title: IL-13KO NP+IgE+ Bcell#79


title: AB7054

status: Public on Jan 27 2021

type: SRA

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic

data_processing:
library strategy: MARS-seq
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes mRNA molecule count values for each Sample
[metadata_s.txt]  Meta data file associating each single cell with its amplification batch and index sorting readouts

molecule: polyA RNA

organism: Homo sapiens

source_name: Bone marrow aspiration

growth_protocol:
(1)  Cells were cultured using an aseptic technique in RPMI medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum, 1mM sodium pyruvate, 2mM L-glutamine, 1% penicillin-streptomycin (ThermoFisher Scientific).
(2)  Bone marrow cells from a relapse refractory myeloma patient (penta-refractory, refractory to bortezomib and carfilzomib) were stained with magnetic CD138+ enrichment beads (Miltenyi). Cells were washed and re-suspended in RPMI 1640 medium (Gibco) supplemented with 15% FBS, 1% Glutamine and 1% penicillin-streptomycin (ThermoFisher Scientific).

extract_protocol:
After informed consent (in accordance with Helsinki declaration), bone marrow aspiration was placed in EDTA-containing tubes (Beckton Dickenson), diluted 1:1 with ice cold FACS buffer (EDTA pH8.0 2mM, BSA 0.5% in PBS), placed on ice and immediately transported to the lab.
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}
single cell RNA-seq for gene expression quantitation

treatment_protocol:
(1)  The designed therapeutic treatment includes a quadruple regimen comprised of Daratumumab, Carfilzomib, Lenalidomide and Dexamethasone (DARA-KRD) (Methods; KYDAR Clinical Trial).
(2)  RPMI-8226 PPIA-/- cells were treated with CFZ, CsA and their combination, and were harvested 4- and 8-hours post treatment.

tag: organ

value: Bone marrow

tag: sample type

value: Bone marrow aspiration

tag: cell type

value: Plasma cells

tag: selection marker

tag: time point

value: Cycle 10

tag: treatment (1)

value: DARA-KRD

tag: replicate id

tag: disease state

value: PRMM


title: IL-13KO NP+IgE+ Bcell#74

city: Yokohama

first: Kosuke

last: Miyauchi

state: Kanagawa

address: 1-7-22 Suehiro-sho

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
HISAT2(version 2.1.0) with default parameters
StringTie(version 2.0)
Genome_build: mm10
Supplementary_files_format_and_content: Fasta files including read sequences of Ig mRNA, and tab-delimited text files include read counts for genes

molecule: total RNA

organism: Mus musculus

extract_protocol:
We transferred IL-13 sufficient or deficient OT-2 TH2 into IgE reporter (Verigem) mice followed by immunization with NP-OVA. At 7 day post immunization, NP specific IgE producing B cells were sorted by flow cytometer.
For scRNA-seq analysis, the single-cells were sorted into each well of 96 well plates using FACS Aria III (BD). The single cells are lysed in a buffer that contains dNTPs and oligo(dT)-tailed oligonucleotides with a universal 5'-anchor sequence. RT is performed, which adds 2–5 untemplated nucleotides to the cDNA 3’ end. A template-switching oligo (TSO) is added, carrying 2 riboguanosines and a modified guanosine to produce a LNA as the last base at the 3’ end. After the first-strand reaction, the cDNA is amplified using a 25 of cycles. Next, Tn5 tagmentation is used to construct sequencing libraries from the amplified cDNA (Nextera XT DNA Library Preparation Kit, illumina). The sequencing was carried out using NovaSeq6000 equipment (SP type, 150PE, Illumina).

tag: strain

tag: tissue

value: spleen

tag: age

value: 8 weeks

tag: genotype

value: IgE repoter (Verigem)


title: EORG-E rep 1 (oestrogen treatment)

city: Vienna

first: Paulina

middle: Anna

last: Latos

address: Schwarzspanierstraße 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

description:
EORG-E-2
CAPW7ANXX_7#51605_GCCAAT

data_processing:
Basecalling performed using RTA 1.18.64.0
Raw reads were trimmed with trimgalore (v0.5.0).
The strand specific reads were depleted of abundant sequences (iGenomes, hg38) by aligning with bowtie2 (v2.3.4.1).
Salmon (v0.11.0) was used to derive TPMs by using the transcriptome based on GRCh38 and Ensembl 94.
Genome_build: GRCh38/Ensembl 94
Supplementary_files_format_and_content: Tab-delimited text files containing gene id and Salmon TPMs.

source_name: EORG-E_oestrogen treatment

growth_protocol: Endometrial organoids (EORG) were established by embedding the isolated epithelial cells of decidua in 60% Matrigel and organoid media (advanced DMEM/F12, 10 mM Hepes, 1xB27, 1x N2 and 20mM Glutamine supplemented with 100 ng/ml R-Spondin, 1 µM A83-01, 100 ng/ml recombinant hEGF, 100 ng/ml Noggin, 10mM CH99021).

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen) with the DNaseI (Qiagen) digest performed on the column according to manufacturer's protocol
mRNA was isolated using the Dyabeads mRNA purification kit (Life Technologies 61006) and prepared into an indexed library using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre SSV21106) according to the manufacturers' instructions. Indexed libraries were pooled and sequenced with a 100-bp single end protocol.

tag: tissue/cell type

value: endometrial organoids

tag: treatment

value: for 7 days with 10nM oestrogen supplemented to standard media

tag: internal id


title: IL-13KO NP+IgE+ Bcell#73


title: IL-13KO NP+IgE+ Bcell#72


title: IL-13KO NP+IgE+ Bcell#71


title: EORG-C-1 rep 3 (control)

description:
EORG-C-3
CAPW7ANXX_51606_CTTGTA


title: IL-13KO NP+IgE+ Bcell#70


title: EORG-C-1 rep 2 (control)

description:
EORG-C-2
CAPW7ANXX_51604_ACTTGA


title: IL-13KO NP+IgE+ Bcell#69


title: EORG-E rep 2 (oestrogen treatment)

description:
EORG-E-1
CAPW7ANXX_7#51603_TGACCA


title: IL-13KO NP+IgE+ Bcell#68


title: AB6887


title: IL-13KO NP+IgE+ Bcell#67


title: EORG-C-1 rep 1 (control)

description:
EORG-C-1
CAPW7ANXX_51602_ATCACG


title: IL-13KO NP+IgE+ Bcell#66


title: AB6886

value: Baseline

tag: cohort

value: Relapse


title: IL-13KO NP+IgE+ Bcell#64


title: EORG-3 rep 3

description:
EORG-3.3
CATK5ANXX_50497_CGATGT


title: EORG-3 rep 2

description:
EORG-3.2
CATK5ANXX_50496_CTTGTA


title: AB6885

value: Cycle 4


title: AB6888


title: AB6884


title: IL-13KO NP+IgE+ Bcell#62


title: IL-13KO NP+IgE+ Bcell#63


title: EORG-3 rep 1

description:
EORG-3.1
CATK5ANXX_50495_GCCAAT


title: IL-13KO NP+IgE+ Bcell#61


title: IL-13KO NP+IgE+ Bcell#60


title: EORG-1 rep 3

description:
EORG-1.3
CATK5ANXX_50494_ACTTGA


title: AB6882


title: IL-13KO NP+IgE+ Bcell#58


title: EORG-1 rep 2

description:
EORG-1.2
CATK5ANXX_50493_TGACCA


title: AB6889


title: AB6883


title: IL-13KO NP+IgE+ Bcell#56


title: IL-13KO NP+IgE+ Bcell#57


title: EORG-1 rep 1

description:
EORG-1.1
CATK5ANXX_50492_ATCACG


title: IL-13KO NP+IgE+ Bcell#55


title: AB6881


title: IL-13KO NP+IgE+ Bcell#65


title: AB6686


title: IL-13KO NP+IgE+ Bcell#53


title: IL-13KO NP+IgE+ Bcell#54


title: EORG-2 rep 3

description:
EORG-2.3
C9N3PANXX_43222_GGCTAC


title: EORG-2 rep 2

description:
EORG-2.2
C9N3PANXX_43221_TAGCTT


title: IL-13KO NP+IgE+ Bcell#51


title: AB6684


title: AB6685


title: AB7057


title: EORG-2 rep 1

description:
EORG-2.1
C9N3PANXX_43220_ACAGTG


title: IL-13KO NP+IgE+ Bcell#50


title: AB6683


title: IL-13KO NP+IgE+ Bcell#48


title: IL-13KO NP+IgE+ Bcell#59


title: IL-13KO NP+IgE+ Bcell#47


title: IL-13KO NP+IgE+ Bcell#46


title: IL-13KO NP+IgE+ Bcell#45


title: AB6682


title: IL-13KO NP+IgE+ Bcell#43


title: MHPJ1: juvenile Mongolian horse pituitary1

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 20 -p 16 --no-discordant. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue <= 0.01.
Genome_build: Ensembl, EquCab2.75
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Equus caballus

source_name: Mongolian horse

extract_protocol:
Each sample was individually ground (mortar and pestle, under continuous liquid N2 chilling) into a fine powder before RNA extraction. Ground samples were stored at -80°C. Total RNA was extracted from 30 mg of ground tissue by using hot phenol method. In brief, cell pellets were resuspended and washed once in Buffer A (50 mM sodium acetate and 10 mM EDTA, pH=5.2). After collecting the cells by centrifugation, the pellets were resuspended in Buffer A containing 1% SDS and immediately added to hot phenol. After incubation at 65°C for 5 minutes followed by centrifugation for 10 minutes at 4°C, the RNA-containing supernatants were transferred to a new tube for ethanol precipitation, washed and then dissolved in DE PC-treated water. The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA we redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). The integrity of the RNA was further verified by 1.5% agarose gel electrophoresis.
Ribosomal RNAs were removed from the RNA samples (10 μg) using a RiboMinus rRNA depletion kit (Ambion), and the resulting samples we are used to prepare directional RNA-Seq libraries. The purified mRNAs were then iron -fragmented at 95°C followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed using RT primers containing a 3' adaptor sequence and a randomized hexamer. The cDNAs were purified and amplified, and all 200-500-bp PCR product s were purified, quantified and stored at -80°C until they were used for sequencing.
For high-throughput sequencing, libraries were prepared following the manufacturer's instructions, and the Illumina NextSeq 500 was used to collect data from 151 nt paired-end sequencing.

value: pituitary

tag: developmental stage

value: juvenile

tag: Sex

value: female


title: AB6680

tag: organ

value: Bone marrow

tag: sample type


title: IL-13KO NP+IgE+ Bcell#42


title: IL-13KO NP+IgE+ Bcell#41


title: MHPA3: adult Mongolian horse pituitary3

value: adult


title: AB6681

value: Bone marrow aspiration

tag: cell type

value: Plasma cells

tag: selection marker


title: MHPJ3: juvenile Mongolian horse pituitary3


title: MHPJ2: juvenile Mongolian horse pituitary2


title: IL-13KO NP+IgE+ Bcell#39


title: AB6679

tag: time point


title: IL-13KO NP+IgE+ Bcell#49


title: AB6678

tag: replicate id


title: IL-13KO NP+IgE+ Bcell#38


title: IL-13KO NP+IgE+ Bcell#37


title: MHPA1: adult Mongolian horse pituitary1


title: MHPA2: adult Mongolian horse pituitary2


title: AB6677

tag: disease state


title: MHLBJ3: juvenile Mongolian horse long bone3

value: epiphysis


title: IL-13KO NP+IgE+ Bcell#35

tag: strain


title: IL-13KO NP+IgE+ Bcell#36

tag: tissue


title: IL-13KO NP+IgE+ Bcell#34

tag: age


title: MHLBJ2: juvenile Mongolian horse long bone2


title: IL-13KO NP+IgE+ Bcell#52

tag: genotype


title: IL-13KO NP+IgE+ Bcell#33


title: IL-13KO NP+IgE+ Bcell#44


title: IL-13KO NP+IgE+ Bcell#40


title: IL-13KO NP+IgE+ Bcell#30


title: AB6676

value: PRMM


title: AB6674


title: IL-13KO NP+IgE+ Bcell#31

value: spleen


title: AB6675


title: IL-13KO NP+IgE+ Bcell#29

value: 8 weeks


title: IL-13KO NP+IgE+ Bcell#32

value: IgE repoter (Verigem)


title: IL-13KO NP+IgE+ Bcell#27


title: IL-13KO NP+IgE+ Bcell#26


title: IL-13KO NP+IgE+ Bcell#25


title: IL-13KO NP+IgE+ Bcell#24


title: IL-13KO NP+IgE+ Bcell#23


title: IL-13KO NP+IgE+ Bcell#21


title: AB6672


title: AB6501


title: AB6673


title: AB6500


title: DPPJ3: juvenile Debao pony pituitary3

source_name: Debao pony


title: MHLBA2: adult Mongolian horse long bone2


title: MHLBJ1: juvenile Mongolian horse long bone1


title: MHLBA3: adult Mongolian horse long bone3


title: DPPJ2: juvenile Debao pony pituitary2


title: MHLBA1: adult Mongolian horse long bone1


title: DPPJ1: juvenile Debao pony pituitary1


title: IL-13KO NP+IgE+ Bcell#28


title: IL-13KO NP+IgE+ Bcell#19


title: AB6499


title: IL-13KO NP+IgE+ Bcell#17


title: IL-13KO NP+IgE+ Bcell#18


title: IL-13KO NP+IgE+ Bcell#16


title: AB6671

tag: treatment (1)

