title: SS2_20_121:B22

first: Louis

last: Faure

address: 321 E 61st Street

data_processing:
The samples were analyzed by first demultiplexing the fastq files using deindexer (http://github.com/ws6/deindexer) using the nextera index adapters and the 384 well layout.
Individual fastq files were then mapped to the relevant genome assembly using the STAR aligner (Dobin et al. Bioinformatics 2013) using 2-pass alignment to have improved performance of de novo splice junction reads, filtered for only uniquely mapping reads that are saved in the BAM  file.
The expression values were computed per gene as described in Ramsköld et al. (2009 PLoS Comp Biol), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo (Storvall et al. 2013 PLoS ONE).
count matrix was processed using scanpy and scFates python packages. This includes QC filtering, normalization, clustering of cells, projection on low embedding for visualization, differential gene expression.
BAM files from each plate were used as input to BRIE2 for counting the isoform specific reads in each splicing event. Variable splicing detection was subsequently performed using the treatment as cell feature.
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts.csv contains compiled unfiltered count data from all plates, plate id is mentioned in cell name. adata.h5ad is the anndata resulting from initial processing pipeline. brie_quant_cell.h5ad is the anndata resulting from BRIE2 pipeline.

source_name: Adrenal Gland - E13.5 - PBS

extract_protocol:
Tissue was added to 500 uL of 0.05% Trypsin/ 0.02% EDTA (Sigma, 59417-C) and incubated at 37° C for 10 min. The tissue was triturated slowly with a P-200 pipette until complete dissociation. Trypsin was deactivated by adding 500 uL of PBS containing 10% FBS.  The cells were pelleted at 500 g +4C for 5 min. The cells were washed 2x with PBS + 10% FBS followed by centrifugation. The non-single cell clusters of cells were removed by filtering through 40 μm-pore size cell strainer. Fluorescent cells were sorted in single cells mode into 384 well plates prefilled with lysis buffer according to previously published protocol (21) using a BD FACSAria III Cell Sorter. One full 384-well plate was sorted and sequenced per organ and per treatment.
RNA libraries were prepared according to Smart-seq2 protocol.

treatment_protocol: Prenatally treated with 5HTP  (40 mg/kg) or vehicle (PBS) for control at E11.5 and E12.5

tag: strain

value: WNT-1 Cre; Rosa26-Tomato

tag: developmental stage

value: Adrenal Gland

value: PBS


title: SS2_20_125:C14

status: Public on Jul 28 2021

type: SRA

city: New York

state: NY

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

source_name: Adrenal Gland - E13.5 - 5HTP

tag: tissue

tag: treatment


title: SS2_20_127:E16

source_name: Zuckerkandl organ - E13.5 - PBS

value: Zuckerkandl organ


title: SS2_20_127:O8


title: SS2_20_123:I24

source_name: Zuckerkandl organ - E13.5 - 5HTP


title: SS2_20_121:G17


title: SS2_20_125:F24


title: SS2_20_127:F17


title: SS2_20_121:H1


title: SS2_20_125:J18


title: SS2_20_123:K10


title: SS2_20_125:E6


title: SS2_20_127:F16


title: SS2_20_125:M19


title: SS2_20_127:D2


title: SS2_20_121:H19


title: SS2_20_123:B14


title: SS2_20_125:K4


title: SS2_20_127:G14


title: SS2_20_121:G2


title: SS2_20_125:H20


title: SS2_20_127:I7


title: SS2_20_123:D17


title: SS2_20_127:L23


title: SS2_20_127:O20


title: SS2_20_125:F21


title: SS2_20_121:I22


title: SAMPLE 7_B74_DI_N

type: RNA

first: Yingjie

last: Zhu

address: 1275 York Avenue

hyb_protocol: The extracted material was sent to Helixio (Saint-Beauzire, France), where it was hybridized with gene arrays (Human SurePrint, Agilent Technologies France, Les Ullis, France)

scan_protocol: not provided

data_processing: Limma package was applied to process Agilent microarray data and identify differentially expressed genes between progressive tumors and tumors with pathological complete response. Background correction was performed on expression intensities before normalization by the parameter of “expnorm”. Median value was taken when a gene has multiple probes. Then, “cyclicloess” method, which applies loess normalization to all possible pairs of arrays, was used to normalize corrected intensities. The probes have been filtered for those close to background and without gene name.

molecule: total RNA

organism: Homo sapiens

source_name: breast

label_protocol: not provided

extract_protocol: Nucleic acids were extracted from frozen tumor tissue (pre-NAT samples) using AllPrep DNA/RNA mini kit (Qiagen France SAS, Courtaboeuf, France) according to the manufacturer’s protocol.

