title: DN-P-701_Well_H12

city: Ede

first: Alphonsus

middle: Chinedu

last: Ugwu

state: osun state

address: redeemers' university ede osun state

department: Biological Sciences

country: Nigeria

institute: Africa Centre of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s 6 University, Ede, Osun State, Nigeria

data_processing:
Sequence data were analysed using the Seven Bridges Genomics bioinformatics platform (BD: Precise Whole Transcriptome Assay Analysis Pipeline v2.0). This pipeline performs all required steps to demultiplex, align, and quantitate sequencing reads from BD™ Precise Whole Transcriptome Assay. After performing a quality control assessment using FastQC, the pipeline filters and demultiplexes sequencing reads based on the sequence of the 8 base sample barcode. It aligns reads from each sample to the transcriptome using STAR, with feature counting by the union rules of HTSeq-count. The initial quantification is performed by counting the unique molecular indices (MI) mapped to each feature. Lastly, the pipeline uses two error correction algorithms to remove MI errors. In brief, MI errors that are derived from sequencing base calls and PCR substitution errors are identified and adjusted to a single MI barcode using Recursive Substitution Error Correction™ (RSEC). Subsequently, MI errors that are derived from library preparation steps or sequencing base deletion errors are adjusted using Distribution-Based Error Correction™ (DBEC).
A cell was considered to be infected if there was at least one GFP sequence read count. This information was then used to define the groups to compare in EdgeR. Differential gene expression was measured between infected and uninfected cells in each subset (Adjusted p-value less than 0.05).
Precise WTA Sample Demultiplexing:Paired-end reads are demultiplexed per well based on the sequence of the sample index. This sample index is found in the first 8 bases of Read 01. The Molecular Index is found in Read 01, in positions 8 to 16. The demultiplexing process also includes a structure filtering step. After filtering, the final step in this process stores the Molecular Index in the demultiplexed FASTQ files by appending the index to the sequence headers of Read 02 FASTQ files. The Read 02s from each well are trimmed by Flexbar to remove any Illumina adapter contaminants and mapped to the reference genome using STAR.
Precise WTA Alignment Quantification: After Read 02s are aligned using STAR, the alignments are assigned to gene counts using a custom implementation of HTSeq-count. The number of reads mapping to each gene is generated in the DBEC Read Mapping Report. The unique counts for molecular indices are calculated in the DBEC Molecular Index Mapping Report
Genome_build: mm9
Supplementary_files_format_and_content: text document (after removal of Molecular indices error using Recursive Substitution Error Correction™ (RSEC) and Distribution-Based Error Correction™ (DBEC))

source_name: Bone marrow derived APC

growth_protocol: BM derived cells were generated by incubating bone marrow stem cells with growth factor (GM-CSF/ IL-4) for 6 days in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10 % foetal calf serum (FCS), 100 U penicillin/ml, 0.1 mg streptomycin/ml and 50 M 2-mercaptoethanol. Differentiated cells were harvested and sorted into the three BM geoups by flow cytometry before infection with LCMV or stimulation with poly (I:C).

extract_protocol:
The cells are collected in WTA single cell encoding plate, RNA secondary structure is done at 65C for 3 minutes (hold at 4C), mastermix containing BD customised RT enzymes is added (PN 650000041) and run at 42C for 30 minutes, heat inactivated at 80C for 5 minutes before holding at 4C. The samples is pooled and purify before library prep.
Libraries of the cellular RNA were made using the BD WTA single cell kit and sequenced using MiSeq V2 from Illumina (BM-DC, BM-M, DN).

treatment_protocol: Sorted CD11c+MHC class II+ bone marrow derived cell populations (dendritic cells [BMDC], macrophages [BM-M], double negative cells [DN]) were infected with LCMV clone 13 expressing GFP, as previously described for 12 and 48hr for single cell (from the 12 h culture) sorting into customised BD WTA single cell encoding plates for RNA extraction and reverse transcription (primary infection) according to manufacturer’s instructions (PN 910000014 Rev. 03). Furthermore, a subset of infected cells (from the 48 h culture) were stimulated with 100 µg poly (I:C)/ml and incubated for another 6hr before single cell sorting as above.

value: Bone marrow derived APC

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: DN-P-701_Well_H11

status: Public on Dec 31 2023

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: strain

tag: treatment


title: 958470-300_lib30909

city: Seattle

first: Naresh

last: Doni Jayavelu

state: WA

address: 1201 9th AVE

department: Systems Immunology/Bioinformatics

country: USA

institute: Benaroya Research Institute at Virginia Mason

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2) was used to remove any remaining adapter sequence.
Reads were aligned by STAR v2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2), and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: raw_counts_ITN_GRASS_nasal_samples.csv is a csv file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

organism: Homo sapiens

source_name: Nasal Brush

extract_protocol:
RNA was extracted from TRIzol following the manufacturer’s protocol (Invitrogen)
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.

tag: tissue

value: Nasal Brush

tag: age

tag: Sex

value: Female

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id

tag: visit number

value: SCIT


title: Adipose 801-A F

city: Bar Harbor

first: Kristen

last: O'Connell

state: ME

address: 600 Main St

institute: The Jackson Laboratory

library_source: genomic

data_processing:
Mouse raw-reads from the 386 samples described above were quality and adapter trimmed with cutadapt v2.3 . Filtered trimmed reads were mapped with Bowtie2 v2.3.5 [PMID: 22388286]. For C57BL/6J samples, reads were mapped to GRCm38 release 98 (ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz). For all other DO founder strains (A/J, 129S1/SvlmJ, NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ), reads were mapped to strain-specific pseudo-references. Pseudo-references for each strain were constructed with g2gtools v0.1.31 (http://churchill-lab.github.io/g2gtools) by patching GRCm38 release 98 with strain-specific SNPs and Indels from the Mouse Genome Project [PMID: 21921910] REL-1807 (ftp://ftp-mouse.sanger.ac.uk/REL-1807-SNPs_Indels/). Mapped reads were filtered to remove PCR duplicates, mtDNA, and the following classes of reads: unmapped, mate unmapped, and non-primary alignment. DeepTools alignmentSieve v3.3.2 [PMID: 27079975] was used to offset all reads aligning to the positive strand by +4bp, and all reads aligning to the negative strand by -5bp to account for Tn5 transposase activity [PMID: 24097267 , PMID: 21143862]. Alignments from non-C57BL/6J samples were then lifted to GRCm38 coordinates with g2gtools. Peak calling was conducted on all pooled alignment files with Macs2 v2.2.7.1 [PMID: 22936215].
Assembly: mm10
Supplementary files format and content: narrowPeak : called peaks of signal enrichment, bed : peaks count matrix, bigwig : read coverage track

molecule: genomic DNA

source_name: adipose

extract_protocol:
Transposed DNA was purified using a QIAGEN MinElute Reaction Cleanup kit (28204).
Adipose, liver, and muscle ATAC libraries were constructed as previously described  [PMID: 27526324] with a few exceptions. Briefly the protocol entails pelleting and washing cells in cold PBS, transposition and adapter addition using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina) with the addition of 0.01% digitonin (2x TDE for adipose), DNA purification using the ChIP DNA Clean & Concentrator Kit (Zymo Research), 11 cycle PCR and clean up using KAPA Pure Beads (Roche). Islet ATAC libraries were constructed as previously described [PMID: 34491912] with a few exceptions. Briefly the protocol entails pelleting and washing approximately islets in cold PBS, incubating in ATAC lysis buffer, trituration with 25-gauge needle, centrifugation to generate crude nuclei pellet, washing in ATAC lysis buffer, transposition and adapter addition using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina), DNA purification using the ChIP DNA Clean & Concentrator Kit (Zymo Research), 11 cycle PCR and clean up using KAPA Pure Beads (Roche).
All libraries were sequenced 100 bp paired end on an Illumina NovaSeq 6000.

treatment_protocol: Male and female mice of each CC founder strain were fed high fat high sugar 45% kcal fat plus 1360% kcal sucrose (Research Diets D19070208) or isocaloric control 10% kcal fat plus 0% kcal sucrose (Research Diets D19072203) diets for 9 weeks prior to tissue harvest and processing for ATAC-seq.

value: adipose

value: Adipose - gonadal fat pad

value: female


title: Adipose 797-A M

value: PWK/PhJ

value: male


title: 966833-300_lib30904

value: Male

value: SLIT


title: Untreated sample used as control donor 1 replicate 1

city: Freiburg

first: Kay

middle: Ole

last: Chmielewski

address: Breisacherstr. 115

department: Institute for transfusion medicine and gene therapy

country: Germany

institute: University clininics Freiburg

description: used as untreated control

data_processing:
Mate paired reads were merged using BBmerge from BBmap (v38.76) software. BBmap  was also used for filtering and trimming as follow: merged reads containing the designer nuclease target site were filtered-in, whereas PCR mispriming products reads were filtered-out. Linker sequences, Illumina adapter sequences, targeted elongation sequence and bad quality reads were trimmed.
Selected reads were aligned to the human genome GRCh38 (hg38) using Bowtie2 (v2.3.4.2) and the very-sensitive preset parameters. Aligned reads with good mapping quality (MAPQ >15) were selected. The aligned BAM file was converted into bed file using bedtools (v2.27.1).
Translocated sites were identified using the CAST-Seq and D-CAST-Seq pipelines with default parameters, as described on https://github.com/AG-Boerries/CAST-Seq
Assembly: hg38
Supplementary files format and content: matrix table of translocation sites detected with CAST-Seq and D-CAST pipelines. It includes the genomic coordinates of translocated sites, read coverage, alignment score against gRNA, translocation event classification and nearest genes annotation.
Library strategy: CAST-Seq

source_name: HSPCs

growth_protocol: All CD34+ HSPCs were cultured in GMP SCGM medium (Cellgenix) supplemented with SCF (100ngml-1), TPO (100ngml-1), Flt3 ligand (100ngml-1), IL-6 (100 ngml-1), and StemRegenin1 (0.75mM). Cells were cultured at 37C, 5% CO2, and 5% O2.

extract_protocol:
Between 2 and 4 days post targeting, gene edited cells were harvested and QuickExtract DNA extraction solution (Epicentre) was used to collect gDNA.
CAST-Seq was performed as previously described (Turchiano et al, 2021) with minor modifications. Briefly, genomic DNA was fragmented by enzymatic digestion (NEBNext® Ultra™ II FS DNA Library Prep Cat.# E7805S) to obtain average fragment lengths of 350-500 bp. After linker ligation (NEBNext®Ultra™ II FS DNA Library Prep Cat.# E7805S) and DNA purification, two rounds of PCR utilizing Q5 polymerase (NEB, Cat.# M0493S) were performed with the following conditions: 20 cycles at 95°C for 15 s, 61°/63°C (g1 or g1+2/g2, first reaction) or 68°C (second reaction) for 20 seconds, 72°C for 20 seconds.
A third PCR introduced the barcoded Illumina adapter for sequencing (NEB, NEBNext Multiplex Oligos for Illumina, Cat.# E7335, E7500, E7710, E7730). Libraries were sequenced by Azenta Life Sciences using the Illumina NovaSeq platform with a 2 x 150 bp configuration.

treatment_protocol: RNPs were complexed at a Cas9/sgRNA molar ratio of 1:2.5 at 25 °C for 10 min before electroporation. CD34+ cells were resuspended in P3 buffer (Lonza) with complexed RNPs. I53 peptide is added directly to the RNP and cell mixture immediately before electroporation. Electroporation was carried out using the Lonza 4D Nucleofector (program DZ-100 for HSPCs).

