title: Healthy control [CTRL107]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL107
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL105]

status: Public on May 25 2021

type: SRA

city: ראשון לציון

first: Iddo

last: Magen

state: Not in US

address: בן אליעזר 32, 17

country: Israel

institute: Weizmann Institute

description:
Healthy control
CTRL105
Controls_only.txt
miR_181_controls.csv

library_source: transcriptomic

data_processing:
Data were aligned to the genome using the GeneGlobe pipeline (https://geneglobe.qiagen.com/us/)
Data were filtered using the following specifications: >50 UMIs in >60% of the samples for longitudinal analysis, >100 UMIs on average for other analyses
Data were corrected for batch using the ComBat function in R and then normalized by DESeq2
Supplementary_files_format_and_content: txt files contain raw UMI counts, after alignment
Supplementary_files_format_and_content: xls files contain batch and DESeq2 corrected UMIs, after filtration of low-abundance miRNAs. Related R code are in the same folder
Supplementary_files_format_and_content: csv files contain categorial values for miRNAs and other clinical features, to be run by an R code for calculation of hazard ratios by COX proportional hazard analysis. Related R codes are in the same folder

molecule: total RNA

organism: Homo sapiens

source_name: Blood plasma

extract_protocol:
Plasma were isolated from blood and total RNA was extracted using the Qiagen miRNeasy micro kit (Cat# 217184)
libraries were prepared from 7.5 ng of total RNA using the QIAseq miRNA library kit and QIAseq miRNA NGS 48 Index IL (Qiagen, Cat# 331505 and 331565), by an experimenter who was blinded to the identity of samples. Samples were randomly allocated to library preparation and sequencing in batches. Libraries with different indices were multiplexed and sequenced on NextSeq 500/550 v2 flow cell or Novaseq SP100 (Illumina), with 75bp single read and 6bp index read.

tag: condition

value: Healthy control


title: Healthy control [CTRL110]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL110
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL103]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL103
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL102]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL102
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL104]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL104
Controls_only.txt
miR_181_controls.csv


title: Healthy control [CTRL101]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL101
Controls_only.txt
miR_181_controls.csv


title: circulating tumor cell P4_4

city: Saarbrücken

first: Tobias

last: Fehlmann

address: Campus E2 1

country: Germany

institute: Saarland University

data_processing:
Basecalls performed with bcl2fastq (2.20.0.422)
Adapter trimming and quality trimming was performed with cutadapt 2.10. Reads were trimmed at the 3’ end with a quality cutoff of 20. In addition to the 3’ adapter, polyA tails, polyG tails, and PCR primers were removed. Trimming was performed up to 3 times per read while allowing an error rate of 10%, at most 2 N bases and requiring a minimum length of 18 bases to keep the read.
The remaining reads were mapped against the primary assembly of the human genome GRCh38 using STAR (2.7.5b) with parameters: “--outFilterMultimapNmax 50 --outFilterScoreMinOverLread 0 --outFilterMultimapScoreRange 0 --outFilterMatchNmin 18 --outFilterMatchNminOverLread 0 --outFilterMismatchNoverLmax 0.04 --alignIntronMax 1 --outSAMstrandField intronMotif”.
For the samples containing miRExplore an additional mapping was performed with RazerS 3 (3.5.3) with parameters:  “--forward -so 1 -dr 0 -rr 100 --percent-identity 80”
Reads were quantified with featureCounts (1.5.2) with parameters -F SAF -O -M -f –fracOverlap 0 -s 0
MiRNAs were quantified with miRMaster 1.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: mir_explore_counts.txt: tab-delimited text file contaiing the raw counts of all miRExplore sequences for each sample.
Supplementary_files_format_and_content: sce_counts.txt: tab-delimited text file containing the raw counts of all RNAs of all single cell equivalent samples.
Supplementary_files_format_and_content: sce_mirna_expr_rpmmm_norm.txt: tab-delimited text file containing the RPMMM normalized miRNA counts for all single cell equivalent samples.
Supplementary_files_format_and_content: sclc_mirna_expr_dedup_counts.txt: tab-delimited text file containing the UMI deduplicated miRNA counts for all circulating tumor cell samples.

source_name: circulating tumor cell

extract_protocol: Single cell miRNA-Seq /w 19 protocols, miRExplore spike-in, single cell equivalents and 67 circulating tumor cells

tag: age

tag: Sex

value: Male

tag: tissue

value: Whole blood

tag: cell line

value: circulating tumor cell

tag: disease

value: small cell lung cancer

tag: sample type

value: single cell

tag: replicate

tag: protocol


title: Reagents only N_1

source_name: not applicable

value: not applicable

value: Reagents only


title: circulating tumor cell P4_1


title: circulating tumor cell P3_9


title: circulating tumor cell P3_3


title: circulating tumor cell P7_1

value: Female


title: circulating tumor cell P7_3


title: circulating tumor cell P3_2


title: circulating tumor cell P3_13


title: Reagents only N_2


title: circulating tumor cell P3_6


title: circulating tumor cell P4_5


title: circulating tumor cell P3_12


title: circulating tumor cell P3_11


title: circulating tumor cell P4_3


title: Primary Tumor 9

type: RNA

city: Kolkata

first: Susanta

last: Roychoudhury

state: West Bengal

address: Mahatma Gandhi Road, Thakurpukur

country: India

institute: Saroj Gupta Cancer Centre & Research Institute

description:
replicate 3
SAMPLE 14

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol in Illumina iScan Microarray scanner

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio 2.0

label: biotin

source_name: Patient

label_protocol: Biotinylated cRNA were prepared with the Epicentre Target Amp Nano Labeling kit for Illumina arrays.

growth_protocol: Primary uterine cervical lesions (n=11) and normal ectocervical tissue (n=5) were collected from the hospital section of Chittaranjan National Cancer Institute (CNCI), Kolkata, India after appropriate approval of the Institutional Ethical Committee and written informed consent from respective patients. Normal ectocervical tissue was obtained from patients who underwent hysterectomy for benign reasons. SiHa (HPV16 positive), HeLa (HPV18 positive) and C33A (HPV negative) cell lines were obtained from NCCS, Pune and were grown and maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with antibiotics and 10% fetal bovine serum and grown at 37 C, 5% CO2.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser/Denaturing RNA agarose gel electrophoresis.

tag: gender

tag: tissue type

value: hrHPV positive cervical squamous cell carcinoma


title: MM106-EaWT-24HPI-rep1_Cy3

city: Angers

first: Alexandre

last: Degrave

address: André Lenôtre

country: France

institute: Agrocampus Ouest

hyb_protocol: The hybridization was performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532 and 635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. Pair-data files were extracted from the scanned images using DEVA 1.2.1 software (Roche).

data_processing: Statistical analyses were performed using R version 2.14.1 (R Development Core Team, 2011) and the package LIMMA 3.10.1 (Smyth G.K., 2005) from the Bioconductor project. Data were normalized by the lowess method from LIMMA.

organism: Malus domestica

source_name: Apple genotype MM106 (susceptible) leaf tissues, infiltrated with Ea CFBP1430 wild type strain, sampled 24 hours after inoculation.

label_protocol: 200ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized.

growth_protocol: Malus × domestica MM106 or ME010 scions, grafted on MM106 rootstocks, were cultivated in greenhouse (semi-controlled conditions, natural photoperiod supplemented with artificial light if needed during a 16h photophase, 23-25 °C day, 17 °C night, watering every 2-4 days with tap water) in standard potting soil. Bacterial strains were grown overnight at 26°C on solid King’s B medium.

extract_protocol: Each sample corresponds to a pool of the youngest expanded leaf from 3 replicate plants per condition. Samples were snap-frozen in liquid nitrogen and further ground to a fine powder in liquid nitrogen using a tissue lyser (Retsch, Haan, Germany) and total RNA were extracted using the Nucleospin® RNA Plant Kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s procedure. Purity and concentration of samples were assayed with a NanoDrop® One.

treatment_protocol: Bacterial suspensions were prepared in reverse osmotic water supplemented by 0.01 % of wetting agent Silwet L-77 from an exponential growth phase culture cultivated on solid King’s B medium overnight at 26 °C. The bacterial titer was adjusted 107 CFU mL-1 and used to inoculate young apple leaves by vacuum infiltration (3 min beyond -0.9 MPa).

value: Leaf

tag: genotype

tag: resistance to ea

value: Susceptible

tag: inoculated

value: Inoculated

tag: bacterial strain

value: Wild type

tag: sampling time


title: MM106-EaWT-6HPI-rep1_Cy3

source_name: Apple genotype MM106 (susceptible) leaf tissues, infiltrated with Ea CFBP1430 wild type strain, sampled 6 hours after inoculation.


title: MM106-no-inoc-rep2_Cy5

source_name: Apple genotype MM106 (susceptible) leaf tissues, untreated samples.

value: Not inoculated


title: ME010-no-inoc-rep1_Cy5

source_name: Apple genotype ME010 (resistant) leaf tissues, untreated samples.

value: Resistant


title: ME010-no-inoc-rep2_Cy3


title: MM106-no-inoc-rep1_Cy3


title: MM106-EaWT-6HPI-rep1_Cy5


title: circulating tumor cell P3_10


title: ME010-EaWT-6HPI-rep1_Cy3

source_name: Apple genotype ME010 (resistant) leaf tissues, infiltrated with Ea CFBP1430 wild type strain, sampled 6 hours after inoculation.


title: ME010-EaWT-6HPI-rep1_Cy5


title: circulating tumor cell P5_4


title: circulating tumor cell P5_2


title: Healthy control [CTRL100]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL100
Controls_only.txt
miR_181_controls.csv


title: circulating tumor cell P1_7


title: circulating tumor cell P1_31


title: Treg_vol307_second_inf_baseline

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

data_processing:
Raw reads were QC assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).  Unwanted primer sequences and homopolymeric tracts were removed using cutadapt v1.9 (parameters:  --no-match-adapter-wildcards -b GTATCAACGCAGAGTAC -B GTATCAACGCAGAGTAC -b NNNNNNNNNNNNNNNNNNNN -B NNNNNNNNNNNNNNNNNNNN -b TTTTTTTTTTTTTTTTTTTT -B TTTTTTTTTTTTTTTTTTTT -b GGGGGGGGGGGGGGGGGGGG -B GGGGGGGGGGGGGGGGGGGG -m 25 -O 10 -n 5; Weblink: https://cutadapt.readthedocs.io/en/stable/).
Read pairs were aligned using bowtie2 (v2.2.7, doi.org/10.1038/nmeth.1923) to the human transcripts set downloaded from ensembl (release 96).  Bowtie2 parameters applied were --very-sensitive -p 24 --no-mixed --no-discordant --no-unal.  Read counts were extracted from the bam files using samtools idxstats (http://www.htslib.org/doc/samtools.html) prior to subsequent manipulation in R.
Pair-wise comparisons of sample groups were performed using the DEseq2 Bioconductor package (doi.org/10.1186/s13059-014-0550-8) after the removal of hemoglobin reads. Alpha value applied was 0.05, logFC shrinkage not applied.
Genome_build: ensembl release 96
Supplementary_files_format_and_content: Tab-delimited text files containing read counts for all transcripts; first column is transcriptID, second column is length of transcript, third column is number of read counts

source_name: blood - flow sorted CD4 T cells

extract_protocol:
Total RNA was extracted using a modified phenol-chloroform protocol (doi.org/10.1038/nprot.2006.83) and RNA quality assessed by Bioanalyser (RIN > 8). cDNA was generated from 1 ng total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio #634894) and amplified using 12 cycles of PCR.
Libraries were constructed from 150 pg of cDNA using the Nextera XT DNA Library Preparation Kit (Illumina #FC-131-1024). Equimolar library pools were sequenced across 4 flow cells at the Wellcome Trust Clinical Research Facility, Western General Hospital (Edinburgh, UK) using the NextSeq 550 platform (Illumina) generating 75 bp paired end reads.

treatment_protocol:
Three CD4 T cell subsets were flow sorted ex vivo from volunteers experimentally infected for the first, second or third time with malaria at baseline before infection and 6-days after drug treatment. RNA from 10,000 T cells was immediately preserved in 1 ml TRIzol reagent (ThermoFisher #15596026) and stored at -80°C.
•     Tm : effector memory (CD3+ CD4+ CD127+ CD25- CCR7- CD45RA-)
•     Tn: naive (Tn: CD3+ CD4+ CD127+ CD25- CCR7+ CD45RA+)
•     Tr: regulatory (Tr: CD3+ CD4+ CD127- CD25+)
See supplementary file for gating strategies. During first malaria infection 30 - 80% of effector memory CD4 T cells and 15 - 35 % of regulatory T cells showed an activated CD38high phenotype. In contrast following second and third infection less than 5% of both T cell subsets were activated.

