title: CoVinh_6

status: Public on Aug 31 2022

type: SRA

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

country: Germany

institute: University Münster

library_source: transcriptomic

data_processing:
Reads were quality checked with package FastQC (version 0.11.4,), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to human genome ENSEMBL hg38 release 91  and to CoV-2 genome EPI_ISL_463008_Cov2_AF, using STAR aligner (Dobin and Gingeras, 2015) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Genome_build: ENSMBL human hg38 release 91 genome and CoV-2 genome EPI_ISL_463008_Cov2_AF
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.

molecule: total RNA

organism: Homo sapiens

growth_protocol: For generation of adult stem cell derived lung organoids, primary cells were isolated from healthy parts of distal lung tissue obtained from lung cancer patients undergoing tumor resection surgery, cells were FACS sorted, counted and seeded in the extracellular matrix substitute. Organoids were kept in an incubator at 37°C, 5 % CO2. Upon growth for 2-3 weeks, the organoids were expanded by enzymatic digestion. Mature human lung organoids were collected on ice to remove remaining matrix.

extract_protocol:
For total RNA isolation, the RNeasy Plus Mini Kit (Qiagen) was used according to the manufacturer`s instructions. Organoids were released from Cultrex with cold PBS, pelleted, and resuspended by vortexing in 350 μl RLT lysis buffer supplemented with β-mercaptoethanol. RNA was eluted in 30 µl water.
PolyA+RNA was purified  from 200 ng total RNA using Poly(A) mRNA Magnetic Isolation module Kit (NEB E7490L, New England Biolabs). The RNA Sequencing library was prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs).
The libraries were sequenced on Illumina Nextseq 2000 using NextSeq2000 P3 Reagent Kit (200 cycles, paired end run 2x 111 bp) with an average of 74.2 M reads per RNA sample.

treatment_protocol: Organoid fragments were either mock-infected or challenged with SARS-CoV-2 (MOI 1, ) Munich/2020/984 strain). After incubation at 37° and 5 % CO2 for 30 min, medium with the respective inhibitor or carrier (PH-797804, VX-702, or DMSO only) was added.

tag: infection

value: SARS

tag: tretament


title: CoVinh_4


title: CoVinh_2

value: mock

value: DMSO


title: CoVinh_14


title: CoVinh_18


title: CoVinh_13

value: CTR


title: CoVinh_16


title: CoVinh_12


title: CoVinh_1


title: 7WB24_B

city: Utrecht

first: Ronald

last: de vries

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: westerdijkinstitute

data_processing:
Data quality was assessed with fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Read-trimming was conducted using bbduk (http://jgi.doe.gov/data-and-tools/bb-tools/).
Reads were aligned to the A. niger NRRL 3 genome (Aguilar‐Pontes et al., 2018) using STAR (https://github.com/alexdobin/STAR).
BAM file outputs were mapped to genes using htseq‐count (Anders et al., 2015) using default settings.
Genome_build: Aspergillus niger NRRL 3 genome (Aguilar‐Pontes et al., 2018)
Supplementary_files_format_and_content: .txt files represent number of raw read counts mapping to each gene

molecule: polyA RNA

organism: Aspergillus niger

source_name: Aspergillus niger N593 delta-kusA

growth_protocol: The strains were grown at 30°C using Minimal Medium (MM, pH 6) or Complete Medium (CM, pH 6) with the appropriate carbon source. When required, media of auxotrophic strains were supplemented with 1.22 g/L uridine. All liquid cultures were incubated in an orbital shaker at 250 rpm and 30°C.

extract_protocol:
Total RNA was extracted from ground mycelial samples using TRIzol® reagent (Invitrogen) and purified with the NucleoSpin® RNA Clean-up Kit (Macherey-Nagel), while contaminant gDNA was removed by rDNase treatment directly on the silica membrane. The RNA quality and quantity were analysed with a RNA6000 Nano Assay using the Agilent 2100 Bioanalyzer (Agilent Technologies).
For RNA‐Seq, The TruSeq stranded mRNA (cat#20020594) was used to generate cDNA library for illumina NextSeq550 platform according to the manufacturer protocol. Single-read sequencing of the cDNA libraries with a read length of 150 was performed with NextSeq 550 Sequencing System using NextSeq 500/550 High Output v2 kit 150 cycles (cat#20024907).

treatment_protocol: The pre-cultures containing 250 ml CM with 2% D-fructose in 1 L Erlenmeyer flasks were inoculated with 106 spores/ml and incubated for 16 h. Subsequently, the mycelia were harvested by filtration on sterile cheesecloth, washed with MM and ~0.5 g (dry weight) was transferred to 250 ml Erlenmeyer flasks containing 50 ml MM supplemented with 1% WB or 1% SBP. All cultures were performed in triplicate. After 2, 8 and 24 h of incubation, the mycelia were harvested by vacuum filtration, dried between tissue paper and frozen in liquid nitrogen.

tag: genotype

value: gaaC/lraC/xkiA/galE/ladB/hxka/glkA

tag: medium

value: 1xMM +1% wheat bran

tag: time point

value: 24 hr


title: 7WB24_C


title: 7WB8_C

value: 8 hr


title: CoVinh_9


title: CoVinh_8


title: 7WB8_B


title: CoVinh_7


title: CoVinh_3


title: 7WB8_A


title: 7SBP24_C

value: 1xMM + 1% sugar beet pulp


title: 7SBP24_B


title: CoVinh_10


title: CoVinh_15


title: 7SBP24_A


title: 7SBP8_C


title: 7SBP8_B


title: 7WB24_A


title: 6WB8_C

value: galE/ladB


title: 6SBP24_A


title: 6SBP8_A


title: 6SBP8_C


title: 6SBP24_B


title: 6SBP24_C


title: 6SBP8_B


title: 5WB8_C

value: hxkA/glkA


title: 5WB24_A


title: 7SBP8_A


title: 6WB24_B


title: 6WB24_C


title: 6WB24_A


title: 5WB8_A


title: 5SBP24_B


title: 5WB24_C


title: 5SBP8_C


title: 5SBP8_B


title: 5SBP8_A


title: 4WB24_C


title: 5SBP24_A


title: 6WB8_B


title: 4WB24_A


title: 4WB8_C


title: 6WB8_A


title: 5WB8_B


title: 5WB24_B


title: 5SBP24_C


title: 4WB8_B


title: 4SBP24_B


title: 4SBP8_A


title: 4WB8_A


title: 4SBP8_B


title: 4SBP24_C


title: 4SBP24_A


title: 3WB8_B

value: gaaC/lraC


title: 4SBP8_C


title: 3WB24_B


title: 3WB24_C


title: 4WB24_B


title: 3WB8_C


title: 3SBP8_A


title: 3WB24_A


title: 3SBP8_B


title: 3WB8_A


title: 2WB24_C

value: lraC


title: 2WB24_B


title: 2WB8_C


title: 3SBP24_C


title: 3SBP24_B


title: 3SBP8_C


title: 2WB8_B


title: 2WB24_A


title: 2SBP24_B


title: 2SBP24_C


title: 2WB8_A


title: 2SBP24_A


title: 2SBP8_B


title: 1WB8_A

value: gaaC


title: 1WB8_B


title: 1WB24_B


title: 1SBP8_A


title: 1SBP24_B


title: 1WB24_C


title: 2SBP8_A


title: 2SBP8_C


title: 3SBP24_A


title: 1WB8_C


title: 1WB24_A


title: 1SBP24_C


title: 1SBP24_A


title: 1SBP8_C


title: 1SBP8_B


title: 2126-Treg_EV-WT-Rep3

type: RNA

city: Luxembourg

first: Etienne

last: Moussay

address: 6 rue Nicolas-Ernest Barblé

department: Cancer Research

country: Luxembourg

institute: Luxembourg Institute of Health

description: Gene expression data from Treg+ T cells incubated with sEV

hyb_protocol: cRNA products were randomly fragmented and labeled prior hybridization onto Affymetrix GeneChips.

scan_protocol: Chips were scanned using GeneChip Scanner 3000

data_processing: CEL files were processed with TAC 4.0

label: biotin

organism: Mus musculus

source_name: Spleen

label_protocol: 100 ng of total RNAs were reverse transcribed into cDNA, then transcribed into cRNAs and labeled into biotinylated cRNA using the GeneChip WT PLUS Reagent kit (Affymetrix) according to the manufacturer’s standard protocols (P/N 703174 Rev.2

extract_protocol: Spleens were removed, gently dissociated on ice, and cells were antibody-stained and sorted by FACS (Aria III). IL-2 (10ng/ml) and extracellular vesicles (50ug/ml) were added in culture for 24h. RNA was harvested using NucleoZOL reagent and columns.

tag: strain

value: Foxp3 YFP/cre


title: 2118-Treg-EV_TCL1-Rep2


title: 2124-Treg_EV-TCL1-Rep1


title: 2116-Treg_EV-TCL1-Rep3


title: 2122-CD8_EV-WT_Rep3

description: Gene expression data from CD8+ T cells incubated with sEV


title: 2120-CD8_EV-TCL1_Rep1


title: 2218-CD4_EV-TCL1_Rep2

description: Gene expression data from CD4+ T cells incubated with sEV


title: 2222-CD19_EV-WT_Rep3

description: Gene expression data from CD19+ T cells incubated with sEV


title: 2121-CD8_EV-WT_Rep2


title: 2217-CD4_EV-TCL1_Rep1


title: 2119-Treg_EV-WT-Rep2


title: 2115-CD8_EV-TCL1_Rep2


title: 2224-CD19_EV-TCL1_Rep2


title: 2225-CD19_EV-TCL1_Rep3


title: 2221-CD19_EV-WT_Rep2


title: 2223-CD19_EV-TCL1_Rep1


title: 2219-CD4_EV-TCL1_Rep3


title: 2123-CD8_EV-TCL1_Rep3


title: 2125-CD8_EV-WT_Rep1


title: 2117-Treg_EV-WT-Rep1


title: 2220-CD19_EV-WT_Rep1


title: 2216-CD4_EV-WT_Rep3


title: 2214-CD4_EV-WT_Rep1


title: 2215-CD4_EV-WT_Rep2


title: Sham-1

city: Niigata

first: Yohko

last: Yoshida

address: 1-757, Asahimachi-dori, Chuo-ku

country: Japan

institute: Niigata University

description: gene expression of BAT at 4 weeks after Sham operation

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE microarray (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 028005_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Brown adipose tissue (BAT) from mouse at 2 weeks after Sham operation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Low Input Quiuck Amp Labeling) (Agilent) according to the manufacturer's instructions.

growth_protocol: Mice were housed at 23℃ with free access to water and normal chow under 12hr light / 12hr dark cycle.

extract_protocol: Total RNA was isolated from BAT with RNeasy Lipid Tissue Mini Kit (QUIAGEN).RNA was quantified using a NanoDrop ND-1000 and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: TAC (Thoracic aortic constriction) or Sham operation was performed in 11-week-old male mice and sample was collected 2 weeks after surgery.

tag: gender

value: Male

tag: age

value: 13 weeks of age

tag: tissue

value: Brown adipose tissue (BAT)


title: Sham-4


title: Trypanosoma brucei gambiense_STIB 386_Resistant_FBS_B

city: Glasgow

first: Nicola

last: Veitch

address: Bearsden Rd

country: United Kingdom

institute: University of Glasgow

data_processing: The processed data files are collated tag sequences and associated tag counts. Tag counts were collated using a custom written script in Perl 5.10.0.

organism: Trypanosoma brucei gambiense

source_name: Trypanosoma brucei gambiense STIB 386 bloodstream-form

growth_protocol: Bloodstream form T. b. gambiense STIB 386 were grown in HMI9 media with 20% fetal bovine serum at 37ºC with 5% CO2 and harvested during mid-log phase (approximately 4,500,000 cells per library). Human serum resistant cells were maintained in HMI9 media with 15% fetal bovine serum and 5 % human serum until 2 weeks before harvest, then they were grown in HMI9 media with 20% fetal bovine serum. The cells were checked for human serum resistance before harvesting for RNA.