tag: age

tag: Stage

value: IIB

tag: tissue type

value: frozen tumor tissue


title: SS2_20_125:O19


title: SS2_20_125:C8


title: SS2_20_121:D19


title: SS2_20_127:H11


title: SS2_20_127:N5


title: SS2_20_125:P20


title: SS2_20_127:O24


title: SS2_20_125:I23


title: SS2_20_123:D7


title: SS2_20_125:A21


title: SS2_20_121:B11


title: SS2_20_123:D5


title: SS2_20_125:O16


title: SS2_20_127:N19


title: SS2_20_121:P12


title: SS2_20_127:H7


title: SS2_20_121:D13


title: SS2_20_125:E15


title: SS2_20_127:N24


title: SS2_20_125:N24


title: SS2_20_123:N22


title: SS2_20_123:B7


title: SS2_20_121:H24


title: SS2_20_121:K23


title: SS2_20_123:J1


title: SS2_20_121:B12


title: SS2_20_127:M16


title: SS2_20_123:B24


title: SS2_20_123:M23


title: SS2_20_121:A22


title: SS2_20_125:P7


title: SS2_20_127:B13


title: SS2_20_125:H3


title: SS2_20_127:K3


title: SS2_20_121:G15


title: SS2_20_121:L1


title: SS2_20_127:L16


title: SS2_20_121:E24


title: SS2_20_127:F23


title: SS2_20_127:P8


title: SS2_20_121:L20


title: SS2_20_125:M9


title: SS2_20_121:F17


title: SS2_20_123:A7


title: SS2_20_127:E4


title: SS2_20_123:C14


title: SS2_20_125:F19


title: SS2_20_127:P4


title: SS2_20_121:E17


title: SS2_20_127:O13


title: SS2_20_123:B8


title: SS2_20_127:N4


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title: SS2_20_127:C13


title: SS2_20_125:M1


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title: SS2_20_121:B19


title: SS2_20_127:N1


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title: SS2_20_125:H6


title: SS2_20_121:I9


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title: SS2_20_123:F14


title: SS2_20_121:M14


title: SS2_20_127:D22


title: SS2_20_125:M5


title: SS2_20_125:C5


title: SS2_20_123:A6


title: SS2_20_125:M4


title: SS2_20_127:A2


title: SS2_20_125:I12


title: SS2_20_127:P6


title: SS2_20_121:L19


title: SS2_20_127:B4


title: SS2_20_125:M10


title: SS2_20_123:G4


title: SS2_20_125:G4


title: SS2_20_123:E5


title: SS2_20_127:L11


title: SS2_20_121:A15


title: SS2_20_125:B21


title: SS2_20_123:O19


title: SS2_20_121:A10


title: SS2_20_127:G20


title: SS2_20_127:F14


title: SS2_20_125:B1


title: SS2_20_127:J15


title: SS2_20_127:H8


title: SS2_20_127:D10


title: SS2_20_121:N1


title: SS2_20_125:A1


title: SS2_20_127:M15


title: SS2_20_123:K18


title: SS2_20_125:O17


title: SS2_20_125:N8


title: SS2_20_123:L5


title: SS2_20_125:P22


title: SS2_20_125:L2


title: SS2_20_121:B16


title: SS2_20_127:B12


title: SS2_20_125:P23


title: SS2_20_127:F18


title: SS2_20_121:B5


title: SS2_20_125:I20


title: SS2_20_125:G18


title: SS2_20_123:L16


title: SS2_20_123:D14


title: SS2_20_127:F11


title: SS2_20_127:K15


title: SS2_20_127:L20


title: SS2_20_123:N12


title: SS2_20_123:K21


title: SS2_20_127:H1


title: SS2_20_125:C21


title: SS2_20_125:A16


title: SS2_20_125:F13


title: SS2_20_125:O8


title: SS2_20_123:I1


title: SS2_20_123:C10


title: SS2_20_121:N23


title: SS2_20_123:A14


title: SS2_20_125:K13


title: SS2_20_121:A23


title: SS2_20_125:M13


title: SS2_20_125:F16


title: SS2_20_127:J21


title: SS2_20_125:D14


title: SS2_20_121:K14


title: SS2_20_127:M2


title: SS2_20_125:L20


title: SS2_20_125:K6


title: SS2_20_123:E12


title: SS2_20_127:K1


title: SS2_20_121:C9


title: SS2_20_121:A1


title: SS2_20_127:F4


title: SS2_20_125:O7


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title: SS2_20_121:C2


title: SS2_20_123:G21


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title: SS2_20_123:G2


title: SS2_20_123:I15


title: SS2_20_127:A14


title: SS2_20_123:I5


title: SS2_20_125:G17


title: SS2_20_125:A8


title: SS2_20_127:K21


title: SS2_20_127:B8


title: SS2_20_127:M24


title: SS2_20_125:P10


title: SS2_20_125:I4


title: SS2_20_123:E7


title: SS2_20_123:G18


title: SS2_20_127:D16


title: SS2_20_125:J5


title: SS2_20_125:P14


title: SS2_20_125:O6


title: SS2_20_127:I6


title: SS2_20_127:G10


title: SS2_20_127:B20


title: SS2_20_123:O24


title: SS2_20_127:H4


title: SS2_20_125:D4


title: SS2_20_121:I10


title: SS2_20_127:G21


title: SS2_20_125:C1


title: SS2_20_121:N11


title: SS2_20_123:L11


title: SS2_20_125:D11


title: SS2_20_125:O14


title: SS2_20_123:H1


title: SS2_20_127:D20


title: SS2_20_121:B21


title: SS2_20_121:D12


title: SS2_20_121:N6


title: SS2_20_121:L22


title: SS2_20_127:C20


title: SS2_20_127:N20


title: SS2_20_125:E5


title: SS2_20_125:E18


title: SS2_20_127:L15


title: SS2_20_125:B24


title: SS2_20_125:I21


title: SS2_20_123:P9


title: SS2_20_127:P3


title: SS2_20_121:E18


title: SS2_20_125:O10


title: SS2_20_121:E4


title: SS2_20_125:M3


title: SS2_20_127:I19


title: SS2_20_123:G23


title: SS2_20_121:M11


title: SS2_20_123:M22


title: SS2_20_125:L3


title: SS2_20_127:N7


title: SS2_20_127:I4


title: SS2_20_121:K24


title: SS2_20_121:O13


title: SS2_20_123:G19


title: SS2_20_125:P6


title: SS2_20_121:H2


title: SS2_20_125:G13


title: SS2_20_121:P16


title: SS2_20_121:D5


title: SS2_20_127:J3


title: SS2_20_125:P18


title: SS2_20_121:H16


title: SS2_20_123:C6


title: SS2_20_121:D14


title: SS2_20_123:L12


title: SS2_20_123:M6


title: SS2_20_125:H18


title: SS2_20_123:O2


title: SS2_20_123:H24


title: SS2_20_125:B18


title: SS2_20_123:P19


title: SS2_20_125:N23


title: SS2_20_121:B13


title: SS2_20_125:B20


title: SS2_20_127:J6


title: SS2_20_121:M5


title: SS2_20_121:J15


title: SS2_20_125:N1


title: SS2_20_127:K7


title: SS2_20_123:J2


title: SS2_20_123:O15


title: SS2_20_123:F7


title: SS2_20_125:P19


title: SS2_20_123:E19


title: SS2_20_127:F10


title: SS2_20_125:O5


title: SS2_20_127:H21


title: SS2_20_125:H23


title: SS2_20_121:N10


title: SS2_20_121:I2


title: SS2_20_123:P7


title: SS2_20_125:M12


title: SS2_20_123:D15


title: SS2_20_127:P5


title: SS2_20_121:P11


title: SS2_20_125:O18


title: SS2_20_127:H15


title: SS2_20_127:M7


title: SS2_20_123:H17


title: SS2_20_127:E3


title: SS2_20_121:H15


title: SS2_20_123:J12


title: SS2_20_121:C17


title: SS2_20_127:M1


title: SS2_20_125:N7


title: SS2_20_125:O9


title: SS2_20_125:A4


title: SS2_20_127:I24


title: SS2_20_123:H14


title: SS2_20_121:M22


title: SS2_20_123:A4


title: SS2_20_123:I20


title: SS2_20_125:L19


title: SS2_20_125:D5


title: SS2_20_127:P11


title: SS2_20_123:D12


title: SS2_20_125:C4


title: SS2_20_123:N16


title: SS2_20_123:P20


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title: SS2_20_123:J21


title: SS2_20_121:I5


title: SS2_20_125:L17


title: SS2_20_123:A19


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title: SS2_20_125:C17


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title: SS2_20_127:A20


title: SS2_20_127:J13


title: SS2_20_123:E20


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title: SS2_20_121:O6


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title: SS2_20_127:K5


title: SS2_20_127:F2


title: SS2_20_127:L24


title: SS2_20_127:B10


title: SS2_20_121:M3


title: SS2_20_127:A6


title: SS2_20_127:G16


title: SS2_20_125:A13


title: SS2_20_125:O13


title: SS2_20_125:N14


title: SS2_20_123:A20


title: SS2_20_127:J7


title: SS2_20_125:C24


title: SS2_20_123:F20


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title: SS2_20_127:O15


title: SS2_20_121:H22


title: SS2_20_121:N24


title: SS2_20_125:H2


title: SS2_20_125:A7


title: SS2_20_125:N15


title: SS2_20_125:G20


title: SS2_20_121:H12


title: SS2_20_123:C21


title: SS2_20_123:B19


title: SS2_20_127:A3


title: SS2_20_125:N5


title: SS2_20_127:C4


title: SS2_20_127:D24


title: SS2_20_125:J17


title: SS2_20_121:B9


title: SS2_20_123:H11


title: SS2_20_123:B13


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title: SS2_20_121:I4


title: SS2_20_127:M11


title: SS2_20_125:D6


title: SS2_20_121:I3


title: SS2_20_127:B15


title: SS2_20_123:O14


title: SS2_20_123:A18


title: SS2_20_125:E11


title: SS2_20_123:H20


title: SS2_20_127:K8


title: SS2_20_127:I12


title: SS2_20_123:N20


title: SS2_20_121:A7


title: SS2_20_121:A9


title: SS2_20_125:K7


title: SS2_20_125:G2


title: SS2_20_123:M2


title: SS2_20_123:B22


title: SS2_20_127:D6


title: SS2_20_121:H21


title: SS2_20_127:J8


title: SS2_20_121:G7


title: SS2_20_127:E22


title: SS2_20_125:H22


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title: SS2_20_121:A13


title: SS2_20_127:A1


title: SS2_20_123:B2


title: SS2_20_121:H3


title: SS2_20_127:P12


title: SS2_20_125:N3


title: SS2_20_121:D21


title: SS2_20_127:C14


title: SS2_20_123:O4


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title: SS2_20_125:L22


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title: SS2_20_127:G24


title: SS2_20_127:J2


title: SS2_20_121:L3


title: SS2_20_125:D17


title: SS2_20_125:E19


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title: SS2_20_127:H14


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title: SS2_20_127:F13


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title: SS2_20_125:K3


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title: SS2_20_121:A16


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title: SS2_20_125:H5


title: SS2_20_125:H14


title: SS2_20_123:M18


title: SS2_20_121:C8


title: SS2_20_123:N6


title: SS2_20_123:E4


title: SS2_20_123:M4


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title: SS2_20_125:E13


title: SS2_20_121:M12


title: SS2_20_123:H2


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title: SS2_20_123:B4


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title: SS2_20_121:B3


title: SS2_20_123:M7


title: SS2_20_123:H15


title: SS2_20_123:E13


title: SS2_20_123:F24


title: SS2_20_121:B15


title: SS2_20_123:D6


title: SS2_20_125:E14


title: SS2_20_125:B4


title: SS2_20_125:F9


title: SS2_20_121:O7


title: SS2_20_127:F22


title: SS2_20_121:K10


title: SS2_20_127:B18


title: SS2_20_121:F22


title: SS2_20_125:P17


title: SS2_20_125:O4


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title: SS2_20_125:D15


title: SS2_20_123:K17


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title: SS2_20_121:G19


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title: SS2_20_123:F21


title: SS2_20_121:L7


title: SS2_20_121:K22


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title: SS2_20_127:H12


title: SS2_20_121:H23


title: SS2_20_121:L13


title: SS2_20_121:L16


title: SS2_20_123:C15


title: SS2_20_123:H6


title: SS2_20_127:C2


title: SS2_20_127:J4


title: SS2_20_123:M3


title: SS2_20_125:P9


title: SS2_20_123:J7


title: SS2_20_123:A22


title: SS2_20_125:M22


title: SS2_20_125:K10


title: SS2_20_127:G12


title: SS2_20_121:K4


title: SS2_20_125:E10


title: SS2_20_125:N16


title: SS2_20_121:A17


title: SS2_20_125:G11


title: SS2_20_125:F15


title: SS2_20_127:G23


title: SS2_20_121:P2


title: SS2_20_123:C2


title: SS2_20_121:N16


title: SS2_20_125:P16


title: SS2_20_127:O22


title: SS2_20_125:I3


title: SS2_20_127:H6


title: SS2_20_127:P21


title: SS2_20_127:F20


title: SS2_20_125:A17


title: SS2_20_121:K6


title: SS2_20_123:B12


title: SS2_20_121:I14


title: SS2_20_125:D2


title: SS2_20_127:K20


title: SS2_20_123:L1


title: SS2_20_121:H11


title: SS2_20_123:B10


title: SS2_20_125:I7


title: SS2_20_123:C18


title: SS2_20_127:I18


title: SS2_20_125:L7


title: SS2_20_127:N13


title: SS2_20_125:L18


title: SS2_20_121:G16


title: SS2_20_127:L12


title: SS2_20_121:F12


title: SS2_20_125:I15


title: SS2_20_123:A11


title: t54

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
Adapter trimming with cutadapt
Mapping with BWA against saura (Anolis carolinensis, Chrysemys picta, Alligator mississippiensis, Ophiophagus hannah) miRNA precursors from miRBase
Genome_build: mirBase 22
Supplementary_files_format_and_content: tabl delimited files contains counts for all samples

organism: Trachemys scripta

source_name: T2 = 36 h after surgery

extract_protocol:
Plasma was thawed on ice and centrifuges at 3000 x g for 5 min at 4°C. An aliquot of 100 mL per sample was transferred in a new tube and small RNA was extracted using miRNeasy Serum/Plasma kit (Qiagen, Cat. No 217184), in accordance with the manufacturer’s instruction.
Small RNA transcripts were converted into barcoded cDNA libraries. Library preparation was performed using the NEBNext Multiplex small RNA Library Prep Set (Cat No NEB#E7560)

value: plasma

tag: Sex

value: female


title: SS2_20_125:O12


title: t52

source_name: T0 = 24 h before surgery


title: t53

source_name: T1 = 2.5 h after surgery


title: SS2_20_121:A18


title: SS2_20_121:E13


title: t50


title: SS2_20_125:C11


title: SS2_20_121:M19


title: SS2_20_121:H17


title: t49


title: SS2_20_127:P19


title: t48


title: t47


title: SS2_20_125:A19


title: SS2_20_127:E1


title: t45


title: t46


title: t44


title: t43


title: t51


title: SS2_20_125:G16


title: t42


title: t40


title: t41


title: SS2_20_125:N11


title: SS2_20_121:H14


title: SS2_20_127:H22


title: t39


title: SS2_20_123:A5


title: SS2_20_121:E19


title: SS2_20_127:L1


title: SS2_20_121:F3


title: t36


title: SS2_20_125:C16


title: SS2_20_121:I19


title: SS2_20_123:F5


title: t38


title: t35


title: SS2_20_125:F7


title: SS2_20_121:H7


title: t33


title: SS2_20_125:F5


title: t37


title: t34


title: SS2_20_123:C12


title: SS2_20_125:K9


title: SS2_20_123:A21


title: SS2_20_125:L23


title: SS2_20_125:E22


title: R3

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

country: Belgium

institute: Ghent University

description: small RNA

data_processing:
Bases were called using the Real Time Analysis 2 software of the HiSeq 3000.
Quality checking was performed using FastQC (version 0.11.8).
Trimming was done using Trimmomatic (version 0.38) setting following parameters: ILLUMINACLIP:3:30:10, MAXINFO:23:1, SLIDINGWINDOW:5:20, MINLEN:17.
STAR (version 2.6.1d) was used for mapping with parameter settings for small RNA mapping: readFilesCommand zcat, outFilterMismatchNoverLmax 0.05, outFilterMatchNmin 16, outFilterScoreMinOverLread 0, outFilterMatchNminOverLread 0, alignIntronMax 1, outSAMmultNmax 1 and runRNGseed
* miRNA analysis: For differential expression analysis of miRNAs, a GTF file was downloaded from miRBase (version 21) with all known mature miRNas in rice 66. The following R packages were then used to create a count table with read counts: rtracklayer (version 1.44.4) to convert the GTF file into a Granges object 67, Rsamtools (version 2.0.3) to create a BamFileList object68 and GenomicAlignments (version 1.20.1) for the summarizeOverlaps function to create the count table 69. The following options were used for counting: mode=’Union’ and singleEnd=TRUE. The DESeq2 package (version 1.24) was used to detect significant differences across conditions using a false discovery rate (FDR) of 0.05 as a threshold (BH correction for multiple testing) 70. Control samples were set as reference samples for log fold change calculations. * siRNA analysis: Differential expression analysis was done by creating an annotation file with the annotated siRNA loci of the plantsmallrnagenes database as well as the Pln24NT database. The differential expression pipeline was as described previously for miRNAs except that the fdrtool package was used for local FDR adjustment.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: Count tables with raw counts.

