title: Mouse5, WT, Small-WT_1 (GeoMx)

description:
B022-B-mouseWTA-003
DSP-1001660005544-A-C01_RIA1443A25-25
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: SH-SY5Y,D6,RNaseR,rep2

status: Public on Mar 04 2024

type: SRA

city: Hefei

first: Yan

last: Yang

state: Anhui

address: No.373 Huangshan Road

country: China

institute: University of Science and Technology of China

library_source: transcriptomic

data_processing:
For poly(A)+ RNA-seq, raw sequence reads were trimmed for adaptor using cutadapt. Trimmed sequence reads were mapped to GRCh38/hg38 using STAR. Read count for each gene was obtained using RSEM. Intron retention in linear RNAs (LIR) was detected using IRFinder.
For RNase R-treated RNA-seq, raw sequence reads were trimmed for adaptor using cutadapt. Trimmed sequence reads were mapped to GRCh38/hg38 using bwa. Circular RNAs (circRNAs) were detected using CIRI2 and Exon-intron circRNAs (EIciRNAs) were detected using FEICP.
Assembly: hg38

molecule: total RNA

organism: Homo sapiens

growth_protocol: cells were cultured with DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S).

extract_protocol:
Total RNA was extracted by Trizol reagent (Invitrogene), according to the standard protocol. The ribosome RNA (rRNA) was removed by Ribominus kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: SY5Y cells were induced differentiation by treatment with 10 μM retinoic acid (RA) in the presence of 1% FBS.

tag: cell line

tag: genotype

value: WT

tag: treatment

value: retinoic acid differentiation


title: WTCHG_900295_205_CT+7_MenACWY_+ve

city: Oxford

first: Irina

last: Chelysheva

address: Roosevelt Dr

department: NDM

country: United Kingdom

institute: University of Oxford

description:
small RNA
stage2

data_processing:
Alignments were performed using bowtie with up to 2 mismatches in best strata mode, and bowtie2 with 2 gaps permitted
Reads were first aligned to the non-coding transcriptome. The bowtie indexes for the non-coding RNAome were built by merging fasta files from the following databases: miRbase (miRNAs), SnOPY (snoRNAs), trRNA_db (tRNAs), RefSeq (snRNAs, yRNAs, vault RNAs, lncRNAs.
Non-aligned reads were then aligned to the mRNA transcriptome, and antisense to the non-coding and mRNA transcriptome
All other reads were collapsed using a "gene_union" approach like those employed in seqCluster and mmQuant.
sRNA features were removed if they did not have an abundance of at least 5 counts per million in at least 20% of samples.
Assembly: GRCh38
Supplementary files format and content: txt file containing raw read counts for each gene for each sample

source_name: Whole blood

extract_protocol:
Peripheral blood (up to 2.5ml) was collected into a PAXgeneTM RNA tube at vaccination (D0), SARS-CoV-2 diagnosis (CT) and 7 days post diagnosis (CT+7). Total RNA was extracted using the PAXgene blood RNA kit (PreAnalytiX, Switzerland) on the QIAsymphony SP (Qiagen) with the PAX_RNA V5 protocol. Eluted RNA was quantified using the Agilent RNA ScreenTape assay on the 4200 TapeStation System (Agilent).
Small RNA libraries were prepared with the NEBNext® Small RNA Library Prep Set for Illumina (catalog #E7330) and run on a single flow cell target of 300 million reads) on the NexTSeq platform using the 75SR configuration with the aim of achieving 5.2 million reads per sample.

tag: tissue

value: Whole blood

tag: timepoint

tag: vaccine

value: MenACWY

tag: naat result

value: +ve

tag: age

tag: Sex

value: Female

tag: participant number


title: WTCHG_900295_204_CT+7_MenACWY_+ve

description:
small RNA
stage2

value: Male


title: SH-SY5Y,D6,RNaseR,rep1


title: Mouse5, WT, Large_1 (GeoMx)

city: Montreal

first: Janusz

last: Rak

state: Quebec

address: 1001 Decarie Blvd. Room E01.4366

department: Department of Pediatrics

country: Canada

institute: McGill University

description:
B022-B-mouseWTA-001
DSP-1001660005544-A-B11_RIA1443A23-23
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx

data_processing:
FASTQ converted to DCC files through Nanostring's pipeline
Assembly: GeoMx NGS Barcode sequencing
Supplementary files format and content: DCC files generated through Nanostring's pipeline
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: brain

extract_protocol:
FFPE GeoMx Digital Spatial Profiling on CD31+ AOIs
GeoMx NGS library preparation with SeqCode Dual Index Primers

value: brain

tag: cell type

value: mesenchymal glioma stem cell

value: EGFR-WT


title: Mouse2, WT, Large_2 (GeoMx)

description:
B022-A-mouseWTA-023
DSP-1001660005544-A-B10_RIA1443A22-22
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: E-In,high-GFP

library_source: genomic

data_processing:
Sequence reads were trimmed for adaptor sequence and sequencing primer using custom python scripts.
Trimmed reads were mapped to sgRNA library using bowtie allowing one mismatch (-v 1).
Read counts for each sgRNA were obtained using custom python scripts.
sgRNA read count was analyzed for enrichment of sgRNAs using MAGeCK test.
Assembly: Brunello sgRNA library
Supplementary files format and content: tab-delimited text file includes raw counts of each sgRNA for each sample

molecule: genomic DNA

extract_protocol:
The genomic DNA were extractd with QIAGEN DNeasy kit according to the manufacturer’s instructions.
sgRNAs were amplified with PCR and PCR products were subjected to standard DNA-seq.

treatment_protocol: Cells were infeted with the lentivirus human CRISPR knockout pooled library. The 4x 10^6 were collected for control, after seven days of puromycin selection. The 4 x 10^7 cells were sorted for collecting the highest GFP fluorescence as experiment grop.


title: Ctrl VSVZ ROI 09

city: Bethesda

first: Yuanyi

last: Feng

state: MD

address: 4301 Jones Bridge Road

country: USA

institute: UNIFORMED SERVICES UNIVERSITY OF THE HEALTH SCIENCES

description:
Experimental Slide 2022-08-18 | 053 | Full ROI
DSP-1001660012009-A-E06

data_processing:
Sequencing data were processed through GeoMx NGS Pipeline according to GeoMx DSP NGS Readout User Manual (MAN-10153-01).
Raw sequencing FASTQ files were converted to digital count conversion (DCC) files and further processed to obtain data for each target probe in each ROI by subtracting the mean of background and normalizing to Q3 of all targets.
Assembly: mm10
Supplementary files format and content: FlnKO CountMatrix.xlsx, DCC files
Library strategy: Spatial Transcriptomics

extract_protocol:
Mouse brains were fixed by transcardial perfusion with nuclease-free PBS and 4% paraformaldehyde. Fixed brains were embedded in OCT, cut to 7-μm cryosections, and placed on a microscope slide.
GeoMx Mouse Whole Transcriptome oligonucleotide probes by NanoString

value: 3 months

tag: region

value: VSVZ

value: Ctrl


title: E-In,input


title: Ctrl VSVZ ROI 10

description:
Experimental Slide 2022-08-18 | 054 | Full ROI
DSP-1001660012009-A-E07


title: Mouse4, WT, Small-WT_4 (GeoMx)

description:
B022-A-mouseWTA-022
DSP-1001660005544-A-B09_RIA1443A21-21
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: WTCHG_900295_203_CT_ChAdOx1_+ve

description:
small RNA
stage2

value: CT


title: SH-SY5Y,D3,RNaseR,rep2


title: SH-SY5Y,D3,RNaseR,rep1


title: Ctrl VSVZ ROI 08

description:
Experimental Slide 2022-08-18 | 052 | Full ROI
DSP-1001660012009-A-E05


title: Ctrl Cx ROI 07

description:
Experimental Slide 2022-08-18 | 057 | Full ROI
DSP-1001660012009-A-E10

value: Upper Cx


title: Mouse4, WT, Small-WT_3 (GeoMx)

description:
B022-A-mouseWTA-021
DSP-1001660005544-A-B08_RIA1443A20-20
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: Ctrl VSVZ ROI 07

description:
Experimental Slide 2022-08-18 | 051 | Full ROI
DSP-1001660012009-A-E04


title: WTCHG_900295_202_CT_MenACWY_+ve

description:
small RNA
stage2


title: P-In,input


title: WTCHG_900295_201_CT+7_ChAdOx1_+ve

description:
small RNA
stage2


title: SH-SY5Y,D0,RNaseR,rep2


title: Mouse4, WT, Small-WT_2 (GeoMx)

description:
B022-A-mouseWTA-020
DSP-1001660005544-A-B07_RIA1443A19-19
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: Ctrl VSVZ ROI 06

description:
Experimental Slide 2022-08-18 | 050 | Full ROI
DSP-1001660012009-A-E03


title: Ctrl VSVZ ROI 11

description:
Experimental Slide 2022-08-18 | 055 | Full ROI
DSP-1001660012009-A-E08


title: SH-SY5Y,D0,RNaseR,rep1


title: SH-SY5Y,D6,polyA,rep2

molecule: polyA RNA


title: Mouse4, WT, Small-WT_1 (GeoMx)

description:
B022-A-mouseWTA-019
DSP-1001660005544-A-B06_RIA1443A18-18
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: Mouse4, WT, Large_4 (GeoMx)

description:
B022-A-mouseWTA-018
DSP-1001660005544-A-B05_RIA1443A17-17
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: WTCHG_900988_283_CT_MenACWY_+ve

description:
small RNA
stage2


title: Ctrl Cx ROI 05

description:
Experimental Slide 2022-08-18 | 049 | Full ROI
DSP-1001660012009-A-E02


title: SH-SY5Y,D6,polyA,rep1


title: Ctrl Cx ROI 04

description:
Experimental Slide 2022-08-18 | 048 | Full ROI
DSP-1001660012009-A-E01


title: WTCHG_900988_282_CT_MenACWY_+ve

description:
small RNA
stage2


title: Ctrl Cx ROI 03

description:
Experimental Slide 2022-08-18 | 047 | Full ROI
DSP-1001660012009-A-D12


title: WTCHG_900988_280_CT+7_MenACWY_+ve

description:
small RNA
stage2


title: WTCHG_900988_281_CT+7_MenACWY_+ve

description:
small RNA
stage2


title: Mouse4, WT, Large_3 (GeoMx)

description:
B022-A-mouseWTA-017
DSP-1001660005544-A-B04_RIA1443A16-16
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: SH-SY5Y,D3,polyA,rep1


title: Ctrl Cx ROI 02

description:
Experimental Slide 2022-08-18 | 046 | Full ROI
DSP-1001660012009-A-D11


title: WTCHG_900988_279_CT_MenACWY_+ve

description:
small RNA
stage2


title: Mouse4, WT, Large_2 (GeoMx)

description:
B022-A-mouseWTA-016
DSP-1001660005544-A-B03_RIA1443A15-15
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: SH-SY5Y,D0,polyA,rep2


title: Ctrl Cx ROI 01

description:
Experimental Slide 2022-08-18 | 045 | Full ROI
DSP-1001660012009-A-D10


title: SH-SY5Y,D0,polyA,rep1


title: Ctrl VSVZ ROI 05

description:
Experimental Slide 2022-08-18 | 044 | Full ROI
DSP-1001660012009-A-D09


title: Mouse3, KO, Large-KO_2 (GeoMx)

description:
B022-A-mouseWTA-015
DSP-1001660005544-A-B02_RIA1443A14-14
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx

value: EGFR-KO


title: WTCHG_900988_277_CT+7_MenACWY_+ve

description:
small RNA
stage2


title: Ctrl VSVZ ROI 04

description:
Experimental Slide 2022-08-18 | 043 | Full ROI
DSP-1001660012009-A-D08


title: Mouse4, WT, Large_1 (GeoMx)

description:
B022-A-mouseWTA-013
DSP-1001660005544-A-A12_RIA1443A12-12
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: Mouse3, KO, Small_3 (GeoMx)

description:
B022-A-mouseWTA-011
DSP-1001660005544-A-A11_RIA1443A11-11
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: SH-SY5Y,D3,polyA,rep2


