title: RTN_d [Batch 5, Sample 10]


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

status: Public on Dec 15 2020

type: SRA

city: ILLKIRCH

first: Jocelyn

last: Laporte

address: 1, rue Laurent Fries

country: France

institute: IGBMC

description:
WT_CTL_n3
Raw_gene_counts_matrix_Cohort_MTM1-c.txt

library_source: transcriptomic

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.

molecule: total RNA

organism: Mus musculus

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: strain

tag: genotype

value: WT

tag: Sex

value: Male

tag: age

tag: tissue

value: Tibialis anterior muscles


title: 12_2_5

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: NA
genomic DNA from buccal samples
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: buccal swab at age 5

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: Female

value: Buccal

value: Age 5

tag: disease state

value: Notexposed

tag: smokingpackyears

tag: category


title: rtn_neuron [Batch 5, Sample 9]

city: Charlottesville

first: Douglas

last: Bayliss

state: VA

address: 1340 Jefferson Park Ave.

department: Pharmacology

country: USA

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

molecule: polyA RNA

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: 12_2_18C

source_name: buccal swab at age 18

value: Age 18


title: Tibialis anterior Mtm1-/y 7w rep4 [MTM1-b]

description:
Mtm1-/y_n4
Mtm1KO_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: 47_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

source_name: whole blood at age 18

value: Blood


title: P2b_neuron [Batch 5, Sample 8]


title: 49_1_450K


title: 12_2_18B

description:
comments: This sample matched with  12_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 47_2_450K


title: Tibialis anterior Mtm1-/y 7w rep3 [MTM1-b]

description:
Mtm1-/y_n3
Mtm1KO_n3
Raw_gene_counts_matrix_Cohort_MTM1-b.txt


title: 13_1_18B

description:
comments: This sample matched with  13_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 13_1_10

source_name: buccal swab at age 10

value: Age 10


title: 12_2_10


title: 46_1_450K


title: 12_1_5

value: Exposed


title: RTN_d [Batch 5, Sample 6]

value: single cell GAD contaminated


title: 46_2_450K


title: RTN_d [Batch 5, Sample 7]


title: 12_1_18C


title: rtn_neuron [Batch 5, Sample 5]


title: Tibialis anterior Mtm1-/y 7w rep1 [MTM1-b]

description:
Mtm1-/y_n1
Mtm1KO_n1
Raw_gene_counts_matrix_Cohort_MTM1-b.txt


title: Tibialis anterior Mtm1-/y 7w rep2 [MTM1-b]

description:
Mtm1-/y_n2
Mtm1KO_n2
Raw_gene_counts_matrix_Cohort_MTM1-b.txt


title: 48_1_450K


title: 12_1_18B

description:
comments: This sample matched with  12_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Tibialis anterior TgBIN1 7w rep 4 [MTM1-b]

description:
TgBIN1_n4
Raw_gene_counts_matrix_Cohort_MTM1-b.txt


title: P2b_neuron [Batch 5, Sample 4]


title: Tibialis anterior Mtm1-/yTgBIN1 rep1 [MTM1-b]

description:
Mtm1-/yTgBIN1_n1
KOTgBIN1_n1
Raw_gene_counts_matrix_Cohort_MTM1-b.txt


title: 48_2_450K


title: Tibialis anterior TgBIN1 7w rep 3 [MTM1-b]

description:
TgBIN1_n3
Raw_gene_counts_matrix_Cohort_MTM1-b.txt


title: 12_1_10


title: P2b_neuron [Batch 5, Sample 3]


title: Tibialis anterior TgBIN1 7w rep 2 [MTM1-b]

description:
TgBIN1_n2
Raw_gene_counts_matrix_Cohort_MTM1-b.txt


title: 11_2_5


title: P2b_neuron [Batch 5, Sample 2]


title: 44_1_450K


title: Tibialis anterior TgBIN1 7w rep 1 [MTM1-b]

description:
TgBIN1_n1
Raw_gene_counts_matrix_Cohort_MTM1-b.txt


title: P2b_neuron [Batch 5, Sample 1]


title: 11_2_18C


title: 43_2_450K


title: 11_2_18B

description:
comments: This sample matched with  11_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: rtn_neuron [Batch 4, Sample 40]


title: Tibialis anterior WT 7w rep3  [MTM1-b]

description:
WT_n3
Raw_gene_counts_matrix_Cohort_MTM1-b.txt


title: Tibialis anterior WT 7w rep2  [MTM1-b]

description:
WT_n2
Raw_gene_counts_matrix_Cohort_MTM1-b.txt


title: 11_2_10

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


title: rtn_neuron [Batch 4, Sample 39]


title: rtn_neuron [Batch 4, Sample 38]


title: 11_1_5


title: 42_1_450K


title: rtn_neuron [Batch 4, Sample 37]


title: 44_2_450K


title: 11_1_18C


title: 13_1_5


title: Tibialis anterior Dnm2+/- 7w rep3 [MTM1-a]

description:
D2Hz_w7_3
Raw_gene_counts_matrix_Cohort_MTM1-a.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-a.txt: Tab-delimited matrix table with raw gene counts for every gene and every sample.


title: Tibialis anterior Dnm2+/- 7w rep2 [MTM1-a]

description:
D2Hz_w7_2
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 41_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: 45_2_450K


title: rtn_neuron [Batch 4, Sample 36]


title: 11_1_18B

description:
comments: This sample matched with  11_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 45_1_450K


title: Tibialis anterior Dnm2+/- 7w rep1 [MTM1-a]

description:
D2Hz_w7_1
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 11_1_10


title: 41_1_450K


title: Tibialis anterior WT 7w rep1  [MTM1-b]

description:
WT_n1
Raw_gene_counts_matrix_Cohort_MTM1-b.txt


title: C1_neuron [Batch 4, Sample 35]


title: Tibialis anterior Mtm1-/yDnm2+/- 7w rep4 [MTM1-a]

description:
M1KOD2Hz_w7_4
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 43_1_450K


title: 40_2_450K


title: rtn_neuron [Batch 4, Sample 34]


title: 42_2_450K


title: 10_2_18C


title: rtn_neuron [Batch 4, Sample 33]


title: 39_2_450K


title: Tibialis anterior Mtm1-/yDnm2+/- 7w rep3 [MTM1-a]

description:
M1KOD2Hz_w7_3
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 40_1_450K


title: Tibialis anterior Mtm1-/yDnm2+/- 7w rep2 [MTM1-a]

description:
M1KOD2Hz_w7_2
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 10_2_18B

description:
comments: This sample matched with  10_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: rtn_neuron [Batch 4, Sample 32]


title: Tibialis anterior Mtm1-/yDnm2+/- 7w rep1 [MTM1-a]

description:
M1KOD2Hz_w7_1
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: rtn_neuron [Batch 4, Sample 31]


title: 10_2_10


title: rtn_neuron [Batch 4, Sample 30]


title: 39_1_450K


title: 38_2_450K


title: Tibialis anterior Mtm1-/y 7w rep5 [MTM1-a]

description:
M1KO_w7_5
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 38_1_450K


title: Tibialis anterior Mtm1-/y 7w rep4 [MTM1-a]

description:
M1KO_w7_4
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 10_1_18C


title: 10_1_5


title: 37_1_450K


title: rtn_neuron [Batch 4, Sample 29]


title: Tibialis anterior Mtm1-/y 7w rep3 [MTM1-a]

description:
M1KO_w7_3
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 10_1_10


title: 10_2_5


title: 37_2_450K


title: rtn_neuron [Batch 4, Sample 28]


title: rtn_neuron [Batch 4, Sample 27]


title: Tibialis anterior Mtm1-/y 7w rep2 [MTM1-a]

description:
M1KO_w7_2
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: Tibialis anterior Mtm1-/y 7w rep1 [MTM1-a]

description:
M1KO_w7_1
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 36_1_450K


title: 10_1_18B

description:
comments: This sample matched with  10_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 9_2_5

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


title: rtn_neuron [Batch 4, Sample 26]


title: Tibialis anterior WT 7w rep5 [MTM1-a]

description:
WT_w7_5
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: C1_neuron [Batch 4, Sample 25]


title: 9_2_18C


title: Tibialis anterior WT 7w rep4 [MTM1-a]

description:
WT_w7_4
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 35_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: 9_2_18B

description:
comments: This sample matched with  9_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: C1_neuron [Batch 4, Sample 24]


title: 35_2_450K


title: 9_2_10


title: Tibialis anterior WT 7w rep2 [MTM1-a]

description:
WT_w7_2
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: rtn_neuron [Batch 4, Sample 22]


title: 9_1_5


title: rtn_neuron [Batch 4, Sample 21]


title: 9_1_18C


title: 34_2_450K


title: 33_1_450K


title: 36_2_450K


title: Tibialis anterior WT 7w rep1 [MTM1-a]

description:
WT_w7_1
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: rtn_neuron [Batch 4, Sample 20]


title: 33_2_450K


title: Tibialis anterior Mtm1-/yDnm2+/- 2w rep4 [MTM1-a]

description:
M1KOD2Hz_w2_4
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: Tibialis anterior Mtm1-/yDnm2+/- 2w rep2 [MTM1-a]

description:
M1KOD2Hz_w2_2
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: Tibialis anterior Mtm1-/yDnm2+/- 2w rep3 [MTM1-a]

description:
M1KOD2Hz_w2_3
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 9_1_10


title: 9_1_18B

description:
comments: This sample matched with  9_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: rtn_neuron [Batch 4, Sample 19]


title: 8_2_5


title: 8_2_18C


title: Tibialis anterior WT 7w rep3 [MTM1-a]

description:
WT_w7_3
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 31_1_450K


title: Tibialis anterior Mtm1-/y 2w rep5 [MTM1-a]

description:
M1KO_w2_5
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: rtn_neuron [Batch 4, Sample 17]


title: rtn_neuron [Batch 4, Sample 23]


title: 32_1_450K


title: 34_1_450K


title: C1_neuron [Batch 4, Sample 16]


title: Tibialis anterior Mtm1-/y 2w rep4 [MTM1-a]

description:
M1KO_w2_4
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 8_2_18B

description:
comments: This sample matched with  8_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 8_2_10


title: Tibialis anterior Mtm1-/y 2w rep3 [MTM1-a]

description:
M1KO_w2_3
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 8_1_5


title: 32_2_450K


title: rtn_neuron [Batch 4, Sample 14]


title: C1_neuron [Batch 4, Sample 18]


title: 30_2_450K


title: 8_1_18C


title: Tibialis anterior Mtm1-/yDnm2+/- 2w rep1 [MTM1-a]

description:
M1KOD2Hz_w2_1
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 30_1_450K


title: Tibialis anterior WT 2w rep4 [MTM1-a]

description:
WT_w2_5
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: Tibialis anterior Mtm1-/y 2w rep1 [MTM1-a]

description:
M1KO_w2_1
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: rtn_neuron [Batch 4, Sample 12]


title: Tibialis anterior Mtm1-/y 2w rep2 [MTM1-a]

description:
M1KO_w2_2
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: rtn_neuron [Batch 4, Sample 13]


title: 8_1_18B

description:
comments: This sample matched with  8_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 29_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: 29_2_450K


title: rtn_neuron [Batch 4, Sample 11]


title: Tibialis anterior WT 2w rep3 [MTM1-a]

description:
WT_w2_4
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 8_1_10

