title: Run-74_H09_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-H09_S93_comb


title: Run-74_F10_CD8_YFV_short_paired-end

status: Public on Jul 17 2017

type: SRA

city: Berkeley

first: Shaked

last: Afik

state: CA

address: Stanley Hall

department: Computational Biology Graduate Group

country: USA

institute: UC Berkeley

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-F10_S70_comb

library_source: transcriptomic

data_processing:
Low quality bases were trimmed with trimmomatic using the following parameters: LEADING:15, TRAILING:15, SLIDINGWINDOW:4:15, MINLEN:16.
Trimmed reads were then aligned to the genome (hg38 or mm10 for human or mouse samples, respectively) with TopHat2 for TCR reconstruction, and aligned to the transcriptome with RSEM for transcriptome quantification.
For transcriptome analysis of the human CMV and YFV donors (donors 1 and 2), low quality cells were filtered out prior to normalization. Cells were filtered out if their read depth was less than 1 million pairs or if the cell expressed less than 20% of all expressed transcript, where a transcript was considered expressed if it had a TPM value of >10 in at least 10% of cells, leaving 353 out of 378 cells for further analysis.
Normalization of TPM values was done with our newly developed normalization framework SCONE. In our study, the chosen normalization first scaled each sample with the DEseq scaling factor to account for differences in sequencing depth. Then, we ran RUVg with k=1.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: Normalized TPM expression matrix of high quality cells from donors 1 and 2.

molecule: polyA RNA

organism: Homo sapiens

source_name: CD8+ YFV-specific T cell donor 2

growth_protocol: Mouse LCMV: Female C57BL/6 mice (The Jackson Laboratory), aged 7 weeks, were infected with 2x105 plaque forming units (PFU) LCMV Armstrong intraperitoneally i.p. or 4x106 PFU LCMV Clone 13 i.v. Human Donor 2: A healthy volunteer was vaccinated with a single dose (0.5 ml containing at least 105 PFU) of 17D live-attenuated yellow fever vaccine strain administered subcutaneously. Seroconversion after vaccination was confirmed by assaying the neutralizing antibody titers for YF-17D. Human Donor 3: Patient 355 (59yr old Male, infected with genotype 1a HCV, baseline viral load 467,000 IU/ml) received a prime vaccination of ChAd3-NSmut (2.5x1010 viral particles) and an MVA-NSmut (2x108 plaque forming units) boost vaccination 8 weeks later.

extract_protocol:
Mouse LCMV: Peripheral blood was obtained from the mice at day 7 post infection (p.i.) and lymphocytes were enriched using LSM density centrifugation. Cells were prestained with a near-IR fixable live/dead marker (Life Technologies, cat# L34976) and an APC- conjugated dextramer reagent for gp33 (Immudex, cat# A2160-APC) according to manufacturer recommendations. The cells were then stained with the following antibodies: FITC 2B4 (BioLegend, cat# 133504), PerCP-Cy5.5 CD44 (BioLegend, cat# 103032), PE KLRG1 (BioLegend, cat# 138408), PE-Cy7 PD1 (BioLegend, cat# 135215), BV421 CD127 (BioLegend, cat# 135024), BV510 CD8A (BioLegend, cat# 100752). Human Donor 1: Blood samples were obtained from a donor with detectable NLV-specific CD8+ T cell response. Lymphocytes were enriched via Ficoll gradient and prestained with a near-IR fixable live/dead marker (Life Technologies, cat# L34976) and an APC-conjugated dextramer reagent (Immudex, cat# WB2132-APC). The cells were then stained with the following antibodies: FITC CD8A (BioLegend, cat# 300906), PerCP-Cy5.5 CCR7 (BioLegend, cat# 353220), PE CD3 (BioLegend, cat# 317308), BV605 CD45RA (BioLegend, cat# 304133). Human Donor 2: A whole blood sample was obtained 9 months post-vaccination and lymphocytes were enriched from whole blood via Ficoll gradient centrifugation and a CD8 negative selection magnetic bead kit (Miltenyi Biotec). Cells were prestained with a live/dead marker (Life Technologies, cat# L34976) and an APC-labeled tetramer reagent (NS4B 214–222 LLWNGPMAV, kindly provided by Dr. Rafi Ahmed). The cells were then stained with the following antibodies: FITC CD8A (BioLegend, cat# 300906), PE CXCR3 (BioLegend, cat# 353705), PE-Cy7 CCR7 (BioLegend, cat# 353226), BV421 IL2Rb (BioLegend, cat# 339009), BV510 CD3 (BioLegend, cat# 317332), BV605 CD95 (BioLegend, cat# 305627), BV780 CD45RA (BioLegend, cat# 304140). Human Donor 3: PBMC were collected 14 weeks post-boost vaccination. PBMC were thawed and prestained with a live/dead marker (Life Technologies, cat# L34976) and a PE-conjugated pentamer reagent (PE-labeled HCV NS31406–1415 (KLSALGINAV; HLA-A*0201)). The cells were then stained with the following antibodies: FITC 2B4 (BioLegend, cat# 329505), PerCP-eFluor 710 LAG3 (eBioscience, cat# 46-2239), PE-Cy7 CCR7 (BioLegend, cat# 329919), APC CD39 (BioLegend, cat# 328209), BV421 PD1 (BioLegend, cat# 329919), BV510 CD3 (BioLegend, cat# 317332), BV605 CD8A (BioLegend, cat# 301040), BV780 CD45RA (BioLegend, cat# 304140).
Single cell lysates were converted to cDNA following capture with Agencourt RNA Clean beads using the SmartSeq2 protocol. The cDNA was amplified using 22-24 PCR enrichment cycles prior to quantification and dual-index barcoding with the Illumina Nextera XT kit. The libraries were enriched with 12 cycles of PCR, then combined in equal volumes prior to final bead cleanup and sequencing.

tag: tissue

value: CD8+ YFV-specific T cell

tag: donor

value: Donor 2

tag: number of cells in sample


title: Run-74_F09_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-F09_S69_comb


title: Run-74_F08_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-F08_S68_comb


title: Run-74_F06_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-F06_S66_comb


title: Run-74_F11_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-F11_S71_comb


title: Run-74_F12_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-F12_S72_comb


title: Run-74_F07_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-F07_S67_comb


title: Run-74_F02_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
NA
NA

source_name: CD8+ Naive T cell donor 2

value: CD8+ Naive T cell


title: Run-74_F03_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-F03_S63_comb

source_name: CD8+ Effector Memory T cell donor 2

value: CD8+ Effector Memory T cell


title: Run-74_E12_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-E12_S60_comb


title: Run-74_F04_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-F04_S64_comb


title: Run-74_E11_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-E11_S59_comb


title: Run-74_F01_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-F01_S61_comb


title: Run-74_G07_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-G07_S79_comb


title: Run-74_E09_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-E09_S57_comb


title: Run-74_E10_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-E10_S58_comb


title: Run-74_E07_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-E07_S55_comb


title: Run-74_E08_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-E08_S56_comb


title: Run-74_E06_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-E06_S54_comb


title: Run-74_E05_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-E05_S53_comb


title: Run-74_E04_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-E04_S52_comb


title: Run-74_E03_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-E03_S51_comb


title: Run-74_D09_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-D09_S45_comb


title: Run-74_D10_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-D10_S46_comb


title: Run-74_D12_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-D12_S48_comb


title: Run-74_D11_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-D11_S47_comb


title: Run-74_E02_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-E02_S50_comb


title: Run-74_E01_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-E01_S49_comb


title: Run-74_F05_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-F05_S65_comb


title: Run-74_D08_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-D08_S44_comb


title: Run-74_D07_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-D07_S43_comb


title: Run-74_C05_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-C05_S29_comb


title: Run-74_C06_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-C06_S30_comb


title: Run-74_D05_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-D05_S41_comb


title: Run-74_D02_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-D02_S38_comb


title: Run-74_C11_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-C11_S35_comb


title: Run-74_D03_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
NA
NA


title: Run-74_D04_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-D04_S40_comb


title: Run-74_C12_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-C12_S36_comb


title: Run-74_C08_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-C08_S32_comb


title: Run-74_C09_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-C09_S33_comb


title: Run-74_C07_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-C07_S31_comb


title: Run-74_D01_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-D01_S37_comb


title: Run-74_C10_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-C10_S34_comb


title: Run-74_C03_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-C03_S27_comb


title: Run-74_C04_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-C04_S28_comb


title: Run-74_C02_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
NA
NA


title: Run-74_D06_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-D06_S42_comb


title: Run-74_B12_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-B12_S24_comb


title: Run-74_C01_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-C01_S25_comb


title: Run-74_B06_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-B06_S18_comb


title: Run-74_B04_CD8_EffectorMemory_short_paired-end


title: Run-74_B02_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
NA
NA


title: Run-74_B05_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-B05_S17_comb


