title: pre B-PLL

city: Kobe

first: Shinichiro

last: Kawamoto

state: Hyogo

address: Chuoh-ku Kusunokicho 7-5-2

department: Department of Transfusion Medicine and Cell Therapy

institute: Kobe University Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Data were filtered as follows: (1) Remove reads containing adaptors; (2) Remove reads containing N > 10% (N represents base that could not be determined);(3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecularlevel information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Cosmic database was used to annotate the differential expressed gene. TFCat is a curated catalog of mouse and human transcription factors (TF) based on a reliable core collection of annotations obtained by expert review of the scientific literature. COSMIC is a database designed to store and display somatic mutation information and related details which contains information relating to human cancers.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table of fold changes in genes with read counts and FPKM values between the primary cells and the recurrent cells.

source_name: B lymphocytic leukemia cells

growth_protocol: Peripheral blood mononuclear cells were isolated from fresh blood samples using Ficoll-Paque PLUS according to the manufacture's instruction.

extract_protocol:
Total RNA was extracted from the cells using RNA purification kit (MACHEREY-NAGEL).
First strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization(1). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.

treatment_protocol: No treatment

value: B lymphocytic leukemia cells

tag: cell subset

value: CD20 positive

value: Leukemia cells at the diagnosis

tag: tls status

value: TLS -


title: post B-PLL

status: Public on Dec 31 2024

type: SRA

country: Japan

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

value: CD20 negative

tag: time

value: Leukemia cells at the relapse

value: TLS +


title: SJ_WT-1

city: New York

first: Shan

last: Zha

state: NY

address: 1130 Saint Nicholas Ave.

country: USA

institute: Columbia University

description: Signal Join junctions on the chromosomal V(D)J recombination substrate pMX-INV

library_source: genomic

data_processing:
Basecalls performed using Illumina RTA version 1.18.54
Miseq reads was first de-multiplexed by fastq-multx tool from ea-util, then adaptor sequence was further trimmed with SeqPrep utility.
Pre-processed reads were then mapped to customized mm9 (for CSR) or mm10 (for chromosomal V(D)J recombination) genome using Bowtie2. The best-path searching algorithm (related to YAHA; G. G. Faust, et al. Bioinformatics 28, 2417-2424 (2012)) was used to identify optimal sequence alignments from Bowtie2-reported top alignments (alignment score > 50).
The reads were then filtered to exclude mis-priming events, germline (unmodified) sequence, sequential joints, and duplicated reads. A “duplicate read” is defined by bait and prey alignment coordinates within 2 nt of another read’s bait and prey alignments. Since signal joint reads number was very low after applying deduplication filter, this filter was not used for SJ analysis. For SJ deletion analyses, the deletion size was capped at 1,000 bp. Since some switch region sequences are very repetitive, the alignments in those regions were filtered out by the mappability filter. But they do unequivocally map to an individual switch region, so to plot all the switch region junctions, we added the ones filtered out by the mappability filter back after deduplication (J. Dong, et al. Nature 525, 134-139 (2015)). MHs are defined as regions of 100% homology between the bait and prey-break site. Insertions are defined as regions containing nucleotides that map to neither the bait nor prey-break site. Blunt junctions are considered to have no MHs or insertions.
Assembly: For SJ analysis, to specifically study the DNA repair junctions on the pMX-INV substrate we added the substrate sequence as an additional chromosome (chrP) on top of the mm10 genome during the alignment process. For CSR analysis, the IgH switch region (from JH4 to the last Cα exon, chr12 114, 494, 415–114, 666, 816; C57/BL6) of customized mm9 genome (mm9sr) was replaced by the corresponding region of 129 strain in NCBI gene accession sequence AJ851868.3.
Supplementary files format and content: .xlsx files generated from tab-delimited text files after analysis for reads distribution.
Library strategy: HTGTS

molecule: genomic DNA

organism: Mus musculus

source_name: Bone marrow

growth_protocol: For SJ analysis, V-abl transformed B cells from mice were cultured in DMEM medium. For CSR analysis, purified splenic B (CD43-) cells from mice were cultured in RPMI medium with cytokines (anti-CD40 (1 µg/mL; BD Pharmingen) and IL-4 (20 ng/mL; R&D)).

extract_protocol:
Genomic DNA was extracted from treated B cells on day 3 for SJ HTGTS analysis and day 4 for CSR analysis.
For SJ analysis, sonicated DNA was linearly amplified with primer (/5Bios/GGCAGCCTACCAAGAACAAC) and nested amplified with primer (5′-CGGTGGTACCTCACCCTTA-3′). Germline sequence was removed with EcoRI (NEB) digestion. For CSR analysis, libraries were prepared according to the protocol in (Hu J, et al. Nat Protoc 11:853–871 (2016)). Linear amplifications were performed using Sμ-specific biotin primer (/5Bios/CAGACCTGGGAATGTATGGT) and followed by nesting PCR with (5′-CACACAAAGACTCTGGACCTC-3′). AflII was used to remove germline sequence.
high-throughput genome translocation sequencing (HTGTS). Sequenced with MiSeq 500v

treatment_protocol: For SJ analysis, V-abl transformed B cells with integrated pMX-INV substrate were treated with STI571 (3 µM; Novartis Pharmaceuticals) for 3 days to arrest cells in G1 phase and induce RAG recombinase expression, generating breaks for V(D)J recombination of the substrate. Cells were analyzed via flow cytometry before DNA extraction. For CSR analysis, cells were cultured for 4 days and analyzed via flow cytometry before DNA extraction.

tag: tissue

value: Bone marrow

tag: cell line

value: v-abl transformed B cell

value: B cells

tag: genotype

value: WT

tag: treatment

value: STI571 for 3 days


title: MG1655, Medium PDMS, 24 hr, rep 1

city: Amherst

first: Lauren

last: Andrews

state: Massachusetts

address: 240 Thatcher Rd Life Sciences Laboratories N265

department: Chemical Engineering

institute: University of Massachusetts Amherst

description:
PD1Int
gRNA_counts_all.csv
PDMS_Med_fitnesses.csv

library_source: other

data_processing:
Base calling and demultiplexing was performed automatically by Illumina Basespace (Illumina.BaseSpace.NativeApp.Core v0.9.0.2, Illumina.BaseSpace.NativeApp.Host v0.9.0.1) and FASTQ files generated by Illumina BaseSpace using Workflow v1.37.0 via GenerateFASTQ v1.1.0.64
Raw reads from the FASTQ files were filtered for an average quality of at least 20 using a custom Python (v3.9) script
For each sample, the counts for each gRNA design in the CRISPRi library were determined using a custom Python script (v3.9) by matching the 20 nucleotide sequence between ACAATTG and GTTTTA (or the reverse complement, if the read is in the reverse direction) to the sequence of a gRNA spacer seqeunce in the designed library, if possible
gRNA with fewer than 20 total counts in the combined four initial library count data were filtered out from downstream analysis
Relative frequencies for each gRNA design in all four initial library samples, the replicates of each selective condition (biomaterial and stiffness or planktonic growth above a biomaterial), and the duplicates of each selective condition were calculated using a custom Python (v3.9) script with a single pseudocount for each gRNA design. Specifically, relative frequency for the four combined initial library samples or a single replicate of a selective condition was calculated as the number of counts of a design in the sample divided by the total number of counts in that sample, with a +1 pseudocount for each gRNA design. Relative frequency for duplicates of a selective condition were calculated as the geometric mean of relative frequencies of both replicates.
Using a custom Python (v3.9) script, gRNA fitness for each gRNA design in each selective condition was then calculated as the log2-fold change in relative frequencies between the combined four initial library samples and the selective condition, normalized to median log2-fold change in relative frequencies for the non-targeting negative control gRNA in that selective condition. This was calculated for both individual replicates and duplicates of a selective condition using the appropriate relative frequency value.
Assembly: Not applicable
Supplementary files format and content: comma-delimited CSV file containing raw counts for all gRNA designs (34,315) and samples (20)
Supplementary files format and content: comma-delimited CSV files containing calculated gRNA fitness values of each replicate and the geometric mean of both replicates for each selective condition (biomaterial and stiffness or planktonic growth)
Library strategy: CRISPRi selection

molecule: other

organism: Escherichia coli

growth_protocol: The MG1655 CRISPRi library was grown in M9 media (6.78 g/L Na2HPO4, 3 g/L KH2PO4, 1 g/L NH4Cl, 0.5 g/L NaCl, 2 µM MgSO4, 0.1 mM CaCl2, 0.2% casamino acids, 0.34 g/L thiamine hydrochloride, 0.4% D-glucose) with 50 µg/mL kanamycin from a starting OD600 of 0.1 A for 2.5 hours at 250 rpm and 37C. A sample of culture was taken as an initial time point ("initial library") and then approximately 1.6X10^8 cells of this culture used to inoculate M9 media with 50 ug/mL kanamycin, 1 mM isopropyl ß-D-1-thiogalactopyranoside (IPTG), and 0.25 ng/mL anhydrotetracycline (aTc) above a biomaterial in a 6-well plate to a total volume of 8 mL. Cultures were then incubated in a stationary incubator at 37C for 24 hours.

extract_protocol:
Plasmid DNA from each cell library sample was extracted using the Qiagen QIAPrep Spin Miniprep kit according to the manufacturer's protocol
The gRNA spacer region of each plasmid pool sample was amplified using custom primers with variable lengths and sequences at the 5′ end to increase nucleotide diversity while maintaining a total amplicon length of 92 base pairs. Amplification was performed using Q5 polymerase (New England Biolabs, NEB) according to the manufacturer's protocol with 18 cycles. Amplicons were then digested using DpnI (NEB) for 8 hours and the PCR products purified using the GenCatch PCR purification kit according to the manufacturer's protocol. The 20 amplicon samples were then prepared for NGS using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to the manufacturer's protocol with 500 ng of starting material and purification of the adaptor-ligated DNA with 0.80X ratio of AMPure XP beads (Beckman Coulter) to for each reaction mixture. NEBNext Multiplex Oligos for Illumina Set 1 or Set 2 primers (NEB) were used to amplify (for 3 cycles) and barcode each sample. DNA concentration was quantified using a Qubit 4 Fluorometer with dsDNA High Sensitivity Quantification assays. All 20 samples were then pooled together in equal mass ratios and sequenced using an Illumina NexSeq500 System with a Mid-150 cycle kit (75 bp X 2 paired end reads) and a 10% PhiX spike-in.

treatment_protocol: Initial library samples were taken prior to inoculating media above biomaterials for selections (time 0 hours). After 24 hours of growth, samples of selections for cellular adhesion were obtained by gently washing biomaterials to remove loosely adhered cells from the surface and harvesting the adhered cells from a 2 cm^2 area on the biomaterial surface using a cell lifter. For each experiment, samples for selection of planktonic growth in stationary media above each biomaterial chemistry were obtained by carefully removing equal volumes of media above each biomaterial (Soft, Medium, and Stiff) in the 6-well plate, being careful to not disturb the biofilm formed on the surface.

tag: strain

tag: selection

value: Cellular adhesion

tag: biomaterial chemistry

value: PDMS

tag: biomaterail stiffness

value: Medium

value: 24 hr

tag: biological replicate


title: MAH022420_001

city: Chicago

first: Gail

middle: B

last: Mahady

state: IL

address: 833 S Wood St

department: Pharmacy Practice

institute: University of Illinois

data_processing:
Raw reads were aligned to human reference genome hg38 using STAR (Dobin et al., 2013). ENSEMBL genes were quantified using FeatureCounts (Liao, Smyth, & Shi, 2014). Differential expression statistics were computed using edgeR (McCarthy, Chen, & Smyth, 2012; Robinson, McCarthy, & Smyth, 2010) on raw expression counts with the exactTest function. P-values were adjusted for multiple testing using the false discovery rate (FDR) correction of Benjamini and Hochberg (Benjamini & Hochberg, 1995).
Genome_build: hg38
Supplementary_files_format_and_content: Table of raw counts per gene – tabular text file

molecule: polyA RNA

extract_protocol:
RNA was isolated and analyzed for integrity using Agilent 4200 TapeStation and RNA Screen Tape
RNA-seq libraries were prepared using a Universal Plus mRNASeq kit, and library fragment size distribution was confirmed by electrophoresis using a 2200 TapeStation system with D1000
Sequencing was carried out on NovaSeq 6000, SP flowcell, 2x50 nt reads. General quality-control metrics were obtained using FastQC and raw reads were aligned to human reference genome hg38 using STAR and BWA MEM. ENSEMBL genes were quantified using FeatureCounts, and differential expression statistics were computed using edgeR. Specific gene expression was measured and verified using qPCR.

