title: Tumor-plate10-46 [EpCam and HIF1a]


title: Tumor-plate10-44 [EpCam and HIF1a]

status: Public on Nov 09 2018

type: SRA

city: Stanford

first: Howard

last: Chang

state: CA

address: 269 Campus Drive

department: Dermatology

country: USA

institute: Stanford University

description: Freshly isolated cells from a breast tumor were fixed, permeabilized and stained against EpCam and HIF1a ,  then sorted into single wells of a 96 well plate for MI-ATAC

library_source: genomic

data_processing:
Paired-end reads were trimmed for Illumina adapter sequences and transposase sequences using an in-house script and mapped to mm9 using Bowtie2 v2.1.0 with parameters –very sensitive. Reads were subsequently filtered for alignment quality of > Q30 and were required to be properly paired. Duplicate reads were removed with Picard (http://picard.sourceforge.net) v1.79. Reads mapping to the mitochondria or chromosome Y were removed and not considered. Peak calling was performed by MACS2 with parameters --call-summits –q 0.05 –nomodel –shift 0. Peaks were filtered using the consensus excludable ENCODE blacklist ( http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and a custom blacklist designed to remove high-signal-causing repeats and mitochondrial homologues. Overlapping peaks from all samples were merged together to a consensus peak list. Then peak region was extended to 500 bp around the summit.
Genome_build: mm9
Supplementary_files_format_and_content: Peak calling was performed by MACS2 with parameters --call-summits –q 0.05 –nomodel –shift 0. Peaks were filtered using the consensus excludable ENCODE blacklist ( http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeMapability/) and a custom blacklist designed to remove high-signal-causing repeats and mitochondrial homologues. Overlapping peaks from all samples were merged together to a consensus peak list. Then peak region was extended to 500 bp around the summit.

molecule: genomic DNA

organism: Mus musculus

source_name: mouse breast cancer

extract_protocol: single cell MI-ATAC of primary mouse breast cancer cells. Single cells were first fixed, then  lysed, followed by staining for respective antibodies and transposition. The transposition reaction is the same as for standard ATAC-seq except with 0.05% Igepal CA-630 in the lysis buffer. After 30 min transposition, at 37 degrees, the reaction was quenched using 40 mM EDTA, then cells were centrifuged and supernatant was discarded. 20 µl of reverse crosslinking solution was added to the cell pellet (with final concentration of 5 ng/ml proteinase K).  Reverse crosslinking was performed 65 degree overnight and inactivated by a 10 min incubation at 80 degrees the next day. The 25 µl PCR master mix (NEB, M0541S) and 5 µl of two unique primer combinations were directly added to the reverse crosslinking mixture and PCR was performed as previous described. The PCR product was purified with Qiagen MinElute purification kit and eluted in 20 µl Qiagen EB elution buffer

tag: tissue

value: single cells were isolated from PyMT mouse breast tumor tissue

tag: antibody

value: EpCam and HIF1a


title: Tumor-plate10-58 [EpCam and HIF1a]


title: Tumor-plate10-55 [EpCam and HIF1a]


title: Tumor-plate10-47 [EpCam and HIF1a]


title: Tumor-plate10-43 [EpCam and HIF1a]


title: Tumor-plate10-40 [EpCam and HIF1a]


title: Tumor-plate10-45 [EpCam and HIF1a]


title: Tumor-plate10-42 [EpCam and HIF1a]


title: Tumor-plate10-41 [EpCam and HIF1a]


title: Tumor-plate10-4 [EpCam and HIF1a]


title: Tumor-plate10-39 [EpCam and HIF1a]


title: Tumor-plate10-37 [EpCam and HIF1a]


title: Tumor-plate10-38 [EpCam and HIF1a]


title: Tumor-plate10-36 [EpCam and HIF1a]


title: Tumor-plate10-35 [EpCam and HIF1a]


title: Tumor-plate10-5 [EpCam and HIF1a]


title: Tumor-plate10-34 [EpCam and HIF1a]


title: Tumor-plate10-30 [EpCam and HIF1a]


title: Tumor-plate10-33 [EpCam and HIF1a]


title: Tumor-plate10-31 [EpCam and HIF1a]


title: Tumor-plate10-32 [EpCam and HIF1a]


title: Tumor-plate10-3 [EpCam and HIF1a]


title: Tumor-plate10-28 [EpCam and HIF1a]


title: Tumor-plate10-29 [EpCam and HIF1a]


title: Tumor-plate10-27 [EpCam and HIF1a]


title: Tumor-plate10-24 [EpCam and HIF1a]


title: Tumor-plate10-23 [EpCam and HIF1a]


title: Tumor-plate10-22 [EpCam and HIF1a]


title: Tumor-plate10-20 [EpCam and HIF1a]


title: Tumor-plate10-2 [EpCam and HIF1a]


title: Tumor-plate10-21 [EpCam and HIF1a]


title: Tumor-plate10-26 [EpCam and HIF1a]


title: Tumor-plate10-17 [EpCam and HIF1a]


title: Tumor-plate10-15 [EpCam and HIF1a]


title: Tumor-plate10-14 [EpCam and HIF1a]


title: Tumor-plate10-18 [EpCam and HIF1a]


title: Tumor-plate10-16 [EpCam and HIF1a]


title: Tumor-plate10-13 [EpCam and HIF1a]


