title: RC43N cells, veh control2 smRNA


title: LNCaP cells, treat3 smRNA

status: Public on Jan 31 2023

type: SRA

city: WEST HOLLYWOOD

first: Moray

last: Campbell

state: CA

address: 8687 Melrose Avenue, Office B227.5G

country: USA

institute: Cedars-Sinai Medical Center

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQC and Trimmomatic
Trimmed sequence reads were mapped to hg38 using Rsubread (with small RNA alignment options)
FASTQ files were aligned to the genome (hg38) using Rsubread (with small RNA alignment options). Expression counts were called against the miRbase consensus miRnome using featureCounts and a standard edgeR pipeline determined differentially expressed miRNA.
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: LNCaP

growth_protocol: All cells were maintained at 37oC and 5.0% CO2 (Sanyo); HPr1AR, RC43N, RC43T,  cells were maintained in keratinocyte serum free media (supplemented with 25mg of Bovine pituitary extract, 10ug EGF and 10% FBS); LNCaP cells were maintained in RPMI 1640 containing 10% FBS. All media contained 100 U/mL Penicillin-Streptomycin. 1α,25(OH)2D3 was kept as 10mM EtOH stocks. Cell lines were authenticated by STR profiling and confirmed mycoplasma free.

extract_protocol:
Total RNA was isolated via TRIzol® reagent
Cell lines were treated as RNA-Seq and library preparation included ligation of 5’ and 3’ RNA adapters to the mature miRNAs 5ʹ‐phosphate and 3ʹ‐hydroxyl groups and 11-13 PCR cycles using a universal primer and a primer containing one of 48 index sequences, which allowed pooling of libraries and multiplex sequencing.  Prior to pooling, each individual sample’s amplified cDNA construct was visualized on a DNA-HS Bioanalyzer DNA chip (Agilent Technologies) for mature miRNA and other small RNA products (140-150bp).  Successful constructs were purified using a Pippen prep (Sage Inc.), using 125 – 160 bp product size settings with separation on a 3% agarose gel. The purified samples were validated for size, purity and concentration using a DNA-HS Bioanalyzer chip.

treatment_protocol: Cells were grown to 70% confluence and treated with 1α,25(OH)2D3 (100nM, 8hr) or EtOH in biological triplicate samples and analyzed by RNA-Seq.

tag: tissue

value: LNCaP

tag: cell line

tag: cell type

value: WT

tag: genotype

value: European American non-malignant prostate

tag: treatment


title: SLG_mu_F rep4

city: Rochester

first: Catherine

middle: E.

last: Ovitt

state: NY

address: 601 Elmwood Ave, Box 611

department: Center for Oral Biology

institute: University of Rochester Medical Center

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using STAR with default parameters
Read counts were used for differential expression analysis
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

organism: Mus musculus

source_name: Female sublingual gland from Nkx2.3 knockout mouse

extract_protocol:
Sublingual salivary glands were removed from female mice, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background strain

value: sublingual gland

tag: Sex

value: female

tag: age

value: 32 weeks


title: SLG_mu_F rep3


title: RC43N cells, veh control3 smRNA

value: African American prostate cancer

value: Vehicle


title: RC43N cells, veh control1 smRNA


title: SLG_mu_F rep1

value: 8 weeks


title: RC43T cells, treat3 smRNA

value: African American non-malignant prostate


title: WNT3

city: Sydney

first: Jinbiao

last: Chen

state: NSW

address: Building 93, RPA Hospital, Missenden Rd

country: Australia

institute: Centenary Institute

data_processing:
The original raw data from Illumina HiSeqTM are transformed to Sequenced Reads by base calling. Raw data are recorded in a FASTQ file, which contains sequence information (reads) and corresponding sequencing quality information.
Raw reads are filtered to remove reads containing adapters or reads of low quality, so that downstream analyses are based on clean reads. The filtering process is as follows: (1) Discard reads with adaptor contamination. (2) Discard reads when uncertain nucleotides constitute more than 10 percents of either read (N > 10%). (3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50 percents of the read.
After quality control procedures, short reads were mapped to mouse genome assembly (mm10) by STAR version 2.7.3a. Mapped reads were quantified by featureCounts version 2.0.0 from Subread package.
Transcripts Per Million (TPM) was used to reduce non-biologically derived variability inherent in RNA sequencing technologies [Wagner GP, et al. Theory Biosci. 2012; 131(4):281-5. Abrams ZB, et al. BMC bioinformatics. 2019; 20(Suppl 24):679]
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each gene and each sample

source_name: wild type non-tumour liver rep3

extract_protocol:
Tissues were flash frozen on dry ice, and total RNA was harvested using Trizol reagent. All samples need to pass through the following four steps before library construction: (1) Nanodrop: tests RNA purity (OD260/OD280)  (2) Agarose Gel Electrophoresis: tests RNA degradation and potential contamination (3) Agilent 2100: checks RNA integrity
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: liver

value: 36 weeks

value: wild type

value: diethylnitrosamine (DEN):25mg/kg body weight, i.p. once, at postnatal day 12


title: RC43T cells, treat2 smRNA


title: RC43T cells, treat1 smRNA


title: WN2

source_name: wild type normal liver rep2

value: untreated


title: RC43T cells, veh control3 smRNA


title: RC43T cells, veh control1 smRNA


title: SLG_mu_F rep2


title: NU03014 Tumor

city: New York

first: Junfei Zhao

last: Zhao

address: 1130 St. Nicholas Ave

institute: Columbia University

data_processing:
Raw fastq files were processed by cellranger count https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count to generate single cell feature counts for each library.
Assembly: GRCh38
Supplementary files format and content: filtered feature-barcode matrices in Hierarchical Data Format (HDF5) generated using cellranger.

molecule: polyA RNA

source_name: Tumor-infiltrating CD45+ immune cells

extract_protocol:
Samples were subjected to scRNA seq library construction on the 10X Genomics platform using Chromium™ Single Cell 3' v3 Reagent Kits and a Chromium instrument according to the manufacturer’s protocol.
scRNA seq library construction was performed according to the 10X Genomics's instructions.

value: Tumor-infiltrating CD45+ immune cells


title: NU02954 PBMC

source_name: PBMC

value: PBMC


title: NU03014 PBMC


title: RC43T cells, veh control2 smRNA


title: RCC, gd T cell sort, pooled samples, scTCRseq

city: San Francisco

first: Marcel

last: Arias Badia

address: 513 Parnassus Ave

institute: UCSF

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Genome Build: GRCh38 3.0.0
Supplementary files format and content: Tab-separated values files and matrix files (gz compressed); comma-separated values and JSON-formatted scTCR annotation files
Library strategy: scTCR-seq

source_name: Renal cell carcinoma

extract_protocol:
Surgical specimens were obtained fresh from the operating field, and dissected in surgical pathology, where tumors were isolated, minced, and transported at room temperature immersed in L15 media with 15 mM HEPES and 600 mg/mL glucose. Resected tumor kidney tissues were further minced using surgical scissors in GentleMACs C Tubes (Miltenyi Biotec) containing RPMI-1640 media with 0.1 mg/mL of Liberase TL and 0.2 mg/mL of DNAse I. Samples were then simultaneously mechanically and enzymatically digested for 1 hour at 37C using a GentleMACS dissociator (Miltenyi Biotec), according to the manufacturer TDK-1 tumor protocol. The digestion reaction was quenched with FACS-buffer (PBS buffer supplemented with 2% heat-inactivated FCS and 2 mM EDTA) and filtered through a 100 μm cell strainer. Samples were resuspended in a 155 mM NH4Cl solution to lyse all erythrocytes and washed in FACS-buffer. Finally, the samples were either frozen for storage or resuspended for flow cytometry staining or scRNAseq.
Libraries were constructed using 10x Genomics Chromium 5’ (v1) and 10x Genomics Chromium V(D)J kit (PN-1000005) according to manufacturer's instructions. For the gd TCR amplication, custom oligonucleotide sequences targeting the gamma and delta constant regions were used.

value: Renal cell carcinoma

value: Live gd T cells


title: evercode whole-transcriptome library 5

city: London

first: Athanasios

last: Dimitriadis

address: 33 Cleveland Street

country: United Kingdom

institute: MRC Prion Unit at UCL

description: Parse Evercode snRNA-seq

library_source: transcriptomic single cell

data_processing:
The fastq files were aligned to the human genome using STAR aligner. The resulting sam files were converted to a binary format and were processed by the SPLiT-seq bioinformatics open-source tools (https://github.com/yjzhang/split-seq-pipeline) to generate a count matrix. Transcriptome GRCh38 (hg38) was used for aligning the human data. The count matrix generated was used as an input for the subsequent analyses.
Assembly: hg38
Supplementary files format and content: comma-separated values files and matrix files

source_name: brain

extract_protocol:
For the post-mortem samples, each human brain was left to partially thaw and removed from the storage cassette. A small slice of the superior frontal gyrus (approximately 50-100 mg) was cut and transferred to a glass 2 mL dounce tissue homogenizer on ice. For the human biopsies, no structure was visible, and a small slice (approximately 50-100 mg) was transferred to a glass 2 mL dounce tissue homogeniser. All following steps were carried out on the ice and using ice-cold solutions. All centrifugation steps were performed at 500 g for 5 minutes at 4oC using a pre-chilled centrifuge unless otherwise specified. 1.5 mL of Nuclei EZ prep was added, and tissue was homogenised using 20 strokes of the loose and 20 strokes of the tight pestle. The suspension was transferred to a 2 mL tube and 0.5 mL of Nuclei EZ prep was added. The suspension was incubated for 5 minutes and then centrifuged. The supernatant was discarded, 2 mL of Nuclei EZ prep were added, and the pellet was resuspended using a P1000 pipette. The suspension was incubated for 5 minutes and then centrifuged. The supernatant was discarded, 0.5 mL of wash buffer (1x PBS, 1% BSA (15260037; Gibco), 0.2 u/μL SUPERase In (AM2694; Invitrogen)) were added without resuspending, and the sample was incubated for 5 min to allow buffer interchange. Then 1.5 mL of wash buffer was added, and the sample was resuspended. The suspension was centrifuged, the supernatant was discarded, the pellet was resuspended in 500 μL wash buffer, and 0.5 mL of 50% OptiPrep Density Gradient Medium solution (D1556; Sigma-Aldrich) was added. The suspension was transferred on top of a 1 mL 29% OptiPrep cushion solution in a new tube and centrifuged at 10,000g for 30 min at 4oC. The supernatant was discarded, and nuclei were resuspended in 750 μL Parse Nuclei Buffer (from the Parse Evercode WT kit) + 0.75% Bovine Albumin Fraction V (15260037; Gibco). Preparation then proceeded following step 7 of the Parse nuclei fixation protocol (page 15 of the protocol; section 7.5.3).  The following steps were performed using the Parse Evercode nuclei fixation kit (Parse Biosciences) according to the manufacturer’s instructions.
The Parse Evercode Whole Transcriptome kit (Parse Biosciences) contains all consumables and a detailed protocol that includes all steps from nuclei fixation up to sequencing, including catalogue numbers of reagents. All steps were carried out according to manufacturer's instructions.
Suspension preparation and split-pool barcoding were carried out in a BSL-3 laboratory. To move the sample to a BSL 2 laboratory, the following prion decontamination procedure was followed: at the end of the Parse Evercode WT user manual chapter 3.4, the resulting solution was incubated with 3 volumes of TRI-reagent at room temperature for 2 hours (R2050-1-50; Zymo Research). The mix was then transferred out of the BSL-3 facilities and nucleic acids were purified using the Direct-zol DNA/RNA miniprep kit (R2080; Zymo Research). The kit columns were substituted with Zymo-Spin IC Columns (C1004-50; Zymo Research) so that smaller elution volumes could be used, following the advice of Zymo customer support. 11 μL of the RNA fraction and 10 μL of the DNA fraction were eluted in the same tube. The resulting solution of 21 μL was used for the PCRs starting at section 3.5 of the Parse Evercode WT user manual.

