title: Biological replicate of whisker follicle in SA-self-administered rat 1

description:
FPKM-all_genes.txt
V-S-1


title: Biological replicate of striatum in MA-self-administered rat 6

status: Public on Aug 27 2021

type: SRA

city: Daegu

first: Taekwon

last: Son

address: 61, Cheomdan-ro, Dong-gu

department: Korea Brain Bank

country: South Korea

institute: Korea Brain Research Institute

description:
FPKM-all_genes.txt
S-M-6

library_source: transcriptomic

data_processing:
Illumina RTA and bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 whole genome using STAR v2.6.0c.
Raw counts were calculated using Cufflinks v2.2.1.
FPKM was calculated using Cufflinks v2.2.1.
Genome_build: rn6
Supplementary_files_format_and_content: Tab-delimited text file include FPKM for all samples

molecule: total RNA

organism: Rattus norvegicus

source_name: striatum

extract_protocol:
Total RNA was extracted from striatum and whisker follicles using TRIzol® RNA Isolation Reagents (Thermo Fisher, Carlsbad, CA).  The quality and concentration of RNA were assessed on a filter-based multi-mode microplate reader (FLUOstar Omega, BMG Labtech, Germany). The isolated total RNA was processed for preparation of an mRNA sequencing library using TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.  In brief, mRNAs were isolated from 1 μg of total RNA on RNA purification beads by polyA capture, followed by enzymatic shearing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: SpragueDawley rats

tag: treatment

value: methamphetamine

tag: tissue

value: striatum


title: PGNs_R2_GAM181115_3NP_A01_1_S1

city: Berlin

first: Alexander

last: Kukalev

address: Hannoversche Str., 28

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max-Delbrueck Center for Molecular Medicine

description:
processed data: PGNs.R2.segregation_at50000.2019-12-05.passed_qc.table
processed data: PGNs.R2.mm10.NPMI.at50Kb.all_chromosomes.gz
processed data: PGNs.R2.mm10.coseg.at250Kb.all_chromosomes.gz

library_source: genomic

data_processing:
Sequenced reads from each GAM library were mapped to the mouse genome assembly GRCm38 (Dec. 2011, mm10) using bowtie2 with all default settings. All non-uniquely mapped reads, reads with mapping quality < 20 were filtered using the command “sed '/XS:/d' | samtools view -q 20 -F 4 -bS -”. PCR duplicates were removed with the “samtools rmdup” command. Samples were checked for contamination using fastq_screen. Number of nucleotides sequenced in each genomic bin was calculated using bedtools coverage command. Genomic windows that were present within ultrathin nuclear slices for each GAM library were identified using gamtools v2. Each dataset was assessed for quality control by determining the percentage of orphan windows, number of uniquely mapped reads to the mouse genome, and cross-well contamination for every sample. For good quality samples we produced raw co-segregation, as well as normalized (NPMI) pair-wise chromatin contact matrices for each cell-type and replicate.
Genome_build: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: pyramidal glutamatergic neurons

extract_protocol: Briefly, we isolated single thin tissue sections by ultrathin cryosectioning (approx. 220 nm) of the mouse brain region of interest, and selected specific cell-types using immunofluorescence with specific AB markers. Following cell identification, 3 nuclear sections (nuclear profiles; NPs) were captured by laser microdissection in individual PCR caps. We then extracted, amplified and sequenced the DNA from each PCR cap.

value: cornus ammonis 1 region of the hippocampus

tag: cell type

value: pyramidal glutamatergic neurons

tag: age

tag: Sex

value: M

tag: genotype

value: passed

tag: cross contamination

value: No

tag: if staining

value: Pan-histo


title: PGNs_R2_GAM181115_3NP_A03_1_S17


title: Biological replicate of striatum in MA-self-administered rat 5

description:
FPKM-all_genes.txt
S-M-5


title: Biological replicate of striatum in MA-self-administered rat 4

description:
FPKM-all_genes.txt
S-M-4


title: PGNs_R2_GAM181115_0NP_A12_1_S89

value: water control

value: failed


title: Biological replicate of striatum in MA-self-administered rat 3

description:
FPKM-all_genes.txt
S-M-3


title: PGNs_R1_GAM180113_3NP_H12_1_S96

description:
processed data: PGNs.R1.segregation_at50000.2019-12-05.passed_qc.table
processed data: PGNs.R1.mm10.NPMI.at50Kb.all_chromosomes.gz
processed data: PGNs.R1.mm10.coseg.at250Kb.all_chromosomes.gz


title: PGNs_R2_GAM181115_0NP_A06_1_S41


title: Biological replicate of striatum in MA-self-administered rat 2

description:
FPKM-all_genes.txt
S-M-2


title: Biological replicate of striatum in SA-self-administered rat 6

description:
FPKM-all_genes.txt
S-S-6

value: saline


title: Biological replicate of striatum in SA-self-administered rat 5

description:
FPKM-all_genes.txt
S-S-5


title: PGNs_R1_GAM180113_3NP_H11_1_S88


title: PGNs_R2_GAM181115_3NP_B01_1_S2


title: PGNs_R1_GAM180113_3NP_H12_2_S192


title: Biological replicate of striatum in SA-self-administered rat 4

description:
FPKM-all_genes.txt
S-S-4


title: PGNs_R1_GAM180113_3NP_H11_2_S184


title: PGNs_R1_GAM180113_3NP_H10_2_S176


title: PGNs_R1_GAM180113_3NP_H09_2_S168


title: PGNs_R1_GAM180113_3NP_H10_1_S80


title: Biological replicate of striatum in SA-self-administered rat 2

description:
FPKM-all_genes.txt
S-S-2


title: PGNs_R1_GAM180113_3NP_H09_1_S72


title: Biological replicate of striatum in SA-self-administered rat 3

description:
FPKM-all_genes.txt
S-S-3


title: PGNs_R1_GAM180113_3NP_H08_1_S64


title: Biological replicate of striatum in SA-self-administered rat 1

description:
FPKM-all_genes.txt
S-S-1


title: PGNs_R1_GAM180113_3NP_H07_2_S152


title: PGNs_R1_GAM180113_3NP_H08_2_S160


title: PGNs_R1_GAM180113_3NP_H06_2_S144


title: Biological replicate of striatum in MA-self-administered rat 1

description:
FPKM-all_genes.txt
S-M-1


title: PGNs_R1_GAM180113_3NP_H06_1_S48


title: Ovarian clear cell carcinoma FFPE [NB15-13182]

type: RNA

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

hyb_protocol: The labelled RNA samples were hybridized at 65°C for at least 16 hours but not more than 48 hours in a thermal cycler.

scan_protocol: Each individual lane was scanned 194 Fields of View (FOV). The system images these FOVs separately, and sums the barcode counts of all FOVs from a single lane to form the final raw data count for each unique barcode target. Finally, the system reports the number of FOVs successfully imaged as FOV Counted.

data_processing: The raw data were processed using NanoString nSolver. The raw data were normalized using positive control and housekeeping genes control.

label: biotin

organism: Homo sapiens

source_name: Ovarian clear cell carcinoma

label_protocol: 100ng of unamplified total FFPE RNA were labelled with nanoString Reporter CodeSet and Capture ProbeSet, procedure as per MAN-10023-11_nCounter_XT_Assay_User_Manual.

extract_protocol: RNA from the FFPE sections were extracted using QIAGEN RNeasy FFPE Kit (Cat No./ID: 73504).

value: Ovarian clear cell carcinoma

tag: histology

value: Clear cell

tag: age (yr)

tag: gender

value: Female


title: Ovarian clear cell carcinoma FFPE [NB08-21864M]


title: Ovarian clear cell carcinoma FFPE [NB09-06409]


title: PGNs_R1_GAM180113_3NP_H04_2_S128


title: PGNs_R1_GAM180113_3NP_H05_1_S40


title: Ovarian clear cell carcinoma FFPE [NB06-05201]


title: Biological replicate of whisker follicle in SA-self-administered rat 2

description:
FPKM-all_genes.txt
V-S-2

source_name: whisker follicle

value: whisker follicle


title: PGNs_R1_GAM180113_3NP_H04_1_S32


title: PGNs_R1_GAM180113_3NP_H03_2_S120


title: PGNs_R1_GAM180113_3NP_H03_1_S24


title: Ovarian clear cell carcinoma FFPE [NB07-15184M]


title: Ovarian clear cell carcinoma FFPE [NB02-07206]


title: Ovarian clear cell carcinoma FFPE [NB04-08931]


title: Ovarian clear cell carcinoma FFPE [NB06-04538]


title: Ovarian clear cell carcinoma FFPE [NB13-05104]


title: PGNs_R1_GAM180113_3NP_H02_2_S112


title: PGNs_R1_GAM180113_3NP_H07_1_S56


title: PGNs_R1_GAM180113_3NP_H02_1_S16


title: Ovarian clear cell carcinoma FFPE [NB15-4124]


title: Ovarian clear cell carcinoma FFPE [NB15-11133]


title: PGNs_R1_GAM180113_3NP_H05_2_S136


title: Ovarian clear cell carcinoma FFPE [NB11-11247M]


title: PGNs_R1_GAM180113_3NP_G12_2_S191


title: Ovarian clear cell carcinoma FFPE [NB10-07719]


title: PGNs_R1_GAM180113_3NP_H01_1_S8


title: PGNs_R1_GAM180113_3NP_G11_2_S183


title: Ovarian clear cell carcinoma FFPE [NB04-07590]


title: Ovarian clear cell carcinoma FFPE [NB15-1021]


title: PGNs_R1_GAM180113_3NP_G11_1_S87


title: PGNs_R1_GAM180113_3NP_G10_2_S175


title: PGNs_R1_GAM180113_3NP_H01_2_S104


title: PGNs_R1_GAM180113_3NP_G08_2_S159


title: PGNs_R1_GAM180113_3NP_G09_1_S71


title: PGNs_R1_GAM180113_3NP_G09_2_S167


title: Ovarian clear cell carcinoma FFPE [NB14-16998]


title: Ovarian clear cell carcinoma FFPE [NB14-1532]


title: Ovarian clear cell carcinoma FFPE [NB14-5263]


title: PGNs_R1_GAM180113_3NP_G12_1_S95


title: PGNs_R1_GAM180113_3NP_G07_1_S55


title: Ovarian clear cell carcinoma FFPE [NB15-2161]


title: PGNs_R1_GAM180113_3NP_G06_2_S143


title: PGNs_R1_GAM180113_3NP_G10_1_S79


title: PGNs_R1_GAM180113_3NP_G07_2_S151


title: Ovarian clear cell carcinoma FFPE [NB13-14828]


title: Ovarian clear cell carcinoma FFPE [NB13-19660]


title: Ovarian clear cell carcinoma FFPE [NB13-20660]


title: Ovarian clear cell carcinoma FFPE [NB13-5104]


title: PGNs_R1_GAM180113_3NP_G06_1_S47


title: PGNs_R1_GAM180113_3NP_G05_1_S39


title: PGNs_R1_GAM180113_3NP_G05_2_S135


title: Ovarian clear cell carcinoma FFPE [NB15-2716]


title: Ovarian clear cell carcinoma FFPE [NB14-10793]


title: Ovarian clear cell carcinoma FFPE [NB14-1306]


title: PGNs_R1_GAM180113_3NP_G04_1_S31


title: PGNs_R1_GAM180113_3NP_G04_2_S127


title: Ovarian clear cell carcinoma FFPE [NB13-19075]


title: PGNs_R1_GAM180113_3NP_G03_1_S23


title: Ovarian clear cell carcinoma FFPE [NB13-1090]


title: Ovarian clear cell carcinoma FFPE [NB12-21643]


title: Ovarian clear cell carcinoma FFPE [NB13-1529]


title: Ovarian clear cell carcinoma FFPE [NB12-15211]


title: Ovarian clear cell carcinoma FFPE [NB12-5838]


title: Ovarian clear cell carcinoma FFPE [NB12-150]


title: PGNs_R1_GAM180113_3NP_G02_1_S15


title: PGNs_R1_GAM180113_3NP_G01_2_S103


title: PGNs_R1_GAM180113_3NP_G02_2_S111


title: PGNs_R1_GAM180113_3NP_G01_1_S7


title: Ovarian clear cell carcinoma FFPE [NB11-16659]