title: Tumor-plate10-12 [EpCam and HIF1a]


title: Tumor-plate10-1 [EpCam and HIF1a]


title: Tumor-plate1-96 [EpCam and HIF1a]


title: Tumor-plate10-10 [EpCam and HIF1a]


title: Tumor-plate10-11 [EpCam and HIF1a]


title: Tumor-plate1-95 [EpCam and HIF1a]


title: Tumor-plate1-94 [EpCam and HIF1a]


title: Tumor-plate1-93 [EpCam and HIF1a]


title: Tumor-plate10-25 [EpCam and HIF1a]


title: Tumor-plate1-92 [EpCam and HIF1a]


title: Tumor-plate10-19 [EpCam and HIF1a]


title: Tumor-plate1-83 [EpCam and HIF1a]


title: Tumor-plate1-81 [EpCam and HIF1a]


title: Tumor-plate1-91 [EpCam and HIF1a]


title: Tumor-plate1-80 [EpCam and HIF1a]


title: Tumor-plate1-8 [EpCam and HIF1a]


title: Tumor-plate1-90 [EpCam and HIF1a]


title: Tumor-plate1-9 [EpCam and HIF1a]


title: Tumor-plate1-89 [EpCam and HIF1a]


title: Tumor-plate1-88 [EpCam and HIF1a]


title: Tumor-plate1-78 [EpCam and HIF1a]


title: Tumor-plate1-84 [EpCam and HIF1a]


title: Tumor-plate1-76 [EpCam and HIF1a]


title: Tumor-plate1-85 [EpCam and HIF1a]


title: Tumor-plate1-87 [EpCam and HIF1a]


title: Tumor-plate1-74 [EpCam and HIF1a]


title: Tumor-plate1-79 [EpCam and HIF1a]


title: Tumor-plate1-82 [EpCam and HIF1a]


title: Tumor-plate1-77 [EpCam and HIF1a]


title: Tumor-plate1-75 [EpCam and HIF1a]


title: Tumor-plate1-73 [EpCam and HIF1a]


title: Tumor-plate1-72 [EpCam and HIF1a]


title: Tumor-plate1-71 [EpCam and HIF1a]


title: Tumor-plate1-86 [EpCam and HIF1a]


title: Tumor-plate1-68 [EpCam and HIF1a]


title: Tumor-plate1-7 [EpCam and HIF1a]


title: Tumor-plate1-64 [EpCam and HIF1a]


title: Tumor-plate1-66 [EpCam and HIF1a]


title: Tumor-plate1-69 [EpCam and HIF1a]


title: Tumor-plate1-67 [EpCam and HIF1a]


title: Tumor-plate1-6 [EpCam and HIF1a]


title: Tumor-plate1-63 [EpCam and HIF1a]


title: Tumor-plate1-70 [EpCam and HIF1a]


title: Tumor-plate1-61 [EpCam and HIF1a]


title: Tumor-plate1-54 [EpCam and HIF1a]


title: Tumor-plate1-55 [EpCam and HIF1a]


title: Tumor-plate1-60 [EpCam and HIF1a]


title: Tumor-plate1-56 [EpCam and HIF1a]


title: Tumor-plate1-65 [EpCam and HIF1a]


title: Tumor-plate1-49 [EpCam and HIF1a]


title: Tumor-plate1-53 [EpCam and HIF1a]


title: Tumor-plate1-51 [EpCam and HIF1a]


title: Tumor-plate1-50 [EpCam and HIF1a]


title: Tumor-plate1-5 [EpCam and HIF1a]


title: Tumor-plate1-46 [EpCam and HIF1a]


title: Tumor-plate1-48 [EpCam and HIF1a]


title: Tumor-plate1-58 [EpCam and HIF1a]


title: Tumor-plate1-44 [EpCam and HIF1a]


title: Tumor-plate1-47 [EpCam and HIF1a]


title: Tumor-plate1-45 [EpCam and HIF1a]


title: Tumor-plate1-43 [EpCam and HIF1a]


title: Tumor-plate1-42 [EpCam and HIF1a]


title: Tumor-plate1-57 [EpCam and HIF1a]


title: Tumor-plate1-62 [EpCam and HIF1a]


title: Tumor-plate1-41 [EpCam and HIF1a]


title: Tumor-plate1-59 [EpCam and HIF1a]


title: Tumor-plate1-40 [EpCam and HIF1a]


title: Tumor-plate1-38 [EpCam and HIF1a]


title: Tumor-plate1-4 [EpCam and HIF1a]


title: Tumor-plate1-52 [EpCam and HIF1a]


title: Tumor-plate1-39 [EpCam and HIF1a]


title: Tumor-plate1-35 [EpCam and HIF1a]


title: Tumor-plate1-34 [EpCam and HIF1a]


title: Tumor-plate1-31 [EpCam and HIF1a]


title: Tumor-plate1-36 [EpCam and HIF1a]


title: Tumor-plate1-33 [EpCam and HIF1a]


title: Tumor-plate1-37 [EpCam and HIF1a]


title: Tumor-plate1-26 [EpCam and HIF1a]


title: Tumor-plate1-27 [EpCam and HIF1a]


title: Tumor-plate1-32 [EpCam and HIF1a]


title: Tumor-plate1-25 [EpCam and HIF1a]