title: WTCHG_900988_278_CT_MenACWY_+ve

description:
small RNA
stage2


title: WTCHG_900988_275_CT_MenACWY_+ve

description:
small RNA
stage2


title: Ctrl VSVZ ROI 03

description:
Experimental Slide 2022-08-18 | 042 | Full ROI
DSP-1001660012009-A-D07


title: Mouse3, KO, Large-KO_1 (GeoMx)

description:
B022-A-mouseWTA-014
DSP-1001660005544-A-B01_RIA1443A13-13
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: HEK293,shSRSF1,polyA,rep1

value: SRSF1 knockdown


title: Mouse3, KO, Small_2 (GeoMx)

description:
B022-A-mouseWTA-010
DSP-1001660005544-A-A10_RIA1443A10-10
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: WTCHG_900988_276_CT_MenACWY_+ve

description:
small RNA
stage2


title: Ctrl VSVZ ROI 02

description:
Experimental Slide 2022-08-18 | 041 | Full ROI
DSP-1001660012009-A-D06


title: HEK293,shCtrl,polyA,rep2

value: WT


title: Mouse2, WT, Small-WT_3 (GeoMx)

description:
B022-A-mouseWTA-009
DSP-1001660005544-A-A09_RIA1443A9-9
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: HEK293,shCtrl,polyA,rep1


title: Ctrl VSVZ ROI 01

description:
Experimental Slide 2022-08-18 | 040 | Full ROI
DSP-1001660012009-A-D05


title: WTCHG_900988_273_CT_ChAdOx1_+ve

description:
small RNA
stage2


title: FlnKO Cx ROI 13

description:
Experimental Slide 2022-08-18 | 039 | Full ROI
DSP-1001660012009-A-D04

value: FlnKO


title: Mouse3, KO, Small_1 (GeoMx)

description:
B022-A-mouseWTA-008
DSP-1001660005544-A-A08_RIA1443A8-8
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: WTCHG_900988_272_CT+7_MenACWY_+ve

description:
small RNA
stage2

value: Whole blood


title: FlnKO Cx ROI 12

description:
Experimental Slide 2022-08-18 | 038 | Full ROI
DSP-1001660012009-A-D03


title: HEK293,shSRSF1,RNaseR,rep2


title: Mouse2, WT, Small-WT_2 (GeoMx)

description:
B022-A-mouseWTA-007
DSP-1001660005544-A-A07_RIA1443A7-7
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: HEK293,shSRSF1,RNaseR,rep1


title: HEK293,shSRSF1,polyA,rep2


title: WTCHG_900988_271_CT_ChAdOx1_+ve

description:
small RNA
stage2


title: FlnKO Cx ROI 11

description:
Experimental Slide 2022-08-18 | 037 | Full ROI
DSP-1001660012009-A-D02


title: Mouse2, WT, Small-WT_1 (GeoMx)

description:
B022-A-mouseWTA-006
DSP-1001660005544-A-A06_RIA1443A6-6
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: WTCHG_900988_270_CT+7_ChAdOx1_+ve

description:
small RNA
stage2


title: WTCHG_900988_269_CT+7_MenACWY_+ve

description:
small RNA
stage2

value: MenACWY


title: FlnKO Cx ROI 10

description:
Experimental Slide 2022-08-18 | 036 | Full ROI
DSP-1001660012009-A-D01


title: WTCHG_900988_274_CT_ChAdOx1_+ve

description:
small RNA
stage2

value: +ve


title: FlnKO Cx ROI 09

description:
Experimental Slide 2022-08-18 | 035 | Full ROI
DSP-1001660012009-A-C12


title: HEK293,polyA,rep2


title: Mouse2, WT, Large_4 (GeoMx)

description:
B022-A-mouseWTA-005
DSP-1001660005544-A-A05_RIA1443A5-5
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: HEK293,shCtrl,RNaseR,rep1


title: WTCHG_900988_267_CT_MenACWY_+ve

description:
small RNA
stage2

value: Female


title: HEK293,polyA,rep1


title: WTCHG_900988_268_CT+7_ChAdOx1_+ve

description:
small RNA
stage2


title: Mouse2, WT, Large_1 (GeoMx)

description:
B022-A-mouseWTA-002
DSP-1001660005544-A-A03_RIA1443A3-3
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: Mouse2, WT, Large_3 (GeoMx)

description:
B022-A-mouseWTA-003
DSP-1001660005544-A-A04_RIA1443A4-4
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: Mouse1, KO, Small (GeoMx)

description:
B022-A-mouseWTA-001
DSP-1001660005544-A-A02_RIA1443A2-2
Mm_R_NGS_WTA_v1.0.pkc
Q3_5% Filtered.xlsx


title: HEK293,RNaseR,rep4


title: FlnKO Cx ROI 08

description:
Experimental Slide 2022-08-18 | 034 | Full ROI
DSP-1001660012009-A-C11


title: WTCHG_900988_266_CT_MenACWY_+ve

description:
small RNA
stage2


title: FlnKO Cx ROI 07

description:
Experimental Slide 2022-08-18 | 033 | Full ROI
DSP-1001660012009-A-C10


title: FlnKO VSVZ ROI 12

description:
Experimental Slide 2022-08-18 | 032 | Full ROI
DSP-1001660012009-A-C09


title: WTCHG_900988_265_CT_MenACWY_+ve

description:
small RNA
stage2


title: anti-PD-1 + anti-Lair1 treatment at Week 4, mouse WTSV_af

city: South San Francisco

first: Lee

middle: Benjamin

last: Rivera

state: CA

address: 333 Oyster Point Blvd.

department: Biology

institute: NGM Bio

data_processing:
RNA-seq data raw reads were filtered using Trim Galore! to remove low quality and adaptor bases and reads shorter than 20 nt were discarded.
Filtered reads were mapped to UCSC mm10 genome sequences using STAR (v2.7.6).
Counts of all samples were generated using featureCounts (v2.0.1), and edgeR (v3.40.1) was used to get normalized counts and perform differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: gene expression read counts in tabular format

source_name: tumor

extract_protocol:
RNA isolation - Total RNA from tumors was isolated using Trizol and was purified using an RNAeasy kit (Qiagen).
Sequencing - Total RNA was then prepared for sequencing using the TailorMix Directional mRNA sample preparation kit (SeqMatic) and sequenced on Illumina NovaSeq V1.5 SP (100bp single-end reads and an average of 40 million reads were generated for each sample).

treatment_protocol: Generation of monocyte derived dendritic cells - Dendritic cells were derived from monocytes, which were purified from PBMCs using a human pan monocyte isolation kit (Miltenyi). DCs were generated by culturing monocytes in X-VIVO 15 media (Lonza) containing 50 ng/mL recombinant human GM-CSF (Peprotech) and 50 ng/mL recombinant human IL-4 (Peprotech) for 5-6 days. 96-well tissue culture plates (Corning) were coated with 5 µg/mL human collagen type 1 (Millipore Sigma) in PBS overnight at 4° C, then washed in PBS. 1 x 105 DCs were added to the plates with anti-LAIR1 or an isotype control antibody at the listed concentrations then incubated for 2 days at 37° C. Conditioned media was collected the next day and analyzed using Luminex (ProcartaPlex, ThermoFisher)

value: tumor

value: anti-Lair1 + anti-PD-1


title: FlnKO VSVZ ROI 11

description:
Experimental Slide 2022-08-18 | 031 | Full ROI
DSP-1001660012009-A-C08

value: brain


title: HEK293,RNaseR,rep2


title: HEK293,shCtrl,RNaseR,rep2


title: WTCHG_900988_264_CT+7_MenACWY_+ve

description:
small RNA
stage2


title: anti-PD-1 + anti-Lair1 treatment at Week 4, mouse WTSV_ae


title: FlnKO VSVZ ROI 10

description:
Experimental Slide 2022-08-18 | 030 | Full ROI
DSP-1001660012009-A-C07


title: HEK293,RNaseR,rep1


title: WTCHG_900988_263_CT+7_MenACWY_+ve

description:
small RNA
stage2

value: Male


title: FlnKO VSVZ ROI 09

description:
Experimental Slide 2022-08-18 | 029 | Full ROI
DSP-1001660012009-A-C06

value: 3 months


title: anti-PD-1 + control anti-KLH treatment at Week 4, mouse LOHM_d

value: anti-KLH + anti-PD-1


title: anti-PD-1 + anti-Lair1 treatment at Week 4, mouse WTSV_ai


title: FlnKO VSVZ ROI 08

description:
Experimental Slide 2022-08-18 | 028 | Full ROI
DSP-1001660012009-A-C05

value: VSVZ


title: Input MN R2

city: Exeter

first: Akshay

last: Bhinge

state: Devon

address: Stocker Road

institute: Living Systems Institute, University of Exeter

description: rRNA depleted total RNA

data_processing:
Adapters were removes using cutadapt and reads were mapped to hg19 using STAR.
Initial peak calling was performed for each sample by CLIPper using only the r1 reads. Peaks with genomic overlap in at least two ePRINT samples were identified and their genomic coordinates merged to define the candidate peak superset using HOMER. These peaks were then filtered using the input retaining those significantly enriched in the ePRINT samples in comparison to the corresponding input samples. The remaining high confidence peaks were then input to DESEQ2 for differential analysis.
Bedgraph files were generated from the r1 reads using bedtools
Assembly: hg19
Supplementary files format and content: bedgraph

source_name: iPSC-derived

growth_protocol: Healthy iPSCs were grown on matrigel in StemFlex and dissociated into small colonies with 0.1 mM EDTA when 70% confluent. Cells were plated as colonies in a 1:6 split.

extract_protocol:
RNA was harvested using Qiazol and rRNA depletion was performed using the NEB rRNA depletion kit.
Libraries were constructed using the NEBNext small RNA sequencing protocol

treatment_protocol: iPSCs were plated as colonies onto Matrigel and treated with neuronal differentiation media (DMEM/F12:Neurobasal in a 1:1 ratio, HEPES 10mM, N2 supplement 1%, B27 supplement 1%, L-glutamine 1%, ascorbic acid 5uM) supplemented with SB431542 (40uM), CHIR9921 (3uM) and LDN8312 (0.2uM) from day 0 till day 4. Cells were caudalized by treatment with 0.1uM retinoic acid starting at day 2 and ventralized with 1uM purmorphamine starting at day 4 and continued till day 8. On day 8, motor neuron progenitors (MNPs) were re-plated onto poly-D-lysine/laminin coated wells. Differentiation was induced by treating the cells with N2B27 media supplemented with retinoic acid, purmorphamine and DAPT 10uM. DAPT treatment was stopped at day 13 and media was changed to N2B27 supplemented with BDNF 10μg/ml, GDNF 10μg/ml. Samples were collected at day 10 (MNP) and day 15 (MN) for ePRINT.

value: iPSC-derived

value: motor neurons

value: differentiation into motor neurons


title: Input MN R1

description: rRNA depleted total RNA


title: WTCHG_900988_260_CT_MenACWY_+ve

description:
small RNA
stage2

value: CT


title: Input MNP R2

description: rRNA depleted total RNA

value: Motor neuron progenitors

value: WT


title: FlnKO VSVZ ROI 07

description:
Experimental Slide 2022-08-18 | 027 | Full ROI
DSP-1001660012009-A-C04

value: FlnKO


title: WTCHG_900988_261_CT+7_MenACWY_+ve

description:
small RNA
stage2

value: Whole blood

value: MenACWY


title: anti-PD-1 + control anti-KLH treatment at Week 4, mouse KWM_a


title: anti-PD-1 + anti-Lair1 treatment at Week 4, mouse WTSV_ah


title: anti-PD-1 + control anti-KLH treatment at Week 4, mouse LOHM_a


title: HEK293,RNaseR,rep3


title: FlnKO PH ROI 14

description:
Experimental Slide 2022-08-18 | 026 | Full ROI
DSP-1001660012009-A-C03

value: PH


title: Input MNP R1

description: rRNA depleted total RNA


title: FlnKO PH ROI 13

description:
Experimental Slide 2022-08-18 | 025 | Full ROI
DSP-1001660012009-A-C02


title: WTCHG_900988_259_CT+7_MenACWY_+ve

description:
small RNA
stage2

value: +ve

value: Female


title: Lymph node cells, EAE mouse 3, VDJ

city: Quebec

first: Luc

last: Vallières

address: 2705 Laurier Boulevard

department: Neuroscience

institute: University Hospital Center of Quebec – Laval University

description: 10× Genomics, single-cell VDJ profile

library_source: transcriptomic single cell

data_processing:
For gene expression libraries, sequencing data were processed, aligned to the mm10 reference genome, and aggregated into a single file using Cell Ranger 4.0 (10× Genomics) with default settings. This file was examined using Loupe Browser 4.2 (10× Genomics) and filtered to remove ambiguous cells (e.g. doublets, phagocytosed cells) based on colocalized cell-specific markers (e.g. Sdc1 [CD138], Ighd, Cd19, Cd3e, C1qa, Siglech, Ccr7, Ly6g, Hbb-bt). Downstream analyses were performed on the filtered data reanalyzed with Cell Ranger.
For V(D)J libraries, sequencing data were processed and aligned to the GRCm38 reference genome using Cell Ranger with default settings. Each sample was separately examined using Loupe V(D)J Browser v3.0 (10× Genomics). Clonotype and lineage data were obtained using Enclone v.0.5.9 (10× Genomics).
Assembly: mm10 (GEX) or GRCm38 (VDJ)
Supplementary files format and content: The .cloupe file is readable with Loupe Browser 4.2 and contains all gene expression data.
Supplementary files format and content: The .vloupe file is readable with Loupe V(D)J Browser v3.0 and contains all VDJ data.

