description: Library name: p22252-s030_RGu18-ROt18-LM98_D8_BAL_CITE

library_source: other

data_processing:
The cellranger v6.1.0 (10X Genomics) pipeline was used for processing the 10X sequencing data and the downstream analysis was performed using the Seurat v4.0.4 R package. A composite reference comprising of Mmul10 from Ensembl release 100 and SARS-CoV2 (strain MT246667.1 - NCBI) was used for alignment with cellranger. The percentage of SARS-CoV-2 reads was determined using the PercentageFeatureSet for SARS-CoV2 genes. For BAL samples, a total of 107,830 cells across all animals passed quality control (QC) and were used for analyses. For lung samples, a total of 101,766 cells passed upstream QC and were used for analysis. For single-cell RNA-Seq, approximately 20,000 cells were loaded onto the 10X Genomics Chromium Controller in the BSL3 facility using the Chromium NextGEM Single Cell 5’ Library & Gel Bead kit according to manufacturer instructions
Gene expression and HTO counts are combined in the cellranger output files.
Assembly: Mmul10, Ensembl annotatation version 100
Assembly: MT246667.1
Supplementary files format and content: cellranger output files: mRNA_and_HTO_barcodes.tsv.gz, mRNA_and_HTO_features.tsv.gz, mRNA_and_HTO_matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

value: HTO

tag: hto

value: Hash4Human_C0254_TotalSeqC (RGu18), Hash5Human_C0255_TotalSeqC (ROt18), Hash6Human_C0256_TotalSeqC (LM98)


status: Public on Dec 31 2024

type: SRA

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

description: Library name: p22252-s029_RJn18-RAu18-RIr18_D7_BAL_CITE

organism: Macaca mulatta

source_name: BAL

extract_protocol:
To collect non necropsy BAL, a 14Fr, sterile, single-use pediatric suction catheter (Covidien #37424) was inserted into the trachea and directed into a mainstem bronchi. The catheter was advanced until it was secured into a distal subsegmental bronchus. 35-70 mL of physiological saline was instilled into the bronchus and then manually aspirated back into a syringe to obtain a minimum of 20 mL of lavage fluid and placed into a 50mL conical. If less than 20mL was recovered, an additional 10-15mL was administered again and a second attempt was taken and placed into a second 50mL conical. BAL was then filtered through a 70uM strainer (Falcon #352350). 1mL of BAL fluid and cells were taken to perform viral load testing by adding RNazol and Acetic Acid into a 5mL microcentrifuge tube. After vigorous vortexing, samples were frozen for later RNA extraction using the RNAzol BD kit. After viral loads were taken, BAL was spun at 300 x g for 10 minutes to pellet the cells. BAL supernatant was collected for MSD and plaque assay. BAL cells were then lysed with the ACK lysis buffer for 10 minutes at 37˚C and the reaction was quenched using DPBS. Cells were then spun and counted in the same manner as PBMCs. At least 100,000 cells were set aside for 10x sequence and the remaining cells were divided between the isotype control and stained panel. At necropsy, an additional 100mL of Post Mortem BAL fluid was taken by placing a large sterile irrigation syringe with the plunger removed into the lungs. Approximately 150 mL of sterile 1 x PBS is poured into the lungs via the syringe to infuse both sides. The syringe is then removed and plunger replaced. The syringe goes back into the trachea opening and the lavage fluid is pulled back and dispensed into 50mL conicals. Post mortem BAL sample is processed the same way as non-necropsy through a 70uM filter and lysing. After samples for viral load, supernatant and 10x were taken for pre-mortem samples, the cells for pre and post mortem were combined together for staining. At necropsy, at least 5 million cells were stained for both the isotype and staining panel with any remaining frozen down using the same freezing media as PBMCs. Caudal lung is processed by following the steps indicated in Voix et al 2023 with the following changes. During the 1 hour 37˚C incubation, samples were placed on a 50mL tube rotator at 10 rpm (Thermo Scientific # 888810001). Samples were run at least 6 times on the pre-loaded M_Lung_02_01 to ensure proper blending of the tissue. After, the tissue is strained over 100uM filters (Falcon # 352360) and the digestion reaction is quenched with R10. Cells are then centrifuged at 1100 x g for 10 minutes. The supernatant is removed and cells are washed again with R10 and centrifuged at 1100 x g for 10 minutes. The cells are lysed using 10mL of ACK lysis and incubated at 37˚C for 10 minutes. Lysing was then quenched using DPBS and cells were spun down at 1100 x g for 10 minutes. Cells were then counted using the same manner as PBMCs and aliquoted for 10x sequencing, bulk RNA sequencing and freezing. Cells were used for 10x sequencing and the extra were saved in the same manner as PBMCs.  Spleen was processed in a similar manner to the lung but without the digestion step. Spleen was dissected using blunt scissors and added to C tubes with 5mL of R10. Using the same M_Lung 02_01 protocol run at least 6 times, spleen was blended then passed through a 100uM filter. Due to the nature of the sample, it is then passed through a 70uM filter and then 40uM filter (Falcon #352340) to remove the debris. Cells were then washed using R10 and then spun at 750 x g for 10 minutes to pellet. Supernatant was removed and the cells were washed with DPBS then centrifuged at 750 x g for 10 minutes. Cells were lysed with 20mL of ACK for 10 minutes. The lysing reaction was quenched with DPBS and cells were pelleted following the same speed and time. Cells were counted and frozen for later use.
Single cell suspensions were prepared and loaded onto the 10X Genomics Chromium Controller in the BSL3 facility using the Chromium NextGEM Single Cell 5’ Library & Gel Bead kit to capture individual cells and barcoded gel beads within droplets (113). The libraries were prepared according to manufacturer instructions, including the preparation of feature barcode libraries for hashtag detection. They were then sequenced on an Illumina NovaSeq 6000 with a paired-end 26x91 configuration targeting a depth of 50,000 reads per cell. Cell Ranger software was used to perform demultiplexing of cellular transcript data, as well as mapping and annotation of UMIs and transcripts for downstream data analysis.

tag: tissue

value: BAL

tag: subject

value: multiplexed

tag: dpi

tag: library type

value: Hash1Human_C0251_TotalSeqC (RJn18), Hash2Human_C0252_TotalSeqC (RAu18), Hash3Human_C0253_TotalSeqC (RIr18)


title: SW620-sh60_1

type: RNA

city: Madrid

first: Javier

last: Robles

state: Madrid

address: Calle Ramiro de Maetzu 9

department: Biomedicine

country: Spain

institute: Biological Research Centre Margarita Salas

hyb_protocol: “Clariom™ S Array, human” (Applied Biosystems).

scan_protocol: “GeneChip® Scanner 3000 7G” (Applied Biosystems).

data_processing: Data analysis was performed with Transcriptome Analysis Console (TAC) Software.

label: Biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Samples were terminal labeled with “GeneChip® WT PLUS Reagent Kit” (Applied Biosystems).

growth_protocol: Cells were grown in DMEM containing 10% FBS (Invitrogen) and antibiotics at 37 °C in a 5% CO2 humidified atmosphere.

extract_protocol: Total RNA was isolated using NucleoSpin RNA kit (Macherey-Nagel). Quality assessment of the RNA was assessed with an Agilent 2100 bio-analyzer.

treatment_protocol: Cell lines were silenced by using TRCN00000555660 shRNA from Open Biosystems.

tag: condition

value: Colorectal cancer


description: Library name: p22252-s028_RGu18-ROt18-LM98_D2_BAL_CITE


title: SW620-sh60_2


description: Library name: p22252-s029_RJn18-RAu18-RIr18_D7_BAL_GEX

library_source: transcriptomic single cell

data_processing:
The cellranger v6.1.0 (10X Genomics) pipeline was used for processing the 10X sequencing data and the downstream analysis was performed using the Seurat v4.0.4 R package. A composite reference comprising of Mmul10 from Ensembl release 100 and SARS-CoV2 (strain MT246667.1 - NCBI) was used for alignment with cellranger. The percentage of SARS-CoV-2 reads was determined using the PercentageFeatureSet for SARS-CoV2 genes. For BAL samples, a total of 107,830 cells across all animals passed quality control (QC) and were used for analyses. For lung samples, a total of 101,766 cells passed upstream QC and were used for analysis. For single-cell RNA-Seq, approximately 20,000 cells were loaded onto the 10X Genomics Chromium Controller in the BSL3 facility using the Chromium NextGEM Single Cell 5’ Library & Gel Bead kit according to manufacturer instructions
Gene expression and HTO counts are combined in the cellranger output files.
Assembly: Mmul10, Ensembl annotatation version 100
Assembly: MT246667.1
Supplementary files format and content: cellranger output files: mRNA_and_HTO_barcodes.tsv.gz, mRNA_and_HTO_features.tsv.gz, mRNA_and_HTO_matrix.mtx.gz

molecule: polyA RNA

value: mRNA


title: batch-1_0052-P

city: Cape Town

first: Valentin

last: Voillet

state: Western Cape

address: First Floor Wembley Square, 3 McKenzie St, Gardens

country: South Africa

institute: cape town hvtn immunology laboratory

library_source: transcriptomic

data_processing:
The `RNASeqPipelineR` was used to perform alignment, quantification and annotation of the RNA sequencing data (RNA-seq) from the whole and mini population RNA-Seq libraries. The RNA-seq data were aligned against the human genome (hg38) using STAR (v2.4.2a), and gene expression quantification was performed using RSEM (v1.2.22).
Reads from a same sample but different batches were aggregated.
Assembly: hg38
Supplementary files format and content: wraw_counts.csv

source_name: PBMC

extract_protocol:
RNA from blood samples was extracted using Paxgene RNA extraction kit and from the BAL samples we used Qiagen RNAEasy micro kit method
Libraries were prepared from RNA samples of both sample types using NEBNext kits

value: PBMC

tag: patient id

tag: disease status

value: LTBI and HIV-positive


title: batch-1_0046-B


title: SW620

city: Guangzhou

first: Yuyi

last: Huang

address: Changgang Street

country: China

institute: The Second Affiliated Hospital of Guangzhou Medical University

description:
The sequencing strategy is PE150
620m

data_processing:
Raw fastq were quality control use fastp.
Expression of genes and transcripts were quantified using Salmon and Tximport.
DESeq2 used to perform differential expression genes analysis.
Gene set enrichment analysis were performed by clusterProfiler.
Assembly: GRCh38
Supplementary files format and content: Read counts of genes for all RNA-Seq samples in csv format.
Supplementary files format and content: TPM of genes for all RNA-Seq samples in csv format.