title: Tumor-plate1-30 [EpCam and HIF1a]


title: Tumor-plate1-23 [EpCam and HIF1a]


title: Tumor-plate1-3 [EpCam and HIF1a]


title: Tumor-plate1-28 [EpCam and HIF1a]


title: Tumor-plate1-24 [EpCam and HIF1a]


title: Tumor-plate1-19 [EpCam and HIF1a]


title: Tumor-plate1-18 [EpCam and HIF1a]


title: Tumor-plate1-20 [EpCam and HIF1a]


title: Tumor-plate1-17 [EpCam and HIF1a]


title: Tumor-plate1-22 [EpCam and HIF1a]


title: Tumor-plate1-16 [EpCam and HIF1a]


title: Tumor-plate1-15 [EpCam and HIF1a]


title: Tumor-plate1-12 [EpCam and HIF1a]


title: Tumor-plate1-13 [EpCam and HIF1a]


title: Tumor-plate1-10 [EpCam and HIF1a]


title: Tumor-plate1-14 [EpCam and HIF1a]


title: Tumor-plate1-11 [EpCam and HIF1a]


title: Tumor-plate1-1 [EpCam and HIF1a]


title: Tumor-plate4-96

description: Freshly isolated cells from a breast tumor were fixed, permeabilized and stained against EpCam and CD45,  then sorted into single wells of a 96 well plate for MI-ATAC

value: EpCam and CD45


title: Tumor-plate1-29 [EpCam and HIF1a]


title: Tumor-plate4-94


title: Tumor-plate4-95


title: Tumor-plate4-92


title: Tumor-plate4-89


title: Tumor-plate1-21 [EpCam and HIF1a]


title: Tumor-plate4-88


title: Tumor-plate4-9


title: Tumor-plate4-87


title: Tumor-plate1-2 [EpCam and HIF1a]