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


title: rtn_neuron [Batch 4, Sample 10]


title: 28_1_450K


title: 7_2_5


title: 31_2_450K


title: rtn_neuron [Batch 4, Sample 15]


title: Tibialis anterior WT 2w rep2 [MTM1-a]

description:
WT_w2_2
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 28_2_450K


title: 7_2_18C


title: rtn_neuron [Batch 4, Sample 9]


title: 27_2_450K


title: 7_2_18B

description:
comments: This sample matched with  7_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 27_1_450K


title: 26_1_450K


title: Tibialis anterior Dnm2+/- E18.5 rep1 [MTM1-a]

description:
D2Hz_w0_1
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: Tibialis anterior WT 2w rep1 [MTM1-a]

description:
WT_w2_1
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: rtn_neuron [Batch 4, Sample 8]


title: Tibialis anterior Dnm2+/- E18.5 rep2 [MTM1-a]

description:
D2Hz_w0_3
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: rtn_neuron [Batch 4, Sample 7]


title: Tibialis anterior Mtm1-/yDnm2+/- E18.5 rep5 [MTM1-a]

description:
M1KOD2Hz_w0_5
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 7_1_18B

description:
comments: This sample matched with  7_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 25_1_450K


title: 25_2_450K


title: 26_2_450K


title: 7_2_10


title: rtn_neuron [Batch 4, Sample 3]


title: rtn_neuron [Batch 4, Sample 6]


title: 7_1_5


title: 24_1_450K


title: Tibialis anterior Mtm1-/yDnm2+/- E18.5 rep3 [MTM1-a]

description:
M1KOD2Hz_w0_3
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: rtn_neuron [Batch 4, Sample 5]


title: rtn_neuron [Batch 4, Sample 2]


title: Tibialis anterior Mtm1-/yDnm2+/- E18.5 rep4 [MTM1-a]

description:
M1KOD2Hz_w0_4
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 6_2_5


title: Tibialis anterior Mtm1-/yDnm2+/- E18.5 rep2 [MTM1-a]

description:
M1KOD2Hz_w0_2
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: Tibialis anterior Mtm1-/yDnm2+/- E18.5 rep1 [MTM1-a]

description:
M1KOD2Hz_w0_1
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: rtn_neuron [Batch 4, Sample 4]


title: 7_1_10


title: 24_2_450K


title: 6_2_18B

description:
comments: This sample matched with  6_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 7_1_18C


title: 6_2_18C


title: 23_2_450K


title: rtn_neuron [Batch 4, Sample 1]


title: Tibialis anterior Mtm1-/y E18.5 rep4 [MTM1-a]

description:
M1KO_w0_5
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: rtn_neuron [Batch 3, Sample 31]


title: rtn_neuron [Batch 3, Sample 30]


title: 6_1_5


title: 23_1_450K


title: 6_2_10


title: rtn_neuron [Batch 3, Sample 32]


title: 22_2_450K


title: Tibialis anterior Mtm1-/y E18.5 rep3 [MTM1-a]

description:
M1KO_w0_4
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: rtn_neuron [Batch 3, Sample 29]


title: 22_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 Mtm1-/y E18.5 rep2 [MTM1-a]

description:
M1KO_w0_3
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: Tibialis anterior Mtm1-/y E18.5 rep1 [MTM1-a]

description:
M1KO_w0_2
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 6_1_18C

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


title: 21_1_450K


title: rtn_neuron [Batch 3, Sample 28]


title: 21_2_450K


title: Tibialis anterior WT E18.5 rep4 [MTM1-a]

description:
WT_w0_4
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 6_1_10


title: Tibialis anterior WT E18.5 rep3 [MTM1-a]

description:
WT_w0_3
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: 6_1_18B

description:
comments: This sample matched with  6_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: rtn_neuron [Batch 3, Sample 27]


title: 20_2_450K


title: 5_2_5


title: rtn_neuron [Batch 3, Sample 26]


title: 19_1_450K


title: 20_1_450K


title: Tibialis anterior WT E18.5 rep1 [MTM1-a]

description:
WT_w0_1
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: Tibialis anterior WT E18.5 rep2 [MTM1-a]

description:
WT_w0_2
Raw_gene_counts_matrix_Cohort_MTM1-a.txt


title: rtn_neuron [Batch 3, Sample 25]


title: rtn_neuron [Batch 3, Sample 24]


title: 19_2_450K


title: 5_2_18B

description:
comments: This sample matched with  5_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 18_1_450K


title: 5_1_5


title: rtn_neuron [Batch 3, Sample 23]


title: 18_2_450K


title: rtn_neuron [Batch 3, Sample 21]


title: 5_2_10


title: 17_2_450K


title: 5_1_18C


title: 5_1_18B

description:
comments: This sample matched with  5_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 16_2_450K


title: rtn_neuron [Batch 3, Sample 18]


title: 5_1_10


title: 4_2_5


title: 17_1_450K


title: rtn_neuron [Batch 3, Sample 17]


title: 5_2_18C


title: 15_1_450K


title: 4_2_18B

description:
comments: This sample matched with  4_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 15_2_450K


title: rtn_neuron [Batch 3, Sample 15]


title: 4_2_18C


title: rtn_neuron [Batch 3, Sample 16]


title: 4_2_10


title: rtn_neuron [Batch 3, Sample 22]


title: 14_2_450K


title: 4_1_5


title: 14_1_450K


title: 4_1_18C


title: rtn_neuron [Batch 3, Sample 14]


title: rtn_neuron [Batch 3, Sample 20]


title: rtn_neuron [Batch 3, Sample 13]


title: rtn_neuron [Batch 3, Sample 19]


title: 16_1_450K


title: 4_1_18B

description:
comments: This sample matched with  4_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 4_1_10


title: 13_1_450K


title: 12_2_450K


title: 3_2_5


title: rtn_neuron [Batch 3, Sample 9]


title: 3_2_18C


title: rtn_neuron [Batch 3, Sample 12]


title: rtn_neuron [Batch 3, Sample 8]


title: 3_2_18B

description:
comments: This sample matched with  3_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: rtn_neuron [Batch 3, Sample 11]


title: rtn_neuron [Batch 3, Sample 7]


title: Tibialis anterior KO_ASO 7w rep3

description:
KO_ASO_3
Raw_gene_counts_matrix_Cohort_BIN1.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_BIN1.txt: Tab-delimited matrix table with raw gene counts for every gene and every sample.

tag: treatment

value: ASO


title: Tibialis anterior KO_ASO 7w rep4

description:
KO_ASO_4
Raw_gene_counts_matrix_Cohort_BIN1.txt


title: 10_2_450K


title: 13_2_450K


title: Tibialis anterior KO_ASO 7w rep2

description:
KO_ASO_2
Raw_gene_counts_matrix_Cohort_BIN1.txt


title: 12_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: rtn_neuron [Batch 3, Sample 6]


title: 3_1_18C


title: 10_1_450K


title: Tibialis anterior KO_ASO 7w rep1

description:
KO_ASO_1
Raw_gene_counts_matrix_Cohort_BIN1.txt


title: rtn_neuron [Batch 3, Sample 5]


title: 9_1_450K


title: 3_1_18B

description:
comments: This sample matched with  3_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: rtn_neuron [Batch 3, Sample 3]


title: 9_2_450K


title: Tibialis anterior KO_PBS 7w rep4

description:
KO_PBS_4
Raw_gene_counts_matrix_Cohort_BIN1.txt

value: PBS


title: Tibialis anterior KO_PBS 7w rep3

description:
KO_PBS_3
Raw_gene_counts_matrix_Cohort_BIN1.txt


title: 3_1_10

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


title: 11_1_450K


title: 11_2_450K


title: P2b_neuron [Batch 3, Sample 4]


title: rtn_neuron [Batch 3, Sample 10]


title: rtn_neuron [Batch 3, Sample 2]


title: 3_2_10


title: 8_1_450K


title: 2_2_5


title: 8_2_450K


title: Tibialis anterior KO_PBS 7w rep1

description:
KO_PBS_1
Raw_gene_counts_matrix_Cohort_BIN1.txt


title: P2b_neuron [Batch 3, Sample 1]


title: Tibialis anterior WT_ASO 7w rep4

description:
WT_ASO_4
Raw_gene_counts_matrix_Cohort_BIN1.txt

value: WT


title: 2_2_18C


title: 7_2_450K

value: Male


title: Tibialis anterior WT_ASO 7w rep3

description:
WT_ASO_3
Raw_gene_counts_matrix_Cohort_BIN1.txt

value: Tibialis anterior muscles


title: 2_2_18B

description:
comments: This sample matched with  2_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Female


title: rtn_neuron [Batch 2, Sample 12]


title: rtn_neuron [Batch 2, Sample 11]


title: 2_2_10

value: Buccal


title: Tibialis anterior WT_ASO 7w rep2

description:
WT_ASO_2
Raw_gene_counts_matrix_Cohort_BIN1.txt


title: Tibialis anterior KO_PBS 7w rep2

description:
_KO_PBS_2
Raw_gene_counts_matrix_Cohort_BIN1.txt


title: 2_1_5

value: Age 5


title: 6_2_450K


title: Tibialis anterior WT_ASO 7w rep1

description:
WT_ASO_1
Raw_gene_counts_matrix_Cohort_BIN1.txt


title: 6_1_450K


title: rtn_neuron [Batch 2, Sample 10]


title: Tibialis anterior WT_PBS 7w rep4

description:
WT_PBS_4
Raw_gene_counts_matrix_Cohort_BIN1.txt


title: 2_1_18B

description:
comments: This sample matched with  2_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 2_1_18C


title: 5_1_450K


title: 2_1_10


title: Tibialis anterior WT_PBS 7w rep3

description:
WT_PBS_3
Raw_gene_counts_matrix_Cohort_BIN1.txt


title: 5_2_450K


title: Tibialis anterior WT_PBS 7w rep2

description:
WT_PBS_2
Raw_gene_counts_matrix_Cohort_BIN1.txt


title: rtn_neuron [Batch 2, Sample 6]


title: 4_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: 1_2_5


title: 7_1_450K


title: Tibialis anterior WT_PBS 7w rep1

description:
WT_PBS_1
Raw_gene_counts_matrix_Cohort_BIN1.txt


title: 1_2_18C


title: rtn_neuron [Batch 2, Sample 5]


title: 1_2_18B

description:
comments: This sample matched with  1_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: HAR257A9_1mo

city: Brisbane

first: Lachlan

middle: Ian

last: Harris

state: QLD

address: 300 Herston Road

department: Cancer Research Program

country: Australia

institute: QIMR Berghofer MRI

data_processing:
TSO contamination was removed from Sample HAR257A3_2mo and Sample HAR257A4_2mo via Cutadapt 1.18.
cellRanger count (Ver. 3.0.2) was used to map the FASTQ files for each individual sample to our custom mouse genome.
Samples aggregrated using cellRanger aggr command.
Genome_build: mm10 (3.0.0) with 4 custom elements. The first element was the GFP coding sequence to detect transcription of Nestin-GFP. The second, was the 5’floxed sequence of the tdtomato allele that detects transcription of the intact tdtomato locus. Finally, we added 3’ regions of the tdtomato locus that are transcribed upon recombination, and encode the woodchuck hepatitis virus post-transcriptional regulatory element (WPRE). The custom genome was made with the cellranger mkref command.
Supplementary_files_format_and_content: compressed filtered feature barcode matrix: the output from aggregated cellRanger count of 8 samples. The 3 files can be placed in a directory and then read directly into R to create a Seurat object.

