title: M_LPS_bio_rep_2

tag: tissue

value: retina

value: 24 hour culture in REM + 0.2ug/mL LPS


title: SA_Y_06_61_BL

status: Public on Dec 01 2024

type: SRA

city: Morgantown

first: Pius

last: Joseph

address: 1000 Frederick Lane

country: USA

institute: NIOSH

library_source: transcriptomic

data_processing:
Basecalls were performed using bcl2fastq/2.19.
Sequence reads were trimmed using Trim Galore!, Cutadapt 3.4 and Trimgalore 0.6.7 using Nextflow 22.10.6 and the nf-core/rnaseq 3.12.0 pipeline.
All sequences were aligned to the Rattus norvegicus Rnor 6.0 genome from Ensembl downloaded from igenomes using Star 2.6.1d within  Nextflow 22.10.6 and the nf-core/rnaseq 3.12.0 pipeline.
Raw gene counts were assigned using Salmon 1.10.1 and Sammtools 1.17 within Nextflow 22.10.6 and the nf-core/rnaseq 3.12.0 pipeline.
Assembly: Rnor6.0
Supplementary files format and content: tsv file including abundance measurements (raw counts)

molecule: total RNA

organism: Rattus norvegicus

source_name: blood

growth_protocol: Healthy male Fischer 344 rats (Charles River Wilmington, MA), weighing 250-300 g were used in this study which was conducted in an Association for Assessment and Accreditation of Laboratory Animal Care International approved animal facility (NIOSH, Morgantown, WV) following a protocol approved by the Animal Care and Use Committee. The rats were housed in pairs/cage and maintained on a 12-hour light-dark cycle in a temperature (68-72oF) and humidity (30-70%) controlled room with free access to filtered tap water and HaCXan Teklad Global 18% protein rodent diet (Harlan Teklad; Madison, WI).

extract_protocol:
Total RNA from the lungs were isolated using the RNeasy Fibrous Mini Kit (Qiagen, Inc, Valencia, CA). RNA from whole blood, collected in K2EDTA BD Vacutainer™ tubes (Becton Dickinson; Franklin Lakes, NJ) and then stored 1 part blood in 3 parts RNALater (ThermoFisher Scientific; Waltham, MA), was isolated using the mouse Ribopure RNA Isolation Kit (Ambion AM1951) with optional DNase treatment using the Invitrogen™ DNA-free™ DNA Removal Kit (Invitrogen by ThermoFisher Scientific; Waltham, MA). Immediately following RNA isolation and DNase treatment, RNA samples were depleted of alpha and beta globin mRNAs using the Ambion® GLOBINclear™-Mouse/Rat Kit, as directed by the manufacturer’s protocol.
Next generation sequencing libraries prepared using TruSeq® Stranded mRNA Library Prep Kit (Illumina, Inc, San Diego, CA) were used in the sequencing.

treatment_protocol: The rats were exposed by whole-body inhalation to filtered air or crystalline silica (Min-U-Sil 5) (15 mg/m3, 6 hours/day, 5 days).

value: blood

tag: strain

value: Fischer 344

tag: time point

value: 6 months

tag: treatment

value: SILICA

tag: Sex

value: male


title: Met_1_4599

city: London

first: Oscar

last: Maiques

address: Charterhouse Square

department: Tumour Microenvironment

country: United Kingdom

institute: Queen Mary's University of London- Cancer Research UK Barts Centre

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.

organism: Mus musculus

source_name: Melanoma lung metastasis

growth_protocol: 4599 murine melanoma cells isolated from different tumour parts (TB, PIF, DIF and MET) were seeded on Fibrillar bovine dermal collagen 1.7 mg/ml (PureCol, Cat. 5005 Advanced BioMatrix) for 24h DMEM+10% FBS.

extract_protocol:
RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA) followed by QIAGEN RNeasy Midi Kit. RNA integrity and quality was evaluated using RNA QubitTM assay.
Sequencing was performed using 150bp paired end sequencing strategy using Illumina sequencing platform and PE150 Technology
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Media was changed to DMEM+1% FBS during 24h before the RNA extraction.

value: Melanoma lung metastasis

tag: cell line

tag: cell type

value: Melanoma

tag: tumour part

value: Met


title: SA_Y_06_60_BL


title: SA-Y-01-42_Lu

source_name: lung

value: lung

value: 1 day

value: AIR


title: split ePE3 at multiple endogenous sites- Rep 1- I1

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake university

library_source: genomic

data_processing:
Traget site and protential off-target sites were amplified by PCR using the primer sequences (Table S1), then sequenced on an Illumina NovaSeq system. Deep sequencing data analysis was processed using CRISPResso2 and untreated cells were used as negative controls to exclude PCR amplification and sequencing errors. Reads were align to the amplicon sequence by crispresso2 using --max_paired_end_reads_overlap 140 --min_paired_end_reads_overlap     10 --exclude_bp_from_left 0 --exclude_bp_from_right 0 --plot_window_size 20 --min_frequency_alleles_around_cut_to_plot 0.2
On-target editing efficiencies, which are greater than 0.1%, were quantified as a percentage of (number of on-target reads) / (number of total reads).
Supplementary files format and content: xlsx files, percentage of total sequencing reads with on-target editing for all libraries, percentage of total sequencing reads with indels for ePE3-hepa.
Library strategy: Amplicon Sequencing

molecule: genomic DNA

organism: Homo sapiens

source_name: HEK293T cell

growth_protocol: HEK293T cell and Hepa1-6 cell were grown in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Gemini #900-108) and 1% GlutaMAX (Thermo #35050061). Cells were passaged every 2-3 days. After one day post-transduction, the medium was changed. Cells were harvested at 72 hours post-transduction.

extract_protocol:
Genomic DNA (gDNA) was isolated using TIANamp Genomic DNA Kit (TIANGEN #DP304) according to the manufacturer’s protocol.
The region that integrated with genomic DNA including RT template was PCR amplified from genomic DNA for HTS. For the first round of PCR, genomic sites of interest were amplified from 150 ng of genomic DNA using Q5 PCR Master Mix (New England Biolabs #M0544S) with the primers containing Illumina forward and reverse adapters. 50 uL of PCR 1 reaction was performed with forward and reverse primers each at 0.25 uM, ~1 uL of genomic DNA extract, and 25 uL of Q5 PCR Master Mix. To add a unique sequencing index, 50 uL of a given PCR 2 contained 2.5 uL of previous step unpurified PCR product; a unique forward or reverse primer pair, each at 0.25 uM; and 25 uL of Q5 PCR Master Mix. Primers are listed in Table S1. PCR 2 products were purified by DNA AMPure XP beads (Beckman Coulter #A63882) and eluted with 25 uL of water. DNA concentration was quantified by Nanodrop One (Thermo Fisher Scientific).

treatment_protocol: Cells were transfected at 60%-70% confluency using 3 uL of Lipofectamine 3000 (Thermo Fisher) with 1500 ng each half of the Split-PE. Three days post transfection, cells were collected.

value: HEK293T cell


title: ERT2CreERT2_Tamoxifen_d3_rep1

city: Seattle

first: Sudarshan

last: Pinglay

state: WA

address: 3720 15th Ave NE

institute: University of Washington

description: Library name: SP000052

data_processing:
Reads were demultiplexed using bcl2fastq (v2.20.0.422). Reads were passed through a custom script (read_extract_iterable.py or read_extract_iterable_4primers.py or amplicon_BCExtract_20240906.py) to extract barcode sequences and UMIs based on matches to the expected preceding and subsequent bases. In the case of 4-primer amplicon-seq, the strand of each read (top-CS2 or bottom-CS1) was also assigned at this step. The identity of the recombination site (loxP, attB, attP, attL or attR) was determined from the combination of bases specific to each site expected to be detected in read 1 and read 2.Total number of reads per barcode pair was taken as the readcount and the total number of unique UMIs detected was taken as the UMI count (df_group.py or df_group_4primers.py). In 4-primer amplicon-seq, the same shuffle cassette can result in two distinct amplicons. We collapsed reads coming from the same shuffle cassette based on the shared set of barcodes and summed up the read counts and UMI counts. Those barcode pairs where we did not detect both types of amplicons were discarded. In all cases, the barcode closest to CS2 was named barcode1 and the barcode closest to CS1 in the shuffle cassette was named barcode2.
Supplementary files format and content: Count of reads, UMIs per shuffle cassette barcode combination without normalization for sequencing depth.

source_name: Bl6xCast mESC

extract_protocol:
Qiagen DNA mini kit
We employed two different strategies for amplicon-seq library construction: 2-primer  and 4-primer. The major difference between these two strategies is that either 2 or 4 primers corresponding to the capture sequences were used to generate the PCR product. In the case of the 2-primer strategy, the P5 Illumina sequencing adapter can only come from the primer that binds CS2 and the P7 adapter can only come from the primer that binds CS1. This precludes identification of recombined shuffle cassettes that contain the same capture sequence on both sides of the loxPsym site. In the 4 primer strategy, primers with P5 and P7 adapters that bind to both CS2 and CS1 are included in the PCR. Theoretically, this would enable us to detect recombined shuffle cassettes with the same capture-sequence on both sides. Two rounds of PCR were performed on genomic DNA extracted from indicated samples to construct sequencing libraries. For the 2-primer experiments, we used 250 ng of genomic DNA prepared using the Qiagen DNeasy kit as input. PCR1 (UMI addition) was performed in a 50 μl reaction with Q5 Polymerase (NEB M0492S), with 2.5 μL of each 10 μM primer (oSP1008 and oSP997) with the following cycling parameters: 98°C - 5 min; 4 cycles of 98°C - 20s, 62°C - 20s, 72°C - 30s; 72°C - 60s. PCRs were cleaned up using AmpureXP beads (1X) and eluted in 11 μl of H2O. PCR2 (sample indexing and sequencing adapter addition) was again performed with Q5 Polymerase in a 50 μl reaction using 10 μl of eluate from the previous step as template and 2.5 μL of each 10 μM sample indexing primer. Progression of PCR2 was monitored in real-time using SYBR green dye and reactions were stopped before saturation (usually 15-18 cycles). Cycling conditions for PCR2:  98°C - 5 min; 15 cycles of 98°C - 10s, 65°C - 10s, 72°C - 20s. Reactions were cleaned up with AmpureXP beads (1X) and eluted in 12 μl of H2O. Sample quality was confirmed on a TapeStation D1000 ScreenTape (Agilent), after which reactions were pooled. Sequencing was performed on an Illumina NextSeq2000 100 cycle kit with the following read lengths: 69 read1, 6 index1, 10 index2 and 53 on read2. For the 4-primer experiments involving loxPsym+ mESCs, 100 ng of genomic DNA prepared using the Qiagen DNeasy kit as used as input. For the 4-primer experiments involving loxPsym+ K562, attB/P+ mESC and attB/P+ K562, 250ng of genomic DNA prepared using the Qiagen DNeasy kit was used as input. PCR1 was performed with a mix of 4 primers (oSP1008, oSP997, oSP1021 and oSP1022) with 0.125 μl of each primer at 100 μM per 50 μl reaction. The rest of the protocol was identical to the 2-primer workflow described above. Primer sequences: oSP1008_996_CS2_Nextera1_10N_F TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG NNNNNNNNNN CCTTAGCCGCTAATAGGTGAGC oSP1021_1014_CS1_Nextera1_10N_F TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG NNNNNNNNNN TTGCTAGGACCGGCCTTAAAGC oSP997_CS1_TruSeq2_R GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC TTGCTAGGACCGGCCTTAAAGC oSP1022_CS2_TruSeq_R GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT CCTTAGCCGCTAATAGGTGAGC

value: Bl6xCast mESC

tag: genotype


title: SA-Y-01-41_Lu


title: DIF_2_4599

source_name: Melanoma orthotopic tumour

value: Melanoma orthotopic tumour

value: DIF


title: ERT2CreERT2_NoTamoxifen_d5_rep1

description: Library name: SP000063


title: Huh7 cells, shKAT7_3

city: Lanzhou

first: He

last: Huang

address: Donggang Street

institute: Lanzhou university

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads
The clean reads were mapped to the reference genome using HISAT
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin solution at 37 °C in a humidified incubator containing 5% CO2

