title: BR1008 Y1 Flu Day 7-9


title: BR1008 Y1 Flu Day 0

status: Public on Apr 24 2025

type: SRA

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

country: USA

institute: Benaroya Research Institute

library_source: transcriptomic

data_processing:
The FASTQs were aligned to the Genome Reference Consortium Human (GRCh) version 38.91, using STAR v.2.4.2a and gene counts were generated using HTSeq-count (v0.4.1) (57, 58). Quality metrics were compiled from PICARD (v1.134FASTQC (v0.11.3) Samtools (v1.2)8, and HTSeq-count. Samples with high median covariance of coverage coverage (>0.6), low total read count (<1 million), and low percent alignment (<92%) were considered low quality and removed from further analysis. Read counts were TMM-normalized (59).
Assembly: GRCh38.91
Supplementary files format and content: gene count matrix

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

growth_protocol: At each visit, peripheral blood was collected into Tempus Blood RNA tubes (Thermo Fisher Scientific).

extract_protocol:
We extracted RNA using the MagMAX RNA Isolation Kit (Thermo Fisher Scientific) then performed globin reduction with the GLOBINclear-Human Kit (Thermo Fisher Scientific).
We generated full-length cDNA from total RNA (0.5 ng). We amplified cDNA using the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) and constructed sequencing libraries using the NexteraXT DNA Library prep kit (Illumina).
We pooled libraries, quantified concentration with a Qubit Fluorometer (Life Technologies), then sequenced on a NextSeq 2000 sequencer (Illumina) with 59-base paired-end reads on a NextSeq P2 flow cell (Illumina). We targeted a depth of 5 million reads per sample.

tag: tissue

value: peripheral blood

tag: donor

tag: timepoint

value: Y1 Flu Day 0

tag: Sex

value: female

tag: age cohort

tag: cmv status

value: Positive


title: BR1057 Y2 Flu Day 80-100

value: Y2 Flu Day 80-100

value: Negative


title: BR1057 Standalone Baseline Visit

value: Standalone Baseline Visit


title: BR1008 Y2 Flu Day 0

value: Y2 Flu Day 0


title: BR1057 Y2 Flu Day 7-9

value: Y2 Flu Day 7-9


title: BR1054 Non-Flu Day 0

value: Non-Flu Day 0

value: male


title: BR1057 Y2 Flu Day 0


title: BR1057 Non-Flu Day 80-100

value: Non-Flu Day 80-100


title: BR1057 Non-Flu Day 7-9

value: Non-Flu Day 7-9


title: BR1057 Non-Flu Day 0


title: BR1057 Y1 Flu Day 80-100

value: Y1 Flu Day 80-100


title: BR1057 Y1 Flu Day 7-9

value: Y1 Flu Day 7-9


title: BR2035 Standalone Baseline Visit


title: BR1057 Y1 Flu Day 0


title: BR1050 Y2 Flu Day 7-9


title: BR2035 Y2 Flu Day 80-100


title: BR1050 Non-Flu Day 7-9


title: BR1050 Non-Flu Day 0


title: BR2035 Y2 Flu Day 0


title: BR2035 Non-Flu Day 7-9


title: BR2035 Non-Flu Day 0


title: BR2035 Y1 Flu Day 80-100


title: BR2035 Y1 Flu Day 7-9


title: BR2035 Y1 Flu Day 0


title: BR2038 Null Y2 Flu Day 7-9

growth_protocol: Peripheral blood was collected directly into control (unstimulated) TruCulture tubes or tubes pre-loaded with 0.4 µg/mL SEB, 1 ng/mL LPS, or 20 µg/mL poly I:C (Rules Based Medicine) for stimulation as previously described

extract_protocol:
We extracted RNA using the MagMAX RNA Isolation Kit (Thermo Fisher Scientific) then performed globin reduction with the GLOBINclear-Human Kit (Thermo Fisher Scientific)
We generated full-length cDNA from total RNA (0.5 ng). We amplified cDNA using the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) and constructed sequencing libraries using the NexteraXT DNA Library prep kit (Illumina).
We pooled libraries, quantified concentration with a Qubit Fluorometer (Life Technologies), then sequenced on a NextSeq 2000 sequencer (Illumina) with 59-base paired-end reads on a NextSeq P2 flow cell (Illumina). We targeted a depth of 5 million reads per sample.

treatment_protocol: After 24 hours of incubation, samples were processed to supernatant and cellular fraction (including RBC).  Cellular fractions were mixed before adding 500 µL to 1.5 mL Tempus solution and stored at -20°C until RNA-seq was performed

