title: SS2.16.227_D14


title: SS2.16.227_D10

status: Public on Jan 27 2021

type: SRA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
Read processing was essentially performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that no UMIs were analysed. and that the reads were not analysed without strand specificity and not trimmed before alignment.
Genome_build: Mmul10
Supplementary_files_format_and_content: Processed data includes raw UMI counts matrix with the assigned celltype clusters, where rows are geneIDs and columns cellIDs. Corresponding annotation text files, where rows are CellIDs and columns different annotation ( sample name, Celltype)

molecule: polyA RNA

organism: Macaca mulatta

source_name: dorsal root ganglion

extract_protocol:
Extracted DRGs were cut once longitudinally (along the nerve) followed by chopping into ~0.5 mm slices. Samples were enzymatically treated for 1 h at 37°C with triturating every 15 min. The resulting cell suspension was then run through 100 µm cell-strainers. 1 ml of 10% Optiprep was loaded under the cell suspension solution using a gel loading tip and centrifugated at 200g for 6 min with a low break. Supernatant was discarded, the cell pellet resuspended and run through a 10 µm strainer. The strainer was rinsed twice and cells were then collected by flushing the filter twice. The cells were kept on ice for 15-20 min, centrifuged for 3 min  at 100 g and resuspended in 900 µl of filtered NMDG-SC/B27/12% optiprep and dispensed immediately into a WaferGen9600 Chip.
RNA libraries were prepared for sequencing using the Smart-Seq2 protocol (Picelli et al, Nat Protoc. 2014)

tag: animal id

tag: age(years)

