title: N5_04_nCOV_OIRRA_Lib37_20200402

description:
N5_04_nCOV_OIRRA_Lib37_20200402_IonXpress_037
processed data file:
user_S5-0093-269-OIRRA_2b_20200402.bcmatrix.csv
user_S5-0093-269-OIRRA_2b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-269-OIRRA_2b_20200402.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

value: M

tag: diagnosis

value: Control (other cause of death)

tag: topography

value: Lung, right superior + inferior lobe

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: copd

tag: smoker

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: Patient Sample, C016_d28

status: Public on Sep 02 2020

type: SRA

city: Boston

first: James

middle: John

last: Kaminski

state: MA

address: 1 Blackfan Circle

department: Hematology / Oncology

country: USA

institute: Boston Children's Hospital

library_source: transcriptomic

data_processing:
Trim reads with trimmomatic. Settings :-phred33 ILLUMINACLIP:Nextera-SE.fa:2:30:10 LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:80
Align to human index using kallisto v0.46.1 (Human index built using Ensembl v99 annotation and GRCh38.p13 reference genome.)
Load matrix of counts into DESeq2 with tximport
Filter matrix to genes with biotype protein_coding or lncRNA.
Retrieve normalized counts from DESeq2
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Bulk_RNASeq_Normalized_Counts.tsv contains normalized RNA-Seq abundances from DESeq2

molecule: total RNA

organism: Homo sapiens

extract_protocol:
We sorted CD8+ T cells from blood samples obtained from hematopoietic cell transplant patients in the placebo-control arm of the ABA2 clinical trial (NCT# NCT01743131)
RNA was isolated from CD4 and CD8 sorted T cells for each patient using the RNeasy Micro kit  (Qiagen) with on-column DNase digestion. RNA quality was assessed using an Agilent  Bioanalyzer and two nanograms of total RNA was used as input for cDNA synthesis using the  Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s  instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using  the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary  electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and  sequenced on an Illumina HiSeq3000 at 100SR, yielding approximately 20 million reads per  sample.

tag: patient id

tag: time

value: 28 days since the patient's hematopoietic cell transplant

tag: tissue

value: blood

tag: cell type

value: CD8+ T cells


title: Sample_5_GCB_H1_DKO_repl1_RNAseq

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to mm10 using STAR with default parameters
TPM were obtained using Rsubread using RefSeq
ChIP-seq reads were aligned to mm10 using BWA with default parameters
Peaks were called using SICER
Genome_build: mm10
Supplementary_files_format_and_content: TPM, SICER peaks

organism: Mus musculus

source_name: GC B cell

extract_protocol:
RNA-seq libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit according to the manufacturer
ChIP-seq libraries for H3K27me3 (C36B11 - Cell Signaling #9733) and H3K36me2 (C75H12 - CellSignaling #2901) were prepared using TrueMicroChip kit according to the manufacturer

treatment_protocol: Included as additional column of SAMPLES section

tag: genotype

value: Constitutive H1c-/-;H1e-/-


title: P4_13_nCOV_OIRRA_Lib35_20200402

city: Liestal

first: Ronny

last: Nienhold

address: Mühlemattstrasse 11

department: Institute of Pathology

country: Switzerland

institute: Cantonal Hospital Baselland

description:
P4_13_nCOV_OIRRA_Lib35_20200402_IonXpress_035
processed data file:
user_S5-0093-269-OIRRA_2b_20200402.bcmatrix.csv
user_S5-0093-269-OIRRA_2b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-269-OIRRA_2b_20200402.rpm.bcmatrix.csv

data_processing:
De-multiplexing and gene expression level quantification were performed with the standard setting of the ImmuneResponseRNA plugin, provided as part of the OIRRA.
Genome_build: hg19
Supplementary_files_format_and_content: comma separated values

source_name: Lung

extract_protocol:
RecoverAll Total Nucleic Acid Isolation Kit (Cat No. AM1975, Thermo Fisher Scientific, Waltham, MA, USA)
Oncomine Immune Response Research Assay (OIRRA, Cat No. A32881, Thermo Fisher Scientific, Waltham, MA, USA)
targeted RNA-seq

tag: material

value: FFPE

tag: age

tag: Sex

tag: diagnosis

value: Other pathology of the lung:Bacterial pneumonia - Lobärpneumonie, Klebsiella pneumoniae

tag: topography

value: Lung, right inferior lobe

tag: time post mortem (h)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf


title: ExVivoBlood_25% Neutron_rep3

type: RNA

first: Sanjay

last: Mukherjee

address: 630 W 168th street

institute: Columbia University

hyb_protocol: 1.65 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 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan setting with eXtended dynamic range, Scan area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not Positive and significant were excluded.  Data were filtered to exclude features not positive and significant in 25% of the samples, or those without at least a 1.5-fold change in expression values across the samples.
Please note that the reduced data set (of 12,905 data rows) resulted from the filtering for bad features. Out of 34184 features 12905 passed through the filtering criteria (Feature Non-uniform outliers or Features not Positive and significant were excluded).

source_name: ExVivoBlood_25% Neutron

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling 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.

growth_protocol: After irradiation, blood samples were diluted 1:1 with RPMI 1640 medium (Mediatech, Herndon, VA) supplemented with 10% heat-inactivated fetal bovine serum (HyClone, Logan, UT), as previously described (Grace et al., Int J Radiat Biol 2002; 78:1011-21; PMID 12456288), and were incubated for 24 h  at 37○ C in a humidified incubator with 5% CO2

extract_protocol: The RNA was prepared using the QiaAmp blood RNA mini kit (Qiagen) following the manufacturer recommendations. This protocol differentially lyses red and white blood cells in whole blood to preferentially deplete   globin mRNA. Remaining globin mRNA was further reduced using GLOBINclear (Ambion Inc., Austin, TX) specifically to remove both a- and b-globin. The RNA was quantified using a NanoDrop-1000 spectrophotometer, and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Peripheral blood from healthy volunteers was drawn into 0.105 mol/l sodium citrate Vacutainer tubes (Becton Dickinson and Company, Franklin Lakes, NJ). The blood was divided into 3-ml aliquots and exposed to neutrons followed by X-ray to a cumulative dose of 3Gy containing different percentges of Neutrons. Pure X-ray of 3Gy exposure was considered as 0% neutron. One aliquote of blood tubes from each donor was Sham-irradiated which served as control.

tag: donor id

value: Donor 3

tag: tissue

value: Peripheral blood

tag: treatment

value: 25%Neutron-X-ray mixed field-irradiated


title: Sample_4_GCB_WT_repl4_RNAseq

tag: genotype

value: WT littermate control


title: ExVivoBlood_25% Neutron_rep2

value: Donor 2


title: ExVivoBlood_25% Neutron_rep1

value: Donor 1


title: P4_10_nCOV_OIRRA_Lib34_20200402

description:
P4_10_nCOV_OIRRA_Lib34_20200402_IonXpress_034
processed data file:
user_S5-0093-269-OIRRA_2b_20200402.bcmatrix.csv
user_S5-0093-269-OIRRA_2b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-269-OIRRA_2b_20200402.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

value: Lung, left inferior lobe

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: copd

tag: smoker

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: C1_3_nCOV_OIRRA_Lib42_20200402

description:
C1_3_nCOV_OIRRA_Lib42_20200402_IonXpress_042
processed data file:
user_S5-0093-269-OIRRA_2b_20200402.bcmatrix.csv
user_S5-0093-269-OIRRA_2b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-269-OIRRA_2b_20200402.rpm.bcmatrix.csv

value: F

tag: topography

tag: time post mortem (h)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

value: Negativ (high Ct value)

tag: hypertension

tag: cvrf


title: Patient Sample, C016_d21

tag: patient id

tag: time

value: 21 days since the patient's hematopoietic cell transplant

tag: tissue

tag: cell type


title: P3_04_nCOV_OIRRA_Lib32_20200402

description:
P3_04_nCOV_OIRRA_Lib32_20200402_IonXpress_032
processed data file:
user_S5-0093-268-OIRRA_b_20200402.bcmatrix.csv
user_S5-0093-268-OIRRA_b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-268-OIRRA_b_20200402.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

value: Other pathology of the lung:Bacterial pneumonia - Lobärpneumonie, Streptococcus pneumoniae

value: Lung, right superior + inferior lobe

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: copd

tag: smoker

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: Sample_3_GCB_WT_repl3_RNAseq

tag: genotype


title: N5_03_nCOV_OIRRA_Lib36_20200402

description:
N5_03_nCOV_OIRRA_Lib36_20200402_IonXpress_036
processed data file:
user_S5-0093-269-OIRRA_2b_20200402.bcmatrix.csv
user_S5-0093-269-OIRRA_2b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-269-OIRRA_2b_20200402.rpm.bcmatrix.csv

value: M

value: Control (other cause of death)

tag: topography

value: Lung, left superior + inferior lobe

tag: time post mortem (h)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf


title: ExVivoBlood_15% Neutron_rep4

source_name: ExVivoBlood_15% Neutron

tag: donor id

value: Donor 4

tag: tissue

tag: treatment

value: 15%Neutron-X-ray mixed field-irradiated


title: P1_23_nCOV_OIRRA_Lib31_20200402

description:
P1_23_nCOV_OIRRA_Lib31_20200402_IonXpress_031
processed data file:
user_S5-0093-268-OIRRA_b_20200402.bcmatrix.csv
user_S5-0093-268-OIRRA_b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-268-OIRRA_b_20200402.rpm.bcmatrix.csv

tag: material

value: FFPE

tag: age

tag: Sex

tag: diagnosis

value: Other pathology of the lung:Tuberculosis

value: Lung, right inferior lobe

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: copd

tag: smoker

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: ExVivoBlood_15% Neutron_rep5

tag: donor id

value: Donor 5

tag: tissue

value: Peripheral blood


title: Patient Sample, C015_d21

tag: patient id

tag: time

value: blood

tag: cell type

value: CD8+ T cells


title: Patient Sample, C015_d28

value: 28 days since the patient's hematopoietic cell transplant


title: Sample_2_GCB_WT_repl2_RNAseq

tag: genotype

value: WT littermate control


title: Patient Sample, C014_d28


title: Patient Sample, C014_d21

value: 21 days since the patient's hematopoietic cell transplant


title: ExVivoBlood_15% Neutron_rep2

value: Donor 2

tag: treatment


title: inlf

city: Madison

first: Xinyu

last: Zhao

state: Wisconsin

address: 1500 HIghland Ave, Wiasman Center North Tower T513

institute: University of Wisconsin Madison

description: input sample

data_processing:
Cluster generation and high-throughput sequencing were performed on a HiSeq 2500 (Illumina), using the single-end 100 bp protocol. RSEM was used to align read pairs to the mm10 transcriptome and estimate gene expression levels (Li and Dewey 2011)
Genome_build: mm10
Supplementary_files_format_and_content: CSV file with TPM values

source_name: dentate gyrus

growth_protocol: We generated the inducible conditional ribosome tagging mice (Tg(Nestin-cre/ERT2)::RPL22HA/WT, simplified as Nes-CreERT2::RiboTag) by crossing transgenic driver Tg(Nes-cre/ERT2) mice (JAX Stock No:016261) (Lagace, Whitman et al. 2007) with RPL22HA/WT  mice (JAX Stock No:029977) (Sanz, Yang et al. 2009). Mice were kept in 12 hours light/12 dark cycle housing.

