title: lncap_p53_ca_enz2

description:
LNCap_6group_gene_exp.txt
p53_ca_enz2_RPKM

value: enzalutamide 1 μM


title: lncap_p53_ca_enz1

status: Public on Jun 22 2023

type: SRA

city: Shanghai

first: Hanling

last: Wang

address: Shanghai

country: China

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Science

description:
LNCap_6group_gene_exp.txt
p53_ca_enz1_RPKM

library_source: transcriptomic

data_processing:
The mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA). And then fragmented to approximately 200bp. Subsequently, the RNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligaion and enrichment with a low-cycleaccording to instructions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina.
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher  Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).
HISAT2 was used to align the clean reads to the mouse reference genome mm10 with default parameters.
HTSeq was subsequently employed to convert aligned short reads into read counts for each gene
Differential expression was assessed by DESeq2 using read counts as input.
Assembly: hg19, mm10
Supplementary files format and content: tab-delimited text files include RPKM or TPM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: LNCap cell line

growth_protocol: LNCap were cultured in RPM1640 media supplemented with 10% FBS at 37°C under 5% CO2. Cancer associated fibroblasts were cultured in DMEM media supplemented with 10% FBS at 37°C under 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. Total RNA was subjected to Hiseq RNA-Seq, performed by RiboBio Co., Ltd.
RNA libraries for RNA-seq were prepared according to instructions of NEBNext® Ultra™ RNA LibraryPrep Kit for Illumina (NEB, USA)

treatment_protocol: For LNCap, enzalutamide (1μM) was added into different conditions, treatment was performed in two biological replicates. For cancer assocciated fibroblasts, enzalutamide (1 μM) and TGF-β1 (5 ng/ml) was added into different conditions, treatment was performed in two biological replicates.

tag: cell line

value: LNCap cell line

tag: cell type

value: epithelial

tag: genotype

value: WT

tag: treatment

value: cocultured with CRPCCAFs

tag: time

value: Day 7


title: AC4-4_Right Atrium

city: South San Francisco

first: Xianglong

last: Zhang

state: CA

address: 1120 Veterans Blvd

country: USA

institute: Amgen Inc

data_processing:
All read files were processed by fastp (v0.19.8) to remove poor quality reads and to trim poor quality 3’ bases. The filtered and trimmed reads were aligned and quantified using OmicSoft’s (Cary, NC, USA) Array Studio software (https://www.omicsoft.com/publish-studio; Oshell.exe v10.0) to reference genome NCBI Macaca_fascicularis_5.0. The transcriptomic annotation NCBI Macaca fascicularis Annotation Release 101 was used as the transcript model reference. The alignment algorithm OSA is documented in an OmicSoft whitepaper (http://omicsoft.com/downloads/whitepaper/OmicsoftAligner.pdf), and the gene/transcript quantification module is an OmicSoft implementation of the RSEM algorithm.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: RNA-Seq data — gene name, read count

organism: Macaca fascicularis

source_name: Right Atrium

extract_protocol:
Total RNA was extracted from 27 snap-froze tissues with RNeasy Micro/Mini Kit (QIAGEN, Germany, Cat. #74004/#74106), according to the manufacturer’s instructions. The quality of the isolated RNA was analyzed by Agilent Bioanalyzer 2100. Only the RNA samples with an RNA Integrity Number (RIN) value of 6.0 or higher were included for RNA sequencing.
RNA-seq libraries were constructed from RNA samples meeting QC criteria based on polyA+ selection of mRNA using a standard strand-specific protocol with VAHTS® Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme, China, Cat. #NR612). The quality of the sequencing libraries was analyzed by Agilent Bioanalyzer 4200 and the peak length ranged from 250~500 bp. Clusters were generated by cBot with the library diluted to 10 pM and then sequenced on Illumina HiSeq 2500 instruments with 2 × 150 bp paired-end sequencing. All libraries were sequenced to an average depth of 52 ± 8.8 (mean ± s.d.) million reads (corresponding to 26 ± 4.4 million paired-end reads).

tag: individual

tag: phenotype

tag: tissue

value: Right Atrium


title: KO CLT_2

city: rochester

first: Roman

last: Thaler

state: MINNESOTA

address: 200 First street SW

institute: Mayo Clinic

data_processing:
Libraries were sequenced on an Illumina HiSeq 4000 instrument and Fastq file quality was checked with FastQC (version 0.72).
Quality and adapter trimming was performed with Trim Galore! (version 0.4.3.1)
Trimmed Fastq files were mapped to the mouse genome (mm10) with RNA STAR (version 2.6.0b-1)
Gene expression was qantified with featureCounts (version 1.6.3)
Differentially expressed genes were defined with DESeq2 (version 2.11.40.2)
Assembly: mm10
Supplementary files format and content: RPKMs all samples.txt

organism: Mus musculus

source_name: Incisors

extract_protocol:
RNA was extraced with commercially available extraction kits (Zymo and Qiagen, respectively).
RNA libraries were prepared for sequencing using standard Illumina protocols;  All deep-sequncing runs were perfomed using the Illumina HiSeq 4000 instrument at the Mayo Clinic Medical Genome Facility Sequencing Core.

value: Dental epithelial cells

tag: strain

value: MED1 knock


title: KO_model 1_Rep1

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

description: KO_model 1_Rep1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to the  mouse mm10 using the STAR aligner. The aligned reads were then assigned to genes using RSEM
Assembly: mm10
Supplementary files format and content: table delimited text file containing the expression of genes

source_name: NRAS/AE9a leukemic cells

growth_protocol: Cells were cultured in RPMI 1640 medium supplied with murine 50 ng/ml SCF, 10 ng/ml IL-3 and IL-6, 1 mg/mL G418, and 2 µg/mL puromycin

extract_protocol:
The total RNA were extracted with QIAzol lysis reagent.
RNA library preparation was conducted using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) following manufacturer's protocols.

value: NRAS/AE9a leukemic cells

value: AML cells

value: Tet2 KO


title: AC4-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: KO CLT_1


title: lncap_p53_enz2

description:
LNCap_6group_gene_exp.txt
p53_enz2_RPKM

value: cocultured with CCAFs


title: RNA-Seq Mbd2-/-_4

city: Ariel

first: Elad

last: Lax

address: 65 Ramat HaGolan st.

department: Molecular Biology

country: Israel

institute: Ariel University

data_processing:
Reads were aligned to the mouse reference transcriptome (mm9) using the STAR aligner
Differential expression was analyzed using DeSeq2 with an FDR of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: Txt file that contains expression level per sample, differential expression between groups and statisitcs.

source_name: Hippocampus

growth_protocol: Mice were housed in groups (3-5/cage) with 12-h light/dark cycles under conditions of constant temperature (23°C) and humidity (50%), and free access to food and water.

extract_protocol:
mice (10-12 weeks of age) were sacrificed, the brains were rapidly removed, and bi-lateral hippocampi were isolated, flesh frozen and stored at -80°C for later analysis. RNA was extracted with AllPrep-DNA/RNA/miRNA-universal kit according to the manufacturer protocol.
RNA concentration was determined by fluorometry on the Qubit system (Invitrogen, Ottawa, ON). Ribosomal RNA was removed using the Ribominus kit (Invitrogen). cDNA libraries (4 per group) were generated and sequenced using an Illumina Hiseq 2500 (100 bp pair-end runs), as instructed by Illumina's RNA-seq protocols

value: Mbd2-/- with C57BL/6 background


title: AC4-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: lncap_p53_enz1

description:
LNCap_6group_gene_exp.txt
p53_enz1_RPKM


title: WT CLT_2

value: control


title: AC4-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: RNA-Seq Mbd2-/-_3


title: WT_rep2

city: Duarte

first: Hung Ping

last: Shih

address: 1500 East Duarte Road

institute: City of Hope

data_processing:
fastq files were aligned to version 79 of mouse reference genome GRCm38 using the STAR aligner.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the TMM function in the edgeR package in R
Differentially expressed genes (³1.5-fold and <5% FDR-adjusted p values) were identified by generalized linear modeling using the edgeR package
Genome_build: version 79 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...

source_name: pancreas

extract_protocol:
Islets were harvested by perfusing pancreta with collagenase P from wildtype and Itgb1 mutant mice
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the  KAPA RNA HyperPrep Kit with RiboErase (HMR) according to the manufacturer’s instructions.

value: pancreas

tag: background strain

value: wild-type

value: islets


title: AC4-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: AC4-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: lncap_p53_c2

description:
LNCap_6group_gene_exp.txt
p53_c2_RPKM

value: LNCap cell line

value: epithelial

value: WT

value: DMSO

value: Day 7


title: KO CLH_2

value: Dental epithelial cells

value: MED1 knock


title: WT CLT_1


title: AC4-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: WT CLH_2


title: RNA-Seq Control_4


title: RNA-Seq Mbd2-/-_1

value: Mbd2-/- with C57BL/6 background


title: lncap_p53_c1

description:
LNCap_6group_gene_exp.txt
p53_c1_RPKM

value: cocultured with CCAFs


title: RNA-Seq Control_3


title: AC4-15_Pituitary Gland

source_name: Pituitary Gland

value: Pituitary Gland


title: KO CLH_1


title: lncap_blank_enz2

description:
LNCap_6group_gene_exp.txt
blank_enz2_RPKM

value: enzalutamide 1 μM

value: blank


title: lncap_blank_enz1

description:
LNCap_6group_gene_exp.txt
blank_enz1_RPKM


title: lncap_blank_c2

description:
LNCap_6group_gene_exp.txt
blank_c2_RPKM


title: AC4-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: AC4-14_Esophagus

source_name: Esophagus

value: Esophagus


title: RNA-Seq Control_2


title: WT CLH_1

value: control


title: N2N1G subcutaneous allograft #3

city: Stanford

first: Siqi

last: Cao

address: 300 Pasteur Drive

institute: Stanford Medical School

description:
N2N1G allograft transplanted into mouse flank subcutis microenvironment via direct injection
s3_gfp

data_processing:
RNA sequencing via HiSeq4000
Cell Ranger alignment based on STAR
Genome_build: mm10 and GFP plasmid
Supplementary_files_format_and_content: barcodes.tsv.gz files contain the cell barcode ID that are the column values for the .mtx files
Supplementary_files_format_and_content: features.tsv.gz files contain the feature (gene) names that are the row values for the .mtx files
Supplementary_files_format_and_content: matrix.mtx.gz contain the gene-barcode matrix data created by cell ranger

molecule: polyA RNA

source_name: cell line allograft

growth_protocol: N2N1G cells were cultured in RPMI-1640 medium supplemented with 10% bovine growth serum and 1% penicillin-streptomycin-glutamine. Cells were transplanted into mice at 1million cells per allograft and harvested 3 weeks after transplantation

extract_protocol:
Single cell suspensions were generated from bulk tumors, healthy single cells were isolated using FACS, and single cell suspensions were sent for 10x dropseq same day
10X Genomics single-cell 3'mRNA-seq methods

tag: cancer type

value: small cell lung cancer

tag: allograft location

value: subcutis


title: ARPE-19 HT-3

city: Guangzhou

first: wenchang

last: Xu

address: Jinsui Road No.7

department: Zhongshan Ophthalmic Center

institute: Sun Yat-Sen University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Reference genome and gene model annotation files were downloaded from genome website directly.
Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed. Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used KOBAS software to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Retinal epithelial cells