value: brain


title: RCC, CD4 T cell sort, pooled samples, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Genome Build: GRCh38 3.0.0
Supplementary files format and content: Tab-separated values files and matrix files (gz compressed); comma-separated values and JSON-formatted scTCR annotation files

value: Live CD4 T cells


title: RCC, gd T cell sort, pooled samples, scRNAseq

description: 10x Genomics


title: NU02954 Tumor


title: Anth_Card_116357

city: Birmingham

first: Smita

last: Bhatia

state: AL

address: 1600 7th Avenue South Lowder 500

department: Pediatrics

institute: University of Alabama at Birmingham

data_processing:
Basecalls were performed using bcl2fastq v2.18.12
Raw sequence files were trimmed using Trim Galore (version 0.6.0) using parameters --paired --trim1 --trim-n
Trimmed sequence files were aligned using STAR (version 2.7.4a) using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from alignment files using HTSeq-count (version 0.11.1) using parameters -m union -r pos - t exon -i gene_id -a 10 -s no -f bam
DESeq2 was used for normalization and pairwsie differential expression following the authors vignette
Assembly: Gencode GRCh38 p7 Release 25
Supplementary files format and content: tab-delimited txt file containing Ensembl ID #s for each gene in each sample

source_name: Whole Blood

extract_protocol:
RNA was isolated using the PAXgene whole blood RNA kit (Qiagen Inc).
Poly-adenylated RNAs were isolated using NEBNext Magnetic Oligo d(T)25 beads. Libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina Inc). Each library was pair-end sequenced  by using the TruSeq SBS Kit v4-HS (Illumina, Inc.), on a Illumina platform
Poly(A) RNA selection RNA-Seq

value: Whole Blood

value: Male

value: Case


title: Leaf sheath_long-day, 1 h_rep1

type: RNA

city: Tsukuba

first: Masao

last: Iwamoto

state: Ibaraki

address: 3-1-3 Kannondai

department: Division of Crop Genome Editing

country: Japan

institute: Institute of Agrobiological Sciences, NARO

hyb_protocol: Agilent protocol G4140-90050. 825 ng of each Cy5- and Cy3-labeled cRNAs were used for hybridization.

scan_protocol: Agilent Technologies Scanner G2505C US90500268

data_processing: The scanned images were analyzed with feature extraction software (version 10.5.1.1, Agilent) to extract signal intensities.

organism: Oryza sativa

label_protocol: 400 ng RNAs were labeled by Low RNA Input Linear Amplification/Labeling Kit (Agilent).

growth_protocol: Plants were grown in soil and maintained in a growth chamber at 28ºC under long day condition (16 h light and 8 h dark).

extract_protocol: Total RNA was extracted using RNeasy Plant Mini Kit (Quigen), according to the manufacturer's instructions.

tag: cultivar

value: Nipponbare

tag: genotype/variation

value: RDD4 overexpressing plant

tag: line

value: RDD4-OX #2

value: 2 weeks

value: leaf sheath


title: Leaf sheath_long-day, 1 h_rep3

value: RDD4-OX #4

value: wild type


title: HOXB9_siHOXB9_MKN1

city: Hong Kong

first: Bonan

address: The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, The People's Republic of China

country: Hong Kong

institute: the Chinese University of Hong Kong

description:
siHOXB9_MKN1_FPKM
siHOXB9_AGS_MKN1_matrix.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed through 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 the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Trimmed sequence reads were mapped to GrCh38/hg38 using lab server.
Read count extraction and normalization were performed using lab server.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using RNA Extraction Kits (QIAGEN). 1 ug of total RNA was used for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: gastric cancer cell

value: HOXB9 knockdown

value: Lipofectamine™ 2000 Transfection


title: TPA+RGRN-305 8

city: Aarhus

first: Hakim

last: Ben Abdallah

state: Denmark

address: Palle Juul-Jensens Boulevard 45

department: Dermatology and Venerology

country: Denmark

institute: Aarhus University Hospital

description: 2x150 Sequence mode to obtain at least 20 million read pairs

data_processing:
R package Subread (version 2.10.3)
Raw reads were aligned to the mouse reference genome (GRCm39 primary assembly)
Gene counts were obtained by uniquely aligned unambiguous reads
Assembly: GRCm39 primary assembly

source_name: Ear

extract_protocol:
Total RNA was isolated using the SV 96 Total RNA Isolation System (Promega) according to the manufacturer’s instructions
RNA sequencing library was prepared with 100 ng of total RNA using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: Ear

value: WT

value: TPA + RGRN-305


title: TPA+RGRN-305 9


title: Anth_Card_765411

value: Female

value: Control


title: Leaf sheath_long-day, 1 h_rep2

value: RDD4-OX #3


title: HOXB9_siScramble_MNK1

description:
siScramble_MKN1_FPKM
siHOXB9_AGS_MKN1_matrix.txt


title: TPA+RGRN-305 7


title: Anth_Card_783953

value: Whole Blood

value: Male


title: RCC, CD8 T cell sort, pooled samples, scRNAseq

description: 10x Genomics

value: Renal cell carcinoma

value: Live CD8 T cells


title: evercode whole-transcriptome library 6

description: Parse Evercode snRNA-seq

value: brain


title: Anth_Card_763538

value: Case


title: TPA+RGRN-305 6


title: evercode whole-transcriptome library 3

description: Parse Evercode snRNA-seq


title: Anth_Card_775912


title: evercode whole-transcriptome library 2

description: Parse Evercode snRNA-seq


title: evercode whole-transcriptome library 4

description: Parse Evercode snRNA-seq


title: Anth_Card_10615


title: TPA+RGRN-305 10


title: TPA+RGRN-305 4


title: H441_RSGL_2

city: Shang Hai

first: zhengke

last: lian

address: 500 Dongchuan Rd

country: China

institute: East China Normal University

data_processing:
Basecalls performed using Illumina NovaSeq 6000
clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Assembly: Hissat2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: lung

growth_protocol: H441 cells were cultured in RPMI 1640 with 10% FBS and 1% Penicillin/Streptomycin (typically 1-3 × 106 cells into a 6cm dish) supplemented with a humidified 95:5 (%; v/v) mixture of air and CO2 at 37℃.

extract_protocol:
Total RNA samples were extracted with RNA TRIzol Reagent (Magen) according to the manufacture’s manual.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: One replicate of H441 was treated with 10μM BSGL orRSGL.

value: lung

value: Non-Small Cell Lung Cancer

value: 10μM RSGL for 24h


title: H441_RSGL_3


title: Anth_Card_767458


title: 67109_control

description: Universal Plus Total RNA-Seq

data_processing:
The raw fastq files were aligned on the human reference genome hg38 using the STAR aligner with default options. The files were converted to binary format (.bam) using samtools. The package GenomicAlignments in R was used to summarize the expression counts and create a SummarizedExperiment object. This was then loaded on DESeq2, size factors were estimated and counts were normalized using the standard call to DESeq2() function with default options and an experimental design formula = ~ experimental_group.
Assembly: hg38
Supplementary files format and content: comma-delimited file of an expression matrix where row names are ENSEMBL transcripts and column names are the sample identifiers

source_name: Brain, Frontal Cortex

extract_protocol:
Frozen frontal cortex brain slices were left to thaw and were hand-dissected. Approximately 50-100 mg of the superior frontal gyrus was homogenised in Tri Reagent (Zymo Research) using a pellet pestle (Kimble) and incubated at room temperature for 2 hours. Total RNA was purified using the Direct-zol RNA miniprep kit (R2050; Zymo Research) following the manufacturer’s instructions. DNAse I treatment was performed in tube followed by column purification (Zymo Research). All RNA samples were subsequently run on a TapeStation 2200 (Agilent, Santa Clara, US) using High Sensitivity RNA ScreenTapes.
100 ng of Total RNA was used as input material to pepare librairies using the Universal Plus Total RNA-Seq with Human AnyDeplete (Tecan) according to the manufacturer’s instructions. Resulting libraries were visualized and quantified on the 2200 TapeStation Instrument and diluted at 2nM concentration and pooled in two batches of 7 libraries each. Each pool was sequenced on the Illumina NextSeq 500 after the addition of 5% PhiX sequencing control library (FC-110-3002; Illumina) using the following settings: paired-end, read 1: 75 nt, read 2: 75 nt.

value: Brain, Frontal Cortex

tag: condition

value: control

value: F


title: H441_BSGL_3

value: 10μM BSGL for 24h


title: evercode whole-transcriptome library 1

description: Parse Evercode snRNA-seq


title: TPA+RGRN-305 5

value: Ear

value: WT

value: TPA + RGRN-305


title: HOXB9_siScramble_AGS

description:
siScramble_AGS_FPKM
siHOXB9_AGS_MKN1_matrix.txt

source_name: AGS

value: AGS

value: gastric cancer cell

value: Lipofectamine™ 2000 Transfection


title: Anth_Card_776437

value: Whole Blood

value: Female


title: H441_BSGL_2


title: HOXB9_siHOXB9_AGS

description:
siHOXB9_AGS_FPKM
siHOXB9_AGS_MKN1_matrix.txt

value: HOXB9 knockdown


title: TPA+RGRN-305 3


title: 67104_control

description: Universal Plus Total RNA-Seq


title: Anth_Card_720000

value: Control


title: TPA+RGRN-305 2


title: 67106_control

description: Universal Plus Total RNA-Seq


title: Anth_Card_779640

value: Case


title: TPA+RGRN-305 1


title: H441_BSGL_1

value: lung

value: Non-Small Cell Lung Cancer


title: Anth_Card_45223


title: Anth_Card_305082


title: TPA 10

value: TPA


title: 67099_control

description: Universal Plus Total RNA-Seq

value: Brain, Frontal Cortex

value: control

value: M


title: 67098_control

description: Universal Plus Total RNA-Seq


title: H441_RSGL_1

value: 10μM RSGL for 24h


title: Anth_Card_769882


title: 67105_control

description: Universal Plus Total RNA-Seq

value: F


title: TPA 9

value: Ear

value: WT


title: 67097_control

description: Universal Plus Total RNA-Seq


title: Anth_Card_50253


title: H441_con_2

value: 0.1% DMSO for 24h


title: 67096_control

description: Universal Plus Total RNA-Seq


title: TPA 8


title: 67094_control

description: Universal Plus Total RNA-Seq


title: Anth_Card_77427


title: H441_con_1


title: TPA 7


title: Anth_Card_129187


title: TPA 6


title: TPA 5


title: 54580_sCJD

description: Universal Plus Total RNA-Seq

value: sCJD


title: 56720_sCJD

description: Universal Plus Total RNA-Seq


title: TPA 4


title: 56093_sCJD

description: Universal Plus Total RNA-Seq


title: 54466_sCJD

description: Universal Plus Total RNA-Seq


title: TPA 3


title: H441_con_3


title: TPA 1


title: TPA 2


title: 53846_sCJD

description: Universal Plus Total RNA-Seq


title: RGRN-305 3


title: RGRN-305 4


title: PDGF-BB induced dedifferentiated human aortic  smooth muscle cell_rep2

city: Beijing

first: zhihua

last: Rong

address: dongdan

institute: peking union medical college hospital

description: PDGFB

data_processing:
Raw sequencing data QC
Mapping Summary: Alignment information of sequence mapping to the reference genome
Identification of tRF & tiRNA
Differential expression analysis of tRF & tiRNA
The scatter plots of differentially expressed tRFs & tiRNAs.
Assembly: Supervised analysis: For each group comparison, we generate a hierarchical clustering heatmap and a volcano plot to display significantly differentially expressed tRFs & tiRNAs .
Supplementary files format and content: tab-delimited text files include count and cpm values for each Sample

source_name: HASMC

growth_protocol: HASMCs were maintained in SMCM supplemented with 2% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) from HASMCs with or without PDGF-BB (50 ng/ml) treatment for 24 h
After pretreatment of tRF that to remove RNA modifications,sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter. The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2100.