title: Ovarian clear cell carcinoma FFPE [NB11-19169]


title: PGNs_R1_GAM180113_3NP_F11_2_S182


title: PGNs_R1_GAM180113_3NP_F12_2_S190


title: PGNs_R1_GAM180113_3NP_F12_1_S94


title: PGNs_R1_GAM180113_3NP_F11_1_S86


title: PGNs_R1_GAM180113_3NP_G03_2_S119


title: Ovarian clear cell carcinoma FFPE [NB11-6123]


title: Ovarian clear cell carcinoma FFPE [NB11-8794]


title: Ovarian clear cell carcinoma FFPE [NB11-7107]


title: Ovarian clear cell carcinoma FFPE [NB11-11247]


title: Ovarian clear cell carcinoma FFPE [NB11-4950]


title: Ovarian clear cell carcinoma FFPE [NB11-1774]


title: PGNs_R1_GAM180113_3NP_F10_2_S174


title: Ovarian clear cell carcinoma FFPE [NB11-1293]


title: Ovarian clear cell carcinoma FFPE [NB10-24976]


title: Ovarian clear cell carcinoma FFPE [NB10-18697]


title: PGNs_R1_GAM180113_3NP_F09_1_S70


title: Ovarian clear cell carcinoma FFPE [NB10-11361]


title: Ovarian clear cell carcinoma FFPE [NB10-4946]


title: PGNs_R1_GAM180113_3NP_F08_1_S62


title: PGNs_R1_GAM180113_3NP_F06_2_S142


title: PGNs_R1_GAM180113_3NP_F06_1_S46


title: PGNs_R1_GAM180113_3NP_F07_2_S150


title: Ovarian clear cell carcinoma FFPE [NB10-3689]


title: Ovarian clear cell carcinoma FFPE [NB10-3863]


title: PGNs_R1_GAM180113_3NP_F04_2_S126


title: PGNs_R1_GAM180113_3NP_F07_1_S54


title: Ovarian clear cell carcinoma FFPE [NB09-21175]


title: PGNs_R1_GAM180113_3NP_F10_1_S78


title: PGNs_R1_GAM180113_3NP_F04_1_S30


title: Ovarian clear cell carcinoma FFPE [NB10-7719]


title: PGNs_R1_GAM180113_3NP_F09_2_S166


title: PGNs_R1_GAM180113_3NP_F03_2_S118


title: PGNs_R1_GAM180113_3NP_F05_2_S134


title: Ovarian clear cell carcinoma FFPE [NB01-6033]


title: Ovarian clear cell carcinoma FFPE [NB09-4451]


title: Ovarian clear cell carcinoma FFPE [NB09-12446]


title: PGNs_R1_GAM180113_3NP_F02_2_S110


title: Ovarian clear cell carcinoma FFPE [NB09-11741]


title: Ovarian clear cell carcinoma FFPE [NB09-11131]


title: Ovarian clear cell carcinoma FFPE [NB09-15468]


title: Ovarian clear cell carcinoma FFPE [NB09-6411]


title: PGNs_R1_GAM180113_3NP_F08_2_S158


title: Ovarian clear cell carcinoma FFPE [NB08-21864]


title: Ovarian clear cell carcinoma FFPE [NB09-6409]


title: Ovarian clear cell carcinoma FFPE [NB09-3335]


title: Ovarian clear cell carcinoma FFPE [NB09-20629]


title: PGNs_R1_GAM180113_3NP_F02_1_S14


title: PGNs_R1_GAM180113_3NP_F01_1_S6


title: PGNs_R1_GAM180113_3NP_F03_1_S22


title: PGNs_R1_GAM180113_3NP_E12_2_S189


title: PGNs_R1_GAM180113_3NP_F05_1_S38


title: Ovarian clear cell carcinoma FFPE [NB08-18827]


title: PGNs_R1_GAM180113_3NP_E11_1_S85


title: Ovarian clear cell carcinoma FFPE [NB08-20432]


title: Ovarian clear cell carcinoma FFPE [NB08-10289]


title: PGNs_R1_GAM180113_3NP_E11_2_S181


title: PGNs_R1_GAM180113_3NP_E12_1_S93


title: PGNs_R1_GAM180113_3NP_E10_2_S173


title: Ovarian clear cell carcinoma FFPE [NB07-9813]


title: PGNs_R1_GAM180113_3NP_E09_2_S165


title: PGNs_R1_GAM180113_3NP_E10_1_S77


title: Ovarian clear cell carcinoma FFPE [NB07-15184]


title: PGNs_R1_GAM180113_3NP_E08_2_S157


title: PGNs_R1_GAM180113_3NP_E09_1_S69


title: Ovarian clear cell carcinoma FFPE [NB07-15866]


title: PGNs_R1_GAM180113_3NP_F01_2_S102


title: Ovarian clear cell carcinoma FFPE [NB07-8920]


title: Ovarian clear cell carcinoma FFPE [NB07-5954]


title: Ovarian clear cell carcinoma FFPE [NB06-17719]


title: PGNs_R1_GAM180113_3NP_E07_2_S149


title: PGNs_R1_GAM180113_3NP_E08_1_S61


title: PGNs_R1_GAM180113_3NP_E07_1_S53


title: PGNs_R1_GAM180113_3NP_E06_2_S141


title: PGNs_R1_GAM180113_3NP_E05_2_S133


title: PGNs_R1_GAM180113_3NP_E06_1_S45


title: PGNs_R1_GAM180113_3NP_E05_1_S37


title: Ovarian clear cell carcinoma FFPE [NB07-6623]


title: PGNs_R1_GAM180113_3NP_E04_1_S29


title: PGNs_R1_GAM180113_3NP_E03_2_S117


title: PGNs_R1_GAM180113_3NP_E04_2_S125


title: PGNs_R1_GAM180113_3NP_E03_1_S21


title: PGNs_R1_GAM180113_3NP_E02_2_S109


title: Ovarian clear cell carcinoma FFPE [NB07-3352]


title: Ovarian clear cell carcinoma FFPE [NB06-5201]


title: Ovarian clear cell carcinoma FFPE [NB06-10947]


title: Ovarian clear cell carcinoma FFPE [NB06-16533]


title: Ovarian clear cell carcinoma FFPE [NB06-8596]


title: Ovarian clear cell carcinoma FFPE [NB06-14531]


title: Ovarian clear cell carcinoma FFPE [NB06-4538]


title: Ovarian clear cell carcinoma FFPE [NB06-12395]


title: Ovarian clear cell carcinoma FFPE [NB05-12788]


title: Ovarian clear cell carcinoma FFPE [NB06-6752]


title: Ovarian clear cell carcinoma FFPE [NB06-2727]


title: PGNs_R1_GAM180113_3NP_E02_1_S13


title: PGNs_R1_GAM180113_3NP_E01_2_S101


title: PGNs_R1_GAM180113_3NP_E01_1_S5


title: Ovarian clear cell carcinoma FFPE [NB05-1018]


title: PGNs_R1_GAM180113_3NP_D12_1_S92


title: Ovarian clear cell carcinoma FFPE [NB03-1792]


title: Ovarian clear cell carcinoma FFPE [NB04-8931]


title: Ovarian clear cell carcinoma FFPE [NB04-7590]


title: PGNs_R1_GAM180113_3NP_D12_2_S188


title: Ovarian clear cell carcinoma FFPE [NB03-13884]


title: Ovarian clear cell carcinoma FFPE [NB02-13500]


title: PGNs_R1_GAM180113_3NP_D11_2_S180


title: PGNs_R1_GAM180113_3NP_D11_1_S84


title: Ovarian clear cell carcinoma FFPE [NB02-13262]


title: PGNs_R1_GAM180113_3NP_D07_2_S148


title: PGNs_R1_GAM180113_3NP_D08_1_S60


title: Ovarian clear cell carcinoma FFPE [NB02-8182]


title: PGNs_R1_GAM180113_3NP_D09_1_S68


title: PGNs_R1_GAM180113_3NP_D10_1_S76


title: PGNs_R1_GAM180113_3NP_D09_2_S164


title: Ovarian clear cell carcinoma FFPE [NB00-3104]

tag: subtype


title: PGNs_R1_GAM180113_3NP_D06_2_S140


title: Ovarian clear cell carcinoma FFPE [NB00-704]


title: PGNs_R1_GAM180113_3NP_D05_2_S132


title: Ovarian clear cell carcinoma FFPE [NB02-7206]


title: Ovarian clear cell carcinoma FFPE [NB01-8419]


title: Ovarian clear cell carcinoma FFPE [NB02-4541]


title: PGNs_R1_GAM180113_3NP_D10_2_S172


title: PGNs_R1_GAM180113_3NP_G08_1_S63


title: Ovarian clear cell carcinoma FFPE [NB05-15412]


title: PGNs_R1_GAM180113_3NP_D08_2_S156


title: PGNs_R1_GAM180113_3NP_D05_1_S36


title: PGNs_R1_GAM180113_3NP_D04_2_S124


title: PGNs_R1_GAM180113_3NP_D03_2_S116


title: PGNs_R1_GAM180113_3NP_D03_1_S20


title: PGNs_R1_GAM180113_3NP_D06_1_S44


title: PGNs_R1_GAM180113_3NP_D02_1_S12


title: PGNs_R1_GAM180113_3NP_D01_2_S100


title: PGNs_R1_GAM180113_3NP_D07_1_S52


title: PGNs_R1_GAM180113_3NP_D02_2_S108


title: PGNs_R1_GAM180113_3NP_C12_2_S187


title: PGNs_R1_GAM180113_3NP_D01_1_S4


title: PGNs_R1_GAM180113_3NP_C12_1_S91


title: PGNs_R1_GAM180113_3NP_C11_2_S179


title: PGNs_R1_GAM180113_3NP_D04_1_S28


title: PGNs_R1_GAM180113_3NP_C10_1_S75


title: PGNs_R1_GAM180113_3NP_C11_1_S83


title: PGNs_R1_GAM180113_3NP_C10_2_S171


title: PGNs_R1_GAM180113_3NP_C09_2_S163


title: PGNs_R1_GAM180113_3NP_C09_1_S67


title: PGNs_R1_GAM180113_3NP_C08_2_S155


title: PGNs_R1_GAM180113_3NP_C07_2_S147


title: PGNs_R1_GAM180113_3NP_C08_1_S59


title: PGNs_R1_GAM180113_3NP_C07_1_S51


title: PGNs_R1_GAM180113_3NP_C06_2_S139


title: GEX_L002

city: New York

first: Samir

last: Parekh

state: NY

address: 1470 Madison Avenue, 5-114, Box 1079

department: Tisch Cancer Institute

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: cDNA (gene expression) replicate 2

data_processing:
Data were analyzed using Cell Ranger v3.1 pipeline, available via the 10X Genomics website.
Genome_build: hg38
Supplementary_files_format_and_content: filtered_feature_bc_matrix.tar.gz: gene barcode matrices and feature barcode matrix; metadata.tar.gz: contains data corresponding to the HTOs and ADTs used, as well as the sample metadata

source_name: peripheral blood mononuclear cells

growth_protocol: Peripheral blood mononuclear cells (PBMC) were Ficoll density separated and cryopreserved.

extract_protocol:
Stained cells were then encapsulated for single-cell reverse transcription using the 10X Chromium platform (5’ v1.0)
cDNA amplification was performed in the presence of 2pM of an antibody oligo specific primer to increase yield of antibody derived tags (ADTs) and 3pM of specific primer to increase yield of HTOs. The amplified cDNA was then separated by SPRI size selection into cDNA fractions containing mRNA derived cDNA (>300bp) and ADT-derived cDNAs (<180bp), which were further purified by additional rounds of SPRI selection. Independent sequencing libraries were generated from the mRNA and ADT cDNA fractions, which were quantified, pooled and sequenced together
OTHER: CITE-seq

treatment_protocol: 5 samples (1 healthy donor, 4 patients) were split into two aliquots and were either "stimulated" or "unstimulated". Stimulated aliquots were incubated for 3hrs at 37ºC with PMA/Ionomycin. Unstimulated aliquots were incubated for 3hrs at 37C with cRPMI.

