title: Juvenile polyposis syndrome stomach 3

first: Won Jae

last: Huh

address: 310 Cedar Street

institute: Yale University

data_processing:
Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality.FASTQ format described by four lines: Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line). Line 2 is the raw sequence letters. Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again. Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence. "e" represents sequencing error rate, "Qphred" represents base quality values of Illunima, the Qphred=-10log10(e). For RNA-seq technology, sequencing error rate distribution has two features, (1)Error rate grows with sequenced reads extension for the consumption of sequencing reagent. The phenomenon is common in the Illumina high-throughput sequencing platform (Erlich Y, Mitra PP et al.2008; Jiang L, Schlesinger F et al.2011.) (2)The first six bases have a relatively high error rate. The reason is incomplete binding of the random hex-primers and RNA template in cDNA synthesis (Jiang et al.). In general, a single base error rate should be lower than 1%. GC-content is used to detect potential AT/GC separation. For RNA-seq, in view of the random interrupted and the principle of G/C, A/T content are respectively equal, G and C, A and T should be equal and content is stable on the whole through the whole sequencing process for non-stranded library (If the library is strand-specific, it may occur AT separation or GC separation). A large variation of sequencing error in the first 6-7 bases is allowed considering the usage of random primer in library construction. It's normal that the first few bases have certain preference in existing highthroughput sequencing technology, for the usage of 6bp random primer in library construction. The Sequenced Reads/raw reads often contain low quality reads or reads with adaptors, which will affect the further analysis results. In order to avoid this, it's necessary to filter the raw reads under conditions to get the clean reads. Raw reads filtering conditions are as follows: (1) Remove reads containing adaptors; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Assembly: Homo sapiens genome assembly GRCh37 (hg19)
Supplementary files format and content: txt file includes FPKM values for each sample.
Supplementary files format and content: txt file includes raw counts for each sample.

source_name: stomach

extract_protocol:
RNA was extracted using RNeasy plus Mini Kit (Qiagen). All the downstream process and sequencing were  performed at the Novogene Corporation Inc.
Briefly, mRNA from Eukaryote organisms is purified from total RNA using poly-T oligo-attached magnetic beads (For prokaryotes, mRNA was purified through the removal of rRNA by using kit). The mRNA is first fragmented randomly by addition of fragmentation buffer. According to demand of customer, we have NEB library and strand specific library to choose.

value: stomach

tag: condition

value: Juvenile polyposis syndrome


title: Juvenile polyposis syndrome stomach 2

status: Public on Nov 03 2025

type: SRA

city: New Haven

state: CT

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: Juvenile polyposis syndrome stomach 1


title: sox17_d008_rep2

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

country: France

institute: Institut Pasteur

library_source: genomic

data_processing:
raw data files format and content: R1 files contain the 1st read, R2 the UMI and R3 the second read (is sequenced as paired end)
Libraries were demultiplexed  using bcl2fastq and adapters trimmed using cutadapt
Reads were aligned to the mm10 genome using bowtie2 in local mode
UMIs were added to the SAM RX tag using AnnotateBamWithUmis, duplicates and reads with MAPQ < 30 filtered using SAMtools
Assembly: mm10
Supplementary files format and content: txt file containing ChIPseq (RPM) for 42403 GATA6 binding sites throughout the ES > iXEN conversion

molecule: genomic DNA

organism: Mus musculus

source_name: ES cells

growth_protocol: ES cells were grown in DMEM supplemented with 15% FCS and 0.01ug/mL LIF on gelatin coated plasticware and mitomycin C-inactivated MEF feeders. XEN cells were cultured in the same condition but without LIF.

extract_protocol:
cells were trypsinised, MEFs were adsorbed on non-gelatinized plasticware for 20 minutes. Cells were washed once in PBS, pelleted and fixed in PBS-2 mM DSG for 50 min followed by 10 min in PBS-1%PFA.
Chromatin Immunoprecipitation was carried out against GATA6, SOX17, OCT4, SOX2, ESRRB and ESRRA as described in material and methods.
Libraries were constructed using the NEBNext Ultra II DNA library prep kit using 0.6 μM annealed adapters for ligaXon
Custom designed Y/forked adapters based on Illumina Truseq indexes with 6-8nt UMI 3’ of the index sequence were used

treatment_protocol: 1ug/mL doxycycline was added to the cell-culture media

value: ES cells

tag: cell line

tag: cell type

value: cells carrying a doxycycline-inducible gata6 expression cassette

tag: strain

tag: treatment

value: dox

tag: time point

tag: antibody


title: young control 2

city: Seongnam

first: Jae Hyun

last: Park

state: Gyeonggi-do

address: 335, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-

country: South Korea

institute: CHA University

description:
Library name: young2
TN1505R0194-1

data_processing:
Reads were mapped to GRCm38 using TopHat
The read counts were normalized to the fragments per kilobase of exon per million (FPKM)
Assembly: GRCm38
Supplementary files format and content: tab-delimited txt file includes raw counts

source_name: hippocampus

extract_protocol:
Mouse brains were snap-frozen in liquid nitrogen. Brains were sliced on a pre-chilled mouse brain matrix using a razor blade. From each slice, the hippocampus was carefully dissected. Hippocampal total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using at Theragen Bio protocl

value: hippocampus

tag: group

value: young

tag: agent

value: control


title: Ménétrier’s disease stomach 3

value: Ménétrier’s disease


title: sox17_d0_rep2


title: sox17_d016_rep1


title: sox17_d008_rep1


title: Ménétrier’s disease stomach 2


title: sox17_d0_rep1


title: Ménétrier’s disease stomach 1


title: oct4_d4_rep2


title: sox2_d0_rep1


title: Normal stomach 3

value: Normal


title: oct4_d2_rep2


title: oct4_d4_rep1


title: Normal stomach 1


title: Normal stomach 2


title: oct4_d2_rep1


title: oct4_d1_rep1


title: oct4_d1_rep2


title: oct4_d016_rep2


title: oct4_d016_rep1


title: oct4_d008_rep2


title: oct4_d008_rep1


title: oct4_d0_rep2


title: oct4_xen_rep1

source_name: XEN cells

value: XEN cells

value: no treatment


title: 993898_mort30_No

type: RNA

city: Philadelphia

first: Blanca

middle: E

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

description: whole blood gene expression data from 161 critically ill sepsis patients

hyb_protocol: Biotinylated cDNA was hybridized onto the whole transcript Affymetrix® Human Gene 2.1 ST arrays.

scan_protocol: GeneChips were scanned using the GeneTitan

data_processing: Raw expression values in .cel files were normalized with Robust Multi-array Average (RMA). Differential expression analysis was performed with Limma to compare expression changes in 1) nonsurvivors versus survivors at 30 days and 2) patients with versus without septic shock, adjusted for age, sex, and absolute neutrophil count.

label: biotin

source_name: whole blood

label_protocol: Biotinylated cDNA were prepared using Affymetrix GeneChip® WT Plus Reagent Kit according to the manufacturer’s protocol.

growth_protocol: Peripheral whole blood was collected in PAXgene™ RNA tubes (PreAnalytix, Hilden, Germany).

extract_protocol: RNA isolation was performed via PAXgene Blood miRNA kit (Qiagen) per protocol. RNA quality (RIN >5 cutoff) was measured via Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).

treatment_protocol: PAXgene blood RNA tubes were left at room temperaturee to defrost (4 hours) while mixing by inversion.

tag: age

tag: Sex

value: female

value: No

tag: shock

value: Yes


title: oct4_d0_rep1


title: input_xen_rep1

value: input


title: input_xen_rep2


title: input_d4_rep2


title: 993888_mort30_No


title: input_d4_rep1


title: input_d2_rep2


title: 993886_mort30_No

value: male


title: input_d2_rep1


title: 993850_mort30_Yes


title: 993824_mort30_No


title: 993820_mort30_No


title: 993778_mort30_No


title: 993749_mort30_Yes


title: 993823_mort30_No


title: input_d1_rep2


title: 993718_mort30_No


title: 993817_mort30_Yes


title: input_d1_rep1


title: 993841_mort30_No


title: 993821_mort30_No


title: 993735_mort30_No


title: input_d016_rep2


title: input_xen_rep2_2


title: 993822_mort30_Yes


title: input_d016_rep1


title: input_d008_rep2


title: input_d008_rep1


title: input_d0_rep2


title: input_d0_rep1


title: 993739_mort30_Yes


title: gata6_xen_rep2


title: 993676_mort30_Yes


title: 993627_mort30_Yes


title: 993730_mort30_Yes


title: 993717_mort30_No


title: 993689_mort30_Yes


title: gata6_xen_rep1


title: 993619_mort30_No


title: gata6_d4_rep1


title: 993603_mort30_Yes


title: gata6_d4_rep2


title: gata6_d4_rep1_2


title: gata6_d2_rep1


title: gata6_d2_rep2


title: gata6_d1_rep2


title: gata6_d1_rep1


title: 993586_mort30_No


title: 993642_mort30_No


title: gata6_d008_rep2


title: gata6_d008_rep1


title: 993513_mort30_No


title: 993542_mort30_No


title: 993508_mort30_Yes


title: 993464_mort30_No


title: 993417_mort30_No


title: 993436_mort30_No


title: esrrb_d4_rep2

value: esrrb


title: esrrb_d4_rep1


title: 993609_mort30_No


title: 993476_mort30_No


title: 993509_mort30_No


title: esrrb_d2_rep1


title: 993543_mort30_No


title: esrrb_d1_rep1


title: 993478_mort30_No


title: 993398_mort30_No


title: esrrb_d2_rep2


title: esrrb_d016_rep2


title: 993390_mort30_No


title: gata6_d0


title: 993387_mort30_Yes


title: 993373_mort30_No


title: 993368_mort30_No


title: 993313_mort30_Yes


title: esrrb_d1_rep2


title: 993296_mort30_No


title: esrrb_d008_rep2


title: 993323_mort30_Yes


title: esrrb_d008_rep1


title: 993319_mort30_Yes


title: esrrb_d016_rep1


title: mnase_d4_rep2

data_processing:
Libraries were demultiplexed  using bcl2fastq and adapters trimmed using cutadapt
Reads were aligned to the mm10 genome using bowtie2 in local mode, duplicates and reads with MAPQ < 30 filtered using SAMtools
Assembly: mm10
Supplementary files format and content: txt file containing read counts (RPM) for 42403 GATA6 binding sites throughout the ES > iXEN conversion

extract_protocol:
Cells were fixed in culture media, washed and resuspended in MNase buffer. 16U MNase was added and samples were incubated at 37˚C for exactly 10 minutes. The digestion was stopped and samples were placed on a rotating wheel overnight at 4˚C for fragment diffusion. Digested chromatin was phenol-chloroform extracted, ethanol precipitated and reverse-crosslinked.
20ng digested DNA was used to construct libraries, briefly, fragments were end-repaired, A-tailed and ligated to 1.25µM adapters. Libraries were amplified by qPCR
Pooled libraries were sequenced by Novogene (PE150 reads)

tag: genotype

value: 96h dox


title: esrrb_d0_rep2

value: ES cells


title: esrrb_d0_rep1

value: cells carrying a doxycycline-inducible gata6 expression cassette


title: mnase_d4_rep1


title: mnase_d4_rep3


title: mnase_d2_rep2

value: 48h dox


title: mnase_d2_rep1


title: mnase_d1_rep3

value: 24h dox


title: mnase_d1_rep1


title: mnase_d1_rep2


title: 993215_mort30_Yes


title: mnase_d016_rep3

value: 16h dox


title: 993229_mort30_Yes


title: 993286_mort30_No


title: mnase_d016_rep2


title: 993167_mort30_No


title: 993231_mort30_Yes


title: mnase_d016_rep1


title: mnase_d008_rep3

value: 8h dox


title: 993217_mort30_Yes


title: mnase_d2_rep3


title: mnase_d008_rep2


title: 993157_mort30_No


title: 993101_mort30_Yes


title: 993183_mort30_No


title: 993196_mort30_No


title: mnase_d008_rep1


title: 993262_mort30_No


title: 993054_mort30_No


title: 993047_mort30_Yes


title: 993145_mort30_Yes


title: 993086_mort30_Yes


title: 993044_mort30_Yes


title: mnase_d0_rep2


title: 993063_mort30_No


title: 993112_mort30_No


title: mnase_d0_rep1


title: atac_xen_rep2

data_processing:
Libraries were demultiplexed  using bcl2fastq and adapters trimmed using cutadapt
Reads were aligned to the mm10 genome using bowtie2 in local mode, duplicates and reads with MAPQ < 30 filtered using SAMtools
Assembly: mm10
Supplementary files format and content: txt file containing ATACseq read counts (RPM) for 42403 GATA6 binding sites throughout the ES > iXEN conversion

extract_protocol:
cells were trypsinised, MEFs were adsorbed in non-gelatinized plasticware for 20 minutes. Cells were washed once in PBS, pelleted and resuspended in 50μL transposition reaction mix. Transposition was carried out for 50 min at 37˚C.
Libraries were prepared by adding 2.5 µL 25 µM primer Ad1.noMX, 2.5 µl 25 µM Ad2 indexing primer and amplified by qPCR while monitoring fluorescence to stop amplification during the log phase.

