title: mTEChi_input-1

value: input


title: WT_mTEChi_03_R03_bulk

status: Public on Feb 19 2021

type: SRA

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
QC was performed using FastQC and Trimmomatic
RNA-seq reads were aligned using HISAT (version 0.1.6) and ChIP-seq peaks were pre-aligned using BWA (version 0.5.9) and Stampy (--bamkeepgoodreads)
Single cell RNA-seq outliers were identified using robust PCA on alignment proportion, ERCC92 spike-in proportion, number of detectable genes, proportion of reads mapping to protein-coding genes, proportion of mitochondrial transcripts, proportion of ribosomal transcripts, 3’ to 5’ coverage bias, transcriptomic variance, cell-to-mean correlation, the proportion of the library accounted for by the top 500 transcripts and GC content
RNA-seq reads were assigned to genes using HTSeq (intersection non-empty)
ChIP-seq bigWig profiles were generated using MACS2 on deduplicated BAM files with MAPQ >10
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited files include counts for RNA-seq samples and bigWig files show ChIP/input signal for ChIP-seq samples

molecule: polyA RNA

organism: Mus musculus

source_name: mTEChi

extract_protocol:
Thymic lobes were cleaned from fatty tissues and incubated with Liberase and DNaseI (Roche Diagnostics; 200μg/ml and 30μg/ml, respectively; 45min, 37ºC) to obtain a cell suspension which was subsequently filtered through a nylon mesh (100micro pore size, Sefar Nitex) to remove debris. TEC were sorted and then RNA was either isolated from ~1,000 cells or single cells using the SMART-seq2 protocol. TEC for ChIP-seq were treated as detailed in Žuklys S et al. Nature Immunology 2016:17(10):1206-1215
RNA-seq libraries were prepared using the appropriate Illumina kit for SMART-seq2 or HiSeq2500 (ChIP-seq). Nextera adapters were used for single cell RNA-seq and ChIP-seq.