tag: tag

value: cDNA (gene expression)


title: PGNs_R1_GAM180113_3NP_C06_1_S43


title: GEX_L001

description: cDNA (gene expression) replicate 1


title: Patient 3_MKX

city: Crawley

first: Andrew

middle: William

last: Stevenson

state: Western Australia

address: Room 112b, Curnow Building, Hackett Drive Carpark Entrance 2, UWA

department: School of Biomedical Sciences

country: Australia

institute: University of Western Australia

data_processing:
Real Time Analysis (RTA) v3.4.4 software used for base-calling. Then the Illumina bcl2fastq  2.20.0.422 pipeline was used to generate the sequence data.
Fastp used for trimming.
STAR used for aligment.
SAMtools used to generate bam files for further analyses.
DESeq2 used for differential gene expresson analyses.
Genome_build: hg19
Supplementary_files_format_and_content: CSV files with raw abundance counts

source_name: Scar tissue

growth_protocol: 3mm punch biopsies were taken from the forearm scar site the attendant physician. Tissue was transported to the lab where it was placed in a petri dish and sliced into three equal sized potions. Pieces of the biopsy were then placed dermis side down in a T-25 (25 cm2) (Greiner Bio-One, Germany) culture flask without any media, and a drop of 100% foetal bovine serum (FBS) added to the surface of each piece. They were then cultured in DMEM with 10% FBS and 5% pen/strep until ready for transfection.

extract_protocol:
RNA was prepared using the RNeasy mini kit (Cat. No. 74104, QIAGEN, Netherlands), as per manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Knockdown of FOXF2 using siRNA was carried out using the FlexiTube GeneSolution siRNA system (QIAGEN, Netherlands) for both FOXF2 (Cat. No. GS2295) and MKX (Cat. No. GS2830780), as well as AllStars Hs Cell Death siRNA (Cat. No. SI04381048) as a positive control and AllStars Negative Control siRNA (Cat. No. SI03650318) as a scrambled negative control.

value: MKX knock out

value: primary fibroblasts


title: PGNs_R1_GAM180113_3NP_C05_2_S131


title: PGNs_R1_GAM180113_3NP_C05_1_S35


title: Patient 2_MKX


title: PGNs_R1_GAM180113_3NP_C04_2_S123


title: Patient 1_MKX


title: PGNs_R1_GAM180113_3NP_C04_1_S27


title: Patient 3_Scrambled

value: Scrambled


title: PGNs_R1_GAM180113_3NP_C03_2_S115

value: cornus ammonis 1 region of the hippocampus


title: Patient 2_Scrambled


title: PGNs_R1_GAM180113_3NP_C03_1_S19

value: pyramidal glutamatergic neurons


title: Sample21.Brown rat.203839170005_R05C01

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Calibration species=Brown rat

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

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

data_processing: noob normalization

label: Cy3 and Cy5

source_name: Calibration

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from premixed DNA standards from EpigenDx Inc (products 80-8060H-PreMixHuman, 80-8060M-PreMixMouse, and Standard80-8060R-PreMixRat Premixed Calibration Standard)

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: dna source

value: premixed DNA standards from EpigenDx Inc (Standard80-8060R-PreMixRat)

tag: proportionmethylated


title: Sample26.Brown rat.203836210094_R02C01


title: PGNs_R1_GAM180113_3NP_C02_1_S11

value: M

value: passed


title: PGNs_R1_GAM180113_3NP_C02_2_S107

value: No

value: Pan-histo


title: Sample13.Mouse.203836210075_R05C01

description: genomic DNA methylation from tissue=Calibration species=Mouse

value: premixed DNA standards from EpigenDx Inc (80-8060M-PreMixMouse)


title: Patient 3_FOXF2

value: FOXF2 knock out


title: Patient 1_Scrambled


title: Patient 2_FOXF2


title: Sample28.Brown rat.203836210094_R04C01


title: PGNs_R1_GAM180113_3NP_C01_2_S99


title: Patient 1_FOXF2


title: Sample14.Mouse.203836210075_R06C01


title: PGNs_R1_GAM180113_3NP_B12_2_S186


title: PGNs_R1_GAM180113_3NP_C01_1_S3


title: H5

city: Shanghai

first: Wansheng

last: Chen

address: 415 Fengyang Road

department: Department of Pharmacy

country: China

institute: Changzheng Hospital, Second Military Medical University

data_processing:
The raw data was checked by FastQC
Clean reads were aligned to the human genome using STAR 2.5
The expression of the transcript was calculated by FPKM using Cuffnorm
Differentially expression transcripts were determined using DESeq v1.22.1
Function and signaling pathway enrichment analysis using GO and KEGG database
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table include FPKM values for every gene and every sample

source_name: colorectal tumor adjacent normal tissue

extract_protocol:
RNA was isolated using the standard TRIzol protocol.
Stand-specific libraries were constructed using the TruSeq RNA sample prepartion kit (Illumina).

value: Male

tag: weight

tag: height

tag: bmi


title: H6


title: H7


title: H4


title: Sample27.Brown rat.203836210094_R03C01


title: PGNs_R1_GAM180113_3NP_B11_2_S178

tag: strain

tag: tissue

tag: treatment


title: PGNs_R1_GAM180113_3NP_B11_1_S82

tag: cell type

tag: age

tag: Sex


title: PGNs_R1_GAM180113_3NP_B12_1_S90

tag: genotype

tag: cross contamination

tag: if staining


title: H1

description: Excluded from the study. As the patient did not use Capecitabine-based adjuvant chemotherapy.

value: unknown


title: Sample20.Brown rat.203839170005_R04C01


title: Sample23.Brown rat.203839170005_R07C01


title: Sample16.Mouse.203836210075_R08C01


title: Sample22.Brown rat.203839170005_R06C01


title: PGNs_R1_GAM180113_3NP_B10_2_S170


title: Sample15.Mouse.203836210075_R07C01


title: PGNs_R1_GAM180113_3NP_B10_1_S74


title: PGNs_R1_GAM180113_3NP_B08_2_S154

value: failed


title: PGNs_R1_GAM180113_3NP_B09_2_S162


title: PGNs_R1_GAM180113_3NP_B08_1_S58


title: Sample17.Mouse.203839170005_R01C01


title: Sample8.Mouse.203440280016_R08C01


title: Sample18.Mouse.203839170005_R02C01


title: G7


title: G4


title: Sample24.Brown rat.203839170005_R08C01


title: Sample19.Brown rat.203839170005_R03C01


title: G3


title: Sample25.Brown rat.203836210094_R01C01


title: Sample11.Mouse.203836210075_R03C01


title: G2


title: G1


title: H3


title: PGNs_R1_GAM180113_3NP_B06_2_S138


title: Sample12.Mouse.203836210075_R04C01


title: PGNs_R1_GAM180113_3NP_B06_1_S42


title: Sample6.Mouse.203440280016_R06C01


title: F7

value: Female


title: PGNs_R1_GAM180113_3NP_B09_1_S66


title: PGNs_R1_GAM180113_3NP_B05_1_S34


title: PGNs_R1_GAM180113_3NP_B04_2_S122


title: G5


title: PGNs_R1_GAM180113_3NP_B05_2_S130


title: Sample10.Mouse.203836210075_R02C01


title: Sample3.Human.203440280016_R03C01

description: genomic DNA methylation from tissue=Calibration species=Human

value: premixed DNA standards from EpigenDx Inc (80-8060H-PreMixHuman)


title: Sample4.Mouse.203440280016_R04C01


title: F6


title: G6


title: Sample5.Mouse.203440280016_R05C01


title: F3


title: F5


title: F4


title: PGNs_R1_GAM180113_3NP_B03_2_S114


title: Sample7.Mouse.203440280016_R07C01


title: Sample9.Mouse.203836210075_R01C01


title: PGNs_R1_GAM180113_3NP_B04_1_S26


title: E7


title: PGNs_R1_GAM180113_3NP_B03_1_S18


title: E6


title: PGNs_R1_GAM180113_3NP_B02_1_S10


title: E4


title: F1


title: F2


title: PGNs_R1_GAM180113_3NP_B02_2_S106


title: Sample1.Human.203440280016_R01C01


title: E3


title: E5


title: PGNs_R1_GAM180113_3NP_B01_2_S98


title: 400_3

city: Rochester

first: O'Banion

last: Kerry

state: United States of America

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
Basecalls: bcl2fastq-2.19.0
Data Cleaning: fastp 0.20.0, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment: STAR_2.7.0f, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification: subread-1.6.4, featurecounts, -s 0 -t exon -g gene_name
DESeq2 was used for differential expression analysis.
Genome_build: Reference Genome: GRCm38.p6 + Gencode-M22 Annotation
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: hippocampal microglia

extract_protocol:
Microglia (CD45int CD11b+) from the hippocampi were isolated through a continuous 40% percoll gradient and sorted with FACSAria II (BD) into RLT Buffer (Qiagen).
Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen) and pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech, Mountain View, CA) per manufacturer’s recommendations. 150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA).

treatment_protocol: Female 3xTg mice (>15 month-old) were treated weekly with 0.1 mg of GA for approximately 8 weeks.

value: GA

value: F

value: hippocampal microglia


title: PGNs_R1_GAM180113_3NP_B01_1_S2

value: cornus ammonis 1 region of the hippocampus


title: 400_2


title: 400_1


title: PGNs_R1_GAM180113_3NP_A12_2_S185

value: pyramidal glutamatergic neurons


title: D7


title: E1


title: 394_2


title: D6


title: PGNs_R1_GAM180113_3NP_A11_2_S177


title: 394_1


title: D5


title: D4


title: D3


title: 388_5

value: PBS


title: PGNs_R1_GAM180113_3NP_A11_1_S81

value: M


title: D2


title: PGNs_R1_GAM180113_3NP_A10_2_S169

value: passed


title: 388_4


title: E2


title: C8


title: PGNs_R1_GAM180113_3NP_A10_1_S73

value: No


title: 388_3


title: C6


title: C5


title: C7


title: C4


title: PGNs_R1_GAM180113_3NP_A09_2_S161

value: Pan-histo


title: 388_2


title: PGNs_R1_GAM180113_3NP_A09_1_S65


title: D1


title: H2


title: Sample2.Human.203440280016_R02C01


title: 388_1


title: C1


title: B8


title: PGNs_R1_GAM180113_3NP_A08_1_S57


title: B7


title: Irf8KO_withLaser_S4

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

data_processing:
FastQC was performed to assess sequencing quality. After removing reads containing adapter sequences and duplicate reads via cutadapt software (GitHub, San Francisco, CA, US) and FastUniq, the filtered reads were mapped to the mouse genome from ENSEMBL (https://www.ensembl.org/Mus_musculus/Info/Index) using bowtie2. The transcripts were functionally annotated with gene transfer formata file version 90, quantified using HTSeq and normalized as transcripts per kilobase million (TPM) via DESeq2. Differential gene expression analysis with threshold (log2 fold change > 1.5 or < -1.5, p < 0.05, TPM ≥ 100 in at least one of the two compared groups) was performed using DESeq2.
Genome_build: GRCm38

source_name: rMG Irf8 KO with laser

extract_protocol:
Fluorescence-activated cell sorting of retinal microglia: Following intracardic perfusion with 1× PBS and enucleation, eyes were dissected in ice-cold 1× PBS to isolate the retinae. For the lasered mice, the central parts (70%) of the retinae were used for FACS while the peripheral parts were omitted. After tissue homogenization and filtration through a 50 µm cell strainer (Sysmex, Goerlitz, Germany), dead cell exclusion was performed by incubation with fixable viability dye 780 (1:1000, 65-0865-14, eBioscience, Waltham, MA, US). Anti-CD16/CD32 Fc block (1:200, 553142, BD Biosciences, Heidelberg, Germany) was used to avoid unspecific binding. Following staining against CD45 (1:200, 103133, BioLegend, San Diego, CA, US), CD11b (1:200, 17-0112-83, eBioscience, Waltham, MA, US), Ly6C (1:200, 560593, BD Bioscience, Heidelberg, Germany) and Ly6G (1:200, 560601, BD Biosciences, Heidelberg, Germany) for 20 minutes at 4 °C, retinal microglia characterized as CD45lowCD11b+Cx3cr1GFP/+Ly6C-Ly6G- were analyzed and sorted into RNA stabilization reagent (QIAGEN, Hilden, Germany) using a MoFlo Astrios EQ High Speed Cell Sorter (Beckman Coulter, Munich, Germany). For RNA Sequencing, an average of 10,000 retinal microglia per sample were obtained from pooling 3 to 4 mice.
RNA extraction: RNA extraction, RNA library preparation and RNA sequencing were performed in collaboration with the Genomics Core Facility "KFB-Center of Excellence for Fluorescent Bioanalytics" (University of Regensburg, Germany). RNA extraction was performed according to manufacturer’s instructions using the RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany). After pelleting the sample by centrifugation, the RNA stabilization reagent was removed and replaced by RLT Plus buffer for lysing of retinal microglia. Genomic DNA was removed selectively and efficiently by using gDNA Eliminator spin columns for RNA purification. After adding Ethanol to the flow-through, the sample was applied to an RNeasy MinElute spin column to collect RNA. Finally, after washing of the column, all purified RNA was eluted in RNase-free water. The quality and integrity of total RNA was assessed with a Agilent 2100 Bioanalyzer in combination with the RNA 6000 Pico LabChip Kit (Agilent, Palo Alto, CA, USA).
RNA sequencing: First-strand cDNA was generated using SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, inc., Mountain View, CA, USA). Double-stand cDNA was amplified with LD PCR and purified with AMPure XP beads. Library preparation was constructed conforming to the Illumina Nextera XT Sample Preparation Guide (Illumina, San Diego, CA, USA). In brief, 150 pg of input cDNA was tagmented via Nextera XT transposome. The products were purified and amplified with a limited-cycle PCR program ro construct sequencing libraries. The libraries were quantified with the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Wobum, MA, USA). Equimolar amounts of each library were pooled for cluster generation on the cBot using the Illumina TruSe SR Cluster Kit v3. The sequencing run was performed on a HiSeq1000 instrument with TruSeq SBS Kit v3 according to the Illumina HiSeq 1000 System User Guide. Illumina image analysis and base calling were recorded in library base call format (.bcl) and further converted to Fastq files via the CASAVA1.8.2 software.