tag: t cell subset

value: regulatory CD4 T cells

tag: volunteer code

tag: number of malaria infections

value: two

tag: a) before (baseline, a) or b) after (t6, b) malaria infection


title: Treg_vol308_third_inf_T6

value: three


title: Treg_vol306_third_inf_baseline


title: Treg_vol306_third_inf_T6


title: Treg_vol307_second_inf_T6


title: circulating tumor cell P1_9

tag: age

tag: Sex

tag: tissue

value: Whole blood


title: circulating tumor cell P1_6

tag: cell line

value: circulating tumor cell

tag: disease

tag: sample type


title: Treg_vol305_third_inf_T6


title: circulating tumor cell P1_4

value: small cell lung cancer

tag: replicate

tag: protocol


title: Treg_vol308_third_inf_baseline


title: circulating tumor cell P5_1

value: single cell


title: Treg_vol305_third_inf_baseline


title: Treg_vol304_third_inf_T6


title: circulating tumor cell P1_30


title: circulating tumor cell P1_5


title: Treg_vol304_third_inf_baseline


title: circulating tumor cell P1_3


title: Treg_vol320_first_inf_T6

value: one


title: Treg_vol302_second_inf_baseline


title: Treg_vol302_second_inf_T6


title: circulating tumor cell P1_28


title: circulating tumor cell P1_27


title: Treg_vol320_first_inf_baseline


title: circulating tumor cell P1_22


title: Treg_vol315_first_inf_T6


title: Treg_vol315_first_inf_baseline


title: circulating tumor cell P1_26


title: circulating tumor cell P1_20


title: circulating tumor cell P1_25


title: circulating tumor cell P1_21


title: Treg_vol301_third_inf_T6


title: circulating tumor cell P1_2


title: Treg_vol310_third_inf_baseline


title: circulating tumor cell P1_19


title: Treg_vol313_first_inf_baseline


title: circulating tumor cell P1_17


title: Treg_vol310_third_inf_T6


title: circulating tumor cell P1_14


title: circulating tumor cell P1_12


title: circulating tumor cell P1_10


title: circulating tumor cell P1_15


title: Tnaive_vol308_third_inf_T6

value: naïve CD4 T cells


title: circulating tumor cell P6_2

value: Male


title: circulating tumor cell P1_24

value: Female


title: circulating tumor cell P2_8


title: circulating tumor cell P1_16


title: Tnaive_vol306_third_inf_T6


title: Tnaive_vol304_third_inf_T6


title: Tnaive_vol307_second_inf_baseline


title: Tnaive_vol306_third_inf_baseline


title: circulating tumor cell P1_11


title: Tnaive_vol308_third_inf_baseline


title: Tnaive_vol305_third_inf_baseline


title: Tnaive_vol305_third_inf_T6


title: circulating tumor cell P1_1


title: circulating tumor cell P2_6


title: Tnaive_vol320_first_inf_T6


title: Tnaive_vol320_first_inf_baseline


title: Tnaive_vol307_second_inf_T6


title: Tnaive_vol304_third_inf_baseline


title: circulating tumor cell P1_13


title: circulating tumor cell P6_6


title: Treg_vol301_third_inf_baseline


title: circulating tumor cell P1_29


title: circulating tumor cell P2_4


title: Tnaive_vol302_second_inf_T6


title: circulating tumor cell P2_9


title: Tnaive_vol302_second_inf_baseline


title: Tnaive_vol301_third_inf_T6


title: Tnaive_vol301_third_inf_baseline


title: circulating tumor cell P2_7


title: circulating tumor cell P2_20


title: circulating tumor cell P2_22


title: Tnaive_vol313_first_inf_baseline


title: Tnaive_vol315_first_inf_baseline


title: Tnaive_vol310_third_inf_baseline


title: circulating tumor cell P2_21


title: Tnaive_vol315_first_inf_T6


title: circulating tumor cell P2_2


title: Tmem_vol308_third_inf_T6

value: effector memory CD4 T cells


title: Tmem_vol307_second_inf_T6


title: circulating tumor cell P2_23


title: circulating tumor cell P2_3


title: circulating tumor cell P2_18


title: circulating tumor cell P2_15


title: Tmem_vol307_second_inf_baseline


title: circulating tumor cell P2_16


title: Tmem_vol305_third_inf_T6


title: Tmem_vol306_third_inf_T6


title: Tmem_vol306_third_inf_baseline


title: circulating tumor cell P2_14


title: Tmem_vol308_third_inf_baseline


title: circulating tumor cell P2_12


title: circulating tumor cell P2_11


title: Tmem_vol304_third_inf_T6


title: circulating tumor cell P2_10


title: Tmem_vol305_third_inf_baseline


title: mammary gland/breast epithelial cell SB_3_SCE

source_name: mammary gland/breast epithelial cell

value: mammary gland/breast epithelial cell

tag: culture collection

value: adenocarcinoma

value: SB

tag: genotype

value: Single cell equivalent


title: mammary gland/breast epithelial cell SB_1_SCE


title: circulating tumor cell P2_1


title: mammary gland/breast epithelial cell SBN_CL_3_SCE


title: mammary gland/breast epithelial cell SB_2_SCE


title: Tnaive_vol310_third_inf_T6


title: Tmem_vol302_second_inf_T6


title: Tmem_vol315_first_inf_T6


title: mammary gland/breast epithelial cell SBN_CL_1_SCE


title: Tmem_vol301_third_inf_baseline


title: mammary gland/breast epithelial cell SBN_3_SCE

value: SBN


title: mammary gland/breast epithelial cell SBN_1_SCE


title: mammary gland/breast epithelial cell SBN_2_SCE


title: circulating tumor cell P2_19


title: Tmem_vol310_third_inf_T6


title: mammary gland/breast epithelial cell 4N_CL_3_SCE


title: Tmem_vol310_third_inf_baseline


title: mammary gland/breast epithelial cell 4N_CL_2_SCE


title: Tmem_vol304_third_inf_baseline


title: Tmem_vol313_first_inf_baseline


title: Tmem_vol302_second_inf_baseline


title: Tmem_vol320_first_inf_T6


title: BD14

city: Athens

first: Maria

middle: G.

last: Tektonidou

state: Please choose a State

address: Mikras Asias 75

country: Greece

institute: National and Kapodistrian University of Athens

description:
BD
N142

data_processing:
Basecalling on Illumina NextSeq550
Alignement with STAR on hg38 with pipeline provided by Lexogen and BlueBee
Bam files summarised to 3’UTR count table with GenomicRanges R package
Gene coubt table normalised with DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: bigWig constructed through metaseqR2 with stranded=FALSE, normTo=1e+08

source_name: PBMCs

extract_protocol:
PBMCs were isolated by Ficoll density gradient centrifugation (Ficoll-Paque PLUS, Sigma-Aldrich). Total RNA was isolated from peripheral blood cells using Trizol reagent (Invitrogen, Life Technologies).
500 ng of total RNA per sample were processed using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen) for library preparation.
RNA sequencing. The kit creates Illumina compatible libraries of sequences close to the 3’ end of polyadenylated RNA.

value: Blood

tag: gender

value: male

tag: disease state

value: Behcet's Disease


title: BD13

description:
BD
N197


title: Tmem_vol320_first_inf_baseline


title: mammary gland/breast epithelial cell 4N_C3_2_SCE


title: mammary gland/breast epithelial cell 4N_C3_1_SCE


title: BD11

description:
BD
N178


title: Tmem_vol315_first_inf_baseline


title: mammary gland/breast epithelial cell 4N_CL_1_SCE


title: BD12

description:
BD
N185


title: mammary gland/breast epithelial cell SBN_CL_2_SCE


title: Tmem_vol301_third_inf_T6

value: three


title: mammary gland/breast epithelial cell 4N_2_SCE


title: BD10

description:
BD
N166


title: mammary gland/breast epithelial cell 4N_3_SCE


title: mammary gland/breast epithelial cell 4N_C3_3_SCE


title: BD9

description:
BD
N161


title: BD7

description:
BD
N146


title: mammary gland/breast epithelial cell CL_3_SCE

value: CL


title: BD8

description:
BD
N158


title: BD6

description:
BD
N145


title: mammary gland/breast epithelial cell SB_4N_3_SCE


title: BD5

description:
BD
N232


title: BD3

description:
BD
N199


title: BD4

description:
BD
N202


title: mammary gland/breast epithelial cell 4N_1_SCE


title: mammary gland/breast epithelial cell SB_4N_2_SCE


title: BD2

description:
BD
N270

value: female


title: mammary gland/breast epithelial cell SB_4N_1_SCE

value: single cell


title: HC11

description:
healthy donor
N258

value: Healthy


title: mammary gland/breast epithelial cell SB_3_ME

value: miRExplore spike-in


title: mammary gland/breast epithelial cell SB_1_ME


title: HC9

description:
healthy donor
N256


title: mammary gland/breast epithelial cell SB_2_ME


title: HC7

description:
healthy donor
N254


title: mammary gland/breast epithelial cell CATS_2_ME

value: CATS


title: mammary gland/breast epithelial cell CATS_1_ME


title: mammary gland/breast epithelial cell CL_2_SCE


title: HC8

description:
healthy donor
N255


title: mammary gland/breast epithelial cell SBN_4N_2_ME


title: mammary gland/breast epithelial cell SBN_4N_1_ME


title: mammary gland/breast epithelial cell CL_1_SCE


title: HC6

description:
healthy donor
N269


title: HC5

description:
healthy donor
N268


title: HC3

description:
healthy donor
N261


title: HC4

description:
healthy donor
N263


title: mammary gland/breast epithelial cell SBN_CL_3_ME


title: mammary gland/breast epithelial cell SBN_CL_2_ME


title: BD1

description:
BD
N267


title: mammary gland/breast epithelial cell SBN_CL_1_ME


title: HC1

description:
healthy donor
N259


title: HC2

description:
healthy donor
N260


title: GPCMV-infection at 35 dGA D

city: Minneapolis

first: Craig

middle: John

last: Bierle

state: Minnesota

address: 2001 6th Street SE

department: Pediatrics

country: USA

institute: University of Minnesota

description:
GPCMV-infection at 35 dGA D
710D.35.21.P

data_processing:
Base calling was completed using bcl2Fastq
FastQ reads were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30. Quality control on raw sequence data for each sample was performed with FastQC.
Read mapping was performed via Hisat2 (v2.1.0) using the “Cavpor3.0” genome (GCF_000151735.1) as reference
Gene quantification was done via Cuffquant for FPKM values and Feature Counts for raw read counts
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen) using raw read counts. The generated list was filtered based on a minimum 2X Absolute Fold Change and False Discovery Rate corrected p < 0.05.
Genome_build: Cavpor3.0 (GCF_000151735.1)
Supplementary_files_format_and_content: Four excel files have been provided. The first contains all normalized gene expression data from the 16 samples (FPKM). The remaining files are pairwise comparisons between groups of tissue, highlighting signficant ≥2-fold differences in gene expression.

organism: Cavia porcellus

source_name: Guinea pig placenta

growth_protocol: Strain 2 female guinea pigs were bred with strain 13 males during postpartum estrus.

extract_protocol:
RNA was extracted using the Rneasy Mini Kit (Qiagen) with the on-column DNase digestion
Dual indexed TruSeq stranded mRNA libraries (Illumina) were prepared and sequenced by Illumina RNA-Seq (NextSeq 550 high-output 75-bp single-end run).

treatment_protocol: Pregnant guinea pigs were infeted with 2E5 PFU of GPCMV (strain 22122) or injected with dPBS at either 21 or 35 days gestation.