source_name: hippocampal neural stem cells  (FLOW-enriched)

extract_protocol:
Hippocampus diassociated with enzymes, fluorescent cells sorted via FLOW cytometry.Samples were prepared using the 10x Chromium Next GEM Single Cell 3ʹ v2.0 or 3.0 kit.
Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer’s instructions.
OTHER: scRNA-Seq

value: 1 month

tag: gem suffix

tag: 10x 3' chemistry

value: Version 3

tag: cells

value: GFP+tdT+ and GFP+tdT-


title: rtn_neuron [Batch 2, Sample 9]

value: Jx99 (Phox2b::GFP)

value: single cell

value: wild type


title: 3_2_450K

value: Blood

value: Age 18


title: rtn_neuron [Batch 2, Sample 4]


title: rtn_neuron [Batch 2, Sample 8]


title: 1_2_10

value: Age 10

value: Exposed


title: HAR257A7_6mo

value: 6 months


title: rtn_neuron [Batch 2, Sample 3]


title: HAR257A6_6mo


title: 3_1_5


title: HAR257A5_6mo


title: 3_1_450K


title: 1_1_5

value: Notexposed


title: rtn_neuron [Batch 2, Sample 2]


title: 2_2_450K


title: rtn_neuron [Batch 2, Sample 7]


title: rtn_neuron [Batch 2, Sample 1]


title: 1_1_18C


title: 4_2_450K

value: Male


title: 1_2_450K


title: 1_1_18B

description:
comments: This sample matched with  1_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 1_1_450K


title: rtn_neuron [Batch 1, Sample 12]

value: pooled cell


title: HAR257A4_2mo

value: 2 months

value: Version 2


title: 1_1_10

value: Female

value: Buccal


title: rtn_neuron [Batch 1, Sample 11]


title: HAR72A2_2mo

value: GFP+tdT-


title: rtn_neuron [Batch 1, Sample 10]


title: 2_1_450K


title: rtn_neuron [Batch 1, Sample 8]


title: rtn_neuron [Batch 1, Sample 7]


title: rtn_neuron [Batch 1, Sample 9]


title: rtn_neuron [Batch 1, Sample 6]


title: HAR257A3_2mo

value: GFP+tdT+ and GFP+tdT-


title: rtn_neuron [Batch 1, Sample 4]

value: Jx99 (Phox2b::GFP)


title: rtn_neuron [Batch 1, Sample 5]

value: single cell


title: HAR72A1_2mo

value: GFP+tdT+ and GFP-tdT-


type: RNA

city: Maastricht

first: Danyel

last: Jennen

address: Universiteitssingel 40

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

description: Gene expression data from HepG2 exposed to tolbutamide for 48 h, biological replicate 1

hyb_protocol: 12.5µg of cRNA were hybridized for 16 hr on 45°C on GeneChip Human Genome U133 Plus 2.0 Array, using Affymetrix® GeneChip® Fluidics Station 450 and the GeneChip Hybridization, Wash and Stain Kit

scan_protocol: Arrays were scanned using genechip scanner 3000 7G

data_processing: Obtained data sets were re-annotated to the Brainarray custom CDF-file V22 ENSEMBL gene ID (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp) (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the R-scripts from ArrayAnalysis.org (Eijssen et al., 2013).

label: biotin

source_name: hepatocellular carcinoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using the 3’ IVT express kit

growth_protocol: HepG2 cells were cultured in 6-well plates in the presence of minimal essential medium (MEM) supplemented with 1% non-essential amino acids, 1% sodium-pyruvate, 2% penicillin/streptomycin and 10% fetal bovine serum (FBS) (all from Gibco BRL, Breda, The Netherlands). The cells were incubated at 37 C and 5% CO2.

extract_protocol: Trizol extraction was performed using the miRNAeasy kit from qiagen accoding to the manufacturer’s protocol

treatment_protocol: When the HepG2 cells were 80% confluent, the medium was replaced with fresh medium containing either compound or solvent (0.5% DMSO)

tag: cell line

tag: compound

value: tolbutamide

tag: dose

tag: time

tag: matching control file


title: identification of  LOXL2 knocked down by genome editing with the CRISPR/Cas9 system target genes in A549 (A549-GE2)

city: Kagoshima

first: Shunsuke

last: Misono

address: 8-35-1, Sakuragaoka

department: Pulmonary Medicine

country: Japan

institute: Kagoshima University Hospital

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 11.5.1.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: control

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or EMEM.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: microRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

tag: cell type

value: lung adenocarcinoma

tag: transfection

value: no genome editing

source_name: LOXL2 genome edited cell line

value: LOXL2 genome editing


description: Gene expression data from HepG2 exposed to tolbutamide for 24 h, biological replicate 3


description: Gene expression data from HepG2 exposed to tolbutamide for 48 h, biological replicate 3


title: rtn_neuron [Batch 1, Sample 3]

tag: strain

tag: age

tag: genotype

value: wild type


description: Gene expression data from HepG2 exposed to tolbutamide for 24 h, biological replicate 2


description: Gene expression data from HepG2 exposed to piperonyl butoxide for 48 h, biological replicate 3

value: piperonyl butoxide


title: AGM_SV1103_Pre, Blood

city: Evry

first: Jorg

last: Tost

address: 2 rue Gaston Cremieux

institute: CEA-Institut de Genomique, Centre National de Genotypage

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium Human Methylation 450 K bead arrays (Illumina Inc., San Diego, CA). Processing was done according to the manufacturer’s protocol using an automated pipeline.  of bisulfite-treated DNA was analyzed using the Infinium  Human Methylation 450 K bead arrays spanning approximately  over 480,000 CpG sites/sample (Illumina Inc., San  Diego, CA). Processing was done according to the manufacturer’s  protocol using an automated pipeline, and the  arrays were scanned on an Illumina iScan platform (Illumina  Inc., San Diego, CA) established at the Life & Brain  Center (Bonn, Germany)

data_processing:
Subset quantile normalization, revised version of Touleimat & tost, Epigenomics 2012
Human Illumina arrays were used for monkey samples. Due to the specificity of probes, the normalized data contains only positions that can be reliably measured in the money species and thus not the expected 450K lines.

organism: Macaca mulatta

source_name: Blood

label_protocol: Standard Illumina Protocol

extract_protocol: Standard Illumina Protocol

tag: gender

value: male

tag: siv infection

value: SIV-negative

tag: timepoint

value: Pre

tag: tissue

value: Blood

value: CD4+ T cell


title: identification of siDONASON-3 target genes in SBC-3

source_name: mock

value: small cell lung cancer

value: no transfection

source_name: siDONSON-3 transfected cell line

value: siDONSON-3 transfection


description: Gene expression data from HepG2 exposed to tolbutamide for 48 h, biological replicate 2


description: Gene expression data from HepG2 exposed to tolbutamide for 24 h, biological replicate 1


title: identification of siDONASON-1 target genes in SBC-3

source_name: siDONSON-1 transfected cell line

value: siDONSON-1 transfection


title: AGM_SV075_Pre, Blood

scan_protocol: the arrays were scanned on an Illumina iScan platform

value: Chronic infection

value: Chr


title: AGM_SV104_Chr, Blood

value: female


title: Identification of miR-150-3p target genes in SK-MES-1

value: lung squamous cell carcinoma

source_name: miR-150-3p transfected cell line

value: miR-150-3p transfection


title: identification of  LOXL2 knocked down by genome editing with the CRISPR/Cas9 system target genes in A549 (A549-GE3)

value: lung adenocarcinoma

value: no genome editing

value: LOXL2 genome editing


description: Gene expression data from HepG2 exposed to piperonyl butoxide for 48 h, biological replicate 1

value: piperonyl butoxide


title: identification of  LOXL2 knocked down by genome editing with the CRISPR/Cas9 system target genes in A549 (A549-GE1)


title: identification of siDONASON-2 target genes in SBC-3

source_name: siDONSON-2 transfected cell line

value: siDONSON-2 transfection


title: AGM_SV1101_Pre, Blood


title: rtn_neuron [Batch 1, Sample 2]

value: Jx99 (Phox2b::GFP)

tag: single cell information

value: single cell

value: wild type


title: Identification of miR-150-3p target genes in EBC-1


title: AGM_SV1103_Pre, Blood

value: male

value: SIV-negative

value: Pre

value: Blood

value: CD4+ T cell


title: AGM_SV074_Chr, Blood

value: Chronic infection

value: Chr


title: NIH-SRF_03FBS

city: Helsinki

first: Maria

last: Sokolova

address: Viikinkaari 5

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

library_source: genomic

data_processing:
ChIP-Seq data sets were aligned using Bowtie2.
Peak calling was performed with MASC2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files were generated using DeepTools.

source_name: NIH 3T3

growth_protocol: Cells were grown in 15cm plates.

extract_protocol:
Ready cells were fixed in 1% paraformaldehyde/PBS for 10 min at RT, crosslinking was stopped by adding cold glycine to a final concentration of 0.125 M for five min, followed by harvesting in 500 ml of ice-cold PBS and spinning at 1000g for 5 min at +4°C. Cell pellets were lysed in 300 µl of RIPA buffer and sonicated with Bioruptor (Diagenode; number of cycles = 15, power = HIGH, ON = 30 sec, OFF = 30 sec). IPs were carried out with 5 µg antibody overnight at 4°C in a rotating wheel.
ChIP libraries were prepared for Illumina NextSeq 500 using NEBNext ChIP-Seq DNA Sample Prep Master Mix Set for Illumina (NEB E6240) and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (NEB E7335) according to the manufacturer’s protocols.

treatment_protocol: Cells were maintained in low-serum medium for 24 hours, then stimulated with serum (15%) for 45 min.

value: NIH 3T3

value: fibroblast

tag: serum %

tag: chip antibody

value: SRF (D71A9) (#5147, Cell Signaling Technology)


title: NIH-SRF_15FBS

tag: cell line


title: AGM_SV1102_Pre, Blood


title: NIH-MRTFA_03FBS

value: MRTFA


description: Gene expression data from HepG2 exposed to piperonyl butoxide for 24 h, biological replicate 3

tag: compound


description: Gene expression data from HepG2 exposed to piperonyl butoxide for 48 h, biological replicate 2

tag: dose


title: rtn_neuron [Batch 1, Sample 1]

value: single cell GAD contaminated


title: NIH-input_15FBS


title: AGM_SV082_Pre, Blood


title: NIH-MRTFA_15FBS


description: Gene expression data from HepG2 exposed to piperonyl butoxide for 24 h, biological replicate 2

value: piperonyl butoxide

tag: time


title: miR-634 Input_2

city: Tokyo

first: Jun

last: Inoue

address: Yushima 1-5-45, Bunkyo-ku

department: Molecular Cytogenetics

institute: Tokyo Medical & dental univ.