treatment_protocol: HCT-116 colon cancer cells were grown and maintained and treated with a combination of Vitamin D2 and D3 and all trans-retinoic acid (ATRA) at 1 µM for four hours.

value: Control


title: MG1655, Initial PDMS, 0 hr, rep 1

description:
PD10; Initial library for PDMS replicate 1 experiment
gRNA_counts_all.csv

value: Initial library

value: Not applicable

value: 0 hr


title: WT_YNB_5min R1

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

country: Canada

institute: Universite de Montreal

description: Library name: WT_YNB_5min_R1

data_processing:
Sequencing reads were filtered with fastp version 0.23.2
Filtered reads were mapped to the reference genome sequence of strain SC5314 with STAR version 2.7.9a
The number of reads mapping on each of the genes was calculated by featurecount version 2.0.1
Differential gene expression was calculated with DESeq2 version 1.26.0.
Assembly: GCF_000182965.3
Supplementary files format and content: Tab-delimited file with normalized read counts for each sample

organism: Candida albicans

growth_protocol: Overnight cultures of WT (SN148-CIp20) strain and smf12 mutant were diluted to an OD600 of 0.1 in 60 ml of fresh SC-Mn medium and grown at 30°C under agitation (200 rpm) to early logarithmic phase (OD600=0.4).

extract_protocol:
Total RNA was extracted using an RNAeasy purification kit (Qiagen) and glass bead lysis in a Biospec Mini 24 bead-beater
The NEBNext UltraTM II RNA Library Prep Kit for Illumina was used to construct the RNA-seq library following the manufacturer’s instruction.

treatment_protocol: Cultures were then either left untreated or exposed to 1 mM MnCl2 and incubated at 30°C for 5 and 90 min. For RNA-seq profiling of Mn excess, overnight cultures of WT cells were diluted to an OD600 of 0.1 in fresh 100 ml YPD and incubated with shaking at 30°C to an OD600 of 0.8 and split into 50-ml cultures. MnCl2 was added to the experimental culture to a final concentration of 7.5 mM, while an equal volume of sterile water was added to the control culture and incubated for 30 min. Cells were harvested by centrifugation and were quick-frozen and stored at -80°C.

value: Yeast cells

value: 90 min in SC-MN


title: SJ_WT-2


title: SAMPLE 12

status: Public on Dec 30 2024

type: RNA

city: Delhi

first: Bhavana

last: Prasher

state: Delhi

address: Sukhdev Vihar

department: Genomics and Molecular Medicine

country: India

institute: CSIR-IGIB

description: Subject 6_After Hypoxia Exposure

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using Illumina iScan System

data_processing: The raw intensity file per chip was background corrected using limma package and was then normalized using Quantiles normalization (normalizeQuantiles) in R

source_name: Peripheral Blood Sample

label_protocol: Biotinylated cRNA were prepared with the IlluminaTotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: RNA was isolated using the PAXgene kit followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Subjects were exposed to graded normobaric hypoxia for 50 minutes (FiO2 ~ 0.19 up till 0.13 in steps of 2% decrement in 10 minutes).

value: Peripheral Blood Sample

tag: age

value: 26 years

tag: gender

value: Male

tag: experiment date

value: After Hypoxia

tag: ID


title: SAMPLE 11

description: Subject 5_After Hypoxia Exposure

value: 24 years


title: SAMPLE 9

description: Subject 3_After Hypoxia Exposure

value: 27 years


title: SAMPLE 6

description: Subject 6_Before Hypoxia Exposure

value: Before Hypoxia


title: SAMPLE 7

description: Subject 1_After Hypoxia Exposure

value: 39 years


title: SAMPLE 3

description: Subject 3_Before Hypoxia Exposure


title: SAMPLE 4

description: Subject 4_Before Hypoxia Exposure

value: 23 years

value: Female


title: SAMPLE 5

description: Subject 5_Before Hypoxia Exposure


title: SAMPLE 1

description: Subject 1_Before Hypoxia Exposure


title: BMDMs, WT, biol replicate3

city: Bethesda

first: Sakshi

last: Chauhan

state: Maryland

address: Building 6A, Room 2A11,6 Center Drive

institute: NICHD

description: Library name: WT3_1

data_processing:
CCBR pipeliner and SARTools
Sequence reads were trimmed for adaptor sequence using cutadapt.
Trimmed sequence reads were mapped to mm10 using STAR aligner.
Assembly: mm10
Supplementary files format and content: tab delimited text file inclues raw count for each sample

source_name: BMDM

extract_protocol:
RNA was purified using Zymogen quick RNA miniprep kit.
NEBNext® rRNA Depletion Kit was used to deplete rRNA. RNA library was prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®.

value: BMDM

value: WT


title: SAMPLE 8

description: Subject 2_After Hypoxia Exposure

value: 32 years


title: BMDMs, H3.3cKO:StingKO, biol rep3

description: Library name: Sting TKO3


title: SAMPLE 2

description: Subject 2_Before Hypoxia Exposure


title: BMDMs, H3.3cKO:StingKO, biol rep2

description: Library name: Sting TKO2


title: BMDMs, WT, biol rep3

description: Library name: WT3


title: BMDMs, WT, biol rep2

description: Library name: WT2


title: BMDMs, cKO, biol rep2

description: Library name: KO2


title: BMDMs, H3.3cKO:MavsKO, biol rep2

description: Library name: Mavs TKO2


title: BMDMs, cKO, biol replicate3

description: Library name: KO3_1


title: BMDMs, cKO, biol replicate2

description: Library name: KO2_1


title: BMDMs, WT, biol replicate2

description: Library name: WT2_1


title: BMDMs, WT, biol rep1

description: Library name: WT1


title: BMDMs, cKO, biol rep1

description: Library name: KO1


title: BMDMs, H3.3cKO:MavsKO, biol rep1

description: Library name: Mavs TKO1


title: BMDMs, cKO, biol rep3

description: Library name: KO3


title: BMDMs, cKO, biol replicate1

description: Library name: KO1_1


title: SAMPLE 10

description: Subject 4_After Hypoxia Exposure


title: BMDMs, H3.3cKO:MavsKO, biol rep3

description: Library name: Mavs TKO3


title: Sample_PG-H5

city: Zurich

first: Hannier

last: Pulido

state: Switzerland

address: Schmelzbergstrasse, 9 / LFO

department: D-USYS

country: Switzerland

institute: ETHZ

description: Da, uninfected

data_processing:
After base calling, adapter content and poor-quality reads were removed from the samples using trimmomatic (Bolger et al., 2014). The samples were then mapped to the reference genome of Glycine max Version 2.0 using tophat2, utilizing genome and annotation files obtained from GenBank (ftp://ftp.ncbi.nlm.nih.gov/genomes/Glycine_max/Assembled_chromosomes/seq/). Coverage files and a count matrix were generated with bedtools. The rlog-normalized feature counts matrix was then utilized for further statistical analysis, gene enrichment analysis, and pathway mapping.
Assembly: Glycine max Version 2.0
Supplementary files format and content: raw counts for each sample

organism: Glycine max

source_name: leave

growth_protocol: Soybean seeds were sterilized for 5 minutes in a 10% sodium hypochlorite solution and washed with copious amounts of ultrapure water. Seeds were germinated in a sterilized growing medium (Premier Pro-mix without mycorrhiza, Griffin Supplies) autoclaved at 120°C for 40 min

extract_protocol:
To assess the effect of rhizobacteria co-inoculation and BPMV on soybean gene expression, we harvested plant leaf tissue from a separate set of untouched undamaged plants at the V4 stage. Tissue sections with weights of 100-200 mg were obtained, and the tissue was flash frozen in liquid nitrogen. The homogenized material was extracted for total RNA using a mirVana miRNA isolation kit (Ambion, Austin, TX). We combined equal amounts of three individual total RNA samples with similar quality and concentration to obtain a pooled replicate sample for each treatment, resulting in a total of five biological pooled replicates per treatment (n = 40). We used a Nanodrop Spectrophotometer (NanoDrop Technologies, Wilmington, DE) to determine RNA concentration and assessed RNA quality using the RNA Integrity Number (RIN) method, which is widely used for RNA quality control (Mueller et al., 2004), in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
To prepare the barcoded libraries for the 40 RNA samples, 100 ng of total RNA was used with a TruSeq Stranded mRNA Library Kit, following the manufacturer's instructions. The concentration of each library was determined by qPCR, and an equimolar pool of the 40 barcoded libraries was created.

treatment_protocol: Three-day old seedlings were transplanted to individual 500 ml pots containing the same growing medium and inoculated with rhizobacteria. One week after rhizobacteria inoculation, seedlings were infected with BPMV or mock-inoculated. Starting from the V1 stage, plants received 50 ml of a modified Hoagland’s nutrient solution three times per week. Plants inoculated with Bj alone or in combination with Da received the same nutrient solution but without nitrogen, as nodulation is inhibited by the presence of nitrates in the soil. This strategy for supplementing nutrient solution to non-rhizobium inoculated plants has also been employed in our previous work and by other studies exploring similar systems. All plants were kept in an insect-free growth chamber at 25°C (day), 23°C (night), a L16:D8 photoperiod and at 70% of relative humidity.

value: leave

value: Da, uninfected


title: BMDMs, WT, biol replicate1

description: Library name: WT1_1


title: BMDMs, H3.3cKO:StingKO, biol rep1

description: Library name: Sting TKO1


title: Sample_PG-H1

description: Da, uninfected


title: Sample_CR-H4

description: Bj, uninfected

value: Bj, uninfected


title: Sample_CR-H2

description: Bj, uninfected


title: Sample_CR-B5

description: Bj, infected

value: Bj, infected


title: Sample_CP-H2

description: Bj+Da, uninfected

value: Bj+Da, uninfected


title: Sample_CP-B5

description: Bj+Da, infected

value: Bj+Da, infected


title: Sample_CP-B4

description: Bj+Da, infected


title: Sample_PG-H4

description: Da, uninfected


title: Sample_PG-H3

description: Da, uninfected


title: Sample_CP-B3

description: Bj+Da, infected


title: Sample_CP-B2

description: Bj+Da, infected


title: Sample_PG-H2

description: Da, uninfected


title: Sample_CR-H1

description: Bj, uninfected


title: Sample_Cn-H5

description: control, uninfected

value: control, uninfected


title: Sample_PG-B5

description: Da, infected

value: Da, infected


title: Sample_PG-B4

description: Da, infected


title: Sample_PG-B3

description: Da, infected


title: Sample_PG-B2

description: Da, infected


title: Sample_PG-B1

description: Da, infected


title: Sample_Cn-H3

description: control, uninfected


title: Sample_Cn-H1

description: control, uninfected


title: Sample_Cn-B5

description: control, infected

value: control, infected


title: Sample_CR-H5

description: Bj, uninfected


title: Sample_Cn-B3

description: control, infected


title: Sample_CR-B3

description: Bj, infected


title: Sample_CR-B1

description: Bj, infected


title: Sample_Cn-B2

description: control, infected


title: Sample_CR-B4

description: Bj, infected


title: Sample_Cn-B1

description: control, infected


title: Sample_CP-H5

description: Bj+Da, uninfected


title: Sample_CP-H4

description: Bj+Da, uninfected


title: THI_Desiccant_4

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

description: Library name: Z4

data_processing:
STAR 2.7.10a
Assembly: AaegL5.0
Supplementary files format and content: read counts in text file format

organism: Aedes aegypti

source_name: Whole body

extract_protocol:
Trizol
PolyA RNA seq library was prepared using NEBNext polyA Module and NEBNext Ultra II RNA Library preparation kit following the manufacturer's recommended procedure