source_name: SW620 cells

growth_protocol: All cell lines were maintained in L15 supplemented with 1×107 U/L penicillin, 10 mg/L streptomycin, and 10 % fetal bovine serum

extract_protocol:
Whole RNA was extracted by Trizol
Construction of transposase RNA library for Illumina high-throughput sequencing platform

tag: cell line

value: SW620 cells

tag: cell type

value: Colorectal cancer cells

tag: genotype

value: wild type


title: SW480 sh RNA 1

description:
The sequencing strategy is PE150
1m

source_name: SW480 sh RNA 1 cells

value: SW480 sh RNA 1 cells

value: Knock down


title: p22252-s028_RGu18-ROt18-LM98_D2_BAL_GEX

description: Library name: p22252-s028_RGu18-ROt18-LM98_D2_BAL_GEX


title: batch-1_0041-P


title: SW620-sh60_3


description: Library name: p22252-s027_RJn18-RAu18-RIr18_D2_BAL_CITE


description: Library name: p22252-s027_RJn18-RAu18-RIr18_D2_BAL_GEX


title: batch-1_0041-B


title: Patient 5 PDX 4

city: Grand Rapids

first: Ian

last: Beddows

state: MI

address: 333 Bostwick

institute: Van Andel Institute

data_processing:
Trim reads with trim_galore v0.6.0
Reads were mapped to GRCh38 with GENCODE release 33 with STAR v2.7.8a basic two-pass mode.
The raw counts were extracted from the reverse strand alignments.
Assembly: hg38
Supplementary files format and content: raw counts

source_name: patient-derived xenograft

growth_protocol: CA-MSC are isolated from patient tumors using platic adherence, exanded then sorted based on expression of CD73, CD90, and CD105.  Isolated CA-MSC are cultured in MEBM media. Immortalized human dermal microvascular endothelial cell line (iHDMEC) TIME (ATCC® CRL-4025™), and immortalized human umbilical vein endothelial cell line (iHUVEC) HUVEC/TERT 2 (ATCC® CRL-4053) were cultured following the manufacturer's instructions.

extract_protocol:
Total RNA was isolated from patient or PDX tumor tissues using RNeasy-mini or RNeasy-Plus-Micro kits (Qiagen). cDNA was synthesized using SuperScript™ III First-Strand Synthesis System (ThermoFisher Scientific, Cat#: 18080051).
After RNA quality control, mRNA was enriched, double-stranded cDNA was synthesized, ends were repaired, poly-A & adaptors were added, fragments were selected, and PCR was performed. cDNA libraries were prepared.  Library construction was performed by NOVOGENE

value: patient-derived xenograft

tag: tumor type

value: High-grade serous ovarian cancer

tag: mouse background

value: BLTS

value: CAMSC

tag: endothelial cells

value: yes

tag: mousesex

value: male

value: Solid

tag: group

value: HuPDX

tag: passage

tag: patient

value: E


title: 99_D0

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

institute: Hospital del Mar Research Institute

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 0

hyb_protocol: Sample was hybridized to Affymetrix Clariom S Mouse array using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

source_name: Total RNA from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 0

label_protocol: 100ng of total RNA from each sample was processed and labelled according to manual GeneChip WT PLUS Reagent kit (P/N 703174 Rev. 2, Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: Total RNA was extracted following Qiagen protocol

tag: disease state

tag: time

tag: tissue

value: peripheral blood


title: 99_D7

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 7

source_name: Total RNA from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 7


title: batch-1_0038-P

value: PBMC

value: LTBI and HIV-negative


description: Library name: p22252-s026_Repeat-run_ROk18-LL60-RHv18_D8_BAL_CITE

value: BAL

tag: subject

value: multiplexed

tag: dpi

tag: library type

value: HTO

tag: hto

value: Hash4Human_C0254_TotalSeqC (ROk18), Hash5Human_C0255_TotalSeqC (LL60), Hash6Human_C0256_TotalSeqC (RHv18)


description: Library name: p22252-s026_Repeat-run_ROk18-LL60-RHv18_D8_BAL_GEX

value: mRNA


title: 91_D7


title: Patient 5 PDX 2

value: patient-derived xenograft

value: NSG

value: no

value: female

value: StndPDX


title: Patient 5 PDX 1

value: High-grade serous ovarian cancer


title: p22252-s024_RFu18_D7_Lung_GEX

description: Library name: p22252-s024_RFu18_D7_Lung_GEX

source_name: Lung

value: Lung


title: batch-1_0036-B

tag: patient id

tag: disease status


title: 90_D0


title: 91_D0


title: Primary Pt. 5 tumor

source_name: primary tumor

value: primary tumor

value: Solid

value: Primary


title: batch-1_0024-P

value: PBMC


description: Library name: p22252-s023_RFu18-RYu18-RZn18_D7_BAL_GEX


title: Primary Pt. 4 tumor

value: D


title: 9_D0

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 0

source_name: Total RNA from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 0

value: peripheral blood


title: SW620-sh60_4

tag: condition

value: Colorectal cancer


title: 89_D7

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 7

source_name: Total RNA from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 7


title: p22252-s021_LL60-RHv18_D2_BAL_CITE

description: Library name: p22252-s021_LL60-RHv18_D2_BAL_CITE

value: BAL

value: multiplexed

value: HTO

value: Hash5Human_C0255_TotalSeqC (LL60), Hash6Human_C0256_TotalSeqC (RHv18)


title: batch-1_0038-B

value: LTBI and HIV-negative


title: Patient 5 PDX 3

value: patient-derived xenograft

tag: tumor type

value: BLTS

value: CAMSC

value: yes

value: male

value: HuPDX

value: E


title: 89_D0


title: Patient 4 PDX 5

value: High-grade serous ovarian cancer

tag: mouse background

value: Hu-NSG

value: female

value: Solid


title: p22252-s021_LL60-RHv18_D2_BAL_GEX

description: Library name: p22252-s021_LL60-RHv18_D2_BAL_GEX

value: mRNA


title: batch-1_0021-P

value: PBMC


title: SW480

description:
The sequencing strategy is PE150
2m

source_name: SW480 cells

tag: cell line

value: SW480 cells

tag: cell type

value: Colorectal cancer cells

tag: genotype

value: wild type


title: batch-1_0036-P

value: LTBI and HIV-negative


title: 85_D7

value: peripheral blood


title: Patient 4 PDX 4

value: patient-derived xenograft

tag: endothelial cells

tag: mousesex

tag: group

tag: passage

value: D


title: p22252-s020_RFu18-RYu18_D2_BAL_CITE

description: Library name: p22252-s020_RFu18-RYu18_D2_BAL_CITE

tag: tissue

value: BAL

value: multiplexed

value: HTO

value: Hash1Human_C0251_TotalSeqC (RFu18), Hash2Human_C0252_TotalSeqC (RYu18)


title: batch-1_0013-P


description: Library name: p22252-s023_RFu18-RYu18-RZn18_D7_BAL_CITE

tag: subject

value: Hash1Human_C0251_TotalSeqC (RFu18), Hash2Human_C0252_TotalSeqC (RYu18), Hash3Human_C0253_TotalSeqC (RZn18)


title: Patient 4 PDX 3

value: High-grade serous ovarian cancer

value: Hu-NSG

value: CAMSC

value: no

tag: patient


title: Patient 4 PDX 2

value: female

value: Solid


title: p22252-s020_RFu18-RYu18_D2_BAL_GEX

description: Library name: p22252-s020_RFu18-RYu18_D2_BAL_GEX

tag: dpi

tag: library type

value: mRNA


title: 85_D0

tag: disease state

tag: time


title: batch-1_0013-B

tag: patient id

tag: disease status


title: 80_D0


title: batch-1_0024-B


title: Patient 4 PDX 1

tag: tumor type

tag: mouse background

value: NSG

value: StndPDX


description: Library name: p22252-s018_Repeat-run_RIn18_D8_Lung_GEX

value: Lung


title: batch-1_0008-P

value: PBMC

value: LTBI and HIV-negative


title: Patient 3 PDX 5

value: patient-derived xenograft

value: yes

value: Ascites

value: HuPDX

value: C


title: batch-1_0003-P


description: Library name: p22252-s017_Repeat-run_RIn18-RBt18-RUv18_D8_BAL_CITE

value: BAL

value: multiplexed

value: HTO

tag: hto

value: Hash4Human_C0254_TotalSeqC (RIn18), Hash5Human_C0255_TotalSeqC (RBt18), Hash6Human_C0256_TotalSeqC (RUv18)


title: batch-1_0003-B


description: Library name: p22252-s017_Repeat-run_RIn18-RBt18-RUv18_D8_BAL_GEX


title: Patient 3 PDX 4

value: High-grade serous ovarian cancer

value: Hu-NSG

value: CAMSC

value: female


title: Patient 3 PDX 3

value: no


title: 71_D0

value: peripheral blood


title: 70_D0


title: 70_D7


title: Control [RNF_S7]

city: Belém

first: Antonio

middle: Carlos Rosário

last: Vallinoto

state: PA

address: Rua Augusto Correa, 01 - Guamá

department: Instituto de Ciencias Biologicas

country: Brazil

institute: Universidade Federal do Pará (UFPA)

data_processing:
FASTQC was used for quality analysis
Bowtie2 was used for the alignment of the reads using the "GCF_000001405.39_GRCh38.p13_genomic" as reference for the human genome
FeatureCounts was used for counting the reads that aligned on each gene using the .GTF file correspnding to the reference used. The seq_id used was the "gene_id" and bases with PHRED quality equal or above 20 were counted
EdgeR was used for DEanalysis considering biological replicates and normalization of the counts by TMM.
Assembly: GCF_000001405.39_GRCh38.p13_genomic
Supplementary files format and content: Tab separeted files with gene counts normalized by TMM

source_name: Blood

extract_protocol:
PBMC samples were previously stored with trizol for RNA conservation. Extraction was performed with the subsequent addition of chloroform (100%), isopropanol (100%) and ethanol (75%), respectively, following incubation and phase separation processes in each sub-process. Finally, the extracted RNA was hydrated with RNAse-free water. A qualitative analysis of the RNA was performed per kit (Agilent RNA 6000 Pico Kit), following the manufacturer's recommendations, samples with integrity (RIN) below 7 were disregarded for sequencing. The RNA was converted into cDNA by kit (High capacity cDNA reverse transcription - Appliedbiosystems) in a cycle at 25ºC/10min, 2x (37ºC/60 min), 85ºC/5 min.
The RNA library was assembled following the recommendations established in the SureSelect Strand-Specific RNA Library Prep System kit protocol (Aligent, Saint Clara, California, USA)

value: Blood

tag: subject status

value: Control

tag: cell type

value: PBMC


description: Library name: p22252-s013_RNw18-MB11_RJr18_D7_BAL_CITE

value: Hash1Human_C0251_TotalSeqC (RNw18), Hash2Human_C0252_TotalSeqC (MB11), Hash3Human_C0253_TotalSeqC (RJr18)


title: Patient 3 PDX 2

value: patient-derived xenograft

tag: endothelial cells

tag: mousesex

value: Ascites


title: p22252-s013_RNw18-MB11_RJr18_D7_BAL_GEX

description: Library name: p22252-s013_RNw18-MB11_RJr18_D7_BAL_GEX

value: mRNA


title: Control [RJSA_S3]


description: Library name: p22252-s019_Repeat-run_RUv18_D8_Lung_GEX

value: Lung


title: 71_D7


title: Patient 3 PDX 1

value: NSG

tag: group

value: StndPDX

tag: passage

value: C


title: Control [MITO_S5]

tag: tissue


title: Primary Pt. 3 ascites

value: primary tumor

value: High-grade serous ovarian cancer

value: Primary

tag: patient


title: p22252-s012_RNw18_D7_Lung_GEX

description: Library name: p22252-s012_RNw18_D7_Lung_GEX

tag: subject

tag: dpi


title: Asymptomatic [RCC_S4]

value: Asymptomatic


title: 7_D0

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 0

tag: disease state


title: Patient 2 PDX 8

value: BLT

value: CAMSC

value: yes

value: female

value: HuPDX

value: B


title: Asymptomatic [MMPS_S1]