value: Placenta

tag: treatment

value: GPCMV

tag: strain

value: Strain 2(F) X Strain 13(M)


title: mammary gland/breast epithelial cell SBN_3_ME

value: mammary gland/breast epithelial cell

value: adenocarcinoma


title: HC10

description:
healthy donor
N257


title: mammary gland/breast epithelial cell CATS_3_ME


title: GPCMV-infection at 35 dGA B

description:
GPCMV-infection at 35 dGA B
713A.35.21.P


title: mammary gland/breast epithelial cell SBN_1_ME


title: Mock-infection at 35 dGA D

description:
Mock-infection at 35 dGA D
716B.35.21.N

value: PBS


title: mammary gland/breast epithelial cell CL_2_ME


title: Mock-infection at 35 dGA C

description:
Mock-infection at 35 dGA C
716A.35.21.N


title: Mock-infection at 35 dGA A

description:
Mock-infection at 35 dGA A
2412C.35.21.N


title: Mock-infection at 35 dGA B

description:
Mock-infection at 35 dGA B
711C.35.21.N


title: mammary gland/breast epithelial cell 4N_2_ME


title: mammary gland/breast epithelial cell CL_1_ME


title: mammary gland/breast epithelial cell SBN_4N_3_ME


title: mammary gland/breast epithelial cell 4N_1_ME


title: mammary gland/breast epithelial cell 4N_3_ME


title: mammary gland/breast epithelial cell CL_3_ME


title: GPCMV-infection at 21 dGA D

description:
GPCMV-infection at 21 dGA D
707C.21.21.P


title: mammary gland/breast epithelial cell 4N_CL_1_ME


title: GPCMV-infection at 35 dGA C

description:
GPCMV-infection at 35 dGA C
714C.35.21.P


title: GPCMV-infection at 21 dGA B

description:
GPCMV-infection at 21 dGA B
703B.21.21.P


title: mammary gland/breast epithelial cell SBN_2_ME

value: SBN


title: GPCMV-infection at 21 dGA A

description:
GPCMV-infection at 21 dGA A
702B.21.21.P


title: GPCMV-infection at 21 dGA C

description:
GPCMV-infection at 21 dGA C
706C.21.21.P


title: mammary gland/breast epithelial cell 4N_CL_2_ME


title: mammary gland/breast epithelial cell 4N_C3_3_ME


title: GPCMV-infection at 35 dGA A

description:
GPCMV-infection at 35 dGA A
712D.35.21.P


title: Mock-infection at 21 dGA C

description:
Mock-infection at 21 dGA C
2364C.21.21.N


title: Mock-infection at 21 dGA A

description:
Mock-infection at 21 dGA A
2363A.21.21.N


title: mammary gland/breast epithelial cell 4N_C3_1_ME


title: Mock-infection at 21 dGA B

description:
Mock-infection at 21 dGA B
2363C.21.21.N


title: mammary gland/breast epithelial cell SB_4N_1_ME


title: mammary gland/breast epithelial cell SB_4N_2_ME


title: mammary gland/breast epithelial cell SB_4N_3_ME


title: mammary gland/breast epithelial cell SB_CL_1_ME


title: MDA-MB-231-0h

city: Seoul

first: Chul Geun

last: Kim

address: wangsimni-ro 222

department: Life Science

country: South Korea

institute: Hanyang University

data_processing:
Illumina NextSeq 500 sequencer used for basecalling.
Tophat 2 and cufflinks were used for reads mapping and expected read counts, respectively.
DEGs were analyzed using an edgeR program.
Functional annotation of genes were achieved using a DAVID program.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM files were genertaed by Tophat 2 and cufflinks.

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 and HepG2 cells were maintained in DMEM (HyClone, SH30243.01) supplemented with 10% fetal bovine serum (FBS; Cellsera. AU-FBS/PG) and 1% penicillin (Sigma Aldrich, P3032)/streptomycin (Sigma Aldrich, S9137).

extract_protocol:
RNA was harvested using QIAZOL reagent (QIAGEN). 400 ng of total RNA was used for the construction of sequencing libraries.
The library was prepared using the RNA seq3’ mRNA-Seq Library Prep Kit FWD standard protocols.

treatment_protocol: ACP52C was dissolved in PBS and treated for 0, 12, 24, and 48 hours as 2 μM in culture medium.

tag: cancer origin type

value: Triple negative cancer cell line

tag: drug (peptide)

tag: drug treated condition

value: 2 µM  for 0 hour


title: MDA-MB-231-12h

value: 2 µM  for 12 hour


title: MDA-MB-231-24h

value: 2 µM  for 24 hour


title: mammary gland/breast epithelial cell SB_CL_3_ME


title: mammary gland/breast epithelial cell CL_Block_2_ME


title: mammary gland/breast epithelial cell CL_Block_3_ME


title: HepG2-12h

source_name: HepG2 cells

value: Liver cancer cell line


title: HepG2-0h


title: mammary gland/breast epithelial cell SB_CL_2_ME


title: mammary gland/breast epithelial cell CL_16C_1_ME


title: patient 4 IgG activation sorted M-MDSCs

city: Rehovot

first: Idit

last: Shachar

address: Herzl 234

department: Immunology

institute: Weizmann Institute of science

description: patient 4 IgG activation

data_processing: none provided by the submitter

source_name: sorted M-MDSCs

extract_protocol:
Samples were seperated by ficoll then sorted for M-MDSCs, thereafter seperated into two samples and treated with anti-CD84 activating antibody or IgG
Libraries were prepared with the MARS-seq protocol (Diego Adhemar Jaitin, 2017) and sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).
MARS-seq

value: Bone marrow


title: mammary gland/breast epithelial cell CL_UMI6_1_ME

value: single cell


title: MDA-MB-231-48h

value: 2 µM for 48 hour


title: HepG2-24h


title: patient 2 IgG activation sorted M-MDSCs

description: patient 2 IgG activation


title: patient 1 IgG activation sorted M-MDSCs

description: patient 1 IgG activation


title: patient 3 IgG activation sorted M-MDSCs

description: patient 3 IgG activation


title: mammary gland/breast epithelial cell CL_16C_3_ME

value: miRExplore spike-in


title: mammary gland/breast epithelial cell 4N_C3_2_ME


title: patient 4 CD84 activation sorted M-MDSCs

description: patient 4 CD84 activation


title: mammary gland/breast epithelial cell CL_UMI6_3_ME


title: patient 3 CD84 activation sorted M-MDSCs

description: patient 3 CD84 activation


title: mammary gland/breast epithelial cell CL_Block_1_ME


title: patient 2 CD84 activation sorted M-MDSCs

description: patient 2 CD84 activation


title: mammary gland/breast epithelial cell CL_C3_1_ME


title: Healthy control [CTRL90]

address: בן אליעזר 32, 17

description:
Healthy control
CTRL90
Controls_only.txt
miR_181_controls.csv

tag: condition

value: Healthy control


title: mammary gland/breast epithelial cell CL_16C_2_ME


title: patient 1 CD84 activation sorted M-MDSCs

description: patient 1 CD84 activation


title: patient 3 CD84 activation sorted G-MDSCs

source_name: sorted G-MDSCs

extract_protocol:
Samples were seperated by ficoll then sorted for G-MDSCs, thereafter seperated into two samples and treated with anti-CD84 activating antibody or IgG
Libraries were prepared with the MARS-seq protocol (Diego Adhemar Jaitin, 2017) and sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).
MARS-seq


title: patient 2 IgG activation sorted G-MDSCs


title: patient 1 IgG activation sorted G-MDSCs


title: patient 1 CD84 activation sorted G-MDSCs


title: patient 2 CD84 activation sorted G-MDSCs


title: mammary gland/breast epithelial cell CL_4N_1_ME


title: mammary gland/breast epithelial cell CL_SB_1_ME


title: mammary gland/breast epithelial cell CL_4N_3_ME


title: mammary gland/breast epithelial cell CL_Rand_1_ME


title: mammary gland/breast epithelial cell CL_Rand_3_ME


title: mammary gland/breast epithelial cell CL_C3_3_ME


title: mammary gland/breast epithelial cell CL_4N_2_ME


title: HepG2-48h


title: mammary gland/breast epithelial cell CL_SB_2_ME


title: cele16h-BAC050117-379

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

data_processing:
We trimmed the adapter sequences of raw sequencing reads using the Trim Galore software (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). We used RSEM to calculate RNA expression levels using scRNA-seq data. We created an RSEM index with the combination of the human hg38 transcriptome (GENCODE version 28) and 3 spike-in molecules. We calculated RNA expression using RSEM 1.3.0 with the default parameters and Bowtie2 as the aligner. We normalized the expression levels of endogenous genes to that of the highest expressed spike-in molecule. Given N single cells, to control the dynamic regulation of endogenous gene expression in single cell k, the TPM value of gene j is normalized to that of spike-in 1 (s), which is the highest spike-in molecule. As the RNA capturing complexity of the scRNA-seq library is ~10% of bulk RNA-seq20, we divided the above-normalized TPM values by 10, and the expression level of gene j in cell k was quantified as the E-value Ejk.
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression E-values

molecule: polyA RNA

growth_protocol: A2780 ovarian endometroid adenocarcinoma cells were a gift from Dr. Chia-Peng Huang Yang at the Albert Einstein College of Medicine obtained from Dr. Elizabeth de Vries at the University Medical Center Groningen. The cells were cultured in RPMI 1640 medium (Thermo Fisher Scientific, Waltham, MA) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific, Waltham, MA) on 35-mm six-well glass bottom plates (Cellvis, Mountain View, CA) until 60 to 85% confluent. All cells were given at least 24 hours to readhere before drug treatment.

extract_protocol:
Cells were treated with 75 μM celecoxib for 2 and 16 hours, 5 nM paclitaxel for 16 and 48 hours, or a combination of 75 μM celecoxib and 5 nM paclitaxel for 16 hours prior to trypsinization and resuspension in growth medium. Cell suspensions were sorted with a C1 single-cell capture system (Fluidigm, South San Francisco, CA) by the University of Illinois at Chicago Genomics Core.
scRNA-seq libraries were prepared according to the Smart-seq2 protocol and sequenced using the NextSeq 500 Sequencing System (Illumina, San Diego, CA) by the University of Illinois at Chicago Sequencing Core. A predesigned set of three polyA-tailed spike-in RNAswas added to each well during the library preparation.
C1 Fluidigm based SMART-seq2

treatment_protocol: Cells were treated with 75 μM celecoxib, 5 nM paclitaxel, or a combination of 75 μM celecoxib and 5 nM paclitaxel for 48 hours.


title: cele16h-BAC050117-382


title: cele16h-BAC050117-380


title: mammary gland/breast epithelial cell CL_SB_3_ME


title: cele16h-BAC050117-381


title: patient 3 IgG activation sorted G-MDSCs


title: mammary gland/breast epithelial cell CL_UMI6_2_ME


title: mammary gland/breast epithelial cell CL_C3_2_ME


title: Mock-infection at 21 dGA D

description:
Mock-infection at 21 dGA D
2370D.21.21.N

value: Placenta


title: mammary gland/breast epithelial cell SB_C3_2_ME


title: cele16h-BAC050117-378


title: mammary gland/breast epithelial cell SB_C3_1_ME


title: mammary gland/breast epithelial cell SB_C3_3_ME


title: cele16h-BAC050117-377


title: cele16h-BAC050117-376


title: mammary gland/breast epithelial cell CL_Rand_2_ME


title: Splenocytes_CD19-Cre_MYD88-L252P_541

city: Limoges

first: Lilian

last: Roland

address: rue Bernard Descottes

department: Haute Vienne

institute: Contrôle de la Réponse Immune B et Lymphoproliférations Limoges

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 120μl of hyb solution to each array • Hybridize 20 hours at 45°• Fluidics washing with Gene Atlas Fluidic Station and WT plus protocol

scan_protocol: Affymetrix Gene Atlas imaging station

data_processing:
Automatic Recognition of the chip by Affymetrix Gene Atlas software
All analyses were performed by LR and JF with the version 1.1.463 of RStudio (Free Software Foundation, Inc, Boston, MA). RMA normalization was done with the “oligo” R package (Carvalho BS, Irizarry RA, Bioinformatics 2010), resulting in a table giving the normalized signal intensity of 770069 probesets, corresponding to 41345 transcripts) for seven mice (three CD19_Cre and four MYD88L252P). After filtering invariant and unannotated probesets, differential analysis was performed with the “Limma” R package (Ritchie ME et al, Nucleic Acid Research, 2015). Then, signal levels of selected probesets were mean-aggregated according the Affymetrix transcript_cluster_id. Kmean clustering was done with the “kmeans” R function, principal component analysis with the “FactoMineR” (Sébastien Le, Julie Josse, François Husson, Journal of statistical software, 2008) and unsupervised clustering with the “EMA” 1.4.5 version (Nicolas Servant et al, (2016) https://CRAN.R-project.org/package=EMA) R package respectively
Processed data file normalized values with ids probeset.id_transcript.clusterID.

label: Biotin

organism: Mus musculus

source_name: MYD88 L252P, splenocyte

label_protocol: Affymetrix Gene Atlas system, Samples were enzymatically fragmented and biotinylated using the WT PlusLabeling Kit (Affymetrix)

growth_protocol: Splenocytes from mice spleen after 1 year of developement

extract_protocol: All samples were prepared using Trizol. cDNA synthesis and amplification was performed using the WT plus reagent kit (Affymetrix).