treatment_protocol: HASMCs were cultured in serum-free and SMGS-free medium for 24 h before treatment with (50 ng/ml) platelet-derived growth factor-BB (PDGF-BB; R&D Systems, USA).

value: HASMC

value: primary smooth muscle cell

value: wt

value: dedifferentiation


title: Differentiated human aortic  smooth muscle cell_rep3

description: PBSC

value: differentiation


title: Differentiated human aortic  smooth muscle cell_rep2

description: PBSB


title: RGRN-305 2


title: PDGF-BB induced dedifferentiated human aortic  smooth muscle cell_rep1

description: PDGFA


title: MN7

city: Los Angeles

first: Michael

last: Neely

address: 4650 Sunset Blvd

institute: Children's Hospital Los Angeles

data_processing:
Libraries were sequenced on an Illumina Hiseq platform at 38 million paired end (2x150 base pair) reads per sample
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0
the gene expression level was estimated using RSEM v1.2.15
Trimmed mean of M values (TMM) method was used for the normalization of the raw count.
Assembly: hg38
Supplementary files format and content: raw count

source_name: BMDM cells, Uninfected, Control, 2 hours

extract_protocol:
Total RNA from Mab-S and Mab-R infected BMDMs and uninfected BMDMs was isolated using STAT-60 RNA kit (AMSBIO Cat# RNASTAT60) following manufacturer’s protocol. Isolated RNA was further purified using the Qiagen RNeasy mini kit using manufacturer’s RNA clean-up protocol and the quality was determined by measuring the RNA integrity number (RIN) using the Agilent bioanalyzer 2100 instrument. RIN was greater than 7.5.
Sequencing libraries were made using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (Cat# E7760), NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat# E7490) and NEBNext Multiplex Oligos (Cat# E7335) using manufacturer’s protocol.
Libraries were sequenced on an Illumina Hiseq platform at 38 million paired end (2x150 base pair) reads per sample.

value: Bone Marrow Derived Macrophages

value: Wild type

value: Uninfected samples


title: MN5

source_name: BMDM cells, Mab-R infected, 2 hours

value: Mab-R infected samples


title: MN6


title: MN4


title: Vehicle 1

value: Vehicle


title: MN9


title: PDGF-BB induced dedifferentiated human aortic  smooth muscle cell_rep3

description: PDGFC


title: MN1

source_name: BMDM cells, Mab-S infected, 2 hours

value: Mab-S infected samples


title: RGRN-305 1


title: Murine primary VSMCs, siPFKFB3-2, 48hrs

city: Guangzhou

first: Dongxing

last: Zhu

state: Guangdong

address: Xinzao, Panyu District

department: School of Basic Medical Sciences

institute: Guangzhou Medical University

data_processing:
The raw reads were further processed with a bioinformatic pipelinetool,BMKCloud(www.biocloud.net) online  platform.
Raw data (raw reads) of fastq format were firstly processed through 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, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were   transformed into clean reads after data processing. These clean reads were then mapped to the reference genome  sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the  reference genome. Hisat2 tools soft were used to map with reference genome  GrCM38/mm10.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped
Assembly: mm10
Supplementary files format and content: Excel files include RPKM values for each Sample

source_name: vascular smooth muscle cells

growth_protocol: Mouse primary VSMCs were isolated using a collagenase digestion method from 12*6-week-old C57BL/6 male mice. Mouse primary VSMCs were cultured in growth medium consisting of α-MEM supplemented with 10% FBS (Gibco, 16000-044), 100 U/ml of penicillin (HyClone, SH40003.01), and 100 mg/ml of streptomycin (Hyclone, SV30010)

extract_protocol:
Total RNA was extracted according to the instruction manual of the TRlzol Reagent (Lifetechnologies, California, USA).1 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina  (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations

treatment_protocol: Scrambled siRNAs (siScrambled) or siRNAs targeting against the mouse Pfkfb3 gene (Gene ID: 170768) were obtained from Guangzhou RiboBio Co., Ltd, China. Mouse VSMCs were seeded at a density of 1.0*105 cells/well in 6-well plates, and transfected with siScarmbled or siPfkfb3 at a final concentration of 20 nM using Lipofectamine RNAiMAX (Invitrogen, 13778) according to the manufacturer’s instructions.

value: vascular smooth muscle cells

value: PFKFB4 knockdown

value: Normal Growth Medium


title: MN8


title: Differentiated human aortic  smooth muscle cell_rep1

description: PBSA


title: HITS-CLIP Flag-Ago2b

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

institute: Omiics ApS

data_processing:
Trimmed using FastX-toolkit: Bases with low quality were trimmed from both ends, then reads with quality score below 20 over 90% of the read were discarded.
Adapter sequence was removed. Reads below 24 bp in length after adapter removal was discarded
Filtered reads were mapped to mouse genome (mm10) using bwa (Burrows-Wheeler Aligner)
To reduce contributions of nonspecifically binding RNA species from cluster detection, any RISC-associated RNA read within 35 bp of 5 or more overlapping reads from the grouped control samples were discarded. Only reads occurring in at least two filtered Flag-Ago2 samples were kept, and 30 nucleotides of genomic sequence was added to each end of the filtered reads. These reads were filtered to only retain clusters composed of minimum 10 overlapping reads.

source_name: Brain

extract_protocol:
In three independent experiments (experiment 1-3), mice that express a Flag-tagged Ago2 protein specifically in Camk2+ neurons in the forebrain (Camk2a-cre; Rosa-Stopfl/fl-Flag_x0002_Ago2) and control mice (Rosa-Stopfl/fl-Flag-Ago2) were sacrificed at 8 to 14 weeks of age. Forebrains were excised, triturated to disrupt tissue, and UV-irradiated three times in a Stratalinker with 400mJ/cm2. Immunoprecipitation was performed as described (8) with the following modifications to the protocol: After UV crosslinking the frozen lysates were sonicated to improve tissue homogenization. RNase digestion with RNase A was performed before IP (using one fourth the concentration of RNase A used by (8)), and after IP (using one twentieth the concentration of RNase A used by (8)). 30µl of magnetic beads pre-coupled to the M2 FLAG antibody (M8823, Sigma) were used for IP on half of one forebrain after pre-blocking the beads with 2% BSA, 1% t-RNAs and 1% salmon sperm for 1.5 hrs at 4o C. RNA was directly de-crosslinked from protein after extensive washing
The small RNA sample preparation kit, version 1.5 (Illumina), was used for library preparation with subtle modifications. Because low concentrations of RNA were purified from the CLIP procedure, as measured by Quant-iT RiboGreen RNA Assay (Invitrogen), the following modifications were made to the small RNA sample preparation kit (Illumina) to allow for low RNA input: Both the v1.5 sRNA 3’ Adapter and the SRA 5’ Adapter were diluted 10 times in nuclease-free water compared to the standard protocol before adapter ligation. The RT reaction was doubled (resulting in a final RT volume of 20 µl instead of the standard 10 µl), all of which was used for the downstream PCR reaction. To allow for the larger volume of RT product, 10 µl less water was used in the PCR step, resulting in a final PCR volume of 50 µl. Instead of the 12 cycles of PCR directed in the standard protocol 15 cycles were performed to increase output. RNA from four CLIP procedures were pooled for each library preparation, amounting to CLIP RNA from two mouse forebrains per library. At the end of the Illumina small RNA protocol, the products were purified from a gel at the size of 110 to 150 bp, containing adapter-linked RISC-associated mRNA target sites

treatment_protocol: Transgenic mice expressing a Cre-inducible FLAG-HA2-tagged Ago2 under the control of the ROSA26 promoter were generated as previously described. The STOP-eGFP-ROSA26TV vector was a gift from K. Rajewsky, Harvard Medical School, Boston, MA. Rosa-Stopfl/fl-Flag-Ago2 mice were bred to Camk2a-cre transgenic mice (kindly provided by G. Schuetz, German Cancer Research Center, Heidelberg, Germany) to generate Camk2a-cre; Rosa-Stopfl/fl-Flag-Ago2 mice.

value: Brain

tag: ip antibody

value: M2 FLAG antibody (M8823, Sigma)

tag: library type

value: HITS-CLIP

value: Camk2a-cre; Rosa-Stopfl/fl-Flag-Ago2)


title: Murine primary VSMCs,  siPFKFB3-3, 48hrs

value: PFKFB5 knockdown


title: HITS-CLIP Flag-Ago2a


title: HITS-CLIP Flag-Ago3b


title: Vehicle 3

value: Ear

value: WT


title: MN2


title: Vehicle 4


title: Murine primary VSMCs, siScarmbled-2, 48hrs


title: Murine primary VSMCs, siPFKFB3-1, 48hrs

value: PFKFB3 knockdown


title: HITS-CLIP Flag-Ago1


title: Vehicle 2


title: MN3

value: Bone Marrow Derived Macrophages


title: HITS-CLIP Flag-Ago3a


title: Murine primary VSMCs, siScarmbled-3, 48hrs


title: HITS-CLIP control2


title: Murine primary VSMCs, siScarmbled-1, 48hrs


title: SS5, romidepsin, replicate 3

city: Ann Arbor

first: Chenguang

last: Wang

state: Michigan

address: 1500E Medical Center Dr, Room 4411

department: Department of Internal Medicine

institute: University of Michigan

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using with Cutadapt (v2.3)
Trimmed reads were mapped to the reference genome GRCh38 (ENSEMBL) using STAR (v2.7.8a) and assigned count estimates to genes using RSEM (v1.3.3) with default parameters.
Differentially expressed genes were determined using expected counts by DESeq2 package (v1.32), p-value <-0.05 and fold-change >=1.5 or <=0.67 were considered statistically significant.
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: primary samples

growth_protocol: Cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 50 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module following manufacturer's protocols.

treatment_protocol: Cells were treated with 1uM belinostat and 1uM romidepsin for 6 hours before harvesting.

