title: LU_m365


title: LU_m366

status: Public on Jan 08 2024

type: SRA

city: Chicago

first: Michihiro

last: Takahama

state: Illinois

department: Pritzker School of Molecular Engineering

country: USA

institute: University of Chicago

library_source: transcriptomic

data_processing:
We used the RNA-seq pipeline in the bcbio-nextgen project version 1.1.5 (https://bcbio-nextgen.readthedocs.io/en/latest/).
Reads were aligned to the mouse mm10 transcriptomes with RapMap.
Transcripts were counted with fasttagcount in umis (https://github.com/vals/umis).
Quality control metrics were compiled with a combination of FastQC (http:bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (https://github.com/ewels/MultiQC).
Assembly: mm10
Supplementary files format and content: 1_counts_LPS_timecourse.txt: counts matrix from experiment1
Supplementary files format and content: 2_counts_CLP_timecourse.txt: counts matrix from experiment2
Supplementary files format and content: 3_counts_Cytokine_combo.txt: counts matrix from experiment3
Supplementary files format and content: 4_counts_Cytokine_combo2.txt: counts matrix from experiment4
Supplementary files format and content: 5_counts_LPS_LPA.txt: counts matrix from experiment5
Supplementary files format and content: 6_counts_LPS_antiPla2g5: counts matrix from experiment6
Supplementary files format and content: 7_counts_LPS_Plasma.txt: counts matrix from experiment7
Supplementary files format and content: 8_counts_LPS_DEX.txt: counts matrix from experiment8
Supplementary files format and content: 9_counts_LPS_KO.txt: counts matrix from experiment9
Supplementary files format and content: 10_counts_LPS_KO2.txt: counts matrix from experiment10
Supplementary files format and content: 11_counts_CLP_timecourse2.txt: counts matrix from experiment11
Supplementary files format and content: 12_counts_CLP_CytoBlock.txt: counts matrix from experiment12
Supplementary files format and content: 13_counts_CLP_CytoBlock2.txt: counts matrix from experiment13
Supplementary files format and content: 14_counts_CLP_antiTNF.txt: counts matrix from experiment14

molecule: polyA RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
Whole-tissue RNA extraction was performed as described previously (Surya et al., 2020). Briefly, tissues stored in RNA-preserving solution were thawed and transferred to 2 mL tubes containing 700-1500 µL (depending on tissue) of PureZOL (Bio-Rad, 7326890) or homemade Trizol-like solution (38% phenol, 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate, 5% glycerol). Tissues were lysed by adding 2.8-mm ceramic beads (OMNI International, 19-646) and running 1-3 cycles of 5-45 s at 3500 rpm on the PowerLyzer 24 (QIAGEN). For liver, brain, and small intestine samples, tissues were lysed with 3-5 mL using M tubes (Miltenyi biotec, 130-096-335) and running 1-4 cycles of the RNA_02.01 program on the gentleMACS Octo Dissociator (Miltenyi biotec). Next, lysates were processed in deep 96-well plates (USA Scientific 1896-2000) by adding chloroform for phase separation by centrifugation, followed by precipitation of total RNA in the aqueous phase using magnetic beads coated with silane (Dynabeads MyOne Silane; TermoFisher Scientific 37002D), buffer RLT (QIAGEN 79216), and ethanol. Genomic DNA contamination was removed by on-bead DNase I (ThermoFisher Scientific AM2239) treatment at 37 °C for 20 min. After washing steps with 80% ethanol, RNA was eluted from beads. This RNA extraction protocol was performed on the Bravo Automated Liquid Handling Platform (Agilent). Sample concentrations were measured using a Nanodrop One (Termo Scientific). RNA quality was confirmed using a Tapestation 4200 (Agilent Technologies).
For each tissue sample, full-length cDNA was synthesized in 20 µl final reaction volume containing the following: (1) 10 µl of 10 ng/µl RNA; (2) 1 µl containing 2 pmoles of a custom RT primer biotinylated in 5’ and containing sequences from 5’ to 3’ for the Illumina read 1 primer, a 6-bp sample barcode (up to 384), a 10-bp unique molecular identifier (UMI), and an anchored oligo(dT)30 for priming; and (3) 9 µl of RT mix containing 4 µl of 5X RT buffer, 1 µl of 10 mM dNTPs, 2 pmoles of template switching oligo (TSO), and 0.25 µl of Maxima H Minus Reverse Trascriptase (Thermo Scientific, EP0753). First, barcoded RT primers were added to RNA, which were then denatured at 72°C for 1 min and snap cooled on ice. Second, the RT mix was added, and plates were incubated at 42°C for 120 min. For each library, double stranded cDNA from up to 384 samples were pooled using DNA Clean & Concentrator-5 columns (Zymo Research, D4013), and residual RT primers were removed using exonuclease I (New England Biolabs, M0293). Full-length cDNAs were amplified with 5 to 8 cycles of single-primer PCR using the Advantage 2 PCR Kit (clontech 639206) and cleaned up using SPRIselect magnetic beads (Beckman Coulter B23318). cDNA was quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific 32851) and 50 ng of cDNA per pool of samples was tagmented using the Tagment DNA Enzyme I (Illumina 20034197) and amplified using the NEBNext Ultra II Q5 Master Mix (NEW ENGLAND BioLabs M0544L). Libraries were gel purified using 2% E-Gel EX Agarose Gels (ThermoFisher Scientific G402002), quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific Q32851) and a Tapestation 4200 (Agilent Technologies), and sequenced on the NextSeq 550 platform (Illumina).

tag: tissue

value: Lung

tag: genotype

value: Wild type

tag: treatment


title: SP_m361

source_name: Spleen

value: Spleen


title: LU_m364


title: LU_m363


title: SP_m20

description:
experiment1
counts_LPS_timecourse.txt

data_processing:
We used the RNA-seq pipeline in the bcbio-nextgen project version 1.1.5 (https://bcbio-nextgen.readthedocs.io/en/latest/).
Reads were aligned to the mouse mm10 transcriptomes with RapMap.
Transcripts were counted with fasttagcount in umis (https://github.com/vals/umis).
Quality control metrics were compiled with a combination of FastQC (http:bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (https://github.com/ewels/MultiQC).
Assembly: mm10
Supplementary files format and content: counts_LPS_timecourse.txt: counts matrix from experiment1
Supplementary files format and content: counts_CLP.txt: counts matrix from experiment2
Supplementary files format and content: counts_Cytokine_combo.txt: counts matrix from experiment3
Supplementary files format and content: counts_Cytokine_combo2.txt: counts matrix from experiment4
Supplementary files format and content: counts_LPS_LPA.txt: counts matrix from experiment5
Supplementary files format and content: counts_LPS_antiPla2g5.txt: counts matrix from experiment6
Supplementary files format and content: counts_LPS_Plasma.txt: counts matrix from experiment7
Supplementary files format and content: counts_LPS_DEX.txt: counts matrix from experiment8
Supplementary files format and content: counts_LPS_KO.txt: counts matrix from experiment9
Supplementary files format and content: counts_LPS_KO2.txt: counts matrix from experiment10