extract_protocol:
RNA from the RiboTag IP was isolated using the Direct-zol™ RNA MicroPrep Kit (Zymo Research Corporation. Irvine, CA, USA).
The libraries were made using SMARTer® Stranded Total RNA-Seq Kit v2 (Takara Bio USA, Inc. Mountain View, CA) according to the user manual.

treatment_protocol: To induce recombination, mice (9–11 weeks old) received Tamoxifen (Sigma-Aldrich) daily for 5 days (160 mg kg–1 i.p., 40 mg ml–1 in 10% ethanol mixed with sunflower oil, Sigma-Aldrich).  Running mice were individually housed in regular mouse cages that contain one running wheel with wireless monitor per cage (Med Associates inc). Sedentary mice were housed in identical cages as running mice except that the wheels were glued (blocked) and without wireless monitor (Med Associates, inc). The mice were kept in 12 hours light/12 dark cycle housing.

value: dentate gyrus

tag: strain

tag: gender

value: female

tag: treatment time

value: 27 days

tag: group

value: sedentary mouse


title: inrf

description: input sample

value: running mouse


title: N4_04_nCOV_OIRRA_Lib29_20200402

description:
N4_04_nCOV_OIRRA_Lib29_20200402_IonXpress_029
processed data file:
user_S5-0093-268-OIRRA_b_20200402.bcmatrix.csv
user_S5-0093-268-OIRRA_b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-268-OIRRA_b_20200402.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

value: M

tag: diagnosis

value: Control (other cause of death)

tag: topography

value: Lung, right superior + inferior lobe

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker


title: ExVivoBlood_15% Neutron_rep3

tag: donor id

value: Donor 3

tag: tissue

tag: treatment

value: 15%Neutron-X-ray mixed field-irradiated


title: inle

description: input sample

tag: strain

tag: gender

tag: treatment time

tag: group


title: ExVivoBlood_15% Neutron_rep1

value: Donor 1

value: Peripheral blood


title: ExVivoBlood_5% Neutron_rep5

source_name: ExVivoBlood_5% Neutron

value: Donor 5

value: 5%Neutron-X-ray mixed field-irradiated


title: N3_03_nCOV_OIRRA_Lib27_20200402

description:
N3_03_nCOV_OIRRA_Lib27_20200402_IonXpress_027
processed data file:
user_S5-0093-268-OIRRA_b_20200402.bcmatrix.csv
user_S5-0093-268-OIRRA_b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-268-OIRRA_b_20200402.rpm.bcmatrix.csv

tag: material

value: FFPE

tag: age

tag: Sex

value: F

tag: diagnosis

tag: topography

value: Lung, left superior + inferior lobe

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: Patient Sample, C012_d28

tag: patient id

tag: time

value: 28 days since the patient's hematopoietic cell transplant

tag: tissue

value: blood

tag: cell type

value: CD8+ T cells


title: inre

description: input sample

value: dentate gyrus

tag: strain

tag: gender

value: female

tag: treatment time

value: 27 days

tag: group


title: N2_03_nCOV_OIRRA_Lib26_20200402

description:
N2_03_nCOV_OIRRA_Lib26_20200402_IonXpress_026
processed data file:
user_S5-0093-268-OIRRA_b_20200402.bcmatrix.csv
user_S5-0093-268-OIRRA_b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-268-OIRRA_b_20200402.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

value: M

tag: diagnosis

value: Control (other cause of death)

tag: topography

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker


title: Sample_1_GCB_WT_repl1_RNAseq

tag: genotype

value: WT littermate control


title: ExVivoBlood_5% Neutron_rep3

tag: donor id

value: Donor 3

tag: tissue

tag: treatment


title: ExVivoBlood_5% Neutron_rep4

value: Donor 4


title: P2_20_nCOV_OIRRA_Lib30_20200402

description:
P2_20_nCOV_OIRRA_Lib30_20200402_IonXpress_030
processed data file:
user_S5-0093-268-OIRRA_b_20200402.bcmatrix.csv
user_S5-0093-268-OIRRA_b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-268-OIRRA_b_20200402.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

value: Other pathology of the lung:ARDS, Candida sepsis

tag: topography

value: Lung, left inferior lobe

tag: time post mortem (h)

tag: bmi

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: inrd

description: input sample

tag: tissue

tag: strain

tag: gender

tag: treatment time

value: 18 days

tag: group

value: running mouse


title: Patient Sample, C011_d28

tag: patient id

tag: time

tag: cell type


title: ExVivoBlood_5% Neutron_rep2

tag: donor id

value: Donor 2

value: Peripheral blood

tag: treatment

value: 5%Neutron-X-ray mixed field-irradiated


title: Patient Sample, C010_d28

value: 28 days since the patient's hematopoietic cell transplant

value: blood


title: N1_03_nCOV_OIRRA_Lib25_20200402

description:
N1_03_nCOV_OIRRA_Lib25_20200402_IonXpress_025
processed data file:
user_S5-0093-268-OIRRA_b_20200402.bcmatrix.csv
user_S5-0093-268-OIRRA_b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-268-OIRRA_b_20200402.rpm.bcmatrix.csv

tag: material

value: FFPE

tag: age

tag: Sex

tag: diagnosis

tag: topography

value: Lung, left superior + inferior lobe

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker


title: N4_03_nCOV_OIRRA_Lib28_20200402

description:
N4_03_nCOV_OIRRA_Lib28_20200402_IonXpress_028
processed data file:
user_S5-0093-268-OIRRA_b_20200402.bcmatrix.csv
user_S5-0093-268-OIRRA_b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-268-OIRRA_b_20200402.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

tag: histology - dad (1 = yes; 0 = no)

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: C12_36_nCOV_OIRRA_Lib21_20200402

description:
C12_36_nCOV_OIRRA_Lib21_20200402_IonXpress_021
processed data file:
user_S5-0093-268-OIRRA_b_20200402.bcmatrix.csv
user_S5-0093-268-OIRRA_b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-268-OIRRA_b_20200402.rpm.bcmatrix.csv

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)


title: inlc

description: input sample

tag: tissue

value: dentate gyrus

tag: strain

tag: gender

value: female

tag: treatment time

tag: group

value: sedentary mouse


title: Patient Sample, C010_d21

tag: patient id

tag: time

value: 21 days since the patient's hematopoietic cell transplant

tag: cell type

value: CD8+ T cells


title: Patient Sample, C013_d28


title: ExVivoBlood_5% Neutron_rep1

tag: donor id

value: Donor 1

tag: treatment


title: inrc

description: input sample


title: Patient Sample, C009_d21


title: inlb

description: input sample

value: 11 days


title: C12_32_nCOV_OIRRA_Lib20_20200402

description:
C12_32_nCOV_OIRRA_Lib20_20200402_IonXpress_020
processed data file:
user_S5-0093-268-OIRRA_b_20200402.bcmatrix.csv
user_S5-0093-268-OIRRA_b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-268-OIRRA_b_20200402.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

value: M

tag: diagnosis

tag: topography

value: Lung, left inferior lobe

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: histology - dad (1 = yes; 0 = no)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd

tag: smoker

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: inld

description: input sample

tag: tissue

tag: strain

tag: gender

tag: treatment time

value: 18 days

tag: group


title: Patient Sample, C008_d28

tag: patient id

tag: time

tag: cell type


title: ExVivoBlood_0% Neutron(3Gy X-ray)_rep4

source_name: ExVivoBlood_0% Neutron(3Gy X-ray)

tag: donor id

value: Donor 4

tag: treatment

value: 3Gy X-ray-irradiated(0% Neutron)


title: C12_31_nCOV_OIRRA_Lib19_20200402

description:
C12_31_nCOV_OIRRA_Lib19_20200402_IonXpress_019
processed data file:
user_S5-0093-268-OIRRA_b_20200402.bcmatrix.csv
user_S5-0093-268-OIRRA_b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-268-OIRRA_b_20200402.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

value: Lung, left superior lobe

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

tag: anamnestic symptom onset to death (days)

tag: hospitalisation time (days)

tag: histopathologic changes in lungs (1 = slight to moderate changes; 2 = moderate changes; 3 = severe changes)

tag: histology - dad (1 = yes; 0 = no)

tag: dad stage (1 = exudative; 2 = proliferating/organizing; 3 = fibrotic)

tag: intraalveolar edema (1 = yes; 0 = no)

tag: intraalveolar hemorrhage (1 = yes; 0 = no)

tag: neutrophils (1 = few; 2 = moderate; 3 = numerous)

tag: sars-cov-2 genomes / 10^6 rnasep copies

tag: hypertension

tag: cvrf

tag: copd


title: Patient Sample, C012_d21

tag: patient id

tag: time

tag: tissue

tag: cell type


title: C13_03_nCOV_OIRRA_Lib22_20200402

description:
C13_03_nCOV_OIRRA_Lib22_20200402_IonXpress_022
processed data file:
user_S5-0093-268-OIRRA_b_20200402.bcmatrix.csv
user_S5-0093-268-OIRRA_b_20200402.mean_hk_scaled_log2_count.csv
user_S5-0093-268-OIRRA_b_20200402.rpm.bcmatrix.csv

tag: material

tag: age

tag: Sex

tag: diagnosis

tag: topography

tag: time post mortem (h)

tag: bmi

tag: pre-existing pulmonary condition(s)

tag: antiviral medication yes (1) / no (0)

value: unclear

value: 1 to 2

tag: smoker

tag: diabetes

tag: malignant tumor

tag: cough

tag: fever

tag: dyspnea / tachypnea


title: inrb

description: input sample

tag: tissue

tag: strain

tag: gender

tag: treatment time

tag: group

value: running mouse


title: ExVivoBlood_0% Neutron(3Gy X-ray)_rep3

tag: donor id

value: Donor 3

value: Peripheral blood

tag: treatment


title: Patient Sample, C008_d21

tag: patient id

tag: time

value: blood

tag: cell type


title: Fx_Callus_d7_CGRP_9

city: Hamburg

first: Thorsten

last: Schinke

address: Martinistr. 52

department: Department of Osteology and Biomechanics

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 h at 45 °C on mouse Clariom D Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0) using  default analysis settings (version 2) and Gene + Exon - SST-RMA as summarization and normalization method.

label: biotin

source_name: left femur, fracture calluse

label_protocol: Proprietary labeled 2nd-cycle ss-cDNA was prepared from 100 ng total RNA using the mouse Clariom D kit according to the GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays user guide (version 23 January 2017) from ThermoFisher Scientific

growth_protocol: All animals were kept at a 12h light /12h dark cycle and fed a standard diet and water ad libitum.

extract_protocol: Snap-frozen callus tissue was homogenized in TRizol using a UltraTurrax (Sigma Aldrich), followed by isolation of total RNA using Rnasy mini Kit (Qiagen).

treatment_protocol: 12-week-old female mice were subjected to controlled bone injury by performing a 0.7 mm osteotomy on the externally fixated left femur. Fracture calli were extracted 7 days post surgery.