value: HSPCs

value: No treatment


title: CAST-seq on samples treated with RNP  in donor 1 replicate 1

value: RNP


title: 970412-300_lib30903


title: Adipose 796-A F


title: 962962-300_lib30901


title: CAST-seq on samples treated with RNP + i53 peptide in donor 1 replicate 1

value: RNP + i53 peptide


title: DN-P-701_Well_H07


title: DN-P-701_Well_H09


title: DN-P-701_Well_H08


title: DN-P-701_Well_H10


title: DN-P-701_Well_H06


title: Adipose 793-A F


title: 958432-300_lib30902


title: Adipose 794-A F


title: 966791-300_lib30900


title: 970417-300_lib30899


title: Adipose 2974-A M

value: WSB/EiJ


title: DN-P-701_Well_H05

value: Bone marrow derived APC


title: 966848-300_lib30898


title: Adipose 2553-A M

value: A/J


title: DN-P-701_Well_H04

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: DN-P-701_Well_H03


title: Adipose 2292-A M

value: CAST/EiJ


title: Adipose 795-A F


title: CAPAN1 inVivo, VC, 3

city: Göttingen

first: Shiv

middle: K.

last: Singh

address: Robert-Koch-Straße 40

department: Gastroenterology, GI-Oncology and Endocrinology

institute: University Medical Center Göttingen

data_processing:
Quality control using FastQC.
For siRNA samples: Alignment to hg38 using STAR v2.7.3a. For in vivo TNF treatment samples: Alignment to hg38 and mm38 using STAR v2.7.3a.
For in vivo TNF treatment samples: Removal of opposite species reads using XenofilteR package v1.6.
Counting of reads using htseq-count v0.11.3.
Assembly: For siRNA samples: hg38. For in vivo TNF treatment samples: hg38 and mm38.
Supplementary files format and content: Tab-delimited text file includes raw counts. Both human (hs) and murine (mm) reads are provided for in vivo TNF treatment samples.

molecule: polyA RNA

source_name: orthotopic tumor

extract_protocol:
For siRNA samples: TRIzol (Invitrogen). For in vivo TNF treatment samples: Direct-ZOL RNA Mini-prep (Zymo Research)
For siRNA samples: the library was made using 500 ng of total RNA and the Illumina TruSeq RNA Library Prep kit. For in vivo TNF treatment samples: libraries were made by Novogene.

value: orthotopic tumor

tag: cell line

value: cell line orthotopically transplanted into pancreas of nude mice

value: VC


title: CAPAN1 inVivo, VC, 2


title: 966821-300_lib30896

value: Nasal Brush

value: Placebo


title: CAPAN1 inVivo, VC, 1


title: 970422-300_lib30897


title: CAST-seq on samples treated with RNP + i53 peptide in donor 1 replicate 2


title: Gene editing, RAG1 intron 1, g9/AAV6 [GE_RAG_14]

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

data_processing:
Reads wuality control checked with FASTQC
trimming with Trim Galore, (parameters --quality 20 --length 25)
Alignment with STAR 2.7.6a (parameters --outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterMismatchNmax 10)
count with featureCounts (parameters -s 2 --minOverlap 10)
Assembly: GENCODE version hg38 primary assembly v35
Supplementary files format and content: tab-delimited text files include read counts values for each Sample

source_name: mPB-hematopoietic stem/progenitor cells -RAG1_Pt2

growth_protocol: Hematopoietic stem/progenitor cells were stimulated for three days before gene editing  in serum-free StemSpan™ SFEM (StemCell Technology) medium supplemented with specific early-acting cytokines

extract_protocol:
RNeasy Plus Mini Kit (QIAgen)
TruSeq Stranded Total RNA with Ribo-Zero Globin (Illumina)

treatment_protocol: Gene editing was perfomed by electroporationa of RNP using P3 Primary Cell 4D-Nucleofector X Kit and Nucleofector device (program EO-100) followed by transduction with the AAV6 corrective donor. Cells were collected before the stimulation phase and 24h after the editing.

value: edited day+1


title: CAPAN1 inVivo, TNF, 3

value: TNF


title: CAPAN1 inVivo, TNF, 2


title: 963011-300_lib30895

value: Male


title: Adipose 1601-A M

value: adipose

value: NZO/HlLtJ

value: Adipose - gonadal fat pad

value: male


title: CAPAN1 inVivo, TNF, 1


title: DN-P-701_Well_H01


title: Gene editing, RAG1 intron 1, g9/AAV6 [GE_RAG_12]

value: mPB-hematopoietic stem/progenitor cells -RAG1_Pt2

value: unedited day-3


title: Adipose 2155-A F

value: female


title: 970490-300_lib30893


title: Adipose 1389-A M

value: NOD/ShiLtJ


title: DN-P-701_Well_G12

value: Bone marrow derived APC

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: DN-P-701_Well_H02


title: Gene editing, RAG1 intron 1, g9/AAV6 [GE_RAG_11]

source_name: mPB-hematopoietic stem/progenitor cells -HD


title: Adipose 1388-A M


title: 966839-300_lib30892


title: Adipose 1387-A M


title: DN-P-701_Well_G10


title: 962921-300_lib30891


title: Gene editing, RAG1 intron 1, g9/AAV6 [GE_RAG_10]

value: mPB-hematopoietic stem/progenitor cells -HD

value: unedited day+1


title: Gene editing, RAG1 intron 1, g9/AAV6 [GE_RAG_9]


title: 958446-300_lib30894

value: Nasal Brush


title: DN-P-701_Well_G09


title: Gene editing, RAG1 intron 1, g9/AAV6 [GE_RAG_13]


title: Adipose 1386-A F


title: 958472-300_lib30890

value: Placebo


title: DN-P-701_Well_G08


title: Gene editing, RAG1 intron 1, g9/AAV6 [GE_RAG_7]

source_name: mPB-hematopoietic stem/progenitor cells -RAG1_Pt1

value: edited day+1


title: DN-P-701_Well_G11


title: DN-P-701_Well_G07


title: Adipose 1385-A F


title: Adipose 1384-A F


title: Adipose 1382-A M


title: LC_14

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read. R2 reads were generated as UMI sequences that were later used to extract PCR duplicates. R1 and R3 reads were used as paired sequencing reads. To assess the read quality, FastQC was run, and low quality reads were removed using sickle with default setting. BBDuk version 36_49  was used to trim/filter low quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the human reference genome GRCh38 was done using HISAT2 version 2.1.0 applying --no-mixed and --no-discordant options. UMI specific workflow that was developed and distributed by Tecan Genomics was used to extract reads that are free from PCR artifacts i.e., deduplication. The resulting deduplicated reads were summarized to each gene using HTseq-count version 0.11.2 by supplementing Ensembl gene annotation GRCh38.78 and ERCC spike-in genes.
Genome_build: GRCh38
Genome_build: mm9
Supplementary_files_format_and_content: Raw read counts are provided in TS_LC_WC_NC.txt and MouseAB_Rawcount.txt files, respectively.
paired-end (R1 and R3, R2 is UMI)

growth_protocol:
Coverslips Fisher Scientific, 12-545-80 were coated with Poly-L-Lysine PLL by incubation in PLL solution 0.01% for 30 minutes at 37°C. TOV-21G ATCC, CRL-11730 cells were grown for 48 hours on cover slips in the Complete Growth Medium [a 1:1 mixture of MCDB 105 1.5 g/L sodium bicarbonate and MCDB 199 2.2 g/L sodium bicarbonate added with fetal bovine serum at a final concentration of 15%] for RNA collection.
Mice were deeply anesthetized with isoflurane Halocarbon. A block of brain containing motor cortex MCx was removed and coronal slices 300 μm thick were cut on a vibrating microtome Leica in ice-cold physiological solution ACSF. The solution contained the following in mM: 130 NaCl, 3 KCl, 1.25 KH2PO4, 20 NaHCO3, 10 glucose, 1.3 MgSO4, 2.5 CaCl2 pH 7.35-7.4, in 95% O2-5% CO2. All solutions were made with nuclease-free, de-ionized, not DEPC-treated water Ambion AM 9938. Slices were incubated for 1 hour at 30°C, then kept at room temperature. For electrophysiological extraction of RNA, slices were held in a chamber on a motorized stage microscope Olympus BX61WI, Gibraltar Burleigh and superfused with ACSF. The location of motor cortex MCx was identified by 1.5-2.0 mm rostral to the start of the hippocampus.

extract_protocol:
For RNA extraction, cultures and slices were held separately in a chamber on a motorized stage on a motorized microscope Olympus BX61WI, Gibraltar Burleigh Thorlabs. Cultures were superfused 2-4 ml/min in a bath solution of in mM: 145 N-methylglucamine NMG, 2 CaCl2, 1 MgCl2, 10 HEPES, 60 glucose pH 7.3, osmolality 300, in 95% O2-5% CO2 . All procedures were performed with a Multiclamp 700B patch-clamp amplifier Molecular Devices, LLC and using borosilicate glass pipettes with filament, OD 1.5 mm, ID 1.10 mm, Sutter and the input resistance was in the range of 3-9 MΩ. RNA was extracted with a 1440A Digidata AD board Molecular Devices, LLC under pClamp v10. Electrodes pipettes were filled with in mM: 100 KCl, 35 N-methylglucamine NMG, 10 EGTA, 1 CaCl2, 4 MgCl2, and 10 HEPES pH 7.3, 290 mOsm for the RNA extraction from the TOV-21G cells. Electrodes were filled with in mM: 130 K-gluconate, 10 KCl, 10 HEPES, 10 EGTA, 2 MgCl2, 2 Na-ATP, 0.2 Na-GTP, and 5 glutathione pH 7.3, 280-290 mOsm for the RNA extraction from the Thy1-YFP L5 neurons. For the RNA extraction from the Thy1-GCaMP6f L2/3 neurons, electrodes were filled with in mM: 110 K-gluconate, 4 KCl, 4 NaCl, 0.2 CaCl2, 10 HEPES, 1.1 EGTA, 2 Mg-ATP, 1 MgCl2, and 5 glutathione pH 7.2-7.3, 300 mOsm. Membrane voltages were corrected for an estimated liquid junction potential of about 10 mV. Perforation was performed using -escin antibiotics 50 M from a stock solution 25 mM respective for each cellular population. All solutions were made with nuclease-free, de-ionized, not DEPC-treated water Ambion AM 9938. Lucifer yellow 50 mM was added to the electrode intracellular working solution for all cellular populations. The intercellular working solution including the antibiotics and dye was prepared fresh daily and used at room temperature and were backfilled into the electrodes for the patch-clamp experiments. Holding potentials for TOV-21G cells and cortical neurons were -80 mV and -70 mV, respectively. Electrodes were made by a PP-830 Narishige puller and positive pressure was applied as the pipettes were advanced to the cell of interest. The leak current Ilk was then used for the holding current in the current-clamp protocol and it was noted before and after the current was injected in all cellular populations. Seven current injection steps of 5 pA each was applied for a duration of 500 ms per step for the RNA extraction. Following RNA extraction, electrodes were slowly retracted while leaving the cell intact in its native environment, and the pipette solution was collected for sequencing. Each sample tube was prefilled with 2 µL of IGEPAL working mixture per tube, and positive pressure was applied to eject the internal contents of the electrode into a sample tube. The IGEPAL working mixture contained 65 µL nuclease-free de-ionized water Ambion, AM9938, 25 µL RNaseOUT™ Recombinant Ribonuclease Inhibitor ThermoFisher, 10 µL IGEPAL CA-630 Alfa Aesar, J61055 and was stored in 4°C for up two weeks. RNA was collected in 0.5 mL tubes Protein LoBind Tube 0.5 mL, Eppendorf, 022431064. After RNA extraction, samples were transferred on dry ice and stored at -80°C. After each RNA extraction, the electrode holder and silver-chloride recording electrode were cleaned with 70% ethanol. Cytosolic extraction for all cellular populations was performed by first doing whole-cell patch-clamp, then applying negative pressure light suction to harvest cellular content into IGEPAL working mixture.
The cDNA libraries were prepared using Ovation SoLo RNA-Seq System Tecan Genomics.  UMIs are used to eliminate possible PCR duplicates in sequencing datasets and facilitate unbiased gene expression profiling. For some experiments, ERCC RNA Spike-In Mix Thermo Fisher Scientific was included in the library preparation. The processed libraries were assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent Technologies. The libraries were pooled and loaded onto a TruSeq SBS v3 flow cells on an Illumina HiSeq 2500 Illumina or an S1 flow cell on an Illumina NovaSeq 6000 Illumina , and run for 2X50 cycles according to the manufacturer's instructions. De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq version 2.18.0.12 allowing no mismatches in the index read.