extract_protocol: Sequence tag preparation was performed with Digital Gene Expression Tag Profile Kit (Illumina) using NlaIII, according to the manufacturer’s instructions.

treatment_protocol: The cells were pelleted at 500g for 10 mins at 4ºC and immediately re-suspended in RLT buffer (Qiagen RNeasy kit). The cells were disrupted by serial passage through a 26 gauge needle and stored at -80ºC before use. RNA was isolated from the cells using RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase treatment step, to ensure that there was no DNA contamination. The RNA was measured for quantity and quality by Nanodrop ND-1000 spectrophotometer and Agilent 2100 Bioanalyzer according to the manufacturer’s instructions.

tag: cell type

value: Bloodstream-form in vitro

value: STIB 386

tag: phenotype

value: resistant to human serum

tag: culture conditions


title: Sham-2


title: 16_18AHC1

city: BANGALORE

first: V L NARASIMHA RAO

last: THOTA

state: KARNATAKA

address: 258/A NARAYANA HRUDAYALAYA, BOMMASANDRA

country: India

institute: Thrombosis Research Institute

hyb_protocol: 1.5 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to sureprint G3 mouse gene expression V2  8 X60K  (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan settings.

data_processing: Data extraction from Images was done using Agilent Feature Extraction software Version 11.5.1.1

source_name: Ascending aorta from 18 week AHC

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP (Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Invitrogen) according to the manufacturer protocol. Total RNA integrity was assessed using RNA 6000 Nano Lab Chip on the 2100 Bioanalyzer (Agilent, Palo Alto, CA) following the manufacturer’s protocol. Total RNA purity was assessed by the NanoDrop® ND-1000 UV-Vis Spectrophotometer (Nanodrop technologies, Rockland, USA). We considered RNA to be good quality based on the rRNA 28S/18S ratios and RNA integrity number (RIN

treatment_protocol: Double knockout mice were fed on High fat diet alone in one group and after 5 oral doses of AHC molecule (ApoB, HSP60, chlamydia pneumonia transcripts in a single scaffold) in another group  for 0, 6, 8, 18 and 30 weeks

value: ascending aorta

value: Double knockout Apobtm2Sgy/Ldltm1Her

value: 18 weeks group (26 weeks)

tag: diet

value: high fat diet

tag: treatment

value: AFC


title: TAC-4

description: gene expression of BAT at 4 weeks after TAC operation

source_name: Brown adipose tissue (BAT) from mouse at 2 weeks after TAC operation


title: Sham-3


title: TAC-3


title: 18_18AHC3


title: TAC-2


title: 19_30HFD1

source_name: Ascending aorta from 30 week HFD

value: 30 weeks group (38 weeks)

value: untreated


title: TAC-1


title: Trypanosoma brucei gambiense_STIB 386_Resistant_FBS_C

value: maintained in HMI9 media with 15% fetal bovine serum and 5 % human serum until 2 weeks before harvest, then they were grown in HMI9 media with 20% fetal bovine serum.


title: 23_30AHC2

source_name: Ascending aorta from 30 week AHC


title: 17_18AHC2


title: 20_30HFD2


title: 21_30HFD3


title: 24_30AHC3


title: Trypanosoma brucei gambiense_Eliane_B

source_name: Trypanosoma brucei gambiense Eliane bloodstream-form

growth_protocol: Bloodstream form Trypanosoma brucei gambiense Eliane and Trypanosoma brucei brucei STIB 247 were grown in HMI9 media with 20% fetal bovine serum at 37ºC with 5% CO2 and harvested during mid-log phase (approximately 4,500,000 cells per library). Eliane was maintained in HMI9 media with 15% fetal bovine serum and 5 % human serum.

treatment_protocol: The cells were pelleted at 500 g for 10 mins at 4ºC and immediately re-suspended in RLT buffer (Qiagen RNeasy kit). The cells were disrupted by serial passage through a 26 gauge needle and stored at -80ºC before use. RNA was isolated from the cells using RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase treatment step, to ensure that there was no DNA contamination. The RNA was measured for quantity and quality by Nanodrop ND-1000 spectrophotometer and Agilent 2100 Bioanalyzer according to the manufacturer’s instructions.

value: Eliane


title: 15_18HFD3

source_name: Ascending aorta from 18 week HFD


title: 22_30AHC1


title: CRC_HC179T

city: Kyoto

first: Makoto

middle: Mark

last: Taketo

state: Kyoto

address: Yoshida-Honmachi, Sakyo

department: Kyoto University Hospital

institute: Kyoto University

description: Large intestine

data_processing:
RNA-seq analysis was performed by Macrogen.
Prepared libraries were paired-end sequencing (2 × 100 bases) to a depth of ~40 million reads/sample using the Illumina HighSeq 2000 sequencer.
The sequence reads were mapped to the hg19 reference genome with HISAT2 program and the transcripts were assembled using StringTie program.
The read counts were scored using featureCounts program.
Assembly: hg19
Supplementary files format and content: A tab-delimited text file include TPM  for each sample

source_name: Colorectal cancer stem cell spheroids

growth_protocol: Collected tumor samples were transferred from the operation room to the laboratory in ice-cold washing medium (DMEM/F12 containing 10% bovine calf serum, 100 U/ml penicillin, and 0.1 mg/ml streptomycin). Fragments of excised tumor were minced and digested by collagenase type I (Thermo Fisher Scientific). Then, epithelial cells were collected and suspended in Matrigel (Corning Inc.) and cultured in the cancer medium (Advanced DMEM/F-12 (Thermo Fisher), 100 units/ml penicillin, 0.1 mg/ml streptomycin, 2 mM L-glutamine, 10 μM Y27632, 10 or 1 μM SB431542, 5 μg/ml Plasmocin (Invivogen, San Diego, CA), and 5% FBS (Thermo Fisher]) with or without 50 ng/mL EGF (PeproTech) and 100 ng/mL basic FGF (PeproTech).

extract_protocol:
After aspiration of the medium, the lysis buffer (Takara Bio Inc., Kusatsu, Japan) was directly added to each well of spheroid culture. RNA was purified using NucleoSpin RNA II kit (Takara).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untreated

value: CRC patient-derived spheroids

value: Untreated

tag: disease state

value: Colorectal cancer


title: CRC_HC127T

description: Large intestine


title: CRC_HC97T

description: Large intestine


title: CRC_HC72T

description: Large intestine


title: 14_18HFD2

value: Male


title: 13_18HFD1


title: 8_6HFD2

source_name: Ascending aorta from 6 week HFD

value: 6 weeks group (14 weeks)


title: Trypanosoma brucei gambiense_STIB 386_Sensitive_C

description: Trypanosoma brucei gambiense STIB 386 bloodstream-form

data_processing: The GEO sample tables are collated tag sequences and associated tag counts. Tag counts were collated using a custom written script in Perl 5.10.0.

source_name: human serum-sensitive Trypanosoma brucei gambiense culture

growth_protocol: Bloodstream form T. b. gambiense STIB 386 were grown in HMI9 media with 20% fetal bovine serum at 37ºC with 5% CO2 and harvested during mid-log phase (approximately 4,500,000 cells per library). Human serum resistant cells were maintained in HMI9 media with 15% fetal bovine serum and 5 % human serum.

extract_protocol: The cells were pelleted at 1100g for 10 mins at 4ºC and immediately re-suspended in RLT buffer (Qiagen RNeasy kit). The cells were disrupted by serial passage through a 26 gauge needle and stored at -80ºC before use. RNA was isolated from the cells using RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase treatment step, to ensure that there was no DNA contamination. The RNA was measured for quantity and quality by Nanodrop ND-1000 spectrophotometer and Agilent 2100 Bioanalyzer according to the manufacturer’s instructions. Sequence tag preparation was performed with Digital Gene Expression Tag Profile Kit (Illumina) using NlaIII, according to the manufacturer’s instructions.

value: Bloodstream-form in vitro

value: sensitive to human serum


title: 3_0HFD3

source_name: Ascending aorta from 0 week HFD

value: 0 weeks group (8 weeks)


title: 7_6HFD1

value: ascending aorta


title: 9_6HFD3

value: Double knockout Apobtm2Sgy/Ldltm1Her


title: 5_0AHC2

source_name: Ascending aorta from 0 week AHC


title: 11_6AHC2

source_name: Ascending aorta from 6 week AHC


title: CRC_HC195T

description: Large intestine


title: 4_0AHC1


title: 10_6AHC1


title: 12_6AHC3


title: 2_0HFD2


title: 1_0HFD1


title: 6_0AHC3


title: CRC_HC178T

description: Large intestine


title: CRC_HC122T

description: Large intestine


title: Trypanosoma brucei gambiense_Eliane_A


title: Trypanosoma brucei gambiense_STIB 386_Sensitive_A

value: STIB 386

value: maintained in HMI9 media with 15% fetal bovine serum and 5 % human serum


title: CRC_HC185T

description: Large intestine


title: CRC_HC46T

description: Large intestine


title: CRC_HC91T

description: Large intestine


title: CRC_HC102T

description: Large intestine


title: CRC_HC172T

description: Large intestine


title: Trypanosoma brucei gambiense_STIB 386_Sensitive_D


title: Trypanosoma brucei gambiense_STIB 386_Resistant_A

source_name: human serum-resistant Trypanosoma brucei gambiense culture

value: resistant to human serum


title: CRC_HC128T

description: Large intestine


title: CRC_HC193T

description: Large intestine


title: CRC_HC90T

description: Large intestine


title: CRC_HC149T

description: Large intestine


title: CRC_HC137T

description: Large intestine


title: CRC_HC35T

description: Large intestine


title: CRC_HC20TT

description: Large intestine

source_name: Colorectal cancer whole tissues

value: CRC whole tissues


title: Trypanosoma brucei gambiense_STIB 386_Resistant_B


title: Healthy_HC20N

description: Large intestine

source_name: Normal colorectal epithelial stem cell spheroids

value: healthy


title: CRC_HC146T

description: Large intestine


title: CRC_HC83T

description: Large intestine


title: Trypanosoma brucei gambiense_STIB 386_Resistant_C


title: Healthy_HC6N

description: Large intestine


title: CRC_HC9TT

description: Large intestine


title: Healthy_HC9N

description: Large intestine


title: CRC_HC24T

description: Large intestine


title: CRC_HC129T

description: Large intestine


title: CRC_HC108T

description: Large intestine


title: CRC_HC106T

description: Large intestine


title: CRC_HC93T

description: Large intestine


title: CRC_HC80T

description: Large intestine


title: CRC_HC6TT

description: Large intestine


title: CRC_HC74T

description: Large intestine


title: CRC_HC120T

description: Large intestine


title: CRC_HC67T

description: Large intestine


title: Trypanosoma brucei brucei_STIB 247

organism: Trypanosoma brucei brucei

source_name: Trypanosoma brucei brucei STIB 247 bloodstream-form

value: STIB 247


title: CRC_HC142T

description: Large intestine


title: CRC_HC73T

description: Large intestine


title: CRC_HC183T

description: Large intestine


title: CRC_HC28T

description: Large intestine


title: CRC_HC117T

description: Large intestine


title: CRC_HC7T

description: Large intestine


title: CRC_HC10T

description: Large intestine


title: CRC_HC40T

description: Large intestine


title: Capan-1 shNDRG3

city: Daejeon

first: Han

last: Koo

address: 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea

country: South Korea

institute: KRIBB

data_processing:
base calling was conducted through an integrated primary analysis software called RTA (Real Time  Analysis).
The BCL (base calls) binary was converted into FASTQ utilizing illumina package bcl2fastq
Adapters are trimmed away with Trim Galore 0.6.4 (>Q30)
Reads are mapped with paired end mapping of STAR 2.7.3a
Mapped reads are quantified and normalized with cufflinks 2.2.1
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Capan-1 cell line

growth_protocol: Each cell line were routinely grown in DMEM or RPMI1640 medium supplemented with 10% fetal bovine serum and 100 U/ml penicillin. Cell lines were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNAs of target cells were extracted using TRIzol reagent according to manufacturer’s protocol. Concentrations of RNA were measured with a spectrophotometer, 3ug of RNAs were used for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For stable knockdown of NDRG3 and GFP, lentiviral particles containing specific shRNA expression vector (pLKO.1) were produced by transfection of the shRNA expression plasmid and lentiviral packaging mix in HEK293T cell line. Each target cell line was incubated with the lentiviral supernatant containing 6 μg/ml polybrene and selected with puromycin (1 μg/ml).

