title: WG17019_E07-W10

description:
single cell
AAGATGGCAGTCG


title: WG17019_E07-W05

status: Public on Mar 11 2021

type: SRA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description:
single cell
AAGATGGCACGCT

library_source: transcriptomic

data_processing:
Reads flagged as invalid by the Illumina HiSeq control software were discarded. In the remaining reads, any 3′ bases with a quality score of B were removed. If any of the six UMI bases in the 5' end had a Phred score <17 the read was discarded, else the UMI was cut away and saved. The following three bases had to be G for the read to be kept. These, as well as any additional up to totally nine (presumably template-switch derived) G:s were cut away. Reads were discarded if the remaining transcript-derived sequence ended in a poly(A) sequence leaving <25 bases, or if the remaining sequence consisted of fewer than six non-A bases or a dinucleotide repeat with fewer than six other bases at either end. The reads were sorted by the well, as defined by the combined two index read barcodes.
Alignment was performed using the Bowtie aligner, allowing for up to three mismatches and up to 24 alternative mappings. Reads with no alignments were realigned against an artificial chromosome, containing all possible splice junctions arising from the exons defined by the UCSC transcript models. The coordinates of aligned splice junctions were translated back to the corresponding genomic positions.
For expression level calculation, the exons of each locus with several transcript variants were merged to a combined model representing total expression of the locus. To account for incomplete cap site knowledge, the 5′ ends of all models were extended by 100 bases, but not beyond the 3′ end of any upstream nearby exon of another gene of the same orientation.
The annotation step was performed separately for each well. For each genomic position and strand combination the number of reads in each UMI was counted. Any multiread that mapped to some repeat outside exons was assigned randomly as one of these repeats and did not contribute to the transcript corresponding to the exon. Else, if the multiread mapped to some exon, and not to any repeat outside exons, it was assigned to the exon where it was closest to the transcript model 5′ end. If it had no exon mapping, it was assigned randomly at one of the mappings. The total number of molecules at each mapping position was determined by the number of distinct UMIs observed. Any UMI represented by only a single read was excluded, in order to reduce false molecules due to PCR and sequencing errors. The raw UMI count was corrected for the UMI collision probability.
Genome_build: rheMac8
Supplementary_files_format_and_content: Processed data consists of a UMI count matrix, where rows are geneIDs and columns cellIDs, and an annotation text file where rows are CellIDs and columns the annotations

molecule: total 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 standard Illumina protocols