organism: Oryza sativa Japonica Group

source_name: Uninfected tissue

growth_protocol: Oryza sativa L. cv ‘Nipponbare’ (GSOR-100, USDA) seeds were germinated for 7 days at 30 °C on paper cloths drenched with tap water. Seedlings were transferred into SAP substrate (sand-absorbent polymer) and grown at 26 °C under a 16 h/8 h light/dark regime

extract_protocol:
Root tips and galls were collected from control and inoculated plants respectively, three days post inoculation (3 dpi). Plant materials were immediately frozen in liquid nitrogen and stored at -80 °C. Three biological replicates of control and treated plants were made. Each biological replicate consisted of ca 9 plants. Frozen samples were ground and total RNA was extracted using the ZR Plant RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions. The bead beater step was performed using a speed of 4 m/s for 45 s. All centrifugal steps were performed at 16 000 x g.  For DNase treatment 1 µg of total RNA per sample was combined with 3.6 µL DNase I buffer + MgCl2 (B43, Thermo Fisher), 1 µL RiboLock RNase Inhibitor (EO0381, Thermo Fisher) and 1 µL DNAse I (EN0521, Thermo Fisher). Afterwards RNase-free water was added until a total volume of 36 µL was reached followed by incubation for 30 minutes at 37 °C. Finally, 4 µL 25 mM EDTA was added before incubating for 10 minutes at 65 °C.
The quality of total RNA of gall and control samples was verified with a RNA 6000 pico chip (Agilent technologies) and the concentration was measured with a Quant-it Ribogreen RNA assay (Life technologies). 350 ng of RNA was used with the Small RNA seq library prep for Illumina (Lexogen) with the use of a small RNA dual indexing kit (Lexogen). Library prep was performed according to manufacturer's instructions. Briefly, 3’ adapters were ligated and excess 3’ adapters were removed. 5’ adapters were then ligated, followed by cDNA synthesis of the ligated RNA. The cDNA was used for enrichment PCR (14 cycles) and purified with  AMPure XP purification (1:1.8) (Beckman Coulter). Adapter dimers were removed using a 8 % native PAGE gel (Life Technologies). The quality was checked with a High sensitivity DNA chip (Agilent technologies). Quantification of the libraries was done with a qPCR assay according to Illumina protocol to enable equimolar pooling of libraries. An additional purification step was performed on E-gel EX agarose gel (2 % agarose). Finally, sequencing was performed on a Hiseq 3000 using 5 % Phix spike-in (single end reads, 50 bp).

treatment_protocol: At two weeks old, ca 500 stage 2 juveniles of root-knot nematode (RKN) Meloidogyne graminicola were used for inoculation per set of three plants. Control plant were mock-inoculated with water. After 36 h, they were transferred to 50 % Hoagland solution in glass tubes to synchronize infection.

value: root

tag: plant age

value: 17 days

tag: replicate number

value: Replicate 3

tag: cultivar

value: Nipponbare


title: R2

description: small RNA

value: Replicate 2


title: R1

description: small RNA

value: Replicate 1


title: SS2_20_127:C17


title: t32


title: SS2_20_123:I14


title: t31


title: G3

description: small RNA

source_name: Infected tissue

value: gall


title: G2

description: small RNA


title: SS2_20_121:J3


title: G1

description: small RNA


title: SS2_20_123:K14


title: SS2_20_123:A13


title: SS2_20_123:N10


title: SS2_20_123:G11


title: SS2_20_121:J6


title: SS2_20_121:P20


title: microglia, female WT, mouse 10

city: 89 Beaumont ave

first: Dimitry

last: Krementsov

state: VT

address: 312C Rowell bldg, 106 Carrigan drive

department: BHSC

institute: University of Vermont

hyb_protocol: Mouse Clariom D arrays were incubated in the Affymetrix® GeneChip® Hybridization Oven 645 at 45° C / 60 RPM for 16-18 hours.

scan_protocol: GeneChips were scanned with the 7G Affymetrix® GeneChip® Scanner 3000

data_processing: Raw intensity CEL files were imported into Expression Console software (Affymetrix, USA), and CHP files were generated for gene level analysis. CHP files were imported into Transcriptome Analysis Console (TAC software v4.0.0.25 (Affymetrix, USA), and gene level expression analysis was performed using the default ANOVA settings

label: Biotin

source_name: microglia, female WT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA

extract_protocol: Total RNA was extracted using the RNAeasy micro kit, Qiagen

treatment_protocol: EAE was induced in mice using MOG35-55/CFA injection

tag: strain background

tag: genotype

value: wildtype

tag: tissue/time point

value: pooled brain and spinal cord, D21 post EAE induction


title: SS2_20_127:F9

value: WNT-1 Cre; Rosa26-Tomato


title: microglia, female WT, mouse 8


title: microglia, female WT, mouse 9


title: SS2_20_121:J10

value: Adrenal Gland


title: microglia, female WT, mouse 6


title: SS2_20_123:J10


title: SS2_20_123:M5


title: microglia, female CKO, mouse 5

source_name: microglia, female CKO

value: p38 CKO


title: SS2_20_125:L4


title: SS2_20_121:A2

value: PBS


title: microglia, female CKO, mouse 4


title: SS2_20_123:G12

value: Zuckerkandl organ


title: SS2_20_123:K1


title: microglia, female CKO, mouse 2


title: microglia, female CKO, mouse 3


title: SS2_20_125:E7


title: SS2_20_125:B17


title: microglia, female CKO, mouse 1


title: SS2_20_127:L19


title: microglia, male CKO, mouse 10

source_name: microglia, male CKO

value: male


title: SS2_20_127:N21


title: microglia, male CKO, mouse 9


title: microglia, female WT, mouse 7


title: microglia, male WT, mouse 6

source_name: microglia, male WT


title: microglia, male CKO, mouse 8


title: SS2_20_125:O1


title: SS2_20_123:N13


title: SS2_20_127:E24


title: SS2_20_127:I22


title: microglia, male CKO, mouse 7


title: microglia, male WT, mouse 5


title: microglia, male WT, mouse 3


title: SS2_20_127:B14


title: SS2_20_127:A19


title: SS2_20_125:C6


title: SS2_20_121:N22


title: EndoC BH1 somatostatin positive sample 4

city: Exeter

first: Lorna

last: Harries

address: RILD Building, Barrack Road,

department: Exeter Medical School

country: United Kingdom

institute: University of Exeter

description: Expression data generated from Applied Biosystems Transcriptome Analysis Console (TAC)

hyb_protocol: RNA was processed and arrays were run by UK Bioinformatics, King's College, London

data_processing: Raw data was analysed using Applied Biosystem Transcriptome Analysis Console (TAC)

label: biotin

source_name: EndoC-BH1 clonal human beta cells

growth_protocol: EndoC BH1 cells were cultured  as follows: The human clonal beta cell line EndoC-βH1 (passage<25) was seeded in T25 flasks at a density of 1.75 x 106 cells/ ml and maintained according to a modified humanised culture protocol. DMEM 1g/ L glucose, 2% Human serum albumin, 10 mM nicotinamide, 50 uM B-2-Mercaptoethanol, 5.5 ug/ uL human transferrin, 6.6 ng/ uL sodium selenite, 100 U/ mL penicillin and 100 ug/ mL streptomycin

extract_protocol: RNA was purified using a column based Zymo Direct-Zol RNA Miniprep kit (Cambridge Bioscience, Cambridge, UK) according to the manufacturer’s instructions to maximise yield.

treatment_protocol: For assessment of the effects of elevated glucose and altered lipids (glucolipotoxicity), cells were treated with a cocktail of 25 mM D-glucose and 0.5 μM palmitic acid for 48 hrs. Controls were maintained in 5 mM glucose media. Each treatment was carried out in 6 biological replicates, along with ethanol vehicle-only controls.

tag: agent

value: Somatostatin


title: microglia, male WT, mouse 2


title: microglia, male WT, mouse 1


title: EndoC BH1 somatostatin positive sample 3

scan_protocol: RNA was processed and arrays were run by UK Bioinformatics, King's College, London


title: SS2_20_123:P18


title: microglia, male WT, mouse 4


title: SS2_20_127:B1


title: EndoC BH1 insulin positive sample 6

label_protocol: RNA was processed and arrays were run by UK Bioinformatics, King's College, London

value: Insulin


title: EndoC BH1 somatostatin positive sample 6


title: EndoC BH1 insulin positive sample 5


title: SS2_20_123:L13


title: SS2_20_125:I13


title: EndoC BH1 insulin positive sample 4


title: SS2_20_127:J23


title: EndoC BH1 insulin positive sample 3


title: SS2_20_127:K17


title: SS2_20_121:A21


title: EndoC BH1 insulin positive sample 1


title: SS2_20_121:D6


title: SS2_20_125:J21


title: EndoC BH1 somatostatin positive sample 1


title: SS2_20_125:B10


title: SS2_20_125:I2


title: OB_KO1

city: Houston

first: Brittney

last: Lozzi

state: TX

address: 1 Baylor Plaza

department: Cell & Gene Therapy

institute: Baylor College of Medicine

data_processing:
Quality control was performed on concatenated fastq files using fastQC and multiQC. Paired end reads were mapped to the mouse genome (mm10) using STAR (v2.5.0a).
Reads Per Million (RPM) were calculated using GenomicAlignments (v1.16.0) and normalized using DESeq2 (v1.20.0).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample

source_name: olfactory bulb astrocytes

extract_protocol:
The olfactory bulb was collected from AAV-GFAP-iCre-P2a-TurboRFP injected Sox9fl/fl mice or C57BL/6J mice 4 weeks after viral injection. Bulbs were dissected and dissociated, and astrocytes were isolated using FACS directly into QIAGEN RLT lysis buffer (Cat# 74004) with 1% ß-Mercaptoethanol. Bulk RNA was isolated using the RNeasy Micro Kit (74004, QIAGEN).
Illumina sequencing libraries were constructed from 10ng of total RNA using the Trio RNA-Seq System (0507-96, NuGEN).

value: Sox9 KO

tag: viral injection

tag: cell type

value: olfactory bulb astrocytes


title: SS2_20_127:E15

tag: strain


title: OB_WT3

value: WT


title: OB_KO2


title: OB_KO3


title: CanAlb_plus_plus_2

city: Zürich

first: Puneet

last: Sharma

state: Zürich

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH

description:
Ribosome profiling
processed data file: Candida_supplementary_count_table.txt

data_processing:
Library strategy: Ribo-Seq
Ribosome profiling reads were processed by clipping the adapter sequence and trimming the 4 randomized nucleotides of the linker using the FASTX-Toolkit version 0.0.13.
Processed yeast reads were mapped to tRNA, rRNA, snRNA and snoRNA; reads from human samples were mapped to rRNA using bowtie version 1.2.1.1.
Residual reads were uniquely mapped to non-dubious ORFs (hg38; SacCer3; C_albicans_SC5314_version_A22;Pombe_ASM294v2) extended by 18 nt into the UTRs.
Genome_build: hg38 (GRCh38); SacCer3 (R64); C_albicans_SC5314_version_A22 (ASM18296v3); Pombe_ASM294v2 (ASM294v2)
Supplementary_files_format_and_content: *_count_table.txt: Tab-delimited text files include raw counts for each sample.

