title: C05_S29_L004


title: C01_S25_L001

status: Public on Jun 01 2024

type: SRA

city: Palo Alto

first: Meng

last: Sun

state: CA

address: Biomedical Innovations Building 1300, 240 Pasteur Drive

country: USA

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
To convert the sequencing read fastq files into single-cell count tables, we used STAR to align with the reference GRCh38.genome.ERCC.fa and an index length of 150bp, and featureCounts to calculate the count tables. The single-cell count tables were imported as a Seurat object in R for downstream analysis89. We filtered cells with unique feature counts over 4000, total counts below 5x105, and mitochondrial counts >5% for doublets, dropouts, and dying cells. CD8 T cells were removed due to a low cell number. We gated CD4 cells based on their CD4 and CD8 flow MFIs.
Assembly: GRCh38.genome.ERCC.fa
Supplementary files format and content: .tsv scRNA-seq raw count table and each row is a cell and each column is a gene.

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
These antigen-specific T cells were FACS-sorted into individual wells of a 96-well PCR plate with lysis buffers. To assess the technical variability, we mixed the lysis buffers with the external RNA control – ERCC RNA Spike-In (a final estimate of ~5000 molecules per well, Thermo Fisher Scientific, Waltham, MA). We used the modified Smart-Seq2 protocol (Clontech Laboratories, Mountain View, CA) to generate the cDNA library. From the library, we took a small aliquot (1 μL) for the nested PCR to amplify and sequence 15 targeted RNAs (TBX21, RORC, GATA3, FOXP3, RUNX1, RUNX3, IFNG, IL2, IL17A, GZMB, PERF, IL4, IL5, IL13, TGFB) and the CDR3 regions of both TCRα and TCRβ chains. Based on the TCR sequences, the Smart-seq2 generated cDNAs of the clonally expanded activated T cells were manually selected only on the ESAT-6/CFP-10-reactive cells for the high-coverage in-depth single-cell full transcriptomic sequencing.
Nextera XT library prep kit (96 index primers; Illumina, San Diego, CA) protocol

tag: tissue

value: PBMC

tag: cell type

value: T-cells

tag: treatment

value: overlapping pipette pool targeting ESAT6/CFP10 of M.tuberculosis


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title: P34-CP5-G05_S77_L002


title: P34-CP5-B09_S21_L003


title: P34-CP5-E11_S59_L002


title: P34-CP5-E09_S57_L002


title: P34-CP5-A10_S10_L002


title: P34-CP5-B12_S24_L004


title: P34-CP5-C06_S30_L001


title: P34-CP5-A12_S12_L001


title: P34-CP5-B04_S16_L002


title: P34-CP5-G04_S76_L003


title: P34-CP5-H01_S85_L004


title: P34-CP5-D09_S45_L001


title: P34-CP5-H08_S92_L004


title: P34-CP5-E08_S56_L003


title: P34-CP5-F04_S64_L001


title: P34-CP5-H06_S90_L001


title: P34-CP5-B10_S22_L002


title: P34-CP5-B11_S23_L004


title: P34-CP5-G07_S79_L003


title: P34-CP5-E05_S53_L003


title: P34-CP5-E06_S54_L001


title: P34-CP5-D07_S43_L001


title: P34-CP5-E06_S54_L002


title: P34-CP5-E04_S52_L001


title: P34-CP5-F01_S61_L003


title: P34-CP5-B02_S14_L003


title: P34-CP5-H10_S94_L002


title: P34-CP5-D12_S48_L003


title: P34-CP5-C07_S31_L001


title: P34-CP5-D04_S40_L004


title: P34-CP5-F10_S70_L001


title: P34-CP3-E03_S51_L003


title: P34-CP3-E08_S56_L001


title: P34-CP3-A11_S11_L003


title: P34-CP5-G01_S73_L004


title: P34-CP3-G06_S78_L001


title: P34-CP3-C12_S36_L003


title: P34-CP3-G10_S82_L004


title: P34-CP3-E02_S50_L002


title: P34-CP3-F01_S61_L002


title: P34-CP3-B04_S16_L001


title: P34-CP3-D05_S41_L001


title: P34-CP3-B08_S20_L003


title: P34-CP5-F05_S65_L002


title: P34-CP3-D09_S45_L001


title: P34-CP3-C07_S31_L002


title: P34-CP3-H10_S94_L004


title: P34-CP5-E10_S58_L003


title: P34-CP3-E01_S49_L001


title: P34-CP3-B05_S17_L004


title: P34-CP3-D04_S40_L003


title: P34-CP3-A03_S3_L003


title: P34-CP3-G11_S83_L004


title: P34-CP5-H06_S90_L002


title: P34-CP3-F03_S63_L004


title: P34-CP3-H07_S91_L004


title: P34-CP3-B03_S15_L003


title: P34-CP3-C01_S25_L001


title: P34-CP3-A01_S1_L004


title: P34-CP3-C01_S25_L002


title: P34-CP3-E12_S60_L003


title: P34-CP3-D05_S41_L003


title: P34-CP3-D11_S47_L002


title: P34-CP3-E01_S49_L003


title: P34-CP3-B09_S21_L004


title: P34-CP3-D01_S37_L002


title: P34-CP3-F02_S62_L004


title: P34-CP3-D07_S43_L004


title: P34-CP3-G03_S75_L003


title: P34-CP3-H11_S95_L001


title: P34-CP3-H05_S89_L003


title: P34-CP3-H02_S86_L004


title: P34-CP3-G04_S76_L004


title: P34-CP3-A05_S5_L003


title: P34-CP3-B06_S18_L004


title: P34-CP3-B07_S19_L004


title: P34-CP3-H01_S85_L002


title: P34-CP3-D07_S43_L001


title: P34-CP3-E06_S54_L002


title: P34-CP3-C02_S26_L001


title: P34-CP3-B05_S17_L002


title: P34-CP3-E06_S54_L001


title: P34-CP3-D03_S39_L004


title: P34-CP3-A10_S10_L002


title: P34-CP3-A06_S6_L001


title: P34-CP3-D11_S47_L004


title: P34-CP3-E11_S59_L002


title: P34-CP3-F05_S65_L003


title: P34-CP3-A07_S7_L003


title: P34-CP3-H04_S88_L004


title: P34-CP3-G10_S82_L003


title: P34-CP3-B12_S24_L003


title: P34-CP3-F05_S65_L001


title: P34-CP3-B03_S15_L002


title: P34-CP3-C08_S32_L004


title: P34-CP3-G05_S77_L004


title: P34-CP3-F07_S67_L004


title: P34-CP3-H02_S86_L001


title: P34-CP3-B08_S20_L004


title: P34-CP3-B05_S17_L001


title: P34-CP3-C06_S30_L004


title: P34-CP3-F10_S70_L002


title: P34-CP3-E07_S55_L004


title: P34-CP3-F04_S64_L001


title: P34-CP3-G12_S84_L004


title: P34-CP3-G08_S80_L001


title: P34-CP3-D01_S37_L001


title: P34-CP3-G05_S77_L001


title: P34-CP3-B01_S13_L004


title: P34-CP3-C02_S26_L003


title: P34-CP3-A12_S12_L002


title: P34-CP3-F12_S72_L002


title: P34-CP3-G07_S79_L001


title: P34-CP3-G11_S83_L003


title: P34-CP3-E05_S53_L001


title: P34-CP3-F02_S62_L002


title: P34-CP3-D10_S46_L004


title: P34-CP3-A12_S12_L003


title: P34-CP3-G01_S73_L001


title: P34-CP3-C09_S33_L003


title: P34-CP3-B10_S22_L001


title: P34-CP3-H12_S96_L003


title: P34-CP3-F12_S72_L001


title: P34-CP3-F06_S66_L002


title: P34-CP3-H03_S87_L001


title: P34-CP3-F10_S70_L004


title: P34-CP3-H06_S90_L003


title: P34-CP3-H10_S94_L002


title: P34-CP3-B02_S14_L003


title: P34-CP3-D06_S42_L002


title: P34-CP3-E07_S55_L002


title: P34-CP3-F08_S68_L003


title: P34-CP3-C05_S29_L004


title: P34-CP3-A12_S12_L004


title: P34-CP3-E12_S60_L001


title: P34-CP3-A07_S7_L002


title: P34-CP3-H04_S88_L001


title: P34-CP3-F03_S63_L003


title: P34-CP3-B07_S19_L002


title: P34-CP3-F11_S71_L001


title: P34-CP3-G09_S81_L003


title: P34-CP3-B09_S21_L001


title: P34-CP3-H03_S87_L004


title: P34-CP3-G09_S81_L002


title: P34-CP3-D06_S42_L004


title: P34-CP3-C03_S27_L003


title: P34-CP3-B04_S16_L002


title: P34-CP3-A11_S11_L001


title: P34-CP3-G12_S84_L001


title: P34-CP3-E01_S49_L002


title: P34-CP3-A08_S8_L002


title: P34-CP3-C10_S34_L001


title: P34-CP3-G08_S80_L003


title: P34-CP3-E05_S53_L003


title: P34-CP3-D10_S46_L003


title: P34-CP3-F07_S67_L003


title: P34-CP3-B03_S15_L004


title: P34-CP3-A04_S4_L003


title: P34-CP3-H10_S94_L001


title: P34-CP3-H01_S85_L004


title: P34-CP3-F11_S71_L002


title: P34-CP3-G03_S75_L004


title: P34-CP3-H07_S91_L002


title: P34-CP3-H10_S94_L003


title: P34-CP3-F02_S62_L001


title: P34-CP3-E06_S54_L004


title: P34-CP3-H07_S91_L003


title: Synechococcus cells, kaiABC knock-out, 8 cycles LD16:8, replicate 3

city: Nashville

first: Carl

middle: Hirschie

last: Johnson

state: Tennessee

address: 465 21st Avenue South, U-8215 BSB/MRBIII

department: Biological Sciences

institute: Vanderbilt University

library_source: transcriptomic

data_processing:
Tuxedo and DESeq
Sequence reads were trimmed for adaptors and low quality reads were removed using trim_galore v. 0.6.10, specifying that the sequences were paired-end
hisa2 v. 2.2.1 was used to build an index using assembly sequences available in NCBI (GenBank assembly accession: GCA_000012525.1) and to align our sequencing reads with the genome (parameters: -S, --dta, --no-spliced-alignment)
samtools v. 1.11.0 was used to convert the generated .sam files into .bam files
stringtie v. 2.1.7 was used to estimate transcript abundances, and the prepDE.py script provided with stringtie was used to generate a read counts matrix
the raw read counts were analyzed with DESeq2 v. 1.36.0 and p-values were calculated using a Wald test followed by multiple-comparisons correction using FDR. Log2FC cvalues were shrunk using adaptive shrinking to account for high levels of variation due to low counts or high dispersion values.
Assembly: GCA_000012525.1
Supplementary files format and content: comma-delimited csv file includes raw counts for the transcripts in each sample

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: bacterial cells

growth_protocol: Cells were maintained in plates of BG-11 and grown in constant light and constant 30ºC, under ~ 40µE of illumination with fluorescent lights.

extract_protocol:
RNA was extracted from cells preserved in RNA Protect (Qiagen) and processed with the Rneasy Mini Kit (Qiagen). DNA contamination was removed with Dnase I (NEB).
Library preparation and rRNA depletion was performed using the NEBNext® rRNA Depletion Kit for Bacteria (New England BioLabs).