tag: tissue

value: dorsal root ganglion

tag: cell type

tag: gender

value: Female

tag: age

value: 4 years 8 months


title: WG17019_F07-W10

description:
single cell
CACCTTTCAACGG


title: WG17019_F07-W06

description:
single cell
CACCTTTCATCCA


title: WG17019_D07-W14

description:
single cell
AAGATGGCAAGGA


title: WG17019_D07-W13

description:
single cell
AAGATGGCAAGCG


title: WG17019_D07-W11

description:
single cell
AAGATGGCAACCT


title: WG17019_D07-W12

description:
single cell
AAGATGGCAACGG


title: WG17019_D07-W09

description:
single cell
AAGATGGCAAACC


title: WG17019_E07-W15

description:
single cell
AGTTGTGGAAGCG


title: WG17019_D07-W10

description:
single cell
AAGATGGCAACAC


title: WG17019_D07-W08

description:
single cell
AAGATGGCATCCA


title: WG17019_D07-W05

description:
single cell
ACAGCGAAAGTCG


title: WG17019_D07-W02

description:
single cell
ACAGCGAAAGACT


title: WG17019_D07-W04

description:
single cell
ACAGCGAAAGCTA

value: ambiguous


title: WG17019_D07-W01

description:
single cell
ACAGCGAAAGAAG

value: non-neuronal


title: WG17019_C07-W14

description:
single cell
ACAGCGAAACTGT


title: WG17019_B08-W18

description:
single cell
TCGGGTGAATCCA


title: WG17019_D07-W17

description:
single cell
AAGATGGCAAGTC


title: WG17019_C07-W06

description:
single cell
ACAGCGAAACGAC


title: WG17019_C07-W13

description:
single cell
ACAGCGAAACTCC


title: WG17019_C07-W01

description:
single cell
ACAGCGAAACAGA


title: WG17019_B07-W25

description:
single cell
ACAGCGAAAAGTC


title: WG17019_C07-W09

description:
single cell
ACAGCGAAACGCT


title: WG17019_C07-W10

description:
single cell
ACAGCGAAACGTA


title: WG17019_C07-W05

description:
single cell
ACAGCGAAACCTG


title: WG17019_C07-W02

description:
single cell
ACAGCGAAACCAT


title: WG17019_B07-W17

description:
single cell
ACAGCGAAAAGCG


title: WG17019_B07-W26

description:
single cell
ACAGCGAAAATGC

value: C-LTMR


title: WG17019_B07-W11

description:
single cell
ACAGCGAAAACAC


title: WG17019_B07-W14

description:
single cell
ACAGCGAAAACGG


title: WG17019_B07-W18

description:
single cell
ACAGCGAAAAGGA


title: WG17019_B07-W10

description:
single cell
ACAGCGAAAAACC


title: WG17019_B07-W13

description:
single cell
ACAGCGAAAACCT


title: WG17019_B07-W08

description:
single cell
TTTCCGAAAAACC


title: WG17019_D07-W06

description:
single cell
ACAGCGAAAGTTC


title: WG17019_B07-W07

description:
single cell
TTTCCGAAATCCA


title: WG17019_B07-W06

description:
single cell
GCTGAGGTAATGC


title: WG17019_B07-W09

description:
single cell
ACAGCGAAATCCA


title: WG17019_B07-W04

description:
single cell
GCTGAGGTATCCA


title: WG17019_B07-W02

description:
single cell
AAGGAGCTACTGT


title: WG17019_B07-W01

description:
single cell
AAGGAGCTACGCT


title: WG17019_B07-W05

description:
single cell
GCTGAGGTAAACC


title: WG17019_A07-W25

description:
single cell
AAGGAGCTACGAC


title: WG17019_A07-W14

description:
single cell
AAGGAGCTAAGCG


title: WG17019_A07-W17

description:
single cell
AAGGAGCTAATGC


title: WG17019_A07-W13

description:
single cell
AAGGAGCTAACGG


title: WG17019_A07-W07

description:
single cell
AAGGAGCTAACAC


title: WG17019_A07-W06

description:
single cell
AAGGAGCTAAACC


title: WG17019_A07-W04

description:
single cell
AAAGGTCCAGTCG


title: WG17019_A07-W05

description:
single cell
AAGGAGCTATCCA


title: WG17019_H06-W02

description:
single cell
AAAGGTCCACGCT


title: WG17019_A07-W03

description:
single cell
AAAGGTCCAGAAG


title: WG17019_G06-W01

description:
single cell
AAAGGTCCAAGGA


title: WG17019_G06-W02

description:
single cell
AAAGGTCCAATGC


title: WG17019_F06-W05

description:
single cell
AAAGGTCCAAACC


title: WG17019_F06-W02

description:
single cell
AAAGGTCCATCCA


title: WG17019_F06-W01

description:
single cell
TCGACATCATGGG


title: WG17019_F06-W09

description:
single cell
AAAGGTCCAACCT


title: WG17019_F06-W10

description:
single cell
AAAGGTCCAACGG

value: injured cell


title: WG17019_F06-W13

description:
single cell
AAAGGTCCAAGCG


title: WG17019_E06-W02

description:
single cell
TCGACATCATGCC


title: WG17019_H06-W01

description:
single cell
AAAGGTCCACGAC


title: WG17019_F06-W06

description:
single cell
AAAGGTCCAACAC


title: WG17019_D06-W10

description:
single cell
TCGACATCAGCTA


title: WG17019_D06-W09

description:
single cell
TCGACATCAGCGT


title: WG17019_A07-W18

description:
single cell
AAGGAGCTACAGA


title: WG17019_D06-W13

description:
single cell
TCGACATCAGGAT


title: WG17019_D06-W14

description:
single cell
TCGACATCAGTCG


title: WG17019_E06-W01

description:
single cell
TCGACATCAGTTC


title: WG17019_A07-W01

description:
single cell
AAAGGTCCACTGT


title: WG17019_D06-W05

description:
single cell
TCGACATCAGACT


title: WG17019_C06-W09

description:
single cell
TCGACATCACTCC


title: WG17019_D06-W02

description:
single cell
TCGACATCAGAAG


title: WG17019_C06-W01

description:
single cell
TCGACATCACGCT


title: WG17019_G06-W10

description:
single cell
AAAGGTCCACAGA


title: WG17019_B06-W13

description:
single cell
TCGACATCACGAC


title: WG17019_B06-W10

description:
single cell
TCGACATCACCTG


title: WG17019_B06-W09

description:
single cell
TCGACATCACCAT


title: WG17019_A06-W10

description:
single cell
TCGACATCAAGGA


title: WG17019_B06-W01

description:
single cell
TCGACATCAAGTC


title: WG17019_H05-W14

description:
single cell
TCGACATCAACAC


title: WG17019_A06-W09

description:
single cell
TCGACATCAAGCG


title: WG17019_A06-W02

description:
single cell
TCGACATCAACGG


title: WG17019_A06-W01

description:
single cell
TCGACATCAACCT


title: WG17019_D06-W01

description:
single cell
TCGACATCACTGT


title: WG17019_H05-W10

description:
single cell
TCGACATCATCCA


title: WG17019_G05-W02

description:
single cell
CGCTAAATAACGG


title: WG17019_F05-W09

description:
single cell
CGCTAAATATCCA


title: WG17019_H05-W05

description:
single cell
CGCTAAATAATGC


title: WG17019_H05-W06

description:
single cell
CGCTAAATACAGA


title: WG17019_H05-W09

description:
single cell
CGCTAAATACGAC


title: WG17019_H05-W01

description:
single cell
CGCTAAATAAGCG


title: WG17019_F05-W10

description:
single cell
CGCTAAATAAACC


title: WG17019_H05-W13

description:
single cell
TCGACATCAAACC


title: WG17019_D05-W13

description:
single cell
CGACTATGAAGCG


title: WG17019_C06-W02

description:
single cell
TCGACATCACGTA


title: WG17019_D05-W09

description:
single cell
CGACTATGATCCA


title: WG17019_E05-W01

description:
single cell
CGACTATGAATGC


title: WG17019_E05-W02

description:
single cell
CGACTATGACAGA


title: WG17019_D05-W06

description:
single cell
CTTTACCTAGTCG


title: WG17019_F05-W05

description:
single cell
GGACCTTAACGAC


title: WG17019_D05-W05

description:
single cell
CTTTACCTACTGT


title: WG17019_B06-W05

description:
single cell
TCGACATCACAGA


title: WG17019_D05-W02

description:
single cell
CTTTACCTACGCT


title: WG17019_D05-W01

description:
single cell
CTTTACCTAATGC


title: WG17019_B06-W02

description:
single cell
TCGACATCAATGC


title: WG17019_C05-W09

description:
single cell
CTTTACCTAACCT


title: WG17019_C05-W13

description:
single cell
CTTTACCTAAGGA


title: WG17019_F05-W01

description:
single cell
CGACTATGACGCT


title: WG17019_C05-W01

description:
single cell
CACTTCCGAATGC


title: WG17019_C05-W02

description:
single cell
CACTTCCGACGAC


title: WG17019_B05-W01

description:
single cell
TTCACCCGACGCT


title: WG17019_B05-W05

description:
single cell
TTCACCCGACTGT


title: WG17019_C05-W10

description:
single cell
CTTTACCTAAGCG


title: WG17019_C05-W14

description:
single cell
CTTTACCTAAGTC


title: WG17019_C05-W06

description:
single cell
CTTTACCTATCCA


title: WG17019_H04-W26

description:
single cell
TTCACCCGAATGC


title: WG17019_C05-W05

description:
single cell
CACTTCCGACTGT


title: WG17019_H04-W17

description:
single cell
TTCACCCGAACAC


title: WG17019_B05-W09

description:
single cell
CACTTCCGATCCA


title: WG17019_B05-W13

description:
single cell
CACTTCCGAACAC


title: WG17019_B05-W10

description:
single cell
CACTTCCGAAACC


title: WG17019_H04-W31

description:
single cell
TTCACCCGACGAC


title: WG17019_H04-W22

description:
single cell
TTCACCCGAAGCG


title: WG17019_H04-W30

description:
single cell
TTCACCCGACAGA


title: WG17019_G04-W14

description:
single cell
CTACATCAACCTG


title: WG17019_H04-W01

description:
single cell
CTACATCAACGAC


title: WG17019_H04-W06

description:
single cell
CTACATCAAGAAG


title: WG17019_H04-W04

description:
single cell
CTACATCAACTGT


title: WG17019_H04-W16

description:
single cell
TTCACCCGAAACC


title: WG17019_H04-W02

description:
single cell
CTACATCAACGCT


title: WG17019_H04-W03

description:
single cell
CTACATCAACGTA


title: WG17019_G04-W13

description:
single cell
CTACATCAACCAT


title: WG17019_H04-W14

description:
single cell
TTCACCCGATCCA


title: WG17019_H04-W09

description:
single cell
CTACATCAAGTCG


title: WG17019_H04-W18

description:
single cell
TTCACCCGAACGG


title: WG17019_F04-W25

description:
single cell
CTACATCAAACAC


title: WG17019_G04-W09

description:
single cell
CTACATCAAATGC


title: WG17019_F04-W12

description:
single cell
GGATACGTAATGC


title: WG17019_F04-W17

description:
single cell
CTACATCAATCCA


title: WG17019_F04-W15

description:
single cell
GGATACGTACGCT


title: WG17019_H04-W10

description:
single cell
CTACATCAAGTTC


title: WG17019_G04-W06

description:
single cell
CTACATCAAAGTC


title: WG17019_F04-W08

description:
single cell
GGATACGTATCCA


title: WG17019_G04-W05

description:
single cell
CTACATCAAAGGA


title: WG17019_G04-W02

description:
single cell
CTACATCAAAGCG


title: WG17019_F04-W18

description:
single cell
CTACATCAAAACC


title: WG17019_G04-W01

description:
single cell
CTACATCAAACGG


title: WG17019_F04-W06

description:
single cell
TGGACTGGACAGA


title: WG17019_F04-W13

description:
single cell
GGATACGTACAGA


title: WG17019_F04-W14

description:
single cell
GGATACGTACGAC


title: WG17019_F04-W11

description:
single cell
GGATACGTAAGCG


title: WG17019_F04-W10

description:
single cell
GGATACGTAACGG


title: WG17019_F04-W05

description:
single cell
TGGACTGGAATGC


title: WG17019_F04-W26

description:
single cell
CTACATCAAACCT


title: WG17019_F04-W02

description:
single cell
TGGACTGGAAACC


title: WG17019_E04-W17

description:
single cell
TGGACTGGATCCA


title: WG17019_F04-W03

description:
single cell
TGGACTGGAACGG


title: WG17019_E04-W05

description:
single cell
CTAATGACAAGCG


title: WG17019_E04-W02

description:
single cell
CTAATGACAACAC


title: WG17019_E04-W03

description:
single cell
CTAATGACAACGG


title: WG17019_E04-W01

description:
single cell
CTAATGACAAACC


title: WG17019_F04-W09

description:
single cell
GGATACGTAAACC


title: WG17019_G04-W10

description:
single cell
CTACATCAACAGA


title: WG17019_F04-W07

description:
single cell
TGGACTGGACGAC


title: WG17019_F04-W04

description:
single cell
TGGACTGGAAGCG


title: WG17019_E04-W14

description:
single cell
CTAATGACACTGT


title: WG17019_E04-W13

description:
single cell
CTAATGACACGCT


title: WG17019_E04-W10

description:
single cell
CTAATGACACGAC


title: WG17019_C04-W13

description:
single cell
CCTGTAACACGCT


title: WG17019_C04-W05

description:
single cell
CCTGTAACACCAT


title: WG17019_E04-W09

description:
single cell
CTAATGACACAGA


title: WG17019_E04-W06

description:
single cell
CTAATGACAATGC


title: WG17019_D04-W17

description:
single cell
CTAATGACATCCA


title: WG17019_D04-W13

description:
single cell
CCTGTAACAGTTC


title: WG17019_B04-W05

description:
single cell
CCTGTAACAACCT


title: WG17019_B04-W10

description:
single cell
CCTGTAACAAGCG


title: WG17019_B04-W06

description:
single cell
CCTGTAACAACGG


title: WG17019_D04-W01

description:
single cell
CCTGTAACACGTA


title: WG17019_D04-W05

description:
single cell
CCTGTAACAGAAG


title: WG17019_C04-W10

description:
single cell
CCTGTAACACGAC


title: WG17019_A04-W17

description:
single cell
CCTATCGTAGACT


title: WG17019_B04-W14

description:
single cell
CCTGTAACAAGTC


title: WG17019_A04-W11

description:
single cell
CCTATCGTACGTA


title: WG17019_B04-W13

description:
single cell
CCTGTAACAAGGA


title: WG17019_B04-W01

description:
single cell
CCTGTAACAACAC


title: WG17019_A04-W29

description:
single cell
CCTGTAACAAACC


title: WG17019_A04-W26

description:
single cell
CCTGTAACATCCA


title: WG17019_A04-W25

description:
single cell
CCTATCGTAGTTC


title: WG17019_A04-W21

description:
single cell
CCTATCGTAGTCG


title: WG17019_A04-W19

description:
single cell
CCTATCGTAGCTA


title: WG17019_A04-W16

description:
single cell
CCTATCGTAGAAG


title: WG17019_D04-W09

description:
single cell
CCTGTAACAGTCG


title: WG17019_A04-W13

description:
single cell
CCTATCGTACTGT


title: WG17019_A04-W07

description:
single cell
CCTATCGTACCAT


title: WG17019_D04-W03

description:
single cell
CCTGTAACACTGT


title: WG17019_C04-W09

description:
single cell
CCTGTAACACCTG


title: WG17019_A04-W12

description:
single cell
CCTATCGTACTCC


title: WG17019_A04-W03

description:
single cell
CCTATCGTAAGGA


title: WG17019_A04-W04

description:
single cell
CCTATCGTAAGTC


title: WG17019_C04-W02

description:
single cell
CCTGTAACACAGA


title: WG17019_A04-W02

description:
single cell
CCTATCGTAAGCG


title: WG17019_A04-W01

description:
single cell
CCTATCGTAACGG


title: WG17019_C04-W01

description:
single cell
CCTGTAACAATGC


title: WG17019_H03-W10

description:
single cell
CCTATCGTAACAC


title: WG17019_A04-W09

description:
single cell
CCTATCGTACGAC


title: WG17019_A04-W06

description:
single cell
CCTATCGTACAGA


title: WG17019_A04-W05

description:
single cell
CCTATCGTAATGC


title: WG17019_A04-W08

description:
single cell
CCTATCGTACCTG


title: WG17019_H03-W14

description:
single cell
CCTATCGTAACCT


title: WG17019_H03-W09

description:
single cell
CCTATCGTAAACC


title: WG17019_H03-W06

description:
single cell
CCTATCGTATCCA


title: WG17019_H03-W02

description:
single cell
GTCGTTGAATGCC


title: WG17019_A04-W10

description:
single cell
CCTATCGTACGCT


title: WG17019_G03-W17

description:
single cell
GTCGTTGAAGTCG


title: WG17019_G03-W13

description:
single cell
GTCGTTGAAGGAT


title: WG17019_H03-W01

description:
single cell
GTCGTTGAAGTTC


title: WG17019_H03-W05

description:
single cell
GTCGTTGAATGGG


title: WG17019_G03-W06

description:
single cell
GTCGTTGAAGACT


title: WG17019_G03-W05

description:
single cell
GTCGTTGAAGAAG


title: WG17019_G03-W03

description:
single cell
GTCGTTGAACTGT


title: WG17019_G03-W02

description:
single cell
GTCGTTGAACTCC


title: WG17019_G03-W01

description:
single cell
GTCGTTGAACGTA


title: WG17019_F03-W26

description:
single cell
GTCGTTGAACGCT


title: WG17019_F03-W18

description:
single cell
GTCGTTGAACCTG


title: WG17019_F03-W25

description:
single cell
GTCGTTGAACGAC


title: WG17019_F03-W11

description:
single cell
GTCGTTGAAATGC


title: WG17019_F03-W10

description:
single cell
GTCGTTGAAAGTC


title: WG17019_F03-W09

description:
single cell
GTCGTTGAAAGGA


title: WG17019_F03-W06

description:
single cell
GTCGTTGAAACCT


title: WG17019_F03-W05

description:
single cell
GTCGTTGAAACAC


title: WG17019_F03-W08

description:
single cell
GTCGTTGAAAGCG


title: WG17019_F03-W07

description:
single cell
GTCGTTGAAACGG


title: WG17019_F03-W03

description:
single cell
GTCGTTGAATCCA


title: WG17019_F03-W01

description:
single cell
TTAGCGGTAATGC


title: WG17019_G03-W10

description:
single cell
GTCGTTGAAGCTA


title: WG17019_F03-W02

description:
single cell
TTAGCGGTACGAC


title: WG17019_E03-W25

description:
single cell
TTAGCGGTAACGG


title: WG17019_E03-W14

description:
single cell
GGCAGACTAACGG


title: WG17019_E03-W18

description:
single cell
TTAGCGGTATCCA


title: WG17019_E03-W13

description:
single cell
AGGGAAGCACTGT


title: WG17019_G03-W09

description:
single cell
GTCGTTGAAGCGT


title: WG17019_E03-W09

description:
single cell
AGGGAAGCAATGC


title: WG17019_E03-W10

description:
single cell
AGGGAAGCACGCT


title: WG17019_E03-W17

description:
single cell
GGCAGACTACAGA


title: WG17019_E03-W07

description:
single cell
AGGGAAGCAAGGA


title: WG17019_E03-W06

description:
single cell
AGGGAAGCAACGG


title: WG17019_F03-W13

description:
single cell
GTCGTTGAACAGA


title: WG17019_F03-W17

description:
single cell
GTCGTTGAACCAT


title: WG17019_E03-W04

description:
single cell
AGGGAAGCAAACC


title: WG17019_E03-W01

description:
single cell
GGAGTTACATCCA


title: WG17019_D03-W26

description:
single cell
CTACCCTCAGTTC


title: WG17019_E03-W03

description:
single cell
GGAGTTACAATGC


title: WG17019_D03-W15

description:
single cell
CTACCCTCACTGT


title: WG17019_D03-W25

description:
single cell
CTACCCTCAGTCG


title: WG17019_D03-W14

description:
single cell
CTACCCTCACGTA


title: WG17019_D03-W17

description:
single cell
CTACCCTCAGAAG


title: WG17019_D03-W11

description:
single cell
CTACCCTCACCAT


title: WG17019_D03-W13

description:
single cell
CTACCCTCACGCT


title: WG17019_D03-W10

description:
single cell
CTACCCTCACAGA


title: WG17019_F03-W04

description:
single cell
GTCGTTGAAAACC


title: WG17019_D03-W12

description:
single cell
CTACCCTCACGAC


title: WG17019_D03-W09

description:
single cell
CTACCCTCAATGC


title: WG17019_D03-W08

description:
single cell
CTACCCTCAAGTC


title: WG17019_D03-W06

description:
single cell
CTACCCTCAAGCG


title: WG17019_D03-W07

description:
single cell
CTACCCTCAAGGA


title: WG17019_D03-W04

description:
single cell
CTACCCTCAACCT


title: WG17019_D03-W01

description:
single cell
CTACCCTCATCCA


title: WG17019_D03-W05

description:
single cell
CTACCCTCAACGG


title: WG17019_C03-W10

description:
single cell
ACAATCCCACGAC


title: WG17019_D03-W03

description:
single cell
CTACCCTCAACAC


title: WG17019_C03-W13

description:
single cell
ACAATCCCACGCT


title: WG17019_C03-W05

description:
single cell
ACAATCCCAATGC


title: WG17019_E03-W02

description:
single cell
GGAGTTACAACGG


title: WG17019_C03-W09

description:
single cell
ACAATCCCACAGA


title: WG17019_D03-W02

description:
single cell
CTACCCTCAAACC


title: WG17019_C03-W01

description:
single cell
ACAATCCCAACGG


title: WG17019_B03-W18

description:
single cell
ACAATCCCATCCA


title: WG17019_B03-W15

description:
single cell
GTCAATCCAATGC


title: WG17019_B03-W25

description:
single cell
ACAATCCCAAACC


title: WG17019_C03-W02

description:
single cell
ACAATCCCAAGCG


title: WG17019_B03-W14

description:
single cell
GTCAATCCAAACC


title: WG17019_B03-W11

description:
single cell
TGATTACCACGAC


title: WG17019_B03-W12

description:
single cell
TGATTACCACGCT


title: WG17019_B03-W10

description:
single cell
TGATTACCACAGA


title: WG17019_B03-W07

description:
single cell
TGATTACCAACGG


title: WG17019_B03-W08

description:
single cell
TGATTACCAAGCG


title: WG17019_B03-W09

description:
single cell
TGATTACCAATGC


title: WG17019_B03-W03

description:
single cell
TCATGCACACGAC


title: WG17019_B03-W02

description:
single cell
TCATGCACACAGA


title: WG17019_B03-W04

description:
single cell
TGATTACCATCCA


title: WG17019_A03-W25

description:
single cell
TCATGCACAACGG


title: WG17019_B03-W01

description:
single cell
TCATGCACAATGC


title: WG17019_A03-W17

description:
single cell
TCATGCACAAACC


title: WG17019_A03-W13

description:
single cell
TCAGTGTGACGAC


title: WG17019_A03-W09

description:
single cell
TCAGTGTGAATGC


title: WG17019_A03-W06

description:
single cell
TCAGTGTGAAACC


title: WG17019_A03-W07

description:
single cell
TCAGTGTGAACGG


title: WG17019_H02-W27

description:
single cell
TACCAGTAAGGAT


title: WG17019_A03-W03

description:
single cell
TACCAGTAATGCC


title: WG17019_H02-W24

description:
single cell
TACCAGTAAGCTA


title: WG17019_A03-W01

description:
single cell
TACCAGTAAGTTC


title: WG17019_H02-W19

description:
single cell
TACCAGTAAGACT


title: WG17019_A03-W05

description:
single cell
TCAGTGTGATCCA


title: WG17019_H02-W22

description:
single cell
TACCAGTAAGCGT


title: WG17019_B03-W13

description:
single cell
GTCAATCCATCCA


title: WG17019_H02-W17

description:
single cell
TACCAGTAAGAAG


title: WG17019_B03-W06

description:
single cell
TGATTACCAAACC


title: WG17019_H02-W14

description:
single cell
TACCAGTAACTCC


title: WG17019_H02-W16

description:
single cell
TACCAGTAACTGT


title: WG17019_H02-W04

description:
single cell
TACCAGTAACGAC


title: WG17019_H02-W10

description:
single cell
TACCAGTAACGCT


title: marR-MeOH-2

city: Saint Paul

first: Jannell

middle: V.

last: Bazurto

state: MINNESOTA

address: 1500 Gortner Ave

department: Plant and Microbial Biology

country: USA

institute: University of Minnesota

description:
ΔttmR
mRNA
Bazurto_ttmR_raw_read_counts.xlsx
Bazurto_ttmR_final_full_dataset.xlsx

data_processing:
FastQC was used to assess the quality of the sequencing data.
Trimmomatic was used to remove the low quality bases and adapter sequences.
HISAT2 was used to align the curated reads to the M. extorquens PA1 genome.
Cuffquant and Cufnorm from the Cufflinks package were used to generate FPKM expression values.
featureCounts from the Rsubread R package was used to generate raw read counts.
DESeq2 was used to convert raw count data to normalized counts.
All further statistical analyses were carried out in R.
Genome_build: GenBank accession: CP000908.1
Supplementary_files_format_and_content: Bazurto_ttmR_raw_read_counts.xlsx: Raw read counts in an Excel file.
Supplementary_files_format_and_content: Bazurto_ttmR_final_full_dataset.xlsx: Fully processed data set comparing wild-type to ΔttmR mutant (includes Log2FC values, p-values, q-values for all genes).

organism: Methylorubrum extorquens PA1

source_name: ΔttmR mutant

growth_protocol: Cells were grown in liquid Methylobacterium PIPES (MP) medium supplemented with 15 mM methanol at 30 ℃ with shaking.

extract_protocol:
The total RNA was extracted with the RNeasy Plus Mini Kit (Qiagen); rRNA was depleted with the Ribo-Zero rRNA removal kit (Illumina); the quality of resulting RNA samples was determined with an Agilent 2100 BioAnalyzer and Qubit assay.
RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR.

tag: strain number

tag: genotype

value: <delta>ttmR

tag: growth phase

value: early exponential

tag: carbon source

value: 15 mM methanol


title: marR-MeOH-1


title: WG17019_G02-W32

description:
single cell
TACCAGTAACCTG


title: WT-MeOH-1

description:
Bazurto_ttmR_raw_read_counts.xlsx
Bazurto_ttmR_final_full_dataset.xlsx

source_name: wild-type

value: wild-type


title: WT-MeOH-2

description:
mRNA
Bazurto_ttmR_raw_read_counts.xlsx
Bazurto_ttmR_final_full_dataset.xlsx


title: WT-MeOH-3


title: marR-MeOH-3


title: WG17019_G02-W31

description:
single cell
TACCAGTAACCAT


title: WG17019_A03-W10

description:
single cell
TCAGTGTGACAGA


title: WG17019_G02-W30

description:
single cell
TACCAGTAACAGA


title: WG17019_H02-W29

description:
single cell
TACCAGTAAGTCG


title: WG17019_G02-W28

description:
single cell
TACCAGTAAAGTC


title: WG17019_G02-W27

description:
single cell
TACCAGTAAAGGA


title: WG17019_G02-W26

description:
single cell
TACCAGTAAAGCG


title: WG17019_A03-W14

description:
single cell
TCATGCACATCCA


title: KidN24_4

city: Chongqing

first: Min-Dian

last: Li

address: 30 Gaotanyan Main Street

department: Cardiology

country: China

institute: Southwest Hospital, Third Military Medical University (Army Medical University)

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.  SOAPnuke:Version v1.5.2  Parameters -l 15 -q 0.2 -n 0.05
The clean reads were mapped to the reference genome using HISAT2.   HISAT2: version: v2.0.4  Parameters：--phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Bowtie2 was applied to align the clean reads to the gene set. The expression level of gene was calculated by RSEM and represented as TPM.  Bowtie2: version: v2.2.5  Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200  RSEM: version: v1.2.12
Genome_build: mm10/GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: adult female kidney

growth_protocol: Special pathogen-free (SPF) mice were purchased from Hunan SJT Laboratory Animal Co. and housed in a SPF barrier facility. C57BL/6J female mice at 7 weeks of age were grouped housed, and entrained to a 12h light:12h dark cycle with normal chow food and water ad libitum for 7 days before assigned to daytime-restricted feeding (DRF) and nighttime-restricted feeding (NRF) groups for additional 7 days.

extract_protocol:
Tissues were dissected, flash frozen liquid nitrogen, and RNA was harvested using Trizol reagent.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at an appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Animals were subjected to daytime-restricted feeding (DRF) or nighttime-restricted feeding (NRF) for 7 days