treatment_protocol: For some experiments, TOV-21G cells were cultured in the Complete Growth Medium added with a IκB kinase IKK inhibitor, IKK-16 IKK Inhibitor VII Sigma-Aldrich at 1 µM for 72 hours before RNA collection.

value: TOV-21G, derived from human ovarian cancer

tag: collection

value: LC-seq


title: LC_23


title: DN-P-701_Well_G06


title: Gene editing, RAG1 intron 1, g9/AAV6 [GE_RAG_5]

value: mPB-hematopoietic stem/progenitor cells -RAG1_Pt1


title: Adipose 1381-A M

value: adipose


title: Gene editing, RAG1 intron 1, g9/AAV6 [GE_RAG_3]


title: LC_12


title: Adipose 1380-A M

value: Adipose - gonadal fat pad


title: Gene editing, RAG1 intron 1, g9/AAV6 [GE_RAG_6]


title: DN-P-701_Well_G03


title: Adipose 1379-A F


title: Gene editing, RAG1 intron 1, g9/AAV6 [GE_RAG_2]


title: ALL_2_3 miRNA

city: Chengdu

first: Hongli

last: Lai

state: Sichuan

address: No. 37, Guoxue Alley

country: China

institute: West China Hospital, Sichuan University

data_processing:
Clean reads were aligned by Bowtie.
Differentially expressed sRNAs were defined as those with |log2-fold change|>1 and p<0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: files of raw gene counts for every gene and every sample

source_name: leukemia cells

extract_protocol:
Long RNA was extracted by a QIAamp RNA Blood Mini Kit (QIAGEN, Germany), and ribosomal RNA was removed.
For small RNA, NEBNext®Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA) was used to construct a sequencing library.

value: bone marrow

tag: state


title: ALL_2_2 miRNA


title: Gene editing, RAG1 intron 1, g9/AAV6 [GE_RAG_1]


title: LC_13


title: Adipose 1378-A F


title: DN-P-701_Well_G02


title: DN-P-701_Well_G05


title: ALL_2_1 miRNA


title: Adipose 1375-A M

value: NZO/HlLtJ

value: male


title: BEAS-2B cells, Dexa+CrudeM, 4hr

city: Taichung city

first: Yu-Fan

last: Liu

address: No.110. Sec 1, Jianguo N. Rd.

department: Biomedical sciences

country: Taiwan

institute: Chung Shan Medical University

data_processing:
Data was mapped to NCBI Human Reference Geonme GRCH38.P13 by Hierarchical Indexing for Spliced Alignment of Transcripts 2 (HISAT2, version 2.2.1) program
Read counts were calculated using featureCounts (version 1.6.2)
Data was further analyzed by DESeq (version 1.38.0)
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes read counts for each sample

source_name: Lung; Bronchus

growth_protocol: BEAS-2B cells were cultured in LHC-9 cell culture medium supplemented with antibiotics at 37°C, 5% CO2.

extract_protocol:
Added 1 ml Tri reagent (Sigma-Aldrich) to the cell culture and incubated for 5 minutes, followed by adding 200μl chloroform, vortexing for 15 seconds, and incubating for 15 minutes.
Subsequently, centrifuged under 16,558 xg for 15 minutes and take the supernatant.
Added 500μl isopropanol and incubated for 10 minutes, then centrifuged for 30 minutes.
Discarded supernatant, added 1 ml 75% ethanol to clean the pellet, and centrifuged again for 30 minutes.
Following the discarded supernatant and drying of the pellet, add 25 μl Diethyl pyrocarbonate (DEPC) to restore the pellet.
The mRNAs were isolated from total RNAs with poly-T probes and were fragmented before first-strand cDNA synthesis with random primers and reverse transcriptase.
The DNA-RNA hybrid products were then synthesized in the second strand cDNAs with DNA polymerase I and ligated adaptors into both ends of cDNAs.

treatment_protocol: The treatment of BEAS-2B cells with HDM allergens (Thermo scientific ImmunoCAP) was carried out in 6 cm cell culture dishes, with a seeding density of 5 x 10^5 cells per dish.

value: Lung; Bronchus

value: epithelial cell

tag: genotype

value: WT

value: Der m + Dexamethasone


title: DN-P-701_Well_F12

value: Bone marrow derived APC

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: DN-P-701_Well_G04


title: BEAS-2B cells, Dexa, 4hr

value: Dexamethasone


title: ALL_1_4 miRNA


title: ALL_2_4 miRNA


title: DN-P-701_Well_F11


title: ALL_1_3 miRNA


title: BEAS-2B cells, CrudeF, 24hr

value: Der f


title: Adipose 1374-A M


title: BEAS-2B cells, CrudeF, 4hr


title: BEAS-2B cells, CrudeP, 24hr

value: Der p


title: Adipose 1373-A M


title: DN-P-701_Well_F10


title: Adipose 1202-A M


title: Adipose 1377-A F

value: NOD/ShiLtJ

value: female


title: DN-P-701_Well_G01


title: BEAS-2B cells, CrudeP, 4hr


title: DN-P-701_Well_F09


title: DN-P-701_Well_F08


title: BEAS-2B cells, CrudeM, 24hr

value: Der m


title: Adipose 1197-A F

value: adipose


title: Adipose 1201-A M

value: Adipose - gonadal fat pad


title: BEAS-2B cells, Mock, 24hr

value: NT


title: Day 35_0 mGy_H3K4me3_ChIPSeq

city: Tsukuba

first: Tomohiro

last: Ito

address: 16-2, Onogawa

country: Japan

institute: National Institute for Environmental Studies

data_processing:
Basecalls performed using CASAVA version 1.4.
ChIP-seq reads were aligned to the hg19 genome assembly.
Data were filtered using the following specifications.
Peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: wig and bigWig files

source_name: pluripotent stem cell

growth_protocol: Human iPS cells were put into 96-well plate to generate embryoid body (EB) to induce differentiation on day 0.

extract_protocol:
After the fixation with 1% paraformaldehyde, they were collected and sonicated. Then, histone-DNA complexes were isolated with histone modification specific antibodies.
The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: On day 4 to 5, they were irradiated with 0, 30 and 180 mGy of gamma-ray for 24 hours.

value: developing retinal ganglion cells

value: no irradiation

tag: time point

value: Day 35

tag: chip antibody


title: Adipose 1185-A M

tag: strain

value: PWK/PhJ

tag: cell type

value: male


title: Adipose 1164-A M

tag: tissue

value: WSB/EiJ

tag: treatment


title: Input DNA


title: DN-P-701_Well_F06

value: Bone marrow derived APC


title: BEAS-2B cells, CrudeM, 4hr

value: Lung; Bronchus

value: epithelial cell

value: WT


title: Day 35_180 mGy_H3K4me3_ChIPSeq

value: 180 mGy irradiation


title: BEAS-2B cells, Mock, 4hr


title: DN-P-701_Well_F07

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: Adipose 1163-A M

tag: Sex


title: DN-P-701_Well_F05


title: ALL_1_2 miRNA

value: bone marrow


title: DN-P-701_Well_F04


title: LPFS_3_8

city: Seocho-gu

first: June-Young

last: Koh

state: Seoul

address: 2575 Nambusunhwan-ro,

country: South Korea

institute: GENOME INSIGHT

description: gDNA for genotyping (demultiplexling)

data_processing:
Libraries were constructed and sequenced at a depth of approximately 50,000 reads per cell using the Novaseq 6000 platform (Illumina, San Diego, CA, USA).
The sequenced data were demultiplexed using the mkfastq function (Cell Ranger, 10X Genomics, v3.0.1) to generate fastq files.
We did not use HTO for demultiplexing. Instead, we performed demultiplexing using genotype information that was submitted. Demultiplexing can be done using tools like the demuxlet algorithm with the provided genotype information.
The feature-barcode matrices of RNA expression were analyzed using the Seurat R package (Seurat, v4.1.1)
Assembly: GRCH38
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, filtered_contig_annotations.csv
Library strategy: DNA-seq

source_name: peripheral blood

extract_protocol:
PBMCs were isolated by Ficoll-Paque (GE Healthcare, Uppsala, Sweden) density-gradient centrifugation
Libraries for scRNA-seq were generated using the Chromium Next GEM Single Cell 5' Kit v2 (10× Genomics, Pleasanton, CA, USA) and Chromium Single Cell Human TCR Amplification Kit (10× Genomics) to read 5'-mRNA and full-length paired T-cell and B-cell receptor sequences following the manufacturer’s instructions

value: PBMC

value: mononuclear cell

value: peripheral blood

tag: responsiveness

value: Long term responder

tag: cycle

tag: patient


title: DN-P-701_Well_F03


title: ALL_1_1 miRNA


title: Adipose 1162-A M

value: adipose

value: Adipose - gonadal fat pad


title: Day 35_0 mGy_H3K27ac_ChIPSeq

value: developing retinal ganglion cells

value: no irradiation

value: Day 35


title: Day 6_180 mGy_H3K4me3_ChIPSeq

value: Day 6


title: LPFS_3_6

description: gDNA for genotyping (demultiplexling)


title: Adipose 1159-A M

value: CAST/EiJ

value: male


title: LPFS_2_8

description: gDNA for genotyping (demultiplexling)


title: Adipose 1160-A F

value: WSB/EiJ

value: female


title: DN-P-701_Well_F02

value: Bone marrow derived APC


title: Day 6_30 mGy_H3K4me3_ChIPSeq

value: 30 mGy irradiation


title: LPFS_2_4

description: gDNA for genotyping (demultiplexling)


title: Day 6_180 mGy_H3K27ac_ChIPSeq

value: 180 mGy irradiation


title: Day 6_0 mGy_H3K4me3_ChIPSeq


title: LPFS_2_2

description: gDNA for genotyping (demultiplexling)

value: PBMC


title: Day 35_180 mGy_H3K27ac_ChIPSeq


title: LPFS_2_6

description: gDNA for genotyping (demultiplexling)

value: mononuclear cell


title: DN-P-701_Well_E11

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: Adipose 1157-A M


title: Day 6_30 mGy_H3K27ac_ChIPSeq


title: DN-P-701_Well_E10


title: DN-P-701_Well_E12


title: Adipose 1153-A M

value: A/J


title: Adipose 1154-A M

value: adipose


title: Day 6_0 mGy_H3K27ac_ChIPSeq


title: LPFS_1_28

description: gDNA for genotyping (demultiplexling)

value: peripheral blood

value: Long term responder


title: LPFS_2_1

description: gDNA for genotyping (demultiplexling)


title: DN-P-701_Well_E08


title: DN-P-701_Well_E09


title: Adipose 1147-A M

value: Adipose - gonadal fat pad


title: 5890_6_sgGCN2_IFNy_TAGCTT_S75_R1_001

city: Amsterdam

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

data_processing:
Library strategy: RiboSeq
Ribo-seq: Preprocessing of fastq files consisted of adapter removal using cutadapt with the parameters (--quality-base=33  -O 7 -e 0.15 -m 20 -q 5) and removal of rRNA and tRNA contaminants by means of alignment against a reference using bowtie2with parameters (--seed 42 -p1 –local). The actual alignment of pre-processed fastq files was done with tophat2  and bowtie2  against GRCh37/hg19  using parameters ( --seed 42 -n 2 -m 1 --no-novel-juncs --no-novel-indels --no-coverage-search --segment-length 25). In a subsequent step the primary aligned reads filtered for a minimum mapping quality of 10.  HTSEQ was used to count reads at exons of genes. Normalization was done using DESEQ.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited txt file containing normalized read counts (DESEQ) for all comparisons

source_name: MD55A3 cells

growth_protocol: MD55A3 was derived from metastatic melanoma tumor resections collected with informed patient consent under a protocol approved by the NIH Institutional Review Board (IRB) Ethics Committee and approved by the MD Anderson IRB (protocol numbers 2012-0846, LAB00-063, and 2004-0069; NCT00338377). MD55A3 was tested regularly for mycoplasma contamination by PCR assay. MD55A3 was maintained in Roswell Park Memorial Institute 1640 Medium (RPMI 1640, Gibco) supplemented with heat-inactivated 10% fetal bovine serum (Sigma), 25mM HEPES (Gibco) and 100 U/mL penicillin/streptomycin (Gibco). MD55A3 was maintained in a humidified atmosphere containing 5% of CO2 at 37°C.