growth_protocol: ARPE-19 cells were expanded in the DMEM/F-12 medium [Dulbecco's Modified Eagle's Medium (DMEM) and Ham's F-12 Nutrient Mixture] (Gibco), 10% fetal bovine serum (FBS) (Gibco) and 1 × Pen/Strep (Gibco)

extract_protocol:
Total RNA was extracted from ARPE-19 cell using the TRIzol reagent according to the manufacturer’s instruction.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: Treated with negative control adenovirus or HTRA1 adenovirus for 24 hours,three replicates for each group

value: Retinal epithelial cells

value: treated with HTRA1 adenovirus for 24 hours


title: N2N1G subcutaneous allograft #2

description:
N2N1G allograft transplanted into mouse flank subcutis microenvironment via direct injection
s2_gfp


title: lncap_blank_c1

description:
LNCap_6group_gene_exp.txt
blank_c1_RPKM

source_name: LNCap cell line

value: LNCap cell line

value: epithelial

value: WT

value: DMSO


title: AC4-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: RNA-Seq Mbd2-/-_2

value: Mbd2-/- with C57BL/6 background


title: AC4-10_Thalamus

source_name: Thalamus

value: Thalamus


title: N2N1G subcutaneous allograft #1

description:
N2N1G allograft transplanted into mouse flank subcutis microenvironment via direct injection
s1_gfp


title: HFF SORSC1 transfected CGH bulk

type: genomic

city: Bordeaux

first: Julian

last: Boutin

state: Nouvelle Aquitaine

address: 146 rue Leo Saignat

country: France

institute: INSERM U1312 BRIC

description:
Test 1
Agilent 60K CGH 021924

hyb_protocol: Labeled DNAs were hybridized onto Agilent oligonucleotide microarrays (8x60K Agilent Genetisure) according to the manufacturer’s instructions (Agilent Technologies)

scan_protocol: Scanning of the microarrays was performed using a G5761A scanner (Agilent Technologies).

data_processing:
Data analysis was carried out with Agilent Technologies software, namely Feature Extraction for Cytogenomics Algorithm v5.0 for the fluorescence ratio calculation and Agilent CytoGenomics v5.2 for the localization of chromosomal imbalances.
Deletions and duplications in the heterozygous state were characterized by values of the log2 ratio of fluorescence intensities (cyanine5/cyanine3) below -0.5 and above +0.3, respectively, with the statistical algorithm ADM2 used at a threshold of five.

molecule: genomic DNA

source_name: SORSC1 CGH bulk

label_protocol: DNA (minimum 125ng) was labeled  (cyanine 3 or cyanine 5) using the Genomic DNA ULS Labeling Kit from Agilent Technologies (Agilent Technologies, Santa Clara, USA)

growth_protocol: HFF cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM with glucose (4.5 g.L-473 1), L-Glutamine (1 g.L-1) and pyruvate supplemented with 20% fetal bovine serum, MEM non-essential 474 amino acids 100X (Gibco® by ThermoFisher scientific, Carlsabad, CA, USA), 100 U/mL penicillin, and 475 100μg/mL streptomycin (all from Eurobio, Courtaboeuf, France)

extract_protocol: DNA was extracted from cultivated cells using the Wizard manual kit (Promega Corporation, Madison, USA).

treatment_protocol: HFF cells were transfected with 16.9 μg Cas9 RNP and 5 μM of Alt-R® Cas9 Electroporation Enhancer by electroporation using the AMAXA™ 4D-499 Nucleofector™ device (Lonza®, Bale, Switzerland) with P3 Primary Cell Line and CZ-167

value: HFF

source_name: WT SORC1 FLUO NEG


title: AC4-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: 9_62_0wk

city: New Haven

first: Taiwo

middle: S

last: Agidigbi

state: Connecticut

address: 330 Cedar street, Orhtopeadic and rehabilitation, Yale college of medicine

department: Orthopaedics and Rehabilitation,

institute: Yale university

description: Samples were collected at 0-wk before initiation of antibiotics therapy, and at 8-wk after therapy to isolate PBMC

data_processing:
Low quality reads were trimmed, and adaptor contamination was removed using Trim Galore (v0.5.0).
Trimmed reads were mapped to the hg38 reference genome using HISAT2 (v2.1.0) (Kim et al., 2015).
Gene expression levels were quantified using StringTie (v 1.3.3b) (Pertea et al., 2015) with gene models from Gencode (v27).
Differentially expressed genes were identified using DESeq2 (v 1.22.1) (Love et al., 2014).
Assembly: hg38
Supplementary files format and content: readcounts

source_name: BLOOD PBMC

extract_protocol:
PBMCs were lysed on ice for 5 mins in 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 0.05% NP-40, and nuclei were spun at 2,500g for 3 mins before being resuspended in QIAzol for RNA isolation using the miRNeasy kit, as directed by the manufacturer (Qiagen
The RNA-seq library was constructed using the Illumina TruSeq RNA Sample Preparation Kit v2 and sequenced on one lane of the HiSeq 2000 platform (100 bp, paired-end)

treatment_protocol: Blood samples from S. aureus infected DFU patient were collected at 0-wk before initiation of antibiotics therapy, and at 8-wk after therapy (as a follow up to treatment response) to isolate PBMC, host immune response were assessed by comparing the transcriptome gene expression at 0-wk vs 8-wk

tag: disease state

value: INFECTED DFU

tag: Stage

value: BEFORE THERAPY


title: ARPE-19 HT-2


title: ARPE-19 HT-1


title: N2N1G liver allograft #3

description:
N2N1G allograft transplanted into mouse liver microenvironment via tail vein
l3_gfp

value: liver


title: 7_59_0wk


title: AC3-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: ARPE-19 nc-3

value: treated with negative control adenovirus for 24 hours


title: 6_58_8wk

value: AFTER THERAPY


title: ARPE-19 nc-2

value: Retinal epithelial cells


title: AC3-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: ARPE-19 nc-1


title: N2N1G brain allograft #2

description:
N2N1G allograft transplanted into mouse brain microenvironment via direct injection
b2_gfp

value: small cell lung cancer

value: brain


title: N2N1G liver allograft #2

description:
N2N1G allograft transplanted into mouse liver microenvironment via tail vein
l2_gfp


title: AC3-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: N2N1G brain allograft #1

description:
N2N1G allograft transplanted into mouse brain microenvironment via direct injection
b1_gfp


title: Non-treated suspension cultured organoid 1

city: Daejeon

first: Ilkyun

last: Im

address: 141 Gajeong-ro, Yuseong-gu

department: Department of Predictive Toxicology

country: South Korea

institute: Korea Institute of Toxicology

data_processing:
Read alignment was performed using HISAT2
Read assemble was performed using StringTie
Read counts were normalized using trimmed mean of M-values
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with FPKM and TPM

source_name: human hepatic organoid

extract_protocol:
Hepatic organoids were harvested and washed by DPBS followed by RNA extraction using NucleoZOL (MN)
Libraries were generated using TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: Iron was treated throughout differentiation process

value: Non-treated

tag: culture condition

value: Suspension


title: 4_57_4wk


title: 5_58_0wk


title: AC3-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: N2N1G liver allograft #1

description:
N2N1G allograft transplanted into mouse liver microenvironment via tail vein
l1_gfp


title: Mbd2_knockout_ChIP-seq 2

library_source: genomic

data_processing:
Reads were aligned to the mouse reference genome using Bowtie
Low quality alignments and alignments for read pairs with multiple possible genomic alignments were omitted. Duplicate read pairs were removed.
Read count peaks corresponding to likely binding sites were identified for each sample by MACS2 with default parameters, and narrow peak calling. Mbd2 knockout mice DNA reads were subtracted from the Mbd2 binding to control for nonspecific peaks
Peaks with false discovery rates less than 0.05 were selected as high-confidence binding sites and were annotated with their genomic locations relative to nearby genes using HOMER with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: txt file annotated peaks

source_name: Hippocampus

extract_protocol:
mice (10-12 weeks of age) were sacrificed, the brains were rapidly removed, and bi-lateral hippocampi were isolated, flesh frozen and stored at -80°C for later analysis. hippocampi (n=8) were pooled, homogenized in 1 X PBS including 1% formaldehyde, and the homogenates were kept for 10 min at 25°C. Cross-linking reactions were stopped by the addition of glycine (125 mM) for 10 min at 25°C. Fixed chromatin samples were then homogenized in cell lysis solution (PIPES 5 mM (pH 8), KCl 85 mM, NP40 0.5%) and centrifuged for 5 min at 3000 rpm, 4°C. Pellets were resuspended in RIPA-light solution (NaCl 150 mM, SDS 0.3%, Tris-HCl 50 mM (pH 8)) and sonicated using a Covaris E220. Sonicated chromatin samples were then centrifuged for 15 min at 14000 rpm, 4°C. Pellets were resuspended in 1 ml of RIPA-light solution. Chromatin samples were pre-cleared with 50 µl of Dynabeads protein G (Life Technologies, Ottawa, ON) pre-blocked with BSA and incubated overnight at 4°C with an anti- Mbd2 (Epigentek-A1007, Burlington, ON) antibody. Input control was treated identically the same way except for not adding an anti-Mbd2 antibody to the solution. Antibodies and chromatin were then mixed with 100 µl of Dynabeads protein G for 3 hours at 4°C. The beads were then washed with RIPA-light solution, then with wash-solution (Tris-HCl 100 mM (pH 8), LiCl 500 mM). Protein–DNA complexes were eluted from the beads, de-cross-linked, treated with proteinase K and purified. The DNA concentration was determined by fluorometry on the Qubit system (Invitrogen, Ottawa, ON).
A total of 10–12 ng DNA were used for the preparation of the libraries. The immunoprecipitated DNA and input DNA were sheared a second time with the Covaris E220 instrument in 53 µl reaction volume (duty factor 10%, Pic Incident Power 175, Cycles per burst 200, time 360 sec) to obtain fragments in the size range of 150 bp followed by purification with AMPure XP beads (×1.8v/v) (Beckman Coulter A63881, Indianapolis, IN). Purified DNA was resuspended in 45 µl elution buffer. Libraries of the chromatin immunoprecipitated and input DNA fragments were prepared using the Tru Seq DNA Low Throughput Protocol (Illumina). PCR enrichment of ligation products was performed using the Illumina Primer Cocktail; 15 cycles of PCR were performed for ChIP libraries and 10 cycles for the input. The libraries were purified using AMPure XP beads ×1.0 v/v. Quality of libraries was validated by 260 nm absorbance measurement, quality control on HSdna chip (Agilent Bioanalyzer: size of libraries around 275bp bp) and quantification by Q-PCR with Kappa Library Quantification kit for Illumina Sequencing Platforms (KAPPA Biosystems). The DNA concentration of the different sequencing libraries was from 40 to 500 nM. Clusters (13.5 pM) were generated using TruSeq PE Cluster Kit v3, for cBot protocol.