title: Tumor-plate4-86


title: Tumor-plate4-84


title: Tumor-plate4-91


title: Tumor-plate4-83


title: Tumor-plate4-82


title: Tumor-plate4-81


title: Tumor-plate4-79


title: Tumor-plate4-80


title: Tumor-plate4-8


title: Tumor-plate4-78


title: Tumor-plate4-75


title: Tumor-plate4-76


title: Tumor-plate4-74


title: Tumor-plate4-77


title: Tumor-plate4-93


title: Tumor-plate4-7


title: Tumor-plate4-73


title: Tumor-plate4-90


title: Tumor-plate4-72


title: Tumor-plate4-70


title: Tumor-plate4-71


title: Tumor-plate4-85


title: Tumor-plate4-66


title: Tumor-plate4-65


title: Tumor-plate4-64


title: Tumor-plate4-67


title: Tumor-plate4-63


title: Tumor-plate4-62


title: Tumor-plate4-69


title: Tumor-plate4-61


title: Tumor-plate4-57


title: Tumor-plate4-56


title: Tumor-plate4-59


title: Tumor-plate4-55


title: Tumor-plate4-54


title: Tumor-plate4-51


title: Tumor-plate4-52


title: Tumor-plate4-49


title: Tumor-plate4-50


title: Tumor-plate4-53


title: Tumor-plate4-5


title: Tumor-plate4-47


title: Tumor-plate4-68


title: Tumor-plate4-48


title: Tumor-plate4-45


title: Tumor-plate4-44


title: Tumor-plate4-42


title: Tumor-plate4-46


title: Tumor-plate4-40


title: Tumor-plate4-41


title: Tumor-plate4-6


title: Tumor-plate4-38


title: Tumor-plate4-36


title: Tumor-plate4-60


title: Tumor-plate4-37


title: Tumor-plate4-58


title: Tumor-plate4-34


title: Tumor-plate4-39


title: Tumor-plate4-31


title: Tumor-plate4-32


title: Tumor-plate4-30


title: Tumor-plate4-29


title: Tumor-plate4-28


title: Tumor-plate4-3


title: Tumor-plate4-26


title: Tumor-plate4-27


title: Tumor-plate4-21


title: Tumor-plate4-24


title: Tumor-plate4-22


title: Tumor-plate4-43


title: Tumor-plate4-23


title: Tumor-plate4-4


title: Tumor-plate4-20


title: Tumor-plate4-2


title: Tumor-plate4-16


title: Tumor-plate4-15


title: Tumor-plate4-12


title: Tumor-plate4-19


title: Tumor-plate4-13


title: Tumor-plate4-35


title: Tumor-plate4-11


title: Tumor-plate4-18


title: Tumor-plate4-33


title: Tumor-plate4-17


title: Tumor-plate4-1


title: Tumor-plate3-96


title: Tumor-plate3-94


title: Tumor-plate4-10


title: Tumor-plate3-95


title: Tumor-plate4-25


title: Tumor-plate3-92


title: Tumor-plate3-93


title: Tumor-plate3-9


title: Tumor-plate3-90


title: Tumor-plate3-88


title: Tumor-plate3-87


title: Tumor-plate3-84


title: Tumor-plate3-83


title: Tumor-plate3-81


title: Tumor-plate3-82


title: Tumor-plate4-14


title: Tumor-plate3-8


title: Tumor-plate3-77


title: Tumor-plate3-78


title: Tumor-plate3-76


title: Tumor-plate3-85


title: Tumor-plate3-86


title: Tumor-plate3-74


title: Tumor-plate3-75


title: Tumor-plate3-73


title: Tumor-plate3-72


title: Tumor-plate3-71


title: Tumor-plate3-70


title: Tumor-plate3-79


title: Tumor-plate3-69


title: Tumor-plate3-91


title: Tumor-plate3-68


title: Tumor-plate3-67


title: Tumor-plate3-89


title: Tumor-plate3-66


title: Tumor-plate3-64


title: Tumor-plate3-62


title: Tumor-plate3-61


title: Tumor-plate3-63


title: Tumor-plate3-80


title: Tumor-plate3-6


title: Tumor-plate3-58


title: Tumor-plate3-59


title: Tumor-plate3-60


title: Tumor-plate3-56


title: Tumor-plate3-55


title: Tumor-plate3-54


title: Tumor-plate3-52


title: Tumor-plate3-7


title: Tumor-plate3-5


title: Tumor-plate3-51


title: Tumor-plate3-57


title: Tumor-plate3-48


title: Tumor-plate3-53


title: Tumor-plate3-47


title: Tumor-plate3-46


title: Tumor-plate3-44


title: Tumor-plate3-43


title: Tumor-plate3-65


title: Tumor-plate3-50


title: Tumor-plate3-45


title: Tumor-plate3-41


title: Tumor-plate3-42


title: Tumor-plate3-40


title: Tumor-plate3-4


title: Tumor-plate3-39


title: Tumor-plate3-37


title: Tumor-plate3-38


title: Tumor-plate3-36


title: Tumor-plate3-35


title: Tumor-plate3-34


title: Tumor-plate3-32


title: Tumor-plate3-49


title: Tumor-plate3-31


title: Tumor-plate3-3


title: Tumor-plate3-33


title: Tumor-plate3-30


title: Tumor-plate3-2


title: Tumor-plate3-27


title: Tumor-plate3-20


title: Tumor-plate3-25


title: Tumor-plate3-16


title: Tumor-plate3-14


title: Tumor-plate3-19


title: Tumor-plate3-28


title: Tumor-plate3-29


title: Tumor-plate3-21


title: Tumor-plate3-23


title: Tumor-plate3-15


title: Tumor-plate3-18


title: Tumor-plate3-22


title: Tumor-plate3-13


title: Tumor-plate3-12


title: Tumor-plate3-24


title: Tumor-plate3-26


title: Tumor-plate3-10


title: Tumor-plate3-1


title: Tumor-plate2-96


title: Tumor-plate3-11


title: Tumor-plate2-95


title: Tumor-plate2-92


title: Tumor-plate2-93


title: Tumor-plate2-91


title: Tumor-plate2-90


title: Tumor-plate2-94


title: Tumor-plate2-9


title: Tumor-plate3-17


title: Tumor-plate2-86


title: Tumor-plate2-85


title: Tumor-plate2-82


title: Tumor-plate2-81


title: Tumor-plate2-76


title: Tumor-plate2-88


title: Tumor-plate2-80


title: Tumor-plate2-89


title: Tumor-plate2-77


title: Tumor-plate2-74


title: Tumor-plate2-73


title: Tumor-plate2-78


title: Tumor-plate2-87


title: Tumor-plate2-83


title: Tumor-plate2-7


title: Tumor-plate2-8


title: Tumor-plate2-75


title: Tumor-plate2-71


title: Tumor-plate2-79


title: Tumor-plate2-70


title: Tumor-plate2-69


title: Tumor-plate2-68


title: Tumor-plate2-72


title: Tumor-plate2-65


title: Tumor-plate2-66


title: Tumor-plate2-64


