title: ExVivoBlood_IGRA+ve_Donor_27_Visit_3

description:
LTBI 27_v3 vs LTBI 28_v1_6475_1_2.txt
27_LTBI_v3_pax


title: ExVivoBlood_IGRA+ve_Donor_22_Visit_3

status: Public on Jan 19 2021

type: RNA

city: London

first: Jackie

last: Cliff

address: Keppel Street

department: Immunology and Infection

country: United Kingdom

institute: London School of Hygiene & Tropical Medicine

description:
LTBI 10_v1 vs LTBI 22_v3_7133_1_4.txt
22_LTBI_v3_pax

hyb_protocol: 300 ng of Cy3 or Cy5-labelled cRNA (specific activity >6.0 pmol Cy3 or Cy5 per ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 μL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression v3 (G4851C) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent).

scan_protocol: Microarray slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using the two colour scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel set to 'red and green',  and PMT set to 100%).

data_processing: Feature Extraction Software 12.0 (Agilent) using default parameters (protocol GE2_1200_Jun14 and grid template: 072363_D_F_20180928) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were   log-2 transformed and normalised using the Agilp expression array processing package in ‘R’ Language and Environment for Statistical Computing 3.5.2

molecule: total RNA

organism: Homo sapiens

label_protocol: Two-color low input Quick Amp Labelling kit (Agilent)

extract_protocol: PAXgene Blood miRNA Kit (Qiagen) with on-column DNAse treatment. Globin-depletion using GLOBINclear Kit (ThermoFisher)

treatment_protocol: Venous Blood was collected into PAXgene RNA tubes (PreAnalytix), inverted repetedly to mix, incubated at room temperature for 2 hours and frozen.

tag: tissue

value: Blood

tag: group

value: IGRA+

tag: timepoint


title: ExVivoBlood_IGRA+ve_Donor_22_Visit_1

description:
LTBI 22_v2 vs LTBI 22_v1_7133_1_3.txt
22_LTBI_v1_pax

value: Week 0


title: ExVivoBlood_IGRA+ve_Donor_16_Visit_3

description:
LTBI 16_v2 vs LTBI 16_v3_7134_2_4.txt
16_LTBI_v3_pax


title: ExVivoBlood_IGRA+ve_Donor_14_Visit_3

description:
LTBI 14_v3 vs LTBI 14_v2_7134_2_1.txt
14_LTBI_v3_pax


title: ExVivoBlood_IGRA+ve_Donor_23_Visit_2

description:
LTBI 23_v1 vs LTBI 23_v2_7135_2_1.txt
23_LTBI_v2_pax

value: Week 2


title: ExVivoBlood_IGRA+ve_Donor_12_Visit_3

description:
LTBI 12_v2 vs LTBI 12_v3_7134_1_2.txt
12_LTBI_v3_pax


title: ExVivoBlood_IGRA+ve_Donor_15_Visit_2

description:
LTBI 15_v1 vs LTBI 15_v2_7134_2_3.txt
15_LTBI_v2_pax


title: ExVivoBlood_IGRA+ve_Donor_22_Visit_2

description:
LTBI 22_v2 vs LTBI 22_v1_7133_1_3.txt
22_LTBI_v2_pax


title: ExVivoBlood_IGRA+ve_Donor_15_Visit_1

description:
LTBI 15_v1 vs LTBI 15_v2_7134_2_3.txt
15_LTBI_v1_pax


title: ExVivoBlood_IGRA+ve_Donor_15_Visit_3

description:
LTBI 32_v1 vs LTBI 15_v3_7135_1_2.txt
15_LTBI_v3_pax


title: P5_Cornea_2_2_8

type: SRA

city: Freiburg

first: Roman

last: Sankowski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University of Freiburg Medical Center

description: library of 192

library_source: transcriptomic

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software 2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

organism: Mus musculus

source_name: Cornea

growth_protocol: SPF mouse facility

extract_protocol:
Isolated myeloid cells were stained with antibodies for CD45 and CD11b. All CD45+ cells were FACS-sorted in 384-well plates.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: CNV mice were to laser lesioning.

tag: strain

tag: age

value: 8 weeks

value: Cornea

tag: cell type

value: CD45+ cells


title: ExVivoBlood_IGRA+ve_Donor_12_Visit_1

description:
LTBI 13_v2 vs LTBI 12_v1_7134_1_4.txt
12_LTBI_v1_pax


title: P4_CB_2_8

description: library of 192

source_name: Ciliary body

value: Ciliary body


title: ExVivoBlood_IGRA+ve_Donor_16_Visit_2

description:
LTBI 16_v2 vs LTBI 16_v3_7134_2_4.txt
16_LTBI_v2_pax


title: ExVivoBlood_IGRA+ve_Donor_12_Visit_2

description:
LTBI 12_v2 vs LTBI 12_v3_7134_1_2.txt
12_LTBI_v2_pax


title: ExVivoBlood_IGRA+ve_Donor_14_Visit_2

description:
LTBI 14_v3 vs LTBI 14_v2_7134_2_1.txt
14_LTBI_v2_pax


title: ExVivoBlood_IGRA+ve_Donor_14_Visit_1

description:
LTBI 14_v1 vs LTBI 13_v3_7134_2_2.txt
14_LTBI_v1_pax


title: P4_CB_1_7

description: library of 192


title: ExVivoBlood_IGRA+ve_Donor_16_Visit_1

description:
LTBI 30_v3 vs LTBI 16_v1_7135_1_1.txt
16_LTBI_v1_pax


title: ExVivoBlood_IGRA+ve_Donor_9_Visit_3

description:
LTBI 8_v1 vs LTBI 9_v3_7133_1_1.txt
9_LTBI_v3_pax


title: ExVivoBlood_IGRA+ve_Donor_10_Visit_2

description:
LTBI 10_v3 vs LTBI 10_v2_7133_1_2.txt
10_LTBI_v2_pax


title: P3_CB_2_8

description: library of 192


title: ExVivoBlood_IGRA+ve_Donor_10_Visit_3

description:
LTBI 10_v3 vs LTBI 10_v2_7133_1_2.txt
10_LTBI_v3_pax


title: P3_CB_1_7

description: library of 192


title: P2_Ret_Mg_2_2

description: library of 192

source_name: Retina Control

value: Retina


title: ExVivoBlood_IGRA+ve_Donor_8_Visit_2

description:
LTBI 8_v3 vs LTBI 8_v2_7132_2_3.txt
8_LTBI_v2_pax


title: ExVivoBlood_IGRA+ve_Donor_7_Visit_3

description:
LTBI 7_v2 vs LTBI 7_v3_7132_2_1.txt
7_LTBI_v3_pax


title: P2_Cornea_2_6

description: library of 192


title: P2_Ret_Mg_1_1

description: library of 192


title: ExVivoBlood_IGRA+ve_Donor_10_Visit_1

description:
LTBI 10_v1 vs LTBI 22_v3_7133_1_4.txt
10_LTBI_v1_pax


title: ExVivoBlood_IGRA+ve_Donor_8_Visit_3

description:
LTBI 8_v3 vs LTBI 8_v2_7132_2_3.txt
8_LTBI_v3_pax


title: ExVivoBlood_IGRA+ve_Donor_28_Visit_2

description:
LTBI 28_v2 vs LTBI 28_v3_6475_1_1.txt
28_LTBI_v2_pax


title: P2_Cornea_1_5

description: library of 192


title: ExVivoBlood_IGRA+ve_Donor_9_Visit_1

description:
LTBI 9_v2 vs LTBI 9_v1_7132_2_4.txt
9_LTBI_v1_pax


title: ExVivoBlood_IGRA+ve_Donor_9_Visit_2

description:
LTBI 9_v2 vs LTBI 9_v1_7132_2_4.txt
9_LTBI_v2_pax


title: ExVivoBlood_IGRA+ve_Donor_8_Visit_1

description:
LTBI 8_v1 vs LTBI 9_v3_7133_1_1.txt
8_LTBI_v1_pax


title: P2_CNV_7d_1_3

description: library of 192

source_name: Retina CNV


title: P2_CNV_7d_2_4

description: library of 192


title: P2_CNV_3d_1_5

description: library of 192


title: ExVivoBlood_IGRA+ve_Donor_7_Visit_2

description:
LTBI 7_v2 vs LTBI 7_v3_7132_2_1.txt
7_LTBI_v2_pax


title: ExVivoBlood_IGRA+ve_Donor_7_Visit_1

description:
LTBI 6_v3 vs LTBI 7_v1_7132_2_2.txt
7_LTBI_v1_pax


title: RPC spheroid 10-cell sample 24

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

country: USA

institute: University of Virginia

data_processing:
Adapters were trimmed using fastq-mcf with the following options:  -q 10 -t 0.01 -k 0 (quality threshold 10, 0.01% occurrence frequency, no nucleotide skew causing cycle removal).
Datasets were aligned to the human (GRCh38.p12)  transcriptome using RSEM. Reference ERCC sequences were also provided for the alignment.
RSEM options  for 10c samples  --bowtie2 --single-cell-prior --paired-end (Bowtie2 transcriptome aligner, single-cell prior to account for dropouts)
Genome_build: GRCm38.82
Supplementary_files_format_and_content: Comma separated file includes read counts from RSEM

molecule: polyA RNA

source_name: Explanted pre-small cell lung cancer cells

extract_protocol:
All samples were cryoembedded and sectioned on to glass slides (8µm sections). Cell samples were isolated with laser capture microdissection and poly(A) RNA extracted, reverse transcribed and poly(A) PCR amplified prior to library preparation
Amplified cDNA samples were diluted to 0.2 µg/ml for tagmentation with the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s earlier recommendation to purify libraries with 180% (vol/vol) SPRI beads

tag: sample name

value: preSCLC RPC spheroid 10-cell sample 1

tag: genotype

tag: sample type

value: 10-cell sample


title: P2_CNV_3d_2_6

description: library of 192


title: P5_Cornea_1_2_7

description: library of 192


title: P1_Ret_Mg_1_1

description: library of 192


title: ExVivoBlood_IGRA+ve_Donor_6_Visit_3

description:
LTBI 6_v3 vs LTBI 7_v1_7132_2_2.txt
6_LTBI_v3_pax


title: RPC spheroid 10-cell sample 23


title: ExVivoBlood_IGRA+ve_Donor_6_Visit_2

description:
LTBI 6_v1 vs LTBI 6_v2_7132_1_4.txt
6_LTBI_v2_pax


title: ExVivoBlood_IGRA+ve_Donor_6_Visit_1

description:
LTBI 6_v1 vs LTBI 6_v2_7132_1_4.txt
6_LTBI_v1_pax


title: P1_CNV_7d_2_8

description: library of 192


title: P1_CNV_7d_1_7

description: library of 192


title: P1_Ret_Mg_2_2

description: library of 192


title: RPC spheroid 10-cell sample 22


title: P1_CNV_3d_2_4

description: library of 192


title: P1_CNV_3d_1_3

description: library of 192


title: RPC spheroid 10-cell sample 21


title: ExVivoBlood_IGRA+ve_Donor_5_Visit_3

description:
LTBI 5_v1 vs LTBI 5_v3_7131_2_2.txt
5_LTBI_v3_pax


title: FACS2018_SNI_3d_2c

city: St Louis

first: Eric

last: Ewan

state: MO

address: 660 S Euclid Ave

department: Neuroscience

institute: Washington University in St Louis

description: ~100 FACS-sorted YFP+ cells

data_processing:
adaptor trimming using cutadapt
sequence quality control using prinseq 0.20.4
map to reference genome using STAR 2.5.3a
generate transcript count matrix using HTSeq 0.6.1
outliers were detected using PcaGrid function  in the rrcov R package
counts of technical replicates were combined
Differential expression was calculated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: transcript count matrix files generated using HTseq

source_name: L4 Dorsal Column Sensory Neurons

extract_protocol:
1 and 3dpi L4 DRG were dissected, dissociated with papain and collagenase, and passed through a 70 um filter. Cells were FACS sorted for YFP-positive cells into Clontech lysis buffer with 5% RiboLock Rnase Inhibitor (Thermo Fisher).
Library prep was performed with ~100 cells collected by flow cytometry in 10 ul of Clontech’s reaction buffer using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Clontech) per manufacturer’s protocol. Three technical replicates of 100 cells each (A-C) were obtained for each biological replicate.