value: Blood

value: PBMC


title: Patient 2 PDX 7

value: patient-derived xenograft

value: Ascites


title: p22252-s011_RNw18-MB11_RJr18_D2_BAL_GEX

description: Library name: p22252-s011_RNw18-MB11_RJr18_D2_BAL_GEX

value: BAL

value: multiplexed

tag: library type

value: mRNA


description: Library name: p22252-s011_RNw18-MB11_RJr18_D2_BAL_CITE

value: HTO

value: Hash4Human_C0254_TotalSeqC (RNw18), Hash5Human_C0255_TotalSeqC (MB11), Hash6Human_C0256_TotalSeqC (RJr18)


title: Asymptomatic [LMC_S10]


title: 7_D7

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 7

tag: time

value: peripheral blood


description: Library name: p22252-s010_RIn18-RBt18-RUv18_D2_BAL_CITE

value: Hash1Human_C0251_TotalSeqC (RIn18), Hash2Human_C0252_TotalSeqC (RBt18), Hash3Human_C0253_TotalSeqC (RUv18)


title: Ham/TSP [NMGRS_S9]

value: Ham/TSP


description: Library name: p22252-s010_RIn18-RBt18-RUv18_D2_BAL_GEX


title: Patient 2 PDX 6

value: High-grade serous ovarian cancer

value: NSG

value: CAMSC

value: male


title: 68_D7

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 7


title: 69_D0


title: 69_D7


title: 67_D0


title: Patient 2 PDX 5

value: BLT

value: no

value: female

value: B


title: p22252-s009_RPb19_D8_Lung_GEX

description: Library name: p22252-s009_RPb19_D8_Lung_GEX

value: Lung


title: Ham/TSP [LSL_S2]

value: Blood

value: PBMC


title: p22252-s008_LM65_D8_Lung_GEX

description: Library name: p22252-s008_LM65_D8_Lung_GEX

value: mRNA


title: Patient 2 PDX 4

value: patient-derived xenograft

value: Ascites


title: Patient 2 PDX 3


title: Ham/TSP [ICD_S8]


description: Library name: p22252-s007_LM65-RIl18-RPb19_D8_BAL_CITE

value: BAL

value: multiplexed

value: HTO

value: Hash4Human_C0254_TotalSeqC (LM65), Hash5Human_C0255_TotalSeqC (RIl18), Hash6Human_C0256_TotalSeqC (RPb19)


title: 68_D0

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 0

value: peripheral blood


title: Patient 2 PDX 2

value: High-grade serous ovarian cancer

value: NSG

value: CAMSC


title: SC13_Input

city: Boston

first: Matthew

last: Ramsey

state: MA

address: 77 Ave Louis Pasteur, HIM 668

department: Dermatology

institute: Brigham and Women's Hospital

description: cell line

library_source: genomic

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq500) were mapped to the genome using the BWA algorithm with default settings. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome were used in the subsequent analysis
5´-ends of the aligned reads (= “tags”) were extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp, depending on the average fragment length in the size selected library.  To identify the density of fragments (extended tags) along the genome, the genome was divided into 32-nt bins and the number of fragments in each bin was determined.
Bound regions were identified using the MACS peak finding algorithm with our default cutoff of p-value = 1e-7
For Tag normalization, the tag number of all samples was reduced (by random sampling) to the number of tags present in the smallest sample.
Overlapping intervals were grouped into “Merged Regions”, which are defined by the start coordinate of the most upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping Intervals). In locations where only one sample has an Interval, this Interval defines the Merged Region.
Assembly: hg38
Supplementary files format and content: bigWig files contain the histogram of fragment densities and genomic regions with local enrichments in tag numbers as determined by MACS

molecule: genomic DNA

source_name: Epidermal Squamous Cell Carcinoma cell line

growth_protocol: All cell lines were grown in k-sfm media + BPE + 0.25ng/ml EGF

extract_protocol:
Genomic DNA from cell lines was purified, sonicated, and then ligated to Illumina barcode adaptors.  Ligated DNA was denatured and incubated with primary antibody overnight at 4oC, and then immunoprecipitated DNA was purified
Immunoprecipitated DNA was sequenced using standard Illumina protocols. Libraries were sequenced on the Illumina NextSeq 500 following the manufacturer's protocols.

treatment_protocol: untreated

tag: antibody

value: input

tag: cell line


title: p22252-s007_LM65-RIl18-RPb19_D8_BAL_GEX

description: Library name: p22252-s007_LM65-RIl18-RPb19_D8_BAL_GEX


title: Patient 2 PDX 1

tag: tumor type

tag: mouse background

value: no

value: female

value: StndPDX


title: Ham/TSP [SNR_S6]

value: Blood

tag: subject status

value: Ham/TSP


title: p22252-s006_RWo17_D7_Lung_GEX

description: Library name: p22252-s006_RWo17_D7_Lung_GEX

value: Lung

value: mRNA


title: SC13_JUNB

description: cell line

value: JUNB antibody:Cell Signaling, 3753

value: Epidermal Squamous Cell Carcinoma cell line


title: 66_D0


title: 63_D7


title: 6_D7


title: 58_D7


title: p22252-s005_RWj18_D7_Lung_GEX

description: Library name: p22252-s005_RWj18_D7_Lung_GEX


title: Primary Pt. 2 ascites

value: primary tumor

value: Ascites

value: Primary

value: B


title: Patient 1 PDX 9

value: patient-derived xenograft

value: High-grade serous ovarian cancer

value: BLT

value: yes

value: Solid

value: HuPDX

value: A


title: 63_D0

value: peripheral blood


title: p22252-s004_RVo18_D7_Lung_GEX

description: Library name: p22252-s004_RVo18_D7_Lung_GEX


title: SC13_FRA1

description: cell line

value: FRA1 antibody:Santa Cruz, sc-605


title: 58_D0


description: Library name: p22252-s003_RWo17-RVo18-RWj18_D7_BAL_CITE

value: BAL

value: multiplexed

value: HTO

tag: hto

value: Hash1Human_C0251_TotalSeqC (RWo17), Hash2Human_C0252_TotalSeqC (RVo18), Hash3Human_C0253_TotalSeqC (RWj18)


title: Patient 1 PDX 7

value: CAMSC

tag: endothelial cells

value: no

value: female


title: SC13_BNC1

description: cell line

value: BNC1 antibody:BW175

value: Epidermal Squamous Cell Carcinoma cell line


title: Patient 1 PDX 8

value: patient-derived xenograft

value: High-grade serous ovarian cancer

value: NSG

tag: mousesex

value: male


description: Library name: p22252-s003_RWo17-RVo18-RWj18_D7_BAL_GEX

value: mRNA


title: G5EpTERT_Input

description: cell line

source_name: Immortalized Epidermal keratinocyte cell line

value: input


title: Patient 1 PDX 6

value: Solid

value: A


title: G5EpTERT_IRF6

description: cell line

value: IRF6 antibody:Novus, NBP1-51911

value: Immortalized Epidermal keratinocyte cell line


title: 57_D7

value: peripheral blood


title: 57_D0

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 0


description: Library name: p22252-s002_LM65-RIl18-RPb19_D2_BAL_CITE

value: BAL

value: multiplexed

value: HTO

value: Hash4Human_C0254_TotalSeqC (LM65), Hash5Human_C0255_TotalSeqC (RIl18), Hash6Human_C0256_TotalSeqC (RPb19)


title: 56_D7


title: 6_D0


title: SC13_IRF6

description: cell line


title: G5EpTERT_BNC1

description: cell line

value: BNC1 antibody:BW175


title: p22252-s002_LM65-RIl18-RPb19_D2_BAL_GEX

description: Library name: p22252-s002_LM65-RIl18-RPb19_D2_BAL_GEX


title: Patient 1 PDX 3

value: CAMSC

value: no

value: female


title: Combination Treated DoHH2 Tumor (biol rep 7)

city: Charlotte

first: Steven

middle: I.

last: Park

state: NC

address: 1021 Morehead Medical Drive

department: Department of Hematologic Oncology and Blood Disorders

institute: Levine Cancer Institute

description:
DoHH2_matrix.txt
The column name of the matrix table is "M23-COM"

data_processing:
Transferred from Illumina BaseSpace Hub to SevenBridges platform for sequence alignment with human (GRh38) and murine (mm10) reference genome using STAR aligner
Paired-end reads exclusively fitting human and mouse reference were processed by removing the common reads mapped to both genomes. Only the reads uniquely mapped to human genome were further used for qunatification.
Significantly expressed genes were clustered across treatment groups in unsupervised manner and further used in Ingenuity pathway analysis (IPA)
Assembly: GRh38 from GENECODE Release 33 (GRCh38.p13) (human) and mm10 GENECODE Release M24 (GRCm38.p6) (murine)
Supplementary files format and content: Gene expression is quanified by StringTie2
Supplementary files format and content: Tab-delimited text files include count values for each Sample

source_name: B cell lymphoma

extract_protocol:
RNA was harvested using miRNeasy Mini Kit (Qiagen) per manufacturer's instructions.
Next generation sequencing libraries were prepared using an Illumina TruSeq Stranded Total RNA kits (Illumina) as directed. The libraries were sequenced on an Illumina NextSeq 500 using High Output Kits v2.5 (150 cycles).

value: B cell lymphoma

tag: cell type

value: B cell

tag: genotype

value: WT

tag: treatment

value: Combination MLN8237 and Venetoclax, 40mg/kg and 50mg/kg respectively


title: Combination Treated DoHH2 Tumor (biol rep 6)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M20-COM"

tag: tissue


title: Patient 1 PDX 2

value: patient-derived xenograft

value: High-grade serous ovarian cancer

value: NSG

value: Solid

tag: group

value: StndPDX

tag: passage

tag: patient


title: Combination Treated DoHH2 Tumor (biol rep 5)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M16-COM"


title: N5,scRNA-seq

city: Kunming

first: Jian

last: Liu

address: Zhiyuan Road,Chenggong

institute: Institute of Primate Translational Medicine, KUST

description: 10x Genomics

data_processing:
Sequencing data were first processed using the 10X Genomics Cell Ranger pipeline(v5.0.1) and sequence was aligned using STAR against the Macaca mulatta reference genome(Ensemble release-102).
Subsequently, unique molecular identifiers (UMI) matrices from each sample were merged in R and imported to Seurat(v3.2).
Assembly: Mmul_10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: vaginal wall

extract_protocol:
The concentration of single cell suspension was counted using Countess (Thermo) and adjusted to 1000 cells/μl.
Cells were loaded according to standard protocol of the Chromium single cell 3’ kit in order to capture between 5000 cells/chip position. The library was constructed with Chromium Single Cell 3' V2 Reagent Kits

value: vaginal wall

tag: age

value: Control


title: Patient 1 PDX 1

value: A


title: Combination Treated DoHH2 Tumor (biol rep 4)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M12-COM"


description: Library name: p22252-s001_RWo17-RVo18-RWj18_D2_BAL_GEX

source_name: BAL

value: BAL

tag: subject

value: multiplexed

tag: dpi

tag: library type

value: mRNA


title: Primary Pt. 1 tumor

value: primary tumor

tag: tumor type

value: no

value: Primary


title: N4,scRNA-seq

description: 10x Genomics


title: Combination Treated DoHH2 Tumor (biol rep 3)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M08-COM"

value: B cell lymphoma

tag: cell line

value: B cell


title: 56_D0

tag: disease state

tag: time

value: peripheral blood


title: N3,scRNA-seq

description: 10x Genomics


title: Combination Treated DoHH2 Tumor (biol rep 2)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M04-COM"

value: WT

value: Combination MLN8237 and Venetoclax, 40mg/kg and 50mg/kg respectively


title: Patient 1 PDX 5

value: patient-derived xenograft

value: High-grade serous ovarian cancer

tag: mouse background

value: NSG

value: CAMSC

tag: endothelial cells

value: female


title: N2,scRNA-seq

description: 10x Genomics

value: vaginal wall

tag: cell type

value: Control


title: 47_D7

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 7


title: 46_D7


title: Survivor post AMI, S55

city: Harbin

first: Maomao

last: Zhang

state: Heilongjiang Province

address: Baojian Road Sub district, Nangang District

institute: The Second Affiliated Hospital of Harbin Medical University

data_processing:
Quality control and mapping using Trimmomatic
Gene-level quantification, analysis of differentially expressed genes (DEGs), cluster analysis, GO and KEGG enrichment using cufflinks,htseq-count,the DESeq (2012) R package,etc.
Transcript-level quantification, analysis of differentially expressed transcript (DEGs),cluster analysis, GO and KEGG enrichment using bowtie2 and eXpress.
Gene structure extension and novel transcripts identification using StringTie and cuffcompare software.
Alternatively splicing analysis and SNP-INDEL calling using ASprofile.
Assembly: human genome (GRCh38)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: blood plasma

extract_protocol:
Total RNA from peripheral blood mononuclear cells (PBMCs) was isolated using TRIzol reagent and the libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions and sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China). 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.