value: DARA-KRD


title: IL-13KO NP+IgE+ Bcell#15


title: IL-13KO NP+IgE+ Bcell#22


title: IL-13KO NP+IgE+ Bcell#14


title: IL-13KO NP+IgE+ Bcell#12


title: IL-13KO NP+IgE+ Bcell#20


title: IL-13KO NP+IgE+ Bcell#11


title: IL-13KO NP+IgE+ Bcell#7


title: IL-13KO NP+IgE+ Bcell#9


title: DPPA3: adult Debao pony pituitary3


title: IL-13KO NP+IgE+ Bcell#8


title: DPPA2: adult Debao pony pituitary2


title: DPPA1: adult Debao pony pituitary1


title: DPLBJ2: juvenile Debao pony long bone2


title: IL-13KO NP+IgE+ Bcell#5


title: AB6498

value: Refractory


title: DPLBJ3: juvenile Debao pony long bone3


title: DPLBA3: adult Debao pony long bone3


title: IL-13KO NP+IgE+ Bcell#6


title: DPLBJ1: juvenile Debao pony long bone1


title: DPLBA2: adult Debao pony long bone2


title: AB6496

value: Baseline


title: IL-13KO NP+IgE+ Bcell#4


title: AB6497


title: AB6491

value: Relapse


title: AB6494


title: IL-13KO NP+IgE+ Bcell#3


title: AB6495


title: IL-13KO NP+IgE+ Bcell#13


title: AB6492


title: AB6493


title: DPLBA1: adult Debao pony long bone1


title: IL-13KO NP+IgE+ Bcell#2


title: AB6490


title: IL-13KO NP+IgE+ Bcell#1


title: WT NP+IgE+ Bcell#384


title: WT NP+IgE+ Bcell#382


title: WT NP+IgE+ Bcell#380


title: WT NP+IgE+ Bcell#381


title: WT NP+IgE+ Bcell#379


title: AB6488


title: AB6489


title: 1_3_K2_48h

city: Frankfurt am Main

first: Klaus

last: Scholich

address: Theodor Stern Kai 7

department: Institute of Clinical Pharmacology

country: Germany

institute: University Hospital Goethe-University Frankfurt

data_processing:
Basecalls performed using Illumina NextSeq500 System.
The raw sequencing reads were preprocessed with the software bcl2fastq using the following command: /opt/illumina/Isas/1.37.0/bcl2fastq2/bin/bcl2fastq --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35 --loading-threads 1 -R "/data/scratch/workspace/RunFolder" --sample-sheet "/data/scratch/workspace/RunFolder/SampleSheet.csv" -o "/data/scratch/workspace/RunFolder/Analysis/Temp_01.01-GenerateFASTQ.FastqGeneration"
Read mapping against the mouse reference genome  was done with the STAR aligner (version2.6.0a 2018/04/23).
The mapped reads were assigned to annotated features (genes) using the Bioconductor package Rsubread (v1.28.1).
Genome_build: Reference genome: primary assembly of the mouse genome sequence as of June 2018 (GRCm38.p6). The genome annotation was downloaded from Gencode (Release M17, GRCm38.p6)
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: Bone marrow-derived mast cells

growth_protocol: Bone marrow cells were isolated from murine femur and tibia from the hind legs of adult mice. The bones were cut open at one end and centrifuged at 10,000 g for 1 min. The cells of a single animal were resuspended in 40 ml of mast cell medium consisting of RPMI 1640 medium supplemented with 10% fetal bovine serum, 100 U/ml penicillin/streptomycin, 4 mM L-Glutamine, 1 mM sodium pyruvate, 1% MEM nonessential amino acids, 50 μM 2-mercaptoethanol and 10 μg/L IL-3 (#213-13, PeproTech). Forty milliliters of medium was added twice a week. The cells were cultivated for 4 to 6 weeks at 37°C with 5% CO2 under humidified conditions.

extract_protocol:
RNA was isolated from the FACS-sorted cells using the RNeasy micro Kit (Qiagen, #74004).
Library preparation was carried out with the QuantSeq 3’ mRNA Library Prep Kit FWD (Lexogen).

treatment_protocol: BMMCs were cultivated for 4 weeks as described, then the cellnumber was adjusted to 8x105 cells/ml and the cells were treated with 10 μg/ml zymosan for 24 h or 48 h or left untreated (0 h). Cells were stained for 1 h with CD117-PE (#130-102-795, Miltenyi Biotec) and FcϵRIa-FITC (#134305, Biolegend) at 4°C  and then sorted using a FACS Aria (BD Biosciences) to obtain a pure population of CD117+/FcϵRIa+ double-positive cells.

value: Bone marrow-derived mast cells

tag: treatment

value: treated with 10 μg/ml zymosan for 48 h


title: 22_2_K1_48h


title: WT NP+IgE+ Bcell#378


title: AB6487

value: Cycle 4


title: 9_2_48h


title: WT NP+IgE+ Bcell#375


title: WT NP+IgE+ Bcell#374


title: WT NP+IgE+ Bcell#373


title: 22_2_K2_48h


title: WT NP+IgE+ Bcell#383


title: AB6484

value: Cycle 10


title: AB6485

value: Bone marrow


title: 1_3_K2_24h

value: treated with 10 μg/ml zymosan for 24 h


title: 22_2_K2_24h


title: AB6483

value: Bone marrow aspiration


title: RAMPAGE_IRBB7_Treated_2

city: Tempe

first: R. Taylor

last: Raborn

state: AZ

address: 727 E Tyler St

department: Center for Mechanisms of Evolution

country: USA

institute: Arizona State University

description: No processed data available for this sample because it failed QC and was thus excluded from the study.

data_processing:
Library strategy: RAMPAGE
RAMPAGE samples were processed from .fastq to coordinate sorted .bam files using the computational workflow listed here (https://github.com/BrendelGroup/AllRice)
TSSs and TSRs were called using TSRchitect (v1.8.9) as part of the GoSTRIPES workflow. TSSs with less than 3 reads were filtered out, and TSSs within 40 bases were clustered into TSRs.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary_files_format_and_content: TSSset*txt: TSRchitect TSS file
Supplementary_files_format_and_content:TSRset*tab: TSRchitect TSR file

organism: Oryza sativa

growth_protocol: The rice cultivar IRBB7 was grown in growth chamber at 28 C, 12 hr light and dark with relative humidity 75%

extract_protocol:
total RNA extraction performed 24h post-innoculations using TRIzol RNA solution according to manufacturers' recommendations
RAMPAGE; after Batut et al., 2013 (PMID: 24510412)

treatment_protocol: Leaves of 3 weeks old plants were inoculated with Xanthomonas oryzae pathovar oryzae strain PXO86, and inoculated leaves were subjected to total RNA extraction

tag: cultivar

value: leaves

value: Young leaves were inoculated with Xanthomonas oryzae pv. oryzae avrXa7 knockout mutant PXO86 (virulent)

tag: input to technology

value: 5 ug

tag: technology

value: RAMPAGE


title: AB6486

value: Plasma cells

value: PRMM


title: RAMPAGE_IRBB7_Treated_1

description:
TSRsetCombined.tab
TSRsetMerged-2.txt


title: WT NP+IgE+ Bcell#377

value: spleen

value: 8 weeks

value: IgE repoter (Verigem)


title: WT NP+IgE+ Bcell#376


title: RAMPAGE_IRBB7_Control_2

description:
TSRsetCombined.tab
TSRsetMerged-1.txt

value: Young leaves were inoculated with Xanthomonas oryzae pv. oryzae avrXa7 knockout mutant MX53 (avirulent)


title: 22_2_K2_0h

value: Bone marrow-derived mast cells

value: untreated


title: RAMPAGE_IRBB7_Treated_3

description:
TSRsetCombined.tab
TSRsetMerged-2.txt


title: AB6480

value: Baseline

tag: cohort

value: Refractory


title: AB6482

tag: organ

value: Bone marrow


title: WT NP+IgE+ Bcell#372


title: WT NP+IgE+ Bcell#371


title: WT NP+IgE+ Bcell#369


title: 1_3_K2_0h


title: WT NP+IgE+ Bcell#368


title: AB6481

tag: sample type


title: AB6479

tag: cell type


title: WT NP+IgE+ Bcell#370


title: 9_2_24h

value: treated with 10 μg/ml zymosan for 24 h


title: WT NP+IgE+ Bcell#367


title: 22_2_K1_0h


title: 22_2_K1_24h


title: WT NP+IgE+ Bcell#366


title: 9_2_0h


title: AB6364

value: Bone marrow aspiration

tag: selection marker

value: Cycle 4

value: DARA-KRD


title: RAMPAGE_IRBB7_Control_1

description:
TSRsetCombined.tab
TSRsetMerged-1.txt

value: leaves

value: 5 ug


title: NonTargetting_Day6_Rep2

city: San Francisco

first: Arthur

middle: Jeremy

last: Willsey

state: CA

address: 675 Nelson Rising Lane, Mail Code 0518

department: Psychiatry

institute: UCSF

description:
ESR2_iPSC_rawcounts.csv
ESR2_iPSC_filtered_cpm.csv

data_processing:
Raw data was processed with the Ion Torrent Suite Server v5.8.0 (ThermoFisher)
Reads were aligned reads to the hg19 AmpliSeq Transcriptome reference (v1.1) with the coverageAnalysis plugin v5.8.0.8 which runs the command `tmap mapall -q 50000 -f hg19_AmpliSeq_Transcriptome_v1.1.fasta -r Sample_1.fastq -s Sample_TMAP.aln.sam stage1 map4`
Reads were quantified using the ampliSeqRNA plugin v5.8.0.3 with default settings.
Genes with greater than 1 count per million in three samples were retained for clustering and DEX analysis; this is represented in the filtered_cpm processed file.
Genome_build: hg19_AmpliSeq_Transcriptome_v1.1.fasta
Supplementary_files_format_and_content: rawcounts.csv, filtered_cpm.csv

source_name: Induced pluripotent stem cells

growth_protocol: DMEM/F12 medium supplemented with 1x N2, 1x B27 -Vitamin A, 1x GlutaMAX, 1x MEM-NEAA, 0.5 mM dibutyryl cAMP, 0.2 mM ascorbic acid, 1 μM PD0325901, 5 μM SU5402, 10 μM DAPT, 20 ng/mL BDNF

extract_protocol:
Qiagen RNeasy Mini kit
Ion AmpliSeq kit
Ion Torrent NGS, Ion GeneStudio S5 System

value: non-targetting

value: Day 6 of neuronal differentiation

tag: passage

value: Induced pluripotent stem cell line GM25256


title: NonTargetting_Day6_Rep3


title: AB6363

value: Plasma cells

tag: time point

tag: replicate id

value: PRMM


title: AB6362

tag: disease state


title: WT NP+IgE+ Bcell#359

tag: strain

tag: tissue

value: spleen

value: 8 weeks

value: IgE repoter (Verigem)


title: WT NP+IgE+ Bcell#363

tag: age

tag: genotype


title: WT NP+IgE+ Bcell#362


title: WT NP+IgE+ Bcell#365


title: WT NP+IgE+ Bcell#364


title: AB6361

tag: treatment (1)


title: WT NP+IgE+ Bcell#361


title: WT NP+IgE+ Bcell#360


title: AB6274


title: AB6275


title: WT NP+IgE+ Bcell#356


title: WT NP+IgE+ Bcell#358


title: WT NP+IgE+ Bcell#355


title: ESR2_Day6_Rep3

value: esr2 knockdown


title: ESR2_Day6_Rep2


title: AB6273

value: Baseline

value: Relapse


title: ESR2_Day6_Rep1


title: WT NP+IgE+ Bcell#354


title: WT NP+IgE+ Bcell#353


title: WT NP+IgE+ Bcell#352


title: NonTargetting_Day6_Rep1


title: NonTargetting_Day0_Rep2

value: Day 0 of neuronal differentiation


title: AB6272

value: Bone marrow

value: Bone marrow aspiration


title: WT NP+IgE+ Bcell#357


title: WT NP+IgE+ Bcell#351


title: WT NP+IgE+ Bcell#350


title: WT NP+IgE+ Bcell#349


title: IL-13KO NP+IgE+ Bcell#10


title: AB6271


title: WT NP+IgE+ Bcell#347


title: AB6270


title: WT NP+IgE+ Bcell#346


title: ESR2_Day0_Rep3


title: WT NP+IgE+ Bcell#345


title: AB6268

value: Cycle 4

value: DARA-KRD


title: AB6269


title: ESR2_Day0_Rep1


title: NonTargetting_Day0_Rep3


title: WT NP+IgE+ Bcell#343


title: NonTargetting_Day0_Rep1


title: AB6267


title: WT NP+IgE+ Bcell#341


title: WT NP+IgE+ Bcell#339


title: WT NP+IgE+ Bcell#338


title: AB6266


title: AB6265


title: WT NP+IgE+ Bcell#348


title: WT NP+IgE+ Bcell#336


title: WT NP+IgE+ Bcell#337


title: AB6264


title: AB6263


title: WT NP+IgE+ Bcell#334


title: WT NP+IgE+ Bcell#331


title: WT NP+IgE+ Bcell#330


title: WT NP+IgE+ Bcell#344


title: WT NP+IgE+ Bcell#332


title: WT NP+IgE+ Bcell#333


title: ESR2_Day0_Rep2


title: WT NP+IgE+ Bcell#342


title: WT NP+IgE+ Bcell#329


title: WT NP+IgE+ Bcell#327


title: WT NP+IgE+ Bcell#328


title: AB6261


title: AB6260


title: WT NP+IgE+ Bcell#340


title: AB6259

value: Refractory


title: WT NP+IgE+ Bcell#324


title: WT NP+IgE+ Bcell#325


title: H10KA: BIOF2 vs Untreated (Dye-swap)

type: RNA

city: Mexico city

first: Ariana

last: Cabrera-Licona

state: Mexico city

address: Patricio Sanz 1582

department: Research

country: Mexico

institute: Esteripharma

description: primary culture of cells isolated from synovial fluid of knees with severe osteoarthritis treated with BIOF2 (US Patent No. 9089580 B1)