treatment_protocol: Mice received either sciatic nerve crush or T9/10 dorsal hemisection spinal cord injury

tag: Sex

value: Female

value: FACS-sorted L4  YFP+ Dorsal Column Sensory Neurons

value: 10-20 weeks


title: FACS2018_SNI_3d_2a

description: ~100 FACS-sorted YFP+ cells


title: RPC spheroid 10-cell sample 20


title: FACS2018_SNI_3d_1c

description: ~100 FACS-sorted YFP+ cells


title: ExVivoBlood_IGRA+ve_Donor_5_Visit_1

description:
LTBI 5_v1 vs LTBI 5_v3_7131_2_2.txt
5_LTBI_v1_pax


title: RPC spheroid 10-cell sample 19


title: FACS2018_SNI_3d_1a

description: ~100 FACS-sorted YFP+ cells


title: ExVivoBlood_IGRA+ve_Donor_5_Visit_2

description:
LTBI 5_v2 vs HC 51_v2_7131_2_4.txt
5_LTBI_v2_pax


title: FACS2018_SNI_3d_1b

description: ~100 FACS-sorted YFP+ cells


title: FACS2018_SNI_1d_2c

description: ~100 FACS-sorted YFP+ cells


title: ExVivoBlood_IGRA+ve_Donor_3_Visit_3

description:
LTBI 3_v3 vs LTBI 3_v2_7131_2_3.txt
3_LTBI_v3_pax


title: RPC spheroid 10-cell sample 18


title: RPC spheroid 10-cell sample 16


title: FACS2018_SNI_1d_1b

description: ~100 FACS-sorted YFP+ cells


title: FACS2018_SNI_1d_2b

description: ~100 FACS-sorted YFP+ cells


title: RPC spheroid 10-cell sample 17


title: FACS2018_SNI_1d_1c

description: ~100 FACS-sorted YFP+ cells


title: ExVivoBlood_IGRA+ve_Donor_3_Visit_2

description:
LTBI 3_v3 vs LTBI 3_v2_7131_2_3.txt
3_LTBI_v2_pax


title: FACS2018_SNI_3d_2b

description: ~100 FACS-sorted YFP+ cells


title: FACS2018_SCI_3d_2c

description: ~100 FACS-sorted YFP+ cells


title: RPC spheroid 10-cell sample 14


title: RPC spheroid 10-cell sample 15


title: ExVivoBlood_IGRA+ve_Donor_3_Visit_1

description:
HC 52_v2 vs LTBI 3_v1_7131_2_1.txt
3_LTBI_v1_pax


title: FACS2018_SNI_1d_1a

description: ~100 FACS-sorted YFP+ cells


title: RPC spheroid 10-cell sample 13


title: FACS2018_SCI_3d_1c

description: ~100 FACS-sorted YFP+ cells


title: FACS2018_SCI_3d_2a

description: ~100 FACS-sorted YFP+ cells


title: ExVivoBlood_IGRA+ve_Donor_2_Visit_3

description:
HC 54_v2 vs LTBI 2_v3_7132_1_1.txt
2_LTBI_v3_pax


title: RPC spheroid 10-cell sample 12


title: FACS2018_SCI_3d_2b

description: ~100 FACS-sorted YFP+ cells


title: ExVivoBlood_IGRA+ve_Donor_2_Visit_1

description:
LTBI 2_v1 vs LTBI 2_v2_7131_1_2.txt
2_LTBI_v1_pax


title: FACS2018_SCI_3d_1b

description: ~100 FACS-sorted YFP+ cells


title: FACS2018_SNI_1d_2a

description: ~100 FACS-sorted YFP+ cells


title: FACS2018_SCI_3d_1a

description: ~100 FACS-sorted YFP+ cells


title: ExVivoBlood_IGRA+ve_Donor_1_Visit_3

description:
LTBI 1_v3 vs HC 54_v1_7132_1_2.txt
1_LTBI_v3_pax


title: RPC spheroid 10-cell sample 11


title: FACS2018_SCI_1d_2a

description: ~100 FACS-sorted YFP+ cells


title: ExVivoBlood_IGRA+ve_Donor_1_Visit_1

description:
HC 51_v1 vs LTBI 1_v1_7135_1_4.txt
1_LTBI_v1_pax


title: ExVivoBlood_HealthyControl_Donor_55_Visit_2

description:
HC 55_v2 vs HC 55_v1_7132_1_3.txt
55_HC_v2_pax

value: Healthy Control


title: FACS2018_SCI_1d_2b

description: ~100 FACS-sorted YFP+ cells


title: RPC spheroid 10-cell sample 10


title: FACS2018_SCI_1d_2c

description: ~100 FACS-sorted YFP+ cells


title: ExVivoBlood_IGRA+ve_Donor_1_Visit_2

description:
LTBI 1_v2 vs HC 52_v1_7131_1_3.txt
1_LTBI_v2_pax


title: ExVivoBlood_IGRA+ve_Donor_2_Visit_2

description:
LTBI 2_v1 vs LTBI 2_v2_7131_1_2.txt
2_LTBI_v2_pax


title: FACS2018_SCI_1d_1a

description: ~100 FACS-sorted YFP+ cells


title: FACS2018_SCI_1d_1b

description: ~100 FACS-sorted YFP+ cells


title: RPC spheroid 10-cell sample 8


title: RPC spheroid 10-cell sample 9


title: RPC spheroid 10-cell sample 7


title: FACS2018_Ctrl_3d_1b

description: ~100 FACS-sorted YFP+ cells


title: FACS2018_Ctrl_1d_1b

description: ~100 FACS-sorted YFP+ cells


title: FACS2018_Ctrl_3d_1a

description: ~100 FACS-sorted YFP+ cells


title: FACS2018_SCI_1d_1c

description: ~100 FACS-sorted YFP+ cells


title: FACS_SNI_3D_2c

description: ~100 FACS-sorted YFP+ cells


title: FACS2018_Ctrl_1d_1c

description: ~100 FACS-sorted YFP+ cells


title: ExVivoBlood_HealthyControl_Donor_54_Visit_1

description:
LTBI 1_v3 vs HC 54_v1_7132_1_2.txt
54_HC_v1_pax


title: ExVivoBlood_HealthyControl_Donor_55_Visit_1

description:
HC 55_v2 vs HC 55_v1_7132_1_3.txt
55_HC_v1_pax


title: FACS_SNI_3D_2b

description: ~100 FACS-sorted YFP+ cells


title: FACS_SNI_3D_2a

description: ~100 FACS-sorted YFP+ cells


title: FACS_SNI_3D_1a

description: ~100 FACS-sorted YFP+ cells


title: FACS_SNI_3D_1c

description: ~100 FACS-sorted YFP+ cells


title: FACS2018_Ctrl_3d_1c

description: ~100 FACS-sorted YFP+ cells


title: RPC spheroid 10-cell sample 4


title: ChIP mock_2

city: Boston

first: Simon

middle: L

last: Dove

state: MA

address: 300 Longwood Ave

department: Division of Infectious Diseases

institute: Boston Children's Hospital and Harvard Medical School

library_source: genomic

data_processing:
Reads were mapped to the PAO1 genome and the pPSV plasmid using bowtie2-2.0.6, allowing up to one mismatch per seed
All the mock IP data (sample 2) was merged and used as background for each biological replicate of sample 1
Regions of enrichment were called using QuEST, version 2.42
Regions in each biological replicate were considered peaks if they were 2.5-fold enriched for reads over background, had a positive peak shift and strand correlation, and had a q-value of less than 0.01.
Custom scripts were used to combine peaks identified in each biological replicate of sample 1, keeping only the minimal region identified in at least two biological replicates (final enriched regions).
Genome_build: NC_002516.2
Supplementary_files_format_and_content: wig files were generated from QuEST and represent normalized sequencing reads. Bed file contains coordinates of final enrichned regions, as described above.

molecule: genomic DNA

organism: Pseudomonas aeruginosa PAO1

source_name: Bacterial cells grown to midlog (OD600 ~ 0.5)

extract_protocol:
Cells were lysed and DNA sheared using a Bioruptor water bath sonicator. Lysates were incubated with anti-IgG beads (GE Healthcare). The co-purifying nucleic acid were purified after crosslink reversal at 65°C overnight.
Libraries were prepared using TruSeq DNA Sample Preparation Guide (Illumina) with the following modification: adapters were diluted 10-fold before ligation, adapter-ligated DNA fragments were amplified by 15-cycle PCR using KOD polymerase (Novagen), and subsequent libraries were gel-purified.

treatment_protocol:
IPTG was added (final concentration 1 mM) to induce AlpA expression and cells were grown for another 30 min
Samples were crosslinked with 1% formaldehyde for 30 min and reactions were quenched with 250 mM glycine for 15 min

tag: plasmid


title: ChIP mock_3

growth_protocol: Bacterial cells grown to midlog (OD600 ~ 0.5)


title: RPC spheroid 10-cell sample 6


title: RPC spheroid 10-cell sample 3


title: FACS2018_Ctrl_1d_1a

description: ~100 FACS-sorted YFP+ cells


title: FACS_SNI_1D_1c

description: ~100 FACS-sorted YFP+ cells


title: FACS_SNI_1D_2a

description: ~100 FACS-sorted YFP+ cells


title: FACS_SNI_3D_1b

description: ~100 FACS-sorted YFP+ cells


title: ChIP AlpA-TAP_3


title: RPC spheroid 10-cell sample 2


title: FACS_SNI_1D_2b

description: ~100 FACS-sorted YFP+ cells


title: RPC spheroid 10-cell sample 5


title: FACS_SNI_1D_1b

description: ~100 FACS-sorted YFP+ cells


title: RPC spheroid 10-cell sample 1


title: FACS_SNI_1D_1a

description: ~100 FACS-sorted YFP+ cells


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 25

source_name: Small cell lung cancer colony in liver

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 25

value: Pool-and-split control


title: FACS_SCI_3D_2c

description: ~100 FACS-sorted YFP+ cells


title: ExVivoBlood_HealthyControl_Donor_53_Visit_1

description:
HC 53_v1 vs HC 53_v2_7131_1_4.txt
53_HC_v1_pax

value: Blood


title: ExVivoBlood_HealthyControl_Donor_53_Visit_2

description:
HC 53_v1 vs HC 53_v2_7131_1_4.txt
53_HC_v2_pax


title: EKO_C2

city: changsha

first: Zijun

last: Wang

state: hunan

address: N0.139 RENMIN MIDDLE ROAD

department: Dermatology

country: China

institute: Second Xiangya Hospital of Central South university

data_processing:
The image data of the sequencing fragment detected by the high-throughput sequencer is converted into sequence data by CASAVA base recognition.
HISAT2 software was performed for genomic localization analysis on the filtered sequencing sequence
featureCounts was utilized for efficient chromosome splitting and feature module techniques.
Genome_build: mm10

source_name: Tfh cells

growth_protocol: For isolation of Tfh cells, total splenocyte naïve CD4+T cells from wild-type and E4BP4-cKO mice were isolated.

extract_protocol:
Total RNA samples were extracted using TRIzol reagent according to the manufacturer’s protocol (Life Technologies) and submitted to Novogene for a microarray analysis.
Using the fragmented mRNA as a template and the random oligonucleotide as a primer, the first strand of cDNA was synthesized in the M-MuLV reverse transcriptase system, and then the RNA strand was degraded by RNaseH, and dNTPs was used in the DNA polymerase I system. The raw material synthesizes the second strand of cDNA. The purified double-stranded cDNA was subjected to terminal repair, A tail was added and the sequencing linker was ligated, and cDNA of about 200 bp was screened with AMPure XP beads, PCR amplification was carried out, and the PCR product was purified again using AMPure XP beads to obtain a library.

treatment_protocol: Isolated naïve CD4+T cells were cultured in 100 ml RPMI 1640 (Life Technologies) supplemented with 10% FBS, 1.2 mM L-glutamine, 1 mM sodium pyruvate, 50 mM 2-ME, 0.1 mM nonessential amino acids, and 10,000 U/ml penicillin/streptomycin, containing IL-6 and IL-21 (10 ng/ml each), anti-IFN-γ, anti-IL-4 (10 ug/ml each) and anti-TGF-β Abs (20 ug/ml each) (all cytokines were purchased from R&D Systems) for three days.