extract_protocol:
1x106 MD55A3 cells were seeded. Cells were rinsed once with PBS and the appropriate medium was added for exactly 48h. After 48h cells were harvested and ribosome profiling was performed based on  Ingolia NT et al, doi:10.1038/nprot.2012.086 (2012). Adjustment to this protocol are as follows: 20μL of fresh cycloheximide (100g/mL) was added to the medium and plates were incubated at 37°C for 1min. Cells were washed twice with PBS containing CHX and harvested into Lysis buffer as described. Samples were centrifuged at 4°C full speed for 10min and the cell pellet was snap frozen in liquid nitrogen. 400µL of lysate was incubated with 3µL of RNAse I (Ambion AM2295 100 U/µL) for 45min at RT in an Eppendorf shaker, 600RPM. Then, the digestion was inactivated by adding 12µL of SUPERaseInhibitor (AM2696, ThermoFisher). Ribosomes were pelleted as described by ultra-centifugation using TLA 100.3 rotor for 1h30, 4°C at 100,000rpm. The pellet was retrieved in 1mL Trizol (Life Technologies). RNA was extracted using manufacturer’s instruction. RNA pellet was resuspended with 15L of 10mM Tris pH-7.  15% TBE-urea gel was pre-run for 20min at 200V. 10µg of RNA maximum was loaded per lane. 2X gel loading buffer was used (AM8547, Invitrogen). 10µM oligos marker of 26nt and 32nt were used as size selection markers. RNA was extracted as described in the protocol using the Rapid Gel extraction. RNA was then precipitated overnight using Isopropanol (Sigma) and Glycoblue (AM9516, ThermoFisher).
The construction of ribosome protected fragments (RPF) libraries were done as previously described in Ingolia NT et al, doi:10.1038/nprot.2012.086 (2012). Possible changes are as follows: For linker ligation, RNA was resuspended into 8µL of 10mM Tris pH 7.0. Then, 1µL of PNK buffer and 1µL of T4 PNK (M0201L, NEB) were added. Samples were incubated for 1h at 37°C. Then, 4µL of 50% PEG-800, 0.5µL of 10X Ligase buffer, 0.2µL of Universal miRNA cloning linker (S1315S, NEB) and 0.75µL of RNL2 Ligase (M0351S, NEB) were added. Samples were incubated for 3h at 25°C. Finally, 0.5µL of Deadenylase (M0331S, NEB) and 2µL of RecJ exonuclease (M0264L, NEB) were added. Samples were incubated at 30°C for 1. RNA was then precipitated overnight as previously described. RNA was resuspended in 6,5µl 10mM Tris pH 7.0 and mixed with 0.75µL of 10X dNTPs and 0.5µL of Reverse transcription primer (50µM solution). Samples were incubated 5min at 65°C. Then, Reverse transcription was performed using SuperScript III RT (18080-051, Life technologies) using manufacturer’s instruction. Then, as described the reaction was separated using and 10% TBE-urea gel and DNA was extracted from gel and precipitated overnight. Then, as described the reaction was separated using and 10% TBE-urea gel and DNA was extracted from gel and precipitated overnight.  Circularization was as described using CircLigase II ssDNA Ligase (CL9021K, epicentre)

treatment_protocol: Tryptophan depletion: 12.048g of Tryptophan depleted medium (Dulbecco’s MEM (DMEM) F-12 w/o Tryptophan powder (Bio-Connect/US biologicals)) and 1.2g of sodium bicarbonate (Sigma) were resuspended into 1L of distilled H20. pH was adjusted to 7,2. Tryptophan-depleted medium was filtered and supplemented with heat-inactivated dialyzed serum (Thermo FisherScientific) and 100U/mL penicillin/streptomycin (Gibco). As control for depletion, medium was supplemented with tryptophan to reach a final concentration of 5μg/ml (T0254-5G, Sigma Aldrich). Phenylalanine depletion: medium was custom-made (Cell Culture technologies). Medium was supplemented with 2mM L-glutamine (Life technologies). All mediums were supplemented with 10% heat-inactivated dialyzed serum and 100U/mL penicillin/streptomycin. GCN1 and GCN2 knockout: For lentivirus production, 3.5 x 106 HEK293T cells were seeded per 100 mm dish, one day prior to transfection. For each transfection, 10 μg of the pCDH reporter, 5 μg of pMDL RRE, 3.5 μg pVSV-G AND 2.5 μg of pRSV-REV plasmids were mixed in 500 μL of serum-free DMEM. Next, 500 μL of serum-free DMEM containing 63 μL of a 1 mg/mL PEI solution was added. The entire mix was vortexed and left for 15 minutes at room temperature, after which it was added to the HEK293T cells to be transfected. The next day, the medium was replaced by RPMI. The lentivirus-containing supernatants were collected 48 and 72 hours post transfection, and snap frozen in liquid nitrogen. Target cells were transduced on two consecutive days by supplementation of the lentiviral supernatant with 8 μg/mL polybrene (Sigma). One day after the last transduction, transduced cells were selected by addition of 5μg/mL blasticidin (Invivogen) or 2μg/mL of puromycin according to the right selection needed. After selection, 10x103 MD55A3 expressing sgNT1 or sgGCN2 were seeded in a 15cm dish. After 10 days, colonies were picked and amplified prior Western Blot analysis of a complete GCN2 knock-out cells. One clone of sgNT1 and one clone of sgGCN2 were used later for ribosome sequencing analysis. For IFNgamma experiments, 1x106 cells were seeded in a 10cm dish. The next day, cells were treated with 250U/mL of IFNgamma (PeproTech) for 48h prior harvesting.

value: Melanoma  cancer cells

value: GCN2 KO + IFNg


title: LPFS_1_19

description: gDNA for genotyping (demultiplexling)


title: LPFS_1_20

description: gDNA for genotyping (demultiplexling)


title: Adipose 1143-A M

value: NZO/HlLtJ


title: 5890_4_sgNT1_IFNy_ACAGTG_S73_R1_001

value: Non-targeting Control + IFNg


title: DN-P-701_Well_F01


title: Adipose 1144-A F


title: DN-P-701_Well_E07


title: Adipose 1158-A M

value: CAST/EiJ

value: male


title: 5890_5_sgGCN1_IFNy_GCCAAT_S74_R1_001

value: GCN1 KO + IFNg


title: 5890_3_sgGCN2_TGACCA_S72_R1_001

value: GCN2 KO


title: DN-P-701_Well_E06

value: Bone marrow derived APC


title: 5890_2_sgGCN1_TTAGGC_S71_R1_001

value: GCN1 KO


title: Adipose 1141-A F

value: female


title: LPFS_1_18

description: gDNA for genotyping (demultiplexling)

value: PBMC

value: mononuclear cell


title: LPFS_1_13

description: gDNA for genotyping (demultiplexling)


title: LPFS_1_11

description: gDNA for genotyping (demultiplexling)


title: Adipose 1142-A M

value: adipose


title: DN-P-701_Well_E04

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: Adipose 1140-A F


title: DN-P-701_Well_E03


title: DN-P-701_Well_E05


title: 5890_1_sgNT1_ATCACG_S70_R1_001

value: Non-targeting Control


title: 5951_3_-F_TGACCA_S63_R1_001

value: Phenylalanine depletion


title: LPFS_1_6

description: gDNA for genotyping (demultiplexling)

value: peripheral blood

value: Long term responder


title: LPFS_1_8

description: gDNA for genotyping (demultiplexling)


title: 5951_2_-W_TTAGGC_S62_R1_001

value: Melanoma  cancer cells

value: Tryptophan depletion


title: Adipose 1139-A F

value: NZO/HlLtJ

value: Adipose - gonadal fat pad


title: 5951_1_CTRL_ATCACG_S61_R1_001

value: Untreated control


title: SPFS_3_7

description: gDNA for genotyping (demultiplexling)

value: Early progressor


title: Adipose 1138-A F


title: SPFS_3_5

description: gDNA for genotyping (demultiplexling)


title: Adipose 1136-A F


title: DN-P-701_Well_D12

value: Bone marrow derived APC

value: 6 hr stimulation with poly (I:C)


title: DN-P-701_Well_E01


title: DN-P-701_Well_D11


title: DN-P-701_Well_E02


title: Adipose 1137-A F

value: female


title: SPFS_3_4

description: gDNA for genotyping (demultiplexling)

value: PBMC


title: Input_unamp_CEM

city: Shanghai

first: Xiang

last: Yu

state: Shanghai

address: 800 DongChuan

institute: Shanghai Jiao Tong University

description: TOP2A-bound DNA (un-amplification)

data_processing:
Raw reads were aligned to the human genome version hg38 using Bowtie2 (version 2.1.0) in default end-to-end mode reporting 1-2 alignments per read. SAM mapping files were converted to BAM files and sorted with SAMtools (version 0.1.19). The BAM files were converted to BED files, filtering sites with multiple reads, and only retaining reads that mapped uniquely.
The Audic and Claverie test was used to measure the statistical significance of the difference in read frequencies. TOP2A cleavage sites were identified as the most 5’ bases (i.e.+1 position of cleavage sites on plus strand, and +1 position of cleavage sites on minus stand corresponding to plus strand position +4; Figure 1A) of all reads that both mapped uniquely and showed a 4X enrichment compared to input with p-value < 0.05 . Adjacent cleavage sites meeting the criteria above were collapsed if separated by ≤200bp, allowing closely spaced cleavage sites to be combined intoCCRssimilar to SPO11 hotspots(Pan et al., 2011). CCR boundaries were defined by the first and last cleavage sites in each cluster. CCRs were subsequently filtered to require a 25 ntlength minimum and 4X enrichmentoverinput.CCR signals were normalized to hits per 10 million reads (HP10M). CCRs from replicates were merged as a union set for each sample. Further analyses were based on the merged CCR data sets.
Genome_build: hg38
Supplementary_files_format_and_content: BED file; TOP2A cleavage cluster regions (CCRs)

source_name: human CEM cell

growth_protocol: CCRF-CEM (ATCC CCL 119) cells were grown to 0.5 x 106 cells/ml in 20 ml of IMDM-10% FSC in T75 flasks.  Stocks of TOP2 poisons in DMSO were added to a final DMSO concentration of 0.05%.

