title: lung from mice with kidney fibrosis rep2 H658 duplicate

city: Houston

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

description:
replicate 2 duplicate, Blab/c, UUO surgery
H658-2-lung

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Genome Studio 5.0
Non-normalzied is the average signal. The normalization is based on rank invariant

source_name: lung from mice with kidney fibrosis

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA was extracted from healthy and fibrotic lungs  and lung from fibrotic kidneys using TRIzol reagent (Life Technologies 15596026) according to the manufacturer’s instructions. An equal amount of RNA was submitted from each cohort to the Microarray core facility at MD Anderson.

treatment_protocol: Lung fibrosis was induced via intratracheal administration of bleomycin. Kidney fibrosis was induced by unilateral ureteral obstruction (UUO) surgery

tag: strain

value: BALB/c

value: lung

tag: disease state

value: mice with kidney fibrosis


title: Neu54yo_ZT24_replicate1

status: Public on Apr 19 2024

type: genomic

city: Vilnius

first: Karolis

last: Koncevičius

address: Saulėtekio al. 7

department: Institute of Biotechnology, Life Sciences Center

country: Lithuania

institute: Vilnius University

description: neutrophils purified with magnetically activated cell sorting

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium HumanMethylationEPIC v1.0 Beadchip using standard Infinium HD Methylation Assay protocol

scan_protocol: Arrays were imaged using iScan Reader using standard recommended Illumina scanner setting

data_processing:
Processeing was done using the R “minfi” package. First, all samples having more than 3% of probes with poor detection p-values (detection p < 0.05) using an alternative detection p-value approach(Heiss and Just 2019) were removed as outliers. Then array normalization was performed using “noob” background correction followed by functional normalization, and signals from the methylated and unmethylated channels were combined to obtain the methylation beta values. Additional outliers were identified by measuring Pearson’s correlations among all the sample pairs and removing samples with an average inter-sample correlation value more than three standard deviations below the mean. Finally, for the datasets that contained technical replicates for every sample, all the samples with only a single replicate remaining after quality control were discarded.
R "minfi" package computed Average Beta values after "noob" background correction and "functional" normalization

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Neutrophils

label_protocol: Standard Infinium HD Methylation Assay protocol

extract_protocol: Neutrophils were isolated from whole blood by immunomagnetic negative selection with EasySep™ Direct Human Neutrophil Isolation Kit (STEMCELL) according to the manufacturer's protocol. The remaining fraction of white blood cells depleted of neutrophils were snap-frozen and stored in -80 °C before DNA extractionDNA was extracted with NucleoSpin® Tissue kit using the standard protocol

tag: Sex

value: male

tag: age

tag: ct


title: Neu54yo_ZT21


title: Neu54yo_ZT21_replicate2


title: Neu54yo_ZT24


title: healthy kidney rep1 H557

type: RNA

country: USA

description:
replicate 1, Blab/c, healthy
H557-kidney

molecule: total RNA

organism: Mus musculus

source_name: healthy kidney

tag: tissue

value: healthy


title: Neu54yo_ZT21_replicate1


title: fibrotic lung rep3 981

description:
replicate 3, Balb/c, intratracheal Bleomycin
981-lung

source_name: fibrotic lung

value: fibrotic


title: lung from mice with kidney fibrosis rep3 H660

description:
replicate 3, Blab/c, UUO surgery
H660-lung


title: Neu54yo_ZT18_replicate2


title: fibrotic lung rep1 A16

description:
replicate 1, Balb/c, intratracheal Bleomycin
A16-lung


title: Neu54yo_ZT18_replicate1


title: healthy lung rep1 H563

description:
replicate 1, Blab/c, healthy
H563-lung

source_name: healthy lung


title: healthy lung rep2 H557

description:
replicate 2, Blab/c, healthy
H557-lung


title: Neu54yo_ZT18


title: fibrotic lung rep2 A18

description:
replicate 2, Balb/c, intratracheal Bleomycin
A18-lung


title: lung from mice with kidney fibrosis rep2 H658

description:
replicate 2, Blab/c, UUO surgery
H658-1-lung


title: healthy kidney rep3 H565

description:
replicate 3, Blab/c, healthy
H565-kidney

value: kidney


title: healthy kidney rep2 H563

description:
replicate 2, Blab/c, healthy
H563-kidney


title: lung from mice with kidney fibrosis rep1 H657

description:
replicate 1, Blab/c, UUO surgery
H657-lung


title: healthy lung rep3 H565

description:
replicate 3, Blab/c, healthy
H565-lung


title: Neu54yo_ZT15


title: Neu54yo_ZT15_replicate1


title: Neu54yo_ZT15_replicate2


title: Neu54yo_ZT12_replicate2


title: kidney from mice with kidney fibrosis rep2 H658

description:
replicate 2, Blab/c, UUO surgery
H658-kidney

source_name: fibrotic kidney


title: Neu54yo_ZT12_replicate1


title: Neu54yo_ZT9_replicate2


title: Neu54yo_ZT12


title: Neu30yo_ZT29_replicate1

description: Neutrophils purified with fluorescence activated cell sorting

extract_protocol: Immediately after collection, the blood samples were processed using Optilyse C™ (Beckman Coulter, CA, USA), both for erythrolysis and mild fixation of the blood cells. These samples were then subsequently sorted for neutrophils via fluorescence activated cell sorting (FACS) using CD15-APC, CD16-PE, and CD45- PE-Cy™7 (BD Pharmingen™, NJ, USA). The neutrophil samples were snap-frozen and stored in -80 °C before DNA extraction.DNA was extracted with NucleoSpin® Tissue kit using the standard protocol


title: Neu30yo_ZT29


title: Neu30yo_ZT26_replicate1


title: Neu30yo_ZT26_replicate2


title: Neu30yo_ZT23_replicate2


title: Neu30yo_ZT26


title: Neu30yo_ZT23_replicate1


title: Neu30yo_ZT23


title: Neu30yo_ZT20_replicate2


title: Neu30yo_ZT20_replicate1


title: Neu30yo_ZT20


title: Neu30yo_ZT17_replicate2


title: Neu30yo_ZT14_replicate2


title: Neu30yo_ZT14


title: Neu30yo_ZT14_replicate1


title: Neu30yo_ZT11_replicate2


title: Neu30yo_ZT17


title: Neu30yo_ZT11


title: Neu30yo_ZT8_replicate2


title: Neu54yo_ZT9_replicate1


title: Neu30yo_ZT8_replicate1


title: Neu30yo_ZT8


title: Neu30yo_ZT29_replicate2


title: 1013_fCortex-SC3_r1

type: SRA

city: Saarbrücken

first: Annika

last: Engel

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

library_source: transcriptomic

data_processing:
Illumina BCL files were converted to FASTQ format using bcl2fastq (2.19.0.316). Reads with unique molecular identifiers (UMIs) had their UMIs incorporated into the header. After adapter and quality trimming with cutadapt (2.1042), reads were mapped to the human genome (GRCh38) using STAR (2.7.5b). RNA classes were assigned using featureCounts (1.5.2) based on annotations from GENCODE, miRBase, piRBase, and GtRNAdb. Unannotated regions were labeled "unmapped" Reads were hierarchically assigned to categories, with prioritization in cases of ambiguity. miRNA expression was quantified with mirquantify (1.0.1) from miRMaster (2.0) [23], and deduplication was performed with UMI-tools (1.0.0). Data were analyzed with and without subsampling using R and Seurat(4.4.0), and various visualizations and analyses were conducted for miRNA variability, clustering, and enrichment.
Assembly: GRCh38
Supplementary files format and content: miRNA_expression_raw.tsv

source_name: fCortex

extract_protocol:
single cell isolation and lysis
The preparation of the single cell miRNA sequencing libraries was performed as described in Hücker et al, 2021, Nature Comm. (Hücker et al. 2021) for the SBN_CL protocol

value: fCortex

tag: sample type

tag: index number

tag: method

value: miRNA-Seq

tag: sequencing type

value: single-cell


title: 1013_fCortex-SC1_r1


title: 1013_fCortex-SC2_r1


title: 1013_Liver-SC20_r1

source_name: Liver

value: Liver


title: 1013_Liver-SC18_r1


title: 1013_Liver-SC17_r1


title: 1013_Liver-SC15_r1


title: 1013_Liver-SC14_r1


title: Neu30yo_ZT17_replicate1


title: 1013_Liver-SC13_r1


title: 1013_Liver-SC12_r1


title: 1013_Liver-SC10_r1


title: 1013_Liver-SC11_r1


title: 1013_Liver-SC7_r1


title: 1013_Liver-SC9_r1


title: 1013_Liver-SC6_r1


title: 1013_Liver-SC8_r1


title: 1013_Liver-SC4_r1


title: 1013_Liver-SC3_r1


title: 1013_Liver-SC2_r1


title: 1013_Liver-SC1_r1


title: 1013_Spleen-SC19_r1

source_name: Spleen

value: Spleen


title: 1013_Spleen-SC18_r1


title: 1013_Spleen-SC16_r1


title: 1013_Spleen-SC17_r1


title: 1013_Spleen-SC10_r1


title: 1013_Liver-SC16_r1


title: 1013_Liver-SC19_r1


title: 1013_Spleen-SC8_r1


title: 1013_Spleen-SC9_r1


title: 1013_Spleen-SC7_r1


title: 1013_Spleen-SC6_r1


title: Sample6: GB rep2

city: Mumbai

first: Dr. Ashish Kumar

last: Srivastava

state: Maharashtra

address: Anushakti Nagar, Trombay

country: India

institute: Bhabha Atomic Research Centre

data_processing:
Adapter and quality trimming using fastp v0.20.1 default parameters
Transcriptome assembly using Trinity v2.11.0 default parameters
Read mapping using Bourtie2 v2.1.0
Expression estimation using Featurecounts v2.0.1
Supplementary_files_format_and_content: Read counts mapped on to the trancripts.

organism: Chlorella sorokiniana

source_name: Gamma radiation treated

growth_protocol: Chlorella sorokiniana cells were grown in BBM solution.

extract_protocol:
Cells were harvested and flash frozen on dryice. RNA
NEB Next Ultra II library prep kit for Illumina is used to generate paired end sequencing libraries from enriched mRNA.

treatment_protocol: For irradiation (UV and Gamma) cells were resuspended in sterile distilled water

tag: time

value: 24 h post irradiation

tag: treatment

value: Gamma (1 kGy)


title: Sample4: UB rep2

source_name: UV radiation treated

value: UV (1 J/cm2)


title: Sample5: GA rep1


title: Neu30yo_ZT11_replicate1


title: Sample3: UA rep1


title: 1013_Liver-SC5_r1


title: 1013_Spleen-SC20_r1


title: BB355 + ifna - 24h - rep2

city: Tübingen

first: Thorsten

last: Stafforst

state: Baden-Württemberg

address: Auf der Morgenstelle 15

department: IFIB

institute: Eberhard Karls University of Tübingen

description:
H_BB355_IFNa_24h_genes.txt
Ctrl_BB355_IFNa_24h_comparison_DESeq2.txt

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20). Adapters were trimmed with Skewer (version 0.2.2) (Jiang et al. 2014).
STAR (v. 2.4.2a)  was used to align RNA-seq reads to the hg19 reference genome and ran RSEM (v. 1.2.21)81 on the alignments to calculate read counts and TPM values.
Using read counts, gene expression for all genes with TPM ≥ 2 (for both replicates) was analyzed with the R package DESeq.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes TPM, FPKM values for replicates for each sample
Supplementary files format and content: tab-delimited text file includes base Mean, log2fold chnage, p-value and padj values for each sample

source_name: HeLa (ACC 57, DSMZ)

growth_protocol: HeLa cells were maintained in DMEM with 10% FBS and 1% Penicillin/Streptomycin (P/S) at 37 °C with 5 % CO2 in a water saturated steam atmosphere

extract_protocol:
RNA was isolated using the Monarch® Total RNA Minprep (New England BioLabs) following manufacturer’s instructions. 25 µl of purified RNA (≥40 ng/µl) was used for poly(A)+mRNA sequencing.
The library was prepared from 200 ng of RNA with the TruSeq stranded mRNA library prep kit (Illumina) and sequenced with a NovaSeq 6000 (25 million reads, 2 × 100 bp paired end; Illumina). Each sample was prepared as biological duplicate.

