title: AVLF_R3b: Aortic Insufficienty rep3b

value: Heart failure, severe mitral and tricuspid valve regurgitation, coronary disease, hypertension


title: Baseline-WT-3

status: Public on Jul 01 2020

type: SRA

city: Leuven

first: Massimiliano

last: Mazzone

address: Herestraat 49

country: Belgium

institute: VIB

description: countData.txt

library_source: transcriptomic

data_processing:
Single-end 75bp reads were quality checked using FastQC (0.11.7) and low quality base calls and adapter contaminations were trimmed using Cutadapt (1.18)
Reads were aligned to the mm10 genome build using HISAT2 (2.1.0)
After an aditional round of quality check with FastQC (0.11.7), read counts were summarized at the gene level using featureCounts of the subread suite (1.6.2)
Genome_build: mm10
Supplementary_files_format_and_content: txt file containing raw read counts summarized on the gene level

molecule: total RNA

organism: Mus musculus

source_name: Muscle

extract_protocol:
Muscles were removed, and macrophages were sorted as F4/80+ , and RNA was harvested using Qiagen Rneasy Micro Kit (Cat#74004).
SMART-Seq V4

tag: cell type

value: Muscle associated macrophages

tag: tissue

value: Normal Muscle

tag: genotype

value: WT


title: Patient P3-derived PDOX rep 1 [P3_X1]

type: RNA

city: Luxembourg

first: Anna

last: Golebiewska

state: Strassen

address: 84 Val Fleuri

department: Department of Oncology

country: Luxembourg

institute: Luxembourg Institute of Health

hyb_protocol: Upon hybridization, microarrays were washed, stained and scanned according to manufacturer’s standard procedures

scan_protocol: Microarrays were scanned with Affymetrix GeneChip Scanner GCS3000 system according to manufacturer standard procedures. Affymetrix GeneChip Command Console Scan Control 4.0.0.1567 was used for image processing

data_processing: Affymetrix CEL files containing hybridization raw signal intensities were processed to gene expression signals using the RMA (robust multichip average) algorithm implemented in the oligo package (version 1.44.0). hugene10sttranscriptcluster.db package version 8.7.0 was then used to map Affymetrix ID to entrez gene ID.

label: Biotin

organism: Homo sapiens

source_name: Human GBM PDOX

label_protocol: the Affymetrix WT Terminal & Labeling kit before being hybridized on Affymetrix arrays according to the manufacturer’s instructions (protocol P/N 702808 Rev.6)

extract_protocol: Total RNA was extracted using the QIAGEN® RNeasy Mini Kit according to the manufacturer’s protocol

tag: tissue/cell type

value: GBM tumor cells grown in mouse brain

tag: sample type

value: FACS-sorted human tumor Cell culture


title: m1_AY_Y3_K18

city: Stanford

first: Michelle

middle: Berkeley

last: Chen

address: 318 Campus Drive

country: USA

institute: Stanford

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: raw count table

source_name: three-mo mouse BEC

growth_protocol: Mice 3 (young)

extract_protocol:
Brain tissues were dissected using Miltenyi neural dissociation kit. Brain endothelial cells were isolated via FACS.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary murine brain endothelial cells


title: AVLF_R3a: Aortic Insufficienty rep3a

city: Palo Alto

first: Kevin

middle: James

last: Jaatinen

state: CA

address: 870 Quarry Rd Ext

department: Cardiothoracic Surgery

institute: Stanford University

data_processing:
The raw sequencing reads were cleaned by removing low-quality reads, adapters, and reads with >10% N.
The reference genome and gene model annotation files were downloaded from human genome websites (http://www.ncbi.nlm.nih.gov, http://uswest.ensembl.org/Homo_sapiens, http://genome.ucsc.edu). Indexes of the reference genome were built using Bowtie v2.0.6
Paired-end clean reads were aligned to the reference genome using STAR.
HTSeq v0.6.1 was used to count the read numbers mapped to each gene.
Fragments per kilobases per million (FPKM) were calculated to estimate the level of gene expression.
Differential gene expression analysis was performed using the DESeq2 R package
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

source_name: Tricuspid Aortic Valve Leaflets

extract_protocol:
Normal control aortic valves were collected from non-matched transplant donor hearts. AS and AI aortic valves were collected from patients undergoing elective aortic valve replacement at our hospital. Total RNA was extracted from the aortic valve leaflets using the PureLink™ RNA Minikit (Thermo Fisher Scientific, USA) with on-column DNAse digestion according to the manufacturer’s instructions. A 10-minute proteinase K digestion was added during the lysis step to further homogenize the tissue. RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent, USA). RNA integrity scores were between 7.4 and 9.2.
A complementary DNA (cDNA) strand-specific library was created in duplicate using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs Inc, USA). After library construction, samples were diluted and quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA). cDNA insert size was detected using an Agilent 2100 Bioanalyzer (Agilent, USA). Library quality was assessed by quantitative polymerase chain reaction (qPCR) ensuring effective concentration >2 nM.
cDNA libraries were sequenced using Illumina HiSeq 2500 (Illumina®, USA). 150-bp paired-ends reads were generated with approximately 30 million reads per sample. Sequencing was performed in duplicate for each sample.

value: Tricuspid Aortic Valve Leaflets

tag: age

tag: Sex

value: M

tag: bmi

tag: degree of aortic valve disease

value: Severe AI

tag: left ventricle ejection fraction

tag: other medical history


title: Patient P3-derived PDOX rep 3 [P3_X3]


title: Patient T101-derived PDOX rep 2 [T101_X2]

value: Tumor tissue


title: Patient T101-derived PDOX rep 1 [T101_X1]


title: Patient T16-derived PDOX [T16_X]


title: Baseline-WT-2

description: countData.txt


title: CTX-KO-4

description: countData.txt

value: CTX injected Muscle

value: GLUD1 KO


title: AVLF_R2b: Aortic Insufficienty rep2b

value: 5.3 cm dilated aortic root, heart failure, coronary disease, hypertension, atrial fibrillation


title: m1_Young2_K15


title: m1_Young1_D14


title: CTX-KO-3

description: countData.txt


title: AVLF_R1b: Aortic Insufficienty rep1b

value: Moderate AI

value: Coronary disease, hypertension, atrial fibrillation


title: AVLF_R2a: Aortic Insufficienty rep2a


title: m1_AY_Y3_A7


title: m1_AY_Y3_B4


title: AVLF_S5b: Aortic Stenosis rep5b

value: F

value: Severe AS

value: Prior coronary bypass surgery, diabetes, hypertension, atrial fibrillation


title: AVLF_R1a: Aortic Insufficienty rep1a


title: CTX-KO-1

description: countData.txt

value: Muscle associated macrophages


title: Patient P3 [P3_B]

source_name: Human GBM patient tumor sample

value: GBM tumor sample


title: Patient P13 [P13_B]

value: GBM tumor cells grown in mouse brain


title: m1_Young1_L6


title: CTX-WT-4

description: countData.txt

value: WT


title: Patient P8 [P8_B ]


title: Patient T185 [T185_B]


title: CTX-WT-3

description: countData.txt


title: Patient T101 [T101_B ]


title: m1_AY_Y3_M6

value: primary murine brain endothelial cells


title: AVLF_S5a: Aortic Stenosis rep5a

value: Tricuspid Aortic Valve Leaflets


title: m1_Young2_B5


title: AVLF_S4b: Aortic Stenosis rep4b

value: M

value: Heart failure, moderate mitral valve regurgitation, severe tricuspid valve regurgitation, hypertension, atrial fibrillation


title: CTX-KO-2

description: countData.txt


title: Normal brain rep 2 [NB_2]

source_name: Human normal brain RNA

value: normal brain

value: Control RNA


title: Normal brain rep 1 [NB_1]


title: CTX-WT-2

description: countData.txt

value: CTX injected Muscle


title: AVLF_S6b: Aortic Stenosis rep6b

value: Coronary disease, diabetes, hypertension, sick sinus syndrome


title: CTX-WT-1

description: countData.txt


title: m1_AY_Y3_O11


title: m1_Young1_F2


title: mESC_ATAC-seq_2iL_rep3

city: Guangzhou

first: Yiwei

last: Lai

state: Guangdong

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine Key Laboratory of Regenerative Biology, CAS

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

library_source: genomic

data_processing:
Illumina bcl2fastq2.17 software was used for base-calling.
Adapter and transposon sequence were trimmed using cutadapt(v 1.1.8).
Data were first aligned to the mm10 mouse genome assembly using Bowtie2 (v2.2.5) with the settings ‘--very-sensitive’. Low quality mapped reads were removed using Samtools with the settings ‘-q 30’. Duplicated reads were collapsed using Picard.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage script of deepTools with the options “ --binSize 10 --normalizeUsingRPKM”.

molecule: genomic DNA

source_name: mouse embryonic stem cells

growth_protocol: ESCs in SL medium were cultured in DMEM/high glucose containing 15% FBS, GlutaMax, nonessential amino acids, sodium pyruvate, β-mercaptoethanol, and 1,000 U/ml LIF on mitomycin-C treated mouse embryonic fibroblasts (MEFs), and they were split onto 0.2% gelatin pre-coated plates prior to the experiment. ESCs in 2iL medium were cultured in a 1:1 mix of DMEM/F12  and Neurobasal medium, with N2 and B27 supplements, GlutaMax, nonessential amino acids, sodium pyruvate, β-mercaptoethanol, 1,000 U/ml LIF, 3 μM, and 1 μM PD0325901 on 0.2% gelatin pre-coated plates.

extract_protocol: A total of 50,000 cells were washed once with cold PBS and re-suspended in 50 μl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) IGEPAL CA-630). The suspension were then centrifuged at 500 g for 10 min at 4°C, following by addition of 50 μl transposition reaction mix of TruePrep DNA Library Prep Kit. Then, samples were incubated at 37°C for 30 mins. Transposition reactions were cleaned up using a MinElute PCR Purification Kit. ATAC-seq libraries were subjected to 5 cycles for pre-amplification and then amplified by PCR for an appropriate number of cycles. The amplified libraries were purified with a QIAquick PCR Purification Kit. Libraries were sequenced on a NextSeq 500 using a NextSeq 500 High Output Kit v2 (150 cycles) according to the manufacturer’s instructions.

value: mouse embryonic stem cells

tag: culture condition

value: cultured with inhibitors of MEK and GSK3 (2iL)


title: Normal liver 1

city: Bronx

first: Sanjeev

last: Gupta

state: NY

address: 1300 Morris Park Ave.

department: Medicine

institute: Albert Einstein College of Medicine

description: Gene expression data from normal sample

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HuGene-1_ST-v1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affy Gene Chip Scanner 3000 7G.

data_processing: The gene expression data were analyzed with Transcriptome Analysis Console (TAC 4.0) (Affymetrix, Applied Biosystems by Thermofisher Scientific) with summarization by the robust multi-array analysis approach (RMA).