title: Run-74_B09_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-B09_S21_comb


title: Run-74_B08_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-B08_S20_comb


title: Run-74_B03_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-B03_S15_comb


title: Run-74_B01_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
NA
NA


title: Run-74_A11_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-A11_S11_comb


title: Run-74_A12_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
NA
NA


title: Run-74_A10_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-A10_S10_comb


title: Run-74_A03_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
NA
NA


title: Run-74_B11_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-B11_S23_comb


title: Run-74_A09_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-A09_S9_comb


title: Run-74_A02_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-A02_S2_comb


title: Run-74_A01_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
NA
NA


title: Run-74_A04_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-A04_S4_comb


title: Run-74_A08_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-A08_S8_comb


title: Run-74_A05_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-A05_S5_comb


title: Run-74_B10_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-B10_S22_comb


title: Run-74_B07_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-B07_S19_comb


title: HCV_355_p3_tet_50_A12_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA

source_name: CD8+ HCV-specific T cell donor 3

value: CD8+ HCV-specific T cell

value: Donor 3


title: HCV_355_p3_tet_1_H12_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_H11_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_H09_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_H08_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: Run-74_A06_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-A06_S6_comb


title: HCV_355_p3_tet_1_H05_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_H03_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_H04_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_G12_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_H06_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_G11_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_G08_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: Run-74_A07_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-A07_S7_comb


title: HCV_355_p3_tet_1_G05_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_G09_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_H10_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_G04_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_F10_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_G10_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_F12_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_G03_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_F11_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_F07_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_F08_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_H07_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_F06_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_F05_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_F04_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_F03_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_E12_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_G07_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_E11_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_E07_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_E10_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_E03_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_E08_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_E05_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_E06_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_G06_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_F09_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_D09_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_D07_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_D12_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_D10_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_D06_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_E09_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_E04_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_D04_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_C09_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_D03_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_C07_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_C05_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_C06_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_D08_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_C10_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_B12_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_C11_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_D11_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_C04_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_B09_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_B07_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_B08_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_B11_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_C03_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_D05_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_A09_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_A11_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_A07_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_B05_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_C12_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_B10_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_C08_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_B06_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_B04_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_A08_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_A05_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_A06_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_A10_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_Naive_1_H02_short_paired-end

description:
CD8+ Naive T cell donor 3
NA
NA

source_name: CD8+ Naive T cell donor 3


title: HCV_355_p3_Naive_50_A01_short_paired-end

description:
CD8+ Naive T cell donor 3
NA
NA


title: HCV_355_p3_Naive_1_H01_short_paired-end

description:
CD8+ Naive T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_B03_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_Naive_1_E02_short_paired-end

description:
CD8+ Naive T cell donor 3
NA
NA


title: HCV_355_p3_Naive_1_F02_short_paired-end

description:
CD8+ Naive T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_A04_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_Naive_1_G01_short_paired-end

description:
CD8+ Naive T cell donor 3
NA
NA


title: HCV_355_p3_Naive_1_G02_short_paired-end

description:
CD8+ Naive T cell donor 3
NA
NA


title: HCV_355_p3_Naive_1_D01_short_paired-end

description:
CD8+ Naive T cell donor 3
NA
NA


title: HCV_355_p3_Naive_1_D02_short_paired-end

description:
CD8+ Naive T cell donor 3
NA
NA


title: HCV_355_p3_tet_1_A03_short_paired-end

description:
CD8+ HCV-specific T cell donor 3
NA
NA


title: HCV_355_p3_Naive_1_C02_short_paired-end

description:
CD8+ Naive T cell donor 3
NA
NA


title: HCV_355_p3_Naive_1_B02_short_paired-end

description:
CD8+ Naive T cell donor 3
NA
NA


title: Bulk_population_CD8_Naive

description:
CD8+ Naive T cell donor 1
NA
NA

source_name: CD8+ Naive T cell donor 1

value: Donor 1

value: Bulk


title: HCV_355_p3_Naive_1_A02_short_paired-end

description:
CD8+ Naive T cell donor 3
NA
NA


title: HCV_355_p3_Naive_1_F01_short_paired-end

description:
CD8+ Naive T cell donor 3
NA
NA


title: 2Plate2_H11_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_H11_CD8_Naive

source_name: CD8+ Naive T cells donor 1


title: 2Plate2_H08_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_H08_CD8_CMVtet

source_name: CD8+ CMV-specific T cell donor 1

value: CD8+ CMV-specific T cell


title: 2Plate2_H10_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_H10_CD8_Naive


title: HCV_355_p3_Naive_1_B01_short_paired-end

description:
CD8+ Naive T cell donor 3
NA
NA


title: 2Plate2_H06_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_H06_CD8_CMVtet


title: 2Plate2_H07_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_H07_CD8_CMVtet


title: HCV_355_p3_Naive_1_E01_short_paired-end

description:
CD8+ Naive T cell donor 3
NA
NA


title: Bulk_population_CD8_CMV

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 2Plate2_H04_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_H04_CD8_CMVtet


title: 2Plate2_H12_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_H12_CD8_Naive


title: HCV_355_p3_Naive_1_C01_short_paired-end

description:
CD8+ Naive T cell donor 3
NA
NA


title: 2Plate2_H09_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_H09_CD8_Naive


title: 2Plate2_G05_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_G05_CD8_CMVtet


title: 2Plate2_H02_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_H02_CD8_CMVtet


title: 2Plate2_G03_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_G03_CD8_CMVtet


title: 2Plate2_G02_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_G02_CD8_CMVtet


title: 2Plate2_G01_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_G01_CD8_CMVtet


title: 2Plate2_H01_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_H01_CD8_CMVtet


title: 2Plate2_F12_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_F12_CD8_Naive


title: 2Plate2_F11_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_F11_CD8_Naive


title: 2Plate2_G12_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_G12_CD8_Naive


title: 2Plate2_F08_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_F08_CD8_CMVtet


title: 2Plate2_F07_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_F07_CD8_CMVtet


title: 2Plate2_H05_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_H05_CD8_CMVtet


title: 2Plate2_G10_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_G10_CD8_Naive


title: 2Plate2_G09_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_G09_CD8_Naive


title: 2Plate2_G11_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_G11_CD8_Naive


title: 2Plate2_F01_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_F01_CD8_CMVtet


title: 2Plate2_F02_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_F02_CD8_CMVtet


title: 2Plate2_E12_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_E12_CD8_Naive


title: 2Plate2_F03_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_F03_CD8_CMVtet


title: 2Plate2_E11_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_E11_CD8_Naive


title: 2Plate2_G08_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_G08_CD8_CMVtet


title: 2Plate2_G07_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_G07_CD8_CMVtet


title: 2Plate2_E10_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_E10_CD8_Naive


title: 2Plate2_E07_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_E07_CD8_CMVtet


title: 2Plate2_G06_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_G06_CD8_CMVtet


title: 2Plate2_E08_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_E08_CD8_CMVtet


title: 2Plate2_F10_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_F10_CD8_Naive


title: 2Plate2_E05_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_E05_CD8_CMVtet


title: 2Plate2_E03_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_E03_CD8_CMVtet


title: 2Plate2_F09_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_F09_CD8_Naive


title: 2Plate2_F06_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_F06_CD8_CMVtet


title: 2Plate2_H03_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_H03_CD8_CMVtet


title: 2Plate2_D11_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_D11_CD8_Naive


title: 2Plate2_D08_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_D08_CD8_CMVtet


title: 2Plate2_F04_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_F04_CD8_CMVtet


title: 2Plate2_D07_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_D07_CD8_CMVtet


title: 2Plate2_F05_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_F05_CD8_CMVtet


title: 2Plate2_D02_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_D02_CD8_CMVtet


title: 2Plate2_G04_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_G04_CD8_CMVtet


title: 2Plate2_D03_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_D03_CD8_CMVtet


title: 2Plate2_D04_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_D04_CD8_CMVtet


title: 2Plate2_C12_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_C12_CD8_Naive


title: 2Plate2_E09_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_E09_CD8_Naive


title: 2Plate2_E06_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_E06_CD8_CMVtet


title: 2Plate2_E04_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_E04_CD8_CMVtet


title: 2Plate2_C08_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_C08_CD8_CMVtet


title: 2Plate2_C11_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_C11_CD8_Naive


title: 2Plate2_E02_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_E02_CD8_CMVtet


title: 2Plate2_D12_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_D12_CD8_Naive


title: 2Plate2_D10_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_D10_CD8_Naive


title: 2Plate2_D09_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
NA
NA


title: WT translatome, replicate 2

city: Heidelberg

first: Kristina

last: Döring

address: Im Neuenheimer Feld 282

department: ZMBH

country: Germany

institute: Heidelberg University

data_processing:
Library strategy: Ribosome profiling
Barcode and linker removal using Cutadapt 1.11
Alignment to rRNA using Bowtie2.2.5.0
Alignment to genome using TopHat2.0.13
center weighting of ribosomal footprints (custom python script)
normalization to total read number per sample (custom python script)
Genome_build: NCBI build3.1
Supplementary_files_format_and_content: NormReads-files: column1: chromosome number, column2: nt position, column3: center weighted reads on plus strand, column4: center weighted reads on minus strand, column5: normalized reads on plus strand, column6: normalized reads on minus strand