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC). The arrays were incubated for 14 h at 42°C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.

scan_protocol: Acquisition and quantification of array images was performed in GenePix 4100A with its accompanying software GenePix from Molecular Devices. All images were captured using 10 µm resolution. For each spot the Alexa555 and Alexa647 density mean value and background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics.

data_processing: For each spot the Alexa555 and Alexa647 density mean value and background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics. Microarray data analysis was performed with genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes.  GenArise software identified differential expressed genes by calculating an intensity-dependent z-score between samples and reference (HDF).

source_name: cells samples from the synovial fluid of severe osteoarthritic knees with no treatment (control)

label_protocol: RNA integrity was analyzed both by agarose gel electrophoresis and by a Bioanalyzer 2100 and only samples with RNA Integrity Numbers (RIN) greater than 8 were used in  these assays. 10μg of total RNA were used for cDNA synthesis incorporating dUTP-Alexa555 or dUTP-Alexa647 employing the First-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647.

growth_protocol: Synovial fluids were seeded in cell culture flask T-25 TC treated (Eppendorf) and incubated in 5% CO2 atmosphere at 37ºC for 24 hrs with 1% penicillin/streptomycin (Gibco). After, washes with sterile 1x PBS pH7.4 (Gibco) were performed to remove unattached cells and Dulbeco`s Modified Eagle Medium F-12 (Gibco) supplemented with 10%SFB (Gibco) and 1% penicillin/streptomycin (100x Gibco) was added. Cells were cultured in 5% CO2 atmosphere at 37ºC until cell outgrowths were well established.

extract_protocol: A pool from untreated or trated cells was made and total RNA was extracted using Trizol ® Reagent (Invitrogen) protocol. Total RNA (30µg) purity was determined by the absorbance 260/absorbance 280 ratio on a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and the integrity was checked by agarose gel electrophoresis and visualized by ChemiDocTM XRS+ and Image LabTM software (BIO-RAD).

treatment_protocol: Cultures with 80% confluence of cells isolated from the synovial fluid of knees with severe osteoarthritis were treated for 48 hours with 5% BIOF2 (US Patent No. 9089580 B1) in DMEM-F12 supplemented with 1% FBS.

value: severe osteoarthritis

source_name: cells samples from the synovial fluid of severe osteoarthritic knees treated with BIOF2 5% (US Patent No. 9089580 B1) in DMEM F-12 for 48 hrs


title: AB6258


title: WT NP+IgE+ Bcell#322


title: WT NP+IgE+ Bcell#323


title: WT NP+IgE+ Bcell#321


title: WT NP+IgE+ Bcell#320


title: WT NP+IgE+ Bcell#335


title: WT NP+IgE+ Bcell#318


title: WT NP+IgE+ Bcell#319


title: AB6257


title: WT NP+IgE+ Bcell#317


title: WT NP+IgE+ Bcell#314


title: WT NP+IgE+ Bcell#315


title: AB6255


title: WT NP+IgE+ Bcell#311


title: AB6253


title: AB6252


title: WT NP+IgE+ Bcell#313


title: WT NP+IgE+ Bcell#309


title: WT NP+IgE+ Bcell#308


title: WT NP+IgE+ Bcell#326


title: AB6251


title: AB6250


title: WT NP+IgE+ Bcell#307


title: WT NP+IgE+ Bcell#306


title: WT NP+IgE+ Bcell#305


title: WT NP+IgE+ Bcell#304


title: AB6256


title: WT NP+IgE+ Bcell#303


title: AB6249


title: AB6248


title: WT NP+IgE+ Bcell#300


title: WT NP+IgE+ Bcell#301


title: AB6246


title: WT NP+IgE+ Bcell#302


title: WT NP+IgE+ Bcell#310


title: WT NP+IgE+ Bcell#298


title: WT NP+IgE+ Bcell#296


title: AB6245


title: WT NP+IgE+ Bcell#295


title: AB6244


title: WT NP+IgE+ Bcell#292


title: WT NP+IgE+ Bcell#299


title: AB6071


title: WT NP+IgE+ Bcell#294


title: WT NP+IgE+ Bcell#291


title: AB6070


title: WT NP+IgE+ Bcell#293


title: WT NP+IgE+ Bcell#290


title: AB6069


title: WT NP+IgE+ Bcell#289


title: WT NP+IgE+ Bcell#312


title: WT NP+IgE+ Bcell#316


title: WT NP+IgE+ Bcell#288


title: WT NP+IgE+ Bcell#286


title: AB6068


title: WT NP+IgE+ Bcell#287


title: WT NP+IgE+ Bcell#285


title: WT NP+IgE+ Bcell#282


title: WT NP+IgE+ Bcell#283


title: WT NP+IgE+ Bcell#284


title: AB6247


title: WT NP+IgE+ Bcell#281


title: WT NP+IgE+ Bcell#280


title: AB6065


title: AB6064


title: AB6063


title: AB6061


title: AB6262


title: WT NP+IgE+ Bcell#277


title: WT NP+IgE+ Bcell#278


title: WT NP+IgE+ Bcell#276


title: AB6060


title: WT NP+IgE+ Bcell#279


title: AB6067


title: AB6062


title: AB6059


title: WT NP+IgE+ Bcell#275


title: WT NP+IgE+ Bcell#271


title: WT NP+IgE+ Bcell#269


title: WT NP+IgE+ Bcell#273


title: WT NP+IgE+ Bcell#274


title: WT NP+IgE+ Bcell#272


title: WT NP+IgE+ Bcell#265


title: WT NP+IgE+ Bcell#263


title: WT NP+IgE+ Bcell#270


title: AB6056


title: AB6066


title: WT NP+IgE+ Bcell#268


title: WT NP+IgE+ Bcell#264


title: WT NP+IgE+ Bcell#267


title: WT NP+IgE+ Bcell#261


title: WT NP+IgE+ Bcell#259


title: WT NP+IgE+ Bcell#257


title: WT NP+IgE+ Bcell#258


title: WT NP+IgE+ Bcell#266


title: WT NP+IgE+ Bcell#256


title: AB6057


title: WT NP+IgE+ Bcell#254


title: AB6054


title: WT NP+IgE+ Bcell#255


title: WT NP+IgE+ Bcell#262


title: AB6051


title: AB6052


title: WT NP+IgE+ Bcell#260


title: AB6053


title: AB6058


title: AB6055


title: AB6048


title: AB6050


title: WT NP+IgE+ Bcell#251


title: WT NP+IgE+ Bcell#247


title: WT NP+IgE+ Bcell#250


title: AB6049


title: WT NP+IgE+ Bcell#252


title: WT NP+IgE+ Bcell#248


title: WT NP+IgE+ Bcell#249


title: WT NP+IgE+ Bcell#253


title: WT NP+IgE+ Bcell#244


title: WT NP+IgE+ Bcell#240


title: WT NP+IgE+ Bcell#246


title: AB6254


title: WT NP+IgE+ Bcell#239


title: WT NP+IgE+ Bcell#237


title: AB6005


title: WT NP+IgE+ Bcell#242


title: WT NP+IgE+ Bcell#241


title: WT NP+IgE+ Bcell#243


title: AB6004


title: AB6000


title: AB6003


title: AB6002


title: WT NP+IgE+ Bcell#234


title: WT NP+IgE+ Bcell#238


title: AB6001


title: WT NP+IgE+ Bcell#231


title: WT NP+IgE+ Bcell#235


title: AB5999


title: WT NP+IgE+ Bcell#245


title: WT NP+IgE+ Bcell#297


title: WT NP+IgE+ Bcell#236


title: AB5995


title: WT NP+IgE+ Bcell#233


title: WT NP+IgE+ Bcell#232


title: AB5998


title: WT NP+IgE+ Bcell#230


title: AB5997


title: AB5996


title: AB5994


title: WT NP+IgE+ Bcell#227


title: WT NP+IgE+ Bcell#228


title: WT NP+IgE+ Bcell#226


title: AB5993


title: WT NP+IgE+ Bcell#224


title: WT NP+IgE+ Bcell#223


title: AB5982


title: WT NP+IgE+ Bcell#222


title: AB5980


title: HaCaT_SM_vs_HaCaT  [aCGH]

type: genomic

city: Munich

first: Hanns Leonhard

last: Kaatsch

address: Neuherbergstraße 11

institute: Bundeswehr Institute of Radiobiology

hyb_protocol: Samples were hybridized on a whole genome array (Agilent®, Santa Clara, CA, USA; SurePrint G3 Human Genome CGH Microarray 2x400K, 5.3 kb spacing).

scan_protocol: Agilent® Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 7.3 March 2014; Agilent® G2505C; Scan Control Version A.8.1.3; resolution 3 µm; 16 bit TIFF; no XDR; Images were quantified using Agilent Feature Extraction Software (version 12.0).

data_processing: Agilent Feature Extraction Software (v 12.0) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

label_protocol: Labelling of DNA and hybridization onto a 400k SurePrint G3 Human CGH Array (Agilent; G4448A-021850) were performed according to the manufacturer’s recommendations (Agilent® Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic Labeling for Blood, Cells, or Tissues, ProtocolVersion 7.3 March 2014).

growth_protocol: HaCaT cells were kindly provided by Prof. Dr. N. Fusenig (German Cancer Research Center, Heidelberg, Germany) and cultivated in Dulbecco’s Modified Eagle Medium supplemented with glutamine and 10 % fetal bovine serum (Gibco, Carlsbad, CA). Cells were maintained at 37 °C and 5 % CO2 in a humidified atmosphere. For cell passaging, HaCaT were detached with 0.05 % trypsin in 1 mM EDTA (Gibco, Carlsbad, CA) for 5 min and reseeded in fresh culture medium twice a week. Human lymphoblastoid cells (GM12878, suspension cells) were obtained from Corriell Institute for medical Research (Camden, New Jersey, USA). Cells were cultivated at 37°C / 5% CO2 in RPMI-1640 2mM L-glutamine and Eagle´s Minimum Essential Medium.

extract_protocol: DNA was isolated using the QIAGEN® Blood & Cell Culture DNA Midi Kit (QIAGEN, Cat No./ID: 13343, Hilden, Germany).

tag: cell line

value: SM-resistant

value: human keratinocyte cell

source_name: human keratinocyte cell line

tag: reference cell line

value: untreated HaCaT cell line


title: Cultured_SatelliteCells_2

city: Los Angeles

first: Albert

middle: Ernesto

last: Almada

address: 1450 Biggy Street

department: Orthopaedic Surgery and Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

description: hindlimb, abdominal, and triceps

hyb_protocol: Hybridization was performed using the Affymetrix WT KIT materials according to manufacterer's protocol

scan_protocol: Samples were scaned on a Gene Chip Scanner 3000 7G system

data_processing:
Microarray data was normalized using the RMA method from the Oligo package in R
pd.mogene.1.0.st.v1

label: biotin

source_name: primary muscle satellite cells

label_protocol: Hybridization and labeling with Biotin was performed using the WT Terminal Labeling kit (Affymetrix)

growth_protocol: Fresh SCs were sorted into pre-coated (Collagen Type 1 (1ug/ml final) and Laminin (10 ug/ml) in PBS for 24 hours) wells containing standard growth media (20% Donor Horse Serum, 1% Penn Strep, 1% GutaMax in F10 media), and supplemented with daily additions of 5 ng/ml of bFGF for 5-days in culture.