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer ’ s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’ s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China)

treatment_protocol: Huh7 cells were transfected with specific shRNAs targeting KAT7 or control shRNA

value: hepatocellular carcinoma cells

value: KAT7 knockdown


title: CreERT2_Tamoxifen_d3_rep1

description: Library name: SP000051


title: SA_Y_06_58_BL

value: blood


title: split ePE3 at multiple endogenous sites- Rep 1- I7


title: Huh7 cells, shKAT7_2


title: SA-Y-01-38_Lu

value: Fischer 344


title: Cre_NoTamoxifen_d5_rep1

description: Library name: SP000061


title: SA_Y_06_56_BL

value: 6 months


title: parental_rep4

description: Library name: SP000044


title: ERT2CreERT2_Tamoxifen_d5_rep1

description: Library name: SP000060


title: parental_rep3

description: Library name: SP000037


title: M_LPS_bio_rep_1

city: Memphis

first: Michael

middle: A

last: Dyer

state: Tennessee

address: 262 Danny Thomas

department: DNB

institute: St. Jude Children's Research Hospital

data_processing:
Read alignment to the reference genome was performed with STAR (version 2.7; PMID: 23104886) software. Gene level quantification was determined using RSEM (version 1.3.1 ; PMID: 21816040).
Assembly: mm10-mouse / GRCh38 – human
Supplementary files format and content: tab delimited text file with raw counts for each sample

source_name: retina

extract_protocol:
Retinal punches were dissolved in 800uL Trizol Reagent (Invitrogen #15596026). 200uL chloroform was added to each sample, inverted, incubated at room temperature for 3 minutes. Samples were then spun down at 12,000 3 g at 4 C for 15 min. The aqueous later was transferred to a new tube and 1uL glycogen and 500 uL isopropanol was added to each sample and mixed by vortex. Samples were incubated at room temperature for 10 minutes and spun down at 12,000 3 g at 4 C for 15 min. The isopropanol was removed and the pellet was washed twice with ice-cold 80% EtOH. The washed pellet was resuspened in water.
Libraries were constructed using Illumina library prep acording to manufacturer protocols

treatment_protocol: Retina were dissected from the eye cup in Retinal Explant Media (REM). 1.5mm punches were taken from each eye using a biopsy punchand were placed on a Nuclepore 1.0uM membrane floating on 2mL of REM in a 12-well dish. The retinal punches were incubated for 24 hours (37C, 5% CO2) for culture control retina. Punches were harvested after 24 hours.

value: retina

value: 24 hour culture in REM + 0.2ug/mL LPS


title: PIF_2_4599

value: PIF


title: SA-Y-01-37_Lu

value: male


title: split ePE3 at multiple endogenous sites- Rep 1- I8


title: 200ngBxb1_d3_rep2

description: Library name: SP000022


title: split ePE3 at multiple endogenous sites- Rep 1- I5


title: CreERT2_Tamoxifen_d5_rep1

description: Library name: SP000059


title: SA_Y_06_54_BL


title: 1ugBxb1_d3_rep2

description: Library name: SP000021


title: PIF_1_4599

value: Melanoma


title: SA_Y_06_63_BL

value: SILICA


title: Met_3_4599

value: Melanoma lung metastasis

value: Met


title: SA_Y_06_62_BL


title: split ePE3 at multiple endogenous sites- Rep 1- I4

value: HEK293T cell


title: CreERT2_NoTamoxifen_d3_rep1

description: Library name: SP000055

value: Bl6xCast mESC


title: split ePE3 at multiple endogenous sites- Rep 1- I3


title: SA_Y_06_53_BL

value: AIR


title: split ePE3 at multiple endogenous sites- Rep 1- I2


title: PBMC, AZ_vaccine with Pd, TCR02

city: Bundang-gu, Seongnam-si

first: Seong Jin

last: Choi

state: Gyeonggi-do

address: Dolma-ro, 172

department: Internal Medicine

country: South Korea

institute: Seoul National University Bundang Hospital

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
(scRNAseq + scTCRseq) Sequenced data were processed by the mkfastq function (Cell Ranger, 10x Genomics, v7.0) to produce fastq files.  (ATACseq) FASTQC (v0.11.9) is used to assess the quality of reads. Sequencing adaptors and low-quality reads are eliminated with skewer (v.0.2.2).
Assembly: (scRNAseq + scTCRseq) Fastq files were then aligned to the human reference genome (GRCh38), with further processing to generate feature-barcode matrices. (ATACseq) Reads are mapped on the hg19 reference genome with bowtie2 (v2.3.5.1) set to the “-very-sensitive” parameter. Aligned read duplicates are eliminated with MarkDuplicates function in PICARD (v 0.24.0). Aligned BAM files are converted into Tag Directory with makeTagDirectory command in HOMER (v 4.11), set size to ‘given’.
Supplementary files format and content: Single-cell sequencing data of ChAdOx1 vaccination patients without corticosteroids is stored in the following folders: 'VACCINE-1', 'VACCINE-2', 'VACCINE-3', 'VACCINE-4', 'VACCINE-5'. There are five patients (VAV01, VAV02, VAV03, VAV04, VAV05) and four time points (D0, D1, D3, D14). The composition of samples in each library is as follows:  VACCINE-1: VAV01-D0, VAV02-D0, VAV03-D0, VAV04-D0 VACCINE-2: VAV05-D0, VAV01-D1, VAV02-D1, VAV03-D1 VACCINE-3: VAV04-D1, VAV05-D1, VAV01-D3, VAV02-D3 VACCINE-4: VAV03-D3, VAV04-D3, VAV05-D3, VAV01-D14 VACCINE-5: VAV02-D14, VAV03-D14, VAV04-D14, VAV05-D14   Single-cell sequencing data of ChAdOx1 vaccination patients with corticosteroids is stored in the following folders: 'VACCINE-PD-D0', 'VACCINE-PD-D1'. There are three patients (VAVPD01, VAVPD02, VAVPD03) and two time points (D0, D1). The composition of samples in each library is as follows:  VACCINE-PD-D0: VAVPD01-D0, VAVPD02-D0, VAVPD03-D0 VACCINE-PD-D1: VAVPD01-D1, VAVPD02-D1, VAVPD03-D1

source_name: PBMC

extract_protocol:
PBMCs were isolated using Ficoll-Paque (GE Healthcare) density-gradient centrifugation.
(scRNAseq + scTCRseq) Sequencing libraries for single-cell and TCR sequencing were prepared using the Chromium Single Cell 5’ Library & Gel Bead Kit (v3.0) and the V(D)J Kit, Human T cell (v3.0) from 10X Genomics, following the manufacturers’ protocols.
(scRNAseq + scTCRseq) Sequencing was carried out on the Novaseq6000 platform (Illumina).  (ATACseq) Libraries were amplified for a total of 10–13 cycles and subjected to high-throughput sequencing on an Illumina Novaseq6000 Sequencer (single end).

value: PBMC

tag: patients

value: VAVPD1, VAVPD2, VAVPD3

value: Day 1

tag: sequencing

value: single cell TCR sequencing

value: ChAdOx1 vaccination + Corticosteroid


title: 200ngCre_d3_rep2

description: Library name: SP000019


title: Cre_NoTamoxifen_d3_rep1

description: Library name: SP000054


title: DIF_3_4599

value: Melanoma orthotopic tumour

value: DIF


title: 4ugCre_d3_rep2

description: Library name: SP000017


title: Lung_ILC2_ChIPseq_PBS_Mother

city: Fukuoka

first: Minako

last: Ito

address: 3-1-1 Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

description: 10x Genomics

data_processing:
Sequencing was then performed by Novaseq 6000 (Illumina) at the Laboratory for Research Support of the Institute of Bioregulatory Medicine, Kyushu University.
All sequencing reads after trimming by TrimGalore and Cutadapt were aligned to the mouse and genome sequences (mm10) using Bowtie 2 with the ‘-q -N 1 -L 25 --no-mixed --no-discordant’ options. After the removal of PCR duplicates using Sambamba with the parameters ‘markdup -r -t 2’. SAMtools was used to manipulate alignments in the SAM and BAM formats. For visualization of ChIP-seq using the Integrative Genomics Viewer, genome coverage tracks were generated using bamCoverage from deepTools with the parameters ‘--scaleFactor Scaling_factor --binSize 50 --normalizeUsing RPKM’.
Assembly: mm10
Supplementary files format and content: bigwig files and narrowPeak files

source_name: Lung

extract_protocol:
Lung tissues were digested in RPMI enzyme solution containing collagenase D (2 mg/ml), DNase I (0.1 mg/ml), and Dispase II (0.2 mg/ml, Roche 04942078001) at 37°C for 40 min (for adults) or 20 min (for fetuses). Digestion was performed by changing the solution every 20 min. And then, lung tissues were digested in RPMI enzyme solution containing collagenase D (2 mg/ml), DNase I (0.1 mg/ml), Dispase II (0.2 mg/ml) and Liberase TH (0.01 mg/ml, Roche 5401151001) at 37°C for 20 min. The digested samples were filtered through 70 µm strainers and suspended in 36% Percoll (Cytiva, 17-0891-01) diluted with RPMI, 72% Percoll diluted with PBS was injected into the bottom and centrifuged at 800 × g for 20 min at 25°C. Cells were collected in the interlayer between 36% and 72% Percoll, washed with RPMI supplemented with FBS (2% v/v), and stained for flow cytometry. In fetal lung cell collection, ILC2 (CD45+, Lin-, ST2+), immune cells (CD45+) and epithelial cells (EpCAM+) were purified using FACSMelody (BD Biosciences).
Snap frozen cell pellets from approximately 3,000 ILC2 with 2-3 µL carryover were lysed by 17 µL of cold Nuclei EZ lysis buffer (Sigma, NUC-101) supplemented with complete EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride. Then, 1 µL of 1% Triton X-100 (Merck 93443) and 1% deoxycholate (Nacalai, 10712-54) mixture solution was added to the samples, and sit on ice for 5 min. The chromatin was fragmented by 4 U/µl MNase (M0247S, NEB) in 1xMNase buffer supplemented with 1% PEG6000 (HAMPTON RESEARCH, HR2-533) and 2 mM DTT (Nacalai) at 37C for 7.5 min. The MNase reaction was stopped by adding 1/10 volume of 100 mM EDTA and 1/12 volume of the 1% Triton X-100 and 1% deoxycholate mixture, and the samples were rest on ice for 15 min. The chromatin lysates were then added with freshly prepared immunoprecipitation buffer (Brind’Amour et al. 2015), and 5% volume was kept for input library construction. To the rest of the lysate, 30 ng of annealed I-SceI carrier DNA was added (Zhu et al. 2021). The forward and reverse strands of the carrier DNA were as follows: /5AmMC6/Gtagggataacagggtaattagggataacagggtaattagggataacagggtaattagggataacagggtaattagggataacagggtaattagggat aacagggtaat*c/3AmMO/ and /5AmMC6/Gattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatcc cta*c/3AmMO/, respectively, where asterisks represent phosphorothioate bonds. The oligos were synthesized by Integrated DNA Technologies. For each immunoprecipitation reaction, 0.25 µL of rabbit anti-H3K4me3 (Active Motif 39159) antibody conjugated to precleared Dynabeads Protein A (Thermo Fisher Scientific, 10006D) and G (Thermo Fisher Scientific, 10007D) mixture was used. After immunoprecipitation at 4C overnight, the chromatin-Dynabeads were washed twice each by the low and high salt wash buffers, and the chromatin was eluted in the freshly prepared ChIP elution buffer at 65C for 1 hr (Brind’Amour et al. 2015). DNA was recovered by phenol-chloroform extraction followed by ethanol precipitation. Adaptor ligation was performed by NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB) in a half scale of the manufacturer’s instruction, and the libraries were purified by 1.8x SPRIselect beads (B23318, Beckman Coulter). The DNA was amplified by KAPA Hifi 2X mater PCR mix (KK2605) for 16 PCR cycles with dual indexing primers (NEBNext Multiplex Oligos for Illumina, E6440). After purification with 0.9x SPRIselect beads, the samples were digested by I-SceI (5 U/µl, NEB, R0694) 37C for 2 hrs followed by heat inactivation at 65C for 20 min and purified by 0.9x SPRIselect beads. The second amplification was not performed.

