title: O_VC_D4_C_rep5

description:
Library name: 2-14C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 5.

value: fractionated abdominal irradiation, 5 × 4 Gy; oral vehicle treatment with water


title: Pooled screen, 103F, v2, CD34+ enriched, GEX

status: Public on Jul 12 2026

type: SRA

city: Cambridge

first: James

last: Briggs

state: MA

address: 75 Ames St

country: USA

institute: Broad Institute

description: Library name: sample_4-3

library_source: transcriptomic single cell

data_processing:
Read processing: generation of transcriptome and TF perturbation count matrices  Single-cell transcriptomes  Raw Illumina sequencing data was processed into cells x genes counts matrices using the 10X genomics cellranger-6.0.1 pipeline with default parameters. Raw BCL files were demultiplexed and converted to FASTQ format using cellranger mkfastq. Cellranger count was then used to generate counts matrices from FASTQ files. GRCh38 (version refdata-gex-GRCh38-2020-A) was used as a human reference genome for read alignment.  Single-cell TF barcodes  For single-cell TF barcode libraries, raw BCL files were demultiplexed and converted to FASTQ format using bcl2fastq2-v2.20.0 with flags: --no-lane-splitting and --mask-short-adapter-reads 10 and --sample-sheet /path/to/samplesheet.csv.  Demultiplexed FASTQ files were processed into cells x TF barcode count arrays using a custom python pipeline: process_dialout_seq.py (see GitHub repository #). Per library, the pipeline takes a R1 and R2 FASTQ path, a list of TF barcodes (from the original lentiviral pool used in the screen), and a list of cell barcodes (i.e., the pass-filter cell barcodes identified by cellranger above) as input. It outputs a dataframe of [cell barcode, TF barcode, UMI count, read count] specifying a cells vs. TF barcode count array.  This pipeline has the following main steps:  Iterate over reads and parse TF barcode, cell barcode, and UMI sequences. Output as dataframe of [TF barcode, cell barcode, UMI] sequences for pass-filter reads.  Identify key sequence (i.e., the constant sequence immediately upstream of TF barcode) in R2 Map 24-bp following key sequence to list of input TF barcodes Extract 16-bp cell barcode from R1 and map to input list of cell barcodes Extract 12-bp UMI sequence from R1 For correctly structured reads store TF barcode, cell barcode, UMI  Iterate over [cell, TF] pairs in parsed fastq and count the number of unique occurrences of each TF barcode using the UMIs. Output dataframe of [cell, TF, UMI count, read count].  Key identification, barcode mapping, and UMI counting are performed with error tolerance to account for sequencing errors. The pipeline has parameters controlling the number of sequence mismatches allowed during identification of key, TF barcode, cell barcode, and UMI sequences. We used selections of 1, 2, 1, and 1 respectively, which added tolerance to sequencing errors without endangering barcode collisions.  The pipeline is implemented to parallelize slow steps and runs in <30 minutes for a 10,000 cell dataset with 50 million reads on mid-tier Google Cloud VM instance.
Count matrix preparation  We loaded and concatenated all single-cell transcriptome count arrays into a shared AnnData object using the ScanPy54 package for single-cell analysis. We stored TF barcode counts in adata.obsm[‘TF_UMIs’] as cells x TF sparse CSR arrays. We stored corresponding TF names in adata.uns[‘TF_names’].  Cell filtering and preprocessing:  We applied the following filters to retain only high-quality cells (threshold values in Extended Data File 2): Depth filter: cell must have > min_UMIs (threshold 1k-10k UMIs) Live filter: cell must have < mito_fraction UMIs assigned to mitochondrial genes (threshold 15-20%) Doublet filter: remove cells predicted to be doublets by Scrublet55.  We scaled each cell to 1 million total UMIs to obtain units of transcripts per million (TPM).   TF barcode filtering and preprocessing:  We applied the following filters to TF barcode count data to exclude background signal (threshold values in Extended Data File 2): Depth filter: TF must be detected with > min_UMIs SNR filter: the fraction of total TF UMIs in the cell assigned to the TF must be > min_fraction  For each unique dial-out TF barcode library, the min_fraction threshold was set by inspecting per cell barcode count histograms and manually selecting a threshold that visually best separates the observed background count distribution (most barcodes observed with very few counts) from likely true signal distribution (few barcodes with significantly higher counts). The manual results were similar to those found by implementing an automated elbow identification function on the same histograms. The min_UMIs threshold was uniformly set to 5, except for one library with lower barcode detection rates that was lowered to 3.  We normalized TF expression such that pass-filter TF UMIs summed to 100 per cell and stored the resulting expression array in adata.obsm[‘TF_UMIs_filt’]. For some analysis, we then assigned an expression value of 1 to pass-filter TFs and 0 otherwise.
Assembly: GRCh38 (version refdata-gex-GRCh38-2020-A)
Supplementary files format and content: Processed .h5ad files provide annotated count matrices for scRNA-seq data. Per sample .h5ad files contain raw count data. The merged all_cells_final_v2.h5ad file contains all single cells across samples and has the following features of interest: - .X : total count normalized to 1e6 counts per cell (excluding highly expressed), then log(TPM+1) transformed - .obs['TF_subpool']: TF library used to transduce sample - .obs['timepoint']: timepoint post transduction that scSeq data was collected (or post-thaw for pHSC samples) - .obs['ddPCR_MOI']: number of TF integrations per cell measured by ddPCR - .obs['min_tot']: cell filtering threshold: minimum total number of UMIs per cell - .obs['max_mito']: cell filtering threshold: maximum allowed fraction of mitochondrial expression - .obs['min_TF_UMIs']: TF filtering threshold: minimum number of UMIs coming from expressed TFs - .obs['min_TF_frac']: TF filtering threshold: minimum fraction of UMIs per cell coming from expressed TFs - .obs['n_counts']: total UMIs detected in cell - .obs['mito_frac']: fraction of reads coming from mitochondrial genes - .obs['doublet_score']: doublet score assigned by Scrublet - .obs['sample']: scSeq library ID - .obsm['TF_UMIs_filt']: filtered to only expressed TFs, normalized so max TF per cell = 100TPMs - .obsm['TF_UMIs']: raw TF UMI expression - .uns['TF_names']: list of column names for TF expression matrices  TF_counts.csv files contain raw cells vs. TFs count matrices output from process_dialout_seq.py run on the TF dialout fastq files.

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
10X genomics 3’ transcriptome kit with v3.1 chemistry (10X genomics #1000268) processing of dissociated single cells, as per the manufacturer’s instructions.
All single-cell RNA-seq libraries were generated using the 10X genomics 3’ transcriptome kit with v3.1 chemistry (10X genomics #1000268) as per the manufacturer’s instructions. We targeted a loading concentration of 10,000 cells / lane and washed cells thoroughly in PBS-/- prior to loading to minimize background RNA contamination. We dual-indexed libraries during PCR2 using the Dual Index Kit TT (Set A; 10X genomics #1000215).  We generated corresponding single-cell TF barcode libraries by performing dial-out PCR on a sample of the 10X PCR1 product. Our primers were designed to generate a ~1.2-kb product compatible with Illumina TruSeq chemistry such that the TF barcode is sequenced by read 2 and the 10X cell barcode by read 1 (Extended Data File 5). The forward primer anneals to the 10X PCR2 adapter sequence upstream of the 10X cell barcode and adds an Illumina p5 adapter, 8-bp barcode, and TruSeq R1 primer annealing site. The reverse primer anneals immediately 5’ of the 24-bp TF barcode and adds an Illumina p7 adapter, 8-bp barcode, TruSeq R2 primer annealing site, and 12-bp stagger to increase sequence diversity. Amplification was performed using NEBNext HiFi polymerase mix (NEB #M0541L). 5% of the total 10X PCR1 product was used template – i.e., 2 uL containing ~50 ng DNA. Primers were used at a 0.25 uM final concentration. Cycling conditions were: 1. 98°C 3 minutes; 2. 20 x [98°C 10 seconds, 60°C 10 seconds, 72°C 1 minute]; 3. 72°C 1 minute. PCR product was purified for sequencing with a 0.8X SPRI selection (Beckman Coulter #B23317). Successful amplification and purification of the expected 1.2-kb product was verified by High-Sensitivity DNA Analysis (Agilent #5067-4626).  Single-cell transcriptome libraries were pooled and sequenced on an Illumina NextSeq. We typically pooled up to 40,000 cells per sequencing run and targeted 20,000 reads/cell sequencing depth. We used High-Output 500/550 v2.5 75-cycle kits with the following read distribution: R1: 28, R2: 44, i7: 10, i5: 10. Corresponding single-cell TF barcode libraries were pooled and sequenced similarly, but with the following read distribution: R1: 28, R2: 53, i7: 0, i5: 8.

tag: cell line

tag: culture media

value: X-vivo 15 (Lonza)

tag: differentiation timepoint_(days)

tag: enrichment

value: CD34 MACS

tag: tf subpool

tag: min umis

tag: max mito_fraction

tag: min tf_umis

tag: min tf_fraction

tag: library type

value: GEX


title: SeMSNs3-Brain

city: Shenyang

first: Jintao

last: Song

address: No. 77, Puhe Road

country: China

institute: China Medical University

description:
Library name: Sample6
B-semsn-4_FPKM

library_source: transcriptomic

data_processing:
Remove the adapter sequences contained in the reads.
Remove the bases at the 3' end with a quality score (Q) lower than 20, that is, the base error rate is less than 0.01. Here, Q = -10 * log(error_ratio).
Remove reads with a length less than 25.
Remove the ribosome RNA reads belonging to the specific species.
Assembly: GRCm38
Supplementary files format and content: processed data.xlsx; FPKM, counts

organism: Mus musculus

source_name: Brain

growth_protocol: The mice were fed on a normal diet.

extract_protocol:
Extract RNA using the Boryou® Total RNA Extraction Kit. 2μg of total RNA was used to construct the sequencing libraries.
The purified Total RNA was subjected to steps such as mRNA isolation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, 3' end addition of A, ligation of adapters, and enrichment, to complete the construction of the mRNA sequencing library. The library concentration was detected using the Qubit 2.0 fluorescence quantitative instrument (Thermo Fisher Scientific), and the distribution of library fragments was detected using the Agilent 4200 TapeStation (Agilent Technologies).

treatment_protocol: The SeMSNs group was given 10mg/kg by gavage daily, while the old control group was given the same amount of normal saline by gavage.

tag: tissue

value: Brain

tag: strain

tag: genotype

value: WT

tag: treatment

value: SeMSNs


title: Cornea Pitx2 -/- female rep1

city: Montpellier

first: Frederic

last: Michon

state: non-US Resident

address: Institute for Neurosciences of Montpellier, 80, rue Augustin Fliche

country: France

institute: Inserm - U1298

description: Library name: F_66_mut

data_processing:
Filtered reads were aligned to the mouse reference genome (Mus_musculus_10090; UCSC mm10 v2201) with HISAT2, and gene-level counts were obtained using HTSeq-count to produce the raw count matrix.
Primary analyses were performed with BGI’s Dr. Tom multi-omics platform (https://biosys.bgi.com). Briefly, clean reads were also aligned against the gene set (including known/novel, coding/non-coding transcripts) using Bowtie2 (Langmead & Salzberg, 2012), and transcript/gene abundance was estimated with RSEM v1.3.1 (Li & Dewey, 2011).
Assembly: Mus_musculus_10090; UCSC mm10 v2201
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: csv fils include FPKM values for each sample

source_name: Cornea

growth_protocol: The mice were kept under a 12-hour light/dark cycle with free access to food and water.