tag: strain

value: 9 weeks

tag: dietary regimen

value: NRF

tag: zeitgeber time in hours


title: KidN24_1


title: KidN20_4


title: KidN24_3


title: KidN24_2


title: WG17019_H02-W12

description:
single cell
TACCAGTAACGTA


title: KidN20_2


title: KidN20_3


title: WG17019_G02-W24

description:
single cell
TACCAGTAAACCT


title: WG17019_G02-W25

description:
single cell
TACCAGTAAACGG


title: WG17019_G02-W23

description:
single cell
TACCAGTAAACAC


title: WG17019_G02-W21

description:
single cell
TACCAGTAATCCA


title: KidN16_4


title: WG17019_G02-W29

description:
single cell
TACCAGTAAATGC


title: KidN16_3


title: KidN16_1


title: WG17019_G02-W22

description:
single cell
TACCAGTAAAACC


title: KidN16_2


title: WG17019_G02-W20

description:
single cell
TGACGTGCCAAGG


title: KidN12_3


title: WG17019_G02-W16

description:
single cell
TGACGTGCATCAG


title: WG17019_G02-W18

description:
single cell
TGACGTGCATGGG


title: KidN12_4


title: WG17019_G02-W17

description:
single cell
TGACGTGCATGCC


title: KidN12_2


title: WG17019_G02-W15

description:
single cell
TGACGTGCATAGC


title: WG17019_G02-W14

description:
single cell
TGACGTGCAGTTC


title: WG17019_G02-W12

description:
single cell
TGACGTGCAGTCG


title: KidN12_1


title: WG17019_G02-W09

description:
single cell
TGACGTGCAGGCA


title: WG17019_G02-W11

description:
single cell
TGACGTGCAGGTG


title: KidN20_1


title: KidN08_1


title: KidN08_2


title: KidN08_4


title: KidN04_4


title: KidN08_3


title: KidN04_3


title: WG17019_G02-W07

description:
single cell
TGACGTGCAGCTA


title: WG17019_G02-W19

description:
single cell
TGACGTGCCAACT


title: WG17019_G02-W08

description:
single cell
TGACGTGCAGGAT


title: WG17019_G02-W06

description:
single cell
TGACGTGCAGCGT


title: WG17019_G02-W04

description:
single cell
TGACGTGCAGACT


title: KidN04_2


title: WG17019_G02-W03

description:
single cell
TGACGTGCAGAAG


title: WG17019_G02-W02

description:
single cell
TGACGTGCACTGT


title: KidN00_3


title: KidN00_4


title: WG17019_G02-W01

description:
single cell
TGACGTGCACTCC


title: KidN04_1


title: KidD24_4

value: DRF


title: KidN00_2


title: KidN00_1


title: WG17019_F02-W26

description:
single cell
TGACGTGCACGTA


title: WG17019_F02-W21

description:
single cell
TGACGTGCACGAC


title: WG17019_F02-W25

description:
single cell
TGACGTGCACGCT


title: KidD24_2


title: KidD24_1


title: KidD20_4


title: WG17019_F02-W18

description:
single cell
TGACGTGCACCTG


title: KidD20_3


title: KidD20_2


title: KidD16_4


title: KidD20_1


title: KidD16_3


title: KidD16_2


title: KidD16_1


title: KidD12_4


title: KidD24_3


title: KidD12_3


title: WG17019_F02-W04

description:
single cell
GATAAGTGACGAC


title: WG17019_F02-W05

description:
single cell
TGACGTGCATCCA


title: WG17019_F02-W12

description:
single cell
TGACGTGCAAGCG


title: WG17019_F02-W16

description:
single cell
TGACGTGCACAGA


title: WG17019_F02-W06

description:
single cell
TGACGTGCAAACC


title: WG17019_F02-W08

description:
single cell
TGACGTGCAACCT


title: WG17019_F02-W17

description:
single cell
TGACGTGCACCAT


title: WG17019_F02-W15

description:
single cell
TGACGTGCAATGC


title: WG17019_F02-W07

description:
single cell
TGACGTGCAACAC


title: WG17019_F02-W13

description:
single cell
TGACGTGCAAGGA


title: KidD12_1


title: WG17019_F02-W02

description:
single cell
GATAAGTGAACGG


title: WG17019_F02-W14

description:
single cell
TGACGTGCAAGTC


title: WG17019_F02-W01

description:
single cell
AGCAAGCGACAGA


title: KidD08_4


title: KidD08_3


title: WG17019_E02-W29

description:
single cell
GCATGATTAGAAG


title: WG17019_F02-W09

description:
single cell
TGACGTGCAACGG


title: WG17019_E02-W30

description:
single cell
AGCAAGCGAAACC


title: KidD08_1


title: WG17019_E02-W25

description:
single cell
GCATGATTACGCT


title: KidD04_4


title: WG17019_E02-W22

description:
single cell
GCATGATTACAGA


title: KidD12_2


title: WG17019_F02-W03

description:
single cell
GATAAGTGAATGC


title: WG17019_E02-W21

description:
single cell
GCATGATTAAGGA


title: KidD04_2


title: KidD00_4


title: KidD04_1


title: KidD00_1


title: HypN24_3

source_name: adult female anterior hypothalamus


title: KidD00_2


title: WG17019_E02-W20

description:
single cell
GCATGATTAAGCG


title: WG17019_E02-W18

description:
single cell
GCATGATTAACAC


title: WG17019_E02-W15

description:
single cell
TCGCTAGTACTGT


title: HypN24_4


title: WG17019_E02-W19

description:
single cell
GCATGATTAACCT


title: HypN24_2


title: WG17019_E02-W14

description:
single cell
TCGCTAGTAATGC


title: KidD00_3


title: HypN20_4


title: WG17019_E02-W17

description:
single cell
GCATGATTAAACC


title: KidD08_2


title: WG17019_E02-W16

description:
single cell
GCATGATTATCCA


title: WG17019_E02-W12

description:
single cell
CGTCGCATATGCC


title: HypN24_1


title: WG17019_E02-W11

description:
single cell
CGTCGCATAGTTC


title: KidD04_3


title: WG17019_E02-W13

description:
single cell
TCGCTAGTAACCT


title: WG17019_E02-W10

description:
single cell
CGTCGCATAGTCG


title: HypN20_3


title: WG17019_E02-W09

description:
single cell
CGTCGCATAGCTA


title: WG17019_E02-W08

description:
single cell
CGTCGCATAGACT


title: HypN20_1


title: WG17019_E02-W05

description:
single cell
CGTCGCATAGAAG


title: HypN16_4


title: WG17019_E02-W03

description:
single cell
CGTCGCATACTCC


title: HypN16_3


title: WG17019_E02-W04

description:
single cell
CGTCGCATACTGT


title: HypN16_1


title: HypN12_4


title: HypN16_2


title: WG17019_D02-W26

description:
single cell
CGTCGCATACGAC


title: WG17019_E02-W02

description:
single cell
CGTCGCATACGTA


title: HypN12_3


title: WG17019_E02-W01

description:
single cell
CGTCGCATACGCT


title: HypN08_4


title: WG17019_D02-W18

description:
single cell
CGTCGCATAATGC


title: HypN08_3


title: HypN12_2


title: HypN12_1


title: WG17019_D02-W19

description:
single cell
CGTCGCATACAGA


title: WG17019_D02-W16

description:
single cell
CGTCGCATAAGGA


title: WG17019_D02-W25

description:
single cell
CGTCGCATACCTG


title: HypN08_2


title: HypN04_4


title: HypN20_2


title: WG17019_D02-W14

description:
single cell
CGTCGCATAACGG


title: WG17019_D02-W15

description:
single cell
CGTCGCATAAGCG


title: WG17019_D02-W13

description:
single cell
CGTCGCATAACCT


title: HypN04_3


title: HypN04_2


title: WG17019_D02-W12

description:
single cell
CGTCGCATAACAC


title: WG17019_D02-W21

description:
single cell
CGTCGCATACCAT


title: WG17019_D02-W17

description:
single cell
CGTCGCATAAGTC


title: WG17019_D02-W11

description:
single cell
CGTCGCATAAACC


title: WG17019_D02-W09

description:
single cell
CAGCGTAGAGTTC


title: WG17019_D02-W10

description:
single cell
CGTCGCATATCCA


title: WG17019_D02-W08

description:
single cell
CAGCGTAGAGTCG


title: HypN08_1


title: WG17019_D02-W07

description:
single cell
CAGCGTAGAGAAG


title: WG17019_D02-W05

description:
single cell
CAGCGTAGACGCT


title: WG17019_D02-W04

description:
single cell
CAGCGTAGACGAC


title: WG17019_D02-W03

description:
single cell
CAGCGTAGACCAT


title: HypN04_1


title: HypD24_1


title: HypD24_2


title: HypN00_4


title: HypD24_4


title: HypD24_3


title: HypD20_3


title: HypN00_1


title: WG17019_D02-W06

description:
single cell
CAGCGTAGACTGT


title: HypN00_3


title: WG17019_C02-W26

description:
single cell
CAGCGTAGAAGTC


title: HypD20_2


title: HypD20_1


title: HypD20_4


title: WG17019_D02-W01

description:
single cell
CAGCGTAGAATGC


title: HypD16_4


title: WG17019_C02-W25

description:
single cell
CAGCGTAGAAGGA


title: WG17019_C02-W22

description:
single cell
CAGCGTAGAAGCG


title: HypN00_2


title: WG17019_C02-W21

description:
single cell
CAGCGTAGAACGG


title: WG17019_C02-W19

description:
single cell
CAGCGTAGAACAC


title: WG17019_C02-W20

description:
single cell
CAGCGTAGAACCT


title: WG17019_D02-W02

description:
single cell
CAGCGTAGACAGA


title: HypD16_1


title: HypD16_3


title: HypD16_2


title: HypD12_4


title: WG17019_C02-W18

description:
single cell
CAGCGTAGAAACC


title: WG17019_C02-W17

description:
single cell
CAGCGTAGATCCA


title: HypD12_2


title: WG17019_C02-W14

description:
single cell
CGTTCTACAATGC


title: WG17019_C02-W11

description:
single cell
CGTTCTACATCCA


title: WG17019_C02-W16

description:
single cell
CGTTCTACACGAC


title: HypD04_4


title: HypD08_1


title: HypD08_3


title: WG17019_C02-W15

description:
single cell
CGTTCTACACAGA


title: WG17019_C02-W09

description:
single cell
TGGTGGCTACAGA


title: HypD08_4


title: HypD08_2


title: WG17019_C02-W10

description:
single cell
TGGTGGCTACGAC


title: HypD04_3


title: WG17019_C02-W08

description:
single cell
TGGTGGCTAATGC


title: HypD04_1


title: WG17019_C02-W07

description:
single cell
TGGTGGCTAACGG


title: HypD12_3


title: HypD00_4


title: WG17019_C02-W05

description:
single cell
TGGTGGCTATCCA


title: HypD00_2


title: HypD12_1


title: HypD00_3


title: WG17019_C02-W13

description:
single cell
CGTTCTACAACGG


title: WG17019_C02-W12

description:
single cell
CGTTCTACAAACC


title: HypD00_1


title: WG17019_C02-W04

description:
single cell
ACTTTGCGACGCT


title: WG17019_C02-W03

description:
single cell
ACTTTGCGACGAC


title: WG17019_B02-W25

description:
single cell
ACTTTGCGAATGC


title: WG17019_B02-W14

description:
single cell
ACTTTGCGAACGG


title: WG17019_B02-W13

description:
single cell
ACTTTGCGAAACC


title: HypD04_2


title: WG17019_B02-W17

description:
single cell
ACTTTGCGAAGCG


title: WG17019_B02-W09

description:
single cell
ACTTTGCGATCCA


title: WG17019_C02-W06

description:
single cell
TGGTGGCTAAACC


title: WG17019_B02-W07

description:
single cell
CAGGACTCAGTTC


title: WG17019_B02-W06

description:
single cell
CAGGACTCAGTCG


title: WT_Control_1

city: Pittsburgh

first: Bernhard

last: Kuhn

state: Pennsylvania

address: 4401 Penn Ave

institute: Children's Hospital of Pittsburgh

data_processing:
RNAseq was performed using the BGISEQ-500 platform combining the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe Anchor Synthesis Sequencing Method.
Quality controlled FASTQ files were aligned to the Ensemble Human reference genome (hg38) using STAR aligner (version 2.5.1). HTSeq-count were used to generate counts of reads uniquely mapped to annotated genes using the GRCh38 annotation gtf file.
Differential gene expression analysis between the different conditions was done using DESeq2 using a model based on the negative binomial distribution.The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate, and differentially expressed genes were determined at the 5% threshold.
Genome_build: Human reference genome (hg38)
Supplementary_files_format_and_content: Tab delimited file showing log2foldchange by the differential gene expression between Gemin5-H913R vs Control
Supplementary_files_format_and_content: Tab delimited file of raw read counts

organism: Homo sapiens

source_name: iPSC line

growth_protocol: GEMIN5-H913R iPSC line was generated by CRISPR/Cas9 technique.The iPSCs were cultured and maintained in mTeSR1 media on Matrigel coated plates. For differentiation, ~ 0.6 million cells were plated and grown for 6 days in Neurobasal/DMEM-F12 basal medium containing  N2, B27, Glutamax and non-essential amino acids (NEAA) along with SB431542, LDN, retinoic acid, smoothened agonist (SAG). For day 7 to 14, cells were supplemented with RA, SAG, DAPT and SU5406. On day 14th , cells were dissociated using TrypLE/ DNase I and cultured on poly-ornithine and laminin coated plates in neuronal media containing neurobasal, N2, B27, Glutamax, NEAA, and ascorbic acid along with human brain-derived neurotrophic factor (BDNF), glial cell derived neurotrophic factor (GDNF), ciliary neurotrophic factor (CNTF).

extract_protocol:
RNA was isolated from GEMIN5His913Arg iPSC-derived differentiated neurons and isogenic controls by using the PureLinkTMRNA mini kit.Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano kit) was used to do the total RNA sample Quality Control (RNA concentration, RIN values, 28S/18S and the fragment length distribution).
For library construction, the poly-A containing mRNAs were purified by using poly-T oligo attached magnetic beads and are fragmented into smaller pieces by divalent cations. The cleaved RNAs are copied into first strand cDNA by reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H and subsequent ligation of the adapter. The products are then purified, enriched by PCR amplification, and pooled together to make a single strand DNA circle (ssDNA). DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study.

value: iPSC-derived differentiated neurons

value: WT


title: Homozygous GEMIN5-H913R_2

value: H913R varaint


title: WG17019_B02-W05

description:
single cell
CAGGACTCAGAAG

value: dorsal root ganglion


title: WG17019_B02-W03

description:
single cell
CAGGACTCACTGT

value: Female


title: WT_Control_2


title: Homozygous GEMIN5-H913R _3


title: Homozygous GEMIN5-H913R_1


title: WG17019_B02-W02

description:
single cell
CAGGACTCACGTA

value: 4 years 8 months


title: WG17019_A02-W31

description:
single cell
CAGGACTCACGAC


title: WG17019_B02-W01

description:
single cell
CAGGACTCACGCT


title: WG17019_C02-W02

description:
single cell
ACTTTGCGACAGA


title: Cr_M_R3_9h

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

institute: Huazhong Agricultural University

description: processed data file: merged_counts_Cru.txt

data_processing:
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to A. thaliana (TAIR10), C. hirsuta (http://chi.mpipz.mpg.de/), C. rubella (Phytozome 10), E. salsugineum (Phytozome10) or individual A. thalianna accession genomes corrected for SNPs usingTopHat2 (v2.1.1) with following parameters: --read-mismatches 10 --read-gap-length 10 --read-edit-dist 20 --read-realign-edit-dist 0  --min-anchor 5 --splice-mismatches 2 --min-intron-length 30 --max-intron-length 10000 --max-insertion-length 20 --max-deletion-length 20 --num-threads 10 --max-multihits 10 --coverage-search --library-type fr-firststrand --segment-mismatches 3 --min-segment-intron 30 --max-segment-intron 10000 --min-coverage-intron 30 --max-coverage-intron 10000 --b2-very-sensitive
reads per gene were counted using HtSeq (v 0.6.0) with default parameters
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.

