title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_DNA#14


title: 36_2_18B

status: Public on Dec 15 2020

type: genomic

city: London

first: Chloe

last: Wong

state: Select a State or Province

address: MRC SGDP Centre, Institute of Psychiatry,

country: United Kingdom

institute: King's College London

description:
comments: This sample matched with  36_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

hyb_protocol: Samples were processed according to the Illumina Infinium Methylation EPIC BeadChip protocol with the exception that 7ul of bisulfite treated material was input into the whole genome amplicifaction reaction instead of 4ul.

scan_protocol: Samples were assessed using the Illumina Infinium MethylationEPIC BeadChip using a Illumina iScan System (Illumina).

data_processing: Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions. Normalized betas using dasen function

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: whole blood at age 18

label_protocol: 500 ng DNA was sodium bisulphite treatedas amplified using the EZ-96 DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer’s standard protocol

extract_protocol: genomic DNA was extracted and purified from buccal and blood samples using standardised protocols.

tag: familyid

tag: twinid

tag: gender

value: Male

tag: tissue

value: Blood

tag: age

value: Age 18

tag: disease state

value: Notexposed

tag: smokingpackyears

tag: category


title: WT-MMI B2CTX_WTH2

type: SRA

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

description: WT-MMI

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads quality was evaluated from FastQC.
Reference Genome was indexed from Bowtie (Langmead B et al. 2009) and sequence reads were aligned using TopHat (Trapnell C et al. 2009). Mapping data quality was evaluated from Qualimap (Garcia-Alcalde F et al. 2012)
We quantified reads to specific genes and transcripts using the Python module HT-SEQ (Anders S et al. 2015).
RNA-Seq data were normalized using Trimmed Mean of M values (Robinson MD and A Oshlack 2010) from EdgeR.
Genome_build: Mouse sequenced genome GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include TMM values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: cerebral cortex

extract_protocol:
Total RNA was isolated using RNeasy Plus Micro Kit (Quiagen) and was quantified and purity checked using a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
500 ng of total RNA were used with the TruSeq RNA Sample Preparation v2 Kit (Illumina, San Diego, CA) to construct index-tagged cDNA libraries. Libraries were quantified using a Quant-iT™ dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and sequence-by-synthesis single reads of 75 base length using the TruSeq SBS Kit v5 (Illumina) were generated on the Genome Analyzer IIx following the standard RNA sequencing protocol. Reads were further processed using the CASAVA package (Illumina) to split reads according to adapter indexes and produce fastq files. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.

value: cerebral cortex

tag: strain

value: WT-SH


title: WT A6CTX_WT8

description: WT

value: WT


title: WT A5CTX_WT7

description: WT


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_DNA#01

city: New York

first: Zhu

last: Chenxu

email: cxzhu@pku.edu.cn, czhu@nygenome.org

state: New York

address: 101 Avenue of the Americas

country: USA

institute: New York Genome Center

library_source: genomic

data_processing:
Cellular barcodes and the linker sequences are read by Read2. The first base of BC#1, BC#2 and BC#3 should locate within 84-87th, 47-50th and 10-13rd base of Read2. We identify the positions of barcodes by matching the linker sequences adjacent to the cellular barcodes.
Cleaned reads were first mapped to a mouse GRCm38 genome reference genome with STAR (version: 2.6.0a) for RNA or bowtie2 for DNA. Mapped DNA reads of H3K4me1, H3K27ac and H3K27me3 were further filtered by mapping quality (MAPK>10). Duplicates were removed based on the mapped position, cellular barcode, PCR index and UMI.
Genome_build: hg19/mm10
Supplementary_files_format_and_content: tab-delimited text files include cell embeddings for each cell.

source_name: Mouse frontal cortex and hippocampus

growth_protocol: HeLa S3 (human, ATCC CCL-2.2) cells were cultured according to standard procedures in Dulbecco’s Modified Eagles’ Medium (Thermo Fisher Scientific, 10569010) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific, 16000044) and 1% penicillin-streptomycin (Thermo Fisher Scientific, 10378016) at 37 °C with 5% CO2.

extract_protocol:
Single-cell suspension were prepared from douncing of the frozen tissues, in Doucing Buffer with Protease/RNase Inhibitor cocktail (DBI: 0.25 M sucrose [Sigma, S7903], 25 mM KCl [Sigma, P9333], 5 mM MgCl2, 10 mM Tris-HCl pH 7.4, 1 mM DTT [Sigma, D9779], 1X Protease Inhibitor, 0.5 U/µL RNase OUT and 0.5 U/µL SUPERase Inhibitor) supplemented with 0.1% Triton-X 100 (Sigma T9284). The cell suspension was then filtered by 30 µm Cell-Tric (Sysmex) and spun-down for 10 min, 1,000 g at 4 °C. After washing the cell pellets with DBI and spun-down again, NIB with 0.2% IGEPAL CA-630 were added to resuspend the nuclei pellets and rotate for 10 min at 4 °C. The nuclei were counted by BioRad TC20 cell counter and proceed to Paired-tag experiments immediately.
Libraries were constructed by Paired-tag workflow, briefly: First, permeabilized nuclei were incubated with antibodies targeting chromatin regions of interest to trigger the targeted binding of protein A-fused Tn5. Tagmentation reaction and reverse transcription (RT) were then sequentially performed: specifically, reactions were carried out in 12 different wells, with the same set of barcodes in transposase adaptors and RT primers, to label different samples or replicates (1st round of barcodes). Next, a ligation-based combinatorial barcoding strategy was used to introduce the 2nd and 3rd rounds of barcodes to nuclei, by sequential attaching well-specific DNA barcodes from 96-well plates to the 5’-end of both DNA fragments and cDNA from RT. Lastly, barcoded nuclei were divided into sub-libraries and lysed, the DNA/cDNA was purified and subjected to an optimized “amplify-and-split” strategy based on that we previously developed, to give rise DNA and RNA libraries for sequencing

treatment_protocol: To prepare nuclei, HeLa S3 cells were harvested by centrifugation, washed with PBS (Thermo Fisher Scientific, 10010-23) and counted using BioRad TC20 cell counter. The cells were then resuspended in cold Nuclei Permeabilization Buffer 1 (NPB1: 10 mM Tris-HCl pH 7.4 [Sigma, T4661], 10 mM NaCl [Sigma, S7653], 3 mM MgCl2 [Sigma, 63069], 1X Protease Inhibitor [Roche, 05056489001], 0.5 U/µL RNase OUT [Invitrogen, 10777-019] and 0.5 U/µL SUPERase Inhibitor [Invitrogen, AM2694]) with 0.1% IGEPAL CA-630 (Sigma, I8896) and centrifuged for 10 min at 1,000 g, 4 °C and proceed to Paired-tag experiments.

tag: chip antibody


title: WT A4CTX_WT6

description: WT


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_DNA#13


title: 36_1_5

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv

source_name: buccal swab at age 5

value: Buccal

value: Age 5

value: Exposed


title: 36_2_10

source_name: buccal swab at age 10

value: Age 10


title: WT A2CTX_WT3

description: WT


title: WT A3CTX_WT4

description: WT


title: 37_1_18B

description:
comments: This sample matched with  37_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Female


title: WT A1CTX_WT1

description: WT


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_DNA#12


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_RNA#13


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_RNA#12


title: 36_1_18C

source_name: buccal swab at age 18


title: 36_1_18B

description:
comments: This sample matched with  36_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 36_1_10


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_RNA#11


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_DNA#11


title: 35_2_5


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_RNA#10


title: 35_2_18C


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_DNA#10


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_RNA#09


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_DNA#09


title: Bd-SiRGS-OE_L2_rep1

city: Saint Louis

first: Sona

last: Pandey

state: MO

address: 975 north warson road

institute: Donald Danforth Plant Science Center

description: Bd-SiRGS-OE_L2_vsBdWT_Bd-SiRGS-OE_Control.csv

data_processing:
The quality control was done using the FastQC software.
Transcripts per million (TPM) abundance was estimated by pseudo-aligning the reads with that of the k-mer index available from the reference genome of B. distachyon from Phytozome using Kallisto.
The differentially expressed genes (DEGs) were sorted using the Sleuth program with likelihood ratio cutoff of false discovery rate (FDR) < 0.05.
Supplementary_files_format_and_content: .csv with TPM values.
Supplementary_files_format_and_content: .h5 and .tsv with abundance.

organism: Brachypodium distachyon

source_name: 2-week-old seedlings

growth_protocol: B. distachyon seedlings were grown on 1/2MS plates at 25ºC growth chamber. Seedlings of 2-week-old transgenic lines with WT as control were collected and total RNA was isolated.

extract_protocol:
Total RNA was extracted from 2-week-old seedlings using RNeasy Mini Kit (QIAGEN).
The RNA-seq library preparation, sequencing and initial quality control analysis were performed by Novogene Inc.

tag: genotype

value: Bd-SiRGS-OE


title: 35_1_5


title: 35_2_10


title: Bd-SiRGS-OE_L2_rep2


title: 35_2_18B

description:
comments: This sample matched with  35_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Bd-SiRGS-OE_L2_rep3


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_RNA#08


title: 35_1_18C


title: Bd-SiRGS-OE_L1_rep2

description: Bd-SiRGS-OE_L1_vsBdWT_Bd-SiRGS-OE_Control.csv


title: Bd-SiRGS-OE_L1_rep1


title: BdWT_rep3_Bd-SiRGS-OE_Control

value: wild-type


title: 3280.D12.R.C1vsI2.R.C1

type: RNA

city: Sao Paulo

first: Augusto

middle: Lima

last: Diniz

state: SP

address: Av Lineu Prestes

department: Biochemistry

country: Brazil

institute: University of Sao Paulo

description: Transcriptome comparation between SP80-3280 roots irrigated for 4 days and SP80-3280 roots submitted to 4 days of drought.

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B Scanner using Agilent Settings and image intensity data were extracted with Feature Extraction Software using Agilent Settings

data_processing: Raw and background corrected data

organism: Saccharum hybrid cultivar (mixed)

label_protocol: CyScribe Post-Labelling Kit Protocol - GE Healthcare

growth_protocol: Greenhouse

extract_protocol: ZENG, Y.; YANG, T. RNA Isolation From Highly Viscous Samples Rich in Polyphenols and Polysaccharides. Plant Molecular Biology Reporter. v.20, p. 417a - 417e, 2002.

treatment_protocol: Samples cultivated in greenhouse condition without irrigation for 4 days

value: Root

tag: variety

tag: collect

value: September 13th, 2011

treatment_protocol: NO


title: 3280.D25.R.C3vsI10.R.C3

description: Transcriptome comparation between SP80-3290 roots irrigated for 8 days and SP80-3290 roots submitted to 6 days of drought followed by 2 days of rehydration.

treatment_protocol: Samples cultivated in greenhouse condition without irrigation for 6 days and then, rehydrated for 2 days

value: September 17th, 2011


title: 3280.D11.R.C1vsI1.R.C1

extract_protocol: ZENG, Y.; YANG, T. RNA Isolation From Highly Viscous Samples Rich in Polyphenols and Polysaccharides. Plant Molecular Biology Reporter. v. 20, p.417a????417e, 2002.


title: 35_1_18B

description:
comments: This sample matched with  35_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Male


title: 3280.D15.R.C2vsI5.R.C2

description: Transcriptome comparation between SP80-3280 roots irrigated for 6 days and SP80-3280 roots submitted to 6 days of drought.

treatment_protocol: Samples cultivated in greenhouse condition without irrigation for 6 days

value: September 15th, 2011


title: 3280.D12.L1.C1vsI2.L1.C1

description: Transcriptome comparation between SP80-3280 leaves irrigated for 4 days and SP80-3280 leaves submitted to 4 days of drought.

