title: 98_DSP-1001250002072-B-E09

city: New Haven

first: Thazin

middle: Nwe

last: Aung

address: 310 Cedar Street

institute: Yale University

data_processing:
The sequencing data were processed with the GeoMx NGS Pipeline (DND) according to the GeoMx®-DSP user manual (MAN-10153-01). Briefly, the pipeline was performed for trimming, merging, and aligning the reads to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicate reads. This program then converted FASTQ files to DCCs, i.e., converting reads into digital counts.
The zipped folder containing the DCC files were transferred back to GeoMx DSP to obtain the read counts.
After uploading the files to GeoMx DSP, the sequencing quality (quality control) allowed for specifying the parameters for evaluating the quality of NGS data and to qualify segments by number of cells or by area. Read counts were filtered setting the threshold for the limit of detection (LoD) in an ROI. This was defined based on the mean and standard deviation (s.d.) of 𝑙𝑜𝑔−10 normalized target group genes. The calculation is: LoD = mean + (2 × s.d.). A gene was filtered/counted as detected only if it exceeded the LoD in at least 10% of all ROIs. ROIs that did not have the filtering criteria were excluded from further analyses
Assembly: hg19
Supplementary files format and content: CD45_0%filter_Yale.xlsx  contains raw, unnormalized read counts from the leukocyte (CD45) compartment
Supplementary files format and content: CD68_0%filter_Yale.xlsx  contains raw, unnormalized read counts from the macrophage (CD68) compartment
Supplementary files format and content: CK_0%filter_Yale.xlsx  contains raw, unnormalized read counts from the tumor (CK) compartment

source_name: Lung Cancer

extract_protocol:
day1:TMA slides were processed using the Nanostring GeoMx DSP manual slide preparation GeoMx®-DSP protocol (MAN-10150-01).Antigen retrieval of the FFPE tissue was performed for 20 minutes followed by deparaffinization and rehydration.Then, the slides were incubated with proteinase K for 20 minutes and RNA probes were placed on slides for overnight in situ hybridization. day2:slides were washed to remove off-target probes for 90 minutes. Morphology markers: CD68 for macrophage compartment (Cy5/666 nm, excitation 645/19 nm, emission 683/30 nm), CD45 for lymphocyte compartment (Texas Red/615 nm, excitation 588/19 nm, emission 623/30 nm), S100B (Cy3/568 nm, excitation 538/19 nm, emission 564/15nm) for tumor compartment to identify the compartments and SYTO 13 for nuclear stain, were added for 1-hour incubation. Slides were loaded onto the GeoMx DSP instrument and after scanning, ROI (region of interest: i.e., CD45, CD68 and S100B) selection and probe collection were performed according to the GeoMx®-DSP user manual protocol (MAN-10088-03). Samples were collected in a 96-well probe aspirate collection plate and each ROI representing a compartment from a patient tumor core was collected in a well.
GeoMx®-DSP user manual (MAN-10117-01); Each GeoMx DSP aspirate in the plate contains photocleaved DNA oligos comprised of an RNA analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. Prior to purification, PCR reactions were pooled into three mixtures, separating CD68, CD45 and S100B ROIs to generate three pooled libraries. The libraries were pooled in a biased manner designed to target the smallest ROI pool with 6 parts of reads for CD68, 3 parts of reads for CD45 and 1 part of reads for S100B. Illumina i5 x i7 system adapter sequences and unique dual sample indices are added when PCR is performed on the probe aspirates. Each photocleaved oligo in the GeoMx DSP collection plate contains a readout tag sequence identifier (RTS ID) that identifies the target. It also includes a unique molecular identifier (UMI), to remove PCR duplicates when converting reads to digital counts. Read 1 (SPR1) and Read 2 (SPR2) are binding sites for Illumina sequencing primers. The GeoMx Seq code primers that hybridize to SPR1 and SPR2 contain i5 or i7 indexing sequences as well as P5 or P7 sequences for binding to Illumina flow cells. Sequencing was performed in both lanes of an Illumina Nova-Seq 6000 S2 flow cell resulting of 3 billion reads

tag: spotid

value: Lung Cancer

value: CK

value: Immunotherapy


title: 99_DSP-1001250002072-B-E12

status: Public on Aug 22 2024

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type

tag: treatment


title: 98_DSP-1001250002072-B-E10


title: 96_DSP-1001250002072-B-E06


title: 96_DSP-1001250002072-B-E07


title: 98_DSP-1001250002072-B-E08


title: 94_DSP-1001250002072-B-E03


title: 94_DSP-1001250002072-B-E04


title: 93_DSP-1001250002072-B-E01


title: 93_DSP-1001250002072-B-D12


title: 96_DSP-1001250002072-B-E05


title: RKO-dox-Cas9, sgERH, nucleus, biol rep 2

city: Vienna

first: Gijs

middle: A.

last: Versteeg

address: Dr. -Bohrgasse 9

department: Department of Microbiology

country: Austria

institute: Max Perutz Labs, University of Vienna

description: RNA input for library preparation: 500 ng

data_processing:
For RNA-seq analysis, reads were pre-processed with fastp (v0.20.1) which was configured to extract 6nt UMIs and trim 4nt from the read 5’-ends along standard quality and adapter trimming settings. Quality controls was done with fastqc (v0.11.8). Reads were mapped to 3’-ends with the nf-core/slamseq pipeline v0.1. For the 3’-end annotations we used the previously published set from Muhar et al, 2018 but extended it with GENCODE annotations for missing genes. Read and UMI counts were collapsed per gene and counted with a custom Python script.
The following software versions were used for the NF-core pipeline: nf-core/slamseq v0.1 Nextflow v21.10.6 FastQC v0.11.9 TrimGalore v0.6.4_dev Slamdunk v0.4.3 R v3.5.1 DESeq2 v1.22.1 MultiQC v1.8
Assembly: hg38 (to download the 3'end genome build: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100708&format=file&file=GSE100708%5Fhg38%5Frefseq%5F062016%5Fensemblv84%5F3UTR%2Ebed%2Egz")
Supplementary files format and content: tab-delimited .tsv files including count and UMI values with Entrez gene ids
Supplementary files format and content: tab-delimited .tsv files including UMI statistics

molecule: nuclear RNA

source_name: Colon carcinoma

growth_protocol: RKO cells were maintained in RPMI 1640 (Thermo Fisher Scientific, 21875) supplemented with  10% FBS (Sigma-Aldrich, F7524),L-glutamine (4 mM, Sigma-Aldrich, G7513), sodium pyruvate (1 mM, Sigma-Aldrich, S8636),  and 1% penicillin/streptomycin (Sigma-Aldrich, P4333) in a humidified incubator at 37 °C and 5% CO2.

extract_protocol:
For subcellular fractionation, ~2x10^6 cells were gently lysed in REAP buffer (0.1% NP-40 in 1x PBS) at 4°C. Nuclei and cytoplasmic fractions were separated through centrifugation at 3k g for 60 sec at 4°C twice. RNA isolation was done with High Performance RNA Isolation kit (Vienna, VBC Molecular Tools Shop, RNAisomag) and a KingFisher Flex robot (Thermo Fisher Scientific).
Generation of 3’ mRNA sequencing libraries was done according to manufacturer’s recommendations (QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina, UMI Second Strand Synthesis Module for QuantSeq FWD, and PCR Add-on Kit for Illumina, Lexogen).

treatment_protocol: Cas9 induced knockouts were generated by 5 days of doxycycline (Sigma-Aldrich,D9891) treatment (100 ng/mL).