treatment_protocol: Female mice aged 6-8 weeks were sensitized by intraperitoneal administration of 200 µL PBS/alum (Thermo, Imject Alum, 77161) containing alum (25 µL) or 200 µL PBS/alum containing OVA (100 µg) (Sigma, A5503) and alum (25 µL) on day -21 and day -7. After the second sensitization, sensitized female mice were bred to untreated male mice. Pregnant mice were given OVA (20 µL PBS containing 500 µg OVA) or PBS intranasally every 2-3 days from day 4 to day 17 of gestation. Lung ILC2 from 7-9 week old offspring were collected.

value: Lung

tag: time

value: 8 weeks old

tag: chip antibody

value: anti-H3K4me3 (Active Motif 39159)

value: adult lung from PBS-tregated mothers


title: SA_Y_06_59_BL

value: blood

value: Fischer 344

value: 6 months

value: SILICA

value: male


title: parental_rep2

description: Library name: SP000016

value: Bl6xCast mESC


title: PBMC, AZ_vaccine, TCR04

description: 10X Genomics

value: PBMC

value: VAV3, VAV4, VAV5, VAV1

value: Day 3 (VAV3, VAV4, VAV5), D14 (VAV1)

value: ChAdOx1 vaccination


title: 200ngBxb1_d3_rep1

description: Library name: SP000015


title: SA_Y_01_45_BL

value: 1 day


title: PIF_3_4599

value: Melanoma orthotopic tumour

value: Melanoma

value: PIF


title: Huh7 cells, shKAT7_1

value: hepatocellular carcinoma cells

value: KAT7 knockdown


title: SA_Y_06_55_BL

value: AIR


title: Huh7 cells, shCtrl_3

value: WT

value: shCtrl


title: DIF_1_4599

value: DIF


title: PBMC, AZ_vaccine, TCR01

description: 10X Genomics

value: VAV1, VAV2, VAV3, VAV4

value: Day 0

value: single cell TCR sequencing


title: TB_3_4599

value: TB


title: Huh7 cells, shCtrl_2


title: 4ugBxb1_d3_rep1

description: Library name: SP000013

value: Bl6xCast mESC


title: Huh7 cells, shCtrl_1


title: 4ugBxb1_d3_rep2

description: Library name: SP000020


title: TB_2_4599


title: PBMC, AZ_vaccine with Pd, GE02

description: 10X Genomics

value: PBMC

value: VAVPD1, VAVPD2, VAVPD3

value: Day 1

value: single cell RNA sequencing

value: ChAdOx1 vaccination + Corticosteroid


title: TB_1_4599

value: Melanoma orthotopic tumour

value: Melanoma


title: SA_Y_06_51_BL

value: blood

value: Fischer 344

value: 6 months

value: male


title: E18_OVA_scATACseq

description: 10x Genomics

data_processing:
Sequencing was then performed by Novaseq 6000 (Illumina) at the Laboratory for Research Support of the Institute of Bioregulatory Medicine, Kyushu University.
From the NGS read data, FASTQ files were generated by CellRanger Arc mkfastq, and then integrated with ATAC and Gene Expression the were generated by Cell Ranger Arc (v2.0.1, 10x Genomics).
Assembly: mm10/EnsDb.Mmusculus.v79
Supplementary files format and content: tsv files and mtx files

extract_protocol:
Lung tissues were digested in RPMI enzyme solution containing collagenase D (2 mg/ml), DNase I (0.1 mg/ml), and Dispase II (0.2 mg/ml, Roche 04942078001) at 37°C for 40 min (for adults) or 20 min (for fetuses). Digestion was performed by changing the solution every 20 min. And then, lung tissues were digested in RPMI enzyme solution containing collagenase D (2 mg/ml), DNase I (0.1 mg/ml), Dispase II (0.2 mg/ml) and Liberase TH (0.01 mg/ml, Roche 5401151001) at 37°C for 20 min. The digested samples were filtered through 70 µm strainers and suspended in 36% Percoll (Cytiva, 17-0891-01) diluted with RPMI, 72% Percoll diluted with PBS was injected into the bottom and centrifuged at 800 × g for 20 min at 25°C. Cells were collected in the interlayer between 36% and 72% Percoll, washed with RPMI supplemented with FBS (2% v/v), and stained for flow cytometry. In fetal lung cell collection, ILC2 (CD45+, Lin-, ST2+), immune cells (CD45+) and epithelial cells (EpCAM+) were purified using FACSMelody (BD Biosciences).
The nuclei were isolated according to the protocol of “Nuclei Isolation from Embroynic Mouse Brain for Single Cell Multiome ATAC + Gene Expression Sequencing, Protocol 1” (10x Genomics, CG000366). Briefly, cells were centrifuged at 500 × g for  5 min at 4°C and removed the supernatant. The pellets were added 100 µl chilled Lysis Buffer (1 mM Tris-HCl (pH 7.4), 1 mM NaCl, 0.3 mM MgCl2, 0.01% Tween-20, 0.01% Nonidet P40 Substitute, 0.001% Digitonin, 0.1% BSA, 0.1 mM DTT, 0.1 U/µl RNase inhibitor), and incubated for 5 min on ice. The lysed cells were washed by 1ml chilled Wash Buffer three times. Libraries were prepared according to the protocol of Chromuim Next GEM Single Cell Multiome ATAC + Gene Expression Kit using a Chromium controller (10x Genomics). Briefly, GEMs were first generated by Master Mix with barcoded Single Cell Multiome Gel Beads (10x Genomics, PN-1000285), neuclei and distribution to Oil to Chromium Next GEM Chip J (PN-1000230). Barcoded cDNA was then generated from the GEM. This cDNA was amplified by PCR reaction to generate Gene Expression library and ATAC library (10x Genomics, PN-1000212, PN-1000215).

treatment_protocol: Female mice aged 6-8 weeks were sensitized by intraperitoneal administration of 200 µL PBS/alum (Thermo, Imject Alum, 77161) containing alum (25 µL) or 200 µL PBS/alum containing OVA (100 µg) (Sigma, A5503) and alum (25 µL) on day -21 and day -7. After the second sensitization, sensitized female mice were bred to untreated male mice. Pregnant mice were given OVA (20 µL PBS containing 500 µg OVA) or PBS intranasally every 2-3 days from day 4 to day 17 of gestation. For fetal analysis, the mother was sacrificed and the fetal lungs were collected on gestation days 18. For the analysis of adult offspring, HDM (20 µL PBS containing 10 µg HDM) or PBS was administered intranasally to 7-9 week old offspring for five consecutive days. The day after final challenge, the lungs were collected.

value: Lung

value: ILC2, immune cells, epthelial cells, fibroblasts

value: Wild type

value: feral lung from OVA-tregated mothers


title: PBMC, AZ_vaccine with Pd, TCR01

description: 10X Genomics

value: Day 0

value: single cell TCR sequencing


title: PBMC, AZ_vaccine with Pd, GE01

description: 10X Genomics

value: PBMC


title: 1ugCre_d3_rep2

description: Library name: SP000018

value: Bl6xCast mESC


title: Lung_ILC2_ChIPseq_OVA_Mother

description: 10x Genomics

value: 8 weeks old

value: anti-H3K4me3 (Active Motif 39159)

value: adult lung from OVA-tregated mothers


title: SA_Y_01_48_BL

value: 1 day

value: SILICA


title: PBMC, AZ_vaccine, TCR05

description: 10X Genomics

value: VAV2, VAV3, VAV4, VAV5

value: Day 14

value: ChAdOx1 vaccination


title: SA_Y_06_52_BL

value: blood

value: Fischer 344

value: 6 months

value: AIR

value: male


title: SA_Y_01_47_BL


title: 200ngCre_d3_rep1

description: Library name: SP000012


title: E18_OVA_snRNAseq

description: 10x Genomics

data_processing:
Sequencing was then performed by Novaseq 6000 (Illumina) at the Laboratory for Research Support of the Institute of Bioregulatory Medicine, Kyushu University.
From the NGS read data, FASTQ files were generated by CellRanger Arc mkfastq, and then integrated with ATAC and Gene Expression the were generated by Cell Ranger Arc (v2.0.1, 10x Genomics).
Assembly: mm10
Supplementary files format and content: tsv files and mtx files

extract_protocol:
Fetal lung tissues were digested in RPMI enzyme solution containing collagenase D (2 mg/ml), DNase I (0.1 mg/ml), and Dispase II (0.2 mg/ml, Roche 04942078001) at 37°C for 20 min. And then, lung tissues were digested in RPMI enzyme solution containing collagenase D (2 mg/ml), DNase I (0.1 mg/ml), Dispase II (0.2 mg/ml) and Liberase TH (0.01 mg/ml, Roche 5401151001) at 37°C for 20 min. The digested samples were filtered through 70 µm strainers and suspended in 36% Percoll (Cytiva, 17-0891-01) diluted with RPMI, 72% Percoll diluted with PBS was injected into the bottom and centrifuged at 800 × g for 20 min at 25°C. Cells were collected in the interlayer between 36% and 72% Percoll, washed with RPMI supplemented with FBS (2% v/v), and stained for flow cytometry. In fetal lung cell collection, ILC2 (CD45+, Lin-, ST2+), immune cells (CD45+) and epithelial cells (EpCAM+) were purified using FACSMelody (BD Biosciences).
The nuclei were isolated according to the protocol of “Nuclei Isolation from Embroynic Mouse Brain for Single Cell Multiome ATAC + Gene Expression Sequencing, Protocol 1” (10x Genomics, CG000366). Briefly, cells were centrifuged at 500 × g for  5 min at 4°C and removed the supernatant. The pellets were added 100 µl chilled Lysis Buffer (1 mM Tris-HCl (pH 7.4), 1 mM NaCl, 0.3 mM MgCl2, 0.01% Tween-20, 0.01% Nonidet P40 Substitute, 0.001% Digitonin, 0.1% BSA, 0.1 mM DTT, 0.1 U/µl RNase inhibitor), and incubated for 5 min on ice. The lysed cells were washed by 1ml chilled Wash Buffer three times. Libraries were prepared according to the protocol of Chromuim Next GEM Single Cell Multiome ATAC + Gene Expression Kit using a Chromium controller (10x Genomics). Briefly, GEMs were first generated by Master Mix with barcoded Single Cell Multiome Gel Beads (10x Genomics, PN-1000285), neuclei and distribution to Oil to Chromium Next GEM Chip J (PN-1000230). Barcoded cDNA was then generated from the GEM. This cDNA was amplified by PCR reaction to generate Gene Expression library and ATAC library (10x Genomics, PN-1000212, PN-1000215).
snRNA-seq

treatment_protocol: Female mice aged 6-8 weeks were sensitized by intraperitoneal administration of 200 µL PBS/alum (Thermo, Imject Alum, 77161) containing alum (25 µL) or 200 µL PBS/alum containing OVA (100 µg) (Sigma, A5503) and alum (25 µL) on day -21 and day -7. After the second sensitization, sensitized female mice were bred to untreated male mice. Pregnant mice were given OVA (20 µL PBS containing 500 µg OVA) or PBS intranasally every 2-3 days from day 4 to day 17 of gestation. For fetal analysis, the mother was sacrificed and the fetal lungs were collected on gestation days 18.