extract_protocol:
Ten million vehicle or TOP2 poison-treated CEM cells were lysed with RIPA buffer and the lysates sonicated to fragment the DNA to 250-750bp. TOP2A was immunocaptured with anti-TOP2A IgG and Protein G magnetic beads, the bead-bound fraction separated, and immunoprecipitation repeated twice on non-bound fractions. The bead-bound fractions were combined and treated with CIP (NEB) to detach the TOP2A-bound DNA from cleavage complexes.
The released DNA and input DNA from sonicated lysates were purified and used directly for library synthesis with an IlluminaTruSeq ChIP library kitor pre-amplified with a SEQXE kit (Sigma) before library preparation. Sequencing was performedon an Illumina HiSeq2500 (SE50 protocol)
CIP-Seq

treatment_protocol: The cells in medium were treated with 25 μM etoposide (Sigma E1318), 2 μM mitoxantrone (Sigma M6545)or 50 μM genistein (Sigma G6776) in DMSO (0.05% final concentration)X1 h, with 8 μM p-benzoquinone (Sigma B10358) in DMSO (0.05% final concentration)X 4 h, or with DMSO (vehicle) X 1 or 4 h. The cells were collected by centrifugation and washed once with PBS at room temperature.  Cell pellets were lysed by addition of 1 ml ice-cold RIPA buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1% Igepal CA-630, 1% Sodium deoxycholate, 0.5% SDS with 1x Roche Complete EDTA-free Protease Inhibitor Cocktail) and transferred to microcentrifuge tubes.  Lysates were incubated on ice X 15 min before being passed 4 times through a 1 ml 25 g needle and then 4 times through a 27 g needle.  Clumps and debris were removed by centrifugation for 20 min at 4°C at 13.2 krpm in an Eppendorf microcentrifuge.  The supernatants were sonicated at high power in a Diagenode Bioruptor to fragment the DNA to peaksizes between 250 and 1000 bp.Fragmentation wasdetermined by electrophoresis in a 1.5 % agarose gel in 1x TAE  buffer (40 mM Tris/31.25 mM sodium acetate/0.1 mM EDTA). The sonicated lysates were frozen overnight at -20°C to enhance subsequent TOP2A immunocapture.

tag: library strategy

value: CIP-Seq

tag: replicate

tag: ngs platform

value: Illumina Hi-Seq2500 50 nt strand-specific


title: SPFS_3_2

description: gDNA for genotyping (demultiplexling)

value: mononuclear cell


title: Input_amp_CEM

description: TOP2A-bound DNA (amplification)


title: DN-P-701_Well_D09


title: DN-P-701_Well_D10


title: VP16_unamp_CEM_rep2

description:
TOP2A-bound DNA (amplification)
CEM_1B_3B_merged_sort_collapse_average.bed


title: SPFS_3_1

description: gDNA for genotyping (demultiplexling)


title: pBQ_unamp_CEM_rep2

description:
TOP2A-bound DNA (amplification)
CEM_1C_3C_merged_sort_collapse_average.bed


title: SPFS_1_27

description: gDNA for genotyping (demultiplexling)


title: Adipose 1054-A M

value: adipose

value: male


title: DN-P-701_Well_D08


title: Adipose 1043-A M

value: A/J


title: DN-P-701_Well_D07


title: SPFS_1_26

description: gDNA for genotyping (demultiplexling)

value: peripheral blood


title: Adipose 1037-A F

value: PWK/PhJ


title: DMSO_unamp_CEM_rep2

description:
TOP2A-bound DNA (un-amplification)
CEM_1A_3A_merged_sort_collapse_average.bed


title: Adipose 1041-A F


title: SPFS_1_23

description: gDNA for genotyping (demultiplexling)


title: VP16_amp_CEM_rep1


title: DN-P-701_Well_D06

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: Adipose 1034-A M


title: SPFS_1_21

description: gDNA for genotyping (demultiplexling)


title: DN-P-701_Well_D05


title: DMSO_amp_CEM_rep1

description:
TOP2A-bound DNA (amplification)
CEM_1A_3A_merged_sort_collapse_average.bed


title: Healthy adult C07_miRNA

city: Beijing

first: xiong

last: liu

state: Beijing

address: No.20，Dongdajie Street，Fengtai District

institute: State Key Laboratory of Pathogen and Biosecurity

data_processing:
Basecalls performed using CASAVA version 1.8
The small RNA tags were mapped to reference sequence by Bowtie v2.0.6 without mismatch to analyze their expression and distribution on the reference
miRNA expression levels were estimated by TPM through the following criteria: Normalization formula: Normalized expression = mapped readcount/Total reads* 1000000.
Genome_build: human NCBI genome build 37
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: Human peripheral blood

extract_protocol:
Whole blood was preserved in Trizol reagent (Ambion). RNA isolation was performed using the miRNeasy mini Kit (Qiagen Cat.No 217004)
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufactures’s recommendations and index codes were added to attribute sequences to each sample. Briefly, NEB 3’ SR Adaptor was directly, and specifically legated to 3’ end of miRNA, siRNA and piRNA. After the 3’ ligation reaction, the SR RT Primer hybridized to the excess oof 3’ SR Adaptor and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H-). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified on an 8% polyacrylamide gel (100V, 80min). DNA fragments corresponding to 140-160bp were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips, the library preparations was sequenced on an Illumina Hiseq 2500 platform and 50bp single-end reads were generated.

tag: disease status

value: Healthy control


title: DN-P-701_Well_D03


title: SPFS_1_17

description: gDNA for genotyping (demultiplexling)


title: SPFS_1_12

description: gDNA for genotyping (demultiplexling)


title: Adipose 1033-A M

value: Adipose - gonadal fat pad


title: DN-P-701_Well_D04


title: Healthy adult C05_miRNA


title: Adipose 1025-A F

value: CAST/EiJ


title: pBQ_amp_CEM_rep1


title: Adipose 1029-A M


title: SPFS_1_5

description: gDNA for genotyping (demultiplexling)

value: Early progressor


title: DN-P-701_Well_D02

value: Bone marrow derived APC


title: Adipose 1030-A M


title: Adipose 1035-A F


title: EVD patient L18_miRNA

value: ebola virus disease


title: SPFS_1_2

description: gDNA for genotyping (demultiplexling)


title: EVD patient L19_miRNA


title: DN-P-701_Well_D01

value: 6 hr stimulation with poly (I:C)


title: Adipose 1021-A F

value: female


title: DN-P-701_Well_C11


title: DN-P-701_Well_C12


title: EVD patient L17_miRNA


title: LPFS_C1D15_1_13_1_19_1_28_2_4_GEX

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Libraries were constructed and sequenced at a depth of approximately 50,000 reads per cell using the Novaseq 6000 platform (Illumina, San Diego, CA, USA).
The sequenced data were demultiplexed using the mkfastq function (Cell Ranger, 10X Genomics, v3.0.1) to generate fastq files.
We did not use HTO for demultiplexing. Instead, we performed demultiplexing using genotype information that was submitted. Demultiplexing can be done using tools like the demuxlet algorithm with the provided genotype information.
The feature-barcode matrices of RNA expression were analyzed using the Seurat R package (Seurat, v4.1.1)
Assembly: GRCH38
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, filtered_contig_annotations.csv

value: PBMC

value: Long term responder


title: Adipose 1020-A F


title: DN-P-701_Well_C10


title: LPFS_C1D15_1_13_1_19_1_28_2_4_TCR

description: 10x Genomics

data_processing:
Libraries were constructed and sequenced at a depth of approximately 50,000 reads per cell using the Novaseq 6000 platform (Illumina, San Diego, CA, USA).
The sequenced data were demultiplexed using the mkfastq function (Cell Ranger, 10X Genomics, v3.0.1) to generate fastq files.
We did not use HTO for demultiplexing. Instead, we performed demultiplexing using genotype information that was submitted. Demultiplexing can be done using tools like the demuxlet algorithm with the provided genotype information.
The feature-barcode matrices of RNA expression were analyzed using the Seurat R package (Seurat, v4.1.1)
Assembly: GRCH38
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, filtered_contig_annotations.csv
Library strategy: scTCR-seq

value: mononuclear cell


title: EVD patient L16_miRNA


title: SPFS_1_10

description: gDNA for genotyping (demultiplexling)


title: Adipose 1019-A F

value: adipose


title: LPFS_C1D15_1_8_1_18_1_20_3_8_TCR

description: 10x Genomics


title: EVD patient L15_miRNA


title: DN-P-701_Well_C09


title: Healthy adult C04_miRNA


title: DN-P-701_Well_C08


title: EVD patient L09_miRNA


title: Adipose 1018-A M

value: male


title: LPFS_C1D15_1_8_1_18_1_20_3_8_GEX

description: 10x Genomics


title: Adipose 1024-A F


title: DN-P-701_Well_C07


title: Adipose 1016-A M


title: LPFS_C1D1_2_1_2_2_2_4_2_6_TCR

description: 10x Genomics


title: EVD patient L08_miRNA


title: EVD patient L07_miRNA


title: DN-P-701_Well_C06


title: Adipose 1014-A F


title: DN-P-701_Well_C05


title: EVD patient L05_miRNA


title: LPFS_C1D1_1_8_1_18_1_20_3_8_TCR

description: 10x Genomics


title: LPFS_C1D1_1_8_1_18_1_20_3_8_GEX

description: 10x Genomics


title: Adipose 1012-A F


title: DN-P-701_Well_C03


title: Adipose 1013-A F


title: LPFS_C1D1_1_6_1_11_1_13_1_19_TCR

description: 10x Genomics


title: EVD patient L04_miRNA


title: DN-P-701_Well_C02


title: EVD patient L03_miRNA


title: LPFS_C1D1_1_6_1_11_1_13_1_19_GEX

description: 10x Genomics


title: 5XFAD, replicate 2, section 3

city: Ann Arbor

first: Mohamed

last: Noureldein

address: 109 Zina Pitcher Place

department: Neurology

institute: University of Michigan

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the spaceranger software v1.3.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files and images
Library strategy: Spatial Transcriptomics

source_name: Brain

extract_protocol:
Brains were sectioned from wild type, 5XFAD mice, 5XFAD mice treated with either vehicle or human neural stem cells (hNSC) at 41 weeks of age and subjected to 10X Visium spatial transcriptomics to get gene expression information.
Briefly, the slides were heated at 37 °C for 1 min on a T100 thermal cycler (BioRad, Hercules, CA, USA) followed by transferring to precooled methanol (Sigma Aldrich, St. Louis, MO) for 30 min followed by hematoxylin and eosin (H&E) using a standard protocol. AGC obtained brightfield images of the H&E stained sections using an AxioObserver (Zeiss, Germany). Permeabilization of tissue sections was performed for 12 min, as experimentally determined using the Visium Spatial Tissue Optimization Slide & Reagent kit (10X Genomics, Pleasanton, CA, USA). Permeabilization resulted in mRNA release from cells to bind to oligonucleotides on the capture areas followed by reverse transcription, second-strand synthesis, denaturation and cDNA amplification as specified in the demonstrated protocol using a T100 thermal cycler with the spatial slide adaptor. Amplified cDNA clean-up was done using SPRIselect (Beckman Coulter, Brea, CA, USA) and library preparation was performed according to the manufacturer’s protocol. The generated cDNA libraries were subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000).

value: Brain cells

value: Brain

tag: age

value: 41 weeks old


title: Adipose 1011-A F


title: 5XFAD, replicate 2, section 1

description: 10x Genomics


title: DN-P-701_Well_C01

data_processing:
Sequence data were analysed using the Seven Bridges Genomics bioinformatics platform (BD: Precise Whole Transcriptome Assay Analysis Pipeline v2.0). This pipeline performs all required steps to demultiplex, align, and quantitate sequencing reads from BD™ Precise Whole Transcriptome Assay. After performing a quality control assessment using FastQC, the pipeline filters and demultiplexes sequencing reads based on the sequence of the 8 base sample barcode. It aligns reads from each sample to the transcriptome using STAR, with feature counting by the union rules of HTSeq-count. The initial quantification is performed by counting the unique molecular indices (MI) mapped to each feature. Lastly, the pipeline uses two error correction algorithms to remove MI errors. In brief, MI errors that are derived from sequencing base calls and PCR substitution errors are identified and adjusted to a single MI barcode using Recursive Substitution Error Correction™ (RSEC). Subsequently, MI errors that are derived from library preparation steps or sequencing base deletion errors are adjusted using Distribution-Based Error Correction™ (DBEC).
A cell was considered to be infected if there was at least one GFP sequence read count. This information was then used to define the groups to compare in EdgeR. Differential gene expression was measured between infected and uninfected cells in each subset (Adjusted p-value less than 0.05).
Precise WTA Sample Demultiplexing:Paired-end reads are demultiplexed per well based on the sequence of the sample index. This sample index is found in the first 8 bases of Read 01. The Molecular Index is found in Read 01, in positions 8 to 16. The demultiplexing process also includes a structure filtering step. After filtering, the final step in this process stores the Molecular Index in the demultiplexed FASTQ files by appending the index to the sequence headers of Read 02 FASTQ files. The Read 02s from each well are trimmed by Flexbar to remove any Illumina adapter contaminants and mapped to the reference genome using STAR.
Precise WTA Alignment Quantification: After Read 02s are aligned using STAR, the alignments are assigned to gene counts using a custom implementation of HTSeq-count. The number of reads mapping to each gene is generated in the DBEC Read Mapping Report. The unique counts for molecular indices are calculated in the DBEC Molecular Index Mapping Report
Genome_build: mm9
Supplementary_files_format_and_content: text document (after removal of Molecular indices error using Recursive Substitution Error Correction™ (RSEC) and Distribution-Based Error Correction™ (DBEC))