tag: region

value: Sacral

tag: gender

value: Female

tag: cell identity

value: A-LTMR


title: SS2.16.227_D11


title: SS2.16.227_D13

value: lowq/nonneuron


title: SS2.16.227_D08


title: SS2.16.227_D06

value: C-LTMR


title: SS2.16.227_D07


title: SS2.16.227_D04


title: SS2.16.227_D01


title: SS2.16.227_D05


title: SS2.16.227_D03


title: SS2.16.227_D22


title: SS2.16.227_C24


title: SS2.16.227_D02


title: SS2.16.227_C23


title: SS2.16.227_C22


title: SS2.16.227_C21


title: SS2.16.227_C20


title: SS2.16.227_C16


title: SS2.16.227_C17


title: SS2.16.227_C14


title: SS2.16.227_C15


title: SS2.16.227_C18


title: SS2.16.227_C12


title: SS2.16.227_D09


title: SS2.16.227_C13


title: SS2.16.227_C10


title: SS2.16.227_C11


title: SS2.16.227_C07


title: SS2.16.227_C06


title: SS2.16.227_C05


title: SS2.16.227_C08


title: SS2.16.227_C09


title: SS2.16.227_C04


title: SS2.16.227_C03


title: SS2.16.227_C01


title: SS2.16.227_B22


title: SS2.16.227_B24


title: SS2.16.227_C19


title: SS2.16.227_B21


title: SS2.16.227_B19


title: SS2.16.227_B23


title: SS2.16.227_B20


title: SS2.16.227_B18


title: SS2.16.227_B13


title: SS2.16.227_B16


title: SS2.16.227_B17


title: SS2.16.227_B14


title: SS2.16.227_B11


title: SS2.16.227_B10


title: SS2.16.227_B09


title: SS2.16.227_B05


title: SS2.16.227_C02


title: SS2.16.227_B08


title: SS2.16.227_B04


title: SS2.16.227_B03


title: SS2.16.227_A24


title: SS2.16.227_B06


title: SS2.16.227_B15


title: SS2.16.227_B01


title: SS2.16.227_B02


title: SS2.16.227_A21


title: SS2.16.227_A22


title: SS2.16.227_B07


title: SS2.16.227_A20


title: SS2.16.227_A17


title: SS2.16.227_B12


title: SS2.16.227_A16


title: SS2.16.227_A18


title: SS2.16.227_A14


title: SS2.16.227_A13


title: SS2.16.227_A15


title: SS2.16.227_A11


title: SS2.16.227_A10


title: SS2.16.227_A12


title: SS2.16.227_A09


title: SS2.16.227_A23


title: SS2.16.227_A04


title: SS2.16.227_A07


title: SS2.16.227_A03


title: SS2.16.227_A05


title: SS2.16.227_A19


title: SS2.16.225_P23

value: Lumbar


title: SS2.16.225_P22


title: SS2.16.225_P24


title: SS2.16.227_A01


title: SS2.16.225_P19


title: SS2.16.225_P21


title: SS2.16.225_P16


title: SS2.16.225_P18


title: SS2.16.225_P17


title: SS2.16.225_P20


title: SS2.16.225_P14


title: SS2.16.225_P12


title: SS2.16.225_P15


title: SS2.16.225_P10


title: SS2.16.227_A08


title: SS2.16.225_P09


title: SS2.16.225_P08


title: SS2.16.225_P06


title: SS2.16.227_A02


title: SS2.16.225_P07


title: SS2.16.225_P04


title: SS2.16.225_P03


title: SS2.16.225_O23


title: SS2.16.225_P02


title: SS2.16.225_P01


title: SS2.16.225_O24


title: SS2.16.225_O22


title: SS2.16.225_O21


title: SS2.16.225_O20


title: SS2.16.225_O13


title: SS2.16.225_O16


title: SS2.16.225_O14


title: SS2.16.225_P13


title: SS2.16.225_P11


title: SS2.16.225_O12


title: SS2.16.225_O18


title: SS2.16.225_O10


title: SS2.16.225_O09


title: SS2.16.225_O15


title: SS2.16.225_O17


title: SS2.16.225_O08


title: SS2.16.225_P05


title: SS2.16.225_O06


title: SS2.16.225_O07


title: SS2.16.225_O11


title: SS2.16.225_O03


title: SS2.16.225_O04


title: SS2.16.225_O01


title: SS2.16.225_N23


title: SS2.16.225_O19


title: SS2.16.225_N24


title: SS2.16.225_O02


title: SS2.16.225_N22


title: SS2.16.225_N20


title: SS2.16.225_N21


title: SS2.16.225_N19


title: SS2.16.225_N18


title: SS2.16.225_N16


title: SS2.16.225_N17


title: SS2.16.225_N13


title: SS2.16.225_N15


title: SS2.16.225_N12


title: SS2.16.225_N14


title: SS2.16.225_N10


title: SS2.16.225_N09


title: SS2.16.225_N08


title: SS2.16.225_N06


title: SS2.16.225_N04


title: SS2.16.225_O05


title: SS2.16.225_N03


title: SS2.16.225_N05


title: SS2.16.227_A06


title: SS2.16.225_N02


title: SS2.16.225_M24


title: SS2.16.225_N01


title: SS2.16.225_M23


title: SS2.16.225_M18


title: SS2.16.225_M19


title: SS2.16.225_M22


title: SS2.16.225_M20


title: SS2.16.225_M21


title: SS2.16.225_M16


title: SS2.16.225_M15


title: SS2.16.225_N11


title: SS2.16.225_M14


title: SS2.16.225_M13


title: SS2.16.225_M08


title: SS2.16.225_M10


title: SS2.16.225_M11


title: SS2.16.225_M12


title: SS2.16.225_N07


title: SS2.16.225_M07


title: SS2.16.225_M06


title: SS2.16.225_M05


title: SS2.16.225_M01


title: SS2.16.225_M02


title: SS2.16.225_M03


title: SS2.16.225_M04


title: SS2.16.225_L23


title: SS2.16.225_L24


title: SS2.16.225_M17


title: SS2.16.225_L19


title: SS2.16.225_L21


title: SS2.16.225_L22


title: SS2.16.225_L18


title: SS2.16.225_L15


title: SS2.16.225_L14


title: SS2.16.225_L16


title: SS2.16.225_L17


title: SS2.16.225_M09


title: SS2.16.225_L11


title: SS2.16.225_L10


title: SS2.16.225_L09


title: SS2.16.225_L08


title: SS2.16.225_L13


title: SS2.16.225_L07


title: SS2.16.225_L06


title: SS2.16.225_L03


title: SS2.16.225_L04


title: SS2.16.225_L02


title: SS2.16.225_K22


title: SS2.16.225_L20


title: SS2.16.225_K19


title: SS2.16.225_K21


title: SS2.16.225_K20


title: SS2.16.225_K23


title: SS2.16.225_K17


title: SS2.16.225_K16


title: SS2.16.225_K15


title: SS2.16.225_K18


title: SS2.16.225_K14


title: SS2.16.225_K11


title: SS2.16.225_K12


title: SS2.16.225_K13


title: SS2.16.225_L05


title: SS2.16.225_K09


title: SS2.16.225_K10


title: SS2.16.225_K08


title: SS2.16.225_L01


title: SS2.16.225_K07


title: SS2.16.225_K04


title: SS2.16.225_K02


title: SS2.16.225_K03


title: SS2.16.225_K05


title: SS2.16.225_K06


title: SS2.16.225_K01


title: SS2.16.225_J24


title: SS2.16.225_K24


title: SS2.16.225_J23


title: SS2.16.225_J21


title: SS2.16.225_J20


title: SS2.16.225_J18


title: SS2.16.225_J19


title: SS2.16.225_J16


title: SS2.16.225_J17


title: SS2.16.225_J13


title: SS2.16.225_J14


title: SS2.16.225_J12


title: SS2.16.225_J15


title: SS2.16.225_J10


title: SS2.16.225_J11


title: SS2.16.225_J09


title: SS2.16.225_J08


title: SS2.16.225_J06


title: SS2.16.225_J07


title: SS2.16.225_J05


title: SS2.16.225_J03


title: SS2.16.225_J04


title: SS2.16.225_J01


title: SS2.16.225_J22


title: SS2.16.225_I24


title: SS2.16.225_I20


title: SS2.16.225_I21


title: SS2.16.225_L12


title: SS2.16.225_I19


title: SS2.16.225_I18


title: SS2.16.225_I17


title: SS2.16.225_I14


title: SS2.16.225_I16


title: SS2.16.225_I13


title: SS2.16.225_I12


title: SS2.16.225_I10


title: SS2.16.225_I11


title: SS2.16.225_I09


title: SS2.16.225_I08


title: SS2.16.225_I23


title: SS2.16.225_I06


title: SS2.16.225_I05


title: SS2.16.225_I07


title: SS2.16.225_J02


title: SS2.16.225_I04


title: SS2.16.225_I22


title: SS2.16.225_I03


title: SS2.16.225_I02


title: SS2.16.225_H22


title: SS2.16.225_I01


title: SS2.16.225_H20


title: SS2.16.225_H23


title: SS2.16.225_H21


title: SS2.16.225_I15


title: SS2.16.225_H17


title: SS2.16.225_H18


title: SS2.16.225_H16


title: SS2.16.225_H19


title: SS2.16.225_H14


title: SS2.16.225_H13


title: SS2.16.225_H12


title: SS2.16.225_H11


title: SS2.16.225_H10


title: SS2.16.225_H08


title: SS2.16.225_H09


title: SS2.16.225_H07


title: SS2.16.225_H06


title: SS2.16.225_H24


title: SS2.16.225_H03


title: SS2.16.225_H05


title: SS2.16.225_H01


title: SS2.16.225_G23


title: SS2.16.225_H02


title: SS2.16.225_G24


title: SS2.16.225_G22


title: SS2.16.225_G21


title: SS2.16.225_G19


title: SS2.16.225_G20


title: SS2.16.225_G17


title: SS2.16.225_H15


title: SS2.16.225_G16


title: SS2.16.225_G11


title: SS2.16.225_G14


title: SS2.16.225_G15


title: SS2.16.225_G09


title: SS2.16.225_G12


title: SS2.16.225_G10


title: SS2.16.225_G06


title: SS2.16.225_G05


title: SS2.16.225_G04


title: SS2.16.225_G08


title: SS2.16.225_H04


title: SS2.16.225_G02


title: SS2.16.225_G01


title: SS2.16.225_G18


title: SS2.16.225_G13


title: SS2.16.225_F24


title: SS2.16.225_F21


title: SS2.16.225_F20


title: SS2.16.225_F19


title: SS2.16.225_F23


title: SS2.16.225_F17


title: SS2.16.225_F22


title: SS2.16.225_F16


title: SS2.16.225_F18


title: SS2.16.225_F14


title: SS2.16.225_F12


title: SS2.16.225_F15


title: SS2.16.225_F13


title: SS2.16.225_F09


title: SS2.16.225_F08


title: SS2.16.225_F11


title: SS2.16.225_F10


title: SS2.16.225_F07


title: SS2.16.225_G03


title: SS2.16.225_F06


title: SS2.16.225_F05


title: SS2.16.225_F01


title: SS2.16.225_F02


title: SS2.16.225_F04


title: SS2.16.225_E24


title: SS2.16.225_E22


title: SS2.16.225_E23


title: SS2.16.225_E20


title: SS2.16.225_E17


title: SS2.16.225_E19


title: SS2.16.225_E16


title: SS2.16.225_E15


title: SS2.16.225_E18


title: SS2.16.225_E21


title: SS2.16.225_E14


title: SS2.16.225_E12


title: SS2.16.225_E13


title: SS2.16.225_E11


title: SS2.16.225_E09


title: SS2.16.225_F03


title: SS2.16.225_E10


title: SS2.16.225_E07


title: SS2.16.225_E08


title: SS2.16.225_E05


title: SS2.16.225_E02


title: SS2.16.225_E03


title: SS2.16.225_E06


title: SS2.16.225_D24


title: SS2.16.225_E01


title: SS2.16.225_D22


title: SS2.16.225_D21


title: SS2.16.225_D20


title: SS2.16.225_D23


title: SS2.16.225_D19


title: SS2.16.225_D18


title: SS2.16.225_D13


title: SS2.16.225_D12


title: SS2.16.225_D15


title: SS2.16.225_D16


title: SS2.16.225_D11


title: SS2.16.225_E04


title: SS2.16.225_D14


title: SS2.16.225_D04


title: SS2.16.225_D10


title: SS2.16.225_D05


title: SS2.16.225_D08


title: SS2.16.225_D07


title: SS2.16.225_D06


title: SS2.16.225_C21


title: SS2.16.225_C24


title: SS2.16.225_C19


title: SS2.16.225_C20


title: SS2.16.225_C23


title: SS2.16.225_D01


title: SS2.16.225_C18


title: SS2.16.225_D03


title: SS2.16.225_C16


title: SS2.16.225_D17


title: SS2.16.225_D09


title: SS2.16.225_C15


title: SS2.16.225_C14


title: SS2.16.225_D02


title: SS2.16.225_C22


title: SS2.16.225_C09


title: SS2.16.225_C10


title: SS2.16.225_C12


title: SS2.16.225_C07


title: SS2.16.225_C08


title: SS2.16.225_C11


title: SS2.16.225_C13


title: SS2.16.225_C17


title: SS2.16.225_C04


title: SS2.16.225_C02


title: SS2.16.225_C06


title: SS2.16.225_C03


title: SS2.16.225_C05


title: SS2.16.225_B24


title: SS2.16.225_B23


title: SS2.16.225_B19


title: SS2.16.225_B20


title: SS2.16.225_B21


title: SS2.16.225_B17


title: SS2.16.225_B18


title: SS2.16.225_B14


title: SS2.16.225_B16


title: SS2.16.225_B13


title: SS2.16.225_B15


title: SS2.16.225_B12


title: SS2.16.225_B11


title: SS2.16.225_B10


title: SS2.16.225_C01


title: SS2.16.225_B09


title: SS2.16.225_B05


title: SS2.16.225_B08


title: SS2.16.225_B04


title: SS2.16.225_B03


title: SS2.16.225_B22


title: SS2.16.225_A24


title: SS2.16.225_A21


title: SS2.16.225_A22


title: SS2.16.225_B01


title: SS2.16.225_A23


title: SS2.16.225_B02


title: SS2.16.225_A15


title: SS2.16.225_A18


title: SS2.16.225_A16


title: SS2.16.225_A14


title: SS2.16.225_A17


title: SS2.16.225_A19


title: SS2.16.225_A13


title: SS2.16.225_B06


title: SS2.16.225_B07


title: SS2.16.225_A06


title: SS2.16.225_A07


title: SS2.16.225_A20


title: SS2.16.225_A12


title: SS2.16.225_A11


title: SS2.16.225_A08


title: SS2.16.225_A10


title: SS2.16.225_A09


title: SS2.16.225_A03


title: SS2.16.225_A05


title: SS2.16.225_A02


title: SS2.16.225_A04


title: SS2.16.225_A01


title: YJF1460 T06

city: Rochester

first: Justin

last: Fay

state: NY

address: 319 Hutchison Hall, University of Rochester

department: Biology

country: USA

institute: University of Rochester

description: Cultures of each strain were taken at each time-point (hours) after inoculation.

data_processing:
Reads were mapped to combined reference genomes using Bowtie2 v2.1.0 using the local alignment setting (--local) and a maximum of one mismatch in the seed alignment (-N 1).
Duplicate reads were marked using PicardTools
Htseq-count was used to quantify allele-specific expression by counting reads that mapped to each allele in the combined reference genomes. Htseq-count was run to remove reads mapping to overlapping features (-mode union) and removal of reads with a mapping quality less than 10 (default).
Genome_build: Reference genomes were generated using the S288c (R64.1.1) genome as a template and GATK’s FastaAlternateReferenceMaker command to incorporate variants present in each strain. Genome annotations were generated using liftOver (PMC4383971) to transfer S288c annotations to each of the three other genomes. For mapping interspecific hybrid reads we used reference genomes and annotations (Scannell et al. 2011) for S. cerevisiae (S288c), S. paradoxus (N17) and S. uvarum (CBS7001).
Supplementary_files_format_and_content: Matrix table with read counts for each strain, gene, allele and time-point

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: Each hybrid strain was cultured in 125 mL YPD at 250 rpm at 30°C with an initial density of ~3x106 cells/mL

extract_protocol:
Approximately ~3x108 cells were taken at each time-point, centrifuged, supernatant removed and flash frozen in liquid nitrogen. RNA was extracted with phenol-chloroform and mRNA purified by oligo-dT (Dynabeads mRNA Direct kit, Invitrogen).
cDNA libraries were made by reverse transcription, fragmentation and adaptor ligation

treatment_protocol: A total of 19 samples were collected during the switch from fermentation to respiration

tag: strain

tag: time-point

tag: medium

value: Rich medium (YPD)


title: YJF1460 T14


title: YJF1460 T18


title: YJF1460 T13


title: YJF1460 T07


title: YJF1460 T19


title: YJF1460 T17


title: YJF1460 T15


title: YJF1460 T10


title: YJF1460 T12


title: YJF1460 T08


title: YJF1460 T05


title: SS2.16.225_G07


title: YJF1460 T04


title: YJF1455 T18


title: YJF1455 T19


title: YJF1455 T17


title: YJF1455 T15


title: YJF1460 T02


title: YJF1460 T01


title: YJF1455 T16


title: YJF1460 T03


title: YJF1455 T13


title: YJF1460 T11


title: YJF1460 T16


title: YJF1460 T09


title: YJF1455 T11


title: YJF1455 T14


title: YJF1455 T12


title: YJF1455 T09


title: YJF1455 T04


title: YJF1455 T03


title: YJF1455 T08


title: YJF1454 T17


title: YJF1454 T18


title: YJF1455 T05


title: YJF1454 T19


title: YJF1455 T06


title: YJF1455 T07


title: YJF1455 T02


title: YJF1455 T10


title: YJF1454 T14


title: YJF1454 T03


title: YJF1454 T15


title: YJF1454 T04


title: YJF1454 T02


title: YJF1454 T10


title: YJF1454 T11


title: YJF1454 T08


title: YJF1454 T09


title: YJF1454 T13


title: YJF1454 T12


title: YJF1454 T05


title: Liver_CONLC_941

city: Braunschweig

first: Fabian

last: Billenkamp

address: Bundesallee 37

country: Germany

institute: Friedrich-Loeffler-Institute

description:
Normalized_Gene_Count_Matrix.txt
RawGeneCountMatrix.txt

data_processing:
sequence quality checks with FastQC
raw reads were trimmed and filtered (minimal Phred scores of 20, minimum read length 30 nt) and adaptor sequence were removed using Trim Galore
alignment of quality filtered reads to the bovine reference UMD3.1 (Ensemble release 93) using default parameters of Hisat2 version 2.1.0
uniquely mapped reads were counted and assigned to gene features using HTSeq version 0.8.0
Detection of differentially expressed genes (>20 assigned reads) using Deseq2 version 1.20.0 in Rstudio version 1.1.456 using following specifications: default shrinkage estimator, p<0.05. Benjamini-Hochberg adjusted p-value (padj)<0.1
Genome_build: UMD3.1 (ensembl release 93)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

organism: Bos taurus

source_name: liver

extract_protocol:
total liver RNA was isolated using NucleoSpin® RNA (Macherey-Nagel GmbH & Co. KG, Düren, Germany), quality and integrity measurement of isolated RNA was assessed (Agilent 2100 Bioanalyzer, Agilent Technologies, Santa Clara, CA, USA)
Two micrograms of total RNA and the TruSeq Stranded mRNA sample preparation kit were used for the preparation of sequencing libraries according to manufacturer’s protocol (Illumina, San Diego, CA, USA)

tag: treatment

value: control

tag: concentrate feed proportion

value: low

tag: tissue

value: liver


title: YJF1454 T06


title: YJF1454 T07


title: YJF1455 T01


title: YJF1454 T16


title: Liver_CONLC_259


title: Liver_CONLC_260


title: Liver_CONLC_169


title: Liver_CONLC_145


title: Liver_CONLC_166


title: Liver_CONLC_60


title: Liver_CONHC_208

value: high


title: YJF1454 T01


title: Liver_CONHC_170


title: Liver_CONHC_134


title: Liver_CONHC_133


title: Liver_CONHC_7


title: Liver_CONHC_41


title: Liver_CONHC_123


title: Liver_GLYLC_912

value: glyphosate


title: Liver_GLYLC_905


title: Liver_GLYHC_127


title: Liver_GLYLC_544


title: Liver_GLYHC_154


title: Liver_GLYLC_209


title: Liver_GLYHC_152


title: Liver_GLYLC_102


title: Liver_GLYLC_42


title: Liver_CONLC_103


title: Liver_GLYHC_117


title: Liver_GLYLC_147


title: Liver_GLYHC_131


title: Liver_GLYHC_159


title: Liver_CONHC_144


title: Liver_GLYHC_37


title: Liver_GLYHC_32


title: T42

city: Seoul

first: Chul-Kee

last: Park

address: 101 Daehak-ro, Jongno-gu

department: Department of Neurosurgery

country: South Korea

institute: Seoul National University College of Medicine

data_processing:
Sequencing reads were aligned by STAR to the human reference genome (GRCh38 primary_assembly) with gene annotation from GENCODE (version 27).
Uniquely-mapped reads were counted for genes by featureCounts.
Transcripts per million was calculated.
Genome_build: hg38
Supplementary_files_format_and_content: Comma seperated file

organism: Homo sapiens

source_name: human brain tissue

extract_protocol:
RNA was isolated in a standard way using RNeasy kit (Qiagen).
RNA-seq library was generted using Illumina TruSeq Stranded Total RNA LT Sample Prep Kit.

value: brain

tag: tumor status

value: Tumor

tag: patient id

tag: pathology

value: Glioblastoma


title: T4


title: N4

value: Normal


title: N40


title: T40


title: T21


title: T16


title: N16


title: N21


title: N14


title: T14


title: T25


title: N25


title: T24


title: N42-1


title: T20


title: T18


title: T22


title: N24


title: T19


title: T12


title: N19


title: N18


title: T13


title: N12


title: N27

value: IDH mutant astrocytoma grade 4


title: N13


title: N6


title: T27


title: N22


title: N41

value: IDH mutant astrocytoma grade 3


title: T41


title: T6


title: T39


title: T17


title: N17


title: N20


title: N39


title: T8


title: T7


title: N7


title: N8


title: T2

value: IDH mutant astrocytoma grade 2


title: T26


title: T1


title: N52


title: N26


title: T51


title: T33

value: oligodendroglioma IDH mutant and 1p/19q-codeleted grade 3


title: N1


title: N51-1


title: T52


title: N32


title: N46-2


title: T47


title: N31


title: N47-2


title: T46


title: T45


title: T49


title: N49


title: N33


title: T44


title: T31


title: T43-1


title: N44


title: N45-2


title: N43-1


title: N55-2

value: oligodendroglioma IDH mutant and 1p/19q-codeleted grade 2


title: T54


title: T32


title: T56


title: T55


title: N54


title: N2


title: T38


title: N35


title: T37


title: N37


title: c8.col: Healthy Control Colonoid from c8

city: Philadelphia

first: Kathryn

middle: Elizabeth

last: Hamilton

state: PA

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to GRCh37 human reference genome using the STAR 2-pass method
Read counts were calculated using RSEM
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file includes raw count values calculated for each sample using RSEM

source_name: Colonoid

growth_protocol: Colonoids were expanded and passaged once prior to washing with ice-cold DMEM/F12 to remove Matrigel and snap-frozen for subsequent RNA isolation

extract_protocol:
RNA isolation was performed using NEBNext Ultra RNA library prep with rRNA depletion
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Healthy Control

tag: cell type

value: Colonoid

tag: group


title: c11.col: Healthy Control Colonoid from c11


title: DMSO

city: Columbus

first: Pu

last: Zhang

address: 1258 Bunkerhill Blvd, AptB

institute: Ohio State University

library_source: genomic

data_processing:
Library strategy: CRISPR screen
sgRNA Sequences: https://www.addgene.org/pooled-library/zhang-human-gecko-v2/
trim the 3p end with skewer, -r 0.2
trim the 5p end with skewer, -r 0.2
count reads with mageck
robust rank algorithm (RRA) with mageck
Supplementary_files_format_and_content: .txt file with read counts of all sgrnas

molecule: genomic DNA

source_name: CRISPR KO HiSeq

growth_protocol: MOLM-13 cells were grown in RPMI media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin/L-glutamine

extract_protocol:
Cells were harvested, DNA extracted via Qiagen Blood & Cell Culture DNA Midi Kit per manufacturer’s instructions, and the sgRNA cassette retrieved via PCR as described by Broad sequencing protocol on Addgene.
The P5 mix and P7 primers design from this protocol were used with the following New England Biolabs NEBNext Indexes: 17, 24, 26, 28, 29, 31, 33, 34, 35, 36, 42.

