title: PVB_before_surgery

city: Riga

first: Raitis

last: Peculis

address: Ratsupites str 1 k-1

country: Latvia

institute: Latvian Biomedical Research and Study Centre

data_processing:
The NGS data were analysed using CLC genomics workbench (v20.0.4.) (Qiagen, Germany)
Adapters were trimmed from 3’ end and any reads with the quality score < 0.02 were discarded
Length based trimming any reads that did not fall into the range of 15 - 55 nucleotides were discarded
miRNA and spike-in quantification the reads to were aligned miRBase (v22) and qiaseq_mirna (v1) spike-ins dataset. For alignment maximum allowed mismatches were set to 2 and for length based isomiRs maximum upstream / downstream bases were set to 2
Differential expression analysis was performed on CLC Genomics Workbench (v20.0.4) which is based on negative binomial distribution and uses trimmed mean of m-values (TMM) normalization method and outputs counts per million values (CPM).
Genome_build: GRCh38; miRBase (v22)
Supplementary_files_format_and_content: xlsx, raw count matrix

source_name: plasma miRNA 24 hours before transsphenoidal PitNET surgery

extract_protocol:
QIAseq miRNA Library QC qPCR Assay Kit includes 8 assays which allows to assess the following conditions: extraction efficiency and uniformity (UniSp100 and UniSp101), cDNA synthesis assessment (UniSp6), evaluation of hemolysis presence (miR-23a-3p and miR-451a), presence of constitutively expressed plasma miRNAs (miR-103a-3p, miR-191-5p, miR-30c-5p).
Plasma located EVs were isolated and their RNA contents were extracted from 0.5 – 1ml plasma samples using exoRNeasy Midi kit (Qiagen, Germany) according to manufacturer’s instructions.
miRNA library preparation was performed using Small RNA-Seq Library Prep Kit (Lexogen, Austria) according to manufacturer’s instructions. To avoid the contamination of adapter dimers and RNAs that exceed the range of small ncRNAs BluePippin electrophoresis (Sage Science, USA) was employed for size selection step.

value: blood plasma

tag: plasma sample acquired from

value: PVB

tag: time

value: before PitNET surgery


title: BIPSS-15-SIN

status: Public on Dec 29 2020

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: bilateral inferior petrosal sinus sampling plasma miRNA from left side of pituitary during the 15th minute after stimulation by CRH

tag: tissue

value: BIPSS, left side of pituitary

value: 15 minutes after CRH


title: PVB_24_hrs_before_BIPSS

source_name: plasma miRNA 24 hours before bilateral inferior petrosal sinus sampling procedure

value: before BIPSS


title: KB2（Control）

city: Zhenjiang

first: Hui

last: Chen

address: Xuefu Road

country: China

institute: jiangsu university

data_processing:
Data filtering was performed on Raw Data, the linker sequences and low-quality reads were removed to obtain high-quality Clean Data.
HISAT2 v2.1.0 was used to sequence alignment.
The reads numbers mapped to each gene were counted by HTSeq v0.6.0.
The number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) was used to estimate the gene expression levels of each gene which was calculated based on the length of the gene and reads count mapped to this gene
Genome_build: ftp://ftp.ensembl.org/pub/release-91/fasta/danio_rerio/dna/Danio_rerio.GRCz10.dna.toplevel.fa
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Danio rerio

source_name: larvae

extract_protocol:
120 hpf F1 larvae were snap frozened in liquid nitrogen, and total RNA was  harvested using Trizol reagent. The sequencing libraries were established with 3 μg RNA per sample by using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)
RNA libraries were sequenced by an Illumina platform and 150 bp paired-end reads (Annoroad Gene Technology Corporation)

tag: strain

value: AB

tag: age

value: 120 h post-fertilization

value: larvae

tag: genotype

value: wild type

tag: agent


title: Day0_Astrocyte_1_Batch2

city: Shanghai

first: Ran

last: Wang

address: 320 Yue Yang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

description: Astrocytes control without virus infection at day 0, sequencing batch 2

data_processing:
Raw reads were mapped to mm10 version of the mouse genome using the Tophat2 v2.0.4 program.
We calculated fragment per kilobase per million (FPKM) as expression level using Cufflinks v2.0.2 with default parameters.
Genes with the FPKM value > 1.0 in at least one sample across all samples were retained for further analysis.
The expression levels were transformed to logarithmic space by using log2(FPKM+1).
Batch effects were corrected using ComBat function in R.
Genome_build: mm10
Supplementary_files_format_and_content: Textfile includes FPKM values for each Sample

organism: Mus musculus

growth_protocol: Astrocyte controls were cultured on 12 cm dish with astrocyte medium (DMEM/F-12+10% FBS+1% PS+ 2% B27 + 10 ng/ml EGF + 10 ng/ml FGF2), and all other induction samples were cultured on 6-well cell plate with inducing medium (DMEM/F-12+1% PS+ 2% B27).

extract_protocol:
Total RNAs were extracted with Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing according to standard Illumina protocols.

treatment_protocol: Astrocyte controls without treatment, and other astrocyte samples were infected with lentivirus FUGW or FUGW-Ascl1.


title: PVB_24_hrs_post_surgery

source_name: plasma miRNA 24 hours after transsphenoidal PitNET surgery

value: after PitNET surgery


title: Piriformospora 21

city: Wuerzburg

first: William

middle: Andrés

last: López Arboleda

state: Bavaria

address: Klara-Oppenheimer-Weg 32

department: Biology

country: Germany

institute: University of Wuerzburg

data_processing:
Quantification of transcripts was performed using Salmon v0.7.2.
Quantification files were read into R environment (version 3.5.1) and formatted to downstream analysis using DESeq2
Condition Mock vs. Infected was tested for all cell layers in each Pathogen
Supplementary_files_format_and_content: Tab-delimited file containing TPM

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Per plate, 50-100 surface-sterilized seeds were placed on the cut surface. After 2 d of stratification in darkness at 4 °C, plants were germinated and seedlings were grown vertically in poly klima ® growth chambers (poly klima GmbH, Germany) at 22 °C ± 1 °C under long day conditions (16 h light / 8 h darkness). As soon as the roots reached the infection channel (9- 11 d old seedlings), the inoculation was started with freshly harvested fungal spores

extract_protocol:
The Infection systems were combined with Translating Ribosome Affinity Purification followed by RNA sequencing (iTRAPseq). Cell-layer specific FLAG-RPL18 expressing lines (pGL2::FLAG-RPL18, pPEP::FLAG-RPL18, pSCR::FLAG-RPL18 and pSHR::FLAG-RPL18) were used to obtain supernatants with purified polysomes. This supernants were transferred for RNA isolation. This step became necessary to remove the ribosomal proteins. For this, the RNeasy ® Micro Kit (Qiagen, Germany) was used according the manufacturer’s instructions. A volume of 15 μl RNA extract was obtained in the end (RNA concentrations > 13 ng/μl).
RNA quality and fragmentation size were checked using an Experion TM RNA HighSens Analysis Kit (Bio-Rad Laboratories, Inc.). Similarly, the quality of cDNA at the end of library preparation was checked with Experion TM DNA Chips (Bio-Rad Laboratories, Inc.). Thereby, cDNA concentrations were determined to pool the samples in equal amounts. High-throughput sequencing was performed on an Illumina Genome Analyzer IIx (GAIIx) platform following the manufacturer’s instructions.

treatment_protocol: Spore solutions were prepared in Milli-Q water supplemented with 1⁄4 MS. Every infection channel was filled with 500 μl of spore solution or a mock solution (Milli-Q water supplemented with 1⁄4 MS without microorganisms). At the indicated time points, roots were collected by removing the leaves with a scalpel, flipping of the medium and carefully plucking the roots out of the Agar with forceps. The material was flash-frozen in liquid nitrogen.

tag: cell layer

value: Rhizodermis

tag: pathogen

value: Serendipita indica

tag: treatment

value: Mock


title: BIPSS-5-SIN

source_name: bilateral inferior petrosal sinus sampling plasma miRNA from left side of pituitary during the 5th minute after stimulation by CRH

value: 5 minutes after CRH


title: DBPG-1(DBP)

value: DBP


title: Normal RGC sample 13

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

country: USA

institute: University of California Los Angeles

description:
Nor.13
Normal RGC sample
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2.
Aligned to mm10 using STAR2.4.0.
Count read using HT-seq0.6.1 using mm10 RefSeq as reference.
Normalization (TMM), and differential expression analysis using EdgeR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Complete_geneList_EdgeR.xlsx: Excel file

source_name: Adult RGCs by FACS

growth_protocol: Adult mice expressing CFP in retinal ganglion cells received treatment or control vehicle after optic nerve crush. Virus-transfected RGCs were selected by FACS (CFP+mCherry) 1, 3, 5 days after nerve injury and treatment.

extract_protocol:
RNA Pico chip. RNA concentration determined by RiboGreen RNA Assay kit (Life Technologies).
NuGen Ovation RNA-Seq System V2 (non-stranded) kit and TruSeq nano DNA Library Prep.
69bp paired-end sequencing.

treatment_protocol: Treatment: AAV2-shPten-mCherry intraocular injection (-14d), optic nerve crush immediately followed by intraocular injection of recombinant oncomodulin + CPT-cAMP. Control: AAV2-mCherry intraocular injection (-14d), optic nerve crush immediately followed by intraocular injection of saline.

tag: cell type

value: Retinal ganglion cells (RGCs)

tag: genotype/variation

value: Cyan-fluorescent protein (CFP) expression in RGCs

value: Adult

value: Normal


title: PVB_24_hrs_after_BIPSS

source_name: plasma miRNA 24 hours after bilateral inferior petrosal sinus sampling procedure

value: blood plasma

value: PVB

value: after BIPSS


title: Piriformospora 19

value: Infected


title: Piriformospora 20


title: WT #3

city: Smithville

first: Sharon

middle: Roth

last: Dent

state: Texas

address: 1808 Park Road 1C

institute: Univ Texas M.D. Anderson Cancer Center

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version HD 3.4.0.38).
The reads were mapped to the mouse genome mm10 by TopHat (version 2.0.10).
The number of fragments in each known gene from GENCODE Release M19 was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genome_build: mm10
Supplementary_files_format_and_content: Number of fragments in each gene

source_name: spleen

extract_protocol:
CD19+ B cells were sorted by flow cytomety, cells were washed and pelleted. RNA was extracted using Qiagen Rneasy minikit.
RNA libraries were prepared for sequencing using Illumina TruSeq stranded Total RNA library Prep kit using standard Illumina protocols.

value: CD19+ B cells

value: WT


title: BIPSS-0-SIN

source_name: bilateral inferior petrosal sinus sampling plasma miRNA from left side of pituitary before stimulation by CRH

value: BIPSS, left side of pituitary

value: before CRH


title: BIPSS-5-DX

source_name: bilateral inferior petrosal sinus sampling plasma miRNA from PitNET side (right) of pituitary during the 5th minute after stimulation by CRH

value: BIPSS, PitNET side (right) of pituitary


title: KB1（Control）

value: AB

value: 120 h post-fertilization

value: larvae

value: wild type


title: BIPSS-0-DX

source_name: bilateral inferior petrosal sinus sampling plasma miRNA from PitNET side (right) of pituitary before stimulation by CRH


title: BIPSS-15-DX

source_name: bilateral inferior petrosal sinus sampling plasma miRNA from PitNET side (right) of pituitary during the 15th minute after stimulation by CRH

value: 15 minutes after CRH


title: Piriformospora 16

value: Cortex

value: Serendipita indica

value: Mock


title: Piriformospora 17


title: Normal RGC sample 12

description:
Nor.12
Normal RGC sample
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Retinal ganglion cells (RGCs)

value: Cyan-fluorescent protein (CFP) expression in RGCs

value: Adult

value: Normal


title: Eµ-Myc Gcn5 Fx/Fx #3

value: CD19+ B cells

value: CD19 CreTg/0; E{mu}-Myc Tg/0; GCN5Fx/Fx


title: WT #2

value: WT


title: Normal RGC sample 11

description:
Nor.11
Normal RGC sample
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx


title: Piriformospora 18


title: Eµ-Myc Gcn5 Fx/Fx #2


title: Normal RGC sample 10

description:
Nor.10
Normal RGC sample
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx


title: Piriformospora 15

value: Infected


title: Eµ-Myc Gcn5 Fx/Fx #1


title: Piriformospora 14


title: Eµ-Myc #2

value: CD19 Cre0/0; E{mu}-MycTg/0; GCN5Fx/+


title: Eµ-Myc #3


title: Piriformospora 13


title: Eµ-Myc #1


title: Control sample 11, 5 days after nerve injury

description:
D5.C11
Control sample, 5 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Control

tag: time point

value: 5 days after nerve injury


title: Control sample 10, 5 days after nerve injury

description:
D5.C10
Control sample, 5 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx


title: Piriformospora 11

value: Endodermis


title: Treatment sample 13, 3 days after nerve injury

description:
D3.T13
Treatment sample, 3 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Treatment

value: 3 days after nerve injury


title: Sample_AN21

city: zhengzhou

first: Ma

last: Linna

address: East of Jianshe Road NO.1

department: Center for Reproductive Medicine

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Basecalls performed using bcl2fastq version 2.17
RNA-seq reads were mapped to human hg38 provided in Ensemble using  hisat2
Data were filtered using cutadapt  version 1.18
Genome_build: human hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: endometrial stromal cell line T-HESC

growth_protocol: Trypsin was used to digest T-HESC in logarithmic growth phase. T-HESC was adjusted to a density of 105 / ml with DME / F-12 medium containing 10% FBS, and was inserted into a 25cm2 cell culture flask a nd incubated overnight at 37 ° C.T-HESC were infected with the LV-PK2, or the control vector (NC). PK2-overexpressing T-HESCs were were measured by RT-PCR.

