title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G3_AD002


title: Whole blood, Day 14, PID 56

status: Public on Nov 15 2020

type: RNA

city: Rixensart

first: Robbert

middle: Gerrit

last: van der Most

address: 89, rue de l'Institut

country: Belgium

institute: GSK

description: 14 days after 1st vaccination

hyb_protocol: After fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on GeneChip_ Human Genome U133 Plus 2.0 arrays following standard procedures.

scan_protocol: Data acquisition was performed using GeneChip Operating Software (Affymetrix).

data_processing: The data were analyzed with R/Bioconductor using GCRMA as summarization/normalization method

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood samples from subject 56 at Day 14

label_protocol: Biotinylated cDNA were prepared according to NuGen Ovation WB amplification protocol from 50ng total RNA

extract_protocol: Total RNA was isolated by PAXgene Blood RNA kit (Qiagen) according to the manufacturer’s protocol. A DNAse treatment was applied on the PAXgene RNA spin column to avoid genomic DNA contamination. RNA was quantified by UV-spectrophotometry.

treatment_protocol: PAXgene preserved whole blood samples were centrifuged, resuspended in lysis buffer and treated with proteinase K.

tag: adjuvant

tag: subject id

tag: time (sample day)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G3_AD001

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: strain

tag: age

tag: tissue

value: brain

tag: source

value: MOp

tag: target

value: SSp

tag: gender

value: male


title: Whole blood, Day 14, PID 8

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 8 at Day 14

value: Alum


title: Whole blood, Day 1, PID 33

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 33 at Day 1


title: Whole blood, Day 14, PID 25

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 25 at Day 14


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G3_AD010

value: SC

value: female


title: Whole blood, Day 30 post, PID 25

description: 30 post

source_name: Whole blood samples from subject 25 at Day 30 post


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G2_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G2_AD010


title: Whole blood, Day 33, PID 60

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 60 at Day 33


title: Whole blood, Day 33, PID 38

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 38 at Day 33


title: Whole blood, Day 1, PID 89

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 89 at Day 1


title: Whole blood, Day 33, PID 92

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 92 at Day 33


title: Whole blood, Day 0 post, PID 76

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 76 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 33, PID 65

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 65 at Day 33


title: Whole blood, Day 0 post, PID 26

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 26 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 30 post, PID 109

description: 30 post

source_name: Whole blood samples from subject 109 at Day 30 post


title: Whole blood, Day 30 post, PID 2

description: 30 post

source_name: Whole blood samples from subject 2 at Day 30 post


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G2_AD008


title: Whole blood, Day 1, PID 76

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 76 at Day 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G2_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G2_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G2_AD004


title: Whole blood, Day 33, PID 45

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 45 at Day 33


title: Whole blood, Day 31, PID 10

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 10 at Day 31


title: Whole blood, Day 1, PID 85

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 85 at Day 1


title: Whole blood, Day 0 post, PID 85

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 85 at Day 0, 3 to 6 hours post vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G2_AD002

source_name: C57BL/6J P56 Mouse Brain


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G2_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G1_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G1_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G1_AD010


title: Whole blood, Day 0 pre, PID 25

description: day of 1st vaccination, before vaccination

source_name: Whole blood samples from subject 25 at Day 0, pre vaccination


title: Whole blood, Day 31, PID 60

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 60 at Day 31


title: Whole blood, Day 30 pre, PID 89

description: day of 2nd vaccination, before vaccination

source_name: Whole blood samples from subject 89 at Day 30, pre vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G1_AD006


title: Whole blood, Day 14, PID 109

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 109 at Day 14


title: Whole blood, Day 33, PID 100

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 100 at Day 33


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G1_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G12_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G1_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G12_AD010


title: Whole blood, Day 1, PID 39

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 39 at Day 1


title: Whole blood, Day 0 post, PID 52

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 52 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 14, PID 2

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 2 at Day 14


title: Whole blood, Day 0 post, PID 60

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 60 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 31, PID 75

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 75 at Day 31


title: Whole blood, Day 0 pre, PID 18

source_name: Whole blood samples from subject 18 at Day 0, pre vaccination


title: Whole blood, Day 30 pre, PID 43

source_name: Whole blood samples from subject 43 at Day 30, pre vaccination


title: Whole blood, Day 33, PID 70

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 70 at Day 33


title: Whole blood, Day 0 pre, PID 2

source_name: Whole blood samples from subject 2 at Day 0, pre vaccination


title: Whole blood, Day 1, PID 91

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 91 at Day 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G1_AD007


title: Whole blood, Day 0 post, PID 43

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 43 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 30 pre, PID 57

source_name: Whole blood samples from subject 57 at Day 30, pre vaccination


title: Whole blood, Day 14, PID 18

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 18 at Day 14


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G1_AD004

source_name: C57BL/6J P56 Mouse Brain


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G12_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G11_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G11_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G12_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G12_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G11_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G11_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G11_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G10_AD004


title: Whole blood, Day 0 pre, PID 75

source_name: Whole blood samples from subject 75 at Day 0, pre vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G10_AD008


title: Whole blood, Day 31, PID 90

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 90 at Day 31


title: Whole blood, Day 0 pre, PID 83

source_name: Whole blood samples from subject 83 at Day 0, pre vaccination


title: Whole blood, Day 14, PID 11

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 11 at Day 14


title: Whole blood, Day 37, PID 29

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 29 at Day 37


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G10_AD010


title: Whole blood, Day 0 pre, PID 62

source_name: Whole blood samples from subject 62 at Day 0, pre vaccination


title: Whole blood, Day 30 pre, PID 90

source_name: Whole blood samples from subject 90 at Day 30, pre vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G10_AD007


title: Whole blood, Day 1, PID 46

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 46 at Day 1


title: Whole blood, Day 30 post, PID 92

description: 30 post

source_name: Whole blood samples from subject 92 at Day 30 post


title: Whole blood, Day 0 pre, PID 60

source_name: Whole blood samples from subject 60 at Day 0, pre vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F9_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G11_AD008


title: Whole blood, Day 0 pre, PID 36

source_name: Whole blood samples from subject 36 at Day 0, pre vaccination


title: Whole blood, Day 31, PID 24

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 24 at Day 31


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F9_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F9_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F9_AD007


title: Whole blood, Day 33, PID 83

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 83 at Day 33


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G10_AD001


title: Whole blood, Day 0 pre, PID 43

source_name: Whole blood samples from subject 43 at Day 0, pre vaccination


title: Whole blood, Day 1, PID 11

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 11 at Day 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F9_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F9_AD010


title: Whole blood, Day 0 post, PID 57

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 57 at Day 0, 3 to 6 hours post vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F8_AD012

source_name: C57BL/6J P56 Mouse Brain


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F9_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F8_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F8_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F8_AD004


title: Whole blood, Day 37, PID 100

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 100 at Day 37


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F8_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F8_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F7_AD012


title: Whole blood, Day 14, PID 59

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 59 at Day 14


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F7_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F7_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F7_AD008


title: Whole blood, Day 0 pre, PID 15

source_name: Whole blood samples from subject 15 at Day 0, pre vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F7_AD006


title: Whole blood, Day 0 post, PID 71

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 71 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 33, PID 19

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 19 at Day 33


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F7_AD004


title: Whole blood, Day 33, PID 13

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 13 at Day 33


title: Whole blood, Day 33, PID 59

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 59 at Day 33


title: Whole blood, Day 14, PID 75

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 75 at Day 14


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F6_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F6_AD012


title: Whole blood, Day 1, PID 15

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 15 at Day 1


title: Whole blood, Day 31, PID 66

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 66 at Day 31


title: Whole blood, Day 37, PID 7

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 7 at Day 37


title: Whole blood, Day 33, PID 4

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 4 at Day 33


title: Whole blood, Day 37, PID 59

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 59 at Day 37


title: Whole blood, Day 0 post, PID 69

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 69 at Day 0, 3 to 6 hours post vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F6_AD007


title: Whole blood, Day 30 pre, PID 46

source_name: Whole blood samples from subject 46 at Day 30, pre vaccination


title: Whole blood, Day 30 pre, PID 22

source_name: Whole blood samples from subject 22 at Day 30, pre vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F6_AD006

source_name: C57BL/6J P56 Mouse Brain


title: Whole blood, Day 37, PID 93

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 93 at Day 37


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F6_AD004


title: Whole blood, Day 1, PID 71

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 71 at Day 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F7_AD001


title: Whole blood, Day 30 post, PID 21

description: 30 post

source_name: Whole blood samples from subject 21 at Day 30 post


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F6_AD001


title: Whole blood, Day 30 pre, PID 39

source_name: Whole blood samples from subject 39 at Day 30, pre vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F5_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F5_AD008


title: Whole blood, Day 0 pre, PID 91

source_name: Whole blood samples from subject 91 at Day 0, pre vaccination


title: Whole blood, Day 0 pre, PID 13

source_name: Whole blood samples from subject 13 at Day 0, pre vaccination


title: Whole blood, Day 30 pre, PID 98

source_name: Whole blood samples from subject 98 at Day 30, pre vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F5_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F5_AD007


title: Whole blood, Day 30 post, PID 17

description: 30 post

source_name: Whole blood samples from subject 17 at Day 30 post


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F5_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F5_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F5_AD002


title: Whole blood, Day 1, PID 20

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 20 at Day 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F5_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F6_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F4_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F4_AD007


title: Whole blood, Day 30 pre, PID 51

source_name: Whole blood samples from subject 51 at Day 30, pre vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F4_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F4_AD004


title: Whole blood, Day 30 pre, PID 35

source_name: Whole blood samples from subject 35 at Day 30, pre vaccination


title: Whole blood, Day 14, PID 35

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 35 at Day 14


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F4_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F3_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F3_AD010


title: Whole blood, Day 0 post, PID 22

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 22 at Day 0, 3 to 6 hours post vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F3_AD008


title: Whole blood, Day 0 post, PID 75

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 75 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 37, PID 41