title: TH_m4

description:
experiment1
counts_LPS_timecourse.txt

source_name: Thymus

value: Thymus


title: SP_m19

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m2

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m362


title: TH_m1

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m18

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m361


title: SP_m17

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m16

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m359

value: TNF KO


title: LU_m360


title: SP_m15

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m358


title: LU_m357


title: SP_m13

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m356


title: SP_m12

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m369

source_name: Liver

value: Liver


title: SP_m11

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m10

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m368


title: SP_m9

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m8

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m6

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m21

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m7

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m5

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m3

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m2

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m14

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m4

description:
experiment1
counts_LPS_timecourse.txt


title: SK_m27

description:
experiment1
counts_LPS_timecourse.txt

source_name: Skin

value: Skin


title: SK_m26

description:
experiment1
counts_LPS_timecourse.txt


title: SK_m25

description:
experiment1
counts_LPS_timecourse.txt


title: SK_m24

description:
experiment1
counts_LPS_timecourse.txt


title: SK_m22

description:
experiment1
counts_LPS_timecourse.txt


title: SK_m23

description:
experiment1
counts_LPS_timecourse.txt


title: SK_m21

description:
experiment1
counts_LPS_timecourse.txt


title: SK_m28

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m364


title: LI_m359


title: LI_m361


title: LI_m358


title: KI_m366

source_name: Kidney

value: Kidney


title: LI_m366


title: KI_m365


title: KI_m364


title: LI_m356


title: KI_m369


title: KI_m367


title: LI_m360


title: LI_m357


title: KI_m368


title: KI_m363


title: LI_m367


title: LI_m365


title: SK_m19

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m362


title: LI_m363


title: KI_m362


title: SK_m18

description:
experiment1
counts_LPS_timecourse.txt


title: SK_m17

description:
experiment1
counts_LPS_timecourse.txt


title: SK_m16

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m360


title: KI_m359


title: SK_m15

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m368

source_name: Inguinal lymph node

value: Inguinal lymph node


title: iLN_m369


title: SK_m6

description:
experiment1
counts_LPS_timecourse.txt


title: SK_m8

description:
experiment1
counts_LPS_timecourse.txt


title: SK_m7

description:
experiment1
counts_LPS_timecourse.txt


title: SK_m5

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m358


title: KI_m357


title: KI_m356


title: SK_m12

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m367


title: SK_m10

description:
experiment1
counts_LPS_timecourse.txt


title: SK_m13

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m365


title: iLN_m363


title: iLN_m364


title: SK_m11

description:
experiment1
counts_LPS_timecourse.txt


title: SK_m4

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m362


title: SK_m14

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m361


title: KI_m361


title: SK_m3

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m360


title: SK_m2

description:
experiment1
counts_LPS_timecourse.txt


title: SK_m9

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m366


title: iLN_m359


title: iLN_m358


title: SI_m27

description:
experiment1
counts_LPS_timecourse.txt

source_name: Small intestine

value: Small intestine


title: HE_m368

source_name: Heart

value: Heart


title: HE_m369


title: SK_m20

description:
experiment1
counts_LPS_timecourse.txt


title: SI_m28

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m357


title: iLN_m356


title: SI_m25

description:
experiment1
counts_LPS_timecourse.txt


title: SI_m24

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m363


title: SI_m23

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m367


title: HE_m362


title: HE_m366


title: SI_m22

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m365


title: SI_m17

description:
experiment1
counts_LPS_timecourse.txt


title: SI_m21

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m360


title: SK_m1

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m364


title: SI_m20

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m359


title: SI_m19

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m357


title: SI_m14

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m361


title: SI_m18

description:
experiment1
counts_LPS_timecourse.txt


title: SI_m12

description:
experiment1
counts_LPS_timecourse.txt


title: SI_m16

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m368

source_name: Bone marrow

value: Bone marrow


title: BM_m367


title: HE_m358


title: BM_m366


title: SI_m13

description:
experiment1
counts_LPS_timecourse.txt


title: SI_m9

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m356


title: BM_m365


title: SI_m7

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m369


title: SI_m11

description:
experiment1
counts_LPS_timecourse.txt


title: SI_m15

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m362


title: SI_m2

description:
experiment1
counts_LPS_timecourse.txt


title: SI_m10

description:
experiment1
counts_LPS_timecourse.txt


title: SI_m3

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m360


title: BM_m358


title: BM_m363


title: SI_m6

description:
experiment1
counts_LPS_timecourse.txt


title: SI_m8

description:
experiment1
counts_LPS_timecourse.txt


title: PBMC_m28

description:
experiment1
counts_LPS_timecourse.txt

source_name: PBMC

value: PBMC


title: BM_m364


title: PBMC_m27

description:
experiment1
counts_LPS_timecourse.txt


title: SI_m26

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m353


title: SI_m5

description:
experiment1
counts_LPS_timecourse.txt


title: SI_m4

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m361


title: TH_m351

value: IL1b KO


title: SI_m1

description:
experiment1
counts_LPS_timecourse.txt


title: PBMC_m18

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m356


title: PBMC_m25

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m355


title: TH_m352


title: PBMC_m23

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m348


title: TH_m349


title: PBMC_m11

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m352


title: PBMC_m21

description:
experiment1
counts_LPS_timecourse.txt


title: PBMC_m17

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m350


title: PBMC_m15

description:
experiment1
counts_LPS_timecourse.txt


title: PBMC_m7

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m359


title: PBMC_m16

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m357


title: SP_m349


title: PBMC_m13

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m353


title: SP_m355


title: PBMC_m8

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m348


title: PBMC_m4

description:
experiment1
counts_LPS_timecourse.txt


title: PBMC_m12

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m353


title: LU_m355


title: LU_m352


title: LU_m351


title: PBMC_m6

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m351


title: SP_m1

description:
experiment1
counts_LPS_timecourse.txt


title: PBMC_m1

description:
experiment1
counts_LPS_timecourse.txt


title: PBMC_m2

description:
experiment1
counts_LPS_timecourse.txt


title: PBMC_m3

description:
experiment1
counts_LPS_timecourse.txt


title: PBMC_m9

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m350


title: LU_m349


title: LU_m28

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m27

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m25

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m350


title: LU_m23

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m355


title: LI_m353


title: LU_m26

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m22

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m21

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m351


title: LU_m20

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m19

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m349


title: LI_m350


title: LU_m17

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m348


title: KI_m353


title: LU_m348


title: KI_m352


title: LU_m15

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m355


title: KI_m349


title: KI_m350


title: LU_m14

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m10

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m352


title: LU_m8

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m9

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m13

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m352


title: LU_m6

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m18

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m351


title: LU_m5

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m349


title: LU_m7

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m348


title: LU_m4

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m3

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m11

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m348


title: HE_m352


title: LU_m2

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m16

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m1

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m350


title: iLN_m353


title: HE_m355


title: HE_m353


title: LI_m28

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m355


title: LI_m25

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m348


title: HE_m351


title: LI_m27

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m26

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m355


title: LI_m23

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m24

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m350


title: LI_m22

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m21

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m349


title: LI_m19

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m353


title: BM_m352


title: LI_m15

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m20

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m14

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m350


title: BM_m349


title: BM_m348


title: TH_m347

value: IL18 KO


title: TH_m344


title: TH_m345


title: LI_m10

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m342

value: IFNg KO


title: LU_m12

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m12

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m13

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m343


title: TH_m341


title: TH_m339


title: LI_m7

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m346


title: TH_m340


title: TH_m338


title: LI_m18

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m351


title: TH_m337


title: LI_m5

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m4

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m6

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m17

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m336


title: LI_m11

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m335


title: SP_m347


title: LI_m3

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m9

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m8

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m342


title: KI_m27

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m345


title: SP_m344


title: SP_m346


title: LI_m2

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m1

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m28

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m343


title: KI_m22

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m338


title: KI_m24

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m340


title: SP_m341


title: SP_m339


title: KI_m21

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m335


title: SP_m336


title: KI_m20

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m19

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m18

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m337


title: KI_m17

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m26

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m25

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m346


title: LU_m344


title: KI_m13

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m343


title: LU_m345


title: KI_m14

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m342


title: KI_m12

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m10

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m16

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m339


title: LU_m338


title: KI_m11

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m7

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m8

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m337


title: KI_m351


title: LU_m335


title: KI_m6

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m347


title: KI_m5

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m341


title: LI_m347


title: KI_m23

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m336


title: KI_m4

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m15

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m346


title: LU_m340


title: KI_m3

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m9

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m345


title: LI_m343


title: KI_m2

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m342


title: LI_m344


title: KI_m1

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m28

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m27

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m25

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m26

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m24

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m339


title: LI_m341


title: LI_m340


title: LI_m337


title: iLN_m22

description:
experiment1
counts_LPS_timecourse.txt


title: LI_m338


title: iLN_m21

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m23

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m347


title: LI_m335


title: LI_m336


title: iLN_m17

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m18

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m345


title: KI_m346


title: iLN_m16

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m15

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m344


title: KI_m343


title: iLN_m14

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m342


title: iLN_m13

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m340


title: iLN_m10

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m339


title: KI_m335


title: KI_m338


title: iLN_m7

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m341


title: iLN_m9

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m6

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m337


title: iLN_m346


title: iLN_m11

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m4

description:
experiment1
counts_LPS_timecourse.txt


title: KI_m336


title: iLN_m19

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m8

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m347


title: iLN_m5

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m3

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m2

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m12

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m343


title: HE_m28

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m1

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m342


title: iLN_m344


title: iLN_m341


title: iLN_m345


title: HE_m27

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m26

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m339


title: HE_m24

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m338


title: iLN_m336


title: HE_m25

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m337


title: HE_m23

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m22

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m335


title: HE_m21

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m346


title: HE_m347


title: HE_m344


title: HE_m20

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m345


title: HE_m18

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m343


title: HE_m19

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m17

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m341


title: HE_m16

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m339


title: HE_m14

description:
experiment1
counts_LPS_timecourse.txt


title: iLN_m340


title: HE_m12

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m338


title: HE_m342


title: HE_m13

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m340


title: HE_m10

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m337


title: HE_m11

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m347


title: HE_m8

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m7

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m346


title: HE_m15

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m6

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m9

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m345


title: HE_m335


title: HE_m5

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m344


title: HE_m4

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m342


title: BM_m343


title: HE_m3

description:
experiment1
counts_LPS_timecourse.txt


title: HE_m2

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m341


title: HE_m1

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m339


title: BM_m340


title: CO_m28

description:
experiment1
counts_LPS_timecourse.txt

source_name: Colon

value: Colon


title: CO_m26

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m338


title: HE_m336


title: CO_m25

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m334


title: BM_m337


title: BM_m335


title: CO_m27

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m331


title: TH_m333


title: CO_m21

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m332


title: CO_m22

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m330


title: BM_m336


title: CO_m20

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m329


title: CO_m16

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m328


title: CO_m17

description:
experiment1
counts_LPS_timecourse.txt


title: CO_m18

description:
experiment1
counts_LPS_timecourse.txt


title: CO_m15

description:
experiment1
counts_LPS_timecourse.txt


title: CO_m14

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m325


title: CO_m23

description:
experiment1
counts_LPS_timecourse.txt


title: CO_m13

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m326


title: CO_m24

description:
experiment1
counts_LPS_timecourse.txt


title: CO_m19

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m324


title: TH_m323


title: CO_m11

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m321


title: CO_m7

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m327


title: CO_m9

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m320


title: TH_m317


title: TH_m319


title: TH_m318


title: CO_m6

description:
experiment1
counts_LPS_timecourse.txt


title: CO_m5

description:
experiment1
counts_LPS_timecourse.txt


title: CO_m3

description:
experiment1
counts_LPS_timecourse.txt


title: CO_m4

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m314


title: TH_m312


title: TH_m316


title: BR_m28

description:
experiment1
counts_LPS_timecourse.txt

source_name: Brain

value: Brain


title: CO_m1

description:
experiment1
counts_LPS_timecourse.txt

value: Wild type


title: CO_m2

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m311


title: CO_m10

description:
experiment1
counts_LPS_timecourse.txt


title: CO_m12

description:
experiment1
counts_LPS_timecourse.txt


title: BR_m25

description:
experiment1
counts_LPS_timecourse.txt


title: BR_m24

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m313


title: TH_m322


title: TH_m309


title: BR_m26

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m308


title: TH_m310


title: BR_m27

description:
experiment1
counts_LPS_timecourse.txt


title: BR_m23

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m315


title: TH_m307


title: BR_m21

description:
experiment1
counts_LPS_timecourse.txt


title: BR_m20

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m303


title: BR_m19

description:
experiment1
counts_LPS_timecourse.txt


title: BR_m18

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m301


title: BR_m16

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m302


title: BR_m15

description:
experiment1
counts_LPS_timecourse.txt


title: BR_m17

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m299


title: TH_m300


title: BR_m12

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m296


title: BR_m14

description:
experiment1
counts_LPS_timecourse.txt


title: TH_m298


title: TH_m306


title: TH_m297


title: TH_m305


title: BR_m22

description:
experiment1
counts_LPS_timecourse.txt


title: BR_m13

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m334

value: Spleen


title: BR_m11

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m332


title: TH_m295

value: Thymus


title: TH_m304


title: BR_m7

description:
experiment1
counts_LPS_timecourse.txt


title: BR_m8

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m331


title: BR_m9

description:
experiment1
counts_LPS_timecourse.txt


title: BR_m6

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m329


title: SP_m328


title: BR_m3

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m326


title: SP_m327


title: BR_m10

description:
experiment1
counts_LPS_timecourse.txt


title: BR_m2

description:
experiment1
counts_LPS_timecourse.txt


title: BR_m5

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m28

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m323


title: BM_m25

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m324


title: SP_m333


title: SP_m321


title: BM_m23

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m27

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m22

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m325


title: BR_m1

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m317


title: BM_m24

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m322


title: SP_m320


title: BM_m19

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m330


title: BM_m18

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m319


title: BM_m20

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m318


title: BM_m13

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m17

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m16

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m312


title: SP_m313


title: BM_m21

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m314


title: BM_m11

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m315


title: BM_m14

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m308


title: BM_m12

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m310


title: SP_m309


title: SP_m316


title: BR_m4

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m306


title: BM_m10

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m305


title: BM_m8

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m304


title: BM_m6

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m303


title: SP_m307


title: BM_m15

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m302


title: BM_m2

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m4

description:
experiment1
counts_LPS_timecourse.txt


title: SP_m299


title: SP_m301


title: SP_m298


title: SP_m300


title: SP_m296


title: BM_m9

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m1

description:
experiment1
counts_LPS_timecourse.txt


title: BM_m3

description:
experiment1
counts_LPS_timecourse.txt


title: SAFB1, SAFB2 and SLTM siRNA treated HEK293 cells

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

country: Germany

institute: Max-Planck-Institut für molekulare Genetik

data_processing:
Base-calling with guppy
Read alignment and downstream prcessing was carried out with FLAIR using directRNA specific options
Assembly: hg38
Supplementary files format and content: Three-column tab-delimited text file with gene identifier and raw read count columns

organism: Homo sapiens

extract_protocol:
Polyadenylated RNA was directly isolated  isolated using Dynabeads mRNA DIRECT purification kit (Thermo Fisher Scientific).
700 ng of freshly isolated polyA enriched mRNA were processed with Direct RNA Sequencing Kit (SQK-RNA002) from Oxford Nanopore according to the manufacturer’s protocol

tag: cell line

tag: sirna

value: SAFB1, SAFB2 and SLTM siRNA


title: SP_m295


title: yhr419w CRAC plus UV replicate 3

city: Paris

first: Gwenael

last: Badis

address: 46 rue d'Ulm

department: Genomique fonctionnelle (Section 2)

country: France

institute: IBENS

data_processing:
demultiplexing using Flexbar
Mapping to the SC288 reference genome Saccer3.fa using STAR standard configuration with option  --alignIntronMax 1500 --alignMatesGapMax 1500 --alignSJoverhangMin 25
Assembly: Saccer3.fa
Supplementary files format and content: wig files contain the profile of each experiment (strand 1 and strand 2 per replicatre)
Supplementary files format and content: Fastq files contains the raw data sequences after demultiplexing.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: 30°C in YPD, exponential phase (OD 600=0,6)

extract_protocol:
cross-linking and analysis of cDNA (CRAC)
cross-linking and analysis of cDNA (CRAC)