organism: Candida albicans

source_name: Yeast

growth_protocol: HEK 293T cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) at 37C. Yeast cultures were grown to mid-exponential phase (optical density 600 [OD600], ~0.4–0.5) at 30C, 200 revolutions per minute in yeast extract peptone dextrose (YPD).

extract_protocol:
For HEK 293T cells, total RNA is extracted using phenol:chloroform method. For yeast, total RNA is extracted using the hot-acid-phenol method.
Ribosome-protected footprints were purified from monosome fractions by size selection and gel extraction. Following 3' dephosphorylation these fragments were subjected to adaptor ligation, RT, circularization and PCR amplification.

treatment_protocol: (+/+) samples are pre-treated with CHX and lyzed in buffer containing CHX; (-/+) samples are lyzed in buffer containing CHX WITHOUT CHX pre-treatment; (-/-) samples are lyzed without CHX pre-treatment in buffer devoid of CHX.

value: Pre-treated with CHX, lyzed in buffer containing CHX


title: SS2_20_123:O18

tag: developmental stage


title: SS2_20_123:G13

tag: tissue


title: CanAlb_plus_plus_1

tag: treatment


title: SS2_20_121:D18

source_name: Adrenal Gland - E13.5 - PBS


title: SS2_20_123:B16


title: SS2_20_123:M17


title: EndoC BH1 insulin positive sample 2


title: SS2_20_127:D3


title: OB_WT1


title: SS2_20_121:K9


title: SS2_20_125:G10

source_name: Adrenal Gland - E13.5 - 5HTP


title: LPS+LEV

city: Higashi-Hiroshima

first: Yasuhiro

last: Ishihara

state: Hiroshima

address: 1-7-1 Kagamiyama

department: Graduate School of Integrated Sciences for Life

country: Japan

institute: Hiroshima University

data_processing:
CAGE tag count data were clustered using the CAGEr (Haberle et al., Nucleic Acids Research 2015, 30:e51) using Paraclu algorithm (Frith et al., Genome Research 2007 18:1-12) with default parameters. Clusters with count per million (CPM) < 0.2 were discarded.
Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
Genome_build: mm9_male
Supplementary_files_format_and_content: *_DESeq.txt: Tab-delimited text files include DESeq2 results.

extract_protocol:
RNA was extracted from BV-2 cells using a High Pure RNA Isolation Kit (Roche Diagnostics K.K., Tokyo, Japan).
The cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5’ cap structures of RNAs were oxidized, and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNA, double-stranded cDNA libraries (CAGE libraries) were constructed.

tag: cell line

value: microglia cell line

value: LPS+LEV for 6 hr


title: LPS

value: LPS for 6 hr


title: SS2_20_125:I5


title: OB_WT2


title: Untreated

value: untreated


title: SS2_20_121:M1


title: SS2_20_125:A23


title: SS2_20_123:C20


title: SS2_20_123:M21


title: SS2_20_125:J23


title: SS2_20_123:J20


title: SS2_20_125:D19


title: SS2_20_127:N2

source_name: Zuckerkandl organ - E13.5 - PBS


title: anti-VEGFA_2

city: Tokyo

first: Tetsuo

last: Mashima

address: 3-8-31, Ariake,Koto-ku

institute: JFCR

description: no additional information

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Gene-level expression signals were obtained by processing of raw data with the MAS5 procedure using GeneSpring GX (Agilent Technologies).

source_name: Human Gastric Cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: MKN45 cells were maintained in RPMI1640 medium supplemented with 10% heat-inactivated fetal bovine serum in a humidified atmosphere of 5% CO2 and 95% air at 37 °C. BALB/c nude mice were subcutaneously injected with MKN45 cells.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: When tumors reached 100-200 mm3, the mice were treated with vehicle, anti-VEGFR2 antibody (DC101) (10mg/kg), anti-VEGF-A antibody (2G11-2A05) (5mg/kg), or the two antibodies together (Dual) (N=2) (twice a week and for two weeks totally).

tag: antibody

value: antiVEGFA


title: SP WT Ly6G intermediate rep 8

city: Glagow

first: John

last: Mackey

address: Switchback Rd, Bearsden

institute: CRUK Beatson Institute

data_processing:
Illumina data were demultiplexed using bcl2fastq version 2.19.0.216, then adaptor sequences were removed using Cutadapt version 0.6.4. Next, quality checks on fastq files were performed using fastqc version 0.11.8.
Paired-end reads were aligned to the mouse genome version GRCm38.95 using HISAT2 version 2.1.0 with the –known-splicesite-infile and –rna-strandness options.
Expression levels were determined using HTseq version 0.11.2 with the -s=reverse, --mode=intersection-nonempty and –type=exon options, then statistically analysed using R version 3.5.1.
Genome_build: GRCm38.95
Supplementary_files_format_and_content: Raw counts matrix

source_name: Spleen-derived neutrophil

extract_protocol:
All mice used for RNA isolation were sacrificed within the same period in the morning (between 07.00-08.30) to minimise circadian-induced gene expression changes between samples. RNA was isolated from Ly6GInt, Ly6GHi and Ly6G+ neutrophil populations that had been FACS sorted from the BM, spleen, liver and peripheral blood. Biological replicates for PBS and LPS bulk Ly6G+ neutrophil RNA-Seq are as follows: PBS: peripheral blood Ly6GHi n=4 mice; BM Ly6GInt n=4 mice; BM Ly6GHi n=4 mice; spleen Ly6GInt n=6 mice; spleen Ly6GHi n=7 mice; liver Ly6G+ n=7 mice. LPS: peripheral blood Ly6GInt n=4 mice; peripheral blood Ly6GHi n=4 mice; BM Ly6GInt n=3 mice; BM Ly6GHi n=3 mice; spleen Ly6GInt n=4 mice; spleen Ly6GHi n=4 mice; liver Ly6G+ n=4 mice. Biological replicates for PDAC model bulk Ly6G+ neutrophil RNA-Seq are as follows: BM: WT Ly6GInt n=10 mice; KPflC Ly6GInt n=5 mice; KPC Ly6GInt n=5 mice; KPC Ly6GHi n=5 mice. Spleen: WT Ly6GInt n=8 mice; KPflC Ly6GInt n=4 mice; KPC Ly6GInt n=5 mice. RNA was extracted from sorted populations using an RNeasy Micro Kit (Qiagen). RNA quality was evaluated using an Agilent Bioanalyser using RNA Pico chips.
Libraries for cluster generation and DNA sequencing were prepared using a TaKaRa SMARTer Stranded Total RNA-Seq – Pico Input Mammalian kit v2.0 as per the manufacturer’s instructions. Quality and quantity of the DNA libraries was assessed on an Agilent 2200 Tapestation (D1000 screentape) and Qubit (Thermo Fisher Scientific) respectively. The libraries were run on the Illumina Next Seq 500 using the High Output 75 cycles kit (2x36 cycles, paired end reads, dual index).

treatment_protocol: Mice were treated with: PBS (150uL i.p.) for 24 hours; LPS (1 mg/kg in PBS, total vol. 150uL i.p.) for 24 hours

value: Spleen-derived neutrophil

tag: genetic background


title: SP WT Ly6G intermediate rep 7


title: SS2_20_127:H17

value: WNT-1 Cre; Rosa26-Tomato


title: anti-VEGFA_1

description: no additional information


title: SS2_20_125:O3

value: Adrenal Gland


title: Dual_2

description: no additional information

value: antiVEGFR2 and antiVEGFA


title: SP WT Ly6G intermediate rep 4


title: SS2_20_121:B10

value: PBS


title: SP WT Ly6G intermediate rep 5


title: SS2_20_123:K5

source_name: Zuckerkandl organ - E13.5 - 5HTP

value: Zuckerkandl organ


title: SP WT Ly6G intermediate rep 3


title: Dual_1

description: no additional information


title: SS2_20_125:O2


title: anti-VEGFR2_2

description: no additional information


title: SS2_20_123:D13


title: SS2_20_123:P11


title: SP WT Ly6G intermediate rep 6


title: SS2_20_121:O15


title: SS2_20_121:A24


title: SP WT Ly6G intermediate rep 1


title: SP WT Ly6G intermediate rep 2


title: SP WT Ly6G high rep 10


title: SS2_20_121:G14


title: SS2_20_121:I20


title: SS2_20_123:I12


title: SP WT Ly6G high rep 9


title: SS2_20_121:E21


title: anti-VEGFR2_1

description: no additional information


title: 135 9553710056_F

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

hyb_protocol: The profiling was done using Illumina HumanHT-12 WG-DASL V4.0 R2 gene expression bead arrays.

scan_protocol: BeadChips were scanned using Illumina BeadArray Reader and the Bead Scan Software

data_processing: Gene expression values were quantile normalized

source_name: Kidney cancer

label_protocol: standard Illumina protocol

extract_protocol: To isolate RNA, 10 µM - thick paraffin slices were trimmed from each FFPE RCC tissue block using microtome. RNA was extracted from FFPE slices using QIAGEN RNeasy FFPE Kit following the manufacturer’s protocol. RNA 6000 Nano or Qubit RNA Assay kits were used to measure RNA concentration. RNA Integrity Number (RIN) was measured using Agilent 2100 bio-Analyzer.