value: Leaves


title: 3280.D11.L1.C1vsI1.L1.C1

description: Transcriptome comparation between SP80-3280 leaves irrigated for 4 days and submitted to 4 days of drought.


title: 3280.D25.L1.C3vsI10.L1.C3

description: Transcriptome comparation between SP80-3290 leaves irrigated for 8 days and SP80-3290 leaves submitted to 6 days of drought followed by 2 days of rehydration.


title: 3280.D16.R.C2vsI6.R.C2


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_RNA#07


title: BdWT_rep1_Bd-SiRGS-OE_Control


title: 3280.D28.L1.C3vsI31.L1.C3


title: 3280.D16.L1.C2vsI6.L1.C2

description: Transcriptome comparation between SP80-3280 leaves irrigated for 6 days and SP80-3280 leaves submitted to 6 days of drought.


title: 3280.D28.R.C3vsI31.R.C3


title: Bd-SiRGS-OE_L1_rep3


title: 3280.D15.L1.C2vsI5.L1.C2


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_RNA#06


title: amiR-BdGalpha_L2_rep2

description: amiR-BdGalpha_L2_vs_BdWT_amiR-BdGalpha_Control.csv

value: amiR-BdGalpha


title: BdWT_rep2_Bd-SiRGS-OE_Control


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_DNA#08


title: 35_1_10

value: Notexposed


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_DNA#06


title: amiR-BdGalpha_L1_rep2

description: amiR-BdGalpha_L1_vs_BdWT_amiR-BdGalpha_Control.csv


title: amiR-BdGalpha_L1_rep1


title: 34_2_18B

description:
comments: This sample matched with  34_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood

value: Age 18


title: 34_2_18C

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv

value: Buccal


title: amiR-BdGalpha_L2_rep1


title: amiR-BdGalpha_L1_rep3


title: amiR-BdGalpha_L2_rep3


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_DNA#07


title: 34_2_5

value: Age 5


title: BdWT_rep2_amiR-BdGalpha_Control


title: BdWT_rep3_amiR-BdGalpha_Control


title: BdWT_rep1_amiR-BdGalpha_Control


title: 34_2_10


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_RNA#05


title: 34_1_5

value: Exposed


title: NDMSC3

city: Suzhou

first: Wenzhuo

last: Zhuang

state: Jiangsu

address: Ren Ai Road 199

department: Department of Cell Biology, School of Biology & Basic Medical Sciences

country: China

institute: Soochow University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.8 mapping to reference genome
Counts counting
Genome_build: GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: MSCs

growth_protocol: Bone marrow–derived MSC cells were cultured (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in DMEM LOW Glucose medium (Hyclone, USA) supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was extracted from cell by Trizol reagent (Invitrogen) separately
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA libraries were then processed for the Proton Sequencing process  according to the commercially available protocols.

value: bone marrow

value: normal


title: NDMSC2


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_DNA#05


title: NDMSC1


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_RNA#04


title: 34_1_18B

description:
comments: This sample matched with  34_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: MMMSC2

value: Multiple Myeloma


title: 34_1_10

value: Age 10


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_RNA#03


title: Individual 6, PMI 24

city: Leuven

first: Bram

last: Bekaert

address: Herestraat 49 - box 7003 71

department: Forensic Biomedical Sciences

country: Belgium

institute: KU Leuven

data_processing:
Read Counts were obtained with BlueBee, so all steps here are part of their pipeline
Read QC is performed over raw reads, then trimmed with Bbduk from the bbmap suite trimming.
Read QC is also performed over trimmed reads.
STAR algorithm was used to align the reads
Gene Read Counting was performed with HTSeq-Count algorithm with kit-specific options
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for each sample

source_name: Vena femoralis left

extract_protocol:
RNA extraction was performed using the PAXgene Blood RNA Kit (IVD)
cDNA libraries were created using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina NextSeq High-Output 75bp (Lexogen) including the Globin Block module to remove the majority of the globin mRNA transcripts

tag: individual

value: Individual 6

value: blood

tag: age (years)

value: male

tag: weight (kg)

tag: height (cm)

tag: bmi

tag: race

value: caucasian

tag: death date (dd-mm-yy)

tag: time of death (tod) (h)

tag: time of death error

tag: sampling date (dd-mm-yy)

tag: post mortem interval (pmi) (h)


title: Individual 7, PMI 0

value: Individual 7

tag: tissue

tag: gender

value: female


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_DNA#03

tag: chip antibody


title: Individual 7, PMI 6


title: Individual 6, PMI 21

source_name: Vena femoralis Right


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_RNA#02


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_DNA#04


title: MMMSC1

tag: age

tag: genotype


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_DNA#02


title: Individual 6, PMI 18

source_name: Vena Subclavian left


title: 33_2_18C

tag: familyid

tag: twinid

value: Female

tag: disease state

tag: smokingpackyears

tag: category


title: Individual 6, PMI 15

tag: individual

tag: age (years)

tag: weight (kg)

tag: height (cm)

tag: bmi


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_RNA#01


title: Individual 6, PMI 12

tag: race

tag: death date (dd-mm-yy)

tag: time of death (tod) (h)

tag: time of death error

tag: sampling date (dd-mm-yy)


title: Individual 6, PMI 9

tag: tissue

tag: gender

tag: post mortem interval (pmi) (h)


title: 34_1_18C

tag: familyid

tag: twinid

value: Male

tag: age


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_DNA#01

tag: chip antibody


title: Individual 6, PMI 3

tag: individual


title: MMMSC3

tag: genotype


title: 33_1_5

tag: disease state

value: Notexposed

tag: smokingpackyears

tag: category


title: 33_2_10


title: Individual 5, PMI 18

value: Individual 5

tag: age (years)

tag: weight (kg)

tag: height (cm)

tag: bmi

tag: race


title: Individual 6, PMI 0

tag: tissue

tag: death date (dd-mm-yy)

tag: time of death (tod) (h)

tag: time of death error

tag: sampling date (dd-mm-yy)


title: Bulk_Brain_H3K9me3_rep2


title: Individual 5, PMI 15

tag: gender

tag: post mortem interval (pmi) (h)


title: 33_2_5

tag: familyid

tag: twinid

value: Buccal

tag: age


title: 32_2_5

value: Age 5

tag: disease state

tag: smokingpackyears


title: Bulk_Brain_H3K27ac_rep2

tag: chip antibody


title: Bulk_Brain_H3K27me3_rep2


title: 33_2_18B

description:
comments: This sample matched with  33_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood

value: Age 18

tag: category


title: 33_1_18B

description:
comments: This sample matched with  33_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Individual 4, PMI 24

tag: individual

value: Individual 4

tag: age (years)

tag: weight (kg)


title: Individual 7, PMI 3

tag: tissue

tag: height (cm)

tag: bmi

tag: race


title: 33_1_18C


title: Individual 5, PMI 9

tag: death date (dd-mm-yy)

tag: time of death (tod) (h)

tag: time of death error

tag: sampling date (dd-mm-yy)


title: 33_1_10

tag: familyid

tag: twinid

tag: gender


title: Individual 4, PMI 18

source_name: Vena sbclavian right

tag: post mortem interval (pmi) (h)


title: Bulk_Brain_H3K9me3_rep1

tag: chip antibody


title: Bulk_Brain_H3K27me3_rep1


title: 32_2_10

tag: age

tag: disease state

value: Exposed

tag: smokingpackyears

tag: category


title: Individual 4, PMI 21

tag: individual

tag: tissue

tag: age (years)

tag: weight (kg)


title: Individual 5, PMI 3

tag: height (cm)

tag: bmi

tag: race

tag: death date (dd-mm-yy)


title: Individual 4, PMI 6

tag: time of death (tod) (h)

tag: time of death error

tag: sampling date (dd-mm-yy)


title: Individual 5, PMI 12

tag: gender

tag: post mortem interval (pmi) (h)


title: Bulk_Brain_H3K27ac_rep1

tag: chip antibody


title: 32_2_18B

description:
comments: This sample matched with  32_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

tag: familyid

tag: twinid

tag: age

tag: disease state


title: 32_2_18C

tag: tissue

tag: smokingpackyears

tag: category


title: Bulk_Brain_H3K4me1_rep2


title: Individual 4, PMI 9

tag: individual

tag: age (years)

tag: weight (kg)


title: Individual 4, PMI 12

tag: race

tag: death date (dd-mm-yy)


title: Individual 4, PMI 15

tag: time of death (tod) (h)

tag: time of death error


title: Individual 5, PMI 6

tag: gender

tag: height (cm)

tag: bmi

tag: sampling date (dd-mm-yy)


title: Individual 5, PMI 0

tag: post mortem interval (pmi) (h)


title: Bulk_Brain_H3K4me1_rep1

tag: chip antibody


title: 32_1_5

tag: familyid

tag: twinid

tag: age

tag: disease state


title: 32_1_18C

tag: tissue

tag: smokingpackyears

tag: category


title: Individual 3, PMI 21

tag: individual

value: Individual 3

tag: age (years)

tag: weight (kg)

tag: race


title: Nagina22_N-W-_shoot

city: New Delhi

first: Amitha Mithra

last: Sevanthi

address: LBS Centre, Pusa Campus

country: India

institute: ICAR - National Institute for Plant Biotechnology

description:
Shoot tissues of 21 day old plants subjected to water stress from days 15-21 and chronic nitrogen stress all along were collected from Nagina 22 genotype from three independent biological replications.
NDS

data_processing:
Base calling done by illumina casava software
The raw data were processed by using the sickle tool for removing adaptors and low-quality reads. The Default parameters were considered for trimming the raw reads
CLC Genomics Workbench 12 used for transcriptome data analysis
Genome_build: IRGSP 1.0
Supplementary_files_format_and_content: Excel files includes TPM,RPKM values and etc for each sample.

organism: Oryza sativa

source_name: Shoot

growth_protocol: Germinated seeds were sown in 4" pots containing vermiculite-perlite mixture and grown in net-house with ammonium nitrate as the only N source and other nutrients as per Yoshida media.

extract_protocol:
Total RNA was isolated from respective tissues using RNeasy Plant Mini Kit (Qiagen, Qiagen India Pvt. Ltd., New Delhi, India). RNA quality assessment was performed by using a RNA 6000 Nano assay kit in Bio analyzer 2100 (Agilent, Santa Clara, CA, USA). Samples with RIN value more than 7 were subjected to RNA-seq libraray construction using Illumina kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wherever nitrogen stress has to be imposed, 0.4 mM ammonium nitrate was supplied; otherwise 0.08 mM ammonium Nitrate was supplied. Simialrly water stress was imposed on 15 day old seelings by limited water supply (10 ml) against 100 ml water supply per day till 21st day.