value: knockout

tag: antibody

value: anti- Mbd2 (Epigentek-A1007)


title: AC3-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: 42_81_4wk

value: INFECTED DFU


title: AC3-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: Non-treated droplet cultured organoid 2

description: Non-treated droplet cultured organoid

value: Droplet


title: 41_81_0wk

value: BEFORE THERAPY


title: Mbd2_knockout_ChIP-seq 1


title: 40_80_8wk


title: AC3-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: Mbd2_WT_ChIP-seq

value: WT


title: Non-treated droplet cultured organoid 1

description: Non-treated droplet cultured organoid


title: Fe treated suspension cultured organoid 2

description: Fe treated suspension cultured organoid

value: Fe treated


title: AC3-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: INS-SMA rep3

city: Ningbo

first: YANG

last: XI

address: Fenghua Road

department: School of medicine

institute: Ningbo University

description: INS-SMA rep3

data_processing:
The sequencing quality were assessed with Fast QC (Version 0.11.5) and then low quality data were filtered using NGSQC (v0.4), quality value of over 50% bases of the read was less than 5, and trimmed the adapter sequence, and removed the reads containing poly-N using in-house perl scripts.
The clean reads were then aligned to the reference genome using HISAT2 (Johns Hopkins University, USA) with default parameters (Liu et al., 2015). The processed reads from each sample were aligned using HISAT (Johns Hopkins University, USA) against the corresponding hg19 reference genome. The gene expression analyses were performed withStringTie. DESeq2 was used to analyze the DEGs between samples. Thousands of independent statistical hypothesis testing were conducted on DEGs, separately. Then a p-value was obtained, which was corrected by FDR method. And Corrected P-value (q-value) was calculated by correcting using BH method. p-value or q-value were used to conduct significance analysis. Parameters for classifying significantly DEGs are ≥2- fold differences (|log2FC|≥1, FC: the fold change of expressions) in the transcript abundance and q < 0.05 (Parreira et al., 2016). By searching the ENSEMBL, NCBI, Uniprot, GO, and KEGG databases, the BLAST (Basic Local Alignment Search Tool) alignment was performed to determine the functional annotation of DEGs. The best matches were selected to annotate the DEGs. Finally, A GO functional enrichment analysis and KEGG pathway enrichment analysis were performed for the DGEs using the Goseq R package and KOBAS 3.0 software (Available online: http://kobas.cbi.pku.edu.cn) . GO terms and pathway terms with P-value(or Q-value ) less than 0.05 were considered significantly enriched by target genes.
Genome_build: rn6
Supplementary_files_format_and_content: count file

organism: Rattus norvegicus

source_name: INS-1 beta cell

growth_protocol: The Rat INS-1 beta cells were cultured in RPMI 1640 medium (Gbico, USA) supplemented with 10 % fetal bovine serum and 100 U/ml penicillin-streptomycin (Gbico, USA) at 37 ℃ in an atmosphere of 5 % CO2.

extract_protocol:
Total RNA were extracted with Trizol (Tiangen, Beijing) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen). Total RNA samples that meet the following requirements were used in subsequent experiments: RNA integrity number (RIN) > 7.0 and a 28S:18S ratio > 1.8.
The cluster formation and sequencing were performed on the NovaSeq 6000 platform following the manufacturer’s standard CapitalBio Technology (Beijing, China) and sequencing protocols.

treatment_protocol: We constructed α-SMA gene expressing cells by lentivirus in INS-1 beta cells.

value: SMA overexpression

value: rat insulinoma cell

tag: passage


title: Non-treated suspension cultured organoid 2


title: 39_80_0wk


title: 38_79_4wk

value: AFTER THERAPY


title: AC3-23_Salivary Gland

source_name: Salivary Gland

value: Salivary Gland


title: Fe treated droplet cultured organoid 2

description: Fe treated droplet cultured organoid


title: INS-SMA rep1

description: INS-SMA rep1

tag: cell line


title: Fe treated suspension cultured organoid 1

description: Fe treated suspension cultured organoid

value: Suspension


title: INS-SMA rep2

description: INS-SMA rep2

tag: cell type


title: INS-MOCK rep3

description: INS-MOCK rep3

tag: genotype

value: wild type


title: 36_78_8wk


title: AC3-21_Colon

source_name: Colon

value: Colon


title: Fe treated droplet cultured organoid 1

description: Fe treated droplet cultured organoid

tag: treatment


title: AC3-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: RNA-Seq Control_1


title: AC3-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: AC3-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: 3_57_0wk

source_name: BLOOD PBMC

value: INFECTED DFU


title: AP.5.NK: AP treated Tumor Natural-Killer Cells Run 1 Rep5

city: Cambridge

first: Dikshant

last: Pradhan

state: MA

address: 70 Dudley Street

institute: Massachusetts Institute of Technology

data_processing:
HiSeq2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNAseq reads were aligned to the mouse transcriptome prepared with the mm10 primary assembly and the Ensembl version 98 annotation using Salmon (Patro, Rob, et al. 2017). Gene expression was summarized with the tximport package (version 1.12.3) in R (version 3.6.1).
Genome_build: mm10 with ensembl v98 annotation
Supplementary_files_format_and_content: cwang_2021_IntCt.xlsx is a comma-separated text file of integer count data
Supplementary_files_format_and_content: cwang_2021_l2tpm.xlsx is a comma-separated text file of log2 tpm data with a plus 1 offset

source_name: Natural-Killer Cells

extract_protocol:
Tumor samples were collected immediately after surgery and submerged in tissue storage solution and were dissociated using the mouse tumor dissociation kit. Briefly, tumors were cut into small pieces (~ 2-4 mm3) and transferred to a gentle MACS C tube containing 2.35 ml RPMI 1640, 100 μl Enzyme D, 50 μl Enzyme R and 12.5 μl Enzyme A. The program 37C_m_TDK_1 was used on a gentle MACS Octo Dissociator with Heaters to fully dissociate tumor tissue. After digestion, the solution was diluted in 10 ml RPMI 1640 and filtered through a prewetted 70 μm filter. Cells were pelleted and used for positive selection of immune cells using mouse CD45 MicroBeads.
RNA libraries were prepared for sequencing using SMART-Seq v2 protocol for Illumina

treatment_protocol: B16F10-bearing C57BL/6 mice were intraperitoneally injected with the tumor targeting antibody 2.5F-Fc (A), MSA-IL-2 (I) and anti-PD-1 (P) or a subcombination of AIP 8 days post tumor inoculation. Tumor infiltrating NK cells and macrophages were collected 3 days post treatment.

value: Natural-Killer Cells

tag: drug treatment

value: AP - Antibody 2.5F-Fc + Anti-PD-1

tag: sequencing run


title: INS-MOCK rep1

description: INS-MOCK rep1


title: 34_76_8wk


title: AC3-18_Biceps Femoris

source_name: Biceps Femoris

tag: individual

tag: phenotype

value: Biceps Femoris


title: AP.4.MF: AP treated Tumor Macrophage Cells Run 1 Rep4

source_name: Macrophage Cells

tag: strain

value: Macrophage Cells


title: AP.3.MF: AP treated Tumor Macrophage Cells Run 1 Rep3


title: 37_79_0wk

value: BEFORE THERAPY


title: AC3-16_Adrenal Gland

source_name: Adrenal Gland

tag: tissue

value: Adrenal Gland


title: AP.3.NK: AP treated Tumor Natural-Killer Cells Run 1 Rep3


title: 35_78_0wk


title: Co-recruit library screen, unused memory screen, unbound R2

first: Adi

middle: Xiyal

last: Mukund

address: 443 via Ortega, Shriram 036

institute: Stanford University

description: 2x150 cycles

data_processing:
Demultiplexed sequencing reads were provided by Admera. Domain 1 and domain 2 reads were aligned separately using bowtie2, trimming 30 base pairs from both 5? and 3? ends, and were then each paired read was identified as a particular library member using a python script iterating over each read pair. "
The total number of reads for each library member was then summed up using another python script. Library members were required to have at least 5 ON reads or 5 OFF reads as well as 50 total reads across both ON and OFF subpopulations to be considered for downstream analysis. For every qualifying library member, the ON or OFF read count was then set to 5 if it was less than 5. Then, ON read counts were normalized by dividing each library member?s read count by the total number of ON reads, and the same was done for OFF counts. Overall enrichment scores were then computed by taking the log2 of the ratio of normalized ON read counts to normalized OFF read counts.
Assembly: hg38
Supplementary files format and content: CSV files for each sample, indicating each domain pair and relevant statistics

growth_protocol: We plated 15 × 106 HEK293T cells on each of 10x 15-cm tissue culture plates in 30 mL DMEM, grew them overnight, and then transfected each with 8 ug of an equimolar mixture of three third-generation packaging plasmids (pMD2.G, psPAX2, pMDLg/pRRE) and 8 ug of rTetR-concatenation library vectors using 50 mL of polyethylenimine (PEI, Polysciences #23966). Packaging plasmids were gifts from Didier Trono. Lentivirus was harvested after 48 and 72 hours of incubation and filtered through a 0.45 mm PVDF filter (Millipore) to remove debris. K562 cells were infected with lentivirus via spinfection for 2 hours, with 2 replicates each spinfected separately.