extract_protocol:
According to the process manual of RNeasy Mini Kit (250) Qiagen # 74106 kit, total RNA was extracted from decidualized cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When the growth of cells reached about 90% fusion, cells were cultivated in DMEM / F12 medium for 48h, and then were finally switched to fresh medium containing 8-Br-cAMP (0.5 mmol / l), MPA (1μmol /l) to induce the decidualization of the T-HESCs for 72 hours.

value: human-derived endometrial stromal cell

tag: treament

value: lentivirus infection


title: Piriformospora 10

value: Serendipita indica

value: Mock


title: Treatment sample 12, 3 days after nerve injury

description:
D3.T12
Treatment sample, 3 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Retinal ganglion cells (RGCs)

value: Cyan-fluorescent protein (CFP) expression in RGCs


title: Control sample 12, 5 days after nerve injury

description:
D5.C12
Control sample, 5 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Adult


title: Piriformospora 12


title: zVAD mock_rep2

city: Berkeley

first: Christopher

last: Duncan-Lewis

state: California

address: Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California Berkeley

description: 4-thiouridine-(4sU-)labeled RNA

data_processing:
Base calling using Illumina CASAVA 2.20
Reads were then trimmed of adaptors using Sickle/1.33
Reads were mapped to human reference genome hg19 and ERCC spike-in list, alignments obtained using STAR genome aligner 2.7.1
Raw gene counts obtained with Cuffquant program in Cufflinks suit 2.2.1
Differential expression values were calculated using Cuffdiff/2
Genome_build: hg19
Supplementary_files_format_and_content: .cbx files with gene counts generated with cuffquant for each sample
Supplementary_files_format_and_content: differential expression files (.diff)  comparing 2 replicates of DMSO/TRAIL samples, and 2 repliactes of zVAD/TRAIL samples

source_name: Colon carcinoma cells

growth_protocol: Cells were cultured to ~90% confluency in 15 cm2 plates in McCoy’s (modified) 5A medium supplemented with 10% FBS and 1 U/mL penicillin-streptomycin

extract_protocol:
Cells from each plate were trypsinized, pelleted, and then lysed with 2 mL TrizolTM reagent (Thermo Fisher Scientific Cat. #15596026). RNA was extracted according to manufacturer protocol and the resultant pellet was dissolved in 800 μL nuclease-free water. RNA was quantified using a Qubit fluorometer, and the 4sU-labeled transcripts from 200 μg total RNA were biotinylated and precipitated with strepdavidin beads according to the protocol detailed by Garibaldi, Carranza, and Hertel (Methods Mol Biol. 2017; 1648: 169–176) and resuspended in 12 μL nuclease free water.
125 ng of 4sU labeled RNA (also quantified by Qubit) from each sample was then used to make barcoded sequencing libraries with KAPA Stranded RNA-Seq Kit with RiboErase (KAPA Biosystems Cat #KR1151) according to manufacturer's instructions. In short, 4sU RNA was depleted of rRNA, fragmented into 300-400 bp segments, reverse transcribed into cDNA, ligated to adapters, and amplified over 13 PCR cycles. Fragment size of the libraries was confirmed via Agilent Bioanalyzer before the libraries were submitted for paired-end sequencing on a NovaSeq 6000 flow cell.

treatment_protocol: Each plate was pretreated with either 20 μM zVAD or equal volume (1:1000) of DMSO for 1 hr, before the addition of either 100 ng/uL SuperKillerTRAIL™ (Enzo Life Sciences Cat. #ALX-201-115-C010) or equal volume (1:1000) of KillerTRAIL storage and dilution buffer (Enzo Life Sciences Cat. #ALX-505-005-R500; "mock") for 2 hr. 50 μM 4sU was added for the last 20 min of the 2 hr TRAIL treatment to label nascent RNA.

tag: cell line

value: zVAD, no TRAIL


title: zVAD TRAIL_rep2

description: 4-thiouridine-(4sU-)labeled RNA

value: zVAD, TRAIL


title: WT #1

value: CD19+ B cells

value: WT


title: Sample_AN23


title: Sample_AN22


title: Sample_AC22

value: untreated


title: Sample_AC1


title: DMSO mock_rep2

description: 4-thiouridine-(4sU-)labeled RNA


title: DMSO TRAIL_rep2

description: 4-thiouridine-(4sU-)labeled RNA

value: TRAIL only


title: FH-AGO2_fPARCLIP_1Uul_RNaseT1_deep

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

data_processing:
Bcl2fastq (v2.20.0) was used to demultiplex and convert BCL basecall files from the sequencer to fastq files
Cutadapt (cutadapt 1.15 with Python 3.6.4) (19) was used to demultiplex adapter barcoded samples (without removing adapters). For demultiplexing libraries with a 5’ adapter barcode, the 5’ adapter barcode anchored to the 5’ end of the read was removed during demultiplexing (without removing UMIs)
PARpipe (https://github.com/ohlerlab/PARpipe) was used for further pre-processing, implementation of paralyzer
To allow the use of additional UMIs in the new protocol and preserve the true number of reads in the final bam file, during preprocessing fastq sequences were collapsed prior to adapter and UMI removal to remove potential PCR duplicates.
Genome_build: hg38
Supplementary_files_format_and_content: clusters(binding sites) csv files

growth_protocol: Flp-In™ 293 T-REx cells with stably integrated transgenic FLAG-HA tagged RBP of interest were cultured at 80% confluency in DMEM supplemented with 10% FBS and1x Pen/Strep

extract_protocol:
Following crosslinking, cells were collected in PBS and centrifuged at 500 x g for 5 minutes at 4°C. For chromatin associated RNPs (e.g U2AF1) cells were lysed by gentle resuspension in a modified HLB buffer (10 mM Tris at pH 7.5, 50 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 10% glycerol) for 2 min and spun for 2 min at 200 x g. The nuclei were washed twice with the same buffer and extracted using MWS buffer (10 mM Tris-HCl at pH 7.0, 4 mM EDTA, 0.3 M NaCl, 1 M urea, and 1% [v/v] NP-40). The chromatin pellet was washed twice in MWS buffer and resuspended in RIPA buffer(10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1%, sodium deoxycholate, 0.1% SDS, 140 mM NaCl supplemented with protease inhibitor cocktail (cOmplete, Sigma Aldrich 4693159001) followed by sonication in a bath sonicator (Bioruptor 300, Diagenode) 3 times for 30 seconds at medium amplitude at 4°C. 0.1 U/µl RNase I was added and incubation for 10 min at 22°C. For KHSRP, the cell pellet was lysed in 3 volumes of RIPA buffer and sonicated followed by addition of 0.1 U/µl RNase I and incubation for 10 min at 22°C. For cytoplasmic RBPs, cells were lysed in 3 volumes of NP40 lysis buffer (20 mM Tris, pH 7.5, 150 mM NaCl, 2 mM EDTA, 1% (v/v) NP40, 0.5 mM DTT) on ice for 15 minutes with optional addition of 0.1 U/µl RNase I and incubation for 10 min at 22°C. The cell extract was cleared at 15,000 x g for 15 minutes at 4°C.
Library conctraction was performed either with the radiolabel protocol or with fPAR-CLIP protocol

treatment_protocol: 8-12 hours before crosslinking, 4-thiouridine (4SU) was added to the cell culture medium at a final concentration of 100 µM. For U2AF1 PAR-CLIP, 4SU-labeling was reduced to 2 hours at a final concentration of 250 µM. Cells were washed once with 1x PBS and crosslinked with 0.3 J/cm2 of 312 or 365 nm UVA or UVB light for PAR-CLIP or 0.3 J/cm2 of 254 nm UVC light for regular CLIP in a Spectrolinker XL-1500 (Spectronics Corporation) or comparable instrument equipped with the appropriate UV lamps

value: Flp-In T-REx 293

tag: protein

tag: protocol

value: fPAR-CLIP-Seq

tag: clip antibody

value: Anti-FLAG® M2 Magnetic Beads, Millipore, M8823

value: NNTGACTGTGGAATTCTCGGGTGCCAAGG


title: FH-AGO2_fCLIP_UV254_1Uul_RNaseT1_deep

value: fCLIP-Seq


title: Piriformospora 9

value: Endodermis

value: Infected


title: Treatment sample 11, 3 days after nerve injury

description:
D3.T11
Treatment sample, 3 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Treatment

value: 3 days after nerve injury


title: Control sample 12, 3 days after nerve injury

description:
D3.C12
Control sample, 3 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Retinal ganglion cells (RGCs)

value: Cyan-fluorescent protein (CFP) expression in RGCs

value: Control


title: Piriformospora 5

value: Stele

value: Serendipita indica

value: Mock


title: Piriformospora 4


title: Piriformospora 8


title: Normal RGC sample 5

description:
Nor.5
Normal RGC sample
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Adult

value: Normal


title: Piriformospora 3


title: Sample_AC23

value: human-derived endometrial stromal cell

value: untreated


title: Piriformospora 7


title: zVAD mock_rep1

description: 4-thiouridine-(4sU-)labeled RNA

value: zVAD, no TRAIL


title: zVAD TRAIL_rep1

description: 4-thiouridine-(4sU-)labeled RNA

value: zVAD, TRAIL


title: Treatment sample 10, 3 days after nerve injury

description:
D3.T10
Treatment sample, 3 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx


title: DMSO TRAIL_rep1

description: 4-thiouridine-(4sU-)labeled RNA

value: TRAIL only


title: DMSO mock_rep1

description: 4-thiouridine-(4sU-)labeled RNA


title: COVID-19 lung scRNA-seq

city: Nashville

first: Jonathan

middle: A

last: Kropski

state: TN

department: Medicine

institute: Vanderbilt University Medical Center

data_processing:
CelRanger v4.0
Seurat v3.1
Genome_build: hg38
Supplementary_files_format_and_content: filtered_feature_bc_matrix - sparse matrix; covid_annotated.rds - analyzed integrated dataset

source_name: peripheral tissue

extract_protocol:
single-cell suspension from fresh tissue removed at the time of organ transplant surgery
10X Genomics 5' v1

value: lung


title: Control sample 13, 3 days after nerve injury

description:
D3.C13
Control sample, 3 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx


title: Zeocin_1

city: Princeton

first: Thomas

last: Shenk

state: New Jersey

address: 119 Lewis Thomas Laboratory, Washington Road

department: Molecular Biology

institute: Princeton University

data_processing:
Illumina Casava1.8+ software used for basecalling.
Barcode-split data was analyzed using Galaxy. RNA STAR aligner was used to map reads to the genome and to repbase sequences.
Counts for genes were obtained using featureCounts application from subread package
Differential expression was computed using the DESeq2 package.
Genome_build: Build 38, gencode annotation
Supplementary_files_format_and_content: tab-delimited text files include raw counts and expression for each sample

source_name: zeocin treated epithelial cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were either infected or treated with zeocin.