treatment_protocol: 2.5×10e6 cells/well were plated in each well of 12-well plates with total cells equal to 400 cells/sgRNA × 76,441 sgRNAs × 100/infection efficiency(%). Media containing lentiviral particles was added at2ug/mL polybrene and spinoculated at 450×g for 90 min. After six hours, cells were centrifuged 300×g for 10 min. and resuspended in complete media. Puromycin selection with 10ug/mL was started after 48 hours and continued for seven days of selection to remove essential and non-transduced cells. Cultures were then exposed to drug for five days or three days if viability fell below 20%.

tag: cell line

tag: passage

tag: crispr library


title: c19.epi: Healthy Control Epithelium from c19

source_name: Epithelium

value: Epithelium


title: c6.col: Healthy Control Colonoid from c6


title: Day0


title: 983A.epi: VEO-IBD Epithelium from 983A

value: inflammatory bowel disease (IBD)

value: VEO-IBD


title: N48-1


title: c18.col: Older Onset IBD Colonoid from c18

value: Older Onset IBD


title: c10.col: Healthy Control Colonoid from c10


title: 6331A.epi: Older Onset IBD Epithelium from 6331A


title: c18.epi: Older Onset IBD Epithelium from c18


title: 983A.col: VEO-IBD Colonoid from 983A


title: 969A.col: Older Onset IBD Colonoid from 969A


title: KPT-9274

description: 50nM KPT-9274


title: 6333A.epi: VEO-IBD Epithelium from 6333A


title: N38


title: 6192A.col: VEO-IBD Colonoid from 6192A


title: 6304A.col: Healthy Control Colonoid from 6304A


title: 6333A.col: VEO-IBD Colonoid from 6333A


title: T35


title: c7.col: Healthy Control Colonoid from c7


title: 6331A.col: Older Onset IBD Colonoid from 6331A


title: 6192A.epi: VEO-IBD Epithelium from 6192A


title: 252A.col: VEO-IBD Colonoid from 252A


title: c19.col: Healthy Control Colonoid from c19


title: ExVivoBlood_withMHE_PC65_rep1

type: RNA

city: El Palmar

first: Teresa

last: Rubio

state: Murcia

address: Av. Buenavista, 32

department: Plataforma de Bioinformática

country: Spain

institute: IMIB

description: Gene expression in whole human blood

hyb_protocol: Following ‘One-Color Microarray-Based Gene Expression Analysis’ protocol Version 6.7 (Agilent p/n G4140-90040), 600 ng of labeled cRNA was hybridized with the SurePrint G3 Human Gene Expression Microarrays v3 8X60K (Agilent p/n G4858A-072363)

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565C) according to the manufacturer’s protocol

data_processing: Data were extracted using Agilent Feature Extraction Software 11.5.1.1 following the Agilent protocol GE1_1105_Oct12, grid template 072363_D_F_20150612 and the QC Metric Set GE1_QCMT_Oct12.

source_name: Peripheral Blood, with Minimal Hepatic Encepalopathy, replicate 1

label_protocol: 200 ng of total RNA were used to produce Cyanine 3-CTP-labeled cRNA using the Low Input Quick Amp Labelling Kit, One-Color (Agilent p/n 5190-2305) according to the manufacturer’s instructions.

extract_protocol: RNA was quantified by spectrometry (NanoDrop ND1000, NanoDrop Technologies, Wilminton, Delaware USA) and quality confirmed by RNA 6000 Nano Bioanalyzer (Agilent Technologies, Palo Alto, California USA) assay.

treatment_protocol: Freshly drawn peripheral blood from patients was taken in BD Vacutainer tubes with EDTA and then centrifuged for 10 min at 1.500 g. Aliquots (500 μl) were immediately separated and kept at −80°C for subsequent analysis.

tag: diagnosis

value: cirrhotic patient with MHE

value: whole blood

tag: gender

value: male

tag: age


title: ExVivoBlood_withMHE_PC75_rep1

description: Gene expression in whole human blood


title: PGC-1α_2_ChIP-Seq

city: Tianjin

first: Bin

last: Han

address: 154 Anshan Road, Heping District

country: China

institute: Tianjin Medical University General Hospital

data_processing:
Base-calling performed using Off-Line Basecaller software (OLB V1.8)
Data were filtered using Solexa CHASTITY quality filter. Individual bases generated from original image files have quality scores which reflect the probability whether a base-call is correct or not. The CHASTITY should be no less than 0.6 in the first 25 bases.
Reads were aligned to Mouse genome (MM10) using BOWTIE software (V2.1.0) with default parameters.
The mapped reads were used for peak detection by MACS V1.4.2 (Model-based Analysis of ChIP-Seq) software. Statistically significant ChIP-enriched regions (peaks) were identified by comparison of IP vs Input or comparison to a Poisson background model (Cut-off p-value=10-4).
Genome_build: MM10
Supplementary_files_format_and_content: The signal profile (at 10 bp resolution) with UCSC WIG file format was generated from ChIP-seq data, which can be visualized on UCSC genome browser or IGB browser (Integrated Genome Browser, Java Runtime Environment needed, http://www.bioviz.org/igb/).

organism: Mus musculus

source_name: Microglia isolated from mPGC-1α mice at 24 h after ischemic stroke

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA samples were end-repaired, A tailed, and adaptor ligated using TruSeq Nano DNA Sample Prep Kit (#FC-121-4002, Illumina), following the manufacturer’s instructions. ~200-1500 bp fragments were size selected using AMPure XP beads. The final size of the library was confirmed by Agilent 2100 Bioanalyzer.

value: Microglia

tag: strain

tag: chip antibody

value: GFP (Abcam, lot ab290)


title: Input_1_ChIP-Seq


title: PGC-1α_1_ChIP-Seq


title: Input_2_ChIP-Seq


title: ExVivoBlood_withMHE_PC77_rep1

description: Gene expression in whole human blood


title: Let7bc2LKO3

city: Bethesda

first: Frank

middle: J

last: Gonzalez

state: Maryland

address: 9000 Rockville Pike

department: Laboratory of Metabolism

institute: National Cancer Institute

data_processing:
Basecalling was performed by Illumina RTA 1.18.64. Demultiplexing was performed by Bcl2fastq v2.17.
Filtering (Adaptor and quality) was performed by Trimmomatic 0.36
Alignment was performed by STAR 2.5.1
RNA Statistics and Duplication Statistics were performed by Picard 1.84
Quantification was performed by RSEM 1.2.22
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is TMM filtered by edgeR. "Expression" column represents TMM normalized value.

source_name: Liver

extract_protocol:
Total RNA was extrated from euthanized mouse livers. RNeasy plus mini kit (Qiagen) was used for preparing high purity RNA.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library Prep

treatment_protocol: Mice were fed with 60% High Fat Diet (Bio-Serve, Cat#F3282) for 8 weeks.

value: 8 weeks old

tag: genotype

value: let7b/c2 hepatocyte knockout

tag: diet

value: HFD

value: Liver


title: Let7bc2LKO1

tag: tissue


title: Wildtype2

value: Wild type


title: Let7bc2LKO2


title: ExVivoBlood_withoutMHE_PC58_rep1

description: Gene expression in whole human blood

source_name: Peripheral Blood, without Minimal Hepatic Encepalopathy, replicate 1

value: cirrhotic patient without MHE


title: Wildtype3


title: Wildtype1


title: Naive B cell

city: Iowa City

first: Noah

last: Butler

state: IL

address: 51 Newton Road

department: Microbiology and Immunology

institute: University of Iowa

data_processing:
Demultiplexing the Illumina sequencer's base call files (BCLs) for each flowcell directory into FASTQ files were performed by "cellranger mkfastq"  (cellranger version 3.02)
Gene counts were calculated using "cellranger count" (cellranger version 3.02) under default setting
Genome_build: mm10
Supplementary_files_format_and_content: h5

source_name: mouse B cells

extract_protocol:
Cells were partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) to achieve single cell resolution for a maximum of 10,000 individual cells per sample.
Utilizing the Chromium Single Cell 5’ Library & Gel Bead Kit (10x genomics, 1000006), poly-adenylated mRNA from an individual cell was tagged with a unique 16 base pair 10x barcode and 10 base pair Unique Molecular Identifier.
The cDNA amplicon size for the library (~700 bp) was optimized using enzymatic fragmentation and size selection and the concentration of the 10x single cell library was determined (Agilent High Sensitivity DNA Kit (Agilent). The single cell 5’ libraries were sequenced on the Illumina HiSeq-4000 sequencer (The NUSeq Core facility, Northwestern University) at 26 x 98 bp, paired end to target more than 50,000 reads per cell. We adopted Cell Ranger 3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) for raw sequencing process

treatment_protocol: Mice (n=3) were infected with P. yoelii and B cell subsets were sorted on day 10 p.i.

tag: treatment

value: P. yoelii-infected

value: Naive B cells (CD19+CD138-IgD+)


title: ExVivoBlood_withMHE_PC25_rep1

description: Gene expression in whole human blood


title: Germinal Center (GC) B cells/Naive B cells

value: GC B cells (CD19+GL7+Fas+)


title: ExVivoBlood_withMHE_PC50_rep1

description: Gene expression in whole human blood


title: ExVivoBlood_withoutMHE_PC57 rep1

description: Gene expression in whole human blood


title: Plasmablasts

value: plasmablasts (CD19+CD138hiIgDneg)


title: ExVivoBlood_withoutMHE_PC55_rep1

description: Gene expression in whole human blood


title: ExVivoBlood_withMHE_PC62_rep1

description: Gene expression in whole human blood


title: ExVivoBlood_withoutMHE_PC56_rep1

description: Gene expression in whole human blood


title: BALBc p18null BRCA1het 316 XIONG

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description:
Agilent-850
mRNA isolated from flash frozen bulk tumors.

hyb_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-125.

data_processing: Data for both channels were Lowess-normalized and then the log(2) ratio was taken. Both channels were filtered for Lowess Normalized Net (Mean) >= 10.

source_name: mammary tumor

growth_protocol: Mammary tumors were harvested for gene expression analysis.

extract_protocol: RNA was extracted using Qiagen RNeasy kits.

value: Balbc

value: mammary tumor

source_name: Normal reference

extract_protocol: Reference

tag: sample type

value: reference

value: normal


title: BALBc p18null BRCA1het 297 XIONG

description:
Agilent-848
mRNA isolated from flash frozen bulk tumors.

scan_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-125.


title: BALBc p18null 228 XIONG

description:
Agilent-847
mRNA isolated from flash frozen bulk tumors.

label_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-125.


title: HaCaT_SM [WGS]

city: Munich

first: Hanns Leonhard

last: Kaatsch

address: Neuherbergstraße 11

institute: Bundeswehr Institute of Radiobiology

data_processing:
Library strategy: WGS
Whole genome sequencing and variant calling: Adapter sequences and low quality bases (Phred <20) were clipped off by means of Trimmomatic. Reads < 40bp after clipping were excluded from further analysis.

source_name: SM-resistant HaCaT cell line

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.

extract_protocol: 2x 125 bp reads were generated for HaCaT and HaCaT/SM on a HiSeq2500 (Illumina).

tag: exposure (yes/no)

value: yes

value: human keratinocyte cell line


title: HaCaT [WGS]

source_name: HaCaT cell line

value: no


title: BALBc p18null BRCA1het 324 XIONG

description:
Agilent-849
mRNA isolated from flash frozen bulk tumors.