tag: individual

value: Survivor post AMI

value: blood

tag: Sex

value: male

value: PBMC

tag: genotype

value: Outcome of AMI within one year


title: 5_D0

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 0

tag: tissue


title: SCD post AMI, D55

tag: group

value: SCD post AMI


title: Combination Treated DoHH2 Tumor (biol rep 1)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M02-COM"

value: B cell lymphoma

value: B cell

tag: treatment


title: N1,scRNA-seq

description: 10x Genomics

tag: age


description: Library name: p22252-s001_RWo17-RVo18-RWj18_D2_BAL_CITE

value: BAL

tag: subject

value: multiplexed

value: HTO

tag: hto

value: Hash1Human_C0251_TotalSeqC (RWo17), Hash2Human_C0252_TotalSeqC (RVo18), Hash3Human_C0253_TotalSeqC (RWj18)


title: 46_D0

value: peripheral blood


title: 47_D0


title: 41_D7

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 7


title: Survivor post AMI, S54

value: WT


title: 42_D0


title: Venetoclax (50 mg/kg) Treated DoHH2 Tumor (biol rep 6)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M28-VEN"

value: Venetoclax (50mg/kg)


title: E4,scRNA-seq

description: 10x Genomics

value: vaginal wall

value: POP


title: SCD post AMI, D54


title: 5_D7


title: E3,scRNA-seq

description: 10x Genomics


title: Venetoclax (50 mg/kg) Treated DoHH2 Tumor (biol rep 5)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M21-VEN"


title: Survivor post AMI, S53

value: Survivor post AMI


title: Venetoclax (50 mg/kg) Treated DoHH2 Tumor (biol rep 4)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M11-VEN"


title: E2,scRNA-seq

description: 10x Genomics


title: SCD post AMI, D53

value: blood


title: Venetoclax (50 mg/kg) Treated DoHH2 Tumor (biol rep 3)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M09-VEN"


title: E1,scRNA-seq

description: 10x Genomics


title: Venetoclax (50 mg/kg) Treated DoHH2 Tumor (biol rep 2)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M06-VEN"


title: Survivor post AMI, S52

value: male


title: 36_D7


title: Patient 1 PDX 4

value: patient-derived xenograft

value: High-grade serous ovarian cancer

value: CAMSC

value: no

tag: mousesex

value: female

value: Solid

tag: passage

tag: patient

value: A


title: SCD post AMI, D52

value: SCD post AMI

value: PBMC

value: Outcome of AMI within one year


title: 34_D7

tag: disease state

value: peripheral blood


title: Venetoclax (50 mg/kg) Treated DoHH2 Tumor (biol rep 1)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M05-VEN"

value: B cell lymphoma

tag: cell line

value: B cell

value: WT

value: Venetoclax (50mg/kg)


title: TNETG3-24

city: Göttingen

first: Hanibal

last: Bohnenberger

address: Robert-Koch-Straße 40

department: Institute of Pathology

country: Germany

institute: University medical center Göttingen

description: The nCounter PanCancer Pathways panel includes 770 genes from 13 canonical pathways and selected reference genes.

hyb_protocol: 5µl of each RNA sample were mixed with 8µl nCounter Reporter probes in hybridization buffer and 2µl nCounter Capture probes and incubated overnight at 65°C . Afterwards purificatin was performed using a two-step magnetic bead-based purification on the nCounter Prep Station (nanoString Technologies).

scan_protocol: The data was collected and quantification was performed on the nCounter Digital Analyzer by counting the individual fluorescent barcodes.

data_processing: Data analysis was performed using the nSolver™ software analysis (freely available from nanoString Technologies). Normalized on housekeeping genes was performed.

label: Nanostring

source_name: thymic neuroendocrine neoplasia

growth_protocol: formalin-fixed and paraffin-embedded (FFPE) tissues

extract_protocol: Qiagen RNeasy FFPE Kit (according to the manufacturer’s protocol)

treatment_protocol: no treatment prior to extraction was performed

tag: histological grading

tag: anatomic origin

value: Thymus


title: TNETG3-23


title: 41_D0

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 0

tag: time


title: MLN8237 (40 mg/kg) Treated DoHH2 Tumor (biol rep 7)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M27-MLN"

tag: cell type


title: Survivor post AMI, S51

tag: individual

value: Survivor post AMI

value: blood

tag: Sex


title: MLN8237 (40 mg/kg) Treated DoHH2 Tumor (biol rep 6)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M19-MLN"

tag: tissue

tag: genotype


title: SCD post AMI, D51

tag: group


title: 34_D0


title: MLN8237 (40 mg/kg) Treated DoHH2 Tumor (biol rep 5)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M18-MLN"

tag: treatment


title: TNETG3-22


title: 30_D7


title: TNETG3-20


title: 30_D0


title: 36_D0


title: SCD post AMI, D50

tag: age

value: male


title: 29_D7


title: TLG19

value: low grade


title: MLN8237 (40 mg/kg) Treated DoHH2 Tumor (biol rep 4)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M17-MLN"


title: Survivor post AMI, S49


title: 29_D0


title: MLN8237 (40 mg/kg) Treated DoHH2 Tumor (biol rep 3)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M14-MLN"


title: SCD post AMI, D49


title: Survivor post AMI, S50


title: TLG17


title: TLG18


title: Survivor post AMI, S48


title: 28_D7

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 7


title: MLN8237 (40 mg/kg) Treated DoHH2 Tumor (biol rep 2)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M10-MLN"


title: SCD post AMI, D48


title: 28_D0

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 0


title: MLN8237 (40 mg/kg) Treated DoHH2 Tumor (biol rep 1)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M07-MLN"


title: Vehicle Treated DoHH2 Tumor (biol rep 7)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M26-CTL"

value: Vehicle


title: TLG15


title: Survivor post AMI, S47


title: Vehicle Treated DoHH2 Tumor (biol rep 6)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M25-CTL"


title: SCD post AMI, D47


title: Vehicle Treated DoHH2 Tumor (biol rep 5)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M24-CTL"


title: TLG13


title: 26_D0


title: 26_D7

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 7


title: Survivor post AMI, S46


title: 25_D7


title: 25_D0


title: Vehicle Treated DoHH2 Tumor (biol rep 4)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M15-CTL"


title: TLG12


title: TLG11


title: Vehicle Treated DoHH2 Tumor (biol rep 3)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M13-CTL"


title: TLG16

description: The nCounter PanCancer Pathways panel includes 770 genes from 13 canonical pathways and selected reference genes.


title: SCD post AMI, D46


title: Vehicle Treated DoHH2 Tumor (biol rep 2)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M03-CTL"


title: Survivor post AMI, S45


title: SCD post AMI, D45


title: 23_D0

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 0


title: TLG10


title: TLG14


title: Vehicle Treated DoHH2 Tumor (biol rep 1)

description:
DoHH2_matrix.txt
The column name of the matrix table is "M01-CTL"


title: TLG09


title: 24_D0


title: TLG06


title: 21_D7


title: 22_D7


title: SCD post AMI, D44


title: Survivor post AMI, S43


title: PHF6 ChIPseq  CCRF-CEM

city: Birmingham

first: Maarten

last: Hoogenkamp

state: West Midlands

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
RNAseq and ChIPseq reads were mapped to the mouse (mm10) or human (hg38) genome using HISAT2.
Transcripts were assembled using Cufflinks 2.0.0 based on the reference genome with quartile normalisation and effective length correction.
A combined gtf file was produced using Cuffmerge 2.1.1 and used for determination of differential gene expression using Cuffdiff 2.0.1.
ChIP-seq peaks were called using MACS2.
Genome_build: Human hg38 (GRCh38), Mouse mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig and tabular files containing FPKM values of all genes and significantly differentially expressed genes between PUER and shPHF6 in pairwise comparisons per day of differentiation.

source_name: T-ALL

extract_protocol:
RNA extraction using columns; AmPure beads for the ChIP-Seq.
According to Illumina Sample Preparation Kit.

value: CCRF-CEM

tag: chip antibody

value: PHF6 (Santa Cruz sc-365237)


title: TLG03


title: TLG05


title: 21_D0


title: PHF6 ChIPseq  ARR

value: ARR


title: Survivor post AMI, S42

value: female


title: 22_D0


title: 18_D7


title: SCD post AMI, D43

value: SCD post AMI

value: PBMC


title: PHF6 ChIPseq  HSB2


title: GATA2 ChIPseq  CCRF-CEM

value: GATA2 (R&D systems AF2046)


title: SCD post AMI, D42

value: Outcome of AMI within one year


title: THG37

value: high grade


title: Survivor post AMI, S44

value: WT


title: GATA2 ChIPseq  HSB2


title: 20_D0

value: peripheral blood


title: THG36

value: Thymus


title: GATA2 ChIPseq  DU.528


title: 18_D0


title: Survivor post AMI, S40

value: Survivor post AMI


title: 16_D0


title: SCD post AMI, D40

value: blood


title: THG26


title: THG25


title: PHF6 ChIPseq  DU.528


title: THG38


title: GATA2 ChIPseq  ARR


title: 17_D0


title: Survivor post AMI, S39


title: LDB1 ChIPseq  CCRF-CEM

value: LDB1 (Abcam ab96799)


title: 15_D7


title: SCD post AMI, D39


title: THG21


title: LLG28

source_name: pulmonary neuroendocrine neoplasia

value: low grade

value: Lung


title: LDB1 ChIPseq  HSB2


title: LLG27


title: Survivor post AMI, S38


title: LDB1 ChIPseq  ARR


title: LDB1 ChIPseq  DU.528


title: 14_D0


title: 14_D7


title: LLG20


title: SCD post AMI, D38


title: Survivor post AMI, S37


title: 1320_D7


title: SCD post AMI, D37


title: TAL1 ChIPseq  CCRF-CEM

value: CCRF-CEM

value: TAL1 (Santa Cruz sc-12984X)


title: TAL1 ChIPseq  HSB2


title: 1320_D0


title: LLG19


title: 15_D0

source_name: Total RNA from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 0


title: LLG18


title: TAL1 ChIPseq  DU.528


title: Survivor post AMI, S36

value: male


title: SCD post AMI, D36


title: LLG17


title: TAL1 ChIPseq  ARR

value: ARR


title: Survivor post AMI, S35

value: female


title: LMO2 ChIPseq  CCRF-CEM

value: LMO2 (R&D systems AF2726)


title: LLG14


title: 1317_D7

source_name: Total RNA from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 7


title: 1317_D0


title: 1307_D0


title: SCD post AMI, D35

value: SCD post AMI

value: PBMC


title: LLG13


title: Survivor post AMI, S34

value: Outcome of AMI within one year


title: LLG16


title: LMO2 ChIPseq  DU.528


title: LMO2 ChIPseq  ARR


title: LLG12


title: LLG15


title: Survivor post AMI, S33

value: WT


title: 1315_D0

value: peripheral blood


title: miR-9/9*-124 2

city: Saint Louis

first: Kitra

last: Cates

state: MO

address: 4523 Clayton Ave, MCD SCI 361

department: Developmental Biology

institute: Washington University in St. Louis

description: Library name: miR-9/9*-124 2 smRNAseq

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custompython demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR.
Data was processed using the CAP-miRseq analysis pipeline (Sun et al. 2014).
Assembly: Ensembl_R76 h_sapien reference build
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: dermal fibroblast

extract_protocol:
Total RNA was extracted using the RNeasy plus micro kit (QIAGEN, USA) as instructed by the manufacturer.
RNA sample integrity was assessed on a 2100 Bioanalyzer (Agilent, USA) before proceeding to library preparation. Small RNAs were prepared for Illumina sequencing using TruSeq Small RNA Library Preparation kit (Illumina, USA). Libraries were sequenced on an HiSeq 2200.