treatment_protocol:
Cells were treated with 1 µg/ml of doxycycline for 24 hrs to induce SA1Q expression. Then the cells were transfected with the respective guide RNAs twice (T1 – 24 h after Doxycycline induction, T2 – 48 h post T1).
24 hrs post T2, cells were treated with IFN-α or -γ for 24 hrs and then lysed for RNA extraction. Control sample was empty transfected and had no IFN treatment.

tag: cell line

value: HeLa (ACC 57, DSMZ)

tag: cell type

value: cervical cancer

tag: genotype

value: gRNA transfection

tag: guide rna

tag: ptmi induced_mutation

value: JAK1 Y1034C

tag: agent

value: IFN-α 24hrs


title: BB349 + ifng - 24h - rep2

description:
H_BB349_IFNg_24h_genes.txt
Ctrl_BB349_IFNg_24h_comparison_DESeq2.txt

value: STAT2 Y690C

value: IFN-γ 24hrs


title: BB304 + ifng - 24h - rep2

description:
H_BB304_IFNg_24h_genes.txt
Ctrl_BB304_IFNg_24h_comparison_DESeq2.txt

value: IFNGR1 Y457C


title: BB349 + ifna - 24h - rep2

description:
H_BB349_IFNa_24h_genes.txt
Ctrl_BB349_IFNa_24h_comparison_DESeq2.txt


title: BB478 + ifna - 24h - rep2

description:
H_BB478_IFNa_24h_genes.txt
Ctrl_BB478_IFNa_24h_comparison_DESeq2.txt

value: STAT1 T288A


title: ctrl + ifng - 24h - rep2

description:
H_IFNg_24h_genes.txt
Ctrl_IFNg_24h_comparison_DESeq2.txt

value: empty transfection

value: no gRNA

value: no PTMi


title: BB355 + ifng - 24h - rep2

description:
H_BB355_IFNg_24h_genes.txt
Ctrl_BB355_IFNg_24h_comparison_DESeq2.txt


title: ctrl + ifna - 24h - rep2

description:
H_IFNa_24h_genes.txt
Ctrl_IFNa_24h_comparison_DESeq2.txt


title: BB305 + ifna - 24h - rep2

description:
H_BB305_IFNa_24h_genes.txt
Ctrl_BB305_IFNa_24h_comparison_DESeq2.txt

value: IFNAR1 Y466C


title: BB180 + ifna - 24h - rep2

description:
H_BB180_IFNa_24h_genes.txt
Ctrl_BB180_IFNa_24h_comparison_DESeq2.txt

value: STAT1 Y701C


title: BB355 + ifng - 24h - rep1


title: ctrl - rep2

value: no IFN


title: BB305 + ifna - 24h - rep1


title: BB478 + ifng - 24h - rep2

description:
H_BB478_IFNg_24h_genes.txt
Ctrl_BB478_IFNg_24h_comparison_DESeq2.txt


title: BB349 + ifna - 24h - rep1


title: BB349 + ifng - 24h - rep1


title: Sample1: CA rep1

source_name: Control (No irradiation)

tag: strain

value: 24 h post irradiation

value: No irradiation


title: Sample2: CB rep2

source_name: Control (No irrdaiation)


title: BB355 + ifna - 24h - rep1

value: HeLa (ACC 57, DSMZ)


title: BB180 + ifng - 24h - rep1

description:
H_BB180_IFNg_24h_genes.txt
Ctrl_BB180_IFNg_24h_comparison_DESeq2.txt

value: cervical cancer


title: BB478 + ifna - 24h - rep1

value: gRNA transfection


title: BB478 + ifng - 24h - rep1


title: BB180 + ifna - 24h - rep1


title: ctrl + ifna - 24h - rep1


title: ctrl - rep1


title: T2

city: Tianjin

first: Zhiqiang

last: Liu

address: 22 Qixiangtai Rd

department: Pathophysiology

country: China

institute: Tianjin Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Homo sapiens hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: human bone marrow

growth_protocol: MSCs were cultured in DMEM medium with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human BMSCs were cocultured with myeloma cells for 24hr.

value: human bone marrow

value: MSC

value: coculture


title: T1


title: VCaP, R1881, rep 2

city: Québec

first: Étienne

last: Audet-Walsh

state: Québec

address: 2705, boulevard Laurier

country: Canada

institute: CRCHU de Québec

data_processing:
Data cleaning: Trim Galore/Cutadapt
Quality control: FastQC and MultiQC
Pseudo-alignment: Kallisto
Normalization and Differential analyses: tximport/DESeq2
Assembly: GRCh38.p10
Supplementary files format and content: normalized_counts.csv.gz: comma separated values containing DESeq2 normalized counts
Supplementary files format and content: raw_counts.csv.gz: comma separated values containing raw counts as called by tximport

molecule: polyA RNA

source_name: VCaP

growth_protocol: Cells were maintained in incubator at 37°C and 5% CO2 for no more than four months in phenol-red DMEM supplemented with 1% penicillin + streptomycin, 1% sodium pyruvate and 5% Fetal Bovine Serum (FBS).

extract_protocol:
24h after treatments, RNA was extracted and purified with the QIAGEN RNeasy Mini Kit.
mRNA was selected and used for library using NEBNext Ultra II Directional RNA library prep kit.

treatment_protocol: Prior to treatments, cells were deprived of steroids using RPMI phenol red-free culture media supplemented with 1% penicillin + streptomycin, 1% sodium pyruvate, and 5% charcoal-stripped serum (CSS) for 48h. Then, cells were treated for 24h with either Ethanol 96%, Estradiol (10 nM) and/or R1881 (10 nM). Estradiol will activate the estrogen receptor alpha (ERa), whereas R1881, a synthetic androgen, will activate the androgen receptor (AR).

value: VCaP

value: Prostate cancer


title: VCaP, Estradiol + R1881, rep 2

value: 17β-Estradiol 10 nM + R1881 10 nM


title: VCaP, R1881, rep 1


title: VCaP, Estradiol + R1881, rep 3


title: VCaP, R1881, rep 3


title: VCaP, Estradiol + R1881, rep 1


title: VCaP, Estradiol, rep 3

value: 17β-Estradiol 10 nM


title: BB304 + ifng - 24h - rep1

value: IFNGR1 Y457C

value: IFN-γ 24hrs


title: Neu54yo_ZT9

description: neutrophils purified with magnetically activated cell sorting

tag: Sex

value: male


title: VCaP, Estradiol, rep 2


title: VCaP, Estradiol, rep 1


title: VCaP, Control, rep 3

value: Ethanol 96 percent


title: VCaP, Control, rep 2


title: VCaP, Control, rep 1


title: ASPS-KY dTAG 6h-3

city: Worcester

first: Matthew

last: Hemming

state: MA

address: 364 Plantation Street

institute: UMass Medical School

library_source: genomic

data_processing:
All ATAC-Seq data were aligned to the human reference genome assembly hg19, GRCh37 (ncbi.nlm.nih.gov/assembly/2758/) using Bowtie2 (version 2.2.1), and gene annotations by gencode annotation release 19 (gencodegenes.org/releases/19.html)
Peak finding was performed using Model-based Analysis for ChIP-Seq (MACS, version 1.4.2).
Assembly: hg19
Supplementary files format and content: Processed ATAC-Seq data files are in wiggle format

source_name: ASPS-KY

growth_protocol: Dulbecco’s modified Eagle’s medium containing 10% FBS, 2 mM L- glutamine, 100 mg/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
Preparation of nuclei from 50,000 viable cells, tagmentation, and library preparation were performed according to manufacturer’s instructions (Zymo Research Cat# D5458).
Libraries were amplified for paired-end 150 bp sequencing on an Illumina NovaSeq.

treatment_protocol: DMSO control or dTAG13 at 500 nM for 6, 24 or 72 hours

value: ASPS-KY


title: ASPS-KY dTAG 24h-2


title: ASPS-KY dTAG 6h-2


title: ASPS-KY dTAG 24h-1


title: ASPS-KY dTAG 72h-1


title: ASPS-KY dTAG 6h-1


title: ASPS-KY dTAG 72h-2


title: kidney from mice with kidney fibrosis rep1 H656

description:
replicate 1, Blab/c, UUO surgery
H656-kidney

value: BALB/c

value: kidney

tag: disease state

value: fibrotic


title: ASPS-KY dTAG DMSO-3

value: DMSO


title: C2

value: control


title: C1

value: human bone marrow


title: ASPS-KY dTAG DMSO-2


title: HEK293OverN3

city: Gothenburg

first: Aishe

last: Sarshad

address: Medicinaregatan 9C

department: Dept.of Biochemistry & Cell Biology

country: Sweden

institute: University of Gothenburg

data_processing:
Illumina Nova-seq 6000 platform was used for sequencing
sequences were aligned to human miRNAs using bowtie2 and quantified using bedtools coverage
normalized counts in excel file
Assembly: hg38
Supplementary files format and content: raw counts file

growth_protocol: HEK293 and A375 cells were cultured in DMEM media supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin. SHSY5Y cells were cultured in RPMI  media supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin

extract_protocol:
cytoplasmic and nuclear fraction was prepared and RNA extracted from HEK293, A375 and SHSY5Y cells. Small RNA libraries was prepared. In terms of HEK293 cells,  AGO proteins were  also enriched by immunoprecipitation with T6B peptide. After washing the beads they were treated with Trizol and the RNA extracted. 3'adapter and 5'adapter were added generating small RNA cDNA library preparation
Ligation products were reverse transcribed and amplified by PCR.

treatment_protocol: no treatemnt

value: WT

value: Confluent


title: HEK293OverN2


title: HEK293OverC2


title: HEK293OverC1


title: HEK293OverN1


title: ASPS-KY dTAG DMSO-1


title: HEK293SubN1

value: Subconfluent


title: HEK293SubN2


title: HEK293SubN3


title: HEK293SubC3


title: HEK293SubC2


title: HEK293SubC1


title: A375OverN2


title: A375OverN1


title: A375OverN3


title: A375SubN2


title: A375OverC1


title: A375SubN3


title: A375SubN1


title: A375OverC2


title: A375SubC3


title: SHSY5YOverN3


title: A375SubC2


title: SHSY5YOverN1


title: SHSY5YOverN2


title: A375SubC1


title: HEK293OverC3


title: SHSY5YOverC3


title: SHSY5YSubN2


title: SHSY5YOverC1


title: SHSY5YSubN3


title: SHSY5YSubN1


title: A375OverC3


title: SHSY5YSubC1


title: SHSY5YSubC3


title: HEK293_Over_total_lysate_biol_rep_1

tag: ip molecule

value: T6B peptide


title: SHSY5YSubC2


title: HEK293_Over_total_lysate_biol_rep_2


title: HEK293_sub_total_lysate_biol_rep_1


title: HEK293_Over_total_lysate_biol_rep_3


title: GLUP_1 ChIP-Seq

city: shanghai

first: yang

last: tang

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
Basecalls were performed using bol2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChiP-seq reads were aligned to the UCSC h19 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seg reads were extended to 150 bp to represent sequenced fragments,renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the sianificance cut-off a-value <=0.01.bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: 1640, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HT Library Preparation Kit complemented with NEXTflex DNA Barcodes from Boo Scientific.10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler.Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter.. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: gastric cancer cell

value: GLUP peptide


title: HEK293_sub_total_lysate_biol_rep_2


title: GLUP_3 ChIP-Seq


title: Ctrl2 ChIP-Seq


title: Ctrl1 ChIP-Seq


title: GLUP_2 ChIP-Seq


title: ctrl + ifng - 24h - rep1

value: HeLa (ACC 57, DSMZ)

value: cervical cancer

value: empty transfection

value: no gRNA

value: no PTMi


title: T4H16

data_processing:
Illumina platform used for base-calling, fastx_toolkit_0.0.14, SeqPrep, and Sickle softwares used for quality control of sequence reads.
Clean data was assambled for mapped data with Hisat2 software, then mapped to hg19 whole genome using Cufflinks software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with RSEM software. Exons from all isoforms of a gene were merged to create one meta-transcript considering paired-end reads, reads length, and fragment length.
Genes were considered significantly differentially expressed under the following criteria: p-adjust < 0.05 & |log2FC| >= 1.
Assembly: hg19
Supplementary files format and content: xls file includes RPKM values for each Sample.