title: ExVivoBlood_withoutMHE_PC59_rep1

description: Gene expression in whole human blood

value: whole blood

value: male


title: Jar

city: Cambridge

first: Qin

last: Li

email: qin_li@harvard.edu, qinli9566@gmail.com

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology Department

institute: Harvard University

data_processing:
The reads were trimmed and aligned to the human reference genome (hg19) with Bowtie2aligner using the option -X2000.
we discarded reads with alignment quality < Q30, improperly paired, mapped to the unmapped contigs, chrY, and mitochondria
Duplicates were removed using MarkDuplicates in Picard tools (http://broadinstitute.github.io/picard/)
To visualize the tracks, the reads were extended by 250bp using igvtools (https://software.broadinstitute.org/software/igv/igvtools)
Genome_build: hg19
Supplementary_files_format_and_content: processed data files format and content

source_name: placenta

growth_protocol: JEG3, BeWo, JAR, HeLa and BJ fibroblasts were cultured in Dulbecco's Modified Eagle Medium (DMEM) (Life Technologies, USA) containing 10% fetal bovine serum and 1% penicillin/streptomycin solution at 37°C with 5% CO2.

extract_protocol:
After transposition reaction with Transposase enzyme (in  Illumina Nextera DNA Preparation kit (Illumina Cat #FC-121-1030), and immediately following transposition incubation, genomic DNA was purified using a Qiagen MinElute PCR purification kit
libraries were prepared with Illumina Nextera DNA Preparation kit (Illumina Cat #FC-121-1030).

treatment_protocol: No treatment was applied to JEG3, BeWo, JAR, HeLa and BJ fibroblasts.

value: Jar

tag: disease

value: choriocarcinoma

value: untreated

tag: malignancy

value: malignant


title: BeWo

value: BeWo


title: Hela

source_name: cervix

value: Hela

value: adenocarcinoma


title: BJ fibroblasts

source_name: skin; foreskin

value: BJ fibroblasts


title: bcell_pbmc_patient_LAU205

city: Epalinges

first: Daniel

middle: E

last: Speiser

state: VD

address: Route de la Corniche 9A

department: Department of Oncology

country: Switzerland

institute: University of Lausanne

data_processing:
Fastq files corresponding to each sample were concatenated to obtain one fastq file per sample.
Target transcript sequences were obtained from ENSEMBL (GRCh38.p10), and transcript abundances were quantified using kallisto (0.43.1) with sequence based bias correction. All other parameters were set to default.
Kallisto's transcript-level estimates were summarized at the gene-level using tximport (1.8.0) from Bioconductor.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: Tab-delimited text file providing gene-by-sample matrix of estimated counts.

extract_protocol:
RNA was extracted using QIAGEN RNeasy Plus Micro kit following the manufacturer's instructions.
Clontech SMART-Seq v4 (Takara)

tag: disease status

value: Melanoma patient

value: PBMC


title: bcell_tumor_patient_LAU392

value: Tumor


title: bcell_pbmc_patient_LAU975


title: bcell_pbmc_patient_LAU576


title: bcell_tumor_patient_LAU371


title: bcell_tumor_patient_LAU576


title: bcell_pbmc_patient_LAU371


title: bcell_tumor_patient_LAU975


title: bcell_tumor_patient_LAU205


title: bcell_pbmc_healthydonor3

value: Healthy donor


title: bcell_pbmc_healthydonor2


title: bcell_pbmc_healthydonor4


title: JEG3

tag: cell line


title: shHOXBLINC-OCI-AML3-RNA-seq-1

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq reads were aligned to the mm9 or hg19 genome assembly using Tophat, and ATAC-seq, ChIP-seq and 4C-seq reads were aligned to the mm9 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples and peaks for ATAC-seq, ChIP-seq and 4C-seq

source_name: MOLM13 leukemia cells

growth_protocol: Total bone marrow cells were taken from WT and Hoxblinc-Tg mice, LSK cells were then sorted using Lin-, Sca1+ and Kit+ markers, and LK cells were sorted using Lin- and Kit+ markers.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I. ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3 antibody (antibody: Anti-H3K4me3, Millipore, Cat No. 04-745). ATAC-seq samples derived according to Nextera Tn5 Transposase kits.    4C seq library samples derived from two enzymes digestion BglII and NlaIII and ligation with T4 ligase.
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594).  ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). 4C-seq libraries were prepared according to  TruSeq ChIP Library Preparation Kit (#IP-202-1012). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Immediately extract RNA from LSK cells without any treatment

tag: cell types

value: Human-derived acute myeloid leukemia

value: peripheral blood

value: acute myeloid leukemia

tag: shRNA

value: shHOXBLINC


title: bcell_pbmc_healthydonor1


title: shHOXBLINC-OCI-AML3-RNA-seq-2


title: Ctrl-OCI-AML3-RNA-seq-2

value: Ctrl


title: Ctrl-OCI-AML3-RNA-seq-1


title: bcell_pbmc_patient_LAU392


title: PT06_TP_402

city: Shanghai

first: Sibo

last: Zhu

state: China

address: songhulu 2005

institute: Fudan University

data_processing:
HiSeq 2500 instrument (Illumina) and single-end 50-bp read flow cells were used in this study
Sequenced reads were trimmed for adaptor sequence by trimmomatic(v0.36), then mapped to human genome(hg19) by Hisat2(V2.0.5), and counted by featureCounts(v1.5.2)
data was filterd under the standization that a gene expressed at least in 3 cells and a cells must express at leat 200 features
Genome_build: hg19
Supplementary_files_format_and_content: csv file include raw count values for each cell

source_name: TP

growth_protocol: tissues collected were transferred into pre-warmed DMEM medium containing 2 mg/ml collagenase P (Roche) and 10 U/µl DNase I (Roche).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We gently pipetted the mixture and then digested for 60 min at 37 °C to fully release single cells. The cell suspension solution was filtered and centrifuged. The pellet was resuspended and 2 mM ethylene diamine tetraacetic acid in phosphate-buffered saline. We employed fluorescence activated cell sorting (FACS) to ensure the living cell selections.

value: Liver

tag: disease state

value: para-tumor

tag: patient id


title: PT06_TP_404


title: PT06_TT_397

source_name: TT

value: tumor


title: PT06_TP_401


title: PT06_TP_403


title: PT06_TT_396


title: PT06_TP_400


title: PT06_TT_395


title: PT06_TT_390


title: PT06_TT_394


title: PT06_TP_398


title: PT06_TT_391


title: PT06_TT_389


title: PT06_TT_387


title: PT06_TT_388


title: PT06_TT_385


title: PT06_TT_384


title: PT06_TP_383


title: PT06_TT_386


title: PT06_TP_381


title: PT06_TP_380


title: PT06_TP_379


title: PT06_TP_377


title: PT06_TT_392


title: PT06_TP_405


title: PT06_TP_376


title: PT06_TP_382


title: PT06_TT_373


title: PT06_TT_367


title: PT06_TT_374


title: PT06_TT_369


title: PT06_TT_368


title: PT06_TT_371


title: PT06_TT_370


title: PT06_TT_364


title: PT06_TT_372


title: PT06_TT_366


title: PT06_TT_361


title: PT06_TP_399


title: PT06_TP_378


title: PT06_TT_355


title: PT06_TT_357


title: PT06_TT_359


title: PT06_TT_358


title: PT06_TP_354


title: PT06_TP_353


title: PT06_TP_352


title: PT06_TT_375


title: PT06_TP_351


title: PT06_TP_350


title: PT06_TT_365


title: PT06_TP_349


title: PT06_TT_360


title: PT06_TP_348


title: PT06_TT_346


title: PT06_TT_345


title: PT06_TT_343


title: PT06_TT_342


title: PT06_TT_338


title: PT06_TT_344


title: PT06_TT_341


title: PT06_TT_340


title: PT06_TT_339


title: PT05_TT_333


title: PT05_TT_335


title: PT05_TT_337


title: PT05_TT_336


title: PT06_TT_356


title: PT05_TT_334


title: PT05_TT_331


title: PT05_TT_332


title: PT05_TT_329


title: PT05_TT_328


title: PT05_TT_330


title: PT05_TT_327


title: PT05_TT_326


title: PT05_TT_325


title: PT06_TP_347


title: PT05_TT_323


title: PT05_TT_324


title: PT05_TT_322


title: PT05_TP_321


title: PT05_TP_318


title: PT05_TP_320


title: PT05_TP_319


title: PT06_TT_362


title: PT05_TP_316


title: PT05_TP_315


title: PT05_TP_317


title: PT05_TP_309


title: PT05_TP_314


title: PT05_TP_307


title: PT05_TP_308


title: PT05_TP_311


title: PT05_TP_310


title: PT05_TP_306


title: PT05_TP_305


title: PT05_TP_302


title: PT05_TP_303


title: PT06_TT_363


title: PT05_TP_304


title: PT05_TP_300


title: PT05_TP_301


title: PT05_TP_299


title: PT05_TT_298


title: PT05_TT_297


title: PT06_TT_393


title: PT05_TT_295


title: PT05_TT_296


title: PT05_TT_294


title: PT05_TT_292


title: PT05_TT_291


title: PT05_TP_312


title: PT05_TP_313


title: PT05_TT_289


title: PT05_TT_288


title: PT04_TT_287


title: PT04_TT_286


title: PT04_TT_284


title: PT04_TT_279


title: PT04_TT_280


title: PT04_TT_281


title: PT04_TT_276


title: PT04_TT_277


title: PT04_TT_283


title: PT04_TT_273


title: PT04_TT_275


title: PT04_TT_272


title: PT04_TT_271


title: PT04_TT_274


title: PT05_TT_293


title: PT04_TT_270


title: PT05_TT_290


title: PT04_TT_266


title: PT04_TT_267


title: PT04_TT_269


title: PT04_TT_265


title: PT04_TP_261


title: PT04_TT_268


title: PT04_TP_262


title: PT04_TT_282


title: PT04_TP_259


title: PT04_TP_264


title: PT04_TT_278


title: PT04_TP_260


title: PT04_TP_257


title: PT04_TP_256


title: PT04_TP_255


title: PT04_TP_263


title: PT04_TT_285


title: PT04_TP_254


title: PT04_TP_253


title: PT04_TP_250


title: PT04_TP_248


title: PT04_TP_249


title: PT04_TP_247


title: PT04_TP_246


title: PT04_TP_252


title: PT04_TP_245


title: PT04_TT_240


title: PT04_TP_243


title: PT04_TP_244


title: PT04_TT_241


title: PT04_TT_238


title: PT04_TT_239


title: PT04_TT_237


title: PT04_TT_236


title: PT04_TT_231


title: PT04_TT_232


title: PT04_TT_230


title: PT04_TT_228


title: PT04_TT_227


title: PT03_TP_226


title: PT03_TP_225


title: PT03_TP_223


title: PT03_TP_222


title: PT03_TP_224


title: PT04_TP_242


title: PT03_TP_217


title: PT03_TP_220


title: PT03_TP_221


title: PT03_TP_219


title: PT03_TP_218


title: PT03_TP_216


title: PT04_TT_234


title: PT04_TT_233


title: PT03_TP_215


title: PT03_TP_213


title: PT03_TP_212


title: PT04_TT_229


title: PT03_TP_209


title: PT03_TP_210


title: PT03_TP_208


title: PT03_TP_207


title: PT03_TT_203


title: PT03_TP_214


title: PT03_TT_202


title: PT03_TT_198


title: PT04_TP_258


title: PT03_TT_195


title: PT03_TT_194


title: PT03_TT_193


title: PT03_TT_188


title: PT03_TT_192


title: PT03_TT_189


title: PT03_TT_196


title: PT03_TT_191


title: PT03_TT_186


title: PT03_TP_206


title: PT03_TT_185


title: PT04_TT_235


title: PT03_TT_182


title: PT03_TT_187


title: PT03_TT_181


title: PT03_TT_179


title: PT03_TT_180


title: PT03_TT_178


title: PT03_TT_211


title: PT03_TT_177


title: PT02_TT_174


title: PT02_TT_175


title: PT02_TT_176


title: PT02_TT_170


title: PT02_TT_171


title: PT02_TT_172


title: PT02_TT_169


title: PT02_TT_168


title: PT03_TT_183


title: PT02_TT_173


title: PT02_TT_166


title: PT03_TT_184


title: PT02_TT_167


title: PT02_TT_165


title: PT02_TT_163


title: KMS34R

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

country: Japan

institute: National cancer center research institute

description:
Human multiple myeloma cells isolated from multiple myeloma patient
Sample 6

data_processing:
Single-end sequenced reads were checked by FastQC.
Mapping was performed using TopHat.
The expression matrix was constructed and normlized by Partek Genomics Suite6.6
Genome_build: hg19
Supplementary_files_format_and_content: expression matrix

source_name: Human multiple myeloma cells

growth_protocol: multiple myeloma cell lines were seeded in culture dishes in RPMI1640 medium (gibco)with 10% fetal bovine serum (gibco) and 1% Antibiotic-Antimycotic solution (gibco) at 37 °C in 5% CO2.