value: dermal fibroblast

value: miR-9/9*-124 expression for 6 days

tag: batch

value: biological replicate 2


title: SCD post AMI, D33

value: blood


title: SCD post AMI, D34


title: 1306_D0


title: LLG11

value: low grade


title: 1315_D7


title: 1306_D7


title: LLG10

value: Lung


title: 1304_D0


title: LMO2 ChIPseq  HSB2


title: LLG09


title: Survivor post AMI, S32

value: Survivor post AMI


title: miR-9/9*-124 1

description: Library name: miR-9/9*-124 1 smRNAseq

value: biological replicate 1


title: 1304_D7


title: miR-NS 3

description: Library name: miR-NS 3 smRNAseq

value: miR-NS expression for 6 days

value: biological replicate 3


title: Survivor post AMI, S31

value: female


title: miR-NS 2

description: Library name: miR-NS 2 smRNAseq


title: LLG07


title: SCD post AMI, D31


title: LLG06


title: miR-NS 1

description: Library name: miR-NS 1 smRNAseq


title: Survivor post AMI, S30


title: mac_control NFS bio rep 4

city: Vienna

first: Georg

last: Stary

address: Spitalgasse 23

country: Austria

institute: Medical University of Vienna

description:
NFS cohort
CL02020_NFS_D3_Macrophages_Control

data_processing:
Single-end reads were trimmed for low quality bases and removal of low-quality reads using ReadTools
Trimmed reads were mapped to the Homo sapiens genome (GRCh38.92 assembly) using STAR (v2.5.3a) mapper
The reads mapped in multiple genomic locations were eliminated by using Samtools (v1.4). PCR duplicates were eliminated from further analysis by using the MarkDuplicates function from the PICARD package
Read counts for features (exons) were generated using the featureCounts function from the Subread package (v 1.22.1)
Assembly: GRCh38.92 assembly
Supplementary files format and content: tab-delimited text files include raw gene count for each sample

source_name: Monocyte-derived macrophage

growth_protocol: 0.4 x 106 CD14+ monocytes per well (Nunclon, 24-well plate) were cultured in VLE RPMI-1640 (Biochrom GmbH) medium supplemented with 10% FCS (Performance Plus, heat inactivated), 1% penicillin-streptomycin (GIBCO), 1% sodium pyruvate (GIBCO) and 1% glutamax (GIBCO)

extract_protocol:
Up to 1.2 x106 CD14+ monocytes or monocyte-derived macrophages from patients and healthy controls were carefully washed, harvested and lysed in 700 ul Qiazol (Qiagen) and stored at -80°C until RNA isolation. CD14+ cells were lysed on the day of sample collection, whereas macrophages were harvested after 3 days of differentiation with GM-CSF. RNA was isolated from the aforementioned samples using the miRNeasy Kit (Qiagen) and concentration and purity assessed using a Nanodrop 2000c Spectrophotometer (Thermo Scientific). RNA quality of the samples was further assessed on the Agilent Bioanalyzer RNA 6000 Nano Electropherogram, and library preparation performed on samples with RIN quality between 8-10.
100ng of total RNA was used for library preparation using the NEBNext Ultra II directional RNA library preparation kit with poly-A tail enrichment.
stranded mRNA 75 bp single read RNA sequencing was performed on the Illumina NextSeq 500 sequencer.

treatment_protocol: CD14-isolated monocytes from 5 chronic sarcoidosis patients and 4 healthy controls were differentiated with 500 IU/mL rhGM-CSF for 3 days.

value: Monocyte-derived macrophage

tag: disease

value: Control

value: GM-CSF dfferentiated macrophages

value: Day 3


title: 1_D0


title: 100_D7


title: 12_D0

source_name: Total RNA from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 0


title: 295

description: Gene expression data from peripheral blood from adult patients with a negative RT-PCR for SARS-CoV-2 and COVID-19

source_name: Total RNA from adult patients with a negative RT-PCR for SARS-CoV-2 and COVID-19


title: SCD post AMI, D30

value: SCD post AMI

value: PBMC

value: WT

value: Outcome of AMI within one year


title: LLG05


title: SCD post AMI, D32

value: male


title: Survivor post AMI, S29

value: blood


title: mac_control NFS bio rep 3

description:
NFS cohort
CL02016_NFS_D3_Macrophages_Control


title: LLG08

value: low grade


title: 244

value: peripheral blood


title: LLG03

value: Lung


title: LLG04


title: mono_control NFS bio rep 3

description:
NFS cohort
CL02015_NFS_D0_Monocytes_Control

source_name: CD14+ Monocyte

value: CD14+ Monocyte

value: Day 0


title: LLG02


title: miR-9/9*-124 3

description: Library name: miR-9/9*-124 3 smRNAseq

value: dermal fibroblast

value: miR-9/9*-124 expression for 6 days

value: biological replicate 3


title: Survivor post AMI, S28

value: Survivor post AMI

value: female


title: mac_control NFS bio rep 2

description:
NFS cohort
CL02014_NFS_D3_Macrophages_Control

value: Monocyte-derived macrophage

value: Control

value: GM-CSF dfferentiated macrophages

value: Day 3


title: mono_control NFS bio rep 4

description:
NFS cohort
CL02019_NFS_D0_Monocytes_Control


title: LLG01


title: Survivor post AMI, S27

value: PBMC

value: WT

value: Outcome of AMI within one year


title: 233


title: LHG30

value: high grade


title: 234

value: peripheral blood


title: mono_control NFS bio rep 2

description:
NFS cohort
CL02013_NFS_D0_Monocytes_Control


title: 271


title: 221


title: mac_control NFS bio rep 1

description:
NFS cohort
CL02012_NFS_D3_Macrophages_Control


title: 223


title: 212


title: SCD post AMI, D29

value: SCD post AMI

value: blood

value: male


title: mono_control NFS bio rep 1

description:
NFS cohort
CL02011_NFS_D0_Monocytes_Control

value: CD14+ Monocyte

value: Day 0


title: SCD post AMI, D27


title: LHG25

value: Lung


title: 216


title: Survivor post AMI, S26

value: Survivor post AMI


title: LHG24


title: SCD post AMI, D28

value: female


title: SCD post AMI, D26


title: 206


title: LHG23


title: 201


title: LHG26


title: LHG22


title: Survivor post AMI, S25


title: mac_disease NFS bio rep 4

description:
NFS cohort
CL02008_NFS_D3_Macrophages_Disease

value: Monocyte-derived macrophage

value: sarcoidosis patient


title: 196

value: Control


title: SCD post AMI, D25


title: mono_disease NFS bio rep 4

description:
NFS cohort
CL02007_NFS_D0_Monocytes_Disease


title: salinity + heat stress + Pseudomonas putida [S+HS+Pp-3]

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

data_processing:
Quality control of reads were performed using FastQC v0.11.7
RNA-seq reads were aligned to Arabidopsis thaliana genome obtained from TAIR using STAR aligner v2.4.0.1
Differential gene expression analysis was performed using DeSeq2 v1.20.0
Assembly: TAIR 10
Supplementary files format and content: tab-deliminated files included mean normalized counts for each sample

organism: Solanum lycopersicum

growth_protocol: Moneymaker tomato seeds used in Pseudomonas putida inoculation experiments were purchased from a commercial nursery (Clemente Viven, Semillas Clemente S.A., Vitoria, Álava, Spain) and were grown up in seedling trays filled with peat moss, perlite, and vermiculite (80:10:10). After germination, seedlings were transplanted to 10-cm diameter pots filled with a mix of sterile autoclaved peat moss and perlite (2:1) and maintained under greenhouse conditions (70% relative humidity, 200 µmol photons m-2· s-1 light intensity, natural photoperiod day/night cycle with temperatures averaging 25.0°C and 18.0°C, respectively). Plants were watered three times a week with half- strength Hoagland solution, and temperature and relative humidity were recorded regularly with a portable USB datalogger (OM-EL-WIN-USB, Omega, NJ, United States).

extract_protocol:
Total RNA was isolated using Plant RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 3-week-old plants were inoculated with Pseudomonas putida KT2240 (OD660 =0.05) through the roots and the rest of the plants were watered with the same amount of M8 buffer 10 days before starting stress treatments. Then, plants were subjected to four different conditions: control (CT), heat stress (37ºC; HS), salinity (150 mM NaCl; S), and the combination of salinity and heat stress (150 mM NaCl + 37ºC; S+HS).  Plants were watered three times a week for 15 days with Hoagland solution or salinity stressor in a half-strength Hoagland solution. For stress combinations that included HS, plants watered in the presence or absence of salinity were subjected to a 3-day treatment of HS (37ºC) in growth chambers. Therefore, eight experimental groups were designed (CT, Pp, HS, HS+Pp, S, S+Pp, HS+S, HS+S+Pp), each stress treatment was imposed on 8 plants and all experiments were repeated at least three times

value: leaf

value: Moneymaker

value: Salinity + heat stress and inoculated with bacteria


title: Survivor post AMI, S24

value: PBMC

value: WT

value: Outcome of AMI within one year


title: LHG21

value: high grade


title: 185

value: peripheral blood


title: mac_disease NFS bio rep 5

description:
NFS cohort
CL02010_NFS_D3_Macrophages_Disease

value: GM-CSF dfferentiated macrophages

value: Day 3


title: mac_disease NFS bio rep 3

description:
NFS cohort
CL02006_NFS_D3_Macrophages_Disease


title: salinity + heat stress + Pseudomonas putida [S+HS+Pp-2]


title: mono_disease NFS bio rep 5

description:
NFS cohort
CL02009_NFS_D0_Monocytes_Disease

value: CD14+ Monocyte

value: Day 0


title: 174


title: SCD post AMI, D24

value: SCD post AMI

value: blood

value: male


title: salinity + heat stress + Pseudomonas putida [S+HS+Pp-1]