value: Pancreatic cancer cell

tag: cell line

value: Pancreas

tag: shRNA

tag: kras mutation

value: Gly12Val (G12V)


title: CRC_HC21T

description: Large intestine

value: CRC patient-derived spheroids

value: Untreated

value: Colorectal cancer


title: Mia PaCa-2 shNDRG3

source_name: Mia PaCa-2 cell line

value: Mia PaCa-2

value: Gly12Cys (G12C)


title: CRC_HC20T

description: Large intestine


title: CRC_HC16T

description: Large intestine


title: CRC_HC11T

description: Large intestine


title: Capan-1 shGFP

value: shGFP


title: CRC_HC8T

description: Large intestine


title: CRC_HC1T

description: Large intestine


title: CRC_HC9T

description: Large intestine


title: BxPC-3shNDRG3

source_name: BxPC-3 cell line


title: Mia PaCa-2 shGFP


title: CRC_HC6T

description: Large intestine


title: Hs-766TshGFP

source_name: Hs-766T cell line

value: Gln61His (Q61H)


title: Hs-766TshNDRG3


title: Treg_EV_TCL1_Rep3

description: incubation with TCL1 sEV

data_processing:
After initial QCs using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/), fastq files were processed using a local Snakemake workflow including the following main steps.
First, raw reads were trimmed from their UMI index, poly A and adapter sequences using a combination of dedicated scripts and cutadapt (v2.10).
Next, filtered reads were submitted for mapping (STAR v2.5.3a) on the Mouse Reference genome (GRCm38).
Collapsing of reads originating from the same fragment was achieved with umi_tools (v 1.0.0) and counting was perfomed with featureCounts (subread v2.0.0).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Table with raw gene counts for every gene and every sample

source_name: Spleen

extract_protocol:
Spleens were removed, gently dissociated on ice, and cells were antibody-stained and sorted by FACS (Aria III). RNA was harvested using NucleoZOL reagent and columns. QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina was used with 500 ng of total RNA for the construction of sequencing libraries. UMI were added to the protocol.
Libraries were prepared for sequencing using standard protocols

value: Foxp3 YFP/cre

value: Foxp3 YFP+ Treg

tag: agent

value: TCL1 sEV


title: BxPC-3shGFP


title: CRC_HC22T

description: Large intestine


title: Ctr_ASO_231_2b_3

city: Davis

first: Sanchita

last: Bhatnagar

state: CA

address: 1275 Health Sciences, Tupper Hall 3134

department: Medical Microbiology and Immunology

country: USA

institute: University of California Davis

description: poly(A) enriched total RNA

data_processing:
Alignment Software: STAR2.5
Quantification Software: HTSeq 0.6.1p1
Differential expression analysis: DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: .txt: table with fpkm for all samples, FC and p-value

source_name: Human Triple Negative Breast Cancer cell line MDA-MB-231_2b

growth_protocol: MDA-MB-231_2b cells were maintained in RPMI Medium with 10% FBS.

extract_protocol:
Cells were grown to ~80% confluency were washed twice with ice-cold PBS. Total RNA was extracted by Rneasy Mini Kit (QIAGEN #74104).
RNA-seq libraries were prepared by Beijing Novogene Co., Ltd. on poly(A) enriched RNA using the Illumina HiSeq instrument.

treatment_protocol: Day 1: Cells were transfected with control or TRIM37 ASO.  Day 2:  Medium was changed. Day 3: Cells were trypsynized and sited on new plates. Day 4: Cells were transfected with control or TRIM37 ASO. Day 5:  Medium was changed. Day 6:  RNA was isolated

tag: source

value: Mouse brain metastasis of MDA-MB-231 cell line

value: Transfected with control ASO


title: TRIM37_ASO_231_2b_2

description: poly(A) enriched total RNA

value: Transfected with anti-TRIM37 ASO


title: TRIM37_ASO_231_2b_1

description: poly(A) enriched total RNA


title: Treg_EV_TCL1_Rep2

description: incubation with TCL1 sEV


title: Treg_EV_WT_Rep2

description: incubation with WT sEV

value: WT sEV


title: Treg_EV_TCL1_Rep1

description: incubation with TCL1 sEV


title: Treg_EV_WT_Rep3

description: incubation with WT sEV


title: Ctr_ASO_231_2b_2

description: poly(A) enriched total RNA


title: patient #31001 day8 replicate3

city: Freiburg

first: Gabriele

last: Greve

address: Hugstetter Str 55

department: Department of Internal Medicine 1

institute: University of Freiburg Medical Center

description: gene expression data from AML patients at day 8 of DAC treatment

hyb_protocol: Samples were hybridized according to manufacturer's protocol (Affymetrix).

scan_protocol: Samples were scanned according to manufacturer's protocol (Affymetrix).

data_processing: Raw data was analyzed with the Partek Genomics Suite.

label: Biotin

source_name: isolated blasts from peripheral blood

label_protocol: Samples were labeled with Biotin according to manufacturer's protocol (Affymetrix).

growth_protocol: Mononuclear cells were isolated out of AML patients' whole blood samples by Pancoll density centrifugation. AML blasts were enriched by automated magnetic sorting using anti-CD34 and -CD117 beads.

extract_protocol: Total RNA was extracted with Trizol Reagent (ThermoScientific)/Chloroform followed by DNase I digestion and column clean-up with the Qiagen RNeasy MinElute Cleanup Kit according to manufacturers' protocols. The subsequent steps were performed in technical triplicates (data only available in duplicates for samples 02_d8, 04_d0, 17_d0 and 17_d8 due to array QC failure)

treatment_protocol: AML patients were treated within the DECIDER trial (NCT00867672) with decitabine ((Decitabine/DAC treatment, 20 mg/m2 intravenous 1-hour infusion over 5 days, with add-on drugs valproic acid and/or all-trans retinoic acid [ATRA] added at day 6).

value: peripheral blood

value: AML

tag: patient id

value: blasts


title: patient #31001 day8 replicate1


title: CD19+EV-TCL1-Rep2

description: incubation with TCL1 sEV

value: CD19+ B cells


title: Ctr_ASO_231_2b_1

description: poly(A) enriched total RNA


title: patient #31001 day8 replicate2


title: Treg_EV_WT_Rep1

description: incubation with WT sEV


title: TRIM37_ASO_231_2b_3

description: poly(A) enriched total RNA


title: CD19+EV-TCL1-Rep3

description: incubation with TCL1 sEV


title: patient #31001 day0 replicate2

description: gene expression data from AML patients at day 0 of DAC treatment


title: CD19+EV-TCL1-Rep1

description: incubation with TCL1 sEV


title: patient #31001 day0 replicate1


title: CD19+EV-Ctrl-Rep2

description: incubation with WT sEV


title: CD8_EV_TCL1_Rep3

description: incubation with TCL1 sEV

value: CD8+ T cells


title: patient #26004 day8 replicate2


title: CD8_EV_TCL1_Rep2

description: incubation with TCL1 sEV


title: patient #26004 day8 replicate1


title: CD8_EV_TCL1_Rep1

description: incubation with TCL1 sEV


title: patient #26004 day0 replicate1


title: CD19+EV-Ctrl-Rep1

description: incubation with WT sEV


title: patient #26004 day0 replicate2


title: CD8_EV_WT_Rep2

description: incubation with WT sEV


title: patient #31001 day0 replicate3


title: CD8_EV_WT_Rep3

description: incubation with WT sEV


title: patient #26002 day8 replicate3


title: CD4_EV_TCL1_Rep1

description: incubation with TCL1 sEV

value: CD4+ T cells


title: patient #26002 day8 replicate2


title: patient #26004 day8 replicate3


title: CD4_EV_TCL1_Rep2

description: incubation with TCL1 sEV


title: CD8_EV_WT_Rep1

description: incubation with WT sEV


title: CD19+EV-Ctrl-Rep3

description: incubation with WT sEV


title: CD4_EV_WT_Rep1

description: incubation with WT sEV


title: CD4_EV_WT_Rep3

description: incubation with WT sEV


title: patient #26002 day8 replicate1


title: patient #26002 day0 replicate1


title: patient #26002 day0 replicate2


title: patient #16005 day8 replicate3


title: CD4_EV_WT_Rep2

description: incubation with WT sEV


title: patient #16005 day8 replicate2


title: IMM-aug20_M17_P23_30hpi

city: Modiin

first: Amichay

last: Afriat

state: non-US Resident

address: Nehar Hayarden Modiin

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description:
single_cell
sequencing protocol: MARSseq

data_processing:
data demultiplexing: bcl2fastq/2.20.0.422 Plate demultiplexing was provided to obtain plate specific reads in two fastq files (read 1 (R1) and read 2 (R2)). Pooled data of scRNAseq were demultiplexed using plate specific barcode. Specific sequences for each cell were demultiplexed using well specific barcode (attached).
data alignment: STAR/2.7.3a & zUMI/0.0.6c alignment of data to a combined pseudo-genome of host + parasite
Genome_build: host: GRCm38.p6
Genome_build: parasite: PBANKA01.43
cleaning, and filtering: custom script on Python 3 using multiple packages. full script in Jupyter notebook at https://github.com/AmichayAfriat/SpatioTemporal_malaria_liver_stage_atlas/
Supplementary_files_format_and_content: tab-delimited csv files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: infected_cells_metadata.csv: list of wells containing infected cells in each plate, wells corresponde to single_cell_384_barcodes_by_well.csv
Supplementary_files_format_and_content: single_cell_384_barcodes_by_well.csv: list of barcodes used for demultiplexing the cells in the single cell RNAseq experiment

source_name: Hepatocytes single cells

growth_protocol: C57bl6 female mice were fed regular chow ad libitum

extract_protocol:
Isolation of hepatocytes was performed as previously decribed (Bahar-Halpern, K. et al. Nature 2017).
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014).