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Cultures were grown in YPD at 30°C and 150 rpm

extract_protocol:
RNA was extracted using the hot acid phenol method (for details see Becker et al. 2013)
DNA libraries were generated following previously published protocoles (Ingolia et al. 2009, Becker et al. 2013)

treatment_protocol: Cultures were filtered, flash frozen and lysed in frozen state using a mixer mill. Ribosomes were pelleted through a sucrose cushion and resuspended. From this a part was used for RNA extraction (total RNCs) and the rest was used to purify GFP-tagged Ssb using a GFP-antibody coupled to sepharose-beads (Ssb-bound RNCs).

tag: strain

tag: genotype

value: wild type


title: 2Plate2_E01_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_E01_CD8_CMVtet


title: WT translatome, replicate 1


title: 2Plate2_C07_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: RACΔ Ssb2 interactome, replicate 2


title: RACΔ Ssb2-GFP translatome, replicate 2


title: 2Plate2_D01_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_D01_CD8_CMVtet


title: 2Plate2_D05_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_D05_CD8_CMVtet


title: 2Plate2_C10_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_C10_CD8_Naive


title: Vehicle_5h_HFF_rep2

city: Bethesda

first: Jesse

middle: H

last: Arbuckle

state: MD

address: 33 North Drive

department: Laboratory of Viral Diseases

institute: National Institute of Allergy and Infectious Diseases, NIH

data_processing:
Trimmomatic program was used to remove adapter sequences and bases with base quality lower than three from the ends.  Bases of reads that don't qualify for window size 4 and mean quality 15 were trimmed using sliding window method.  Read lengths shorter than 36bp were removed.  Trimmed reads were mapped (Partek-Flow, Partek Inc., v. 5.016.1003) to a reference genome (hg38 or mm10) with STAR (2.4.1d) and quantified with the Partek E/M algorithm.  Differential analysis was done using Partek GSA from three independent replicates.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each sample

growth_protocol: HFF cells and ganglia were cultured in DMEM with 10% FBS.

extract_protocol:
Total RNA from HFF cells was isolated with Isolate II RNA Kit (Bioline, Cat # BIO-52073).  Ganglia were homogenized in TriPure Reagent (Roche, 11667165001) with Lysing Matrix D (MP Biomedicals, 6913-100) using a FastPrep-24 Instrument (MP Biomedicals).  Total RNA was further purified with Isolate II RNA Kit.
Libraries were generated with TruSeq Stranded Total RNA with Ribo-Zero according manufacturer’s instructions (Illumina).

treatment_protocol: HFF cells seeded into a 6-well dish and grown for 3 days (37 degrees C, 5% CO2).  HFF cells were then treated with GSK126 or vehicle (DMSO) for 1, 2, and 5 hours.  Total RNA was then isolated with Isolate II RNA Kit (Bioline, Cat # BIO-52073).  Mock or latently HSV-1 infected trigeminal ganglia were harvested from BALB/c mice 30-45 days after clearance of the primary infection and explanted in culture media for 12 hours (37 degrees C, 5% CO2).  Ganglia were homogenized in TriPure Reagent (Roche, 11667165001) with Lysing Matrix D (MP Biomedicals, 6913-100) using a FastPrep-24 Instrument (MP Biomedicals).  Total RNA was further purified with Isolate II RNA Kit.  RNA quality (RNA Integrity Number > 8.5) was verified by Bioanalyzer for all samples.

tag: treatment

value: Vehicle

tag: time

value: 5 h

tag: infection

value: Mock

tag: cell line

value: HFF


title: 2Plate2_C09_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_C09_CD8_Naive


title: ssb1Δssb2Δ translatome, replicate 2

value: ssb1delta::LEU2 ssb2delta::natMX4


title: Sequencing of the transduced sgRNAs post-selection (Screen C)

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

description:
Single Lane Sequencing
MiSeq
Neg C

library_source: genomic

data_processing:
The sgRNA reads (which had 5' and 3' flanking regions that matched the sgRNA expression lentivirus vector) were quality filtered and mapped to a reference table of sgRNA sequences provided in Konermann et al, Nature 2015 (supplementary table 6).
Read numbers were normalized by dividing by the total read depth to give a percentage of total reads (displayed in the "percentage of reads" column in the processed data tables).
Supplementary_files_format_and_content: Raw and normalized read numbers

molecule: genomic DNA

organism: Mus musculus

source_name: A549 Cells

growth_protocol: Cells were grown under standard laboratory conditions and stably transfected with CRISPR components.

extract_protocol:
Cells were sorted via flow cytometry, genomic DNA was extracted, and PCR for the sgRNA sequences was performed.
Illumina adaptors and barcodes were incorporated into the PCR primers.
PCR amplified libraries were generated with independent barcodes to allow multiplexing.  50% PhiX DNA was included in the sequencing run, as low diversity libraries were expected.

treatment_protocol: Cells were transduced with sgRNA lentivirus and subsequently infected with influenza A virus (PR8 strain).

tag: sample type


title: NACΔ Ssb2 interactome, replicate 2

value: egd1delta::hisMX6 btt1delta::phleo egd2delta::LEU2 Ssb2-GFP::kanMX4


title: GSK126_5h_HFF_rep3


title: ssb1Δssb2Δ translatome, replicate 1


title: NACΔ  Ssb1 interactome, replicate 2

value: egd1delta::hisMX6 btt1delta::phleo egd2delta::LEU2 Ssb1-GFP::kanMX4


title: NACΔ Ssb2-GFP translatome, replicate 2


title: Vehicle_5h_HFF_rep3


title: 2Plate2_D06_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_D06_CD8_CMVtet


title: RACΔ  Ssb1 interactome, replicate 2


title: 2Plate2_C05_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_C05_CD8_CMVtet


title: WT Ssb2 interactome, replicate 2


title: 2Plate2_C06_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_C06_CD8_CMVtet


title: 2Plate2_C02_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_C02_CD8_CMVtet


title: Vehicle_5h_HFF_rep1


title: 2Plate2_C01_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_C01_CD8_CMVtet


title: 2Plate2_C03_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_C03_CD8_CMVtet


title: 2Plate2_C04_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_C04_CD8_CMVtet


title: WT Ssb2-GFP translatome, replicate 2


title: RACΔ  Ssb1 interactome, replicate 1


title: RACΔ Ssb1-GFP  translatome, replicate 2


title: RACΔ Ssb2 interactome, replicate 1


title: GSK126_5h_HFF_rep2


title: NACΔ Ssb1-GFP  translatome, replicate 2


title: RACΔ Ssb2-GFP translatome, replicate 1


title: GSK126_5h_HFF_rep1


title: Vehicle_2h_HFF_rep2

value: 2 h


title: Vehicle_2h_HFF_rep3


title: 2Plate2_B10_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_B10_CD8_Naive


title: WT Ssb1 interactome, replicate 2


title: RACΔ Ssb1-GFP translatome, replicate 1


title: Vehicle_2h_HFF_rep1


title: NACΔ Ssb2-GFP translatome, replicate 1


title: GSK126_2h_HFF_rep3


title: 2Plate2_B12_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_B12_CD8_Naive


title: WT Ssb2 interactome, replicate 1


title: WT Ssb1-GFP  translatome, replicate 2


title: GSK126_2h_HFF_rep2


title: 2Plate2_B11_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_B11_CD8_Naive


title: NACΔ Ssb2 interactome, replicate 1


title: WT Ssb2-GFP translatome, replicate 1


title: WT Ssb1-GFP  translatome, replicate 1


title: ssb1∆ Ssb2-GFP translatome, replicate 2

value: Ssb2-GFP::kanMX4 ssb1delta::LEU2


title: 2Plate2_B07_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_B07_CD8_CMVtet


title: 2Plate2_B09_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_B09_CD8_Naive

value: CD8+ Naive T cell


title: Vehicle_1h_HFF_rep1

value: 1 h


title: ssb1∆ Ssb2 interactome, high salt, replicate 2


title: 2Plate2_B05_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_B05_CD8_CMVtet


title: Vehicle_1h_HFF_rep3


title: 2Plate2_B03_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: GSK126_1h_HFF_rep2


title: 2Plate2_B08_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_B08_CD8_CMVtet


title: 2Plate2_B04_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_B04_CD8_CMVtet