value: Whole body


title: THI_Desiccant_2

description: Library name: Z2


title: Sample_Cn-H4

description: control, uninfected


title: THI_Desiccant_5

description: Library name: Z5


title: THI_Control_4

description: Library name: X4


title: THI_Desiccant_1

description: Library name: Z1


title: Sample_CP-H3

description: Bj+Da, uninfected


title: THI_Control_2

description: Library name: X2


title: Sample_CR-H3

description: Bj, uninfected


title: Sample_CP-B1

description: Bj+Da, infected


title: Sample_CR-B2

description: Bj, infected


title: Sample_CP-H1

description: Bj+Da, uninfected


title: Sample_Cn-H2

description: control, uninfected


title: PK10_Control_6

description: Library name: W6


title: PK10_Control_3

description: Library name: W3


title: PK10_Desiccant_2

description: Library name: Y2


title: Sample_Cn-B4

description: control, infected


title: THI_Desiccant_6

description: Library name: Z6


title: THI_Desiccant_3

description: Library name: Z3


title: THI_Control_6

description: Library name: X6


title: THI_Control_1

description: Library name: X1


title: PK10_Desiccant_4

description: Library name: Y4


title: PK10_Desiccant_6

description: Library name: Y6


title: THI_Control_5

description: Library name: X5


title: PK10_Desiccant_5

description: Library name: Y5


title: THI_Control_3

description: Library name: X3


title: IR_Fors_D5_2

city: Los Angeles

first: Frank

last: Pajonk

state: CA

address: 10833 Le Conte Ave

institute: UC Los Angeles

description: Library name: IR_Fors_D5_2

data_processing:
Novogene Standard RNA-Seq pipeline
Assembly: Homo_sapiens_hg38
Supplementary files format and content: standard BAM files

source_name: Glioblastoma

growth_protocol: HK-374 cells were grown in DMEM containing 10% FBS, 1% pen/strep media at 37°C in a 5% CO2 incubator. Cells were grown as monolayers and plated into 6-well plates at 40,000 cells per well.

extract_protocol:
Total RNA was isolated using Trizol reagent. The treated cells were lysed in 1 ml of Trizol reagent, rocked for 5 min to obtain a homogenous mixture and then transferred to RNAeasy mini kit (Qiagen) colimns for RNA isolation by following manufacturer's protocol.
The RNA sequencing library was generated using NEBNext® Ultra RNA Library Prep Kit (New England Biolabs) according to manufacturer’s protocols. The library concentration was quantified using a Qubit 3.0 fluorometer (Life Technologies), and then diluted to 1 ng/uL before checking insert size on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany) and quantifying to greater accuracy by quantitative Q-PCR (library molarity >2 nM). The library was sequenced on Illumina NovaSeq6000 with an average of 20M reads per RNA sample.

treatment_protocol: 4 days after seeding the cells were irradiated with 4 Gy. Controls were sham irradiated. 48 hours later cells were treated with either forskolin or DMSO for 5 consecutive days.

value: Glioblastoma

value: patient-derived


title: IR_Fors_D5_3

description: Library name: IR_Fors_D5_3


title: IR_D5_2

description: Library name: IR_D5_2


title: DMSO_D5_3

description: Library name: DMSO_D5_3


title: PK10_Desiccant_3

description: Library name: Y3


title: PK10_Control_5

description: Library name: W5


title: PK10_Control_4

description: Library name: W4


title: IR_D5_1

description: Library name: IR_D5_1


title: PK10_Control_1

description: Library name: W1


title: DMSO_D5_2

description: Library name: DMSO_D5_2


title: PK10_Control_2

description: Library name: W2


title: PK10_Desiccant_1

description: Library name: Y1


title: IR_Fors_D5_1

description: Library name: IR_Fors_D5_1


title: DMSO_D5_1

description: Library name: DMSO_D5_1


title: IR_D5_3

description: Library name: IR_D5_3


title: hLUC7L overexpression replicate 3

city: Cambridge

first: Connor

middle: J

last: Kenny

state: MA

address: 31 Ames Street

department: Biology

institute: MIT

description: Library name: L1_FLAG-3

data_processing:
Aligned with star v2.7.3a.
Analyzed with rmats- v.4.1.1.
Assembly: hg38 and TAIR10
Supplementary files format and content: rmats tables with corrected dPSI estimates.

source_name: HEK293T RMCE

growth_protocol:
Cell line: HEK293T RMCE cell lines were cultured in Advanced DMEM supplemented with 5% FBS, 25 mM HEPES and Glutamax. For each experiment, cells were plated 24 hours in advance in 24-well plates.
Seedlings: Seeds of Wildtype Col0, luc7 single mutants (luc7a-1, luc7a-2, luc7b-1 and luc7rl-1), luc7 double mutants (luc7a-1 luc7b-1, luc7a-2 luc7b-1, luc7a-1 luc7rl-1 and luc7b-1 luc7rl-1) and a luc7 triple mutant (luc7a-2 luc7b-1 luc7rl-1) were surface sterilized with chlorine-gas and then grown on half-strength Murashige Skoog (MS) plates containing 0.8% phytoagar in continuous light at 22°C for 10 days.

extract_protocol:
Cell line: RNA was extracted 24 hours after transfection using the Qiagen RNeasy Mini kit (cat. no. 74104) according to the manufacturer’s instructions with the optional on-column DNase digestion (cat. No 79254). Seedlings: Seedlings were collected and flash frozen in liquid nitrogen. Total RNA was isolated using RNeasy® Plant Mini Kit (Qiagen, cat. nos. 74904) according to the manufacturer’s instructions.
Cell line: Illumina-compatible libraries were prepared by MIT BioMicroCenter using NEB II Ultra Directional RNA with poly(A) selection and sequenced on NovaSeq 6000 with 2 x 150 bp reads. Seedlings: mRNA stranded library preparation and sequencing (PE150) was done by Novogene (Cambridge, United Kingdom) using an Illumina Novaseq6000 system.

value: HEK293T RMCE

value: embryonic kidney epithelial

value: hLUC7L overexpression


title: hLUC7L2 overexpression replicate 3

description: Library name: L2_FLAG-3

value: hLUC7L2 overexpression


title: hLUC7L3 overexpression replicate 1

description: Library name: L3_FLAG-1

value: hLUC7L3 overexpression


title: hLUC7L2 overexpression replicate 1

description: Library name: L2_FLAG-1


title: hLUC7L3 overexpression replicate 3

description: Library name: L3_FLAG-3


title: hLUC7L2 overexpression replicate 2

description: Library name: L2_FLAG-2


title: hLUC7L3 overexpression replicate 2

description: Library name: L3_FLAG-2


title: hLUC7L overexpression replicate 2

description: Library name: L1_FLAG-2


title: hLUC7L overexpression replicate 1

description: Library name: L1_FLAG-1


title: control overexpression replicate 3

description: Library name: eGFP-3

value: control overexpression


title: AR002859_0001

city: Rochester

first: Aaron

last: Pennington

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
Data Formatting - bcltofastq-2.19.0
Data Cleaning - Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35
Genome Alignment - STAR_2.6.0c, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 - subread-1.6.1, featurecounts, -s 0 -t exon -g gene_name
Read Quantification2 - subread-1.6.1, featurecounts, -M -s 0 -t exon -g gene_name
Assembly: hg38
Supplementary files format and content: raw gene counts

source_name: Bone Marrow Aspirate

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Valencia, CA) per the manufacturer’s recommendations. The Total RNA (1 ng) was pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech, Mountain View, CA) per manufacturer’s recommendations.
RNA libraries for RNA-seq were prepared using Clontech-Nextera Library Prep v2 following manufacturer's protocols.

value: Bone Marrow Aspirate

value: Transitional B Cell

tag: participant id

tag: disease state

value: SLE


title: AR002754_0001

source_name: Blood (Whole)

value: Blood (Whole)

tag: cell type

value: Plasmablast cells

value: Healthy


title: control overexpression replicate 2

description: Library name: eGFP-2


title: AR002863_0001


title: AR002753_0001

value: CD19- Long-Lived Plasma Cells


title: AR001657_0001


title: control overexpression replicate 1

description: Library name: eGFP-1


title: AR002861_0001


title: AR001343_0001


title: AR001655_0001

value: CD19+ Long-Lived Plasma Cells


title: AR002752_0001


title: AR001656_0001


title: AR001654_0001


title: AR002751_0001


title: AR001341_0001


title: AR002862_0001


title: AR001342_0001


title: AR001281_0001


title: AR001280_0001


title: AR002860_0001


title: AR001278_0001


title: AR001216_0001


title: AR001217_0002


title: AR001279_0001


title: AR001340_0001


title: AR001218_0002


title: AR001106_0001


title: AR001107_0001


title: AR001105_0001


title: AR001214_0001


title: AR001215_0001


title: AR001104_0001


title: AR001038_0001


title: AR000891_0001


title: AR000899_0001


title: AR001031_0001


title: AR001344_0001


title: AR000813_0001


title: AR000811_0001


title: AR001039_0002


title: AR001032_0001


title: AR000890_0001


title: AR000888_0001


title: AR000889_0001


title: AR000805_0001


title: AR000669_0001


title: AR000668_0001


title: AR000651_0001


title: ADMSC, Aripiprazole

city: Seongnam

first: Hyun-Ju

last: An

state: --- Select One ---

address: Seongnam-si, 13496

country: South Korea

institute: CHA university

description: Aripiprazole-treated ADMSC

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: hg19
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: ADMSC

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: ADMSC

value: Mesenchymal stem cell

value: Aripiprazole


title: ADMSC, DMSO

description: DMSO-treated ADMSC

value: DMSO


title: s-TFE TFE3 input_rep2

city: Boston

first: Dipanjan

last: Chowdhury

address: 4 Blackfan Circle

institute: Dana-Farber Cancer Institute

data_processing:
Before alignment, raw ChIP-sequencing reads were qualified by FastQC. Trimmomatic was used to trim adaptor and low-quality reads. Trimmed reads were aligned to hg38 human genome assembly using Bowtie2, with parameters “--very-sensitive --end-to-end --mm -X 2000 --no-unal”. Proper paired and high-quality mapped reads (MAPQ >30) were extracted by samtools with parameter “-F 1804 -f 2 -q 30”. PCR duplicates were marked and further removed by picard tools, then reads were subjected to peak calling by MACS2 with “q 0.01” for H3K27ac ChIP and “p 1e-4” for TFE3 ChIP-seq. Signal tracks for each example were generated using the MACS2 pileup function and were normalized to 1 million reads. Bigwig files were generated using the bedGraphToBigWig command for visualization. H3K27ac and TFE3 ChIP-seq signal at selected genomic loci were visualized using IGV. Peak annotation was performed using annotatePeaks function from homer. Enrichment analysis was performed on annotated genes proximal to TFE3 peaks using Enrichr. Profile plot for TFE3 at annotated OXPHOS, glutathione metabolism and PPP genes were drawn with deeptools.
Assembly: hg38
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak

source_name: Cell line

extract_protocol:
cells were fixed with 1% formaldehyde for 5 minutes, After quenching and cell lysis, chromatin was sonicated using a E220 covaris
ChIP libraries were prepared using using NEBNext® Ultra™ II DNA Library Prep Kit complemented with NEB DNA Barcodes.1 ng of DNA was used as starting material for input and ChIP samples. Libraries were amplified using 15 cycles on the thermocycler.Post amplification libraries were size selected at 200-400bp in length using AMPure XP beads from Beckman Coulter. Libraries were validated using the High sensitivity DNA Kit.