tag: age

value: 12 months

value: Spleen


title: cele16h-BAC050117-375


title: Splenocytes_CD19-Cre_MYD88-L252P_540

tag: tissue


title: cele16h-BAC050117-374

tag: cell line


title: Splenocytes_CD19-Cre_MYD88-L252P_539


title: Splenocytes_CD19-Cre_MYD88-L252P_4830


title: cele16h-BAC050117-371


title: Splenocytes_CD19-Cre_4633

source_name: CD19 Cre, splenocyte


title: Wistar_SON_dehydrated_rep5

city: Bristol

first: Audrys

middle: G

last: Pauza

state: Somerset

address: University of Bristol, The Dorothy Hodgkin Building, Whitson Street

department: Bristol Medical School (THS)

institute: University of Bristol

data_processing:
RNAseq reads were processed using RTA and CASAVA from Illumina’s suite of sequencing software. This produced a series of compressed FASTQ files per library. All raw reads were merged per library, and pre-processed for quality assessment, adaptor removal, quality trimming and size selection using the FastQC toolkit to generate quality plots for all read libraries (35). We adopted a phred30 quality cutoff (99.9% base call accuracy).
Post-trimming, reads were aligned to Rn6 rat reference genome using RNA STAR aligner.
FeatureCounts is used to generate read counts for each gene present in the Rn6 genome annotation.
DEseq2 (v1.28.1) package in R was used to call differentially expressed genes betweem Wistar-Han rat SON transcriptomes in euhydrated and dehydrated (72h) conditions
Genome_build: Rn6
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each sample as originally generated using FeatureCounts

organism: Rattus norvegicus

source_name: Hypothalamic supraoptic nucleus (SON)

extract_protocol:
All rats were humanely euthanised by striking of the cranium (stunning), and then immediately decapitated with a small animal guillotine. Brains were rapidly removed from the cranium and placed into a chilled rat brain matrix for separation of the forebrain from the hindbrain. The forebrain was placed cut edge down onto aluminium foil resting on pellets of dry ice and covered with powdered dry ice (within 3 minutes of stunning). By using a cryostat, bilateral punches of the SON were collected from 12 coronal slices with a 1 mm sample corer.  Animal experiments were performed between 10 am-12 pm.
Illumina TruSeq Stranded mRNA Library prep (Cat. no. 20020594) following manufacturer's protocol.

treatment_protocol: Rat cages were randomly assigned to two groups: control (free access to drinking water) and dehydrated (removal of drinking water for 72 hours).

value: Wistar Han

value: Brain

tag: brain region

value: Supraoptic nucleus

value: 72h dehydrated


title: Wistar_SON_dehydrated_rep2


title: cele16h-BAC050117-365


title: cele16h-BAC050117-369


title: Wistar_SON_dehydrated_rep3


title: cele16h-BAC050117-366


title: Wistar_SON_dehydrated_rep4


title: cele16h-BAC050117-368


title: Wistar_SON_dehydrated_rep1


title: cele16h-BAC050117-363


title: Wistar_SON_euhydrated_rep3

value: Euhydrated (control)


title: cele16h-BAC050117-364


title: Wistar_SON_euhydrated_rep5


title: Wistar_SON_euhydrated_rep4


title: cele16h-BAC050117-361


title: Wistar_SON_euhydrated_rep2


title: cele16h-BAC050117-362


title: cele16h-BAC050117-367


title: cele16h-BAC050117-370


title: Rat neurons topo_2

city: Saint Louis

first: Ya-Lin

last: Lu

state: MO

address: 660 S. Euclide Avenue

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Raw reads were aligned to Ensembl release 76  by STAR (Dobin and Gingeras, 2015).
Counts were normalized by trimmed mean of M-values (TMM) using edgeR (Robinson et al., 2010).
EdgeR (Robinson et al., 2010) was used to identify differentially expressed genes.
Genome_build: Ensembl release 76
Supplementary_files_format_and_content: Count matrix

source_name: Rat neurons

growth_protocol: E18 rat cortical neurons were resuspended in STEMdiffTM Neural Induction Medium for plating. After 24hrs, cells were cultured in BrainPhys Neuronal Medium and SM1 supplement.

extract_protocol:
Total RNA was extracted using a combination of Trizol (Invitrogen, USA) and RNeasy plus micro kit (QIAGEN, USA).
RNA was prepared for sequencing using TruSeq Small RNA Library Preparation Kits (San Diego, CA).

treatment_protocol: Cell treated with either DMSO or TOPO (topotecan)

tag: cell type

value: BrainBits, FSDECX1M, E18 rat cortex

value: Topotecan

value: Rat neurons


title: cele16h-BAC050117-358


title: Splenocytes_CD19-Cre_4643


title: Splenocytes_CD19-Cre_4640


title: cele16h-BAC050117-372


title: cele16h-BAC050117-359


title: Rat neurons topo_1


title: cele16h-BAC050117-360


title: cele16h-BAC050117-373


title: Rat neurons dmso_2

value: DMSO


title: cele16h-BAC050117-356


title: cele16h-BAC050117-354


title: cele16h-BAC050117-353


title: Wistar_SON_euhydrated_rep1


title: cele16h-BAC050117-352


title: Rat neurons dmso_1


title: cele16h-BAC050117-350


title: cele16h-BAC050117-349


title: v818_12: vol818_second_inf_memory

data_processing:
Raw reads were QC assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Read pairs were aligned using bowtie2 (v2.2.7, doi.org/10.1038/nmeth.1923) to the human transcripts set downloaded from ensembl (release 98).  Bowtie2 parameters applied were --very-sensitive -p 24 --no-mixed --no-discordant --no-unal.  Read counts were extracted from the bam files using samtools idxstats (http://www.htslib.org/doc/samtools.html) prior to subsequent manipulation in R.
Pair-wise comparisons of sample groups were performed using the DEseq2 Bioconductor package (doi.org/10.1186/s13059-014-0550-8) after the removal of hemoglobin reads. Alpha value applied was 0.05, logFC shrinkage not applied.
Genome_build: ensembl release 98
Supplementary_files_format_and_content: Tab-delimited text files containing read counts for all transcripts; first column is transcriptID, second column is length of transcript, third column is number of read counts

source_name: whole blood after second inf (memory)

extract_protocol:
Total whole blood RNA was extracted using the Tempus™ Spin RNA isolation reagent kit (ThermoFisher #4380204) according to manufacturer’s instructions. RNA integrity assessed using an Agilent Bioanalyzer 2100 (RNA 6000 nano kit Agilent #5067-1511). Our average RNA integrity number (RIN) was 9 (98% of samples > 8, lowest RIN 7).
Libraries were constructed by Edinburgh Genomics (Edinburgh, UK) from approximately 500 ng of RNA using the TruSeq® Stranded mRNA library prep kit (Illumina #20020595). Stranded library preparation allows transcripts expression to be estimated more accurately; in particular it is more effective in quantifying anti-sense gene expression, properly assigning transcripts to putative coding genes and to resolve ambiguity in reads from overlapping genes (Zhao, S., et al., Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap. BMC Genomics, 2015, PMID: 26334759). Libraries were sequenced using the NovaSeq 6,000 Illumina® platform yielding 50 bp paired end (PE) reads.

treatment_protocol: Venous blood was drawn into K2EDTA-coated vacutainers (Becton Dickinson #367835). To preserve RNA for whole blood transcriptome analysis 1 ml of blood was mixed thoroughly with 2 ml Tempus™ reagent (ThermoFisher #4342792) and samples were stored at -80°C. Note that no more than 2-hours passed between blood draw and RNA preservation.

tag: volunteer code

tag: number of malaria infections

value: two

tag: timepoint

value: whole blood


title: v818_11: vol818_second_inf_T6

source_name: whole blood after second inf (T6)


title: cele16h-BAC050117-348


title: v818_9: vol818_second_inf_C8

source_name: whole blood after second inf (C8)


title: cele16h-BAC050117-346


title: cele16h-BAC050117-351


title: cele16h-BAC050117-347


title: v818_10: vol818_second_inf_diagnosis

source_name: whole blood after second inf (diagnosis)


title: 3 samples: KTx, HC, ESRD

city: Changsha

first: 皓

last: 李

state: China

address: Changsha Organ Transplantation Center, Third Xiangya Hospital, Changsha, Hunan，China

country: China

institute: the third Xiangya hospital

description: 3 samples

data_processing:
Using BD pipeline (Bowtie2 v2.2.9)to processing the raw data to gene expression matrix
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: matrix data with every gene counts for every cell

source_name: PBMC

extract_protocol:
peripheral blood was collected into EDTA-anticoagulant tubes, after red blood cells lysis, lymphocyte separation medium (TBD, LTS1077), blood and phosphate buffered saline 1X (Hyclone, SH30256.01) were slowly added to centrifuge tube separately at ratio of 2:1:1. After centrifuged at 450g for 20 minutes (min), PBMCs were aspirated from the middle of centrifuge tubes.
Libraries were prepared according to Illumina's protocol

value: blood


title: cele16h-BAC050117-357


title: cele16h-BAC050117-345


title: Cglutamicum_ pAN6-cg1978_vs_pAN6_A

city: Jülich

first: Max

last: Hünnefeld

address: Wilhelm-Johnen-Straße

department: Institute for Bio- and Geosciences 1: Biotechnology

institute: Forschungszentrum Jülich

hyb_protocol: RNA sample preparation, labelling, hybridization and comparative transcriptome analysis was performed as described previously (Vogt et al., 2014).

scan_protocol: Fluorescence of hybridized DNA microarrays was determined at 532 nm (Cy3) and 635 nm (Cy5) at 5 μm resolution with a GenePix 4000B laser scanner and GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA). Fluorescence images were saved to raw data files in TIFF format (GenePix Pro 6.0). Quantitative TIFF image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0).

data_processing: For ratio calculation and ratio normalization, GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

organism: Corynebacterium glutamicum ATCC 13032

source_name: ATCC13032 pAN6-cg1978 CGXII glucose

growth_protocol: For transcriptome analysis, C. glutamicum ATCC13032 pAN6-cg1978 and ATCC13032 pAN6 cells were grown in 5 ml BHI (Brain Heart Infusion, Difco) with 25 µg/ml Kanamycin for about 8 hours at 30°C. A second precultivation was performed in CGXII minimal medium containing 2% (w/v) glucose as carbon source with 25 µg/ml Kanamycin. The main cultures were inoculated to an OD600 of 1 in CGXII minimal medium with 2% (w/v) glucose, 25 µg/ml Kanamycin and 50 µM IPTG. At OD600 of 6, the cells were centrifuged and harvested on ice and the cell pellet was subsequently frozen in liquid nitrogen and stored at -80°C.

treatment_protocol: see growth protocol

tag: overexpression

source_name: ATCC13032 pAN6 CGXII glucose

value: pAN6 empty vector


title: Cglutamicum_ pAN6-cg1978_vs_pAN6_B

label_protocol: RNA sample preparation, labelling, hybridization and comparative transcriptome analysis was performed as described previously (Vogt et al., 2014).


title: cele16h-BAC050117-343


title: PCFCL

city: Vienna

first: Natalia

last: Alkon

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GrCh38) and counted using Cell Ranger (version 3.0.2; 10x Genomics).
Genome_build: GrCh38
Supplementary_files_format_and_content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids)

source_name: Skin Biopsy

extract_protocol:
Single cell suspensions were generated using the Skin Dissociation Kit by Miltenyi Biotech (Bergisch Gladbach, Germany) according to the manufacturer’s instructions, except for the time of enzymatic digestion, which was reduced to a total of 1 hour at 37°C.
Single cell suspensions were subjected to scRNA-seq using the Chromium Single Cell Controller and Single Cell 5’ Library & Gel Bead Kit according to the manufacturer’s protocol.T cell-receptor (TCR) and B cell-receptor (BCR) sequences were enriched from the cDNA using the respective reagents, and following the instructions of the VDJ Kit workflow by 10X Genomics

tag: diagnosis

value: Primary cutaneous follicle center lymphoma

value: Skin cells

tag: chemistry

value: Single Cell 5' PE


title: MF

value: Mycosis fungoides


title: cele16h-BAC050117-344

tag: treatment


title: cele16h-BAC050117-342


title: Cglutamicum_ pAN6-cg1978_vs_pAN6_C_csw

extract_protocol: RNA sample preparation, labelling, hybridization and comparative transcriptome analysis was performed as described previously (Vogt et al., 2014).