label: biotin

source_name: FFPE adult liver sections

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted from FFPE sections with RecoverAll Total Nucleic Acid Isolation kit (Ambion, cat. #AM1975) according to the manufacturer's instruction manual

value: Liver

tag: disease state

value: normal


title: Patient T16 [T16_B]

value: Tumor tissue


title: AVLF_S2b: Aortic Stenosis rep2b

value: F

value: Severe AS

value: Hypertension


title: AVLF_S6a: Aortic Stenosis rep6a


title: m1_AY_Y3_E2


title: Normal liver 2

description: Gene expression data from normal sample


title: Normal liver 3

description: Gene expression data from normal sample


title: mESC_ATAC-seq_2iL_rep1


title: AVLF_S4a: Aortic Stenosis rep4a


title: AVLF_S2a: Aortic Stenosis rep2a


title: m1_AY_Y3_B18


title: m1_Young1_L17


title: m1_Young1_C10


title: mESC_ATAC-seq_SL_rep3

value: cultured with serum/LIF (SL)


title: mESC_ATAC-seq_SL_rep2


title: ALF liver 3

description: Gene expression data from ALF sample

value: acute liver failure


title: AVLF_S1a: Aortic Stenosis rep1a

source_name: Bicuspid Aortic Valve Leaflets

value: Bicuspid Aortic Valve Leaflets

value: Bicuspid aortic valve, coronary disease, hypertension


title: mESC_ATAC-seq_SL_rep1


title: m1_Young1_K1

value: primary murine brain endothelial cells


title: AVLF_S1b: Aortic Stenosis rep1b


title: m1_AY_Y3_G1


title: ALF liver 1

description: Gene expression data from ALF sample


title: ALF liver 2

description: Gene expression data from ALF sample


title: mESC_ATAC-seq_2iL_rep2


title: m1_Young2_A8


title: m1_AY_Y3_K5


title: AVLF_D5a: Normal Control rep5a

value: Tricuspid Aortic Valve Leaflets

value: Normal

value: Intracranial hemorrhage


title: MDA_112

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 47231 probes on the Human-H12 V4.0 were used.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: disease

value: hepatocellular carcinoma (HCC)


title: AVLF_D4: Normal Control rep4b

value: Tonsillar herniation after drug overdose


title: AVLF_D4a: Normal Control rep4a


title: m1_Young1_E16


title: m1_Young2_E5


title: Uncorrected

city: Boston

first: George

last: Murphy

state: MA

address: 670 Albany Street

institute: Center for Regenerative Medicine of Boston University and Boston Medical Center

description: total RNA

data_processing:
Due to the limited length of R1 reads, they were discarded from the analysis. R2 Reads were demultiplexed using a script provided by Fluidigm and aligned to the human genome (hg19) and quantified using the STAR aligner
Genome_build: hg19
Supplementary_files_format_and_content: raw counts matrix, cell metadata

source_name: day 16 ATTR amyloidosis patient-specific iPSC-derived HLCs

extract_protocol:
Day 16 corrected and uncorrected TTR-L55P HLCs were exposed to 0.25% trypsin for approximately 10 minutes. After trypsinization, inactivation reagent (50% IMDM, 50% FBS) was added to each well and gently pipetted to dislodge cells. Cells were centrifuged at 200 x g at 4ºC for 5 minutes and resuspended in 1 mL day 13-18 media supplemented with ROCK inhibitor and propidium iodide (PI). Cells were applied to a 70 µm filter and sorted for size, singlets, PI- (i.e. live cells), and GFP+ (i.e. TTR expressing cells).
Single Cell RNA sequencing libraries were prepared using the Fluidigm C1 HT platform. Libraries were sequenced using the Illumina Nextseq 500.

tag: cell line

tag: treatment

value: Uncorrected


city: Jeungpyoung

first: Sung-Gook

last: Cho

address: 61 University RD

country: South Korea

institute: KNUT

description:
549-C
A549 cells transfected with control siRNAs

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: A549 human lung cancer cell line

growth_protocol: Cells were cultured in DMEM with 10% fetal bovine serum, 1% antibiotics and antimycoplasma

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: ADGRF4 gene silencing was conducted by transfecting control or ADGRF4 siRNAs

value: control siRNAs


title: MDA_113


title: AVLF_D5b: Normal Control rep5b


title: Corrected

description: total RNA

source_name: day 16 ATTR amyloidosis patient-specific iPSC-derived HLCs corrected at the TTR locus

value: Corrected


title: AVLF_D3b: Normal Control rep3b

value: M

value: Anoxic brain injury, diabetes, hypertension, intravenous drug use


title: m1_Young1_L13


title: m1_Young2_J15


title: AVLF_D2b: Normal Control rep2b

value: F

value: Anoxic brain injury


title: MDA_111


title: MDA_108


description:
549-KD
A549 cells transfected with ADGRF4 siRNAs

value: ADGRF4 siRNAs


title: 52_t13_d

city: Seattle

first: Richard

middle: G

last: James

state: WA

address: 1900 9th ave

institute: Seattle Children's Research Institute

description:
transfection 13, region 9-exon 4, dmso
52_t13_d_S45
processed data file: TableS2_dmso.xlsx

data_processing:
Library strategy: Amplicon
Illumina bcl2fastq v2.16 for base calling and demultiplex.
Paired-End read to mergeR algorithm to align read 1 and read 2 (https://www.h-its.org/downloads/pear-academic/).
Custom python scripts were used to keep sequences from homology directed repair and to trim to the editing region. Briefly, we kept entries that contained both the silent sgRNA blocking changes that we introduced for each sgRNA and a single additional NNK substitution within a single codon in the repair region associated with the ssODN library. Note that sequences containing the silent sgRNA blocking change without additional changes were also preserved. All remaining sequences were then trimmed so that they only contained the repair region associated with the ssODN library. Finally, we reverse complemented some fastq files so that all of the individual sequences corresponded with the coding strand, regardless of sequencing orientation.
To filter sequence by quality (minimum single base quality 25, average read quality 30) and extract counts for each variant present in fastq files from sequencing of gDNA from samples at day 2 and day 14, as well as in RNA at day 2, we used the Enrich2 software package (https://github.com/FowlerLab/Enrich2).
We used custom python scripts to scale, normalize and log transform the data from the growth and ibrutinib screens. For each variant in each replicate, we calculated fold-change by dividing the number of counts at day 14 by those at day 2. Next, the data generated from each replicate in each library was scaled (min-max) based on the average of the highest and lowest 2.5% of the measurements. For each replicate in each library, we then normalized each individual measurement to the scaled fold-change calculation of the silent guide blocking HDR sequence (‘_wt’). At this point, we log2-transformed each replicate. To calculate the “functional score” cited in the text and tables, we took the mean of the log2-transformed replicates. Lastly, for each variant, the lower bound of the 90% confidence interval was calculated by multiplying the standard error by the critical t-value (based on the number of degrees of freedom for each measurement) and subtracting this from the “functional score”. Likewise, the upper bound of the 90% confidence interval was calculated by multiplying the standard error by the critical t-value and adding this to the “functional score”.
Genome_build: GRCh38
Supplementary_files_format_and_content: *xlsx: Excel files include counts, normalized variant frequencies, scores for all variants.

growth_protocol: TMD8 lymphoma cells were cultured at 37C in Iscove’s modified Dulbecco’s medium (IMDM) (Thermo Fisher Scientific) supplemented with 10% FBS and 55 mM beta-mercaptoethanol.

extract_protocol:
Zymo Research Genomic DNA Clean and Concentrator and Quick DNA/RNA kits.
Each sample was first amplified for 18 cycles with primers (see Table S6 for sequences) that generated 700-980bp amplicons using GXL PrimSTAR Polymerase (TaKaRa). Samples were then purified with Agencourt AMPure XP reagent (Beckman Coulter) at 0.8x beads to sample volume ratio according to manufacturer’s protocol and amplified for another 7 cycles with locus-specific primers containing Illumina adaptor sequences. The amplicons were purified with 1X AMPure beads, and reamplified for 7 cycles using primers containing Illumina p5 and p7 sequences and a unique sample index.

treatment_protocol: For each region, 2 x 10e6 human TMD8 cells were electroporated using a Neon (Invitrogen) with 2.5uM Cas9-gRNA complex (2.1:1.2 ratio) and 100pmol of ssODNs (equimolar mix of oligonucleotides). Exons 3-5 of CARD11 were divided into 9 regions to be targeted with a single gRNA (sgRNA). For each sgRNA, libraries of ssODNs for each amino acid position were ordered from IDT with mixed bases NNK (N= A, C, G, or T; K = G or T), or NNM for non target strands (M = A or C) to generate HDR templates with each of the 20 possible amino acids and one of the STOP codons. Each ssODN introduced (i) two synonymous substitutions at and near the PAM site to prevent Cas9-mediated cleavage of repaired DNA and (ii) a single NNK/NNM amino acid variant. Two days post transfection, a portion of the cells were lysed and their genomic DNA (gDNA) and mRNA isolated using Quick DNA Kit (Zymo Research) or AllPrep DNA/RNA Micro Kit (QIAGEN). The remainder of the cells were cultured in either IMDM with 50nM Ibrutinib or IMDM with vehicle (DMSO). On day 16 post transfection, gDNA from the cells was harvested again.

value: lymphoma

value: DMSO

tag: guide rna


title: 52_t13_i

description:
transfection 13, region 9-exon 4, ibrutinib
52_t13_i_S54
processed data file: TableS1_ibrutinib.xlsx

tag: cell type

value: ibrutinib


title: 52_t13_2

description:
transfection 13, region 9-exon 4, day 2
52_t13_2_S36
processed data file: TableS2_dmso.xlsx

value: untreated


title: MDA_110


title: MDA_109


title: m1_Young2_N12

value: primary murine brain endothelial cells


title: AVLF_D2a: Normal Control rep2a

tag: tissue

value: Tricuspid Aortic Valve Leaflets

value: Normal


title: MDA_107

value: hepatocellular carcinoma (HCC)


title: 52_t12_i

description:
transfection 12, region 9-exon 4, ibrutinib
52_t12_i_S27
processed data file: TableS1_ibrutinib.xlsx


title: m1_Young1_H15


title: MDA_106


title: AVLF_D1b: Normal Control rep1b

value: Ruptured internal carotid artery aneurysm, diabetes, hypertension


title: m1_Young1_N6


title: 52_t12_2

description:
transfection 12, region 9-exon 4, day 2
52_t12_2_S9
processed data file: TableS2_dmso.xlsx


title: MDA_105


title: AVLF_D1a: Normal Control rep1a


title: 52_t12_d

description:
transfection 12, region 9-exon 4, dmso
52_t12_d_S18
processed data file: TableS2_dmso.xlsx


title: AVLF_D3a: Normal Control rep3a


title: m1_AY_Y3_D10


title: HEMn-LP_shRKIP_p8

city: Leioa

first: cristina

last: penas lago

state: Vizcaya

address: Barrio Sarriena

country: Spain

institute: UPV/EHU

description: RKIP silenced human epidermal melanocytes from neonatal foreskin in passage 8

data_processing:
RNA-Seq: FASTQC Report (v.0.11.8) was used to assess  the quality of the FASTQ files. Sequenced reads were trimmed for adaptor sequence with TrimGalore! (v.0.6.2), and mapped to mm10 whole genome using hisat2 (v.2.1.0). Transcripts assembly was carried out using StringTie (v.1.3.6) and transcripts reads count was quantified using featureCounts (v.1.6.4) software. Differential expressed genes were called using edgeR (v.3.26.4)
Integrative analyises were performed using BioJupies  and EnrichR Websites.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: RNA-Seq: Raw counts matrix text file

source_name: HEMn-LP

growth_protocol: All primary human melanocytes were grown in Cascade Medium 254 supplemented with Cascade Human Melanocyte Growth Supplement  in the absence of antibiotics. Two days after infection, the cells were selected with 5 µg/mL of Puromycin to get stable purified cell lines.

extract_protocol:
Total RNA was extracted using RNase Mini Kit from Qiagen
RNA  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human melanocytes were transduced with RKIP shRNA Lentiviral Particles (sc-36430-V, 2 MOI) or Control shRNA Lentiviral Particles (sc-108080 2MOI) (Santa Cruz Biotechnology Inc., Dallas, TX, USA )

tag: transfection

value: RKIP silencing


title: 52_t11_i [S88]

description:
transfection 11, region 9-exon 4, ibrutinib
52_t11_i_S88
processed data file: TableS1_ibrutinib.xlsx


title: HEMn-LP_shRKIP_p6

description: RKIP silenced human epidermal melanocytes from neonatal foreskin in passage 6


title: MDA_102


title: MDA_103


title: 52_t11_i [S58]

description:
transfection 11, region 9-exon 4, ibrutinib
52_t11_i_S58
processed data file: TableS1_ibrutinib.xlsx


title: m1_Young2_F1


title: m1_Young2_K8


title: MDA_100


title: MDA_101


title: m1_Young2_N13


title: 52_t11_d

description:
transfection 11, region 9-exon 4, dmso
52_t11_d_S77
processed data file: TableS2_dmso.xlsx


title: m1_AY_Y3_H15


title: HEMn-LP_shCTR_p6

description: transfection control of human epidermal melanocytes from neonatal foreskin in passage 6

value: scramble


title: 52_t11_2

description:
transfection 11, region 9-exon 4, day 2
52_t11_2_S68
processed data file: TableS2_dmso.xlsx


title: D456_Glut3_C

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Wau

institute: HudsonAlpha Institute

data_processing:
adapter trimming using trimgalore v0.4.1
fastqc v0.10.1 for quality score assessment
star version v2,5,2b for alignment
ht-seq-gene v 0.5.3 to consoldiate reads to features
Genome_build: hg37
Supplementary_files_format_and_content: raw count table at the gene level for all 9 samples

molecule: polyA RNA

source_name: D456 GBM xenograft cells

growth_protocol: DMEM/F12 basal media (Invitrogen) supplemented with epidermal growth factor (EGF), fibroblast growth factor, sodium pyruvate, penicillin/streptomycin, and the B27 equivalent GEM21 (Gemini Bio Products)

extract_protocol:
RNA was extracted with TRIzol.
NEBNext Ultra RNA Library Prep Kit for Illumina with polyA selection

treatment_protocol: Cells were transiently co-transfected with psPAX2, pCMV-VSVG and pLX304 lentiviral plasmids containing GLUT3 or GLUT1 (Genecopia) using FuGENE® HD Transfection Reagent (Promega)

value: D456 GBM xenograft cells

value: GLUT3 Overexpression vector

tag: replicate #


title: 51_t9_i

description:
transfection 9, region 8-exon 4, ibrutinib
51_t9_i_S58
processed data file: TableS1_ibrutinib.xlsx


title: MDA_099

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 47231 probes on the Human-H12 V4.0 were used.