value: Cell line

value: s-TFE

value: cancer cell


title: s-TFE TFE3 ChIP_rep2


title: s-TFE TFE3 ChIP_rep1


title: s-TFE TFE3 input_rep1


title: FU-UR-1 TFE3 input_rep1


title: FU-UR-1 TFE3 input_rep2


title: UOK109 TFE3 ChIP_rep2


title: FU-UR-1 TFE3 ChIP_rep1


title: AR000812_0001


title: UOK109 TFE3 ChIP_rep1


title: FU-UR-1 TFE3 ChIP_rep2


title: UOK109 TFE3 input_rep2


title: s-TFE H3K27ac input_rep2


title: s-TFE H3K27ac input_rep1


title: FU-UR-1 H3K27 Input rep2


title: AR000670_0001


title: FU-UR-1 H3K27 Input rep1


title: s-TFE H3K27ac ChIP_rep2


title: FU-UR-1 H3K27 ChIP rep2


title: FU-UR-1 H3K27 ChIP rep1


title: UOK146 H3K27ac ChIP_rep1


title: UOK146 H3K27ac input_rep2


title: 786-O H3K27ac ChIP_rep1


title: N3-1

city: Guangzhou

first: Jianfang

last: Luo

state: Please Select

address: # 106 Zhongshan Second Road, Yuexiu District

country: China

institute: Guangdong Provincial People's hospital

data_processing:
Basecalls performed using CASAVA version 1.4
Raw fastq files were processed using fastp 0.20.0 with default parameters
RNA-seq reads were mapped to GRCh38 human reference genome using hisat2 2.1.0
Differential expression analysis
GO and KEGG enrichment analysis of differentially expressed genes
Assembly: hg38
Supplementary files format and content: read counts

source_name: aorta

extract_protocol:
Smooth muscle cell was extracted from normal human aorta
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: (1) PDGFBB (2) PDGFBB+GMRSP overexpressing

value: aorta

value: Smooth muscle cell

value: PDGFBB+NC


title: N1-1


title: G5-1

value: PDGFBB+GMRSP


title: 786-O H3K27ac input_rep2


title: UOK146 H3K27ac input_rep1


title: UOK109 H3K27ac ChIP_rep2


title: UOK109 H3K27ac ChIP_rep1


title: G4-1


title: s-TFE H3K27ac ChIP_rep1


title: UOK109 H3K27ac input_rep2


title: G3-1


title: 786-O H3K27ac input_rep1


title: UOK109 TFE3 input_rep1


title: G2-1


title: G1-1


title: PHH_donor_2_rep1

city: Shanghai

first: hexin

last: Yan

address: Pujian Road

institute: Shanghai Reji Hospital

data_processing:
Bioinformatics data analysis was provided by NewCore BioTech. (Shanghai, China). Briefly, fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads.
STAR software (v2.7.9a) was used to align the high-quality clean reads to the mouse (mm39) reference genome.
featureCounts software (v2.0) was used to get the raw gene level mRNA expression counts.
Assembly: mm39
Supplementary files format and content: txt format raw counts of each gene
Supplementary files format and content: Expression.txt

source_name: liver

growth_protocol: hepatocytes were isolated from non-transplantable liver tissue using a customized two-step collagenase perfusion technique. The donor tissue, sourced through approved channels, ensured the integrity of the process. Then, the viability of these hepatocytes was over 70%, as determined by Trypan blue staining (Sigma-Aldrich).

extract_protocol:
mRNA high throughput sequencing was performed by NewCore Biotech. (Shanghai, China). Briefly, total RNA was extracted using Trizol Reagent (ThermoFisher, 15596026). The mRNAs were purified using a NEBNext Poly(A) mRNA Magnetic Isolation Module Kit (NEB, E7490) according to the user manual.
mRNA libraries were constructed by using Illumina TrueSeq mRNA sample preparation kit (Cat. No. RS-122-2101) according to the manufacturer’s instructions. Library sequencing was performed on an Illumina NovaSeq 6000 instrument.

treatment_protocol: Hepatocytes were plated on CellBIND® surface 150 cm2 cell culture flasks (Corning) at 0.1-0.2x105 cells/cm2 within an optimized culture system containing animal-free growth factors based on Transition and Expansion Medium (TEM) as described previously.Over a 14-day period, under the induction of small molecules cocktail, hepatocytes progressively converted into an expandable liver progenitor cell state (designated as HepLPCs).

value: liver

value: primary human hepatocytes


title: PHH_donor_1_rep1

value: hepatocytes were isolated from non-transplantable liver tissue using a customized two-step collagenase perfusion technique.


title: HepLPCs_donor_2_rep2

value: liver progenitor cells

value: cultured in an optimized culture system containing animal-free growth factors based on Transition and Expansion Medium (TEM) as described previously


title: HepLPCs_donor_2_rep1


title: N2-1


title: HepLPCs_donor_1_rep2


title: PHH_donor_2_rep2


title: UOK146 H3K27ac ChIP_rep2


title: UOK109 H3K27ac input_rep1


title: N5-1


title: HepLPCs_donor_1_rep1


title: w17437

city: Changchun

first: Jing

last: Jiang

state: Jilin

address: No.1 Xinmin Street

department: Division of Clinical Epidemiology

institute: First Hospital of Jilin University

data_processing:
raw sequencing reads were trimmed for adaptor sequences using Trimmomatic Low quality bases were also trimmed to a minimum length of 30 bp, followed by alignment to the current human genome reference (hg19) using Bowtie2 [24] with the end-to-end alignment mode,Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length.
Alignments with Mapping Quality Score ≥ 10 were counted for gene bodies, according to the gene start and gene end annotations by the GENCODE Project [25](release 19), using featureCounts [26] without strand information.peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Assembly: hg19
Supplementary files format and content: Processed_Data rpm_allsample is a data frame with fields: 1) gene (official gene symbol; for 23 pairs of genes sharing the same official gene symbol, one from each pair assigned a new gene symbol as original_gene_symbol.dup); 2) sample name; 3) raw rpms of samples at genes. Reports hydroxy-methylation levels.Processed_Data count_allsample is a data frame with fields: 1) gene (official gene symbol; for 23 pairs of genes sharing the same official gene symbol, one from each pair assigned a new gene symbol as original_gene_symbol.dup); 2) sample name; 3) rawcounts of samples at genes. Reports hydroxy-methylation levels.
Library strategy: 5hmC-Seal (selective 5hmC chemical labeling)

source_name: plasma cfDNA, gastric cancer patient

extract_protocol:
The plasma cfDNA was isolated using the QIAamp Circulating Nucleic Acid Kit (Qiagen) according to the manufacturer’s protocol.
5hmC-Seal libraries were constructed according to established protocol.DNA samples were first repaired and ligated with adaptors. Next, the T4 bacteriophage enzyme β-glucosyltransferase was used to transfer an engineered glucose moiety containing an azide-group to 5hmC in duplex DNA. A biotin tag was then added to the azide group using Huisgen cycloaddition (“Click”) chemistry. Finally, the 5hmC-containing DNA fragments with biotin tags were captured by avidin beads. The 5hmC-Seal libraries were constructed through PCR amplification

treatment_protocol: Plasma sample was prepared within 6h by centrifuging twice at 3000rpm for 15min, and then centrifuging at 3000rpm for 15min. The prepared plasma samples (about 4ml/subject) were immediately stored at -80°C

value: plasma cfDNA

value: gastric cancer

tag: Sex

value: male


title: w17429

tag: tissue

value: female


title: w17432


title: w17431


title: w17433


title: PHH_donor_1_rep2


title: w17430


title: w17409


title: w17408


title: w17428


title: w17410


title: w17347


title: w17407


title: w17412


title: w17349


title: w17346


title: w17351


title: w17350


title: 786-O H3K27ac ChIP_rep2

tag: cell line


title: w17348


title: w17296


title: w17289


title: w17306


title: w17295


title: w17291


title: w17294


title: w17293


title: w17300


title: w17297


title: w17299


title: w17302


title: N4-1


title: w17303


title: w17301


title: w17298


title: w17290


title: w17292


title: w15333


title: w17230


title: w17305


title: w17287


title: w15332


title: w17231


title: w17229


title: w15341


title: w15337


title: w15336


title: w15335


title: w15334


title: w15340


title: w15339


title: w15338


title: w17286

source_name: plasma cfDNA, benign gastric disease

value: benign gastric disease


title: w17235


title: w17288


title: w17411


title: w17227


title: w17232

source_name: plasma cfDNA, healthy

value: healthy


title: w17233


title: w17208


title: w17219


title: w17221


title: w17209


title: w17212


title: w17207


title: w17211


title: w17215


title: w17223


title: w17214


title: w17217


title: w17225


title: w17210


title: w17206


title: w17222


title: w17226


title: w17205


title: w17193


title: w17202


title: w17216


title: w17224


title: w17220


title: w17201


title: w17204


title: w17218


title: w17195


title: w17234


title: w17203


title: w17200


title: w17199


title: w15342


title: w17198


title: w15348


title: w17196


title: w17213


title: w15346


title: w15347


title: w15344


title: w15345


title: w15381


title: w15380


title: w15379


title: Aorta normal No.3

source_name: normal ascending aorta

extract_protocol:
fresh aortic tissues were collected and stored at  liquid nitrogen.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: normal ascending aorta


title: 184T

type: genomic

city: Seoul

first: Dawon

last: Kim

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

institute: Yonsei University

description: cancer

hyb_protocol: Bisulphite converted DNA was hybridized to Illumina EPIC BeadChip according to manufacturer's protocol.

scan_protocol: Standard Illumina iScan scanning protocol.

data_processing:
Normalized Average Beta using Functional Normalization Method in Bioconductor minfi R package.
totalliver_funnorm_beta850_2022NT.txt: Normalized Average Beta

label: Cy5 and Cy182

source_name: HCC 184

label_protocol: Illumina Protocol.

extract_protocol: Genomic DNA was extracted using MagListo™ 5M Genomic DNA Extraction Kit (Bioneer) according to manufacturer's protocol.

value: Male

tag: diagnosis

value: Hepatocellular carcinoma (HCC)

value: Hepatocellular carcinoma

tag: patient


title: Aortic dissection No.3

source_name: dissected ascending aorta

value: dissected ascending aorta


title: Aortic dissection No.2


title: Aortic dissection No.1


title: 182T

description: cancer

label: Cy5 and Cy180

source_name: HCC 182


title: w17197


title: 181T

description: cancer

label: Cy5 and Cy179

source_name: HCC 181


title: Aorta normal No.2


title: 178T

description: cancer

label: Cy5 and Cy176

source_name: HCC 178


title: 176T

description: cancer

label: Cy5 and Cy174

source_name: HCC 176


title: w15343


title: 179T

description: cancer

label: Cy5 and Cy177

source_name: HCC 179


title: 183T

description: cancer

label: Cy5 and Cy181

source_name: HCC 183


title: 172T

description: cancer

label: Cy5 and Cy170

source_name: HCC 172


title: 175T

description: cancer

label: Cy5 and Cy173

source_name: HCC 175


title: 174T

description: cancer

label: Cy5 and Cy172

source_name: HCC 174


title: 173T

description: cancer

label: Cy5 and Cy171

source_name: HCC 173


title: Aorta normal No.1


title: 170T

description: cancer

label: Cy5 and Cy168

source_name: HCC 170


title: 168T

description: cancer

label: Cy5 and Cy166

source_name: HCC 168


title: 164T

description: cancer

label: Cy5 and Cy162

source_name: HCC 164

value: Female


title: 167T

description: cancer

label: Cy5 and Cy165

source_name: HCC 167


title: 163T

description: cancer

label: Cy5 and Cy161

source_name: HCC 163


title: 177T

description: cancer

label: Cy5 and Cy175

source_name: HCC 177


title: 165T

description: cancer

label: Cy5 and Cy163

source_name: HCC 165


title: 171T

description: cancer

label: Cy5 and Cy169

source_name: HCC 171


title: 180T

description: cancer

label: Cy5 and Cy178

source_name: HCC 180


title: 162T

description: cancer

label: Cy5 and Cy160

source_name: HCC 162


title: 161T

description: cancer

label: Cy5 and Cy159

source_name: HCC 161


title: 159T

description: cancer

label: Cy5 and Cy157

source_name: HCC 159


title: 169T

description: cancer

label: Cy5 and Cy167

source_name: HCC 169


title: 160T

description: cancer

label: Cy5 and Cy158

source_name: HCC 160


title: 158T

description: cancer

label: Cy5 and Cy156

source_name: HCC 158


title: 154T

description: cancer

label: Cy5 and Cy152

source_name: HCC 154


title: 153T

description: cancer

label: Cy5 and Cy151

source_name: HCC 153


title: 156T

description: cancer

label: Cy5 and Cy154

source_name: HCC 156


title: 157T

description: cancer

label: Cy5 and Cy155

source_name: HCC 157


title: 155T

description: cancer

label: Cy5 and Cy153

source_name: HCC 155


title: 151T

description: cancer

label: Cy5 and Cy149

source_name: HCC 151


title: 166T

description: cancer

label: Cy5 and Cy164

source_name: HCC 166


title: 146T

description: cancer

label: Cy5 and Cy145

source_name: HCC 146


title: 145T

description: cancer

label: Cy5 and Cy144

source_name: HCC 145


title: 144T

description: cancer

label: Cy5 and Cy143

source_name: HCC 144


title: 141T

description: cancer

label: Cy5 and Cy140

source_name: HCC 141


title: Liver, PH80_HC, POD3, FLR2

city: Brussels

first: Isabelle

last: Leclercq

address: Avenue E. Mounier

country: Belgium

institute: UCLouvain

data_processing:
Illumina output FASTQ files were analyzed using the RNA-seq Alignment app from Illumina Basespace to ultimately create the raw count tables. To obtain the differentially expressed genes, the raw counts were analyzed with the DESeq2. We retained genes expressed in at least 3 samples.
Assembly: GRCm38_mm10
Supplementary files format and content: tab-delimited text file containing the normalized counts obtained by DESeq2