value: wild type


title: 992926_mort30_Yes


title: atac_xen_rep3


title: atac_xen_rep1


title: atac_d4_rep2


title: atac_d4_rep1


title: 992922_mort30_No


title: atac_d2_rep2

value: 72h dox


title: atac_d2_rep3


title: atac_d2_rep1


title: SOX17_siOCT4_rep2

description: Library name: SOX17_siOCT4_rep2

data_processing:
raw data files format and content: R1 files contain the 1st read, R2 the UMI and R3 the second read (is sequenced as paired end)
Libraries were demultiplexed using bcl2fastq and adapters trimmed using cutadapt
Reads were aligned to the mm10 genome using bowtie2 in local mode
UMIs were added to the SAM RX tag using AnnotateBamWithUmis, duplicates and reads with MAPQ < 30 filtered using SAMtools
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: txt file containing ChIPseq (RPM) for 42403 GATA6 binding sites throughout the ES > iXEN conversion

growth_protocol: ES cells were grown in DMEM supplemented with 15% FCS and 0.01ug/mL LIF on gelatin coated plasticware and mitomycin C-inactivated MEF feeders

extract_protocol:
cells were trypsinised, MEFs were adsorbed on non-gelatinized plasticware for 20 minutes. Cells were washed once in PBS, pelleted and fixed in PBS-2 mM DSG for 50 min followed by 10 min in PBS-1%PFA. Chromatin Immunoprecipitation was carried out against GATA6 and SOX17as described in material and methods.
Libraries were constructed using the NEBNext Ultra II DNA library prep kit using 0.6 μM annealed adapters for ligation. Custom designed Y/forked adapters based on Illumina Truseq indexes with 6-8nt UMI 3’ of the index sequence were used

treatment_protocol: 1µg/mL dox + control or oct4 siRNA

value: oct4 siRNA + 1µg/mL dox


title: 992851_mort30_No


title: atac_d1_rep3


title: 992895_mort30_Yes


title: SOX17_siOCT4_rep1

description: Library name: SOX17_siOCT4_rep1


title: 992833_mort30_No


title: 992875_mort30_Yes


title: 992813_mort30_Yes


title: atac_d1_rep1


title: 992890_mort30_Yes


title: 992974_mort30_No


title: SOX17_siCTL_rep1

description: Library name: SOX17_siCTL_rep1

value: control siRNA + 1µg/mL dox


title: SOX17_siCTL_rep2

description: Library name: SOX17_siCTL_rep2


title: atac_d016_rep3


title: input_siOCT4_rep2

description: Library name: input_siOCT4_rep2


title: atac_d016_rep2


title: input_siCTL_rep2

description: Library name: input_siCTL_rep2


title: 992798_mort30_No


title: 992808_mort30_No

value: female


title: 992748_mort30_No

value: No


title: 992805_mort30_No

value: Yes


title: atac_d1_rep2


title: 992791_mort30_Yes


title: 992788_mort30_No


title: 992753_mort30_Yes


title: 992815_mort30_Yes


title: 992742_mort30_No


title: input_siCTL_rep1

description: Library name: input_siCTL_rep1


title: atac_d016_rep1


title: GATA6_siOCT4_rep2

description: Library name: GATA6_siOCT4_rep2


title: GATA6_siCTL_rep1

description: Library name: GATA6_siCTL_rep1


title: GATA6_siOCT4_rep1

description: Library name: GATA6_siOCT4_rep1


title: GATA6_siCTL_rep2

description: Library name: GATA6_siCTL_rep2


title: il2_timecourse

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Library name: il2_timecourse

library_source: genomic single cell

data_processing:
Sequencing data were converted to fastq files, aligned to the mm10 reference genome, and quantified per cell using Cell Ranger ATAC software (10x Genomics, v2.1).
To enable comparisons across conditions and datasets, we used a common set of Treg-specific open chromatin regions, defined previously (Chowdhary et al., 2023) by supplementing pan-immunocyte OCRs from the ImmGen consortium(Yoshida et al., 2019) with additional peaks from Treg spleen and colon scATAC-seq data in (Chowdhary et al., 2023). To arrive at the final peak set, we also called peaks on the data generated in this study, using Archr v1.0.1(Granja et al., 2021) and MACS2 v2.2.7.1(Zhang et al., 2008) to call fixed-width peaks of 250bp within cell clusters. Any new OCRs not overlapping with the previous peak sets were added to the final merged peak set used for downstream analysis.
scATACseq data analysis was performed using Signac v1.4(Stuart et al., 2021). For quality control, only cells with at least 1x103 fragments per cell (depending on sequencing depth of experiment), greater than 25 percent reads in peaks, TSS enrichment score greater than 2, nucleosome signal less than 10, and ratio of blacklist-region reads less than 0.05 were retained for further analysis. Putative doublets identified by ArchR v1.0.1(Granja et al., 2021) and non-Treg, non-Tconv contaminant cells were also removed. We used the latent semantic indexing approach as previously described (Cusanovich et al., 2018; Stuart et al., 2019). Binarized count matrices were normalized using the term frequency-inverse document frequency (TF-IDF) transformation and reduced in dimensionality by singular value decomposition (SVD). As the first component was highly correlated with sequencing depth, SVD components 2-30 were used to generate a shared nearest neighbor (SNN) graph for clustering and as input into UMAP(McInnes et al., 2018) with cosine distance metric for visualization.
We used Seurat label-transfer using group identities (PBS, early, mid, late) from the scRNA-seq data to identify corresponding cells in the scATAC-seq data. Gene scores were calculated using ArchR v1.0.1.
Assembly: mm10
Supplementary files format and content: .mtx ATAC counts matrices, peaks.txt files have OCR locations, barcodes.txt files have cell barcodes
Supplementary files format and content: fragments.tsv.gz files have raw ATAC fragments, fragments.tsv.gz.tbi files are index of fragments files
Supplementary files format and content: MetaData.txt files have relevant metadata, including timepoint assignment and UMAP coordinates.

source_name: Spleen

extract_protocol:
ImmGen standard protocols (http://www.immgen.org) for cell preparation and sorting were followed to generate data for all conditions – IL2/JES6-1, IL2 immuno-cytokine treatment/IL2 anti-FITC controls or PBS control. Whole spleens were harvested and homogenized through 70um filter and centrifuged before red blood cells were removed using ACK lysis buffer for 3 minutes on ice and centrifugation. Remaining cells were washed once with 5mL of FACS buffer (Phenol red-free DMEM, 2% FBS, 0.1% azide, and 10 mM Hepes, pH 7.9) and then resuspended in FACS buffer to be stained for 20 minutes on ice with antibodies for flow cytometry. Stained cell suspensions were sorted once for ATACSeq or twice for RNASeq to obtain pure samples of T regulatory cells. Splenic cell suspensions from FOXP3-IRES-GFP mice were stained on ice for 20minutes with anti-CD4, anti-TCRb+, anti-CD19, anti-CD8a, anti-CD11c, NK1.1, and propidium iodide (PI) as a viability dye. Cells were sorted as PI-Dump [CD19-CD8a-CD11c-NK1.1]-CD4+TCRb+GFP+].
Nuclei isolation, transposition, GEM generation, and library construction targeting capture of 10000 cells were carried out as detailed in the Chromium Next GEM Single Cell ATAC manual (10x Genomics) with modifications to allow sample hashtagging (see below). Libraries were pooled and sequenced on an Illumina NovaSeq 6000 to a final median depth of approximately 20-30,000 paired-end reads per cell. Sequencing data were converted to fastq files, aligned to the mm10 reference genome, and quantified per cell using Cell Ranger ATAC software (10x Genomics, v2.1). To include multiple experimental conditions in the same scATAC run, we hashtagged cells using a modification of the ASAP-seq strategy (Mimitou et al., 2021) for low cell input primary cell samples. Before sorting, cells were hashtagged with mouse TotalSeqA DNA-barcoded hashtag antibodies at the same time as staining with fluorophore-conjugated antibodies (BioLegend). Cells were sorted into RPMI + 5% FCS in DNA Lo-Bind tubes (Eppendorf, cat # 022431021). After spinning down for 5 min at 500g in a refrigerated centrifuge at 4°C, cells were resuspended in 100 μl chilled 0.1x Omni Lysis buffer (1x Omni Lysis buffer (10mM Tris-HCl, 10mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP40 substitute/IGEPAL, 0.01% Digitonin, 1% BSA in nuclease free water) diluted 1:10 in Wash/Lysis Dilution Buffer (10mM Tris-HCl, 10mM NaCl, 3 mM MgCl2, 1% BSA in nuclease free water), gently mixed by pipetting, and incubated on ice for 6.5 min. Following lysis, 100 μl chilled wash buffer was added and gently mixed by pipetting. Cells were spun down for 5 min at 500g at 4°C, all but 5 μl of supernatant was removed, and 45 μl of chilled 1x nuclei buffer (10x Genomics) was added without mixing. After one more centrifugation step at 500g, 4°C for 5 min, supernatant was removed, and samples were resuspended in 7ul 1x nuclei buffer for cell counting and input into transposition, barcoding, and library preparation according to the Chromium Next GEM Single Cell ATAC manual (10x Genomics). Modifications to the original 10X protocol were made as described in the original ASAP-seq publication (Mimitou et al., 2021) and as detailed at https://citeseq.files.wordpress.com/2020/09/asap_protocol_20200908.pdf. Briefly, 0.5 μl of 1uM BOA bridge oligo was spiked into the barcoding reaction. During GEM incubation, an additional 5 min incubation at 40°C was added to the beginning of the protocol. 43.5 instead of 40.5 μl of Elution Solution I was added during silane bead elution to recover 43 μl. 40 μl was used for SPRI clean up as indicated in the protocol, while 3 μl was set aside. During SPRI cleanup, the supernatant was saved. The bead bound fraction was processed as in the protocol, while for the supernatant fraction, 32 μl SPRI was added for 5 min. Beads were collected on a magnet, washed twice with 80% ethanol, and eluted in 42 μl EB. This 42 μl was combined with the 3 μl set aside from the previous step as input into the HTO indexing reaction. HTO Indexing PCR was run with partial P5 and indexed Rpxx primers (https://citeseq.files.wordpress.com/2020/09/asap_protocol_20200908.pdf) as: 95°C 3 min, 12-14 cycles of (95°C 20 sec, 60°C 30 sec, 72°C 20 sec), 72°C 5 min. The PCR product was cleaned up with 1.6X SPRI purification for quantification and sequencing alongside ATAC libraries.

value: Spleen

value: Treg

value: Male


title: atac_d008_rep2


title: Gene expression

city: Hanover

first: Brittany

last: Goods

state: New Hampshire

address: 15 Thayer Dr.

institute: Dartmouth College

description: Library name: Pooled_GEX

library_source: transcriptomic single cell

data_processing:
Cell Ranger was used for demultiplexing raw sequencing data and alignment.
Cells with >5% mitochondrial gene expression, fewer than 500 total expression counts, and multiple or no hashtag oligos  were excluded from further analysis.
Data were then normalized and scaled using SCTransform, regressing out mitochondrial genes, ribosomal genes, and HTO classification.
Assembly: GRCh38
Supplementary files format and content: h5 matrix

molecule: nuclear RNA

source_name: Macrophage

extract_protocol:
Cultured cells from 3 female donors were washed with PBS, then incubated on ice for 5min with 100ul hypotonic buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40). After 5min incubation, wells were loosely scraped with a pipette tip and 200ul of wash buffer (PBS 1X, 1% BSA, 0.2U/ul Protector RNAse Inhibitor) and counted using a Cellometer K2 with AO/PI live/dead reagent. Technical replicates "well A" and "well B" for each donor were sequenced and combined for downstream analysis.
Nuclei tagging was done using the MULTIseq methodology in tandem with the Curiox washing system (Curiox Biosystems). In brief, anchor lipid-oligo and Barcoding oligos specific to each sample were incubated together then added to the respective samples to get incorporated into the nuclei membrane. A Co-anchor lipid-oligo was added to the mix to stabilize the tagging before transferring the samples to individual wells of a Curiox washing strip. Nuclei were incubated 40min on ice to bind oligos and allow nuclei to settle in the wells. Nuclei were washed 25x at flow rate of 1ul/s with PBS + 1% BSA prior to recovery, counting and pooling in equal proportions.

