: Mn-PO-r3-Sat-252-ATCTCAGG-CTTAATAG


title: H9_clone2-3_Day3 (MiSeq, Sample 129)


title: H9_clone2-1_Day3 (MiSeq, Sample 127)


title: H9_clone2-2_Day3 (MiSeq, Sample 128)


title: Mn-PO-r3-Sat-250-GTAGAGGA-CTTAATAG


title: Mn-PO-r3-Sat-249-AAGAGGCA-CTTAATAG


title: H9_clone2-3_Day2_Dox (MiSeq, Sample 126)


title: H9_clone2-2_Day2_Dox (MiSeq, Sample 125)


title: Mn-PO-r3-Sat-248-CGAGGCTG-CTTAATAG


title: H9_clone2-1_Day2_Dox (MiSeq, Sample 124)


title: Mn-PO-r3-Sat-246-TAGGCATG-CTTAATAG


title: Mn-PO-r3-Sat-244-TCCTGAGC-CTTAATAG


title: Mn-PO-r3-Sat-245-GGACTCCT-CTTAATAG


title: Mn-PO-r3-Sat-247-CTCTCTAC-CTTAATAG


title: H9_clone2-3_Day2 (MiSeq, Sample 123)


title: Mn-PO-r3-Sat-243-AGGCAGAA-CTTAATAG


title: H9_clone2-3_Day1_Dox (MiSeq, Sample 120)


title: Mn-PO-r3-Sat-242-CGTACTAG-CTTAATAG


title: H9_clone2-1_Day2 (MiSeq, Sample 121)


title: H9_clone2-2_Day2 (MiSeq, Sample 122)


title: Mn-PO-r3-Sat-241-TAAGGCGA-CTTAATAG


title: H9_clone2-2_Day1_Dox (MiSeq, Sample 119)


title: H9_clone2-1_Day1_Dox (MiSeq, Sample 118)


title: H9_clone2-3_Day1 (MiSeq, Sample 117)


title: H9_clone2-2_Day1 (MiSeq, Sample 116)


title: H9_clone2-1_Day1 (MiSeq, Sample 115)


title: Mn-PO-r3-Sat-24-ATCTCAGG-AGAGGATA


title: Mn-PO-r3-Sat-239-GCTCATGA-TCTTACGC


title: Mn-PO-r3-Sat-240-ATCTCAGG-TCTTACGC


title: Mn-PO-r3-Sat-238-GTAGAGGA-TCTTACGC


title: Mn-PO-r3-Sat-25-TAAGGCGA-CTCCTTAC


title: Mn-PO-r3-Sat-237-AAGAGGCA-TCTTACGC


title: H9_wt (MiSeq, Sample 114)


title: H9_clone2-3_Day4_Dox (MiSeq, Sample 113)


title: Mn-PO-r3-Sat-236-CGAGGCTG-TCTTACGC


title: Mn-PO-r3-Sat-235-CTCTCTAC-TCTTACGC


title: H9_clone2-1_Day4_Dox (MiSeq, Sample 111)


title: H9_clone2-3_Day4 (MiSeq, Sample 110)


title: H9_clone2-2_Day4 (MiSeq, Sample 109)


title: Mn-PO-r3-Sat-232-TCCTGAGC-TCTTACGC


title: H9_clone2-1_Day4 (MiSeq, Sample 108)


title: Mn-PO-r3-Sat-231-AGGCAGAA-TCTTACGC


title: Mn-PO-r3-Sat-233-GGACTCCT-TCTTACGC


title: H9_clone2-2_Day3_Dox (MiSeq, Sample 106)


title: Mn-PO-r3-Sat-230-CGTACTAG-TCTTACGC


title: H9_clone2-1_Day3_Dox (MiSeq, Sample 105)


title: H9_clone2-3_Day3 (MiSeq, Sample 104)


title: Mn-PO-r3-Sat-228-ATCTCAGG-ACTCTAGG


title: H9_clone2-2_Day3 (MiSeq, Sample 103)


title: Mn-PO-r3-Sat-227-GCTCATGA-ACTCTAGG


title: H9_clone2-1_Day3 (MiSeq, Sample 102)


title: Mn-PO-r3-Sat-226-GTAGAGGA-ACTCTAGG


title: H9_clone2-3_Day2_Dox (MiSeq, Sample 101)


title: H9_clone2-2_Day4_Dox (MiSeq, Sample 112)


title: H9_clone2-2_Day2_Dox (MiSeq, Sample 100)


title: Mn-PO-r3-Sat-229-TAAGGCGA-TCTTACGC


title: H9_clone2-1_Day2_Dox (MiSeq, Sample 99)


title: Mn-PO-r3-Sat-224-CGAGGCTG-ACTCTAGG


title: Mn-PO-r3-Sat-223-CTCTCTAC-ACTCTAGG


title: Mn-PO-r3-Sat-234-TAGGCATG-TCTTACGC


title: H9_clone2-3_Day2 (MiSeq, Sample 98)


title: Mn-PO-r3-Sat-221-GGACTCCT-ACTCTAGG


title: Mn-PO-r3-Sat-23-GCTCATGA-AGAGGATA


title: H9_clone2-3_Day3_Dox (MiSeq, Sample 107)


title: H9_clone2-2_Day2 (MiSeq, Sample 97)


title: Mn-PO-r3-Sat-220-TCCTGAGC-ACTCTAGG


title: H9_clone2-3_Day1_Dox (MiSeq, Sample 95)


title: H9_clone2-2_Day1_Dox (MiSeq, Sample 94)


title: Mn-PO-r3-Sat-22-GTAGAGGA-AGAGGATA


title: Mn-PO-r3-Sat-218-CGTACTAG-ACTCTAGG


title: H9_clone2-1_Day1_Dox (MiSeq, Sample 93)


title: Mn-PO-r3-Sat-219-AGGCAGAA-ACTCTAGG


title: H9_clone2-3_Day1 (MiSeq, Sample 92)


title: Mn-PO-r3-Sat-216-ATCTCAGG-AGCTAGAA


title: Mn-PO-r3-Sat-225-AAGAGGCA-ACTCTAGG


title: H9_clone2-2_Day1 (MiSeq, Sample 91)


title: Mn-PO-r3-Sat-215-GCTCATGA-AGCTAGAA


title: H9_clone4-3_Day4_Dox (MiSeq, Sample 90)

description: Exon 4 time course


title: Mn-PO-r3-Sat-214-GTAGAGGA-AGCTAGAA


title: Mn-PO-r3-Sat-213-AAGAGGCA-AGCTAGAA


title: Mn-PO-r3-Sat-222-TAGGCATG-ACTCTAGG


title: H9_clone4-1_Day4_Dox (MiSeq, Sample 88)

description: Exon 4 time course


title: Mn-PO-r3-Sat-212-CGAGGCTG-AGCTAGAA


title: H9_clone4-2_Day4 (MiSeq, Sample 86)

description: Exon 4 time course


title: H9_clone4-3_Day4 (MiSeq, Sample 87)

description: Exon 4 time course


title: Mn-PO-r3-Sat-210-TAGGCATG-AGCTAGAA


title: Mn-PO-r3-Sat-211-CTCTCTAC-AGCTAGAA


title: H9_clone2-1_Day2 (MiSeq, Sample 96)


title: H9_clone4-1_Day4 (MiSeq, Sample 85)

description: Exon 4 time course


title: Mn-PO-r3-Sat-21-AAGAGGCA-AGAGGATA


title: H9_clone4-3_Day3_Dox (MiSeq, Sample 84)

description: Exon 4 time course


title: Mn-PO-r3-Sat-209-GGACTCCT-AGCTAGAA


title: H9_clone4-2_Day3_Dox (MiSeq, Sample 83)

description: Exon 4 time course


title: H9_clone4-1_Day3_Dox (MiSeq, Sample 82)

description: Exon 4 time course


title: Mn-PO-r3-Sat-208-TCCTGAGC-AGCTAGAA


title: H9_clone4-3_Day3 (MiSeq, Sample 81)

description: Exon 4 time course


title: Mn-PO-r3-Sat-207-AGGCAGAA-AGCTAGAA


title: Mn-PO-r3-Sat-206-CGTACTAG-AGCTAGAA


title: Mn-PO-r3-Sat-205-TAAGGCGA-AGCTAGAA


title: H9_clone4-1_Day3 (MiSeq, Sample 79)

description: Exon 4 time course


title: H9_clone4-2_Day3 (MiSeq, Sample 80)

description: Exon 4 time course


title: H9_clone4-2_Day4_Dox (MiSeq, Sample 89)