extract_protocol: RNA was extracted using Trizol Reagent

value: skeletal muscle (hind-limbs, abdominal, and triceps)

value: Cultured (5-days) SCs


title: Cultured_SatelliteCells_3

description: hindlimb, abdominal, and triceps


title: Cultured_SatelliteCells_1

description: hindlimb, abdominal, and triceps


title: WT NP+IgE+ Bcell#225

value: spleen

value: 8 weeks


title: HaCaT_SM  [aCGH]

value: sulfur mustard (SM) - resistant

source_name: GM12878 cell line

value: human lymhoblastoid cell


title: Fresh_SatelliteCells_2

description: hindlimb, abdominal, and triceps

value: Fresh SCs


title: AB5978

value: Plasma cells

value: Baseline

value: PRMM


title: AB5981

value: Bone marrow

value: Bone marrow aspiration


title: WT NP+IgE+ Bcell#229

value: IgE repoter (Verigem)


title: HaCaT [aCGH]

source_name: HaCaT


title: WT NP+IgE+ Bcell#221


title: WT NP+IgE+ Bcell#220


title: ADC 1970C44

city: Ramat Gan

first: Michael

last: Gurevich

address: Tel Hashomer

department: Multiple Sclerosis Center

institute: Sheba Medical Center

description:
ADC
PBMC gene expression from ADC patients

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Following scanning of the arrays, the microarray raw data were initially normalized by R Bioconductor Packages, all arrays were normalized serially using a single sample microarray normalization approach designed for personal medicine workflows (SCAN Normalization). An empirical Bayes approach (ComBat algorithm) was used to minimize the batch effect in the data

source_name: PBMC from ADC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: PBMC were purified from  Ficoll hypaque gradient (Invitrogen, USA)

tag: gender

value: Female

tag: age (years)


title: ADC 2463C48

value: Male


title: Fresh_SatelliteCells_3

description: hindlimb, abdominal, and triceps


title: ADC 12952C191


title: Fresh_SatelliteCells_1

description: hindlimb, abdominal, and triceps


title: AB5979

tag: organ

tag: cohort

value: Refractory


title: ADC 2717C50


title: AB5976

tag: sample type

tag: cell type


title: WT NP+IgE+ Bcell#219


title: WT NP+IgE+ Bcell#218


title: WT NP+IgE+ Bcell#217


title: AB5977

tag: selection marker


title: WT NP+IgE+ Bcell#215


title: AB5972

tag: time point


title: ADC 12918C190


title: AB5973

tag: replicate id


title: WT NP+IgE+ Bcell#216


title: AB5975

tag: disease state


title: ADC 3075C55


title: AB5789


title: AB5971


title: AB5974


title: AB5788


title: ADC 2601C52


title: WT NP+IgE+ Bcell#214

tag: strain


title: WT NP+IgE+ Bcell#213

tag: tissue


title: ADC 12902C189


title: WT NP+IgE+ Bcell#212

tag: age


title: Blood9

data_processing:
10x genomics pipeline
hg38
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Patient 9 blood

extract_protocol:
For each patient approximately 20 ml of BAL fluid was obtained, stored at room temperature and processed within 2 hours in a BSL-3 laboratory. An unprocessed aliquot was used for bacterial cul-ture. The BAL fluid was filtered 2 times through a nylon gauze and a 100-μm nylon cell strainer to remove clumps and debris. The supernatant was then washed with PBS 1x and centrifuged. RBCs were lysed with 4 mL of 0.2% NaCl solution (3 minutes, RT) and the reaction was blocked by adding 9 mL of 1.2% NaCl solution. The cells were washed with PBS 1x, re-suspended in RPMI 1640 me-dium supplemented with 5% bovine serum albumin and counted. Cell viability was determined by Trypan blue exclusion. BAL fluids of patients with COVID-19 infection contained a heterogeneous number of cells ranging from 0.83 x106 to 22 x106 of cells. Cells were re-suspended at a concentration of 1 × 106 /ml for single cell analysis. Peripheral blood (PB) from COVID-19 patients and HDs was collected in EDTA-coated tubes. 2 ml of PB was washed once with PBS 1x and the RBCs lysis was performed twice adding 15 mL of 0.2% NaCl solution (3 minutes, RT) and the reaction was blocked by adding 35 mL of 1.2% NaCl solution. The cells were washed with PBS 1x, re-suspended in RPMI 1640 medium supplemented with 5% bovine serum albumin, filtered through a 100-μm nylon cell strainer and counted. Cell viability was determined by Trypan blue exclusion. Cells were re-sus-pended at a concentration of 1 × 106 /ml for single cell analysis
For each sample, cells were resuspended in RPMI supplemented with 5% FBS to a final concentration of 1000 cells per ml and processed using the 10x Genomics Chromium Controller and the Chromium NextGEM Single Cell 3′ GEM, Library& Gel Bead kit v3.1 (Pleasanton, California, United States) following the stand-ard manufacturer’s instructions. In brief, 10,000 live cells were loaded onto the Chromium controller to recover 4,000 single cell GEMs per inlet uniquely barcoded. After synthesis of cDNA, sequencing libraries were generated. Final 10X library quality was assessed using the Fragment Analyzer High Sensitivity NGS kit (Agilent Technologies, Santa Clara, CA, USA) and then sequenced on the Illu-mina NextSeq500 (Illumina, San Diego CA, USA) generating 75 base pair paired-end reads (28bp read1 and 91bp read2) at a depth of 50,000 reads/cell.
Single cell RNA-seq 3’ : 28bp R1 and 91 bp R2

tag: clinic status

value: Severe COVID

value: Blood

tag: subject id

value: Patient 9

tag: sofa score

tag: Sex

tag: clinical outcome

value: Alive


title: WT NP+IgE+ Bcell#210

value: spleen

value: 8 weeks

tag: genotype


title: ADC 12954C191

tag: gender

tag: age (years)


title: AB5787

tag: organ

tag: sample type

tag: cohort


title: WT NP+IgE+ Bcell#211


title: WT NP+IgE+ Bcell#208


title: WT NP+IgE+ Bcell#209


title: Blood8

source_name: Patient 8 blood

value: Patient 8


title: Blood7

source_name: Patient 7 blood

value: Patient 7

value: Dead


title: Blood6

source_name: Patient 6 blood

value: Patient 6


title: WT NP+IgE+ Bcell#207


title: WT NP+IgE+ Bcell#205


title: Blood5

source_name: Patient 5 blood

value: Patient 5


title: WT NP+IgE+ Bcell#206


title: WT NP+IgE+ Bcell#202


title: WT NP+IgE+ Bcell#203


title: WT NP+IgE+ Bcell#204


title: Blood41

source_name: Patient 41 blood

value: Healthy control

value: Patient 41


title: Blood4

source_name: Patient 4 blood

value: Patient 4


title: Blood40

source_name: Patient 40 blood

value: Patient 40


title: WT NP+IgE+ Bcell#200

value: IgE repoter (Verigem)


title: Blood42

source_name: Patient 42 blood

value: Patient 42

value: Male


title: Blood39

source_name: Patient 39 blood

value: Blood

value: Patient 39


title: Blood38

source_name: Patient 38 blood

value: Patient 38


title: WT NP+IgE+ Bcell#197

value: spleen


title: ADC 3648C64

value: Female


title: ADC 5564C109


title: ADC 3068C54


title: ADC 1732C44


title: ADC 12983C191


title: WT NP+IgE+ Bcell#199

value: 8 weeks


title: Blood37

source_name: Patient 37 blood

value: Mild COVID

value: Patient 37


title: ADC 4201C69


title: ADC 12915C190


title: ADC 5622C109


title: ADC 2152C52


title: WT NP+IgE+ Bcell#198


title: WT NP+IgE+ Bcell#201


title: Blood33

source_name: Patient 33 blood

value: Patient 33


title: ADC 3639C64


title: Blood35

source_name: Patient 35 blood

value: Patient 35


title: ADC 13410NMS203


title: ADC 3320C58


title: ADC 3071C54


title: ADC 12966C191


title: Blood36

source_name: Patient 36 blood

value: Patient 36


title: ADC 5565C108


title: WT NP+IgE+ Bcell#196


title: Blood34

source_name: Patient 34 blood

value: Patient 34


title: WT NP+IgE+ Bcell#194


title: WT NP+IgE+ Bcell#195


title: WT NP+IgE+ Bcell#191


title: WT NP+IgE+ Bcell#193


title: Blood32

source_name: Patient 32 blood

value: Patient 32


title: Blood31

source_name: Patient 31 blood

value: Patient 31


title: WT NP+IgE+ Bcell#190

value: IgE repoter (Verigem)


title: ADC 5369C98

source_name: PBMC from ADC


title: WT NP+IgE+ Bcell#187


title: WT NP+IgE+ Bcell#192


title: ADC 3070C56


title: Blood23

source_name: Patient 23 blood

value: Severe COVID

value: Patient 23

value: Alive


title: Blood24

source_name: Patient 24 blood

value: Blood

value: Patient 24

value: Male

value: Dead


title: Blood3

source_name: Patient 3 blood

value: Patient 3

value: Female


title: WT NP+IgE+ Bcell#189

value: spleen

value: 8 weeks


title: Blood27

source_name: Patient 27 blood

value: Patient 27


title: ADC 12899C189


title: ADC 2720C50


title: ADC 13408NMS203


title: WT NP+IgE+ Bcell#188


title: Blood25

source_name: Patient 25 blood

value: Patient 25


title: Blood29

source_name: Patient 29 blood

value: Patient 29


title: Blood2

source_name: Patient 2 blood

value: Patient 2


title: Blood22

source_name: Patient 22 blood

value: Patient 22


title: WT NP+IgE+ Bcell#184

value: IgE repoter (Verigem)


title: ADC 2120C46


title: ADC 1566C46


title: Blood18

source_name: Patient 18 blood

value: Severe COVID

value: Patient 18


title: WT NP+IgE+ Bcell#186


title: ADC 4200C69


title: ADC 2467C56


title: ADC 4489C73


title: ADC 3326C58


title: WT NP+IgE+ Bcell#182


title: WT NP+IgE+ Bcell#181


title: Blood16

source_name: Patient 16 blood

value: Patient 16

value: Alive


title: WT NP+IgE+ Bcell#180


title: ADC 2466C48


title: Blood17

source_name: Patient 17 blood

value: Blood

value: Patient 17


title: ADC 1571C44

value: Male


title: WT NP+IgE+ Bcell#185


title: Blood10

source_name: Patient 10 blood

value: Patient 10

value: Dead


title: Blood14

source_name: Patient 14 blood

value: Patient 14


title: ADC 1891-Control

value: Female


title: Blood1

source_name: Patient 1 blood

value: Patient 1


title: ADC 5368C98


title: ADC 13409NMS203


title: ADC 3069C55


title: ADC 1568-Control


title: BAL8

source_name: Patient 8 BAL

value: BAL

value: Patient 8


title: WT NP+IgE+ Bcell#179

value: spleen

value: 8 weeks


title: WT NP+IgE+ Bcell#183

value: IgE repoter (Verigem)


title: WT NP+IgE+ Bcell#178


title: Blood11

source_name: Patient 11 blood

value: Severe COVID

value: Patient 11


title: BAL9

source_name: Patient 9 BAL

value: Patient 9


title: WT NP+IgE+ Bcell#177


title: BAL5

source_name: Patient 5 BAL

value: Patient 5

value: Alive


title: BAL4

source_name: Patient 4 BAL

value: Patient 4


title: WT NP+IgE+ Bcell#173


title: WT NP+IgE+ Bcell#174


title: WT NP+IgE+ Bcell#172


title: BAL7

source_name: Patient 7 BAL

value: Patient 7

value: Male


title: BAL6

source_name: Patient 6 BAL

value: Patient 6


title: WT NP+IgE+ Bcell#175


title: ADC 4491C73

source_name: PBMC from ADC


title: PDC 13381C205

description:
PDC
PBMC gene expression from PDC patients

source_name: PBMC from PDC


title: ADC 12912C190


title: BAL3

source_name: Patient 3 BAL

value: Patient 3

value: Dead


title: BAL27

source_name: Patient 27 BAL

value: Patient 27


title: PDC 13406C204

value: Female


title: PDC 13436PDC211


title: ADC 6291PDC212


title: WT NP+IgE+ Bcell#176


title: PDC 13434C206


title: PDC 6309PDC211


title: ADC 5645C108


title: WT NP+IgE+ Bcell#169


title: WT NP+IgE+ Bcell#171


title: WT NP+IgE+ Bcell#168


title: WT NP+IgE+ Bcell#170


title: WT NP+IgE+ Bcell#165


title: PDMS-norec 10351PDMS212

description:
PDMS-norec
PBMC gene expression from PDMS-norec patients

source_name: PBMC from PDMS-norec


title: BAL24

source_name: Patient 24 BAL

value: BAL

value: Patient 24


title: BAL25

source_name: Patient 25 BAL

value: Patient 25


title: PDC 6303PDC210_


title: WT NP+IgE+ Bcell#164

value: spleen

value: 8 weeks

value: IgE repoter (Verigem)