value: human retinal pigment epithelial cells

tag: passage

value: zeocin

tag: virus accession number


title: Control sample 10, 3 days after nerve injury

description:
D3.C10
Control sample, 3 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: 3 days after nerve injury


title: Piriformospora 2

value: Infected


title: Normal RGC sample 2

description:
Nor.2
Normal RGC sample
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Retinal ganglion cells (RGCs)

value: Cyan-fluorescent protein (CFP) expression in RGCs


title: Control_Female_rep1 (array)

type: genomic

city: Bangkok

first: Nakarin

last: Kitkumthorn

address: Yothee road

department: Oral Biology

country: Thailand

institute: Mahidol University

description:
PBMC from  female
control_HT29_1

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

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

data_processing: GenomeStudio software version 2011.1

label: Cy5 and Cy3

molecule: genomic DNA

source_name: PBMC

label_protocol: Standard Illumina Protocol

growth_protocol: The human colorectal adenocarcinoma cell lines were obtained from the American Type Culture Collection (ATCC) including HT29 (ATCC® HTB-38™) and SW480 (ATCC® CCL-228™). The Cells were grown with DMEM medium (Gibco BRL, USA) supplemented with 10% FBS at 37°C in a 5% CO2 in air atmosphere in culture flask. The cells were harvested at 80% confluence by using 0.05% Trypsin (with 0.5 mM EDTA) and washed by using phosphate buffer saline (PBS). All of this were used for maintaining cells.

extract_protocol: PBMCs were collected from Transwell culture six well plates and DNA was extracted and purified using Phenol-Chloroform.

treatment_protocol: Indirect or co-culture human colorectal adenocarcinoma cells with PBMC were performed in Transwell culture six well plates (Costar, France). The  human colorectal adenocarcinoma cells were seeded into plate (100,000 cells) with DMEM in experiment wells but not in control wells and then incubated overnight at 37°C in a 5% CO2 in air atmosphere. The PBMC were plated on permanent membrane culture of Transwell (2 × 100,000 cells) and incubated for 4 hours at 37°C in a 5% CO2 in air atmosphere.

tag: gender

value: Female

value: PBMC


title: Piriformospora 1

value: Stele

value: Serendipita indica


title: Zeocin_2


title: Mock_1

source_name: mock infected epithelial cells

value: mock


title: LP351 MSC; a3cced37-4d05-4392-a4bb-f69e369c3413

city: Boston

first: Fasih

middle: Mubtasim

last: Ahsan

state: MA

address: 185 Cambridge Street, CPZN 6500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

description: a3cced37-4d05-4392-a4bb-f69e369c3413.rsem.txt.gz

data_processing:
Pre-Processing: Fibroblasts, iPSCs, and MSCs were each sequenced in biological triplicates and technical duplicates (n = 60 total samples) to account for variation in extraction and culturing. Raw sequencing reads were converted into fastq files and filtered for low quality reads and Illumina sequencing adapter contamination using bcl2fastq (Illumina). Reads were then quasi-mapped and quantified to the Homo sapiens GENCODE 28 (GRCh38.p12, Ensembl 92, April 2018) transcriptome using the alignment-free transcript level quantifier Salmon v0.9.1 (Harrow et al., 2012; Mudge and Harrow, 2015; Patro et al., 2017). A quasi-mapping index was prepared using parameters ?salmon index -k 31 ?type quasi?, and comprehensive transcript level estimates were calculated using parameters ?salmon quant -l A ?seqBias ?gcBias --discardOrphansQuasi?. Transcript level counts were collapsed to gene level (HGNC) counts, transcripts per million abundances (TPM) and estimated lengths using R Bioconductor package tximport v1.6.0 (Soneson et al., 2015).
Differential Gene Expression Analysis: The resulting sample gene count matrix was size factor normalized and analyzed for pairwise differential gene expression using R Bioconductor package DESeq2 v1.18.1. Expression changes were estimated using an empirical Bayes procedure to generate moderated fold change values with design ?~ Batch + Sample?, modeling batch effect variation due to day of RNA extraction (Huber et al., 2015; Love et al., 2014).  Significance testing was performed using the Wald test, and resulting P values were adjusted for multiple testing using the Benjamini-Hochberg procedure (Benjamini and Hochberg, 1995). DEGs were filtered using an adjusted false discovery rate (FDR) q value < 0.05 and an absolute log2 transformed fold-change > 1.
Gene Expression PCA: Variance stabilized transform (VST) values in the gene count matrix were calculated and plotted for principal component analysis (PCA) using R Bioconductor packages DESeq2, FactoMineR, and factoextra, as described in the metabolomics methods (Huber et al., 2015; Love et al., 2014). PCA of nuclear-encoded mitochondrial protein and mtDNA transcripts were extracted using localization evidence derived from MitoMiner v4.0, subsetting VST matrices using genes listed in MitoCarta 2.0 (Calvo et al., 2016; Smith and Robinson, 2016). Scatterplots and MA plots of gene expression fold-changes between fibroblasts, iPSCs, and MSCs were performed, and Pearson/Spearman correlation coefficients calculated, using R package ggpubr v0.1.6 (https://cran.r-project.org/web/packages/ggpubr/index.html). Genes of interest were extracted and averaged clonal heatmaps were prepared using R Bioconductor packages pheatmap v1.0.8 and gplots v3.0.1 (Gregory Warnes, 2016; Kolde, 2015). Venn diagram intersections of DEG lists were generated using Venny 2.1.0 (http://bioinfogp.cnb.csic.es/tools/venny/index.html)
Metabolic Transcript GSVA: GSVA on metabolic transcripts were performed similarly to metabolomics data as noted above. Pathway-level metabolic gene set enrichment analysis was performed using R Bioconductor package GSVA v1.26.0 function gsva() with parameters ?method = gsva, rnaseq = FALSE, abs.ranking = FALSE, min.sz = 5, max.sz = 500?  using a log2(TPM + 1) transformed gene expression matrix (Hanzelmann et al., 2013). GSVA pathway enrichment scores per sample were extracted and assessed for significance using R Bioconductor package limma v3.34.9, as described above except with a Benjamini-Hochberg adjusted P value threshold = 0.01. Pathway metabolite sets were constructed using the KEGG PATHWAY Database, utilizing gene sets annotated to the metabolic pathways overview map HSA01100 (Kanehisa et al., 2012). Significance testing across clones and conditions for each gene set were calculated using Kruskal-Wallis ANOVA.
Gene Set Overrepresentation Analysis: DEGs were extracted and analyzed for pathway/gene ontology (GO) term overrepresentation using the R Bioconductor package clusterProfiler v3.6.0 and ReactomePA v1.22.0, using a background gene set of all genes expressed with at least one read count in the sample gene count matrix (Yu and He, 2016; Yu et al., 2012). Overrepresented Reactome/KEGG pathways and GO terms were identified across DEG lists and conditions using clusterProfiler function compareCluster() with significance testing cutoffs of P < 0.05, and an adjusted FDR < 0.25.
CellNet Classification Analysis: We performed the CellNet algorithm to assess the similarity of cell-and-tissue (C/T) type specific gene regulatory networks (GRNs) between established C/T cohorts and our transfer samples (Cahan et al., 2014; Morris et al., 2014; Radley et al., 2017). All raw RNA-seq sample FASTQs were re-quantified and quasi-mapped to a modified Homo sapiens Ensembl 80 transcriptome pre-packaged with the CellNet R package using Salmon v0.8.2 (Patro et al., 2017). Transcript counts were then collapsed to gene level counts using tximport v1.6.0 and downsampled per 100,000 reads for CellNet input (Soneson et al., 2015). Samples were then benchmarked and classified against provided C/T type samples from the CellNet Processor repository (June 20th, 2017), using a random forest classifier to assess classification probability of a sample to a given C/T type.
HLA Class I Genotyping: MHC Class I HLA genotypes were identified using OptiType v1.3.1(Szolek et al., 2014). All raw RNA-seq sample FASTQs were aligned to the HLA Class I reference transcriptome packaged in OptiType using BWA MEM v0.7.17 with standard parameters (Li and Durbin, 2010). HLA subset reads were then analyzed for Class I genotype using OptiType in paired-end RNA mode with standard parameters.
Genome_build: Homo sapiens GENCODE 28 (GRCh38.p12, Ensembl 92, April 2018)
Supplementary_files_format_and_content: Salmon v0.9.1 quantification output files for each respective sample after quasi-mapping to the GENCODE 28 reference transcriptome. Columns are (in order): (1) Name of transcript from GENCODE 28 reference, (2) Length of the transcript (nt), (3) Effective length of the transcript, correcting for sequencing and GC fragment bias, (4) transcripts per million of the transcript (TPM), and (5) number of estimated reads mapping to each quantified transcript.

source_name: Differentiated in vitro mesenchymal stem cell (MSC) lines

growth_protocol: HEK293T expressing mitochondrial-targeted DsRed protein (Human Embryonic Kidney, pMitoDsRed, Clontech Laboratories) were generated as previously described (Miyata et al., 2014). BJ (Human Foreskin Fibroblast, CRL-2522), ADF (Adult Dermal Fibroblast, PCS-201-012), NDF (Neonatal Dermal Fibroblast,  PCS-201-010).  BJ, NDF, ADF, and HEK293T DsRed cells were cultured in “complete media” containing DMEM (Corning, Cat. # 10013CV) supplemented with 10% Fetal Bovine Serum (FBS, Hyclone, Cat. # SH30088.03HI0), penicillin-streptomycin (Corning, Cat. # 30-002-CI), GlutaMax (ThermoFisher, Cat. # 35050-061), and non-essential amino acids (MEM NEAA, ThermoFisher, Cat. # 11-140-050). BJ ρ0, NDF ρ0, and ADF ρ0 fibroblasts were cultured in complete media supplemented with 50 µg/ml uridine (Sigma, Cat. # U3003). IPSCs were cultured on matrigel (Corning, Cat. # 356234) coated plates in mTeSR1 media (StemCell Technologies, Cat. # 85850) according to manufacturer’s protocol. MSCs were cultured in defined, MesenCult-ACF media (StemCell Technologies, Cat. # 05449) following manufacturer’s protocol. Cells were tested frequently for mycoplasma using a universal mycoplasma detection kit (ATCC,  Cat. # 30-1012K).

extract_protocol:
Fibroblasts, iPSCs, and MSCs were grown in biological triplicates and technical duplicates to 70-80% confluence and purified using the RNeasy Mini Kit (Qiagen, Cat. # 74104) and RNase-free DNase (Qiagen, Cat. # 79254) following manufacturer’s protocols. All samples showed a A260/280 ratio > 1.99 (Nanodrop; Thermo Scientific). Prior to library preparation, quality control of the RNA was performed using the Advanced Analytical Technologies Fragment Analyzer (Advanced Analytical, Inc.) and analyzed using PROSize 2.0.0.51 software. RNA Quality Numbers (RQNs) were computed per sample with final scores between 8.1-10, indicating intact total RNA per sample prior to library preparation.
Strand-specific ribosomal RNA (rRNA) depleted RNA-Seq libraries were prepared from 1 µg of total RNA using the KAPA Stranded RNA-Seq Kit with Ribo-Erase (Kapa Biosystems, Roche). Briefly, rRNA was depleted from total RNA samples, the remaining RNA was heat fragmented, and strand-specific cDNA was synthesized using a first strand random priming and second strand dUTP incorporation approach. Fragments were then A-tailed, adapters were ligated, and libraries were amplified using high-fidelity PCR. All libraries were prepared in technical duplicates per sample (n = 60 samples, 120 libraries total), and resulting raw sequencing reads merged for downstream alignment and analysis. Libraries were paired-end sequenced at 2x150 bp on an Illumina NovaSeq 6000.

treatment_protocol: For mtDNA depleted BJ fibroblast generation: A 1000x stock of 2’,3’-dideoxycytidine (ddC, Sigma, Cat. # D5782) was prepared in water. BJ cells cultured in complete media with 50 µg/ml uridine were added ddC to an appropriate final concentration. Cells were passaged every 3-4 d and fresh ddC added over the course of 3 weeks. After ddC treatment, total DNA was extracted (Qiagen, Cat. # 69504) and mtDNA quantified using SYBR Select Master Mix for CFX (Life Technologies, Cat. # 4472942). For mitochondria transfer generation: Mitochondria were harvested from HEK293T DsRed cells, LP351 PBMC, or LP298 PBMC using a Qproteome Mitochondria Isolation Kit (Qiagen, Cat. # 37612) following manufacturer’s protocol. Mitochondrial pellets were resuspended in PBS at a concentration ~1 mg total protein/mL. Mitochondrial suspensions were delivered into ρ0 fibroblast cells using a mitochondrial transfer tool developed by NanoCav, LLC. Transferred fibroblasts were cultured in complete media with 50 μg/mL uridine for 4 d following mitochondria delivery. On day 5, cells were shifted to uridine-free complete media prepared with 10% dialyzed FBS (Life Technologies, Cat. #26400-044). On day 8, cells were shifted to glucose-free, galactose-containing medium (DMEM without glucose (Gibco, Cat. # 11966025) supplemented with 10% dialyzed FBS and 4.5 g/l galactose). Colonies emerged ~10 d post-delivery and cells were shifted back to uridine-free medium before colonies were counted by microscopy or isolated using cloning rings. For iPSC reprogramming: Fibroblast lines were reprogrammed to iPSCs using StemRNA-NM Reprogramming kit (Stemgent, Cat. # 00-0076) following manufacturer’s protocol. Briefly, fibroblasts were plated on a matrigel (Corning, Cat. # 356234) coated 6-well plate at 2 x 105 cells/well on Day 0. Daily transfections of non-modified (NM)-RNA reprogramming cocktail were carried out from days 1-4 using Lipofectamine RNAiMAX (ThermoFisher, Cat. # 13778100. On days 10-12, iPSC colonies were identified by staining with Tra 1-60 antibody (Stemgent, Cat. # 09-0068). Tra 1-60+ iPSC colonies were picked and re-plated on matrigel coated 12-well plates and maintained in mTeSR 1 (Stemcell Technologies, 85850). For MSC differentiation: MSC lines were generated from iPSCs using STEMdiff Mesenchymal Progenitor Kit (Stemcell Technologies, Cat. #05240) following manufacturer’s protocol. The provided substrate was used for the initial differentiation but the cells were plated on plastic for further passaging.