value: Lung

value: ILC2, immune cells, epthelial cells

value: Wild type

value: feral lung from OVA-tregated mothers


title: PBMC, AZ_vaccine, GE04

description: 10X Genomics

value: PBMC

value: VAV3, VAV4, VAV5, VAV1

value: Day 3 (VAV3, VAV4, VAV5), D14 (VAV1)

value: single cell RNA sequencing


title: parental_rep1

description: Library name: SP000009

value: Bl6xCast mESC


title: E18_Lung_scRNAseq_Tag

description:
10x Genomics
HashTag

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: tsv files and mtx files

extract_protocol:
For the preparation of lung immune cells for flow cytometry analysis and scRNA-seq, lung tissue was digested in RPMI enzyme solution containing collagenase D (2 mg/ml, Roche, 11088882001) and DNase I (0.1 mg/ml, Roche, 10104159001) at 37°C for 60 min (for adults) or 40 min (for fetuses). Digestion was performed by changing the solution every 20 min. The digested samples were filtered through 70 µm strainers and suspended in 36% Percoll (Cytiva, 17-0891-01) diluted with RPMI, 72% Percoll diluted with PBS was injected into the bottom and centrifuged at 800 × g for 20 min at 25°C. Cells were collected in the interlayer between 36% and 72% Percoll, washed with RPMI supplemented with FBS (2% v/v), and stained for flow cytometry. The tags were assigned as follows: C0301, fetal lung from DEX-treated mother 1; C0302, fetal lung from DEX-treated mother 2; C0307, fetal lung from PBS-treated mother 1; C0308, fetal lung from PBS-treated mother 2. ILC2s (FVD-CD45+Lin- ST2+) were purified by FACSMelody (BD Biosciences).
Libraries were prepared according to the protocol of Chromuim Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) (10x Genomics, PN-1000263) using a Chromium controller (10x Genomics). Briefly, GEMs were first generated by Master Mix with barcoded Single Cell VDJ 5' Gel Beads, cells and distribution to Oil to Chromium Next GEM Chip K (10x Genomics, PN-1000286). Barcoded cDNA was then generated from the GEM. This cDNA was amplified by PCR reaction to generate, 5' Gene Expression library and Feature Barcode library (10x Genomics, PN-1000190, -1000256, -1000215, and -1000250). Sequencing was then performed by Novaseq 6000 (Illumina).

treatment_protocol: For DEX administration, untreated 9-week-old pregnant mice were obtained and DEX was administered in drinking water from day 12 of gestation (DEX was dissolved in PBS to a concentration of 10 mg/ml and further diluted to 1.3 µg/ml in drinking water). Fetal lungs were harvested on gestation day 18 from each of two mice that had received water containing DEX or PBS since gestation day 12. Fetal lungs (DEX-1, n = 8; DEX-2, n = 9; PBS-1, n = 5; PBS-2, n = 8) were pooled per sample.

value: feral lung from DEX- or PBS-tregated mothers


title: SA_Y_01_39_BL

value: 1 day


title: SA_Y_01_46_BL

value: SILICA


title: PBMC, AZ_vaccine, TCR03

description: 10X Genomics

value: VAV4, VAV5, VAV1, VAV2

value: Day 1 (VAV4, VAV5), Day 3 (VAV1, VAV2)

value: single cell TCR sequencing

value: ChAdOx1 vaccination


title: PBMC, AZ_vaccine, GE02

description: 10X Genomics

value: VAV5, VAV1, VAV2, VAV3

value: Day 0 (VAV5), D1 (VAV1, VAV2, VAV3)


title: SA_Y_01_38_BL

value: blood

value: Fischer 344

value: AIR

value: male


title: BMMs, RANKL+NVP-BHG712 2, Day2

city: Jinan

first: Yueran

last: Zhao

state: Shandong

address: 44 Wenhua West Road

department: Center for Reproductive Medicine

institute: Shandong University

data_processing:
Store raw data in fastq file format. HISTA2 software was used for sequence alignment with the reference genome, and StringTie software was used to assemble and quantify the reads on the pair. The alignment results of transcriptome sequencing Reads and the reference genome sequence were stored in BAM format.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts values for each Sample
Supplementary files format and content: tab-delimited text files includes FPKM values for each Sample

source_name: Bone marrow

growth_protocol: Bone marrow macrophages were maintained in αMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using trizol.5μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Osteoclastogenic differentiation was inducdced by M-CSF for 3days . Cells were treated with RANKL or RANKL +NVP-BHG712 for 2days.

value: Bone marrow

value: BMM

value: Macrophage

value: WT


title: 1ugBxb1_d3_rep1

description: Library name: SP000014

value: Bl6xCast mESC


title: Adult_OVA_scATACseq

description: 10x Genomics

value: Lung

value: 8 weeks old

value: ILC2, immune cells, epthelial cells, fibroblasts

value: Wild type

value: adlut lung from OVA-tregated mothers


title: NF1KOAE6_TDM1_3

city: Milan

first: Luca

last: Mazzarella

state: M

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: IEO European Institute of Oncology IRCCS

data_processing:
Translational Oncology lab custom RNA-Seq pipeline
Alignment performed with STAR (command: STAR --genomeDir $genomeDir --readFilesIn $workdir/$d/${d}_R1.fastq.gz $workdir/$d/${d}_R2.fastq.gz --outFileNamePrefix $workdir/$d/${d}_ --runThreadN 12)
SAM file were processed with htseq-count to obtain count files (command: htseq-count -f sam -m intersection-strict -s reverse -t exon -i gene_id -r pos ${d}_Aligned.out.sorted.sam $gtfFileUCSC > ${d}_strict_counts.txt)
To obtain the degs data were processed using DESeq2 R package
Assembly: hg19
Supplementary files format and content: tab-delimeted text file with DESeq2 differential expressed genes

extract_protocol:
RNA extraction was performed using QIAGEN RNeasy Kit (Qiagen) following the manufacturer ’s protocol. Then RNA Integrity Number (RIN) was measured using Agilent 2100 bio-Analyzer. Qubit RNA Assay Kits were used to measure RNA concentration.
mRNA-seq libraries were prepared according to the TruSeq low sample protocol (Illumina, San Diego, CA, USA), starting with 1 µg of total RNA per sample.

value: Breast Cancer

value: KO

tag: agent

tag: batch

value: RNP


title: SA_Y_01_44_BL

value: blood

value: 1 day

value: SILICA


title: S3012

city: Helsinki

first: Fred

last: Asiegbu

address: Latokartanonkaari 7

country: Finland

institute: University of Helsinki

data_processing:
All samples need to pass through the following three steps before library construction
mRNA  is enriched using oligo(dT) beads. The mRNA  is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase.
The original raw data from Illumina are transformed to Sequenced Reads by base calling
Raw reads are filtered to remove reads with adapter contamination or reads with low quality. Only clean reads were used in the downstream analyses.
Perform alignments with HISAT2 to the reference
Genome_build: Pabies01
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Picea abies

source_name: Norway spruce needles

extract_protocol:
Needles were flash frozen in liquid nitrogen, and RNA was harvested using CTAB reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: clone

tag: age

value: 3 years

value: needles


title: PBMC, AZ_vaccine, TCR02

description: 10X Genomics

tag: tissue

value: PBMC

value: VAV5, VAV1, VAV2, VAV3

value: Day 0 (VAV5), D1 (VAV1, VAV2, VAV3)

value: single cell TCR sequencing

value: ChAdOx1 vaccination


title: S3313


title: E18_Lung_scRNAseq_GEX

description:
10x Genomics
GEX

value: Lung

value: feral lung from DEX- or PBS-tregated mothers


title: S1611


title: SA_Y_01_43_BL

tag: strain

value: Fischer 344

value: male


title: R1528


title: SA_Y_01_42_BL

tag: time point

value: AIR


title: BMMs, RANKL 2, Day2

value: Bone marrow

value: BMM

value: Macrophage

value: WT

tag: treatment

value: osteoclastogenic


title: BMMs, RANKL 1, Day2


title: FSDE_FSDE_294_27

data_processing:
Basecalls were performed using bcl2fastq/2.19.
Sequence reads were trimmed using Trim Galore!, Cutadapt 3.4 and Trimgalore 0.6.7 using Nextflow 22.10.6 and the nf-core/rnaseq 3.12.0 pipeline.
All sequences were aligned to the Rattus norvegicus Rnor 6.0 genome from Ensembl downloaded from igenomes using Star 2.6.1d within  Nextflow 22.10.6 and the nf-core/rnaseq 3.12.0 pipeline.
Raw gene counts were assigned using Salmon 1.10.1 and Sammtools 1.17 within Nextflow 22.10.6 and the nf-core/rnaseq 3.12.0 pipeline.
Assembly: Rnor6.0
Supplementary files format and content: CSVt file including abundance measurements (raw counts) in a matrix containing all samples

growth_protocol: Healthy male Sprague-Dawley rats (Hilltop Lab Animals, Scottdale, PA), weighing 200-250 g were used in this study which was conducted in an Association for Assessment and Accreditation of Laboratory Animal Care International approved animal facility (NIOSH, Morgantown, WV) following a protocol approved by the Animal Care and Use Committee. The rats were housed in pairs and maintained on a 12-hour light-dark cycle in a temperature (68-72oF) and humidity (30-70%) controlled room with free access to filtered tap water and HaCXan Teklad Global 18% protein rodent diet (Harlan Teklad; Madison, WI).

extract_protocol:
Total RNA was isolated from a piece of the lung tissue using the RNeasy Fibrous Mini Kit (Qiagen, Inc, Valencia, CA) following the procedure provided by the manufacturer.
Next generation sequencing libraries prepared using TruSeq® Stranded mRNA Library Prep Kit (Illumina, Inc, San Diego, CA) were used in the sequencing.

treatment_protocol: The rats were exposed by whole-body inhalation to filtered air or DEP at concentrations 1.0 mg/m3 combined with FSD at concentrations of 30 mg/m3, 6 hours/day for 4 days.

value: lung

value: Sprague-Dawley

tag: time (days)

value: 30 mg/m3 fracking sand dust + 1.0 mg/m3 of diesel particles


title: NF1KOAE6_TDM1_1

tag: cell line

value: Breast Cancer

value: KO

value: RNP


title: 1ugCre_d3_rep1

description: Library name: SP000011

value: Bl6xCast mESC


title: E18_PBS_scATACseq

description: 10x Genomics

value: Lung

tag: cell type

value: ILC2, immune cells, epthelial cells, fibroblasts

value: Wild type

value: feral lung from PBS-tregated mothers


title: Adult_PBS_scATACseq

description: 10x Genomics

value: 8 weeks old

value: adlut lung from PBS-tregated mothers


title: NF1KOAE6_ctrl_2

value: untreated


title: SA_Y_01_41_BL

value: blood

value: Fischer 344

value: 1 day

value: AIR

tag: Sex

value: male


title: PBMC, AZ_vaccine, GE05

description: 10X Genomics

value: PBMC

value: VAV2, VAV3, VAV4, VAV5

value: Day 14

value: single cell RNA sequencing

value: ChAdOx1 vaccination


title: 4ugCre_d3_rep1

description: Library name: SP000010

value: Bl6xCast mESC

tag: genotype


title: SA_Y_01_40_BL


title: SWT_veh_biol rep 3

city: Shenzhen

first: Aolin

last: Yang

address: 66 Gongchang Road

institute: Sun Yat-sen University

data_processing:
Reads were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to rRNA database. The rRNA mapped reads then will be removed.
Paired-end clean reads were mapped Ensembl_release107 using HISAT2. 2.4
Assembly: Ensembl_release107
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: gastrocnemius

growth_protocol: All mice were maintained group-housed under specific pathogen free (SPF) conditions with a 12h/12h light dark cycle at 23°C with free access to food and water at the Laboratory Animal Center of SUN YAT-SEN UNIVERSITY, China.

