title: tumor, IgG2b, control, id 146

status: Public on Feb 29 2024

type: SRA

city: Bethesda

first: Teresa

last: Przytycka

state: MD

address: 8600 Rockville Pike

department: NLM

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
Bcl2fastq v2.17 was used for sample demultiplexing
Adapters from the samples were trimmed using Trimmomatic
Genome mapping and transcript annotation were using STAR v2.5.1 with mouse reference genome mm10
The gene expression quantification analysis was performed for all samples using RSEM 1.2.22
Assembly: mm10 with Gencode vM9 GTF
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample
Supplementary files format and content: comma-delimited csv file includes RPKM values for each Sample

molecule: polyA RNA

organism: Mus musculus

growth_protocol: B2905 cells are cultured in RPMI medium with 10% FBS and supplement of glutamine at 2mM.

extract_protocol:
TruSeq Stranded Total RNA Kit RS-122-2201 from Illumina following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Kit RS-122-2201 from Illumina following manufacturer's protocols.

treatment_protocol: The antibodies (see experimental design) were given to mice at the dose 10mg/kg.

tag: cell line

tag: treatment


title: tumor, anti-CTLA-4, non-responder, id 143


title: tumor, IgG2b, control, id 152


title: tumor, anti-CTLA-4, non-responder, id 150


title: tumor, IgG2b, control, id 145


title: tumor, IgG2b, control, id 166


title: tumor, anti-CTLA-4, non-responder, id 139


title: tumor, anti-CTLA-4, non-responder, id 138


title: tumor, IgG2b, control, id 168


title: tumor, anti-CTLA-4, non-responder, id 172


title: tumor, anti-CTLA-4, stable, id 173


title: tumor, anti-CTLA-4, stable, id 167


title: tumor, anti-CTLA-4, responder, id 169


title: tumor, anti-CTLA-4, responder, id 163


title: tumor, anti-CTLA-4, responder, id 165


title: tumor, anti-CTLA-4, stable, id 137


title: TDC_3

city: Medellín

first: Sara

last: Zuluaga

department: Antioquia

country: Colombia

institute: Universidad de Antioquia

data_processing:
Trimmage trimmomatic-0.39.jar
Trinity --seqType fq
Alignment-free abundance estimation methods SALMON
Assembly: de novo
Supplementary files format and content: MATRIX  file included raw counts for each sample

molecule: total RNA

organism: Triatoma dimidiata

source_name: whole insect

growth_protocol: The insects were obtained when they were three days old, ensuring their color and weight were homogeneous, and stored at -80°C until processing

extract_protocol:
RNA extraction was performed using the Quick-RNA Miniprep kit (Zymo Research, USA), and DNA traces were removed by adding DNase I, following the manufacturer's instructions.
The library preparation was performed using the TruSeq Stranded LT Sample Preparation Kit (Illumina, USA), following the manufacturer's instructions.

tag: tissue

value: whole insect

tag: population

value: Field

tag: time

value: Day 3


title: tumor, anti-CTLA-4, responder, id 161


title: TDC_2


title: tumor, anti-CTLA-4, responder, id 160


title: tumor, anti-CTLA-4, responder, id 142


title: tumor, anti-CTLA-4, stable, id 158


title: TDP_3

value: Lambda-cyhalothrin pressure population


title: tumor, anti-CTLA-4, responder, id 140


title: tumor, anti-CTLA-4, non-responder, id 162


title: TDL_3

value: Laboratory- Control


title: TDP_2


title: tumor, anti-CTLA-4, responder, id 149


title: TDC_1


title: tumor, anti-CTLA-4, stable, id 155


title: tumor, anti-CTLA-4, stable, id 136


title: TDL_1


title: TDL_2


title: SK-LMS-1_sEV

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

data_processing:
The CLC Genomics Workbench version 9.5.3 program (Qiagen GmbH) was used for adaptor trimming and mapping to the miRbase 21 database, which allowed up to two mismatches.
Assembly: miRbase 21 database
Supplementary files format and content: a txt file includes raw read count of each sample

organism: Homo sapiens

source_name: small EV

growth_protocol: SKN and SK-LMS-1 were purchased from the Japanese Collection of Research Bioresources Cell Bank (Tokyo, Japan) and the American Type Culture Collection (Manassas, VA, USA), respectively. The cells were maintained in RPMI 1640 (Nacalai tesque, Kyoto, Japan) containing 10% fetal bovine serum (FBS) and penicillin-streptomycin (Wako, Osaka, Japan) at 37℃ with 5% CO2. For EV extraction, the cells were washed twice with D-PBS (Nacalai tesque), and the culture medium was replaced with advanced RPMI 1640 medium (Thermo Fisher Scientific, Waltham, MA, USA). After incubation for 48 h, the conditioned medium was then used for EV isolation.

extract_protocol:
Total RNA was extracted from EVs and cultured cells using QIAzol Lysis Reagent and the miRNeasy Mini Kit (QIAGEN, Hilden, Germany). RNA concentration was measured using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific).
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s instructions. The small RNA libraries (cDNAs) were purified using a QIAquick PCR Purification Kit (Qiagen) and separated by gel electrophoresis (6% TBE gel, 120 V, 60 min). DNA fragments corresponding to 140–160 bp (the length of small noncoding RNA plus the 3′ and 5′ adaptors) were recovered and the cDNA concentration was measured using the Qubit dsDNA HS Assay Kit with a Qubit 4 Fluorometer (Thermo Fisher Scientific).

treatment_protocol: The conditioned medium was centrifuged at 500 g for 15 min at 4℃ to thoroughly remove cellular debris. To isolate medium/large EVs, the supernatant was centrifuged at 10,000 g for 40 min at 4℃ in a refrigerated high-speed ultracentrifuge (Model 7000, KUBOTA CO., Tokyo, Japan). The pellets containing medium/large EVs were washed with D-PBS, centrifuged at 10,000 g for 40 min at 4℃, and resuspended in PBS. To isolate small EVs, the supernatant from the previous centrifugation was filtered through a 0.22 μm filter and centrifuged at 32,000 rpm using a SW32Ti rotor (Beckman Coulter, Inc., CA, USA) for 2 h at 4℃. The pellets containing small EVs were washed with PBS, centrifuged at 32,000 rpm using a SW32Ti rotor for 2 h at 4℃, and resuspended in PBS.

value: small EV

tag: cell type


title: SK-LMS-1_cell

source_name: cell

value: cell


title: SK-LMS-1_mlEV

source_name: medium/large EV

value: medium/large EV


title: SKN_sEV

value: SKN


title: SKN_mlEV


title: SKN_cell


title: TDP_1


title: 48.HPr1AR.miR96.2

city: WEST HOLLYWOOD

first: Moray

last: Campbell

state: CA

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center

data_processing:
Differentially enriched miR-96 binding sites were identified with csaw and annotated to genes (ChIPpeakAnno), and only those retained that directly overlapped with a transcript. Shared binding with other features (e.g. m6A) was determined with a minimum of 1bp in common between peaks.
Assembly: hg38
Supplementary files format and content: bed
Library strategy: IMPACT-Seq

source_name: prostate

growth_protocol: LNCaP were obtained from the ATCC and maintained in RPMI-1640 media supplemented with 10% FBS and penicillin/ streptomycin. Non-malignant HPr1AR cells were maintained in keratinocyte serum free medium supplemented with penicillin/streptomycin/gentamicin.

extract_protocol:
RNA was then extracted from washed beads using Trizol LS and treated with T4 Polynucleotide Kinase to obtain 5’ phosphate ends for subsequent ligations and passed through NucAway columns to remove RNAs <20 nt in length.
Small RNA libraries were generated using NEBNext Multiplex Small RNA Library Prep following the manufacturer’s recommendations for 100ng input material. PCR-amplified small RNA libraries were size selected to 130-200 bp fragments.
Libraries characterized on an Agilent Tape Station on a DNA1000 High-Sensitivity Screen Tape and quantified by Qubit were pooled and sequenced at 75 bp read length on the MiSeq platform

treatment_protocol: 5x106 cells transfected with 3' biotinylated miRIDIAN miR-96 mimic or scramble control (50 nM, 24h and 48h) using Lipofectamine 2000.

value: prostate

value: non-malignant prostate

tag: genotype

value: WT

value: biotin miR-96  (50nM, 48h)


title: 48.HPr1AR.miR96.1


title: 48.HPr1AR.Ct.2

value: biotin scramble control (50nM, 48h)


title: Gold-seedCoat_endosperm_rep_3 [GC3]

city: Saskatoon

first: Ioanni

last: Mavraganis

address: 110 Gymnasium Place

country: Canada

institute: National Research Council

data_processing:
Raw data was mapped end-to-end to the reference genome using STAR version 2.7.10, using default parameters
Read counts was performed using the STAR quantMode GeneCounts
Assembly: lentil genome version v2
Supplementary files format and content: Tab-delimited text files include raw counts

organism: Lens culinaris

source_name: Seed Coat – Endosperm

extract_protocol:
Total RNA was extracted using the Rneasy plant mini kit (Qiagen, Germany)
RNA libraries for RNAseq were constructed using a TruSeq RNA Sample Preparation kit v2

value: Seed Coat – Endosperm

value: CDC Gold


title: Redmoon-seedCoat_endosperm_rep_3 [RC3]

value: CDC Redmoon


title: Redmoon-Embryo_rep_2 [RE2]

source_name: Embryo

value: Embryo


title: Redmoon-seedCoat_endosperm_rep_2 [RC2]


title: Redmoon-Embryo_rep_3 [RE3]


title: Gold-seedCoat_endosperm_rep_1 [GC1]


title: Redmoon-seedCoat_endosperm_rep_1 [RC1]


title: Gold-seedCoat_endosperm_rep_2 [GC2]


title: 48.HPr1AR.Ct.3


title: 48.LNCaP.miR96.1

value: LNCaP

value: prostate cancer


title: 48.HPr1AR.Ct.1


title: Gold-Embryo_rep 3 [GE3]


title: 48.LNCaP.miR96.3


title: Gold-Embryo_rep 1 [GE1]


title: 48.LNCaP.miR96.2


title: 48.LNCaP.Ct.1


title: 48.LNCaP.Ct.2


title: Eleven-seedCoat_endosperm_rep_2 [EC2]


title: 48.LNCaP.Ct.3


title: Eleven-seedCoat_endosperm_rep_3 [EC3]


title: Eleven-seedCoat_endosperm_rep_1 [EC1]


title: 24.HPr1AR.miR96.1

value: biotin miR-96  (50nM, 24h)


title: 48.HPr1AR.miR96.3


title: 24.HPr1AR.miR96.2


title: Eleven-Embryo_rep 3 [EE3]


title: Redmoon-Embryo_rep_1 [RE1]


title: Eleven-Embryo_rep 2 [EE2]


title: 24.HPr1AR.Ct.3

value: biotin scramble control (50nM, 24h)


title: 24.HPr1AR.Ct.2


title: Gold-Embryo_rep 2 [GE2]


title: 24.LNCaP.miR96.2


title: Eleven-Embryo_rep 1 [EE1]


title: 24.LNCaP.Ct.1


title: 24.LNCaP.Ct.2


title: 24.LNCaP.Ct.3


title: hamster,S2_infection, 25mg/kg Ganetespib at 72hd.p.i., rep3

city: Berlin

first: Luiz Gustavo

last: Teixeira Alves

address: Hannoversche Strasse 28

country: Germany

institute: MDC Berlin

data_processing:
Reads were aligned to the human reference genome hg38 (GRCh38) and the hamster genome (MesAur1.0) using hisat2.
Gene expression was quantified using the package featureCounts from Rsubread and analyzed by DESeq2.
Differentially expressed genes were defined by an absolute fold change in mRNA abundance greater than 1.5 (log2 fold change of 0.58 - using DESeq2 shrunken log2 fold changes) and an adjusted p-value of less than 0.05 (Benjamini-Hochberg corrected)
Assembly: hg38 and MesAur1.0
Supplementary files format and content: tab-delimited text files including raw values or normalized values for each Sample

organism: Mesocricetus auratus

source_name: blood

extract_protocol:
RNA isolation was performed using Trizol reagent according to the manufacturer’s instructions and RNA extracted with
Libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs)

value: blood

value: whole blood

value: 25mg/kg Ganetespib at 72hd.p.i.