tag: strain

tag: sample type

value: bulk

tag: zsgreen status

value: negative


title: mTEChi_K27me3-1

description: mTEChi_K27me3-1_merged_signal_mapq_10_FE.bw

library_source: genomic

molecule: genomic DNA

value: H3K27me3 IP


title: mTEChi_input-2


title: mTEChi_input-3


title: mTEChi_input-4


title: WT_mTEChi_02_R02_bulk


title: mTEChi_input-5


title: WT_mTEChi_02_R01_bulk


title: WT_mTEChi_03_R01_bulk


title: WT_mTEChi_03_R02_bulk


title: Eed_ZsG_neg_mTEChi_02_bulk_seq_repl


title: WT_mTEChi_01_R03_bulk


title: WT_mTEChi_01_R01_bulk


title: Eed_ZsG_pos_mTEChi_04_bulk

value: positive


title: SCGC1381_mTEChi_WT_P8

value: single cell


title: Eed_ZsG_pos_mTEChi_03_bulk


title: Eed_ZsG_neg_mTEChi_03_bulk


title: SCGC1381_mTEChi_WT_P9


title: Eed_ZsG_pos_mTEChi_01_bulk


title: Eed_ZsG_neg_mTEChi_01_bulk


title: Eed_ZsG_neg_mTEChi_04_bulk


title: WT_mTEChi_01_R02_bulk


title: SCGC1381_mTEChi_WT_P7


title: Eed_ZsG_neg_mTEChi_02_bulk


title: SCGC1381_mTEChi_WT_P5


title: SCGC1381_mTEChi_WT_P4


title: SCGC1381_mTEChi_WT_P3


title: SCGC1381_mTEChi_WT_P2


title: SCGC1381_mTEChi_WT_P18


title: SCGC1381_mTEChi_WT_P17


title: SCGC1381_mTEChi_WT_P22


title: SCGC1381_mTEChi_WT_P20


title: SCGC1381_mTEChi_WT_P15


title: SCGC1381_mTEChi_WT_P14


title: SCGC1381_mTEChi_WT_P21


title: SCGC1381_mTEChi_WT_P12


title: SCGC1381_mTEChi_WT_P16


title: Eed_ZsG_pos_mTEChi_02_bulk


title: SCGC1381_mTEChi_WT_P6


title: SCGC1381_mTEChi_WT_P11


title: SCGC1381_mTEChi_WT_P1


title: SCGC1381_mTEChi_WT_O9


title: SCGC1381_mTEChi_WT_O8


title: SCGC1381_mTEChi_WT_O6


title: SCGC1381_mTEChi_WT_O7


title: SCGC1381_mTEChi_WT_P10


title: SCGC1381_mTEChi_WT_O3


title: SCGC1381_mTEChi_WT_O4


title: SCGC1381_mTEChi_WT_O24


title: SCGC1381_mTEChi_WT_O21


title: SCGC1381_mTEChi_WT_O22


title: SCGC1381_mTEChi_WT_P13


title: SCGC1381_mTEChi_WT_P19


title: SCGC1381_mTEChi_WT_O20


title: SCGC1381_mTEChi_WT_O19


title: SCGC1381_mTEChi_WT_O17


title: SCGC1381_mTEChi_WT_O16


title: SCGC1381_mTEChi_WT_O18


title: SCGC1381_mTEChi_WT_O12


title: SCGC1381_mTEChi_WT_O13


title: SCGC1381_mTEChi_WT_O14


title: SCGC1381_mTEChi_WT_O10


title: SCGC1381_mTEChi_WT_O11


title: SCGC1381_mTEChi_WT_O1


title: SCGC1381_mTEChi_WT_N8


title: SCGC1381_mTEChi_WT_O5


title: SCGC1381_mTEChi_WT_N6


title: SCGC1381_mTEChi_WT_O23


title: SCGC1381_mTEChi_WT_N7


title: SCGC1381_mTEChi_WT_N9


title: SCGC1381_mTEChi_WT_N3


title: SCGC1381_mTEChi_WT_N24


title: SCGC1381_mTEChi_WT_N5


title: SCGC1381_mTEChi_WT_N4


title: SCGC1381_mTEChi_WT_N22


title: SCGC1381_mTEChi_WT_N23


title: SCGC1381_mTEChi_WT_N20


title: SCGC1381_mTEChi_WT_N18


title: SCGC1381_mTEChi_WT_N21


title: SCGC1381_mTEChi_WT_O15


title: SCGC1381_mTEChi_WT_N19


title: SCGC1381_mTEChi_WT_O2


title: SCGC1381_mTEChi_WT_N17


title: SCGC1381_mTEChi_WT_N16


title: SCGC1381_mTEChi_WT_N15


title: SCGC1381_mTEChi_WT_N1


title: SCGC1381_mTEChi_WT_N14


title: SCGC1381_mTEChi_WT_N13


title: SCGC1381_mTEChi_WT_N11


title: SCGC1381_mTEChi_WT_N10


title: SCGC1381_mTEChi_WT_M9


title: SCGC1381_mTEChi_WT_M8


title: SCGC1381_mTEChi_WT_M7


title: SCGC1381_mTEChi_WT_M6


title: SCGC1381_mTEChi_WT_M5


title: SCGC1381_mTEChi_WT_M4


title: SCGC1381_mTEChi_WT_M3


title: SCGC1381_mTEChi_WT_M23


title: SCGC1381_mTEChi_WT_N2


title: SCGC1381_mTEChi_WT_M24


title: SCGC1381_mTEChi_WT_M22


title: SCGC1381_mTEChi_WT_M2


title: SCGC1381_mTEChi_WT_M19


title: SCGC1381_mTEChi_WT_M21


title: SCGC1381_mTEChi_WT_M18


title: SCGC1381_mTEChi_WT_M20


title: SCGC1381_mTEChi_WT_M17


title: SCGC1381_mTEChi_WT_M15


title: SCGC1381_mTEChi_WT_M14


title: SCGC1381_mTEChi_WT_M16


title: SCGC1381_mTEChi_WT_M12


title: SCGC1381_mTEChi_WT_M13


title: SCGC1381_mTEChi_WT_M11


title: SCGC1381_mTEChi_WT_N12


title: SCGC1381_mTEChi_WT_L6


title: SCGC1381_mTEChi_WT_L5


title: SCGC1381_mTEChi_WT_L7


title: SCGC1381_mTEChi_WT_L3


title: SCGC1381_mTEChi_WT_L24


title: SCGC1381_mTEChi_WT_L22


title: SCGC1381_mTEChi_WT_L21


title: SCGC1381_mTEChi_WT_L4


title: SCGC1381_mTEChi_WT_L2


title: SCGC1381_mTEChi_WT_L19


title: SCGC1381_mTEChi_WT_L17


title: SCGC1381_mTEChi_WT_L15


title: SCGC1381_mTEChi_WT_L12


title: SCGC1381_mTEChi_WT_L13


title: SCGC1381_mTEChi_WT_L14


title: SCGC1381_mTEChi_WT_L23


title: SCGC1381_mTEChi_WT_M10


title: SCGC1381_mTEChi_WT_L11


title: SCGC1381_mTEChi_WT_M1


title: SCGC1381_mTEChi_WT_L16


title: SCGC1381_mTEChi_NTC_P24

value: no template control


title: SCGC1381_mTEChi_NTC_P23


title: SCGC1381_mTEChi_EedZsGpos_F8


title: SCGC1381_mTEChi_EedZsGpos_F9


title: SCGC1381_mTEChi_WT_L10


title: SCGC1381_mTEChi_EedZsGpos_F7


title: SCGC1381_mTEChi_EedZsGpos_F6


title: SCGC1381_mTEChi_WT_L8


title: SCGC1381_mTEChi_WT_L9


title: SCGC1381_mTEChi_EedZsGpos_F4


title: SCGC1381_mTEChi_WT_L18


title: SCGC1381_mTEChi_EedZsGpos_F3


title: SCGC1381_mTEChi_EedZsGpos_F24


title: SCGC1381_mTEChi_EedZsGpos_F23


title: SCGC1381_mTEChi_WT_L20


title: SCGC1381_mTEChi_EedZsGpos_F20


title: SCGC1381_mTEChi_EedZsGpos_F22


title: SCGC1381_mTEChi_EedZsGpos_F21


title: SCGC1381_mTEChi_EedZsGpos_F19


title: SCGC1381_mTEChi_WT_L1


title: SCGC1381_mTEChi_EedZsGpos_F17


title: SCGC1381_mTEChi_EedZsGpos_F18


title: SCGC1381_mTEChi_EedZsGpos_F14


title: SCGC1381_mTEChi_EedZsGpos_F15


title: SCGC1381_mTEChi_EedZsGpos_F13


title: SCGC1381_mTEChi_EedZsGpos_F11


title: SCGC1381_mTEChi_EedZsGpos_F12


title: SCGC1381_mTEChi_EedZsGpos_E9


title: SCGC1381_mTEChi_EedZsGpos_F5


title: SCGC1381_mTEChi_EedZsGpos_E8


title: SCGC1381_mTEChi_EedZsGpos_E7


title: SCGC1381_mTEChi_EedZsGpos_E4


title: SCGC1381_mTEChi_EedZsGpos_E3


title: SCGC1381_mTEChi_EedZsGpos_E5


title: SCGC1381_mTEChi_EedZsGpos_E24


title: SCGC1381_mTEChi_EedZsGpos_F2


title: SCGC1381_mTEChi_EedZsGpos_F1


title: SCGC1381_mTEChi_EedZsGpos_E23


title: SCGC1381_mTEChi_EedZsGpos_F16


title: SCGC1381_mTEChi_EedZsGpos_E20


title: SCGC1381_mTEChi_EedZsGpos_E2


title: SCGC1381_mTEChi_EedZsGpos_E21


title: SCGC1381_mTEChi_EedZsGpos_E22


title: SCGC1381_mTEChi_EedZsGpos_E19


title: SCGC1381_mTEChi_EedZsGpos_E17


title: SCGC1381_mTEChi_EedZsGpos_E18


title: SCGC1381_mTEChi_EedZsGpos_E11


title: SCGC1381_mTEChi_EedZsGpos_E15


title: SCGC1381_mTEChi_EedZsGpos_E10


title: SCGC1381_mTEChi_EedZsGpos_E12


title: SCGC1381_mTEChi_EedZsGpos_E14


title: SCGC1381_mTEChi_EedZsGpos_F10


title: SCGC1381_mTEChi_EedZsGpos_E13


title: SCGC1381_mTEChi_EedZsGpos_E6


title: SCGC1381_mTEChi_EedZsGpos_E1


title: SCGC1381_mTEChi_EedZsGpos_D6


title: SCGC1381_mTEChi_EedZsGpos_D9


title: SCGC1381_mTEChi_EedZsGpos_D7


title: SCGC1381_mTEChi_EedZsGpos_D8


title: SCGC1381_mTEChi_EedZsGpos_D5


title: SCGC1381_mTEChi_EedZsGpos_D4


title: SCGC1381_mTEChi_EedZsGpos_D24


title: SCGC1381_mTEChi_EedZsGpos_D3


title: SCGC1381_mTEChi_EedZsGpos_D23


title: SCGC1381_mTEChi_EedZsGpos_D21


title: SCGC1381_mTEChi_EedZsGpos_D20


title: SCGC1381_mTEChi_EedZsGpos_E16


title: SCGC1381_mTEChi_EedZsGpos_D22


title: SCGC1381_mTEChi_EedZsGpos_D2


title: SCGC1381_mTEChi_EedZsGpos_D18


title: SCGC1381_mTEChi_EedZsGpos_D16


title: SCGC1381_mTEChi_EedZsGpos_D17


title: SCGC1381_mTEChi_EedZsGpos_D15


title: SCGC1381_mTEChi_EedZsGpos_D14


title: SCGC1381_mTEChi_EedZsGpos_D13


title: SCGC1381_mTEChi_EedZsGpos_D12


title: SCGC1381_mTEChi_EedZsGpos_D11


title: SCGC1381_mTEChi_EedZsGpos_D10


title: SCGC1381_mTEChi_EedZsGpos_D1


title: SCGC1381_mTEChi_EedZsGpos_C8


title: SCGC1381_mTEChi_EedZsGpos_C9


title: SCGC1381_mTEChi_EedZsGpos_C7


title: SCGC1381_mTEChi_EedZsGpos_C5


title: SCGC1381_mTEChi_EedZsGpos_C6


title: SCGC1381_mTEChi_EedZsGpos_C3


title: SCGC1381_mTEChi_EedZsGpos_C4


title: SCGC1381_mTEChi_EedZsGpos_C22


title: SCGC1381_mTEChi_EedZsGpos_C21


title: SCGC1381_mTEChi_EedZsGpos_C23


title: SCGC1381_mTEChi_EedZsGpos_C19


title: SCGC1381_mTEChi_EedZsGpos_C2


title: SCGC1381_mTEChi_EedZsGpos_D19


title: SCGC1381_mTEChi_EedZsGpos_C20


title: SCGC1381_mTEChi_EedZsGpos_C17


title: SCGC1381_mTEChi_EedZsGpos_C24


title: SCGC1381_mTEChi_EedZsGpos_C18


title: SCGC1381_mTEChi_EedZsGpos_C16


title: SCGC1381_mTEChi_EedZsGpos_C15


title: SCGC1381_mTEChi_EedZsGpos_C1


title: SCGC1381_mTEChi_EedZsGpos_C13


title: SCGC1381_mTEChi_EedZsGpos_C12


title: SCGC1381_mTEChi_EedZsGpos_C11


title: SCGC1381_mTEChi_EedZsGpos_C10


title: SCGC1381_mTEChi_EedZsGposBulk70_A3

value: small bulk


title: SCGC1381_mTEChi_EedZsGposBulk100_A1


title: SCGC1381_mTEChi_EedZsGpos_C14


title: SCGC1381_mTEChi_EedZsGpos_B7


title: SCGC1381_mTEChi_EedZsGposBulk100_A2


title: SCGC1381_mTEChi_EedZsGpos_B6


title: SCGC1381_mTEChi_EedZsGpos_B9


title: SCGC1381_mTEChi_EedZsGpos_B8


title: SCGC1381_mTEChi_EedZsGpos_B5


title: SCGC1381_mTEChi_EedZsGpos_B20


title: SCGC1381_mTEChi_EedZsGpos_B3


title: SCGC1381_mTEChi_EedZsGpos_B24


title: SCGC1381_mTEChi_EedZsGpos_B22


title: SCGC1381_mTEChi_EedZsGpos_B19


title: SCGC1381_mTEChi_EedZsGpos_B17


title: SCGC1381_mTEChi_EedZsGpos_B15


title: SCGC1381_mTEChi_EedZsGpos_B14


title: SCGC1381_mTEChi_EedZsGpos_B18


title: SCGC1381_mTEChi_EedZsGpos_B16


title: SCGC1381_mTEChi_EedZsGpos_B21


title: SCGC1381_mTEChi_EedZsGpos_B13


title: SCGC1381_mTEChi_EedZsGpos_B10


title: SCGC1381_mTEChi_EedZsGpos_B12


title: SCGC1381_mTEChi_EedZsGpos_B11


title: SCGC1381_mTEChi_EedZsGpos_A8


title: SCGC1381_mTEChi_EedZsGpos_A9


title: SCGC1381_mTEChi_EedZsGpos_A6


title: SCGC1381_mTEChi_EedZsGpos_A22


title: SCGC1381_mTEChi_EedZsGpos_A5


title: SCGC1381_mTEChi_EedZsGpos_A7


title: SCGC1381_mTEChi_EedZsGpos_B1


title: SCGC1381_mTEChi_EedZsGpos_B4


title: SCGC1381_mTEChi_EedZsGpos_A4


title: SCGC1381_mTEChi_EedZsGpos_B23


title: SCGC1381_mTEChi_EedZsGpos_A21


title: SCGC1381_mTEChi_EedZsGpos_A20


title: SCGC1381_mTEChi_EedZsGpos_B2


title: SCGC1381_mTEChi_EedZsGpos_A17


title: SCGC1381_mTEChi_EedZsGpos_A19


title: SCGC1381_mTEChi_EedZsGpos_A18


title: SCGC1381_mTEChi_EedZsGpos_A16


title: SCGC1381_mTEChi_EedZsGpos_A23


title: SCGC1381_mTEChi_EedZsGneg_K8


title: SCGC1381_mTEChi_EedZsGpos_A14


title: SCGC1381_mTEChi_EedZsGneg_K9


title: SCGC1381_mTEChi_EedZsGpos_A10


title: SCGC1381_mTEChi_EedZsGpos_A12


title: SCGC1381_mTEChi_EedZsGpos_A13


title: SCGC1381_mTEChi_EedZsGpos_A15


title: SCGC1381_mTEChi_EedZsGpos_A11


title: SCGC1381_mTEChi_EedZsGneg_K4


title: SCGC1381_mTEChi_EedZsGneg_K7


title: SCGC1381_mTEChi_EedZsGneg_K21


title: SCGC1381_mTEChi_EedZsGpos_A24


title: SCGC1381_mTEChi_EedZsGneg_K3


title: SCGC1381_mTEChi_EedZsGneg_K6


title: SCGC1381_mTEChi_EedZsGneg_K2


title: SCGC1381_mTEChi_EedZsGneg_K5


title: SCGC1381_mTEChi_EedZsGneg_K23


title: SCGC1381_mTEChi_EedZsGneg_K17


title: SCGC1381_mTEChi_EedZsGneg_K22


title: SCGC1381_mTEChi_EedZsGneg_K24


title: SCGC1381_mTEChi_EedZsGneg_K15


title: SCGC1381_mTEChi_EedZsGneg_K14


title: SCGC1381_mTEChi_EedZsGneg_K13


title: SCGC1381_mTEChi_EedZsGneg_K20


title: SCGC1381_mTEChi_EedZsGneg_K19


title: SCGC1381_mTEChi_EedZsGneg_K12


title: SCGC1381_mTEChi_EedZsGneg_K16


title: SCGC1381_mTEChi_EedZsGneg_K11