hyb_protocol: 0,6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K (G4851C) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61 x 21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-107) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNAeasy

value: human carcinoma cell line

tag: genotype/variation

value: overexpressing miR-634

tag: rip antibody

value: normal rabbit IgG antibody


title: miR-634 Input_1

tag: cell type


description: Gene expression data from HepG2 exposed to 4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one for 48 h, biological replicate 1

tag: matching control file


description: Gene expression data from HepG2 exposed to 4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one for 48 h, biological replicate 3


title: NIH-IgG_15FBS

value: Normal rabbit IgG (sc-2027, Santa Cruz Biotechnology)


title: miR-NC RIP_2

source_name: miR-NC-RIP

value: miR-NC

value: AGO2 antibody


title: AGM_SV072_Chr, Blood

value: female

value: SIV-negative

value: Pre


description: Gene expression data from HepG2 exposed to piperonyl butoxide for 24 h, biological replicate 1


title: NIH-input_03FBS


title: AGM_SV071_Pre, Blood

value: male

value: Chronic infection

value: Blood

value: CD4+ T cell


description: Gene expression data from HepG2 exposed to 4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one for 48 h, biological replicate 2


title: miR-634 RIP_2


title: NIH-IgG_03FBS

value: NIH 3T3

value: fibroblast


title: AGM_O7199_Chr, Blood


title: AGM_O7199_Pre, Blood

value: Chr


title: miR-NC Input_2

source_name: miR-NC-Input


description: Gene expression data from HepG2 exposed to 4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one for 24 h, biological replicate 2


title: AGM_SV084_D64, Blood


title: miR-NC RIP_1


title: AGM_AGM SV092_Pre, Blood


title: MDF_WT_POL2S5P_15FBS

source_name: MDF

value: Mouse dermal fibroblast

value: Lap2alpha WT

value: POL2S5P (4H8; ab5408, Abcam)


title: miR-634 RIP_1

value: human carcinoma cell line

value: overexpressing miR-634


title: miR-NC Input_1

value: miR-NC

value: normal rabbit IgG antibody


title: AGM_AGM SV092_Chr, Blood

value: female


title: MDF_WT_POL2S5P_03FBS


title: Meniscus_26w_RESECT7_rep1

city: Haikou

first: Fang

middle: Ye

last: Han

state: Hainan

address: No. 19 Xiuhua Road

department: Department of Orthopaedic Surgery

country: China

institute: Hainan Provincial People’s Hospital

description:
7Ba
Gene expression of meniscus 26 weeks after resection of anterior cruciate ligament and lateral collateral ligament.

hyb_protocol: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 7 out of 14 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

organism: Sus scrofa

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.

growth_protocol: A visit was carried out twice a day after operation. All animals had been treated with penicillin (Kerui Animal Pharmaceutical Co., Ltd, Chengdu, Sichuan Province, China) and tramadol (Duoduo Pharmaceutical Co., Ltd, Jiamusi, Heilongjiang Province, China) for 7 days. After the wound was completely healed, the animal could move freely in the pig pen.

extract_protocol: Total RNA from the meniscal tissue was extracted using an E.Z.N.A Total RNA Kit II (Omega Bio-Tek, Inc., USA) according to the manufacturer’s instructions, including a DNase digestion step. The quantity and quality of RNA were assessed using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technology, Rockland, DE). RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: After the surgical sites were shaved and sterilized, the right rear limbs (Ba-Group) were operated upon using a medial parapatellar approach of approximately 10.0cm from the patella to the tuberositas tibiae. The joint was then opened by partly luxating the patella to the lateral. The ACL was then fixed by a clamp and cut at the distal end and resected 1.0cm. Then, the lateral collateral ligament was separated and exposed along the joint line, and a length of 1.0cm was resected. Following washing with 100 ml of sterile saline solution, the articular capsule was then sutured intermittently and independently with 3-0 silk sutures (Aipu Medical Equipment Co., Ltd., Hangzhou, China). The sham operation was carried out on the left knee joint (Aa-Group) with a similar incision to the articular capsule, but no manipulation was made to the ligaments, menisci or articular cartilage.

tag: breed

value: Wuzhishan

value: medial meniscus

tag: age

tag: treatment

value: resection of ACL and LCL


title: AGM_SV073_Chr, Blood

tag: gender

tag: siv infection

value: Chronic infection


title: AGM_SV084_Pre, Blood

organism: Chlorocebus sabaeus

source_name: lymph node

tag: timepoint

tag: tissue

value: Blood


title: MDF_WT_MRTFA_15FBS

tag: serum %

value: MRTFA


description: Gene expression data from HepG2 exposed to nifedipine for 48 h, biological replicate 3

value: nifedipine


description: Gene expression data from HepG2 exposed to nifedipine for 48 h, biological replicate 2


title: MDF_WT_Lap2alpha_15FBS

tag: chip antibody


title: MDF_WT_MRTFA_03FBS


title: AGM_A8533_Euth, lymph node

value: Euth

value: lymph node

value: CD4+ T cell


description: Gene expression data from HepG2 exposed to nifedipine for 48 h, biological replicate 1

tag: cell line


title: Meniscus_26w_RESECT6_rep1

description:
6Ba
Gene expression of meniscus 26 weeks after resection of anterior cruciate ligament and lateral collateral ligament.

value: male


title: MDF_KO_POL2S5P_15FBS

value: Mouse dermal fibroblast

value: Lap2alpha KO

value: POL2S5P (4H8; ab5408, Abcam)


description: Gene expression data from HepG2 exposed to 4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one for 24 h, biological replicate 3

tag: compound


title: MDF_KO_POL2S5P_03FBS


description: Gene expression data from HepG2 exposed to nifedipine for 24 h, biological replicate 3

tag: dose


title: Meniscus_26w_RESECT4_rep1

description:
4Ba
Gene expression of meniscus 26 weeks after resection of anterior cruciate ligament and lateral collateral ligament.


title: AGM_B2338_Euth, lymph node


title: Meniscus_26w_RESECT5_rep1

description:
5Ba
Gene expression of meniscus 26 weeks after resection of anterior cruciate ligament and lateral collateral ligament.


title: Meniscus_26w_RESECT3_rep1

description:
3Ba
Gene expression of meniscus 26 weeks after resection of anterior cruciate ligament and lateral collateral ligament.


title: AGM_O7249_D64, Blood


description: Gene expression data from HepG2 exposed to nifedipine for 24 h, biological replicate 2

tag: time


description: Gene expression data from HepG2 exposed to methapyrilene hydrochloride for 48 h, biological replicate 2

value: methapyrilene hydrochloride


description: Gene expression data from HepG2 exposed to nifedipine for 24 h, biological replicate 1


title: Meniscus_26w_SHAM7_rep1

description:
7Aa
Gene expression of meniscus 26 weeks after sham operation.

value: sham operation


title: Meniscus_26w_RESECT2_rep1

description:
2Ba
Gene expression of meniscus 26 weeks after resection of anterior cruciate ligament and lateral collateral ligament.


title: MDF_KO_MRTFA_15FBS

tag: genotype/variation


title: Meniscus_26w_SHAM6_rep1

description:
6Aa
Gene expression of meniscus 26 weeks after sham operation.


title: AGM_06003-3_Pre, lymph node

value: SIV-negative

value: Pre


title: AGM_A7737_Euth, lymph node

value: female


title: AGM_O7249_Pre, Blood


description: Gene expression data from HepG2 exposed to 4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one for 24 h, biological replicate 1


title: Meniscus_26w_SHAM5_rep1

description:
5Aa
Gene expression of meniscus 26 weeks after sham operation.

value: Wuzhishan

value: medial meniscus


description: Gene expression data from HepG2 exposed to methapyrilene hydrochloride for 48 h, biological replicate 1


title: AGM_SV082_D14, lymph node

value: Acute infection


title: AGM_SV084_D65, lymph node

value: Chronic infection


title: Meniscus_26w_RESECT1_rep1

description:
1Ba
Gene expression of meniscus 26 weeks after resection of anterior cruciate ligament and lateral collateral ligament.

value: resection of ACL and LCL


title: MDF_KO_Lap2alpha_15FBS


title: MDF_KO_MRTFA_03FBS

value: MRTFA


title: AGM_SV082_D65, lymph node

value: lymph node


title: MDF_KO_input_15FBS


title: 11-Lap2-si-15percent

description: Replicate 2

data_processing:
RNA-seq data sets were aligned using TopHat2.
Counting aligned reads per genes were performed with HTSeq.
Differential expression analysis was performed with DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.tsv: Tab-delimited text files of expression values per sample in RPKM format.

growth_protocol: NIH 3T3 cells were plated onto 10 cm plates with 10% FBS.

extract_protocol:
Total RNA was extracted with a Nucleospin RNA kit from Macherey-Nagel.
Illumina NextSeq 500 using Ribo-Zero rRNA Removal Kit (Illumina) and the NEBNext Ultra Directional RNA Library Prep.

treatment_protocol: The following day, cells were transfected with siRNA.

value: NIH 3T3

value: fibroblast

tag: sirna


title: 12-Lap2-si-15percent

description: Replicate 3

tag: cell type


title: AGM_SV081_D65, lymph node

value: male

value: CD4+ T cell


title: Meniscus_26w_SHAM4_rep1

description:
4Aa
Gene expression of meniscus 26 weeks after sham operation.


title: MOLM13_AF10-PZP

city: San Diego

first: Aniruddha

last: Deshpande

state: California

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq  Sequence reads were aligned to  human genome assembly hg19 using Bowtie (Langmead et al., 2009)
Reads that aligned to multiple loci in the genome were discarded.
Genome_build: Hg19
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using pybedtools

source_name: MOLM13 cells

growth_protocol: MOLM13 cells were grown in RPMI supplemented with 10% FBS and 5% Penicilin+ Streptomycin  (typically 1  million cells into a T25 flask).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina following the manufacturer's protocols.

treatment_protocol: No treatments were done

value: human AML cell line

value: Custom AF10 PZP N-terminal Antibody


description: Gene expression data from HepG2 exposed to methapyrilene hydrochloride for 24 h, biological replicate 3

value: methapyrilene hydrochloride

tag: matching control file


title: 9-Lap2-si-0-3percent

description: Replicate 3


title: 10-Lap2-si-15percent

description: Replicate 1


title: Meniscus_26w_SHAM3_rep1

description:
3Aa
Gene expression of meniscus 26 weeks after sham operation.

tag: breed

value: sham operation


title: Meniscus_26w_SHAM2_rep1

description:
2Aa
Gene expression of meniscus 26 weeks after sham operation.

tag: age


title: 8-Lap2-si-0-3percent

description: Replicate 2


title: CD14-derived macrophages: control 3

city: Moscow

first: Evgeny

last: Karpulevich

address: Alexandra Solzhenitsina

department: Information Systems

country: Russia

institute: ISP RAS

data_processing:
Raw data processing with https://github.com/nf-core/rnaseq (default settings)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: blood

growth_protocol: CD14+ monocytes were isolated with magnetic beads. CD14-derived macrophages were obtained after 7 days of incubation of CD14+ monocytes with MCSF (5 ng/ml).

extract_protocol:
Total mRNA was isolated from CD14-derived macrophages using QIAzol lysis reagent and Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column deoxyribonuclease I step (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: On the 7th day LPS (100 ng/ml) was added to experimental cells. Control cells were intact.