title: hamster,S2_infection, 25mg/kg Ganetespib at 72hd.p.i., rep2


title: hamster,S2_infection, Mock-treatment at 72hd.p.i., rep2

value: DMSO


title: hamster,S2_infection, 25mg/kg Ganetespib at 72hd.p.i., rep4


title: hamster,S2_infection, 25mg/kg Ganetespib at 48hd.p.i., rep4

value: 25mg/kg Ganetespib at 48hd.p.i.


title: hamster,S2_infection, Mock-treatment at 72hd.p.i., rep1


title: hamster,S2_infection, 25mg/kg Ganetespib at 72hd.p.i., rep1


title: hamster,S2_infection, 25mg/kg Ganetespib at 48hd.p.i., rep3


title: hamster,S2_infection, 25mg/kg Ganetespib at 48hd.p.i., rep2


title: 24.HPr1AR.miR96.3

value: prostate

value: non-malignant prostate


title: 24.HPr1AR.Ct.1

value: WT


title: 24.LNCaP.miR96.1


title: AT, 21

city: Huddinge

first: Likun

last: Du

address: Halsovagen 7C, Floor 7, NEO, group PHA

department: BioNut

country: Sweden

institute: Karolinska Institutet

description: Library name: LD102

library_source: genomic

data_processing:
LAM-HTGTS pipeline from Hu. et al Nat. Protoc, 2016.
Assembly: hg19
Supplementary files format and content: xls file containing location of breakpoints.
Library strategy: LAM-HTGTS

molecule: genomic DNA

source_name: PBMCs

extract_protocol:
Genomic DNA were extracted by using Qiagen Dneasy blood and tissue kits.
CSR fragment were linear amplified and adaptor ligated in 3' end. Illumina sequencing primer were added by PCR, and libraries were extracted after gel purification.
Illumina Miseq 300

value: PBMCs

tag: condition

value: AT patient

value: no


title: AT, 24a

description: Library name: LD103


title: 24.LNCaP.miR96.3


title: Control, 237

description: Library name: LD107

value: control


title: AT, 62

description: Library name: LD96


title: AT, 55a

description: Library name: LD100


title: AT, 10

description: Library name: LD92


title: AT, 06

description: Library name: LD95


title: Control. 042

description: Library name: LD104


title: hamster,S2_infection, 25mg/kg Ganetespib at 48hd.p.i., rep1


title: Control, 013

description: Library name: LD99


title: patient_4_normal

type: RNA

city: Guilin

first: Erlin

last: Song

address: No. 15 Lequn Road, Xiufeng District, Guilin, China

country: China

institute: Affiliated Hospital of Guilin Medical University

hyb_protocol: Array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

scan_protocol: The array were scanned immediately after washing and fixing with the Agilent Microarray Scanner (Agilent p/n G2565BA) and data were exacted using Agilent Feature Extraction Software(V11.0.1.1)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies)

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY鈩?Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/渭g cRNA) were measured by NanoDrop ND-1000.

extract_protocol: TRIzol reagents (Invitrogen) was used to extracted total RNA from the tumor and normal tissue of 5 patient_matched samples. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: kidney


title: patient_5_normal


title: P23-1

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

data_processing:
Sequencing reads were mapped using STAR against the human genome reference (hg19), and gene level quantification was performed with featureCounts. Total counts mapped to protein-coding genes were used for downstream analysis.
Assembly: hg19
Supplementary files format and content: Comma-separated values (CSV) file with featureCounts for protein-coding genes

source_name: Plasma extracellular vesicles

growth_protocol: Not applicable

extract_protocol:
RNA was isolated using Invitrogen total exosome RNA & Protein Isolation kit according to the manufacturer protocol
SMART-Seq® v4 Ultra® low input RNA kit followed by Illumina Nextera XT DNA Library Preparation

treatment_protocol: Not applicable

value: Plasma extracellular vesicles

tag: disease stage

value: Metastatic colorectal cancer

tag: disease status

value: At the time of surgery (hepatectomy)


title: P25-1


title: P24-1


title: P22-1

description: other label: P47-1


title: Mouse vessels, Cldn5 iECKO, rep3

city: Stockholm

first: Michael

last: Vanlandewijck

address: Blickagången 6

department: Department of Medicine

institute: Karolinska Institute

description: Dual index

library_source: transcriptomic single cell

data_processing:
Demultiplexing with Cellranger mkfastq
Alignment with Cellranger count
Loading of the samples into the R Seurat package
Seurat object with min.cells=3 and min.features=500
subset cells with nFeature_RNA > 500 and percent.mt < 10
FindVariableFeatures(bind, selection.method = "vst", nfeatures = 2000)
FindNeighbors(cells, dims = 1:30)
FindClusters(cells, resolution = 0.8)
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz contains the UMI barcodes used
Supplementary files format and content: features.tsv.gz contains the gene names included in the matrix assembly
Supplementary files format and content: matrix.mtx.gz contyains the gene expression data of every sample

source_name: Brain microvessels

extract_protocol:
The brain tissue was mechanically and enzymatically digested with Collagenase type II (1 mg/ml, cat. #C6885, Sigma). On ice, the washed microvascular fragments (MVFs) were isolated using sheep anti-rat magnetic Dynabeads® (50 µl/brain, cat. #11035, Invitrogen) bound to rat anti-mouse PECAM1 antibody (10 µl/brain, cat. #553370, BD Biosciences) and a DynaMag 2 magnet (Invitrogen). The washed MVFs were then further dissociated with Collagenase IV (1 mg/ml, cat. #17104-019, Gibco) and TrypLE (cat. #A1217701, Gibco) to remove the magnetic beads and obtain single cell solutions.
Libraries were constructed as per manufacurers' recommendation (10x Genomics Gene expression v3.1)

treatment_protocol: In all analyzed mice, Cldn5 deletion was achieved through oral gavage of 100 µl of a 20 mg/ml Tamoxifen (cat. #T5648, Sigma-Aldrich) solution in 90% peanut oil (cat. #C8267, Sigma-Aldrich) and 10% ethanol for 3 consecutive days at around 3 months of age.

value: Brain microvessels

value: C57Bl6 Cdh5-creERT2+, Cldn5 fl/fl, R26 YFP/YFP

value: Gavage with Tamoxifen


title: Control, 291

description: Library name: LD106


title: patient_4_tumor


title: patient_5_tumor


title: Mouse vessels, Control, rep3

description: Dual index

value: C57Bl6 Cldn5 fl/fl, R26 YFP/YFP


title: P20-1


title: patient_2_normal


title: Mouse vessels, Cldn5 iECKO, rep2

description: Dual index


title: patient_2_tumor


title: P19-1


title: patient_1_normal


title: P18-1

description: other label: P67-1


title: patient_1_tumor


title: Mouse vessels, Control, rep2

description: Dual index


title: patient_3_tumor


title: P17-1


title: Mouse vessels, Cldn5 iECKO, rep1

description: Dual index


title: Mouse vessels, Control, rep1

description: Dual index


title: P16-1


title: patient_3_normal


title: P21-1


title: Ctrl_2, Muscle biopsy, Control Patient

city: San Sebastian

first: Lorea

last: Blazquez

address: Dr Begiristain

country: Spain

institute: Biogipuzkoa Health Research Institute

description: Column in NORM_COUNTS-SNUPN_MUSCLES.tab: CTR_MUS_b

data_processing:
Raw reads obtained from RNA-sequencing experiments were filtered to remove adaptor sequences, contamination and low-quality reads
For quantification of gene expression, RNA-seq reads were mapped with Salmon (v0.14.1)
In order to quantify the expression of snRNA genes, RNA-seq reads were mapped to the GRCh38 transcriptome using STAR (v2.7.7a), allowing for multi-mapping (--outFilterMultimapNmax 100). Expression was quantified with featureCounts (v2.0.1), allowing multi-mappers with the -M and -F command-line flags. Differential gene expression analysis was then carried out using DESeq2 (v1.40.2), after normalisation with the VST method.
Alternative splicing analysis was performed using vast-tools (v2.5.1). FASTQ reads were aligned with vast-tools align using human VASTDB library (vastdb.hs2.23.06.20). Differentially regulated events were identified using vast-tools compare.
Assembly: GRCh38
Supplementary files format and content: tab delimited file with TPMs

source_name: Muscle biopsy

extract_protocol:
Rneasy Mini Kit
Ribo-Zero Plus rRNA depletion kit
single end, 100nt

value: Muscle biopsy

tag: tissue source

value: vastus lateralis

tag: age


title: Ctrl_3, Muscle biopsy, Control Patient

description: Column in NORM_COUNTS-SNUPN_MUSCLES.tab: CTR_MUS_c

value: semitendinosus


title: P13-1

description: other label: P57-1


title: FI.II.2, Muscle biopsy, Affected Patient

description: Column in NORM_COUNTS-SNUPN_MUSCLES.tab: MUS_b

value: SNUPN c.926T>G Hom


title: P14-1


title: Ctrl_1, Muscle biopsy, Control Patient

description: Column in NORM_COUNTS-SNUPN_MUSCLES.tab: CTR_MUS_a

value: WT


title: P12-1


title: FI.II.1, Muscle biopsy, Affected Patient

description: Column in NORM_COUNTS-SNUPN_MUSCLES.tab: MUS_a


title: P10-1


title: PC3shTIMP1_Veh2

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

country: Switzerland

institute: Institute of oncology research

data_processing:
The tool FastQC (https:// www.bioinformatics.babraham.ac.uk/projects/fastqc/) was run to assess the global quality of sequencing reads. Sequences were aligned to the human genome (GRCh38) by exploiting STAR (v.2.7.10a).
Transcript quantification was performed at the gene level by taking advantage of the comprehensive annotations from Gencode. More precisely, we exploited the v39 release of the Gene Transfer File (GTF).
We processed the raw counts with R software to perform differential expression analysis by running the DESeq2 package. Genes characterized by zero expression were removed and features with low mean normalized counts were sorted out by Independent Filtering strategy present in DESeq2 (alpha = 0.05).
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file with raw counts for each samples

growth_protocol: PC3 shTIMP1 cells were kept in culture in RPMI + 1% Pen/Strep + 10% FBS medium.

extract_protocol: RNAs were prepared using RNeasy Mini Kit (Qiagen, 74106), and DNA contaminations were removed with RNase-Free DNase (Qiagen, 79254). NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs Inc.) was used with the NEBNext Multiplex Oligos for Illumina (New England BioLabs Inc.) and NEBNext® Poly(A) mRNA Magnetic Isolation Module for cDNA synthesis; barcode sequences were also included. The sequencing of the prepools was carried out by exploiting the NextSeq2000 (Illumina, San Diego, CA, USA) with the P2 reagents kit V3 (100 cycles; Illumina). Samples were processed starting from stranded, single-ended 120bp-long sequencing reads with the P2 reagents kit V3 (100 cycles; Illumina). Samples were processed starting from stranded, single-ended 120bp-long sequencing reads

treatment_protocol: PC3 shTIMP1 cells were treated with vehicle, Docetaxel (1 nM), Adapalene (5 μM) or the combination of Docetaxel and Adapalene for 48 hours

value: epithelial prostate cancer cells

value: Vehicle


title: PC3shTIMP1_Doce4

value: Docetaxel


title: PC3shTIMP1_Doce3


title: PC3shTIMP1_Veh1


title: P8-1


title: P7-1


title: PC3shTIMP1_Doce1


title: P6-1


title: P5-1


title: PC3shTIMP1_Doce2


title: PC3shTIMP1_Combo3

value: Combo


title: P4-1


title: P15-1


title: PC3shTIMP1_Combo2


title: P3-1


title: PC3shTIMP1_Combo1


title: PC3shTIMP1_Adapalene3

value: Adapalene


title: P11-1

value: Plasma extracellular vesicles


title: P2-1

description: other label: P77-1

value: Metastatic colorectal cancer


title: PC3shTIMP1_Adapalene2


title: PC3shTIMP1_Veh3


title: P1-1

value: At the time of surgery (hepatectomy)


title: P9-1


title: PC3shTIMP1_Adapalene1


title: LATS-IN-1+BAY1125976_1

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

institute: Kyoto University

data_processing:
TPM
Assembly: hg38
Supplementary files format and content: CSV files incude count values and TPM for each sample.

growth_protocol: FACS-isolated iPSC-derived GFP-positive AT2 cells (P1) were seeded onto Matrigel-coated 96-well plates at the cell densities of 1x10^4 cells/well for "On-Gel" culture. Cells were cultured in DCIK+3i medium: Ham's F12 (Fujifilm Wako, 087-08335) containing 50 nM dexamethasone, 100 μM 8-Br-cAMP, 100 μM 3-isobutyl-1-methylxanthine, 10 ng/mL KGF, 1% B-27 supplement, 0.25% BSA (Thermo Fisher Scientific, 15260-037), 15 mM HEPES (Thermo Fisher Scientific, 17557-94), 0.8 mM CaCl2, 0.1% ITS premix (Corning) and 50 U/mL Penicillin/Streptomycin plus 3i (3 μM CHIR99021, 10 μM SB431542 and 10 μM Y27632).