tag: cultivar

value: Nagina 22

value: Shoot

tag: growth stage

value: Seedling

tag: stress

value: Nitorgen and drought stress


title: Individual 3, PMI 24

value: blood

tag: gender

value: male

tag: height (cm)

tag: bmi

value: caucasian

tag: death date (dd-mm-yy)

tag: time of death (tod) (h)

tag: time of death error

tag: sampling date (dd-mm-yy)


title: Individual 4, PMI 3

tag: tissue

value: female

tag: post mortem interval (pmi) (h)


title: Individual 3, PMI 18


title: Nagina22_N-W-_root

description:
Root tissues of 21 day old plants subjected to water stress from days 15-21 and chronic nitrogen stress all along were collected from Nagina 22 genotype from three independent biological replications.
NDR

source_name: Root

value: Root


title: 32_1_10

tag: familyid

tag: twinid

value: Male

tag: age

value: Age 10

tag: disease state

value: Notexposed

tag: smokingpackyears

tag: category


title: Individual 3, PMI 9

tag: individual

tag: age (years)

tag: weight (kg)

tag: race


title: Individual 4, PMI 0

tag: gender


title: Individual 3, PMI 12

tag: height (cm)

tag: bmi

tag: death date (dd-mm-yy)


title: Individual 3, PMI 6

tag: time of death (tod) (h)

tag: time of death error

tag: sampling date (dd-mm-yy)


title: Individual 2, PMI 24

value: Individual 2

tag: tissue

tag: post mortem interval (pmi) (h)


title: Individual 3, PMI 15


title: 32_1_18B

description:
comments: This sample matched with  32_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

tag: familyid

tag: twinid

value: Blood

tag: age

value: Age 18


title: 31_2_5

value: Female

value: Buccal

value: Age 5

tag: disease state

value: Exposed

tag: smokingpackyears

tag: category


title: Nagina22_N+W-_root

description:
Root tissues of 21 day old plants subjected to water stress from days 15-21 were collected from Nagina 22 genotype from three independent biological replications.
NCR

tag: cultivar

value: Nagina 22

tag: growth stage

value: Seedling

tag: stress

value: Drought stress


title: Nagina22_N-W+_shoot

description:
Shoot tissues of 15 day old plants grown under chronic nitrogen stress (0.04 mM NH4NO3) were collected from Nagina 22 genotype from three independent biological replications.
NBS

value: Shoot

value: Nitrogen stress


title: Individual 3, PMI 3

tag: individual

value: Individual 3

value: blood

tag: age (years)

tag: gender

value: male

tag: weight (kg)

tag: height (cm)

tag: race

value: caucasian


title: Nagina22_N-W+_root

description:
Root tissues of 15 day old plants grown under chronic nitrogen stress (0.04 mM NH4NO3) were collected from Nagina 22 genotype from three independent biological replications.
NBR

tag: tissue

value: Root


title: Individual 3, PMI 0

tag: bmi

tag: death date (dd-mm-yy)

tag: time of death (tod) (h)

tag: time of death error

tag: sampling date (dd-mm-yy)

tag: post mortem interval (pmi) (h)


title: Individual 2, PMI 18

value: Individual 2


title: Individual 2, PMI 21


title: Nagina22_N+W+_shoot

description:
Shoot tissues of 15 day old plants were collected from Nagina 22 genotype from three independent biological replications
NAS

value: No stress


title: 31_2_18B

description:
comments: This sample matched with  31_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

tag: familyid

tag: twinid

value: Blood

tag: age

value: Age 18

tag: disease state

tag: smokingpackyears

tag: category


title: Wild-type TIFseq return to growth replicate 2

first: Folkert

last: van Werven

address: 1 Midland Road

institute: Francis Crick Institute

description: TIF seq

data_processing:
First we collapsed all 5’-end or 3’-end sequence reads in each sample according to the indexes.
Cutadapt (v1.16) was utilized to trim TIF-seq2 sequencing primer (-AGGTGACCGGCAGGTGT) and Illumina TruSeq adapter (-AGATCGGAAG).
After extracting 8 bp of unique molecular identifiers (UMIs) with UMItools (v0.5.4) from the 5’ ends and removing extra A stretches in the 3’ ends caused by poly(A) slippery during PCR amplification, we kept reads over 20 bp for alignment.
We used STAR (v2.5.3a) for aligning paired-end reads separately to theSK1 assembly. Alignment setting was adjusted as below, --alignIntronMax 1 --alignMatesGapMax 0 --alignEndsType Extend5pOfReads12 --outSAMattributes NH HI NM AS.
We then linked paired-end reads and kept the uniquely mapped pairs that are in the same chromosome.
Covert alignment BAM files to BEDPE format using "bedtools bamtobed".
Genome_build: SK1 assembly from Keeney lab (http://cbio.mskcc.org/public/SK1_MvO/)
Supplementary_files_format_and_content: BEDPE format files containing the 5' and 3' ends of transcript isoforms. See data processing step for more details.

organism: Saccharomyces cerevisiae

source_name: yeast strains in small batch culture

growth_protocol: Cells were grown in regular YPD  (2.0% (wt/vol) glucose) and grown to exponential phase (OD600 < 2.0) at 30°C and 300 rpm. Approximately 0.05 OD of exponentially growing yeast were inoculated into new flasks containing reduced glucose YPD (1.0% (wt/vol) glucose). After 16-18 hours, cells were then pelleted, washed with sterile miliQ water, and re-suspended in supplemented sporulation (SPO) media at an OD600 of 2.5.

extract_protocol:
Cell pellets were washed once with sterile water and snap-frozen in liquid nitrogen. Total RNA was extracted using hot acid phenol:chloroform:isoamyl alcohol (25:24:1) and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in RNAse-free sterile water.
Briefly, we selected the capped RNA and used dT primer to generate cDNA. We then circularized the cDNA and broke them with sonication. The joined fragments, which consisted of the docking site of the 5’ and 3’ end of cDNA, were selected by streptavidin beads and used for library preparation.In detail, we took 2.5 µg total RNA per sample as input. To prevent genomic DNA contamination, input RNA was incubated with Turbo DNase(0.12U/µl)(Takara) for 20min at 37˚C. After inactivation of DNase, we filtered out the RNA degradation intermediate via dephosphorylating the exposed 5’ phosphomonoesters by Alkaline Phosphatase, Calf Intestinal(0.3U/µl)(CIP from NEB). Then we performed two rounds of phenol-chloroform RNA extraction to remove CIP residues in the reaction system completely. The 5’Cap of mature RNA was later removed by incubating with Cap-Clip(0.125U/µl) at 37˚C for 60min. Cap-clip treatment exposed the 5’ phosphomonoester of mature RNA and allowed for ligation to RNA adaptor in the following steps. After phenol-chloroform purification, mature RNA was then ligated overnight at 16˚C at 5’with single strand DNA_RNA chimeric adaptor, which introduced an 8 mer unique molecular identifier(UMI) and a common anchor sequence for subsequent PCR amplification.On the second day, the ligated RNA was purified with 1.8X Ampure XP beads according to the manufacturer instruction. Purified mature RNA worked as the template for reverse transcription(RT) to generate first-strand cDNA with custom barcoded oligo dT primers, which introduce the sequencing primer 1, 3’index, NOT1 endonuclease digestion site and a 3’ universal anchor sequence for subsequent PCR reaction. For details of RT, RNA template was first mixed with primer and dNTPs. The mixture was denatured at 65˚C for 5min and then put on ice. After adding first strand buffer, Trehalose and Risosafe, the reaction system was first incubated at 42˚C for 2min, and then 2 µl of superscript II enzyme was added to each reaction. The RT system went through 42 ˚C for 50min, 50 ˚C for 30 min, 55 ˚C for 30min. Then the RT enzyme was inactivated at 70 ˚C for 15min. To remove the RNA template, 0.5ul RNase H(5U/µl) and 0.5µl RNase cocktail were added and incubated at 37 ˚C for 30min. First-strand cDNA was then purified with 2X Ampure XP beads according to manufacturer instruction.We stored half of cDNA as a backup. The left half was split into two as the template for following PCR amplification with TERA(Takara). First, denature at 98 ˚C for 2min, then 98 ˚C 20s, 60 ˚C 30s 68 ˚C 5min (+10s/cycle) for 16 cycles and final extension was performed at 72 ˚C for 5min. Pool the two PCR system for the same sample together and purify with 1X Ampure XP beads according to manufacturer instruction. The PCR products are then quantified with qubit dsDNA HS assay. PCR products from different samples are then pooled together with equal mass. The pooled PCR products were then subjected to NOT1 HF (NEB) endonuclease digestion at 37˚C for one hour. After inactivation of NOT1 at 65 ˚C for 20 min, we used 1.8X Ampure XP beads to purify.To favour intramolecular ligation, the PCR products with sticky ends were highly diluted to a final concentration less than 1ng/µl and ligated with a high concentration of T4 DNA ligase(NEB)(66.6U/µl) at 16 ˚C for at least 16 hours. To remove the unligated linear PRC products, for every 100 µl system, 0.5 µl plasmid-safe were added and incubated at 37 ˚C for 1h. After inactivation at 70 ˚C for 30min, the self-circularized cDNA was purified with phenol-chloroform. Circularized cDNA was fragmented by Covaris ME220 sonicator (Duration 240s, peak power 30, duty factor 10, Avg Power(W) 6). The fragments were then purified with 1X Ampure XP beads according to manufacturer instruction. As the fragment of 5’ and 3’ docking site are labelled with biotin, these specific fragments are selected via streptavidin beads by incubating with M280 streptavidin beads (Invitrogen) for 30 min. The fragments of docking site were then subjected to end repair, dA tailing and ligation of the barcoded partially forked adaptor with a common sequence to anneal to each other and the grafting part to anchor to Illumina sequencer flowcells. After final amplification using Phusion High Fidelity Master Mix with PCR graft P5 and P7 as primers for 18 cycles, the library was ready to load onto the sequencer. The final PCR parameter was as following, first, denature at 98 ˚C for 30s, then 98 ˚C 20s, 65 ˚C 30s, 72 ˚C 30s for 18 cycles and a final extension at 72 ˚C for 5min.The library is ready to load onto sequencer after purification with 1X Ampure beads according to manufacturer instruction. We used four custom sequencing oligoes. We added 15Ts to illumine read1 sequencing oligo and named it as SeqR1+15T. The sequencing oligoes for index1, index2 and read2(SeqR2) are exactly the same as Illumina oligoes. We diluted the oligoes according to manufacturer instruction. We made two mixtures of sequencing oligoes. Mixture 1 was composed of SeqR1+15T and SeqR2 in a 1:1 ratio. Mixture 2 was composed of index1 and index2 sequencing primer in 1:1 ratio. The mixture 1 was loaded into both positions for custom read1 and read2 primers on sequecing kit. The mixture2 was loaded on index primer on sequencing kit.TIF2 library was denatured, diluted and loaded according to manufacturer instruction.we used stand alone configuration of NextSeq 500 machine. We checked read1, index1, index2 and read2 as custom sequencing oligoes. For paired end, we set as read1 76bp, read2 76bp, index1 6bp, index2 6bp.
TIF-Seq

treatment_protocol: For the regular WT time course, 50 μM CuSO4 was added after 2h in SPO and 1 μM β-estradiol was added after 6h in SPO for synchronous sporulation. For the mutant samples and their controls,  50 μM CuSO4 was added after 2h in SPO. Additionally after 2h in SPO, all cells with the SPT16-AID allele were treated with 3-indole-acetic acid (3-IAA, Sigma-Aldrich I3750) to a final concentration of 500 μM from a 1 M stock dissolved in DMSO.