value: CD14-derived macrophages


title: CD14-derived macrophages: LPS 2

value: female


description: Gene expression data from HepG2 exposed to methapyrilene hydrochloride for 24 h, biological replicate 2


title: 7-Lap2-si-0-3percent

description: Replicate 1


title: CD14-derived macrophages: LPS 3


title: 6-CTRL-si-15percent

description: Replicate 3

value: Control


title: 5-CTRL-si-15percent

description: Replicate 2


title: 4-CTRL-si-15percent

description: Replicate 1


title: AGM_O7249_D14, lymph node


title: CD14-derived macrophages: LPS 1


title: CD14-derived macrophages: control 1


title: AGM_O7249_D65, lymph node


description: Gene expression data from HepG2 exposed to DMSO for 48 h, exposure 1, biological replicate 2

value: DMSO


description: Gene expression data from HepG2 exposed to DMSO for 48 h, exposure 2, biological replicate 1


title: AGM_O7199_D14, lymph node

value: Acute infection


description: Gene expression data from HepG2 exposed to DMSO for 48 h, exposure 1, biological replicate 1


description: Gene expression data from HepG2 exposed to DMSO for 24 h, exposure 2, biological replicate 1


description: Gene expression data from HepG2 exposed to DMSO for 48 h, exposure 2, biological replicate 3


title: AGM_SV082_Pre, lymph node

value: SIV-negative

value: Pre


description: Gene expression data from HepG2 exposed to DMSO for 48 h, exposure 2, biological replicate 2


title: 2-CTRL-si-0-3percent

description: Replicate 2


title: MDF_WT_input_15FBS

value: Mouse dermal fibroblast

value: Lap2alpha WT


description: Gene expression data from HepG2 exposed to DMSO for 24 h, exposure 2, biological replicate 3


title: Meniscus_26w_SHAM1_rep1

description:
1Aa
Gene expression of meniscus 26 weeks after sham operation.

value: Wuzhishan

value: medial meniscus

tag: treatment


description: Gene expression data from HepG2 exposed to methapyrilene hydrochloride for 24 h, biological replicate 1


description: Gene expression data from HepG2 exposed to DMSO for 24 h, exposure 2, biological replicate 2


title: S12_EX_008_MCI: Patient with mild cognitive impairment #5

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: mild cognitive impairment (MCI)

data_processing:
FASTQ files were extracted using bcl2fastq v2.18.0.12
Adapters were trimmed using Cutadapt version v1.18
Aligned to human genome hg19 Ensembl v82 using STAR v2.4.0j
FeatureCounts was used to create gene counts file
Genome_build: hg19
Supplementary_files_format_and_content: Text files containing counts for each gene

source_name: Extracellular vesicle derived from patients with mild cognitive impairment (MCI)

extract_protocol:
Total extracellular vesicle RNAs are isolated from plasma using exoRNeasy Serum/Plasma Maxi kits (Cat# 77164, QIAGEN)
RNA libraries were prepared for sequencing using Ovation RNA-Seq System V2 (NuGEN) kit following the manufacturer’s instructions. The amplified cDNA was fragmented using a Bioruptor (Diagenode), adapters were ligated to cDNA using TruSeq ChIP Sample Preparation kit (Illumina, San Diego, CA, USA), the DNA fragments were size-selected (300–350 bp) after electrophoresis on a 2.5% agarose gel, and the selected DNA was subjected to 17 cycles of PCR amplification.  Library quality was determined using a Bioanalyzer 2100 instrument and the final libraries were sequenced using the Illumina HiSeq 2500 instrument.

value: Extracellular vesicle from plasma

tag: diagnosis

value: mild cognitive impairment (MCI)

tag: Sex

value: Male

tag: clinical stage

value: aMCI


description: Gene expression data from HepG2 exposed to DMSO for 48 h, exposure 1, biological replicate 3

source_name: hepatocellular carcinoma cell line


title: AGM_SV084_Pre, lymph node

tag: gender

tag: siv infection

tag: timepoint

tag: tissue

value: lymph node

value: CD4+ T cell


title: 3-CTRL-si-0-3percent

description: Replicate 3

tag: cell line

value: NIH 3T3

value: fibroblast

tag: serum %


title: 1-CTRL-si-0-3percent

description: Replicate 1

value: Control


title: AGM_O7199_Pre, lymph node

value: male


description: Gene expression data from HepG2 exposed to methapyrilene hydrochloride for 48 h, biological replicate 3

tag: compound

value: methapyrilene hydrochloride

tag: dose

tag: time


title: S12_EX_019_MCI: Patient with mild cognitive impairment #2

description: mild cognitive impairment (MCI)

value: Female

value: multidomain MCI


title: AGM_SV081_D14, lymph node

value: Acute infection

tag: cell type


title: S11_EX_010_MCI: Patient with mild cognitive impairment #1

description: mild cognitive impairment (MCI)


title: AGM_O7249_Pre, lymph node

value: SIV-negative

value: Pre


title: MAC_O90528_Pre, Blood

value: female

value: Blood


description: Gene expression data from HepG2 exposed to DMSO for 24 h, exposure 1, biological replicate 2

value: DMSO


title: MAC_VI219_Chr, Blood

value: Chronic infection

value: Chr


description: Gene expression data from HepG2 exposed to DMSO for 24 h, exposure 1, biological replicate 1


title: CD TIL8

city: Boston

first: Alison

last: Ringel

state: MA

address: 240 Longwood Ave

department: Cell Biology

institute: Harvard Medical School

data_processing:
Samples were run on an Illumina NextSeq sequencer using 50bp single end reads
Samples were analyzed with CLC Genomics Workbench 8.0.1 software utilizing standard RNA-seq pipeline alignment (mismatch cost=2, insertion cost=3, deletion cost=3, length fraction=0.8, similarity fraction=0.8)
Samples were normalized as reads per million
Genome_build: mm10
Supplementary_files_format_and_content: Tab-deliminated file containing exonic reads per million

source_name: tumor-infiltrating CD8+ T lymphocyte

growth_protocol: CD8+ T cells from dissociated MC38 tumors or tumor-draining lymph node were sorted 12 days post-implantation and RNA immediately extracted.

extract_protocol:
CD8+ T cells from dissociated MC38 tumors or tumor-draining lymph node were sorted 12 days post-implantation from MC38 tumors in C57BL6/J mice.
RNA-libraries were constructed by enriching for mRNA using OligoDT beads, samples were fragmented, barcoded and then amplified

treatment_protocol: Female C57BL6/J mice were fed a control or high-fat diet starting at 5 weeks of age for 8-10 weeks.

tag: strain

value: subcutaneous MC38 tumor

tag: diet

value: Control Diet


title: S12_EX_025_MCI: Patient with mild cognitive impairment #3

description: mild cognitive impairment (MCI)

value: Extracellular vesicle from plasma

value: mild cognitive impairment (MCI)

tag: age

value: Male

value: aMCI


title: MAC_98R0078_Chr, Blood

value: CD4+ T cell


title: CD TIL7


title: S09_EX_030_AD: Patient with Alzheimer's disease #4

description: Alzheimer's disease

source_name: Extracellular vesicle derived from patient with Alzheimer's disease (AD)

value: Alzheimer's disease (AD)

value: Female

value: Mild Dementia


title: CD TIL5


title: S10_EX_042_AD: Patient with Alzheimer's disease #5

description: Alzheimer's disease


description: Gene expression data from HepG2 exposed to clonidine for 48 h, biological replicate 2

value: clonidine

tag: matching control file


title: MAC_54410_Pre, Blood

source_name: Blood

value: SIV-negative

value: Pre


title: S08_EX_020_AD: Patient with Alzheimer's disease #3

description: Alzheimer's disease

tag: diagnosis


title: MAC_98R0016_Chr, Blood

value: female

value: Blood


title: CD TIL4

tag: Sex


title: S07_EX_007_AD: Patient with Alzheimer's disease #2

description: Alzheimer's disease

tag: clinical stage


description: Gene expression data from HepG2 exposed to clonidine for 48 h, biological replicate 3


title: CD TIL3


description: Gene expression data from HepG2 exposed to DMSO for 24 h, exposure 1, biological replicate 3

value: DMSO


title: MAC_90874_Pre, Blood

tag: gender


title: MAC_504034_Chr, Blood

tag: siv infection

value: Chronic infection

value: Chr


title: S05_EX_4783_healthy: Healthy donor #5

description: Healthy Donor

source_name: Extracellular vesicle derived from Healthy donor

value: Healthy

value: Healthy Donor


title: S06_EX_001_AD: Patient with Alzheimer's disease #1

description: Alzheimer's disease

value: Extracellular vesicle from plasma


description: Gene expression data from HepG2 exposed to clonidine for 24 h, biological replicate 2


description: Gene expression data from HepG2 exposed to clonidine for 24 h, biological replicate 1


title: MAC_503052_Chr, Blood

tag: timepoint


title: MAC_503068_Chr, Blood

tag: tissue


description: Gene expression data from HepG2 exposed to clonidine for 24 h, biological replicate 3

tag: cell line


title: CD TIL2

value: subcutaneous MC38 tumor

value: Control Diet


title: CD TIL1


title: MAC_54189_Pre, Blood

value: CD4+ T cell


title: MAC_81998_Pre, Blood


title: S04_EX_1845_healthy: Healthy donor #4

description: Healthy Donor

value: Male


title: HFD TIL6

value: High-fat Diet


title: S03_EX_1096_healthy: Healthy donor #3

description: Healthy Donor


title: S12_EX_041_MCI: Patient with mild cognitive impairment #4

description: mild cognitive impairment (MCI)

value: mild cognitive impairment (MCI)

value: multidomain MCI


title: CD14-derived macrophages: control 2

value: CD14-derived macrophages


title: HFD TIL5


title: HFD TIL3


title: MAC_98R0078_Chr, lymph node

value: lymph node


description: Gene expression data from HepG2 exposed to 2-nitrofluorene for 48 h, biological replicate 3


title: HFD TIL2

value: female


description: Gene expression data from HepG2 exposed to 2-nitrofluorene for 24 h, biological replicate 3


title: S01_EX_7816_healthy: Healthy donor #1

description: Healthy Donor

value: Female


title: MAC_O90528_Pre, lymph node

value: SIV-negative

value: Pre


description: Gene expression data from HepG2 exposed to 2-nitrofluorene for 48 h, biological replicate 2


title: hSpS at day 53 of differentiation

city: Palo Alto

first: Jimena

last: Andersen

state: CA

address: 318 Campus Drive, Clark Center, 2nd floor/W200

institute: Stanford University

data_processing:
Quality control, UMI counting of Ensemble genes and aggregation of samples were performed by count and aggr functions in the Cell Ranger software (version 3.1.0 with default settings)
Genome_build: Human: GRCh38
Supplementary_files_format_and_content: Count matrices, barcodes, and features

source_name: hSpS derived from hiPS cells; day 53

extract_protocol:
Dissociated single cells from were loaded onto a Chromium Single cell 3’ chip (Chromium Chip B Single Cell Kit, 10x Genomics, PN-1000154) with Chromium Single Cell 3’ Library & Gel Bead kit v3 (10x Genomics, PN-1000075) and proceeded according to manufacturer’s instructions.
cDNA library was generated with the Chromium Single Cell 3’ GEM, Library & Gel Bead kit v3 (10x Genomics, PN-1000078) according to manufacturer’s instructions.
Single-cell RNAseq

value: hiPS-derived spinal cord cells (hSpS)


description: Gene expression data from HepG2 exposed to 2-nitrofluorene for 48 h, biological replicate 1


title: S02_EX_6182_healthy: Healthy donor #2

description: Healthy Donor

value: Healthy


title: HFD TIL1


title: hSpS at day 45 of differentiation_no DAPT

data_processing:
BD Rhapsody pipeline for whole transcriptome analysis was used to identify the molecular index sequences (position 49-56) and align reads to predefined cell label sequences (position 1-8,22-30,43-51) on Read1, and to align reads (Read2) to the human transcriptome (hg19, gencode annotation) using STAR with default parameters. A unique cell label is a combination of the cell label sequences in the 3 indicated positions on Read1.
See the file "cell_ID_info.xlsx" on the series record for the numbered sequences for each position (1-8, 22-30 and 43-51).
Reads with the identical cell label, molecular index, and gene identity, are collapsed and counted as 1 molecule
Counts of molecule per gene per cell label are organized in a cell by gene matrix format, which is the final processed data file
Genome_build: hg19
Supplementary_files_format_and_content: Data tables containing number of molecules per gene per cell. Cell IDs are composed of the 3 sequence numbers for each position: (1-8)-(22-30)-(43-51). Sequence numbers for each sequence are available in the file "cell_ID_info.xlsx".