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 41 at Day 37


title: Whole blood, Day 37, PID 102

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 102 at Day 37


title: Whole blood, Day 14, PID 3

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 3 at Day 14


title: Whole blood, Day 37, PID 65

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 65 at Day 37


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F3_AD007

source_name: C57BL/6J P56 Mouse Brain


title: Whole blood, Day 1, PID 59

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 59 at Day 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F3_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F3_AD004


title: Whole blood, Day 0 pre, PID 53

source_name: Whole blood samples from subject 53 at Day 0, pre vaccination


title: Whole blood, Day 0 post, PID 38

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 38 at Day 0, 3 to 6 hours post vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F2_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F3_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F3_AD002


title: Whole blood, Day 0 pre, PID 86

source_name: Whole blood samples from subject 86 at Day 0, pre vaccination


title: Whole blood, Day 30 pre, PID 19

source_name: Whole blood samples from subject 19 at Day 30, pre vaccination


title: Whole blood, Day 30 pre, PID 91

source_name: Whole blood samples from subject 91 at Day 30, pre vaccination


title: Whole blood, Day 14, PID 19

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 19 at Day 14


title: Whole blood, Day 1, PID 24

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 24 at Day 1


title: Whole blood, Day 30 post, PID 24

description: 30 post

source_name: Whole blood samples from subject 24 at Day 30 post


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F2_AD007


title: Whole blood, Day 1, PID 45

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 45 at Day 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_G12_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F2_AD006


title: Whole blood, Day 30 post, PID 57

description: 30 post

source_name: Whole blood samples from subject 57 at Day 30 post


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F1_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F2_AD001


title: Whole blood, Day 0 pre, PID 80

source_name: Whole blood samples from subject 80 at Day 0, pre vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F2_AD002


title: Whole blood, Day 30 post, PID 76

description: 30 post

source_name: Whole blood samples from subject 76 at Day 30 post


title: Whole blood, Day 30 pre, PID 106

source_name: Whole blood samples from subject 106 at Day 30, pre vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F1_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F2_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F1_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F2_AD008


title: Whole blood, Day 14, PID 60

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 60 at Day 14


title: Whole blood, Day 1, PID 19

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 19 at Day 1


title: Whole blood, Day 30 pre, PID 60

source_name: Whole blood samples from subject 60 at Day 30, pre vaccination


title: Whole blood, Day 1, PID 6

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 6 at Day 1


title: Whole blood, Day 14, PID 105

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 105 at Day 14


title: Whole blood, Day 30 pre, PID 24

source_name: Whole blood samples from subject 24 at Day 30, pre vaccination


title: Whole blood, Day 0 pre, PID 76

source_name: Whole blood samples from subject 76 at Day 0, pre vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F1_AD004

source_name: C57BL/6J P56 Mouse Brain


title: Whole blood, Day 0 post, PID 45

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 45 at Day 0, 3 to 6 hours post vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F1_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F12_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F1_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F1_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F12_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F12_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F12_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F12_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F12_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F11_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F11_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F11_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F11_AD006


title: Whole blood, Day 14, PID 76

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 76 at Day 14


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F11_AD004


title: Whole blood, Day 31, PID 76

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 76 at Day 31


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F10_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F10_AD008


title: Whole blood, Day 30 post, PID 45

description: 30 post

source_name: Whole blood samples from subject 45 at Day 30 post


title: Whole blood, Day 14, PID 106

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 106 at Day 14


title: Whole blood, Day 30 pre, PID 100

source_name: Whole blood samples from subject 100 at Day 30, pre vaccination


title: Whole blood, Day 30 post, PID 4

description: 30 post

source_name: Whole blood samples from subject 4 at Day 30 post


title: Whole blood, Day 1, PID 18

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 18 at Day 1


title: Whole blood, Day 0 pre, PID 19

source_name: Whole blood samples from subject 19 at Day 0, pre vaccination


title: Whole blood, Day 30 post, PID 100

description: 30 post

source_name: Whole blood samples from subject 100 at Day 30 post


title: Whole blood, Day 30 post, PID 106

description: 30 post

source_name: Whole blood samples from subject 106 at Day 30 post


title: Whole blood, Day 0 pre, PID 3

source_name: Whole blood samples from subject 3 at Day 0, pre vaccination


title: Whole blood, Day 0 pre, PID 4

source_name: Whole blood samples from subject 4 at Day 0, pre vaccination


title: Whole blood, Day 1, PID 60

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 60 at Day 1


title: Whole blood, Day 37, PID 106

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 106 at Day 37


title: Whole blood, Day 31, PID 45

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 45 at Day 31


title: Whole blood, Day 37, PID 57

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 57 at Day 37


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F11_AD001

source_name: C57BL/6J P56 Mouse Brain


title: Whole blood, Day 31, PID 106

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 106 at Day 31


title: Whole blood, Day 0 post, PID 59

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 59 at Day 0, 3 to 6 hours post vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F10_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F10_AD010


title: Whole blood, Day 0 post, PID 91

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 91 at Day 0, 3 to 6 hours post vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F11_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F10_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F10_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_F10_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E9_AD012


title: Whole blood, Day 33, PID 75

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 75 at Day 33


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E9_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E9_AD008


title: Whole blood, Day 30 pre, PID 45

source_name: Whole blood samples from subject 45 at Day 30, pre vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E9_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E9_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E9_AD004


title: Whole blood, Day 31, PID 91

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 91 at Day 31


title: Whole blood, Day 30 pre, PID 6

source_name: Whole blood samples from subject 6 at Day 30, pre vaccination


title: Whole blood, Day 33, PID 6

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 6 at Day 33


title: Whole blood, Day 0 pre, PID 100

source_name: Whole blood samples from subject 100 at Day 0, pre vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E8_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E8_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E8_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E8_AD007


title: Whole blood, Day 33, PID 76

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 76 at Day 33


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E8_AD004


title: Whole blood, Day 0 post, PID 24

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 24 at Day 0, 3 to 6 hours post vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E8_AD006


title: Whole blood, Day 30 post, PID 68

description: 30 post

source_name: Whole blood samples from subject 68 at Day 30 post


title: Whole blood, Day 30 post, PID 60

description: 30 post

source_name: Whole blood samples from subject 60 at Day 30 post


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E8_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E8_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E7_AD012


title: Whole blood, Day 0 pre, PID 45

source_name: Whole blood samples from subject 45 at Day 0, pre vaccination


title: Whole blood, Day 0 post, PID 6

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 6 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 31, PID 100

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 100 at Day 31


title: Whole blood, Day 0 pre, PID 34

source_name: Whole blood samples from subject 34 at Day 0, pre vaccination


title: Whole blood, Day 1, PID 100

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 100 at Day 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E7_AD010

source_name: C57BL/6J P56 Mouse Brain


title: Whole blood, Day 14, PID 100

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 100 at Day 14


title: Whole blood, Day 37, PID 4

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 4 at Day 37


title: Whole blood, Day 31, PID 6

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 6 at Day 31


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E7_AD008


title: Whole blood, Day 37, PID 6

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 6 at Day 37


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E7_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E7_AD004


title: Whole blood, Day 0 pre, PID 11

source_name: Whole blood samples from subject 11 at Day 0, pre vaccination


title: Whole blood, Day 14, PID 4

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 4 at Day 14


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E7_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E6_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E6_AD012


title: Whole blood, Day 31, PID 19

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 19 at Day 31


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E6_AD008


title: Whole blood, Day 30 pre, PID 11

source_name: Whole blood samples from subject 11 at Day 30, pre vaccination


title: Whole blood, Day 0 pre, PID 57

source_name: Whole blood samples from subject 57 at Day 0, pre vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E6_AD006


title: Whole blood, Day 30 post, PID 19

description: 30 post

source_name: Whole blood samples from subject 19 at Day 30 post


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E6_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E6_AD007


title: Whole blood, Day 30 post, PID 83

description: 30 post

source_name: Whole blood samples from subject 83 at Day 30 post


title: Whole blood, Day 30 post, PID 11

description: 30 post

source_name: Whole blood samples from subject 11 at Day 30 post


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E6_AD002


title: Whole blood, Day 31, PID 17

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 17 at Day 31


title: Whole blood, Day 37, PID 74

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 74 at Day 37


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E7_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E5_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E5_AD010


title: Whole blood, Day 0 pre, PID 27

source_name: Whole blood samples from subject 27 at Day 0, pre vaccination


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E6_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E5_AD006


title: Whole blood, Day 33, PID 37

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 37 at Day 33


title: Whole blood, Day 1, PID 83

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 83 at Day 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E5_AD004

source_name: C57BL/6J P56 Mouse Brain


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E5_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E5_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E5_AD001


title: Whole blood, Day 30 pre, PID 49

source_name: Whole blood samples from subject 49 at Day 30, pre vaccination


title: Whole blood, Day 1, PID 9

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 9 at Day 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E3_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E3_AD007


title: Whole blood, Day 0 post, PID 78

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 78 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 0 post, PID 65