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen).
The sequence library was prepared with Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina), and the quality of the library was checked with High Sensitivity D500 kit and 4200 TapeStation (Agilent).

treatment_protocol: "On-Gel" alveolar epithelial spheroids were cultured in DCIK+3i medium for the first 3 days, and Y-27632 was withdrawn from day 3. Then, the spheroids were cultured in DCIK medium from day 6 to 12, and treated with each compound at 10 µM for the last 3 days.

value: iPSC-derived AT2 cells

value: SFTPC:GFP, AGER:mCherry dual reporter

value: co-treatment with 10 uM LATS-IN-1 and 10 uM BAY1125976


title: BAY1125976_3


title: LATS-IN-1+BAY1125976_2


title: LATS-IN-1+BAY1125976_3


title: BAY1125976_2


title: LATS-IN-1_3

value: 10 uM LATS-IN-1


title: LATS-IN-1_2


title: LATS-IN-1_1


title: BAY1125976_1


title: DMSO_3

value: DMSO


title: DMSO_2


title: DMSO_1


title: On-Gel_3

growth_protocol: FD-AOs were cultured in DCIK medium: Ham's F12 (Fujifilm Wako, 087-08335) containing 50 nM dexamethasone, 100 μM 8-Br-cAMP, 100 μM 3-isobutyl-1-methylxanthine, 10 ng/mL KGF, 1% B-27 supplement, 0.25% BSA (Thermo Fisher Scientific, 15260-037), 15 mM HEPES (Thermo Fisher Scientific, 17557-94), 0.8 mM CaCl2, 0.1% ITS premix (Corning), and 50 U/mL Penicillin/Streptomycin for 14 days. FF-AOs and "On-Gel" spheroids were cultured in DCIK+3i (3 μM CHIR99021, 10 μM SB431542 and 10 μM Y27632) medium for 12 days.

extract_protocol:
Total RNA was extracted using RNeasy mini kit or micro kit (Qiagen).
The sequence library was prepared with Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina), and the quality of the library was checked with High Sensitivity D500 kit and 4200 TapeStation (Agilent).

value: Cells in On-Gel culture


title: hamster,S2_infection, Mock-treatment at 72hd.p.i., rep3

value: blood

value: whole blood


title: On-Gel_1


title: On-Gel_2


title: FF-AO_3

value: Cells of FF-AO


title: FF-AO_2


title: FF-AO_1


title: FD-AO_EpCAM+_3

value: EpCAM-positive cells of FD-AO


title: FD-AO_EpCAM+_2


title: CPMhigh_LungProgenitor_3

value: iPSC-derived CPMhigh cells


title: Airway_BA.1_4 [SARS-CoV-2]

data_processing:
Illumina RTA version 3.9.25 and bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by Cutadapt v4.1. The trimmed reads were mapped to the human reference genome sequences (hg38) and SARS-CoV-2/Hu/DP/Kng/19-027 RNA complete genome (LC528233.1) with the GENCODE (Release 32 (GRCh38.p13)) gtf file using STAR v2.7.10a.
The raw counts for the genes was calculated using htseq-count v2.0.2 with the GENCODE gtf file and annotation data based on LC528233.1.
Assembly: hg38, LC528233.1
Supplementary files format and content: RawCounts_for_GEO_upload.txt: Matrix table with raw counts for every gene and every sample.

growth_protocol: The MACS-isolated iPSC-derived lung progenitor cells (LPs) were seeded in the 24-well micro-patterned plates for "2.5-dimensional culture" (Tosoh Co., Ltd.) with multiple round-shaped cell-attachment areas in 100 diameter pre-coated with 0.5 ug/cm2 of iMatrix-511 silk (TaKaRa bio, 892021) at the cell densities ranging from 1 or 3 x10^5 cells/well. The LPs were differentiated into alveolar epithelial cells in DCIK+3i medium or airway epithelial cells in PAL medium.

extract_protocol:
Each total RNA sample was isolated from human iPSC-derived airway and alveolar cells in the micro-patterned culture plates using ISOGENE (NIPPON GENE).
The library preparation was performed using a TruSeq Stranded mRNA Sample Prep Kit (Illumina), according to the manufacturer’s instructions.

treatment_protocol: The iPSC-derived pulmonary epithelial cells were infected with SARS-CoV-2 (0.1 MOI) in the micro-pattern culture plate.

value: Micro-patterned airway epithelial cells

value: SARS-CoV-2 BA.1 variant


title: CPMhigh_LungProgenitor_2


title: CPMhigh_LungProgenitor_1


title: FD-AO_EpCAM+_1


title: Airway_BA.1_3 [SARS-CoV-2]


title: Airway_BA.1_1 [SARS-CoV-2]


title: Airway_B.1.617.2_2 [SARS-CoV-2]

description: Micro-patterned alveolar epithelial cells infected with delta variant.

value: SARS-CoV-2 B.1.617.2 variant


title: Airway_BA.1_2 [SARS-CoV-2]


title: Airway_B.1.617.2_4 [SARS-CoV-2]


title: Airway_mock_4 [SARS-CoV-2]

value: Mock


title: Airway_B.1.617.2_1 [SARS-CoV-2]


title: Airway_mock_3 [SARS-CoV-2]


title: Alveolar_BA.1_3 [SARS-CoV-2]

value: Micro-patterned alveolar epithelial cells


title: Airway_mock_1 [SARS-CoV-2]


title: Airway_mock_2 [SARS-CoV-2]


title: Alveolar_BA.1_1 [SARS-CoV-2]


title: Alveolar_BA.1_4 [SARS-CoV-2]


title: Alveolar_B.1.617.2_3 [SARS-CoV-2]


title: Alveolar_B.1.617.2_2 [SARS-CoV-2]


title: Airway_B.1.617.2_3 [SARS-CoV-2]


title: Alveolar_mock_4 [SARS-CoV-2]


title: Alveolar_mock_3 [SARS-CoV-2]


title: Alveolar_mock_2 [SARS-CoV-2]


title: Alveolar_B.1.617.2_4 [SARS-CoV-2]


title: Alveolar_mock_1 [SARS-CoV-2]


title: Pt15 - Day 28 - Arm C

city: Cambridge

first: Ce

last: Gao

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

data_processing:
FASTQ files were obtained by Illumina bcl2fastq2.
STAR and RSEM were used to align to GRCh38 and to calculate the raw counts for genes, respectively.
Assembly: GRCh38
Supplementary files format and content: raw counts and TPM in csv

source_name: PBMC

extract_protocol:
Total RNA was extracted from the isolated CD4T cells using a commercial PicoPure RNA Isolation Kit
RNA-Seq libraries were generated as described in a previous study. Briefly, whole transcriptome amplification (WTA) and tagmentation-based library preparation was performed using SMART-seq2, followed by sequencing with a 100-cycle kit on a NextSeq 2000 instrument (Illumina, CA). The quantification of transcript abundance was conducted using RSEM software (v1.2.22) supported by the STAR aligner software (STAR_2.4.2a). The raw reads were aligned to the Hg38 human genome database.

value: PBMC

value: CD4 T cells

value: Day 28

tag: participant id

tag: group

value: Arm C

tag: participant treatment


title: Pt17 - Day 28 - Arm C


title: Pt10 - Day 28 - Arm B

value: Arm B

value: panobinostat + IFN-α2A


title: Pt06 - Day 28 - Arm B


title: Pt01 - Day 28 - Arm A

value: Arm A

value: panobinostat


title: Alveolar_B.1.617.2_1 [SARS-CoV-2]


title: Pt03 - Day 28 - Arm A


title: Pt08 - Day 28 - Arm B


title: Pt12 - Day 28 - Arm B


title: Pt17 - Day 4 - Arm C

value: Day 4


title: Alveolar_BA.1_2 [SARS-CoV-2]


title: Pt15 - Day 4 - Arm C


title: Pt06 - Day 4 - Arm B


title: Pt12 - Day 4 - Arm B


title: Pt08 - Day 4 - Arm B


title: Pt01 - Day 4 - Arm A


title: Pt15 - Day 0 - Arm C

value: Day 0


title: Pt10 - Day 4 - Arm B


title: Pt03 - Day 4 - Arm A


title: Pt06 - Day 0 - Arm B


title: hamster,S2_infection, Mock-treatment at 72hd.p.i., rep4

value: blood

value: whole blood

value: DMSO


title: Pt17 - Day 0 - Arm C


title: Pt08 - Day 0 - Arm B


title: Pt12 - Day 0 - Arm B


title: Pt10 - Day 0 - Arm B


title: Pt03 - Day 0 - Arm A


title: Pt01 - Day 0 - Arm A


title: Pt14 - Day 28 - Arm C


title: Pt16 - Day 28 - Arm C


title: Pt05 - Day 28 - Arm B


title: Pt09 - Day 28 - Arm B


title: Pt11 - Day 28 - Arm B


title: Pt04 - Day 28 - Arm A


title: Pt13 - Day 28 - Arm B


title: Pt02 - Day 28 - Arm A


title: Pt14 - Day 4 - Arm C


title: Pt16 - Day 4 - Arm C


title: Pt05 - Day 4 - Arm B


title: Pt07 - Day 4 - Arm B


title: Pt09 - Day 4 - Arm B


title: Pt11 - Day 4 - Arm B


title: Pt02 - Day 4 - Arm A


title: Pt14 - Day 0 - Arm C


title: Pt13 - Day 4 - Arm B


title: Pt04 - Day 4 - Arm A


title: Pt16 - Day 0 - Arm C


title: Pt05 - Day 0 - Arm B


title: Pt07 - Day 0 - Arm B


title: Pt09 - Day 0 - Arm B


title: Pt13 - Day 0 - Arm B


title: Pt11 - Day 0 - Arm B


title: Pt02 - Day 0 - Arm A


title: Pt04 - Day 0 - Arm A


title: Pt07 - Day 28 - Arm B


title: PRS Regen 1

city: MAYWOOD

first: SEBY

last: EDASSERY

state: IL

address: CTRE121,2160 S FIRST AVE

institute: Loyola University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through Novogene in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content for the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome (Genome assembly: PapAnu2.0 (GCA_000264685.1)) and gene model annotation files were downloaded from the genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus, and featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Greater than 70 million mapped reads at a total mapping rate > 93% from each sample were obtained. We obtained gene expression quantitation for 12,008 genes from all samples after removing genes with any missing values.
Assembly: PapAnu2.0
Supplementary files format and content: tab delimited text file contain the read count for each sample

organism: Papio anubis

source_name: Urinary bladder

extract_protocol:
Native urinary bladder tissue and cell-seeded or bowel-augmented grafts (~50mg each for each animal) were submitted to Novogene (Novogene Corporation Inc) for total RNA extraction, quality control (QC), library preparation, sequencing, and quantitation as per the in-house standard protocol for gene expression analysis. Briefly, RNA degradation and contamination were assessed on 1% agarose gels and RNA purity was determined by NanoPhotometer® spectrophotometer (IMPLEN, CA). RNA integrity and quantitation was performed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA).  Library preparation and sequencing were only carried forward if the sample passed the QC step and as per the Novogene in-house protocol as follows (44, 45). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. Clustering and sequencing: (Novogene Experimental Department) The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: Urinary bladder

value: Primary bone marrow cells

value: MSC/CD34+ HSPC

value: WT

value: MSC/CD34+ HSPC graft


title: PRS Native 2


title: PRS Regen 2


title: PRS Regen 3


title: PRS Native 3


title: PRS Native 4


title: PRS Regen 4


title: SIS Regen 5


title: SIS Regen 1


title: SIS Regen 3


title: SIS Regen 2


title: SIS Native 4


title: SIS Native 3


title: SIS Native 2


title: SIS Native 1


title: Entero Ileum 5

value: Ileum graft


title: Entero Ileum 4


title: Entero Ileum 3


title: Entero Ileum 2


title: Entero Ileum 1


title: HA_TCF1_4

city: Philadelphia

first: Katherine

middle: Paige

last: Mueller

state: Pennsylvania

address: 3501 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

data_processing:
Reads were trimmed for quality and adapter sequences using fastQC.
Trimmed reads were aligned to the mm10 reference genome using bowtie2.
Aligned reads were deduplicated using Picard.
Peakswere called using MACS2 from the paired endbed file (bedpe) using a false discovery thresh-old of 0.05 (-q 0.05).
Normalized bigwig files were created by normalizing the coverage track of the bedpe file by reads in peaks.
Assembly: hg38
Supplementary files format and content: Normalized bigwig files.