tag: strain/background

value: FW2795 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3) Sk1 derivative

tag: treatment

value: no treatment


title: 31_2_10

tag: gender

value: Female

value: Buccal

value: Age 10

value: Exposed


title: Individual 2, PMI 15

tag: individual

tag: age (years)

tag: weight (kg)

tag: height (cm)

tag: race


title: Nagina22_N+W-_shoot

description:
Shoot tissues of 21 day old plants subjected to water stress from days 15-21 were collected from Nagina 22 genotype from three independent biological replications.
NCS

tag: cultivar

value: Nagina 22

tag: tissue

value: Shoot

tag: growth stage

value: Seedling

tag: stress

value: Drought stress


title: 31_2_18C

tag: familyid

tag: twinid


title: Nagina22_N+W+_root

description:
Root tissues of 15 day old plants were collected from Nagina 22 genotype from three independent biological replications
NAR


title: Wild-type TIFseq return to growth replicate 1

description: TIF seq


title: IR64_N-W-_shoot

description:
Shoot tissues of 21 day old plants subjected to water stress from days 15-21 and chronic nitrogen stress all along were collected from IR 64 genotype from three independent biological replications.
IDS

value: IR 64

value: Nitorgen and drought stress


title: Individual 2, PMI 9

source_name: Vena subclavian right

value: blood

value: male

tag: bmi

value: caucasian

tag: death date (dd-mm-yy)

tag: time of death (tod) (h)

tag: time of death error

tag: sampling date (dd-mm-yy)

tag: post mortem interval (pmi) (h)


title: Individual 2, PMI 12

tag: individual

value: Individual 2

tag: gender


title: Wild-type TIFseq mid-late meiotic replicate 1

description: TIF seq

tag: strain/background

value: FW2795 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3) SK1 derivative

tag: treatment


title: 31_1_5

tag: age

value: Age 5

tag: disease state

tag: smokingpackyears

tag: category


title: IR64_N+W-_shoot

description:
Shoot tissues of 21 day old plants subjected to water stress from days 15-21 were collected from IR 64 genotype from three independent biological replications.
ICS

tag: cultivar

tag: tissue

tag: growth stage

tag: stress


title: Wild-type TIFseq early meiotic replicate 2

description: TIF seq

value: no treatment


title: 31_1_18C

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv

tag: familyid

tag: twinid

value: Female

value: Age 18


title: 30_2_5

value: Buccal

value: Notexposed


title: Wild-type TIFseq mid-late meiotic replicate 2

description: TIF seq


title: 31_1_10

value: Age 10

value: Exposed


title: IR64_N-W+_shoot

description:
Shoot tissues of 15 day old plants grown under chronic nitrogen stress (0.04 mM NH4NO3) were collected from IR 64 genotype from three independent biological replications.
IBS

value: Shoot

value: Seedling

value: Nitrogen stress


title: 30_2_18C


title: 31_1_18B

description:
comments: This sample matched with  31_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: Individual 2, PMI 6

source_name: Vena subclavian left

value: blood

tag: age (years)

tag: weight (kg)

tag: height (cm)

tag: bmi

tag: race

tag: death date (dd-mm-yy)

tag: time of death (tod) (h)

tag: time of death error


title: IR64_N-W-_root

description:
Root tissues of 21 day old plants subjected to water stress from days 15-21 and chronic nitrogen stress all along were collected from IR 64 genotype from three independent biological replications.
IDR

value: IR 64

value: Root

value: Nitorgen and drought stress


title: Individual 2, PMI 3

tag: individual

value: Individual 2

tag: gender

value: male

value: caucasian

tag: sampling date (dd-mm-yy)

tag: post mortem interval (pmi) (h)


title: Individual 1, PMI 24

value: Individual 1

tag: tissue


title: IR64_N+W-_root

description:
Root tissues of 21 day old plants subjected to water stress from days 15-21 were collected from IR 64 genotype from three independent biological replications.
ICR

tag: cultivar

tag: growth stage

value: Drought stress


title: Wild-type TIFseq early meiotic replicate 1

description: TIF seq

tag: strain/background

value: FW2795 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3) Sk1 derivative

tag: treatment

value: no treatment


title: Wild-type TIFseq premeiotic replicate 2

description: TIF seq

value: FW2795 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3) SK1 derivative


title: Wild-type TIFseq premeiotic replicate 1

description: TIF seq


title: IR64_N-W+_root

description:
Root tissues of 15 day old plants grown under chronic nitrogen stress (0.04 mM NH4NO3) were collected from IR 64 genotype from three independent biological replications.
IBR

tag: stress


title: 30_2_18B

description:
comments: This sample matched with  30_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

source_name: whole blood at age 18

tag: familyid

tag: twinid

value: Female

tag: age

value: Age 18

tag: disease state

value: Notexposed

tag: smokingpackyears

tag: category


title: Individual 1, PMI 21

source_name: Vena femoralis right

tag: age (years)

tag: weight (kg)

tag: height (cm)

tag: bmi

tag: race

tag: death date (dd-mm-yy)

tag: time of death (tod) (h)

tag: time of death error


title: IR64_N+W+_shoot

description:
Shoot tissues of 15 day old plants were collected from IR 64 genotype from three independent biological replications
IAS

tag: cultivar

tag: tissue

value: Shoot

tag: growth stage

value: Seedling

value: No stress


title: Citeseq human GBM: recurrent + newly diagnosed

city: Brussels

first: Daliya

last: Kancheva

address: Pleinlaan 2

institute: Vrije Universiteit Brussel

description: glioblastoma

data_processing:
Raw data bcl files were first demultiplexed using Cellranger mkfastq
Demultiplexed data was then processed using the Cellranger count pipeline
The output count matrices of Cell Ranger count were then aggregated using Cellranger aggr
Genome_build: mm10 (mouse) / GRCh38 (human)
Supplementary_files_format_and_content: comma-delimited text files including raw counts for the aggregated samples (output Cellranger aggr) and annotation metadata with information per cell

source_name: glioblastoma

extract_protocol:
All methods listed in Antunes et al. Single-cell multi-omic profiling of glioblastoma-associated myeloid cells across species and disease stage reveals macrophage competition and functional specialization. Nature Neuroscience. 2020.
All methods listed in Antunes et al. Single-cell multi-omic profiling of glioblastoma-associated myeloid cells across species and disease stage reveals macrophage competition and functional specialization. Nature Neuroscience. 2020.

tag: genotype

value: IDH WT

value: resected glioblastoma tissue

value: Grade IV glioblastoma

tag: platform

value: 10x Genomics

tag: number of cells


title: Individual 1, PMI 18

tag: individual

value: blood

tag: gender

value: male

tag: sampling date (dd-mm-yy)

tag: post mortem interval (pmi) (h)


title: human newly diagnosed GBM

description: glioblastoma

tag: disease state


title: IR64_N+W+_root

description:
Root tissues of 15 day old plants were collected from IR 64 genotype from three independent biological replications
IAR

value: IR 64

value: Root

tag: stress


title: Individual 2, PMI 0

value: Individual 2

tag: age (years)

tag: weight (kg)

tag: height (cm)

tag: bmi

value: caucasian


title: 30_1_5

source_name: buccal swab at age 5

tag: familyid

tag: twinid

value: Buccal

tag: age

value: Age 5

value: Exposed

tag: smokingpackyears

tag: category


title: Individual 1, PMI 15

value: Individual 1

tag: tissue

tag: race

tag: death date (dd-mm-yy)

tag: time of death (tod) (h)

tag: time of death error


title: human recurrent GBM

description: glioblastoma

tag: genotype

tag: platform

tag: number of cells


title: Thyroid tumor, TC63 (RNA-seq)

city: Moscow

first: Daniil

last: Nikitin

address: Miklucho-Maklaya

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

data_processing:
RNA sequencing FASTQ files were processed with STAR aligner in ‘GeneCounts’ mode with the Ensembl human transcriptome annotation
Ensembl gene IDs were converted to HGNC gene symbols using Complete HGNC dataset (https://www.genenames.org, database version of July 13, 2017
Genome_build: Build version GRCh38 and transcript annotation GRCh38.89
Supplementary_files_format_and_content: raw read counts

source_name: Thyroid tumor

extract_protocol:
Tissue specimens were formalin fixed and embedded in paraffin.
RNA was extracted from the FFPE samples using RecoverAllâ¢ Total Nucleic Acid Isolation  Kit. KAPA  RNA Hyper with RiboErase (KAPA Biosystem) Kit was used for further depletion of ribosomal  RNA and library preparation. Different adaptors were used for multiplexing samples in one  sequencing run.
Illumina Library prep kit

tag: disease

value: Thyroid tumor


title: 30_1_18C

source_name: buccal swab at age 18

tag: gender

value: Female

value: Age 18

tag: disease state


title: HLO_Day50_replicate_2

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

data_processing:
UMIs were extracted from the fastq.gz files with umi_tools, and cutadapt was used to remove short and low-quality reads.
The reads were aligned to human GENCODE v.34 reference genome using STAR aligner, and the duplicate reads were collapsed using umi_tools.
Gene level counts were measured using HTSeq and compared using DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data is provided as a (.csv) file.

source_name: hPSC-derived Lung Organoid

growth_protocol: Human lung organoids (HLO) were derived from hPSCs as previously described (Carvalho et al., 2019; Jacob et al., 2017; Miller et al., 2019), with minor modifications. Briefly, H9 hPSCs were maintained in mTeSR Plus media and were seeded on Day 0 onto matrigel (Corning) coated surface. On Days 1-4 cells were treated with 100 ng/mL Activin A and increasing concentration of defined FBS (dFBS, HyClone) in RPMI 1640 medium (Thermo), to induce definitive endoderm formation (Day 1: 3 µM CHIR99021 and no dFBS; Day 2: 0.2% dFBS; Days 3-4: 2% dFBS). On Day 4, cells were >95% double positive for CXCR4/CD184 and c-Kit/CD117 as determined by flow cytometry. On Days 5-9 cells were treated with anterior foregut induction medium, containing 10 µM SB431542, 100 nM LDN193189, 2 µM CHIR99021, 1 µM SAG, 500 ng/mL FGF4 in Foregut Basal Medium (Advanced DMEM, 1x B27, 1x N2, 10 mM HEPES, 1x Glutagro (all Thermo), 50 µg/mL ascorbic acid (Sigma), 0.4 µM monothioglycerol (Sigma)). On Day 9, anterior foregut spheroids were harvested by gentle pipetting and transferred into an ultra-low attachment plate, in Lung Organoid Medium I (3 µM CHIR99021, 10 ng/mL BMP4, 10 ng/mL FGF7, 10 ng/mL FGF10, 50 nM all-trans retinoic acid, in Foregut Basal Medium). The medium was changed every two days until Day 15. On Day 15, the medium was changed to Lung Organoid Medium II (3 µM CHIR99021, 10 ng/mL FGF7, 10 ng/mL FGF10, in Foregut Basal Medium). On Day 25 the organoids were embedded in matrigel, in transwell inserts, and grown in Lung Organoid Medium III (3 µM CHIR99021, 10 ng/mL FGF7, 10 ng/mL FGF10, 50 nM dexamethasone (Sigma), 100 µM 8-bromo-cAMP (Sigma), 100 µM IBMX (Sigma), in Foregut Basal Medium). The medium was changed every 3 days. The CHIR99021 was withdrawn on Days 35-42. All media components were from Stem Cell Technologies unless noted otherwise.

extract_protocol:
RNA was extracted using Quick-RNA 96 Kit (Zymo) with on-column DNaseI treatment.
QuantSeq FWD Kit (with UMI module, Lexogen) was used for RNAseq library preparation.