value: primary samples

value: Sezary Sydrome

value: PBMC

value: romidepsin

value: 6 hours


title: SS5, romidepsin, replicate 2


title: SS5, romidepsin, replicate 1


title: SS4, belinostat, replicate 3

value: belinostat


title: HITS-CLIP control3


title: Testis, in vitro D30, CSF, rep1

city: Paris

first: Hélène

last: Lopez-Maestre

address: 25-28 rue du Dr Roux

country: France

institute: Institut Pasteur

description:
in_vitro_D30_CSF-1
Read length: 50

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Statistical Filtration of Global DEGs Analysis. The statistical filtration of the genes showing a differential expression across experimental samples was performed using the Annotation, Mapping, Expression and Network (AMEN) suite of tools (Chalmel and Primig, 2008). Out of 12,565 genes were extracts in the dataset and the final expression matrix were explored by hierarchical clustering to identify a potential grouping of samples.
Bioinformatics Analysis. Reads were aligned against the reference genome (GRCm38) using STAR (2.7.3a; Dobin et al., 2013) with default parameters. Gene expression was then calculated with HTseq (0.12.4; Anders et al., 2015) with --mode intersection-nonempty.
Principal Component Analysis and Sample Distance Map. The raw count data from all samples were transformed with the varianceStabilizingTransformation (vst) function from DESeq2. We then calculated the Euclidean distance between samples on the transformed counts and the samples were then clustered using the R function hclust. We also performed a PCA on the vst transformed counts using the 500 most variable genes. The biological samples who did not meet the quality checks were therefore eliminated from this bioinformatic analysis.
Differential Analysis Fold-chance. Differential analysis was then performed with R, using DESeq2. Each condition was compared to another, and raw p-values were adjusted by the method of Benjamini and Hochberg to control a false discovery rate (FDR) (Benjamini and Hochberg, 1995). DEGs selected for Volcano Plots analysis have a |Log2 fold change| greater or equal to 2.0 and a |Log10 padj| greater or equal to 3.0.
Functional Profiling. The g:GOSt function was used to known functional information sources and detects statistically significantly enriched terms using g:SCS threshold fixed at 0.05. In order to consider only the elements that emerge from the batch for in vitro vs. in vivo, DEGs selected for this analysis have a padj<6×10-8. The g:GOSt database versions used in the present study are Ensembl 104 and Ensembl Genomes 51. In addition to GO Terms with the use of biological process (BP), cellular component (CC), and molecular function (MF), the g:GOSt includes pathways from Reactome (REAC), and WikiPathways (WP) up-to-date data sources.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include matrix_raw_count of all samples with ENTREZID genes

source_name: Testis

growth_protocol: The culture media used for this study was a medium composed of α-MEM plus 10% (v/v) KnockOut™ serum replacement (KSR) (10828-010; Gibco®), 5 µg/mL gentamicin (G1397; Sigma-Aldrich®), and Rol (all-trans retinol; R7632; Sigma-Aldrich®) at a concentration of 10-6 M. An alternate supplementation of Rol was performed every 8 days to mimic the physiological timing of entry into differentiation of spermatogonia.

extract_protocol:
Total RNA was extracted from testicular samples using RNeasy Micro kit (74004; Qiagen, Courtabœuf, France) according to the manufacturer’s instructions and stored at -20°C until use. For in vitro cultured testicular explants, the central necrotic area (inherent of long-term culture system) was carefully removed before RNA extraction. To avoid contamination with genomic DNA, extracted RNA was incubated with two units of TURBO DNA-free™ kit (AM1907; Life Technologies™, Carlsbad, California, USA) for 45 min at 37°C.
RNA-Seq libraries were generated from 800 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94°C for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: Testis

value: Germ and somatic cells

tag: in vivo_or_in_vitro

value: in vitro

tag: corresponding time_(dpp)

tag: state of_tissue

value: controlled slow frozen

value: wt


title: SS4, belinostat, replicate 2

tag: tissue

tag: cell line


title: SS4, belinostat, replicate 1

tag: cell type

tag: genotype


title: Testis, in vitro D30, FT, rep3

description:
in_vitro_D30_FT-3
Read length: 50

value: fresh


title: SS3, vehicle control, replicate 2

value: control

tag: treatment


title: Testis, in vitro D30, FT, rep2

description:
in_vitro_D30_FT-2
Read length: 50


title: Testis, in vitro D16, FT, rep2

description:
in_vitro_D16_FT-2
Read length: 50


title: SS3, vehicle control, replicate 1


title: 6921

city: Pamplona

first: Cristina

last: Perez

address: Av. Pio XII 55

country: Spain

institute: Cima Universidad de Navarra

description: SureSelectXT

library_source: genomic

data_processing:
Sample demultiplexing, alignment to the reference genome and single-cell gene count was performed using the Cell Ranger Single-Cell Software Suite v.2.0.1 (https://www.10xgenomics.com/). Expression matrixes were analyzed with the R package seurat 4.0 (https://satijalab.org/seurat/) and cells were filtered according to < 10% mitochondrial expression and at least 200 (but less than 2500) mRNA counts per cell. Once scaled and normalized, a genelist including the most variable genes was obtained by the FindVariableFeatures function. After removing genes belonging to the immunoglobulin families (which could work as a confounding factor during clustering), the genelist was used to derive the principal component analysis (PCA) vectors for each sample. The first 100 PCA were used to align samples (batch removal) using the R package harmony. The new harmonized coordinates were used to develop UMAPs (dimensionality reduction). The shared nearest neighbor (SNN) algorithm based on 50 batch-corrected dimensions was used for clustering the cells into homogeneous groups that were manually identified according to the expression of canonical genes (see Supplemental Information) obtained from curated gene-sets. A sequential subclustering strategy (which consists basically in repeating the same steps as before on a specific subpopulation) to focus on clonotypic T cells was performed. Reconstruction of T cell trajectories was performed by ordering single cells in “pseudotime” according to their RNA expression through Monocle 2 R package. This package accurately resolves biological processes (ordering cells) by learning an explicit principal graph from the single cell genomics data through Reverse Graph Embedding algorithm.
Assembly: mm10
Supplementary files format and content: BM_T_mice.rds

molecule: genomic DNA

source_name: bone marrow

extract_protocol:
scRNA-seq + scTCR-seq were performed in 13 bone marrow aspirates from 2 healthy (Ycɣ1), 3 MGUS (BIcɣ1), 3 MM (BIcɣ1), 3 MGUS (MIC) and 2 MM (MIC) bearing mice. Cells were FACS sorted (a mix of 0.8x10^5 T cells + 0.8x10^5 NK cells + 0.25x10^5 monocytes + 0.15x10^5 B cells) in 100 µL of PBS+0.05% BSA. Samples with at least 90% viability were processed using the 10X Genomics (CA, USA) scRNA/TCRseq kit, following the manufacturer’s instructions (Chromium Next GEM Single Cell V(D)J v1.1 protocol rev F for human samples and Chromium Next GEM Single Cell 5’ v2 Dual Index protocol rev B for mice samples). Quality control was performed with Qubit Fluorometric Quantification (ThermoFisher Scientific, MA, USA) using the double-stranded DNA high-sensitivity assay kit, and with TapeStation (Agilent, Santa Clara, CA) using high-sensitivity screentapes. Libraries were sequenced on a NextSeq 550 (Illumina, San Diego, CA).
WES was performed in 71 BM samples isolated from GFP+ CD138+B220− PCs (purity, >99%), including 62 samples from the MM stage, 3 samples of pooled PCs from nine mice at the MGUS stage (3 mice with similar genotype were included on each pooled sample), and 6 samples from MM-derived cell lines. As MM reference controls, 5TGM1 and 12598Vk*Myc cell lines were also characterized.
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 5’ v2 Dual Index protocol rev B, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Of note, according to TCR-seq protocol from manufacturer, we further sequenced (after specific amplification) CDR3 sequences from each CD3+ T cells.
scRNA-seq, scTCR-seq, WES

value: bone marrow

value: bone marrow immune cells

value: tumor plasma cells

value: BIc


title: Testis, in vitro D30, FT, rep1

description:
in_vitro_D30_FT-1
Read length: 50


title: UTHBC0073 BA9

city: Houston

first: Consuelo

last: Walss-Bass

state: Texas

address: 1941 East Road Rm. 3110

department: Louis A. Faillace Department of Psychiatry and Behavioral Sciences

institute: University of Texas Health Science Center at Houston

description:
UTHBC0073
BA9_CUD_GEO-counts.csv

data_processing:
Reads were mapped to the GRCh38 genome using STAR version 1.7.10a. (Dobin et al., 2013)
Gene and transcript counts were obtained using featureCounts (Liao et al., 2014), and from the raw counts, gene lengths, library size, and counts per million were calculated.
Genes with CPM > 1 in at least 1 sample were kept for analysis.
Assembly: GRCh38
Supplementary files format and content: BA9_CUD_GEO-counts.csv: Raw counts matrix of postmortem cocaine use disorder Brodmann Area 9 samples from the UTHealth Brain collection. Columns refer to individual UTH Brain Collection ID for each subject
Supplementary files format and content: counts-cells-GEO_1-26-23.csv: Raw counts matrix of postmortem-derived fibroblast, iPSC, NPC, and Neuron lines from the UTHealth Brain Collection. Columns refer to individual cell line samples and whether they were treated or untreated with corresponding drug (morphine or cocaine)