title: v818_7: vol818_second_inf_C6

source_name: whole blood after second inf (C6)


title: v818_6: vol818_second_inf_baseline

source_name: whole blood before second inf (baseline)


title: v818_8: vol818_second_inf_C7

source_name: whole blood after second inf (C7)


title: v818_5: vol818_first_inf_diagnosis

source_name: whole blood after first inf (diagnosis)

value: one


title: cele16h-BAC050117-341


title: cele16h-BAC050117-340


title: v818_4: vol818_first_inf_C8

source_name: whole blood after first inf (C8)


title: cele16h-BAC050117-338


title: cele16h-BAC050117-339


title: v818_3: vol818_first_inf_C7

source_name: whole blood after first inf (C7)


title: v818_1: vol818_first_inf_baseline

source_name: whole blood before first inf (baseline)


title: v818_2: vol818_first_inf_C6

source_name: whole blood after first inf (C6)


title: cele16h-BAC050117-337


title: v806_14: vol806_second_inf_memory


title: cele16h-BAC050117-336


title: v806_13: vol806_second_inf_T6


title: cele16h-BAC050117-355


title: cele16h-BAC050117-335


title: v806_11: vol806_second_inf_C11

source_name: whole blood after second inf (C11)


title: v806_10: vol806_second_inf_C10

source_name: whole blood after second inf (C10)


title: cele16h-BAC050117-334


title: v806_8: vol806_second_inf_C6


title: v806_9: vol806_second_inf_C9

source_name: whole blood after second inf (C9)


title: v806_6: vol806_first_inf_diagnosis


title: v806_5: vol806_first_inf_C10

source_name: whole blood after first inf (C10)


title: v806_4: vol806_first_inf_C9

source_name: whole blood after first inf (C9)


title: cele16h-BAC050117-333


title: cele16h-BAC050117-328


title: cele16h-BAC050117-330


title: cele16h-BAC050117-332


title: v806_3: vol806_first_inf_C8


title: cele16h-BAC050117-327


title: cele16h-BAC050117-329


title: cele16h-BAC050117-326


title: cele16h-BAC050117-324


title: cele16h-BAC050117-323


title: v6032_19: vol6032_third_inf_memory

source_name: whole blood after third inf (memory)

value: three


title: v806_2: vol806_first_inf_C6


title: v806_1: vol806_first_inf_baseline


title: v806_12: vol806_second_inf_diagnosis

source_name: whole blood after second inf (diagnosis)


title: cele16h-BAC050117-325


title: cele16h-BAC050117-331


title: v6032_18: vol6032_third_inf_T6

source_name: whole blood after third inf (T6)


title: cele16h-BAC050117-322


title: cele16h-BAC050117-320


title: cele16h-BAC050117-321


title: cele16h-BAC050117-319


title: v6032_17: vol6032_third_inf_diagnosis

source_name: whole blood after third inf (diagnosis)


title: v806_7: vol806_second_inf_baseline


title: v6032_16: vol6032_third_inf_C9

source_name: whole blood after third inf (C9)


title: cele16h-BAC050117-318


title: v6032_14: vol6032_third_inf_C7

source_name: whole blood after third inf (C7)


title: cele16h-BAC050117-317


title: PacCele16h-BAC050117-312


title: PacCele16h-BAC050117-313


title: PacCele16h-BAC050117-310


title: v6032_13: vol6032_third_inf_C6

source_name: whole blood after third inf (C6)


title: v6032_12: vol6032_third_inf_baseline

source_name: whole blood before third inf (baseline)


title: PacCele16h-BAC050117-309


title: v6032_11: vol6032_second_inf_diagnosis


title: v6032_7: vol6032_second_inf_baseline

source_name: whole blood before second inf (baseline)


title: v6032_9: vol6032_second_inf_C7

source_name: whole blood after second inf (C7)


title: PacCele16h-BAC050117-311


title: v6032_15: vol6032_third_inf_C8

source_name: whole blood after third inf (C8)


title: PacCele16h-BAC050117-307


title: v6032_10: vol6032_second_inf_C8

source_name: whole blood after second inf (C8)


title: v6032_8: vol6032_second_inf_C6

source_name: whole blood after second inf (C6)


title: v6032_4: vol6032_first_inf_C8

source_name: whole blood after first inf (C8)


title: PacCele16h-BAC050117-306


title: v6032_6: vol6032_first_inf_diagnosis

source_name: whole blood after first inf (diagnosis)


title: cele16h-BAC050117-316


title: v6032_5: vol6032_first_inf_C9


title: PacCele16h-BAC050117-308


title: PacCele16h-BAC050117-304


title: PacCele16h-BAC050117-305


title: v6032_2: vol6032_first_inf_C6

source_name: whole blood after first inf (C6)


title: PacCele16h-BAC050117-303


title: v6032_1: vol6032_first_inf_baseline

source_name: whole blood before first inf (baseline)


title: PacCele16h-BAC050117-302


title: v320_8: vol320_first_inf_memory

source_name: whole blood after first inf (memory)


title: PacCele16h-BAC050117-301


title: v320_7: vol320_first_inf_T6

source_name: whole blood after first inf (T6)


title: PacCele16h-BAC050117-300


title: PacCele16h-BAC050117-299


title: v6032_3: vol6032_first_inf_C7

source_name: whole blood after first inf (C7)


title: v320_3: vol320_first_inf_C7


title: v320_5: vol320_first_inf_C9

source_name: whole blood after first inf (C9)


title: v315_8: vol315_first_inf_memory


title: v320_4: vol320_first_inf_C8


title: PacCele16h-BAC050117-298


title: v315_7: vol315_first_inf_T6


title: PacCele16h-BAC050117-297


title: PacCele16h-BAC050117-292


title: PacCele16h-BAC050117-291


title: PacCele16h-BAC050117-293


title: PacCele16h-BAC050117-295


title: PacCele16h-BAC050117-296


title: v320_2: vol320_first_inf_C6


title: v320_1: vol320_first_inf_baseline


title: v315_4: vol315_first_inf_C8


title: v315_5: vol315_first_inf_C9


title: PacCele16h-BAC050117-289


title: v315_3: vol315_first_inf_C7


title: PacCele16h-BAC050117-288


title: v315_2: vol315_first_inf_C6


title: PacCele16h-BAC050117-287


title: PacCele16h-BAC050117-294


title: v320_6: vol320_first_inf_diagnosis


title: v315_6: vol315_first_inf_diagnosis


title: v315_1: vol315_first_inf_baseline


title: PacCele16h-BAC050117-285


title: v313_7: vol313_first_inf_T6


title: PacCele16h-BAC050117-290


title: v313_4: vol313_first_inf_C8


title: v313_6: vol313_first_inf_diagnosis


title: PacCele16h-BAC050117-280


title: PacCele16h-BAC050117-279


title: PacCele16h-BAC050117-284


title: v313_5: vol313_first_inf_C9


title: PacCele16h-BAC050117-282


title: v313_2: vol313_first_inf_C6


title: PacCele16h-BAC050117-278


title: v313_8: vol313_first_inf_memory


title: PacCele16h-BAC050117-277


title: v313_3: vol313_first_inf_C7


title: PacCele16h-BAC050117-281


title: v1075_20: vol1075_third_inf_memory

source_name: whole blood after third inf (memory)


title: PacCele16h-BAC050117-276


title: v1075_19: vol1075_third_inf_T6

source_name: whole blood after third inf (T6)


title: PacCele16h-BAC050117-286


title: PacCele16h-BAC050117-283


title: PacCele16h-BAC050117-275


title: PacCele16h-BAC050117-274


title: v1075_17: vol1075_third_inf_C14

source_name: whole blood after third inf (C14)


title: PacCele16h-BAC050117-273


title: v313_1: vol313_first_inf_baseline


title: PacCele16h-BAC050117-272


title: v1075_16: vol1075_third_inf_C12

source_name: whole blood after third inf (C12)


title: v1075_15: vol1075_third_inf_C10

source_name: whole blood after third inf (C10)


title: v1075_14: vol1075_third_inf_C8


title: PacCele16h-BAC050117-271


title: v1075_13: vol1075_third_inf_C6

source_name: whole blood after third inf (C6)


title: PacCele16h-BAC050117-269


title: v1075_18: vol1075_third_inf_diagnosis

source_name: whole blood after third inf (diagnosis)


title: v1075_11: vol1075_second_inf_diagnosis

source_name: whole blood after second inf (diagnosis)


title: PacCele16h-BAC050117-270


title: PacCele16h-BAC050117-267


title: PacCele16h-BAC050117-266


title: v1075_9: vol1075_second_inf_C10

source_name: whole blood after second inf (C10)


title: v1075_8: vol1075_second_inf_C8

source_name: whole blood after second inf (C8)


title: PacCele16h-BAC050117-265


title: v1075_6: vol1075_second_inf_baseline

source_name: whole blood before second inf (baseline)


title: v1075_7: vol1075_second_inf_C6

source_name: whole blood after second inf (C6)


title: PacCele16h-BAC050117-262


title: v1075_4: vol1075_first_inf_C10

source_name: whole blood after first inf (C10)


title: PacCele16h-BAC050117-263


title: v1075_5: vol1075_first_inf_diagnosis

source_name: whole blood after first inf (diagnosis)


title: PacCele16h-BAC050117-261


title: v1075_2: vol1075_first_inf_C6

source_name: whole blood after first inf (C6)


title: v1075_3: vol1075_first_inf_C8

source_name: whole blood after first inf (C8)


title: PacCele16h-BAC050117-259


title: PacCele16h-BAC050117-257


title: v1075_12: vol1075_third_inf_baseline

source_name: whole blood before third inf (baseline)


title: PacCele16h-BAC050117-260


title: v1075_10: vol1075_second_inf_C12

source_name: whole blood after second inf (C12)


title: PacCele16h-BAC050117-258


title: PacCele16h-BAC050117-268


title: PacCele16h-BAC050117-264


title: v1068_17: vol1068_third_inf_memory

source_name: whole blood after third inf (memory)


title: PacCele16h-BAC050117-255


title: PacCele16h-BAC050117-256


title: v1068_15: vol1068_third_inf_diagnosis


title: v1068_16: vol1068_third_inf_T6

source_name: whole blood after third inf (T6)


title: v1068_12: vol1068_third_inf_C6


title: Pac16h-BAC050117-252


title: v1068_11: vol1068_third_inf_baseline


title: v1068_14: vol1068_third_inf_C8

source_name: whole blood after third inf (C8)


title: v1075_1: vol1075_first_inf_baseline

source_name: whole blood before first inf (baseline)


title: v1068_13: vol1068_third_inf_C7

source_name: whole blood after third inf (C7)


title: Pac16h-BAC050117-249


title: v1068_9: vol1068_second_inf_C8


title: Pac16h-BAC050117-251


title: v1068_10: vol1068_second_inf_diagnosis


title: Pac16h-BAC050117-247


title: v1068_8: vol1068_second_inf_C7

source_name: whole blood after second inf (C7)


title: Pac16h-BAC050117-246


title: Pac16h-BAC050117-250


title: Pac16h-BAC050117-248


title: Pac16h-BAC050117-243


title: Pac16h-BAC050117-242


title: v1068_4: vol1068_first_inf_C8


title: v1068_3: vol1068_first_inf_C7

source_name: whole blood after first inf (C7)


title: v1068_5: vol1068_first_inf_diagnosis


title: v1068_2: vol1068_first_inf_C6


title: Pac16h-BAC050117-241


title: v1068_7: vol1068_second_inf_C6


title: v1068_1: vol1068_first_inf_baseline


title: Pac16h-BAC050117-245


title: v1068_6: vol1068_second_inf_baseline


title: v1067_12: vol1067_second_inf_memory

source_name: whole blood after second inf (memory)


title: Pac16h-BAC050117-238


title: Pac16h-BAC050117-240


title: Pac16h-BAC050117-237


title: v1067_11: vol1067_second_inf_diagnosis

source_name: whole blood after second inf (diagnosis)


title: Pac16h-BAC050117-235


title: v1067_9: vol1067_second_inf_C8

source_name: whole blood after second inf (C8)


title: v1067_10: vol1067_second_inf_C9

source_name: whole blood after second inf (C9)


title: Pac16h-BAC050117-234


title: Pac16h-BAC050117-236


title: Pac16h-BAC050117-233


title: Pac16h-BAC050117-244


title: v1067_8: vol1067_second_inf_C7


title: Pac16h-BAC050117-232


title: v1067_7: vol1067_second_inf_C6

source_name: whole blood after second inf (C6)


title: v1067_5: vol1067_first_inf_diagnosis

source_name: whole blood after first inf (diagnosis)


title: v1067_4: vol1067_first_inf_C8


title: Pac16h-BAC050117-231


title: Pac16h-BAC050117-230


title: Pac16h-BAC050117-239


title: Pac16h-BAC050117-228


title: v1067_2: vol1067_first_inf_C6

source_name: whole blood after first inf (C6)


title: Pac16h-BAC050117-229


title: Pac16h-BAC050117-225


title: v1067_3: vol1067_first_inf_C7


title: Pac16h-BAC050117-224


title: v1065_13: vol1065_second_inf_memory


title: v1067_1: vol1067_first_inf_baseline


title: v1067_6: vol1067_second_inf_baseline

source_name: whole blood before second inf (baseline)


title: Pac16h-BAC050117-226


title: Pac16h-BAC050117-227


title: v1065_9: vol1065_second_inf_C8


title: v1065_12: vol1065_second_inf_diagnosis


title: v1065_10: vol1065_second_inf_C9


title: v1065_11: vol1065_second_inf_C10

source_name: whole blood after second inf (C10)


title: Pac16h-BAC050117-222


title: Pac16h-BAC050117-223


title: v1065_8: vol1065_second_inf_C6


title: v1065_7: vol1065_second_inf_baseline


title: v1065_5: vol1065_first_inf_C10

source_name: whole blood after first inf (C10)


title: v1065_3: vol1065_first_inf_C8

source_name: whole blood after first inf (C8)