extract_protocol:
Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA quantity and quality were evaluated with a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
TruSeq Stranded mRNA Sample Prep Kit

treatment_protocol: Lenalidomide-resistant cell lines were continued to be exposed to low concentrations of lenalidomide.

value: multiple myeloma patient

tag: group

value: Resistant


title: KMS27R

description:
Human multiple myeloma cells isolated from multiple myeloma patient
Sample 4


title: PT02_TT_162


title: KMS27

description:
Human multiple myeloma cells isolated from multiple myeloma patient
Sample 3

value: Parental


title: PT02_TT_161


title: KMS21R

description:
Human multiple myeloma cells isolated from multiple myeloma patient
Sample 2


title: PT02_TT_159


title: PT02_TT_157


title: PT02_TT_158


title: KMS21

description:
Human multiple myeloma cells isolated from multiple myeloma patient
Sample 1


title: KMS34

description:
Human multiple myeloma cells isolated from multiple myeloma patient
Sample 5


title: PT03_TT_197


title: PLC8024_V

city: Hong Kong

first: XIA

last: WANG

address: 21 Sassoon Rd, Pokfulam

department: Clinical Oncology

country: Hong Kong

institute: The University of Hong Kong

data_processing:
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: Homo_sapiens.GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: HCC cell line

growth_protocol: PLC-8024 cells were cultured in DMEM medium with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PLC-8024 was infected with RALYL lentivirus or vecter control lentivirus, and selected by puromycin.

tag: transfection

value: vector control lentivirus


title: PT03_TT_190


title: PLC8024_R

value: RALYL lentivirus


title: NPM1-KI-ATAC-seq-LSK-2

source_name: Bone marrow Lin- Sca1+ Kit+ cells

value: Mouse-derived Bone marrow cells

value: Bone marrow

tag: strain

value: Lin- Sca1+ Kit+ cells


title: NPM1-KI-ATAC-seq-LSK-1

tag: genotype


title: PT02_TT_164


title: PT02_TT_156


title: PT02_TT_154


title: WT-ATAC-seq-LSK-2

value: WT


title: PT02_TT_155


title: PT02_TT_153


title: WT-ATAC-seq-LSK-1


title: NPM1-KI-RNA-seq-LSK-2


title: PT02_TT_152


title: PT02_TT_151


title: PT02_TT_150


title: WT-RNA-seq-LSK-1


title: WT-RNA-seq-LSK-2


title: PT02_TT_149


title: PT02_TT_148


title: PT02_TT_146


title: PT03_TP_204


title: attachment [E1]

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

description:
Bulk Mars-Seq (3' end-RNA-seq)
processed data file: MARseq_day14.5_crudeReadCount.txt

data_processing:
Bulk Mars-Seq (3' end-RNA-seq):
Bcl files were converted into fastq by bcl2fastq v2.17.1.14. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).
Adapters and low quality bases were removed from the raw reads using cutadapt
The remaining reads (raw data submitted)  were aligned to the Mus musculus genome (mm9) using Bowtie
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file (downloaded from igenomes UCSC), which was modified to contain a window surrounding the 3' UTR. Duplicate reads were marked and filtered based on having the same UMI and mapping to the same gene, using a python script.
Genes were filtered out if their sum counts after UMI filter <=10 or  maximum value <= 5. Normalization and differential expression analysis was performed using the DESeq2 R-package. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 (after adjusment with fdrtools).
ATAC-seq:
Bcl files were converted into fastq by bcl2fastq v2.17.1.14 following demultiplexing.
Adapters and low quality bases were removed from the raw reads using cutadapt
The remaining reads (raw data submitted)  were aligned to the Mus musculus genome (mm10) using Bowtie
Non-mitochondrial, unique aligned read-pairs with an inter-distance of <120 bp were selected for peak calling
peak calling was performed using MACS2. The number of reads per peak was calculated using bamtools.
A set of reproducible peaks ( shred in >=50% of the replicates of each condition) were obtained Peaks were merged and quantified using bedtools
read count was normalized using DESeq2.
Genome_build: mm9 (RNA-seq); mm10 (ATAC-seq)
Supplementary_files_format_and_content: text file with crude read count

source_name: Scx-Col2- LCM isolated attachment cells from prominent deltoid tuberosity and greater tuberosity of the humerus from E14.5 forelimb

growth_protocol:
Bulk Mars-Seq (3' end-RNA-seq): For collcetion of cells by laser capture microdissection (LCM), E14.5 Col2a1-tdTomato-Scx-GFP mouse forelimbs were dissected, shortly fixated in 4% PFA, washed with PBS and cryo-embedded. Next, samples were cryo-sectioned and mounted on LCM slides (PET, Zeiss), washed with RNase-free water and EtOH (Arcturus dehydration component kit) according to an altered protocol of Pazin et al 2012. LCM (PALM MicroBeam C system, Zeiss) was calibrated for refined tissue cutting. Isolated cells were collected to LCM caps (Adhesive Cap 500 clear, Zeiss) and RNA was purified using RNeasy FFPE Kit (Qiagen).
ATAC-seq: For collection of cells by FACS, forelimbs were dissected and suspended in cold PBS. To extract cells from tissues, PBS was replaced with 1 ml heated 0.05% trypsin and collagenase type V (dissolved in DMEM, Sigma) and incubated for 15 min at 37˚C, gently agitated every 5 minutes. Tissues were then dissociated by vigorous pipetting using 1 ml tips. Next, 4 ml of DMEM supplemented with 10% FBS and 1% Pen-Strep was added and cell suspensions were filtered with 40 μm filter net. Finally, tubes were centrifuged at 1,000 rpm for 7 minutes, supernatant was removed and cells were resuspended in 1 ml of cold PBS and used immediately for FACS.

extract_protocol:
Bulk Mars-Seq (3' end-RNA-seq): RNA was purified using RNeasy FFPE Kit (Qiagen) according to manufacture guidelines (Protocol:Protocol: Purification of Total RNA from Microdissected FFPE Tissue Sections).
Bulk Mars-Seq (3' end-RNA-seq): Purified RNA was stored at -80C. For library preparation RNA was used for the bulk MARS-seq  protocol (Jaitin et al. 2014 Science.343:776-9, Keren-Shaul et al. 2019 Nature Protocols). MARS-seq libraries were sequenced using  Hiseq 2500 SR50 cycles kit (Illumina)
For ATAC-seq protocol we used a modified protocol of Buenrostro et al., 2015 Curr Protoc Mol Biol.

tag: strain background

value: A mixed background of C57BL/6 and B6.129 (ICR)

tag: genotype/variation

tag: age

tag: cell type

value: attachment


title: remote chondrocyte [C2]

source_name: Col2a1+ LCM from prominent deltoid tuberosity and greater tuberosity of the humerus from E14.5 forelimb

value: remote chondrocyte


title: adjacent chondrocyte [D2]

value: adjacent chondrocyte


title: attachment [E2]


title: PT02_TT_144

tag: tissue


title: adjacent tenocyte [B2]

source_name: Scx+ LCM from prominent deltoid tuberosity and greater tuberosity of the humerus from E14.5 forelimb

value: adjacent tenocyte


title: PT02_TT_145

value: Liver


title: NPM1-KI-RNA-seq-LSK-1


title: PT02_TT_142


title: PT02_TT_141


title: remote tenocyte [A1]

value: remote tenocyte


title: PT02_TT_140

value: tumor


title: WT-CHIRP-seq

data_processing:
Library strategy: CHIRP-seq
Standard Illumina software base-calling and quality-control filtering were applied Sequences (Paired end).
Paired end RNA-seq reads were aligned to the mm9 genome assembly using Tophat, and ATAC-seq, ChIRP-seq, ChIP-seq and 4C-seq reads were aligned to the mm9 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1).
Genome coverage tracks were created using deepTools version 3.0.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples and peaks for ATAC-seq, ChIP-seq and 4C-seq.

extract_protocol:
RNA samples extracted with Trizol and treated with DNase I. ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3 antibody (antibody: Anti-H3K4me3, Millipore, Cat No. 04-745). ATAC-seq samples derived according to Nextera Tn5 Transposase kits. 4C seq library samples derived from two enzymes digestion BglII and NlaIII and ligation with T4 ligase.
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). 4C-seq libraries were prepared according to TruSeq ChIP Library Preparation Kit (#IP-202-1012). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Immediately extract RNA from LSK cells without any treatment.


title: PT02_TT_138


title: IL-13KO NP+IgE+ Bcell#380

city: Yokohama

first: Kosuke

last: Miyauchi

state: Kanagawa

address: 1-7-22 Suehiro-sho

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

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).

value: spleen

value: 8 weeks

value: IgE repoter (Verigem)


title: IL-13KO NP+IgE+ Bcell#382


title: IL-13KO NP+IgE+ Bcell#384


title: Hoxblinc-Tg-CHIRP-seq

value: Hoxblinc-Tg


title: PT02_TT_139


title: Control_FreshSC_2

city: Los Angeles

first: Albert

middle: Ernesto

last: Almada

state: CA

address: 1450 Biggy Street

department: Orthopaedic Surgery and Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

description: Sample 13

data_processing:
Adaptor sequences were trimmed from sequence reads
Resulting FASTQ files were aligned to the mouse reference genome using STAR (2.5.0c) aligner software with default parameters and exported into BAM format.
HTSeq (0.6.1), was used to count the number of aligned reads per gene, specifically using the htseq-count function with options -s (no), -m (intersection-nonempty), -t (“Exons”).
To measure differential gene expression, gene read count tables generated by HTSeq were used as input for the R package DESeq2 (1.20.0). Differentially expressed genes were defined as those genes displaying > 50% (FosGFP+/GFP-) or > 2 (FoscKO/Control) Fold-Changed in either direction with an adjusted p-value < 0.05 (Benjamin-Hochberg).
Genome_build: Ensembl GRCm38.87 assembly
Supplementary_files_format_and_content: csv files containing Differentially Expressed Genes determined by Limma (Microarray) or DeSeq2 (RNA-Seq).

source_name: primary muscle satellite cells

extract_protocol:
RNA was extracted from Fresh SCs using the RNeasy mico kit
cDNA libraries were prepared and amplified using Smart-Seq v4 Ultra Low Input RNA Kit for sequencing, and fragmented, adaptor tagged, amplified,and barcoded using Nextera XT kit (#FC-131-1096). Pooled libraries were then quantified using a 2100 BioAnalyzer, and subjected to massively, paralleled sequencing using Illumina’s HiSeq 2500 platform.

value: Control

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

value: Fresh SCs


title: Control_FreshSC_3

description: Sample 14


title: IL-13KO NP+IgE+ Bcell#381


title: PT03_TT_199


title: remote tenocyte [A2]