extract_protocol:
Total mRNA was extracted using TRIZOL Reagent (Cat#15596-018) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies). Illumina Hiseq 4000 SBS Kit (Cat#FC-410-1003) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: gastric cancer cells


title: Ctrl3 ChIP-Seq


title: T4H15


title: T4ctrl2


title: T4H14


title: SHSY5YOverC2


title: T4ctrl3


title: T4ctrl1


title: NCH16


title: NCctrl2


title: NCH15


title: NCH14


title: NCctrl3


title: HEK293_sub_total_lysate_biol_rep_3


title: HGC-27 GLUP_3

data_processing:
Illumina platform used for base-calling, fastx_toolkit_0.0.14, SeqPrep, and Sickle softwares used for quality control of sequence reads.
Clean data was assambled for mapped data with Hisat2 software, then mapped to GRCh38.p10 whole genome using Cufflinks software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with RSEM software. Exons from all isoforms of a gene were merged to create one meta-transcript considering paired-end reads, reads length, and fragment length.
Genes were considered significantly differentially expressed under the following criteria: p-adjust < 0.05 & |log2FC| >= 1.
Assembly: GRCh38.p10
Supplementary files format and content: xls file includes RPKM values for each Sample.


title: HGC-27 Con_3


title: HGC-27 Con_2


title: NCctrl1


title: HGC-27 GLUP_1


title: HGC-27 Con_1


title: HEK293WT confluent biol rep1

data_processing:
RNAseq data were preprocessed using the RNAseq nf-core pipeline  (https://nf-co.re/rnaseq)
Assembly: hg38
Supplementary files format and content: format: tsv content: TPM

growth_protocol: HEK293 and A375 cells were cultured in DMEM media supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin, while SHSY5Y cells were  cultured in RPMI media supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin.

extract_protocol:
Total RNA was extracted using Quick-RNA Miniprep Kit (BioSite-R1055, Zymo Research).
Libraries were prepared from 300 ng RNA using the Illumina Stranded Total RNA library preparation kit, including Ribo-Zero Plus treatment (20040525/20040529, Illumina Inc.) according to manufacturer’s instructions. For indexing Unique Dual Indexes (20040553/20040554, Illumina Inc.) were used.

value: no


title: SHSY5Y WT confluent biol rep1


title: SHSY5Y WT sub biol rep1


title: HEK293WT sub biol rep2


title: HEK293WT sub biol rep3


title: SHSY5Y WT confluent biol rep3


title: SHSY5Y WT confluent biol rep2


title: A375 WT confluent biol rep2


title: SHSY5Y WT sub biol rep2


title: HEK293WT confluent biol rep2


title: A375 WT confluent biol rep1


title: A375 WT confluent biol rep3


title: HEK293WT sub biol rep1


title: A375 WT sub biol rep3


title: A375 WT sub biol rep2


title: A375 WT sub biol rep1


title: HGC-27 GLUP_2


title: BC rep 32

city: Xuhui District

first: Kun

last: Zheng

state: Shanghai

address: No. 600, Yishan Road, Xuhui District, Shanghai

department: Department of Urology

institute: Shanghai 6th Peoples Hospital Affiliated to Shanghai Jiao Tong University

description: Low-grade papillary urothelial carcinoma

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

source_name: Bladder

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture er's protocols.

treatment_protocol: Surgery

tag: tissue

value: Bladder

value: Male

tag: tumor stage

value: Ta

value: Surgery

tag: batch


title: BC rep 31

description: High-grade papillary urothelial carcinoma


title: HEK293WT confluent biol rep3

value: WT


title: BC rep 30

value: Female

value: Low-grade papillary urothelial carcinoma


title: BC 31

value: High-grade papillary urothelial carcinoma


title: BC 29


title: BC rep 28


title: BC rep 29


title: BC 28


title: BC 30


title: SHSY5Y WT sub biol rep3


title: BC rep 27

description: High-grade invasive urothelial carcinoma


title: BC 27

value: High-grade invasive urothelial carcinoma


title: BC 26


title: Curtobacterium_Wood_21_T3_R3

city: Irvine

first: Nicholas

middle: C

last: Scales

state: CA

address: 321 Steinhaus Hall

department: Ecology & Evolutionary Biology

institute: UC Irvine

description: there are two sets of paired-end reads for each sample, for increased depth. These are technical replicates and can be combined

data_processing:
Raw reads were QC'ed and low quality reads were removed using trimmomatic.
Bowtie2 was used to remove rRNA by mapping the reads to the SILVA v0.2 ssRNA database
Fully closed reference genomes were annotated using PROKKA
Salmon was used to map mRNA to the reference genome
DESeq was used in R for differential abundance testing
Assembly: GCA_001864975.1
Supplementary files format and content: The processed data file is one combined DESeq differential abundance table for all the strains. Day 0 was used as the control, representing the unstressed mid-log cells, and the two constasts are day 1 vs day 0 and day 32 vs day 0
Supplementary files format and content: The DESeq output underwent the LFC processing step as recommended in their manual

organism: Curtobacterium

source_name: Bacterial isolate

growth_protocol: Isolates were streaked from frozen (-80C) glycerol stock and then grown in Luria Broth and harvested at mid-log phase

extract_protocol:
We used the ZymoBiomics Quick-RNA Fungal/Bacterial Kit. We lysed the cells by bead beating for 5 min at 6.5 m/sec in a MPBio FastPrep bead beater and in the final protocol step eluted into 10µL DNase/RNase free water
9 µL of total RNA was mixed with 1 µL 10x Turbo DNase Buffer and 1 µL of Turbo DNase Enzyme. The enzymatic digestion proceeded for 30 minutes at 37C in a PCR machine. We inactivated the reaction by mixing in 2 µL of DNase Inactivation buffer. Subsequently, we followed the Kapa RNA Hyper Prep Protocol. For fragmentation we incubated the total RNA with the Fragment Prime Elute Buffer for 6 minutes at 85°C

treatment_protocol: They were then centrifuged at 2808 rcf for 15 minutes, washed twice in 0.9% saline, and resuspended in 0.9% saline. They were subjected to up to 32 days inside a desiccation chamber on glass slides. Saline was added to the slides to remove the cells, and they were added to a ZymoBiomics ZR Bashing Bead Tube and flash frozen in liquid nitrogen, and then stored in the freezer (-80C)

value: Bacterial isolate

tag: clade

value: I

tag: timepoint

tag: days

tag: replicate


title: BC 32

tag: treatment


title: Curtobacterium_Salt_16_T3_R3

tag: cell type


title: Curtobacterium_Pine_43_T0_R1

value: IV


title: BC 24

tag: genotype


title: BC 23


title: BC rep 26


title: BC 25


title: Curtobacterium_Desert_3_T0_R3

value: V


title: Curtobacterium_Salt_16_T1_R2


title: BC rep 22


title: Curtobacterium_Wood_52_T0_R3


title: BC 22


title: Curtobacterium_Salt_16_T1_R1


title: Curtobacterium_Desert_3_T3_R2


title: BC 21


title: BC 20


title: Curtobacterium_Pine_43_T0_R3


title: BC rep 21


title: Curtobacterium_Wood_21_T1_R1


title: BC 19


title: BC rep 19


title: Curtobacterium_Desert_3_T1_R1


title: BC rep 25


title: Curtobacterium_Desert_35_T1_R2


title: BC rep 17


title: Curtobacterium_Desert_3_T0_R2


title: BC rep14

description: Urothelial carcinoma in situ

value: Tis

value: Urothelial carcinoma in situ


title: Curtobacterium_Desert_35_T1_R1


title: Curtobacterium_Wood_52_T1_R2


title: BC 17


title: BC 14

description: Urothelial carcinoma in situ


title: Curtobacterium_Wood_52_T3_R1


title: Curtobacterium_Desert_3_T1_R2


title: BC 13


title: Curtobacterium_Desert_40_T3_R2


title: BC rep 12


title: Curtobacterium_Pine_43_T1_R3


title: BC rep 13


title: BC 12


title: Curtobacterium_Salt_16_T3_R1


title: Curtobacterium_Desert_40_T0_R3


title: Curtobacterium_Wood_21_T0_R2


title: Curtobacterium_MMLR14_002_T3_R1


title: BC 18

description: Urothelial neoplasms of low malignant potential


title: BC 10


title: Curtobacterium_Grass_32_T3_R3


title: BB180 + ifng - 24h - rep2

tag: cell line

value: HeLa (ACC 57, DSMZ)

value: cervical cancer

value: gRNA transfection

tag: guide rna

value: STAT1 Y701C

value: IFN-γ 24hrs


title: BC rep 11

value: Bladder

value: Male

value: Surgery


title: BC 11


title: Curtobacterium_MMLR14_002_T3_R2


title: BC 16

value: Female

value: Ta

value: Low-grade papillary urothelial carcinoma


title: UF_10_FSH_136

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

data_processing:
Rna-seq reads were aligned with STAR-aligner using the genome build Ensembl Ovis aries Oar3.1 Release 89
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: Ovis aries Ensembl Oar3.1 Release 89
Supplementary files format and content: Tab-delimited .txt files include 5 columns, ensemble transcripts identifier, transcript length, effective transcript length, estimated counts and transcripts per million.

organism: Ovis aries

source_name: endometrial caruncule

extract_protocol:
Total RNA was isolated using TRIzol reagent, according to the manufacturer’s instructions. Extracted RNA was prepared for sequencing using the Illumina Truseq mRNA Library assay following manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: endometrial caruncule

value: FSH stimulated (SOV)


title: UF_10_FSH_119


title: UF_10_FSH_147


title: BC 9

value: High-grade papillary urothelial carcinoma


title: Curtobacterium_Desert_40_T1_R3

value: Bacterial isolate

value: V


title: UF_10_C_88

value: Control (untreated with FSH)


title: BC 8


title: UF_10_C_67


title: Curtobacterium_Desert_40_T0_R2


title: UF_10_C_41


title: BC 7


title: BC rep 4

value: High-grade invasive urothelial carcinoma


title: UF_10_C_27


title: Curtobacterium_Wood_52_T3_R3

value: IV


title: OF_10_FSH_120


title: OF_10_FSH_118


title: OF_10_FSH_101


title: Curtobacterium_Salt_16_T0_R1

value: I


title: OF_10_C_77


title: BC 6

description: Inverted urothelial papilloma

value: Inverted urothelial papilloma


title: Curtobacterium_Grass_32_T1_R2


title: BC rep 5

description: Urothelial carcinoma in situ

value: Tis

value: Urothelial carcinoma in situ


title: OF_10_C_53


title: Curtobacterium_Wood_21_T0_R1


title: OF_10_C_20


title: BC 5

description: Urothelial carcinoma in situ

value: Bladder

value: Male


title: OF_10_C_45


title: NF_5_C_74


title: OF_10_C_28


title: NF_5_C_51


title: Curtobacterium_Wood_52_T1_R1


title: BC 4

value: Female

value: Surgery


title: Curtobacterium_MMLR14_002_T0_R2


title: BC rep 3

value: Ta


title: NF_5_C_31

value: endometrial caruncule


title: Curtobacterium_Desert_40_T3_R1


title: NF_10_FSH_143

value: FSH stimulated (SOV)


title: OF_10_FSH_146


title: NF_5_C_42


title: NF_10_FSH_140


title: BC 3

value: High-grade papillary urothelial carcinoma


title: Curtobacterium_MMLR14_002_T1_R2

value: Bacterial isolate


title: NF_5_C_3


title: NF_10_FSH_137


title: Curtobacterium_Desert_40_T3_R3

value: V


title: BC 2

description: Inverted urothelial papilloma


title: NF_10_FSH_110


title: NF_10_C_78

value: Control (untreated with FSH)