tag: condition

value: MSC

tag: transfer status

value: LP351 Transfer

tag: clonality

value: LP351 Transfer MSC Clone 11


title: LP351 MSC; d3487a8f-6d5e-44e3-9c6b-567078334cf1

description: d3487a8f-6d5e-44e3-9c6b-567078334cf1.rsem.txt.gz

value: Differentiated in vitro mesenchymal stem cell (MSC) lines

value: LP351 Transfer MSC Clone 2


title: Cancer_HT29_rep2 (array)

description:
PBMC from female co-culture with HT29
cancer_HT29_2


title: Phytoph_2.5hpi 15

tag: cell layer

value: Rhizodermis

value: Phytophtora parasitica

value: Mock


title: Cancer_SW480_rep2 (array)

description:
PBMC from male co-culture with SW480
cancer_SW480_2

value: Male


title: Untreated_1

source_name: untreated epithelial cells

value: human retinal pigment epithelial cells


title: HCMV_2

source_name: CMV infected epithelial cells

value: infected with virus CMV strain TB40


title: Phytoph_2.5hpi 16

source_name: Root

tag: pathogen


title: Cancer_SW480_rep1 (array)

description:
PBMC from male co-culture with SW480
cancer_SW480_1


title: Control_Male_rep1 (array)

description:
PBMC from  male
control_SW480_1


title: Cancer_HT29_rep1 (array)

description:
PBMC from female co-culture with HT29
cancer_HT29_1


title: HCMV_1

tag: treatment


title: Control_Female_rep2 (array)

description:
PBMC from  female
control_HT29_2

tag: cell type


title: Control_Male_rep2 (array)

description:
PBMC from  male
control_SW480_2


title: Normal RGC sample 4

description:
Nor.4
Normal RGC sample
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

source_name: Adult RGCs by FACS

value: Retinal ganglion cells (RGCs)

tag: genotype/variation

value: Cyan-fluorescent protein (CFP) expression in RGCs

tag: age

value: Adult

value: Normal


title: Untreated_2


title: Normal RGC sample 3

description:
Nor.3
Normal RGC sample
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx


title: Phytoph_2.5hpi 14

value: Infected


title: Mock_2

value: mock


title: HEK Transfer MSC; 15abb767-7694-4a8b-b3bc-cd923f40dda2

description: 15abb767-7694-4a8b-b3bc-cd923f40dda2.rsem.txt.gz

value: MSC

value: HEK Transfer

value: HEK Transfer MSC Clone 4


title: Normal RGC sample 1

description:
Nor.1
Normal RGC sample
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx


title: Phytoph_2.5hpi 13


title: BJ MSC; b4cd8875-d973-44d5-869c-73b7f8c4da93

description: b4cd8875-d973-44d5-869c-73b7f8c4da93.rsem.txt.gz

value: Differentiated in vitro mesenchymal stem cell (MSC) lines

value: BJ

value: BJ MSC


title: LP351 MSC; fcc59924-e4a6-4319-8c47-98c44c84a104

description: fcc59924-e4a6-4319-8c47-98c44c84a104.rsem.txt.gz

value: LP351 Transfer

value: LP351 Transfer MSC Clone 1


title: BJ MSC; 4c017238-ed3d-4143-adc2-da1bfad4c853

description: 4c017238-ed3d-4143-adc2-da1bfad4c853.rsem.txt.gz


title: Control sample 4, 5 days after nerve injury

description:
D5.C4
Control sample, 5 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Control

tag: time point

value: 5 days after nerve injury


title: Treatment sample 4, 5 days after nerve injury

description:
D5.T4
Treatment sample, 5 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Treatment


title: HEK Transfer MSC; e01a17f0-8487-4c96-9bdf-ed0f8780d4ed

description: e01a17f0-8487-4c96-9bdf-ed0f8780d4ed.rsem.txt.gz

value: HEK Transfer MSC Clone 1


title: Phytoph_2.5hpi 11

value: Cortex

value: Phytophtora parasitica

value: Mock


title: LP351 Transfer iPSC; 1f27bdc2-15f8-46a3-bc75-72c5a2994caf

description: 1f27bdc2-15f8-46a3-bc75-72c5a2994caf.rsem.txt.gz

source_name: Reprogrammed in vitro induced pluripotent stem cell (iPSC) lines

value: iPSC

value: LP351 Transfer iPSC Clone 1


title: Phytoph_2.5hpi 9

value: Infected


title: Treatment sample 2, 5 days after nerve injury

description:
D5.T2
Treatment sample, 5 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Retinal ganglion cells (RGCs)

value: Cyan-fluorescent protein (CFP) expression in RGCs

value: Adult


title: BJ iPSC; 9725b625-dc29-4b44-8e4e-cd9ac791820f

description: 9725b625-dc29-4b44-8e4e-cd9ac791820f.rsem.txt.gz

value: Reprogrammed in vitro induced pluripotent stem cell (iPSC) lines

value: BJ

value: BJ iPSC


title: HEK Transfer iPSC; 3f211dea-da0b-4d7d-b4af-fd8dd6f47cb9

description: 3f211dea-da0b-4d7d-b4af-fd8dd6f47cb9.rsem.txt.gz

value: HEK Transfer

value: HEK Transfer iPSC Clone 1


title: Phytoph_2.5hpi 7

value: Endodermis


title: HEK Transfer MSC; b99c3284-40e2-4e10-b209-e0d8f715484f

description: b99c3284-40e2-4e10-b209-e0d8f715484f.rsem.txt.gz

value: Differentiated in vitro mesenchymal stem cell (MSC) lines

value: MSC

value: HEK Transfer MSC Clone 2


title: Piriformospora 6

value: Stele

value: Serendipita indica


title: Treatment sample 3, 5 days after nerve injury

description:
D5.T3
Treatment sample, 5 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Treatment

value: 5 days after nerve injury


title: Treatment sample 1, 5 days after nerve injury

description:
D5.T1
Treatment sample, 5 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx


title: LP351 Transfer iPSC; 5e0a2969-5c32-4833-b6cf-c63e2ceb556a

description: 5e0a2969-5c32-4833-b6cf-c63e2ceb556a.rsem.txt.gz

value: iPSC

value: LP351 Transfer

value: LP351 Transfer iPSC Clone 2


title: Phytoph_2.5hpi 10

value: Cortex

value: Phytophtora parasitica

value: Infected


title: HEK Transfer iPSC; 2f89aa1b-6509-42b6-89a9-868e861b6145

description: 2f89aa1b-6509-42b6-89a9-868e861b6145.rsem.txt.gz

value: Reprogrammed in vitro induced pluripotent stem cell (iPSC) lines

value: HEK Transfer iPSC Clone 4


title: LP351 Transfer iPSC; 29c74692-c15b-4bb5-b46e-2a8d01a3d13e

description: 29c74692-c15b-4bb5-b46e-2a8d01a3d13e.rsem.txt.gz

value: LP351 Transfer iPSC Clone 11


title: Control sample 3, 5 days after nerve injury

description:
D5.C3
Control sample, 5 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Retinal ganglion cells (RGCs)

value: Cyan-fluorescent protein (CFP) expression in RGCs

value: Adult

value: Control


title: Treatment sample 1, 3 days after nerve injury

description:
D3.T1
Treatment sample, 3 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: 3 days after nerve injury


title: Control sample 2, 5 days after nerve injury

description:
D5.C2
Control sample, 5 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx


title: Phytoph_2.5hpi 12

value: Mock


title: Phytoph_2.5hpi 8

value: Endodermis


title: BJ iPSC; aff49441-7784-4e39-9dda-114811ef33da

description: aff49441-7784-4e39-9dda-114811ef33da.rsem.txt.gz

value: BJ

value: BJ iPSC


title: Control sample 1, 5 days after nerve injury

description:
D5.C1
Control sample, 5 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: 5 days after nerve injury


title: Phytoph_2.5hpi 3

value: Stele


title: BJ MSC; 6cdc6d3c-6af9-4fcb-89ab-18a16d164186

description: 6cdc6d3c-6af9-4fcb-89ab-18a16d164186.rsem.txt.gz

value: Differentiated in vitro mesenchymal stem cell (MSC) lines

value: MSC

value: BJ MSC


title: BJ iPSC; d3652ec5-d670-4544-9fc6-3716fb05cd02

description: d3652ec5-d670-4544-9fc6-3716fb05cd02.rsem.txt.gz

value: Reprogrammed in vitro induced pluripotent stem cell (iPSC) lines

value: iPSC


title: HEK Transfer iPSC; 45c90384-25ab-4c7f-8392-28a87a9b3c3d

description: 45c90384-25ab-4c7f-8392-28a87a9b3c3d.rsem.txt.gz

value: HEK Transfer

value: HEK Transfer iPSC Clone 2


title: BJ Rho Null Fibs; cd3c684e-26fe-4ea8-81df-fffc3dff959b

description: cd3c684e-26fe-4ea8-81df-fffc3dff959b.rsem.txt.gz

source_name: BJ neonatal foreskin fibroblast (CRL-2522)

value: Fibs

value: Rho Null

value: BJ Rho Null Fibroblast


title: LP351 Transfer Fibs; 1fa07146-0416-4a4c-8f15-20a0e44f4c57

description: 1fa07146-0416-4a4c-8f15-20a0e44f4c57.rsem.txt.gz

value: BJ neonatal foreskin fibroblast (CRL-2522)

value: LP351 Transfer

value: LP351 Transfer Fibroblast


title: BJ Fibs; 94799a70-74de-411e-bff1-e6c4ed715f0d

description: 94799a70-74de-411e-bff1-e6c4ed715f0d.rsem.txt.gz

value: BJ

value: BJ Fibroblast


title: Treatment sample 4, 3 days after nerve injury

description:
D3.T4
Treatment sample, 3 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Retinal ganglion cells (RGCs)

value: Cyan-fluorescent protein (CFP) expression in RGCs

value: Adult

value: Treatment

value: 3 days after nerve injury


title: Phytoph_2.5hpi 6

value: Endodermis

value: Phytophtora parasitica

value: Infected


title: LP351 Transfer Fibs; 2600a68f-7fa9-4217-8a48-ba7161abce84

description: 2600a68f-7fa9-4217-8a48-ba7161abce84.rsem.txt.gz


title: BJ Rho Null Fibs; 5491c6d3-31f1-483c-b4f7-b778e10c4272

description: 5491c6d3-31f1-483c-b4f7-b778e10c4272.rsem.txt.gz


title: LP351 Transfer Fibs ; 44ab6f65-74b0-46b9-a4f2-7804f5827acf

description: 44ab6f65-74b0-46b9-a4f2-7804f5827acf.rsem.txt.gz


title: Treatment sample 3, 3 days after nerve injury

description:
D3.T3
Treatment sample, 3 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx


title: Phytoph_2.5hpi 5


title: LP351 MSC; 52f558cb-1b97-4f8d-81be-13b8a0e9732c

description: 52f558cb-1b97-4f8d-81be-13b8a0e9732c.rsem.txt.gz

value: Differentiated in vitro mesenchymal stem cell (MSC) lines

value: MSC

value: LP351 Transfer MSC Clone 11


title: LP351 MSC; c7432564-97f0-45e6-b332-3e2753ee08ed

description: c7432564-97f0-45e6-b332-3e2753ee08ed.rsem.txt.gz

value: LP351 Transfer MSC Clone 2


title: Treatment sample 3, one day after nerve injury

description:
D1.T3
Treatment sample, one day after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: 1 day after nerve injury