value: Colon carcinoma

tag: cell line

value: RKO

tag: genotype

value: sgERH

value: non-treated

tag: time

value: 5 days dox


title: 93_DSP-1001250002072-B-D11


title: 9_DSP-1001250002072-B-D07


title: 9_DSP-1001250002072-B-D08


title: 90_DSP-1001250002072-B-D09


title: 99_DSP-1001250002072-B-F01


title: 9_DSP-1001250002072-B-D06


title: 90_DSP-1001250002072-B-D10


title: 88_DSP-1001250002072-B-D05


title: 88_DSP-1001250002072-B-D04


title: RKO-dox-Cas9, sgAAVS1, cytoplasm, biol rep 3

molecule: cytoplasmic RNA


title: 99_DSP-1001250002072-B-E11


title: 87_DSP-1001250002072-B-D03


title: 87_DSP-1001250002072-B-D02


title: 81_DSP-1001250002072-B-C11


title: 81_DSP-1001250002072-B-C12


title: 87_DSP-1001250002072-B-D01


title: 80_DSP-1001250002072-B-C07


title: 77_DSP-1001250002072-B-C03


title: 80_DSP-1001250002072-B-C08


title: 8_DSP-1001250002072-B-C05


title: 94_DSP-1001250002072-B-E02


title: 77_DSP-1001250002072-B-C04


title: 72_DSP-1001250002072-B-B12


title: 71_DSP-1001250002072-B-B10


title: 70_DSP-1001250002072-B-B09


title: 72_DSP-1001250002072-B-C01


title: 8_DSP-1001250002072-B-C06


title: 70_DSP-1001250002072-B-B07


title: 70_DSP-1001250002072-B-B08


title: 71_DSP-1001250002072-B-B11


title: 77_DSP-1001250002072-B-C02


title: 69_DSP-1001250002072-B-B06


title: 69_DSP-1001250002072-B-B04


title: 69_DSP-1001250002072-B-B05


title: 58_DSP-1001250002072-B-A12


title: 67_DSP-1001250002072-B-B01


title: 58_DSP-1001250002072-B-A11


title: 67_DSP-1001250002072-B-B02


title: 80_DSP-1001250002072-B-C09


title: 81_DSP-1001250002072-B-C10


title: 55_DSP-1001250002072-B-A10


title: 55_DSP-1001250002072-B-A09


title: 53_DSP-1001250002072-B-A08


title: 51_DSP-1001250002072-B-A04


title: 51_DSP-1001250002072-B-A05


title: 49_DSP-1001250002072-B-A02


title: No Template Control_DSP-1001250002072-B-A01

value: No Template Control


title: 67_DSP-1001250002072-B-B03


title: 48_DSP-1001250002073-A-H10


title: 49_DSP-1001250002073-A-H12


title: 49_DSP-1001250002073-A-H11


title: 46_DSP-1001250002073-A-H06


title: 48_DSP-1001250002073-A-H08


title: 48_DSP-1001250002073-A-H09


title: 45_DSP-1001250002073-A-H03


title: 42_DSP-1001250002073-A-G12


title: 45_DSP-1001250002073-A-H04


title: 45_DSP-1001250002073-A-H02


title: 42_DSP-1001250002073-A-G11


title: 40_DSP-1001250002073-A-G10


title: 4_DSP-1001250002073-A-G07


title: 4_DSP-1001250002073-A-G05


title: 53_DSP-1001250002072-B-A07


title: 4_DSP-1001250002073-A-G06


title: 40_DSP-1001250002073-A-G08


title: 53_DSP-1001250002072-B-A06


title: 35_DSP-1001250002073-A-G04


title: 40_DSP-1001250002073-A-G09


title: 35_DSP-1001250002073-A-G03


title: 51_DSP-1001250002072-B-A03


title: 46_DSP-1001250002073-A-H07


title: 46_DSP-1001250002073-A-H05


title: 33_DSP-1001250002073-A-F12


title: 32_DSP-1001250002073-A-F10


title: 33_DSP-1001250002073-A-G01


title: 32_DSP-1001250002073-A-F09


title: 30_DSP-1001250002073-A-F07


title: 33_DSP-1001250002073-A-F11


title: 32_DSP-1001250002073-A-F08


title: 35_DSP-1001250002073-A-G02


title: 42_DSP-1001250002073-A-H01


title: 3_DSP-1001250002073-A-F04


title: 3_DSP-1001250002073-A-F03


title: 27_DSP-1001250002073-A-F01


title: 3_DSP-1001250002073-A-F05


title: 27_DSP-1001250002073-A-E12


title: 27_DSP-1001250002073-A-F02


title: 25_DSP-1001250002073-A-E10


title: 25_DSP-1001250002073-A-E11


title: 23_DSP-1001250002073-A-E05


title: 24_DSP-1001250002073-A-E08


title: 24_DSP-1001250002073-A-E07


title: 23_DSP-1001250002073-A-E06


title: 25_DSP-1001250002073-A-E09


title: 23_DSP-1001250002073-A-E04


title: 22_DSP-1001250002073-A-E03


title: 22_DSP-1001250002073-A-E02


title: 21_DSP-1001250002073-A-D12


title: 21_DSP-1001250002073-A-D10


title: 21_DSP-1001250002073-A-D11


title: 30_DSP-1001250002073-A-F06


title: 20_DSP-1001250002073-A-D09


title: 2_DSP-1001250002073-A-D07


title: 17_DSP-1001250002073-A-D03


title: 18_DSP-1001250002073-A-D04


title: 15_DSP-1001250002073-A-D01


title: 20_DSP-1001250002073-A-D08


title: 17_DSP-1001250002073-A-D02


title: 15_DSP-1001250002073-A-C12


title: 15_DSP-1001250002073-A-C11


title: 2_DSP-1001250002073-A-D06


title: 18_DSP-1001250002073-A-D05


title: 120_DSP-1001250002073-A-C08


title: 120_DSP-1001250002073-A-C09


title: 119_DSP-1001250002073-A-C06


title: 120_DSP-1001250002073-A-C10


title: 119_DSP-1001250002073-A-C05


title: 117_DSP-1001250002073-A-B12


title: 118_DSP-1001250002073-A-C04


title: 22_DSP-1001250002073-A-E01


title: 117_DSP-1001250002073-A-C01


title: 118_DSP-1001250002073-A-C03


title: 117_DSP-1001250002073-A-B11


title: 118_DSP-1001250002073-A-C02


title: 116_DSP-1001250002073-A-B09


title: 116_DSP-1001250002073-A-B10


title: 116_DSP-1001250002073-A-B08


title: 109_DSP-1001250002073-A-B07


title: 109_DSP-1001250002073-A-B06


title: 109_DSP-1001250002073-A-B05


title: 103_DSP-1001250002073-A-B02


title: 103_DSP-1001250002073-A-B04


title: 102_DSP-1001250002073-A-B01


title: 119_DSP-1001250002073-A-C07


title: 103_DSP-1001250002073-A-B03


title: 102_DSP-1001250002073-A-A12


title: 101_DSP-1001250002073-A-A08


title: 101_DSP-1001250002073-A-A09


title: 101_DSP-1001250002073-A-A10


title: 100_DSP-1001250002073-A-A07


title: 1_DSP-1001250002073-A-A04


title: 102_DSP-1001250002073-A-A11


title: 100_DSP-1001250002073-A-A06


title: 1_DSP-1001250002073-A-A03


title: 100_DSP-1001250002073-A-A05


title: 1_DSP-1001250002073-A-A02


title: No Template Control_DSP-1001250002073-A-A01


title: 99_DSP-1001250002070-D-E12


title: 98_DSP-1001250002070-D-E10


title: 96_DSP-1001250002070-D-E06


title: 98_DSP-1001250002070-D-E09


title: 98_DSP-1001250002070-D-E08


title: 96_DSP-1001250002070-D-E07


title: 94_DSP-1001250002070-D-E04


title: 96_DSP-1001250002070-D-E05


title: 93_DSP-1001250002070-D-E01


title: 94_DSP-1001250002070-D-E03


title: 94_DSP-1001250002070-D-E02


title: 93_DSP-1001250002070-D-D12


title: 9_DSP-1001250002070-D-D07


title: 90_DSP-1001250002070-D-D10


title: 99_DSP-1001250002070-D-E11


title: 90_DSP-1001250002070-D-D09


title: 88_DSP-1001250002070-D-D05


title: 9_DSP-1001250002070-D-D06


title: 9_DSP-1001250002070-D-D08


title: 93_DSP-1001250002070-D-D11


title: 87_DSP-1001250002070-D-D03


title: 81_DSP-1001250002070-D-D01


title: 88_DSP-1001250002070-D-D04


title: 80_DSP-1001250002070-D-C10


title: 80_DSP-1001250002070-D-C11


title: 81_DSP-1001250002070-D-C12


title: 81_DSP-1001250002070-D-D02


title: 79_DSP-1001250002070-D-C06


title: 79_DSP-1001250002070-D-C05


title: 79_DSP-1001250002070-D-C04


title: 77_DSP-1001250002070-D-C03


title: 77_DSP-1001250002070-D-C01


title: 72_DSP-1001250002070-D-B11


title: 8_DSP-1001250002070-D-C07


title: 72_DSP-1001250002070-D-B12


title: 71_DSP-1001250002070-D-B08


title: 70_DSP-1001250002070-D-B07


title: 70_DSP-1001250002070-D-B06


title: 67_DSP-1001250002070-D-B01


title: 71_DSP-1001250002070-D-B09


title: 80_DSP-1001250002070-D-C09


title: 72_DSP-1001250002070-D-B10


title: 67_DSP-1001250002070-D-A12


title: 8_DSP-1001250002070-D-C08


title: 69_DSP-1001250002070-D-B04


title: 69_DSP-1001250002070-D-B03


title: 69_DSP-1001250002070-D-B02


title: 63_DSP-1001250002070-D-A07


title: 66_DSP-1001250002070-D-A08


title: 77_DSP-1001250002070-D-C02


title: 66_DSP-1001250002070-D-A09


title: 63_DSP-1001250002070-D-A05


title: 66_DSP-1001250002070-D-A10


title: 55_DSP-1001250002070-D-A02


title: 55_DSP-1001250002071-C-H11


title: 55_DSP-1001250002071-C-H12


title: 53_DSP-1001250002071-C-H10


title: 58_DSP-1001250002070-D-A04


title: 67_DSP-1001250002070-D-A11


title: 53_DSP-1001250002071-C-H09


title: No Template Control_DSP-1001250002070-D-A01


title: 70_DSP-1001250002070-D-B05


title: 53_DSP-1001250002071-C-H08


title: 51_DSP-1001250002071-C-H07


title: 51_DSP-1001250002071-C-H06


title: 51_DSP-1001250002071-C-H05


title: 49_DSP-1001250002071-C-H04


title: 63_DSP-1001250002070-D-A06


title: 46_DSP-1001250002071-C-G10


title: 48_DSP-1001250002071-C-H01


title: 49_DSP-1001250002071-C-H02


title: 58_DSP-1001250002070-D-A03


title: 48_DSP-1001250002071-C-G12


title: 49_DSP-1001250002071-C-H03


title: 48_DSP-1001250002071-C-G11


title: 45_DSP-1001250002071-C-G07


title: 46_DSP-1001250002071-C-G09


title: 42_DSP-1001250002071-C-G04


title: 45_DSP-1001250002071-C-G05


title: 42_DSP-1001250002071-C-G03


title: 40_DSP-1001250002071-C-G02


title: 40_DSP-1001250002071-C-F12


title: 4_DSP-1001250002071-C-F10


title: 4_DSP-1001250002071-C-F09


title: 4_DSP-1001250002071-C-F11


title: 40_DSP-1001250002071-C-G01


title: 35_DSP-1001250002071-C-F06


title: 35_DSP-1001250002071-C-F07


title: 33_DSP-1001250002071-C-F05


title: 35_DSP-1001250002071-C-F08


title: 32_DSP-1001250002071-C-F03


title: 32_DSP-1001250002071-C-F02


title: 45_DSP-1001250002071-C-G06


title: 46_DSP-1001250002071-C-G08


title: 3_DSP-1001250002071-C-E12


title: 3_DSP-1001250002071-C-E11


title: 27_DSP-1001250002071-C-E09


title: 3_DSP-1001250002071-C-E10


title: 25_DSP-1001250002071-C-E05


title: 27_DSP-1001250002071-C-E07


title: 25_DSP-1001250002071-C-E04


title: 27_DSP-1001250002071-C-E08


title: 25_DSP-1001250002071-C-E06


title: 24_DSP-1001250002071-C-E02


title: 24_DSP-1001250002071-C-E01


title: 23_DSP-1001250002071-C-D12


title: 22_DSP-1001250002071-C-D11


title: 33_DSP-1001250002071-C-F04


title: 20_DSP-1001250002071-C-D08


title: 22_DSP-1001250002071-C-D09


title: 18_DSP-1001250002071-C-D03


title: 20_DSP-1001250002071-C-D07


title: 18_DSP-1001250002071-C-D04


title: 32_DSP-1001250002071-C-F01


title: 18_DSP-1001250002071-C-D05


title: 17_DSP-1001250002071-C-D02


title: 20_DSP-1001250002071-C-D06


title: 17_DSP-1001250002071-C-C12


title: 15_DSP-1001250002071-C-C11


title: 24_DSP-1001250002071-C-E03


title: 15_DSP-1001250002071-C-C09


title: 15_DSP-1001250002071-C-C10


title: 119_DSP-1001250002071-C-C07


title: 120_DSP-1001250002071-C-C08


title: 119_DSP-1001250002071-C-C06


title: 117_DSP-1001250002071-C-C01


title: 118_DSP-1001250002071-C-C02


title: 117_DSP-1001250002071-C-B12


title: 118_DSP-1001250002071-C-C04


title: 117_DSP-1001250002071-C-B11


title: 119_DSP-1001250002071-C-C05


title: 22_DSP-1001250002071-C-D10


title: 109_DSP-1001250002071-C-B07


title: 116_DSP-1001250002071-C-B09


title: 109_DSP-1001250002071-C-B06


title: 17_DSP-1001250002071-C-D01


title: 109_DSP-1001250002071-C-B05


title: 103_DSP-1001250002071-C-B04


title: 103_DSP-1001250002071-C-B03


title: 102_DSP-1001250002071-C-A12


title: 116_DSP-1001250002071-C-B08


title: 101_DSP-1001250002071-C-A09


title: 103_DSP-1001250002071-C-B02


title: 102_DSP-1001250002071-C-A11


title: 102_DSP-1001250002071-C-B01


title: 101_DSP-1001250002071-C-A10


title: 101_DSP-1001250002071-C-A08


title: 100_DSP-1001250002071-C-A05


title: 1_DSP-1001250002071-C-A04


title: 1_DSP-1001250002071-C-A03


title: 118_DSP-1001250002071-C-C03


title: 100_DSP-1001250002071-C-A07


title: No Template Control_DSP-1001250002071-C-A01


title: 99_DSP-1001660003116-F-E11


title: 98_DSP-1001660003116-F-E10


title: 116_DSP-1001250002071-C-B10


title: 98_DSP-1001660003116-F-E09


title: 99_DSP-1001660003116-F-E12


title: 96_DSP-1001660003116-F-E07


title: 96_DSP-1001660003116-F-E05


title: 1_DSP-1001250002071-C-A02