organism: Capsella rubella

source_name: Capsella rubella

extract_protocol:
seedlings were flash frozen in liquid nitrogen and RNA was extracted using peqGOLD TriFast reagent
library preparation was performed with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs)

treatment_protocol: Eleven-day-old seedlings were transferred from ½ MS-Agar to 24-well plates each with 1.6 ml of ½ MS-Medium 24 h prior to treatments. Five to ten seedlings were transferred per well. For the flg22 treatment 800 µl of 3 µM flg22 solution was added to the medium containing the seedlings resulting in a final concentration of 1 µM flg22. For mock treatments 800 µl 1/2 MS medium was added to the wells. Three well were combined to create one sample.

value: seedling

value: 12 day old

tag: treatment

value: mock

tag: timepoint

tag: replicate


title: Cr_M_R3_24h


title: Cr_M_R2_24h


title: Cr_T_R3_1h


title: WG17019_A02-W30

description:
single cell
CAGGACTCACCTG


title: Cr_T_R3_9h


title: Cr_T_R3_24h


title: Cr_M_R3_1h


title: Cr_T_R2_24h


title: Cr_T_R2_9h


title: Cr_M_R2_9h


title: WG17019_A02-W29

description:
single cell
CAGGACTCACCAT


title: Cr_T_R2_1h


title: WG17019_A02-W28

description:
single cell
CAGGACTCACAGA


title: Cr_M_R2_1h


title: WG17019_A02-W27

description:
single cell
CAGGACTCAATGC


title: Cr_T_R1_24h


title: WG17019_A02-W26

description:
single cell
CAGGACTCAAGTC


title: Cr_M_R1_24h


title: Cr_T_R1_9h


title: WG17019_A02-W24

description:
single cell
CAGGACTCAAGCG


title: WG17019_A02-W23

description:
single cell
CAGGACTCAACGG

value: ambiguous


title: WG17019_A02-W22

description:
single cell
CAGGACTCAACCT


title: WG17019_A02-W25

description:
single cell
CAGGACTCAAGGA


title: Cr_M_R1_9h


title: WG17019_A02-W20

description:
single cell
CAGGACTCAAACC


title: MET1 [miRNA]

type: RNA

city: Essen

first: Jan

last: Gravemeyer

address: Universitätstraße 1

country: Germany

institute: DKZF

description: miRNA expression was analyzed using the nCounter Human v2 miRNA Expression Assay kit

hyb_protocol: Hybridization was done following the NanoString hybridization protocol that is specific for miRNA hybridization. CodeSet hybridization is achieved by the application of probe pairs that consist of a reporter probe, which carries the color code signal on it’s 5’ end, and a capture probe which carries biotin on it’s 3’end.

data_processing: Raw data was extracted from the nCounter RCC Collector file using the nSolver software and analyzed in R. Gene expression was normalized by using the four most stably expressed microRNAs identified by the GeNorm algorithm

label: capture probe with biotin

source_name: cell line

label_protocol: miR sample preparation was done according to the manufacture’s instructions

growth_protocol: The vMCC (MCC13, MCC26 ) and cMCC (WaGa, PeTa, MKL-1, MKL-2, BroLi and UKE-MCC-1a) cell lines were maintained in RPMI-1640 (Pan Biotech, Aidenbach, Germany) supplemented with 10% fetal bovine serum (Sigma, St. Lous, MO, USA) and 1% penicillin/streptomycin (Pan Biotech, Aidenbach, Germany). The SCC cell lines (Met-1, HSC-1, SCL-1) were maintained in DMEM (Pan Biotech, Aidenbach, Germany), supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol: RNA was isolated using the PeqGOLD total RNA kit (Peqlab, Erlangen, Germany).

treatment_protocol: no treatment

tag: sample type

value: Squamous cell carcinoma


title: WG17019_A02-W21

description:
single cell
CAGGACTCAACAC

value: C-LTMR


title: WG17019_A02-W19

description:
single cell
CAGGACTCATCCA


title: WG17019_A02-W17

description:
single cell
GTGTGAGAAGTCG


title: SCL1 [miRNA]


title: WG17019_A02-W14

description:
single cell
GTGTGAGAACGAC


title: 794_rep2

city: Shanghai

first: Mengzhu

last: Xue

address: No.100, Haike Road

institute: Shanghai Advanced Research Institute

data_processing:
Fastqc was taken to Check the RNA sequencing quality
Reads were mapped to hg19 by RSEM, then TPM values were calculated to characterize gene expression profiles.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Human hepatoma cells

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols, and Illumina TruSeq RNA Sample Prep Kit was used for library construction.

treatment_protocol: HepG2 cells were treated with BRD4 inhibitor at 4000nM, CHIR98014 at 4000nM, BRD4 inhibitor at 4000nM and CHIR98014 at 72nM, BRD4 inhibitor at 25nM and CHIR98014 at 4000nM, respectively.

value: Drug combination with BRD4 inhibitor at 25nM and CHIR98014 at 4000nM


title: Cr_M_R1_1h


title: HSC1 [miRNA]


title: Cr_T_R1_1h


title: WG17019_A02-W16

description:
single cell
GTGTGAGAACTGT


title: WG17019_A02-W15

description:
single cell
GTGTGAGAACGCT


title: MKL-2 [miRNA]

value: classical Merkel cell carcinoma


title: 794_rep1


title: WG17019_A02-W12

description:
single cell
GTGTGAGAAATGC


title: WG17019_A02-W13

description:
single cell
GTGTGAGAACAGA


title: BroLi [miRNA]


title: 749_rep2

value: Drug combination with BRD4 inhibitor at 4000nM and CHIR98014 at 72nM


title: MKL-1 [miRNA]


title: WG17019_A02-W10

description:
single cell
GTGTGAGAAAGCG


title: WG17019_A02-W09

description:
single cell
GTGTGAGAAACGG


title: 94_rep2


title: PeTa [miRNA]


title: WG17019_A02-W08

description:
single cell
GTGTGAGAAACAC


title: WaGa [miRNA]


title: WG17019_A02-W07

description:
single cell
GTGTGAGAAAACC


title: WG17019_A02-W05

description:
single cell
ACGAGTCTCAAGG


title: WG17019_A02-W03

description:
single cell
ACGAGTCTCAACT


title: 74_rep2

value: BRD4 inhibitor at 4000nM


title: WG17019_A02-W02

description:
single cell
ACGAGTCTATGGG


title: 94_rep1


title: WG17019_A02-W11

description:
single cell
GTGTGAGAAAGGA


title: WG17019_A02-W06

description:
single cell
GTGTGAGAATCCA


title: NC_rep2

value: Control


title: UKE-MCC-1a [miRNA]


title: WG17019_H01-W10

description:
single cell
ACGAGTCTAGTTC


title: 74_rep1


title: MCC13 [miRNA]

value: variant Merkel cell carcinoma


title: WG17019_H01-W17

description:
single cell
ACGAGTCTATAGC


title: WG17019_H01-W08

description:
single cell
ACGAGTCTAGTCG


title: WG17019_H01-W05

description:
single cell
ACGAGTCTAGGTG


title: NC_rep1


title: WG17019_H01-W18

description:
single cell
ACGAGTCTATCAG


title: MCC26 [miRNA]


title: WG17019_A02-W01

description:
single cell
ACGAGTCTATGCC


title: WG17019_G01-W31

description:
single cell
ACGAGTCTAGCTA


title: WG17019_G01-W32

description:
single cell
ACGAGTCTAGGAT


title: WG17019_G01-W29

description:
single cell
ACGAGTCTAGCGT


title: rep2_HepG2_BETi

value: Human hepatoma cells


title: rep1_HepG2_BETi


title: rep2_HepG2_control


title: Tumor vs Normal patient ID 294

city: Villejuif

first: Shai

last: Magidi

address: rue Guy Moquet

country: France

institute: WIN Consortium

description:
Tumor vs Normal Head and Neck - 294
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

hyb_protocol: Hybridizations were performed as dual-dye-swapped (direct and inversed labeling) experiments with direct cohybridization of equal amounts of labeled tumor and normal probes.

scan_protocol: Microarrays were read using the Agilent 2000 scanner version C.

data_processing: Data was processed with Agilent Feature extractions software

source_name: Cancer tissue

label_protocol: Of each tumor and normal tissue, 100 ng total RNA was used to generate double-stranded complementary DNA using MMLV reverse transcriptase and oligo DT primers coupled with the promoter sequence of T7 RNA. Probe labeling and linear amplification were generated using Agilent Technologies reagents and T7 RNA polymerase that generated labeled complementary labeled RNAs (tumor labeled with Cy5 and normal tissue with complementary RNAs with Cy3).

extract_protocol: The tissue biopsies were lysed with a Polytron, by homogenization in the lysis buffer RLT Plus provided in the kit, and DNA was obtained with a specific affinity silica matrix column, specifically retaining the DNA, whereas RNAs and proteins were collected from the through flow. DNA was washed and eluted. The through flow containing RNAs was mixed with tri-reagent and, subsequently, RNA was obtained by isopropanol precipitation. This procedure enables the collection of all types of RNAs, including mRNAs and small microRNA species. RNAs pelleted through centrifugation were washed with ethanol 75% and solved in nuclease-free water

value: Head and Neck

value: Male

source_name: Organ-matched normal tissue

value: Tongue


title: 749_rep1


title: rep1_HepG2_control


title: Tumor vs Normal patient ID 259

description:
Tumor vs Normal Head and Neck - 259
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

value: Female


title: WG17019_G01-W27

description:
single cell
ACGAGTCTAGAAG

value: dorsal root ganglion

value: 4 years 8 months


title: WG17019_G01-W23

description:
single cell
ACGAGTCTACGCT


title: WG17019_G01-W25

description:
single cell
ACGAGTCTACTCC


title: rep2_Hep3B_BETi


title: WG17019_G01-W26

description:
single cell
ACGAGTCTACTGT


title: WG17019_H01-W04

description:
single cell
ACGAGTCTAGGCA


title: WG17019_G01-W28

description:
single cell
ACGAGTCTAGACT


title: Tumor vs Normal patient ID 270

description:
Tumor vs Normal Colon - 270
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

value: Colon

value: Rectal/colon mucosa


title: WG17019_G01-W22

description:
single cell
ACGAGTCTACGAC


title: WG17019_G01-W20

description:
single cell
ACGAGTCTACCTG


title: rep1_Hep3B_BETi


title: rep2_Hep3B_control


title: WG17019_G01-W19

description:
single cell
ACGAGTCTACCAT


title: WG17019_G01-W17

description:
single cell
ACGAGTCTAATGC


title: WG17019_G01-W18

description:
single cell
ACGAGTCTACAGA


title: Tumor vs Normal patient ID 237

description:
Tumor vs Normal Head and Neck - 237
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.


title: Tumor vs Normal patient ID 235

description:
Tumor vs Normal Lung - 235
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

value: Lung

value: Bronchial mucosa


title: WG17019_G01-W14

description:
single cell
ACGAGTCTAAGGA


title: Tumor vs Normal patient ID 228

description:
Tumor vs Normal Colon - 228
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.


title: WG17019_G01-W13

description:
single cell
ACGAGTCTAAGCG

value: ambiguous


title: Tumor vs Normal patient ID 227

description:
Tumor vs Normal Liposarcoma - 227
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

value: Liposarcoma

value: Adipose tissue


title: Tumor vs Normal patient ID 247

description:
Tumor vs Normal GI - 247
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

value: GI Tract / Esophagus

value: esophagus


title: PE-treated NRVCs infected with control virus for ad-sORF8_nsRNA_seq_rep3

city: Guangzhou

first: Youchen

last: Yan

state: Guangdong

address: No.58 Zhongshan Road II

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%.
The clean reads were mapped to the rat genome (NCBI_GCF_000001895.5_Rnor_6.0) using HISAT2(v2.0.4). Expression level of gene was calculated by RSEM (v1.2.12).
Differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
GO and KEGG enrichment analysis of annotated different expressed gene was performed by Phyper based on Hypergeometric test.The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni.
Genome_build: Rattus_norvegicus.Rnor_6.0

organism: Rattus norvegicus

source_name: Neonatal rat ventricular cardiomyocytes

growth_protocol: NRVCs were isolated by enzymatic disassociation repeatedly. All isolated cells were plated for 1 hours to remove non-cardiomyocytes. Non-adherent cells were then plated on 0.5% gelatin-coated plates and cultured in DMEM high glucose medium (Gibco) supplemented with sodium pyruvate(1X), GlutaMAX(1X) and 10% fetal bovine serum with antibiotics.