extract_protocol:
Frozen corneas were shipped on dry ice to Beijing Genomics Institute (BGI, Shenzhen, China) for library construction and sequencing on the DNBseq platform. Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
Polyadenylated RNA was captured with oligo(dT)-coupled magnetic beads and fragmented. RNA integrity and fragment-size distributions were assessed on a Fragment Analyzer; only samples meeting predefined QC thresholds advanced to library preparation. Libraries were generated with the BGI Optimal Dual-mode mRNA Library Prep Kit and sequenced on a DNBSEQ-T7 (paired-end 2×100 bp; ~50 million clean reads per sample). Adapters, contaminants, and low-quality bases/reads were removed with SOAPnuke (Li et al., 2008).

value: Cornea


title: CD4+ T cells from healthy control 3, untreated

city: Tianjin

first: Weiwei

last: Jiang

address: No. 354, Beima Road, Hongqiao District, Tianjin

department: Dermatology

institute: Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital

description: Library name: HC_3_Clean

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM X PLUS sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Homo sapiens.GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

source_name: CD4+ T cells

growth_protocol: Purified CD4+ T cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BP group: Cells from BP patients cultured with standard medium. HC group: Cells from healthy controls cultured with standard medium. BP + C176 group: Cells from BP patients treated with the STING inhibitor C176 (5μM) for 24 hours. HC + C176 group: Cells from healthy controls treated with C176 (same concentration and duration).

tag: cell type

value: CD4+ T cells

value: BP

value: untreated

tag: batch


title: O_VC_D4_C_rep4

city: Adelaide

first: Yan

last: Zhou

state: South Australia

address: 108 North Terrace

department: Biological science

country: Australia

institute: Adelaide University

description:
Library name: 2-13C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 4.

data_processing:
Adapter and low-quality sequences were trimmed using BBDuk with parameters hdist=1, mink=11, ktrim=r, qtrim=rl, trimq=20, minlen=25, and trimpolyg=20.
Trimmed reads were aligned to the Rattus norvegicus reference genome using STAR v2.7.10a with mismatchNoverLmax set to 0.03 and alignIntronMax set to 10000.
Gene counts were generated from aligned reads and lowly expressed genes were filtered before downstream analysis.
Assembly: Rattus norvegicus reference genome mRatBN7.2 (Ensembl release 107)
Supplementary files format and content: The file contains the raw read count matrix for all genes across all samples.

organism: Rattus norvegicus

source_name: colon epithelium

growth_protocol: Sprague Dawley rats were maintained under standard laboratory conditions with access to food and water according to the approved animal ethics protocol.

extract_protocol:
Total RNA was extracted from colon and jejunum epithelial tissues. RNA quality and quantity were assessed before library preparation. Samples passing quality-control criteria were used for bulk RNA sequencing.
RNA-seq libraries were prepared from total RNA using a transcriptome library preparation protocol and sequenced on a DNBSEQ-G400 platform using paired-end 150 bp sequencing.

treatment_protocol: Rats received fractionated abdominal irradiation at 5 × 4 Gy from day 0 to day 4. Compound Kushen powder, compound Kushen injection, or corresponding vehicle treatments were administered according to the experimental design. Colon and jejunum epithelial tissues were collected at day 4 or day 7 after irradiation.

value: colon epithelium


title: Trigeminal Ganglion Pitx2 -/- male rep5

department: Institute for Neurosciences of Montpellier

description: Library name: TG_M_194_MutA

extract_protocol:
Frozen trigeminal ganglia were shipped on dry ice to Beijing Genomics Institute (BGI, Shenzhen, China) for library construction and sequencing on the DNBseq platform. Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
Polyadenylated RNA was captured with oligo(dT)-coupled magnetic beads and fragmented. RNA integrity and fragment-size distributions were assessed on a Fragment Analyzer; only samples meeting predefined QC thresholds advanced to library preparation. Libraries were generated with the BGI Optimal Dual-mode mRNA Library Prep Kit and sequenced on a DNBSEQ-T7 (paired-end 2×100 bp; ~50 million clean reads per sample). Adapters, contaminants, and low-quality bases/reads were removed with SOAPnuke (Li et al., 2008).


title: Huh-7, G1/S, macroH2A1, Rep1 (Chip)

city: Minhang

first: deng

last: yongzhuo

state: Shanghai

address: DongchuanoRoad N0.800

institute: Shanghai Jiao Tong University

description: Library name: Huh-7_G1/S_macroH2A1_Chip, Rep1

library_source: genomic

data_processing:
Utilize TrimGalore to remove sequencing adapter sequences and low-quality bases from your reads (Q<20)
Use Bowtie2 to align the trimmed pair-end reads to human genome
Use Samtools to remove the unknown chromosome segments mapped reads, unmappable reads and multi-mapped reads The mapped reads are converted to bam format.
mapped reads are used to identidfy macroH2A1/2 enriched domains  by normR after normalization by the control (input nucleosome DNA). Genome is divided into 2kb bins,regimeR is used for calling peaks,  significant bins identified by Fisher’s test (P < 0.05) are use exportR to output into Bed files and BigWig files
Assembly: Homo_sapiens.GRCh38.114
Supplementary files format and content: BigWig

molecule: genomic DNA

source_name: human hepatocellular carcinoma cells

growth_protocol: The human hepatocellular carcinoma cell line Huh-7 (CL-0120) was obtained from iCell Bioscience Inc. (Shanghai, China). Huh7 cells were cultured in Dulbecco’s Modified Eagle medium (DMEM; Gibco, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS; Gibco, Carlsbad, CA, USA) and 1% penicillin–streptomycin antibiotics (Pen/Strep; Gibco, Carlsbad, CA, USA) in an atmosphere of 95% humidified air and 5% CO2 at 37 °C.

extract_protocol:
For mitotic samples, synchronized cells were collected by mechanical shake-off, swollen in hypotonic buffer (75 mM KCl), and resuspended in polyamine buffer. Cells were homogenized using a Dounce homogenizer, filtered (10 μm and 5 μm membranes), and centrifuged to isolate purified mitotic chromosomes. Chromosomes were digested with MNase (3000 gel units/mL) at 4 °C overnight in MNase buffer; the reaction was quenched with 20 mM EDTA.  For G1/S samples, synchronized cells were harvested via trypsinization, washed with ice-cold PBS, and permeabilized in MNase buffer containing 0.5% NP-40 to release chromatin. Chromatin was digested with MNase (2000 gel units/mL) at 4 °C overnight. Both mitotic and G1/S digestion products were centrifuged at 10,000 rpm for 7 min at 4 °C, and supernatants containing mononucleosomes were collected. Mononucleosome preparations from G1/S or mitotic phases were subjected to native ChIP. Protein A/G magnetic beads were pre-incubated with target antibodies (anti-mH2A1 or anti-mH2A2) for 1 h at 4 °C, followed by overnight incubation with the mononucleosomes at 4 °C. After immunoprecipitation, beads were washed, and bound nucleosomes were eluted for subsequent sequencing library preparation.
Input mononucleosomes and ChIP-enriched nucleosomes were treated with 100 μg/mL RNase A (Invitrogen, Carlsbad, CA, USA) to remove RNA contamination, followed by overnight digestion with 1% SDS and 200 μg/mL Proteinase K (Invitrogen) at 56 °C. DNA was purified by phenol-chloroform extraction and ethanol precipitation. Sequencing libraries were prepared using approximately 1 ng of purified DNA per sample with the NEBNext® Multiplex Oligos (E7500S, NEB, Ipswich, MA, USA). Libraries were sequenced on the MGI® DNBSEQ-T7 platform.

treatment_protocol: For G1/S state synchronization, cells were first subjected to serum starvation in DMEM containing 0.5% FBS and 1% Pen/Strep for 2 days. Cells were then released into fresh complete medium supplemented with 1% Aphidicolin (Abcam, Cambridge, MA, USA) for 18 h before harvest. For mitotic synchronization, cells were cultured to approximately 80% confluence and treated with 100 ng/mL colcemid (Sigma-Aldrich, St. Louis, MO, USA) for 12 h. Mitotic cells were then collected by mechanical shake-off and used for subsequent mitotic chromosome purification..

value: human hepatocellular carcinoma cells

value: epithelial cells


title: O_CKP_D4_J_rep3

description:
Library name: 1-21J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 3.

source_name: jejunum epithelium

value: jejunum epithelium

value: fractionated abdominal irradiation, 5 × 4 Gy; oral compound Kushen powder treatment


title: CD4+ T cells from healthy control 2, untreated

description: Library name: HC_2_Clean


title: O_CKP_D4_J_rep2

description:
Library name: 1-20J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 2.


title: Pooled screen, 103F, v1, CD34+ enriched, TF dialout

description: Library name: sample_3-4

library_source: other

molecule: other

value: TF dialout PCR


title: O_VC_D4_C_rep3

description:
Library name: 1-15C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 3.

value: fractionated abdominal irradiation, 5 × 4 Gy; oral vehicle treatment with water


title: Trigeminal Ganglion Pitx2 -/- male rep4

description: Library name: TG_M_170_MutA


title: Huh-7, G1/S, macroH2A1 (input)

description: Library name: Huh-7_G1/S_macroH2A1_Control, input


title: CD4+ T cells from healthy control 1, untreated

description: Library name: HC_1_Clean


title: Trigeminal Ganglion Pitx2 +/+ male rep5

description: Library name: TG_M_137_CTRLA


title: O_VC_D4_C_rep2

description:
Library name: 1-14C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 2.


title: CD4+ T cells from BP patient 3, untreated

description: Library name: BP_3_Clean


title: NIC-QUE-DSS r8

city: Zhengzhou

first: huanhuan

last: ma

address: Cuizhu street

institute: china tobacco quality supervision and test center

description: Library name: sample22

data_processing:
RNA-seq
Offline data quality control
Matching genome
Modification site identification (RNA quantification)
Differential site identification (differential RNA identification)
Assembly: Functional enrichment analysis
Supplementary files format and content: Genomic version

organism: Musculus

source_name: colon

extract_protocol:
Appropriate amount of tissue was ground into powder under liquid nitrogen, then transferred into a 2ml EP tube containing 1.5ml of TRIzol, standing for 5 minutes. For cell samples, the TRIzol was directly added to the cell sample with the amount 1 mL per 1×10^6 cells, followed by vortex mixing and standing for 5-minute. The mixture was centrifuged at 4°C at 12,000xg for 5 minutes, and the supernatant was transferred to a new EP tube for extraction. 300μl of chloroform/isoamyl alcohol (24:1) was added into the transferred supernatant and the mixture was vigorously vortexed to ensure thorough mixing. Then the mixture was centrifuged at 4°C and 12,000xg for 8 minutes. Take the clear upper aqueous layer and repeat the above process one time. After centrifugation, the final upper aqueous layer  was carefully transferred to a new 1.5ml EP tube with a 2/3 supernatant volume of isopropanol (for low amount of tissues/ cell, 2µL 5mg/mL glycogen can be added for precipitation), gently inverted to mix well, placed in a -20°C refrigerator for 2 hours. Next, the precipitation mixture was centrifuged with 17500xg at 4°C for 25 minutes. The supernatant was discarded, and the precipitation was washed with 0.9ml of 75% ethanol. The precipitation was suspended by inverting the tube up and down several times. Then the precipitation was collected by centrifuging at 17500g for 3 minutes at 4°C and discarding the supernatant. Repeat the centrifugation to remove supernatant completely and the precipitation was dried in the biosafety cabinet for 3-5 minutes. Finally, 20µL~200µL of DEPC-treated or RNase-free water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Fragment Analyzer or Agilent 2100 Bioanalyzer (Agilent, CA, USA), or Qseq-400 (Bioptic, Taiwan, China).
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA are treated with DNase I to digest DNA, and then rRNA is removed using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (VAZYME-Nanjing, China) (for mammal) / TIANSeq rRNA Depletion Kit (Animal) (TIANGEN-Beijing, China) (for non-mammal). After reacting at a suitable temperature for a fixed time period, the rRNA removed RNAs are fragmented with fragmentation reagents. Then First-strand cDNA is generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis in a new reaction system containing dUTP. The synthesized double strand cDNA is subjected to end repairment reaction. After cDNA end repairment, a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments through A tailing reaction. Then the reaction system for adaptor ligation is configured to ligate adaptors with the cDNAs, and finally, the library products are amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded circularized DNA products. Any single stranded linear DNA molecules will be digested. The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and sequencing reads of PE 100/150 bases length are generated on G400/T7/T10 platform (BGI-Shenzhen, China).