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 65 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 31, PID 54

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 54 at Day 31


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E3_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E3_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E3_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E3_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E2_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E2_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E2_AD008


title: Whole blood, Day 0 post, PID 17

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 17 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 33, PID 101

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 101 at Day 33


title: Whole blood, Day 37, PID 101

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 101 at Day 37


title: Whole blood, Day 37, PID 5

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 5 at Day 37


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E2_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E2_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E3_AD006


title: Whole blood, Day 37, PID 48

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 48 at Day 37


title: Whole blood, Day 0 post, PID 36

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 36 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 30 post, PID 102

description: 30 post

source_name: Whole blood samples from subject 102 at Day 30 post


title: CD8 T DhxP3

city: Xi’an

first: Anjun

last: Jiao

state: Shaanxi

address: No. 28, Xianning West Road, Xi'an City, Shaanxi Province

country: China

institute: Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University

library_source: transcriptomic

data_processing:
Illumina Hiseq 2000 sequencer software used for basecalling.
The double-stranded cDNA library was finished through PCR enrichment and size selection. The prepared cDNA library was sequenced with the Illumina Hiseq 2000 sequencer (Illumina HiSeq 2000 v4 Single-Read 50 bp) after pooling according to its expected data volume and effective concentration.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CD8+ T cells from the spleens 8 days post infection

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration was detected by the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen). After quality control by RNase free agarose gel and Agilent 2100 (Agilent Technologies, Palo Alto, CA, USA), RNA-Seq libraries were prepared using 200ng total RNA with the TruSeq RNA sample prep kit according to manufacturer’s instructions (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD44+CD62- effector CD8+ T cells were sorted from the spleens of LCMV-Armstrong-infected CD4Cre+Dhx9 f/f mice and wild-type littermates

value: spleen

tag: genotype/variation

value: Dhx9 deficient


title: Whole blood, Day 0 pre, PID 102

source_name: Whole blood samples from subject 102 at Day 0, pre vaccination


title: BC_Patient4012_Genearray5

city: Dortmund

first: Jan

middle: G.

last: Hengstler

address: Ardeystrasse 67

country: Germany

institute: Leibniz Research Centre for Working Environment and Human Factors

hyb_protocol: 11 µg   of fragmented aRNA was hybridized to the Human Genome U133 plus 2.0 microarrays in the Genechip Hybridisation Oven-645 (Affymetrix, United Kingdom) for 16 h   at 45° C.

scan_protocol: Arrays were washed and stained with phycoerythrin with the Fluidics Station 450 and scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions.

data_processing: CEL-files were normalized with R/Bioconductor using frozen robust multi-array average implemented in the Bioconductor package 'fRMA' with default settings.

label: biotin

source_name: Pretreatment biopsy

label_protocol: 100-200 ng total RNA was used for aRNA amplification with the GeneChip® 3’ IVT Express Kit (Affymetrix, United Kingdom) according to the manufacturer’s instructions. After 16 h   of biotinylated in vitro transcription, aRNA was purified using magnetic beads and 15 µg   of purified aRNA was fragmented with fragmentation buffer.

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen).

tag: response cycle 3

value: cPR

tag: response cycle 6

tag: pathological response

value: pNC

tag: tumor type

value: invasive ductal

tag: menopausal status

value: pre-menopausal

tag: ct stage

tag: cn stage

tag: cm stage

tag: tumor grade

tag: er status

tag: pr status

tag: her2 status

tag: pam50 subtypes

value: LumB


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E2_AD004

tag: strain

tag: age

tag: tissue

tag: source


title: BC_Patient2019_Genearray5

tag: response cycle 3

value: pPR

value: post-menopausal

value: LumA


title: BC_Patient4005_Genearray5

tag: response cycle 6

value: cCR


title: BC_Patient4003_Genearray5

tag: pathological response

value: pCR

value: Normal


title: BC_Patient6001_Genearray5

tag: tumor type


title: CD8 T DhxP2

tag: genotype/variation


title: BC_Patient1024_Genearray5

value: cNC

value: invasive mucinous

tag: menopausal status

tag: ct stage


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E2_AD002

value: brain

value: MOp

tag: target

value: SSp

tag: gender

value: male


title: CD8 T DhxP1

value: spleen

value: Dhx9 deficient


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E2_AD001


title: BC_Patient9009_Genearray5

value: cPR

value: invasive ductal

tag: cn stage

tag: cm stage

tag: tumor grade

tag: er status


title: CD8 T DhxN3

tag: strain

value: wild-type


title: BC_Patient8009_Genearray4

value: pPR

value: invasive lobular

tag: age

tag: pr status

tag: her2 status

tag: pam50 subtypes


title: CD8 T DhxN2

tag: tissue


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E1_AD010

tag: source

value: SC

value: female


title: CD8 T DhxN1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E1_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E1_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E1_AD006


title: TBI_PLX5622_1

city: Columbus

first: Kristina

middle: Grace

last: Witcher

state: OH

address: 460 Medical Center Dr

department: Neuroscience

institute: Ohio State University

data_processing:
Sequencing reads were aligned to the mm10 mouse genome and count matrices generated using CellRanger's count protocol (10X Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: column index (barcodes), row index (features) and matrix

molecule: polyA RNA

growth_protocol: Adult (8-10-week-old) male C57BL/6 mice were purchased from Charles River Breeding Laboratories (Wilmington, MA, USA). Mice were housed in groups of 4 and kept under a 12/12 light-dark cycle with ad  libitumaccess  to  food  and  water.  All  procedures  were  performed  in  accordance  with  the National Institute of Health Guidelines for the Care and Use of Laboratory Animals and  were  approved  by  The  Ohio  State  University IACUC.

extract_protocol:
Mice  were  perfused  with  ice-cold  PBS,  brains were rapidly removed, and the cortex was microdissected. The cortex was dissociated using the Adult Mouse Brain Dissociation Kit for mouse and rat per manufacturer’s instructions with minor modifications(Miltenyi  Biotec,Bergisch  Gladbach,  Germany). aCSF  (as  described  below)  was used  to  make  up  enzyme  solutions.  Dissected  cortex was  immediately  placed  into  pre-warmed (37°C) Enzyme P solution, Enzyme A solution was added, and tissue was dissociated in C-tubes at  37°C  using  a  gentleMACS  dissociator(Miltenyi  Biotec).  Density  centrifugation  was  used  to remove myelin debris, remaining red blood cells were lysed, and cell viability and concentration was determined using a hemocytometer. Approximately 3,000-7,000 cells were recovered from each cortical homogenate.
Single-cell cortical suspension was loaded onto a 10X chip  and  run  on  a  Chromium  Controller  to  generate  gel-bead  emulsions  (10X  Genomics, 12Pleasanton, CA, USA). Protocol for UMI barcoding, cDNA amplification, and library construction followed the 10X Genomics Single Cell 3’ v2 reagent kit protocol. Library quality was determined by Agilent High Sensitivity DNA BioAnalyzer chip.
RNA-sequencing was performed using an Illumina HiSeq by Novogene per 10x Single Cell 3' v2 specifications

treatment_protocol: PLX5622  was  provided  by  Plexxikon  Inc.  (Berkley,  CA,  USA)  and formulated in AIN-76A rodent chow byResearch Diets at a concentration of 1200 mg/kg. Standard AIN-76A  diet  was  provided  as  a  vehicle control.  Mice  were  provided ad  libitumaccess  to PLX5622 or vehicle diet for 14 days to deplete microglia prior to TBI. Mice were maintained on the experimental diets for the duration of the study. Mice  received  a  midline  diffuse  TBI  using  a  fluid percussion  injury  (FPI)  apparatus  (Custom  Design  &  Fabrication,  Richmond,  VA,  USA)  as  we previously described (Fenn et al., 2014; Fenn et al., 2015; Rowe et al., 2016; Witcher et al., 2018).  In  brief,  a  midline  craniectomy  was performed with a 3 mm outerdiameter trephine and a rigid Luer-loc needle hub was secured over the  craniectomy.  After  recovery,  injury  was  induced  by  filling  the  injury  hub  with  saline  and imposing a 10ms pulse of saline (1.2 atmospheres; 670-720 mV) onto the dura through the hub (Fenn et al., 2014; Lifshitz et al., 2007b; Rowe et al., 2016; Witgen et al., 2006). Immediately after injury, the hub was removed, dural integrity was confirmed, and mice were evaluated for injury severity using the self-righting test (Lifshitz et al., 2007a).