title: SCGC1381_mTEChi_EedZsGneg_K10


title: SCGC1381_mTEChi_EedZsGneg_J3


title: SCGC1381_mTEChi_EedZsGneg_J5


title: SCGC1381_mTEChi_EedZsGneg_J4


title: SCGC1381_mTEChi_EedZsGneg_J23


title: SCGC1381_mTEChi_EedZsGneg_K18


title: SCGC1381_mTEChi_EedZsGneg_J24


title: SCGC1381_mTEChi_EedZsGneg_J8


title: SCGC1381_mTEChi_EedZsGneg_J20


title: SCGC1381_mTEChi_EedZsGneg_J2


title: SCGC1381_mTEChi_EedZsGneg_J18


title: SCGC1381_mTEChi_EedZsGneg_J19


title: SCGC1381_mTEChi_EedZsGneg_J15


title: SCGC1381_mTEChi_EedZsGneg_J11


title: SCGC1381_mTEChi_EedZsGneg_J6


title: SCGC1381_mTEChi_EedZsGneg_J22


title: SCGC1381_mTEChi_EedZsGneg_J7


title: SCGC1381_mTEChi_EedZsGneg_J10


title: SCGC1381_mTEChi_EedZsGneg_J12


title: SCGC1381_mTEChi_EedZsGneg_K1


title: SCGC1381_mTEChi_EedZsGneg_J1


title: SCGC1381_mTEChi_EedZsGneg_J14


title: SCGC1381_mTEChi_EedZsGneg_J17


title: SCGC1381_mTEChi_EedZsGneg_J21


title: SCGC1381_mTEChi_EedZsGneg_J9


title: SCGC1381_mTEChi_EedZsGneg_J16


title: SCGC1381_mTEChi_EedZsGneg_I9


title: SCGC1381_mTEChi_EedZsGneg_I7


title: SCGC1381_mTEChi_EedZsGneg_I8


title: SCGC1381_mTEChi_EedZsGneg_J13


title: SCGC1381_mTEChi_EedZsGneg_I6


title: SCGC1381_mTEChi_EedZsGneg_I4


title: SCGC1381_mTEChi_EedZsGneg_I5


title: SCGC1381_mTEChi_EedZsGneg_I21


title: SCGC1381_mTEChi_EedZsGneg_I24


title: SCGC1381_mTEChi_EedZsGneg_I3


title: SCGC1381_mTEChi_EedZsGneg_I23


title: SCGC1381_mTEChi_EedZsGneg_I2


title: SCGC1381_mTEChi_EedZsGneg_I20


title: SCGC1381_mTEChi_EedZsGneg_I17


title: SCGC1381_mTEChi_EedZsGneg_I19


title: SCGC1381_mTEChi_EedZsGneg_I18


title: SCGC1381_mTEChi_EedZsGneg_I15


title: SCGC1381_mTEChi_EedZsGneg_I16


title: SCGC1381_mTEChi_EedZsGneg_I12


title: SCGC1381_mTEChi_EedZsGneg_I11


title: SCGC1381_mTEChi_EedZsGneg_I10


title: SCGC1381_mTEChi_EedZsGneg_I1


title: SCGC1381_mTEChi_EedZsGneg_I13


title: SCGC1381_mTEChi_EedZsGneg_H9


title: SCGC1381_mTEChi_EedZsGneg_H8


title: SCGC1381_mTEChi_EedZsGneg_H6


title: SCGC1381_mTEChi_EedZsGneg_H5


title: SCGC1381_mTEChi_EedZsGneg_H7


title: SCGC1381_mTEChi_EedZsGneg_H23


title: SCGC1381_mTEChi_EedZsGneg_H4


title: SCGC1381_mTEChi_EedZsGneg_I22


title: SCGC1381_mTEChi_EedZsGneg_H19


title: SCGC1381_mTEChi_EedZsGneg_H20


title: SCGC1381_mTEChi_EedZsGneg_H22


title: SCGC1381_mTEChi_EedZsGneg_H21


title: SCGC1381_mTEChi_EedZsGneg_I14


title: SCGC1381_mTEChi_EedZsGneg_H14


title: SCGC1381_mTEChi_EedZsGneg_H2


title: SCGC1381_mTEChi_EedZsGneg_H18


title: SCGC1381_mTEChi_EedZsGneg_H11


title: SCGC1381_mTEChi_EedZsGneg_H17


title: SCGC1381_mTEChi_EedZsGneg_H13


title: SCGC1381_mTEChi_EedZsGneg_H16


title: SCGC1381_mTEChi_EedZsGneg_H12


title: SCGC1381_mTEChi_EedZsGneg_H3


title: SCGC1381_mTEChi_EedZsGneg_H10


title: SCGC1381_mTEChi_EedZsGneg_H24


title: SCGC1381_mTEChi_EedZsGneg_G3


title: SCGC1381_mTEChi_EedZsGneg_G8


title: SCGC1381_mTEChi_EedZsGneg_G9


title: SCGC1381_mTEChi_EedZsGneg_G6


title: SCGC1381_mTEChi_EedZsGneg_G7


title: SCGC1381_mTEChi_EedZsGneg_G5


title: SCGC1381_mTEChi_EedZsGneg_G24


title: SCGC1381_mTEChi_EedZsGneg_G21


title: SCGC1381_mTEChi_EedZsGneg_G23


title: SCGC1381_mTEChi_EedZsGneg_G22


title: SCGC1381_mTEChi_EedZsGneg_G20


title: SCGC1381_mTEChi_EedZsGneg_H15


title: SCGC1381_mTEChi_EedZsGneg_G18


title: SCGC1381_mTEChi_EedZsGneg_G19


title: SCGC1381_mTEChi_EedZsGneg_G2


title: SCGC1381_mTEChi_EedZsGneg_G16


title: SCGC1381_mTEChi_EedZsGneg_G15


title: SCGC1381_mTEChi_EedZsGneg_H1


title: SCGC1381_mTEChi_EedZsGneg_G14


title: SCGC1381_mTEChi_EedZsGneg_G4


title: SCGC1381_mTEChi_EedZsGneg_G13


title: SCGC1381_mTEChi_EedZsGneg_G1


title: SCGC1381_mTEChi_EedZsGneg_G11


title: SCGC1380_mTEChi_WT_P9


title: SCGC1380_mTEChi_WT_P3


title: SCGC1380_mTEChi_WT_P6


title: SCGC1380_mTEChi_WT_P8


title: SCGC1380_mTEChi_WT_P21


title: SCGC1380_mTEChi_WT_P22


title: SCGC1380_mTEChi_WT_P5


title: SCGC1380_mTEChi_WT_P4


title: SCGC1380_mTEChi_WT_P17


title: SCGC1380_mTEChi_WT_P18


title: SCGC1380_mTEChi_WT_P16


title: SCGC1380_mTEChi_WT_P20


title: SCGC1380_mTEChi_WT_P19


title: SCGC1380_mTEChi_WT_P2


title: SCGC1380_mTEChi_WT_P15


title: SCGC1380_mTEChi_WT_P14


title: SCGC1380_mTEChi_WT_P13


title: SCGC1380_mTEChi_WT_P12


title: SCGC1381_mTEChi_EedZsGneg_G12


title: SCGC1381_mTEChi_EedZsGneg_G10


title: SCGC1380_mTEChi_WT_P10


title: SCGC1380_mTEChi_WT_P1


title: SCGC1380_mTEChi_WT_P11


title: SCGC1380_mTEChi_WT_O9


title: SCGC1381_mTEChi_EedZsGneg_G17


title: SCGC1380_mTEChi_WT_P7


title: SCGC1380_mTEChi_WT_O8


title: SCGC1380_mTEChi_WT_O7


title: SCGC1380_mTEChi_WT_O6


title: SCGC1380_mTEChi_WT_O5


title: SCGC1380_mTEChi_WT_O4


title: SCGC1380_mTEChi_WT_O24


title: SCGC1380_mTEChi_WT_O20


title: SCGC1380_mTEChi_WT_O21


title: SCGC1380_mTEChi_WT_O2


title: SCGC1380_mTEChi_WT_O23


title: SCGC1380_mTEChi_WT_O17


title: SCGC1380_mTEChi_WT_O16


title: SCGC1380_mTEChi_WT_O19


title: SCGC1380_mTEChi_WT_O18


title: SCGC1380_mTEChi_WT_O15


title: SCGC1380_mTEChi_WT_O13


title: SCGC1380_mTEChi_WT_O12


title: SCGC1380_mTEChi_WT_O1


title: SCGC1380_mTEChi_WT_O11


title: SCGC1380_mTEChi_WT_N6


title: SCGC1380_mTEChi_WT_N8


title: SCGC1380_mTEChi_WT_N7


title: SCGC1380_mTEChi_WT_N9


title: SCGC1380_mTEChi_WT_N24


title: SCGC1380_mTEChi_WT_N22


title: SCGC1380_mTEChi_WT_N3


title: SCGC1380_mTEChi_WT_N4


title: SCGC1380_mTEChi_WT_O3


title: SCGC1380_mTEChi_WT_N20


title: SCGC1380_mTEChi_WT_N21


title: SCGC1380_mTEChi_WT_N2


title: SCGC1380_mTEChi_WT_N19


title: SCGC1380_mTEChi_WT_N17


title: SCGC1380_mTEChi_WT_N16


title: SCGC1380_mTEChi_WT_O14


title: SCGC1380_mTEChi_WT_N15


title: SCGC1380_mTEChi_WT_O10


title: SCGC1380_mTEChi_WT_N13


title: SCGC1380_mTEChi_WT_N12


title: SCGC1380_mTEChi_WT_O22


title: SCGC1380_mTEChi_WT_N11


title: SCGC1380_mTEChi_WT_N10


title: SCGC1380_mTEChi_WT_N5


title: SCGC1380_mTEChi_WT_N1


title: SCGC1380_mTEChi_WT_M7


title: SCGC1380_mTEChi_WT_M9


title: SCGC1380_mTEChi_WT_M8


title: SCGC1380_mTEChi_WT_M5


title: SCGC1380_mTEChi_WT_M4


title: SCGC1380_mTEChi_WT_N23


title: SCGC1380_mTEChi_WT_M3


title: SCGC1380_mTEChi_WT_M22


title: SCGC1380_mTEChi_WT_M21


title: SCGC1380_mTEChi_WT_N18


title: SCGC1380_mTEChi_WT_M19


title: SCGC1380_mTEChi_WT_M23


title: SCGC1380_mTEChi_WT_M20


title: SCGC1380_mTEChi_WT_M2


title: SCGC1380_mTEChi_WT_N14


title: SCGC1380_mTEChi_WT_M18


title: SCGC1380_mTEChi_WT_M16


title: SCGC1380_mTEChi_WT_M15


title: SCGC1380_mTEChi_WT_M17


title: SCGC1380_mTEChi_WT_M11


title: SCGC1380_mTEChi_WT_M12


title: SCGC1380_mTEChi_WT_M13


title: SCGC1380_mTEChi_WT_M14


title: SCGC1380_mTEChi_WT_L9


title: SCGC1380_mTEChi_WT_M10


title: SCGC1380_mTEChi_WT_L7


title: SCGC1380_mTEChi_WT_M6


title: SCGC1380_mTEChi_WT_L8


title: SCGC1380_mTEChi_WT_M24


title: SCGC1380_mTEChi_WT_L6


title: SCGC1380_mTEChi_WT_L4


title: SCGC1380_mTEChi_WT_L3


title: SCGC1380_mTEChi_WT_L23


title: SCGC1380_mTEChi_WT_L24


title: SCGC1380_mTEChi_WT_L22


title: SCGC1380_mTEChi_WT_L20


title: SCGC1380_mTEChi_WT_L18


title: SCGC1380_mTEChi_WT_L19


title: SCGC1380_mTEChi_WT_L17


title: SCGC1380_mTEChi_WT_L2


title: SCGC1380_mTEChi_WT_L15


title: SCGC1380_mTEChi_WT_L14


title: SCGC1380_mTEChi_WT_L16


title: SCGC1380_mTEChi_WT_L12


title: SCGC1380_mTEChi_WT_L10


title: SCGC1380_mTEChi_WT_M1


title: SCGC1380_mTEChi_WT_K8


title: SCGC1380_mTEChi_WT_K9


title: SCGC1380_mTEChi_WT_K7


title: SCGC1380_mTEChi_WT_L1


title: SCGC1380_mTEChi_WT_K5


title: SCGC1380_mTEChi_WT_L13


title: SCGC1380_mTEChi_WT_K4


title: SCGC1380_mTEChi_WT_K24


title: SCGC1380_mTEChi_WT_K23


title: SCGC1380_mTEChi_WT_K21


title: SCGC1380_mTEChi_WT_L21


title: SCGC1380_mTEChi_WT_K20


title: SCGC1380_mTEChi_WT_K19


title: SCGC1380_mTEChi_WT_K2


title: SCGC1380_mTEChi_WT_L5


title: SCGC1380_mTEChi_WT_K18


title: SCGC1380_mTEChi_WT_K17


title: SCGC1380_mTEChi_WT_K15


title: SCGC1380_mTEChi_WT_K16


title: SCGC1380_mTEChi_WT_L11


title: SCGC1380_mTEChi_WT_K14


title: SCGC1380_mTEChi_WT_K13


title: SCGC1380_mTEChi_WT_K10


title: SCGC1380_mTEChi_WT_K1


title: SCGC1380_mTEChi_WT_K12


title: SCGC1380_mTEChi_WT_K6


title: SCGC1380_mTEChi_WT_J2


title: SCGC1380_mTEChi_WT_J7


title: SCGC1380_mTEChi_WT_J6


title: SCGC1380_mTEChi_WT_J4


title: SCGC1380_mTEChi_WT_K3


title: SCGC1380_mTEChi_WT_K11


title: SCGC1380_mTEChi_WT_J3


title: SCGC1380_mTEChi_WT_J5


title: SCGC1380_mTEChi_WT_J1


title: SCGC1380_mTEChi_NTC_P24


title: SCGC1380_mTEChi_EedZsGpos_F9


title: SCGC1380_mTEChi_NTC_A3


title: SCGC1380_mTEChi_NTC_A2


title: SCGC1380_mTEChi_EedZsGpos_F8


title: SCGC1380_mTEChi_WT_K22


title: SCGC1380_mTEChi_NTC_A1


title: SCGC1380_mTEChi_EedZsGpos_F7


title: SCGC1380_mTEChi_NTC_P23


title: SCGC1380_mTEChi_EedZsGpos_F4


title: SCGC1380_mTEChi_EedZsGpos_F6


title: SCGC1380_mTEChi_EedZsGpos_F24


title: SCGC1380_mTEChi_EedZsGpos_F5


title: SCGC1380_mTEChi_EedZsGpos_F23


title: SCGC1380_mTEChi_EedZsGpos_F21


title: SCGC1380_mTEChi_EedZsGpos_F22


title: SCGC1380_mTEChi_EedZsGpos_F19


title: SCGC1380_mTEChi_EedZsGpos_F20


title: SCGC1380_mTEChi_EedZsGpos_F2


title: SCGC1380_mTEChi_EedZsGpos_F18


title: SCGC1380_mTEChi_EedZsGpos_F13


title: SCGC1380_mTEChi_EedZsGpos_F15


title: SCGC1380_mTEChi_EedZsGpos_F16


title: SCGC1380_mTEChi_EedZsGpos_F10


title: SCGC1380_mTEChi_EedZsGpos_F14


title: SCGC1380_mTEChi_EedZsGpos_F1


title: SCGC1380_mTEChi_EedZsGpos_F12


title: SCGC1380_mTEChi_EedZsGpos_E9


title: SCGC1380_mTEChi_EedZsGpos_E4


title: SCGC1380_mTEChi_EedZsGpos_E6


title: SCGC1380_mTEChi_EedZsGpos_E3


title: SCGC1380_mTEChi_EedZsGpos_E24


title: SCGC1380_mTEChi_EedZsGpos_E7


title: SCGC1380_mTEChi_EedZsGpos_E8


title: SCGC1380_mTEChi_EedZsGpos_E5


title: SCGC1380_mTEChi_EedZsGpos_F3


title: SCGC1380_mTEChi_EedZsGpos_E22


title: SCGC1380_mTEChi_EedZsGpos_E21


title: SCGC1380_mTEChi_EedZsGpos_E2


title: SCGC1380_mTEChi_EedZsGpos_E19


title: SCGC1380_mTEChi_EedZsGpos_F17


title: SCGC1380_mTEChi_EedZsGpos_E20


title: SCGC1380_mTEChi_EedZsGpos_E16


title: SCGC1380_mTEChi_EedZsGpos_E13


title: SCGC1380_mTEChi_EedZsGpos_F11


title: SCGC1380_mTEChi_EedZsGpos_E17


title: SCGC1380_mTEChi_EedZsGpos_E23


title: SCGC1380_mTEChi_EedZsGpos_E18


title: SCGC1380_mTEChi_EedZsGpos_E11


title: SCGC1380_mTEChi_EedZsGpos_D9


title: SCGC1380_mTEChi_EedZsGpos_E1


title: SCGC1380_mTEChi_EedZsGpos_E12


title: SCGC1380_mTEChi_EedZsGpos_D6


title: SCGC1380_mTEChi_EedZsGpos_D8


title: SCGC1380_mTEChi_EedZsGpos_D5


title: SCGC1380_mTEChi_EedZsGpos_D3


title: SCGC1380_mTEChi_EedZsGpos_D24


title: SCGC1380_mTEChi_EedZsGpos_D23


title: SCGC1380_mTEChi_EedZsGpos_D22


title: SCGC1380_mTEChi_EedZsGpos_D21


title: SCGC1380_mTEChi_EedZsGpos_D20


title: SCGC1380_mTEChi_EedZsGpos_D4


title: SCGC1380_mTEChi_EedZsGpos_E15


title: SCGC1380_mTEChi_EedZsGpos_D2


title: SCGC1380_mTEChi_EedZsGpos_D19


title: SCGC1380_mTEChi_EedZsGpos_E14


title: SCGC1380_mTEChi_EedZsGpos_D18


title: SCGC1380_mTEChi_EedZsGpos_D16


title: SCGC1380_mTEChi_EedZsGpos_D17


title: SCGC1380_mTEChi_EedZsGpos_D7