treatment_protocol: Prior to collection, cells were grown in plates containing solid BG-11 media for different amounts of LD cycles, being exposed to either short (LD8:16; 8h of light, 16h of darkness) or long (LD16:8) days. In order to account for differential growth caused by the higher amount of light in LD16:8, as well as the different numbers of LD cycles, the plates either received supplemental constant light prior to being given their LD cycles, or were replated in the middle of their treatment, such that by the time the cells were collected, they had been allowed to grow for ~60h of light.

value: bacterial cells

tag: time

value: collected 1h before midday of their respective photoperiod

tag: genotype

value: kaiABC knock-out

value: 8 cycles of LD16:8


title: Timecourse scRNAseq, days 0 to 15

city: Boston

first: Merrick

middle: Pierson

last: Smela

state: MA

address: 3 Blackfan Circle

institute: Harvard University

description: Three differentiating hiPSC lines, sampled every 24 hours from days 0 to 15, inclusive (48 samples total). Cells were pooled and split into 8 sublibraries for sequencing. Sample barcode wells are given in the file: sample_wells.txt Software to process the raw data is available from Parse Biosciences (Parse pipeline version 1.2.1).

data_processing:
Parse Biosciences pipeline, version 1.2.1
During read alignment with STAR, --outFilterScoreMinOverLread and outFilterMatchNminOverLread were set to 0.25
After processing the sublibraries individually, output was combined using the Parse Biosciences pipeline, version 1.2.1, in mode "--combine"
Assembly: GrCh38 v110 plus transgene sequences (BCL2, MEIOC, HOXB5, BOLL, mGreenLantern, tdTomato, TET3G-P2A-Puro)
Supplementary files format and content: all_genes.csv.gz: list of genes (column information for the count matrix)
Supplementary files format and content: cell_metadata.csv.gz: list of cells with associated sample information (row information for the count matrix)
Supplementary files format and content: count_matrix.mtx.gz: count matrix

molecule: polyA RNA

source_name: F2, F3, and PGP1

growth_protocol: Plasmids for constitutive expression of BCL2 and doxycycline-inducible expression of HOXB5, BOLL, and MEIOC were integrated into F2 D4TDZG, F3 D4TT2G, and PGP1 D4TR8G reporter hiPSCs. The iPSCs were seeded at 50,000 cells/cm2 on Matrigel-coated plates in mTeSR1 supplemented with 5 µM GSK3484862, 1 µg/mL doxycycline, and 10 µM Y-27632. For 6-well plates, 1.5 mL of medium was used per well. After one day, the media was replaced with APEL2 containing 5 µM GSK3484862 and 1 µg/mL doxycycline. A 50% media change was performed every 2 days, and GSK3484862 was withdrawn starting on day 7. At each day from day 0 (hiPSC) to day 15, cells were harvested for scRNAseq. Samples for scRNAseq were counted and fixed using the Parse Biosciences fixation kit. Library preparation was performed using the Parse Biosciences WT v3 kit. Sequencing was performed on two lanes of a Novaseq X Plus 25B PE150 flowcell.

extract_protocol: Parse WT v3 kit

treatment_protocol: Cells were fixed using the Parse Biosciences fixation kit and stored at -80°C prior to sequencing

tag: cell line

value: F2, F3, and PGP1

value: Differentiating hiPSCs and meiotic cells

value: meiosis differentiation, days 0 to 15


title: P34-CP3-H02_S86_L003


title: Synechococcus cells, kaiABC knock-out, 8 cycles LD16:8, replicate 2


title: P34-CP3-D11_S47_L003


title: P34-CP3-G10_S82_L001


title: P34-CP3-F07_S67_L001


title: Synechococcus cells, kaiABC knock-out, 4 cycles LD16:8, replicate 3

value: 4 cycles of LD16:8


title: Synechococcus cells, kaiABC knock-out, 8 cycles LD16:8, replicate 1


title: P34-CP3-C12_S36_L002


title: Synechococcus cells, kaiABC knock-out, 4 cycles LD16:8, replicate 2


title: Synechococcus cells, kaiABC knock-out, 4 cycles LD16:8, replicate 1


title: P34-CP3-G02_S74_L002


title: P34-CP3-E09_S57_L003


title: P34-CP3-E12_S60_L004


title: Synechococcus cells, kaiABC knock-out, 1 cycle LD16:8, replicate 2

value: 1 cycle of LD16:8


title: P34-CP3-E09_S57_L001


title: P34-CP3-B11_S23_L004


title: P34-CP3-C03_S27_L001


title: Synechococcus cells, kaiABC knock-out, 1 cycle LD16:8, replicate 1


title: Synechococcus cells, kaiABC knock-out, 8 cycles LD8:16, replicate 2


title: Synechococcus cells, kaiABC knock-out, 8 cycles LD8:16, replicate 3


title: Synechococcus cells, kaiABC knock-out, 8 cycles LD8:16, replicate 1


title: P34-CP3-A09_S9_L001


title: P34-CP3-D03_S39_L002


title: Synechococcus cells, kaiABC knock-out, 4 cycles LD8:16, replicate 3

value: 4 cycles of LD8:16


title: P34-CP3-H05_S89_L004


title: Synechococcus cells, kaiABC knock-out, 1 cycle LD16:8, replicate 3


title: P34-CP3-D04_S40_L002


title: Synechococcus cells, kaiABC knock-out, 4 cycles LD8:16, replicate 2


title: Synechococcus cells, kaiABC knock-out, 4 cycles LD8:16, replicate 1


title: P34-CP3-C01_S25_L004


title: Synechococcus cells, kaiABC knock-out, 1 cycle LD8:16, replicate 2

value: 1 cycle of LD8:16


title: P34-CP3-D07_S43_L003


title: Synechococcus cells, kaiABC knock-out, 1 cycle LD8:16, replicate 3


title: P34-CP3-B01_S13_L001


title: P34-CP3-D12_S48_L004


title: Synechococcus cells, wild-type, 8 cycles LD16:8, replicate 3

value: wild-type


title: P34-CP3-H04_S88_L002


title: Synechococcus cells, kaiABC knock-out, 1 cycle LD8:16, replicate 1


title: Synechococcus cells, wild-type, 8 cycles LD16:8, replicate 2


title: P34-CP3-F10_S70_L001


title: Synechococcus cells, wild-type, 8 cycles LD16:8, replicate 1


title: Synechococcus cells, wild-type, 4 cycles LD16:8, replicate 2


title: Synechococcus cells, wild-type, 4 cycles LD16:8, replicate 3


title: P34-CP3-D05_S41_L002


title: P34-CP3-F10_S70_L003


title: P34-CP3-C02_S26_L002


title: Synechococcus cells, wild-type, 4 cycles LD16:8, replicate 1


title: P34-CP3-H12_S96_L002


title: Synechococcus cells, wild-type, 1 cycle LD16:8, replicate 3


title: Synechococcus cells, wild-type, 1 cycle LD16:8, replicate 2


title: P34-CP3-C08_S32_L001


title: P34-CP3-D09_S45_L002


title: Synechococcus cells, wild-type, 8 cycles LD8:16, replicate 3


title: P34-CP3-E05_S53_L004


title: P34-CP3-H02_S86_L002


title: Synechococcus cells, wild-type, 8 cycles LD8:16, replicate 2


title: P34-CP3-G06_S78_L002


title: P34-CP3-F06_S66_L001


title: Synechococcus cells, wild-type, 4 cycles LD8:16, replicate 3


title: Synechococcus cells, wild-type, 4 cycles LD8:16, replicate 2


title: P34-CP3-G04_S76_L003


title: P34-CP3-A04_S4_L002


title: P34-CP3-C06_S30_L002


title: P34-CP3-D03_S39_L003


title: Synechococcus cells, wild-type, 1 cycle LD8:16, replicate 3


title: P34-CP3-G01_S73_L003


title: Synechococcus cells, wild-type, 4 cycles LD8:16, replicate 1


title: Synechococcus cells, wild-type, 1 cycle LD8:16, replicate 2


title: P34-CP3-A04_S4_L004


title: Synechococcus cells, wild-type, 1 cycle LD8:16, replicate 1


title: P34-CP3-G12_S84_L002


title: P34-CP3-G04_S76_L002


title: P34-CP3-C07_S31_L003


title: P34-CP3-B05_S17_L003


title: A2AM28

type: protein

city: Bronx

first: Jacqueline

last: Achkar

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description:
IgG
D01

hyb_protocol: Arrays were blocked with 3% BSA overnight, and diluted samples was incubated on the array for 4 hours at 37 C and gentle agitation (100 RPM).  Slides were then washed with PBS contain 0.05% Tween (PBST).  After washing, bound antibodies were detected by Alexa 647-labeled goat anti-human IgG (Jackson Immunoresearch). Slides were then washed with PBST, spun dry in a centrifuge, and scanned.

scan_protocol: The GenePix 4000 Microarray scanner system (Molecular Devices, CA) was used for scanning.

data_processing: We analyzed images using GenePix Pro 7.3.0.0 to measure median pixel intensity (MPI) and neighboring background pixel intensity (BPI) of individual spots. The median fluorescence intensity (MFI), representing AM-epitope specific reactivity, was calculated using the MPI minus the BPI and averaged from the triplicate spots. A minimun value was set at 100.