extract_protocol:
RNA was extracted from liver or gastrocnemius with Total RNA Extraction Reagent.
RNA library for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacture's protocols.

treatment_protocol: SWT and SKO mice were treated 3 times per week with Calcipotriol or vehicle for 20 weeks.

value: gastrocnemius

value: vehicle


title: FSDE_FSDE_291_27

value: lung

value: Sprague-Dawley

value: 30 mg/m3 fracking sand dust + 1.0 mg/m3 of diesel particles


title: PBMC, AZ_vaccine, GE03

description: 10X Genomics

tag: patients

value: VAV4, VAV5, VAV1, VAV2

value: Day 1 (VAV4, VAV5), Day 3 (VAV1, VAV2)


title: BMMs, RANKL+NVP-BHG712 3, Day2

value: Bone marrow

value: BMM

value: Macrophage

value: WT


title: SWT_veh_biol rep 2

value: male

value: Wild type


title: S1623

value: 3 years

value: needles


title: SA_Y_01_37_BL

value: blood

value: Fischer 344

value: 1 day

value: AIR


title: PBMC, AZ_vaccine, GE01

description: 10X Genomics

value: PBMC

value: VAV1, VAV2, VAV3, VAV4

value: Day 0

tag: sequencing

value: single cell RNA sequencing

value: ChAdOx1 vaccination


title: E18_PBS_snRNAseq

description: 10x Genomics

value: Lung

tag: time

value: ILC2, immune cells, epthelial cells

value: feral lung from PBS-tregated mothers


title: BMMs, RANKL+NVP-BHG712 1, Day2

value: Bone marrow

value: BMM

value: Macrophage

value: WT


title: FSDE_FSDE_296_27

value: lung

value: Sprague-Dawley

value: 30 mg/m3 fracking sand dust + 1.0 mg/m3 of diesel particles


title: NF1KO3_TDM1_3

value: Breast Cancer

value: KO

value: P


title: BMMs, RANKL 3, Day2

value: osteoclastogenic


title: FSDE_FSDE_295_27


title: NF1KOAE6_TDM1_2

value: RNP


title: SWT_veh_biol rep 1

value: gastrocnemius

value: male

value: Wild type

value: vehicle


title: NF1KO3_TDM1_2


title: FSDE_FSDE_289_27


title: AIR_FSDE_288_27

value: air


title: FSDE_FSDE_293_27


title: R3037

value: 3 years

value: needles


title: FSDE_FSDE_292_27


title: SKO_veh_biol rep 3

value: SOD1 knockout


title: scRNASeq

city: Houston

first: Benjamin

middle: R

last: Schrank

state: TX

address: 1400 Pressler St

institute: MD Anderson Cancer Center

description: Cells from three treatmen groups were barcoded, pooled and captured in the same chip lane. One library is generated and later were demultiplexed by CellRanger

data_processing:
The alignment, barcodeing process, and gene counting were made using CellRanger 7.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-flex-multi-frp)
Assembly: mm10
Supplementary files format and content: tabs-separated values files and matrix files

source_name: mammary

growth_protocol: Orthotopic mammary fat pad tumours were established by injecting mouse breast cancer cells EO771 in C57BL/6J mice,  at 1×10^6 cells in 50μl PBS per mouse..

extract_protocol:
Tumour tissues were prepared for Single Cell Fixed RNA profiling following manufacturer instructions (10X Genomics, product no. 1000414).
Chromium Fixed RNA Profiling Reagent Kits (CG000527)

treatment_protocol: EO771 tumour-bearing C57BL6 female mice were treated with 25microgram of IgG, anti-CD47, or CD47-LLO via intratumoural injection on days 10, 12, and 14 post tumour inoculation. On day 16, mice were euthanized, and tumours were excised, cut into small pieces, and filtered into a single cell suspension following manufacturer instructions. Single cell suspensions were labelled with AQUA and anti-CD45-PE, and fixed per manufacturer instructions. Fluorescence-activated cell sorting collected 100,000 AQUA negative CD45-PE+ cells per tumour. Four tumours were collected per treatment condition which were pooled into three samples for scRNA-seq analysis.

value: mammary

value: mammary carcinoma cell line

value: WT

value: IgG, CD47, CD47-LLO


title: FFPE kidney allograft, Normal, n4

city: Pittsburgh

first: Elodie

last: Bailly

state: PA

address: BST 200 lothrop street

department: Surgery

institute: Starzl Transplant Institute

description: Illumina NSQ 500/550 Mid Output KT v2.5 (150 CYS) kit (FC-404-2001)

data_processing:
Demultiplexing and FASTQ file generation was carried out via Illumina Sequencing Analysis Viewer.
Stranded reads were checked for quality using FastQC (v0.11.5) and they were trimmed for quality and adapters using Cutadapt (v1.12).
Each sample was mapped to the Homo Sapien Ensembl reference genome GRCh38 using the fast alignment tool HISAT2 v2.1.0 with default settings
Genes in GRCh38 were quantified by HTSeq v0.9.0 using default settings
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include counts for each sample

source_name: Kidney allograft

extract_protocol:
Formalin fixed paraffin embedded (FFPE) biopsy tissue section was cut in 14uM thick, then Qiagen RNeasy® FFPE Kit (Cat# 73504) was used to extract total RNA.
Stranded RNAseq libraries were prepared from 40ng of RNA using the SMARTer Stranded Total RNA-Seq Kit v2 (cat# 634413) from Takara Bio USA, Inc. following manufacturer’s instructions. During this process depletion of ribosomal cDNA is carried out with ZapR v2 and R-Probes v2. Prior to denaturation and dilution for sequencing libraries were pooled at a concentration of 4 nM.

value: Kidney allograft

tag: developmental stage

value: adult

value: M

value: F

tag: time post transplantation (month)

tag: anti-hla donor specific antibodies

value: no

tag: diagnosis

tag: disease state

value: Stable, DSA-, C4d negative

tag: banff type

value: Negative

tag: glomerulitis

tag: peritubular capillaritis

tag: interstitial inflammation

tag: tubulitis

tag: intimal arteritis

tag: transplant glomerulopathy

tag: mesangial matrix increase

tag: interstitial fibrosis

tag: tubular atrophy

tag: chronic vasculopathy

tag: arteriolar hyaline thickening

tag: c4d score


title: R1316

tag: clone

tag: age

tag: tissue


title: AIR_FSDE_285_27

value: lung

tag: strain

value: Sprague-Dawley

tag: time (days)

tag: treatment


title: FFPE kidney allograft, TCMR, n9

tag: developmental stage

tag: time post transplantation (month)

tag: anti-hla donor specific antibodies

tag: diagnosis

tag: disease state

value: Acute TCMR, Banff 1A

tag: banff type

tag: glomerulitis

tag: peritubular capillaritis


title: R291

value: 3 years


title: NF1KOAE6_ctrl_3

tag: cell line

tag: cell type

value: Breast Cancer

tag: genotype

value: KO

tag: agent

value: untreated

tag: batch

value: RNP


title: NF1KOAE6_ctrl_1


title: FSDE_FSDE_290_27

tag: tissue

value: 30 mg/m3 fracking sand dust + 1.0 mg/m3 of diesel particles


title: mock_TDM1_3

value: WT


title: FFPE kidney allograft, TCMR, n8

value: Kidney allograft

tag: interstitial inflammation

tag: tubulitis

tag: intimal arteritis

tag: transplant glomerulopathy

tag: mesangial matrix increase

tag: interstitial fibrosis

tag: tubular atrophy

tag: chronic vasculopathy

tag: arteriolar hyaline thickening

tag: c4d score


title: FFPE kidney allograft, Normal, n5

tag: developmental stage

value: adult

tag: time post transplantation (month)

tag: anti-hla donor specific antibodies

tag: diagnosis

tag: disease state

tag: banff type

tag: glomerulitis

tag: peritubular capillaritis


title: FFPE kidney allograft, Normal, n6

tag: tissue

value: M

tag: interstitial inflammation

tag: tubulitis

value: X


title: SKO_veh_biol rep 1

value: gastrocnemius

tag: strain

tag: Sex

value: male

tag: genotype

value: SOD1 knockout

tag: treatment

value: vehicle


title: SWT_Cal_biol rep 3

value: Wild type

value: Calcipotriol


title: SKO_veh_biol rep 2


title: mock_TDM1_2

tag: cell line

tag: cell type

tag: agent

tag: batch


title: NF1KO3_TDM1_1

value: P


title: FFPE kidney allograft, Normal, n3

tag: developmental stage

value: F

tag: time post transplantation (month)

tag: anti-hla donor specific antibodies

value: no

value: Stable, DSA-, C4d negative

value: Negative

tag: intimal arteritis

tag: transplant glomerulopathy

tag: mesangial matrix increase

tag: interstitial fibrosis

tag: tubular atrophy

tag: chronic vasculopathy

tag: arteriolar hyaline thickening

tag: c4d score


title: AIR_FSDE_282_27

tag: tissue

value: lung

tag: strain

value: Sprague-Dawley

tag: time (days)

value: air


title: AIR_FSDE_287_27

tag: treatment


title: SWT_Cal_biol rep 2

tag: Sex

tag: genotype


title: NF1KO3_ctrl_3

tag: cell line

tag: cell type

value: Breast Cancer

value: KO

tag: agent

value: untreated

tag: batch


title: FFPE kidney allograft, Normal, n2

value: Kidney allograft

tag: developmental stage

value: adult

value: M

tag: time post transplantation (month)

tag: anti-hla donor specific antibodies

tag: diagnosis

tag: disease state

tag: banff type

tag: glomerulitis

tag: peritubular capillaritis

tag: interstitial inflammation

tag: tubulitis

tag: intimal arteritis

tag: transplant glomerulopathy


title: SWT_Cal_biol rep 1

tag: tissue

value: gastrocnemius

tag: strain

tag: Sex

value: male

tag: genotype

tag: treatment


title: SKO_Cal_biol rep 1

value: SOD1 knockout

value: Calcipotriol


title: AIR_FSDE_286_27

tag: time (days)


title: NF1KO3_ctrl_2

tag: cell line

tag: cell type

tag: agent

tag: batch

value: P


title: FFPE kidney allograft, Normal, n1

tag: developmental stage

value: F

tag: time post transplantation (month)

tag: anti-hla donor specific antibodies

value: no

tag: diagnosis

tag: disease state

tag: banff type

tag: mesangial matrix increase

tag: interstitial fibrosis

tag: tubular atrophy

tag: chronic vasculopathy

tag: arteriolar hyaline thickening

tag: c4d score


title: NF1KO3_ctrl_1

tag: genotype


title: AIR_FSDE_284_27

tag: tissue

tag: strain

tag: time (days)

tag: treatment


title: FH1_KO1

city: San Francisco

first: Juliana

last: Sucharov Costa

state: California

address: 2351 Powell Street, Apt 513

institute: UCSF

data_processing:
The raw base sequence calls were demultiplexed into sample-specific cDNA files with bcl2fastq/mkfastq sample sheet using Cell Ranger 7.1 (10x Genomics). Raw FASTQ files were processed using the Cell Ranger software package (10x Genomics) for the RNA expression matrix, including introns in analysis. 13,100 – 15,950 nuclei were sequenced per sample with an average read depth of 27,00 reads per nuclei and 44% sequencing saturation. Further QC and analysis were performed on R 4.2.2. Ambient RNA was removed with the SoupX package and data from the four samples was integrated using Seurat (2000 variable features, 1:20 dimensions). Data were processed to remove doublets and unwanted sources of variation by removing nuclei with more than 5,000 and fewer than 300 genes per cell and regressing on number of UMIs. Genes expressed in fewer than three nuclei were filtered out. Nuclei with a percentage of mitochondrial genes of higher than 2% were removed. Final nuclei counts of 14,591 (Control 1), 15,773 (Control2), 12,936 (Ftl1 KO1), and 14,840 (Ftl1 KO2) were used for gene expression analysis. The matrices of data were log-normalized in a sparse data matrix and PCA was applied to reduce dimensionality. The first 20 PCA components were used to cluster cells by Louvain clustering implemented in Seurat while UMAP plots were independently generated to aid in 2D representation of multidimensional data independent of the clustering
Assembly: mm10
Supplementary files format and content: Filtered and raw tab-separated values and matrix files