tag: Sex

tag: injury

value: TBI

tag: treatment

value: Cortex


title: TBI_PLX5622_2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E1_AD004


title: TBI_Vehicle_2

value: Vehicle


title: BC_Patient4016_Genearray4

tag: response cycle 3

value: cNC

tag: response cycle 6

tag: pathological response

value: pNC

tag: tumor type

tag: menopausal status

value: post-menopausal

tag: ct stage

value: LumB


title: BC_Patient7001_Genearray4

value: pre-menopausal

tag: cn stage

tag: cm stage

tag: tumor grade

tag: er status


title: BC_Patient4001_Genearray4

value: cPD

tag: age

tag: pr status

tag: her2 status

value: LumA


title: BC_Patient2013_Genearray4

value: cPR

value: cCR

value: pCR

tag: pam50 subtypes

value: Basal


title: BC_Patient1009_Genearray4

value: pPR

value: invasive ductal

value: Normal


title: BC_Patient2006_Genearray4


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E1_AD012

tag: strain

tag: tissue

value: brain

tag: source

value: SSp

tag: target

value: SC

tag: gender

value: female


title: BC_Patient3011_Genearray4

tag: response cycle 3

value: cNC

tag: response cycle 6

tag: pathological response


title: BC_Patient1012_Genearray4

tag: tumor type

tag: menopausal status

tag: ct stage


title: TBI_Vehicle_1

tag: Sex

value: male

tag: injury

value: TBI

tag: treatment

value: Vehicle

value: Cortex


title: BC_Patient1002_Genearray4

tag: age

value: post-menopausal

tag: cn stage

tag: cm stage

tag: tumor grade

tag: er status

tag: pr status

value: LumB


title: BC_Patient2005_Genearray4

value: cPR

tag: her2 status

tag: pam50 subtypes

value: LumA


title: BC_Patient6002_Genearray4

tag: response cycle 3


title: BC_Patient8008_Genearray4

tag: response cycle 6

value: pNC

value: invasive lobular


title: Control_PLX5622_2

tag: strain

value: Control

tag: tissue


title: BC_Patient3010_Genearray4

tag: pathological response

value: pCR

tag: tumor type

value: invasive ductal

tag: menopausal status

value: pre-menopausal

value: Normal


title: BC_Patient1025_Genearray4

tag: ct stage


title: BC_Patient8001_Genearray4


title: BC_Patient7002_Genearray4

value: cCR


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E1_AD002

value: brain

tag: source

value: MOp

tag: target

value: SSp

tag: gender


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E12_AD012

tag: age

value: SC

value: female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E1_AD001

value: male


title: Control_Vehicle_2

tag: Sex

tag: injury

tag: treatment

value: Vehicle

value: Cortex


title: Control_PLX5622_1


title: Control_Vehicle_1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E12_AD010


title: BC_Patient8006_Genearray4

value: cPR

value: cNC

value: pPR

value: micropapillary

value: post-menopausal

tag: cn stage

tag: cm stage

tag: tumor grade

tag: er status

tag: pr status

tag: her2 status

value: LumB


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E12_AD008

tag: strain

tag: tissue


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E12_AD007


title: BC_Patient4009_Genearray3

tag: response cycle 3

tag: response cycle 6

tag: pathological response

tag: tumor type

value: invasive ductal

tag: menopausal status

value: pre-menopausal

tag: pam50 subtypes


title: BC_Patient2018_Genearray3

value: cCR

tag: age

tag: ct stage

value: LumA


title: Smed-exoc3(RNAi) rep2

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2fastq v1.8.4. Read mapping was done with STAR (version 2.7.2b, parameters: --alignIntronMax 100000 --outSJfilterReads --outSAMmultNmax Unique --outFilterMismatchNoverLmax 0.04) to the S. mediterranea S2F2 genome assembly (dd_Smes_g4) with the repeat filtered version of the smes_v2_SMEG gene annotation (PlanMine). Read counting was performed with FeatureCounts (version 1.6.5, multi-mapping or multi-overlapping reads were not counted, stranded mode was set to “–s 2”).
genome_build: dd_Smes_g4
processed_data_files_format_and_content: tsv (tabulator-separated values) file for each sample containing the gene id (1st column) and the number of asigned reads (=counts, 2nd column)

organism: Schmidtea mediterranea

growth_protocol: Planarians maintained in MilliQ water which constituted of 1.6mM NaCl, 1mM CaCl2, 1mM MgSO4, 0.1mM MgCl2, 0.1mM KCl and 0.1gr NaHCO3 at an ambient temperature of 19°C with 12 hours light and 12 hours dark cycles.

extract_protocol:
Total RNA was extracted from X1 cells using the Trizol reagent by following the manufacturer's instruction.
Library preparation was done using Illumina’s TruSeq Stranded mRNA library preparation kit following the manufacturer’s description.

treatment_protocol: 5 to 5.5mm planarians measured with the use of millimeter paper were utilized to inject dsRNA against exoc3 as described previously (Sánchez Alvarado and Newmark 1999). All animals were injected ventrally at different pre- and post-pharyngeal positions to rule out the possibility that the defects observed were related to the place of injection. As a control, dsRNA against gfp was used as its sequence does not align with planarian genome. Smed-exoc3 dsRNA were injected in planarians following the conventional schedule of three consecutive days of injections followed by another round of injection for three consecutive days twelve days later of the first round of injections.

tag: irradiation sensitivity

value: irradiation sensitive

tag: cell cycle

value: mitotically active

tag: depletion


title: Smed-exoc3(RNAi) rep1


title: Smed-exoc3(RNAi) rep3


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E12_AD006

value: brain

tag: source

value: MOp

tag: target

value: SSp

tag: gender


title: BC_Patient1005_Genearray3

tag: cn stage

tag: cm stage

tag: tumor grade

tag: er status

tag: pr status

tag: her2 status


title: BC_Patient1021_Genearray3

tag: response cycle 3

tag: response cycle 6

tag: pathological response

value: pNC

tag: tumor type


title: BC_Patient3002_Genearray3

tag: age

tag: menopausal status

tag: ct stage

tag: pam50 subtypes


title: BC_Patient4007_Genearray3

value: pCR


title: BC_Patient4010_Genearray3

value: cPR


title: BC_Patient2015_Genearray3


title: BC_Patient4011_Genearray3

value: cNC


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E12_AD004

tag: strain

tag: tissue

tag: source

value: male


title: BC_Patient2010_Genearray3

value: pPR

tag: cn stage

value: Normal


title: gfp(RNAi) rep3

tag: irradiation sensitivity

tag: cell cycle

tag: depletion

value: gfp (control)


title: BC_Patient1004_Genearray3

value: invasive ductal

tag: cm stage

tag: tumor grade

tag: er status

tag: pr status

value: LumB


title: BC_Patient1001_Genearray3

tag: response cycle 3

tag: response cycle 6

tag: pathological response

value: post-menopausal

tag: her2 status


title: BC_Patient3013_Genearray3

value: cCR

tag: tumor type

tag: age

tag: menopausal status

value: pre-menopausal

tag: ct stage

value: Basal


title: BC_Patient8002_Genearray3

tag: pam50 subtypes


title: gfp(RNAi) rep2

value: irradiation sensitive

value: mitotically active


title: BC_Patient9011_Genearray3

tag: cn stage


title: BC_Patient9019_Genearray3

value: invasive ductal; multicenter

value: LumA


title: gfp(RNAi) rep1

tag: irradiation sensitivity


title: BC_Patient9016_Genearray3

value: invasive lobular


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E11_AD008

tag: strain

tag: tissue

value: brain

tag: source

value: SSp

tag: target

value: SC

tag: gender


title: BC_Patient9007_Genearray3

value: cPR

value: pPR

tag: cm stage

tag: tumor grade

tag: er status

tag: pr status


title: BC_Patient3004_Genearray2

tag: response cycle 3

value: cNC

tag: response cycle 6

tag: pathological response

tag: her2 status


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E12_AD001

tag: age

value: MOp

value: male


title: BC_Patient4006_Genearray3

value: pCR

tag: tumor type

value: invasive ductal

tag: menopausal status

tag: ct stage

tag: pam50 subtypes

value: Normal


title: BC_Patient9021_Genearray5

value: pre-menopausal

tag: cn stage


title: BC_Patient4017_Genearray3

value: Basal


title: BC_Patient9017_Genearray3

value: cCR


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E11_AD007

tag: strain

tag: tissue

tag: source


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E11_AD004

tag: target

tag: gender


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E11_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E11_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E10_AD010

value: female


title: 739_PLX5622_TBI_7d

hyb_protocol: standard Nanostring protocol

scan_protocol: standard Nanostring protocol

data_processing: Gene expression was quantified using the NanoString neuropathology panel, with 30 added custom genes (NanoString Technologies, Seattle, WA, USA). Technical normalization was first performed to positive and negative controls per manufacturer’s protocols. Housekeeping genes were validated based on strong correlation with total counts and 7 were used to normalize data (Aars, Asb7, Ccdc127, Cnot10, Csnk2a2, Lars, Mto1). Data were normalized and differential expression testing was performed using DESeq2 in R (Love et al., 2014).

label: fluorescent tag barcodes

label_protocol: standard Nanostring protocol

growth_protocol: Adult (8-10-week-old) male C57BL/6 mice were purchased from Charles River Breeding Laboratories (Wilmington, MA, USA). Mice were housed in groups of 4 and kept under a 12/12 light-dark cycle with ad libitum access to food and water. All procedures were performed in accordance with the National Institute of Health Guidelines for the Care and Use of Laboratory Animals and the Public Health Service’s Policy on Humane Care and Use of Laboratory Animals and Guide for the Care use of Laboratory Animals and were approved by The Ohio State University Institutional Laboratory Animal Care and Use Committee.

