title: EACBEwt-Rag1ko-DN-DpnII-HiC-rep2

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Hi-C data process pipline. For each sample, reads were obtained following quality filtering and adapter trimming using fastp (v0.20.0). Hi-C mapping, filtering, correction, and binning were performed with Hi-C-Pro (v2.11.1). The paired-end reads were mapped to the mouse mm10 genome. Self-circle ligation, dangling ends, re-ligation, and the other dumped types were filtered out with Hi-C-Pro after mapping. We generated raw contact matrices at 10 kb, 20 kb, 50 kb, 100 kb, 500 kb, 1 Mb resolutions. For raw contact matrix correction, we used the iterative correction method (ICE). The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox hic format at fragment resolution. Heatmap, differential analysis and visualization of local interactions from Hi-C data were obtained using HiTC (v1.34.0) R package. A/B compartment analysis was performed at 100 kb resolution using a publicly available script runHiCpca.pl that performs PCA analysis with HOMER (v4.10.4). Then, we used the first principal component (PC1) to predict regions of active (A compartments) and inactive chromatin (B compartments). The TAD structure (insulation) was defined by the insulation score. The matrices which were used to calculate the insulation score were normalized by ICE method for discarding the bias of raw matrices. And then, the insulation score was computed at 10 kb resolution. The script matrix2insulation.pl was used to detect TAD boundaries, with the following options: ‘--is 100001 --ids 20001 --nt 0.3 -ss 0 --im mean’. TADs were called using normalized Hi-C matrices at 10 kb resolution with insulation2tads.pl. Chromatin loops were called using Fit-Hi-C (v2.0.7). Input files of Fit-Hi-C were created by using a publicly available script hicpro2fithic.py from Hi-C-Pro. Next, loops were called using fixed-size bin resolutions from 10 kb in all cell types. Briefly, significant interaction loops (P < 0.0001 and contact frequencies > = 5) were identified through jointly modeling the contact probability using raw contact frequencies and ICE normalization vectors with the Fit-Hi-C algorithm.
3C-HTGTS data processing for pairwise chromatin interactions. Paired-end Illumina sequencing fastq data were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads again were extracted from the sequence file after quality control with Cutadapt (v1.18). Paired-end reads containing nested primer or adapter primer were merged manually using restriction enzyme recognition sequences into single reads with Pear (v0.9.6), then the first digested fragment behind the bait was obtained by splitting the single reads into fragments according to restriction enzyme recognition sequences. The remaining single-end reads were aligned to the enzyme-digested mm10 reference genome with Bowtie2 (v2.4.5, parameter: -p 8 --sensitive), and mouse genome sequence (mm10) was retrieved from the UCSC and we extracted concordantly exact alignments using SAMtools (v1.9). Self-ligation reads and off-targeted reads were filtered after mapping. For visualization, we converted the final bam files into bedGraph files using Bedtools (v2.29.2). The signal peak bedGraph file was obtained by post-comparison filtering, signal statistics, and standardization. We normalized bedGraph files using the CPM (Counts Per Million in cis) normalization method and visualized them on the IGV genome browser. Differential pair-wise interactions were identified by the R package R.4Cker (v1.0.0, k=30) with the function nearBaitAnalysis called to define domains of interaction with the bait and DESeq2 (v1.34.0, p < 0.05). Finally, we organized the results report and visualized it with the Bioconductor package ggplot2 (v3.3.6).
3C-HTGTS data processing for three-way chromatin interactions. Paired-end Illumina sequencing reads were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads were extracted from the file after quality control with Cutadapt (v1.18). Paired-end reads containing nested primer or adapter primer were merged at restriction enzyme cut sites into single reads with Pear (v0.9.6), then fragments with multiple MboI cut sites were split and each fragment was aligned to the enzyme-digested mm10 reference genome by Bowtie2 (v2.4.5, parameter: -p 8 --sensitive). We extracted concordantly exact alignments using SAMtools (v1.9). We converted the final bam files into bed files using Bedtools (v2.29.2). Self-ligation and off-targeted fragments were filtered. Subsequently, we put all fragments retrieved from the same read according to the unique ID of each read on one line, then removed the continuous fragments. To create contact matrices, we extracted the first two digested fragments after the bait fragment, or a variety of combinations of three fragments were obtained by arranging all fragments from the same read. Raw contact matrices were generated at 3 kb, 5 kb, and 10 kb resolutions. For raw contact matrices correction, these interaction counts were normalized for a total of 1,000,000 interactions at the same resolutions. Similar to a Hi-C matrix, coverage was represented in a 2-dimensional matrix where each point represented the number of interactions found between two bins meaning a specific resolution. Differential analysis and visualization of local interactions from three-way interactions were obtained using the R package GENOVA (v1.0.0). Loops seen on the IGV genome browser were called using fixed-size bin resolutions from 3 kb to 10 kb. Briefly, interaction loops (contact frequencies >= 5) were identified by using raw contact frequencies.
ATAC-Seq data process pipline. Raw sequence reads were initially processed for removing adapter sequences and poor quality reads by fastp (v0.20.0). Subsequently, the remaining reads were mapped to the human genome hg38 using Bowtie2 (v2.4.5, parameter: -p 8 --sensitive). PCR duplicated fragments were filtered by Picard (v2.22.8). Then, we filtered the unmapped, multi-mapped reads and mapping to the reads on chrM. FRiP (Fragments Ratio in Peaks) value was calculated by using Bedtools (v2.29.2) and awk (v4.0.2). We used deepTools (v3.5.0) to generate bigWig file with CPM normalization, and these files can be visualized in IGV. SAM files were converted to BAM format using SAMtools (v1.9) and used for peak calling. MACS2 (v2.2.4) with parameters (--nomodel --shift -100 --extsize 200 -B --keep-dup all --broad --broad-cutoff 0.1) was used to call peaks.
HTGTS-VDJ data process pipline. The raw data were filtered by fastp (v0.20.0). Trimmed reads again that nested primer and adapter primer were removed were extracted from the sequence file after quality control with Cutadapt (v1.18). Contamination, and low-quality reads were also removed. T-cell receptor beta chain V, D, and J gene identification, CDR3 sequence extraction in clean reads were performed using MiXCR (v3.0.11). The corresponding germline sequences were mapped to the reference sequences derived from international ImMunoGeneTics (IMGT) information.
Assembly: mm10
Supplementary files format and content: The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox .hic format.
Supplementary files format and content: BedGraph files were generated using Bedtools (v2.29.2) with normalized values for each sample.
Supplementary files format and content: BigWig files were generated using bamCoverage with normalized values for each sample.

source_name: Thymus


title: PANC-1 cells, shControl, biol rep 1

status: Public on Apr 27 2024

type: SRA

city: Beijing

first: Chengqi

last: Yi

address: Yiheyuan Road

department: School of Life Sciences

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
Adaptor and low-quality reads were trimmed using cutadapt
FastQC was used for quality control of the sequencing data.
Reads were aligned to the human (GRCh38) reference genome using STAR (v2.7.2b)
Mapped reads were assigned to genes using featureCounts (v2.0.1)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for all samples

molecule: total RNA

organism: Homo sapiens

growth_protocol: H1299 and PANC-1 were maintained in DMEM(CORNING), supplemented with 10% FBS(PAN) in a 37℃ incubator with 5 % (v/v) CO2.

extract_protocol:
Total RNA was isolated from cultured cells using Trizol (Invitrogen, 10296010).
After quality check, samples were sent to library preparation using the NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530L, NEB, USA).

tag: cell line

tag: cell type

value: pancreatic adenocarcinoma cells

tag: genotype

value: WT


title: Nor1-input (A)

city: Xi’an

first: wang

middle: gui

last: hu

address: No.157#, The West 5th Road

department: The Second Affiliated Hospital

institute: Xi'an Jiaotong University

library_source: genomic

data_processing:
Reads were aligned to Human genome (HG19) using BOWTIE software (V2.1.0).
peak detection by MACS V1.4.2 (Model-based Analysis of ChIP-Seq) software. Statistically significant ChIP-enriched regions (peaks) were identified by comparison of IP vs Input or comparison to a Poisson background model (Cut-off p-value=10-3.
Contains the nearest gene annotation of the peaks using the newest UCSC RefSeq database
Read count extraction and normalization were performed using CLC genomic benchwork
Contains all the ChIP-seq signal densities in WIG format for visualizing the ChIP-seq profiles of each sample in UCSC Genome Browser (*.wig files).
Assembly: hg38
Supplementary files format and content: The peaks in samples were annotated by the nearest gene using the newest UCSC RefSeq database (This data was in EXCEL format, it can be found from the Peaks_Annotation.xls file)
Supplementary files format and content: Human_ChIP-Sequencing_Summary_Report is saved in a word file

molecule: genomic DNA

source_name: Spleen

growth_protocol: Spleen macrophages are sorted by CD11b+magnetic beads,The Chip-IP use Magna ChIP™ A/G (Catalog # 17-10085)

extract_protocol:
The sorted cells were lysed using ultrasound and broken into 150-200bp fragments，The mapped 150 bp reads represent enriched DNA fragments by ChIP experiment.  using a  Magna ChIP™ A/G (Catalog # 17-10085) reagent kit；
Sequencing Library Preparation，DNA samples were end-repaired, A tailed, and adaptor ligated using TruSeq Nano DNA Sample Prep Kit (#FC-121-4002, Illumina), following the manufacturer’s instructions. ~200-1500 bp fragments were size selected using AMPure XP beads. The final size of the library was confirmed by Agilent 2100 Bioanalyzer.

tag: tissue

value: Spleen

value: macrophage

tag: chip-antibody

tag: condition

value: Spleen-injury


title: 20c_scp

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

country: USA

institute: Lieber Institute for Brain Development

library_source: transcriptomic single cell

data_processing:
FASTQ files were pre-processed with the 10x CellRanger pipeline
Reads were aligned to reference genome GRCh38
Assembly: GRCh38
Supplementary files format and content: Raw FASTQ files and data processed with the 10x CellRanger pipeline with barcode, feature, and matrix files for each donor.

molecule: polyA RNA

source_name: brain (hippocampus)

extract_protocol:
Anterior hippocampus was dissected from fresh frozen postmortem human tissue. 100 micron coronal sections of hippocampus from fresh frozen postmortem human tissue were obtained by cryosectioning. Nuclei were isolated and barcoded with 10x Genomics Chromium.
Libraries were prepared using 10x Chromium Next GEM Single Cell 3’ v3.1 (dual-index) kit according to manufacturer's instructions.
single-nucleus RNA-sequencing

value: brain (hippocampus)


title: Liver, oral, 14 days, CK_2

city: Guiyang

first: Gongzhen

last: Chen

address: Dongqing South-Road 4#

institute: Guizhou University of Traditional Chinese Medicine

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: Mus musculus
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

organism: Mus musculus

source_name: liver tissue

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: liver tissue

tag: treatment

value: control


title: PANC-1 cells, shFOSL1, biol rep 3

value: FOSL1 knockdown


title: BPS_D

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
DESeq2 was used for differential expression analysis between the control and treatments.
Assembly: homo_sapiens_grch38_p12_gca_000
Supplementary files format and content: BPSvDMSO excel files containing read count, fpkm, log2 fold change, p-value, BPFvDMSO excel files containing read count, fpkm, log2 fold change, p-value

source_name: neuronal

extract_protocol:
Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer (ThermoFisher/Invitrogen, Grand Island, NY), and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.). RNA samples with a measured 28S/18S > 1 and RNA integrity number (RIN) ≥ 7 were used for RNAseq library construction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library"
Total RNA was used for mRNA isolation using the NEBNext Ploy(A) mRNA Magnetic Isolation module (New England Biolabs, catalog # E7490). RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 (Illumina Inc., CA, U.S.A). Sequencng was performed by Novogene.