treatment_protocol: UV crosslink

value: yeast

tag: cell type

value: MATa, ura3d0, his3d1, leu2d0, met15d0, Ylr419w-TAP:HIS3MX6

value: no


title: control siRNA treated HEK293 cells

value: control


title: yhr419w CRAC minus UV replicate 3


title: LU_m333

value: Lung


title: BM_m7

description:
experiment1
counts_LPS_timecourse.txt


title: LU_m334


title: LU_m332


title: yhr419w CRAC minus UV replicate 2

value: UV crosslink


title: yhr419w CRAC plus UV replicate 1


title: yhr419w CRAC plus UV replicate 2


title: SP_m311


title: LU_m330


title: BM_m5

description:
experiment1
counts_LPS_timecourse.txt

value: Bone marrow


title: yhr419w CRAC minus UV replicate 1


title: LU_m329


title: WT5SC

city: Los Angeles

first: Brendan

middle: H

last: Grubbs

state: CA

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

data_processing:
quality assessment: FastQC
adapter removal: Cutadapt
read quality trimming: Trimmomatic
alignment to Gencode h28: STAR
generation of RPKM: edgeR
Genome_build: Gencode h28 (GRCh38.p12)
Supplementary_files_format_and_content: Raw counts, RPKM

source_name: Wilms Tumor

extract_protocol: Kapa low input total RNA kit

tag: age

value: 14 years old

tag: Sex

value: Male

tag: tumor type

value: Non-anaplastic Chemo Treates COG Stage IV


title: WT4SC

value: 3 years old

value: non-anaplastic COG Stage III


title: WT3SC

value: 6 years old

value: anaplastic COG Stage I


title: SP_m297

value: Spleen

value: Wild type


title: LU_m328


title: LU_m323


title: LU_m331


title: LU_m326


title: LU_m325


title: LU_m324


title: LU_m327


title: LU_m322


title: LU_m315


title: LU_m314


title: LU_m321


title: LU_m320


title: LU_m319


title: Uninjured, MRL/MpJ, muscle, 3

city: Bethesda

first: Kaitlyn

last: Sadtler

state: Maryland

address: 50 S Drive, Room 4341

department: NIBIB

institute: NIH

data_processing:
Sequence reads were quality chekced for basecall accuracy greater than 30
Sequence reads were mapped to GRCm39 using Kalisto
Genes were annotated using EnsDb.Mmusculus.v79
Genes with less than 1 cpm in at least 3 samples were filtered out
Counts were log2 transformed and normalized using the TMM method
Assembly: mm39
Supplementary files format and content: compressed csv file contains filtered, log2 transformed, normalized counts for each gene across all samples

source_name: Quadriceps muscle

growth_protocol: Does not apply

extract_protocol:
total RNA isolation was performed at Azenta Life Sciences
Illumina library preperation for RNA with PolyA selection with ERCC spike in was performed at Azenta Life Sciences

treatment_protocol: Mice were treated either with Saline, decellularized ECM or Polyethylene powder

value: Quadriceps muscle

tag: strain

value: MRL/MpJ

value: Uninjured


title: Control, MRL/MpJ, muscle, day21, 3

value: Saline


title: ECM, MRL/MpJ, muscle, day21, 1

value: ECM


title: ECM, MRL/MpJ, muscle, day21, 2


title: Uninjured, MRL/MpJ, muscle, 1


title: Control, MRL/MpJ, muscle, day21, 1


title: LU_m317

value: Lung


title: LU_m316


title: Control, C57BL/6, muscle, day21, 3


title: Control, C57BL/6, muscle, day21, 2


title: LU_m318


title: LU_m311


title: PE, MRL/MpJ, muscle, day21, 2

value: PE


title: PE, MRL/MpJ, muscle, day21, 3


title: Control, MRL/MpJ, muscle, day21, 2


title: Control, C57BL/6, muscle, day21, 1


title: PE, MRL/MpJ, muscle, day21, 1


title: ECM, MRL/MpJ, muscle, day21, 3


title: Uninjured, MRL/MpJ, muscle, 2


title: LU_m313


title: PE, C57BL/6, muscle, day21, 2


title: LU_m310


title: LU_m312


title: PE, C57BL/6, muscle, day21, 1


title: Uninjured, C57BL/6, muscle, 3


title: LU_m309


title: PE, C57BL/6, muscle, day21, 3


title: LU_m308


title: LU_m306


title: LU_m305


title: Uninjured, C57BL/6, muscle, 1


title: ECM, C57BL/6, muscle, day21, 1


title: ECM, C57BL/6, muscle, day21, 2


title: LU_m307


title: LU_m303


title: LU_m304


title: ECM, C57BL/6, muscle, day21, 3


title: LU_m302


title: 300BCG325_d14_PBMC

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

library_source: genomic

data_processing:
ATAC-seq reads were trimmed using Skewer and aligned to the GRCh38 assembly of the human genome using Bowtie 2 with the “-very-sensitive” parameter. Duplicate reads were removed using the sambamba “markdup” command, and only reads with mapping quality ≥ 30 and alignment to the genome were kept. Peak calling was performed with MACS2 using the “-nomodel” and “-extsize 147” parameters, and peaks overlapping blacklisted features as defined by the ENCODE project were discarded.
For quality control, the fraction of reads in peaks (FRiP) was calculated as the fraction of transposase cutting events overlapping identified peaks. Similarly, we quantified the fraction of transposase cutting events overlapping regions defined in the Ensembl Regulatory Build v20190329 and overlapping promoters. We defined the TSS enrichment statistic as the maximum value of the TSS enrichment plot, which is a histogram of transposase cutting events falling within ±1,000 bp from a reference set of TSSs normalized by the average tail value (calculated as the average coverage on the last 100 bp of both tails of the histogram). We then selected all samples with at least 5,000 called peaks and a TSS enrichment statistic of at least 4.5 for further analysis.
The chromatin accessibility peaks were combined into a single consensus region set by merging the peak summits, extended by 250 bp on both sides, across all samples that passed the quality control. This procedure yielded a consensus set.
Assembly: GRCh38
processed data files format and content: countData_ATAC_allsamples.csv : comma-separated count file of the ATAC-seq data
processed data files format and content: region_annotations.csv : comma-separated information on the genomic location and length of each region in the ATAC-seq data

molecule: genomic DNA

extract_protocol:
Briefly, at all three time points, 50,000 PBMCs were washed once in 50 μl cold PBS and lysed in a transposase reaction mix containing 10.25 μl nuclease free water, 12.50 μl 2 × Tagment DNA Buffer (Illumina), 2 μl Tagment DNA Enzyme (Illumina), and 0.25 μl 1% digitonin (Promega) for 30 minutes at 37 °C. Upon DNA purification with the MinElute kit (Qiagen), 1 μl of eluted DNA was used in a qPCR reaction in order to estimate the optimum number of amplification cycles. Next, the remaining 10 μl of each library was amplified for the number of cycles corresponding to the Cq value (the cycle number at which fluorescence has increased above background levels) from the qPCR.
Library amplification was followed by SPRI (Beckman Coulter) size selection to exclude fragments exceeding 1,200 bp in length. DNA concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers. Libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 3000/4000 platform and the 50-bp single-end configuration.