title: Tumor-plate2-63


title: Tumor-plate2-67


title: Tumor-plate2-62


title: Tumor-plate2-84


title: Tumor-plate2-61


title: Tumor-plate2-60


title: Tumor-plate2-59


title: Tumor-plate2-58


title: Tumor-plate2-56


title: Tumor-plate2-6


title: Tumor-plate2-55


title: Tumor-plate2-52


title: Tumor-plate2-53


title: Tumor-plate2-57


title: Tumor-plate2-5


title: Tumor-plate2-48


title: Tumor-plate2-49


title: Tumor-plate2-44


title: Tumor-plate2-50


title: Tumor-plate2-41


title: Tumor-plate2-46


title: Tumor-plate2-45


title: Tumor-plate2-4


title: Tumor-plate2-39


title: Tumor-plate2-38


title: Tumor-plate2-37


title: Tumor-plate2-40


title: Tumor-plate2-43


title: Tumor-plate2-42


title: Tumor-plate2-36


title: Tumor-plate2-35


title: Tumor-plate2-51


title: Tumor-plate2-54


title: Tumor-plate2-47


title: Tumor-plate2-34


title: Tumor-plate2-33


title: Tumor-plate2-30


title: Tumor-plate2-32


title: Tumor-plate2-29


title: Tumor-plate2-28


title: Tumor-plate2-26


title: Tumor-plate2-3


title: Tumor-plate2-25


title: Tumor-plate2-22


title: Tumor-plate2-24


title: Tumor-plate2-21


title: Tumor-plate2-20


title: Tumor-plate2-2


title: Tumor-plate2-19


title: Tumor-plate2-17


title: Tumor-plate2-16


title: Tumor-plate2-15


title: Tumor-plate2-18


title: Tumor-plate2-14


title: Tumor-plate2-11


title: Tumor-plate2-10


title: Tumor-plate2-31


title: Tumor-plate2-12


title: Tumor-plate2-1


title: Tumor-plate2-13


title: Tumor-plate2-27


title: Tumor-plate1-94


title: Tumor-plate1-93


title: Tumor-plate1-95


title: Tumor-plate1-91


title: Tumor-plate1-96


title: Tumor-plate1-92


title: Tumor-plate2-23


title: Tumor-plate1-90


title: Tumor-plate1-9


title: Tumor-plate1-89


title: Tumor-plate1-85


title: Tumor-plate1-86


title: Tumor-plate1-87


title: Tumor-plate1-88


title: Tumor-plate1-84


title: Tumor-plate1-82


title: Tumor-plate1-79


title: Tumor-plate1-78


title: Tumor-plate1-81


title: Tumor-plate1-83


title: Tumor-plate1-8


title: Tumor-plate1-77


title: Tumor-plate1-76


title: Tumor-plate1-70


title: Tumor-plate1-73


title: Tumor-plate1-71


title: Tumor-plate1-75


title: Tumor-plate1-74


title: Tumor-plate1-72


title: Tumor-plate1-68


title: Tumor-plate1-67


title: Tumor-plate1-65


title: Tumor-plate1-66


title: Tumor-plate1-69


title: Tumor-plate1-63


title: Tumor-plate1-80


title: Tumor-plate1-62


title: Tumor-plate1-64


title: Tumor-plate1-6


title: Tumor-plate1-60


title: Tumor-plate1-58


title: Tumor-plate1-57


title: Tumor-plate1-59


title: Tumor-plate1-56


title: Tumor-plate1-54


title: Tumor-plate1-55


title: Tumor-plate1-52


title: Tumor-plate1-51


title: Tumor-plate1-5


title: Tumor-plate1-7


title: Tumor-plate1-49


title: Tumor-plate1-48


title: Tumor-plate1-47


title: Tumor-plate1-45


title: Tumor-plate1-44


title: Tumor-plate1-46


title: Tumor-plate1-42


title: Tumor-plate1-61


title: Tumor-plate1-43


title: Tumor-plate1-39


title: Tumor-plate1-40


title: Tumor-plate1-38


title: Tumor-plate1-4


title: Tumor-plate1-37


title: Tumor-plate1-34


title: Tumor-plate1-33


title: Tumor-plate1-53


title: Tumor-plate1-50


title: Tumor-plate1-32


title: Tumor-plate1-30


title: Tumor-plate1-36


title: Tumor-plate1-29


title: Tumor-plate1-28


title: Tumor-plate1-26


title: Tumor-plate1-25


title: Tumor-plate1-24


title: Tumor-plate1-23


title: Tumor-plate1-22


title: Tumor-plate1-41


title: Tumor-plate1-2


title: Tumor-plate1-21


title: Tumor-plate1-20


title: Tumor-plate1-19


title: Tumor-plate1-35


title: Tumor-plate1-16


title: Tumor-plate1-18


title: Tumor-plate1-17


title: Tumor-plate1-12


title: Tumor-plate1-14


title: Tumor-plate1-13


title: Tumor-plate1-15


title: Splenocytes-CD45-96

description: freshly isolated splenocytes were fixed, permeabilized and stained against CD45,  then sorted into single wells of a 96 well plate for MI-ATAC

data_processing:
Paired-end reads were trimmed for Illumina adapter sequences and transposase sequences using an in-house script and mapped to mm9 using Bowtie2 v2.1.0 with parameters –very sensitive. Reads were subsequently filtered for alignment quality of > Q30 and were required to be properly paired. Duplicate reads were removed with Picard (http://picard.sourceforge.net) v1.79. Reads mapping to the mitochondria or chromosome Y were removed and not considered. Peak calling was performed by MACS2 with parameters --call-summits –q 0.05 –nomodel –shift 0. Peaks were filtered using the consensus excludable ENCODE blacklist ( http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeMapability/) and a custom blacklist designed to remove high-signal-causing repeats and mitochondrial homologues. Overlapping peaks from all samples were merged together to a consensus peak list. Then peak region was extended to 500 bp around the summit.
Genome_build: mm9
Supplementary_files_format_and_content: Peak calling was performed by MACS2 with parameters --call-summits –q 0.05 –nomodel –shift 0. Peaks were filtered using the consensus excludable ENCODE blacklist ( http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeMapability/) and a custom blacklist designed to remove high-signal-causing repeats and mitochondrial homologues. Overlapping peaks from all samples were merged together to a consensus peak list. Then peak region was extended to 500 bp around the summit.