value: renal cell carcinoma tissue


title: 128 9553710081_L


title: SP WT Ly6G high rep 8


title: SS2_20_127:J11


title: 122 9553710056_L


title: Vehicle_1

description: no additional information

value: Vehicle


title: 97 9553710081_F


title: Vehicle_2

description: no additional information


title: SS2_20_121:N12


title: SS2_20_123:G8


title: SS2_20_127:E13


title: SS2_20_123:M13


title: 94 9553710081_K


title: SP WT Ly6G high rep 6


title: SS2_20_121:D22


title: SS2_20_121:C20


title: 91 9553976007_A


title: SP WT Ly6G high rep 5


title: SS2_20_123:J6


title: SS2_20_121:A19


title: SS2_20_123:N3


title: SS2_20_125:E4


title: SP WT Ly6G high rep 4


title: SP WT Ly6G high rep 7


title: SP WT Ly6G high rep 3


title: SS2_20_123:J11


title: SS2_20_125:M14


title: SP WT Ly6G high rep 2


title: 88 9553710081_E


title: SS2_20_121:B17


title: SS2_20_127:D4


title: 74 9553976002_G


title: 72 9553976002_L


title: SP WT Ly6G high rep 1


title: SS2_20_127:H16


title: 73 9553976002_I


title: 62 9553976003_E


title: SS2_20_123:H23


title: SP KPflC Ly6G intermediate rep 4

value: KrasG12D/+; Trp53fl/+; Pdx1-Cre


title: SS2_20_121:N18


title: 60 9553710071_B


title: SS2_20_121:J18


title: SP KPflC Ly6G intermediate rep 3


title: SS2_20_123:K19


title: SS2_20_127:B2


title: SS2_20_123:A2


title: 58 9553710060_L


title: SP KPflC Ly6G intermediate rep 1


title: SS2_20_127:O21


title: SS2_20_127:O9


title: SP KPflC Ly6G high rep 5


title: SS2_20_125:H16


title: SS2_20_127:B9


title: 49 9553976007_J


title: SS2_20_127:G9


title: 46 9553710071_E


title: EndoC BH1 somatostatin positive sample 5

value: Somatostatin


title: 54 9553710071_I


title: SP KPflC Ly6G intermediate rep 2


title: SS2_20_121:P5


title: SS2_20_123:N8


title: SP KPflC Ly6G high rep 4


title: SP KPflC Ly6G high rep 3


title: SS2_20_125:N20


title: SP KPflC Ly6G high rep 2


title: 31 9992555041_A


title: SS2_20_123:I8


title: SS2_20_125:B11


title: 27 9992555037_J


title: SP KPflC Ly6G high rep 1


title: SS2_20_121:J19


title: SS2_20_123:C9


title: SS2_20_123:B20


title: SP KPC Ly6G intermediate rep 5

value: KrasG12D/+; Trp53R172H/+; Pdx1-Cre


title: 37 9992555041_I


title: SS2_20_123:K4


title: SS2_20_125:J1


title: SP KPC Ly6G intermediate rep 4


title: SS2_20_125:J16


title: 18 9992555037_C


title: SS2_20_123:E14


title: SS2_20_123:O8


title: 36 9992555041_G


title: SP KPC Ly6G intermediate rep 3


title: SP KPC Ly6G intermediate rep 2


title: SS2_20_127:K4


title: SS2_20_127:O16


title: SS2_20_127:P15


title: SS2_20_123:K6


title: SP KPC Ly6G intermediate rep 1


title: SS2_20_127:G1


title: SS2_20_127:F12


title: SP KPC Ly6G high rep 5


title: 26 9992555037_H


title: SS2_20_121:D11


title: SP KPC Ly6G high rep 4


title: 35S::GUS roots Replicate 2c

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

country: France

institute: INRAE

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

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. NimbleScan Software v2.4 was used to extract pair-data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

organism: Medicago truncatula

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: Seeds were sterilized, grown and transformed according to Boisson-Dernier et al (2001). Germinated and transformed roots seeds were cultivated with Fahräeus medium, with appropriated antibiotics, with sixteen hours of photoperiod, at 20°C.

extract_protocol: Roots total RNA was extract with Macherey-Nagel's Nucleospin Plant II Kit according manufacturer's recommandations.

treatment_protocol: Binary vector pK7GW2D (Karimi et al, 2002) containing the full-lenght GUS gene was introduced in Arqua1 strain of Agrobacterium rhizogenes by a freeze-thaw method. Thirty hours age old apex roots were cut and scrapped on fourty eight hours age old transformed ARqua1 culture before being placed on culture medium

value: roots

tag: phenotype

value: GUS

tag: age

value: 4 weeks

tag: harvest date


title: 35S::SF2 roots Replicate 1


title: 35S::SF2 roots Replicate 2


title: SS2_20_123:C24


title: SS2_20_121:O1


title: SP KPC Ly6G high rep 3


title: SS2_20_123:B3


title: SS2_20_125:P4


title: SP KPC Ly6G high rep 2


title: SS2_20_121:J12


title: SS2_20_121:L14


title: SS2_20_127:M14


title: SS2_20_121:F8


title: 35S::GUS roots Replicate 1c


title: SS2_20_127:I9


title: 35S::SF3 roots Replicate 3


title: SS2_20_125:H8


title: PBS treated SP Ly6G intermediate rep 5

value: WT

value: PBS (150uL i.p. 24hrs)


title: SS2_20_125:L11


title: SP KPC Ly6G high rep 1


title: SS2_20_121:F13


title: SS2_20_121:O3


title: EndoC BH1 somatostatin positive sample 2


title: 35S::SF3 roots Replicate 2


title: 35S::GUS roots Replicate 3b


title: PBS treated SP Ly6G intermediate rep 4


title: SS2_20_121:D20


title: 35S::SF1 roots Replicate 3


title: 35S::SF3 roots Replicate 1


title: 35S::GUS roots Replicate 1b


title: 35S::GUS roots Replicate 2b


title: PBS treated SP Ly6G intermediate rep 6


title: SS2_20_127:K22


title: SS2_20_123:P6


title: SS2_20_123:D2


title: PBS treated SP Ly6G intermediate rep 1


title: SS2_20_125:I17


title: SS2_20_121:E3


title: PBS treated SP Ly6G high rep 7


title: PBS treated SP Ly6G intermediate rep 2


title: PBS treated SP Ly6G intermediate rep 3


title: SS2_20_123:K24


title: 35S::SF1 roots Replicate 1


title: 35S::SF1 roots Replicate 2


title: Sample_15-00461

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
bam files are converted to fastq files
Reads were mapped to ABL1 exon sequences using bowtie2 (v.2.1.1)
Counted the reads mapped to exon-exon, exon-intron boundaries
Supplementary_files_format_and_content: ABL1 alternative splicing reads quantification.xlsx
Supplementary_files_format_and_content: FASTA BCR-ABL1 splice variant junctions.txt

source_name: Peripheral Blood

growth_protocol: Following informed consent, primary research specimens were collected from Ph+ leukemia patients by peripheral blood draw, bone marrow aspirate, or leukapheresis.

extract_protocol:
For mononuclear cells, cells were isolated by Ficoll gradient from other blood components by centrifugation, multiply washed with IMDM, aliquotted, and flash frozen and stored at -80C as either cell pellets or frozen GTC cell lysate. These were later thawed on ice and total RNA was isolated by Qiagen RNeasy protocol. For samples derived from total white blood cells, peripheral blood was colleted and lysed directly in PAXgene tubes to stabilize total RNA, and RNA was subsequently also extracted by Qiagen protocol. Sample RNA concentrations were determined by Nanodrop spectrophotometer and then flash frozen and stored at -80C until sequencing.
CML patient RNA was subjected to 2x125 bp paired-end Illumina sequencing using the KAPA Stranded Total RNASeq kit at the New York Genome Sequencing Center.

treatment_protocol: Samples were not treated ex vivo prior to other processing and extraction of RNA.

value: White Blood Cells

value: Peripheral Blood

tag: disease state

value: CML, TKI resistant


title: PBS treated SP Ly6G high rep 6

value: Spleen-derived neutrophil


title: SS2_20_127:K24

value: WNT-1 Cre; Rosa26-Tomato


title: SS2_20_123:J5


title: SS2_20_123:I7


title: SS2_20_121:K5

value: Adrenal Gland

value: PBS


title: PBS treated SP Ly6G high rep 5


title: SS2_20_123:H19

value: Zuckerkandl organ


title: SS2_20_125:L10


title: Sample_15-00460


title: 35S::GUS roots Replicate 3a


title: 35S::GUS roots Replicate 1a


title: SS2_20_127:F3


title: Sample_15-00459


title: Sample_15-00458


title: 35S::GUS roots Replicate 2a


title: SS2_20_125:G9


title: SS2_20_125:M23


title: SS2_20_127:L9


title: SS2_20_127:H9


title: SS2_20_121:B23


title: Sample_15-00457


title: PBS treated SP Ly6G high rep 3


title: PBS treated SP Ly6G high rep 4


title: Sample_15-00456


title: PBS treated LV neutrophil rep 7

source_name: Liver-derived neutrophil

value: Liver-derived neutrophil


title: SS2_20_127:G17


title: SS2_20_123:N17


title: SS2_20_123:F6


title: PBS treated SP Ly6G high rep 1


title: Sample_15-00455


title: SS2_20_127:J9


title: SS2_20_123:F19


title: Sample_15-00453


title: PBS treated LV neutrophil rep 6


title: Sample_15-00452


title: SS2_20_121:C19


title: SS2_20_123:I4


title: PBS treated SP Ly6G high rep 2


title: PBS treated LV neutrophil rep 5


title: Sample_15-00451


title: SS2_20_123:P12


title: Sample_15-00450


title: PBS treated LV neutrophil rep 4


title: SS2_20_125:B16


title: SS2_20_127:O18


title: SS2_20_121:F20


title: PBS treated LV neutrophil rep 3


title: Sample_15-00448


title: SS2_20_123:O3


title: PBS treated LV neutrophil rep 1


title: SS2_20_121:P10


title: Sample_15-00446


title: SS2_20_127:I8


title: PBS treated BM neutrophil rep 4

source_name: Bone Marrow-derived neutrophil

value: Bone Marrow-derived neutrophil


title: SS2_20_121:M9


title: SS2_20_125:K12


title: SS2_20_123:N21


title: SS2_20_127:D5


title: PBS treated BM neutrophil rep 3


title: SS2_20_123:P22


title: Sample_15-00441


title: Sample_15-00442


title: Sample_15-00443


title: SS2_20_127:P24


title: SS2_20_127:G5


title: Sample_15-00434


title: PBS treated BM neutrophil rep 1


title: SS2_20_123:I19


title: PBS treated BM Ly6G high rep 4


title: Sample_15-00346

value: Mononuclear Cells

value: CML, Newly diagnosed / TKI naive


title: SS2_20_121:J11


title: SS2_20_121:O23


title: PBS treated LV neutrophil rep 2


title: SS2_20_125:G7


title: SS2_20_121:B1


title: PBS treated BM Ly6G high rep 3


title: Sample_15-00290


title: SS2_20_127:A17


title: SS2_20_121:G13


title: SS2_20_127:D17


title: PBS treated BM neutrophil rep 2


title: SS2_20_127:M6


title: PBS treated BM Ly6G high rep 2


title: SS2_20_127:F5


title: Sample_15-00289


title: Sample_15-00236


title: PBS treated BM Ly6G high rep 1


title: SS2_20_123:B23


title: PBS treated BL neutrophil rep 8

source_name: Blood-derived neutrophil

value: Blood-derived neutrophil


title: Sample_15-00183


title: SS2_20_127:K6


title: SS2_20_127:P7


title: PBS treated BL neutrophil rep 7


title: Sample_15-00152

source_name: Bone Marrow Aspirate

value: Bone Marrow Aspirate


title: SS2_20_123:K8


title: Sample_15-00314


title: SS2_20_127:C19


title: PBS treated BL neutrophil rep 6


title: Sample_15-00122


title: SS2_20_123:O12


title: SS2_20_121:O4


title: PBS treated BL neutrophil rep 5


title: Sample_15-00110

value: Ph+ ALL, TKI resistant


title: PBS treated BL neutrophil rep 4

value: WT


title: SS2_20_121:D8


title: SS2_20_123:A12


title: Sample_15-00109


title: PBS treated BL neutrophil rep 3

value: PBS (150uL i.p. 24hrs)