value: PBMC

tag: individual

tag: time point

tag: protocol

value: ATAC

tag: flowcell

tag: batch id

tag: pcr cq

tag: filtered peaks

tag: tss enrichment

tag: frip


title: LU_m301

tag: tissue

tag: genotype

tag: treatment


title: LU_m299


title: 300BCG326_d90_PBMC

tag: cell type


title: 300BCG326_d14_PBMC


title: 300BCG327_d14_PBMC


title: 300BCG327_d0_PBMC


title: LU_m296


title: 300BCG326_d0_PBMC


title: 300BCG325_d90_PBMC


title: LU_m300


title: LU_m298


title: LU_m297


title: 300BCG324_d90_PBMC


title: LU_m295


title: 300BCG325_d0_PBMC


title: LI_m334

value: Liver


title: Uninjured, C57BL/6, muscle, 2


title: LI_m333


title: 300BCG324_d14_PBMC


title: 300BCG327_d90_PBMC


title: 300BCG324_d0_PBMC


title: LI_m332


title: 300BCG323_d90_PBMC


title: LI_m331


title: 300BCG323_d14_PBMC


title: LI_m330


title: 300BCG323_d0_PBMC


title: LI_m329


title: LI_m328


title: 300BCG322_d14_PBMC


title: 300BCG321_d90_PBMC


title: 300BCG322_d0_PBMC


title: 300BCG321_d14_PBMC


title: 300BCG321_d0_PBMC


title: LI_m326


title: LI_m327


title: LI_m325


title: LI_m324


title: LI_m323


title: 300BCG320_d14_PBMC


title: 300BCG320_d0_PBMC


title: LI_m322


title: LI_m319


title: LI_m321


title: LI_m320


title: 300BCG318_d90_PBMC


title: LI_m318


title: 300BCG319_d0_PBMC


title: 300BCG319_d90_PBMC


title: 300BCG319_d14_PBMC


title: LI_m316


title: LI_m314


title: LI_m315


title: 300BCG318_d0_PBMC


title: LI_m317


title: 300BCG317_d90_PBMC


title: 300BCG320_d90_PBMC


title: 300BCG317_d14_PBMC


title: LI_m312


title: LI_m311


title: 300BCG316_d90_PBMC


title: 300BCG316_d14_PBMC


title: LI_m310


title: 300BCG316_d0_PBMC


title: LI_m313


title: 300BCG315_d14_PBMC


title: 300BCG315_d90_PBMC


title: LI_m309


title: LI_m307


title: LI_m308


title: LI_m306


title: 300BCG315_d0_PBMC


title: 300BCG318_d14_PBMC


title: 300BCG314_d14_PBMC


title: LI_m304


title: 300BCG314_d0_PBMC


title: LI_m303


title: LI_m305


title: 300BCG313_d14_PBMC


title: 300BCG313_d0_PBMC


title: LI_m302


title: LI_m301


title: 300BCG312_d90_PBMC


title: 300BCG313_d90_PBMC


title: LI_m300


title: 300BCG317_d0_PBMC


title: 300BCG312_d0_PBMC


title: 300BCG311_d90_PBMC


title: LI_m299


title: LI_m297


title: LI_m298


title: 300BCG311_d0_PBMC


title: LI_m296


title: 300BCG310_d90_PBMC


title: 300BCG310_d0_PBMC


title: 300BCG309_d90_PBMC


title: 300BCG309_d0_PBMC


title: KI_m334

value: Kidney


title: LI_m295


title: KI_m332


title: 300BCG308_d90_PBMC


title: 300BCG307_d90_PBMC


title: 300BCG307_d0_PBMC


title: 300BCG308_d0_PBMC


title: KI_m329


title: KI_m331


title: KI_m330


title: KI_m328


title: 300BCG306_d0_PBMC


title: 300BCG305_d90_PBMC


title: KI_m325


title: 300BCG305_d0_PBMC


title: 300BCG304_d90_PBMC


title: 300BCG304_d0_PBMC


title: 300BCG303_d90_PBMC


title: KI_m324


title: KI_m323


title: 300BCG303_d0_PBMC


title: KI_m322


title: KI_m319


title: KI_m327


title: KI_m333


title: KI_m320


title: KI_m318


title: KI_m314


title: KI_m316


title: KI_m326


title: KI_m315


title: 300BCG306_d90_PBMC


title: 300BCG301_d0_PBMC


title: 300BCG302_d90_PBMC


title: 300BCG301_d90_PBMC


title: 300BCG300_d90_PBMC


title: 300BCG300_d0_PBMC


title: KI_m313


title: 300BCG299_d0_PBMC


title: KI_m312


title: KI_m311


title: KI_m321


title: 300BCG298_d0_PBMC


title: KI_m310


title: KI_m309


title: 300BCG298_d90_PBMC


title: KI_m308


title: 300BCG302_d0_PBMC


title: 300BCG297_d90_PBMC


title: 300BCG298_d14_PBMC


title: 300BCG297_d14_PBMC


title: KI_m307


title: KI_m306


title: 300BCG297_d0_PBMC


title: 300BCG299_d90_PBMC


title: 300BCG296_d14_PBMC


title: 300BCG296_d90_PBMC


title: KI_m303


title: KI_m304


title: 300BCG296_d0_PBMC


title: 300BCG299_d14_PBMC


title: KI_m302


title: KI_m301


title: 300BCG295_d0_PBMC


title: 300BCG295_d14_PBMC


title: KI_m299


title: 300BCG294_d14_PBMC


title: 300BCG293_d90_PBMC


title: 300BCG294_d90_PBMC


title: KI_m298


title: 300BCG294_d0_PBMC


title: 300BCG293_d14_PBMC


title: KI_m295


title: iLN_m334

value: Inguinal lymph node


title: 300BCG292_d90_PBMC


title: iLN_m332


title: 300BCG292_d0_PBMC


title: KI_m297


title: iLN_m331


title: 300BCG291_d14_PBMC


title: iLN_m330


title: KI_m300


title: 300BCG291_d0_PBMC


title: iLN_m329


title: 300BCG290_d90_PBMC


title: iLN_m328


title: iLN_m333


title: 300BCG290_d14_PBMC


title: iLN_m326


title: 300BCG293_d0_PBMC


title: KI_m296


title: iLN_m327


title: 300BCG292_d14_PBMC


title: iLN_m325


title: iLN_m324


title: 300BCG289_d90_PBMC


title: 300BCG289_d14_PBMC


title: 300BCG289_d0_PBMC


title: iLN_m323


title: 300BCG288_d90_PBMC


title: iLN_m322


title: iLN_m320


title: 300BCG288_d14_PBMC


title: 300BCG291_d90_PBMC


title: iLN_m319


title: KI_m317


title: 300BCG287_d14_PBMC


title: 300BCG287_d90_PBMC


title: 300BCG290_d0_PBMC


title: iLN_m318


title: iLN_m317


title: iLN_m316


title: 300BCG287_d0_PBMC


title: iLN_m315


title: iLN_m314


title: KI_m305


title: 300BCG286_d14_PBMC


title: iLN_m312


title: iLN_m311


title: 300BCG285_d0_PBMC


title: 300BCG284_d90_PBMC


title: iLN_m310


title: iLN_m309


title: iLN_m308


title: 300BCG284_d0_PBMC


title: iLN_m313


title: 300BCG285_d90_PBMC


title: 300BCG283_d90_PBMC


title: iLN_m307


title: 300BCG288_d0_PBMC


title: iLN_m306


title: iLN_m305


title: 300BCG283_d0_PBMC


title: 300BCG282_d90_PBMC


title: iLN_m303


title: 300BCG282_d14_PBMC


title: iLN_m304


title: 300BCG286_d90_PBMC


title: 300BCG285_d14_PBMC


title: iLN_m302


title: 300BCG284_d14_PBMC


title: 300BCG281_d90_PBMC


title: iLN_m299


title: 300BCG281_d0_PBMC


title: iLN_m301


title: iLN_m297


title: iLN_m300


title: iLN_m295


title: 300BCG279_d90_PBMC


title: 300BCG280_d14_PBMC


title: iLN_m296


title: HE_m334

value: Heart


title: 300BCG283_d14_PBMC


title: HE_m333


title: HE_m332


title: 300BCG279_d0_PBMC


title: 300BCG278_d14_PBMC


title: HE_m331


title: 300BCG282_d0_PBMC


title: 300BCG278_d0_PBMC


title: 300BCG277_d14_PBMC


title: 300BCG281_d14_PBMC


title: 300BCG277_d90_PBMC


title: HE_m330


title: HE_m329


title: HE_m328


title: 300BCG280_d90_PBMC


title: 300BCG277_d0_PBMC


title: HE_m326


title: 300BCG276_d90_PBMC


title: HE_m325


title: HE_m327


title: HE_m324


title: 300BCG279_d14_PBMC


title: 300BCG276_d0_PBMC


title: 300BCG280_d0_PBMC


title: 300BCG275_d14_PBMC


title: 300BCG275_d90_PBMC


title: HE_m321


title: HE_m323


title: HE_m322


title: HE_m320


title: 300BCG275_d0_PBMC


title: HE_m319


title: 300BCG274_d90_PBMC


title: 300BCG274_d0_PBMC


title: 300BCG274_d14_PBMC


title: HE_m318


title: 300BCG273_d0_PBMC


title: HE_m317


title: HE_m316


title: 300BCG272_d90_PBMC


title: 300BCG272_d14_PBMC


title: HE_m313


title: 300BCG271_d90_PBMC


title: HE_m315


title: HE_m312


title: 300BCG276_d14_PBMC


title: HE_m314


title: HE_m311


title: 300BCG272_d0_PBMC


title: 300BCG271_d14_PBMC


title: 300BCG270_d90_PBMC


title: 300BCG270_d14_PBMC


title: HE_m310


title: HE_m309


title: 300BCG269_d90_PBMC


title: 300BCG270_d0_PBMC


title: HE_m307


title: 300BCG269_d14_PBMC


title: HE_m306


title: HE_m308


title: 300BCG268_d90_PBMC


title: HE_m305


title: 300BCG269_d0_PBMC


title: HE_m302


title: HE_m303


title: 300BCG268_d14_PBMC


title: HE_m304


title: 300BCG268_d0_PBMC


title: 300BCG267_d90_PBMC


title: HE_m299


title: 300BCG267_d0_PBMC


title: HE_m301


title: HE_m300


title: 300BCG266_d14_PBMC


title: 300BCG271_d0_PBMC


title: 300BCG266_d90_PBMC


title: 300BCG266_d0_PBMC


title: HE_m296


title: HE_m295


title: 300BCG265_d90_PBMC


title: BM_m334

value: Bone marrow


title: 300BCG264_d90_PBMC


title: BM_m332


title: 300BCG264_d14_PBMC


title: BM_m333


title: BM_m331


title: 300BCG265_d0_PBMC


title: 300BCG263_d90_PBMC


title: 300BCG264_d0_PBMC


title: 300BCG263_d14_PBMC


title: 300BCG267_d14_PBMC


title: BM_m330


title: BM_m328


title: 300BCG262_d14_PBMC


title: 300BCG263_d0_PBMC


title: HE_m298


title: BM_m325


title: HE_m297


title: BM_m329


title: BM_m326


title: 300BCG261_d90_PBMC


title: 300BCG262_d0_PBMC


title: BM_m327


title: 300BCG261_d0_PBMC


title: 300BCG260_d90_PBMC


title: BM_m323


title: BM_m324


title: BM_m321


title: 300BCG261_d14_PBMC


title: 300BCG260_d14_PBMC


title: BM_m320


title: 300BCG260_d0_PBMC


title: 300BCG259_d90_PBMC


title: BM_m319


title: 300BCG259_d14_PBMC


title: BM_m317


title: 300BCG259_d0_PBMC


title: BM_m318


title: BM_m316


title: 300BCG258_d90_PBMC


title: BM_m314


title: BM_m315


title: 300BCG258_d0_PBMC


title: 300BCG257_d14_PBMC


title: 300BCG258_d14_PBMC


title: 300BCG256_d90_PBMC


title: 300BCG257_d90_PBMC


title: BM_m313


title: BM_m312


title: BM_m322


title: 300BCG256_d0_PBMC


title: BM_m311


title: 300BCG257_d0_PBMC


title: BM_m308


title: 300BCG254_d90_PBMC


title: BM_m309


title: BM_m307


title: 300BCG255_d0_PBMC


title: BM_m306


title: BM_m305


title: BM_m303


title: VS40GAMS

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

institute: INSERM U1236-MOBIDIC

description:
All processed data files are available on the *MM samples.
VS40_MIG1.tar.gz

data_processing:
Demultiplexing and UMIs tag extraction with Migec v1.2.9  (Shugay et al., 2014). (java -jar migec.jar Checkout -cute path/to/barcode.txt path/to/reads.fq.gz outdir)
UMI-guided consensus assembly with Migec v1.2.9 (Shugay et al., 2014). (java -jar migec.jar Assemble --filter-collisions -m 1 path/to/checkout/read_R1.fq.gz path/to/checkout/read_R2.fq.gz outdir)
Annotation of the consensus with the IMGT HighV-QUEST tools v3.5.19. Parameters : Locus:IG, species: Homo sapiens, other parameters as default values.
Supplementary files format and content: IMGT HighV-QUEST output archive, containing tabular files

extract_protocol:
Total mRNA was extracted from blood samples (3 mL) using TempusTM spin RNA isolation kit (Thermofisher).
For each blood sample, Ig mRNA was reverse-transcribed to cDNA by a 5’RACE PCR with consensus reverse primers for IgH Cμ, Cɣ and Cα constant region and a cap race primer carrying unique molecular identifiers (UMIs), amplified by PCR using a universal forward primer and a nested reverse primer selected within the CH1 exon of the Cμ, Cɣ and Cα genes and sequenced with an Illumina MiSeq, standard Illumina sequencing primers and MiSeq Reagent Kit v3 (600 cycles).

value: blood b cell

tag: disease state

value: Healthy sample

tag: timepoint

value: Day 0

tag: splice variant

value: secreted repertoire


title: BM_m302

value: Wild type


title: 300BCG254_d14_PBMC


title: VS39GAMS

description:
All processed data files are available on the *MM samples.
VS39_MIG1.tar.gz


title: VS38GAMS

description:
All processed data files are available on the *MM samples.
VS38_MIG1.tar.gz


title: VS40GAMM

value: membrane repertoire


title: VS39GAMM


title: VS38GAMM


title: 300BCG254_d0_monocyte

source_name: monocyte

value: monocyte


title: 300BCG254_d0_nkcell

source_name: nkcell

value: nkcell


title: VS37GAMS

description:
All processed data files are available on the *MM samples.
VS37_MIG1.tar.gz


title: BM_m304


title: BM_m310


title: 300BCG256_d14_PBMC


title: 300BCG254_d0_PBMC


title: VS37GAMM


title: BM_m300


title: 300BCG253_d90_PBMC


title: BM_m301


title: 300BCG253_d14_PBMC


title: VS36GAMM

description:
All processed data files are available on the *MM samples.
VS36_MIG1.tar.gz


title: 300BCG253_d0_PBMC


title: VS36GAMS


title: BM_m299


title: BM_m298


title: VS35GAMM

description:
All processed data files are available on the *MM samples.
VS35_MIG1.tar.gz


title: VS34GAMS

description:
All processed data files are available on the *MM samples.
VS34_MIG1.tar.gz


title: 300BCG253_d0_nkcell


title: VS34GAMM


title: 300BCG253_d0_monocyte


title: VS33GAMM

description:
All processed data files are available on the *MM samples.
VS33_MIG1.tar.gz


title: VS33GAMS


title: 300BCG252_d90_PBMC


title: BM_m297


title: BM_m296


title: VS32GAMS

description:
All processed data files are available on the *MM samples.
VS32_MIG1.tar.gz


title: VS32GAMM


title: VS30GAMS

description:
All processed data files are available on the *MM samples.
VS30_MIG1.tar.gz


title: 300BCG252_d0_PBMC


title: VS30GAMM


title: VS29GAMS

description:
All processed data files are available on the *MM samples.
VS29_MIG1.tar.gz


title: VS31GAMS

description:
All processed data files are available on the *MM samples.
VS31_MIG1.tar.gz


title: VS31GAMM


title: 300BCG251_d90_PBMC


title: 300BCG252_d0_monocyte


title: VS28GAMS

description:
All processed data files are available on the *MM samples.
VS28_MIG1.tar.gz


title: Lung Cancer, 20210915MCX011

city: Guangzhou

first: Bin

last: Yang

address: Guangzhou 510700

country: China

institute: Vision Medicals Co., Ltd.