title: mono_disease NFS bio rep 3

description:
NFS cohort
CL02005_NFS_D0_Monocytes_Disease

value: sarcoidosis patient


title: Survivor post AMI, S23

value: Survivor post AMI

value: female


title: mac_disease NFS bio rep 2

description:
NFS cohort
CL02004_NFS_D3_Macrophages_Disease

value: Monocyte-derived macrophage


title: mono_disease NFS bio rep 2

description:
NFS cohort
CL02003_NFS_D0_Monocytes_Disease


title: SCD post AMI, D23


title: salinity + heat stress [S+HS-3]

source_name: salinity + heat stress

value: leaf

value: Moneymaker

value: Salinity + heat stress


title: salinity + heat stress [S+HS-2]


title: Survivor post AMI, S22

value: PBMC

value: WT

value: Outcome of AMI within one year


title: 170

value: Control

value: peripheral blood


title: salinity + heat stress [S+HS-1]


title: heat stress + Pseudomonas putida [HS+Pp-3]

source_name: heat stress + Pseudomonas putida

value: Heat stress and inoculated with bacteria


title: SCD post AMI, D22


title: Survivor post AMI, S21


title: 164


title: mac_disease NFS bio rep 1

description:
NFS cohort
CL02002_NFS_D3_Macrophages_Disease

value: GM-CSF dfferentiated macrophages

value: Day 3


title: 181

description: Gene expression data from peripheral blood from adult patients with a negative RT-PCR for SARS-CoV-2 and COVID-19


title: 154


title: mac_control bio rep 3

description:
FS external
CL01010_FS_D3_Macrophages_Control


title: 163


title: mono_disease bio rep 1

description:
NFS cohort
CL02001_NFS_D0_Monocytes_Disease

value: CD14+ Monocyte

value: Day 0


title: SCD post AMI, D21

value: SCD post AMI

value: blood


title: mac_disease FS bio rep 2

description:
FS cohort
CL01009_FS_D3_Macrophages_Disease

value: sarcoidosis patient


title: heat stress + Pseudomonas putida [HS+Pp-1]


title: Survivor post AMI, S20

value: Survivor post AMI

value: male


title: heat stress  [HS-3]

source_name: heat stress

value: leaf

value: Moneymaker

value: Heat stress


title: mac_control bio rep 2

description:
FS cohort
CL01007_FS_D3_Macrophages_Control

value: Monocyte-derived macrophage


title: heat stress  [HS-2]


title: SCD post AMI, D20

value: PBMC

value: WT

value: Outcome of AMI within one year


title: mac_disease FS bio rep 1

description:
FS cohort
CL01008_FS_D3_Macrophages_Disease


title: Survivor post AMI, S19


title: mac_control bio rep 1

description:
FS cohort
CL01006_FS_D3_Macrophages_Control

value: Control


title: SCD post AMI, D19


title: 148

value: peripheral blood


title: mono_control bio rep 3

description:
FS external
CL01005_FS_D0_Monocytes_Control


title: salinity + Pseudomonas putida  [S+Pp-3]

source_name: salinity + Pseudomonas putida

value: Salinity and inoculated with bacteria


title: 153


title: Survivor post AMI, S18


title: 152


title: 150


title: salinity + Pseudomonas putida  [S+Pp-2]


title: 142


title: 143


title: SCD post AMI, D18


title: 128


title: Survivor post AMI, S17


title: mono_disease FS bio rep 2

description:
FS cohort
CL01004_FS_D0_Monocytes_Disease

value: CD14+ Monocyte


title: mono_disease FS bio rep 1

description:
FS cohort
CL01003_FS_D0_Monocytes_Disease

value: Day 0


title: mono_control  bio rep 2

description:
FS cohort
CL01002_FS_D0_Monocytes_Control


title: salinity [S-3]

source_name: salinity

value: Salinity


title: SCD post AMI, D17

value: SCD post AMI

value: blood


title: 126


title: Normal-USMSC-3

city: Shanghai

first: Haibin

last: Tian

address: 1239 Siping Road

institute: Tongji University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome
Assembly: hg38
Supplementary files format and content: RNA-SEQ TPM.TXT

source_name: Umbilical cord

extract_protocol:
Total RNA was isolated from the samples and RNA integrity was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Umbilical cord

value: USMSC


title: mono_control  bio rep 1

description:
FS cohort
CL01001_FS_D0_Monocytes_Control


title: SCD post AMI, D16

source_name: blood plasma

value: male


title: Survivor post AMI, S16

value: Survivor post AMI


title: 113


title: 122


title: control + Pseudomonas putida  [CT+Pp-3]

source_name: control + Pseudomonas putida

value: leaf

value: Moneymaker

value: Inoculated with bacteria


title: Normal-USMSC-2


title: salinity + Pseudomonas putida  [S+Pp-1]


title: control + Pseudomonas putida  [CT+Pp-2]


title: Normal-USMSC-1


title: 106


title: salinity [S-1]


title: 112


title: SCD post AMI, D15

value: PBMC

value: WT


title: APS-USMSC-4


title: Survivor post AMI, S13

value: Outcome of AMI within one year


title: APS-USMSC-3


title: salinity [S-2]


title: control + Pseudomonas putida  [CT+Pp-1]


title: control [CT-3]

source_name: control

value: No treatment


title: 108

value: Control

value: peripheral blood


title: 104


title: SCD post AMI, D13


title: APS-USMSC-2


title: control [CT-2]


title: 92


title: 94


title: APS-USMSC-1


title: Survivor post AMI, S12

value: female


title: Survivor post AMI, S15


title: control [CT-1]


title: H146-RXRG cells

first: Hong

last: Wang

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-sen University

data_processing:
sample1-8:single sequencing was performed with Illumina HiSeq 3000 (RiboBio Co, Ltd). TopHat2 and HTSeq were used for RNA-seq data analysis with GRCh38/hg19 as the reference genome. Differential analysis of the RNA-seq data was performed using DESeq2 analysis.
Assembly: hg38
Supplementary files format and content: sample1-8:tab-delimited text files include TPM values for each Sample

source_name: Homo sapiens

growth_protocol: SCLC cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
sample1-8:Total RNA was isolated using TRIzol reagent according to the manufacturer’s instruction (15596026, Invitrogen, USA).
sample1-8:DNase I was used for column digestion to ensure RNA quality. RNA library preparation was performed using the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (E7420L). RNA libraries were prepared for paired-end sequencing using standard Illumina protocols.

treatment_protocol: (1) H128 cells were treated with HX531 for 48 h or transfected with RXRG siRNA or vehicle siRNA for 48 h. (2) H146 cells and H146 RXRG overexpression cells.

value: Homo sapiens

value: tumor cells


title: SW620 cells, shFH #3

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

data_processing:
Basecalls performed using Rsubread v2.12.3
Sequencing read quality was inspected using fastp v0.23.4. Adapter removal and read trimming were performed. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the hg38. FeatureCounts (Rsubread) was used to count the reads numbers mapped to each gene. And then FPKM/TPM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read-counts values for each Sample.
Supplementary files format and content: NA

extract_protocol:
RNA was harvested using Trizol reagent(Life Technologies). Illumina NEB Ultra directional RNA library Prep Kit was used with 1 ug of total RNA for the construction sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: colorectal cancer cells

value: FH knockdown


title: Survivor post AMI, S11

value: blood


title: H146 cells


title: 85


title: SW620 cells, shFH #1


title: H128 cells, HX531-10μM


title: Survivor post AMI, S10


title: 86


title: SW620 cells, shControl #3


title: SCD post AMI, D12

value: SCD post AMI


title: SCD post AMI, D10


title: H128 cells,Con


title: SW620 cells, shControl #2


title: Survivor post AMI, S9

value: Survivor post AMI


title: 78


title: heat stress  [HS-1]

value: leaf

value: Heat stress


title: SCD post AMI, D9


title: H128 cells, siRXRG3


title: SW620 cells, shFH #2


title: SCD post AMI, D11

value: male


title: SCC13-tet-shBNC1-486-shFRA1-12

description: Squamous Cell Carcinoma cell line

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36, then mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted
Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes
Assembly: GRCh38
Supplementary files format and content: xlsx files containing differential expression analysis of all comparisons used in this project
Supplementary files format and content: tab-delimited text files include hit count values for each Sample

source_name: epidermal SCC

extract_protocol:
RNA STAT-60 was used for RNA extraction
Following Ribosomal depletion, RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were treated with10ng/mL Doxycycline for 96 hours to induce shRNA expression

tag: shRNA


title: SW620 cells, shControl #1


title: H128 cells, siRXRG2


title: Survivor post AMI, S8

value: PBMC


title: 84

tag: disease state


title: H128 cells, siCont

tag: cell line


title: 72


title: 66


title: 80


title: 61


title: 62


title: SCD post AMI, D8

value: WT


title: 65


title: SCC13-tet-shBNC1-486-shFRA1-10

description: Squamous Cell Carcinoma cell line


title: LM31-CAP3

city: Beijing

first: xinyu

last: mang

address: Dongdan Three

institute: Peking Union Medical College,

description:
LM3_exp_count.txt
LM3_exp_TPM.txt

data_processing:
The hisat2 Genomic Analysis Software v2.2.1 was used to align the reads to the genome, generate raw counts corresponding to each known gene
calculate the Transcript per million(TPM) values.
Assembly: grch38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Hepatocellular carcinoma cells

growth_protocol: SMMC7721, HepG2 and LM3 cells were cultured in Dulbecco’s modified eagle medium (DMEM, Corning, USA) supplemented with 10% fetal bovine serum (FBS, Gibco, USA) and penicillin-streptomycin (Gibco, USA), and maintained in an incubator with 5% CO2 at 37°C.

extract_protocol:
The total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The SMMC7721, HepG2 and LM3 cells were seeded in 6-well plates overnight and then treated with Piezo-CAP (0 and 60 s) for 24 h.

value: Hepatocellular carcinoma cells

value: Piezoeletric Cold Atmospheric Plasma (CAP)


title: Survivor post AMI, S7

value: Outcome of AMI within one year


title: 74_D0

description: Gene expression data from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 7

source_name: Total RNA from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 0

value: peripheral blood


title: SCD post AMI, D7

value: female


title: LM31-CAP1

description:
LM3_exp_count.txt
LM3_exp_TPM.txt


title: 48

value: Control


title: 37


title: SCC13-tet-shBNC1-486-shFRA1-11

description: Squamous Cell Carcinoma cell line


title: LM31-CAP2

description:
LM3_exp_count.txt
LM3_exp_TPM.txt


title: batch-1_0021-B

city: Cape Town

first: Valentin

last: Voillet

address: First Floor Wembley Square, 3 McKenzie St, Gardens

institute: cape town hvtn immunology laboratory

data_processing:
The `RNASeqPipelineR` was used to perform alignment, quantification and annotation of the RNA sequencing data (RNA-seq) from the whole and mini population RNA-Seq libraries. The RNA-seq data were aligned against the human genome (hg38) using STAR (v2.4.2a), and gene expression quantification was performed using RSEM (v1.2.22).
Reads from a same sample but different batches were aggregated.
Assembly: hg38
Supplementary files format and content: wraw_counts.csv

source_name: BAL

extract_protocol:
RNA from blood samples was extracted using Paxgene RNA extraction kit and from the BAL samples we used Qiagen RNAEasy micro kit method
Libraries were prepared from RNA samples of both sample types using NEBNext kits

value: BAL

tag: patient id

tag: disease status

value: LTBI and HIV-negative


title: SCC13-tet-shBNC1-486-shSCR-7

description: Squamous Cell Carcinoma cell line


title: LM3-Control3

description:
LM3_exp_count.txt
LM3_exp_TPM.txt

value: control

value: No treatment


title: Survivor post AMI, S6

value: blood

tag: time


title: SCD post AMI, D6

value: SCD post AMI

tag: cell type


title: SCC13-tet-shSCR-shFRA1-6

description: Squamous Cell Carcinoma cell line


title: Survivor post AMI, S5

tag: individual

value: Survivor post AMI


title: SCC13-tet-shSCR-shFRA1-5

description: Squamous Cell Carcinoma cell line


title: LM3-Control2

description:
LM3_exp_count.txt
LM3_exp_TPM.txt


title: 26

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

extract_protocol: Total RNA was extracted following Qiagen protocol


title: LM3-Control1

description:
LM3_exp_count.txt
LM3_exp_TPM.txt


title: SCC13-tet-shSCR-shFRA1-4

description: Squamous Cell Carcinoma cell line


title: fib1-3-/- fib2-4+/- replicate 1

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and to Arabidopsis genome annotation Araport11 (https://www.araport.org) using bowtie v2 with default parameters
Both ends of read-through reads and 5' ends of longer reads were counted for ScoreMean calculation using an R package "RNAmodR.RiboMethSeq" (https://github.com/FelixErnst/RNAmodR.RiboMethSeq).
To minimize false positives brought by RNA secondary structures, over 3 consecutive nucleotides with ScoreMean over 0.5 were filtered out. Among the remaining sites, those with ScoreMean over 0.8 were retained as positive signals. IGV 2.6.0 was used to visualize the distribution of read ends and ScoreMean
Genome_build: Araport 11
Supplementary_files_format_and_content: WIG file containing the read end coverage