source_name: hiPS-derived 3D culture

growth_protocol: Differentiation of human iPS cells into hSpS

extract_protocol:
Dissociated single cells from were loaded onto the BD Rhapsody single cell gene expression analysis system
mRNA from individual cells were captured by barcoded oligo probes on a BD Rhapsody bead. Capture probes contain cell labels (total of 27 bases) and molecule index (8 randomers) such that when cDNAs were extended by reverse transcriptase, each cDNA molecule was tagged with a cell specific sequence and a molecular index sequence. cDNA were then universally amplified following by adaptor ligation. 3' end of transcripts were enriched using random priming and sequenced on Illumina HiSeq2500.

treatment_protocol: Patterning for spinal cord single cell trituration (no reporter used)


title: MAC_98R0016_Chr, lymph node

value: Chronic infection

value: Chr


title: CD LN8

source_name: CD8+ T lymphocyte from tumor draining lymph node

value: tumor draining lymph node


title: hSpS at day 45 of differentiation with DAPT treatment


title: CD LN7

value: Control Diet


title: SKGT4 rad 1

city: Bedford Park

first: George

last: Mayne

state: SA

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

department: Surgery

institute: Flinders University of South Australia

description:
ionising radiation
microRNA

data_processing:
Fluorescence data was exported to comma delimited text files and then analysed using R statistical software (version 3.4.3), and Microsoft Excel for Mac (version 16). The cycle threshold (Ct) value for each PCR assay was determined using the qpcR package v1.4 in R (https://cran.r-project.org/web/packages/qpcR/index.html). The relative levels of the miRNAs were determined using the formula 2^(40-Ct), and were normalized using the geometric means of the relative levels of selected HKGs.
Fold-change data set reports differences between cell lines chosen to be treated with cisplatin and 5-FU (treated samples not included here). This is because we chose to use the 2 most sensitive and 2 most resistant cell lines for each treatment (out of the of 8 cell lines that were tested), for our RNA investigations (in this case, miRNAs), and so we used different cell lines for cisplatin and 5-FU.
Normalized data set reports the House Keeping Gene normalised miRNA relative levels

label: FAMTM

source_name: oesophageal adenocarcinoma cell line

label_protocol: For cell line experiments, high throughput QuantStudio™ 12K Flex OpenArray® PCR custom made plates were used for miRNA profiling. These arrays were comprised of a panel of 112 miRNA probes (miRBase version 22 miRNA names, seed sequences, and miRBase accession numbers are in Supplementary file 2) that were selected based upon their abundance in OAC patient samples from our previous study on serum small extracellular vesicle associated miRNAs [94]. For each sample, 3.35 μl of RNA was reverse transcribed using a matching Custom OpenArray® miRNA RT pool (Life Technologies cat # A25630) and the TaqMan® microRNA Reverse Transcription Kit (Life Technologies cat # 4366596). cDNA Pre-amplifications were carried out with a matching Custom OpenArray® PreAmp pool (Life Technologies cat # 4485255) and TaqMan PreAmp Master Mix (Life Technologies cat # 4488593) on 7.5 μl complementary DNA (cDNA)/sample for each pool. The pre-amplified products (4 μl per sample) were diluted at the recommended 1:40 dilution with 156 μl of RNase-free ultra pure water before mixing with TaqMan OpenArray Real-Time PCR Master Mix (Life Technologies cat # 4462164) and loading onto a 384-well TaqMan OpenArray loading plate. PCR runs were performed using a QuantStudio™ 12K Flex Real-Time PCR System.

growth_protocol: All cell lines were cultured using RPMI 1640 medium  supplemented with 10 % fetal bovine serum (FBS) , 50 U/ml penicillin , 50 µg/ml streptomycin , and 100 µg/ml normocin.

extract_protocol: Total RNA isolation from untreated cell samples at time of treatment, including DNase digestion, was performed using the miRNeasy Mini Kit (Qiagen, #217004, Chadstone, Australia) and RNase-free DNase Set (Qiagen, #79254, Chadstone, Australia) as instructed by the manufacturer.

treatment_protocol: These are untreated cells. These samples were taken at the same time as a parallel set of samples were treated so that we could investigate the treatment naive RNA levels in these cells that may have contributed to their treatment responses. We collected 2 sets of samples from cells grown to different cell densities appropriate to either radiation treatment or chemotherapuetic drug treatment.

value: oesophageal adenocarcinoma

tag: treatment

value: untreated


title: OE33 rad 2

description:
ionising radiation
microRNA


title: SKGT4 rad 2

description:
ionising radiation
microRNA


title: OE19 rad 2

description:
ionising radiation
microRNA


title: OE19 rad 1

description:
ionising radiation
microRNA


description: Gene expression data from HepG2 exposed to 2-nitrofluorene for 24 h, biological replicate 1

tag: compound


title: MAC_503052_Chr, lymph node

value: CD4+ T cell


title: MAC_VI219_Euth, lymph node

value: Euth


description: Gene expression data from HepG2 exposed to 2-nitrofluorene for 24 h, biological replicate 2

tag: dose


title: MAC_504034_Chr, lymph node


title: MAC_503068_Chr, lymph node


title: CD LN4


title: OE33 rad 1

description:
ionising radiation
microRNA


title: IPH 27

first: Han

last: Jin

address: P. Debyelaan 25

description:
plaque with intraplaque haemorrhage
SAMPLE 43

hyb_protocol: Hybridization and washing were performed according to the Illumina standard assay procedure.

scan_protocol: Scanning was performed on the Illumina BeadStation 500 (Illumina, Inc., San Diego, CA, U.S.A.).

data_processing: Image analysis and extraction of raw expression data was performed with Illumina Beadstudio v3 Gene Expression software with default settings (no background substraction) and no normalization. Transcriptomic data were analysed using the R Bioconductor lumi package (v2.38.0).

source_name: carotid plaque

label_protocol: The RNA labeling, hybridisation and data extraction were performed at ServiceXS (Leiden, The Netherlands). Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin, TX, U.S.A.) according to the manufacturer's specifications starting with 100 ng total RNA. Per sample 750 ng of cRNA was used for hybridization.

extract_protocol: RNA of the 24 sample pairs was isolated using Guanidium Thiocyanate lysis followed by Cesium Chloride gradient centrifugation. After the extracting procedure, the RNA was further purified using the Nucleospin RNAII kit (Macherey-Nagel GmbH & Co. KG). RNA concentration was measured using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, U.S.A). The RNA quality and integrity was determined using Lab-on-Chip analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, U.S.A.). Samples that had an RNA Integrity Number (RIN) lower than 5.6 were excluded from the study. In total 43 samples (16 paired) from 24 patients were eligible for submission to the transcriptomics platform.

treatment_protocol: The endarterectomy specimens were cut into parallel, transverse segments of 5 mm thickness. Each alternating segment was snap frozen in liquid nitrogen and stored at -80 degrees C, their flanking segments fixed in formalin and processed for histological evaluation. Hematoxylin-Eosin (H.E) stained slides from these flanking segments have their plaques staged using the Virmani classification criteria by a cardiovascular pathologist (MD) and two experienced researchers in cardiovascular pathology (VH, JS). Segments designated as IPH or non-IPH based on the presence/absence of intraplaque haemorrhage.

tag: classification

value: IPH


title: CD LN5


title: IPH 26

description:
plaque with intraplaque haemorrhage
SAMPLE 42


title: MAC_9813552_Euth, lymph node

tag: cell type


title: CD LN2

tag: strain


title: JHEso Ad1 rad 1

description:
ionising radiation
microRNA

value: JHEso Ad1


title: FLO-1 rad 2

description:
ionising radiation
microRNA


title: JHEso Ad1 rad 2

description:
ionising radiation
microRNA


title: CD LN1

tag: diet


title: MAC_9808282_Euth, lymph node

value: lymph node


title: MAC_85696_D63, Blood

value: male

value: Blood


title: CD TIL6

value: female

value: subcutaneous MC38 tumor


title: IPH 24

description:
plaque with intraplaque haemorrhage
SAMPLE 40


title: IPH 25

description:
plaque with intraplaque haemorrhage
SAMPLE 41


title: HFD LN5

value: High-fat Diet


title: MAC_9801046_Euth, lymph node


description: Gene expression data from HepG2 exposed to clonidine for 48 h, biological replicate 1

value: clonidine

tag: time


title: IPH 21

description:
plaque with intraplaque haemorrhage
SAMPLE 37


title: FLO-1 rad 1

description:
ionising radiation
microRNA


title: ESO51 rad 2

description:
ionising radiation
microRNA


title: IPH 23

description:
plaque with intraplaque haemorrhage
SAMPLE 39


title: IPH 22

description:
plaque with intraplaque haemorrhage
SAMPLE 38


title: HFD LN4


title: MAC_54410_D14, Blood

value: Acute infection


title: MAC_85696_Pre, Blood

value: SIV-negative

value: Pre


title: MAC_85696_D14, Blood (RM85696-J14)


title: IPH 20

description:
plaque with intraplaque haemorrhage
SAMPLE 36


title: MAC_54189_D14, Blood


title: ESO26 rad 2

description:
ionising radiation
microRNA


title: MAC_53482_D65, Blood

value: Chronic infection


title: HFD LN3

value: tumor draining lymph node


title: HFD LN2


title: ESO26 rad 1

description:
ionising radiation
microRNA

value: oesophageal adenocarcinoma

value: untreated


title: HFD LN1


title: SK-GT-4 chemo 2

description:
chemotherapeutic drugs
microRNA


title: MAC_54410_D65, Blood

value: CD4+ T cell


title: HFD-Sample13

source_name: MC38 tumor

growth_protocol: GFP+ MC38 tumor cells were sorted from dissociated tumors 12 days post-implantation and RNA immediately extracted.