data_processing:
high-quality data were aligned to the human genome hg38 using HISAT2 with default parameters. Gene-level quantification was performed using FeatureCounts. The gene counts were aggregated using the featureCounts program from the Subread package release 2.0.0.
Assembly: hg38
Supplementary files format and content: Tab-delimited text includes raw per-gene counts for each sample.

source_name: BALF

extract_protocol:
1 mL BALF sample was centrifuged at 12,000 rpm for 10 min. Then, 200 μL of the precipitate was lysed in TRIzol LS (Thermo Fisher Scientific, Carlsbad, CA, USA), followed by RNA extraction using a Direct-zol RNA Miniprep kit (Zymo Research, Irvine, CA, USA) according to the manufacturer's instructions.
According to the manufacturer's instructions,  10 μL of purified RNA was used for cDNA generation and library preparation with an Ovation Trio RNA-Seq Library Preparation Kit (NuGEN, CA, USA).   A Qubit dsDNA HS Assay Kit was used to measure the library concentration.   The library quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and a High Sensitivity DNA kit.   The library was sequenced using an Illumina NextSeq 550 sequencer with a 75-cycle single-end sequencing strategy.

value: BALF

value: Lung Cancer


title: VS28GAMM


title: VS27GAMS

description:
All processed data files are available on the *MM samples.
VS27_MIG1.tar.gz


title: VS35GAMS


title: VS29GAMM


title: Lung Cancer, 20210910MCX010


title: Lung Cancer, 20210909MCX012


title: Lung Cancer, 20210910MCX007


title: 300BCG251_d14_PBMC

value: PBMC


title: Lung Cancer, 20210907MCX013


title: VS27GAMM


title: 300BCG251_d0_PBMC

value: ATAC


title: BM_m295


title: Lung Cancer, 20210827MCX014


title: 300BCG251_d0_monocyte


title: Lung Cancer, 20210816MCX011


title: 300BCG252_d14_PBMC


title: VS26GAMS

description:
All processed data files are available on the *MM samples.
VS26_MIG1.tar.gz


title: 300BCG251_d0_nkcell


title: VS26GAMM


title: 300BCG250_d0_PBMC


title: VS14GAMS

description:
All processed data files are available on the *MM samples.
VS14_MIG1.tar.gz


title: VS16GAMS

description:
All processed data files are available on the *MM samples.
VS16_MIG1.tar.gz


title: 300BCG250_d0_monocyte


title: VS16GAMM


title: VS13GAMS

description:
All processed data files are available on the *MM samples.
VS13_MIG1.tar.gz


title: VS12GAMS

description:
All processed data files are available on the *MM samples.
VS12_MIG1.tar.gz


title: VS12GAMM


title: Lung Cancer, 20210812MCX008


title: 300BCG249_d90_PBMC


title: VS15GAMM

description:
All processed data files are available on the *MM samples.
VS15_MIG1.tar.gz


title: 300BCG249_d14_PBMC


title: VS15GAMS


title: VS11GAMS

description:
All processed data files are available on the *MM samples.
VS11_MIG1.tar.gz


title: VS25GAMS

description:
All processed data files are available on the *MM samples.
VS25_MIG1.tar.gz


title: Lung Cancer, 20210807MCX014


title: VS14GAMM


title: Lung Cancer, 20210827MCX009


title: VS25GAMM


title: Lung Cancer, 20210714MCX008


title: VS1GAMS

description:
All processed data files are available on the *MM samples.
VS1_MIG1.tar.gz


title: VS13GAMM


title: VS10GAMM

description:
All processed data files are available on the *MM samples.
VS10_MIG1.tar.gz


title: 300BCG249_d0_nkcell


title: 300BCG250_d14_PBMC


title: Lung Cancer, 20210730MCX017


title: Lung Cancer, 20210804MCX003


title: Lung Cancer, 20210729MCX011


title: 300BCG249_d0_PBMC


title: VS10GAMS


title: Lung Cancer, 20210713MCX013


title: 300BCG249_d0_monocyte

value: HWVYNBBXX


title: VS1GAMM


title: Lung Cancer, 20210712MCX011


title: C19-037  GAMS

description:
All processed data files are available on the *MM samples.
C19_037_GAM_MS.tar.gz

value: With ARDS

value: Day 7


title: 300BCG248_d90_PBMC


title: C19-037  GAMM


title: VS11GAMM


title: J0-C19-037  GAMM

description:
All processed data files are available on the *MM samples.
J0_C19_037_GAM_MS.tar.gz


title: Lung Cancer, 20210702MCX009


title: 300BCG248_d14_PBMC


title: C19-036  GAMS

description:
All processed data files are available on the *MM samples.
C19_036_GAM_MS.tar.gz

value: Without ARDS


title: Lung Cancer, 20210628MCX011


title: J0-C19-036  GAMS

description:
All processed data files are available on the *MM samples.
J0_C19_036_GAM_MS.tar.gz


title: 300BCG248_d0_PBMC


title: Lung Cancer, 20210623MCX012


title: J0-C19-036  GAMM


title: J4-35-GAMS

description:
All processed data files are available on the *MM samples.
J4_MIG1_35_GAMMS.tar.gz

value: Day 4


title: J4-35-GAMM

value: blood b cell


title: 300BCG248_d0_monocyte


title: C19-035  GAMM

description:
All processed data files are available on the *MM samples.
C19_035_GAM_MS.tar.gz


title: C19-035  GAMS


title: Lung Cancer, 20210618MCX005


title: 300BCG247_d90_PBMC


title: J0-C19-035  GAMS

description:
All processed data files are available on the *MM samples.
J0_C19_035_GAM_MS.tar.gz


title: J0-C19-035  GAMM


title: J0-C19-037  GAMS


title: Lung Cancer, 20210528MCX007


title: C19-033  GAMM

description:
All processed data files are available on the *MM samples.
C19_033_GAM_MS.tar.gz


title: J0-C19-033  GAMS

description:
All processed data files are available on the *MM samples.
J0_C19_033_GAM_MS.tar.gz


title: Lung Cancer, 20210507MCX008


title: C19-036  GAMM


title: J4-32-GAMS

description:
All processed data files are available on the *MM samples.
J4_MIG1_32_GAMMS.tar.gz


title: 300BCG247_d0_PBMC


title: C19-032  GAMS

description:
All processed data files are available on the *MM samples.
C19_032_GAM_MS.tar.gz


title: C19-033  GAMS


title: 300BCG246_d90_PBMC


title: Lung Cancer, 20210410MCX001


title: 300BCG246_d14_PBMC


title: J4-32-GAMM


title: J0-C19-033  GAMM


title: Lung Cancer, 20210330MCX005


title: Lung Cancer, 20210618MCX008


title: 300BCG248_d0_nkcell


title: 300BCG246_d0_nkcell


title: 300BCG246_d0_PBMC


title: Lung Cancer, 20210330MCX004


title: C19-032  GAMM


title: J0-C19-032  GAMM

description:
All processed data files are available on the *MM samples.
J0_C19_032_GAM_MS.tar.gz


title: Lung Cancer, 20210526MCX014


title: C19-029  GAMS

description:
All processed data files are available on the *MM samples.
C19_029_GAM_MS.tar.gz


title: J0-C19-032  GAMS


title: J4-29-GAMS

description:
All processed data files are available on the *MM samples.
J4_MIG1_29_GAMMS.tar.gz


title: 300BCG246_d0_monocyte


title: J4-29-GAMM


title: C19-029  GAMM


title: J0-C19-029  GAMS

description:
All processed data files are available on the *MM samples.
J0_C19_029_GAM_MS.tar.gz


title: 300BCG246_d0_cd8t

value: HWVYYBBXX


title: 300BCG247_d14_PBMC


title: J0-C19-029  GAMM

value: Day 0


title: J4-25-GAMS

description:
All processed data files are available on the *MM samples.
J4_MIG1_25_GAMMS.tar.gz

value: secreted repertoire


title: Lung Cancer, 20210325MCX003


title: 300BCG245_d90_PBMC


title: Lung Cancer, 20210319MCX011


title: J4-25-GAMM


title: C19-025  GAMS

description:
All processed data files are available on the *MM samples.
J7_25_MIG1_GAMMS.tar.gz


title: C19-025  GAMM


title: 300BCG245_d0_PBMC


title: Lung Cancer, 20220226MCX019


title: J0-C19-025  GAMM

description:
All processed data files are available on the *MM samples.
J0_C19_025_GAM_MS.tar.gz


title: J4-24-GAMS

description:
All processed data files are available on the *MM samples.
J4_MIG1_24_GAMMS.tar.gz


title: Lung Cancer, 20210329MCX004


title: Lung Cancer, 20220219MCX016


title: J4-24-GAMM


title: Lung Cancer, 20220217MCX012


title: C19-024  GAMS

description:
All processed data files are available on the *MM samples.
C19_024_GAM_MS.tar.gz


title: 300BCG244_d14_PBMC


title: 300BCG244_d90_PBMC


title: J0-C19-024  GAMS

description:
All processed data files are available on the *MM samples.
J0_C19_024_GAM_MS.tar.gz


title: Lung Cancer, 20210326MCX005


title: J0-C19-024  GAMM


title: Lung Cancer, 20220127MCX030


title: C19-020  GAMM

description:
All processed data files are available on the *MM samples.
C19_020_GAM_MS.tar.gz


title: 300BCG244_d0_PBMC


title: Lung Cancer, 20220122MCX014


title: J0-C19-025  GAMS


title: 300BCG244_d0_monocyte


title: Lung Cancer, 20220121MCX009


title: 300BCG245_d14_PBMC


title: J4-18-GAMS

description:
All processed data files are available on the *MM samples.
J4_MIG1_18_GAMMS.tar.gz


title: J0-C19-020  GAMM

description:
All processed data files are available on the *MM samples.
J0_C19_020_GAM_MS.tar.gz


title: 300BCG245_d0_monocyte


title: 300BCG243_d90_PBMC


title: Lung Cancer, 20220115MCX016


title: Lung Cancer, 20220121MCX008


title: C19-024  GAMM


title: C19-020  GAMS


title: 300BCG243_d14_PBMC


title: 300BCG244_d0_cd8t


title: 300BCG243_d0_PBMC


title: J0-C19-018  GAMM

description:
All processed data files are available on the *MM samples.
J0_C19_018_GAM_MS.tar.gz


title: 300BCG244_d0_nkcell


title: J0-C19-018  GAMS


title: Lung Cancer, 20220127MCX024


title: J4-16-GAMM

description:
All processed data files are available on the *MM samples.
J4_MIG1_16_GAMMS.tar.gz


title: C19-018  GAMM

description:
All processed data files are available on the *MM samples.
J7_18_MIG1_GAMMS.tar.gz


title: J4-18-GAMM


title: C19-018  GAMS


title: C19-016  GAMS

description:
All processed data files are available on the *MM samples.
J7_16_MIG1_GAMMS.tar.gz


title: Lung Cancer, 20220113MCX017


title: Lung Cancer, 20220115MCX009


title: C19-016  GAMM


title: 300BCG242_d90_PBMC


title: J0-C19-020  GAMS


title: C19-014  GAMS

description:
All processed data files are available on the *MM samples.
J7_14_MIG1_GAMMS.tar.gz


title: J4-16-GAMS


title: Lung Cancer, 20220105MCX011


title: 300BCG242_d14_PBMC


title: J0-C19-016  GAMS

description:
All processed data files are available on the *MM samples.
J0_C19_016_GAM_MS.tar.gz


title: Lung Cancer, 20220112MCX016


title: C19-014  GAMM


title: J0-C19-016  GAMM


title: Lung Cancer, 20211231MCX012


title: Lung Cancer, 20211230MCX010


title: C19-012  GAMS

description:
All processed data files are available on the *MM samples.
C19_012_GAM_MS.tar.gz