description: Exon 4 time course


title: H9_clone4-2_Day2_Dox (MiSeq, Sample 77)

description: Exon 4 time course


title: Mn-PO-r3-Sat-203-GCTCATGA-CTAGTCGA


title: H9_clone4-1_Day2_Dox (MiSeq, Sample 76)

description: Exon 4 time course


title: Mn-PO-r3-Sat-202-GTAGAGGA-CTAGTCGA


title: Mn-PO-r3-Sat-201-AAGAGGCA-CTAGTCGA


title: H9_clone4-3_Day2 (MiSeq, Sample 75)

description: Exon 4 time course


title: Mn-PO-r3-Sat-200-CGAGGCTG-CTAGTCGA


title: H9_clone4-2_Day2 (MiSeq, Sample 74)

description: Exon 4 time course


title: H9_clone4-3_Day1_Dox (MiSeq, Sample 72)

description: Exon 4 time course


title: H9_clone4-1_Day2 (MiSeq, Sample 73)

description: Exon 4 time course


title: Mn-PO-r3-Sat-199-CTCTCTAC-CTAGTCGA


title: Mn-PO-r3-Sat-2-CGTACTAG-ATAGAGAG


title: H9_clone4-2_Day1_Dox (MiSeq, Sample 71)

description: Exon 4 time course


title: Mn-PO-r3-Sat-198-TAGGCATG-CTAGTCGA


title: Mn-PO-r3-Sat-197-GGACTCCT-CTAGTCGA


title: Mn-PO-r3-Sat-196-TCCTGAGC-CTAGTCGA


title: Mn-PO-r3-Sat-195-AGGCAGAA-CTAGTCGA


title: H9_clone4-2_Day1 (MiSeq, Sample 68)

description: Exon 4 time course


title: H9_clone4-3_Day1 (MiSeq, Sample 69)

description: Exon 4 time course


title: H9_clone4-1_Day1 (MiSeq, Sample 67)

description: Exon 4 time course


title: Mn-PO-r3-Sat-194-CGTACTAG-CTAGTCGA


title: H9_clone4-1_Day1_Dox (MiSeq, Sample 70)

description: Exon 4 time course


title: H9_clone4-3_Day2_Dox (MiSeq, Sample 78)

description: Exon 4 time course


title: H9_Exon1 (MiSeq, Sample 66)

description: Exon 1-2 time course


title: Mn-PO-r3-Sat-204-ATCTCAGG-CTAGTCGA


title: Mn-PO-r3-Sat-192-TCGACGTC-CGGAGAGA


title: Mn-PO-r3-Sat-191-TGCAGCTA-CGGAGAGA


title: H9_clone1-3_Day4 (MiSeq, Sample 62)

description: Exon 1-2 time course


title: H9_clone1-2_Day4_Dox (MiSeq, Sample 64)

description: Exon 1-2 time course


title: Mn-PO-r3-Sat-190-CGATCAGT-CGGAGAGA


title: H9_clone1-1_Day4_Dox (MiSeq, Sample 63)

description: Exon 1-2 time course


title: Mn-PO-r3-Sat-189-CCTAAGAC-CGGAGAGA


title: Mn-PO-r3-Sat-20-CGAGGCTG-AGAGGATA


title: Mn-PO-r3-Sat-188-ACTGAGCG-CGGAGAGA


title: H9_clone1-1_Day4 (MiSeq, Sample 60)

description: Exon 1-2 time course


title: H9_clone1-3_Day3_Dox (MiSeq, Sample 59)

description: Exon 1-2 time course


title: H9_clone1-2_Day4 (MiSeq, Sample 61)

description: Exon 1-2 time course


title: Mn-PO-r3-Sat-187-TAGCGCTC-CGGAGAGA


title: Mn-PO-r3-Sat-185-TACGCTGC-CGGAGAGA


title: H9_clone1-1_Day3_Dox (MiSeq, Sample 57)

description: Exon 1-2 time course


title: Mn-PO-r3-Sat-184-CGGAGCCT-CGGAGAGA


title: H9_clone1-3_Day4_Dox (MiSeq, Sample 65)

description: Exon 1-2 time course


title: Mn-PO-r3-Sat-193-TAAGGCGA-CTAGTCGA


title: H9_clone1-3_Day3 (MiSeq, Sample 56)

description: Exon 1-2 time course


title: Mn-PO-r3-Sat-183-GCGTAGTA-CGGAGAGA


title: H9_clone1-2_Day3 (MiSeq, Sample 55)

description: Exon 1-2 time course


title: Mn-PO-r3-Sat-18-TAGGCATG-AGAGGATA


title: Mn-PO-r3-Sat-181-ACTCGCTA-CGGAGAGA


title: Mn-PO-r3-Sat-182-GGAGCTAC-CGGAGAGA


title: Mn-PO-r3-Sat-179-TGCAGCTA-ATTAGACG


title: H9_clone1-2_Day2_Dox (MiSeq, Sample 52)

description: Exon 1-2 time course


title: H9_clone1-3_Day2_Dox (MiSeq, Sample 53)

description: Exon 1-2 time course


title: Mn-PO-r3-Sat-178-CGATCAGT-ATTAGACG


title: Mn-PO-r3-Sat-177-CCTAAGAC-ATTAGACG


title: H9_clone1-3_Day2 (MiSeq, Sample 50)

description: Exon 1-2 time course


title: H9_clone1-2_Day2 (MiSeq, Sample 49)

description: Exon 1-2 time course


title: Mn-PO-r3-Sat-176-ACTGAGCG-ATTAGACG


title: Mn-PO-r3-Sat-175-TAGCGCTC-ATTAGACG


title: H9_clone1-2_Day3_Dox (MiSeq, Sample 58)

description: Exon 1-2 time course


title: Mn-PO-r3-Sat-174-ATGCGCAG-ATTAGACG


title: Mn-PO-r3-Sat-186-ATGCGCAG-CGGAGAGA


title: H9_clone1-3_Day_Dox (MiSeq, Sample 47)

description: Exon 1-2 time course


title: H9_clone1-2_Day1_Dox (MiSeq, Sample 46)

description: Exon 1-2 time course


title: Mn-PO-r3-Sat-173-TACGCTGC-ATTAGACG


title: H9_clone1-1_Day_Dox (MiSeq, Sample 45)

description: Exon 1-2 time course


title: Mn-PO-r3-Sat-172-CGGAGCCT-ATTAGACG


title: H9_clone1-1_Day3 (MiSeq, Sample 54)

description: Exon 1-2 time course


title: H9_clone1-2_Day1 (MiSeq, Sample 43)

description: Exon 1-2 time course


title: H9_Cl-3_Day4+Dox (MiSeq, Sample 41)

description: Exon 1-1 time course


title: Mn-PO-r3-Sat-17-GGACTCCT-AGAGGATA


title: Mn-PO-r3-Sat-170-GGAGCTAC-ATTAGACG


title: H9_clone1-1_Day2_Dox (MiSeq, Sample 51)

description: Exon 1-2 time course


title: H9_clone1-3_Day1 (MiSeq, Sample 44)

description: Exon 1-2 time course


title: H9_clone1-1_Day1 (MiSeq, Sample 42)

description: Exon 1-2 time course


title: H9_Cl-2_Day4 (MiSeq, Sample 38)

description: Exon 1-1 time course


title: Mn-PO-r3-Sat-169-ACTCGCTA-ATTAGACG


title: Mn-PO-r3-Sat-167-TGCAGCTA-AGGCTTAG


title: Mn-PO-r3-Sat-168-TCGACGTC-AGGCTTAG


title: H9_clone1-1_Day2 (MiSeq, Sample 48)

description: Exon 1-2 time course


title: H9_Cl-3_Day3+Dox (MiSeq, Sample 37)

description: Exon 1-1 time course


title: Mn-PO-r3-Sat-166-CGATCAGT-AGGCTTAG


title: H9_Cl-2_Day3+Dox (MiSeq, Sample 36)

description: Exon 1-1 time course


title: Mn-PO-r3-Sat-164-ACTGAGCG-AGGCTTAG


title: Mn-PO-r3-Sat-165-CCTAAGAC-AGGCTTAG


title: H9_Cl-3_Day4 (MiSeq, Sample 39)

description: Exon 1-1 time course


title: H9_Cl-3_Day3+Dox (MiSeq, Sample 35)

description: Exon 1-1 time course


title: H9_Cl-2_Day3 (MiSeq, Sample 32)

description: Exon 1-1 time course


title: H9_Cl-2_Day3+Dox (MiSeq, Sample 34)