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: SPFS_C1D15_1_21_3_7_LPFS_1_11_1_6_TCR

description: 10x Genomics

value: peripheral blood

value: Early progressor, Long term responder


title: LPFS_C1D1_2_1_2_2_2_4_2_6_GEX

description: 10x Genomics


title: DN-P-701_Well_B12

value: 48hr treatment with Phosphate buffer saline (PBS)


title: SPFS_C1D15_1_21_3_7_LPFS_1_11_1_6_GEX

description: 10x Genomics


title: EVD patient L06_miRNA


title: L126H_YPEG_Rep3

city: Los Angeles

first: Siavash

last: Kurdistani

state: CA

address: 615 Charles Young Dr. South

department: Department of Biological Chemistry

institute: David Geffen School of Medicine at UCLA

description:
L126H_YPEG3
raw_counts.csv
normalized_counts_DESeq2.csv

data_processing:
Genomic alignment of FASTQ using HISAT2. Strand-specific alignment.
Assignment to open reading frames and counting using featureCounts. Strand-specific assignment.
Differential expression analysis performed with DESeq2, with strain (WT, L126M, L126H) and batch (rep1, rep2, rep3, rep4) as variables.
Assembly: sacCer3
Supplementary files format and content: csv

organism: Saccharomyces cerevisiae

source_name: whole yeast cells

growth_protocol: Cells were grown to 2-3 doublings before collection

extract_protocol:
RNA was extracted from whole yeast cells using hot acid phenol, followed by a further phenol-cholorform extraction and ethanol precipitation.
Prior to preparing RNA-seq libraries for Illumina NovaSeq sequencing, contaminating DNA was digested using Turbo DNase (Thermo Fisher). RNA quality was assessed by Agilent 2200 Tapestation. Stranded mRNA (Poly-A) libraries were constructed with automated NGS library construction and sequenced by UCLA Technology Center for Genomics & Bioinformatics

value: whole yeast cells

value: YPEG (oxidative medium)


title: DN-P-701_Well_B11

source_name: Bone marrow derived APC

value: Bone marrow derived APC


title: hNSC, replicate 3, section 2

description: 10x Genomics

value: hNSC


title: SPFS_C1D1_3_4_LPFS_C1D1_1_28_2_8_3_6_TCR

description: 10x Genomics


title: L126H_YPEG_Rep2

description:
L126H_YPEG2
raw_counts.csv
normalized_counts_DESeq2.csv


title: SPFS_C1D1_3_4_LPFS_C1D1_1_28_2_8_3_6_GEX

description: 10x Genomics


title: L126H_YPEG_Rep1

description:
L126H_YPEG1
raw_counts.csv
normalized_counts_DESeq2.csv


title: Adipose 1015-A M

data_processing:
Mouse raw-reads from the 386 samples described above were quality and adapter trimmed with cutadapt v2.3 . Filtered trimmed reads were mapped with Bowtie2 v2.3.5 [PMID: 22388286]. For C57BL/6J samples, reads were mapped to GRCm38 release 98 (ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz). For all other DO founder strains (A/J, 129S1/SvlmJ, NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ), reads were mapped to strain-specific pseudo-references. Pseudo-references for each strain were constructed with g2gtools v0.1.31 (http://churchill-lab.github.io/g2gtools) by patching GRCm38 release 98 with strain-specific SNPs and Indels from the Mouse Genome Project [PMID: 21921910] REL-1807 (ftp://ftp-mouse.sanger.ac.uk/REL-1807-SNPs_Indels/). Mapped reads were filtered to remove PCR duplicates, mtDNA, and the following classes of reads: unmapped, mate unmapped, and non-primary alignment. DeepTools alignmentSieve v3.3.2 [PMID: 27079975] was used to offset all reads aligning to the positive strand by +4bp, and all reads aligning to the negative strand by -5bp to account for Tn5 transposase activity [PMID: 24097267 , PMID: 21143862]. Alignments from non-C57BL/6J samples were then lifted to GRCm38 coordinates with g2gtools. Peak calling was conducted on all pooled alignment files with Macs2 v2.2.7.1 [PMID: 22936215].
Assembly: mm10
Supplementary files format and content: narrowPeak : called peaks of signal enrichment, bed : peaks count matrix, bigwig : read coverage track

value: Adipose - gonadal fat pad


title: hNSC, replicate 3, section 1

description: 10x Genomics


title: SPFS_C1D15__3_2_3_4_1_10_1_26_TCR

description: 10x Genomics

value: PBMC

value: Early progressor


title: DN-P-701_Well_B09


title: DN-P-701_Well_B08


title: DN-P-701_Well_B07


title: hNSC, replicate 1, section 2

description: 10x Genomics


title: L126M_YPEG_Rep3

description:
L126M_YPEG3
raw_counts.csv
normalized_counts_DESeq2.csv


title: L126M_YPEG_Rep2

description:
L126M_YPEG2
raw_counts.csv
normalized_counts_DESeq2.csv


title: L126H_YPEG_Rep4

description:
L126H_YPEG4
raw_counts.csv
normalized_counts_DESeq2.csv


title: L126M_YPEG_Rep4

description:
L126M_YPEG4
raw_counts.csv
normalized_counts_DESeq2.csv


title: DN-P-701_Well_B06


title: SPFS_C1D15_1_2_1_27_3_1_3_5_TCR

description: 10x Genomics

value: mononuclear cell


title: SPFS_C1D15__3_2_3_4_1_10_1_26_GEX

description: 10x Genomics


title: SPFS_C1D15_1_2_1_27_3_1_3_5_GEX

description: 10x Genomics


title: SPFS_C1D1_1_2_1_27_3_1_3_5_TCR

description: 10x Genomics


title: Vehicle, replicate 1, section 2

description: 10x Genomics

value: vehicle


title: WT_YPEG_Rep4

description:
WT_YPEG4
raw_counts.csv
normalized_counts_DESeq2.csv

value: Wild type


title: L126M_YPEG_Rep1

description:
L126M_YPEG1
raw_counts.csv
normalized_counts_DESeq2.csv


title: DN-P-701_Well_C04


title: DN-P-701_Well_B10


title: hNSC, replicate 2, section 2

description: 10x Genomics

value: Brain cells


title: SPFS_C1D1_1_2_1_27_3_1_3_5_GEX

description: 10x Genomics


title: DN-P-701_Well_B04


title: hNSC, replicate 2, section 1

description: 10x Genomics

value: Brain


title: Vehicle, replicate 1, section 1

description: 10x Genomics

value: 41 weeks old


title: WT, replicate 1, section 2

description: 10x Genomics


title: WT_YPEG_Rep3

description:
WT_YPEG3
raw_counts.csv
normalized_counts_DESeq2.csv


title: WT, replicate 1, section 1

description: 10x Genomics


title: WT_YPEG_Rep2

description:
WT_YPEG2
raw_counts.csv
normalized_counts_DESeq2.csv


title: DN-P-701_Well_B02


title: SPFS_C1D1_1_21_1_23_1_26_3_2_TCR

description: 10x Genomics


title: hNSC, replicate 1, section 1

description: 10x Genomics


title: DN-P-701_Well_B05


title: 5XFAD, replicate 1, section 2

description: 10x Genomics


title: L126H_YPD_Rep4

description:
L126H_YPD4
raw_counts.csv
normalized_counts_DESeq2.csv

value: YPD (fermentative medium)


title: SPFS_C1D1_1_5_1_10_1_12_1_17_GEX

description: 10x Genomics

value: peripheral blood


title: DN-P-701_Well_A12

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: SPFS_C1D1_1_5_1_10_1_12_1_17_TCR

description: 10x Genomics


title: DN-P-701_Well_B01

value: 48hr treatment with Phosphate buffer saline (PBS)


title: L126H_YPD_Rep2

description:
L126H_YPD2
raw_counts.csv
normalized_counts_DESeq2.csv

value: whole yeast cells


title: DN-P-701_Well_A11


title: PD16_rep3

city: Wuhan

first: changjiu

last: he

state: Hubei

address: 1 Shizishan street, Hongshan District

department: College of Animal Science and Technology

institute: Huazhong Agricultural University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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 FPKM values for each Sample .

source_name: Granulosa cells

extract_protocol:
Granulosa cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Kunming

value: ovary

value: postnatal day 16


title: PD16_rep2


title: L126H_YPD_Rep3

description:
L126H_YPD3
raw_counts.csv
normalized_counts_DESeq2.csv


title: DN-P-701_Well_B03

city: Ede

first: Alphonsus

last: Ugwu

address: redeemers' university ede osun state

institute: Africa Centre of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s 6 University, Ede, Osun State, Nigeria

extract_protocol:
The cells are collected in WTA single cell encoding plate, RNA secondary structure is done at 65C for 3 minutes (hold at 4C), mastermix containing BD customised RT enzymes is added (PN 650000041) and run at 42C for 30 minutes, heat inactivated at 80C for 5 minutes before holding at 4C. The samples is pooled and purify before library prep.
Libraries of the cellular RNA were made using the BD WTA single cell kit and sequenced using MiSeq V2 from Illumina (BM-DC, BM-M, DN).

value: Bone marrow derived APC


title: L126H_YPD_Rep1

description:
L126H_YPD1
raw_counts.csv
normalized_counts_DESeq2.csv


title: L126M_YPD_Rep4

description:
L126M_YPD4
raw_counts.csv
normalized_counts_DESeq2.csv


title: DN-P-701_Well_A10


title: PD15_rep3

value: postnatal day 15


title: IL2 stimulated CAR NK -2

first: Jianhua

last: Luo

address: 800 Xiangyin Road

institute: National Key Laboratory of Immunology & Inflammation, Institute of Immunology

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to GRCh38 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: human cell line

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
According to the instructions of the experiment, the purified Total RNA was separated into mRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

value: human cell line

tag: cell line

value: non-Hodgkin's lymphoma

value: IL-2 stimulated


title: DN-P-701_Well_A09


title: Neo-2/15  stimulated CAR NK 2-2

value: Neo-2/15  stimulated


title: SPFS_C1D1_1_21_1_23_1_26_3_2_GEX

description: 10x Genomics

value: PBMC

value: mononuclear cell

value: Early progressor


title: 5XFAD, replicate 1, section 1

description: 10x Genomics

value: Brain cells

value: Brain

value: 41 weeks old


title: DN-P-701_Well_A08

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: WT_YPEG_Rep1

description:
WT_YPEG1
raw_counts.csv
normalized_counts_DESeq2.csv

value: whole yeast cells

tag: genotype

value: Wild type

value: YPEG (oxidative medium)


title: PD15_rep2

value: Kunming

value: ovary


title: IL2 stimulated CAR NK 1-1


title: L126M_YPD_Rep3

description:
L126M_YPD3
raw_counts.csv
normalized_counts_DESeq2.csv

value: YPD (fermentative medium)


title: DN-P-701_Well_A07

value: Bone marrow derived APC


title: Neo-2/15-NK-92, H3K4me3, Cut&Tag

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Fastx v0.0.13, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2.2.6. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were renormalized (to reads per million, rpkm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.2.7.1 with the significance cut-off p-value <=0.01
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&Tag

growth_protocol: Alpha Minimum Essential medium (BasalMedia, L540KJ) with final a concentration of 0.2 mM inositol, 0.1 mM 2-mercaptoethanol; 0.02 mM folic acid, 20ng/ml recombinant IL-2 (Novoprotein, C013), 12.5% horse serum (Gibco, 26050088) and 12.5% fetal bovine serum (Gibco, 10091).