tag: genotype

value: alpha-CGRP KO

value: Fracture callus day 7


title: inla

description: input sample

value: dentate gyrus

value: female

value: sedentary mouse


title: Fx_Callus_d7_CGRP_8


title: ExVivoBlood_0% Neutron(3Gy X-ray)_rep5

value: Donor 5


title: inra

description: input sample

value: 11 days


title: Patient Sample, C006_d28

value: 28 days since the patient's hematopoietic cell transplant

value: CD8+ T cells


title: lf

description: Ribosome IP sample

source_name: immature neurons in dentate gyrus

value: immature neurons in dentate gyrus

value: 27 days


title: ExVivoBlood_0% Neutron(3Gy X-ray)_rep1

value: Donor 1

value: 3Gy X-ray-irradiated(0% Neutron)


title: ExVivoBlood_Control_rep5

value: sham-irradiated(control)


title: Fx_Callus_d7_WT_10

value: Wildtype


title: Patient Sample, C006_d21

value: 21 days since the patient's hematopoietic cell transplant


title: Fx_Callus_d7_WT_9


title: Fx_Callus_d7_CGRP_7


title: ExVivoBlood_0% Neutron(3Gy X-ray)_rep2

value: Donor 2

value: Peripheral blood


title: rf

description: Ribosome IP sample

value: running mouse


title: le

description: Ribosome IP sample


title: Patient Sample, C004_d28

value: blood


title: Patient Sample, C005_d21


title: ExVivoBlood_Control_rep4

value: Donor 4


title: Patient Sample, C004_d21


title: ExVivoBlood_Control_rep2


title: ExVivoBlood_Control_rep3

value: Donor 3


title: re

description: Ribosome IP sample

value: female


title: ExVivoBlood_Control_rep1


title: Fx_Callus_d7_WT_7

value: Fracture callus day 7


title: Patient Sample, C007_d28

value: 28 days since the patient's hematopoietic cell transplant


title: ATAC-seq BFF2

city: Nanning

first: Zhiqiang

last: Wang

address: No. 6 TaoYuan Rd.

country: China

institute: Guangxi Academy of Medical Sciences and the People’s Hospital of Guangxi Zhuang Autonomous Region

library_source: genomic

data_processing:
CHIP-seq:
Basecalls performed using bcl2fastq2 version 2.20
Data were filtered using inhouse scripts with adaptor pollution bases<=5 bp, Q<=19 base rates<=0.5 Ns rates<=0.05
ChIP-seq reads were aligned to the buffalo genome assembly using bowtie2 version 2.1.0 with the following configurations:-x Genome.fa –S sample.sam –N 1 -1 -2
peaks were called using MACS2 version 2.1.1 with the following setting: –t IP.bam –c input.bam -f BAM -g genome_size -n sample_name -p 1e-5
ATAC-seq:
Basecalls performed using bcl2fastq2 version 2.20
Data were filtered using inhouse scripts with adaptor pollution bases<=5 bp, Q<=19 base rates<=0.5 Ns rates<=0.05
ATAC-seq reads were aligned to the buffalo genome assembly using bowtie2 version 2.1.0 with the following configurations:-x Genome.fa –S sample.sam –N 1 -1 -2
peaks were called using MACS2 version 2.1.1 with the following setting:-f BAM -g genome_size -n sample_name -p 1e-5
Genome_build: GCA_003121395.1
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Bubalus bubalis

source_name: Fibroblasts with high cloning efficiency

growth_protocol: Buffalo fetal fibroblasts (BFFs) with different cloning efficiency were culture on 100  mm tissue culture dishes (Nunc, Roskilde, Denmark) in high glucose-DMEM(Gibco) supplemented with 0.06 mg/ml Penicillin, 0.1 mg/ml Streptomycin and 10% FBS.

extract_protocol:
Cells were picked and treated with the lysis buffer for STAR ChIP-seq
a total of 50,000 cells were washed once with 50 mL cold PBS and re-suspended in 50 mL lysis buffer for start ATAC-seq
ChIP-Seq libraries were prepared using NEXTflex® Rapid DNA-Seq Kit (Bioo Scientific) following the manufacturer’s procedure
ATAC-Seq libraries were prepared using Nextera DNA library Preparation Kit (96 samples) (FC-121-1031, Illumina) following the manufacturer’s procedure

treatment_protocol: Untreatment

value: Swamp buffalo

value: Buffalo fetal fibroblasts (BFFs)

tag: cloning efficiency

value: high


title: ATAC-seq BFF1

source_name: Fibroblasts with low cloning efficiency

value: low


title: Patient Sample, C003_d21

value: CD8+ T cells


title: rd

description: Ribosome IP sample

value: immature neurons in dentate gyrus

value: 18 days


title: BFF2 input

tag: chip antibody


title: Mock_M_12hr_5

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

institute: PNNL

hyb_protocol: Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). 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. 100μl 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 with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the biological replicates was performed independently of the other.

source_name: Primary normal human bronchial epithelial cells, with macrophage cells, mock-inoculated, 12hr, bioreplicate 5

label_protocol: Total RNA was labeled according to Agilent’s Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

extract_protocol: Influenza A/Vietnam/1203/2004 (H5N1, VN1203) or influenza A/California/04/2009 (H1N1, CA04) viral stocks were used to infect NHBE cells at a multiplicity of infection (MOI) of 1. Infections were allowed to progress for 1 hour. Next, 500,000 PBMC-derived macrophages were place onto each apical transwell surface in a final volume of 500 ul to create co cultures. The co-cultures at a ratio of approximately 2 NHBE cells for every PBMC-derived macrophage were allowed to progress for an additional 11, 15 and 23 hours respectively (12, 16, 24 hours post-infection). An n=5 was used for each condition, which included infection with either H1N1, H5N1, or mock uninfected, of either NHBE-only monocultures or NHBE + PBMC-macrophage co-cultures. In total this infection scheme represented a total of 90 samples for microarray analysis. At the specified time points, 1 ml of TRlzol RNA isolation reagent (Thermo Fischer, 15596-018) that lead to inactivation of samples.

tag: virus


title: FOXO1 KO 2 MK ext0897

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description: LME-1 FOXO1 KO clone 2 treated with 2,5 µM MK2206

hyb_protocol: 200 ng of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

source_name: Human Multiple myeloma celline LME-1

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: Cells were incubated O/N in IMDM supplementend with 10% FCS; 100 µ/ml penicillin; 2 mM L-glutamine

extract_protocol: RNA was extrated using Tri-reagent according to manufacturers protocol and then purified using the RNAeasy mini kit.

treatment_protocol: Cells were treated with 2.5 µM MK2206 (AKT inhibitor) O/N and subsequently transfered to Tri-reagent .

tag: clone

value: Foxo1 KO 2


title: Patient Sample, C002_d21

value: 21 days since the patient's hematopoietic cell transplant


title: BFF1 input


title: FOXO1 KO 1 MK ext0896

description: LME-1 FOXO1 KO clone 1 treated with 2,5 µM MK2206

value: Foxo1 KO 1


title: rc

description: Ribosome IP sample

value: running mouse


title: ChIP-seq BFF2

value: H3K9ac (CST, Cat#9649)


title: CTRL 2 MK ext0895

description: LME-1 Control clone 2 treated with 2,5 µM MK2206

value: Control 2


title: lb

description: Ribosome IP sample

value: 11 days

value: sedentary mouse


title: ld

description: Ribosome IP sample

value: female


title: ChIP-seq BFF1


title: la

description: Ribosome IP sample


title: rb

description: Ribosome IP sample


title: Patient Sample, C001_d21

value: blood


title: ra

description: Ribosome IP sample


title: FOXO1 KO 2 ext0893

description: LME-1 FOXO1 KO clone 2 untreated

value: untreated


title: iSLK BAC16 KO no tx

city: Daejeon

first: Yun Hee

last: Kang

address: 77 Gyeryong-ro 771 beon-gil, Jung-gu

department: Eulji Biomedical Science Research Institute

country: South Korea

institute: Eulji University School of Mdicine

data_processing:
HISAT v2.1.0(1). 1000000019358 v02 software used for basecalling.
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using Fastx_trimmer), then mapped to mm10 whole genome using Tophat.
Read count extraction and normalization were performed using edgeR.
Genome_build: USSC hg19
Supplementary_files_format_and_content: tab-delimited excel files inclued read count values for each sample.

source_name: Renal carcinoma

growth_protocol: iSLK BAC16 cultured in Dulbecco`s modified Eagle`s medium, supplemented with 10% Fetal bovine serum, 1% antibiotics. iSLK BAC16 were maintained by adding 1.2 mg/ml hygromycin B, 250 ug/ml geneticin, 1 ug/ml puromycin.

extract_protocol:
Total RNA was collected from cultured cells using Ribospin II (geneall).
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit.

treatment_protocol: HMGB1 wild type and Knock-out iSLK BAC16 cells were induced for 48 hours by 1.2 mM sodium butyrate(sigma) and 50 ug/ml Doxycycline(sigma).

tag: cell line

value: iSLK BAC16

value: HMGB1 KO

tag: viral replication state

value: latent


title: iSLK BAC16 KO induction

value: lytic


title: lc

description: Ribosome IP sample

tag: tissue

value: immature neurons in dentate gyrus


title: FOXO1 KO 1 ext0892

description: LME-1 FOXO1 KO clone 1 untreated


title: iSLK BAC16 WT induction

value: HMGB1 WT


title: Patient Sample, C001_d28

value: 28 days since the patient's hematopoietic cell transplant

value: CD8+ T cells


title: CTRL 2 ext0891

description: LME-1 Control clone 2 untreated


title: iSLK BAC16 WT no tx


title: Patient Sample, C002_d28


title: MYH7b_sp_infection_2

city: Boulder

first: Lindsey

middle: Joe

last: Broadwell

state: CO

address: 3415 Colorado Avenue, Apt, Suite, Bldg. (optional)

department: Biochemistry

institute: University of Colorado Boulder

data_processing:
nf-core/rnaseq v1.4.2
DEseq2/R
Genome_build: v33/GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text file summarizing TPM for each sample and gene
Supplementary_files_format_and_content: comma separated file summarizing differential expression for scrambled vs knockdown samples

molecule: polyA RNA

source_name: WTC-11_hiPSC cardiomyocytes_MYH7b_sp

growth_protocol: iPSCs were differentiated to cardiomyocytes using the small molecule protocol then matured for 35 days before treatment.

extract_protocol:
Trizol
poly-A selection

treatment_protocol: Infected at 400 MOI with adenoviruses expressing either GFP or MYH7b_sp.

value: induced pluripotent stem cell (hiPSC) cardiomyocyte

value: MYH7b_sp adenovirus


title: Exposed-maternal diabetes+high fat diet_replicate3

city: Sioux Falls

first: Randolph

middle: S

last: Faustino

state: SD

address: 2301 East 60th Street North

department: Genetics and Genomics

institute: Sanford Research

hyb_protocol: Labeled cRNA, synthesized and amplified from the double-stranded cDNA template, was fragmented and hybridized onto GeneChip Rat Gene 1.0 ST arrays according to manufacturer’s protocol. Briefly, fragmented cRNA and control oligonucleotide B2 were added along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and BSA to the hybridization buffer. The hybridization mixture was heated at 99°C for 5 min followed by incubation at 45°C for 5 min, before sample was injected into the microarray. Hybridization was carried out at 45°C for 16 hours, mixing on a rotisserie at 60 rpm. After hybridization, solutions were removed and arrays were washed and stained with streptavidin-phycoerythrin (Invitrogen).