tag: stimulation


title: BR2038 Poly I:C Y2 Flu Day 7-9

value: Poly I:C


title: BR2038 Null Y2 Flu Day 0


title: BR2038 Poly I:C Y2 Flu Day 0


title: BR2038 SEB Y2 Flu Day 0

value: SEB


title: BR2038 LPS Y2 Flu Day 0

value: peripheral blood

value: LPS


title: BR1018 Null Non-Flu Day 80-100


title: BR2015 Poly I:C Non-Flu Day 80-100

value: female


title: BR2015 SEB Non-Flu Day 80-100


title: BR2015 LPS Non-Flu Day 80-100


title: BR2015 Null Non-Flu Day 80-100


title: BR1006 SEB Non-Flu Day 80-100


title: BR1006 Poly I:C Non-Flu Day 80-100


title: BR2032 SEB Non-Flu Day 80-100


title: BR2035 Non-Flu Day 80-100

value: Positive


title: BR2032 Null Non-Flu Day 80-100


title: BR2032 Poly I:C Non-Flu Day 80-100


title: BR2035 Y2 Flu Day 7-9


title: BR2046 Poly I:C Y2 Flu Day 7-9


title: BR2046 SEB Y2 Flu Day 7-9


title: BR2032 LPS Non-Flu Day 80-100


title: BR2046 LPS Y2 Flu Day 7-9


title: BR2038 SEB Y2 Flu Day 7-9


title: BR2046 Poly I:C Y2 Flu Day 0


title: BR2046 Null Y2 Flu Day 7-9


title: BR2046 LPS Y2 Flu Day 0


title: BR2046 Null Y2 Flu Day 0


title: BR2038 LPS Y2 Flu Day 7-9


title: BR1002 Poly I:C Y2 Flu Day 7-9


title: BR1002 SEB Y2 Flu Day 7-9


title: BR1006 Null Non-Flu Day 80-100


title: BR2019 Poly I:C Y1 Flu Day 7-9


title: BR2019 SEB Y1 Flu Day 7-9


title: BR1002 LPS Y2 Flu Day 7-9


title: BR1002 Null Y2 Flu Day 7-9


title: BR2044 SEB Non-Flu Day 0


title: BR2019 LPS Y1 Flu Day 7-9


title: BR2044 LPS Non-Flu Day 0


title: BR1050 LPS Non-Flu Day 7-9


title: BR1050 Null Non-Flu Day 7-9


title: BR1050 SEB Non-Flu Day 7-9


title: BR2044 Poly I:C Non-Flu Day 0


title: BR2038 Null Non-Flu Day 7-9


title: BR1050 Poly I:C Non-Flu Day 7-9


title: BR2038 Poly I:C Non-Flu Day 7-9


title: BR2038 LPS Non-Flu Day 7-9


title: BR2046 SEB Y2 Flu Day 0


title: BR2039 Poly I:C Y1 Flu Day 7-9


title: BR2039 LPS Y1 Flu Day 7-9


title: BR2003 SEB Y2 Flu Day 7-9


title: BR2039 Null Y1 Flu Day 7-9


title: BR2003 Poly I:C Y2 Flu Day 7-9


title: BR2003 LPS Y2 Flu Day 7-9


title: BR1044 SEB Y1 Flu Day 0

value: Y1 Flu Day 0


title: BR1044 Poly I:C Y1 Flu Day 0


title: BR1044 LPS Y1 Flu Day 0


title: BR2019 Null Y1 Flu Day 7-9


title: BR1028 SEB Y1 Flu Day 0

value: Negative


title: BR2044 Null Non-Flu Day 0


title: BR1044 Null Y1 Flu Day 0


title: BR1028 Poly I:C Y1 Flu Day 0


title: BR1028 LPS Y1 Flu Day 0


title: BR1002 SEB Standalone Baseline Visit

value: Standalone Baseline Visit


title: BR1002 Poly I:C Standalone Baseline Visit


title: BR2038 SEB Non-Flu Day 7-9


title: BR1002 Null Standalone Baseline Visit


title: BR1002 LPS Standalone Baseline Visit


title: BR1040 SEB Non-Flu Day 0


title: BR1028 Null Y1 Flu Day 0


title: BR2003 Null Y2 Flu Day 7-9


title: BR1040 LPS Non-Flu Day 0


title: BR1023 Poly I:C Y1 Flu Day 7-9


title: BR1023 LPS Y1 Flu Day 7-9


title: BR1058 SEB Non-Flu Day 7-9


title: BR2039 SEB Y1 Flu Day 7-9


title: BR1040 Poly I:C Non-Flu Day 0


title: BR1040 Null Non-Flu Day 0


title: BR1058 Null Non-Flu Day 7-9


title: BR1023 Null Y1 Flu Day 7-9


title: BR1058 Poly I:C Non-Flu Day 7-9


title: BR1023 SEB Y1 Flu Day 7-9


title: BR1026 Poly I:C Non-Flu Day 80-100


title: BR1026 LPS Non-Flu Day 80-100


title: BR1026 Null Non-Flu Day 80-100


title: BR2042 SEB Y1 Flu Day 7-9


title: BR2042 Null Y1 Flu Day 7-9


title: BR2042 Poly I:C Y1 Flu Day 7-9


title: BR1058 LPS Non-Flu Day 7-9


title: BR2042 LPS Y1 Flu Day 7-9


title: BR2042 Poly I:C Y1 Flu Day 0


title: BR2042 SEB Y1 Flu Day 0


title: BR2042 Null Y1 Flu Day 0


title: BR1026 SEB Non-Flu Day 80-100


title: BR2010 Poly I:C Y1 Flu Day 7-9


title: BR2010 SEB Y1 Flu Day 7-9


title: BR2010 Null Y1 Flu Day 7-9


title: BR2042 LPS Y1 Flu Day 0


title: BR2010 LPS Y1 Flu Day 7-9


title: BR2021 SEB Y1 Flu Day 7-9


title: BR2021 Poly I:C Y1 Flu Day 7-9


title: BR1048 SEB Y1 Flu Day 0


title: BR2021 Null Y1 Flu Day 7-9


title: BR2035 SEB Y1 Flu Day 0


title: BR1048 Null Y1 Flu Day 0


title: BR2035 Null Y1 Flu Day 0


title: BR2021 LPS Y1 Flu Day 7-9


title: BR2035 Poly I:C Y1 Flu Day 0


title: BR1023 SEB Non-Flu Day 80-100


title: BR1023 Null Non-Flu Day 80-100


title: BR1051 Poly I:C Y1 Flu Day 0


title: BR1051 SEB Y1 Flu Day 0


title: BR1023 LPS Non-Flu Day 80-100


title: BR2035 LPS Y1 Flu Day 0


title: BR1051 Null Y1 Flu Day 0


title: BR1051 LPS Y1 Flu Day 0


title: BR1006 SEB Y2 Flu Day 7-9


title: BR1006 Poly I:C Y2 Flu Day 7-9


title: BR2010 Null Y1 Flu Day 0


title: BR1006 Null Y2 Flu Day 7-9


title: BR2010 Poly I:C Y1 Flu Day 0


title: BR2010 SEB Y1 Flu Day 0


title: BR2010 LPS Y1 Flu Day 0


title: BR1006 LPS Y2 Flu Day 7-9


title: BR2045 SEB Non-Flu Day 0


title: BR2045 Null Non-Flu Day 0


title: BR1025 SEB Y1 Flu Day 7-9


title: BR2045 LPS Non-Flu Day 0


title: BR2045 Poly I:C Non-Flu Day 0


title: BR1025 LPS Y1 Flu Day 7-9


title: BR1025 Poly I:C Y1 Flu Day 7-9


title: BR2005 Null Non-Flu Day 80-100


title: BR1023 Poly I:C Non-Flu Day 80-100


title: BR2005 SEB Non-Flu Day 80-100


title: BR2047 SEB Y1 Flu Day 7-9


title: BR2005 LPS Non-Flu Day 80-100


title: BR2047 Poly I:C Y1 Flu Day 7-9


title: BR2047 Null Y1 Flu Day 7-9


title: BR1008 Poly I:C Y2 Flu Day 7-9


title: BR1008 Null Y2 Flu Day 7-9


title: BR1008 LPS Y2 Flu Day 7-9


title: BR2035 Poly I:C Non-Flu Day 80-100


title: BR2035 Null Non-Flu Day 80-100


title: BR1040 Poly I:C Y1 Flu Day 7-9


title: BR1040 Null Y1 Flu Day 7-9


title: BR1040 LPS Y1 Flu Day 7-9


title: BR2035 SEB Non-Flu Day 80-100


title: BR1040 SEB Y1 Flu Day 7-9


title: BR2049 SEB Y1 Flu Day 0


title: BR1034 LPS Non-Flu Day 80-100


title: BR2035 LPS Non-Flu Day 80-100


title: BR2049 Poly I:C Y1 Flu Day 0


title: BR1034 Poly I:C Non-Flu Day 80-100


title: BR2005 Poly I:C Non-Flu Day 80-100


title: BR1034 Null Non-Flu Day 80-100


title: BR1025 Null Y1 Flu Day 7-9


title: BR1034 SEB Non-Flu Day 80-100


title: BR2049 LPS Y1 Flu Day 0


title: BR2016 SEB Y1 Flu Day 7-9


title: BR2016 Null Y1 Flu Day 7-9


title: BR2016 Poly I:C Y1 Flu Day 7-9


title: BR2052 Poly I:C Y1 Flu Day 7-9


title: BR2047 LPS Y1 Flu Day 7-9


title: BR1008 SEB Y2 Flu Day 7-9


title: BR2052 SEB Y1 Flu Day 7-9


title: BR2052 Null Y1 Flu Day 7-9


title: BR2039 SEB Y1 Flu Day 0


title: BR2039 Poly I:C Y1 Flu Day 0


title: BR2039 LPS Y1 Flu Day 0


title: BR2049 Null Y1 Flu Day 0


title: BR2031 SEB Y1 Flu Day 0


title: BR1003 LPS Y2 Flu Day 0

value: Y2 Flu Day 0


title: BR1003 Poly I:C Y2 Flu Day 0


title: BR1003 SEB Y2 Flu Day 0


title: BR1003 Null Y2 Flu Day 0


title: BR2016 LPS Y1 Flu Day 7-9


title: BR2052 LPS Y1 Flu Day 7-9


title: BR2031 Poly I:C Y1 Flu Day 0


title: BR2015 LPS Y1 Flu Day 7-9


title: BR2015 Null Y1 Flu Day 7-9


title: BR2031 LPS Y1 Flu Day 0


title: BR2008 Null Y1 Flu Day 7-9


title: BR2015 Poly I:C Y1 Flu Day 7-9


title: BR2015 SEB Y1 Flu Day 7-9


title: BR1010 SEB Non-Flu Day 7-9


title: BR2008 SEB Y1 Flu Day 7-9


title: BR2031 Null Y1 Flu Day 0


title: BR1010 Null Non-Flu Day 7-9


title: BR2008 LPS Y1 Flu Day 7-9


title: BR1007 SEB Non-Flu Day 80-100


title: BR1010 LPS Non-Flu Day 7-9


title: BR2008 Poly I:C Y1 Flu Day 7-9


title: BR1007 Null Non-Flu Day 80-100


title: BR1007 Poly I:C Non-Flu Day 80-100


title: BR1024 Poly I:C Non-Flu Day 80-100


title: BR1007 LPS Non-Flu Day 80-100


title: BR1024 SEB Non-Flu Day 80-100


title: BR2039 Null Y1 Flu Day 0


title: BR2023 SEB Y1 Flu Day 0


title: BR2023 Poly I:C Y1 Flu Day 0


title: BR1024 LPS Non-Flu Day 80-100


title: BR1057 SEB Non-Flu Day 0


title: BR1057 LPS Non-Flu Day 0


title: BR1057 Null Non-Flu Day 0


title: BR1004 SEB Y2 Flu Day 0


title: BR1003 SEB Y2 Flu Day 7-9

value: Y2 Flu Day 7-9


title: BR1012 Null Y2 Flu Day 0


title: BR1004 Null Y2 Flu Day 0


title: BR1003 LPS Y2 Flu Day 7-9


title: BR2012 Poly I:C Y1 Flu Day 7-9


title: BR1004 LPS Y2 Flu Day 0


title: BR1003 Poly I:C Y2 Flu Day 7-9


title: BR1003 Null Y2 Flu Day 7-9


title: BR1004 Poly I:C Y2 Flu Day 0


title: BR2012 SEB Y1 Flu Day 7-9


title: BR2012 Null Y1 Flu Day 7-9


title: BR2013 Poly I:C Y1 Flu Day 0


title: BR2012 LPS Y1 Flu Day 7-9


title: BR2028 SEB Y1 Flu Day 7-9


title: BR2013 Null Y1 Flu Day 0


title: BR1012 SEB Y2 Flu Day 0


title: BR1012 LPS Y2 Flu Day 0


title: BR2013 LPS Y1 Flu Day 0


title: BR1024 Null Non-Flu Day 80-100


title: BR2028 Poly I:C Y1 Flu Day 7-9


title: BR1012 Poly I:C Y2 Flu Day 0


title: BR2023 LPS Y1 Flu Day 0


title: BR2013 SEB Y1 Flu Day 0


title: BR2028 Null Y1 Flu Day 7-9


title: BR2010 Null Non-Flu Day 80-100


title: BR2028 LPS Y1 Flu Day 7-9


title: BR1045 Poly I:C Y1 Flu Day 7-9


title: BR1017 SEB Y1 Flu Day 7-9


title: BR1045 LPS Y1 Flu Day 7-9


title: BR2010 SEB Non-Flu Day 80-100


title: BR1045 Null Y1 Flu Day 7-9


title: BR1016 SEB Y1 Flu Day 0


title: BR1017 LPS Y1 Flu Day 7-9


title: BR2004 SEB Non-Flu Day 80-100


title: BR2004 LPS Non-Flu Day 80-100


title: BR2010 LPS Non-Flu Day 80-100


title: BR2004 Null Non-Flu Day 80-100


title: BR2004 Poly I:C Non-Flu Day 80-100


title: BR1017 Poly I:C Y1 Flu Day 7-9


title: BR1016 Null Y1 Flu Day 0


title: BR1016 Poly I:C Y1 Flu Day 0


title: BR2037 SEB Y1 Flu Day 0


title: BR1016 LPS Y1 Flu Day 0


title: BR2037 Poly I:C Y1 Flu Day 0


title: BR2012 SEB Non-Flu Day 80-100


title: BR2010 Poly I:C Non-Flu Day 80-100


title: BR2012 Null Non-Flu Day 80-100


title: BR2037 Null Y1 Flu Day 0