description: Exon 1-1 time course


title: Mn-PO-r3-Sat-163-TAGCGCTC-AGGCTTAG


title: Mn-PO-r3-Sat-162-ATGCGCAG-AGGCTTAG


title: Mn-PO-r3-Sat-161-TACGCTGC-AGGCTTAG


title: H9_Cl-3_Day3 (MiSeq, Sample 33)

description: Exon 1-1 time course


title: H9_Cl-3_Day2 (MiSeq, Sample 31)

description: Exon 1-1 time course


title: Mn-PO-r3-Sat-171-GCGTAGTA-ATTAGACG


title: H9_Cl-2_Day2 (MiSeq, Sample 30)

description: Exon 1-1 time course


title: H9_Cl-2_Day4+Dox (MiSeq, Sample 40)

description: Exon 1-1 time course


title: Mn-PO-r3-Sat-159-GCGTAGTA-AGGCTTAG


title: H9_Cl-3_Day1+Dox (MiSeq, Sample 29)

description: Exon 1-1 time course


title: Mn-PO-r3-Sat-158-GGAGCTAC-AGGCTTAG


title: H9_Cl-2_Day1+Dox (MiSeq, Sample 28)

description: Exon 1-1 time course


title: Mn-PO-r3-Sat-16-TCCTGAGC-AGAGGATA


title: Mn-PO-r3-Sat-157-ACTCGCTA-AGGCTTAG


title: H9_Cl-3_Day1 (MiSeq, Sample 27)

description: Exon 1-1 time course


title: H9_Cl-3_Day0 (MiSeq, Sample 25)

description: Exon 1-1 time course


title: H9_Cl-2_Day1 (MiSeq, Sample 26)

description: Exon 1-1 time course


title: H9_clone2-3_Day4+Dox (MiSeq, Sample 23)

description: Exon 2 time course


title: Mn-PO-r3-Sat-156-TCGACGTC-TACTCCTT


title: Mn-PO-r3-Sat-154-CGATCAGT-TACTCCTT


title: Mn-PO-r3-Sat-152-ACTGAGCG-TACTCCTT


title: H9_clone2-3_Day4 (MiSeq, Sample 22)

description: Exon 2 time course


title: Mn-PO-r3-Sat-155-TGCAGCTA-TACTCCTT


title: Mn-PO-r3-Sat-151-TAGCGCTC-TACTCCTT


title: H9_Cl-2_Day0 (MiSeq, Sample 24)

description: Exon 1-1 time course


title: Mn-PO-r3-Sat-160-CGGAGCCT-AGGCTTAG


title: Mn-PO-r3-Sat-153-CCTAAGAC-TACTCCTT


title: H9_clone2-3_Day3+Dox (MiSeq, Sample 21)

description: Exon 2 time course


title: H9_clone2-3_Day3 (MiSeq, Sample 20)

description: Exon 2 time course


title: H9_clone2-3_Day2 (MiSeq, Sample 18)

description: Exon 2 time course


title: H9_clone2-3_Day2+Dox (MiSeq, Sample 19)

description: Exon 2 time course


title: Mn-PO-r3-Sat-149-TACGCTGC-TACTCCTT


title: Mn-PO-r3-Sat-150-ATGCGCAG-TACTCCTT


title: Mn-PO-r3-Sat-15-AGGCAGAA-AGAGGATA


title: H9_clone2-3_Day1 (MiSeq, Sample 17)

description: Exon 2 time course


title: Mn-PO-r3-Sat-148-CGGAGCCT-TACTCCTT


title: Mn-PO-r3-Sat-147-GCGTAGTA-TACTCCTT


title: H9_clone2-2_Day4 (MiSeq, Sample 15)

description: Exon 2 time course


title: H9_clone2-2_Day4+Dox (MiSeq, Sample 16)

description: Exon 2 time course


title: Mn-PO-r3-Sat-145-ACTCGCTA-TACTCCTT


title: Mn-PO-r3-Sat-144-TCGACGTC-TATGCAGT


title: H9_clone2-2_Day3+Dox (MiSeq, Sample 14)

description: Exon 2 time course


title: Mn-PO-r3-Sat-143-TGCAGCTA-TATGCAGT


title: H9_clone2-2_Day3 (MiSeq, Sample 13)

description: Exon 2 time course


title: H9_clone2-2_Day2+Dox (MiSeq, Sample 12)

description: Exon 2 time course


title: Mn-PO-r3-Sat-139-TAGCGCTC-TATGCAGT


title: Mn-PO-r3-Sat-140-ACTGAGCG-TATGCAGT


title: H9_clone2-1_Day4 (MiSeq, Sample 7)

description: Exon 2 time course


title: H9_clone2-2_Day1+Dox (MiSeq, Sample 10)

description: Exon 2 time course


title: Mn-PO-r3-Sat-142-CGATCAGT-TATGCAGT


title: H9_clone2-2_Day1 (MiSeq, Sample 9)

description: Exon 2 time course


title: H9_clone2-1_Day4+Dox (MiSeq, Sample 8)

description: Exon 2 time course


title: Mn-PO-r3-Sat-141-CCTAAGAC-TATGCAGT


title: Mn-PO-r3-Sat-138-ATGCGCAG-TATGCAGT


title: H9_clone2-1_Day3+Dox (MiSeq, Sample 6)

description: Exon 2 time course


title: H9_clone2-1_Day2+Dox (MiSeq, Sample 4)

description: Exon 2 time course


title: H9_clone2-1_Day2 (MiSeq, Sample 3)

description: Exon 2 time course


title: H9_clone2-1_Day3 (MiSeq, Sample 5)

description: Exon 2 time course


title: H9_clone2-1_Day1+Dox (MiSeq, Sample 2)

description: Exon 2 time course


title: Mn-PO-r3-Sat-146-GGAGCTAC-TACTCCTT


title: Mn-PO-r3-Sat-137-TACGCTGC-TATGCAGT


title: Mn-PO-r3-Sat-136-CGGAGCCT-TATGCAGT


title: Mn-PO-r3-Sat-134-GGAGCTAC-TATGCAGT


title: Mn-PO-r3-Sat-133-ACTCGCTA-TATGCAGT


title: T3049HDMCx

description:
Gr2MCx_combinedisos.tsv
HumMCx_all_gene_coverageGr2.tsv
MCxgr2_analyzed_isos.tsv
MCxgr2_analyzed_DE.tsv

value: Huntington's disease grade 2


title: Mn-PO-r3-Sat-132-TCGACGTC-CTCCTTAC


title: T289HDMCx


title: Mn-PO-r3-Sat-131-TGCAGCTA-CTCCTTAC


title: Mn-PO-r3-Sat-14-CGTACTAG-AGAGGATA


title: H9_clone2-2_Day2 (MiSeq, Sample 11)

description: Exon 2 time course


title: T273HDMCx


title: Mn-PO-r3-Sat-13-TAAGGCGA-AGAGGATA


title: Mn-PO-r3-Sat-130-CGATCAGT-CTCCTTAC


title: Mn-PO-r3-Sat-128-ACTGAGCG-CTCCTTAC


title: Mn-PO-r3-Sat-126-ATGCGCAG-CTCCTTAC


title: T1482HDMCx


title: Mn-PO-r3-Sat-129-CCTAAGAC-CTCCTTAC


title: Mn-PO-r3-Sat-135-GCGTAGTA-TATGCAGT


title: Mn-PO-r3-Sat-123-GCGTAGTA-CTCCTTAC


title: Mn-PO-r3-Sat-127-TAGCGCTC-CTCCTTAC


title: Mn-PO-r3-Sat-124-CGGAGCCT-CTCCTTAC


title: Mn-PO-r3-Sat-122-GGAGCTAC-CTCCTTAC


title: Mn-PO-r3-Sat-12-ATCTCAGG-ATAGAGAG


title: Mn-PO-r3-Sat-117-CCTAAGAC-AGAGGATA


title: Mn-PO-r3-Sat-118-CGATCAGT-AGAGGATA


title: Mn-PO-r3-Sat-119-TGCAGCTA-AGAGGATA


title: Mn-PO-r3-Sat-121-ACTCGCTA-CTCCTTAC


title: Mn-PO-r3-Sat-116-ACTGAGCG-AGAGGATA


title: H9_clone2-1_Day1 (MiSeq, Sample 1)