source_name: Hippocampus

extract_protocol:
Neuronal nuclei were isolated based on the demonstrated protocol by 10x Genomics with modifications. Briefly, flash-frozen dissected hippocampi were dounce homogenized (Wheaton, Cat# 357538) in 500μL of NP40 lysis buffer (10mM Tris-HCl (pH = 7.4), 10mM NaCl, 3mM MgCl2, 0.1% Nonidet P40 Substitute), 1mM DTT, 1x RNAse Inhibitor, Nuclease-free H2O) with 20 strokes of the loose pestle and 25 strokes of the tight pestle. 500 μL of NP40 lysis buffer was added and samples incubated for 7 minutes on ice. Samples were filtered through a 40 μm filter and centrifuged at 500 RCF for 5 min at 4°C. Samples were resuspended in 1ml of Wash Buffer (PBS, 1%BSA, 1xRNAse Inhibitor) and incubated for 5 min on ice. Samples were centrifuged at 500 RCF for 5 min at 4°C, supernatant was removed, and samples were resuspended in 400 uL of Wash Buffer with 1:10,000 dilution of Hoescht 44,432 and incubated for five minutes before filtering through a 35μm FACS tube filter and sorting on a BD FACSAria II. Nuclei that were both Hoechst+ and NeuN+ (neuronal nuclei isolation) or only Hoechst+ (single nucleus isolation) were sorted.
Isolated nuclei were given to the UCSF-IHG Genomics Core for analysis with the 10x Genomics Chromium Single Cell Expression Solution 3′ kit and the libraries were constructed according to the manufacturer’s instructions (single nucleus 3’ v protocol, 10x Genomics). 10,000 cells were loaded per sample. The final library pool was sequenced on the NovaSeq 6000 S2 system.

treatment_protocol: Aged Rosa26-fl-stop-fl-Cas9-eGFP mice were infected with a high-titer lentivirus encoding a Synapsin-driven Cre and a gRNA against Ftl1 or a non-targeting gRNA to create neuronal specific Ftl1 knockout mice and littermate controls.

value: Hippocampus

value: aged temporally controlled neuron specific conditional Ftl1 genetic knockout mice (FTL1 cKO)

value: Synapsin-Cre + Ftl1 gRNA


title: SKO_Cal_biol rep 3

tag: Sex


title: FFPE kidney allograft, TCMR, n7

tag: developmental stage

tag: time post transplantation (month)

value: Acute TCMR, Banff 1A

tag: glomerulitis

tag: peritubular capillaritis

tag: interstitial inflammation

tag: tubulitis

tag: intimal arteritis

tag: transplant glomerulopathy


title: FFPE kidney allograft, TCMR, n1

tag: anti-hla donor specific antibodies

tag: diagnosis

tag: disease state

tag: banff type

tag: mesangial matrix increase

tag: interstitial fibrosis

tag: tubular atrophy

tag: chronic vasculopathy


title: CTR2

tag: tissue

tag: genotype

value: control

tag: treatment

value: Synapsin-Cre + NT gRNA


title: FFPE kidney allograft, TCMR, n2

tag: developmental stage

tag: time post transplantation (month)

tag: glomerulitis

tag: arteriolar hyaline thickening

tag: c4d score


title: CTR1


title: AIR_FSDE_283_27

value: lung

tag: strain

value: Sprague-Dawley

tag: time (days)

value: air


title: FFPE kidney allograft, TCMR, n6

value: Kidney allograft

value: adult

value: M

tag: anti-hla donor specific antibodies

tag: diagnosis

tag: peritubular capillaritis

tag: interstitial inflammation

tag: tubulitis

tag: intimal arteritis

tag: transplant glomerulopathy


title: mock_ctrl_3

tag: cell line

tag: cell type

value: Breast Cancer

value: WT

tag: agent

value: untreated

tag: batch

value: RNP


title: SKO_Cal_biol rep 2

tag: tissue

value: gastrocnemius

tag: Sex

value: male

tag: genotype

value: SOD1 knockout

tag: treatment

value: Calcipotriol


title: mock_ctrl_2


title: FSDE_FSDE_280_07

tag: strain

value: 30 mg/m3 fracking sand dust + 1.0 mg/m3 of diesel particles


title: AIR_FSDE_281_27

tag: time (days)


title: mock_TDM1_1


title: FSDE_FSDE_279_07


title: FSDE_FSDE_278_07


title: FH1_KO2

value: Hippocampus

value: aged temporally controlled neuron specific conditional Ftl1 genetic knockout mice (FTL1 cKO)

value: Synapsin-Cre + Ftl1 gRNA


title: mock_ctrl_1


title: FSDE_FSDE_275_07

value: lung

value: Sprague-Dawley


title: FFPE kidney allograft, TCMR, n3

value: Kidney allograft

tag: developmental stage

value: F

tag: time post transplantation (month)

tag: anti-hla donor specific antibodies

value: no

value: RA2 12M

tag: disease state

value: Acute TCMR, Banff 1A

tag: banff type

tag: glomerulitis

tag: mesangial matrix increase

tag: interstitial fibrosis

tag: tubular atrophy

tag: chronic vasculopathy

tag: arteriolar hyaline thickening

tag: c4d score


title: FFPE kidney allograft, TCMR, n5

tag: tissue

value: adult

tag: diagnosis

tag: peritubular capillaritis

tag: interstitial inflammation

tag: tubulitis

tag: intimal arteritis

tag: transplant glomerulopathy


title: THP-1_H37Ra Infection_3

city: shanghai

first: Tianxian

last: Liu

address: meilong road 130

institute: east china university of science and technology

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp) with default parameters.
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software.
The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) .
All the alternative splice events were identified by using recently releases program rMATS.
RSEM was used to quantify gene abundances and differential expression analysis was performed using the DESeq2.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology (Shanghai, China). High-quality RNA sample was used to construct sequencing library following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.
Messenger RNA was isolated using oligo(dT) beads and then fragmented by fragmentation buffer. Double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA). Then the synthesized cDNA was subjected to end-repair, phosphorylation, and ‘A’ base addition. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified

tag: cell line

tag: infection

value: Mtb


title: FFPE kidney allograft, TCMR, n4

tag: developmental stage

value: M

tag: time post transplantation (month)

tag: anti-hla donor specific antibodies

tag: disease state

tag: banff type


title: THP-1_Control_2

value: control


title: THP-1_H37Ra Infection_2


title: FSDE_FSDE_276_07

tag: strain

tag: time (days)

tag: treatment


title: FSDE_FSDE_277_07

tag: tissue


title: FFPE kidney allograft, mixed ABMR, n11

value: yes

tag: diagnosis

value: RH1diffuse RA2RC3g2cg0, C4d+

value: Mixed ABMR-TCMR

tag: glomerulitis

tag: mesangial matrix increase

tag: interstitial fibrosis

tag: tubular atrophy

tag: chronic vasculopathy

tag: arteriolar hyaline thickening

tag: c4d score


title: FFPE kidney allograft, mixed ABMR, n13

tag: developmental stage

value: RH1-d, C4d+

tag: peritubular capillaritis

tag: interstitial inflammation

tag: tubulitis

tag: intimal arteritis

value: X

tag: transplant glomerulopathy


title: THP-1_Control_1

tag: cell line

tag: infection


title: THP-1_H37Ra Infection_1


title: scRNA-Seq of mus musculus: bone marrow cells_CRS_3

first: Xinjiang

last: Lu

address: Yuhangtang road No.866

institute: Zhejiang University

description: Singleron

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope v1.9.0 pipeline (https://github.com/singleron-RD/CeleScope).
The mouse reference genome GRCm38 v92 was used for mapping reads.
The R package Seurat (v. 4.3.0) was utilized to process the profiles of cell expression.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
LK cells from the bone marrow of mice were FACS sorted into 1.5 mL tubes. Cell suspensions with PBS were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System.
The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron).Individual libraries were pooled and sequenced on Illumina Novaseq 6000 with 150 bp paired end reads.

treatment_protocol: We performed scRNA-seq in flow cytometry sorted LK cells from bone marrow of mice explored to CRS and CUMS for 4 weeks.

tag: tissue

value: bone marrow

value: bone marrow cells

tag: cell type

tag: genotype

value: CRS

tag: treatment

value: chronic restraint stress


title: FSDE_FSDE_274_07

first: Pius

last: Joseph

address: 1000 Frederick Lane

institute: NIOSH

value: lung

tag: strain

value: Sprague-Dawley

tag: time (days)

value: 30 mg/m3 fracking sand dust + 1.0 mg/m3 of diesel particles


title: THP-1_Control_3


title: scRNA-Seq of mus musculus: bone marrow cells_CUMS_5

description: Singleron

value: CUMS

value: chronic unpredicted mild stress


title: scRNA-Seq of mus musculus: bone marrow cells_CUMS_6

description: Singleron


title: scRNA-Seq of mus musculus: bone marrow cells_CRS_4

description: Singleron


title: H_B.Hen_bio_rep_1

value: retina

value: 24 hour culture in REM + 100CFU/mL B. Henslae


title: FSDE_FSDE_273_07


title: FFPE kidney allograft, mixed ABMR, n12

value: Kidney allograft

value: adult

value: M

value: F

tag: time post transplantation (month)

tag: anti-hla donor specific antibodies

tag: diagnosis

value: RH1-F Plasma cells RA3, C4d+

tag: disease state

tag: glomerulitis

tag: mesangial matrix increase

tag: interstitial fibrosis

tag: tubular atrophy

tag: chronic vasculopathy


title: FFPE kidney allograft, mixed ABMR, n8

tag: developmental stage

value: yes

value: RH1 diffuse, C4d+

value: Mixed ABMR-TCMR

tag: banff type

tag: peritubular capillaritis

tag: interstitial inflammation

tag: tubulitis

tag: intimal arteritis

tag: transplant glomerulopathy

tag: arteriolar hyaline thickening

tag: c4d score


title: FFPE kidney allograft, mixed ABMR, n9

tag: tissue

tag: time post transplantation (month)

tag: anti-hla donor specific antibodies

value: RH1 Focal, C4d+


title: scRNA-Seq of mus musculus: bone marrow cells_control_2

description: Singleron

value: bone marrow

tag: cell line

value: bone marrow cells

tag: cell type

tag: genotype

value: control

tag: treatment


title: H_Glut_bio_rep_1

value: 24 hour culture in REM + 100U/mL IFN g


title: AIR_FSDE_271_07

value: lung

tag: strain

value: Sprague-Dawley

tag: time (days)

value: air


title: H_C.Albic_bio_rep_1

value: retina

value: 24 hour culture in REM + 100CFU/mL C. Albicans


title: AIR_FSDE_270_07


title: scRNA-Seq of mus musculus: bone marrow cells_control_1

description: Singleron


title: RNA-Seq of mus musculus: bone marrow_CUMS_3

description: Total 6 bone marrow samples were analyzed in this study. 3 samples as negtive control, 8 samples as CUMS.