label: Alexa 647

molecule: protein

source_name: monoclonal antibody

label_protocol: Alexa 647

extract_protocol: MAb expressed in HEK293 cell

treatment_protocol: 5 ug/ml

tag: sample type

value: Antibody


title: Synechococcus cells, wild-type, 1 cycle LD16:8, replicate 1


title: P34-CP3-F09_S69_L002


title: P34-CP3-D03_S39_L001


title: Synechococcus cells, wild-type, 8 cycles LD8:16, replicate 1


title: P34-CP3-B02_S14_L004


title: A2AM10

description:
IgG
D01


title: A1AM16

description:
IgG
B07


title: T2AM15

description:
IgG
B07


title: P34-CP3-G02_S74_L004


title: P34-CP3-F09_S69_L004


title: A2AM30

description:
IgG
D01


title: T2AM11

description:
IgG
B07


title: P34-CP3-F12_S72_L004


title: A1AM23

description:
IgG
B07


title: P34-CP3-E02_S50_L001


title: P34-CP3-E11_S59_L004


title: A2AM08

description:
IgG
D01


title: IT25_OS56dpl repeat

description:
IGRA+ OS56 depletion
IgG

source_name: Plasma

extract_protocol: Plasma was obtained from peripheral blood samples

treatment_protocol: Diluted 1:100

tag: infection states

value: Asymptomatic controlled Mtb infection


title: P34-CP3-F03_S63_L001

value: PBMC


title: A2AM31

description:
IgG
D01


title: IT219_OS56dpl

description:
Active TB OS56 depletion
IgG

value: Symptomatic Mtb infection


title: IT219_OS9dpl

description:
Active TB OS9 depletion
IgG


title: P34-CP3-F03_S63_L002

value: T-cells

value: overlapping pipette pool targeting ESAT6/CFP10 of M.tuberculosis


title: IT219_OS1dpl

description:
Active TB OS1 depletion
IgG


title: P34-CP3-C03_S27_L004


title: P34-CP3-H05_S89_L002


title: IT25_Biodpl repleat

description:
IGRA+ Biotin depletion
IgG


title: IT219_OS6dpl

description:
Active TB OS6 depletion
IgG


title: P34-CP3-D07_S43_L002


title: P34-CP3-H06_S90_L004


title: IT219_Biodpl

description:
Active TB Biotin depletion
IgG


title: P34-CP3-C10_S34_L003


title: P34-CP3-G11_S83_L001


title: IT173_OS56dpl

description:
Active TB OS56 depletion
IgG


title: IT173_OS9dpl

description:
Active TB OS9 depletion
IgG


title: T1AM65

description:
IgG
B09


title: P34-CP3-D01_S37_L004


title: P34-CP3-A06_S6_L004


title: P34-CP3-D08_S44_L002


title: T2AM02

description:
IgG
B07


title: P34-CP3-F09_S69_L003


title: IT173_OS6dpl

description:
Active TB OS6 depletion
IgG


title: IT173_Biodpl

description:
Active TB Biotin depletion
IgG


title: P34-CP3-H08_S92_L001


title: P34-CP3-G03_S75_L002


title: IT105_OS56dpl

description:
Active TB OS56 depletion
IgG


title: IT105_OS9dpl

description:
Active TB OS9 depletion
IgG


title: P34-CP3-B10_S22_L004


title: P34-CP3-E01_S49_L004


title: IT105_OS6dpl

description:
Active TB OS6 depletion
IgG


title: P34-CP3-C05_S29_L003


title: P34-CP3-H12_S96_L004


title: IT105_OS1dpl

description:
Active TB OS1 depletion
IgG


title: P34-CP3-H06_S90_L002


title: IT105_Biodpl

description:
Active TB Biotin depletion
IgG


title: P34-CP3-E10_S58_L002


title: P34-CP3-E07_S55_L001


title: P34-CP3-F08_S68_L002


title: IT61_OS56dpl

description:
Active TB OS56 depletion
IgG


title: P34-CP3-B02_S14_L001


title: IT173_OS1dpl

description:
Active TB OS1 depletion
IgG


title: IT61_OS1dpl

description:
Active TB OS1 depletion
IgG


title: IT61_OS6dpl

description:
Active TB OS6 depletion
IgG


title: P34-CP3-H03_S87_L002


title: IT61_OS9dpl

description:
Active TB OS9 depletion
IgG


title: IT58_OS56dpl

description:
Active TB OS56 depletion
IgG


title: P34-CP3-A09_S9_L003


title: P34-CP3-C04_S28_L002


title: IT58_OS6dpl

description:
Active TB OS6 depletion
IgG


title: P34-CP3-B01_S13_L003


title: IT58_Biodpl

description:
Active TB Biotin depletion
IgG


title: P34-CP3-D12_S48_L002


title: IT58_OS1dpl

description:
Active TB OS1 depletion
IgG


title: P34-CP3-G01_S73_L002


title: IT41_OS56dpl

description:
Active TB OS56 depletion
IgG


title: P34-CP3-F04_S64_L004


title: P34-CP3-E05_S53_L002


title: IT41_OS1dpl

description:
Active TB OS1 depletion
IgG


title: IT41_OS9dpl

description:
Active TB OS9 depletion
IgG


title: P34-CP3-D01_S37_L003


title: IT41_Biodpl

description:
Active TB Biotin depletion
IgG


title: IT41_OS6dpl

description:
Active TB OS6 depletion
IgG


title: IT61_Biodpl

description:
Active TB Biotin depletion
IgG


title: P34-CP3-C09_S33_L004


title: P34-CP3-G04_S76_L001


title: P34-CP3-C12_S36_L004


title: IT215_OS56dpl

description:
IGRA+ OS56 depletion
IgG


title: P34-CP3-F12_S72_L003


title: IT58_OS9dpl

description:
Active TB OS9 depletion
IgG


title: IT215_OS9dpl

description:
IGRA+ OS9 depletion
IgG


title: P34-CP3-A03_S3_L001


title: IT215_OS6dpl

description:
IGRA+ OS6 depletion
IgG


title: IT215_Biodpl

description:
IGRA+ Biotin depletion
IgG


title: IT175_OS9dpl

description:
IGRA+ OS9 depletion
IgG


title: IT215_OS1dpl

description:
IGRA+ OS1 depletion
IgG


title: IT175_OS56dpl

description:
IGRA+ OS56 depletion
IgG


title: P34-CP3-H08_S92_L002


title: P34-CP3-C10_S34_L002


title: P34-CP3-A05_S5_L002


title: IT175_OS1dpl

description:
IGRA+ OS1 depletion
IgG


title: P34-CP3-H11_S95_L003


title: IT175_Biodpl

description:
IGRA+ Biotin depletion
IgG


title: P34-CP3-G06_S78_L004


title: P34-CP3-H11_S95_L002


title: IT175_OS6dpl

description:
IGRA+ OS6 depletion
IgG


title: IT107_OS9dpl

description:
IGRA+ OS9 depletion
IgG


title: P34-CP3-G01_S73_L004


title: P34-CP3-G02_S74_L003


title: IT107_OS1dpl

description:
IGRA+ OS1 depletion
IgG


title: IT107_OS6dpl

description:
IGRA+ OS6 depletion
IgG


title: P34-CP3-H05_S89_L001


title: IT107_Biodpl

description:
IGRA+ Biotin depletion
IgG


title: IT48_OS56dpl

description:
IGRA+ OS56 depletion
IgG


title: P34-CP3-D12_S48_L003


title: IT48_OS9dpl

description:
IGRA+ OS9 depletion
IgG


title: P34-CP3-A01_S1_L002


title: P34-CP3-D02_S38_L004


title: IT48_OS6dpl

description:
IGRA+ OS6 depletion
IgG


title: P34-CP3-B12_S24_L004


title: P34-CP3-A12_S12_L001


title: P34-CP3-E04_S52_L004


title: IT48_OS1dpl

description:
IGRA+ OS1 depletion
IgG


title: P34-CP3-B10_S22_L003


title: P34-CP3-F11_S71_L003


title: IT107_OS56dpl

description:
IGRA+ OS56 depletion
IgG


title: IT48_Biodpl

description:
IGRA+ Biotin depletion
IgG


title: P34-CP3-E04_S52_L002


title: IT39_OS9dpl

description:
IGRA+ OS9 depletion
IgG


title: IT39_OS6dpl

description:
IGRA+ OS6 depletion
IgG


title: IT39_OS56dpl

description:
IGRA+ OS56 depletion
IgG


title: P34-CP3-F06_S66_L004


title: P34-CP3-D02_S38_L002


title: IT39_OS1dpl

description:
IGRA+ OS1 depletion
IgG


title: IT39_Biodpl

description:
IGRA+ Biotin depletion
IgG


title: IT207_OS56dpl

description:
IGRA- OS56 depletion
IgG


title: P34-CP3-D09_S45_L003


title: P34-CP3-D04_S40_L001


title: IT207_OS9dpl

description:
IGRA- OS9 depletion
IgG


title: P34-CP3-B04_S16_L003


title: IT207_OS6dpl

description:
IGRA- OS6 depletion
IgG


title: IT207_OS1dpl

description:
IGRA- OS1 depletion
IgG


title: P34-CP3-C08_S32_L003


title: IT207_Biodpl

description:
IGRA- Biotin depletion
IgG


title: P34-CP3-E03_S51_L004


title: P34-CP3-H08_S92_L004


title: P34-CP3-C02_S26_L004


title: IT25_OS9dpl

description:
IGRA+ OS9 depletion
IgG


title: P34-CP3-C09_S33_L002


title: P34-CP3-C10_S34_L004


title: IT25_Biodpl

description:
IGRA+ Biotin depletion
IgG


title: IT25_OS1dpl

description:
IGRA+ OS1 depletion
IgG


title: P34-CP3-G09_S81_L004


title: P34-CP3-A02_S2_L004


title: IT18_OS56dpl

description:
IGRA+ OS56 depletion
IgG


title: P34-CP3-B08_S20_L002


title: P34-CP3-E04_S52_L003


title: P34-CP3-F07_S67_L002


title: IT18_OS9dpl

description:
IGRA+ OS9 depletion
IgG


title: IT18_OS1dpl

description:
IGRA+ OS1 depletion
IgG


title: P34-CP3-C05_S29_L001


title: IT02_OS9dpl

description:
IGRA+ OS9 depletion
IgG


title: P34-CP3-E09_S57_L004


title: IT18_Biodpl

description:
IGRA+ Biotin depletion
IgG


title: IT02_OS56dpl

description:
IGRA+ OS56 depletion
IgG


title: IT25_OS56dpl

description:
IGRA+ OS56 depletion
IgG


title: P34-CP3-C04_S28_L004


title: IT02_OS6dpl

description:
IGRA+ OS6 depletion
IgG


title: P34-CP3-B11_S23_L003


title: IT02_OS1dpl

description:
IGRA+ OS1 depletion
IgG


title: IT25_OS6dpl

description:
IGRA+ OS6 depletion
IgG


title: P34-CP3-D04_S40_L004


title: IT02_Biodpl

description:
IGRA+ Biotin depletion
IgG


title: P34-CP3-D10_S46_L002


title: IT86_OS56dpl

description:
IGRA- OS56 depletion
IgG


title: IT18_OS6dpl

description:
IGRA+ OS6 depletion
IgG


title: IT86_OS6dpl

description:
IGRA- OS6 depletion
IgG


title: IT86_OS9dpl

description:
IGRA- OS9 depletion
IgG


title: P34-CP3-E09_S57_L002


title: P34-CP3-C11_S35_L001


title: P34-CP3-F04_S64_L003


title: P34-CP3-C11_S35_L003


title: P34-CP3-C11_S35_L004


title: IT86_OS1dpl

description:
IGRA- OS1 depletion
IgG


title: P34-CP3-E03_S51_L002


title: IT86_Biodpl

description:
IGRA- Biotin depletion
IgG


title: IT43_OS9dpl

description:
IGRA- OS9 depletion
IgG


title: P34-CP3-A02_S2_L002


title: P34-CP3-C07_S31_L004


title: IT43_OS56dpl

description:
IGRA- OS56 depletion
IgG


title: P34-CP3-F06_S66_L003


title: P34-CP3-A07_S7_L001


title: P34-CP3-F05_S65_L002


title: IT43_Biodpl

description:
IGRA- Biotin depletion
IgG


title: IT43_OS6dpl

description:
IGRA- OS6 depletion
IgG


title: IT43_OS1dpl

description:
IGRA- OS1 depletion
IgG


title: P34-CP3-D05_S41_L004


title: IT12_OS56dpl

description:
IGRA- OS56 depletion
IgG


title: P34-CP3-A06_S6_L002


title: P34-CP3-F11_S71_L004


title: IT12_OS6dpl

description:
IGRA- OS6 depletion
IgG


title: IT12_Biodpl

description:
IGRA- Biotin depletion
IgG


title: IT12_OS1dpl

description:
IGRA- OS1 depletion
IgG


title: P34-CP3-C06_S30_L001


title: IT11_OS56dpl

description:
IGRA- OS56 depletion
IgG


title: P34-CP3-H04_S88_L003


title: P34-CP3-A08_S8_L003


title: P34-CP3-B07_S19_L001


title: IT11_OS6dpl

description:
IGRA- OS6 depletion
IgG


title: P34-CP3-A02_S2_L001


title: IT11_OS9dpl

description:
IGRA- OS9 depletion
IgG


title: IT11_Biodpl

description:
IGRA- Biotin depletion
IgG


title: IT08_OS56dpl

description:
IGRA- OS56 depletion
IgG


title: IT11_OS1dpl

description:
IGRA- OS1 depletion
IgG


title: IT12_OS9dpl

description:
IGRA- OS9 depletion
IgG


title: P34-CP3-B12_S24_L001


title: P34-CP3-G07_S79_L002


title: P34-CP3-H09_S93_L004


title: IT08_Biodpl

description:
IGRA- Biotin depletion
IgG


title: P34-CP3-F08_S68_L004


title: IT08_OS6dpl

description:
IGRA- OS6 depletion
IgG


title: P34-CP3-E11_S59_L003


title: P34-CP3-E08_S56_L004


title: P34-CP3-C07_S31_L001


title: IT08_OS1dpl

description:
IGRA- OS1 depletion
IgG


title: G10_S82_L001


title: IT05_OS56dpl

description:
IGRA- OS56 depletion
IgG


title: F01_S61_L004


title: F01_S61_L003


title: F01_S61_L002


title: IT05_OS9dpl

description:
IGRA- OS9 depletion
IgG


title: IT05_OS6dpl

description:
IGRA- OS6 depletion
IgG


title: IT08_OS9dpl

description:
IGRA- OS9 depletion
IgG


title: IT05_OS1dpl

description:
IGRA- OS1 depletion
IgG


title: D09_S45_L004


title: IT05_Biodpl

description:
IGRA- Biotin depletion
IgG


title: D09_S45_L003


title: D09_S45_L001


title: NSCLC,total,pacbio,rep2

city: Ipswich

first: Zhiyi

state: MASSACHUSETTS

address: 240 County Road

department: Research

institute: New England Biolabs

data_processing:
PacBio consensus reads were generated using the SMRT tools (version 10.2.0.133434). Raw nanopore data were basecalled in high accuracy mode with Dorado 7.0.9 and filtered by average quality (≥ 7).
Sequencing reads in FASTQ format from either PacBio or Nanopore were first mapped to the rDNA reference sequences using minimap2 and the unmapped reads were kept for downstream circRNA analysis.
Then circular consensus sequences and candidate circRNAs were identified using the CIRI-long bioinformatics pipeline. We applied an additional filter to remove consensus sequences that were called from any read that contains fewer than 2 copies of repeat sequences. Candidate circRNA sequences were identified based on the GRCh38 reference genome sequence and annotation. Then all candidate circRNA sequences from the subsets were aggregated together using the CIRI-long collapse program to determine BSJ sites and calculate the relative isoform usage index of each BSJ.
Finally, for each BSJ, the read counts of its isoforms were calculated from the isoform usage index (*collapse.isoforms file) and the total read counts of that BSJ as isoform expression = isoform usage index * BSJ read counts.
Assembly: GRCh38/hg38
Supplementary files format and content: Tabular data file with circRNA isoform counts
Library strategy: Induro-RT mediated circRNA-sequencing (IMCR-seq)

source_name: lung tumor

extract_protocol:
NEB Monarch Total RNA Miniprep Kit was used for home made HEK293 cell RNA, guanidine thiocyanate tecnniques were reported to be used for commercially obtained RNA and Quick-cfRNA Serum & Plasma Kit from Zymo Research was used for RNA extraction from plasma
Total RNA or rRNA depleted, RNaseR treated RNA were reverse transcribed with a group II intron RT then the cDNAs were sized selected with SPRI beads. Second strand synthesis and amplification were done with Phi29 DNA polymerase. T7 endonuclease I was used to digest the branched DNA into double stranded DNA and ONT and PacBio library preparation kits for dsDNA were used to make libraries for sequencing.

value: lung tumor


title: NSCLC,total,pacbio,rep3


title: NSCLC,total,pacbio,rep1


title: HEK293,RNaseR,pacbio,rep2

library_source: other

molecule: other


title: healthy plasma, total,pacbio

source_name: plasma

value: plasma


title: D09_S45_L002


title: D01_S37_L004


title: D01_S37_L003


title: HEK293,RNaseR,pacbio,rep1


title: HEK293,total,pacbio,rep3


title: G10_S82_L002


title: D01_S37_L001


title: nsclc plasma, total, pacbio


title: D01_S37_L002


title: HEK293,total,pacbio,rep1


title: A08_S8_L004


title: HEK293,total,pacbio,rep2


title: A08_S8_L003


title: F01_S61_L001


title: brain,RNaseR,pacbio,rep3

source_name: brain

value: brain


title: A08_S8_L001


title: A07_S7_L004


title: A08_S8_L002


title: HEK293,RNaseR,pacbio,rep3


title: brain,total,pacbio,rep3


title: brain,RNaseR,pacbio,rep1


title: brain,total,pacbio,rep2


title: brain,RNaseR,pacbio,rep2


title: A07_S7_L001


title: A07_S7_L002


title: A07_S7_L003


title: Amyloid Body ePAT 28S-1

city: Miami

first: Stephen

last: Lee

state: FL

department: Biochemistry & Molecular Biology

institute: University of Miami

data_processing:
For tail analysis, reverse primers were removed using Cutadapt for both forward and reverse sequences.
Grep was used to select sequences containing 28S rRNA sequence which contained A instead of 28S sequence indicating start of tailing.
This sequences as well as sequence from before this sequence was removed to isolate tails using grep commands. Sequences and reverse adpater primer sequence within tail were also removed to isolate pure tails. Awk and Grep functions were used to analyze tail length and nucleotide composition.
Supplementary files format and content: Text file containing ePAT products from 28S-3' end.
Supplementary files format and content: Text file containing isolated tails from ePAT product
Library strategy: Epat

source_name: Breast

growth_protocol: Cells were propagated in Dulbecco’s Modified Eagle Media (DMEM) (HyClone) with 10% fetal bovine serum (Omega Scientific) and 1% penicillin–streptomycin (HyClone).

extract_protocol:
Amyloid-bodies were purified and then RNA was extracted using TRIzol.
1ug of RNA and 1uL of Reverse-ePAT anchored (100uM) primer were heated at 80°C for 5 min. Samples were cooled to room temperature, incubated with 4uL dH2O. 4uL SuperScript IV Reverse Transcriptase Buffer (Life Technologies), 1uL 100mM DTT, 1uL 10mM dTNPs, 1ul RNaseOUT (Life Technologies) 1uL Klenow polymerase (NEB). Samples were incubated at 25°C for 1 hr. Polymerase was then inactivated at 80°C for 10 min, followed by cooling to 55°C for 1 min. Heating block was maintained at 55°C and 1uL of  SuperScript IV was added and incubated for 1 hr then inactivated at 80°C for 10min. ePAT reactions, ePAT reactions were done with Barcoded Reverse-ePAT anchored primer and PCR amplified with Barcoded forward and reverse primers. Reactions were PCR cleaned using NEB PCR purification kit. Samples were prepared for Pacbio sequencing (SMRTbell Template Prep Kit)
ePAT followed by PacBio sequencing

treatment_protocol: Cells were maintained at 37 °C in a 5% CO2 humidified incubator (Unstressed). Cells were subjected to heat shock by translocation to a 5% CO2 humidified incubator at 43°C for indicated times.

value: Breast

value: Adenocarcinoma

value: Heat Shocked (43deg for 1hr.)


title: brain,total,pacbio,rep1


title: Amyloid-bodies Rep2

description:
All three replicates for each unstresssed and stressed were pooled into one processed file from each peak of interest respectively.  Then another processed file was  generated containing isolated corrresponding tails
HS

data_processing:
FLAM-seq processing pipeline using default settings. https://github.com/rajewsky-lab/FLAMAnalysis
Reads were aligned to GRCh38.primary_assembly and GL000220.1 was visualized using IGV.
To analyze tails of rRNA sequence, peaks within GL000220.1 were chosen to be searched manually. Both forward and reverse complement sequences were searched and oriented so that tails began with As
Reads from within each peak were trimmed to remove GI tailed sequence using Sed command. Awk command was used to remove sequences before AAAAA, indicating tailing. Reads were inspected to ensure no genomic sequence was retained.
As a final cleaning step, reads still containing initial genomic sequence searched were removed. Awk and Grep commands were used to analyze tail length and nucleotide composition.
Assembly: GRCh38.primary_assembly.genome.fa
Supplementary files format and content: Text file containing reads aligning to respective peaks in GL00220.1 from untreated (UN) and heat shocked (HS) samples pooled together.  DNA sequence of file name corresponds to rDNA sequence.
Supplementary files format and content: Text file containing corresponding tails from respective rRNA reads in untreated (UN) and heat shocked (HS) samples pooled together.  DNA sequence of file name corresponds to rDNA sequence for peaks called.
Library strategy: FLAM-seq

extract_protocol:
Nucleoli and Amyloid-bodies were purified and then RNA was extracted using TRIzol.
Poly(A)-RNA was selected (Illumina Truseq mRNA preparation kit), followed by GI tailing (USB poly(A) tail length assay, Thermo Fisher), cDNA synthesis (SMARTscribe). Samples were barcoded and prepared using Pacbio sequencing (SMRTbell Template Prep Kit).


title: Amyloid-bodies Rep1


title: Amyloid-bodies Rep3


title: A05_S5_L001


title: A05_S5_L004


title: Nucleoli -Rep3

description:
All three replicates for each unstresssed and stressed were pooled into one processed file from each peak of interest respectively.  Then another processed file was  generated containing isolated corrresponding tails
UN

value: Unstressed (37deg)


title: H12_S96_L004


title: Nucleoli -Rep1


title: Nucleoli -Rep2


title: H12_S96_L001


title: H12_S96_L003


title: H12_S96_L002


title: A05_S5_L002


title: A05_S5_L003


title: H02_S86_L004


title: H02_S86_L003


title: H02_S86_L002


title: H02_S86_L001


title: G01_S73_L004


title: G01_S73_L002


title: G01_S73_L001


title: E05_S53_L004


title: E05_S53_L003


title: clean air (vehicle) replicate 4, GFP+ cells from 3 mice

type: RNA

city: Lexington

first: Tim

last: McClintock

state: KY

address: 780 Rose St.

department: Physiology

institute: University of Kentucky

description: mRNA abundance data

hyb_protocol: after fragmentation cRNA was hybridized for 16 hr at 45C on Clariom S Arrays. These were washed and stained in an Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix GCS3000 7G Scanner

data_processing: The data were analyzed with Affymetrix Gene Expression Console software using default analysis settings and global scaling as normalization method.

label: biotin

organism: Mus musculus

source_name: Olfactory mucosa; Vehicle-stimulated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 50 - 100 ng of total RNA.

growth_protocol: 24 mice of both sexes, ages 7 - 12 weeks, were placed individuallly in clean air chambers for 40 hrs under air flow of 3.1L/min

extract_protocol: Mice were euthanized, olfactory mucosa were dissected, dissociated, and subjected to FACS.

treatment_protocol: After 26 hrs, the mice were intermittently stimulated with vehicle (filtered air) or odorant for 10 sec every 20 min.