title: Curtobacterium_Wood_21_T1_R2


title: NF_10_C_69


title: BC 1


title: Curtobacterium_Desert_35_T1_R3


title: NF_10_C_63


title: Curtobacterium_Salt_16_T3_R2


title: PROTAC experiment, KELLY cells, GSK6991, MYCN antibody, 6 hours, replicate 2

city: Cambridge

first: Gabriela

last: Alexe

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

description: Sequencing performed at the Molecular Biology Core Facilities (MBCF) at Dana-Farber Cancer institute (DFCI)

data_processing:
ChIP-Seq data analysis was performed in alignment with the ENCODE Consortium standards (https://www.encodeproject.org/chip-seq/). Quality control tests for unmapped sequences were performed by using the FastQC v.0.11.9 software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). All samples passed the QC, except MYCN replicate 2 for the PROTAC experiment on KELLY cells treated with DMSO at 6h. The MYCN replicate 2 for the PROTAC experiment on KELLY cells treated with DMSO at 6h was removed.
The ChIP-sequences were aligned to the GRCh38/hg38 genome and to the spiked-in dm6 Drosophila melanogaster genome using bowtie2-2.3.5 (Langmead and Salzberg, 2012) with the standard options.  PCR duplicates were removed with the Picard Mark Duplicates method   implemented in the sambamba v0.7.1 tool (Tarasov et al., 2015). The alignments with MAPQ < 5 were skipped.
The mapped reads were normalized in units of reads per kilobase per million (RPKM or rpm/bp) and coverage tracks for the RPKM signal were created as bigwig files for bins of size 20 base pairs by using the bamCoverage tool available in deepTools v3.5.1 (Ramírez et al., 2016). The Active Motif Spike-in Normalization protocol was then applied to each hg38 sample. The dm6 genome-wide counts distribution on 200 bp size bins was computed with the multiBamSummary function available from the deepTools v3.5.1. The dm6 uniquely mapped reads were summed up from all the bins with at least 10 mapped dm6 reads. Each hg38 sample was normalized by multiplying the human tag counts with the scaling factor derived from the Drosophila reads as ratio between the average of the uniquely mapped dm6 counts across all samples vs. the dm6 uniquely mapped reads counts for that sample.
Peak calling was performed against the input control using the model-based MACS2 v2.1.1.20160309 software (Zhang et al., 2008), with the significance cut-off FDR ≤ 0.01. Area under the curve (AUC) RPKM normalized signal across genomic regions was computed with the bwtool software (Pohl and Beato, 2014). Each set of MACS2 peaks  was curated by removing the binding regions with low area under curve RPKM coverage (log2(AUC+1)< 13) and the regions overlapping with the  ENCODE black-listed regions for hg38 (available at https://www.encodeproject.org/annotations/ENCSR636HFF/). Quality control tests for the peaks were performed by using the ChIPQC library available from Bioconductor v3.9 (Carroll et al., 2014).
The peaks were annotated with the closest hg38 genes by using the annotatePeaks function implemented in the Homer v4.11 platform (Heinz et al., 2010) and the GREAT annotation platform (McLean et al., 2010).  Binding peaks and normalized binding signal were visualized on the Integrative Genomic Viewer (IGV) v2.12.3 platform (Thorvaldsdóttir et al., 2013).  Gene promoter regions were defined as the +/- 3.0 kb intervals around the hg38 gene transcription start site (TSS). Enhancer regions were defined as the H3K27ac binding regions outside TSS +/- 3.0 kb gene promoter regions. The samtools v1.9 (Li et al., 2009) and the BEDTools v2.29 suite (Quinlan and Hall, 2010) were used to perform various mapping and genomic region analyses (indexing, sorting, intersection, merging).
Per each antibody, the binding sites identified by MACS2 for treatment and control conditions across time points were merged into the antibody’s set of aggregated peaks.  A peak by sample counts matrix was created by counting the reads overlapping each aggregated peak with the multiBamSummary tool available from deepTools. The counts matrix was used to perform differential peak analysis. For a specific genomic region, the changes in signal between two conditions were classified as increase, decrease or not significant  based on the absolute cut-off 1.5 for the delta area under curve scores; the significance was quantified based on the cut-off p-value ≤ 0.10 for the differences in the mapped reads by using edgeR v3.36.0 with the  glmLRT model (Robinson et al., 2010).   Heatmaps of AUC ChIP-seq normalized signal occupancy on genomic regions were created using the computeMatrix and the plotHeatmap tools available in deepTools v3.5.1. The plotProfile tool from deepTools v3.5.1 was used to create metaplots based on the average normalized scores across genomic regions. Differences between metaplots were estimated based on the t-test with Welch correction (cutoff P-value ≤ 0.05) for the area under curve (AUC) RPKM normalized signal across the regions for the conditions.  Motif enrichment analysis was performed for genomic regions and gene promoters using the Homer v4.11 platform (Heinz et al., 2010) and the  MEME Suite v5.4.1 platform (FIMO method) (Bailey et al., 2015) with the adjusted p-value cutoff ≤ 0.01.
Assembly: hg38
Supplementary files format and content: bigWig RPKM binding signal

source_name: KELLY

growth_protocol: Neuroblastoma cell lines were grown in 15 cm plates.

extract_protocol:
20 million cells were cross-linked with 1% formaldehyde in 22 mL warm media for 10 minutes with rotation followed by quenching with the addition of 1.1 mL of 2.5 M glycine for 5 minutes. Cells were pelleted by centrifugation at 600xg and resuspended in 1 mL cold PBS supplemented with protease inhibitors (Thermo Fisher # 78430) and 1 mM PMSF (Sigma Aldrich #P7626). This wash was repeated twice for a total of three washes in PBS. Cells were resuspended in cytoplasmic and then nuclear lysis buffer, and cells were sheared on an E220 Covaris sonicator (Duty cycle: 5%; Peak power: 140W; Cycles per Burst:200; Temp: 4C; time 15 min). Sheared lysates were cleared by centrifugation at 15,000g for 10 minutes at 4C and incubated overnight with rotation at 4C with magnetic beads prebound with antibody, spike-in antibody (Active Motif #61686), and spike-in chromatin (Active Motif #53083). Following overnight incubation, beads were washed twice with low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tri-HCl pH8.1, 150 mM NaCl), twice with high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tri-HCl pH8.1, 500 mM NaCl), twice with LiCl wash buffer (0.25 M LiCl, 1% IGEPAL-CA 630, 1% deoxycholic acid, 10 mM Tri-HCl ph8.1, 1 mM EDTA), and once with TE. DNA was eluted in elution buffer (1% SDS, 0.1 M NaHCO3). Cross linking was reversed overnight at 65C with 0.9% RNAse A, 0.9% Proteinase K, and 0.182 M NaCl. DNA was isolated by adding Agencourt AMPure XP beads (Beckman Coulter A63880) at 1.2x volume, incubating 20 minutes, washing twice with 80% ethanol, and eluting into 10-20 µl TE.
ChIP-Seq libraries were prepared using Swift S2 Acel reagents on a Beckman Coulter Biomek i7 liquid handling platform from approximately 1ng of DNA according to manufacturer’s protocol and 14 cycles of PCR amplification. Finished sequencing libraries were quantified by Qubit fluorometer and Agilent TapeStation 2200.  Subsequently, libraries were paired end sequenced on Illumina NovaSeq 6000.

treatment_protocol: Antibodies used for ChIP were HA-tag (Cell Signaling Technologies, #3724), H3K9ac (Abcam #ab4441), H3K27ac (Abcam #ab4729), and MYCN (Abcam #ab16898). For HA-tag ChIP in KELLY, 5 µg of HA antibody was used for 20 million cells. For NGP and NB1 HA-tag ChIPs, 50 µl of HA antibody was used for 20 million cells. For MYCN, 10 µg of antibody was used per sample of 20 million cells. For H3K9ac, 5 µg of antibody was used per sample of 5 million cells. For H3K9ac, 7.5 µl of spike-in chromatin was used per sample. For MYCN, 3 µl of spike-in chromatin was used per sample. For HA ChIP, 10 µl of spike-in chromatin was used per sample of 20 million cells. For H3K27ac, 5 µg antibody and 2 µl of spike-in chromatin was used for 10 million cells. For each sample, protein A or protein G beads (Life Technologies #10003D) were prepared by washing three times in BSA blocking solution, then resuspended in 250 µl/sample BSA blocking solution with appropriate antibody and spike-in antibody. Beads were incubated overnight with rotation, washed four times with BSA blocking solution, and resuspended in 100 µl/sample BSA blocking solution. Spike-in chromatin was added to the beads two hours before adding sheared human chromatin and incubated with rotation at 4C.

value: KELLY

value: Neuroblastoma, MYCN amplified

tag: chip antibody

value: MYCN (Abcam #ab16898)

tag: spike-in antibody

value: spike-in antibody (Active Motif cat.#61686)


title: NF_10_C_49


title: Nip_endosperm, polyA RNA, untreated, rep2

city: Chicago

first: CHUAN

last: HE

state: Illinois

address: 929 East 57th Street, GCIS E313

institute: University of Chicago

data_processing:
m6A sites were detected using the method previously published (https://github.com/y9c/m6A-SACseq) 18. The analysis utilized the reference genome downloaded from the Ensembl database, with assembly versions TAIR10 and IRGSP-1.0 employed for Arabidopsis and rice respectively.
Assembly: IRGSP-1.0
Supplementary files format and content: TSV

organism: Oryza sativa Japonica Group

extract_protocol:
A total of 50 ug total RNA for each of the two biological replicates was used for mRNA capture (Dynabeads mRNA DIRECT Purification Kit (Invitrogen)) following the manufacturer′ s instructions with modification. Briefly, 50 ug total RNA was diluted with H2O in 100ul volume and then denatured under 65°C for 2 min, and immediately put on the ice for exactly 2 min. Next, a total of 100ul Dynabeads were washed twice with 200ul lysis/binding buffer provided in the above kit. The washed beads were then eluted in 100ul lysis/binding buffer, which further mixed with the denatured total RNA. Then, the sample was put on the rotor to binding for 15 min at room temperature. After binding, wash buffer B was used to wash the beads for twice. 30ul H2O was used to elute the beads and immediately put on the 75°C for 2min. The eluted mRNA was collected after magnetic separation. The mRNA capture process was repeated as described above to obtain the more purified mRNA.
50ng mRNAs of each replicate were used for the library construction. All these libraries were constructed exactly following the previously published protocols


title: PROTAC experiment, KELLY cells, GSK6991, MYCN antibody, 6 hours, replicate 1


title: Nip_endosperm, polyA RNA, untreated, rep1


title: Curtobacterium_Wood_21_T0_R3

tag: strain

value: I


title: Curtobacterium_Grass_32_T0_R2

value: IV


title: Nip_endosperm, polyA RNA, treated, rep2


title: BC rep 1

value: Bladder

tag: Sex


title: Nip_endosperm, polyA RNA, treated, rep1


title: Nip_embryo, polyA RNA, untreated, rep2


title: Nip_embryo, polyA RNA, untreated, rep1


title: PROTAC experiment, KELLY cells, GSK6991, Input, 6 hours, replicate 1

description: Sequencing performed at Novogene Co


title: Nip_embryo, polyA RNA, treated, rep2


title: Curtobacterium_Wood_21_T3_R1


title: Curtobacterium_Grass_32_T1_R3


title: PROTAC experiment, KELLY cells, GSK6991, H3K9ac antibody, 6 hours, replicate 1

description: Sequencing performed at Novogene Co

value: H3K9ac (Abcam cat.# ab4441)


title: Curtobacterium_Desert_3_T3_R3


title: Nip_seedling_2Week, polyA RNA, untreated, rep2


title: PROTAC experiment, KELLY cells, GSK6991, H3K27ac antibody, 6 hours, replicate 2

description: Sequencing performed at Novogene Co

value: H3K27ac (Abcam #ab4729)