source_name: Brain Brodmann Area 9

growth_protocol:
At autopsy, three 3 millimeter (mm) skin punches were collected from the forearm of Subject 1 and Subject 2 and dermal fibroblasts were cultured and expanded. Briefly, punches were dissected into 0.5 mm pieces in phosphate buffered saline (PBS) without calcium and magnesium (Corning, Corning, NY) with 100 micrograms (µg)/ milliliter (mL) primocin (InvivoGen, San Diego, CA) and 1x Pen/Strep (Gibco-Thermo Fisher Scientific, Waltham, MA), incubated in 2units/mL type 2 collagenase (Worthington Biochemical, Lakewood, NJ) in Dulbecco’s Modified Eagle Media (DMEM, Corning) overnight, rinsed in DMEM and plated on 3 wells of a of a 24-well culture plate coated with Bovine plasma fibronectin (EMD Millipore, Darmstadt, Germany). Cells were cultured in fibroblast media consisting of 10% FBS (Gibco) and 1x PenStrep (Gibco) in DMEM and passaged and expanded using 0.05% Trypsin/0.53 millimolar (mM) EDTA (Corning) chemical dissociation. Cells were expanded into T-125 flasks and frozen to -80°C in a Mr. FrostyTM freezing container (ThermoFisher) at passage 3 in 1mL of 10% dimethylsufoxide (DMSO, Sigma-Aldrich, St. Louis, MO) at 1.5 million cells per cryovial. Cells were transferred after 24 hours (hr) to long term storage in liquid nitrogen until use when they were thawed quickly in a 37°C water bath, immediately diluted in fibroblast media, and centrifuged before plating to remove DMSO.
Postmortem fibroblasts were induced to iPSCs using the Cyto-TuneTM-iPS 2.0 Sendai Reprogramming Kit (Invitrogen-Thermo Fisher Scientific, Waltham, MA), following manufacturer’s protocol. Briefly, fibroblasts were thawed and plated at passage 4 on 3 wells of a 6-well plates to 50% confluency and then were transfected overnight with the Cyto-TuneTM-iPS 2.0 Sendai viral vectors in fibroblast media at the following Multiplicity of Infection (MOI): KOS = 5, hc-Myc = 5, hKlf4 = 3. After 6 days, cells were replated on 60mm dishes coated with GeltrexTM LDEV-Free Reduced Growth Factor Basement Membrane Matrix (Gibco). Cells were maintained in TeSRTM-E8TM media (StemCell Technologies, Vancouver, BC, Canada) and media was changed daily until iPSC colony formation (10-28 days). Colony clones were manually selected based on morphology and subsequently expanded in mTeSRTM Plus media (StemCell Technologies). Colonies were passaged for expansion using 10 micromolar (µM) EDTA in PBS without calcium and magnesium and gentle mechanical dissociation with a P1000 pipette. 2 clones from each line were selected based on morphology and iPSC marker positivity for expansion and differentiation into neural cells.
Neural progenitor cells (NPC) were generated using StemCell Technologies AggrewellTM plates to generate embryoid bodies (EBs) and then cultured using the StemDiffTM SMADi Neural Induction Kit, following manufacturer’s protocol as previously described (Stertz et al., 2021). After 7 days, EBs were plated in Geltrex-coated 6-well plates in STEMDiff Neural Induction Medium + SMADi, and rosettes were manually selected 7 days later and replated on Geltrex-coated wells for expansion. NPCs were passaged at 80-90% confluence using Accutase cell detachment solution (Innovative Cell Tech, San Diego, CA) and expanded in Neural Basal (NB) media (50% DMEM/F12 (Corning), 50% Neurobasal Medium (Gibco), 1x GlutaMAX (Gibco), 1x NEAA (Gibco), 1x PenStrep (Gibco), 1x N-2 (Gibco), 1x B27 minus vitamin A (Gibco) supplemented with 20ng/mL of recombinant human FGF-Basic (1-155 a.a, PeproTech, Cranbury, NJ).
Cortical neurons were differentiated as previously described (Stertz et al., 2021). NPCs were plated on Laminin/Poly-L-Ornithine coated 6-well plates at a density of 20,000 cells/cm2 and media was replaced the next day with Neuron Differentiation (ND) media consisting of NB media without FGF-Basic supplemented with 20 nanogram (ng)/ml BDNF (PeproTech), 20 ng/ml GDNF (PeproTech), 1 mM dibutyryl-cyclic AMP (Sigma-Aldrich), 200 nanomolar (nM) ascorbic acid (Sigma-Aldrich), 10 ng/mL IGF-1 (PeproTech), and 10 ng/ml WNT-3A (R&D Systems, Minneapolis, MN). ND media was changed every other day until the final neuron time points of Day 7, Day 14, or Day 21.
To avoid cell passage number affecting epigenetic age and cellular maturity, all cell samples were collected, induced and differentiated at the same passage number: passage 4 for fibroblasts, passage 16 for iPSCs, and passage 4 for NPCs.

extract_protocol:
RNA was extracted from 50mg of BA9 tissue using RNeasy Plus Mini kits (Qiagen, Hilden, Germany) and RNA integrity number (RIN) was measured for RNA quality (Agilent Bioanalyzer 2100 system, Agilent Technologies, Santa Clara, CA).
1 μg RNA per sample was used for mRNA library construction using NEBNext® Ultra™ RNA Library Prep Kit (Illumina Inc, San Diego, CA).
For cell samples: Cells were lifted in Trypsin, Accutase or 10 µM EDTA in PBS without calcium and magnesium, pelleted in 1.5mL tubes and stored at -80oC until use. Fibroblasts were pelleted at 1.5 million cells, iPSCs were pelleted from 2 wells of a 6 well plate at 60-80% confluence, NPCs were pelleted from 2 wells of a 6 well plate at 100% confluence, and neurons were pelleted from 2 wells of each 6 well differentiation plate.
For cell samples: RNA was collected from dry frozen pellets using the RNeasy Plus Mini kits (Qiagen, Hilden, Germany).
For Brain Tissue: RNA was extracted from 50mg of BA9 tissue using RNeasy Plus Mini kits (Qiagen, Hilden, Germany) and RNA integrity number (RIN) was measured for RNA quality (Agilent Bioanalyzer 2100 system, Agilent Technologies, Santa Clara, CA).
For Cells: 400ng RNA per sample was used for mRNA library construction using NEBNext® Ultra™ RNA Library Prep Kit (Illumina Inc, San Diego, CA). Paired-end sequencing reads (150bp) were generated on an Illumina HiSeq2000 platform (Novogene Bioinformatics Institute, Chula Vista, CA).
For Brain Tissue: 1 μg RNA per sample was used for mRNA library construction using NEBNext® Ultra™ RNA Library Prep Kit (Illumina Inc, San Diego, CA).

treatment_protocol: 10mM morphine stocks were prepared by dissolving morphine sulfate (Sigma-Aldrich, M8777) in PBS. 10mM cocaine stocks were prepared by dissolving cocaine hydrochloride (Sigma-Aldrich C5776) in PBS. Stocks of cocaine and morphine were stored at 4C until use at which time either morphine or cocaine was diluted in NDM to produce a final concentration of 10µM. To model chronic drug exposure in OUD and CUD, Neuron lines derived from two iPSC clones from one individual with OUD who died of an opioid overdose (morphine and hydrocodone, Table 1, Subject 2) were treated with 10µM morphine or left untreated for 7 days during differentiation from day 14 to day 21 of the neuron differentiated protocol. Morphine-containing or morphine-free media was changed daily for 7 days. Neuron lines derived from two iPSC clones from one individual with CUD who died of a cocaine overdose (Table 1, Subject 1) were treated with 10µM cocaine or left untreated for 7 days during differentiation from day 14 to day 21 of the neuron differentiated protocol. Cocaine-containing or cocaine-free media was changed daily for 7 days. For each cell line, treated and untreated cells were pelleted at day 21 of differentiation for RNA seq analysis.

tag: uthbc subject_id

value: Brain Brodmann Area 9

tag: ethnicity

value: Black

tag: Sex

value: Male

tag: age at_time_of_death

tag: postmortem interval_(hours)

tag: rna integrity_number

tag: brain cerebellar_ph

tag: postmortem consenus_diagnosis

value: Cocaine Use Disorder


title: UTHBC0090 BA9

description:
UTHBC0090
BA9_CUD_GEO-counts.csv


title: H9 cells, romidepsin, replicate 3

value: cutaneous T cell lymphoma cells

value: cell line

value: romidepsin

value: 6 hours


title: UTHBC0071 BA9

description:
UTHBC0071
BA9_CUD_GEO-counts.csv

value: White


title: Testis, in vitro D16, FT, rep1

description:
in_vitro_D16_FT-1
Read length: 50

value: Testis

value: Germ and somatic cells

value: in vitro


title: UTHBC0063 BA9

description:
UTHBC0063
BA9_CUD_GEO-counts.csv


title: MIC124

description: SureSelectXT

value: MIc


title: 6916

description: SureSelectXT

value: bone marrow

value: KrasBIc


title: HITS-CLIP control1

value: Brain

tag: ip antibody

value: M2 FLAG antibody (M8823, Sigma)

tag: library type

value: HITS-CLIP


title: Testis, in vitro D4, FT, rep3

description:
in_vitro_D4_FT-3
Read length: 50

tag: in vivo_or_in_vitro

tag: corresponding time_(dpp)

value: fresh

value: wt


title: UTHBC0069 BA9

description:
UTHBC0069
BA9_CUD_GEO-counts.csv

tag: tissue

value: Brain Brodmann Area 9

value: Black

value: Female

value: Cocaine Use Disorder


title: UTHBC0052 BA9

description:
UTHBC0052
BA9_CUD_GEO-counts.csv

tag: cell line


title: H9 cells, belinostat, replicate 3

value: cutaneous T cell lymphoma cells

tag: cell type

value: cell line

value: belinostat

value: 6 hours


title: 6841

description: SureSelectXT

value: bone marrow immune cells

value: tumor plasma cells

tag: genotype


title: H9 cells, romidepsin, replicate 2

value: romidepsin

tag: treatment


title: Testis, in vivo 36.5 dpp, FT, rep2

description:
in_vivo_365_dpp_FT-2
Read length: 50

value: Testis

value: Germ and somatic cells

value: in vivo

tag: state of_tissue


title: Testis, in vitro D4, FT, rep2

description:
in_vitro_D4_FT-2
Read length: 50

value: in vitro


title: 6741

description: SureSelectXT

value: bone marrow

value: BIc


title: NPC-L2C1

description:
NPC-L2C1
counts-cells-GEO_1-26-23.csv

source_name: iPSC-NPC

extract_protocol:
Cells were lifted in Trypsin, Accutase or 10 µM EDTA in PBS without calcium and magnesium, pelleted in 1.5mL tubes and stored at -80oC until use. Fibroblasts were pelleted at 1.5 million cells, iPSCs were pelleted from 2 wells of a 6 well plate at 60-80% confluence, NPCs were pelleted from 2 wells of a 6 well plate at 100% confluence, and neurons were pelleted from 2 wells of each 6 well differentiation plate. RNA was collected from dry frozen pellets using the RNeasy Plus Mini kits (Qiagen, Hilden, Germany).
400ng RNA per sample was used for mRNA library construction using NEBNext® Ultra™ RNA Library Prep Kit (Illumina Inc, San Diego, CA). Paired-end sequencing reads (150bp) were generated on an Illumina HiSeq2000 platform (Novogene Bioinformatics Institute, Chula Vista, CA).
For cell samples: Cells were lifted in Trypsin, Accutase or 10 µM EDTA in PBS without calcium and magnesium, pelleted in 1.5mL tubes and stored at -80oC until use. Fibroblasts were pelleted at 1.5 million cells, iPSCs were pelleted from 2 wells of a 6 well plate at 60-80% confluence, NPCs were pelleted from 2 wells of a 6 well plate at 100% confluence, and neurons were pelleted from 2 wells of each 6 well differentiation plate.
For cell samples: RNA was collected from dry frozen pellets using the RNeasy Plus Mini kits (Qiagen, Hilden, Germany).
For Brain Tissue: RNA was extracted from 50mg of BA9 tissue using RNeasy Plus Mini kits (Qiagen, Hilden, Germany) and RNA integrity number (RIN) was measured for RNA quality (Agilent Bioanalyzer 2100 system, Agilent Technologies, Santa Clara, CA).
For Cells: 400ng RNA per sample was used for mRNA library construction using NEBNext® Ultra™ RNA Library Prep Kit (Illumina Inc, San Diego, CA). Paired-end sequencing reads (150bp) were generated on an Illumina HiSeq2000 platform (Novogene Bioinformatics Institute, Chula Vista, CA).
For Brain Tissue: 1 μg RNA per sample was used for mRNA library construction using NEBNext® Ultra™ RNA Library Prep Kit (Illumina Inc, San Diego, CA).