source_name: mouse fresh isolated splenocytes

extract_protocol: single cell MI-ATAC of 4T1 and splenocytes. Single cells were first fixed, then  lysed, followed by staining for respective antibodies and transposition. The transposition reaction is the same as for standard ATAC-seq except with 0.05% Igepal CA-630 in the lysis buffer. After 30 min transposition, at 37 degrees, the reaction was quenched using 40 mM EDTA, then cells were centrifuged and supernatant was discarded. 20 µl of reverse crosslinking solution was added to the cell pellet (with final concentration of 5 ng/ml proteinase K).  Reverse crosslinking was performed 65 degree overnight and inactivated by a 10 min incubation at 80 degrees the next day. The 25 µl PCR master mix (NEB, M0541S) and 5 µl of two unique primer combinations were directly added to the reverse crosslinking mixture and PCR was performed as previous described. The PCR product was purified with Qiagen MinElute purification kit and eluted in 20 µl Qiagen EB elution buffer

tag: cell line

value: mouse splenocytes

tag: cell type


title: Tumor-plate1-1


title: Tumor-plate1-10


title: Tumor-plate1-27


title: Splenocytes-CD45-95


title: Tumor-plate1-3


title: Splenocytes-CD45-93


title: Splenocytes-CD45-94


title: Splenocytes-CD45-92


title: Splenocytes-CD45-9


title: Splenocytes-CD45-90


title: Splenocytes-CD45-89


title: Tumor-plate1-31


title: Splenocytes-CD45-87


title: Splenocytes-CD45-86


title: Splenocytes-CD45-83


title: Splenocytes-CD45-85


title: Splenocytes-CD45-84


title: Splenocytes-CD45-81


title: Tumor-plate1-11


title: Splenocytes-CD45-76


title: Splenocytes-CD45-79


title: Splenocytes-CD45-8


title: Splenocytes-CD45-75


title: Splenocytes-CD45-72


title: Splenocytes-CD45-7


title: Splenocytes-CD45-73


title: Splenocytes-CD45-74


title: Splenocytes-CD45-70


title: Splenocytes-CD45-69


title: Splenocytes-CD45-77


title: Splenocytes-CD45-91


title: Splenocytes-CD45-88


title: Splenocytes-CD45-65


title: Splenocytes-CD45-67


title: Splenocytes-CD45-68


title: Splenocytes-CD45-64


title: Splenocytes-CD45-71


title: Splenocytes-CD45-63


title: Splenocytes-CD45-66


title: Splenocytes-CD45-82


title: Splenocytes-CD45-61


title: Splenocytes-CD45-6


title: Splenocytes-CD45-59


title: Splenocytes-CD45-60


title: Splenocytes-CD45-78


title: Splenocytes-CD45-58


title: Splenocytes-CD45-80


title: Splenocytes-CD45-57


title: Splenocytes-CD45-54


title: Splenocytes-CD45-55


title: Splenocytes-CD45-53


title: Splenocytes-CD45-52


title: Splenocytes-CD45-51


title: Splenocytes-CD45-50


title: Splenocytes-CD45-47


title: Splenocytes-CD45-5


title: Splenocytes-CD45-46


title: Splenocytes-CD45-45


title: Splenocytes-CD45-62


title: Splenocytes-CD45-48


title: Splenocytes-CD45-44


title: Splenocytes-CD45-43


title: Splenocytes-CD45-40


title: Splenocytes-CD45-4


title: Splenocytes-CD45-38


title: Splenocytes-CD45-39


title: Splenocytes-CD45-41


title: Splenocytes-CD45-36


title: Splenocytes-CD45-33


title: Splenocytes-CD45-35


title: Splenocytes-CD45-31


title: Splenocytes-CD45-32


title: Splenocytes-CD45-34


title: Splenocytes-CD45-56


title: Splenocytes-CD45-37


title: Splenocytes-CD45-28


title: Splenocytes-CD45-3


title: Splenocytes-CD45-29


title: Splenocytes-CD45-49


title: Splenocytes-CD45-30


title: Splenocytes-CD45-26


title: Splenocytes-CD45-25


title: Splenocytes-CD45-42


title: Splenocytes-CD45-23


title: Splenocytes-CD45-22


title: Splenocytes-CD45-21


title: Splenocytes-CD45-24


title: Splenocytes-CD45-19


title: Splenocytes-CD45-20


title: Splenocytes-CD45-2


title: Splenocytes-CD45-16


title: Splenocytes-CD45-14


title: Splenocytes-CD45-15


title: Splenocytes-CD45-12


title: Splenocytes-CD45-1


title: Splenocytes-CD45-10


title: Splenocytes-CD45-13


title: 4T1-EpCam-95

description: 4T1 cells were fixed, permeabilized and stained against EpCam,  then sorted into single wells of a 96 well plate for MI-ATAC