title: Curtobacterium_Desert_40_T0_R1


title: Nip_seedling_2Week, polyA RNA, untreated, rep1


title: Nip_embryo, polyA RNA, treated, rep1


title: PROTAC experiment, KELLY cells, GSK6991, H3K9ac antibody, 6 hours, replicate 2

description: Sequencing performed at Novogene Co


title: Nip_seedling_2Week, polyA RNA, treated, rep2


title: Curtobacterium_Grass_32_T3_R1


title: Nip_panicle, polyA RNA, untreated, rep2


title: PROTAC experiment, KELLY cells, GSK6991, H3K27ac antibody, 6 hours, replicate 1

description: Sequencing performed at Novogene Co


title: Curtobacterium_Grass_32_T3_R2


title: Nip_panicle, polyA RNA, untreated, rep1


title: PROTAC experiment, KELLY cells, GSK6991, Input, 6 hours, replicate 2

description: Sequencing performed at Novogene Co


title: Nip_panicle, polyA RNA, treated, rep2


title: Nip_panicle, polyA RNA, treated, rep1


title: PROTAC experiment, KELLY cells, DMSO, MYCN antibody, 6 hours, replicate 1


title: Nip_plumule_dark, polyA RNA, untreated, rep2


title: PROTAC experiment, KELLY cells, DMSO, Input, 6 hours, replicate 2

description: Sequencing performed at Novogene Co


title: Nip_plumule_dark, polyA RNA, untreated, rep1


title: Curtobacterium_Desert_35_T0_R3


title: Nip_plumule_dark, polyA RNA, treated, rep2


title: Nip_seedling_2Week, polyA RNA, treated, rep1


title: Nip_plumule_light, polyA RNA, untreated, rep2


title: Curtobacterium_Desert_40_T1_R2


title: PROTAC experiment, KELLY cells, DMSO, H3K9ac antibody, 6 hours, replicate 2

description: Sequencing performed at Novogene Co


title: Nip_plumule_dark, polyA RNA, treated, rep1


title: Nip_plumule_light, polyA RNA, treated, rep2


title: Nip_plumule_light, polyA RNA, treated, rep1


title: PROTAC experiment, KELLY cells, DMSO, H3K9ac antibody, 6 hours, replicate 1

description: Sequencing performed at Novogene Co


title: Nip_flagleaf, polyA RNA, untreated, rep2


title: Nip_flagleaf, polyA RNA, untreated, rep1


title: PROTAC experiment, KELLY cells, DMSO, H3K27ac antibody, 6 hours, replicate 2

description: Sequencing performed at Novogene Co


title: Curtobacterium_Desert_3_T3_R1


title: Curtobacterium_MMLR14_002_T0_R1


title: Nip_flagleaf, polyA RNA, treated, rep2


title: PROTAC experiment, KELLY cells, DMSO, H3K27ac antibody, 6 hours, replicate 1

description: Sequencing performed at Novogene Co


title: Nip_flagleaf, polyA RNA, treated, rep1


title: Curtobacterium_Wood_52_T3_R2


title: Curtobacterium_MMLR14_002_T1_R1


title: Nip_seedling, polyA RNA, untreated, rep2


title: PROTAC-RNA, KELLY cells, GSK-699-1, 72 hours, replicate 3

data_processing:
RNA-Seq data analysis was performed in alignment with the ENCODE Consortium standards (https://www.encodeproject.org/chip-seq/). Quality control tests for unmapped reads were performed based on the FastQC v.0.11.9 software (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and summarized with multiQC v1.9 PMID: 27312411.  All samples except the CRISPR KO and sg LacZ at 12 days were spiked-in with the ERCC RNA Spike-In Mix1 (ThermoFisher Cat. No.: 4456740, https://tools.thermofisher.com/content/sfs/manuals/ERCC92.zip). The spiked human reads were mapped to hg38/gencode v30 and to the ERCC genome  using STAR v2.7.2b  PMID: 23104886
Quality control for the mapped reads and for replicate reproducibility were performed using SARTools v1.7.3 PMID: 27280887.
Gene level reads were summarized by counting the reads that overlapped the hg38/gencode v30 gene exons by using the featureCounts v1.6.3 method implemented in the Subread v2.0.0 package (http://subread.sourceforge.net) PMID: 24227677.
Gene counts were normalized and used to quantify the differential genes between the experimental and control conditions using DESeq2 v1.32.0 PMID: 25516281. Gene expression was estimated based on the log2(TPM+1) scores for normalized reads PMID: 34158060. The expressed genes were identified as the genes with  maximum log2(TPM+1)  expression ≥ 1 across  conditions.
The gene differentiability was assessed with DESeq2 based on the robust shrunken log2 fold change scores  and  the approximate posterior estimation for GLM coefficients (apeglm v1.6)  method for effect size PMID: 25516281. The cutoffs for gene differentiability were |fold change expression| ≥ 1.5 and adj P-value ≤ 0.10.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts and log2(TPM+1) values for each sample.

extract_protocol:
RNeasy PLUS Mini Kit from Qiagen (#74134)
Illumina TruSeq Stranded Total RNA Library Prep

value: neuroblastoma cell line

value: KAT2A/KAT2B targeted

tag: time

value: 72 hours


title: Nip_seedling, polyA RNA, untreated, rep1

tag: tissue


title: PROTAC experiment, KELLY cells, DMSO, Input, 6 hours, replicate 1

description: Sequencing performed at Novogene Co


title: Nip_seedling, polyA RNA, treated, rep2


title: Curtobacterium_Wood_52_T1_R3


title: Nip_seedling, polyA RNA, treated, rep1


title: NTL12-SRDX_2

city: Berkeley

first: Yangnan

last: Gu

state: California

address: 371 Koshland Hall, Berkeley, CA 94720, Department of Plant & Microbial Biology

institute: UC Berkeley

data_processing:
Clean mRNA-seq reads were aligned to the Arabidopsis thaliana reference genome (TARI10) using HISAT2 (v2.0.4) with default parameters.
Gene-level read counts were calculated with HTseq (v0.6.1p1) with the union mode.
Assembly: TAIR 10
Supplementary files format and content: raw counts, normalized abundance measurements

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Plants grown on soil

extract_protocol:
Total RNA was extracted from about 50 mg samples of 4-week-old leaves using RNAprep pure Plant Kit (Genesee Scientific, Catalog #11– 330).
mRNA-Seq(Strand-Specific) libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: leaves

tag: age

value: 35S:NTL2-SRDX pnet2_ab_2


title: Curtobacterium_Desert_35_T3_R2

value: Bacterial isolate


title: Nip_plumule_light, polyA RNA, untreated, rep1


title: PROTAC-RNA, KELLY cells, GSK-699-1, 72 hours, replicate 1


title: NTL12-SRDX_1

value: 35S:NTL12-SRDX pnet2_ab_1


title: Curtobacterium_MMLR14_002_T1_R3


title: PROTAC-RNA, KELLY cells, DMSO, 72 hours, replicate 3

value: WT

value: DMSO


title: NTL9-SRDX_1

value: 35S:NTL9-SRDX pnet2_ab_1


title: Curtobacterium_Wood_52_T0_R2


title: NTL6-SRDX_2

value: 35S:NTL6-SRDX pnet2_ab_2


title: PROTAC-RNA, KELLY cells, DMSO, 72 hours, replicate 2

value: KELLY


title: NTL6-SRDX_1

value: 35S:NTL6-SRDX pnet2_ab_1


title: Curtobacterium_Desert_3_T1_R3

value: V


title: pnet2_2


title: PROTAC-RNA, KELLY cells, DMSO, 72 hours, replicate 1


title: PROTAC-RNA, KELLY cells, GSK-699-1, 24 hours, replicate 3

value: 24 hours


title: Curtobacterium_Pine_43_T0_R2

value: IV


title: PROTAC-RNA, KELLY cells, GSK-699-1, 72 hours, replicate 2


title: Curtobacterium_Salt_16_T0_R3

value: I


title: WT_2


title: WT_1


title: T24-hNectin4 (ADC-control) mouse 6

city: Bothell

first: John

last: Gosink

email: john@gosink.org, john.gosink@pfizer.com

state: WA

department: Computational Biology

institute: Pfizer

data_processing:
Adaptors removed with cutadapt
Reads were aligned and quantitated with STAR/RSEM
Assembly: hg38 mm10 composite genome
Supplementary files format and content: matrix of TPMs for both human and mouse reads

organism:
Homo sapiens
Mus musculus

source_name: xenograft

growth_protocol: T24-hNectin-4 cells were resuspended in 50% Matrigel before subcutaneous injection of 5×106 T24-hNectin-4 xenograft tumor cells (0.1 mL volume) in the flanks of athymic nude female mice (Envigo, BALB/cAnNHsd). Tumor pieces were passaged via trocar needle two times to establish consistent engraftment.

extract_protocol:
Tumors were harvested 5 days after treatment and processed via polyA selection.
Standard paired end read preparation by Azenta.

treatment_protocol: On Day 15 post implantation, tumor volumes reached ~200 mm3 (calculated using 0.5 × [length] × [width]2), and the mice were treated with a single intraperitoneal (IP) dose of 3 mg/kg enfortumab vedotin. As a control, mice were treated with 3 mg/kg IgG-MMAE.

value: xenograft

value: non-binding ADC control at 3 mg/kg


title: Curtobacterium_Wood_21_T3_R2


title: T24-hNectin4 (ADC-control) mouse 7


title: T24-hNectin4 (ADC-control) mouse 5


title: PROTAC-RNA, KELLY cells, GSK-699-1, 24 hours, replicate 1

value: neuroblastoma cell line

value: KAT2A/KAT2B targeted


title: T24-hNectin4 (ADC-control) mouse 4


title: Curtobacterium_Grass_32_T0_R1


title: T24-hNectin4 (ADC-control) mouse 3


title: PROTAC-RNA, KELLY cells, DMSO, 24 hours, replicate 3


title: PROTAC-RNA, KELLY cells, DMSO, 24 hours, replicate 2


title: T24-hNectin4 (ADC-control) mouse 1


title: PROTAC-RNA, KELLY cells, GSK-699-1, 24 hours, replicate 2


title: NTL9-SRDX_2

value: leaves

value: 35S:NTL9-SRDX pnet2_ab_2


title: Curtobacterium_Pine_43_T1_R2

value: Bacterial isolate


title: pnet2_1


title: T24-hNectin4 (ADC-treated) mouse 7

value: ASG-22C3E at 3.0 mg/kg


title: T24-hNectin4 (ADC-treated) mouse 6


title: PROTAC-RNA, KELLY cells, DMSO, 24 hours, replicate 1

value: WT

value: DMSO


title: T24-hNectin4 (ADC-treated) mouse 5


title: T24-hNectin4 (ADC-control) mouse 2


title: Curtobacterium_Desert_35_T0_R2


title: T24-hNectin4 (ADC-treated) mouse 1


title: Curtobacterium_Pine_43_T3_R2


title: T24-hNectin4 (untreated) mouse 7

value: Untreated


title: PROTAC-RNA. KELLY cells, GSK-699-1, 6 hours, replicate 2

value: KELLY

value: 6 hours


title: T24-hNectin4 (ADC-treated) mouse 4


title: Curtobacterium_Desert_35_T0_R1

value: V


title: PROTAC-RNA. KELLY cells, GSK-699-1, 6 hours, replicate 3


title: T24-hNectin4 (untreated) mouse 6


title: Curtobacterium_Grass_32_T1_R1


title: PROTAC-RNA. KELLY cells, GSK-699-1, 6 hours, replicate 1


title: T24-hNectin4 (ADC-treated) mouse 3


title: Curtobacterium_Salt_16_T1_R3


title: Curtobacterium_Desert_40_T1_R1


title: T24-hNectin4 (ADC-treated) mouse 2


title: PROTAC-RNA, KELLY cells, DMSO, 6 hours, replicate 3


title: T24-hNectin4 (untreated) mouse 2


title: T24-hNectin4 (untreated) mouse 4


title: PROTAC-RNA, KELLY cells, DMSO, 6 hours, replicate 2


title: T24-hNectin4 (untreated) mouse 3


title: Curtobacterium_Wood_52_T0_R1


title: PROTAC-RNA, KELLY cells, DMSO, 6 hours, replicate 1


title: Curtobacterium_Pine_43_T1_R1


title: NK cells ; RMA-KR 2 ; Late D+14 [TRWR79]