tag: uthbc subject_id

value: iPSC-NPC

value: untreated

tag: ethnicity

value: White

value: Opioid Use Disorder, severe; Borderline Personality Disorder


title: Testis, in vitro D4, FT, rep1

description:
in_vitro_D4_FT-1
Read length: 50

value: fresh

value: wt


title: H9 cells, vehicle control, replicate 2

value: cutaneous T cell lymphoma cells

value: cell line

value: control


title: 6805

description: SureSelectXT

value: bone marrow immune cells

value: tumor plasma cells


title: H9 cells, romidepsin, replicate 1

value: romidepsin

value: 6 hours


title: NPC-L1C1

description:
NPC-L1C1
counts-cells-GEO_1-26-23.csv

tag: Sex

value: Female

tag: age at_time_of_death


title: Testis, in vivo 36.5 dpp, FT, rep1

description:
in_vivo_365_dpp_FT-1
Read length: 50

value: Testis

value: Germ and somatic cells

value: in vivo


title: 6723

description: SureSelectXT

value: bone marrow

value: MmsetBIc


title: H9 cells, vehicle control, replicate 3


title: Testis, in vivo 22.5 dpp, FT, rep3

description:
in_vivo_225_dpp_FT-3
Read length: 50


title: 6719

description: SureSelectXT


title: UTHBC0029 BA9

description:
UTHBC0029
BA9_CUD_GEO-counts.csv

value: Brain Brodmann Area 9

value: Black

value: Male

tag: postmortem interval_(hours)

tag: rna integrity_number

value: Cocaine Use Disorder


title: UTHBC0049 BA9

description:
UTHBC0049
BA9_CUD_GEO-counts.csv

value: Hispanic

tag: brain cerebellar_ph

tag: postmortem consenus_diagnosis


title: NPC-L2C2

description:
NPC-L2C2
counts-cells-GEO_1-26-23.csv

value: iPSC-NPC

value: untreated

value: White

value: Opioid Use Disorder, severe; Borderline Personality Disorder


title: H9 cells, vehicle control, replicate 1

value: cutaneous T cell lymphoma cells

value: cell line

value: control


title: NPC-L1C2

description:
NPC-L1C2
counts-cells-GEO_1-26-23.csv

value: Female


title: Neuron-L2C1 Day7

description:
Neuron-L2C1 Day7
counts-cells-GEO_1-26-23.csv

source_name: iPSC-Neuron

value: iPSC-Neuron


title: H9 cells, belinostat, replicate 1

value: belinostat

value: 6 hours


title: 6714

description: SureSelectXT

value: bone marrow

value: bone marrow immune cells

value: tumor plasma cells

value: MmsetBIc


title: 6539

description: SureSelectXT


title: Testis, in vivo 22.5 dpp, FT, rep1

description:
in_vivo_225_dpp_FT-1
Read length: 50

value: Testis

value: Germ and somatic cells

value: in vivo

value: fresh

value: wt


title: 733819

source_name: Whole Blood

value: Whole Blood

value: Case


title: Testis, in vivo 10.5 dpp, FT, rep3

description:
in_vivo_105_dpp_FT-3
Read length: 50


title: Neuron-L2C1 Day21 Untreated

description:
Neuron-L2C1 Day21 Untreated
counts-cells-GEO_1-26-23.csv

value: untreated

value: White

value: Opioid Use Disorder, severe; Borderline Personality Disorder


title: Testis, in vivo 10.5 dpp, FT, rep2

description:
in_vivo_105_dpp_FT-2
Read length: 50


title: 741706

value: Female

value: Control


title: H9 cells, belinostat, replicate 2

value: cutaneous T cell lymphoma cells

value: cell line

value: belinostat

value: 6 hours


title: Testis, in vivo 22.5 dpp, FT, rep2

description:
in_vivo_225_dpp_FT-2
Read length: 50


title: 740656

value: Male


title: Neuron-L2C2 Day7

description:
Neuron-L2C2 Day7
counts-cells-GEO_1-26-23.csv

value: iPSC-Neuron


title: 6452

description: SureSelectXT

value: bone marrow

value: bone marrow immune cells

value: tumor plasma cells


title: 6195

description: SureSelectXT

value: BIc


title: 6383

description: SureSelectXT

value: MmsetBIc


title: 6101

description: SureSelectXT


title: 6225

description: SureSelectXT


title: 757828

value: Whole Blood


title: Testis, in vivo 6.5 dpp, CSF, rep2

description:
in_vivo_65_dpp_CSF-2
Read length: 50

value: Testis

value: Germ and somatic cells

value: in vivo

value: controlled slow frozen

value: wt


title: Neuron-L2C2 Day14

description:
Neuron-L2C2 Day14
counts-cells-GEO_1-26-23.csv

value: untreated

value: White

value: Female

value: Opioid Use Disorder, severe; Borderline Personality Disorder


title: Neuron-L2C2 Day21 Untreated

description:
Neuron-L2C2 Day21 Untreated
counts-cells-GEO_1-26-23.csv


title: 788473

value: Control


title: Testis, in vivo 6.5 dpp, FT, rep3

description:
in_vivo_65_dpp_FT-3
Read length: 50

value: fresh


title: Testis, in vivo 6.5 dpp, CSF, rep1

description:
in_vivo_65_dpp_CSF-1
Read length: 50


title: 6392

description: SureSelectXT

value: bone marrow


title: Testis, in vivo 6.5 dpp, CSF, rep3

description:
in_vivo_65_dpp_CSF-3
Read length: 50


title: Neuron-L2C1 Day14

description:
Neuron-L2C1 Day14
counts-cells-GEO_1-26-23.csv

value: iPSC-Neuron


title: Testis, in vivo 10.5 dpp, FT, rep1

description:
in_vivo_105_dpp_FT-1
Read length: 50


title: Neuron-L2C1 Day21 Morphine Treated

description:
Neuron-L2C1 Day21 Treated
counts-cells-GEO_1-26-23.csv

value: 10 micromolar morphine, 7 Days


title: 776612


title: 793203


title: Neuron-L2C2 Day21 Morphine Treated

description:
Neuron-L2C2 Day21 Treated
counts-cells-GEO_1-26-23.csv


title: 6042

description: SureSelectXT

value: bone marrow immune cells

value: tumor plasma cells


title: Testis, in vivo 6.5 dpp, FT, rep2

description:
in_vivo_65_dpp_FT-2
Read length: 50


title: 815855

value: Whole Blood

value: Male


title: Neuron-L1C1 Day7

description:
Neuron-L1C1 Day7
counts-cells-GEO_1-26-23.csv

value: Black

value: Cocaine Use Disorder


title: 5566

description: SureSelectXT

value: MmsetBIc


title: Testis, in vivo 6.5 dpp, FT, rep1

description:
in_vivo_65_dpp_FT-1
Read length: 50

value: Testis

value: Germ and somatic cells

value: in vivo

value: wt


title: 857347


title: 66287

value: Female

value: Case


title: Neuron-L1C1 Day21 Untreated

description:
Neuron-L1C1 Day21 Untreated
counts-cells-GEO_1-26-23.csv

value: untreated


title: Neuron-L1C1 Day21 Cocaine Treated

description:
Neuron-L1C1 Day21 Treated
counts-cells-GEO_1-26-23.csv

value: 10 micromolar cocaine, 7 Days


title: 5277_6577

description: SureSelectXT

value: bone marrow


title: 5278_6578

description: SureSelectXT


title: CPT1a-/- t7 rep 2

first: Andreas

last: Wack

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
Read trimming and adaptor removal was performed with Trimmomatic (v 0.36)
Read alignment was carried out with STAR ( v 2.5.2a) and gene quantification with RSEM( v 1.2.31)
Assembly:
Supplementary files format and content: Table of log transformed normalized counts per gene per sample
Assembly: GRCm38, Ensembl, release 89

source_name: airway epithelia

growth_protocol: Primary cells isolated from tracheas by enzymatic treatment were seeded onto 0.4 μm pore size clear polyester membrane  coated with a collagen solution. At confluence, media was removed from the upper chamber to establish an air- liquid interface (ALI). Cells were collected at day o, 5 and 7 post air-exposure.

extract_protocol: RNA was isolated from MTEC cultures by directly lysing the cells in the transwells, using the Qiagen RNeasy mini kit

value: airway epithelia

tag: strain

value: primary epithelia

value: Cpt1a KO

value: day 7


title: CPT1a-/- t7 rep 3


title: Neuron-L1C1 Day14

description:
Neuron-L1C1 Day14
counts-cells-GEO_1-26-23.csv

value: iPSC-Neuron

value: Male


title: Neuron-L1C2 Day21 Untreated

description:
Neuron-L1C2 Day21 Untreated
counts-cells-GEO_1-26-23.csv

value: Black

value: Cocaine Use Disorder


title: 757813

value: Whole Blood

value: Control


title: 1389

description: SureSelectXT

value: bone marrow immune cells

value: tumor plasma cells

value: BIc


title: CPT1a-/- t5 rep 1

value: day 5


title: 783341


title: 767854

value: Female


title: 1978

description: SureSelectXT


title: CPT1a-/- t5 rep 2


title: 772242


title: CPT1a-/- t7 rep 1


title: 5275_6575

description: SureSelectXT


title: 1162

description: SureSelectXT


title: 1278

description: SureSelectXT


title: Neuron-L1C2 Day14

description:
Neuron-L1C2 Day14
counts-cells-GEO_1-26-23.csv

value: untreated


title: IPSC-L2C1

description:
IPSC-L2C1
counts-cells-GEO_1-26-23.csv

source_name: iPSC

value: iPSC

value: White

value: Opioid Use Disorder, severe; Borderline Personality Disorder


title: 748157


title: 8535-MAFB2IC

description: SureSelectXT

value: bone marrow

value: MafBIc


title: CPT1a-/- t5 rep 3

value: airway epithelia

value: primary epithelia

value: Cpt1a KO


title: Neuron-L1C2 Day21 Cocaine Treated

description:
Neuron-L1C2 Day21 Treated
counts-cells-GEO_1-26-23.csv

value: iPSC-Neuron

value: 10 micromolar cocaine, 7 Days

value: Black

value: Male

value: Cocaine Use Disorder


title: IPSC-L1C1

description:
IPSC-L1C1
counts-cells-GEO_1-26-23.csv


title: CPT1a-/- t0 rep 1

value: day 0


title: 8192-MAFB2IC

description: SureSelectXT

value: bone marrow immune cells

value: tumor plasma cells


title: IPSC-L1C2

description:
IPSC-L1C2
counts-cells-GEO_1-26-23.csv

value: untreated


title: CPT1a-/- t0 rep 3


title: wt T7 rep3

value: wt

value: day 7


title: 832836

value: Whole Blood

value: Case


title: 792261

value: Control


title: 726642


title: wt t5 rep3

value: airway epithelia

value: day 5


title: CPT1a-/- t0 rep 2

value: primary epithelia

value: Cpt1a KO


title: 705919

value: Female


title: IPSC-L2C2

description:
IPSC-L2C2
counts-cells-GEO_1-26-23.csv

value: iPSC

value: White

value: Opioid Use Disorder, severe; Borderline Personality Disorder


title: HK-2-WT-3

city: Zhanjiang

first: Ji-Xin

last: Tang

address: No.57, Renmin Avenue

institute: Affiliated Hospital of Guangdong Medical University

data_processing:
Transcriptome sequencing procedures include RNA extraction, RNA sample quality detection, library construction, library purification, li-brary detection, library quantification, generation of sequencing clusters, and comput-er sequencing. In order to ensure the accuracy and reliability of source data, we carried out strict quality control for each step of the experimental process.
Different libraries were mixed according to the requirements of effective concen-tration and target data volume and then sequencing by Illumina.
Bcl2fastq (v2.17.1.14) was used for image Base Calling for preliminary quality analysis to obtain the original sequencing Data (Pass Filter Data), and the results were stored in FASTQ file format. It contains sequencing sequence information and its corresponding sequencing quality information. The sequencing data quality was evaluated by FastQC (v0.10.1) software.
Raw data was preprocessed using Cutadapt (version 1.9.1) software and low quality data was filtered to remove contamination and joint sequences. The filtered sequenc-ing Clean Data was compared with the reference genome for analysis.
Hisat2(v2.0.1) software was used to compare short reads with the default parameters. Gene expres-sion was calculated using Cuffdiff software (v2.2.1), which calculated gene expression using FPKM (Fragments Per Kilo bases per Million reads)[38]. Genetic difference anal-ysis was performed using cuffdiff(v2.2.1), which was based on a negative binomial distribution model. The detection results were screened according to the differential significance criteria (differential gene expression changes of more than 2 times and qvalue(fdr, padj<=0.05), and the down-regulation of significant differential gene ex-pression was counted.
Assembly: Homo_sapiens.GRCh37
Supplementary files format and content: all.fpkm_anno.txt contains the count value and fpkm value of each sample, and the corresponding gene ID.