source_name: Liver

extract_protocol:
RNA was extracted using the RNAse Mini kit (Qiagen ref. 74104)
Libraries were prepared starting from 100 ng of total RNA and using the TruSeq Stranded mRNA kit (Illumina, San Diego, CA) following the standard protocol (Part#15031047 Rev.E)

value: Liver

tag: genotype

value: WT

tag: strain

tag: treatment

value: M

tag: time

value: POD 3


title: 149T

description: cancer

label: Cy5 and Cy148

source_name: HCC 149


title: Liver, PH80_G+H, POD3, FLR2


title: 143T

description: cancer

label: Cy5 and Cy142

source_name: HCC 143


title: Liver, PH80_G+H, POD3, FLR1


title: 142T

description: cancer

label: Cy5 and Cy141

source_name: HCC 142


title: 137T

description: cancer

label: Cy5 and Cy136

source_name: HCC 137


title: Liver, PH80_HC, POD3, FLR1


title: 140T

description: cancer

label: Cy5 and Cy139

source_name: HCC 140


title: 152T

description: cancer

label: Cy5 and Cy150

source_name: HCC 152


title: Liver, PH80_HC, POD3, FLR3


title: Liver, PH80, POD3, FLR2


title: Liver, PH80, POD3, FLR1


title: 139T

description: cancer

label: Cy5 and Cy138

source_name: HCC 139


title: Liver, PH70, POD3, FLR1


title: 138T

description: cancer

label: Cy5 and Cy137

source_name: HCC 138


title: 148T

description: cancer

label: Cy5 and Cy147

source_name: HCC 148


title: Liver, PH70, POD3, FLR2


title: Liver, PH70, POD3, FLR3


title: 136T

description: cancer

label: Cy5 and Cy135

source_name: HCC 136


title: 135T

description: cancer

label: Cy5 and Cy134

source_name: HCC 135


title: Liver, PH80_G+H, POD3, FLR3


title: 147T

description: cancer

label: Cy5 and Cy146

source_name: HCC 147


title: 134T

description: cancer

label: Cy5 and Cy133

source_name: HCC 134


title: Liver, PH80, POD3, FLR3


title: 132T

description: cancer

label: Cy5 and Cy131

source_name: HCC 132


title: 130T

description: cancer

label: Cy5 and Cy129

source_name: HCC 130


title: 133T

description: cancer

label: Cy5 and Cy132

source_name: HCC 133


title: 120T

description: cancer

label: Cy5 and Cy119

source_name: HCC 120


title: 122T

description: cancer

label: Cy5 and Cy121

source_name: HCC 122


title: 125T

description: cancer

label: Cy5 and Cy124

source_name: HCC 125


title: 124T

description: cancer

label: Cy5 and Cy123

source_name: HCC 124


title: 121T

description: cancer

label: Cy5 and Cy120

source_name: HCC 121


title: 129T

description: cancer

label: Cy5 and Cy128

source_name: HCC 129


title: sorted cells from 4 patients before treatment with Methylprednisolone hashtags [Pool_PreMP_CITE]

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

country: Germany

data_processing:
CellRanger v5.0.0 functions count and aggr were used in default settings
Assembly: hg19
Supplementary files format and content: *.h5 files containing the information needed to evaluate date in R using Seurat (e.g.)
Supplementary files format and content: *.fasta files containing the DNA information for the samples
Supplementary files format and content: *.csv files containing the B-cell receptor informations for the samples.

molecule: protein

source_name: sorted cells from peripheral blood

extract_protocol:
Frozen PBMC from 11 MIS-C patients and from 4 patients who were 6 weeks post-infection with SARS-CoV-2 without developing MIS-C were thawed in RPMI 1640 with 20%v/v FCS. Cells were washed once in PBS containing 1%w/v BSA, 2mM EDTA and 2µg/ml Actinomycin D. Cells were incubated with human FcR blocking reagent and stained for 30 min at 4°C with fluorophore-coupled anti-human antibodies. Simultaneously, cells were incubated with DNA barcoded antibodies for Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq). DAPI was added before sorting to allow dead cell exclusion. Activated T cells were identified as DAPI-, CD14-, CD19-, CD3+, CD38+ and HLA-DRhigh, memory B cells were identified as DAPI-, CD14-, CD3-, CD19+, CD27+ (and CD38high for plasmablasts), and monocytes were identified as DAPI-, CD14+. For identifying methylprednisolone effects on activated cells For identifying methylprednisolone effects on activated cells, instead of plasmablasts, lineage- HLA-DRhigh cells were sorted (identified as DAPI-, CD14-, CD19-, CD3-, and HLA-DRhigh). After sorting of the cells using FACS technology, the cells were then applied to the 10X Genomics platform using the Single Cell 5’ Library & Gel Bead Kit (v2, dual index) following the manufacturer’s instructions. Some PBMC were first stimulated with virus-specific peptide-pools for 16 hours in the presence of blocking antibodies for CD28 and CD40. These cells were sorted for expression of DAPI- and dump- (CD14 and CD19) and CD3+, CD154+ and CD69+.
The purified cDNA was amplified and then used for 5’ gene expression (GEX), CITE-Seq and TCR library preparation using the Single Cell 5’ Library & Gel Bead Kit (v2, 10x Genomics). TCR target enrichment was achieved using the Chromium Single Cell V(D)J Enrichment Kit for Human T cells. Through fragmentation, adapter ligation and index PCR the final GEX and TCR libraries were obtained. The CITE-Seq libraries were obtained only by index PCR. The quality of single cell 5’ GEX, CITE-Seq and BCR libraries was assessed by Qubit quantification and Bioanalyzer fragment analysis (HS DNA Kit, Agilent).
The sequencing was performed on a NextSeq2000 (or NextSeq500) device (Illumina) using NextSeq 1000/2000 P3 reagent kits (200 Cycles, Illumina) with the recommended sequencing conditions for 5’ GEX and Cite-Seq libraries (read1: 26nt, read2: 90nt, index1: 10nt, index2: 10nt) and NextSeq 1000/2000 P3 reagent kits.

treatment_protocol: Patients were treated accodring to standard of care. For dataset before and after Methylprednisolone puls children were treated with methylprednisolon 20-30 mg/kg(bodyweight)/day for 3 consecutive days. B07 (MIS-C patient Berlin 07), B09 and B 10 were captured before treatment with methylprednisolone, B08 was treated with 1-2mg/kg methylprednisolone for 2 days, B06 was treated with 1-2 mg/kg methylprednisolone for 3 days. Patients B01, B02 B04, B05 and B11 were treated with 20-30 mg/kg methylprednisolone for 1 day and B03 was treated with 20-30 mg/kg methylprednisolone for 4 days before capturing.

value: sorted cells from peripheral blood

tag: hto


title: 116T

description: cancer

label: Cy5 and Cy115

source_name: HCC 116


title: 119T

description: cancer

label: Cy5 and Cy118

source_name: HCC 119


title: 113T

description: cancer

label: Cy5 and Cy112

source_name: HCC 113


title: 126T

description: cancer

label: Cy5 and Cy125

source_name: HCC 126


title: 131T

description: cancer

label: Cy5 and Cy130

source_name: HCC 131


title: 112T

description: cancer

label: Cy5 and Cy111

source_name: HCC 112


title: 127T

description: cancer

label: Cy5 and Cy126

source_name: HCC 127


title: sorted cells from 4 patients after treatment with Methylprednisolone mRNA expression [Pool_PosMP]

library_source: transcriptomic single cell


title: 110T

description: cancer

label: Cy5 and Cy109

source_name: HCC 110


title: 114T

description: cancer

label: Cy5 and Cy113

source_name: HCC 114


title: 115T

description: cancer

label: Cy5 and Cy114

source_name: HCC 115


title: 123T

description: cancer

label: Cy5 and Cy122

source_name: HCC 123


title: 128T

description: cancer

label: Cy5 and Cy127

source_name: HCC 128


title: sorted cells from 4 patients after treatment with Methylprednisolone hashtags [Pool_PosMP_CITE]


title: sorted cells from 4 controls 6 weeks after infection with SARS-CoV-2 TCR [PIMS_Pool4_TCR]


title: sorted cells from 4 patients before treatment with Methylprednisolone mRNA expression [Pool_PreMP]


title: 111T

description: cancer

label: Cy5 and Cy110

source_name: HCC 111


title: 117T

description: cancer

label: Cy5 and Cy116

source_name: HCC 117


title: 118T

description: cancer

label: Cy5 and Cy117

source_name: HCC 118


title: 109T

description: cancer

label: Cy5 and Cy108

source_name: HCC 109


title: 108T

description: cancer

label: Cy5 and Cy107

source_name: HCC 108


title: sorted cells from 4 controls 6 weeks after infection with SARS-CoV-2 BCR [PIMS_Pool4_BCR]

source_name: sorted cells from peripheral blood


title: sorted cells from 4 controls 6 weeks after infection with SARS-CoV-2 hashtags [PIMS_Pool4_CITE]


title: 107T

description: cancer

label: Cy5 and Cy106

source_name: HCC 107


title: 106T

description: cancer

label: Cy5 and Cy105

source_name: HCC 106


title: sorted cells from 4 controls 6 weeks after infection with SARS-CoV-2 mRNA expression [PIMS_Pool4]


title: sorted cells from 4 MIS-C patients 8-11 TCR [PIMS_Pool3_TCR]


title: 105T

description: cancer

label: Cy5 and Cy104

source_name: HCC 105


title: sorted cells from 4 MIS-C patients 8-11 BCR [PIMS_Pool3_BCR]


title: 101T

description: cancer

label: Cy5 and Cy100

source_name: HCC 101


title: 102T

description: cancer

label: Cy5 and Cy101

source_name: HCC 102


title: 104T

description: cancer

label: Cy5 and Cy103

source_name: HCC 104


title: 98T

description: cancer

label: Cy5 and Cy97

source_name: HCC 98


title: 99T

description: cancer

label: Cy5 and Cy98

source_name: HCC 99


title: sorted cells from 3 MIS-C patients + 1 other 5-7 TCR [PIMS_Pool2_TCR]


title: sorted cells from 3 MIS-C patients + 1 other 5-7 BCR [PIMS_Pool2_BCR]


title: 103T

description: cancer

label: Cy5 and Cy102

source_name: HCC 103


title: sorted cells from 3 MIS-C patients + 1 other 5-7 mRNA expression [PIMS_Pool2]


title: 97T

description: cancer

label: Cy5 and Cy96

source_name: HCC 97


title: sorted cells from 4 MIS-C patients 8-11 mRNA expression [PIMS_Pool3]