extract_protocol: RNA was extracted from microdissected regions of cortex containing hypertrophied and rod-shaped microglia (Witcher et al., 2018). At time of sacrifice, brains were rapidly removed and snap-frozen in dry ice-cooled isopentane. Fresh-frozen tissue was cryosectioned at alternating thicknesses of 30 um and 200 um onto charged slides. Thin sections, or guide slides, were labeled for CD11b (1:300, biotinylated) and visualized using an ABC solution (Vector Laboratories, Burlingame, CA, USA) and a diaminobenzidine (DAB) peroxidase substrate kit (Vector Laboratories, Burlingame, CA, USA). Labeled guide slides were used to identify regions of interest in the frozen thick sections, which were then microdissected, immediately lysed, and RNA was extracted (PicoPure RNA extraction kit, Thermo Fisher). RNA integrity was confirmed by Agilent BioAnalyzer and pre-amplification cycles were determined using expression of housekeeping genes (Gapdh, Actb).

treatment_protocol: PLX5622 was provided by Plexxikon Inc. (Berkley, CA, USA) and formulated in AIN-76A rodent chow by Research Diets at a concentration of 1200 mg/kg. Standard AIN-76A diet was provided as a vehicle control. Mice were provided ad libitum access to PLX5622 or vehicle diet for 14 days to deplete microglia prior to TBI. Mice were maintained on the experimental diets for the duration of the study. This dose and time was validated in our lab to deplete ~96% of microglia in C57BL/6 mice (McKim et al., 2017).

tag: Sex

tag: mouse group

value: injured (TBI)

tag: treatment

value: Cortex

tag: nanostring cartridge

tag: rna extraction batch


title: 740_PLX5622_TBI_1d


title: 742_Vehicle_Control

value: control (naive)

value: Vehicle


title: 741_Vehicle_TBI_1d


title: BC_Patient9014_Genearray2

tag: response cycle 3

tag: response cycle 6

tag: pathological response

value: post-menopausal

tag: cm stage

tag: tumor grade

tag: er status

tag: pr status

tag: her2 status

value: LumB


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E10_AD006

tag: strain

tag: age

tag: tissue

value: brain

value: SSp


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E10_AD012

tag: source

tag: target

value: SC

tag: gender


title: BC_Patient2017_Genearray2

value: cPR

value: pNC

tag: tumor type

tag: menopausal status

tag: ct stage

tag: cn stage

tag: pam50 subtypes


title: BC_Patient1022_Genearray2

tag: response cycle 3

value: cNC

tag: response cycle 6

tag: pathological response

value: invasive ductal


title: BC_Patient4013_Genearray3

value: pPR

value: invasive lobular

tag: cm stage

tag: tumor grade

tag: er status


title: BC_Patient1015_Genearray2

value: pCR

value: pre-menopausal

tag: pr status

tag: her2 status

value: Basal


title: BC_Patient1003_Genearray2

tag: age


title: BC_Patient1027_Genearray2


title: 737_Vehicle_Control

tag: strain

tag: Sex

value: male

tag: mouse group

tag: treatment

tag: tissue

value: Cortex

tag: nanostring cartridge

tag: rna extraction batch


title: 736_PLX5622_Control

value: control (naive)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E10_AD007

tag: source

tag: target

tag: gender


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E10_AD004

value: MOp


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_E10_AD001


title: 734_PLX5622_TBI_7d

value: injured (TBI)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D9_AD012

value: brain

value: female


title: 735_Vehicle_TBI_7d

value: Vehicle


title: 732_Vehicle_Control


title: 733_PLX5622_TBI_30d


title: BC_Patient1020_Genearray2

tag: response cycle 3

value: cPR

tag: response cycle 6

tag: pathological response

tag: tumor type

tag: menopausal status

tag: ct stage

tag: cn stage

tag: pam50 subtypes

value: LumA


title: BC_Patient2008_Genearray2

tag: age

value: post-menopausal

tag: cm stage

tag: tumor grade

tag: er status

tag: pr status

tag: her2 status


title: BC_Patient9018_Genearray2

value: invasive left basal phenotype


title: BC_Patient1016_Genearray2

value: pNC

value: invasive ductal


title: BC_Patient9022_Genearray2

value: cNC


title: BC_Patient1014_Genearray2

value: cCR

value: pCR

value: pre-menopausal

value: Normal


title: BC_Patient2001_Genearray2

value: pPR

value: Basal


title: BC_Patient1028_Genearray2


title: 731_PLX5622_Control

tag: strain

tag: Sex

value: male

tag: mouse group

value: control (naive)

tag: treatment

tag: tissue

value: Cortex

tag: nanostring cartridge

tag: rna extraction batch


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D9_AD006

value: brain

tag: source

value: MOp

tag: target

value: SSp

tag: gender


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D9_AD007

value: SC


title: 730_Vehicle_TBI_7d

value: injured (TBI)

value: Vehicle


title: BC_Patient4014_Genearray2

tag: response cycle 3

value: cPR

tag: response cycle 6

tag: pathological response

value: pNC

tag: tumor type

value: invasive ductal

tag: menopausal status

value: post-menopausal

tag: ct stage

tag: cn stage

tag: pam50 subtypes

value: LumA


title: BC_Patient8010_Genearray2

tag: age

tag: cm stage

tag: tumor grade

tag: er status

tag: pr status

tag: her2 status

value: Normal


title: BC_Patient2016_Genearray2

value: cNC

value: pPR

value: invasive lobular


title: BC_Patient2004_Genearray2

value: pCR

value: Basal


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D9_AD008

tag: strain

tag: tissue

value: brain

tag: source

value: male


title: BC_Patient2002_Genearray2

tag: response cycle 3


title: BC_Patient9020_Genearray1

tag: response cycle 6

value: invasive ductal; multicenter


title: 729_PLX5622_TBI_7d

tag: Sex

tag: mouse group

tag: treatment

value: Cortex

tag: nanostring cartridge

tag: rna extraction batch


title: BC_Patient9013_Genearray1

tag: pathological response

tag: tumor type

tag: menopausal status

value: pre-menopausal

tag: ct stage

tag: cn stage

tag: pam50 subtypes


title: 728_Vehicle_TBI_30d

value: injured (TBI)

value: Vehicle


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D9_AD004

tag: age

value: MOp

tag: target

value: SSp

tag: gender


title: BC_Patient9015_Genearray1

value: cPR

value: invasive ductal

tag: cm stage

tag: tumor grade

tag: er status

tag: pr status

tag: her2 status

value: LumB


title: BC_Patient4004_Genearray2

tag: response cycle 3

tag: response cycle 6

value: post-menopausal


title: BC_Patient9008_Genearray1


title: 727_PLX5622_TBI_30d

tag: strain

tag: Sex

tag: mouse group

tag: treatment

tag: tissue

tag: nanostring cartridge

tag: rna extraction batch


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D8_AD012

tag: age

tag: source

value: SC

value: female


title: 726_Vehicle_TBI_1d


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D8_AD010

tag: target

tag: gender


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D8_AD008


title: 725_PLX5622_TBI_1d


title: 724_Vehicle_TBI_7d


title: 723_PLX5622_TBI_7d


title: BC_Patient9005_Genearray2

tag: pathological response

value: pPR

tag: tumor type

tag: menopausal status

tag: ct stage

tag: cn stage

tag: cm stage

tag: tumor grade

tag: pam50 subtypes


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D8_AD006

tag: strain


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D9_AD001


title: 722_Vehicle_TBI_30d

tag: Sex

tag: mouse group

tag: treatment


title: BC_Patient8011_Genearray1

tag: response cycle 3

tag: response cycle 6

value: cCR

value: pNC

tag: er status

tag: pr status

tag: her2 status

value: LumA


title: BC_Patient2014_Genearray1

value: cNC

tag: pathological response

value: pCR

value: invasive lobular

tag: age


title: BC_Patient3008_Genearray1

tag: tumor type

tag: menopausal status


title: BC_Patient2011_Genearray1

tag: ct stage

tag: cn stage


title: BC_Patient2009_Genearray1

tag: cm stage

tag: tumor grade


title: BC_Patient3001_Genearray1

value: pre-menopausal

tag: pam50 subtypes


title: BC_Patient4002_Genearray1


title: BC_Patient9012_Genearray1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D8_AD007

tag: strain

tag: tissue

value: brain

tag: source

tag: target

tag: gender

value: male


title: 721_PLX5622_TBI_30d

tag: Sex

tag: mouse group

value: injured (TBI)

tag: treatment

value: Cortex

tag: nanostring cartridge

tag: rna extraction batch


title: BC_Patient1018_Genearray1

tag: response cycle 3

value: cPR

tag: response cycle 6

tag: pathological response

tag: tumor type

value: invasive ductal

tag: age

tag: er status

tag: pr status

tag: her2 status


title: 720_Vehicle_TBI_1d

tag: strain

value: Vehicle

tag: tissue


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D8_AD001

tag: source

value: MOp

tag: target

value: SSp


title: IM24h: DE83NGSUKBR106058

city: Bonn

first: Reiner

last: Schneider

address: Venusberg-Campus 1

department: Surgery Department

institute: University Clinics Bonn

data_processing:
PARTEK FLOW software with a lexogen generated pipeline using Poly-A-Sequence for trimming and ensemble (95) as database for aliment.
Supplementary_files_format_and_content: Excel file with list of discussed genes

source_name: intestinal manipulation 24h

growth_protocol: Bl6 mice 8-12 weeks old.