value: colon


title: O_VC_D4_C_rep1

description:
Library name: 1-13C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 1.


title: NIC-QUE-DSS r7

description: Library name: sample21


title: Trigeminal Ganglion Pitx2 -/- male rep3

description: Library name: TG_M_98_MutA


title: CD4+ T cells from BP patient 2, untreated

description: Library name: BP_2_Clean


title: NT_D7_J_rep6

description:
Library name: 2-21J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 6.

value: abdominal irradiation only; no drug treatment


title: CBMS1 mESC, scRepli-seq, untreated singleS 012

status: Public on Jul 13 2026

city: Kobe

first: Jothivanan

last: Elumalai

state: Hyogo

address: 2-2-3, Minatojima Minamimachi, Chuo-ku

department: Biosystems Dynamics Research (BDR)

country: Japan

institute: RIKEN

data_processing:
We used only one end of the paired-end sequenced reads for our analysis. Raw fastq files were subjected to quality assessment with FastQC v0.11.5 , and the cutadapt program v1.15 was used to eliminate SEQXE and Illumina adapters. Mapping to the hg19 or mm9 genome was carried out using bwa v0.7.17-r1188 (bwa-aln command). The resulting mapped reads were sorted using samtools v1.7, and duplicate reads were flagged using picard-tools v2.8.1.
For single-G1 karyotype analysis: After marking the duplicate reads, copy number analysis was conducted using the AneuFinder package v1.22.0 within R v4.1.3. Initially, duplicate reads, blacklist regions (available at https://github.com/Boyle-Lab/Blacklist) and reads with a mapping quality (MAPQ) below 10 were filtered out. Uniquely mapped reads were counted within each 500-Kb genomic window, adjusted for GC content (GC.BSgenome=BSgenome.Hsapiens.UCSC.hg19 for humans and BSgenome.Mmusculus.UCSC.mm9 for mouse, method="loess"), and copy number segmentation was executed using the "findCNVs" function (method='edivisive', R=50) of the AneuFinder package. For quality control (QC), multivariate clustering was applied, and clusters with a spikiness value exceeding 1 were eliminated.
For Log2percentile RT: We followed our established procedure to generate binarized replication timing (RT) profiles for each of the 14 fractions of S-phase or single-cells under analysis, along with their respective percentage replication scores (Miura et al, Nat. Protoc. 2020). The percentage replication score of each S-phase fraction or single-cells was utilized to compute their raw, non-binarized replication timing profile, termed as "log2repliscore RT".
Assembly: hg19, mm9
Supplementary files format and content: CNV states (.txt)
Supplementary files format and content: log2percentile RT (.txt)
Library strategy: scRepli-seq

source_name: Embryo

growth_protocol: Human osteosarcoma cells (U2OS) were cultured in DMEM (Nacalai, 08459-64) supplemented with 10% FBS (Sigma, 172012) and maintained at 37°C with 5% CO2. CBMS1 mouse embryonic stem cells (mESCs) have been described (Murakami et al, Development, 2011) and grown in 2i/LIF medium as described (Hayashi et al, Nat. Protoc. 2013).

extract_protocol:
Single cells were sorted with a Sony SH800 or MA900 cell sorter. Sample preparations were performed as described (Miura et al, Nat. Protoc. 2020). DNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE).
NGS libraries were constructed for amplied DNA using an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions.

treatment_protocol: Cells were subjected to treatment with or without 0.4 μM aphidicolin for 24 hours and labelled with 10 μM EdU for 60 and 15 minutes before harvesting, respectively.

value: Embryo

value: CBMS1 mESC

value: Embryonic Stem Cells

value: Untreated


title: NIC-QUE-DSS r6

description: Library name: sample20


title: Trigeminal Ganglion Pitx2 -/- male rep2

description: Library name: TG_M_91_MutA

value: Cornea


title: 2_Rep1-4

city: Hiroshima

first: Yasuo

last: Kitajima

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

institute: Hiroshima University

description:
Library name: family-2
CaMKII-KO-Pre_training

data_processing:
Read1(10bp of UMI + 9bp of barcode) was assigned to Read2(insert read) by following command "umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC".
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver.0.6.10).
Reads were mapped to the GRCm38 reference using HISAT2 (ver.2.2.1).
Gene count was obtaind by featureCounts(ver.2.0.6) and UMI duplication was ramoved by using UMI tools (ver.1.1.4).
Assembly: GRCm38
Supplementary files format and content: compressed tab separated files(.tsv.gz, .txt.gz)

source_name: Gastrocnemius muscle

extract_protocol:
tissue sections were lysed in ISOGEN II reagent kit (NIPPON GENE) and extract RNA by using RNeasy Mini Kit (QIAGEN).
Libraries were prepared by BRB-Seq(Alpern D, et al.) method. Individual samples were reverse transcribed using dT primer with unique cell barcodes. Then replicate were mixed and amplified by PCR. 10nt of UMI followedby 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.

value: Gastrocnemius muscle


title: NT_D7_J_rep5

description:
Library name: 2-20J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 5.


title: CD4+ T cells from BP patient 1, untreated

description: Library name: BP_1_Clean

value: CD4+ T cells

value: BP


title: Trigeminal Ganglion Pitx2 -/- male rep1

description: Library name: TG_M_90_MutA


title: NIC-QUE-DSS r5

description: Library name: sample19


title: NT_D7_J_rep4

description:
Library name: 2-19J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 4.


title: PC-9  cells, PAX5 OE3

city: hangzhou

first: ailing

last: wu

address: yuhangtang street

institute: hangzhou normal university

description: Library name: Sample6

data_processing:
Illumina Casava 1.8 software used for basecalling
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.
Reference genome and gene model annotation files were downloaded from genome website. Use HISAT2 (2.2.1) to build the index of the reference genome, and use HISAT2 to align paired-end clean reads to3 the reference genome.
featureCounts (2.0.6) 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.
For DESeq2 with biological replicates: Differential expression analysis for two conditions/groups was performed using the DESeq2 R package(1.42.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

extract_protocol:
Total RNA was isolated using TRIzol (TIANGEN) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2 following manufacturer's protocols.

value: human lung adenocarcinoma cell

value: PAX5 overexpressing


title: Trigeminal Ganglion Pitx2 +/+ male rep4

description: Library name: TG_M_85_CTRLA


title: O_VC_D4_J_rep2

description:
Library name: 1-14J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 2.


title: Cornea Pitx2 -/- female rep5

description: Library name: F_97_mut


title: NIC-QUE-DSS r4

description: Library name: sample18


title: PC-9  cells, PAX5 OE2

description: Library name: Sample5


title: NT_D7_J_rep3

description:
Library name: 1-6J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 3.


title: Huh-7, G1/S, macroH2A1, Rep2 (Chip)

description: Library name: Huh-7_G1/S_macroH2A1_Chip, Rep2

value: human hepatocellular carcinoma cells

value: epithelial cells


title: Trigeminal Ganglion Pitx2 +/+ male rep3

description: Library name: TG_M_84_CTRLA


title: PC-9  cells, PAX5 OE1

description: Library name: Sample4


title: NIC-QUE-DSS r3

description: Library name: sample17


title: NT_D7_J_rep2

description:
Library name: 1-5J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 2.

value: jejunum epithelium


title: Huh-7, Meta, macroH2A2 (input)

description: Library name: Huh-7_Meta_macroH2A2_Control, input


title: Trigeminal Ganglion Pitx2 +/+ male rep2

description: Library name: TG_M_79_CTRLA


title: Trigeminal Ganglion Pitx2 +/+ male rep1

description: Library name: TG_M_78_CTRLA


title: NIC-QUE-DSS r1

description: Library name: sample15


title: PC-9  cells, Control2

description: Library name: Sample2

value: WT


title: Trigeminal Ganglion Pitx2 -/- female rep5

description: Library name: TG_F_99_MutA


title: NT_D7_C_rep6

description:
Library name: 2-21C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 6.

value: colon epithelium


title: CBMS1 mESC, scRepli-seq, untreated singleS 004


title: PC-9  cells, Control1

description: Library name: Sample1


title: NT_D7_C_rep5

description:
Library name: 2-20C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 5.


title: DSS r7

description: Library name: sample13

value: colon


title: DSS r8

description: Library name: sample14


title: Trigeminal Ganglion Pitx2 -/- female rep4

description: Library name: TG_F_97_MutA


title: NT_D7_C_rep4

description:
Library name: 2-19C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 4.

value: abdominal irradiation only; no drug treatment


title: Trigeminal Ganglion Pitx2 -/- female rep3

description: Library name: TG_F_96_MutA


title: DSS r6

description: Library name: sample12


title: MDA-MB-231-cGAS-KO+WT-cGAS+shJunB-2

city: Chapel Hill

first: Pengda

last: Liu

state: NC

address: 21-246 Lineberger Building, 450 West Drive, CB7295 450 West Drive, CB7295

department: Biochemistry and Biophysics

institute: The University of North Carolina at Chapel Hill

description: Library name: W2

data_processing:
Data quality control: 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.
Reads mapping to the reference genome: Use HISAT2 (2.2.1) to build the index of the reference genome, and use HISAT2 to align paired-end clean reads to the reference genome.
Quantification of gene expression level: eatureCounts (2.0.6) was used to count the reads numbers mapped to each gene.
Differential expression analysis: Differential expression analysis for two conditions/groups was performed using the DESeq2 R package (1.42.0).
GO and KEGG enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler (4.8.1), in which gene length bias was corrected. KEGG is performed using http://www.genome.jp/kegg/. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO, KEGG data set were used for GSEA independently.
Assembly: hg38
Supplementary files format and content: .xls and .tsv

source_name: breast

growth_protocol: MDA-MB-231 cells are cultured in DMEM medium supplemented with 10% FBS,100 units of penicillin and 100 mg/mL streptomycin at 37 oC with 5% CO2.

extract_protocol:
Biobasic EZ-10 DNAaway RNA Miniprep Kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. 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.

value: breast

value: breast cancer cell

value: cGAS-KO+WT-cGAS-shJunB


title: Trigeminal Ganglion Pitx2 -/- female rep2

description: Library name: TG_F_95_MutA


title: NT_D7_C_rep3

description:
Library name: 1-6C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 3.


title: DSS r5

description: Library name: sample11


title: NT_D7_C_rep2

description:
Library name: 1-5C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 2.


title: MDA-MB-231-cGAS-KO+WT-cGAS+shJunB-1

description: Library name: W1


title: Trigeminal Ganglion Pitx2 -/- female rep1

description: Library name: TG_F_94_MutA


title: MDA-MB-231-cGAS-KO+F491AF503A-cGAS-3

description: Library name: J3


title: NT_D7_C_rep1

description:
Library name: 1-4C
Colon epithelium sample collected at D7 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 1.