value: Macrophage


title: input_siOCT4_rep1

description: Library name: input_siOCT4_rep1

value: ES cells


title: atac_d008_rep1

value: cells carrying a doxycycline-inducible gata6 expression cassette


title: Hashtag oligo data

description: Library name: Pooled_HTO

library_source: other

molecule: protein


title: atac_d0_rep3

value: no treatment


title: Male donor 3, M1 macrophage, IFNg 20 ng/mL + LPS 100 ng/mL

description:
Library name: M3_IFNg_LPS100
Smart-Seq2

data_processing:
BCL files were converted to FASTQs that were merged and demultiplexed. FASTQs were assessed for size to ensure that sequencing depth was comparable across all samples
Libraries were aligned to GRCh38.p14 genome using STAR with count matrixes generated with HT-seq
Assembly: GRCh38
Supplementary files format and content: combined count matrix and metadata file

extract_protocol:
Cultured cells were lysed in RLT buffer (Qiagen) and RNA was extracted using the RNeasy mini kit (Qiagen).
RNA-seq libraries were generated using SMART-Seq2 protocol (Trombetta et al., 2014). Briefly, cDNA was reversed transcribed from single cells using Superscript III (Thermo Fisher Scientific) and whole transcriptome amplification (WTA) was performed. WTA products were purified using the Agencourt AMPure XP beads (Beckman Coulter, IN, USA) and used to prepare paired-end libraries with Nextera XT  (Illumina, CA, USA).


title: Male donor 3, M1 macrophage, IFNg 20 ng/mL + LPS 10 ng/mL

description:
Library name: M3_IFNg_LPS10
Smart-Seq2


title: Male donor 3, M0 macrophage, 50ng/mL M-CSF

description:
Library name: M3_50_Pep
Smart-Seq2


title: atac_d0_rep2


title: Male donor 3, M0 macrophage, 25ng/mL M-CSF

description:
Library name: M3_25_Pep
Smart-Seq2


title: atac_d008_rep3


title: Male donor 1, M2 macrophage, IL-4 20ng/mL

description:
Library name: M1_IL420
Smart-Seq2


title: atac_d0_rep1


title: Male donor 1, M1 macrophage, IFNg 20 ng/mL + LPS 10 ng/mL

description:
Library name: M1_IFNg_LPS10
Smart-Seq2


title: Male donor 1, M1 macrophage, IFNg 20 ng/mL + LPS 100 ng/mL

description:
Library name: M1_IFNg_LPS100
Smart-Seq2


title: t8_xen_rep2

data_processing:
libraries were demultiplexed using bcl2fastq
adapters were trimmed with cutadapt
read were aligned using STAR
read counts were calculated with rsem
Assembly: mm10
Supplementary files format and content: TPM counts
Supplementary files format and content: demultiplexed fastq

molecule: polyA RNA

extract_protocol:
cells were trypsinised, MEFs were adsorbed on non-treated plasticware for 20 minutes. Cells were washed once in PBS and lysed in TRIzol. Total RNAs were purified by pheno-chloroform extraction and precipitated.
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. Then the second strand cDNA was synthesized using dUTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification, following NOVOGENE library construction workflow.
NovogenestrandedRNAkit:250~300bpinsertstrandedspecificlibrary(directional)

value: XEN cells


title: Male donor 1, M0 macrophage, 50ng/mL M-CSF

description:
Library name: M1_50_Pep
Smart-Seq2


title: t8_xen_rep1


title: Male donor 1, M0 macrophage, 25ng/mL M-CSF

description:
Library name: M1_25_Pep
Smart-Seq2


title: Male donor 3, M2 macrophage, IL-4 20ng/mL

description:
Library name: M3_IL420
Smart-Seq2


title: 992705_mort30_Yes

value: male


title: Female donor 3, M2 macrophage, IL-4 20ng/mL

description:
Library name: F3_IL420
Smart-Seq2


title: 992732_mort30_No


title: 992729_mort30_Yes


title: Female donor 3, M1 macrophage, IFNg 20 ng/mL + LPS 10 ng/mL

description:
Library name: F3_IFNg_LPS10
Smart-Seq2


title: t7_168h_rep2

value: 168h dox


title: t7_168h_rep1


title: Female donor 3, M0 macrophage, 25ng/mL M-CSF

description:
Library name: F3_25_Pep
Smart-Seq2


title: Female donor 2, M0 macrophage, 50ng/mL M-CSF

description:
Library name: F2_50_Pep
Smart-Seq2


title: t6_96h_rep3

value: 96h dox


title: t7_168h_rep3


title: Female donor 1, M1 macrophage, IFNg 20 ng/mL + LPS 100 ng/mL

description:
Library name: F1_IFNg_LPS100
Smart-Seq2


title: t6_96h_rep2


title: Female donor 1, M2 macrophage, IL-4 20ng/mL

description:
Library name: F1_IL420
Smart-Seq2


title: 992695_mort30_No


title: Female donor 3, M1 macrophage, IFNg 20 ng/mL + LPS 100 ng/mL

description:
Library name: F3_IFNg_LPS100
Smart-Seq2


title: 992722_mort30_No


title: MCF7dCas9Halo,sgRNAMYC-NTC,Cl-PDS2, R3

city: London

first: Marco

last: Di Antonio

state: United Kingdom

address: 80 Wood Lane

department: Chemistry

country: United Kingdom

institute: Imperial College London

data_processing:
Data Quality Control: filtering reads containing adapter or with low quality with Fastp
Mapping Reads to Reference Genome with HISAT2
Gene Expression Quantification with FeatureCounts
Differential Expression Analysis (two or more groups of samples) with DESeq2
Assembly: GRCh38-NCBI:GCA_000001405.27
Supplementary files format and content: A xls data file including  counts for each samples and gene ID

growth_protocol: MCF7 cells were mantained in  DMEM GlutaMAX™ supplemented with 1x β-Estradiol, 1x penicillin streptomycin and 10% (vol/vol) fetal bovine serum (FBS) and maintained at 37 ℃, 5% CO2.

extract_protocol:
RNeasy mini kit (Qiagen)
Novogene kit for library preparation

treatment_protocol: Samples were treated with either 0.5%DMSO, 7.5 μM of DC34 or 2.5 μM of PyPDS or 2.5 μM of Cl-PDS2

value: Breast cancer cell

value: dCas9-Halo stably expressed

value: sgRNA-NTC, +Cl-PDS2


title: Female donor 1, M1 macrophage, IFNg 20 ng/mL + LPS 10 ng/mL

description:
Library name: F1_IFNg_LPS10
Smart-Seq2


title: 992678_mort30_No


title: t6_96h_rep1


title: 992692_mort30_Yes

value: female


title: 992680_mort30_Yes


title: Female donor 3, M0 macrophage, 50ng/mL M-CSF

description:
Library name: F3_50_Pep
Smart-Seq2


title: MCF7dCas9Halo,sgRNAMYC-NTC,Cl-PDS2, R2


title: MCF7dCas9Halo,sgRNAMYC-NTC,Cl-PDS2, R1


title: t5_72h_rep3

value: 72h dox


title: MCF7dCas9Halo,sgRNAMYC-NTC,DMSO, R3

value: sgRNA-NTC, +DMSO


title: Female donor 2, M0 macrophage, 25ng/mL M-CSF

description:
Library name: F2_25_Pep
Smart-Seq2


title: 992659_mort30_No

value: No


title: 992632_mort30_No

value: Yes


title: 992635_mort30_No


title: 992660_mort30_Yes


title: 992656_mort30_Yes


title: MCF7dCas9Halo,sgRNAMYC-NTC,DMSO, R2


title: 992619_mort30_Yes


title: t5_72h_rep2


title: MCF7dCas9Halo,sgRNAMYC-19,Cl-PDS2, R2

value: sgRNAMyc-19, +Cl-PDS2


title: t4_48h_rep3

value: 48h dox


title: MCF7dCas9Halo,sgRNAMYC-19,Cl-PDS2, R1


title: MCF7dCas9Halo,sgRNAMYC-19,DMSO, R3

value: sgRNAMyc-19, +DMSO


title: t5_72h_rep1

value: ES cells

value: cells carrying a doxycycline-inducible gata6 expression cassette


title: t4_48h_rep2


title: MCF7dCas9Halo,sgRNAMYC-19,DMSO, R1


title: MCF7dCas9Halo,sgRNAMYC-19,DMSO, R2


title: t4_48h_rep1


title: MCF7, PyPDS, R3

value: WT

value: PyPDS


title: 992622_mort30_Yes

value: male


title: t3_24h_rep3

value: 24h dox


title: MCF7, PyPDS, R1

value: Breast cancer cell


title: MCF7dCas9Halo,sgRNAMYC-19,Cl-PDS2, R3

value: dCas9-Halo stably expressed


title: MCF7dCas9Halo,sgRNAMYC-NTC,DMSO, R1


title: MCF7, DC34, R3


title: t3_24h_rep2


title: t3_24h_rep1


title: MCF7, DMSO, R2

value: DMSO


title: MCF7, DMSO, R3


title: MCF7, DMSO, R1


title: t2_16h_rep3

value: 16h dox


title: MCF7, PyPDS, R2


title: Treg_Sp_PBS_2h_1

description: Library name: Treg_Sp_PBS_2h_1

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

extract_protocol:
For each sample, 1000 cells were sorted directly into the lysis buffer [5uL TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Sigma)]. Total RNA was purified using RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and then reverse transcribed to cDNA. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina).
Libraries were constructed following the Smart-seq2 RNA-seq library preparation protocol.

treatment_protocol: Tregs,NK, and B cells were isolated by smashing spleen in 70um filter, ACK lysis buffer, filter 40um

value: Spleen

tag: cell name

value: CD4 TReg Cell

value: Male

value: 2hrs PBS IV Injection, retroorbital


title: Treg_Sp_PBS_2h_2

description: Library name: Treg_Sp_PBS_2h_2


title: t2_16h_rep2


title: mnase_d0_rep3

value: no treatment


title: MCF7, DC34, R2


title: Treg_Sp_IL2_JES6_1h_2

description: Library name: Treg_Sp_IL2_1h_2

value: 1hr IL2_JES6 IV Injection, retroorbital


title: t2_16h_rep1


title: Treg_Sp_IL2_JES6_1h_1

description: Library name: Treg_Sp_IL2_1h_1


title: 992594_mort30_No

value: No


title: 992526_mort30_No

value: Yes


title: Treg_Sp_IL2_JES6_2h_1

description: Library name: Treg_Sp_IL2_2h_1

value: 2hrs IL2_JES6 IV Injection, retroorbital


title: 992557_mort30_Yes


title: 992558_mort30_No


title: Treg_Sp_IL2_JES6_4h_2

description: Library name: Treg_Sp_IL2_4h_2

value: 4hrs IL2_JES6 IV Injection, retroorbital


title: t1_0h_rep3

value: ES cells

value: cells carrying a doxycycline-inducible gata6 expression cassette


title: Treg_Sp_IL2_JES6_4h_1

description: Library name: Treg_Sp_IL2_4h_1


title: 992500_mort30_Yes

value: male


title: MCF7, DC34, R1

value: Breast cancer cell

value: WT


title: 992536_mort30_No


title: 992535_mort30_No


title: Treg_Sp_IL2_JES6_8h_2

description: Library name: Treg_Sp_IL2_8h_2

value: 8hrs IL2_JES6 IV Injection, retroorbital


title: 992593_mort30_No


title: Treg_Sp_IL2_JES6_8h_1

description: Library name: Treg_Sp_IL2_8h_1


title: 992565_mort30_No


title: t1_0h_rep1


title: 992504_mort30_No

value: female


title: Treg_Sp_IL2_JES6_16h_1

description: Library name: Treg_Sp_IL2_16h_1

value: Spleen

value: 16hrs IL2_JES6 IV Injection, retroorbital


title: Treg_Sp_IL2_JES6_16h_2

description: Library name: Treg_Sp_IL2_16h_2

value: CD4 TReg Cell

value: Male


title: Treg_Sp_PBS_128h_1

description: Library name: Treg_Sp_PBS_128h_1

value: 128hrs PBS IV Injection, retroorbital


title: Treg_Sp_IL2_JES6_24h_2

description: Library name: Treg_Sp_IL2_24h_2

value: 24hrs IL2_JES6 IV Injection, retroorbital


title: Day2_Group4_4_GEX

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
Gene expression libraries were mapped to the mouse genome mm10 with STAR (version v2.7.9a) with default parameters, except: soloUMIlen=12, soloBarcodeReadLength=0, outFilterMultimapNmax=10, outFilterScoreMin=30, soloUMIfiltering=MultiGeneUMI_CR, soloUMIdedup=1MM_CR, soloCellFilter=None . The mm10 genome reference was supplemented with the human MLL-AF9 fusion gene and with the EGFP Enhanced green fluorescent protein gene.  ADT/HTO libraries were processed and mapped using the STARsolo tool  (version v2.7.9a) with default parameters except: soloCBmatchWLtype=1MM_multi_Nbase_pseudocounts, soloUMIfiltering= MultiGeneUMI_CR, soloUMIdedup=1MM_CR, soloCellFilter=None, clipAdapterType=False, soloType=CB_UMI_Simple, soloBarcodeReadLength=0, soloUMIlen=12, clip5pNbases=10, clip3pNbases=76 (for 101nt reads) or 65 (for 90nt reads). Read counting was done using Ensembl 102 gene models with in addition the two extra genes (MLL-AF9 and EGFP).
All subsequent analyses were performed using the R software (version 4.2.0) and Bioconductor 3.15 packages.
Assembly: mm10
Supplementary files format and content: Gene_counts.tsv.gz: gzipped text file with tab-separated RNA-seq raw read counts for each gene; each row contains the Ensembl 102 gene annotation and raw counts per gene; columns correspond to cells. Counts on the two extra genes (MLL-AF9 and EGPF) are listed at the end of the file.
Supplementary files format and content: ADT_counts.tsv.gz: gzipped text file with tab-separated RNA-seq raw read counts for each Antibody-Derived Tags  (ADT); each row contains a ADT and the raw counts per protein; columns correspond to cells
Supplementary files format and content: CellSurfaceProtein_barcode.tsv:  text file with tab-separated ADT/HTO sequence name (1st colum), the corresponding Toltal-seqB barcode name (2nd column), the sequence (3rd column) and the type of cell surface protein (4th column).
Supplementary files format and content: SingleCellExperiment.rds: rds file of single cell experiment object.  The object contains  raw gene counts, cell and gene metadata information after demultiplexing, prior to QC filtering.