title: Treatment sample 2, 3 days after nerve injury

description:
D3.T2
Treatment sample, 3 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx


title: HEK Transfer Fibs; 5cd6540c-abe9-4768-ac60-d34f39047287

description: 5cd6540c-abe9-4768-ac60-d34f39047287.rsem.txt.gz

value: BJ neonatal foreskin fibroblast (CRL-2522)

value: Fibs

value: HEK Transfer

value: HEK Transfer Fibroblast


title: LP351 MSC; bec88e7e-17ac-40b8-901f-eb9143c2ae49

description: bec88e7e-17ac-40b8-901f-eb9143c2ae49.rsem.txt.gz

value: LP351 Transfer

value: LP351 Transfer MSC Clone 1


title: HEK Transfer Fibs; 33cd518a-88f7-4984-941a-bbdf4c00a1d7

description: 33cd518a-88f7-4984-941a-bbdf4c00a1d7.rsem.txt.gz


title: BJ Fibs; 81198c14-b0ef-45ad-9042-cb7821bb64b0

description: 81198c14-b0ef-45ad-9042-cb7821bb64b0.rsem.txt.gz

value: BJ

value: BJ Fibroblast


title: Phytoph_2.5hpi 4

value: Stele

value: Mock


title: Treatment sample 2, one day after nerve injury

description:
D1.T2
Treatment sample, one day after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Retinal ganglion cells (RGCs)

value: Cyan-fluorescent protein (CFP) expression in RGCs

value: Adult

value: Treatment


title: HEK Transfer Fibs; 2012771c-8d8d-426e-b083-3393e44c31df

description: 2012771c-8d8d-426e-b083-3393e44c31df.rsem.txt.gz


title: Verticillium_2dpi 15

value: Rhizodermis

value: Verticillium longisporum

value: Infected


title: Treatment sample 1, one day after nerve injury

description:
D1.T1
Treatment sample, one day after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: 1 day after nerve injury


title: BJ Fibs ; 0a788839-3eb4-4b27-9ad5-f8b23da97d67

description: 0a788839-3eb4-4b27-9ad5-f8b23da97d67.rsem.txt.gz

value: BJ neonatal foreskin fibroblast (CRL-2522)

value: Fibs


title: Control sample 1, 3 days after nerve injury

description:
D3.C1
Control sample, 3 days after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Control

value: 3 days after nerve injury


title: BJ Rho Null Fibs; 15cd734e-a53d-4033-b103-415614b373b4

description: 15cd734e-a53d-4033-b103-415614b373b4.rsem.txt.gz

value: Rho Null

value: BJ Rho Null Fibroblast


title: Phytoph_2.5hpi 2

value: Phytophtora parasitica


title: HEK Transfer MSC; 49a57add-fd64-4609-937c-7b8bef7ee7f4

description: 49a57add-fd64-4609-937c-7b8bef7ee7f4.rsem.txt.gz

value: Differentiated in vitro mesenchymal stem cell (MSC) lines

value: MSC

value: HEK Transfer

value: HEK Transfer MSC Clone 2


title: BJ MSC; 597999d5-2013-45a6-aa9d-2ad0c05cc4dd

description: 597999d5-2013-45a6-aa9d-2ad0c05cc4dd.rsem.txt.gz

value: BJ

value: BJ MSC


title: Treatment sample 5, one day after nerve injury

description:
D1.T5
Treatment sample, one day after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Retinal ganglion cells (RGCs)

value: Cyan-fluorescent protein (CFP) expression in RGCs

value: Adult

value: Treatment


title: Phytoph_2.5hpi 1

value: Stele

value: Infected


title: BJ MSC; fb4f8f80-ec69-4cae-a0c7-2f743b3844d7

description: fb4f8f80-ec69-4cae-a0c7-2f743b3844d7.rsem.txt.gz


title: Treatment sample 4, one day after nerve injury

description:
D1.T4
Treatment sample, one day after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: 1 day after nerve injury


title: Verticillium_2dpi 17

value: Rhizodermis

value: Verticillium longisporum

value: Mock


title: Verticillium_2dpi 13

value: Cortex


title: LP351 Transfer iPSC; 0f9cb841-ff39-4b48-bfd5-faf2bad51109

description: 0f9cb841-ff39-4b48-bfd5-faf2bad51109.rsem.txt.gz

value: Reprogrammed in vitro induced pluripotent stem cell (iPSC) lines

value: iPSC

value: LP351 Transfer

value: LP351 Transfer iPSC Clone 11


title: Control sample 3, one day after nerve injury

description:
D1.C3
Control sample, one day after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Control


title: HEK Transfer MSC; 5245244d-170b-4258-ba53-b6fe1398349e

description: 5245244d-170b-4258-ba53-b6fe1398349e.rsem.txt.gz

value: Differentiated in vitro mesenchymal stem cell (MSC) lines

value: MSC

value: HEK Transfer

value: HEK Transfer MSC Clone 4


title: LP351 Transfer iPSC; a0db8844-9056-42dc-bf36-654061617b1b

description: a0db8844-9056-42dc-bf36-654061617b1b.rsem.txt.gz

value: LP351 Transfer iPSC Clone 1


title: Verticillium_2dpi 16


title: BJ MSC; 7c463e9b-d7e7-46ad-af69-97efd6efb931

description: 7c463e9b-d7e7-46ad-af69-97efd6efb931.rsem.txt.gz

value: BJ

value: BJ MSC


title: HEK Transfer MSC; 7feb6877-39dc-445b-bfb5-f6755851592d

description: 7feb6877-39dc-445b-bfb5-f6755851592d.rsem.txt.gz

value: HEK Transfer MSC Clone 1


title: HEK Transfer iPSC; e0a67304-7019-44cf-a2c9-d5bf91c36ea7

description: e0a67304-7019-44cf-a2c9-d5bf91c36ea7.rsem.txt.gz

value: HEK Transfer iPSC Clone 4


title: Verticillium_2dpi 14

value: Rhizodermis

value: Verticillium longisporum

value: Infected


title: HEK Transfer iPSC; c9a75556-39c7-44e8-8ec1-9b88bf79ce37

description: c9a75556-39c7-44e8-8ec1-9b88bf79ce37.rsem.txt.gz

value: Reprogrammed in vitro induced pluripotent stem cell (iPSC) lines

value: HEK Transfer iPSC Clone 2


title: Control sample 4, one day after nerve injury

description:
D1.C4
Treatment sample, one day after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Retinal ganglion cells (RGCs)

value: Cyan-fluorescent protein (CFP) expression in RGCs

value: Adult

value: 1 day after nerve injury


title: HEK Transfer iPSC; d0a731cc-9d22-411f-bef9-c2ee1207f745

description: d0a731cc-9d22-411f-bef9-c2ee1207f745.rsem.txt.gz

value: iPSC

value: HEK Transfer iPSC Clone 1


title: Verticillium_2dpi 12

value: Cortex

value: Mock


title: Control sample 2, one day after nerve injury

description:
D1.C2
Control sample, one day after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx

value: Control


title: LP351 Transfer iPSC; 2c708981-49e5-4691-95d1-ed04676bcdc6

description: 2c708981-49e5-4691-95d1-ed04676bcdc6.rsem.txt.gz

value: LP351 Transfer

value: LP351 Transfer iPSC Clone 2


title: BJ iPSC; d09bdbb2-0881-4ba5-b77f-38e1a39fe29a

description: d09bdbb2-0881-4ba5-b77f-38e1a39fe29a.rsem.txt.gz

value: BJ

value: BJ iPSC


title: BJ iPSC; 90fe80c9-2f5d-4faa-9b6e-aa52ef99acfb

description: 90fe80c9-2f5d-4faa-9b6e-aa52ef99acfb.rsem.txt.gz


title: BJ iPSC; 96c524a0-9ec2-4af4-a29f-e5b58171da84

description: 96c524a0-9ec2-4af4-a29f-e5b58171da84.rsem.txt.gz


title: Control sample 1, one day after nerve injury

description:
D1.C1
Control sample, one day after nerve injury
mCherry
mRNA
processed data file: Complete_geneList_EdgeR.xlsx


title: Verticillium_2dpi 11

value: Verticillium longisporum


title: Verticillium_2dpi 10

value: Infected


title: LP351 Transfer Fibs; d094adc5-496c-45c1-8da9-fc61204b3ee6

description: d094adc5-496c-45c1-8da9-fc61204b3ee6.rsem.txt.gz

value: BJ neonatal foreskin fibroblast (CRL-2522)

value: Fibs

value: LP351 Transfer Fibroblast


title: LP351 Transfer Fibs; 7cfb6f23-8670-43e2-ac43-9b9cb27de3e8

description: 7cfb6f23-8670-43e2-ac43-9b9cb27de3e8.rsem.txt.gz


title: Verticillium_2dpi 7

value: Endodermis


title: HEK Transfer Fibs; 36659ffa-4d9d-48b6-9af7-ee69add64a31

description: 36659ffa-4d9d-48b6-9af7-ee69add64a31.rsem.txt.gz

value: HEK Transfer

value: HEK Transfer Fibroblast


title: HEK Transfer Fibs; a9cdeb6a-0b30-4bcd-8d91-73bffed920fd

description: a9cdeb6a-0b30-4bcd-8d91-73bffed920fd.rsem.txt.gz


title: LP351 Transfer Fibs ; 158c0cda-a7f9-4a0f-81e3-50d946a1452f

description: 158c0cda-a7f9-4a0f-81e3-50d946a1452f.rsem.txt.gz


title: TT_IPF_RNA

city: Denver

first: Sarah

last: Sasse

state: CO

address: 1400 Jackson St., K720

institute: National Jewish Health

description: snRNA-seq.rds

data_processing:
For single nucleus RNA-seq fastq files were trimmed, quality-filtered and aligned to the hg38 reference genome using standardized Cell Ranger analysis pipelines from 10X Genomics. The output of this pipeline included a sparse count table containing cellular barcodes by gene IDs.
For single nucleus RNA-seq count tables were imported into Seurat (v. 3; https://satijalab.org/seurat), selected to exclude samples with >10% mitochondrial reads and integrated using the sctransform wrapper (Seurat v. 3), which applies a regularized, negative binomial regression approach to per-cell read depth as a normalization across samples. Principle components were calculated and selected by looking at the inflection point of a histogram of principal components by standard deviation. Dimensionality was reduced and cell groups defined by unbiased hierarchical clustering using the Uniform Manifold Approximation and Projection method (UMAP; available through Seurat v. 3).
For single nucleus RNA-seq cell types were identified using several approaches, including marker analysis to summarize discriminating genes between clusters and graphical approaches testing for known cell type-specific markers. Details of this analysis are included in the manuscript.
For single nucleus ATAC-seq, fastq files were trimmed, filtered, and aligned to the hg38 reference genome using SnapATAC (https://github.com/r3fang/SnapATAC). Resulting BAM files were converted into fragment files using Sinto (https://timoast.github.io/sinto/index.html), and peak calls and counts tables for each sample were constructed with Genrich (https://github.com/jsh58/Genrich#atacseq).
For single nucleus ATAC-seq, count matrices were imported into Signac (v. 0.1.6; https://github.com/timoast/signac), unaligned counts were removed, and cells with nucleosome signal >10, transcription start site enrichment <2, alignment to error-prone regions >5% and <15% read fractions in peaks were filtered out. Sample integration and dimensionality reduction were performed in Signac using term frequency-inverse document frequency (TF-IDF) weighted integration, singular value decomposition, and latent semantic indexing dimensionality reduction.
Cell type labels were transferred from cells labeled using the snRNA-seq pipeline above by performing canonical correlation analysis across datasets with UMAP. All statistical analyses utilized R (v. 3.6.1; R Foundation for Statistical Computing, Vienna, Austria).
Genome_build: GRCh38
Supplementary_files_format_and_content: For RNA-seq, raw matrix, barcode, and feature files are included for each sample, and an aggregated, normalized R analysis object is provided as a processed data file. For ATAC-seq, raw fragment files and peak ranges are included for each sample, and an aggregated, normalized R analysis object is provided (excluding the failed Sample2/TT_Control) as a processed data file.