scan_protocol: GeneChip 3000 scanner (Affymetrix) was used to scan and quantitatively analyze images of hybridized GeneChip arrays. Intensity values for each probe cell in the arrays were calculated by GeneChip software.

data_processing: Data normalization and analysis was performed using GeneSpring GX 14.01 (Agilent Technologies). Probe cell intensities were used to calculate an average intensity for each set of probe pairs representing a gene. Quality control filtering was performed on the normalized intensity values and entities were clustered into conditions. Gene expression profiles for each condition were visualized as volcano plots to identify genes significantly upregulated or downregulated in each group. Statistical analysis was performed using the unpaired unequal variance t-test (Welch test). The hierarchical clustering for groups and entities was performed using Euclidean distance metric and Ward’s linkage algorithm.

label: Biotin

organism: Rattus norvegicus

source_name: Rat newborn heart

label_protocol: Total isolated RNA (100 ng) from each sample was converted to cDNA utilizing SuperScript III First Strand Synthesis Supermix (Invitrogen). Biotinylated complimentary RNA (cRNA) was then synthesized using an RNA transcript labeling reagent (Affymetrix).

growth_protocol: Hearts were extracted from newborn, postnatal day one (P1), rats.

extract_protocol: Total RNA was extracted from the whole heart with TRIzol and purified using an affinity resin column (Qiagen RNeasy Mini kit, Germantown, MD) according to manufacturer’s protocol.

treatment_protocol: Young adult female rats received either control or high fat diet (Teklad, Harlan Laboratories) for at least 28 days before mating and throughout pregnancy. Gestational day (GD) zero was determined by a positive vaginal swab for spermatozoa. On GD14, after confirmation of pregnancy through ultrasound, dams received either citrate buffer (0.09 M) or 65 mg/kg of intraperitoneal streptozotocin (Sigma Life Sciences) to induce late gestational diabetes. Hyperglycemia was partially controlled with twice daily insulin treatments to keep glucose levels in a target range of 200-400 mg/dl. Delivery (GD22) yielded postnatal day one (P1) offspring from four distinct groups: exposed to maternal diabetes alone, exposed to maternal high fat diet alone, exposed to combination of both maternal diabetes and high fat diet, and control group. Hearts were harvested from each treatment group and immediately snap frozen in liquid nitrogen, and stored at -80C until RNA extraction.

value: Heart

tag: developmental stage

value: Newborn postnatal day 1

tag: exposure

value: Maternal diabetes+high-fat diet


title: FOXO3 KO 2 EXT0910

description: MM1.S FOXO3 KO clone 2 untreated

source_name: Human Multiple myeloma celline MM1.S

value: Foxo3 KO 2


title: CTRL 1 MK ext0894

description: LME-1 Control clone 1 treated with 2,5 µM MK2206

value: Control 1


title: FOXO3 KO 2 MK EXT0911

description: MM1.S FOXO3 KO clone 2 treated with 2,5 µM MK2206


title: CTRL 1  ext0890

description: LME-1 Control clone 1 untreated


title: MYH7b_sp_infection_1


title: Exposed-maternal diabetes+high fat diet_replicate4


title: FOXO3 KO 1 MK EXT0909

description: MM1.S FOXO3 KO clone 1 treated with 2,5 µM MK2206

value: Foxo3 KO 1


title: Exposed-maternal diabetes+high fat diet_replicate5


title: GFP_infection_1

source_name: WTC-11_hiPSC cardiomyocytes_GFP

value: GFP adenovirus


title: GFP_infection_2


title: FOXO3 KO 1 EXT0908

description: MM1.S FOXO3 KO clone 1 untreated

value: untreated


title: Exposed-maternal high fat diet_replicate5

value: Maternal high-fat diet


title: CTRL 2 MK EXT0907

description: MM1.S Control clone 2 treated with 2,5 µM MK2206

value: Control 2


title: Exposed-maternal diabetes+high fat diet_replicate1


title: CTRL 2 EXT0906

description: MM1.S Control clone 2 untreated


title: Cell line SNU61 treated with DMSO

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description: SST RMA expression values at the gene-level derived using Expression Console software

hyb_protocol: Samples were hybridized onto Affymetrix Human Transcriptome 2.0 Arrays according to the manufacturer's protocol (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's protocol (Affymetrix).

data_processing: Gene-level expression signals were obtained from raw data CEL files by the SST RMA procedure implemented in the Affymetrix Expression Console software.

label_protocol: RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip HT WT User Guide.

growth_protocol: 250,000 - 400,000 cells were seeded in 60 mm cell culture dishes (Falcon, #353002) in DMEM/F12 growth media (Thermo Fischer Scientific #31330038) supplemented with 15% Fetal Bovine Serum (Thermo Fischer Scientific #10270106) and 100 U/ml penicillin-streptomycin (Thermo Fischer #15140122). The cells were recovered for 24h before treatment.

extract_protocol: Total RNA was isolated from cell pellets using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).

treatment_protocol: Cells were incubated with 100 and 1000 nM talazoparib (MedChemExpress, #HY-16106) or 0.005% DMSO (Sigma, #D5879) for 48h. After the drug incubation, cells were washed twice with 1xPBS (Gibco, #20010019) and collected after trypsinization.

value: Colorectal cancer cell

value: DMSO


title: Exposed-maternal high fat diet_replicate4


title: CTRL 1 MK EXT0905

description: MM1.S Control clone 1 treated with 2,5 µM MK2206


title: Cell line SW1222 treated with 100nM talazoparib

value: 100nM talazoparib


title: Cell line SW1222 treated with DMSO


title: Exposed-maternal diabetes+high fat diet_replicate2


title: Cell line SW1222 treated with 1000nM talazoparib

value: 1000nM talazoparib


title: Cell line SNU61 treated with 100nM talazoparib


title: SFC840_clone5_MSAamp

city: Oxford

first: Devika

last: Agarwal

address: JR hospital, Headley way

department: The MRC Weatherall Institute of molecular medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Pairend end files (151 bp) were geenerated for each sample
Kallisto  was used to estimate transcript abundance for Ensembl (release 88) protein-coding genes from RNAseq reads
Count data was imported into R using tximport and genes with less than 10 reads across the six samples used in the comparison were filtered out
Differential gene expression was performed in DESeq2 using the Wald test with an FDR threshold of 0.05 and a log2 fold change threshold on 0.25
Genome_build: GRCh38 (Ensemble release 88)
Supplementary_files_format_and_content: Kallisto quantification files  (HDF5 binary files ) for each sample with transcript abundance estimates, bootstrap estimates, and transcript length information length

extract_protocol: NOT PROVIDED; REQUESTED

tag: donor

value: Control

value: Aggregation

tag: treatment condition/type

value: MSAamp

value: iPSC-derived midbrain dopaminergic neurons

tag: replicate


title: SFC840_clone5_WTPFF

tag: treatment

value: WTPFF


title: Cell line SNU61 treated with 1000nM talazoparib


title: SFC840_clone5_PDamp

value: PDamp


title: Exposed-maternal high fat diet_replicate3

value: Heart

value: Newborn postnatal day 1


title: CTRL 1  EXT0904

description: MM1.S Control clone 1 untreated

value: Control 1


title: Exposed-maternal diabetes_replicate6

value: Maternal diabetes


title: FOXO3 KO 2 ext0980

description: XG3 FOXO3 KO clone 2 untreated

source_name: Human Multiple myeloma celline XG-3

value: Foxo3 KO 2

value: untreated


title: Exposed-maternal high fat diet_replicate1

value: Maternal high-fat diet


title: Cell line SKCO1 treated with 1000nM talazoparib

value: Colorectal cancer cell


title: OX3_clone9_MSAamp


title: SFC840_clone5_NSC

value: NSC


title: Exposed-maternal high fat diet_replicate2


title: OX3_clone9_PDamp


title: Cell line SKCO1 treated with DMSO

value: DMSO


title: FOXO3 KO 1 MK ext0979

description: XG3 FOXO3 KO clone 1 treated with 2,5 µM MK2206

value: Foxo3 KO 1


title: OX3_clone9_WTPFF

value: Control


title: FOXO3 KO 2 MK ext0981

description: XG3 FOXO3 KO clone 2 treated with 2,5 µM MK2206


title: OX3_clone9_NSC


title: Exposed-maternal diabetes_replicate5


title: Cell line SKCO1 treated with 100nM talazoparib

value: 100nM talazoparib


title: LR-V_EL38_A

city: Beijing

first: Run-Ze

last: Sun

address: No.20 Nanxincun, Xiangshan, Haidian District

department: Institute of Botany

institute: Chinese Academy of Sciences

data_processing:
Bowtie2 v2.2.5 was used to map clean reads to reference, allowing no more than two nucleotides mismatched.
Level of gene expression was calculated using the FPKM (expected fragments per kilobase of transcript per million fragments mapped) method.
Genome_build: Vitis vinifera  (PN40024) genome V2 download from Grape Genome Database (CRIBI)
Supplementary_files_format_and_content: excel file (.xlsx) include the FPKM values and annotations of all genes

organism: Vitis vinifera

source_name: LR-V-EL38_grape berries

growth_protocol: Field experiments were conducted in a commercial vineyard of V. vinifera L. Cabernet Sauvignon located in Manas Country (44◦170 North, 86◦120 East, 475 m above sea level), the wine-producing region of Xinjiang province, China, for three consecutive growing seasons (2011, 2012, and 2013). The ownrooted vines in this vineyard were planted in 2000, managed on a modified Vertical-Shoot-Positioned (M-VSP) trellis system with a spur-pruned cordon retaining 15 nodes per linear meter, arranged in north-south rows with 2.5 m × 1 m vine spacing and equipped with a furrow irrigated system. Nutrition and pest management was carried out according to industry standards for this cultivar and the region.

extract_protocol:
For each biological replicate, 600 berries were randomly separated from both sunny and shade sides of at least 100 clusters within 15 vines. The sampling time  was fixed at 10:00 to 11:00 am, and three biological replicates were collected with the same method at each sampling date. After being washed with distilled water, a sub-sample of 100 berries from each biological replicate was subjected to the physiological measurements, including berry fresh weight, total soluble solids (TSS) content and titratable acidity (TA), the rest were frozen in liquid nitrogen immediately and transported to the lab in dry ice for the subsequent metabolites determination and transcriptional analysis.
cDNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Leaf removal and half leaf removal treatments were carried out by removing the first one to six basal leaves from the main shoots with clusters and three basal leaves from the first, third, and fifth of each shoot with clusters, respectively. For leaf moving treatment, the first one to six basal leaves of each shoot with clusters were moved aside by the use of nylon zipties, in order to increase the sunlight exposure of grape clusters without affecting the photosynthetic carbon assimilation to the fruit. Each treatment was arranged in a completely randomized experimental design with three biological replicates. In each biological replicate, treatment was applied to 15 vines randomly  selected from the vineyard's south and north sites.