source_name: Bone marrow

growth_protocol: iKMT2A-MLLT3;IRES-GFP mice were sacrificed at age of 8-11 weeks.

extract_protocol:
Lin-BM cells from KME mice were stained for FACS sorting of LSK Flt3- population. Additionally, CITE-seq HTO labelling of LT-HSC was added to the staining mix for 1h at 4°C. Each sample was also labelled individually with a different CD45 Hashtag HTO antibody. After washing, cells were resuspended in one sample in FACS buffer and sorted on a SORPAria.
TotalSeq-B Antibodies

treatment_protocol: 2 or 5 days before sacrifice, mice were injected i.p. in single doses with PBS or TPO. At the same day, doxycyclin (DOX) was given as food to induce KMT2A-MLLT3 fusion.

value: Bone marrow

value: LSK Flt3-


title: 992493_mort30_No

value: No

value: Yes


title: 992479_mort30_No


title: 992461_mort30_Yes


title: t1_0h_rep2

value: ES cells

value: no treatment


title: Treg_Sp_IL2_JES6_24h_1

description: Library name: Treg_Sp_IL2_24h_1


title: Day2_Group4_3_GEX


title: Treg_Sp_IL2_JES6_64h_1

description: Library name: Treg_Sp_IL2_64h_1

value: 64hrs IL2_JES6 IV Injection, retroorbital


title: Treg_Sp_IL2_JES6_64h_2

description: Library name: Treg_Sp_IL2_64h_2


title: Day2_Group4_2_GEX


title: Treg_Sp_IL2_JES6_128h_2

description: Library name: Treg_Sp_IL2_128h_2

value: 128hrs IL2_JES6 IV Injection, retroorbital


title: Treg_Sp_IL2_JES6_128h_1

description: Library name: Treg_Sp_IL2_128h_1


title: 4hD2FITCF10Bcell_a

description: Library name: 4hD2FITCF10Bcell_a

value: TCRB-, CD19+

value: B cells

value: 4hrs IL2-IC retroorbital injection


title: 992444_mort30_No

value: male


title: Day2_Group4_3_CellSurfaceProtein

value: female


title: 4hD2FITCF10NK_a

description: Library name: 4hD2FITCF10NK_a

value: Spleen

value: NK


title: 4hD2FITCF10Treg_a

description: Library name: 4hD2FITCF10Treg_a

value: TCRB+, CD4+, CD8-, FoxP3+

value: Tregs

value: Male


title: 992498_mort30_No


title: Day2_Group4_2_CellSurfaceProtein

value: Bone marrow

value: LSK Flt3-


title: 4hD2FITCF5111Bcell_a

description: Library name: 4hD2FITCF5111Bcell_a


title: 992485_mort30_No

value: No

value: Yes


title: Day2_Group4_4_CellSurfaceProtein


title: 4hD2FITCF5111Treg_a

description: Library name: 4hD2FITCF5111Treg_a


title: Day2_Group3_4_CellSurfaceProtein


title: 4hD2F5111Bcell_a

description: Library name: 4hD2F5111Bcell_a


title: 4hD2FITCF5111NK_a

description: Library name: 4hD2FITCF5111NK_a


title: 4hD2F5111NK_a

description: Library name: 4hD2F5111NK_a


title: Day2_Group3_3_CellSurfaceProtein


title: 4hD2F5111Treg_a

description: Library name: 4hD2F5111Treg_a


title: 4hD2HF10Bcell_a

description: Library name: 4hD2HF10Bcell_a


title: 4hD2HF10NK_a

description: Library name: 4hD2HF10NK_a


title: Day2_Group3_1_CellSurfaceProtein


title: 4hD2PBSBcell_a

description: Library name: 4hD2PBSBcell_a

value: 4hrs PBS retroorbital injection


title: 4hD2PBSNK_a

description: Library name: 4hD2PBSNK_a


title: Day2_Group3_4_GEX


title: 4hD2PBSTreg_a

description: Library name: 4hD2PBSTreg_a


title: 4hD1FITCF10NK_a

description: Library name: 4hD1FITCF10NK_a


title: 4hD1FITCF10Bcell_a

description: Library name: 4hD1FITCF10Bcell_a


title: 992403_mort30_No


title: 992423_mort30_No


title: 4hD1FITCF5111Bcell_a

description: Library name: 4hD1FITCF5111Bcell_a


title: 4hD1FITCF10Treg_a

description: Library name: 4hD1FITCF10Treg_a


title: Day2_Group3_2_GEX


title: 992352_mort30_Yes


title: Day2_Group3_3_GEX


title: Day2_Group3_1_GEX


title: 4hD1FITCF5111NK_a

description: Library name: 4hD1FITCF5111NK_a


title: 992370_mort30_No


title: 992439_mort30_No


title: 992313_mort30_Yes


title: 992317_mort30_Yes


title: Day2_Group3_2_CellSurfaceProtein


title: 992106_mort30_No


title: 992253_mort30_No


title: 992088_mort30_Yes


title: 4hD1F5111Bcell_a

description: Library name: 4hD1F5111Bcell_a


title: 992131_mort30_No


title: 992107_mort30_No


title: 4hD1FITCF5111Treg_a

description: Library name: 4hD1FITCF5111Treg_a


title: Day2_Group2_3_CellSurfaceProtein


title: 4hD1HF10Bcell_a

description: Library name: 4hD1HF10Bcell_a


title: 4hD2HF10Treg_a

description: Library name: 4hD2HF10Treg_a


title: 4hD1F5111NK_a

description: Library name: 4hD1F5111NK_a


title: 4hD1HF10NK_a

description: Library name: 4hD1HF10NK_a


title: Day2_Group2_2_CellSurfaceProtein


title: Day2_Group2_2_GEX


title: 4hD1HF10Treg_a

description: Library name: 4hD1HF10Treg_a


title: 992073_mort30_No


title: 4hD1PBSBcell_a

description: Library name: 4hD1PBSBcell_a


title: 4hD1PBSTreg_a

description: Library name: 4hD1PBSTreg_a


title: 4hD1PBSNK_a

description: Library name: 4hD1PBSNK_a


title: 4hD1F5111Treg_a

description: Library name: 4hD1F5111Treg_a


title: Day2_Group1_2_CellSurfaceProtein


title: 24hrFITCF10NK_a

description: Library name: 24hrFITCF10NK_a

value: 24hrs IL2-IC retroorbital injection


title: 992016_mort30_No


title: 24hrFITCF10Bcell_a

description: Library name: 24hrFITCF10Bcell_a


title: 24hrFITCF10Treg_a

description: Library name: 24hrFITCF10Treg_a


title: Day2_Group1_1_CellSurfaceProtein


title: 24hrFITCF5111Bcell_a

description: Library name: 24hrFITCF5111Bcell_a


title: 24hrFITCF5111Treg_a

description: Library name: 24hrFITCF5111Treg_a


title: 24hrF5111Bcell_a

description: Library name: 24hrF5111Bcell_a


title: 992066_mort30_No


title: Day2_Group2_3_GEX


title: Day2_Group1_1_GEX


title: 991981_mort30_No


title: 24hrF5111NK_a

description: Library name: 24hrF5111NK_a


title: 24hrF5111Treg_a

description: Library name: 24hrF5111Treg_a


title: 991968_mort30_No


title: 24hrHF10Bcell_a

description: Library name: 24hrHF10Bcell_a


title: 24hrHF10NK_a

description: Library name: 24hrHF10NK_a


title: 991904_mort30_No


title: 991901_mort30_No


title: 992033_mort30_No


title: Day5_Group3_1_GEX


title: 24hrPBSBcell_a

description: Library name: 24hrPBSBcell_a

value: 24hrs PBS retroorbital injection


title: Day2_Group1_2_GEX


title: 24hPBSTreg_a

description: Library name: 24hPBSTreg_a


title: 24hPBSNK_a

description: Library name: 24hPBSNK_a


title: 24hrFITCF5111NK_a

description: Library name: 24hrFITCF5111NK_a


title: Day5_Group3_2_GEX


title: 991915_mort30_Yes


title: 24hrHF10Treg_a

description: Library name: 24hrHF10Treg_a


title: Day5_Group2_2_CellSurfaceProtein


title: Day5_Group3_2_CellSurfaceProtein


title: Ad-CMV-GOL_highdose_infection_3

city: München

first: sainitin

last: donakonda

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Immunology

country: Germany

institute: TUM

data_processing:
Dropseq tools v1.12 was used for mapping the raw sequence reads to the reference genome and to generate transcript counts
DESeq2 v1.14.1 R package was utilized to identify differentially expressed genes
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab delimited text file include sequence read counts of each sample

source_name: hepatic CD8 T cells_highdose_infection

extract_protocol:
Samples for RNA-seq were sorted in 1.5 mL reaction tubes including lysis buffer (2xTCL buffer (Qiagen, #1070498) + RNase-free water + beta-mercaptoethanol (1% total volume)).
Library preparation for bulk 3’-sequencing of poly(A)-RNA was done as described previously in Drop-Seq pipeline. Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adapter. 5’ ends of the cDNAs were extended by a template switch oligo (TSO) and after pooling of all samples full-length cDNA was amplified with primers binding to the TSO-site and the adapter. cDNA was tagmented with the Nextera XT kit (Illumina) and 3’-end-fragments finally amplified using primers with Illumina P5 and P7 overhangs. The P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 75 cycles for the cDNA in read1 and 16 cycles for the barcodes and UMIs in read2.

value: liver

value: CD8 T cells

tag: infection status

value: 13 weeks


title: Ad-CMV-GOL_highdose_infection_1


title: Ad-CMV-GOL_highdose_infection_2


title: Day5_Group2_1_CellSurfaceProtein


title: Ad-CMV-GOL_lowdose_infection_3

source_name: hepatic CD8 T cells_lowdose_infection


title: 991815_mort30_No


title: 991803_mort30_No

value: male


title: Ad-CMV-GOL_lowdose_infection_2


title: 991806_mort30_Yes


title: Day5_Group3_1_CellSurfaceProtein

value: female


title: Day5_Group2_2_GEX


title: Day5_Group2_1_GEX


title: Ad-CMV-GOL_lowdose_infection_1


title: 991798_mort30_No


title: orb2-delta-zz 2-3h, rep1

city: Toronto

first: Howard

middle: D

last: Lipshitz

state: ON

address: 661 University Ave

department: Molecular Genetics

country: Canada

institute: University of Toronto

description:
Library name: orb2-delta-zz_2-3h_1
Column name in all Processed_file 2-3hr.txt: zz_3h.1

data_processing:
Sequencing adapter trimming and quality control were carried out using Trimgalore (Version 0.6.5) with default parameters
The Drosophila melanogaster 7SLRNA, rRNA, pseudogene-rRNA, tRNA, mtRNA and other species of rRNAs (rRNA_databases, https://github.com/sortmerna/sortmerna/tree/master/data/rRNA_databases) were pre-filtered by sortMeRNA (version 2.1)
The reads were aligned to FlyBase release 6.23 transcriptome RNA (FB2018_04) using Salmon (Version 1.9.1). With corrects for fragment GC-content bias and selective alignment to decoy-aware transcriptome. The whole genome was used as decoy.
TPM and normlized count extraction used the R package tximeta (version 1.20.3) and DEseq2 (version 1.42.1)
Assembly: FlyBase release 6.23 (FB2018_04) transcriptome RNA
Supplementary files format and content: tab-delimited text file include DEsrq2 normlized count for each sample
Supplementary files format and content: tab-delimited text file include TPM  for each sample

organism: Drosophila melanogaster

source_name: embryos

growth_protocol: Flies were kept at 25ºC on a 12 hour light/dark cycle

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) following the manufacturer’s protocol.
RNA libraries were prepared using a NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina and following the manufacturer’s protocol. The protocol for depletion of rRNA and other abundant non-coding RNAs was performed as described in Haugen et al. (2024) RNA 30: 866-890.