title: SCGC1380_mTEChi_EedZsGpos_D11


title: SCGC1380_mTEChi_EedZsGpos_D13


title: SCGC1380_mTEChi_EedZsGpos_D12


title: SCGC1380_mTEChi_EedZsGpos_D1


title: SCGC1380_mTEChi_EedZsGpos_D15


title: SCGC1380_mTEChi_EedZsGpos_D10


title: SCGC1380_mTEChi_EedZsGpos_C6


title: SCGC1380_mTEChi_EedZsGpos_C7


title: SCGC1380_mTEChi_EedZsGpos_C5


title: SCGC1380_mTEChi_EedZsGpos_C4


title: SCGC1380_mTEChi_EedZsGpos_C8


title: SCGC1380_mTEChi_EedZsGpos_E10


title: SCGC1380_mTEChi_EedZsGpos_C3


title: SCGC1380_mTEChi_EedZsGpos_C21


title: SCGC1380_mTEChi_EedZsGpos_C24


title: SCGC1380_mTEChi_EedZsGpos_C20


title: SCGC1380_mTEChi_EedZsGpos_C2


title: SCGC1380_mTEChi_EedZsGpos_C19


title: SCGC1380_mTEChi_EedZsGpos_D14


title: SCGC1380_mTEChi_EedZsGpos_C17


title: SCGC1380_mTEChi_EedZsGpos_C23


title: SCGC1380_mTEChi_EedZsGpos_C22


title: SCGC1380_mTEChi_EedZsGpos_C9


title: SCGC1380_mTEChi_EedZsGpos_C15


title: SCGC1380_mTEChi_EedZsGpos_C16


title: SCGC1380_mTEChi_EedZsGpos_C14


title: SCGC1380_mTEChi_EedZsGpos_C18


title: SCGC1380_mTEChi_EedZsGpos_C13


title: SCGC1380_mTEChi_EedZsGpos_C10


title: SCGC1380_mTEChi_EedZsGpos_C11


title: SCGC1380_mTEChi_EedZsGpos_C12


title: SCGC1380_mTEChi_EedZsGpos_B8


title: pac1-ts#2 37 °C

city: Namur

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

department: Medecine

country: Belgium

institute: Namur University

data_processing:
Raw paired reads were trimmed using trimmomatic against the appropriate adapter sequences with options PE ILLUMINACLIP:$adapters:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Trimmed reads were then mapped on S. pombe genome (version ASM294v2.26) using HISAT244 with option --RNA-strandness RF --min-intronlen 20 --max-intronlen 3000 --no-mixed --no-discordant.
Mapped reads were summarized at the gene level using featureCounts45 with options -s 2 -p -P -d 0 -D 5000 -C.
Gene-level read count matrix was then inputed into DESeq2 that uses a median of ratio method to compute size factors (normalization factor). Based on these size factors, we used deepTools to create strand-specific normalized coverage files (.bigwig) with options bamCoverage --samFlagExclude 256 --maxFragmentLength --scaleFactor $size_factor --filterRNAstrand [forward,reverse] -bs 1 -of bigwig.
Differential expression analysis was carried out in DEseq2 using a generalized linear model of the form expression ~ strain + temperature + temperature:strain to accounts for the interaction between the thermosensitive mutation and the temperature in the case of the pac1-ts dataset, and of the form expression ~ strain for the other datasets.
Genome_build: ASM294v2.26
Supplementary_files_format_and_content: Strand-specific genome coverage files in bigWig format.

molecule: total RNA

organism: Schizosaccharomyces pombe

source_name: S.pombe cells

growth_protocol: Cells were grown at 30 °C in Edinburgh minimal media (EMM) supplemented with adenine, uracil, histidine, and leucine. Cells were collected at OD600nm of ∼0.6–0.7.

extract_protocol:
Total RNA was extracted using the hot-acid phenol method.
RNA-seq libraries were prepared following manufacturer’s instructions using either the Zymo-Seq RiboFree Total RNA Library Kit (for the pac1-ts RNA-seq experiment) or Illumina Truseq Stranded Total RNA-sequencing after ribodeletion with the RiboZero Yeast ribodepletion (Epicentre). RNA-seq libraries were sequenced in paired-end (2x50nt) using illumine technologies (MiSeq or NovaSeq) at Genome Québec.

treatment_protocol: The Pac1 protein fused to the anchor-away system was relocalized in the cytoplasm by a two hours rapamycin treatment at a final concentration of 2.5 µg/ml. Conditional strains in which the nmt81 promoters control the expression of genes of interests were repressed by 12-15h treatment with 60 µM of thiamine.

tag: genotype

value: h+ S. pombe:ade6M210 leu1-32 ura4-D18 his3-D1 pac1-G1024A

tag: condition

value: EMM 37°C 2h


title: SCGC1380_mTEChi_EedZsGpos_C1


title: SCGC1380_mTEChi_EedZsGpos_B7


title: SCGC1380_mTEChi_EedZsGpos_B9


title: pac1-ts#2 30 °C

value: EMM 30°C


title: SCGC1380_mTEChi_EedZsGpos_B6


title: pac1-ts#1 30 °C


title: pac1-ts#1 37 °C


title: SCGC1380_mTEChi_EedZsGpos_B5


title: SCGC1380_mTEChi_EedZsGpos_B4


title: CD335 subset of Sheep  at day 5

city: Karnal

first: Ravi Kumar

last: Gandham

state: Haryana

address: Makrampur

country: India

institute: ICAR-NBAGR

description: Gene expression in CD335

data_processing: Initially, the quality-filtered reads from control and infected samples (0 days and 5 days post vaccination) were mapped to Goat/Sheep genome using Bowtie2. The mapped reads were then assembled using RNA-Seq by expectation maximization (RSEM).

organism: Ovis aries

source_name: PBMCs of Sheep at day 5

extract_protocol:
Total RNA from each subset-CD4+, CD8+, CD14+, CD21+ and CD335+ of PBMCs of control (Goat & Sheep) and vaccinated (Goat & Sheep) were isolated using the RNeasy Mini kit (Qiagen GmbH, Germany). The integrity and quantity of isolated RNA were assessed  based on a Bioanalyzer (Agilent Technologies, Inc). The RNA integrity number (RIN) value of all the samples were found greater than 8.
Library was prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NewEngland Biolabs Inc.) following the manufacturer’s protocol. Approximately, 100ng of RNA from each sample was used for RNA library preparation. The quality of the libraries was assessed on Bioanalyzer and further quantified using a Qubit 2.0 Fluorometer (Life technologies). Libraries were sequenced on Illumina – NextSeq500  following manufacturer’s protocol.

treatment_protocol: Goat and Sheep were subjected to Sungri/96 PPRV vaccination and PBMCs were isolated from them at 0 day (control i.e. just before vaccination) and before the development of antibody response (5 days post vaccination i.e. 5dpv). The RNA was  isolated from each subsets of PBMCs of both species.

tag: cell type

tag: infection status

value: 5 day


title: CD335 subset of Sheep  at day 0

description: Gene expression in CD335

source_name: PBMCs of Sheep at day 0

value: 0 day


title: CD21 subset of Sheep  at day 5

description: Gene expression in CD21


title: SCGC1380_mTEChi_EedZsGpos_B3


title: SCGC1380_mTEChi_EedZsGpos_B24


title: SCGC1380_mTEChi_EedZsGpos_B23


title: CD21 subset of Sheep  at day 0

description: Gene expression in CD21


title: CD14 subset of Sheep  at day 5

description: Gene expression in CD14


title: SCGC1380_mTEChi_EedZsGpos_B2


title: SCGC1380_mTEChi_EedZsGpos_B22


title: SCGC1380_mTEChi_EedZsGpos_B20


title: CD8 subset of Sheep  at day 5

description: Gene expression in CD8


title: CD8 subset of Sheep at day 0

description: Gene expression in CD8


title: SCGC1380_mTEChi_EedZsGpos_B18


title: CD4 subset of Sheep  at day 5

description: Gene expression in CD4


title: SCGC1380_mTEChi_EedZsGpos_B19


title: SCGC1380_mTEChi_EedZsGpos_B15


title: CD4 subset of Sheep  at day 0

description: Gene expression in CD4


title: SCGC1380_mTEChi_EedZsGpos_B17


title: SCGC1380_mTEChi_EedZsGpos_B14


title: Nr29_control_0557

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

country: Germany

institute: Justus-Liebig University Gießen

data_processing:
All reads were trimmed for quality and adaptor sequences using trimmomatic
Reads were mapped to the Rhodobacter sphaeroides 2.4.1 whole genome (NC_007493.2, NC_007494.2, NC_009007.1, NC_007488.2, NC_007489.1, NC_007490.2, and NC_009008.1) using the READemption pipeline (version 0.4.3) subcommand align with the integrated mapper segemehl (version 0.2.0)
READemption (version 0.4.3) was used for gene quantification, subcommand gene_quanti
READemption (version 0.4.3) was used to compute the coverage files, subcommand coverage
Genome_build: GCF_000012905.2 ASM1290v2

organism: Cereibacter sphaeroides 2.4.1

source_name: wildtype

growth_protocol: All cultures were grown in malate minimal medium under microaerobic conditions (25 μM dissolved oxygen) at 32°C and 140 rpm in the dark.

extract_protocol:
Total RNA was isolated using the phenol method and remaining DNA was removed by a DNaseI treatment (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were harvested during exponential growth phase. Cell-pellets were resuspended in 2 ml of cold lysis buffer (20 mM Tris pH 7.5, 150 mM KCl, 1 mM MgCl2, 1 mM DTT) and disrupted by sonication (Pfeiffer, 2007). Cell lysate was centrifuged for 10 min at 13000 rpm and 4°C, followed by a ultra-centrifugation step (100000 rpm, 1 h, 4°C). Afterwards the supernatant was mixed with 40 µl of ANTI-FLAG M2 Magnetic Beads (Sigma-Aldrich) and incubated for 2 h at 4°C under rotation. Following five washing steps with 500 µl of lysis buffer, magnetic beads were resuspended in 500 µl of lysis buffer and RNA was isolated with phenol and chloroform-isoamylalcohol before precipitation with 1/10x vol. 3 M sodium acetate pH 4.5 and 2.5x vol. 96% Ethanol overnight.

tag: plasmid


title: SCGC1380_mTEChi_EedZsGpos_B16


title: L1900796_Nr_1_CoIP_RSP_6037

data_processing:
All reads were trimmed for quality and adaptor sequences using trimmomatic
Reads were mapped to the Rhodobacter sphaeroides 2.4.1 whole genome (NC_007493.2, NC_007494.2, NC_009007.1, NC_007488.2, NC_007489.1, NC_007490.2, and NC_009008.1) using the READemption pipeline (version 0.4.3) subcommand align with the integrated mapper segemehl (version 0.2.0)
READemption (version 0.4.3) was used for gene quantification, subcommand gene_quanti
READemption (version 0.4.3) with DESeq2 (version 1.22.1) was used to perform the differential gene expression analysis, subcommand deseq
READemption (version 0.4.3) was used to compute the coverage files, subcommand coverage
Genome_build: GCF_000012905.2 ASM1290v2
Supplementary_files_format_and_content: csv contains gene quantification and DESeq2 analysis


title: Nr23_OECcsr_32GradC_exp2

description: deseq_comp_OECcsr_32GradC_vs_WT_old_exp_with_annotation_and_countings.csv

data_processing:
All reads were trimmed for adaptor sequences using trim-galore (version 0.6.3), low-quality reads have been rejected in the same data processing step. Options were set to -q 10 --length 15 -j 8
Reads were mapped to the Rhodobacter sphaeroides 2.4.1 whole genome (NC_007493.2, NC_007494.2, NC_009007.1, NC_007488.2, NC_007489.1, NC_007490.2, and NC_009008.1) using the READemption pipeline (version 0.4.3) subcommand align with the integrated mapper segemehl (version 0.2.0)
READemption (version 0.4.3) was used for gene quantification with parameters gene_quanti --features CDS,tRNA,rRNA,tmRNA,ncRNA,sRNA --skip_antisense
READemption (version 0.4.3) with DESeq2 (version 1.22.1) was used to perform the differential gene expression analysis, subcommand deseq
Genome_build: GCF_000012905.2 ASM1290v2
Supplementary_files_format_and_content: csv contains raw counts and DESeq2 analysis

organism: Cereibacter sphaeroides

extract_protocol:
Total RNA was isolated using the hot phenol method and remaining DNA was removed by a DNaseI treatment (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were harvested during exponential growth phase.