value: hepatocyte

tag: Sex

value: female

value: post natal 1.5 month

value: infected with P. berghaei spz


title: CD4_EV_TCL1_Rep3

description: incubation with TCL1 sEV

tag: strain

value: Foxp3 YFP/cre


title: patient #16005 day8 replicate1


title: patient #16005 day0 replicate3


title: patient #16005 day0 replicate2


title: patient #16005 day0 replicate1


title: IMM-aug20_M17_P20_30hpi


title: IMM-aug20_M16_P19_mock

value: injected with mosquito salivary gland debris


title: IMM-aug20_M17_P22_30hpi


title: IMM-aug20_M17_P21_30hpi


title: patient #26004 day0 replicate3


title: patient #14008 day8 replicate2


title: IMM-aug20_M16_P18_mock


title: patient #14008 day0 replicate3


title: IMM-aug20_M16_P17_mock


title: patient #14008 day0 replicate2


title: IMM-aug20_M16_P16_mock


title: IMM-aug20_M15_P15_2hpi


title: CRC_HC94T

description: Large intestine

source_name: Colorectal cancer stem cell spheroids

value: CRC patient-derived spheroids

value: Untreated

value: Colorectal cancer


title: IMM-aug20_M15_P14_2hpi


title: IMM-aug20_M15_P13_2hpi


title: IMM-aug20_M15_P12_2hpi


title: patient #14007 day8 replicate3


title: patient #14007 day0 replicate2


title: patient #14007 day8 replicate1


title: patient #14008 day8 replicate3


title: patient #14008 day8 replicate1


title: patient #14001 day8 replicate2


title: IMM-aug20_M13_P5_36hpi


title: patient #14007 day0 replicate1


title: patient #14001 day0 replicate2


title: patient #14007 day0 replicate3


title: patient #14001 day0 replicate1


title: patient #14007 day8 replicate2


title: patient #14001 day8 replicate1


title: patient #11011 day8 replicate3


title: IMM-aug20_M15_P11_2hpi


title: patient #11011 day0 replicate3


title: IMM-feb20_M10_P33_24hpi


title: IMM-feb20_M10_P34_24hpi


title: IMM-feb20_M10_P35_24hpi


title: IMM-feb20_M10_P32_24hpi


title: IMM-aug20_M14_P7_2hpi


title: IMM-aug20_M13_P4_36hpi


title: patient #11011 day0 replicate2


title: IMM-feb20_M10_P30_24hpi


title: patient #04012 day8 replicate3


title: IMM-feb20_M10_P31_24hpi


title: patient #11011 day0 replicate1


title: IMM-aug20_M13_P1_36hpi


title: IMM-feb20_M10_P29_24hpi


title: IMM-aug20_M13_P2_36hpi


title: IMM-feb20_M9_P28_2hpi


title: IMM-aug20_M13_P3_36hpi


title: patient #11011 day8 replicate1


title: patient #04012 day0 replicate3


title: IMM-feb20_M9_P27_2hpi


title: patient #04012 day8 replicate2


title: patient #11011 day8 replicate2


title: patient #04012 day0 replicate2


title: IMM-feb20_M9_P26_2hpi


title: patient #03005 day8 replicate2


title: IMM-feb20_M10_P36_24hpi


title: patient #04012 day0 replicate1


title: IMM-feb20_M9_P22_2hpi


title: IMM-feb20_M9_P25_2hpi


title: patient #03005 day0 replicate3


title: IMM-feb20_M9_P23_2hpi


title: IMM-feb20_M9_P24_2hpi


title: IMM-feb20_M8_P21_36hpi


title: patient #03005 day0 replicate2


title: patient #04012 day8 replicate1


title: IMM-feb20_M8_P20_36hpi


title: patient #03005 day0 replicate1


title: patient #01999 day8 replicate3


title: IMM-feb20_M8_P17_36hpi


title: IMM-feb20_M8_P18_36hpi


title: patient #01999 day0 replicate3


title: patient #01999 day8 replicate2


title: patient #01999 day8 replicate1


title: IMM-feb20_M8_P16_36hpi


title: IMM-feb20_M7_P9_NI

value: untreated


title: IMM-feb20_M8_P15_36hpi


title: patient #01999 day0 replicate1


title: patient #01999 day0 replicate2


title: patient #03005 day8 replicate1


title: patient #01888 day8 replicate3


title: IMM-feb20_M7_P13_NI


title: patient #01888 day8 replicate1


title: IMM-feb20_M7_P12_NI


title: IMM-feb20_M6_P8_12hpi


title: IMM-feb20_M7_P10_NI


title: IMM-feb20_M7_P11_NI


title: patient #01888 day0 replicate2


title: IMM-feb20_M6_P7_12hpi


title: IMM-feb20_M8_P19_36hpi


title: IMM-feb20_M6_P6_12hpi


title: patient #01888 day0 replicate1


title: patient #01777 day8 replicate3


title: IMM-feb20_M6_P5_12hpi


title: patient #01777 day8 replicate1


title: patient #01777 day8 replicate2


title: patient #01777 day0 replicate3


title: patient #01888 day8 replicate2


title: IMM-feb20_M6_P2_12hpi


title: IMM-feb20_M6_P1_12hpi


title: IMM-feb20_M6_P3_12hpi


title: patient #01777 day0 replicate1


title: IMM-nov18_M3_P5_13hpi


title: IMM-nov18_M4_P3_2hpi


title: patient #01888 day0 replicate3


title: patient #01039 day8 replicate2


title: patient #01039 day8 replicate3


title: patient #01039 day0 replicate3


title: IMM-nov18_M3_P4_13hpi


title: patient #01039 day8 replicate1


title: patient #01039 day0 replicate1


title: patient #01039 day0 replicate2


title: IMM-nov18_M1_P5_22hpi


title: patient #01038 day8 replicate3


title: IMM-feb20_M6_P4_12hpi


title: patient #01038 day8 replicate2


title: patient #01777 day0 replicate2


title: IMM-nov18_M1_P1_22hpi


title: patient #01038 day8 replicate1


title: patient #01038 day0 replicate2


title: IMM-nov18_M4_P4_2hpi


title: patient #01033 day8 replicate2


title: patient #01033 day8 replicate3


title: patient #01038 day0 replicate3


title: patient #01033 day8 replicate1


title: patient #01033 day0 replicate2


title: patient #01033 day0 replicate3


title: patient #01033 day0 replicate1


title: patient #01032 day8 replicate1


title: patient #01032 day8 replicate2


title: patient #01032 day8 replicate3


title: IMM-nov18_M2_P1_26hpi


title: IMM-nov18_M3_P3_13hpi


title: patient #01032 day0 replicate3


title: patient #01032 day0 replicate2


title: patient #01038 day0 replicate1


title: patient #01032 day0 replicate1


title: patient #01030 day8 replicate3


title: COM-24h-rep1

city: Wuhan

first: xueao

last: zheng

state: Not US or Canada

address: Shizishan

country: China

institute: Huazhong agricultural university

data_processing:
Raw reads were processed and aligned to the Arabidopsis genome (https://www.arabidopsis.org) using STAR (v.2.6.1a).
Genes with over 10 reads were filtered and processed using DESeq2 (R package, v.1.22.2) to identify the differentially expressed genes (p-value < 0.05, |Log2FoldChange| > Log21.5).
Assembly: tair10
Supplementary files format and content: RNA_normalized_counts_total.CSV: Comma-separated text file includes RPKM values for each Sample.

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: The plants were grown under long-day conditions at 22°C (16 h of light/8 h of dark; supplied by white-light tubes).

extract_protocol:
Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Aidlab Biotechnologie, Beijing, China).
Library preparation and RNA-sequencing were performed by Novogene (Beijing, China).

treatment_protocol: Pathogen infection: The third and fourth leaves of the three-week-old Arabidopsis were infiltrated with Psm ES4326 (OD600 = 0.0002) using a needleless syringe. Bacterial growth was tested 3 days after infection.

value: leaf

value: 21 days

value: pathogen infection

tag: genotype

value: complementation line


title: COM-24h-rep2

tag: age


title: cgb-24h-rep1

tag: tissue

value: cgb mutant


title: cgb-24h-rep3


title: cgb-24h-rep2


title: B cells, Day 7, 2

city: Shanghai

first: Minxiang

last: Xie

address: Dongan Road 130

institute: Fudan University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2).
The clean reads were mapped to the reference genome using HISAT2.
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference.
Expression level of gene was calculated by RSEM (v1.2.12).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary cell

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
Purified mRNA was used for the construction of sequencing libraries according to the manufacture's instructions.

value: primary cell

tag: cell type

value: B cells

value: WT

value: DSS induction

tag: time

value: Day 7


title: B cells, Day 10, 2

value: Day 10


title: B cells, Day 7, 3


title: B cells, Day 10, 3


title: B cells, Day 10, 1


title: patient #01030 day8 replicate2

value: peripheral blood

value: AML

value: blasts


title: B cells, Day 7, 1


title: B cells, Day 4, 3

value: Day 4


title: patient #01030 day8 replicate1


title: COM-24h-rep3


title: B cells, Day 4, 2


title: B cells, Day 4, 1


title: COM-0h-rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end strand-specific RNA-sequencing data were aligned to the Arabidopsis genome using STAR (v.2.6.1a)
Genes over 10 read counts were filtered and processed using DESeq2 (R package, v.1.22.2) for differential expression analysis.
Genome_build: Araport11
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

growth_protocol: For growth of the plants, seedlings were transferred to soil and grown in growth chambers with a 16-h-light/ 8-h-dark cycle.

extract_protocol:
The third and fourth leaves of three weeks plants (n = 8) were sampled for RNA-sequencing. The total RNA was extracted with Trizol reagent according to the manufacturer’s instructions (Aidlab Biotechnologie, Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: COM-0h-rep2


title: patient #01030 day0 replicate3


title: B cells, Day 0, 3

value: Day 0


title: B cells, Day 0, 2


title: patient #01030 day0 replicate2


title: COM-0h-rep1


title: B cells, Day 0, 1


title: MDA-MB-231 siSTAT3+HMGN5 Rep3

city: Haining

first: Chaochen

last: Wang

address: 718 East Haizhou Rd

department: ZJU-UoE Institute

institute: Zhejiang University

data_processing:
RNA-Seq reads were aligned to the GRCh38 human reference transcriptome using salmon (v1.4.0) for count matrix generation
Genome_build: hg38
Supplementary_files_format_and_content: raw counts
Basecalls performed using the CASAVA software  ChIP-seq reads were aligned to the hg38 genome assembly using the Bowtie2 program (Langmead et al., Nature method, 2012)
The HOMER ((http://homer.salk.  edu/homer/) software was used to convert alignment map files into bedGraph files with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: BedGraph files can be used to check ChIP-seq peaks through the UCSC genome browser.

growth_protocol: Cells are maintained in L15 medium (Invitrogen, USA) supplemented with 10% fetal bovine serum (Gibco) at 37 °C in air

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen).
For RNA-Seq, libraries were prepared for sequencing using standard Illumina protocols. For Cut&Tag, 50,000 cells were harvested and the CUT&Tag assay was performed using a commercial kit (Vazyme, China, TD901-TD902) according to the manufacturer’s protocol.

treatment_protocol: 30nM synthesized siRNAs were transfected with Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer’s instructions.

value: STAT3 siRNA + HMGN5


title: cgb-0h-rep3

value: leaf


title: patient #01030 day0 replicate1


title: MDA-MB-231 siSTAT3+HMGN5 Rep2


title: MDA-MB-231 siSTAT3+Vector Rep3

value: STAT3 siRNA + control Vector


title: MDA-MB-231 siSTAT3+HMGN5 Rep1


title: patient #01016 day8 replicate3


title: cgb-0h-rep2

value: 21 days


title: MDA-MB-231 siSTAT3+Vector Rep2


title: MDA-MB-231 Ctrl+Vector Rep2

value: control siRNA + control Vector


title: MDA-MB-231 siSTAT3+Vector Rep1


title: patient #01016 day8 replicate2


title: MDA-MB-231 Ctrl+Vector Rep3


title: MDA-MB-231 Ctrl+Vector Rep1


title: cgb-0h-rep1

value: cgb mutant


title: MDA-MB-231 siSTAT3 Rep1

value: STAT3 siRNA


title: MDA-MB-231 siHMGN5 Rep2

value: HMGN5 siRNA


title: MDA-MB-231 siSTAT3 Rep2


title: patient #01016 day8 replicate1


title: patient #01016 day0 replicate3


title: patient #01016 day0 replicate2


title: patient #01016 day0 replicate1


title: MDA-MB-231 siHMGN5 Rep1


title: MDA-MB-231 Ctrl Rep3

value: control siRNA


title: MDA-MB-231 Ctrl Rep2


title: MDA-MB-231 Ctrl Rep4


title: patient #01015 day8 replicate3


title: MDA-MB-231 Ctrl Rep1


title: patient #01015 day8 replicate2


title: Covid55L18AUG2020_ROI_024_well_H07

city: Seattle

first: Tyler

last: Hether

state: WA

address: 530 Fairview Ave N

department: Translational Sciences

institute: NanoString Technologies, Inc.

description: Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation

data_processing:
library strategy: GeoMx Seq
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27"
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1"
Genome_build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx COVID19 Immune Response Atlas v1 Platform files (GeoMx_Hs_CTAv1.1.pkc and GeoMx_COVID19_v1.0.pkc)
Supplementary_files_format_and_content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: Values represented in the collapsed target counts tab (in GeoMx_processed_data.xlsx) are the geometric mean of the probes for a given, removing any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments.