title: GSK126_1h_HFF_rep1


title: NACΔ Ssb1-GFP  translatome, replicate 1


title: ssb2∆ Ssb1-GFP translatome, replicate 2

value: Ssb1-GFP::kanMX4 ssb2delta::natMX4


title: 2Plate2_B01_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_B01_CD8_CMVtet


title: ssb2∆ Ssb1 interactome, high salt, replicate 2


title: WT Ssb1 interactome, replicate 1


title: GSK126_2h_HFF_rep1


title: Vehicle_1h_HFF_rep2


title: 2Plate2_A12_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_A12_CD8_Naive


title: 2Plate2_B06_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: GSK126_1h_HFF_rep3


title: ssb1∆ Ssb2 interactome, low salt, replicate 2


title: NACΔ  Ssb1 interactome, replicate 1


title: 2Plate2_A10_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_A10_CD8_Naive


title: LCMV_clone13_H12_long_single-end

description:
CD8+ clone 13 LCMV-specific T cell mouse 1
NA
NA

value: CD8+ clone 13 LCMV-specific T cell

value: Mouse 1


title: 2Plate2_A09_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_A09_CD8_Naive

value: Donor 1


title: ssb1∆ Ssb2-GFP translatome, replicate 1


title: 2Plate2_A08_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_A08_CD8_CMVtet

value: CD8+ CMV-specific T cell


title: LCMV_clone13_H11_short_paired-end

source_name: CD8+ clone 13 LCMV-specific T cell mouse 1


title: LCMV_clone13_H11_long_single-end


title: ssb2∆ Ssb1-GFP translatome, replicate 1


title: 2Plate2_A11_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_A11_CD8_Naive


title: ssb1∆ Ssb2 interactome, low salt, replicate 1


title: ssb1∆ Ssb2 interactome, high salt, replicate 1


title: ssb2∆ Ssb1 interactome, high salt, replicate 1


title: 2Plate2_B02_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_B02_CD8_CMVtet


title: Sequencing of the plasmid sgRNA library_lane 1

description:
Double Lane Sequencing
HiSeq2000 Rapid Run
Plasmid NH

value: plasmid sgRNA library


title: ssb2∆ Ssb1 interactome, low salt, replicate 1


title: ssb2∆ Ssb1 interactome, low salt, replicate 2


title: LCMV_clone13_H10_short_paired-end


title: LCMV_clone13_H10_long_single-end


title: LCMV_clone13_H09_short_paired-end


title: 2Plate2_A07_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_A07_CD8_CMVtet


title: LCMV_clone13_H12_short_paired-end


title: 2Plate2_A05_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_A05_CD8_CMVtet


title: 2Plate2_A03_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_A03_CD8_CMVtet


title: LCMV_clone13_H09_long_single-end


title: ΔSMG6L

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

country: China

institute: Institute of hydrobiology, CAS

data_processing:
Basecalls performed using CASAVA version 1.8
The adaptor sequences were trimmed, and low-quality reads (contianing over 10% of N, or the quality score of over 50% of base is lower than 5) were discarded to get clean reads for downstream analysis
RNA-seq reads were aligned to the Tetrahymena macronuclear genome assembly (version:June2014) using Tophat (v2.0.9) with the following parameters : tophat -o -p 4 --coverage-search --library-type fr-unstranded.
Reference guided transcript assembly performed using Cufflinks (v2.1.1) with the following paprameters: cufflinks bam_file -g T_thermophila_June2014.gtf -p 10 -o. The "T_thermophila_June2014.gtf" file was downloaded from the Tetrahymena Genome Database (http://ciliate.org/index.php/home/downloads)
The genome annotation files generated from previous step using wild type RNA-seq reads and ΔUPF1a RNA-seq reads were merged with reference genome annotation file  by cufflinks (v2.1.1) with following parameters: cuffmerge Genome_annotation_list (a list containing the path to genome annotation files) -g T_thermophila_June2014.gtf -p 20–o Merged.gtf
The merged annotation file generated from previous step was compared with reference genome annotation file (T_thermophila_June2014.gtf) using cuffcompare algorithm (included in Cufflinks v2.1.1) with default settings to identify potential novel isoforms.
The fragments per kilobase of transcript per million mapped reads (FPKM) for each gene and transcript was determined using cuffdiff algorithm with default settings.
The exon usage was determined using DEXSeq (v1.12.1) . Briefly, prior to the DEXSeq analysis, the .bam files were indexed and sorted using samtools with the following parameters (1. samtools index; 2. samtools view -h). The genome annotation file (merged.gtf) was then modified using dexseq_prepare_annotation.py script, a phython script provided in DEXSeq package. The sequencing reads assigned to each exon in WT and ΔUPF1a samples were calculated using a phython script provided in DEXSeq package, dexseq_count.py, with the following parameter: -p yes. At last, the exon usage was calculated using DEXSeq algorithm in R (v3.1.1). The FDR value was set to 0.05.
Genome_build: Tetrahymena macronuclear genome assembly (version:June2014; downloaded from Tetrahymena Genome Database)
Supplementary_files_format_and_content: Tab-delimited Excel files include FPKM values for each sample; WTvsUPF1aKO_DEXSeq.csv contains quantification of exon usage.

organism: Tetrahymena thermophila

source_name: Tetrahymena thermophila whole cell

growth_protocol: The Tetrahymena B2086 wild-type (WT) strain (obtained from the Tetrahymena Stock Center at Cornell University) and mutant strains (Supplemental Table 1) were maintained in Super Proteose Peptone (SPP) medium (1% Proteose peptone, 0.2% Glucose, 0.1% Yeast extract, 0.003% Sequestrene) at 30°C on a rotary shaker at 135 rpm.

extract_protocol:
Total RNA was extracted from 5ml of vegetative Tetrahymena WT and mutant cells (density: 2.5 x 105 cells/mL) using an RNeasy Plus Mini Kit (Qiagen, Valencia, CA, USA)
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structurewere ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers andIndex (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: genetic background

value: Somatic SMG6L gene knockout

tag: knockout gene accession number


title: 2Plate2_A04_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_A04_CD8_CMVtet


title: SMG6L-NYNmu

value: Somatic truncation of NYN nuclease domain coding sequence in SMG6L gene


title: ΔMAG1

value: Somatic MAG1 gene knockout


title: LCMV_clone13_H08_short_paired-end


title: LCMV_clone13_H08_long_single-end


title: 2Plate2_A02_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_A02_CD8_CMVtet


title: LCMV_clone13_H07_long_single-end


title: 2Plate2_A01_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_A01_CD8_CMVtet


title: LCMV_clone13_G12_short_paired-end


title: ΔUPF1a-Rep1

description: The processed data for this sample contains data for both GSM2417231 and GSM2417232. DEXSeq output for wildtype vs UPK1a KO is available on the series record.

value: Somatic UPF1a gene knockout


title: LCMV_clone13_H07_short_paired-end


title: LCMV_clone13_G12_long_single-end


title: WT-Rep2

description: The processed data for this sample can be found on sample GSM2417229. DEXSeq output for wildtype vs UPK1a KO is available on the series record.

value: Wild type


title: WT-Rep1

description: The processed data for this sample contains data for both GSM2417229 and GSM2417230. DEXSeq output for wildtype vs UPK1a KO is available on the series record.


title: CAG_TB_rep1

city: Toyonaka

first: Koji

last: Nagao

state: Osaka

address: 1-1 Machikaneyama

department: Graduate School of Science

country: Japan

institute: Osaka University

data_processing:
RNA-seq reads were mapped to a concatenated custom reference, including strain-specific genomes and sequences spanning splice junctions based on RefSeq genes, using BWA. The coordinates of mapped reads were converted to mm9 genomic coordinates using custom scripts.
The numbers of maternal and paternal allele-specific reads for each gene were counted using custom scripts.
Gene expression was quantified in a non-allelic manner using Cufflinks v2.2.1 cuffdiff with option '--library-type ff-firststrand --library-norm-method classic-fpkm --multi-read-correct'.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include average of % paternal reads (avePat) and average of FPKM values (aveFPKM) for each genotype; FDR adjusted p-value (qVal) for comparison with wild-type; % paternal reads (Pat), the total number of allele-specific reads, both maternal and paternal (ASreads), and FPKM value (FPKM) for each sample.

source_name: E7.5 trophoblast

extract_protocol:
Trophoblasts were isolated from E7.5 embryos. RNA was prepared using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#15027078) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: trophoblast

value: Xist +/CAG

value: JF1 x C57BL6/J

tag: Sex

value: female


title: deltaA_TB_rep5

value: Xist +/deltaA


title: 1Plate1_H12_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
NA
NA

value: CD8+ Naive T cell


title: 1Plate1_H11_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: LCMV_clone13_G11_short_paired-end


title: 1Plate1_H11_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_H11_CD8_Naive


title: LCMV_clone13_G11_long_single-end


title: RNASeq_riboM_lin-41(xe11);let-7(n2853)_36hr

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing: The RNA-seq data (50bp read length) were mapped to the C. elegans genome (ce6) with the R package QuasR (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html) using the included spliced alignment algorithm SpliceMap. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6",splicedAlignment=TRUE)". Gene expression (ce_geneExpression_riboM_rawCounts.txt) was quantified by counting the number of reads that started within any of the exons beloning to a particular gene (WormBase, WS190). The command used to create the count table was qCount(proj,exons,orientation="same"). To compensate for differences in the read depths of the various libraries, we divided each sample by the total number of reads and multiplied by the average library size. Log2 expression levels (ce_geneExpression_riboM_normalized.txt) were calculated after adding a pseudocount of 8 (y=log2(x+8)). This was done to minimize the large differences in expression that would otherwise be caused by genes with small number of counts. The N2 time-course experiment corresponding to let-7(n2853)_18hr-36hr is not part of this series as it was previously published (GSM1277189-GSM1277198).