tag: cultivar

value: cv. Cabernet Sauvignon

value: leaf removal at véraison (LR-V)

value: grape berries


title: LR-V_EL38_C


title: LR-V_EL38_B


title: AH017_clone7_MSAamp

value: Aggregation

value: MSAamp

value: iPSC-derived midbrain dopaminergic neurons


title: Exposed-maternal diabetes_replicate3

value: Heart

value: Newborn postnatal day 1


title: Ventral Hippocampus - Stress Group - 3rd replicate

city: Nouzilly

first: Hugues

last: Dardente

address: INRA

department: INRAE - Centre Val de Loire

country: France

institute: INRAE

data_processing:
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina). Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
A splice junction mapper, TopHat 2.1.1 (using Bowtie 2.3.5.1), was used to align the RNA-Seq reads to the Ovis aries genome (NCBI, Oar_rambouillet v1.0) with a set of gene model annotations (genes.gtf downloaded from NCBI on May 25 2020 ; release 103).
Final read alignments having more than 6 mismatches were discarded. Samtools (v1.9) was used to sort the alignment files. Then, the counting was performed with Featurecounts 2.0.0. As the data is from a strand-specific assay, the read has to be mapped to the opposite strand of the gene (-s 2 option).
Genome_build: Oar_rambouillet v1.0
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene and every sample

organism: Ovis aries

source_name: Brain - Hippocampus

extract_protocol:
TriReagent
Libraries were constructed using the Truseq stranded mRNA sample prep kit (Illumina, San Diego, CA,USA) according to the manufacturer instructions.

tag: breed

value: Ile-de-France

tag: age

value: adult ewes

tag: group

value: chronic stress

value: Ventral Hippocampus


title: CTRL 2 MK ext0977

description: XG3 Control clone 2 treated with 2,5 µM MK2206

value: Control 2


title: AH017_clone7_PDamp

tag: genotype

value: PDamp

tag: cell type


title: Exposed-maternal diabetes_replicate4

value: Maternal diabetes


title: Exposed-maternal diabetes_replicate2


title: CTRL 1 MK ext0975

description: XG3 Control clone 1 treated with 2,5 µM MK2206

value: Control 1


title: Cell line LS513 treated with 100nM talazoparib

value: Colorectal cancer cell

value: 100nM talazoparib


title: AH017_clone7_WTPFF

value: Control

value: WTPFF


title: Ventral Hippocampus - Stress Group - 2nd replicate


title: Ventral Hippocampus - Stress Group - 1st replicate


title: AH017_clone7_NSC

value: NSC


title: Cell line LS513 treated with DMSO

value: DMSO


title: LR-V_EL37_A

source_name: LR-V-EL37_grape berries

value: cv. Cabernet Sauvignon

value: leaf removal at véraison (LR-V)

value: grape berries


title: LR-V_EL37_C


title: LR-V_EL37_B


title: Exposed-maternal diabetes_replicate1

value: Heart

value: Newborn postnatal day 1


title: FOXO3 KO 1 ext0978

description: XG3 FOXO3 KO clone 1 untreated

value: Foxo3 KO 1

value: untreated


title: CTRL 2 ext0976

description: XG3 Control clone 2 untreated

value: Control 2


title: Control_replicate7


title: Control_replicate6


title: Ventral Hippocampus - Control Group - 3rd replicate

value: Ile-de-France

value: adult ewes

value: control

value: Ventral Hippocampus


title: Triplication_clone5_MSAamp

source_name: Triplication SNCA_MSAamp

value: Triplication SNCA

value: Aggregation

value: MSAamp

value: iPSC-derived midbrain dopaminergic neurons


title: Ventral Hippocampus - Control Group - 2nd replicate


title: Control_replicate4

value: Control


title: Control_replicate5


title: Cell line LS513 treated with 1000nM talazoparib

value: Colorectal cancer cell

value: 1000nM talazoparib


title: Triplication_clone5_PDamp

source_name: Triplication SNCA_PDamp

value: PDamp


title: Ventral Hippocampus - Control Group - 1st replicate


title: LR-V_EL36_B

source_name: LR-V-EL36_grape berries

value: cv. Cabernet Sauvignon

value: leaf removal at véraison (LR-V)

value: grape berries


title: LR-V_EL36_C


title: Control_replicate3

value: Heart

value: Newborn postnatal day 1


title: CTRL 1  ext0974

description: XG3 Control clone 1 untreated

value: Control 1

value: untreated


title: Triplication_clone5_WTPFF

source_name: Triplication SNCA_WTPFF

value: WTPFF


title: LR-V_EL36_A


title: Dorsal Hippocampus - Stress Group - 3rd replicate

value: Ile-de-France

value: adult ewes

value: chronic stress

value: Dorsal Hippocampus


title: Triplication_clone5_NSC

source_name: Triplication SNCA_NSC

value: Triplication SNCA

value: NSC

value: iPSC-derived midbrain dopaminergic neurons


title: Alb128_pol12A2_H3K56ac_eSPAN_S45

first: zhiguo

last: zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

description: 30C 45' HU MNase

data_processing:
CUT&TAG, OK-Seq and eSPAN reads were mapped using bowtie2. RNA-Seq reads were mapped using STAR.
Read count on gene body or promoters were calculated by FeatureCount.
Differential genes and log fold change were calculated by DEseq2
Read coverage in each bin was calculated using the R package of Rsamtools. Histone bias was computed from trimmed, mapped, unique reads in each bin as Bias=(W-C)/(W+C), where W and C are the number of reads mapped on Crick and Watson strand in each bin, respectively.
Genome_build: For mouse, reads were mapped to mm10. For yeast, reads were mapped to saccer3.
Supplementary_files_format_and_content: bw files, the score represents reads coverage at each genomic position. Read coverage on plus strand, minus strand and total were calculated seperately.

organism: Saccharomyces cerevisiae

growth_protocol: Mouse E14 ES cells (a gift from Dr. Tom Fazzio, University of Massachusetts Medical School, Worcester, MA) were cultured in DMEM (Corning) medium supplemented with 15% (vol/vol) fetal bovine serum (FBS), 1% penicillin/streptomycin (Invitrogen), 1 mM sodium pyruvate (Cellgro), 2 mM L-glutamine (Cellgro), 1% MEM non-essential amino acids (Invitrogen), 55 µM β-Mercaptoethanol (Sigma), 10 ng/mL mouse leukemia inhibitory factor (mLIF) on gelatin-coated dishes in a 37°C incubator with a humidified, 5% CO2 atmosphere. Yeast cells were synchronized and cultured following the standard protocol (Dunham et al., 2015).

extract_protocol:
eSPAN in yeast was performed exactly as previously described (Yu et al., 2014). Total RNA samples were purified the same as for RT-PCR. OK-seq was performed as previously described with some modifications (Petryk et al., 2016).
RNA-seq libraries were prepared and deep sequencing was performed by Columbia University Genome Center. For eSPAN libraries, the supernatants were purified with ChIP DNA concentrator columns and library PCR was performed using standard Illumina Nextera Dual Indexing primers. Samples were pooled and sequenced using paired-end sequencing on Illumina NextSeq 500 platforms at Columbia University Genome Center.
RNA-Seq, ChIP-Seq, CUT&TAG, OK-Seq, eSPAN

tag: condition

tag: experiments


title: Triplication_clone3_MSAamp

value: Aggregation

value: MSAamp


title: Control_replicate2

value: Control


title: Dorsal Hippocampus - Stress Group - 2nd replicate


title: LM-V_EL38_C

source_name: LM-V-EL38_grape berries

value: cv. Cabernet Sauvignon

value: leaf moving at véraison (LM-V)


title: LM-V_EL38_B

value: grape berries


title: Dorsal Hippocampus - Stress Group - 1st replicate


title: LM-V_EL38_A


title: Dorsal Hippocampus - Control Group - 3rd replicate

value: control


title: Triplication_clone3_PDamp

value: PDamp


title: Alb125_pol12A2_H3K56ac_ChIP_S45

description: 30C 45' HU MNase


title: Alb126_pol12A2_Brdu_S45

description: 30C 45' HU MNase

value: Brdu


title: Alb127_pol12A2_H3K4me3_eSPAN_S45

description: 30C 45' HU MNase


title: Control_replicate1

value: Heart

value: Newborn postnatal day 1


title: Dorsal Hippocampus - Control Group - 2nd replicate

value: Ile-de-France

value: adult ewes


title: Triplication_clone3_NSC


title: Alb123_pol12A2_Input_S45

description: 30C 45' HU MNase

value: Input


title: LM-V_EL37_B

source_name: LM-V-EL37_grape berries


title: LM-V_EL37_C


title: Triplication_clone1_MSAamp

value: Triplication SNCA


title: Dorsal Hippocampus - Control Group - 1st replicate

value: Dorsal Hippocampus


title: Alb124_pol12A2_H3K4me3_ChIP_S45

description: 30C 45' HU MNase


title: LM-V_EL37_A


title: Triplication_clone1_PDamp

value: iPSC-derived midbrain dopaminergic neurons


title: Alb122_pol12A2_H3K4me3_ChIP_G1

description: G1 MNase


title: LM-V_EL36_C

source_name: LM-V-EL36_grape berries


title: Alb121_pol12A2_Input_G1

description: G1 MNase


title: Tolerized kidney rep 2

city: Durham

first: Shyni

last: Varghese

state: NC

address: 203 Research Drive

department: Department of Biomedical Engineering

institute: Duke University

data_processing:
.bcl files from instrument NextSeq application version 2.2.0.4. RTA version 2.4.11. Bcl files were converted to fastqs using CellRanger’s mkfastq (version 2.1.1 for naive kidney samples; version 3.0.1 for other four samples) command-line tool (bcl2fastq)
Resulting .fastqs were aligned to mm10 reference transcriptome using CellRanger Count command-line tool (version 2.1.1 for naive kidney samples; version 3.0.1 for other four samples). Putative doublets were removed using DoubletDecon version 1.1.3
Genome_build: mm10
Supplementary_files_format_and_content: gzip2-compressed .mtx files containing single cell information (raw gene counts for all cells)

source_name: kidney allograft

extract_protocol:
Kidney allografts from untreated and tolerized WT B6  recipients were retrieved on d15 post-transplant, perfused by cold PBS and a single cell suspension was prepared using ‘multi tissue dissociation kit 2’ (Miltenyi  Biotec, Auburn CA) as per manufacturer’s protocol. Naïve B6 kidneys retrieved from WT B6 mice were similarly processed to serve as a control. Cell suspension was subjected to RBC lysis followed by washing. Cell viability was confirmed to be >90%, and cell concentration was adjusted to 2,000 cells/μl.
In brief, 10X Genomics microfluidic platform combines single cells with barcoded gel beads containing essential components for cDNA preparation including barcodes to tag individual transcripts from the cells, a Unique Molecular Identifier (UMI) to identify PCR products, and primers for amplification of resulting cDNA. cDNA libraries were checked for quality using Agilent D5000 Tape Station analyzer. cDNA libraries of ~400bp size were subjected to Illumina NextSeq 550 sequencer using NextSeq500/550 High Output Kit v2.5 (150 Cycles).

tag: strain

value: BALB/c [I-Ad] --> B6

value: 6-7 weeks

tag: Sex

value: male

value: Same as sample 5 with additional treatment:BALB/c splenocytes (SP) were treated with ethylenecarbodiimide (ECDI, Calbiochem, 150 mg/mL per 3.2x108) on ice for 1h with agitation and washed. 108 BALB/c ECDI-SP cells were infused to the B6 recipient intravenously on day 7 and day +1,  while day 0 was designated as the day of transplantation.