title: 51_t9_d

description:
transfection 9, region 8-exon 4, dmso
51_t9_d_S50
processed data file: TableS2_dmso.xlsx


title: MDA_098


title: D456_Glut3_A


title: MDA_097


title: MDA_096


title: HEMn-LP_shCTR_p8

description: transfection control of human epidermal melanocytes from neonatal foreskin in passage 8


title: 51_t9_2

description:
transfection 9, region 8-exon 4, day 2
51_t9_2_S42
processed data file: TableS2_dmso.xlsx


title: m1_AY_Y3_F17


title: D456_Glut1_C

value: GLUT1 Overexpression vector


title: MDA_094


title: D456_Glut1_B


title: MDA_095


title: 51_t14_i

description:
transfection 14, region 8-exon 4, ibrutinib
51_t14_i_S21
processed data file: TableS1_ibrutinib.xlsx


title: m1_Young1_C9


title: m1_Young1_F18


title: D456_Glut1_A


title: m1_AY_Y3_O17


title: D456_Glut3_B


title: 51_t14_d

description:
transfection 14, region 8-exon 4, dmso
51_t14_d_S14
processed data file: TableS2_dmso.xlsx


title: m1_Young1_G2


title: m1_Young1_D18


title: D456_EV_C

value: Empty Vector Control


title: m1_Young2_K9


title: 51_t13_i

description:
transfection 13, region 8-exon 4, ibrutinib
51_t13_i_S53
processed data file: TableS1_ibrutinib.xlsx


title: MDA_091


title: 51_t14_2

description:
transfection 14, region 8-exon 4, day 2
51_t14_2_S7
processed data file: TableS2_dmso.xlsx


title: D456_EV_B


title: D456_EV_A


title: m1_Young1_L16


title: MDA_090


title: m1_AY_Y3_P5


title: MDA_089


title: 51_t13_2

description:
transfection 13, region 8-exon 4, day 2
51_t13_2_S35
processed data file: TableS2_dmso.xlsx


title: m1_Young1_L1


title: MDA_092


title: 51_t12_d

description:
transfection 12, region 8-exon 4, dmso
51_t12_d_S17
processed data file: TableS2_dmso.xlsx


title: MDA_087


title: LumbarDiscNP_DS4

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: nucleus pulposus

extract_protocol:
Frozen tissue biopsies were ground into a powder using a mortar and pestle and homogenized in Qiazol reagent (Qiagen, Hilden, Germany) and homogenized. Total RNA was extracted from research biopsies using the miRNeasy minikit (Qiagen, Hilden, Germany)
mRNA version 2 library prep kit (Illumina)

value: nucleus pulposus

tag: clinical diagnosis

value: Degenerative spondylolisthesis

value: M

tag: age (year)


title: m1_AY_Y3_O5


title: 51_t12_i

description:
transfection 12, region 8-exon 4, ibrutinib
51_t12_i_S26
processed data file: TableS1_ibrutinib.xlsx

value: lymphoma


title: MDA_088


title: LumbarDiscNP_DS3

tag: Sex


title: 51_t11_i [S87]

description:
transfection 11, region 8-exon 4, ibrutinib
51_t11_i_S87
processed data file: TableS1_ibrutinib.xlsx

value: ibrutinib


title: 51_t11_i [S57]

description:
transfection 11, region 8-exon 4, ibrutinib
51_t11_i_S57
processed data file: TableS1_ibrutinib.xlsx


title: LumbarDiscNP_DS2


title: MDA_085


title: LumbarDiscNP_DS1


title: MDA_082


title: LumbarDiscNP_DH5

value: Disc herniation


title: MDA_081


title: MDA_083


title: MDA_084


title: LumbarDiscNP_DS5


title: 51_t11_2

description:
transfection 11, region 8-exon 4, day 2
51_t11_2_S67
processed data file: TableS2_dmso.xlsx

value: untreated


title: m1_Young1_D13

value: primary murine brain endothelial cells


title: LumbarDiscNP_DH4


title: 42_t9_i

description:
transfection 9, region 7-exon 3, ibrutinib
42_t9_i_S57
processed data file: TableS1_ibrutinib.xlsx


title: 42_t9_d

description:
transfection 9, region 7-exon 3, dmso
42_t9_d_S49
processed data file: TableS2_dmso.xlsx

value: DMSO


title: m1_AY_Y3_B3


title: m1_Young1_D9


title: m1_Young2_F14


title: 42_t9_2

description:
transfection 9, region 7-exon 3, day 2
42_t9_2_S41
processed data file: TableS2_dmso.xlsx


title: m1_Young1_J12


title: m1_Young1_O4


title: LumbarDiscNP_DH1


title: LumbarDiscNP_DH2


title: 42_t16_g

description:
transfection 16, region 7-exon 3, gDNA
42_t16_g_S35
processed data file: TableS3_RNA.xlsx


title: 51_t11_d

description:
transfection 11, region 8-exon 4, dmso
51_t11_d_S76
processed data file: TableS2_dmso.xlsx


title: m1_Young1_G12


title: LumbarDiscNP_DH3

value: F


title: 42_t16_c

description:
transfection 16, region 7-exon 3, RNA
42_t16_c_S49
processed data file: TableS3_RNA.xlsx


title: m1_Young2_H7


title: U266 DMSO_1

city: San Francisco

first: Esther

middle: T

last: Chan

state: California

address: 1500 Owens Street, Suite 500

institute: Celgene Corporation

description: Various B-cell lymphoma cell lines were cultured, treated with CC-115 or vehicle (DMSO), and harvested. Samples were transferred to NeoGenomics for library preparation withTruSeq Stranded mRNA kits and paired-end sequencing on Illumina HiSeq 2500.

data_processing:
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence using cutadapt 1.15 and evaluated using FastQC v 0.10.1. Alignment was performed using STAR (v2.5.2b) on a reference genome that contains the primary assembly of the human genome (hg38) using the trimming options that the tool provides. We used Gencode v24 for the gene annotation and gene/isoform related analyses. QC on the aligned reads was performed using a variety of tools from the Picard tools suite (v2.18). Pseudoalignments using Salmon (v0.7) were performed on reads where Illumina adapters were trimmed.
Read counts are loaded from STAR (using the defined strandness for each sample), and Salmon. In the case of Salmon first the transcript TPMs are loaded from the fields and subsequenctly summarized using the tximport package from Bioconductor. The generated pseudocounts have been scaled for the average transcript length over samples and the library size using the argument lengthScaledTPM and were then summarized to gene level.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include scaled counts for each Sample generated by Salmon and tximport for transcripts (GSE140184_CountsSalmon.isoforms.lengthScaledTPM.txt) and genes (GSE140184_CountsSalmon.lengthScaledTPM.txt)

source_name: U266 DMSO

extract_protocol:
poly-A selected mRNA was extracted from the cell lines by NeoGenomics.
Stranded, paired-end libraries were prepared using Illumina TruSeq Stranded mRNA kit

treatment_protocol: Cell lines were treated with CC-115 or vehicle control (DMSO) for 6 hours in technical replicate.

value: male

value: B-cell lymphoma cell line

value: 6 hours


title: 42_t15_g

description:
transfection 15, region 7-exon 3, gDNA
42_t15_g_S28
processed data file: TableS3_RNA.xlsx


title: U266 DMSO_2


title: m1_AY_Y3_K14


title: MDA_079

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 47231 probes on the Human-H12 V4.0 were used.

value: hepatocellular carcinoma (HCC)


title: MDA_078


title: MDA_080


title: m1_Young2_M13


title: 42_t15_c

description:
transfection 15, region 7-exon 3, RNA
42_t15_c_S42
processed data file: TableS3_RNA.xlsx


title: MDA_076


title: 42_t14_i

description:
transfection 14, region 7-exon 3, ibrutinib
42_t14_i_S20
processed data file: TableS1_ibrutinib.xlsx


title: m1_AY_Y3_F4


title: m1_Young2_O15


title: U266 CC115_2


title: MDA_077


title: RPMI8226 DMSO_2

source_name: RPMI8226 DMSO


title: U266 CC115_1


title: 42_t14_d

description:
transfection 14, region 7-exon 3, dmso
42_t14_d_S13
processed data file: TableS2_dmso.xlsx


title: MDA_074


title: m1_Young2_F15


title: 42_t14_2

description:
transfection 14, region 7-exon 3, day 2
42_t14_2_S6
processed data file: TableS2_dmso.xlsx


title: RPMI8226 DMSO_1


title: 42_t13_i

description:
transfection 13, region 7-exon 3, ibrutinib
42_t13_i_S52
processed data file: TableS1_ibrutinib.xlsx


title: RPMI8226 CC115_2


title: RPMI8226 CC115_1


title: 42_t13_d

description:
transfection 13, region 7-exon 3, dmso
42_t13_d_S43
processed data file: TableS2_dmso.xlsx


title: RAMOS DMSO_2

source_name: RAMOS DMSO

value: Ramos


title: m1_AY_Y3_N14


title: MDA_073


title: MDA_075


title: MDA_072


title: m1_Young1_I16


title: MDA_071


title: MDA_069


title: MDA_068


title: MDA_070


title: RAMOS DMSO_ 1


title: RAMOS CC115_2

source_name: RAMOS CC115


title: 42_t12_i

description:
transfection 12, region 7-exon 3, ibrutinib
42_t12_i_S25
processed data file: TableS1_ibrutinib.xlsx


title: m1_Young2_E18

source_name: three-mo mouse BEC


title: m1_Young2_F9


title: m1_AY_Y3_K12


title: RAMOS CC115_1


title: 42_t12_2

description:
transfection 12, region 7-exon 3, day 2
42_t12_2_S7
processed data file: TableS2_dmso.xlsx


title: m1_AY_Y3_N3


title: MDA_066


title: 42_t13_2

description:
transfection 13, region 7-exon 3, day 2
42_t13_2_S34
processed data file: TableS2_dmso.xlsx


title: m1_Young1_H2


title: MDA_067


title: Jiyoye DMSO_2

source_name: Jiyoye DMSO

value: Jiyoye


title: MDA_065


title: MDA_064


title: m1_Young2_I13


title: MDA_063


title: 42_t12_d

description:
transfection 12, region 7-exon 3, dmso
42_t12_d_S16
processed data file: TableS2_dmso.xlsx


title: m1_Young1_M12


title: 42_t11_i [S86]

description:
transfection 11, region 7-exon 3, ibrutinib
42_t11_i_S86
processed data file: TableS1_ibrutinib.xlsx


title: 42_t11_i [S56]

description:
transfection 11, region 7-exon 3, ibrutinib
42_t11_i_S56
processed data file: TableS1_ibrutinib.xlsx


title: m1_Young1_J1


title: 42_t11_2

description:
transfection 11, region 7-exon 3, day 2
42_t11_2_S66
processed data file: TableS2_dmso.xlsx


title: Jiyoye CC115_1

data_processing:
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence using cutadapt 1.15 and evaluated using FastQC v 0.10.1. Alignment was performed using STAR (v2.5.2b) on a reference genome that contains the primary assembly of the human genome (hg38) using the trimming options that the tool provides. We used Gencode v24 for the gene annotation and gene/isoform related analyses. QC on the aligned reads was performed using a variety of tools from the Picard tools suite (v2.18). Pseudoalignments using Salmon (v0.7) were performed on reads where Illumina adapters were trimmed.
Read counts are loaded from STAR (using the defined strandness for each sample), and Salmon. In the case of Salmon first the transcript TPMs are loaded from the fields and subsequenctly summarized using the tximport package from Bioconductor. The generated pseudocounts have been scaled for the average transcript length over samples and the library size using the argument lengthScaledTPM and were then summarized to gene level.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include scaled counts for each Sample generated by Salmon and tximport for transcripts (GSE140184_CountsSalmon.isoforms.lengthScaledTPM.txt) and genes (GSE140184_CountsSalmon.lengthScaledTPM.txt)’

source_name: Jiyoye CC115

value: female


title: Jiyoye DMSO_1


title: 41_t9_i

description:
transfection 9, region 6-exon 3, ibrutinib
41_t9_i_S56
processed data file: TableS1_ibrutinib.xlsx


title: m1_Young2_K10


title: MDA_061


title: MDA_060


title: m1_Young1_L18


title: JEKO-1 DMSO_1

description: Various B-cell lymphoma cell lines were cultured, treated with CC-115 or vehicle (DMSO), and harvested. Samples were transferred to NeoGenomics for library preparation withTruSeq Stranded mRNA kits and paired-end sequencing on Illumina HiSeq 2500.