title: BR2012 Poly I:C Non-Flu Day 80-100


title: BR2037 LPS Y1 Flu Day 0


title: BR2012 LPS Non-Flu Day 80-100


title: BR1011 Poly I:C Y2 Flu Day 7-9


title: BR2030 SEB Standalone Baseline Visit


title: BR1045 SEB Y1 Flu Day 7-9


title: BR2030 Null Standalone Baseline Visit


title: BR1011 SEB Y2 Flu Day 7-9


title: BR1011 LPS Y2 Flu Day 7-9


title: BR2030 LPS Standalone Baseline Visit


title: BR1011 Null Y2 Flu Day 7-9


title: BR1032 SEB Y1 Flu Day 7-9


title: BR1032 Null Y1 Flu Day 7-9


title: BR2045 SEB Y1 Flu Day 0


title: BR1057 Poly I:C Non-Flu Day 0

value: Non-Flu Day 0


title: BR2045 Poly I:C Y1 Flu Day 0


title: BR2045 Null Y1 Flu Day 0


title: BR2045 LPS Y1 Flu Day 0


title: BR2020 Null Standalone Baseline Visit

value: male


title: BR2020 Poly I:C Standalone Baseline Visit


title: BR2020 SEB Standalone Baseline Visit


title: BR2020 LPS Standalone Baseline Visit


title: BR2050 SEB Y1 Flu Day 0


title: BR2050 LPS Y1 Flu Day 0


title: BR2029 SEB Standalone Baseline Visit


title: BR2050 Null Y1 Flu Day 0


title: BR2029 Poly I:C Standalone Baseline Visit


title: BR2029 LPS Standalone Baseline Visit


title: BR2029 Null Standalone Baseline Visit


title: BR2030 Poly I:C Standalone Baseline Visit


title: BR1013 SEB Y2 Flu Day 7-9


title: BR1032 Poly I:C Y1 Flu Day 7-9


title: BR1013 Null Y2 Flu Day 7-9


title: BR1013 LPS Y2 Flu Day 7-9


title: BR2041 Poly I:C Y1 Flu Day 0


title: BR1013 Poly I:C Y2 Flu Day 7-9


title: BR2041 SEB Y1 Flu Day 0


title: BR1032 LPS Y1 Flu Day 7-9


title: BR1002 SEB Y2 Flu Day 0


title: BR1002 LPS Y2 Flu Day 0


title: BR2041 LPS Y1 Flu Day 0


title: BR1019 SEB Y1 Flu Day 0


title: BR1002 Poly I:C Y2 Flu Day 0


title: BR1002 Null Y2 Flu Day 0


title: BR1019 Null Y1 Flu Day 0


title: BR1011 Poly I:C Y2 Flu Day 0


title: BR1011 Null Y2 Flu Day 0


title: BR1021 SEB Non-Flu Day 80-100

value: Non-Flu Day 80-100


title: BR1019 LPS Y1 Flu Day 0


title: BR1021 Poly I:C Non-Flu Day 80-100


title: BR1011 LPS Y2 Flu Day 0


title: BR1021 Null Non-Flu Day 80-100


title: BR1017 Null Y1 Flu Day 7-9


title: BR1018 Poly I:C Y2 Flu Day 0


title: BR1021 LPS Non-Flu Day 80-100


title: BR1018 SEB Y2 Flu Day 0


title: BR2041 Null Y1 Flu Day 0


title: BR1018 Null Y2 Flu Day 0


title: BR1018 LPS Y2 Flu Day 0


title: BR1051 SEB Y1 Flu Day 7-9


title: BR1051 Poly I:C Y1 Flu Day 7-9


title: BR1019 Poly I:C Y1 Flu Day 0


title: BR2050 Null Y1 Flu Day 7-9


title: BR2050 SEB Y1 Flu Day 7-9


title: BR1032 LPS Y1 Flu Day 0


title: BR1051 LPS Y1 Flu Day 7-9


title: BR1032 Null Y1 Flu Day 0


title: BR1011 SEB Y2 Flu Day 0


title: BR1051 Null Y1 Flu Day 7-9


title: BR2050 Poly I:C Y1 Flu Day 7-9


title: BR1041 SEB Y1 Flu Day 0


title: BR1032 Poly I:C Y1 Flu Day 0


title: BR2050 LPS Y1 Flu Day 7-9


title: BR1041 Null Y1 Flu Day 0


title: BR2037 Poly I:C Non-Flu Day 0


title: BR2037 Null Non-Flu Day 0


title: BR2037 SEB Non-Flu Day 0


title: BR2037 LPS Non-Flu Day 0


title: BR1048 SEB Y1 Flu Day 7-9


title: BR1019 SEB Standalone Baseline Visit


title: BR1048 Poly I:C Y1 Flu Day 7-9


title: BR1048 LPS Y1 Flu Day 7-9


title: BR1032 SEB Y1 Flu Day 0


title: BR1019 Poly I:C Standalone Baseline Visit


title: BR1019 Null Standalone Baseline Visit


title: BR2024 SEB Y1 Flu Day 0


title: BR1019 LPS Standalone Baseline Visit


title: BR2024 Poly I:C Y1 Flu Day 0


title: BR2024 LPS Y1 Flu Day 0


title: BR2024 Null Y1 Flu Day 0


title: BR1034 Poly I:C Y1 Flu Day 7-9


title: BR1034 LPS Y1 Flu Day 7-9


title: BR1034 Null Y1 Flu Day 7-9


title: BR1041 Poly I:C Y1 Flu Day 0


title: BR1034 LPS Y1 Flu Day 0


title: BR2049 SEB Y1 Flu Day 7-9


title: BR1034 Poly I:C Y1 Flu Day 0


title: BR1048 Null Y1 Flu Day 7-9


title: BR1054 SEB Non-Flu Day 0


title: BR1034 SEB Y1 Flu Day 0


title: BR1054 LPS Non-Flu Day 0


title: BR2049 Null Y1 Flu Day 7-9


title: BR2049 LPS Y1 Flu Day 7-9


title: BR1054 Poly I:C Non-Flu Day 0


title: BR2021 LPS Y1 Flu Day 0


title: BR2021 Null Y1 Flu Day 0


title: BR2021 Poly I:C Y1 Flu Day 0


title: BR2044 Poly I:C Y1 Flu Day 0


title: BR2044 LPS Y1 Flu Day 0


title: BR2044 SEB Y1 Flu Day 0


title: BR2044 Null Y1 Flu Day 0


title: BR1034 SEB Y1 Flu Day 7-9


title: BR1041 LPS Y1 Flu Day 0


title: BR1034 Null Y1 Flu Day 0


title: BR1004 SEB Non-Flu Day 0


title: BR2049 Poly I:C Y1 Flu Day 7-9


title: BR1004 Poly I:C Non-Flu Day 0


title: BR1054 Null Non-Flu Day 0


title: BR1004 Null Non-Flu Day 0


title: BR2021 SEB Y1 Flu Day 0


title: BR2025 LPS Non-Flu Day 0


title: BR1037 Null Y1 Flu Day 7-9


title: BR1037 LPS Y1 Flu Day 7-9


title: BR1014 SEB Y2 Flu Day 0


title: BR2014 SEB Standalone Baseline Visit


title: BR2014 Poly I:C Standalone Baseline Visit


title: BR1014 LPS Y2 Flu Day 0


title: BR1010 Poly I:C Y2 Flu Day 7-9


title: BR1010 SEB Y2 Flu Day 7-9


title: BR2014 Null Standalone Baseline Visit


title: BR1037 Poly I:C Y1 Flu Day 7-9


title: BR1010 Null Y2 Flu Day 7-9


title: BR1010 LPS Y2 Flu Day 7-9


title: BR1010 SEB Y2 Flu Day 0


title: BR1010 LPS Y2 Flu Day 0


title: BR2025 Null Non-Flu Day 0


title: BR1010 Poly I:C Y2 Flu Day 0


title: BR1010 Null Y2 Flu Day 0


title: BR1026 SEB Y1 Flu Day 7-9


title: BR1026 Poly I:C Y1 Flu Day 7-9


title: BR1014 Poly I:C Y2 Flu Day 0


title: BR1026 LPS Y1 Flu Day 7-9


title: BR2021 SEB Standalone Baseline Visit


title: BR1004 LPS Non-Flu Day 0


title: BR2014 LPS Standalone Baseline Visit


title: BR1014 Null Y2 Flu Day 0


title: BR2021 Poly I:C Standalone Baseline Visit


title: BR2021 Null Standalone Baseline Visit


title: BR1026 Null Y1 Flu Day 7-9


title: BR1037 SEB Y1 Flu Day 7-9


title: BR1045 SEB Y1 Flu Day 0


title: BR1045 Null Y1 Flu Day 0


title: BR1045 Poly I:C Y1 Flu Day 0


title: BR1045 LPS Y1 Flu Day 0


title: BR2021 LPS Standalone Baseline Visit


title: BR1013 Poly I:C Y2 Flu Day 0


title: BR1013 SEB Y2 Flu Day 0


title: BR1013 LPS Y2 Flu Day 0


title: BR2032 SEB Y1 Flu Day 7-9


title: BR1013 Null Y2 Flu Day 0


title: BR2032 Poly I:C Y1 Flu Day 7-9


title: BR2032 Null Y1 Flu Day 7-9


title: BR2032 LPS Y1 Flu Day 7-9


title: BR2025 Poly I:C Y1 Flu Day 7-9


title: BR2025 SEB Y1 Flu Day 7-9


title: BR2024 Null Standalone Baseline Visit


title: BR2025 LPS Y1 Flu Day 7-9


title: BR2024 SEB Standalone Baseline Visit


title: BR2025 Null Y1 Flu Day 7-9


title: BR2024 Poly I:C Standalone Baseline Visit


title: BR1037 Poly I:C Y1 Flu Day 0


title: BR1037 Null Y1 Flu Day 0


title: BR2024 LPS Standalone Baseline Visit


title: BR1037 LPS Y1 Flu Day 0


title: BR1037 SEB Y1 Flu Day 0


title: BR1037 Poly I:C Non-Flu Day 80-100


title: BR1037 SEB Non-Flu Day 80-100


title: BR1037 LPS Non-Flu Day 80-100


title: BR1011 SEB Non-Flu Day 80-100


title: BR1011 LPS Non-Flu Day 80-100


title: BR2022 SEB Y1 Flu Day 0


title: BR1037 Null Non-Flu Day 80-100


title: BR1011 Poly I:C Non-Flu Day 80-100


title: BR2022 Poly I:C Y1 Flu Day 0


title: BR2022 Null Y1 Flu Day 0


title: BR2022 LPS Y1 Flu Day 0


title: BR1058 LPS Y1 Flu Day 0


title: BR1058 Null Y1 Flu Day 0


title: BR1058 Poly I:C Y1 Flu Day 0


title: BR1058 SEB Y1 Flu Day 0


title: BR2025 Poly I:C Non-Flu Day 0


title: BR2048 SEB Non-Flu Day 7-9

value: Non-Flu Day 7-9


title: BR2048 Null Non-Flu Day 7-9


title: BR2048 Poly I:C Non-Flu Day 7-9


title: BR2048 LPS Non-Flu Day 7-9


title: BR1025 SEB Y1 Flu Day 0


title: BR1025 Null Y1 Flu Day 0


title: BR1025 Poly I:C Y1 Flu Day 0


title: BR1025 LPS Y1 Flu Day 0


title: BR1013 SEB Y1 Flu Day 80-100

value: Y1 Flu Day 80-100


title: BR1011 Null Non-Flu Day 80-100


title: BR1013 Null Y1 Flu Day 80-100


title: BR2022 SEB Standalone Baseline Visit


title: BR1013 LPS Y1 Flu Day 80-100


title: BR1013 Poly I:C Y1 Flu Day 80-100


title: BR2022 Null Standalone Baseline Visit


title: BR2008 SEB Y1 Flu Day 0


title: BR2022 Poly I:C Standalone Baseline Visit


title: BR2022 LPS Standalone Baseline Visit


title: BR2008 Null Y1 Flu Day 0


title: BR2053 Poly I:C Non-Flu Day 0


title: BR2053 Null Non-Flu Day 0


title: BR2053 LPS Non-Flu Day 0


title: BR1054 SEB Y1 Flu Day 0


title: BR1054 LPS Y1 Flu Day 0


title: BR1054 Null Y1 Flu Day 0


title: BR1009 LPS Y2 Flu Day 7-9


title: BR1009 Null Y2 Flu Day 7-9


title: BR1009 SEB Y2 Flu Day 7-9


title: BR2033 Poly I:C Y1 Flu Day 0


title: BR2033 SEB Y1 Flu Day 0


title: BR2033 Null Y1 Flu Day 0


title: BR1009 Poly I:C Y2 Flu Day 7-9


title: BR2033 LPS Y1 Flu Day 0


title: BR1031 SEB Y1 Flu Day 0


title: BR1031 Poly I:C Y1 Flu Day 0


title: BR1031 Null Y1 Flu Day 0


title: BR1044 Poly I:C Non-Flu Day 80-100


title: BR1031 LPS Y1 Flu Day 0


title: BR2008 Poly I:C Y1 Flu Day 0


title: BR1044 LPS Non-Flu Day 80-100


title: BR1044 Null Non-Flu Day 80-100


title: BR2053 SEB Non-Flu Day 0


title: BR2009 Poly I:C Y1 Flu Day 7-9

value: Y1 Flu Day 7-9


title: BR2008 LPS Y1 Flu Day 0


title: BR1054 Poly I:C Y1 Flu Day 0

value: Poly I:C


title: BR2009 Null Y1 Flu Day 7-9


title: BR2009 LPS Y1 Flu Day 7-9


title: BR2009 SEB Non-Flu Day 80-100

value: SEB


title: BR2009 Poly I:C Non-Flu Day 80-100

value: peripheral blood


title: BR1049 SEB Y1 Flu Day 0


title: BR2009 LPS Non-Flu Day 80-100

value: LPS


title: BR1049 Poly I:C Y1 Flu Day 0


title: BR2028 SEB Standalone Baseline Visit


title: BR1049 LPS Y1 Flu Day 0


title: BR2028 Null Standalone Baseline Visit


title: BR2028 LPS Standalone Baseline Visit