extract_protocol:
GFP+ MC38 colorectal cancer cells were sorted 12 days post-implantation from MC38 tumors in C57BL6/J mice.
RNA-libraries were constructed by enriching for mRNA using OligoDT beads, samples were fragmented, barcoded and then amplified

value: High Fat Diet


title: HFD-Sample14


title: IPH 18

description:
plaque with intraplaque haemorrhage
SAMPLE 34

value: IPH


title: HFD-Sample12


title: MAC_54189_D62, Blood


title: IPH 15

description:
plaque with intraplaque haemorrhage
SAMPLE 31


title: IPH 17

description:
plaque with intraplaque haemorrhage
SAMPLE 33


title: HFD-Sample11


title: OE 33 chemo 2

description:
chemotherapeutic drugs
microRNA

value: OE 33


title: IPH 14

description:
plaque with intraplaque haemorrhage
SAMPLE 30


title: MAC_54189_D14, lymph node

value: lymph node


title: MAC_85696_D14, Blood (85696_D14)

value: male

value: Blood


title: MAC_54410_D65, lymph node

value: female


title: MAC_53482_Pre, Blood


title: OE 19 chemo 1

description:
chemotherapeutic drugs
microRNA

value: OE 19


title: MAC_53482_D65, lymph node


title: IPH 16

description:
plaque with intraplaque haemorrhage
SAMPLE 32


title: OE 33 chemo 1

description:
chemotherapeutic drugs
microRNA


title: OE 19  chemo 2

description:
chemotherapeutic drugs
microRNA


title: MAC_53482_D14, lymph node


title: HFD-Sample10

value: subcutaneous MC38 tumor


title: MAC_54410_D14, lymph node

value: Acute infection


title: IPH 11

description:
plaque with intraplaque haemorrhage
SAMPLE 27


title: CD-Sample7

value: Control Diet


title: IPH 10

description:
plaque with intraplaque haemorrhage
SAMPLE 26


title: MAC_85696_Pre, lymph node

value: SIV-negative

value: Pre


title: JHEso Ad1 chemo 2

description:
chemotherapeutic drugs
microRNA

value: JHEso Ad1


title: MAC_54189_D65, lymph node

value: Chronic infection


title: MAC_85696_D65, lymph node


title: CD-Sample8


title: HFD-Sample9


title: OACP4C chemo 2

description:
chemotherapeutic drugs
microRNA

value: oesophageal adenocarcinoma

value: untreated


title: CD LN3

value: tumor draining lymph node


title: IPH 7

description:
plaque with intraplaque haemorrhage
SAMPLE 23

value: IPH


title: CD-Sample5


title: CD-Sample4


title: MAC_54410_Pre, lymph node

value: CD4+ T cell


title: Liver

city: Kobe

first: Gusty

middle: Rizky Teguh

last: Ryanto

state: Hyogo

address: 7-5-1, Kusunoki, Chuo

department: Cardiovascular Medicine

institute: Kobe University

hyb_protocol: 600 ng of cRNAs was used for hybridization with microarray chips (SurePrint G3 Human GE; G4851B; Agilent Technologies) for 17 h

scan_protocol: After washing, signals were scanned using an Agilent DNA microarray scanner (Agilent Technologies)

data_processing: Data were analyzed using Feature Extraction ver. 10.7.1.1 (Agilent Technologies)

source_name: Liver Tissue

label_protocol: Labeled cRNA was prepared using 1 vial of the mixed RNAs for each sample according to the One-Color Microarray-Based Gene Expression Analysis ver. 6.5 protocol

growth_protocol: RNAs for 5-donor pooled human lungs, heart, kidneys, and liver of were commercially obtained

extract_protocol: No additional extraction was performed to the samples. Concentrations were analyzed using NanoDrop ND-1000 (NanoDrop Technologies)

treatment_protocol: No treatment was done to the samples

tag: cell source

value: Commercially available RNA (BioTech Institute)


title: Flo-1 chemo 2

description:
chemotherapeutic drugs
microRNA


title: IPH 8

description:
plaque with intraplaque haemorrhage
SAMPLE 24


title: CD LN6


title: Flo-1 chemo 1

description:
chemotherapeutic drugs
microRNA


title: CD-Sample6


title: CD-Sample2


title: IPH 9

description:
plaque with intraplaque haemorrhage
SAMPLE 25


title: OACP4C chemo 1

description:
chemotherapeutic drugs
microRNA


title: CD-Sample1


title: H1

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of multiple sequencing runs were performed using the Cell Ranger analysis pipeline (v1.2)
Ambient RNA correction was performed using the SoupX package (v1.2.2)
Data normalization, dimension reduction, and differential expression analysis were performed using the Seurat R package (v3.1.5)
Genome_build: mm10
Supplementary_files_format_and_content: Files contain raw counts generated from Cell Ranger output. Files containing "matrix.mtx" are count matrices in sparse matrix format. Files containing "barcodes.tsv" are lists of barcodes for each sample. Files containing "genes.tsv" are lists of genes detected in samples.

source_name: tumor-infiltrating CD45+ leukocytes

growth_protocol: CD45+ leukocytes were enriched from dissociated MC38 tumors by MACS positive selection 12 days post-implantation into female C57BL6/J mice. Cells were immediately loaded on the 10X Chromium controller for single cell encapsulation.

extract_protocol:
CD45+ leukocytes from dissociated MC38 tumors were isolated by positive MACS selection (Miltenyi) 12 days post-implantation from female C57BL6/J mice fed control or high-fat diet for 8-10 weeks. Cells were immediately loaded on the 10X Chromium controller for single cell encapsulation.
Library construction was performed as per standard 10x protocol for single-cell 3' RNA-seq v2 (Manual CG00052 Rev B)

value: High-fat Diet


title: MAC_54189_Pre, lymph node

source_name: lymph node

value: lymph node


title: JHEso Ad1 chemo 1

description:
chemotherapeutic drugs
microRNA


title: C2

value: female


title: Eso 26 chemo 1

description:
chemotherapeutic drugs
microRNA

value: Eso 26


title: IPH 2

description:
plaque with intraplaque haemorrhage
SAMPLE 18


title: CD-Sample3

value: subcutaneous MC38 tumor


title: Kidney

source_name: Kidney Tissue


title: MAC_53482_Pre, lymph node

value: male


title: IPH 19

description:
plaque with intraplaque haemorrhage
SAMPLE 35


title: Heart

source_name: Heart Tissue


title: ESo 51 chemo 2

description:
chemotherapeutic drugs
microRNA

value: ESo 51


title: ESO51 rad 1

description:
ionising radiation
microRNA


title: ESo 51 chemo 1

description:
chemotherapeutic drugs
microRNA


title: Day5_M3

first: Bo

last: Zhu

address: 1 Blackfan Circle

department: Biology of Vascular Program

institute: Boston Children's Hospital

data_processing:
Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2
Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads.
Reads were aligned to Danio rerio genome version GRCz10 from Ensemble using tophat2
Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package.
Genome_build: GRCz10 (Ensembl build 84)
Supplementary_files_format_and_content: raw counts and normalized read counts for each sample in CSV/TSV format

organism: Danio rerio

source_name: ybx-/-_5 day

growth_protocol: The ybx1 F3 larvae ( ybx1+/+, ybx1+/-, and ybx1-/-) were maintained the ZebTEC multilinking rack system under an artificial photoperiod of 14 h light:10 h dark, and fed by paramecia and artemia.

extract_protocol:
Total RNA from day5 ybx1+/+, day6 ybx1+/+, day5 ybx1-/- larvae were extracted using Tri-Reagent according to the protocol of the manufacturer and our previous report (Wang & Ge, 2003).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: perform genotype screening among ybx1 F3, and separation of larvae with three different genotypes, day5 WT, day6 WT, and day5 ybx1-/- were used total RNA extraction.

tag: genotype/variation

value: ybx-/-

tag: age

value: 5 day

value: larvae


title: E13.5_male_IR_rep3

first: Victor

last: Navarro

address: 221 Longwood Ave

department: Division of Endocrinology

institute: Brigham and Women's Hospital

description:
MC3
E13.5_counttable_FPKM.xlsx

data_processing:
RNA-seq gene expression analysis with DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: excel count tables

source_name: E13.5 male primordial germ cells

extract_protocol:
Ribosomal RNA was subtracted by hybridization from total RNA samples using the RiboZero Magnetic Gold H/M/R Kit (Illumina)
TruSeq-barcoded RNA-seq libraries were generated with the NEBNext Ultra II RNA Library Prep Kit

treatment_protocol: samples were either treated with ionizing radiation (IR) or left untreated to serve as controls

value: E13.5 primordial germ cells

tag: Sex

tag: condition

value: ionizing radiation


title: Eso 26 chemo 2

description:
chemotherapeutic drugs
microRNA

value: oesophageal adenocarcinoma

value: untreated


title: E13.5_male_IR_rep1

description:
MC1
E13.5_counttable_FPKM.xlsx


title: non-IPH 15

description:
plaque without intraplaque haemorrhage
SAMPLE 15

value: non-IPH


title: Day5_M1


title: IPH 1

description:
plaque with intraplaque haemorrhage
SAMPLE 17

value: IPH


title: IPH 6

description:
plaque with intraplaque haemorrhage
SAMPLE 22


title: Lung

source_name: Lung Tissue

value: Commercially available RNA (BioTech Institute)


title: IPH 5

description:
plaque with intraplaque haemorrhage
SAMPLE 21


title: IPH 4

description:
plaque with intraplaque haemorrhage
SAMPLE 20


title: CAEC

hyb_protocol: 600 ng of cRNAs was used for hybridization with microarray chips (SurePrint G3 Human GE; G4851B; Agilent Technologies) for 17 hours

source_name: Coronary Artery Endothelial Cells

growth_protocol: PAECs and CAECs were cultured in HuMedia-EG2 (Kurabo), and hMVECs-L and hMVECs-D were cultured in EGM-MV2 (Lonza). Cells were cultured until subconfluency (~90%).

extract_protocol: When the cells became subconfluent (~90%), RNA was extracted from cultured ECs using TRIzol (Invitrogen) followed by RNeasy Mini Kit (Qiagen), and concentrations were analyzed using NanoDrop ND-1000 (NanoDrop technologies).

treatment_protocol: No treatment was done to the cells

value: Commercially available human cell lines (Clonetics)


title: 14dpi animal #3, lung sample for single-cell RNA-seq

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al, 2015)
Sequencing reads were aligned to the MesAur 1.0 version of the Mesocricetus auratus genome using standard parameter, using the Refseq gtf file downloaded from ENSEMBL, with the following adjustments to extend 3' UTR lengthes:
cat ../MesAur/Mesocricetus_auratus.MesAur1.0.99.gtf | perl -ane 'print if (!($F[2] =~ m/five_prime_utr/ || $F[2] =~ m/gene/ || $F[2] =~ m/three_prime_utr/ || $F[2] =~ m/transcript/))' | bedtools sort -i /dev/stdin > ma1_genes.gtf
cat ma1_genes.gtf | perl -ane 'print if ($F[6] eq "+")' > ma1_genes_plus.gtf
cat ma1_genes.gtf | perl -ane 'print if ($F[6] eq "-")' > ma1_genes_minus.gtf
cat ma1_genes_plus.gtf | perl -ne 'm/transcript_id \"([^\"]*)\"/; print "$1\n";' | sort -u > transcripts_plus.txt
cat ma1_genes_minus.gtf | perl -ne 'm/transcript_id \"([^\"]*)\"/; print "$1\n";' | sort -u > transcripts_minus.txt
samtools faidx genome-ma1.fa
for t in `cat transcripts_plus.txt`; do grep $t ma1_genes_plus.gtf > temp_plus.gtf; chr=`cut -f 1 temp_plus.gtf | head -1`; l=`grep -P "^$chr\t" genome-ma1.fa.fai | cut -f 2`; export l; s=`tac temp_plus.gtf | grep -P "\texon\t" | head -1`; r=`tac temp_plus.gtf | grep -P "\texon\t" | head -1 | perl -F'\t' -ane '$l=$ENV{"l"}; $F[4]+=1000; if ($F[4] > $l-1) {$F[4] = $l-1} print(join("\t", @F));'`; export s; export r; cat temp_plus.gtf | perl -ne 'chomp; chomp $s; chomp $r; $s=$ENV{"s"}; $r=$ENV{"r"}; if ($_ eq $s) {print "$r\n"} else {print "$_\n"}'; done > ma1_genes_longer_plus.gtf
for t in `cat transcripts_minus.txt`; do grep $t ma1_genes_minus.gtf > temp_minus.gtf; s=`cat temp_minus.gtf | grep -P "\texon\t" | head -1`; r=`cat temp_minus.gtf | grep -P "\texon\t" | head -1 | perl -F'\t' -ane '$F[3]-=1000; if ($F[3] < 1) {$F[3] = 1} print(join("\t", @F));'`; export s; export r; cat temp_minus.gtf | perl -ne 'chomp; chomp $s; chomp $r; $s=$ENV{"s"}; $r=$ENV{"r"}; if ($_ eq $s) {print "$r\n"} else {print "$_\n"}'; done > ma1_genes_longer_minus.gtf
cat ma1_genes_longer_plus.gtf ma1_genes_longer_minus.gtf | bedtools sort -i /dev/stdin > ma1_genes_longer.gtf
The 3'-UTR of the Ifit2 gene was in addition manually extended for 1000 nt
Reads were then quantified using quasR (Gaidatzis et al, 2015)
For SARS-CoV-2 alignements, GenBank entry MN908947 was used
For single-cell RNA-sequencing data, fastq files were processed using a merged MesAur/SARS-CoV-2 genome by applying CellRanger 3.1.0 with standard parameters
Genome_build: MesAur 1.0
Genome_build: SARS-CoV-2 MN908947
Supplementary_files_format_and_content: ma1_genes_longer.gtf
readcounts_ma.tsv
h5 matrix