source_name: JEKO-1 DMSO


title: MDA_062


title: JEKO-1 CC115_2

source_name: JEKO-1 CC115


title: m1_AY_Y3_F14


title: Jiyoye CC115_2

data_processing:
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence using cutadapt 1.15 and evaluated using FastQC v 0.10.1. Alignment was performed using STAR (v2.5.2b) on a reference genome that contains the primary assembly of the human genome (hg38) using the trimming options that the tool provides. We used Gencode v24 for the gene annotation and gene/isoform related analyses. QC on the aligned reads was performed using a variety of tools from the Picard tools suite (v2.18). Pseudoalignments using Salmon (v0.7) were performed on reads where Illumina adapters were trimmed.
Read counts are loaded from STAR (using the defined strandness for each sample), and Salmon. In the case of Salmon first the transcript TPMs are loaded from the fields and subsequenctly summarized using the tximport package from Bioconductor. The generated pseudocounts have been scaled for the average transcript length over samples and the library size using the argument lengthScaledTPM and were then summarized to gene level
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include scaled counts for each Sample generated by Salmon and tximport for transcripts (GSE140184_CountsSalmon.isoforms.lengthScaledTPM.txt) and genes (GSE140184_CountsSalmon.lengthScaledTPM.txt)


title: m1_AY_Y3_D18


title: 41_t9_d

description:
transfection 9, region 6-exon 3, dmso
41_t9_d_S48
processed data file: TableS2_dmso.xlsx


title: MDA_059

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 47231 probes on the Human-H12 V4.0 were used.


title: 41_t9_2

description:
transfection 9, region 6-exon 3, day 2
41_t9_2_S40
processed data file: TableS2_dmso.xlsx


title: 42_t11_d

description:
transfection 11, region 7-exon 3, dmso
42_t11_d_S75
processed data file: TableS2_dmso.xlsx


title: JEKO-1 DMSO_2


title: Human_Universal_Reference


title: m1_AY_Y3_E5


title: m1_Young2_D1


title: JEKO-1 CC115_1


title: 41_t16_g

description:
transfection 16, region 6-exon 3, gDNA
41_t16_g_S34
processed data file: TableS3_RNA.xlsx


title: m1_AY_Y3_N6


title: 41_t15_g

description:
transfection 15, region 6-exon 3, gDNA
41_t15_g_S27
processed data file: TableS3_RNA.xlsx


title: 41_t16_c

description:
transfection 16, region 6-exon 3, RNA
41_t16_c_S48
processed data file: TableS3_RNA.xlsx


title: GRANTA DMSO_2

source_name: GRANTA DMSO


title: MDA_057


title: GRANTA DMSO_1


title: m1_AY_Y3_J2


title: MDA_054


title: GRANTA CC115_2

source_name: GRANTA CC115


title: MDA_055


title: MDA_056


title: 41_t15_c

description:
transfection 15, region 6-exon 3, RNA
41_t15_c_S41
processed data file: TableS3_RNA.xlsx


title: 51_t12_2

description:
transfection 12, region 8-exon 4, day 2
51_t12_2_S8
processed data file: TableS2_dmso.xlsx


title: MDA_058


title: 41_t14_i

description:
transfection 14, region 6-exon 3, ibrutinib
41_t14_i_S19
processed data file: TableS1_ibrutinib.xlsx


title: GRANTA CC115_1


title: m1_Young1_E17


title: m1_Young1_C8


title: MDA_053


title: glia control [504]

city: New York

first: Yasmin

last: Hurd

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

description: ATACseq data from human putamen

data_processing:
Reads were mapped to the gender appropriate reference genome hg19 using STAR aligner version 2.5.0, by disabling spliced alignments (setting --alignIntronMax 1) and prohibiting soft-clipping of the reads (setting --alignEndsType EndToEnd). Reads that (1) mapped to more than one locus, (2) were duplicated, and/or (3) mapped to the mitochondrial genome were excluded.
We retained peaks passing a p-value cutoff 4.7 x 10-6 as defined previously based on Irreproducibility Discovery Rate (IDR) analysis on technical replicates (github.com/nboley/idr).
We used the featureCounts function from the Rsubread package to generate a sample-by-peak read count matrix (36 samples by 143,003 peak regions). We counted fragments (defined from pair-end reads), instead of individual reads, that overlapped with the final consensus set of peaks.
Scaling normalization to remove composition biases in sequencing data was applied to log(CPM) (Counts Per Million total reads) using the trimmed mean of M-values method.
-
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: putamen

extract_protocol:
ATAC-seq (assay for transposase accessible chromatin) reactions were performed using Illumina Cat #FC-121-1030
Libraries amplified using the Nextera index kit (Illumina Cat #FC-121-1011). ATACseq libraries were sequenced on Hi-Seq2500 (Illumina) obtaining 50 bp paired-end reads.
ATAC-seq on FACS-sorted neuronal (N) and glial (G) cell populations. All libraries were loaded onto two separate lanes of a flow cell.

tag: gender

tag: group

value: control

tag: subject id

value: glia


title: 41_t14_d

description:
transfection 14, region 6-exon 3, dmso
41_t14_d_S12
processed data file: TableS2_dmso.xlsx


title: 41_t14_2

description:
transfection 14, region 6-exon 3, day 2
41_t14_2_S5
processed data file: TableS2_dmso.xlsx


title: m1_Young1_L2


title: m1_Young1_C18


title: MDA_052


title: 41_t13_i

description:
transfection 13, region 6-exon 3, ibrutinib
41_t13_i_S51
processed data file: TableS1_ibrutinib.xlsx


title: MDA_051


title: glia control [499]

description: ATACseq data from human putamen


title: MDA_050


title: m1_Young1_G16


title: m1_Young2_P12


title: MDA_049


title: MDA_048


title: glia heroin [497]

description: ATACseq data from human putamen

value: heroin


title: neuron control [499]

description: ATACseq data from human putamen

value: neuron


title: m1_Young2_D15


title: neuron heroin [497]

description: ATACseq data from human putamen


title: MDA_047


title: glia heroin [488]

description: ATACseq data from human putamen


title: neuron control [504]

description: ATACseq data from human putamen


title: 41_t12_i

description:
transfection 12, region 6-exon 3, ibrutinib
41_t12_i_S24
processed data file: TableS1_ibrutinib.xlsx

value: lymphoma

value: ibrutinib


title: 41_t12_d

description:
transfection 12, region 6-exon 3, dmso
41_t12_d_S15
processed data file: TableS2_dmso.xlsx


title: 41_t12_2

description:
transfection 12, region 6-exon 3, day 2
41_t12_2_S6
processed data file: TableS2_dmso.xlsx

value: untreated


title: m1_Young1_D4

value: primary murine brain endothelial cells


title: MDA_046


title: neuron heroin [488]

description: ATACseq data from human putamen


title: 41_t11_i [S85]

description:
transfection 11, region 6-exon 3, ibrutinib
41_t11_i_S85
processed data file: TableS1_ibrutinib.xlsx


title: 41_t13_d

description:
transfection 13, region 6-exon 3, dmso
41_t13_d_S42
processed data file: TableS2_dmso.xlsx

value: DMSO


title: glia heroin [487]

description: ATACseq data from human putamen


title: 41_t13_2

description:
transfection 13, region 6-exon 3, day 2
41_t13_2_S33
processed data file: TableS2_dmso.xlsx


title: m1_Young2_H6


title: m1_Young1_I10


title: neuron heroin [487]

description: ATACseq data from human putamen


title: 41_t11_d

description:
transfection 11, region 6-exon 3, dmso
41_t11_d_S74
processed data file: TableS2_dmso.xlsx


title: MDA_043

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 47231 probes on the Human-H12 V4.0 were used.


title: MDA_042


title: m1_AY_Y3_L17


title: glia heroin [484]

description: ATACseq data from human putamen


title: m1_Young1_K13


title: MDA_041


title: m1_Young2_C13


title: neuron heroin [484]

description: ATACseq data from human putamen


title: MDA_045


title: 34_t9_i

description:
transfection 9, region 5-exon 2, ibrutinib
34_t9_i_S55
processed data file: TableS1_ibrutinib.xlsx


title: MDA_044


title: 41_t11_i [S55]

description:
transfection 11, region 6-exon 3, ibrutinib
41_t11_i_S55
processed data file: TableS1_ibrutinib.xlsx


title: 34_t9_d

description:
transfection 9, region 5-exon 2, dmso
34_t9_d_S47
processed data file: TableS2_dmso.xlsx


title: m1_Young2_G12


title: neuron heroin [481]

description: ATACseq data from human putamen


title: MDA_040


title: m1_Young1_J9


title: 34_t9_2

description:
transfection 9, region 5-exon 2, day 2
34_t9_2_S39
processed data file: TableS2_dmso.xlsx


title: glia heroin [477]

description: ATACseq data from human putamen


title: m1_AY_Y3_C15


title: MDA_038


title: 34_t16_g

description:
transfection 16, region 5-exon 2, gDNA
34_t16_g_S33
processed data file: TableS3_RNA.xlsx


title: 41_t11_2

description:
transfection 11, region 6-exon 3, day 2
41_t11_2_S65
processed data file: TableS2_dmso.xlsx


title: m1_Young1_I13


title: MDA_036


title: glia heroin [468]

description: ATACseq data from human putamen


title: neuron heroin [477]

description: ATACseq data from human putamen


title: MDA_035


title: MDA_037


title: glia heroin [481]

description: ATACseq data from human putamen


title: 34_t16_c

description:
transfection 16, region 5-exon 2, RNA
34_t16_c_S47
processed data file: TableS3_RNA.xlsx


title: 34_t14_i

description:
transfection 14, region 5-exon 2, ibrutinib
34_t14_i_S18
processed data file: TableS1_ibrutinib.xlsx


title: 34_t14_d

description:
transfection 14, region 5-exon 2, dmso
34_t14_d_S11
processed data file: TableS2_dmso.xlsx


title: m1_AY_Y3_C16


title: MDA_034


title: MDA_039


title: m1_AY_Y3_M7


title: glia control [457]

description: ATACseq data from human putamen


title: m1_Young2_E13


title: neuron control [457]

description: ATACseq data from human putamen


title: m1_AY_Y3_N9


title: m1_Young1_M8


title: glia control [456]

description: ATACseq data from human putamen


title: 34_t13_i

description:
transfection 13, region 5-exon 2, ibrutinib
34_t13_i_S50
processed data file: TableS1_ibrutinib.xlsx