value: hPSC-derived Lung Organoid

tag: cell line

tag: replicate

tag: time


title: Thyroid tumor, TC116 (RNA-seq)


title: Individual 1, PMI 12

tag: individual

tag: age (years)

tag: weight (kg)

tag: height (cm)

tag: bmi

tag: sampling date (dd-mm-yy)

tag: post mortem interval (pmi) (h)


title: 30_1_18B

description:
comments: This sample matched with  30_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

tag: familyid

tag: twinid

tag: tissue

value: Blood

tag: age

tag: smokingpackyears

tag: category


title: Individual 1, PMI 6

tag: gender

tag: race

tag: death date (dd-mm-yy)

tag: time of death (tod) (h)

tag: time of death error


title: 30_1_10

source_name: buccal swab at age 10

value: Age 10

tag: disease state


title: HLO_Day50_replicate_1

tag: cell line

tag: replicate

tag: time


title: Individual 1, PMI 3

tag: individual

tag: age (years)

tag: weight (kg)

tag: height (cm)

tag: bmi

tag: sampling date (dd-mm-yy)


title: HLO_Day35_replicate_2

tag: tissue


title: HLO_Day35_replicate_1


title: 29_2_18C

tag: familyid

tag: twinid

tag: age

tag: smokingpackyears

tag: category


title: 30_2_10

tag: gender

value: Notexposed


title: 117_2_450K

description:
comments: NA
genomic DNA from blood samples
Overlaping_probes_normalised_seperately_450K_betas.csv, Overlaping_probes_normalised_together_450K_EPIC_betas.csv

tag: disease state


title: 118_1_450K

value: Male


title: Individual 1, PMI 0

source_name: Vena Subclavian Right

value: blood

value: male

tag: race

tag: death date (dd-mm-yy)

tag: time of death (tod) (h)

tag: time of death error

tag: post mortem interval (pmi) (h)


title: HLO_Day25_replicate_2

tag: cell line

tag: replicate

tag: time


title: 117_1_450K


title: 29_2_18B

description:
comments: This sample matched with  29_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: PsA-3849

city: Toronto

first: Vinod

last: Chandran

state: Ontario

address: 399 Bathurst Street

department: Krembil Research Institute

country: Canada

institute: University Health Network

data_processing:
FASTQ data files were aligned to the human genome (GRCh38) using the STAR aligner (STAR v2.5.2b).
Feature-barcode (Gene-barcode) expression matrices were obtained using the CELLRANGER (v3.0.2) pipeline.
Genome_build: GRCh38
Supplementary_files_format_and_content: Barcodes files containing cellular barcode sequences corresponding to the column indices of the filtered feature-barcode matrix
Supplementary_files_format_and_content: Features files containing feature annotation and correspond to the row indices of the filtered feature-barcode matrix
Supplementary_files_format_and_content: Matrix files containing values of the filtered feature-barcode matrix (without background and cell-associated barcodes)

source_name: Synovial fluid

extract_protocol:
Synovial fluid was obtained during routine joint aspirations
10X Genomics Chromium platform. A total of 1000 cells were captured for each sample and sequencing was performed to a depth of 60,000 reads per cell on the Illumina NextSeq 500.

tag: disease

value: Psoriatic arthritis

value: Synovial fluid


title: 116_1_450K

tag: tissue


title: PsA-3830


title: Individual 1, PMI 9

source_name: Vena femoralis left

tag: individual

tag: age (years)

tag: weight (kg)

tag: height (cm)

tag: bmi

value: caucasian

tag: sampling date (dd-mm-yy)


title: PsA-22228


title: 115_2_450K

tag: familyid

tag: twinid

tag: gender

tag: age

tag: disease state

tag: smokingpackyears

tag: category


title: 118_2_450K


title: 29_1_5

value: Buccal


title: 29_2_5

value: Age 5


title: 29_1_18C

value: Exposed


title: HLO_Day9_replicate_2

tag: cell line

tag: replicate


title: 29_1_18B

description:
comments: This sample matched with  29_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 115_1_450K


title: HAL-8_2

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

country: Germany

institute: Martin Luther University Halle-Wittenberg

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20 --trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters  -p 6 --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.89)
Gene expression was assessed using R/edgeR using TMM normalization and FPKM transformation
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including FPKM values for each sample

source_name: GBM-derived cell line

growth_protocol: HAL cells were cultured in neural stem cell (NSC) medium (DMEM/F-12 and Neurobasal medium (1:1) supplemented with B27 supplement, bFGF and EGF (20 ng/ml each)). Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
1µg of total RNA served as input for rRNA depletion using RiboCop v1.2 (Lexogen). NEBNext Ultra Directional RNA Library kit (NEB) was used for library generation. Sequencing was performed on the Illumina NextSeq platform

treatment_protocol: 1x10^6 cells were used for RNA extraction.

tag: primary cell line

tag: brain tumor

value: patient-derived GBM 8


title: HAL-8_1


title: 114_2_450K

tag: tissue


title: 29_1_10


title: HLO_Day25_replicate_1

tag: time


title: 113_1_450K


title: HLO_Day9_replicate_1


title: HAL-4_2

value: patient-derived GBM 4


title: HAL-4_1


title: 28_2_5

value: Female


title: HLO_Day5_replicate_2


title: 113_2_450K

value: Age 18


title: HAL-1_2

value: patient-derived GBM 1


title: 29_2_10


title: HLO_Day5_replicate_1

value: hPSC-derived Lung Organoid


title: HLO_Day15_replicate_2


title: HLO_Day0_replicate_2


title: 116_2_450K

value: Blood


title: HLO_Day15_replicate_1


title: 28_2_18C

value: Notexposed


title: 112_1_450K


title: 28_2_18B

description:
comments: This sample matched with  28_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: HAL-1_1


title: 112_2_450K


title: KNS-42_2 [miRNA-Seq]

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 16
the first and the last 4 nucleotides added during the NextFlex library preparation were trimmed off using Cutadapt (v 1.14) with parameters -m 16 -u 4/-4
Trimmed reads were mapped against the human genome (hg38 UCSC) usingBowtie2 (v 2.3.3) with parameters -N 1 --un-gz
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 1-T 6  -t miRNA -g ID and miRBase annotations (v21)
Gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization and CPM transformation
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including CPM values for each sample

growth_protocol: HAL cells were cultured in neural stem cell (NSC) medium (DMEM/F-12 and Neurobasal medium (1:1) supplemented with B27 supplement, bFGF and EGF (20 ng/ml each)). KNS42 cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
2µg of total RNA served as input for library generation with NEXTFLEX® Small RNA-Seq Kit v3 for Illumina® Platforms (PerkinElmer). Sequencing was performed on an Illumina NextSeq platform

value: cell line


title: HLO_Day0_replicate_1


title: 28_2_10

value: Age 10


title: 111_2_450K

value: Male


title: 28_1_5


title: 111_1_450K


title: KNS-42_1 [miRNA-Seq]


title: IPF F18536 CD45+

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

data_processing:
FASTQ files were generated using the Cell Ranger v3.0.2 (10X Genomics) bcl2fastq (Illumina) wrapper.
Sequencing reads were assembled and aligned against the GENCODE basic human reference using Cell Ranger v3.0.2 (10X Genomics) to generate count matrices.
Genome_build: GRCh38
Supplementary_files_format_and_content: HDF5 gene count matrices

source_name: lung explant

extract_protocol:
After bronchoalveolar lavage, fresh lung explant tissue was stored in complete media on wet ice overnight. The tissue was washed in HBSS and then thoroughly minced in digestion buffer (HBSS, 2.5mg/mL Collagenase D, 100ug/mL DNAse). Minced tissue was rocked 45 minutes at 37C. Residual tissue material was transferred into fresh digestion buffer and rocked another 45 minutes at 37C. Single cells from both rounds of digest were combined and utilized for downstream analyses. Single cell preparations were labeled with a cocktail of fluorescently labeled antibodies including, CD45(BUV421), EpCAM(PE) , CD31(PE-CY7) , CD90(APC), Live/Dead(eFluor 780), and then subjected to fluorescence-activated cell sorting (FACS) to isolate specific populations.
Single-cell RNA-seq library preparation was performed using the 10x Genomics Chromium platform with the Single Cell 3’ Library and Gel bead kit v2 following the manufacturer’s user guide.

tag: disease

value: IPF

value: lung

tag: cell type


title: IPF F18536 Unsorted

value: Unsorted


title: HAL-8_2 [miRNA-Seq]


title: HAL-8_1 [miRNA-Seq]


title: IPF F18536 CD31+


title: 28_1_18B

description:
comments: This sample matched with  28_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

extract_protocol: genomic DNA was extracted and purified from buccal and blood samples using standardised protocols.


title: 28_1_18C

value: Buccal


title: IPF F18536 EPCAM+

value: EPCAM+


title: 110_1_450K


title: HAL-4_2 [miRNA-Seq]


title: 28_1_10


title: 109_2_450K


title: 27_2_5

value: Age 5


title: IPF F18536 Triple-

value: Triple-


title: 109_1_450K


title: HAL-4_1 [miRNA-Seq]

value: patient-derived GBM 4


title: 27_2_18C

value: Female


title: 108_2_450K

value: Age 18


title: HAL-1_2 [miRNA-Seq]

value: patient-derived GBM 1


title: Control N1865 Unsorted

source_name: transplant rejection lung

value: Control


title: HAL-1_1 [miRNA-Seq]


title: 27_2_18B

description:
comments: This sample matched with  27_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: Control N1865 CD31+


title: Control N1865 CD45+


title: 27_2_10

value: Notexposed


title: 110_2_450K


title: Control N1865 EPCAM+


title: 27_1_5

value: Exposed


title: MGC8

city: Tallinn

first: Ilmatar

last: Rooda

address: Akadeemia tee 15

department: Chemistry and Biotechnology

country: Estonia

institute: Tallinn University of Technology

data_processing:
Raw FASTQ files were quality-filtered with Trimmomatic v 0.39  with the options of SLIDINGWINDOW:2:20.  Adapter sequences (3´adapter AACTGTAGGCACCATCAAT and 5´ adapter GTTCAGAGTTCTACAGTCCGACGATC) were removed and reads below 17 nucleotides in length were discarded and the remaining filtered and trimmed reads were counted and mapped to the primary assembly of human genome GRCh38 using miRDeep2 with standard settings
Count tables from individual samples were merged using edgeR package v.3.28.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw miRNA counts for every gene and every sample

source_name: Ovarian follicle

extract_protocol:
FF containing all cellular material was collected from the first aspirated follicle visibly clear of blood contamination. The sample was first centrifuged 10 minutes at 300g to remove large cells. The supernatant was subsequently centrifuged 10 minutes at 2000g to remove cell debris. The final cell-free FF was stored at -80°C until further analysis. The cell pellets (MGC) were lysed using QIAzol Lysis Reagent (QIAGEN, Hilden, Germany) and stored at -80°C until RNA extraction. For extracellular vesicles extraction five hundred µl of each FF sample was concentrated to 150 µl using Amicon® Ultra 2 centrifugal filter units (10 kDa) (Merck Millipore Ltd, Ireland). Commercially available size exclusion chromatography (SEC) column (qEVsingle/70 nm by Izon Sciences, UK) was used for the isolation of EVs. The column was prewashed with 10 ml filtered (0.2 µm Ministart® syringe filters) Dulbecco’s phosphate-buffered saline (DPBS, Sigma® Life Science, UK) and 150 µl of the concentrated sample was added to the top of the column filter until it passed down the filter.  DPBS was added immediately on the top of the column filter and a total of 20 fractions, 200 µl each, was collected separately. From all sample types RNA was extracted using miRNEASY Micro kit (QIAGEN).
Small RNA libraries were prepared with QIAseq miRNA Library Kit (QIAGEN) according to the manufacturer’s protocol. Starting amount of RNA in library preparation was 10ng from cellular small RNA fraction and 5µl of RNA from EV and FF samples. The size of libraries was estimated with Agilent DNA High Sensitivity chips on the Agilent 2100 Bioanalyzer system (Agilent Technologies). Library concentrations were measured using Qubit High Sensitivity Assay kit (ThermoFisher Scientific) before pooling in equimolar amounts. Single-end sequencing of 75 bp length was performed on NextSeq 500 platform with NextSeq 500/550 High Output Kit v2.5 (Illumina, San Diego, CA, USA).

tag: group

value: PCOS

value: mural granulosa cells


title: 107_1_450K

data_processing: Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions. Normalized betas using dasen function

value: Male


title: Control N1865 Triple-

value: lung


title: MGC7


title: IPF F18545 Unsorted

value: IPF

value: Unsorted


title: 107_2_450K


title: 106_2_450K


title: MGC6


title: 27_1_18B

description:
comments: This sample matched with  27_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 27_1_18C