title: 94_DSP-1001660003116-F-E03


title: 93_DSP-1001660003116-F-E02


title: 96_DSP-1001660003116-F-E06


title: 90_DSP-1001660003116-F-D09


title: 90_DSP-1001660003116-F-D11


title: 9_DSP-1001660003116-F-D06


title: 90_DSP-1001660003116-F-D10


title: 9_DSP-1001660003116-F-D07


title: 100_DSP-1001250002071-C-A06


title: 88_DSP-1001660003116-F-D05


title: 87_DSP-1001660003116-F-D04


title: 86_DSP-1001660003116-F-D02


title: 79_DSP-1001660003116-F-C04


title: 86_DSP-1001660003116-F-D03


title: 9_DSP-1001660003116-F-D08


title: 98_DSP-1001660003116-F-E08


title: 53_DSP-1001660003047-E-H12


title: 49_DSP-1001660003047-E-H09


title: 81_DSP-1001660003116-F-D01


title: 49_DSP-1001660003047-E-H08


title: 51_DSP-1001660003047-E-H10


title: 51_DSP-1001660003047-E-H11


title: 48_DSP-1001660003047-E-H06


title: 93_DSP-1001660003116-F-E01


title: 93_DSP-1001660003116-F-D12


title: 94_DSP-1001660003116-F-E04


title: 48_DSP-1001660003047-E-H05


title: 46_DSP-1001660003047-E-H02


title: 46_DSP-1001660003047-E-H01


title: 48_DSP-1001660003047-E-H04


title: 46_DSP-1001660003047-E-H03


title: 45_DSP-1001660003047-E-G12


title: 42_DSP-1001660003047-E-G09


title: 42_DSP-1001660003047-E-G08


title: 45_DSP-1001660003047-E-G11


title: 40_DSP-1001660003047-E-G07


title: 40_DSP-1001660003047-E-G06


title: 45_DSP-1001660003047-E-G10


title: 4_DSP-1001660003047-E-G03


title: 4_DSP-1001660003047-E-G04


title: 35_DSP-1001660003047-E-G01


title: 4_DSP-1001660003047-E-G02


title: 49_DSP-1001660003047-E-H07


title: 35_DSP-1001660003047-E-F11


title: 35_DSP-1001660003047-E-F12


title: 3_DSP-1001660003047-E-F04


title: 30_DSP-1001660003047-E-F05


title: 33_DSP-1001660003047-E-F09


title: 33_DSP-1001660003047-E-F10


title: 32_DSP-1001660003047-E-F08


title: 27_DSP-1001660003047-E-F01


title: 32_DSP-1001660003047-E-F07


title: 32_DSP-1001660003047-E-F06


title: 3_DSP-1001660003047-E-F03


title: 25_DSP-1001660003047-E-E08


title: 27_DSP-1001660003047-E-E11


title: 27_DSP-1001660003047-E-E12


title: 3_DSP-1001660003047-E-F02


title: 25_DSP-1001660003047-E-E09


title: 40_DSP-1001660003047-E-G05


title: 24_DSP-1001660003047-E-E07


title: 24_DSP-1001660003047-E-E06


title: 20_DSP-1001660003047-E-D12


title: 20_DSP-1001660003047-E-D10


title: 21_DSP-1001660003047-E-E01


title: 2_DSP-1001660003047-E-D09


title: 18_DSP-1001660003047-E-D07


title: 21_DSP-1001660003047-E-E02


title: 17_DSP-1001660003047-E-D05


title: 22_DSP-1001660003047-E-E03


title: 20_DSP-1001660003047-E-D11


title: 18_DSP-1001660003047-E-D08


title: 17_DSP-1001660003047-E-D04


title: 25_DSP-1001660003047-E-E10


title: 15_DSP-1001660003047-E-C12


title: 120_DSP-1001660003047-E-C11


title: 120_DSP-1001660003047-E-C10


title: 22_DSP-1001660003047-E-E04


title: 119_DSP-1001660003047-E-C09


title: 15_DSP-1001660003047-E-D02


title: 22_DSP-1001660003047-E-E05


title: 119_DSP-1001660003047-E-C07


title: 118_DSP-1001660003047-E-C06


title: 118_DSP-1001660003047-E-C05


title: 118_DSP-1001660003047-E-C04


title: 117_DSP-1001660003047-E-C03


title: 116_DSP-1001660003047-E-B11


title: 117_DSP-1001660003047-E-C02


title: 17_DSP-1001660003047-E-D03


title: 117_DSP-1001660003047-E-C01


title: 111_DSP-1001660003047-E-B07


title: 15_DSP-1001660003047-E-D01


title: 116_DSP-1001660003047-E-B12


title: 103_DSP-1001660003047-E-B03


title: 18_DSP-1001660003047-E-D06


title: 111_DSP-1001660003047-E-B09


title: 111_DSP-1001660003047-E-B08


title: 102_DSP-1001660003047-E-B01


title: 119_DSP-1001660003047-E-C08


title: 102_DSP-1001660003047-E-A11


title: 116_DSP-1001660003047-E-B10


title: 109_DSP-1001660003047-E-B06


title: 101_DSP-1001660003047-E-A09


title: 109_DSP-1001660003047-E-B05


title: 103_DSP-1001660003047-E-B02


title: 102_DSP-1001660003047-E-A12


title: 100_DSP-1001660003047-E-A06


title: 101_DSP-1001660003047-E-A10


title: 100_DSP-1001660003047-E-A05


title: 101_DSP-1001660003047-E-A08


title: 99_DSP-1001660003045-D-E08


title: 100_DSP-1001660003047-E-A07


title: 96_DSP-1001660003045-D-E03


title: 96_DSP-1001660003045-D-E04


title: 96_DSP-1001660003045-D-E02


title: No Template Control_DSP-1001660003047-E-A01


title: 94_DSP-1001660003045-D-D12


title: 1_DSP-1001660003047-E-A03


title: 1_DSP-1001660003047-E-A04


title: 1_DSP-1001660003047-E-A02


title: 94_DSP-1001660003045-D-E01


title: 98_DSP-1001660003045-D-E06


title: 90_DSP-1001660003045-D-D08


title: 98_DSP-1001660003045-D-E05


title: 93_DSP-1001660003045-D-D10


title: 9_DSP-1001660003045-D-D07


title: 9_DSP-1001660003045-D-D05


title: 88_DSP-1001660003045-D-D03


title: 90_DSP-1001660003045-D-D09


title: 86_DSP-1001660003045-D-D01


title: 93_DSP-1001660003045-D-D11


title: 98_DSP-1001660003045-D-E07


title: 81_DSP-1001660003045-D-C10


title: 88_DSP-1001660003045-D-D04


title: 109_DSP-1001660003047-E-B04


title: 81_DSP-1001660003045-D-C09


title: 80_DSP-1001660003045-D-C07


title: 8_DSP-1001660003045-D-C04


title: 80_DSP-1001660003045-D-C05


title: 8_DSP-1001660003045-D-C02


title: 87_DSP-1001660003045-D-D02


title: 86_DSP-1001660003045-D-C12


title: 79_DSP-1001660003045-D-B12


title: 86_DSP-1001660003045-D-C11


title: 77_DSP-1001660003045-D-B10


title: 80_DSP-1001660003045-D-C06


title: 71_DSP-1001660003045-D-B06


title: 81_DSP-1001660003045-D-C08


title: 72_DSP-1001660003045-D-B08


title: 70_DSP-1001660003045-D-B03


title: 9_DSP-1001660003045-D-D06


title: 69_DSP-1001660003045-D-B01


title: 69_DSP-1001660003045-D-A12


title: 67_DSP-1001660003045-D-A10


title: 79_DSP-1001660003045-D-C01


title: 67_DSP-1001660003045-D-A09


title: 79_DSP-1001660003045-D-B11


title: 8_DSP-1001660003045-D-C03


title: 67_DSP-1001660003045-D-A11


title: 66_DSP-1001660003045-D-A08


title: 70_DSP-1001660003045-D-B05


title: 72_DSP-1001660003045-D-B09


title: 71_DSP-1001660003045-D-B07


title: No Template Control_DSP-1001660003045-D-A01


title: 66_DSP-1001660003045-D-A06


title: 69_DSP-1001660003045-D-B02


title: 66_DSP-1001660003045-D-A07


title: 53_DSP-1001660003044-C-H10


title: 53_DSP-1001660003044-C-H09


title: 70_DSP-1001660003045-D-B04


title: 55_DSP-1001660003045-D-A02


title: 51_DSP-1001660003044-C-H08


title: 51_DSP-1001660003044-C-H07


title: 55_DSP-1001660003044-C-H12


title: 63_DSP-1001660003045-D-A05


title: 63_DSP-1001660003045-D-A04


title: 48_DSP-1001660003044-C-H02


title: 45_DSP-1001660003044-C-G08


title: 48_DSP-1001660003044-C-H03


title: 45_DSP-1001660003044-C-G10


title: 46_DSP-1001660003044-C-H01


title: 53_DSP-1001660003044-C-H11


title: 49_DSP-1001660003044-C-H06


title: 42_DSP-1001660003044-C-G07


title: 42_DSP-1001660003044-C-G06


title: 49_DSP-1001660003044-C-H05


title: 48_DSP-1001660003044-C-H04


title: 40_DSP-1001660003044-C-G05


title: 4_DSP-1001660003044-C-G01


title: 46_DSP-1001660003044-C-G11


title: 45_DSP-1001660003044-C-G09


title: 32_DSP-1001660003044-C-F07


title: 58_DSP-1001660003045-D-A03


title: 4_DSP-1001660003044-C-G02


title: 40_DSP-1001660003044-C-G04


title: 27_DSP-1001660003044-C-E12


title: 35_DSP-1001660003044-C-F11


title: 35_DSP-1001660003044-C-F10


title: 35_DSP-1001660003044-C-F12


title: 4_DSP-1001660003044-C-G03


title: 46_DSP-1001660003044-C-G12


title: VERO_NSP12_2

city: shanghai

first: ql

last: zheng

address: xiangyin

country: China

institute: immunity

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19 and Cercopithecus aethiops
Supplementary_files_format_and_content: xlsx files containing include RPKM values for each Sample

organism: Chlorocebus aethiops

source_name: VERO

growth_protocol: Cells were grown in RIPM-1640 media supplemented with 10% FBS

extract_protocol:
Total RNA was isolated from the above treated cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HEK293T or VERO cells were transfected with Control or NSP12 overexpression plasmid

value: VERO

tag: overexpression

value: NSP12 overexpression


title: 32_DSP-1001660003044-C-F06


title: 30_DSP-1001660003044-C-F05


title: 24_DSP-1001660003044-C-E07


title: 32_DSP-1001660003044-C-F08


title: 24_DSP-1001660003044-C-E06


title: 3_DSP-1001660003044-C-F02


title: VERO_Control_1

value: control


title: 3_DSP-1001660003044-C-F03


title: 24_DSP-1001660003044-C-E05


title: 27_DSP-1001660003044-C-F01


title: 25_DSP-1001660003044-C-E10


title: 27_DSP-1001660003044-C-E11


title: 25_DSP-1001660003044-C-E09


title: VERO_NSP12_1


title: Non-treated gshA:Tn cells replicate 1

city: Fresno

first: Mamta

last: Rawat

state: CA

address: 2555 E. San Ramon Ave. MS S/B 73

department: Biology

institute: California State University, Fresno

description:
gshA 1
raw_counts.txt
PAO1_processed.xlsx

data_processing:
Reads were mapped to the reference genome for P. aeruginosa (RefSeq GCF_000006765.1) using Rsubread version 2.4.0.
EdgeR was used to normalize gene expression using trimmed means of M-values (TMM) and to identify differentially expressed genes and statistical analysis
Only mapped reads equal to or greater than 10 counts per million reads, and a cut-off of p-value < 0.05 were considered for further analysis.
Assembly: RefSeq GCF_000006765.1
Supplementary files format and content: raw_counts.txt contains the raw counts for each set of aligned reads for each individual sample.
Supplementary files format and content: BT_processed.xlsx contains an excel file containing the gene ID, gene description, log2FC of the mutants compared to the wildtype strain, and p-value. There are three different sheets in the file, one for each mutant vs wildtype.

organism: Pseudomonas aeruginosa

source_name: whole bacterial cell

growth_protocol: Pseudmonas aeruginosa was grown in TSB and collected at mid-logarithmic phase (OD600 0.4 - 0.6) grown while shaken at 37C

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to manufacturer instructions with the following exception: samples were lysed by bead-beating using a BeadBlaster 24 (Benchmark Scientific). To remove ribosomal RNAs, high-quality total RNA was processed using Illumina’s Ribo-Zero Bacteria kit (Illumina, San Diego, CA).
cDNA libraries were generated with rRNA depleted mRNA using the KAPA RNA Hyper Plus Kit (Roche, Indianapolis, IN) following the manufacturer’s instructions

treatment_protocol: No treatments were applied, rather a comparison between the wildtype and transposon mutated strain were compared.

tag: strain

value: whole bacterial cell

tag: growth condition

value: 37C, shaken, logarithmic growth


title: 23_DSP-1001660003044-C-E03


title: Non-treated wildtype cells replicate 2

description:
wildtype 2
raw_counts.txt
PAO1_processed.xlsx

value: wild-type


title: 25_DSP-1001660003044-C-E08


title: 23_DSP-1001660003044-C-E02


title: Non-treated gshA:Tn cells replicate 2

description:
gshA 2
raw_counts.txt
PAO1_processed.xlsx


title: 3_DSP-1001660003044-C-F04


title: 23_DSP-1001660003044-C-E04


title: Non-treated gshA:Tn cells replicate 3

description:
gshA 3
raw_counts.txt
PAO1_processed.xlsx


title: Non-treated wildtype cells replicate 3

description:
wildtype 3
raw_counts.txt
PAO1_processed.xlsx


title: 22_DSP-1001660003044-C-D12


title: VERO_Control_2


title: Non-treated wildtype cells replicate 1

description:
wildtype 1
raw_counts.txt
PAO1_processed.xlsx


title: KAPA_TR_V

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 0900 Euclid Ave.