title: 34_t14_2

description:
transfection 14, region 5-exon 2, day 2
34_t14_2_S4
processed data file: TableS2_dmso.xlsx


title: 34_t13_d

description:
transfection 13, region 5-exon 2, dmso
34_t13_d_S41
processed data file: TableS2_dmso.xlsx


title: m1_AY_Y3_G10


title: 34_t13_2

description:
transfection 13, region 5-exon 2, day 2
34_t13_2_S32
processed data file: TableS2_dmso.xlsx


title: 34_t12_i

description:
transfection 12, region 5-exon 2, ibrutinib
34_t12_i_S23
processed data file: TableS1_ibrutinib.xlsx


title: m1_Young1_N12


title: MDA_032


title: MDA_031


title: MDA_033


title: neuron control [448]

description: ATACseq data from human putamen


title: glia control [448]

description: ATACseq data from human putamen


title: MDA_029


title: MDA_030


title: glia control [446]

description: ATACseq data from human putamen


title: m1_AY_Y3_P16


title: neuron control [446]

description: ATACseq data from human putamen


title: m1_Young1_N18


title: neuron control [456]

description: ATACseq data from human putamen


title: glia control [444]

description: ATACseq data from human putamen


title: m1_AY_Y3_F13


title: m1_Young2_E1


title: 34_t12_d

description:
transfection 12, region 5-exon 2, dmso
34_t12_d_S14
processed data file: TableS2_dmso.xlsx


title: m1_AY_Y3_H9


title: 34_t11_i

description:
transfection 11, region 5-exon 2, ibrutinib
34_t11_i_S84
processed data file: TableS1_ibrutinib.xlsx


title: m1_Young2_L11


title: 34_t12_2

description:
transfection 12, region 5-exon 2, day 2
34_t12_2_S5
processed data file: TableS2_dmso.xlsx


title: m1_Young1_D12


title: glia control [440]

description: ATACseq data from human putamen


title: neuron control [440]

description: ATACseq data from human putamen


title: 34_t11_2

description:
transfection 11, region 5-exon 2, day 2
34_t11_2_S64
processed data file: TableS2_dmso.xlsx


title: neuron control [444]

description: ATACseq data from human putamen


title: 33_t9_i

description:
transfection 9, region 4-exon 2, ibrutinib
33_t9_i_S54
processed data file: TableS1_ibrutinib.xlsx


title: m1_Young1_F13


title: 33_t9_d

description:
transfection 9, region 4-exon 2, dmso
33_t9_d_S46
processed data file: TableS2_dmso.xlsx


title: m1_Young1_E8


title: 34_t11_d

description:
transfection 11, region 5-exon 2, dmso
34_t11_d_S73
processed data file: TableS2_dmso.xlsx


title: 33_t9_2

description:
transfection 9, region 4-exon 2, day 2
33_t9_2_S38
processed data file: TableS2_dmso.xlsx


title: neuron heroin [439]

description: ATACseq data from human putamen


title: MDA_027

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 47231 probes on the Human-H12 V4.0 were used.


title: MDA_026


title: m1_AY_Y3_N4


title: MDA_028


title: neuron heroin [468]

description: ATACseq data from human putamen


title: MDA_024


title: MDA_025


title: MDA_023


title: m1_Young2_G18


title: glia control [431]

description: ATACseq data from human putamen


title: 33_t16_g

description:
transfection 16, region 4-exon 2, gDNA
33_t16_g_S32
processed data file: TableS3_RNA.xlsx


title: MDA_021


title: MDA_020


title: 33_t16_c

description:
transfection 16, region 4-exon 2, RNA
33_t16_c_S46
processed data file: TableS3_RNA.xlsx


title: MDA_019


title: glia heroin [439]

description: ATACseq data from human putamen


title: m1_Young2_O4


title: MDA_022


title: neuron control [431]

description: ATACseq data from human putamen


title: m1_AY_Y3_C3


title: 33_t15_c

description:
transfection 15, region 4-exon 2, RNA
33_t15_c_S39
processed data file: TableS3_RNA.xlsx


title: 33_t15_g

description:
transfection 15, region 4-exon 2, gDNA
33_t15_g_S25
processed data file: TableS3_RNA.xlsx


title: MDA_018


title: neuron control [430]

description: ATACseq data from human putamen


title: m1_Young1_G11


title: m1_AY_Y3_B6


title: glia heroin [371]

description: ATACseq data from human putamen


title: neuron heroin [371]

description: ATACseq data from human putamen


title: 33_t14_i

description:
transfection 14, region 4-exon 2, ibrutinib
33_t14_i_S17
processed data file: TableS1_ibrutinib.xlsx


title: 33_t14_d

description:
transfection 14, region 4-exon 2, dmso
33_t14_d_S10
processed data file: TableS2_dmso.xlsx


title: MDA_016


title: m1_Young2_N3


title: MDA_015


title: 33_t14_2

description:
transfection 14, region 4-exon 2, day 2
33_t14_2_S3
processed data file: TableS2_dmso.xlsx


title: glia control [430]

description: ATACseq data from human putamen


title: m1_Young1_J8


title: glia heroin [343]

description: ATACseq data from human putamen


title: neuron heroin [343]

description: ATACseq data from human putamen


title: m1_Young1_K3


title: 33_t13_i

description:
transfection 13, region 4-exon 2, ibrutinib
33_t13_i_S49
processed data file: TableS1_ibrutinib.xlsx


title: NCCIT Teton-shOCT4 DOX (+) OCT4 S236D rescue

city: Gyeonggi-do

first: Hyonchol

last: Jang

address: 323, Ilsan-ro, Ilsandong-gu, Goyang-si

institute: National Cancer Center

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Homo sapiens using TopHat 2.0.13, which is capable of reporting split-read alignments across splice junctions and determined using Cufflinks 2.2.1 software in default options.
The reference genome sequence of Homo sapiens (hg19) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: germ cell cancer with expressing mut-OCT4

extract_protocol:
Total RNAs were extracted from germ cell cancer of Homo sapiens. Poly(A) mRNA isolation from total RNA (2 µg) and fragmentation were performed using the Illumina Truseq Stranded mRNA LT Sample Prep Kit with poly-T oligo-attached magnetic beads, according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina Truseq Stranded mRNA LT Sample Prep Kit, according to the manufacturer’s protocol.

value: Breast

tag: genotype/variation

value: rescued by phosphorylation mimicking OCT4 mutants (S236D)

value: NCCIT


title: 33_t13_d

description:
transfection 13, region 4-exon 2, dmso
33_t13_d_S40
processed data file: TableS2_dmso.xlsx


title: NCCIT Teton-shOCT4 DOX (+) OCT4 WT rescue

source_name: germ cell cancer with expressing WT-OCT4

value: rescued by wild type OCT4


title: m1_Young2_J7


title: 33_t13_2

description:
transfection 13, region 4-exon 2, day 2
33_t13_2_S31
processed data file: TableS2_dmso.xlsx


title: m1_Young1_O6


title: MDA_014

value: hepatocellular carcinoma (HCC)


title: MDA_017


title: m1_AY_Y3_D4


title: HMVEC-L-pod(-)

city: Oralndo

first: Junko

last: Sawada

state: Florida

address: 6400 Sanger Rd

institute: SBP Discovery MRI

data_processing:
Illumina Real-Time Analysis (RTA) was used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to hg19 whole genome using Partek Flow software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by using Partek Flow software.
Genome_build: hg19

source_name: HMVEC

growth_protocol: Human Lung Microvascular Endothelial Cells (HMVEC-L) was obtained from Lonza and cultured with EGM2-MV medium. To remove the lymphatic endothelial population, cells were stained with anti-Podoplanin antibody (eBioscience) and FACS sorted (BD FACS ARIA II Sorter) to collect Podoplanin-negative cells. Cells were cultured for 3 days, and total RNA was used for RNA-seq

extract_protocol:
RNA was extracted from cells with Direct-zol RNA (Genesee Scientific).
To construct multiplexed Libraries, 1 µg of total RNA was used for TruSeq Stranded Total RNA Library Prep Kit (Illumina). Multiplexed libraries are pooled and single-end 50-bp sequencing was performed on one flow-cell of Illumina Hiseq 2500.

value: podoplanin negative


title: 33_t12_d

description:
transfection 12, region 4-exon 2, dmso
33_t12_d_S13
processed data file: TableS2_dmso.xlsx


title: NCCIT Teton-shOCT4 DOX (-)

source_name: germ cell cancer with expressing OCT4

value: harbor endogenous OCT4


title: NCCIT Teton-shOCT4 DOX (+)

source_name: germ cell cancer without expressing OCT4

value: OCT4 is depleted


title: 33_t12_2

description:
transfection 12, region 4-exon 2, day 2
33_t12_2_S4
processed data file: TableS2_dmso.xlsx


title: 33_t11_i

description:
transfection 11, region 4-exon 2, ibrutinib
33_t11_i_S83
processed data file: TableS1_ibrutinib.xlsx


title: m1_AY_Y3_B15

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: raw count table


title: MDA_013


title: MDA_012


title: MDA_011


title: m1_AY_Y3_P11


title: miPEP31 KO-rep 3

city: shanghai

first: Hong

last: Zhou

address: South Chongqing road

department: Immunology

institute: Shanghai Insititute of immunology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The data were analyzed on the free online platform of Majorbio I-Sanger Cloud Platform (www.i-sanger.com)
Genome_build: mm8
Supplementary_files_format_and_content: expression of miR-31 target gene were anlaed on the online platform of Majorbio I-Sanger Cloud Platform.

source_name: spleen

extract_protocol:
RNA extraction using trizoll
TruseqTM RNA sample prep kit

treatment_protocol: activated by anti-CD3/28 for 48 hours

tag: strain

tag: genotype

tag: age

value: 8 weeks

value: spleen


title: m1_AY_Y3_H13


title: MDA_010

tag: disease


title: MDA_009


title: MDA_008


title: 33_t11_d

description:
transfection 11, region 4-exon 2, dmso
33_t11_d_S72
processed data file: TableS2_dmso.xlsx

tag: cell line

tag: treatment


title: miPEP31 KO-rep 2


title: 33_t11_2

description:
transfection 11, region 4-exon 2, day 2
33_t11_2_S63
processed data file: TableS2_dmso.xlsx

tag: cell type

tag: guide rna


title: m1_AY_Y3_K6


title: MDA_007


title: MDA_005


title: m1_AY_Y3_A4


title: miPEP31 KO-rep 1

tag: tissue


title: WT-rep 3

value: wild type


title: m1_Young2_I9


title: WT-rep 2


title: 32_t9_i

description:
transfection 9, region 3-exon 2, ibrutinib
32_t9_i_S53
processed data file: TableS1_ibrutinib.xlsx


title: MDA_004

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 47231 probes on the Human-H12 V4.0 were used.


title: MDA_006


title: m1_Young2_L10


title: m1_Young2_G16


title: WT-rep 1


title: 32_t9_2

description:
transfection 9, region 3-exon 2, day 2
32_t9_2_S37
processed data file: TableS2_dmso.xlsx


title: m1_Young2_F11


title: 32_t16_g

description:
transfection 16, region 3-exon 2, gDNA
32_t16_g_S31
processed data file: TableS3_RNA.xlsx


title: E11: CD8_2_WT_combo_Day9

first: Asaf

last: Madi

address: 60 Fenwood Road, BTM 10016F

department: Neurology

institute: BWH

data_processing:
RNA-seq reads were aligned using Tophat(Trapnell et al., 2009) (to mouse genome version mm9), and expression levels were calculated using RSEM(Li and Dewey, 2011) using annotated transcripts (mm9), followed by further processing using the Bioconductor package DESeq in R(Anders and Huber, 2010). The data was normalized using TMM normalization
mm9
Genome_build: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CD8+ T cells

growth_protocol: wild type (E8i-Cre-Nr3c1fl/fl) or E8i-Cre+Nr3c1fl/fl CD8+ T cells activated in the presence or absence of glucocorticoid (GC;dexamethasone) for 72hrs and wild type CD8+ T cell  9 days activated in the presence or absence of glucocorticoid (GC;dexamethasone), IL27 or both

extract_protocol: 1,000 cells were sorted into 5 µL of Buffer TCL (Qiagen) supplemented with 1% 2 mercaptoethanol. Plates were thawed on ice for one minute and spun down at 2,000 rpm for one minute. Immediately following, RNA lysate was purified using a 2.2x RNAClean SPRI bead ratio (Beckman Coulter Genomics). The RNA captured beads were processed using a modified SMART-Seq2 protocol(Picelli et al., 2013) entailing RNA secondary structure denaturation (72˚C for three minutes), reverse transcription with Maxima Reverse Transcriptase (Life Technologies), and whole-transcription amplification (WTA) with KAPA HiFi HotStart ReadyMix 2X (Kapa Biosystems) for 11 cycles. WTA products were purified with Ampure XP beads (Beckman Coulter), quantified with a Qubit dsDNA HS Assay Kit (ThermoFisher), and quality accessed with a high-sensitivity DNA chip (Agilent). 0.2 ng of purified WTA product was used as input for the Nextera XT DNA Library Preparation Kit (Illumina). Uniquely barcoded libraries were pooled and sequenced with a NextSeq 500 high output V2 75 cycle kit (Illumina) using 38 and 38 paired end reads(Picelli et al., 2013).