tag: strain

value: S100a5-tauGFP mice

value: Olfactory mucosa

value: FACS sample, GFP+

value: exposed to clean air (vehicle)


title: E05_S53_L002


title: E05_S53_L001


title: D10_S46_L004


title: clean air (vehicle) replicate 4, GFP- cells from 3 mice

description: mRNA abundance data

value: FACS sample, GFP-


title: D10_S46_L002


title: clean air (vehicle) replicate 3, GFP- cells from 3 mice

description: mRNA abundance data


title: clean air (vehicle) replicate 3, GFP+ cells from 3 mice

description: mRNA abundance data


title: 2-pentanone-stimulated, Odor replicate 3, GFP+ cells from 3 mice

description: mRNA abundance data

value: exposed to odor 2-pentanone


title: clean air (vehicle) replicate 1, GFP+ cells from 3 mice

description: mRNA abundance data


title: clean air (vehicle) replicate 1, GFP- cells from 3 mice

description: mRNA abundance data


title: 2-pentanone-stimulated, Odor replicate 3, GFP- cells from 3 mice

description: mRNA abundance data


title: 2-pentanone-stimulated, Odor replicate 2, GFP- cells from 3 mice

description: mRNA abundance data


title: D10_S46_L001

value: PBMC


title: G01_S73_L003


title: clean air (vehicle) replicate 2, GFP- cells from 3 mice

description: mRNA abundance data


title: 2-pentanone-stimulated, Odor replicate 4, GFP- cells from 3 mice

description: mRNA abundance data


title: 2-pentanone-stimulated, Odor replicate 4, GFP+ cells from 3 mice

description: mRNA abundance data


title: clean air (vehicle) replicate 2, GFP+cells from 3 mice

description: mRNA abundance data


title: 2-pentanone-stimulated, Odor replicate 2, GFP+ cells from 3 mice

description: mRNA abundance data


title: 2-pentanone-stimulated, Odor replicate 1, GFP- cells from 3 mice

description: mRNA abundance data


title: 2-pentanone-stimulated, Odor replicate 1, GFP+ cells from 3 mice

description: mRNA abundance data


title: B11_S23_L003


title: B11_S23_L002


title: D10_S46_L003


title: B11_S23_L001


title: B01_S13_L004


title: Vehicle replicate 4, GFP- cells from 3 mice (pentanol)

description: mRNA abundance data


title: Vehicle replicate 4, GFP+ cells from 3 mice (pentanol)

description: mRNA abundance data


title: Vehicle replicate 3, GFP- cells from 3 mice (pentanol)

description: mRNA abundance data


title: B01_S13_L003


title: B11_S23_L004


title: Vehicle replicate 2, GFP- cells from 3 mice (pentanol)

description: mRNA abundance data


title: B01_S13_L002


title: B01_S13_L001


title: A06_S6_L002


title: Vehicle replicate 1, GFP- cells from 3 mice (pentanol)

description: mRNA abundance data


title: A06_S6_L004


title: A06_S6_L001


title: Vehicle replicate 1, GFP+ cells from 3 mice (pentanol)

description: mRNA abundance data


title: A06_S6_L003


title: Odor replicate 4, GFP- cells from 3 mice (pentanol)

description: mRNA abundance data

source_name: Olfactory mucosa; pentanol-stimulated


title: G03_S75_L003


title: G03_S75_L002


title: Vehicle replicate 3, GFP+ cells from 3 mice (pentanol)

description: mRNA abundance data


title: F11_S71_L004


title: G03_S75_L004


title: F11_S71_L003


title: Odor replicate 2, GFP+ cells from 3 mice (pentanol)

description: mRNA abundance data


title: F11_S71_L002


title: F11_S71_L001


title: Vehicle replicate 2, GFP+cells from 3 mice (pentanol)

description: mRNA abundance data


title: Odor replicate 3, GFP+ cells from 3 mice (pentanol)

description: mRNA abundance data


title: Vehicle replicate 3, GFP+ cells from 3 mice (pentanoic)

description: mRNA abundance data


title: Vehicle replicate 4, GFP- cells from 3 mice (pentanoic)

description: mRNA abundance data


title: F10_S70_L004


title: Vehicle replicate 3, GFP- cells from 3 mice (pentanoic)

description: mRNA abundance data


title: Vehicle replicate 2, GFP- cells from 3 mice (pentanoic)

description: mRNA abundance data


title: Vehicle replicate 4, GFP+ cells from 3 mice (pentanoic)

description: mRNA abundance data


title: G03_S75_L001


title: F10_S70_L002


title: Odor replicate 2, GFP- cells from 3 mice (pentanol)

description: mRNA abundance data


title: Odor replicate 4, GFP+ cells from 3 mice (pentanol)

description: mRNA abundance data


title: Odor replicate 1, GFP+ cells from 3 mice (pentanol)

description: mRNA abundance data


title: Odor replicate 1, GFP- cells from 3 mice (pentanol)

description: mRNA abundance data


title: Odor replicate 3, GFP- cells from 3 mice (pentanol)

description: mRNA abundance data


title: F10_S70_L001


title: Vehicle replicate 1, GFP- cells from 3 mice (pentanoic)

description: mRNA abundance data


title: Vehicle replicate 1, GFP+ cells from 3 mice (pentanoic)

description: mRNA abundance data


title: Vehicle replicate 2, GFP+cells from 3 mice (pentanoic)

description: mRNA abundance data


title: Odor replicate 4, GFP- cells from 3 mice (pentanoic)

description: mRNA abundance data

source_name: Olfactory mucosa; pentanoic acid-stimulated


title: F04_S64_L003


title: F04_S64_L004


title: F04_S64_L002


title: Odor replicate 3, GFP- cells from 3 mice (pentanoic)

description: mRNA abundance data


title: F10_S70_L003


title: F04_S64_L001


title: E09_S57_L004


title: E09_S57_L003


title: Odor replicate 3, GFP+ cells from 3 mice (pentanoic)

description: mRNA abundance data


title: E09_S57_L001


title: E09_S57_L002


title: D12_S48_L004


title: Odor replicate 4, GFP+ cells from 3 mice (pentanoic)

description: mRNA abundance data


title: Odor replicate 2, GFP- cells from 3 mice (pentanoic)

description: mRNA abundance data


title: Odor replicate 2, GFP+ cells from 3 mice (pentanoic)

description: mRNA abundance data


title: Odor replicate 1, GFP- cells from 3 mice (pentanoic)

description: mRNA abundance data


title: D12_S48_L001


title: C10_S34_L004


title: C10_S34_L003


title: Vehicle replicate 4, GFP- cells from 3 mice (octanol)

description: mRNA abundance data


title: Vehicle replicate 4, GFP+ cells from 3 mice (octanol)

description: mRNA abundance data


title: C10_S34_L002


title: Vehicle replicate 3, GFP- cells from 3 mice (octanol)

description: mRNA abundance data


title: B05_S17_L004


title: Vehicle replicate 2, GFP+cells from 3 mice (octanol)

description: mRNA abundance data


title: Vehicle replicate 3, GFP+ cells from 3 mice (octanol)

description: mRNA abundance data


title: Vehicle replicate 2, GFP- cells from 3 mice (octanol)

description: mRNA abundance data


title: C10_S34_L001


title: D12_S48_L002


title: B05_S17_L002


title: B05_S17_L001


title: D12_S48_L003


title: Vehicle replicate 1, GFP+ cells from 3 mice (octanol)

description: mRNA abundance data


title: B05_S17_L003


title: B02_S14_L003


title: Odor replicate 1, GFP+ cells from 3 mice (pentanoic)

description: mRNA abundance data


title: Odor replicate 3, GFP- cells from 3 mice (octanol)

description: mRNA abundance data

source_name: Olfactory mucosa; octanol-stimulated


title: Odor replicate 4, GFP- cells from 3 mice (octanol)

description: mRNA abundance data


title: Vehicle replicate 1, GFP- cells from 3 mice (octanol)

description: mRNA abundance data


title: B02_S14_L001


title: B02_S14_L002


title: Odor replicate 1, GFP+ cells from 3 mice (octanol)

description: mRNA abundance data


title: G02_S74_L003


title: Vehicle replicate 4, GFP- cells from 3 mice (octanone)

description: mRNA abundance data


title: Odor replicate 1, GFP- cells from 3 mice (octanol)

description: mRNA abundance data


title: G02_S74_L004


title: B02_S14_L004


title: Odor replicate 4, GFP+ cells from 3 mice (octanol)

description: mRNA abundance data


title: G02_S74_L001


title: Vehicle replicate 4, GFP+ cells from 3 mice (octanone)

description: mRNA abundance data


title: Odor replicate 3, GFP+ cells from 3 mice (octanol)

description: mRNA abundance data


title: Odor replicate 2, GFP- cells from 3 mice (octanol)

description: mRNA abundance data


title: Odor replicate 2, GFP+ cells from 3 mice (octanol)

description: mRNA abundance data


title: E11_S59_L003


title: E11_S59_L002


title: E11_S59_L004


title: E03_S51_L004


title: Vehicle replicate 3, GFP- cells from 3 mice (octanone)

description: mRNA abundance data


title: E11_S59_L001


title: E03_S51_L002


title: Vehicle replicate 1, GFP- cells from 3 mice (octanone)

description: mRNA abundance data


title: Vehicle replicate 3, GFP+ cells from 3 mice (octanone)

description: mRNA abundance data


title: Odor replicate 4, GFP- cells from 3 mice (octanone)

description: mRNA abundance data

source_name: Olfactory mucosa; 2-octanone-stimulated


title: B08_S20_L003


title: B08_S20_L002


title: Odor replicate 4, GFP+ cells from 3 mice (octanone)

description: mRNA abundance data


title: B08_S20_L004


title: E03_S51_L001


title: Vehicle replicate 2, GFP+cells from 3 mice (octanone)

description: mRNA abundance data


title: G12_S84_L004


title: Odor replicate 3, GFP+ cells from 3 mice (octanone)

description: mRNA abundance data


title: Odor replicate 3, GFP- cells from 3 mice (octanone)

description: mRNA abundance data


title: G12_S84_L003


title: E03_S51_L003


title: Odor replicate 2, GFP- cells from 3 mice (octanone)

description: mRNA abundance data


title: Odor replicate 1, GFP- cells from 3 mice (octanone)

description: mRNA abundance data


title: G12_S84_L002


title: Odor replicate 1, GFP+ cells from 3 mice (octanone)

description: mRNA abundance data


title: Odor replicate 2, GFP+ cells from 3 mice (octanone)

description: mRNA abundance data


title: Vehicle replicate 4, GFP- cells from 3 mice (octanoic)

description: mRNA abundance data


title: Vehicle replicate 3, GFP- cells from 3 mice (octanoic)

description: mRNA abundance data


title: Vehicle replicate 4, GFP+ cells from 3 mice (octanoic)

description: mRNA abundance data


title: G12_S84_L001


title: Vehicle replicate 3, GFP+ cells from 3 mice (octanoic)

description: mRNA abundance data


title: B08_S20_L001


title: F07_S67_L004


title: F07_S67_L002


title: F07_S67_L003


title: Vehicle replicate 2, GFP- cells from 3 mice (octanoic)

description: mRNA abundance data


title: F07_S67_L001


title: Vehicle replicate 1, GFP+ cells from 3 mice (octanoic)

description: mRNA abundance data


title: Vehicle replicate 1, GFP- cells from 3 mice (octanoic)

description: mRNA abundance data


title: E07_S55_L004


title: E07_S55_L003


title: E07_S55_L002


title: Odor replicate 4, GFP+ cells from 3 mice (octanoic)

description: mRNA abundance data

source_name: Olfactory mucosa; octanoic acid-stimulated


title: E01_S49_L004


title: E07_S55_L001


title: Odor replicate 3, GFP- cells from 3 mice (octanoic)

description: mRNA abundance data


title: E01_S49_L003


title: Vehicle replicate 2, GFP+cells from 3 mice (octanoic)

description: mRNA abundance data


title: C06_S30_L004


title: Odor replicate 2, GFP+ cells from 3 mice (octanoic)

description: mRNA abundance data


title: Odor replicate 2, GFP- cells from 3 mice (octanoic)

description: mRNA abundance data


title: C06_S30_L003


title: C06_S30_L002


title: Odor replicate 1, GFP- cells from 3 mice (octanoic)

description: mRNA abundance data


title: C06_S30_L001


title: Vehicle replicate 4, GFP- cells from 3 mice (hexanone)

description: mRNA abundance data


title: Odor replicate 4, GFP- cells from 3 mice (octanoic)

description: mRNA abundance data


title: Vehicle replicate 4, GFP+ cells from 3 mice (hexanone)