title: BAL2

source_name: Patient 2 BAL

value: Severe COVID

value: Patient 2


title: BAL29

source_name: Patient 29 BAL

value: Patient 29


title: BAL16

source_name: Patient 16 BAL

value: Patient 16

value: Alive


title: BAL23

source_name: Patient 23 BAL

value: Patient 23

value: Male


title: BAL22

source_name: Patient 22 BAL

value: Patient 22


title: WT NP+IgE+ Bcell#167


title: BAL18

source_name: Patient 17 BAL

value: Patient 17

value: Dead


title: WT NP+IgE+ Bcell#166


title: WT NP+IgE+ Bcell#162


title: WT NP+IgE+ Bcell#161


title: PDC 13364C204


title: BAL14

source_name: Patient 14 BAL

value: Patient 14


title: BAL11

source_name: Patient 11 BAL

value: BAL

value: Patient 11


title: WT NP+IgE+ Bcell#160


title: PDC 13380C205

value: Female


title: WT NP+IgE+ Bcell#163

value: spleen


title: BAL17


title: ADMS-norec 12833ADMS211

description:
ADMS-norec
PBMC gene expression from ADMS-norec patients

source_name: PBMC from ADMS-norec


title: ADMS-norec 5219ADMS211


title: PDMS-norec 10868PDMS212


title: ADMS-norec 13546ADMS210_


title: PDMS-norec 6275PDMS213


title: BAL1

source_name: Patient 1 BAL

value: Patient 1


title: PDMS-norec 12822PDMS211


title: WT NP+IgE+ Bcell#156

value: 8 weeks

value: IgE repoter (Verigem)


city: Ithaca

first: Praveen

last: Sethupathy

state: New York

address: 618 Tower Road, T7006

institute: Cornell University

description:
intestinal orgnaoid - duodenum
polyA RNA
RNAseq_DESeq2_normalized_counts_spheroids&HIO.txt

data_processing:
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
ChRO-seq samples were aligned using Burrows-Wheeler Aligner (BWA) and counts were normalized by the length of the gene bodies
Genome_build: hg38 for RNA-seq; hg38 plus a single copy of the Pol I ribosomal RNA transcription unit (GenBank U13369.1) for ChRO-seq
Supplementary_files_format_and_content: DESeq2 normalized counts for each of the samples in the RNA-seq study; TPM (transcripts per million) counts normalized by the length of the gene bodies for each of the samples in the ChRO-seq study

source_name: intestinal orgnaoid - duodenum

extract_protocol: NEBNext Ultra II Directional Library Prep Kit

tag: cell type

value: intestinal orgnaoid - duodenum


title: PDMS-norec 1788PDMS213


title: BAL10

source_name: Patient 10 BAL

value: Severe COVID

value: Patient 10


title: WT NP+IgE+ Bcell#158


title: PDMS-norec 13324PDMS213


title: WT NP+IgE+ Bcell#155


title: PDMS-norec 10760PDMS213


title: WT NP+IgE+ Bcell#159


title: WT NP+IgE+ Bcell#154


title: intestnal orgnaoid - ileum polyA RNA

description:
intestnal orgnaoid - ileum
polyA RNA
RNAseq_DESeq2_normalized_counts_spheroids&HIO.txt

source_name: intestnal orgnaoid - ileum

value: intestnal orgnaoid - ileum


title: WT NP+IgE+ Bcell#157


title: ADMS-norec 7701ADMS213


title: ADMS-norec 6069ADMS213


description:
intestinal spheriods -  ileum Rep#2
polyA RNA
RNAseq_DESeq2_normalized_counts.txt

source_name: intestinal spheriods -  ileum

value: intestinal spheriods -  ileum


description:
intestinal spheriods -  ileum Rep#4
polyA RNA
RNAseq_DESeq2_normalized_counts.txt


title: WT NP+IgE+ Bcell#151


description:
intestinal spheriods -  ileum Rep#1
polyA RNA
RNAseq_DESeq2_normalized_counts.txt


title: WT NP+IgE+ Bcell#153


title: WT NP+IgE+ Bcell#152


title: ADMS-norec 7820ADMS212

value: Male


title: PDC 13405C206

source_name: PBMC from PDC


description:
intestinal spheriods - duodenum Rep#5
polyA RNA
RNAseq_DESeq2_normalized_counts.txt

source_name: intestinal spheriods - duodenum

value: intestinal spheriods - duodenum


description:
intestinal spheriods - duodenum Rep#4
polyA RNA
RNAseq_DESeq2_normalized_counts.txt


title: WT NP+IgE+ Bcell#149


description:
intestinal spheriods -  ileum Rep#3
polyA RNA
RNAseq_DESeq2_normalized_counts.txt


description:
intestinal spheriods - duodenum Rep#6
polyA RNA
RNAseq_DESeq2_normalized_counts.txt


title: WT NP+IgE+ Bcell#148


title: WT NP+IgE+ Bcell#150


title: ADMS-norec 7675ADMS211


title: WT NP+IgE+ Bcell#146


title: PDMS-rec 13511PDMS210_

description:
PDMS-rec
PBMC gene expression from PDMS-rec patients

source_name: PBMC from PDMS-rec


title: WT NP+IgE+ Bcell#147


description:
intestinal spheriods - duodenum Rep#3
polyA RNA
RNAseq_DESeq2_normalized_counts.txt


title: ADMS-norec 10677ADMS210_


title: WT NP+IgE+ Bcell#143


title: definitive endoderm Rep#1 polyA RNA

description:
definitive endoderm Rep#1
polyA RNA
RNAseq_DESeq2_normalized_counts.txt

source_name: definitive endoderm

value: definitive endoderm


title: WT NP+IgE+ Bcell#145


description:
intestinal spheriods - duodenum Rep#1
polyA RNA
RNAseq_DESeq2_normalized_counts.txt


title: WT NP+IgE+ Bcell#142


title: definitive endoderm Rep#2 polyA RNA

description:
definitive endoderm Rep#2
polyA RNA
RNAseq_DESeq2_normalized_counts.txt


title: definitive endoderm Rep#3 polyA RNA

description:
definitive endoderm Rep#3
polyA RNA
RNAseq_DESeq2_normalized_counts.txt


description:
human embryonic stem cells Rep#2
polyA RNA
RNAseq_DESeq2_normalized_counts.txt

source_name: human embryonic stem cells

value: human embryonic stem cells


title: WT NP+IgE+ Bcell#141


title: WT NP+IgE+ Bcell#144


description:
intestinal spheriods - duodenum Rep#2
polyA RNA
RNAseq_DESeq2_normalized_counts.txt


title: PDMS-rec 3445PDMS211


title: WT NP+IgE+ Bcell#140


description:
human embryonic stem cells Rep #1
polyA RNA
RNAseq_DESeq2_normalized_counts.txt


title: ADMS-rec 8125ADMS212

description:
ADMS-rec
PBMC gene expression from ADMS-rec patients

source_name: PBMC from ADMS-rec


title: WT NP+IgE+ Bcell#139


title: PDMS-rec 2125PDMS212


description:
intestinal spheriods -  ileum Rep#2
nuclear RNA
ChROseq_GenesBodies_TPM.txt

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349125


title: WT NP+IgE+ Bcell#138


title: WT NP+IgE+ Bcell#137


title: ADMS-rec 6495ADMS211


description:
intestinal spheriods -  ileum Rep#1
nuclear RNA
ChROseq_GenesBodies_TPM.txt

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349124


title: ADMS-rec 13653ADMS210_


description:
intestinal spheriods - duodenum Rep#2
nuclear RNA
ChROseq_GenesBodies_TPM.txt

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349122


title: ADMS-rec 1662ADMS213


title: ADMS-rec 11283ADMS213


title: MYB117 2

city: Victoria

first: C. Peter

last: Constabel

state: British Columbia

address: 3800 Finnerty Rd

department: Biology

country: Canada

institute: University of Victoria

data_processing:
The alignment of sequence was performed using Hisat2 version 2.1.0. A P. tremula genome sequence (version 1.0) was used as reference genome (Sjödin et al., 2009; http://popgenie.org/).
Cufflinks and Cuffmerge (version 2.2.1.OSX_x86_64) were used to generate a reference transcriptome and use a Populus tremula transcriptome as reference (http://popgenie.org/).
Htseq-count (version 0.6.1) was used to calculate the raw count.
Supplementary_files_format_and_content: raw count in csv files

organism: Populus tremula x Populus tremuloides

source_name: leaves LPI7-10

growth_protocol: Hybrid poplar were transfer from tissue culture to mist chamber and grew for one month. They were then transfer to greenhouse for two months before harvest.

extract_protocol:
Leaves number 7-10 (LPI 7-10) were harvested. Total RNA was extracted from frozen poplar hairy roots or ground leaf powder using the modified cetyl trimethyl ammonium bromide method for polyphenol-rich plant tissue described by Muoki et al. (2012).
MagJET enrichment kit (ThermoScientific) was used to purify mRNA from crude RNA. The mRNA was fragmented by heating the samples at 94℃ for 5 minutes. To make cDNA libraries with adaptors NEBNext ultra RNA Library Prep Kit for Illumina (NEB) was used. GeneJET NGS Cleanup Kit (ThermoScientific) was used to clean the extra adaptors.  Primers for RNA-Seq were added to cDNA using NEBNext Multiplex Oligo kit (NEB). MagJET NGS Cleanup and Size Selection kit (ThermoScientific) was used to select DNA fragments around 350bp. Six libraries with same concentration (250ng/ul) each were pooled and sent to McGill University/GenomeQuébec

treatment_protocol: To generate MYB117-overexpressing poplars, the binary vectors pMDC32 with MYB117 were transformed into the Agrobacterium tumefaciens strain GV3101::pMP90 by electroporation. P. tremula x P. tremuloides  (clone INRA 353-38) leaves were excised and transformed using the method describe in (James et al., 2018).

tag: genotype/variation

tag: growth condition

value: greenhouse


title: PDMS-rec 2704PDMS212


title: WT NP+IgE+ Bcell#135

tag: strain


title: PDMS-rec 3411PDMS211


title: PDMS-rec 6893PDMS210_


title: MYB117 3


description:
intestinal spheriods - duodenum Rep#3
nuclear RNA
ChROseq_GenesBodies_TPM.txt

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349123


description:
intestinal spheriods - duodenum Rep#1
nuclear RNA
ChROseq_GenesBodies_TPM.txt

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349121


title: ADMS-rec 7618ADMS212


title: PDMS-rec 13183PDMS211


title: definitive endoderm Rep #4 nuclear RNA

description:
definitive endoderm Rep #4
nuclear RNA
ChROseq_GenesBodies_TPM.txt

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349120


title: WT 3

value: wild type


title: WT NP+IgE+ Bcell#136

extract_protocol:
We transferred IL-13 sufficient or deficient OT-2 TH2 into IgE reporter (Verigem) mice followed by immunization with NP-OVA. At 7 day post immunization, NP specific IgE producing B cells were sorted by flow cytometer.
For scRNA-seq analysis, the single-cells were sorted into each well of 96 well plates using FACS Aria III (BD). The single cells are lysed in a buffer that contains dNTPs and oligo(dT)-tailed oligonucleotides with a universal 5'-anchor sequence. RT is performed, which adds 2–5 untemplated nucleotides to the cDNA 3’ end. A template-switching oligo (TSO) is added, carrying 2 riboguanosines and a modified guanosine to produce a LNA as the last base at the 3’ end. After the first-strand reaction, the cDNA is amplified using a 25 of cycles. Next, Tn5 tagmentation is used to construct sequencing libraries from the amplified cDNA (Nextera XT DNA Library Preparation Kit, illumina). The sequencing was carried out using NovaSeq6000 equipment (SP type, 150PE, Illumina).

tag: tissue


title: MYB117 1


description:
intestinal spheriods -  ileum Rep#3
nuclear RNA
ChROseq_GenesBodies_TPM.txt

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349126


title: WT NP+IgE+ Bcell#134

tag: age


title: PDMS-rec 5532PDMS210_

description:
PDMS-rec
PBMC gene expression from PDMS-rec patients


title: WT NP+IgE+ Bcell#132


title: definitive endoderm Rep #2 nuclear RNA

description:
definitive endoderm Rep #2
nuclear RNA
ChROseq_GenesBodies_TPM.txt

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349118


title: definitive endoderm Rep #3 nuclear RNA

description:
definitive endoderm Rep #3
nuclear RNA
ChROseq_GenesBodies_TPM.txt

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349119


title: WT NP+IgE+ Bcell#133


title: WT NP+IgE+ Bcell#130


description:
human embryonic stem cells Rep #2
nuclear RNA
ChROseq_GenesBodies_TPM.txt