title: DSS r3

description: Library name: sample9


title: DSS r4

description: Library name: sample10


title: MDA-MB-231-cGAS-KO+F491AF503A-cGAS-2

description: Library name: J2


title: Trigeminal Ganglion Pitx2 +/+ female rep5

description: Library name: TG_F_88_CTRLA


title: Trigeminal Ganglion Pitx2 +/+ female rep4

description: Library name: TG_F_87_CTRLA


title: CD4+ T cells from BP patient 2, C176 treated

description: Library name: BP_c176_2

value: STING inhibitor C176, 5μM, 24h


title: MDA-MB-231-cGAS-KO+F491AF503A-cGAS-1

description: Library name: J1


title: DSS r2

description: Library name: sample8


title: Cornea Pitx2 +/+ female rep1

description: Library name: F_82_ctrl

value: Cornea


title: O_VC_D4_C_rep6

description:
Library name: 2-15C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the oral vehicle control group; biological replicate 6.

value: fractionated abdominal irradiation, 5 × 4 Gy; oral vehicle treatment with water


title: NT_D4_J_rep5

description:
Library name: 2-11J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 5.


title: Trigeminal Ganglion Pitx2 +/+ female rep3

description: Library name: TG_F_86_CTRLA


title: DSS r1

description: Library name: sample7


title: I_CKI_D4_J_rep3

description:
Library name: 3-6J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen injection treatment group; biological replicate 3.

value: fractionated abdominal irradiation, 5 × 4 Gy; intraperitoneal compound Kushen injection treatment


title: NT_D4_J_rep4

description:
Library name: 2-10J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 4.


title: Trigeminal Ganglion Pitx2 +/+ female rep2

description: Library name: TG_F_83_CTRLA


title: CON r6

description: Library name: sample6


title: NT_D4_J_rep3

description:
Library name: 1-9J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 3.


title: Trigeminal Ganglion Pitx2 +/+ female rep1

description: Library name: TG_F_82_CTRLA


title: CON r5

description: Library name: sample5


title: MDA-MB-231-cGAS-KO+WT-cGAS-1

description: Library name: F1

value: cGAS-KO+WT-cGAS


title: MDA-MB-231-cGAS-KO+WT-cGAS-2

description: Library name: F2


title: CON r4

description: Library name: sample4


title: CON r3

description: Library name: sample3


title: NT_D4_J_rep1

description:
Library name: 1-7J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 1.


title: GDB1331b control male batch 185

city: Napoli

first: Emile

last: Danvin

state: NAPOLI

address: Sergio pansini 5

department: Molecular medicine

country: Italy

institute: Federico II University of Naples

description: Library name: GDB1331b_ctrl_REP1

data_processing:
Raw reads processed using nf-core/rnaseq v3.14.0. Adapter and quality trimming with Trim Galore v0.6.7, Reads aligned to GRCh38 (GENCODE v46) using STAR v2.7.9a. Transcript abundances estimated with Salmon v1.10.1 and summarized to gene-level counts with tximeta
Technical replicates (3 donors sequenced in both batches) collapsed by summing raw counts, yielding 16 unique donors. Batch correction using RUVSeq v1.32.0 (k=2 factors). Differential expression with DESeq2 v1.38.3, design: ~ W1 + W2 + sex + status. Log2FC shrinkage with ashr v2.2.63. Batch correction using RUVSeq v1.32.0 (k=2 factors). Differential expression with DESeq2 v1.38.3, design: ~ W1 + W2 + sex + status. Log2FC shrinkage with ashr v2.2.63.
Genes with FDR < 0.05 and |log2FC| > 1.0 considered differentially expressed. GO enrichment with clusterProfiler v4.6.2.
Assembly: GRCh38 (GENCODE release 46)
Supplementary files format and content: B01_collapsed_counts.tsv: gene-level raw counts matrix (63,086 genes × 16 donors).
Supplementary files format and content: B02_RNA_DE_results.csv: full DESeq2 differential expression results for 17,495 tested genes (baseMean, log2FC, SE, Wald statistic, p-value, padj).
Supplementary files format and content: B01_gene_map.tsv: Ensembl gene ID to HGNC symbol mapping from GENCODE v46.
Supplementary files format and content: B01_collapsed_metadata.csv: sample metadata with donor ID, sex, disease status, batch information.

source_name: dermal fibroblast

growth_protocol: Primary skin fibroblasts were cultured in DMEM/F-12 supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin, and 2 mM L-glutamine at 37°C; 5% CO2.

extract_protocol:
Total RNA was extracted using the Maxwell RSC simplyRNA Cells Kit (Promega) following manufacturer's instructions. RNA concentration was assessed by NanoDrop and RNA integrity was evaluated on an Agilent TapeStation 4150. All RNAs had RINe > 7
Sequencing libraries were prepared from 150 ng of total RNA using the SureSelect XT HS2 mRNA System (Agilent Technologies), which combines poly(A) enrichment with strand-specific library construction. Indexed libraries were pooled at equimolar concentrations and sequenced on an Illumina NextSeq 550 in a 2×75 bp paired-end configuration.

value: dermal fibroblast

value: wild-type


title: NT_D4_C_rep6

description:
Library name: 2-12C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 6.


title: CON r2

description: Library name: sample2


title: TF_1

city: Jinan, Shandong Province

first: yun

middle: xiu

last: li

address: No.238 Jingshi East Road, Jinan City

institute: Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

organism: Candida albicans

growth_protocol: Overnight grown C. albicans CA10，fluconazole treated C. albicans  CA10,iravacycline hydrochloride  treated C. albicans  CA10, and fluconazole combined with iravacycline hydrochloride treated C. albicans  CA10  were diluted to 1E6 cells per milliliter using RPMI1640 medium and cultured for 6 h at 35℃.

extract_protocol:
RNA was extracted using a RiboPure-Yeast kit (Ambion) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CA10 was treated fluconazole  and iravacycline hydrochloride


title: NT_D4_C_rep5

description:
Library name: 2-11C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 5.


title: GDB339 control female batch 185

description: Library name: GDB339_ctrl_REP2


title: CON r1

description: Library name: sample1


title: NT_D4_C_rep4

description:
Library name: 2-10C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 4.


title: T_3

treatment_protocol: Overnight grown C. albicans CA10，fluconazole treated C. albicans  CA10,iravacycline hydrochloride  treated C. albicans  CA10, and fluconazole combined with iravacycline hydrochloride treated C. albicans  CA10  were diluted to 1E6 cells per milliliter using RPMI1640 medium and cultured for 6 h at 35℃.

value: CA10 was treated iravacycline hydrochloride


title: NT_D4_C_rep3

description:
Library name: 1-9C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 3.


title: T_1


title: F_3

value: CA10 was treated fluconazole


title: GDB447 Kabuki syndrome male batch 185

description: Library name: GDB447_KS_REP2

value: KMT2D c.472delT p.Cys158ValfsX50


title: Y308F Rep 1

city: Charlottesville

first: Brooke

last: O'Donnell

state: Virginia

address: 409 Lane Rd.

department: Robert M. Berne Cardiovascular Research Center

institute: University of Virginia

description:
Library name: Y323798
resY308FvControl_Y308F.csv

data_processing:
Paired-end 150 base pair reads were mapped to the Genome Reference Consortium Mouse Build 39 (GRCm39; Accession ID GCA_000001635.9) reference genome using STAR software (v2.7.9a).
Gene counts were generated using featureCounts in the Rsubread (v2.20.0) software package.
Differentially expressed genes (DEGs, Padj < 0.05) were identified using DESeq2 (v1.46.0).
The org.Mm.eg.db package was used to convert Ensemble IDs to gene symbols.
Assembly: GRCm39
Supplementary files format and content: Feature_Counts.csv includes raw count files for each dataset
Supplementary files format and content: NormCounts.csv includes counts normalized with DESeq2
Supplementary files format and content: resKOvWT.csv includes differential expression results of global Panx1 KO mesenteric arteries compared to WT controls.
Supplementary files format and content: resY198FvControl.csv includes differential expression results of Y198F mesenteric arteries compared to controls.
Supplementary files format and content: resS205AvControl_S205A.csv includes differential expression results of S205A mesenteric arteries compared to controls.
Supplementary files format and content: resY308FvControl_Y308F.csv includes differential expression results of Y308F mesenteric arteries compared to controls.

source_name: mesenteric arteries

extract_protocol:
RNeasy MinElute Cleanup Kit (QIAGEN, #74204)
Paired-end 150 base pair reads were generated using the Illumina NovoSeq X platform.

value: mesenteric arteries


title: F_2


title: NT_D4_C_rep1

description:
Library name: 1-7C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 1.

value: colon epithelium


title: Y308F Control Rep 3

description:
Library name: WTY323818
resY308FvControl_Y308F.csv


title: GDB380 Kabuki syndrome male batch 185

description: Library name: GDB380_KS_REP2

value: KMT2D c.588delC p.Cys197Alafs*11


title: NI_J_rep6

description:
Library name: 2-9J
Jejunum epithelium sample from a non-irradiated, non-treated Sprague Dawley rat; biological replicate 6.

value: jejunum epithelium

value: non-irradiated; non-treated


title: NIC-QUE-DSS r2

description: Library name: sample16

value: colon


title: F_1


title: NT_D7_J_rep1

description:
Library name: 1-4J
Jejunum epithelium sample collected at D7 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 1.

value: abdominal irradiation only; no drug treatment


title: PC-9  cells, Control3

description: Library name: Sample3

value: human lung adenocarcinoma cell

value: WT


title: Y308F Control Rep 2

description:
Library name: WTY323817
resY308FvControl_Y308F.csv


title: GDB491 Kabuki syndrome male batch 185

description: Library name: GDB491_KS_REP1

value: KMT2D c.16528T>G p.Tyr5510Asp


title: Y308F Control Rep 1

description:
Library name: WTY323812
resY308FvControl_Y308F.csv


title: MDA-MB-231-cGAS-KO+WT-cGAS+shJunB-3

description: Library name: W3

value: breast

value: breast cancer cell

value: cGAS-KO+WT-cGAS-shJunB


title: GDB598 Kabuki syndrome male batch 84

description: Library name: GDB598_KS_REP1

value: dermal fibroblast


title: NI_J_rep4

description:
Library name: 2-7J
Jejunum epithelium sample from a non-irradiated, non-treated Sprague Dawley rat; biological replicate 4.


title: S205A Rep 4

description:
Library name: S22534
resS205AvControl_S205A.csv


title: GDB587 Kabuki syndrome female batch 84

description: Library name: GDB587_KS_REP1

value: KMT2D c.12966delA p.Gln4322HisfsX62


title: NI_J_rep3

description:
Library name: 1-3J
Jejunum epithelium sample from a non-irradiated, non-treated Sprague Dawley rat; biological replicate 3.


title: Con_2

value: CA10 without compound


title: Con_1


title: S205A Rep 3

description:
Library name: S22425
resS205AvControl_S205A.csv


title: GDB447 Kabuki syndrome male batch 84

description: Library name: GDB447_KS_REP1

value: KMT2D c.472delT p.Cys158ValfsX50


title: NT_D4_J_rep6

description:
Library name: 2-12J
Jejunum epithelium sample collected at D4 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 6.


title: NI_J_rep2

description:
Library name: 1-2J
Jejunum epithelium sample from a non-irradiated, non-treated Sprague Dawley rat; biological replicate 2.