value: laser


title: B6


title: PGNs_R1_GAM180113_3NP_B07_2_S146


title: B4


title: B5


title: PGNs_R1_GAM180113_3NP_A07_2_S145


title: Irf8KO_withLaser_S2


title: Irf8KO_withLaser_S3


title: PGNs_R1_GAM180113_3NP_A07_1_S49


title: C3


title: B3


title: PGNs_R1_GAM180113_3NP_A06_2_S137


title: PGNs_R1_GAM180113_3NP_A06_1_S41


title: A8


title: B2


title: PGNs_R1_GAM180113_3NP_A05_2_S129


title: C2


title: PGNs_R1_GAM180113_3NP_A08_2_S153


title: A5


title: Irf8KO_withoutLaser_S1

source_name: rMG Irf8 KO without laser

value: untreated


title: Irf8KO_withoutLaser_S2


title: A4


title: PGNs_R1_GAM180113_3NP_A05_1_S33


title: B1

value: Male


title: A2


title: PGNs_R1_GAM180113_3NP_A04_2_S121


title: A3


title: A6


title: A7

value: unknown


title: A1


title: PGNs_R1_GAM180113_3NP_A03_2_S113


title: KRp2-99

city: Houston

first: Jianfeng

last: Xu

state: Texas

address: one baylor plaza

institute: Baylor College of Medicine

data_processing:
For each plasma sample, after trimming adaptor and low-quality bases, we use BSMAP (2.90) to align bisulfite sequencing reads to hg19 human genome assembly. The methylation ratio of CpG site is calculated by the methratio.py script (from BSMAP package). The CpG methylation ratios supported by less than 4 reads are discarded before the downstream analysis
Genome_build: hg19
Supplementary_files_format_and_content: methratio output produced by using methratio.py of BSMAP

molecule: other

source_name: GC

extract_protocol:
The plasma was transferred to 2-mL microcentrifuge tube and centrifuged at 16,000g for 10 minutes at 4°C to remove any cellular debris. Circulating cell-free DNA (10–50 ng) was extracted from 1-2 ml plasma using the QIAamp Circulating Nucleic Acid kit (Qiagen) and quantified using the Quant-iT high-sensitivity Picogreen double-stranded DNA Assay Kit (Invitrogen by Thermo Fisher Scientific) according to manufacturer instructions.
For targeted methylation sequencing, 10 ng plasma cell-free DNA was first bisulfite treated using the ZYMO Gold Kit per the manufacturer’s protocol. We adapted Swift Bioscience Methyl-Seq library preparation kit to generate individual libraries incorporating 13 PCR cycles and overnight ligation. Custom targeted CpG methylation probes were designed using Roche Nimblegen target capture kit, Custom SeqCap Epi Choice 30 MB. Libraries were quantified using Quant-iT high-sensitivity Picogreen double-stranded DNA Assay Kit before equimolarly pooling 10 individual libraries per capture consisting of 2 ug total DNA. Hybridization and capture were performed using VK SeqCap Epi Reagent Kit Plus and SeqCap EZ hybridization/wash kit from Roche Nimblegen following manufacturer recommendations. For blocking, we used universal blocker from IDT technologies. We sequenced the pooled libraries on Illumina NovaSeq S4 using paired-end 100-base-pair reads incorporating 150 individual libraries per lane.

value: GC

tag: Stage

value: #N/A

tag: alternate id

tag: assayed molecule

value: cell-free DNA


title: Exosomes3 [A103-06]

city: Hangzhou

first: Wang

last: zhengguang

address: Yuhangtang

institute: Zhejiang university

data_processing:
Illumina Casava1.7 software used for basecalling.
Use Bowtie tools soft, The Clean Reads respectively with Silva database, GtRNAdb database, Rfam database and Repbase database sequence alignment, filter ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats. The remaining reads were used to detect known miRNA and new miRNA predicted by comparing with known miRNAs from miRbase and Human Genome (GRCh38), respectively.
Read count for each miRNA was obtained from the mapping results, and TPM was calculated.
Supplementary_files_format_and_content: raw counts

source_name: Exosomes

growth_protocol: HTR8/SVneo cells were cultured in RPMI-1640 medium supplemented with 5%fetal bovine serum (FBS). In order to isolate exosomes from trophoblast cell culture medium, cells were cultured with 5% exosome-free FBS for 48h. exosomes-depleted FBS was prepared by ultracentrifugation at 100,000g, 4℃ overnight. The culture supernant was collected and centrifuged at 500g for 10min to remove dead cells, and 2000g for 20 min to remove cellular debris, and 10,000g for 35 min at 4℃ to remove microvesicles. Next, the supernatant was filtered using a 0.22mm filter and centrifuged at 120000g for 75min at 4℃. The pellets were re-suspended in PBS and centrifuged at 120,000g for 75min at 4℃ again. The final pellets containing exosomes were re-suspended with PBS for further usages.

extract_protocol:
The total RNA  was extracted using miRNeasy® Mini kit (Qiagen, cat. No. 217004)  according to the manufacturer’s protocol. The total RNA was then reverse transcribed to synthesize cDNA using PrimeScript™ RT reagent Kit (Perfect Real Time) (TAKARA, RR037A).
A total amount of 250pg - 10ng RNA per sample was used as input material for sequencing libraries using the SMARTer Stranded Total RNA-Seq Kit (Takara Bio USA, Inc.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. For small RNA libraries, a total amount of 1ng-500ng RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using QIAseq miRNA Library Kit (Qiagen, Frederick, MD) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. At last, library quality was assessed on the Agilent Bioanalyzer 2100 and qPCR. The clustering of the index-coded samples was performed on acBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.

tag: sample type

value: exosomes

tag: molecule type

value: miRNA


title: Exosomes1 [A103-04]


title: Htr8/Svneo cells3 [A103-03]

source_name: Htr8/Svneo cells

value: Trophoblast cell lines

value: cell line


title: KRp2-96

source_name: ESCC

value: ESCC


title: KRp2-97

source_name: PDAC

value: PDAC

value: IV


title: Htr8/Svneo cells2 [A103-02]


title: KRp2-95


title: PGNs_R1_GAM180113_3NP_A02_1_S9

value: cornus ammonis 1 region of the hippocampus

value: pyramidal glutamatergic neurons

value: M

value: passed


title: KRp2-93


title: Irf8KO_withLaser_S1

value: laser


title: Htr8/Svneo cells1 [A103-01]


title: KRp2-92

source_name: CRC

value: CRC

value: I


title: KRp2-94

value: IIB


title: KRp2-91


title: PGNs_R1_GAM180113_3NP_A01_2_S97

value: No

value: Pan-histo


title: KRp2-98

value: GC

value: #N/A

value: cell-free DNA


title: PGNs_R1_GAM180113_3NP_A04_1_S25


title: Exosomes2 [A103-05]

value: exosomes

value: miRNA


title: R4V3

city: Cleveland

first: Ruth

last: Keri

state: OH

address: 9500 Euclid Avenue

department: Cancer Biology

institute: Cleveland Clinic Lerner Research Institute

description: RNA isolated 48h post treatment

data_processing:
fastq files were aligned to version hg19 for both the RNA-Seq
For RNA-Seq, Differential expression was determined using the DESeq2 R package, where differentially expressed genes were deemed significantly changed if the Benjamini-Hochberg adjusted p-value was <0.05.
Genome_build: hg19

source_name: epithelial breast cancer cell line; derived from metasatic pleural effusion

growth_protocol: sensitive and resistant MDA-MB-231 and MDA-MB-468 cells were cultured in RPMI-1640 supplmented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol: RNA was isolated using a trizol extraction and precipitation protocal. Illumina platform was used with Pair-end reads and mapped to hg19.

treatment_protocol: Resistant cell lines were developed by treating the sensitive/parental cell lines with increasing doses of THZ1 (CDK7 inhibitor) over a 2-month period to a final concentration of 250nM THZ1. Cells were treated with vehicle after the establishment of resistance.