source_name: Inguinal lymph nodes

extract_protocol:
Cells were processed with the Chromium Single Cell Chip A and Chromium Controller (10× Genomics) according to the manufacturer's protocols.
RNA samples were pooled for reverse transcription and amplification to generate gene expression and V(D)J libraries using the Single Cell 5’ Library Kit and Single Cell V(D)J Enrichment Kit (10× Genomics) according to the manufacturer's protocols.

treatment_protocol: Mice received a total of 200 µl of emulsion, injected subcutaneously into each flank. Emulsion was made by mixing equal volumes of Freund's adjuvant supplemented with 5 mg/ml of killed Mycobacterium tuberculosis H37Ra and PBS containing 4.5 mg/ml of bMOG. Mice were injected intraperitoneally with 20 µg/kg of pertussis toxin immediately before immunization and 2 days later.

value: Inguinal lymph nodes

value: Mix enriched in CD138+ cells

tag: strain

value: 8-9 weeks

value: bMOG immunization

tag: time point

value: Day 8 post-immunization


title: Lymph node cells, EAE mouse 4, VDJ

description: 10× Genomics, single-cell VDJ profile

value: Male


title: FlnKO PH ROI 12

description:
Experimental Slide 2022-08-18 | 024 | Full ROI
DSP-1001660012009-A-C01

value: brain

value: 3 months


title: ep MN R2

description: rRNA depleted total RNA

value: iPSC-derived

value: motor neurons

value: differentiation into motor neurons


title: WTCHG_900988_258_CT+7_MenACWY_+ve

description:
small RNA
stage2


title: ep MN R1

description: rRNA depleted total RNA

value: WT


title: WTCHG_900988_257_CT_MenACWY_+ve

description:
small RNA
stage2

value: Whole blood

value: CT


title: Lymph node cells, EAE mouse 2, VDJ

description: 10× Genomics, single-cell VDJ profile


title: FlnKO PH ROI 11

description:
Experimental Slide 2022-08-18 | 023 | Full ROI
DSP-1001660012009-A-B12

value: PH

value: FlnKO


title: ep MNP R2

description: rRNA depleted total RNA

value: Motor neuron progenitors


title: WTCHG_900988_262_CT+7_MenACWY_+ve

description:
small RNA
stage2

value: MenACWY

value: +ve

value: Female


title: Lymph node cells, EAE mouse 1, VDJ

description: 10× Genomics, single-cell VDJ profile

value: Inguinal lymph nodes

value: Mix enriched in CD138+ cells

value: 8-9 weeks

value: bMOG immunization


title: ep MNP R1

description: rRNA depleted total RNA


title: WTCHG_900988_254_CT_MenACWY_+ve

description:
small RNA
stage2


title: FlnKO PH ROI 09

description:
Experimental Slide 2022-08-18 | 021 | Full ROI
DSP-1001660012009-A-B10

value: brain

value: 3 months


title: Lymph node cells, EAE mouse 4, GEX

description:
10× Genomics, single-cell gene expression profile
GEX1-4.cloupe

value: Male

value: Day 8 post-immunization


title: WTCHG_900988_252_D0_ChAdOx1_D0_only

description:
small RNA
stage2


title: input 293T siFUS R2

description: rRNA depleted total RNA

growth_protocol: Cells were grown in DMEM and 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

treatment_protocol: Cells were transfected with the control and FUS siRNAs (Silencer Select siRNA, Thermo Fisher) at a conc of 5nM using Calcium Phosphate. Media was changed at 24 hours and samples were collected 72 hours post-transfection.

value: Human embryonic Kidney

value: WT

value: FUS siRNA


title: input 293T siFUS R1

description: rRNA depleted total RNA


title: Lymph node cells, EAE mouse 2, GEX


title: Lymph node cells, EAE mouse 3, GEX


title: input 293T siNeg R2

description: rRNA depleted total RNA

value: control siRNA


title: FlnKO VSVZ ROI 06

description:
Experimental Slide 2022-08-18 | 019 | Full ROI
DSP-1001660012009-A-B08

value: VSVZ

value: FlnKO


title: WTCHG_900988_251_D0_ChAdOx1_D0_only

description:
small RNA
stage2

value: Whole blood


title: Lymph node cells, EAE mouse 1, GEX


title: FlnKO VSVZ ROI 05

description:
Experimental Slide 2022-08-18 | 018 | Full ROI
DSP-1001660012009-A-B07


title: input 293T siNeg R1

description: rRNA depleted total RNA


title: FlnKO VSVZ ROI 04

description:
Experimental Slide 2022-08-18 | 017 | Full ROI
DSP-1001660012009-A-B06


title: WTCHG_900988_249_D0_ChAdOx1_D0_only

description:
small RNA
stage2


title: WTCHG_900988_250_D0_MenACWY_D0_only

description:
small RNA
stage2

value: MenACWY


title: WT, 6Day, 3

city: LITTLE ROCK

first: Zijing

last: Zhang

address: 4301 W Markham St

institute: University of Arkansas for Medical Sciences

data_processing:
The samples were sequenced and analyzed by Novogene.  The reads were mapped using STAR (v2.5) to the reference genome and HTSeq (v0.6.1) as used to count the reads mapped to each gene. FPKM of each gene was calculated and differential expression analysis performed using DESeq2 (v2_1.6.3). The resulting p-values were adjusted using the Benjamini and Hochberg's approach for controlling the False Discovery Rate (FDR). Genes with an adjusted p-value < 0.05 were considered differentially expressed.
Assembly: mm10
Supplementary files format and content: excel file including fpkm of genes.

source_name: lung

extract_protocol:
Each mouse lung sample was treated with 1mL of TRIZzol reagent at room temperature for 30 min. Total RNAs were then isolated according to the manufacturer's instruction.
The RNA samples were checked for quality using Bioanalyzer (Agilent 2100) and were sent to Novogene for library construction per company's protocol.

value: lung

value: 6 days post infection


title: ep 293T siFUS R2

description: rRNA depleted total RNA


title: WT, 6Day, 2


title: FlnKO VSVZ ROI 03

description:
Experimental Slide 2022-08-18 | 016 | Full ROI
DSP-1001660012009-A-B05


title: WT, 6Day, 1


title: ep 293T siFUS R1

description: rRNA depleted total RNA


title: WTCHG_900988_248_D0_MenACWY_D0_only

description:
small RNA
stage2


title: FlnKO PH ROI 10

description:
Experimental Slide 2022-08-18 | 022 | Full ROI
DSP-1001660012009-A-B11

value: PH


title: WTCHG_900988_253_D0_ChAdOx1_D0_only

description:
small RNA
stage2


title: WTCHG_900988_247_D0_MenACWY_D0_only

description:
small RNA
stage2

value: Female


title: ep 293T siNeg R2

description: rRNA depleted total RNA


title: WT, 4Day, 3

value: 4 days post infection


title: FlnKO VSVZ ROI 01

description:
Experimental Slide 2022-08-18 | 014 | Full ROI
DSP-1001660012009-A-B03

value: brain


title: FlnKO VSVZ ROI 02

description:
Experimental Slide 2022-08-18 | 015 | Full ROI
DSP-1001660012009-A-B04

value: 3 months


title: FlnKO PH ROI 08

description:
Experimental Slide 2022-08-18 | 020 | Full ROI
DSP-1001660012009-A-B09


title: WTCHG_900988_245_D0_MenACWY_D0_only

description:
small RNA
stage2


title: WT, 4Day, 2


title: ep 293T siNeg R1

description: rRNA depleted total RNA


title: WTCHG_73825358_CT_MenACWY_+ve

data_processing:
The sequencing data were aligned against the whole human (Homo sapiens) genome build GRCh38 using STAR (version 2.7.3a).
Gene features were counted using HTSeq (version 0.11.1), using human gene annotation general transfer format version GRCh38.92.
Genes with low counts across most libraries were removed by only retaining genes with abundance greater than 3 counts per million in 9 or more samples.
Ribosomal RNA (rRNA), sex chromosome genes, mitochondrial RNA and haemoglobin genes were excluded from downstream analysis.
Assembly: GRCh38
Supplementary files format and content: txt file containing normalised expression (rpkm - reads per kilobase per million) for each gene for each sample

extract_protocol:
Peripheral blood (up to 2.5ml) was collected into a PAXgeneTM RNA tube at vaccination (D0), SARS-CoV-2 diagnosis (CT) and 7 days post diagnosis (CT+7). Total RNA was extracted using the PAXgene blood RNA kit (PreAnalytiX, Switzerland) on the QIAsymphony SP (Qiagen) with the PAX_RNA V5 protocol. Eluted RNA was quantified using the Agilent RNA ScreenTape assay on the 4200 TapeStation System (Agilent).
RNA was ribodepleted and globin depleted using Ribo-ZeroTM Gold rRNA removal Kit (Illumina, USA). RNA was converted to cDNA, second-strand cDNA synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated and prior to amplification, samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and quality controlled before 150bp paired-end sequencing (NovaSeq6000).

value: CT

value: +ve


title: WTCHG_900988_246_D0_ChAdOx1_D0_only

description:
small RNA
stage2


title: WT, 4Day, 1


title: FlnKO Cx ROI 05

description:
Experimental Slide 2022-08-18 | 012 | Full ROI
DSP-1001660012009-A-B01

value: Upper Cx


title: WTCHG_900988_244_D0_ChAdOx1_D0_only

description:
small RNA
stage2

value: Male


title: WTCHG_73815357_CT_MenACWY_+ve


title: WT, Mock, 3

value: mock infection


title: FlnKO Cx ROI 04

description:
Experimental Slide 2022-08-18 | 011 | Full ROI
DSP-1001660012009-A-A12


title: FlnKO Cx ROI 03

description:
Experimental Slide 2022-08-18 | 010 | Full ROI
DSP-1001660012009-A-A11


title: WTCHG_900988_255_CT_MenACWY_+ve

description:
small RNA
stage2


title: WTCHG_73805356_CT7_MenACWY_+ve


title: WTCHG_900988_243_D0_MenACWY_D0_only

description:
small RNA
stage2


title: WT, Mock, 2


title: WTCHG_73125384_CT7_MenACWY_+ve


title: WTCHG_900988_242_D0_ChAdOx1_D0_only

description:
small RNA
stage2


title: WT, Mock, 1


title: FlnKO Cx ROI 02

description:
Experimental Slide 2022-08-18 | 009 | Full ROI
DSP-1001660012009-A-A10


title: WTCHG_73115383_CT_MenACWY_+ve


title: WTCHG_900988_241_D0_ChAdOx1_D0_only

description:
small RNA
stage2


title: DownSyndrome, 6Day, 3


title: FlnKO Cx ROI 06

description:
Experimental Slide 2022-08-18 | 013 | Full ROI
DSP-1001660012009-A-B02