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seedlings for RiboMeth seq were grown on Murashige and Skoog (MS) plates containing 1% (v/w) sucrose and 0.7% (v/w) agar at 23°C under long day conditions for 14 days.

extract_protocol:
RNAs were extracted using Trizol reagent. NEBNext Small RNA Library Prep Set (Cat#E7330L) was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using protocols described in "High-Throughput Mapping of 2′-O-Me Residues in RNA Using Next-Generation Sequencing, Alexandra Lusser (ed.), RNA Methylation: Methods and Protocols, Methods in Molecular Biology, vol. 1562, DOI 10.1007/978-1-4939-6807-7_12"

tag: developmental stage

value: 14-day-old seedlings

tag: cultivar

value: seedlings


title: SCD post AMI, D5

tag: tissue

tag: Sex

value: PBMC

tag: genotype


title: 27

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

institute: Hospital del Mar Research Institute

source_name: Total RNA from adult patients with a negative RT-PCR for SARS-CoV-2 and COVID-19


title: 18


title: fib1-2-/- fib2-4+/- replicate 2


title: HepG2-CAP3

description:
HepG2_exp_count.txt
HepG2_exp_TPM.txt

value: WT

tag: treatment


title: SCC13-et-shBNC1-486-shSCR-9

description: Squamous Cell Carcinoma cell line


title: Survivor post AMI, S4

tag: group

tag: age


title: SCC13-tet-shBNC1-486-shSCR-8

description: Squamous Cell Carcinoma cell line


title: 5


title: SCC13-tet-shSCR-shSCR-3

description: Squamous Cell Carcinoma cell line

value: shScr


title: fib1-2-/- fib2-4+/- replicate 1


title: HepG2-CAP2

description:
HepG2_exp_count.txt
HepG2_exp_TPM.txt

value: Hepatocellular carcinoma cells

value: Piezoeletric Cold Atmospheric Plasma (CAP)


title: SCD post AMI, D4

value: Outcome of AMI within one year


title: SCC13-tet-shSCR-shSCR-2

description: Squamous Cell Carcinoma cell line


title: heat stress + Pseudomonas putida [HS+Pp-2]

value: leaf

value: Moneymaker

value: Heat stress and inoculated with bacteria


title: Survivor post AMI, S3

value: female


title: SCC13-tet-shSCR-shSCR-1

description: Squamous Cell Carcinoma cell line


title: fib2-3 replicate 1


title: fib1-1 replicate 1


title: HepG2-CAP1

description:
HepG2_exp_count.txt
HepG2_exp_TPM.txt


title: SCD post AMI, D3


title: HepG2-Control2

description:
HepG2_exp_count.txt
HepG2_exp_TPM.txt

value: control


title: SCC68-tet-shBNC1_24

description: Squamous Cell Carcinoma cell line

source_name: oral SCC


title: Survivor post AMI, S2


title: HepG2-Control1

description:
HepG2_exp_count.txt
HepG2_exp_TPM.txt

value: No treatment


title: SCD post AMI, D2

value: blood


title: wild type replicate 1

value: wild type


title: SCC68-tet-shBNC1_22

description: Squamous Cell Carcinoma cell line


title: Dehydrated Male 08

city: Bristol

first: Benjamin

middle: Thomas

last: Gillard

address: Dorothy Hodgkin Building

department: Bristol Medical School

institute: University of Bristol

data_processing:
BBDuk, read trimming
FastQC, read quality control
Rsubread, Alignment to Jac genome (GCA_00028075.1)
FeatureCounts Read summarisation
DESeq2 Differential Expression Analysis
Assembly: GCA_00028075.1
Supplementary files format and content: Featurecounts raw counts file
Supplementary files format and content: DESeq2 results from dehydration vs control comparison
Supplementary files format and content: DESeq2 results from rehydration vs control comparison

organism: Jaculus jaculus

source_name: Supraoptic nucleus (hypothalamus)

growth_protocol: All animals were kept single housed at 25°C constant temperature, 12-hour light cycle, with free access to dry food pellets throughout.

extract_protocol: Fresh frozen brains were sliced on the coronal plane at 100microns on a cryostat. Twelve bilateral punches of the SON were taken using a 1mm sample core within the cryostat chamber kept at -20C and kept on dry ice. A pestle and mortar with liquid nitrogen was used to break up the sample. Powdered tissue was lysed using no more than 100ml/mg of Trizol. Chloroform phase separation was used to isolate RNA then cleaned up using Zymo Direct-Zol RNA miniprep kit as per manufacturer's instructions. All storage was at -80C.

treatment_protocol: Animals were randomly assigned to three experimental groups: Control (access to water ad libitum), Dehydrated (water restriction 11 days), and Rehydration (water restriction 7 days followed by access to water ad libitum 3 days).

value: Supraoptic nucleus (hypothalamus)

value: Male

value: Dehydrated


title: SMMC7721-CAP3

description:
SMC7721_exp_count.txt
SMC7721_exp_TPM.txt


title: SCC13-tet-shBNC1_21

first: Matthew

last: Ramsey

address: 77 Ave Louis Pasteur, HIM 668

institute: Brigham and Women's Hospital

description: Squamous Cell Carcinoma cell line


title: Dehydrated Male 05


title: SMMC7721-CAP2


title: SCD post AMI, D1

value: SCD post AMI

value: male

value: PBMC


title: Control Male 06

value: Control


title: SCC13-tet-shBNC1_19

description: Squamous Cell Carcinoma cell line


title: HepG2-Control3

description:
HepG2_exp_count.txt
HepG2_exp_TPM.txt

value: Hepatocellular carcinoma cells

value: WT


title: SMMC7721-Control3


title: SMMC7721-CAP1

value: Piezoeletric Cold Atmospheric Plasma (CAP)


title: Dehydrated Male 02

description:
Ignore library name - female animal
DHM02

value: Female


title: HCT116 sh_AL1_2_IP

city: Guangzhou

first: Dingcheng

last: Shen

address: 26 Yuancun Erheng Road

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

data_processing:
Index of the reference genome was built using BWA v0.7.12 and clean reads were aligned to the reference genome (Ensemble_GRCh38.104) using BWA mem v 0.7.12. The m6A peaks were detected by exomePeak R package (version 2.16.0). The motif search was detected by HOMER (version 4.9.1). Differential peak calling was performed using exomePeak R package (version 2.16.0)
Assembly: Ensemble_GRCh38.104
Supplementary files format and content: Transcripts where differential m6A peak was identified between shALKBH5 cells and shNC cells

growth_protocol: HCT116 cells were maintained Mc5A supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for MeRIP-seq were prepared using NovaSeq mRNA-Seq Library Prep Kit following manufacturer's protocols.
Chemically fragmented RNA (100 nucleotides) was incubated with m6A antibody for immunoprecipitation according to the standard protocol of the Magna methylated RNA immune-precipitation (MeRIP) m6A Kit (Merck Millipore). Enrichment of m6A containing mRNA was then analyzed either through quantitative reverse-transcription polymerase chain reaction (qRTPCR) or by high-throughput sequencing. For highthroughput sequencing, purified RNA fragments from m6A-MeRIP were used for library construction with the NEBNext Ultra RNA library Prep kit from Illumina and were sequenced with Illumina HiSeq 2000.

treatment_protocol: HCT116 cells with stable knocksown of ALKBH5 and control cells were collected (two replications; labeled as shAL and shNC, respectively). More than 250 μg of total RNA was extracted from each group, and mRNA was further purified with the NEBNext Poly(A) mRNA. Magnetic Isolation Module (NEB#E7490) using oligo (dT) beads. Concentration and integrity of RNA were evaluated using NanoDrop Spectrophotometer and Agilent 2100 Bioanalyzer (Agilent, USA). The mRNA was then chemically fragmented into ~ 150 nts nucleotides with fragmentation buffer. After 10% of fragmented mRNA was saved as input, m6A-modified mRNA was immunoprecipitated with anti-m6A antibodies (Synaptic System, #202003) and eluted.

value: ALKBH5 knockdown

tag: antibody

value: Anti-N6-methyladenosine (m6A) Antibody (ABE572, Sigma-Aldrich)


title: HCT116 sh_AL1_2_Input


title: SCC68-tet-shScr_18

description: Squamous Cell Carcinoma cell line

tag: shRNA

value: shScr


title: SMMC7721-Control2

value: control

value: No treatment


title: Rehydrated Male 04

value: Rehydrated


title: SCC68-tet-shBNC1_23

description: Squamous Cell Carcinoma cell line


title: SCC68-tet-shScr_17

description: Squamous Cell Carcinoma cell line


title: Control Male 05

description:
Ignore library name - female animal
CM05

value: Supraoptic nucleus (hypothalamus)


title: SMMC7721-Control1


title: Dehydrated Male 06

value: Male


title: HCT116 sh_AL1_1_Input


title: Survivor post AMI, S1

value: Survivor post AMI

value: blood

value: Outcome of AMI within one year


title: SCC68-tet-shScr_16

description: Squamous Cell Carcinoma cell line


title: Control Male 04


title: SCC13-tet-shScr_15

description: Squamous Cell Carcinoma cell line


title: HCT116 sh_NC_2_Input


title: Rehydrated Female 06


title: SCC13-tet-shScr_14

description: Squamous Cell Carcinoma cell line


title: HCT116 sh_AL1_1_IP


title: SCC13-tet-shScr_13

description: Squamous Cell Carcinoma cell line


title: HCT116 sh_NC_1_IP


title: Rehydrated Female 05


title: SCC13-tet-shBNC1_20

description: Squamous Cell Carcinoma cell line


title: Ovarian yolk sac tumor, patient 4

first: Kezhe

last: Tan

address: Luding Road 355, Shanghai, China

institute: Shanghai Children's Hospital

description: Gene expression after 12hr  in 8Gy-irradiated human blood

hyb_protocol: Hybridzation was performed as follows: 1. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar; 2. Slowly dispense all of the volume of the hybridization sample onto the gasket well in the center; 3. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned; 4. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces; 5. Firmly hand-tighten the clamp onto the chamber;6. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. If necessary, tap the assembly on a hard surface to move stationary bubbles; 7. Place assembled slide chamber in rotisserie in a hybridization oven set to 55°C. Set your hybridization rotator to rotate at 20rpm; 8. Hybridize at 55°C for 20 hours.