value: Spleen

value: Tfh cells

tag: genotype/variation

value: wild-type


title: ExVivoBlood_HealthyControl_Donor_54_Visit_2

description:
HC 54_v2 vs LTBI 2_v3_7132_1_1.txt
54_HC_v2_pax

value: Week 2


title: FACS_SCI_3D_2b

description: ~100 FACS-sorted YFP+ cells


title: FACS_SCI_3D_2a

description: ~100 FACS-sorted YFP+ cells


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 24

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 24


title: FACS_SCI_3D_1b

description: ~100 FACS-sorted YFP+ cells


title: ChIP mock_1


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 23

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 23


title: EKO2

value: E4BP4-conditional knockout


title: ChIP AlpA-TAP_2


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 21

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 21


title: FACS_SCI_3D_1a

description: ~100 FACS-sorted YFP+ cells


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 22

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 22


title: EKO1


title: FACS_SCI_1D_2a

description: ~100 FACS-sorted YFP+ cells


title: FACS_SCI_1D_1c

description: ~100 FACS-sorted YFP+ cells


title: ExVivoBlood_HealthyControl_Donor_51_Visit_2

description:
LTBI 5_v2 vs HC 51_v2_7131_2_4.txt
51_HC_v2_pax


title: ExVivoBlood_HealthyControl_Donor_51_Visit_1

description:
HC 51_v1 vs LTBI 1_v1_7135_1_4.txt
51_HC_v1_pax

value: Week 0


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 20

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 20


title: FACS_SCI_3D_1c

description: ~100 FACS-sorted YFP+ cells

value: Female

value: FACS-sorted L4  YFP+ Dorsal Column Sensory Neurons


title: ChIP AlpA-TAP_1


title: FACS_SCI_1D_1b

description: ~100 FACS-sorted YFP+ cells

value: 10-20 weeks


title: EKO_C1


title: FACS_Ctrl_3D_2c

description: ~100 FACS-sorted YFP+ cells


title: FACS_Ctrl_3D_2a

description: ~100 FACS-sorted YFP+ cells


title: FACS_SCI_1D_1a

description: ~100 FACS-sorted YFP+ cells


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 18

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 18


title: FACS_SNI_1D_2c

description: ~100 FACS-sorted YFP+ cells


title: FACS_Ctrl_3D_2b

description: ~100 FACS-sorted YFP+ cells


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 16

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 16

value: Pool-and-split control


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 15

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 15


title: FACS_SCI_1D_2b

description: ~100 FACS-sorted YFP+ cells


title: FACS_Ctrl_1D_2b

description: ~100 FACS-sorted YFP+ cells


title: FACS_Ctrl_3D_1a

description: ~100 FACS-sorted YFP+ cells


title: FACS_Ctrl_1D_1c

description: ~100 FACS-sorted YFP+ cells


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 14

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 14


title: FACS_Ctrl_1D_2c

description: ~100 FACS-sorted YFP+ cells


title: FACS_Ctrl_1D_2a

description: ~100 FACS-sorted YFP+ cells


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 11

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 11


title: DRG_1d_SCI_3

description: L4 DRG

data_processing:
adaptor trimming using cutadapt
sequence quality control using prinseq 0.20.4
map to reference genome using STAR 2.5.3a
generate transcript count matrix using HTSeq 0.6.1
Differential expression was calculated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: transcript count matrix files generated using HTseq

source_name: L4 Dorsal Root Ganglion

extract_protocol:
L4 DRG were dissected and homogenized in 300μl of lysis buffer on ice and RNA purified using the PureLink RNA Mini kit. RNA quality was assessed using an Agilent Bioanalyzer (RIN > 8). Samples were subjected to DNase treatment. rRNA depletion was achieved with the Ribo-Zero rRNA removal kit.
Library preparation was performed from purified RNA using the SMARTer kit for Illumina sequencing (Clontech) per manufacturer's instructions.

value: L4 Dorsal Root Ganglion

value: 10-12 weeks

value: wild type


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 13

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 13


title: FACS_Ctrl_1D_1a

description: ~100 FACS-sorted YFP+ cells


title: DRG_1d_SCI_4

description: L4 DRG


title: FACS_Ctrl_1D_1b

description: ~100 FACS-sorted YFP+ cells


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 12

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 12


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 10

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 10


title: DRG_1d_SCI_2

description: L4 DRG


title: FACS_Ctrl_3D_1c

description: ~100 FACS-sorted YFP+ cells


title: DRG_1d_SCI_1

description: L4 DRG


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 17

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 17


title: DRG_1d_Ctrl_4

description: L4 DRG


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 9

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 9


title: DRG_1d_Ctrl_1

description: L4 DRG

value: Female


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 8

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 8


title: FACS_Ctrl_3D_1b

description: ~100 FACS-sorted YFP+ cells

value: FACS-sorted L4  YFP+ Dorsal Column Sensory Neurons

value: 10-20 weeks


title: DRG_1d_Ctrl_3

description: L4 DRG


title: DRG_1d_Ctrl_2

description: L4 DRG


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 7

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 7


title: 412-4403

city: Los Angeles

first: Karolina Elzbieta

middle: Kaczor

last: Urbanowcz

state: CA

address: 10833 Le Conte Avenue

institute: UCLA

data_processing:
Cut adapters: Trimmomatic-0.39
Quality check:  FastQC v0.11.8
Alligment: Bowtie2 2.2.5 -N 1 -p 8
Generate counts: Htseq 0.9.1 --nonunique=all  --format=bam --stranded=no --type=exon --idattr=gene_id -a 0  --order=pos
Differential expression: R 3.8, Deseq2

source_name: kidney

extract_protocol:
kidneys were removed, flash frozen on dry ice, and RNA was harvested using Qiagen Rneasy kit.
cDNA libraries were prepared using the Illumina TruSeq kits (Illumina, San Diego, CA).

treatment_protocol: 4-weeks old female apoEKO mice were fed various diets for 14 weeks

value: apoEKO on C57BL/6J background

value: kidney

value: 18 weeks old

value: apoE knockout

tag: treatment

value: Adenine + IMC


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 6

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 6

value: Pool-and-split control


title: 410-4401


title: 409-4303

value: Adenine


title: 403-4103

value: Control


title: 407-4301


title: 404-4201

value: Control + IMC


title: 311-3402


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 4

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 4


title: 302-3102


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 3

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 3


title: 304-3201


title: 310-3401


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 2

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 2


title: 301-3101


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 1

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 1


title: 212-2403


title: KP1 F1 liver colony 10-cel sample 33

value: mSCLC1 F1 liver colony 10-cel sample 33

value: 10-cell sample


title: 207-2301


title: 211-2402


title: 408-4302


title: 208-2302


title: KP1 F1 liver colony 10-cel sample 30

value: mSCLC1 F1 liver colony 10-cel sample 30


title: 206-2203

value: apoEKO on C57BL/6J background


title: RNA PAO1 alpA[stop] + cipro [JP_1139_A_cip]

data_processing:
Sequencing reads from each pooled sample were demulitplexed based on their associated barcod sequence using custom scripts; allowing up to 1 mismatch in the barcode, provided this did not make assignemtn of the read to a different barcode possible. Barcode sequencese were subsequently trimmed from the first read as were terminal G's from the second read that may have been added by SMARTScirbe during template switching.
Reads were aligned to the PAO1 reference genome (NCBI RefSeq NC_002516) using BWA
Read counds were assigned to the genes and other genomic features using custom scripts
Differential expression analysis was conducted with DESeq2.
Genome_build: NC_002516.2
Supplementary_files_format_and_content: tab-delimited text file includes read counts assigned to each feature for each sample

source_name: Bacterial cells grown to OD ∼0.3 to 0.5

growth_protocol: overnight cultures were back-diluted to OD600 of 0.01 in 3 mL LB and grown to mid-log-phase (OD600 of ~0.5)

extract_protocol:
Total RNA was extracted via Direct-Zol RNA Miniprep Kit (Zymo Research)
Illumina cDNA libraries were generated using a modified version of the RNAtag-Seq protocol. 500 ng - 1 µg total RNA was fragmented, depleted of genomic DNA, dephosphorylated and ligated to DNA adapters carrying 5'-AN8-3' barcodes of known sequence with a 5' phosphate and a 3' blocking group. Barcoded RNAs were pooled and depleted of rRNA using the RiboZero rRNA depletion kit (EpiCentre). Pools of barcoded RNAs were converted to Illumina cDNA libraries in 2 main steps: (i) reverse transcription of the RNA using a primer designed to the constant region of the barcode adaptor with addition of an adapter to the 3' end of the cDNA by template switching using SMARTScribe (Clonetech); (ii) PCR amplification using primers whose 5' ends target the constant region of the 3' or 5' adaptors and whose 3' ends contain the full Illumina P5 or P7 sequences.

treatment_protocol: mid-log cultures were treated with ciprofloxacin at a final concentration of 1 ug/mL for 120 minutes

value: PAO1 with early stop codon in alpA

tag: molecule subtype

value: rRNA-depleted RNA


title: 205-2202

value: kidney

value: 18 weeks old

value: apoE knockout


title: KP1 F1 liver colony 10-cel sample 32

value: mSCLC1 F1 liver colony 10-cel sample 32


title: RNA PAO1 alpA[stop] + cipro [JP_1139_B_cip]


title: KP1 F1 liver colony 10-cel sample 31

value: mSCLC1 F1 liver colony 10-cel sample 31


title: 201-2101

value: Control


title: KP1 F1 liver colony 10-cell pool-and-split control replicate 5

value: mSCLC1 F1 liver colony 10-cell pool-and-split control replicate 5

value: Pool-and-split control


title: 308-3302

value: Adenine


title: RNA PAO1 ∆alpA + cipro replicate C

value: deletion of alpA


title: RNA PAO1 ∆alpA + cipro replicate A


title: RNA PAO1 + cipro replicate C

value: wild-type


title: KP1 F1 liver colony 10-cel sample 29

value: mSCLC1 F1 liver colony 10-cel sample 29


title: Mus musculus with MHV at day 7dpi and rescue with medicine. (302.BAM)

city: Beijing

first: Xuefei

last: Guo

state: Bejing

address: Xueyuan road, haidian district

department: Institute of Systems Biomedicine

institute: Peking university health science center

description:
"left" represents the left lung
N2004949_GZR_80-481563826.xlsx

data_processing:
fastqc, cutadapt and fastx_trimmer were used for raw data quality control
tophat2 was used for mapping rads to the genome
the R package Rsubread was used for counts the reads
the GFOLD, a Linux program was used for analyzed DEGs
Genome_build: mm10 and rheMac10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

growth_protocol: All animals were kept and bred in specific pathogen-free conditions.

extract_protocol:
Lungs were removed, flash frozen on dry ice, and RNA was harvested using RNeasy Mini Kit (Qiagen NO. 74104).The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme Biotech Co.,Ltd, Nanjing, China) following the manufacturer's recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Experiments with live SARS-CoV-2 viruses were carried out in the enhanced biosafety level 3 (P3+) facilities. WT Rhesus macaques were inoculated intranasally with SARS-CoV-2 (10^6 TCID50/ml) after anesthesia and  lungs were harvested at 0 dpi, 3 dpi and 5 dpi. WT and hACE2 mice were inoculated intranasally with IAV (10^5 TCID50) and MHV (MHV-a59)  after anesthesia and  lungs were harvested at 0 hour, 6 hour,24, 48hour, 3day, 5day, 7 day post-infection.