title: BR2002 Null Non-Flu Day 80-100

value: female


title: BR1044 SEB Non-Flu Day 80-100

value: Positive


title: BR2028 Poly I:C Standalone Baseline Visit


title: BR2009 SEB Y1 Flu Day 7-9


title: BR2002 Poly I:C Non-Flu Day 80-100


title: BR2002 LPS Y2 Flu Day 7-9


title: BR2002 Null Y2 Flu Day 7-9


title: BR1032 Poly I:C Non-Flu Day 80-100


title: BR1032 Null Non-Flu Day 80-100


title: BR1032 SEB Non-Flu Day 80-100


title: BR2002 SEB Y2 Flu Day 7-9


title: BR1032 LPS Non-Flu Day 80-100


title: BR2051 Null Y1 Flu Day 7-9


title: BR2051 SEB Y1 Flu Day 7-9


title: BR2051 LPS Y1 Flu Day 7-9


title: BR2044 SEB Y1 Flu Day 7-9


title: BR2002 LPS Non-Flu Day 80-100


title: BR2051 Poly I:C Y1 Flu Day 7-9


title: BR2044 Poly I:C Y1 Flu Day 7-9


title: BR1028 Null Y1 Flu Day 7-9


title: BR1028 SEB Y1 Flu Day 7-9


title: BR2044 Null Y1 Flu Day 7-9


title: BR2044 LPS Y1 Flu Day 7-9


title: BR1028 Poly I:C Y1 Flu Day 7-9


title: BR1028 LPS Y1 Flu Day 7-9


title: BR2002 SEB Non-Flu Day 80-100


title: BR1019 Null Y1 Flu Day 7-9


title: BR2025 Null Y1 Flu Day 0

value: Y1 Flu Day 0


title: BR2025 LPS Y1 Flu Day 0

value: Negative


title: BR1019 SEB Y1 Flu Day 7-9


title: BR2025 SEB Y1 Flu Day 0


title: BR1019 Poly I:C Y1 Flu Day 7-9


title: BR1019 LPS Y1 Flu Day 7-9


title: BR2030 SEB Y1 Flu Day 7-9


title: BR2030 Poly I:C Y1 Flu Day 7-9


title: BR2030 Null Y1 Flu Day 7-9


title: BR2030 LPS Y1 Flu Day 7-9


title: BR1015 SEB Y1 Flu Day 0


title: BR1015 Null Y1 Flu Day 0


title: BR1015 LPS Y1 Flu Day 0


title: BR1015 Poly I:C Y1 Flu Day 0


title: BR2025 Poly I:C Y1 Flu Day 0


title: BR1047 SEB Non-Flu Day 80-100


title: BR2036 LPS Non-Flu Day 0


title: BR2036 Poly I:C Non-Flu Day 0


title: BR2036 SEB Non-Flu Day 0


title: BR1057 Null Y1 Flu Day 0


title: BR1057 Poly I:C Y1 Flu Day 0


title: BR1041 SEB Y1 Flu Day 7-9


title: BR2043 LPS Y1 Flu Day 0


title: BR2040 LPS Y1 Flu Day 0


title: BR2043 Null Y1 Flu Day 0


title: BR2043 SEB Y1 Flu Day 0


title: BR1041 Poly I:C Y1 Flu Day 7-9


title: BR1041 LPS Y1 Flu Day 7-9


title: BR1042 Null Y1 Flu Day 0


title: BR1042 SEB Y1 Flu Day 0


title: BR1042 Poly I:C Y1 Flu Day 0


title: BR1042 LPS Y1 Flu Day 0


title: BR1047 Null Non-Flu Day 80-100


title: BR2003 Poly I:C Y2 Flu Day 0


title: BR2003 SEB Y2 Flu Day 0


title: BR2003 LPS Y2 Flu Day 0


title: BR2003 Null Y2 Flu Day 0


title: BR2035 SEB Y1 Flu Day 7-9


title: BR1057 LPS Y1 Flu Day 0


title: BR1057 SEB Y1 Flu Day 0


title: BR2035 Null Y1 Flu Day 7-9


title: BR2007 Poly I:C Non-Flu Day 80-100


title: BR2035 Poly I:C Y1 Flu Day 7-9


title: BR2007 LPS Non-Flu Day 80-100


title: BR2007 Null Non-Flu Day 80-100


title: BR2007 SEB Non-Flu Day 80-100


title: BR2015 LPS Y1 Flu Day 0


title: BR2036 Null Non-Flu Day 0


title: BR2035 LPS Y1 Flu Day 7-9


title: BR2015 Poly I:C Y1 Flu Day 0


title: BR2015 SEB Y1 Flu Day 0


title: BR2015 Null Y1 Flu Day 0


title: BR2028 SEB Y1 Flu Day 0


title: BR2028 Poly I:C Y1 Flu Day 0


title: BR2018 Null Y1 Flu Day 7-9


title: BR2019 Poly I:C Standalone Baseline Visit

value: Standalone Baseline Visit


title: BR2019 SEB Standalone Baseline Visit


title: BR2018 SEB Y1 Flu Day 7-9


title: BR2028 Null Y1 Flu Day 0


title: BR2018 Poly I:C Y1 Flu Day 7-9


title: BR2019 Null Standalone Baseline Visit


title: BR2023 SEB Y1 Flu Day 7-9


title: BR2019 LPS Standalone Baseline Visit


title: BR2023 LPS Y1 Flu Day 7-9


title: BR2023 Poly I:C Y1 Flu Day 7-9


title: BR2023 Null Y1 Flu Day 7-9


title: BR2040 Poly I:C Non-Flu Day 80-100


title: BR2040 SEB Non-Flu Day 80-100


title: BR2040 Null Non-Flu Day 80-100


title: BR2040 LPS Non-Flu Day 80-100


title: BR2047 Poly I:C Y1 Flu Day 0


title: BR2047 Null Y1 Flu Day 0


title: BR2047 SEB Y1 Flu Day 0


title: BR2031 SEB Standalone Baseline Visit


title: BR2031 LPS Standalone Baseline Visit


title: BR2031 Poly I:C Standalone Baseline Visit


title: BR2047 LPS Y1 Flu Day 0


title: BR2007 Null Y1 Flu Day 7-9


title: BR2007 SEB Y1 Flu Day 7-9


title: BR2007 Poly I:C Y1 Flu Day 7-9


title: BR2018 LPS Y1 Flu Day 7-9


title: BR2007 LPS Y1 Flu Day 7-9


title: BR2028 LPS Y1 Flu Day 0


title: BR1021 SEB Y1 Flu Day 0


title: BR1021 Null Y1 Flu Day 0


title: BR1021 Poly I:C Y1 Flu Day 0


title: BR1056 Poly I:C Y1 Flu Day 7-9


title: BR1021 LPS Y1 Flu Day 0


title: BR1056 LPS Y1 Flu Day 7-9


title: BR1056 Null Y1 Flu Day 7-9


title: BR1054 SEB Y1 Flu Day 7-9


title: BR1054 LPS Y1 Flu Day 7-9


title: BR1005 Poly I:C Y2 Flu Day 0

value: Y2 Flu Day 0


title: BR1054 Null Y1 Flu Day 7-9


title: BR1054 Poly I:C Y1 Flu Day 7-9


title: BR1005 SEB Y2 Flu Day 0


title: BR1005 Null Y2 Flu Day 0


title: BR1005 LPS Y2 Flu Day 0


title: BR2031 Null Standalone Baseline Visit


title: BR1052 SEB Y1 Flu Day 0


title: BR1050 SEB Y1 Flu Day 0


title: BR1050 Null Y1 Flu Day 0


title: BR1052 Null Y1 Flu Day 0


title: BR1050 LPS Y1 Flu Day 0


title: BR1050 Poly I:C Y1 Flu Day 0


title: BR1052 Poly I:C Y1 Flu Day 0


title: BR1057 Null Y1 Flu Day 7-9


title: BR2034 SEB Non-Flu Day 80-100


title: BR1057 SEB Y1 Flu Day 7-9


title: BR1056 SEB Y1 Flu Day 7-9


title: BR1057 LPS Y1 Flu Day 7-9


title: BR2034 Null Non-Flu Day 80-100


title: BR2034 Poly I:C Y1 Flu Day 0


title: BR2034 SEB Y1 Flu Day 0


title: BR2034 Null Y1 Flu Day 0


title: BR1049 SEB Non-Flu Day 7-9


title: BR1049 Poly I:C Non-Flu Day 7-9


title: BR2034 LPS Y1 Flu Day 0


title: BR1049 Null Non-Flu Day 7-9


title: BR1049 LPS Non-Flu Day 7-9


title: BR1023 SEB Y1 Flu Day 0


title: BR1023 Poly I:C Y1 Flu Day 0


title: BR1023 Null Y1 Flu Day 0


title: BR1023 LPS Y1 Flu Day 0


title: BR1026 Poly I:C Y1 Flu Day 0


title: BR1026 LPS Y1 Flu Day 0


title: BR1056 SEB Y1 Flu Day 0


title: BR1057 Poly I:C Y1 Flu Day 7-9


title: BR1056 Null Y1 Flu Day 0


title: BR1052 LPS Y1 Flu Day 0


title: BR2034 Poly I:C Non-Flu Day 80-100


title: BR2036 Poly I:C Y1 Flu Day 7-9


title: BR2045 SEB Y1 Flu Day 7-9


title: BR1056 Poly I:C Y1 Flu Day 0


title: BR1026 Null Y1 Flu Day 0


title: BR2045 Poly I:C Y1 Flu Day 7-9


title: BR2036 LPS Y1 Flu Day 7-9


title: BR1056 LPS Y1 Flu Day 0


title: BR2043 Poly I:C Y1 Flu Day 7-9


title: BR2045 LPS Y1 Flu Day 7-9


title: BR2043 LPS Y1 Flu Day 7-9


title: BR1031 SEB Y1 Flu Day 7-9


title: BR1026 SEB Y1 Flu Day 0


title: BR1031 Null Y1 Flu Day 7-9


title: BR1031 LPS Y1 Flu Day 7-9


title: BR2005 Poly I:C Y1 Flu Day 7-9


title: BR2005 Null Y1 Flu Day 7-9


title: BR2036 SEB Y1 Flu Day 7-9


title: BR2034 SEB Y1 Flu Day 7-9


title: BR2034 Poly I:C Y1 Flu Day 7-9


title: BR2022 SEB Y1 Flu Day 7-9


title: BR2022 LPS Y1 Flu Day 7-9


title: BR2043 SEB Y1 Flu Day 7-9


title: BR2045 Null Y1 Flu Day 7-9


title: BR2022 Null Y1 Flu Day 7-9


title: BR1024 SEB Y1 Flu Day 7-9


title: BR1024 Null Y1 Flu Day 7-9


title: BR2022 Poly I:C Y1 Flu Day 7-9


title: BR2018 SEB Y1 Flu Day 0


title: BR2034 LPS Y1 Flu Day 7-9


title: BR2018 Poly I:C Y1 Flu Day 0


title: BR1024 Poly I:C Y1 Flu Day 7-9


title: BR1024 LPS Y1 Flu Day 7-9


title: BR2029 SEB Y1 Flu Day 7-9


title: BR1031 Poly I:C Y1 Flu Day 7-9


title: BR2029 Poly I:C Y1 Flu Day 7-9


title: BR2018 Null Y1 Flu Day 0


title: BR2043 Null Y1 Flu Day 7-9


title: BR2005 SEB Y1 Flu Day 7-9


title: BR2005 LPS Y1 Flu Day 7-9


title: BR2029 Null Y1 Flu Day 7-9


title: BR2003 Poly I:C Standalone Baseline Visit


title: BR2003 SEB Standalone Baseline Visit


title: BR2003 Null Standalone Baseline Visit


title: BR2034 Null Y1 Flu Day 7-9


title: BR2003 LPS Standalone Baseline Visit


title: BR2041 SEB Non-Flu Day 80-100


title: BR2041 LPS Non-Flu Day 80-100


title: BR2018 LPS Y1 Flu Day 0


title: BR2041 Null Non-Flu Day 80-100


title: BR2012 SEB Y1 Flu Day 0


title: BR2012 Null Y1 Flu Day 0


title: BR2041 Poly I:C Non-Flu Day 80-100


title: BR2012 LPS Y1 Flu Day 0


title: BR1028 LPS Non-Flu Day 80-100


title: BR2032 SEB Y1 Flu Day 0


title: BR2032 Poly I:C Y1 Flu Day 0


title: BR2032 LPS Y1 Flu Day 0


title: BR1040 SEB Y1 Flu Day 0


title: BR1040 Poly I:C Y1 Flu Day 0


title: BR2049 SEB Non-Flu Day 0


title: BR2049 Poly I:C Non-Flu Day 0


title: BR1028 Null Non-Flu Day 80-100


title: BR1040 Null Y1 Flu Day 0


title: BR2029 LPS Y1 Flu Day 7-9


title: BR2049 LPS Non-Flu Day 0


title: BR2049 Null Non-Flu Day 0


title: BR2036 LPS Y1 Flu Day 0


title: BR2036 Poly I:C Y1 Flu Day 0


title: BR2036 SEB Y1 Flu Day 0


title: BR2036 Null Y1 Flu Day 0


title: BR2002 Null Y2 Flu Day 0


title: BR2002 SEB Y2 Flu Day 0


title: BR2002 LPS Y2 Flu Day 0


title: BR2002 Poly I:C Y2 Flu Day 0


title: BR1028 SEB Non-Flu Day 80-100


title: BR2042 SEB Non-Flu Day 0


title: BR2042 Null Non-Flu Day 0


title: BR2042 LPS Non-Flu Day 0


title: BR2051 SEB Non-Flu Day 0


title: BR2051 Poly I:C Non-Flu Day 0


title: BR2051 LPS Non-Flu Day 0


title: BR2051 Null Non-Flu Day 0


title: BR2023 SEB Standalone Baseline Visit


title: BR2023 LPS Standalone Baseline Visit


title: BR2023 Null Standalone Baseline Visit


title: BR2023 Poly I:C Standalone Baseline Visit


title: BR1050 SEB Y1 Flu Day 7-9


title: BR1050 LPS Y1 Flu Day 7-9


title: BR2026 SEB Y1 Flu Day 7-9


title: BR1050 Poly I:C Y1 Flu Day 7-9


title: BR2026 Null Y1 Flu Day 7-9


title: BR2026 LPS Y1 Flu Day 7-9


title: BR2026 Poly I:C Y1 Flu Day 7-9


title: BR1044 SEB Y1 Flu Day 7-9


title: BR1044 Poly I:C Y1 Flu Day 7-9