title: sorted cells from 4 MIS-C patients 1-4 TCR [PIMS_Pool1_TCR]


title: 100T

description: cancer

label: Cy5 and Cy99

source_name: HCC 100


title: sorted cells from 4 MIS-C patients 8-11 hashtags [PIMS_Pool3_CITE]


title: 96T

description: cancer

label: Cy5 and Cy95

source_name: HCC 96


title: 94T

description: cancer

label: Cy5 and Cy93

source_name: HCC 94


title: sorted cells from 4 MIS-C patients 1-4 BCR [PIMS_Pool1_BCR]


title: sorted cells from 3 MIS-C patients + 1 other 5-7 hashtags [PIMS_Pool2_CITE]


title: 95T

description: cancer

label: Cy5 and Cy94

source_name: HCC 95


title: Plasmablasts from 3 MIS-C patients + two other samples hashtags [PIMS_plasmablasts_CITE]

source_name: primary plasmablasts

value: primary plasmablasts


title: 93T

description: cancer

label: Cy5 and Cy92

source_name: HCC 93


title: sorted cells from 4 MIS-C patients 1-4 hashtags [PIMS_Pool1_CITE]

source_name: sorted cells from peripheral blood


title: sorted cells from 4 MIS-C patients 1-4 mRNA expression [PIMS_Pool1]


title: Plasmablasts from 3 MIS-C patients + two other samples mRNA expression [PIMS_plasmablasts]


title: 92T

description: cancer

label: Cy5 and Cy91

source_name: HCC 92


title: 91T

description: cancer

label: Cy5 and Cy90

source_name: HCC 91


title: EBV specific T cells from donor 1-5 hashtags [PIMS_actTcells_EBV_CITE]

source_name: primary T cells

value: primary T cells


title: 90T

description: cancer

label: Cy5 and Cy89

source_name: HCC 90


title: 89T

description: cancer

label: Cy5 and Cy88

source_name: HCC 89


title: EBV specific T cells from donor 1-5 mRNA expression [PIMS_actTcells_EBV]


title: 87T

description: cancer

label: Cy5 and Cy86

source_name: HCC 87


title: SARS-CoV-2 specific T cells from donor 1-4 hashtags [Covid_T_Cite]

tag: adt


title: CMV specific T cells from donor 1-5 TCR [CMV_2nd_hTCR]


title: 82T

description: cancer

label: Cy5 and Cy81

source_name: HCC 82

tag: gender


title: CMV specific T cells from donor 1-5 mRNA expression [PIMS_actTcells_CMV_GEX]


title: 83T

description: cancer

label: Cy5 and Cy82

source_name: HCC 83


title: CMV specific T cells from donor 1-5 hashtags [PIMS_actTcells_CMV_CITE]


title: 84T

description: cancer

label: Cy5 and Cy83

source_name: HCC 84


title: 80T

description: cancer

label: Cy5 and Cy79

source_name: HCC 80


title: 86T

description: cancer

label: Cy5 and Cy85

source_name: HCC 86


title: SARS-CoV-2 specific T cells from donor 1-4 TCR [Covid_T_TCR]


title: Adenovirus specific TCR [AdV_hTCR]


title: SARS-CoV-2 specific T cells from donor 1-4 mRNA expression [Covid_T_GEX]


title: 85T

description: cancer

label: Cy5 and Cy84

source_name: HCC 85


title: Stage 15 gonad, Male producing temperature

first: Rafael

middle: Domínguez

last: Acemel

address: Hannoversche Str. 28

department: Berlin Institute of Medical Systems Biology (BIMSB)

institute: Max Delbrück Center for Molecular Medicine (MDC)

description: 10x genomics

data_processing:
The demultiplexing, barcoded processing, alignment to genome and transcriptome, gene counting and aggregation was performed using the Cell Ranger software (v3.1.0)
Assembly: CAS_Tse_1.0 (GCF_013100865.1)
Supplementary files format and content: Barcode and feature tsv files and matrix files from filtered CellRanger output.

organism: Trachemys scripta elegans

source_name: Embryonic gonad

growth_protocol: Freshly laid red-eared slider turtle (Trachemys scripta elegans) eggs were obtained from Concordia Turtle Farms (Jonesville, LA, with permission from the Louisiana Department of Agriculture). The day after oviposition, fertilized eggs were randomly placed into trays of moist pearlite and housed in incubators kept at either 26˚C (male-producing temperature) or 31˚C (female-producing temperature), with humidity maintained at 70-80%.

extract_protocol:
For all experiments, embryos were removed from eggshells, immediately decapitated, and moved to sterile PBS for gonad dissection. GMCs were dissected from MPT and FPT embryos at St. 15, St. 18 and St. 23 in ice-cold PBS. The mesonephros was removed using sterile syringe tips. A minimum of two replicates of 8-12 gonads per incubation treatment and stage were pooled in 500ul of cold DPBS. DPBS was removed and 20ul of 5% BSA/DPBS was added to each tube. 250ul of 0.05% Trypsin/EDTA was added and gonads incubated were incubated at MPT or FPT, respective to the original incubation treatment of the egg, for 5-7 minutes (until tissue was completely dissociated). Trypsin was removed and 300 ul of 5% BSA/DPBS was added. Cell suspension was collected using a p1000 and filtered into a new Eppendorf tube using a 40um Flowmi® cell strainer (Sigma-Aldrich; BAH136800040). Cells were precipitated at 3,000 RPM for 5 mins at 4°C and supernatant was discarded. Cells were fixed in methanol and stored in -80˚C.
Once rehydrated from methanol storage, around 10,000 cells were loaded on a 10x Chromium controller and sc-RNA libraries were prepared using the Chromium Next Gem Single Cell 3’ Reagent Kit v3.1 (PN-1000128) following the manufacturer's instructions. Finally, libraries were sent for sequence.
10x Genomics

value: Embryonic gonad

value: 26ºC incubation (MPT)

value: Stage 15


title: 81T

description: cancer

label: Cy5 and Cy80

source_name: HCC 81


title: Stage 18 gonad, Male producing temperature

description: 10x genomics

value: Stage 18


title: EBV specific T cells from donor 1-5 TCR [EBV_hTCR]


title: 79T

description: cancer

label: Cy5 and Cy78

source_name: HCC 79


title: 78T

description: cancer

label: Cy5 and Cy77

source_name: HCC 78


title: Stage 23 gonad, Female producing temperature

description: 10x genomics

value: 32ºC incubation (FPT)

value: Stage 23


title: Stage 18 gonad, Female producing temperature

description: 10x genomics


title: Stage 23 gonad, Male producing temperature

description: 10x genomics

value: Male


title: 88T

description: cancer

label: Cy5 and Cy87

source_name: HCC 88

value: Hepatocellular carcinoma (HCC)

value: Hepatocellular carcinoma


title: 77T

description: cancer

label: Cy5 and Cy76

source_name: HCC 77


title: 76T

description: cancer

label: Cy5 and Cy75

source_name: HCC 76


title: Stage 15 gonad, Female producing temperature

description: 10x genomics

value: Female


title: 75T

description: cancer

label: Cy5 and Cy74

source_name: HCC 75


title: 74T

description: cancer

label: Cy5 and Cy73

source_name: HCC 74


title: 73T

description: cancer

label: Cy5 and Cy72

source_name: HCC 73


title: 71T

description: cancer

label: Cy5 and Cy70

source_name: HCC 71


title: 72T

description: cancer

label: Cy5 and Cy71

source_name: HCC 72


title: 69T

description: cancer

label: Cy5 and Cy68

source_name: HCC 69


title: 68T

description: cancer

label: Cy5 and Cy67

source_name: HCC 68


title: 66T

description: cancer

label: Cy5 and Cy65

source_name: HCC 66


title: 70T

description: cancer

label: Cy5 and Cy69

source_name: HCC 70


title: 65T

description: cancer

label: Cy5 and Cy64

source_name: HCC 65


title: 67T

description: cancer

label: Cy5 and Cy66

source_name: HCC 67


title: 63T

description: cancer

label: Cy5 and Cy62

source_name: HCC 63


title: 64T

description: cancer

label: Cy5 and Cy63

source_name: HCC 64


title: 62T

description: cancer

label: Cy5 and Cy61

source_name: HCC 62


title: P4(SRCC-US1)

city: shanghai

first: ren

last: xiangyu

address: 盘山路8号

institute: naval medical university

description: un-secreted subclones

data_processing:
Basecalls performed using CASAVA version 1.8
Sequencing quality control: (1) Remove Reads containing joints;(2) Removal of low-quality Reads (including Reads with N removal ratio greater than 10%;Remove more than 50% of Reads with mass value Q≤10.
Transcriptome data were compared with reference genome sequences:TopHat2 ,which is based on comparison software Bowtie2 was used to sequence Clean Reads with the reference genome to obtain the location information on the reference genome or genes, as well as the sequence characteristic information of the sequenced samples.
Based on the Beta Negative Binomial Distribution mathematical model, using the Cufflinks Cuffquant and Cuffnorm components, the Mapped Reads location information on genes,The transcription and gene expression levels were quantified.  Normalize the number of Mapped Reads and transcript length in the sample.Cuffquant and Cuffnorm used FPKM (Fragments Per Kilobase of transcript Per Million Fragments Mapped) to measure the level of transcription or gene expression.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: un-secreted subclones

growth_protocol: The specimens of tumor and small normal nodes were isolated and delivered on ice to perform subsequent primary cell culture.

extract_protocol:
the qualified genome DNA was randomly fragmented into 150bp to 200bp.
Based on the Sequencing By Synthesis (SBS) technology, the cDNA library was sequenced By Illumina HiSeq high-throughput Sequencing platform

treatment_protocol: A total of 15 SRCC single cell subclones were successfully isolated, which were then determined as secreted or un-secreted clones according to the supernatant of cell culture visibly viscous or not.

value: sarcomatoid renal cell carcinoma cell line SRCC


title: P5(SRCC-US2)

description: un-secreted subclones


title: 61T

description: cancer

label: Cy5 and Cy60

source_name: HCC 61


title: P3(SRCC-S2)

description: secreted subclones

source_name: secreted subclones


title: Blastocysts from intrafollicular transfer of immature oocytes _replicate3

city: Bonn

first: Dessie Salilew

last: Wondim

address: Endenicher Allee 15

institute: University of Bonn

description: Fragmented ss-cDNA was then labeled with terminal deoxynucleotidyl transferase (TdT) using the biotin-linked labeling reagent

hyb_protocol: Hybridization, washing and staining were performed with the GeneChip® Hybridization, Wash and Stain Kit (P/N 900720-C, Affymetrix Inc., Santa Clara, CA).

scan_protocol: Array scanning was performed  using Affymetrix GeneChip® scanner 3000 7G.

data_processing: The Affymetrix GeneChip® Command Console™ (AGCC) software was used to evaluate the array images and to export the spot intensity data in the CEL file format. Probe to transcript level annotation was performed following Affymetrix annotation algorithm.  The Cytoscape plugin ClueGO was used to export the significantly enriched gene ontologies

label: biotin

organism: Bos taurus

source_name: Blastocysts produced after intrafollicular transfer of immature oocytes into dominant follicle_replicate3

label_protocol: About 15 ng total RNA from each of the biological replicates of each embryo group was subjected to the first-strand cDNA followed by synthesis of double-strand cDNA using DNA polymerase with the presence of RNase H followed by in vitro transcription using T7 RNA polymerase. Following subsequent steps, fragmented ss-cDNA was  labeled with terminal deoxynucleotidyl transferase (TdT) using the biotin-linked labeling reagent.

growth_protocol: Blastocyst were generated  after intrafollicular transfer of immature oocytes (IFOT-IM) into dominant follicles or transfer of in vitro matured oocytes (IFOT-M) into preovulatory follicles for in vitro maturation, fertilization and development up to the blastocyst stage, fully in vitro or fully in  vivo following superovulation and AI.