extract_protocol:
Genomic DNA was extracted with the QIAgen Blood Maxi Kit following the manufacturer?s instructions with up to 1 × 108 cells per column. Domain sequences were amplified by PCR with primers containing Illumina adapters as extensions. 27-55x 100uL PCRs were set up on ice, with the genomic DNA available for each experiment dictating the number of reactions. 10 ug of genomic DNA, 0.5 uL of each 100M primer, and 50uL of NEBnext Ultra 2x Master Mix (NEB) was used in each reaction. Samples were thermocycled at 98C for 3m; 33 cycles of 98C for 10s, 63C for 1m, 72C for 30s; and 72C for 2m. PCR reactions were pooled and run on a 1% TAE gel, the 600bp band was excised, and DNA was purified using QIAquick gel extraction kit (Qiagen) and eluted into nonstick tubes (Ambion). Samples were sequenced on an Illumina HiSeq (2×150bp, Admera Health).
Library members were chosen from the Nuclear Pfam library described in21. A total of 20 negative control domains, 10 randomers and 10 tiles of the DMD protein; 30 activator domains; and 50 repressor domains were chosen for cloning. Of the 50 repressors, 6 were discovered to have errors introduced during design, and were discarded from downstream analysis. All domains, including those eventually discarded, are listed in Supplementary Table 1. After library assembly, DNAChisel77 was used to optimize coding sequences by removing duplicates, 7xC homopolymers, BsmBI and BbsI restriction sites, and rare codons. Codon usage was matched to human codon prevalence and GC content was restricted to be between 20% and 75% in any 50-nucleotide window and between 25% and 65% globally.
Cloning for the combinatorial screen proceeded in two stages; in the first, domain-linker-domain concatenations were assembled, and in the second, concatenations were placed into a lentiviral backbone. Domains in the N-terminal and C-terminal position were synthesized as 2 separate oligonucleotide pools (Twist Biosciences). Each pool was PCR amplified in a clean PCR hood to avoid DNA contamination. Each pool was split into 6x 50 uL reactions that were PCR amplified for 21 cycles with 5 ng template, 1 uL of each 10mM primer, 1uL of Herculase II polymerase (Agilent), 1 uL of DMSO, 1 uL of 10mM dNTPs, and 10 uL of 5x Herculase buffer (Agilent). Reaction mixes were thermocycled at 98C for 3m; then 21x cycles of 98C for 20s, 61C for 20s, and 72C for 30s; and, finally, 72C for 3m. Reaction products were pooled and gel extracted by loading a 1% TAE gel, excising the 300 bp band, and purifying using a Zymo Research gel extraction kit. Each of the 2 extraction products (N-terminal and C-terminal) were then amplified for 23x cycles each using the same protocol in order to generate sufficient DNA for downstream reactions. To generate concatenations, 5 uL of 15 ng/uL product from each product, N-terminal and C-terminal, were mixed with 4 uL T4 buffer (NEB B0202S), 4 uL BbsI-HF (NEB R3539L, 1 uL T4 ligase (NEB M0202M), and 1uL of an XTEN linker-encoding DNA amplicon. This linker was encoded with variable nucleotides in codon wobble positions to permit variable DNA sequence in between domains and prevent lentiviral recombination without varying the amino acid sequence of the linker. To complete the GoldenGate reaction, the mix was thermocycled for 65x cycles at 37C for 5m, then 16C for 5m, before a series of incubations at 37C for 1h, 65C for 20m, and 16C for 1h. The reaction product was run on a 1% TAE gel and the 600bp band of domain pair concatenations was extracted with a Zymo gel extraction kit. The concatenation product was then PCR amplified as before, using the outer primers, for 15x cycles. Amplification products were then split into 12x GoldenGate reactions, each consisting of 75ng (1.33 uL) Bsmbi-v2 digested pJT039 lentiviral backbone, 10 ng (0.64 uL) concatenation amplicon, 2 uL T4 buffer, 1 uL BsmbI-v2 Golden Gate Assembly Kit (NEB E1602L), and 15.03 uL nuclease free H2O. Reactions were thermocycled with 65x cycles at 42C for 5m and 16C for 5m, before a final incubation at 42C for 5m and 70C for 20m. The reactions were then pooled and purified with a QIAgen MinElute column, eluting in 6 uL ddH2O. 2 uL of eluent was then electroporated into each of 2 tubes of 50 uL Endura electrocompetent cells (Lucigen, Cat#60242-2) as per manufacturer?s instructions. Cells were then plated onto 4x large 10? x 10? LB plates with carbenicillin. After overnight growth colonies were scraped into a collection bottle and plasmid pools were extracted using a plasmid maxiprep kit (Qiagen #12662). 2 smaller plates of LB with carbenicillin were also prepared with 1:20 diluted cells to count colonies and confirm transformation efficiency. Approximately 50 colonies were Sanger sequenced (Quintara) to estimate cloning efficiencies and the proportion of empty backbone plasmids in the pool.

treatment_protocol: After 48 hours of growth, infected cells were selected with 10 mg/mL blasticidin (Gibco). Infection and selection efficiency were monitored each day with flow cytometry using a Biorad ZE5 flow cytometer. Infection coverage was approximately 600x for each replicate, while maintenance coverage was maintained between 10,000 and 20,000x cells per library element. On day 8 post-infection, cells were treated with 1000 ng/mL doxycycline (Fisher Scientific) for 2 days for activation or 5 days for repression.

value: blasticidin 7d, dox 5d, wait 5d


title: Co-recruit library screen, unused memory screen, unbound R1

description: 2x150 cycles


title: Co-recruit library screen, unused memory screen, bound R2

description: 2x150 cycles


title: INS-MOCK rep2

description: INS-MOCK rep2

value: rat insulinoma cell


title: 30_70_8wk

value: AFTER THERAPY


title: 31_71_0wk


title: AP.2.MF: AP treated Tumor Macrophage Cells Run 1 Rep2


title: AP.5.MF: AP treated Tumor Macrophage Cells Run 1 Rep5


title: AP.2.NK: AP treated Tumor Natural-Killer Cells Run 1 Rep2


title: AC3-14_Esophagus

source_name: Esophagus

value: Esophagus


title: Co-recruit library screen, repression screen, unbound R2

description: 2x150 cycles

value: blasticidin 7d, then dox 5d


title: Co-recruit library screen, unused memory screen, bound R1

description: 2x150 cycles


title: 29_70_0wk


title: AC3-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: 28_82_8wk


title: AP.1.MF: AP treated Tumor Macrophage Cells Run 1 Rep1


title: AC3-12_Optic Nerve

source_name: Optic Nerve

value: Optic Nerve


title: 33_76_0wk


title: Co-recruit library screen, repression screen, bound R2

description: 2x150 cycles


title: 32_71_8wk


title: AC3-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: AC3-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: AC3-15_Pituitary Gland

source_name: Pituitary Gland

value: Pituitary Gland


title: Co-recruit library screen, repression screen, bound R1

description: 2x150 cycles


title: AC3-10_Thalamus

source_name: Thalamus

value: Thalamus


title: IP.5.MF: IP treated Tumor Macrophage Cells Run 1 Rep5

value: IP - MSA-IL-2 + Anti-PD-1


title: 25_69_0wk

value: INFECTED DFU


title: Co-recruit library screen, activation screen, unbound, R2

description: 2x150 cycles

value: blasticidin 7d, then dox 2d


title: IP.5.NK: IP treated Tumor Natural-Killer Cells Run 1 Rep5

value: Natural-Killer Cells


title: 27_82_0wk

value: BEFORE THERAPY


title: IP.4.MF: IP treated Tumor Macrophage Cells Run 1 Rep4

value: Macrophage Cells


title: IP.4.NK: IP treated Tumor Natural-Killer Cells Run 1 Rep4


title: AC2-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: 26_69_8wk


title: Co-recruit library screen, activation screen, bound, R2

description: 2x150 cycles


title: AC2-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: Co-recruit library screen, repression screen, unbound R1

description: 2x150 cycles


title: Co-recruit library screen, activation screen, unbound, R1

description: 2x150 cycles


title: 24_64_8wk

value: AFTER THERAPY


title: Co-recruit library screen, activation screen, bound, R1

description: 2x150 cycles


title: 22_51_8wk


title: AC2-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: 21_51_0wk


title: IP.3.NK: IP treated Tumor Natural-Killer Cells Run 1 Rep3


title: IP.2.MF: IP treated Tumor Macrophage Cells Run 1 Rep2


title: AC2-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: IP.2.NK: IP treated Tumor Natural-Killer Cells Run 1 Rep2


title: Molm13_GADD45g

city: Tianjin

first: Dan

last: Guo

state: Tianjin

address: 288 Nanjing Road

department: State Key Laboratory of Experimental Hematology

institute: Institute of Hematology & Blood Diseases Hospital

data_processing:
Clean reads of transcriptome were mapped to reference genome by Tophat. The expression level of genes among samples were calculated by cuffnorm as FPKM(Fragments Per Kilobase per Million).
The differential expression analysis was performed by cuffdiff.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: cell line: AML cell line

growth_protocol: Cells were grown in RPMI supplemented with 10% Feval bovine serum (FBS)

extract_protocol:
Total RNA from cells was isolated using the RNeasy Mini Kit. Quality of the RNA samples was assessed by 260/280 nm and 260/230 nm absorption spectrum profiles using a NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with or without 1 mg/ml dox for 4 days.

value: 1 mg/ml dox for 4 days


title: Molm13_GADD45g-1


title: 20_49_8wk

source_name: BLOOD PBMC


title: AC3-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: AC2-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: Molm13_Control-1

value: no treatment


title: AC2-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: Molm13_Control


title: 19_49_0wk


title: IP.1.NK: IP treated Tumor Natural-Killer Cells Run 1 Rep1

source_name: Natural-Killer Cells


title: ATAC_HMEC_rep2

first: YEONWOO

last: KIM

address: 291 Daehak-ro, Yuseong-gu

department: Department of Biological Sciences

institute: Korea Advanced Institute of Science and Technology

data_processing:
The adaptors of raw reads were trimmed with cutadapt.
They were mapped to the human genome (hg19) via Bowtie2 (version 2.5.0) with default parameters.
The aligned bam files are merged and sorted with samtools.
We used the bam2wig tool of the RseQC tool to make bigwig files.
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: Describe the positions of the peaks in ATAC-seq.

source_name: Breast

extract_protocol:
The pelleted nuclei were incubated in 25 μl fresh TD buffer (10 mM Tris-HCl, pH 8.0, 5 mM MgCl2, and 10% dimethylformamide) with 2.5 μl Tn5 transposase for 30 min at 37℃. Purify DNA fragments using a QIAquick PCR purification kit (Qiagen, Cat. No. 28106).
The library was amplified as described in the provided manual using the KAPA HiFi HotStart ReadyMix (Roche, KK2061). There was additional purification with a QIAquick PCR purification kit.

value: Breast

value: HMEC

value: primary mammary epithelial cells


title: AC2-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: 17_48_0wk

value: INFECTED DFU


title: 18_48_8wk


title: 23_64_0wk

value: BEFORE THERAPY


title: IP.3.MF: IP treated Tumor Macrophage Cells Run 1 Rep3

source_name: Macrophage Cells

value: Macrophage Cells

value: IP - MSA-IL-2 + Anti-PD-1


title: 16_46_8wk


title: AI.5.NK: AI treated Tumor Natural-Killer Cells Run 1 Rep5

value: Natural-Killer Cells

value: AI - Antibody 2.5F-Fc + MSA-IL-2


title: ATAC_HMEC_rep1


title: AI.5.MF: AI treated Tumor Macrophage Cells Run 1 Rep5


title: AC2-24_Bone Marrow, Femur

source_name: Bone Marrow

value: Bone Marrow


title: AI.4.MF: AI treated Tumor Macrophage Cells Run 1 Rep4


title: AC2-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: 9_1 KO veh_3395

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
Data Formatting - bcltofastq-2.19.0
Data Cleaning - fastp 0.20.0, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment - STAR_2.7.0f, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 - subread-1.6.4, featurecounts, -s 2 -t exon -g gene_name
Assembly: Mg38 + Gencode-M22 Annotation
Supplementary files format and content: raw gene counts

source_name: heart

extract_protocol:
RNA was extracted from heart tissue, CMs or CFs using either RNeasy kit (Qiagen)
The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size. Amplified libraries were sequenced using the NextSeq 550 sequencer (Illumina, San Diego, CA) on the High flow cell to obtain approximately 25 to 30 million reads per sample.

treatment_protocol: Male or female C57BL/6J PDE10A-WT or PDE10A-KO mice were received pretreatment of TP-10 (3.2mg/kg/day) or same volume of vehicle (10% DMSO in 40% β-cyclodextrin) via subcutaneous injection before DOX treatment for 2 days via intra-peritoneal injection and then continuously received the same treatment for another 5 days. TP-10 was dissolved in a vehicle consisting of 10% DMSO and 40% β cyclodextrin. After pretreatment mice received DOX treatment (15mg/kg) in one bolus via intra-peritoneal injection for 7 days.