city: Lyon

first: Kévin

last: Pouxvielh

state: France

address: 50 Avenue Tony Garnier

country: France

institute: U1111 - Centre International de Recherche en Infectiologie (CIRI)

data_processing:
raw data were preprocessed using cutadapt 1.10 in order to remove adaptor and low595 quality sequences (Phred quality score below 20). Reads shorter than 40 bp were removed for further analysis. Remaining reads were mapped to mouse rRNA sequences using bowtie 2.2.8 and reads mapped to rRNA sequences were discarded for further analysis. Remaining reads were aligned to mm10 assembly of the mouse genome with STAR 2.5.3a. Gene quantification was performed with htseq-count 0.6.1p1 using “union” mode and Ensembl 96 annotations. Differential gene expression analysis between groups of samples was performed using method implemented in the Bioconductor R package DESeq2 1.16.1, with the following non602 default options: betaPrior=TRUE, alpha=0.05. P-values were adjusted for multiple testing using the Benjamini and Hochberg method.
Assembly: mm10
Supplementary files format and content: A TSV (tab-separated values) file provides raw read counts and normalized read counts for each gene together with gene annotations and the p-value, adjusted p-value and log2 fold-change for each performed comparison. This file contains only genes with at least one read count in one sample. It can be opened with a spreadsheet software like Excel or Calc. The “,” character is used as decimal separator in numeric columns. This file contains the following columns:
Supplementary files format and content: Ensembl Gene ID Ensembl identifier of the gene, corresponding to Ensembl release 96.
Supplementary files format and content: Raw read counts Number of reads that have been assigned to the gene.
Supplementary files format and content: Normalized read counts Number of reads that have been assigned to the gene, normalized to make these counts comparable between samples.
Supplementary files format and content: Normalized read counts divided by median of transcripts length in kb Number of reads that have been assigned to the gene, normalized between samples and divided by transcript length in kb (cal culated as the median of the length of all transcripts corresponding to this gene). These expression estimates can be compared across genes and samples.
Supplementary files format and content: Median of transcripts length Median of the length of all transcripts corresponding to this gene (in bp).
Supplementary files format and content: Gene name Common gene name.
Supplementary files format and content: Description Description of the gene.
Supplementary files format and content: Chromosome name Name of the chromosome where the gene is located.
Supplementary files format and content: Start gene position Start coordinate of the gene.
Supplementary files format and content: End gene position End coordinate of the gene.
Supplementary files format and content: Gene biotype Biotype of the gene as defined in Ensembl4.
Supplementary files format and content: GO:biological process Biological process Gene Ontology terms associated with this gene. A biological process term describes a series of events accomplished by one or more organized assemblies of molecular functions.
Supplementary files format and content: GO:molecular function Molecular function Gene Ontology terms associated with this gene. A molecular function term describes activities that occur at the molecular level.
Supplementary files format and content: GO:cellular component Cellular component Gene Ontology terms associated with this gene. A cellular component term describes a location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function.
Supplementary files format and content: log2 FC Log2 of the expression fold change estimated, reflecting differential expression between the two compared conditions.
Supplementary files format and content: pvalue P-value of the statistical test.
Supplementary files format and content: padj P-value of the statistical test, adjusted for multiple testing

extract_protocol:
Total RNA was purified using the Direct-Zol RNA microprep kit (Ozyme) according to manufacturer instructions and was quantified using QuantiFluor RNA system (Promega).
RNAseq libraries were generated using mRNAseq library Prep Kit V2 (LEXOGEN). Tagged library quality was checked on D1000 screen tape and analyzed on Tape station 4200 (Agilent).

value: Spleen

value: NK cells

value: Bearing RMA-KR tumor cells


title: NK cells ; RMA-KR 3 ; Late D+14 [TRWR80]


title: K104421/K109177_ROI_6_well_B05

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

description: Library name:  DSP-1008870999731-D-B05

data_processing:
dcc-metadata = true
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Supplementary files format and content: dcc
Library strategy: GeoMx Seq

source_name: Breast tissues from healthy woman

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

value: Breast tissues from healthy donor donated 10 years apart

tag: disease state

value: healthy donor

tag: slide id

tag: roi number

tag: segment type

value: Full ROI

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Curtobacterium_Salt_16_T0_R2

tag: cell type

tag: strain

tag: clade

value: I

tag: timepoint

tag: days

tag: replicate


title: Curtobacterium_Desert_3_T0_R1


title: NK cells ; RMA-KR 1 ; Late D+14 [TRWR78]

tag: tissue

tag: genotype

tag: treatment


title: T24-hNectin4 (untreated) mouse 5

value: xenograft

tag: cell line


title: NK cells ; RMA-KR 5 ; Intermediate D+7 [TRWR77]


title: K104421/K109177_ROI_5_well_B04

description: Library name:  DSP-1008870999731-D-B04

tag: disease state

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate


title: Curtobacterium_Pine_43_T3_R3

tag: cell type

value: IV


title: K104421/K109177_ROI_4_well_B03

description: Library name:  DSP-1008870999731-D-B03

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: NK cells ; RMA-KR 3 ; Intermediate D+7 [TRWR75]

tag: tissue

tag: genotype


title: Curtobacterium_Wood_21_T1_R3

value: Bacterial isolate

tag: strain

tag: clade

tag: timepoint

tag: days

tag: replicate


title: K104421/K109177_ROI_3_well_B02

description: Library name:  DSP-1008870999731-D-B02

tag: disease state

tag: slide id

tag: roi number

tag: segment type

tag: area


title: NK cells ; RMA-KR 4 ; Intermediate D+7 [TRWR76]

tag: cell type

tag: treatment


title: NK cells ; RMA-KR 2 ; Intermediate D+7 [TRWR74]


title: NK cells ; RMA 3 ; Late D+9 [TRWR72]

value: Bearing RMA tumor cells


title: K104421/K109177_ROI_2_well_B01

description: Library name:  DSP-1008870999731-D-B01

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: NK cells ; RMA 2 ; Late D+9 [TRWR71]

tag: tissue

tag: genotype

value: WT


title: NK cells ; RMA 1 ; Late D+9 [TRWR70]


title: NK cells ; RMA-KR 1 ; Intermediate D+7 [TRWR73]


title: Curtobacterium_Desert_35_T3_R3

tag: strain

tag: clade

tag: timepoint

tag: days


title: Curtobacterium_Grass_32_T0_R3

tag: replicate


title: T24-hNectin4 (untreated) mouse 1

tag: cell line


title: K104421/K109177_ROI_1_well_A12

description: Library name:  DSP-1008870999731-D-A12

tag: disease state

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: stitchedreads

tag: sequencingsaturation


title: NK cells ; RMA 3 ; Intermediate D+4 [TRWR69]

tag: cell type

tag: treatment


title: Curtobacterium_MMLR14_002_T0_R3


title: Curtobacterium_Pine_43_T3_R1


title: K105467/K109184_ROI_10_well_A11

description: Library name:  DSP-1008870999731-D-A11

tag: tissue

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: NK cells ; RMA-KR 3 ; Early D+2 [TRWR66]

tag: genotype


title: NK cells ; RMA 1 ; Intermediate D+4 [TRWR67]


title: NK cells ; RMA-KR 1 ; Early D+2 [TRWR64]


title: Curtobacterium_Desert_35_T3_R1

tag: strain

tag: clade

tag: timepoint

tag: days

tag: replicate


title: K105467/K109184_ROI_9_well_A10

description: Library name:  DSP-1008870999731-D-A10

tag: disease state

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: stitchedreads


title: NK cells ; RMA-KR 2 ; Early D+2 [TRWR65]

tag: tissue

tag: cell type

tag: treatment


title: NK cells ; RMA 3 ; Early D+2 [TRWR63]


title: NK cells ; RMA 2 ; Early D+2 [TRWR62]


title: NK cells ; RMA 2 ; Intermediate D+4 [TRWR68]


title: NK cells ; RMA 1 ; Early D+2 [TRWR61]


title: K105467/K109184_ROI_7_well_A08

description: Library name:  DSP-1008870999731-D-A08

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: K105467/K109184_ROI_5_well_A06

description: Library name:  DSP-1008870999731-D-A06

tag: trimmedreads


title: NK cells ; Control 4 [TRWR60]

tag: genotype

value: Not treated


title: NK cells ; Control 3 [TRWR59]


title: NK cells ; Control 1 [TRWR57]


title: MKN28_shLTBP1_3

city: Yangsan

first: Sae-Ock

last: Oh

state: Gyeongsangnam-do

department: Anatomy

country: South Korea

institute: Pusan National University School of Medicine

data_processing:
FastQC v0.10.1.
STAR version 2.7.3a RSEM version 1.3.1, default parameter
RSEM 1.3.1 in the units of TPM
DEseq2
Genome_build: hg38 and Ensembl v.102
Supplementary_files_format_and_content: csv, nomalized value

source_name: MKN28 gastric cancer cells

growth_protocol: MKN28 cells were maintained in RPMI 1640 Medium containing 10% fetal bovine serum (FBS), 25 mM HEPES, and 100 μg/ml of penicillin/streptomycin in a 5% CO2 atmosphere at 37 °C.

extract_protocol:
Total RNAs wee extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA)
0.1 ug total RNA was used  for libraries using MGIEasy RNA Directional Library Prep Kit(MGI)

tag: cell line

tag: plasmid

value: shLTBP1 plasmid-expressing stable cells


title: K105467/K109184_ROI_6_well_A07

description: Library name:  DSP-1008870999731-D-A07

tag: disease state

tag: slide id

tag: roi number


title: Curtobacterium_MMLR14_002_T3_R3

tag: strain

tag: clade

tag: timepoint

tag: days

tag: replicate


title: NK cells ; Control 2 [TRWR58]

source_name: Spleen

tag: tissue

tag: cell type

tag: treatment


title: MKN28_shLTBP1_2


title: K105467/K109184_ROI_4_well_A05

description: Library name:  DSP-1008870999731-D-A05

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: stitchedreads


title: WT, Saline, 12mo, rep 5

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

data_processing:
Sequencing adapters were trimmed from the raw reads with skewer (version 0.2.2).
Unique molecular identifiers (UMIs) were extracted from each read with the umi2index tool (Lexogen). Quality control of the trimmed reads was performed using FastQC (version 0.11.5).
Reads were aligned to the mouse genome version GRCm38_p6. A STAR index (version 2.7.1a) was built with the –sjdbOverhang=50 argument. Splice junctions from Gencode gene models (release M17) were provided via the –sjdbGTFfile argument. STAR alignments were generated with the following parameters: –outFilterType BySJout, –quantMode TranscriptomeSAM, –outFilterIntronMotifs RemoveNoncanonicalUnannotated, –outSAMstrandField intronMotif, –outSAMattributes NH HI AS nM MD XS and –outSAMunmapped Within. Alignments were obtained with the following parameters: –readFilesCommand zcat –outFilterType BySJout –outFilterMultimapNmax 20 –alignSJoverhangMin 8 –alignSJDBoverhangMin 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.6 –alignIntronMin 20 –alignIntronMax 1000000 –alignMatesGapMax 1000000 –quantMode GeneCounts –outSAMunmapped Within –outSAMattributes NH HI AS nM MD XS –outSAMstrandField intronMotif –outSAMtype BAM SortedByCoordinate –outBAMcompression 6.
Alignments sharing the same UMI and genomic coordinate were deduplicated using the collapse_UMI_bam tool (Lexogen). Post-alignment quality control reports were generated using MultiQC (version 1.0).
The raw gene expression matrix was constructed from the 'forward' column of STAR's ReadsPerGene.out.tab output files using R (version 4.2). Gene symbols and biotype information were extracted from the Gencode GTF file. To calculate normalized counts per million (CPM) TMM normalization was applied across all genes annotated as protein_coding with the edgeR R package (version 3.40.2).
Assembly: GRCm38
Supplementary files format and content: Microsoft excel format with three worksheets: 1) sample annotations, 2) raw counts, 3) normalized counts (CPMs)

source_name: cortex

growth_protocol: All animal experiments were performed either according to German animal welfare law and approved by the government of upper Bavaria (Vet_02-17-106) or by the Denali Therapeutics Institutional Animal Care and Use Committee. Mice were kept under standard housing conditions; standard pellet food and water was provided ad libitum.