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: FFPE Rapid Autopsy Tissue

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

tag: virus

value: yes

value: 1. Covid55L

tag: roi number

tag: segment type

value: Geometric Segment

value: Alveolar

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: notes

value: Aveolar Zone/Endothelial cells


title: Covid55L18AUG2020_ROI_023_well_H06

tag: patient id


title: INFG_ID_379

hyb_protocol: 1.5 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Raw data were normalized using the R package ‘limma’ using the function backgroundCorrect with parameters: method=normexp, offset=50.

source_name: peripheral blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Whole blood RNA was extracted from PAX gene tubes as described in the manufacturer’s protocol (QIAGEN PreAnalytiX).

treatment_protocol: A 2.5 ml peripheral blood sample (into PAXgene tubes) was obtained from each study participant. Routine investigations were performed, as determined by the admitting physician. Airway samples were tested for bacterial pathogens and common respiratory viruses.

tag: tissue

value: whole blood

tag: Sex

value: m

tag: age

tag: disease state

value: viral


title: INFG_ID_380

value: missing


title: patient #01015 day0 replicate3

value: peripheral blood

value: AML

tag: cell type

value: blasts


title: Covid55L18AUG2020_ROI_022_well_H05

tag: virus

tag: roi number

tag: segment type


title: INFG_ID_376

value: f


title: INFG_ID_375


title: INFG_ID_378


title: patient #01015 day0 replicate2


title: Covid55L18AUG2020_ROI_021_well_H04

tag: condition

tag: roi x coordinate

tag: roi y coordinate


title: Covid55L18AUG2020_ROI_018_well_H01

tag: rawreads

tag: trimmedreads

tag: stitchedreads

value: Aveolar Zone with Type 2 Hyperplasia


title: Covid55L18AUG2020_ROI_017_well_G12

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Covid55L18AUG2020_ROI_016_well_G11

tag: patient id

tag: tissue

tag: notes


title: patient #01015 day0 replicate1

tag: disease state


title: Covid55L18AUG2020_ROI_019_well_H02


title: Covid55L18AUG2020_ROI_020_well_H03


title: Covid55L18AUG2020_ROI_015_well_G10


title: patient #01007 day8 replicate3

tag: cell type


title: Covid55L18AUG2020_ROI_013_well_G08

tag: virus


title: Covid55L18AUG2020_ROI_014_well_G09

tag: roi number


title: patient #01015 day8 replicate1


title: Covid55L18AUG2020_ROI_012_well_G07

tag: segment type


title: Covid55L18AUG2020_ROI_011_well_G06

tag: condition


title: INFG_ID_374

tag: Sex

tag: age

value: bac


title: patient #01007 day8 replicate2


title: Covid55L18AUG2020_ROI_010_well_G05

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: patient #01007 day8 replicate1


title: INFG_ID_371


title: patient #01007 day0 replicate3


title: Covid55L18AUG2020_ROI_006_well_G01

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

value: Aveolar Zone with hyaline membranes


title: Covid55L18AUG2020_ROI_008_well_G03

tag: patient id

tag: deduplicatedreads

tag: sequencingsaturation


title: Covid55L18AUG2020_ROI_007_well_G02

tag: tissue

tag: notes


title: INFG_ID_370

tag: disease state


title: INFG_ID_365


title: INFG_ID_364


title: INFG_ID_366


title: patient #01007 day0 replicate2

tag: cell type


title: patient #01007 day0 replicate1


title: patient #01006 day8 replicate3


title: Covid55L18AUG2020_ROI_004_well_F11

tag: virus

tag: roi number

tag: segment type


title: INFG_ID_363

tag: Sex

tag: age


title: patient #01006 day8 replicate2


title: INFG_ID_362


title: INFG_ID_361


title: INFG_ID_356


title: Covid86L18AUG2020_ROI_023_well_F06

value: 4. Covid86L

tag: condition

tag: roi x coordinate

tag: roi y coordinate


title: Covid55L18AUG2020_ROI_001_well_F08

value: yes

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: Covid55L18AUG2020_ROI_003_well_F10

tag: patient id

value: 1. Covid55L

tag: alignedreads

tag: deduplicatedreads


title: INFG_ID_360

tag: tissue


title: INFG_ID_359

tag: disease state


title: Covid86L18AUG2020_ROI_024_well_F07

value: Geometric Segment

tag: sequencingsaturation

tag: notes


title: patient #01006 day8 replicate1

tag: cell type


title: Covid86L18AUG2020_ROI_020_well_F03

tag: virus

tag: roi number

tag: segment type

value: Alveolar

value: Aveolar Zone with macrophages


title: Covid86L18AUG2020_ROI_021_well_F04

tag: condition

value: Aveolar Zone/Endothelial cells


title: Covid86L18AUG2020_ROI_022_well_F05

tag: roi x coordinate


title: Covid55L18AUG2020_ROI_005_well_F12

tag: roi y coordinate


title: patient #01006 day0 replicate3


title: Covid55L18AUG2020_ROI_002_well_F09

tag: rawreads


title: Covid86L18AUG2020_ROI_016_well_E11

tag: trimmedreads


title: INFG_ID_353

value: whole blood

tag: Sex

tag: age


title: INFG_ID_355


title: Covid55L18AUG2020_ROI_009_well_G04

tag: patient id

tag: stitchedreads

tag: alignedreads


title: Covid86L18AUG2020_ROI_019_well_F02

tag: tissue

tag: deduplicatedreads


title: Covid86L18AUG2020_ROI_018_well_F01

tag: sequencingsaturation

tag: notes


title: patient #01006 day0 replicate2

tag: disease state

tag: cell type


title: Covid86L18AUG2020_ROI_013_well_E08

tag: virus

tag: roi number

tag: segment type


title: Covid86L18AUG2020_ROI_012_well_E07

tag: condition

tag: roi x coordinate

tag: roi y coordinate


title: patient #01006 day0 replicate1


title: Covid86L18AUG2020_ROI_017_well_E12

tag: rawreads

tag: trimmedreads


title: patient #01004 day8 replicate2

tag: patient id


title: INFG_ID_354

tag: Sex

tag: age


title: INFG_ID_352

tag: tissue


title: Covid86L18AUG2020_ROI_015_well_E10

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: patient #01004 day8 replicate3

tag: disease state


title: INFG_ID_351


title: patient #01004 day8 replicate1

tag: cell type


title: Covid86L18AUG2020_ROI_014_well_E09

tag: virus

tag: sequencingsaturation

tag: notes


title: Covid86L18AUG2020_ROI_011_well_E06

tag: roi number

tag: segment type

tag: condition


title: INFG_ID_350


title: patient #01004 day0 replicate3


title: Covid86L18AUG2020_ROI_008_well_E03

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: Covid86L18AUG2020_ROI_009_well_E04

tag: patient id

tag: trimmedreads


title: Covid86L18AUG2020_ROI_007_well_E02

tag: tissue


title: Covid86L18AUG2020_ROI_006_well_E01

tag: stitchedreads


title: patient #01004 day0 replicate2


title: Covid86L18AUG2020_ROI_005_well_D12

tag: alignedreads


title: INFG_ID_349

tag: Sex

tag: age


title: INFG_ID_348

tag: disease state


title: patient #01004 day0 replicate1

tag: cell type


title: INFG_ID_347


title: Covid86L18AUG2020_ROI_004_well_D11

tag: virus

value: Segment 1

value: Large Airway

tag: deduplicatedreads

tag: sequencingsaturation


title: Covid86L18AUG2020_ROI_003_well_D10

tag: roi number

tag: segment type


title: Covid86L18AUG2020_ROI_002_well_D09

tag: condition

tag: roi x coordinate


title: Covid86L18AUG2020_ROI_010_well_E05

tag: roi y coordinate

tag: rawreads

tag: notes


title: Covid86L18AUG2020_ROI_001_well_D08

tag: patient id

tag: tissue

tag: trimmedreads


title: Covid73L18AUG2020_ROI_018_well_D07

value: 3. Covid73L

tag: stitchedreads

tag: alignedreads


title: INFG_ID_345

tag: Sex

value: missing

tag: age

tag: disease state


title: control-2

city: Sendai

first: Mitsuyo

last: Matsumoto

address: 2-1 Seiryo-machi Aoba-ku

department: Biochemistry

institute: Tohoku university school of medicine

data_processing:
Alignment of reads to reference hg19 were performed using the RNASeqAnalysis plugin from the Ion torrent suite software. Files format of final downloaded data (raw data) from Ion Proton was BAM.
Read counts were performed using Htseq version 0.9.1 htseq-count (samtools view -F4 [raw_file(BAM)] | htseq-count -q -t exon -I gene_id - hg19.gtf).
Assembly: hg19
Supplementary files format and content: text (Matrix data containing raw counts data of all sample)

source_name: AsPC-1 cell line

growth_protocol: AsPC1 was cultured at 37°C in 5% CO2 in RPMI 1640 medium (Sigma Aldrich, MO, USA) with 20% fetal bovine serum (FBS, Sigma Aldrich) and 1% penicillin/streptomycin (P/S, GIBCO, NY, USA).

extract_protocol:
Total RNA was isolated using a RNeasy Plus Mini kit (QIAGEN) following the instruction manual. Ribosomal RNA (rRNA) of five microgram of total RNA was removed using a  RiboMinus Eukaryote System v2 (Thermo Fisher). One hundred ng of rRNA-depleted RNA was incubated at 95 ºC for 10 min for fragmentation and was purified by Magnetic Beads Cleanup Module (Life Technologies).
The libraries were constructed using Ion Total RNA-seq kit for AB Libraly builer system (Thermo Fisher Scientific Inc.) and were barcoded with Ion Xpress RNA-seq BC primer ((Thermo Fisher Scientific Inc., 16 PCR cycles). Barcoded library fragment with the size range of 100-200 bp was selected with Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). Templates were prepared using Ion PI Hi-Q Chef Kit (Thermo Fisher Scientific Inc.) on Ion Chef (Thermo Fisher Scientific Inc.). Sequencing was performed on an Ion Proton system by the P1 chip v3 (Thermo Fisher Scientific Inc.) using Hi-Q Sequensing kit (Thermo Fisher Scientific Inc.).

treatment_protocol: TBK1 specific siRNA (Stealth RNAiTMsiRNA Duplex Oligoribonucleotides, Invitrogen, CA, USA) was transfected using Lipofectamine RNAiMAX (Thermo Fisher Scientific Inc., MA, USA). Stealth RNAi siRNA Negative Control, Low GC (Thermo Fisher Scientific) was used as a control. 24 hours later, the cells were harvested for RNA isolation.

tag: genotype

value: Control

value: Pancreatic ductal adenocarcinoma


title: INFG_ID_344


title: siTBK1-2

value: TBK1 knockdown


title: siTBK1-1


title: INFG_ID_346


title: Covid73L18AUG2020_ROI_014_well_D03

tag: virus

tag: deduplicatedreads

tag: sequencingsaturation

value: Aveolar Zone with Type 2 Hyperplasia


title: INFG_ID_343


title: Covid73L18AUG2020_ROI_012_well_D01

tag: roi number

tag: segment type

tag: condition


title: INFG_ID_342


title: INFG_ID_341


title: Covid73L18AUG2020_ROI_011_well_C12

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: Covid73L18AUG2020_ROI_013_well_D02

tag: patient id

tag: tissue

tag: notes


title: Covid73L18AUG2020_ROI_010_well_C11

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: HTG group R2 [T2]

city: Beijing

first: Aiping

last: Chen

address: No. 11, Bei San Huan Road, Chaoyang District

institute: Beijing University of Chinese Medicine

data_processing:
Raw data (raw reads) were processed using Trimmomatic.
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
DEGs were identified using the DESeq[6] R package functions estimateSizeFactors and nbinomTest.
The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was performed using ASprofile
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Counts values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: blood

extract_protocol:
Total RNA was extracted and purified from the blood of mice in OVA group and 4.2 g/kg/day HTG group using Trizol (Tiangen Biotech, Beijing, China), respectively.
cDNA libraries were constructed from high-quality RNA and qualified with a Bioanalyzer 2100 system (Agilent Technologies, CA, USA). High-quality cDNA libraries were sequenced using a HiSeqTM 2500 sequencer (Illumina, NEB, USA).