title: WTCHG_900988_240_D0_MenACWY_D0_only

description:
small RNA
stage2


title: FlnKO Cx ROI 01

description:
Experimental Slide 2022-08-18 | 008 | Full ROI
DSP-1001660012009-A-A09


title: DownSyndrome, 6Day, 2


title: WTCHG_73095381_CT7_MenACWY_+ve


title: WTCHG_900988_239_D0_ChAdOx1_D0_only

description:
small RNA
stage2


title: DownSyndrome, 6Day, 1


title: FlnKO PH ROI 06

description:
Experimental Slide 2022-08-18 | 006 | Full ROI
DSP-1001660012009-A-A07


title: DownSyndrome, 4Day, 3


title: FlnKO PH ROI 05

description:
Experimental Slide 2022-08-18 | 005 | Full ROI
DSP-1001660012009-A-A06


title: WTCHG_900988_237_D0_ChAdOx1_D0_only

description:
small RNA
stage2


title: WTCHG_73075379_CT_MenACWY_+ve


title: DownSyndrome, 4Day, 2


title: WTCHG_73065378_CT_ChAdOx1_+ve


title: WTCHG_73055377_CT_ChAdOx1_+ve


title: FlnKO PH ROI 02

description:
Experimental Slide 2022-08-18 | 002 | Full ROI
DSP-1001660012009-A-A03


title: DownSyndrome, 4Day, 1


title: FlnKO PH ROI 03

description:
Experimental Slide 2022-08-18 | 003 | Full ROI
DSP-1001660012009-A-A04


title: WTCHG_900988_234_CT+7_ChAdOx1_+ve

description:
small RNA
stage2


title: WTCHG_900988_235_D0_MenACWY_D0_only

description:
small RNA
stage2


title: DownSyndrome, Mock, 3


title: FlnKO PH ROI 07

description:
Experimental Slide 2022-08-18 | 007 | Full ROI
DSP-1001660012009-A-A08


title: FlnKO PH ROI 01

description:
Experimental Slide 2022-08-18 | 001 | Full ROI
DSP-1001660012009-A-A02


title: DownSyndrome, Mock, 2


title: WTCHG_900988_233_CT_ChAdOx1_+ve

description:
small RNA
stage2


title: WTCHG_73035375_CT_ChAdOx1_+ve


title: WTCHG_73085380_CT_MenACWY_+ve


title: DownSyndrome, Mock, 1


title: WTCHG_900988_238_D0_ChAdOx1_D0_only

description:
small RNA
stage2


title: Immunocompetent_GeneExpression_Library2

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: 237 Tower Rd

department: Meinig School of Biomedical Engineering

institute: Cornell University

description:
Immunocompetent_multi_raw_feature_bc_matrix.h5
Immunocompetent_multi_assignment_confidence_table.csv

data_processing:
Raw sequencing data was aligned to a combined human and mouse genome reference (assembly: GRCh38 and mm10) using the Cell Ranger 6.1.1 pipeline (10x Genomics) to obtain single-cell gene expression matrices for individual samples. Cell multiplexing oligo sequencing data was used to demultiplex the raw gene expression data for individual samples using the multi command in Cell Ranger 6.1.1 pipeline. The cell multiplexing oligo IDs were provided in a config file to the CellRanger multi command and min-assignment-confidence was set to 0.9 (recommended default).
Assembly: GRCh38 and mm10
Supplementary files format and content: HDF5 file containing single-cell gene expression count matrix (UMI counts)
Supplementary files format and content: CSV file containing demulitplexing results for cellplex experiment

source_name: Mineralized and deminerlaised bone scaffolds

growth_protocol: Differently mineralized bone matrix scaffolds were fabricated as previously described. Briefly, 6mm diameter cylindrical subchondral bone plug biopsies were extracted from 1-3 day old neonatal bovine femurs, flushed with deionized water to remove marrow, and cut into 1mm thick sections. Cells and debris were removed by incubation in an extraction buffer of 20 mM NaOH and 0.5% Triton X-100 in PBS at 37 °C. Scaffolds were then treated with 20 U/mL DNase I to remove residual DNA, washed 5 times with PBS and labeled as “M-Bone''. To produce “DM-Bone” scaffolds, mineral-containing “M-Bone” scaffolds were demineralized at physiological pH in a solution of 9.5% ethylenediaminetetraacetic acid (EDTA), then washed 5 times in PBS. Before use, scaffolds were sterilized by overnight incubation in 70% ethanol, then washed with PBS and pre-incubated in complete culture medium. MDA-MB231 breast cancer cells (ATCC) expressing RFP and luciferase were routinely cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S) in a 5% CO2 incubator. 400,000 cells (P12) were seeded onto M-Bone and DM-Bone scaffolds and cultured overnight before implantation. Bone-tropic Balb/C-syngeneic 4T1.2 cells expressing GFP and luciferase were routinely cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS)  and 1% penicillin/streptomycin (P/S) in a 5% CO2 incubator. 50,000 cells (P4) were seeded onto M-Bone and DM-Bone scaffolds and cultured overnight before implantation.

extract_protocol:
Mice implanted with scaffolds were sacrificed on day 14 post implantation and the scaffolds with tumor microenvironment were isolated aseptically for single-cell RNA sequencing experiments. One half of the collected scaffolds from each condition was minced into 1-2 mm pieces and transferred to 1.5 ml Eppendorf tube for dissociation into a single cell suspension. Tissue pieces were then digested in a tissue dissociation media with 5mg/mL dispase, 2.5 mg/mL collagenase I, and 2.5 mg/mL collagenase II in 1x basal culture medium in a 37°C incubator. At the end of the digestion, the cells were passed through a 40 µm filter and centrifuged into a pellet. To remove erythrocytes from the suspension, samples were resuspended in an ammonium-chloride-potassium (ACK) lysis buffer for 3-5 minutes and centrifuged at 180g for 6 minutes. For immunocompromised mice, samples were then washed 3x in PBS with 0.04% BSA and then resuspended at 1 × 106 cells per ml. Cells from each sample were stained with Trypan Blue and cell viability was calculated on an automated cell counter (Countess II) before loading the cells on 10x Chromium. We used these cell viabilities to adjust the number of cells loaded on 10x Chromium to get the desired number of transcriptomes from viable cells for each sample (5000 cells per sample). For immunocompetent mice, samples were washed twice in PBS with 0.04% BSA and then resuspended at 0.5 × 106 cells in 1 ml total buffer. The cells were then centrifuged and the supernatant was removed without disturbing the pellet. Distinct 10x Genomics Cell Multiplexing Oligos were then added to all samples and incubated for 5 minutes at room temperature. Samples Control-M-Bone, Control-DM-Bone, Tumor-M-Bone, Tumor-DM-Bone were tagged with CMO301, CMO302, CMO303, and CMO304 respectively. Labeled cell suspensions were then washed 3x in pre-chilled wash and resuspension buffer containing 1% BSA in 1x PBS as recommended in the manufacturer’s Cell Multiplexing Oligo Labeling protocol for Single-cell RNA Sequencing. The cells were resuspended in the resuspension buffer at 1500 cells/ul and were counted on an automated cell counter (Countess II). Labeled cells from individual samples were pooled in equal proportions, stained with Trypan Blue, and cell viability was calculated on an automated cell counter (Countess II) before loading the cells on 10x Chromium. We used these cell viabilities to adjust the number of cells loaded on 10x Chromium to get the desired number of transcriptomes from viable cells for each sample (5000 cells per sample; 20,000 total cells for four samples).
For immunocompromised mice, single-cell suspensions for individual samples were directly loaded on the Chromium platform (10x Genomics) with one microfluidic channel per condition and ~5000 target cells per channel. Single-cell mRNA libraries were made using the Chromium Next GEM Single Cell 3’ Library Construction V3.1 Kit according to the manufacturer’s protocol. Sequencing Libraries sequenced on an Illumina NextSeq 500/550 using 75 cycle high output kits (Index 1 = 8bp, Index2 =8bp, Read 1 = 28, and Read 2 = 55bp). Raw sequencing data was aligned to a combined human and mouse genome reference (assembly: GRCh38 and mm10) using the Cell Ranger 6.1.1 pipeline (10x Genomics) to obtain single-cell gene expression matrices for individual samples. For immunocompetent mice, oligo-tagged and pooled single-cell suspension derived from all four experiment conditions was loaded on a single microfluidic channel of the Chromium platform (10x Genomics) with a target of ~16,000 cells (~4,000 cells per experiment condition). A single-cell mRNA library and a cell multiplexing oligo library were made using the Chromium Next GEM Single Cell 3’ Library Construction V3.1 Kit with Feature Barcode technology for Cell Multiplexing, according to the manufacturer’s protocol. Sequencing Libraries sequenced on an Illumina NextSeq 500/550 using 75 cycle high output kits (Index 1 = 10bp, Index2 =10bp, Read 1 = 28, and Read 2 = 90bp). Raw sequencing data was aligned to a combined human and mouse genome reference (assembly: GRCh38 and mm10) and demultiplexed using the Cell Ranger 6.1.1 pipeline (10x Genomics).

treatment_protocol: For immunocompromised experiments, pre-seeded scaffolds were implanted on the subcutaneous flank of 6-8 week old female athymic nude-Foxn1nu mice. Bioluminescence images were taken with an in vivo imaging system once weekly 10 minutes following intraperitoneal (IP) injection of 150 mg/kg D-luciferin in DPBS. For immunocompetent experiments, pre-seeded scaffolds were implanted on the subcutaneous flank of 6-8 week old female Balb/C mice. Bioluminescence images were taken twice weekly 15 minutes following IP injection of 150 mg/kg D-luciferin in DPBS. Implants were followed for 14 days and candidates for sequencing were identified by bioluminescent signal. Samples for single-cell transcriptomics were processed as below.

value: None and 4T1.2

value: Balb/C

value: 14 days post-implantation

tag: condition

value: Tumor-free and 4T1.2-seeded


title: WTCHG_73025374_CT+7_ChAdOx1_+ve

value: Whole blood


title: WTCHG_900988_232_CT+7_ChAdOx1_+ve

description:
small RNA
stage2


title: Immunocompetent_CellplexOligo_Library2

value: Mineralized and deminerlaised bone scaffolds


title: ATAC of HEK293 TNFa with TRAFTAC against NfkB, rep2

city: Zürich

first: Pierre-Luc

last: Germain

address: Winterthurerstrasse 190

department: D-HEST Institute for Neuroscience

country: Switzerland

institute: ETH Zürich

data_processing:
Adapters were removed with trimmomatic before alignment on GRCh38.p10 using bowtie2 with --dovetail --no-mixed --no-discordant -I 15 -X 2000. Duplicates were marked with picard.
Peaks were called on the merge of reads from all samples using MACS2.
Bigwig files of (shifted) insertion sites (normalized to library size) were generated using the epiwraps R package.
Assembly: GRCh38
Supplementary files format and content: Peaks (called on the merge of all samples), per-sample bigwig files of insertion sites
Supplementary files format and content: peakCounts.SE.rds.gz is a R object containing a SummarizedExperiment of the peak counts.

growth_protocol: HEK293 cells were cultured in Dulbecco's Modified Eagles Medium (DMEM) with 10% Fetal Bovine serum (FBS) (Gibco,10500064) and 1% Penicillin/Streptomycin (P/S) (Gibco,15140122). All of the incubation steps were performed at 37 Celsius and 5% CO2.

extract_protocol:
30 min before harvest, cells were treated with 200 units/ml DNase (Sigma, DN25). HEK293 cells were then washed twice with PBS (Gibco, 10010023) and detached with TrypLE (Gibco, 12605010). Enzymatic digestion was quenched with growth medium and cells were washed once again with PBS.
ATAC libraries were prepared from 50 000 cells per sample according to the published OmniATAC protocol (Corces et al., 2017) with minor adaptations. In short, samples were washed with cold 50 ul of PBS, afterwards cells were incubated in 50 ul lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin) for 3 min on ice. Cells were washed with 1 ml of lysis buffer without Digitonin and NP-40. Transposition was done in 50 ul reaction buffer (1x tagmentation buffer (Diagenode, C01019043), 0.1% Tween-20, 0.01% and 2.5 ul Tn5 (Diagenode, C01070012)) for 30 min at 37 Celsius and 1000 RPM shaking. Subsequent DNA purification was performed with MinElute Reaction Cleanup Kit (Qiagen, 28204). PCR amplification was done with NEBNext High Fidelity 2X PCR Master mix (NEB, M0541) and UDI primer (Diagenode, #C01011034) with concentrations according to manufacturer's recommendation. Total number of needed amplification cycles (8x) was controlled with qPCR. Library purification and fragment size selection was done with AMPure XP beads (Beckmann, A63880). 20 ul of 10 nM was sent for sequencing externally with Novogene (Cambridge, UK). A minimum of 20 Mio PE reads were sequenced per sample.