extract_protocol:
Cell total RNA was isolated using Trizol reagent.
RNA libraries were prepared for sequencing using standard BGIseq protocols

treatment_protocol: NRVCs treated with PE (20uM)) for 24h

value: Sprague-Dawley

value: cardiac ventricle

value: ventricular cardiomyocytes

value: post natal day 2

value: treated with PE for 24 hours

tag: infection

value: control virus for ad-sORF


title: rep1_Hep3B_control

value: Human hepatoma cells


title: WG17019_G01-W24

description:
single cell
ACGAGTCTACGTA

value: dorsal root ganglion

value: Female

value: 4 years 8 months


title: Tumor vs Normal patient ID 223

description:
Tumor vs Normal Head and Neck - 223
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

value: Head and Neck

value: Tongue


title: WG17019_G01-W12

description:
single cell
ACGAGTCTAACGG


title: PE-treated NRVCs infected with control virus for ad-sORF8_nsRNA_seq_rep2


title: WG17019_G01-W11

description:
single cell
ACGAGTCTAACCT


title: PE-treated NRVCs infected with control virus for ad-sORF8_nsRNA_seq_rep1


title: WG17019_G01-W10

description:
single cell
ACGAGTCTAACAC


title: WG17019_G01-W08

description:
single cell
ACGAGTCTATCCA

value: C-LTMR


title: WG17019_G01-W09

description:
single cell
ACGAGTCTAAACC

value: injured cell


title: Tumor vs Normal patient ID 183

description:
Tumor vs Normal Colon - 183
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

value: Colon

value: Male

value: Rectal/colon mucosa


title: Tumor vs Normal patient ID 203

description:
Tumor vs Normal GI - 203
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

value: GI Tract / Small Intestine neuroendocrine tumor


title: Tumor vs Normal patient ID 156

description:
Tumor vs Normal Lung - 156
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

value: Lung

value: Bronchial mucosa


title: WG17019_G01-W05

description:
single cell
CTAGGAATACTGT


title: WG17019_G01-W07

description:
single cell
GCGTCTAAACAGA

value: ambiguous


title: WG17019_G01-W15

description:
single cell
ACGAGTCTAAGTC


title: Tumor vs Normal patient ID 149

description:
Tumor vs Normal GI - 149
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

value: GI Tract / Rectum


title: WG17019_G01-W06

description:
single cell
CTAGGAATAGAAG


title: WG17019_G01-W04

description:
single cell
CTAGGAATACGCT


title: PE-treated NRVCs infected with ad-sORF8_nsRNA_seq_rep3

value: Sprague-Dawley

value: cardiac ventricle

value: ventricular cardiomyocytes

value: post natal day 2

value: treated with PE for 24 hours

value: ad-sORF


title: PE-treated NRVCs infected with ad-sORF8_nsRNA_seq_rep2


title: WG17019_G01-W01

description:
single cell
CTAGGAATAAGGA

value: dorsal root ganglion

value: Female

value: 4 years 8 months


title: PE-treated NRVCs infected with control virus for ad-sORF7_nsRNA_seq_rep2

value: control virus for ad-sORF


title: WG17019_F01-W26

description:
single cell
GAATCACGATCCA


title: PE-treated NRVCs infected with control virus for ad-sORF7_nsRNA_seq_rep1


title: Tumor vs Normal patient ID 136

description:
Tumor vs Normal Lung - 136
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

value: Male


title: Tumor vs Normal patient ID 148

description:
Tumor vs Normal Neuroendocrine - 148
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

value: Neuroendocrine

value: Rectal/colon mucosa


title: PE-treated NRVCs infected with ad-sORF8_nsRNA_seq_rep1


title: WG17019_G01-W03

description:
single cell
CTAGGAATACAGA


title: PE-treated NRVCs infected with control virus for ad-sORF7_nsRNA_seq_rep3


title: WG17019_F01-W27

description:
single cell
GAATCACGAAACC


title: WG17019_G01-W02

description:
single cell
CTAGGAATAATGC


title: Tumor vs Normal patient ID 100

description:
Tumor vs Normal Lung - 100
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

value: Lung


title: Tumor vs Normal patient ID 088

description:
Tumor vs Normal Lung - 088
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

value: Bronchial mucosa


title: WG17019_F01-W25

description:
single cell
TCCCATGGAGTTC


title: Tumor vs Normal patient ID 117

description:
Tumor vs Normal Head and Neck - 117
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

value: Head and Neck

value: Tongue


title: Tumor vs Normal patient ID 090

description:
Tumor vs Normal Head and Neck - 090
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.


title: Tumor vs Normal patient ID 118

description:
Tumor vs Normal Lung - 118
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.


title: WG17019_F01-W23

description:
single cell
TCCCATGGAGTCG


title: WG17019_F01-W21

description:
single cell
TCCCATGGAGACT

value: C-LTMR


title: WG17019_F01-W29

description:
single cell
CTAGGAATATCCA


title: PE-treated NRVCs infected with ad-sORF7_nsRNA_seq_rep2

value: Sprague-Dawley

value: cardiac ventricle


title: PE-treated NRVCs infected with ad-sORF7_nsRNA_seq_rep3

value: ventricular cardiomyocytes

value: post natal day 2


title: WG17019_F01-W18

description:
single cell
TCCCATGGACTGT


title: WG17019_F01-W30

description:
single cell
CTAGGAATAACCT


title: Tumor vs Normal patient ID 083

description:
Tumor vs Normal Head and Neck - 083
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.


title: PE-treated NRVCs infected with control virus for ad-sORF6_nsRNA_seq_rep3

value: treated with PE for 24 hours


title: PE-treated NRVCs infected with ad-sORF7_nsRNA_seq_rep1

value: ad-sORF


title: WG17019_F01-W19

description:
single cell
TCCCATGGAGAAG

value: dorsal root ganglion

value: Female


title: WG17019_F01-W17

description:
single cell
TCCCATGGACTCC

value: 4 years 8 months


title: WG17019_F01-W16

description:
single cell
TCCCATGGACGTA


title: WG17019_F01-W22

description:
single cell
TCCCATGGAGCTA


title: Tumor vs Normal patient ID 006

description:
Tumor vs Normal Unknown Primary - 006
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

value: Leiomyosarcoma

value: Skeletal muscle


title: PE-treated NRVCs infected with control virus for ad-sORF6_nsRNA_seq_rep2

value: control virus for ad-sORF


title: ABE_HBF_LOW_rep1

city: Memphis

first: Yong

last: Cheng

state: Tennessee

address: 262 Danny Thomas Place

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

description: gRNA screening

library_source: genomic

data_processing:
Library strategy: pooled sgRNA screening
Reads were mapped to the reference sgRNA library and normalized to control sgRNAs by using MAGeCK (v0.5.9) count. The significance (FDR) of the difference in gRNA abundance between the HbF-high and HbF-low populations was calculated with the MAGeCK RRA test with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tsv

molecule: genomic DNA

growth_protocol: HUDEP-2–ABEmax cells were transduced with the library at a low multiplicity of infection (MOI) of 0.3 to minimize the transduction of cells with more than one vector particle and to achieve an approximately 1000-fold coverage of the sgRNA library. After 24 h, transduced cells were selected in puromycin (1 µg/mL) for 2 additional days and then maintained in the expansion medium for 5 days. Erythroid maturation was induced in differentiation medium for 5 days. Cells were then stained for HbF as indicated above and sorted into HbF-high and HbF-low populations.

extract_protocol:
Genomic DNA was extracted with the PureLink Genomic DNA Mini Kit (Life Technologies). sgRNAs were amplified for 27 cycles, using barcoded lentiGuide-Puro–specific primers with 400 ng of genomic DNA per reaction. The PCR products were then pooled for each sample. The barcoded libraries were pooled at an equimolar ratio, gel purified, and subjected to massively parallel sequencing with a MiSeq instrument (Illumina)
Oligonucleotide PCR products were gel purified and cloned into a BsmBI-digested and gel-purified pLentiGuide-Puro5 vector (Addgene cat. #52963), which encodes a puromycin resistance cassette, by Gibson assembly using NEBuilder HiFi DNA Assembly Master Mix (NEB). The assembly products were transformed into NEB stable competent cells, then the plasmids were extracted. Lentiviral particles were generated by transfecting HEK293T cells with the library plasmid, pVSVG, pRevtat, and pGagpol, using Lipofectamine 2000 (Life Technologies). Viral vector titers were determined by serial dilution.

tag: cell line

tag: population

value: HBF-low


title: Tumor vs Normal patient ID 025

description:
Tumor vs Normal Head and Neck - 025
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

tag: tissue

value: Male


title: ABE_HBF_LOW_rep2

description: gRNA screening


title: ABE_HBF_HIGH_rep2

description: gRNA screening

value: HBF-high


title: WG17019_F01-W13

description:
single cell
TCCCATGGACGAC

tag: cell type

tag: gender


title: WG17019_F01-W09

description:
single cell
TCCCATGGACCAT

tag: age


title: WG17019_F01-W07

description:
single cell
TCCCATGGACAGA


title: ABE_HBF_HIGH_rep1

description: gRNA screening


title: PE-treated NRVCs infected with control virus for ad-sORF6_nsRNA_seq_rep1


title: WG17019_F01-W06

description:
single cell
TCCCATGGAATGC


title: Bufexamac 3

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

institute: Ludwig-Maximilians-Universität München

data_processing:
Read were demultiplexed and 9 nt were trimmed from the 5'-end of each read.
The output was mapped to the human reference genome (hg19) using STAR (v.2.5.2b-0) with default settings and the gene annotation obtained from Illumina's iGenomes project.
Transcript abundance was counted using HTSeq-count (v.1.0.0) with reverse strand specifity and union mode.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq-count

source_name: act. CD4+ T cell (4-donor pool)

growth_protocol: For isolation of CD4+ T cells, blood cells were diluted with PBS (Gibco) and T cells were isolated via the Easy-SepTM Rosette Human CD4+ T cell enrichment kit (Stemcell Technologies, Canada) according to manufacturer´s protocols. Purity of isolated CD4+ T cells was controlled on a FACSverseTM flow cytometer (BD Biosciences) using BD Tritest CD4/CD8/CD3 antibody stain (BD Biosciences). CD4+ T cells were further cultivated and activated for 4 days in RPMI Glutamax medium (Gibco) containing 10 % heat-inactivated FCS (Sigma Aldrich), antibiotics (100 U/ml Penicillin, 100 mg/ml Streptomycin (Merck KgAa)), IL-2 (100 U/ml; Biomol, Germany), and phytohemagglutinin-P (PHA-P) (5 µg/ml; Sigma Aldrich). Subsequently, medium was exchanged to RPMI Glutamax medium (Gibco) containing 10 % heat-inactivated FCS (Sigma Aldrich), antibiotics (100 U/ml penicillin, 100 mg/ml streptomycin (Merck KgAa)), and IL-2 (100 U/ml; Biomol, Germany) without PHA-P and cells were cultivated for another 1-4 days.

extract_protocol:
RNA was isolated from trizol lysates of cells using Direct-zol RNA Miniprep Kit (Zymo Research) following manufacturer’s instructions. Isolated RNA was additionally purified using Agencourt RNAClean XP beads (Beckman Coulter) following manufacturer’s instructions. After quantification (Nanodrop), the RNA was quality controlled using a Bioanalyzer (Agilent Technologies).
Good quality RNA (RIN > 7) was used to generate sequencing libraries by using 500 ng total RNA in a Sense mRNA Seq Libarary Prep Kit V2 for Illumina platforms (Lexogen) following manufacture’s instructions.

treatment_protocol: 4-donor pools of act. CD4+ T cells were cultivated (at 37°C in 5 % CO2) for 48 h in RPMI Glutamax medium (Gibco) containing 10 % heat-inactivated FCS (Sigma Aldrich), antibiotics (100 U/ml penicillin, 100 mg/ml streptomycin (Merck KgAa)), and IL-2 (100 U/ml; Biomol, Germany) supplemented either with 1.95 mM sodium butyrate or 0.04 mM bufexamac. Untreated cells served as control.