source_name: 4T1 mouse breast cancer cell line

value: 4T1 mouse breast cancer cell

value: EpCam


title: Splenocytes-CD45-27


title: Splenocytes-CD45-11


title: 4T1-EpCam-94


title: 4T1-EpCam-96


title: 4T1-EpCam-9


title: 4T1-EpCam-90


title: 4T1-EpCam-91


title: 4T1-EpCam-93


title: 4T1-EpCam-92


title: 4T1-EpCam-86


title: 4T1-EpCam-88


title: 4T1-EpCam-89


title: 4T1-EpCam-87


title: 4T1-EpCam-85


title: 4T1-EpCam-84


title: 4T1-EpCam-83


title: Splenocytes-CD45-18


title: Splenocytes-CD45-17


title: 4T1-EpCam-8


title: 4T1-EpCam-82


title: 4T1-EpCam-78


title: 4T1-EpCam-80


title: 4T1-EpCam-74


title: 4T1-EpCam-73


title: 4T1-EpCam-72


title: 4T1-EpCam-71


title: 4T1-EpCam-76


title: 4T1-EpCam-7


title: 4T1-EpCam-77


title: 4T1-EpCam-70


title: 4T1-EpCam-67


title: 4T1-EpCam-68


title: 4T1-EpCam-69


title: 4T1-EpCam-75


title: 4T1-EpCam-63


title: 4T1-EpCam-66


title: 4T1-EpCam-65


title: 4T1-EpCam-64


title: 4T1-EpCam-62


title: 4T1-EpCam-61


title: 4T1-EpCam-81


title: 4T1-EpCam-58


title: 4T1-EpCam-6


title: 4T1-EpCam-55


title: 4T1-EpCam-57


title: 4T1-EpCam-60


title: 4T1-EpCam-79


title: 4T1-EpCam-56


title: 4T1-EpCam-53


title: 4T1-EpCam-54


title: 4T1-EpCam-59


title: 4T1-EpCam-52


title: 4T1-EpCam-50


title: 4T1-EpCam-51


title: 4T1-EpCam-5


title: 4T1-EpCam-49


title: 4T1-EpCam-47


title: 4T1-EpCam-45


title: 4T1-EpCam-46


title: 4T1-EpCam-44


title: 4T1-EpCam-43


title: 4T1-EpCam-40


title: 4T1-EpCam-42


title: 4T1-EpCam-41


title: 4T1-EpCam-39


title: 4T1-EpCam-38


title: 4T1-EpCam-37


title: 4T1-EpCam-36


title: 4T1-EpCam-4


title: 4T1-EpCam-35


title: 4T1-EpCam-34


title: 4T1-EpCam-33


title: 4T1-EpCam-31


title: 4T1-EpCam-30


title: 4T1-EpCam-3


title: 4T1-EpCam-32


title: 4T1-EpCam-29


title: 4T1-EpCam-27


title: 4T1-EpCam-28


title: 4T1-EpCam-26


title: 4T1-EpCam-48


title: 4T1-EpCam-25


title: 4T1-EpCam-24


title: 4T1-EpCam-23


title: 4T1-EpCam-21


title: 4T1-EpCam-19


title: 4T1-EpCam-20


title: 4T1-EpCam-14


title: 4T1-EpCam-16


title: 4T1-EpCam-15


title: 4T1-EpCam-17


title: 4T1-EpCam-11


title: 4T1-EpCam-13


title: 4T1-EpCam-10


title: bulk_MI-ATAC-seq_72h_rep2

description:
No antibody used
72h_4T1.sorted.q0.05_peaks.narrowPeak

data_processing:
Paired-end reads were trimmed for Illumina adapter sequences and transposase sequences using an in-house script and mapped to mm9 using Bowtie2 v2.1.0 with parameters –very sensitive. Reads were subsequently filtered for alignment quality of > Q30 and were required to be properly paired. Duplicate reads were removed with Picard (http://picard.sourceforge.net) v1.79. Reads mapping to the mitochondria or chromosome Y were removed and not considered. Peak calling was performed by MACS2 narrow peak mode with parameters –q 0.01 –nomodel –shift 0. Peaks were filtered using the consensus excludable ENCODE blacklist ( http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeMapability/) and a custom blacklist designed to remove high-signal-causing repeats and mitochondrial homologues. Overlapping peaks from all samples were merged together to a consensus peak list, and normalized using DESeq. The number of unique and properly paired reads mapped to each peak for each individual samples was quantified to calculate the Pearson Correlation
Genome_build: mm9
Supplementary_files_format_and_content: narrow.peak files were generated by MACS2 narrow peak mode with parameters –q 0.01 –nomodel –shift 0. Replicates were merged. Then peaks were filtered using the consensus excludable ENCODE blacklist.

source_name: hypoxic culture (1%O2) for indicated time

extract_protocol: bulk MI-ATAC of 4T1 cells, cells were first fixed in hypoxia, then counted and lysed, followed by transposition. The transposition reaction is the same as for standard ATAC-seq except with 0.05% Igepal CA-630 in the lysis buffer. After 30 min transposition, at 37 degrees, the reaction was quenched using 40 mM EDTA, then cells were centrifuged and supernatant was discarded. 20 µl of reverse crosslinking solution was added to the cell pellet (with final concentration of 5 ng/ml proteinase K).  Reverse crosslinking was performed 65 degree overnight and inactivated by a 10 min incubation at 80 degrees the next day. The 25 µl PCR master mix (NEB, M0541S) and 5 µl of two unique primer combinations were directly added to the reverse crosslinking mixture and PCR was performed as previous described12. The PCR product was purified with Qiagen MinElute purification kit and eluted in 20 µl Qiagen EB elution buffer

treatment_protocol: 4T1 cell line were cultured in a Ruskinn Invivo2 workstation maintained at 1% O2 and 5% CO2, and cells were collected with trypsin digestion in the Ruskinn Invivo2 workstation and fixed immediately after 6hs, 12hs, 24hs, 36hs, 48hs and 72hs incubation