treatment_protocol: Embryos were collected from two groups: orb2-delta-zz and w1118 (pre-injected control). Extract was prepared from embryos collected 0 to 3 hours post egg-lay with 1-hour intervals (0-1h, 1-2h, 2-3h), dechorionated with ice cold 100% bleach for 2 minutes, washed with 0.1% Triton X-100, and disrupted by crushing using 0.5 g embryos per mL of lysis buffer (150 mM KCl, 20 mM HEPES-KOH (pH 7.4), 1 mM MgCl2, 1 mM DTT, 1 mM AEBSF, 2 mM benzamidine, 2 μg/mL pepstatin, 2 μg/mL leupeptin).

value: embryos

tag: time


title: 991807_mort30_Yes


title: orb2-delta-zz 2-3h, rep2

description:
Library name: orb2-delta-zz_2-3h_2
Column name in all Processed_file 2-3hr.txt: zz_3h.2


title: Day5_Group1_2_CellSurfaceProtein


title: orb2-delta-zz 1-2h, rep3

description:
Library name: orb2-delta-zz_1-2h_3
Column name in all Processed_file 1-2hr.txt: zz_2h.3


title: orb2-delta-zz 2-3h, rep3

description:
Library name: orb2-delta-zz_2-3h_3
Column name in all Processed_file 2-3hr.txt: zz_3h.3


title: 991785_mort30_No


title: Day5_Group1_1_CellSurfaceProtein


title: orb2-delta-zz 1-2h, rep2

description:
Library name: orb2-delta-zz_1-2h_2
Column name in all Processed_file 1-2hr.txt: zz_2h.2


title: orb2-delta-zz 0-1h, rep3

description:
Library name: orb2-delta-zz_0-1h_3
Column name in all Processed_file 0-1hr.txt: zz_1h.3


title: orb2-delta-zz 1-2h, rep1

description:
Library name: orb2-delta-zz_1-2h_1
Column name in all Processed_file 1-2hr.txt: zz_2h.1


title: Day5_Group1_2_GEX


title: 991774_mort30_No


title: 991783_mort30_No


title: orb2-delta-zz 0-1h, rep2

description:
Library name: orb2-delta-zz_0-1h_2
Column name in all Processed_file 0-1hr.txt: zz_1h.2


title: orb2-delta-zz 0-1h, rep1

description:
Library name: orb2-delta-zz_0-1h_1
Column name in all Processed_file 0-1hr.txt: zz_1h.1


title: Day5_Group1_1_GEX


title: 991770_mort30_Yes


title: wild type 2-3h, rep1

description:
Library name: wt_2-3h_1
Column name in all Processed_file 2-3hr.txt: wt_3h.1

value: wild type


title: 991753_mort30_No


title: 991761_mort30_No


title: wild type 2-3h, rep3

description:
Library name: wt_2-3h_3
Column name in all Processed_file 2-3hr.txt: wt_3h.3


title: wild type 2-3h, rep2

description:
Library name: wt_2-3h_2
Column name in all Processed_file 2-3hr.txt: wt_3h.2


title: B cells, severe asthma 3

city: Nanjing

first: Xijie

last: Zhang

address: 300 Guangzhou Road, Gulou District

department: Department of Respiratory and Critical Care Medicine

country: China

institute: the First Affiliated Hospital of Nanjing Medical University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includeTPM and raw counts for each Sample

source_name: lung

extract_protocol:
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China)according to the manufacturer’s protocol.
mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA). And then fragmented to approximately 200bp. Subsequently, theRNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycleaccording to instructions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina.

treatment_protocol: For the induction of a murine model with severe allergic airway inflammation, 10 μg of LPS (L4391, Escherichia coli 0111:B4, Sigma-Aldrich, St. Louis, MO, USA) and 25 μg of HDM was dissolved in 35μl of sterile PBS. During the stage of sensitization, mice were treated with the above-mentioned allergens once daily for three days (days 0-2, i.t.). During challenge, 25 μg of HDM added into 35 µl of PBS was administered from airway once daily for 8 days (days 7-14). The control mice received PBS alone intratracheally throughout the process.

value: lung

value: severe asthma

value: B cells

value: WT

value: LPS/HDM


title: wild type 1-2h, rep1

description:
Library name: wt_1-2h_1
Column name in all Processed_file 1-2hr.txt: wt_2h.1


title: B cells, severe asthma 1


title: B cells, severe asthma 2


title: wild type 1-2h, rep2

description:
Library name: wt_1-2h_2
Column name in all Processed_file 1-2hr.txt: wt_2h.2


title: B cells, control 2

value: control


title: AtTEGFR_EGF_18h_Rep1

city: Montreal

first: Arthur

middle: Jules

last: Gouhier

state: Quebec

address: 110 Avenue des Pins

institute: IRCM

description: Library name: AtTEGFR_EGF_18h_Rep1

data_processing:
RNAseq reads were trimmed with Trimmomatic 0.22 and aligned against the mm10 mouse genome using Tophat 2.0.8.
Raw read counts per gene were calculated with HTSeq-count from HTSeq 0.5.4.
Raw counts were normalized relative to library size and tested for differential expression with DESeq.
Assembly: mm10
Supplementary files format and content: TSV (gene expression in FPKM)

growth_protocol: AtT-20 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % fetal bovine serum (FBS) and antibiotics (penicillin, streptomycin).

extract_protocol:
RNA was extracted using RNeasy mini extraction columns (Qiagen) according to the manufacturer's instructions. 100-200 ng of total RNA were utilized to generate cDNA using the Superscript III reverse transcriptase (Invitrogen, 18080-044) following the manufacturer's recommendations.
Libraries and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendation

value: Corticotrope

value: EGFR

value: EGF 18h


title: wild type 0-1h, rep3

description:
Library name: wt_0-1h_3
Column name in all Processed_file 0-1hr.txt: wt_1h.3


title: B cells, control 3


title: wild type 0-1h, rep1

description:
Library name: wt_0-1h_1
Column name in all Processed_file 0-1hr.txt: wt_1h.1


title: AtTEGFR_EGF_18h_Rep2

description: Library name: AtTEGFR_EGF_18h_Rep2


title: AtTEGFR_H2O_3h_Rep2

description: Library name: AtTEGFR_H2O_3h_Rep2


title: B cells, control 1


title: AtTEGFR_EGF_3h_Rep2

description: Library name: AtTEGFR_EGF_3h_Rep2

value: EGF 3h


title: wild type 1-2h, rep3

description:
Library name: wt_1-2h_3
Column name in all Processed_file 1-2hr.txt: wt_2h.3


title: AtTEGFR_EGF_3h_Rep1

description: Library name: AtTEGFR_EGF_3h_Rep1


title: 991740_mort30_Yes

description: whole blood gene expression data from 161 critically ill sepsis patients

value: Yes

value: No


title: AtTEGFR_H2O_3h_Rep1

description: Library name: AtTEGFR_H2O_3h_Rep1


title: 991711_mort30_No


title: AtTNeo_H2O_3h_Rep2

description: Library name: AtTNeo_H2O_3h_Rep2

value: Neo (control)


title: 991724_mort30_No


title: wild type 0-1h, rep2

description:
Library name: wt_0-1h_2
Column name in all Processed_file 0-1hr.txt: wt_1h.2


title: AtTNeo_H2O_3h_Rep1

description: Library name: AtTNeo_H2O_3h_Rep1


title: Hep-G2_SG34-48-replicate_2

city: kunming

first: shunkai

last: chen

address: wujiaying

department: school of life sciences

institute: Yunnan university

description: Library name: Hep-G2_SG34-48-replicate_2

data_processing:
Sequence reads were trimmed by Trim Galore(v0.6.10)
Clean reads were mapped to GRCm39 using STAR (v2.7.11b)
Read count extraction were performed using featureCounts (v1.6.3)
Reads normalization and differentially-expressed gene calling were performed using DESeq2 (v1.40.2)
Assembly: GRCm39/GRCh38
Supplementary files format and content: tab-delimited text files include gene expression for each Sample

extract_protocol:
Total RNAs were extracted from embryos at specific stages utilizing TRIzol reagent.  Each RNA sample (500 ng total RNA) underwent rRNA depletion.
Strand-specific libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for ILLUMINA, following the manufacturer's instructions.


title: Hep-G2_SG34-48-replicate_3

description: Library name: Hep-G2_SG34-48-replicate_3


title: Hep-G2_SG34-48-replicate_1

description: Library name: Hep-G2_SG34-48-replicate_1


title: 991752_mort30_Yes


title: PKO_D8_Rep2

city: Harrisburg

first: Jessenia

last: Chavez

state: Pennsylvania

address: 4261 Williamsburg Dr, Apt. A

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

data_processing:
Libraries were loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500.
These cells were run for 50 cycles using the pair-end recipe according to the manufacturer's instructions.
Raw reads were aligned to the Mus musculus genome (UCSC mm10) using TopHat (version 2.1.1) (14) with default parameters.
Subsequently, the relative abundances (FPKM/TPM) of the transcripts and genes were estimated with Cufflinks (version 2.2.1)
Assembly: mm10
Supplementary files format and content: A single tab-delimited text files containing the FPKM/TPM values for all samples

source_name: neural precursor cell

extract_protocol:
Total RNA was extracted using 0.5mL of TRIzol per 5-10x10^6 cells. The homogenized sample was incubated at RT, followed by the addition of chloroform. Samples were centrifuged at 4ºC. After centrifugation, the upper aqueous phase was discarded, and 100% Isopropanol was added to the RNA fraction. Samples were then incubated at RT and then centrifuged at 4ºC. After spin, the supernatant was discarded, and the pellet was washed using 75% Ethanol. The sample was spun at 4ºC, and the ethanol was removed. The pellet was then air-dried at RT. The pellet was resuspended using diH2O and RNA concentration was measured and standardized across all samples. cDNA was synthesized using the SuperScript III system (Invitrogen, Cat# 18080).
cDNA libraries were prepared using the NEXTflex™ Illumina Rapid Directional RNA-Seq Library Prep Kit (BioO Scientific) according to the manufacturer’s instructions. Libraries were loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500. The samples were run for 50 cycles using either pair-end recipe according to the manufacturer's instructions.

value: neural precursor cell

value: POGZ KO


title: 991709_mort30_Yes

data_processing: Raw expression values in .cel files were normalized with Robust Multi-array Average (RMA). Differential expression analysis was performed with Limma to compare expression changes in 1) nonsurvivors versus survivors at 30 days and 2) patients with versus without septic shock, adjusted for age, sex, and absolute neutrophil count.

extract_protocol: RNA isolation was performed via PAXgene Blood miRNA kit (Qiagen) per protocol. RNA quality (RIN >5 cutoff) was measured via Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).

value: male


title: PKO_D8_Rep3


title: PKO_D0_Rep2

source_name: embryonic stem cell

value: embryonic stem cell


title: Hep-G2_replicate_3

description: Library name: Hep-G2_replicate_3


title: 991702_mort30_No

value: female


title: PKO_D0_Rep1


title: Hep-G2_replicate_2

description: Library name: Hep-G2_replicate_2


title: ATCC_D8_Rep1

value: POGZ WT


title: ATCC_D0_Rep2


title: ATCC_D8_Rep2


title: whole kidney, Pkd1 KO (Pkd1flox/flox.Pax8rtTA.Tet-O-Cre), sample 3

city: Freiburg

first: Katharina

last: Moos

address: Breisacherstr. 153

department: Medical Faculty

institute: University of Freiburg

data_processing:
Raw RNA sequencing reads were quality-controlled with FastQC (v0.11.8) and pre-processed with cutadapt (v4.0) to trim low-quality bases from both ends, trim adapter sequences, remove low-quality reads (more than 1 expected error and/or more than 30% N-bases) and remove short reads (less than 20 nucleotides).
Processed reads were aligned against the mouse reference genome GRCm39 from Ensembl (v108) using STAR (v2.6.1e).
The number of reads per gene were counted during the alignment process, using the STAR option “--quantMode GeneCounts”.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file containing raw counts (as generated by the STAR aligner)
Supplementary files format and content: tab-delimited text file containing raw counts of the sample's second sequencing run (as generated by the STAR aligner)

source_name: kidney

growth_protocol: Mice were housed in a specific pathogen-free facility, fed ad libitum, and housed at constant ambient temperature in a 12-hour day/night cycle.

extract_protocol:
Total RNAs were obtained from whole snap-frozen mouse kidneys using RNeasy Mini Kit (Qiagen). RNA quantification and quality was performed using Nanodrop photometer.
Purification of poly-A containing mRNA molecules, mRNA fragmentation, randomly primed cDNA synthesis, adapter ligation and adapter-specific PCR.

treatment_protocol: From post-natal day 28 (P28) to P42, mice received doxycycline hydrochloride (Fagron) via the drinking water (2 mg/ml with 5% sucrose, protected from light) for a period of 14 days.

value: kidney


title: whole kidney, Pkd1 KO (Pkd1flox/flox.Pax8rtTA.Tet-O-Cre), sample 2


title: 41901_N

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

description:
Library name: 41901_N
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mmul10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Macaca mulatta

source_name: BAL cells

extract_protocol:
BAL was performed with 80 mL of sterile saline in BSL3 on NHPs at weeks 5, 11, 13 and necropsy after Mtb infection. The BAL was filtered, centrifuged (1,200 rpm, 10 min at 4C), lysed for red blood cells (RBCs) using ACK lysis buffer (GibcoTM) and resuspended in 2 mL final volume of RPMI 1640 media (GibcoTM). The cells were counted and stored in internally threaded cryovials in liquid nitrogen for downstream scRNA-seq processing using 10x Genomics platform.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Target about 5-10K cells per sample.