institute: Case Western Reserve University

library_source: genomic

data_processing:
trim fastq using fastp with Qxyg option
map the trimmed reads to galGal6 genome
extract mapped alignments in bed format using bedtools
Assembly: galGal6
Supplementary files format and content: bed coordinates and mapping read sequences

molecule: genomic DNA

organism: Tyrannosaurus rex

source_name: vessels

extract_protocol:
Tyrannosaurus rex (MOR1125) and Brachylophosaurus canadensis (MOR 2598) were prepared and analyzed in separate laboratories from the extant material, with separate buffers, reagents and instruments, by investigators wearing all protective lab garb (coats, hair covers, masks, gloves, etc.) and following aseptic procedures. Samples were prepared in the BioGard hood. Cortical bone fragments from each dinosaur were subjected to demineralization by incubation in 0.5 M EDTA (pH 8.0). Debris remaining from demineralization was filtered through a 40 µm cell strainer (BD Falcon 352340), and filtrate was centrifuged and washed with E-pure water to collect cells. Vessels were isolated from debris trapped within the cell strainer and washed. Both cells and vessels were incubated with the iron chelator pyridoxal isonicotinoyl hydrazone (PIH) in solution (5 mM PIH in 50 mM NaOH) (1,2,3) to remove iron, and then were prepared with "Protocol for preparing non-mammalian samples for Omni-C sequencing and do novo genome reconstruction— 2/22/2021, adopted by Berkley Gryder from Dovetail protocol used in the DNA zoo project" beginning at step 3, as above.
KAPA HyperPlus Kit protocol (Roche 07962401001)

value: vessels


title: 22_DSP-1001660003044-C-E01


title: SRSLY_TR_O

source_name: osteocytes

value: osteocytes


title: 20_DSP-1001660003044-C-D07

value: Lung Cancer


title: Blood, Beta, rep7

city: Toronto

first: Stephen

last: Matthews

address: 1 King's College Circle, Rm 3302

country: Canada

institute: University of Toronto

data_processing:
Quality control of data was performed using Trim Galore to trim low-quality reads (Phred <30) and accessory sequences from adaptors. Reads that did not contain an MspI site signature at the 5’ end were removed using a script provided by NuGEN (https://github.com/nugentechnologies/NuMetRRBS/blob/master/ trimRRBSdiversityAdaptCustomers.py). The reads were then aligned using Bismark (version 0.16.0) and Bowtie2 (v2.3.4.3) and sorted by Samtools (v1.9). We then used MethPipe (version 3.4.2) to identify significant differentially methylated CpG sites (DMCs). DMCs were filtered for those with at least 10X reads with FDR < 0.05. CompEpitool was used to annotate the differentially methylated CpG sites to the guinea pig genome (cavPor3).
Assembly: cavPor3
Supplementary files format and content: Tab-delimited text files of DMCs with at least 10X reads (formatted as "chr", "loc", "fdr", "MethDiff")

organism: Cavia porcellus

source_name: Whole Blood Spot

extract_protocol:
DNA from a dried blood spot of each animal was extracted using Quick-DNA™ Microprep Plus Kit (Zymo Research).
RRBS libraries were generated from 100ng of high-quality dsDNA using the RRBS Methyl_seq System 1-16 (Ovation: Part #0353) and EpiTect Fast DNA Bisulfite kit (Qiagen: Cat. #59824) following the manufacturer’s protocols.

treatment_protocol: Pregnant guinea pigs were administered betamethasone or saline on gestational day 50/51.

value: Whole Blood Spot


title: SRSLY_TR_V_S


title: SRSLY_TR_V


title: KAPA_TR_O


title: SRSLY_TR_O_S


title: 21_DSP-1001660003044-C-D10

value: Immunotherapy


title: 21_DSP-1001660003044-C-D09

value: CK


title: 21_DSP-1001660003044-C-D08


title: Blood, Beta, rep6


title: 20_DSP-1001660003044-C-D06


title: 22_DSP-1001660003044-C-D11


title: 2_DSP-1001660003044-C-D05


title: Blood, Beta, rep4


title: 2_DSP-1001660003044-C-D04


title: 2_DSP-1001660003044-C-D03


title: Blood, Beta, rep5


title: 18_DSP-1001660003044-C-D02


title: Blood, Beta, rep2


title: 18_DSP-1001660003044-C-C12


title: 18_DSP-1001660003044-C-D01


title: liver_fructose_nitrite_3

type: RNA

city: Novy Hradek

first: Tomas

last: Hrncir

address: Doly 183

department: Laboratory of Gnotobiology

country: Czech Republic

institute: Institute of Microbiology of the Czech Academy of Sciences

description: Gene expression data from mouse liver.

hyb_protocol: 3.8 µg of fragmented and labeled ss cDNA were hybridized to Applied Biosystems GeneChip Clariom S mouse arrays for 16 h at 45°C and 60 rpm in an Applied Biosystems GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Applied Biosystems GeneChip Fluidics Station FS450. The fluorescent signals were measured with an Applied Biosystems GeneChip Scanner 3000 7G System. Fluidics and scan functions were controlled by the Applied Biosystems GeneChip Command Console v5.0 software.

data_processing: Summarized probe set signals in log2 scale were calculated using the GCCN-SST-RMA algorithm with the Applied Biosystems GeneChip Expression Console v1.4 Software. The SST-RMA method includes GC4 (GC Correction Version 4) background reduction and SST (Signal Space Transformation) intensity normalization in the expression data processing workflow. Data were analyzed using Transcriptome Analysis Console (TAC), 4.0.2.

label: biotin

organism: Mus musculus

source_name: liver, fructose_nitrite

label_protocol: Sample preparation was carried out using the Applied Biosystems GeneChip Whole Transcript (WT) PLUS Reagent Kit. 200 ng of total RNA was used to generate double-stranded cDNA. 20 µg of subsequently synthesized cRNA were purified and reverse transcribed into single-stranded (ss) cDNA, incorporating unnatural dUTP residues. Purified ss cDNA was fragmented using uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1), followed by terminal labeling with biotin.

growth_protocol: Mice were colonized with human microbiota and maintained in plastic isolators. They were given ad libitum access to food and water and maintained on a 12-hour light/dark cycle.

extract_protocol: Total RNA was extracted from mouse liver tissue stabilized in RNAlater buffer using the RNeasy Micro Kit (QIAGEN, Hilden, Germany). Tissue was disrupted and homogenized in 600 µl RLT buffer containing 1% beta-mercaptoethanol with Precellys CK14 ceramic beads (2 cycles of 15 seconds at 6500 rpm; 30 seconds break) using a Precellys 24 Homogenizator. After centrifugation, 300 µl of the cleared supernatant was processed through RNeasy MinElute spin columns, including an on-column DNase digestion step. Total RNA was eluted in 14 μl of nuclease-free water.

treatment_protocol: 10% fructose (w/v) was administered from 3 weeks of age for 11 weeks. Fructose was given ad libitum in the drinking water. Food preservatives (sodium benzoate, sodium nitrite, or potassium sorbate) were administered together with the fructose, adjusted to the estimated maximum daily intake for the European population.

tag: age

value: 11 weeks


title: liver_fructose_sorbate_3

description: Gene expression data from mouse liver.

source_name: liver, fructose_sorbate


title: liver_fructose_benzoate_3

description: Gene expression data from mouse liver.

source_name: liver, fructose_benzoate

value: fructose-benzoate


title: liver_fructose_sorbate_1

description: Gene expression data from mouse liver.


title: liver_fructose_nitrite_2

description: Gene expression data from mouse liver.


title: liver_fructose_sorbate_2

description: Gene expression data from mouse liver.


title: liver_fructose_nitrite_1

description: Gene expression data from mouse liver.


title: liver_fructose_benzoate_1

description: Gene expression data from mouse liver.


title: Blood, Beta, rep1


title: liver_fructose_benzoate_2

description: Gene expression data from mouse liver.


title: 17_DSP-1001660003044-C-C11


title: liver_fructose_3

description: Gene expression data from mouse liver.

source_name: liver, fructose

value: fructose


title: Blood, Beta, rep3


title: Blood, Saline, rep6


title: 17_DSP-1001660003044-C-C10


title: 17_DSP-1001660003044-C-C09


title: liver_fructose_2

description: Gene expression data from mouse liver.


title: Blood, Saline, rep5


title: Blood, Saline, rep7


title: liver_control_3

description: Gene expression data from mouse liver.

source_name: liver, water

value: water


title: Blood, Saline, rep4


title: 15_DSP-1001660003044-C-C07


title: liver_control_2

description: Gene expression data from mouse liver.


title: Blood, Saline, rep3


title: liver_fructose_1

description: Gene expression data from mouse liver.


title: 120_DSP-1001660003044-C-C06


title: 120_DSP-1001660003044-C-C05


title: R1

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

hyb_protocol: Labeled fragments were hybridized to Affymetrix Clariom S arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: C57BL/6 wildtype

label_protocol: We used the Affymetrix Clariom S kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: B16.F10 luc+GFP+ melanoma cells were maintained in DMEM (with 10 % FCS and 1 % PenStrep) with a confluency up to 90 % for one week prior to injection

extract_protocol: RNA was isolated using the miRNeasy Mini kit (Qiagen). RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent 141 Technologies). RNA samples with an RNA quality number (RQN) greater than 9 were further processed for Affymetrix microarrays.

treatment_protocol: Mice were treated intraperitoneally with anti-PD-1 on day 1, 4 and 8 after melanoma injection and treated orally with RG7112 or vehicle (corn oil + 5 % DMSO) every second day for 6 days (two days after B16.F10 melanoma injection)

tag: srtrain

tag: tissues

value: subcutaneous tumor (melanoma)

value: mixture of:melanoma tumor cells and infiltrating immune cells

value: 10 weeks

value: Wildtype

value: treated with anti-PD-1 + RG7112


title: 5FC derivative clone R2, bio rep 3

first: Trinh

last: Phan-Canh

email: phancanht99@univie.ac.at, phancanhtrinh@gmail.com, karl.kuchler@univie.ac.at, karl.kuchler@univie.ac.at

state: Vienna

address: Dr.-Bohr-Gasse 9

department: Max Perutz Labs Vienna, Campus Vienna Biocenter

institute: Medical University of Vienna

data_processing:
The quality of raw reads were analyzed using FastQC (Andrews, 2010).
TrueSeq (Illumina) adapters were trimmed by using cutadapt v2.8 (https://cutadapt.readthedocs.io/en/stable/; settings: -q 30 -O 1). The reads were then mapped to C. auris genome (B8441) using NextGenMap (Sedlazeck et al., 2013), settings: -b -Q 30.
Optical read duplicates were removed using Picard tools (Broad Institute, https://broadinstitute.github.io/picard/, settings: MarkDuplicates REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT). Read counting was done using HTseq (Anders et al., 2014) in the union mode and the genomic annotation from C. auris B8441 (settings: -f bam -t gene -i ID).
Assembly: Differential gene expression analysis was done using the glm approach in edgeR (Robinson et al., 2009)
Supplementary files format and content: tab delimited .txt files containing the output of the HTSeq analysis (read counts)
Assembly: Candida auris B8441 - Genome version: s01-m01-r22 from Candida Genome Database
Supplementary files format and content: Matrix files are provided for each sample, comprising two columns: GeneID (Candida Genome Database) and raw read count.

molecule: polyA RNA

organism: Candidozyma auris

source_name: 1133/P/13R, 5FC-induced mutant

growth_protocol: YPD, 37°C, 200 rpm, exponential phase

extract_protocol:
The total RNA was isolated from frozen samples using TRIZOL reagent.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: comparing different genotypes

value: 1133/P/13R, 5FC-induced mutant

value: planktonic cell at exponential phase

value: 5FC-induced mutant

value: YPD


title: R3


title: 5FC derivative clone I1, bio rep 2


title: 5FC derivative clone R2, bio rep 2


title: liver_control_1

description: Gene expression data from mouse liver.


title: R2


title: 119_DSP-1001660003044-C-C04

value: Lung Cancer


title: 5FC derivative clone S1, bio rep 2


title: 5FC derivative clone R2, bio rep 1


title: 15_DSP-1001660003044-C-C08


title: muscle,excersised

city: Hangzhou

first: Fangling

last: Zhao

state: Zhejiang province

address: Jie Fang Road NO.88

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Gastrocnemius in old mice

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: Gastrocnemius in old mice

value: primary culture cell

value: Muscle cells

value: WT

value: adipogenic differentiation


title: 119_DSP-1001660003044-C-C03

value: CK

value: Immunotherapy


title: Blood, Saline, rep1

value: Whole Blood Spot


title: 5FC derivative clone I1, bio rep 1


title: 5FC derivative clone S1, bio rep 1


title: 5FC derivative clone R1, bio rep 3


title: 5FC derivative clone R1, bio rep 2


title: V4

value: subcutaneous tumor (melanoma)

value: mixture of:melanoma tumor cells and infiltrating immune cells

value: treated with anti-PD-1 + vehicle (corn oil + 5 % DMSO)


title: 119_DSP-1001660003044-C-C02


title: 5FC derivative clone R1, bio rep 1


title: WT, biol rep 3

source_name: 1133/P/13R, clinical isolate

value: 1133/P/13R, clinical isolate


title: 118_DSP-1001660003044-C-C01


title: V3

value: 10 weeks

value: Wildtype


title: 2ko--d1

city: Shanghai

first: Yijin

last: Hou

address: No. 168, Changhai Road

institute: Department of Traumatic Orthopedics, Changhai Hospital, Naval Medical University

data_processing:
Stringtie（version:1.3.0）
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: FPKM values for each sample

source_name: cell

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1.3 ug of total RNA was used for the construction of sequencing libraries
RNA lilbraries for RNA-seg were prepared using SMARTER mRNA-Seg Lilbrary Prep Kit folowing manufacturer's protocols.