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Arrested L1 stage larvae were obtained by extracting embryos from gravid adults with bleaching solution (30% (v/v) sodium hypochlorite (5% chlorine) reagent, 750 mM KOH) and hatching overnight in the absence of food, at room temperature in M9 buffer (42 mM Na2HPO4, 22 mM KH2PO4, 86 mM NaCl, 1 mM MgSO4). Synchronized arrested L1 larvae were then plated on enriched peptone plates with Escherichia coli NA22 bacteria and harvested after incubation at 25 °C for the desired time (referred to as hours of development).

extract_protocol:
Total RNA isolation was performed using Tri-Reagent (MRC). To obtain ribosomal RNA (rRNA)-depleted total RNA, a DNase-treatment was performed with the RNase-Free DNase Set (Qiagen) and the RNeasy MiniKit (Qiagen), before using the Ribo-Zero rRNA Removal Kit (Epicentre) to remove rRNA.
Library preparation was performed using the ScriptSeq v2 RNA-Seq library preparation kit (Epicentre) according to the manufacturer's protocol

treatment_protocol: Worms were washed off the plates and subsequently washed three additional times with M9 buffer before lysis (Aeschimann et al., Methods, 2015)

tag: time in development

value: 36 hours


title: RNASeq_riboM_lin-41(xe11);let-7(n2853)_38hr

value: 38 hours


title: RNASeq_riboM_lin-41(xe11);let-7(n2853)_34hr

value: 34 hours


title: ΔUPF1a-Rep2

description: The processed data for this sample can be found on sample GSM2417231. DEXSeq output for wildtype vs UPK1a KO is available on the series record.


title: 1Plate1_H10_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_H10_CD8_Naive

value: Donor 1


title: 1Plate1_H12_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: LCMV_clone13_G10_short_paired-end

description:
CD8+ clone 13 LCMV-specific T cell mouse 1
NA
NA

value: CD8+ clone 13 LCMV-specific T cell

value: Mouse 1


title: LCMV_clone13_G10_long_single-end


title: deltaA_TB_rep2


title: deltaA_TB_rep3


title: 1Plate1_H10_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: deltaA_TB_rep4


title: RNASeq_riboM_lin-41(xe11);let-7(n2853)_32hr

value: 32 hours


title: deltaA_TB_rep1


title: LCMV_clone13_G09_short_paired-end


title: LCMV_clone13_G09_long_single-end


title: CAGdelta5_TB_rep7

value: Xist +/CAGdelta5'


title: RNASeq_riboM_lin-41(xe11);let-7(n2853)_26hr

value: 26 hours


title: 1Plate1_H09_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_H09_CD8_Naive


title: 1Plate1_H08_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA

value: CD8+ CMV-specific T cell


title: LCMV_clone13_G08_short_paired-end


title: RNASeq_riboM_lin-41(xe11);let-7(n2853)_24hr

value: 24 hours


title: 2Plate2_A06_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
2Plate2_A06_CD8_CMVtet


title: 1Plate1_H08_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_clone13_G08_long_single-end


title: CAGdelta5_TB_rep5

value: trophoblast


title: CAGdelta5_TB_rep4


title: 1Plate1_H07_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_H07_CD8_CMVtet


title: 1Plate1_H07_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_H06_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: CAGdelta5_TB_rep3


title: RNASeq_riboM_lin-41(xe11);let-7(n2853)_22hr

value: 22 hours


title: RNASeq_riboM_lin-41(xe11);let-7(n2853)_20hr

value: 20 hours


title: RNASeq_riboM_lin-41(xe11);let-7(n2853)_18hr

value: 18 hours


title: CAGdelta5_TB_rep2

value: JF1 x C57BL6/J

value: female


title: RNASeq_riboM_lin-41(xe11);let-7(n2853)_30hr

value: 30 hours


title: 1Plate1_H09_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA

value: CD8+ Naive T cell


title: 1Plate1_H06_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_clone13_F12_long_single-end


title: RNASeq_riboM_lin-41(xe11)_38hr

value: 38 hours


title: CAGdelta5_TB_rep6


title: RNASeq_riboM_lin-41(xe11);let-7(n2853)_28hr

value: 28 hours


title: RNASeq_riboM_lin-41(xe11)_36hr

value: 36 hours


title: WT_TB_rep3

value: Xist +/+


title: LCMV_clone13_F11_short_paired-end

value: CD8+ clone 13 LCMV-specific T cell

value: Mouse 1


title: LCMV_clone13_F11_long_single-end


title: LCMV_clone13_G07_short_paired-end


title: WT_TB_rep2


title: CAGdelta5_TB_rep1

value: Xist +/CAGdelta5'


title: 1Plate1_H05_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA

value: CD8+ CMV-specific T cell

value: Donor 1


title: WT_TB_rep1

value: trophoblast


title: RNASeq_riboM_lin-41(xe11)_32hr

value: 32 hours


title: LCMV_clone13_F12_short_paired-end


title: 1Plate1_H04_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_clone13_G07_long_single-end


title: LCMV_clone13_F10_short_paired-end


title: LCMV_clone13_F09_short_paired-end


title: LCMV_clone13_F09_long_single-end


title: RNASeq_riboM_lin-41(xe11)_30hr


title: RNASeq_riboM_lin-41(xe11)_28hr


title: 1Plate1_H03_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_H03_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_H03_CD8_CMVtet


title: 1Plate1_H02_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: RNASeq_riboM_lin-41(xe11)_22hr

value: 22 hours


title: 1Plate1_H05_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_H05_CD8_CMVtet


title: RNASeq_riboM_lin-41(xe11)_26hr

value: 26 hours


title: LCMV_clone13_F07_short_paired-end


title: RNASeq_riboM_lin-41(xe11)_20hr

value: 20 hours


title: 1Plate1_H04_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_H04_CD8_CMVtet


title: 1Plate1_H01_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_clone13_F08_long_single-end


title: LCMV_clone13_F10_long_single-end


title: LCMV_clone13_F07_long_single-end


title: RNASeq_riboM_N2_36hr


title: RNASeq_riboM_N2_38hr


title: LCMV_clone13_E12_short_paired-end


title: 1Plate1_G12_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_G12_CD8_Naive


title: RNASeq_riboM_N2_34hr

value: 34 hours


title: RNASeq_riboM_lin-41(xe11)_18hr

value: 18 hours


title: LCMV_clone13_E12_long_single-end


title: RNASeq_riboM_lin-41(xe11)_24hr

value: 24 hours


title: 1Plate1_G11_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_G11_CD8_Naive

value: CD8+ Naive T cell


title: 1Plate1_H02_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_H02_CD8_CMVtet


title: 1Plate1_G10_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_G10_CD8_Naive


title: LCMV_clone13_E11_short_paired-end


title: 1Plate1_G12_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: 1Plate1_G10_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: 1Plate1_G11_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: LCMV_clone13_E10_short_paired-end


title: RNASeq_riboM_N2_30hr

value: 30 hours


title: 1Plate1_H01_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_H01_CD8_CMVtet


title: RNASeq_riboM_N2_28hr

value: 28 hours


title: LCMV_clone13_E09_short_paired-end


title: RNASeq_riboM_N2_26hr


title: 1Plate1_G08_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_clone13_E08_short_paired-end


title: 1Plate1_G08_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_G08_CD8_CMVtet


title: LCMV_clone13_E10_long_single-end


title: LCMV_clone13_E11_long_single-end


title: LCMV_clone13_E09_long_single-end


title: RNASeq_riboM_N2_24hr


title: 1Plate1_G07_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_G07_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_G07_CD8_CMVtet


title: RNASeq_riboM_N2_20hr


title: 1Plate1_G06_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_G06_CD8_CMVtet