title: SS2_20_125:J3


title: PBS treated BL neutrophil rep 2


title: SS2_20_121:F21


title: SS2_20_127:E20


title: SS2_20_123:K7


title: PBS treated BL neutrophil rep 1


title: Sample_15-00100


title: Sample_15-00099


title: SS2_20_127:M21


title: SS2_20_125:J7


title: SS2_20_125:E16


title: Sample_15-00098


title: PBS treated BL Ly6G high rep 3


title: SS2_20_121:H5


title: SS2_20_123:A9


title: SS2_20_127:M23


title: Sample_15-00097


title: SS2_20_127:B6


title: SS2_20_127:G3


title: PBS treated BL Ly6G high rep 4


title: PBS treated BL Ly6G high rep 2


title: Sample_15-00096


title: SS2_20_121:J8


title: PBS treated BL Ly6G high rep 1


title: SS2_20_123:B5


title: SS2_20_121:K1


title: Sample_15-00106


title: Sample_15-00094


title: LPS treated SP Ly6G intermediate rep 4

value: LPS (1mg/kg, i.p., 24hrs)


title: Sample_15-00093

value: Peripheral Blood


title: SS2_20_125:F23


title: SS2_20_121:E11


title: SS2_20_123:N23


title: SS2_20_121:C10


title: LPS treated SP Ly6G intermediate rep 3


title: SS2_20_125:G19


title: LPS treated SP Ly6G intermediate rep 2


title: Sample_15-00091

value: CML, TKI resistant


title: SS2_20_125:L16


title: SS2_20_127:J19


title: SS2_20_121:F5


title: Sample_15-00089


title: LPS treated SP Ly6G high rep 4

value: Spleen-derived neutrophil


title: LPS treated SP Ly6G intermediate rep 1


title: Sample_14-00770


title: SS2_20_127:E23

value: WNT-1 Cre; Rosa26-Tomato


title: SS2_20_123:F16


title: SS2_20_123:J3


title: SS2_20_123:M11


title: LPS treated SP Ly6G high rep 3


title: SS2_20_121:K8

value: Adrenal Gland


title: SS2_20_121:M10

value: PBS


title: LPS treated SP Ly6G high rep 2


title: Sample_14-00696


title: SS2_20_127:K16

value: Zuckerkandl organ


title: SS2_20_121:M23


title: Sample_15-00092


title: SS2_20_127:A10


title: LPS treated SP Ly6G high rep 1


title: SS2_20_123:H9


title: LPS treated LV neutrophil rep 4

value: Liver-derived neutrophil


title: Sample_14-00294


title: Sample_14-00293


title: LPS treated LV neutrophil rep 3


title: SS2_20_121:O11


title: SS2_20_127:D13


title: Sample_14-00172


title: SS2_20_123:E11


title: SS2_20_123:F22


title: SS2_20_125:K18


title: Sample_14-00011


title: Sample_14-00722


title: Sample_14-00009


title: SS2_20_127:P22


title: SS2_20_125:C2


title: Sample_13-00534


title: SS2_20_125:J9


title: LPS treated BM Ly6G intermediate rep 3

value: Bone Marrow-derived neutrophil


title: LPS treated LV neutrophil rep 1


title: LPS treated BM Ly6G intermediate rep 2


title: SS2_20_121:E12


title: SS2_20_125:K8


title: Sample_13-00427

value: Mononuclear Cells


title: LPS treated BM Ly6G intermediate rep 1


title: LPS treated BM Ly6G high rep 3


title: SS2_20_123:L22


title: SS2_20_123:A17


title: Sample_13-00320

value: CML, Newly diagnosed / TKI naive


title: SS2_20_125:D13


title: SS2_20_127:G18


title: LPS treated LV neutrophil rep 2


title: LPS treated BM Ly6G high rep 2


title: Sample_13-00261


title: SS2_20_123:L17


title: SS2_20_125:F6


title: LPS treated BM Ly6G high rep 1


title: Sample_13-00248


title: Sample_13-00135

value: CML, TKI responder


title: SS2_20_121:D7


title: LPS treated BL neutrophil rep 4

value: Blood-derived neutrophil


title: SS2_20_125:N19


title: SS2_20_127:E7


title: SS2_20_123:A1


title: SS2_20_123:B1


title: Sample_13-00120


title: LPS treated BL neutrophil rep 2


title: Sample_13-00069

value: Bone Marrow Aspirate


title: SS2_20_123:N24


title: LPS treated BL neutrophil rep 3

value: WT


title: Sample_13-00035


title: SS2_20_123:H21


title: LPS treated BL neutrophil rep 1


title: SS2_20_125:P13


title: SS2_20_127:P2


title: SS2_20_123:C13


title: SS2_20_125:F2


title: SS2_20_127:M22


title: LPS treated BL Ly6G intermediate rep 4


title: SS2_20_123:C5


title: SS2_20_123:A3


title: Sample_12-00341


title: Sample_13-00024


title: LPS treated BL Ly6G intermediate rep 3


title: Sample_12-00337


title: SS2_20_121:G1


title: SS2_20_123:N7


title: Sample_12-00328


title: LPS treated BL Ly6G intermediate rep 1


title: SS2_20_127:E17


title: Sample_12-00322


title: Sample_12-00299


title: SS2_20_125:H4


title: LPS treated BL Ly6G high rep 3


title: LPS treated BL Ly6G high rep 4


title: SS2_20_127:G7


title: SS2_20_121:G24


title: LPS treated BL Ly6G high rep 2


title: SS2_20_121:O21


title: LPS treated BL Ly6G intermediate rep 2


title: Sample_12-00271


title: SS2_20_125:H1


title: SS2_20_123:J19


title: Sample_12-00293


title: LPS treated BL Ly6G high rep 1


title: SS2_20_125:O20


title: SS2_20_123:L8


title: SS2_20_125:N2


title: Sample_12-00257


title: Sample_12-00233


title: BM WT Ly6G intermediate rep 10


title: BM WT Ly6G intermediate rep 9


title: SS2_20_121:F10


title: SS2_20_127:G2


title: SS2_20_125:D16


title: SS2_20_121:I13


title: SS2_20_123:F3


title: Sample_12-00222


title: SS2_20_125:N13


title: SS2_20_121:C14


title: Sample_12-00200

value: Ph+ ALL, TKI resistant


title: SS2_20_127:O1


title: BM WT Ly6G intermediate rep 7


title: Sample_12-00186


title: SS2_20_125:A10


title: SS2_20_127:H13


title: Sample_12-00174


title: SS2_20_123:C3


title: BM WT Ly6G intermediate rep 4


title: BM WT Ly6G intermediate rep 6


title: Sample_12-00149

value: Ph+ ALL, Newly diagnosed / TKI naive


title: SS2_20_121:M17


title: BM WT Ly6G intermediate rep 5


title: SS2_20_123:N19


title: SS2_20_125:B19


title: SS2_20_121:G4


title: SS2_20_125:L1


title: Sample_11-00508

value: Peripheral Blood


title: BM WT Ly6G intermediate rep 3


title: Sample_12-00056

value: CML, TKI resistant


title: SS2_20_127:P1


title: Sample_11-00270


title: BM WT Ly6G intermediate rep 8


title: SS2_20_121:G11


title: BM WT Ly6G intermediate rep 1


title: Sample_11-00259


title: SS2_20_125:J20


title: SS2_20_125:C9


title: SS2_20_123:M15


title: BM WT Ly6G high rep 10


title: Mnase-seq in AtT-20 expressing Pax7

city: Montreal

first: Amandine

last: Bemmo

state: QC

address: 110 Avenue des Pins

country: Canada

institute: IRCM

library_source: genomic

data_processing:
Sequence reads were trimmed for adapter sequences.
The resulting 50bp reads were trimmed to obtain high quality reads and then mapped to the mm10 mouse genome build using Bowtie with the following parameter: -t -p 4 --trim5 12 --trim3 1  mm10 -S --chunkmbs 1024
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using makeUCSCfile with the following parameters : -o auto -fsize 1e20 -bigWig mm10.chrom.sizes

molecule: genomic DNA

source_name: AtT-20 cells expressing 3x flag-Pax7

growth_protocol: AtT-20 cells were plated on adherent culture dishes to obtain about 70% confluence after 3 days. They are cultured in DMEM + 10% FBS.

extract_protocol:
Nuclei lysates from 3×106 cells were digested in micrococcal nuclease.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocols to obtain 50bp paired end reads.

value: pituitary corticotroph cell

tag: passages

tag: genotype/variation

value: expressing 3x flag-Pax7


title: Mnase-seq in AtT-20 with empty vector (neo)

source_name: AtT-20 cells with empty vector

value: empty vector


title: BM WT Ly6G high rep 9

tag: genotype


title: Sample_10-00219


title: ATAC-seq in AtT-20 expressing Pax7 S264E

data_processing:
Reads trimmed using Trimmomatic/0.36 (Bolger et al. 2014)
Reads aligned to the mouse mm10 reference genome using Bowtie/2.3.5 (--very-sensitive --no-mixed --no-unal) (Langmead et al. 2009)
Duplicated reads removed using MarkDuplicates from Picard/2.17.3 (Broad Institute)
Bam files created using view from SAMtools/1.9 (Li et al. 2009) and bigwig files using bamCoverage (--normalizeUsing RPKM -bs 10 -e) from deepTools/3.3.0 (Ramirez et al. 2016)
Peaks called against sequenced input DNA or control Flag ChIP using callpeaks (-f BAMPE -p {1e-3|1e-5} -g mm) from MACS/2.1.1 (Zhang et al. 2008)
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig

extract_protocol:
50,000 nuclei were extracted and treated as described in doi.org/10.1038/s41467-019-11791-9
Librairies were prepared as described in doi.org/10.1038/s41467-019-11791-9 and sequenced on Illumina HiSeq/NovaSeq following Illumina's instructions

value: expressing Pax7 S264E


title: ATAC-seq in AtT-20 expressing Pax7 G43A

value: expressing Pax7 G43A


title: Sample_10-00218


title: SS2_20_127:D19

value: WNT-1 Cre; Rosa26-Tomato

value: Zuckerkandl organ

value: PBS


title: Pax7 ChIPseq in AtT-20 expressing Pax7 S264E

description:
HI.4804.006_AtTPax7_JA2565
AtT-20 cells cells expressing 3x flag-Pax7 R56L

source_name: AtT-20 cells expressing 3x flag-Pax7 S264E

extract_protocol:
Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific antibodies. Fragments of 200-400bp were kept for library preparation
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocols to obtain 50bp paired end reads.