tag: cell line

tag: phenotype

value: resistant

value: Veh


title: PGNs_R1_GAM180113_3NP_A03_1_S17

source_name: pyramidal glutamatergic neurons

value: cornus ammonis 1 region of the hippocampus


title: R4V2

description: RNA isolated 48h post treatment


title: Irf8KO_withoutLaser_S3

value: untreated


title: KRp2-86

value: II


title: KRp2-90

value: PDAC


title: KRp2-89

value: IV


title: KRp2-85

value: CRC


title: S4V3

description: RNA isolated 48h post treatment

value: sensitive


title: KRp2-87

value: IIA


title: KRp2-9


title: PGNs_R1_GAM180113_3NP_A01_1_S1

value: pyramidal glutamatergic neurons

value: M

value: passed

value: No


title: PGNs_R1_GAM180113_0NP_A12_1_S89

value: water control

value: failed

value: Pan-histo


title: PGNs_R1_GAM171130_3NP_H04_2_S128


title: R4V1

description: RNA isolated 48h post treatment

value: resistant


title: S4V2

description: RNA isolated 48h post treatment

value: Veh


title: KRp2-83

value: ESCC

value: #N/A

value: cell-free DNA


title: KRp2-80

value: PDAC


title: KRp2-82


title: S4V1

description: RNA isolated 48h post treatment


title: PGNs_R1_GAM171130_3NP_H03_2_S120

value: cornus ammonis 1 region of the hippocampus


title: PGNs_R1_GAM180113_3NP_B07_1_S50


title: KRp2-81

value: IIB


title: KRp2-78


title: KRp2-79


title: R2_V_3

description: RNA isolated 48h post treatment


title: PGNs_R1_GAM180113_0NP_A02_2_S105


title: PGNs_R1_GAM171130_3NP_G04_2_S127


title: KRp2-77

value: CRC

value: IV


title: R2_V_2

description: RNA isolated 48h post treatment


title: KRp2-76

value: III


title: KRp2-84

source_name: EAC

value: EAC


title: PGNs_R1_GAM171130_3NP_G03_2_S119

value: pyramidal glutamatergic neurons

value: M

value: passed


title: R2_V_1

description: RNA isolated 48h post treatment


title: KRp2-72


title: PGNs_R1_GAM171130_3NP_G01_2_S103

value: No


title: PGNs_R1_GAM171130_3NP_F04_2_S126

value: Pan-histo


title: S2V_3

description: RNA isolated 48h post treatment

value: sensitive


title: KRp2-75


title: PGNs_R1_GAM171130_3NP_F03_2_S118


title: KRp2-69

value: II


title: KRp2-73


title: KRp2-70


title: KRp2-71

value: GC


title: KRp2-68


title: PGNs_R1_GAM171130_3NP_F01_2_S102


title: RKO_C20_sgPSMA3_2_rep3

city: Vienna

first: Tobias

last: Neumann

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description: RNA-Seq

data_processing:
RNA-seq
The 3' adaptors were removed using cutadapt (v1.4.2, Read1: cutadapt --match-read-wildcards -O 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) and trimmed reads with a length of less than 18bp were discarded.
The trimmed reads were filtered with a contaminants database consisting of rDNA sequences (KY962518.1, NR_023363.1 and the ERCC.fa) with bowtie2 (v2.1.0 --very-sensitive-local).
The recovered non matching reads were aligned to the genome/transcriptome using STAR-align (v2.4.2a, STAR  --outSAMstrandField None --outFilterIntronMotifs RemoveNoncanonical --outFilterMismatchNoverLmax 0.1 --outFilterMismatchNmax 10 --outFilterScoreMinOverLread 0.30 --outFilterMatchNminOverLread 0.30 --outFilterMatchNmin 30 --chimSegmentMin 15 --quantMode TranscriptomeSAM --chimJunctionOverhangMin 15 --twopassMode Basic --outSAMtype SAM --outSAMattributes All --outReadsUnmapped Fastx intronMotif --alignIntronMax 200000  --outSJfilterIntronMaxVsReadN 10000 20000 30000 50000 --outSJfilterOverhangMin 20 12 12 12 --outFilterType BySJout --alignMatesGapMax 0  --outFilterMultimapNmax 20).
The STAR-index used for alignment was generated from the human genome build NCBI GRCh38 (GCA_000001405.15) and a transcriptome GTF file from ENSEMBL build 78.
Differential gene expression analysis: Read counts for genes were quantified using featureCounts  v1.6.4.
As a reference, we downloaded all human hg38 refSeq genes from the UCSC table browser (https://genome.ucsc.edu/cgi-bin/hgTables) on May 2, 2016.
Differential gene expression analysis was performed with DESeq2 v1.22.2 and shrinking log2-foldchanges with apeglmv1.4.2.
Genome_build: NCBI hg38
Supplementary_files_format_and_content: Tab-delimited table with TPMs and DESeq2 log2-foldchanges, adjusted p-values and control TPMs

molecule: polyA RNA

source_name: human colon carcinoma cell line

growth_protocol: RKO cells were cultured in RPMI 1640 (Gibco) and 10% fetal calf serum (FCS; Sigma). Fresh medium was added to cells 12-24h before harvest.

extract_protocol:
RNA was isolated using in-house magnetic RNA isolation beads
NGS libraries were prepared with NEBNext Ultra RNA kit (NEB) according to manufacturer’s instructions and sequenced on a HiSeq2500 platform (Illumina)

treatment_protocol: To assess transcriptional effects of AKIRIN2, RKO cells expressing dox-inducible Cas9 were lentivirally transduced with AKIRIN2-, PSMA3- or AAVS1-targeting sgRNA and sgRNA+ cells were selected with G418. For each sgRNA, Cas9 expression was induced with dox and 2 (sgAKIRIN2 and sgAAVS1) or 3 (sgPSMA3) days post Cas9 induction cells were washed, harvested, pelleted and snap-frozen.

value: Colon Carcinoma

value: RKO

value: PSMA3 sgRNA knockout - Day 3

tag: method

value: RNA was isolated using in-house magnetic RNA isolation beads and NGS libraries were prepared with NEBNext Ultra RNA kit (NEB) according to manufacturer’s instructions and sequenced on a HiSeq2500 platform (Illumina)


title: KRp2-8

value: PDAC

value: cell-free DNA


title: PGNs_R1_GAM171130_3NP_E04_2_S125

tag: strain

value: cornus ammonis 1 region of the hippocampus


title: PGNs_R1_GAM171130_3NP_E03_2_S117

tag: tissue


title: KRp2-66

value: CRC

value: IV


title: KRp2-64


title: KRp2-67

value: III


title: KRp2-63

value: IIB


title: RKO_C20_sgPSMA3_2_rep2

description: RNA-Seq

tag: treatment


title: KRp2-74


title: RKO_C20_sgPSMA3_2_rep1

description: RNA-Seq


title: S2V_1

description: RNA isolated 48h post treatment

value: Veh


title: KRp2-7


title: KRp2-6

value: #N/A


title: PGNs_R1_GAM171130_3NP_D04_2_S124

tag: cell type

value: pyramidal glutamatergic neurons

value: M

value: passed

value: No

value: Pan-histo


title: KRp2-60

value: ESCC

tag: age


title: KRp2-58


title: KRp2-62

value: II


title: KRp2-61


title: RKO_C20_sgAKIRIN2_2_rep2

description: RNA-Seq

value: Colon Carcinoma

value: RKO

value: AKIRIN2 sgRNA knockout - Day 2

value: RNA was isolated using in-house magnetic RNA isolation beads and NGS libraries were prepared with NEBNext Ultra RNA kit (NEB) according to manufacturer’s instructions and sequenced on a HiSeq2500 platform (Illumina)


title: RKO_C20_sgAKIRIN2_2_rep1

description: RNA-Seq


title: KRp2-57

value: CRC

value: I

value: cell-free DNA


title: KRp2-55

value: PDAC

value: IIA


title: KRp2-56


title: PGNs_R1_GAM171130_3NP_H02_2_S112

value: cornus ammonis 1 region of the hippocampus

tag: Sex


title: PGNs_R1_GAM171130_3NP_D01_2_S100

value: pyramidal glutamatergic neurons

tag: genotype


title: RKO_C20_sgAAVS1_3_rep2

description: RNA-Seq

value: AAVS1 sgRNA knockout - Day 2


title: KRp2-65

value: IIB


title: KRp2-53

value: III


title: PGNs_R1_GAM171130_3NP_D02_2_S108

value: M

value: passed

tag: cross contamination

value: No

value: Pan-histo


title: KRp2-52


title: S2V_2

description: RNA isolated 48h post treatment

value: sensitive

value: Veh


title: PGNs_R1_GAM171130_3NP_C04_2_S123

tag: if staining


title: RKO_C20_sgAAVS1_3_rep1

description: RNA-Seq

value: Colon Carcinoma

value: RKO

value: RNA was isolated using in-house magnetic RNA isolation beads and NGS libraries were prepared with NEBNext Ultra RNA kit (NEB) according to manufacturer’s instructions and sequenced on a HiSeq2500 platform (Illumina)


title: KRp2-50

value: CRC

tag: Stage

value: cell-free DNA


title: PGNs_R1_GAM171130_3NP_E01_2_S101


title: KRp2-51

tag: alternate id


title: PGNs_R1_GAM171130_3NP_D03_2_S116


title: RKO_C20_sgAAVS1_3_rep3

description: RNA-Seq


title: RKO_C20_sgAKIRIN2_2_rep3

description: RNA-Seq

value: AKIRIN2 sgRNA knockout - Day 2


title: KRp2-5

value: I

tag: assayed molecule


title: PGNs_R1_GAM171130_3NP_C02_2_S107

value: cornus ammonis 1 region of the hippocampus

value: pyramidal glutamatergic neurons


title: PGNs_R1_GAM171130_3NP_E02_2_S109


title: KRp2-49

value: PDAC

value: IIB


title: PGNs_R1_GAM171130_3NP_C01_2_S99

value: M


title: KRp2-47

value: III


title: PGNs_R1_GAM171130_3NP_B03_2_S114

value: passed

value: No


title: KRp2-46


title: KRp2-43

value: II


title: KRp2-44


title: KRp2-42

value: IV


title: KRp2-40


title: KRp2-4

value: #N/A


title: PGNs_R1_GAM171130_3NP_B02_2_S106

value: Pan-histo


title: KRp2-39


title: PGNs_R1_GAM171130_3NP_B01_2_S98


title: a_MCAO_2

city: Beijing

first: Haiping

last: Zhao

address: 45 Changchun Street

institute: Xuanwu Hospital of Capital Medical University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: excel,expression profiles

organism: Macaca mulatta

source_name: plasma

growth_protocol: adult rhesus monkeys

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: As described previously by us in NHPs models, a Prowler-10 micro-catheter (Codman) with a SilverSpeedTM-10 Hydrophilic micro-wire was introduced into the guiding catheter and navigated to the distal end of M1 segment of the right MCA. Next, the clot was transferred into micro-catheter and flushed into the end of M1 segment with 2mL saline

value: blood

value: adult

tag: condition

value: after ischemia


title: a_MCAO_1


title: a_MCAO_3


title: b_MCAO_2

value: before ischemia


title: KBM-7_Input_H3K27me3

city: Cambridge

first: Iva

last: Tchasovnikarova

address: Tennis Court Road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: Input for H3K27me3 ChIP-seq

data_processing:
Reads were trimmed of adaptor sequences using Cutadapt
Reads were aligned to the reference human genome using Bowtie2
Uniquely mapping reads (MAPQ score >20) were imported into SeqMonk
Peaks were called using the implementation of the MACS peak caller in SeqMonk, with the exception of H3K27me3 and H3K9me3 (GSE60056), for which peaks were called using the hiddenDomains tool. The coordinates of the peaks were used to create a merged bed file; regions of the genome that were not enriched for any of the tested modifications were annotated as 'None'.
Genome_build: GRCh38
Supplementary_files_format_and_content: bed file containing the coordinates of all histone modification peaks, as well as genomic regions that were not enriched for any of the tested modifications

source_name: KBM-7 cells

growth_protocol: KBM-7 cells were growm in IMDM supplemented with 10% fetal calf serum (FCS) and penicillin/streptomycin (100 U/ml)

extract_protocol:
Formaldehye-crosslinked chromatin was sheared by sonication to an average size of ~300bp and then immunoprecipitated with the following antibodies:
NEBNext Ultra II DNA Library Prep Kit (NEB)

tag: chip antibody


title: KRp2-48

value: GC

value: cell-free DNA


title: b_MCAO_3


title: KBM-7_Input_K27ac_K4me1_K4me2_K36me3_K16ac

description: Input for H3K27ac, H3K4me1, H3K4me2, H3K36me3 and H4K16ac

tag: cell line


title: KBM-7_Input_K9ac_K4me3_K79me2

description: Input for H3K9ac, H3K4me3 and H3K79me2


title: PGNs_R1_GAM171130_3NP_A02_2_S105

value: cornus ammonis 1 region of the hippocampus

value: pyramidal glutamatergic neurons


title: KRp2-33

value: PDAC

value: IIB


title: KRp2-45


title: KRp2-41

value: CRC


title: KRp2-38


title: HeLa Ctrl_2nd

city: Wuhan

first: Dong

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description:
expressed_gene_FPKM.txt
expressed_gene_reads.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 20 -p 16 --no-discordant. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue <= 0.01 Qvalue <= 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: hela cell

growth_protocol: The human HeLa cell line was purchased from the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China. Cells were seeded into a petridish (100 mm) at a density of 1 × 105 cells/mL per well, and cultured at 37 ℃with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) (Hyclone), penicillin (100 U/ml) and streptomycin (100 g/ml). TFRC overexpression plasmid transfection of HeLa cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Transfected cells were harvested after 48 h.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

value: HeLa

tag: genotype/variation

value: control plasmid


title: KRp2-34


title: KRp2-35


title: KBM-7_H3K27me3


title: KRp2-32


title: KBM-7_H4K16ac

value: H4K16ac (EMD Millipore, 07-329)


title: HeLa TFRC_2nd

value: TFRC overexpression


title: HeLa Ctrl_1st


title: PGNs_R1_GAM171130_3NP_C03_2_S115

value: M

value: passed

value: No


title: KRp2-30

value: II


title: KRp2-28


title: KBM-7_H3K79me2


title: KBM-7_H3K36me3

value: H3K36me3 (Abcam, ab9050)


title: HeLa TFRC_1st


title: KRp2-29

value: III


title: PGNs_R1_GAM171130_3NP_A01_2_S97

value: Pan-histo


title: KRp2-27

value: #N/A

value: cell-free DNA


title: OPC (Ad-GFP treated animal) [20-K198-7]

city: BRONX

first: Praveen

last: Ballabh

state: New York

address: 1410 Pelham Parkway South

department: Pediatrics and Neuroscience

institute: ALBERT EINSTEIN COLLEGE OF MEDICINE

data_processing:
Hiseq Control software was used for basecalling.
Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Sequenced reads were trimmed for adaptor sequence, trimmed reads were mapped to the Rabbit Oryctolagus reference genome available on ENSEMBL using the STAR aligner version 2.5.2b.
Unique gene hit counts were calculated by using feature counts from Subread package version 1.5.2.
Gene counts were normalized to the median and the average expression level and coefficient of variation among biological replicas.
Genome_build: OryCun 2.0
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include raw counts.