extract_protocol:
ACCORDING TO PROTOCOL:vazyme TD903:Add 5 μl Proteinase K, 100 μl Buffer L/B and 20 μl DNA Extract Beads to the fragmented sample, vortex thoroughly and incubate at 55°C for 10 min, inverting and mixing 2 to 3 times. Remove the sample from the magnetic stand, add 200 µl Buffer WA, vortex and mix thoroughly, centrifuge briefly to collect the reaction solution, place the 8-tube strip on the magnetic stand, let stand for 2 minutes, and discard the supernatant. Remove the above samples from the magnetic stand, add 200 µl Buffer WB, vortex and mix thoroughly, centrifuge briefly to collect the reaction solution, place 8 strips of tubes on the magnetic stand, let stand for 2 minutes, and discard the supernatant. repeat. Open the lid and let it sit at room temperature for 5 - 10 minutes until there is no liquid remaining in the tube and there is no reflection on the surface of the magnetic beads. Remove the above sample from the magnetic stand, add 22 μl of sterilized ultrapure water, pipet and mix with a pipette, and elute at room temperature for 5 minutes, shaking gently 2 to 3 times during this period. Place the 8-strip tube on the magnetic stand. After the solution is clarified (about 1 minute), pipet 20 μl of the supernatant into a new 8-strip tube. The sample can be stored at -30 ~ -15°C for a long time to avoid repeated freezing and thawing.
ChIP-Seq libraries were prepared using the vazyme TD903 kit

value: human cell line

value: non-Hodgkin's lymphoma


title: L126M_YPD_Rep1

description:
L126M_YPD1
raw_counts.csv
normalized_counts_DESeq2.csv


title: Neo-2/15-NK-92, XBP1,Cut&Tag 3

value: Neo-2/15  stimulated


title: DN-P-701_Well_A06


title: PD15_rep1

value: postnatal day 15


title: WT_YPD_Rep4

description:
WT_YPD4
raw_counts.csv
normalized_counts_DESeq2.csv


title: Neo-2/15  stimulated CAR NK 2-1


title: PD16_rep1

value: postnatal day 16


title: PD14_rep2

value: postnatal day 14


title: Neo-2/15-NK-92, XBP1,Cut&Tag 1


title: DN-P-701_Well_A05


title: DN-P-701_Well_A04


title: PD14_rep1


title: DN-P-701_Well_A03


title: Neo-2/15-NK-92, IgG, Cut&Tag (IgG negative control group)


title: BMDM cells, K7M2-EVs treated, biol rep 3

city: Guangzhou

first: Chuangzhong

last: Deng

state: Guangdong China

address: 651 Dongfeng East Rd

department: Department of Musculoskeletal Oncology

institute: Sun Yat-sen University Cancer Center

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTP
mRNA-seq reads were aligned to the GRCm38.91 genome assembly using Hisat2 version 2.1.0 with default parameters
Gene abundance measurements were generationed and normalized  using stringtie version 1.3.4b Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR function package in R program version 3.4.3
Assembly: GRCm38.91
Supplementary files format and content: tab-delimited text files include normalized FPKM values for each Sample

source_name: primary cultured bone marrow derived macrophage

growth_protocol: To obtain bone marrow-derived macrophages (BMDMs), bone marrow cells were flushed out from the femurs and tibias of 5- to 8-week-old BALB/C mice. After red blood cell lysis and filtration, cells were cultured in RPMI 1640 supplemented with 10% heat-inactivated FBS and M-CSF (25 ng/ml) for 6 days

extract_protocol:
Total RNA from BMDMs were isolated by TRIzol (No.:15596026, Thermo Fisher Scientific, USA) and extracted by chloroform. RNA degradation and contamination were monitored on 1% agarose gels and purity was checked by the NanoPhotometer spectrophotometer (IMPLEN, CA USA). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer(Life Technologies, CA, USA) and integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzeer 2100 system (Agilent Technologies, CA, USA ).
Sequencing libraries were generated using NEBNest UltraTM RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Macrophage polarization was induced by treatment with K7M2-EVs (10 μg) or PBS control for 24 hours

value: BMDM

value: WT

tag: polarization

value: macrophage polarization


title: DN-P-701_Well_A02

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: WT_YPD_Rep3

description:
WT_YPD3
raw_counts.csv
normalized_counts_DESeq2.csv

value: whole yeast cells


title: WT_YPD_Rep2

description:
WT_YPD2
raw_counts.csv
normalized_counts_DESeq2.csv

value: Wild type


title: WT_YPD_Rep1

description:
WT_YPD1
raw_counts.csv
normalized_counts_DESeq2.csv


title: IL-2-NK-92, H3K4me3, Cut&Tag

value: IL-2 stimulated


title: DN-P-701_Well_A01


title: BMDM cells, K7M2-EVs treated, biol rep 2


title: IL-2-NK-92, XBP1,Cut&Tag 3


title: L126M_YPD_Rep2

description:
L126M_YPD2
raw_counts.csv
normalized_counts_DESeq2.csv


title: BMDM cells, K7M2-EVs treated, biol rep 1


title: PD14_rep3

value: Kunming


title: Neo-2/15-NK-92, XBP1,Cut&Tag 2


title: IL-2-NK-92, XBP1,Cut&Tag 2


title: DN-701_Well_H11

value: 12hr infection with LCMV Cl 13


title: exercise4weeks_B_2

first: André

last: Fischer

state: Niedersachsen

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

institute: Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE)

description: 10x Genomics

data_processing:
Raw BCL files weredemultiplexed (using cellranger mkfastq), mapped and counts files were generated using cellranger count (cellranger-4.0.0), using default settings.
Assembly: mm10
Supplementary files format and content: The processed data files include the filtered feature-barcode matrices in the MEX (Market Exchange) file format ouputted by CellRanger.

source_name: whole hippocampus, tissue from adult mice brain

extract_protocol:
Nuclei from frozen mouse brain tissues were isolated according to the previously published protocol with certain modifications (Sakib et al., 2021 [PMID: 33554149]). Briefly, frozen tissues were Dounce homogenized in 500 µl EZ prep lysis buffer (Sigma NUC101) supplemented with 1:200 RNAse inhibitor (Promega, N2615) for 45 times in a 1.5 mL Eppendorf tube using micro pestles. The volume was increased with lysis buffer up to 2000 µl and incubated on ice for 5 min. Lysates were centrifuged for 5 min at 500 × g at 4 °C and supernatants were discarded. The pellet was resuspended into 2000 µl lysis buffer and incubated for 5 min on ice. After 5 min of centrifugation (500 × g at 4 °C), the resulting pellet was resuspended into 1500 µl nuclei suspension buffer (NSB, 0.5 % BSA, 1:100 Roche protease inhibitor, 1:200 RNAse inhibitor in 1×PBS) and centrifuged again for 5 min (500 × g at 4 °C). The pellet was finally resuspended into 500 µl NSB and stained with 7AAD (Invitrogen, Cat: 00-6993-50). Single nuclei were sorted using BD FACS Aria III sorter. Sorted nuclei were counted in Countess II FL Automated Counter.
Approximately 4000 single nuclei per sample were used for GEM generation, barcoding, and cDNA libraries according to 10X Chromium Next GEM Single Cell 3ʹ Reagent v3.1 protocol. Pooled libraries were sequenced in Illumina NextSeq 550 in order to achieve >50,000 reads/nuclei.
10X genomics snRNA-seq

value: C57BL/6J , WT

value: exercise


title: exercise4weeks_B_3

description: 10x Genomics

value: whole hippocampus, tissue from adult mice brain


title: exercise4weeks_B_4

description: 10x Genomics


title: BMDM cells, PBS treated, biol rep 2

value: PBS


title: DN-701_Well_H10

value: Bone marrow derived APC


title: BMDM cells, PBS treated, biol rep 1


title: exercise4weeks_B_1

description: 10x Genomics


title: E14.5 mouse cerebral cortex, Brg1 cKO,bio rep3

city: jinan

first: Yecheng

last: Jin

address: No.44 West Wenhua Road

institute: Shandong university

data_processing:
Raw data (raw reads) in the fastq format were first processed using in-house Perl scripts. Clean reads were obtained by removing reads containing adapters, reads containing poly-N, and low-quality reads from raw data.
Paired-end clean reads were aligned to mm10 genome assembly using Hisat2 v2.0.5.
Feature Counts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Subsequently, the FPKM of each gene was calculated based on the length of the gene, and the read count was mapped to this gene.
Assembly: mm10
Supplementary files format and content: matrix table files include FPKM values for each Sample

source_name: cerebral cortex

extract_protocol:
The cerebral cortex at E14.5 was dissected and total RNA was extracted using Trizol reagent (Ambion, 15596) following the manufacturer’s protocol. A total of 1 μg RNA per sample was used as the input material for the RNA sample preparations.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was implemented using divalent cations under elevated temperatures in the First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H). Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3’ ends of DNA fragments, an adaptor with a hairpin loop structure was ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA) to select cDNA fragments of 370–420 bp in length. PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. PCR products were purified (AMPure XP system), and library quality was assessed using the Agilent Bioanalyzer 2100 system.

value: cerebral cortex

tag: developmental stage

value: embryonic day 14.5

value: neural progenitor

value: Brg1 knockout

value: no treanment


title: IL-2-NK-92, IgG, Cut&Tag (IgG negative control group)

value: human cell line

value: non-Hodgkin's lymphoma


title: IL-2-NK-92, XBP1,Cut&Tag 1


title: urine_chronic_03

city: Medellín

first: Carlos

last: Carmona

address: Cl. 62 #52-59, La Candelaria, Medellín

department: Inmunología Celular e Inmunogenética

country: Colombia

institute: Universidad de Antioquia

data_processing:
Spliced Transcripts Aligned to a Reference (STAR) sofware
Sequence reads were trimmed for adaptor sequence/low quality sequence using STAR.
Trimmed sequences were mapped to GRCh38/hg38 using STAR.
Read count extraction was performed using STAR.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample listed.

source_name: Urine

extract_protocol:
RNA was obtained using Tri Reagent+2uL glycogen, following manufacturer's protocols.
Libraries were prepared using the SureSelect RNA Direct_Human kit  following manufacturer's protocols.

treatment_protocol: Samples were taken at the moment of biopsy in a clinical setting.

value: Urine

tag: condition

value: Chronic rejection

value: Urinary sediment


title: E14.5 mouse cerebral cortex, Brg1 cKO,bio rep2

tag: cell type


title: DN-701_Well_H09

tag: strain


title: DN-701_Well_H07

tag: treatment


title: DN-701_Well_H08


title: control4weeks_A_2

city: Göttingen

description: 10x Genomics

tag: tissue

value: control


title: urine_chronic_01


title: control4weeks_A_1

description: 10x Genomics


title: biopsy_chronic_03

source_name: Renal biopsy

value: Renal biopsy

value: Renal cells obtained from the whole tissue


title: E14.5 mouse cerebral cortex, control,bio rep3

value: WT


title: biopsy_chronic_02


title: Ovary, postnatal day 65 3

city: Omaha

first: So-Youn

last: Kim

state: Nebraska

address: DRC2 4016, 601 South Saddle Creek RD

institute: University of Nebraska Medical center

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Ovary

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NuGEN Universal Plus mRNA-Seq library Kit following manufacturer's protocols.