value: cell

value: Bone Marrow-Derived Macrophages

value: bone marrow derived macrophage(BMDM)

value: Zmat1 ko

value: M-CSF;RANKL,1 day


title: 2ko--d0

value: M-CSF


title: 1WT--d0

value: wilde type


title: 1WT--d1


title: Thyroid MPRA rep 3 [thy_3]

city: Stanford

first: Paul

last: Khavari

address: 269 Campus Drive, CCSR, Room 2150

department: Dermatology

institute: Stanford University

data_processing:
library strategy: Massively parallel reporter assay (MPRA)
Read 1 was unzipped and trimmed to the first 20bp containing the barcode using fastx_trimmer (fastx_trimmer -f 1 -l 20 -Q33)
Reverse complement of barcode was taken (fastx_reverse_complement -Q33)
UMI was extracted from index 2 (umi_tools extract --bc-pattern=NNNNNNNNNNNN)
Reads were aligned to the barcode library using bowtie2 (bowtie2 -p 8 -k 1 --norc -x)
Sam file was converted to a bam file (samtools view -S -b)
Bam file was sorted and indexed (samtools sort, samtools index)
Reads were deduplicated (umi_tools dedup -I --out-sam --no-sort-output)
File was converted to a tsv  (awk '$1 !~ /^@/ {print $1"\t"$3}')
Counts per barcode were tabulated (umi_tools count_tab)
Genome_build: NA
Supplementary_files_format_and_content: Tab-delimited files with barcode counts for each oligo in each condition

source_name: Thyroid MPRA

growth_protocol: Cells were grown in Cell Biologics Human Epithelial Cell Medium, passed before 95% confluence. Cells were infected with 16ul 50x virus per 200k cells with 8ug/ml polybrene. At least 12M cells were reverse infected, plated onto 15cm plates and selected with 1ug/ml puromycin. Cells were harvested in Qiagen Buffer RLT Plus.

extract_protocol:
Total RNA and DNA representing roughly 12 million cells were isolated using Qiagen’s AllPrep DNA/RNA Mini Kit. mRNA was then isolated from the total RNA using Dynabeads mRNA DIRECT purification kit (Thermo Fisher)
Reactions containing 500ng mRNA and 100nM of a gene-specific primer containing a sample index and UMI (GGW610-501 – GGW610-508, Table S5) were reverse transcribed using Superscript IV (Thermo Fisher), along with a no reverse transcriptase control. Reactions were incubated with 1ul thermolabile exonuclease I (NEB) for 10 min at 37C, followed by heat inactivation for 5min at 85C. The cDNA was cleaned with Ampure XP beads (Beckman Coulter) at a ratio of 1:1.1 sample to beads and eluted in the initial volume. The cDNA was amplified in 50ul reactions containing 5ul cDNA, LK612 at 80nM, one of LK134-701-LK134-712 at 80nM (Table S5), SYBR green (Thermo Fisher), and PrimeStar Max DNA Polymerase (Takara Bio). The reactions were amplified until they were just beginning to rise, then they were pooled and concentrated. The libraries were then gel purified and quantified using the KAPA library quantification kit (Roche). The 42 samples were put into 3 pools which were sequenced using an Illumina NextSeq Sequencer.

value: Human primary thyroid epithelial cells (Cell Biologics)


title: 5FC derivative clone S1, bio rep 3

value: 1133/P/13R, 5FC-induced mutant

value: planktonic cell at exponential phase

value: 5FC-induced mutant

value: YPD


title: 118_DSP-1001660003044-C-B12

source_name: Lung Cancer

value: Lung Cancer

value: CK

value: Immunotherapy


title: WT, biol rep 1

value: 1133/P/13R, clinical isolate

value: WT


title: 1ko--d1

value: cell


title: Renal MPRA rep 3 [renal_3]

source_name: Renal MPRA

growth_protocol: Cells were grown in Cell Biologics Human Epithelial Cell Medium, passed before 95% confluence. Cells were infected with 32ul 50x virus per 200k cells with 8ug/ml polybrene. At least 12M cells were reverse infected, plated onto 15cm plates and selected with 1ug/ml puromycin. Cells were harvested in Qiagen Buffer RLT Plus.

value: Human primary proximal tubular epithelial cells (Cell Biologics)


title: 3WT-3d

value: Bone Marrow-Derived Macrophages

value: bone marrow derived macrophage(BMDM)

value: M-CSF;RANKL,3 days


title: 117_DSP-1001660003044-C-B10


title: Renal MPRA rep 1 [renal_1]


title: Renal MPRA rep 2 [renal_2]


title: Thyroid MPRA rep 1 [thy_1]


title: 117_DSP-1001660003044-C-B09


title: Prostate MPRA rep 3 [pros_3]

source_name: Prostate MPRA

growth_protocol: Cells were grown in ATCCProstate Epithelial Cell Basal Medium with Prostate Epithelial Cell Growth Kit, passed before 95% confluence. Cells were infected with 4ul 50x virus per 150k cells with 8ug/ml polybrene. At least 12M cells were reverse infected, plated onto 15cm plates and selected with 1ug/ml puromycin. Cells were harvested in Qiagen Buffer RLT Plus.

value: Primary prostate epithelial cells (ATCC)


title: 3WT-0d

value: wilde type

value: M-CSF


title: WT, biol rep 2


title: Prostate MPRA rep 2 [pros_2]


title: Prostate MPRA rep 1 [pros_1]


title: Pancreas MPRA rep 3 [panc_3]

source_name: Pancreas MPRA

growth_protocol: Cells were grown in Cell Biologics Human Epithelial Cell Medium, passed before 95% confluence. Cells were infected with 8ul 50x virus per 150k cells with 8ug/ml polybrene. At least 12M cells were reverse infected, plated onto 15cm plates and selected with 1ug/ml puromycin. Cells were harvested in Qiagen Buffer RLT Plus.

value: Human primary pancreatic epithelial cells (Cell Biologics)


title: 117_DSP-1001660003044-C-B08


title: Thyroid MPRA rep 2 [thy_2]

value: Human primary thyroid epithelial cells (Cell Biologics)


title: 3KO-3d

value: Zmat1 ko


title: 3KO-1d

value: M-CSF;RANKL,1 day


title: Ovarian MPRA rep 3 [ov_3]

source_name: Ovarian MPRA

value: Human primary ovarian epithelial cells (Cell Biologics)


title: Pancreas MPRA rep 1 [panc_1]


title: 3KO-0d


title: Ovarian MPRA rep 2 [ov_2]


title: 116_DSP-1001660003044-C-B07

value: Lung Cancer


title: 116_DSP-1001660003044-C-B05

value: Immunotherapy


title: 2WT-3d


title: Ovarian MPRA rep 1 [ov_1]


title: 111_DSP-1001660003044-C-B04


title: Melanocyte MPRA rep 2 [mc_2]

source_name: Melanocyte MPRA

growth_protocol: Cells were grown in Medium 254 with Human Melanocyte Growth Supplement and 1% Pen/Strep. Cells were infected with 8ul 50x virus per 200k cells with 8ug/ml polybrene. At least 12M cells were reverse infected, plated onto 15cm plates and selected with 1.5ug/ml puromycin. Cells were harvested in Qiagen Buffer RLT Plus.

value: Neonatal foreskin derived melanocytes


title: Melanocyte MPRA rep 1 [mc_1]


title: 111_DSP-1001660003044-C-B03

value: CK


title: 118_DSP-1001660003044-C-B11


title: 293T MPRA rep 3 [lx_3]

source_name: 293T MPRA

growth_protocol: Cells were grown in DMEM with 10% FBS and 1% Pen/Strep. Cells were infected with 16ul 50x virus per 200k cells with 8ug/ml polybrene. At least 12M cells were reverse infected, plated onto 15cm plates and selected with 1.5ug/ml puromycin. Cells were harvested in Qiagen Buffer RLT Plus.

value: 293T LentiX (Takara)


title: 2WT-1d

value: cell


title: 293T MPRA rep 2 [lx_2]


title: Pancreas MPRA rep 2 [panc_2]


title: Melanocyte MPRA rep 3 [mc_3]


title: 111_DSP-1001660003044-C-B02


title: 293T MPRA rep 1 [lx_1]


title: 116_DSP-1001660003044-C-B06


title: 1WT-3d

value: Bone Marrow-Derived Macrophages


title: Keratinocyte MPRA rep 3 [kc_3]

source_name: Keratinocyte MPRA

growth_protocol: Cells were grown in Keratinocyte-SFM and Medium 154 with pen/strep and antimycotic. Cells were infected with 16ul 50x virus per 200k cells with 8ug/ml polybrene. At least 12M cells were reverse infected, plated onto 15cm plates and selected with 1.5ug/ml puromycin. Cells were harvested in Qiagen Buffer RLT Plus.

value: Neonatal foreskin derived keratinocytes


title: Keratinocyte MPRA rep 2 [kc_2]


title: Keratinocyte MPRA rep 1 [kc_1]


title: 109_DSP-1001660003044-C-B01


title: HMEC MPRA rep 3 [hmec_3]

source_name: HMEC MPRA

growth_protocol: Cells were grown in Lonza Mammary Epithelial Cell Medium, passed before 95% confluence. Cells were infected with 8ul 50x virus per 200k cells with 8ug/ml polybrene. At least 12M cells were reverse infected, plated onto 15cm plates and selected with 1.5ug/ml puromycin. Cells were harvested in Qiagen Buffer RLT Plus.

value: Human mammary epithelial cells (Lonza)


title: 109_DSP-1001660003044-C-A12


title: 1WT-1d

value: bone marrow derived macrophage(BMDM)


title: HMEC MPRA rep 2 [hmec_2]


title: 103_DSP-1001660003044-C-A11


title: H9 MPRA rep 3 [h9_3]

source_name: H9 MPRA

growth_protocol: Cells were grown on Corning ES-qualified matrigel and lifted with accutase. Cells were infected with 200ul virus/130k cells with 10uM rock inhibitor. Cells were then selected with 0.5ug/ml puromycin. Cells were harvested by lifting with Accutase and lysing in Qiagen buffer RLT Plus.

value: H9 human ES cells


title: HMEC MPRA rep 1 [hmec_1]


title: 2WT-0d

value: wilde type

value: M-CSF


title: 103_DSP-1001660003044-C-A10


title: 1KO-0d


title: H9 MPRA rep 2 [h9_2]


title: GM12878 MPRA rep 3 [gm_3]

source_name: GM12878 MPRA

growth_protocol: Cells were grown in RPMI 1640 supplemented with 15% non-heat inactivated FBS, 2mM L-glutamine and 1% pen/strep. At least 20M cells were spinfected with 1ml/million cells of freshly harvested 1x virus at 300g for 2hours at room temperature with 4ug/ml polybrene. Cells were selected with 2ug/ml puromycin. RNA was harvested in Qiagen Buffer RLT Plus.

value: GM12878 B lymphoblastoid line


title: H9 MPRA rep 1 [h9_1]


title: 102_DSP-1001660003044-C-A09


title: 2KO-3d

value: Zmat1 ko

value: M-CSF;RANKL,3 days


title: 6847974_tumor_CD45+_cells_scTCRseq

city: Tarrytown

first: Qingqing

last: Wang

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

description: 10x Genomics

data_processing:
For scRNAseq, raw fastq files were processed with Cell Ranger Single-Cell Software Suite (10X Genomics, v6.1.2) for sample demultiplexing, alignment,filtering and UMI counting. Specifically, alignment was performed against a custom-built genome reference using cellranger mkref as instructed by 10X Genomics, where the humanized LAG3 and PDCD1 sequences were provided in additional to the default mouse genome. Data from multiple samples were merged and further cleaned up to remove dead cell populations, doublets and small tumor sample contaminations, and clustered, analyzed and visualized following the standard analysis workflow of Seurat v4 (cite). Cell identities were annotated using known cell functional markers.
For V(D)J profiling data, Cell Ranger (v6.1.2) was used to perform sample demultiplexing, de novo assembly of read pairs into contigs, alignment and annotation of contigs against the germline segment V(D)J reference sequences from IMGT, labeling and location of CDR3 regions and grouping of clonotypes. Single cell TCR clonotypes data were further analyzed using scRepertoire (v1.13.0) (cite) for clonal analysis. A TCR clonotype is defined as the combination of V(D)J genes comprising the TCR and the nucleotide sequence of the CDR3 region (gene+nucleotide) for paired TCR alpha and beta chains.
Assembly: Mm10
Supplementary files format and content: genes.tsv file, 10X gene file for raw UMI counts
Supplementary files format and content: matrix.mtx file, 10X format, raw UMI counts
Supplementary files format and content: barcodes.tsv file, 10X barcodes file for raw UMI counts
Supplementary files format and content: Metadata.txt file, phenotypic metadata for cells in dataset
Supplementary files format and content: UMAP_coordinates.txt file, UMAP coordinates of cells in dataset, from unsupervised clustering based on gene expression profiles
Supplementary files format and content: filtered_contig_annoatations.csv file, filtered VDJ contig information analyzed by Cell ranger v.3.0.2

source_name: tumor

growth_protocol: For tumor studies, unless otherwise indicated, different mouse strains were implanted with tumor cells resuspended in HBSS (GibcoTM 14025076) by subcutaneous injection on the right flank. The following tumor cell numbers were used: MC38 (3x105 cells), B16F10 (3x105 cells), MCA205 (1x106 cells), TRAMP-C2 (1x106 cells), Colon26 (1x106 cells). When tumors were established, mice were randomized based on tumor size and treated with indicated molecules and doses on the indicated days via intraperitoneal injection. For the ID8-VEGF/huMUC16D studies, human CD3/MUC16 knock-in mice were subcutaneously implanted with 1x107 tumor cells, resuspended in RMPI1640 medium, and treatments were administered via intravenous injection. Tumor growth was monitored over time using caliper measurements and calculated as (length x width2)/2. Mice were euthanized when tumors reached >2000mm3 or became severely ulcerated. For tumor rechallenge experiments, 3x105 MC38 cells or 1x107 ID8-VEGF cells were implanted on the left flanks of corresponding tumor-free mice more than 75 days after they received and rejected their primary tumor challenges.