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 FPKM values for each sample

extract_protocol:
Total RNA was extracted using TRIZOL Reagent according the manufacturer’s instructions (Invitrogen). RNA-seq transcriptome libraries were prepared using 1 μg of total RNA following TruSeq RNA Sample Prep Kit from Illumina (San Diego, CA, USA).
The DNA library was then sequenced using Illumina Novaseq 6000 with 2 × 151 bp read length.

treatment_protocol: Chronic unpredicted mild stress (CUMS) was performed to induce depression in mice for 4 weeks.

value: Bone marrow

value: Bone marrow cells

value: CUMS

value: depression


title: FFPE kidney allograft, mixed ABMR, n10

value: Kidney allograft

tag: developmental stage

value: adult

value: F

value: yes

tag: diagnosis

value: RH1 focal g2ptc2-3cg0 RA2RC4, C4d+

tag: disease state

tag: banff type

tag: glomerulitis

tag: mesangial matrix increase

tag: interstitial fibrosis

tag: tubular atrophy

tag: chronic vasculopathy


title: AIR_FSDE_269_07

tag: tissue


title: AIR_FSDE_267_07


title: FFPE kidney allograft, mixed ABMR, n5

value: M

tag: time post transplantation (month)

tag: anti-hla donor specific antibodies

value: RH1 diffuse RA3RC3RC7CG1, C4d+

value: Mixed ABMR-TCMR

tag: peritubular capillaritis

tag: interstitial inflammation

tag: tubulitis

tag: intimal arteritis

tag: transplant glomerulopathy

tag: arteriolar hyaline thickening

tag: c4d score


title: AIR_FSDE_272_07

value: lung

tag: strain

tag: time (days)

tag: treatment


title: RNA-Seq of mus musculus: bone marrow_CUMS_2

description: Total 6 bone marrow samples were analyzed in this study. 3 samples as negtive control, 7 samples as CUMS.

tag: cell line

tag: cell type

tag: genotype


title: FFPE kidney allograft, mixed ABMR, n6

tag: developmental stage

tag: diagnosis

value: RH1 focal g2 cg1, C4d+

tag: disease state

tag: banff type

tag: glomerulitis

tag: mesangial matrix increase

tag: interstitial fibrosis

tag: tubular atrophy

tag: chronic vasculopathy


title: RNA-Seq of mus musculus: bone marrow_CUMS_1

description: Total 6 bone marrow samples were analyzed in this study. 3 samples as negtive control, 6 samples as CUMS.

tag: tissue


title: H_Gluc_bio_rep_1

data_processing:
Read alignment to the reference genome was performed with STAR (version 2.7; PMID: 23104886) software. Gene level quantification was determined using RSEM (version 1.3.1 ; PMID: 21816040).
Assembly: mm10-mouse / GRCh38 – human
Supplementary files format and content: tab delimited text file with raw counts for each sample

extract_protocol:
Retinal punches were dissolved in 800uL Trizol Reagent (Invitrogen #15596026). 200uL chloroform was added to each sample, inverted, incubated at room temperature for 3 minutes. Samples were then spun down at 12,000 3 g at 4 C for 15 min. The aqueous later was transferred to a new tube and 1uL glycogen and 500 uL isopropanol was added to each sample and mixed by vortex. Samples were incubated at room temperature for 10 minutes and spun down at 12,000 3 g at 4 C for 15 min. The isopropanol was removed and the pellet was washed twice with ice-cold 80% EtOH. The washed pellet was resuspened in water.
Libraries were constructed using Illumina library prep acording to manufacturer protocols

value: 24 hour culture in REM at pH 7.70


title: FFPE kidney allograft, mixed ABMR, n4

tag: time post transplantation (month)

tag: anti-hla donor specific antibodies

value: RH1 focal RA1RH1, C4d+

value: Bordeline

tag: peritubular capillaritis

tag: interstitial inflammation

tag: tubulitis

tag: intimal arteritis

tag: transplant glomerulopathy

tag: arteriolar hyaline thickening

tag: c4d score


title: AIR_FSDE_266_07

tag: strain

value: Sprague-Dawley

tag: time (days)

tag: treatment

value: air


title: H_pH715_bio_rep_1

value: retina

value: 24 hour culture in REM + 0.2ug/mL LPS


title: H_pH770_bio_rep_1

value: 24 hour culture in REM at pH 7.15


title: RNA-Seq of mus musculus: bone marrow_control_2

description: Total 6 bone marrow samples were analyzed in this study. 3 samples as negtive control, 4 samples as CUMS.

value: Bone marrow

tag: cell line

value: Bone marrow cells

tag: cell type

tag: genotype

value: control

value: negative control


title: FFPE kidney allograft, mixed ABMR, n3

value: Kidney allograft

tag: developmental stage

value: adult

value: M

value: F

value: yes

tag: diagnosis

value: RH1 focal, C4d+

tag: disease state

tag: banff type

tag: glomerulitis

tag: mesangial matrix increase

tag: interstitial fibrosis

tag: tubular atrophy

tag: chronic vasculopathy


title: AIR_FSDE_265_07

tag: tissue

value: lung


title: FFPE kidney allograft, mixed ABMR, n7

tag: time post transplantation (month)

tag: anti-hla donor specific antibodies

value: RH1diffuse RA3RA7 g1ptc2cg0, C4d+

value: Mixed ABMR-TCMR

tag: peritubular capillaritis

tag: interstitial inflammation

tag: tubulitis

tag: intimal arteritis

tag: transplant glomerulopathy

tag: arteriolar hyaline thickening

tag: c4d score


title: FFPE kidney allograft, mixed ABMR, n2

tag: developmental stage

tag: diagnosis

tag: disease state


title: H_LPS_bio_rep_1

tag: treatment

value: 24 hour culture in REM at 33 degrees Celcius


title: FFPE kidney allograft, mixed ABMR, n1

tag: banff type

tag: glomerulitis

tag: mesangial matrix increase

tag: interstitial fibrosis


title: RNA-Seq of mus musculus: bone marrow_control_1

description: Total 6 bone marrow samples were analyzed in this study. 3 samples as negtive control, 3 samples as CUMS.

tag: tissue

tag: cell line

tag: cell type

tag: genotype


title: RNA-Seq of mus musculus: PB_neutrophil_AVP_3

description: Total 6 PB samples were analyzed in this study. 3 samples as negtive control, 3 samples as AVP treatment.

source_name: PB

treatment_protocol: Transcriptome analysis of blood neutrophils was performed after 30-day AVP administration.

value: PB

value: Neutrophils

value: AVP

value: AVP treatment


title: FSDE_FSDE_263_01

tag: strain

value: Sprague-Dawley

tag: time (days)

value: 30 mg/m3 fracking sand dust + 1.0 mg/m3 of diesel particles


title: H_MeOH_bio_rep_1

value: retina

value: 24 hour culture in REM + 20mM Glucose


title: FSDE_FSDE_264_01


title: SK-OV-3-BAY-850 treated replicate 3

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each Sample

source_name: SK-OV-3-BAY-850 treated

growth_protocol: PA-1 and SK-OV-3 cells were grown in DMEM medium and RPMI medium respectively with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacturer and then purified using RNAeasy mini columns (Qiagen) as per the manufacturer's instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: PA-1 and SK-OV-3 cells were treated with  ATAD2 inhibitor (5 micomolar) BAY-850 for 48 hours,  were harvested and were used for preparing the total RNA and to perfrom RNA Seq.

value: ovarian cancer cell

value: BAY-850 treated, 5 micromolar, 48 hours


title: RNA-Seq of mus musculus: PB_neutrophil_AVP_2


title: H_bio_rep_13C_bio_rep_1

value: 24 hour culture in REM at 2.3% Oxygen


title: H_bio_rep_2.3%O2_bio_rep_1

value: 24 hour culture in REM + 70uM Ouabain


title: RNA-Seq of mus musculus: bone marrow_control_3

description: Total 6 bone marrow samples were analyzed in this study. 3 samples as negtive control, 5 samples as CUMS.

value: Bone marrow

value: Bone marrow cells

value: control

value: negative control


title: H_IFN_bio_rep_1

value: 24 hour culture in REM + 8uM Formic Acid


title: RNA-Seq of mus musculus: PB_neutrophil_AVP_1

value: PB


title: H_Kcl_bio_rep_1

value: 24 hour culture in REM + 80mM Kcl


title: SK-OV-3-BAY-850 treated replicate 2


title: SK-OV-3-BAY-850 treated replicate 1


title: FSDE_FSDE_260_01

city: Morgantown

value: lung


title: H_40C_bio_rep_1

value: 24 hour culture in REM at 40% Oxygen


title: AIR_FSDE_268_07

value: Sprague-Dawley

value: air


title: SK-OV-3-DMSO treated replicate 2

source_name: SK-OV-3-DMSO treated

value: DMSO treated


title: RNA-Seq of mus musculus: PB_neutrophil_control_3

value: Neutrophils


title: FSDE_FSDE_259_01

source_name: lung

value: 30 mg/m3 fracking sand dust + 1.0 mg/m3 of diesel particles


title: RNA-Seq of mus musculus: PB_neutrophil_control_1


title: FSDE_FSDE_262_01


title: H_Ouabain_bio_rep_1

value: retina

value: 24 hour culture in REM at 40 degrees Celcius


title: SK-OV-3-DMSO treated replicate 1

value: ovarian cancer cell


title: FSDE_FSDE_258_01


title: CP3

city: Xi'an

first: Xiaolong

address: 127 West Changle Road

department: Urology

institute: Xijing Hospital

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome,Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: testis

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 1ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: testis

value: Spermatocyte

value: WT

value: 2 mM cyclophosphamide for 24 hours


title: CP2


title: FSDE_FSDE_261_01


title: AIR_FSDE_256_01


title: PA-1-BAY-850 treated replicate 3

source_name: PA-1-BAY-850 treated

value: BAY-850 treated, 5 micromolar, 48 hours


title: H_Control_bio_rep_1

value: 24 hour culture in REM


title: H_T0_bio_rep_1

value: Normal human retina


title: AIR_FSDE_255_01

value: lung


title: CP1


title: H_B.Hen_bio_rep_2

value: 24 hour culture in REM + 100CFU/mL B. Henslae


title: SK-OV-3-DMSO treated replicate 3


title: RNA-Seq of mus musculus: PB_neutrophil_control_2

city: Hangzhou

value: PB

value: control

value: negative control


title: Sal_CP3

value: 2 mM cyclophosphamide and 100μM salidroside for 24 hours


title: AIR_FSDE_252_01

value: Sprague-Dawley

value: air


title: Sal_CP1


title: H_40pct_bio_rep_1

value: retina


title: AIR_FSDE_254_01


title: PA-1-BAY-850 treated replicate 1

value: ovarian cancer cell


title: PA-1-DMSO treated replicate 3

source_name: PA-1-DMSO treated

value: DMSO treated


title: Sal_CP2

value: testis

value: Spermatocyte


title: AIR_FSDE_251_01


title: PA-1-DMSO treated replicate 2


title: H_IFN_bio_rep_2

source_name: retina

value: 24 hour culture in REM + 8uM Formic Acid


title: H_MeOH_bio_rep_2

value: 24 hour culture in REM + 20mM Glucose


title: AIR_FSDE_253_01


title: wt_ms_rep3

city: guangzhou

first: yizhi

last: chen

state: guangdong

address: No.601, West Huangpu Avenue

department: Guangdong-Hong Kong-Macau Institute of CNS Regeneration

institute: Jinan university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through Trimmomatic v0.39[2]. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-A and low quality reads from raw data. FastQC v0.11.9[3] software was used to perform quality control on raw data and clean data respectively. Q20, Q30 and GC content were calculated through in-house python scripts. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from Ensembl website directly. Index of the reference genome was built using Hisat2 v2.2.1[4] and clean reads were aligned to the reference genome using Hisat2 v2.2.1 to generate a .sam or .bam files containing the alignments.
The gene expression level quantification was performed separately for each sample using the featureCounts v2.0.1[5] software in the subRead package, and the reads count of each gene was obtained with the parameter "-t exon -g gene_id -s 1". Then results of all samples were combined to obtain the expression matrix of all samples. The RPM (Reads per million mapped reads) of each gene was based on the reads count mapped to this gene and sequencing depth.
Assembly: Sus_scrofa.Sscrofa11.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: polyA RNA

source_name: striatum

extract_protocol:
Total RNAs from striatum of mice, and striatum of pigs were extracted using the Trizol method (Thermo Fisher Scientific, MA, USA).
Sequencing libraries were generated using the SEQUMED ® MustSeq ® 3'mRNA DEG kit（Sequmed，China）.The first step is to capture polyA mRNA with polyT primer and reverse transcript it to form DNA-RNA heterozygous chain. The primer consists of oligo-dT, a sample barcode, a unique and the Illumina-compatible 5ʹ adaptor. Then RNA is removed, the sample is purified with 1X magnetic beads.After the RNA removal,the random primer is used for two-chain synthesis,and the P5 and P7 adaptor that are suitable for the Illumina platform are used for PCR amplification.At last, PCR products were purified 250bp-1000bp fragments for sequencing library.