organism: Oryctolagus cuniculus

source_name: OPC isolated by FACS

extract_protocol:
RNA extraction, library preparations, sequencing reactions and bioinformatic analysis were carried out by GENEWIZ, LLC (South Plainfield, NJ, USA). RNA samples were extracted using Trizol (Invitrogen, Carlsbad, CA). Extracted samples were quantified by Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was measured using the RNA Screen Tape on Agilent 2200 TapeStation (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared and validated using DNA Analysis Screen Tape on the Agilent 2200 TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by qPCR (KAPA Biosystems, Wilmington, MA, USA). The pooled libraries were clustered on a flowcell, which were loaded on the Illumina HiSeq instrument (4000) according to manufacturer’s instructions and sequenced using a 2x150 bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS).

treatment_protocol: The rabbit kits with moderate-to-severe IVH were treated with intracerebroventricular (ICV) Ad-GFP or Ad-PPARg-GFP (CMV promoter, 5 µl volume) 1 mm ant., 4 mm lateral and 3 mm deep from Bregma under anesthesia. We compared Ad-GFP and Ad-PPARg-GFP treated kits.

tag: breed

value: New Zealand

tag: disease state

value: Intraventricular hemorrhage (IVH)

value: Brain

value: O4-positive oligodendrocyte progenitor cells

value: Ad-GFP

tag: antibody

value: mouse anti-O4-APC, Miltenyi Biotec, 130-118-978


title: KRp2-25

tag: tissue

value: PDAC


title: KRp2-24

value: ESCC


title: KRp2-26

value: IIB


title: KRp2-31

value: IV


title: OPC (Ad-GFP treated animal) [19-K198-5]

tag: cell type

tag: treatment


title: KBM-7_H3K4me2

value: H3K4me2 (Abcam, ab7766)


title: KRp2-22

tag: age


title: KRp2-20


title: KBM-7_H3K4me3


title: OPC (Ad-GFP treated animal) [18-K195-11]


title: KBM-7_H3K4me1

value: H3K4me1 (Abcam, ab8895)


title: KRp2-23

value: CRC


title: OPC (Ad-GFP treated animal) [17-K195-9]


title: KRp2-192

value: GC


title: KRp2-2


title: KRp2-191


title: KBM-7_H3K9ac


title: KRp2-36


title: KBM-7_H3K27ac

value: H3K27ac (Active Motif, 39134)


title: OPC (Ad-PPAR-r treated animal) [15-K197-4]

value: Ad-PPARg


title: OPC (Ad-PPAR-r treated animal) [K196-12]


title: control_3

city: Huzhou

first: weifei

last: wu

state: Zhejiang Province

address: 1588, 3rd Ring North Road, Wuxing District

institute: Huzhou Hospital, Zhejiang University School of Medicine

data_processing:
The raw data were quality controlled by removing adapters, Q20 less than 80% to obtain clean reads.
The clean reads were aligned to miRBase (version 22.0). The expression of miRNAs were estimated using transcript per million (TPM).
The miRNAs with |log2FoldChange|≥0.58 and p<0.05 were regarded as differences miRNAs.
Genome_build: hg38
Supplementary_files_format_and_content: excel file include expression values for each sample.

growth_protocol: All patients were recruited from the Peritoneal Dialysis Center of Huzhou Central Hospital, diagnosed with end-stage renal failure and treated with maintenance peritoneal dialysis. 3 patients developed peritoneal ultrafiltration failure during the treatment of maintenance PD (CAPD). The diagnosis was confirmed by the peritoneal balance test. Type I peritoneal ultrafiltration failure, and recruited 3 patients with normal peritoneal ultrafiltration with matching age and other general conditions at the same period. Collect 500ml overnight peritoneal dialysis effluent (PDE) from all Patients.

extract_protocol:
Overnight PDE, separate the exosomes by ultracentrifugation. Supernatant were collected by differential centrifugation (300xg at 4℃ for 10min, 3000xg at 4℃ for 15min, 12000xg at 4℃ for 30min). Filtrated with a 0.22um sterile filter, added into the ultra-high speed centrifuge tube, centrifuged at 4℃ for 60min at 120000xg and discarded the supernatant. Finally, depending on the amount of precipitation,pre-cooled sterile PBS was added for resuspended suspension, which was high purity EVs. Total RNA was isolated from exosomes using TRIzol reagent. 1 ml TRIzol and 25 fmol cel-mir-39-3p standards were used to crack exosome suspension, then chloroform (200 µl) was added to separate the liquid phase and the upper liquid was added with isopropanol to precipitate RNA in the exosome suspension. Then the sediment was resuspended with 75% ethyl alcohol and centrifuged at 12,000 g at 4 ℃ for 5 min. The pellets were dissolved with 20 µl sterile water. Finally, the RNA concentration was calculated using the 260/280 optical density (OD) ratio.
The 3′adapters were added and the 36–44 nt RNAs were enriched. The 5′adapters were then ligated to the RNAs as well. The ligation products were reverse-transcribed by PCR amplification, and the 140–160 bp size PCR products were enriched to generate a cDNA library. The cDNA fragments were purified with PCR extraction kit, poly(A) added and ligated to Illumina sequencing adapters.

treatment_protocol: Collect 500ml overnight PDE from three type I peritoneal ultrafiltration failure patients and three controls with stable peritoneal function.

value: Control

value: peritoneal dialysis effluent (PDE)


title: KRp2-184

source_name: Normal

value: Normal

value: #N/A

value: cell-free DNA


title: b_MCAO_1

value: blood

value: adult

value: before ischemia


title: KRp2-187


title: KRp2-186


title: KRp2-181


title: OPC (Ad-PPAR-r treated animal) [14-K197-3]

value: New Zealand

value: Intraventricular hemorrhage (IVH)

value: Brain

value: O4-positive oligodendrocyte progenitor cells

value: mouse anti-O4-APC, Miltenyi Biotec, 130-118-978


title: KRp2-179


title: KRp2-180


title: KRp2-18

value: CRC

value: IV


title: OPC (Ad-PPAR-r treated animal) [11-K188-11]


title: control_2

source_name: controls with stable peritoneal function


title: KRp2-177

value: GC


title: microglia (Ad-GFP treated animal) [8-K195-11]

source_name: microglia isolated by FACS

value: CD11-positive CD45-low microglia

value: Ad-GFP

value: mouse anti-rabbit CD45, Bio-Rad, MCA808GA; Rat anti-CD11b-dylight550, Novus, NB600-1327R


title: control_1

value: Control

value: peritoneal dialysis effluent (PDE)


title: KRp2-178

value: PDAC

value: #N/A

value: cell-free DNA


title: microglia (Ad-GFP treated animal) [10-K198-7]


title: KRp2-174


title: disease_3

source_name: type I peritoneal ultrafiltration failure


title: KRp2-175

source_name: HCC

value: HCC

value: I


title: disease_2

value: type I peritoneal ultrafiltration failure


title: KRp2-176

source_name: GC


title: microglia (Ad-GFP treated animal) [7-K195-9]

value: New Zealand

value: Intraventricular hemorrhage (IVH)

value: Brain


title: KRp2-19

value: CRC

value: II


title: KRp2-172

source_name: ESCC

value: ESCC


title: KRp2-173


title: disease_1


title: microglia (Ad-GFP treated animal) [6-K193-5]

value: CD11-positive CD45-low microglia


title: KRp2-171


title: microglia (Ad-PPAR-r treated animal) [5-K197-4]

value: Ad-PPARg


title: KRp2-170


title: CD_villus

city: Neuherberg

first: Sophie

last: Tritschler

address: Ingolstädter Landstrasse 1

institute: Helmholtz Zentrum Munich

description:
Polyadenylated RNA's
processed data file:
adata_villus_raw.h5
adata_villus_processed.h5

data_processing:
The 10X Genomics core computational software Cellranger v.2.0 was used for alignment and processing of next generation sequencing reads of the scRNA-seq data as recommended (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). For read 2 150bp were considered for alignment.
For QC, filtering, normalization and batch correction of crypt samples the scanpy python package v.1.0.4 and anndata v0.5.10 and a python implementation of Combat were used.   For QC, filtering and normalization of villi samples the scanpy python package v.1.4.4 and anndata v0.7.1 were used.   Scripts for preprocessing with detailed descriptions are available here: https://github.com/theislab/2021_Aliluev_Tritschler_gut_HFD
Genome_build: mm10
Supplementary_files_format_and_content: anndata (annotated data matrix) object saved in h5ad-file format. File contains raw or preprocessed and annotated count data for all experiments.

source_name: Single cells of small intestinal villi

extract_protocol:
Small intestines were removed, washed with cold PBS and villi were scraped off with a glass slide. Villi were scraped off with a glass slide. The remaining tissue was cut into 2-cm pieces, washed several times with cold PBS and incubated in 2 mM EDTA/PBS for 35 min at 4 °C. Subsequently, crypts were harvested by rigorous shaking and filtered through a 70-µm mesh to remove villous fragments. For single cell suspension, isolated crypts were incubated with TrypLE (Life technologies, #12605) for 5 min on ice and then 5 min at 37 °C and treated with 10 µg/ml DNase in crypt complete medium (DMEM/F-12 containing 10 % FCS) for 5 min at 37 °C. For flow cytometry, cells were colleced in 1-2ml FACS buffer (2% FCS, 2mM EDTA in PBS) (Sigma-Aldirch, #Y0503) and passed through the 40µm cell strainer caps of FACS tubes. Small intestinal crypt cells were sorted using FACS-Aria III (BD Bioscience) with a 100 μm nozzle. For all experiments, single cells were gated according to their FSC-A (front scatter area) and SSC-A (side scatter area). Singlets were gated dependent on the FSC-W (front scatter width) and FSC- H (front scatter height) and dead cells were excluded using the 7-AAD marker (eBioscience, #00-6993-50). To obtain FVF-enriched small intestinal crypt cell samples for single-cell RNA sequencing, we sorted 30,000 FVF+ (FVFlow and FVFhigh) cells followed by sorting 30,000 live crypt cells per sample. Cells were sorted into modified FACS buffer (2 % FCS, 0.02 mM EDTA in PBS).
Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 (PN #120237) from 10x Genomics. Libraries were sequenced on the HiSeq4000 (Illumina) with 150bp paired-end sequencing of read2.

tag: strain

tag: source tissue

value: small intestine

tag: developmental day

value: adult


title: KRp2-167

value: Normal

tag: Stage


title: KRp2-17

source_name: PDAC

value: PDAC

value: IIB

tag: alternate id


title: microglia (Ad-PPAR-r treated animal) [4-K197-3]

value: mouse anti-rabbit CD45, Bio-Rad, MCA808GA; Rat anti-CD11b-dylight550, Novus, NB600-1327R


title: KRp2-163

value: #N/A

tag: assayed molecule

value: cell-free DNA


title: KRp2-162


title: microglia (Ad-PPAR-r treated animal) [3-K196-4]


title: KRp2-156

value: GC


title: KRp2-150


title: KRp2-161


title: microglia (Ad-PPAR-r treated animal) [1-K188-11]

value: New Zealand


title: KRp2-16

value: IIA


title: HFD_villus

value: 12 weeks high-fat-high-sugar diet


title: KRp2-145


title: KRp2-141


title: KRp2-149


title: KRp2-148

value: HCC


title: KRp2-140


title: KRp2-14

source_name: CRC

value: CRC

value: III


title: Thirty month old_adipose_smallRNA1

city: Xinyang

first: Yun

last: Ma

address: Shihe

institute: Xinyang Normal University

description: adipose _4

data_processing:
The primer and adaptor sequence as well as the junk reads and fragments < 18 nt and > 26 nt were removed. For the buffalo genome was not available, the remaining 18~26 nt reads were screened against and mapped to the cattle genome (UMD3.1) by Bowtie software.
To discard rRNA, tRNA, snRNA, ncRNA and other snoRNA sequences, the reads mapped to the reference genome were further filtered by blasting against the Rfam database, RepBase database, mRNA database, miRBase database, respectively.
The clean miRNA reads were further used for novel miRNAs prediction by miRDeep.
Transcripts per kilobase million (TPM) was used as the index to calculate the expression level of each miRNA in every library. The expression level was indicated as log2TPM.
Genome_build: UMD3.1
Supplementary_files_format_and_content: log2TPMs of miRNAs

organism: Bubalus bubalis

source_name: Thirty month old adipose tissue

growth_protocol: Three muscle samples three adipose samples from Chinese swamp buffalo were collected from Benniu abattoir, a local slaughterhouse of Xinayang, P.R. China. Tissue samples were snap-frozen in liquid nitrogen and stored at –80°C freezer until use.