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349115


title: WT NP+IgE+ Bcell#131


title: WT 2


title: WT 1


title: WT NP+IgE+ Bcell#127


title: WT NP+IgE+ Bcell#125


description:
human embryonic stem cells Rep #3
nuclear RNA
ChROseq_GenesBodies_TPM.txt

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349116


title: definitive endoderm Rep #1 nuclear RNA

description:
definitive endoderm Rep #1
nuclear RNA
ChROseq_GenesBodies_TPM.txt

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349117


title: ADMS-norec 4956ADMS212

description:
ADMS-norec
PBMC gene expression from ADMS-norec patients

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.


title: GBM_4275

city: Calgary

first: Marco

last: Gallo

state: Alberta

address: 3330 Hospital Drive NW, Heritage Medical Research Building

department: Cumming School of Medicine

institute: University of Calgary

library_source: genomic

data_processing:
All raw base call (BCL) files generated by Illumina® sequencers were converted to FASTQ files using cellranger-atac mkfastq function, a wrapper around bcl2fastq from Illumina®, with additional 10x Genomics-specific features. Next, read filtering and alignment, barcode counting, and identification of transposase cut sites were detected using cellranger-atac count function using the cellranger-atac-specific hg19 reference package.
Genome_build: refdata-cellranger-atac-hg19-1.1.0 (hg19 with pre-generated indices and other data required to run CellRanger-ATAC)
Supplementary_files_format_and_content: Filtered peak-barcode matrix output from CellRanger-ATAC (containing only detected cellular barcodes)

source_name: scATAC-seq of primary patient-derived adult glioblastoma tissue

extract_protocol:
Cryopreserved primary GBM samples were washed at 1000 RPM for 5 minutes in PBS to remove DMSO, and then transferred to 1.5 mL tubes. Samples were resuspended in cold ATAC resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, 1% BSA in PBS) on ice and dissociated using a wide-bore P1000 pipette tip and vortexing, followed by 10 minutes of incubation on ice. Cells were spun down at 500x g for 5 minutes at 4 C, washed in the ATAC resuspension buffer, spun down again, and resuspended in ATAC-Tween wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA in PBS), then passed through a cell strainer top FACS tube (Falcon; #38030) to remove debris. Nuclei quality and quantity was evaluated using trypan blue on an Invitrogen Countess II device in duplicate, and a subset of nuclei was spun down in a fresh tube and resuspended in 10X sample dilution buffer.
Libraries were prepared according to 10X Genomics Chromium Single Cell ATAC Library & Gel Bead Kit Chemistry. Briefly, single nuclei were first treated in bulk with Tn5 transposase to preferentially insert sequencing adaptors into accessible DNA regions. Transposed nuclei are then partitioned into GEMs in the 10x Chromium Controller. All the DNA fragments from the same nucleus share a common 10x barcode. The barcoded, accessible DNA fragments are subsequently pooled for downstream processing and library preparation. Next generation sequencing was performed using Illumina HiSeq 4000 PE with a targeted sequencing depth of >10,000 median fragments per cell. 77.4% of the fragments overlapped a targeted region and fraction of transposition events in peaks was 53.2%.

tag: diagnosis

value: glioblastoma

value: primary glioblastoma tissue


title: WT NP+IgE+ Bcell#129

value: spleen


title: WT NP+IgE+ Bcell#124


title: WT NP+IgE+ Bcell#128


title: WT NP+IgE+ Bcell#123


title: Forskolin 3

city: Leeds

first: Lee

last: Roberts

state: Yorkshire

address: Level 7 LIGHT Laboratories, University of Leeds

department: LICAMM

country: United Kingdom

institute: University of Leeds

description: replicate 3

data_processing:
Data was collected as Bcl files and converted to Fastq files. The quality control of the reads was done using FastQC [1] v0.11.4. Reads were trimmed using TrimGalore [2] v0.4.1. TrimGalore trimms off low-quality base calls from the 3’ end of the reads before the adapter removal. Next, it finds and removes adapter sequences from the 3’ end of reads. If reads after trimming are less than 20 bases long, they are discarded from the dataset. Additionally to the default trimming, QuantSeq 3’ mRNA-Seq Libraries require trimming of the first 12 bases of all reads.
The tool used for mapping in this analysis is STAR. STAR does local alignment and clipping of 3’-end of reads in case that such an alignment gives a better score. This means that the majority of polyA sequences are clipped from reads during the alignment step. For this reason it is not strictly necessary to trim polyA sequences from the reads. However polyA sequences were trimmed before the mapping with the tool prinseq.
Reads were mapped using STAR [3] v2.5.2a. Ensembl Homo_sapiens.GRCh38.dna.primary_assembly.fa (release 85) reference genome file was used to do the mapping of reads, using the annotated transcripts from the ensembl Homo_sapiens.GRCh38.85.gtf. The number of reads that map to genomic features is calculated using HTSeq[6] v0.6.0. A feature is considered as the union of all gene’s exons whose genomic coordinates are determined from the ensembl Homo_sapiens.GRCh38.85.gtf. Reads with a mapping quality less than 10, that map to multiple loci or to overlapping gene regions are discarded to avoid ambiguity and false positives
Differential Gene Expression Analysis was done using the counted reads and the R package edgeR [8] v3.8.6. The standard pipeline follows the next steps:    Filter genes with low count of reads. Genes having more than 1 cpm (i. e. counts per million) in at least 1 sample were kept.    Calculate normalization factors. EdgeR computes effective library sizes using TMM (i.e trimmed mean of M-values) normalization. The normalization factors account for sequencing depth and RNA composition.    Data exploration. MDS and scatter plots to show sample relationships. MDS plots show distances in terms of BCV (i. e. biological coefficient of variation, which represents the square root of the common dispersion described in step 4 below). For both plots, data is filtered and normalised within each comparison. Scatter plots use normalised and log-2 transformed cpm values.    Estimate dispersion of each gene across samples and common dispersion. The common dispersion is the average dispersion across genes. A plot is shown for each comparison. Each gene’s average log-counts per million across samples (x-axis) is plotted against its coefficient of variation (BCV), so each point (refered to as tagwise in the plot legend) corresponds to a gene. The red line is the common dispersion. It indicates the overall variability in the dataset.    Perform differential gene expression. We used the exact test edgeR approach to make pairwise comparisons between groups. This involves adjusting for multiple testing. EdgeR uses FDR approach for multiple testing correction. Please refer to the edgeR documentation to know more about statistical principles of the procedure.  A table of the top 10 genes is shown for each comparison with the following information:  Ensembl ID  Gene name  logFC, which indicates the log difference between the two groups. The baseline group is always the control group, which means that negative values indicate higher expression in control samples.  logCPM, which is the log-average abundance across samples  Pvalue for the differential expression test  FDR, which is the adjusted p-value for multiple testing.  Following columns show the normalised non-log cpm value for each gene for each sample.
Parameters were as follows: TrimGalore - --gzip; --fastqc; --fastqc_args '--nogroup --extract'; --clip_R1 12; prinseq -trim_right 8; STAR --runThreadN 4; --outSAMtype BAM SortedByCoordinate; --readFilesCommand zcat; HTSeq  HTSeq -a 10; -m union; -s yes; -t exon
Genome_build: Ensembl Homo_sapiens.GRCh38.dna.primary_assembly.fa (release 85) reference genome file was used to do the mapping of reads, using the annotated transcripts from the ensembl Homo_sapiens.GRCh38.85.gtf.
Supplementary_files_format_and_content: abundance

source_name: Human Primary Adipocytes

growth_protocol: Human white primary preadipocytes (PromoCell, Heidelberg, Germany) were seeded (10,000-15,000 cells/cm2) and grown to confluence (37°C, 5% CO2) in preadipocyte growth medium (0.05ml/ml fetal calf serum, 0.004ml/ml endothelial cell growth supplement, 10ng/ml epidermal growth factor, 1µg/ml hydrocortisone, 90µg/ml heparin). Preadipocytes were differentiated according to supplier’s instructions. Briefly, growth medium was replaced by differentiation media (8µg/ml d-biotin, 0.5µg/ml insulin, 400ng/ml dexamethasone, 44µg/ml isobutylmethylxanthine, 9ng/ml L-thyroxine, 3µg/ml ciglitazone) for 48 hours. Differentiation medium was replaced with adipocyte nutrition media (0.03ml/ml fetal calf serum, 8µg/ml d-biotin, 0.5µg/ml insulin, 400ng/ml dexamethasone) for 12 days until cells were fully differentiated. Media was changed every 48 hours.

extract_protocol:
Total RNA was isolated using the Qiagen Lipis Tissue Rneasy kit according to the manufacturers instructions.
RNA libraries were prepared using the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina according to the manufacturers' instructions

treatment_protocol: Human white primary adipocytes were treated with 1 μM forskolin on days 10 - 12 of differentiation or remained untreated (control).

tag: vendor

value: PromoCell

value: differentiated stromal vascular fraction preadipocytes

tag: passage

value: Passages 3 - 5

tag: agent

value: forskolin


description:
human embryonic stem cells Rep #1
nuclear RNA
ChROseq_GenesBodies_TPM.txt

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349114


title: P0_wt_rep5

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description:
Gene expression data from pancreas from wild-type mice at postnatal day 0
P0_wt_10

hyb_protocol: According to the Affymetrix expression protocol (HWS kit) including minor modifications as suggested in the Encore Biotion protocol

scan_protocol: According to the Affymetrix expression protocol, Scanner 3000 7G

data_processing: SST-RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.4.1.46) including median polish and Sketch-Quantile normalisation

source_name: Pancreas from wild-type mice at postnatal day 0

label_protocol: Ovation PicoSL WTA System V2 and Encore Biotin Module (NuGEN Technologies, Inc, San Carlos, CA, USA)

growth_protocol: Animals per housed under spf conditions

extract_protocol: RNeasy Lipid Tissue Kit (Qiagen)

treatment_protocol: As described in the paper. Briefly, for embryonic samples the mother was starved for 2 h before dissection and P0 pups were starved for 5 h

value: not determined

value: Iir +/+

value: pancreas


title: WT NP+IgE+ Bcell#122

value: 8 weeks

value: IgE repoter (Verigem)


title: GBM_4349


title: Forskolin 2

description: replicate 2


title: WT NP+IgE+ Bcell#120


title: WT NP+IgE+ Bcell#118


title: WT NP+IgE+ Bcell#121


title: GBM_4250


title: Forskolin 1

description: replicate 1


title: P0_wt_rep3

description:
Gene expression data from pancreas from wild-type mice at postnatal day 0
P0_wt_07


title: WT NP+IgE+ Bcell#115


title: WT NP+IgE+ Bcell#126


title: GBM_4218


title: Control 3

description: replicate 3

value: untreated


title: WT NP+IgE+ Bcell#114


title: WT NP+IgE+ Bcell#119


title: Control 2

description: replicate 2


title: P0_wt_rep4

description:
Gene expression data from pancreas from wild-type mice at postnatal day 0
P0_wt_08


title: P0_wt_rep1

description:
Gene expression data from pancreas from wild-type mice at postnatal day 0
P0_wt_03


title: WT NP+IgE+ Bcell#113


title: WT NP+IgE+ Bcell#112


title: P0_wt_rep2

description:
Gene expression data from pancreas from wild-type mice at postnatal day 0
P0_wt_04


title: P0_ko_rep2

description:
Gene expression data from pancreas from inceptor-deficient mice at postnatal day 0
P0_ko_02

source_name: Pancreas from inceptor-deficient mice at postnatal day 0

value: Iir -/-


title: eSMGs, Control rep1

city: Seoul

first: Kyungpyo

last: Park

address: Jongno-Gu Daehak-Ro 101

country: South Korea

institute: Seoul National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
tab-delimited text files include read count values for each Sample
Genome_build: mm10
Supplementary_files_format_and_content: read count values

source_name: eSMGs, Control

extract_protocol:
Embryonic submandibular glands were extracted from E14 embryos and were harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: ICR

value: embryonic day 14

value: embryonic submandibular glands (eSMGs)

tag: treatment

value: control


title: P0_ko_rep6

description:
Gene expression data from pancreas from inceptor-deficient mice at postnatal day 0
P0_ko_12

tag: genotype


title: WT NP+IgE+ Bcell#116

data_processing:
HISAT2(version 2.1.0) with default parameters
StringTie(version 2.0)
Genome_build: mm10
Supplementary_files_format_and_content: Fasta files including read sequences of Ig mRNA, and tab-delimited text files include read counts for genes


title: Control 1

description: replicate 1


title: P0_ko_rep1

description:
Gene expression data from pancreas from inceptor-deficient mice at postnatal day 0
P0_ko_01

tag: gender


title: P0_ko_rep4

description:
Gene expression data from pancreas from inceptor-deficient mice at postnatal day 0
P0_ko_06


title: P0_ko_rep5

description:
Gene expression data from pancreas from inceptor-deficient mice at postnatal day 0
P0_ko_11