extract_protocol:
Single cells suspended in PBS with 0.04% BSA were loaded on a Chromium Single Cell Instrument (10x Genomics).
RNA-seq and V(D)J libraries were prepared using Chromium Single Cell 5’ Library, Gel Beads & Multiplex Kit (10X Genomics). After amplification, cDNA was split into RNA-seq and V(D)J library aliquots. To enrich the V(D)J library aliquot for TCR a/b, the cDNA was split into two 20 ng aliquots and amplified in two rounds using primers designed in-house. Specifically, for first round amplification the primers used were MP147 (ACACTCTTTCCCTACACGACGC) for short R1, MP120 (GCAGACAGACTTGTCACTGGA) for human TRAC, and MP121(CTCTGCTTCTGATGGCTCAAACA) for human TRBC. For second round amplification, 20 ng aliquots from the first round were amplified using MP147, MP128 (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCAGGGTCAGGGTTCTGGATA) a nested R2 plus human TRAC, and MP129 (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCAGGGTCAGGGTTCTGGATA) a nested R2 plus human TRABC. V(D)J libraries were prepared from 25 ng each hTRAC and hTRBC amplified cDNA. Paired-end sequencing was performed on Illumina NextSeq500 for RNA-seq libraries (Read 1 26-bp for UMI and cell barcode, 8-bp i7 sample index, and Read 2 55-bp transcript read) and V(D)J libraries (Read 1 150-bp, 8-bp i7 sample index, and Read 2 150-bp read). For RNA-seq libraries, Cell Ranger Single-Cell Software Suite (10X Genomics, v2.2.0) was used to perform sample demultiplexing, alignment, filtering, and UMI counting. The human GRCh38 genome assembly and RefSeq gene model for human were used for the alignment. For V(D)J libraries, Cell Ranger Single-Cell Software Suite (10x Genomics, v2.2.0) was used to perform sample de-multiplexing, de novo assembly of read pairs into contigs, align and annotate contigs against the germline segment V(D)J reference sequences from IMGT, label and locate CDR3 regions, group clonotypes.
RNA-seq and V(D)J seq

treatment_protocol: Human PD-1 knock-in mice bearing established MC38 tumors (200 mm3) were grouped (4 mice per group) and intraperitoneally injected with two doses of either isotype (10 mg/kg), anti-PD1 (10mg/kg), NT-IL2Ra-IL2 (0.5mg/kg), or PD1-IL2Ra-IL2 (0.5mg/kg) on days 0 and 3. On day 6, tumors were excised and dissociated. Enriched CD45+ immune cells from tumors were subjected to single-cell RNA and TCR sequencing analyses

value: tumor


title: GM12878 MPRA rep 1 [gm_1]


title: 6815976_tumor_CD45+_cells_scTCRseq

description: 10x Genomics


title: GM12878 MPRA rep 2 [gm_2]


title: 102_DSP-1001660003044-C-A08

value: Lung Cancer


title: Esophageal MPRA rep 3 [eso_3]

source_name: Esophageal MPRA

growth_protocol: Cells were grown in Cell Biologics Human Epithelial Cell Medium, passed before 95% confluence. Cells were infected with 8ul 50x virus per 200k cells with 8ug/ml polybrene. At least 12M cells were reverse infected, plated onto 15cm plates and selected with 1ug/ml puromycin. Cells were harvested in Qiagen Buffer RLT Plus.

value: Human primary esophageal epithelial cells (Cell Biologics)


title: 101_DSP-1001660003044-C-A07

value: Immunotherapy


title: 101_DSP-1001660003044-C-A06

value: CK


title: Esophageal MPRA rep 2 [eso_2]


title: 1KO-3d


title: Endometrial MPRA rep 3 [endo_3]

source_name: Endometrial MPRA

growth_protocol: Cells were grown in Lifeline ReproLife Reproductive Medium, passed before 95% confluence. Cells were infected with 16ul 50x virus per 200k cells with 8ug/ml polybrene. At least 12M cells were reverse infected, plated onto 15cm plates and selected with 1ug/ml puromycin. Cells were harvested in Qiagen Buffer RLT Plus.

value: Normal human endometrial epithelial cells (Lifeline)


title: 101_DSP-1001660003044-C-A05


title: Endometrial MPRA rep 1 [endo_1]


title: 6815952_tumor_CD45+_cells_scTCRseq

description: 10x Genomics


title: Colon MPRA rep 3 [colon_3]

source_name: Colon MPRA

value: Primary colonic epithelial cells (Cell Biologics)


title: 6815945_tumor_CD45+_cells_scTCRseq

description: 10x Genomics


title: 100_DSP-1001660003044-C-A04


title: Colon MPRA rep 2 [colon_2]


title: 6815939_tumor_CD45+_cells_scTCRseq

description: 10x Genomics


title: 100_DSP-1001660003044-C-A02


title: 6815935_tumor_CD45+_cells_scTCRseq

description: 10x Genomics


title: 100_DSP-1001660003044-C-A03


title: Astrocyte MPRA rep 3 [ast_3]

source_name: Astrocyte MPRA

growth_protocol: Cells were grown in Lonza Astrocyte Growth Medium BulletKit, passed before 95% confluence. Cells were infected with 8ul 50x virus per 200k cells with 8ug/ml polybrene. At least 12M cells were reverse infected, plated onto 15cm plates and selected with 1ug/ml puromycin. Cells were harvested in Qiagen Buffer RLT Plus.

value: Normal human astrocytes (Lonza)


title: Astrocyte MPRA rep 1 [ast_1]


title: 6815959_tumor_CD45+_cells_scTCRseq

description: 10x Genomics


title: Astrocyte MPRA rep 2 [ast_2]


title: Airway MPRA rep 2 [airway_2]

source_name: Airway MPRA

growth_protocol: Cells were grown in ATCC Airway Epithelial Cell Basal Medium with Bronchial Epithelial Cell Growth Kit, passed before 95% confluence. Cells were infected with 8ul 50x virus per 150k cells with 8ug/ml polybrene. At least 12M cells were reverse infected, plated onto 15cm plates and selected with 1ug/ml puromycin. Cells were harvested in Qiagen Buffer RLT Plus.

value: Primary bronchial/tracheal epithelial cells (ATCC)


title: No Template Control_DSP-1001660003044-C-A01

source_name: Lung Cancer

value: No Template Control

value: immunotherapy


title: Endometrial MPRA rep 2 [endo_2]


title: 6815930_tumor_CD45+_cells_scTCRseq

description: 10x Genomics


title: Airway MPRA rep 1 [airway_1]


title: Airway MPRA rep 3 [airway_3]


title: Esophageal MPRA rep 1 [eso_1]


title: RA1 VDJ

city: London

first: Lucy

last: Durham

address: 1st Floor, New Hunt's House, Guy's Campus, Newcommen Street

department: Centre for Inflammation Biology and Cancer Immunology

country: United Kingdom

institute: King's College London

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 6.1.1. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: .csv files containing VDJ information

source_name: Blood, synovial fluid, synovial tissue

extract_protocol:
Patient recruitment: Patients with PsA (n=5) and RA (n=1) were recruited from Guy’s and St Thomas’ NHS Foundation Trust, London, UK, to donate peripheral blood (PB) and ST and SF from an inflamed knee. Five patients underwent US-guided ST biopsies and one (PsA 1) donated ST during arthroplasty. Cell isolation: PB and SF mononuclear cells (PBMC and SFMC) were isolated using LymphoprepTM (Axis-Shield). US-guided ST biopsies were processed fresh by 30-minute digestion in culture media (RPMI) containing 1% penicillin/streptomycin/L‐glutamine (Gibco), 0.3mg/ml Liberase and 0.1mg/ml DNase (both Roche) on the gentleMACS dissociator (Miltenyi Biotech). The one ST sample obtained from surgery was cut into ~1-2mm3 sized pieces which were cryopreserved in culture media containing 50% FCS and 10% dimethyl sulfoxide (Fisher Scientific). Upon thawing, all subsequent steps were the same as for US-guided biopsy samples. Sample staining: Samples were stained with fluorescently labelled, TotalSeqC and hashtag antibodies in the presence of Fc-receptor blocker (Biologend). Samples containing > 2x106 cells were stained in duplicate using different hashtags to enhance doublet detection. Prior to sorting, replicate cells from tissues stained with different hashtags were pooled, and DAPI (Thermo Fisher Scientific) was added. Fluorescent-Activated Cell Sorting: Memory T-cells (CD45RA-CD27+, CD45RA-CD27- and CD45RA+CD27-) were sorted on BD Aria cell sorter using an 85μm nozzle for ST digests and a 70μm nozzle for PBMC and SFMC. Cells from all tissues were pooled and retained on ice pending library preparation.
Library was performed according to the manufacter’s instructions (single cell 5’ v1.1 protocol with feature barcoding and VDJ sequencing, 10x Genomics).

value: Blood, synovial fluid, synovial tissue

tag: disease

value: psoriatic arthritis

value: memory CD8+ T cells


title: HaCat cells, SDR42E1 knockout, biol rep2

city: Doha

first: Georges

middle: Michel

last: Nemer

state: Qatar

department: CHLS

country: Qatar

institute: HBKU

data_processing:
CLC Genomics Workbench version 22.0.2 software.
Raw sequence reads were trimmed to eliminate contaminant DNA, PCR duplicates, and adaptor sequences. Reads with a quality lower than Q20 were filtered using CLC Genomics Workbench software.
CLC Genomics Workbench was employed for assembly and mapping of all paired end reads against the latest version of the human genome (Homo sapiens, GRCh38). Genes with average raw counts below 10 were excluded.
Read counts were extracted utilizing CLC Genomics Workbench with default parameters.
Assembly: GRCh38
Supplementary files format and content: Comma-separated values (CSV) file contains raw counts for all samples.

source_name: human epidermal keratinocyte line

growth_protocol: All cells were cultured in DMEM with (4.5 g/L) high D-Glucose, (2 mM) Glutamine, and (1 mM) Sodium Pyruvate, supplemented with 10% fetal bovine serum (FBS) and (1X) antibiotic-antimycotic (Gibco). All cell lines were grown under sterile conditions in a monolayer culture at 37°C, with a 5% CO2 atmosphere and 95% air humidity. At 70% to 80% confluency, all cells were harvested through treatment with 0.25% EDTA.

extract_protocol:
Total RNA was isolated from cell lines using 1 mL TRIzol reagent (Invitrogen), according to the manufacturer's guidelines. Subsequently, equivalent amounts of high-quality RNA pools (100–200 ng) were precipitated in a 75% ethanol solution and shipped to Macrogen Inc. (http://macrogen.com, Korea) for total RNA-sequencing library construction and next-generation sequencing.
RNA sequencing libraries were prepared with the TruSeq Stranded Total RNA Library Prep Kit (1000000040499, Illumina), following the instructions.