extract_protocol:
Qiagen RNA extraction protocol
QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina

treatment_protocol: intestinal manipulation 3h or 24h

value: muscularis externa of the small intestine


title: BC_Patient1011_Genearray1

value: pPR

tag: menopausal status

value: post-menopausal

tag: ct stage

tag: cn stage

tag: cm stage

tag: tumor grade

tag: pam50 subtypes


title: BC_Patient2007_Genearray1

tag: response cycle 3

tag: response cycle 6

value: pNC

value: LumA


title: BC_Patient2012_Genearray1

tag: pathological response

tag: tumor type

value: LumB


title: BC_Patient1013_Genearray1

tag: age

tag: er status

value: Basal


title: IM3h: DE79NGSUKBR107003_S108

source_name: intestinal manipulation 3h


title: BC_Patient1008_Genearray1

value: cNC

tag: pr status

tag: her2 status


title: BC_Patient1010_Genearray1

value: cCR

value: pCR

value: trabecular


title: 719_PLX5622_TBI_1d

tag: strain

tag: Sex

value: male

tag: mouse group

value: injured (TBI)

tag: treatment

tag: tissue

value: Cortex

tag: nanostring cartridge

tag: rna extraction batch


title: BC_Patient9001_Genearray1

value: invasive ductal

tag: menopausal status

value: pre-menopausal

tag: ct stage

tag: cn stage

tag: cm stage

tag: tumor grade


title: Control: DE56NGSUKBR106059

source_name: sham operated


title: BC_Patient1007_Genearray1

tag: response cycle 3

tag: response cycle 6

value: cPR

tag: pathological response

tag: tumor type

tag: pam50 subtypes


title: IM3h: DE52NGSUKBR107004_S109

tag: strain

value: muscularis externa of the small intestine


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D7_AD010

source_name: C57BL/6J P56 Mouse Brain

tag: age

value: brain

tag: source

value: SSp

tag: target

value: SC

tag: gender

value: female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D7_AD008

tag: tissue


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D7_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D8_AD004

value: MOp


title: 717_PLX5622_TBI_7d

tag: Sex

tag: mouse group

tag: treatment

tag: nanostring cartridge

tag: rna extraction batch


title: 718_Vehicle_TBI_7d

value: Vehicle


title: Control: DE29NGSUKBR106060_S182


title: IM3h: DE09NGSUKBR107002_S107


title: ATP: DE77NGSUKBR106069

source_name: enteric glia from primary culture

growth_protocol: Enteric glia were cultures as described in doi: 10.1371/journal.pone.0151335. eCollection 2016 and doi: 10.1053/j.gastro.2013.09.030. Epub 2013 Sep 22.

treatment_protocol: 6h with 100µM ATP (SIGMA)

value: enteric glia from primary culture


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D7_AD007


title: 715_PLX5622_TBI_30d


title: Control: DE02NGSUKBR106061


title: 716_Vehicle_TBI_30d


title: IM24h: DE13NGSUKBR106057


title: ATP: DE83NGSUKBR107319_S45


title: ATP: DE13NGSUKBR107318_S44


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D7_AD004


title: ATP: DE56NGSUKBR107320_S46


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D7_AD002


title: ATP: DE66NGSUKBR106073


title: 714_Vehicle_Control

value: control (naive)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D7_AD001


title: Control: DE94NGSUKBR107315_S41


title: Control: DE67NGSUKBR107316_S42


title: 712_Vehicle_TBI_1d


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D6_AD012


title: 711_PLX5622_TBI_1d


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D7_AD006


title: Control: DE21NGSUKBR107174_S115


title: Control: DE40NGSUKBR107317_S43


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D6_AD008


title: Control: DE91NGSUKBR107175_S116


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D6_AD010


title: ATP: DE23NGSUKBR106071


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D6_AD007


title: Tnfaip2-/- EBs with PA/PC treatment rep1 [KO_EB_PAPC_1]

description:
KO_EB_PAPC_1
palmitic acid (PA) and palmitoyl-L-carnitine (PC) treatment

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2fastq v2.20.0.422. Read mapping was done with STAR (version 2.7.2b, parameters: --alignIntronMax 100000 --outSJfilterReads --outSAMmultNmax Unique --outFilterMismatchNoverLmax 0.04) to the mouse reference genome (GRCm38) with the Ensembl gene annotation (release 99). Read counting was performed with FeatureCounts (version 1.6.5, multi-mapping or multi-overlapping reads were not counted, stranded mode was set to “–s 2”).
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file containing read counts per gene over all samples

source_name: embryoid bodies

growth_protocol: ES cells were plated on gelatin-coated plates and cultured using mouse ES cell medium containing 15% KnockOut™ D-MEM supplemented with Knockout Serum Replacement, L-glutamine, penicillin/streptomycin, nonessential amino acids, β-mercaptoethanol, and 1,000 U/ml Leukemia Inhibitory Factor.

extract_protocol:
Total RNA was extracted from embryoid bodies using the Masterpure RNA Purification Kit (Epicentre) as per manufacturer’s instruction.
Library preparation was done using Illumina’s TruSeq RNA v2 library preparation kit following the manufacturer’s description.

treatment_protocol: 3.75 × 10,000 ES cells/ml were re-suspended and rows of 27μl drops (1000 cells per drop)  on the up-turned inner surface of the lid of the 10cm tissue culture dish were made and incubated at 37°C for 3 days to form EBs. The EBs (at day 0) were plated onto 0.1% gelatin coated tissue culture dishes to initiate in vitro differentiation by incubating for another 3 days at 37°C MEF medium containing 15% KnockOut™ D-MEM supplemented with Knockout Serum Replacement, L-glutamine, penicillin/streptomycin, nonessential amino acids. For the rescue experiments (samples KO_EB_PAPC_1,2,3), the EBs were supplemented with 8μM each of palmitic acid  (PA) and palmitoyl-L-carnitine (PC). After 3 days of in vitro differentiation the EBs were harvested.

tag: cell type

value: embryonic stem cells

tag: genotype

tag: agent


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D6_AD006


title: 710_Vehicle_TBI_7d


title: 713_PLX5622_Control


title: Tnfaip2-/- EBs with PA/PC treatment rep2 [KO_EB_PAPC_2]

description:
KO_EB_PAPC_2
palmitic acid (PA) and palmitoyl-L-carnitine (PC) treatment


title: Tnfaip2-/- EBs with PA/PC treatment rep3 [KO_EB_PAPC_3]

description:
KO_EB_PAPC_3
palmitic acid (PA) and palmitoyl-L-carnitine (PC) treatment


title: WT EBs rep1 [WT_EB_1]

value: WT


title: Huh7 cells, YFVC 2

city: New York

first: Diego

last: Mourão

state: NY

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
ATAC-seq reads were aligned to the hg19 genome from the Bsgenome.Hsapiens.UCSC.hg19 Bioconductor package (version 1.4.0) using Rsubread's align method in paired-end mode with fragments between 1 to 5000 base-pairs considered properly paired
Normalized, fragment signal bigWigs were created using the rtracklayer package. Peak calls were made with MACS2 software in BAMPE mode
Genome_build: Bsgenome.Hsapiens.UCSC.hg19
Supplementary_files_format_and_content: BigWig

source_name: Huh7 cells

growth_protocol: Huh-7 cells, Huh-7 YFV-C and Huh-7 YFV-C K4RK8R cells were grown at 37˚C and 5% CO2

extract_protocol:
cells were lysed in ATAC lysis buffer for 5 min and then transposed with TN5 transposase (Illumina) for 30 min
Samples were barcoded and the sequencing library was prepared according to manufacturer’s guidelines (Illumina) and sequenced on an Illumina HiSeq 2500

treatment_protocol: 48 hours with 10ug/ml doxycycline.

tag: cell line

value: Human hepatoma cell line Huh7

value: 10µg/ml of doxycycline for 48h to induce  YFV capsid protein


title: Huh7 cells, YFVC 3


title: WT EBs rep3 [WT_EB_3]


title: Tnfaip2-/- EBs rep3 [KO_EB_3]


title: Huh7 cells, YFVC 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D6_AD001

value: male


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D6_AD004


title: Tnfaip2-/- EBs rep2 [KO_EB_2]


title: 708_PLX5622_TBI_30d

value: injured (TBI)

value: Cortex


title: 709_PLX5622_TBI_7d


title: 707_Vehicle_TBI_30d


title: 706_Vehicle_Control


title: IM24h: DE40NGSUKBR106056


title: WT EBs rep2 [WT_EB_2]


title: Huh7 cells, YFVC mutant 3

value: 10µg/ml of doxycycline for 48h to induce mutant YFV capsid protein


title: Tnfaip2-/- EBs rep1 [KO_EB_1]