value: neuronal


title: PANC-1 cells, shFOSL1, biol rep 2


title: BPS_B


title: PANC-1 cells, shFOSL1, biol rep 1


title: Liver, oral, 14 days, ST_2

value: water extract of Emilia sonchifolia


title: Liver, oral, 14 days, CK_1


title: H1299 cells, shControl, biol rep 2

value: lung adenocarcinoma cells


title: BPF_D


title: BPF_C


title: B3_output_3

city: Barcelona

first: Antoni

last: Beltran

address: Dr Aiguader, 88

country: Spain

institute: CRG Barcelona

description: genomic and plasmid DNA

data_processing:
DiMSum (Demultiplex with Cutadapt)
DiMSum (QC raw reads with FastQC)
DiMSum (Trim reads with Cutadapt)
DiMSum (Process and analyse variants with DiMSum)
Assembly: NA
Supplementary files format and content: Variant growth rates table: Tabular format; contains the raw counts and dimsum fitness estimates per replicate and aggregated and their corresponding errors.
Library strategy: Amplicon-seq

organism: Saccharomyces cerevisiae

source_name: log phase culture

growth_protocol: BY4741 cells were transformed with the Domainome libraries cloned in the abundancePCA assay plasmid at a coverage of at least 20x and transferred to selective media for ~24h. The resulting cell population was transferred to input media (SC -ura-ade 2% glucose) and grown overnight to an OD of at least 1.6. A small volume of cells was saved to inoculate outputs and the rest of cells were split in two, harvested by centrifugation, and frozen at -20C as input samples. The remainder of cells were then inoculated at an OD=0.05 in selective media (SC -ura-ade+MTX 2% glucose), and grown to an OD=1.6 at which point cells were harvested and stored as output samples as described for the inputs.

extract_protocol:
Cell pellets (one for each experiment input/output replicate) were re-suspended in 1 mL of DNA extraction buffer (2% Triton-X, 1% SDS, 100mM NaCl, 10mM Tris-HCl pH8, 1mM EDTA pH8), and freeze-cracked by liquid nitrogen freezing followed by 62ºC incubation for 10 min in a water bath, twice. Subsequently, 1 mL of Phenol/Chloro/Isoamyl 25:24:1 (equilibrated in 10mM Tris-HCl, 1mM EDTA, pH8) was added, together with 1 g of acid-washed glass beads (Sigma Aldrich) and the samples were vortexed for 10 minutes. Samples were centrifuged at RT for 30 minutes at 4,000 rpm and the aqueous phase was transferred into new tubes. The same step was repeated twice. 0.1 mL of NaOAc 3M and 2.2 mL of pre-chilled absolute ethanol were added to the aqueous phase. The samples were gently mixed and incubated at -20ºC for 30 minutes. After that, they were centrifuged for 30 min at full speed at 4ºC to precipitate the DNA. The ethanol was removed and the DNA pellet was vacuum-dried. DNA pellets were resuspended in 0.6 mL TE 1X and treated with 5 uL of RNaseA (10mg/mL, Thermo Scientific) for 30 minutes at 37ºC. To desalt and concentrate the DNA solutions, QIAEX II Gel Extraction Kit was used (30 μL of QIAEX II beads). The samples were washed twice with PE buffer and eluted in 200 μL of 10 mM Tris-HCI buffer, pH 8.5.
Plasmid concentrations in the total DNA extract (that also contained yeast genomic DNA) were quantified by qPCR using the primer pair oGJJ152-oGJJ153, that binds to the ori region of the plasmids. We performed 2 consecutive PCR reactions for each sample. The first PCR (PCR1) is used to amplify the amplicons for sequencing, to add a part of the Illumina sequencing adaptors to the amplicon and to increase nucleotide complexity for the sequencing reaction by introducing frame-shift bases between the adapters and the sequencing region of interest. The second PCR (PCR2) is used to add the remainder of the Illumina adaptor and to add demultiplexing indexes (dual-indexed). The amplicon libraries were run on a 2% agarose gel for quality control and quantification, and were pooled by block and size selected on a 2% agarose gel. Bands were purified using QIAEX II Gel Extraction Kit (QIAGEN) and using 30uL of QIAEX II beads for each sample. The purified amplicons were subjected to Illumina 150bp paired-end NextSeq sequencing at the CRG Genomics Core Facility.

treatment_protocol: abundancePCA (High-resolution mapping of protein concentration reveals principles of proteome architecture and adaptation, Levy and Michnick, 2014)

tag: strain

value: log phase culture


title: H1299 cells, shControl, biol rep 1


title: PANC-1 cells, shControl, biol rep 2


title: BPF_B


title: H1299 cells, shHDAC2, biol rep 3

value: HDAC2 knockdown


title: H1299 cells, shHDAC2, biol rep 2


title: Cerebrum, P7, female, F1i, m6A-seq, Input

status: Public on Apr 26 2024

first: Ying

last: Zhang

state: Guangdong

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

data_processing:
Preparation of high-confidence SNPs and the N-masked genome were performed using SNPsplit package (v. 0.3.2).
UMIs were extracted using fastp (v.0.21.0)
Read alignment was performed using hisat2(v.2.1.0).
Peak calling was performed using MACS2 (v.2.1.2).
The alignments were split into respective alleles using SNPsplit (v.0.3.2)
Allelically aligned reads for each m6A site were counted by featureCounts (v.1.6.0)
Assembly: mm10
Supplementary files format and content: narrowPeak
Library strategy: m6A-seq

source_name: Cerebrum

extract_protocol:
Tissues were collected and separately homogenized in the presence of TRNzol Universal reagent (TianGen, #DP424).Total RNA was extracted in Trizol reagent following the manufacturer’s protocol. Poly(A)+ RNA was then isolated using Dynabeads mRNA Purification Kit (Invitrogen, #61006).
Synthesized 3′-adapter encoded with 6-nt barcode was pre-adenylated using 5′ DNA Adenylation Kit (NEB, E2610S). 200 ng RNA was fragmented to approximately 150~200 nt using RNA fragmentation reagents (Invitrogen, #AM8740). Fragmented RNA was purified and then repaired using T4 Polynucleotide Kinase (NEB, #M0201S). After cleanup, end-prepared RNA was ligated to adenylated 3′-adapter by T4 RNA Ligase 2, truncated KQ (NEB, #M0373S) incubated at 25 ℃ for 2 h, followed by 4 ℃ overnight. The 3′-adapters with 6-nt barcode and 5'-adapters with 8-nt unique molecular identifier (UMI) were synthesized by Sangon Biotech and Hippo Bio, respectively. To remove redundant adapter, 2 ml of Lambda Exonuclease (NEB, #M0262S) and 1 ml of 5′ Deadenylase (NEB, #M0331S) were added to each ligation mix. The reaction was incubated at 30 ℃ for 30 min, then at 37 ℃ for 30 min and finally 70 ℃ for 10 min to inactivate the enzymes. Subsequently, the samples were pooled to perform cleanup together and 10% of the sample pool was reserved as input sample. Multiplexed m6A immunoprecipitation (IP) was conducted 2 rounds. After immunoprecipitation, input and IP samples were respectively ligated to pre-heated 5′-adapter with T4 RNA Ligase 1 (NEB, #M0204S), and subjected to reverse transcription using HiScript III 1st Strand cDNA Synthesis Kit (Vazyme, #R312-01) and RT primer without cleanup. Library amplification was conducted with KAPA HiFi HotStart ReadyMix (KAPA Biosystems, #KK2601) with the universal primer and the indexed primer.

value: Cerebrum

tag: developmental stage

tag: Sex

value: female

tag: hybrid


title: Cerebrum, P7, female, F1r, m6A-seq, Ip


title: Cerebrum, P0, female, F1r, GLORI

data_processing:
Calling m6A sites was conducted using GLORI-tools (v.1.0; https://github.com/liucongcas/GLORI-tools), with GENCODE (v26; downloaded from https://www.gencodegenes.org/mouse/) as annotation.
Two sets of m6A sites were obtained by using two reference genomes for read mapping: the mm10 (C57 strain) and PWK-mm10 genomes. The PWK-mm10 genome was generated by replacing each SNP site in the mm10 genome with the corresponding base from the PWK genome. Calling m6A sites using this genome could detect PWK-specific adenosines with m6A modification.
m6A sites with a methylation rate > 0.1 and read count > 8 in the union of these two sets were retained for downstream analysis
Assembly: mm10
Supplementary files format and content: bed file includes the identified m6a sites
Library strategy: Glori-seq

extract_protocol:
Tissues were collected and separately homogenized in the presence of TRNzol Universal reagent (TianGen, #DP424).Total RNA was extracted in Trizol reagent following the manufacturer’s protocol. Poly(A)+ RNA was then isolated using Dynabeads mRNA Purification Kit (Invitrogen, #61006).
Glyoxal and nitrite-mediated deamination treatment were conducted on mRNA samples. For library construction, 50 ng of the GLORI-treated RNA sample was firstly repaired and ligated to pre-adenylated 3′-adapter. After the redundant adapter was digested by Lambda Exonuclease (NEB, #M0262S) and 5′ Deadenylase (NEB, #M0331S), the RNA samples were ligated to a pre-heated 5′-adapter without cleanup. Reverse transcription was then carried out using HiScript III 1st Strand cDNA Synthesis Kit (Vazyme, #R312-01) and RT primer. Finally, the library was amplified using Q5 High-Fidelity DNA Polymerases with GC enhancer (NEB, #M0491S) and subjected to size selection using a 6% polyacrylamide gel, retaining fragments longer than 150 nt.