value: blood

tag: strain

value: AR mouse model

tag: time

value: day 27

tag: treatment

value: Huanggui Tongqiao Gragunles (HTG) 4.2 g/kg/day


title: HTG group R1 [T1]

value: Huanggui Tongqiao Gragunles (HTG) 2.1 g/kg/day


title: Covid73L18AUG2020_ROI_017_well_D06

tag: virus

value: yes

value: Geometric Segment

value: Alveolar

tag: deduplicatedreads


title: Covid73L18AUG2020_ROI_009_well_C10

tag: roi number

tag: sequencingsaturation


title: Covid73L18AUG2020_ROI_016_well_D05

tag: segment type

tag: condition


title: Covid73L18AUG2020_ROI_006_well_C07

tag: roi x coordinate

tag: roi y coordinate


title: Covid73L18AUG2020_ROI_008_well_C09

tag: patient id

tag: rawreads


title: HTG group R3 [T3]

tag: tissue

value: Huanggui Tongqiao Gragunles (HTG) 8.4 g/kg/day


title: INFG_ID_340

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

institute: University Münster

value: whole blood

tag: Sex

tag: age

tag: disease state


title: Covid73L18AUG2020_ROI_015_well_D04

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: notes


title: Covid73L18AUG2020_ROI_007_well_C08

tag: virus

tag: deduplicatedreads


title: Model group R7 [M7]

tag: strain

tag: time

tag: treatment

value: 0.9%  saline


title: Covid73L18AUG2020_ROI_005_well_C06

value: 3. Covid73L

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: sequencingsaturation


title: INFG_ID_339

tag: tissue

tag: Sex

value: missing


title: INFG_ID_338

tag: age

tag: disease state


title: Covid73L18AUG2020_ROI_004_well_C05

tag: patient id

value: Segment 1

value: Large Airway

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: Model group R2 [M2]

tag: strain


title: Covid73L18AUG2020_ROI_002_well_C03

tag: virus

tag: alignedreads

tag: deduplicatedreads


title: Covid73L18AUG2020_ROI_003_well_C04

tag: roi number

tag: segment type


title: Model group R1 [M1]

tag: time

tag: treatment


title: Covid73L18AUG2020_ROI_001_well_C02

tag: tissue

tag: condition

tag: roi x coordinate

tag: sequencingsaturation


title: INFG_ID_337

tag: Sex

tag: age

tag: disease state


title: INFG_ID_336

value: bac


title: Covid59L18AUG2020_ROI_024_well_C01

tag: patient id

value: 2. Covid59L

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: notes

value: Aveolar Zone/Endothelial cells


title: Covid59L18AUG2020_ROI_023_well_B12

tag: virus

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: Covid59L18AUG2020_ROI_022_well_B11

tag: roi number

tag: segment type


title: Covid59L18AUG2020_ROI_020_well_B09

tag: tissue

tag: condition


title: Covid59L18AUG2020_ROI_019_well_B08

tag: roi x coordinate

tag: sequencingsaturation


title: INFG_ID_334

tag: Sex

tag: age


title: Covid59L18AUG2020_ROI_018_well_B07

tag: patient id

value: Aveolar Zone with Type 2 Hyperplasia


title: INFG_ID_333

tag: disease state


title: Covid59L18AUG2020_ROI_014_well_B03

tag: roi y coordinate

tag: rawreads


title: Covid59L18AUG2020_ROI_017_well_B06

tag: trimmedreads

tag: notes


title: INFG_ID_335


title: Covid59L18AUG2020_ROI_021_well_B10

tag: virus

tag: stitchedreads


title: Covid59L18AUG2020_ROI_016_well_B05

tag: alignedreads

tag: deduplicatedreads


title: Covid59L18AUG2020_ROI_013_well_B02

tag: roi number

tag: segment type


title: Covid59L18AUG2020_ROI_012_well_B01

tag: tissue

tag: condition

value: Aveolar Zone with hyaline membranes


title: Covid59L18AUG2020_ROI_011_well_A12

tag: roi x coordinate

tag: sequencingsaturation


title: Primary cortical cells, Whole Cell Extract, Triptolide-3hrs, Bicuculline-1hr, rep1

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description:
Whole cell extract polyA RNAs
S1_W_Bic

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Count on FAST DB gene annotations (GenoSplice) and normalization using FPKM
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes FPKM normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2018_1 were also provide

source_name: brain

growth_protocol: primary cortical cells were isolated from embryonic stage 16.5 embryos and maintained for 14 days in culture

extract_protocol:
Cells were lysed using Trizol reagent (Sigma, T9424). Total RNAs were isolated and DNase treated on columns (RNeasy micro kit, Qiagen, 74004) following the manufacturer’s instructions.
Library preparation was performed, starting from 200ng total RNAs, using the TruSeq Stranded mRNA Library Kit (Illumina, 20020595) and the TruSeq RNA UD Indexes (Illumina, 20022371).

treatment_protocol: DRB (50uM), Triptolide (1uM), Bicuculline (20uM), BDNF(50ng/mL)

value: brain

tag: cell type

value: Primary cortical cells

tag: genotype

value: wild type

tag: treatment

value: Triptolide-3hrs, Bicuculline-1hr


title: Primary cortical cells, Whole Cell Extract, Triptolide-3hrs, Bicuculline-1hr, rep2

description:
Whole cell extract polyA RNAs
S2_W_Bic


title: Primary cortical cells, Nucleus, Triptolide-3hrs, Bicuculline-1hr, rep3

description:
Nuclear polyA RNAs
S4_N_Bic


title: Primary cortical cells, Cytosol, Triptolide-3hrs, Bicuculline-1hr, rep3

description:
Cyplasmic polyA RNAs
S4_C_Bic


title: Primary cortical cells, Whole Cell Extract, Triptolide-3hrs, Bicuculline-1hr, rep3

description:
Whole cell extract polyA RNAs
S4_W_Bic


title: Primary cortical cells, Nucleus, Triptolide-3hrs, Bicuculline-1hr, rep2

description:
Nuclear polyA RNAs
S2_N_Bic


title: INFG_ID_326

tag: Sex

tag: age

tag: disease state


title: Primary cortical cells, Nucleus, Triptolide-3hrs, Bicuculline-1hr, rep1

description:
Nuclear polyA RNAs
S1_N_Bic


title: INFG_ID_327


title: INFG_ID_332


title: INFG_ID_325


title: Primary cortical cells, Cytosol, Triptolide-3hrs, Bicuculline-1hr, rep1

description:
Cyplasmic polyA RNAs
S1_C_Bic


title: INFG_ID_331


title: Primary cortical cells, Cytosol, Triptolide-3hrs, Bicuculline-1hr, rep2

description:
Cyplasmic polyA RNAs
S2_C_Bic


title: Covid59L18AUG2020_ROI_015_well_B04

value: yes

tag: patient id

value: Geometric Segment

value: Alveolar

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: notes


title: Covid59L18AUG2020_ROI_006_well_A07

tag: virus

tag: roi number

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: Covid59L18AUG2020_ROI_005_well_A06

tag: segment type

tag: tissue

tag: condition

tag: roi x coordinate

tag: sequencingsaturation


title: Primary cortical cells, Whole Cell Extract, Triptolide-3hrs, unstimulated, rep1

description:
Whole cell extract polyA RNAs
S1_W_Ctl

tag: cell type

tag: genotype

tag: treatment

value: Triptolide-3hrs, Unstimulated


title: Covid59L18AUG2020_ROI_009_well_A10

tag: patient id

tag: roi y coordinate


title: NormalARCHOL103_050820_ROI_022_well_H12

value: no

value: 4. NormalARCHOL103

value: Segment 2

value: Normal

tag: rawreads

tag: trimmedreads


title: Covid59L18AUG2020_ROI_008_well_A09

tag: virus

tag: notes


title: Covid59L18AUG2020_ROI_010_well_A11

tag: roi number

tag: stitchedreads


title: Primary cortical cells, Nucleus, Triptolide-3hrs, unstimulated, rep2

description:
Nuclear polyA RNAs
S2_N_Ctl


title: INFG_ID_324

value: whole blood

tag: Sex

value: missing

tag: age

tag: disease state

value: bac


title: NormalARCHOL103_050820_ROI_019_well_H09

tag: segment type

value: Segment 1

tag: tissue

tag: condition

tag: alignedreads

tag: deduplicatedreads


title: Covid59L18AUG2020_ROI_003_well_A04

value: 2. Covid59L

value: Large Airway

tag: roi x coordinate

tag: sequencingsaturation


title: Covid59L18AUG2020_ROI_001_well_A02

tag: patient id

tag: roi y coordinate


title: control-1

tag: genotype

value: Control

value: Pancreatic ductal adenocarcinoma


title: Covid59L18AUG2020_ROI_004_well_A05

tag: virus

tag: rawreads

tag: trimmedreads


title: NormalARCHOL103_050820_ROI_021_well_H11

tag: roi number

tag: stitchedreads


title: INFG_ID_319

tag: Sex

tag: age


title: Primary cortical cells, Nucleus, Triptolide-3hrs, unstimulated, rep3

description:
Nuclear polyA RNAs
S4_N_Ctl

value: brain

tag: cell type

value: Primary cortical cells

value: wild type

tag: treatment


title: NormalARCHOL103_050820_ROI_018_well_H08

tag: segment type

tag: tissue

value: Alveolar

tag: condition


title: NormalARCHOL103_050820_ROI_016_well_H06

tag: roi x coordinate

tag: alignedreads

tag: deduplicatedreads


title: Primary cortical cells, Whole Cell Extract, Triptolide-3hrs, unstimulated, rep3

description:
Whole cell extract polyA RNAs
S4_W_Ctl

value: Triptolide-3hrs, Unstimulated


title: Covid59L18AUG2020_ROI_007_well_A08

value: yes

tag: patient id

value: Geometric Segment

tag: roi y coordinate

tag: sequencingsaturation

tag: notes

value: Aveolar Zone with hyaline membranes


title: NormalARCHOL103_050820_ROI_017_well_H07

tag: virus

value: no

value: 4. NormalARCHOL103

value: Normal

tag: rawreads

tag: trimmedreads


title: Primary cortical cells, Nucleus, Triptolide-3hrs, unstimulated, rep1

description:
Nuclear polyA RNAs
S1_N_Ctl

tag: genotype


title: Covid59L18AUG2020_ROI_002_well_A03

tag: roi number

tag: stitchedreads


title: Primary cortical cells, Whole Cell Extract, Triptolide-3hrs, unstimulated, rep2