value: Ovary

value: Oocyte-specific PIK3CA* gene knockin

tag: postnatal day


title: BMDM cells, PBS treated, biol rep 3

value: BMDM

value: macrophage polarization

value: PBS


title: DN-701_Well_H04

value: Bone marrow derived APC

value: 12hr infection with LCMV Cl 13


title: Ovary, postnatal day 65 2


title: E14.5 mouse cerebral cortex, control,bio rep1

value: cerebral cortex

value: embryonic day 14.5

value: neural progenitor

value: no treanment


title: E14.5 mouse cerebral cortex, Brg1 cKO,bio rep1

value: Brg1 knockout


title: biopsy_chronic_01

value: Chronic rejection


title: DN-701_Well_H03


title: Ovary, postnatal day 65 1


title: urine_chronic_02

value: Urine

value: Urinary sediment


title: control4weeks_A_4

description: 10x Genomics

value: whole hippocampus, tissue from adult mice brain

value: C57BL/6J , WT

value: control


title: DN-701_Well_H06


title: DN-701_Well_H02


title: Ovary, postnatal day 50 3

value: Ovary

value: Oocyte-specific PIK3CA* gene knockin


title: control4weeks_A_3

description: 10x Genomics


title: Ovary, postnatal day 50 2


title: G317-4Micro

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

institute: Penn State University

description:
G317-4Micro
controls  replicate2

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.20.0) allowing no mismatches in the index read. For mRNA-seq, BBDuk was used to trim/filter low-quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the mouse reference genome (mouse Ensembl release 67 (GRCm37 / NCBIM37 / mm9)) was done using HISAT2 (version 2.1.0) applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq by supplementing Ensembl gene annotation (release 67: "Mus_musculus.Ensembl.NCBIM37.67.gtf"). For microRNA-seq, sequencing reads were subjected to quality filtering, quality trimming and adapter trimming by FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit), conducted by fastq_quality_filter function, fastq_quality_trimmer function, and fastq_clipper function, respectively, 4 bases were trimmed from both 5’ and 3’ ends of the sequencing reads by fastq_trimmer function. Oasis 2.0 suite (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2047-z) was used to align and count raw reads of all expressed small RNAs.
Assembly: mouse Ensembl release 67 (GRCm37 / NCBIM37 / mm9)
Supplementary files format and content: csv file containing raw read counts for each sample ("EG_merged.HTSeq.out.csv" for mRNA-seq, "EGmicro.out.csv" for microRNA-seq)

source_name: 8 hour_cont_2

growth_protocol: Mice were purchased from Jackson laboratory and housed in a room with an ambient temperature of 25 C, 30–70% humidity, a 12-h light–dark cycle, and ad libitum access to rodent chow

extract_protocol:
Animal was sacrificed, decapitated and brain was removed from skull. Hippocampus isolation was done  in PBS, right and left halves of hippocampus were flash frozen.Total RNA isolation waswere carried out from the leftfrom left hippocampus with Trizol reagent (15596018, Ambion, Carlsbad, CA, USA) as described in the vendor’s manual. The quality of RNA was assessed on an Agilent Bioanalyzer and confirmed fof their samples with RNA integrity numbers were between greater than 7.9.
For mRNA-seq, the libraries were prepared using the Illumina® Stranded mRNA Prep, Ligation kit (Illumina) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 200 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique dual index sequences (IDT® for Illumina® RNA UD Indexes Set A, Ligation, Illumina) were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). For microRNA-seq, the libraries were prepared using the NEXTflexTM Small RNA Library Prep Kit v3 (BioO Scientific) as per the manufacturer's instructions. The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).
The denatured libraries were loaded onto an S1 flow cell on a NovaSeq 6000 or a Rapid flow cell on a HiSeq2500 (Illumina) and run for 2X53 cycles (for mRNA-seq) or for 1X49-65 cycles (for microRNA-seq) according to the manufacturer's instructions.

treatment_protocol: C57BL/6j male and female mice 6-7weeks old   injected intraperitoneal  with pilocarpine (350 mg/kg) or vehicle (0.9% bacteriostatic sodium chloride)

value: adult 6-7 weeks

value: hippocampus

tag: molecule subtype

value: micro-RNA

tag: time

tag: batch


title: DN-701_Well_H01

value: Bone marrow derived APC

value: 12hr infection with LCMV Cl 13


title: DN-701_Well_G12


title: blood_chronic_01

source_name: Peripheral blood

value: Peripheral blood

value: Leukocytes


title: E14.5 mouse cerebral cortex, control,bio rep2

value: cerebral cortex

value: embryonic day 14.5

value: neural progenitor

value: WT

value: no treanment


title: C317-1Micro

description:
C317-1Micro
pilocarpine seizure replicate 1

source_name: 8 hour seizure_1

value: Pilocarpine


title: C317-3Micro

description:
C317-3Micro
pilocarpine seizure replicate 2

source_name: 8 hour seizure_2


title: G317-2Micro

description:
G317-2Micro
controls  replicate1

source_name: 8 hour_cont_1


title: DN-701_Well_G11


title: Ovary, postnatal day 50 1


title: G545_08_t120_exp

description:
G545_08_t120_exp
pilocarpine seizure replicate 3

source_name: 120hour seuzure_3

value: mRNA


title: Ovary, postnatal day 8 3


title: DN-701_Well_H05


title: urine_acute_03

value: Urine

value: Acute rejection

value: Urinary sediment


title: urine_acute_01


title: urine_acute_02


title: Ovary, postnatal day 8 1

value: Ovary

value: Oocyte-specific PIK3CA* gene knockin


title: G545_02_t120_exp

description:
G545_02_t120_exp
pilocarpine seizure replicate 1

source_name: 120hour seuzure_1

value: adult 6-7 weeks

value: hippocampus


title: Ovary, postnatal day 8 2


title: DN-701_Well_G09

value: Bone marrow derived APC

value: 12hr infection with LCMV Cl 13


title: G545_03_t120_exp

description:
G545_03_t120_exp
pilocarpine seizure replicate 2

source_name: 120hour seuzure_2


title: blood_chronic_03

value: Peripheral blood

value: Chronic rejection

value: Leukocytes


title: biopsy_acute_04

value: Renal biopsy

value: Renal cells obtained from the whole tissue


title: blood_chronic_02


title: biopsy_acute_03


title: DN-701_Well_G08

source_name: Bone marrow derived APC


title: D3 lung2

city: Valhalla

first: Sudhir

last: Jain

state: New York

address: 15 Dana Rd

department: Pathology, Microbiology and Immunology

institute: New York Medical Collage

data_processing:
Kallisto pseudo-alignment was used with Ensembl mouse transcriptome reference GRCm38
DESeq2 was used for differential gene expression
Genome_build: GRCm38
Supplementary_files_format_and_content: TPM for gene expression level in a csv file

source_name: lung tissue

extract_protocol:
RNA was extracted using Qiagen RNAeasy Kit
Illumina TruSeq Stranded Total RNA Library Preparation using the polyadenylated mRNA pull-down.

tag: group

value: Haplotype-II aged+LVS

value: lung


title: G545_06_t36_exp

description:
G545_06_t36_exp
pilocarpine seizure replicate 3

source_name: 36 hour seizure_3

value: Pilocarpine

value: mRNA


title: D2 lung2


title: biopsy_acute_02

value: Acute rejection


title: DN-701_Well_G06


title: DN-701_Well_G10


title: D1 lung2


title: G545_04_t36_exp

description:
G545_04_t36_exp
pilocarpine seizure replicate 1

source_name: 36 hour seizure_1


title: biopsy_acute_01


title: DN-701_Well_G05


title: blood_acute_04


title: DN-701_Well_G04


title: G545_09_t0_cont

description:
G545_09_t0_cont
controls  replicate3


title: B3 lung2

value: Haplotype-II aged


title: B2 lung2


title: G545_07_t0_cont

description:
G545_07_t0_cont
controls  replicate2


title: blood_acute_03


title: blood_acute_02


title: DN-701_Well_G03


title: B1 lung2


title: G545_01_t0_cont

description:
G545_01_t0_cont
controls  replicate1


title: DN-701_Well_G02


title: DN-701_Well_G07


title: D4 kidney2

source_name: Kidney tissue

value: Haplotype-II aged+western diet

value: kidney


title: blood_acute_01


title: D3 kidney2


title: G545_05_t36_exp

description:
G545_05_t36_exp
pilocarpine seizure replicate 2

source_name: 36 hour seizure_2

value: adult 6-7 weeks


title: G317_3_t8_exp

description:
G317_3_t8_exp
pilocarpine seizure replicate 2

value: hippocampus


title: G317_1_t8_exp

description:
G317_1_t8_exp
pilocarpine seizure replicate 1


title: B5L32

city: Houston

first: Zejuan

last: Li

state: Texas

address: 6565 Fannin St, MC227

department: Department of Pathology and Genomic Medicine

institute: Houston Methodist Hospital

data_processing:
Basecalls were converted using bcl2fastq2.
Sequencing quality of raw reads were evaluated using FastQC, and trimmed adaptors and low quality reads (Phred quality score < 15) using Trimmomatic
High quality reads were mapped to hg38  genome using bowtie2 with end-to-end mode
Duplicate reads were removed using samtools.
The reads were counted into gene body regions of RefSeq genes using featureCounts.
Assembly: hg38
Supplementary files format and content: txt file for all sample with raw reads count summarised to gene body regions of Refseq genes.

source_name: Plasma

extract_protocol:
Plasma was separated from whole blood by centrifuge 1350 g for 10 minutes at 4 °C. Plasma cfDNA was extracted using QIAamp Circulating Nucleic Acid Kit (QIAGEN, Germantown, MD) following manufacturer’s instructions.
Briefly, cfDNA was ligated with barcode adaptors after end repair and A-tailing. Then cfDNA was purified and was incubated with 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, 100 μM N3-UDP-azide-glucose and 1 μM T4 Phage β-gulcosyltransferase at 37 °C for 1 hour. After purification, cfDNA was incubated with 1 μL DBCO-PEG4-DBCO (a click chemistry tool, 4.5 mM stock in DMSO) at 37 °C for 2 hours. Next, the cfDNA was purified and incubated with 5 μL pre-washed C1 Streptavidin beads (Thermo Fisher Scientific, Waltham, MA) for 15 min. The beads were subsequently washed for 5 minutes eight times. The captured DNA fragments were amplified with 15-18 cycles of PCR. The PCR products were purified with AMPure XP beads according to the manufacturer’s instructions. The concentration of DNA library was measured using a Qubit Fluorometer with dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA) and Bioanalyzer 2100 with Agilent High Sensitivity Kit (Agilent Technologies, Santa Clara, CA).
nano-hmC-Seal

tag: diagnosis

value: Acute myeloid leukemia

tag: gender (1 = male, 2 = female)


title: DN-701_Well_G01

value: Bone marrow derived APC

value: 12hr infection with LCMV Cl 13


title: DN-701_Well_F12


title: G317_4_t8_cont

description:
G317_4_t8_cont
controls  replicate3

source_name: 8 hour_cont_3

tag: age


title: B5L26


title: DN-701_Well_F11


title: D2 kidney2


title: D1 kidney2


title: B5L13


title: DN-701_Well_F10


title: C4 kidney2

value: Haplotype-II adult+western diet


title: G511_01_t8_cont

description:
G511_01_t8_cont
controls  replicate1


title: B5L71


title: C3 kidney2


title: G511_03_t1_exp

description:
G511_03_t1_exp
pilocarpine seizure replicate 3

source_name: 1 hour seizure_3


title: B5L5


title: DN-701_Well_F08


title: C2 kidney2


title: DN-701_Well_F09