title: BR1044 LPS Y1 Flu Day 7-9


title: BR2024 SEB Y1 Flu Day 7-9


title: BR2024 Poly I:C Y1 Flu Day 7-9


title: BR1021 Poly I:C Y1 Flu Day 7-9


title: BR2024 LPS Y1 Flu Day 7-9


title: BR2024 Null Y1 Flu Day 7-9


title: BR1021 SEB Y1 Flu Day 7-9


title: BR1044 Null Y1 Flu Day 7-9


title: BR1021 Null Y1 Flu Day 7-9


title: BR1021 LPS Y1 Flu Day 7-9


title: BR1030 Null Y1 Flu Day 7-9


title: BR1030 LPS Y1 Flu Day 7-9


title: BR1030 SEB Y1 Flu Day 7-9


title: BR1017 SEB Y1 Flu Day 0


title: BR1050 Null Y1 Flu Day 7-9


title: BR1017 LPS Y1 Flu Day 0


title: BR1017 Poly I:C Y1 Flu Day 0


title: BR1004 Poly I:C Y2 Flu Day 7-9

value: Y2 Flu Day 7-9


title: BR1030 Poly I:C Y1 Flu Day 7-9


title: BR1004 SEB Y2 Flu Day 7-9


title: BR1017 Null Y1 Flu Day 0


title: BR1004 Null Y2 Flu Day 7-9


title: BR1041 SEB Non-Flu Day 0

value: Non-Flu Day 0


title: BR1041 Poly I:C Non-Flu Day 0


title: BR1004 LPS Y2 Flu Day 7-9

value: male


title: BR1041 LPS Non-Flu Day 0


title: BR2040 Null Y1 Flu Day 7-9


title: BR2040 SEB Y1 Flu Day 7-9


title: BR2040 Poly I:C Y1 Flu Day 7-9


title: BR1041 Null Non-Flu Day 0


title: BR2039 SEB Non-Flu Day 0


title: BR1042 Poly I:C Y1 Flu Day 7-9


title: BR2039 LPS Non-Flu Day 0


title: BR1042 LPS Y1 Flu Day 7-9


title: BR2039 Poly I:C Non-Flu Day 0


title: BR2005 SEB Y1 Flu Day 0


title: BR2039 Null Non-Flu Day 0


title: BR2005 Poly I:C Y1 Flu Day 0


title: BR2005 Null Y1 Flu Day 0


title: BR2014 SEB Y1 Flu Day 0


title: BR2014 Null Y1 Flu Day 0


title: BR2053 LPS Y1 Flu Day 0


title: BR2053 Poly I:C Y1 Flu Day 0


title: BR2053 SEB Y1 Flu Day 0


title: BR2053 Null Y1 Flu Day 0


title: BR1024 SEB Y1 Flu Day 0


title: BR1024 Null Y1 Flu Day 0


title: BR2040 LPS Y1 Flu Day 7-9


title: BR1006 SEB Y2 Flu Day 0


title: BR1006 Poly I:C Y2 Flu Day 0


title: BR1024 LPS Y1 Flu Day 0


title: BR1006 Null Y2 Flu Day 0


title: BR1006 LPS Y2 Flu Day 0


title: BR1056 SEB Non-Flu Day 7-9


title: BR1056 Poly I:C Non-Flu Day 7-9


title: BR1056 LPS Non-Flu Day 7-9


title: BR1047 SEB Y1 Flu Day 0


title: BR1056 Null Non-Flu Day 7-9


title: BR1047 Poly I:C Y1 Flu Day 0


title: BR2005 LPS Y1 Flu Day 0


title: BR2014 Poly I:C Y1 Flu Day 0


title: BR1047 Null Y1 Flu Day 0


title: BR1047 LPS Y1 Flu Day 0


title: BR2014 LPS Y1 Flu Day 0


title: BR1005 SEB Y2 Flu Day 7-9


title: BR2026 SEB Standalone Baseline Visit


title: BR1005 Null Y2 Flu Day 7-9


title: BR1024 Poly I:C Y1 Flu Day 0


title: BR1005 Poly I:C Y2 Flu Day 7-9


title: BR1043 SEB Y1 Flu Day 7-9


title: BR2026 Poly I:C Standalone Baseline Visit


title: BR2026 Null Standalone Baseline Visit


title: BR1043 Poly I:C Y1 Flu Day 7-9


title: BR1043 Null Y1 Flu Day 7-9


title: BR1043 LPS Y1 Flu Day 7-9


title: BR2026 LPS Standalone Baseline Visit


title: BR1014 Null Y2 Flu Day 7-9


title: BR1014 LPS Y2 Flu Day 7-9


title: BR1014 SEB Y2 Flu Day 7-9


title: BR1014 Null Y1 Flu Day 80-100


title: BR1014 SEB Y1 Flu Day 80-100


title: BR1014 Poly I:C Y2 Flu Day 7-9


title: BR1014 Poly I:C Y1 Flu Day 80-100


title: BR1012 SEB Y2 Flu Day 7-9


title: BR1014 LPS Y1 Flu Day 80-100


title: BR1005 LPS Y2 Flu Day 7-9


title: BR1012 LPS Y2 Flu Day 7-9


title: BR1012 Null Y2 Flu Day 7-9


title: BR2013 Poly I:C Y1 Flu Day 7-9


title: BR1012 Poly I:C Y2 Flu Day 7-9


title: BR2013 SEB Y1 Flu Day 7-9


title: BR2013 Null Y1 Flu Day 7-9


title: BR2013 LPS Y1 Flu Day 7-9


title: BR1051 SEB Non-Flu Day 0


title: BR1030 SEB Y1 Flu Day 0


title: BR1051 Null Non-Flu Day 0


title: BR1051 LPS Non-Flu Day 0


title: BR1051 Poly I:C Non-Flu Day 0


title: BR1030 Poly I:C Y1 Flu Day 0


title: BR1030 LPS Y1 Flu Day 0


title: BR1031 SEB Standalone Baseline Visit


title: BR1031 Poly I:C Standalone Baseline Visit


title: BR1017 LPS Non-Flu Day 80-100

value: Non-Flu Day 80-100


title: BR1031 Null Standalone Baseline Visit


title: BR1017 Null Non-Flu Day 80-100


title: BR2037 Poly I:C Y1 Flu Day 7-9


title: BR1043 SEB Y1 Flu Day 0


title: BR2037 SEB Y1 Flu Day 7-9


title: BR2037 LPS Y1 Flu Day 7-9


title: BR1043 Null Y1 Flu Day 0


title: BR1043 LPS Y1 Flu Day 0


title: BR2053 Poly I:C Y1 Flu Day 7-9


title: BR1043 Poly I:C Y1 Flu Day 0


title: BR2053 Null Y1 Flu Day 7-9


title: BR2012 Poly I:C Y1 Flu Day 0


title: BR1030 Null Y1 Flu Day 0


title: BR1007 Poly I:C Y2 Flu Day 7-9


title: BR1007 SEB Y2 Flu Day 7-9


title: BR2053 LPS Y1 Flu Day 7-9


title: BR1017 SEB Non-Flu Day 80-100


title: BR1017 Poly I:C Non-Flu Day 80-100


title: BR1007 LPS Y2 Flu Day 7-9


title: BR1031 LPS Standalone Baseline Visit


title: BR1007 SEB Y2 Flu Day 0


title: BR1007 Poly I:C Y2 Flu Day 0


title: BR1007 Null Y2 Flu Day 0


title: BR2037 Null Y1 Flu Day 7-9


title: BR2053 SEB Y1 Flu Day 7-9


title: BR1007 Null Y2 Flu Day 7-9


title: BR2018 Poly I:C Standalone Baseline Visit


title: BR2018 SEB Standalone Baseline Visit


title: BR2043 Poly I:C Non-Flu Day 7-9

value: Non-Flu Day 7-9


title: BR2018 Null Standalone Baseline Visit


title: BR2018 LPS Standalone Baseline Visit


title: BR2043 SEB Non-Flu Day 7-9


title: BR2043 LPS Non-Flu Day 7-9


title: BR2043 Null Non-Flu Day 7-9


title: BR2052 SEB Non-Flu Day 7-9


title: BR2052 Null Non-Flu Day 7-9


title: BR1025 SEB Non-Flu Day 80-100


title: BR1025 Poly I:C Non-Flu Day 80-100


title: BR2052 Poly I:C Non-Flu Day 7-9


title: BR1025 Null Non-Flu Day 80-100


title: BR1043 LPS Non-Flu Day 7-9


title: BR1012 Null Non-Flu Day 0


title: BR1043 SEB Non-Flu Day 7-9


title: BR2052 LPS Non-Flu Day 7-9


title: BR1048 Null Non-Flu Day 7-9


title: BR1048 LPS Non-Flu Day 7-9


title: BR1043 Poly I:C Non-Flu Day 7-9


title: BR1048 Poly I:C Non-Flu Day 7-9


title: BR1012 SEB Non-Flu Day 0


title: BR1025 LPS Non-Flu Day 80-100


title: BR1012 Poly I:C Non-Flu Day 0


title: BR1012 LPS Non-Flu Day 0


title: BR2013 SEB Non-Flu Day 80-100


title: BR1048 SEB Non-Flu Day 7-9


title: BR1043 Null Non-Flu Day 7-9


title: BR2013 Poly I:C Non-Flu Day 80-100


title: BR2013 Null Non-Flu Day 80-100


title: BR2013 LPS Non-Flu Day 80-100


title: BR2008 Null Non-Flu Day 80-100


title: BR2008 Poly I:C Non-Flu Day 80-100


title: BR2046 Poly I:C Non-Flu Day 0


title: BR2046 Null Non-Flu Day 0


title: BR2046 SEB Non-Flu Day 0


title: BR2046 LPS Non-Flu Day 0


title: BR2008 LPS Non-Flu Day 80-100


title: BR2048 Null Y1 Flu Day 0


title: BR2048 Poly I:C Y1 Flu Day 0


title: BR2048 LPS Y1 Flu Day 0


title: BR1052 LPS Y1 Flu Day 7-9


title: BR2029 Null Y1 Flu Day 0


title: BR1016 Poly I:C Y1 Flu Day 7-9


title: BR1016 LPS Y1 Flu Day 7-9


title: BR2029 LPS Y1 Flu Day 0


title: BR1052 SEB Y1 Flu Day 7-9


title: BR1016 Null Y1 Flu Day 7-9


title: BR2029 Poly I:C Y1 Flu Day 0


title: BR2041 LPS Y1 Flu Day 7-9


title: BR2041 Poly I:C Y1 Flu Day 7-9


title: BR1007 LPS Y2 Flu Day 0


title: BR1016 SEB Y1 Flu Day 7-9


title: BR2041 Null Y1 Flu Day 7-9


title: BR1052 Null Y1 Flu Day 7-9


title: BR2008 SEB Non-Flu Day 80-100


title: BR2041 SEB Y1 Flu Day 7-9


title: BR2009 Poly I:C Y1 Flu Day 0


title: BR2009 SEB Y1 Flu Day 0


title: BR2009 LPS Y1 Flu Day 0


title: BR2007 SEB Y1 Flu Day 0


title: BR2009 Null Y1 Flu Day 0


title: BR2007 Poly I:C Y1 Flu Day 0


title: BR2007 Null Y1 Flu Day 0


title: BR2007 LPS Y1 Flu Day 0


title: BR2029 SEB Y1 Flu Day 0


title: BR1018 SEB Y2 Flu Day 7-9


title: BR1018 Null Y2 Flu Day 7-9


title: BR1058 SEB Y1 Flu Day 7-9


title: BR1018 LPS Y2 Flu Day 7-9


title: BR1058 Poly I:C Y1 Flu Day 7-9


title: BR1018 Poly I:C Y2 Flu Day 7-9


title: BR1058 LPS Y1 Flu Day 7-9


title: BR1058 Null Y1 Flu Day 7-9


title: BR1015 LPS Y1 Flu Day 7-9


title: BR2016 SEB Y1 Flu Day 0


title: BR1015 Null Y1 Flu Day 7-9


title: BR1015 SEB Y1 Flu Day 7-9


title: BR2016 Poly I:C Y1 Flu Day 0


title: BR1015 Poly I:C Y1 Flu Day 7-9


title: BR2019 Poly I:C Y1 Flu Day 0


title: BR2016 Null Y1 Flu Day 0


title: BR2016 LPS Y1 Flu Day 0


title: BR1009 Poly I:C Y2 Flu Day 0


title: BR2019 Null Y1 Flu Day 0


title: BR1009 Null Y2 Flu Day 0


title: BR1009 SEB Y2 Flu Day 0


title: BR2019 LPS Y1 Flu Day 0


title: BR1009 LPS Y2 Flu Day 0


title: BR2020 Null Y1 Flu Day 7-9


title: BR2050 Poly I:C Non-Flu Day 0


title: BR2050 Null Non-Flu Day 0


title: BR2050 LPS Non-Flu Day 0


title: BR2027 Poly I:C Standalone Baseline Visit


title: BR2027 LPS Standalone Baseline Visit


title: BR2027 Null Standalone Baseline Visit


title: BR2019 SEB Y1 Flu Day 0


title: BR2027 SEB Standalone Baseline Visit


title: BR1008 SEB Y2 Flu Day 0


title: BR2014 SEB Y1 Flu Day 7-9


title: BR2014 Null Y1 Flu Day 7-9


title: BR1008 Poly I:C Y2 Flu Day 0


title: BR1059 Poly I:C Y1 Flu Day 7-9


title: BR1047 Null Y1 Flu Day 7-9


title: BR1059 SEB Y1 Flu Day 7-9


title: BR2014 LPS Y1 Flu Day 7-9


title: BR1059 LPS Y1 Flu Day 7-9


title: BR1047 SEB Y1 Flu Day 7-9


title: BR2020 SEB Y1 Flu Day 7-9


title: BR1008 LPS Y2 Flu Day 0


title: BR1047 LPS Y1 Flu Day 7-9


title: BR2016 SEB Non-Flu Day 0


title: BR2016 Poly I:C Non-Flu Day 0


title: BR2020 LPS Y1 Flu Day 7-9


title: BR2050 SEB Non-Flu Day 0


title: BR2016 Null Non-Flu Day 0


title: BR2016 LPS Non-Flu Day 0


title: BR1030 SEB Non-Flu Day 80-100


title: BR1030 Poly I:C Non-Flu Day 80-100


title: BR2014 Poly I:C Y1 Flu Day 7-9


title: BR1008 Null Y2 Flu Day 0


title: BR2020 SEB Y1 Flu Day 0


title: BR2020 Poly I:C Y1 Flu Day 0