description: Exon 2 time course


title: Mn-PO-r3-Sat-112-CGGAGCCT-AGAGGATA


title: Mn-PO-r3-Sat-114-ATGCGCAG-AGAGGATA


title: Mn-PO-r3-Sat-111-GCGTAGTA-AGAGGATA


title: Mn-PO-r3-Sat-110-GGAGCTAC-AGAGGATA


title: Mn-PO-r3-Sat-113-TACGCTGC-AGAGGATA


title: Mn-PO-r3-Sat-11-GCTCATGA-ATAGAGAG


title: Mn-PO-r3-Sat-109-ACTCGCTA-AGAGGATA


title: Mn-PO-r3-Sat-108-TCGACGTC-ATAGAGAG


title: Mn-PO-r3-Sat-106-CGATCAGT-ATAGAGAG


title: Mn-PO-r3-Sat-107-TGCAGCTA-ATAGAGAG


title: Mn-PO-r3-Sat-105-CCTAAGAC-ATAGAGAG


title: Mn-PO-r3-Sat-103-TAGCGCTC-ATAGAGAG


title: Mn-PO-r3-Sat-102-ATGCGCAG-ATAGAGAG


title: Mn-PO-r3-Sat-125-TACGCTGC-CTCCTTAC


title: Mn-PO-r3-Sat-101-TACGCTGC-ATAGAGAG


title: Mn-PO-r3-Sat-100-CGGAGCCT-ATAGAGAG


title: Mn-PO-r3-Sat-1-TAAGGCGA-ATAGAGAG


title: Mn-PO-r3-Sat-104-ACTGAGCG-ATAGAGAG


title: Lung_WR_dropletBased_pool1_exp3

data_processing:
(SCRB-seq)  Mapping of read 2 on mRNA refseq using BWA.  Parsing the output based on cell barcode stored in read 1 (first 6bp).  Gene expression computation based on Unique Molecular Identifier (UMI) counts stored in read 1 (base 7 to 16).
(inDrops)  The full procedure for data processing can be found at https://github.com/indrops/indrops (library version v2).  Reads were filtered based on presence in read 1 of two sample barcode components separated by the W1 adaptor sequence (GAGTGATTGCTTGTGACGCCTT).  Read 2 was trimmed using Trimomatic (arguments; LEADING: "28", SLIDINGWINDOW: "4:20", MINLEN: "16").  Barcodes for each read were matched against a list of the 3842 pre-determined barcodes, and errors of up to two nucleotides mismatch were corrected.   Reads with a barcode separated by more than two nucleotides from the reference list were discarded.   The reads were then split into barcode-specific files for mapping and UMI filtering.  The trimmed reads were aligned using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 1000 -m 200 -best -strata -a) to the mouse transcriptome.   The reference transcriptome was built using all annotated transcripts (extended with a 125bp poly-A tail) from the UCSC mm10 genome assembly.  We used a custom Python and PySAM script to process mapped reads into counts of UMI-filtered transcripts per gene (arguments: m = 10, u = 2, d = 400, split-ambigs: False).
Genome_build: Genome_build: mm10 (SCRB-seq), GRCm38.85 from Ensembl (inDrops)
Supplementary_files_format_and_content: Tab-delimited text files include raw unique molecular identifier (UMI) counts across all cells. Rows = genes, and columns = single cells.

extract_protocol:
Live memory CD8+ T cells (DAPI-CD45+CD3e+CD8a+CD62L-CD44+) from lung or liver single cell suspensions were sorted by FACS as: (1) one per well into 96-well plates containing 2 µL of lysis buffer for plate-based scRNA-seq based on a modified SCRB-seq protocol (Soumillon et al., bioRxiv, 2014 - doi:10.1101/003236); or (2) as bulk populations in PBS followed by droplet-based encapsulation for scRNA-seq using the inDrops method (Zilionis et al. (2017). Nat Protoc 12, 44–73).
For plate-based scRNA-seq, sequencing libraries from single CD8+ memory T cells were prepared based on the SCRB-seq protocol (Soumillon et al., bioRxiv, 2014 - doi:10.1101/003236) with modifications using the following workflow: (1) oligo(dT)-primed RT reaction with cell and molecular barcoding followed by pooling of 384 cells; (2) single primer PCR amplication; and (3) full-length cDNA tagmentation and amplication by PCR. For droplet-based scRNA-seq, we followed the inDrops protocol for cell encapsulation followed by library preparation (Zilionis et al. (2017). Nat Protoc 12, 44–73).

tag: treatment

value: MVA s.c. 21d + WR i.n. 16h

tag: protocol id

value: inDrops

tag: cell number


title: Lung_PBS_dropletBased_pool2_exp3

value: MVA s.c. 21d + PBS i.n. 16h


title: Mn-PO-r3-Sat-10-GTAGAGGA-ATAGAGAG


title: Lung_PBS_plateBased_exp2

value: MVA s.c. 24d + PBS i.n. 16h

value: SCRB-seq


title: Liver_PBS_plateBased_exp2

source_name: Liver


title: Lung_WR_plateBased_exp2

value: MVA s.c. 24d + WR i.n. 16h


title: Lung_B8R_plateBased_exp1

value: MVA s.c. 41d + B8R i.n. 16h


title: Liver_WR_plateBased_exp2


title: Lung_WR_plateBased_exp1

value: MVA s.c. 41d + WR i.n. 16h


title: Lung_PBS_plateBased_exp1

value: MVA s.c. 41d + PBS i.n. 16h


title: LV_WT_G3_MW1_5_M20_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt

extract_protocol:
For whole organs, samples were lysed in Trizol and total RNA was extracted by phenol-chloroform extraction followed by purification with Dynabeads MyOne Silane beads (Thermoscientific). For sorted cell populations, CD8+ T cell populations (5,000-10,000 cells per sample) were lysed in RLT buffer (Qiagen) containing 1% beta-mercaptoethanol and total RNA was extracted with Dynabeads MyOne Silane beads. After bead-based enrichment, total RNA samples were purified by on-bead DNase I treatment followed by cleanup with 80% ethanol. RNA concentration was normalized across samples prior library construction.
Total RNA was heat-fragmented to an average size of 500 bp fragments and reverse transcribed with barcoded oligo(dT) primers containing an Illumina-compatible adapter sequence. After RNA degradation, barcoded, single-stranded cDNA samples were pooled and flanked by an Illumina-compatible adapter sequence in their 3’ end using a ‘primer extension’ method with DNA Pol I, Large Klenow Fragment exo minus. cDNA pools flanked on both ends with illumina sequences were then amplified by PCR and sequenced on Illumina sequencers.


title: LV_WT_G3_MW1_5_M21_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_Il22_G3_MW1_5_M25_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt

value: Il22 KO


title: LV_Il15ra_G2_MW1_5_M17_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt

value: Il15ra KO


title: LV_B6129_G2_MW1_5_M16_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_Il15ra_G2_MW1_5_M18_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_Il22_G3_MW1_5_M23_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_B6129_G2_MW1_5_M15_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_Il22_G3_MW1_5_M24_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_WT_G3_MW1_5_M22_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_Il15ra_G2_MW1_5_M19_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: Lung_WR_dropletBased_pool2_exp3


title: LV_Ifng_G1_MW1_5_M11_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt

value: Ifng KO


title: LV_Ifng_G1_MW1_5_M12_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: Lung_PBS_dropletBased_pool1_exp3


title: LV_Csf2_G1_MW1_5_M10_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt

value: Csf2 KO


title: LV_Ifng_G1_MW1_5_M13_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_B6129_G2_MW1_5_M14_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_Csf2_G1_MW1_5_M9_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_Csf2_G1_MW1_5_M8_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_WT_G1_MW1_5_M7_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_WT_G1_MW1_5_M6_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_WT_G1_MW1_5_M5_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_ctrl_M4_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt

value: Uninfected


title: LU_Il22_G3_MW1_5_M23_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_Il22_G3_MW1_5_M24_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_ctrl_M2_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_ctrl_M3_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LV_ctrl_M1_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_Ifng_G1_MW1_5_M13_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_WT_G3_MW1_5_M20_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_Ifng_G1_MW1_5_M12_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_B6129_G2_MW1_5_M16_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_Il15ra_G2_MW1_5_M18_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_B6129_G2_MW1_5_M14_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_Csf2_G1_MW1_5_M9_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_Csf2_G1_MW1_5_M8_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_WT_G1_MW1_5_M7_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_Csf2_G1_MW1_5_M10_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_Ifng_G1_MW1_5_M11_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_WT_G3_MW1_5_M22_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_WT_G1_MW1_5_M5_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_WT_G3_MW1_5_M21_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_Il15ra_G2_MW1_5_M19_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_Il15ra_G2_MW1_5_M17_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_B6129_G2_MW1_5_M15_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_ctrl_M4_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_ctrl_M2_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_WT_G1_MW1_5_M6_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_ctrl_M1_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: LU_ctrl_M3_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: dLN_CD44pos_CD62Lpos_M4_exp4