title: S205A Rep 2

description:
Library name: S22229
resS205AvControl_S205A.csv

value: mesenteric arteries


title: Splenic CD27-CD11b+ Ly49C-Ly49I-NKG2A- (TN) NK cells from B2m knockout mouse, biol rep 2

city: Berkeley

first: Yeara

last: Jo

state: CA

address: 485 Weill Hall

institute: University of California, Berkeley

description:
Library name: Sample 17
Column name in tpm_table_with_symbol.csv: KO2_TN

data_processing:
Reads were aligned to the mouse reference genome GRCm39 by using STAR aligner with the following parameters: “--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000”. Gene- and transcript-level quantification was performed using RSEM.
Assembly: GRCm39
Supplementary files format and content: csv files include TPM values for each sample

source_name: Spleen

extract_protocol:
Total RNA was extracted by using miRNeasy Micro Kit (Qiagen) following manufacturer's instructions. RNA integrity was assessed by using bioanalyzer and 50ng RNA from the samples with RIN score > 7 were used to construct sequencing libraries.
RNA-seq libraries were prepared using KAPA MRNA HyperPrep kit (Roche) following manufacturer's instructions.

value: Spleen

value: Natural Killer cells

value: B2m knockout


title: GDB425 Kabuki syndrome female batch 84

description: Library name: GDB425_KS_REP1

value: KMT2D c.7903C>T p.Arg2635X


title: NI_J_rep1

description:
Library name: 1-1J
Jejunum epithelium sample from a non-irradiated, non-treated Sprague Dawley rat; biological replicate 1.

value: jejunum epithelium

value: non-irradiated; non-treated


title: S205A Rep 1

description:
Library name: S24048
resS205AvControl_S205A.csv


title: MDA-MB-231-cGAS-KO+WT-cGAS-3

description: Library name: F3

value: cGAS-KO+WT-cGAS


title: GDB380 Kabuki syndrome male batch 84

description: Library name: GDB380_KS_REP1

value: KMT2D c.588delC p.Cys197Alafs*11


title: Splenic CD27-CD11b+ Ly49C-Ly49I-NKG2A- (TN) NK cells from B2m knockout mouse, biol rep 1

description:
Library name: Sample 16
Column name in tpm_table_with_symbol.csv: KO1_TN


title: NI_C_rep6

description:
Library name: 2-9C
Colon epithelium sample from a non-irradiated, non-treated Sprague Dawley rat; biological replicate 6.

value: colon epithelium


title: TF_3

value: CA10 was treated fluconazole  and iravacycline hydrochloride


title: S205A Control Rep 4

description:
Library name: WTS23558
resS205AvControl_S205A.csv


title: GDB374 Kabuki syndrome male batch 84

description: Library name: GDB374_KS_REP1

value: KMT2D c.5652dup p.Lys1885Glnfs*18


title: TF_2


title: NI_C_rep5

description:
Library name: 2-8C
Colon epithelium sample from a non-irradiated, non-treated Sprague Dawley rat; biological replicate 5.


title: S205A Control Rep 3

description:
Library name: WT22238
resS205AvControl_S205A.csv


title: NI_C_rep4

description:
Library name: 2-7C
Colon epithelium sample from a non-irradiated, non-treated Sprague Dawley rat; biological replicate 4.


title: Splenic CD27-CD11b+ Ly49C-Ly49I+NKG2A- (SP) NK cells from B2m knockout mouse, biol rep 3

description:
Library name: Sample 15
Column name in tpm_table_with_symbol.csv: KO3_SP


title: GDB813 control male batch 84

description: Library name: GDB813_ctrl_REP1

value: wild-type


title: Splenic CD27-CD11b+ Ly49C-Ly49I+NKG2A- (SP) NK cells from B2m knockout mouse, biol rep 2

description:
Library name: Sample 14
Column name in tpm_table_with_symbol.csv: KO2_SP


title: S205A Control Rep 2

description:
Library name: WT22231
resS205AvControl_S205A.csv


title: GDB809 control female batch 84

description: Library name: GDB809_ctrl_REP1

value: dermal fibroblast


title: NI_C_rep3

description:
Library name: 1-3C
Colon epithelium sample from a non-irradiated, non-treated Sprague Dawley rat; biological replicate 3.


title: Splenic CD27-CD11b+ Ly49C-Ly49I+NKG2A- (SP) NK cells from B2m knockout mouse, biol rep 1

description:
Library name: Sample 13
Column name in tpm_table_with_symbol.csv: KO1_SP


title: Y308F Rep 3

description:
Library name: Y323821
resY308FvControl_Y308F.csv


title: T_2

value: CA10 was treated iravacycline hydrochloride


title: GDB728 control female batch 185

description: Library name: GDB728_ctrl_REP1


title: GDB418 control female batch 84

description: Library name: GDB418_ctrl_REP1


title: S205A Control Rep 1

description:
Library name: WT22230
resS205AvControl_S205A.csv


title: GDB682 control female batch 185

description: Library name: GDB682_ctrl_REP1


title: NI_C_rep2

description:
Library name: 1-2C
Colon epithelium sample from a non-irradiated, non-treated Sprague Dawley rat; biological replicate 2.


title: Splenic CD27-CD11b+ Ly49C+Ly49I+NKG2A+ (TP) NK cells from B2m knockout mouse, biol rep 3

description:
Library name: Sample 12
Column name in tpm_table_with_symbol.csv: KO3_TP


title: Y198F Rep 3

description:
Library name: Y122504
resY198FvControl.csv


title: GDB424 control female batch 185

description: Library name: GDB424_ctrl_REP1


title: GDB339 control female batch 84

description: Library name: GDB339_ctrl_REP1


title: NT_D4_C_rep2

description:
Library name: 1-8C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the irradiated non-treated control group; biological replicate 2.

value: abdominal irradiation only; no drug treatment


title: NI_C_rep1

description:
Library name: 1-1C
Colon epithelium sample from a non-irradiated, non-treated Sprague Dawley rat; biological replicate 1.


title: Y308F Rep 2

description:
Library name: Y323820
resY308FvControl_Y308F.csv


title: Y198F Rep 2

description:
Library name: Y122503
resY198FvControl.csv


title: GDB598 Kabuki syndrome male

description: Library name: GDB598_KS

data_processing:
Raw reads processed using nf-core/atacseq v2.1.2. Adapter and quality trimming with Trim Galore v0.6.7. Reads aligned to GRCh38 using BWA-MEM v0.7.17. Duplicates removed with Picard v3.0.0. Mitochondrial reads and ENCODE blacklist regions excluded.
Peaks called per sample using MACS2 v2.2.7.1 in broad-peak mode. Consensus peak set derived using DiffBind v3.8.4 with 250 bp windows centered on peak summits.
Differential accessibility with DESeq2 using RUVSeq correction (k=2, 5000 empirical invariant peaks). Design: ~ W1 + W2 + sex + status. Log2FC shrinkage with ashr. Peaks with FDR < 0.05 and |log2FC| > 1.0 considered differentially accessible.
Peaks annotated using ChIPseeker v1.34.1 with TxDb.Hsapiens.UCSC.hg38.knownGene. GO enrichment with clusterProfiler v4.6.2.
Assembly: GRCh38
Supplementary files format and content: B03_ATAC_DA_peaks.csv: differential accessibility results for all consensus peaks.
Supplementary files format and content: B03_ATAC_DA_peaks_annotated.csv: DA peaks with ChIPseeker annotations.
Supplementary files format and content: Per-sample broadPeak files: MACS2 broad peak calls for each library.
Supplementary files format and content: Per-sample broadPeak files: MACS2 broad peak calls for each library.
Supplementary files format and content: KS_GAINED.bed: genomic coordinates of significantly opening chromatin regions (FDR < 0.05, log2FC > 1.0).
Supplementary files format and content: KS_LOST.bed: genomic coordinates of significantly closing chromatin regions (FDR < 0.05, log2FC < -1.0).
Supplementary files format and content: normalization_factors.csv: DiffBind normalization factors applied to count matrix.

extract_protocol:
Cells were harvested, washed in cold PBS, and viability assessed by trypan blue exclusion. 50,000 viable cells per sample were used for library preparation.
Sequencing libraries were prepared using the ATAC-Seq Express Kit (Active Motif) following manufacturer's instructions. Post-amplification libraries were purified with SPRI beads and quantified using Qubit dsDNA HS Assay. Equimolar pools were sequenced on Illumina NextSeq 550 in 2×75 bp paired-end configuration across four lanes per library.


title: Splenic CD27-CD11b+ Ly49C+Ly49I+NKG2A+ (TP) NK cells from B2m knockout mouse, biol rep 2

description:
Library name: Sample 11
Column name in tpm_table_with_symbol.csv: KO2_TP


title: Splenic CD27-CD11b+ Ly49C+Ly49I+NKG2A+ (TP) NK cells from B2m knockout mouse, biol rep 1

description:
Library name: Sample 10
Column name in tpm_table_with_symbol.csv: KO1_TP


title: Rat_hp_30 hippocampus RRBS, Low intrinsic aerobic capacity, female, aged 23-24 months

city: Budapest

first: Zsolt

last: Radák

address: Budapest, Alkotás u. 42-48, 1123

department: Research Center for Molecular Exercise Science

country: Hungary

institute: University of sports science, Hungary

description:
Library name: Rat_hp_30
Hippocampal genomic DNA from aged female rat; intrinsic aerobic capacity group: Low

data_processing:
Raw RRBS reads were assessed by FastQC and aggregated with MultiQC.
Adapter and low-quality bases were trimmed with Trim Galore v0.6.10 using RRBS-specific (--rrbs) and paired-end (--paired) settings; bases with Phred score <20 were removed.
Trimmed reads were aligned to the Rattus norvegicus reference genome mRatBN7.2/rn7 using Bismark with Bowtie2.
Methylation calls were extracted with bismark_methylation_extractor using the --no_overlap option to generate coverage files.
Downstream methylation analysis was conducted in R with methylKit using non-overlapping 1 kb tiles; significant DMRs were defined by FDR < 0.1 and methylation difference >= 5%.
Assembly: mRatBN7.2/rn7
Supplementary files format and content: Methylation_Matrix_1kb_Tiles.xlsx:containing genome-wide non-overlapping 1 kb tile methylation percentages for all samples. Columns correspond to library names and rows are traceable by rn7 genomic coordinates (chr, start, end, strand).
Supplementary files format and content: *.bismark.cov.gz:  CpG-level methylation coverage files generated by bismark_methylation_extractor.

source_name: hippocampus

growth_protocol: Selectively bred high- and low-running-capacity rats (44th generation) were housed in temperature-controlled rooms under a 12:12-h light-dark cycle with ad libitum access to standard chow and water. Female rats aged 23–24 months were used.

extract_protocol:
Hippocampal tissue was snap-frozen and stored at -80C. Total genomic DNA was extracted using the PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific, USA) according to the manufacturer's instructions.
RRBS libraries were prepared using the Premium RRBS Kit V2 (Diagenode, Seraing, Belgium). Briefly, 100 ng genomic DNA was digested with MspI, followed by end repair, adapter ligation, size selection using Agencourt AMPure XP beads, bisulfite conversion, purification, and PCR amplification. Final library quality was assessed by Qubit dsDNA HS Assay and Agilent Bioanalyzer. Sequencing was performed on an Illumina HiSeq 2500 in paired-end mode.

treatment_protocol: No experimental treatment was applied before tissue collection. Samples represent intrinsic aerobic capacity phenotypes: High and Low.