treatment_protocol: For the transfection cells at a confluency of 70-90% were incubated for 6h with 1 ug/mL of a plasmid encoding N-terminal HA-HaloTag7-containing dCas9 fusion protein and 25 nM TRAFTAC using Lipofectamine 3000 following the suppliers' instructions. The plasmid used was published and kindly provided by the Crews lab (Samarasinghe et al., 2021). Cells were then incubated for 19h with 5 ng/mL of TNF-alpha (Sigma-Aldrich, H8916) and 25 uM HP14 (dissolved in DMSO) (WuXiAppTec) respectively DMSO.

tag: knockdown

value: NFkB

value: TNF-alpha activation


title: WTCHG_73015373_CT+7_MenACWY_+ve

value: MenACWY

value: Female


title: WTCHG_900988_231_CT+7_MenACWY_+ve

description:
small RNA
stage2


title: WTCHG_73045376_CT+7_MenACWY_+ve


title: Immunocompetent_GeneExpression_Library1


title: WTCHG_73005372_CT+7_ChAdOx1_+ve


title: WTCHG_900988_230_CT+7_MenACWY_+ve

description:
small RNA
stage2


title: WTCHG_72995371_CT_MenACWY_+ve


title: WTCHG_900988_229_CT+7_ChAdOx1_+ve

description:
small RNA
stage2


title: Immunocompetent_CellplexOligo_Library1


title: ATAC of HEK293 TNFa with scrambled TRAFTAC, rep1


title: ATAC of HEK293 TNFa with scrambled TRAFTAC, rep2


title: Immunocompromised_Tumor_DM-Bone

source_name: Deminerlaised bone scaffold

value: Deminerlaised bone scaffold

value: Athymic Nude-Foxn1nu


title: WTCHG_900988_228_CT+7_ChAdOx1_+ve

description:
small RNA
stage2


title: WTCHG_72985370_CT_MenACWY_+ve

value: CT


title: WTCHG_72975369_CT_MenACWY_+ve

value: +ve


title: WTCHG_900988_227_CT_MenACWY_+ve

description:
small RNA
stage2


title: scRNAseq_FL_E125_dCas9P300TSS

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

institute: University of Geneva

data_processing:
10× Genomics Cell Ranger 6.1.2 software was used for demultiplexing, alignment, filtering barcode, and UMI counting
Assembly: mm39
Supplementary files format and content: 10× Genomics Cell Ranger 6.1.2 software output

source_name: Embryonic Limb Bud

growth_protocol: Limbs from 40-45 somite-stage (E12.5) mouse embryos were microdissected in PBS.

extract_protocol:
Two replicates of forelimb buds of E12.5 of Pitx1-Inv1+/- embryos and one replicate of E12.5 Shox2-dCas9P300-ColA1-sgRNAs forelimb bud were micro-dissected and incubated for 12 minutes in 400l trypsin-EDTA 0.25% (Thermo Fischer Scientific, 25300062), supplemented with 40l of 5% BSA. During incubation tissues were disrupted by pipetting after 6 minutes of incubation and at the end of the 12 minutes. Trypsin was then inactivated by adding 2x volume of 5% BSA and single cell suspension was obtained by passing cells in a 40m cell strainer. Cells were then spun at 250g for 5 minutes at 4° and resuspended in 1%BSA in PBS. Cells were then counted using an automatized cell counter and a 1% BSA 1400cells/ul suspension was prepared.
Single-cell libraries were prepared using the Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 following the manufacture’s protocol (10X Genomics, PN-1000075). Briefly, Gel beads in EMulsion (GEMs) are generated by combining Single Cell 3ʹ v3.1 Gel Beads, a Master Mix containing cells, and Partitioning Oil onto Chromium Chip B. Incubation of the GEMs produced from the poly-adenylated mRNA barcoded, full-length cDNA. Immediately, gel beads are dissolved and cDNA is amplified via PCR followed by library construction and sequencing. Libraries were paired-end sequenced on a HiSeq 4000. On average, 7000 cells were loaded on the Chromium Chip and between 25000-35000 mean reads were obtained.

value: Embryonic Limb Bud

value: embryonic limb cell


title: WTCHG_72965368_CT7_MenACWY_+ve


title: Immunocompromised_Tumor_M-Bone

source_name: Minerlaized bone scaffold

value: Minerlaized bone scaffold


title: CHiC-mESC-Inv2

description: mESC

data_processing:
*library strategy: capture Hi-C
Sequencing reads were mapped to reference genome mm9, filtered and deduplicated using the HiCUP pipeline v6.1.0. The pipeline was set up with Bowtie2 v2.3.4.2 for short read mapping.  In case replicates were available, they were combined before the processing with the HiCUP pipeline. Juicer command line tools v1.7.6 was used to generate binned contact maps from valid and unique reads pairs with MAPQ≥30 and to normalize maps by Knights and Ruiz matrix balancing. For binning and normalization, only the genomic region chr13: 54,000,001-57,300,000 was considered.  Afterwards, KR normalized maps, as well as raw count maps, were exported for 5 kb resolution. Subtraction maps were produced from theKR normalized maps and scaled together across their subdiagonals. cHiC maps of count values, as well as subtraction maps, were visualized as heatmaps in which values above the 99-th  percentile were truncated for visualization purposes.
Assembly: mm9
Supplementary files format and content: Text files indicating interaction frequency of valid pairs of the binned contact map

source_name: mESC

growth_protocol: Limbs from 40-45 somite-stage (E12.5) mouse embryos were microdissected in PBS. After producing cell suspention, cells were FACS sorted according to GFP status or processed directly for the extraction protocol (see below).

extract_protocol:
Tissues were homogenized in typsin-EDTA solution, fixes with 2% FA at room temperature, 10 min and the cells were lysed in custom-made lysis buffer (10mM Tris pH7.5, 10mM NaCl, 5mM MgCl2, 0.1mM EGTA, Protease Inhibitor). Upon PBS wash, samples were frozen and stored at -80°C. Samples were then digested with DpnII, re-ligated, de-crosslinked and purified.
The 3C-library was then sheared and adaptors were added to the sheared DNA and amplified according to Agilent instructions for Illumina sequencing. The library was hybridized to the custom-designed SureSelect beads and indexed for sequencing (50 to 100 bp paired-end) following Agilent instructions.

value: mESC


title: WTCHG_900988_226_CT_MenACWY_+ve

description:
small RNA
stage2


title: CHiC_mESC_Inv1

description: mESC


title: WTCHG_72955367_CT7_MenACWY_+ve

value: Male


title: Immunocompromised_Control_M-Bone

value: 14 days post-implantation

value: Tumor-free


title: ATAC of HEK293 TNFa with TRAFTAC against NFkB, rep1


title: WTCHG_900988_225_CT_ChAdOx1_+ve

description:
small RNA
stage2

value: Whole blood


title: CHiC_mESC_Pitx1GFP

description: mESC


title: RPE1_trisomy21_passage50 [Rtr21p50]

type: genomic

city: Kaiserslautern

first: Jan-Eric

last: Boekenkamp

address: Paul-Ehrlich-Strasse 24

department: Molecular Genetics

country: Germany

institute: University of Kaiserslautern-Landau

description: CGH probe signal intensities of hTERT RPE-1 cells with one added copy of chromosome 21 after 50 passages compared with female human gDNA (#G1521, Promega)

hyb_protocol: After purification, equal volumes of the corresponding Cyanine-5- and Cyanine-3-labeled samples were mixed. Human Cot-1 DNA (Invitrogen) was added to block repetitive sequences in the DNA. The combined samples were pre-hybridized before Two-Color based hybridization (Oligo aCGH Hybridization Kit, Agilent Technologies). All combinations were hybridized at 65°C for 24 hrs on Agilent Human Genome CGH Microarrays (4x44K format, AMADID 014950). The hybridized microarrays were washed with increasing stringency using Oligo aCGH Wash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies).

data_processing: The Agilent Genomic Workbench 7.0.4.0 was used to normalize and process the extracted singnals, applying probe filtering, as well as GC correction and re-centralization of log2 ratios.

source_name: RPE-1 cell line, trisomy 21, passage 50

label_protocol: Equal amounts of genomic DNA for both the experimental and reference samples were sheared by enzymatic digestion. 1.0 µg gDNA of each sample was treated with a combination of Alu I and Rsa I at 37°C for 2 hours. The Genomic DNA Enzymatic Labeling Kit (Agilent Technologies) uses random primers and the exo-Klenow fragment to differentially label the digested gDNA samples with fluorescent_x0002_labeled nucleotides. Cyanine-5 dUTP (dUTP = 2’-deoxyuridine 5’-triphosphate) was used for   all experimental samples , whereas Cyanine-3 dUTP was used for the reference samples.

growth_protocol: Both HCT116 and RPE-1 cell lines were cultured in DMEM (supplemented with 10% FBS) at 5% CO2, 37°C

extract_protocol: Cells were collected with trypsin and centrifuged. The pellet was washed twice with PBS. DNA isolation was performed using the Qiagen DNA easy Blood and Tissue Kit (Hilden, Germany) following manufacturer’s instructions.

treatment_protocol: no treatment

value: hTERT RPE-1

tag: gender

value: female

value: Eye; Pigmented epithelium; Retina

tag: disease

value: Normal

tag: transferred chromosomes

tag: in-vitro evolution

value: passage 50

source_name: human genomic DNA, female (#G1521, Promega)


title: WTCHG_900988_224_CT+7_MenACWY_+ve

description:
small RNA
stage2

tag: tissue

value: MenACWY

value: Female


title: WTCHG_72945366_CT7_MenACWY_+ve

tag: timepoint


title: WTCHG_900988_223_CT+7_MenACWY_+ve

description:
small RNA
stage2

tag: vaccine


title: WTCHG_72935365_CT7_MenACWY_+ve

tag: naat result


title: CHiC_pFL_E125_dCas9P300TSS

description: bulk limb

source_name: embryonic limb bud

value: embryonic limb bud

tag: cell line

tag: genotype


title: Immunocompromised_Control_DM-Bone

value: Deminerlaised bone scaffold

value: Athymic Nude-Foxn1nu


title: WTCHG_900988_222_CT+7_MenACWY_+ve

description:
small RNA
stage2

value: +ve

tag: age

tag: Sex

tag: participant number


title: CHiC_pFL_E125_Eed

description: bulk limb

tag: cell type

value: embryonic limb cell

value: Prx1-CRE, Eedflox/-


title: WTCHG_853846_296_CT_ChAdOx1_-ve

description:
small RNA
stage1

value: CT

value: -ve


title: CHiC_pFL_E125_WT

description: bulk limb

value: WT


title: WTCHG_72905362_CT7_MenACWY_+ve

value: Whole blood


title: WTCHG_72915363_CT7_MenACWY_+ve


title: RPE1_WT_passage50 [Rp50]

description: CGH probe signal intensities of hTERT RPE-1 cells after 50 passages compared with female human gDNA (#G1521, Promega)

source_name: RPE-1 cell line, near-diploid, passage 50

value: hTERT RPE-1


title: WTCHG_853846_295_D0_ChAdOx1_-ve

description:
small RNA
stage1


title: CHiC_pFL_E125_dCas9P300

description: bulk limb


title: RPE1_WT_passage0 [RPE1]

description: CGH probe signal intensities of hTERT RPE-1 cells compared with female human gDNA (#G1521, Promega)

scan_protocol: Fluorescent signal intensities were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (Agilent Technologies).