description:
Sorted CD44+CD62L+ CD8+ T cells
raw_counts_exp4_sortedCD8.txt

source_name: draining lymph node (inguinal)


title: dLN_CD44neg_CD62Lpos_M1_exp4

description:
Sorted CD44-CD62L+ CD8+ T cells
raw_counts_exp4_sortedCD8.txt


title: dLN_CD44neg_CD62Lpos_M4_exp4


title: LU_Il22_G3_MW1_5_M25_exp5

description:
Whole tissue
raw_counts_exp5_KOs.txt


title: dLN_CD44neg_CD62Lpos_M3_exp4


title: dLN_CD44neg_CD62Lpos_M2_exp4


title: SP_M107_5d_WR_exp1

description:
Whole tissue
raw_counts_exp1_day7_day21.txt

source_name: Spleen

value: WR


title: SP_M106_5d_WR_exp1


title: dLN_CD44pos_CD62Lpos_M3_exp4


title: dLN_CD44pos_CD62Lpos_M2_exp4


title: SP_M84_3d_WR_exp1


title: SP_CD44neg_CD62Lpos_M3_exp4


title: SP_CD44neg_CD62Lpos_M4_exp4


title: SP_CD44neg_CD62Lpos_M2_exp4


title: dLN_CD44pos_CD62Lpos_M1_exp4


title: SP_CD44pos_CD62Lpos_M4_exp4


title: SP_M22_12h_WR_exp1


title: SP_M87_3d_MVA_WR_exp1


title: SP_M58_36h_WR_exp1


title: SP_M81_3d_WR_exp1


title: SP_M86_3d_MVA_WR_exp1


title: SP_M21_12h_WR_exp1


title: SP_M111_5d_MVA_WR_exp1


title: SP_M110_5d_MVA_WR_exp1


title: SP_CD44pos_CD62Lpos_M2_exp4


title: SP_CD44pos_CD62Lpos_M1_exp4


title: SP_M28_12h_MVA_WR_exp1


title: SP_M25_12h_MVA_WR_exp1


title: SP_CD44pos_CD62Lneg_M2_exp4

description:
Sorted CD44+CD62L- CD8+ T cells
raw_counts_exp4_sortedCD8.txt


title: SP_M104_5d_MVA_exp1

value: MVA


title: SP_M102_5d_MVA_exp1


title: SP_M59_36h_WR_exp1


title: LV_CD44neg_CD62Lpos_M4_exp4


title: SP_CD44neg_CD62Lpos_M1_exp4


title: SP_CD44pos_CD62Lpos_M3_exp4


title: SP_M79_3d_MVA_exp1


title: LV_CD44neg_CD62Lpos_M3_exp4


title: LV_CD44neg_CD62Lpos_M2_exp4


title: SP_M54_36h_MVA_exp1


title: LV_CD44neg_CD62Lpos_M1_exp4


title: SP_M18_12h_MVA_exp1


title: LV_CD44pos_CD62Lpos_M4_exp4


title: SP_M17_12h_MVA_exp1


title: SP_M55_36h_MVA_exp1


title: LV_CD44pos_CD62Lpos_M3_exp4


title: SP_CD44pos_CD62Lneg_M4_exp4


title: SP_M4_0h_exp1


title: SP_M140_0h_exp1


title: LV_CD44pos_CD62Lpos_M1_exp4


title: LV_CD44pos_CD62Lneg_M4_exp4


title: SP_CD44pos_CD62Lneg_M3_exp4


title: LV_CD44pos_CD62Lpos_M2_exp4


title: LV_CD44pos_CD62Lneg_M3_exp4


title: SP_CD44pos_CD62Lneg_M1_exp4


title: SP_M61_36h_MVA_WR_exp1


title: LV_CD44pos_CD62Lneg_M2_exp4


title: Sk_d_WR_5d_M108_exp1

source_name: Skin


title: LV_CD44pos_CD62Lneg_M1_exp4


title: Sk_d_WR_5d_M109_exp1


title: Sk_d_WR_5d_M107_exp1


title: SP_M138_0h_exp1


title: SP_M77_3d_MVA_exp1


title: LU_CD44neg_CD62Lpos_M3_exp4


title: LU_CD44neg_CD62Lpos_M4_exp4


title: Sk_d_WR_3d_M84_exp1


title: Sk_d_WR_3d_M83_exp1


title: Sk_d_WR_3d_M82_exp1


title: LU_CD44neg_CD62Lpos_M1_exp4


title: Sk_d_WR_5d_M106_exp1


title: LU_CD44neg_CD62Lpos_M2_exp4


title: LU_CD44pos_CD62Lpos_M4_exp4


title: Sk_d_WR_1_5d_M60_exp1


title: Sk_d_WR_1_5d_M58_exp1


title: Sk_d_WR_0_5d_M24_exp1


title: LU_CD44pos_CD62Lneg_M3_exp4


title: LU_CD44pos_CD62Lpos_M2_exp4


title: LU_CD44pos_CD62Lpos_M3_exp4


title: Sk_d_WR_1_5d_M57_exp1


title: LU_CD44pos_CD62Lneg_M2_exp4


title: Sk_d_WR_1_5d_M59_exp1


title: LU_CD44pos_CD62Lpos_M1_exp4


title: LU_CD44pos_CD62Lneg_M4_exp4


title: Sk_d_WR_0_5d_M23_exp1


title: LU_CD44pos_CD62Lneg_M1_exp4


title: Sk_d_WR_0_5d_M22_exp1


title: SP_KO_MW1_5_M12_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt

value: TCRa KO


title: SP_KO_MW1_5_M11_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: Sk_d_MVA_WR_5d_M113_exp1


title: Sk_d_MVA_WR_5d_M112_exp1


title: SP_WT_MW1_5_M08_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: SP_KO_MW1_5_M09_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: Sk_d_WR_3d_M81_exp1


title: Sk_d_MVA_WR_5d_M110_exp1


title: Sk_d_MVA_WR_3d_M88_exp1


title: SP_WT_MW1_5_M07_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: SP_WT_MW1_5_M06_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: SP_WT_MW1_5_M05_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: Sk_d_MVA_WR_3d_M87_exp1


title: SP_WT_ctrl_M04_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: Sk_d_MVA_WR_3d_M85_exp1


title: SP_WT_ctrl_M03_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: Sk_d_MVA_WR_1_5d_M64_exp1


title: Sk_d_MVA_WR_1_5d_M63_exp1


title: Sk_d_MVA_WR_3d_M86_exp1


title: Sk_d_MVA_WR_1_5d_M62_exp1


title: Sk_d_MVA_WR_1_5d_M61_exp1


title: LV_KO_MW1_5_M12_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: LV_KO_MW1_5_M11_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: Sk_d_WR_0_5d_M21_exp1


title: Sk_d_MVA_WR_0_5d_M27_exp1


title: SP_WT_ctrl_M01_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: LV_KO_MW1_5_M09_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: SP_KO_MW1_5_M10_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: Sk_d_MVA_WR_0_5d_M26_exp1


title: LV_WT_MW1_5_M08_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: Sk_d_MVA_WR_5d_M111_exp1


title: Sk_d_MVA_WR_0_5d_M25_exp1


title: LV_WT_MW1_5_M07_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: Sk_d_MVA_5d_M104_exp1


title: LV_WT_MW1_5_M05_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: Sk_d_MVA_5d_M103_exp1


title: SP_WT_ctrl_M02_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: LV_WT_MW1_5_M06_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: Sk_d_MVA_5d_M102_exp1


title: Sk_d_MVA_3d_M77_exp1


title: Sk_d_MVA_3d_M80_exp1


title: Sk_d_MVA_3d_M78_exp1


title: LU_KO_MW1_5_M12_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: LV_WT_ctrl_M04_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: LV_KO_MW1_5_M10_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: LV_WT_ctrl_M02_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: Sk_d_MVA_1_5d_M55_exp1


title: Sk_d_MVA_3d_M79_exp1


title: Sk_d_MVA_1_5d_M54_exp1


title: LU_KO_MW1_5_M09_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: LU_KO_MW1_5_M11_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: LU_KO_MW1_5_M10_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: Sk_d_MVA_1_5d_M53_exp1


title: Sk_d_MVA_5d_M105_exp1


title: Sk_d_MVA_0_5d_M20_exp1


title: LU_WT_MW1_5_M08_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: Sk_d_MVA_0_5d_M18_exp1