value: hippocampus

tag: phenotype

value: LCR


title: Y198F Rep 1

description:
Library name: Y122502
resY198FvControl.csv

value: mesenteric arteries


title: GDB587 Kabuki syndrome female

description: Library name: GDB587_KS

value: KMT2D c.12966delA p.Gln4322HisfsX62


title: Rat_hp_26 hippocampus RRBS, Low intrinsic aerobic capacity, female, aged 23-24 months

description:
Library name: Rat_hp_26
Hippocampal genomic DNA from aged female rat; intrinsic aerobic capacity group: Low


title: Splenic CD27-CD11b+ Ly49C-Ly49I-NKG2A- (TN) NK cells from WT mouse, biol rep 3

description:
Library name: Sample 9
Column name in tpm_table_with_symbol.csv: WT3_TN

value: Spleen

value: Natural Killer cells

value: WT


title: Y198F Control Rep 3

description:
Library name: WTY123780
resY198FvControl.csv


title: GDB447 Kabuki syndrome male

description: Library name: GDB447_KS

value: KMT2D c.472delT p.Cys158ValfsX50


title: Rat_hp_24 hippocampus RRBS, Low intrinsic aerobic capacity, female, aged 23-24 months

description:
Library name: Rat_hp_24
Hippocampal genomic DNA from aged female rat; intrinsic aerobic capacity group: Low


title: Splenic CD27-CD11b+ Ly49C-Ly49I-NKG2A- (TN) NK cells from WT mouse, biol rep 2

description:
Library name: Sample 8
Column name in tpm_table_with_symbol.csv: WT2_TN


title: Y198F Control Rep 2

description:
Library name: WTY123779
resY198FvControl.csv


title: GDB425 Kabuki syndrome female

description: Library name: GDB425_KS

value: KMT2D c.7903C>T p.Arg2635X


title: Rat_hp_22 hippocampus RRBS, Low intrinsic aerobic capacity, female, aged 23-24 months

description:
Library name: Rat_hp_22
Hippocampal genomic DNA from aged female rat; intrinsic aerobic capacity group: Low


title: Splenic CD27-CD11b+ Ly49C-Ly49I-NKG2A- (TN) NK cells from WT mouse, biol rep 1

description:
Library name: Sample 7
Column name in tpm_table_with_symbol.csv: WT1_TN


title: Y198F Control Rep 1

description:
Library name: WTY124039
resY198FvControl.csv


title: GDB380 Kabuki syndrome male

description: Library name: GDB380_KS

value: KMT2D c.588delC p.Cys197Alafs*11


title: Splenic CD27-CD11b+ Ly49C-Ly49I+NKG2A- (SP) NK cells from WT mouse, biol rep 3

description:
Library name: Sample 6
Column name in tpm_table_with_symbol.csv: WT3_SP


title: Con_3

value: CA10 without compound


title: Rat_hp_19 hippocampus RRBS, High intrinsic aerobic capacity, female, aged 23-24 months

description:
Library name: Rat_hp_19
Hippocampal genomic DNA from aged female rat; intrinsic aerobic capacity group: High

value: HCR


title: NI_J_rep5

description:
Library name: 2-8J
Jejunum epithelium sample from a non-irradiated, non-treated Sprague Dawley rat; biological replicate 5.

value: jejunum epithelium

value: non-irradiated; non-treated


title: O_CKP_D4_C_rep4

description:
Library name: 2-16C
Colon epithelium sample collected at D4 after fractionated abdominal irradiation from the compound Kushen pill treatment group; biological replicate 4.

value: colon epithelium

value: fractionated abdominal irradiation, 5 × 4 Gy; oral compound Kushen powder treatment


title: Splenic CD27-CD11b+ Ly49C-Ly49I+NKG2A- (SP) NK cells from WT mouse, biol rep 2

description:
Library name: Sample 5
Column name in tpm_table_with_symbol.csv: WT2_SP


title: GDB374 Kabuki syndrome male

description: Library name: GDB374_KS

value: dermal fibroblast

value: KMT2D c.5652dup p.Lys1885Glnfs*18


title: Global Panx1 KO Rep 3

description:
Library name: GKO3
resKOvWT.csv

value: Panx1 KO


title: Rat_hp_18 hippocampus RRBS, Low intrinsic aerobic capacity, female, aged 23-24 months

description:
Library name: Rat_hp_18
Hippocampal genomic DNA from aged female rat; intrinsic aerobic capacity group: Low

value: hippocampus

value: LCR


title: GDB813 control male

description: Library name: GDB813_ctrl

value: wild-type


title: Global Panx1 KO Rep 2

description:
Library name: GKO2
resKOvWT.csv

value: mesenteric arteries


title: Rat_hp_15 hippocampus RRBS, High intrinsic aerobic capacity, female, aged 23-24 months

description:
Library name: Rat_hp_15
Hippocampal genomic DNA from aged female rat; intrinsic aerobic capacity group: High


title: GDB809 control female

description: Library name: GDB809_ctrl


title: Global Panx1 KO Rep 1

description:
Library name: GKO1
resKOvWT.csv


title: Splenic CD27-CD11b+ Ly49C+Ly49I+NKG2A+ (TP) NK cells from WT mouse, biol rep 3

description:
Library name: Sample 3
Column name in tpm_table_with_symbol.csv: WT3_TP

value: Spleen

value: Natural Killer cells

value: WT


title: Splenic CD27-CD11b+ Ly49C-Ly49I+NKG2A- (SP) NK cells from WT mouse, biol rep 1

description:
Library name: Sample 4
Column name in tpm_table_with_symbol.csv: WT1_SP


title: Rat_hp_12 hippocampus RRBS, Low intrinsic aerobic capacity, female, aged 23-24 months

description:
Library name: Rat_hp_12
Hippocampal genomic DNA from aged female rat; intrinsic aerobic capacity group: Low


title: Global WT Rep 3

description:
Library name: GWT3
resKOvWT.csv


title: Rat_hp_11 hippocampus RRBS, High intrinsic aerobic capacity, female, aged 23-24 months

description:
Library name: Rat_hp_11
Hippocampal genomic DNA from aged female rat; intrinsic aerobic capacity group: High


title: Splenic CD27-CD11b+ Ly49C+Ly49I+NKG2A+ (TP) NK cells from WT mouse, biol rep 2

description:
Library name: Sample 2
Column name in tpm_table_with_symbol.csv: WT2_TP


title: Global WT Rep 2

description:
Library name: GWT2
resKOvWT.csv


title: GDB418 control female

description: Library name: GDB418_ctrl


title: GDB339 control female

description: Library name: GDB339_ctrl


title: Splenic CD27-CD11b+ Ly49C+Ly49I+NKG2A+ (TP) NK cells from WT mouse, biol rep 1

description:
Library name: Sample 1
Column name in tpm_table_with_symbol.csv: WT1_TP


title: Rat_hp_1 hippocampus RRBS, High intrinsic aerobic capacity, female, aged 23-24 months

description:
Library name: Rat_hp_1
Hippocampal genomic DNA from aged female rat; intrinsic aerobic capacity group: High


title: Human IgG PhIP-Seq for participant 24, timepoint w36, replicate 1

status: Public on Jul 11 2026

city: Boston

first: Stephen

last: Elledge

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: Library name: Sample_3_698

data_processing:
Seuqencing reads were aligned to library reference files by bowtie.
Read counts were obtained using samtools.
Read counts from multiple samples were merged to generate the read count files.
Assembly: custom peptide library
Supplementary files format and content: * samples from `run id` "IgA Vir 1" or "IgA Vir 2" (sample titles start with "Viral IgA...") use the same "vir3_metadata_geo.csv".
Supplementary files format and content: * samples from `run id` "IgA Hum 1" (sample titles start with "Human IgA...") use "hum_260k_metadata_geo.csv" which has ids ranging from 1 to 259345.
Supplementary files format and content: * samples from `run id` "IgG Hum 1" or "IgG Hum 2" (sample titles start with "Human IgG...") use a variation of the human library for which the reference fasta is attached "hu600_50nt.fasta" with ids ranging from "hu_1" to "hu_605375".
Supplementary files format and content: counts

source_name: blood

extract_protocol:
Phage display libraries were mixed with human sera to allow antibodies from sera to bind to displayed peptides. These complexes were then immunoprecipitated using Dynabeads coated either with protein A/G (for IgG) or strepavidin conjugated to biotinylated anti-IgA antibody (for IgA). Phage were then lysed and the contained DNA coding for the displayed peptides were amplified and barcoded by PCR, pooled, gel extracted, and prepared for Illumina sequencing.
Peptide libraries tiling across the proteins from viruses that infect humans (VirScan) and the human proteome were packaged in T7 bacteriophage and expanded as described in Xu et al (DOI:10.1126/science.aaa0698) and Larman et al (DOI: 10.1038/nbt.1856).

value: blood

tag: phip isotype

value: IgG

tag: participant id

tag: time point

tag: replicate

tag: run id

value: IgG Hum 1

tag: outcome

value: birth

tag: series


title: Global WT Rep 1

description:
Library name: GWT1
resKOvWT.csv


title: Human IgG PhIP-Seq for participant 24, timepoint Post, replicate 1

description: Library name: Sample_3_697

value: Post


title: Human IgG PhIP-Seq for participant 24, timepoint w20, replicate 1

description: Library name: Sample_3_696


title: Human IgG PhIP-Seq for participant 24, timepoint w12, replicate 1

description: Library name: Sample_3_695


title: Human IgG PhIP-Seq for participant 24, timepoint Pre, replicate 1

description: Library name: Sample_3_691

value: Pre


title: Human IgG PhIP-Seq for participant 24, timepoint w0, replicate 1

description: Library name: Sample_3_693


title: Human IgG PhIP-Seq for participant 24, timepoint w4, replicate 1

description: Library name: Sample_3_694


title: Human IgG PhIP-Seq for participant 23, timepoint Post, replicate 1

description: Library name: Sample_3_689


title: Human IgG PhIP-Seq for participant 20, timepoint w4, replicate 1

description: Library name: Sample_3_692


title: Human IgG PhIP-Seq for participant 23, timepoint w20, replicate 1

description: Library name: Sample_3_688


title: Human IgG PhIP-Seq for participant 23, timepoint w4, replicate 1

description: Library name: Sample_3_686


title: Human IgG PhIP-Seq for participant 23, timepoint w12, replicate 1

description: Library name: Sample_3_687


title: Human IgG PhIP-Seq for participant 23, timepoint w0, replicate 1

description: Library name: Sample_3_685


title: Human IgG PhIP-Seq for participant 23, timepoint w36, replicate 1

description: Library name: Sample_3_690


title: Splenic CD27-CD11b+ Ly49C-Ly49I-NKG2A- (TN) NK cells from B2m knockout mouse, biol rep 3

description:
Library name: Sample 18
Column name in tpm_table_with_symbol.csv: KO3_TN