title: IL-13KO NP+IgE+ Bcell#383


title: IL-13KO NP+IgE+ Bcell#378


title: FoscKO_FreshSC_3

description: Sample 11

value: FoscKO


title: PT02_TT_134


title: PT02_TT_137


title: FoscKO_FreshSC_2

description: Sample 10


title: PT02_TT_136


title: IL-13KO NP+IgE+ Bcell#377


title: IL-13KO NP+IgE+ Bcell#371


title: IL-13KO NP+IgE+ Bcell#376


title: PT02_TT_143


title: PT02_TT_135


title: IL-13KO NP+IgE+ Bcell#375


title: IL-13KO NP+IgE+ Bcell#379


title: PT03_TT_200


title: IL-13KO NP+IgE+ Bcell#374


title: IL-13KO NP+IgE+ Bcell#369


title: PT02_TT_132


title: PT02_TT_133


title: Control_FreshSC_1

description: Sample 12


title: IL-13KO NP+IgE+ Bcell#370


title: FoscKO_FreshSC_1

description: Sample 9


title: PT04_TP_251

value: para-tumor


title: FosGFP_negative_FreshSC_4

description: Sample 8

value: FosGFP-


title: IL-13KO NP+IgE+ Bcell#372


title: IL-13KO NP+IgE+ Bcell#368


title: PT02_TT_131


title: IL-13KO NP+IgE+ Bcell#367


title: PT02_TT_130


title: IL-13KO NP+IgE+ Bcell#366


title: PT02_TT_147


title: IL-13KO NP+IgE+ Bcell#365


title: FosGFP_negative_FreshSC_2

description: Sample 6


title: IL-13KO NP+IgE+ Bcell#364


title: PT02_TT_129


title: IL-13KO NP+IgE+ Bcell#363


title: FosGFP_negative_FreshSC_1

description: Sample 5


title: IL-13KO NP+IgE+ Bcell#362


title: PT02_TT_128


title: IL-13KO NP+IgE+ Bcell#361


title: FosGFP_positive_FreshSC_4

description: Sample 4

value: FosGFP+


title: IL-13KO NP+IgE+ Bcell#360


title: PT03_TT_201


title: FosGFP_positive_FreshSC_3

description: Sample 3


title: PT02_TT_126


title: IL-13KO NP+IgE+ Bcell#359


title: IL-13KO NP+IgE+ Bcell#358


title: FosGFP_negative_FreshSC_3

description: Sample 7


title: IL-13KO NP+IgE+ Bcell#357


title: FosGFP_positive_FreshSC_2

description: Sample 2


title: IL-13KO NP+IgE+ Bcell#356


title: PT02_TT_125


title: FosGFP_positive_FreshSC_1

description: Sample 1


title: IL-13KO NP+IgE+ Bcell#355


title: IL-13KO NP+IgE+ Bcell#353


title: PT02_TT_124


title: IL-13KO NP+IgE+ Bcell#354


title: IL-13KO NP+IgE+ Bcell#351


title: PT02_TT_127


title: PT02_TT_123


title: PT02_TT_122


title: IL-13KO NP+IgE+ Bcell#350


title: IL-13KO NP+IgE+ Bcell#349


title: PT02_TT_160


title: IL-13KO NP+IgE+ Bcell#348


title: IL-13KO NP+IgE+ Bcell#346


title: PT02_TT_120


title: PT02_TT_121


title: IL-13KO NP+IgE+ Bcell#345


title: PT03_TP_205


title: PT02_TP_119


title: IL-13KO NP+IgE+ Bcell#343


title: IL-13KO NP+IgE+ Bcell#342


title: PT02_TP_118


title: IL-13KO NP+IgE+ Bcell#352


title: IL-13KO NP+IgE+ Bcell#341


title: IL-13KO NP+IgE+ Bcell#340


title: PT02_TP_117


title: IL-13KO NP+IgE+ Bcell#347


title: IL-13KO NP+IgE+ Bcell#338


title: IL-13KO NP+IgE+ Bcell#339


title: IL-13KO NP+IgE+ Bcell#344


title: IL-13KO NP+IgE+ Bcell#336


title: IL-13KO NP+IgE+ Bcell#335


title: YAMC_wt_T.g.16h vs. YAMC_wt_ni

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: polarity(-)

hyb_protocol: SurePrint G3 Mouse Gene Expression v2 Microarrays  (Agilent-014868) were done according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range (XDR) using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA  (Agilent Technologies). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware). Intra-array data were normalized with the  extraction protocol and interarray normalization was done by the mean of trimmed positive non-flagged/non-control reporters.

label_protocol: RNA labeling was performed with the  Quick-Amp Labeling Kit  (Agilent Technologies) according supplier's instructions.

growth_protocol:
The natural life cycle of Eimeria falciformis was maintained by continuous passage in NMRI mice. Oocysts were purified from animal feces by NaOCl floatation method. Sporozoites were excysted by incubating sporocyst preparations with 0.25% trypsin and 0.04% sodium tauroglycocholate (MP Biomedicals) in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 2 mM glutamine, 100 µg/mL streptomycin and 100 U/mL penicillin (37°C, 2 h). Tachyzoites of Toxoplasma gondii were maintained in confluent monolayers of human foreskin fibroblast (HFF) cells
Human foreskin fibroblast  (HFF) cells were cultured in DMEM with 4.5 g/L glucose, 10% FCS, 2 mM glutamine, 1x MEM non-essential amino acids, 100 µg/mL streptomycin and 100 U/mL penicillin in a humidified incubator (37°C, 5% CO2). Young adult mouse colonic epithelial cells (YAMC) were cultured in RPMI medium containing glucose (4.5 g/L), FCS (5%), insulin (1 µg/mL), α-thioglycerol (10 µM), hydrocortisone (1 µM) and IFNγ (5 U/mL) (33°C, 5% CO2).  Wildtype cFos+/+ 1-98M (wt) and cFos-/- 7-98M mutant (ko) murine embryonic fibroblast cells (MEF) were maintained in DMEM supplemented with 4.5 g/L glucose, 10% FCS, 2 mM glutamine, 100 µg/mL streptomycin and 100 U/mL penicillin (37°C and 5% CO2).

extract_protocol: Total RNA was isolated from uninfected and infected cells suspended in TRIzol (PureLink RNA kit, Life Technologies)

treatment_protocol: Young adult mouse colonic epithelial cells (YAMC) , wildtype cFos+/+ 1-98M (wt) and cFos-/- 7-98M mutant (ko) murine embryonic fibroblast (MEF) cells were seeded into wells for 24 h, and then infected with Eimeria falciformis sporozoites or Toxoplasma gondii tachyzoites at a MOI of 6 and 2 respectively.

value: young adult mouse colonic epithelial cells

value: wildtype

tag: infection

value: Toxoplasma gondii

tag: time point

tag: biol. replicate

value: non infected


title: PT02_TP_115

value: Liver


title: YAMC_wt_ni vs. YAMC_wt_T.g.4h

description: polarity(+)


title: YAMC_wt_T.g.4h vs. YAMC_wt_ni

description: polarity(+)


title: YAMC_wt_ni vs. YAMC_wt_T.g.16h

description: polarity(-)


title: IL-13KO NP+IgE+ Bcell#334


title: YAMC_wt_E.f.16h vs. YAMC_wt_ni

description: polarity(-)

value: Eimeria falciformis


title: YAMC_wt_E.f.4h vs. YAMC_wt_ni

description: polarity(+)


title: YAMC_wt_ni vs. YAMC_wt_E.f.16h

description: polarity(-)


title: PT02_TP_114


title: IL-13KO NP+IgE+ Bcell#333

value: spleen


title: IL-13KO NP+IgE+ Bcell#332

value: 8 weeks


title: PT02_TP_113


title: YAMC_wt_ni vs. YAMC_wt_E.f.4h

description: polarity(+)


title: PT02_TP_116


title: IL-13KO NP+IgE+ Bcell#337

value: IgE repoter (Verigem)


title: IL-13KO NP+IgE+ Bcell#331


title: PT02_TP_112


title: IL-13KO NP+IgE+ Bcell#373


title: IL-13KO NP+IgE+ Bcell#329


title: IL-13KO NP+IgE+ Bcell#330


title: IL-13KO NP+IgE+ Bcell#328


title: PT02_TP_111


title: IL-13KO NP+IgE+ Bcell#327


title: MEF_ko _ni vs. MEF_wt_ni_1_4

description: polarity(-)

source_name: MEF_ko _ni

value: mouse embryonic fibroblast cells

value: cFos knockout


title: PT02_TP_110


title: MEF_wt_ni vs. MEF_ko _ni_1_3

description: polarity(+)


title: IL-13KO NP+IgE+ Bcell#326


title: IL-13KO NP+IgE+ Bcell#324


title: IL-13KO NP+IgE+ Bcell#323


title: IL-13KO NP+IgE+ Bcell#325


title: IL-13KO NP+IgE+ Bcell#320


title: IL-13KO NP+IgE+ Bcell#321


title: PT02_TP_108


title: PT02_TP_107


title: MEF_ko _ni vs. MEF_wt_ni_1_2

description: polarity(-)


title: IL-13KO NP+IgE+ Bcell#319


title: PT02_TP_105


title: PT02_TP_106


title: IL-13KO NP+IgE+ Bcell#322


title: PT02_TP_109


title: MEF_wt_ni vs. MEF_ko _ni_1_1

description: polarity(+)


title: IL-13KO NP+IgE+ Bcell#318


title: MEF_ko _ni vs. MEF_ko _E.f.16h

description: polarity(+)

source_name: MEF_ko _E.f.16h


title: IL-13KO NP+IgE+ Bcell#316


title: MEF_ko _E.f.16h vs. MEF_ko _ni

description: polarity(-)


title: PT02_TP_104


title: MEF_ko _ni vs. MEF_ko _E.f.4h

description: polarity(+)

source_name: MEF_ko _E.f.4h


title: MEF_wt_E.f.16h vs. MEF_wt_ni

description: polarity(-)


title: MEF_ko _E.f.4h vs. MEF_ko _ni

description: polarity(-)


title: MEF_wt_E.f.4h vs. MEF_wt_ni

description: polarity(-)


title: IL-13KO NP+IgE+ Bcell#315


title: PT02_TP_103


title: IL-13KO NP+IgE+ Bcell#317


title: IL-13KO NP+IgE+ Bcell#312


title: IL-13KO NP+IgE+ Bcell#313


title: IL-13KO NP+IgE+ Bcell#311


title: MEF_wt_ni vs. MEF_wt_E.f.16h

description: polarity(+)


title: adjacent tenocyte [B1]

value: A mixed background of C57BL/6 and B6.129 (ICR)

value: adjacent tenocyte


title: PT02_TP_102


title: IL-13KO NP+IgE+ Bcell#314


title: IL-13KO NP+IgE+ Bcell#310


title: IL-13KO NP+IgE+ Bcell#308


title: IL-13KO NP+IgE+ Bcell#309


title: MEF_ko _T.g.16h vs. MEF_ko _ni

description: polarity(-)

source_name: MEF_ko _T.g.16h


title: MEF_wt_ni vs. MEF_wt_E.f.4h

description: polarity(+)


title: IL-13KO NP+IgE+ Bcell#307


title: IL-13KO NP+IgE+ Bcell#306


title: PT02_TP_101


title: remote chondrocyte [C1]

value: remote chondrocyte


title: MEF_ko _ni vs. MEF_ko _T.g.16h

description: polarity(+)


title: IL-13KO NP+IgE+ Bcell#305


title: PT02_TP_099

value: para-tumor


title: IL-13KO NP+IgE+ Bcell#304


title: PT02_TT_096

value: tumor


title: PT02_TP_098


title: IL-13KO NP+IgE+ Bcell#301


title: IL-13KO NP+IgE+ Bcell#303


title: MEF_ko _ni vs. MEF_ko _T.g.4h

description: polarity(+)

source_name: MEF_ko _T.g.4h


title: IL-13KO NP+IgE+ Bcell#302


title: IL-13KO NP+IgE+ Bcell#297


title: IL-13KO NP+IgE+ Bcell#298


title: IL-13KO NP+IgE+ Bcell#299


title: PT02_TT_095


title: IL-13KO NP+IgE+ Bcell#296


title: IL-13KO NP+IgE+ Bcell#294


title: IL-13KO NP+IgE+ Bcell#295


title: PT02_TT_094


title: IL-13KO NP+IgE+ Bcell#293


title: IL-13KO NP+IgE+ Bcell#292


title: MEF_wt_T.g.16h vs. MEF_wt_ni

description: polarity(-)


title: MEF_wt_ni vs. MEF_wt_T.g.4h

description: polarity(+)


title: PT02_TP_100


title: PT02_TP_097


title: BALBc p18null BRCA1het 855 XIONG

description:
Agilent-273
mRNA isolated from flash frozen bulk tumors.

source_name: mammary tumor

value: Balbc

value: mammary tumor

source_name: Normal reference

tag: sample type

value: reference

value: normal


title: IL-13KO NP+IgE+ Bcell#300


title: BALBc p18null BRCA1het 384 XIONG

description:
Agilent-110
mRNA isolated from flash frozen bulk tumors.


title: PT02_TT_093


title: IL-13KO NP+IgE+ Bcell#291


title: PT02_TT_092


title: IL-13KO NP+IgE+ Bcell#289


title: IL-13KO NP+IgE+ Bcell#287


title: IL-13KO NP+IgE+ Bcell#288


title: PT02_TT_091


title: PT02_TT_090


title: IL-13KO NP+IgE+ Bcell#284


title: IL-13KO NP+IgE+ Bcell#285


title: IL-13KO NP+IgE+ Bcell#283


title: BALBc p18null BRCA1het 853-8-2 XIONG biorep

description:
Agilent-129
mRNA isolated from flash frozen bulk tumors.


title: PT02_TT_089


title: IL-13KO NP+IgE+ Bcell#281


title: IL-13KO NP+IgE+ Bcell#282


title: PT01_TT_088


title: IL-13KO NP+IgE+ Bcell#290


title: PT01_TT_087


title: IL-13KO NP+IgE+ Bcell#280


title: IL-13KO NP+IgE+ Bcell#279


title: BALBc p18null BRCA1het 348 XIONG

description:
Agilent-127
mRNA isolated from flash frozen bulk tumors.


title: BALBc p18null BRCA1het 347 XIONG

description:
Agilent-1896
mRNA isolated from flash frozen bulk tumors.


title: BALBc p18null BRCA1het 349 XIONG

description:
Agilent-126
mRNA isolated from flash frozen bulk tumors.