description:
Whole cell extract polyA RNAs
S2_W_Ctl

tag: cell type

tag: treatment


title: Primary cortical cells, Cytosol, Triptolide-3hrs, unstimulated, rep3

description:
Cyplasmic polyA RNAs
S4_C_Ctl

tag: tissue


title: NormalARCHOL103_050820_ROI_020_well_H10

tag: segment type

tag: condition


title: INFG_ID_317

value: whole blood

tag: Sex

value: missing

tag: age

tag: disease state


title: INFG_ID_320

value: bac


title: INFG_ID_323


title: INFG_ID_318


title: NormalARCHOL103_050820_ROI_014_well_H04

tag: patient id

value: Segment 2

tag: roi x coordinate

tag: roi y coordinate

tag: alignedreads

tag: deduplicatedreads


title: INFG_ID_321


title: INFG_ID_322


title: NormalARCHOL103_050820_ROI_015_well_H05

tag: virus

value: Segment 1

tag: rawreads

tag: trimmedreads

tag: sequencingsaturation


title: NormalARCHOL103_050820_ROI_013_well_H02

tag: roi number

tag: stitchedreads


title: NormalARCHOL103_050820_ROI_013_well_H03

tag: tissue


title: Primary cortical cells, Cytosol, Triptolide-3hrs, unstimulated, rep1

description:
Cyplasmic polyA RNAs
S1_C_Ctl

tag: cell type

tag: genotype

tag: treatment


title: NormalARCHOL103_050820_ROI_012_well_H01

tag: segment type

tag: condition


title: NormalARCHOL103_050820_ROI_011_well_G12

tag: patient id


title: INFG_ID_316

tag: Sex

tag: age

tag: disease state


title: NormalARCHOL103_050820_ROI_010_well_G11

tag: roi x coordinate

tag: roi y coordinate

tag: alignedreads

tag: deduplicatedreads


title: NormalARCHOL103_050820_ROI_009_well_G10

tag: virus

tag: rawreads

tag: trimmedreads

tag: sequencingsaturation


title: Primary cortical cells, Cytosol, Triptolide-3hrs, unstimulated, rep2

description:
Cyplasmic polyA RNAs
S2_C_Ctl

tag: tissue

tag: cell type


title: Control 3

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

institute: Universitätsklinikum des Saarlandes

data_processing:
Fastq files were imported into Partek Flow (Partek Incorporated, Missouri, USA).
Quality analysis and quality control were performed on all reads to assess read quality and to determine the amount of trimming required (both ends: 13 bases 5´and 1 base 3´).
rRNA and mtRNA were filtered out of trimmed reads using STAR v2.4.1d aligner and were further aligned against the Mmu10 genome using the STAR v2.4.1d aligner. Unaligned reads were further processed using Bowtie 2 v2.2.5 aligner.
Aligned reads were combined before quantifying the expression against the ENSEMBL (release 95) database by the Partek Expectation-Maximization algorithm using the counts per million normalization.
Genes with missing values and with a mean expression less than one were filtered out
Genome_build: mmu10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was isolated using Qiagen kit
500 ng total RNA was processed using the TruSeq RNA Sample Preparation v2 Kit (low-throughput protocol; Illumina, San Diego, USA) to prepare the barcoded libraries.
Libraries were validated and quantified using DNA 1000 and high-sensitivity chips on a Bioanalyzer (Agilent, Böblingen, Germany); 7.5 pM denatured libraries were used as input into cBot (Illumina), followed by deep sequencing using HiSeq 2500 (Illumina) for 101 cycles, with an additional seven cycles for index reading.

tag: baff status

value: control


title: NormalARCHOL103_050820_ROI_006_well_G07

tag: roi number

tag: segment type

value: Vascular

tag: stitchedreads


title: NormalARCHOL103_050820_ROI_007_well_G08

tag: patient id

tag: condition


title: NormalARCHOL103_050820_ROI_005_well_G06


title: NormalARCHOL103_050820_ROI_008_well_G09


title: Control 2


title: NormalARCHOL103_050820_ROI_004_well_G05


title: NormalARCHOL103_050820_ROI_003_well_G04

value: Large Airway


title: Control 1


title: Baff 3

value: over expression


title: INFG_ID_313

tag: Sex

tag: age

tag: disease state


title: NormalARCHOL103_050820_ROI_001_well_G02

value: Segment 3

tag: roi x coordinate

tag: roi y coordinate

tag: alignedreads


title: Baff 1


title: ARDS02_050820_ROI_017_well_F10

tag: virus

value: 3. ARDS02

value: Alveolar

value: Non-viral

tag: rawreads

tag: deduplicatedreads


title: INFG_ID_311

tag: tissue


title: Baff 2


title: INFG_ID_315


title: INFG_ID_310


title: ARDS02_050820_ROI_018_well_F11

tag: trimmedreads

tag: sequencingsaturation


title: INFG_ID_307


title: INFG_ID_308


title: INFG_ID_309


title: INFG_ID_302


title: ARDS02_050820_ROI_013_well_F06

tag: roi number


title: ARDS02_050820_ROI_014_well_F07

tag: segment type


title: ARDS02_050820_ROI_015_well_F08

tag: stitchedreads


title: ARDS02_050820_ROI_013_well_F05

tag: patient id


title: GCN2 KO MEFs_input_Leu

city: Chicago

first: Soroush

last: Tahmasebi

state: IL

address: 909 S Wolcott Ave

department: Department of Pharmacology and Regenerative Medicine

institute: University of Illinois at Chicago

library_source: genomic

data_processing:
Reads were aligned to the mouse genome assembly mm10 using BWA v0.7.12.
Peaks were called using MACS v2.1.0 with default parameters (mfold=[5,50]; FDR cutoff=0.05, --nomodel) using sequenced libraries of either WT or GCN2 KO input DNA as control.
Peak annotations, tag directory, bed files and de novo motif discovery were performed using HOMER v4.7.
Peak list intersections were done using the R package GenomicRanges v1.26.4.
Binding intensity heatmaps and tag density plots were generated using the R package Genomation v1.9.3 with an estimated fragment length of 200.
Genome_build: mm10
Supplementary_files_format_and_content: BedGraphs for input and ChIPs as well as peak text files corrected using input controls

molecule: genomic DNA

source_name: Mouse embryonic fibroblasts (MEFs)

growth_protocol: WT of GCN2 KO MEFs were grown in DMEM +/- Leucine fo 24h.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with an ATF4-specific antibody.
Libraries were prepared at the Genome Quebec Innovation Centre (McGill University) using the TruSeq DNA sample preparation kit according to Illumina's recommendations and sequenced as single 50bp reads on an Illumina HiSeq 2500 sequencer.

tag: strain

tag: cell type

value: Mouse embryonic fibroblasts (MEFs)

tag: genotype

tag: treatment

value: Complete DMEM for 24h

tag: chip antibody


title: GCN2 KO MEFs_ATF4 ChIP-seq_No Leu

value: DMEM without Leucine for 24h

value: ATF4 (sc-200, Santa-Cruz)


title: INFG_ID_301

value: whole blood

tag: Sex

tag: age

tag: disease state


title: INFG_ID_306

value: missing


title: ARDS02_050820_ROI_019_well_F12

tag: virus

value: no

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads


title: ARDS02_050820_ROI_020_well_G01

tag: roi number

tag: segment type

tag: tissue

tag: trimmedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: WT MEFs_input_Leu

tag: strain

tag: cell type

tag: genotype

value: Wild-type

tag: treatment


title: ARDS02_050820_ROI_012_well_F04

tag: patient id

value: Segment 2

tag: stitchedreads


title: INFG_ID_296

tag: Sex

tag: age

tag: disease state

value: bac


title: NormalARCHOL103_050820_ROI_002_well_G03

tag: virus

value: 4. NormalARCHOL103

tag: condition

value: Normal

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: ARDS02_050820_ROI_011_well_F01