source_name: RPE-1 cell line, near-diploid, passage 0

value: female

value: passage 0


title: HCT116_tetrasomy5_colonyselection [Hte5cs]

description: CGH probe signal intensities of HCT116 cells with two added copies of chromosome 5 after colony selection with male human gDNA (#G1471, Promega)

source_name: HCT116 cell line, tetrasomy 5, colony selection

value: male

value: Large intestine; Colon

value: Carcinoma; Colorectal

value: colony selection

source_name: human genomic DNA, male (#G1471, Promega)


title: FlnKO PH ROI 04

description:
Experimental Slide 2022-08-18 | 004 | Full ROI
DSP-1001660012009-A-A05

source_name: brain

value: brain

value: 3 months

tag: region

value: PH

value: FlnKO

tag: treatment


title: WTCHG_853846_294_CT+7_MenACWY_+ve

description:
small RNA
stage1

source_name: Whole blood

value: MenACWY

value: +ve

value: Female


title: CHiC_FL_E125_Rel3_GFPn

description: GFP-

value: embryonic limb bud

value: embryonic limb cell

value: FACS sorted


title: WTCHG_72895361_CT_MenACWY_+ve

value: Whole blood

value: CT

value: Male


title: RPE1_trisomy5_passage50 [Rtr5p50]

description: CGH probe signal intensities of hTERT RPE-1 cells with one added copy of chromosome 5 after 50 passages compared with female human gDNA (#G1521, Promega)

source_name: RPE-1 cell line, trisomy 5, passage 50

value: hTERT RPE-1

value: female

value: Eye; Pigmented epithelium; Retina

value: Normal

value: passage 50


title: CHiC_FL_E125_Rel3_GFPp

description: GFP+


title: RPE1_trisomy5_passage0 [Rtr5]

description: CGH probe signal intensities of hTERT RPE-1 cells with one added copy of chromosome 5 compared with female human gDNA (#G1521, Promega)

source_name: RPE-1 cell line, trisomy 5, passage 0

value: passage 0


title: WTCHG_72925364_CT_MenACWY_+ve


title: WTCHG_70965072_CT+7_ChAdOx1_+ve


title: WTCHG_853846_293_CT_MenACWY_+ve

description:
small RNA
stage1


title: HCT116_tetrasomy5_passage0 [Hte5]

description: CGH probe signal intensities of HCT116 cells with two added copies of chromosome 5 after compared with male human gDNA (#G1471, Promega)

source_name: HCT116 cell line, tetrasomy 5, passage 0

value: male

value: Large intestine; Colon

value: Carcinoma; Colorectal


title: WTCHG_70955071_CT+7_MenACWY_+ve

value: MenACWY

value: +ve


title: WTCHG_73105382_CT_MenACWY_+ve

value: Female


title: WTCHG_853846_292_D0_MenACWY_+ve

description:
small RNA
stage1


title: HCT116_trisomy5_colonyselection [Htr5cs]

description: CGH probe signal intensities of HCT116 cells with one added copy of chromosome 5 after colony selection compared with male human gDNA (#G1471, Promega)

source_name: HCT116 cell line, trisomy 5, colony selection

value: colony selection


title: WTCHG_70945070_CT+7_MenACWY_+ve


title: WTCHG_853846_291_CT+7_ChAdOx1_+ve

description:
small RNA
stage1


title: HCT116_trisomy5_passage0 [Htr5]

description: CGH probe signal intensities of HCT116 cells with one added copy of chromosome 5 compared with male human gDNA (#G1471, Promega)

source_name: HCT116 cell line, trisomy 5, passage 0


title: CHiC_FL_E125_Inv2_GFPn

description: GFP-

value: embryonic limb bud

value: embryonic limb cell

value: FACS sorted


title: WTCHG_853846_290_CT_ChAdOx1_+ve

description:
small RNA
stage1

value: Whole blood

value: CT


title: WTCHG_70935069_CT+7_ChAdOx1_+ve


title: HCT116_WT_colonyselection [Hcs]

description: CGH probe signal intensities of wild-type HCT116 cells after colony selection compared with male human gDNA (#G1471, Promega)

source_name: HCT116 cell line, near-diploid, colony selection


title: CHiC_FL_E125_Inv2_GFPp

description: GFP+


title: WTCHG_70925068_CT+7_ChAdOx1_+ve

value: Male


title: WTCHG_853846_289_D0_ChAdOx1_+ve

description:
small RNA
stage1


title: HCT116_tetrasomy5_passage50 [Hte5p50]

description: CGH probe signal intensities of HCT116 cells with two added copies of chromosome 5 after 50 passages with male human gDNA (#G1471, Promega)

source_name: HCT116 cell line, tetrasomy 5, passage 50


title: HCT116_WT_passage0 [HCT116]

description: CGH probe signal intensities of wild-type HCT116 cells compared with male human gDNA (#G1471, Promega)

source_name: HCT116 cell line, near-diploid, passage 0


title: CHiC_FL_E125_Inv1_GFPn

description: GFP-


title: WTCHG_853846_250_CT+7_MenACWY_+ve

description:
small RNA
stage1


title: CHiC_FL-E125_Inv1_GFPp

description: GFP+


title: CHiC_FL_E125_Rel2_GFPn

description: GFP-


title: WTCHG_853846_249_CT_MenACWY_+ve

description:
small RNA
stage1


title: RPE1_trisomy21_passage0 [Rtr21]

description: CGH probe signal intensities of hTERT RPE-1 cells with one added copy of chromosome 21 compared with female human gDNA (#G1521, Promega)

hyb_protocol: After purification, equal volumes of the corresponding Cyanine-5 and Cyanine-3 labeled samples were mixed. Human Cot-1 DNA (Invitrogen) was added to block repetitive sequences in the DNA. The combined samples were pre-hybridized beforeTwo-Color based hybridization (Oligo aCGH Hybridization Kit, Agilent Technologies). All combinations were hybridized at 65°C for 24 hrs on Agilent SurePrint G3 Human CGH Microarrays (4x180K format). The hybridized microarrays were washed with increasing stringency using Oligo aCGH Wash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.1 Software (Agilent Technologies).

source_name: RPE-1 cell line, trisomy 21, passage 0

value: hTERT RPE-1

value: female

value: Eye; Pigmented epithelium; Retina


title: WTCHG_70905066_CT_MenACWY_+ve


title: scRNAseq_FL_E125_Inv1_R2

source_name: Embryonic Limb Bud

value: Embryonic Limb Bud


title: CHiC_FL_E125_Rel2_GFPp

description: GFP+

source_name: embryonic limb bud


title: WTCHG_70895065_CT_ChAdOx1_+ve


title: H3K27ac-FL-E125-Rel3-GFPp

description: GFP+

data_processing:
Single-end reads were mapped to the reference genome GRCm39/mm39 using Bowtie2 version 2.3.4.2, filtered for mapping quality q ≥ 25 and duplicates were removed with SAMtools 1.9. Reads were extended to 250 bp and scaled (1 million/total of unique reads) to produce coverage tracks.
Assembly: mm39
Supplementary files format and content: BigWig

growth_protocol: Limbs from 40-45 somite-stage (E12.5) mouse embryos were microdissected in PBS. After producing cell suspention, cells were FACS sorted according to GFP status.

extract_protocol:
After sorting, cells were centrifuged for 5’ at 400g at 4°C and supernatant was discarded. Cells for ChIP-seq were resuspended in 10% FCS/PBS and fixed in 1% formaldehyde at room temperature. The fixation was blocked by the addition of 1.25M glycine, cells were isolated by centrifugation (1000g, at 4°C for 8’), resuspended in cold lysis buffer (10 mM Tris, pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, Protease Inhibitor (Roche, 04693159001)) and incubated on ice for 10’ to isolate the cell nuclei. The nuclei were isolated by centrifugation (1000g, at 4°C for 3’), washed in cold 1X PBS, centrifuged again (1000g, at 4°C for 1’) and stored frozen at -80°C after removal of the PBS supernatant.
500000 fixed nuclei were sonicated to a 200-500bp length with the Bioruptor Pico sonicator (Diagenode). H3K27Ac ChIP was (Diagenode C15410174) was performed as previously described (Lee et al. 2006; Rouco et al. 2021) with the addition of 5mM of Na-Butyrate to all buffers. Libraries were then prepared following the Illumina ChIP TruSeq protocol and sequenced as 50bp single-end reads on an Illumina NovaSeq 6000. Libraries were prepared starting with below <10ng quantities of ChIP-enriched DNA as starting material and processed with the Illumina TruSeq ChIP kit according to manufacturer specifications. Libraries were validated on a Tapestation 2200 (Agilent) and a Qubit fluorimeter (Invitrogen – Thermofisher Scientific). Libraries were pooled at 2 nM and loaded for clustering on a Single-read Illumina Flow cell. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina NovaSeq 6000 sequencer.


title: WTCHG_853846_248_CT_MenACWY_+ve

description:
small RNA
stage1


title: scRNAseq_FL_E125_Inv1_R1


title: WTCHG_70885064_CT+7_MenACWY_+ve


title: WTCHG_853846_247_CT+7_MenACWY_+ve

description:
small RNA
stage1


title: FL_E125_dCas9P300_r2

description: bulk limb

data_processing:
Reads from RNA-seq were mapped using the STAR 2.7.2b mapper with default settings to the GRCm39/mm39 genome
Assembly: mm39
Supplementary files format and content: BigWig

extract_protocol:
After sorting, cells were centrifuged for 5’ at 400g at 4°C, supernatant was discarded and cells frozen at -80°C. Total RNA from 1,5 x10^5 cells was isolated using the RNeasy Micro Kit (QIAGEN, ID:74004) following manufacturer’s instructions and then stored frozen at -80°C. Total RNA was quantified with a Qubit (fluorimeter from Life Technologies) and RNA integrity assessed with a Bioanalyzer (Agilent Technologies).
The SMART-Seq v4 kit from Clontech was used for the reverse transcription and cDNA amplification according to manufacturer’s specifications, starting with 5 ng of total RNA as input. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina. Library molarity and quality was assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM and loaded for clustering on a Single-read Illumina Flow cell for an average of 35 mio reads / library. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina NovaSeq 6000 sequencer.


title: H3K27ac-FL-E125-Inv1-GFPn

description: GFP-


title: WTCHG_853846_246_CT_MenACWY_+ve

description:
small RNA
stage1


title: WTCHG_70875063_CT+7_MenACWY_+ve


title: FL_E125_dCas9P300_r1

description: bulk limb


title: WTCHG_70865062_CT+7_MenACWY_+ve


title: H3K27ac-FL-E125-Inv1-GFPp

description: GFP+


title: FL_E125_dCas9P330TSS_r2

description: bulk limb


title: WTCHG_70915067_CT_MenACWY_+ve


title: FL_E125_dCas9P300TSS_r1

description: bulk limb


title: WTCHG_853846_244_CT_MenACWY_+ve

description:
small RNA
stage1


title: NTOC supernatant, IL-12 + IL-18, day 6, ADT

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

country: Belgium

institute: Ghent University

description:
Antibody-derived oligonucleotide (ADT)
PTO008_filtered_feature_bc_matrix.h5

library_source: other

data_processing:
genome_build/assembly: n/a
The Cell Ranger pipeline (10x Genomics, version 3.1.0) was used to perform sample 996 demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index for the gene 997 expression and cell surface protein libraries.
Read 2 of the gene expression libraries was mapped to the mouse reference genome.
Subsequent barcode processing, unique molecular identifiers filtering and gene counting were performed using the Cell Ranger suite.
CITE-seq reads were quantified using the feature-barcoding functionality.
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format files as produced by the Cellranger pipeline of 10X Genomics
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Neonatal Thymus Organ Culture

growth_protocol: Neonates were euthanized by decapitation at P0.5 and thymic lobes were extracted, and cleaned before setup. Three neonatal thymus lobes were cultured per well unless otherwise stated. Only intact neonatal thymic lobes were cultured on top of a 0.8 μm IsoporeTM Membrane Filter (Cat# ATTP01300, Merck Millipore), which was suspended on top of 2 mL NTOC medium in 12-well plates and cultured at 37°C with 5% CO2.