source_name: Tissue-nucleus

extract_protocol:
Nuclei were isolated from frozen lung tissue by pulverizing in liquid nitrogen using a mortar and pestle, lysed in PBS containing 2% BSA, 0.1% TritonX-100, 1X protease inhibitors (Roche), 0.2 U/µl RNase inhibitor (Promega), and 1 mM DTT. Nuclei were washed by centrifugation at 500 x g, resuspended in PBS containing 2% BSA, 1 mM EDTA, 0.2 U/µl RNase inhibitor, and 1:100 DRAQ7 (Cell Signaling) and isolated for DRAQ7+ nuclei using a microfluidic Sony SH800 cell sorter. Nuclei were collected in PBS containing 5% BSA and 1 U/µl RNase inhibitor and quantified prior to library preparation.
For snRNA-seq, nuclei were loaded onto a 10X Chromium platform for 3-prime library preparation per manufacturer protocols. For snATAC-seq, 2K nuclei were resuspended in 17% dimethylformamide-containing buffer and incubated with 1 µl Tn5 transposase containing combinatorial barcodes.
For snRNA-seq, libraries were sequenced on an Illumina HiSeq4000 sequencer using 50 bp paired-end reads and custom sequencing primers at the University of California San Diego Institute for Genomic Medicine.
For ATAC-seq, libraries were sequenced on a NextSeq500 sequencer using 50 bp paired-end reads and custom sequencing primers at the University of California San Diego Institute for Genomic Medicine.

tag: source barcode

tag: Sex

value: male

tag: race

value: white

tag: ethnicity

value: non-hispanic

tag: disease

value: ipf

tag: genotype

value: TT


title: Verticillium_2dpi 6


title: HEK Transfer Fibs; 1ad3cd29-2eda-4a71-9c7d-deaa3cc6ab6f

description: 1ad3cd29-2eda-4a71-9c7d-deaa3cc6ab6f.rsem.txt.gz


title: GG_IPF_RNA

description: snRNA-seq.rds

value: GG


title: BJ Fibs; c9d94a14-38ea-4ef4-8045-1f68b6ca36e0

description: c9d94a14-38ea-4ef4-8045-1f68b6ca36e0.rsem.txt.gz

value: BJ Fibroblast


title: BJ Fibs; 1bd36e15-65bc-475f-9b59-024ac2038dae

description: 1bd36e15-65bc-475f-9b59-024ac2038dae.rsem.txt.gz

value: BJ


title: TT_control_RNA

description: snRNA-seq.rds

value: normal


title: BJ Fibs ; d8e86411-8f83-44ab-a4e0-be587a3e69a5

description: d8e86411-8f83-44ab-a4e0-be587a3e69a5.rsem.txt.gz


title: BJ Rho Null Fibs; 73c987bf-fdd2-4674-a3c5-3352c8f7e96a

description: 73c987bf-fdd2-4674-a3c5-3352c8f7e96a.rsem.txt.gz

value: Rho Null

value: BJ Rho Null Fibroblast


title: Verticillium_2dpi 4

value: Stele

value: Verticillium longisporum

value: Mock


title: Verticillium_2dpi 5


title: GG_control_RNA

description: snRNA-seq.rds


title: BJ Rho Null Fibs; 255d874b-6966-4235-b809-d26a97fc4b52

description: 255d874b-6966-4235-b809-d26a97fc4b52.rsem.txt.gz

value: BJ neonatal foreskin fibroblast (CRL-2522)

value: Fibs


title: Verticillium_2dpi 9

value: Endodermis


title: BJ Rho Null Fibs; b8a9e771-5e64-4973-a459-f2de0182d439

description: b8a9e771-5e64-4973-a459-f2de0182d439.rsem.txt.gz


title: Verticillium_2dpi 3

value: Infected


title: Verticillium_2dpi 8


title: Verticillium_2dpi 1


title: 79_K

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumor Immunology

institute: Charité University Medicine

description:
all_final_DESeq2~batch+response_all_countsNormalized.txt
all_final_DESeq2~patient+treatment_all_countsNormalized.txt
responders_final_DESeq2~patient+treatment_all_countsNormalized.txt
untreated_final_DESeq2~batch+response_all_countsNormalized.txt

data_processing:
Read alignment to hg19 was performed using STAR’s two-pass alignment (STAR version 2.4.2a) with transcriptome annotation from GENCODE release 19.
Read counts were generated by STAR during alignment.
Read counts were normalized using DESeq2 (version 1.18.1) in R (version 3.4.4).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files containing normalized counts of each sample and comparison performed. Note that all_final_DESeq2~batch+response_all_countsNormalized.txt and all_final_DESeq2~patient+treatment_all_countsNormalized.txt are identical and only both included for the sake of completeness.

molecule: polyA RNA

source_name: peripheral blood lymphocytes

extract_protocol:
RNA was isolated with TriPure Isolation Reagent (Roche) and chloroform and dissolved in water.
Libraries were prepared from 1μg of total RNA per sample, as detailed in the TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, CA, USA).

tag: patient id

tag: unified patient id, as used in the manuscript

value: P

tag: patient diagnosis

value: Treatment-naive chronic lymphocytic leukemia

tag: in vitro dasatinib treatment

value: no

tag: patient's in vitro response to dasatinib

value: sensitive

value: peripheral blood lymphocytes

tag: batch


title: Uveal Melanoma 67

type: RNA

city: Genoa

first: Adriana

middle: Agnese

last: Amaro

address: Largo Rosanna Benzi 10

department: Molecular Pathology

country: Italy

institute: IRCCS Ospedale Policlinico SAN MARTINO - IST - NATIONAL CANCER RESEARCH INSTITUTE

hyb_protocol: Hybridization at 56 °C for 16 h in the HS‐400 Pro system (Tecan) was followed by washing and nitrogen drying according to the manufacturer's protocol (Exiqon).

scan_protocol: Scanned on Axon Genepix 4000B scanner and dedicated software was used

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal and processed Green signal. Axon and R/BioConductor software were used.

source_name: Uveal Melanoma

label_protocol: For labeling of the miRNAs, we used the miRCURY™ LNA microRNA Array Power labeling kit (Exiqon) according to the recommendations of the manufacturer.

extract_protocol: Total RNA extracted using Trizol and MiRNeasy kit (Qiagen, Hilden, Germany) following manufacturer's instructions

tag: disease state

value: uveal melanoma

tag: tissue

value: eye tumor

tag: gender

value: Male

tag: status

value: Metastases

source_name: Total RNA from pool of 20 different cell lines

value: ecotdermal, mesenchymal and endodermal origin

tag: cell line

value: pool of 20 different cell lines


title: Uveal Melanoma 78


title: Verticillium_2dpi 2

tag: cell layer

value: Stele

tag: pathogen

value: Verticillium longisporum

tag: treatment


title: Uveal Melanoma 73

value: No Metastases


title: Uveal Melanoma 68


title: 79_Dasa

description:
all_final_DESeq2~batch+response_all_countsNormalized.txt
all_final_DESeq2~patient+treatment_all_countsNormalized.txt
responders_final_DESeq2~patient+treatment_all_countsNormalized.txt
treated_final_DESeq2~batch+response_all_countsNormalized.txt

value: yes

tag: cell type


title: 76_K

value: O


title: Uveal Melanoma 62

value: Female


title: HepG2 Se+ Day3 rep2

city: Ankara

first: Damla

last: Gözen

state: Tr

address: Hayrabolu cad. Konutkent 2 sit. A5 blok No:6 Cayyolu

country: Turkey

institute: METU

description: gene expression data from HepG2 cells.

hyb_protocol: According to the Affymetrix standard protocol (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array).

data_processing: The qualities of arrays were checked using simpleaffy package available in R (Miller, 2020). Robust Multi-Array Average (RMA) background correction and quantiles normalization of the data were performed.

label: biotin

source_name: HepG2 cells

growth_protocol: HepG2-2.2.15 and HepG2 cell lines were grown in DMEM medium with 0.01% FCS  in duplicates at 37°C in an incubator containing 5% CO2.

extract_protocol: Cells were harvested on the 1st, 2nd and 3rd days of the treatment, and Trizol extraction of total RNA was performed according to the manufacturer's protocol.

treatment_protocol: Cells were either supplemented with 0.1 μM Na2SeO3 (Se positive) or not (Se negative) for 3 days.

tag: hbv-integration

value: No

tag: selenium

value: Se +

tag: day


title: Uveal Melanoma 65


title: Uveal Melanoma 64


title: Uveal Melanoma 60


title: HepG2 Se+ Day2 rep2

description: gene expression data from HepG2 cells.

scan_protocol: According to the Affymetrix standard protocol (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array).


title: 76_Dasa

tag: patient id

tag: unified patient id, as used in the manuscript

value: Treatment-naive chronic lymphocytic leukemia


title: HepG2 Se+ Day1 rep2

description: gene expression data from HepG2 cells.

label_protocol: According to the Affymetrix standard protocol (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array).


title: 75_K

description:
all_final_DESeq2~batch+response_all_countsNormalized.txt
all_final_DESeq2~patient+treatment_all_countsNormalized.txt
nonresponders_final_DESeq2~patient+treatment_all_countsNormalized.txt
untreated_final_DESeq2~batch+response_all_countsNormalized.txt

value: N

tag: patient diagnosis

tag: in vitro dasatinib treatment

value: no

value: resistant


title: Uveal Melanoma 54

value: uveal melanoma

value: eye tumor


title: Uveal Melanoma 32

value: Male


title: Uveal Melanoma 48

value: ecotdermal, mesenchymal and endodermal origin


title: Uveal Melanoma 53

value: pool of 20 different cell lines


title: Uveal Melanoma 49


title: HepG2 Se- Day2 rep2

description: gene expression data from HepG2 cells.

value: Se -


title: HepG2 Se- Day3 rep2

description: gene expression data from HepG2 cells.


title: HepG2 Se- Day1 rep2

description: gene expression data from HepG2 cells.


title: Uveal Melanoma 46


title: 75_Dasa

description:
all_final_DESeq2~batch+response_all_countsNormalized.txt
all_final_DESeq2~patient+treatment_all_countsNormalized.txt
nonresponders_final_DESeq2~patient+treatment_all_countsNormalized.txt
treated_final_DESeq2~batch+response_all_countsNormalized.txt

tag: patient's in vitro response to dasatinib

value: peripheral blood lymphocytes

tag: batch


title: HepG2-2.2.15 Se+ Day3 rep2

description: gene expression data from HepG2-2.2.15 cells.

source_name: HepG2-2.2.15 cells

value: Yes


title: Uveal Melanoma 29

tag: disease state

tag: tissue

value: No Metastases


title: 50_Dasa

value: M

value: yes


title: Uveal Melanoma 58

tag: gender

tag: status

value: Metastases


title: Uveal Melanoma 19

tag: cell line


title: Uveal Melanoma 17

value: Female


title: Uveal Melanoma 9


title: 49_Dasa

value: L

value: Treatment-naive chronic lymphocytic leukemia


title: 49_K

value: no


title: HepG2-2.2.15 Se+ Day2 rep2

value: Se +


title: HepG2-2.2.15 Se+ Day1 rep2


title: 50_K

value: resistant


title: 46_K

value: K


title: Mycelium-C2-MACE

city: Pontevedra

first: Pilar

last: Soengas

state: Pontevedra

address: Palacio de Salcedo

department: Brassica Genetic and Biochemistry

country: Spain

institute: CSIC

data_processing:
Library strategy: MACE
HCS from Illumina HiSeq 2000
Reads aligned to Sclerotinia sclerotiorum genome ("Sclerotinia_sclerotiorum.ASM14694v1.dna.toplevel.fa") . The assembly was done with Trinity RNA-Seq (https://github.com/trinityrnaseq/trinityrnaseq/wiki).
Consensus sequences were annotated via BLASTX to the Uniprot database (Swiss-Prot and TrEMBL). Reads that did not match the genome were taken into a de novo assembly step and annotated via BLASTX to the Uniprot database (Swiss-Prot and TrEMBL)
Differential expression analysis was performed with the R package DESeq (Anders and Huber 2010) with the standard parameters
Genome_build: Sclerotinia_sclerotiorum.ASM14694v1.dna.toplevel.fa (https://fungi.ensembl.org/Sclerotinia_sclerotiorum/Info/Index)
Supplementary_files_format_and_content: Tab-delimited text files including Gene annotation, Expression values, logFC and FDR

organism: Sclerotinia sclerotiorum

source_name: Mycelium

growth_protocol: Fungus was grown in PDA medium supplemented with each isothiocyanate (100 µM). Petri dishes were coated with one layer of cellophane membrane (Bio-Rad Catalog No. 165–0963). Agar plugs of 2.5 mm diameter containing fresh fungus colonies were transferred to petri dishes and incubated at 24°C in darkness. After 5 days mycelium mass was harvested from cellophane membranes and homogenized in liquid nitrogen. The resultant material was used immediately for isolation of RNAs. Two replicates per treatment and control samples were carried out.