title: 300BCG242_d0_cd8t


title: J4-11-GAMS

description:
All processed data files are available on the *MM samples.
J4_MIG1_11_GAMMS.tar.gz


title: Lung Cancer, 20211229MCX015


title: 300BCG242_d0_PBMC


title: J0-C19-014  GAMS

description:
All processed data files are available on the *MM samples.
J0_14_MIG1_GAMMS.tar.gz


title: 300BCG241_d90_PBMC


title: 300BCG241_d0_PBMC


title: 300BCG241_d14_PBMC


title: C19-011  GAMS

description:
All processed data files are available on the *MM samples.
J7_11_MIG1_GAMMS.tar.gz


title: J0-C19-014  GAMM


title: 300BCG242_d0_nkcell


title: J0-C19-012  GAMS

description:
All processed data files are available on the *MM samples.
J0_C19_012_GAM_MS.tar.gz


title: J4-12-GAMM

description:
All processed data files are available on the *MM samples.
J4_MIG1_12_GAMMS.tar.gz


title: J0-C19-011  GAMM

description:
All processed data files are available on the *MM samples.
J0_C19_011_GAM_MS.tar.gz


title: 300BCG242_d0_monocyte


title: Lung Cancer, 20211230MCX011


title: J4-11-GAMM


title: C19-010 GAMS

description:
All processed data files are available on the *MM samples.
J7_10_MIG1_GAMMS.tar.gz


title: C19-012  GAMM


title: Lung Cancer, 20211229MCX016


title: Lung Cancer, 20211222MCX007


title: J0-C19-012  GAMM


title: J0-C19-011  GAMS


title: 300BCG241_d0_nkcell


title: C19-010 GAMM


title: C19-011  GAMM


title: 300BCG241_d0_monocyte


title: Lung Cancer, 20211209MCX019


title: Lung Cancer, 20211210MCX014


title: Lung Cancer, 20211218MCX011


title: J0-C19-010 GAMM

description:
All processed data files are available on the *MM samples.
J0_C19_010_GAM_MS.tar.gz


title: Lung Cancer, 20211207MCX012


title: C19-009  GAMS

description:
All processed data files are available on the *MM samples.
J7_09_MIG1_GAMMS.tar.gz


title: 300BCG240_d90_PBMC


title: J0-C19-010 GAMS


title: 300BCG241_d0_cd8t

value: HYGNWBBXX


title: J4-9-GAMS

description:
All processed data files are available on the *MM samples.
J4_MIG1_9_GAMMS.tar.gz


title: Lung Cancer, 20211208MCX010


title: J4-6-GAMS

description:
All processed data files are available on the *MM samples.
J4_MIG1_6_GAMMS.tar.gz


title: Lung Cancer, 20211126MCX011


title: J4-9-GAMM

value: membrane repertoire


title: Lung Cancer, 20211125MCX012


title: C19-006  GAMS

description:
All processed data files are available on the *MM samples.
J7_06_MIG1_GAMMS.tar.gz


title: C19-009  GAMM


title: 300BCG240_d14_PBMC


title: J0-C19-009  GAMS

description:
All processed data files are available on the *MM samples.
J0_C19_009_GAM_MS.tar.gz


title: Lung Cancer, 20211127MCX010


title: J0-C19-009  GAMM


title: 300BCG239_d14_PBMC


title: Lung Cancer, 20211113MCX008


title: J0-C19-006  GAMM

description:
All processed data files are available on the *MM samples.
J0_C19_006_GAM_MS.tar.gz


title: J4-6-GAMM


title: J4-5-GAMS

description:
All processed data files are available on the *MM samples.
J4_MIG1_5_GAMMS.tar.gz


title: Lung Cancer, 20211117MCX010


title: J0-C19-006  GAMS


title: 300BCG239_d0_nkcell


title: 300BCG239_d0_monocyte

value: monocyte


title: Lung Cancer, 20211110MCX010


title: J4-5-GAMM


title: C19-005  GAMM

description:
All processed data files are available on the *MM samples.
J7_05_MIG1_GAMMS.tar.gz


title: C19-005  GAMS


title: 300BCG239_d90_PBMC


title: Lung Cancer, 20211109MCX016


title: J0-C19-005  GAMS

description:
All processed data files are available on the *MM samples.
J0_C19_005_GAM_MS.tar.gz


title: 300BCG239_d0_cd8t


title: 300BCG238_d90_PBMC


title: Lung Cancer, 20211109MCX014


title: J0-C19-005  GAMM


title: Lung Cancer, 20211106MCX007


title: J4-4-GAMS

description:
All processed data files are available on the *MM samples.
J4_MIG1_4_GAMMS.tar.gz


title: C19-004  GAMS

description:
All processed data files are available on the *MM samples.
J7_04_MIG1_GAMMS.tar.gz


title: J4-4-GAMM


title: 300BCG239_d0_PBMC


title: C19-004  GAMM


title: C19-006  GAMM


title: 300BCG238_d0_PBMC


title: 300BCG238_d14_PBMC


title: Lung Cancer, 20211029MCX010


title: Lung Cancer, 20211029MCX014


title: 300BCG238_d0_nkcell

value: nkcell


title: J0-C19-004  GAMS

description:
All processed data files are available on the *MM samples.
J0_04_MIG1_GAMMS.tar.gz


title: R9Qunc-16_replicate_2

city: Beijing

first: Yongping

last: Chai

state: Beijing

address: Tsinghua University

institute: Tsinghua University 清华大学

data_processing:
The raw sequencing reads were trimmed using Trim_galore (version 0.4.4) to remove the low-quality bases and adaptor sequences
Paired-end reads with at least 20 nucleotides long were aligned to C. elegans reference genome (ce11) using STAR (2.5.4b).
The numbers of reads that aligned to genes were quantified by HTSeq (version 0.9.1).
Assembly: ce11
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole animal

extract_protocol:
Animal were lysed in 400μL TRIzol reagent (Invitrogen). Total RNA was extracted according to the manufacturer’s protocol.
library was constructed using KAPA RNA HyperPrep Kit (KAPA Biosystems), according to the manufacturer's protocol.

value: whole animal

value: no


title: R9Qunc-16_replicate_1


title: 300BCG238_d0_monocyte


title: Lung Cancer, 20211028MCX015

value: BALF

value: Lung Cancer


title: R9QG265R_replicate_2


title: Lung Cancer, 20211026MCX013


title: Lung Cancer, 20211022MCX015


title: R9Q_replicate_1


title: 300BCG237_d90_PBMC

value: PBMC

value: ATAC


title: Lung Cancer, 20211020MCX013


title: 300BCG237_d14_PBMC


title: R9QT102I_replicate_2


title: R9QT102I_replicate_1


title: 300BCG238_d0_cd8t


title: R9Q_replicate_2


title: Lung Cancer, 20211019MCX016


title: 300BCG237_d0_PBMC


title: J0-C19-004  GAMM

value: With ARDS


title: WT_replicate_1

value: WT


title: Lung Cancer, 20211016MCX015


title: 300BCG237_d0_nkcell


title: 300BCG237_d0_monocyte

value: HWVYNBBXX


title: Run3-ME586L

city: Ottawa

first: Lauren

middle: E

last: Carter

state: Ontario

address: 251 SIR FREDERICK BANTING

department: 251 Sir Frederick Banting Driveway

country: Canada

institute: Health Canada

data_processing:
Quality filtering and trimming Bbduk (38.84) maq=12 qtrim=rl trimq=12 minlength=20 tpe tbo
Alignment STAR (2.7.1a) OutFilterScoreMinOverLread=0.25 outFilterMatchNminOverLread=0.25
Gene reads counting FeatureCounts (2.0.0)
Differential Expression calling DESeq2 (1.26.0) alpha=0.05 min_reads_gene=5 min_reads_library=1000000 shrinkage=apeglm
Assembly: Rnor_6.0
Supplementary files format and content: gene counts assigned by featureCounts and differentially expressed genes assigned by DESeq2

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Total RNA was extracted from flash frozen tissue samples using Qiagen miRNeasy kits.  20mg of frozen liver was placed in pre-filled tube containing Qiazol reagent and Zirconium beads, then homogenized 2 x for 20 seconds.  Subsequent steps were followed as per manufacture's instructions.
3-methylfuran cDNA libraries were constructed using Illumina TruSeq Stranded mRNA protocol. Furan cDNA libraries were prepared with the Illumina Stranded mRNA prep kit (updated release).