value: GLORI+


title: Cerebellum, P0, female, F1r, GLORI

source_name: Cerebellum

value: Cerebellum


title: Cerebrum, P7, male, F1r, m6A-seq, Ip

value: male


title: DMSO_A


title: Cerebrum, P7, female, F1r, m6A-seq, Input


title: BPS_C


title: Cerebrum, P7, male, F1i, m6A-seq, Ip


title: H1299 cells, shControl, biol rep 3

value: WT


title: Cerebrum, P7, male, F1i, m6A-seq, Input


title: Cerebrum, P7, male, F1r, m6A-seq, Input


title: Cerebrum, P0, female, F1r, m6A-seq, Ip


title: Cerebrum, P0, female, F1i, m6A-seq, Ip


title: BPS_A


title: Cerebrum, P0, female, F1r, m6A-seq, Input


title: Cerebrum, P0, male, F1i, m6A-seq, Input


title: BPF_A


title: Cerebrum, P0, male, F1r, m6A-seq, Input


title: H1299 cells, shHDAC2, biol rep 1


title: Cerebrum, P0, male, F1r, m6A-seq, Ip


title: Cerebellum, P7, female, F1i, m6A-seq, Ip


title: Cerebellum, P7, female, F1r, m6A-seq, Input


title: Cerebrum, P7, female, F1i, m6A-seq, Ip


title: DMSO_B


title: Cerebellum, P0, male, F1r, m6A-seq, Ip


title: Cerebellum, P7, male, F1r, m6A-seq, Input


title: Cerebellum, P7, female, F1i, m6A-seq, Input


title: Cerebellum, P7, male, F1i, m6A-seq, Ip


title: Cerebellum, P7, male, F1i, m6A-seq, Input


title: Cerebellum, P0, male, F1i, m6A-seq, Ip


title: Cerebellum, P0, male, F1i, m6A-seq, Input


title: Cerebrum, P0, female, F1i, m6A-seq, Input


title: Cerebellum, P0, male, F1r, m6A-seq, Input


title: Cerebellum, P7, female, F1r, m6A-seq, Ip


title: Cerebrum, P0, male, F1i, m6A-seq, Ip


title: B16-OVA, 12h, rep1

city: Shenzhen

first: Xuefei

last: Li

address: 1068 Xueyuan Avenue, Shenzhen University Town, Nanshan

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

data_processing:
The raw sequencing reads were trimmed to remove sequences with low quality and short read lengths using Fastp (version 0.20.0). Subsequently, HISAT2 was employed to map the high-quality reads (clean reads) onto the mouse reference genome mm10. The read count matrix corresponding to the genes and samples was generated using featureCounts. Next, we transformed the count matrix into an RPKM matrix to qualify the expression levels with in-house scripts.
Assembly: mm10
Supplementary files format and content: CSV file includes RPKM values for each sample

extract_protocol:
After qualifying the total RNA samples, purification is performed based on the characteristics of mRNA from different sources. Eukaryotic mRNA, which has a polyA tail at the 3' end, is enriched and purified using magnetic beads with oligo(dT).
Fragmentation Buffer is added to the purified mRNA to fragment it into short fragments. Then, using the fragmented RNA as a template, the first-strand cDNA synthesis is achieved through reverse transcription with random primers. The second strand of cDNA is synthesized by adding Second Strand Marking Buffer and Second Strand/End Repair Enzyme Mix. After end repair, addition of base A, and sequencing adapter ligation, the target fragments are recovered by magnetic bead selection and subjected to PCR amplification, thus completing the entire library construction process.  Following library construction, the library is initially quantified using Qubit 3.0 and diluted to 1ng/μl. Subsequently, the insert size of the library is detected using Agilent 2100. Once the insert size meets expectations, accurate quantification of the effective concentration of the library is performed using a Bio-RAD CFX 96 fluorescence quantitative PCR instrument and Bio-RAD KIT iQ SYBR GRN for Q-PCR. This ensures precise quantification of the library's effective concentration (>10 nM) to guarantee library quality.

value: Melanoma

value: OVA

value: B16-F10 overexpressing ovalbumin by lentivirus infection


title: OT-1-T, 12h, rep1

source_name: spleen

value: spleen

value: OT-I

value: CD8+ T lymphocytes

value: OT-1 activated, co-culture with B16-WT cancer cells for 12h


title: OVA-OT-1-T, 12h, rep2

value: OT-1 activated, co-culture with B16-OVA cancer cells for 12h


title: OVA-OT-1-T, 12h, rep1


title: B16cancer, scRNA, 12h

data_processing:
Raw data (Raw Reads) of fastq files were assembled from the Raw BCL files using Illumina’s bcl2fastq converter. For Raw data, firstly processed through primary quality control. The monitored quality assessment parameters were, (i) contain N more than 3; (ii) the proportion of base with quality value below 5 is more than 20%; (iii) adapter sequence. All the downstream analyses were based on the clean data with high quality.
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger) using default parameters.
Assembly: mm10-2020-A
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

extract_protocol:
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics), according to the manufacturer’s instructions.
Cells were captured in droplets at a targeted cell recovery of cells. After the reverse transcription step, emulsions were broken and Barcoded-cDNA was purified with Dynabeads, followed by PCR amplification. Amplified cDNA was then used for 3’gene expression library construction. For gene expression library construction, 50 ng of amplified cDNA was fragmented and end-repaired, double-size selected with SPRIselect beads, and sequenced on an NovaSeq platform (Illumia) to generate 150 bp paired-end Reads.

treatment_protocol: Prepare the sample into single-cell suspension, requiring uniform cell size and less than 5% cell clusters and fragments. Use Countess® II Automated Cell Counter for cell counting and viability assessment, requiring cell viability ≥85%, cell concentration, and total count ≥1×10^6 cells/mL.


title: B16-OVA, 12h, rep2


title: B16ctl, scRNA, 12h


title: OVActl, scRNA,12h


title: Cerebellum, P7, male, F1r, m6A-seq, Ip


title: B16-WT, 12h, rep1


title: OT-1-T, 12h, rep2


title: B16-WT, 12h, rep2


title: OVA-OT-1-T, 6h, rep2

value: OT-1 activated, co-culture with B16-OVA cancer cells for 6h


title: OVA-OT-1-T, 6h, rep1


title: Zebrafish, RNAseq, high dose, dsRNA1

city: Qingdao

first: tong

last: lu

address: 72, binghai rd

institute: ShanDong University

description:
dsR1
high-doseun-VS-dsR_DE_anno.txt
RNAseq-high dose-all.fpkm_anno.txt

data_processing:
Each library was amplified by a 11-cycle PCR, and 150 bp paired-end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data.
Differential expression was calculated with DESeq2 and edgeR.
Assembly: GRCz10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C

extract_protocol:
Total RNAs were extracted from 6 hpf embryos using TRIzol reagent (Invitrogen), and were precipitated by cold isopropanol (50%, v/v) in the presence of carrier glycogen (20 µg/each sample). Polyadenylated mRNAs were purified by the poly(A) mRNA Magnetic Isolation Module (NEB).
The mRNA libraries were then generated using NEBNext Ultra RNA Library Prep Kit for lllumina following manufacturer’s instruction. Briefly, mRNA fragmentation and priming were carried out via NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. ProtoScript II Reverse Transcriptase and Second Strand Synthesis Enzyme Mix were used to synthesize first and second strand cDNAs. AxyPrep Mag PCR Clean-up (Axygen) kit were then used to purify the cDNAs. After that, cDNAs were treated with End Prep Enzyme Mix to repair 3’ and 5’ ends, followed by dA-tailing and adaptor ligation. Following size selection by AxyPrep Mag PCR Clean-up (Axygen) kit, fragments haboring around 300 bp inserts were recovered.

treatment_protocol: Zebrafish embryos injected with dsRNA were maintained in 1/3x Ringer's at 28.5C

value: whole embryo

value: 50% epi stage

value: embryonic cell

value: wild type

value: dsRNA


title: Zebrafish, RNAseq, high dose, dsRNA3

description:
dsR3
high-doseun-VS-dsR_DE_anno.txt
RNAseq-high dose-all.fpkm_anno.txt


title: Zebrafish, RNAseq, high dose, dsRNA2

description:
dsR2
high-doseun-VS-dsR_DE_anno.txt
RNAseq-high dose-all.fpkm_anno.txt


title: OT-1-T, 6h, rep1

value: OT-1 activated, co-culture with B16-WT cancer cells for 6h


title: OT-1-T, 6h, rep2


title: Zebrafish, RNAseq, high dose, uninj1

description:
un1
high-doseun-VS-dsR_DE_anno.txt
RNAseq-high dose-all.fpkm_anno.txt

value: uninjected


title: Zebrafish, RNAseq, high dose, uninj2

description:
un2
high-doseun-VS-dsR_DE_anno.txt
RNAseq-high dose-all.fpkm_anno.txt


title: B16-OVA, 6h, rep2


title: Zebrafish, RNAseq, low dose, dsRNA3

description:
dsR3
low-dose-un-VS-dsR_DE_anno.txt
RNAseq-low dose-all.fpkm_anno.txt


title: Zebrafish, RNAseq, high dose, uninj3

description:
un3
high-doseun-VS-dsR_DE_anno.txt
RNAseq-high dose-all.fpkm_anno.txt


title: OVAcancer, scRNA, 12h

value: B16-10 overexpressing ovalbumin by lentivirus infection


title: Zebrafish, RNAseq, low dose, dsRNA2

description:
dsR2
low-dose-un-VS-dsR_DE_anno.txt
RNAseq-low dose-all.fpkm_anno.txt


title: Zebrafish, RNAseq, low dose, dsRNA1

description:
dsR1
low-dose-un-VS-dsR_DE_anno.txt
RNAseq-low dose-all.fpkm_anno.txt


title: B16-WT, 6h, rep1

value: Melanoma

value: WT


title: B16-WT, 6h, rep2


title: Zebrafish, RNAseq, low dose, uninj3

description:
un3
low-dose-un-VS-dsR_DE_anno.txt
RNAseq-low dose-all.fpkm_anno.txt


title: CTLs, 0h, rep2

value: OT-1 activated, co-culture 0h


title: B16-OVA, 0h, rep1

value: OVA

value: B16-F10 overexpressing ovalbumin by lentivirus infection


title: Zebrafish, RNAseq, low dose, uninj2

description:
un2
low-dose-un-VS-dsR_DE_anno.txt
RNAseq-low dose-all.fpkm_anno.txt


title: Zebrafish, RNAseq, low dose, uninj1

description:
un1
low-dose-un-VS-dsR_DE_anno.txt
RNAseq-low dose-all.fpkm_anno.txt


title: B16-WT, 0h, rep2


title: B16-OVA, 0h, rep2


title: B16-OVA, 6h, rep1


title: B16-WT, 0h, rep1


title: PGC rep2

city: Bron

first: Clémence

last: Kress

address: 18 avenue du Doyen Lépine

country: France

institute: INRAE, Inserm

data_processing:
Basecalls were performed using bcl2fastq-1.8.4.Quality control was performed on fastq files using the MultiQC 1.7 software.
Reads were mapped to the transcriptome using TopHat associated with Bowtie.
Read count was performed using FeatureCounts.
Differential gene expression analysis was performed using the DESeq2 R package.
Assembly: Gallus_gallus-5.0
Supplementary files format and content: raw counts for all samples (csv format)
Supplementary files format and content: differential gene expression analysis results including fold change (PGC vs ESC), p-values and adjusted counts (csv format)

organism: Gallus gallus

source_name: primordial germ cells

extract_protocol:
Total RNA was extracted using TRIzol reagent.
Libraries were prepared from total RNA according to the Illumina procedure by Eurofins Genomics (https://www.eurofinsgenomics.eu/).

value: primordial germ cells


title: PGC rep3


title: Beta 23 9/13 CR0001 Starting rep2

city: Beachwood

first: Trailhead

last: Biosystems

state: Ohio

address: 23215 Commerce Park Rd

institute: Trailhead Biosystems Inc

data_processing:
processed the raw data with nextflow nf-core/rnaseq (v 3.6) pipeline, with default parameters. Netxflow version 22.05.0-edge.5704.
Trim Galore (v.0.6.7) was used for adaptor trimming and quality control
STAR (v 2.6.1) was used for alignment and counting within nf-core/rnaseq pipeline
Assembly: GRCh38
Supplementary files format and content: Tab delimited raw count files for each sample

source_name: hiPSC

growth_protocol: Cells were maintained in E8 medium on vitronectin coated 6 well plate and dissociated with TrypLE to be seeded in bioreactors for a 2day growth protocol. The bioreactor had E8 medium and the treated bioreactor had E8 medium + PEG + Heparin

extract_protocol:
RNA was qualified using Qubit™ RNA BR Assay Kit. Isolated RNA's quality validated with 4200 TapeStation System.
Library preparation done with Illumina Stranded mRNA Prep.