treatment_protocol: CD8+ T cells from splenocytes and lymph nodes were isolated using CD8 microbeads (Miltenyi). Cells were further stained with antibodies against CD8, CD62L and CD44, and CD8+CD62LhiCD44- naive cells were sorted by BD FacsAria (BD Biosciences). Sorted cells were cultured for 9 days as described below in DMEM supplemented with 10% (vol/vol) FCS, 50 mM mercaptoethanol, 1 mM sodium pyruvate, nonessential amino acids, L-glutamine, and 100 U/ml penicillin and 100 g/ml streptomycin. Specifically, naive CD8+ cells were stimulated with plate bound anti-CD3 (145-2C11, 1 μg/ml) and anti-CD28 (PV-1, 1μg/ml) in the presence of either 10 nM dexamethasone (Sigma), 100 nM Corticosterone (Fisher Scientific), 25 ng/ml IL-27 (R&D), or both dexamethasone and IL27  for 3 days. Cells were then rested in the presence of 5 ng/ml IL2 (Miltenyi) for 3 days followed by re-stimulation with plate bound anti-CD3 (145-2C11, 1 μg/ml) and anti-CD28 (PV-1, 1μg/ml) in the presence of either 10nM dexamethasone ( Sigma), 100 nM Corticosterone (Fisher Scientific), 25 ng/ml IL-27 (R&D), or both dexamethasone and IL27   for an additional 3 days.

value: CD8+ T cells

tag: time-point

value: Day 9


title: E10: CD8_1_WT_combo_Day9


title: E12: CD8_3_WT_combo_Day9


title: E9: CD8_3_WT_IL27_Day9


title: Murine cDC1 cells from MLN - 09

city: Copenhagen

first: Søren

last: Brunak

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Protein Research

country: Denmark

institute: University of Copenhagen

data_processing:
FASTQ files were quality checked using FastQC.
Reads of the FASTQ files were aligned to the Mus Musculus ENSEMBL genome using STAR (v 2.4.2a), which also quantified the gene expression.
Genome_build: Mus Musculus - GRCm38 release 89
Supplementary_files_format_and_content: The processed files are tab-delimited text files (.tab) showing the gene expression as read counts. Gene annotation is ENSEMBL.

source_name: Conventional Dendritc Cell lineage 1

extract_protocol:
Cells in suspension from murine mesenteric lymph nodes were stained with a cocktail of antibodies to CD45 (30-F11), CD3 (17A2), CD19 (6D5), B220 (RA3-6B2), TER-119 (TER-119), NK-1.1 (PK136), MHC II (IA/I-E) (M5/114.15.2), CD11b (M1/70), CD11c (N418), CD103 (M290), CD64 (X54-5/7.1), F4/80 (BM8), SIRPa (P84), XCR1 (ZET). CD11c+MHCIIhiXCR-1+CD103+ cDC1 were flow cytometry cell sorted on a FACSAriaII (BD Biosciences) after exclusion of dead cells stained by fixable live/dead near-infrared dye (Life technologies) and cell aggregates (identified on FSC-A versus FSC-W scatterplots).
Total RNA was isolated using the RNeasy Micro kit (QIAGEN). Briefly, frozen pellets of sorted cells were resuspended in RLT buffer. Buffer and cells were mixed for 30 sec through pipetting and left on the bench for 5 min to assure proper lysis. Extraction was performed according to manufacturer’s protocol with an on-column DNAse digestion step added after the first wash buffer step. RNA quality and quantity were measured using the 2100 BioAnalyzer equipped with RNA6000 Pico chip (Agilent Technologies). RNA was subjected to whole transcriptome amplification using Ovation RNA-Seq System V2 (NuGEN) kit, following the manufacturer’s protocol. This kit employs a single primer isothermal amplification (SPIA) method to amplify RNA into double stranded cDNA. Amplified cDNA samples were purified using the MinElute Reaction Cleanup kit (Qiagen) according to manufacturer’s instructions. Quantity and quality of the cDNA samples were measured using the 2100 BioAnalyzer equipped with DNA1000 chip (Agilent technologies) and the Nanodrop (ThermoFisher Scientific). Libraries to sequence with Illumina platform were constructed the Ovation Ultralow system V2 kit (NuGEN), following manufacturer’s instructions. 100ng of amplified cDNA were fragmented by sonication using a Bioruptor Pico (Diagenode). The sheared cDNA was end-repaired to generate blunt ends, then ligated to Illumina adaptors with indexing tags, followed by AMPure XP beads purification. The final size distribution of the libraries was evaluated using 2100 Bioanalyzer equipped with DNA1000 chip (Agilent technologies) and quantified using KAPA library Quantification Kit Illumina platforms (Kapa Biosystems).

value: mesenteric lymph node

value: female

value: 7-10 weeks old


title: m1_AY_Y3_G3

city: Stanford

first: Michelle

last: Chen

address: 318 Campus Drive

institute: Stanford

extract_protocol:
Brain tissues were dissected using Miltenyi neural dissociation kit. Brain endothelial cells were isolated via FACS.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary murine brain endothelial cells


title: Murine cDC1 cells from MLN - 07

value: untreated


title: 32_t15_g

description:
transfection 15, region 3-exon 2, gDNA
32_t15_g_S24
processed data file: TableS3_RNA.xlsx

value: lymphoma


title: 32_t16_c

description:
transfection 16, region 3-exon 2, RNA
32_t16_c_S45
processed data file: TableS3_RNA.xlsx


title: 32_t9_d

description:
transfection 9, region 3-exon 2, dmso
32_t9_d_S45
processed data file: TableS2_dmso.xlsx

value: DMSO


title: m1_Young1_B8


title: 32_t15_c

description:
transfection 15, region 3-exon 2, RNA
32_t15_c_S38
processed data file: TableS3_RNA.xlsx


title: E8: CD8_2_WT_IL27_Day9


title: m1_Young2_J3


title: m1_Young2_M7


title: E6: CD8_3_WT_Dex_Day9

value: Dex


title: E7: CD8_1_WT_IL27_Day9


title: m1_Young1_J10


title: E5: CD8_2_WT_Dex_Day9


title: m1_Young2_O3


title: Murine cDC1 cells from MLN - 08


title: E4: CD8_1_WT_Dex_Day9


title: E3: CD8_3_WT_Ctrl_Day9

value: Ctrl


title: m1_Young1_E14


title: Murine cDC1 cells from MLN - 04


title: Murine cDC1 cells from MLN - 02


title: Murine cDC1 cells from MLN - 03


title: Murine cDC1 cells from MLN - 06


title: m1_AY_Y3_N17


title: Murine cDC1 cells from MLN - 01


title: Murine cDC1 cells from MLN - 05


title: E2: CD8_2_WT_Ctrl_Day9


title: isp1-vrk1-3

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

institute: KAIST

data_processing:
Sequencing reads were aligned to the C. elegans trascriptome and genome WBcel235.87 (ce11) by using HISAT2 (v.2.0.5). Aligned transcripts were assembled and quantified by using SeqMonk
Genome_build: WBcel235.87 (ce11)
Supplementary_files_format_and_content: txt files with read counts were generated by using SeqMonk

organism: Caenorhabditis elegans

source_name: Whole body

growth_protocol: Worms were grown on NGM plates as previously described in 'Maintenance of C. elegans (Stiernagle T, WormBook, 2006)'.

extract_protocol:
RNA extraction was performed as previously described (Son et al., Nature Comm, 2017). Total RNA in the animals was extracted using RNAiso plus (Takara, Seta, Kyoto, Japan).
Libraries were constructed with TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, CA, USA) by Macrogen Inc. (Seoul, South Korea) following the manufacture’s instruction.

treatment_protocol: Wild-type N2 and isp-1(qm150) mutant animals were synchronized by using an embryo bleaching method, and synchronized larvae were fed with either control or vrk-1 RNAi bacteria until the worms reached young adult stage. To induce RNAi, 10 mM IPTG was treated on the bacteria seeded NGM plates. Worms were harvested with M9 buffer, washed to remove remaining bacteria.

tag: developmental stage

value: Day 0 adult

value: vrk-1 RNAi


title: 32_t14_i

description:
transfection 14, region 3-exon 2, ibrutinib
32_t14_i_S51
processed data file: TableS1_ibrutinib.xlsx

value: ibrutinib


title: 32_t14_2

description:
transfection 14, region 3-exon 2, day 2
32_t14_2_S89
processed data file: TableS2_dmso.xlsx


title: 32_t14_d

description:
transfection 14, region 3-exon 2, dmso
32_t14_d_S31
processed data file: TableS2_dmso.xlsx


title: 32_t13_i

description:
transfection 13, region 3-exon 2, ibrutinib
32_t13_i_S48
processed data file: TableS1_ibrutinib.xlsx


title: m1_Young2_D7

source_name: three-mo mouse BEC


title: 32_t13_d

description:
transfection 13, region 3-exon 2, dmso
32_t13_d_S39
processed data file: TableS2_dmso.xlsx


title: 32_t12_i

description:
transfection 12, region 3-exon 2, ibrutinib
32_t12_i_S21
processed data file: TableS1_ibrutinib.xlsx


title: 32_t13_2

description:
transfection 13, region 3-exon 2, day 2
32_t13_2_S30
processed data file: TableS2_dmso.xlsx


title: MDA_003

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

value: hepatocellular carcinoma (HCC)


title: m1_Young2_D9


title: D12: CD8_6_cKO_Dex_Day3

value: Day 3


title: MDA_001


title: m1_Young2_H9


title: isp1-vrk1-2


title: 32_t12_d

description:
transfection 12, region 3-exon 2, dmso
32_t12_d_S12
processed data file: TableS2_dmso.xlsx


title: 32_t12_2

description:
transfection 12, region 3-exon 2, day 2
32_t12_2_S3
processed data file: TableS2_dmso.xlsx


title: isp1-vrk1-1


title: m1_AY_Y3_I5


title: MDA_002


title: isp1-ctrl-3

value: control RNAi


title: 32_t11_2

description:
transfection 11, region 3-exon 2, day 2
32_t11_2_S62
processed data file: TableS2_dmso.xlsx


title: isp1-ctrl-2


title: D11: CD8_5_cKO_Dex_Day3

value: CD8+ T cells


title: m1_Young1_I17


title: 31b_t9_i

description:
transfection 9, region 2-exon 2, ibrutinib
31b_t9_i_S52
processed data file: TableS1_ibrutinib.xlsx


title: E1: CD8_1_WT_Ctrl_Day9

value: Day 9


title: isp1-ctrl-1


title: m1_Young1_H1


title: 31b_t9_d

description:
transfection 9, region 2-exon 2, dmso
31b_t9_d_S44
processed data file: TableS2_dmso.xlsx


title: N2-vrk1-3

value: wild type


title: D8: CD8_5_cKO_Ctrl_Day3


title: D7: CD8_4_cKO_Ctrl_Day3


title: m1_AY_Y3_O15


title: N2-vrk1-2


title: D6: CD8_3_WT_Dex_Day3


title: N2-vrk1-1


title: D5: CD8_2_WT_Dex_Day3


title: N2-ctrl-3


title: 31b_t16_c

description:
transfection 16, region 2-exon 2, RNA
31b_t16_c_S44
processed data file: TableS3_RNA.xlsx