title: v1065_4: vol1065_first_inf_C9

source_name: whole blood after first inf (C9)


title: v1065_6: vol1065_first_inf_diagnosis


title: v1065_2: vol1065_first_inf_C6


title: v1065_1: vol1065_first_inf_baseline


title: v1061_17: vol1061_third_inf_T6

source_name: whole blood after third inf (T6)


title: v1061_18: vol1061_third_inf_memory

source_name: whole blood after third inf (memory)


title: v1061_16: vol1061_third_inf_diagnosis

source_name: whole blood after third inf (diagnosis)


title: Pac16h-BAC050117-215


title: Pac16h-BAC050117-220


title: v1061_14: vol1061_third_inf_C9

source_name: whole blood after third inf (C9)


title: Pac16h-BAC050117-218


title: Pac16h-BAC050117-221


title: Pac16h-BAC050117-217


title: Pac16h-BAC050117-212


title: Pac16h-BAC050117-211


title: Pac16h-BAC050117-219


title: Pac16h-BAC050117-209


title: Pac16h-BAC050117-213


title: v1061_11: vol1061_third_inf_baseline

source_name: whole blood before third inf (baseline)


title: Pac16h-BAC050117-214


title: Pac16h-BAC050117-207


title: Pac16h-BAC050117-206


title: v1061_9: vol1061_second_inf_C9


title: v1061_10: vol1061_second_inf_diagnosis


title: Pac16h-BAC050117-205


title: v1061_8: vol1061_second_inf_C8


title: Pac16h-BAC050117-204


title: v1061_15: vol1061_third_inf_C10

source_name: whole blood after third inf (C10)


title: v1061_13: vol1061_third_inf_C8

source_name: whole blood after third inf (C8)


title: Pac16h-BAC050117-202


title: Pac16h-BAC050117-203


title: Pac16h-BAC050117-208


title: v1061_6: vol1061_second_inf_baseline


title: v1061_7: vol1061_second_inf_C6


title: Pac16h-BAC050117-200


title: Pac16h-BAC050117-199


title: Pac16h-BAC050117-201


title: v1061_1: vol1061_first_inf_baseline

source_name: whole blood before first inf (baseline)


title: v1061_2: vol1061_first_inf_C6


title: v1061_3: vol1061_first_inf_C8


title: Pac16h-BAC050117-196


title: v1040_21: vol1040_third_inf_memory


title: v1040_20: vol1040_third_inf_T6


title: Pac16h-BAC050117-195


title: Pac16h-BAC050117-197


title: Pac16h-BAC050117-198


title: Cele2h-BAC050117-191


title: v1040_18: vol1040_third_inf_C10


title: v1040_19: vol1040_third_inf_diagnosis


title: Cele2h-BAC050117-192


title: v1040_17: vol1040_third_inf_C9


title: Cele2h-BAC050117-189


title: Cele2h-BAC050117-190


title: Pac16h-BAC050117-216


title: Cele2h-BAC050117-187


title: v1040_16: vol1040_third_inf_C8


title: v1040_14: vol1040_third_inf_baseline


title: v1061_5: vol1061_first_inf_diagnosis


title: v1040_15: vol1040_third_inf_C6

source_name: whole blood after third inf (C6)


title: Cele2h-BAC050117-188


title: v1061_4: vol1061_first_inf_C9


title: Cele2h-BAC050117-186


title: v1040_13: vol1040_second_inf_diagnosis

source_name: whole blood after second inf (diagnosis)


title: Cele2h-BAC050117-185


title: Cele2h-BAC050117-184


title: v1040_12: vol1040_second_inf_C18

source_name: whole blood after second inf (C18)


title: v1040_10: vol1040_second_inf_C12

source_name: whole blood after second inf (C12)


title: v1040_11: vol1040_second_inf_C15

source_name: whole blood after second inf (C15)


title: v1040_9: vol1040_second_inf_C9

source_name: whole blood after second inf (C9)


title: Cele2h-BAC050117-182


title: Cele2h-BAC050117-181


title: Cele2h-BAC050117-180


title: v1040_6: vol1040_first_inf_diagnosis

source_name: whole blood after first inf (diagnosis)


title: v1040_8: vol1040_second_inf_C6

source_name: whole blood after second inf (C6)


title: Cele2h-BAC050117-178


title: Cele2h-BAC050117-179


title: v1040_5: vol1040_first_inf_C11

source_name: whole blood after first inf (C11)


title: Cele2h-BAC050117-176


title: v1040_4: vol1040_first_inf_C10

source_name: whole blood after first inf (C10)


title: Cele2h-BAC050117-177


title: A baumannii 17978 WT2

city: Daegu

first: Md.

middle: Maidul

last: Islam

address: 680 Gukchaebosang-Ro, Jung-gu

department: Department of Microbiology

institute: Kyungpook National University

data_processing:
Illumina NovaSeq 6000
For quality check used FastQC v0.11.7
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data (Trimmomatic 0.38)
Data assessment (Error rate, AT and GC content distribution, daat filtration)Mapping to reference genome (Bowtie1.1.2 software)
Expression quantification (HTSeq version 0.10.0 software)
Genome_build: GCF_000015425.1_ASM1542v1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Acinetobacter baumannii

source_name: Liqiud bacterial culture

growth_protocol: Bacteria were cultured in LB under shaking conditions at 200 rpm at 37ºC for overnight. Fresh culture by 1/100 dilution with LB and culture upto OD600=1.0

extract_protocol:
Total RNA was extracted using the RNAeasy Mini kit (QIAGEN) following the manufacturer instructions. RNA integrity was assessed using the Agilent Technologies 2100 Bioanalyzer (or 2200 TapeStation) (Agilent Technologies, CA, USA).Sequencing libraries were generated using TruSeq Stranded Total RNA (NEB Microbe) library kit and NovaSeq 6000 S4 Reagent Kit following manufacturer’s recommendations. mRNA was purified from total RNA using ribo-zero rRNA removal kit. Fragmentation was carried out using divalent cations under elevated temperature.Reverse transcribe  onto cDNA. Nat Rev Genet. 2011 Sep 7;12(10):671-82
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNAprotect (Qiagen) before RNA extraction

tag: strain background

tag: genotype/variation

value: wild-type

tag: growth stage

value: Optical density at 600= 1.00


title: v1040_3: vol1040_first_inf_C9

source_name: whole blood after first inf (C9)


title: Cele2h-BAC050117-174


title: ∆A1S_1874 Mutant3

value: RNAprotect (Qiagen) before RNA extraction


title: Cele2h-BAC050117-175


title: A baumannii 17978 WT3


title: Cele2h-BAC050117-173


title: Cele2h-BAC050117-172


title: Cele2h-BAC050117-183


title: v1040_2: vol1040_first_inf_C6

source_name: whole blood after first inf (C6)


title: v1040_1: vol1040_first_inf_baseline


title: Cele2h-BAC050117-169


title: v1039_18: vol1039_third_inf_memory

source_name: whole blood after third inf (memory)


title: Cele2h-BAC050117-167


title: Cele2h-BAC050117-170


title: Cele2h-BAC050117-171


title: Cele2h-BAC050117-166


title: v1039_17: vol1039_third_inf_T6

source_name: whole blood after third inf (T6)


title: v1039_16: vol1039_third_inf_diagnosis

source_name: whole blood after third inf (diagnosis)


title: v1039_15: vol1039_third_inf_C9

source_name: whole blood after third inf (C9)


title: Cele2h-BAC050117-162


title: v1039_14: vol1039_third_inf_C8

source_name: whole blood after third inf (C8)


title: Cele2h-BAC050117-160


title: Cele2h-BAC050117-164


title: Cele2h-BAC050117-163


title: Cele2h-BAC050117-159


title: v1039_13: vol1039_third_inf_C7

source_name: whole blood after third inf (C7)


title: Cele2h-BAC050117-161


title: Cele2h-BAC050117-155


title: Cele2h-BAC050117-158


title: ∆A1S_1874 Mutant2


title: v1039_12: vol1039_third_inf_C6

source_name: whole blood after third inf (C6)


title: Cele2h-BAC050117-154


title: Cele2h-BAC050117-156


title: Cele2h-BAC050117-168


title: Cele2h-BAC050117-157


title: Cele2h-BAC050117-153


title: v1039_11: vol1039_third_inf_baseline

source_name: whole blood before third inf (baseline)


title: Cele2h-BAC050117-152


title: v1039_10: vol1039_second_inf_diagnosis

source_name: whole blood after second inf (diagnosis)


title: v1039_9: vol1039_second_inf_C8

source_name: whole blood after second inf (C8)


title: Cele2h-BAC050117-150


title: Cele2h-BAC050117-165


title: Cele2h-BAC050117-149


title: v1039_8: vol1039_second_inf_C7

source_name: whole blood after second inf (C7)


title: v1061_12: vol1061_third_inf_C6


title: Cele2h-BAC050117-148


title: Cele2h-BAC050117-147


title: Cele2h-BAC050117-146


title: ACHN_siMEX3A_2_rep.2

city: guangzhou

first: yuntan

last: qiu

state: guangdong

address: 107 Yanjiang West Road, Guangzhou City, Guangdong Province

department: Research Center of Medicine

institute: Sun Yat-Sen Memorial Hospital

data_processing:
RNA-Seq data were aligned and quantified using RSEM as well as STAR against the GRCh37 human reference genome and annotation (GTF format) downloaded from GENCODE official website. Gene counts were then used for downstream analysis.
Genome_build: hg19

source_name: ACHN

extract_protocol:
After transfection for 48 h, total RNA was extracted using RNAiso Plus (Takara, #9108Q) according to the manufacturer’s instructions.
mRNA library construction and single end sequencing were executed by BGI (Wuhan, China).

value: ACHN

tag: sirna treatment


title: v1039_7: vol1039_second_inf_C6

source_name: whole blood after second inf (C6)


title: Cele2h-BAC050117-145


title: v1039_6: vol1039_second_inf_baseline

source_name: whole blood before second inf (baseline)


title: Cele2h-BAC050117-144


title: ACHN_siMEX3A_1_rep.2


title: Cele2h-BAC050117-142


title: v1039_5: vol1039_first_inf_diagnosis

source_name: whole blood after first inf (diagnosis)


title: ACHN_siMEX3A_2_rep.1


title: Cele2h-BAC050117-143


title: Cele2h-BAC050117-141


title: Cele2h-BAC050117-151


title: v1039_4: vol1039_first_inf_C8

source_name: whole blood after first inf (C8)


title: Cele2h-BAC050117-139


title: ACHN_siMEX3A_1_rep.1


title: ACHN_NC_rep.2

value: negative control


title: Cele2h-BAC050117-138


title: v1039_3: vol1039_first_inf_C7

source_name: whole blood after first inf (C7)


title: v1039_2: vol1039_first_inf_C6

source_name: whole blood after first inf (C6)


title: Cele2h-BAC050117-136


title: ACHN_NC_rep.1


title: v1039_1: vol1039_first_inf_baseline

source_name: whole blood before first inf (baseline)


title: Cele2h-BAC050117-137


title: Cele2h-BAC050117-135


title: PA324_MZL 9B

city: Uppsala

first: Lena

last: Claesson-Welsh

address: Dag Hammarskjölds väg 20

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description: CHP files genearated by SST-RMA in the Transcript analysis Console  (TAC v4.0.1.36)

hyb_protocol: Clariom D Human Arrays were hybridized for 16 hours in a 45 degrees C incubator, rotated at 60 rpm. According to the GeneChip TM Expression Wash, Stain  and Scan Manual (PN 702731, ThermoFisher Scientific Inc., Life Technologies, Carlsbad, CA 92008 USA) the arrays were then washed and stained using the GeneChip  TM Fluidics Station 450.

scan_protocol: Scanning was performed using the GeneChip™ Scanner 3000 7G.

data_processing: The raw data was background corrected and  normalized in th Transription Analysis Console (TAC v4.0.1.36), provided by Thermofisher using the SST-RMA version of the robust multi-array average (RMA) method.

source_name: Splenic marginal zone lymphoma

label_protocol: 50 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip TM WT Pico Reagent Kit manual Target Preparation for GeneChip TM Whole Transcript (WT) Expression Arrays User Guide (P/N 703262, ThermoFisher Scientific Inc., Life Technologies, Carlsbad, CA 92008 USA).