treatment_protocol: After 2 days of seeding iPSCs , differentiation was started using the differentiation protocol indicated in manuscript. The treatment included seeding single cells in a vertical wheel 100ml bioreactor

value: hiPSC

value: Pluripotent stem cell

value: Wild Type

value: iPSC


title: EN5 Mice study 9/21 rep3

value: Pancreatic beta cell

value: Bioreactor


title: EN5 Mice study 9/21 rep4


title: Beta 23 9/13 CR0001 Starting rep1


title: EN5 Mice study 9/21 rep1


title: Beta 23 Harvest CR0001 Plate CDM2 rep3

value: Adherent Control


title: Beta 23 Harvest CR0001 Plate CDM2 rep1


title: ESC rep2

source_name: embryonic stem cells

value: embryonic stem cells


title: Beta 23 Harvest CR0001 Plate CDM2 rep2


title: CTLs, 0h, rep1

value: spleen

value: OT-I

value: CD8+ T lymphocytes


title: Lrp10 KO, CD8+ TILs, paired single cell TCR seq

city: Dallas

first: Evan

last: Nair-Gill

state: Texas

address: 5323 Harry Hines Blvd

department: Center for the Genetics of Host Defense

institute: UT Southwestern Medical Center

description:
KO_TCR
10XGenomics

library_source: other

data_processing:
*library strategy: scTCR-seq
scRNAseq FASTQ files were processed with Cell Ranger v. 7.1.0 (10x Genomics) using default settings for 5’ RNA gene expression analysis. scTCRseq files were processd with Cell Ranger V(D)J v7.1.0 using Single Cell V(D)J-T (alpha Beta) and default settings.
Assembly: mm10 (scRNAseq), and Mouse (GRCm38) v7.0.0 (scTCRseq)
Supplementary files format and content: Tab separated CVS tables and matrix files

molecule: other

source_name: MC38 tumors

extract_protocol:
1.5 x 10^4 live CD8 T cells were FACS sorted from dissociated D12 MC38 tumors.
scRNAseq and scTCRseq libraries were generated using the Chromium Next GEM Single Cell 5’ kit (10X Genomics) according to the manufacturer’s protocol. Purified libraries sequenced together on one S4 lane of a NovaSeq sequencing instrument with the run configuration 150x10x10x150

value: CD8+ tumor infiltrating lymphocytes

value: Lrp10 KO

value: MC38 tumors


title: Lrp10 KO, CD8+ TILs

description:
KO
10XGenomics

data_processing:
scRNAseq FASTQ files were processed with Cell Ranger v. 7.1.0 (10x Genomics) using default settings for 5’ RNA gene expression analysis. scTCRseq files were processd with Cell Ranger V(D)J v7.1.0 using Single Cell V(D)J-T (alpha Beta) and default settings.
Assembly: mm10 (scRNAseq), and Mouse (GRCm38) v7.0.0 (scTCRseq)
Supplementary files format and content: Tab separated CVS tables and matrix files


title: Lrp10 WT, CD8+ TILs, paired single cell TCR seq

description:
WT_TCR
10XGenomics

value: Lrp10 WT


title: Beta 23 9/13 CR0001 Starting rep3


title: Lrp10 WT, CD8+ TILs

description:
WT
10XGenomics


title: Mouse2_PulmonaryEpithelialCell_BioRep2

city: San Francisc

first: David

last: Julius

state: CA

institute: UCSF

data_processing:
Quality was checked with fastqc and adapter/low quality reads were trimmed with Cutadapt via TrimGalore
Assembly: mm10 containing exogenous sequence for tdTomato
Supplementary files format and content: Reads were aligned to reference genome using StarAlign
Supplementary files format and content: Processed data file is a normalized read count for each sample, which was generated using rsem-calculate-expression function of RSEM-1.3.3 in Rstudio

source_name: Lung

extract_protocol:
Cells were sorted directed into Takara Smart Seq lysis buffer and then flash frozen. See Seeholzer and Julius 2024 for further details.
We performed cDNA synthesis with Smart-Seq v4 kit according to the protocol recommendatioons (Takara Bio, 634890). cDNA library was generated by using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024).  See Seeholzer and Julius 2024 for further details.

value: Lung

value: EpCam+/tdTomto- Cell

value: tamoxifen


title: Mouse1_PulmonaryEpithelialCell_BioRep1


title: WHIM6_mouse passage A [re-analysis]

type: RNA

city: st louis

first: Cynthia

last: Ma

state: Missouri

address: 4515 Mckinley, 4515 Mckinley

department: Medical Oncology

institute: Washington University

description:
re-analysis of GSM4486594
HIM_6A

hyb_protocol: Agilent 60-mer oligo microarray processing protocol

scan_protocol: Microarrays were scanned with an Agilent Scanner.

data_processing: txt files from Agilent Feature Extraction software were loaded into the UNC-CH Microarray Database. Final loess, normalized log2 ratios (Cy5-sample/Cy3-control) for each probe were retrieved.

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

label_protocol: Agilent Low Input Linear Amplification Kit and protocol

extract_protocol: Trizol extractions followed by Dnase treatment and column purification.

value: Total RNA from 10 human cell lines:1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte.  Also, mRNA spiked in from MCF7 and ME16C.

tag: molecule type

value: Generated labeled cRNA from reference sample

source_name: WU PDX WHIM6_passage A

tag: tissue type

value: xenograft

value: oct block from human:mouse xenograft which contained at least 50% tumor cellularity

value: Total RNA from which cy5 labeled cRNA was generated


title: WHIM6_mouse passage C [re-analysis]

description:
re-analysis of GSM4486595
HIM_6C

source_name: WU PDX WHIM6_passage B


title: Mouse2_PulmonaryNE_BioRep2

value: tdTomato+ Cell


title: Mouse3_PulmonaryNE_BioRep3


title: WHIM6_mouse passage E [re-analysis]

description:
re-analysis of GSM4486596
HIM_6E

source_name: WU PDX WHIM6_passage E


title: Mouse1_PulmonaryNE_BioRep1


title: WHIM52_mouse passage C

source_name: WU PDX WHIM52_passage C


title: R-4

first: Yubo

last: Hu

address: 74 Zhongshaner Rd

data_processing:
Library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated
clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Assembly: GRCm38.100   Mus musculus
Supplementary files format and content: tab-delimited text file includes counts for each Sample

source_name: brain

extract_protocol:
RNA was extracted using RNeasy Micro Kit following the manufacturer's protocols
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations

value: brain

value: retrieval


title: R-3


title: WHIM4_mouse passage E [re-analysis]

description:
re-analysis of GSM4486588
HIM_4E

source_name: WU PDX WHIM4_passage E


title: R-2


title: Mouse3_PulmonaryEpithelialCell_BioRep3


title: R-1


title: non-R-4

value: non-retrieval


title: non-R-3


title: non-R-2


title: non-R-1


title: 3MO MPP #2

city: Austin

first: Lauren

last: Ehrlich

state: TX

address: Neural and Molecular Sciences building

institute: University of Texas at Austin

data_processing:
Data processed using Nextflow, steps described below: https://github.com/nf-core/rnaseq
QC performed with FastQC
UMI extraction with UMI-tools
Adapter and quality trimming with Trim Galore!
Removal of genome contaminants with BBSplit and removal of ribosomal RNA with SortMeRNA
Alignment and quantification with STAR > Salmon
Additional quality control and differential expression analysis with DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files (all samples in a single file) showing gene-level TPM

source_name: Bone marrow

extract_protocol:
Total RNA was extracted using Direct-zol RNA Microprep kit (Zymo Research). 32ng ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared at the University of Texas Genomic Sequencing and Analysis Facility according to manufacturer’s instructions for the NEBNext Ultra II Direction RNA kit (NEB, product number E7760).

value: Bone marrow

value: Flk2+ MPPs

value: WT


title: 3MO MPP #3


title: 3MO CLP #3

value: Ly6d- CLPs


title: 3MO CLP #2


title: 3MO CLP #1


title: 3MO MPP #1


title: 1MO MPP #3


title: resistant e6 bio rep 2

city: Brasília

first: Camila

middle: Maurmann

last: de Souza

state: Distrito Federal

address: QS 07, Lote 01, Taguatinga Sul

department: Biotechnology

country: Brazil

institute: Universidade Católica de Brasília

data_processing:
The quality of raw reads was assessed using FastQC.
The RNA reads were align using Bowtie2.
The counts were generated using HTseq.
Assembly: kp03  acession numbers SAMN41007404, SAMN41007405, and SAMN41007406
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Klebsiella pneumoniae

source_name: lineage e6 rep 2

extract_protocol:
RNA was extracted using Rneasy Mini Kit (Qiagen)
The libraries were generated using Stranded Total RNA Prep with Ribozero (Illumina)  following manufacture’s protocol.

value: lineage e6 rep 2

value: bacteria culture

value: resistant

value: amikacin and polymyxin B


title: resistant e6 bio rep 3

source_name: lineage e6 rep 3

value: lineage e6 rep 3


title: 1MO MPP #1


title: 1MO MPP #2


title: 1MO CLP #3


title: resistant e6 bio rep 1

source_name: lineage e6 rep 1

value: lineage e6 rep 1


title: control c1 bio rep 2

source_name: lineage c1 bio rep 2

value: lineage c1 bio rep 2

value: susceptible


title: control c1 bio rep 1

source_name: lineage c1 bio rep 1

value: lineage c1 bio rep 1


title: control c1 bio rep 3

source_name: lineage c1 bio rep 3

value: lineage c1 bio rep 3


title: WHIM4_mouse passage D [re-analysis]

description:
re-analysis of GSM4486587
HIM_4D

value: Total RNA from 10 human cell lines:1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte.  Also, mRNA spiked in from MCF7 and ME16C.

value: Generated labeled cRNA from reference sample

source_name: WU PDX WHIM4_passage D

value: xenograft

value: oct block from human:mouse xenograft which contained at least 50% tumor cellularity

value: Total RNA from which cy5 labeled cRNA was generated


title: 1MO CLP #2

value: Bone marrow

value: WT


title: 1MO CLP #1

value: Ly6d- CLPs


title: snRNA-seq KO

city: Ann Arbor

first: Xiaoxue

last: Qiu

state: MI

address: 210 Washtenaw

department: Life Sciences Institute

institute: University of Michigan

description:
ko
ave.UMI_snliver_integrated.txt

data_processing:
FastQC was used to asses the sequencing qualtiy on fastq files; STAR was used for alignment to generate bam files; The reads aligned to each gene feature were counted by Rsubread package (version 2.0.1); DESeq2 pacakge was used for differential gene expression analysis
snRNA-seq fastq files were processed by CellRanger to generate aligned matrix data that were further analyzed using Seurat package (version 4.0.1).
Assembly: mm10
Supplementary files format and content: DEseq2 normalized reads counts for bulk RNA-seq data
Supplementary files format and content: average UMI counts for snRNA-seq data

source_name: Liver, NASH diet, 22 weeks, three liver samples pooled

extract_protocol:
Nuclei were isolated from frozen liver tissues using salt-Tris based protocol. Isolated nuclei were stained with propidium iodide before FACS sorting. Sorted nuclei were processed for snRNA sequencing. Total liver RNA was extracted from frozen tissues using RNA extract kit (Invitrogen, Cat: 12183025)
Bulk RNA libraries were prepared using high-throughput sequenicng set following the user manual; snRNA libraries were prepared using standard Illumina and 10X genomics Chromium single cell guide

value: liver tissue

value: Ms4a7 KO

value: NASH diet for 22 weeks


title: snRNA-seq WT

description:
wt
ave.UMI_snliver_integrated.txt

value: wild type


title: mycelia - N1617GFP-eed_Input

city: Hangzhou

first: mengting

last: xu

state: ZheJiang

address: Zhejiang University

institute: mengtingxu

data_processing:
High-throughput sequencing was carried out using Illumina Hiseq-PE150 by Novogene Corporation (Beijing, China) for Illumina (Langmead et al., 2009).
The clean read pairs were mapped to the reference genome with Bowtie2 (Version 2.3.5) (Langmead and Salzberg, 2012)
Enriched peaks were called by HOMER (Version 4.9.1) with default parameters (Heinz, 2010).
Assembly: MG8
Supplementary files format and content: peak text files
Supplementary files format and content: bedGraph

organism: Pyricularia oryzae

growth_protocol: The Pyricularia oryzae strains were grown on CM medium at 28℃ in the dark for 2 days, followed by growth under continuous lights for 5 days. Then taking 10-12 pieces of mycelia and culture them in liquid CM medium for 2 days.The mycelia were harvested by 2-3 layers of Miracloth.