title: LU_WT_MW1_5_M07_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: LU_WT_MW1_5_M06_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: LU_WT_MW1_5_M05_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: LU_WT_ctrl_M04_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: Sk_d__control_M139_exp1


title: Sk_d__control_M138_exp1


title: LU_WT_ctrl_M03_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: LV_WT_ctrl_M03_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: Sk_d__control_M1_exp1


title: Sk_d__control_M140_exp1


title: LV_WT_ctrl_M01_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: LU_WT_ctrl_M02_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: LU_WT_ctrl_M01_exp3

description:
Whole tissue
raw_counts_exp3_TcraKO.txt


title: SP_d80_control_d0_M8_exp2

description:
Whole tissue
raw_counts_exp2_day21_day80.txt


title: SP_d80_control_d0_M7_exp2


title: SI_WR_5d_M107_exp1

source_name: Small intestine


title: SI_WR_3d_M84_exp1


title: SI_WR_3d_M83_exp1


title: SI_WR_5d_M108_exp1


title: SI_WR_3d_M81_exp1


title: SP_d80_MVA_WR_d1_5_M4_exp2


title: Sk_d_MVA_1_5d_M56_exp1


title: SP_d80_control_d0_M5_exp2


title: SP_d80_MVA_WR_d1_5_M3_exp2


title: SI_WR_1_5d_M60_exp1


title: SP_d80_MVA_WR_d1_5_M2_exp2


title: SP_d80_MVA_WR_d1_5_M1_exp2


title: SI_WR_1_5d_M59_exp1


title: SI_WR_1_5d_M58_exp1


title: SI_WR_1_5d_M57_exp1


title: medLN_d80_control_d0_M7_exp2

source_name: Mediastinal lymph node


title: medLN_d80_MVA_WR_d1_5_M4_exp2


title: SI_WR_0_5d_M24_exp1


title: SI_WR_0_5d_M22_exp1


title: medLN_d80_control_d0_M8_exp2


title: medLN_d80_control_d0_M5_exp2


title: SI_WR_0_5d_M23_exp1


title: SI_WR_5d_M109_exp1


title: SP_d80_control_d0_M6_exp2


title: medLN_d80_MVA_WR_d1_5_M1_exp2


title: SI_WR_3d_M82_exp1


title: medLN_d80_MVA_WR_d1_5_M3_exp2


title: medLN_d80_MVA_WR_d1_5_M2_exp2


title: SI_MVA_WR_5d_M113_exp1


title: SI_MVA_WR_5d_M112_exp1


title: SI_MVA_WR_3d_M88_exp1


title: SI_MVA_WR_5d_M111_exp1


title: SI_MVA_WR_3d_M86_exp1


title: SI_MVA_WR_5d_M110_exp1


title: SI_MVA_WR_3d_M87_exp1


title: LU_d80_control_d0_M8_exp2


title: SI_WR_0_5d_M21_exp1


title: LU_d80_control_d0_M6_exp2


title: LU_d80_control_d0_M7_exp2


title: LU_d80_MVA_WR_d1_5_M3_exp2


title: LU_d80_MVA_WR_d1_5_M4_exp2


title: SI_MVA_WR_1_5d_M62_exp1


title: SI_MVA_WR_1_5d_M61_exp1


title: SI_MVA_WR_3d_M85_exp1


title: LI_d80_control_d0_M6_exp2


title: LU_d80_MVA_WR_d1_5_M2_exp2


title: SI_MVA_WR_1_5d_M63_exp1


title: LI_d80_MVA_WR_d1_5_M4_exp2


title: LI_d80_control_d0_M5_exp2


title: LU_d80_control_d0_M5_exp2


title: SI_MVA_WR_0_5d_M28_exp1


title: LI_d80_MVA_WR_d1_5_M3_exp2


title: SI_MVA_WR_0_5d_M27_exp1


title: SI_MVA_WR_0_5d_M26_exp1


title: LI_d80_MVA_WR_d1_5_M1_exp2


title: LI_d80_MVA_WR_d1_5_M2_exp2


title: SI_MVA_5d_M105_exp1


title: SP_d21_MVA_WR_d1_5_M16_exp2


title: SI_MVA_WR_1_5d_M64_exp1


title: SP_d21_MVA_WR_d1_5_M14_exp2


title: SI_MVA_3d_M80_exp1


title: SP_d21_MVA_WR_d1_5_M15_exp2


title: SP_d21_MVA_WR_d0_5_M12_exp2


title: SP_d21_MVA_WR_d1_5_M13_exp2


title: SI_MVA_5d_M102_exp1


title: LU_d80_MVA_WR_d1_5_M1_exp2


title: SI_MVA_5d_M104_exp1


title: SI_MVA_5d_M103_exp1


title: SI_MVA_3d_M77_exp1


title: SP_d21_MVA_d21_M8_exp2


title: SP_d21_MVA_WR_d0_5_M11_exp2


title: SP_d21_MVA_d21_M7_exp2


title: SI_MVA_1_5d_M55_exp1


title: SI_MVA_1_5d_M54_exp1


title: SP_d21_MVA_WR_d0_5_M10_exp2


title: SP_d21_MVA_d21_M5_exp2


title: SP_d21_MVA_d21_M6_exp2


title: SI_MVA_1_5d_M53_exp1


title: SI_MVA_WR_0_5d_M25_exp1


title: SP_d21_control_d0_M4_exp2


title: SI_MVA_0_5d_M19_exp1


title: SP_d21_control_d0_M3_exp2


title: SI_MVA_0_5d_M20_exp1


title: SI_MVA_0_5d_M18_exp1


title: SI_MVA_3d_M79_exp1


title: SI_MVA_0_5d_M17_exp1


title: SI_d21_MVA_WR_d1_5_M14_exp2


title: SI__control_M139_exp1


title: SI__control_M1_exp1


title: LV_WR_5d_M109_exp1


title: SI_d21_MVA_WR_d1_5_M15_exp2


title: SP_d21_control_d0_M2_exp2


title: SI_MVA_3d_M78_exp1


title: SI_d21_MVA_WR_d1_5_M13_exp2


title: SI_d21_MVA_WR_d1_5_M16_exp2


title: SP_d21_control_d0_M1_exp2


title: SI__control_M138_exp1


title: LV_WR_5d_M108_exp1


title: LV_WR_5d_M106_exp1


title: LV_WR_3d_M84_exp1


title: SI_d21_MVA_WR_d0_5_M11_exp2


title: LV_WR_5d_M107_exp1


title: SI_d21_MVA_WR_d0_5_M10_exp2


title: SI_d21_control_d0_M4_exp2


title: SI_d21_control_d0_M2_exp2


title: SI_d21_control_d0_M3_exp2


title: SI_d21_control_d0_M1_exp2


title: LV_WR_3d_M83_exp1


title: LV_WR_3d_M82_exp1


title: medLN_d21_MVA_WR_d1_5_M15_exp2


title: LV_WR_1_5d_M60_exp1


title: medLN_d21_MVA_WR_d1_5_M14_exp2


title: medLN_d21_MVA_WR_d1_5_M16_exp2


title: LV_WR_1_5d_M58_exp1


title: medLN_d21_MVA_WR_d1_5_M13_exp2


title: LV_WR_1_5d_M59_exp1


title: LV_WR_0_5d_M24_exp1


title: LV_WR_0_5d_M22_exp1


title: medLN_d21_MVA_WR_d0_5_M9_exp2


title: medLN_d21_MVA_WR_d0_5_M10_exp2


title: medLN_d21_MVA_WR_d0_5_M11_exp2


title: LV_MVA_WR_5d_M113_exp1


title: medLN_d21_MVA_d21_M6_exp2


title: LV_WR_0_5d_M21_exp1


title: medLN_d21_MVA_WR_d0_5_M12_exp2


title: medLN_d21_MVA_d21_M7_exp2


title: LV_WR_0_5d_M23_exp1


title: medLN_d21_control_d0_M4_exp2


title: medLN_d21_control_d0_M3_exp2


title: medLN_d21_MVA_d21_M8_exp2


title: medLN_d21_MVA_d21_M5_exp2


title: LV_MVA_WR_5d_M110_exp1


title: LV_MVA_WR_5d_M111_exp1


title: LV_MVA_WR_3d_M87_exp1


title: LV_MVA_WR_3d_M88_exp1