tag: roi number

tag: segment type

value: Segment 1

tag: tissue

tag: trimmedreads

tag: alignedreads


title: ARDS02_050820_ROI_010_well_E12

tag: deduplicatedreads

tag: sequencingsaturation


title: WT MEFs_ATF4 ChIP-seq_No Leu

tag: strain

tag: cell type

tag: genotype

tag: treatment

tag: chip antibody


title: ARDS02_050820_ROI_011_well_F02

tag: virus

tag: patient id

tag: stitchedreads


title: GCN2 KO MEFs_ATF4 ChIP-seq_Leu


title: ARDS02_050820_ROI_016_well_F09

tag: condition

tag: roi x coordinate

tag: roi y coordinate


title: WT MEFs_ATF4 ChIP-seq_Leu


title: ARDS02_050820_ROI_009_well_E10

tag: roi number

tag: segment type

tag: rawreads


title: ARDS02_050820_ROI_012_well_F03

tag: tissue

tag: trimmedreads

tag: alignedreads


title: INFG_ID_312

tag: Sex

tag: age

tag: disease state


title: INFG_ID_293


title: ARDS02_050820_ROI_007_well_E08

tag: deduplicatedreads

tag: sequencingsaturation


title: ARDS02_050820_ROI_009_well_E11

tag: virus


title: ARDS02_050820_ROI_003_well_E04

tag: patient id

value: Segment 3

value: Large Airway


title: ARDS02_050820_ROI_006_well_E07

value: 3. ARDS02

value: Vascular

tag: stitchedreads


title: ARDS02_050820_ROI_004_well_E05

tag: condition

value: Non-viral


title: ARDS02_050820_ROI_001_well_E02

tag: roi x coordinate


title: INFG_ID_294


title: ARDS02_050820_ROI_005_well_E06

tag: roi y coordinate


title: Covid21_050820_ROI_020_well_D09

value: yes

value: 2. Covid21

tag: roi number

value: Geometric Segment

value: Alveolar

tag: notes

value: Aveolar Zone with Type 2 Hyperplasia


title: Covid21_050820_ROI_018_well_D07

tag: segment type

tag: rawreads


title: Covid21_050820_ROI_023_well_D12

tag: tissue

tag: trimmedreads


title: INFG_ID_289

value: whole blood

tag: Sex

value: missing


title: Covid21_050820_ROI_024_well_E01

tag: alignedreads


title: ARDS02_050820_ROI_008_well_E09

value: no


title: INFG_ID_291

tag: age

tag: disease state

value: bac


title: INFG_ID_292


title: INFG_ID_290


title: Covid21_050820_ROI_019_well_D08

tag: deduplicatedreads

tag: sequencingsaturation


title: Covid21_050820_ROI_015_well_D04

tag: virus

tag: patient id


title: ARDS02_050820_ROI_002_well_E03

tag: condition

tag: stitchedreads


title: Covid21_050820_ROI_017_well_D06

tag: roi x coordinate

tag: roi y coordinate


title: Covid21_050820_ROI_021_well_D10

tag: roi number

tag: notes


title: Covid21_050820_ROI_016_well_D05

tag: segment type

tag: rawreads


title: Covid21_050820_ROI_022_well_D11

tag: tissue

tag: trimmedreads


title: INFG_ID_285

tag: Sex


title: Covid21_050820_ROI_014_well_D03

tag: alignedreads


title: INFG_ID_295

tag: age

tag: disease state


title: INFG_ID_284

value: viral


title: INFG_ID_283


title: INFG_ID_287


title: INFG_ID_282

value: m


title: INFG_ID_288


title: INFG_ID_281


title: Covid21_050820_ROI_012_well_D01

tag: deduplicatedreads

tag: sequencingsaturation


title: Covid21_050820_ROI_009_well_C10

tag: virus

tag: patient id


title: Covid21_050820_ROI_010_well_C11

tag: condition

tag: stitchedreads


title: Covid21_050820_ROI_007_well_C08

tag: roi x coordinate

tag: roi y coordinate


title: Covid21_050820_ROI_005_well_C06

tag: roi number

value: Segment 1


title: Covid21_050820_ROI_011_well_C12

tag: segment type

tag: notes


title: Covid21_050820_ROI_008_well_C09

tag: tissue

tag: rawreads


title: Covid21_050820_ROI_003_well_C04

tag: trimmedreads


title: Covid21_050820_ROI_004_well_C05

tag: alignedreads


title: Covid17_050820_ROI_024_well_C01

value: 1. Covid17


title: Covid17_050820_ROI_023_well_B12


title: Covid17_050820_ROI_022_well_B11


title: Covid21_050820_ROI_002_well_C03

value: Large Airway


title: Covid21_050820_ROI_001_well_C02


title: Covid21_050820_ROI_006_well_C07


title: Covid17_050820_ROI_021_well_B10


title: Covid17_050820_ROI_020_well_B09


title: Covid21_050820_ROI_013_well_D02


title: Covid17_050820_ROI_019_well_B08


title: Covid17_050820_ROI_017_well_B06


title: INFG_ID_277

tag: Sex

value: f

tag: age


title: Covid17_050820_ROI_018_well_B07

tag: deduplicatedreads


title: Covid17_050820_ROI_016_well_B05

tag: sequencingsaturation


title: INFG_ID_280

tag: disease state


title: INFG_ID_278


title: INFG_ID_275


title: INFG_ID_279


title: Covid17_050820_ROI_015_well_B04

tag: virus

tag: patient id


title: INFG_ID_274


title: INFG_ID_276


title: INFG_ID_273


title: Covid17_050820_ROI_010_well_A11

tag: condition

tag: stitchedreads


title: INFG_ID_271


title: Covid17_050820_ROI_008_well_A09

tag: roi x coordinate

tag: roi y coordinate


title: Covid17_050820_ROI_012_well_B01

tag: roi number

tag: segment type


title: Covid17_050820_ROI_013_well_B02

tag: tissue

tag: notes


title: Covid17_050820_ROI_014_well_B03

tag: rawreads

tag: trimmedreads


title: INFG_ID_272

tag: Sex


title: INFG_ID_268

tag: age


title: Covid17_050820_ROI_005_well_A06

value: Vascular

tag: alignedreads

tag: deduplicatedreads


title: Covid17_050820_ROI_004_well_A05

tag: sequencingsaturation


title: Covid17_050820_ROI_006_well_A07

tag: virus


title: Covid17_050820_ROI_007_well_A08

tag: patient id


title: INFG_ID_269

tag: disease state


title: Covid17_050820_ROI_002_well_A03

tag: condition

tag: stitchedreads


title: INFG_ID_270


title: Covid17_050820_ROI_003_well_A04

tag: roi x coordinate

tag: roi y coordinate


title: INFG_ID_267


title: NormalARCHOL104)_050720_ROI_023_well_H12

value: 4. NormalARCHOL104

tag: roi number

tag: segment type

value: Normal


title: NormalARCHOL104)_050720_ROI_021_well_H10

tag: tissue


title: Covid17_050820_ROI_001_well_A02

value: yes

tag: rawreads


title: NormalARCHOL104)_050720_ROI_022_well_H11

tag: trimmedreads


title: NormalARCHOL104)_050720_ROI_020_well_H09


title: INFG_ID_263

tag: Sex


title: INFG_ID_266

tag: age


title: INFG_ID_265


title: NormalARCHOL104)_050720_ROI_019_well_H08

tag: alignedreads


title: INFG_ID_264


title: NormalARCHOL104)_050720_ROI_017_well_H06

tag: deduplicatedreads


title: INFG_ID_262


title: NormalARCHOL104)_050720_ROI_015_well_H04

tag: sequencingsaturation


title: NormalARCHOL104)_050720_ROI_016_well_H05

tag: virus


title: NormalARCHOL104)_050720_ROI_018_well_H07

tag: patient id


title: NormalARCHOL104)_050720_ROI_014_well_H03


title: NormalARCHOL104)_050720_ROI_012_well_H01


title: NormalARCHOL104)_050720_ROI_013_well_H02


title: INFG_ID_259

tag: disease state


title: INFG_ID_260


title: INFG_ID_261


title: NormalARCHOL104)_050720_ROI_011_well_G12

tag: condition


title: NormalARCHOL104)_050720_ROI_010_well_G11

tag: stitchedreads


title: NormalARCHOL104)_050720_ROI_009_well_G10

tag: roi x coordinate


title: NormalARCHOL104)_050720_ROI_008_well_G09

tag: roi y coordinate


title: NormalARCHOL104)_050720_ROI_007_well_G08

tag: roi number


title: INFG_ID_258


title: NormalARCHOL104)_050720_ROI_005_well_G06

tag: segment type


title: NormalARCHOL104)_050720_ROI_006_well_G07

tag: tissue


title: INFG_ID_257


title: NormalARCHOL104)_050720_ROI_004_well_G05

tag: rawreads


title: NormalARCHOL104)_050720_ROI_001_well_G02

tag: trimmedreads


title: NormalARCHOL104)_050720_ROI_002_well_G03


title: NormalARCHOL104)_050720_ROI_003_well_G04


title: INFG_ID_256

tag: Sex


title: ARDS03_050720_ROI_020_well_G01

value: 3. ARDS03

value: Non-viral


title: ARDS03_050720_ROI_018_well_F11

value: Alveolar


title: ARDS03_050720_ROI_019_well_F12


title: INFG_ID_254

value: whole blood

tag: age


title: ARDS03_050720_ROI_017_well_F10

tag: alignedreads


title: ARDS03_050720_ROI_015_well_F08

tag: deduplicatedreads


title: ARDS03_050720_ROI_012_well_F05

tag: sequencingsaturation


title: ARDS03_050720_ROI_011_well_F04

tag: virus


title: ARDS03_050720_ROI_014_well_F07

tag: patient id


title: NAc, Caudate, and Putamen [1180P]

city: Pittsburgh

first: WEI

last: ZONG

state: PA

address: 130 De Soto St

institute: UNIVERSITY OF PITTSBURGH

data_processing:
Quality control using FastQC
Trim data using Trimmomatic
Alignment with HISAT2
Read counts using HTSeq
Assembly: Ensembl GRh38
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

source_name: Putamen

extract_protocol:
Total RNA was extracted from the tissue samples using a combination of Trizol (Invitrogen, Carlsbad, CA) and RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany).
Libraries were prepped for RNA-sequencing using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, CA). 75bp paired-end dual-indexed sequencing was performed using the NextSeq 500 platform (Illumina, San Diego, CA).

tag: gender

value: Female

value: Putamen

tag: race

value: White

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Suicide


title: ARDS03_050720_ROI_013_well_F06

value: no

tag: roi number

tag: segment type

tag: tissue

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: NAc, Caudate, and Putamen [931P]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

value: Accidental


title: NAc, Caudate, and Putamen [933P]

value: Male

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

value: Natural


title: ARDS03_050720_ROI_009_well_F02

tag: virus

tag: patient id

tag: roi number

tag: segment type

value: Segment 1

tag: tissue

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: ARDS03_050720_ROI_010_well_F03

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: NAc, Caudate, and Putamen [930P]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: tissuestoragetime

tag: manner of death


title: ARDS03_050720_ROI_016_well_F09

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: tissue

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: NAc, Caudate, and Putamen [878P]

tag: age

tag: gender

tag: bmi

tag: ph


title: ARDS03_050720_ROI_008_well_F01

value: Segment 2

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: ARDS03_050720_ROI_006_well_E09

tag: virus

tag: patient id


title: ARDS03_050720_ROI_008_well_E12

tag: roi number

tag: segment type


title: ARDS03_050720_ROI_007_well_E10

tag: tissue

tag: alignedreads


title: ARDS03_050720_ROI_007_well_E11

tag: deduplicatedreads

tag: sequencingsaturation


title: INFG_ID_253

tag: Sex

value: f

tag: age

tag: disease state

value: viral


title: INFG_ID_248


title: INFG_ID_255


title: INFG_ID_252


title: INFG_ID_249


title: INFG_ID_251

value: m


title: INFG_ID_164


title: INFG_ID_167


title: INFG_ID_160


title: NAc, Caudate, and Putamen [843P]

tag: gender

tag: race

tag: pmi

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: NAc, Caudate, and Putamen [822P]

tag: tissue

value: Black

value: match control


title: ARDS03_050720_ROI_006_well_E08

tag: virus

tag: patient id

value: 3. ARDS03

tag: roi number

tag: segment type

value: Alveolar

tag: condition

value: Non-viral

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: INFG_ID_159

value: whole blood

tag: Sex

tag: age

tag: disease state


title: INFG_ID_250


title: ARDS03_050720_ROI_004_well_E05

value: Vascular

tag: deduplicatedreads

tag: sequencingsaturation


title: ARDS03_050720_ROI_005_well_E06

tag: tissue


title: ARDS03_050720_ROI_005_well_E07

tag: virus


title: ARDS03_050720_ROI_003_well_E04

tag: patient id


title: NAc, Caudate, and Putamen [787P]

tag: gender

value: Putamen

tag: race

tag: pmi

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Suicide


title: INFG_ID_156

tag: Sex

tag: age


title: INFG_ID_154

tag: disease state


title: ARDS03_050720_ROI_002_well_E03

value: no

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Flu02_050720_ROI_020_well_E01

tag: virus

value: yes

tag: patient id

tag: tissue

value: Flu


title: Flu02_050720_ROI_019_well_D12

value: Segment 1


title: NAc, Caudate, and Putamen [739P]

tag: gender

value: Male

tag: race

value: White

tag: pmi

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Natural


title: NAc, Caudate, and Putamen [722P]

tag: age

tag: disease state


title: NAc, Caudate, and Putamen [700P]


title: Flu02_050720_ROI_018_well_D11

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: Flu02_050720_ROI_016_well_D09

tag: virus

tag: patient id

tag: tissue

tag: sequencingsaturation


title: Flu02_050720_ROI_015_well_D08


title: Flu02_050720_ROI_017_well_D10


title: NAc, Caudate, and Putamen [697P]

tag: gender

tag: race

tag: pmi

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: INFG_ID_148

tag: Sex

value: f

tag: age

tag: disease state


title: Flu02_050720_ROI_014_well_D07

tag: virus

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: INFG_ID_149

tag: tissue

value: m


title: NAc, Caudate, and Putamen [694P]

tag: gender

tag: race

tag: pmi

value: match control

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime


title: Flu02_050720_ROI_013_well_D05

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: sequencingsaturation


title: Flu02_050720_ROI_012_well_D04

tag: tissue

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: NAc, Caudate, and Putamen [656P]

tag: age

tag: gender

value: Female

tag: race

value: Black

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: manner of death


title: Flu02_050720_ROI_013_well_D06

tag: virus

tag: patient id

tag: roi number

tag: segment type

value: Segment 2

tag: tissue

value: Alveolar

tag: condition

tag: roi x coordinate

tag: sequencingsaturation


title: Flu02_050720_ROI_011_well_D03

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: INFG_ID_145

value: whole blood

tag: Sex

tag: age

tag: disease state


title: ARDS03_050720_ROI_001_well_E02

tag: virus

value: 3. ARDS03

value: Large Airway

value: Non-viral


title: INFG_ID_140


title: Flu02_050720_ROI_011_well_D02

value: yes

tag: patient id


title: INFG_ID_151


title: NAc, Caudate, and Putamen [604P]

tag: gender

value: Putamen

tag: race

tag: pmi

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: INFG_ID_143

tag: tissue


title: INFG_ID_138


title: Flu02_050720_ROI_010_well_D01

tag: roi number

tag: segment type

tag: condition

value: Flu

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Flu02_050720_ROI_010_well_C12

tag: virus

tag: patient id

value: Segment 1


title: INFG_ID_121

tag: Sex

tag: age

tag: disease state

value: viral


title: NAc, Caudate, and Putamen [625P]

tag: gender

value: Male

tag: tissue

tag: race

tag: pmi

tag: sequence id

value: HGCTCBGXF

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Natural


title: NAc, Caudate, and Putamen [587P]


title: Flu02_050720_ROI_007_well_C09

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Flu02_050720_ROI_008_well_C10

tag: virus

tag: patient id

tag: tissue


title: Flu02_050720_ROI_007_well_C08


title: NAc, Caudate, and Putamen [1834P]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

value: match control

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

value: Undetermined


title: INFG_ID_115

tag: Sex

value: f


title: INFG_ID_117


title: NAc, Caudate, and Putamen [1807P]

value: Black

tag: tissuestoragetime

tag: manner of death

value: Suicide


title: Flu02_050720_ROI_006_well_C07

tag: roi number

tag: segment type

value: Vascular

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Flu02_050720_ROI_004_well_C05

tag: virus

tag: patient id

tag: tissue


title: NAc, Caudate, and Putamen [1789P]

tag: age

tag: gender

value: Female

tag: race

value: White

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph


title: INFG_ID_114

value: whole blood

tag: Sex


title: Flu02_050720_ROI_002_well_C03

value: yes

tag: roi number

tag: segment type

value: Large Airway

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: NAc, Caudate, and Putamen [1687P]

tag: age

tag: gender

tag: tissue

value: Putamen

tag: race

tag: pmi

tag: tissuestoragetime

tag: manner of death


title: Flu02_050720_ROI_009_well_C11

tag: virus

tag: patient id

value: Segment 1

value: Alveolar

value: Flu

tag: deduplicatedreads

tag: sequencingsaturation