extract_protocol:
The ChIP experiments with mycelia cultured in liquid CM for 2 days were conducted as previous reports with minor modification (He et al., 2018; Tao et al., 2017). Briefly, 1.0 g mycelia were crosslinked with 1% formaldehyde for 20 mins and stopped with 125 mM glycine for 5 mins at room temperature. Samples were ground with liquid nitrogen and resuspended in nuclei isolating buffer. Subsequently the precipitated nuclei were used to total chromatin extraction with 1mL lysis buffer. The lysis chromatin was sonicated into DNA fragments between 200-500 bp using Diagenode Bioruptor. 20μL chromatin was used to input DNA extraction and the remainder was pre-cleared with 10μL protein A Dynabeads (Thermofisher, 10001D) for 1 hour. Subsequently the chromatin was incubated with anti-H3K27me3 (Abcam, ab6002) or anti-H3K4ac (Active Motif, 39381) overnight at 4°C. Another 20μL protein A Dynabeads was used capture protein-DNA mixture and followed by three washing. Protein-DNA mixture was reverse-crosslinked, and DNA was recovered with phenol-chloroform extraction. The recovery DNA was used as template for followed ChIP-qPCR and ChIP-seq. Two biological repeats were conducted.
The purified DNA was used as libraries construction with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L).

treatment_protocol: The mycelia were crosslinked with 1% formaldehyde for 20 mins and stopped with 125 mM glycine for 5 mins at room temperature.

value: mycelia

value: complement

value: GFP


title: mycelia - N1617GFP-eed_rep2_IP


title: mycelia - N1617GFP-eed_rep1_IP


title: mycelia - N1617GFP-eed_rep3_IP


title: WHIM6_human counterpart [re-analysis]

description:
re-analysis of GSM4486597
HIM_6Hu

source_name: WU WHIM6_human counterpart tumor

value: oct blocks from biopsy which contained at least 50% tumor cellularity


title: WHIM4_human counterpart [re-analysis]

description:
re-analysis of GSM4486589
HIM_4Hu

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: WU WHIM4_human counterpart tumor


title: mycelia - N1617GFP-ash1_rep1_IP


title: ATAC-seq_MCD rep 1

city: Madison

first: Jeffrey

last: Dilworth

state: Wisconsin

address: 1111 Highland Ave

institute: University of Wisconsin

data_processing:
Quality-control with FastQC
Adapters were trimmed from quality-controlled paired-end reads with Cutadapt v2.6;
Reads were aligned to mm10 using Bowtie2 v2.4.4; BigWigs were generated using BamCoverage (deeptools v3.5.1);
Peaks were called using MACS3 v3.0.0;
Differential peaks were found using DiffBind (R 4.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: BigWigs (.bw) as a .tar.gz file - Counts per million (CPM) normalization; differential peaks (.csv)

source_name: RAW  267.4 macrophagte

extract_protocol:
50,000 RAW 267.4 macrophages were lysed in the presence of 10 mM NaCl 0.1% IGEPAL CA-630. Tagementation was performed usign TDE1 transposase as per manufacturer recommendations.Tagmented DNA was prepared using Zymo-spin concentrator 5 columns
Purified tagmented DNA was amplified with KAPA HIFI polymerase (12 PCR cycles) and Unique Dual Primers from Illumina (Cat number 20332088). Size-selection (L:1.1; R :0.6) was performed with KAPA Pure beads and size distribution of the final libraries was assessed on bioanalyzer (Agilent). Libraries were quantified by qPCR and loaded equimolarly on a S4 Novaseq flowcell. Each library was sequenced with a coverage of 50M paired-end reads (PE100).

treatment_protocol: RAW 267.4 macrophage cells were maintained in DMEM supplemented with 10% FCS at 37 °C in a 5% CO2 incubator. Cells were treated with MCD (5 mM) in 1 mg/ml BSA for 1 hour.

value: tissue culture

value: macrophages

value: MCD


title: ATAC-seq_ctl rep 1

growth_protocol: RAW 267.4 macrophage cells were maintained in DMEM supplemented with 10% FCS at 37 °C in a 5% CO2 incubator.


title: statin LPS rep 2

data_processing:
Read alignment to mm10 was performed with STAR v2.5.3;
HTSeq v0.9.1 was used for transcript quantification;
DESeq2 v1.18.1 was used for differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq counts + tabluar format with DESeq2 output

source_name: RAW macrophages

extract_protocol:
Total RNA was isolated using a total RNA isolation kit (ThermoFisher cat. No. 12183020)
Total RNA (approx. 350 ng per sample) underwent rRNA depletion with a Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat) (Illumina cat. No. MRZG12324). RNA library preparation proceeded with a KAPA stranded RNA-seq kit (roche 07962169001-KAPA KK8401). Fragmentation/1st strand / 2nd strand end-repair and A-tailing steps proceeded, followed with ligation to  Illumina TruSeq LT Indexes (Illumina FC-121-2001 / FC-121-2002) followed by 8 cycles of PCR enrichment.

treatment_protocol: RAW 267.4 macrophage cells were maintained in DMEM supplemented with 10% FCS at 37 °C in a 5% CO2 incubator. Cells were treated with MCD (5 mM) in 1 mg/ml BSA for 1 hour or statin (7 υM) plus lipoprotein deficient serum (LPDS).  For LPS, cells were stimulated with 100 ng/ml LPS in DMEM supplemented with 1 mg/ml BSA for 3 h.

value: RAW macrophages

value: statin + LPS


title: ATAC-seq_MCD rep 2


title: statin LPS rep 1


title: ATAC-seq_ctl rep 2


title: mycelia - N1617GFP-ash1_Input


title: mycelia - N1617GFP-ash1_rep3_IP


title: mycelia - N1617GFP-ash1_rep2_IP


title: Figure 7-8,Dual tumor model,  T-Platin-M-NP+T-Mito-DCA-NP 3 [Brain_408]

city: Miami

first: Shanta

last: Dhar

state: Florida

address: 1011 NW 15th Street, Room 437

department: Biochemistry

institute: University of Miami

description:
Figure 7-8 cluster_fpkm-whole genome-average data-raw file.csv
figure 7-8 ALL_FPKM.csv

data_processing:
Quality Control and adapter trimming was performed with FastQC and fastp. The filtered clean reads were mapped to reference genome by HISAT2. HTseq-count was used to quantify transcripts and gene expression levels using mapped reads’ positional information on the reference genome and we used DESeq to analyze the Differentially Expressed Genes (DEGs) for samples with biological replicates. Functional annotation for DEGs was performed with HMMER, DIAMOND, EggNOG-mapper, clusterProfiler and KofamKOALA. Gene Ontology (GO) and Kyoto Encycloepedia of Genes and Genomes (KEGG) analysis was done with clusterProfiler and KofamKOALA.
Assembly: hg38
Supplementary files format and content: Text file include raw counts and fpkm for each sample or Z score values

source_name: Cancer cells

growth_protocol: MDA-MB-231-BR cells were grown in DMEM media supplimented with 10% fetal bovine serum(FBS) and antibiotics in 5% CO2 atmosphere at 37 C. Animals care and handling was followed in accordance with the guide for the care and use of laboratory animals of American association of accreditation of laboratory animal care( AAALAC)  after the experimenta protocol was approved by Institutional Animal Care  and Use Committe(IACUC).

extract_protocol:
RNeasy Mini Kit
Total RNA proceeds to library construction. The Poly-A containing mRNA molecules are purified using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA. Adapter ligation prepares the ds cDNA for hybridization onto a flow. The products are enriched with PCR and purified to create the final cDNA library. Final library was quantified and library quality was evaluated by TapeStation D1000 ScreenTape. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina NovaSeq S4 with a read length configuration of 150 PE for 20M PE reads per sample (20M in each direction)
TruSeq Stranded mRNA Library

treatment_protocol:
MDA-MB-231-BR cells were treated with cisplatin (10 μM) and T-Platin-M-NP (10 μM  with repsct to Platin-M) and trypsinized and pellets were used for sequencing.
The single tumor mouse model was established using MDA-MB-231-BR cells which where implanted subcutaneously in the right flank of the mice. The treatment groups were saline, cisplatin at a dosage of 5 mg/kg, T-Platin-M-NPs (10 mg/kg with respect to Platin-M), 2-DG (10 mg/kg ) or a combination of T-Platin-M-NPs (at a dosage of 10 mg/kg with respect to Platin-M) and 10 mg/kg of 2-DG, respectively. 2-DG was injected 24 h post T-Platin-M-NP injection in the combiantion group. All the test articles were injected twice weekly for 3 weeks via tail i.v. route.
The dual tumor mouse model was established using MDA-MB-231BRLuc cells where the primary tumor was implanted subcutaneously in the right flank of the mice and once the primary tumor was established, the secondary tumor was implanted in the brain orthotopically via stereotactic intracranial injection. The treatment groups were saline, cisplatin  at a dosage of 5 mg/kg, and a combination of T-Platin-M-NPs + T-Mito-DCA-NPs at a dosage of 10 mg/kg with respect to Platin-M and 30 mg/kg with respect to Mito-DCA, respectively. T-Mito-DCA-NPs were injected 24 h post T-Platin-M-NP injection. All the test articles were injected twice weekly for 3 weeks via tail i.v. route.

value: Cancer cells

value: Breast cancer brain metastasis

value: Luciferase tagged

value: T-Platin-M-NP and T-Mito-DCA-NP


title: WHIM3_mouse passage C [re-analysis]

description:
re-analysis of GSM4486583
HIM_3C

value: Total RNA from 10 human cell lines:1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte.  Also, mRNA spiked in from MCF7 and ME16C.