description: mRNA abundance data


title: Vehicle replicate 3, GFP+ cells from 3 mice (hexanone)

description: mRNA abundance data


title: Vehicle replicate 3, GFP- cells from 3 mice (hexanone)

description: mRNA abundance data


title: Vehicle replicate 2, GFP- cells from 3 mice (octanone)

description: mRNA abundance data


title: C02_S26_L004


title: C02_S26_L003


title: E01_S49_L001


title: Vehicle replicate 2, GFP- cells from 3 mice (hexanone)

description: mRNA abundance data


title: C02_S26_L002


title: Vehicle replicate 2, GFP+cells from 3 mice (hexanone)

description: mRNA abundance data


title: Vehicle replicate 1, GFP- cells from 3 mice (hexanone)

description: mRNA abundance data


title: E01_S49_L002


title: Odor replicate 3, GFP+ cells from 3 mice (octanoic)

description: mRNA abundance data


title: C02_S26_L001


title: H08_S92_L004


title: H08_S92_L003


title: Vehicle replicate 1, GFP+ cells from 3 mice (hexanone)

description: mRNA abundance data


title: H08_S92_L001


title: Odor replicate 4, GFP- cells from 3 mice (hexanone)

description: mRNA abundance data

source_name: Olfactory mucosa; 2-hexanone-stimulated


title: Odor replicate 4, GFP+ cells from 3 mice (hexanone)

description: mRNA abundance data


title: E06_S54_L004


title: E06_S54_L003


title: E06_S54_L001


title: Odor replicate 1, GFP+ cells from 3 mice (octanoic)

description: mRNA abundance data


title: D11_S47_L004


title: Odor replicate 3, GFP- cells from 3 mice (hexanone)

description: mRNA abundance data


title: D11_S47_L002


title: Odor replicate 3, GFP+ cells from 3 mice (hexanone)

description: mRNA abundance data


title: D11_S47_L001


title: H08_S92_L002


title: D03_S39_L003


title: Odor replicate 2, GFP- cells from 3 mice (hexanone)

description: mRNA abundance data


title: Odor replicate 1, GFP- cells from 3 mice (hexanone)

description: mRNA abundance data


title: Vehicle replicate 4, GFP- cells from 3 mice (hexanol)

description: mRNA abundance data

treatment_protocol: After 26 hrs, half the mice were intermittently stimulated with vehicle (filtered air) or odorant for 10 sec every 20 min.


title: E06_S54_L002


title: D03_S39_L002


title: Vehicle replicate 2, GFP- cells from 3 mice (hexanol)

description: mRNA abundance data


title: Vehicle replicate 3, GFP+ cells from 3 mice (hexanol)

description: mRNA abundance data


title: Vehicle replicate 3, GFP- cells from 3 mice (hexanol)

description: mRNA abundance data


title: Vehicle replicate 1, GFP- cells from 3 mice (hexanol)

description: mRNA abundance data


title: D03_S39_L001


title: Odor replicate 1, GFP+ cells from 3 mice (hexanone)

description: mRNA abundance data


title: Vehicle replicate 2, GFP+cells from 3 mice (hexanol)

description: mRNA abundance data


title: B12_S24_L004


title: B12_S24_L003


title: D03_S39_L004


title: Vehicle replicate 1, GFP+ cells from 3 mice (hexanol)

description: mRNA abundance data


title: D11_S47_L003


title: Odor replicate 4, GFP+ cells from 3 mice (hexanol)

description: mRNA abundance data

source_name: Olfactory mucosa; hexanol-stimulated


title: Vehicle replicate 4, GFP+ cells from 3 mice (hexanol)

description: mRNA abundance data


title: Odor replicate 4, GFP- cells from 3 mice (hexanol)

description: mRNA abundance data


title: B12_S24_L002

source_name: PBMC


title: Odor replicate 3, GFP+ cells from 3 mice (hexanol)

description: mRNA abundance data


title: Odor replicate 3, GFP- cells from 3 mice (hexanol)

description: mRNA abundance data


title: B12_S24_L001


title: B09_S21_L002


title: E10_S58_L003


title: B09_S21_L001


title: G02_S74_L002


title: E10_S58_L004


title: E10_S58_L002


title: E10_S58_L001


title: Odor replicate 2, GFP+ cells from 3 mice (hexanone)

description: mRNA abundance data


title: B09_S21_L003


title: D04_S40_L004


title: B09_S21_L004


title: Odor replicate 2, GFP+ cells from 3 mice (hexanol)

description: mRNA abundance data


title: Odor replicate 2, GFP- cells from 3 mice (hexanol)

description: mRNA abundance data


title: D04_S40_L003


title: D04_S40_L001


title: Vehicle replicate 1, GFP+ cells from 3 mice (octanone)

description: mRNA abundance data


title: B04_S16_L004


title: Vehicle replicate 3, GFP+ cells from 3 mice (hexanoic)

description: mRNA abundance data


title: Odor replicate 1, GFP- cells from 3 mice (hexanol)

description: mRNA abundance data


title: Vehicle replicate 4, GFP- cells from 3 mice (hexanoic)

description: mRNA abundance data


title: B04_S16_L003


title: Vehicle replicate 2, GFP+cells from 3 mice (hexanoic)

description: mRNA abundance data


title: Vehicle replicate 1, GFP- cells from 3 mice (hexanoic)

description: mRNA abundance data


title: Vehicle replicate 4, GFP+ cells from 3 mice (hexanoic)

description: mRNA abundance data


title: Vehicle replicate 3, GFP- cells from 3 mice (hexanoic)

description: mRNA abundance data


title: Odor replicate 4, GFP- cells from 3 mice (hexanoic)

description: mRNA abundance data

source_name: Olfactory mucosa; hexanoic acid-stimulated


title: Odor replicate 4, GFP+ cells from 3 mice (hexanoic)

description: mRNA abundance data


title: Vehicle replicate 2, GFP- cells from 3 mice (hexanoic)

description: mRNA abundance data


title: B04_S16_L002


title: Odor replicate 1, GFP+ cells from 3 mice (hexanol)

description: mRNA abundance data


title: Odor replicate 3, GFP- cells from 3 mice (hexanoic)

description: mRNA abundance data


title: Vehicle replicate 1, GFP+ cells from 3 mice (hexanoic)

description: mRNA abundance data


title: B04_S16_L001


title: Odor replicate 3, GFP+ cells from 3 mice (hexanoic)

description: mRNA abundance data


title: D04_S40_L002


title: A10_S10_L004


title: A10_S10_L002


title: A10_S10_L003


title: A10_S10_L001


title: Odor replicate 2, GFP- cells from 3 mice (hexanoic)

description: mRNA abundance data


title: Odor replicate 1, GFP- cells from 3 mice (hexanoic)

description: mRNA abundance data


title: Vehicle replicate 4, GFP- cells from 3 mice (heptanone)

description: mRNA abundance data


title: H07_S91_L004


title: H07_S91_L003


title: Odor replicate 1, GFP+ cells from 3 mice (hexanoic)

description: mRNA abundance data


title: H07_S91_L002


title: H07_S91_L001


title: H06_S90_L004


title: Odor replicate 2, GFP+ cells from 3 mice (hexanoic)

description: mRNA abundance data


title: H06_S90_L002


title: H06_S90_L003


title: F08_S68_L004


title: H06_S90_L001


title: F08_S68_L002


title: F08_S68_L003


title: Vehicle replicate 2, GFP- cells from 3 mice (heptanone)

description: mRNA abundance data


title: Vehicle replicate 3, GFP+ cells from 3 mice (heptanone)

description: mRNA abundance data


title: Odor replicate 4, GFP- cells from 3 mice (heptanone)

description: mRNA abundance data


title: Odor replicate 2, GFP- cells from 3 mice (heptanone)

description: mRNA abundance data


title: D05_S41_L003


title: D05_S41_L002


title: D05_S41_L004


title: Odor replicate 2, GFP+ cells from 3 mice (heptanone)

description: mRNA abundance data


title: Vehicle replicate 3, GFP- cells from 3 mice (heptanone)

description: mRNA abundance data


title: D05_S41_L001


title: C4_2D_Noc3

first: Yanquan

last: Zhang

address: 760 Press Ave, Rm 352/HKRB

department: Toxicology and Cancer Biology

institute: U of Kentucky

description:
BRD4 2D upon nocodazole treatment
expressions_expected_count.txt
expressions_TPM.txt

data_processing:
Sequencing reads were trimmed and filtered using Trimmomatic (V0.39) to remove adapters and low quality reads.
Reads from the samples were mapped to Ensembl GRCh38 transcripts annotation using RSEM.
Assembly: GRCh38r98
Supplementary files format and content: expressions_expected_count.txt: whole-transcriptomic expected counts matrix
Supplementary files format and content: expressions_TPM.txt: whole-transcriptomic TPM (transcripts per million) matrix

growth_protocol: C4-2 cells stable expressing BRD4 WT, S24/1100A, or S24/1100D were maintained in RPMI 1640 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 RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
RNA-seq. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: The cells were treated with 200 ng/mL nocodazole for 18 hours before harvest

value: prostate cancer cells

value: 200 ng/mL nocodazole


title: C4_2D_Noc2


title: F08_S68_L001

value: T-cells

value: overlapping pipette pool targeting ESAT6/CFP10 of M.tuberculosis


title: C4_2D_Noc1


title: Odor replicate 3, GFP- cells from 3 mice (heptanone)

description: mRNA abundance data


title: Vehicle replicate 1, GFP- cells from 3 mice (heptanone)

description: mRNA abundance data


title: Vehicle replicate 2, GFP+cells from 3 mice (heptanone)

description: mRNA abundance data


title: Odor replicate 3, GFP+ cells from 3 mice (heptanone)

description: mRNA abundance data


title: Odor replicate 1, GFP- cells from 3 mice (heptanone)

description: mRNA abundance data


title: C4_2A_Noc3

description:
BRD4 2A upon nocodazole treatment
expressions_expected_count.txt
expressions_TPM.txt


title: Odor replicate 4, GFP+ cells from 3 mice (heptanone)

description: mRNA abundance data


title: Vehicle replicate 4, GFP+ cells from 3 mice (heptanol)

description: mRNA abundance data


title: Vehicle replicate 4, GFP- cells from 3 mice (heptanol)

description: mRNA abundance data


title: Vehicle replicate 2, GFP- cells from 3 mice (heptanol)

description: mRNA abundance data


title: Vehicle replicate 3, GFP- cells from 3 mice (heptanol)

description: mRNA abundance data


title: Vehicle replicate 2, GFP+cells from 3 mice (heptanol)

description: mRNA abundance data


title: Vehicle replicate 3, GFP+ cells from 3 mice (heptanol)

description: mRNA abundance data


title: C4_2A_Noc2


title: C4_WT_Noc3

description:
BRD4 WT upon nocodazole treatment
expressions_expected_count.txt
expressions_TPM.txt

value: WT


title: C4_WT_Noc2


title: Odor replicate 1, GFP+ cells from 3 mice (heptanone)

description: mRNA abundance data


title: C4_WT_Noc1


title: HCT116 cells, siNONO, Set 1

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

country: South Korea

institute: Hanyang University

data_processing:
The Illumina sequences generates raw images utilizing sequencing control software for system control and base calling, through integratd primary analysis software called RTA (Real Time Analysis)
The BCL/cBCL (base call) binary files are converted into FASTQ files using bcl2fastq, which is an illumina provided package.
Reads were initially processed by sickle version 1.33, which is a windowed adaptive trimming tool for FASTQ files using quality, with "-q 20 "-l 20" option
Gene expression levels were estimaed from processed RNA-seq using RSEM version 1.3.1 using STAR to align RNA-seq reads to transcriptome (Gencode version 34, GRCh37)
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file that includes gene_id, transcript_id(s), length, effective_length, expected count(raw count), TPM, FPKM

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

extract_protocol:
RNA was isolated using TRIzol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manafacturer's protocols

treatment_protocol: siRNAs were treated at final concentration of 20 nM with 5 ul/ml of lipofectamine RNAiMAX transfection reagent.

value: Colorectal cancer cells

value: NONO knockdown

value: siRNA treatment


title: HCT116 cells, siControl, Set 3


title: HCT116 cells, siNONO, Set 2


title: Vehicle replicate 1, GFP- cells from 3 mice (heptanol)

description: mRNA abundance data


title: Odor replicate 4, GFP+ cells from 3 mice (heptanol)

description: mRNA abundance data

source_name: Olfactory mucosa; heptanol-stimulated


title: C4_2A_Noc1


title: HCT116 cells, siControl, Set 1


title: Parental hTERT-RPE1, treated with siCENPF and siFOXM1 rep 3

city: Chicago

first: Sakshi

last: Khurana

state: IL

address: SQBRC Room 7-400, 303 E Superior St.