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv

value: Buccal


title: IPF F18545 CD45+


title: MGC5

value: donor


title: 106_1_450K


title: 26_2_5

value: Age 5


title: 27_1_10

value: Age 10


title: 105_2_450K


title: IPF F18545 EPCAM+

value: EPCAM+


title: IPF F18545 CD31+


title: MGC4


title: 108_1_450K

value: Age 18


title: MGC9


title: 105_1_450K


title: IPF F18545 Triple-

value: Triple-


title: 104_2_450K


title: 26_2_18C

value: Female


title: 104_1_450K

value: Blood


title: 26_2_18B

description:
comments: This sample matched with  26_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: IPF F18555 Unsorted


title: 26_2_10


title: MGC2


title: 103_1_450K


title: 26_1_5

value: Notexposed


title: MGC16


title: IPF F18555 CD45+


title: 26_1_18C


title: MGC14


title: 103_2_450K


title: MGC15


title: IPF F18555 EPCAM+


title: IPF F18555 CD31+


title: MGC3


title: 26_1_18B

description:
comments: This sample matched with  26_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 102_2_450K


title: MGC13


title: IPF F18555 Triple-


title: 102_1_450K


title: 26_1_10


title: MGC12


title: 25_2_5


title: 101_1_450K


title: Control N1857 CD45+

value: Control


title: 101_2_450K


title: MGC11

value: PCOS


title: Control N1857 Unsorted


title: 25_2_18C


title: 100_1_450K


title: Control N1857 CD31+


title: MGC10

value: mural granulosa cells


title: 25_2_18B

description:
comments: This sample matched with  25_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 100_2_450K


title: FF8

value: follicular fluid


title: 99_1_450K


title: Control N1857 Triple-

value: lung


title: FF7


title: 25_2_10


title: 25_1_5


title: SSc-ILD S19578 CD45+

value: SSc-ILD


title: 98_1_450K

value: Male


title: 25_1_18B

description:
comments: This sample matched with  25_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: SSc-ILD S19578 CD31+


title: SSc-ILD S19578 EPCAM+


title: FF5


title: FF4


title: FF6


title: 25_1_10

value: Buccal


title: 24_2_5


title: 98_2_450K


title: 97_2_450K


title: SSc-ILD S19578 CD90+


title: Control N1857 EPCAM+


title: 24_2_18C


title: FF9


title: FF2

value: donor


title: SSc-ILD S19584 CD31+


title: 96_2_450K


title: FF3


title: FF16


title: 99_2_450K


title: 24_2_10


title: 96_1_450K


title: 25_1_18C


title: FF15


title: 95_1_450K


title: SSc-ILD S19584 Triple-


title: 24_2_18B

description:
comments: This sample matched with  24_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 24_1_5

value: Age 5

value: Exposed


title: FF14


title: 24_1_18C


title: 95_2_450K


title: 97_1_450K


title: SSc-ILD S19584 CD45+


title: 94_1_450K


title: FF13


title: 24_1_18B

description:
comments: This sample matched with  24_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 94_2_450K


title: FF11


title: SSc-ILD S19600 Triple-


title: SSc-ILD S19600 CD31+


title: SSc-ILD S19600 CD45+


title: 24_1_10

value: Age 10


title: SSc-ILD S19584 EPCAM+

value: EPCAM+


title: FF12


title: FF10


title: 23_2_5


title: SSc-ILD S19600 EPCAM+HT2-280-


title: SSc-ILD S19600 EPCAM+HT2-280+


title: 93_2_450K

value: Age 18


title: 23_2_18B

description:
comments: This sample matched with  23_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Female


title: 92_1_450K

value: Blood


title: EV8

value: extracellular vesicles


title: Control N1902 CD45+

value: Control


title: EV9

value: PCOS


title: 92_2_450K


title: 23_2_10


title: 91_1_450K


title: 93_1_450K


title: EV7


title: Control N1902 EPCAM+


title: EV6


title: 23_1_5


title: 91_2_450K


title: 90_2_450K


title: 23_2_18C


title: Control N1902 CD90+


title: 23_1_18C


title: EV5


title: EV4


title: 23_1_10


title: IPF F19609 CD45+

value: IPF


title: Control N1902 Triple-

value: Triple-


title: 89_1_450K


title: 23_1_18B

description:
comments: This sample matched with  23_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: EV2


title: Control N1902 CD31+

value: lung


title: 22_2_5


title: 89_2_450K


title: IPF F19609 CD90+


title: 22_2_18C


title: EV16


title: 88_2_450K


title: IPF F19609 EPCAM+SAbGAL-

value: EPCAM+SAbGAL-


title: EV15


title: 88_1_450K

value: Male


title: 22_2_10

value: Buccal


title: IPF F19609 EPCAM+SAbGAL+

value: EPCAM+SAbGAL+


title: EV14

value: donor


title: 22_2_18B

description:
comments: This sample matched with  22_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Exposed


title: EV3


title: 22_1_5

value: Age 5

value: Notexposed


title: 90_1_450K

description:
comments: NA
genomic DNA from blood samples
Overlaping_probes_normalised_seperately_450K_betas.csv, Overlaping_probes_normalised_together_450K_EPIC_betas.csv

value: Age 18


title: 87_2_450K

value: Female


title: 22_1_18C


title: PRO-seq_rep1

city: Cold Spring Harbor

first: Yixin

last: Zhao

state: NEW YORK

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
Library strategy: PRO-seq
For PRO-seq, raw data files in fastq format were trimmed using Cutadapt (Martin 2011) with parameters (-j 0 -e 0.10 --minimum-length=10 -a GGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAG).
For PRO-seq and RNA-seq, clean reads were then aligned to human genome (GRCh38) using HISAT2 (Kim et al. 2019) with default parameters.
HTSeq (Anders et al. 2015) was used for read counting with parameters (-m union -f bam -s reverse --order pos). The coordinates of the longest transcript for every gene were used for read counting. Importantly, for PRO-seq, we omitted the first 500 bases downstream of the TSS and 500 bases upstream of TES to avoid a bias in read counts from promoter proximal pausing and polymerase deceleration.
Genome_build: GRCh38
Supplementary_files_format_and_content: *counts.txt: Tab-delimited text files include transcript name and read (raw) count for each sample.

growth_protocol: Human K562 cells were cultured using standard cell culture procedures and sterile techniques. The cells were cultured in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
For PRO-seq, RNA preparation follows protocol from Mahat et al. (2016). Library construction follows method from Chu et al. (2018). Sequencing was done by Novogene on a HiSeq instrument with paired-end reads of 2×150bp.
For RNA-seq, RNA was extracted using the Trizol method (see https://assets.thermofisher.com/TFS-Assets/LSG/manuals/trizol_reagent.pdf), followed by rRNA depletion using the Ribozero HMR Gold kit. Libraries were prepared using the NEB kit with TruSeq RNAseq adaptors. Single-end sequencing (length=75) was performed on a NextSeq500 instrument by the RNA Sequencing Core at the College of Veterinary Medicine, Cornell University.

treatment_protocol: No specific treatments performed for this study.

value: Chronic myelogenous leukemic cell line


title: EV13

value: extracellular vesicles


title: 86_2_450K

first: Chloe

last: Wong

institute: King's College London

value: Blood


title: EV11

value: PCOS


title: IPF F19609 CD31+

value: IPF


title: 22_1_18B

description:
comments: This sample matched with  22_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Microglia + Mg-TAM subset of mouse CCR2 WT GBM: tumor surrounding brain (different sample)

description:
WT5wb_K13
Microglia + Mg-TAM subset of mouse CCR2 WT GBM: tumor (same samples as in Mouse_GBM) + tumor surrounding brain (different sample)

source_name: glioblastoma/tumor surrounding brain

tag: strain background

value: glioblastoma/tumor surrounding brain tissue

tag: platform

value: 10x Genomics


title: 87_1_450K

tag: familyid

tag: twinid


title: EV12


title: mouse GBM: CCR2 knockout 3

description:
KO3_K9
processed data file:
Mouse.GBM.KO1_2_3.WT1_2_3.filtered.gene.bc.matrix.csv
annot.Mouse.GBM.KO1_2_3.WT1_2_3.csv

tag: genotype

value: CCR2 knockout

value: glioblastoma tissue

value: Grade IV glioblastoma

tag: number of cells


title: 86_1_450K

tag: gender

tag: age

tag: disease state

tag: smokingpackyears


title: 85_1_450K

value: Male

tag: category


title: mouse GBM: CCR2 knockout 2

description:
KO2_K8
processed data file:
Mouse.GBM.KO1_2_3.WT1_2_3.filtered.gene.bc.matrix.csv
annot.Mouse.GBM.KO1_2_3.WT1_2_3.csv


title: RNA-seq_rep4

data_processing:
For PRO-seq, raw data files in fastq format were trimmed using Cutadapt (Martin 2011) with parameters (-j 0 -e 0.10 --minimum-length=10 -a GGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAG).
For PRO-seq and RNA-seq, clean reads were then aligned to human genome (GRCh38) using HISAT2 (Kim et al. 2019) with default parameters.
HTSeq (Anders et al. 2015) was used for read counting with parameters (-m union -f bam -s reverse --order pos). The coordinates of the longest transcript for every gene were used for read counting. Importantly, for PRO-seq, we omitted the first 500 bases downstream of the TSS and 500 bases upstream of TES to avoid a bias in read counts from promoter proximal pausing and polymerase deceleration.
Genome_build: GRCh38
Supplementary_files_format_and_content: *counts.txt: Tab-delimited text files include transcript name and read (raw) count for each sample.

tag: cell line


title: 21_2_5

tag: tissue

value: Buccal


title: PRO-seq_rep2


title: 21_2_18C

value: Exposed


title: mouse GBM: CCR2 knockout 1

description:
KO1_K2
processed data file:
Mouse.GBM.KO1_2_3.WT1_2_3.filtered.gene.bc.matrix.csv
annot.Mouse.GBM.KO1_2_3.WT1_2_3.csv


title: mouse GBM: WT 3

description:
WT3_K7
processed data file:
Mouse.GBM.KO1_2_3.WT1_2_3.filtered.gene.bc.matrix.csv
annot.Mouse.GBM.KO1_2_3.WT1_2_3.csv

value: WT


title: RNA-seq_rep2


title: 84_1_450K


title: RNA-seq_rep3


title: 84_2_450K


title: 21_2_18B

description:
comments: This sample matched with  21_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: mouse GBM: WT 2

description:
WT2_K6
processed data file:
Mouse.GBM.KO1_2_3.WT1_2_3.filtered.gene.bc.matrix.csv
annot.Mouse.GBM.KO1_2_3.WT1_2_3.csv


title: 83_2_450K


title: RNA-seq_rep1


title: 22_1_10

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv

value: Age 10

value: Notexposed


title: 21_1_5

value: Age 5


title: 21_2_10


title: mouse GBM: WT 1

description:
WT1_K1
processed data file:
Mouse.GBM.KO1_2_3.WT1_2_3.filtered.gene.bc.matrix.csv
annot.Mouse.GBM.KO1_2_3.WT1_2_3.csv


title: ARC185-WCL

city: Stanford

first: Jennifer

last: Shadrach

address: 290 Jane Stanford Way, Room E365

department: Neurosurgery

institute: Stanford University

data_processing:
Reads were aligned to the mm10 genome using STAR version 2.5.2a
Bam files were generated using SAMtools version 0.1.19
Statistical analyses of enriched or differentially expressed genes were performed using cuffdiff in cufflinks version 2.2.1
Data were extracted and visualized using cummeRbund version 2.7.2
Gene ontology analyses were performed using ClueGO
Genome_build: mm10
Supplementary_files_format_and_content: Text files containing per-gene expression values and statistical analysis results