organism: Mesocricetus auratus

source_name: Syrian gold hamster

growth_protocol:
Clinical evaluation of hamsters included twice-daily monitoring and weighting. Animals with >15 % body weight loss for over 48 h were euthanized in accordance with the animal use protocol. Naïve hamsters (n = 3) and hamsters at time points 2, 3, 5 and 14 days post infection (dpi) (n = 3, each) were selected randomly.
Euthanasia prior analysis occurred by exsanguination under anesthesia as previously described  (Osterrieder et al. 2020). 1 mL peripheral blood was collected in EDTA-coated syringes and lung lobes were collected for follow-up analyses, in which the left lobe was used for histopathology, the right caudal lobe for single-cell analysis, the right cranial lobe for virological assessments and the right medial for bulk RNA and proteomics analysis.

extract_protocol:
10xGenomics Chromium v3.1 single cell 3' gene expression kit
For isolation of cells from whole blood, 250 µL blood were lysed in red blood cell lysis buffer (BioLegend), washed and centrifuged according to the manufacturer’s instructions. Resulting RBC-free pellets were resuspended in low-BSA buffer (1× PBS, 0.04 % BSA), filtered with 40 µm FloMi filters (Merck) suitable for volumes below 500 µL and counted microscopically by hemocytometer in trypan blue.
For isolation of single cells lobus caudalis of the right lung was removed and placed in storage medium (1× PBS, 0.5 % BSA) until further processing. Storage and isolation media contained 2 µg/mL ActinomycinD. Tissues and cells were always spun at 350 x g for 6 minutes at 4 °C. Mechanical dissociation of lung lobes was achieved by clapping motions with tweezers for 2 minutes in enzymatic digestion medium (3,4 mg/mL Collagenase Cls II (Merck), 1 mg/mL DNase I (PanReac AppliChem), in 2 mL Dispase medium per lung lobe (Corning), 50 Caseinolytic Units/mL followed by 30 minutes incubation at 37°C and 5 % CO2.
Further tissue dissociation was achieved by repeated pipetting of digested lung tissue with 5 mL pipettes and passing of cell suspension with plungers through 70 µm cell strainers. Cells were pelleted from suspension by centrifugation and resuspended in red blood cell lysis buffer (BioLegend). Lysis reaction was stopped and cells washed with excessive volumes of PBS/BSA. Cells were centrifuged, resuspended in low-BSA buffer (1× PBS, 0.04 % BSA), filtered with 40 µm FloMi filters (Merck) suitable for low volumes and quantified microscopically in trypan blue.
For Lung RNA Bulk Sequencing the lobus medialis of the right lung lobe was removed carefully and stored in RNA Later Solution for a maximum of 24 hours at 4°C (Thermofisher). Lung Tissue was homogenized using the TissueLyser II system (Qiagen) and the homogenate stored in Trizol reagent.
For WBC RNA Bulk Sequencing, white blood cells were isolated as described for scSeq followed by lysis in Trizol reagent.
RNA was extracted using the DirectZol kit (Zymo research)
Bulk and single-cell RNA-sequencing libraries were constructed using commercial kits (New England Biolabs, 10xGenomics), see column "library construction protocol" in the SAMPLES section.

treatment_protocol: At 10–12 weeks of age hamsters were infected intranasally as previously described (Osterrieder et al. 2020). Briefly, hamster received 1 x 105 pfu SARS-CoV-2 intranasally under anesthesia.

tag: sars-cov-2 infection

value: yes

tag: sampling timepoint

value: lung


title: non-IPH 13

description:
plaque without intraplaque haemorrhage
SAMPLE 13


title: PAEC

source_name: Pulmonary Artery Endothelial Cells

value: Commercially available human cell lines (PromoCell)


title: MVEC_D

source_name: Microvascular Endothelial Cells of the Dermis


title: C1

value: female

tag: tissue

value: subcutaneous MC38 tumor

value: Control Diet


title: IPH 3

description:
plaque with intraplaque haemorrhage
SAMPLE 19


title: 14dpi animal #2, lung sample for single-cell RNA-seq


title: IPH 12

description:
plaque with intraplaque haemorrhage
SAMPLE 28


title: non-IPH 16

description:
plaque without intraplaque haemorrhage
SAMPLE 16


title: SK-GT-4 chemo 1

description:
chemotherapeutic drugs
microRNA

tag: cell line


title: 14dpi animal #3, blood sample for single-cell RNA-seq

value: blood


title: MVEC_L

source_name: Microvascular Endothelial Cells of the Lung


title: Day5_M2

value: ybx-/-

value: 5 day


title: 14dpi animal #1, blood sample for single-cell RNA-seq


title: E13.5_male_IR_rep2

description:
MC2
E13.5_counttable_FPKM.xlsx

value: E13.5 primordial germ cells

value: male


title: E13.5_male_noIR_rep2

description:
MIR2
E13.5_counttable_FPKM.xlsx


title: Day6_3

source_name: WT_6 day

value: WT

value: 6 day

value: larvae


title: E13.5_male_noIR_rep3

description:
MIR3
E13.5_counttable_FPKM.xlsx


title: non-IPH 11

description:
plaque without intraplaque haemorrhage
SAMPLE 11

value: non-IPH


title: Day6_2


title: 14dpi animal #2, blood sample for single-cell RNA-seq


title: non-IPH 14

description:
plaque without intraplaque haemorrhage
SAMPLE 14


title: 5dpi animal #3, blood sample for single-cell RNA-seq


title: Day5_2

source_name: WT_5 day


title: non-IPH 12

description:
plaque without intraplaque haemorrhage
SAMPLE 12

source_name: carotid plaque


title: E13.5_male_noIR_rep1

description:
MIR1
E13.5_counttable_FPKM.xlsx


title: 5dpi animal #1, blood sample for single-cell RNA-seq


title: non-IPH 10

description:
plaque without intraplaque haemorrhage
SAMPLE 10


title: E13.5_female_noIR_rep3

description:
FC3
E13.5_counttable_FPKM.xlsx

source_name: E13.5 female primordial germ cells


title: Day5_3


title: 14dpi animal #1, lung sample for single-cell RNA-seq


title: Day5_1


title: non-IPH 9

description:
plaque without intraplaque haemorrhage
SAMPLE 9


title: Day6_1


title: E13.5_female_noIR_rep2

description:
FC2
E13.5_counttable_FPKM.xlsx


title: non-IPH 7

description:
plaque without intraplaque haemorrhage
SAMPLE 7


title: non-IPH 8

description:
plaque without intraplaque haemorrhage
SAMPLE 8


title: E13.5_female_noIR_rep1

description:
FC1
E13.5_counttable_FPKM.xlsx


title: 5dpi animal #2, blood sample for single-cell RNA-seq


title: 5dpi animal #3, lung sample for single-cell RNA-seq


title: non-IPH 6

description:
plaque without intraplaque haemorrhage
SAMPLE 6


title: E13.5_female_IR_rep2

description:
FIR2
E13.5_counttable_FPKM.xlsx

value: ionizing radiation


title: Wildtype replicate 3

city: Zürich

first: Christian

last: Mosimann

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

country: Switzerland

institute: University of Zürich

description:
Wildtype replicate 3
W3

data_processing:
reads were mapped to the UCSC Danio rerio danRer10 genome with the TopHat v.2.0.11 software
normalization and differential expression analysis were performed with R/Bioconductor package EdgeR v. 3.14
the gene features were counted with HTSeq v.0.6.1 (htseq-count) on the UCSC danRer10 gene annotation
Genome_build: danRer10

source_name: anterior structures

growth_protocol: All zebrafish embryos were raised and mainteined in E3 medium at 28.5 °C without light cycle.

extract_protocol:
Zebrafish embryos from bcl9∆29/wt crosses were dissected at 56 hpf: a cut was made between the anterior part of the embryo. The anterior tissues were directly snap-frozen in liquid nitrogen in single tubes of PCR 8-tube strips. The posterior trunks and tails were transferred in 50 mM NAOH and genomic DNA was extracted with alkaline lysis for genotyping.  All snap-frozen anterior parts of bcl9∆29 mutants and of wildtypes were pooled in two separate tubes and RNA isolation performed with the RNeasy Plus Mini Kit (Qiagen). The whole procedure was repeated for a total of three clutches making three independent replicates.
TruSeq mRNA stranded kit from Illumina was used for the library preparation with 250 ng of total RNA as input.

value: wildtype

tag: developmental stage

value: embryo at 54 hpf


title: Mutant replicate 2

description:
Mutant replicate 2
M2


title: 5dpi animal #1, lung sample for single-cell RNA-seq

value: yes

value: lung


title: Mutant replicate 3

description:
Mutant replicate 3
M3


title: E13.5_female_IR_rep1

description:
FIR1
E13.5_counttable_FPKM.xlsx

value: E11.5 primordial germ cells

value: female


title: 5dpi animal #2, lung sample for single-cell RNA-seq


title: E11.5_noIR_rep3

description:
E11.5_noIR3.bam
E11.5_counttable_FPKM.xlsx

source_name: E11.5 primordial germ cells


title: Wildtype replicate 2

description:
Wildtype replicate 2
W2


title: 3dpi animal #3, blood sample for single-cell RNA-seq


title: Mutant replicate 1

description:
Mutant replicate 1
M1


title: 3dpi animal #2, blood sample for single-cell RNA-seq


title: 3dpi animal #1, blood sample for single-cell RNA-seq


title: Wildtype replicate 1

description:
Wildtype replicate 1
W1


title: non-IPH 4

institute: Maastricht University

description:
plaque without intraplaque haemorrhage
SAMPLE 4


title: E11.5_noIR_rep1

description:
E11.5_noIR1.bam
E11.5_counttable_FPKM.xlsx


title: 3dpi animal #2, lung sample for single-cell RNA-seq