value: striatum

value: wt

value: untreated


title: PA-1-DMSO treated replicate 1


title: attB/P_K562_Lane2_GEX

city: Seattle

first: Sudarshan

last: Pinglay

address: 3720 15th Ave NE

institute: University of Washington

description: Library name: SP000328

data_processing:
10x Genomics 3’ gene expression (transcriptome) libraries were processed using cellranger-6.0.1 count function (with reference refdata-cellranger-mm10-3.0.0 for mESC cells [loxPsym+ mESC experiment 1 and attB/P+ mESC/K562 experiment lane 1] and refdata-gex-GRCh38-2020-A for K562 cells [attB/P+ mESC/K562 experiment lane 1 & 2]). Resulting raw count matrices were converted to a Seurat (v4.3.1) object using functions Read10X and CreateSeuratObject (options: min.cells=3, min.features=50). The mitochondrial fraction was computed and cell barcodes with >1500 and >1000 transcriptome UMI/cell (K562 and mESC respectively) and with 2-8% and 1.3-6% mitochondrial fraction (K562 and mESC respectively) were retained. For loxPsym+ mESC experiment 1, cell barcodes with >1000 transcriptome UMI/cell and with 1-12% mitochondrial fraction were retained. Scrublet 0.2.3 was run on filtered cells, and cells with doublet score <0.4 were retained for further analysis. For the lane 1 mESC+K562 barnyard experiment, the following criteria were further used to unambiguously assign species identity to cells: cell barcodes passing each separate species singlet processing thresholds were retained, and any cell barcodes removed as a putative scrublet-called doublet in one species but not the other were further marked as doublets (e.g., cell called as singlet in K562 mapping but flagged as a doublet in mESC mapping). Total transcriptome UMIs mapping to both species from all these cell barcodes were then inspected, showing clear separation between singlet and doublet. Initial assignment from the single species threshold was finely refined to stringently identify cells as doublets if transcriptome UMI ratios were not sufficiently separate (threshold selected by inspection): mm10/hg38 <1.42 or hg38/mm10<3.  To obtain the BC-by-cell-count matrix, we first modified the fastq files to separate the cell barcode and shuffle barcodes in two distinct files (original read structure -- read 1: first 28 cycles [cell barcode]-umi, remaining cycles 29 to 75 to read [capture sequence]-BC-[att site]; read 2: cycles 1 to 47 cycles to [read capture sequence]-BC-[att site]). Modified fastq content -- read 1: 28 cyclces [cell barcode]-umi, read 2: cycles 1 to 47 cycles to [read capture sequence]-BC-[att site] followed by original cycles 29 to 75 from original read 1. The merge was generated using seqtk version 1.4 and the following script (appending line number to join and retaining only desired information in final fastq (seqtk trimfq -b 28 file_R1_001.fastq.gz | join <(zcat file_R2_001.fastq.gz | nl) <(cat - | nl) | awk -F ' ' '{if ($2 ~ /^@VH00979/ ) {print $4" "$5;} else {print $2$3;}}' | gzip > file_w_47bpR1R2transfer_R2_001.fastq.gz).  T7-BC sequencing data was then processed using cellranger-6.0.1 count to perform error correction on the cell barcodes. The unmapped reads with error-corrected cell barcodes were selected from the sorted BAM file output, and barcodes sequences were extracted for each read from the shuffle cassette by looking for matches for constant surrounding sequences. From the read 1 portion (searching in cyles 48 to 95 appended to read 2 as described above): attP CS2 if TGAGC(.{20})GTGG, attB CS2 if TGAGC(.{20})GGCC, attP CS1 if AAAGC(.{20})TGGG, attB CS1 if AAAGC(.{20})CCGG. From the original read 2 (searching in cycles 15 to 47): attB CS1 if AAAGC(.{20})CCGG, attP CS1 if AAAGC(.{20})TGGG, attP CS2 if AAAGC(.{20})TGGG, attB CS2 if TGAGC(.{20})GGCC. The resulting two (barcode)-(capture sequence)-(recombinase site) combinations were stored and joined to the error-corrected cell barcode and umi from the read. Reads counts and total set of UMIs for all cellBC/BC1/BC2/capture/recombinase site combinations were then tallied, discarding likely chimeric UMIs (taken to be UMIs for which the proportion of reads associated to a given BC1/BC2/capture-orientation all other BC1/BC2/capture/recombinase site in the specified cell barcode falls below 0.2). The number of error-corrected UMIs for a given BC1/BC2/capture/recombinase site was then taken as the number of connected components in a graph created by connecting all UMIs associated with that combination with a Hamming distance≤1. To filter out spurious molecules (sequencing errors or PCR chimeras, only cell barcode BC1/BC2 combinations with reads/UMI ≥15 and ≥9 for Lane 1 and Lane 2 respectively were retained commensurate with the level of sequencing saturation in both libraries).
Assembly: mm10 or hg38
Supplementary files format and content: For gene expression libraries, the processed file is a seurat object. For T7 libraries, processed file is a matrix containing count of reads, UMIs per shuffle cassette barcode combination, per cell barcode.

extract_protocol:
For loxPsym+ mESC scRNA-seq experiment, 300,000 parental cells were transfected in 6-well plates as described above with 1 μg of Cre and 200 ng of the reporter per transfection. 10 individual wells were transfected. At 24 hours post transfection, 5 wells were treated with 20 μM Pifithrin-α for 48 hours total. At 72 hours post transfection, both Pifithrin-α treated and untreated cells were harvested and approximately 500,000 RFP positive cells were FACS sorted into a combined tube based on the activity of the Cre reporter. Untransfected parental cells were harvested, and 1 million cells were used as input in parallel with Cre-sorted cells for the protocol.  For the attB/P+ K562 and attB/P+ mESC “Lane 1” experiment, 200,000 parental cells were nucleofected (2 reactions) or transfected (3 reactions) with 1 μg of Bxb1 plasmid as described above. All cells were harvested at day 3 post-transfection and used as input for the protocol. For the “Lane 2” experiment, attB/P+ K562 populations bottlenecked to 1000 cells after Bxb1 treatment were thawed and split once before being used as input in the protocol. For both Lanes, 500,000 cells from each population were mixed and were used for the subsequent steps.  After washing twice with cold 1X PBS (Gibco), 1 million cells per sample were resuspended in 400 μl of cold PBS. Cells were fixed with 1600 μl of cold 100% methanol, added dropwise with swirling. Cells were left on ice to fix with gentle swirling to mix every 5 minutes during the incubation. Cells were rehydrated with 4 mL of cold 1X PBS added slowly with gentle swirling of the tube. Cells were spun down and resuspended in 60 μl of PBS. For the loxPsym+ mESC experiment, approximately 60,000 cells and 380,000 cells in total were counted in the Cre and parental samples respectively using a Countess automated cell counter (Thermo) of which all and 100,000 cells in 18 μl of PBS were used for T7 IVT respectively. For the attB/P+ K562/mESC experiment, approximately 600,000 and 450,000 cells were counted of which, 100,000 cells per sample in 18 μl of PBS were used for T7 IVT. IVT reactions were set up in 30 μl total volume with the HiScribe T7 High Yield RNA Synthesis Kit (NEB E2040S) with 2 μl of each NTP, buffer and enzyme. Reactions were incubated at 37°C for 1 hour in a thermocycler. Cells were immediately moved to ice and 20 μl of cold PBS was added to each sample. Approximately 40,000 cells were processed per lane of a 10X Genomics Single Cell 3’ HT with Feature Barcoding kit.
Transcriptome libraries were prepared as per the manufacturer’s protocol. To prepare libraries from T7 transcripts captured using CS1 and CS2, we started with the supernatant from the clean-up after cDNA amplification of the standard 10X Genomics feature barcoding protocol for the loxPsym+ mESC experiment. For the attB/P+ K562/mESC experiment, we spiked in two construct specific primers (oSP1059, oSP1060) at 0.5 μM into the cDNA amplification step. Two rounds of PCR were performed with primers specific to the shuffle cassette. In PCR1, oSP997 (CS1-TruSeq2), oSP1022 (CS2-TruSeq2) and oSP1061 (feature-cDNA primer F) primers were used (1.25 μl of 10 μM each) in a 50 μl Q5 polymerase reaction with 5 μl of template. Cycling conditions: 98°C - 45 s; cycles of 98°C - 20s, 60°C - 5s, 72°C - 5s; 72°C - 60s, 4°C - hold. 15 cycles of PCR1 were performed for the loxPsym+ mESC experiment and 12 cycles for the attB/P+ K562/mESC experiment. loxPsym+ mESC  were cleaned up with AmpureXP beads (1X) and eluted in 15 μl of Qiagen buffer EB. attB/P+ K562/mESC reactions were cleaned up with AmpureXP beads (1X) and eluted in 30 ul of buffer EB. In PCR2, 5 μl of PCR1 eluate was used as input into either one or two (loxPsym+ mESC experiment)  50 μl Q5 Polymerase reactions per sample with sample index primers (1.25 μl of 10 μM each) that add Illumina adapters. Reaction progress was monitored using SYBR green and was stopped before saturation. Cycling conditions for the loxPsym+ mESC experiment: 98°C - 5 min; 9 cycles of 98°C - 10s, 65°C - 10s, 72°C - 20s; 72°C - 60s, 4°C - hold. Cycling conditions for the attB/P+ K562/mESC experiment: 98°C - 1 min; 8 cycles of 98°C - 20s, 63°C - 20s, 72°C - 1min; 72°C - 60s, 4°C - hold. After a clean up with AmpureXP beads (1X), quality of the libraries was confirmed (prominent single-peak) by running them on a TapeStation D1000 ScreenTape (Agilent).  Primer sequences:  oSP997_CS1_TruSeq2_R GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC TTGCTAGGACCGGCCTTAAAGC oSP1022_CS2_TruSeq_R GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT CCTTAGCCGCTAATAGGTGAGC oSP1061_FeaturecDNA_Primer1 TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG oSP1059_CS2_SpikeIn GGGGGGTTTTTTTTTTCCTTAGCC oSP1060_CS1_SpikeIn GGGGGGTTTTTTTTTTGCTAGGAC


title: wt_ms_rep2


title: H_Gluc_bio_rep_2

city: Memphis

first: Michael

address: 262 Danny Thomas

institute: St. Jude Children's Research Hospital

value: 24 hour culture in REM at pH 7.70


title: wt_ms_rep1


title: AIR_FSDE_250_01

value: lung


title: H_Glut_bio_rep_2

value: 24 hour culture in REM + 100U/mL IFN g


title: H_C.Albic_bio_rep_2

value: 24 hour culture in REM + 100CFU/mL C. Albicans


title: H_pH770_bio_rep_2

value: 24 hour culture in REM at pH 7.15


title: AIR_FSDE_249_01

value: Sprague-Dawley