extract_protocol: RNA was extracted from frozen tissue samples with the Thermo Fischer RecoverAll kit

value: Splenic marginal zone lymphoma

tag: hrg expression

value: HRG negative


title: Cele2h-BAC050117-133


title: muc17888_GenExpr

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

institute: Boehringer Ingelheim

description:
*** Raw data not available due to patient privacy concerns ***
cell culture: Peripheral blood mononuclear cells (PBMC) were isolated from EDTA whole blood by gradient density centrifugation according to manufacturer’s instructions (Biocoll, Biochrom) and frozen in FCS + 10% DMSO (Merck) for liquid nitrogen storage. After freezing-thawing procedure, T cells were cultured in RPMI 1640 (Gibco) supplemented with 5% human serum, 0.025% l- glutamine, 0.1% HEPES, 0.001% gentamycin and 0.002% streptomycin (hereafter RPMI-HS).
antigen-specific stimulation: PBMCs were stimulated with 0.6nmol of SARS-CoV-2 spike protein peptide mix (PepTivator®SARS-CoV-2 Prot_S, Miltenyi). For the unstimulated condition, PBMCs were only cultured in RPMI-HS. After stimulation for 4h at 37°C, surface staining was conducted for 20min with the following fluorochrome conjugated antibodies: CD3-APC, CD4-PE, CD56-FITC (Life Technologies), CD8-eFluor450 (Biolegend) and CD19-ECD (Beckman Coulter). Propidium iodide (Invitrogen) was used for live/dead discrimination. Flow sorting of CD4+ and CD8+ cells from the stimulated and unstimulated condition was conducted on a MoFlo Astrios EQ (Beckman Coulter) under biosafety level 3.
peripheral blood T cell processing : CD3+ CD4+ and CD8+ T cells were sorted by flow cytometry, centrifuged and the supernatant was carefully removed. Cells were resuspended in the Mastermix + 37.8 μl of water before 70 μl of the cell suspension were transferred to the chip (step 1.1 and 1.2 of the original protocol). After each step, the integrity of the pellet was checked under the microscope to ensure that all cells are loaded onto the chip. From here on, 10x experiments have been performed according to the manufacturer’s protocol (Chromium next GEM Single Cell VDJ V1.1, Rev D). Quality control has been performed with a high sensitivity DNA Kit (Agilent #5067-4626) on a Bioanalyzer 2100 as recommended in the protocol and libraries were quantified with the Qubit dsDNA hs assay kit (life technologies #Q32851). All steps have been performed using RPT filter tips (Starlab #S1181-3710) and DNA LoBind tubes (Sigma #EP0030108051, #EP0030108078, #EP0030124359).
tracheal aspirate processing : Tracheal aspirates were digested with 4ml dispase (50 units/ml) (Corning, #354235) and 25 μl DNase (30 μg/ml) (Qiagen, #79254) at 37°C for 10 min with occasional shaking. The digestion was then stopped with 10 ml of ice-cold 10% FCS/PBS. To obtain single cell suspensions, the digestion mix was passed through a 70 μm cell strainer. Red blood cell lysis was performed only when necessary by incubating the cells with 3 ml RBL buffer at RT for 1 min. The cells were counted, diluted to 1,000 cells/μl and loaded on the 10x Chromium Next GEM Chip G with a targeted cell recovery of 10,000. The following steps were completed according to manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1).

data_processing:
The processing of next generation sequencing reads of the scRNA-seq data was performed using CellRanger version 3.1.0 (10X Genomics) with a customized reference genome. To account for transcripts originating from the virus, the genes of the SARS-CoV-2 genome (NCBI Reference Sequence: NC_045512.2) were manually added to the hg38 (GRCh38.99) human reference genome’s GTF files. For the Blood samples, we filtered genes that were expressed in at least 10 cells, scaled cell-wise expression vectors to a total count of 10,000, and logp1-transformed the data. For the tracheal aspirates, we excluded barcodes with less than 200 detected genes and a high proportion (> 10%) of  mitochondria-encoded genes. Genes were only considered if they were expressed in at least 3 cells in the data set.
Genome_build: hg38 + NC_045512.2
Supplementary_files_format_and_content: Raw count matrix (TcellReversePT_raw_counts_Munich.mtx) from 10x experiments with 46190 genes and 40800 cells in market matrix format and corresponding column (TcellReversePT_genes_allCohorts.txt) and row (TcellReversePT_barcodes_Munich.txt) labels. Cell-level metadata (TcellReversePT_metadata_munich.txt).

extract_protocol:
Single cells were diluted in PBS, supplemented with 0.04% bovine serum albumin up to a final concentration of 100 cells/µl. Using a microfluidic PDMS device (Nanoshift), single cells were co-encapsulated in droplets with barcoded beads (Chemgenes Corporation, Wilmington, MA) at a final concentration of 120 beads/uL. Droplets were collected for 15 min/sample. After droplet breakage, beads were harvested, washed, and prepared for on bead mRNA reverse transcription (Maxima RT, Thermo Fisher). Following an exonuclease I (New England Biolabs) treatment for the removal of unused primers, beads were treated with Klenow enzyme to improve single cell transcript quality; thereafter, beads were counted, aliquoted (2000 beads/reaction, equals ~100 cells/reaction), and pre-amplified by 12 PCR cycles (primers, chemistry, and cycle conditions identical to those previously described in Macosko et al., 2015).
Libraries have been pooled according to their minimal required read counts (35,000 or 50,000 reads/cell for 3’ gene expression libraries, 20,000 reads/cell for 5’ gene expression libraries and 5,000 reads/cell for TCR libraries). Illumina paired end sequencing was performed with 150 or 200 (3’ gene expression) and 100 cycles (5’ gene expression and TCR libraries) on a NovaSeq 6000.

tag: sample type

value: tracheal aspirate

tag: antigenic stimulation

tag: number of cells


title: Cele2h-BAC050117-140

tag: cell line


title: PA324_MZL 8B

tag: tissue


title: Cele2h-BAC050117-131


title: Cele2h-BAC050117-132


title: PA324_MZL 7B


title: PA324_MZL 6B

value: HRG positive


title: Cele2h-BAC050117-128


title: Cele2h-BAC050117-130


title: Cele2h-BAC050117-129


title: muc17887_GenExpr


title: muc17886_GenExpr


title: muc17885_GenExpr


title: Cele2h-BAC050117-127


title: PA324_MZL 5B


title: Pac48h-BAC050117-123


title: Pac48h-BAC050117-124


title: Cele2h-BAC050117-134


title: PA324_MZL 4B


title: muc17884_GenExpr


title: Pac48h-BAC050117-122


title: Muc_10x_GT_8_GenExpr

source_name: GT_5 TA_2


title: Pac48h-BAC050117-120


title: Pac48h-BAC050117-119


title: PA324_MZL 3B (qia)


title: Pac48h-BAC050117-118


title: PA324_MZL 2B


title: Muc_10x_GT_6_GenExpr

source_name: GT_6 TA_2


title: Pac48h-BAC050117-117


title: Pac48h-BAC050117-116


title: PA324_MZL 1B


title: Pac48h-BAC050117-115


title: Muc_10x_GT_5_GenExpr

source_name: GT_5 TA_1


title: PA324_H4417


title: Pac48h-BAC050117-114


title: Pac48h-BAC050117-113


title: Pac48h-BAC050117-112


title: Pac48h-BAC050117-111


title: Muc_10x_GT_4_GenExpr

source_name: GT_6 TA_1


title: PA324_H2267-04


title: Pac48h-BAC050117-121


title: Sample_20063a012_01_TCR

source_name: GT PBMC_1

value: PBMC

value: stimulated


title: Pac48h-BAC050117-109


title: Pac48h-BAC050117-110


title: Pac48h-BAC050117-107


title: Muc_10x_GH_7_GenExpr

source_name: GH_7 TA


title: Sample_20063a011_01_TCR

value: unstimulated


title: Sample_20063a010_01_TCR

source_name: GT_6 PBMC_2

value: stimulted


title: Pac48h-BAC050117-106


title: Pac48h-BAC050117-105


title: Pac48h-BAC050117-104


title: Sample_20063a009_01_TCR

source_name: GT_6 PBMC_1


title: PA324_H2676-13

source_name: MALT lymphoma

value: MALT lymphoma


title: Pac48h-BAC050117-102


title: Pac48h-BAC050117-103


title: Pac48h-BAC050117-101


title: Pac48h-BAC050117-108


title: Pac48h-BAC050117-100


title: Pac48h-BAC050117-099


title: Pac48h-BAC050117-097


title: Pac48h-BAC050117-096


title: Tumor_free_sample_2

city: Essen

first: Sied

last: Kebir

address: Hufelandstr. 55

institute: DKFZ-Division Translational Neurooncology at the West German Cancer Center (WTZ)

data_processing:
Read alignment to the hg38 human reference genome, counts, cell-calling, dimensionality reduction (t-SNE) and clustering were computed using the 10x Genomics Cell Ranger 4.0.0 pipeline.
for each samples with the “cellranger count” command and default parameters. Median UMI counts per cell in all samples ranged from 14188 to 19610.
Genome_build: hg38

growth_protocol: CD34+ and CD45+ cells from two fresh glioblastoma tissues, one tumor-free region tissue, healthy bone marrow monouclear cells (CD34+ Lonza, 2M-101A) and one healthy PBMC sample ( Lonza, 4W-270) were used for scRNAseq studies

extract_protocol:
After isolation, samples were stored at -80°C in freezing medium (15 % DMSO and 20 % FBS in IMDM) until further processing. Before library preparation, samples were inspected for dead cells using trypan blue exclusion.
Library preparation was performed with all samples using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics). Appropriate volume for the recovery of 770 cells was loaded onto a chip and DNA libraries were prepared according to the manufacturers protocol. Quality control of prepared libraries was performed using the Agilent 2100 Bioanalyzer prior to sequencing.

treatment_protocol: Tissue samples were dissociated as previously described. CD34+ / CD45+ positive magnetic selection was performed using the REAlease® CD45 (TIL) MicroBead Kit (Miltenyi Biotec, 130-121-563) and, immediately after removal of the CD45 complex, using the CD34 MicroBead Kit UltraPure (Miltenyi Biotec, 130-100-453) on the CD45 positively-selected samples, according to the manufacturer’s instructions.

value: tumor free sample


title: Pac48h-BAC050117-095


title: Tumor_free_sample_3


title: Tumor_free_sample_1


title: Glioblastoma_sample_4

value: glioblastoma


title: Tumor_free_sample_4


title: Pac48h-BAC050117-094


title: Pac48h-BAC050117-093


title: PID14 miR-9/9*-124 shCTL biological rep2

hyb_protocol: Labelled cDNAs were hybridized onto the Human Clariom D array according to the manufacturer's instructions.

scan_protocol: Array was scanned using GeneChip Scanner 3000.

data_processing: Array data was analyzed using manufacturer’s software, Expression Console followed by Transcriptome Analysis Console (TAC) using RMA gene analysis setting.

source_name: adult fibroblast

label_protocol: GeneChip WT PLUS reagent kit was used to prepare RNA samples to biotinylated cDNAs according to the manufacturer's instructions.

growth_protocol: Human adult fibroblasts (GM02171) obtained from NIGMS Coreill Institute were maintained high glucose Dulbecco’s Modified Eagle Medium (Gibco, 11960044) containing 10% FBS (Gibco, 10437028), MEM non-essential amino acids (Gibco, 11140050), sodium pyruvate (Gibco, 11360070), GlutaMAX (Gibco, 35050061), HEPES (Gibco, 15630080), penicillin-streptomycin (Gibco, 15130122), and 2-mercaptoethanol (Gibco, 21985023).