title: 31b_t16_g

description:
transfection 16, region 2-exon 2, gDNA
31b_t16_g_S30
processed data file: TableS3_RNA.xlsx


title: m1_AY_Y3_P17


title: D9: CD8_6_cKO_Ctrl_Day3


title: D3: CD8_3_WT_Ctrl_Day3


title: m1_AY_Y3_J13


title: m1_Young2_B15


title: D10: CD8_4_cKO_Dex_Day3


title: N2-ctrl-1


title: D2: CD8_2_WT_Ctrl_Day3


title: N2-ctrl-2


title: 31b_t9_2

description:
transfection 9, region 2-exon 2, day 2
31b_t9_2_S36
processed data file: TableS2_dmso.xlsx


title: m1_AY_Y3_I17


title: m1_AY_Y3_F18


title: D1: CD8_1_WT_Ctrl_Day3


title: m1_AY_Y3_L10


title: m1_Young1_G5


title: Dm.TraPR.2.R1

first: Stefan

last: Oberlin

address: 505 Parnassus Ave

department: Department of Microbiology and Immunology

institute: University of California, San Francisco

description: processed data file: Dm_miRNA_counts.csv

data_processing:
Illumina Casava1.8 software used for basecalling.
Trimming of reads with Trimmomatic 0.36
Mapping to the Arabidopsis thaliana genome (TAIR10) with Bowtie 1.2.1.1
Mapping to the Drosophila melanogaster genome (BDGP6) with Bowtie 1.2.1.1
Mapping to the Mus musculus genome (GRCm38) with Bowtie 1.2.1.1
Read counting to miRBase annotation with Rsubread 1.26.1
Read normalization with DEseq2.
Genome_build: TAIR10
Genome_build: BDGP6
Genome_build: GRCm38
Supplementary_files_format_and_content: comma separated text files of library and log2 normalized miRNA read counts

organism: Drosophila melanogaster

extract_protocol:
RNA was extracted with the standard TRIzol method or with the TRaPR isolation method.
Libraries were prepared with from TRIzol or TRaPR isolated RNA with the TRUseq or Lexogen sRNA library preparation kits or with a custom library preparation protocol.

value: ovaries

tag: library preparation

value: custom

tag: rna isolation

value: TraPR

tag: molecule subtype

value: small RNA


title: 31b_t13_i

description:
transfection 13, region 2-exon 2, ibrutinib
31b_t13_i_S47
processed data file: TableS1_ibrutinib.xlsx

data_processing:
Library strategy: Amplicon
Illumina bcl2fastq v2.16 for base calling and demultiplex.
Paired-End read to mergeR algorithm to align read 1 and read 2 (https://www.h-its.org/downloads/pear-academic/).
Custom python scripts were used to keep sequences from homology directed repair and to trim to the editing region. Briefly, we kept entries that contained both the silent sgRNA blocking changes that we introduced for each sgRNA and a single additional NNK substitution within a single codon in the repair region associated with the ssODN library. Note that sequences containing the silent sgRNA blocking change without additional changes were also preserved. All remaining sequences were then trimmed so that they only contained the repair region associated with the ssODN library. Finally, we reverse complemented some fastq files so that all of the individual sequences corresponded with the coding strand, regardless of sequencing orientation.
To filter sequence by quality (minimum single base quality 25, average read quality 30) and extract counts for each variant present in fastq files from sequencing of gDNA from samples at day 2 and day 14, as well as in RNA at day 2, we used the Enrich2 software package (https://github.com/FowlerLab/Enrich2).
We used custom python scripts to scale, normalize and log transform the data from the growth and ibrutinib screens. For each variant in each replicate, we calculated fold-change by dividing the number of counts at day 14 by those at day 2. Next, the data generated from each replicate in each library was scaled (min-max) based on the average of the highest and lowest 2.5% of the measurements. For each replicate in each library, we then normalized each individual measurement to the scaled fold-change calculation of the silent guide blocking HDR sequence (‘_wt’). At this point, we log2-transformed each replicate. To calculate the “functional score” cited in the text and tables, we took the mean of the log2-transformed replicates. Lastly, for each variant, the lower bound of the 90% confidence interval was calculated by multiplying the standard error by the critical t-value (based on the number of degrees of freedom for each measurement) and subtracting this from the “functional score”. Likewise, the upper bound of the 90% confidence interval was calculated by multiplying the standard error by the critical t-value and adding this to the “functional score”.
Genome_build: GRCh38
Supplementary_files_format_and_content: *xlsx: Excel files include counts, normalized variant frequencies, scores for all variants.

value: lymphoma


title: 31b_t15_c

description:
transfection 15, region 2-exon 2, RNA
31b_t15_c_S37
processed data file: TableS3_RNA.xlsx

value: untreated


title: 31b_t15_g

description:
transfection 15, region 2-exon 2, gDNA
31b_t15_g_S23
processed data file: TableS3_RNA.xlsx


title: 31b_t13_2

description:
transfection 13, region 2-exon 2, day 2
31b_t13_2_S29
processed data file: TableS2_dmso.xlsx


title: Dm.TraPR.5.R2


title: 709_2_Adad2_mutant

city: New Brunswick

first: Elizabeth

middle: M

last: Snyder

state: NJ

address: 59 Dudley Rd Foran Hall 328

department: Animal Science

institute: Rutgers University

data_processing:
RNA-seq reads from triplicate juvenile testis samples were aligned to an expanded testis transcriptome (Gamble, et al, Reproduction, 2020) via RSEM.
RSEM exp. counts were summarized by RSEM to generate the count matrix (gene and isoform level)
Differential gene expression was calculated by EBSeq (gene and isoform level)
Genome_build: GRCm38 genome

source_name: late juvenile whole testis

extract_protocol:
Samples were stored in RNAlater® (Life Technologies, Grand Island, NY) at -20° C until extraction. Total RNA extraction via the mirVana RNA isolation kit (Life Technologies, Grand Island, NY) was performed per manufacturer’s instructions.
RNA sequencing libraries for 100 bp paired-end sequencing were produced using the TruSeq RNA Sample prep Kit v2 Set A and B (Illumina, San Diego, CA).
Paired-end RNA sequencing was performed on an Illumina HiSeq 2000 at The Jackson Laboratory (Bar Harbor, ME).

value: Adad2 mutant

value: testis

tag: developmental state

value: 25 dpp


title: D4: CD8_1_WT_Dex_Day3

value: Dex


title: 31b_t12_i

description:
transfection 12, region 2-exon 2, ibrutinib
31b_t12_i_S20
processed data file: TableS1_ibrutinib.xlsx

value: ibrutinib


title: m1_Young1_C17

value: primary murine brain endothelial cells


title: m1_Young1_N14


title: 709_1_Adad2_mutant


title: Dm.TraPR.5.R1


title: 610_3_Adad2_mutant


title: Dm.TraPR.10.R2


title: 31b_t12_d

description:
transfection 12, region 2-exon 2, dmso
31b_t12_d_S11
processed data file: TableS2_dmso.xlsx

value: DMSO


title: 31b_t12_2

description:
transfection 12, region 2-exon 2, day 2
31b_t12_2_S2
processed data file: TableS2_dmso.xlsx


title: Dm.TraPR.2.R2


title: Dm.TraPR.10.R1


title: 31a_t16_g

description:
transfection 16, region 1-exon 2, gDNA
31a_t16_g_S29
processed data file: TableS3_RNA.xlsx


title: 31b_t13_d

description:
transfection 13, region 2-exon 2, dmso
31b_t13_d_S38
processed data file: TableS2_dmso.xlsx


title: 722_3_Wildtype

value: Wildtype


title: m1_Young2_N2


title: Dm.TraPR.25.R2


title: Dm.TraPR.25.R1


title: Dm.TraPR.50.R2


title: m1_Young1_F4


title: 31a_t15_g

description:
transfection 15, region 1-exon 2, gDNA
31a_t15_g_S22
processed data file: TableS3_RNA.xlsx


title: 31a_t16_c

description:
transfection 16, region 1-exon 2, RNA
31a_t16_c_S43
processed data file: TableS3_RNA.xlsx


title: m1_Young1_F15


title: 33_t12_i

description:
transfection 12, region 4-exon 2, ibrutinib
33_t12_i_S22
processed data file: TableS1_ibrutinib.xlsx


title: Cranio/Cervico/Thoracic E12.5 PlpcreERT2;Tom [SS2_15_0073]

city: Stockholm

first: Saida

last: Hadjab

address: Solnav. 9

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description: corresponding raw files include SS2_15_0073 in the filename

data_processing:
The samples were analyzed by first demultiplexing the fastq files using deindexer (http://github.com/ws6/deindexer) using the nextera index adapters and the 384 well layout.
Individual fastq files were then mapped to the relevant genome assembly using the STAR aligner (Dobin et al. Bioinformatics 2013) using 2-pass alignment to have improved performance of de novo splice junction reads, filtered for only uniquely mapping reads that are saved in the BAM  file.
The expression values were computed per gene as described in Ramsköld et al. (2009 PLoS Comp Biol), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo (Storvall et al. 2013 PLoS ONE).
BAM files from each plate were processed using python command-line velocity tool10, using run-smartseq2 command with GENCODE M21 genome and repeat masker annotation files
count matrix was pre-processed using PAGODA2 package, which includes normalization, clustering of cells, and projection on low embedding for visualization
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts.csv contains compiled count data from all plates, plate id is mentionned in cell name. p2w_sensory are R readable rds file and pagoda2 web app bin file, which can be opened on http://pklab.med.harvard.edu/nikolas/pagoda2/frontend/current/pagodaLocal/index.html. adata_sensory.loom contains spliced and unspliced count matrices for RNA velocity inference

extract_protocol:
Brachial DRGs were dissected (from E11 embryos), embryonic trunks (E10.5 and younger) and cranio/cervico/thoracic (E12.5) parts from the embryo were collected in Leibovit’z L-15 medium (Life technologies) on ice. The tissue was incubated in 0.05% trypsin-EDTA (1×) (Life technologies) for 5, 7, 10 and 15 min for tissue obtained from E9.5, E10.5, E11.5 and E12.5, respectively, at 37 °C, in a thermomixer comfort (Eppendorf) at 700 RPM. After spinning down the samples at 100 RCF for 5 min, the supernatant was removed and replaced by Leibovit’z L-15 medium (Life technologies). The tissue following enzymatic digestion was physically triturated using two different sizes of pipettes previously coated with 0.2% bovine serum albumin until the solution homogenized. The cell suspension was then filtered through a 70-μm cell strainer (BD Biosciences) to remove the clusters of cells.
RNA libraries were prepared according to Smart-seq2 protocol.


title: 610_4_Wildtype


title: m1_AY_Y3_M18


title: m1_AY_Y3_C6


title: Dm.ribodep.oxid.R2

value: custom; ribodepleted & oxidized

value: TRIzol & size selection


title: 31a_t15_c

description:
transfection 15, region 1-exon 2, RNA
31a_t15_c_S36
processed data file: TableS3_RNA.xlsx


title: 722_6_Wildtype


title: m1_Young2_P2


title: m1_Young2_L5


title: DRG E12.5 Ntrk3cre;Tom [SS2_16_384]

description: corresponding raw files include SS2_16_384 in the filename

source_name: DRG E12.5 Ntrk3cre;Tom

extract_protocol:
Brachial DRGs were dissected (from E11 embryos), embryonic trunks (E10.5 and younger) and cranial parts the embryo were collected in Leibovit’z L-15 medium (Life technologies) on ice. The tissue was incubated in 0.05% trypsin-EDTA (1×) (Life technologies) for 5, 7, 10 and 15 min for tissue obtained from E9.5, E10.5, E11.5 and E12.5, respectively, at 37 °C, in a thermomixer comfort (Eppendorf) at 700 RPM. After spinning down the samples at 100 RCF for 5 min, the supernatant was removed and replaced by Leibovit’z L-15 medium (Life technologies). The tissue following enzymatic digestion was physically triturated using two different sizes of pipettes previously coated with 0.2% bovine serum albumin until the solution homogenized. The cell suspension was then filtered through a 70-μm cell strainer (BD Biosciences) to remove the clusters of cells.
RNA libraries were prepared according to Smart-seq2 protocol.