tag: chip antibody

value: FlagM2 Sigma F1365


title: ATAC-seq in AtT-20 expressing Pax7 R56L

value: expressing Pax7 R56L


title: Sample_09-00619

value: Mononuclear Cells


title: BM WT Ly6G high rep 8

value: Bone Marrow-derived neutrophil


title: BM WT Ly6G high rep 6

value: WT


title: BM WT Ly6G high rep 5


title: Pax7 ChIPseq in AtT-20 expressing Pax7 G43A

description:
HI.4804.006_AtTPax7_JA2563
AtT-20 cells cells expressing 3x flag-Pax7 G43A

source_name: AtT-20 cells expressing 3x flag-Pax7 G43A


title: Pax7 ChIPseq in AtT-20 expressing Pax7

description:
HI.4804.006_AtTPax7_JA2225
AtT-20 cells cells expressing 3x flag-Pax7

value: expressing Pax7


title: NoV∆B2: suckling C57BL/6 4dpi

city: Shanghai

first: Yang

last: Li

address: 2005 Songhu Road

country: China

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to virus genome using bowtie 1.1.2 with perfect match.
Supplementary_files_format_and_content: mapping results

source_name: hindlimb muscle

extract_protocol:
Total RNA was extracted from mice hindlimb muscle tissue or 293T cells using TRIzol reagent.
Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.

value: NoV∆B2 virus


title: NoV：B2-IP(suckling BALB/c 3dpi)

value: BALB/c

value: NoV virus


title: BM WT Ly6G high rep 4


title: NoV：Ago-IP(suckling BALB/c 3dpi)


title: Sample_11-00218

value: Peripheral Blood

value: CML, TKI resistant


title: BM WT Ly6G high rep 3


title: NoV∆B2：Ago-IP(suckling BALB/c 3dpi)


title: NoV: suckling C57BL/6 Lgp2-/- 4dpi


title: BM WT Ly6G intermediate rep 2


title: Sample_08-00306


title: Pax7 ChIPseq in AtT-20 expressing Pax7 R56L

description:
HI.4804.006_AtTPax7_JA2564
AtT-20 cells cells expressing 3x flag-Pax7 R56L

source_name: AtT-20 cells expressing 3x flag-Pax7 R56L

value: pituitary corticotroph cell


title: BM WT Ly6G high rep 7


title: BM WT Ly6G high rep 2


title: Sample_07-00345


title: NoV∆B2：suckling BALB/c 3dpi


title: STM815 nifA mutant in symbiosis with bean rep2

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

institute: University of Zürich

description:
20180920.B-Bphy_nifA2_nod_R1 trimmed (GE)_phym: mapping to STM815 genome
20180920.B-Bphy_nifA2_nod_R1 trimmed (GE)_bean: mapping to Pvulgaris genome

data_processing:
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer
Sequencing reads were mapped to the Pp STM815 genome using CLC Genomics Workbench v7.0 (CLCbio) allowing up to 2 mismatches per read
RNA-Seq count data were subsequently analyzed with the DESeq software (Anders & Huber 2010)
Genome_build: STM815 genome sequence (accession no. NC_010622.1, NC_010623.1, NC_010625.1 and NC_010627.1); P. vulgaris genome (accession no. GCA_000499845))
Supplementary_files_format_and_content: tab-delimited text files include RPKM and mean values for each sample

organism:
Phaseolus vulgaris
Paraburkholderia phymatum STM815

source_name: Pp STM815 symbiosis

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using hot phenol protocol (Pessi et al 2007) . For RNA extracted from nodules, first nodules were disrupted with TissueLyzer and then rRNA of plants was removed using Ribo-zero kit (Epicentre). The cDNA was produced and nugen libraries obtained.
RNA libraries were prepared using Encore Complete Prokaryotic RNA-Seq DR Muliplex System
NuGen

value: nifA mutant

tag: growth

value: nodules harvested 21 days post infection

tag: medium

value: inside bean nodules


title: BM WT Ly6G high rep 1

tag: cell type


title: Sample_07-00103

source_name: Leukapheresis

value: Leukapheresis


title: STM815 wt in symbiosis with bean rep2

description:
20150521.A-201505_Bp_nod_o_R1 trimmed (GE)_phym: mapping to STM815 genome
20150521.A-201505_Bp_nod_o_R1 trimmed (GE)_bean: mapping to Pvulgaris genome

tag: strain

value: wt


title: Sample_09-00184

tag: tissue

value: Bone Marrow Aspirate


title: STM815 wt in symbiosis with bean rep1

description:
20150521.A-201505_Bp_nod_n_R1 trimmed (GE)_phym: mapping to STM815 genome
20150521.A-201505_Bp_nod_n_R1 trimmed (GE)_bean: mapping to Pvulgaris genome


title: Sample_09-00225


title: Sample_07-00003


title: BM KPflC Ly6G intermediate rep 5

value: KrasG12D/+; Trp53fl/+; Pdx1-Cre

tag: treatment


title: BM KPflC Ly6G intermediate rep 4


title: ms11_3 [111171_O]

city: Würzburg

first: Dagmar

middle: Hannelore Irmgard

last: Beier

address: Am Hubland

department: Chair of Microbiology

country: Germany

institute: Biocenter, University of Würzburg

data_processing:
Adapters were removed using cutadapt.
Reads were mapped using Bowtie2, and were indexed with Samtools.
bedtools and featureCount was used to generate gene coverages.
DEseq2 was used to identify differentially expressed genes.
Genome_build: ASM15685v2;RefSeq assembly accession: GCF_000156855.2
Supplementary_files_format_and_content: tab-delimited text files include Reads for each annotation.

organism: Neisseria gonorrhoeae

source_name: wild-type_not induced

growth_protocol: Bacteria were grown to an OD550 = 0.4 in PPM containing 1% vitamin mix and 0.04% (w/v) NaHCO3.

extract_protocol:
Bacteria were harvested by centrifugation and RNA was isolated using the miRNeasy Micro Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 200 ng/ml anhydrous tetracycline were added to WT, sRNA deletion mutants and the sRNA overexpressing strains and incubation was continued for 30 min.

value: wild-type

tag: induction

value: not induced


title: ms11_1 [111171_M]


title: Sample_06-00361

value: Mononuclear Cells


title: Sample_09-00157

value: Ph+ ALL, Newly diagnosed / TKI naive


title: BM KPflC Ly6G intermediate rep 3

value: Bone Marrow-derived neutrophil


title: dd_3 [111171_R]

source_name: mutant ΔΔ162/163_not induced


title: Sample_06-00277


title: dd_2 [111171_Q]


title: dd_1 [111171_P]


title: BM KPflC Ly6G intermediate rep 2


title: 163aie_3 [111171_X]

source_name: mutant ΔΔ162/163, Ptet-163_induced

value: mutant:{delta}{delta}162/163, Ptet-163

value: induced


title: STM815 nifA mutant in symbiosis with bean rep1

description:
20180920.B-Bphy_nifA1_nod_R1 trimmed (GE)_phym: mapping to STM815 genome
20180920.B-Bphy_nifA1_nod_R1 trimmed (GE)_bean: mapping to Pvulgaris genome


title: 163aie_2 [111171_W]


title: Sample_06-00203

value: Peripheral Blood

value: CML, Newly diagnosed / TKI naive


title: BM KPflC Ly6G intermediate rep 1


title: Sample_06-00196


title: 163aie_1 [111171_V]


title: BM KPflC Ly6G high rep 5


title: 162aie_3 [111171_U]

source_name: mutant ΔΔ162/163, Ptet-162_induced

value: mutant:{delta}{delta}162/163, Ptet-162


title: 162aie_1 [111171_S]


title: ms11_2 [111171_N]


title: 162aie_2 [111171_T]


title: BM KPflC Ly6G high rep 4


title: 237aie_3 [111171_AD]

source_name: mutant Δ237, Ptet-237_induced

value: mutant:{delta}237, Ptet-237


title: Sample_06-00179

value: CML, TKI resistant


title: Sample_06-00028


title: 237aie_2 [111171_AC]


title: BM KPflC Ly6G high rep 3


title: 237aie_1 [111171_AB]


title: Sample_06-00023


title: d237_3  [111171_AA]

source_name: mutant Δ237_not induced


title: BM KPflC Ly6G high rep 2

source_name: Bone Marrow-derived neutrophil


title: d237_2  [111171_Z]


title: Sample_05-00255

source_name: Peripheral Blood


title: Sample_05-00225

source_name: Bone Marrow Aspirate


title: BM KPflC Ly6G high rep 1


title: RNA-seq_p11_4

city: St. Louis

first: Guoyan

last: Zhao

state: MO

address: 660 South Euclid Ave.

department: Genetics & Neurology

institute: Washington University

data_processing:
adapter-trimming using Cutadapt 1.16
sequence quality control using PRINSEQ 0.20.4
align to rat genome using STAR 2.5.3a
Reads in features were counted using HTseq 0.6.1
Genome_build: Rattus norvegicus (Norway rat) genome assembly Rnor_6.0 (rn6)
Supplementary_files_format_and_content: HTseq output text file with gene expression counts

organism: Rattus norvegicus

source_name: Retinal Ganglion Cell

extract_protocol:
Total RNA from 700,000 to 1.25 million RGCs per sample was isolated using the Qiagen RNAeasy kit from Qiagen, which included a 15 minutes On-column DNAse step. Ribodepletion and RiboErase (human, mouse, rat) were used to remove ribosomal RNA.
Libraries were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq. All samples were sequenced in the same lane.

value: postnatal day P11

value: retina

value: Retinal Ganglion Cell


title: BM KPC Ly6G intermediate rep 5

value: KrasG12D/+; Trp53R172H/+; Pdx1-Cre


title: 42725-P2-D13

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences and mapped to the Mmul_8.0.1 genome sequence using STAR-2.5.2b with --quantMode GeneCounts --outSAMtype None and all other paramters default
Genome_build: Mmul_8.0.1
Supplementary_files_format_and_content: tab-delimited text files (STAR output) include transcript raw count values for each sample

organism: Macaca mulatta

source_name: Peripheral blood mononuclear cells

extract_protocol:
Total RNA was extracted from PBMC using RNEasy Mini kit reagents on a QIAcube instrument
cDNA libraries were constructed from 300 ng total RNA using Lexogen QuantSeq 3' FWD and sequenced on an Illumina HiSeq 4000 acquiring single-strand 65-bp reads (targeting > 10M reads/sample).

value: SIP-JuvenilePartnered

value: Peripheral blood mononuclear cells


title: Sample_05-00148

value: Bone Marrow Aspirate


title: BM KPC Ly6G intermediate rep 4


title: RNA-seq_p11_3


title: Sample_05-00128

value: Mononuclear Cells


title: RNA-seq_p11_1


title: BM KPC Ly6G intermediate rep 3


title: 42725-P2-D8


title: Sample_05-00125


title: BM KPC Ly6G intermediate rep 2


title: Sample_05-00130


title: RNA-seq_e21_4

value: embryonic E21 day


title: BM KPC Ly6G intermediate rep 1

value: Bone Marrow-derived neutrophil


title: d237_1  [111171_Y]

value: not induced


title: 42725-P1-D8

value: SIP-Isolated


title: BM KPC Ly6G high rep 5


title: 42725-P1-D2


title: Sample_05-00109

value: CML, TKI responder


title: RNA-seq_e21_2


title: 42725-P2-FC


title: RNA-seq_e21_3


title: 42725-P1-FC


title: Sample_05-00106


title: RNA-seq_e21_1


title: 42725-P2-D2


title: BM KPC Ly6G high rep 3


title: Sample_05-00082


title: 42725-P1-D13


title: 42652-P2-D13


title: BM KPC Ly6G high rep 2


title: Sample_05-00115


title: Sample_05-00075

value: Peripheral Blood


title: BM KPC Ly6G high rep 1


title: 42652-P2-D2


title: 42652-P2-D8


title: Sample_05-00070


title: 42652-P2-FC


title: Sample_05-00060


title: BM KPC Ly6G high rep 4


title: primary_fSCs

city: Boston

first: Simona

last: Cristea

state: Massachusetts

address: 450 Brookline Ave.