treatment_protocol: Coinfected NHPs received a drug regimen consisting of 20 mg/kg of (R)-9-(2-phosphonylmethoxypropyl) adenine (PMPA, tenofovir, Gilead Sciences), 30 mg/kg of 2′,3′-dideoxy-5-fluoro-3′-thiacytidine (FTC, emtricitabine, Gilead Sciences), and 2.5 mg/mL of the integrase inhibitor DTG (ViiV Healthcare). The macaques also recevied once weekly isoniazid and rifapentine for 12 weeks orally.

value: BAL cells

value: 4.88 years


title: whole kidney, Pkd1 KO (Pkd1flox/flox.Pax8rtTA.Tet-O-Cre), sample 1


title: 991694_mort30_No


title: 991693_mort30_Yes


title: 41901_Wk13

description:
Library name: 41901_Wk13
10x Genomics


title: 991691_mort30_No


title: 991697_mort30_No


title: whole kidney, control (Pkd1flox/flox.Tet-O-Cre), sample 3


title: whole kidney, control (Pkd1flox/flox.Tet-O-Cre), sample 2


title: 41901_Wk11

description:
Library name: 41901_Wk11
10x Genomics


title: whole kidney, control (Pkd1flox/flox.Tet-O-Cre), sample 1


title: X2 695MB-L3 Lesion

city: WOOLLOONGABBA

first: Mitchell

middle: S

last: Stark

state: QLD

address: 37 Kent St

department: Frazer Institute

country: Australia

institute: The University of Queensland

description:
Library name: Sample 2
10xGenomics

data_processing:
Raw base calls from the NextSeq 500 sequencer were demultiplexed with the cellranger mkfastq pipeline into library-specific Fastq files
The Fastq files were aligned to the refdata-gex-GRCh38-2020-A human reference dataset from 10X genomics using cellranger count version 7.0.1 to create quality control metrics, Loupe Browser files and filtered gene barcode matrices.
The filtered gene barcode matrices were loaded into the Seurat package in R and merged into a single matrix.
Cells with more than 10% mitochondrial reads or less than 500 features were removed and counts were normalized using the sctransform v2 method.
Assembly: GRCh38
Supplementary files format and content: filtered gene barcode matrices in MEX format

source_name: cell line

extract_protocol:
One pair of stable nevus and perilesional melanocyte cultures were grown in MCBD 153 media supplemented as described above. Cells were grown to 75% confluency to ensure they were in the growth phase before being scraped, pelleted, and resuspended in media containing 12% FCS + 2mM EDTA. Sufficient cells were sorted with a BD FACSAria™ Fusion Flow Cytometer (BD Biosciences, New Jersey, U.S.) to achieve 200,000-300,000 viable cells. No cell surface markers were used since all cells were considered to be melanocytic in origin based upon cell morphology and growth characteristics. Only a cell viability marker was used to ensure a high proportion of live cells required for single cell Gel Bead-In-Emulsion (GEM) preparation.
The single cell suspensions were loaded onto a 10X Genomics Single Cell A Chip and partitioned along with oligo-containing Gel Beads into nanolitre-scale droplets using the 10X Chromium Controller. Next, a reverse transcription reaction was performed using oligos contained within the Gel Bead. This process tagged each cDNA molecule with an identical 10X barcode and a random Unique Molecular Identifier (UMI). After the generation of full-length barcoded cDNA molecules inside the GEMs, the emulsion was broken and cDNA from single cells was pooled for subsequent sequencing library preparation. Single cell sequencing libraries, containing standard Illumina P5 and P7 sequencing adapters, were generated with the 10X Chromium 3’ Single Cell Library Kit.  Each sample was given a unique sample index using the 10X Chromium i7 multiplex kit, allowing for multiplexing of different samples on a single sequencing run. Resulting sequencing libraries were assessed with an Agilent BioAnalyzer DNA High Sensitivity chip, pooled as desired, and quantified with a qPCR KAPA Library Quantification Kit. Denatured libraries were loaded onto an Illumina NextSeq-500 and sequenced using a 150-cycle High-Output Kit with the following protocol steps: 26bp (Read1), 8bp (i7 index), 98bp (Read2).  Read1 supplies the cell barcode and UMI, i7 the sample index, and Read2 the 3’ sequence of the transcript.

value: cell line

value: melanocytes

value: Lesion-naevocytes


title: 991713_mort30_Yes


title: X1 695MB-PL4 Perilesion

description:
Library name: Sample 1
10xGenomics

value: Perilesion-melanocytes


title: 991679_mort30_Yes


title: EndoCBH1 cells, siMNX1-3

city: Paris

first: Farah

last: Kobaisi

address: 123 Bvd Port Royal

institute: Institute Cochin

description:
Library name: Sample 6
coloumn name in normalized counts-all samples.tsv: MN3

data_processing:
STAR algorithm (version 2.7.6a)
Reads were then count using RSEM (v1.3.1) and the statistical analyses on the read counts were performed with R (version 3.6.3) and the DESeq2 package (DESeq2_1.26.0) to determine the proportion of differentially expressed genes between two conditions.
We used the standard DESeq2 normalization method (DESeq2’s median of ratios with the DESeq function)
Assembly: the Ensembl Homo Sapiens GRCh38 reference, release 101.
Supplementary files format and content: txt file including RSEM normalized counts for all samples

extract_protocol:
RNA was extracted using RNeasy Mini kit (Qiagen)  For library construction, 5ng of total RNA for each sample in triplicate
RNA libraries were prepared using Ovation Solo RNA-seq Kit (NuGEN) according to the manufacturer’s instructions. library amplification, rRNA was depleted using AnyDeplete (NuGEN)

value: pancreatic beta cell line

value: MNX1 knock down


title: ATCC_D0_Rep1


title: Hep-G2_replicate_1

description: Library name: Hep-G2_replicate_1


title: orb2-delta-zz  2-3h rep3_pool1

description:
Library name: zz_3h_4_1
Column name in all processed file: zz_3h.4_1
Processed_polysome_DEseq2_NormlizedCount_zw_3h.txt
Processed_polysome_DEseq2_TPM_zw_3h.txt

data_processing:
Sequencing adapter trimming and quality control were carried out using Trimgalore (Version 0.6.5) with default parameters
The Drosophila melanogaster 7SLRNA, rRNA, pseudogene-rRNA, tRNA, mtRNA and other species of rRNAs (rRNA_databases, https://github.com/sortmerna/sortmerna/tree/master/data/rRNA_databases) were pre-filtered by sortMeRNA (version 2.1)
The reads were aligned to FlyBase release 6.23 transcriptome RNA (FB2018_04) using Salmon (Version 1.9.1). With corrects for fragment GC-content bias and selective alignment to decoy-aware transcriptome. The whole genome was used as decoy.
TPM and normlized count extraction used the R package tximeta (version 1.20.3) and DEseq2 (version 1.42.1)
Assembly: FlyBase release 6.23 (FB2018_04)
Supplementary files format and content: tab-delimited text file includeDEseq2 normlized count for each sample
Supplementary files format and content: tab-delimited text file include TPM  for each sample

extract_protocol:
The polysome gradient protocol was adapted from Chen et al., 2014, with modifications. See paper MATERIALS AND METHODS.
RNA libraries were prepared using a NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina and following the manufacturer’s protocol. Ribosomal RNA depletion was performed using the QIAseq FastSelect rRNA Fly Kit (QIAGEN, Cat# 333265 (96 rxns) following the manufacturer’s protocol.

treatment_protocol: Embryos were collected from two groups: orb2∆ZZ and w1118 (pre-injected control). Extract was prepared from embryos collected 0 to 3 hours post egg-lay with 1-hour intervals (0-1h, 1-2h, 2-3h), dechorionated with ice cold 100% bleach for 2 minutes, washed with 0.1% Triton X-100, and disrupted by crushing using 0.5 g embryos per mL of polysome lysis buffer ( 7.5 mM MgCl2, 500 mM NaCl, 25 mM Tris (pH 7.5), 1 mM DTT, 1 mM AEBSF, 2 μg/mL leupeptin, 2 mM benzamidine, 2 μg/mL pepstatin A, 2 mg/mL heparin, 0.5 mg/mL cycloheximide).

value: embryos

value: 15-45% sucrose gradient


title: EndoCBH1 cells, siMNX1-2

description:
Library name: Sample 5
coloumn name in normalized counts-all samples.tsv: MN2


title: 991688_mort30_No

value: No

value: Yes


title: EndoCBH1 cells, siMNX1-1

description:
Library name: Sample 4
coloumn name in normalized counts-all samples.tsv: MN1


title: EndoCBH1 cells, siNT3

description:
Library name: Sample 3
coloumn name in normalized counts-all samples.tsv: NT3

value: WT

value: siNT


title: orb2-delta-zz  2-3h rep2_pool3

description:
Library name: zz_3h_2_3
Column name in all processed file: zz_3h.2_3
Processed_polysome_DEseq2_NormlizedCount_zw_3h.txt
Processed_polysome_DEseq2_TPM_zw_3h.txt


title: 41898_Wk13

description:
Library name: 41898_Wk13
10x Genomics

value: 4.93 years


title: 991682_mort30_Yes

value: male


title: 991678_mort30_Yes


title: orb2-delta-zz  2-3h rep3_pool3

description:
Library name: zz_3h_4_3
Column name in all processed file: zz_3h.4_3
Processed_polysome_DEseq2_NormlizedCount_zw_3h.txt
Processed_polysome_DEseq2_TPM_zw_3h.txt


title: EndoCBH1 cells, siNT2

description:
Library name: Sample 2
coloumn name in normalized counts-all samples.tsv: NT2


title: 41898_Wk11

description:
Library name: 41898_Wk11
10x Genomics


title: 41901_Wk5

description:
Library name: 41901_Wk5
10x Genomics


title: EndoCBH1 cells, siNT1

description:
Library name: Sample 1
coloumn name in normalized counts-all samples.tsv: NT1


title: Subject 36

city: Pamplona

first: Goren

last: Saenz-Pipaon

state: Navarra

address: Av. Pio XII 55

department: Atherothrombosis

country: Spain

institute: CIMA University of Navarra

description: UMI sequence (8 bp) in Read 2

data_processing:
First, polyA tails and short reads (less than 20 bp) were removed using Cutadapt software.
The resulting reads were aligned to the GRCh38.p12 reference genome with STAR software, obtaining BAM files with uniquely aligned reads.
De-duplication was performed with UMI-tools software, using dedup function and default options.
Gene expression was quantified from de-duplicated BAM files using quant3p script (github.com/ctlab/quant3p) and Ensembl gene annotation (release 92).
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Excel file (.xlsx) contains the raw counts for each gene (rows) and sample (columns).

source_name: Plasma extracellular vesicles

extract_protocol:
Medium/large size extracellelular vesicles were isolated from 400 µL platelet-free plasma by two serial centrifugations of 20,000g for 90 minutes.
RNA-Seq was performed following MARS-Seq protocol adapted from Jaitin et al., 2014. Briefly, poly-A RNA from plasma-derived extracellular vesicles was reverse-transcribed (RT) using poly-dT oligos carrying a 7 bp index and 8 bp unique molecular identifier (UMI, sequence in read 2). Pooled samples were subjected to linear amplification by in vitro transcription. Resulting amplified RNA was fragmented and dephosphorylated. Ligation of partial Illumina adaptor sequences was followed by a second RT reaction. Full Illumina adaptor sequences were added during final library amplification. RNA-Seq libraries were quantified by Qubit 3.0 Fluorometer (Life Technologies) and size profiles examined by 4200 TapeStation System (Agilent). Libraries were sequenced in an Illumina NextSeq 500 at a sequence depth of 10 million reads per sample.