value: human epidermal keratinocyte line

value: HaCat

value: spontaneously immortalized, human keratinocyte line

value: Homozygous SDR42E1 knockout


title: 6794397_tumor_CD45+_cells_scTCRseq

description: 10x Genomics

value: tumor


title: 6794403_tumor_CD45+_cells_scTCRseq

description: 10x Genomics


title: RA1 GEX

description: 10x Genomics


title: PSA5 VDJ

description: 10x Genomics


title: Colon MPRA rep 1 [colon_1]


title: RA1 CSP

description: 10x Genomics


title: 6794390_tumor_CD45+_cells_scTCRseq

description: 10x Genomics


title: 6780115_tumor_CD45+_cells_scTCRseq

description: 10x Genomics


title: HaCat cells, SDR42E1 knockout, biol rep1


title: PSA5 CSP

description: 10x Genomics


title: HaCat cells, control, biol rep2

value: wild-type control


title: 6780108_tumor_CD45+_cells_scTCRseq

description: 10x Genomics


title: PSA4 CSP

description: 10x Genomics

source_name: Blood, synovial fluid, synovial tissue, skin


title: HaCat cells, control, biol rep3


title: PSA4 GEX

description: 10x Genomics

value: Blood, synovial fluid, synovial tissue, skin


title: HaCat cells, SDR42E1 knockout, biol rep3


title: PSA4 VDJ

description: 10x Genomics


title: PSA3b CSP

description: 10x Genomics


title: PSA5 GEX

description: 10x Genomics


title: 6780107_tumor_CD45+_cells_scTCRseq

description: 10x Genomics


title: 6780103_tumor_CD45+_cells_scTCRseq

description: 10x Genomics


title: PSA3b GEX

description: 10x Genomics


title: PSA3b VDJ

description: 10x Genomics


title: 143B_XD23_48h_c

city: Shenzhen

first: jianhui

last: liang

state: Guangdong

address: 1068 Xueyuan Avenue, Nanshan District

institute: Shenzhen Institute of Science and Technology

data_processing:
All of the analyses were performed using an in-house pipeline from Shanghai Applied Protein Technology。Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. Inthis step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html), DEGs with | log2FC | > 1 and Padj < 0.05 were considered to be significantly different expressed genes.
The GO and KEGG enrichment analysis of differential genes can explain the functional enrichment of differential genes and clarify the differences between samples at the gene function level. We use clusterProfiler R software package for GO function enrichment and KEGG pathway enrichment analysis. When P<0.05, it is considered that the GO or KEGG function is significantly enriched.
Transcription factor is a kind of proteins that can bind to specific DNA sequences, widely existing in organisms. It can be recognized and bound to the cis-acting elements in the upstream regulatory region of genes through specific functional domains, which can activate or hinder the expression of genes. TF analysis of DEGs are extracted directly from the AnimalTFDB (http://bioinfo.life.hust.edu.cn/AnimalTFDB/) /PlantTFDB database(http://planttfdb.cbi.pku.edu.cn/) .
For the species are not existed in the database,fistly, we annotate the genes in the Pfam database (http://pfam.xfam.org/) by interscan tool to find the genes and the DBD database (https://dblp.uni- trier.de/rec/journals/nar/KummerfeldT06.html) to screen for transcription factors.
PPI analysis is used to study whether there is interaction between gene products -- proteins. The analysis is based on the protein information corresponding to genes. Based on the STRING database (https://www.string-db.org/) , which known and predicted Protein-Protein Interactions. For the species existing in the database, we construct the networks by extract the target gene list from the database. For species not included in the database, the target gene set sequence is first aligned with the reference sample protein sequence contained in the STRING protein interaction database with blastx, and the protein interaction relationship of the reference species is used to establish an interaction network.Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein.
rMATS (http://rnaseq-mats.sourceforge.net/index.html) is a variable splicing analysis software suitable for RNA-Seq data. It can not only classify variable splicing events, but also classify deformable splicing events as follows: Skipped exon (SE), Alternative 5 splice site (A5SS), Alternative 3 splice site (A3SS), mutually exclusion exon (MXE) , Retained intron (RI).
Assembly: hg38
Supplementary files format and content: gene_fpkm.txt

growth_protocol: The 143B cell lines were propagated in RPMI-1640 medium enriched with 10% fetal bovine serum (Gibco, US) and 1% penicillin-streptomycin (Gibco, US).

extract_protocol:
The cell samples were homogenized in Trizol (Invitrogen) and processed for RNA extraction according to the manufacturer’s instructions.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapterligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system

treatment_protocol: 143B cells were treated with 0.5μM XD23 for 24h or 48h.

value: human osteosarcoma cell line


title: HaCat cells, control, biol rep1


title: 33_DSP-1001660003044-C-F09

value: Lung Cancer

value: CK

value: Immunotherapy


title: Blood, Saline, rep2

source_name: Whole Blood Spot

value: Whole Blood Spot


title: 143B_XD23_48h_b


title: PSA3a VDJ

description: 10x Genomics


title: PSA2 CSP

description: 10x Genomics


title: PSA2 VDJ

description: 10x Genomics


title: PSA3a CSP

description: 10x Genomics


title: PSA3a GEX

description: 10x Genomics


title: 6815976_tumor_CD45+_cells_scRNAseq

description: 10x Genomics


title: PSA2 GEX

description: 10x Genomics


title: 6815959_tumor_CD45+_cells_scRNAseq

description: 10x Genomics


title: 143B_XD23_24h_c


title: PSA1 VDJ

description: 10x Genomics


title: 6815952_tumor_CD45+_cells_scRNAseq

description: 10x Genomics


title: Patski cells, Xist O-MAP RIP, Pulldown, Rep3

city: Seattle

first: Evan

middle: Erik

last: Kania

state: WA

address: 1959 NE Pacific Street, HSB K554, Box 357750

department: Pharmacology

institute: University of Washington

data_processing:
Raw RNA-seq FASTA files were aligned to mm10 using HISAT2 version 2.2.1, in the paired-end setting with default parameters.
The resulting SAM files were converted to BAM format and sorted using Samtools version 1.15.1.
Mapped reads were quantified using StringTie version 2.2.1 and the StringTie output was prepared for differential expression analysis using the prepDE.py function. The resulting gene count matrices were used for differential expression analysis using DESeq2 with an FDR cutoff of 0.05.
Assembly: mm10
Supplementary files format and content: csv containing read counts for each gene.
Library strategy: O-MAP RIP

organism: Mus musculus x Mus spretus

source_name: Patski

extract_protocol:
For RNA isolation, pellets were thawed on ice and resuspended by gentle pipetting in 1000 µL ice cold RIPA Buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.1% (w/v) SDS, 0.5% (w/v) Sodium Deoxycholate, 1% (v/v) Triton X-100, 5 mM EDTA, 0.5 mM DTT), supplemented with 1x EDTA-Free Halt Protease Inhibitor Cocktail, 0.1 U/µL RNase-OUT, and 10mM Sodium Azide, and rocked end-over-end at 4°C for five minutes. Samples were then sheared using a Branson Digital Sonifier 250 outfitted with a double stepped microtip, at 10–12 Watts for 30 s intervals (0.7 s on; 1.3 s off), with 30 s resting steps between intervals, seven intervals total. Samples were held in ice-cold metal thermal blocks throughout sonication. Lysates were then clarified by centrifugation at 15,000 x g for 10 min at 4°C, moved to fresh tubes and diluted with 1 mL Native Lysis Buffer (NLB: 25 mM Tris-HCl pH 7.5, 150 mM KCl, 0.5% (v/v) NP-40, 5 mM EDTA, 0.5 mM DTT), supplemented with 1X Halt Protease Inhibitor Cocktail, 0.1 U/µL RNase-OUT and 10 mM sodium azide. For each sample, 5% was removed as "input," and to the remainder was added 100 µL of Pierce streptavidin magnetic bead slurry (ThermoFisher Scientific) that had been equilibrated by two washes in 1:1 RIPA:NLB. Samples were incubated for 2 hr at room temperature with end-over-end agitation. Beads were then washed with the following series of buffers (1 mL each, 5 min per wash at room-temperature with end-over-end agitation). All buffers were supplemented with 1x EDTA-Free Halt protease inhibitor cocktail, 0.1 U/µL RNase-OUT, and 0.5 mM DTT, unless otherwise noted: (1) RIPA, supplemented with 10 mM Sodium Azide; (2) RIPA alone (3) High Salt Buffer (1 M KCl, 50 mM Tris-HCl pH 7.5, 5 mM EDTA) (4) Urea Buffer (2 M Urea, 50mM Tris-HCl pH 7.5, 5 mM EDTA) (5) 1:1 RIPA:NLB, without protease inhibitors (6) NLB, without protease inhibitors, (7–8) two washes in TE buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA), without protease inhibitors. RNA was isolated from both input and O-MAP-enriched samples by proteolysis in 100 µL Elution Buffer (2% (v/v) N-lauryl sarcoside, 10 mM EDTA, 5 mM DTT, 200 μg proteinase K, in 1x PBS). Reactions were shaken at 700 rpm in a Mixer HC for 1 hour at 42°C, followed by 1 hour at 60°C. RNA was then extracted once with 25:24:1 phenol:chloroform:isoamyl alcohol, and twice thereafter with 24:1 chloroform:isoamyl alcohol. Reactions were supplemented with 15 µg Glycoblue and NaCl to 300 mM, and ethanol precipitated at –20°C overnight. RNA was harvested by centrifugation at 15,000 x g for 30 minutes at 4°C, washed once with 70% ethanol, and resuspended in 84.75 µL nuclease free water. Contaminating DNA was removed by digestion with 5 U RQ1 RNase-free DNase I in 100 µL of the manufacturer’s supplied buffer (1x final concentration) at 37°C for 30 min, and this reaction was terminated by addition of EDTA to 15 mM, final. RNA was purified by phenol extraction and ethanol precipitation, as described above, and resuspended in 15 µL nuclease free water. rRNA was removed using a NEBNext rRNA Depletion Kit (NEB; E6310), according to the manufacturer’s protocol. Purified RNA samples were quality assessed using an Agilent 4200 TapeStation with a ‘RNA High Sensitivity’ kit. Samples were quantified on a Nanodrop prior to library preparation and 300ng of RNA per sample was used during library preparation. Libraries were prepared using the NebNext Ultra II Directional RNA Library Prep Kit (NEB) according to manufacturer’s instructions. Each library was given a unique index during synthesis. Library concentration was measured using an NebNext Library Quant Kit for Illumina (NEB). Quality was confirmed using an Agilent 4200 TapeStation with a ‘RNA High Sensitivity’ kit.
Sequencing libraries were prepared from 300 ng RNA using the NEBNext Ultra II Directional RNA Library Prep Kit and NEBNext Multiplex Oligos for Illumina, according to the manufacturer’s instructions. Three biological replicates were used for each experimental condition; each library was given a unique index. Libraries were quantified using the NEBNext Library Quant Kit for Illumina, following the manufacturer's instructions, and the quality of these libraries was confirmed using an Agilent 4200 TapeStation with an "DNA High Sensitivity" kit.

treatment_protocol: Cells were first briefly washed with 1X DPBS and then fixed with 2% PFA in 1X PBS for 10 minutes. Fixation was quenched by two five-minute washes with 250 mM glycine in PBS. Cells were then briefly washed with 1X DPBS and permeabilized with 0.5% (v/v) triton-X 100 in PBS, then washed five minutes with DPBS three times. To inactivate endogenous peroxidases, samples were treated with 0.5% (v/v) H2O2, in 1x PBS, for 10 minutes with gentle rocking, and washed twice with 1X DPBS. Samples were then equilibrated in Formamide Wash Buffer (40% (v/v) deionized formamide; 2x SSC; 0.1% (v/v) Tween-20), for five minutes. This buffer was then aspirated, and each sample was treated with 114 µL of Probe Mix (0.1 µM primary oligo probe pool for Xist, in 1x Hybridization Buffer: (40% deionized formamide; 2x SSC; 0.1% (v/v) Tween-20; 10% (w/v) dextran sulfate) and this mix was gently spread over the sample by covering with a clean, 30 mm diameter #1.5 thickness glass cover slip. A Formamide Wash Buffer-soaked kimwipe was placed between the wells to maintain humidity during hybridization. Plates were then sealed with Parafilm and incubated without agitation for 8 hours at 42°C. Following primary hybridization, coverslips were removed and cells were washed three times with pre-warmed 30% Formamide Wash Buffer, 10 minutes per wash, at 37°C with gentle rocking. Each well was treated with 50 µL O-MAP Secondary Probe Mix (100 nM SABER1–HRP oligo, in 30% Formamide Hybridization Buffer), and covered with a clean coverslip, as above. Samples were incubated for 1 hour at 37°C, with gentle rocking. Coverslips were then removed, and samples were washed four times with PBST (0.1% (v/v) Tween-20 in 1x PBS), 15 minutes per wash, with gentle rocking at room temperature. Buffer was aspirated, and in situ biotinylation induced by addition of 1 mL Labeling Solution (0.8 µM biotinyl-tyramide, 1 mM H2O2, 1x PBST), and incubation at room temperature for 10 minutes. Biotinylation was halted by addition of PBSTq (Sodium Azide and Sodium Ascorbate (10 mM each, final) in 1x PBST). Cells were harvested by scraping into PBSTq and pelleted by centrifugation at 3,000 x g for 10 minutes. Buffer was aspirated and cells were flash frozen in liquid nitrogen and stored at –80°C until use.