value: treated with bufexamac

tag: agebt

value: IL-2, PHA activated

value: blood cell


title: PE-treated NRVCs infected with ad-sORF6_nsRNA_seq_rep3

value: Sprague-Dawley

value: cardiac ventricle


title: WG17019_F01-W05

description:
single cell
TCCCATGGAAGTC

value: C-LTMR


title: WG17019_F01-W14

description:
single cell
TCCCATGGACGCT


title: WG17019_F01-W04

description:
single cell
TCCCATGGAAGGA


title: PE-treated NRVCs infected with ad-sORF6_nsRNA_seq_rep2

value: ventricular cardiomyocytes

value: post natal day 2

value: treated with PE for 24 hours


title: PE-treated NRVCs infected with ad-sORF6_nsRNA_seq_rep1

value: ad-sORF


title: WG17019_F01-W02

description:
single cell
TCCCATGGAACGG

value: dorsal root ganglion

value: Female

value: 4 years 8 months


title: WG17019_F01-W01

description:
single cell
TCCCATGGAACCT


title: WG17019_F01-W03

description:
single cell
TCCCATGGAAGCG


title: WG17019_E01-W13

description:
single cell
TCCCATGGAACAC

value: ambiguous


title: Bufexamac 2


title: WG17019_E01-W10

description:
single cell
TCCCATGGAAACC


title: WG17019_F01-W11

description:
single cell
TCCCATGGACCTG

value: injured cell


title: 888_2_RNA

city: Dallas

first: Kuanqing

last: Liu

state: Texas

address: 5323 Harry Hines Blvd

department: Biochemistry

institute: UT Southwestern Medical Center

description:
rRNA depleted total RNA
rpkm_mrna_masked.txt

data_processing:
FASTX-clipper and -barcode splitter (http://hannonlab.cshl.edu/fastx toolkit/) were used to remove the linker sequences and de-multiplex ribosome profiling data, respectively.
Unique molecular identifiers and sample barcodes were subsequently removed using a custom Python script.
Reads corresponding to rRNAs and tRNAs were excluded using Bowtie v1.1.2 (http://bowtie-bio.sourceforge.net/) and the remaining reads were aligned to Saccharomyces cerevisiae genome using tophat v2.1.1 (https://ccb.jhu.edu/software/tophat/).
We then used the plastid cs program (Dunn and Weissman, 2016) to calculate counts per gene and normalized counts per gene (in Reads Per Kilobase per Million mapped reads, or RPKM), with counts assigned to the ribosome P-site determined by the plastid psite program.
Genome regions that could not be uniquely mapped from a 26-base read with two mismatches were identified by the plastid crossmap program, which, together with the first 30 and last five codons of each CoDing Sequence (CDS), were excluded from count assignments and RPKM calculations. RNA-seq data were analyzed similarly. However, because of the TruSeq Stranded chemistry, the reads had to be reverse-complemented prior to plastid analysis, and counts were assigned to the 5’-most aligned base.
Genome_build: sacCer3
Supplementary_files_format_and_content: txt files containing RPKM data for both ribosome profiling and RNA-seq

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast cells were grown in sulfur free medium supplemented with 1 mM methionine to log phase and then starved in sulfur free medium for two hours.

extract_protocol:
Frozen cell pellets were cryogenically pulverized on a SPEX 6870 Freezer/Mill for one minute at 15 cycles per minute and frozen droplets of lysis buffer (20 mM Tris-HCl pH 8.0, 140 mM KCl, 5 mM MgCl2, 1 mM dithiothreitol, 100 mg ml-1 cycloheximide, 1% Triton X-100, and 0.025 U ml-1 Turbo DNase) were added. The cell lysate was thawed, and cell debris was removed by two sequential centrifugation steps at 4°C: first at 3000 x g for five minutes and then at 20,000 x g for ten minutes.
For ribosome profiling, ribosome-protected RNA fragments ranging from ∼15-34 nt were isolated after RNase I digestion and denaturing PAGE separation. Cloning linkers with 3’ barcode sequences were ligated to RNA footprints and samples of unique barcodes were pooled together post-ligation whenever possible. rRNA was depleted sequentially using Ribo-Zero Gold for Yeast (Illumina) and biotinylated antisense oligos against rRNA species that co-migrate with ribosome footprints. For RNA-seq, RNA was extracted from the clarified lysates using TRIzol (Invitrogen) and rRNA was depleted using Ribo-Zero Gold for Yeast (Illumina). The processed RNA was then used to generate TruSeq Stranded libraries (Illumina) following the manufacturer’s recommendations. Libraries of ribosome profiling and RNA-seq were sequenced on an Illumina HiSeq 4000 in single read 50-base mode. Each set of matched ribosome profiling and RNA-seq data are derived from a single biological sample (two biological replicates in total for each strain under each condition).

treatment_protocol: Cells were collected by rapid filtration on a 0.45 μm cellulose nitrate membrane filter followed by snap freezing in liquid nitrogen.

tag: strain background

tag: genotype (dim1)

tag: note

value: D87E strain #888

tag: growth

value: without methionine for two hours


title: WG17019_E01-W09

description:
single cell
TCCCATGGATCCA


title: Sodium butyrate 3

value: treated with sodium butyrate


title: WG17019_E01-W06

description:
single cell
TATAGGACAGTCG


title: 888_0_RNA

value: with methionine


title: WG17019_E01-W05

description:
single cell
TATAGGACAGAAG


title: 887_2_RNA

value: D87E strain #887


title: WG17019_E01-W02

description:
single cell
TATAGGACACTGT


title: Sodium butyrate 2

value: IL-2, PHA activated

value: blood cell


title: WG17019_E01-W01

description:
single cell
TATAGGACACGCT


title: Sodium butyrate 1


title: WG17019_D01-W30

description:
single cell
TATAGGACACGAC


title: 887_0_RNA


title: Control 3

value: untreated


title: Bufexamac 1

value: treated with bufexamac


title: WG17019_D01-W29

description:
single cell
TATAGGACACAGA


title: Control 2


title: WG17019_D01-W26

description:
single cell
TATAGGACAATGC


title: 625_2_RNA

value: E85Q strain #625


title: Control 1


title: WG17019_D01-W19

description:
single cell
TATAGGACAACCT


title: WG17019_D01-W20

description:
single cell
TATAGGACAACGG


title: 625_0_RNA


title: WG17019_D01-W22

description:
single cell
TATAGGACAAGGA


title: WG17019_D01-W21

description:
single cell
TATAGGACAAGCG


title: 623_0_RNA

value: E85Q strain #623


title: 623_2_RNA


title: WG17019_D01-W17

description:
single cell
TATAGGACAAACC


title: WG17019_D01-W18

description:
single cell
TATAGGACAACAC


title: LVAD153

type: genomic

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy3, Cy5

source_name: genomic DNA from cardiac left ventricle

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from Human Left Ventricle Pre-LVAD samples using Qiagen DNeasy Kit according to standard instructions

tag: race

value: Caucasian American

value: Left Ventricle Endocardium


title: WG17019_D01-W14

description:
single cell
CACGGTGTAATGC

value: dorsal root ganglion

value: Female


title: WG17019_D01-W16

description:
single cell
TATAGGACATCCA

value: 4 years 8 months


title: 600_2_RNA

value: WT

value: WT strain #600


title: WG17019_D01-W12

description:
single cell
CACGGTGTATCCA


title: LVAD141


title: WG17019_D01-W15

description:
single cell
CACGGTGTACAGA


title: LVAD142


title: WG17019_D01-W09

description:
single cell
TTGTACAGAGTTC


title: LVAD157

value: African American


title: 172_2_RNA

value: WT strain #172

value: without methionine for two hours


title: WG17019_D01-W13

description:
single cell
CACGGTGTAAACC


title: 172_0_RNA

value: with methionine


title: LVAD133


title: WG17019_D01-W08

description:
single cell
TTGTACAGAGTCG


title: WG17019_D01-W07

description:
single cell
TTGTACAGAGGAT

value: injured cell


title: LVAD132


title: WG17019_D01-W03

description:
single cell
TTGTACAGAGACT


title: WG17019_D01-W05

description:
single cell
TTGTACAGAGCTA


title: WG17019_D01-W04

description:
single cell
TTGTACAGAGCGT

value: ambiguous


title: 887_2_RFP

description:
ribosome footprint
rpkm_footprints_masked_18to34nt.txt

data_processing:
Library strategy: ribosome profiling
FASTX-clipper and -barcode splitter (http://hannonlab.cshl.edu/fastx toolkit/) were used to remove the linker sequences and de-multiplex ribosome profiling data, respectively.
Unique molecular identifiers and sample barcodes were subsequently removed using a custom Python script.
Reads corresponding to rRNAs and tRNAs were excluded using Bowtie v1.1.2 (http://bowtie-bio.sourceforge.net/) and the remaining reads were aligned to Saccharomyces cerevisiae genome using tophat v2.1.1 (https://ccb.jhu.edu/software/tophat/).
We then used the plastid cs program (Dunn and Weissman, 2016) to calculate counts per gene and normalized counts per gene (in Reads Per Kilobase per Million mapped reads, or RPKM), with counts assigned to the ribosome P-site determined by the plastid psite program.
Genome regions that could not be uniquely mapped from a 26-base read with two mismatches were identified by the plastid crossmap program, which, together with the first 30 and last five codons of each CoDing Sequence (CDS), were excluded from count assignments and RPKM calculations. RNA-seq data were analyzed similarly. However, because of the TruSeq Stranded chemistry, the reads had to be reverse-complemented prior to plastid analysis, and counts were assigned to the 5’-most aligned base.
Genome_build: sacCer3
Supplementary_files_format_and_content: txt files containing RPKM data for both ribosome profiling and RNA-seq

value: D87E strain #887


title: 888_0_RFP

value: D87E strain #888


title: 888_2_RFP


title: WG17019_C01-W32

description:
single cell
TTGTACAGACTCC


title: WG17019_D01-W11

description:
single cell
TTGTACAGATGCC


title: WG17019_D01-W01

description:
single cell
TTGTACAGACTGT


title: WG17019_D01-W02

description:
single cell
TTGTACAGAGAAG

value: non-neuronal


title: 600_0_RNA


title: LVAD127


title: LVAD125


title: WG17019_C01-W31

description:
single cell
TTGTACAGACGTA


title: LVAD140


title: 887_0_RFP


title: LVAD122


title: WG17019_C01-W29

description:
single cell
TTGTACAGACGAC


title: WG17019_C01-W28

description:
single cell
TTGTACAGACCTG


title: LVAD130


title: WG17019_C01-W26

description:
single cell
TTGTACAGACAGA


title: LVAD121


title: WG17019_C01-W27

description:
single cell
TTGTACAGACCAT


title: WG17019_C01-W25

description:
single cell
TTGTACAGAATGC


title: 625_2_RFP

value: E85Q strain #625


title: 625_0_RFP


title: WG17019_C01-W24

description:
single cell
TTGTACAGAAGTC

value: C-LTMR


title: LVAD119

value: Eastern African

value: Left Ventricle Endocardium


title: WG17019_C01-W23

description:
single cell
TTGTACAGAAGGA

value: dorsal root ganglion

value: Female


title: 623_2_RFP

value: E85Q strain #623


title: 623_0_RFP


title: WG17019_C01-W30

description:
single cell
TTGTACAGACGCT

value: 4 years 8 months


title: WG17019_C01-W21

description:
single cell
TTGTACAGAACGG


title: LVAD106

value: African American


title: LVAD092

value: Caucasian American


title: WG17019_C01-W20

description:
single cell
TTGTACAGAACCT


title: WG17019_C01-W19

description:
single cell
TTGTACAGAACAC


title: 600_2_RFP

value: WT

value: WT strain #600

value: without methionine for two hours


title: 600_0_RFP

value: with methionine


title: WG17019_C01-W18

description:
single cell
TTGTACAGAAACC


title: LVAD111


title: 172_2_RFP

value: WT strain #172


title: WG17019_C01-W17

description:
single cell
TTGTACAGATCCA


title: LVAD090

value: Asian American


title: WG17019_C01-W16

description:
single cell
CTTGAAGGAGTCG


title: WG17019_C01-W22

description:
single cell
TTGTACAGAAGCG


title: WG17019_C01-W15

description:
single cell
CTTGAAGGACTGT


title: LVAD087


title: LVAD084


title: WG17019_C01-W13

description:
single cell
CTTGAAGGACGCT


title: WG17019_C01-W09

description:
single cell
CTTGAAGGAATGC


title: RNA-seq Sample 45 Hilar lymph node

city: Amsterdam

first: Tesa

last: Severson

address: 121 Plesmanlaan

department: Molecular Carcinogensis

country: Netherlands

institute: Netherlands Cancer Institute

description:
RNAseq_45_Hilar_LN
RNA-seq for AR in Sample 45_Hilar_LN
processed data file: rna_seq_processed_data_counts_matrix.txt

data_processing:
Sequencing library was sequenced on Applied Biosystems SOLiD (V3) with paired-end 34 x 74 bp reads.
Sequencing reads were aligned to hg18 (NCBI36) and raw counts were generated using Bioscope.
Raw counts were normalized with DESeq2 (v1.22.2). All genes not expressed across all samples were removed (normalized count data < 10). Subsequently data were log transformed.
Genome_build: hg18 (NCBI36)
Supplementary_files_format_and_content: rna_normalized_log_transformed_ge_matrix.txt: Gene expression matrix of normalized and log transformed counts.