value: heart

value: PDE10A Knockout

value: Vehicle


title: 8-1 KO veh_3394


title: 15_46_0wk


title: AI.4.NK: AI treated Tumor Natural-Killer Cells Run 1 Rep4


title: AC2-21_Colon

data_processing:
All read files were processed by fastp (v0.19.8) to remove poor quality reads and to trim poor quality 3’ bases. The filtered and trimmed reads were aligned and quantified using OmicSoft’s (Cary, NC, USA) Array Studio software (https://www.omicsoft.com/publish-studio; Oshell.exe v10.0) to reference genome NCBI Macaca_fascicularis_5.0. The transcriptomic annotation NCBI Macaca fascicularis Annotation Release 101 was used as the transcript model reference. The alignment algorithm OSA is documented in an OmicSoft whitepaper (http://omicsoft.com/downloads/whitepaper/OmicsoftAligner.pdf), and the gene/transcript quantification module is an OmicSoft implementation of the RSEM algorithm.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: RNA-Seq data — gene name, read count

source_name: Colon

extract_protocol:
Total RNA was extracted from 27 snap-froze tissues with RNeasy Micro/Mini Kit (QIAGEN, Germany, Cat. #74004/#74106), according to the manufacturer’s instructions. The quality of the isolated RNA was analyzed by Agilent Bioanalyzer 2100. Only the RNA samples with an RNA Integrity Number (RIN) value of 6.0 or higher were included for RNA sequencing.
RNA-seq libraries were constructed from RNA samples meeting QC criteria based on polyA+ selection of mRNA using a standard strand-specific protocol with VAHTS® Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme, China, Cat. #NR612). The quality of the sequencing libraries was analyzed by Agilent Bioanalyzer 4200 and the peak length ranged from 250~500 bp. Clusters were generated by cBot with the library diluted to 10 pM and then sequenced on Illumina HiSeq 2500 instruments with 2 × 150 bp paired-end sequencing. All libraries were sequenced to an average depth of 52 ± 8.8 (mean ± s.d.) million reads (corresponding to 26 ± 4.4 million paired-end reads).

value: Colon


title: AI.3.MF: AI treated Tumor Macrophage Cells Run 1 Rep3


title: 7 KO veh_3393


title: 14_45_8wk

value: AFTER THERAPY


title: IP.1.MF: IP treated Tumor Macrophage Cells Run 1 Rep1


title: AC2-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: AC2-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: 5-1 WT Dox_24

value: PDE10A WT

value: Doxorubicin


title: 4-1 WT Dox_22


title: 1_54_0wk

value: INFECTED DFU


title: AC2-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: 12_63_8wk


title: 3 WT veh_3


title: 13_45_0wk

value: BEFORE THERAPY


title: AI.2.MF: AI treated Tumor Macrophage Cells Run 1 Rep2

value: Macrophage Cells


title: AI.2.NK: AI treated Tumor Natural-Killer Cells Run 1 Rep2

value: Natural-Killer Cells


title: AC2-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: AI.1.MF: AI treated Tumor Macrophage Cells Run 1 Rep1

value: AI - Antibody 2.5F-Fc + MSA-IL-2


title: P128, Pre treatment

city: Philadelphia

first: Gregory

middle: L

last: Beatty

state: PA

institute: University of Pennsylvania

data_processing:
Pre-processing operations included a quality check (FastQC), removal of adapter content (used during sequencing), and quality thresholding (removal of bad quality reads (Phred Score <30)).
Reads that passed quality thresholds were deemed suitable for further analyses and were mapped to the human reference genome hg38 (GRCh38.p12, Ensembl), using Bowtie2 and Tophat 2.1.1.
Expression of assembled transcriptomes was estimated using Cufflinks 2.2.1.
Normalization was performed using the Classic FPKM (Fragments Per Kilobases per Million fragments) method, followed by Log2 transformation of the value.
Gene-level differential expression between conditions was estimated based on the Log2 transformed FPKM of transcripts using deseq2 in R (version 4.0.3).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: tumor

extract_protocol:
RNA was extracted from FFPE tissue samples using the Norgen FFPE DNA/RNA Purification Plus Kit (Norgen Biotek, Ontario, Canada).
Libraries were constructed with KAPA RNA HyperPrep with Riboerase and performed based on manufacturer’s recommendations.

value: tumor

tag: subject id

tag: subject status

value: patients with treatment-naïve pancreatic carcinoma

tag: time point

value: Pre


title: AC2-23_Salivary Gland

first: Xianglong

last: Zhang

institute: Amgen Inc

source_name: Salivary Gland

value: Salivary Gland


title: P136, Pre treatment


title: AI.1.NK: AI treated Tumor Natural-Killer Cells Run 1 Rep1


title: P145, Post treatment

value: Post


title: AC2-15_Pituitary Gland

source_name: Pituitary Gland

value: Pituitary Gland


title: AIP.5.MF: AIP treated Tumor Macrophage Cells Run 1 Rep5

value: AIP - Antibody 2.5F-Fc + MSA-IL-2 + Anti-PD-1


title: 1-1 WT veh_1

value: heart

value: Vehicle


title: P145, Pre treatment


title: 13 WT Dox_21

value: PDE10A WT

value: Doxorubicin


title: 12-1 KO Dox_20

value: PDE10A Knockout


title: AI.3.NK: AI treated Tumor Natural-Killer Cells Run 1 Rep3


title: AC2-14_Esophagus

source_name: Esophagus

value: Esophagus


title: AIP.5.NK: AIP treated Tumor Natural-Killer Cells Run 1 Rep5


title: P143, Post treatment


title: AC2-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: AC2-12_Optic Nerve

source_name: Optic Nerve

value: Optic Nerve


title: 2 WT veh_2


title: AIP.4.MF: AIP treated Tumor Macrophage Cells Run 1 Rep4

value: Macrophage Cells


title: P143, Pre treatment


title: AIP.4.NK: AIP treated Tumor Natural-Killer Cells Run 1 Rep4

source_name: Natural-Killer Cells

value: Natural-Killer Cells


title: P142, Post treatment

value: tumor


title: 10-1 KO Dox_18


title: AC2-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: P142, Pre treatment

value: patients with treatment-naïve pancreatic carcinoma

value: Pre


title: OmpGFP_WT_RNASeq_Rep2

city: SAN FRANCISCO

first: Lea

last: Kiefer

address: 1651 4th Street, Weill Neurosci RM 471A

institute: UCSF

data_processing:
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. Crosslinked ChIP-Seq samples were aligned with Bowtie2 (2.3.2) with default parameters. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20. HiC samples were aligned and processed using HiC-Pro (Servant et al. 2015 Genome Biology). 10x single cell RNA-seq was processed using cellranger.
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1). For ChIP-seq, duplicate reads were marked with Picard and removed with samtools.
For ChIP-Seq, bigWig files  were generated using HOMER (4.7) (-fsize 1e20 -fragLength given). For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: mOSNs

extract_protocol:
For RNA-seq: RNA  was  isolated  from  tissue  using  TRIzol.  Cell  lysate  was  extracted  with  bromo-chloropropane and RNA was precipitated with 100% isopropanol supplemented with 10 μg of glycobluefor 10 min at room temperature and then pelleted at 16,000 x g for 30 min at  4°C.  The  RNA  pellet  was  washed  once  with  75%  ethanol  and  then  resuspended  in RNase-free water to a maximal concentration of 200 ng/μl. Genomic DNA contaminants were   removed   by   Turbo   DNase.   Removal   of   Turbo   DNase   was   performed   by phenol:chloroform  extraction  and  RNA  was  precipitated  as  described  above  and resuspended in RNase-free water and stored at -80°C.   For Raphe RNA-seq: RNA  was  isolated  from  coronal  sections  of  the  Raphe  (20  μm  thick)  obtainedfrom paraformaldehyde-fixed   brain   (described   in   more   detail   below,   see   paragraph “Preparation of Mouse Brain Tissue Sections”). After 3x 5 minutes washes of the slides with 1X PBS, a small portion of each section containing approximately the Raphe region was extracted. Then, the RNA was isolated using  RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Invitrogen) as instructed by the manufacturer.   For in situ HiC was carried out according to Rao et al. 2014.  For ChIP-seq: Cells were crosslinked with 1% formaldehyde for  10 minutes  at room  temperature. Formaldehyde  was  quenched  by  adding  glycine to  a  final concentration of 0.125 M for 5 minutes at room temperature. Cells were then washed with 1X cold PBS with protein inhibitors twice and pelleted. Cell pellets were stored at -80°C till use. Cells were lysed in lysis buffer (50 mM Tris pH 7.5, 140 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) for 10 minutes. Nuclei were spun for 10 minutes at 1000 x g and resuspended in the sonication buffer (10 mM Tris pH 7.5, 0.5% SDS) as 5million nuclei per 300 μl sonication buffer. Chromatin was sheared by Covaris (Peak power 105.0; Duty Factor 2.0; Cycle/Burst 200; Treatment 960 sec; Temperature 4-8°C). Following a spin at 13,000 x g for 10 minutes to remove debris, the sheared chromatin was diluted such that the final binding buffer concentration was 15 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS) and incubated for 2 hours with dynabeads G pre-equilibrated in the binding buffer for pre-clearing of the chromatin. Post-cleared chromatin was then incubated with the specific antibody overnight (1 μg of antibody was used per 5 million nuclei). The next day, dynabeads G were added to the chromatin-antibody mix for 2 hours. A total of four washes with 1X wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) and one wash with TE buffer (10 mM Tris pH 7.5, 1 mM EDTA) were performed. The elution was performed at65°C for 1 hour in the elution buffer (1% SDS, 250 mM NaCl, 2 mM DTT).  All steps, with the exception of the elution, were performed at 4°C. All buffers, with the exception of the TE and elution buffer contained 1X protease inhibitors. The eluted chromatin was reverse-crosslinked overnight at 65°C and the DNA was purified with AMPure  XP  beads  (Beckman  Coulter).
For RNA-Seq experiments, raw FASTQ files were aligned with either Tophat or STAR using hg19 or mm10 reference genomes. When libraries were made following the SMARTer Stranded Total RNA-Seq, the initial 4 base pairs of both paired reads were trimmed prior to alignment.   For single cell RNA-seq, raw FASTQ files were analyzed using cellranger.  For ChiP-Seq experiments, raw FASTQ files were aligned using Bowtie2 using hg19 reference genome upon adapter sequences removal using CutAdapt. Uniquely aligning reads were selected using Samtools and reads with alignment quality below 30 (-q 30) were removed. The HOMER software package was used to generate signal tracks.   For in situ Hi-C experiments, raw FASTQ files were analyzed using HiC-Pro and hic files were generated (Servant et al. 2015).