source_name: HA CD8 CAR-T

growth_protocol: Primary human T cells were grown in AIM-V media supplemented with 5% FBS, 10mM HEPES, 1x Penicillin-Streptomycin-Glutamate, and 100U/mL recombinant human IL-2. T cells were activated with anti-CD3/CD28 beads immediately after thawing from liquid nitrogen, then at 48 and 72 hours post-activation were transduced with retroviruses containing CARs and transcription factors of interest. 96 hours post-activation, beads were removed; subsequently, T cells were resuspended at a concentration of 0.5e6 cells/mL every 2-3 days in the above described media. For experiments requiring magnetic sorting, isolations were performed using Miltenyi MACS or StemCell EasySep magnetic sorting systems. 150,000 T cells were slow-frozen in BamBanker cell preservation media prior to ATAC-seq specific preparation.

extract_protocol:
Nuclei were isolated with ChIP lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0).
DNA was quantified by Qubit and 10 ng DNA was used for sequencing library construction with the Ovation Ultralow Library System V2 (Tecan) using 12 PCR cycles.

treatment_protocol: All cells in this sample were treated the same, the only difference between the cells is which virus they were transduced with (CAR, transcription factor)

value: HA CD8 CAR-T


title: HA_TCF1_1


title: PRS Native 1


title: HA_FOXO1-WT_4


title: HA_NGFR_4


title: HA_TCF1_3


title: HA_NGFR_2


title: SIS Regen 4


title: Entero Native 4


title: SIS Native 5


title: HA_FOXO1-WT_1


title: CD19_TCF1_1


title: CD19_TCF1_3


title: CD19_TCF1_4


title: Entero Native 5


title: Entero Native 3


title: HA_FOXO1-WT_2


title: CD19_NGFR_3


title: CD19_NGFR_4


title: Entero Native 1


title: Neutrophils, RS-6

city: ALBANY

first: Bibhuti

middle: B

last: Mishra

state: NEW YORK

address: 49 New Scotland Ave

department: Immunology and Microbial Disease

institute: Albany Medical College

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. T
The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fall within exon regions were counted.
Assembly: GRCm39
Supplementary files format and content: Normalized abundance measurements. Output obtained from DESeq2 analysis of gene expression between the indicated groups of samples
Supplementary files format and content: Text document of hit counts

organism: Mus

source_name: Spleen

extract_protocol:
8-10 wks old C57BL/6 (IL1R1+/+) and IL1R1-/- mice were infected with low dose aerosol of Mycobacterium tuberculosis strain HN878. Four weeks post infection, neutrophils were  isolated  by magnetic cell sorting and total RNA was extracted using the RNAeasy mini plus kit (Qiagen, USA) according to the manufacturer’s instructions. RNA quality was ensured by Agilent bioanalyzer and RNA samples with a RIN value>8.0 was used for library preparation and sequencing.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: Spleen

value: Neutrophils

tag: infection

value: Mycobacterium tuberculosis HN878


title: HA_NGFR_1


title: Neutrophils, RS-3


title: Neutrophils, RS-5


title: CD19_NGFR_1


title: CD19_FOXO1-WT_1


title: Neutrophils, RL-6

source_name: Lung

value: Lung


title: CD19_FOXO1-WT_2


title: Neutrophils, RL-3


title: Neutrophils, RL-5


title: Entero Native 2


title: Neutrophils, RBM-6

source_name: Bone Marrow

value: Bone Marrow


title: Neutrophils, RL-2


title: HA_OE_NGFR_Donor_8

data_processing:
Fastq files were aligned to a mm10 transcriptome index with STAR
The abundance of transcripts was quantified using Salmon
Transcript-level abundance estimates were imported and summarized using tximport v1.16.1
Differential expression was determined using the DESeq2 package v1.28.11 in Bioconductor v.3.11.
Assembly: hg38
Supplementary files format and content: Raw and normalized counts(.csv).

growth_protocol: Primary human T cells were grown in AIM-V media supplemented with 5% FBS, 10mM HEPES, 1x Penicillin-Streptomycin-Glutamate, and 100U/mL recombinant human IL-2. T cells were activated with anti-CD3/CD28 beads immediately after thawing from liquid nitrogen. Then, at 48 and 72 hours post-activation were transduced with retroviruses containing CARs and transcription factors of interest. 96 hours post-activation, beads were removed; subsequently, T cells were resuspended at a concentration of 0.5e6 cells/mL every 2-3 days in the above described media. For experiments requiring magnetic sorting, isolations were performed using Miltenyi MACS or StemCell EasySep magnetic sorting systems. 5e5-1e6 TCs were pelleted and flash frozen prior to RNA seq prep

extract_protocol:
Total RNA was isolated with Trizol, followed by precipitation with isopropanol. RNA was washed with 75% Ethanol and pellet was dried and dissolved in nulcease-free water.
Approximately 20ng total RNA was used for library preparation with Ovation Ultralow RNA-seq V2 (Tecan) from two biological replicates. Libraries were generated according to the manufacturer’s instructions. Approximately 50ng amplified cDNA was subjected to Ovation Ultralow V2 library generation and manufacturer’s instructions were followed. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 6000 instrument.


title: Neutrophils, RBM-3


title: HA_OE_NGFR_Donor_7


title: Neutrophils, RBM-2


title: Neutrophils, BS-6

tag: strain


title: HA_OE_DBDmut_Donor_8


title: Neutrophils, BS-4


title: HA_OE_FOXO1_Donor_8


title: HA_OE_DBDmut_Donor_5


title: CD19.28Z_FOXO1_OE_TCF7_KO_Donor_ND578

growth_protocol: Primary human T cells were grown in AIM-V media supplemented with 5% FBS, 10mM HEPES, 1x Penicillin-Streptomycin-Glutamate, and 100U/mL recombinant human IL-2. T cells were activated with anti-CD3/CD28 beads immediately after thawing from liquid nitrogen. 48hrs post-activation, CRISPR-Cas9-based knockout was performed on the cells using a Lonza electroporation kit and electroporator. Then, at 48 and 72 hours post-activation were transduced with retroviruses containing CARs and transcription factors of interest. 96 hours post-activation, beads were removed; subsequently, T cells were resuspended at a concentration of 0.5e6 cells/mL every 2-3 days in the above described media. Since FOXO1 KO cells uniformly exhibited low CD62L surface expression, we used CD62L as a surrogate marker for FOXO1 editing and applied magnetic bead negative selection to enrich for CD62Llo/FOXO1KO cells using a StemCell EasySep magnetic sorting kit. 5e5-1e6 TCs were pelleted and flash frozen prior to RNA seq prep.

extract_protocol:
Pellets were thawed on ice and processed using either a RNEasy Plus Mini Kit or an AllPrep DNA/RNA Micro Kit (for simultaneous DNA and RNA isolation) (Qiagen) according to the manufacturer’s instructions. Total RNA was quantified using either a Qubit Fluorometer or a DeNovix DS-11 FX Spectrophotometer/Fluorometer
Sequencing was outsourced to Novogene - US. Libraries were prepared by the vendor and sequenced on a NovoSeq 6000 instrument.

treatment_protocol: Cells were treated the same, the only difference being which sgRNA was used for CRISPR knockout (sgAAVS1 vs. sgTCF7)


title: Neutrophils, BM-4


title: Neutrophils, BS-3


title: Neutrophils, BS-2


title: CD19.28Z_NGFR_OE_TCF7_KO_Donor_ND578


title: CD19.28Z_NGFR_OE_AAVS1_KO_Donor_ND578


title: HA_OE_DBDmut_Donor_7


title: CD19_FOXO1-WT_3


title: HA_OE_NGFR_Donor_5


title: Neutrophils, RS-2


title: CD19.28Z_FOXO1_OE_AAVS1_KO_Donor_ND578


title: Neutrophils, BM-2


title: Neutrophils, BM-3


title: CD19.28Z_NGFR_OE_TCF7_KO_Donor_TMP503


title: Neutrophils, BL-6


title: Neutrophils, BL-4


title: HA_OE_FOXO1_Donor_5


title: Neutrophils, RBM-5


title: CD19.28Z_FOXO1_OE_TCF7_KO_Donor_TMP503


title: HA_OE_FOXO1_Donor_7


title: CD19.28Z_NGFR_OE_AAVS1_KO_Donor_TMP503


title: Neutrophils, BL-3


title: CD19.28Z_FOXO1_OE_AAVS1_KO_Donor_TMP503


title: Neutrophils, BM-6


title: Neutrophils, BL-2


title: CD19.28Z_NGFR_OE_TCF7_KO_Donor_TMP502


title: CD19.28Z_FOXO1_OE_TCF7_KO_Donor_TMP502


title: CD19.28Z_NGFR_OE_AAVS1_KO_Donor_TMP502


title: CD19.28Z_FOXO1_OE_AAVS1_KO_Donor_TMP502


title: TCF1-HA_Rep3

data_processing:
Fastq files were aligned to a mm10 transcriptome index with STAR
The abundance of transcripts was quantified using Salmon
Transcript-level abundance estimates were imported and summarized using tximport v1.16.1
Differential expression was determined using the DESeq2 package v1.28.11 in Bioconductor v.3.11.
Assembly: hg38
Supplementary files format and content: Raw and normalized counts(.xls).

growth_protocol: Primary human T cells were grown in AIM-V media supplemented with 5% FBS, 10mM HEPES, 1x Penicillin-Streptomycin-Glutamate, and 100U/mL recombinant human IL-2. T cells were activated with anti-CD3/CD28 beads immediately after thawing from liquid nitrogen. 48hrs post-activation, CRISPR-Cas9-based knockout was performed on the cells using a Lonza electroporation kit and electroporator. Then, at 48 and 72 hours post-activation were transduced with retroviruses containing CARs and transcription factors of interest. 96 hours post-activation, beads were removed; subsequently, T cells were resuspended at a concentration of 0.5e6 cells/mL every 2-3 days in the above described media. For experiments requiring magnetic sorting, isolations were performed using Miltenyi MACS or StemCell EasySep magnetic sorting systems. 5e5-1e6 TCs were pelleted and flash frozen prior to RNA seq prep

treatment_protocol: Cells were treated the same, the only difference being which viruses they were transduced with (CAR/transcription factor)


title: TCF1-HA_Rep2


title: NGFR-HA_Rep3


title: NGFR-HA_Rep2


title: NGFR-HA_Rep1


title: FOXO1WT-HA_Rep3


title: FOXO1WT-HA_Rep2


title: FOXO1WT-HA_Rep1


title: TCF1-CD19_Rep2

source_name: CD19 CD8 CAR-T

value: CD19 CD8 CAR-T


title: TCF1-CD19_Rep3


title: TCF1-CD19_Rep1


title: NGFR-CD19_Rep3


title: NGFR-CD19_Rep2


title: NGFR-CD19_Rep1


title: FOXO1WT-CD19_Rep2


title: FOXO1WT-CD19_Rep1


title: FOXO1WT-CD19_Rep3


title: HA_NGFR_5

treatment_protocol: All cells in this sample were treated the same, the only difference between the cells is which virus they were transduced with (thus which version of FOXO1 they were transduced with).