title: LM-V_EL36_B

value: cv. Cabernet Sauvignon

value: leaf moving at véraison (LM-V)

tag: tissue


title: Triplication_clone1_WTPFF

value: Aggregation

value: WTPFF


title: Rejecting kidney rep 2

value: BALB/c [I-Ad] mouse kidney transplanted into bilaterally nephrectomized B6 male recipient


title: Alb556_pol12A2_H3K56ac_eSPAN_S30

description: 25C 30' MNase


title: LM-V_EL36_A

tag: developmental stage

value: grape berries


title: Naive kidney rep 2

source_name: kidney

value: 10-12 weeks

value: Naive untransplanted kidney


title: Triplication_clone1_NSC

value: Control

value: NSC


title: Triplication_clone3_WTPFF

value: Triplication SNCA


title: O25v3SpD

city: New Haven

first: Yang-Hui

last: Yeh

state: CT

address: 295 Congress Ave.

department: Microbial Pathogenesis

institute: Yale University

description:
DEseq2_Pt_normalized_DM.txt
Pt_IR_SpvsDM_D.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 release 91 plus HIV-1 sequence (HXB2 or HIV-1-dsGFP) whole genome using STAR 2.6.1d or 2.7.0f with parameters --readFilesCommand gunzip -c --outSAMtype BAM SortedByCoordinate --chimOutType SeparateSAMold --runThreadN 20 --outFilterType BySJout --alignSJoverhangMin 5 --alignSJDBoverhangMin 3 --chimSegmentMin 15 --outSAMstrandField intronMotif --outSAMattributes All --quantMode GeneCounts
DEseq2 normalized count: Total gene count and normalization of STAR aligned bam file was obtained using HTseq (htseq-count -r pos -f bam -s reverse) and DESeq2 with human genome assembly hg38 release 91. Genes with the sum of read count smaller than 10 were filtered out.
Intron retention: Quality trimmed fastq files were analyzed with IRFinder 1.2.5 using STAR-built indexes with human genome assembly hg38 release 91.gtf as reference annotation (77). Up to triplicates of treatments were compared. Output files were filtered with following criteria in Rstudio (1.1.463): `A-IRratio` >= 0.1 & `A-IntronCover` >= 0.7 & `A-IntronDepth` >= 6 & `A-SplicesExact` >= 2 & `B-IRratio` < 0.1 & `B-SplicesExact` >=2. Unequal variance t-test of IRratio between two treatment groups were applied and intron-retained regions with significant difference (p < 0.05) were reported.
Genome_build: hg38 release 91 + HIV-1 sequence (HXB2 and HIV-1-dsGFP)
Supplementary_files_format_and_content: DEseq2 normalized counts: tab-delimited txt files; Intron retention: tab-delimited txt files:
DEseq2_8B10_normalized_DM.txt (DEseq2_normalized gene counts_cell line 8B10 for differential expression, IPA, and GSEA)
DEseq2_Pt_normalized_DM.txt (DEseq2_normalized gene counts_clinical samples for differential expression, IPA, and GSEA)
8B10_IR_FivsDM_D.txt (Intron retention analysis_cell line 8B10)
8B10_IR_RuvsDM_D.txt (Intron retention analysis_cell line 8B10)
8B10_IR_SpvsDM_D.txt (Intron retention analysis_cell line 8B10)
8B10_IR_MAvsDM_D.txt (Intron retention analysis_cell line 8B10)
Pt_IR_FivsDM_D.txt (Intron retention analysis_clinical samples)
Pt_IR_RuvsDM_D.txt (Intron retention analysis_clinical samples)
Pt_IR_SpvsDM_D.txt (Intron retention analysis_clinical samples)
Pt_IR_MAvsDM_D.txt (Intron retention analysis_clinical samples)

source_name: CD4+ T cells

growth_protocol: Jurkat_clones: RPMI1640 high glucose + 10% FBS, passage every 3-4 days. CD4+ T cells ex vivo culture: RPMI1640 high glucose + 10% FBS

extract_protocol:
Cells were solublized in 300µl TRIzol per million cells then extracted with Direct-zol RNA microprep kits.
Approximately 500 ng of total RNA was used to generate cDNA library using TruSeq mRNA Library Prep kit (Illumina) for Illumina HiSeq 4000 2x100 bp sequencing or NEBNext Ultra II directional mRNA library prep kit (NEB) for Novaseq 6000 2x150 bp sequencing

treatment_protocol: Cells were treated with HIV-1-suppressing drugs (filgotinib, ruxolitinib, spironolactone, mycophenolic acid) for 24 hours in culture media incubated at 37oC with 5% CO2

tag: cell state

value: Isolated resting CD4+ T cells by negative selection

tag: hiv-1 infection status

value: estimated 1-100 intact provius per million cells

tag: drug treatment

value: Spironolactone

value: CD4+ T cells


title: Tolerized kidney rep 1

value: BALB/c [I-Ad] --> B6

value: 6-7 weeks

value: male

value: Same as sample 2 with additional treatment:BALB/c splenocytes (SP) were treated with ethylenecarbodiimide (ECDI, Calbiochem, 150 mg/mL per 3.2x108) on ice for 1h with agitation and washed. 108 BALB/c ECDI-SP cells were infused to the B6 recipient intravenously on day 7 and day +1,  while day 0 was designated as the day of transplantation.


title: Alb577_pol12A2_BrdU_S30

description: 25C 30' MNase

value: BrdU


title: Alb578_pol12A2_H3K4me3_eSPAN_S30

description: 25C 30' MNase


title: CK_EL38_B

source_name: CK-EL38_grape berries

value: cv. Cabernet Sauvignon

value: control group


title: CK_EL38_C

value: grape berries


title: Rejecting kidney rep 1

value: BALB/c [I-Ad] mouse kidney transplanted into bilaterally nephrectomized B6 male recipient


title: O25v3RuD

description:
DEseq2_Pt_normalized_DM.txt
Pt_IR_RuvsDM_D.txt

value: Ruxolitinib


title: Naive kidney rep 1

value: 10-12 weeks

value: Naive untransplanted kidney


title: O25v3MAD

description:
DEseq2_Pt_normalized_DM.txt
Pt_IR_MAvsDM_D.txt

value: Mycophenolic acid


title: CK_EL38_A


title: Alb575_pol12A2_H3K4me3_ChIP_S30

description: 25C 30' MNase


title: Alb576_pol12A2_H3K56ac_ChIP_S30

description: 25C 30' MNase


title: Sample_43_GCB_H1_DKO_H3K9me3_CutAndRun

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
library strategy: Cut&Run
Illumina Casava1.8 software used for basecalling.
ATAC-seq paired-end sequencing reads were trimmed to remove adapter sequences using NGmerge with option “-a”, and trimmed reads were aligned to mm10 reference genome using bowtie2 with options “-X2000 –local”. Alignments were filtered using samtools v1.8 to retain only uniquely mapping read pairs and to discard mitochondrial mapping reads. Read duplicates were detected and removed using the MarkDuplicates program in Picard Tools 2.18.11.
ATAC-seq peaks were called using MACS2
Cut and Run reads from two replicated aligned to mm10 using Bowtie2 and merged, filtering out non-unique and blacklist regions (PMID:31249361)
ChIP-seq reads were aligned to mm10 using BWA with default parameters
ChIP-seq peaks were called using narrow MACS2 for H3K4me3 and H3K27Ac and SICER2 for H3K9me2 and H3K9me3
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited

extract_protocol:
RNA-seq libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit according to the manufacturer
Cut and Run libraries for H3K4me3 (EpiCypher 13-0041), H3K9me2 (Millipore 05-1249), and H3K9me3 (Abcam 176916) were prepared using EpiCypher CUTANA v1.5.1 protocol
ChIP-seq libraries for H3K27ac (pAb 39133 Active Motif) were prepared using TrueMicroChip kit according to the manufacturer

value: Constitutive H1c-/-;H1e-/-

value: GC B cell

tag: anitbody


title: Alb574_pol12A2_Input_S30

description: 25C 30' MNase

value: Input


title: O25v3DMD

description:
DEseq2_Pt_normalized_DM.txt
Pt_IR_FivsDM_D.txt
Pt_IR_RuvsDM_D.txt
Pt_IR_SpvsDM_D.txt
Pt_IR_MAvsDM_D.txt

value: Isolated resting CD4+ T cells by negative selection

value: estimated 1-100 intact provius per million cells

value: DMSO

value: CD4+ T cells


title: CK_EL37_C

source_name: CK-EL37_grape berries

tag: treatment


title: CK_EL37_B

tag: cultivar


title: O25v3FiD

description:
DEseq2_Pt_normalized_DM.txt
Pt_IR_FivsDM_D.txt

value: Filgotinib


title: Sample_41_GCB_H1_DKO_H3K4me3_CutAndRun


title: Alb573_pol12A2_H3K4me3_ChIP_G1

description: G1 MNase


title: Sample_42_GCB_H1_DKO_H3K9me2_CutAndRun


title: O24v2SpD

value: Spironolactone


title: CK_EL37_A

value: cv. Cabernet Sauvignon


title: Sample_40_GCB_WT_H3K9me3_CutAndRun

value: WT littermate control


title: Sample_39_GCB_WT_H3K9me2_CutAndRun


title: O24v2RuD


title: O24v2MAD


title: Alb308_pol12A2_H3K56ac_eSPAN_S30

description: 25C 30' MNase


title: Alb307_pol12A2_H3K4me3_eSPAN_S30

description: 25C 30' MNase


title: CK_EL36_C

source_name: CK-EL36_grape berries

value: control group

value: grape berries


title: CK_EL36_B


title: Sample_38_GCB_WT_H3K4me3_CutAndRun


title: O24v2FiD


title: Alb306_pol12A2_BrdU_S30

description: 25C 30' MNase

value: BrdU


title: O24v2DMD


title: O21v2SpD


title: CK_EL36_A


title: Alb305_pol12A2_H3K56ac_ChIP_S30

description: 25C 30' MNase


title: card1_2_DMBQ_3

city: Yokohama

first: Anuphon

last: Laohavisit

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN

data_processing:
50 bp single-ends reads were sequenced by Illumina Hiseq 4000 and basecalls performed using CASAVA bcl2fastq_v2.17
Quality filtering was performed using the Fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Low Quality nucleotides (quality score < 30) were removed from the 3’end. Short reads (< 40 bp) and reads which showed at least 95 % nucleotides with low quality score (quality score < 20) were removed.
Filtered reads were mapped onto Arabidopsis genome (TAIR10) with Tophat2 v2.1.1 (http://ccb.jhu.edu/software/tophat) with the following settings: -i 20 -I 5000
Mapped reads were counted using HTseq v0.6.1 (13) (https://htseq.readthedocs.io/) with default settings.
Genome_build: TAIR10
Supplementary_files_format_and_content: comma separate values, HTseq read count values

organism: Arabidopsis thaliana

source_name: 7-day old liquid-grown seedlings

growth_protocol: Arabidopsis seedling (WT-expressing aequorin, card1-1 and card1-2) were grown in liquid media containing half-strength Murashige-Skoog supplemented with 0.25 % sucrose. After 2 days stratification, seedlings were grown at 16 hr: 8 hr, light: dark, 22 C, 50 µE for 7 days

extract_protocol:
Extraction was carried out prepared as previously described in Townsley et al., 2015 Front. Plant Sci. (https://doi.org/10.3389/fpls.2015.00366)
Libraries were prepared as previously described in Townsley et al., 2015 Front. Plant Sci. (https://doi.org/10.3389/fpls.2015.00366)