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For RNA-seq, dissociated cells were washed once with sort media (PBS + 2% Fetal Bovine Serum) and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical)  and 500ng/mL DAPI (Invitrogen). For Crosslinked-ChIP and HiC samples, cells were fixed prior to sorting. For fixation, dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 10 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting.

value: mOSNs

value: ompgfp


title: Ompcre_Rad21cKO_TdTom_singlecellRNA

description: single cell RNA-Seq

source_name: mOSNs with conditional Rad21 deletion

value: mOSNs with conditional Rad21 deletion


title: AC2-10_Thalamus

source_name: Thalamus

value: Thalamus


title: AC2-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: P141, Post treatment

value: Post


title: AIP.3.MF: AIP treated Tumor Macrophage Cells Run 1 Rep3

source_name: Macrophage Cells

value: AIP - Antibody 2.5F-Fc + MSA-IL-2 + Anti-PD-1


title: AIP.3.NK: AIP treated Tumor Natural-Killer Cells Run 1 Rep3


title: AIP.2.NK: AIP treated Tumor Natural-Killer Cells Run 1 Rep2


title: P141, Pre treatment


title: AC1-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: AIP.1.MF: AIP treated Tumor Macrophage Cells Run 1 Rep1


title: OmpGFP_WT_RNASeq_Rep1


title: AC1-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: 11-1 KO Dox_19

source_name: heart

value: heart

value: PDE10A Knockout

value: Doxorubicin


title: P138, Post treatment


title: UT.5.MF: Untreated Tumor Macrophage Cells Run 1 Rep5

value: Macrophage Cells

value: Untreated


title: P138, Pre treatment

value: tumor


title: AC1-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: P134, Post treatment

source_name: tumor

value: patients with treatment-naïve pancreatic carcinoma


title: UT.4.MF: Untreated Tumor Macrophage Cells Run 1 Rep4


title: AC1-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: Tubal fluid_S306224exo_NS

type: RNA

city: shanghai

first: yiqin

last: zhang

address: No. 910, Hengshan Rd

institute: International Peace Maternity and Child Health Hospital

description: Exosomal miRNA microarray intubal fluid

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings. Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna(López-Romero, P. BMC Genomics. 2011.).

data_processing: Putative target genes of miRNAs were predicted by miRanda. R package ClusterProfiler was used to perform enrichment analysis of Gene Ontology (GO) functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Pathways were also enriched by DAVID (https://david.ncifcrf.gov). KEGG analysis was performed simultaneously using the ClusterProfiler package of R software and the DAVID website to predict the pathways.

source_name: Tubal fluid_exosome

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit without phenol (Cat # AM1561, Ambion, Austin, TX, US), following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Exosomes were separated from tubal fluid by gradient centrifugation and ultracentrifugation as MISEV reported (Witwer et al., 2021)(Théry et al., 2018). We used nanoparticle tracking analysis (NTA) ZetaVIEW S/N 17-310 (Particle Meerbusch, Germany) to measure the diameter of exosomes (Supplementary Fig.1A). Exosomes were also dyed by uranyl acetate and detected by TEM (Supplementary Fig.1B&C) (Di Pietro, 2016).

tag: group

value: Control

tag: source

value: Tubal fluid


title: Tubal fluid_S306515exo_NS

description: Exosomal miRNA microarray intubal fluid


title: AC2-1_Left Ventricle

city: South San Francisco

address: 1120 Veterans Blvd

source_name: Left Ventricle

value: Left Ventricle


title: P133, Post treatment


title: AC1-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: UT.2.MF: Untreated Tumor Macrophage Cells Run 1 Rep2


title: UT.3.MF: Untreated Tumor Macrophage Cells Run 1 Rep3


title: Tubal fluid_S305643exo_NS

description: Exosomal miRNA microarray intubal fluid


title: P133, Pre treatment

value: Pre


title: UT.1.MF: Untreated Tumor Macrophage Cells Run 1 Rep1


title: AC1-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: P132, Post treatment

value: Post


title: P132, Pre treatment


title: UT.T.NK.3: Untreated Tumor Natural-Killer Cells Run 2 Rep3

source_name: Natural-Killer Cells

value: Natural-Killer Cells


title: AC1-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: AC1-24_Bone Marrow, Femur

source_name: Bone Marrow

value: Bone Marrow


title: Tubal fluid_S303534exo_NS

description: Exosomal miRNA microarray intubal fluid


title: UT.T.NK.2: Untreated Tumor Natural-Killer Cells Run 2 Rep2


title: UT.4.NK: Untreated Tumor Natural-Killer Cells Run 1 Rep4


title: P134, Pre treatment


title: AC1-23_Salivary Gland

source_name: Salivary Gland

value: Salivary Gland


title: AC1-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: HFF SORSC1 transfected CGH clone 4

description:
Test 3
Agilent 180K CGH + SNP 85591

hyb_protocol: Labeled DNAs were hybridized onto Agilent oligonucleotide microarrays (Agilent 180K CGH + SNP) according to the manufacturer’s instructions (Agilent Technologies)

data_processing:
Data analysis was carried out with Agilent Technologies software, namely Feature Extraction for Cytogenomics Algorithm v5.0 for the fluorescence ratio calculation and Agilent CytoGenomics v5.2 for the localization of chromosomal imbalances and LOH.
Deletions and duplications in the heterozygous state were characterized by values of the log2 ratio of fluorescence intensities (cyanine5/cyanine3) below -0.5 and above +0.3, respectively, with the statistical algorithm ADM2 used at a threshold of five. LOH was evaluated with the statistical algorithm ADM2 used at a threshold of 6 (Default Analysis Method v2)

source_name: SNP clone 4

value: HFF

source_name: Agilent Male control

value: primary


title: Tubal fluid_S308632zuo_NS

description: Exosomal miRNA microarray intubal fluid

value: Tubal endometriosis


title: P124, Post treatment

value: tumor

value: patients with treatment-naïve pancreatic carcinoma


title: Tubal fluid_S305896exo_NS

description: Exosomal miRNA microarray intubal fluid


title: Tubal fluid_S305044exo_NS

description: Exosomal miRNA microarray intubal fluid

value: Control


title: P124, Pre treatment


title: AC1-21_Colon

source_name: Colon

value: Colon


title: Tubal fluid_S129922exo_NS

description: Exosomal miRNA microarray intubal fluid

value: Tubal fluid


title: Tubal fluid_S302873exo_NS

description: Exosomal miRNA microarray intubal fluid


title: HFF SORSC1 transfected CGH clone  3

description:
Test 2
Agilent 180K CGH + SNP 85591

source_name: SNP clone 3


title: UT.T.NK.1: Untreated Tumor Natural-Killer Cells Run 2 Rep1

value: Untreated


title: AIP.T.MF.3: AIP treated Tumor Macrophage Cells Run 2 Rep3

source_name: Macrophage Cells

value: Macrophage Cells

value: AIP - Antibody 2.5F-Fc + MSA-IL-2 + Anti-PD-1


title: AIP.T.MF.2: AIP treated Tumor Macrophage Cells Run 2 Rep2


title: P120, Post treatment

value: Post


title: AC1-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: HFF SORSC1 transfected CGH bulk before editing

description:
Test 1
Agilent 180K CGH + SNP 85591

source_name: SNP WT


title: HFF ABRAXAS2 transfected CGH clone 3 (CN + dup)

description: Test 3

hyb_protocol: Labeled DNAs were hybridized onto Agilent oligonucleotide microarrays (8x60K Agilent Genetisure or 180K CGH + SNP) according to the manufacturer’s instructions (Agilent Technologies)

source_name: ABRAXAS2 CGH clone 2

source_name: Control agilent Male


title: P120, Pre treatment

source_name: tumor

value: Pre


title: AC1-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: AC1-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: HFF ABRAXAS2 transfected CGH clone 1 (del terminale)

description: Test 2

source_name: ABRAXAS2 CGH clone 1


title: UT.T.MF.3: Untreated Tumor Macrophage Cells Run 2 Rep3


title: P119, Post treatment


title: AC1-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: UT.T.MF.2: Untreated Tumor Macrophage Cells Run 2 Rep2


title: AC1-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: P136, Post treatment


title: UT.T.MF.1: Untreated Tumor Macrophage Cells Run 2 Rep1


title: AC1-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: AIP.T.NK.3: AIP treated Tumor Natural-Killer Cells Run 2 Rep3

source_name: Natural-Killer Cells

value: Natural-Killer Cells


title: AIP.T.NK.2: AIP treated Tumor Natural-Killer Cells Run 2 Rep2


title: P128, Post treatment

value: tumor


title: AC1-15_Pituitary Gland

source_name: Pituitary Gland

value: Pituitary Gland


title: patient progressed to TKIs, nC_P27_2

city: Barcelona

first: Miguel

middle: A

last: Molina-Vila

state: Barcelona

address: Sabino de Arana 16, -1.7

country: Spain

institute: Hospital Universitario Dexeus

description: nCounter analysis of patients progressed to TKIs

hyb_protocol: Total RNA was hybridized with a custom-designed  mixture of biotinylated capture tags and fluorescently labeled reporter probes (Elements  Chemistry) Amplified cDNA was denatured at 95ºC for 5 minutes and hybridized at 67ºC for 18-24 hours with a customized nCounter panel including probes for housekeeping genes, common ALK, ROS1 or RET fusion transcripts and METΔex14 transcripts.

scan_protocol: All processes of hybridization, capture, clean-up and digital data acquisition  were performed with nCounter Prep Station® and Digital Analyzer® (NanoString  Technologies) according to the manufacturer’s instructions. The hybridization mixture  included specific probes for fusions, MET-wt and METΔex14 target sequences

data_processing:
Reporter counts were uploaded into the nSolver analysis software version 2.6 and converted into an Excel Sheet.
Samples were considered not evaluable if the geometrical mean (geomean) of counts corresponding to the housekeeping genes was lower than 100. Counts from MET probes were normalized in two steps and subjected to a logarithmic transformation to obtain the log-MET mRNA expression values

source_name: liquid biopsy sample

label_protocol: not applicable

extract_protocol: The protocol used is as follows, In the case of liquid biopsies (LBx), blood samples were collected in a 10-mL sterile Vacutainer tubes (BD) while pleural effusions and cerebrospinal fluids were collected in sterile tubes or containers with no additives or anticoagulants. Samples were centrifuged twice for 10 min at 500 xg and the circulating-free RNA (cfRNA) was isolated from 4 mL of supernatant using the QIAsymphony® DSP Virus/Pathogen Midi Kit in a QIAsymphony robot (Qiagen), following the manufacturer’s instructions. Final elution volume was 50 μL in all cases. RNA concentration was estimated by Qubit™

tag: disease state

value: NSCLC

value: blood

tag: gender

value: male

tag: age


title: patient progressed to TKIs, nC_P28_1

value: female

value: UNK


title: AIP.T.NK.1: AIP treated Tumor Natural-Killer Cells Run 2 Rep1

tag: cell type

value: AIP - Antibody 2.5F-Fc + MSA-IL-2 + Anti-PD-1


title: patient progressed to TKIs, nC_P26_1


title: NFO120-P: NFO120-P_HD#7_CLIP-AbR

city: Copenhagen

first: Nicolas

last: Fossat

address: Blegdamsvej 3B

country: Denmark

institute: University of Copenhagen

description: Single-end 1 x 150bp

data_processing:
Library strategy: CLIP-Seq
CLIP-Seq: Removal of poor quality sequence and adaptors using Trimmomatic. Mapping to the mm10 mouse reference genome using bowtie. PCR duplicates collapsed using tools developed in-house or found in galaxy. Collapsed mapped reads were then grouped into clusters depending on their location, followed by quantification of the number of reads for each region for each sample. Clusters were then annotated, and their size normalised to the sample size before subsequent analyses and comparisons between samples. Significance of overlap was assessed by Fisher’s exact test.
RNA-Seq: Removal of poor quality sequence and adaptors using Trimmomatic. Mapping to the mm10 mouse reference genome using RNA STAR (v2.7.3) following the two-pass alignment protocol. BAM files were imported in SeqMonk (v 1.45.4,  Babraham Institute) where data was assessed for data integrity (RNA-Seq QC pipeline), and quantified using the RNA-Seq quantitation pipeline to generate raw counts to mRNA and setting library type to “opposing strand specific”. Differentially expressed genes were calculated using SeqMonk edgeR via the “statistical test on replicated data” script as generated via SeqMonk. For differentially expressed exons and introns we quantified data in SeqMonk to a collapsed exon reference and then performed edgeR analysis.
Genome_build: mm10

source_name: Brain

extract_protocol:
Whole brains were collected as fast as possible from euthanasied mice, bissected longitudinally, then cells were gently dissociated and processed as described in the "overall design" section above. For RNA-Seq, total RNA was extracted using RNAeasy micro kit (Qiagen #74004).
For CLIP-Seq, library was constructed following a custom-made protocol (see PMID: 24407355). For RNA-Seq, library was constructed following protocol described chapter 2 of NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB #E7760S).