source_name: Sample 45 Hilar lymph node

extract_protocol: Purified RNA was used to prepare a sequencing library and sequenced on Applied Biosystems SOLiD (V3).

tag: disease state

value: Metastatic castration resistant prostate cancer

value: Hilar lymph node


title: RNA-seq Sample 40 lung

description:
RNAseq_40_lung
RNA-seq for AR in Sample 40_lung
processed data file: rna_seq_processed_data_counts_matrix.txt

source_name: Sample 40 lung

value: Lung


title: WG17019_C01-W08

description:
single cell
CTTGAAGGAAGGA

source_name: dorsal root ganglion


title: WG17019_C01-W10

description:
single cell
CTTGAAGGACAGA


title: LVAD083


title: RNA-seq Sample 5 liver

description:
RNAseq_5_liver
RNA-seq for AR in 5_liver
processed data file: rna_seq_processed_data_counts_matrix.txt

source_name: Sample 5 liver

value: Liver


title: LVAD079

value: Left Ventricle Endocardium


title: WG17019_C01-W07

description:
single cell
CTTGAAGGAAGCG

value: dorsal root ganglion


title: RNA-seq Sample 38 Perigastric lymph node

description:
RNAseq_38_Perigastric_LN
RNA-seq for AR in Sample 38_Perigastric_LN
processed data file: rna_seq_processed_data_counts_matrix.txt

source_name: Sample 38 Perigastric lymph node

value: Perigastric lymph node


title: WG17019_C01-W05

description:
single cell
CTTGAAGGAACAC

value: Female


title: 172_0_RFP


title: LVAD075


title: WG17019_C01-W04

description:
single cell
CTTGAAGGAAACC

value: injured cell

value: 4 years 8 months


title: WG17019_C01-W06

description:
single cell
CTTGAAGGAACGG


title: LVAD067

value: Caucasian American


title: WG17019_C01-W02

description:
single cell
GGTATTCACAACT


title: WG17019_C01-W12

description:
single cell
CTTGAAGGACGAC


title: LVAD066

value: African American


title: WG17019_C01-W01

description:
single cell
GGTATTCAATGGG


title: LVAD060


title: WG17019_B01-W30

description:
single cell
GGTATTCAATAGC


title: WG17019_B01-W29

description:
single cell
GGTATTCAAGTTC


title: WG17019_B01-W31

description:
single cell
GGTATTCAATCAG


title: LVAD058


title: WG17019_B01-W32

description:
single cell
GGTATTCAATGCC


title: LVAD032


title: WG17019_B01-W27

description:
single cell
GGTATTCAAGGTG


title: LVAD054


title: WG17019_B01-W28

description:
single cell
GGTATTCAAGTCG


title: LVAD013


title: WG17019_B01-W25

description:
single cell
GGTATTCAAGGAT


title: LVAD006


title: WG17019_C01-W03

description:
single cell
CTTGAAGGATCCA


title: WG17019_B01-W24

description:
single cell
GGTATTCAAGCTA


title: LVAD001


title: LVAD014


title: WG17019_B01-W26

description:
single cell
GGTATTCAAGGCA


title: WG17019_B01-W22

description:
single cell
GGTATTCAAGACT


title: WG17019_B01-W23

description:
single cell
GGTATTCAAGCGT


title: WG17019_B01-W20

description:
single cell
GGTATTCAACTGT


title: WG17019_B01-W19

description:
single cell
GGTATTCAACTCC


title: Salluit S1A cDNA

city: Tachikawa-shi,

first: Shu-Kuan

last: Wong

state: Tokyo

address: 10-3, Midori-cho,

country: Japan

institute: National Polar Research Institute

description: Low Arctic: Salluit

hyb_protocol: Each dried and labelled DNA sample was resuspended in 42 µL of hybridization solution. This solution consisted of 1 x HI-RPM hybridization buffer, 1 x comparative genome hybridization blocking agent, 0.05 µg・µL-1 Cot-1 DNA, 10 pM universal standard, and 10% formamide (final concentrations). The solution was later denatured by remaining at 95 ℃ for 3 min. To remove the bubbles created during the denaturation process, the conditions were maintained at 37 ℃ for 30 min. The hybridizations were carried out at 67 ℃ for 24 h

scan_protocol: The scanned images of the GeoChip hybridizations were obtained and converted by means of the Agilent Feature Extraction 11.5 software (Agilent Technologies, California, USA)

data_processing: The signal intensities, used as a proxy of abundances, were quantified and processed based on previous pipelines48 as follows: (i) removing probes with a signal-to-noise ratio of less than 2.0; (ii) normalizing the signal intensity of each probe by dividing the total signal intensity of a sample and multiplying by a constant

organism: soil metagenome

source_name: Soil

label_protocol: The DNA from each sample (500 ng) was labelled with the fluorescent dye Cy-3 by random priming.

growth_protocol: Samples collected directly from the environment

extract_protocol: Total DNA and RNA were extracted from each soil sample using ZymoBIOMICS DNA & RNA kit. The total RNA extracted were subjected to DNAse I treatment and cDNA was generated from the RNA template using SuperScript IV First-Strand Synthesis System for RT-PCR according to the manufacturer’s instruction.

treatment_protocol: Soil samples were collected using a sterile scoop and placed into a 5 mL sampling tube containing RNAlater Stabilization Solution

tag: source material

value: Environmental soil

tag: location

value: low Arctic region of Salluit

tag: molecule subtype

value: complementary DNA


title: Salluit S2B cDNA

description: Low Arctic: Salluit


title: WG17019_B01-W18

description:
single cell
GGTATTCAACGTA


title: Salluit S3A cDNA

description: Low Arctic: Salluit


title: 621H::goxR-strep_ChAP

city: Jülich

first: Angela

last: Kranz

state: NRW

address: Wilhelm-Johnen-Strasse

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

data_processing:
Library strategy: ChAP-seq
Read processing and quality trimming was performed with the CLC Genomics Workbench (Qiagen Aarhus A/S). For the mapping to the G. oxydans 621H reference genome (NC_006672.1-NC_006677.1) one mismatch per read was allowed.
The expected peak width was estimated via the following procedure: (i) all the peaks higher than 3-fold mean coverage were detected. (ii) Points at which their coverage dropped below 1/2  of the maximal peak height were found and the distance between them was considered as a peak width.
Peak intensity is the highest read coverage for a peak normalized to the average coverage of non-peak genomic area.
Genome_build: NC_006672.1-NC_006677.1
Supplementary_files_format_and_content: Peak tsv file

organism: Gluconobacter oxydans

growth_protocol: For preparation of ChAP-Seq samples, the strain G. oxydans 621H::goxR-strep was used. A preculture was inoculated in 15 ml mannitol medium and incubated for 8 h at 30°C. Subsequently, 1 ml of the first preculture was transferred into 50 ml mannitol medium. After cultivation overnight, this second preculture was used to inoculate the main culture (1 l in a 5 l baffled Erlenmeyer flask) to an OD600 of 0.5. The culture was incubated at 30°C and 130 rpm. In the late exponential phase (OD600 ca. 2.8), cells were harvested by centrifugation and washed once in 40 ml PBS (137 mM NaCl, 2.7 mM KCl, 1.5 mM KH2PO4, 8 mM Na2HPO4, pH 7.4).

extract_protocol:
Cell disruption, sonication of the DNA, purification of DNA bound to Strep-tagged GoxR, and the final DNA purification after digestion of protein was performed as described (PMID: 32453397).
The obtained DNA fragments were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturer´s protocol for DNA fragments without size selection. Adapter-ligated DNA was amplified by using 15 PCR cycles. Quantification of the resulting libraries was performed with the KAPA library quantification kit and sequenced on a MiSeq (Illumina) using paired-end sequencing with a read-length of 2 × 150 bases.

treatment_protocol: Afterwards, the cell pellet was resuspended in 20 ml PBS with 1% (v/v) formaldehyde incubated for 20 min at room temperature to crosslink the Strep-tagged GoxR protein to DNA. To stop the crosslinking, glycine was added to a final concentration of 125 mM followed by incubation for 5 min at room temperature. Afterwards, cells were washed twice with 40 ml buffer A (100 mM Tris-HCl, pH 8.0, 1 mM EDTA) and pellets were stored overnight at -80°C.

tag: strain

tag: genotype


title: Salluit S1B cDNA

description: Low Arctic: Salluit


title: WG17019_B01-W17

description:
single cell
GGTATTCAACGCT

data_processing:
Reads flagged as invalid by the Illumina HiSeq control software were discarded. In the remaining reads, any 3′ bases with a quality score of B were removed. If any of the six UMI bases in the 5' end had a Phred score <17 the read was discarded, else the UMI was cut away and saved. The following three bases had to be G for the read to be kept. These, as well as any additional up to totally nine (presumably template-switch derived) G:s were cut away. Reads were discarded if the remaining transcript-derived sequence ended in a poly(A) sequence leaving <25 bases, or if the remaining sequence consisted of fewer than six non-A bases or a dinucleotide repeat with fewer than six other bases at either end. The reads were sorted by the well, as defined by the combined two index read barcodes.
Alignment was performed using the Bowtie aligner, allowing for up to three mismatches and up to 24 alternative mappings. Reads with no alignments were realigned against an artificial chromosome, containing all possible splice junctions arising from the exons defined by the UCSC transcript models. The coordinates of aligned splice junctions were translated back to the corresponding genomic positions.
For expression level calculation, the exons of each locus with several transcript variants were merged to a combined model representing total expression of the locus. To account for incomplete cap site knowledge, the 5′ ends of all models were extended by 100 bases, but not beyond the 3′ end of any upstream nearby exon of another gene of the same orientation.
The annotation step was performed separately for each well. For each genomic position and strand combination the number of reads in each UMI was counted. Any multiread that mapped to some repeat outside exons was assigned randomly as one of these repeats and did not contribute to the transcript corresponding to the exon. Else, if the multiread mapped to some exon, and not to any repeat outside exons, it was assigned to the exon where it was closest to the transcript model 5′ end. If it had no exon mapping, it was assigned randomly at one of the mappings. The total number of molecules at each mapping position was determined by the number of distinct UMIs observed. Any UMI represented by only a single read was excluded, in order to reduce false molecules due to PCR and sequencing errors. The raw UMI count was corrected for the UMI collision probability.
Genome_build: rheMac8
Supplementary_files_format_and_content: Processed data consists of a UMI count matrix, where rows are geneIDs and columns cellIDs, and an annotation text file where rows are CellIDs and columns the annotations


title: Salluit S2A cDNA

description: Low Arctic: Salluit