value: Generated labeled cRNA from reference sample

source_name: WU PDX WHIM3_passage C

value: xenograft

value: oct block from human:mouse xenograft which contained at least 50% tumor cellularity

value: Total RNA from which cy5 labeled cRNA was generated


title: WHIM4_mouse passage C [re-analysis]

description:
re-analysis of GSM4486586
HIM_4C

source_name: WU PDX WHIM4_passage C


title: ctl LPS rep 2

value: LPS


title: WHIM34_human counterpart [re-analysis]

description:
re-analysis of GSM4486604
HIM_34Hu_Redo

source_name: WU WHIM34_human counterpart tumor


title: WHIM12_human counterpart [re-analysis]

description:
re-analysis of GSM4486565
HIM_12Hu

source_name: WU WHIM12_human counterpart tumor


title: ctl LPS rep 1


title: Figure 7-8,Dual tumor model,  T-Platin-M-NP+T-Mito-DCA-NP 2 [TNP2_406]


title: WHIM3_mouse passage B [re-analysis]

description:
re-analysis of GSM4486582
HIM_3B

source_name: WU PDX WHIM3_passage B


title: WHIM3_mouse passage A [re-analysis]

description:
re-analysis of GSM4486581
HIM_3A

source_name: WU PDX WHIM3_passage A


title: WHIM29_mouse passage A [re-analysis]

description:
re-analysis of GSM4486611
HIM_29A

source_name: WU PDX WHIM29_passage A


title: WHIM10_mouse passage A [re-analysis]

description:
re-analysis of GSM4486560
HIM_10A

source_name: WU PDX WHIM10_passage A


title: Figure 7-8, Dual tumor model,  Cisplatin 3 [CP3_407]

value: Cisplatin


title: WHIM4_mouse passage A [re-analysis]

description:
re-analysis of GSM4486585
HIM_4A

source_name: WU PDX WHIM4_passage A


title: WHIM29_human counterpart [re-analysis]

description:
re-analysis of GSM4486612
HIM_29Hu

source_name: WU WHIM29_human counterpart tumor

value: oct blocks from biopsy which contained at least 50% tumor cellularity


title: WHIM10_mouse passage D [re-analysis]

description:
re-analysis of GSM4486562
HIM_10D

source_name: WU PDX WHIM10_passage D


title: Figure 7-8, Dual tumor model,  Cisplatin 2 [CP2_401]


title: WHIM10_mouse passage C [re-analysis]

description:
re-analysis of GSM4486561
HIM_10C

source_name: WU PDX WHIM10_passage C


title: Figure 7-8,Dual tumor model,  T-Platin-M-NP+T-Mito-DCA-NP 1 [TNP_412]


title: WHIM29_mouse passage B [re-analysis]

description:
re-analysis of GSM4486607
HIM_29B

source_name: Stratagene Human Universal Reference spiked with MCF7 and  ME16C mRNA

source_name: WU PDX WHIM29_passage B


title: statin rep 2

value: tissue culture

value: statin


title: WHIM34_mouse passage E [re-analysis]

description:
re-analysis of GSM4486598
HIM_34E

source_name: WU PDX WHIM34_passage E


title: Figure 7-8, Dual tumor model,  Cisplatin 1 [CP1_404]


title: statin rep 1

source_name: RAW macrophages


title: Ctrl rep 2


title: Ctrl rep 1


title: Figure 7-8, Dual tumor model,  Saline 2 [Sal2_458]

source_name: Cancer cells

value: Control


title: MCD-LPS rep2

value: RAW macrophages

value: MCD + LPS


title: Figure 7-8, Dual tumor model,  Saline 1 [Sal1_411]

value: Cancer cells


title: MCD-LPS rep1


title: LPS rep 2


title: Figure 4, Single tumor model, T-Platin-M-NP+2-DG 3 [('sample15,NP+2-DG,Perturbation')]

description: Figure 4 z -score values.xlsx

value: Breast cancer brain metastasis

value: WT

value: T-Platin-M-NP and 2-DG


title: WHIM34_mouse passage A [re-analysis]

description:
re-analysis of GSM4486603
HIM_34A

value: Total RNA from 10 human cell lines:1_Adenocarcinoma, mammary gland 2_Hepatoblastoma, liver 3_Adenocarcinoma, cervix 4_Embryonal carcinoma, testis 5_Glioblastoma, brain 6_Melanoma 7_Liposarcoma 8_Histiocytic Lymphoma; macrophage; histocyte 9_ Lymphoblastic leukemia, T lymphoblast 10_Plasmacytoma; myeloma; B lymphocyte.  Also, mRNA spiked in from MCF7 and ME16C.

source_name: WU PDX WHIM34_passage A


title: WHIM12_mouse passage C [re-analysis]

description:
re-analysis of GSM4486564
HIM_12C

value: Generated labeled cRNA from reference sample

source_name: WU PDX WHIM12_passage C


title: Figure 4, Single tumor model, T-Platin-M-NP 3 [('sample12,NP,Perturbation')]

description: Figure 4 z -score values.xlsx

value: T-Platin-M-NP


title: MCD rep 2

value: MCD


title: Figure 4, Single tumor model, T-Platin-M-NP+2-DG 1 [('sample13,NP+2-DG,Perturbation')]

description: Figure 4 z -score values.xlsx


title: LPS rep 1


title: Figure 4, Single tumor model, T-Platin-M-NP 2 [('sample11,NP,Perturbation')]

description: Figure 4 z -score values.xlsx


title: ctl rep2


title: ctl rep1


title: MCD rep 1


title: WHIM3_mouse passage E [re-analysis]

description:
re-analysis of GSM4486584
HIM_3E

source_name: WU PDX WHIM3_passage E

value: xenograft

value: oct block from human:mouse xenograft which contained at least 50% tumor cellularity

value: Total RNA from which cy5 labeled cRNA was generated


title: Figure 4, Single tumor model, T-Platin-M-NP 1 [('sample10,NP,Perturbation')]

description: Figure 4 z -score values.xlsx


title: WHIM52_mouse passage A

source_name: WU PDX WHIM52_passage A


title: MKP PD DT rep2

city: Munich

first: Anne

last: Dueck

state: Bavaria

address: Biedersteiner Str.29

department: Institute of Pharmacology and Toxicology

country: Germany

institute: TUM

data_processing:
Single-read 75 cycles (SR75) run was performed using a SP flowcell. Cluster generation and sequencing were operated under the control of the NovaSeq® Control Software (NVCS) v1.7.0
CLC Genomics Workbench 20.0.4 (CLC bio, a Qiagen company) was used for read mapping and analysis of differential gene expression
Reads were mapped against GRCm38.p4 using CLC Genomics Workbench (Qiagen) with the following parameters: mismatch cost 2, insertion/deletion cost 3, length fraction 0.8, similarity fraction 0.8, global alignment “no”, strand specific “both”, maximum number of hits per read 5
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: RPKM values in tab-delimited text format

source_name: Megakaryocyte progenitor cells

extract_protocol:
Total RNA was isolated from the cell pellets using the RNeasy Micro Kit (Qiagen) or using the Monarch Total RNA Miniprep Kit (New England Biolabs) according to the manufacturer’s instructions. For cells in RNAlater, Monarch Total RNA Miniprep Kit (New England Biolabs) was used according to the manufacturer’s instructions. DNaseI digestions were performed on column.
Library preparation was performed with the NEBNext Single Cell / Low Input RNA technology (New England Biolabs), according to the manufacturer's protocol.

value: pDC-DTR

tag: cell type depletion

value: platelet depletion + plasmacytoid dendritic cell depletion

value: R300 + diphteria toxin


title: Figure 4, Single tumor model, 2-DG 1 [('sample7,2-DG,Perturbation')]

description: Figure 4 z -score values.xlsx


title: MKP PD DT rep1


title: Figure 4, Single tumor model, 2-DG 3 [('sample9,2-DG,Perturbation')]

description: Figure 4 z -score values.xlsx


title: MKP PD rep3

value: platelet depletion


title: Figure 4, Single tumor model, Cisplatin 3 [('sample6,Cisplatin,Perturbation')]

description: Figure 4 z -score values.xlsx

value: Cisplatin


title: Figure 4, Single tumor model, 2-DG 2 [('sample8,2-DG,Perturbation')]

description: Figure 4 z -score values.xlsx


title: MKP PD rep2


title: MKP control rep2

value: no depletion

value: untreated/control


title: WHIM12_mouse passage A [re-analysis]

description:
re-analysis of GSM4486563
HIM_12A

source_name: WU PDX WHIM12_passage A


title: Figure 4, Single tumor model, Cisplatin 2 [('sample5,Cisplatin,Perturbation')]

description: Figure 4 z -score values.xlsx

value: Cancer cells

value: Breast cancer brain metastasis


title: MKP control rep1


title: MKP PD rep1


title: Figure 4, Single tumor model, Cisplatin 1 [('sample4,Cisplatin,Perturbation')]

description: Figure 4 z -score values.xlsx

value: WT


title: Figure 4, Single tumor model, Control 1 [('sample1,Control,Control')]

description: Figure 4 z -score values.xlsx

value: Control


title: Figure 4, Single tumor model, Control 2 [('sample2,Control,Control')]

description: Figure 4 z -score values.xlsx


title: Figure 2, MDA-MB-231-BR,  T-Platin-M-NP 3 [T.PM.NP3]

description:
Figure 2 C vs PM geneDE_results.chr.xls
Figure 2 CP vs PM geneDE_results.chr.xls


title: Figure 2, MDA-MB-231-BR,  T-Platin-M-NP 1 [T.PM.NP1]


title: Figure 2, MDA-MB-231-BR, Control 3 [C3]

description:
Figure 2 C vs CP geneDE_results.chr.xls
Figure 2 C vs PM geneDE_results.chr.xls


title: Figure 4, Single tumor model, T-Platin-M-NP+2-DG 2 [('sample14,NP+2-DG,Perturbation')]

description: Figure 4 z -score values.xlsx

value: T-Platin-M-NP and 2-DG


title: Figure 2, MDA-MB-231-BR, Cisplatin 1 [CP1]

description:
Figure 2 C vs CP geneDE_results.chr.xls
Figure 2 CP vs PM geneDE_results.chr.xls


title: Figure 4, Single tumor model, Control 3 [('sample3,Control,Control')]

description: Figure 4 z -score values.xlsx


title: 231-09 Plate4 NK 8

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
The fastq files were aligned to MacaM v7 using STAR aligner v 2.5.2b. The raw counts from ReadsPerGene output of STAR was used for downstream analysis using Seurat v4.0.4.
Assembly: MacaM v7
Supplementary files format and content: The ReadsPerGene output from STAR for each cell was combined as separate columns in ReadCounts.txt.The MacaM v7.8.2 gtf was used to convert gene id to gene names.

organism: Macaca mulatta

source_name: NK

extract_protocol:
RNA was purified using RNACleanXP Solid Phase Reversible Immobilization (SPRI) beads (Beckman Coulter). Beads with bound RNA were re-suspended in 5 ul of RSB buffer.
Single-cell RNA sequencing was performed by Medgenome using a modified version of the ClonTech SMART-Seq Single Cell Kit that utilized miniaturization to ¼ volumes using a MANTIS Liquid Handler (Formulatrix). Amplified cDNA was fragmented and appended with dual-indexed barcodes using Illumina Nextera kits.