treatment_protocol: Seedlings (7-day old) were treated with 5 µM DMBQ or DMSO (volume equivalent) for 10 minutes

tag: ecotype

tag: agent

value: 5 microM DMBQ

tag: genotype/variation

tag: time point

value: 10 min

tag: replicate

value: replicate 3


title: 194; PBMC

city: new york

first: Mamta

last: Giri

state: new york

address: 1470 madison ave

department: Institute of Personalized medicine

institute: Mount Sinai hospital

data_processing:
FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grch38 human
Cell barcodes and unique molecular identifiers (UMIs) were extracted and “Raw” UMI matrix generated for each sample
extracted cell-barcodes associated with at least 800 UMIs from the “Raw” output UMI matrices of CellRanger
Epithelial cells, Red blood cells and cell-barcodess associated with high mitochondrial mRNA content were excluded by "in-silico" gating precedure which computes that fractoin of UMIs assocated with each gene signature. Thresholds and genes lists are detailed in the manuscripts.
Genome_build: Grch38

source_name: PBMC

extract_protocol:
10X genomics V1 or V2 protocol following manufacturer recommendations
10x Genomics Library Kits
Single-cell RNA-sequencing

treatment_protocol: Lamina prorpia single cell suspensions were prepared from PBMC from Crohn's disease patients. Fifteen to twenty mucosal biopsies sampled all along the resected specimens using a biopsy forceps (EndoChoice, Alpharetta, GA). Epithelial cells were dissociated by incubating the biopsies in an EDTA-enriched dissociation medium (HBSS w/o Ca2+ Mg2+ (Life Technologies, Carlsbad, CA) - HEPES 10mM (Life Technologies) - EDTA 5mM (Life Technologies)) at +37oC under 100 rpm agitation for two cycles of 15 minutes. After each cycle, biopsies were hand-shaken for 30s and then vortexed vigorously for another 30s. Biopsies were then washed in complete RPMI media previously put at RT, and transferred in digestion medium (HBSS with Ca2+ Mg2+ - FCS 2% - DNase I 0.5mg/ml (Sigma-Aldrich, St. Louis, MO) – Collagenase IV 0.5mg/ml (Sigma-Aldrich)) for 40 minutes at +37oC under 100 rpm agitation. After digestion, the cell suspension was filtered through a 70mm cell strainer, washed in DBPS/ 2% FCS/ 1mM EDTA and spun down at 400g for 10 minutes. After red blood cell lysis (BioLegend, San Diego, CA), cells were washed as before. Dead cells were depleted from the suspension using the dead cell depletion kit (Miltenyi Biotec, Bergisch Gladbach, Germany), following manufacturer’s recommendations. Viability of the final cell suspension was calculated using a hemocytometer and Trypan blue (Corning) exclusion and was routinely > 85%.

tag: patient id

value: Blood

tag: 10x chemistry


title: card1_2_DMBQ_2

value: replicate 2


title: 191; PBMC


title: O21v2RuD

value: Ruxolitinib

tag: cell type


title: Alb303_pol12A2_Input_S30

city: New York

institute: Columbia University

description: 25C 30' MNase

tag: condition

tag: genotype

tag: experiments

value: Input


title: Alb304_pol12A2_H3K4me3_ChIP_S30

description: 25C 30' MNase


title: 185; PBMC

tag: tissue


title: O21v2MAD

tag: cell state

value: Isolated resting CD4+ T cells by negative selection

tag: hiv-1 infection status

value: estimated 1-100 intact provius per million cells

value: Mycophenolic acid


title: Alb572_pol12A2_Input_G1

description: G1 MNase


title: card1_2_DMBQ_1

value: replicate 1


title: Alb302_pol12A2_H3K4me3_ChIP_G1

description: G1 MNase


title: O21v2FiD

tag: drug treatment

value: Filgotinib

value: CD4+ T cells


title: card1_1_DMBQ_4

value: replicate 4


title: 179; PBMC


title: 157; PBMC


title: Alb301_pol12A2_Input_G1

description: G1 MNase


title: O21v2DMD

value: DMSO


title: card1_2_DMBQ_4


title: card1_1_DMBQ_2


title: Alb571_WT_H3K56ac_eSPAN_S30

description: 25C 30' MNase

value: WT


title: 134; PBMC


title: JurMAD3

description: only used for IGV plot

source_name: T lymphoblastoid

value: immortal cell line

value: T lymphoblastoid


title: 127; PBMC


title: card1_1_DMBQ_1

value: 5 microM DMBQ

value: 10 min


title: JurMAD2

description: only used for IGV plot


title: 126; PBMC

value: Blood


title: WT_DMBQ_4

value: WT-expressing aequorin


title: Alb569_WT_BrdU_S30

description: 25C 30' MNase

value: BrdU


title: JurMAD1

description: only used for IGV plot


title: 67; PBMC


title: Alb568_WT_H3K56ac_ChIP_S30

description: 25C 30' MNase


title: JurSpD3

description: only used for IGV plot

value: Spironolactone


title: WT_DMBQ_3

value: replicate 3


title: WT_DMBQ_2

value: replicate 2


title: JurSpD2

description: only used for IGV plot


title: Alb567_WT_H3K4me3_ChIP_S30

description: 25C 30' MNase


title: crKO 3

city: London

first: Florence

last: Enjalbert

state: London

address: 4 Newark Street

institute: QMUL

data_processing:
Hisat2 (v 2.0.4, paired-end mode)
htseq-count (v0.6.0)
DESeq2
Genome_build: GRCh38 (v 93)
Supplementary_files_format_and_content: Excel file include gene names normalized counts

source_name: organotypic 3D model

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

value: CRISPR-Cas9 ABCA12 KO

value: hTert cells


title: crKO 1


title: Alb566_WT_Input_S30

description: 25C 30' MNase

value: Input


title: JurSpD1

description: only used for IGV plot


title: crKO 2


title: card1_1_DMBQ_3


title: card1_2_mock_4

value: mock (DMSO)


title: JurRuD3

description: only used for IGV plot

value: Ruxolitinib


title: WT_DMBQ_1

value: replicate 1


title: Alb570_WT_H3K4me3_eSPAN_S30

description: 25C 30' MNase

value: WT


title: card1_2_mock_3


title: Alb565_WT_H3K4me3_ChIP_G1

description: G1 MNase


title: Alb564_WT_Input_G1

description: G1 MNase


title: Alb350_WT_H3K56ac_eSPAN_S30

description: 25C 30' MNase


title: crWT 3

value: Wildtype


title: JurRuD1

description: only used for IGV plot

value: immortal cell line

value: T lymphoblastoid


title: crWT 1


title: Alb349_WT_H3K4me3_eSPAN_S30

description: 25C 30' MNase


title: JurRuD2

description: only used for IGV plot


title: card1_2_mock_1

value: 10 min


title: HI 4

data_processing:
Hisat2 (v 2.0.4, paired-end mode)
htseq-count (v0.6.0)
DESeq2
Genome_build: GRCh38 (v 93)
Supplementary_files_format_and_content: Excel file with normalized counts

source_name: HI skin (HI)

tag: diagnosis

value: Harlequin Ichrthyosis

value: skin


title: card1_1_mock_4

value: replicate 4


title: Alb348_WT_BrdU_S30

description: 25C 30' MNase

value: BrdU


title: card1_1_mock_3

value: replicate 3


title: 8B10MAD1

description:
DEseq2_8B10_normalized_DM.txt
8B10_IR_MAvsDM_D.txt

value: permanent defected HIV-1-infected cell line

value: Mycophenolic acid


title: Alb347_WT_H3K56ac_ChIP_S30

description: 25C 30' MNase


title: Alb346_WT_H3K4me3_ChIP_S30

description: 25C 30' MNase


title: card1_1_mock_2

value: replicate 2


title: HI 1


title: 8B10SpD3

description:
DEseq2_8B10_normalized_DM.txt
8B10_IR_SpvsDM_D.txt

value: Spironolactone


title: crWT 2

value: hTert cells


title: card1_1_mock_1

value: mock (DMSO)


title: 8B10SpD2


title: card1_2_mock_2


title: NS 9

source_name: Normal skin (NS)

value: Normal


title: Alb344_WT_H3K4me3_ChIP_G1

description: G1 MNase

value: WT


title: Alb345_WT_Input_S30

description: 25C 30' MNase

value: Input


title: 8B10SpD1

value: immortal cell line


title: WT_mock_4

value: WT-expressing aequorin


title: Alb343_WT_Input_G1

description: G1 MNase


title: 8B10RuD3

description:
DEseq2_8B10_normalized_DM.txt
8B10_IR_RuvsDM_D.txt

value: Ruxolitinib

value: T lymphoblastoid


title: NS 6

value: skin


title: 8B10MAD3


title: WT_mock_2

value: 10 min


title: 8B10MAD2


title: HI 3

value: Harlequin Ichrthyosis


title: 8B10RuD2


title: HI 2


title: WT_mock_1

value: replicate 1


title: 8B10RuD1

value: permanent defected HIV-1-infected cell line


title: Arecoline

city: Ishikari-Tobetsu

first: Durga

last: Paudel

state: Hokkaido

address: Kanazawa

institute: Health Sciences University of Hokkaido

hyb_protocol: According to Agilent protocol

scan_protocol: According to Agilent protocol

data_processing:
Feature extraction software from Agilent using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628 012391_D_20060331)
Normalization was performed using software R. The quantile method was used for normalization.

label: Agilent Low Input QuickAmp Labeling Kit

source_name: Human Gingival Epithelial Cell

label_protocol: 50 ng of total RNA was was labelled using Agilent low input QuickAmp, one color

growth_protocol: Human gingival epithelial progenitors  were cultured in CnT-Prime epithelial cell culture medium  containing antibiotics (5% penicillin-streptomycin at 37˚C in an incubator supplied with 5% CO2

extract_protocol: Total RNA was extracted with the acid guanidine thiocyanate/phenol-chloroform method using TRIzol Reagent (Invitrogen Corporation, USA)

treatment_protocol: The cells were  treated with 50 μg/ml arecoline hydrobromide  for 3 days and without arecoline for another 3 days for a total period of 1 month

value: Gingiva

value: Human Gingival Epithelial Cell

tag: treatment

value: 50 μg/ml arecoline for 1 month


title: NS 2


title: psAP2 vector control rep 3

status: Public on Sep 01 2020

city: Tokyo

first: Kumiko

last: Nakada-Tsukui

address: 1-23-1, Toyama, Shinjyuku-ku

institute: National Institute of Infectious Diseases

data_processing:
Real-time analysis (RTA) software was used for base calling.
Sequenced reads were trimmed for TruSeq adaptor sequence, and masked for low-complexity and low-quality sequence by using cutadapt software ver. 1.13, then further analyzed for the quality by using FastQC software ver. 0.11.5.
Quality controlled reads were mapped to E. histolytica genome release version 1.3 in AmoebaDB using TopHat software ver. 2.1.1 (Bowtie software ver. 2.3.3.1).
Mapped reads were assembled using Cufflinks software ver. 2.2.1. Assembled data were merged and transcripts were predicted using cuffmerge tool in the Cufflinks software.
The differential gene expression analysis was performed using cuffdiff tool to analyse the difference between mock vector and rab7d gene silencing plasmid transfected cells.
Genome_build: E. histolytica genome release version 1.3
Supplementary_files_format_and_content: genes_read_group_tracking: Excel file, raw fragment counts of transcripts in 6 samples (at the 4th column).
Supplementary_files_format_and_content: genes.fpkm_tracking: Excel file, normalized and averaged FPKM value of the mock vector transfected and rab7d gene silenced strain.
Supplementary_files_format_and_content: gene_exp.diff: Excel file, analyzed data for differentially expressed genes in mock vector transfected and rab7d gene sileced strain.