title: HA_DBO_5


title: HA_NGFR_6


title: HA_FOXO1-WT_6


title: TCF1-HA_Rep1


title: HA_NGFR_7


title: HA_DBO_7


title: HA_FOXO1-WT_7


title: HA_DBO_6


title: CD19_FOXO1KO_Donor_ND612

description: FOXO1 KO CD19.BBz CAR T cells were isolated on day 15 post activation. Since FOXO1 KO cells uniformly exhibited low CD62L surface expression, we used CD62L as a surrogate marker for FOXO1 editing and applied magnetic bead negative selection to enrich for CD62Llo/FOXO1KO cells using a StemCell EasySep magnetic sorting kit. 5e5-1e6 TCs were pelleted and flash frozen prior to RNA seq prep.

source_name: Primary human T cells

treatment_protocol: Cells were treated the same, the only difference being which sgRNA was used for CRISPR knockout (sgAAVS1 vs. sgFOXO1)

value: Primary human T cells

value: FOXO1 KO


title: CD19_FOXO1KO_Donor_ND607


title: CD19_FOXO1KO_Donor_ND500


title: CD19_AAVS1_Donor_ND607

description: FOXO1 WT (AAVS1 KO) CD19.BBz CAR T cells were isolated on day 15 post activation. 5e5-1e6 TCs were pelleted and flash frozen prior to RNA seq prep.

value: FOXO1 WT


title: HA_TCF1_55

source_name: HA.28z CD4 CAR T cells

value: HA.28z CD4 CAR T cells


title: CD19_AAVS1_Donor_ND500


title: HA_NGFR_56

value: NGFR


title: HA_NGFR_55


title: HA_NGFR_46


title: HA_FOXO1-WT_46


title: HA_FOXO1-WT_56


title: HA_FOXO1-WT_55


title: HA_FOXO1-WT_5


title: CD19_AAVS1_Donor_ND612


title: HA_TCF1_56


title: HA_TCF1_46


title: kaku4-2

city: Beijing

first: Zhen

last: Su

address: #2 Yuanmingyuan Xilu

department: College of Biological Sciences

institute: China Agricultural University

data_processing:
All clean ChIP-seq reads were mapped to the Arabidopsis genome TAIR10 using BOWTIE2 software with default parameters. The MACS program was used to shift the reads to identify peaks.
RNA-seq data with 3 biological replicates were generated. The paired-end clean reads of RNA-seq were aligned to the reference genome (TAIR10) by TopHat2 v2.0.9 software. FPKM values were calculated using Cufflinks.
Supplementary files format and content: bw
Supplementary files format and content: FPKM

organism: Arabidopsis thaliana

source_name: 30-day-old leaves

extract_protocol:
Total RNA was isolated using TRIZOL® reagent (Invitrogen, CA, USA) and purified using Qiagen RNeasy columns (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Sequencing libraries were constructed by the Beijing Genomics Institute and sequenced using an IlluminaHiSeq™ 2000 with 150-bp pair-end reads.

value: 30-day-old leaves


title: Endo2

first: James

last: Garifallou

address: 3615 Civic Center Boulevard, ARC1014

department: Neonatology

data_processing:
Sequencing data was demultiplexed into separate per library fastq files using the mkfastq command of the cell ranger 6.0.0 pipeline (10x Genomics)
Reads in fastq files were aligned to the GRCh38 transcriptome and creation of feature barcode matrices using cell ranger 6.0.0 (10x Genomics)
Secondary analysis of the feature barcode matrices was performed using the Seurat package (Hao, 2021) within the R statistical computing environment. Cells were filtered for quality, normalized, scaled and clustered in an ubiased manner to generate a UMAP plot.
Assembly: GRCh38
Supplementary files format and content: filtered cell barcode by gene matrices

source_name: Mid-secretory (implantation window) endometrium

extract_protocol:
Endometrial and decidual tissues were grossly dissected and washed in PBS, then finely minced before being digested in a shaking 37°C water bath for 15-30 mins in sterile medium containing 0.28WU/mL Liberase TM (Roche, Catalog  # 05401127001) and 30ug/mL DNase (Roche, catalog # 10104159001)]. A large-bore transfer pipet was used to pipet tissue up and down during digestion to break down tissue. Digested tissue was pelleted, subjected to RBC lysis, and then filtered through a 70μm filter. For the fresh/unfrozen tissue, cells were immediately processed within 2 hours for flow sorting. Frozen samples were similarly processed within 2 hours, and frozen in cryotubes at a concentration of 1x107/mL in 1mL of freezing medium, consisting of 90% RPMI (ThermoFisher, Catalog # 11875085), 10% DMSO (Sigma, Catalog # D2650-100mL), and 1mg/mL BSA (Sigma, A9418)]. Samples were frozen in a Mr.Frosty freezing container for 24 hours before being placed in a -120℃ freezer for up to 6 months. Immediately prior to flow sorting, cryovials were thawed for 30 seconds in a 37ºC water bath and immediately washed in PBS to remove DMSO.
Next-generation sequencing libraries were prepared using the 10× Genomics Chromium Single Cell 3’ Library and Gel Bead kit v3, per manufacturer’s “Chromium Single Cell Reagent Kits” protocol. Libraries were uniquely indexed using the Chromium i7 Sample Index Kit, pooled, and sequenced on the Illumina NovaSeq 6000 sequencer (v1.5 chemistry) in a paired-end, single indexing run. Sequencing targeted 20,000 mean reads per cell.

value: Sort-purified CD45+ cells from mid-secretory (implantation window) endometrium


title: Endo4

value: Mid-secretory (implantation window) endometrium


title: FT4

source_name: First-trimester decidua

value: First-trimester decidua

value: Sort-purified CD45+ cells from first-trimester elective termination decidua


title: Endo1


title: FT1


title: Endo3


title: LNCaP_C.m6.1

data_processing:
Differentially enriched m6A binding sites were identified with csaw and annotated to genes (ChIPpeakAnno), and only those retained that directly overlapped with a transcript. Shared binding with other features (e.g. miR-96 binding sites) was determined with a minimum of 1bp in common between peaks.
Assembly: hg38
Supplementary files format and content: bed

source_name: prostate

growth_protocol: LNCaP and 22Rv1 were obtained from the ATCC and maintained in RPMI-1640 media supplemented with 10% FBS and penicillin/ streptomycin. Non-malignant HPr1AR cells were maintained in keratinocyte serum free medium supplemented with penicillin/streptomycin/gentamicin.

extract_protocol:
m6A seq was performed on 2x107 cells using EpiMark N6-methyladenosine enrichment kit (New England Biolabs).
The libraries were prepared from purified DNA, using the NEB Ultra II Library Prep Kit (New England Biolabs) per manufacturer's instructions and the libraries were sequenced at 50 bp read length and were sequenced on an NovaSeq SP with a target of ~40M PE reads per sample.

treatment_protocol: Cells were grown to 70% confluence in biological triplicate samples

value: prostate

tag: cell line

value: LNCaP

value: prostate cancer

value: WT

tag: rip antibody

value: vehicle


title: LNCaP_C.m6.3

tag: tissue

tag: treatment


title: RV1_C.C.2

value: IgG


title: LNCaP_C.C.3


title: RV1_C.m6.3


title: LNCaP_C.m6.2


title: RV1_C.m6.1


title: LNCaP_C.C.2


title: kaku4-1


title: LNCaP_C.C.1


title: HPR_C.m6.3

value: non-malignant prostate


title: FT3


title: HPR_C.m6.2


title: WT-3

value: col


title: FT2


title: WT-2


title: kaku4-3


title: HPR_C.C.3


title: HPR_C.C.2


title: RV1_C.C.3


title: RV1_C.C.1


title: WT-1


title: HPR_C.C.1


title: Arabidopsis seedlings, control, 48hr, rep2

city: Tainan City

first: Hao-Jen

last: Huang

address: No. 1., University Road

country: Taiwan

institute: National Cheng Kung University

data_processing:
Reads were trimmed by Trimmomatic v3.6
Trimmed reads were mapped to Arabidopsis reference genome by tophat
Gene expression was calculated by cufflink
Assembly: Arabidopsis_thaliana.TAIR10.dna.toplevel.fa
Supplementary files format and content: tab-delimited text files include FPKM value for each sample

source_name: whole seedling

extract_protocol:
RNA was harvested using RNeasy Plant Mini kit (Qiagen)
RNA libraries were prepared in Illunima Hiseq platform following manufacturer's protocols

value: whole seedling


title: Arabidopsis seedlings, control, 48hr, rep1


title: A375 cells, shALKBH5 IP 3

city: Guangzhou

first: Julin

last: Xie

state: State...

address: Zhongshan 2nd Road, Yuexiu District, Guangzhou city, Guangdong Province, China

institute: First Affiliated Hospital of Sun Yat-sen University

description:
A375_shALKBH5VSA375_shCtrl_diffPeak_result.txt
A375_shALKBH5_IPVSA375_shALKBH5_input_peak.txt

data_processing:
Remove reads with adapters
Remove reads containing N (N represents base information that cannot be determined) with a proportion greater than 5%
Remove low-quality reads (alkaline bases with a mass value Q ≤ 10 account for more than 20% of the entire read)
Calculate the original sequencing quantity, effective sequencing quantity, Q20, Q30, GC content, and conduct a comprehensive evaluation
Assembly: mm10
Supplementary files format and content: text file includes FPKM value and m6A peaks for each sample
Supplementary files format and content: text file includes differential m6A peaks between samples

source_name: skin

growth_protocol: A375 melanoma cells were maintained in DMEM with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was extracted by TRIzol (Invitrogen, USA) following the manufacturer’s instructions.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
MeRIP-Seq/RNA-Seq

value: skin

value: melanoma cells

value: ALKBH5 knockdown


title: Arabidopsis seedlings, mVCs, 48hr, rep1


title: HPR_C.m6.1

city: WEST HOLLYWOOD

first: Moray

last: Campbell

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center


title: Arabidopsis seedlings, mVCs, 48hr, rep2


title: A375 cells, shALKBH5 IP 1

value: m6A-specific antibody (No. 202003, Synaptic Systems, Germany)


title: A375 cells, shALKBH5 IP 2


title: Arabidopsis seedlings, mVCs, 24hr, rep2


title: Arabidopsis seedlings, control, 24hr, rep2


title: Arabidopsis seedlings, mVCs, 24hr, rep1


title: A375 cells, shCtrl IP 3

description:
A375_shALKBH5VSA375_shCtrl_diffPeak_result.txt
A375_shCtrl_IPVSA375_shCtrl_input_peak.txt

value: wild type


title: iHLCS, Alcohol Cirrhotic AC1

city: Rockville

first: Bani

last: Mukhopadhyay

address: 5625 Fishers lane.Rockville.MD, 3S24-

department: LNG

institute: NIH,NIAAA

data_processing:
STAR software is used to accomplish the mapping. The alignment by STAR performs precise and effective in positioning junction reads for RNA sequencing data analysis
Assembly: Human genome build 38
Supplementary files format and content: Geosamplefpkm.xlsx

source_name: iHLCs

extract_protocol:
RNA was harvested from Zymo kit
Novogene service protocol

value: iHLCs

value: Hepatocyte like cells

tag: disease state

value: Alcohol Cirrhotic


title: iHLCs, Healthy 4

tag: cell type

value: Healthy


title: iHLCS, Alcohol Cirrhotic AC2


title: iHLCS, Alcohol Cirrhotic AC4


title: iHLCS, Alcohol Cirrhotic AC3


title: iHLCS, Alcohol Cirrhotic AC6


title: A375 cells, shCtrl IP 2

tag: genotype


title: Arabidopsis seedlings, control, 24hr, rep1


title: A375 cells, shCtrl IP 1


title: A375 cells, shALKBH5 input 3

description: A375_shALKBH5_inputVSA375_shCtrl_input_Gene_differential_expression.txt