value: B2m knockout


title: Human IgG PhIP-Seq for participant 23, timepoint Pre, replicate 1

description: Library name: Sample_3_684


title: Human IgG PhIP-Seq for participant 22, timepoint w36, replicate 1

description: Library name: Sample_3_683


title: Human IgG PhIP-Seq for participant 20, timepoint w0, replicate 1

description: Library name: Sample_3_681


title: Human IgG PhIP-Seq for participant 22, timepoint Post, replicate 1

description: Library name: Sample_3_682


title: Human IgG PhIP-Seq bead control S192, run IgG Hum 1

description: Library name: Sample_3_680

value: beads

value: error


title: Human IgG PhIP-Seq bead control S191, run IgG Hum 1

description: Library name: Sample_3_679


title: Human IgG PhIP-Seq bead control S190, run IgG Hum 1

description: Library name: Sample_3_678


title: Human IgG PhIP-Seq bead control S189, run IgG Hum 1

description: Library name: Sample_3_676


title: Human IgG PhIP-Seq bead control S188, run IgG Hum 1

description: Library name: Sample_3_675


title: Human IgG PhIP-Seq bead control S187, run IgG Hum 1

description: Library name: Sample_3_674


title: Human IgG PhIP-Seq bead control S186, run IgG Hum 1

description: Library name: Sample_3_673


title: Human IgG PhIP-Seq bead control S184, run IgG Hum 1

description: Library name: Sample_3_671


title: Human IgG PhIP-Seq bead control S182, run IgG Hum 1

description: Library name: Sample_3_669


title: Human IgG PhIP-Seq bead control S183, run IgG Hum 1

description: Library name: Sample_3_670


title: Human IgG PhIP-Seq for participant 22, timepoint w20, replicate 1

description: Library name: Sample_3_677


title: Human IgG PhIP-Seq bead control S179, run IgG Hum 1

description: Library name: Sample_3_665


title: Human IgG PhIP-Seq for participant 19, timepoint w8, replicate 1

description: Library name: Sample_3_663

value: loss


title: Human IgG PhIP-Seq for participant 22, timepoint w12, replicate 1

description: Library name: Sample_3_666


title: Human IgG PhIP-Seq for participant 19, timepoint w4, replicate 1

description: Library name: Sample_3_662


title: Human IgG PhIP-Seq bead control S181, run IgG Hum 1

description: Library name: Sample_3_668


title: Human IgG PhIP-Seq for participant 7, timepoint w4, replicate 1

description: Library name: Sample_3_657


title: Human IgG PhIP-Seq for participant 22, timepoint w4, replicate 1

description: Library name: Sample_3_655


title: Human IgG PhIP-Seq bead control S180, run IgG Hum 1

description: Library name: Sample_3_667


title: Human IgG PhIP-Seq for participant 7, timepoint w12, replicate 1

description: Library name: Sample_3_659


title: Human IgG PhIP-Seq for participant 7, timepoint Pre, replicate 1

description: Library name: Sample_3_654


title: Human IgG PhIP-Seq for participant 13, timepoint w8, replicate 1

description: Library name: Sample_3_653


title: Human IgG PhIP-Seq for participant 13, timepoint Pre, replicate 1

description: Library name: Sample_3_650


title: Human IgG PhIP-Seq for participant 18, timepoint w4, replicate 1

description: Library name: Sample_3_648


title: Human IgG PhIP-Seq for participant 18, timepoint Pre, replicate 1

description: Library name: Sample_3_646


title: Human IgG PhIP-Seq for participant 18, timepoint w8, replicate 1

description: Library name: Sample_3_649


title: Human IgG PhIP-Seq for participant 1, timepoint w0, replicate 1

description: Library name: Sample_3_642


title: Human IgG PhIP-Seq bead control S178, run IgG Hum 1

description: Library name: Sample_3_664


title: Human IgG PhIP-Seq for participant 8, timepoint w0, replicate 1

description: Library name: Sample_3_634


title: Human IgG PhIP-Seq for participant 3, timepoint w8, replicate 1

description: Library name: Sample_3_631


title: Human IgG PhIP-Seq for participant 8, timepoint Pre, replicate 1

description: Library name: Sample_3_632


title: Human IgG PhIP-Seq for participant 3, timepoint w0, replicate 1

description: Library name: Sample_3_629


title: Human IgG PhIP-Seq for participant 3, timepoint Pre, replicate 1

description: Library name: Sample_3_628


title: Human IgG PhIP-Seq bead control S143, run IgG Hum 1

description: Library name: Sample_3_626


title: Human IgG PhIP-Seq bead control S142, run IgG Hum 1

description: Library name: Sample_3_625


title: Human IgG PhIP-Seq bead control S141, run IgG Hum 1

description: Library name: Sample_3_624


title: Human IgG PhIP-Seq bead control S140, run IgG Hum 1

description: Library name: Sample_3_623


title: Human IgG PhIP-Seq for participant 21, timepoint w36, replicate 1

description: Library name: Sample_3_622


title: Human IgG PhIP-Seq bead control S139, run IgG Hum 1

description: Library name: Sample_3_621


title: Human IgG PhIP-Seq bead control S138, run IgG Hum 1

description: Library name: Sample_3_620


title: Human IgG PhIP-Seq bead control S185, run IgG Hum 1

description: Library name: Sample_3_672


title: Human IgG PhIP-Seq for participant 19, timepoint Pre, replicate 1

description: Library name: Sample_3_660


title: Human IgG PhIP-Seq for participant 19, timepoint w0, replicate 1

description: Library name: Sample_3_661


title: Human IgG PhIP-Seq for participant 7, timepoint w0, replicate 1

description: Library name: Sample_3_656


title: Human IgG PhIP-Seq for participant 7, timepoint w8, replicate 1

description: Library name: Sample_3_658


title: Human IgG PhIP-Seq bead control S137, run IgG Hum 1

description: Library name: Sample_3_619


title: Human IgG PhIP-Seq for participant 13, timepoint w0, replicate 1

description: Library name: Sample_3_651


title: Human IgG PhIP-Seq for participant 31, timepoint w12, replicate 1

description: Library name: Sample_3_617


title: Human IgG PhIP-Seq bead control S136, run IgG Hum 1

description: Library name: Sample_3_618


title: Human IgG PhIP-Seq for participant 13, timepoint w4, replicate 1

description: Library name: Sample_3_652


title: Human IgG PhIP-Seq for participant 31, timepoint w4, replicate 1

description: Library name: Sample_3_616


title: Human IgG PhIP-Seq for participant 22, timepoint w0, replicate 1

description: Library name: Sample_3_644


title: Human IgG PhIP-Seq for participant 18, timepoint w0, replicate 1

description: Library name: Sample_3_647


title: Human IgG PhIP-Seq for participant 31, timepoint w0, replicate 1

description: Library name: Sample_3_615


title: Human IgG PhIP-Seq for participant 1, timepoint w4, replicate 1

description: Library name: Sample_3_643


title: Human IgG PhIP-Seq for participant 1, timepoint w8, replicate 1

description: Library name: Sample_3_645


title: Human IgG PhIP-Seq for participant 31, timepoint Pre, replicate 1

description: Library name: Sample_3_614


title: Human IgG PhIP-Seq for participant 30, timepoint Post, replicate 1

description: Library name: Sample_3_612


title: Human IgG PhIP-Seq for participant 30, timepoint w36, replicate 1

description: Library name: Sample_3_613


title: Human IgG PhIP-Seq for participant 12, timepoint w8, replicate 1

description: Library name: Sample_3_640


title: Human IgG PhIP-Seq for participant 1, timepoint Pre, replicate 1

description: Library name: Sample_3_641


title: Human IgG PhIP-Seq for participant 12, timepoint w4, replicate 1

description: Library name: Sample_3_639


title: Human IgG PhIP-Seq for participant 21, timepoint Post, replicate 1

description: Library name: Sample_3_611


title: Human IgG PhIP-Seq for participant 12, timepoint w0, replicate 1

description: Library name: Sample_3_638


title: Human IgG PhIP-Seq for participant 12, timepoint Pre, replicate 1

description: Library name: Sample_3_637


title: Human IgG PhIP-Seq for participant 8, timepoint w8, replicate 1

description: Library name: Sample_3_636


title: Human IgG PhIP-Seq for participant 8, timepoint w4, replicate 1

description: Library name: Sample_3_635


title: Human IgG PhIP-Seq for participant 30, timepoint w12, replicate 1

description: Library name: Sample_3_609


title: Human IgG PhIP-Seq for participant 30, timepoint w20, replicate 1

description: Library name: Sample_3_610


title: Human IgG PhIP-Seq for participant 30, timepoint w4, replicate 1

description: Library name: Sample_3_608


title: Human IgG PhIP-Seq for participant 30, timepoint w0, replicate 1

description: Library name: Sample_3_607


title: Human IgG PhIP-Seq for participant 30, timepoint Pre, replicate 1

description: Library name: Sample_3_606


title: Human IgG PhIP-Seq for participant 22, timepoint Pre, replicate 1

description: Library name: Sample_3_633


title: Human IgG PhIP-Seq for participant 29, timepoint w36, replicate 1

description: Library name: Sample_3_605


title: Human IgG PhIP-Seq for participant 3, timepoint w4, replicate 1

description: Library name: Sample_3_630


title: Human IgG PhIP-Seq for participant 29, timepoint Post, replicate 1

description: Library name: Sample_3_604


title: Human IgG PhIP-Seq for participant 29, timepoint w20, replicate 1

description: Library name: Sample_3_603


title: Human IgG PhIP-Seq for participant 29, timepoint w4, replicate 1

description: Library name: Sample_3_601


title: Human IgG PhIP-Seq for participant 21, timepoint w20, replicate 1

description: Library name: Sample_3_600


title: Human IgG PhIP-Seq for participant 29, timepoint w12, replicate 1

description: Library name: Sample_3_602


title: Human IgG PhIP-Seq for participant 28, timepoint w36, replicate 1

description: Library name: Sample_3_597


title: Human IgG PhIP-Seq for participant 29, timepoint w0, replicate 1

description: Library name: Sample_3_599


title: Human IgG PhIP-Seq for participant 28, timepoint Post, replicate 1

description: Library name: Sample_3_596


title: Human IgG PhIP-Seq for participant 28, timepoint w20, replicate 1

description: Library name: Sample_3_595


title: Human IgG PhIP-Seq for participant 29, timepoint Pre, replicate 1

description: Library name: Sample_3_598


title: Human IgG PhIP-Seq for participant 28, timepoint w12, replicate 1

description: Library name: Sample_3_594


title: Human IgG PhIP-Seq for participant 28, timepoint Pre, replicate 1

description: Library name: Sample_3_591


title: Human IgG PhIP-Seq for participant 28, timepoint w4, replicate 1

description: Library name: Sample_3_593


title: Human IgG PhIP-Seq for participant 27, timepoint w36, replicate 1

description: Library name: Sample_3_590


title: Human IgG PhIP-Seq for participant 21, timepoint w12, replicate 1

description: Library name: Sample_3_589


title: Human IgG PhIP-Seq for participant 27, timepoint Post, replicate 1

description: Library name: Sample_3_588


title: Human IgG PhIP-Seq for participant 28, timepoint w0, replicate 1

description: Library name: Sample_3_592


title: Human IgG PhIP-Seq for participant 27, timepoint w20, replicate 1

description: Library name: Sample_3_587


title: Human IgG PhIP-Seq for participant 27, timepoint w12, replicate 1

description: Library name: Sample_3_586


title: Human IgG PhIP-Seq for participant 27, timepoint w0, replicate 1

description: Library name: Sample_3_584


title: Human IgG PhIP-Seq for participant 27, timepoint w4, replicate 1

description: Library name: Sample_3_585


title: Human IgG PhIP-Seq bead control S144, run IgG Hum 1

description: Library name: Sample_3_627


title: Human IgG PhIP-Seq for participant 27, timepoint Pre, replicate 1