value: Plasma

tag: batch

tag: age (years)

value: CLI

value: M


title: 41898_Wk5

description:
Library name: 41898_Wk5
10x Genomics

value: BAL cells


title: Subject 35

description: UMI sequence (8 bp) in Read 2

tag: tissue


title: 41898_N

description:
Library name: 41898_N
10x Genomics

tag: cell type


title: orb2-delta-zz  2-3h rep1_pool3

description:
Library name: zz_3h_1_3
Column name in all processed file: zz_3h.1_3
Processed_polysome_DEseq2_NormlizedCount_zw_3h.txt
Processed_polysome_DEseq2_TPM_zw_3h.txt


title: Subject 34

description: UMI sequence (8 bp) in Read 2


title: orb2-delta-zz  2-3h rep1_pool1

description:
Library name: zz_3h_1_1
Column name in all processed file: zz_3h.1_1
Processed_polysome_DEseq2_NormlizedCount_zw_3h.txt
Processed_polysome_DEseq2_TPM_zw_3h.txt


title: Subject 33

description: UMI sequence (8 bp) in Read 2


title: 991666_mort30_No


title: 41882_N

description:
Library name: 41882_N
10x Genomics

value: 4.13 years


title: Subject 32

description: UMI sequence (8 bp) in Read 2


title: orb2-delta-zz  1-2h rep3_pool3

description:
Library name: zz_2h_4_3
Column name in all processed file: zz_2h.4_3
Processed_polysome_DEseq2_NormlizedCount_zw_2h.txt
Processed_polysome_DEseq2_TPM_zw_2h.txt


title: Subject 31

description: UMI sequence (8 bp) in Read 2


title: 41882_Wk13

description:
Library name: 41882_Wk13
10x Genomics


title: orb2-delta-zz  2-3h rep2_pool1

description:
Library name: zz_3h_2_1
Column name in all processed file: zz_3h.2_1
Processed_polysome_DEseq2_NormlizedCount_zw_3h.txt
Processed_polysome_DEseq2_TPM_zw_3h.txt


title: Subject 30

description: UMI sequence (8 bp) in Read 2


title: Subject 29

description: UMI sequence (8 bp) in Read 2


title: 41882_Wk11

description:
Library name: 41882_Wk11
10x Genomics


title: orb2-delta-zz  1-2h rep3_pool1

description:
Library name: zz_2h_4_1
Column name in all processed file: zz_2h.4_1
Processed_polysome_DEseq2_NormlizedCount_zw_2h.txt
Processed_polysome_DEseq2_TPM_zw_2h.txt


title: Subject 28

description: UMI sequence (8 bp) in Read 2


title: Subject 26

description: UMI sequence (8 bp) in Read 2


title: orb2-delta-zz  1-2h rep2_pool3

description:
Library name: zz_2h_3_3
Column name in all processed file: zz_2h.3_3
Processed_polysome_DEseq2_NormlizedCount_zw_2h.txt
Processed_polysome_DEseq2_TPM_zw_2h.txt


title: Subject 25

description: UMI sequence (8 bp) in Read 2


title: 41879_N

description:
Library name: 41879_N
10x Genomics

value: 5.61 years


title: Subject 27

description: UMI sequence (8 bp) in Read 2

value: F


title: orb2-delta-zz  1-2h rep2_pool1

description:
Library name: zz_2h_3_1
Column name in all processed file: zz_2h.3_1
Processed_polysome_DEseq2_NormlizedCount_zw_2h.txt
Processed_polysome_DEseq2_TPM_zw_2h.txt


title: Subject 24

description: UMI sequence (8 bp) in Read 2

value: IC


title: 41879_WK13

description:
Library name: 41879_WK13
10x Genomics


title: orb2-delta-zz  1-2h rep1_pool3

description:
Library name: zz_2h_2_3
Column name in all processed file: zz_2h.2_3
Processed_polysome_DEseq2_NormlizedCount_zw_2h.txt
Processed_polysome_DEseq2_TPM_zw_2h.txt


title: Subject 22

description: UMI sequence (8 bp) in Read 2


title: 41879_Wk11

description:
Library name: 41879_Wk11
10x Genomics


title: orb2-delta-zz  1-2h rep1_pool1

description:
Library name: zz_2h_2_1
Column name in all processed file: zz_2h.2_1
Processed_polysome_DEseq2_NormlizedCount_zw_2h.txt
Processed_polysome_DEseq2_TPM_zw_2h.txt


title: Subject 23

description: UMI sequence (8 bp) in Read 2


title: Whole Lung Homogenate, LPS, TCDD

city: Columbia

first: Chloe

last: Weyer-Nichols

state: South Carolina

address: 6311 Garners Ferry Rd

department: Pathology, Microbiology, and Immunology

institute: University of South Carolina School of Medicine

description:
Library name: Sample 2
10x Genomics

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using the Cell Ranger (v4.0.0) pipeline (10x Genomics)
Assembly: mouse mm10
Supplementary files format and content: table separated values files and matrix files

source_name: Lung

extract_protocol:
Following perfusion with heparinized buffer, whole lungs were brought to a single cell suspension using Miltenyi Biotec's Lung Dissociation kit according to the manufacturer's protocol.
Single-cell RNA sequencing (scRNA-seq) was performed using the Chromium Next GEM Single Cell 5' Kit v2 (10X Genomics, Pleasanton, CA)]. In brief, whole lung homogenate samples with ≥70% cell viability, which the manufacturer considers acceptable viability, were included for sequencing (n = 3 per treatment group). Approximately 3,000 cells per treatment group were loaded onto the Chromium Controller to generate single-cell Gel Bead-In Emulsions (GEMs), and gene expression libraries were prepared according to the manufacturer's protocol.

value: Lung

tag: strain

value: Female

value: 8-10 weeks

value: TCDD

tag: disease state

value: LPS-ARDS


title: Subject 20

description: UMI sequence (8 bp) in Read 2


title: 41879_Wk5

description:
Library name: 41879_Wk5
10x Genomics


title: orb2-delta-zz  0-1h rep3_pool1

description:
Library name: zz_1h_4_1
Column name in all processed file: zz_1h.4_1
Processed_polysome_DEseq2_NormlizedCount_zw_1h.txt
Processed_polysome_DEseq2_TPM_zw_1h.txt

value: embryos

tag: treatment

value: 15-45% sucrose gradient


title: 41876_N

description:
Library name: 41876_N
10x Genomics

value: 5.10 years


title: Whole Lung Homogenate, LPS, VEH

description:
Library name: Sample 1
10x Genomics

value: Vehicle


title: Subject 19

description: UMI sequence (8 bp) in Read 2

value: Plasma


title: 991786_mort30_Yes

city: Philadelphia

first: Blanca

last: Himes

address: 423 Guardian Dr

institute: University of Pennsylvania

description: whole blood gene expression data from 161 critically ill sepsis patients

value: male

value: Yes


title: Input, rep3

description:
Library name: Lipshitz_HL18_S9
Column name in processed_file: Input_3

data_processing:
Sequencing adapter trimming and quality control were carried out using Trimgalore (Version 0.6.5) with default parameters
The Drosophila melanogaster 7SLRNA, rRNA, pseudogene-rRNA, tRNA, mtRNA and other species of rRNAs (rRNA_databases, https://github.com/sortmerna/sortmerna/tree/master/data/rRNA_databases) were pre-filtered by sortMeRNA (version 2.1)
The reads were aligned to FlyBase release 6.23 transcriptome RNA (FB2018_04) using Salmon (Version 1.9.1). With corrects for fragment GC-content bias and selective alignment to decoy-aware mRNA transcriptome. The whole genome was used as decoy.
TPM and normlized count extraction used the R package tximeta (version 1.20.3) and DEseq2 (version 1.42.1)
Assembly: FlyBase release 6.23 (FB2018_04) transcriptome RNA
Supplementary files format and content: tab-delimited text file include DEseq2 normlized count
Supplementary files format and content: tab-delimited text file include TPM

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) following the manufacturer’s protocol.
RNA was prepared for sequencing using Ribo-Zero Gold rRNA depletion kit and TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to manufacturer’s instructions

treatment_protocol: Embryo lysate used in this study was collected from embryos laid and aged at 25°C. Extract was prepared from embryos collected 0 to 3 hours post egg-lay on apple juice agar plates, dechorionated with 100% bleach for 2 minutes, washed with 0.1% Triton X-100, and disrupted by crushing in minimal volume of lysis buffer consisting of 150 mM KCl, 20 mM HEPES-KOH (pH 7.4), 1 mM MgCl2, 1 mM DTT, and protease inhibitors (1 mM AEBSF, 2 mM benzamidine, 2 μg/mL pepstatin, 2 μg/mL leupeptin). The lysate was cleared by centrifugation at 4°C, 13 000 RPM for 15 minutes, and the supernatant was collected and either used immediately, or stored at -80°C.

value: wild type


title: 41876_Wk13

description:
Library name: 41876_Wk13
10x Genomics

value: BAL cells


title: orb2-delta-zz  0-1h rep2_pool3

description:
Library name: zz_1h_3_3
Column name in all processed file: zz_1h.3_3
Processed_polysome_DEseq2_NormlizedCount_zw_1h.txt
Processed_polysome_DEseq2_TPM_zw_1h.txt


title: 41882_Wk5

description:
Library name: 41882_Wk5
10x Genomics

value: 4.13 years


title: Subject 18

description: UMI sequence (8 bp) in Read 2

value: M


title: Input, rep2

description:
Library name: Lipshitz_HL17_S8
Column name in processed_file: Input_2


title: 41876_Wk11

description:
Library name: 41876_Wk11
10x Genomics


title: 41876_Wk5

description:
Library name: 41876_Wk5
10x Genomics


title: Subject 17

description: UMI sequence (8 bp) in Read 2

value: IC


title: orb2-delta-zz  0-1h rep2_pool1

description:
Library name: zz_1h_3_1
Column name in all processed file: zz_1h.3_1
Processed_polysome_DEseq2_NormlizedCount_zw_1h.txt
Processed_polysome_DEseq2_TPM_zw_1h.txt


title: Subject 21

description: UMI sequence (8 bp) in Read 2

value: F


title: Subject 16

description: UMI sequence (8 bp) in Read 2


title: orb2-delta-zz  0-1h rep1_pool3

description:
Library name: zz_1h_2_3
Column name in all processed file: zz_1h.2_3
Processed_polysome_DEseq2_NormlizedCount_zw_1h.txt
Processed_polysome_DEseq2_TPM_zw_1h.txt


title: control_IP, rep3

description:
Library name: Lipshitz_HL15_S6
Column name in processed_file: C1_3

tag: ip antibody

value: Fab anti-EGFR-C1

value: immunoprecipitation


title: Subject 15

description: UMI sequence (8 bp) in Read 2

tag: group


title: orb2-delta-zz  0-1h rep3_pool3

description:
Library name: zz_1h_4_3
Column name in all processed file: zz_1h.4_3
Processed_polysome_DEseq2_NormlizedCount_zw_1h.txt
Processed_polysome_DEseq2_TPM_zw_1h.txt


title: 34561_Wk13

description:
Library name: 34561_Wk13
10x Genomics

value: 7.90 years


title: 34561_N

description:
Library name: 34561_N
10x Genomics


title: Subject 14

description: UMI sequence (8 bp) in Read 2


title: orb2-delta-zz 0-1h rep1_pool1

description:
Library name: zz_1h_2_1
Column name in all processed file: zz_1h.2_1
Processed_polysome_DEseq2_NormlizedCount_zw_1h.txt
Processed_polysome_DEseq2_TPM_zw_1h.txt


title: control_IP, rep2

description:
Library name: Lipshitz_HL14_S5
Column name in processed_file: C1_2


title: orb2_IP, rep3

description:
Library name: Lipshitz_HL12_S3
Column name in processed_file: orb2_3

value: Fab anti-orb2 E8


title: Subject 13

description: UMI sequence (8 bp) in Read 2


title: wt 2-3h rep3_pool1

description:
Library name: LWG_3h_4_1
Column name in all processed file: LWG_3h.4_1
Processed_polysome_DEseq2_NormlizedCount_zw_3h.txt
Processed_polysome_DEseq2_TPM_zw_3h.txt

value: embryos


title: control_IP, rep1

description:
Library name: Lipshitz_HL13_S4
Column name in processed_file: C1_1


title: Subject 12

description: UMI sequence (8 bp) in Read 2

value: Control


title: 34561_Wk5

description:
Library name: 34561_Wk5
10x Genomics


title: wt 2-3h rep2_pool3

description:
Library name: LWG_3h_2_3
Column name in all processed file: LWG_3h.2_3
Processed_polysome_DEseq2_NormlizedCount_zw_3h.txt
Processed_polysome_DEseq2_TPM_zw_3h.txt

value: 15-45% sucrose gradient


title: Monocytes_KL_1

city: Wuhan

first: 鹏

last: 王

email: wangp00678@163.com, wangp94@whu.edu.cn

state: 湖北省

address: 169 Donghu nan road,Wucang District

institute: 武汉大学

description: Monocytes.xlsx

data_processing:
Illumina Hiseq X Ten platform for sequencing with 150-bp paired-end reads strategy (Novogene)
Quality control of mRNA-seq data was performed by using Fatsqc (v0.11.9) and low-quality bases were trimmed by Trim_galore (0.6.4_dev)
All RNA-seq data were mapped to the mouse genome (Mus_musculus_Ensemble_94) by Hisat2 (v.2.0.5) and allowed a maximum of two mismatches per read
Gene expression level was calculated by FeatureCounts (v.2.0.0) with default parameters and normalized by FPKM (Fragments Per Kilobase of exon model per Million mapped fragments).
Assembly: Mus_musculus_Ensemble_94
Supplementary files format and content: excel with FPKM for every gene (Rows) and every sample (Columns)