title: iHLCS, Alcohol Cirrhotic AC5


title: iHLCs, Healthy 3


title: iHLCs, Healthy 2


title: Zhx5-6, liver, Y3KO+CCL4

city: Nanjing

first: Xiang

last: Zhong

state: Jiangsu

address: Tongwei Road

institute: Nanjing agricultural university

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

source_name: liver

extract_protocol:
Trial procedures were performed with minor modifications, as previously reported.10 Liver tissue samples, each weighing 200 mg, were immediately frozen in liquid nitrogen and physically disrupted in 1.5 mL of lysis buffer. The buffer composition included 1% NP-40, 200 mM KOAc, 25 mM HEPES-KOH pH 7.2, 10 mM MgCI2, and 4 mM CaCI2. Following a 5-min incubation of the liver tissue on ice in the lysis buffer, the lysate was centrifuged at 9000 rpm for 5 min at 4°C. The resulting supernatant was separated into two 200 μL aliquots to generate an input sample and a Ribo-bound sample.  The sample was then diluted with ddH2O at a 1:1 ratio, and MNase was added at a final concentration of 0.2 U/μL lysate, followed by a incubation at 37°C for 30 min. RNA extraction was carried out using Trizol. The RNA was resuspended in a 10 μL PNK solution (1 μL 10X buffer A, 1 μL PNK, 1 μL ATP, and RNA in 7 μL H2O), with a subsequent 30-min incubation at 37°C. A total of 10 μL of RNA loading dye was added to the mixture. Gel electrophoresis was performed at 180 V for 75 min. The gel was immersed in 25 mL 1X TBE with a 1:10000 SybrGold solution for 5 min, exposed under UV light, printed at actual size, and placed in a tube.  Subsequently, 400 μL of 400 mM NaOAc was added, and the gel slice was frozen at -80°C for 10 min and thawed at 95°C for 5 min. The gel slice was then thoroughly homogenized using a pestle or pipet tip and subjected to RNA extraction through three cycles of heating (95°C, 5 min, 20 min of shaking). The extracted gel slice was loaded onto a SpinX column, centrifuged for 10 min at maximum speed, treated with 1 mL ethanol and 1 μL Glycogen, and incubated for 1 h at -20°C. After centrifugation for 15 min at 4°C and washing with cold 80% ethanol, the pellet was dried for 10 min before being resuspended in 7 μL of water.
NEB Next Small RNA Library Prep Set for Illumina was employed for library construction.

value: liver


title: Arabidopsis seedlings, mVCs, 3hr, rep2


title: A375 cells, shALKBH5 input 2


title: iHLCs, Healthy 1


title: Zhx5-5, liver, Y3KO+CCL4


title: Arabidopsis seedlings, mVCs, 3hr, rep1


title: A375 cells, shALKBH5 input 1


title: Zhx5-4, liver, Y3KO+CCL4


title: A375 cells, shCtrl input 3


title: Arabidopsis seedlings, control, 3hr, rep2


title: A375 cells, shCtrl input 2


title: A375 cells, shCtrl input 1


title: Zhx5-3, liver, WT+CCL4


title: Arabidopsis seedlings, control, 3hr, rep1


title: Zhx5-2, liver, WT+CCL4


title: Input-control

city: Wuhan

first: Maoqing

last: Tian

address: 238 Jiefang Road, Wuchang District

institute: Renmin Hospital of Wuhan University

description: Input is the purified DNA from the input chromatin, and IP is the DNA enriched with antibodies

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output
Chl-seg reads were trimmed from 3' end untl the final base had a quality score > 30, using Trmmomatic v0.36, discarding reads left with < 20 bp
CHIP-seq reads were aligned to the UCSC hg38 foxk1 genome using Bwa (version 0.7.15). Only uniquely mapping reads with at most two mismatches  were retained.
Peaks were called uing MACS version 2.1.1.20160309 with the significance cut-off q-value <0.05
Assembly: hg38
Supplementary files format and content: bedGraph

growth_protocol: Cells were cultured in DMEM/F12 medium with 10% fetal bovine serum and 1% penicillin-streptomycin in a 37 °C incubator with 5% CO2

extract_protocol:
Cultured HK-2 cells underwent indicated treatment were fixed with 1% paraformaldehyde.
ChIP assays were performed with Pierce Magnetic ChIP kit (Thermo scientific, Cat. 26157) according to manufacturer’s protocol.  After the lysis and MNase digestion, chromatin was sonicated on ice with three 20-second pulses at 3 watts power (using Sonicator 3000 Instrument). Immunoprecipitation was performed overnight at 4 °C.

treatment_protocol: treatment with or without 10 ng/ml TGF-β1 for 24 hours.

tag: antibody

value: Proximal tubular epithelial cells

value: control


title: PAL_Day14

description: 10x Genomics

data_processing:
The 10X Genomics Cell Ranger pipeline (version 7.1.0) was used to perform sample demultiplexing, alignment to the hg38 human reference genome (refdata-gex-GRCh38-2020-A from 10X Genomics) and the reporter sequences, barcode/UMI processing, and gene counting for each cell.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: The MACS-isolated iPSC-derived lung progenitor cells(LPs) were seeded in the 24-well micro-patterned plates for "2.5-dimensional culture" (Tosoh Co., Ltd.) with multiple round shaped cell-attachment areas in 100 μm diameter pre-coated with 0.5 ug/cm2 of iMatrix-511 silk (TaKaRa bio, 892021) at the cell densities 1x10^5 or 3x10^5 cells/well. The LPs were differentiated into alveolar or airway epithelial cells in "DCIK+3i" or "PAL" medium for 7 or 14 days, respectively.

extract_protocol:
The cell suspension after CPM MACS sorting was used as "CPM_MACS_progenitor". The micro-patterned cultured cells were dissociated by 0.5 mM EDTA/PBS and Accutase treatment and subjected to scRNA-seq.
The collected cells were loaded into a 10X Genomics Chromium system. The scRNA-seq libraries were constructed using Single Cell 3' Reagent Kits (v.3.1, 10X Genomics).

value: Micro-patterned airway epithelial cells

tag: medium

value: PAL


title: Input-treat


title: Zhx5-1, liver, WT+CCL4

value: WT


title: IP-control


title: DCIK+3i_Day14

description: 10x Genomics

value: Micro-patterned alveolar epithelial cells


title: PAL_Day7

description: 10x Genomics


title: 99_site1_core1

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
All_Sample_Raw_Counts.csv
All_Samples_TMM_log2_CPM.csv

data_processing:
Fastq files have been trimmed of adapters using TrimGalore, then aligned to hg38 using STAR (v2.4.2a).
FASTQC has also been run on each of the samples. Genes with 0 counts across all samples were filtered out.
The gene-level counts from all studies were then normalized using TMM with edgeR. Log2 transformed TMM-normalized counts per million [log2 (TMM-CPM + 1)] were used for analysis.
Assembly: hg38
Supplementary files format and content: csv file includes raw counts of each sample
Supplementary files format and content: csv file includes TMM normalized log2 (CPM+1) value of each sample

source_name: Breast tumor tissue

extract_protocol:
Total RNA was isolated from 295 formalin-fixed paraffin-embedded (FFPE) tissue specimens; each sample consisted of seven 4µm sections scraped from individual slides. Paraffin wax was removed with two rounds of xylene extraction. Samples were incubated in lysis buffer containing proteinase-K, and RNA was purified using miRNeasy FFPE (QIAGEN) kits following the manufacturer’s recommended procedure. RNA purity and concentration were measured by UV absorbance. RNA integrity (fragment size) was assessed using a 2100 Bioanalyzer (Agilent Technologies) and RNA 6000 Nano and 6000 Pico kits. DV200 values (% fragments > 200 bases) were calculated using the 2100 Bioanalyzer Expert Software (Agilent Technologies). DV200 values ranged from 7 to 66% with 221 samples having a value ≥ 30%.
Libraries were prepared using the Illumina RNA with Enrichment, Tagmentation protocol (Illumina) with the Illumina Exome Panel - Enrichment Oligos (Illumina). Libraries were profiled on a Bioanalyzer (Agilent) and quantified with an NGS Quantification Kit (Roche/Kapa Biosystems) using a StepOnePlus Real Time PCR Workstation (Thermo/ABI).

value: Breast tumor tissue

value: early-stage HER2-positive breast cancer

value: Pre-treatment

tag: patient id

tag: her2 heterogeneity

value: No

tag: pcr


title: 98_site2_core1

value: Yes


title: 99_site2_core1


title: 98_site1_core1


title: 97_site1_core2


title: 97_site2_core2


title: brain_14d_BYHWD_rep2

city: Changsha

first: Zhe

last: Yu

address: Kaifu District, Xiangya Road, No.87

institute: Central South University

data_processing:
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software
The trimmed reads were aligned to reference genome with bowtie software
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) )
Raw reads were normalized by calculated CPM value
Differential expression analysis of miRNAs between groups was performed using edgeR with settings of 1.5-fold difference, p-value < 0.05 and within-group CPM mean of 1 to screen for differentially expressed miRNAs.
Assembly: hg38
Supplementary files format and content: Microsoft excel file includes the counts per million (CPM) reads of miRNAs in all samples.
Supplementary files format and content: Differential expression analysis of miRNAs between groups was performed using edgeR. For differentially expressed miRNA were screened with the significant threshold to 1.5-fold difference, p-value ≤ 0.05 and the mean CPM within the group ≥ 1

source_name: brain

growth_protocol: Mice were housed in a well-ventilated room (four rats in one cage) at a constant room temperature (25 ± 1℃) and controlled humidity (50 ± 10%), with a 12 h light/dark cycle. All procedures involving the use and care of animals were performed in accordance with the guidelines of Central South University for the care and use of animals and were approved by the Medical Ethics Committee of Central South University (Animal ethical number: 2020sydw0929).

extract_protocol:
Total RNA was extracted from exosome pellet using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE). Small RNA libraries were constructed using New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencers and the NEB standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135   155 bp PCR amplified fragments (corresponding to 15   35 nt small RNAs).

treatment_protocol: Mice were randomly assigned to three groups: sham, ICH, and BYHWD. In the BYHWD group, BYHWD powder was dissolved in distilled water and administered to mice (6.19 g/kg) by oral gavage once per day for 14 days. The sham and ICH groups were gavaged with an equal dose of distilled water. The mice were sacrificed under 0.3% pentobarbital sodium (60 mg/kg, intraperitoneally) on the 14th day, and transcardially perfused with saline. Brains were harvested and the ipsilateral basal ganglia were isolated immediately.

value: brain

value: BYHWD-H

value: gavaged 6.19 g/kg BYHWD daily


title: 96_site2_core1


title: brain_14d_BYHWD_rep1


title: brain_14d_BYHWD_rep5


title: LNCaP_Mir96.3

data_processing:
Transcript abundance estimates were normalized and differentially expressed genes (DEGs) identified using a standard edgeR pipeline, and gene set enrichment analysis (GSEA) performed. For transcript-aware analyses, the FASTQ files were aligned with salmon(59) and differentially enriched transcripts were identified using DRIMSeq(60) in a similar workflow to edgeR.
Assembly: hg38
Supplementary files format and content: csv file includes CPM values for each Sample

extract_protocol:
Total RNA was extracted E.Z.N.A.® Total RNA Kit I, Omega Bio-tek®) and subjected to DNase treatment and purification by the RNA Clean & Concentrator kit (Zymo Research) to yield high-quality RNA for library preparation. RNA-seq libraries were prepared using Illumina’s TruSeq Stranded protocol. ~70 million paired-end 150 bp sequence reads were generated for each library on the HiSeq 4000 platform.
RNA-seq libraries were prepared using Illumina’s TruSeq Stranded protocol.

treatment_protocol: Cells were grown to 70% confluence in biological triplicate samples in the presence of miR-96 mimic/scramble (50nM) by transient transfection in HPr1-AR, LNCaP and 22Rv1 cells and RNA harvested at 48h.