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen, 15596026) in combination with RNeasy mini kit (Qiagen, 74104). RNA quality (RIN > 9.6) was determined with 2100 Bioanalyzer (Agilent).

treatment_protocol: MiRNA-mediated direct conversion of fibroblasts into neurons was initiated by treating fibroblasts with lentiviral reprogramming cocktail of reverse tetracycline-controlled transactivator rtTA (Addgene, 66810) with 1) inducible pT-miR-NS, 2) pT-miR-9/9*-124 with shCTL, or 3) pT-miR-9/9*-124 with shPTBP2. The day following lentiviral transduction, media change was supplemented with doxycycline (Sigma-Aldrich, D9891). Three days following initial transduction, media was changed again and supplemented with doxycycline and antibiotics. Five days post transduction, cells were plated onto poly-l-ornithine (Sigma-Aldrich, P4957), fibronectin (Sigma-Aldrich, F4759), and laminin (Sigma-Aldrich, L2020) coated coverslips followed by full media switch to neuronal media (ScienCell, 1521) the following day supplemented with 200 M dibutyl-cyclic AMP (cAMP; Sigma-Aldrich, D0627), 1 mM valproic acid (VPA; Sigma Aldrich, P4543), 10 ng/mL human BDNF (PeproTech, 450-02), 10 ng/mL human NT-3 (Peprotech, 450-03), 1 M retinoic acid (RA; Sigma-Aldrich, R2625), RevitaCell supplement (Gibco, A2644501), and antibiotics. DOX was supplemented every 2 days while half media changes occurred every 4 days until day 14 when cells were collected for RNA extraction.

tag: age

tag: gender

value: female


title: PID14 miR-9/9*-124 shPTBP2 biological rep2


title: PID14 miR-9/9*-124 shPTBP2 biological rep1


title: PID14 miR-9/9*-124 shCTL biological rep1


title: Pac48h-BAC050117-091


title: YPW2798_rep4 [120031]

city: Ann Arbor

first: Patricia

middle: J

last: Wittkopp

state: MI

address: 1105 N University Ave

department: Department of Molecular, Cellular, and Developmental Biology

institute: University of Michigan

description:
120031_TCTCGCGC-GTACTGAC_S51_L005
processed data file: Strain_2798.txt

data_processing:
Raw reads were run through the fastqc (version 0.11.5) read quality software, which indicated high quality reads for all samples sequenced. Reads were then trimmed using cutadapt (version 1.10)
Reads were pseudo-mapped to the a transcriptome index generated using salmon (version 0.9.1) on S. cerevisiae cDNA (Ensemble, release 38)
Read counts from salmon were imported into R using TxDb (version 3.2.2). Read counts for the entire dataset were supplied to DESeq2 to model gene expression levels. The DESeq2 ‘contrast’ wrapper was then used to estimate log2 fold changes for each strain relative to its appropriate reference and identify differentially expressed genes.
Genome_build: S. cerevisiae s288c cDNA (Ensemble, release 38, retrieved from ftp://ftp.ensemblgenomes.org/pub/release-38/fungi/fasta/saccharomyces_cerevisiae/cdna/).
Supplementary_files_format_and_content: three types of processed data files are provided: output of differential expression measures for each strain relative to the appropriate wild type reference as calculated by DESeq2 as tab delimited text files, read count abundance measures as output from salmon for both the endogenous and transgenes present as .sf files, and a raw read count matrix for all samples also as a tab delimited text file.

organism: Saccharomyces cerevisiae

source_name: haploid yeast culture_YPW2798

growth_protocol: For a total of four replicates, each replicate set of strains, including mutants and controls, were randomly arrayed across the inner wells of a 96 well plate surrounded by an outer row of wells filled with non-inoculated media. Each of the four plate arrays was grown to saturation in YPD, and then glycerol stocked in 80% glycerol and stored at -80C. The glycerol stocks were thawed by transfer using a pin tool onto solid YPG agar plates and strains were grown up for ~3 days at 30C. Strains were then transferred by pin tool again into 500uL liquid YPD in 1mL 96-well plates with glass beads and grown at 30C while shaking at 250rpms for 2 days, until all strains were once again at saturation. 100uL of the saturated culture was then transferred to a Costar 96 well plate and OD measured using a Tecan Sunrise. The OD was then used to calculate cell density. A separate 1mL 96 well plate was then filled with  500uL of YPD in each well, and each well inoculated with a volume of the saturated culture calculated to grow to a cell density of 5x10^6 cell per mL (an OD of about 0.4) after 12.5hr, based on empirical determination of each strain’s growth rate. These cultures were then grown spinning on a wheel at 30C for 12.5hrs, after which 100uL was removed and used to measure OD to ensure all cultures were between an OD of 0.26 to 0.48. Plates were then spun down for 5min at 3000g, and liquid media pipetted off. Remaining cell pellets were frozen by plunging the entire plate containing cell pellets into liquid nitrogen. Plates were sealed with foil and stored at -80C until RNA extractions were performed.

extract_protocol:
Frozen cell pellets were resuspended in 700uL of a lysis buffer containing beta-mercaptoethanol and transferred to a plate containing ~250uL of acid-washed 425-600um beads. Beaded plates were beaten 10x for 1min each with 1min on ice in between. Plates were spun down at 3000rpm at 4C for 4min, and 400uL of lysis supernatant were removed and transferred into a new 96 well plate containing oligodT magnetic beads (Dynabeads mRNA DIRECT Kit, Ambion, cat# 61011). Beads and lysate were incubated at room temperature with agitation for 5 minutes, and then placed on a magnetic stand. Beads were then washed according to the Dynabeads mRNA direct kit user guide. After extraction, several representative samples were run on Agilent Bioanalyzer to check RNA quality and concentration before moving on to library preparation. In addition, selected wells were tested for the presence of NAT or KAN resistance markers present in distinct strains and controls by RT-PCR and visualized on a gel to ensure well-cross contamination had not taken place at any step previous to library prep.
RNA sequencing libraries were prepared using a modified, ⅓ volume reaction TruSeq RNA Sample Preparation v2 Guide, and using multiplexable adapters from the TruSeq RNA CD Index Plate (cat# 20019792).

tag: cell type

value: alpha

value: trans-regulatory mutant to TDH3


title: YPW2506_rep4 [120032]

description:
120032_AGCGATAG-GTACTGAC_S52_L005
processed data file: Strain_2506.txt

source_name: haploid yeast culture_YPW2506


title: Pac48h-BAC050117-090


title: YPW3016r3_rep4 [120030]

source_name: haploid yeast culture_YPW3016r3

value: alpha wild type control


title: Pac48h-BAC050117-098


title: YPW3191r2_rep4 [120029]

description:
120029_CGGCTATG-GTACTGAC_S49_L005
processed data file: Strain_3191.txt

source_name: haploid yeast culture_YPW3191r2


title: Pac48h-BAC050117-089


title: Glioblastoma_sample_1


title: Glioblastoma_sample_3


title: Glioblastoma_sample_2


title: Pac48h-BAC050117-092


title: Bone marrow_3

source_name: Bone marrow_3

value: bone marrow


title: Pac48h-BAC050117-087


title: Pac48h-BAC050117-086


title: Bone marrow_4

source_name: Bone marrow_4


title: YPW3191r1_rep4 [120027]

description:
120027_CTGAAGCT-GTACTGAC_S47_L005
processed data file: Strain_3191.txt

source_name: haploid yeast culture_YPW3191r1


title: YPW3245_rep4 [120028]

description:
120028_TAATGCGC-GTACTGAC_S48_L005
processed data file: Strain_3245.txt

source_name: haploid yeast culture_YPW3245


title: Pac48h-BAC050117-085


title: Pac48h-BAC050117-084


title: YPW2800r1_rep4 [120026]

description:
120026_GAATTCGT-GTACTGAC_S46_L005
processed data file: Strain_2800.txt

source_name: haploid yeast culture_YPW2800r1


title: Pac48h-BAC050117-083


title: Pac48h-BAC050117-088


title: Bone marrow_2

source_name: Bone marrow_2


title: Pac48h-BAC050117-082


title: Pac48h-BAC050117-081


title: Bone marrow_1

source_name: Bone marrow_1


title: Pac48h-BAC050117-080


title: PID14 miR-NS biological rep1


title: PID14 miR-NS biological rep2


title: Blood_4

value: blood


title: Pac48h-BAC050117-079


title: Pac48h-BAC050117-078


title: Pac48h-BAC050117-077


title: YPW2504r1_rep4 [120024]

description:
120024_GAGATTCC-GTACTGAC_S44_L005
processed data file: Strain_2504.txt

source_name: haploid yeast culture_YPW2504r1


title: Pac48h-BAC050117-076


title: Pac48h-BAC050117-074


title: YPW2794_rep4 [120023]

description:
120023_CGCTCATT-GTACTGAC_S43_L005
processed data file: Strain_2794.txt

source_name: haploid yeast culture_YPW2794


title: Blood_2


title: Blood_1


title: Pac48h-BAC050117-075


title: YPW3161_rep4 [120021]

description:
120021_ATTACTCG-GTACTGAC_S41_L005
processed data file: Strain_3161.txt

source_name: haploid yeast culture_YPW3161


title: Pac48h-BAC050117-072


title: Pac48h-BAC050117-070


title: YPW3016r2_rep4 [120022]

source_name: haploid yeast culture_YPW3016r2


title: Pac48h-BAC050117-071


title: Pac48h-BAC050117-073


title: YPW3275_rep4 [120019]

description:
120019_TCTCGCGC-CAGGACGT_S39_L005
processed data file: Strain_3275.txt

source_name: haploid yeast culture_YPW3275


title: Pac48h-BAC050117-069


title: YPW3016r4_rep4 [120025]

source_name: haploid yeast culture_YPW3016r4


title: Patient 33 Blood

city: Aurora

first: Kristine

middle: A

last: Kuhn

state: Colorado

address: 1775 Aurora Ct. Mail Stop B115

department: Medicine

institute: University of Colorado School of Medicine

description: All.combined.metadata.csv

data_processing:
10X Genomics library sequence fastq files aligned and cell gene expression matrices generated with Cellranger v2.0.0 cellranger count with default settings
Created Seurat object for each sample with Seurat Read10X
Subset each seurat object to keep nFeature_RNA >200 and <4000, percent.mt<10 & nCount_RNA<20000
Removed batch effects with FindIntegrationAnchors, dims=1:20 and IntegrateData, dims=1:20
Clusters defined with FindNeighbors, reduction=“pca”, dims=1:20 and FindClusters, resolution=0.25

source_name: Periperhal Blood

extract_protocol:
For colon tissue: 30 pinch biopsies were tkaen from the rectoSignoid colon of each patient. Tissue was frozen in liquid nitrogen until use. Thawed tissue was treated with type 4 collagenase for 30 minutes and strained through a 100 micron filter. Cells were stained for Viability and CD45 and sorted for live CD45+ on an Astrios EQ
For Peripheral blood: Whole blood was collewcted in a Potassium EDTA tube, blood was layered on ficolla and centrifuged at 1200RPM for 20 minutes. Buffy Coat layer was collected and stained for CD45 and viability. CD45+ live cells were collected on an Astrios EQ.

tag: disease state

value: Co-morbid Crohn's and Spondyloarthritis


title: Pac48h-BAC050117-068


title: Patient 33 Colon

description: All.combined.metadata.csv

source_name: Retrosigmoid Colon


title: Blood_3


title: YPW3241_rep4 [120020]

description:
120020_AGCGATAG-CAGGACGT_S40_L005
processed data file: Strain_3241.txt

source_name: haploid yeast culture_YPW3241


title: YPW3287_rep4 [120018]

description:
120018_TCCGCGAA-CAGGACGT_S38_L005
processed data file: Strain_3287.txt

source_name: haploid yeast culture_YPW3287


title: Pac48h-BAC050117-067


title: Patient 27 Blood

description: All.combined.metadata.csv

value: Spondyloarhtritis


title: Patient 27 Colon

description: All.combined.metadata.csv


title: YPW3298r2_rep4 [120017]

description:
120017_CGGCTATG-CAGGACGT_S37_L005
processed data file: Strain_3298.txt

source_name: haploid yeast culture_YPW3298r2

value: A

value: TDH2/3 double deletion


title: Pac48h-BAC050117-065


title: Pac48h-BAC050117-064


title: Pac48h-BAC050117-066


title: Pac48h-BAC050117-063


title: Pac48h-BAC050117-061


title: Pac48h-BAC050117-062


title: Pac48h-BAC050117-060


title: YPW2728_rep4 [120015]

description:
120015_CTGAAGCT-CAGGACGT_S35_L005
processed data file: Strain_2728.txt

source_name: haploid yeast culture_YPW2728


title: Patient 23 Colon

description: All.combined.metadata.csv

value: Crohn's Disease


title: Patient 23 Blood

description: All.combined.metadata.csv


title: YPW1200_rep4 [120016]

description:
120016_TAATGCGC-CAGGACGT_S36_L005
processed data file: Strain_1200.txt

source_name: haploid yeast culture_YPW1200

value: cis-regulatory mutant to TDH3


title: YPW2504r2_rep4 [120013]

description:
120013_ATTCAGAA-CAGGACGT_S33_L005
processed data file: Strain_2504.txt

source_name: haploid yeast culture_YPW2504r2


title: YPW3016r1_rep4 [120014]

source_name: haploid yeast culture_YPW3016r1


title: Ctrl-BAC050117-057

value: Ctrl


title: Patient 21 Blood

description: All.combined.metadata.csv

value: Healthy Control


title: Ctrl-BAC050117-056


title: Ctrl-BAC050117-055


title: Ctrl-BAC050117-054


title: Patient 21 Colon

description: All.combined.metadata.csv


title: Ctrl-BAC050117-051


title: YPW3228_rep4 [120012]

description:
120012_GAGATTCC-CAGGACGT_S32_L005
processed data file: Strain_3228.txt

source_name: haploid yeast culture_YPW3228


title: Ctrl-BAC050117-050


title: Ctrl-BAC050117-053


title: Ctrl-BAC050117-052


title: YPW3272_rep4 [120011]

description:
120011_CGCTCATT-CAGGACGT_S31_L005
processed data file: Strain_3272.txt

source_name: haploid yeast culture_YPW3272


title: YPW3286_rep4 [120010]

description:
120010_TCCGGAGA-CAGGACGT_S30_L005
processed data file: Strain_3286.txt

source_name: haploid yeast culture_YPW3286


title: Patient 7 Blood

description: All.combined.metadata.csv


title: Ctrl-BAC050117-045