title: LCMV_clone13_F08_short_paired-end


title: LCMV_clone13_D12_short_paired-end


title: RNASeq_riboM_let-7(n2853)_36hr

value: 36 hours


title: LCMV_clone13_E08_long_single-end

value: CD8+ clone 13 LCMV-specific T cell


title: RNASeq_riboM_N2_32hr


title: RNASeq_riboM_N2_18hr


title: 1Plate1_G09_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_G09_CD8_Naive


title: RNASeq_riboM_let-7(n2853)_32hr


title: LCMV_clone13_D12_long_single-end

value: Mouse 1


title: LCMV_clone13_E07_short_paired-end


title: LCMV_clone13_D11_short_paired-end


title: 1Plate1_G05_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_G04_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_G04_CD8_CMVtet


title: RNASeq_riboM_let-7(n2853)_28hr


title: RNASeq_riboM_let-7(n2853)_34hr


title: 1Plate1_G05_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_G05_CD8_CMVtet


title: LCMV_clone13_D10_short_paired-end

description:
CD8+ clone 13 LCMV-specific T cell mouse 1
NA
NA


title: 1Plate1_G09_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: RNASeq_riboM_lin-41(xe11)_34hr


title: 1Plate1_G06_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: RNASeq_riboM_N2_22hr


title: RNASeq_riboM_let-7(n2853)_30hr


title: 1Plate1_G03_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_G03_CD8_CMVtet


title: LCMV_clone13_E07_long_single-end


title: RNASeq_riboM_let-7(n2853)_20hr


title: LCMV_clone13_D08_short_paired-end


title: 1Plate1_G03_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: RNASeq_riboM_let-7(n2853)_26hr


title: LCMV_clone13_D10_long_single-end


title: 1Plate1_G02_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: RNASeq_riboM_let-7(n2853)_24hr


title: LCMV_clone13_D11_long_single-end


title: RNASeq_riboM_let-7(n2853)_18hr


title: 1Plate1_G04_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: Footprint_lin-41(xe11);let-7(n2853)_38hr

data_processing: The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) was removed from the reads using the function preprocessReads from within the bioconductor package QuasR (default parameters). The short fragments (about 30bp length) were mapped to the C. elegans genome (ce6) with the R package QuasR (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html) using the included aligner bowtie allowing only for uniquely mapping reads. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6")". Gene expression (ce_geneExpression_riboM_rawCounts.txt) was quantified by counting the number of reads that started within any of the exons beloning to a particular gene (WormBase, WS190). The command used to create the count table was qCount(proj,exons,orientation="same"). To compensate for differences in the read depths of the various libraries, we divided each sample by the total number of reads and multiplied by the average library size. Log2 expression levels (ce_geneExpression_riboM_normalized.txt) were calculated after adding a pseudocount of 8 (y=log2(x+8)). This was done to minimize the large differences in expression that would otherwise be caused by genes with small number of counts. The N2 time-course experiment corresponding to let-7(n2853)_18hr-36hr is not part of this series as it was previously published (GSM1277907-GSM1277916).

source_name: Whole-worm

extract_protocol:
Worms were lysed and monosomes purified according to our detailed published protocol (Aeschimann et al., Methods, 2015). Monosomes were purified using linear sucrose density gradients for the first time course experiment (let-7(n2853) animals) and using size-exclusion chromatography for the second time course experiment (N2, lin-41(xe11) and lin-41(xe11); let-7(n2853) animals).
Performed as described in our detailed published protocol (Aeschimann et al., Methods, 2015).

value: 38 hours


title: LCMV_clone13_C12_short_paired-end


title: Footprint_lin-41(xe11);let-7(n2853)_28hr


title: LCMV_clone13_D09_long_single-end


title: LCMV_clone13_D08_long_single-end


title: 1Plate1_F12_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_F12_CD8_Naive


title: 1Plate1_G02_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_G02_CD8_CMVtet

value: CD8+ CMV-specific T cell


title: 1Plate1_G01_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_G01_CD8_CMVtet

value: Donor 1


title: LCMV_clone13_D07_short_paired-end


title: Footprint_lin-41(xe11);let-7(n2853)_34hr


title: Footprint_lin-41(xe11);let-7(n2853)_26hr


title: 1Plate1_G01_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: Footprint_lin-41(xe11);let-7(n2853)_36hr


title: Footprint_lin-41(xe11);let-7(n2853)_24hr


title: Footprint_lin-41(xe11);let-7(n2853)_32hr


title: LCMV_clone13_C10_short_paired-end


title: LCMV_clone13_C10_long_single-end


title: 1Plate1_F12_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: Footprint_lin-41(xe11);let-7(n2853)_30hr


title: LCMV_clone13_D09_short_paired-end


title: LCMV_clone13_C12_long_single-end


title: 1Plate1_F09_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
NA
NA


title: RNASeq_riboM_let-7(n2853)_22hr


title: LCMV_clone13_C11_long_single-end


title: LCMV_clone13_C11_short_paired-end


title: 1Plate1_F10_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_F10_CD8_Naive


title: Footprint_lin-41(xe11);let-7(n2853)_20hr


title: 1Plate1_F11_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_F11_CD8_Naive


title: 1Plate1_F10_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: 1Plate1_F09_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: Footprint_lin-41(xe11);let-7(n2853)_22hr


title: LCMV_clone13_C08_short_paired-end


title: LCMV_clone13_C09_short_paired-end


title: 1Plate1_F11_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: Footprint_lin-41(xe11);let-7(n2853)_18hr


title: LCMV_clone13_C09_long_single-end


title: Footprint_lin-41(xe11)_38hr


title: 1Plate1_F08_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_F08_CD8_CMVtet


title: LCMV_clone13_C08_long_single-end


title: LCMV_clone13_C07_short_paired-end


title: Footprint_lin-41(xe11)_34hr


title: 1Plate1_F07_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_F07_CD8_CMVtet


title: Footprint_lin-41(xe11)_32hr


title: 1Plate1_F07_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: Footprint_lin-41(xe11)_30hr


title: LCMV_clone13_C07_long_single-end


title: 1Plate1_F06_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: Footprint_lin-41(xe11)_28hr


title: LCMV_clone13_B12_short_paired-end


title: 1Plate1_F06_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_F06_CD8_CMVtet


title: Footprint_lin-41(xe11)_26hr


title: LCMV_clone13_B11_short_paired-end


title: 1Plate1_F08_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_F05_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_clone13_B11_long_single-end


title: LCMV_clone13_B12_long_single-end


title: Footprint_lin-41(xe11)_24hr


title: 1Plate1_F04_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_F04_CD8_CMVtet


title: LCMV_clone13_B10_short_paired-end


title: Footprint_lin-41(xe11)_20hr


title: 1Plate1_F04_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_clone13_B10_long_single-end


title: 1Plate1_F03_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_F03_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_F03_CD8_CMVtet


title: 1Plate1_F02_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_F02_CD8_CMVtet


title: Footprint_N2_38hr


title: 1Plate1_F02_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: Footprint_N2_34hr


title: LCMV_clone13_B09_long_single-end


title: LCMV_clone13_B08_long_single-end


title: LCMV_clone13_B08_short_paired-end


title: LCMV_clone13_B09_short_paired-end


title: Footprint_N2_36hr


title: LCMV_clone13_B07_short_paired-end


title: 1Plate1_F01_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_F01_CD8_CMVtet


title: Footprint_N2_32hr


title: 1Plate1_F01_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_clone13_A12_short_paired-end


title: 1Plate1_E12_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_E12_CD8_Naive


title: Footprint_lin-41(xe11)_22hr


title: Footprint_lin-41(xe11)_36hr


title: 1Plate1_E11_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_E11_CD8_Naive


title: Footprint_N2_26hr


title: Footprint_N2_28hr


title: 1Plate1_E12_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: Footprint_N2_24hr


title: LCMV_clone13_D07_long_single-end


title: 1Plate1_E11_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: Footprint_lin-41(xe11)_18hr


title: LCMV_clone13_A12_long_single-end


title: LCMV_clone13_A11_short_paired-end


title: Footprint_N2_22hr


title: LCMV_clone13_A11_long_single-end


title: Footprint_N2_30hr


title: 1Plate1_E10_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_E10_CD8_Naive


title: 1Plate1_E10_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: Footprint_N2_18hr


title: Footprint_let-7(n2853)_36hr


title: 1Plate1_F05_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_clone13_A10_long_single-end

description:
CD8+ clone 13 LCMV-specific T cell mouse 1
NA
NA


title: Footprint_N2_20hr


title: LCMV_clone13_B07_long_single-end


title: 1Plate1_E09_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: LCMV_clone13_A10_short_paired-end


title: Footprint_let-7(n2853)_34hr


title: 1Plate1_E08_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_E08_CD8_CMVtet


title: Footprint_let-7(n2853)_32hr


title: LCMV_clone13_A09_short_paired-end


title: LCMV_clone13_A08_short_paired-end


title: 1Plate1_E09_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_E09_CD8_Naive