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Data was processed using the Ceto pipeline (https://github.com/ebartom/NGSbartom)
Base calls were performed using bcl2fastq2.20 for HiSeq output
Demultiplexed fastq files were trimmed according to trailing quality scores with Trimmomatic and then reads were aligned to hg38 with Tophat
Read counts and differential gene expression profiling analysis was conducted using EdgeR
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKMS for each sample

extract_protocol:
Qiagen Rneasy Kit
1ug RNA was used as input, using NEBNext polyA isolation kit and Ultra II RNA library kit following manufacturer protocol

treatment_protocol: 20nM siRNA treatment overnight, cells collected 48 hours after siRNA treatment

value: epithelial

value: Double KD

value: siCENPF + siFOXM1


title: Parental hTERT-RPE1, treated with siCENPF and siFOXM1 rep 2


title: Vehicle replicate 4, GFP+ cells from 3 mice (heptanone)

description: mRNA abundance data


title: Odor replicate 4, GFP- cells from 3 mice (heptanol)

description: mRNA abundance data


title: Odor replicate 3, GFP- cells from 3 mice (heptanol)

description: mRNA abundance data


title: Odor replicate 3, GFP+ cells from 3 mice (heptanol)

description: mRNA abundance data


title: Vehicle replicate 1, GFP+ cells from 3 mice (heptanol)

description: mRNA abundance data


title: Odor replicate 2, GFP+ cells from 3 mice (heptanol)

description: mRNA abundance data


title: Odor replicate 2, GFP- cells from 3 mice (heptanol)

description: mRNA abundance data


title: Vehicle replicate 4, GFP- cells from 3 mice

description: mRNA abundance data


title: Odor replicate 1, GFP+ cells from 3 mice (heptanol)

description: mRNA abundance data


title: Odor replicate 1, GFP- cells from 3 mice (heptanol)

description: mRNA abundance data


title: Vehicle replicate 4, GFP+ cells from 3 mice

description: mRNA abundance data


title: HCT116 cells, siNONO, Set 3


title: Vehicle replicate 3, GFP- cells from 3 mice

description: mRNA abundance data


title: Parental hTERT-RPE1, treated with siFOXM1 rep 3

value: FOXM1 KD


title: Parental hTERT-RPE1, treated with siFOXM1 rep 2


title: Parental hTERT-RPE1, treated with siCENPF rep 3

value: CENP-F KD

value: siCENPF


title: Parental hTERT-RPE1, treated with siFOXM1 rep 1


title: Parental hTERT-RPE1, treated with siCENPF rep 2


title: Parental hTERT-RPE1, treated with siCENPF and siFOXM1 rep 1


title: Parental hTERT-RPE1, treated with siCENPF rep 1


title: Vehicle replicate 2, GFP- cells from 3 mice

description: mRNA abundance data

value: FACS sample, GFP-


title: Vehicle replicate 2, GFP+cells from 3 mice

description: mRNA abundance data

value: FACS sample, GFP+


title: Odor replicate 4, GFP- cells from 3 mice

description: mRNA abundance data

source_name: Olfactory mucosa; heptanoic acid-stimulated


title: Vehicle replicate 1, GFP- cells from 3 mice

description: mRNA abundance data


title: Parental hTERT-RPE1, treated with siNeg rep 3

value: siNeg


title: Vehicle replicate 1, GFP+ cells from 3 mice

description: mRNA abundance data


title: Odor replicate 3, GFP+ cells from 3 mice

description: mRNA abundance data


title: Parental hTERT-RPE1, treated with siNeg rep 2


title: NeuroD1_MCAO-rep3

city: Guangzhou

first: He

last: Xiaosong

state: Guangdong

address: Xinzao Road

department: Department Of Anatomy

country: China

institute: Guangzhou Medical University

data_processing:
The filtered reads were aligned against mouse reference genome GRCm38 using HISAT2 (v.2.0.1) and summarized using feature counts (v.1.5.0). Differential expression analysis was processed using DESeq2 (v.1.16.1)
Assembly: GRCm38
Supplementary files format and content: gene counts for each sample

source_name: Brain

extract_protocol:
RNA extractions were performed using the Macherey-Nagel NucleoSpin® RNA kit according to the manufacture. The concentration and purity of the samples were measured using NanoDropTM 2000 spectrophotometers (Thermo Fisher Scientific, Waltham, USA).
RNA libraries were prepared for sequencing usingstandard Illumina protocols performed at the UCLA Technology Center for Genomics and Bioinformatics.

value: Brain

tag: condition

value: MCAO


title: NeuroD1_MCAO-rep2


title: Odor replicate 3, GFP- cells from 3 mice

description: mRNA abundance data


title: NeuroD1_MCAO-rep1


title: GFP_MCAO-rep3

value: GFP


title: Parental hTERT-RPE1, treated with siNeg rep 1


title: hTERT-RPE1, RbIgG ChIP, rep 2

library_source: genomic

data_processing:
Data was processed using the nf-core/chipseq pipeline (https://nf-co.re/chipseq/2.0.0)
Base calls were performed using bcl2fastq2.20 for HiSeq output
Demultiplexed fastq files were trimmed according to trailing quality scores with TrimGalore and then reads were aligned to GRCh38 with BWA
Bigwig files were produced using bedtools and peak calling was done using Macs2
Assembly: GRCh38
Supplementary files format and content: bigWig for each sample

molecule: genomic DNA

extract_protocol:
Cells were fixed with 1% formaldehyde and sonicated using the E220 Covaris ultrasonicator. Protein-DNA complexes were then immunoprecipitated with respective antibodies overnight.
ChIP DNA was extracted using Qiagen PCR Purification Kit and library prepped using NEBNext DNA Ultra II Library Preperation Kit

tag: chip-antibody

value: Normal Rabbit IgG#2729 (CST)


title: GFP_MCAO-rep2


title: hTERT-RPE1, RbIgG ChIP, rep 3


title: GFP_MCAO-rep1


title: Odor replicate 2, GFP- cells from 3 mice

description: mRNA abundance data


title: WT biol rep 3

city: Wuhan

first: Fei

last: Liu

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

institute: Institute of Hydrobiology, Chinese Academy of Sciences

data_processing:
Raw reads in fastq format were firstly processed by Cutadapt (v1.15) to remove adapters, reads containing ploy-N, and low-quality reads. The resulting clean reads were used for all downstream analyses.
Clean reads were mapped to the zebrafish reference genome (DanRer11) using STAR (v2.6.1a) according to the user manual with the default parameters. featureCounts (v1.6.0) was adopted to count the mapped reads. Stringtie (v1.3.3b) was executed to calculate the FPKM values of genes.
Differential expression analysis was performed by DESeq2 R package (v1.22.1). The significantly DEGs between WT and Bcas2-KO embryos were identified by using the threshold fold change > 2 and adjusted p-values < 0.05.
Alternative splicing patterns were identified and calculated by rMATs python package (v4.0.2). The threshold of inclusion level change > 0.10 and adjusted p-values < 0.05 was used to identify significant DSEs.
GO and KEGG enrichment analysis was performed by using the RDAVIDWebService R package.
Assembly: GRCz11 (GCA_000002035.4)
Supplementary files format and content: raw_counts.txt is a tab-delimited text file for read count numbers of each gene.
Supplementary files format and content: FPKMs_allsamples.txt is a tab-delimited text file for quantitative expression (FPKM) of each gene.

organism: Danio rerio

source_name: embryo

extract_protocol:
After genotyping, for each WT and bcas2-KO sample, 10 zebrafish embryos were used to isolate total RNA using the TRIzol reagent (Invitrogen, USA) according to the manufacturer’s protocol.
Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s technical guide.
The library preparations were then sequenced on an Illumina Hiseq platform using the 2 x 150 bp paired-end configuration according to the manufacturer’s protocol. For each cDNA library, 6 G base paired-end raw reads were generated.

value: embryo

value: WT

tag: age

value: 3 dpf


title: hTERT-RPE1, RbIgG ChIP, rep 1


title: Odor replicate 2, GFP+ cells from 3 mice

description: mRNA abundance data


title: Odor replicate 1, GFP- cells from 3 mice

description: mRNA abundance data


title: Vehicle replicate 3, GFP+ cells from 3 mice

description: mRNA abundance data


title: WT biol rep 2


title: IP_Naive_Tra2b

city: Farmington

first: Anthony

last: Vella

state: Connecticut

address: 263 Farmington Ave

department: Immunology

institute: UConn Health

description: Total RNA from CD8+ T cells

data_processing:
Sequences were analyzed using the original eCLIP analysis pipeline (Eclipse Data Analysis Protocol). Significant eCLIP peaks (Tra2β binding events) were identified by Clipper using the strict threshold set by Eclipse Bioinnovations of log2 fold change ≥ 3 and -log10(p-value) ≥ 3.
Assembly: mm10
Supplementary files format and content: Bigwig files

source_name: CD8+ T cell

extract_protocol: RBP-eCLIP protocol (Eclipsebio RBP-eCLIP Protocol v2.01R)

treatment_protocol: Cells were UV crosslinked on ice at 400 mJ/cm2 using a Stratagene UV Stratalinker 2400 and sent to Eclipse BioinnovationsInc. for processing using their RBP-eCLIP protocol (RBP-eCLIP Protocol v2.01 R). Immunoprecipitation was performed using the anti-Tra2beta rabbit polyclonal antibody (Santa Cruz Biotechnology, Dallas TX, cat. #sc-166829) and anti-IgG rabbit antibody (Thermo Fisher Scientific, Waltham, MA, cat. #02-6102).