value: Liver

value: Diet E - 1.0 mg/kg bw/day 3-methylfuran


title: Run3-ME592L


title: Run3-ME591L


title: Run3-ME590L


title: Run3-ME587L


title: Lung Cancer, 20211016MCX013


title: Lung Cancer, 20211011MCX008


title: Run3-ME583L


title: 300BCG237_d0_cd8t

value: HWVYYBBXX


title: Run3-ME584L


title: R9QG265R_replicate_1


title: WT_replicate_2


title: Lung Cancer, 20211006MCX010


title: Run3-MC512L

value: Diet C - Control 0


title: Run3-ME582L


title: 300BCG236_d90_PBMC


title: Lung Cancer, 20211004MCX018


title: Run3-MC510L


title: Run3-MC511L


title: Lung Cancer, 20210928MCX012


title: 300BCG236_d0_PBMC


title: 300BCG236_d14_PBMC


title: Run3-MC506L


title: Run3-MC508L


title: Run3-MC503L


title: 300BCG236_d0_monocyte


title: Run3-MC502L


title: 300BCG236_d0_cd8t


title: Lung Cancer, 20210928MCX006


title: Run3-MB551L

value: Diet B - 0.075 mg/kg bw/day 3-methylfuran


title: Lung Cancer, 20210924MCX016


title: Run3-MB552L


title: Run3-MB549L


title: Lung Cancer, 20210922MCX011


title: Run3-MB546L


title: 300BCG235_d14_PBMC


title: Run3-MB548L


title: Run3-MB545L


title: Lung Cancer, 20210915MCX010


title: 300BCG235_d0_nkcell


title: Run3-MB541L


title: Run3-MC507L


title: Lung Cancer, 20210914MCX010


title: Lung Cancer, 20210928MCX009


title: Run3-MB542L


title: Run3-MA532L

value: Diet A - 0.02 mg/kg bw/day 3-methylfuran


title: Run3-MA531L


title: 300BCG235_d0_PBMC


title: Lung Cancer, 20210913MCX015


title: 300BCG235_d0_monocyte

value: monocyte


title: Run3-MA528L


title: Lung Cancer, 20210910MCX019


title: Run3-MA525L


title: 300BCG235_d0_cd8t


title: 300BCG235_d90_PBMC


title: 300BCG234_d0_PBMC


title: Run3-MA522L


title: Run3-MA521L


title: Lung Cancer, 20210910MCX015


title: Run3-MA524L


title: 300BCG234_d0_nkcell

value: nkcell


title: Run2-ME592L


title: Run2-ME591L


title: Lung Cancer, 20210910MCX012


title: Run2-ME590L


title: 300BCG234_d0_cd8t


title: Lung Cancer, 20210910MCX011


title: Lung Cancer, 20210908MCX019


title: Run2-ME583L


title: Run2-ME582L


title: Run3-MA529L


title: Lung Cancer, 20210907MCX017


title: Run2-ME586L


title: Run2-ME587L


title: 300BCG233_d90_PBMC


title: 300BCG233_d14_PBMC


title: Run2-ME584L


title: Run2-MC512L


title: 300BCG233_d0_PBMC


title: Run2-MC510L


title: Run2-MC511L


title: Lung Cancer, 20210906MCX015


title: Lung Cancer, 20210910MCX013


title: 300BCG233_d0_nkcell


title: Run2-MC507L


title: Lung Cancer, 20210826MCX011


title: Run2-MC506L


title: Lung Cancer, 20210827MCX010


title: Run2-MC503L


title: 300BCG233_d0_monocyte


title: 300BCG234_d0_monocyte


title: Lung Cancer, 20210826MCX009


title: Run2-MB552L


title: 300BCG233_d0_cd8t

value: HYGGCBBXX


title: Run2-MC502L


title: 300BCG232_d14_PBMC


title: Run2-MB546L


title: Run2-MB548L


title: Run2-MB549L


title: Run2-MB551L


title: Lung Cancer, 20210814MCX014


title: Lung Cancer, 20210819MCX009


title: Run2-MB545L


title: 300BCG232_d0_monocyte


title: Lung Cancer, 20210805MCX014


title: Run2-MC508L


title: Lung Cancer, 20210802MCX012


title: 300BCG232_d0_nkcell


title: Run2-MB542L


title: Run2-MB541L


title: Lung Cancer, 20210731MCX007


title: Run2-MA532L


title: 300BCG231_d14_PBMC


title: Run2-MA531L


title: Lung Cancer, 20210730MCX018


title: 300BCG232_d0_cd8t


title: Run2-MA525L


title: 300BCG232_d0_PBMC


title: Lung Cancer, 20210730MCX009


title: 300BCG231_d0_PBMC


title: Run2-MA522L


title: Run2-MA524L


title: Run2-MA521L


title: Run1-ME592L


title: 300BCG231_d0_monocyte


title: Lung Cancer, 20210723MCX015


title: Run1-ME590L


title: 300BCG231_d0_cd8t


title: Run1-ME591L


title: Run2-MA528L


title: Run1-ME587L


title: Run2-MA529L


title: Run1-ME586L


title: Lung Cancer, 20210710MCX009


title: Lung Cancer, 20210716MCX014


title: 300BCG230_d14_PBMC


title: Run1-ME584L


title: Run1-ME583L


title: 300BCG230_d0_PBMC


title: Lung Cancer, 20210703MCX008


title: RNA-517

city: Iowa City

first: Yann

last: Vanrobaeys

state: IA

address: 169 Newton Road

department: Neuroscience and Pharmacology

institute: University of Iowa

description:
RNA-517
rna_counts16p.txt

data_processing:
We trimmed the Ribo-Seq reads using cutadaptv3.5 to remove the Illumina the 3’ adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC), the Poly-A inserted between the footprint sequence and the 3’ adapter sequence (AAAAAAAAAA), the first three 5’ nucleotides of the read (“GGG” 5’ trimer – more generally G/C-trimer - added during library construction) with the parameter -u 3, and we discarded trimmed reads shorter than 15 nt with the parameter -m 15. Afterwards, we remove trimmed reads mapping to abundant sequences (rRNA, tRNA, and mtRNA) using bowtie2 with a seed length of 22 (-L 20). The unmapped reads to abundant sequences were then mapped to the mouse mm39 reference genome with a seed length of 22 (-L 20). Aligned reads were quantified to generate a raw count matrix for each protein coding gene.
Assembly: mm39
Supplementary files format and content: ribo_counts16p.txt
Supplementary files format and content: ribo_counts3g.txt
Supplementary files format and content: rna_counts16p.txt
Supplementary files format and content: rna_counts3g.txt
Supplementary files format and content: sample_info16p.txt
Supplementary files format and content: sample_info3g.txt
Supplementary files format and content: Raw count matrix of the ribo part for the comparison between 16p11.2 del/+ and wild-type male mice.
Supplementary files format and content: Raw count matrix of the ribo part for the comparison between 3g KO and wild-type male mice.
Supplementary files format and content: Raw count matrix of the rna part for the comparison between 16p11.2 del/+ and wild-type male mice.
Supplementary files format and content: Raw count matrix of the rna part for the comparison between 16p11.2 del/+ and wild-type male mice.
Supplementary files format and content: Sample information of 16p11.2 del/+ and wild-type male mice for differential analysis.
Supplementary files format and content: Sample information of 3g KO and wild-type male mice for differential analysis.
Library strategy: RIBO-seq

source_name: Striatum

extract_protocol:
Total RNA was extracted from sampled human brains using miRNeasy Mini Kite and homogenized in Qiazol using stainless steel beads. Chloroform was then used for phase separation. RNA containing an aqueous layer was further purified using the RNeasy MinElute spin column. RNA was finally eluted in RNase-free water.
RNA-seq libraries were prepared in parallel from the same lysate used to prepare RIBO-seq libraries. RIBO-seq and RNA-seq libraries were pooled and sequenced on a NovaSeq6000 sequencer, single read, 1x50 cycles, for a total of ≥ 130M reads/RIBO-seq and ≥ 50M reads/RNA-seq library. Library prep and sequencing were performed at TB-SEQ (Palo Alto, CA).

value: Striatum

tag: Sex

value: Male

tag: strain

tag: condition

value: Wild type


title: RNA-516

description:
RNA-516
rna_counts16p.txt


title: Lung Cancer, 20210701MCX010

value: BALF

value: Lung Cancer


title: Run1-MC512L


title: RNA-506

description:
RNA-506
rna_counts16p.txt


title: 300BCG231_d0_nkcell

tag: individual

tag: time point

tag: protocol

value: ATAC


title: Lung Cancer, 20210728MCX012


title: Run1-MC511L


title: 300BCG230_d0_monocyte

tag: flowcell

tag: batch id

tag: pcr cq


title: Lung Cancer, 20210619MCX010


title: Run1-MC510L


title: 300BCG230_d0_cd8t

tag: filtered peaks

tag: tss enrichment

tag: frip


title: Lung Cancer, 20210618MCX007

tag: tissue


title: 300BCG229_d14_PBMC

tag: cell type

value: PBMC

tag: genotype


title: Run1-MC508L

tag: treatment


title: Lung Cancer, 20210617MCX009

tag: disease state


title: RNA-499

description:
RNA-499
rna_counts16p.txt

tag: Sex


title: Run1-MC507L


title: 300BCG229_d0_PBMC


title: RNA-498

description:
RNA-498
rna_counts16p.txt

tag: strain


title: Run1-ME582L


title: 300BCG229_d0_monocyte

value: HWVYNBBXX


title: 300BCG230_d0_nkcell


title: Lung Cancer, 20210604MCX011


title: Run1-MC503L

value: Liver


title: RNA-319

description:
RNA-319
rna_counts3g.txt

tag: condition

value: 3 genes hemideletion knockout


title: Lung Cancer, 20210603MCX008


title: RNA-318

description:
RNA-318
rna_counts3g.txt


title: Lung Cancer, 20210630MCX015


title: Run1-MC502L


title: RNA-505

description:
RNA-505
rna_counts16p.txt


title: Lung Cancer, 20210602MCX013


title: RNA-303

description:
RNA-303
rna_counts3g.txt


title: 300BCG229_d0_cd8t

tag: individual

value: HWVYYBBXX


title: RNA-504

description:
RNA-504
rna_counts16p.txt


title: Run1-MB552L


title: Run1-MB551L


title: 300BCG228_d14_PBMC

tag: time point


title: 300BCG228_d0_PBMC

tag: protocol


title: RNA-301

description:
RNA-301
rna_counts3g.txt


title: Lung Cancer, 20210430MCX009


title: 300BCG228_d0_nkcell

tag: flowcell


title: Run1-MB549L


title: 300BCG229_d0_nkcell

tag: batch id


title: RNA-300

description:
RNA-300
rna_counts3g.txt


title: Run1-MC506L

value: Diet C - Control 0


title: 300BCG228_d0_cd8t

tag: pcr cq


title: Lung Cancer, 20210429MCX009


title: Run1-MB548L

value: Diet B - 0.075 mg/kg bw/day 3-methylfuran


title: RIBO-517

description:
RIBO-517
ribo_counts16p.txt


title: Lung Cancer, 20210603MCX006


title: Run1-MB546L


title: Lung Cancer, 20210415MCX002


title: RIBO-516

description:
RIBO-516
ribo_counts16p.txt


title: Lung Cancer, 20210330MCX002


title: Run1-MB545L


title: Lung Cancer, 20210323MCX007


title: 300BCG227_d0_PBMC

tag: filtered peaks


title: RIBO-506

description:
RIBO-506
ribo_counts16p.txt


title: J4-12-GAMS

value: blood b cell

value: Without ARDS

tag: timepoint

value: Day 4

tag: splice variant

value: secreted repertoire


title: Lung Cancer, 20210524MCX007

tag: tissue


title: Run1-MB542L


title: Lung Cancer, 20210309MCX007


title: 300BCG227_d0_monocyte

tag: cell type

value: monocyte

tag: tss enrichment

tag: frip


title: RIBO-504

description:
RIBO-504
ribo_counts16p.txt

value: Striatum

value: Male


title: Run1-MA532L

tag: treatment

value: Diet A - 0.02 mg/kg bw/day 3-methylfuran


title: 300BCG227_d0_cd8t

tag: genotype


title: RNA-302

description:
RNA-302
rna_counts3g.txt

tag: Sex

tag: strain


title: 300BCG227_d0_nkcell

value: nkcell

tag: individual


title: 300BCG227_d14_PBMC

tag: time point

value: ATAC


title: RIBO-498

description:
RIBO-498
ribo_counts16p.txt

tag: condition

value: Wild type


title: Pulmonary Tuberculosis, 230603MCX00015

value: BALF

tag: disease state

value: Pulmonary Tuberculosis


title: RIBO-505

description:
RIBO-505
ribo_counts16p.txt


title: Run1-MB541L

value: Liver


title: Run1-MA528L


title: RIBO-318

description:
RIBO-318
ribo_counts3g.txt


title: Pulmonary Tuberculosis, 230606MCX00030


title: Run1-MA525L


title: RIBO-499

description:
RIBO-499
ribo_counts16p.txt


title: RIBO-303

description:
RIBO-303
ribo_counts3g.txt

value: 3 genes hemideletion knockout


title: Run1-MA524L


title: RIBO-302

description:
RIBO-302
ribo_counts3g.txt


title: Pulmonary Tuberculosis, 230606MCX00022


title: 300BCG226_d0_cd8t

tag: protocol

tag: flowcell

value: HWVYYBBXX

tag: batch id


title: Run1-MA522L


title: RIBO-301

description:
RIBO-301
ribo_counts3g.txt


title: 300BCG226_d90_PBMC

value: PBMC

tag: pcr cq

tag: filtered peaks


title: Run1-MA531L

tag: tissue


title: Run1-MA529L


title: 300BCG225_d14_PBMC

tag: cell type


title: 300BCG226_d14_PBMC

tag: tss enrichment


title: RIBO-319

description:
RIBO-319
ribo_counts3g.txt


title: Pulmonary Tuberculosis, 230530MCX00020


title: 300BCG226_d0_PBMC

tag: frip


title: in3127_25_mmTG_sars_48hrs

city: Berkeley

first: Diana

last: Bautista

state: California

address: University Avenue

institute: University of California, Berkeley

description:
SARSMouseTG48hr_rawcounts.csv
viral_transcipts_mmTG_tpm.csv

data_processing:
Mouse trigeminal ganglia gene expression sequences are aligned to grcm39 using defaut settings of STAR
Calu-3 cells gene expression sequences are aligned to grch38 using defaut settings of STAR
SARS-CoV-2 transcripts are aligned to ASM985889v3 using Kallisto
Assembly: grcm39, grch38, ASM985889v3
Supplementary files format and content: Two comma-separated values file (csv) includes raw counts for each sample. One for the mouse TG, another for the Calu-3.
Supplementary files format and content: Two comma-separated values file (csv) includes TPM of Viral Transcripts for each sample. One for the mouse TG, another for the Calu-3.