title: WT NP+IgE+ Bcell#117


title: WT NP+IgE+ Bcell#110


title: eSMGs, AMD3100 rep2

source_name: eSMGs, AMD3100


title: WT NP+IgE+ Bcell#109


title: eSMGs, AMD3100 rep1


title: eSMGs, Control rep3


title: eSMGs, AMD3100 rep3


title: P0_ko_rep3

description:
Gene expression data from pancreas from inceptor-deficient mice at postnatal day 0
P0_ko_05


title: E18.5_wt_rep3

description:
Gene expression data from pancreas from wild-type mice at embryonic day 18.5
E18.5_wt_20

source_name: Pancreas from wild-type mice at embryonic day 18.5


title: WT NP+IgE+ Bcell#106


title: WT NP+IgE+ Bcell#111


title: E18.5_wt_rep1

description:
Gene expression data from pancreas from wild-type mice at embryonic day 18.5
E18.5_wt_13


title: WT NP+IgE+ Bcell#104


title: eSMGs, Control rep2


title: D21C

city: Cuernavaca

first: Fernanda

last: Cornejo

address: Av Universidad 2001

institute: Instituto de Biotecnología UNAM

data_processing:
Quality filtering with Trimmomatic, remotion of adapters and ambiguous bases.
Alignment to M. tuberculosis genome with SMALT
Read counts
Abundance of expression was normalized by RPKM
Genome_build: The genome was submitted under BioProject PRJNA669742, BioSample SAMN16457620. GFF with gene IDs and coordinates is available on the series record.
Supplementary_files_format_and_content: normalized abundance measurements RPKM

source_name: mouse lung

extract_protocol:
Total RNA was extracted from infected mice lungs using one of three protocols: direct extraction, differential lysis or differential lysis and probe hybridization
Libraries were prepared following the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs)

value: lung

tag: rna extraction method

tag: infectious strain

value: M. tuberculosis H37Rv


title: D21B

value: differential lysis and probe hybridization


title: E18.5_wt_rep4

description:
Gene expression data from pancreas from wild-type mice at embryonic day 18.5
E18.5_wt_21


title: E1C

value: differential lysis


title: D21A


title: E18.5_wt_rep2

description:
Gene expression data from pancreas from wild-type mice at embryonic day 18.5
E18.5_wt_14


title: WT NP+IgE+ Bcell#102

city: Yokohama

first: Kosuke

last: Miyauchi

address: 1-7-22 Suehiro-sho

institute: RIKEN Center for Integrative Medical Sciences

value: spleen


title: WT NP+IgE+ Bcell#108


title: E1B


title: E18.5_ko_rep4

description:
Gene expression data from pancreas from inceptor-deficient mice at embryonic day 18.5
E18.5_ko_19

source_name: Pancreas from inceptor-deficient mice at embryonic day 18.5


title: MPLW515L STK11 -/- plating 6 rep 1

city: Memphis

first: Lance

middle: E

last: Palmer

state: TN

address: 262 Danny Thomas Place

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Read Quality Control with FastQC 0.11.5
Read Alignment with STAR 2.6.0 using standard parameters to produce BAM files coordinate sorted.
Read Summarization performed with featureCounts from subread 1.6.1.
Within R differential expression analysis was carried out using EdgeR 3.26.8
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing raw reads count matrix for every gene and every sample.

source_name: Hematopoietic cells from Colony Forming Assay

growth_protocol: HSPCs were sorted 36 hrs after transduction, plated in Methocult M3434 methylcellulose media and colonies grown for 7 days. At day 7 cells were harvested from the methylcellulose media for RNA extraction.

extract_protocol:
Total RNA was extracted using the Zymo Research Direct-zol RNA Miniprep Kit using manifacturer instructions
Libraries were prepared by the Northwestern University NUSeq Core Facility with the Illumina TruSeq Stranded mRNA Library Preparation Kit using 100 ng of total RNA.

value: Hematopoietic cells

value: MPLW515L STK11 -/-

tag: plating


title: WT NP+IgE+ Bcell#107


title: MM.1S_GSK126+UNC0638_replicate2

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Normalization and background subtraction for intra-array data were performed according to Agilent Feature Extraction Software (v 10.7) protocol. For inter-array normalization, 75% percentile shift was performed.

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: RPMI-8226 and MM.1S cells were cultured in RPMI-1640 supplemented with 10% heat-inactivated fetal bovine serum.  The cultures were incubated at 37ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy Mini Kits (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: RPMI-8226 and MM.1S cells treated with GSK126 (1 μM), UNC0638 (1 μM) or their combination (1 μM each) for 6 days.

tag: cell line


title: E18.5_ko_rep5

description:
Gene expression data from pancreas from inceptor-deficient mice at embryonic day 18.5
E18.5_ko_22

value: not determined


title: E18.5_ko_rep3

description:
Gene expression data from pancreas from inceptor-deficient mice at embryonic day 18.5
E18.5_ko_18

value: pancreas


title: MPLW515L STK11 -/- plating 3 rep 3

tag: cell type


title: WT NP+IgE+ Bcell#105

value: 8 weeks


title: E0

value: direct RNA extraction


title: WT NP+IgE+ Bcell#103

value: IgE repoter (Verigem)


title: MPLW515L STK11 -/- plating 6 rep 3


title: MPLW515L STK11 -/- plating 3 rep 1


title: WT NP+IgE+ Bcell#99


title: E18.5_ko_rep1

description:
Gene expression data from pancreas from inceptor-deficient mice at embryonic day 18.5
E18.5_ko_15

value: Iir -/-


title: WT NP+IgE+ Bcell#98


title: E18.5_ko_rep2

description:
Gene expression data from pancreas from inceptor-deficient mice at embryonic day 18.5
E18.5_ko_17


title: MPLW515L STK11 -/- plating 1 rep 2


title: MPLW515L STK11 -/- plating 6 rep 2


title: WT NP+IgE+ Bcell#101


title: E1A


title: MM.1S_GSK126_replicate1


title: WT NP+IgE+ Bcell#96


title: WT NP+IgE+ Bcell#95


title: MPLW515L STK11 -/- plating 1 rep 1


title: MM.1S_UNC0638_replicate2


title: MM.1S_GSK126+UNC0638_replicate1


title: WT NP+IgE+ Bcell#100


title: MPLW515L STK11 -/- plating 3 rep 2


title: WT NP+IgE+ Bcell#94


title: MM.1S_UNC0638_replicate1


title: MM.1S_GSK126_replicate2


title: MPLW515L STK11 -/- plating 1 rep 3


title: WT NP+IgE+ Bcell#97


title: WT NP+IgE+ Bcell#93


title: WT cells plating 1 rep 2

value: WT


title: WT cells plating 1 rep 1


title: WT NP+IgE+ Bcell#90


title: WT NP+IgE+ Bcell#89


title: WT cells plating 1 rep 3


title: MPLW515L plating 1  rep 3

value: MPLW515L overxpressing


title: MPLW515L plating 1  rep 1


title: WT NP+IgE+ Bcell#92


title: MM.1S_DMSO_replicate1

value: DMSO


title: MPLW515L plating 1  rep 2


title: RPMI-8226_GSK126+UNC0638_replicate2


title: RPMI-8226_UNC0638_replicate1


title: RPMI-8226_UNC0638_replicate2


title: MM.1S_DMSO_replicate2


title: RPMI-8226_DMSO_replicate2


title: RPMI-8226_GSK126+UNC0638_replicate1


title: 7m_Mcoln1_KO_72

city: Rehovot

first: Anthony

last: Futerman

address: Herzl

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200)
Reads were mapped to genome
The pipeline quantifies the genes annotated in RefSeq (that have expanded with 1000 bases toward 5’ edge and 100 bases toward 3’ bases)
We used the 3 end (1000bp) of the transcripts for counting the number of reads per gene. Read count was performed with HTSeq-count
UTAP: User-friendly Transcriptome Analysis Pipeline. Refael Kohen, Jonathan Barlev, Gil Hornung, Gil Stelzer, Ester Feldmesser, Kiril Kogan, Marilyn Safran and Dena Leshkowitz (in revision BMC Bioinformatics)
Genome_build: mm10
Supplementary_files_format_and_content: Raw_counts
Supplementary_files_format_and_content: Normalized
Supplementary_files_format_and_content: Differentially_expressed

source_name: Mcoln1 mice C57Bl/6J

extract_protocol:
Brain tissue was homogenized using a GentleMACS dissociator and mRNA was isolated using the RNeasy mini kit. RNA concentration (260/230 and 260/280 nm ratios)  were measured using a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). RNA integrity was evaluated using an RNA screen tape on a Tapestation 2200 (Agilent, Santa Clara, California, USA).
A bulk variation of MARSseq was used to construct RNAseq libraries: Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, et al. Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types. Science. American Association for the Advancement of Science; 2014;343:776–9.

value: 7 months

value: Brain

tag: background strain

value: Mcoln1 -/-

tag: protocol

value: MARS-seq


title: 7m_Mcoln1_KO_21


title: severely contused muscel at 168h , biological rep3

city: Jinzhong

first: Jun-hong

last: Sun

state: Shanxi Province

address: 98 University Street, Yuci District, Jinzhong

department: School of Forensic Medicine

institute: Shanxi Medical University

description: Gene expression at 168h after severe contusion

hyb_protocol: Hybridization for array plates (Gene 2.0 ST Arrays;Affymetrix®) was used the GeneChip® Hybridization, Wash and Stain Kit according to the manufacturer’s protocol.

scan_protocol: GeneChips were scanned by GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Transcriptome Analysis Console software (version 4.0.1;  Affymetrix®)

organism: Rattus norvegicus

source_name: skeletal muscle from wound site, severely contused, 168h

label_protocol: The Ambion WT Expression Kit generates purified sense-strand cDNA (with incorporated dUTP) that is ready for fragmentation and labeling using the Affymetrix GeneChip WT Terminal Labeling Kit.

extract_protocol: Total RNA was extracted from the skeletal muscle specimens

treatment_protocol: (1) Control group (n = 3): no treatment before sampling;  (2) Mild contusion group (n = 15): a 500-g counterpoise weight (diameter, 0.8 cm) fell from a height of 15 cm through a clear Lucite tube onto the thigh muscles of the right posterior limb, with an energy of ~0.74 J (calculated by E = mgh) transferred to the limb;   (3) Severe contusion group (n = 15): a 500-g counterpoise weight (diameter, 1.1 cm ) fell from a height of 50 cm through a clear Lucite tube onto the thigh muscles of the right posterior limb, with an energy of ~2.45 J transferred to the limb (n = 15).

value: 168h after severe contusion

value: 10-12 weeks


title: WT NP+IgE+ Bcell#91

extract_protocol:
We transferred IL-13 sufficient or deficient OT-2 TH2 into IgE reporter (Verigem) mice followed by immunization with NP-OVA. At 7 day post immunization, NP specific IgE producing B cells were sorted by flow cytometer.
For scRNA-seq analysis, the single-cells were sorted into each well of 96 well plates using FACS Aria III (BD). The single cells are lysed in a buffer that contains dNTPs and oligo(dT)-tailed oligonucleotides with a universal 5'-anchor sequence. RT is performed, which adds 2–5 untemplated nucleotides to the cDNA 3’ end. A template-switching oligo (TSO) is added, carrying 2 riboguanosines and a modified guanosine to produce a LNA as the last base at the 3’ end. After the first-strand reaction, the cDNA is amplified using a 25 of cycles. Next, Tn5 tagmentation is used to construct sequencing libraries from the amplified cDNA (Nextera XT DNA Library Preparation Kit, illumina). The sequencing was carried out using NovaSeq6000 equipment (SP type, 150PE, Illumina).