title: BR2020 Null Y1 Flu Day 0


title: BR2020 LPS Y1 Flu Day 0


title: BR1047 Poly I:C Y1 Flu Day 7-9


title: BR1059 Null Y1 Flu Day 7-9


title: BR2026 Poly I:C Y1 Flu Day 0


title: BR2026 SEB Y1 Flu Day 0


title: BR1003 Poly I:C Standalone Baseline Visit


title: BR2031 SEB Y1 Flu Day 7-9


title: BR2026 LPS Y1 Flu Day 0


title: BR2031 Poly I:C Y1 Flu Day 7-9


title: BR1003 SEB Standalone Baseline Visit


title: BR2031 LPS Y1 Flu Day 7-9


title: CD68

status: Public on Apr 02 2025

city: La Jolla, CA 92093

first: Pradipta

last: Ghosh

state: CA

address: 9500 Gilman Drive (MC 0651)

department: Departments of Medicine and Cellular and Molecular Medicine

institute: University of California San Diego

description:
Library name: CD68
CD68

data_processing:
Low quality sequences were trimmed or removed with Trimmomatic; STAR (version 2.6.0a) was used to align reads on reference genome (human genome hsGRCh38_94 ); The resulting transcriptome-aligned sequences were used for expression quantification by using RSEM (version 1.3.3) with “–forward-prob 0 ” option
Assembly: GRCh38
Supplementary files format and content: Normalized count

source_name: Patient-derived organoids

growth_protocol: CD organoids were embedded in matrigel and cultured for 7 days using WNT, R-Spondin, Noggin conditioned media.

extract_protocol:
total RNA
cDNA

treatment_protocol: Organoids were allowed to proliferate for 7 days.

value: Patient-derived organoids


title: CD19

description:
Library name: CD19
CD19


title: BR1030 Null Non-Flu Day 80-100


title: CD26

description:
Library name: CD26
CD26


title: CD28

description:
Library name: CD28
CD28


title: CD27

description:
Library name: CD27
CD27


title: CD21

description:
Library name: CD21
CD21


title: BR1030 LPS Non-Flu Day 80-100


title: CD63

description:
Library name: CD63
CD63


title: CD20

description:
Library name: CD20
CD20


title: CD52

description:
Library name: CD52
CD52


title: CD50

description:
Library name: CD50
CD50


title: CD24

description:
Library name: CD24
CD24


title: CD11

description:
Library name: CD11
CD11


title: CD60

description:
Library name: CD60
CD60


title: CD59

description:
Library name: CD59
CD59


title: CD30

description:
Library name: CD30
CD30


title: BR1003 Null Standalone Baseline Visit


title: CD47

description:
Library name: CD47
CD47


title: CD74

description:
Library name: CD74
CD74


title: BR2026 Null Y1 Flu Day 0


title: BR2031 Null Y1 Flu Day 7-9

value: Y1 Flu Day 7-9


title: CD69

description:
Library name: CD69
CD69


title: CD61

description:
Library name: CD61
CD61


title: CD35

description:
Library name: CD35
CD35


title: CD23

description:
Library name: CD23
CD23


title: CD58

description:
Library name: CD58
CD58


title: CD32

description:
Library name: CD32
CD32


title: iNKT Multi Tissue Targeted Data

status: Public on Mar 22 2025

city: St. Louis

first: Melissa

last: Mavers

state: MO

address: 660 Euclid Ave

department: Pediatrics

institute: Washington University School of Medicine

description: BD Rhapsody

library_source: transcriptomic single cell

data_processing:
Expression tables (RSEC_MolsPerCell.csv) and sample tags (Sample_Tag_Calls.csv) were downloaded from Seven Bridges and analyzed using Seurat (v4.4.0). First, separate assays were created using the CreateSeuratObject function and percent mitochondrial DNA, nCount_RNA and nFeature_RNA were evaluated for each cell. Cells were maintained for downstream processing if they met the following criteria: nFeature_RNA > 200; nFeature_RNA < 4000; nCount_RNA < 20000; percent.mito < 20. Cells with sample tags labeled “Undetermined” or “Multiplets” were filtered out. Each sample was scaled and normalized using Seurat’s ‘SCTransform’ function to correct for batch effects (with parameters: vars.to.regress = c("nCount_RNA"), dims = 1:20). Any merged analysis or subsequent subsetting of cells/samples underwent the same scaling and normalization method. Cells were clustered using the original Louvain algorithm and top 10 PCA dimensions via ‘FindNeighbors’ and ‘FindClusters’ (with parameters: resolution = 0.5) functions. After initial subsetting and clustering, a clear population of infiltrating macrophages were identified exhibiting higher expression of FCGR3A, LYN, FCR1G, IL1B. The macrophage cluster was filtered out and we subsequently used Harmony (group.by.vars = "Sample_Tag", reduction = "pca", assay.use = "SCT") before rerunning RunUMAP, FindNeighbors and FindClusters to annotate final object (dims=1:20). The resulting merged and normalized matrix was used for the subsequent analysis. To evaluate cluster resolution we utilized clustree before settling on cluster assignment. ADT data was normalized using NormalizeData command with method = “CLR” and a margin of 2.
Assembly: GRCh38
Supplementary files format and content: gene expression matrices, genes and barcodes files

source_name: Multi Tissue

growth_protocol: Isolated iNKTs

extract_protocol:
Human iNKT cells were enriched by magnetic bead-based positive selection (Stem Cell Technologies EasySep™ Release Human PE Positive Selection Kit) utilizing PE-conjugated anti-V11 antibody (Beckman Coulter, C21), followed by bead release, additional staining with fluorochrome-conjugated and oligomer-conjugated antibodies, and fluorescence activated cell sorting for CD24-CD3+V11+V24+ cells. Antibodies included APC-H7 CD14 (BD Biosciences, MoP9), APC-Cy7 CD19 (BD Biosciences, SJ25C1), APC-Cy7-CD24 (Biolegend, ML5), PerCP-Cy5.5 CD3 (Biolegend, UCHT1), FITC V24 (Beckman Coulter, C15), PE V11 (Beckman Coulter, C21), Oligo-CD4 (BD AbSeq, SK3), Oligo-CD8 (BD AbSeq, RPAT8), Oligo-CD45RA (BD AbSeq, HI100), and Oligo-CD45RO (BD AbSeq, UCHL1). Samples were sorted individually, cell counts roughly normalized, and then pooled for sequencing.
Refer to BD Rhapsody for library construction parameters

value: Multi Tissue

tag: cell type

value: iNKT


title: iNKT Multi Tissue Whole Transcriptome Data

description: BD Rhapsody


title: CD42

description:
Library name: CD42
CD42


title: 8911-JF-16

status: Public on Mar 21 2025

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description:
Library name: 8911-JF-16
mixed (single cell)

data_processing:
“BCL Convert Software (Illumina) was used to generate de-multiplexed Fastq files and the CellRanger Pipeline (10X Genomics) was used to align reads and generate count matrices.”
CellRanger was used to map the reads (paired end) to the reference genome to generate the bam files.
Assembly: hg19
Supplementary files format and content: cellranger output format

molecule: polyA RNA

source_name: biopsies from secondary syphilis

extract_protocol:
https://cdn.10xgenomics.com/image/upload/v1721078231/support-documents/CG000632_DemonstratedProtocol_SamplePrep_from__FFPETissueSections_RevD.pdf    Protocol Overview: gentleMACS Octo Dissociator for Isolation of Cells from FFPE Tissue Sections
https://cdn.10xgenomics.com/image/upload/v1722287750/support-documents/CG000527_Chromium_FixedRNAProfiling_MultiplexedSamples_UserGuide_Rev_F.pdf

value: human skin


title: 8911-JF-15

description:
Library name: 8911-JF-15
mixed (single cell)


title: 8821-JF-27

description:
Library name: 8821-JF-27
mixed (single cell)


title: 8911-JF-14

description:
Library name: 8911-JF-14
mixed (single cell)


title: 8911-JF-13

description:
Library name: 8911-JF-13
mixed (single cell)


title: 8821-JF-25

description:
Library name: 8821-JF-25
mixed (single cell)


title: 8821-JF-26

description:
Library name: 8821-JF-26
mixed (single cell)


title: 8325-JF-2

description:
Library name: 8325-JF-2
mixed (single cell)


title: 8821-JF-24

description:
Library name: 8821-JF-24
mixed (single cell)


title: scRNAseq of tagged library: 12hr after ligand, replicate 2, batch2

status: Public on Mar 10 2025

city: Philadelphia

first: david

last: smith

state: Pennsylvania

address: 3501 Civic Center Blvd

institute: CHOP

description:
Library name: sc_12hr_2_batch2
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.

data_processing:
For single cell experiments, CellRanger v7 was used
For bulk sequencing experiments, the nf-core/rnaseq pipeline was used
Assembly: GRCh38-2020-A
Supplementary files format and content: sc_data.tar.gz, contains the counts, cell barcodes, and feature names for sample listed in "library name". Sequence guide RNA counts are appended to the counts.
Supplementary files format and content: out_counts_remap.csv, contains the nf-core/rnaseq pipeline output, renamed to match library ids

source_name: HEK 293

growth_protocol: Cells were lifted with TrypLE Express (Thermo Fisher Scientific, 12605010), pelleted for 5 minutes at 300 × g, and washed in PBS with 0.04% BSA. Cells were diluted and strained through a 40 μm strainer.

extract_protocol:
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering
Chromium Next GEM Single Cell 3' HT Kit

treatment_protocol: We treated cells with 25 μM HyT36 for 2 and 12 hours in order to capture the breadth of acute responses to misfolding stress across the different cell compartments.

value: HEK 293

tag: cell line

tag: treatment


title: scRNAseq of untagged cells, batch2

description:
Library name: sc_2hr_untag_batch2
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: scRNAseq of control: no ligand, batch2

description:
Library name: sc_2hr_ctrl_batch2
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.