extract_protocol:
Total RNA was extracted using TRIzol reagent. Total RNA was assessed by electrophoresis on a denaturing agarose gel and quantified by NanoDrop spectrophotometer (NanoDrop, USA) and Agilent 2100 Bioanalyzer. The total RNA samples (3 mg) were treated with the epicentre Ribo-ZeroTM Kit to remove rRNA before constructing the RNA-seq libraries.
Approximately 1 μg total RNA per sample was used for small RNA library construction according to protocol of the TruSeq® miRNA Sample Prep Kit v2 (Illumina, USA). Briefly, the 5’ and 3’ adaptors were ligated using T4 RNA ligase. Then the modified small RNA was subjected to RT-PCR for amplification. The 145-160 bp cDNA fragment was extracted and purified from the polyacrylamide gel electrophoresis.
The enriched cDNA was sequenced in a HiSeq 2500 sequencing system (Illumina, San Diego, USA) at the Genergy Biotechnology Co., Ltd. (Shanghai, China).

value: adipose tissue

value: Thirty month old


title: Thirty month old_muscle_smallRNA3

description: muscle _3

source_name: Thirty month old muscle tissue

value: muscle tissue


title: KRp2-137

value: IV


title: Thirty month old_muscle_smallRNA2

description: muscle _2


title: KRp2-138

value: ESCC


title: Thirty month old_muscle_smallRNA1

description: muscle _1


title: KRp2-136

value: I


title: KRp2-135


title: PC9_low_rep4

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

description: Gene expression in ALDH-low cell populations of PC9 cells.

hyb_protocol: 0.6µg of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/µg cRNA) was fragmented at 60˚C for 30 minutes in a reaction volume of 25µl containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 25µl of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE microarry 8x60K Ver. 3.0 (G4858A #72363, Agilent Technologies) for 17 hours at 65˚C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37˚C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 1 x 60K array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentG3_GX_1Color) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered with three filters with GeneSpring software 12.1 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than 20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was excluded. In the last filter, when the value (log scale) of CV was over 50 percent in both conditions, the probe was excluded. After filtering, control probes were excluded, and log scale values were transformed into normal scale.

source_name: PC9, ALDH-low cell population, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2µg RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 10% FBS RPMI-1640 + 100 units/mL penicillin, and 100 μg/mL streptomycin

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

value: Cancer cell line

tag: aldh status

value: low


title: Recurrent HCC tissue from patient No.29

city: Tianjin

first: Tao

last: Liu

address: 24 Fu-Kang Road, Nan-Kai District

department: First Central Hospital

institute: Nankai University

description:
mRNA and lncRNA expression in recurrent HCC tissue
large RNA (>200 nt)
Rawdata_P29.txt

hyb_protocol: DNA in hybridization solution was denatured at 95°C for 3 min prior to loading onto a microarray. Arrays were hybridized in an Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42°C, and were washed with two consecutive solutions (0.2% SDS, 2× SSC at 42°C for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Slides were scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Recurrent HCC tissue, replicate 2

label_protocol: cDNA labeled with a fluorescent dye (Cy5-dCTP or Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: Tissue RNA was extracted and large RNA (>200 nt) was isolated using the mirVana miRNA isolation kit (Invitrogen) following the manufacturer's instructions.  RNA was quantified using a Beckman Coulter DU800 spectrophotometer.

value: hepatocellular carcinoma tissue

tag: gender

value: male


title: Primary HCC tissue from patient No.22

description:
mRNA and lncRNA expression in the corresponding primary HCC tissue
large RNA (>200 nt)
Rawdata_P22.txt

source_name: Primary HCC tissue, replicate 1


title: PC9_low_rep3

source_name: PC9, ALDH-low cell population, replicate 3

tag: cell line


title: KRp2-134

value: #N/A

value: cell-free DNA


title: Primary HCC tissue from patient No.29

description:
mRNA and lncRNA expression in the corresponding primary HCC tissue
large RNA (>200 nt)
Rawdata_P29.txt

source_name: Primary HCC tissue, replicate 2


title: Recurrent HCC tissue from patient No.22

description:
mRNA and lncRNA expression in recurrent HCC tissue
large RNA (>200 nt)
Rawdata_P22.txt

source_name: Recurrent HCC tissue, replicate 1


title: KRp2-133

value: II


title: KRp2-131

value: IIIA


title: Cancer-Associated Fibroblast [DanaCosteaud25]

city: Bergen

first: Saroj

last: Rajthala

state: Hordaland

address: Jonas Lies vei 87

department: Department of Clinical Medicine

country: Norway

institute: University of Bergen

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R.

source_name: Oral Squamous Cell Carcinoma lesions

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Cancer-Associated Fibroblast


title: KRp2-127

value: PDAC


title: KRp2-125

value: GC


title: KRp2-130


title: KRp2-126


title: KRp2-129


title: PC9_high_rep4

description: Gene expression in ALDH-high cell populations of PC9 cells.

source_name: PC9, ALDH-high cell population, replicate 4

value: high


title: KRp2-124


title: Dysplastic Oral Fibroblast [DanaCosteaud21]

source_name: Oral Dysplastic lesions

value: Dysplastic Oral Fibroblast


title: PC9_high_rep3

source_name: PC9, ALDH-high cell population, replicate 3


title: Cancer-Associated Fibroblast [DanaCosteaud24]


title: Dysplastic Oral Fibroblast [DanaCosteaud22]


title: PC9_high_rep2

source_name: PC9, ALDH-high cell population, replicate 2


title: PC9_low_rep1

source_name: PC9, ALDH-low cell population, replicate 1


title: PC9_high_rep1

source_name: PC9, ALDH-high cell population, replicate 1


title: KRp2-123

source_name: PDAC


title: Dysplastic Oral Fibroblast [DanaCosteaud20]


title: KRp2-122

source_name: EAC

value: EAC


title: KRp2-12

value: IIB


title: PC9_low_rep2

source_name: PC9, ALDH-low cell population, replicate 2


title: KRp2-117

source_name: ESCC

value: ESCC


title: PC9M2_low_rep4

description: Gene expression in ALDH-low cell populations of PC9M2 cells.

source_name: PC9M2, ALDH-low cell population, replicate 4


title: KRp2-118


title: KRp2-119


title: Normal Oral Fibroblast [DanaCosteaud19]

source_name: Normal Oral Mucosa

value: Normal Oral Fibroblast


title: Normal Oral Fibroblast [DanaCosteaud18]


title: KRp2-116

source_name: HCC

value: HCC


title: PC9M2_low_rep3

source_name: PC9M2, ALDH-low cell population, replicate 3

value: Cancer cell line

value: low


title: PC9M2_low_rep2

source_name: PC9M2, ALDH-low cell population, replicate 2


title: Normal Oral Fibroblast [DanaCosteaud17]


title: KRp2-120


title: KRp2-114


title: KRp2-115

source_name: GC


title: Normal Oral Fibroblast [DanaCosteaud16]


title: Normal Oral Fibroblast [DanaCosteaud15]


title: KRp2-112

value: I


title: KRp2-111


title: KRp2-110

value: #N/A


title: PC9M2_high_rep4

description: Gene expression in ALDH-high cell populations of PC9M2 cells.

source_name: PC9M2, ALDH-high cell population, replicate 4


title: KRp2-11

source_name: CRC

value: CRC

value: cell-free DNA


title: Normal Oral Fibroblast [DanaCosteaud14]


title: KRp2-109

value: IIIA


title: KRp2-108


title: KRp2-113


title: KRp2-107


title: Cancer-Associated Fibroblast [DanaCosteaud13]

source_name: Oral Squamous Cell Carcinoma lesions

value: Cancer-Associated Fibroblast


title: KRp2-106


title: PC9M2_low_rep1

source_name: PC9M2, ALDH-low cell population, replicate 1


title: KRp2-104

value: II


title: PC9M2_high_rep3

source_name: PC9M2, ALDH-high cell population, replicate 3


title: KRp2-15


title: KRp2-105

value: PDAC

value: III


title: Cancer-Associated Fibroblast [DanaCosteaud12]


title: KRp2-102


title: Cancer-Associated Fibroblast [DanaCosteaud10]


title: Cancer-Associated Fibroblast [DanaCosteaud9]


title: Sample42.Brown rat.203877620010_R05C01

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

institute: University of California, Los Angeles

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

source_name: Calibration

extract_protocol: genomic DNA was extracted

tag: dna source

value: premixed DNA standards from EpigenDx Inc (Standard80-8060R-PreMixRat)

tag: proportionmethylated


title: KRp2-103


title: PC9M2_high_rep2

source_name: PC9M2, ALDH-high cell population, replicate 2

value: high


title: Sample45.Brown rat.203877620010_R02C02


title: PC9M2_high_rep1

source_name: PC9M2, ALDH-high cell population, replicate 1


title: Sample44.Brown rat.203877620010_R01C02


title: Cancer-Associated Fibroblast [DanaCosteaud8]


title: Sample43.Brown rat.203877620010_R06C01


title: KRp2-1

source_name: PDAC

value: IIA


title: Cancer-Associated Fibroblast [DanaCosteaud11]


title: KRp1-97

value: GC


title: Sample41.Brown rat.203877620010_R04C01


title: KRp1-98


title: KRp2-10

value: IV


title: Cancer-Associated Fibroblast [DanaCosteaud7]


title: Sample40.Brown rat.203877620010_R03C01


title: Dysplastic Oral Fibroblast [DanaCosteaud6]

source_name: Oral Dysplastic lesions

value: Dysplastic Oral Fibroblast


title: Sample39.Brown rat.203877620010_R02C01


title: KRp1-99

value: IIB


title: Dysplastic Oral Fibroblast [DanaCosteaud5]


title: KRp2-101

value: HCC


title: KRp1-93

value: I


title: KRp1-94

value: #N/A


title: KRp1-95

source_name: Normal

value: Normal


title: Normal Oral Fibroblast [DanaCosteaud4]

value: Normal Oral Fibroblast


title: Normal Oral Fibroblast [DanaCosteaud3]


title: KRp1-96

value: cell-free DNA


title: KRp1-92


title: Thirty month old_adipose_smallRNA3

description: adipose _6

source_name: Thirty month old adipose tissue

value: adipose tissue

value: Thirty month old


title: KRp1-91

source_name: ESCC

value: ESCC


title: Sample38.Brown rat.203877620010_R01C01


title: Thirty month old_adipose_smallRNA2

description: adipose _5


title: KRp1-9


title: KRp1-88

source_name: HCC


title: KRp1-87


title: KRp1-85


title: Normal Oral Fibroblast [DanaCosteaud2]

source_name: Normal Oral Mucosa


title: KRp1-84


title: Sample36.Brown rat.203877620035_R05C02


title: KRp1-83


title: KRp1-86


title: Sample37.Brown rat.203877620035_R06C02


title: RNA-seq_NK_E Stage 5 EOMES

city: Ghent

first: Wouter

last: Van Loocke

state: East Flanders

address: C. Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Ghent University

description: Sample 24

data_processing:
Fastq files were aligned to human reference genome GRCh38 using STARv2.42 and gencode v25 as guide gtf
Counts were generated on the fly by STAR
QC of fastq files was done with FastQC
Genome_build: GRCh38
Supplementary_files_format_and_content: a tab separated raw count matrix file

source_name: Natural Killer cells

growth_protocol: HPC were obtained by isolating peripheral blood monocytes form umbilical cord blood by density gradient centrifugation and subsequently CD34+ HPC were enriched by magnetic activated cell sorting (MACS). Isolated cord blood-derived CD34+ HPC were cultured in complete IMDM containing 10% FCS and supplemented with thrombopoietin (TPO) (20 ng/ml), stem cell factor (SCF) (100 ng/ml) (all from Peprotech, London, UK.) and FMS-like tyrosine kinase 3 ligand (FLT3-L) (100 ng/ml, R&D Systems, Minneapolis, MN, U.S.A.) for 48 hours. Sucessfully transduced HPC were sorted and co-cultured with mitomycin-inactivated EL08.1D2 cells in Dulbecco’s modified Eagle medium plus Ham’s F-12 medium (2:1 ratio), supplemented with 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM glutamine, 10 mM sodium pyruvate (all from Life Technologies), 20% of heat-inactivated human AB serum (Biowest, Nuaillé, France), 24 μM β-mercaptoethanol, 20 μg/mL ascorbic acid and 50 ng/mL sodium selenite (all from Sigma-Aldrich). The following cytokines were added: IL-3 (5 ng/mL, first week only, R&D systems), IL-7 (20 ng/mL), IL-15 (10 ng/mL) (all from Miltenyi Biotec), SCF (20 ng/mL; Peprotech, London, UK.), and Flt3-L (10 ng/mL; R&D Systems, Minneapolis, MN, U.S.A.) . Culture medium was refreshed on day 7 by addition of the same volume of fresh medium with cytokines. At day 14 the non-adherent cells were harvested and transferred to new mitomycin-treated EL08.1D2 feeder cells.