value: prostate

value: LNCaP

value: prostate cancer

value: vehicle

tag: mimic


title: brain_14d_BYHWD_rep3

tag: group


title: 22RV1_Mir96.2


title: 22RV1_Mir96.1


title: 22RV1_Scr.2

value: Scr


title: 22RV1_Scr.3


title: 22RV1_Mir96.3


title: 22RV1_Scr.1


title: IP-treat

value: Proximal tubular epithelial cells


title: DCIK+3i_Day7

description: 10x Genomics


title: brain_14d_BYHWD_rep4


title: CPM_MACS_progenitor

description: 10x Genomics

value: iPSC-derived CPM+


title: brain_14d_ICH_rep1

value: ICH

value: WT

value: gavaged distilled water daily


title: LNCaP_Mir96.2


title: 95_site2_core2

value: Breast tumor tissue

value: early-stage HER2-positive breast cancer


title: 96_site1_core1

value: Pre-treatment

value: No


title: 94_site1_core2


title: LNCaP_Mir96.1


title: brain_14d_ICH_rep5

value: brain


title: 93_site2_core1


title: brain_14d_ICH_rep4


title: 92_site2_core1


title: 93_Residual_Disease


title: 93_site1_core1


title: LNCaP_Scr.3


title: brain_14d_ICH_rep3


title: brain_14d_ICH_rep2


title: LNCaP_Scr.2


title: 92_site1_core1


title: 91_Residual_Disease


title: 91_site1_core1


title: 90_Residual_Disease


title: brain_14d_sham_rep5

value: Sham


title: 90_site1_core1


title: 91_site2_core2


title: LNCaP_Scr.1


title: brain_14d_sham_rep4


title: HPr1-AR_Mir96.2

value: non-malignant prostate


title: 89_site1_core2

value: Yes


title: brain_14d_sham_rep3


title: 89_site2_core2


title: HPr1-AR_Mir96.1

value: prostate


title: 87_site2_core1


title: 87_site1_core2


title: HPr1-AR_Scr.3


title: brain_14d_sham_rep1


title: brain_14d_sham_rep2


title: 86_site2_core2


title: HPr1-AR_Scr.2


title: 86_site1_core1


title: 85_site1_core2


title: NCR_PD1_F_1_S14(PD1+)

city: Melbourne

first: Cyril

last: Seillet

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

description: ILC3 NCR- PD1+ #2

data_processing:
Alignment from raw FASTQ files
Genes with counts per million (CPM) larger than 0.5 in at least one group of samples were kept, and genes related to immunoglobulins (Igh, Igkv) were filtered out.
Differential gene expression was performed in R studio with Bioconductor package DESeq2 (version 1.34.0).
Regularized log transformation (base 2) was conducted in significantly differentially expressed genes (log2 fold change > 1 and adjusted p value < 0.1) for heatmap visualization.
Pathway-enrichment analysis with KEGG database (Kyoto Encyclopedia of Genes and Genomes) was perform on these significantly differentially expressed genes with Bioconductor package clusterProfiler (version 4.2.1).
Heatmap of differentially expressed genes and bar plot of pathway enrichment results were generated by R package pheatmap (version 1.0.12) and Bioconductor enrichplot (version 1.14.1), respectively.
Assembly: mm10
Supplementary files format and content: Tab-delimited csv file includes raw data for each sample

source_name: Small intestine

extract_protocol:
Small intestine and colon were digested and single cell suspension were stained with appropriate antibodies. Cells were FACS-sorted . Purified cells were centrifuge and store at -80. RNA was isolated using a QIAGEN RNeasy Micro kit.
Libraries were generated using the Clontech SMART-Seq v4 Ultra Low Input RNA Kit preparation, following the manufacturer’s instructions

value: Small intestine

tag: Sex

value: Female

tag: age

value: 6-8 week old

value: Rorc(gt)+/GFP


title: 84_site2_core1


title: NCR_PD1_F_2_S17(PD1+)

description: ILC3 NCR- PD1+ #1

tag: strain


title: 84_site1_core2


title: HPr1-AR_Scr.1

tag: cell line

value: vehicle

value: Scr


title: 83_site2_core1

value: WT


title: 83_site1_core2


title: 84_Residual_Disease


title: NCR_PD1_F_1_S15(PD1-)

description: ILC3 NCR- PD1- #2


title: HPr1-AR_Mir96.3


title: 81_site1_core1


title: NCR_PD1_F_2_S18(PD1-)

description: ILC3 NCR- PD1- #1


title: neurons, HIF1CKO_5

city: Vestec

first: Valéria

last: Fabríciová

address: Průmyslová 595

country: Czech Republic

institute: Institute of biotechnology CAS

description: Hif1CKO 5

data_processing:
RNA-Seq reads in FASTQ files were mapped to the mouse genome GRCm38 primary assembly release M8 using STAR [version 2.7.0c ]. Using cutadapt v1.18, the number of reads (minimum, 32 million; maximum, 73 million), Illumina sequencing adaptors were trimmed, subsequently reads shorter than 20 bp were filtered out using TrimmomaticPE version 0.36. Ribosomal RNA and reads mapping to UniVec database were filtered out using bowtie v1.2.2. (parameters -S -n 1) and SortMeRNA. A count table was generated by Rsubread v2.0.1 package using default parameters without counting multi mapping reads.
Assembly: mm10/GRCm38
Supplementary files format and content: tab-delimited text file with raw counts for each Sample

source_name: sympathetic neurons

extract_protocol:
Sympathetic ganglia dissected from E14.5 embryos Hif1aCKO-Ai14;Prph-eGFP (n = 3) and Control-Ai14;Prph-eGFP (n = 2). Sympathetic chains were homogenized and neuronal cells were dissociated using 0.1% collagenase (C9263, Sigma-Aldrich, UK) and 0.05% trypsin in Dulbecco’s PBS for 7 minutes (T4799, Sigma-Aldrich, UK). Enzymatic activity was stopped by adding FACS buffer (2% FBS in Dulbecco’s PBS and 10 mM EGTA). Fluorescence-activated cell sorting (FACS) of eGFP and tdTomato positive cells was performed on a BD FACS Aria Fusion flow cytometer operated with BD FACSDiva™ Software. 100 eGFP+ and tdTomato+ cells per each biological sample were collected into individual wells of 96-well plate containing 5 µl of lysis buffer of NEB Next single-cell low input RNA library prep kit for Illumina (New England Biolabs #E6420). Plates were frozen immediately on dry ice and stored at −80 °C. The total time from euthanasia to cell collection was ∼3 hrs.
The NEB Next single-cell low input RNA library prep kit for Illumina was used for library generation. The libraries were sequenced on an Illumina NextSeq 500 next-generation sequencer with NextSeq 500/550 High Output kit 75 cycles (Illumina #200024906).

treatment_protocol: We used experimental model of the conditional deletion of Hif1a (Hif1aCKO) the genotype Isl1tm1(cre)Sev/+;Hif1a loxP/loxP. Briefly, floxed Hif1atm3Rsjo with exon 2 of the Hif1a gene flanked by loxP sites on a mixed C57BL/6J; C57BL/6N genetic background were obtained from Jackson Laboratories (#Strain 007561). Isl1Cre/+ mice were on the FVB background. Hif1a loxP/+ or Hif1a loxP/loxP mice without the Isl1-Cre allele individuals were used as the Control. Breeding scheme: Female mice Hif1a loxP/loxP were crossed with Hif1a loxP/+; Isl1Cre/+ males, in which the Isl1-Cre knock-in allele was inherited paternally to minimize the potential influence of maternal genotype on the developing embryos. To visualize sympathetic neurons, we used tdTomatoAi14 reporter mice with Rosa-CAG-LSL-tdTomato allele (Ai14, B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze, Stock No: 7914 Jackson Laboratory) to generate the reporter Hif1aCKO-Ai14 (genotype: Hif1a loxP/loxP; Isl1Cre; tdTomatoAi14) and control-Ai14 mice (genotype: Hif1a loxP/+; Isl1Cre; TdtomatoAi14). To examine the formation of the secondary sympathetic chain, we used peripherin-EGFP (Prph-eGFP) genomic reporter transgenic mice and crossed them with the Hif1a mutant line.

value: sympathetic neurons


title: 82_site2_core2

value: Breast tumor tissue


title: 81_site2_core2

value: early-stage HER2-positive breast cancer


title: 82_site1_core1

value: Pre-treatment


title: STBI_Sample_7

city: Bethesda

first: Manish

last: Bhomia

address: 4301 Jones bRidge Road

department: Pathology

institute: Uniformed Services University of the Health Sciences

data_processing:
Cutadapt and perl scripts were used to control the quality of bases
Sequence quality was verified used FastQC
Bowtie and Tophat were used to map reads to the human genome, and the mapped reads were then assembled using StringTie
Mapped reads assembled using StringTie were merged to construct a comprehensive transcriptome  gffcompare and perl
StringTie and Ballgown were used to estimate the expression levels of the resulting transcripts
Assembly: homo sapien(Version: v90)
Supplementary files format and content: Complete RNA sequencing analysis files that includes information for each sample that includes raw read counts, reference mapping information, transcript expression and Quality control information for Fastq files and RNAseq analysis.
Supplementary files format and content: excel files include FPMK values for each sample

source_name: Blood

extract_protocol:
RNA was extracted uing Trizol reagent (Invitrogen) per the manufaturer's recommended protocol.
Cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with dUTP method.

value: Blood


title: STBI_Sample_6


title: STBI_Sample_5


title: STBI_Sample_8


title: 80_site1_core1

value: No


title: neurons, HIF1CKO_4

description: Hif1CKO 4


title: STBI_Sample_4


title: 80_site2_core2


title: 75_site1_core1


title: neurons, HIF1CKO_3

description: Hif1CKO 3


title: 80_Residual_Disease


title: STBI_Sample_3


title: 74_site2_core2


title: 74_site1_core2


title: neurons, control_6

description: Control 6

value: control


title: STBI_Sample_2


title: 74_Residual_Disease


title: neurons, control_5

description: Control 5


title: 73_site2_core2


title: STBI_Sample_1


title: 73_site1_core1


title: E18 LK PBS

city: New York

first: Melissa

last: Proven

institute: Columbia Unversity

data_processing:
The demulitplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v 7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: fetal liver

extract_protocol:
Cells were sorted into HBSS with 2% FBS and allowed to rest on ice for 1 hr prior to centrifugation. Cells were pelleted at 350 x g for 5 min at 4 degrees and resuspended in 0.04% BSA in PBS and pelleted again at 350 x g for 5 min at 4 degrees. Supernatant was removed, and the pelleted cells were lysed by adding 45 ul of chilled lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40 Substitute, 0.01% Digitonin, 1% BSA, 1 mM DTT, 1 U/ul RNase inhibitor) and pipetted gently 3 times before being incubated on ice for 3 minutes. Resulting nuclei were washed by adding 50 ul of chilled wash buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 1 mM DTT, 1 U/ul RNase inhibitor). Nuclei were pelleted at 500 x g for 10 min at 4 degrees and washed in diluted nuclei buffer (10X Genomics).
Multiome GEM generation and library preparation was performed according to 10X Genomics protocol CG000338, targeting 5000 cell data recovery.