value: DMSO


title: scRNAseq of tagged library: 2hr after ligand, replicate 3, batch2

description:
Library name: sc_2hr_3_batch2
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: scRNAseq of tagged library: 2hr after ligand, replicate 2, batch2

description:
Library name: sc_2hr_2_batch2
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: scRNAseq of tagged library: 12hr after ligand, replicate 1, batch2

description:
Library name: sc_12hr_1_batch2
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: scRNAseq of untagged cells, batch1

description:
Library name: sc_2hr_untag_batch1
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: scRNAseq of tagged library: 2hr after ligand, replicate 1, batch2

description:
Library name: sc_2hr_1_batch2
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: scRNAseq of tagged library: 12hr after ligand, replicate 3, batch1

description:
Library name: sc_12hr_3_batch1
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: scRNAseq of tagged library: 12hr after ligand, replicate 2, batch1

description:
Library name: sc_12hr_2_batch1
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: scRNAseq of tagged library: 2hr after ligand, replicate 3, batch1

description:
Library name: sc_2hr_3_batch1
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: scRNAseq of control: no ligand, batch1

description:
Library name: sc_2hr_ctrl_batch1
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: scRNAseq of tagged library: 2hr after ligand, replicate 2, batch1

description:
Library name: sc_2hr_2_batch1
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: scRNAseq of tagged library: 2hr after ligand, replicate 1, batch1

description:
Library name: sc_2hr_1_batch1
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: scRNAseq of tagged library: 12hr after ligand, replicate 1, batch1

description:
Library name: sc_12hr_1_batch1
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: bulk RNAseq of tagged library: received ligand, replicate 3, clone5

description:
Library name: cl5_HyT_3
Cell pellets were frozen on dry ice and submitted for standard RNA sequencing by Azenta Life Sciences. RNA was purified by PolyA selection and libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)


title: bulk RNAseq of tagged library: received ligand, replicate 1, clone5

description:
Library name: cl5_HyT_1
Cell pellets were frozen on dry ice and submitted for standard RNA sequencing by Azenta Life Sciences. RNA was purified by PolyA selection and libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)


title: bulk RNAseq of tagged library: no ligand, replicate 2, clone5

description:
Library name: cl5_DMSO_2
Cell pellets were frozen on dry ice and submitted for standard RNA sequencing by Azenta Life Sciences. RNA was purified by PolyA selection and libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)


title: bulk RNAseq of tagged library: no ligand, replicate 3, clone5

description:
Library name: cl5_DMSO_3
Cell pellets were frozen on dry ice and submitted for standard RNA sequencing by Azenta Life Sciences. RNA was purified by PolyA selection and libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)


title: bulk RNAseq of tagged library: no ligand, replicate 1, clone5

description:
Library name: cl5_DMSO_1
Cell pellets were frozen on dry ice and submitted for standard RNA sequencing by Azenta Life Sciences. RNA was purified by PolyA selection and libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)


title: bulk RNAseq of tagged library: received ligand, replicate 3, clone4

description:
Library name: cl4_HyT_3
Cell pellets were frozen on dry ice and submitted for standard RNA sequencing by Azenta Life Sciences. RNA was purified by PolyA selection and libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)


title: bulk RNAseq of tagged library: received ligand, replicate 2, clone4

description:
Library name: cl4_HyT_2
Cell pellets were frozen on dry ice and submitted for standard RNA sequencing by Azenta Life Sciences. RNA was purified by PolyA selection and libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)


title: bulk RNAseq of tagged library: received ligand, replicate 1, clone4

description:
Library name: cl4_HyT_1
Cell pellets were frozen on dry ice and submitted for standard RNA sequencing by Azenta Life Sciences. RNA was purified by PolyA selection and libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)


title: bulk RNAseq of tagged library: no ligand, replicate 3, clone4

description:
Library name: cl4_DMSO_3
Cell pellets were frozen on dry ice and submitted for standard RNA sequencing by Azenta Life Sciences. RNA was purified by PolyA selection and libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)


title: bulk RNAseq of tagged library: no ligand, replicate 2, clone4

description:
Library name: cl4_DMSO_2
Cell pellets were frozen on dry ice and submitted for standard RNA sequencing by Azenta Life Sciences. RNA was purified by PolyA selection and libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)


title: scRNAseq of tagged library: 12hr after ligand, replicate 3, batch2

description:
Library name: sc_12hr_3_batch2
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: guide sequences, 2hr, dmso

description:
Library name: guide_2hr_untag
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.

library_source: other

molecule: other


title: bulk RNAseq of tagged library: no ligand, replicate 1, clone4

description:
Library name: cl4_DMSO_1
Cell pellets were frozen on dry ice and submitted for standard RNA sequencing by Azenta Life Sciences. RNA was purified by PolyA selection and libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)


title: guide sequences, 2hr, control

description:
Library name: guide_2hr_ctrl
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: guide sequences, 12hr,  replicate 1

description:
Library name: guide_12hr_1
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: guide sequences, 2hr, replicate 3

description:
Library name: guide_2hr_3
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: guide sequences, 2hr, replicate 1

description:
Library name: guide_2hr_1
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: guide sequences, 2hr, replicate 2

description:
Library name: guide_2hr_2
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


title: H3WT_hemi_P2

status: Public on Mar 05 2025

type: other

city: Boston

first: Carlos Alberto

middle: Oliveira de

last: Biagi Junior

state: MA

address: 360 Longwood Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

description: n.a.

hyb_protocol: Xenium Analyzer is fully automated. The user marks regions for analysis by manually selecting sample location on an initial low-resolution image. After loading consumable reagents and slides, internal sample and liquid handling mechanics control experiment progression. Data collection occurs in cycles of fluorescently labeled probe binding, image acquisition, and probe stripping. Localized points of fluorescence intensity detected during the rounds of imaging are then defined as potential RNA puncta. Each gene on the panel has a unique fluorescence pattern across the image channels. Puncta that match a specific pattern are then decoded and labeled according to the gene ID. All image FOVs (4240 x 2960 pixels) and associated detected transcripts are computationally stitched together via the DAPI-stained image. Detailed instructions on instrument operation and consumable preparation can be found in 10X Genomics’ Demonstrated Protocol CG000582.

scan_protocol: During every Xenium Analyzer run, image processing, and decoding are performed real time on-instrument.

data_processing: Downstream analysis were done using Seurat pipeline and house-made scripts.

label_protocol: A total of 343 unique genes were included in the analysis of this dataset. 319 genes came from an early version of the Xenium human brain base panel and 100 genes from a custom designed panel. The custom panel was curated based on Ependymoma single cell analysis data (Gojo, Johannes, et al. 2020), selecting for genes useful in programs identification. Gene panel probe hybridization occurred overnight for 18 hours at 50°C (Bio-Rad DNA Engine Tetrad 2). Subsequent washes the next day removed unbound probes. Ligase was added to circularize the paired ends of bound probes (2 hours at 37°C) and followed by enzymatic rolling circle amplification (2 hours at 30°C). Slides were washed in TE buffer before background fluorescence was chemically quenched; autofluorescence is a known issue in lung tissue as well as a byproduct of formalin-fixation (Davis et al. 2014). Following PBS and PBS-T washes, DAPI was used to stain sample nuclei. Finalized slides were stored in PBS-T in the dark at 4°C for ≤5 days until being loaded onto the Xenium Analyzer instrument. Stepwise Xenium FFPE preparation guidelines and buffer recipes can be found in 10X Genomics Demonstrated Protocol CG000578.

extract_protocol: For fresh frozen samples, tissue sections were cut at a thickness of 10µM with a Leica CM3050S cryostat and collected onto Fisherbrand™ Superfrost™ Plus microscope slides, 10um tissue sections were placed onto a Xenium slide followed by fixation and permeabilization. For FFPE blocks, 5 µm tissue sections on a Xenium slide underwent deparaffinization and permeabilization. A mix of pre-designed and custom gene expression probe hybridization occurred at 50°C overnight. After multiple washing to remove un-hybridized probes, ligation of probes and annealing of rolling circle amplification (RCA) primer occurred at 37°C for 2 hours. Circularized probes were then enzymatically amplified at 30°C for 2 hours, after which background autofluorescence was quenched chemically. Slide was then loaded into the Xenium Analyzer following nuclei staining.

tag: age

tag: gender

value: Female

tag: type

value: frozen

tag: sampling

value: Primary

value: Diffuse High Grade Glioma

tag: subtype


title: guide sequences, 12hr,  replicate 3

description:
Library name: guide_12hr_3
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


status: Public on Feb 27 2025

city: Meblourne

first: Alistair

middle: Morgan

last: Chalk

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

description:
Hek 293T B2S184A KI, DMEM High Glc 10% FBS basal, Technical rep 4
B2Sr4_NL8

data_processing:
Reads were trimmed using fastp "--detect_adapter_for_pe".
Reads were quantified using salmon (v 1.10.2) quant using gcBias against gencode v40 transcriptome.
Degust to perform differential expression (edgeR).
Assembly: GRCh38
Supplementary files format and content: transcript_counts.txt : Salmon counts.
Supplementary files format and content: gene_counts.txt : Salmon counts

source_name: cell line

growth_protocol: Hek 293T cells were maintained inw DMEM Hihg Glucose supplemented with 10% Fetabl Bovine Serum (FBS) in humidified atomosphere with 5% CO2 at 37C

extract_protocol:
RNeasy Mini Kit (Qiagen)
NEBNext®Ultra™II RNA Library Prep Kit for Illumina®

treatment_protocol: No Treatment

value: cell line

value: Hek 293T

value: Human embryonic kidney 293 cells

tag: genotype

value: AMPK B2S184A KI

value: No treatment, Basal


title: guide sequences, 12hr, replicate 2

description:
Library name: guide_12hr_2
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering. Targeted amplification of sgRNA sequences from the CROPseq backbone was performed in order to reliably identify the tag in each cell. Sequencing libraries were prepared from three sequential PCR reactions starting from cDNA obtained during the 10x single cell processing protocol. The number of cycles for each PCR reaction was optimized by qPCR with EvaGreen on a CFX Opus 96 Real-Time PCR System.


description:
Hek 293T B2S184A KI, DMEM High Glc 10% FBS basal, Technical rep 3
B2Sr3_NL7


title: PFA_P3

description: n.a.

source_name: Ependymoma, Posterior Fossa -A,

value: Ependymoma

value: Posterior Fossa, A


description:
Hek 293T B2S184A KI, DMEM High Glc 10% FBS basal, Technical rep 1
B2Sr1_NL5


title: ST-Z/R_P2

description: n.a.

source_name: Ependymoma, Primary

value: Male

value: ZFTA-RELA


title: H3K27M_P6

description: n.a.

source_name: H3K27M-mutated, Autopsy

value: Autopsy


description:
Hek 293T B2S184A KI, DMEM High Glc 10% FBS basal, Technical rep 2
B2Sr2_NL6


description:
Hek 293T WT, DMEM High Glc 10% FBS basal, Technical rep 4
WTr4_NL4

value: WT


description:
Hek 293T WT, DMEM High Glc 10% FBS basal, Technical rep 1
WTr1_NL1


description:
Hek 293T WT, DMEM High Glc 10% FBS basal, Technical rep 2
WTr2_NL2


title: DBD+ Micro-C rep 8 [Micro-C]

city: Columbus

first: Ariunaa

last: Bayanjargal

state: OH

address: 700 Children's Dr

institute: Nationwide Childrens Hospital

library_source: genomic

data_processing:
Fastq files were aligned to hg19 reference genome using BWA-MEMalgorithmwith options -5SP tomapmates independently
Parse module from pairtools was used to find ligation junctions in Micro-C libraries with options min-mapq 40 and max-inter-align-gap 30.
The parsed pair is then sorted using pairtools sort and PCR duplicates were removed with pairtools dedup.
The pairtools split command was used to split the final .pairsam into .bam (then sorted with samtools sort) and .pairs files.
Using Juicer Tools, .pairs files were converted into HiC contact matrices.
Assembly: hg19
Supplementary files format and content: A text file with stats of processing steps.
Supplementary files format and content: HiC files created with Juicer Tools
Supplementary files format and content: TSV files of GI objects used in plotting MDS
Supplementary files format and content: Bedpe files of differentially interacting regions compared to KD at 500kb
Supplementary files format and content: Bed files of differential TADs called
Supplementary files format and content: Bed files of loops called with Mustache
Supplementary files format and content: Bed files of differential loops called with Mustache
Library strategy: Micro-C

molecule: genomic DNA

source_name: pulmonary metastasis a cervical tumor

growth_protocol: TTC466 cells were grown at 37C, 5% CO2 in DMEM with 10% fetal bovine serum, 1% P/S/Q, and 1% sodium pyruvate.

extract_protocol:
Micro-C kits (Catalog 21006) purchased from Dovetail Genomics were used to prepare Micro-C libraries. Specifically, the cells were lysed and the chromatin was captured with beads to perform proximity ligation
Libraries were prepared per the protocol of Micro-C kit and each library was indexed with unique primer pairs from IDT (10009816 and 10010147)

treatment_protocol: For knockdown of endogenous EWS::ERG in TTC466, cells were infected with RNAi virus and subsequently infected with the cDNA-containing virus to rescue the cells. After 48 hours, cells were selected with puromycin (1 μg/ul) and hygromycin (150 μg/ul); and allowed to grow for ~10 days prior to collection

value: pulmonary metastasis a cervical tumor

value: Ewing sarcoma cell line

value: KD + DBD+ rescue

value: DBD+ rescue


title: DBD Micro-C rep 8 [Micro-C]

value: KD + DBD rescue

value: DBD rescue


title: KD Micro-C rep 8 [Micro-C]

value: KD of EWS::ERG

value: empty vector rescue


title: SMARCAL1_KO_3

status: Public on Feb 19 2025

first: Yu-Xin

last: Xu

state: United States

address: 185 Cambridge Street Simches Research Building, CPZN 5.500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

description: SMARCAL1 KO 123A

data_processing:
Base calling:  RTA-1.18.64.0
FASTQ generation:  bcl2fastq-1.8.4
Read trimming:  trimmomatic-0.35
Read QC:  fastQC-0.10.1
Alignment:  STAR-2.4.2
Mapping statistics:  bamtools-2.3.0
Differential expression:  cufflinks-2.2.1
Assembly: hg19
Supplementary files format and content: tab-delimited gene-level differential expression output from Cuffdiff

source_name: SMARCAL1KO Huh7 cell clone transfected with lentivirus containing CRISPR/cas9 and EDEM3 sgRNA

growth_protocol: Standard culture with DMEM medium suppplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer’s procedures
Ilumina TruSeq Stranded Total RNA with Ribo-Zero Globin

treatment_protocol: The cells were infected with lentiviruses containing CRISPR/cas9 with control and SMARCAL1 sgRNAs.