scan_protocol: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 14.8, Agilent Technologies) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were chosen for further data analysis.

data_processing: Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test. The threshold set for up- and down-regulated genes was a fold change >= 2.0 and a P value <= 0.05. Target genes of differentially expressed miRNAs were the intersection predicted with  2 databases (miRDB, miRWalk). GO analysis and KEGG analysis were applied to determine the roles of these target genes. Hierarchical Clustering was performed to show the distinguishable miRNAs expression pattern among samples.

source_name: Ovarian yolk sac tumor, patient 4

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP. After purification the labeled RNAs were hybridized onto the microarray. After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted from ten 10-µm-thick sections of FFPE samples using an RecoverAll FFPE Kit (Thermo Fisher Scientific, USA, #AM1975). The RNA concentration and quality were measured using an Agilent 2100 bioanalyzer (Agilent, USA, #G2939BA) according to the manufacturer’s instruction. Quality control was set as follows: 1) mass>130ng; 2) concentration>17ng/μL; 3) A260/280 value between 1.8 and 2.1.

treatment_protocol: The enrolled patients underwent tumor resection and the samples were collected, including 18 cases using the formalin-fixed, paraffin-embedded (FFPE) approach, of which 2 cases of ovarian cyst, 3 cases of mature teratoma, 6 cases of immature teratoma, 3 cases of yolk sac tumor, 3 cases of juvenile granulosa cell tumor, and 1 case of dysgerminoma; 2 cases were fresh frozen tissue samples preserved in -81℃ environment, including one mature teratoma and one yolk sac tumor.

value: tissue

tag: gender

value: female

tag: age (year)


title: Ovarian yolk sac tumor, patient 3

source_name: Ovarian yolk sac tumor, patient 3


title: Rehydrated Female 04


title: HCT116 sh_NC_2_IP

tag: cell line


title: Rehydrated Female 03


title: OKF6TERT-tet-shBNC1_12

description: Immortalized keratinocyte cell line

source_name: oral keratinocytes


title: HCT116 sh_NC_1_Input


title: MDM tolerance

city: Melbourne

first: Jarny

last: Choi

state: Victoria

address: The University of Melbourne

department: Anatomy and Neuroscience

country: Australia

institute: Centre for Stem Cell Systems

description: 10x Genomics Next GEM Single Cell 5/ v2 (Dual Index)

data_processing:
Two Sequencing runs were performed using Novaseq6000
Data processing and merging of sequencing runs were carried out through CellRanger v6.0.2
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood monocyte

extract_protocol:
in vitro derived macrophages from peripheral blood monocytes and induced pluripotent stem cells were extracted by washing cells with PBS before incubation at 37 degrees celsius for 5 minutes in 10mM EDTA.
Single cell RNA-sequencing libraries were prepared using the Chromium Next GEM Single Cell 5’ v2 (Dual Index) protocol as per manufacturer’s instructions. Cell suspensions were prepared for a target recovery of 6000 cells per sample. Libraries were quality checked and quantified using the Agilent Tapestation D5000 High Sensitivity Tape.

value: macrophage

value: peripheral blood monocyte

value: Re-stimulated with LPS


title: Ovarian yolk sac tumor, patient 2

source_name: Ovarian yolk sac tumor, patient 2


title: OKF6TERT-tet-shBNC1_10

description: Immortalized keratinocyte cell line


title: OKF6TERT-tet-shBNC1_11

description: Immortalized keratinocyte cell line


title: Ovarian yolk sac tumor, patient 1

source_name: Ovarian yolk sac tumor, patient 1


title: MDM 18 hour

value: 18 hour LPS stimulation


title: NTERT-tet-shBNC1-9

description: Immortalized keratinocyte cell line

source_name: epidermal keratinocytes


title: Dehydrated Female 06

value: Female

value: Dehydrated


title: MDM acute

value: 2 hour LPS stimulation


title: MDM control

value: unstimulated


title: Control Male 03

value: Control


title: NTERT-tet-shBNC1-8

description: Immortalized keratinocyte cell line


title: Dehydrated Female 07


title: Ovarian mature teratoma, patient 4

source_name: Ovarian mature teratoma, patient 4


title: Dehydrated Female 05


title: Ovarian mature teratoma, patient 2

description: Gene expression after 6hr in 5Gy-irradiated human blood

source_name: Ovarian mature teratoma, patient 2


title: NTERT-tet-shBNC1-7

description: Immortalized keratinocyte cell line


title: Ovarian mature teratoma, patient 3

description: Gene expression after 6hr in 8Gy-irradiated human blood

source_name: Ovarian mature teratoma, patient 3


title: PSCM tolerance

source_name: pluripotent stem cell

value: pluripotent stem cell


title: Dehydrated Female 04

value: Supraoptic nucleus (hypothalamus)


title: OKF6TERT-tet-shScr-6

description: Immortalized keratinocyte cell line

value: shScr


title: Ovarian mature teratoma, patient 1

description: Gene expression after 6hr in 2Gy-irradiated human blood

source_name: Ovarian mature teratoma, patient 1


title: PSCM acute


title: Ovarian immature teratoma, patient 6

description: Gene expression after 6hr in 0.5Gy-irradiated human blood

source_name: Ovarian immature teratoma, patient 6


title: Dehydrated Female 03


title: OKF6TERT-tet-shScr-5

description: Immortalized keratinocyte cell line


title: PSCM 18 hour


title: PSCM control


title: Control Female 06


title: Control Female 05


title: H128 cells, HX531-5μM

source_name: Homo sapiens

value: Homo sapiens

value: tumor cells


title: OKF6TERT-tet-shScr-4

description: Immortalized keratinocyte cell line


title: A-eMSCs Scr3

city: Nanjing

first: Tao

last: Gui

state: Jiangsu

address: NO.100 Shizi Street, Hongshan Road

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine

data_processing:
Illumina NovaSeq6000 sequencer was used and the sequencing mode was PE150.
Quality control standard: the data volume is about 6G/ sample, and the proportion of each base mass greater than 20 (Q20 ratio) is not less than 90%.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: Eutopic endometrium from patients with adenomyosis

growth_protocol: A-eMSCs were maintained in DMEM/F12 supplemented with 10% fetal bovine serum and 100 µg/ml streptomycin and 100 IU/ml penicillin at 37˚C in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using MagBeads Total RNA Extraction Kit (Cat#T02-096) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries for RNA-seq were prepared using KAPA RNA HyperPrep Kit following manufacturer's protocols. The concentration was detected and quatified by Qubit® 2.0 Fluorometerand Labchip.

treatment_protocol: Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),

value: Endometrial mesenchymal stem cells (eMSCs)

value: Adenomyotic eutopic endometrial mesenchymal stem cells (A-eMSCs)

value: WT

value: Control lentivirus


title: Control Female 03

description:
Ignore library name - male animal
CF03

value: Male


title: NTERT-tet-shSCR-3

city: Boston

description: Immortalized keratinocyte cell line


title: Ovarian immature teratoma, patient 4

source_name: Ovarian immature teratoma, patient 4

value: tissue

value: female


title: A-eMSCs Scr2

value: Eutopic endometrium from patients with adenomyosis


title: Control Female 02

source_name: Supraoptic nucleus (hypothalamus)

value: Female


title: A-eMSCs Scr1


title: NTERT-tet-shSCR-1

description: Immortalized keratinocyte cell line


title: Ovarian immature teratoma, patient 3

source_name: Ovarian immature teratoma, patient 3


title: A-eMSCs EGR1-KD-3

value: Lentivirus-mediated EGR1 knockdown


title: HeLa_NOAA_mRNAseq_biological-replicate2

city: Los Angeles

first: Siavash

last: Kurdistani

state: CA

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

description: mRNA

data_processing:
Reads were mapped to the Human genome (hg19) and to spike-in reference sequences using default parameters of TopHat. SAMMate software was used to determine the transcript RPKM (reads per kilobase of exon per million of reads) for mRNA-seq libraries. The sums of RPKM values from the spike-in controls were used to normalize across samples and to adjust transcripts RPKM.
Genome_build: hg19
Supplementary_files_format_and_content: Excel workbook with normalized RPKM values for all samples except the chromRNAseq samples. For chromRNAseq samples, we used mapped counts around the gene regions to illustrate newly synthesized transcripts.   Therefore, processed data for those two libraries are mapped read coverage in wig format (available on the sample records).

source_name: Cell line

growth_protocol: HeLa cells were maintained in DMEM (Cellgro #10-013-CV) supplemented with 10% fetal bovine serum (FBS) (Thermo Fisher HyClone #SV30014.03).

extract_protocol:
Total RNA was extracted using the Trizol reagents (Ambion #15596026) and treated with TURBO DNase (Ambion #AM2239).
1 μg of total RNA was used to prepare sequencing library using the Illumina TruSeq RNA sample preparation kit. A mixture of external RNA spike-in controls (Ambion #4456740) was added to total RNA prior to library preparation. Libraries were sequenced with Illumina Hi-seq platforms to obtain 50 bp-long reads. No spike-in control was added to biological replicate 2, and 100 bp-long reads were obtained from those two libraries.  For chromatin RNA-seq, chromatin subcellular fractionation was isolated. Total RNA-seq libraries were prepared and sequenced with Illumina Hi-seq platforms to obtain 50 bp-long reads.

treatment_protocol: Media containing complete amino acids (AA) were made from DMEM powder (US Biological #D9802) and supplemented with an additional 3.5 g/L D-glucose (for a total of 4.5 g/L), 1 mM sodium pyruvate (Gibco #11360070), 3.7 g/L sodium bicarbonate, and 0.0159 g/L sodium phenol red (US Biological #P4040). Media without AA were made from DMEM without amino acids powder (US Biological #D9800-013) and supplemented with an additional 3.5 g/L D-glucose, 1 mM sodium pyruvate (Gibco #11360070), and 3.7 g/L sodium bicarbonate. pH of media was adjusted to 7.2 by the addition of HCl before being filter sterilized and supplemented with 10% dialyzed FBS (Gibco #26400-044).

value: HeLa

value: without AA

tag: sirna mediated knockdown and plasmid


title: Rehydrated Male 08

value: Rehydrated


title: Ovarian granulosa cell tumor, patient 3

source_name: Ovarian granulosa cell tumor, patient 3


title: Ovarian immature teratoma, patient 1

source_name: Ovarian immature teratoma, patient 1


title: Ovarian granulosa cell tumor, patient 2

source_name: Ovarian granulosa cell tumor, patient 2


title: Ovarian immature teratoma, patient 5

description: Gene expression after 6hr in 0Gy-irradiated human blood

source_name: Ovarian immature teratoma, patient 5


title: HeLa_AA_mRNAseq_biological-replicate2

description: mRNA

value: AA


title: Rehydrated Male 05

value: Supraoptic nucleus (hypothalamus)


title: NTERT-tet-shSCR-2

description: Immortalized keratinocyte cell line

source_name: epidermal keratinocytes

value: shScr


title: HeLa_NOAA_chromRNAseq

description: total RNA


title: A-eMSCs EGR1-KD-1


title: Control Male 01

value: Control