description: Library name: Sample_3_583


title: Human IgG PhIP-Seq for participant 26, timepoint w36, replicate 1

description: Library name: Sample_3_582


title: Human IgG PhIP-Seq for participant 26, timepoint w20, replicate 1

description: Library name: Sample_3_580


title: Human IgG PhIP-Seq for participant 26, timepoint Post, replicate 1

description: Library name: Sample_3_581


title: Human IgG PhIP-Seq for participant 26, timepoint w12, replicate 1

description: Library name: Sample_3_579


title: Human IgG PhIP-Seq for participant 20, timepoint Pre, replicate 1

description: Library name: Sample_3_577


title: Human IgG PhIP-Seq for participant 21, timepoint w4, replicate 1

description: Library name: Sample_3_578


title: Viral IgA PhIP-Seq for participant 15, timepoint w0, replicate 2

description: Library name: Sample_3_575

value: IgA

value: IgA Vir 2


title: Viral IgA PhIP-Seq bead control S96, run IgA Vir 2

description: Library name: Sample_3_573


title: Viral IgA PhIP-Seq bead control S95, run IgA Vir 2

description: Library name: Sample_3_572


title: Viral IgA PhIP-Seq for participant 116, timepoint w36, replicate 2

description: Library name: Sample_3_571


title: Viral IgA PhIP-Seq for participant 112, timepoint w36, replicate 2

description: Library name: Sample_3_570


title: Viral IgA PhIP-Seq for participant 112, timepoint w20, replicate 2

description: Library name: Sample_3_568


title: Viral IgA PhIP-Seq for participant 98, timepoint Post, replicate 2

description: Library name: Sample_3_567


title: Viral IgA PhIP-Seq for participant 102, timepoint w0, replicate 2

description: Library name: Sample_3_566


title: Viral IgA PhIP-Seq for participant 89, timepoint w36, replicate 2

description: Library name: Sample_3_564


title: Viral IgA PhIP-Seq for participant 89, timepoint Post, replicate 2

description: Library name: Sample_3_563


title: Viral IgA PhIP-Seq for participant 89, timepoint w12, replicate 2

description: Library name: Sample_3_561


title: Viral IgA PhIP-Seq bead control S84, run IgA Vir 2

description: Library name: Sample_3_560


title: Viral IgA PhIP-Seq bead control S82, run IgA Vir 2

description: Library name: Sample_3_558


title: Viral IgA PhIP-Seq for participant 108, timepoint w36, replicate 2

description: Library name: Sample_3_557


title: Viral IgA PhIP-Seq for participant 102, timepoint Pre, replicate 2

description: Library name: Sample_3_555


title: Viral IgA PhIP-Seq for participant 89, timepoint w20, replicate 2

description: Library name: Sample_3_562


title: Viral IgA PhIP-Seq for participant 108, timepoint w4, replicate 2

description: Library name: Sample_3_552


title: Viral IgA PhIP-Seq for participant 108, timepoint w0, replicate 2

description: Library name: Sample_3_551


title: Viral IgA PhIP-Seq for participant 108, timepoint Pre, replicate 2

description: Library name: Sample_3_550


title: Viral IgA PhIP-Seq for participant 112, timepoint w12, replicate 2

description: Library name: Sample_3_549


title: Viral IgA PhIP-Seq for participant 112, timepoint w0, replicate 2

description: Library name: Sample_3_547


title: Viral IgA PhIP-Seq for participant 112, timepoint Pre, replicate 2

description: Library name: Sample_3_546


title: Viral IgA PhIP-Seq for participant 111, timepoint Post, replicate 2

description: Library name: Sample_3_543


title: Viral IgA PhIP-Seq for participant 101, timepoint w36, replicate 2

description: Library name: Sample_3_544


title: Viral IgA PhIP-Seq for participant 111, timepoint w36, replicate 2

description: Library name: Sample_3_545


title: Viral IgA PhIP-Seq for participant 110, timepoint w36, replicate 2

description: Library name: Sample_3_537


title: Viral IgA PhIP-Seq for participant 110, timepoint Post, replicate 2

description: Library name: Sample_3_536


title: Viral IgA PhIP-Seq for participant 101, timepoint Post, replicate 2

description: Library name: Sample_3_533


title: Viral IgA PhIP-Seq for participant 110, timepoint w4, replicate 2

description: Library name: Sample_3_532


title: Viral IgA PhIP-Seq for participant 109, timepoint Post, replicate 2

description: Library name: Sample_3_528


title: Viral IgA PhIP-Seq for participant 110, timepoint w0, replicate 2

description: Library name: Sample_3_531


title: Viral IgA PhIP-Seq for participant 109, timepoint w20, replicate 2

description: Library name: Sample_3_527


title: Viral IgA PhIP-Seq for participant 109, timepoint w4, replicate 2

description: Library name: Sample_3_525


title: Viral IgA PhIP-Seq for participant 109, timepoint w0, replicate 2

description: Library name: Sample_3_524


title: Viral IgA PhIP-Seq for participant 109, timepoint Pre, replicate 2

description: Library name: Sample_3_523


title: Viral IgA PhIP-Seq for participant 101, timepoint w20, replicate 2

description: Library name: Sample_3_522


title: Viral IgA PhIP-Seq for participant 107, timepoint Post, replicate 2

description: Library name: Sample_3_520


title: Viral IgA PhIP-Seq for participant 107, timepoint w20, replicate 2

description: Library name: Sample_3_519


title: Viral IgA PhIP-Seq for participant 107, timepoint w4, replicate 2

description: Library name: Sample_3_517


title: Viral IgA PhIP-Seq for participant 107, timepoint w0, replicate 2

description: Library name: Sample_3_516


title: Viral IgA PhIP-Seq for participant 107, timepoint Pre, replicate 2

description: Library name: Sample_3_515


title: Viral IgA PhIP-Seq for participant 106, timepoint w36, replicate 2

description: Library name: Sample_3_514


title: Viral IgA PhIP-Seq for participant 106, timepoint Post, replicate 2

description: Library name: Sample_3_513


title: Viral IgA PhIP-Seq for participant 111, timepoint w20, replicate 2

description: Library name: Sample_3_542


title: Viral IgA PhIP-Seq for participant 106, timepoint w20, replicate 2

description: Library name: Sample_3_512


title: Viral IgA PhIP-Seq for participant 101, timepoint w12, replicate 2

description: Library name: Sample_3_511


title: Viral IgA PhIP-Seq for participant 111, timepoint w4, replicate 2

description: Library name: Sample_3_540


title: Viral IgA PhIP-Seq for participant 111, timepoint w0, replicate 2

description: Library name: Sample_3_539


title: Viral IgA PhIP-Seq for participant 110, timepoint w20, replicate 2

description: Library name: Sample_3_535


title: Viral IgA PhIP-Seq for participant 106, timepoint w4, replicate 2

description: Library name: Sample_3_509


title: Viral IgA PhIP-Seq for participant 109, timepoint w36, replicate 2

description: Library name: Sample_3_529


title: Viral IgA PhIP-Seq for participant 106, timepoint w0, replicate 2

description: Library name: Sample_3_508


title: Viral IgA PhIP-Seq for participant 110, timepoint Pre, replicate 2

description: Library name: Sample_3_530


title: Viral IgA PhIP-Seq for participant 106, timepoint w12, replicate 2

description: Library name: Sample_3_510


title: Viral IgA PhIP-Seq for participant 106, timepoint Pre, replicate 2

description: Library name: Sample_3_507


title: Viral IgA PhIP-Seq for participant 105, timepoint w36, replicate 2

description: Library name: Sample_3_506


title: Viral IgA PhIP-Seq for participant 105, timepoint Post, replicate 2

description: Library name: Sample_3_505


title: Viral IgA PhIP-Seq for participant 105, timepoint w20, replicate 2

description: Library name: Sample_3_504


title: Viral IgA PhIP-Seq for participant 105, timepoint w12, replicate 2

description: Library name: Sample_3_503


title: Viral IgA PhIP-Seq for participant 101, timepoint w4, replicate 2

description: Library name: Sample_3_500


title: Viral IgA PhIP-Seq for participant 105, timepoint w0, replicate 2

description: Library name: Sample_3_501


title: Viral IgA PhIP-Seq for participant 104, timepoint w36, replicate 2

description: Library name: Sample_3_498


title: Viral IgA PhIP-Seq for participant 104, timepoint Post, replicate 2

description: Library name: Sample_3_497


title: Viral IgA PhIP-Seq for participant 104, timepoint w20, replicate 2

description: Library name: Sample_3_496


title: Viral IgA PhIP-Seq for participant 104, timepoint Pre, replicate 2

description: Library name: Sample_3_492


title: Viral IgA PhIP-Seq for participant 103, timepoint Post, replicate 2

description: Library name: Sample_3_490


title: Viral IgA PhIP-Seq for participant 103, timepoint w36, replicate 2

description: Library name: Sample_3_491


title: Viral IgA PhIP-Seq for participant 101, timepoint w0, replicate 2

description: Library name: Sample_3_489


title: Viral IgA PhIP-Seq bead control S192, run IgA Vir 2

description: Library name: Sample_3_488


title: Viral IgA PhIP-Seq for participant 81, timepoint w36, replicate 2

description: Library name: Sample_3_487


title: Viral IgA PhIP-Seq for participant 81, timepoint Post, replicate 2

description: Library name: Sample_3_486


title: Viral IgA PhIP-Seq for participant 81, timepoint w20, replicate 2

description: Library name: Sample_3_484


title: Viral IgA PhIP-Seq for participant 68, timepoint w12, replicate 2

description: Library name: Sample_3_483


title: Viral IgA PhIP-Seq for participant 52, timepoint w20, replicate 2

description: Library name: Sample_3_482


title: Viral IgA PhIP-Seq for participant 39, timepoint w12, replicate 2

description: Library name: Sample_3_481


title: Viral IgA PhIP-Seq for participant 30, timepoint Post, replicate 2

description: Library name: Sample_3_479


title: Viral IgA PhIP-Seq for participant 30, timepoint w36, replicate 2

description: Library name: Sample_3_480


title: Viral IgA PhIP-Seq for participant 30, timepoint w20, replicate 2

description: Library name: Sample_3_478


title: Viral IgA PhIP-Seq for participant 105, timepoint w4, replicate 2

description: Library name: Sample_3_502


title: Viral IgA PhIP-Seq for participant 105, timepoint Pre, replicate 2

description: Library name: Sample_3_499


title: Viral IgA PhIP-Seq for participant 27, timepoint w36, replicate 2

description: Library name: Sample_3_477


title: Viral IgA PhIP-Seq for participant 27, timepoint Post, replicate 2

description: Library name: Sample_3_476


title: Viral IgA PhIP-Seq for participant 104, timepoint w12, replicate 2

description: Library name: Sample_3_495


title: Viral IgA PhIP-Seq bead control S180, run IgA Vir 2

description: Library name: Sample_3_475


title: Viral IgA PhIP-Seq for participant 104, timepoint w4, replicate 2

description: Library name: Sample_3_494


title: Viral IgA PhIP-Seq for participant 104, timepoint w0, replicate 2

description: Library name: Sample_3_493


title: Viral IgA PhIP-Seq bead control S179, run IgA Vir 2

description: Library name: Sample_3_473


title: Viral IgA PhIP-Seq for participant 103, timepoint w12, replicate 2

description: Library name: Sample_3_474


title: Viral IgA PhIP-Seq bead control S177, run IgA Vir 2

description: Library name: Sample_3_471


title: Viral IgA PhIP-Seq bead control S178, run IgA Vir 2

description: Library name: Sample_3_472


title: Viral IgA PhIP-Seq for participant 15, timepoint w4, replicate 2

description: Library name: Sample_3_576


title: Viral IgA PhIP-Seq for participant 112, timepoint Post, replicate 2

description: Library name: Sample_3_569


title: Viral IgA PhIP-Seq bead control S176, run IgA Vir 2

description: Library name: Sample_3_470