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D5_AD012


title: Tnfaip2-/- EBs rep3

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2fastq v1.8.4.
The raw reads were quality-trimmed and filtered for low complexity with the tool preprocess from the SGA assembler v0.10.13 (-q 30 -m 50 --dust)
The passed reads were mapped to the mouse reference genome (GRCm38) with the Ensembl gene annotation (release90) with TopHat2 v2.1.0.
All reads mapping uniquely to an Ensembl gene were counted using FeatureCounts v1.5.0 (Liao et al., 2014).
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file containing read counts per gene over all samples

treatment_protocol: 50000 ES cells were re-suspended in ES cell medium and rows of 30μl drops (300 cells per drop) on the up-turned inner surface of the lid of the 10cm tissue culture dish were made and incubated at 37°C for 3 days to form EBs. The EBs (at day 0) were plated onto 0.1% gelatin coated tissue culture dishes to initiate in vitro differentiation by incubating for another 3 days at 37°C MEF medium containing 15% KnockOut™ D-MEM supplemented with Knockout Serum Replacement, L-glutamine, penicillin/streptomycin, nonessential amino acids . After 3 days of in vitro differentiation the EBs were harvested.

tag: shape

value: spherical

tag: genotype/variation


title: Huh7 cells, YFVC mutant 2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D5_AD010

tag: strain

value: brain


title: 704_Vehicle_TBI_1d


title: Huh7 cells, control 3

value: 10µg/ml of doxycycline for 48h to induce HA-Flag fusion protein


title: Tnfaip2-/- EBs rep2


title: 703_PLX5622_TBI_1d


title: Huh7 cells, YFVC mutant 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D5_AD007

tag: age

value: SSp

value: SC


title: WT EBs rep3

value: wild type


title: 705_PLX5622_Control


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D5_AD006

tag: source

value: MOp


title: Huh7 cells, control 2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D5_AD002

tag: target


title: 702_Vehicle_TBI_7d

value: Vehicle


title: Huh7 cells, control 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D5_AD004

tag: gender


title: WT EBs rep1


title: 700_PLX5622_TBI_30d

tag: tissue


title: Tnfaip2-/- EBs rep1


title: Late_patient3

description:
surgery samples of patients at late timepoint of a pancreatectomy
3b_DE17NGSUKBR110350_S146_R1_001

data_processing:
Partek pipline from Illumina
https://www.lexogen.com/quantseq-umi-pipeline-is-now-available-on-partek-flow/
genome build: hg19
Supplementary_files_format_and_content: Excel, gene counts of all samples

source_name: small intestine

extract_protocol:
RNA isolation with Trizol
QuantSeq 3’ mRNA-Seq Library Prep Kit

treatment_protocol: Collection on ice and directly freezing in liquid nitrogen.

value: small intestine

tag: surgery

value: pancreaticoduodenectomy

tag: time point

value: late time


title: 698_PLX5622_Control

tag: Sex

tag: mouse group

value: control (naive)

tag: treatment


title: 701_PLX5622_TBI_7d

tag: nanostring cartridge

tag: rna extraction batch


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D5_AD001


title: WT EBs rep2

tag: cell type

value: embryonic stem cells


title: 697_Vehicle_TBI_1d

value: male


title: 696_PLX5622_TBI_1d

value: injured (TBI)


title: Early_patient3

description:
surgery samples of patients at early timepoint of a pancreatectomy
3a_DE44NGSUKBR110349_S145_R1_001

value: early


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D4_AD012

value: female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D4_AD010


title: Late_patient2

description:
surgery samples of patients at late timepoint of a pancreatectomy
2b_DE71NGSUKBR110348_S144_R1_001


title: 695_Vehicle_Control_7d

value: Cortex


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D4_AD008

value: brain


title: GFP+ sorted cells - bulk RNAseq 6

first: Dieter

last: Egli

state: New York

address: 701 West 168th Street

institute: Columbia University

description:
Differentiation day 24. Experiment number A79. Genotype HNF1A Het
hESC-HNF1A-HET (A79)-DB004
processed data file: DB004_genes.csv

data_processing:
Bulk RNA-seq: the reads were mapped to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.  The relative abundance (aka expression level) of genes and splice isoforms is estimated using cufflinks6 (version 2.0.2) with default settings.
Single Cell RNA-seq: the raw fastq files was processed via 10X Cell Ranger pipeline (cellranger-2.1.1). To note that GRCh38 reference genome was applied for the whole analysis. “cellranger count” with “--expect-cells=3000” was run for each library respectively and “cellranger aggr” with default parameters was run to aggregate results generated from multiple libraries. A normalized umi-count matrix for all the cells was then generated.  As for the quality control, cell and gene filtering process, cells with umi-count<5000 and umi-count>40000 and cells with <2000 detected genes were removed. Also, genes with <~1% (25) non-zero counts across all the cells were eliminated from the analysis. To get rid of the Mitochondria cells, cells with more than 10% Mitochondria genes’ count were also removed.
Genome_build: GRCh38 for single cell RNA-seq, GRCh37 for bulk RNA-seq
Supplementary_files_format_and_content: .csv files are the processed raw count files with label information.

source_name: Endocrine cells

growth_protocol: The initial stages of differentiation were conducted in planar culture (d0-d11). For definitive endoderm stage (d1-d3) cells were cultured using STEMdiffTM Definitive Endoderm Differentiation Kit (Stemcell Technologies, 05110). For primitive gut stage (d4-d6), cells were cultured in RPMI containing GlutaMAX (Life Technology, 61870-127), 1% (v/v) Penicillin-Streptomycin (PS) (Thermo Fisher Scientific, 15070-063), 1% (v/v) B27 Serum-Free Supplement (50x) (Life Technology, 17504044) and 50 ng/ml FGF7 (R&D System, 251-KG). For posterior foregut stage (d7-d8), cells were cultured in DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27, 0.25 μM KAAD-Cyclopamine (Stemgent, 04-0028), 2 μM Retinoic acid (Stemgent, 04-0021) and 0.25 μM LDN193189 (Stemgent, 04-0074). For pancreatic progenitor stage (d9-d11), cells were cultured in DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27 and 50 ng/ml EGF (R&D System, 236-EG). Cells were then dissociated using TrypLE™ Express (Life Technology, 12605036) and seeded into low-attachment 96 well-plates (Corning, 7007) (1 well of 6 well-plate to 60 wells of 96-well-plate) for clustering step to form aggregates or clusters of endocrine cells in DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27, 0.25 μM Cyclopamine, 1 μM thyroid hormone (T3) (Sigma, T6397), 10 μM Alk5i, 10 μM Zinc sulfate (Sigma-Aldrich, Z4750) and 10 μg/ml Heparin (Sigma-Aldrich, H3149) for 2 days (d12-d13). For pancreatic endocrine stage (d14-20) cells were cultured using DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27, 100 nM LDN, 1 μM T3, 10 μM Alk5i, 10 μM Zinc sulfate, 10 μg/ml Heparin and 100 nM gamma-secretase inhibitor (DBZ) (EMD Millipore, 565789). For mature pancreatic endocrine stage (d21-d27) cells were cultured using DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27, 1 μM T3, 10 μM Alk5i, 10 μM Zinc sulfate, 10 μg/ml Heparin, 1 mM N-acetyl cysteine (N-Cys) (Sigma-Aldrich, A9165-5G), 10 μM Trolox (EMD Millipore, 648471-500MG) and 2 μM R428 (Tyrosine kinase receptor AXL inhibitor) (ApexBio, A8329). From d1 to d11 media was changed every day and from d12 to d27 media was changed every other day. All differentiations were done for 27 to 30 days.

extract_protocol:
Single Cell RNA-seq: around 100 clusters of cells per genotype at day 27 of differentiation are dissociated. Single cells were suspended in PBS+0.04% BSA. Cellular suspensions (~6,000 cells) were loaded on a Chromium Single Cell Instrument (10X Genomics) to generate single cell GEMs. Single-cell RNAseq libraries were prepared using Chromium Single cell 3¢ Library, Gel beads & Mutiplex kit (10X Genomics). Sequencing was performed on Illumina NextSeq500 using the following read length: 59-bp Read1 for transcript read, 14-bp I7 Index for Cell Barcode read, 8-bp I5 Index for sample index read, and 10-bp Read2 for UMI read. The samples were sequenced in ten different libraries (batches). Among all these samples, Batch 980379 and Batch 993091 (2 libraries) are HNF1A mutants (R200Q), Batch 980380 and Batch 993090 (2 libraries) are HNF1A knockouts (KO) while Batch 989516 and Batch 993089 (2 libraries) are HNF1A wildtype cells (WT).
Bulk RNA-seq: around 200 clusters of cells are dissociated and sorted for GFP using BD FACS Aria II cell sorter. Sorted cells are pelleted by centrifugation and RNA extracted using total the RNA purification micro (Norgen Biotek, 35300) kit according to the manufactures protocol. RNA quality and concentration is determined by an Agilent bioanalyzer and RNAseq performed by the Columbia University Genome Center. A poly-A pull-down was used to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using an Illumina HiSeq2000.  RTA (Illumina) was used for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming.