tag: infection

value: MHV

tag: time

value: 7 dpi

value: lung


title: RNA PAO1 ∆alpA + cipro replicate B


title: KP1 F1 liver colony 10-cel sample 28

value: mSCLC1 F1 liver colony 10-cel sample 28

value: 10-cell sample


title: Mus musculus with MHV at day 7dpi and rescue with medicine. (301.BAM)

description:
"right" represents the left lung
N2004949_GZR_80-481563826.xlsx


title: RNA PAO1 alpA[stop] + cipro [JP_1139_C_cip]

value: PAO1 with early stop codon in alpA

value: rRNA-depleted RNA


title: Mus musculus with MHV at day 7dpi and rescue with medicine. (303.BAM)


title: KP1 F1 liver colony 10-cel sample 27

value: mSCLC1 F1 liver colony 10-cel sample 27


title: RNA PAO1 + cipro replicate B


title: KP1 F1 liver colony 10-cel sample 26

value: mSCLC1 F1 liver colony 10-cel sample 26


title: Mus musculus with MHV at day 7dpi and rescue with medicine. (300.BAM)


title: RNA PAO1 + cipro replicate A


title: KP1 F1 liver colony 10-cel sample 25

value: mSCLC1 F1 liver colony 10-cel sample 25


title: KP1 F1 liver colony 10-cel sample 24

value: mSCLC1 F1 liver colony 10-cel sample 24


title: Mus musculus with IAV at 1dpi, 3dpi, 5dpi, 7dpi. (WT.BAM)

description:
WT
N2003508_GZR_80-461790558.xlsx

value: IAV

value: 0 dpi


title: KP1 F1 liver colony 10-cel sample 22

value: mSCLC1 F1 liver colony 10-cel sample 22


title: Mus musculus with IAV at 1dpi, 3dpi, 5dpi, 7dpi. (Day7.BAM)

description:
IAV
N2003508_GZR_80-461790558.xlsx


title: 202-2102

value: apoEKO on C57BL/6J background

value: kidney

value: 18 weeks old

value: apoE knockout

value: Control


title: KP1 F1 liver colony 10-cel sample 21

value: mSCLC1 F1 liver colony 10-cel sample 21


title: CA_3

first: dongfang

last: zhao

address: No.35 Tsinghua East Road. Haidian Distric

institute: Beijing Forestry University

data_processing:
Illumina Casava software used for basecalling.Fastx_toolkit_0.0.14 was used to analyze the base quality, A/T/G/C base content, and base error rate distribution for each sample, as well as the Q20, Q30, and GC contents. SeqPrep and Sickle were used to eliminate raw sequencing data
All sequenced reads after quality control were performed de novo assembly using Trinity_v2.8.5. TransRate _v1.0.3 was used to filter and optimize the sequences obtained from the de novo assembly of the transcriptome. CD-HIT_v4.5.7 was used to remove redundant and similar sequences by a sequence clustering method. The assembly integrity of single-copy orthologs was evaluated using BUSCO_3.0.2 to obtain references for subsequent analyses.
Bowtie2_2.3.5.1 was used to compare the sequence data after quality control with assembled non-redundant transcriptome sequences. According to mapped reads, RSEM 1.2.31 was used to evaluate expression levels based on FPKM (Fragments Per Kilobase per Million mapped reads). The FPKM method can be used for standardization to eliminate the effect of gene length and sequencing volume on estimates of expression levels.
Genome_build: A fasta file the generate with Trinity, named Trinity.fasta
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with assembly sequence for every gene and every sample

organism: Dendroctonus valens

source_name: Dendroctonus valens adult

extract_protocol:
Total RNA was extracted from D. valens collected in January and May using TRIzol reagent (Ambion, Austin, TX, USA) and the RNeasy Plus Mini Kit (No. 74134; Qiagen, Hilden, Germany) following the manufacturers’ instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole adult

tag: developmental stage

value: adult

tag: isolate

value: cold


title: Mus musculus with IAV at 1dpi, 3dpi, 5dpi, 7dpi. (Day5.BAM)

description:
IAV
N2003508_GZR_80-461790558.xlsx

value: 5 dpi

tag: tissue

value: lung


title: NA_2

value: normal


title: KP1 F1 liver colony 10-cel sample 23

value: mSCLC1 F1 liver colony 10-cel sample 23

value: 10-cell sample


title: CA_2


title: KP1 F1 liver colony 10-cel sample 20

value: mSCLC1 F1 liver colony 10-cel sample 20


title: KP1 F1 liver colony 10-cel sample 19

value: mSCLC1 F1 liver colony 10-cel sample 19


title: CA_1


title: KP1 F1 liver colony 10-cel sample 18

value: mSCLC1 F1 liver colony 10-cel sample 18


title: Mus musculus with IAV and MHV at 6h, 24h, 48h. (WTMHV-48-BMDM)

description:
"MHV" represents the MHV-a59 virus
N2001796_YFP_80-434295367.xlsx

value: IAV and MHV

value: 48 hpi


title: NL_2

source_name: Dendroctonus valens larva

value: whole larva

value: mature larva


title: KP1 F1 liver colony 10-cel sample 17

value: mSCLC1 F1 liver colony 10-cel sample 17


title: Mus musculus with IAV and MHV at 6h, 24h, 48h. (WTMHV-24-BMDM)

value: 24 hpi


title: Mus musculus with IAV at 1dpi, 3dpi, 5dpi, 7dpi. (Day1.BAM)

description:
IAV
N2003508_GZR_80-461790558.xlsx

value: IAV

value: 1 dpi


title: Mus musculus with IAV and MHV at 6h, 24h, 48h. (WT-MHV-6H)

value: 6 hpi


title: Mus musculus with IAV at 1dpi, 3dpi, 5dpi, 7dpi. (Day3.BAM)

description:
IAV
N2003508_GZR_80-461790558.xlsx

value: 3 dpi


title: KP1 F1 liver colony 10-cel sample 16

value: mSCLC1 F1 liver colony 10-cel sample 16


title: NL_3

value: normal


title: NA_3

value: whole adult

value: adult


title: Mus musculus with IAV and MHV at 6h, 24h, 48h. (WT-IV-6H)

description:
"IV" represents the IAV virus
N2001796_YFP_80-434295367.xlsx

value: lung


title: NA_1


title: NL_1


title: KP1 F1 liver colony 10-cel sample 15

value: mSCLC1 F1 liver colony 10-cel sample 15

value: 10-cell sample


title: Mus musculus with IAV and MHV at 6h, 24h, 48h. (WT-IV-24)

value: IAV and MHV


title: CL_3

value: cold


title: CL_1

value: whole larva


title: Mus musculus with IAV and MHV at 6h, 24h, 48h. (WT-IAV48-BMDM)

description:
"BMDM" represents the Bone marrow derived macrophages
N2001796_YFP_80-434295367.xlsx

value: 48 hpi


title: KP1 F1 liver colony 10-cel sample 14

value: mSCLC1 F1 liver colony 10-cel sample 14


title: CL_2

value: mature larva


title: KP1 F1 liver colony 10-cel sample 12

value: mSCLC1 F1 liver colony 10-cel sample 12


title: Mus musculus with IAV and MHV at 6h, 24h, 48h. (IBDM-WT-CON)

description:
"IBMDM" represents the  Bone marrow derived macrophages
N2001796_YFP_80-434295367.xlsx

value: 0 dpi


title: KP1 F1 liver colony 10-cel sample 13

value: mSCLC1 F1 liver colony 10-cel sample 13


title: cKO_rep1

city: hangzhou

first: lie

last: wang

state: zhejiang

address: Zijingang Campus, Zhejiang University，Yuhangtang Road 866

department: immunology

institute: zhejiang universiry

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 using SOAPnuke with parameters -l 15 -q 0.5 -n 0.1
Aligned to the mm10 genome assembly using BOWTIE2 version 2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Finded different expressed genes using PossionDis with parameters Fold Change >= 2.00 and FDR <= 0.001
Genome_build: mm10

source_name: CD4+ T cell

extract_protocol:
Total RNA was extracted from naïve CD4+ T cells with anti-CD3 stimulated for 4h using the RNeasy kit (Qiagen).
Library construction and sequencing were performed on a BGISEQ-500 platform by the Wuhan Genomic Institution (www.genomics.org.cn, BGI, Shenzhen, China).

value: Zfp281 cKO

value: CD4+ T cell


title: KP1 F1 liver colony 10-cel sample 11

value: mSCLC1 F1 liver colony 10-cel sample 11


title: cKO_rep2


title: WT_rep1

value: wild type


title: hACE2 transgenic mice with SARS-CoV2 at 1dpi, 2dpi, 3dpi, 5dpi and 7dpi. (ACE2-5.BAM)

description:
"ACE2" represents the hACE2 mice
N2001794_YFP_80-434287925.xlsx

value: 5 dpi


title: Mn_2

first: Zhengfan

last: Jiang

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

data_processing:
online_YX developed by Beijing Genomics Institute was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GCF_000001635.25_GRCm38.p5 (mm10) reference using Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Fragments per kilobase of exon per million reads mapped (FPKM) were calculated by RSEM using a protocol from  Langmead, B. et al., Nat. Methods, 2012 and Li, B. & Dewey, C. N., BMC Bioinformatics, 2011.
Genome_build: GCF_000001635.25_GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: tumor infiltrating CD8+ T cells

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using Smart-seq2 protocols

value: tumor infiltrating CD8+ T cells

value: 14days after tumor inoculation

value: MnCl2 5mg/kg, intranasally, every two days


title: hACE2 transgenic mice with SARS-CoV2 at 1dpi, 2dpi, 3dpi, 5dpi and 7dpi. (ACE2-3.BAM)

value: 3 dpi

value: lung


title: KP1 F1 liver colony 10-cel sample 10

value: mSCLC1 F1 liver colony 10-cel sample 10

value: 10-cell sample


title: KP1 F1 liver colony 10-cel sample 6

value: mSCLC1 F1 liver colony 10-cel sample 6


title: KP1 F1 liver colony 10-cel sample 7

value: mSCLC1 F1 liver colony 10-cel sample 7


title: KP1 F1 liver colony 10-cel sample 5

value: mSCLC1 F1 liver colony 10-cel sample 5


title: WT_rep2


title: Mus musculus with MHV at 0 dpi,  1dpi, 3 dpi and 7 dpi. (WML3)

description:
"WML" represents the wt MHV lung
N2001787_YFP_80-434261329.xlsx

value: MHV


title: hACE2 transgenic mice with SARS-CoV2 at 1dpi, 2dpi, 3dpi, 5dpi and 7dpi. (ACE2-1.BAM)

value: 1 dpi


title: con_1

value: saline, intranasally, every two days


title: KP1 F1 liver colony 10-cel sample 3

value: mSCLC1 F1 liver colony 10-cel sample 3


title: hACE2 transgenic mice with SARS-CoV2 at 1dpi, 2dpi, 3dpi, 5dpi and 7dpi. (ACE2-20-1.BAM)

description:
"ACE2-20" represents the hACE2 mice control
N2001794_YFP_80-434287925.xlsx

value: 0 dpi


title: Mus musculus with MHV at 0 dpi,  1dpi, 3 dpi and 7 dpi. (WML7)

value: 7 dpi


title: Mus musculus with MHV at 0 dpi,  1dpi, 3 dpi and 7 dpi. (WML1)


title: KP1 F1 liver colony 10-cel sample 4

value: mSCLC1 F1 liver colony 10-cel sample 4


title: PAO1 ∆relA pPSV38_2

data_processing:
Sequenced reads were trimmed for adaptor sequences and mapped to the LVS genome using bowtie2 v. 2.3.5.1 with parameters -N 1 -L 10 -i S,1,1.00 -D 20
Read counds were assigned to the genes and other genomic features using custom scripts using HTSeq-count
Differential expression analysis was performed with DESeq2
For visualization, the bam alignment files were sorted using samtools (version 1.3.1).
The sorted reads were split by strand and convereted to the bedgraph file format using bedtools (version 2.27.1).
Read depth was normalized to the total number of mapping fragments in sample 1A using custom R scripts.
The normalized bedgraph files were converted to the bigwig file format using the bedgraphToBigWig executable (downloaded from the USCS database) for visualization in a genome brower.
Genome_build: NC_002516.2
Supplementary_files_format_and_content: bgwig files were generated using the bedgraphtobigwig script package from UCSC; Scores represent normalized RNASeq read density

growth_protocol: Overnight cultures were back-diluted to an OD600 of 0.01 in 200 mL LB with 30 µg/mL gentamicin and grown at 37°C with shaking for 2 hrs.

extract_protocol:
Total RNA was extracted using Tri Reagent
Ribosomal RNAs were depleted using the Ribo-Zero Magnetic Kit (Bacteria) (Epicentre). Remaining RNA was used to generate libraries using the NEB-Next Multiplex Small RNA Library Prep Kit for Illumina (New England Biolabs). Libraries were sized-selected by PAGE, isolating fragments corresponding to 150–300 bp.