extract_protocol:
Total RNA was extracted from frozen brain powder using the Qiagen RNeasy plus kit (Qiagen, 74034). Quality and quantity were assessed with a 4200 TapeStation System (Agilent).
Next generation sequencing libraries were generated with the QuantSeq 3' mRNA-seq Library Prep Kit FWD for Illumina (Lexogen A01173), with the UMI second strand synthesis module in order to identify and remove PCR duplicates. Library quantity and quality were assessed with the 4200 TapeStation system (Agilent). Libraries were pooled in equimolar ratios for sequencing.

treatment_protocol: AAV was applied intravenously via tail vain injection (max. 200 µl). For tissue collection, mice were anesthetized with either Ketamine/Xylazine or tribromoethanol. Mice were transcardiacally perfused with chilled PBS before organ collection. Tissues and fluids were stored at -80°C until further use.

value: cortex

tag: genotype

value: Grn WT

value: Saline

tag: treatment dose

tag: rin

tag: age

value: 12.93 months


title: WT, Saline, 12mo, rep 6


title: KO, AAV, 12mo, rep 5

value: Grn KO

value: 12.0 months


title: KO, Saline, 12mo, rep 5


title: KO, AAV, 12mo, rep 4

value: 12.23 months


title: K105467/K109184_ROI_3_well_A04

description: Library name:  DSP-1008870999731-D-A04

value: Breast tissues from healthy donor donated 10 years apart

tag: disease state

value: healthy donor

tag: slide id

tag: roi number

tag: trimmedreads

tag: sequencingsaturation


title: MKN28_shLTBP1_1

tag: cell line

tag: plasmid


title: KO, Saline, 12mo, rep 4

tag: tissue

tag: treatment

value: 12.7 months


title: WT, Saline, 12mo, rep 4


title: MKN28_shSCR_3

value: shSCR (control) plasmid-expressing stable cells


title: KO, AAV, 12mo, rep 3


title: KO, Saline, 12mo, rep 3

value: 12.67 months


title: K105467/K109184_ROI_1_well_A02

description: Library name:  DSP-1008870999731-D-A02

tag: segment type

value: Full ROI

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: MKN28_shSCR_2


title: K105467/K109184_ROI_8_well_A09

description: Library name:  DSP-1008870999731-D-A09

tag: alignedreads

tag: deduplicatedreads

tag: stitchedreads


title: KO, Saline, 12mo, rep 2

tag: genotype

tag: treatment dose

tag: rin

tag: age

value: 12.2 months


title: KO, AAV, 12mo, rep 2


title: K105467/K109184_2_ROI_2_well_A03

description: Library name:  DSP-1008870999692-B-A03

tag: disease state

tag: slide id

tag: roi number

tag: trimmedreads

tag: sequencingsaturation


title: WT, Saline, 12mo, rep 3

tag: tissue

tag: treatment

value: 12.43 months


title: MKN28_shSCR_1

tag: cell line

tag: plasmid


title: KO, AAV, 12mo, rep 1


title: WT, Saline, 12mo, rep 2


title: K106272/K109169_ROI_13_well_C07

description: Library name:  DSP-1008870999691-D-C07

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: KO, Saline, 12mo, rep 1

tag: genotype

tag: treatment dose


title: K106272/K109169_ROI_12_well_C06

description: Library name:  DSP-1008870999691-D-C06

tag: alignedreads

tag: deduplicatedreads

tag: stitchedreads


title: K105467/K109184_ROI_2_well_A03

description: Library name:  DSP-1008870999731-D-A03

tag: disease state

tag: slide id

tag: roi number


title: zhx12

city: Nanjing

first: Xiang

last: Zhong

state: Jiangsu

address: Tongwei Road

institute: Nanjing agricultural university

description: Input

data_processing:
Reads were quality controlled using FastQC (v0.11.5) and TrimGalore (v0.6.0).
rRNA sequence were removed by using bowtie2(v2.3.4.1) with --ungz or --un-conc-gz parameter.
The retained reads were aligned to GRCm38/mm10 by HISAT2 (v2.2.1) with default parameters.
Bigwig files were obtained by using bamCoverage function in deepTools (v3.5.1) and visualized in IGV (v11.0.19).
Read counts were quantified by using featureCounts (v1.6.0).
Assembly: Sscrofa 11.1,porcine_rotavirus
Supplementary files format and content: bigwig

organism: Sus scrofa

extract_protocol:
The experiment was carried out according to the procedure previously reported. mRNA was isolated from total RNA using the Dynabeads™ mRNA DIRECT™ kit (Ambion, Cat NO. 61012). The purified mRNA was then fragmented by 30 cycles of ultrasound, with each cycle comprising 30 s on and 30 s off. The concentration of fragmented mRNA was determined using a QubitTM RNA HS assay kit (Invitrogen, Cat NO. Q32852). Next, 500 ng of mRNA was taken as the Input control for sequencing. A total of 950 ng of fragmented mRNA was incubated with 1 μL of m6A antibody (NEB, Cat. E1610S) at 4°C for 1 h. After incubation, the mixture was washed twice in reaction buffer (150 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40), twice in low salt buffer (50 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40), and twice in high salt buffer (500 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40). Bound mRNA was eluted using 100 μL of elution buffer (QIAGEN, Cat. 1015762). Library preparation was conducted using the SMARTer Stranded Total RNA-Seq Kit version 2-Pico Input Mammalian (Takara) per the manufacturer’s instructions. Briefly, the immunoprecipitated mRNA fragments and an equal amount of input control were subjected to cDNA synthesis using the kit components SMART Pico Oligos Mix v2, 5X First-Strand Buffer, SMART TSO Mix v2, and SMARTScribe Reverse Transcriptase. The cDNA was then ligated with Illumina adapters and indexes, followed by PCR amplification. The libraries were then purified using AMPure beads to remove excess primers and nucleotides. Ribosomal cDNA removal was performed using the ZapR v2 and R-Probes v2 reagents provided in the kit. The library fragments underwent a second round of PCR enrichment to amplify the libraries to sufficient quantity for sequencing. Before sequencing on an Illumina HiSeq4000, the libraries were analyzed on an Agilent 2100 Bioanalyzer (Agilent Technologies).
Library preparation was performed using the SMARTer Stranded Total RNA-Seq Kit version 2-Pico Input Mammalian (Takara), according to the manufacturer’s protocol.
m6a-seq


title: zhx13

description: Input


title: WT, Saline, 12mo, rep 1

tag: tissue

tag: rin

tag: age


title: BMDM, 250 ng/ml FST, day 6 3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).  Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (ensemble release 101) using STAR 2.7.9a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 2.0.2 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.30.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2). Only genes with a minimum fold change of +- 2 (log2 = +-1), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Assembly: mm10
Supplementary files format and content: library size normalized counts

source_name: bone marrow

growth_protocol: Bone marrow progenitor cells were isolated from adult C57BL6/J mice and cultured in complete RPMI-1640 medium (Gibco).

extract_protocol:
RNA was harvested using the RNeasy Mini Kit (Qiagen)
4µg of total RNA was used as input for VAHTS Stranded mRNA-seq Library preparation following manufacture’s protocol (Vazyme).

treatment_protocol: BMDM were generated by treating the progenitor cells with 50 ng/ml mouse recombinant M-CSF, and then stimulating with 50 ng/ml reombinant activin A, 250 ng/ml FST288, or combination of both for 6 days.

value: bone marrow

tag: cell line

value: BMDM

tag: cell type

value: bone marrow derived macrophages

value: WT


title: BMDM, 250 ng/ml FST, day 6 2


title: BMDM, 250 ng/ml FST, day 6 1


title: BMDM, 50 ng/ml activin A, 250 ng/ml FST, day 6 2


title: K106272/K109169_ROI_10_well_C04

description: Library name:  DSP-1008870999691-D-C04

tag: segment type

tag: area

tag: trimmedreads

tag: sequencingsaturation


title: BMDM, 50 ng/ml activin A, 250 ng/ml FST, day 6 3

tag: genotype


title: K106272/K109169_ROI_11_well_C05

description: Library name:  DSP-1008870999691-D-C05

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: BMDM, 50 ng/ml activin A, 250 ng/ml FST, day 6 1


title: zhx10

description: Input

tag: treatment


title: zhx11

description: Input


title: zhx9

description: Input


title: BMDM, 50 ng/ml activin A, day 6 2


title: BMDM, 50 ng/ml activin A, day 6 3


title: K105467/K109184_2_ROI_1_well_A02

description: Library name:  DSP-1008870999692-B-A02

tag: disease state

tag: alignedreads

tag: deduplicatedreads

tag: stitchedreads


title: zhx14

description: Input


title: K106272/K109169_ROI_8_well_C02

description: Library name:  DSP-1008870999691-D-C02

tag: tissue

tag: slide id

tag: roi number


title: BMDM, untreated, day 6 3

tag: cell line

tag: cell type


title: BMDM, 50 ng/ml activin A, day 6 1


title: zhx6

description: immunoprecipitation


title: BMDM, untreated, day 6 2


title: K106272/K109169_ROI_7_well_C01

description: Library name:  DSP-1008870999691-D-C01

tag: segment type

tag: area


title: BMDM, untreated, day 6 1


title: K106272/K109169_ROI_6_well_B12

description: Library name:  DSP-1008870999691-D-B12

tag: trimmedreads

tag: sequencingsaturation


title: mta_seedling, polyA RNA, input, rep2

description:
At11-sac-mta_seedling-rep2-input
Arabidopsis_mta_gene_expression.tsv.gz
Arabidopsis_mta_m6a_modification.tsv.gz

data_processing:
m6A sites were detected using the method previously published (https://github.com/y9c/m6A-SACseq) 18. The analysis utilized the reference genome downloaded from the Ensembl database, with assembly versions TAIR10 and IRGSP-1.0 employed for Arabidopsis and rice respectively.
Assembly: TAIR-10
Supplementary files format and content: TSV

tag: ecotype


title: zhx4

description: immunoprecipitation


title: K106272/K109169_ROI_9_well_C03

description: Library name:  DSP-1008870999691-D-C03

tag: roi x coordinate

tag: roi y coordinate


title: mta_seedling, polyA RNA, input, rep1

description:
At11-sac-mta_seedling-rep1-input
Arabidopsis_mta_gene_expression.tsv.gz
Arabidopsis_mta_m6a_modification.tsv.gz


title: mta_seedling, polyA RNA, treated, rep2

description:
At11-sac-mta_seedling-rep2-treated
Arabidopsis_mta_gene_expression.tsv.gz
Arabidopsis_mta_m6a_modification.tsv.gz

data_processing:
m6A sites were detected using the method previously published (https://github.com/y9c/m6A-SACseq) 18. The analysis utilized the reference genome downloaded from the Ensembl database, with assembly versions TAIR10 and IRGSP-1.0 employed for Arabidopsis and rice respectively.
Assembly: TAIR-10
Supplementary files format and content: TSV
Library strategy: SAC-seq


title: K106272/K109169_ROI_5_well_B11

description: Library name:  DSP-1008870999691-D-B11

tag: rawreads


title: mta_seedling, polyA RNA, treated, rep1

description:
At11-sac-mta_seedling-rep1-treated
Arabidopsis_mta_gene_expression.tsv.gz
Arabidopsis_mta_m6a_modification.tsv.gz


title: zhx3

description: immunoprecipitation

tag: treatment


title: At10 Arabidopsis_seedling, polyA RNA, input, rep2

description:
At10-sac-Col_0_seedling-rep2-input
Arabidopsis_mta_gene_expression.tsv.gz
Arabidopsis_mta_m6a_modification.tsv.gz