extract_protocol:
All viable (DAPI negative) cells from Day 6 NTOC supernatant treated with (1) Vehicle, (2) IL-12, (3) IL-18, and (4) IL-12+IL-18 were sorted (Aria III, BD Biosciences) and pelleted by centrifugation at 400g for 5min at 4°C. When CITE-seq was to be performed, cells were then stained with CD16/CD32 mAb (Cat# 553142, BD Bioscience) to block nonspeceific Fc receptor binding of CITE-seq antibodies for 20mins at 4°C, before being washed in excess PBS with 2% FCS used directly in downstream CITE-seq analysis
Following sorting, both the NTOC supernatant cells and ex vivo tissue comparison cells were stained with mouse cell surface protein TotalSeq-A antibodies panels containing 9 isotype controls and 77 (NTOC) or 174 (tissue) oligo-conjugated antibodies (TotalSeq-A, Biolegend). The sorted single-cell suspensions were resuspended at a final estimated conc. of 1500 and 1100 cells/µl for NTOC and tissues, respectively. The cells were loaded on a Chromium GemCode Single Cell Instrument (10x Genomics) to create single-cell gel beads-in-emulsion (GEM). The scRNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library kit, version 3 (NTOC) and version NextGEM 3.1 (tissue) (10x Genomics) according to the manufacturer’s instructions with the addition of amplification primer (3 nM, 5’CCTTGGCACCCGAGAATT*C*C) during cDNA amplification to enrich the TotalSeq-A cell surface protein oligos.

treatment_protocol: Cytokines were used at the following concentrations: IL-12 [4 ng/mL], and IL-18 [40 ng/mL]. The NTOC medium was composed of DMEM (Cat# 31330-038, GIBCO) supplemented with 20 % FCS (Lot# 71133 and 90439, Brand: TICO EUROPE, Greiner and Int Medical), 20μM L-glutamine, 50 μM β- mercapto-ethanol, 0.8 % penicillin-streptomycin (#Cat P4333, Sigma-Aldrich), 0.4 mM Na pyruvate (#Cat S-8636, Sigma-Aldrich), 1x non-essential amino acids (#Cat M7145, Sigma-Aldrich). Different types of FCS were tested for optimal cellular output of the NTOC to ensure it supported ILC1 development.

value: Neonatal Thymus Organ Culture

tag: strain


title: WTCHG_70845060_CT+7_MenACWY_+ve


title: NTOC supernatant, IL-18, day 6, ADT

description:
Antibody-derived oligonucleotide (ADT)
PTO006_filtered_feature_bc_matrix.h5


title: WTCHG_70855061_CT+7_ChAdOx1_+ve


title: bFL_E125_Rel3_r2

description: GFP+


title: WTCHG_853846_243_CT+7_ChAdOx1_+ve

description:
small RNA
stage1

data_processing:
Alignments were performed using bowtie with up to 2 mismatches in best strata mode, and bowtie2 with 2 gaps permitted
Reads were first aligned to the non-coding transcriptome. The bowtie indexes for the non-coding RNAome were built by merging fasta files from the following databases: miRbase (miRNAs), SnOPY (snoRNAs), trRNA_db (tRNAs), RefSeq (snRNAs, yRNAs, vault RNAs, lncRNAs.
Non-aligned reads were then aligned to the mRNA transcriptome, and antisense to the non-coding and mRNA transcriptome
All other reads were collapsed using a "gene_union" approach like those employed in seqCluster and mmQuant.
sRNA features were removed if they did not have an abundance of at least 5 counts per million in at least 20% of samples.
Assembly: GRCh38
Supplementary files format and content: txt file containing raw read counts for each gene for each sample

extract_protocol:
Peripheral blood (up to 2.5ml) was collected into a PAXgeneTM RNA tube at vaccination (D0), SARS-CoV-2 diagnosis (CT) and 7 days post diagnosis (CT+7). Total RNA was extracted using the PAXgene blood RNA kit (PreAnalytiX, Switzerland) on the QIAsymphony SP (Qiagen) with the PAX_RNA V5 protocol. Eluted RNA was quantified using the Agilent RNA ScreenTape assay on the 4200 TapeStation System (Agilent).
Small RNA libraries were prepared with the NEBNext® Small RNA Library Prep Set for Illumina (catalog #E7330) and run on a single flow cell target of 300 million reads) on the NexTSeq platform using the 75SR configuration with the aim of achieving 5.2 million reads per sample.


title: WTCHG_70835059_CT_ChAdOx1_+ve


title: NTOC supernatant, IL-12, day 6, ADT

description:
Antibody-derived oligonucleotide (ADT)
PTO005_filtered_feature_bc_matrix.h5


title: H3K27ac-FL-E125-Rel2-GFPp

description: GFP+


title: WTCHG_853846_242_CT_ChAdOx1_+ve

description:
small RNA
stage1


title: WTCHG_70825058_CT+7_MenACWY_+ve


title: bFL_E125_Rel2_r2

description: GFP+


title: WTCHG_853846_240_CT_MenACWY_+ve

description:
small RNA
stage1


title: NTOC supernatant, IL-18, day 6, RNA

description:
poly A RNA
PTO006_filtered_feature_bc_matrix.h5

data_processing:
genome_build/assembly: mm10-3.0.0
The Cell Ranger pipeline (10x Genomics, version 3.1.0) was used to perform sample 996 demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index for the gene 997 expression and cell surface protein libraries.
Read 2 of the gene expression libraries was mapped to the mouse reference genome.
Subsequent barcode processing, unique molecular identifiers filtering and gene counting were performed using the Cell Ranger suite.
CITE-seq reads were quantified using the feature-barcoding functionality.
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format files as produced by the Cellranger pipeline of 10X Genomics
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)


title: WTCHG_70805056_CT+7_MenACWY_+ve


title: WTCHG_853846_245_CT+7_MenACWY_+ve

description:
small RNA
stage1


title: WTCHG_900988_236_D0_ChAdOx1_D0_only

description:
small RNA
stage2


title: bFL_E125_Rel3_r1

description: GFP+


title: FL_E125_Rel3_GFPp_r2

description: GFP+


title: WTCHG_853846_241_CT+7_MenACWY_+ve

description:
small RNA
stage1


title: NTOC supernatant, IL-12 + IL-18, day 6, RNA

description:
poly A RNA
PTO008_filtered_feature_bc_matrix.h5


title: NTOC supernatant, IL-12, day 6, RNA

description:
poly A RNA
PTO005_filtered_feature_bc_matrix.h5


title: bFL_E125_Rel2_r1

description: GFP+


title: WTCHG_70795055_CT_MenACWY_+ve


title: WTCHG_70815057_CT+7_ChAdOx1_+ve


title: WTCHG_853846_238_CT+7_MenACWY_+ve

description:
small RNA
stage1


title: NTOC supernatant, Control, day 6, RNA

description:
poly A RNA
PTO003_filtered_feature_bc_matrix.h5

value: Control


title: FL_E125_Rel3_GFPp_r1

description: GFP+


title: FL_E125_Rel2_GFPp_r2

description: GFP+


title: WTCHG_70785054_CT_MenACWY_+ve


title: WTCHG_853846_237_CT_MenACWY_+ve

description:
small RNA
stage1


title: WTCHG_853846_236_CT_MenACWY_+ve

description:
small RNA
stage1


title: Clone88

city: Frederick

first: Yongmei

last: Zhao

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

data_processing:
Illumina RTA v3.4.4 software was used fro base calling, Bcl2fastq v2.17 was used for sample demultiplexing
Adapters from the samples were trimmed using Trimmomatic v0.36 software
Genome mapping and transcript annotation were using STAR v2.5.1 with mouse reference genome mm10
The gene expression quantification analysis was performed for all samples using RSEM 1.3.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RSEM raw count values for each Sample

source_name: mESC clones

growth_protocol: mESC clones mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were resuspended with QIAzol (QIAGEN, Hilden, Germany) and RNA was extracted (Zymo Direct-zol RNA miniprep kit).
RNA libraries were prepared for sequencing using standard Illumina TruSeq Stranded mRNA library protocol.

treatment_protocol:
Mirin Pretreatment was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: mESC clones

value: mouse embryonic stem cells

value: Mirin Pretreatment

tag: time

value: Passage 1


title: NTOC supernatant, Control, day 6, ADT

description:
Antibody-derived oligonucleotide (ADT)
PTO003_filtered_feature_bc_matrix.h5


title: Clone95


title: WTCHG_70765052_CT_ChAdOx1_+ve

value: +ve

value: Female


title: WTCHG_70775053_CT_MenACWY_+ve

value: MenACWY


title: WTCHG_853846_235_CT+7_MenACWY_+ve

description:
small RNA
stage1


title: FL_E125_Rel2_GFPp_r1

description: GFP+

value: embryonic limb bud

value: embryonic limb cell

value: FACS sorted


title: FL_E125_Rel1_GFPp_r2

description: GFP+


title: Clone94


title: WTCHG_853846_239_CT_ChAdOx1_+ve

description:
small RNA
stage1

value: Whole blood

value: CT

value: Male


title: WTCHG_853846_234_CT_MenACWY_+ve

description:
small RNA
stage1


title: FL_E125_Rel1_GFPp_r1

description: GFP+


title: Clone91


title: WTCHG_853846_233_CT+7_MenACWY_-ve

description:
small RNA
stage1

value: -ve


title: WTCHG_70745050_CT_MenACWY_+ve


title: Clone83


title: WTCHG_70735049_CT+7_MenACWY_+ve


title: FL_E125_Inv2_GFPp_r1

description: GFP+


title: Clone70


title: WTCHG_853846_232_CT_MenACWY_-ve

description:
small RNA
stage1


title: FL_E125_Inv2_GFPp_r2

description: GFP+


title: WTCHG_70725048_CT_MenACWY_+ve


title: WTCHG_853846_231_CT+7_MenACWY_-ve

description:
small RNA
stage1


title: Clone7


title: WTCHG_853846_230_CT_MenACWY_-ve

description:
small RNA
stage1


title: Clone67


title: WTCHG_70705046_CT_ChAdOx1_+ve


title: Clone6


title: WTCHG_853846_229_CT_MenACWY_-ve

description:
small RNA
stage1


title: WTCHG_70695045_CT+7_MenACWY_+ve


title: WTCHG_853846_228_CT+7_ChAdOx1_+ve

description:
small RNA
stage1


title: WTCHG_70685044_CT+7_MenACWY_+ve


title: FL_E125_Inv1_GFPp_r1

description: GFP+


title: WTCHG_853846_227_CT_ChAdOx1_+ve

description:
small RNA
stage1


title: WTCHG_70755051_CT+7_ChAdOx1_+ve


title: Clone58


title: MUT Input ChIP

city: Guanghzou

first: Zeng

last: Pengguihang

address: No.74, Zhongshan 2nd Road, Guangzhou, Guangdong

institute: Sun Yat-Sen University

description: CTCF.peaks.DESeq.txt

data_processing:
Raw fastq files were under adapter trimming and quality control by Trim Galore 0.4.4_dev, using default parameters.
Trimmed reads were mapped to mm9 genome assembly by Bowtie2 2.3.4.1, using default parameters.
Mapped ChIP-seq reads peakcalling were performed by macs2 2.1.1.20160309 with a modified pipeline including use of spikein scale factors. Differential enriched peaks were identified by DESeq2 1.38.0, using default parameters.
Bigwig files were converted from uniquely mapped reads by deeptools 3.1.1 bamCoverage tool and multiplied by spike-in scale factors.
Assembly: mm9
Supplementary files format and content: ChIP-seq coverage bigwig files, peaks and differential enriched peaks

source_name: ESC

growth_protocol: ESC lines was cultured in gelatin-coated dish with ESC medium, which consisted of DMEM (Hyclone), 15% (v/v) fetal bovine serum (FBS, Lonsera), 0.1 mM β-mercaptoethanol (Sigma), 2 mM L-glutamine (Thermo Fisher), 0.1 mM nonessential amino acids (Thermo Fisher), 1% (v/v) nucleoside mix (Sigma), 1,000 U/mL recombinant LIF (Millipore).

extract_protocol:
1% formaldehyde in PBS was used to crosslink the cells. Antibody enrich DNA fragments overnight from Sonicated lysates. Drosophila spike-in chromatin was uesed for normalization.
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The MUT_CTCF cells was mutated the CTCF at T668.