value: 12 weeks old

tag: Sex

value: Male

tag: genotype

value: R6/2 (Huntington's disease)

tag: animal id

value: Brain

tag: experiment

value: CLIP-Seq

tag: antibody

value: Rabbit anti-RBM5 antibody (AbR)


title: AIP.T.MF.1: AIP treated Tumor Macrophage Cells Run 2 Rep1

value: Macrophage Cells

tag: drug treatment

tag: sequencing run


title: NFO120-R: NFO120-R_HD#9_CLIP-AbR

description: Single-end 1 x 150bp

tag: strain

tag: tissue


title: Treatment_A8

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

data_processing:
Overrepresented adapters were checked using FastQC and adapters were trimmed using AdapterRemoval when required.
Quasi-aligment of dataset to the GENCODE mouse transcriptome and transcript quantification via Salmon.
Expression profiles and differential gene expression were assessed with limma 62 and edgeR.
Genome_build: GRCm38.p6, M25 release
Supplementary_files_format_and_content: tabular, transcript read count output of Salmon

source_name: peri-ovulatory granulosa cells

growth_protocol: 21 days old mice

extract_protocol:
RNA was extracted using the RNeasy Mini kit (QIAGEN)
RNA was subjected to rRNA depletion using a modified Ribozero method and library preparation using Clontech SMARTer Stranded RNA-Seq Kits (Takara Bio, Shiga, Japan).

treatment_protocol: mice were injected with 5 IU eCG, after 46 hours mice were either humanely killed (0h treatment) or injected with 5 IU hCG. hCG-injected mice were humanely killed 8 h post-treatment. All mice were then dissected and ovaries were punctured for granulosa cell collection.

tag: treatment

value: 6hr hCG Treatment

value: CBA x C57BL/6 F1


title: patient progressed to TKIs, nC_P24_1


title: patient progressed to TKIs, nC_P27_1


title: NFO120-O: NFO120-O_WT#4_CLIP-AbR

description: Single-end 1 x 150bp

value: Wild-type


title: AC1-14_Esophagus

source_name: Esophagus

tag: individual

tag: phenotype

value: Esophagus


title: patient progressed to TKIs, nC_P23_2

value: NSCLC


title: AC1-12_Optic Nerve

source_name: Optic Nerve

value: Optic Nerve


title: Treatment_A7


title: NFO120-N: NFO120-N_WT#3_CLIP-AbR

description: Single-end 1 x 150bp


title: P119, Pre treatment

value: tumor

tag: subject id

tag: subject status

value: patients with treatment-naïve pancreatic carcinoma

tag: time point

value: Pre


title: AC1-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: NFO120-M: NFO120-M_WT#2_CLIP-AbR

description: Single-end 1 x 150bp

tag: age

value: 12 weeks old


title: AC1-10_Thalamus

source_name: Thalamus

value: Thalamus


title: Treatment_A6


title: Treatment_A5


title: patient progressed to TKIs, nC_P22_2

tag: disease state

value: blood

tag: gender

value: male

value: UNK


title: NFO120-Q: NFO120-Q_HD#8_CLIP-AbR

description: Single-end 1 x 150bp

tag: Sex

value: Male

tag: genotype

value: R6/2 (Huntington's disease)

value: Brain

value: CLIP-Seq

value: Rabbit anti-RBM5 antibody (AbR)


title: AC1-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: AC1-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: NFO120-L: NFO120-L_HD#9_CLIP-AbM

description: Single-end 1 x 150bp

tag: animal id

tag: experiment

value: Mouse anti-RBM5 antibody (AbM)


title: Control_A4

value: Control

value: CBA x C57BL/6 F1


title: NFO120-K: NFO120-K_HD#8_CLIP-AbM

description: Single-end 1 x 150bp

tag: antibody


title: patient progressed to TKIs, nC_P22_1

value: NSCLC


title: NFO120-J: NFO120-J_HD#7_CLIP-AbM

description: Single-end 1 x 150bp


title: patient progressed to TKIs, nC_P20_1

value: female


title: NFO120-I: NFO120-I_WT#4_CLIP-AbM

description: Single-end 1 x 150bp

value: 12 weeks old

value: Wild-type


title: Control_A2


title: Patient31 meningioma

city: Los Angeles

first: Michelle

middle: Ariana

last: Wedemeyer

state: California

address: 1200 N State St, Suite 3300

department: Neurosurgery

institute: University of Southern California

description: meningioma

hyb_protocol: standard Illumina HumanOmni-Express v12.1 BeadChip SNP array protocol

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

data_processing:
Data were analyzed in Illumina GenomeStudio v2.0.5 with cnvPartition Plug-in v3.2.1
Genotype: AA,AB,BB,or NC (no call)

label: Cy5 and Cy3

source_name: meningioma

extract_protocol: Tumor/dura samples were obtained at the time of surgery.  DNA was extracted using Qiagen DNeasy Blood & Tissue Kit (Cat No./ID: 69506).

tag: prior sample id

value: FEMALE

tag: who grade

value: II

tag: reoperation

value: Unknown

tag: progression


title: Patient30 meningioma

description: meningioma

label_protocol: standard Illumina HumanOmni-Express v12.1 BeadChip SNP array protocol


title: Patient29 meningioma

description: meningioma

value: I

value: No


title: NFO120-H: NFO120-H_WT#3_CLIP-AbM

description: Single-end 1 x 150bp

tag: strain

value: Male

tag: tissue

value: Brain


title: Control_A1

tag: treatment


title: patient progressed to TKIs, nC_P23_1

value: blood

value: male

value: UNK


title: NFO120-G: NFO120-G_WT#2_CLIP-AbM

description: Single-end 1 x 150bp

value: CLIP-Seq

value: Mouse anti-RBM5 antibody (AbM)


title: patient progressed to TKIs, nC_P16_1


title: Patient27 meningioma

description: meningioma


title: patient progressed to TKIs, nC_P15_1


title: Patient26 meningioma

description: meningioma


title: Mbd2_ChIP-seq

city: Ariel

first: Elad

last: Lax

address: 65 Ramat HaGolan st.

institute: Ariel University

data_processing:
Reads were aligned to the mouse reference genome using Bowtie
Low quality alignments and alignments for read pairs with multiple possible genomic alignments were omitted. Duplicate read pairs were removed.
Read count peaks corresponding to likely binding sites were identified for each sample by MACS2 with default parameters, and narrow peak calling. Input DNA  reads were subtracted from the Mbd2 binding to control for nonspecific peaks
Peaks with false discovery rates less than 0.05 were selected as high-confidence binding sites and were annotated with their genomic locations relative to nearby genes using HOMER with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: txt file annotated peaks

source_name: Hippocampus

value: 10-12 weeks

value: Hippocampus

tag: chip antibody

value: anti- Mbd2 (Epigentek-A1007) antibody


title: Input


title: patient progressed to TKIs, nC_P14_1

value: NSCLC


title: Patient25 meningioma

description: meningioma


title: patient progressed to TKIs, nC_P13_1

value: female


title: NFO120-E: NFO120-E_HD#8_CLIP-IgG

description: Single-end 1 x 150bp

value: 12 weeks old

value: R6/2 (Huntington's disease)

value: Non-specific antibody


title: Control_A3

value: Control

value: CBA x C57BL/6 F1


title: NFO120-F: NFO120-F_HD#9_CLIP-IgG

description: Single-end 1 x 150bp

value: Male


title: Mbd2-/- 1

data_processing:
Reads were aligned to mm9 reference genome using Bsmap v2.89
Output data were strand-sorted, filtered, and deduplicated with Picard tools
Methylation levels and coverage levels were extracted with methratio.py command in Bsmap
Differential methylation cytosines were analyzed with methylKit R package
Genome_build: mm9
Supplementary_files_format_and_content: Txt files contain methylation level and differentail methylation per CpG

extract_protocol:
mice (10-12 weeks of age) were sacrificed, the brains were rapidly removed, and bi-lateral hippocampi were isolated, flesh frozen and stored at -80°C for later analysis. DNA was extracted with AllPrep-DNA/RNA/miRNA-universal kit according to the manufacturer protocol.
The SeqCap Epi Enrichment System (Roche NimbleGen, Laval, QC) for targeted bisulfite sequencing of promoters and enhancers in the mouse genome was used. Mouse target probes (mm9) were custom designed based on H3K4me1 and H3K4me3 signals from mouse public ChIP-seq data. A total of 83276 regions were targeted by the probes which spans 64760111 base pairs. Biotinylated target probes were designed for both strands of bisulfite converted genomic DNA. Bisulfite treated genomic DNA was ligated to methylated next generation sequencing (NGS) adaptors, hybridized to the biotinylated oligonucleotide probes followed by a series of washes of off-target DNA sequences and unbound DNA. Isolated DNA then underwent PCR amplification and sequenced on Illumina Hiseq 2000 with pair-end 50bp reads and replication with 125bp pair-end reads was performed as well.