value: Patski

value: Fibroblasts derived from hybrid embryonic kidney

value: Xist O-MAP

tag: fraction

value: Pulldown


title: PSA1 GEX

description: 10x Genomics

value: psoriatic arthritis

value: memory CD8+ T cells


title: PSA1 CSP

description: 10x Genomics


title: 143B_XD23_24h_a


title: 6780091_tumor_CD45+_cells_scTCRseq

description: 10x Genomics


title: 6815945_tumor_CD45+_cells_scRNAseq

description: 10x Genomics


title: Patski cells, Xist O-MAP RIP, Pulldown, Rep1


title: 6847974_tumor_CD45+_cells_scRNAseq

description: 10x Genomics


title: 143B_con_c

value: con


title: 6815939_tumor_CD45+_cells_scRNAseq

description: 10x Genomics


title: Patski cells, Xist O-MAP RIP, Input, Rep3

value: Input


title: Patski cells, Xist O-MAP RIP, Pulldown, Rep2


title: 143B_con_b


title: Patski cells, Xist O-MAP RIP, Input, Rep2


title: Patski cells, Xist O-MAP RIP, Input, Rep1


title: 6815935_tumor_CD45+_cells_scRNAseq

description: 10x Genomics


title: Patski cells, Xist O-MAP ChIP, Pulldown, Rep2

description:
Patski_Xist_OMAP_ChIP_Rep2_L2FC.bw
Patski_Xist_OMAP_ChIP_Rep2.broadPeak

data_processing:
Deep sequencing reads were trimmed using TrimGalore! with parameters -q 30 --phred33.
Trimmed reads were mapped to mm10 Bowtie2 version 2.4.4. with arguments -N 1 -L 25.
Duplicate reads were removed with the Picard MarkDuplicates function before peak calling.
The deepTools bamcoverage function was used to create coverage bigWig files with the parameters  --ignoreDuplicates -p max --normalizeUsing RPKM.
The deepTools bamcompare function was used to create log2 fold change bigWig files with the parameters --ignoreDuplicates --scaleFactorsMethod None -bs 1 -p max --normalizeUsing RPKM
Deduplicated BAM files were sorted and indexed with samtools version 1.15.1.
Regions of enrichment were called using MACS2 with the broadpeak setting.
Assembly: mm10
Supplementary files format and content: bigWig, broadPeak
Library strategy: O-MAP ChIP

extract_protocol:
For DNA isolation, thawed pellets were gently resuspended by pipetting in 1000 µL of CLB (20mM Tris pH 8.0, 85mM KCl, 0.5% NP40) supplemented with 1X Halt protease inhibitor cocktail (ThermoFisher Scientific) and 10 mM NaN3 for 10 minutes. Lysates were then clarified by centrifugation at 3,000 x g for 5 minutes at 4℃. Supernatant was aspirated, and lysates were subjected to another round of CLB lysis, clarification, and supernatant aspiration. Lysates were then lysed by gentle pipeting in 1000 µL of NLB (10mM Tris-HCl pH 7.5, 1% NP40, 0.5% Na Deoxycholate, 0.1% SDS) for 10 minutes. Samples were then sheared using a Branson sonicator at 10-12 Watts for 18 30 s intervals (0.7 s on +1.3 s off), with 30 s resting steps between intervals. Samples were held in ice-cold metal thermal blocks throughout sonication. Lysates were then clarified by centrifugation at 15,000 x g for 10 min at 4℃ and moved to fresh tubes. For each sample, 10% was removed as ‘input’; to the remainder was added 100 µL of streptavidin-coated magnetic bead slurry (ThermoFisher Scientific) that had been equilibrated by two washes in NLB. Samples were incubated for 2 hr at room-temperature with end-over-end agitation. Beads were subsequently washed with the following series of buffers (1 mL each, 5 min per wash, room-temperature, with gentle end-over-end agitation): (1) NLB + 5mM EDTA, 10mM NaN3, 1X Halt protease inhibitor cocktail, 150mM NaCl, (2) NLB + 5mM EDTA, 10mM NaN3, 1X Halt protease inhibitor cocktail, (3+4) 1M KCl, 10mM Tris-HCl pH 7.5, 5mM EDTA, (5+6) 2M Urea, 10mM Tris-HCl pH 7.5, 5mM EDTA, (7) 10mM Tris-HCl, 1% SDS, (8+9) 10mM Tris-HCl pH 7.5, 1mM EDTA. Enriched DNA was released from the beads by proteolysis in 100uL of Elution Buffer (2% N-lauryl sarcoside, 10 mM EDTA, 5 mM DTT, in 1X PBS, supplemented with 200 μg proteinase K (ThermoFisher Scientific)) at 65℃, shaking in a Mixer HC (USA Scientific) 700 rpm for 1 hour. Samples were then placed in a thermocycler overnight at 65℃ for proteinase K treatment. DNA was then extracted using 1:1 phenol:chloroform, and a second chloroform cleanup. Samples were then EtOH precipitated in 300mM NaCl supplemented with glycoblue at -20C overnight. DNA was precipitated by centrifugation at 15,000 x g for 30 minutes at 4℃, washed with 70% EtOH, and resuspended in 20 uL nuclease free water. Each sample then received 1 µL RNaseA (ThermoFisher) and incubated at 37℃ for 1 hour. DNA was then extracted using 1:1 phenol:chloroform with two rounds of chloroform cleanup. Samples were then EtOH precipitated in 300mM NaCl supplemented with glycoblue at -20C overnight, washed in 70% EtOH, and resuspended in 20 µL nuclease free water.
Purified DNA samples were quality assessed using agarose electrophoresis to ensure chromatin sheared size was ~200bp. Samples were quantified on a Nanodrop (ThermoFisher) prior to library preparation and 300ng of DNA per sample was used during library preparation. Libraries were prepared using the NebNext Ultra II DNA Library Prep Kit (NEB) according to manufacturer’s instructions. Each library was given a unique index during synthesis. Library concentration was measured using an NebNext Library Quant Kit for Illumina (NEB). Quality was confirmed using an Agilent 4200 TapeStation with a ‘DNA High Sensitivity’ kit.


title: 6815930_tumor_CD45+_cells_scRNAseq

description: 10x Genomics


title: 143B_XD23_24h_b


title: 143B_con_a


title: Enriched myeloid cells from mouse 19121, T. gondii infected

city: Charlottesville

first: Hui

last: Zong

state: Virginia

address: 7042 Pinn Hall

department: Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

description:
toxo_notoxo_macrophages_fpm.csv
M_19121_S10

data_processing:
All sequence reads files (in fastq format) successfully passed ‘Basic Statistic’ check by FastQC (v0.11.5)
The reads were aligned to the mouse genome assembly (mm10) using STAR (v2.7.9a) and quantified with RSEM (v1.3.0)
Differential gene expression analysis was conducted using the standard DESeq2 (v1.36.0) pipeline to identify differentially expressed genes with a false discovery rate less than 0.05
To correct for possible differences between females and males, sex was included in DESeq2 as a covariance.
Assembly: mm10
Supplementary files format and content: DE_toxo_vs_notoxo_macrophages_plus_sex_covariance.csv contains a table with fold changes and p-values for infected vs. PBS comparison as calculated by DESeq2
Supplementary files format and content: toxo_notoxo_macrophages_fpm.csv containes table with fpm walues for all the genes in all the smaples as calculated by DEseq2

source_name: Tumor

extract_protocol:
RNA were extracted using the RNeasy micro kit (QIAGEN) according to the manufacturer’s instruction. For each sample, 200 ng of total RNAs was used for the construction of sequencing libraries. RNA quality was assessed by Bioanalyzer (Agilent Technologies) with RNA integrity number (RIN) of ≥ 6.5 were selected for library construction.
Illumina TruSeq Stranded Total RNA Library prep kit (#20020596, Illumina) was used to prepare the libraries per Illumina protocol specifications. Ribozero beads, included in the kit, were used to deplete the rRNA. Concentrations of the libraries were determined using the Qubit Flex (#Q33327, Fisher) and the Qubit 1X dsDNA HS Assay kit (#Q33230, fisher).

value: Tumor

value: Myeloid cells

tag: Sex

value: Male

value: Animal infected with T. gondii

value: 27 days after treatment


title: PML_rep2, RCC4

city: Milan

first: Rosa

last: Bernardi

address: via Olgettina 60

country: Italy

institute: San Raffaele Scientific Institute

data_processing:
Base-calling was performed on NovaSeq 6000 Illumina machine.
ChIP-seq reads were trimmed using BBDuk from BBTools suite version 37.36 with suggested settings (ktrim=r k=23 mink=11 hdist=1).
ChIP-seq reads were aligned to the UCSC hg38 genome using BWA-MEM version 0.7.12-r1039 . Uniquely mapped reads were selected with MarkDuplicates from Picard Tools version 1.104
Filtering was done on reads mapping in regions present in the ENCODE hg38 blacklist and regions flagged as not primary alignment or with mapping quality score less than 15.
Mapped reads were used to call domain using the Enriched Domain Detector.
Assembly: bigWig files were generated using bamCompare from Deeptools.
Supplementary files format and content: hg38
Supplementary files format and content: EDD peaks

growth_protocol: DMEM, 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 2 mM Di(N-succinimidyl) glutarate for 45 min at RT and with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using the Diagenode Bioruptor 300.
ChIP-seq libraries were prepared using ChIPSeq Illumina protocol. Libraries were validated using the High Sensitivity D5000 ScreenTape (Agilent Technologies).

value: Human kidney cancer

tag: chip antibody

value: anti-PML Santa Cruz Biotechnology 71910


title: Enriched myeloid cells from mouse 19116, T. gondii infected

description:
toxo_notoxo_macrophages_fpm.csv
M_19116_S9

value: Female


title: Patski cells, Xist O-MAP ChIP, Pulldown, Rep1

description:
Patski_Xist_OMAP_ChIP_Rep1_L2FC.bw
Patski_Xist_OMAP_ChIP_Rep1.broadPeak


title: 6794403_tumor_CD45+_cells_scRNAseq

description: 10x Genomics

value: tumor


title: Enriched myeloid cells from mouse 19190, T. gondii infected

description:
toxo_notoxo_macrophages_fpm.csv
M_19190_S8


title: Enriched myeloid cells from mouse 19193, T. gondii infected

description:
toxo_notoxo_macrophages_fpm.csv
M_19193_S7


title: NKCs, Donor 3 (uG)

city: Winston-Salem

first: Kimberly

middle: D

last: Reeves

state: North Carolina

address: Medical Center Blvd

institute: Wake Forest School of Medicine

data_processing:
Raw sequence reads were imported into Partek Flow (Version: 10.0.23.0720) for analysis.
CUTADAPT was used to trim sequence reads based on quality and to remove sequencing adapters; rDNA and mtrDNA contaminants were filtered out using Bowtie 2.
High-quality reads were mapped to the human GENCODE reference database (release 36) using STAR (Spliced Transcripts Alignment to a Reference).
Aligned reads were quantified using the Partek E/M algorithm and then normalized with the median-of-ratios method used in DESeq2.
Assembly: hg38 GENCODE Genes, release 36
Supplementary files format and content: The 'Normalized_Log2Transformed_Genes.txt' processed data file contains normalized and log2-transformed read counts for genes identified in each of the samples. The first column contains the gene symbol, the second column includes the havana gene ID, the third column includes the hgnc ID, and the subsequent columns contain the normalized counts for each designated gene.
Supplementary files format and content: The 'Normalized_Log2Transformed_Transcripts.txt' processed data file contains normalized and log2-transformed read counts for transcripts identified in each of the samples. The first column contains the gene symbol, second column includes ensembl transcript ID, third column includes ensembl gene ID, fourth column includes havana transcript ID, fifth column includes havana gene ID, sixth column includes hgnc ID, seventh column includes transcript type, and the subsequent columns contain the normalized counts for each designated transcript.

source_name: Blood

extract_protocol:
RNA was extracted using a Qiagen RNeasy Kit. The quantity of the RNA extracts was determined using a NanoDrop Spectrophotometer, and the integrity of each extract was determined using an Agilent 4200 TapeStation and reagents.
cDNA libraries were prepared using a Perkin Elmer NEXTFLEX Combo-Seq mRNA/miRNA Kit. Proper sizing of cDNA libraries were validated using an Agilent 4200 TapeStation, and library quantities were determined by qPCR using a KAPA Library Quantification Kit (Roche). The cDNA libraries were then normalized prior to pooling to ensure equal library representation. Pooled cDNA libraries were sequenced using an Illumina NovaSeq 6000 System, generating 76-bp single-end reads.

value: Blood

tag: individual

value: Donor 3

value: Natural Killer Cells

value: Simulated Microgravity


title: 6794397_tumor_CD45+_cells_scRNAseq

description: 10x Genomics

tag: tissue


title: Patski cells, Xist O-MAP ChIP, Input, Rep2

value: Patski

tag: cell type

value: Fibroblasts derived from hybrid embryonic kidney

value: Xist O-MAP


title: 6794390_tumor_CD45+_cells_scRNAseq

description: 10x Genomics

tag: treatment


title: PML_rep1, RCC4

tag: cell line


title: Patski cells, Xist O-MAP ChIP, Input, Rep1

value: Input


title: 6780115_tumor_CD45+_cells_scRNAseq

description: 10x Genomics


title: Enriched myeloid cells from mouse 19198, T. gondii infected

description:
toxo_notoxo_macrophages_fpm.csv
M_19198_S6

value: Tumor