treatment_protocol: IPTG was added (final concentration 1 mM) and cells were grown for another 90 min to mid-log-phase (i.e. an OD600 of ∼0.3 to 0.5)

value: deltarelA

value: pPSV38 (empty vector)


title: hACE2 transgenic mice with SARS-CoV2 at 1dpi, 2dpi, 3dpi, 5dpi and 7dpi. (ACE2-7.BAM)


title: PAO1 ∆relA pPSV38_3


title: KP1 F1 liver colony 10-cel sample 1

value: mSCLC1 F1 liver colony 10-cel sample 1


title: hACE2 transgenic mice with SARS-CoV2 at 1dpi, 2dpi, 3dpi, 5dpi and 7dpi. (ACE2-20-2.BAM)


title: Mus musculus with MHV at 0 dpi,  1dpi, 3 dpi and 7 dpi. (WIL1)

description:
"WCL" represents the wt IAV lung
N2001787_YFP_80-434261329.xlsx


title: FACS_SCI_1D_2c

description: ~100 FACS-sorted YFP+ cells

value: Female

value: FACS-sorted L4  YFP+ Dorsal Column Sensory Neurons

value: 10-20 weeks


title: KP1 nude liver colony 10-cell pool-and-split control replicate 37

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 37

value: Pool-and-split control


title: PAO1 ∆relA pAlpA_3

value: pAlpA


title: PAO1 ∆relA pPSV38_1


title: KP1 F1 liver colony 10-cel sample 9

value: mSCLC1 F1 liver colony 10-cel sample 9

value: 10-cell sample


title: PAO1 ∆relA pAlpA_2


title: Mus musculus with MHV at 0 dpi,  1dpi, 3 dpi and 7 dpi. (EIL1)

description:
"EIL" represents the WT IAV lung
N2001787_YFP_80-434261329.xlsx

value: MHV

value: 1 dpi

value: lung


title: KP1 nude liver colony 10-cell pool-and-split control replicate 35

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 35


title: KP1 nude liver colony 10-cell pool-and-split control replicate 34

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 34


title: KP1 nude liver colony 10-cell pool-and-split control replicate 36

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 36


title: PAO1 ∆relA pAlpA_1

value: deltarelA


title: PAO1 pPSV38_3

value: wild-type

value: pPSV38 (empty vector)


title: PAO1 pPSV38_2


title: KP1 nude liver colony 10-cell pool-and-split control replicate 33

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 33


title: Mus musculus with MHV at 0 dpi,  1dpi, 3 dpi and 7 dpi. (WCL0)

description:
"WCL" represents the wt control lung
N2001787_YFP_80-434261329.xlsx

value: 0 dpi


title: PAO1 pAlpA_1


title: KP1 nude liver colony 10-cell pool-and-split control replicate 32

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 32


title: KP1 nude liver colony 10-cell pool-and-split control replicate 29

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 29


title: PAO1 pPSV38_1


title: KP1 nude liver colony 10-cell pool-and-split control replicate 30

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 30

value: Pool-and-split control


title: PAO1 pAlpA_2

value: pAlpA


title: KP1 nude liver colony 10-cell pool-and-split control replicate 31

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 31


title: KP1 nude liver colony 10-cell pool-and-split control replicate 28

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 28


title: KP1 nude liver colony 10-cell pool-and-split control replicate 27

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 27


title: KP1 nude liver colony 10-cell pool-and-split control replicate 26

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 26


title: KP1 nude liver colony 10-cell pool-and-split control replicate 25

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 25


title: PAO1 pAlpA_3


title: KP1 nude liver colony 10-cell pool-and-split control replicate 20

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 20


title: KP1 nude liver colony 10-cell pool-and-split control replicate 22

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 22


title: SCNT4C-1

city: Nanjing

first: Mingtian

last: Deng

state: Jiangsu

address: Weigang No.1

department: College of Animal Science and Technology

institute: Nanjing Agricultural University

data_processing:
Reads quality control using fastp
reads that passed quality control were mapped to the goat reference genome (ARS1, NCBI) using hisat2 (version 2.2.1)
Uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation using HTSeq
Gene expression levels were quantiﬁed by calculating normalized fragments per kilobase of exon per million mapped fragments (FPKM) values
Genome_build: ars1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Capra hircus

extract_protocol:
directly lysed embryos were used for cDNA synthesis
smart-seq2

tag: tissue/genotype

value: 4-cell embryos

value: SCNT


title: IVF4C-2

value: IVF


title: SCNT4C-2


title: MGO 5mM -4

city: Aichi-gun

first: Shuichi

last: Matsuyama

address: 94 Hatajiri, Morowa

country: Japan

institute: Nagoya University

hyb_protocol: For microarray hybridization, 1650 ng of Cy3-labeled cRNA was fragmented and hybridized on a slide of bovine 4 × 44K microarray (Agilent Technologies; 023647) at 65°C for 17 hours.

scan_protocol: Slides were scanned on the Agilent G2505C DNA microarray scanner.

data_processing:
Background correction of the Cy3 raw signals was performed using the Agilent Feature Extraction software (version 10.5.1.1). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The raw signal intensity of all probes was subjected to 75 percentile normalization and the baseline was transformed to the median of all samples.

organism: Bos taurus

source_name: Endometrial tissue in cow_8

label_protocol: One-color spike-mix was added to the total RNA prior to the labeling reaction. Labeling was performed using a Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from the endometrial samples using RNeasy Plus Universal Mini kit (Qiagen) according to the manufacturer’s instructions. Total RNA quality and quantity were confirmed using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and a NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA), respectively.

value: endometrium

value: MGO 5mM


title: KP1 nude liver colony 10-cell pool-and-split control replicate 19

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 19


title: IVF4C-1


title: MGO 5mM -2

source_name: Endometrial tissue in cow_6


title: KP1 nude liver colony 10-cell pool-and-split control replicate 21

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 21


title: MGO 5mM -1

source_name: Endometrial tissue in cow_5


title: MGO 5mM -3

source_name: Endometrial tissue in cow_7


title: MGO 0mM -4

source_name: Endometrial tissue in cow_4

value: MGO 0mM


title: SCNT8C-1

value: 8-cell embryos


title: total RNA from sorted BM, kras 1014

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

hyb_protocol: Affymetrix GeneChip miRNA 4.0 Array (Cat No. 902412);  Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720);   Affymetrix Genechip®  fluidics station 450: protocol FS450_0002 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC 4.0.0)

data_processing: Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.

label: Biotin

source_name: BM HSPC

label_protocol: 300ng for Affymetrix FlashTaq Biotin RNA Labeling Kit for Affymetrix GeneChip miRNA Arrays 4.0  P/N 703095 Rev3, (Cat No. 901911)

growth_protocol: standard

extract_protocol: miRNeasy Mini Kit (Qiagen; Hilden, Germany; Cat No. 217004)

treatment_protocol: 250µl pIpC injection 40d after brith

value: hematopoietic stem and progenitor cells


title: MGO 0mM -2

source_name: Endometrial tissue in cow_2


title: total RNA from sorted BM, kras 1013


title: total RNA from sorted BM, kras 1021


title: IVF8C-2


title: MGO 0mM -3

source_name: Endometrial tissue in cow_3


title: total RNA from sorted BM, wt-1023

value: wildtype


title: total RNA from sorted BM, kras 980


title: total RNA from sorted BM, wt-942


title: total RNA from sorted BM, wt-978


title: MGO 0mM -1

source_name: Endometrial tissue in cow_1


title: total RNA from sorted BM, wt-984


title: KO

city: Xi’an

first: Huilong

last: Yin

state: Shaanxi

address: No.169, Changle West Road

institute: Fourth Military Medical University

description:
1868_YHL
B16 tumor from mice

data_processing:
Data was demultiplexed using CellRanger software based on 10X sample indexes and paired-end FASTQ files were generated.
Low quality cells, doublets and potentially dead cells were removed. Cells with  less than or equal 10% percentage of mitochondrial genes and more than or equal 200 genes  detected were retained for subsequent analyses.
Normalization, dimensionality reduction and clustering of single cells were also performed by cellranger.
Differentially expressed genes between each group of cells and other groups of cells were identified bySeurat-Bimod statistical test.
TopGO R package was used for Gene ontology enrichment analysis for these significant differentially expressed genes. The Hypergeometric test in R. Significantly enriched GO terms was used for KEGG pathway enrichment analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: B16 tumor

extract_protocol:
Tumors from WT or KO mice were digested and stained with anti-CD45 antibody and 7-AAD. Live CD45+ cells were sorted by flowcytometry
RNA libraries were prepared with Chromium Single cell 3' Reagent v3 Kits according to the manufacturer's protocol

value: 8 weeks

value: METTL3 deficient


title: WT

description:
1869_YHL
B16 tumor from mice

value: WT


title: F_PKLR_rep2

first: Calvin

last: Pan

address: 675 Charles Young Dr South

description: PKLR.sex.counts.txt

data_processing:
Alignment was performed using HISAT2 against genome build GRCm38.
Quantification and differential expression was performed using DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: PKLR.sex.counts.txt: Feature counts were generated using DESeq2.

source_name: liver

extract_protocol:
Upon sacrifice, tissues were instantly frozen in liquid nitrogen. Frozen tissues were homogenized in QIAzol, and following chloroform phase separation RNA was prepared from the pink phase using Qiagen miRNeasy kits as per original protocol. Total RNA quality was validated with BioAnalyzer (all samples had eRIN >7).
RNA libraries were prepared using Illumina Stranded Total RNA Kit.

tag: strain

value: Female

value: 16 weeks

value: Liver

tag: aav

value: PKLR

tag: diet

value: High fat, high sucrose


title: KP1 nude liver colony 10-cell pool-and-split control replicate 17

data_processing:
Adapters were trimmed using fastq-mcf with the following options:  -q 10 -t 0.01 -k 0 (quality threshold 10, 0.01% occurrence frequency, no nucleotide skew causing cycle removal).
Datasets were aligned to the human (GRCh38.p12)  transcriptome using RSEM. Reference ERCC sequences were also provided for the alignment.
RSEM options  for 10c samples  --bowtie2 --single-cell-prior --paired-end (Bowtie2 transcriptome aligner, single-cell prior to account for dropouts)
Genome_build: GRCm38.82
Supplementary_files_format_and_content: Comma separated file includes read counts from RSEM

source_name: Small cell lung cancer colony in liver

extract_protocol:
All samples were cryoembedded and sectioned on to glass slides (8µm sections). Cell samples were isolated with laser capture microdissection and poly(A) RNA extracted, reverse transcribed and poly(A) PCR amplified prior to library preparation
Amplified cDNA samples were diluted to 0.2 µg/ml for tagmentation with the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s earlier recommendation to purify libraries with 180% (vol/vol) SPRI beads

tag: sample name

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 17

value: Pool-and-split control


title: KP1 nude liver colony 10-cell pool-and-split control replicate 15

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 15

tag: genotype


title: KP1 nude liver colony 10-cell pool-and-split control replicate 16

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 16

tag: sample type


title: F_PKLR_rep1

description: PKLR.sex.counts.txt

tag: Sex

tag: age


title: F_PKLR_rep4

description: PKLR.sex.counts.txt


title: F_PKLR_rep3

description: PKLR.sex.counts.txt


title: SCNT8C-2

value: SCNT


title: F_GFP_rep3

description: PKLR.sex.counts.txt

value: GFP


title: D100E

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

data_processing:
kallisto version 0.43.1 was first used to build an index file for the rat reference transcriptome Rnor_6.0 as downloaded from the Ensembl web site (www.ensembl.org). The sequence reads for each sample were then quantified with the quant function of kallisto.
For each sample, an in-house Perl script was used to sum the kallisto read counts at the transcript level for each gene.
Each sample was assessed with the quality control software RNA-SeQC (DeLuca et al., 2012) and the PtR script from the trinity suite (Grabherr et al., 2011).
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab separated text file with ensembl gene id and counts from kallisto

organism: Rattus norvegicus

source_name: exsanguinated heart

extract_protocol:
Animals were followed for 4 days before termination at which time blood was collected and hearts exsanguinated.
Total RNA from 4 control, 6 D55, and 6 D100 rats was isolated using TRIzol. Sequencing libraries were prepared from 400 ng total RNA using the TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, CA). Libraries were multiplexed and sequenced on the NextSeq 500 (Illumina).

treatment_protocol: Under halothane anesthesia, adult male Wistar rats (240-260 g) were made diabetic with a single dose of 55 (D55) or 100 (D100) mg/kg STZ into the tail vein. After 24 hours, hyperglycemia (>13 mmol/L) was confirmed using a glucometer and glucose test strips.