value: pRK4352_CcsR1-4  (constitutively overexpression of the sRNAs CcsR1-4)


title: SCGC1380_mTEChi_EedZsGpos_B12


title: SCGC1380_mTEChi_EedZsGpos_B13


title: SCGC1380_mTEChi_EedZsGpos_B21


title: CD14 subset of Sheep  at day 0

description: Gene expression in CD14


title: SCGC1380_mTEChi_EedZsGpos_B11


title: Nr20_OE6037_32GradC_exp2

description: deseq_comp_OE6037_32GradC_vs_WT_old_exp_with_annotation_and_countings.csv

value: pRK4352_RSP_6037 (constitutively overexpression of RSP_6037)


title: Nr19_OE6037_32GradC_exp1


title: Nr22_OECcsr_32GradC_exp1


title: Nr03_WT_old_exp3

description:
deseq_comp_OE6037_32GradC_vs_WT_old_exp_with_annotation_and_countings.csv
deseq_comp_OECcsr_32GradC_vs_WT_old_exp_with_annotation_and_countings.csv

value: no plasmid


title: SCGC1380_mTEChi_EedZsGpos_A9


title: SCGC1380_mTEChi_EedZsGpos_A8


title: SCGC1380_mTEChi_EedZsGpos_A7


title: SCGC1380_mTEChi_EedZsGpos_B10


title: Nr02_WT_old_exp2


title: Nr01_WT_old_exp1


title: SCGC1380_mTEChi_EedZsGpos_A6


title: Nr24_OECcsr_32GradC_exp3


title: SCGC1380_mTEChi_EedZsGpos_A5


title: L1900797_Nr_2_CoIP_RSP_0557


title: Nr28_ctr


title: SCGC1380_mTEChi_EedZsGpos_A24


title: SCGC1380_mTEChi_EedZsGpos_A23


title: SCGC1380_mTEChi_EedZsGpos_A20


title: SCGC1380_mTEChi_EedZsGpos_A18


title: SCGC1380_mTEChi_EedZsGpos_A19


title: SCGC1380_mTEChi_EedZsGpos_A22


title: SCGC1380_mTEChi_EedZsGpos_A16


title: SCGC1380_mTEChi_EedZsGpos_A15


title: SCGC1380_mTEChi_EedZsGpos_B1


title: SCGC1380_mTEChi_EedZsGpos_A14


title: Nr21_OE6037_32GradC_exp3


title: SCGC1380_mTEChi_EedZsGpos_A4


title: SCGC1380_mTEChi_EedZsGpos_A12


title: SCGC1380_mTEChi_EedZsGpos_A13


title: SCGC1380_mTEChi_EedZsGpos_A11


title: SCGC1380_mTEChi_EedZsGpos_A17


title: SCGC1380_mTEChi_EedZsGpos_A10


title: SCGC1380_mTEChi_EedZsGneg_J9


title: SCGC1380_mTEChi_EedZsGpos_A21


title: SCGC1380_mTEChi_EedZsGneg_J23


title: SCGC1380_mTEChi_EedZsGneg_J17


title: SCGC1380_mTEChi_EedZsGneg_J21


title: SCGC1380_mTEChi_EedZsGneg_J20


title: SCGC1380_mTEChi_EedZsGneg_J22


title: SCGC1380_mTEChi_EedZsGneg_J18


title: SCGC1380_mTEChi_EedZsGneg_J16


title: SCGC1380_mTEChi_EedZsGneg_J19


title: SCGC1380_mTEChi_EedZsGneg_J12


title: SCGC1380_mTEChi_EedZsGneg_J15


title: SCGC1380_mTEChi_EedZsGneg_J14


title: SCGC1380_mTEChi_EedZsGneg_J13


title: SCGC1380_mTEChi_EedZsGneg_I9


title: SCGC1380_mTEChi_EedZsGneg_J10


title: SCGC1380_mTEChi_EedZsGneg_I6


title: SCGC1380_mTEChi_EedZsGneg_I5


title: SCGC1380_mTEChi_EedZsGneg_I8


title: SCGC1380_mTEChi_EedZsGneg_J8


title: SCGC1380_mTEChi_EedZsGneg_J11


title: SCGC1380_mTEChi_EedZsGneg_J24


title: SCGC1380_mTEChi_EedZsGneg_I7


title: SCGC1380_mTEChi_EedZsGneg_I4


title: SCGC1380_mTEChi_EedZsGneg_I3


title: SCGC1380_mTEChi_EedZsGneg_I21


title: SCGC1380_mTEChi_EedZsGneg_I19


title: SCGC1380_mTEChi_EedZsGneg_I23


title: SCGC1380_mTEChi_EedZsGneg_I20


title: SCGC1380_mTEChi_EedZsGneg_I2


title: SCGC1380_mTEChi_EedZsGneg_I24


title: SCGC1380_mTEChi_EedZsGneg_I16


title: SCGC1380_mTEChi_EedZsGneg_I11


title: SCGC1380_mTEChi_EedZsGneg_I12


title: SCGC1380_mTEChi_EedZsGneg_I13


title: SCGC1380_mTEChi_EedZsGneg_I14


title: SCGC1380_mTEChi_EedZsGneg_I17


title: SCGC1380_mTEChi_EedZsGneg_I15


title: SCGC1380_mTEChi_EedZsGneg_I10


title: SCGC1380_mTEChi_EedZsGneg_I1


title: SCGC1380_mTEChi_EedZsGneg_H9


title: SCGC1380_mTEChi_EedZsGneg_H8


title: SCGC1380_mTEChi_EedZsGneg_I22


title: SCGC1380_mTEChi_EedZsGneg_H7


title: SCGC1380_mTEChi_EedZsGneg_I18


title: SCGC1380_mTEChi_EedZsGneg_H6


title: SCGC1380_mTEChi_EedZsGneg_H5


title: SCGC1380_mTEChi_EedZsGneg_H4


title: SCGC1380_mTEChi_EedZsGneg_H3


title: SCGC1380_mTEChi_EedZsGneg_H24


title: SCGC1380_mTEChi_EedZsGneg_H23


title: SCGC1380_mTEChi_EedZsGneg_H22


title: Tregs coculture with control SVEC4-10 cells

city: Tokyo

first: Takuro

last: Miyazaki

address: 1-5-8 Hatanodai, Shinagawa-ku

department: Biochemistry

country: Japan

institute: Showa University School of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using trimmomatic (ver. 0.39)
BWA(ver. 0.7.17) was used for mapping the reads to reference sequence
Genome_build: GRCm39
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CD4+CD25+ Tregs

growth_protocol: Isolated splenic CD4+CD25+ cells were cocultured with SVEC4-10 cells for 5 days.

extract_protocol:
Total RNA in cocultured Tregs were isolated using an RNeasy mini kit (Qiagen) with on-column DNaseI digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SVEC4-10 cells  were subjected to siRNA against Capns1 or control oligo.

value: splenic CD4+CD25+ Tregs

tag: treatment

value: coculture with control SVEC4-10 cells


title: Tregs coculture with Capns1-knockdown SVEC4-10 cells


title: SCGC1380_mTEChi_EedZsGneg_H20


title: Sox9fl:flAcanCreER-P13

city: Philadelphia

first: Véronique

last: Lefebvre

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC 912

department: Division of Orthopaedic Surgery

country: USA

institute: The Children's Hospital of Philadelphia Research Institute

data_processing:
Alignment, demultiplexing, barcode assignment and UMI quantification: Cell Ranger (10X Genomics)
Clustering and gene expression analysis: Seurat v3
Pseudotime analysis: Monocle 3
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files as Matrix (.mtx) format and gene expression analysis from Seurat as Excel Spreadsheet (.xlsx)

source_name: Tibial and femur epiphyses

extract_protocol:
Tibial and femur epihyses were disssected out from control and mutant neonate mice and then digested with Liberase.  Dissociated cells in a single cell suspension were loaded into the Chromium Single Cell v3 microfluidics chip. cDNA libraries were sequenced by NovaSeq using 100 cycle paired-end read
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Tibial and femur epiphyses

tag: age

value: Postnatal 13 days

value: Sox9fl:fl AcanCreERT2/+


title: WT-P13

value: wild type


title: WT-P19

value: Postnatal 19 days


title: Sox9fl:flAcanCreER-P19


title: SCGC1380_mTEChi_EedZsGneg_H18

value: single cell

value: negative


title: ka120_mature leaf_rep2

type: RNA

city: Berkeley

first: Yangnan

last: Gu

state: CA

address: 371 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

hyb_protocol: Following fragmentation, 10 ug of aRNA were hybridized on Affymetrix ATH1 GeneChip (Santa Clara, CA, U.S.A) for 16 hours at 45C with rotation at 60rpm.

scan_protocol: Immediately following hybridization, the hybridized probe arrays undergo an automated washing and staining protocol on the GeneChip® FS450 fluidic station and are then scanned on the GeneChip® Scanner 3000 7G Plus where patterns of hybridization are detected.

data_processing: The data were normalized using affy package in R

label: biotin

organism: Arabidopsis thaliana

source_name: ka120_mature leaf

label_protocol: RNA probes were labelled using MessageAmp Premier RNA Amplification Kit (Ambion)

growth_protocol: Arabidopsis plants were grown on soil (Metro Mix 360) at 22˚C under a 12/12 hr light/dark cycle for 4 weeks

extract_protocol: The RNA was extracted with TRIzol (Ambion)

treatment_protocol: No treatment

value: mature leaf


title: ka120_mature leaf_rep3


title: Treated-KO Replicate 2

city: Columbus

first: Pearlly

last: Yan

state: OH

department: Division of Hematology

institute: The Ohio State University

description:
IP: 5uL per gram bodyweight (3mg/mL) stock
X6528_SparreboomA_53_V1N

data_processing:
Basecalls performed using Casava 1.8.2
Reads were trimmed using AdapterRemoval v2.2.0 to remove sequencing adapters
Reads were aligned against the mouse decontaminome using HISAT2 v2.0.6 using default parameters
Unaligned deconaminome reads were aligned against the mouse genome using HISAT2 v2.0.6 using default parameters
Reads were quantified using Subread FeatureCounts using GENCODE release M14
Genome_build: GRCm38p4
Supplementary_files_format_and_content: TSV Counts tables generated using Subread FeatureCounts, Unfiltered

source_name: Oct3-M (Slc22a3) null mice of FVB inbred strain (8 week)

growth_protocol: Animals were maintained on standard lab chow and water ad libitum

extract_protocol:
Heart tissue dissected and immediately snap frozen in LN2. RNA isolated according to protocol: Omega Bio-Tek EZNA Total RNA Kit I (SKU: R6834-01)
Total RNA quantified using the Invitrogen Qubit RNA HS Assay kit (Invitrogen, Carlsbad, CA) was serially diluted to masses characteristic of single- and low cell number RNA-Seq (1ng). The Clontech SMARTer v4 kit (Takara Bio USA, Inc., Mountain View, CA) was used for global preamplification. Illumina sequencing library was derived from the resultant cDNA using the Illumina Nextera XT DNA Library Prep Kit (Cat. # 15031942).

treatment_protocol: IP: 5uL per gram bodyweight of saline or 15 mg/kg doxorubicin

tag: input rna mass

value: heart

value: doxorubicin (in saline)


title: Treated-WT Replicate 3

description:
IP: 5uL per gram bodyweight (3mg/mL) stock
X6526_SparreboomA_43_V1N

source_name: FVB-M (FVB/Ntac); Inbred strain (8 week)


title: WT_mature leaf_rep2

source_name: WT_mature leaf

value: WT


title: WT_mature leaf_rep1


title: SCGC1380_mTEChi_EedZsGneg_H15


title: Treated-KO Replicate 1

description:
IP: 5uL per gram bodyweight (3mg/mL) stock
X6527_SparreboomA_48_V1N


title: Treated-KO Replicate 3

description:
IP: 5uL per gram bodyweight (3mg/mL) stock
X6529_SparreboomA_58_V1N


title: ka120_mature leaf_rep1


title: Treated-WT Replicate 1

description:
IP: 5uL per gram bodyweight (3mg/mL) stock
X6524_SparreboomA_33_V1N


title: SCGC1380_mTEChi_EedZsGneg_H14


title: Treated-WT Replicate 2

description:
IP: 5uL per gram bodyweight (3mg/mL) stock
X6525_SparreboomA_38_V1N


title: Untreated-KO Replicate 3

description:
IP: 5uL per gram bodyweight
X6523_SparreboomA_28_V1N

value: vehicle (saline)


title: SCGC1380_mTEChi_EedZsGneg_H13


title: SCGC1380_mTEChi_EedZsGneg_H21


title: SCGC1380_mTEChi_EedZsGneg_H12


title: WT_mature leaf_rep3


title: SCGC1380_mTEChi_EedZsGneg_H2


title: Untreated-KO Replicate 2

description:
IP: 5uL per gram bodyweight
X6522_SparreboomA_23_V1N


title: SCGC1380_mTEChi_EedZsGneg_H11


title: SCGC1380_mTEChi_EedZsGneg_H19


title: Untreated-KO Replicate 1

description:
IP: 5uL per gram bodyweight
X6521_SparreboomA_18_V1N


title: Untreated-WT Replicate 3

description:
IP: 5uL per gram bodyweight
X6520_SparreboomA_WT3_V1N


title: SCGC1380_mTEChi_EedZsGneg_H1


title: Untreated-WT Replicate 2

description:
IP: 5uL per gram bodyweight
X6519_SparreboomA_WT2_V1N


title: SCGC1380_mTEChi_EedZsGneg_H10


title: SCGC1380_mTEChi_EedZsGneg_H17


title: SCGC1380_mTEChi_EedZsGneg_G9


title: SCGC1380_mTEChi_EedZsGneg_H16


title: Untreated-WT Replicate 1

description:
IP: 5uL per gram bodyweight
X6518_SparreboomA_WT1_V1N


title: SCGC1380_mTEChi_EedZsGneg_G8


title: SCGC1380_mTEChi_EedZsGneg_G5


title: SCGC1380_mTEChi_EedZsGneg_G7


title: Sox8fl/flSox9fl/flAcanCreER-GP-14days [Growth plate cartilage]

data_processing:
Sequence alignment,  Reads Per Kilobase of exons per millon of total reads (NRPKM) and differential genes expression were calculated using a Strand NGS software.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes NRPKM values for each sample.