treatment_protocol: Cells are untreated

value: ES-derived endocrine cells

tag: passages

tag: chip antibody

tag: differentiation day

value: HNF1A Het


title: YFVC 1

data_processing:
Transcript expressions were calculated using the Salmon quantification software (version 0.8.2)
gene expression levels as TPMs and counts retrieved using Tximport (version 1.8.0)
Normalization and rlog transformation of raw read counts in genes were performed using DESeq2 (version 1.20.0) and between sample variability assessed with hierarchical clustering and heat maps of between sample distances implemented in the Pheatmap R package (1.0.10)
RNA-seq reads are aligned to the genome using Rsubread's subjunc method (version 1.30.6) and exported as bigWigs normalised to total mapped reads using the rtracklayer package (version 1.40.6)
Genome_build: Bsgenome.Hsapiens.UCSC.hg19
Supplementary_files_format_and_content: Bigwig files

source_name: Huh-7 YFV-C cells

extract_protocol:
Total RNA was extracted using Qiagen mini Rneasy protocol
RNA was analyzed on the Agilent 2100 Bioanalyzer and all samples had RNA integrity number higher than 8.0. 100 ng of total RNA was used to generate RNA-Seq libraries using Illumina TruSeq stranded mRNA LT kit (Cat#RS-122-2101).  Libraries prepared with unique barcodes were pooled at equal molar ratios.  The pool was denatured and sequenced on Illumina NextSeq 500 sequencer using high output V2 reagents and NextSeq Control Software v1.4 to generate 75 bp single reads, following manufactures protocol (Cat# 15048776 Rev.E).

treatment_protocol: 10µg/ml of doxycycline for 48h to induce  YFV capsid protein

tag: cell line

value: Human hepatoma

tag: induced expression

value: YFV capsid protein


title: YFVC 2


title: YFVC 3


title: Late_patient1

description:
surgery samples of patients at late timepoint of a pancreatectomy
1b_DE28NGSUKBR110346_S142_R1_001


title: YFVC mutant 3

source_name: Huh-7 YFV-C K4RK8R cells

treatment_protocol: 10µg/ml of doxycycline for 48h to induce mutant YFV capsid protein

value: mutant YFV capsid protein


title: 694_PLX5622_TBI_7d

tag: strain


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D4_AD007

tag: age

tag: source

value: SSp

tag: target

value: SC


title: YFVC mutant 2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D4_AD004

tag: tissue

value: MOp

tag: gender


title: Early_patient1

description:
surgery samples of patients at early timepoint of a pancreatectomy
1a_DE55NGSUKBR110345_S141_R1_001

value: small intestine

tag: surgery

value: pancreaticoduodenectomy

tag: time point


title: Early_patient2

description:
surgery samples of patients at early timepoint of a pancreatectomy
2a_DE98NGSUKBR110347_S143_R1_001


title: ALR_456_B

city: Toronto

first: Aaron

last: Schimmer

state: ON

address: 610 University avenue

country: Canada

institute: University Health Network

data_processing:
Reads adapters were removed using Trim Galore v. 0.4.0 and reads were aligned against hg19 using Tophat v. 2.0.11. Read counts per gene were obtained through htseq-count v.0.6.1p2 in the mode “intersection_nonempty”.
After removing genes whose cpm (counts per million reads) were less than 0.5, edgeR R package v.3.8.6 was used to normalize the data using the TMM (trimmed mean of M values) method and to estimate differential expression by applying a generalized linear model between the control TEX samples and the TEX cells isolated after MTCH2 knockdown.
Raw gene counts are loaded and sample-normalized using DESeq v.1.18.0
False Discovery Rate, calculated by Benjamini-Hochberg method (useful for hits selection)
Two-condition differential expression was done with the edgeR R package, v.3.8.6
Genome_build: hg19 (RefSeq gene models)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Patient derived cell line

growth_protocol: OCI-AML2 leukemic cell lines were cultured in Iscove’s modified Dulbecco’s medium (IMDM) containing 10% fetal calf serum (FCS), 100 units/mL streptomycin and 100 µg/mL penicillin

extract_protocol:
RNeasy Plus Mini Kit. Quality of total RNA samples were checked on an Agilent Bioanalyzer 2100 RNA Nano chip following Agilent Technologies’ recommendation. Concentration was measured by Qubit RNA HS Assay ona Qubit fluorometer (ThermoFisher)
RNA library preparation was performed following the NEB NEBNext Ultra Directional Library Preparation protocol

treatment_protocol: shRNA knockdown was performed with lentiviral infections. 2 mL of virus was added to 5 mL of media containing 5.0 x 106 cells and protamine sulfate (5 µg/mL) followed by overnight incubation (37C, 5% CO2). The following day, cells were centrifuged and washed, and re-suspended in 25 mL fresh medium with appropriate puromycin concentration (2.0 ug/ml) and subjected to selection for 3 days.

value: OCI-AML2 cell line

tag: genetic modification

value: ALR shRNA


title: 693_PLX5622_TBI_1d

tag: Sex

value: male

tag: mouse group

value: injured (TBI)

tag: treatment

tag: nanostring cartridge


title: ALR_456_A


title: ALR_325_B


title: 691_Vehicle_Control

value: control (naive)

value: Vehicle

tag: rna extraction batch


title: 690_PLX5622_Control

value: Cortex


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D4_AD002

value: brain


title: YFVC mutant 1

tag: cell type


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D4_AD001


title: control 3

treatment_protocol: 10µg/ml of doxycycline for 48h to induce HA-Flag fusion protein

tag: cell line

value: HA-Flag fusion protein


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D3_AD012

value: female


title: control 2

value: Human hepatoma

tag: induced expression


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D4_AD006

tag: strain


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D3_AD010

tag: age


title: ALR_GFP_B

value: Scrambled shRNA


title: control 1


title: 686_Vehicle_TBI_7d


title: 687_PLX5622_TBI_7d


title: 688_PLX5622_TBI_1d


title: Spleen_1_06

status: Public on Nov 14 2020

city: Austin

first: Anna

last: Battenhouse

state: TX

address: 100 East 24th St., Stop A5000

department: Center for Biomedical Research Support

institute: The University of Texas at Austin

data_processing:
Quality control was performed on the sequencing fastq files using FastQC (ver. 0.11.9, Babraham Bioinformatics).
Paired-end pseudo alignment was performed using kallisto (ver. 0.45.0) with the -rf-stranded option, against the mouse transcriptome (GENCODE M24 transcript sequences).
Downstream analysis of kallisto estimated counts was performed in R (ver. 3.4.4).
The tximport package was used to roll up transcript-level counts into gene-level counts provided to the DESeq2 package (ver. 1.18.1).
Before DESeq2 analysis, count data matrices were filtered to remove genes with fewer than 1 read across all included samples.
Genome_build: GENCODE M24 transcriptome (transcript sequences and main gene annotation set)
Supplementary_files_format_and_content: Tab-delimited transcript_abundance.tsv text files provide kallisto per-transcript estimated counts and transcripts per million values for each sample.

source_name: Spleen

growth_protocol: C57BL/6N Dusp11tm1a(EUCOMM)Wtsi mice were generated by IVF using frozen sperm (EM: 09991) obtained from the European Mouse Mutant Archive and maintained on the C57BL/6N.  (Taconic) background. Age/sex-matched C57BL/6N wild-type and homozygote Dusp11 tm1a/tm1a mice were used experiments.

extract_protocol:
Total RNA from mouse tissue samples were extracted using TRIzol reagent. Snap frozen tissue samples were thawed and homogenized in the lysing matrix tubes containing TRIzol prior to RNA extraction.
mRNAs were isolated using oligo(dT)-attached magnetic beads, fragmented and reverse-transcribed for cDNA synthesis. Adapter-ligated cDNA fragments were PCR amplified and libraries were validated using the Agilent 2100 Bioanalyzer. Qualified double-stranded PCR products were then circularized to produce the final single strand circle DNA library. Libraries were amplified with phi29 to generate DNA nanoballs and were loaded onto BGISEQ-500 DNBseq platform (BGI) flow cells for 100 bp paired end sequencing.

treatment_protocol: Mice were either treated with in vitro transcribed VSV 5’-triphosphate PAMP RNA, complexed with in vivo-JetPEI (PolyPlus) using an N/P (nitrogen/phosphate) ratio of 8, or mock-treated with RNA lacking immunostimulatory activity complexed with in vivo-JetPEI (mock-treated), or not treated at all (untreated).

value: spleen

tag: genotype

value: DUSP11 tm1a/tm1a

value: mock-treated

tag: age (months)


title: Spleen_1_05

tag: tissue


title: ALR_GFP_A


title: Spleen_1_03

value: wild-type


title: Spleen_1_04


title: Spleen_1_02


title: Liver_3_05

source_name: Liver

value: liver

value: untreated


title: 685_PLX5622_TBI_30d


title: 684_Vehice_TBI_30d

value: Vehice


title: Spleen_1_01


title: Liver_3_06

value: male


title: Liver_3_03


title: Liver_3_02


title: Liver_3_01


title: Liver_3_04


title: Liver_2_11

value: 5'-ppp RNA-stimulated


title: Liver_2_12


title: Liver_2_10


title: Liver_2_09


title: Liver_2_08


title: Liver_2_07


title: Liver_2_04


title: Liver_2_06


title: Liver_2_05


title: Liver_2_01


title: Liver_1_06


title: Liver_1_05


title: Liver_1_04


title: Liver_1_02


title: ALR_325_A

value: OCI-AML2 cell line

value: ALR shRNA