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute

data_processing:
sequenced reads were aligned to the mm10 reference genome using CellRanger version 3.0.2.
The filtered reads assigned to cell barcodes were analyzed with the R package Seurat, version 4.0.0 (Hao, 2020). In an initial quality control step, all cells with less than 300 genes expressed were removed, as well as all genes expressed in less than 10 cells (in CreateSeuratObject function). In a second step, only cells with less than 20% percentage mitochondria expression were retained.
The data was normalized using SCTransform (Hafemeister and Satija, 2019) and decomposed using PCA.
UMAP (McInnes, 2020)  embeddings were then computed using the first 30 dimensions as input. Based on the UMAP embedding, further quality control was performed by removing clusters of contaminating cells (identified by differential expression and relevant marker genes of contaminating populations) and of poor-quality cells (identified as outliers by number of genes expressed or percentage mitochondria).
Genome_build: mm10
Supplementary_files_format_and_content: text files containing SCT-normalized expression values (the 'data' slot in the Seurat object) for each analyzed cell after QC.

source_name: skeletal muscle tissue

growth_protocol: MEFs harboring Rosa-rtTA, Col1a1-tetO-MyoD and Pax7-nGFP were isolated from E13.5 embryos and were maintained in DMEM (GIBCO) containing 1X glutaMAX (GIBCO), 1X MEM non essential Amino Acid Solution (GIBCO), 100 U/ml penicillin, 100 μg/mL streptomycin (GIBCO), 0.1% β-mercaptoethanol (GIBCO) and 10% Fetal Bovine Serum (HyClone). For dedifferentiation into iMPCs, MEFs were maintained in knockout DMEM (GIBCO) containing 1X glutaMAX (GIBCO), 1X MEM non essential Amino Acid Solution (GIBCO), 100 U/ml penicillin, 100 μg/mL streptomycin (GIBCO), 0.1% β-mercaptoethanol (GIBCO), 10% KnockOut Serum Replacement (GIBCO), 10% Fetal Bovine Serum (HyClone), 10ng/ml basic FGF (Peprotech), 5μM Forskolin (Sigma), 5μM RepSox (Sigma), 3μM GSK3β inhibitor CHIR99021 (Tocris) and 2μg/ml Doxycycline (Sigma). For transdifferentiation into myotubes, MEFs were maintained in knockout DMEM (GIBCO) containing 1X glutaMAX (GIBCO), 1X MEM non essential Amino Acid Solution (GIBCO), 100 U/ml penicillin, 100 μg/mL streptomycin (GIBCO), 0.1% β-mercaptoethanol (GIBCO), 10% KnockOut Serum Replacement (GIBCO), 10% Fetal Bovine Serum (HyClone), 10ng/ml basic FGF (Peprotech) and 2μg/ml Doxycycline (Sigma). Hypoxia experiments were performed in 5% O2 level. Freshly isolated satellite cells (fSCs) were isolated from adult Pax7-nGFP mice (10-12 weeks). Cultured satellite cells (cSCs) were maintained in F10 (GIBCO) with 20% Horse Serum (GIBCO), 1X glutaMAX (GIBCO) and 100 U/ml penicillin, 100 μg/mL streptomycin (GIBCO). 5ng/ml basic FGF (Sigma) was daily added. For differentiating cSCs, cSCs were cultured in 2% horse serum differentiation medium for 2 days.

extract_protocol:
Cells (1000 cells/μl) were resuspended with PBS and were loaded into Chromium 10x system.
scRNA-seq libraries were generated from approximately 5000 cells per sample using Chromium 10x instrument with version 3.0 kit.
single cell RNA-sequencing

value: Skeletal muscles (8-10 weeks age of mice)

value: muscle stem cells freshly isolated from skeletal muscles

value: not cultured in vitro (freshly isolated from in vivo)


title: 42652-P1-D13


title: G14_37_3

city: Wuxi

first: Nai-Xin

last: Lin

address: lihu avenue

institute: Jiangnan University

data_processing:
Illumina Casava software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.  And then FPKM of each gene was calculated based on the length of the gene and  reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and  is currently the most commonly used method for estimating gene expression levels.
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCA_000223565.1/

organism: Komagataella phaffii GS115

source_name: cell pellet

growth_protocol: Flask-batch fermentation in BMGY/BMMY medium

extract_protocol: Standard illumina protocols

treatment_protocol: Induction temperature: 28℃ and 37℃

value: oxidative and thermal stress cross-tolerant mutant

value: induction temperature 37 degrees C

tag: time


title: Sample_05-00013

value: CML, TKI resistant


title: Sample_04-00274


title: LRNA_mTORi_2d_rep1

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
mapping reads to mm9 using STAR/v2.7.3a with parameters --outFilterScoreMinOverLread 0.2 --outFilterMatchNminOverLread 0.2 --outFilterMismatchNmax 1 --alignEndsType EndToEnd --outSAMattributes NH HI NM MD  (>80% uniquely mapped rates)
kallisto/0.46.2
rtracklayer/1.46.0, Rsamtools/2.2.3
GemonicRanges/1.38.0, GenomicAlignments/1.22.1, STAN/2.14.0
generate bigwig files using deepTools/v3.3.1 bamCoverage command with default settings
Genome_build: mm9
Supplementary_files_format_and_content: Genomic tracks in bigwig format with spike-in normalization

source_name: mESC

growth_protocol: Serum medium was used to culture mouse embryonic stem cells (mESCs) with feeder-free in 0.1% gelatin-coated flasks (Sigma, G1890) under standard conditions (10% CO2, 90% humidity, 37 °C) in KnockOut DMEM (LifeTechnologies, 10829018), 2 mM Alanyl-glutamine (Sigma, G8541), 0.1 mM non-essential amino acids (Sigma, M7145) 15% fetal bovine serum (FBS) (Sigma, F7524), 0.1 mM β-mercaptoethanol (Sigma, M3148), ESGRO Leukemia Inhibitory Factor (LIF) (Millipore, ESG1107), Penicillin-Streptomycin (Sigma, P4333).

extract_protocol:
TT-seq was performed as described before (Schwalb et al., 2016). In short, cells were seeded in 5 million per 15 cm dish for 2 days. After recording the cell number, cells were supplemented with 500 µM of 4-thiouracil (4sU) (Sigma-Aldrich, T4509) for 5 min at 37°C and 5\% CO2, then immediately quenched 4sU incorporation with TRIzol (ThermoFisher, 15596018). Total RNA extraction were fragmented to about 1 kb with Bioruptor (Diagenode), then incubated with HPDP-Biotin (ThermoFisher, 21341) for 2 hours at room temperature. A small aliquot was saved as fragmented total RNA and the rest was subjected to µMACS streptavidin beads (Miltenyi Biotec, 130-074-101) and purified with miRNeasy Micro Kit (Qiagen, 217084) with DNase digestion (Qiagen, 79254).
Ovation Universal RNA-Seq System 1-16 (NuGEN, #0348).
Stranded Ribo-minus RNA-Seq

treatment_protocol: mESCs were switched to 2i medium with ESGRO Complete Basal Medium (Millipore, SF002), 1 μM MEK inhibitor PD0325901 (Sigma, PZ0162) and 3 μM GSK3 inhibitor CHIR99021 (Sigma, SML1046), 0.1 mM β-mercaptoethanol (Sigma, M3148), ESGRO Leukemia Inhibitory Factor (LIF) (Millipore, ESG1107), Penicillin-Streptomycin (Sigma, P4333). mES mTORi cells were treated with 200nM INK128 (VWR, CAYM11811) in the serum LIF medium as described above.

value: mouse embryonic stem cells

tag: assay

value: TT-seq labeled RNA

tag: culture

value: 2 days culture in mTORi medium


title: MDXC1 sample 1.1

city: Bethesda

first: Donald

middle: P

last: Bottaro

state: MD

address: Bldg 10 CRC Rm 2-3952, 10 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute

hyb_protocol: As decribed in MAN-10100-02; http://blog.nanostring.com/geomx-online-user-manual-v1.5/Content/PDF_downloads/MAN-10100-02_GeoMx-Protein-Slide-Prep_QS.pdf

scan_protocol: Hybridized panels (770 genes and 30 control genes) were read at maximum field count (555 FOV).

data_processing: nCounter software version 2.0 and 3.0

label: Nanostring bar code

source_name: MDXC1 cell mRNA

growth_protocol: Cells were grown to near confluence, then serum-deprived for 16 h.

extract_protocol: Total RNA was extracted and samples were processed and analyzed per the manufacturer’s protocol (Nanostring nCounter profiling arrays, manual MAN-10100-02).

treatment_protocol: Cells were untreated for all samples.

tag: sample type

value: 90% confluent culture


title: G14_37_2


title: J82 sample 1.1

source_name: J82 cell mRNA

label_protocol: As decribed in MAN-10100-02; http://blog.nanostring.com/geomx-online-user-manual-v1.5/Content/PDF_downloads/MAN-10100-02_GeoMx-Protein-Slide-Prep_QS.pdf


title: J82 sample 1.2


title: LRNA_mTORi_1d_rep2

value: 1 day culture in mTORi medium


title: Sample_04-00268

value: Mononuclear Cells

value: Bone Marrow Aspirate


title: G14_37_1


title: MDXC1 sample 1.2


title: Sample_04-00267


title: 42652-P1-FC

value: Peripheral blood mononuclear cells


title: LRNA_mTORi_1d_rep1


title: G14_28_3

value: induction temperature 28 degrees C


title: LRNA_mTORi_2d_rep2


title: 42652-P1-D2

value: SIP-Isolated


title: 42634-P2-D13

value: SIP-JuvenilePartnered


title: Sample_04-00225

value: CML, Newly diagnosed / TKI naive


title: G14_28_2


title: LRNA_SL_rep2

value: culture in SL medium


title: 42634-P2-D8


title: 42652-P1-D8


title: Sample_04-00165

value: CML, TKI responder


title: 42634-P2-D2


title: Sample_04-00155


title: Parent_28_3

value: parent


title: G14_28_1

value: oxidative and thermal stress cross-tolerant mutant


title: LRNA_SL_rep1


title: LRNA_2i_7d_rep1

value: 7 days culture in 2i medium


title: 42634-P2-FC


title: RNA-seq_p11_2

tag: age

value: postnatal day P11

value: retina

value: Retinal Ganglion Cell


title: Sample_04-00129

tag: disease state


title: LRNA_2i_2d_rep2

value: mouse embryonic stem cells

value: TT-seq labeled RNA

value: 2 days culture in 2i medium


title: 42634-P1-D13


title: Parent_28_2