source_name: Growth plate cartilage

extract_protocol:
Knee joints were harvested from control and mutant mice and were snap frozen in OCT compound. Frozen sections were cut and then processed for laser-caputure microdissection. Articular and growth plate cartilage area were removed using laser-capture mirodissection, flash frozen on dry ice, and RNA was harvested using Qiagen Kit RNeasy Plus Micro Kit. SMARTer Stranded Total RNA-seq v2  Pico Input Mammalian kit (Takara Bio) was used with 10 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Growth plate cartilage

value: Adult 3 months

value: Sox8fl/fl Sox9fl/fl AcanCreERT2/+


title: SCGC1380_mTEChi_EedZsGneg_G4


title: Sox8fl/flSox9fl/fl-GP-14days [Growth plate cartilage]

value: Sox8fl/fl Sox9fl/fl


title: Sox8fl/flSox9fl/fl-AC-14days [Articular cartilage]

source_name: Articular cartilage

value: Articular cartilage


title: SCGC1380_mTEChi_EedZsGneg_G3


title: Sox9fl/flAcanCreER-AC-14days [Articular cartilage]

value: Sox9fl/fl AcanCreERT2/+


title: Sox9fl/fl-GP-14days [Growth plate cartilage]


title: SCGC1380_mTEChi_EedZsGneg_G22


title: Sox9fl/flAcanCreER-GP-7days [Growth plate cartilage]


title: Sox8fl/flSox9fl/flAcanCreER-AC-14days [Articular cartilage]


title: SCGC1380_mTEChi_EedZsGneg_G23


title: Sox9fl/flAcanCreER-GP-14days [Growth plate cartilage]


title: Sox9fl/fl-AC-14days [Articular cartilage]


title: SCGC1380_mTEChi_EedZsGneg_G20


title: Sox9fl/fl-GP-7days [Growth plate cartilage]


title: SCGC1380_mTEChi_EedZsGneg_G2


title: Sox9fl/fl-AC-7days [Articular cartilage]


title: SCGC1380_mTEChi_EedZsGneg_G21


title: Rbbp4KO rep3

city: Nanjing

first: Su

last: Ting

address: No. 12, Xuefu Road, Pukou District

department: Model Animal Research Center

country: China

institute: Nanjing University

data_processing:
FastQc were used for data quality control.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SeqPrep and Sickle.
Paired-end clean reads were aligned to the reference genome using the HISAT2 2.1.0; RSEM was used to calculate FPKM.
Differential expression analysis was performed using the DESeq v1.26.0.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: Embryonic stem cells

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA sample prep kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Embryonic stem cells


title: SCGC1380_mTEChi_EedZsGneg_G18


title: SCGC1380_mTEChi_EedZsGneg_G19


title: SCGC1380_mTEChi_EedZsGneg_G17


title: SCGC1380_mTEChi_EedZsGneg_G6


title: Rbbp4KO rep1


title: Rbbp4KO rep2


title: SCGC1380_mTEChi_EedZsGneg_G16


title: Rbbp4F/F rep3


title: SCGC1380_mTEChi_EedZsGneg_G15


title: SCGC1380_mTEChi_EedZsGneg_G24


title: SCGC1380_mTEChi_EedZsGneg_G14


title: Rbbp4F/F rep1


title: SCGC1380_mTEChi_EedZsGneg_G12


title: Sox9fl/flAcanCreER-AC-7days [Articular cartilage]


title: SCGC1380_mTEChi_EedZsGneg_G10


title: SCGC1380_mTEChi_EedZsGneg_G11


title: SCGC1380_mTEChi_EedZsGneg_G1


title: SCGC1379_mTEChi_WT_P9


title: SCGC1379_mTEChi_WT_P8


title: SCGC1379_mTEChi_WT_P7


title: SCGC1379_mTEChi_WT_P6


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H8_ad012

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: ACA,PL,ILA

tag: Sex

value: male


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H9_ad004


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H8_ad001


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H9_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H9_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H9_ad002


title: SCGC1379_mTEChi_WT_P5


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H8_ad010


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H8_ad006


title: Rbbp4F/F rep2


title: SCGC1379_mTEChi_WT_P4


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H8_ad004


title: SCGC1380_mTEChi_EedZsGneg_G13


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H8_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H9_ad010


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H8_ad002


title: SCGC1379_mTEChi_WT_P22


title: SCGC1379_mTEChi_WT_P21


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H7_ad012


title: SCGC1379_mTEChi_WT_P2


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H7_ad001


title: SCGC1379_mTEChi_WT_P19


title: SCGC1379_mTEChi_WT_P20


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H7_ad007


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H7_ad010


title: SCGC1379_mTEChi_WT_P17


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H7_ad008


title: SCGC1379_mTEChi_WT_P14


title: SCGC1379_mTEChi_WT_P15


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H6_ad007


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H6_ad010


title: SCGC1379_mTEChi_WT_P16


title: SCGC1379_mTEChi_WT_P13


title: SCGC1379_mTEChi_WT_P3


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H6_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H6_ad004


title: SCGC1379_mTEChi_WT_P12


title: SCGC1379_mTEChi_WT_P11


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H6_ad002


title: SCGC1379_mTEChi_WT_P10


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H6_ad008


title: SCGC1379_mTEChi_WT_O9


title: SCGC1379_mTEChi_WT_P1


title: SCGC1379_mTEChi_WT_O8


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H5_ad001


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H5_ad012


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H5_ad007


title: SCGC1379_mTEChi_WT_P18


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H5_ad010


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H7_ad006


title: SCGC1379_mTEChi_WT_O7


title: SCGC1379_mTEChi_WT_O6


title: SCGC1379_mTEChi_WT_O5


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H5_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H5_ad002


title: SCGC1379_mTEChi_WT_O3


title: SCGC1379_mTEChi_WT_O24


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H5_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H4_ad012


title: SCGC1379_mTEChi_WT_O23


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H4_ad001


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H5_ad004


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H4_ad007


title: SCGC1379_mTEChi_WT_O21


title: SCGC1379_mTEChi_WT_O22


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H4_ad010


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H4_ad006


title: SCGC1379_mTEChi_WT_O20


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H4_ad004


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H4_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H4_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H9_ad001


title: SCGC1379_mTEChi_WT_O17


title: SCGC1379_mTEChi_WT_O18


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H3_ad012


title: SCGC1379_mTEChi_WT_O19


title: SCGC1379_mTEChi_WT_O16


title: SCGC1379_mTEChi_WT_O15


title: SCGC1379_mTEChi_WT_O14


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H3_ad001


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H3_ad007


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H3_ad010


title: SCGC1379_mTEChi_WT_O13


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H3_ad006


title: SCGC1379_mTEChi_WT_O4


title: SCGC1379_mTEChi_WT_O12


title: SCGC1379_mTEChi_WT_O11


title: SCGC1379_mTEChi_WT_O2


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H3_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H3_ad002


title: SCGC1379_mTEChi_WT_O10


title: SCGC1379_mTEChi_WT_O1


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H2_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H2_ad001


title: SCGC1379_mTEChi_WT_N6


title: SCGC1379_mTEChi_WT_N5


title: SCGC1379_mTEChi_WT_N4


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H2_ad007


title: SCGC1379_mTEChi_WT_N8


title: SCGC1379_mTEChi_WT_N7


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H2_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H12_ad012


title: SCGC1379_mTEChi_WT_N9


title: SCGC1379_mTEChi_WT_N3


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H12_ad010


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H12_ad008


title: SCGC1379_mTEChi_WT_N24


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H2_ad002


title: SCGC1379_mTEChi_WT_N23


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H12_ad007


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H3_ad004


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H2_ad004


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H12_ad006


title: SCGC1379_mTEChi_WT_N21


title: SCGC1379_mTEChi_WT_N20


title: SCGC1379_mTEChi_WT_N2


title: SCGC1379_mTEChi_WT_N22


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H12_ad004


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H12_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H12_ad001


title: SCGC1379_mTEChi_WT_N19


title: SCGC1379_mTEChi_WT_N18


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H11_ad012


title: SCGC1379_mTEChi_WT_N17


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H11_ad010


title: SCGC1379_mTEChi_WT_N16


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H11_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H11_ad007


title: SCGC1379_mTEChi_WT_N14


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H11_ad004


title: SCGC1379_mTEChi_WT_N13


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H10_ad012


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H11_ad002


title: SCGC1379_mTEChi_WT_N12


title: SCGC1379_mTEChi_WT_N11


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H10_ad010


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H10_ad008


title: SCGC1379_mTEChi_WT_N1


title: SCGC1379_mTEChi_WT_M9


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H10_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H10_ad007


title: SCGC1379_mTEChi_WT_M8


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H10_ad001


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H10_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H10_ad004


title: SCGC1379_mTEChi_WT_M7


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H1_ad007


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H6_ad012


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H1_ad010


title: SCGC1379_mTEChi_WT_N15


title: SCGC1379_mTEChi_WT_M3


title: SCGC1379_mTEChi_WT_M4


title: SCGC1379_mTEChi_WT_M24


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H1_ad006


title: SCGC1379_mTEChi_WT_M23


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H1_ad004


title: SCGC1379_mTEChi_WT_M22


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H1_ad008


title: SCGC1379_mTEChi_WT_M21


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G9_ad012


title: SCGC1379_mTEChi_WT_N10


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G9_ad001


title: SCGC1379_mTEChi_WT_M2


title: SCGC1379_mTEChi_WT_M19


title: CEMBA190108_6A_3_CEMBA190108_6A_4_H1_ad012


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G9_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G9_ad007


title: SCGC1379_mTEChi_WT_M6


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G9_ad004


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G9_ad010


title: SCGC1379_mTEChi_WT_M18


title: SCGC1379_mTEChi_WT_M17


title: SCGC1379_mTEChi_WT_M5


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G9_ad002


title: SCGC1379_mTEChi_WT_M14


title: SCGC1379_mTEChi_WT_M11


title: SCGC1379_mTEChi_WT_M12


title: SCGC1379_mTEChi_WT_M16


title: SCGC1379_mTEChi_WT_L9


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G8_ad007


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G8_ad012


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G8_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G9_ad008


title: SCGC1379_mTEChi_WT_M13


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G8_ad004


title: SCGC1379_mTEChi_WT_L6


title: SCGC1379_mTEChi_WT_L7


title: SCGC1379_mTEChi_WT_M20


title: SCGC1379_mTEChi_WT_M1


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G8_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G7_ad007


title: SCGC1379_mTEChi_WT_M15


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G7_ad012


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G7_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G7_ad010


title: SCGC1379_mTEChi_WT_L8


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G7_ad001


title: SCGC1379_mTEChi_WT_L4


title: SCGC1379_mTEChi_WT_L5


title: SCGC1379_mTEChi_WT_L24


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G8_ad010


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G8_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G7_ad004


title: SCGC1379_mTEChi_WT_L21


title: SCGC1379_mTEChi_WT_L23


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G6_ad001


title: SCGC1379_mTEChi_WT_L19


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G6_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G7_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G6_ad004


title: SCGC1379_mTEChi_WT_L16


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G7_ad008


title: SCGC1379_mTEChi_WT_L22


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G6_ad012


title: SCGC1379_mTEChi_WT_L12


title: SCGC1379_mTEChi_WT_L17


title: SCGC1379_mTEChi_WT_L20


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G6_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G5_ad007


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G5_ad010


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G6_ad007


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G5_ad004


title: SCGC1379_mTEChi_WT_L15


title: SCGC1379_mTEChi_WT_L18


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G5_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G6_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G5_ad006


title: SCGC1379_mTEChi_WT_L14


title: SCGC1379_mTEChi_WTBulk100_L3

value: small bulk


title: SCGC1379_mTEChi_WTBulk100_L2


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G5_ad001


title: SCGC1379_mTEChi_WT_L13

value: single cell


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G4_ad001


title: SCGC1379_mTEChi_WT_L11

value: negative


title: SCGC1379_mTEChi_WT_L10


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G5_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G4_ad007


title: SCGC1379_mTEChi_WTBulk100_L1


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G4_ad012


title: SCGC1379_mTEChi_NTC_P23

value: no template control


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G4_ad004


title: SCGC1379_mTEChi_NTC_A3


title: SCGC1379_mTEChi_EedZsGpos_K8

value: positive


title: SCGC1379_mTEChi_NTC_A2


title: SCGC1379_mTEChi_NTC_A1


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G4_ad010


title: SCGC1379_mTEChi_EedZsGpos_K7


title: SCGC1379_mTEChi_EedZsGpos_K6


title: SCGC1379_mTEChi_NTC_P24


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G4_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G4_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G3_ad010