value: Mbd2-/- with C57BL/6 background


title: Mbd2-/- 2


title: Patient24 meningioma

description: meningioma

value: MALE

value: II

value: No


title: patient progressed to TKIs, nC_P11_1

value: blood

value: male

value: UNK


title: NFO120-D: NFO120-D_HD#7_CLIP-IgG

description: Single-end 1 x 150bp

value: Brain

value: CLIP-Seq


title: Patient28 meningioma

description: meningioma

value: FEMALE

value: I

value: Yes


title: patient progressed to TKIs, nC_P19_1

value: NSCLC


title: WT_2


title: NFO120-B: NFO120-B_WT#3_CLIP-IgG

description: Single-end 1 x 150bp

value: 12 weeks old

value: Wild-type

value: Non-specific antibody


title: WT_4


title: patient progressed to TKIs, nC_P17_1

value: female


title: NFO120-C: NFO120-C_WT#4_CLIP-IgG

description: Single-end 1 x 150bp

value: Male


title: Patient22 meningioma

description: meningioma

value: MALE

value: Unknown


title: patient progressed to TKIs, nC_P10_1


title: leaf blade, VOC exposed, rep3

city: Nanjing

first: Paul

last: Daly

state: Jiangsu

address: 50 Zhongling St

institute: Jiangsu Academy of Agricultural Sciences

description: matrix column name: GAQ1_VOCS_R3

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic (Bolger et al., 2014) and the low-quality reads were removed to obtain the clean reads.
Then, about 48 M clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the Zingiber officinale reference genome (GCF_018446385.1_Zo_v1.1_genomic.fna) (Cheng et al., 2021) using HISAT2 (Kim et al., 2015) and > 90% of the reads mapped to the genome from all the samples.
FPKM (Roberts et al., 2011) of each gene was calculated using Cufflinks (Trapnell et al., 2010), and the read counts of each gene were obtained by HTSeq-count (Anders et al., 2015).
The GFF file "GCF_018446385.1_Zo_v1.1_genomic.gff " was used.
Assembly: GCF_018446385.1_Zo_v1.1
Supplementary files format and content: tab-delimited text file of read counts for all samples
Supplementary files format and content: tab-delimited text file of FPKM values for all samples

organism: Zingiber officinale

source_name: leaf blade

growth_protocol: The effect of P. oligandrum GAQ1 volatile compounds (VOCs) on ginger was evaluated by following the method described by Park et al., (2015). Glass jars containing V8 agar medium were inoculated with a 5 mm actively growing mycelial plug of P. oligandrum whereas the non-inoculated glass jars containing only V8 medium were used as a control. Six small 2 mm holes were made at the bottom of the plastic pots (270 mL) to allow the roots to be exposed to the VOCs produced by P. oligandrum. Two sterilized filter paper pieces (Cat no. 99-102-150, Cytiva, USA) were placed inside the bottom of the plastic pot to avoid the leakage of contaminating liquid through the holes into the glass jar. Equal-sized ginger seedlings were transferred to the plastic pots containing sterilized vermiculite and organic matter (3:1) and placed on the glass jars containing either P. oligandrum or only V8 agar medium as control. The pot-jar assembly was then firmly sealed by wrapping at least nine times with parafilm (PARAFILM M, Bemis, USA) to avoid the escape of VOCs produced by P. oligandrum. The pot-jar assembly was then placed at 16 h light and 8 h dark cycles at 25ºC and watered with sprayer. Plants were watered by wetting the surface of the soil to avoid contamination by leakage of water through holes into the glass jar. Plants were grown for 21 days. Leaf material was collected and frozen at -80°C for subsequent analysis of gene expression. Three replicate samples were collected for each treatment, i.e., three samples for VOCs-exposed and three samples for non-exposed (control) plants. The leaf blades from the two uppermost leaves of the plants grown for 21 days with and without exposure to VOCs were collected, flash-frozen in liquid nitrogen, and stored at -80°C. See publication connected with our GEO submission for images of the ginger plants. Park, Y. S., Dutta, S., Ann, M., Raaijmakers, J. M., and Park, K. (2015). Promotion of plant growth by Pseudomonas fluorescens strain SS101 via novel volatile organic compounds. Biochem. Biophys. Res. Commun. 461, 361–365. doi: 10.1016/j.bbrc.2015.04.039.

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantity were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA) and RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, USA) according to the manufacturer’s instructions.

treatment_protocol: See the growth protocol for the description of treatments.

value: leaf blade

value: Laiwu variety

value: P oligandrum VOC-exposed


title: Patient21 meningioma

description: meningioma


title: patient progressed to TKIs, nC_P9_1

value: blood


title: Patient23 meningioma

description: meningioma

value: No


title: patient progressed to TKIs, nC_P8_2


title: patient progressed to TKIs, nC_P8_1


title: NFO120-A: NFO120-A_WT#2_CLIP-IgG

description: Single-end 1 x 150bp

value: Brain

value: CLIP-Seq


title: Patient19 meningioma

description: meningioma

value: FEMALE

value: III


title: Patient18 meningioma

description: meningioma

value: Yes


title: Patient20 meningioma

description: meningioma

value: I


title: Mbd2-/-_3_targeted_bis_seq

value: Mbd2-/- with C57BL/6 background


title: Mbd2-/-_2_targeted_bis_seq


title: Mbd2-/-_1_targeted_bis_seq


title: WT_5_targeted_bis_seq


title: leaf blade, VOC exposed, rep1

description: matrix column name: GAQ1_VOCS_R1


title: leaf blade, non-VOC exposed, rep3

description: matrix column name: Control_R3

value: not VOC-exposed


title: leaf blade, VOC exposed, rep2

description: matrix column name: GAQ1_VOCS_R2


title: leaf blade, non-VOC exposed, rep2

description: matrix column name: Control_R2


title: Patient17 meningioma

description: meningioma


title: WT_3_targeted_bis_seq


title: Patient16 meningioma

description: meningioma


title: WT_4_targeted_bis_seq


title: Patient15 meningioma

description: meningioma


title: Patient14 meningioma

description: meningioma


title: WT_2_targeted_bis_seq


title: patient progressed to TKIs, nC_P7_1

value: NSCLC

value: not provided

value: UNK


title: patient progressed to TKIs, nC_P6_1

value: female


title: patient progressed to TKIs, nC_P6_2


title: leaf blade, non-VOC exposed, rep1

description: matrix column name: Control_R1

value: leaf blade


title: HFF WT CGH-SNP before editing

city: Bordeaux

first: Julian

last: Boutin

address: 146 rue Leo Saignat

institute: INSERM U1312 BRIC

hyb_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on NextSeq550 (Illumina).

scan_protocol: Genomic DNA extracted cultured cells was genotyped using Infinium HumanCytoSNP850K v1.2 BeadChips (Illumina). The Beadchips were scanned on NextSeq 550 (Illumina) according to manufacturer's recommandations. Genotype: AA,AB,BB,or NC (no call)

data_processing:
Data were analysed using BlueFuseMulti v4.5 (Illumina) and the Illumina CytoSNP-850K_v1.2
Genome Studio 2.0 software computed normalized signal intensities

label: Streptavidin-green,DNP-red

label_protocol: 250ng of genomic DNA was amplified in an overnight reaction at 37°C. After incubation, the amplified DNA was fragmented with digestion mix(FMS) for 1H at 37°C, precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1). All steps were performed according to manufacturer's recommendations (Illumina). RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Illumina, France).

extract_protocol: Extraction of genomic DNA from fresh cultured cells was performed using Macherey-Nagel DNA extraction and purification kit.

tag: cell type

value: HFF


title: patient progressed to TKIs, nC_P5_1

tag: age


title: WT_1_targeted_bis_seq


title: patient progressed to TKIs, nC_P3_1

tag: disease state


title: patient progressed to TKIs, nC_P2_1

tag: gender


title: patient progressed to TKIs, nC_P1_1


title: Patient13 meningioma

description: meningioma

tag: Sex

value: MALE

value: Unknown


title: HFF ABRAXAS2 transfected CGH-SNP Fluorescent positive cell sorting


title: steE_inf_bulk

status: Public on Jun 21 2023

city: Rehovot

first: Noa

last: Bossel Ben-Moshe

address: Hertzl Street

institute: Weizmann

data_processing:
Library strategy: scPAIR-seq
Fastq reads were demultiplexed to samples based on the CEL-Seq barcode located in positions 7-12 of R1.
R2 reads were filtered to contain the GFP sequence preceding the MIB (positions 1-37 of R2; GFP sequence: TGGGATTACACATGGCATGGATGAACTATACAAATAA, for ∆sseJ the sequence is TGGGATCACACATGGCATGGATGAACTATACAAATAA due to mutation in the plasmid during cloning). To account for sequencing errors, 1 mismatch was allowed for the GFP sequence identification.
The sequence of 10 nucleotides following the GFP (positions 38-47 of R2) is the bacterial barcode, i.e., the MIB sequence. In each sample, we counted the number of reads that correspond to each bacterial barcode allowing 1 mismatch in the MIB sequence
Using this procedure, we generated a matrix with the counts of each mutant (MIB) in each sample
Supplementary files format and content: Text files include MIB counts per sample

organism: synthetic construct

source_name: infected BMDMs

growth_protocol: BMDMs (8x[10^5] cells/well) were plated in non-tissue culture treated six–well plates supplemented with DMEM containing 20% FBS and 25 ng/ml rmM-CSF

extract_protocol:
Cells were harvested 4 hours post infection by a PBS wash followed by incubation of 10 min with ice-cold EDTA (5mM) and analyzed by flow cytometry (BD FACS Aria III) under continuous cooling at 4°C. Infected cells were sorted into 1.7ml low–bind tubes containing 25μl of lysis buffer (0.1% Triton in RNase-free water), placed immediately on dry ice and stored in minus 80.
scPAIR-seq relies on the CEL-seq library preparation protocol (Hashimshony et al., 2016) up to in-vitro transcription (IVT) step. After IVT, amplified RNA (aRNA) was treated with EXO-SAP enzyme (15 min at 37°C) to remove unused primers leftovers. aRNA sample was split and half of the sample volume (11 µl) was used to perform nucleic acid purification with RNAClean XP beads. The purified aRNA was converted to cDNA using superscript Ⅲ with specific GFP primer and cDNA was purified with AMPure XP beads. MIB library was amplified by 25 PCR cycles using a nested GFP primer to improve specificity of MIB amplification. To ensure exclusive sequencing of MIB reads by a custom GFP primer in the downstream steps, the nested GFP-primer was attached with a 5′-tail containing Illumina 3′-adaptor that was modified in its binding site for the Illumina sequencing primer

treatment_protocol: LB-grown cultures of WT or each of 24 MIB-tagged SPI-2 mutant strains were opsonized with 20% mouse serum for 30 min and washed with PBS. BMDMs were infected with each of SPI-2 mutants separately at MOIs of 5:1 and spun down for 5 min at 400g to synchronize internalization. After 30 min, cells were washed with media containing 50 μg/ml gentamicin to remove S.Tm that were not internalized. Fresh media containing 50 μg/ml gentamicin was then added back to the cells for the duration of infection

tag: infected with

value: ∆steE


title: steC_inf_bulk

value: ∆steC


title: HFF ABRAXAS2 transfected CGH-SNP bulk


title: control_inf_bulk

value: control


title: steB_inf_bulk

value: ∆steB


title: sseL_inf_bulk

value: ∆sseL


title: sseJ_inf_bulk

value: ∆sseJ


title: sspH2_inf_bulk


title: steA_inf_bulk

value: ∆steA


title: sseK1_inf_bulk


title: sseI_inf_bulk

value: ∆sseI


title: ssaV_inf_bulk

value: ∆ssaV


title: srfJ_inf_bulk

value: ∆srfJ


title: sseF_inf_bulk

value: ∆sseF


title: slrP_inf_bulk

value: ∆slrP


title: spvB_inf_bulk

value: ∆spvB


title: sseG_inf_bulk

value: ∆sseG


title: sopD2_inf_bulk


title: pipB_inf_bulk

value: ∆pipB


title: spvD_inf_bulk

value: ∆spvD


title: pipB2_inf_bulk


title: sifB_inf_bulk

value: ∆sifB


title: gtgA_inf_bulk

value: ∆gtgA


title: gogB_inf_bulk

value: ∆gogB


title: WT_inf_bulk

value: WT