value: dorsal root ganglion


title: DRG E11.5 Ntrk3cre;Tom [SS2_16_385]

description: corresponding raw files include SS2_16_385 in the filename

source_name: DRG E11.5 Ntrk3cre;Tom


title: Dm.ribodep.oxid.R1

description: processed data file: Dm_miRNA_counts.csv

value: ovaries


title: m1_Young1_M7


title: Dm.ribodep.R2

value: custom; ribodepleted


title: DRG E10.5 Isl1cre;Tom [SS2_17_433]

description: corresponding raw files include SS2_17_433 in the filename

source_name: DRG E10.5 Isl1cre;Tom


title: Cranio/Cervico/Thoracic E12.5 PlpcreERT2;Tom [SS2_15_0169]

description: corresponding raw files include SS2_15_0169 in the filename


title: m1_Young2_J13


title: 31a_t13_i

description:
transfection 13, region 1-exon 2, ibrutinib
31a_t13_i_S46
processed data file: TableS1_ibrutinib.xlsx

extract_protocol:
Zymo Research Genomic DNA Clean and Concentrator and Quick DNA/RNA kits.
Each sample was first amplified for 18 cycles with primers (see Table S6 for sequences) that generated 700-980bp amplicons using GXL PrimSTAR Polymerase (TaKaRa). Samples were then purified with Agencourt AMPure XP reagent (Beckman Coulter) at 0.8x beads to sample volume ratio according to manufacturer’s protocol and amplified for another 7 cycles with locus-specific primers containing Illumina adaptor sequences. The amplicons were purified with 1X AMPure beads, and reamplified for 7 cycles using primers containing Illumina p5 and p7 sequences and a unique sample index.


title: 31a_t13_d

description:
transfection 13, region 1-exon 2, dmso
31a_t13_d_S37
processed data file: TableS2_dmso.xlsx


title: 31a_t12_i

description:
transfection 12, region 1-exon 2, ibrutinib
31a_t12_i_S19
processed data file: TableS1_ibrutinib.xlsx


title: DRG E10.5 Isl1cre;Tom [SS2_17_432]

description: corresponding raw files include SS2_17_432 in the filename


title: Dm.ribodep.R1


title: Dm.TraPR.50.R1

value: custom

value: TraPR


title: 31a_t12_d

description:
transfection 12, region 1-exon 2, dmso
31a_t12_d_S10
processed data file: TableS2_dmso.xlsx

value: lymphoma


title: DRG E10.5 Isl1cre;Tom [SS2_16_688]

description: corresponding raw files include SS2_16_688 in the filename


title: DRG E10.5 Isl1cre;Tom [SS2_16_769]

description: corresponding raw files include SS2_16_769 in the filename


title: m1_Young1_J16


title: 31a_t12_2

description:
transfection 12, region 1-exon 2, day 2
31a_t12_2_S1
processed data file: TableS2_dmso.xlsx

value: untreated


title: m1_AY_Y3_H11


title: m1_AY_Y3_L9


title: DRG E9.5 Isl1cre;Tom [SS2_17_435]

description: corresponding raw files include SS2_17_435 in the filename

source_name: DRG E9.5 Isl1cre;Tom


title: 31a_t13_2

description:
transfection 13, region 1-exon 2, day 2
31a_t13_2_S28
processed data file: TableS2_dmso.xlsx


title: m1_Young2_E3


title: RNA-seq: Spn1-AID + DMSO 2

first: Fred

last: Winston

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
RNA-seq of the Spn1-AID strain treated with DMSO.

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). The random hexamer molecular barcode on the 5′ end of each read was removed and processed using a custom Python script. Cutadapt was then used to remove adapter sequences and low-quality base calls from the 3′ end of the read, as well as poly-A sequences from the 5′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using TopHat2 without a reference transcriptome, and uniquely mapping alignments were selected using SAMtools. Alignments mapping to the same location as another alignment with the same molecular barcode were identified as PCR duplicates and removed using a custom Python script. Coverage corresponding to the 3′-most base of the RNA fragment sequenced as well as the entire interval for each alignment was extracted using BEDTools genomecov and normalized to the total number of alignments uniquely mapping to the S. pombe genome.
"Minus" and "plus" bigWig files are spike-in normalized coverage of entire RNA-seq alignments mapping to the minus and plus strands, respectively.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

organism: Saccharomyces cerevisiae

source_name: RNA-seq: Spn1-AID + DMSO 2

extract_protocol:
Total RNA was prepared by hot acid phenol extraction, and a portion of each sample was treated with RQ1 DNase and used for subsequent steps (Promega, M6101). Ribosomal RNA was depleted using a Ribo-Zero kit for yeast (Illumina, MRZY1324) as per manufacturer instructions, except all volumes were halved.
Library preparation was carried out according to a previously published method (doi:10.1002/0471142727.mb0414s98), except fragmentation was performed prior to linker ligation for RNA-seq. Briefly, alkaline fragmentation (2x fragmentation buffer: 100 mM NaCO3 pH 9.2, 2 mM EDTA pH 8.0) was performed to obtain 40-70-nucleotide fragments that were subsequently size-selected and dephosphorylated with T4 PNK (NEB, M0201S) for ligation of a 3’ DNA linker containing a random hexamer molecular barcode to allow detection of PCR duplicates. First-strand cDNA was synthesized with SuperScriptIII (Invitrogen, #56575) using a primer with sequence complimentary to the 3’ linker and with an additional adapter sequence. cDNA was circularized with CircLigase (Epicentre, CL4111K). DNA libraries were amplified by PCR for 6-10 cycles with Phusion HF DNA Polymerase (NEB, M0530) using Illumina TruSeq indexing primers for multiplexing. Libraries were gel-purified and run on Agilent Bioanalyzer and/or TapeStation to assess size distribution, quality, and concentration.

treatment_protocol: Cells were grown in YPD at 30°C to ~ 3.5 x 107 cells/mL, diluted back to OD600 ≈ 0.3 in pre-warmed YPD, treated with DMSO, and grown for an additional 90 minutes.

value: MATa leu2delta1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6


title: Human iPSCs [SC_2_1]

city: Aurora

first: Edward

last: Lau

state: CO

address: 12700 E19th Av RCII Rm 8004

department: Medicine/Cardiology

institute: University of Colorado

description:
SC_2_1
small RNA
processed data file: transcript_count_matrix.csv

data_processing:
Indexing GRCh38 for 75nt single end using STAR v.2.7.3a.
Alignment to indexed genome using STAR v.2.7.3a (--outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1 --clip3pAdapterSeq TGGAATTCTCGGGTGCCAAGG --clip3pAdapterMMp 0.1).
Remove 5' genomically trimmed reads, convert to sorted bam using samtools v.1.10.
Quantify transcripts using StringTie v.2.11 against miRBase v.22.1 annotations (-e -b).
Genome_build: GRCh38
Supplementary_files_format_and_content: transcript_count_matrix.csv: Comma-separated text file output by Stringtie containing transcript counts mapped to miRBase v22.1.

source_name: Induced pluripotent stem cells

growth_protocol: Human induced pluripotent stem cells were passaged using standard protocols then differentiated into cardiomyocytes, endothelial cells, and fibroblasts in vitro using published protocols from the Wu lab.

extract_protocol:
Exosomes were extracted from culture medium supernatant, followed by Qiagen miRNeasy isolation of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq small RNA).

treatment_protocol: Untreated

value: Induced pluripotent stem cells exosomes

tag: biological replicate


title: RNA-seq: Spn1-AID + IAA 1

city: Boston

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
RNA-seq of the Spn1-AID strain treated with IAA.

source_name: RNA-seq: Spn1-AID + IAA 1

treatment_protocol: Cells were grown in YPD at 30°C to ~ 3.5 x 107 cells/mL, diluted back to OD600 ≈ 0.3 in pre-warmed YPD, treated with IAA at a final concentration of 25 μM, and grown for an additional 90 minutes.

value: 25 microM IAA


title: RNA-seq: Spn1-AID + DMSO 1

source_name: RNA-seq: Spn1-AID + DMSO 1


title: RNA-seq: Spn1-AID + IAA 2

source_name: RNA-seq: Spn1-AID + IAA 2


title: Human iPSCs [SC_1_2]

description:
SC_1_2
small RNA
processed data file: transcript_count_matrix.csv


title: m1_Young2_O17


title: RNA-seq: Spn1-noAID + IAA 2

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1
RNA-seq of the Spn1-noAID strain treated with IAA.

source_name: RNA-seq: Spn1-noAID + IAA 2

value: MATa leu2delta1 ura3-52 CgLEU2::OsTIR1


title: Human iPSCs [SC_1_1]

description:
SC_1_1
small RNA
processed data file: transcript_count_matrix.csv


title: m1_Young2_E11


title: Human iPSCs [SC_2_2]

description:
SC_2_2
small RNA
processed data file: transcript_count_matrix.csv


title: Trunk E10.5 Wnt1cre;Tom [SS2_18_109]

description: corresponding raw files include SS2_18_109 in the filename

source_name: Trunk E10.5 Wnt1cre;Tom

value: trunk


title: m1_AY_Y3_C12

value: primary murine brain endothelial cells


title: Trunk E10.5 Wnt1cre;Tom [SS2_18_108]

description: corresponding raw files include SS2_18_108 in the filename


title: DRG E9.5 Isl1cre;Tom [SS2_16_767]

description: corresponding raw files include SS2_16_767 in the filename


title: Human iPSC-Fibroblasts [FB_2_2]

description:
FB_2_2
small RNA
processed data file: transcript_count_matrix.csv

value: iPSC-derived fibroblasts exosomes


title: m1_Young1_E10


title: Human iPSC-Fibroblasts [FB_2_1]

description:
FB_2_1
small RNA
processed data file: transcript_count_matrix.csv


title: RNA-seq: Spn1-noAID + DMSO 2

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1
RNA-seq of the Spn1-noAID strain treated with DMSO.

source_name: RNA-seq: Spn1-noAID + DMSO 2

value: DMSO


title: RNA-seq: Spn1-noAID + IAA 1

source_name: RNA-seq: Spn1-noAID + IAA 1


title: RNA-seq: Spn1-noAID + DMSO 1

source_name: RNA-seq: Spn1-noAID + DMSO 1


title: Trunk E9.5 Wnt1cre;Tom [SS2_15_0085]

description: corresponding raw files include SS2_15_0085 in the filename

source_name: Trunk E9.5 Wnt1cre;Tom


title: Human iPSC-Fibroblasts [FB_1_2]

description:
FB_1_2
small RNA
processed data file: transcript_count_matrix.csv


title: m1_AY_Y3_J14

source_name: three-mo mouse BEC


title: Human iPSC-Cardiomyocytes [FB_1_1]

description:
FB_1_1
small RNA
processed data file: transcript_count_matrix.csv


title: m1_AY_Y3_M14


title: RNA-seq: wild type + IAA 2

description:
MATa leu2∆1 ura3-52
RNA-seq of a wild type strain treated with IAA.

source_name: RNA-seq: wild type + IAA 2

value: MATa leu2delta1 ura3-52


title: Human iPSC-Endothelial Cells [EC_2_1]

description:
EC_2_1
small RNA
processed data file: transcript_count_matrix.csv

value: iPSC-derived endothelial cells exosomes


title: m1_AY_Y3_P10


title: RNA-seq: wild type + DMSO 2

description:
MATa leu2∆1 ura3-52
RNA-seq of a wild type strain treated with DMSO.

source_name: RNA-seq: wild type + DMSO 2


title: m1_Young2_A17


title: RNA-seq: wild type + DMSO 1

source_name: RNA-seq: wild type + DMSO 1


title: Human iPSC-Endothelial Cells [EC_1_2]

description:
EC_1_2
small RNA
processed data file: transcript_count_matrix.csv


title: Trunk E10.5 Wnt1cre;Tom [SS2_18_107]

description: corresponding raw files include SS2_18_107 in the filename