value: heart

tag: dose (mg/kg)

tag: agent

value: streptozotocin

value: male

tag: tag

value: Wistar


title: F_GFP_rep4

description: PKLR.sex.counts.txt


title: IVF8C-1

value: 8-cell embryos

tag: treatment

value: IVF


title: D100F


title: KP1 nude liver colony 10-cell pool-and-split control replicate 12

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 12


title: D100B


title: KP1 nude liver colony 10-cell pool-and-split control replicate 14

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 14


title: D100D


title: D100C


title: KP1 nude liver colony 10-cell pool-and-split control replicate 10

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 10


title: D55F


title: D100A


title: KP1 nude liver colony 10-cell pool-and-split control replicate 18

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 18


title: M_PKLR_rep4

description: PKLR.sex.counts.txt

value: Male

value: 16 weeks

value: Liver

value: PKLR

value: High fat, high sucrose


title: KP1 nude liver colony 10-cell pool-and-split control replicate 9

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 9

value: Pool-and-split control


title: D55E

value: heart


title: F_GFP_rep1

description: PKLR.sex.counts.txt

value: Female

value: GFP


title: KP1 nude liver colony 10-cell pool-and-split control replicate 13

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 13


title: D55D

value: streptozotocin

value: male

value: Wistar


title: KP1 nude liver colony 10-cell pool-and-split control replicate 8

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 8


title: KP1 nude liver colony 10-cell pool-and-split control replicate 7

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 7


title: D55B


title: D55C


title: M_PKLR_rep3

description: PKLR.sex.counts.txt


title: KP1 nude liver colony 10-cell pool-and-split control replicate 11

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 11


title: M_PKLR_rep1

description: PKLR.sex.counts.txt

value: Male


title: M_GFP_rep4

description: PKLR.sex.counts.txt

value: 16 weeks


title: Control2


title: KP1 nude liver colony 10-cell pool-and-split control replicate 3

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 3


title: M_GFP_rep3

description: PKLR.sex.counts.txt

value: Liver


title: KP1 nude liver colony 10-cell pool-and-split control replicate 6

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 6


title: Control4


title: M_PKLR_rep2

description: PKLR.sex.counts.txt

value: PKLR

value: High fat, high sucrose


title: M_GFP_rep2

description: PKLR.sex.counts.txt


title: F_GFP_rep2

description: PKLR.sex.counts.txt


title: KP1 nude liver colony 10-cell pool-and-split control replicate 4

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 4

value: Pool-and-split control


title: Control3

value: heart


title: M_GFP_rep1

description: PKLR.sex.counts.txt

value: GFP


title: PKLR rep4

description:
replicate 4
PKLR.overexpression.counts.txt

data_processing:
Alignment was performed using HISAT2 against genome build GRCm38
Quantification and differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: feature counts were generated using DESeq2

value: liver


title: PKLR rep5

description:
replicate 5
PKLR.overexpression.counts.txt


title: KP1 nude liver colony 10-cell pool-and-split control replicate 1

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 1


title: KP1 nude liver colony 10-cell sample 35

value: mSCLC1 nude liver colony 10-cell sample 35

value: 10-cell sample


title: acute_myeloid_leukemia [Cyto99]

type: genomic

city: Meldola

first: Giorgia

last: Simonetti

state: FC

address: Via Piero Maroncelli, 40

country: Italy

institute: IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"

description: Genomic data from bone marrow cells of AML patients at diagnosis

hyb_protocol: DNA was processed through the following steps: digestion, ligation, amplification and purification, fragmentation, labeling, hybridization in each array according to the manufacturer's instructions. The volume of 10x Fragmentation Buffer and Fragmentation Reagent has been increased compared to the standard protocol in order to improve the quality of the fragmented DNA, according to the  Affymetrix Technical Support’s suggestion.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files (SNP 6.0 and Cytoscan HD Array) were processed with Genotyping console (GTC) 4.1 and Chromosome Analysis Suite (ChAS) v. 4.1 to obtain CN5.CNCHP and cyhd.cychp files, respectively. CN5.CNCHP and cyhd.cychp were used to check QC, thresholds and MAPD. CEL files were used to produce raw segments files for the analysis as described in the correspective papers.
CEL, CN5.CNCHP and cyhd.cychp files obtained from SNP 6.0 and Cytoscan HD were uploaded.

label: biotin

source_name: mononuclear cells

label_protocol: As per manufacturer (Affymetrix, Thermo Fisher Scientific)

extract_protocol: Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit or the DNA Blood Mini Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: disease

value: acute myeloid leukemia

tag: gender

value: male


title: D55A

value: streptozotocin

value: Wistar


title: acute_myeloid_leukemia [Cyto98]

value: female


title: KP1 nude liver colony 10-cell sample 34

value: mSCLC1 nude liver colony 10-cell sample 34


title: acute_myeloid_leukemia [Cyto97]


title: PKLR rep3

description:
replicate 3
PKLR.overexpression.counts.txt


title: KP1 nude liver colony 10-cell sample 33

value: mSCLC1 nude liver colony 10-cell sample 33


title: PKLR rep2

description:
replicate 2
PKLR.overexpression.counts.txt

value: PKLR


title: acute_myeloid_leukemia [Cyto95]


title: KP1 nude liver colony 10-cell pool-and-split control replicate 5

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 5


title: KP1 nude liver colony 10-cell pool-and-split control replicate 2

value: mSCLC1 nude liver colony 10-cell pool-and-split control replicate 2


title: PKLR rep1

description:
replicate 1
PKLR.overexpression.counts.txt


title: acute_myeloid_leukemia [Cyto94]


title: acute_myeloid_leukemia [Cyto90]


title: acute_myeloid_leukemia [Cyto93]


title: GFP rep5


title: KP1 nude liver colony 10-cell sample 28

value: mSCLC1 nude liver colony 10-cell sample 28


title: acute_myeloid_leukemia [Cyto89]


title: KP1 nude liver colony 10-cell sample 30

value: mSCLC1 nude liver colony 10-cell sample 30


title: GFP rep4

value: GFP


title: KP1 nude liver colony 10-cell sample 29

value: mSCLC1 nude liver colony 10-cell sample 29


title: GFP rep3

value: liver


title: Control1

value: heart


title: KP1 nude liver colony 10-cell sample 32

value: mSCLC1 nude liver colony 10-cell sample 32

value: 10-cell sample


title: KP1 nude liver colony 10-cell sample 27

value: mSCLC1 nude liver colony 10-cell sample 27


title: acute_myeloid_leukemia [Cyto88]

value: acute myeloid leukemia


title: GFP rep2


title: GFP rep1


title: KP1 nude liver colony 10-cell sample 26

value: mSCLC1 nude liver colony 10-cell sample 26


title: B-71 (mRNA)

city: Amsterdam

first: Giulia

last: Mantini

address: De Boelelaan

country: Netherlands

institute: Amsterdam UMC

description:
intron.spanning.rawcounts.txt
mRNA.raw_counts.txt

data_processing:
Intron-spanning reads were detected using the ThromboSeq pipeline while gene counts were detected using STAR and HTSeq counts
filtering steps are described in the material and methods section
Genome_build: Homo_sapiens.GRCh38.77.gtf
Supplementary_files_format_and_content: txt files were rows are intron-reads / genes and columns are the samples.
intron.spanning.rawcounts.txt:  raw counts on intron spanning reads
mRNA.raw_counts.txt:  raw counts on mRNA
miRNA.canonical.rawcounts.txt:  raw counts on canonical miRNAs
isomiRs.rawcounts.txt:  raw counts on isomiRs

source_name: Blood Platelets

extract_protocol:
Total RNA was extracted from platelets using the MiRVAna kit (Ambion) while the protein fraction was stored for proteomics analysis after removal of RNA
thromboSeq protocol described previously (Best et al. Nature Protocols 2019)

tag: disease type

value: Benign

value: F

tag: age at biopsy

tag: cell type

value: platelets


title: acute_myeloid_leukemia [Cyto87]

value: female


title: B-97 (mRNA)


title: shPKLR rep5

description:
replicate 5
shPKLR.knockdown.counts.txt

tag: tissue

tag: strain

value: shPKLR


title: KP1 nude liver colony 10-cell sample 25

first: Kevin

last: Janes

address: Box 800759 Health System

value: mSCLC1 nude liver colony 10-cell sample 25


title: acute_myeloid_leukemia [Cyto86]

value: male


title: acute_myeloid_leukemia [Cyto85]


title: shPKLR rep4

description:
replicate 4
shPKLR.knockdown.counts.txt

tag: aav


title: KP1 nude liver colony 10-cell sample 24

tag: sample name

value: mSCLC1 nude liver colony 10-cell sample 24


title: B-98 (mRNA)


title: shPKLR rep3

description:
replicate 3
shPKLR.knockdown.counts.txt


title: B-82 (mRNA)


title: acute_myeloid_leukemia [Cyto76]


title: acute_myeloid_leukemia [Cyto75]


title: B-10 (mRNA)

value: M


title: B-35 (mRNA)


title: KP1 nude liver colony 10-cell sample 23

value: mSCLC1 nude liver colony 10-cell sample 23

tag: genotype


title: shPKLR rep1

description:
replicate 1
shPKLR.knockdown.counts.txt

value: liver


title: KP1 nude liver colony 10-cell sample 21

value: mSCLC1 nude liver colony 10-cell sample 21

tag: sample type


title: shLUC rep5

description:
replicate 5
shPKLR.knockdown.counts.txt

value: shLUC


title: KP1 nude liver colony 10-cell sample 22

value: mSCLC1 nude liver colony 10-cell sample 22

value: 10-cell sample


title: acute_myeloid_leukemia [Cyto74]

value: acute myeloid leukemia


title: KP1 nude liver colony 10-cell sample 20

value: mSCLC1 nude liver colony 10-cell sample 20


title: acute_myeloid_leukemia [Cyto73]


title: B-2 (mRNA)

value: Benign


title: acute_myeloid_leukemia [Cyto69]


title: shLUC rep4

description:
replicate 4
shPKLR.knockdown.counts.txt


title: KP1 nude liver colony 10-cell sample 18

value: mSCLC1 nude liver colony 10-cell sample 18


title: shLUC rep3

description:
replicate 3
shPKLR.knockdown.counts.txt


title: B-118 (mRNA)

value: F

value: platelets


title: acute_myeloid_leukemia [Cyto68]


title: KP1 nude liver colony 10-cell sample 17

value: mSCLC1 nude liver colony 10-cell sample 17


title: KP1 nude liver colony 10-cell sample 16

value: mSCLC1 nude liver colony 10-cell sample 16


title: B-40 (mRNA)


title: shPKLR rep2

description:
replicate 2
shPKLR.knockdown.counts.txt

value: shPKLR


title: acute_myeloid_leukemia [Cyto67]

value: male


title: shLUC rep1

description:
replicate 1
shPKLR.knockdown.counts.txt


title: B-1 (mRNA)


title: PDAC-26 (mRNA)

value: PDAC

tag: Stage

value: IIB


title: shLUC rep2

description:
replicate 2
shPKLR.knockdown.counts.txt

value: liver


title: KP1 nude liver colony 10-cell sample 15

value: mSCLC1 nude liver colony 10-cell sample 15


title: PDAC-22 (mRNA)

value: M


title: KP1 nude liver colony 10-cell sample 14

value: mSCLC1 nude liver colony 10-cell sample 14


title: acute_myeloid_leukemia [Cyto62]


title: KP1 nude liver colony 10-cell sample 19

value: mSCLC1 nude liver colony 10-cell sample 19

value: 10-cell sample


title: PDAC-17 (mRNA)

value: IA


title: Th1_KO1

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

data_processing:
The quality of RNA-Seq libraries was assessed by FastQC (v0.11.5).
RNA-Seq libraries were mapped to mouse genome mm10 (version M17) using TopHat (v2.1.1).
Expression levels of all genes were estimated by HTseq (v0.6.1), and Reads Per Kilobase per Million mapped reads (RPKM) counts were calculated.
Genome_build: mm10

source_name: Th1 cells

extract_protocol:
Tfh cells (SLAM-loCD44+CD62L-CD4+) and Th1 cells (SLAM-hiCD44+CD62L-CD4+) were directly sorted into TRIzol reagent by a FACSAriaII sorter, and total RNA was extracted using standard Qiagen RNease columns.
RNA libraries were prepared for sequencing using standard Illumina protocols。

tag: stain

tag: genotype/variation

value: Mettl3 KO

value: splenic Th1 cells


title: PDAC-11 (mRNA)