extract_protocol:
Total mRNA was extracted using the RNeasy micro kit (Qiagen). The concentration and quality of the total extracted RNA was checked by using the Quant-it ribogreen RNA assay (Life Technologies) and the RNA 6000 nano chip (Agilent Technologies, Santa Clara, CA, U.S.A), respectively.
Illumina sequencing library preparation was performed using the QuantSeq 3' mRNA-Seq Library Prep Kits (Lexogen, Vienna, Austria) according to manufacturer's protocol. Libraries were quantified by qPCR.

treatment_protocol: CD34+ HPC underwent retroviral transduction with T-BET or EOMES overexpression vectors or the control vector. After 48 hours, eGFP+CD34+ HPC were sorted by FACS cell sorting.

value: Natural Killer cells

tag: day of culture

value: Day 21

tag: donor

value: Donor E

value: retroviral transduction


title: Sample35.Mouse.203877620035_R04C02

value: premixed DNA standards from EpigenDx Inc (80-8060M-PreMixMouse)


title: RNA-seq_NK_E Stage 5 T-BET

description: Sample 23


title: Sample34.Mouse.203877620035_R03C02


title: RNA-seq_NK_E Stage 5 Ctrl

description: Sample 22


title: KRp1-82

source_name: GC

tag: tissue

value: GC


title: Sample32.Mouse.203877620035_R01C02


title: KRp2-100

value: PDAC

value: IIA


title: KRp1-81


title: KRp1-8


title: KRp1-79


title: RNA-seq_NK_D Stage 5 EOMES

description: Sample 21

tag: cell type

value: Donor D


title: RNA-seq_NK_D Stage 5 T-BET

description: Sample 20

tag: treatment


title: Sample33.Mouse.203877620035_R02C02


title: KRp1-78

tag: age

value: IV


title: Normal Oral Fibroblast [DanaCosteaud1]


title: KRp1-80

value: HCC

value: I


title: KRp1-76


title: RNA-seq_NK_C Stage 5 EOMES

description: Sample 18

value: Donor C


title: KRp1-74

value: Normal

value: #N/A

value: cell-free DNA


title: KRp1-77


title: RNA-seq_NK_D Stage 5 Ctrl

description: Sample 19


title: Sample29.Mouse.203877620035_R04C01


title: KRp1-73

value: IIIB


title: KRp1-7


title: KRp1-75

value: ESCC


title: Sample30.Mouse.203877620035_R05C01


title: KRp1-71


title: Sample31.Mouse.203877620035_R06C01


title: KRp1-69

value: IIB


title: KRp1-67


title: RNA-seq_NK_C Stage 5 T-BET

description: Sample 17

value: Natural Killer cells

value: Day 21


title: RNA-seq_NK_B Stage 5 EOMES

description: Sample 15

value: Donor B

value: retroviral transduction


title: KRp1-66

source_name: EAC

value: EAC


title: Sample25.Brown rat.202897220127_R05C01

value: premixed DNA standards from EpigenDx Inc (Standard80-8060R-PreMixRat)


title: Sample27.Mouse.203877620035_R02C01

value: premixed DNA standards from EpigenDx Inc (80-8060M-PreMixMouse)


title: Sample24.Brown rat.202897220127_R04C01


title: KRp1-65


title: KRp1-68


title: KRp1-63


title: RNA-seq_NK_B Stage 5 T-BET

description: Sample 14


title: RNA-seq_NK_B Stage 5 Ctrl

description: Sample 13


title: KRp1-61


title: RNA-seq_NK_E Stage 4 EOMES

description: Sample 12

value: Donor E


title: RNA-seq_NK_C Stage 5 Ctrl

description: Sample 16


title: KRp1-59


title: RNA-seq_NK_E Stage 4 T-BET

description: Sample 11


title: Sample26.Mouse.203877620035_R01C01


title: KRp1-56


title: KRp1-55


title: KRp1-58

value: HCC

value: IIIA


title: RNA-seq_NK_E Stage 4 Ctrl

description: Sample 10


title: KRp1-54


title: RNA-seq_NK_D Stage 4 EOMES

description: Sample 9

value: Donor D


title: Sample22.Brown rat.202897220127_R02C01


title: KRp1-50


title: Sample20.Mouse.202897220059_R04C02


title: Sample23.Brown rat.202897220127_R03C01


title: KRp1-62

value: Normal


title: KRp1-53


title: KRp1-49

value: #N/A


title: KRp1-5

value: cell-free DNA


title: RNA-seq_NK_D Stage 4 T-BET

description: Sample 8


title: KRp1-57


title: RNA-seq_NK_C Stage 4 EOMES

description: Sample 6

value: Donor C


title: Sample18.Mouse.202897220059_R02C02


title: KRp1-52


title: KRp1-48

value: ESCC


title: Sample19.Mouse.202897220059_R03C02


title: KRp1-42


title: Sample28.Mouse.203877620035_R03C01


title: RNA-seq_NK_D Stage 4 Ctrl

description: Sample 7


title: RNA-seq_NK_C Stage 4 T-BET

description: Sample 5


title: KRp1-44


title: KRp1-37

value: I


title: Sample16.Mouse.202897220059_R06C01


title: Sample14.Mouse.202897220059_R04C01


title: KRp1-35


title: KRp1-34


title: Sample13.Mouse.202897220059_R03C01


title: KRp1-36

value: PDAC


title: KRp1-4


title: KRp1-33


title: KRp1-30


title: Sample17.Mouse.202897220059_R01C02


title: KRp1-3


title: KRp1-32


title: KRp1-28


title: KRp1-27


title: RNA-seq_NK_B Stage 4 Ctrl

description: Sample 1

value: Natural Killer cells

value: Day 21


title: RNA-seq_E EOMES

source_name: Hematopoietic stem cell

growth_protocol: HPC were obtained by isolating peripheral blood monocytes form umbilical cord blood by density gradient centrifugation and subsequently CD34+ HPC were enriched by magnetic activated cell sorting (MACS). Isolated cord blood-derived CD34+ HPC were cultured in complete IMDM containing 10% FCS and supplemented with thrombopoietin (TPO) (20 ng/ml), stem cell factor (SCF) (100 ng/ml) (all from Peprotech, London, UK.) and FMS-like tyrosine kinase 3 ligand (FLT3-L) (100 ng/ml, R&D Systems, Minneapolis, MN, U.S.A.) for 48 hours.

treatment_protocol: Pre-cultured CD34+ HPC were harvested, transferred to RetroNectin (Takara Bio, Saint-Germain-en-Laye, France)-coated plates and viral supernatant was added. Additional cytokines were added to keep the concentrations constant after virus addition. The plates were centrifuged at 950 g and 32°C during 90 min. Another 48 hours after transduction, lineage-(CD3/CD14/CD19/CD56) CD34+eGFP+ HPC were sorted using a BD FACSAria™ Fusion cell sorter (BD Biosciences).

value: umbilical cord blood

value: Hematopoietic stem cell

value: Retroviral transduction


title: RNA-seq_NK_C Stage 4 Ctrl

description: Sample 4

value: retroviral transduction


title: Sample11.Mouse.202897220059_R01C01

value: premixed DNA standards from EpigenDx Inc (80-8060M-PreMixMouse)


title: KRp1-26


title: RNA-seq_E T-BET

value: Donor E


title: KRp1-25

value: IIB


title: RNA-seq_NK_B Stage 4 EOMES

description: Sample 3

value: Donor B


title: Sample9.Human.202897220084_R03C02

value: premixed DNA standards from EpigenDx Inc (80-8060H-PreMixHuman)


title: Sample21.Brown rat.202897220127_R01C01

value: premixed DNA standards from EpigenDx Inc (Standard80-8060R-PreMixRat)


title: KRp1-22

value: Normal

value: #N/A

value: cell-free DNA


title: Sample12.Mouse.202897220059_R02C01


title: Sample8.Human.202897220084_R02C02


title: RNA-seq_E Control


title: Sample10.Human.202897220084_R04C02


title: RNA-seq_D EOMES

value: Donor D


title: KRp1-21

value: PDAC


title: KRp1-20

value: GC


title: KRp1-189


title: KRp1-2


title: Sample15.Mouse.202897220059_R05C01


title: KRp1-24

value: III


title: KRp1-190


title: RNA-seq_D Control

value: umbilical cord blood


title: Sample7.Human.202897220084_R01C02


title: KRp1-188


title: KRp1-187

value: ESCC


title: KRp1-186

value: HCC

value: II


title: Sample5.Human.202897220084_R05C01


title: Sample6.Human.202897220084_R06C01


title: KRp1-185


title: RNA-seq_C EOMES

value: Hematopoietic stem cell

value: Donor C

value: Retroviral transduction


title: RNA-seq_C T-BET


title: mpk1Δ_12h_2_Strand_specific

city: beijing

first: lei

last: chen

address: NO.1 Beichen West  Road, Chaoyang District, Beijing 100101, China

institute: the institute of microbiology chinese academy of sciences

data_processing:
Basecalls performed using CASAVA version 1.4
Standard sequencing for samples contain wildtype at seven time points with 3 repeats and wildtype. Strand-specific sequencing for crz1Δ, mpk1Δ, znf2Δ at one time point with two repeats. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, and then ~2 GB of clean data of each sample (representing over 100 × coverage) was mapped to the genome sequence of H99 using STATR_2.6.0c.  All unigenes were subsequently aligned against the well-annotated genome of H99.
The gene expression level was measured in TPM to determine unigenes by StringTie v1.3.3.
The differentially expressed genes (DEGs) were assessed using the DEseq2 v1.16.1 Bioconductor package and defined based on the fold change criterion.
Genome_build: H99
Supplementary_files_format_and_content: TPM values for each Sample

organism: Cryptococcus neoformans H99

growth_protocol: Strains were cultured in YPD liquid medium at 30°C for 12 hrs. The cells were collected, washed twice with ddH2O, and diluted to A600 = 5.0. The diluted cells were spotted on YPGlcN medium and incubated at 30°C

extract_protocol:
Total RNA was subsequently extracted from the cells collected at different time points. The RNA concentration of each sample was assessed using a Qubit RNA Assay Kit on a Qubit 2.0 Fluorometer (Life Technologies, CA, USA). The RNA integrity was evaluated using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The transcriptome libraries were generated using the VAHTS mRNA-seq v2 Library Prep Kit (Vazyme Biotech Co., Ltd, Nanjing, China) following the manufacturer’s instructions. Transcriptome library sequencing was performed by Annoroad Gene Technology Co., Ltd (Beijing, China). The samples were clustered using VAHRS RNA adapters set1/set2 and then sequenced on an Illumina platform.

tag: strain background

tag: mating type

value: Mating type alpha

tag: genotype/variation

value: YPGlcN (2% GlcN) at 30°C, 12h


title: RNA-seq_C Control