extract_protocol:
Total cellular RNA was extracted from cultured cells using RNAiso Plus (Takara, 9108, Japan) according to the manufacturer’s protocol.
The RNA concentra-tion and purity were quantified using NanoDrop 2000 ultrafine spectrophotometer (Thermo Scientific, Massachusetts, America). And then the genome DNA was elimi-nated with the RNase-free DNase H. The RNA was then reverse-transcribed with 5× FastKing-RT SuperMix kit (TIANGEN, KR118–01, Beijing, China) according to the manufacturer’s protocols. The reverse-transcribed cDNA was used as template for qPCR using Genious 2X SYBR Green Fast qPCR Mix (ABclonal, RK21204) according to the manufacturer’s protocol. LightCycler 480 II real-time fluorescence quantitative PCR instrument was used for PCR reaction. The primer sequences used for amplifying the target fragments and GAPDH as internal control were listed in Table1. Gene’s rela-tive expression levels were calculated by the 2-ΔΔCt (threshold cycle) method.

value: WT


title: 745396

extract_protocol:
RNA was isolated using the PAXgene whole blood RNA kit (Qiagen Inc).
Poly-adenylated RNAs were isolated using NEBNext Magnetic Oligo d(T)25 beads. Libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina Inc). Each library was pair-end sequenced  by using the TruSeq SBS Kit v4-HS (Illumina, Inc.), on a Illumina platform
Poly(A) RNA selection RNA-Seq


title: 800113

value: Male


title: 8074-MAFB2IC

description: SureSelectXT

value: bone marrow

value: bone marrow immune cells

value: tumor plasma cells

value: MafBIc


title: wt T7 rep2

value: wt

value: day 7


title: Fibroblast-2

description:
Fibroblast-2
counts-cells-GEO_1-26-23.csv

source_name: Postmortem Dermal Fibroblasts

value: Postmortem Dermal Fibroblasts

value: untreated


title: 3191-CD1B2IC

description: SureSelectXT


title: HK-2-WT-2


title: HK-2-KO-ZKSCAN3-3


title: HK-2-WT-1


title: 5629-CD1B2IC

description: SureSelectXT


title: 3075-CD1B2IC

description: SureSelectXT


title: Fibroblast-1

description:
Fibroblast-1
counts-cells-GEO_1-26-23.csv

value: Black

value: Cocaine Use Disorder


title: 60213

value: Whole Blood

value: Control


title: 115185


title: 738442

value: Female


title: HK-2-KO-ZKSCAN3-2


title: 68497


title: wt t5 rep2

value: airway epithelia

value: primary epithelia

value: day 5


title: YFP-47

description: SureSelectXT


title: 66651


title: wt t0 rep2

value: day 0


title: 5302-B2IKC

description: SureSelectXT

value: bone marrow

value: KrasBIc


title: 12598-VKMYC

description: SureSelectXT

value: bone marrow immune cells

value: tumor plasma cells


title: wt T7 rep1

value: wt


title: 6425-B2IKC

description: SureSelectXT


title: Hela-WT-3

source_name: Hela

value: Hela

value: WT


title: wt t0 rep3


title: wt t5 rep1


title: sc20_B2IC

description: SureSelectXT

value: BIc


title: HK-2-KO-ZKSCAN3-1


title: wt t0 rep1


title: 6434_B2IKC

description: SureSelectXT


title: Hela-WT-2


title: 776984


title: Hela-WT-1


title: 766608

value: Male


title: 739719


title: 33315


title: MTEC ALI t0 rep3

description:
ALI t0
CRO118A9_S11_L001

data_processing:
Read trimming and adaptor removal was performed with Trimmomatic (v 0.36)
Read alignment was carried out with STAR ( v 2.5.2a) and gene quantification with RSEM( v 1.2.31)
Assembly: GRCm38, Ensembl, release 89
Supplementary files format and content: Table of log transformed normalized counts per gene per sample

growth_protocol: Primary cells isolated from tracheas by enzymatic treatment were seeded onto 0.4 μm pore size clear polyester membrane  coated with a collagen solution. At confluence, media was removed from the upper chamber to establish an air- liquid interface (ALI). Cells were collected at day 10 post air-exposure.

extract_protocol:
RNA was isolated from sorted cells  , using the Qiagen RNeasy mini kit
RNA (200 ng) was used to prepare cDNA libraries using the TruSeq Stranded mRNA HT Library Preparation Kit (Illumina). Libraries were normalized, pooled and then clustered using the HiSeq® 3000/4000 PE Cluster Kit (Illumina). The libraries were imaged and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq® 3000/4000 SBS kit (Illumina) at a minimum of 25 million paired-end reads (75 bp/100 bp) per sample.

treatment_protocol: Cultures were trypzinazed and sorted into CD49f+NGFR+ and CD49f-NGFR- subsets

tag: cell subtype

value: MTEC


title: 771899

data_processing:
Basecalls were performed using bcl2fastq v2.18.12
Raw sequence files were trimmed using Trim Galore (version 0.6.0) using parameters --paired --trim1 --trim-n
Trimmed sequence files were aligned using STAR (version 2.7.4a) using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from alignment files using HTSeq-count (version 0.11.1) using parameters -m union -r pos - t exon -i gene_id -a 10 -s no -f bam
DESeq2 was used for normalization and pairwsie differential expression following the authors vignette
Assembly: Gencode GRCh38 p7 Release 25
Supplementary files format and content: tab-delimited txt file containing Ensembl ID #s for each gene in each sample

value: Whole Blood


title: 3869_MMSETB2IC

description: SureSelectXT

value: MmsetBIc


title: 3426_B2IKC

description: SureSelectXT


title: YFP-49

description: SureSelectXT


title: 6430_B2IKC

description: SureSelectXT


title: CD49f+NGFR+ cells rep 3

description:
ALI t10 sorted
CRO118A3_S3_L001


title: 6174_PB2IC

description: SureSelectXT


title: Hela-KO-ZKSCAN3-2


title: CD49f-NGFR- cells rep1

description:
ALI t10 sorted
CRO118A4_S4_L001


title: CD49f-NGFR- cells rep3

description:
ALI t10 sorted
CRO118A6_S6_L001


title: Hela-KO-ZKSCAN3-1


title: 3086_MMSETB2IC

description: SureSelectXT


title: CD49f-NGFR- cells rep2

description:
ALI t10 sorted
CRO118A5_S5_L001


title: Hela-KO-ZKSCAN3-3


title: 711532

value: Female

value: Control


title: YFP-48

description: SureSelectXT


title: 741121


title: YFP-42

description: SureSelectXT


title: CD49f+NGFR+ cells rep 2

description:
ALI t10 sorted
CRO118A2_S2_L001

value: airway epithelia

value: primary epithelia


title: 700711


title: 756527


title: 751008


title: Mutant 2 [Fb_S3]

first: Fei

last: Pei

address: 2250 Alcazar St

institute: USC

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were trimmed and aligned using TopHat (Version 2.0.8) with the mm10 genome
RPKM was used to normalize the data and differential expression was calculated by selecting transcripts that changed with p < 0.05
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include lognormal with shrinkage mean value for each feature in individual sample.

source_name: incisor

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol:
Incisor samples from Fgfr1fl/fl (control) and Gli1-Cre;Fgfr1fl/fl (mutant) mice were collected 1 week after TMX for RNA isolation with RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol
cDNA library preparation and sequencing were performed at the Technology Center for Genomics & Bioinformatics at the University of California, Los Angeles (UCLA).

treatment_protocol: Not applicable

tag: genotype/variation

value: incisor

tag: age


title: YFP-43

description: SureSelectXT

tag: tissue

value: bone marrow

tag: cell line


title: Fzd6 Wild Type-Tomato replicate 1, scRNAseq

city: New Haven

first: Barani Kumar

last: Rajendran

state: CT

address: 10 Amistad Street, New Haven, , Yale University

department: Pharmacology

institute: Yale University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.1.0 (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: lung

extract_protocol:
Mouse right ventricles were perfused with 10 ml of PBS, excised, gently disrupted by teasing and resuspended in RPMI-1640 medium supplemented with 250 U/ml of collagenase, 400 U/ml elastase and 50 U/ml of DNAse. Lungs were then enzymatically digested for 40 min at 37oC. Dispersed cells were filtered through a 70-μm cell strainer to eliminate clumps and debris, and erythrocytes were lysed using lysing buffer. Cells in single cell suspension were resuspend cells in cold 0.1% BSA/PBS. Following live/dead staining with viability dye (Fixable Viability Dye eFluor 506, eBioscience), cells were incubated with a Fc-blocking reagent (BD Biosciences) for 5 minutes at 4 oC and then incubated with an anti-CD45.2 mAb-PE-Cy7 antibodies for 1 hour at 4oC. Cells were sorted using a 100 μm nozzle and 40 psi pressure (FACSAria instrument, BD Biosciences).
Single-cell 3’ RNA-seq libraries were prepared using Chromium Single Cell V3 Reagent Kit and Controller (10x Genomics). Libraries were assessed for quality and then sequenced on HiSeq 4000 instruments (Illumina).