source_name: Spinal Cord Input

extract_protocol:
Mice were transcardially perfused with phosphate-buffered saline (PBS). The entire spinal cord was rapidly isolated by hydraulic extrusion and then the lumbar segment was further dissected for subsequent analysis (Injury L3-L6, ALS entire lumbar cord). Spinal cord samples were snap frozen in liquid nitrogen. Tissues were placed into IP buffer (50 mM Tris, pH 7.4, 100 mM KCl, 12 mM MgCl2, 1% Nonidet P-40 [NP-40] supplemented with 200 U/mL Promega RNasin, 1 mg/mL heparin, 100µg/mL cycloheximide, and protease inhibitor mixture [Sigma-Aldrich]) and subjected to Dounce homogenization. Samples were then rotated at 4°C for 15-20 minutes followed by centrifugation at 10,000 x g for 10 min at 4°C to generate a postmitochondrial supernatant. A 50µl aliquot of the input was saved and processed separately for RNA isolation. The remainder of the sample was precleared with Protein G magnetic beads (25 µl of beads per 200 µl of supernatant, New England Biolabs) for 1 hour under constant rotation at 4°C. After preclearing, samples were separated from the magnetic beads and incubated with an HA antibody (1:150 dilution, #MMS-101P, BioLegend) by toppling at 4°C for 4 hours. Protein G magnetic beads were then added and allowed to incubate under rotation at 4°C overnight. The IP product associated with the magnetic beads was then washed 3 times in high salt buffer (50 mM Tris, pH 7.4, 300 mM KCl, 12 mM MgCl2, 1% NP-40 supplemented with 100 µg/mL cycloheximide). RNA associated with the HA IP and from the input lysates was isolated using the RNeasy Plus Micro Kit (Qiagen) per manufacturer instructions.
The purity and quality of isolated RNA was confirmed by Bioanalyzer or TapeStation (Agilent Genomics). SMART-Seq v4 Ultra Low input RNA kit (Takara) was used to synthesize cDNA from 4ng of RNA using 11 cycles of cDNA amplification, according to manufacturer’s protocols. The cDNA was sheared by Covaris and quantitated by Qbit dsDNA HS Assay kit (ThermoFisher). Libraries were prepared from 5 ng cDNA using SMARTer ThruPLEX DNA-Seq kit (Takara) with 8 cycles of PCR according to manufacturer’s protocols. Final libraries were checked for quality and quantity by the Bioanalyzer or TapeStation (Agilent Genomics) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (#KK4835, Kapa Biosystems).

tag: strain

tag: injury/age

value: RiboWT


title: 21_1_18C

city: London

address: MRC SGDP Centre, Institute of Psychiatry,

value: Age 18


title: EV10

value: extracellular vesicles


title: 83_1_450K

source_name: whole blood at age 18

value: Female

value: Blood


title: ARC179-WCL


title: H226 FIBULIN-3 KD 1

city: Syracuse

first: Mariano

middle: S

last: Viapiano

state: NY

address: 505 Irving Ave Rm 4604

department: Neuroscience and Physiology

institute: SUNY Upstate Medical University

description: polyA RNA was isolated and used for library prep

data_processing:
Samples were barcoded and run in the 4 lanes of NextSeq 500, generating 4 FASTQ files per sample. FASTQ files were not merged until gene quantification step
Basecalls were performed using Illumina's Real-Time Analysis (RTA) v2 in the NextSeq 500 instrument
Sequenced reads (75 bases, single-end) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the human hg38 genome using  Bowtie 1.0.0 with parameters: -S -q -n 2 -l 30 -e 70 --tryhard -k 1 --best
Aligned reads were quantified to the annotation model using Partek E/M tool (Partek Flow) to generate total gene counts and total transcript counts, using parameters: --feature_type RefSeq --min_unexplained 30 --require_proper_pair --strand_specific auto --check_junctions --exon_overlap percent --overlap_percent 95 --overlap_bases 100 --min_coverage 1
Total gene counts were re-scaled in Partek Flow to remove batch effect (removed factors: cell line and total counts), in order to identify changes caused by fibulin-3 knockdown that were common to both cell lines
Batch-corrected gene counts were compared by ANOVA with multiple-comparison corrections (Q value <= 0.05).
Genes differentially expressed between control and KD conditions (Q<=0.05 and change <=-1.5 fold or >=1.5 fold) were uploaded to GO Consortium to identify geneset enrichment
Genes differentially expressed between control and KD conditions (Q<=0.05 and change <=-1.5 fold or >=1.5 fold) were uploaded to KEGG database to identify pathway enrichment
Genome_build: Human hg38
Supplementary_files_format_and_content: Tab-delimited files represent total gene counts or total transcript counts (before normalization and after batch-adjustement)
Supplementary_files_format_and_content: MM cells_PartekEM_total gene counts_raw.txt: Total gene counts per sample, before normalization
Supplementary_files_format_and_content: MM cells_PartekEM_total transcript counts_raw.txt: Total transcript counts per sample, before normalization
Supplementary_files_format_and_content: MM cells_PartekEM_total gene counts_batch-adjusted.txt: Total gene counts per sample, batch-adjusted
Supplementary_files_format_and_content: MM cells_PartekEM_total transcript counts_batch-adjusted.txt: Total transcript counts per sample, batch-adjusted

molecule: polyA RNA

source_name: Human mesothelioma cells

growth_protocol: Cells were seeded in triplicate in 60mm dishes at a density of 5x10E5 cells/ml (3 ml total volume) and were cultured until sub-confluent. Culture medium was DMEM (glucose 4.5 g/L) + 10% fetal bovine serum and standard antibiotics

extract_protocol:
Total RNA isolated from frozen cell pellets was extracted using Invitrogen PureLink RNA Mini Kit Spin Column 250 (cat #12-183-025). RNA was quantified and assesed for integrity using the  Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA).
Libraries were constructed using Illumina TruSeq stranded RNA kit with Ribo-Zero Globin kit following the manufacturer's instructions (Illumina, San Diego CA)

treatment_protocol: Each cell plate was independently transfected with a mixture of two fibulin-3 siRNAs or a non-targeting control siRNA (Qiagen AllStars negative control), using Lipofectamine 2000. Culture medium was changed to Opti-MEM 24h after transfection and the cells were collected after 24h in Opti-MEM (i.e., 48h after transfection).

tag: genotype/variation

value: fibulin-3 knockdown

tag: tumor type

value: Malignant mesothelioma


title: 82_2_450K


title: H226 FIBULIN-3 KD 3


title: 21_1_18B

description:
comments: This sample matched with  21_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: H226 FIBULIN-3 KD 2


title: 82_1_450K


title: 21_1_10


title: H226 CONTROL 3

value: control


title: ARC132-WCL


title: 81_1_450K


title: ARC185

source_name: Spinal Cord IP


title: 81_2_450K


title: 20_2_5

source_name: buccal swab at age 5


title: 20_2_18C


title: ARC179


title: H226 CONTROL 1


title: 80_2_450K


title: 20_2_18B

description:
comments: This sample matched with  20_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 20_2_10


title: H2595 FIBULIN-3 KD3


title: ARC170-WCL

value: RiboALS


title: 80_1_450K


title: ARC132


title: 20_1_5


title: ARC171-WCL


title: H2595 FIBULIN-3 KD2


title: 78_1_450K


title: 79_2_450K


title: ARC171


title: ARC139-WCL


title: H2595 FIBULIN-3 KD1


title: 79_1_450K


title: H2595 CONTROL 3


title: 20_1_18C


title: 20_1_18B

description:
comments: This sample matched with  20_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 78_2_450K


title: H2595 CONTROL 2


title: H226 CONTROL 2


title: ARC139


title: 77_2_450K


title: 20_1_10


title: 19_2_5


title: Sample 18 OAC TRG 5

city: Bedford Park

first: George

last: Mayne

state: SA

address: Room 3D213, Dept of Surgery, Flinders Medical Center

department: Surgery

country: Australia

institute: Flinders University of South Australia

data_processing:
Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq software (Illumina inc.). FASTQ data were checked using the FastQC tool.
Cutadapt (1.11) was used to extract information of adapter and unique molecular identifiers in raw reads, and the output from Cutadapt was used to remove adapter sequences and to collapse reads by the unique molecular identifiers.
Bowtie2 (2.2.2) was used for mapping the reads against the human reference genome (Gencode GRCh37) using miRBase version 20 annotation.
Differential expression analysis was performed using the EdgeR statistical software package (Bioconductor, http://bioconductor.org/). For normalization, the trimmed mean of M-values method based on log-fold and absolute gene-wise changes in expression levels between samples (TMM normalization) was used. Mann Whitney U tests were used to determine the significance of differential expression.
Genome_build: Gencode GRCh37
Supplementary_files_format_and_content: read counts

source_name: serum small extracellular vesicles

extract_protocol:
Extraction of miRNA from small EVs was performed using the commercial miRNeasy Serum/Plasma kit (QIAGEN, #217184) according to the manufacturer’s protocol.  Five microlitres (0.1 picomole) of each of the synthetic RNA molecules ath-miR-159a and cel-miR-54 (Shanghai Genepharma Co.Ltd.) were added to the 500 µl QIAzol vesicle lysate before further processing. Twenty-four µl of RNase-free ultrapure water was used for the final RNA elution step.
The library preparation was done using the QIAseq miRNA Library Kit (QIAGEN). A total of 5µL total RNA was converted into miRNA NGS libraries. Adapters containing unique molecular identifiers were ligated to the RNA. Then RNA was converted to cDNA, and the cDNA was amplified, with the addition of indices, using 22 cycles of PCR. The samples were then purified, and library preparation QC was performed using a Bioanalyzer 2100 (Agilent). The libraries were pooled in equimolar ratios based on the quality of the inserts and the concentration measurements.

treatment_protocol: Patients received a nCRT protocol that included radiation (41.4 Gy), carboplatin and paclitaxel.

tag: tumor response grade (mandard)

value: TRG 5

tag: pre-treatment tnm staging


title: ARC85-WCL


title: 77_1_450K

tag: familyid

value: Male


title: Sample 17 OAC TRG 5


title: 19_2_18C

source_name: buccal swab at age 18

tag: twinid

value: Buccal


title: 19_2_18B

description:
comments: This sample matched with  19_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 76_2_450K


title: ARC77-WCL

tag: genotype


title: ARC76-WCL


title: ARC98-WCL


title: 75_1_450K


title: Sample 14 OAC TRG 4

value: TRG 4


title: 19_1_5


title: 19_2_10


title: ARC170


title: Sample 15 OAC TRG 5


title: H2595 CONTROL 1


title: Sample 13 OAC TRG 4


title: 74_1_450K


title: ARC85


title: ARC77


title: 19_1_18B

description:
comments: This sample matched with  19_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 74_2_450K

description:
comments: NA
genomic DNA from blood samples
Overlaping_probes_normalised_seperately_450K_betas.csv, Overlaping_probes_normalised_together_450K_EPIC_betas.csv


title: Sample 12 OAC TRG 4


title: Sample 11 OAC TRG 4


title: 19_1_10


title: 76_1_450K


title: Sample 10 OAC TRG 4


title: Sample 16 OAC TRG 5


title: ARC98


title: 73_1_450K


title: ARC82-WCL


title: 73_2_450K


title: Sample 9 OAC TRG 4


title: 18_2_18B

description:
comments: This sample matched with  18_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Exposed


title: 75_2_450K


title: 18_2_18C


title: ARC99-WCL


title: 72_1_450K


title: 19_1_18C


title: ARC81-WCL


title: Sample 8 OAC TRG 4


title: ARC82


title: 18_2_10

value: Age 10


title: Sample 7 OAC TRG 4


title: ARC76


title: Sample 6 OAC TRG 1

value: TRG 1

value: TNM


title: 71_1_450K


title: 18_1_5

value: Age 5

value: Notexposed


title: ARC81


title: 18_2_5


title: Sample 5 OAC TRG 1


title: ARC99


title: 18_1_18C

value: Age 18


title: 70_1_450K

value: Female


title: 18_1_18B

description:
comments: This sample matched with  18_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: 70_2_450K