source_name: Trigeminal Ganglion

growth_protocol: Mouse trigeminal ganglia were dissected and incubated in warmed Collagenase P (Roche) in Hanks calcium-free balanced salt solution followed by incubation in 0.25% trypsin with gentle agitation. Cells were washed, triturated, and plated in MEM Eagle's with Earle's BSS medium, supplemented with 10% horse serum (vol/vol), MEM vitamins, penicillin/streptomycin and L-glutamine. Cells were plated on poly-D-Lysine and laminin-coated 96-well plates for infection. Human airway epithelial cell and primary mouse neuron infection: Human adenocarcinoma lung epithelial (Calu-3) cells (ATCC, HTB-55) were maintained with RPMI (Fisher Scientific) supplemented with fetal bovine serum (FBS), L-glutamine, penicillin/streptomycin.

extract_protocol:
RNA are harvest using DNA/RNA Shield (Zymo Research).
lncRNA library with rRNA removal are prepared by Novogene

treatment_protocol: Approximately 500,000 Calu-3 cells were incubated with SARS-CoV-2 (WA1) in medium (10% heat-inactivated FBS, sodium pyruvate, HEPES, L-glutamine, penicillin/streptomycin) diluted in phenol-red free RPMI to an MOI of 1 for 24 or 48 hours. Mouse trigeminal ganglia cells were cultured as described above and plated in a 96-well plate. Eight trigeminal ganglia from 4 animals were combined and plated into 8 wells. TG cultures were infected with 500,000 SARS-CoV-2 virions or medium (mock infection) for 48 hours.

value: Trigeminal Ganglion

tag: treatment


title: Run2-ME092_L

value: Diet E - 2.0 mg/kg bw/day furan


title: Pulmonary Tuberculosis, 230526MCX00012


title: 300BCG226_d0_nkcell

tag: genotype


title: Run2-ME089_L


title: Pulmonary Tuberculosis, 230510MCX00020


title: Pulmonary Tuberculosis, 230518MCX00014


title: 300BCG226_d0_monocyte

value: HWVYNBBXX


title: Pulmonary Tuberculosis, 230517MCX00023


title: 300BCG225_d0_monocyte


title: in3127_23_mmTG_sars_48hrs


title: Run2-ME086_L


title: in3127_22_mmTG_sars_48hrs


title: Pulmonary Tuberculosis, 230505MCX00035


title: 300BCG224_d90_PBMC


title: Pulmonary Tuberculosis, 230517MCX00018


title: RIBO-300

description:
RIBO-300
ribo_counts3g.txt

tag: Sex


title: Pulmonary Tuberculosis, 230504MCX00021


title: in3127_21_mmTG_mock_48hrs


title: 300BCG225_d0_PBMC


title: Pulmonary Tuberculosis, 230512MCX00018


title: Run2-ME082_L


title: Run1-MA521L


title: Run2-ME081_L


title: in3127_19_mmTG_mock_48hrs


title: Pulmonary Tuberculosis, 20211203MCX011


title: in3127_20_mmTG_mock_48hrs


title: 300BCG223_d90_PBMC


title: 300BCG225_d0_nkcell


title: Run2-MD072_L

value: Diet D - 0.5 mg/kg bw/day furan


title: in3127_24_mmTG_sars_48hrs


title: 300BCG223_d14_PBMC


title: Run2-MD071_L


title: Run2-ME085_L


title: 300BCG225_d0_cd8t


title: Pulmonary Tuberculosis, 230509MCX00022


title: 300BCG223_d0_PBMC


title: Pulmonary Tuberculosis, 20211204MCX004


title: Run2-MD067_L


title: 300BCG224_d14_PBMC


title: Pulmonary Tuberculosis, 20211022MCX006


title: Run2-MD064_L


title: 300BCG222_d14_PBMC


title: whole-body section, untreated, sample1

data_processing:
Resulting libraries were sequenced on the NovaSeq 6000 (Illumina) and sequencing data was pre-processed using STAR/STARsolo 2.7.10a79 (https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md) for read alignment using the GRCm39 mouse reference genome, spatial barcode demultiplexing, and unique molecular identifier (UMI) counting.
Resulting ST data was normalized, processed for differential expression analysis, and visualized using custom Python 3.8.5 (http://www.python.org) scripts and existing packages, including Scanpy, scikit-image, and Seaborn.
Assembly: GRCm39
Supplementary files format and content: All_Samples.h5ad: filtered feature-barcode matrices
Library strategy: Spatial transcriptomics

source_name: Whole-body

extract_protocol:
In brief, After transfer, sections were fixed in methanol, stained with hematoxylin and eosin, and imaged on an Olympus VS2000 slide scanner (20X magnification). Sections were permeabilized (1% pepsin), incubated for in-tissue reverse transcription, and treated with Proteinase K for tissue removal. Resulting full-length, single-stranded cDNAs were denatured and retrieved from the array using KOH and purified by column clean up (Zymo Research).
cDNA was processed for single-primer PCR amplication followed by sequencing library construction using tagmentation (Nextera DNA Library Prep Kit) and final PCR amplification.

treatment_protocol: Mice injected with LPS or left untreated as control were euthanized with CO2, frozen in a dry ice-hexane bath after removing all body hair, and stored at -80°C until use. Frozen section preparation and section transfer were carried out according to Kawamoto’s film method77,78. Frozen mice were embedded in a cryo-embedding medium and sectioned (10-µm thickness) using a Leica CM3600-XP cryomacrotome. Resulting whole-mouse sections were transferred onto custom, large-format microarrays for spatial transcriptomics (ST) (30-µm spot diameter with 45 µm center-to-center distance between spots).

value: Whole-body

value: Wild-type (C57BL/6J)

value: Untreated


title: 300BCG224_d0_PBMC


title: whole-body section, LPS, sample2

value: LPS (5 mg/kg, 24 hours)


title: Pulmonary Tuberculosis, 20211112MCX010


title: Pulmonary Tuberculosis, 20211130MCX010


title: in3127_18_mmTG_mock_48hrs


title: Run2-ME083_L


title: whole-body section, untreated, sample2


title: Run2-MD069_L


title: Pulmonary Tuberculosis, 20211124MCX019


title: Pulmonary Tuberculosis, 20210526MCX015


title: Run2-MD063_L


title: er_fl_hsc2

city: Lund

first: Mohamed

last: Eldeeb

address: DMH, BMC B12

country: Sweden

institute: Lund University

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one sample greater than one count-per-million were excluded from further analysis. The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights. The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals.
Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Assembly: Mouse GRCm38
Supplementary files format and content: Tab-delimited file includes normalized counts (CPM)

source_name: Hematopoietic

extract_protocol:
Cells were harvested, lysed, and RNA extraction was performed using the Norgen single cell RNA purification kit (51800, Norgen Biotech).
Library preparation was performed using SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (634418, TaKaRa). Library concentration was measured using QuantIT 1X dsDNA HS Assay Kit (Q33232, Thermo Fisher), and quality was assessed on 5200 Fragment Analyzer™ 12-capillary (M3510AA, Agilent) using DNF-930 dsDNA Reagent Kit, 75 bp – 20,000 bp (K0500, Agilent).
The library pool was diluted to a final concentration of 1.25 nM and sequenced on a NovaSeq 6000 System (20012850, Illumina) using NovaSeq 6000 S2 Reagent Kit (2x100 paired end cycles) (20012861, Illumina).

value: Hematopoietic

value: Dox


title: whole-body section, LPS, sample1


title: 300BCG222_d0_PBMC

value: ATAC


title: Pulmonary Tuberculosis, 20210813MCX009

value: BALF


title: er_fl_hsc3


title: Pulmonary Tuberculosis, 20220104MCX015

value: Pulmonary Tuberculosis


title: 300BCG221_d90_PBMC


title: Run2-MD062_L

value: Liver


title: 300BCG222_d90_PBMC


title: Run2-MC012_L

value: Diet C - Control 0


title: Pulmonary Tuberculosis, 20210414MCX013


title: er_fl_hsc1


title: Pulmonary Tuberculosis, 20210430MCX011


title: Pulmonary Tuberculosis, 230510MCX00019


title: Pulmonary Tuberculosis, 20211022MCX010


title: 300BCG220_d90_PBMC


title: 300BCG220_d14_PBMC


title: Run2-MC011_L


title: 300BCG221_d0_PBMC


title: er_abm_hsc1


title: Run2-MC008_L


title: Run2-MC009_L


title: er_abm_hsc2


title: Run2-MC010_L


title: Pulmonary Tuberculosis, 20210723MCX017


title: 300BCG221_d14_PBMC


title: er_abm_hsc3


title: wt_fl_hsc3

value: WT


title: 300BCG220_d0_PBMC

value: PBMC


title: Pulmonary Tuberculosis, 20210630MCX014


title: 300BCG219_d90_PBMC


title: Run2-MC007_L


title: 300BCG219_d14_PBMC


title: Pulmonary Tuberculosis, 20210422MCX007


title: Pulmonary Tuberculosis, 20211126MCX009


title: wt_fl_hsc2


title: wt_fl_hsc1


title: 300BCG219_d0_PBMC


title: Run2-MC003_L


title: Run2-MC004_L


title: 300BCG218_d90_PBMC


title: wt_abm_hsc3


title: Run2-MB052_L

value: Diet B - 0.12 mg/kg bw/day furan


title: Run2-MB050_L


title: Pulmonary Tuberculosis, 20210713MCX010


title: Pulmonary Tuberculosis, 20220226MCX020


title: 300BCG218_d14_PBMC


title: Pulmonary Tuberculosis, 20211222MCX010


title: 300BCG218_d0_PBMC


title: Run2-MB048_L


title: Pulmonary Tuberculosis, 20211104MCX017


title: 300BCG217_d90_PBMC


title: Dox_ER_HSCs_02_S5

data_processing:
Demultiplexing was performed using the bcl2fastq2 software with default settings, and a raw quality control was performed.
Alignment to the Mouse GRCm38 was performed using the HISAT2 software.
Assembly of the alignments into full transcripts and quantification was performed using the StringTie software.
Differentially expressed genes analysis was performed using DESeq2. Gene set enrichment analysis was performed as previously described (Eldeeb et al., 2023; Subramanian et al., 2005).
Assembly: Mouse GRCm38
Supplementary files format and content: Tab-delimited file includes normalized counts (TPM)

extract_protocol:
RNA extraction was performed using the Norgen single cell RNA purification kit (51800, Norgen Biotech)
Library preparation was performed using SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (634418, TaKaRa). Library concentration was measured using QuantIT 1X dsDNA HS Assay Kit (Q33232, Thermo Fisher), and quality was assessed on 5200 Fragment Analyzer™ 12-capillary (M3510AA, Agilent) using DNF-930 dsDNA Reagent Kit, 75 bp – 20,000 bp (K0500, Agilent).
The library pool was diluted to a final concentration of 1.25 nM and sequenced on a NovaSeq 6000 System (20012850, Illumina) using NovaSeq 6000 S2 Reagent Kit (2x100 paired end cycles) (20012861, Illumina).

value: HSC

value: Dox food for 2 weeks


title: Dox_ER_HSCs_03_S6


title: Run2-MB046_L


title: 300BCG217_d14_PBMC


title: Dox_ER_HSCs_01_S4


title: Pulmonary Tuberculosis, 20210714MCX007


title: Pulmonary Tuberculosis, 20210910MCX014


title: 300BCG217_d0_PBMC


title: Run2-MB045_L


title: Run2-MB044_L


title: Pulmonary Tuberculosis, 20210924MCX017


title: NoDox_ER_HSCs_03_S3


title: NoDox_ER_HSCs_02_S2


title: Pulmonary Tuberculosis, 20210507MCX009


title: Run2-MB042_L


title: 300BCG216_d14_PBMC


title: wt_abm_hsc2


title: NoDox_ER_HSCs_01_S1


title: Run2-MB041_L


title: 300BCG216_d0_PBMC


title: Run2-MA030_L

value: Diet A - 0.03 mg/kg bw/day furan


title: Pulmonary Tuberculosis, 20210428MCX011