tag: cell type

value: CD45-negative and Tdtomat-positive cells sorted from lung digest

value: lung

tag: genotype

value: 12 weeks


title: Fzd6 Knock-Out-Tomato replicate 1, scRNAseq

description: 10x Genomics


title: Pool1-B2IC

description: SureSelectXT

value: bone marrow immune cells

value: tumor plasma cells

value: MGUS pool1 BIc


title: MTEC ALI t0 rep1

description:
ALI t0
CRO118A7_S7_L001

value: wt


title: CD49f+NGFR+ cells rep 1

description:
ALI t10 sorted
CRO118A1_S1_L001


title: Mutant 3 [Fc_S4]


title: MTEC ALI t0 rep2

description:
ALI t0
CRO118A8_S8_L001


title: 746908

first: Smita

address: 1600 7th Avenue South Lowder 500

institute: University of Alabama at Birmingham

tag: treatment

value: Case


title: WTCD45 positive replicate 1, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (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: Lung

value: CD45-positive cells sorted from lung digest

value: Lung

value: Fzd6 (fl/fl)

value: 14 weeks old


title: Pool2-B2IC

description: SureSelectXT

value: MGUS pool2 BIc


title: WTCD45 negative replicate 1, scRNAseq

description: 10x Genomics

value: CD45-negative cells sorted from lung digest


title: MIC71

description: SureSelectXT

value: MIc


title: Mutant 1 [Fa_S2]

value: incisor


title: 61948

value: Whole Blood

value: Female

value: Control


title: 776270


title: Control 1 [Ctrl_2_S1]

value: wild type


title: Control 3 [Ctrl_4_S3]


title: Control3

description: SureSelectXT

value: bone marrow

value: bone marrow immune cells


title: MIXPB2ICCPMGUS

description: SureSelectXT

value: tumor plasma cells

value: MGUS pool Trp53BIc


title: 747703


title: 9530_B2IKC

description: SureSelectXT

value: KrasBIc


title: KOCD45 negative replicate 1, scRNAseq

description: 10x Genomics

value: Fzd6 (fl/fl)Mx1Cre


title: IFITM3 KO rep3

city: Columbus

first: Jacob

last: Yount

state: OH

address: 460 W 12th Ave, BRT 790

department: Microbial Infection and Immunity

institute: The Ohio State University

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt file with  normalized counts for each sample and each gene, includes gene annotations
Supplementary_files_format_and_content: csv file with raw counts for each sample and each gene

extract_protocol:
TRIzol RNA extraction from lung tissue.
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was loaded onto the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

value: IFITM3 KO

value: lung

tag: infection

tag: time

value: 2 day post infection


title: Control 2 [Ctrl_3_S2]


title: MIX_PB2IC_CP-

description: SureSelectXT

value: CP- control


title: 781270

last: Bhatia


title: MIC70

description: SureSelectXT


title: 111102

value: Male

value: Case


title: 782428


title: 783376


title: KOCD45 positive replicate 1, scRNAseq

description: 10x Genomics

value: CD45-positive cells sorted from lung digest

value: Lung

value: 14 weeks old


title: IFITM3 KO rep1


title: 778787

value: Whole Blood


title: end-stage split-seq library 3

city: London

first: Athanasios

last: Dimitriadis

address: 33 Cleveland Street

institute: MRC Prion Unit at UCL

description: SPLiT-seq

data_processing:
The fastq files were aligned to the mouse genome using STAR aligner. The resulting sam files were converted to a binary format and were processed by the SPLiT-seq bioinformatics open-source tools (https://github.com/yjzhang/split-seq-pipeline) to generate a count matrix. Transcriptome GRCm39 (mm39) was used for aligning the mouse data. The count matrix generated was used as an input for the subsequent analyses.
Assembly: mm39
Supplementary files format and content: comma-separated values files and matrix files

source_name: Brain frontal lobe

extract_protocol:
Flash-frozen mouse brain was left to partially thaw. The olfactory bulb removed, and a small slice of the frontal cortex was cut and transferred to a glass 2 mL dounce tissue homogenizer on ice. All following steps were carried out on ice and using ice-cold solutions. All centrifugation steps were performed at 500 g for 5 minutes at 4oC using a pre-chilled centrifuge, unless otherwise specified. 2 mL of Nuclei EZ prep was added, and tissue was homogenised using 20 strokes of the loose and 20 strokes of the tight pestle. The suspension was transferred to a 15 mL tube and 2 mL of Nuclei EZ prep was added. The suspension was incubated for 5 minutes and then centrifuged. The supernatant was discarded, 4 mL of Nuclei EZ prep was added, and the pellet was resuspended using a P1000 pipette. The suspension was incubated for 5 minutes and then centrifuged. The supernatant was discarded, and the pellet was resuspended in 4 mL Nuclei Suspension Buffer (NSB; 1x PBS, 0.01% BSA (Cambridge Bioscience; 227-10210) and 0.1% NxGen RNAse inhibitor (Lucigen; 30281-2)). The suspension was centrifuged, the supernatant discarded, and the pellet resuspended in 1 mL NSB. The suspension was filtered through a 35 um filter (Fisher Scientific; 10585801), and stored on ice. For nuclei fixation, 3 mL of 1.33% formalin solution were added to the 1 mL of nuclei suspension. The suspension was incubated on ice for 10 minutes. 169 uL of 5% Triton-X was added to the fixed nuclei, the solution was mixed by pipetting and then incubated on ice for 3 minutes. Nuclei were centrifuged at 500g for 5 minutes at 4oC, supernatant was discarded, and the pellet was resuspended in 500 uL cold NSB. 500 uL of cold 100 mM Tris and 20 uL of 5% Triton-X were added. Nuclei were centrifuged again under the same conditions; supernatant was discarded, and the pellet was resuspended in 400 uL of cold 0.5X PBS. Nuclei were filtered through a 35 um filter, counted using a Neubauer-Improved haemocytometer, and diluted to a final concentration of 2000 nuclei/uL using cold 0.5x PBS supplemented with 0.2 units/uL SUPERase In RNAse inhibitor. The nuclei were stored frozen at -80oC until library preparation.
Sequencing libraries from the mouse brain samples were prepared using the SPLiT-seq protocol (version 3) (Rosenberg et al. 2018). A summary of the methodology and optimisations is given below.
For the reverse transcription, 4 uL the first 24 wells of Stock plate 1 were transferred to a new PCR plate on ice. 8 uL of RT mix (per reaction: 4 uL Maxima 5x RT buffer, 0.124 uL NxGen RNAse inhibitor, 0.25 uL SUPERase In, 1 uL 10 mM Takara dNTPs, 2 uL Maxima H minus enzyme, 0.625 uL H2O) was added to each well and then 8 uL of fixed nuclei suspension. The plate was placed in a thermocycler and PCR was carried out as per protocol instructions. All wells were then pooled together, Triton-X was added to a final concentration of 0.1% and suspension was centrifuged for 3 minutes at 500g. The supernatant was discarded, and nuclei were resuspended in 2 mL 1x NEBuffer 3.1 (New England Biolabs; B7203S) + 20uL NxGen RNase Inhibitor.
For ligation round 1, the ligation mix (1337.5 uL water, 500 uL 10x T4 ligase buffer (included with ligase enzyme), 100 uL T4 DNA Ligase (New England Biolabs; M0202L), 100 uL BSA 10 mg/mL, 12.5 SUPERase In, 40 uL NxGen RNAse inhibitor) was added to the nuclei suspension and into a basin. 40 uL of the suspension were pipetted in each well of the Ligation round 1 barcode plate and the plate was incubated in a plate shaker at 37oC for 30 minutes and 300 rpm rotation. Then 10 uL of the Ligation Round 1 blocking solution (316.8 uL 100 uM BC_0216, 300 uL 10x Ligase buffer, 583.2 uL water) were added to each well and the plate was incubated again under the same conditions.
For ligation round 2, the nuclei suspensions were pooled in a 15 mL Falcon and passed through a 40 um strainer to another Falcon. 100 uL T4 DNA ligase was added and the mix was transferred to a basin. 50 uL of the mix was added to each well of the Ligation Round 2 barcode plate. The plate was incubated as previously. Then 20 uL of the Ligation Round 2 blocking solution (369 uL 100 uM BC_0066, 800 uL 0.5 M EDTA, 2031 uL water) was added to each well. The wells were pooled in a 15 mL Falcon and passed through a 40 um strainer into another Falcon.
70 uL 10% Triton-X was added to the mix and nuclei were centrifuged for 5 minutes at 1000g. The supernatant was aspirated, and nuclei were washed with 4 mL wash buffer (4 mL 1x PBS, 40 uL 10% Triton-X, 10 uL SUPERase In) and centrifuged again under the same conditions. Supernatant was aspirated and nuclei were resuspended in 100 uL 1x PBS + 2 uL SUPERase In. Nuclei were counted using a Neubauer-Improved haemocytometer and a desired number of them was aliquoted in each 1.5 mL Eppendorf tube. PBS was used to fill each tube up to 50 uL. Each tube is referred to as a “sublibrary”.
For nuclei lysis, 50 uL 2x lysis buffer (final concentrations: 20 mM Tris pH 8, 400 mM NaCl, 100 mM EDTA pH 8, 4.4% SDS (Thermo Fisher Scientific; AM9822)) were added to each tube followed by 10 uL 20 mg/mL Proteinase K. The mix was incubated at 55oC for 2 hours with shaking at 300 rpm. Lysates were frozen at -80oC and processed the following day.
5 uL 100 uM AEBSF (Abcam; ab141403) was used to stop proteinase reaction. Dynabeads MyOne Streptavidin C1 (Thermo Fisher Scientific; 65002) were washed and used to bind the barcoded transcripts as per protocol. Beads were resuspended in 200 uL Template Switch mix (88 uL water, 44 uL 5x Maxima buffer, 44 uL 20% Ficoll PM-400, 22 uL 10 mM Takara dNTPs, 5.5 uL NxGen RNAse inhibitor, 5.5 uL 100 μM Template Switch Oligo, 11 uL Maxima H minus enzyme) and incubated at a rotating incubator at room temperature for 30 minutes and at 42oC for 1.5 hours.
The sample was then washed, resuspended in PCR mix (121 uL 2x Kapa Hifi Master Mix, 9.68 uL 10 uM BC_0108, 9.68 uL 10 uM BC_0062, water up to 242 uL) and split equally in 4 different wells of a PCR plate. The following PCR programme was then used: 3 min at 95oC, then 20 s at 98oC, 45 s at 65oC, 3 min at 72oC for a total of 5 cycles, and then hold at 4oC. Reactions were combined in a single tube, cleaned with 0.6x AMPure XP beads as per manufacturer’s instructions, eluted in 20 uL water, mixed with 180 uL of the same PCR mix and split in 4 wells (50 uL per well). 2.5 uL EvaGreen (Biotium; #31000) was added to each well and amplification continued in a QuantStudio 7 Flex qPCR machine (Thermo Fisher Scientific) until signal plateaued out of exponential amplification using the following programme: 3 min at 95oC, then 20 s at 98oC, 20 s at 67oC, 3 min at 72oC until signal plateaus out of exponential amplification, then 5 min at 72oC, hold at 4oC. Reactions were combined in a single tube, cleaned with 0.6x AMPure XP beads as per manufacturer’s instructions, eluted in 10 uL water and analysed at TapeStation 2200 using a gDNA tape.
600 pg of each sample was used for tagmentation using the Nextera XT sample prep kit using custom primers one of BC_0076-BC_0083 and BC_0118, according to manufacturer’s instructions. Resulting libraries were analysed on a TapeStation 2200 using a high sensitivity D1000 tape or a high sensitivity D5000 tape.

value: Brain frontal lobe

tag: days post_inoculation

value: variable

tag: Sex

value: Female

value: FVB/NHan Hsd


title: 9275

description: SureSelectXT

value: bone marrow

value: bone marrow immune cells

value: tumor plasma cells


title: IFITM3 KO rep2

value: IFITM3 KO


title: 120dpi split-seq library 3

description: SPLiT-seq


title: end-stage split-seq library 1

description: SPLiT-seq


title: 8994_MIC

description: SureSelectXT

value: MIc


title: WT rep2

value: WT

value: lung

value: 2 day post infection


title: 82494

city: Birmingham

value: Male

value: Control


title: end-stage split-seq library 2

description: SPLiT-seq


title: WT rep3


title: 120dpi split-seq library 2

description: SPLiT-seq


title: 769663

value: Case


title: 80dpi split-seq library 2

description: SPLiT-seq


title: 8795_CMAFB2IKC

description: SureSelectXT

value: MafBIc


title: 120dpi split-seq library 1

description: SPLiT-seq


title: 758535

value: Whole Blood


title: 80dpi split-seq library 1

description: SPLiT-seq

value: Brain frontal lobe


title: 72844


title: 761525