title: At10 Arabidopsis_seedling, polyA RNA, input, rep1

description:
At10-sac-Col_0_seedling-rep1-input
Arabidopsis_mta_gene_expression.tsv.gz
Arabidopsis_mta_m6a_modification.tsv.gz


title: zhx2

description: immunoprecipitation


title: At10 Arabidopsis_seedling, polyA RNA, treated, rep2

description:
At10-sac-Col_0_seedling-rep2-treated
Arabidopsis_mta_gene_expression.tsv.gz
Arabidopsis_mta_m6a_modification.tsv.gz


title: K106272/K109169_ROI_1_well_B08

description: Library name:  DSP-1008870999691-D-B08

tag: disease state

tag: alignedreads


title: Arabidopsis_root, polyA RNA, input, rep2

description:
At9-sac-root-input2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: DU2

city: Fuzhou

first: Zhimin

last: Chen

address: Chazhong Road NO.20

institute: the First Affiliated Hospital, Fujian Medical University, Fuzhou

library_source: transcriptomic single cell

data_processing:
The data matrix processed by Seurat is output through R language
Assembly: mm10
Supplementary files format and content: tab delimited text file includes data value for each sample
Supplementary files format and content: text file includes data value for each sample

source_name: kidney

extract_protocol:
Harvested cells at the required densities were combined with gel beads  containing the barcoded information along with a mixture of cells and  enzymes. Oil surfactant droplets in a microfluidic double-cross system were used for encapsulation to generate Gel Beads-In-Emulsions (GEMs). GEMs were passed through a reservoir and collected while the gel beads were lysed to release the barcode sequence.
The cDNA fragment was then reverse transcribed before the sample was labeled. The gel beads and the oil droplets are ruptured and PCR amplification was performed using the generated cDNA as a template. The products of all GEMs were mixed and a standard sequencing library is constructed. The cDNA was first enzymatically digested into fragments of about 200300 base pairs (bp), together with the library building process of traditional secondgeneration sequencing such as sequencing junction and primers. Finally, the DNA library was generated by PCR amplification

value: kidney

tag: genotype

value: wild type


title: Arabidopsis_root, polyA RNA, input, rep1

description:
At9-sac-root-input1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz

tag: tissue


title: K106272/K109169_ROI_2_well_B09

description: Library name:  DSP-1008870999691-D-B09

tag: slide id

tag: deduplicatedreads

tag: stitchedreads


title: At10 Arabidopsis_seedling, polyA RNA, treated, rep1

description:
At10-sac-Col_0_seedling-rep1-treated
Arabidopsis_mta_gene_expression.tsv.gz
Arabidopsis_mta_m6a_modification.tsv.gz


title: zhx5

description: immunoprecipitation

tag: cell line


title: K106194/K109187_ROI_12_well_B07

description: Library name:  DSP-1008870999691-D-B07

tag: roi number

tag: segment type


title: DU1


title: Arabidopsis_root, polyA RNA, treated, rep2

description:
At9-sac-root-treated2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: Arabidopsis_root, polyA RNA, treated, rep1

description:
At9-sac-root-treated1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: K106194/K109187_ROI_11_well_B06

description: Library name:  DSP-1008870999691-D-B06

tag: area

tag: trimmedreads


title: K106194/K109187_ROI_10_well_B05

description: Library name:  DSP-1008870999691-D-B05

tag: sequencingsaturation


title: K106272/K109169_ROI_4_well_B10

description: Library name:  DSP-1008870999691-D-B10

tag: roi x coordinate


title: K106194/K109187_ROI_9_well_B04

description: Library name:  DSP-1008870999691-D-B04

tag: roi y coordinate


title: Arabidopsis_shoot, polyA RNA, input, rep1

description:
At8-sac-shoot-input1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz

tag: ecotype


title: zhx1

description: immunoprecipitation

tag: treatment


title: Arabidopsis_shoot, polyA RNA, treated, rep1

description:
At8-sac-shoot-treated1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: Arabidopsis_shoot, polyA RNA, treated, rep2

description:
At8-sac-shoot-treated2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: scMO_MM_CD8_controlled [MM4_1_atac]

city: Seattle

first: Geoffrey

middle: R

last: Hill

address: 1100 Fairview Ave N

institute: Fred Hutch Cancer Center

description: 10x Genomics

library_source: genomic single cell

data_processing:
BCL files were demultiplexed and features were counted using either cellranger count, arc, or mulit (RNA, multiome, RNA + TCR + HTO + ADT) Filtered feature matrices were used for gene expression counts and underwent data normalization. ATAC fragments were used to create peak matrices and underwent data normalization.
Assembly: mm10
Supplementary files format and content: Normalized count matrices for all assays and metadata of cells passing quality control metrics with corresponding cell type labels and UMAP coordinates are provided.

extract_protocol:
Primary mouse CD8 T cells were harvested from BM by manually flushing marrow with 2%FBS RMPI. Cells were then sort purified (Polyclonal CD8 T) or selected using an anti-PE MACs selection kit (CD19 CAR T).
Libraries were constructed according to 10X genomics manufacturers instructions.

value: Primary cells

tag: cell type

value: CD8 T cells

value: stem cell transplantation


title: scMO_MM_CD8_relapse [MM3_2_gex]

description: 10x Genomics

molecule: nuclear RNA


title: scMO_MM_CD8_controlled [MM4_1_gex]

description: 10x Genomics


title: scMO_MM_CD8_free [MM4_2_atac]

description: 10x Genomics


title: Arabidopsis_seed, polyA RNA, input, rep2

description:
At7-sac-seed-input2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: K106194/K109187_ROI_6_well_B01

description: Library name:  DSP-1008870999691-D-B01

value: Breast tissues from healthy donor donated 10 years apart

tag: disease state

tag: rawreads

tag: alignedreads


title: scMO_MM_CD8_relapse [MM3_2_atac]

description: 10x Genomics

tag: tissue

tag: genotype


title: Arabidopsis_seed, polyA RNA, input, rep1

description:
At7-sac-seed-input1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: K106194/K109187_ROI_7_well_B02

description: Library name:  DSP-1008870999691-D-B02

value: healthy donor

tag: slide id

tag: deduplicatedreads

tag: stitchedreads


title: K106194/K109187_ROI_5_well_A12

description: Library name:  DSP-1008870999691-D-A12

tag: roi number

tag: segment type


title: K106194/K109187_ROI_8_well_B03

description: Library name:  DSP-1008870999691-D-B03

tag: area

tag: trimmedreads


title: scRNA_MM_CD8_relapse [MM_relapse]

description: 10x Genomics

tag: cell line


title: scRNA_TCR_MM_CD19_CAR_T [SM_4]

description: 10x Genomics

value: CD19 CAR T cell


title: 10-KO-cr

city: Tianjin

first: Zhiqiang

last: Liu

address: 22 Qixiangtai Rd

institute: Tianjin Medical University

data_processing:
Basecalls performed using Illumina NovaSeq 6000
Clean reads were aligned to mouse mm39 reference genome using bowtie2 software (v2.2.4).
Assembly: Mus musculus (mm39)
Supplementary files format and content: bigwig files were generated using macs2; Scores represent an average read coverage
Library strategy: CUT&Tag

growth_protocol: BMSCs were cultured in αMEM medium with 10% FBS.

extract_protocol:
Clarify the lysate from the nucleus treated with Protein A-Tn5 enzyme and isolate the histone DNA complex with antibodies.
Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, China) was used to perform the CUT&Tag assay. Briefly, a total of 50 000 cells were harvested and enriched by ConA magnetic beads. The samples were incubated with primary H3K18ac or H3K18cr antibody at 4°C overnight and secondary antibody at room temperature for 1 hour. Cells were incubated with the protein A-Tn5 transposon at room temperature for 1 hour, and washed thrice in Dig-300 buffer. The cells were resuspended in 50 μL of fragmentation buffer, incubated at 37 °C for 1 hour and then terminated with 1 μL of 10% SDS at 55 °C for 10 min. DNA Extract Beads Pro was used to extract the ~250bp DNA fragments. The libraries were used for sequencing on an Illumina NovaSeq 6000 platform at Novogene Science.

value: HDGFR2 knockout

value: BMSC

tag: cut&tag antibody

value: H3K18cr(PTM BIO, PTM-540)


title: scMO_MM_CD8_free [MM4_2_gex]

description: 10x Genomics


title: K106194/K109187_ROI_3_well_A10

description: Library name:  DSP-1008870999691-D-A10

value: Full ROI

tag: roi x coordinate

tag: roi y coordinate

tag: sequencingsaturation


title: Arabidopsis_seed, polyA RNA, treated, rep2

description:
At7-sac-seed-treated2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz

tag: ecotype


title: Arabidopsis_shoot, polyA RNA, input, rep2

description:
At8-sac-shoot-input2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: iAT1 72hr

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

description: iPSC-derived iAT1s in 3D 72hr post media change to L+DCI

data_processing:
The sample was processed using the standard Cellranger v.3 pipeline
Reads were mapped to GRCh38 supplemented with sequences for GFP and tdTomato reporters
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38
Supplementary files format and content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5  format

source_name: iPSC-derived

growth_protocol: BU3 NGAT iPSCs were differentiated into iAT2s grown in 3D matrigel. iAT2s were passaged as single cells and collected 3 days post plating as iAT2s. Media on remaining cells was changed to L+DCI and cells were collected 24. 48, and 72 hours post media change

extract_protocol:
Cells were dissociated to single cell using 0.05% trypsin for 3D samples. Each were sorted for live cells using Calcein blue.
Single cells were captured for sequencing library preparation using a 10X Chromium (10X Genomics, Pleasanton, CA) instrument at the BUMC Single Cell Core. Library preperation was done on separate days for each sample, but sequencing was done together. Single-cell RNA-seq libraries were prepared according to the Single Cell 3’ v2 Reagent Kits User Guide (10X Genomics). Sequence libraries were constructed using the Chromium Single-Cell 3’ Library Kit (10X Genomics). Sequencing libraries were loaded on a NextSeq500 (Illumina) to obtain a sequencing depth of~50K reads per cell. 685 cells from CKDCI 3D, 1340 cells from LDCI 3D, 643 cells from LDCI ALI p0, and 1093 cells from LDCI ALI p1 were captured and sequenced.

value: iPSC-derived

value: BU3 NGAT

tag: cell type

tag: treatment

value: LDCI 72hr


title: 9-KO-cr

tag: tissue

value: bone marrow


title: Arabidopsis_seed, polyA RNA, treated, rep1

description:
At7-sac-seed-treated1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: K106194/K109187_ROI_4_well_A11

description: Library name:  DSP-1008870999691-D-A11

tag: disease state

tag: rawreads

tag: alignedreads


title: 8-KO-ac

tag: genotype

value: H3K18ac(PTM BIO, # PTM-158)


title: iAT1 48hr

description: iPSC-derived iAT1s in 3D 48hr post media change to L+DCI

value: LDCI 48hr


title: K106194/K109187_ROI_2_well_A09

description: Library name:  DSP-1008870999691-D-A09

tag: slide id

tag: roi number

tag: deduplicatedreads

tag: stitchedreads


title: 7-WT-cr

value: wildtype


title: Arabidopsis_rosetta_leaf, polyA RNA, input, rep2

description:
At6-sac-rosetta_leaf-input2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: iAT1 24hr

description: iPSC-derived iAT1s in 3D 24hr post media change to L+DCI

tag: cell line

value: LDCI 24hr


title: K106194/K109187_ROI_1_well_A08

description: Library name:  DSP-1008870999691-D-A08

tag: segment type

tag: area

tag: trimmedreads


title: Arabidopsis_rosetta_leaf, polyA RNA, input, rep1

description:
At6-sac-rosetta_leaf-input1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: 6-WT-cr

tag: cut&tag antibody


title: iAT2 3D

description: iPSC-derived iAT2s in 3D

value: iPSC-derived iAT2s in 3D

value: CKDCI