extract_protocol: Total RNA was extracted using the Single Cell RNA Purification Kit (Norgen, P/N 51800) according to the manufacturer’s instructions. the RNA integrity was verified on an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA) using RNA 6000 Pico Kit. The RIN values of ≥ 7.0 with rRNA ratio of ≥ 1.5 were considered for microarray target preparation

treatment_protocol: Blastocyst were grouped into four groups: Those derived after intrafollicular transfer of immature oocytes (IFOT-IM) or vitro matured oocytes (IFOT-M) or completely developed under in vitro condition (VITRO) or in vivo (VIVO)

value: Blastocyst embryo


title: Blastocysts from intrafollicular transfer of in vitro matured oocytes_replicate3

source_name: Blastocysts produced after intrafollicular transfer of in vitro matured oocytes into dominant follicles_replicate3


title: In vivo developed blastocysts_replicate3

source_name: Blastocysts produced in vivo after superovulation and AI_replicate3


title: In vitro blastocysts_replicate3

source_name: In vitro produced blastocysts_replicate3


title: 59T

description: cancer

label: Cy5 and Cy58

source_name: HCC 59


title: Blastocysts from intrafollicular transfer of immature oocytes _replicate1

source_name: Blastocysts produced after intrafollicular transfer of immature oocytes into dominant follicle_replicate1


title: P1(SRCC)

description: primary SRCC cells

source_name: Self-established renal sarcomatoid carcinoma cell lines


title: 0Gy_DMSO_d21_1-3, 0Gy_Forskolin_d21_1-3, 4Gy_DMSO_d21_1-3, 4Gy_Forskolin_d21_1-3

description:
Library name: 0Gy_DMSO_d21_1
10x Genomics

data_processing:
Sequencing reads from the mRNA libraries were mapped to the human genome (hg38) using the Parse Biosciences pipeline (split-pipe vers. 1.1.1) to generate cell by gene counts matrices. Data analysis was performed using the R package Seurat (version 4.3.3). Matrices were filtered for cells with high mitochondrial and ribosomal gene count and doublets were removed using DoubletFinder R package.
Assembly: human genome (hg38)
Supplementary files format and content: FASTQ and matrix files

source_name: Glioblastoma

growth_protocol: Patient-derived HK-374 gliomaspheres were cultured in serum-free conditions in ultra-low adhesion plates in DMEM/F12, supplemented with SM1 Neuronal Supplement, EGF, bFGF and heparin.

extract_protocol:
At day 21, the gliomaspheres in the suspension culture were collected and dissociated with TrypLE (no phenol red), and the adherent differentiated cells were washed with HBSS and de-attached with Trypsin/EDTA. The cells were then pooled and filtered through a 40-µm strainer and fixed with EvercodeTM Cell Fixation v2 kit (#ECF2101, Parse Biosciences), following the manufacturer’s guidelines.
Library was performed according to the manufacter's instructions for the EvercodeTM Whole Transcriptome Mini kit (#EC-W01010, Parse Biosciences).

treatment_protocol: HK-374 gliomaspheres were plated onto the Poly-D-Lysine/Laminin 6-well plate and irradiated with 4 Gy the next day. 48 hours after the irradiation, the cells were treated with forskolin (10 µM) for 21 consecutive days.

value: Glioblastoma

value: patient-derived cell line

value: WT


title: In vitro blastocysts_replicate1

source_name: In vitro produced blastocysts_replicate1


title: Blastocysts from intrafollicular transfer of in vitro matured oocytes_replicate2

source_name: Blastocysts produced after intrafollicular transfer of in vitro matured oocytes into dominant follicles_replicate2


title: Blastocysts from intrafollicular transfer of immature oocytes _replicate2

source_name: Blastocysts produced after intrafollicular transfer of immature oocytes into dominant follicle_replicate2


title: 58T

description: cancer

label: Cy5 and Cy57

source_name: HCC 58


title: In vivo developed blastocysts_replicate2

source_name: Blastocysts produced in vivo after superovulation and AI_replicate2


title: In vivo developed blastocysts_replicate1

source_name: Blastocysts produced in vivo after superovulation and AI_replicate1


title: 57T

description: cancer

label: Cy5 and Cy56

source_name: HCC 57


title: In vitro blastocysts_replicate2

source_name: In vitro produced blastocysts_replicate2


title: 0Gy_DMSO_d5_1-3, 0Gy_Forskolin_d5_1-3, 4Gy_DMSO_d5_1-3, 4Gy_Forskolin_d5_1-3

description:
Library name: 0Gy_DMSO_1
10x Genomics

extract_protocol:
At day 5, the gliomaspheres in the suspension culture were collected and dissociated with TrypLE (no phenol red), and the adherent differentiated cells were washed with HBSS and de-attached with Trypsin/EDTA. The cells were then pooled and filtered through a 40-µm strainer and fixed with EvercodeTM Cell Fixation v2 kit (#ECF2101, Parse Biosciences), following the manufacturer’s guidelines.
Library was performed according to the manufacter's instructions for the EvercodeTM Whole Transcriptome Mini kit (#EC-W01010, Parse Biosciences).

treatment_protocol: HK-374 gliomaspheres were plated onto the Poly-D-Lysine/Laminin 6-well plate and irradiated with 4 Gy the next day. 48 hours after the irradiation, the cells were treated with forskolin (10 µM) for 5 consecutive days.


title: PHH biol rep 2

city: Guangdong

first: Wu

last: Haibin

state: 广州

address: No. 382 Waihuan East Rd., Guangzhou University City, Panyu District, Guangzhou, Guangdong, P.R.China

institute: South China University of technology

data_processing:
Sequencing was performed by Novogene (China) on an Illumina HiSeq X-Ten sequencer with 150 bp paired-end sequencing reaction.
The reads were mapped to the human reference genome using HISAT2.
Reads Counts for each gene in each sample were counted by featureCounts, and FPKM (Fragments Per Kilobase Million Mapped Reads) and then were calculated to estimate the expression level of genes in each sample.
Differentially expressed genes (DEGs) were analyzed by DESeq2 using counts. Genes with P value ≤ 0.05 and |log2 Fold Change| ≥1.5 were identified as DEGs.
Heatmap was performed with the R package. TBtools software and DAVID database were used to test the statistical enrichment of differential expression genes in KEGG pathways. Principle component analysis (PCA) and Gene Set Enrichment Analysis (GSEA) were performed using the OmicShare tools at www.omicshare.com/tools .
Assembly: GRCh38
Supplementary files format and content: processed_counts_data.xlsx: Excel file includes raw counts for each sample.

source_name: Primary human hepatocytes

extract_protocol:
Total RNA of H9 cells, HB-orgs cultured with or without Matrigel, P-hep-orgs and NP-hep-spheres were extracted using RNAiso Plus kit according to the manufacturer’s instructions.
The cDNA libraries for RNA sequencing were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB).

value: Primary human hepatocytes


title: 55T

description: cancer

label: Cy5 and Cy54

source_name: HCC 55


title: PHH biol rep 1


title: Blastocysts from intrafollicular transfer of in vitro matured oocytes_replicate1

source_name: Blastocysts produced after intrafollicular transfer of in vitro matured oocytes into dominant follicles_replicate1


title: P2(SRCC-S1)

description: secreted subclones

source_name: secreted subclones


title: 54T

description: cancer

label: Cy5 and Cy53

source_name: HCC 54


title: 53T

description: cancer

label: Cy5 and Cy52

source_name: HCC 53


title: Pheporg biol rep 2

source_name: H9 differentiated cells (P-hep-orgs)

value: H9 differentiated cells (P-hep-orgs)


title: 60T

description: cancer

label: Cy5 and Cy59

source_name: HCC 60


title: Pheporg biol rep 1


title: 44T

description: cancer

label: Cy5 and Cy43

source_name: HCC 44


title: 49T

description: cancer

label: Cy5 and Cy48

source_name: HCC 49


title: 48T

description: cancer

label: Cy5 and Cy47

source_name: HCC 48


title: MG+ Hborg biol rep 3

source_name: H9 differentiated cells (HB-orgs)

value: H9 differentiated cells (HB-orgs)

tag: condition

value: With Matrigel


title: 52T

description: cancer

label: Cy5 and Cy51

source_name: HCC 52


title: MG- Hborg biol rep 1

value: Without Matrigel


title: 42T

description: cancer

label: Cy5 and Cy41

source_name: HCC 42


title: Nphepsphere biol rep 2

source_name: H9 differentiated cells (NP-hep-spheres)


title: H9 biol rep 2

value: hESC


title: 51T

description: cancer

label: Cy5 and Cy50

source_name: HCC 51


title: 47T

description: cancer

label: Cy5 and Cy46

source_name: HCC 47


title: MG- Hborg biol rep 3


title: H9 biol rep 1


title: Nphepsphere biol rep 1

value: H9 differentiated cells (NP-hep-spheres)


title: 43T

description: cancer

label: Cy5 and Cy42

source_name: HCC 43


title: 50T

description: cancer

label: Cy5 and Cy49

source_name: HCC 50


title: MG+ Hborg biol rep 2


title: 46T

description: cancer

label: Cy5 and Cy45

source_name: HCC 46


title: 40T

description: cancer

label: Cy5 and Cy39

source_name: HCC 40


title: MG+ Hborg biol rep 1


title: 56T

description: cancer

label: Cy5 and Cy55

source_name: HCC 56


title: Pheporg biol rep 3


title: Retinoic acid-induced N2a cells, RSL3-3

city: jining

first: gao

last: xu

state: Shandong

address: 89 Guhuai Road

institute: Affiliated Hospital of Jining Medical University

description: Library name: RSL3-3

data_processing:
Illumina cyclers produce raw sequencing in FASTQ format. Assess the quality of the raw sequencing for each sample upon amplification All columns will be counted Q30: Q=-10log1o(P) For example, Q=30 means that the probability of incorrect identification is 0.1%, that is, the error rate is 0.1% and the accuracy rate is 99.9%.
After sequencing quality control, the raw data is preprocessed after QC (use cutadapt to remove the 3’ adapter sequence and filter out short fragments <17 bp) The trimmed reads were obtained and aligned to the reference genome using bowtie. The statistical information of the alignment is listed in the table below. Comparison of general sample reads The rate is about 40~90%. The comparison rate is affected by many factors, including sample RNA quality, library construction method, sequencing method, comparison software and parameters etc. can affect the comparison rate.
Quantification of miRNA expression was obtained by comparing the results to known genomes using software mirdeep2 and conducting statistics. The miRNA expression threshold is The miRNAs with a mean CPM value exceeding ≥1 in each group were considered to be expressed in the group and subjected to statistical analysis. The specific calculation formula of Counts per million reads (CPM) is as follows: CPM=(C*10^6)/N C: The number of reads mapped to a certain gene. N: The total number of reads mapped to all genes.
Use edgeR to perform differential expression analysis of miRNAs between groups. Set the threshold to 1.5-fold difference, p-yalue<0.05 and mean CPM within the group>1 to screen differentially expressed miRNAs
Assembly: GRCm38
Supplementary files format and content: The csv format file contains the CPM value of gene in every sample

source_name: N2a cells

growth_protocol: The cells were maintained in high glucose-DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin (100 units/mL)/streptomycin (100 μg/mL) at 37°C in a humidified 5% CO2-containing atmosphere.

extract_protocol:
After extracting the total RNA samples, undergo agarose electrophoresis and Nanodrop quality inspection and quantification, construct a library, use Agilent 2100 Bioanalyzer to measure the library quality, mix the sequencing libraries of different samples, and generate single-stranded DNA through 0.1M NaOH denaturation. According to the supply Commercial Instructions for 50-Cycle Sequencing on the Illumina NextSeq 500 Sequencer
Prepare a miRNA sequencing library using total RNA from each sample, including the following steps: 1)3' connector connection: 2) 5' joint connection; 3) cDNA synthesis: 4) PCR amplification: 5) Select 135 ~ 155 bp PCR amplified fragments (corresponding to 15 ~ 35 nt small RNAs): The library was denatured into single-stranded DNA molecules, captured on an Illumina flow cell, amplified in situ into clusters, and according to the supplier's instructions, Sequencing was performed for 50 cycles on an Illumina NextSeq 500 sequencer.