title: ARC161-WCL

value: RiboWT


title: Sample 4 OAC TRG 1


title: Sample 3 OAC TRG 1


title: 69_2_450K


title: ARC153-WCL


title: 17_2_5


title: 69_1_450K


title: ARC145-WCL


title: Sample 2 OAC TRG 1


title: 71_2_450K


title: 17_2_18C


title: Sample 1 OAC TRG 1


title: ARC161


title: 17_2_18B

description:
comments: This sample matched with  17_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: ARC153


title: CLL_CPT1_M27

city: TOULOUSE

first: Anne

last: QUILLET-MARY

state: Select

address: Av Hubert Curien, CS 53717, CS 53717

department: INSERM U1037/CNRS ERL5294

country: France

institute: CRCT

data_processing:
Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v3.0.2).
Fastq files were then run with count application (Cell Ranger v3.0.2) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and antibodies

source_name: Peripheral Blood mononuclear cells

growth_protocol: frozen PBMCs

extract_protocol: Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 14 cycles used for cDNA amplification and 12 cycles for library amplification

treatment_protocol: in vivo Ibrutinib treatment

tag: time point

value: 27 months

tag: agent

value: Ibrutinib


title: 68_1_450K

tag: gender

tag: age


title: 68_2_450K

tag: disease state

tag: smokingpackyears


title: 17_2_10

source_name: buccal swab at age 10

tag: category


title: CLL_CPT1_M3

value: 3 months


title: ARC145


title: 67_2_450K

tag: tissue


title: CLL_CPT1_M0

value: Before treatment


title: 17_1_18C


title: 67_1_450K


title: 18_1_10

value: Male


title: ARC160-WCL

tag: strain

value: RiboALS


title: ARC159-WCL

tag: injury/age


title: 66_2_450K


title: 66_1_450K


title: 16_2_5

value: Buccal


title: ARC152-WCL


title: 17_1_10

value: Exposed


title: 65_2_450K


title: ARC160


title: ARC152


title: 16_2_18C


title: 72_2_450K


title: 65_1_450K


title: 64_1_450K


title: 16_2_18B

description:
comments: This sample matched with  16_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: ARC159


title: 16_2_10

value: Age 10


title: UNT-RC179-WCL

value: UNJ

value: RiboHO;ChATCre+


title: 17_1_5

value: Age 5


title: 63_2_450K


title: UNT-RC176-WCL


title: 16_1_5

value: Notexposed


title: 17_1_18B

description:
comments: This sample matched with  17_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Age 18


title: 63_1_450K

value: Female


title: UNT-RC179


title: UNT-RC177-WCL


title: 62_1_450K

value: Blood


title: 16_1_18C


title: 62_2_450K


title: UNT-RC176


title: 16_1_10


title: 61_1_450K


title: 15_2_5


title: 16_1_18B

description:
comments: This sample matched with  16_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 61_2_450K


title: D7-RC176-WCL


title: 64_2_450K


title: UNT-RC177


title: 85_2_450K


title: 15_2_18C


title: D7-RC179-WCL


title: 60_1_450K


title: D7-RC177-WCL


title: 15_2_18B

description:
comments: This sample matched with  15_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 60_2_450K


title: C1_neuron [Batch 5, Sample 31]

city: Charlottesville

first: Douglas

last: Bayliss

state: VA

address: 1340 Jefferson Park Ave.

department: Pharmacology

institute: University of Virginia

data_processing:
fastq files were quasi-mapped to the mouse refernce transcriptome (Ensemble GRCm38)  using salmon  with parameters quant -p 12 --seqBias --gcBias -l A
Transcript abundance was summarized to   the gene level normalized as transcripts per  million (TPM), according to Soneson et al.  F1000Res  4:1521 (2015)
Genome_build: GRCm38
Supplementary_files_format_and_content: tpm-all-genes

source_name: RTN region

growth_protocol: mice kept in standard UVA vivarium, food ad lib and 12:12 light dark schedule

extract_protocol:
brainstem slice preparation; GFP-expressing cells harvested into micropipette under fluorescence microscopy
Nextera XT DNA Library kit (Illumina, catlog #FC-131-1096; RRID:SCR_010233)

value: Jx99 (Phox2b::GFP)

tag: single cell information

value: single cell

value: wild type


title: D7-RC176


title: rtn_neuron [Batch 5, Sample 32]


title: P2b_neuron [Batch 5, Sample 30]

value: single cell GAD contaminated


title: 15_2_10


title: 15_1_5


title: 59_1_450K


title: 59_2_450K


title: 15_1_18C


title: P2b_neuron [Batch 5, Sample 29]


title: D7-RC179


title: D7-RC177


title: 58_1_450K


title: 58_2_450K


title: 15_1_18B

description:
comments: This sample matched with  15_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: RTN_d [Batch 5, Sample 27]


title: P2b_neuron [Batch 5, Sample 28]

value: single cell bad data


title: 14_2_5

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv


title: Tibialis anterior Mtm1-/y + TAM 7w rep 3 [MIM1-c]

city: ILLKIRCH

first: Jocelyn

last: Laporte

address: 1, rue Laurent Fries

institute: IGBMC

description:
KO_TAM_n3
Raw_gene_counts_matrix_Cohort_MTM1-c.txt

data_processing:
Reads were preprocessed in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20). After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10. Reads were mapped to spike sequences using bowtie version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR version 2.5.3a.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Raw_gene_counts_matrix_Cohort_MTM1-c.txt: Tab-delimited matrix table with raw gene counts for every gene and every sample.

source_name: Tibialis anterior

extract_protocol:
RNA was extracted from Tibialis anterior muscles using TRI Reagent (Molecular Research Center, Cincinnati, USA).
RNA sequencing library have been prepared using the TruSeq Stranded mRNA Sample Preparation Kit.

tag: Sex

value: Male

value: Tibialis anterior muscles

tag: treatment

value: Tamoxifen


title: Tibialis anterior Mtm1-/y + TAM 7w rep 2 [MIM1-c]

description:
KO_TAM_n2
Raw_gene_counts_matrix_Cohort_MTM1-c.txt


title: rtn_neuron [Batch 5, Sample 26]


title: 56_2_450K


title: P2b_neuron [Batch 5, Sample 25]


title: 55_2_450K


title: 14_2_18B

description:
comments: This sample matched with  14_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Exposed


title: C1_neuron [Batch 5, Sample 24]


title: C1_neuron [Batch 5, Sample 23]


title: 54_1_450K


title: Tibialis anterior Mtm1-/y 7w rep 2 [MIM1-c]

description:
KO_CTL_n2
Raw_gene_counts_matrix_Cohort_MTM1-c.txt


title: C1_neuron [Batch 5, Sample 22]


title: 14_1_5

value: Buccal


title: 54_2_450K


title: Tibialis anterior Mtm1-/y 7w rep 1 [MIM1-c]

description:
KO_CTL_n1
Raw_gene_counts_matrix_Cohort_MTM1-c.txt


title: 14_1_18C


title: rtn_neuron [Batch 5, Sample 21]


title: 15_1_10

value: Age 10


title: Tibialis anterior WT+TAM 7w rep 4 [MIM1-c]

description:
WT_TAM_n4
Raw_gene_counts_matrix_Cohort_MTM1-c.txt

value: WT


title: 53_2_450K


title: 56_1_450K


title: Tibialis anterior Mtm1-/y + TAM 7w rep 1 [MIM1-c]

description:
KO_TAM_n1
Raw_gene_counts_matrix_Cohort_MTM1-c.txt


title: 14_2_18C


title: P2b_neuron [Batch 5, Sample 20]


title: Tibialis anterior Mtm1-/y 7w rep 4 [MIM1-c]

description:
KO_CTL_n4
Raw_gene_counts_matrix_Cohort_MTM1-c.txt


title: 53_1_450K

description:
comments: NA
genomic DNA from blood samples
Overlaping_probes_normalised_seperately_450K_betas.csv, Overlaping_probes_normalised_together_450K_EPIC_betas.csv


title: Tibialis anterior WT+TAM 7w rep 2 [MIM1-c]

description:
WT_TAM_n2
Raw_gene_counts_matrix_Cohort_MTM1-c.txt


title: RTN_d [Batch 5, Sample 19]


title: 52_2_450K


title: P2b_neuron [Batch 5, Sample 18]


title: 14_1_10


title: 14_1_18B

description:
comments: This sample matched with  14_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 14_2_10


title: 55_1_450K


title: Tibialis anterior WT+TAM 7w rep 1 [MIM1-c]

description:
WT_TAM_n1
Raw_gene_counts_matrix_Cohort_MTM1-c.txt


title: 52_1_450K


title: rtn_neuron [Batch 5, Sample 17]


title: 13_2_18C


title: Tibialis anterior WT 7w rep 4 [MIM1-c]

description:
WT_CTL_n4
Raw_gene_counts_matrix_Cohort_MTM1-c.txt


title: 51_1_450K


title: 13_2_18B

description:
comments: This sample matched with  13_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: rtn_neuron [Batch 5, Sample 16]


title: 51_2_450K


title: 13_2_10


title: rtn_neuron [Batch 5, Sample 15]


title: Tibialis anterior WT 7w rep 2 [MIM1-c]

description:
WT_CTL_n2
Raw_gene_counts_matrix_Cohort_MTM1-c.txt


title: Tibialis anterior WT+TAM 7w rep 3 [MIM1-c]

description:
WT_TAM_n3
Raw_gene_counts_matrix_Cohort_MTM1-c.txt


title: 50_2_450K


title: rtn_neuron [Batch 5, Sample 14]


title: rtn_neuron [Batch 5, Sample 13]


title: Tibialis anterior WT 7w rep 1 [MIM1-c]

description:
WT_CTL_n1
Raw_gene_counts_matrix_Cohort_MTM1-c.txt


title: 50_1_450K


title: 13_2_5

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv

value: Age 5


title: 13_1_18C

value: Notexposed


title: Tibialis anterior Mtm1-/yTgBIN1 rep4 [MTM1-b]

description:
Mtm1-/yTgBIN1_n4
KOTgBIN1_n4
Raw_gene_counts_matrix_Cohort_MTM1-b.txt

data_processing:
Reads were preprocessed in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20). After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10. Reads were mapped to spike sequences using bowtie version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Reads were mapped onto the mm10 assembly of Mus musculus genome and BIN1 gene of Homo sapiens (hg38 – ENSG00000136717) genome using STAR version 2.5.3a.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Raw_gene_counts_matrix_Cohort_MTM1-b.txt: Tab-delimited matrix table with raw gene counts for every gene and every sample.


title: 49_2_450K

value: Age 18


title: RTN_d [Batch 5, Sample 12]


title: Tibialis anterior Mtm1-/yTgBIN1 rep3 [MTM1-b]

description:
Mtm1-/yTgBIN1_n3
KOTgBIN1_n3
Raw_gene_counts_matrix_Cohort_MTM1-b.txt


title: rtn_neuron [Batch 5, Sample 11]


title: Tibialis anterior Mtm1-/y 7w rep 3 [MIM1-c]

description:
KO_CTL_n3
Raw_gene_counts_matrix_Cohort_MTM1-c.txt


title: Tibialis anterior Mtm1-/yTgBIN1 rep2 [MTM1-b]

description:
Mtm1-/yTgBIN1_n2
KOTgBIN1_n2
Raw_gene_counts_matrix_Cohort_MTM1-b.txt