extract_protocol:
RNA was extracted with SpectrumTM Plant Total RNA Kit (Sigma MO, USA).
Massive Analysis of 3′-cDNA Ends (MACE) libraries were generated using GenXPro’s MACE kit (GenXPro GmbH, Frankfurt, Germany) as described by Zawada et al., (2014).

treatment_protocol: Three different treatments were studied: allyl isothiocyanate (100 µM, Sigma-Aldrich, 36682), indol-3-carbinol (100 µM, Sigma-Aldrich, I7256-5G) and control.

tag: strain

value: Mycelium

value: control

tag: day of harvest


title: Mycelium-I3C2-MACE

tag: treatment


title: Mycelium-C1-MACE


title: Mycelium-I3C1-MACE


title: HepG2-2.2.15 Se- Day2 rep2

tag: hbv-integration


title: HepG2-2.2.15 Se- Day1 rep2

tag: selenium


title: Mycelium-AITC2-MACE

value: allyl-isothiocyanate


title: Brain_Sevoflurane_rep3

city: Beijing

first: Cheng

last: Ni

state: Beijing

address: No.49 North Garden Road

institute: Peking University Third Hospital

description: Gene expression data from hipppcampus of  18-month old rat after 4 hours of sevoflurane treatment

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to the Affymetrix® Rat Transcriptome Array Strip (45 oC /24 h), and up to 25 unique probes sequences were hybridized to a single transcript. Following hybridization, each array strip was washed and stained using the Fluidics Station of GeneChip® Scanner 3000 7G system (Affymetrix, Santa Clara, CA).

scan_protocol: The array strips were scanned using the Imaging Station of the GeneChip® Scanner 3000 7G system.

data_processing: Data were analyzed with Microarray Suite 5 (MAS5) and Robust Multi-array Average (RMA) using Affymetrix Expression Console 1.4.1. Affymetrix default analysis settings were used.

organism: Rattus norvegicus

source_name: Rat hippocampus after 4 hours sevoflurane

label_protocol: The obtained cDNA was used for biotin labeling and fragmentation by Affymetrix GeneChip® WT Terminal Labeling and Hybridization.

growth_protocol: Male Sprague-Dawley rats, 18-month old, weighing 550–600 g, were used in the studies. Before sevoflurane anesthesia, the rats were maintained on a standard housing condition with food and water ad libitum for 2 weeks. C6 rat glioma cells were used in the studies. The cells were cultured in F-12K medium (Gibco™, Thermo Fisher Scientific, Waltham, MA, USA) containing 2.5% fetal bovine serum, 15% horse serum, 100 U/ml penicillin, and 100 μg/ml streptomycin. Before treatments, cells were seeded in 6-well plates, with one million cells in 1.5 ml cell culture media per well.

extract_protocol: Total RNAs were isolated from the hippocampi and cells using TRIzol reagent (Invitrogen, Carlsbad, CA), then digested with RNase-Free DNase to remove residual DNAs. The RNA concentrations were analyzed using the Nanodrop 2000 (Thermo Fisher Scientific), then total RNA (2 μg) was reverse-transcribed using the GoScriptTM Reverse Transcription System (Promega).

treatment_protocol: The rats were randomly assigned to the sevoflurane anesthesia or control group. In our study, rats in sevoflurane group received 2.5% sevoflurane in 100% oxygen for 4 hours in an anesthetizing chamber, and the control group received 100% oxygen at an identical flow rate for 4 h in an identical chamber. The rats breathed spontaneously, and sevoflurane and oxygen concentrations were monitored continuously (Datex, Tewksbury, MA, USA). Temperature of the anesthetizing chamber was controlled to maintain rectal temperature of the animals at 37 ± 0.5 °C. Anesthesia was terminated by discontinuing sevoflurane and placing animals in a chamber containing 100% oxygen until 20 minutes after recovery of consciousness. The animals were then returned to individual home cages until sacrifice. Rats were sacrificed by decapitation 3 h after anesthesia. The brain tissues were removed rapidly, and the hippocampus was dissected out and frozen in liquid nitrogen.

value: Sprague-Dawley

tag: age

value: 18-month old

value: sevoflurane anesthesia

value: hippocampus


title: 46_Dasa

description:
Merged two technical replicates.
all_final_DESeq2~batch+response_all_countsNormalized.txt
all_final_DESeq2~patient+treatment_all_countsNormalized.txt
nonresponders_final_DESeq2~patient+treatment_all_countsNormalized.txt
treated_final_DESeq2~batch+response_all_countsNormalized.txt

tag: patient id

tag: cell type

value: peripheral blood lymphocytes


title: Brain_Control_rep3

description: Gene expression data from hipppcampus of  18-month old rat

source_name: Rat hippocampus


title: Brain_Control_rep2


title: Brain_Control_rep1


title: Brain_Sevoflurane_rep1


title: 45_K

description:
Merged two technical replicates.
all_final_DESeq2~batch+response_all_countsNormalized.txt
all_final_DESeq2~patient+treatment_all_countsNormalized.txt
responders_final_DESeq2~patient+treatment_all_countsNormalized.txt
untreated_final_DESeq2~batch+response_all_countsNormalized.txt

tag: unified patient id, as used in the manuscript

value: J

tag: patient diagnosis

value: sensitive


title: Brain_Sevoflurane_rep2


title: Mycelium-AITC1-MACE


title: HepG2 Se+ Day3 rep1

description: gene expression data from HepG2 cells.

value: No

tag: day


title: HepG2 Se+ Day2 rep1

description: gene expression data from HepG2 cells.


title: 32_K

value: I

tag: in vitro dasatinib treatment

tag: patient's in vitro response to dasatinib

tag: batch


title: HepG2 Se+ Day1 rep1

description: gene expression data from HepG2 cells.


title: 32_Dasa

description:
Merged two technical replicates.
all_final_DESeq2~batch+response_all_countsNormalized.txt
all_final_DESeq2~patient+treatment_all_countsNormalized.txt
responders_final_DESeq2~patient+treatment_all_countsNormalized.txt
treated_final_DESeq2~batch+response_all_countsNormalized.txt

value: Treatment-naive chronic lymphocytic leukemia

value: yes


title: HepG2 Se- Day3 rep1

description: gene expression data from HepG2 cells.

value: Se -


title: 31_Dasa

value: H

value: resistant


title: HepG2 Se- Day2 rep1

description: gene expression data from HepG2 cells.


title: HepG2-2.2.15 Se+ Day3 rep1

value: Yes

value: Se +


title: HepG2-2.2.15 Se- Day3 rep2


title: 31_K

value: no


title: HepG2 Se- Day1 rep1

description: gene expression data from HepG2 cells.


title: 45_Dasa


title: patient45_whole-blood_day56 [p45D56]

city: Paris

first: Jeremy

last: Manry

address: 24 boulevard du Montparnasse

country: France

institute: INSERM, Institut Imagine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
We used the lumi package of R for variance-stabilization transformation (VST) and quantile normalization of the crude data. Only probes corresponding to autosomes, mapping to unique locations and expressed at levels above background noise (p-value < 0.05) in at least 10 samples (10%) were retained. Probes not matching any unique Ensembl gene or Hugo ID were excluded. For genes with several probes, we retained the median expression value.
quantile normalized. Probes with Detection P val < 0.05 in at least 10 samples were kept for analysis.

source_name: whole-blood cells, day 56 after start of treatment

label_protocol: RNA samples were labeled with the Illumina TotalPrep RNA Amplification Kit from Ambion

extract_protocol: Total RNA was extracted with the Tempus Sample kit (Applied Biosystem).

tag: subject id

tag: subject status

value: patient diagnosed with Buruli ulcer

tag: gender

value: female

tag: time point

value: day 56 after start of treatment

tag: tissue/cell type

value: whole-blood cells


title: patient45_whole-blood_day0 [p45D0]

source_name: whole-blood cells, day 0 after start of treatment

value: day 0 after start of treatment


title: patient45_whole-blood_day150 [p45D150]

source_name: whole-blood cells, day 150 after start of treatment

value: day 150 after start of treatment


title: patient44_whole-blood_day150 [p44D150]


title: H_K

value: G

value: peripheral blood lymphocytes


title: patient44_whole-blood_day90 [p44D90]

source_name: whole-blood cells, day 90 after start of treatment

value: day 90 after start of treatment


title: HepG2-2.2.15 Se- Day3 rep1

tag: cell line


title: H_Dasa

value: Treatment-naive chronic lymphocytic leukemia


title: patient44_whole-blood_day0 [p44D0]


title: patient43_whole-blood_day90 [p43D90]


title: patient44_whole-blood_day56 [p44D56]


title: patient43_whole-blood_day120 [p43D120]

source_name: whole-blood cells, day 120 after start of treatment

value: day 120 after start of treatment


title: G_Dasa

value: F

value: yes


title: HepG2-2.2.15 Se- Day1 rep1

tag: hbv-integration

value: Se -


title: patient42_whole-blood_day150 [p42D150]


title: HepG2-2.2.15 Se+ Day1 rep1

value: Yes

tag: selenium


title: HepG2-2.2.15 Se+ Day2 rep1

value: Se +


title: patient43_whole-blood_day56 [p43D56]

tag: age


title: patient42_whole-blood_day90 [p42D90]


title: patient43_whole-blood_day150 [p43D150]


title: patient42_whole-blood_day56 [p42D56]


title: patient43_whole-blood_day0 [p43D0]


title: F_K

tag: patient id

value: E

value: no

value: resistant


title: F_Dasa

tag: cell type


title: HepG2-2.2.15 Se- Day2 rep1


title: E_K

tag: unified patient id, as used in the manuscript

value: D


title: patient42_whole-blood_day0 [p42D0]

value: patient diagnosed with Buruli ulcer

value: female

value: whole-blood cells


title: D_K

value: C

tag: patient diagnosis

value: sensitive


title: G_K

value: G

value: peripheral blood lymphocytes


title: E_Dasa

value: Treatment-naive chronic lymphocytic leukemia


title: patient41_whole-blood_day0 [p41D0]

value: male

value: day 0 after start of treatment


title: patient40_whole-blood_day56 [p40D56]

value: day 56 after start of treatment


title: patient40_whole-blood_day0 [p40D0]


title: patient39_whole-blood_day56 [p39D56]


title: CL1-0 cells expressing PSAT1

city: Taipei

first: Michael

last: Hsiao

address: Academia Road, Section 2, Nankang, Taipei, 115, Ta

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description: Gene expression data from CL1-0 cells expressing PSAT1 vector

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Lung  adenocarcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with puromycin for two weeks.  Stably transduced cells were use for this experiment.

tag: shRNA

value: PSAT1 vector

value: Type II alveolar cell


title: D_Dasa

tag: in vitro dasatinib treatment

value: yes


title: patient38_whole-blood_day90 [p38D90]

value: day 90 after start of treatment


title: ein2-5+Glc-2

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 17 and length >= 25 bp). Clean reads were mapped to the Arabidopsis genome sequence (TAIR10) using TopHat. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed and only genes with an expression level of at least 1 RPM (reads per million) in at least two samples were kept for further analysis.
Supplementary_files_format_and_content: Tab-delimited text file include RPM(Reads per Million) values for 12 Samples .