title: LV_WR_3d_M81_exp1


title: LV_MVA_WR_5d_M112_exp1


title: medLN_d21_control_d0_M1_exp2


title: medLN_d21_control_d0_M2_exp2


title: LV_WR_1_5d_M57_exp1


title: LV_MVA_WR_3d_M86_exp1


title: Sk_d_MVA21_WR_1_5d_M16_exp1


title: LV_MVA_WR_3d_M85_exp1


title: Sk_d_MVA21_WR_1_5d_M15_exp1


title: Sk_d_MVA21_WR_1_5d_M14_exp1


title: LV_MVA_WR_1_5d_M64_exp1


title: LV_MVA_WR_1_5d_M63_exp1


title: Sk_d_MVA21_WR_0_5d_M9_exp1


title: LV_MVA_WR_1_5d_M62_exp1


title: LV_MVA_WR_1_5d_M61_exp1


title: Sk_d_MVA21_WR_0_5d_M12_exp1


title: Sk_d_MVA21_WR_0_5d_M11_exp1


title: LV_MVA_WR_0_5d_M28_exp1


title: Sk_d_MVA21_WR_0_5d_M10_exp1


title: LV_MVA_5d_M104_exp1


title: LV_MVA_WR_0_5d_M27_exp1


title: LV_MVA_WR_0_5d_M25_exp1


title: Sk_d_MVA_21d_M6_exp1


title: LV_MVA_5d_M105_exp1


title: Sk_d_MVA_21d_M5_exp1


title: Sk_d_MVA_21d_M7_exp1


title: LV_MVA_WR_0_5d_M26_exp1


title: Sk_d_MVA_21d_M8_exp1


title: LV_MVA_5d_M103_exp1


title: Sk_d_control_M2_exp1


title: Sk_d_control_M1_exp1


title: Sk_d_control_M3_exp1


title: LV_MVA_5d_M102_exp1


title: Sk_d_control_M4_exp1


title: LV_MVA_3d_M80_exp1


title: LV_MVA21_WR_1_5d_M16_exp1


title: LV_MVA21_WR_1_5d_M15_exp1


title: Sk_d_MVA21_WR_1_5d_M13_exp1


title: LV_MVA_3d_M79_exp1


title: LV_MVA_1_5d_M56_exp1


title: LV_MVA_3d_M77_exp1


title: LV_MVA_3d_M78_exp1


title: LV_MVA_1_5d_M55_exp1


title: LV_MVA21_WR_1_5d_M14_exp1


title: LV_MVA21_WR_1_5d_M13_exp1


title: LV_MVA21_WR_0_5d_M9_exp1


title: LV_MVA21_WR_0_5d_M12_exp1


title: LV_MVA21_WR_0_5d_M10_exp1


title: LV_MVA21_WR_0_5d_M11_exp1


title: LV_MVA_0_5d_M19_exp1


title: LV_MVA_0_5d_M18_exp1


title: LV_MVA_0_5d_M17_exp1


title: LV_MVA_21d_M7_exp1


title: LV_MVA_0_5d_M20_exp1


title: LV_MVA_21d_M8_exp1


title: LV_MVA_21d_M6_exp1


title: LV__control_M138_exp1


title: LV_MVA_21d_M5_exp1


title: LV_control_M4_exp1


title: LV__control_M139_exp1


title: LV__control_M1_exp1


title: LV_control_M3_exp1


title: LU_WR_5d_M108_exp1


title: LV_MVA_1_5d_M54_exp1


title: LV_control_M2_exp1


title: LU_WR_5d_M106_exp1


title: LU_MVA21_WR_1_5d_M16_exp1


title: LV_MVA_1_5d_M53_exp1


title: LU_MVA21_WR_1_5d_M15_exp1


title: LU_WR_3d_M84_exp1


title: LU_MVA21_WR_1_5d_M14_exp1


title: LU_WR_3d_M83_exp1


title: LV__control_M140_exp1


title: LU_MVA21_WR_1_5d_M13_exp1


title: LU_WR_1_5d_M60_exp1


title: LU_WR_3d_M81_exp1


title: LU_WR_3d_M82_exp1


title: LU_MVA21_WR_0_5d_M11_exp1


title: LU_WR_1_5d_M59_exp1


title: LU_MVA21_WR_0_5d_M10_exp1


title: LU_WR_5d_M109_exp1


title: LU_WR_1_5d_M57_exp1


title: LU_MVA_21d_M7_exp1


title: LU_WR_1_5d_M58_exp1


title: LU_MVA_21d_M8_exp1


title: LU_MVA_21d_M6_exp1


title: LU_WR_5d_M107_exp1


title: LV_control_M1_exp1


title: LU_WR_0_5d_M23_exp1


title: LU_WR_0_5d_M24_exp1


title: LU_WR_0_5d_M22_exp1


title: LU_MVA_21d_M5_exp1


title: LU_control_M4_exp1


title: LU_control_M3_exp1


title: LU_control_M2_exp1


title: LU_WR_0_5d_M21_exp1


title: LU_MVA_WR_5d_M113_exp1


title: LU_control_M1_exp1


title: LU_MVA21_WR_0_5d_M9_exp1


title: BR_MVA21_WR_1_5d_M16_exp1

source_name: Brain


title: LU_MVA_WR_5d_M112_exp1


title: BR_MVA21_WR_1_5d_M15_exp1


title: LU_MVA21_WR_0_5d_M12_exp1


title: BR_MVA21_WR_1_5d_M13_exp1


title: LU_MVA_WR_5d_M111_exp1


title: BR_MVA21_WR_1_5d_M14_exp1


title: BR_MVA21_WR_0_5d_M9_exp1


title: LU_MVA_WR_3d_M87_exp1


title: LU_MVA_WR_5d_M110_exp1


title: BR_MVA21_WR_0_5d_M11_exp1


title: LU_MVA_WR_1_5d_M64_exp1


title: BR_MVA21_WR_0_5d_M12_exp1


title: LU_MVA_WR_3d_M86_exp1


title: BR_MVA21_WR_0_5d_M10_exp1


title: LU_MVA_WR_3d_M85_exp1


title: LU_MVA_WR_1_5d_M62_exp1


title: BR_MVA_21d_M8_exp1


title: BR_MVA_21d_M7_exp1


title: LU_MVA_WR_0_5d_M27_exp1


title: BR_MVA_21d_M6_exp1


title: LU_MVA_WR_1_5d_M61_exp1


title: LU_MVA_WR_0_5d_M26_exp1


title: LU_MVA_WR_0_5d_M28_exp1


title: BR_MVA_21d_M5_exp1


title: LU_MVA_WR_0_5d_M25_exp1


title: BR_control_M4_exp1


title: BR_control_M3_exp1


title: LU_MVA_WR_3d_M88_exp1


title: BR_control_M2_exp1


title: BR_control_M1_exp1


title: LU_MVA_5d_M103_exp1


title: LU_MVA_5d_M104_exp1


title: LU_MVA_3d_M80_exp1


title: LU_MVA_3d_M78_exp1


title: BM_MVA21_WR_1_5d_M15_exp1

source_name: Bone marrow


title: BM_MVA21_WR_1_5d_M13_exp1


title: LU_MVA_1_5d_M56_exp1


title: LU_MVA_1_5d_M55_exp1


title: LU_MVA_3d_M77_exp1


title: BM_MVA21_WR_0_5d_M12_exp1


title: BM_MVA21_WR_0_5d_M9_exp1


title: LU_MVA_1_5d_M54_exp1


title: BM_MVA21_WR_0_5d_M10_exp1


title: BM_MVA_21d_M6_exp1


title: LU_MVA_0_5d_M20_exp1


title: BM_MVA_21d_M5_exp1


title: LU_MVA_5d_M105_exp1


title: BM_MVA_21d_M8_exp1


title: LU_MVA_1_5d_M53_exp1


title: LU_MVA_0_5d_M18_exp1


title: LU_MVA_0_5d_M19_exp1


title: BM_control_M4_exp1


title: BM_control_M3_exp1


title: BM_control_M2_exp1


title: LU__control_M139_exp1


title: LU_MVA_0_5d_M17_exp1


title: LU_MVA_5d_M102_exp1


title: BM_MVA21_WR_1_5d_M16_exp1


title: LU__control_M1_exp1


title: BM_MVA21_WR_1_5d_M14_exp1


title: dLN_WR_5d_M109_exp1


title: Villin-Cre+_ infected_18h_Salmonella_intestinal_epithelial_cells_3

first: Daniel

last: Mucida

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
reads were aligned to Mouse Ensembl genes using the STAR version 2.3.0 software
Differential expression was determined by use of the Cufflinks software with default settings
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes RPKM