source_name: lungs

extract_protocol:
Tumor cells, TRMs, MDMs, Monocytes and CD8+ T cells were isolated from tumor of KL and KLG4 mice based FACS. the cells were homogenized in 2 ml of TRIzol (Invitrogen). Total RNAs were prepared and the quality of RNAs was determined by agarose gel electrophoresis and spectrophotometer analysis. Poly(A) mRNA was subsequently purified from 10μg total RNA using NEBNext Oligo d(T)25 Magnetic Beads Isolation Module. First-strand complementary DNA was synthesized with NEBNext RNA First-Strand Synthesis Module. NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module was used for the synthesis of the complementary strand of first-strand cDNA. The resulting double-stranded DNA was purified and Vazyme TruePrep DNA Library Prep kit V2 was used to prepare libraries followed by sequencing on an Illumina Hiseq X Ten platform with 150-bp paired-end reads strategy (Novogene)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lungs

tag: cell line

value: primary cells

value: Monocytes

value: primary cells from tumor lungs 10 weeks after intranasal injection of Ad-Cre and Tamoxifen treatment


title: Input, rep1

description:
Library name: Lipshitz_HL16_S7
Column name in processed_file: Input_1

value: wild type


title: orb2_IP, rep2

description:
Library name: Lipshitz_HL11_S2
Column name in processed_file: orb2_2


title: Subject 11

description: UMI sequence (8 bp) in Read 2

value: Plasma


title: orb2_IP, rep1

description:
Library name: Lipshitz_HL10_S1
Column name in processed_file: orb2_1


title: Subject 10

description: UMI sequence (8 bp) in Read 2


title: CD8+_T_KL_2

description: CD8+ T cells_Gene_expr_with_pval.xlsx

value: CD8+ T cells


title: wt 2-3h rep1_pool1

description:
Library name: LWG_3h_1_1
Column name in all processed file: LWG_3h.1_1
Processed_polysome_DEseq2_NormlizedCount_zw_3h.txt
Processed_polysome_DEseq2_TPM_zw_3h.txt


title: CD8+_T_KLG4_1

description: CD8+ T cells_Gene_expr_with_pval.xlsx


title: Subject 9

description: UMI sequence (8 bp) in Read 2

value: M


title: Subject 8

description: UMI sequence (8 bp) in Read 2


title: wt 2-3h rep3_pool3

description:
Library name: LWG_3h_4_3
Column name in all processed file: LWG_3h.4_3
Processed_polysome_DEseq2_NormlizedCount_zw_3h.txt
Processed_polysome_DEseq2_TPM_zw_3h.txt


title: Culture 3, LPGRN

city: Birmingham

first: Andrew

last: Arrant

state: AL

address: 1825 University Blvd SHEL 1106

institute: University of Alabama at Birmingham

description:
Library name: LPGRN3
column name in GL_P_normalized_counts_cpm.csv : GL_3S7

data_processing:
nf-core/rnaseq pipeline, v.3.1.0
Reads were screened for quality, trimmed, and processed for contamination removal with BBSplit (v 39.01)
Files were aligned to the rn7 genome (v107) using STAR (v 2.7.9a)
Reads were quantified with Salmon (v 1.9.0) with the following parameters enabled: `--seqBias --gcBias`
Quantified counts were imported to R (v 4.3.0) with tximport (v 1.28.0) and differential gene expression was assessed using limma-voom (v 3.56.2).
Assembly: rn7 (v107)
Supplementary files format and content: csv file includes cpm for all samples

organism: Rattus norvegicus

source_name: Primary hippocampal astrocyte

growth_protocol: Primary hippocampal astrocytes from E19 rat embryos were cultured for 7 days in DMEM with 10% FBS and 1% penicillin-streptomycin in T25 flasks. Cultures were shaken at 240 rpm for 6 hours, then passaged to 24 well plates and cultured in Neurobasal medium with B27 supplement, 2 mM L-glutamine, 1% penicillin/streptomycin, and 5 ng/mL heparin-binding EGF-like growth factor. After 4 days, astrocytes were transduced with lentiviral vectors expressing GFP or L-PGRN, then cultured for 3 more days. Cultures were then switched to media mimicking neuronal co-culture (Neurobasal A medium with B27 supplement, 2 mM L-glutamine, and 2.5% fetal bovine serum) for 4 days before harvesting RNA.

extract_protocol:
RNA was isolated using the Qiagen Rneasy mini kit, then processed for poly-A selection before library construction.
Libraries were prepared using the NEB Next Ultra II Directional kit (New England Biolabs), according to the manufacturer’s instructions.

treatment_protocol: Cultures were transduced with lentiviral vectors expressing GFP (RRID: Addgene_12252) or L-PGRN (RRID: Addgene_234873) under the PGK promoter by incubating overnight at an MOI of 5000.

value: Primary hippocampal astrocyte

value: L-PGRN lentivirus

tag: culture


title: Culture 4, LPGRN

description:
Library name: LPGRN4
column name in GL_P_normalized_counts_cpm.csv : GL_4S8


title: CD8+_T_KL_1

description: CD8+ T cells_Gene_expr_with_pval.xlsx


title: wt 1-2h rep3_pool1

description:
Library name: LWG_2h_4_1
Column name in all processed file: LWG_2h.4_1
Processed_polysome_DEseq2_NormlizedCount_zw_2h.txt
Processed_polysome_DEseq2_TPM_zw_2h.txt


title: MDMs_KLG4_2

value: MDMs


title: wt 1-2h rep3_pool3

description:
Library name: LWG_2h_4_3
Column name in all processed file: LWG_2h.4_3
Processed_polysome_DEseq2_NormlizedCount_zw_2h.txt
Processed_polysome_DEseq2_TPM_zw_2h.txt


title: Subject 6

description: UMI sequence (8 bp) in Read 2

tag: Sex

value: F


title: Subject 7

description: UMI sequence (8 bp) in Read 2


title: 34561_Wk11

description:
Library name: 34561_Wk11
10x Genomics

value: BAL cells

tag: age

value: 7.90 years


title: Culture 1, LPGRN

description:
Library name: LPGRN1
column name in GL_P_normalized_counts_cpm.csv : GL_1S5


title: MDMs_KLG4_1

tag: genotype


title: Culture 4, GFP

description:
Library name: GFP4
column name in GL_P_normalized_counts_cpm.csv : P_4S4

value: GFP lentivirus


title: Subject 5

description: UMI sequence (8 bp) in Read 2

value: Control


title: wt 2-3h rep2_pool1

description:
Library name: LWG_3h_2_1
Column name in all processed file: LWG_3h.2_1
Processed_polysome_DEseq2_NormlizedCount_zw_3h.txt
Processed_polysome_DEseq2_TPM_zw_3h.txt

value: embryos

value: 15-45% sucrose gradient


title: wt 1-2h rep2_pool3

description:
Library name: LWG_2h_3_3
Column name in all processed file: LWG_2h.3_3
Processed_polysome_DEseq2_NormlizedCount_zw_2h.txt
Processed_polysome_DEseq2_TPM_zw_2h.txt


title: wt 1-2h rep2_pool1

description:
Library name: LWG_2h_3_1
Column name in all processed file: LWG_2h.3_1
Processed_polysome_DEseq2_NormlizedCount_zw_2h.txt
Processed_polysome_DEseq2_TPM_zw_2h.txt


title: Culture 3, GFP

description:
Library name: GFP3
column name in GL_P_normalized_counts_cpm.csv : P_3S3


title: MDMs_KL_2

value: lungs

value: primary cells


title: CD8+_T_KLG4_2

description: CD8+ T cells_Gene_expr_with_pval.xlsx

value: primary cells from tumor lungs 10 weeks after intranasal injection of Ad-Cre and Tamoxifen treatment


title: Subject 4

description: UMI sequence (8 bp) in Read 2


title: wt 1-2h rep1_pool3

description:
Library name: LWG_2h_1_3
Column name in all processed file: LWG_2h.1_3
Processed_polysome_DEseq2_NormlizedCount_zw_2h.txt
Processed_polysome_DEseq2_TPM_zw_2h.txt

value: wild type


title: wt 2-3h rep1_pool3

description:
Library name: LWG_3h_1_3
Column name in all processed file: LWG_3h.1_3
Processed_polysome_DEseq2_NormlizedCount_zw_3h.txt
Processed_polysome_DEseq2_TPM_zw_3h.txt


title: Culture 2, GFP

description:
Library name: GFP2
column name in GL_P_normalized_counts_cpm.csv : P_2S2


title: Culture 2, LPGRN

description:
Library name: LPGRN2
column name in GL_P_normalized_counts_cpm.csv : GL_2S6


title: MDMs_KL_1


title: wt 1-2h rep1_pool1

description:
Library name: LWG_2h_1_1
Column name in all processed file: LWG_2h.1_1
Processed_polysome_DEseq2_NormlizedCount_zw_2h.txt
Processed_polysome_DEseq2_TPM_zw_2h.txt


title: wt 0-1h rep3_pool3

description:
Library name: LWG_1h_4_3
Column name in all processed file: LWG_1h.4_3
Processed_polysome_DEseq2_NormlizedCount_zw_1h.txt
Processed_polysome_DEseq2_TPM_zw_1h.txt


title: TRMs_KLG4_2

value: TRMs


title: Subject 2

description: UMI sequence (8 bp) in Read 2

value: Plasma


title: Subject 3

description: UMI sequence (8 bp) in Read 2

value: M


title: Culture 1, GFP

description:
Library name: GFP1
column name in GL_P_normalized_counts_cpm.csv : P_1S1

value: Primary hippocampal astrocyte


title: LT-HSCs, Piezo1 KO, rep3

city: Hangzhou

first: Xinjiang

last: Lu

address: Yuhangtang road No.866

institute: Zhejiang University

description:
Library name: KO3
Total 6 samples were analysed in this study. 3 samples as control, 3 samples as Piezo5 KO groups.

data_processing:
Demultiplexing and adapter trimming were performed with bcl2fastq v2.19. No quality trimming was performed for deposited fastq files.
Sequenced reads were quality trimmed using Cutadapt v1.16.5.
Reads were mapped to mm10 whole genome using HISAT2 v2.1 with default settings for paired-end reverse strand specific libraries.
featureCounts v1.6.4 and DESeq2 v2.11.40.6 were applied for differentially expression analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text file inclueds raw counts for each sample

extract_protocol:
Total RNA was extracted using TRIZOL Reagent according to the manufacturer’s instructions (Invitrogen). RNA libraries were prepared for sequencing using the TruSeq RNA Sample Prep Kit.
RNA-seq

treatment_protocol: LT-HSCs were sorted from the bone marrow of control and Piezo1 KO mice.

value: Bone marrow

value: LT-HSCs

value: Bone marrow cells

value: Piezo3 knockout


title: TRMs_KLG4_1


title: Subject 1

description: UMI sequence (8 bp) in Read 2

value: F


title: LT-HSCs, Piezo1 KO, rep2

description:
Library name: KO2
Total 6 samples were analysed in this study. 3 samples as control, 3 samples as Piezo4 KO groups.

value: Piezo2 knockout


title: wt 0-1h rep3_pool1

description:
Library name: LWG_1h_4_1
Column name in all processed file: LWG_1h.4_1
Processed_polysome_DEseq2_NormlizedCount_zw_1h.txt
Processed_polysome_DEseq2_TPM_zw_1h.txt


title: wt 0-1h rep2_pool3

description:
Library name: LWG_1h_3_3
Column name in all processed file: LWG_1h.3_3
Processed_polysome_DEseq2_NormlizedCount_zw_1h.txt
Processed_polysome_DEseq2_TPM_zw_1h.txt


title: TRMs_KL_2


title: CUH124 Nasal cells HIV infected, ART greater than 1 year

city: Blantyre

first: Joseph

middle: Aston

last: Phiri

state: Southern Region

address: Chipatala Avenue

country: Malawi

institute: Malawi Liverpool Wellcome Programme

description:
Library name: CUH124
10x Genomics

data_processing:
Data demultiplexing, barcoded cunting, gene counting were made using cellranger count (cellranger version 8.0.1). https://www.10xgenomics.com/support/jp/software/cell-ranger/downloads#download-links
Assembly: Human reference (GRCh38) - 2024-A
Supplementary files format and content: Tab seprated values files and matrix files

source_name: Inferior turbinate nasal cells

extract_protocol:
Nasal cells collected using nasal currette were dislodged by pipetting liquid up and down the tip of the curette, and cells were centrifuged at 500g for 10 min at 4 °C. The supernatant was completely removed, and cells were resuspended in 500 µl of PBS (Fisher Scientific) counted snd loaded onto a chromium controller.
Single-cell RNA libraries were prepared using the Chromium Next GEM Single Cell 5′ Reagent Kit v2 and Chromium Controller (10× Genomics), following the manufacturer’s protocol. We loaded 10,000-16,000 nasal single-cell suspensions, with a minimum viability greater than 80%, into microfluidic chips to generate Gel Beads-in-Emulsion (GEMs), where individual cells were lysed, and mRNA barcoded using oligo(dT) primers with unique molecular identifiers (UMIs) and cell barcodes. Template switching was facilitated by a template switch oligonucleotide (TSO) to enable full-length cDNA synthesis. GEMs were broken, and barcoded cDNA was recovered and amplified by PCR.

value: Inferior turbinate nasal cells

value: Immune, epithelial cells


title: TRMs_KL_1