treatment_protocol: N2a cells were cultured in six-well plates for 24 hours. DMEM+2% FBS and 10 μM retinoic acid induced differentiation. The culture medium was changed every day for 96 hours. Retinoic acid-treated, and control cells were imaged every day. Cells with axon length at least twice the diameter of the cell body were considered differentiated cells. Moreover, 5 μM RSL3  was used for 24 hours to establish ferroptosis in the RA-induced neuronal cells, and the same DMSO concentration was maintained in control cells.

value: N2a cells

value: Neuron


title: Retinoic acid-induced N2a cells, RSL3-2

description: Library name: RSL3-2


title: 39T

description: cancer

label: Cy5 and Cy38

source_name: HCC 39

value: Male

value: Hepatocellular carcinoma (HCC)


title: Retinoic acid-induced N2a cells, DMSO-3

description: Library name: DMSO-3

value: DMSO


title: Retinoic acid-induced N2a cells, RSL3-1

description: Library name: RSL3-1


title: 41T

description: cancer

label: Cy5 and Cy40

source_name: HCC 41

value: Hepatocellular carcinoma


title: 45T

description: cancer

label: Cy5 and Cy44

source_name: HCC 45

value: Female


title: MG- Hborg biol rep 2


title: 37T

description: cancer

label: Cy5 and Cy36

source_name: HCC 37


title: Retinoic acid-induced N2a cells, DMSO-2

description: Library name: DMSO-2


title: Retinoic acid-induced N2a cells, DMSO-1

description: Library name: DMSO-1


title: 38T

description: cancer

label: Cy5 and Cy37

source_name: HCC 38


title: 35T

description: cancer

label: Cy5 and Cy34

source_name: HCC 35


title: BMDMs, H3.3cKO:Irf7KO, biol rep1

city: Bethesda

first: Sakshi

last: Chauhan

address: Building 6A, Room 2A11,6 Center Drive

institute: NICHD

description: Library name: Irf7 TKO1

data_processing:
CCBR pipeliner and SARTools
Sequence reads were trimmed for adaptor sequence using cutadapt.
Trimmed sequence reads were mapped to mm10 using STAR aligner.
Assembly: mm10
Supplementary files format and content: tab delimited text file inclues raw count for each sample

source_name: BMDM

extract_protocol:
RNA was purified using Zymogen quick RNA miniprep kit.
NEBNext® rRNA Depletion Kit was used to deplete rRNA. RNA library was prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®.

value: BMDM


title: 33T

description: cancer

label: Cy5 and Cy32

source_name: HCC 33


title: BMDMs, H3.3cKO:Irf7KO, biol rep3

description: Library name: Irf7 TKO3


title: BMDMs, cKO, biological rep2

description: Library name: KO2_2


title: 31T

description: cancer

label: Cy5 and Cy30

source_name: HCC 31


title: BMDMs, H3.3cKO:Irf7KO, biol rep2

description: Library name: Irf7 TKO2


title: 32T

description: cancer

label: Cy5 and Cy31

source_name: HCC 32


title: 30T

description: cancer

label: Cy5 and Cy29

source_name: HCC 30


title: 28T

description: cancer

label: Cy5 and Cy27

source_name: HCC 28


title: 29T

description: cancer

label: Cy5 and Cy28

source_name: HCC 29


title: BMDMs, cKO, biological rep1

description: Library name: KO1_2


title: 26T

description: cancer

label: Cy5 and Cy25

source_name: HCC 26


title: BMDMs, WT, biological rep1

description: Library name: WT1_2


title: BMDMs, WT, biological rep2

description: Library name: WT2_2


title: BMDMs, cKO, biological rep3

description: Library name: KO3_2


title: 27T

description: cancer

label: Cy5 and Cy26

source_name: HCC 27


title: BMDMs, WT, biological rep3

description: Library name: WT3_2


title: 25T

description: cancer

label: Cy5 and Cy24

source_name: HCC 25


title: BMDMs, cKO, IFNAR1 antibody, biol rep3

description: Library name: KO3_IFNAR1 antibody


title: BMDMs, cKO, IFNAR1 antibody, biol rep1

description: Library name: KO1_IFNAR1 antibody


title: 24T

description: cancer

label: Cy5 and Cy23

source_name: HCC 24


title: BMDMs, WT, IFNAR1 antibody, biol rep3

description: Library name: WT3_IFNAR1 antibody


title: 36T

description: cancer

label: Cy5 and Cy35

source_name: HCC 36


title: 34T

description: cancer

label: Cy5 and Cy33

source_name: HCC 34


title: 23T

description: cancer

label: Cy5 and Cy22

source_name: HCC 23


title: BMDMs, WT, IFNAR1 antibody, biol rep2

description: Library name: WT2_IFNAR1 antibody


title: BMDMs, WT, IFNAR1 antibody, biol rep1

description: Library name: WT1_IFNAR1 antibody


title: BMDMs, cKO, control antibody, biol rep3

description: Library name: KO3_control antibody


title: 17T

description: cancer

label: Cy5 and Cy18

source_name: HCC 17


title: BMDMs, cKO, control antibody, biol rep1

description: Library name: KO1_control antibody


title: BMDMs, cKO, control antibody, biol rep2

description: Library name: KO2_control antibody


title: 16T

description: cancer

label: Cy5 and Cy17

source_name: HCC 16


title: BMDMs, cKO, IFNAR1 antibody, biol rep2

description: Library name: KO2_IFNAR1 antibody


title: BMDMs, WT, control antibody, biol rep3

description: Library name: WT3_control antibody


title: BMDMs, WT, control antibody, biol rep2

description: Library name: WT2_control antibody


title: BMDMs, cKO, no antibody, biol rep3

description: Library name: KO3_no antibody


title: 14T

description: cancer

label: Cy5 and Cy15

source_name: HCC 14


title: 15T

description: cancer

label: Cy5 and Cy16

source_name: HCC 15


title: BMDMs, cKO, no antibody, biol rep1

description: Library name: KO1_no antibody

source_name: BMDM


title: BMDMs, cKO, no antibody, biol rep2

description: Library name: KO2_no antibody


title: 12T

description: cancer

label: Cy5 and Cy13

source_name: HCC 12


title: 13T

description: cancer

label: Cy5 and Cy14

source_name: HCC 13


title: 11T

description: cancer

label: Cy5 and Cy12

source_name: HCC 11


title: 10T

description: cancer

label: Cy5 and Cy11

source_name: HCC 10


title: BMDMs, WT, control antibody, biol rep1

description: Library name: WT1_control antibody


title: 9T

description: cancer

label: Cy5 and Cy10

source_name: HCC 9


title: BMDMs, WT, no antibody, biol rep3

description: Library name: WT3_no antibody


title: BMDMs, WT, no antibody, biol rep2

description: Library name: WT2_no antibody


title: 8T

description: cancer

label: Cy5 and Cy9

source_name: HCC 8


title: BMDMs, WT, no antibody, biol rep1

description: Library name: WT1_no antibody


title: 19T

description: cancer

label: Cy5 and Cy20

source_name: HCC 19


title: 6T

description: cancer

label: Cy5 and Cy7

source_name: HCC 6


title: 18T

description: cancer

label: Cy5 and Cy19

source_name: HCC 18


title: 7T

description: cancer

label: Cy5 and Cy8

source_name: HCC 7


title: Peritoneal macrophaes, cKO, biol rep3

description: Library name: KO3_Peritoneal macrophages

source_name: Peritoneal macrophages

value: Peritoneal macrophages


title: Peritoneal macrophaes, cKO, biol rep2

description: Library name: KO2_Peritoneal macrophages


title: 4T

description: cancer

label: Cy5 and Cy5

source_name: HCC 4


title: 5T

description: cancer

label: Cy5 and Cy6

source_name: HCC 5


title: 3T

description: cancer

label: Cy5 and Cy4

source_name: HCC 3


title: 2T

description: cancer

label: Cy5 and Cy3

source_name: HCC 2


title: Peritoneal macrophaes, cKO, biol rep1

description: Library name: KO1_Peritoneal macrophages


title: Peritoneal macrophaes, WT, biol rep3

description: Library name: WT3_Peritoneal macrophages

value: WT


title: Peritoneal macrophaes, WT, biol rep1

description: Library name: WT1_Peritoneal macrophages


title: Peritoneal macrophaes, WT, biol rep2

description: Library name: WT2_Peritoneal macrophages


title: 148N

source_name: Normal liver 148

value: normal liver tissue adjacent to the tumor (NAT)


title: 145N

source_name: Normal liver 145


title: BMDMs, cKO, day8, IFNγ treatment 12 hrs,biol rep1

description: Library name: KO1_day8_IFNγ_12hrs

source_name: BMDM


title: 147N

source_name: Normal liver 147


title: 143N

source_name: Normal liver 143


title: BMDMs, WT, day8,IFNγ treatment 12 hrs, biol rep2

description: Library name: WT2_day8_IFNγ_12hrs


title: 146N

source_name: Normal liver 146


title: BMDMs, cKO, day8,biol rep3

description: Library name: KO3_day8_IFNγ_12hrs


title: BMDMs, cKO, day8, IFNγ treatment 12 hrs, biol rep2

description: Library name: KO2_day8_IFNγ_12hrs


title: 144N

source_name: Normal liver 144


title: BMDMs, WT, day8, IFNγ treatment 12 hrs,biol rep3

description: Library name: WT3_day8_IFNγ_12hrs


title: 141N

source_name: Normal liver 141


title: BMDMs, cKO, day8,IFNγ treatment 12 hrs, biol rep3

description: Library name: KO3_day8


title: 142N

source_name: Normal liver 142


title: BMDMs, cKO, day8, biol rep2

description: Library name: KO2_day8


title: 136N

source_name: Normal liver 136


title: 135N

source_name: Normal liver 135


title: 140N

source_name: Normal liver 140


title: BMDMs, cKO, day8,biol rep1

description: Library name: KO1_day8


title: 133N

source_name: Normal liver 133


title: BMDMs, WT, day8, biol rep2

description: Library name: WT2_day8


title: 134N

source_name: Normal liver 134


title: BMDMs, cKO, day7,biol rep3

description: Library name: KO3_day7


title: 132N

source_name: Normal liver 132


title: BMDMs, cKO, day7, biol rep2

description: Library name: KO2_day7


title: 131N

source_name: Normal liver 131


title: 130N

source_name: Normal liver 130


title: BMDMs, cKO, day7,biol rep1

description: Library name: KO1_day7


title: BMDMs, WT, day8,IFNγ treatment 12 hrs, biol rep1

description: Library name: WT1_day8_IFNγ_12hrs


title: 128N

source_name: Normal liver 128


title: BMDMs, WT, day7,biol rep3

description: Library name: WT3_day7


title: BMDMs, WT, day7, biol rep2

description: Library name: WT2_day7


title: 124N

source_name: Normal liver 124


title: BMDMs, WT, day7, biol rep1

description: Library name: WT1_day7

source_name: BMDM


title: 123N

source_name: Normal liver 123


title: BMDM progeniors, cKO, day5, biol rep2

description: Library name: KO2_day5

source_name: BMDM progenitors

value: BMDM progenitors


title: BMDM progeniors, cKO, day5, biol rep1

description: Library name: KO1_day5


title: 122N

source_name: Normal liver 122


title: BMDMs, WT, day8,biol rep3

description: Library name: WT3_day8


title: 120N

source_name: Normal liver 120


title: BMDM progeniors, WT, day5,biol rep3

description: Library name: WT3_day5


title: BMDM progeniors, WT, day5, biol rep2

description: Library name: WT2_day5


title: BMDM progeniors, WT, day5, biol rep1

description: Library name: WT1_day5


title: BMDMs, WT, day8, biol rep1

description: Library name: WT1_day8


title: 117N

source_name: Normal liver 117


title: BMDM progeniors, cKO, day3, biol rep3

description: Library name: KO3_day3


title: 115N

source_name: Normal liver 115


title: 125N

source_name: Normal liver 125


title: 126N

source_name: Normal liver 126


title: BMDM progeniors, cKO, day3, biol rep2

description: Library name: KO2_day3