source_name: ein2-5+Glc_4d old seedlings

growth_protocol: 22-23℃, 12h/12h (Light/Dark), liqiud 1/2MS without glucose

extract_protocol:
TRIZOL regent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 15 mM glucose for 2 hours

tag: ecotype background

tag: genotype/variation

value: ein2-5 mutant

tag: tissue

value: 4-day old seedligns

tag: treated with

value: 15 mM glucose for 2 hours


title: patient38_whole-blood_day0 [p38D0]

tag: subject id

tag: subject status

value: patient diagnosed with Buruli ulcer

tag: gender

value: female


title: patient41_whole-blood_day60 [p41D60]

source_name: whole-blood cells, day 60 after start of treatment

tag: time point

value: day 60 after start of treatment

tag: tissue/cell type

value: whole-blood cells


title: B_K

value: B

value: no

tag: patient's in vitro response to dasatinib

value: sensitive

tag: batch


title: patient36_whole-blood_day150 [p36D150]

tag: age

value: male

value: day 150 after start of treatment


title: ein2-5+Glc-1


description: Gene expression data from CL1-5 cells expressing PSAT1 shRNA vector

value: PSAT1 shRNA vector

tag: cell line

tag: cell type


title: ein2-5-Glc-3

source_name: ein2-5-Glc_4d old seedlings


title: patient38_whole-blood_day56 [p38D56]

value: day 56 after start of treatment


title: patient39_whole-blood_day0 [p39D0]

value: day 0 after start of treatment


title: CL1-0 cells expressing vector control [VC]

description: Gene expression data from CL1-0 cells expressing control vector

value: vector

value: Type II alveolar cell


title: CL1-5 cells expressing Non-silencing shRNA vector [NS]

description: Gene expression data from CL1-5 cells expressing non-silencing shRNA vector

value: non-silencing shRNA vector


title: patient36_whole-blood_day100 [p36D100]

source_name: whole-blood cells, day 100 after start of treatment

value: day 100 after start of treatment


title: ein2-5+Glc-3

value: ein2-5 mutant

value: 4-day old seedligns

value: 15 mM glucose for 2 hours


title: ein2-5-Glc-2


title: patient36_whole-blood_day56 [p36D56]

value: patient diagnosed with Buruli ulcer


title: patient36_whole-blood_day90 [p36D90]

value: day 90 after start of treatment

value: whole-blood cells


title: patient35_whole-blood_day90 [p35D90]


title: patient35_whole-blood_day0 [p35D0]


title: B_Dasa

source_name: peripheral blood lymphocytes

tag: patient id

value: B

tag: unified patient id, as used in the manuscript

tag: patient diagnosis

value: Treatment-naive chronic lymphocytic leukemia

value: yes

value: peripheral blood lymphocytes


title: patient36_whole-blood_day0 [p36D0]

value: male


title: A_K

value: A

tag: in vitro dasatinib treatment

value: no

value: sensitive


title: patient33_whole-blood_day90 [p33D90]

value: female


title: ein2-5-Glc-1

tag: ecotype background

tag: genotype/variation


title: Col-0+Glc-2

source_name: Col-0+Glc_4d old seedlings

value: Wild type

tag: tissue

tag: treated with


title: patient33_whole-blood_day56 [p33D56]

tag: subject id

tag: subject status

value: day 56 after start of treatment


title: A_Dasa


title: Col-0+Glc-3


title: IghTer5H∆TM/Ter5H∆TM;Ragko/ko _Bone_Marrow_ProB_rep1_Experiment_4

city: Amsterdam

first: Heinz

last: jacobs

address: Plesmanlaan 121

country: Netherlands

institute: NKI

data_processing:
Sample 1-16: The 51 bp single end reads were mapped to the aligned against the mouse reference genome (Ensembl build 37) using TopHat (version 2.0.6).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 66. Additional parameters --prefilter-multihits and –no coverage were used.
Genecounts were generated using HTSeq-count.
Sample 17-40: The 51/65 bp single end reads were mapped to the aligned against the mouse reference genome (Ensembl build 38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
Genecounts were generated using a custom script that gives the same output as HTSeq-count.
Genome_build: Ensembl build 37 / build 38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample.

growth_protocol: Single cells suspensions were prepared from the Bone Marrow of 6-8-week-old mice and subjected to erylysis.

extract_protocol:
Pro or PreB cells were flow cytometrically sorted and resuspended in Trizol (Ambion Life Technologies) for the subsequent extraction of total RNA using Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001). Total RNA was extracted using according to the manufacturer’s protocol.
Library preparation was performed on RNA samples with a measured RNA Integrity Number (RIN) between 8.0 and 10.0 as assessed by the 2100 Bioanalyzer using a Nano chip (Agilent). Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc.) according to manufacturer’s instructions (Illumina, Part # 15031047 Rev. E). RNA libraries were prepared using standard Illumina protocols, analyzed for size and quantity of cDNAs on a 2100 Bioanalyzer using a DNA 7500 chip (Agilent), diluted and pooled in multiplex sequencing pools. The libraries were sequenced as 65 base single reads on a HiSeq2500 (Illumina).

treatment_protocol: Following erythrocyte lysis, Bone marrow cells were stained with flourescence conjugated monoclonal atibodies against CD19, B220, IgM, c-Kit and CD25 to identify their cell surface expression. ProB cells were identified as CD19+B220+IgM-c-Kit+CD25- and PreB cells were identified as CD19+B220+IgM-c-Kit-CD25+.

tag: strain

value: Bone Marrow

tag: genotype


title: Col-0-Glc-3

source_name: Col-0-Glc_4d old seedlings

value: 4-day old seedligns


title: patient36_whole-blood_day120 [p36D120]

tag: gender

tag: time point

value: day 120 after start of treatment

tag: tissue/cell type


title: patient31_whole-blood_day250 [p31D250]

source_name: whole-blood cells, day 250 after start of treatment

value: patient diagnosed with Buruli ulcer

tag: age

value: day 250 after start of treatment


title: Col-0-Glc-2


title: IghTer5H∆TM/Ter5H∆TM;Ragko/ko _Bone_Marrow_ProB_rep2_Experiment_4

tag: cell type


title: Col-0+Glc-1

value: 15 mM glucose for 2 hours


title: patient31_whole-blood_day150 [p31D150]

value: day 150 after start of treatment

value: whole-blood cells


title: patient31_whole-blood_day120 [p31D120]


title: patient33_whole-blood_day0 [p33D0]

value: day 0 after start of treatment


title: Rag1ko/ko_Bone_Marrow_ProB_rep2_Experiment_4


title: patient31_whole-blood_day90 [p31D90]

value: day 90 after start of treatment


title: CONTROL7

city: Guangzhou

first: Qi

last: Guo

address: Yanjiangxi Road

institute: Sun Yat-sen University

description: Gene expression in healthy control plasma

hyb_protocol: The biotinylated cRNA targets were then hybridized with the slides.

scan_protocol: After hybridization, slides were scanned on the Agilent Microarray Scanner (Agilent Technologies, Santa Clara, USA).

data_processing: Data were extracted with Feature Extraction software 12.0.3.1 (Agilent Technologies, Santa Clara, USA).

source_name: plasma, healthy controls7

label_protocol: RNA samples from each group were then used to generate biotinylated cRNA targets for the LC Human ceRNA array (version 1.0).

extract_protocol: Total RNA was isolated using a Plasma RNA Purification Mini Kit (Norgen, Thorold, Canada) according to the manufacturer’s instructions and purified using an RNeasy Mini Kit (Qiagen, GmBH, Germany).

treatment_protocol: Whole blood was collected in venous blood collection tubes containing EDTA after fasting overnight, and plasma was separated by centrifugation.

tag: disease

value: healthy

value: plasma


title: CONTROL4

source_name: plasma, healthy controls4


title: IghTer5H∆TM/Ter5H∆TM;Ragko/ko _Bone_Marrow_ProB_rep3_Experiment_4


title: patient30_whole-blood_day90 [p30D90]

value: male


title: Col-0-Glc-1


title: Rag1ko/ko_Bone_Marrow_ProB_rep3_Experiment_4


title: CONTROL3

source_name: plasma, healthy controls3


title: patient31_whole-blood_day60 [p31D60]

value: day 60 after start of treatment


title: Rag1ko/ko_Bone_Marrow_ProB_rep1_Experiment_4


title: CONTROL5

source_name: plasma, healthy controls5

value: female


title: IghTer5H∆TM/ Ter5H∆TM _Bone_Marrow_ProB_rep2_Experiment_3

source_name: IghTer5H∆TM/ Ter5H∆TM _Bone_Marrow

value: IghTer5H{delta}TM/ Ter5H{delta}TM


title: IghTer5H∆TM/ Ter5H∆TM _Bone_Marrow_ProB_rep3_Experiment_3


title: patient31_whole-blood_day0 [p31D0]

source_name: whole-blood cells, day 0 after start of treatment


title: CONTROL6

source_name: plasma, healthy controls6


title: patient30_whole-blood_day60 [p30D60]


title: CONTROL1

source_name: plasma, healthy controls1


title: patient30_whole-blood_day0 [p30D0]


title: TS543

city: La Jolla

first: Tao

last: Long

address: 9500 Gilman Dr

institute: University of California at San Diego

description: PTEN-WT

data_processing:
QC of raw fastq files with MultiQC
Alignment with STAR
TPM calling with RSEM
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: text files include TPM values for each gene

growth_protocol: GBM-neurospheres were cultured in DMEM/F12 medium supplemented with B27 (GIBCO/Life Technologies) and human recombinant EGF (20 ng/ml), bFGF (10 ng/ml) and 2 mg/mL heparin (Stemcell Technologies), and dissociated with Accutase (Stemcell Technologies).

extract_protocol:
Total RNA was extracted from GBM-spheres using RNeasy Plus Mini Kit (Qiagen # 74134). 2000 ng of total RNA dissolved in RNase-free ddH2O was shipped for sequencing to Novogene Corporation Inc.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.
The qualified libraries are fed into HiSeq/MiSeq sequencers after pooling according to its effective concentration and expected data volume.

value: Glioblastoma stem cells

value: Brain

tag: disease state

value: Cancer (glioblastoma)

tag: treatment

value: Untreated

value: PTEN-WT


title: TS543-2C4

description: PTEN-KO

value: PTEN-KO


title: patient29_whole-blood_day120 [p29D120]

source_name: whole-blood cells, day 120 after start of treatment

value: patient diagnosed with Buruli ulcer

value: day 120 after start of treatment


title: HCM14

description: Gene expression in hypertrophic cardiomyopathy patient plasma

source_name: plasma, hypretrophic cardiomyopathy14

value: hypretrophic cardiomyopathy


title: TS528

description: PTEN-WT


title: IghTer5H∆TM/ Ter5H∆TM _Bone_Marrow_ProB_rep1_Experiment_3

value: Bone Marrow


title: CONTROL2

source_name: plasma, healthy controls2


title: Rag1ko/ko_Bone_Marrow_ProB_rep2_Experiment_3


title: Rag1ko/ko_Bone_Marrow_ProB_rep1_Experiment_3


title: TS576-1A3

description: PTEN-KO


title: IghTer5H/Ter5H _Bone_Marrow_ProB_rep3_Experiment_3

source_name: IghTer5H/Ter5H _Bone_Marrow


title: patient29_whole-blood_day100 [p29D100]

source_name: whole-blood cells, day 100 after start of treatment

value: day 100 after start of treatment

value: whole-blood cells


title: TS576-1A1

description: PTEN-KO


title: HK412

description: PTEN-NULL

value: PTEN-NULL


title: Rag1ko/ko_Bone_Marrow_ProB_rep3_Experiment_3


title: IghTer5H/Ter5H _Bone_Marrow_ProB_rep2_Experiment_3


title: GBM39

description: PTEN-WT


title: TS576

description: PTEN-WT


title: HCM13

source_name: plasma, hypretrophic cardiomyopathy13

value: plasma

value: male


title: HCM10

source_name: plasma, hypretrophic cardiomyopathy10

value: female


title: patient29_whole-blood_day80 [p29D80]

source_name: whole-blood cells, day 80 after start of treatment

value: day 80 after start of treatment


title: HK385

description: PTEN-NULL

value: Glioblastoma stem cells


title: HCM9

source_name: plasma, hypretrophic cardiomyopathy9


title: patient28_whole-blood_day60 [p28D60]

source_name: whole-blood cells, day 60 after start of treatment

value: day 60 after start of treatment


title: IghTer5 /wt;Rag1ko/ko_Bone_Marrow_ProB_rep3_Experiment_2

source_name: IghTer5 /wt;Rag1ko/ko_Bone_Marrow

value: IghTer5 /wt;Rag1ko/ko


title: HK305

description: PTEN-NULL

value: Brain

value: Cancer (glioblastoma)

value: Untreated


title: HCM12

source_name: plasma, hypretrophic cardiomyopathy12


title: HCM11

source_name: plasma, hypretrophic cardiomyopathy11


title: patient29_whole-blood_day56 [p29D56]

source_name: whole-blood cells, day 56 after start of treatment

value: patient diagnosed with Buruli ulcer

value: day 56 after start of treatment


title: HK301

description: PTEN-NULL


title: HK296

description: PTEN-NULL


title: patient28_whole-blood_day0 [p28D0]

source_name: whole-blood cells, day 0 after start of treatment

value: day 0 after start of treatment


title: IghTer5 /wt;Rag1ko/ko_Bone_Marrow_ProB_rep1_Experiment_2

value: Bone Marrow


title: IghTer5H/Ter5H _Bone_Marrow_ProB_rep1_Experiment_3


title: Rag1ko/ko_Bone_Marrow_ProB_rep2_Experiment_2


title: TS600

description: PTEN-NULL


title: GSC11-PTEN

description: PTEN-OVEREXPRESSION

value: PTEN-OVEREXPRESSION