value: NK


title: 231-09 Plate4 NK 9


title: 231-09 Plate4 NK 3


title: 231-09 Plate4 NK 19


title: Ramos cells, R-Lv-control-H3K4m2_L1

city: Lanzhou

first: caiyue

last: que

state: 甘肃

address: 天水南路222号

institute: 兰州大学

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt[1]（version 1.9.1）to be high quality clean data.
Mapping:  Firstly, reference genome sequences and gene model annotation files of relative species are downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, bowtie2-build is used to index reference genome sequence. Finally, clean data is aligned to reference genome via software Bowtie2 (version 2.2.6).
Peaks analysis: Use MACS[2](V2) to analyze peaks quality control, peaks calling and peaks annotation.
Assembly: GRCh38.p13
Supplementary files format and content: final_peaks.txt; anno.peaks.txt; sort_q_peaks.txt
Library strategy: CUT&Tag

source_name: Ramos

extract_protocol:
CUT&Tag DNA samples were quantified using a Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) and qualified by Agilent Bioanalyzer 2100(Agilent Technologies, Palo Alto, CA, USA). Next generation sequencing library preparations were constructed following the manufacturer’s protocol. For each sample, CUT&Tag product was used for library preparation. The CUT&Tag product was treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and dAtailing in one reaction, followed by ligation to adaptors with a “T” base overhang. Adaptor-ligated DNA was then recovered using Beads. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flowcell to perform bridge PCR and P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit 3.0 Fluorometer.
Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq/Novaseq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA) or a MGI2000 instrument according to manufacturer’s instructions (MGI, Shenzhen, China) . Sequencing was carried out using a 2x150 paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument，image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB +GAPipeline-1.6 (Illumina) on the NovaSeq instrument，image analysis and base calling were conducted by the Zebeacall on the MGI2000 instrument.

value: Ramos

value: B lymphocytes

value: Vector

tag: antibody


title: Ramos cells, R-control-H3K4m2_L1


title: 231-09 Plate4 NK 4


title: 231-09 Plate4 NK 16


title: 231-09 Plate4 NK 21


title: 231-09 Plate4 NK 6


title: Figure 2, MDA-MB-231-BR, Control 1 [C1]


title: 231-09 Plate4 NK 1


title: 231-09 Plate4 NK 7


title: Figure 2, MDA-MB-231-BR, Control 2 [C2]


title: 231-09 Plate4 NK 15


title: Ramos cells, R-Lv-ZEBRA-H3K4m2_L1

value: ZEBRA


title: Ramos cells, ZEBRA-Input_L1

description:
Ramos-ZEBRA-H3K9me2-VS-Ramos-ZEBRA-Input_final_peaks.txt
Ramos-ZEBRA-H3K9me2-VS-Ramos-ZEBRA-Input_anno.peaks.txt
Ramos-ZEBRA-H3K9me2-VS-Ramos-ZEBRA-Input_sort_q_peaks.txt

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments and bases quality lower than 20, PF(pass filter) data of fastq format were processed by Cutadapt[1]（version 1.9.1）to be high quality clean data.
Mapping: Firstly, reference genome sequences and gene model annotation files of relative species are downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, bowtie2-build is used to index reference genome sequence. Finally, clean data is aligned to reference genome via software Bowtie2 (version 2.2.6).
Different peak analysis:Combine the peaks of two different experimental groups with bedtools (version, 2.25.0)  software, and then readcounts are counted in the combined peaks area. Difference analysis was performed using edgeR (V3.4.6) of the Bioconductor software package.
Merging peaks:To find the common and unique peaks of several groups, HOMER(V2) toolkit is used to treat the peaks with 200bp overlapping peaks as common and vice versa.
Assembly: GRCh38.p13
Supplementary files format and content: final_peaks.txt; anno.peaks.txt; sort_q_peaks.txt; bw

extract_protocol:
ChIP DNA samples were quantified using a Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) and qualified by Agilent Bioanalyzer 2100(Agilent Technologies, Palo Alto, CA, USA). Next generation sequencing library preparations were constructed following the manufacturer’s protocol. For each sample, ChIP product was used for library preparation. The ChIP product was treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and dA-tailing in one reaction, followed by ligation to adaptors with a “T” base overhang. Adaptorligated DNA was then recovered using Beads. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flowcell to perform bridge PCR and P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit 3.0 Fluorometer.
Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq/Novaseq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA) or a MGI2000 instrument according to manufacturer’s instructions (MGI, Shenzhen, China) . Sequencing was carried out using a 2x150 paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument，image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB +GAPipeline-1.6 (Illumina) on the NovaSeq instrument，image analysis and base calling were conducted by the Zebeacall on the MGI2000 instrument.

tag: chip antibody


title: 231-09 Plate4 NK 18


title: 231-09 Plate4 NK 12


title: Ramos cells, Ctrl-Input_L1

description:
Ramos-Ctrl-H3K9me2-VS-Ramos-Ctrl-Input_final_peaks.txt
Ramos-Ctrl-H3K9me2-VS-Ramos-Ctrl-Input_anno.peaks.txt
Ramos-Ctrl-H3K9me2-VS-Ramos-Ctrl-Input_sort_q_peaks.txt


title: Ramos cells, ZEBRA-H3K9me2_L1


title: Ramos cells, Ctrl-H3K9me2_L1


title: 231-09 Plate4 NK 11


title: 231-09 Plate4 NK 10


title: Ramos cells, Vector-H3K9me2_L1

description:
Ramos-Vector-H3K9me2-VS-Ramos-Vector-Input_final_peaks.txt
Ramos-Vector-H3K9me2-VS-Ramos-Vector-Input_anno.peaks.txt
Ramos-Vector-H3K9me2-VS-Ramos-Vector-Input_sort_q_peaks.txt


title: 231-09 Plate4 NKB 9

source_name: NKB

value: NKB


title: Ramos cells, Vector-Input_L1


title: 231-09 Plate4 NK 13


title: AGS cells, GPAT3SiRNA3

city: Chongqing

first: yuan

last: zhuang

address: Gaotanyan Street

institute: Third Military Medical University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
clean data were mapped to the reference genome of Homo sapiens from GRCh38 using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Assembly: GRCh38
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

source_name: AGS

growth_protocol: AGS cells were cultured in complete RPMI 1640 medium supplemented with 10% FBS in a humidified environment containing 5% CO2 at 37 °C.

extract_protocol:
Total RNAs were extracted  using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).2 μg total RNAs were used for stranded RNA sequencing library
RNA libraries for RNA-seg were prepared using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 (Vazyme Biotech, NR612-02)  following manufacturer's protocols.

treatment_protocol: AGS cells were pre-treated with GPAT3 siRNA or non-specific control siRNA (NC) (40 nM) for 24 h.

value: AGS

value: gastric epithelial cells

value: GPAT3 siRNA


title: AGS cells, GPAT3SiRNA2


title: 231-09 Plate4 NKB 43


title: AGS cells, NC_1

value: control


title: 231-09 Plate4 NK 14


title: AGS cells, NC_2


title: 231-09 Plate4 NKB 8


title: 231-09 Plate4 NKB 4


title: 231-09 Plate4 NKB 7


title: AGS cells, GPAT3SiRNA1


title: HuCCT-1 cells,C4A-3

city: Shanghai

first: Bonan

last: Xu

address: 415，Fengyang Road

department: gastroenterology

institute: Shanghai Changzheng Hospital

data_processing:
The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4).
. The fragments of genes were counted using stringtie(v1.3.3b) followed by TMM (trimmed mean of M values) normalization
Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q< 0.05) and fold-change >2 using edgeR software.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

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

tag: infection


title: 231-09 Plate4 NKB 39


title: 231-09 Plate4 NKB 6


title: AGS cells, NC_3

tag: cell line


title: 231-09 Plate4 NKB 40

tag: cell type


title: HuCCT-1 cells,C4A-2


title: fetal pancreas,sample #11, ewe#328, NTS-RNAi

city: Fort Collins

first: Victoria

last: Kennedy

state: Colorado

address: 1683 Campus Delivery

institute: Colorado State University

data_processing:
CLC Genomics Workbench v21
trimming of raw sequencing reads based on quality score (Q‐score > 30), read length (≥ 15 nucleotides), and removal of adapter sequences
Raw sequence reads were mapped to the reference ovine genome (Ovis aries, Oar.ra_1.0, Baylor College of Medicine)
Expression data was normalized using the trimmed mean of M-values (TMM) normali-zation method and presented as transcripts per kilobase per million mapped reads (TPM)
CLC Genomics Workbench Differential Expression tool and compared with DESeq2 package in R studio
Assembly: Ovis aries, Oar.ra_1.0, Baylor College of Medicine, NCBI RefSeq assembly GCF_002742125.1
Supplementary files format and content: xlsx file including TPM counts for each sample

organism: Ovis aries

source_name: fetal pancreas

extract_protocol:
RNA was extracted  using RNeasy Mini Kit (Ref# 74104; QIAGEN)
Assessment of the RNA samples integrity and quality, library generation and RNA-Seq (2x150 cycles, 80 million paired-end reads/sample; NovSeq6000, Illumina, San Diego, CA, USA) was conducted by the Genomics Shared Resource Core Facility, Uni-versity of Colorado Anschutz Medical Campus (Aurora, CO)

treatment_protocol: day 9 hatched blastocysts were infected with lentiviral constructs containing either non-targeting sequence (NTS) or SLC1A3-RNAi. Fetal pancreases were collected at mid-gestation (75 days) under general anesthesia before euthanasia

value: fetal pancreas

tag: genotype

value: NTS-RNAi

value: 75 days gestational age


title: HuCCT-1 cells,C4A-1


title: 231-09 Plate4 NKB 3


title: fetal pancreas,sample #8, ewe#323, NTS-RNAi

tag: tissue


title: fetal pancreas,sample #7, ewe#263, NTS-RNAi


title: HuCCT-1 cells, NC3

value: AdGFP


title: 231-09 Plate4 NKB 44


title: 231-09 Plate4 NKB 41


title: HuCCT-1 cells, NC1


title: fetal pancreas, sample #12,ewe#333, NTS-RNAi


title: 231-09 Plate4 NKB 38


title: HuCCT-1 cells, NC2


title: fetal pancreas,sample #5, ewe#317, 472-RNAi


title: 22_0769_TM

city: Houston

first: Alice

middle: Yuxuan

last: Tian

email: ayt2@rice.edu, alicet.3993@gmail.com

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: 10x Genomics

data_processing:
Raw sequencing reads were processed using the CellRanger v6.1.2 (10X Genomics) pipeline, against the hg38 reference genome (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz)
quality control was performed separately for each sample through a quality control pipeline (https://github.com/lijinbio/cellqc). Briefly, empty cells were filtered by dropkick v1.2.8 and ambient RNA was removed using SoupX v1.6.2. Doublets were detected and removed using DoubletFinder. After merging all samples, cells were further filtered manually (features > 300, transcript (UMI) counts > 500, mitochondrial percentage < 5%)
Assembly: hg38
Supplementary files format and content: A .h5ad file of count matrix.

source_name: post-mortem tissue

extract_protocol:
Primary hTM cells were isolated from human donor corneal rims deemed unsuitable for transplantation, and characterized. All donor tissues were procured from Saving Sight eye bank (Kansas city, MO). All donor cells used in this study were isolated (between 2012 and 2021), validated, stored in liquid nitrogen, or used in prior studies from our lab. Prior to single cell sequencing, frozen cells were thawed with 15ml pre-warmed media (37C, DMEM:F12=1:1, with 20%FBS, 1%Penn/Step/fungizone) and centrifuged at 300g, 4C for 5min. Cells were washed with media again and suspended in 0.04% BFA and ready for single cell RNA sequencing. Cell viability was checked with trypan blue.
Resuspended single cells were loaded on a 10X Chromium controller for obtaining single cell Gel Beads-In-Emulsions. scRNA-seq libraries were generated using 10X Chromium Single Cell 3’ reagent kits v3.1 (10X Genomics) following the manufacturer’s recommendations (https://www.10xgenomics.com). Sequencing was performed on Illumina Novaseq 6000 (http://www.illumina.com) at the Single Cell Genomics Core at Baylor College of Medicine.