organism: Entamoeba histolytica

source_name: Trophozoite

growth_protocol: Standard protocl for E. histolytica axenic cuture with BIS medium.

extract_protocol:
Logarithmic growth phase of E. histolytica trophozoites were harvested then total RNA was extracted using Trizol reagent.
RNA-seq libraries were generated by using TruSeq stranded mRNA kit. The protocol included polyA plus RNA purification, RNA fragmentation, random hexamer primed cDNA synthesis, linker ligation, PCR amplification, and gel purification. The libraries were then subjected to 100 nt paired-end sequencing using an Illumina HiSeq2500.

tag: strain

tag: transfected plasmid

value: psAP2 (empty vector)

tag: expression of rab7d

value: normal


title: rab7d gene-silenced strain rep 3

value: psAP2-Rab7D (vector for silencing rab7d)

value: silenced


title: rab7d gene-silenced strain rep 2


title: psAP2 vector control rep 1


title: rab7d gene-silenced strain rep 1


title: psAP2 vector control rep 2


title: NS 7

value: Normal


title: WT_mock_3

tag: ecotype

tag: agent

value: mock (DMSO)

tag: genotype/variation

tag: time point

value: replicate 3


title: 4-24-124a-1 [mRNA]

city: Sacramento

first: Pui Yan

last: Ho

state: CA

address: 2700 Stockton Blvd., Rm2120B

institute: UC Davis

data_processing:
Sequence reads were mapped to reference human genome assembly (Feb. 2009, GRCh37/hg19) with BWA.
Read counts derived from transfected recombinant RNAs were mapped to sequence reads from FASTQ-formatted data to the using a PERL script
Differentially expressed mRNAs between phenotypes were computed using EdgeR. Parameters: log2FC > 1.2 or log2FC < 0.8, P < 0.05, and log2CPM > 5.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts (CPM), fold change (FC), p-value, and FDR values generated by EdgeR.

growth_protocol: 293T and Dicer-KO 293T cells were maintained in DMEM media supplemented with 10% FBS and 10ug/ml gentamycin, routinely passaged, and plated onto 6-well plates for treatment

extract_protocol:
RNA was harvested using TRIzol-chloroform.
Sequencing libraries were constructed by BGI using 1 ug of total RNA to isolate mRNAs using poly-T oligo-attached magnetic beads. Following mRNA fragmentation, cDNA was generated using random primers and an adapter was ligated at the 3' end of the fragment. Products were then purified, enriched by PCR amplification, and used to create DNB-based nanoarrays by RCR. Stepwise sequencing was performed using the combinatorial probe-anchor ligation (cPAL) approach and read on the BGISEQ-500 system.

treatment_protocol: cells were treated with 20nM of control tRNA, nCAR/miR-34a-5p, or nCAR/miR-34a-3p and harvested 48h post-transfection

tag: cell type

value: Embryonic kidney cells

tag: passage

value: 293/Dicer KO


title: 4-24-124a-3 [mRNA]

tag: genotype


title: 4-24-MSA-2 [mRNA]

value: control tRNA (MSA)


title: 4-24-124a-2 [mRNA]


title: 4-24-34a-2 [mRNA]


title: 4-24-MSA-1 [mRNA]


title: 4-24-34a-1 [mRNA]


title: 4-24-34a-3 [mRNA]


title: 293T-MSA-3 [mRNA]


title: NS 4

value: skin


title: 293T-MSA-1 [mRNA]


title: 293T-MSA-2 [mRNA]


title: 293T-124-3 [mRNA]


title: 293T-124-2 [mRNA]


title: 293T-34a-3 [mRNA]


title: 293T-34a-1 [mRNA]


title: 4-24-MSA-3 [mRNA]


title: 4-24-MSA-3

description:
4-24-MSA-3
match_MSA_107nt_matrix_ReadCount

data_processing:
Read counts of known miRNAs were analyzed using the miRDeep module
Read counts derived from transfected recombinant RNAs were mapped to sequence reads from FASTQ-formatted data to the using a PERL script
Differentially expressed miRNAs between phenotypes were computed using EdgeR. Parameters: P < 0.05 and log2CPM > 6.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts (CPM), fold change (FC), p-value, and FDR values generated by EdgeR.

source_name: Embryonic kidney cells

extract_protocol:
RNA was harvested using TRIzol-chloroform.
Sequencing libraries were constructed by BGI following the BGI-500 kit, using 1 ug of total RNA subjected to isolation of small RNAs less than 30 nt by gel separation (15% Urea-PAGE). Small RNA fragments were ligated to adenylated 3’ adapters annealed to unique barcodes, followed by the ligation of 5’ adapters and reverse transcription (RT). Samples were pooled to make a single strand DNA circle (ssDNA circle) to yield the final small RNA library, after a second size selection by gel separation. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and single-end reads of 50bp were read on the BGISEQ-500 platform.

value: Dicer KO

value: control tRNA


title: 4-24-MSA-2

description:
4-24-MSA-2
match_MSA_107nt_matrix_ReadCount


title: Control

value: control


title: 4-24-MSA-1

description:
4-24-MSA-1
match_MSA_107nt_matrix_ReadCount


title: 4-24-124a-3

description:
4-24-124a-3
match_124a_180nt_matrix_ReadCount


title: 4-24-34a-2

description:
4-24-34a-2
match_34a_180nt_matrix_ReadCount


title: 4-24-34a-3

description:
4-24-34a-3
match_34a_180nt_matrix_ReadCount


title: 4-24-34a-1

description:
4-24-34a-1
match_34a_180nt_matrix_ReadCount


title: 4-24-124a-2

description:
4-24-124a-2
match_124a_180nt_matrix_ReadCount


title: 293T-MSA-3

description:
293T-MSA-3
match_MSA_107nt_matrix_ReadCount

value: Dicer WT


title: 4-24-124a-1

description:
4-24-124a-1
match_124a_180nt_matrix_ReadCount


title: 293T-34a-2

description:
293T-34a-2
match_34a_180nt_matrix_ReadCount


title: 293T-MSA-1

description:
293T-MSA-1
match_MSA_107nt_matrix_ReadCount


title: 293T-34a-3

description:
293T-34a-3
match_34a_180nt_matrix_ReadCount


title: 293T-124-2

description:
293T-124-2
match_124a_180nt_matrix_ReadCount


title: 293T-MSA-2

description:
293T-MSA-2
match_MSA_107nt_matrix_ReadCount


title: 293T-124-3

description:
293T-124-3
match_124a_180nt_matrix_ReadCount


title: 293T-124-1

description:
293T-124-1
match_124a_180nt_matrix_ReadCount


title: 293T-124-1 [mRNA]


title: 293T-34a-1

description:
293T-34a-1
match_34a_180nt_matrix_ReadCount


title: 293T-34a-2 [mRNA]


title: IsoCS_testis_18C_replicate 3

city: Houston

first: Richard

last: Meisel

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

data_processing:
RNA-seq reads were aligned to the housefly reference genome Musca_domestica-2.02 using HISAT2
Aligned reads were sorted with SAMtools
Sorted reads were assigned to annotated genes using htseq-count
Gene counts were analysed with DESeq2
Genome_build: Musca_domestica-2.0.2 (GCF_000371365.1)
Supplementary_files_format_and_content: CSV file with read counts for each replicate and results of a statistical test for genotype-by-environment interactions on expression

organism: Musca domestica

source_name: Testis

extract_protocol:
Direct-zol RNA Mini Prep (Zymo Research) was used to extract RNA from head and testis samples homogenized in TRIzol reagent (Life Technologies)
Library preparation was carried out using TruSeq Stranded mRNA Kit (Illumina). Quality of libraries were assessed using a 2100 Bioanalyzer.

value: IsoCS

tag: developmental temperature

value: Testis


title: IsoCS_testis_29C_replicate 3

tag: tissue


title: CSrab_testis_18C_replicate 2

value: CSrab


title: CSrab_testis_18C_replicate 1


title: CSrab_testis_29C_replicate 1


title: IsoCS_testis_29C_replicate 1


title: IsoCS_testis_18C_replicate 1


title: CSrab_testis_29C_replicate 2


title: CSrab_testis_29C_replicate 3


title: IsoCS_testis_18C_replicate 2


title: CSrab_testis_18C_replicate 3


title: IsoCS_testis_29C_replicate 2


title: Progressive.9

first: Vitor

middle: H

last: Teixeira

address: 5 University Street

department: Medicine

institute: University College London

hyb_protocol: Thermofisher/Affymetrix Human Clariom D GeneChip as per manufacturer's instructions [Fluidics Station 450]

scan_protocol: Affymetrix Scanner 3000 7G as per manufacturer's instructions

data_processing: Processing was performed using R and Bioconductor. Raw data in CEL format were read using the read.celfiles method from the oligo package, and normalised using RMA.

source_name: Human preinvasive lung squamous cell carcinoma lesions - matched stroma

label_protocol: Thermofisher/Affymetrix WT Pico Kit Biotin labelling module as per manufacturer's instructions

extract_protocol: Laser-capture micro-dissection (LCM) was used to selectively isolate stromal regions adjacent to known CIS for molecular analysis. RNA was extracted using the High Pure FFPE RNA Kit (Roche Applied Science, West Sussex, UK) according to manufacturer’s protocol. Quantification was carried out using the Quant-iT RNA assay kit and the Qubit® 2.0 fluorometer (Life Technologies, Paisley, UK).

value: Preinvasive lung squamous cell carcinoma lesions - matched stroma

tag: lesion outcome

value: Progression

tag: matched cis lesion

value: Progressive 42


title: Progressive.3

value: Progressive 36


title: Regressive.9.2

value: Regression

value: Regressive 59


title: Progressive.7

value: Progressive 40


title: Progressive.8

value: Progressive 41


title: IsoCS_head_18C_replicate 3

source_name: Head

value: Head


title: Regressive.11

value: Regressive 63


title: Progressive.2

value: Progressive 35


title: Progressive.5

value: Progressive 38


title: IsoCS_head_18C_replicate 2


title: IsoCS_head_18C_replicate 1


title: IsoCS_head_29C_replicate 3


title: IsoCS_head_29C_replicate 2


title: CSrab_head_18C_replicate 3


title: CSrab_head_18C_replicate 1


title: CSrab_head_18C_replicate 2


title: Progressive.12

value: Progressive 46


title: CSrab_head_29C_replicate 1


title: Progressive.4

value: Progressive 37


title: Regressive.10

value: Regressive 62


title: Regressive.2

value: Regressive 51


title: Regressive.8

value: Regressive 58


title: Regressive.12

value: Preinvasive lung squamous cell carcinoma lesions - matched stroma

value: Regressive 64


title: IsoCS_head_29C_replicate 1

value: IsoCS


title: Progressive.6

value: Progression

value: Progressive 39


title: Regressive.3

value: Regression

value: Regressive 52