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G3_ad004


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G3_ad001


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G3_ad007


title: SCGC1379_mTEChi_EedZsGpos_K24


title: SCGC1379_mTEChi_EedZsGpos_K3


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G4_ad002


title: SCGC1379_mTEChi_EedZsGpos_K4


title: SCGC1379_mTEChi_EedZsGpos_K22


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G3_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G2_ad001


title: SCGC1379_mTEChi_EedZsGpos_K9


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G2_ad010


title: SCGC1379_mTEChi_EedZsGpos_K20


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G3_ad012


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G2_ad004


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G2_ad006


title: SCGC1379_mTEChi_EedZsGpos_K5


title: SCGC1379_mTEChi_EedZsGpos_K2


title: SCGC1379_mTEChi_EedZsGpos_K19


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G2_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G2_ad008


title: SCGC1379_mTEChi_EedZsGpos_K16


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G12_ad012


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G12_ad010


title: SCGC1379_mTEChi_EedZsGpos_K15


title: SCGC1379_mTEChi_EedZsGpos_K18


title: SCGC1379_mTEChi_EedZsGpos_K17


title: SCGC1379_mTEChi_EedZsGpos_K23


title: SCGC1379_mTEChi_EedZsGpos_K14


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G2_ad012


title: SCGC1379_mTEChi_EedZsGpos_K12


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G12_ad006


title: SCGC1379_mTEChi_EedZsGpos_K11


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G12_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G12_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G12_ad001


title: SCGC1379_mTEChi_EedZsGpos_K21


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G12_ad004


title: SCGC1379_mTEChi_EedZsGpos_K10


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G11_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G11_ad010


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G11_ad007


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G11_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G11_ad012


title: SCGC1379_mTEChi_EedZsGpos_K1


title: SCGC1379_mTEChi_EedZsGpos_J6


title: SCGC1379_mTEChi_EedZsGpos_J8


title: SCGC1379_mTEChi_EedZsGpos_J9


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G11_ad004


title: SCGC1379_mTEChi_EedZsGpos_K13


title: SCGC1379_mTEChi_EedZsGpos_J3


title: SCGC1379_mTEChi_EedZsGpos_J5


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G11_ad001


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G10_ad012


title: SCGC1379_mTEChi_EedZsGpos_J24


title: SCGC1379_mTEChi_EedZsGpos_J4


title: SCGC1379_mTEChi_EedZsGpos_J23


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G11_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G10_ad010


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G10_ad004


title: SCGC1379_mTEChi_EedZsGpos_J20


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G10_ad007


title: SCGC1379_mTEChi_EedZsGpos_J22


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G10_ad002


title: SCGC1379_mTEChi_EedZsGpos_J2


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G10_ad001


title: SCGC1379_mTEChi_EedZsGpos_J7


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G1_ad012


title: SCGC1379_mTEChi_EedZsGpos_J17


title: SCGC1379_mTEChi_EedZsGpos_J18


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G1_ad001


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G1_ad007


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G10_ad008


title: SCGC1379_mTEChi_EedZsGpos_J16


title: SCGC1379_mTEChi_EedZsGpos_J14


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G1_ad004


title: CEMBA190108_6A_3_CEMBA190108_6A_4_F9_ad012


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G1_ad006


title: SCGC1379_mTEChi_EedZsGpos_J13


title: SCGC1379_mTEChi_EedZsGpos_J11


title: SCGC1379_mTEChi_EedZsGpos_J1


title: SCGC1379_mTEChi_EedZsGpos_J15


title: SCGC1379_mTEChi_EedZsGpos_J21


title: CEMBA190108_6A_3_CEMBA190108_6A_4_F9_ad007


title: CEMBA190108_6A_3_CEMBA190108_6A_4_F9_ad010


title: SCGC1379_mTEChi_EedZsGpos_J12


title: CEMBA190108_6A_3_CEMBA190108_6A_4_F9_ad006


title: SCGC1379_mTEChi_EedZsGpos_I9


title: SCGC1379_mTEChi_EedZsGpos_I8


title: CEMBA190108_6A_3_CEMBA190108_6A_4_F9_ad002


title: SCGC1379_mTEChi_EedZsGpos_I7


title: SCGC1379_mTEChi_EedZsGpos_I6


title: SCGC1379_mTEChi_EedZsGpos_J19


title: CEMBA190108_6A_3_CEMBA190108_6A_4_F9_ad004


title: CEMBA190108_6A_3_CEMBA190108_6A_4_F8_ad012


title: CEMBA190108_6A_3_CEMBA190108_6A_4_F8_ad001


title: CEMBA190108_6A_3_CEMBA190108_6A_4_G1_ad010


title: SCGC1379_mTEChi_EedZsGpos_I5


title: SCGC1379_mTEChi_EedZsGpos_I4


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title: SCGC1379_mTEChi_EedZsGneg_C6


title: CEMBA190108_6A_3_CEMBA190108_6A_4_E10_ad004


title: SCGC1379_mTEChi_EedZsGneg_C2


title: SCGC1379_mTEChi_EedZsGneg_C4


title: SCGC1379_mTEChi_EedZsGneg_C24


title: SCGC1379_mTEChi_EedZsGneg_C18


title: SCGC1379_mTEChi_EedZsGneg_C20


title: CEMBA190108_6A_3_CEMBA190108_6A_4_E1_ad002


title: SCGC1379_mTEChi_EedZsGneg_C14


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D9_ad007


title: SCGC1379_mTEChi_EedZsGneg_C3


title: SCGC1379_mTEChi_EedZsGneg_C19


title: CEMBA190108_6A_3_CEMBA190108_6A_4_E10_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_E11_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D9_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_E10_ad002


title: SCGC1379_mTEChi_EedZsGneg_C1


title: SCGC1379_mTEChi_EedZsGneg_B9


title: CEMBA190108_6A_3_CEMBA190108_6A_4_E10_ad001


title: SCGC1379_mTEChi_EedZsGneg_C17


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D9_ad012


title: SCGC1379_mTEChi_EedZsGneg_C16


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D9_ad001


title: SCGC1379_mTEChi_EedZsGneg_C13


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D8_ad012


title: SCGC1379_mTEChi_EedZsGneg_B6


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D9_ad010


title: SCGC1379_mTEChi_EedZsGneg_C11


title: SCGC1379_mTEChi_EedZsGneg_B5


title: SCGC1379_mTEChi_EedZsGneg_C12


title: SCGC1379_mTEChi_EedZsGneg_B3


title: CEMBA190108_6A_3_CEMBA190108_6A_4_E10_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D9_ad006


title: SCGC1379_mTEChi_EedZsGneg_C10


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D9_ad004


title: SCGC1379_mTEChi_EedZsGneg_B24


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D8_ad001


title: SCGC1379_mTEChi_EedZsGneg_B8


title: SCGC1379_mTEChi_EedZsGneg_C15


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D8_ad004


title: SCGC1379_mTEChi_EedZsGneg_B7


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D7_ad007


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D8_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D8_ad007


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D8_ad002


title: SCGC1379_mTEChi_EedZsGneg_B20


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D8_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D7_ad012


title: SCGC1379_mTEChi_EedZsGneg_B4


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D7_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D7_ad001


title: SCGC1379_mTEChi_EedZsGneg_B23


title: SCGC1379_mTEChi_EedZsGneg_B22


title: SCGC1379_mTEChi_EedZsGneg_B16


title: CEMBA190108_6A_3_CEMBA190108_6A_4_E5_ad001


title: SCGC1379_mTEChi_EedZsGneg_B14


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D7_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D6_ad006


title: SCGC1379_mTEChi_EedZsGneg_B13


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D6_ad008


title: SCGC1379_mTEChi_EedZsGneg_B21


title: SCGC1379_mTEChi_EedZsGneg_B10


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D7_ad004


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D7_ad010


title: SCGC1379_mTEChi_EedZsGneg_B2


title: SCGC1379_mTEChi_EedZsGneg_B1


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D6_ad012


title: SCGC1379_mTEChi_EedZsGneg_B18


title: SCGC1379_mTEChi_EedZsGneg_B19


title: SCGC1379_mTEChi_EedZsGneg_A9


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D6_ad001


title: SCGC1379_mTEChi_EedZsGneg_A8


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D6_ad004


title: SCGC1379_mTEChi_EedZsGneg_B12


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D6_ad007


title: SCGC1379_mTEChi_EedZsGneg_B17


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D5_ad006


title: SCGC1379_mTEChi_EedZsGneg_A7


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D6_ad010


title: SCGC1379_mTEChi_EedZsGneg_A6


title: SCGC1379_mTEChi_EedZsGneg_B15


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D5_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D6_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D5_ad012


title: SCGC1379_mTEChi_EedZsGneg_B11


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D5_ad001


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D5_ad010


title: SCGC1379_mTEChi_EedZsGneg_A23


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D5_ad007


title: SCGC1379_mTEChi_EedZsGneg_A4


title: SCGC1379_mTEChi_EedZsGneg_A22


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D4_ad001


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D4_ad007


title: SCGC1379_mTEChi_EedZsGneg_A5


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D5_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D4_ad012


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D4_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D5_ad004


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D4_ad010


title: SCGC1379_mTEChi_EedZsGneg_A20


title: SCGC1379_mTEChi_EedZsGneg_A18


title: SCGC1379_mTEChi_EedZsGneg_A21


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D4_ad004


title: SCGC1379_mTEChi_EedZsGneg_A19


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D4_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D4_ad002


title: SCGC1379_mTEChi_EedZsGneg_A17


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D3_ad012


title: SCGC1379_mTEChi_EedZsGneg_A16


title: SCGC1379_mTEChi_EedZsGneg_A24


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D3_ad001


title: SCGC1379_mTEChi_EedZsGneg_A15


title: SCGC1379_mTEChi_EedZsGneg_A14


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D3_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D3_ad007


title: SCGC1379_mTEChi_EedZsGneg_A11


title: SCGC1379_mTEChi_EedZsGneg_A13


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D3_ad010


title: SCGC1379_mTEChi_EedZsGneg_A12


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D3_ad002


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D3_ad004


title: SCGC1373_mTEChi_WT_P9


title: SCGC1379_mTEChi_EedZsGneg_A10


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D2_ad012


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D2_ad001


title: SCGC1373_mTEChi_WT_P8


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D2_ad007


title: SCGC1373_mTEChi_WT_P6


title: SCGC1373_mTEChi_WT_P7


title: SCGC1373_mTEChi_WT_P5


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D2_ad006


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D2_ad010


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D2_ad004


title: SCGC1373_mTEChi_WT_P4


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D2_ad002


title: SCGC1373_mTEChi_WT_P3


title: SCGC1373_mTEChi_WT_P22


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D2_ad008


title: CEMBA190108_6A_3_CEMBA190108_6A_4_D12_ad012


title: SCGC1373_mTEChi_WT_P21


title: SCGC1373_mTEChi_WT_P2


title: Pnmt81-dhp1 thiamine

value: h- ade6-M210 leu1-32 ura4-D18 his3-D1 P81nmt1-dhp1::kanMX6

value: EMM + 60 µM of thiamine


title: Pnmt81-dhp1 Pnmt81-dis3 thiamine

value: h? ade6-M? leu1-32 ura4-D18 his3-D1 P81nmt1-dhp1::kanMX6 P81nmt1-dis3::natMX6


title: WT thiamine


title: SCGC1373_mTEChi_WT_P18


title: Pac1-AA rapa #2

value: h- torSE::KanMX6 fkh1::URA+ leu1-32::(nmt1-rpl13-2FKBP12-leu1+) ura4-D18 leu1-32 ade6-M210 Pac1-FRB-GFP::natMX6

value: EMM + rapamycin 2.5µg/mL 2h


title: Pnmt81-dis3 thiamine

value: h? ade6? leu1-32 ura4-D18 his3-D1 p81nmt1::kanMX6-dis3


title: SCGC1373_mTEChi_WT_P17


title: SCGC1373_mTEChi_WT_P15


title: CTL rapa #2

value: h- torSE::KanMX6 fkh1::URA+ leu1-32::(nmt1-rpl13-2FKBP12-leu1+) ura4-D18 leu1-32 ade6-M210


title: SCGC1373_mTEChi_WT_P16


title: CTL rapa #1


title: Pac1-AA rapa #1


title: SCGC1373_mTEChi_WT_P14


title: SCGC1373_mTEChi_WT_P13


title: WT 30 °C

value: h+ S. pombe:ade6M210 leu1-32 ura4-D18 his3-D1

value: EMM 30°C


title: SCGC1373_mTEChi_WT_P11


title: SCGC1373_mTEChi_WT_P12


title: WT 37 °C

value: EMM 37°C 2h


title: SCGC1373_mTEChi_WT_P10


title: SCGC1373_mTEChi_WT_P1


title: Input CTL

data_processing:
Raw reads were trimmed using trimmomatic against the appropriate adapter sequences with options SE ILLUMINACLIP:$adapters:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Trimmed reads were then mapped on S. pombe genome (version ASM294v2.26) using HISAT2 with option --no-splice-alignment.
For input-controlled peak calling of the Pac1-TAP ChIP experiments, MACS2 was used on individual replicates with options -f BAM -t IP.bam -c INPUT.bam -g 12000000 -B -q 0.01 -m 1 10 --fe-cutoff 2 --keep-dup all.
Individual narrowPeak files (MACS2 output) were converted into bed format and combined using MSPC (Multiple Sample Peak Calling)50 using parameters  -r bio -s 1E-8 -w 1E-4 -c 2 to obtain the final list of Pac1-associated loci presented in the supplementary file Pac1_associated_genes.txt
Genome_build: ASM294v2.26
Supplementary_files_format_and_content: Strand-specific genome coverage files in bigWig format.