tag: antibody

value: ESC

value: embryonic stem cells

value: MUT


title: Clone57

value: mESC clones


title: WTCHG_70675043_CT_ChAdOx1_+ve


title: MUT CTCF ChIP rep2

description: CTCF.peaks.DESeq.txt

value: CTCF


title: Clone55

value: mouse embryonic stem cells

value: Mirin Pretreatment


title: WTCHG_853846_226_CT+7_ChAdOx1_+ve

description:
small RNA
stage1

value: +ve


title: Clone54

value: Passage 1


title: WTCHG_853846_224_CT_ChAdOx1_+ve

description:
small RNA
stage1


title: WTCHG_70655041_CT+7_ChAdOx1_+ve

value: Female


title: WTCHG_853846_225_CT_ChAdOx1_+ve

description:
small RNA
stage1


title: WT Input ChIP

description: CTCF.peaks.DESeq.txt

value: WT


title: WTCHG_70715047_CT_MenACWY_+ve

value: MenACWY


title: WTCHG_70665042_CT_MenACWY_+ve


title: Clone53


title: FL_E125_Inv1_GFPp_r2

description: GFP+

value: embryonic limb bud

value: embryonic limb cell

value: FACS sorted


title: WTCHG_853846_223_CT+7_ChAdOx1_-ve

description:
small RNA
stage1

value: Whole blood


title: WTCHG_70645040_CT+7_ChAdOx1_+ve


title: WT CTCF ChIP rep2

description: CTCF.peaks.DESeq.txt


title: WTCHG_70635039_CT+7_ChAdOx1_+ve


title: Clone43


title: WTCHG_853846_221_D0_ChAdOx1_-ve

description:
small RNA
stage1

value: -ve


title: WTCHG_853846_222_CT_ChAdOx1_-ve

description:
small RNA
stage1

value: CT


title: WTCHG_70625038_CT+7_MenACWY_+ve


title: Clone45


title: Clone36


title: WTCHG_70615037_CT+7_ChAdOx1_+ve

value: Male


title: WT CTCF ChIP rep1

description: CTCF.peaks.DESeq.txt

value: ESC

value: embryonic stem cells


title: MUT ATAC rep1

data_processing:
Raw fastq files were under adapter trimming and quality control by Trim Galore 0.4.4_dev, using default parameters.
Trimmed reads were mapped to mm9 genome assembly by Bowtie2 2.3.4.1, using default parameters.
Bigwig files were converted from uniquely mapped reads by deeptools 3.1.1 bamCoverage tool.
Assembly: mm9
Supplementary files format and content: ATAC-seq coverage bigwig files

extract_protocol:
The TruePrepTM DNA Library Prep Kit V2 for Illumina® (Vazyme, #TD501) was uesed.
Libraries were prepared for sequencing using standard Illumina protocols.

value: MUT


title: MUT CTCF ChIP rep1

description: CTCF.peaks.DESeq.txt

value: CTCF


title: Clone35

value: mESC clones

value: mouse embryonic stem cells

value: Mirin Pretreatment


title: WTCHG_70605036_CT+7_MenACWY_+ve

value: +ve

value: Female


title: WTCHG_853846_219_CT_ChAdOx1_-ve

description:
small RNA
stage1


title: Clone3

value: Passage 1


title: WTCHG_70595035_CT+7_ChAdOx1_+ve


title: WT ATAC rep2

value: WT


title: WTCHG_853846_217_CT_ChAdOx1_-ve

description:
small RNA
stage1


title: WTCHG_70585034_CT+7_ChAdOx1_+ve


title: WTCHG_853846_218_D0_ChAdOx1_-ve

description:
small RNA
stage1


title: Clone25


title: WTCHG_70575033_CT_MenACWY_+ve

value: MenACWY


title: MUT RNA rep2

data_processing:
Raw fastq files were under adapter trimming and quality control by Trim Galore 0.4.4_dev, using default parameters.
Trimmed reads were mapped to mm9 genome assembly by STAR2 020201, using default parameters.
Mapped RNA-seq reads were counted by HTSeq-count 0.9.1, using default parameters.
Assembly: mm9
Supplementary files format and content: RNA-seq raw counts and edgeR differential expression gene list.

extract_protocol:
Total RNA was extracted from cell pellets using RNAzol reagent.
Libraries were prepared for sequencing using standard Illumina protocols.


title: MUT RNA rep1


title: WTCHG_853846_216_CT_MenACWY_-ve

description:
small RNA
stage1


title: Clone12


title: MUT ATAC rep2


title: Clone26


title: WTCHG_70565032_CT+7_MenACWY_+ve


title: WTCHG_853846_215_CT_MenACWY_-ve

description:
small RNA
stage1


title: WTCHG_853846_220_CT+7_ChAdOx1_-ve

description:
small RNA
stage1


title: WT RNA rep2


title: WT RNA rep1


title: WTCHG_70555031_CT+7_MenACWY_+ve


title: WTCHG_70545030_CT+7_MenACWY_+ve


title: WTCHG_853846_214_D0_MenACWY_-ve

description:
small RNA
stage1


title: KO-rep3

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

country: France

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

data_processing:
The libraries were sequenced on Illumina Hiseq 4000 sequencer as single-end 50 bp reads following Illumina's instructions.
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Adapter dimer reads were removed using DimerRemover v0.9.2.
Reads were mapped to the mouse genome (mm9) using Tophat v2.0.14 and Bowtie v2-2.1.0.
Quantification of gene expression was performed using HTSeq v0.6.1 and gene annotations from Ensembl release 67.
Assembly: mm9
Supplementary files format and content: Processed expression data were summarized in one single Excel file containing the following informations for each sample: gene name/ensemble_gene_id/raw read count/normalized read count/log2 fold change/p-value/p-value adjusted for multi-testing.

source_name: Tibialis anterior

extract_protocol:
To extract total RNA, 500 µl of TRI Reagent (Sigma) was added to frozen tibialis anterior and homogenized with PreCellys (Bertin Technologies) (6500 RPM, 3 × 10 s) in tube containing ceramics beads (Lysing Matrix D – MP biomedicals). After centrifugation, TRI Reagent was removed and beads were washed one time with 500 µl of TRI reagent. Total RNA was then extracted following provider’s instruction
Libraries of template molecules suitable for strand-specific high-throughput DNA sequencing were created using a TruSeq Stranded Total RNA with Ribo-Zero Gold Prep Kit (RS-122-2301; Illumina)

value: Tibialis anterior

value: 12 months-old


title: Clone11


title: WTCHG_853846_213_CT+7_ChAdOx1_+ve

description:
small RNA
stage1

value: Whole blood


title: KO-rep2


title: WTCHG_70535029_CT_ChAdOx1_+ve

value: CT


title: WTCHG_853846_212_CT_ChAdOx1_+ve

description:
small RNA
stage1

value: Male


title: WT ATAC rep1

value: ESC


title: VSV_HUB

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: 10x Genomics

data_processing:
Post sequencing, the 10x Genomics "cellranger" tool suite (v7.2) was used to generate expression counts per known gene (refdata-gex-mm10-2020-A) per sample.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: rostral rhinal hub

growth_protocol: All mice used in this study were handled in accordance with the guidelines established by the NIH Animal Care and Use Committee and the recommendations of AAALAC for the Care and Use of Laboratory Animals. The animal study protocol was approved by the NINDS Animal Care and Use Committee. Mice were bred and maintained within individually ventilated cages in the specific pathogen-free animal facilities at the NIH.

extract_protocol:
Meningeal rostral-rhinal hubs from twelve 15-week-old naïve or d8 VSV-infected mice B6 mice transcardially perfused with 20 ml of ice-cold PBS were carefully collected under a dissection microscope. Upon isolation, meningeal hub samples were pooled for each experimental group and dissociated with a mouse Tumor Dissociation Kit (Miltenyi Biotec) using the gentleMACS Octo Dissociator (Miltenyi Biotec). After dissociation, the samples were then filtered through 100µm meshes and washed with 2% fetal bovine serum in RPMI and resuspended in 0.05% BSA PBS solution. Cell number and viability were checked with the Luna-FX7 (Logos Bio).
cDNA libraries were prepared from single-cell suspensions following the 10x Genomics 3′ v3 protocol using either single indices or dual indicies (www.10xgenomics.com) and sequenced on a Illumina NextSeq 550 (www.illumina.com).

treatment_protocol: C57BL/6J mice were either uninfected or infected intranasally in each nostril with 10 ul of PBS containing 5x10^5 plaque forming units of VSV-OVA serotype Indiana

value: rostral rhinal hub

value: leukocytes

tag: infection

value: day 8 post intranasal VSV infection


title: KO-rep1


title: WTCHG_70525028_CT+7_ChAdOx1_+ve

data_processing:
The sequencing data were aligned against the whole human (Homo sapiens) genome build GRCh38 using STAR (version 2.7.3a).
Gene features were counted using HTSeq (version 0.11.1), using human gene annotation general transfer format version GRCh38.92.
Genes with low counts across most libraries were removed by only retaining genes with abundance greater than 3 counts per million in 9 or more samples.
Ribosomal RNA (rRNA), sex chromosome genes, mitochondrial RNA and haemoglobin genes were excluded from downstream analysis.
Assembly: GRCh38
Supplementary files format and content: txt file containing normalised expression (rpkm - reads per kilobase per million) for each gene for each sample

source_name: Whole blood


title: WTCHG_853846_211_D0_ChAdOx1_+ve

description:
small RNA
stage1


title: Men_VSV

description: 10x Genomics


title: WTCHG_70515027_CT_ChAdOx1_+ve


title: WT-rep2

value: H2A-Z.1flox/flox :H2A-Z.2 flox/flox HSA Cre WT


title: WTCHG_853846_210_CT+7_MenACWY_-ve

description:
small RNA
stage1

value: -ve


title: Men_naive

description: 10x Genomics

value: uninfected


title: IMQ mouse deliveried EPIC repeat2

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Remove low quality bases and adaptor sequences via Trimmomatic.
Align trimmed data to rRNA sequene to remove reads from ribosomal RNAs.
Align clean data to mm10 genome by HISAT2 then calculate FPKM of linear RNAs.
The unmapped reads were realignment to mm10 mouse genome by TopHat-Fusion and identify circRNAs via CIRCexplorer3.
Assembly: mm10
Supplementary files format and content: Text file cotains FPKM.

source_name: spleen

growth_protocol: Wild-type C57BL/6 mice received a daily topical dose of 62.5 mg IMQ cream (5%; Aldara; 3M Pharmaceuticals) on the shaved dorsal skin for 2 days, then EPIC-LNP was delivered (i.v.) at D1.5.

extract_protocol:
Total RNAs from spleens of mice were extracted with TRIzol (Life technologies) according to the manufacturer’s protocol.
For total RNA Ribo– RNA-seq libraries were prepared with TruSeq® Stranded Total RNA Library Prep Gold Kit. Deep sequencing was performed on Illumina NovaSeq.

treatment_protocol: Spleen samples were minced through a 70-μm mesh to obtain single-cell suspensions. Then obtained single-cell suspensions were treated with Red cell lysis buffer (TIANGEN) and washed with PBS for following experiments.

value: spleen

value: IMQ (imiquimod) treatment at day 0 and day 1, and delivered (i.v.) EPIC by LNP at 1.5 day


title: WT-rep1


title: WTCHG_70495025_CT_ChAdOx1_+ve

first: Irina

last: Chelysheva

address: Roosevelt Dr

institute: University of Oxford

extract_protocol:
Peripheral blood (up to 2.5ml) was collected into a PAXgeneTM RNA tube at vaccination (D0), SARS-CoV-2 diagnosis (CT) and 7 days post diagnosis (CT+7). Total RNA was extracted using the PAXgene blood RNA kit (PreAnalytiX, Switzerland) on the QIAsymphony SP (Qiagen) with the PAX_RNA V5 protocol. Eluted RNA was quantified using the Agilent RNA ScreenTape assay on the 4200 TapeStation System (Agilent).
RNA was ribodepleted and globin depleted using Ribo-ZeroTM Gold rRNA removal Kit (Illumina, USA). RNA was converted to cDNA, second-strand cDNA synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated and prior to amplification, samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and quality controlled before 150bp paired-end sequencing (NovaSeq6000).

value: +ve