title: Th1_KO2


title: KP1 nude liver colony 10-cell sample 13

institute: University of Virginia

value: mSCLC1 nude liver colony 10-cell sample 13


title: KP1 nude liver colony 10-cell sample 12

value: mSCLC1 nude liver colony 10-cell sample 12


title: acute_myeloid_leukemia [Cyto59]

value: acute myeloid leukemia


title: Th1_WT2

value: wild-type


title: Th1_WT1


title: PDAC-91 (mRNA)

value: IIA

value: F

value: platelets


title: B-127 (mRNA)

value: Benign


title: PDAC-18 (mRNA)

value: PDAC


title: KP1 nude liver colony 10-cell sample 11

value: mSCLC1 nude liver colony 10-cell sample 11


title: acute_myeloid_leukemia [Cyto64]

value: male


title: Mettl3-KO_Eff-CD4-miCLIP_m6A_rep2

data_processing:
m6A-miCLIP-SMARTer-seq data (paired-end) were analyzed as previously described  (Moore et al., Nat Protoc, 2014)
Adapters were removed with Cutadapt (v1.7.1).
fastq2collapse (CTK Tool Kit, v1.0.9) was used to remove duplicated reads, afterwards barcodes of reads were removed.
Reads were mapped to the reference genome (mm10) using BWA (v0.7.12-r1039) with the parameter: -n 0.06.
The mutation information was extracted and PCR duplicates according to BWA’s results were removed separately by parseAlignment.pl (--map-qual 1 --min-len 18) and tag2collapse.pl (-EM 30 --seq-error-model alignment). CIMS.pl was used to calculate the coverage (n) of mutation site and transition number (m). Mutation sites with parameters, m ≥ 3, k/m ≥ 0.01 and k/m ≤ 0.5, were kept. The remaining sites within the RRACH motif sequence were considered as m6A.
Genome_build: mm10
Supplementary_files_format_and_content: bw format

source_name: effector CD4+ T cells

extract_protocol:
Total RNAs were isolated from effector CD4+ T cells of GP61-primed Ctrl or Mettl3fl/flCd4-Cre SMARTA mice, and subjected to m6A-miCLIP-SMARTer-seq protocol.
Approximately 100 ng of mRNAs were used for miCLIP library preparation using a SMARTer smRNA-Seq Kit (Clontech) according to the manufacturer's protocol.

value: splenic effector CD4 T cells


title: Mettl3-KO_Eff-CD4-miCLIP_m6A_rep1


title: KP1 nude liver colony 10-cell sample 10

value: mSCLC1 nude liver colony 10-cell sample 10


title: PDAC-95 (mRNA)


title: acute_myeloid_leukemia [Cyto60]


title: KP1 nude liver colony 10-cell sample 9

value: mSCLC1 nude liver colony 10-cell sample 9

value: 10-cell sample


title: acute_myeloid_leukemia [Cyto56]

value: female


title: Mettl3-WT_Eff-CD4-miCLIP_m6A_rep2


title: acute_myeloid_leukemia [Cyto39]


title: Mettl3-WT_Eff-CD4-miCLIP_m6A_rep1


title: acute_myeloid_leukemia [Cyto3]


title: KO3

data_processing:
The quality of RNA-Seq libraries was assessed by FastQC (v0.11.5).
RNA-Seq libraries were mapped to mouse genome mm10 (version M17) using TopHat (v2.1.1).
Expression levels of all genes were estimated by HTseq (v0.6.1), and Reads Per Kilobase per Million mapped reads (RPKM) counts were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements

source_name: Mettl3 KO_splenic Tfh cells

extract_protocol:
Tfh cells (SLAM-loCD44+CD62L-CD4+) were directly sorted into TRIzol reagent by a FACSAriaII sorter, and total RNA was extracted using standard Qiagen RNease columns.
RNA libraries were prepared for sequencing using standard Illumina protocols。

tag: stain background

value: Mettl3 KO

value: splenic Tfh cells


title: PDAC-9 (mRNA)

value: M


title: KP1 nude liver colony 10-cell sample 7

value: mSCLC1 nude liver colony 10-cell sample 7


title: PDAC-94 (mRNA)

value: IIB


title: KP1 nude liver colony 10-cell sample 5

value: mSCLC1 nude liver colony 10-cell sample 5


title: acute_myeloid_leukemia [Cyto38]

value: acute myeloid leukemia


title: PDAC-4 (mRNA)

value: F

value: platelets


title: KO2


title: acute_myeloid_leukemia [Cyto58]


title: PDAC-8 (mRNA)

value: PDAC


title: acute_myeloid_leukemia [Cyto37]


title: 150250 Cohort 2

city: Toronto

first: Stephanie

middle: Zhi-Juan

last: Xie

state: ON

address: 101 College St. TMDT 8-401

institute: University Health Network

data_processing:
Samples were aligned using STAR 2.5.2b9 against GRCh38 and transcript sequences downloaded from Ensembl build 90. Default parameters were used except for the following: “--chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --chimSegmentReadGapMax parameter 3 --alignSJstitchMismatchNmax 5 -1 5 5”.
Counts were the obtained using HTSeq v0.7.2
HTSeq counts were imported into R (3.4.1) and normalized using RLE
Supplementary_files_format_and_content: normalized counts

source_name: Acute myeloid leukemia

extract_protocol:
AML patient samples were obtained as viably frozen material from the Leukemia Tissue Bank at Princess Margaret Cancer Centre/ University Health Network and  thawed by dropwise addition of X-VIVO + 50% fetal calf serum supplemented with DNase (100μg/mL final concentration, Roche).
RNA was extracted from bulk peripheral blood mononuclear cells (PBMC) using the RNeasy Micro Kit (Qiagen Inc.).
A paired-end 50 base-pair flow-cell lane Illumina High seq 2000 yielded an average of 240 million sequence reads aligning to genome per sample at the Genome Sciences Centre, BC Cancer Agency for cohort 1. Cohort 2 was subjected to 125 bp, paired-end RNA-sequencing on the Illumina HiSeq 2500 with an average of 50 million reads/sample at the Centre for Applied Genomics, Sick Kids Hospital.

tag: sample material

value: peripheral blood

tag: cohort

value: Cohort 2

tag: rnaseq sample name


title: acute_myeloid_leukemia [Cyto36]

tag: disease

tag: gender

value: male


title: KO1


title: acute_myeloid_leukemia [Cyto57]


title: KP1 nude liver colony 10-cell sample 3

value: mSCLC1 nude liver colony 10-cell sample 3


title: WT3

source_name: wild-type_splenic Tfh cells

value: wild-type


title: 150238 Cohort 2


title: KP1 nude liver colony 10-cell sample 8

value: mSCLC1 nude liver colony 10-cell sample 8

value: 10-cell sample


title: 141104 Cohort 2


title: KP1 nude liver colony 10-cell sample 2

value: mSCLC1 nude liver colony 10-cell sample 2


title: KP1 nude liver colony 10-cell sample 1

value: mSCLC1 nude liver colony 10-cell sample 1


title: acute_myeloid_leukemia [Cyto2]


title: acute_myeloid_leukemia [Cyto32]

value: female


title: acute_myeloid_leukemia [Cyto23]


title: 140171 Cohort 2


title: acute_myeloid_leukemia [268_SNP6.0]


title: acute_myeloid_leukemia [Cyto22]


title: 140005 Cohort 2


title: KP1 spheroid 10-cell pool-and-split control replicate 20

source_name: Explanted small cell lung cancer

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 20

value: Pool-and-split control


title: KP1 spheroid 10-cell pool-and-split control replicate 19

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 19


title: KP1 nude liver colony 10-cell sample 4

value: mSCLC1 nude liver colony 10-cell sample 4


title: acute_myeloid_leukemia [Cyto20]

value: acute myeloid leukemia


title: acute_myeloid_leukemia [Cyto179]


title: acute_myeloid_leukemia [213_SNP6.0]


title: KP1 spheroid 10-cell pool-and-split control replicate 17

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 17


title: 130311 Cohort 2


title: KP1 spheroid 10-cell pool-and-split control replicate 18

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 18


title: 120287 Cohort 2

value: peripheral blood


title: acute_myeloid_leukemia [Cyto178]


title: WT2

value: splenic Tfh cells


title: WT1


title: KP1 spheroid 10-cell pool-and-split control replicate 16

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 16


title: 130926 Cohort 2

value: Cohort 2


title: acute_myeloid_leukemia [210_SNP6.0]


title: KP1 spheroid 10-cell pool-and-split control replicate 15

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 15


title: acute_myeloid_leukemia [211_SNP6.0]


title: acute_myeloid_leukemia [270_SNP6.0]

value: male


title: acute_myeloid_leukemia [Cyto176]


title: acute_myeloid_leukemia [212_SNP6.0]


title: 130607 Cohort 2


title: KP1 spheroid 10-cell pool-and-split control replicate 14

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 14


title: 130826 Cohort 2


title: 121020 Cohort 2


title: acute_myeloid_leukemia [209_SNP6.0]


title: acute_myeloid_leukemia [177_SNP6.0]


title: acute_myeloid_leukemia [Cyto175]


title: KP1 spheroid 10-cell pool-and-split control replicate 13

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 13


title: acute_myeloid_leukemia [Cyto174]


title: KP1 spheroid 10-cell pool-and-split control replicate 12

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 12


title: acute_myeloid_leukemia [176_SNP6.0]

value: female


title: 130712 Cohort 2


title: acute_myeloid_leukemia [175_SNP6.0]


title: 120858 Cohort 2


title: KP1 spheroid 10-cell pool-and-split control replicate 11

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 11


title: acute_myeloid_leukemia [Cyto173]


title: acute_myeloid_leukemia [Cyto172]


title: KP1 spheroid 10-cell pool-and-split control replicate 10

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 10

value: Pool-and-split control


title: acute_myeloid_leukemia [174_SNP6.0]


title: 130695 Cohort 2


title: acute_myeloid_leukemia [Cyto177]


title: KP1 spheroid 10-cell pool-and-split control replicate 9

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 9


title: acute_myeloid_leukemia [Cyto171]

value: acute myeloid leukemia


title: acute_myeloid_leukemia [173_SNP6.0]


title: 130578 Cohort 2


title: acute_myeloid_leukemia [Cyto170]


title: acute_myeloid_leukemia [172_SNP6.0]


title: KP1 spheroid 10-cell pool-and-split control replicate 8

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 8


title: 120347 Cohort 2


title: 120899 Cohort 2


title: acute_myeloid_leukemia [171_SNP6.0]


title: KP1 spheroid 10-cell pool-and-split control replicate 7

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 7


title: 120791 Cohort 2

value: peripheral blood


title: acute_myeloid_leukemia [170_SNP6.0]


title: acute_myeloid_leukemia [Cyto167]


title: KP1 spheroid 10-cell pool-and-split control replicate 5

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 5


title: acute_myeloid_leukemia [Cyto166]


title: KP1 spheroid 10-cell pool-and-split control replicate 4

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 4


title: acute_myeloid_leukemia [163_SNP6.0]


title: 110120 Cohort 2

value: Cohort 2


title: acute_myeloid_leukemia [Cyto169]


title: acute_myeloid_leukemia [Cyto165]


title: acute_myeloid_leukemia [161_SNP6.0]


title: KP1 spheroid 10-cell pool-and-split control replicate 3

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 3


title: 100474 Cohort 2


title: 130262 Cohort 2


title: acute_myeloid_leukemia [165_SNP6.0]

value: male


title: acute_myeloid_leukemia [Cyto164]


title: KP1 spheroid 10-cell pool-and-split control replicate 2

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 2


title: acute_myeloid_leukemia [160_SNP6.0]


title: acute_myeloid_leukemia [Cyto168]


title: 90156 Cohort 2


title: acute_myeloid_leukemia [Cyto163]


title: KP1 spheroid 10-cell pool-and-split control replicate 6

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 6


title: KP1 spheroid 10-cell pool-and-split control replicate 1

value: mSCLC1 spheroid 10-cell pool-and-split control replicate 1


title: acute_myeloid_leukemia [159_SNP6.0]


title: 5786 Cohort 2


title: acute_myeloid_leukemia [Cyto162]

value: female


title: KP1 spheroid 10-cell sample 28

value: mSCLC1 spheroid 10-cell sample 28

value: 10-cell sample


title: acute_myeloid_leukemia [146_SNP6.0]


title: 120093 Cohort 2


title: acute_myeloid_leukemia [Cyto161]


title: acute_myeloid_leukemia [145_SNP6.0]