value: post-mortem tissue

value: healthy

value: unknown


title: 231-09 Plate4 NKB 37


title: fetal pancreas, sample #2, ewe#221, 472-RNAi


title: fetal pancreas,sample #6, ewe#215, 472-RNAi


title: 22_0688_TM

description: 10x Genomics


title: fetal pancreas,sample #3, ewe#336, 472-RNAi


title: 231-09 Plate4 NKB 36


title: 231-09 Plate4 NKB 34


title: 22_0500_TM

description: 10x Genomics


title: PolySeq~tg_18~L124~PolySeq_7.5%EtOH~BY4741~30C~15min~mock~BR2~Poly

city: Chicago

first: D Allan

last: Drummond

state: IL

address: 929 E 57th Street

institute: University of Chicago

data_processing:
Sequencing reads were trimmed using TrimGalore (v0.6.10, https://github.com/FelixKrueger/TrimGalore) using default settings (e.g. trim_galore --paired --fastqc_args '--outdir fastqc/' -j 4 -o trimmed --basename F02 AD-JB-F02_S44_R1_001.fastq.gz AD-JB-F02_S44_R2_001.fastq.gz). They were mapped using STAR v2.7.10b(Dobin et al. 2013) (e.g. STAR --outSAMtype BAM Unsorted --readFilesCommand gunzip -c  --sjdbGTFfile spike_saccharomyces_cerevisiae_R64-3-1_20210421_geneid.gff3 --sjdbGTFtagExonParentTranscript Parent --sjdbGTFfeatureExon CDS --sjdbGTFtagExonParentGene gene_id --runThreadN 4 --alignMatesGapMax 20000 --limitBAMsortRAM 1445804817 --genomeDir STAR_spike_saccharomyces_cerevisiae_R64-3-1_20210421 --outFileNamePrefix mapped_reads/F02/F02_ --readFilesIn trimmed/F02_val_1.fq.gz trimmed/F02_val_2.fq.gz). The estimated counts and TPMs were generated using kallisto v0.48.0(Bray et al. 2016) (e.g. kallisto quant -i spike_Scerevisiae_orf_coding_all_Scerevisiae_rna_coding.fasta.idx -o kallisto_quant/F02 --fr-stranded --bootstrap-samples=50 -t 1 trimmed/F02_val_1.fq.gz trimmed/F02_val_2.fq.gz).
S. pombe total RNA was added and reads were mapped to saccharomyces_cerevisiae_R64-3-1_20210421_Schizosaccharomyces_pombe_all_chromosomes_relabelled.fasta (STAR) using the annotation file saccharomyces_cerevisiae_R64-3-1_20210421_Schizosaccharomyces_pombe_all_chromosomes_relabelled_geneid.gff3, and Scerevisiae_orf_coding_all_Scerevisiae_rna_coding_Spombe_cds.fasta (kallisto).
In general, sequencing reads were mapped to the transcriptome using kallisto to extract estimated counts and TPMs.
Assembly: S288C R64.3.1
Supplementary files format and content: estimated counts and TPMs per RNA sample

source_name: yeast cells

growth_protocol: Cells were grown overnight at 30¬∞C with shaking for at least 12 hours to OD600 = 0.4 in synthetic complete dextrose media (SCD) before being exposed to stress.

extract_protocol:
Around 100 mg of frozen yeast that was collected by vacuum filtration was transferred to a pre-chilled 2 ml Eppendorf Safe-Lock tube. Cells were lysed with a pre-chilled 7 mM stainless steel ball (Retsch #05.368.0035) by 5x90sx30Hz pulses in a Retsch MM100 mixer mill, chilling in liquid nitrogen (LN2) between pulses. Sample was resuspended in 10:1 (v/w) polysome lysis buffer (20 mM HEPES-KOH (pH 7.4), 100 mM KCl, 5 mM MgCl2, 200 Œºg/mL heparin (Sigma #H3149), 1% triton X-100, 0.5 mM TCEP (Goldbio #TCEP25), 100 Œºg/mL cycloheximide (Sigma #C7698-5G), 20 U/ml SUPERase‚Ä¢In (Invitrogen #AM2696), 1:200 Millipore protease inhibitor IV #539136). The lysate was clarified by centrifugation at 3000 g for 30 s, and the clarified lysate was transferred to new tube and aliquots were flash frozen in LN2. A 10‚Äì50% continuous sucrose gradient in polysome gradient buffer (5 mM HEPES-KOH (pH 7.4), 140 mM KCl, 5 mM MgCl2, 100 Œºg/ml cycloheximide, 10 U/ml SUPERase‚Ä¢In, 0.5 mM TCEP) was prepared in SW 28.1 tubes (Seton #7042) using a Biocomp Gradient Master and allowed to cool to 4¬∞C. Clarified lysate (200 ¬µL) was loaded on top of the gradient, and gradients were spun in a SW28.1 rotor at 27,500 rpm for 3.5 hr at 4¬∞C. Gradients were fractionated into 0.6mL fractions using a Biocomp Piston Gradient Fractionator with UV monitoring at 254 nm, and fractions were flash frozen in LN2. UV traces were normalized to the total signal starting with the 40S peak. The samples were generated by pooling 50 ¬µL of each fraction from the free fraction (before the monosome peak) and either separately pooling the fractions with 3+ ribosomes bound and the mono/di-some fractions (for the heat shock experiments), or by combining all ribosome-bound fractions together (azide and ethanol stresses). The spike-in (50 ng of S. pombe total RNA) was then added to each pooled sample. RNA was purified via ethanol precipitation (final concentrations of 0.3 M sodium acetate pH 5.2, 0.3 ¬µg/mL glycoblue (Invitrogen #AM9516), and 70% ethanol) at -20¬∞C overnight followed by centrifugation at 4¬∞C for 30 minutes at 21,000 g. The pellet was washed with 1 mL of 70% ethanol before being resuspended in water. The purified RNA was then treated with Dnase I (NEB) before purifying again using an NEB RNA clean and concentrate kit (NEB #T2030).
Sequencing libraries were prepared by the University of Chicago Genomics Facility from DNase I treated RNA using Qiagen FastSelect (Qiagen #334215) and Illumina Stranded mRNA Prep (Illumina #20020595) kits.  Paired end 200 bp sequencing was performed on an Illumina NovaSeq 6000.
In general, cells were first lysed by cryo-grinding with a steel ball. When appropriate, fractionation by sedimentation or sucrose gradients was performed and RNA was dissolved in Trizol. The RNA was then purified using Zymo Direct-Zol columns. For more details, please see the protocol associated with each sample.
In general, RNA sequencing libraries were prepared using either Illumina RNA sequencing kits or NEBNext Ultra II RNA sequencing kits.

treatment_protocol: Ethanol stresses were completed by resuspending centrifuged cell pellets in SCD made with either 5%, 7.5%, 10%, or 15% ethanol for 15 min. Control cells were mock treated by resuspending in normal SCD.

value: yeast cells


title: 231-09 Plate4 NKB 32


title: PolySeq~tg_18~L123~PolySeq_7.5%EtOH~BY4741~30C~15min~EtOH_7.5%~BR1~Poly


title: 10x3V31_OHSU_GTM_2019_0461

description: 10x Genomics

source_name: primary cell culture

value: primary cell culture

value: glaucoma


title: PolySeq~tg_18~L124~PolySeq_7.5%EtOH~BY4741~30C~15min~mock~BR2~Free


title: PolySeq~tg_18~L122~PolySeq_7.5%EtOH~BY4741~30C~15min~mock~BR1~Poly


title: PolySeq~tg_18~L125~PolySeq_7.5%EtOH~BY4741~30C~15min~EtOH_7.5%~BR2~Poly


title: PolySeq~tg_18~L123~PolySeq_7.5%EtOH~BY4741~30C~15min~EtOH_7.5%~BR1~Free


title: 10x3v31_hTM_9691_P1

description: 10x Genomics


title: 10x3v31_hTM_9355_P1

description: 10x Genomics

value: OS


title: PolySeq~tg_18~L125~PolySeq_7.5%EtOH~BY4741~30C~15min~EtOH_7.5%~BR2~Free


title: PolySeq~tg_18~L122~PolySeq_7.5%EtOH~BY4741~30C~15min~mock~BR1~Free


title: 10x3v31_hTM_9632_P2

description: 10x Genomics


title: PolySeq~tg_18~L125~PolySeq_7.5%EtOH~BY4741~30C~15min~EtOH_7.5%~BR2~Total


title: PolySeq~tg_18~L123~PolySeq_7.5%EtOH~BY4741~30C~15min~EtOH_7.5%~BR1~Total


title: 10x3V31_hTM_7987_P2

description: 10x Genomics


title: PolySeq~tg_18~L122~PolySeq_7.5%EtOH~BY4741~30C~15min~mock~BR1~Total


title: 231-09 Plate4 NKB 2


title: 231-09 Plate4 NKB 28


title: PolySeq~tg_17~L117~PolySeq_0.8%Azide~BY4741~30C~30min~Azide_0.8%_pH6.8~BR2~Poly


title: 10x3V31_hTM_659_P1_DCR

description: 10x Genomics


title: 231-09 Plate4 NKB 29


title: PolySeq~tg_17~L115~PolySeq_0.8%Azide~BY4741~30C~30min~Azide_0.8%_pH6.8~BR1~Poly


title: PolySeq~tg_17~L117~PolySeq_0.8%Azide~BY4741~30C~30min~Azide_0.8%_pH6.8~BR2~Free


title: 231-09 Plate4 NKB 33


title: 10x3V31_hTM_74M_P2

description: 10x Genomics

value: OD


title: 231-09 Plate4 NKB 30

value: NKB


title: PolySeq~tg_17~L117~PolySeq_0.8%Azide~BY4741~30C~30min~Azide_0.8%_pH6.8~BR2~Total


title: PolySeq~tg_17~L116~PolySeq_0.8%Azide~BY4741~30C~30min~mock~BR2~Poly


title: 10x3v31_hTM_11701_P2

description: 10x Genomics


title: 231-09 Plate4 NKB 31


title: PolySeq~tg_17~L115~PolySeq_0.8%Azide~BY4741~30C~30min~Azide_0.8%_pH6.8~BR1~Total


title: PolySeq~tg_18~L124~PolySeq_7.5%EtOH~BY4741~30C~15min~mock~BR2~Total


title: PolySeq~tg_17~L114~PolySeq_0.8%Azide~BY4741~30C~30min~mock~BR1~Poly


title: 10x3v31_hTM_2180

description: 10x Genomics


title: PolySeq~tg_17~L115~PolySeq_0.8%Azide~BY4741~30C~30min~Azide_0.8%_pH6.8~BR1~Free


title: 231-09 Plate4 NKB 26


title: 231-09 Plate4 NKB 25


title: PolySeq~tg_17~L114~PolySeq_0.8%Azide~BY4741~30C~30min~mock~BR1~Free


title: 10x3v31_hTM_11703_P2

description: 10x Genomics


title: 231-09 Plate4 NKB 27


title: 10x3V31_hTM_0114_P1

description: 10x Genomics


title: PolySeq~tg_17~L116~PolySeq_0.8%Azide~BY4741~30C~30min~mock~BR2~Total


title: PolySeq~tg_17~L114~PolySeq_0.8%Azide~BY4741~30C~30min~mock~BR1~Total


title: 231-09 Plate4 NKB 23


title: 10x3V31_GTM_7445

description: 10x Genomics