title: 1Plate1_E08_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: Footprint_let-7(n2853)_30hr


title: LCMV_clone13_A08_long_single-end


title: 1Plate1_E07_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_E07_CD8_CMVtet


title: Footprint_let-7(n2853)_26hr


title: 1Plate1_E07_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: Footprint_let-7(n2853)_24hr


title: LCMV_clone13_A07_short_paired-end


title: 1Plate1_E06_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_E06_CD8_CMVtet


title: LCMV_clone13_A07_long_single-end


title: 1Plate1_E06_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_armstrong_H05_short_paired-end

description:
CD8+ armstrong LCMV-specific T cell mouse 2
NA
NA

value: CD8+ armstrong LCMV-specific T cell

value: Mouse 2


title: Footprint_let-7(n2853)_22hr

value: 22 hours


title: LCMV_armstrong_H06_short_paired-end

source_name: CD8+ armstrong LCMV-specific T cell mouse 2


title: LCMV_armstrong_H06_long_single-end


title: 1Plate1_E05_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_E05_CD8_CMVtet


title: Footprint_let-7(n2853)_20hr


title: LCMV_clone13_A09_long_single-end


title: LCMV_armstrong_H05_long_single-end


title: Footprint_let-7(n2853)_18hr


title: Vehicle_Mock_Ganglia_rep2

value: BALB/c

value: Vehicle

value: Mock

value: Trigeminal ganglia


title: 1Plate1_E04_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_E04_CD8_CMVtet


title: 1Plate1_E03_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_E03_CD8_CMVtet


title: LCMV_armstrong_H03_short_paired-end


title: Vehicle_Mock_Ganglia_rep1


title: Footprint_let-7(n2853)_28hr


title: Vehicle_Mock_Ganglia_rep3


title: 1Plate1_E04_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_E03_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: GSK126_Mock_Ganglia_rep3


title: LCMV_armstrong_H03_long_single-end


title: GSK126_Mock_Ganglia_rep2


title: LCMV_armstrong_H02_short_paired-end


title: LCMV_armstrong_H02_long_single-end


title: GSK126_Mock_Ganglia_rep1


title: 1Plate1_E02_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_E02_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_E02_CD8_CMVtet


title: LCMV_armstrong_H04_short_paired-end


title: 1Plate1_E01_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_armstrong_H01_long_single-end


title: Vehicle_HSV1_Ganglia_rep1


title: LCMV_armstrong_H04_long_single-end


title: LCMV_armstrong_H01_short_paired-end


title: 1Plate1_E01_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_E01_CD8_CMVtet


title: 1Plate1_D12_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_D12_CD8_Naive


title: Vehicle_HSV1_Ganglia_rep3


title: LCMV_armstrong_G06_short_paired-end


title: Vehicle_HSV1_Ganglia_rep2


title: 1Plate1_D12_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: GSK126_HSV1_Ganglia_rep3


title: LCMV_armstrong_G06_long_single-end


title: 1Plate1_D11_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_D11_CD8_Naive


title: GSK126_HSV1_Ganglia_rep2


title: LCMV_armstrong_G05_short_paired-end


title: 1Plate1_D11_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: GSK126_HSV1_Ganglia_rep1


title: Sequencing of the transduced sgRNAs post-selection (Screen B)_lane 2

description:
Double Lane Sequencing
HiSeq2000 Rapid Run
Neg B NH


title: 1Plate1_D10_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_D10_CD8_Naive


title: LCMV_armstrong_G04_short_paired-end


title: Sequencing of the transduced sgRNAs post-selection (Screen B)_lane 1


title: 1Plate1_D10_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: LCMV_armstrong_G05_long_single-end


title: LCMV_armstrong_G03_short_paired-end


title: 1Plate1_D09_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_D09_CD8_Naive


title: 1Plate1_D09_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: Sequencing of the transduced sgRNAs post-selection (Screen A)_lane 2

description:
Double Lane Sequencing
HiSeq2000 Rapid Run
Neg A NH


title: LCMV_armstrong_G02_short_paired-end


title: Sequencing of the transduced sgRNAs pre-selection_lane 2

description:
Double Lane Sequencing
HiSeq2000 Rapid Run
Transduced NH

value: transduced sgRNAs pre-selection


title: LCMV_armstrong_G03_long_single-end


title: 1Plate1_D08_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_D08_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_D08_CD8_CMVtet


title: LCMV_armstrong_G01_short_paired-end


title: 1Plate1_D07_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_D07_CD8_CMVtet


title: LCMV_armstrong_G02_long_single-end


title: LCMV_armstrong_G01_long_single-end


title: Sequencing of the plasmid sgRNA library_lane 2

description:
Double Lane Sequencing
HiSeq2000 Rapid Run
Plasmid NH

value: plasmid sgRNA library


title: 1Plate1_D07_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: Sequencing of the transduced sgRNAs pre-selection_lane 1


title: LCMV_armstrong_F06_short_paired-end


title: LCMV_armstrong_F06_long_single-end


title: 1Plate1_D06_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_D06_CD8_CMVtet


title: LCMV_armstrong_F05_short_paired-end

description:
CD8+ armstrong LCMV-specific T cell mouse 2
NA
NA


title: 1Plate1_D06_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_D05_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_D05_CD8_CMVtet


title: LCMV_armstrong_G04_long_single-end


title: LCMV_armstrong_F04_short_paired-end


title: LCMV_armstrong_F05_long_single-end


title: 1Plate1_D04_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_D04_CD8_CMVtet


title: LCMV_armstrong_F04_long_single-end


title: 1Plate1_D04_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: Sequencing of the transduced sgRNAs post-selection (Screen A)_lane 1


title: 1Plate1_D03_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_D03_CD8_CMVtet


title: 1Plate1_D03_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_armstrong_F03_short_paired-end


title: 1Plate1_D02_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_armstrong_F02_short_paired-end


title: 1Plate1_D02_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_D02_CD8_CMVtet


title: LCMV_armstrong_F02_long_single-end


title: LCMV_armstrong_F01_short_paired-end


title: 1Plate1_D01_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_D01_CD8_CMVtet


title: 1Plate1_D01_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_D05_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_C12_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_C12_CD8_Naive

value: CD8+ Naive T cell


title: 1Plate1_C12_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: LCMV_armstrong_E06_short_paired-end


title: LCMV_armstrong_E06_long_single-end


title: At_p35S_Mock2

city: College Park

first: James

middle: N

last: Culver

address: 4291 Fieldhouse Dr.

department: Plant Science and Landscape Architecture

institute: University of Maryland, College Park

description: polysomal RNA from leaf tissue mock inoculated with sterile water

data_processing:
CASAVA 1.8.2 was used for bcl conversion and demultiplexing
Reads were mapped to the Arabidopsis thaliana Col-0 genome reference TAIR10 using the CLC Genomics Workbench v 7.5.1 RNA-seq analysis tool and default parameters. (Mismatch cost 2, Insertion cost 3, Deletion Cost 3, Length fraction 0.8, Similarity fraction 0.8, Max hits for a read 10)
Genome_build: Col-0 TAIR10
Supplementary_files_format_and_content: tab-delimited text files include Gene ID, Chromosome, Region, RPKM value, Total gene reads, and Total exon reads.

organism: Arabidopsis thaliana

growth_protocol: Transgenic plants expressing promoter:His6FLAG-RPL18 (ecotype Shahdara) were maintained in growth chambers for a 12-h photoperiod, light 100 µmol s-1 m-2, at 24°C.  Biological replicates were grown in different months under the same growth chamber conditions.

extract_protocol:
Frozen tissue was homogenized in Polysome Extraction Buffer (PEB; 200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM ethylene glycol tetraacetic acid (EGTA) pH 8.0, 35 mM MgCl2, 1% (v/v) octylphenyl-polyethylene glycol (Igepal CA-630), 1% (v/v) polyoxyethylene 10 tridecyl ether, 1% (v/v) sodium deoxycholate, 5 mM dithiothereitol (DTT), 1 mM PMSF, 50 ug/mL cycloheximide, 50 ug/mL chloramphenicol, 0.5 mg/mL heparin) using 10 mL PEB per 5 g of tissue.  Homogenates were clarified by centrifugation at 16,000 g for 15 min and filtered with cheesecloth. Anti-FLAG magnetic beads, 50 μL, (Sigma Chemical Company, St. Louis, MO USA) were added to the clarified supernatant and incubated at 4oC overnight with gentle rocking.  The beads were recovered using a magnet and washed four times for 5 min with 5 mL of wash buffer (200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM EGTA, 35 mM MgCl2, 5 mM DTT, 50 μg/mL cycloheximide, 50 μg/mL chloramphenicol).  The complexes were eluted by treatment of the magnetic beads with 100 uL of elution buffer (100 uL wash buffer, 10 uL of 5mg/mL FLAG3 peptide - Sigma Chemical Company, St. Louis, MO USA, 0.5 uL of 2 U/mL RNAse OUT - Thermo Fisher Scientific Cleveland, Ohio, USA).  RLT buffer plus 2-Mercaptoethanol from the Qiagen RNeasy kit (Qiagen, Valencia, CA USA) was added to the eluted complexes.  A 0.5 X volume of 100% ethanol was then added and the sample transferred to Qiagen RNeasy columns.  Washes and RNA elutions were performed according to the manufacturer’s instructions.  Isolated RNA was measured on a NanoDrop 1000 and the quality of the RNA confirmed using a 2100 Bioanalyzer Eukaryotic Total RNA Nanochip (Agilent Technologies Palo Alto, CA USA).
cDNA libraries were prepared by the by the UM-IBBR Sequencing Core at University of Maryland, College Park (http://ibbr.umd.edu/facilities/sequencing) using the Illuminia TrueSeq RNA library kit according to the manufacturer's instructions.