title: 110625 Cohort 2


title: 110500 Cohort 2


title: KP1 spheroid 10-cell sample 27

value: mSCLC1 spheroid 10-cell sample 27


title: KP1 spheroid 10-cell sample 26

value: mSCLC1 spheroid 10-cell sample 26


title: acute_myeloid_leukemia [132_SNP6.0]

value: acute myeloid leukemia


title: acute_myeloid_leukemia [Cyto160]


title: 110484 Cohort 2


title: acute_myeloid_leukemia [Cyto159]


title: acute_myeloid_leukemia [107_SNP6.0]


title: KP1 spheroid 10-cell sample 25

value: mSCLC1 spheroid 10-cell sample 25


title: 120846 Cohort 2


title: acute_myeloid_leukemia [Cyto158]


title: KP1 spheroid 10-cell sample 24

value: mSCLC1 spheroid 10-cell sample 24


title: acute_myeloid_leukemia [Cyto153]


title: 110555 Cohort 2

value: peripheral blood


title: KP1 spheroid 10-cell sample 22

value: mSCLC1 spheroid 10-cell sample 22


title: 90240 Cohort 2

value: peritoneal fluid


title: acute_myeloid_leukemia [105_SNP6.0]


title: acute_myeloid_leukemia [Cyto152]


title: 598 Cohort 2

value: Cohort 2


title: acute_myeloid_leukemia [106_SNP6.0]


title: acute_myeloid_leukemia [103_SNP6.0]


title: acute_myeloid_leukemia [Cyto139]


title: 90543 Cohort 2


title: KP1 spheroid 10-cell sample 21

value: mSCLC1 spheroid 10-cell sample 21


title: acute_myeloid_leukemia [101_SNP6.0]

value: male


title: 90191 Cohort 2


title: acute_myeloid_leukemia [102_SNP6.0]


title: KP1 spheroid 10-cell sample 20

value: mSCLC1 spheroid 10-cell sample 20


title: acute_myeloid_leukemia [Cyto151]


title: acute_myeloid_leukemia [Cyto138]


title: acute_myeloid_leukemia [99_SNP6.0]


title: KP1 spheroid 10-cell sample 19

value: mSCLC1 spheroid 10-cell sample 19


title: acute_myeloid_leukemia [Cyto136]


title: acute_myeloid_leukemia [Cyto134]


title: acute_myeloid_leukemia [81_SNP6.0]


title: DFX05

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

institute: University of Trieste

description: Replicate DFX -05

data_processing:
1 Raw Data    The original raw data from Illumina are transformed to Sequenced Reads by base calling. Raw data are recorded in a FASTQ file, which contains sequence information (reads) and corresponding sequencing quality information.    Every read in FASTQ format is stored in four lines as follows:    @HWI-ST1276:71:C1162ACXX:1:1101:1208:2458 1:N:0:CGATGT     ANTTGTTAACAGGTCAAAATGCAGATCTTCGTGAAGACCCTGACCGGCAAGACCATCACCCTAGAGGTGGAGCCCAGTGACACCATCGAGAACGTGAAG  +  F#,FFFFFFFFFFFFF:FFFF::FFFFF:FFFFFFFFFFFFFFFFFF:F,FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FF:FFFFFF:FFFFFFF    Line 1 begins with a '@' character and is followed by the Illumina Sequence Identifiers and an optional description.  Line 2 is the raw sequence read.  Line 3 begins with a '+' character and is optionally followed by the same sequence identifier and description.  Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of characters as there are bases in the sequence.
2 Data Filtering    Raw reads are filtered to remove reads with adapter contamination or reads with low quality. Only clean reads were used in the downstream analyses.    The filtering process is as follows:  (1) Discard reads with adaptor contamination.  (2) Discard reads when uncertain nucleotides constitute more than 10% of either read (N > 10%).  (3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50% of the read.
3 Mapping To Reference Genome    Mapping the clean reads to the reference genome or the transcriptome is the basis for the next following analysis. Novogene use STAR to accomplish the mapping. For the Human species, if only need the differential expression significant genes, can map reads to the transcriptome directly. In order to avoid losing a lot of effective junction reads, Novogene use STAR software to alignment for RNA-seq sequencing data analysis, the junction reads can be positioned precisely, as shown below.
4 Quantification  Gene expression level is measured by transcript abundance. The greater the abundance, the higher is the gene expression level. In our RNA-seq analysis, the gene expression level is estimated by counting the reads that map to genes or exons. Read count is not only proportional to the actual gene expression level, but is also proportional to the gene length and the sequencing depth. In order for the gene expression levels estimated from different genes and experiments to be comparable, the FPKM is used.    HTSeq software was used to analyze the gene expression levels in this experiment, using the union mode.    The result files present the number of genes with different expression levels and the expression level of single genes.  In general, an FPKM value of 0.1 or 1 is set as the threshold for determining whether the gene is expressed or not.    Comparison between Gene Expression Levels: To compare gene expression levels under different conditions, an FPKM distribution diagram and violin Plot are used. For biological replicates, the final FPKM would be the mean value.

Genome_build: Homo Sapiens (GRCh37/hg19)
Supplementary_files_format_and_content: genes.FPKM.annot.xlsx: FPMK + Gene annotations (Excel format)
Supplementary_files_format_and_content: genes.readcount.annot.xlsx: Readcounts + Gene annotations (Excel format)

source_name: immortalized human Pompe Disease fibroblasts

growth_protocol: Human fibroblasts were cultured in RPMI 1640 medium supplemented with 10% (v/v) fetal calf serum and 50 mg/ml penicillin/streptomycin (Gibco, Paisley, UK). HeLa cells were grown in Dulbecco’s modified Eagle’s medium high glucose medium (Gibco, Paisley, UK) supplemented with 10% (v/v) fetal bovine serum, 50 mg/ml penicillin/streptomycin and 2 mM l-glutamine (Gibco, Paisley, UK). Cells were maintained at 37°C in a humidified atmosphere enriched with 5% (v/v) CO2

extract_protocol:
Total RNA was isolated using the TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
RNA sequencing  (150PE, 60M read pair per sample) was performed by Novogene (https://en.novogene.com/).  RNA libraries were prepared for sequencing using standard Illumina protocols.  Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies).  Insert size was checked on an Agilent 2100 and quantified using quantitative PCR (Q-PCR).

treatment_protocol: After exposure of human PD fibroblasts to 10 µM Deferoxamine or 0.1% DMSO (control condition) for three days, cells were harvested.

value: fibroblast

tag: treatment

value: Deferoxamine 10 microM


title: KP1 spheroid 10-cell sample 17

value: mSCLC1 spheroid 10-cell sample 17


title: acute_myeloid_leukemia [80_SNP6.0]


title: DFX06

description: Replicate DFX -06

tag: cell type


title: KP1 spheroid 10-cell sample 23

value: mSCLC1 spheroid 10-cell sample 23

value: 10-cell sample


title: DFX04

description: Replicate DFX -04


title: KP1 spheroid 10-cell sample 16

value: mSCLC1 spheroid 10-cell sample 16


title: acute_myeloid_leukemia [56_SNP6.0]

value: acute myeloid leukemia

value: female


title: acute_myeloid_leukemia [Cyto133]


title: acute_myeloid_leukemia [55_SNP6.0]


title: acute_myeloid_leukemia [Cyto126]


title: CTR03Fib

description: Replicate DMSO (Control)-03

value: DMSO  0.1%


title: CTR02Fib

description: Replicate DMSO (Control)-02


title: KP1 spheroid 10-cell sample 15

value: mSCLC1 spheroid 10-cell sample 15


title: acute_myeloid_leukemia [Cyto125]


title: acute_myeloid_leukemia [3_SNP6.0]


title: acute_myeloid_leukemia [Cyto123]


title: KP1 spheroid 10-cell sample 14

value: mSCLC1 spheroid 10-cell sample 14


title: KP1 spheroid 10-cell sample 12

value: mSCLC1 spheroid 10-cell sample 12


title: acute_myeloid_leukemia [Cyto124]


title: KP1 spheroid 10-cell sample 13

value: mSCLC1 spheroid 10-cell sample 13


title: acute_myeloid_leukemia [52_SNP6.0]


title: RRBS_dermalfibroblasts_control_15-11C

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated MethylSeq pipeline based on Bismark and methylation extractor from Babraham (https://www.bioinformatics.babraham.ac.uk/projects/bismark/)
Bismark aligns reads to the genome via Bowtie2 and maps bisulfite converted sequence reads and determine cytosine methylation states producing coverage files
Coverage files from Bismark were analyzed via the  Biconducotr R package RnBeads
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited .txt files include BISMARK output for each Sample

source_name: cultured dermal fibroblasts

growth_protocol: Primary dermal fibroblasts lines were established from skin biopsies taken from healthy control donors or patients with systemic sclerosis (scleroderma). Fibroblasts were cultured for 3 passages in DMEM + 20% FBS + Antibiotic-Antimycotic , then DNA was isolated.

extract_protocol:
DNA was isolated using DNeasy kit (Qiagen) following the manufacturer’s protocols. RRBS was performed using the Ovation® RRBS Methyl-Seq System 1–16 (NuGEN Technologies) following the manufacture’s procedure.
Library construction was done following Ovation® RRBS Methyl-Seq System (part no. 0353)

tag: disease status

value: control

tag: disease subtype

tag: Sex

tag: age at skin biopsy

tag: passage


title: CTR01Fib

description: Replicate DMSO (Control)-01

tag: genotype


title: RRBS_dermalfibroblasts_SSc_15-14A

value: systemic sclerosis

value: diffuse


title: KP1 spheroid 10-cell sample 11

city: Charlottesville

tag: sample name

value: mSCLC1 spheroid 10-cell sample 11

tag: sample type


title: KP1 spheroid 10-cell sample 18

value: mSCLC1 spheroid 10-cell sample 18


title: acute_myeloid_leukemia [2_SNP6.0]

value: male


title: acute_myeloid_leukemia [Cyto121]


title: RRBS_dermalfibroblasts_control_14-9C


title: KP1 spheroid 10-cell sample 10

value: mSCLC1 spheroid 10-cell sample 10


title: Macaca mulatta lung with SARS-CoV and SARS-CoV2. (Du-1.BAM)

first: Xuefei

last: Guo

address: Xueyuan road, haidian district

description:
"Du-1" represents the rhesus macaques lung-control 1
N2003482_YFP_80-461806545.xlsx

data_processing:
fastqc, cutadapt and fastx_trimmer were used for raw data quality control
tophat2 was used for mapping rads to the genome
the R package Rsubread was used for counts the reads
the GFOLD, a Linux program was used for analyzed DEGs
Genome_build: mm10 and rheMac10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Macaca mulatta

source_name: Lung

extract_protocol:
Lungs were removed, flash frozen on dry ice, and RNA was harvested using RNeasy Mini Kit (Qiagen NO. 74104).The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme Biotech Co.,Ltd, Nanjing, China) following the manufacturer's recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: infection

value: SARS-CoV and SARS-CoV-2

value: WT

tag: time

value: 0 dpi

tag: tissue

value: lung


title: acute_myeloid_leukemia [Cyto118]

value: acute myeloid leukemia

value: female


title: Macaca mulatta with SARS-CoV2 detected in different parts. (G.BAM)

description:
"G" represents the rhesus macaques lung-dpi 5-4
N2002260_YFP_80-440791514.xlsx

value: 5 dpi


title: KP1 spheroid 10-cell sample 9

value: mSCLC1 spheroid 10-cell sample 9

value: 10-cell sample


title: KP1 spheroid 10-cell sample 8

value: mSCLC1 spheroid 10-cell sample 8


title: acute_myeloid_leukemia [Cyto117]


title: Macaca mulatta with SARS-CoV2 detected in different parts. (C.BAM)

description:
"C" represents the rhesus macaques lung-dpi 3-5
N2002260_YFP_80-440791514.xlsx

value: 3 dpi


title: RRBS_dermalfibroblasts_SSc_14-13A

value: systemic sclerosis

value: sine


title: acute_myeloid_leukemia [Cyto116]


title: RRBS_dermalfibroblasts_SSc_13-11A

value: diffuse


title: KP1 spheroid 10-cell sample 7

value: mSCLC1 spheroid 10-cell sample 7


title: acute_myeloid_leukemia [Cyto122]


title: RRBS_dermalfibroblasts_control_12-IC

value: control