value: fetal liver

value: pooled male and female

value: Linneg cKitpos

value: C57BL/6 wildtype

value: PBS


title: Control_Sample_8


title: 72_site2_core1

value: Yes


title: E18 LK LPS 16 hrs

value: 16 hrs LPS in vivo


title: 70_site1_core2


title: 72_site1_core2


title: Control_Sample_7


title: Control_Sample_6


title: 69_site2_core2


title: 69_Residual_Disease


title: 68_site2_core1


title: Adult LK PBS

value: 8-12 weeks


title: Control_Sample_5


title: 68_site1_core2


title: 69_site1_core2


title: Control_Sample_4


title: 68_Residual_Disease


title: 67_site1_core2


title: Uterus,SMAD5-KI,PA,rep2

city: Houston

first: Martin

middle: M

last: Matzuk

state: TX

address: One Baylor Plaza

department: Pathology and Immunolodgy

institute: Baylor College of Medicine

data_processing:
Basecalls were performed using bcl2fastq v2.20 for NextSeq500 output.
Raw sequencing reads were aligned to the mm10 reference genome using bowtie2/2.2.7 in paired-end mode with parameters --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
Raw sequencing reads for Spike-in were aligned to the  E. coli genome U00096.3 using bowtie2/2.2.7 in paired-end mode with parameters --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
Duplicated reads were removed, and only uniquely mapped reads were kept.
Spike-in normalization was achieved through multiply primary genome coverage by scale factor (100000 / fragments mapped to E. coli genome).Then normalized alignments were converted into fragments using bedtools bamtobed(v2.29.2)
bigWig files were generated using the bedGraphToBigWig tool. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
peaks were called by SECAR using IgG input as background and with the parameters of -norm -stringent -output
Assembly: MM10
Supplementary files format and content: bigwig
Supplementary files format and content: bed file for the peak

source_name: Uterus

extract_protocol:
Uteri were harvested from two pregnant mice at 4.5 days post coitus and washed with cold swelling buffer (10 mM Tris-HCl pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 1X Protease Inhibitor Cocktail (PIC, Roche, 11836170001)) immediately after collection. Then tissue was cut into small pieces (~2-3mm) using scissors, while submerged in cold swelling buffer. Nuclear extract was prepared by dounce homogenization in cold swelling buffer (using a size 7 dounce) and filtered using the cell strainer (100 μm, BD Biosciences). Lysate was centrifuged at 400 g for 10 min, then resuspended in lysis buffer (swelling buffer with 10% glycerol and 1% CA-630, 1X PIC) using an end-cut or wide-bore tips and incubated on ice for 5 min. Nuclei were washed twice with lysis buffer and resuspended in lysis buffer and incubated with activated concanavalin A beads for 10 min at room temperature. Bead-nuclei complexes were then resuspended in antibody buffer containing 0.01% digitonin, 1ug of each antibody was added to individual aliquots, and tubes were rotated at 4°C overnight. The following day, targeted chromatin digestion and release were performed with 2.5 ul of Cutana pA/G-MNase and 1 ul of 100 mM CaCl2. Genomic DNA with 0.5ng of Spike-in DNA together was purified with phenol-chloroform and ethanol precipitatation method.
Sequencing libraries were prepared using  NEBNext Ultra II DNA Library Prep Kit (NEB E7645) following manufacture's protocol.
CUT&RUN-Seq

value: Uterus

value: 4.5 dpc


title: Control_Sample_3


title: 66_site2_core1

value: WT


title: Uterus,SMAD1-KI,PR,rep2


title: 66_site1_core2

value: Breast tumor tissue


title: 65_site2_core2

value: early-stage HER2-positive breast cancer


title: Uterus,SMAD5-KI,IgG,rep2


title: Control_Sample_2


title: Uterus,SMAD1-KI,HA,rep2


title: 65_site1_core1

value: Pre-treatment


title: 63_site2_core2


title: 64_site1_core2


title: Uterus,SMAD5-KI,PA,rep1


title: 64_site2_core1


title: Uterus,SMAD1-KI,IgG,rep2


title: 63_Residual_Disease


title: Adult LK LPS 16 hrs


title: 62_site2_core2


title: 63_site1_core1


title: 67_site2_core1


title: 62_site1_core1


title: Library 16 cell hashing

city: Leuven

first: Bart

last: De Strooper

address: Herestraat 49 box 602

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

description:
10x Genomics
Mancuso2022_RNAcounts.mtx.gz
Mancuso2022_RNAcounts_genes.txt
Mancuso2022_RNAcounts_cellbarcodes.txt
Mancuso2022_NormExpr.mtx.gz
Mancuso2022_NormExpr_genes.txt
Mancuso2022_NormExpr_cellbarcodes.txt

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: Genome build: Human reference, hg19 (Ensembl 87), downloaded from 10x Genomics pre-built Cell Ranger reference packages (3.0.0).
Supplementary files format and content: *.mtx.gz: Raw or SCT normalised gene expression counts per cell in a gzipped tab-separated values file.
Supplementary files format and content: *genes.txt: row names (genes) for raw or SCT normalised gene expression matrices, in txt files.

source_name: Brain

extract_protocol:
Human microglia were freshly isolated from the mouse brain of AppNL-G-F, Apphu/hu or AppNL-G-FApoE-/-  mice. In brief, mice were anesthetized with an overdose of sodium pentobarbital and perfused with ice-cold 1x DPBS (+5U heparin). Freshly collected mouse brains were placed in ice-cold FACS buffer (1x DPBS + 2% FCS + 2 mM EDTA) + 5 μM Actinomycin D (ActD, Sigma, Cat#A1410-5MG). After removal of olfactory bulbs and cerebellum, tissue was dissociated using the Miltenyi neural tissue dissociation kit P (Miltenyi, Cat#130-092-628) by means of mechanical and enzymatic dissociation. Cell suspension was filtered and washed with FACS buffer + 5 μM Actinomycin D and spun at 300g for 5 minutes at 4o degrees. Of note, 5 μM Actinomycin D was kept during collection, dissociation and washing and was removed afterwards to avoid cellular toxicity. After washing, cell pellet was resuspended in 30% isotonic Percoll and centrifuged for 5 minutes at 300g to remove cell debris and myelin layers. Pelleted cells were incubated for 10 minutes with mouse FcR blockers (1:10 in FACS Buffer, Miltenyi, Cat#130- 092-575) on ice. After washing, cell pellet was stained with: PE-PanCD11b (1:50, Miltenyi, Cat#130-113-806), BV421-mCD45 (1:500, BD Biosciences, Cat#563890), APC-hCD45 (1:50, BD Biosciences, Cat#555485), TotalSeqTM-A cell hashing antibodies (1:500, Biolegend) and viability dye (eFluor 780, Thermo Fisher Scientific, Cat#65-0865-14) in cold FACS buffer during 30 minutes at 4°C. Cells were washed in ice-cold FACS buffer and resuspended and filtered on a 35 μm strainer with 500 ml of FACS buffer for sorting. Alive human microglia sorting was done on a MACSQuant Tyto Cartridge and human cells were sorted based on CD11b and hCD45 expression at 4 °C.
In this manuscript, we generated a total of 20 libraries containing 95 biological replicates for single cell RNA sequencing. In brief, we sorted 15000-20000 alive human microglia (CD11b+, hCD45+) per mouse and adjusted the final concentration to 1000 cells/µl. Out of each mouse, 2000 sorted cells were loaded into the Chromium Next GEM Chip G (PN #2000177). Since all the individual replicates were hashed using TotalSeqTM-A cell hashing antibodies, we pooled different samples into the same library. Libraries were prepared using manufacturer’s instructions (CG000204 Chromium Next GEM Single Cell 3’ Reagent Kits v3.1). For hashtag oligo libraries, we followed manufacturers’ instructions (BioLegend - TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 3.1 Protocol) using 16 cycles for the index PCR. Libraries were sequenced on a HiSeq4000 or NovaSeq6000 (Illumina) platform with the recommended read lengths by 10X Genomics workflow targeting 90% mRNA and 10% hashtag library (50,000 reads/cell).

value: Brain

value: Microglia

tag: mouse host genotype

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F , Rag2- /- Il2r{gamma}-/- hCSF1KI Apphu/hu

tag: human cells gender

value: female

tag: mouse host gender

value: female and male

tag: timepoint

value: 6 months

tag: injection

tag: multiplexed samples

tag: samples used for this study


title: Unmigrated, scRNAseq

first: Navin

last: Varadarajan

address: 4726 Calhoun Rd

department: William A Brookshire Chemical and Biomolecular Engineering Department

institute: University of Houston

description: 10X Genomics

data_processing:
The demultiplexing, barcode extraction, and gene alignment was performed using the CellRanger package v7.1.0.
Assembly: hg38
Supplementary files format and content: Tab-separated value files and matrix files.

source_name: CD28z-CAR T cell

extract_protocol:
Stimulated CD19-CD28z-CAR T cells were starved overight in serum-free media. Cells were seeded in a 5 um pore size transwell insert with full serum media at the bottom of the wells for 6 hours. Cells were collected and washed with PBS. We used the Miltenyi Dead Cell Removal kit to remove dead cells from the samples and the cells were resuspended in FACS buffer with 2% FBS. Cells from the 8 transwells were pooled based on migrated versus unmigrated cells.
We performed library preparation for the two populations. We did transcriptome capturing using 10X Chromium platform (10X Genomics) according to the manufacturer's instructions for Single Cell 3' v2 protocol.

value: CD28z-CAR T cell

value: Unmigrated


title: Migrated, scRNAseq

description: 10X Genomics

value: Migrated


title: Library 4 cell hashing

tag: tissue

tag: cell type

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F

value: male


title: Uterus,SMAD1-KI,PR,rep1

value: Uterus

tag: genotype

tag: treatment


title: Uterus,SMAD1-KI,HA,rep1

value: 4.5 dpc


title: 61_site1_core2

tag: disease state

value: WT

tag: patient id

tag: her2 heterogeneity

value: No

tag: pcr

value: Yes


title: 61_site2_core2

value: Breast tumor tissue

value: early-stage HER2-positive breast cancer

value: Pre-treatment


title: 62_Residual_Disease


title: 60_site2_core2


title: Uterus,SMAD1-KI,IgG,rep1


title: 60_site2_core1


title: Control_Sample_1

value: Blood


title: Library Mancuso et al., 2019, Nat Neuro - sAb

value: Brain

value: Microglia

value: Rag2- /- Il2r{gamma}-/- hCSF1KI

value: female

value: 2 months

value: Soluble amyloid-β aggregates

value: 1 (pool of 3)

value: all


title: interscapular brown adipose tissue, 10day cold exposed, Mafbf/f-LysMcre 3

city: Tsukuba

first: Michito

last: Hamada

state: Ibaraki

address: 1-1-1 Tennodai,

department: Department of Anatomy and Embryology

institute: University of Tsukuba

description: Single bam file generated for each sample using STAR, from paired-end two separate fastq files

data_processing:
STAR version=STAR_2.6.1a_08-27
Sequence read were alligned and mapped using default paramaters of STAR version STAR_2.6.1a_08-27
Read count performed by STAR
Normalization and DEG analysis done by edgeR tool
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count and TPM values for each Sample

source_name: interscapular brown adipose tissue

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 500ng of total RNA was used for the construction of sequencing libraries.
Library construction and RNA seq peformed by University of Tsukuba, RNA seq service

value: interscapular brown adipose tissue

tag: strain

value: tissue

value: Mafbf/f-LysMcre

value: 10 days, 4 degree cold exposure


title: Library Mancuso et al., 2019, Nat Neuro - Scrambled

tag: cell line

value: female and male

value: Scrambled peptide


title: 59_Residual_Disease

value: Breast tumor tissue

value: early-stage HER2-positive breast cancer

value: WT

value: No


title: Uterus,SMAD5-KI,IgG,rep1

value: Uterus

value: 4.5 dpc


title: 58_site2_core1

value: Pre-treatment

value: Yes


title: interscapular brown adipose tissue, 10day cold exposed, Mafbf/f-LysMcre 2


title: Library 16 mRNA

value: Brain

value: Microglia

tag: mouse host genotype

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F , Rag2- /- Il2r{gamma}-/- hCSF1KI Apphu/hu

value: female

value: 6 months


title: 58_site1_core1


title: 57_site1_core1


title: 57_site2_core2


title: interscapular brown adipose tissue, 10day cold exposed, Mafbf/f-LysMcre 1

value: interscapular brown adipose tissue

value: tissue

value: Mafbf/f-LysMcre


title: Library 3 cell hashing

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F

tag: human cells gender

value: male

value: female and male


title: 57_Residual_Disease

value: Breast tumor tissue

value: early-stage HER2-positive breast cancer

value: WT


title: Library 3 mRNA

tag: mouse host gender


title: 56_site2_core1

value: No


title: 55_site2_core2

value: Pre-treatment


title: interscapular brown adipose tissue, 10day cold exposed, Mafbf/f, 2

value: Mafbf/f

value: 10 days, 4 degree cold exposure