title: IL-13KO NP+IgE+ Bcell#278


title: IL-13KO NP+IgE+ Bcell#286


title: BALBc p18null BRCA1het 326 XIONG

description:
Agilent-1897
mRNA isolated from flash frozen bulk tumors.


title: BALBc p18null BRCA1het 350 XIONG

description:
Agilent-125
mRNA isolated from flash frozen bulk tumors.


title: PT01_TT_086


title: IL-13KO NP+IgE+ Bcell#277


title: IL-13KO NP+IgE+ Bcell#276


title: IL-13KO NP+IgE+ Bcell#275


title: BALBc p18null 854 XIONG

description:
Agilent-272
mRNA isolated from flash frozen bulk tumors.


title: PT01_TT_085


title: IL-13KO NP+IgE+ Bcell#274


title: PT01_TT_084


title: IL-13KO NP+IgE+ Bcell#273


title: BALBc p18null 474 XIONG

description:
Agilent-4858-2
mRNA isolated from flash frozen bulk tumors.


title: IL-13KO NP+IgE+ Bcell#272


title: MEF_wt_ni vs. MEF_wt_T.g.16h

description: polarity(+)

value: wildtype

value: non infected

value: Toxoplasma gondii


title: PT01_TT_083

value: Liver


title: BALBc p18null 426 XIONG

description:
Agilent-4855
mRNA isolated from flash frozen bulk tumors.


title: IL-13KO NP+IgE+ Bcell#271

value: spleen

value: 8 weeks


title: IL-13KO NP+IgE+ Bcell#269

value: IgE repoter (Verigem)


title: PT01_TT_082


title: IL-13KO NP+IgE+ Bcell#270


title: IL-13KO NP+IgE+ Bcell#268


title: PT01_TT_080


title: IL-13KO NP+IgE+ Bcell#266


title: IL-13KO NP+IgE+ Bcell#264


title: PT01_TT_079


title: BALBc p18null 426-5.851 XIONG

description:
Agilent-615
mRNA isolated from flash frozen bulk tumors.


title: IL-13KO NP+IgE+ Bcell#263


title: IL-13KO NP+IgE+ Bcell#267


title: BALBc p18null 205 XIONG

description:
Agilent-4843
mRNA isolated from flash frozen bulk tumors.


title: PT01_TT_078


title: IL-13KO NP+IgE+ Bcell#261


title: IL-13KO NP+IgE+ Bcell#260


title: MEF_wt_T.g.4h vs. MEF_wt_ni

description: polarity(-)

value: mouse embryonic fibroblast cells


title: BALBc p18het 181 XIONG

description:
Agilent-1898
mRNA isolated from flash frozen bulk tumors.


title: BALBc p18null 411 bRep XIONG

description:
Agilent-128
mRNA isolated from flash frozen bulk tumors.


title: IL-13KO NP+IgE+ Bcell#259


title: MEF_ko _T.g.4h vs. MEF_ko _ni

description: polarity(-)

value: cFos knockout


title: IL-13KO NP+IgE+ Bcell#258


title: PT01_TT_081


title: BALBc p18null 200 XIONG

description:
Agilent-4857
mRNA isolated from flash frozen bulk tumors.


title: IL-13KO NP+IgE+ Bcell#257


title: IL-13KO NP+IgE+ Bcell#256


title: IL-13KO NP+IgE+ Bcell#265


title: IL-13KO NP+IgE+ Bcell#255


title: BALBc p18null 250 XIONG

description:
Agilent-1899
mRNA isolated from flash frozen bulk tumors.


title: IL-13KO NP+IgE+ Bcell#262


title: PT01_TT_075


title: Hacat_SM_HiC

data_processing: Analysis of chromosomal translocations by in situ Hi-C: The hiC-data was analyzed using Juicer applying the default setting.

source_name: SM-resistant HaCaT cell line

extract_protocol: Genome wide probability of spatial proximity of chromosomal segments was done by means of in situ Hi-C following the protocol developed by Rao and colleagues using 1mio cells of HaCaT and HaCaT/SM, respectively.

tag: exposure (yes/no)

value: yes

tag: cell line

value: human keratinocyte cell line


title: IL-13KO NP+IgE+ Bcell#254


title: PT01_TT_077

tag: disease state


title: IL-13KO NP+IgE+ Bcell#252


title: PT01_TT_076

tag: patient id


title: PT01_TT_073


title: IL-13KO NP+IgE+ Bcell#253


title: EA1096_03

city: Bunkyo-ku

first: Takuma

last: Nakatsuka

department: Gastroenterology

institute: The University of Tokyo

description: Gene expression data from G9aKO mouse non-tumorous liver

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using GeneChip 3’IVT Express Kit User Manual.

data_processing: The data were analyzed using MAS5 Statistical Algorithm according to Affymetrix default analysis settings.

label: biotin

source_name: Alb-Cre; G9aflox/flox

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: The mice were maintained on a regular chow diet and autoclaved water provided ad libitum in a temperature controlled environment with 12 h light and dark cycles.

extract_protocol: Total RNA was extracted from mouse liver tissue using NucleoSpin® RNAII (Takara).

treatment_protocol: WT and G9aKO mice were injected with DEN in combination with 22 weekly injections of CCl4

value: liver

value: non-tumorous


title: EA1096_04


title: IL-13KO NP+IgE+ Bcell#251


title: EA1096_02

description: Gene expression data from WT mouse non-tumorous liver

source_name: Alb-Cre; G9a+/+

value: WT


title: IL-13KO NP+IgE+ Bcell#250


title: PT01_TT_072

source_name: TT

value: tumor


title: IL-13KO NP+IgE+ Bcell#249


title: IL-13KO NP+IgE+ Bcell#248


title: IL-13KO NP+IgE+ Bcell#247


title: IL-13KO NP+IgE+ Bcell#246


title: bulk_P3_EM

city: Stockholm

first: Marcus

last: Buggert

address: C2:94; Karolinska Universitetssjukhuset Huddinge

department: Microbiology

institute: Karolinska Institutet

data_processing:
Sequencing reads were aligned to the hg38 reference genome using STAR 2.5.2a
Data was normalized using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated text file include normalized read counts for each sample

source_name: Donor 3, Effector memory CD8+ T cell

growth_protocol: Cells were thawed and rested overnight at 37C in RPMI + 10% FBS + 1% L-glut + 1% Pen/Strep media

value: Effector memory CD8+ T cell


title: bulk_P3_CM

source_name: Donor 3, Central memory CD8+ T cell

value: Central memory CD8+ T cell


title: PT01_TT_070


title: bulk_P3_EMRA

source_name: Donor 3, Effector (RA+) CD8+ T cell

value: Effector (RA+) CD8+ T cell


title: IL-13KO NP+IgE+ Bcell#244


title: Hacat_H_HiC

source_name: HaCaT cell line

value: no


title: PT01_TT_069


title: IL-13KO NP+IgE+ Bcell#243


title: bulk_P3_Naive

source_name: Donor 3, Naïve CD8+ T cell

value: Naive CD8+ T cell


title: bulk_P2_EMRA

source_name: Donor 2, Effector (RA+) CD8+ T cell


title: IL-13KO NP+IgE+ Bcell#242


title: IL-13KO NP+IgE+ Bcell#240


title: PT01_TT_068

value: Liver


title: PT01_TT_067


title: IL-13KO NP+IgE+ Bcell#241

value: spleen


title: bulk_P2_EM

source_name: Donor 2, Effector memory CD8+ T cell


title: IL-13KO NP+IgE+ Bcell#239

value: 8 weeks


title: bulk_P2_CM

source_name: Donor 2, Central memory CD8+ T cell


title: PT01_TT_071


title: IL-13KO NP+IgE+ Bcell#237

value: IgE repoter (Verigem)


title: IL-13KO NP+IgE+ Bcell#238


title: IL-13KO NP+IgE+ Bcell#236


title: IL-13KO NP+IgE+ Bcell#235


title: PT01_TT_066


title: bulk_P2_Naive

source_name: Donor 2, Naïve CD8+ T cell


title: PT01_TT_064


title: bulk_P1_EMRA

source_name: Donor 1, Effector (RA+) CD8+ T cell


title: PT01_TT_065


title: IL-13KO NP+IgE+ Bcell#233


title: bulk_P1_CM

source_name: Donor 1, Central memory CD8+ T cell


title: IL-13KO NP+IgE+ Bcell#232


title: PT01_TT_063


title: IL-13KO NP+IgE+ Bcell#231


title: IL-13KO NP+IgE+ Bcell#230


title: PT01_TT_062


title: bulk_P1_EM

source_name: Donor 1, Effector memory CD8+ T cell


title: IL-13KO NP+IgE+ Bcell#228


title: IL-13KO NP+IgE+ Bcell#245


title: PT01_TT_061


title: IL-13KO NP+IgE+ Bcell#227


title: bulk_P1_Naive

source_name: Donor 1, Naïve CD8+ T cell


title: MB231-KO2+MK rep3

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

data_processing:
Sequenced data was processed based on the RNAseq pipeline implemented in Pipeliner (Federico et al., PMID 31316552).
In particular, sequencing reads were checked for quality with FastQC, were trimmed with TrimGalore, then aligned to the reference genome hg38 with HISAT2, and quantified with featureCounts.
After alignment, mapping quality was checked with RSeQC, and a comprehensive summary report of all samples was generated with MultiQC.
Genome_build: hg38
Supplementary_files_format_and_content: count_matrix.txt

growth_protocol: Cells were maintained in DMEM with 4.5 g/L glucose and L-glutamine and 10% FBS at 37°C and 5% CO2.

extract_protocol:
Total RNA was harvested from cultured cells using Qiagen RNeasy Plus Mini Kit according to the manufacturer’s instructions.
Libraries were prepared using Kapa RNA HyperPrep Kit with RiboErase.

treatment_protocol: 3 replicates each of MB231-GPS2KO1 and KO2 were treated with 10uM MK2206 for 4h prior to sample collection.

value: MDA-MB-231 breast cancer cell line

tag: genotype (modification)

value: GPS2 knockout, sgRNA set 2

tag: treatment


title: PT01_TT_060


title: MB231-KO2+MK rep2

value: treated with 10uM MK2206 for 4h prior to sample collection


title: IL-13KO NP+IgE+ Bcell#225

tag: strain


title: IL-13KO NP+IgE+ Bcell#224

tag: genotype


title: IL-13KO NP+IgE+ Bcell#223


title: MB231-KO2+MK rep1


title: IL-13KO NP+IgE+ Bcell#222


title: PT01_TT_058


title: PT01_TT_059


title: IL-13KO NP+IgE+ Bcell#221


title: IL-13KO NP+IgE+ Bcell#220


title: IL-13KO NP+IgE+ Bcell#229


title: PT01_TT_057


title: PT01_TT_056


title: MB231-KO1+MK rep1

value: GPS2 knockout, sgRNA set 1


title: MB231-KO1+MK rep2


title: IL-13KO NP+IgE+ Bcell#217


title: IL-13KO NP+IgE+ Bcell#218


title: PT01_TT_055


title: IL-13KO NP+IgE+ Bcell#219


title: MB231-myrAKT rep3

value: myristoylated AKT

value: untreated


title: IL-13KO NP+IgE+ Bcell#226


title: IL-13KO NP+IgE+ Bcell#214


title: IL-13KO NP+IgE+ Bcell#216


title: PT01_TT_054


title: IL-13KO NP+IgE+ Bcell#215


title: EA1096_01

value: liver

value: non-tumorous

value: WT


title: MB231-myrAKT rep2


title: MB231-myrAKT rep1


title: IL-13KO NP+IgE+ Bcell#210


title: MB231-KO1+MK rep3


title: IL-13KO NP+IgE+ Bcell#212


title: PT01_TT_053

value: tumor


title: MB231-KO2 rep3


title: IL-13KO NP+IgE+ Bcell#209


title: PT01_TT_052


title: IL-13KO NP+IgE+ Bcell#211


title: IL-13KO NP+IgE+ Bcell#208


title: PT01_TT_051


title: IL-13KO NP+IgE+ Bcell#207


title: PT01_TT_050


title: IL-13KO NP+IgE+ Bcell#206


title: PT01_TT_049


title: IL-13KO NP+IgE+ Bcell#205


title: IL-13KO NP+IgE+ Bcell#204


title: MB231-KO1 rep3


title: MB231-KO2 rep1


title: IL-13KO NP+IgE+ Bcell#203


title: IL-13KO NP+IgE+ Bcell#202


title: MB231-KO1 rep2


title: IL-13KO NP+IgE+ Bcell#213


title: IL-13KO NP+IgE+ Bcell#200


title: IL-13KO NP+IgE+ Bcell#201


title: IL-13KO NP+IgE+ Bcell#199


title: PT01_TT_047


title: IL-13KO NP+IgE+ Bcell#198


title: PT01_TT_046


title: IL-13KO NP+IgE+ Bcell#197


title: IL-13KO NP+IgE+ Bcell#195


title: IL-13KO NP+IgE+ Bcell#196


title: MB231-WT rep2


title: MB231-KO2 rep2


title: PT01_TT_045


title: IL-13KO NP+IgE+ Bcell#194


title: PT01_TT_048


title: IL-13KO NP+IgE+ Bcell#193


title: MB231-WT rep1


title: IL-13KO NP+IgE+ Bcell#192


title: PT01_TT_043


title: IL-13KO NP+IgE+ Bcell#190


title: PT01_TT_044


title: IL-13KO NP+IgE+ Bcell#191


title: AB8204

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

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

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

value: Bone marrow aspiration

value: Plasma cells

tag: selection marker

value: Baseline

tag: replicate id

value: NDMM


title: AB8205

tag: cell type


title: IL-13KO NP+IgE+ Bcell#188

tag: tissue

value: spleen

tag: age

value: 8 weeks


title: PT01_TT_041

value: Liver


title: MB231-KO1 rep1

value: MDA-MB-231 breast cancer cell line


title: IL-13KO NP+IgE+ Bcell#186

value: IgE repoter (Verigem)