value: Human Huh7 hepatoma cells

value: SMARCAL1 KO


title: KD Micro-C rep 2 [Micro-C]


title: SMARCAL1_KO_5

description: SMARCAL1 KO 124Y6


title: SMARCAL1_KO_4

description: SMARCAL1 KO 123B


title: SMARCAL1_KO_2

description: SMARCAL1 KO 124Y6


title: SMARCAL1_KO_0

description: SMARCAL1 KO 123A


title: Control 5

description: SMARCAL1 WT3

source_name: SMARCAL1 WT Huh7 cell clone transfected with lentivirus containing CRISPR/cas9 and control sgRNA

value: WT SMARCAL1


title: Control 2

description: SMARCAL1 WT3


title: Control 4

description: SMARCAL1 WT2


title: Control 1

description: SMARCAL1 WT2


title: H3K27M_P9

status: Public on Feb 17 2025

description: fresh single whole cell RNA-seq: 10X Genomics

data_processing:
Illumina bcl2fastq 1.5 is used for demultiplexing
RNA-seq sequenced reads were mapped to hg19 using hisat2(2.1.0) with parameters --met 5 -k 10 --mp 1,1 --np 1 --score-min L,0,-0.1 --secondary --no-mixed --no-softclip --no-discordant --rdg 99999999,99999999 --rfg 99999999,99999999 --no-spliced-alignment --seed 12345
RNA-seq TPM were calculated using RSEM (v1.3.0) with parameters --estimate-rspd --paired-end -sam
Supplementary files: tab-delimited text files include TPM values for all cells passing QC (immune and tumor) separately for samples profiled by SmartSeq2 and/or 10X Genomics
tab-delimited text files for metadata for all cells passing QC (tumor and immune) separately for samples profiled by SmartSeq2 and/or 10X Genomics
Assembly: hg19
Supplementary files format and content: Tab-separated count matrix files and metadata files

source_name: Human tissue H3-K27-Altered

extract_protocol:
Smart-seq2 protocol, 10X Genomics protocol
Smart-seq2: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol). Briefly: RNA was purified with Agencourt RNAClean. Oligo-dT primed reverse transcription (RT) was performed using Maxima H Minus reverse transcriptase (Life Technologies) and a template-switching oligonucleotide (TSO; Qiagen). For the reverse transcription step, Maxima RNaseH-minus RT (200 U/ml) was used as the RT enzyme at 2U/ml. The RT step was performed at 50 Celsius degree for 90 minutes followed by 85 Celsius degree for 5 minutes. In the PCR pre-amplification step, an ISPCR primer was used at 0.2 mM and PCR was performed for 21 cycles. ). PCR purification was performed using AMpure XP beads at 0.8X. Libraries were enriched with dual indexes using Illumina Nextera XT Library Prep kits
10X Genomics: The isolated single cells (T cells, Myeloid cells, or tumor cells) were loaded into separate channels of a Single Cell Chip A with reverse transcriptase reagent mixture and 50ul gel beads according to the manufacturer’s protocol.Chips were next loaded into the 10X Genomics Chromium Controller for single-cell partitioning, immediately followed by emulsion recovery from the chip and incubated in a Thermocycler for the RT reaction. cDNA isolation and library preparation were completed as per the manufacturer’s protocol. Isolated cDNA was amplified (13 cycles). cDNA was allocated for preparation of a gene expression library or TCR enrichment/library preparation with the Chromium Single Cell V(D)J TCR kit (10X Genomics)

value: 9 years old

value: pediatric high grade glioma


title: H3K27M_P5

description: fresh single whole cell RNA-seq: SmartSeq2

source_name: Human tissue H3-K27 mutated

value: 6 years old


title: H3G34R_P2

source_name: Human tissue H3-G34 mutated

value: 16 years old


title: H3WT_hemi_P2

source_name: Human tissue GBM

value: 7 years old


description:
Hek 293T WT, DMEM High Glc 10% FBS basal, Technical rep 3
WTr3_NL3

value: cell line

value: Hek 293T

value: Human embryonic kidney 293 cells

value: WT

value: No treatment, Basal


title: Control 0

description: SMARCAL1 WT1


title: H3G34R_P1

value: 15 years old


title: DBD+ Micro-C rep 2 [Micro-C]

value: pulmonary metastasis a cervical tumor

value: Ewing sarcoma cell line

value: KD + DBD+ rescue

value: DBD+ rescue


title: H3K27M_P4

value: 4 years old


title: Control 3

description: SMARCAL1 WT1

value: Human Huh7 hepatoma cells

value: WT SMARCAL1


title: H3WT_hemi_P1

value: 2 years old

value: pediatric high grade glioma


title: H3K27M_P6

value: 12 years old


title: DBD Micro-C rep 2 [Micro-C]

value: KD + DBD rescue

value: DBD rescue


title: H3K27M_P1

value: 10 years old


title: H3WT_mid_P1

source_name: Human tissue H3-K27 Altered

value: 13 years old


title: H3WT_hemi_P5_R3

value: 16 years old


title: SMARCAL1_KO_1

description: SMARCAL1 KO 123B

value: SMARCAL1 KO


title: H3K27M_P3

value: 7 years old


title: H3WT_hemi_P5_R2

value: 15 years old


title: Arabidopsis root cells - sc_71

status: Public on Jan 26 2025

city: Los Angeles

first: Rachel

last: Shahan

state: California

address: 610 Charles E. Young Dr. S

institute: University of California, Los Angeles

description: Chromium Single Cell 3ʹ GEM Kit v3

data_processing:
Processed by COPILOT (https://github.com/ohlerlab/COPILOT)
Assembly: TAIR10
Supplementary files format and content: Seurat object

organism: Arabidopsis thaliana

source_name: Root tip

growth_protocol: Arabidopsis accession Columbia-0 (Col-0) was used as wild type.  Seeds were sterilized using 50% (v/v) bleach with 0.05% Tween-20 for 10-15 minutes, plated on 1/2 Linsmaier and Skoog (LSP03-1LT, Caisson Labs; pH 5.7), 1% sucrose media, and stratified 2-4 days at 4°C in the dark. Plates were kept vertically in a Percival growth chamber set to 22°C, 16 hours light/8 hours dark, and grown for 5-7 days.

extract_protocol:
For each sample, 0.2-0.5cm root tips were harvested from 1000-3000 roots and placed into a 35mm petri dish containing a 70 μm cell strainer and 4.5mL enzyme solution (1.5% [w/v] cellulase [ONOZUKA R-10, GoldBio], 0.1% Pectolyase [Sigma P3026], 0.4 M mannitol, 20 mM MES (pH 5.7), 20 mM KCl, 10 mM CaCl2, 0.1% bovine serum albumin, and 0.000194% (v/v) beta-mercaptoethanol). The digestion was incubated on an 85 rpm shaker at 25°C for one hour with additional stirring every 15-20 minutes. The resulting cell solution was filtered twice through 40 μm cell strainers and centrifuged for 5 minutes at 500g in a swinging bucket rotor. The pellet was washed with 2mL washing solution (0.4 M mannitol, 20 mM MES (pH 5.7), 20 mM KCl, 10 mM CaCl2, 0.1% bovine serum albumin, and 0.000194% (v/v) beta-mercaptoethanol), centrifuged again at 500g for 3 minutes, and the pellet resuspended in washing solution at a concentration of 1000-2000 cells/uL. We loaded 16,000 cells, with the aim to capture 10,000 cells per sample with the 10X Genomics Chromium 3` Gene expression v3 or v3.1 kits. 32,000 cells were loaded with the aim of capturing 20,000 cells for 10X Genomics v3.1 HT kits. Cell barcoding and library construction were performed following the manufacturer’s instructions. cDNA and final library quality were verified using a Bioanalyzer High Sensitivity DNA Chip (Agilent) and sequenced on an Illumina NextSeq 500 or NovaSeq 6000 instrument to produce 100bp paired-end reads.
Chromium Single Cell 3ʹ GEM Kit v3 and v3.1

treatment_protocol: Plants were grown on 100 μm nylon mesh (Nitex 03-100/44) on the plates to facilitate root collection

value: Root tip

value: All cell types of root

value: WT


title: H3WT_hemi_P3

description: fresh single whole cell RNA-seq: SmartSeq2 and 10X Genomics

value: 8 days old


title: YNN1 replicate 2 60nM Pho4

status: Public on Jan 16 2025

city: State College

first: Shane

middle: Douglas

last: Stoeber

address: 406 South Frear Building

department: BMMB

institute: Penn State

description: Library name: YNN1 replicate 2 60nM Pho4 MNase-seq

data_processing:
Paired-end reads were aligned to the corresponding reference sequence (Widom 601 or YNN with or without factor binding site) with Bowtie2 on galaxy (https://usegalaxy.org/) in paired-end mode.
Unpaired and unmapped reads were removed using samtools view in galaxy (https://usegalaxy.org/).
Nucleosome coverage was calculated from the read counts normalized to total reads in BPM using bamCoverage. The minimum and maximum fragment length was set to 130 bp and 160 bp respectively unless otherwise stated to enrich reads for mono-nucleosome fragments. Files were outputted as a bedgraph and plotted to visualize nucleosome occupancy.
The dyad position for each sequence was calculated using bamCoverage –MNase in which only the three center bp of each fragment was used for analysis and were normalized to total reads in BPM. Files were outputted as a bedgraph and plotted to visualize dyad location.
Supplementary files format and content: All nucleosome coverage and dyad analysis are bedgraph

organism: synthetic construct

source_name: PCR generated DNA molecule

extract_protocol:
Nucleosome binding experiments were performed by incubating 60 nM nucleosome with 0 nM or 60 nM of TFs (Reb1, Cbf1, or Pho4) for 20 minutes at room temperature. Nucleosomes-TF binding was confirmed on a 5% acrylamide native gel. The incubated samples were then digested with 0.3 U, 1 U, 3 U, 10 U of MNase (New England Biolabs) for 8 minutes at 37 ⁰C and immediately quenched by adding quench buffer (0.1 % SDS, 20 mM EDTA pH8.0, 0.01 U proteinase K). Proteinase K digestion was carried out by incubating the quenched samples for 1 hour at 50 ⁰C. The final digested samples were analyzed by agarose gel electrophoresis with a 1.5% gel in 0.5x TAE buffer (20 mM Tris base, 10 mM acetic acid, 0.5 mM EDTA pH 8.0) (Figure S4). The digest DNA samples were then purified by agarose gel electrophoresis and then gel extraction with a Freeze 'N Squeeze DNA extraction kit (Bio-Rad).
After gel purification of the MNase digested samples, sequencing libraries were prepared using NEBNext ® Ultra™ II DNA Library Prep Kit for Illumina® (Catalog # E7645L) according to the manufacturer’s instructions. The sequencing libraries were sequenced on a NextSeq 2000 machine in 2 x 50 bp paired-end sequencing mode at the Genomics Research Incubator at The Pennsylvania State University.

value: 1 unit micrococcal nuclease

value: 60nM Pho4


title: 601

description: Library name: 601 MNase-seq


title: YNN1 replicate 1 0nM Pho4

description: Library name: YNN1 replicate 1 0nM Pho4 MNase-seq

value: 0nM Pho4


title: YNN1 replicate 2 0nM Pho4

description: Library name: YNN1 replicate 2 0nM Pho4 MNase-seq