value: CD8+ T cell

tag: clip antibody

value: anti-Tra2β rabbit polyclonal antibody (Santa Cruz Biotechnology, Dallas TX, cat. #sc-166829)


title: hTERT-RPE1, MYBL2 ChIP, rep 3

value: epithelial

value: B-Myb Polyclonal antibody 18896-1-AP (Proteintech)


title: WT biol rep 1


title: HCT116 cells, siControl, Set 2

value: Colorectal cancer cells

value: siRNA treatment


title: Odor replicate 1, GFP+ cells from 3 mice

description: mRNA abundance data


title: Odor replicate 4, GFP+ cells from 3 mice

description: mRNA abundance data


title: bcas2-KO biol rep 2


title: Input__Naive_Tra2b

description: Total RNA from CD8+ T cells


title: bcas2-KO biol rep 1


title: Vehicle replicate 1, GFP+ cells from 3 mice (heptanone)

description: mRNA abundance data


title: hTERT-RPE1, MYBL2 ChIP, rep 2


title: hTERT-RPE1, MYBL2 ChIP, rep 1


title: IP_Effector_Tra2b_2

description: Total RNA from CD8+ T cells


title: Synovial fluid PTOA

city: Raleigh

first: Shannon

middle: S

last: Connard

state: NC

address: 1060 William Moore Drive

department: Clinical Sciences

institute: North Carolina State University

data_processing:
Raw reads obtained from miRNA sequencing were processed by removing contamination and adapter sequences. Statistical analysis on lengths and counts of the filtered reads as well as data volume was performed as part of data quality control. The filtered reads were aligned to the miRbase database, composed of known miRNA sequences, and followed by miRNA annotation. Additionally, the reads were aligned to Rfam database to study non-coding RNA (ncRNA) distribution. For novel miRNA prediction, the sequences were aligned to the Equus caballus genome and subject to RNA folding and secondary structure analysis. miRNA differential expression (DE), clustering, and target gene prediction were also analyzed. The original image data were analyzed using Bcl2fastq for base calling and preliminary quality analysis. During the sequencing process, the quality of the first 25 bases of each read determined whether the read was retained or discarded via Illumina built-in software. Trimmomatic v0.30 was used to process the raw data to clean data for subsequent data analysis. ncRNAs were classified and annotated by aligning clean reads to the Rfam database using blastn. The best query-reference match was used as the alignment result. To remove the repetitive sequences in the small RNAs (sRNAs), the sRNA sequences were aligned to the repetitive sequence reference of the given species or predicted based on the sequence of the reference Equus caballus genome. The miRNA sequences were aligned to mRNA exons and introns to identify the original mRNA of the miRNA fragment. miRNA prediction was performed by aligning the reads to the reference genome, then utilizing miRDeep2 V2.0.0.7 to model all the possible secondary structures of miRNA precursors based on the alignment information. The secondary structures were then subject to a scoring system for evaluation to determine the novel miRNA sequence. miRNA family classification was then performed on the annotated known miRNAs to explore the presence of the miRNA family in other species. Miranda v3.3a was used to predict target sites based on miRNA sequences and the corresponding genomic cDNA sequences.
The miRNA expression was analyzed in clusters to examine the differences across all miRNAs within the same cluster. The read count from the miRNA expression analysis was used as the input for this analysis. Differentially expressed (DE) miRNAs were analyzed using DESeq2 V1.16.1. Due to the use of a single pooled sample containing EVs from 6 horses for each group, statistical analysis could not be performed; however, each sample was treated as a replicate for estimation of dispersion. DE miRNAs were identified based on the criteria of fold change > 2 between groups (control and PTOA) in order to explore the upregulated and downregulated genes.
Assembly: Horse reference genome Equus caballus
Supplementary files format and content: Data files include mature read counts, transcript per million (TPM), log2 fold change (FC), log2 counts per million (CMP), p-value, false discovery rate (FDR), and regulation for each sample and DE miRNAs between groups.

organism: Equus caballus

source_name: Synovial fluid extracellular vesicles

growth_protocol: NA - EVs were isolated from plasma and synovial fluid from horses with (n = 6) and without (n = 6) PTOA

extract_protocol:
RNA was isolated using the Quick-RNA Miniprep Kit (Zymo Research Corporation) and analyzed using an Agilent 2100 Bioanalyzer and an RNA 6000 Pico kit (Agilent Technologies) to determine RNA concentration, purity, and integrity per manufacturer’s instructions.
Samples from the control horses and horses with PTOA were pooled and shipped according to company protocols to GENEWIZ, a division of Azenta Life Sciences, for small RNA-sequencing. Library preparation included ligation of sequencing adapters to 5’ phosphate ends. The RNA fragments were then converted to cDNA libraries prior to sequencing to target small RNA products of 18-30bp.

treatment_protocol: NA - Synovial fluid samples were treated with 10 µg/ml hyaluronidase; plasma and hyaluronidase-treated synovial fluid EVs were isolated by stepwise ultracentrifugation

value: Synovial fluid extracellular vesicles

value: Synovial fluid

value: PTOA


title: Synovial fluid control

value: Control (no PTOA)


title: GLV, BXD, rep3

city: Beijing

first: Shutao

last: Pan

address: Liangxiang University Town, Fangshan District, Beijing, 102488, China

institute: Beijing University of Chinese Medicine

data_processing:
High-quality clean reads were filtered by SOAPnuke (v1.5.2 ; https://github.com/BGI-flexlab/SOAPnuke) with a low-quality base ratio (≤5) of >20%, and an unknown base ("N" base) ratio of > 5%.
The reads were mapped to ribosome RNA (rRNA) database by Bowtie2 (v2.2.5; http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and then the rRNA mapped reads were removed.
Reads were mapped onto the Rattus norvegicus reference genome using HISAT2 (version 2.2.4), and >80% alignment was achieved.
The gene expression levels were normalized as fragments per kilobase of transcript per million (FPKM).
Assembly: Rnor_6.0
Supplementary files format and content: Excel file include FPKM values for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: Gastric lymphatic vessel (GLV)

growth_protocol: Male Sprague-Dawley rats (180-220 g) were purchased from SPF (Beijing) Biotechnology Co., Ltd. (Beijing, China, Animal Production License No. SCXK2019-0010) and underwent an adaption period of 3d under standard conditions of temperature (22 ± 2 °C) and humidity (40-70%) with 12 h light and dark cycles and free access to standard rodent pellet chow and water

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and purified by chloroform/isoamyl alcohol extraction and 75% ethanol precipitation. 1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA.
RNA quality was detected by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). The qualified RNA samples are denatured at suitable temperature, and the mRNA is enriched by oligo (dT) -attached magnetic beads. The target mRNA fragments were reverse transcribed into cDNA, and the complementary cDNA chain was synthesized. The cDNA fragments were purified with the QiaQuick PCR extraction kit and eluted with EB buffer. The purified cDNA was end-repaired and the poly(A) were added. Suitable fragments were selected, purified, and subsequently PCR-amplified to establish cDNA library template. The prepared DNA library was sequenced on the Illumina HiSeq2500 platform.

treatment_protocol: The rats were randomly assigned into a normal control group (CON), a model group (MOD), a BXD treated group (BXD), and an anti-ulcer positive control drug (omeprazole) group (OME) with 6 rats in each group (n = 6). All rats were fasted for 12h before the experiment. On the day of the experiment, the rats in the CON group were left without intervention, and the other 3 groups were subjected to a classical water-immersion stress modeling process (Rajagopal et al., 2018). Briefly, the rats were placed individually in an opaque 13×13 cm cubic pool of 40 cm height filled with water up to 15 cm for 4h. The water temperature was maintained at 22 ± 2 °C. Afterwards, all rats were removed from the pool, wiped by dry towel, and put into their original cages. Any rats that may have appeared to drown would have been removed from the experiment, but no such outcomes occurred. 30 min afterward, the rats in the BXD and OME groups were administered BXD or omeprazole respectively at a dose of 10ml/kg body weight by gavage, and rats in the CON and MOD groups were administered the same dose of distilled water. All the gavage solutions were kept in a 37 °C water bath before use.

value: Gastric lymphatic vessel (GLV)

value: SIGU modeling+BXD gavage


title: hTERT-RPE1, FOXM1 ChIP, rep 3

value: FoxM1 (D12D5) XPRabbit mAb#5436 (CST)


title: IP_Effector_Tra2b_1

description: Total RNA from CD8+ T cells


title: Plasma control

source_name: Plasma extracellular vesicles

value: Plasma extracellular vesicles

value: Plasma


title: GLV, BXD, rep2

value: WT


title: hTERT-RPE1, FOXM1 ChIP, rep 2


title: IP_Effector_IgG

description: Total RNA from CD8+ T cells

value: anti-IgG rabbit antibody (Thermo Fisher Scientific, Waltham, MA, cat. #02-6102)


title: GLV, BXD, rep1


title: Input_Effector_Tra2b_2

description: Total RNA from CD8+ T cells

value: CD8+ T cell


title: hTERT-RPE1, FOXM1 ChIP, rep 1


title: bcas2-KO biol rep 3

value: embryo

value: 3 dpf


title: GLV, model, rep3

value: SIGU modeling+saline gavage


title: Input_Effector_Tra2b_1

description: Total RNA from CD8+ T cells

value: anti-Tra2β rabbit polyclonal antibody (Santa Cruz Biotechnology, Dallas TX, cat. #sc-166829)


title: GLV, model, rep2


title: Input_Effector_IgG

description: Total RNA from CD8+ T cells


title: hTERT-RPE1, Input, rep 3

value: epithelial


title: hTERT-RPE1, Input, rep 2


title: Heart, Ric-8b(flx/flx)MCM, KO6

city: London

first: Alison

last: Thomas

address: Charterhouse Square, William Harvey Heart Centre, 1st Floor

department: Clinical Pharmacology and Precision Medicine

country: United Kingdom

institute: QMUL

data_processing:
PartekFlow was used for data processing.
Contaminants filtered and quality controlled using Bowtie2
Sequences aligned to the mouse reference genome (Mm10) using STAR (v3.7.1)
Genes were annotated and counted using PartekFlow Quantify to annotation model (Partek E/M) and Ensembl 102.
DeSeq2 used for differential expression within PartekFlow.
Assembly: Mm10
Supplementary files format and content: tab delimited text file containing gene counts for each sample.

source_name: Heart

extract_protocol:
RNA was extracted using Rneasy Fibrous Tissue mini kit (Qiagen).
Library preparation for RNA-seq was carried out using NEB Next UltraTM II RNA library prep kit (New England Biolabs) following manufacturer's protocols.

treatment_protocol: 1mg tamoxifen/25g body weight was injected intraperitoneally in mice for 3 consecutive days. Two days after the last injection, hearts were removed and stored in RNAlater.

value: Heart

value: Ric-8b (flx/flx) MCM


title: Plasma PTOA

value: PTOA


title: GLV, control, rep3

value: Blank


title: hTERT-RPE1, siFOXM1, ATAC-seq, rep 2

data_processing:
Data was processed using the nf-core/atacseq pipeline (https://nf-co.re/atacseq/2.1.2)
Base calls were performed using bcl2fastq2.20 for HiSeq output
Demultiplexed fastq files were trimmed according to trailing quality scores with TrimGalore and then reads were aligned to GRCh38 with BWA
Bigwig files were produced using bedtools
Assembly: GRCh38
Supplementary files format and content: bigWig for each sample

extract_protocol:
Transposition was conducted with Tagment DNA Enzyme and Buffer Kit from Illumina and purified using Qiagen MinElute Reaction Cleanup Kit
Transposed DNA was PCR amplified and library prepped using Nextera adaptors from Illumina

value: FOXM1 KD


title: Heart, Ric-8b(flx/flx)MCM, KO4


title: hTERT-RPE1, siFOXM1, ATAC-seq, rep 1


title: Heart, Ric-8b(flx/flx)MCM, KO5


title: Heart, Ric-8b(flx/flx)MCM, KO3


title: GLV, control, rep2

value: Gastric lymphatic vessel (GLV)


title: Heart, Ric-8b(flx/flx)MCM, KO2


title: GLV, control, rep1


title: hTERT-RPE1, siCENP-F, ATAC-seq, rep 1

value: CENP-F KD

value: siCENPF


title: Heart, Ric-8b(flx/flx)MCM, KO1