title: IL-13KO NP+IgE+ Bcell#187


title: AB8203

tag: time point


title: IL-13KO NP+IgE+ Bcell#234


title: MB231-WT rep3


title: PT01_TT_040


title: AB8202

value: Cycle 4

tag: treatment (1)

value: DARA-KRD

value: PRMM


title: PT01_TT_039


title: AB8201

tag: sample type


title: IL-13KO NP+IgE+ Bcell#185


title: PT01_TT_038


title: AB8200

value: Cycle 10


title: PT01_TT_042


title: IL-13KO NP+IgE+ Bcell#184


title: IL-13KO NP+IgE+ Bcell#180


title: PT01_TT_037


title: IL-13KO NP+IgE+ Bcell#181


title: IL-13KO NP+IgE+ Bcell#189


title: PT01_TT_036


title: IL-13KO NP+IgE+ Bcell#178


title: IL-13KO NP+IgE+ Bcell#177


title: AB8199


title: AB8198


title: IL-13KO NP+IgE+ Bcell#176


title: IL-13KO NP+IgE+ Bcell#175


title: PT01_TT_074


title: PT01_TT_035


title: PT01_TT_034


title: IL-13KO NP+IgE+ Bcell#173


title: IL-13KO NP+IgE+ Bcell#183


title: AB8117


title: AB8116


title: IL-13KO NP+IgE+ Bcell#182


title: PT01_TT_033


title: IL-13KO NP+IgE+ Bcell#171


title: AB8115


title: IL-13KO NP+IgE+ Bcell#172


title: PT01_TT_032


title: IL-13KO NP+IgE+ Bcell#179


title: IL-13KO NP+IgE+ Bcell#167


title: IL-13KO NP+IgE+ Bcell#169


title: IL-13KO NP+IgE+ Bcell#168


title: IL-13KO NP+IgE+ Bcell#165


title: IL-13KO NP+IgE+ Bcell#174


title: IL-13KO NP+IgE+ Bcell#166


title: PT01_TP_030

source_name: TP

value: para-tumor


title: IL-13KO NP+IgE+ Bcell#164


title: AB7740


title: AB7739


title: PT01_TT_031


title: PT01_TP_029


title: AB8114


title: IL-13KO NP+IgE+ Bcell#159


title: IL-13KO NP+IgE+ Bcell#160


title: AB7737


title: AB7738


title: IL-13KO NP+IgE+ Bcell#163


title: IL-13KO NP+IgE+ Bcell#162


title: PT01_TP_028


title: AB7736

tag: cohort

value: Refractory


title: IL-13KO NP+IgE+ Bcell#158


title: PT01_TP_026


title: IL-13KO NP+IgE+ Bcell#170


title: IL-13KO NP+IgE+ Bcell#157


title: AB7735


title: IL-13KO NP+IgE+ Bcell#156


title: PT01_TP_027


title: IL-13KO NP+IgE+ Bcell#161


title: PT01_TP_025


title: IL-13KO NP+IgE+ Bcell#154


title: IL-13KO NP+IgE+ Bcell#155


title: IL-13KO NP+IgE+ Bcell#153


title: IL-13KO NP+IgE+ Bcell#152


title: IL-13KO NP+IgE+ Bcell#151


title: IL-13KO NP+IgE+ Bcell#149


title: PT01_TP_023


title: IL-13KO NP+IgE+ Bcell#147


title: PT01_TP_022


title: PT01_TP_021


title: AB7733


title: IL-13KO NP+IgE+ Bcell#148


title: AB7734


title: IL-13KO NP+IgE+ Bcell#145


title: PT01_TP_020


title: AB7731


title: AB7730


title: IL-13KO NP+IgE+ Bcell#144


title: PT01_TP_019


title: IL-13KO NP+IgE+ Bcell#142


title: PT01_TP_024


title: IL-13KO NP+IgE+ Bcell#150


title: AB7483


title: IL-13KO NP+IgE+ Bcell#141


title: IL-13KO NP+IgE+ Bcell#143


title: AB7732


title: PT01_TP_017


title: IL-13KO NP+IgE+ Bcell#140


title: IL-13KO NP+IgE+ Bcell#146


title: IL-13KO NP+IgE+ Bcell#139


title: AB7481


title: IL-13KO NP+IgE+ Bcell#137


title: AB7480


title: IL-13KO NP+IgE+ Bcell#136


title: IL-13KO NP+IgE+ Bcell#138


title: AB7482


title: IL-13KO NP+IgE+ Bcell#135


title: IL-13KO NP+IgE+ Bcell#132


title: AB7299


title: IL-13KO NP+IgE+ Bcell#134


title: PT01_TP_018


title: PT01_TP_014


title: IL-13KO NP+IgE+ Bcell#133


title: PT01_TP_016


title: PT01_TP_013


title: AB7479


title: AB7729


title: AB7298


title: IL-13KO NP+IgE+ Bcell#128


title: PT01_TP_015


title: PT01_TP_011


title: IL-13KO NP+IgE+ Bcell#129


title: AB7297


title: IL-13KO NP+IgE+ Bcell#131


title: PT01_TP_012


title: AB7296


title: IL-13KO NP+IgE+ Bcell#126


title: IL-13KO NP+IgE+ Bcell#125


title: AB7295


title: PT01_TP_010


title: IL-13KO NP+IgE+ Bcell#120


title: IL-13KO NP+IgE+ Bcell#122


title: IL-13KO NP+IgE+ Bcell#121


title: IL-13KO NP+IgE+ Bcell#124


title: PT01_TP_009


title: IL-13KO NP+IgE+ Bcell#123


title: PT01_TP_008


title: AB7293

value: Relapse


title: IL-13KO NP+IgE+ Bcell#119


title: AB7294

value: Bone marrow


title: IL-13KO NP+IgE+ Bcell#130


title: PT01_TT_006

value: tumor


title: IL-13KO NP+IgE+ Bcell#117


title: IL-13KO NP+IgE+ Bcell#127


title: IL-13KO NP+IgE+ Bcell#116


title: PT01_TT_005


title: AB7291

value: Bone marrow aspiration

value: Plasma cells


title: IL-13KO NP+IgE+ Bcell#115


title: IL-13KO NP+IgE+ Bcell#114


title: AB7290


title: AB7292

value: Baseline


title: PT01_TT_004


title: IL-13KO NP+IgE+ Bcell#113

value: spleen


title: PT01_TT_007


title: PT01_TT_003


title: IL-13KO NP+IgE+ Bcell#112

value: 8 weeks


title: IL-13KO NP+IgE+ Bcell#118


title: AB7288


title: PT01_TT_002

value: Liver


title: AB7287


title: IL-13KO NP+IgE+ Bcell#108


title: PT01_TT_001


title: IL-13KO NP+IgE+ Bcell#110


title: IL-13KO NP+IgE+ Bcell#109


title: AB7286


title: IL-13KO NP+IgE+ Bcell#107


title: HC-5

city: Wuhu

first: Xueqin

address: 2 Western Zheshan Road

institute: wannan medical college

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
Total clean reads were mapped to the human reference genome using the bwa aligner.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org), piRBase(http://www.regulatoryrna.org/database/piRNA/index.html) and MINTbase(https://cm.jefferson.edu/MINTbase/) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes RPMs for each Sample

source_name: serum

extract_protocol:
Exosome was isolated from serum using the RiboTM Exosome Isolation Reagent (Ribobio),and Exosomal RNA was extracted by the MagZol (Magen) according to the manufacturer's protocol. RNA purity was assessed using the K5500.RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, USA) and each sample had the RINe above 7.0.
RNAs were ligated with 3’RNA adapter, and followed by 5’adapter ligation. Subsequently, the adapter-ligated RNAs were subjected to RT-PCR and amplified with a low-cycle. Then the PCR products were size selected by PAGE gel according to instructions of NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Illumina, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and diluted to 10 pM for cluster generation in situ on the HiSeq2500 single-end flow cell followed by sequencing (1×50 bp) on HiSeq 2500.

value: control

value: serum

value: serum exosomes


title: IL-13KO NP+IgE+ Bcell#105

value: IgE repoter (Verigem)


title: AB7285

value: PRMM


title: HC-4


title: IL-13KO NP+IgE+ Bcell#104


title: AB7289

value: Cycle 10

value: DARA-KRD


title: IL-13KO NP+IgE+ Bcell#102


title: AB7284

value: Refractory


title: IL-13KO NP+IgE+ Bcell#100


title: IL-13KO NP+IgE+ Bcell#103


title: HC-2


title: IL-13KO NP+IgE+ Bcell#101


title: HC-3


title: IL-13KO NP+IgE+ Bcell#111


title: AB7108

value: Cycle 4


title: IL-13KO NP+IgE+ Bcell#106


title: IL-13KO NP+IgE+ Bcell#99


title: AB7107

value: Bone marrow


title: HC-1


title: IL-13KO NP+IgE+ Bcell#96


title: IL-13KO NP+IgE+ Bcell#97


title: AB7106

value: Relapse


title: FM-5

value: fulminant myocarditis (FM)


title: IL-13KO NP+IgE+ Bcell#94


title: IL-13KO NP+IgE+ Bcell#98


title: IL-13KO NP+IgE+ Bcell#95


title: FM-4


title: AB7105

value: Bone marrow aspiration

value: Plasma cells


title: IL-13KO NP+IgE+ Bcell#92

value: spleen


title: IL-13KO NP+IgE+ Bcell#91

value: 8 weeks


title: IL-13KO NP+IgE+ Bcell#90


title: FM-2


title: IL-13KO NP+IgE+ Bcell#88


title: FM-3


title: AB7104


title: FM-1


title: Hoxblinc-KRAB-RNA-seq-2

data_processing:
Standard Illumina software base-calling and quality-control filtering were applied Sequences (Paired end).
Paired end RNA-seq reads were aligned to the mm9 genome assembly using Tophat, and ATAC-seq, ChIRP-seq, ChIP-seq and 4C-seq reads were aligned to the mm9 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1).
Genome coverage tracks were created using deepTools version 3.0.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples and peaks for ATAC-seq, ChIP-seq and 4C-seq.

source_name: OCI-AML3 leukemia cells

tag: cell line

value: Human-derived acute myeloid leukemia cell line

tag: genotype/variation

value: Hoxblinc-KRAB


title: AB7103

tag: disease state


title: IL-13KO NP+IgE+ Bcell#85


title: IL-13KO NP+IgE+ Bcell#89


title: IL-13KO NP+IgE+ Bcell#93


title: IL-13KO NP+IgE+ Bcell#84


title: AB7101


title: IL-13KO NP+IgE+ Bcell#87


title: AB7059


title: Hoxblinc-KRAB-RNA-seq-1


title: AB7102


title: IL-13KO NP+IgE+ Bcell#86


title: IL-13KO NP+IgE+ Bcell#83


title: WT-OCIAML3-RNA-seq-2

value: WT


title: IL-13KO NP+IgE+ Bcell#82


title: AB7058


title: IL-13KO NP+IgE+ Bcell#81


title: IL-13KO NP+IgE+ Bcell#80


title: WT-OCIAML3-RNA-seq-1


title: IL-13KO NP+IgE+ Bcell#78


title: AB7056


title: IL-13KO NP+IgE+ Bcell#77


title: EORG-E rep 3 (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-3
CAPW7ANXX_7#51607_CGATGT

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

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

tag: internal id


title: AB7055

value: PRMM


title: IL-13KO NP+IgE+ Bcell#75

tag: strain

value: IgE repoter (Verigem)


title: IL-13KO NP+IgE+ Bcell#76

tag: genotype