treatment_protocol: Plant leaves were inoculated with tobacco mosaic virus (1 mg/ml) or mock inoculated with sterile water. Inoculated leaves were harvested 6 days post infection and immediately frozen in liquid nitrogen.

tag: ecotype

value: Shahdara

value: 5-week-old plants

tag: genotype/variation

tag: infected with

value: leaf


title: At_pSUC2_Mock2

description: polysomal RNA from leaf phloem tissue mock inoculated with sterile water

tag: tissue

value: leaf phloem


title: At_pSULTR22_Mock1


title: At_pSUC2_Mock1


title: At_pSULTR22_Mock2


title: 1Plate1_C11_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_C11_CD8_Naive

tag: donor

tag: number of cells in sample


title: LCMV_armstrong_E05_long_single-end

value: CD8+ clone 13 LCMV-specific T cell


title: LCMV_armstrong_E05_short_paired-end


title: 1Plate1_C10_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_C10_CD8_Naive


title: At_pSULTR22_TMV2

description: polysomal RNA from leaf phloem tissue inoculated with tobacco mosaic virus

value: Tobacco mosaic virus


title: LCMV_armstrong_E04_short_paired-end


title: 1Plate1_C10_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA

value: Donor 1


title: LCMV_armstrong_F03_long_single-end


title: At_pSULTR22_TMV1


title: LCMV_armstrong_F01_long_single-end


title: LCMV_armstrong_E04_long_single-end


title: 1Plate1_C09_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
NA
NA


title: LCMV_armstrong_E03_short_paired-end

value: CD8+ armstrong LCMV-specific T cell


title: 1Plate1_C09_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: At_pSUC2_TMV2


title: At_p35S_Mock1


title: At_p35S_TMV1

description: polysomal RNA from leaf tissue inoculated with tobacco mosaic virus


title: LCMV_armstrong_E03_long_single-end

value: Mouse 2


title: 1Plate1_C11_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: 1Plate1_C08_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA

value: CD8+ CMV-specific T cell


title: LCMV_armstrong_E02_short_paired-end


title: 1Plate1_C07_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_C07_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_C07_CD8_CMVtet


title: 1Plate1_C08_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_C08_CD8_CMVtet


title: LCMV_armstrong_E01_short_paired-end


title: LCMV_armstrong_D06_short_paired-end


title: LCMV_armstrong_D06_long_single-end


title: LCMV_armstrong_D05_short_paired-end


title: 1Plate1_C06_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_C06_CD8_CMVtet


title: LCMV_armstrong_E01_long_single-end


title: 1Plate1_C05_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_C05_CD8_CMVtet


title: 1Plate1_C05_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: At_pSUC2_TMV1


title: LCMV_armstrong_D05_long_single-end

description:
CD8+ armstrong LCMV-specific T cell mouse 2
NA
NA


title: 1Plate1_C04_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_C04_CD8_CMVtet


title: 1Plate1_C04_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_armstrong_D04_long_single-end


title: LCMV_armstrong_D04_short_paired-end


title: At_p35S_TMV2


title: LCMV_armstrong_E02_long_single-end


title: LCMV_armstrong_D03_short_paired-end


title: LCMV_armstrong_D03_long_single-end


title: LCMV_armstrong_D02_short_paired-end


title: LCMV_armstrong_D02_long_single-end


title: 1Plate1_C03_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_C03_CD8_CMVtet


title: 1Plate1_C01_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_C01_CD8_CMVtet


title: 1Plate1_C06_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_C01_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_armstrong_C06_short_paired-end


title: 1Plate1_B12_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_B12_CD8_Naive


title: 1Plate1_C02_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_armstrong_D01_long_single-end


title: 1Plate1_B12_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: LCMV_armstrong_D01_short_paired-end


title: 1Plate1_B11_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_B11_CD8_Naive


title: LCMV_armstrong_C05_long_single-end


title: 1Plate1_B11_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: LCMV_armstrong_C04_short_paired-end


title: 1Plate1_B10_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_B10_CD8_Naive


title: LCMV_armstrong_C05_short_paired-end


title: LCMV_armstrong_C04_long_single-end


title: LCMV_armstrong_C03_short_paired-end


title: 1Plate1_B09_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_B09_CD8_Naive


title: 1Plate1_C03_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_C02_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_C02_CD8_CMVtet


title: 1Plate1_B09_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: LCMV_armstrong_C03_long_single-end


title: LCMV_armstrong_C02_short_paired-end


title: 1Plate1_B08_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_B08_CD8_CMVtet


title: 1Plate1_B08_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_armstrong_C01_short_paired-end


title: LCMV_armstrong_C06_long_single-end


title: LCMV_armstrong_B06_short_paired-end


title: 1Plate1_B07_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_B06_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_armstrong_C01_long_single-end


title: LCMV_armstrong_C02_long_single-end


title: LCMV_armstrong_B06_long_single-end


title: 1Plate1_B10_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: LCMV_armstrong_B05_short_paired-end


title: LCMV_armstrong_B05_long_single-end


title: 1Plate1_B05_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_B05_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_B05_CD8_CMVtet


title: LCMV_armstrong_B04_short_paired-end


title: LCMV_armstrong_B04_long_single-end


title: 1Plate1_B04_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_armstrong_B03_short_paired-end


title: LCMV_armstrong_B02_short_paired-end


title: LCMV_armstrong_B03_long_single-end


title: 1Plate1_B02_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_B02_CD8_CMVtet


title: 1Plate1_B03_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_B02_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_armstrong_B02_long_single-end


title: 1Plate1_B07_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_B07_CD8_CMVtet


title: LCMV_armstrong_B01_short_paired-end


title: 1Plate1_B06_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_B06_CD8_CMVtet


title: 1Plate1_B01_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_B01_CD8_CMVtet


title: 1Plate1_B01_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_armstrong_B01_long_single-end


title: LCMV_armstrong_A06_short_paired-end


title: 1Plate1_B04_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_B04_CD8_CMVtet


title: 1Plate1_A12_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: 1Plate1_A12_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_A12_CD8_Naive


title: LCMV_armstrong_A06_long_single-end

description:
CD8+ armstrong LCMV-specific T cell mouse 2
NA
NA


title: LCMV_armstrong_A05_long_single-end


title: 1Plate1_B03_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_B03_CD8_CMVtet


title: LCMV_armstrong_A04_short_paired-end


title: 1Plate1_A11_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: 1Plate1_A10_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_A10_CD8_Naive


title: 1Plate1_A09_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_A09_CD8_Naive


title: 1Plate1_A09_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: 1Plate1_A10_CD8_Naive_long_single-end

description:
CD8+ Naive T cell donor 1
NA
NA


title: LCMV_armstrong_A04_long_single-end


title: LCMV_armstrong_A03_short_paired-end


title: LCMV_armstrong_A03_long_single-end


title: LCMV_armstrong_A02_short_paired-end


title: 1Plate1_A08_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: LCMV_armstrong_A02_long_single-end


title: 1Plate1_A08_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_A08_CD8_CMVtet


title: LCMV_armstrong_A01_short_paired-end


title: 1Plate1_A07_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_A07_CD8_CMVtet


title: LCMV_armstrong_A01_long_single-end


title: 1Plate1_A07_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA


title: 1Plate1_A11_CD8_Naive_short_paired-end

description:
CD8+ Naive T cells donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_A11_CD8_Naive


title: LCMV_armstrong_A05_short_paired-end


title: 1Plate1_A06_CD8_CMVtet_short_paired-end

description:
CD8+ CMV-specific T cell donor 1
Norm.TPM.cmv.yfv.xlsx
1Plate1_A06_CD8_CMVtet


title: 1Plate1_A06_CD8_CMVtet_long_single-end

description:
CD8+ CMV-specific T cell donor 1
NA
NA