extract_protocol:
50 mL of cultures were incubated for 20 min at room temperature with 1% formaldehyde. After quenching the reaction with glycine, cells were washed cold Tris-buffered saline (20 mM Tris–HCl pH 7.5, 150 mM NaCl) and snap-freezed. Frozen pellets were thawned and resuspended in 500 μL of lysis buffer (50 mM HEPES-KOH at pH 7.5, 140 mM NaCl, 1 mM EDTA at pH 8.0, 1% Triton X-100, 0.1% Na-deoxycholate) containing protease inhibitors, disrupted using a FastPrep instrument, and sonicated 12 times for 10 sec at 20% intensity using a Branson digital sonifier. Sonicated chromatin was incubated overnight at 4°C with 50 µL of magnetic beads only for Pac1-TAP immunoprecipitation, or with magnetic beads coupled with 2 µg of 8WG16 antibody. After the beads were washed twice with 1 mL of lysis buffer, twice with 1 mL of lysis buffer plus 500 mM NaCl, twice with 1 mL of wash buffer (10 mM Tris-HCl at pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, and 1 mM EDTA), and once with 1 mL of Tris-EDTA (TE; 10 mM Tris-HCl at pH 8.0, 1 mM EDTA), the co-immunoprecipitated chromatin was eluted by incubating the beads 15 minutes in elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1% SDS) at 65°C. After overnight incubation at 65°C for reverse-crosslinking, treatment with proteinase K and DNA extraction by phenol-chloroform, the samples were treated with RNaseA and purified on PCR purification column (Qiagen).
Libraries were prepared using the SPARK DNA Sample Prep Kit Illumina Platform (Quantabio) according to the manufacturer’s instructions and sequenced in single-end (50nt) using Illumina technologies (MiSeq or NovaSeq) at Genome Québec.

treatment_protocol: The Pac1 protein fused to the anchor-away system was relocalized in the cytoplasm by a two hours rapamycin treatment at a final concentration of 2.5 µg/ml.

tag: ip

value: input


title: SCGC1373_mTEChi_WT_P20


title: Input Pac1-TAP#1

value: h+ ade6-M216 leu1-32 ura4-D18 his3-D1 Pac1-TAP-natMX6

value: EMM


title: SCGC1373_mTEChi_WT_O9

value: single cell


title: IP 8WG16 Pac1-AA


title: SCGC1373_mTEChi_WT_O8

value: negative


title: Input Pac1-TAP#2


title: IP 8WG16 CTL


title: SCGC1373_mTEChi_WT_P19


title: SCGC1373_mTEChi_WT_O7


title: IP Pac1-TAP#2


title: SCGC1373_mTEChi_WT_O5


title: IP Pac1-TAP#1


title: SCGC1373_mTEChi_WT_O6


title: SCGC1373_mTEChi_WT_O24


title: skin_T_727_day365

city: Vienna

first: Georg

last: Stary

address: Spitalgasse 23

department: Dermatology

country: Austria

institute: Medical University of Vienna

data_processing:
Single-end reads were trimmed for low quality bases and removal of low-quality reads using ReadTools
Trimmed reads were mapped to the Homo sapiens genome (GRCh38.92 assembly) using STAR (v2.5.3a) mapper
The reads mapped in multiple genomic locations were eliminated by using Samtools (v1.4)
Read counts for features (exons) were generated using the featureCounts function from the Subread package (v 1.22.1)
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene count matrix was generated using featureCounts function from the Subread package (v 1.22.1) with Ensembl Known Gene models (version GRCh38.92) as reference annotations

organism: Homo sapiens

source_name: T cells

growth_protocol: freshly isolated cells from human tissue

extract_protocol:
cells were isolated from heparinized blood using ficoll gradient and from skin biopsies using collagenase IV + mesh filtering
Illumina
SMART-seq

value: skin

tag: time

value: Day 365 (after transplantation)


title: Input Pac1-AA


title: skin_T_723_day365


title: SCGC1373_mTEChi_WT_O23


title: skin_T_722_day365


title: SCGC1373_mTEChi_WT_O3


title: skin_T_721_day365


title: SCGC1373_mTEChi_WT_O22


title: skin_T_719_day365


title: skin_T_718_day365


title: SCGC1373_mTEChi_WT_O20


title: skin_T_713_day365


title: SCGC1373_mTEChi_WT_O2


title: SCGC1373_mTEChi_WT_O19


title: skin_T_728_day14

value: Day 14 (after transplantation)


title: skin_T_712_day365


title: skin_T_727_day14


title: SCGC1373_mTEChi_WT_O18


title: skin_T_723_day14


title: SCGC1373_mTEChi_WT_O16


title: skin_T_721_day14


title: skin_T_722_day14


title: SCGC1373_mTEChi_WT_O4


title: SCGC1373_mTEChi_WT_O17


title: SCGC1373_mTEChi_WT_O15


title: skin_T_728_day365


title: SCGC1373_mTEChi_WT_O14


title: skin_T_719_day14


title: SCGC1373_mTEChi_WT_O12


title: skin_T_718_day14


title: SCGC1373_mTEChi_WT_O21


title: SCGC1373_mTEChi_WT_O1


title: skin_T_713_day14


title: SCGC1373_mTEChi_WT_O11


title: skin_T_717_day14


title: skin_T_728_day100

value: Day 100 (after transplantation)


title: SCGC1373_mTEChi_WT_O10


title: SCGC1373_mTEChi_WT_N6


title: SCGC1373_mTEChi_WT_N9


title: skin_T_721_day100


title: skin_T_719_day100


title: skin_T_727_day100


title: SCGC1373_mTEChi_WT_N24


title: SCGC1373_mTEChi_WT_O13


title: skin_T_712_day100


title: skin_T_722_day100


title: SCGC1373_mTEChi_WT_N5


title: skin_T_723_day100


title: SCGC1373_mTEChi_WT_N4


title: skin_T_718_day100


title: skin_T_717_day100


title: skin_T_710_day100


title: SCGC1373_mTEChi_WT_N3


title: SCGC1373_mTEChi_WT_N22


title: skin_T_728_day0

value: Day 0 (day of transplantation)


title: skin_T_710_day14


title: SCGC1373_mTEChi_WT_N8


title: skin_T_723_day0


title: SCGC1373_mTEChi_WT_N19


title: SCGC1373_mTEChi_WT_N7


title: skin_T_721_day0


title: SCGC1373_mTEChi_WT_N18


title: skin_T_722_day0


title: SCGC1373_mTEChi_WT_N20


title: skin_T_718_day0


title: skin_T_713_day100


title: SCGC1373_mTEChi_WT_N17


title: SCGC1373_mTEChi_WT_N2


title: skin_T_719_day0


title: SCGC1373_mTEChi_WT_N16


title: SCGC1373_mTEChi_WT_N15


title: skin_T_717_day0


title: SCGC1373_mTEChi_WT_N14


title: SCGC1373_mTEChi_WT_N13


title: skin_T_727_day-7

value: Baseline


title: skin_T_710_day0


title: skin_T_728_day-7


title: SCGC1373_mTEChi_WT_N11


title: SCGC1373_mTEChi_WT_N10


title: SCGC1373_mTEChi_WT_N21


title: skin_T_722_day-7


title: SCGC1373_mTEChi_WT_N1


title: skin_T_723_day-7


title: skin_T_721_day-7


title: SCGC1373_mTEChi_WT_M9


title: SCGC1373_mTEChi_WT_N23


title: SCGC1373_mTEChi_WT_M8


title: skin_T_713_day-7


title: skin_T_718_day-7


title: SCGC1373_mTEChi_WT_M5


title: skin_T_712_day0


title: SCGC1373_mTEChi_WT_M7


title: skin_T_717_day-7


title: SCGC1373_mTEChi_WT_M6


title: SCGC1373_mTEChi_WT_M4


title: SCGC1373_mTEChi_WT_M3


title: blood_T_727_day365

value: blood


title: SCGC1373_mTEChi_WT_N12


title: skin_T_710_day-7


title: blood_T_723_day365


title: SCGC1373_mTEChi_WT_M24


title: SCGC1373_mTEChi_WT_M23


title: blood_T_728_day365


title: SCGC1373_mTEChi_WT_M22


title: blood_T_722_day365


title: blood_T_721_day365


title: SCGC1373_mTEChi_WT_M21


title: blood_T_718_day365


title: blood_T_717_day365


title: blood_T_719_day365


title: skin_T_719_day-7


title: SCGC1373_mTEChi_WT_M2


title: SCGC1373_mTEChi_WT_M19


title: SCGC1373_mTEChi_WT_M20


title: SCGC1373_mTEChi_WT_M18


title: blood_T_713_day365


title: blood_T_712_day365


title: SCGC1373_mTEChi_WT_M17


title: SCGC1373_mTEChi_WT_M16


title: reanalysis blood_T_727_day14


title: SCGC1373_mTEChi_WT_M14


title: SCGC1373_mTEChi_WT_M15


title: SCGC1373_mTEChi_WT_M12


title: reanalysis blood_T_721_day14


title: reanalysis blood_T_719_day14


title: SCGC1373_mTEChi_WT_M13


title: SCGC1373_mTEChi_WT_M10


title: reanalysis blood_T_713_day14


title: SCGC1373_mTEChi_WT_M1


title: SCGC1373_mTEChi_WT_L9


title: SCGC1373_mTEChi_WT_L8


title: SCGC1373_mTEChi_WT_L7


title: reanalysis blood_T_712_day14


title: SCGC1373_mTEChi_WT_L5


title: SCGC1373_mTEChi_WT_L6


title: reanalysis blood_T_727_day100


title: reanalysis blood_T_723_day100


title: reanalysis blood_T_722_day100


title: SCGC1373_mTEChi_WT_L4


title: reanalysis blood_T_728_day14


title: reanalysis blood_T_723_day14


title: reanalysis blood_T_721_day100


title: SCGC1373_mTEChi_WT_L24


title: SCGC1373_mTEChi_WT_L23


title: reanalysis blood_T_722_day14


title: reanalysis blood_T_719_day100


title: reanalysis blood_T_718_day100


title: SCGC1373_mTEChi_WT_L22


title: reanalysis blood_T_718_day14


title: reanalysis blood_T_717_day14


title: SCGC1373_mTEChi_WT_M11


title: reanalysis blood_T_717_day100


title: SCGC1373_mTEChi_WT_L20


title: SCGC1373_mTEChi_WT_L21


title: SCGC1373_mTEChi_WT_L19


title: reanalysis blood_T_713_day100


title: reanalysis blood_T_712_day100


title: SCGC1373_mTEChi_WT_L18


title: reanalysis blood_T_728_day100


title: reanalysis blood_T_728_day0


title: SCGC1373_mTEChi_WT_L16


title: reanalysis blood_T_727_day0


title: reanalysis blood_T_723_day0


title: SCGC1373_mTEChi_WT_L15


title: reanalysis blood_T_722_day0


title: SCGC1373_mTEChi_WT_L14


title: SCGC1373_mTEChi_WT_L13


title: SCGC1373_mTEChi_WT_L12


title: reanalysis blood_T_719_day0


title: SCGC1373_mTEChi_WT_L10


title: SCGC1373_mTEChi_WT_L11


title: reanalysis blood_T_718_day0


title: reanalysis blood_T_717_day0


title: SCGC1373_mTEChi_WTBulk100_L3

value: small bulk


title: SCGC1373_mTEChi_WTBulk100_L2


title: reanalysis blood_T_712_day0


title: reanalysis blood_T_713_day0


title: reanalysis blood_T_710_day100


title: reanalysis blood_T_710_day0


title: reanalysis blood_T_728_day-7


title: SCGC1373_mTEChi_WTBulk100_L1


title: reanalysis blood_T_727_day-7


title: SCGC1373_mTEChi_WT_L17


title: reanalysis blood_T_723_day-7


title: SCGC1373_mTEChi_NTC_P23

value: no template control


title: SCGC1373_mTEChi_NTC_P24


title: SCGC1373_mTEChi_EedZsGpos_K9

value: positive


title: SCGC1373_mTEChi_EedZsGpos_K8


title: reanalysis blood_T_722_day-7


title: SCGC1373_mTEChi_EedZsGpos_K7


title: reanalysis blood_T_721_day-7


title: reanalysis blood_T_719_day-7


title: reanalysis blood_T_721_day0