tag: strain

value: spleen


title: 7m_Mcoln1_KO_68

tag: tissue


title: severely contused muscel at 168h , biological rep2

value: the thigh muscles of the right posterior limb

tag: age


title: WT NP+IgE+ Bcell#88


title: 7m_Mcoln1_KO_66


title: WT NP+IgE+ Bcell#87


title: WT NP+IgE+ Bcell#82


title: WT NP+IgE+ Bcell#86


title: RPMI-8226_DMSO_replicate1


title: 7m_Mcoln1_WT_74

value: Mcoln1 +/+


title: 7m_Mcoln1_KO_69


title: severely contused muscel at 168h , biological rep1


title: severely contused muscel at 24h , biological rep3

description: Gene expression at 24h after severe contusion

source_name: skeletal muscle from wound site, severely contused, 24h

value: 24h after severe contusion


title: severely contused muscel at 48h , biological rep2

description: Gene expression at 48h after severe contusion

source_name: skeletal muscle from wound site, severely contused, 48h

value: 48h after severe contusion


title: severely contused muscel at 48h , biological rep1


title: RPMI-8226_GSK126_replicate1


title: 7m_Mcoln1_Het_71

value: Mcoln1 +/-


title: 3m_Mcoln1_KO_3

value: 3 months


title: RPMI-8226_GSK126_replicate2


title: WT NP+IgE+ Bcell#85

value: 8 weeks

value: IgE repoter (Verigem)


title: severely contused muscel at 48h , biological rep3


title: WT NP+IgE+ Bcell#83


title: 7m_Mcoln1_Het_12


title: 7m_Mcoln1_Het_29


title: 3m_Mcoln1_KO_1


title: WT NP+IgE+ Bcell#81


title: WT NP+IgE+ Bcell#80


title: WT NP+IgE+ Bcell#84


title: WT NP+IgE+ Bcell#74


title: WT NP+IgE+ Bcell#75


title: WT NP+IgE+ Bcell#79


title: 3m_Mcoln1_Het_2


title: WT NP+IgE+ Bcell#78


title: WT NP+IgE+ Bcell#73


title: 3m_Mcoln1_Het_1


title: 7m_Mcoln1_WT_75


title: severely contused muscel at 1h , biological rep3

description: Gene expression at 1h after severe contusion

source_name: skeletal muscle from wound site, severely contused, 1h

value: 1h after severe contusion


title: severely contused muscel at 1h , biological rep2


title: severely contused muscel at 24h , biological rep2


title: severely contused muscel at 24h , biological rep1


title: severely contused muscel at 3h , biological rep1

description: Gene expression at 3h after severe contusion

source_name: skeletal muscle from wound site, severely contused, 3h

value: 3h after severe contusion


title: severely contused muscel at 3h , biological rep3


title: WT NP+IgE+ Bcell#77


title: 3m_Mcoln1_KO_2


title: severely contused muscel at 1h , biological rep1


title: severely contused muscel at 3h , biological rep2


title: mildly contused muscel at 168h , biological rep3

description: Gene expression at 168h after mild contusion

source_name: skeletal muscle from wound site, mildly contused, 168h

value: 168h after mild contusion


title: 3m_Mcoln1_Het_4

value: Brain


title: 3m_Mcoln1_Het_3


title: WT NP+IgE+ Bcell#72


title: WT NP+IgE+ Bcell#70


title: WT NP+IgE+ Bcell#69


title: WT NP+IgE+ Bcell#71


title: mildly contused muscel at 48h , biological rep2

description: Gene expression at 48h after mild contusion

source_name: skeletal muscle from wound site, mildly contused, 48h

value: 48h after mild contusion


title: WT NP+IgE+ Bcell#66


title: 2m_Mcoln1_Het_4

value: 2 months

value: MARS-seq


title: mildly contused muscel at 168h , biological rep2

value: 10-12 weeks


title: 2m_Mcoln1_KO_4

value: Mcoln1 -/-


title: 1m_Mcoln1_KO_4

value: 1 month


title: mildly contused muscel at 48h , biological rep1

value: the thigh muscles of the right posterior limb


title: 2m_Mcoln1_KO_1


title: WT NP+IgE+ Bcell#76

value: spleen


title: WT NP+IgE+ Bcell#68


title: WT NP+IgE+ Bcell#63


title: WT NP+IgE+ Bcell#64


title: 2m_Mcoln1_KO_3


title: 2m_Mcoln1_Het_3


title: mildly contused muscel at 24h , biological rep3

description: Gene expression at 24h after mild contusion

source_name: skeletal muscle from wound site, mildly contused, 24h

value: 24h after mild contusion


title: WT NP+IgE+ Bcell#65


title: 2m_Mcoln1_Het_2

value: Mcoln1 +/-


title: mildly contused muscel at 24h , biological rep1


title: mildly contused muscel at 24h , biological rep2


title: mildly contused muscel at 168h , biological rep1


title: WT NP+IgE+ Bcell#67


title: mildly contused muscel at 48h , biological rep3


title: 2m_Mcoln1_Het_1


title: 1m_Mcoln1_KO_1


title: mildly contused muscel at 3h , biological rep3

description: Gene expression at 3h after mild contusion

source_name: skeletal muscle from wound site, mildly contused, 3h

value: 3h after mild contusion


title: 1m_Mcoln1_Het_4


title: 1m_Mcoln1_Het_3


title: 2m_Mcoln1_KO_2


title: WT NP+IgE+ Bcell#58

value: 8 weeks


title: mildly contused muscel at 3h , biological rep2


title: mildly contused muscel at 3h , biological rep1


title: mildly contused muscel at 1h , biological rep3

description: Gene expression at 1h after mild contusion

source_name: skeletal muscle from wound site, mildly contused, 1h

value: 1h after mild contusion


title: WT NP+IgE+ Bcell#57

value: IgE repoter (Verigem)


title: 1m_Mcoln1_KO_3


title: WT NP+IgE+ Bcell#62


title: WT NP+IgE+ Bcell#55


title: WT NP+IgE+ Bcell#56


title: WT NP+IgE+ Bcell#61


title: 1m_Mcoln1_KO_2


title: Ssc 4 T2 CD8+

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Library strategy: TCR-seq
Raw paired-end reads were assembled using Paired-End reAd mergeR (PEAR)
As part of our protocol, both reads contain barcodes/UMIs.
Sample specific barcode correction was performed using the ‘umi_group_ec’ command from the Recover T Cell Receptor (RTCR) pipeline, allowing zero mismatches in the barcode seed sequence for UMI detection.
Barcode sequence reads having the same UMI were collapsed into consensus sequences using the RTCR pipeline to accurately recover TCRβ sequences
Barcode and UMI sequences for each sample are contained in the file Barcodes_GEOsubmission_pandit.txt which is available from the series record.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited file containing TCRβ sequences and counts after error correction and post-processing using the RTCR pipeline

source_name: CD8+ non-naive T-cells peripheral blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation on Ficoll-PlaqueTM Plus (GE Healthcare Life Sciences). pDCs, mDCs, B-cells and monocytes were first depleted by magnetic bead sorting using the autoMACs Pro Separator (Miltenyi Biotec) according to the manufacturer’s protocol. The remaining peripheral blood lymphocytes (PBLs) were resuspended in freezing medium (80% FCS, Sigma / 20% DMSO, Sigma) and stored in sterile cryovials in liquid nitrogen (-196°C) until further use. PBLs were thawed in RPMI 1640 (Thermo Fisher Scientific) supplemented with 20% FCS (Sigma), and washed with PBS. Cells were resuspended in FACS buffer (PBS supplemented with 1% BSA (Sigma-Aldrich) and 0.1% sodium azide (Sigma-Aldrich)) and stained using the following antibodies: CD3-AF700 (clone UCHT1, Biolegend), CD4-BV711 (clone OKT4, Sony Biotechnology), CD8-V500 (clone RPA-T8, BD), CD56-PE-CF594 (clone B159, BD), CD16-BV785 (clone 3G8, Sony Biotechnology), CD14-PerCP-Cy5.5 (clone HCD14, Biolegend), HLADR-BV421 (clone L243, Biolegend), CD45RO-PE-Cy7 (clone L243, BD), CD27- APC-eFluor780 (clone O323, eBioscience). Multiparametric flow cytometry sorting of CD4+ and CD8+ non-naive T-cells was performed on the BD FACSAria II (BD Biosciences). After sorting, cells were washed in PBS, lysed in TRIzol™ Reagent (Invitrogen), and stored at -20°C. RNA was isolated and using the RNeasy Mini Kit (Qiagen) by adding ethanol to the upper aqueous phase of processed TRIzol samples and transferring directly to the RNeasy spin columns.
cDNA was generated by RACE using a primer directed to the TCRβ constant region. Thirteen nucleotide long unique molecular identifiers (UMIs) were incorporated during cDNA synthesis. Subsequently, two-stage semi-nested PCR amplification was performed including a size selection/agarose gel purification step after the first PCR. To minimize cross-sample contamination, 5-nucleotide sample specific barcodes were introduced at two steps during the library preparation process. Resulting TCR amplicons were subjected to high-throughput sequencing using the Ovation Low Complexity Sequencing System kit from NuGEN (San Carlos) according to the manufacturer’s instructions, and the Illumina MiSeq system (San Diego), using indexed paired-end 300 cycle runs.

value: CD8+ non-naive T-cells peripheral blood

tag: diagnosis

value: lcSSc

tag: subject id

value: Ssc 4

tag: timepoint

value: T2 (46 months from baseline)

value: female


title: WT NP+IgE+ Bcell#54


title: mildly contused muscel at 1h , biological rep1


title: mildly contused muscel at 1h , biological rep2


title: Macrophage M2

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description:
Macrophage M2
M2_ctrl

data_processing:
Trimming adaptor sequences and removing reads of low quality were performed by cutadapt (v2.4).
Quantified reads were aligned to the mouse genome (GRCm38) by STAR (v2.7.2a) and then gene-level read counts were generated based on the annotations of Gencode (vM19).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file includes gene-level read counts.

source_name: Mouse bone marrow-derived macrophages with IL4

growth_protocol: Mouse bone marrow-derived macrophages were polarized with IFN-gamma + LPS or IL4 for 24 h to induce M1 or M2 phenotypes, respectively.

extract_protocol:
Total RNA was extracted from frozen snaps using an AllPrep DNA/RNA mini kit (Qiagen,  Hilden, Germany).
Libraries were constructed using Illumina TruSeq Stranded mRNA kit according to the manufacturers

treatment_protocol: macrophages were treated with DMSO and regorafenib

value: control

value: macrophage

tag: subtype


title: skeletal muscle of control group, biological rep1

description: Gene expression form control group

source_name: skeletal muscle from the site same as wound site

tag: treatment

value: control group

value: 10-12 weeks


title: WT NP+IgE+ Bcell#59

tag: genotype


title: WT NP+IgE+ Bcell#60


title: Macrophage M1

description:
Macrophage M1
M1_ctrl

source_name: Mouse bone marrow-derived macrophages with IFN-gamma + LPS


title: WT NP+IgE+ Bcell#52


title: 1m_Mcoln1_Het_2

value: 1 month

value: Brain

value: MARS-seq


title: Ssc 4 T0 CD8+

value: T0 (0 months from baseline)

tag: gender


title: WT NP+IgE+ Bcell#50

value: spleen


title: Ssc 4 T0 CD4+

source_name: CD4+ non-naive T-cells peripheral blood

value: CD4+ non-naive T-cells peripheral blood


title: Macrophage M0

description:
Macrophage M0
M0_ctrl

source_name: Mouse bone marrow-derived macrophages


title: 1m_Mcoln1_Het_1

source_name: Mcoln1 mice C57Bl/6J

value: Mcoln1 +/-


title: Macrophage M2 treated with regorafenib

description:
Macrophage M2 treated with regorafenib
M2_rego

value: regorafenib


title: Ssc 3 T2 CD8+

value: CD8+ non-naive T-cells peripheral blood

value: Ssc 3

value: T2 (42 months from baseline)


title: skeletal muscle of control group, biological rep3

description: Gene expression form control group

value: the thigh muscles of the right posterior limb


title: skeletal muscle of control group, biological rep2

description: Gene expression form control group


title: Ssc 4 T2 CD4+

value: lcSSc

value: Ssc 4

value: T2 (46 months from baseline)

value: female


title: Ssc 3 T1 CD8+

value: T1 (18 months from baseline)


title: Ssc 4 T1 CD8+

value: T1 (15 months from baseline)


title: Reg5_antiPD1_p101_rep1

description: BNL-MEA tumor-bearing Balb/c mice treated with 5 mg regorafenib and anti-PD1 (p101)

value: BNL-MEA tumor-bearing Balb/c mice

value: regorafenib + anti-PD1

value: hepatocellular carcinoma

tag: batch


title: Macrophage M1 treated with regorafenib

description:
Macrophage M1 treated with regorafenib
M1_rego

value: macrophage


title: Ssc 3 T1 CD4+

value: CD4+ non-naive T-cells peripheral blood


title: WT NP+IgE+ Bcell#53

value: spleen

value: 8 weeks

value: IgE repoter (Verigem)


title: Ssc 3 T0 CD8+

value: CD8+ non-naive T-cells peripheral blood

value: Ssc 3

value: T0 (0 months from baseline)


title: antiPD1_p101_rep2

description: BNL-MEA tumor-bearing Balb/c mice treated with anti-PD1 (p101)


title: Ssc 4 T1 CD4+

value: lcSSc


title: WT NP+IgE+ Bcell#51


title: WT NP+IgE+ Bcell#45


title: Ssc 3 T0 CD4+


title: WT NP+IgE+ Bcell#44


title: antiPD1_p101_rep1

source_name: BNL-MEA tumor-bearing Balb/c mice treated with anti-PD1 (p101)


title: Reg5_p101_rep3

description: BNL-MEA tumor-bearing Balb/c mice treated with 5 mg regorafenib (p101)

value: regorafenib 5 mg/kg/day


title: Reg5_p101_rep2

source_name: BNL-MEA tumor-bearing Balb/c mice treated with 5 mg regorafenib (p101)


title: Ssc 3 T2 CD4+

value: T2 (42 months from baseline)