extract_protocol:
Intraepithelial lymphocytes were isolated as previously described(Mucida et al., 2007). Briefly, small and large intestines were removed and placed in chilled HBSS media (Gibco) containing 2% FCS. The intestines were carefully cleaned from the mesentery and flushed of fecal content.  Intestines were opened longitudinally and then cut into 1 cm pieces. The intestinal tissue was transferred to a 50 ml Falcon tubes containing 25 ml of cold HBSS complemented with 2% FCS and 5 mM EDTA and shaken (2x) at 230 rpm for 20 min at 37°C. The tissue suspension was passed through a stainless steel sieve into 50-ml conical tubes and the cells were pelleted by centrifugation at 1200 rpm for 10 min at 4°C. The cell pellet was resuspended in complete HBSS, layered over a discontinuous 40/70% Percoll gradient, and centrifuged at 2000 rpm for 30 min. Cells from the 40/70% interface were collected, washed and resuspended in complete RPMI media. These purified cells constituted the intraepithelial lymphocyte (IEL) population.  Cells were sorted using a FACS ARIAII with markers as shown above. Total RNA was extracted using the RNAeasy kit from Qiagen.
For total RNA from TCRgd IELs, RNA libraries were prepared using the SMART-Seq™ v4 Ultra™ Low Input RNA kit (ClonTech Labs) . For total RNA from intestinal epithelial cells, RNA libraries were prepared using TruSeq® Stranded mRNA Sample Preparation.  All samples were sequenced using 75 base pair single end reading on a NextSeq 500 instrument (Illumina) at High Output setting.

treatment_protocol: Mice were orally inoculated with 10^8 CFU of S. enterica serovar Typhimurium (SL1344) .  Gene expression analysis was performed 18 hours after inoculation as indicated. Briefly, a single aliquot of Salmonella was grown in 3 ml of LB overnight at 37ºC with agitation, and then the bacteria were sub-cultured (1:30) into 3 ml of LB for 3.5h at 37ºC with agitation. The bacteria were next diluted to final concentration in 1 ml of DPBS. Bacteria were inoculated by gavage into recipient mice in a total volume of 100µl.

tag: genotype/variation

value: Salmonella

value: Small intestine

value: intestinal epithelial cells

tag: flow cytrometry markers


title: dLN_WR_3d_M84_exp1


title: dLN_WR_5d_M108_exp1


title: dLN_WR_5d_M106_exp1


title: Villin-Cre+_ infected_18h_Salmonella_intestinal_epithelial_cells_2


title: dLN_WR_3d_M82_exp1


title: Villin-Cre-_ infected_18h_Salmonella_intestinal_epithelial_cells_2


title: dLN_WR_3d_M81_exp1


title: WT_infected_18h_Salmonella_intestinal_epithelial_cells_3

value: wildtype


title: dLN_WR_1_5d_M59_exp1


title: dLN_WR_1_5d_M60_exp1


title: WT_naïve_intestinal_epithelial_cells_3

value: naïve


title: dLN_WR_1_5d_M58_exp1


title: WT_infected_18h_Salmonella_intestinal_epithelial_cells_2


title: WT_infected_18h_Salmonella_intestinal_epithelial_cells_1


title: dLN_WR_1_5d_M57_exp1


title: dLN_WR_0_5d_M24_exp1


title: BM_control_M1_exp1


title: dLN_WR_0_5d_M23_exp1


title: Villin-Cre+_ infected_18h_Salmonella TCRgd+_2

source_name: Villin-Cre+_ infected_18h_Salmonella TCRgd+ T cells

value: intraepithelial lymphocytes


title: WT_naïve_intestinal_epithelial_cells_2


title: WT_naïve_intestinal_epithelial_cells_1


title: Villin-Cre+_ infected_18h_Salmonella_intestinal_epithelial_cells_1


title: dLN_WR_0_5d_M22_exp1


title: Villin-Cre+_ infected_18h_Salmonella TCRgd+_1


title: dLN_WR_0_5d_M21_exp1


title: dLN_WR_3d_M83_exp1


title: Villin-Cre-_ infected_18h_Salmonella_intestinal_epithelial_cells_3


title: Villin-Cre-_ infected_18h_Salmonella TCRgd+_2

source_name: Villin-Cre-_ infected_18h_Salmonella TCRgd+ T cells


title: Villin-Cre-_ infected_18h_Salmonella TCRgd+_1


title: dLN_MVA_WR_5d_M113_exp1


title: dLN_MVA_WR_5d_M112_exp1


title: Villin-Cre-_ infected_18h_Salmonella_intestinal_epithelial_cells_1


title: dLN_MVA_WR_5d_M111_exp1


title: WT_infected_18h_Salmonella TCRgd+_2


title: WT_infected_18h_Salmonella TCRgd+_1


title: dLN_MVA_WR_5d_M110_exp1


title: WT_naïve_TCRgd+_3

source_name: WT_naïve_TCRgd+ T_cells


title: dLN_MVA_WR_3d_M87_exp1


title: WT_naïve_TCRgd+_1


title: dLN_MVA_WR_3d_M86_exp1


title: WT_naïve_TCRgd+_2


title: dLN_MVA_WR_3d_M85_exp1


title: dLN_MVA_WR_1_5d_M63_exp1


title: SpiB KO rep2

source_name: SpiB KO_activated B cells

value: Spi1fl/fl Cd23+/+ Spib-/-

value: lymph node

value: Activated B cells


title: PU.1 cKO rep2

source_name: PU.1 cKO_activated B cells

value: Spi1fl/fl Cd23T/+


title: WT_infected_18h_Salmonella TCRgd+_3


title: PU.1 SpiB DKO rep1

source_name: PU.1 SpiB DKO_activated B cells

value: Spi1fl/fl Cd23T/+ Spib-/-


title: SpiB KO rep1


title: dLN_MVA_WR_0_5d_M27_exp1


title: Control rep2

source_name: Control_activated B cells


title: dLN_MVA_WR_0_5d_M28_exp1


title: dLN_MVA_WR_1_5d_M61_exp1


title: dLN_MVA_WR_1_5d_M62_exp1


title: dLN_MVA_WR_0_5d_M26_exp1


title: PU.1 cKO rep1


title: dLN_MVA_5d_M105_exp1


title: dLN_MVA_5d_M103_exp1


title: dLN_MVA_5d_M102_exp1


title: Control rep1


title: dLN_MVA_5d_M104_exp1


title: dLN_MVA_3d_M79_exp1


title: dLN_MVA_3d_M80_exp1


title: dLN_MVA_WR_1_5d_M64_exp1


title: dLN_MVA_3d_M77_exp1


title: dLN_MVA_3d_M78_exp1


title: dLN_MVA_1_5d_M56_exp1


title: dLN_MVA_1_5d_M54_exp1


title: dLN_MVA_1_5d_M53_exp1


title: PU.1 SpiB DKO rep2


title: dLN_MVA_WR_3d_M88_exp1


title: dLN_MVA_0_5d_M20_exp1


title: dLN_MVA_0_5d_M19_exp1


title: dLN_MVA_0_5d_M17_exp1


title: dLN_MVA_0_5d_M18_exp1


title: dLN_MVA_WR_0_5d_M25_exp1


title: dLN__control_M139_exp1


title: dLN__control_M138_exp1


title: BR_WR_3d_M83_exp1


title: BR_WR_5d_M106_exp1


title: BR_WR_5d_M109_exp1


title: BR_WR_5d_M108_exp1


title: BR_WR_5d_M107_exp1


title: BR_WR_3d_M84_exp1


title: BR_WR_3d_M82_exp1


title: BR_WR_1_5d_M58_exp1


title: BR_WR_1_5d_M60_exp1


title: BR_WR_1_5d_M57_exp1


title: dLN_MVA_1_5d_M55_exp1


title: BR_WR_1_5d_M59_exp1


title: BR_WR_3d_M81_exp1


title: BR_WR_0_5d_M23_exp1


title: BR_WR_0_5d_M21_exp1


title: BR_MVA_WR_5d_M111_exp1


title: BR_MVA_WR_5d_M112_exp1


title: BR_MVA_WR_3d_M88_exp1


title: BR_MVA_WR_3d_M87_exp1


title: BR_MVA_WR_5d_M113_exp1


title: BR_MVA_WR_3d_M85_exp1


title: BR_MVA_WR_1_5d_M64_exp1


title: BR_MVA_WR_1_5d_M62_exp1


title: BR_MVA_WR_1_5d_M63_exp1


title: BR_MVA_WR_1_5d_M61_exp1


title: BR_MVA_WR_0_5d_M28_exp1


title: BR_MVA_WR_0_5d_M27_exp1


title: BR_MVA_WR_0_5d_M26_exp1