value: breast cancer cells

tag: timepoint


title: 4T1-EpCam-2


title: bulk_MI-ATAC-seq_72h_rep1


title: 4T1-EpCam-1


title: bulk_MI-ATAC-seq_48h_rep1

description:
No antibody used
48h_4T1.sorted.q0.05_peaks.narrowPeak


title: 4T1-EpCam-22


title: bulk_MI-ATAC-seq_48h_rep2


title: bulk_MI-ATAC-seq_12h_rep2

description:
No antibody used
12h_4T1.sorted.q0.05_peaks.narrowPeak


title: bulk_MI-ATAC-seq_24h_rep1

description:
No antibody used
24h_4T1.sorted.q0.05_peaks.narrowPeak


title: bulk_MI-ATAC-seq_6h_rep1

description:
No antibody used
6h_4T1.sorted.q0.05_peaks.narrowPeak


title: bulk_MI-ATAC-seq_36h_rep1

description:
No antibody used
36h_4T1.sorted.q0.05_peaks.narrowPeak


title: bulk_MI-ATAC-seq_36h_rep2


title: bulk_MI-ATAC-seq_12h_rep1


title: 4T1-EpCam-18


title: bulk_MI-ATAC-seq_Ctrl_rep2

description:
No antibody used
Ctrl_4T1.sorted.q0.05_peaks.narrowPeak

source_name: normoxic culture


title: 4T1-EpCam-12


title: bulk_MI-ATAC-seq_24h_rep2


title: bulk_MI-ATAC-seq_6h_rep2


title: 2018_Inf_SF_04

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

description: processed data file: FibrInflRlog.txt

library_source: transcriptomic

data_processing:
Illumina RTA 1.18.66.3 used for basecalling
Illumina bcl2fastq v2.17.1.14 used for demultiplexing
bwa mem 0.7.14-r1136 used for filter mapping
fqtrim 0.9.5 used for quality triming
STAR 2.5.2b used for mapping
subread v1.5.1 featureCounts to get raw read counts
Genome_build: Ensembl GRCh37.85
Supplementary_files_format_and_content: tab-delimited text file containing rlog normalized reads from DESeq2

molecule: total RNA

organism: Homo sapiens

source_name: Synovial fibroblasts

extract_protocol:
Human dermal fibroblasts were isolated from systemic sclerosis patients (fibrotic fibroblasts) and age- and sex-matched healthy volunteers (resting fibroblasts). After enzymatic digestion of the skin biopsies with collagenase type II (Merck, Darmstadt, 676 Germany) for 3h at 37°C, the digested tissues were filtered and centrifuged at 1400 rpm for 5 min. The pellet was resuspended in DMEM/F-12 medium containing 10% heat inactivated fetal bovine serum (FBS), 25 mM HEPES, 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine, 2.5 μg/ml amphotericin B (Thermo Fisher Scientific, Dreieich, Germany) and 0.2 mM ascorbic acid (Sigma-Aldrich, Steinheim, Germany). Synovial fibroblasts (inflammatory fibroblasts) were isolated from inflamed joints of patients with rheumatoid arthritis. Fibroblasts were cultured for 3 passages and then quality checked for a pure fibroblast population before using them in experiments. Fibroblasts were negative for CD31, CD45, CD326 (EpCAM) and KRT14 and positive for collagen-1, PDGFRα and vimentin.
RNA libraries were prepared for sequencing using Illumina stranded mRNA protocols

value: Synovial fibroblasts

tag: phenotype

value: Inflammatory


title: 2018_Inf_SF_03

description: processed data file: FibrInflRlog.txt


title: bulk_MI-ATAC-seq_Ctrl_rep1


title: 2018_Inf_SF_01

description: processed data file: FibrInflRlog.txt


title: 2016_DB_DF_08

description: processed data file: FibrInflRlog.txt

source_name: Dermal fibroblasts

tag: subject status

value: systemic sclerosis patient

value: Dermal fibroblasts

value: Fibrotic

tag: treatment

value: PU.1 inhibitor DB1976


title: 2018_Inf_SF_02

description: processed data file: FibrInflRlog.txt


title: C40280_atac_seq

city: Chicago

first: Irene

last: Gallego Romero

state: IL

address: 920 E 58th St, CLSC 317

department: Human Genetics

institute: University of Chicago

description: Tn5-transposase treated nuclear DNA

data_processing:
We mapped all reads independently to either the human (hg19) or chimpanzee (panTro 2.1.3) genomes using BWA 0.7.9a-r786, allowing a maximum of two mismatches per read and a maximum fragment size of 5000 base pairs for paired-end mates.
Reads with mapping quality < 30, unmapped reads, multi-mapping reads and reads that mapped outside the autosomes and X chromosome were discarded. We also discarded all reads that mapped to mitochondrial DNA for the main analyses reported in the text. Next, we identified and removed reads produced by PCR duplicates with Picard Tools (version 1.129; http://broadinstitute.github.io/picard/).
Additionally, to control for differences in genome assembly quality, and to ensure fair comparisons between the two species, we retained only those reads that fell within a defined set of windows with high orthology between human and chimpanzee. The list of windows was generated by first retrieving the hg19toPanTro3 liftOver chain file from the UCSC Genome Browser, and using the regions that are part of the chain to generate non-overlapping 100 bp windows, for a total of 27.2 million 100bp windows. We then used liftOver to test whether each of these windows could be lifted over to a single site in the chimpanzee genome, and from there back to its original location in the human genome, allowing for a maximum 20% change in size during each lift over process. Windows that failed either of these steps were discarded. In parallel, we calculated the uniqueness of every 50-mer in the chimpanzee and human genomes using the GEM suite. Windows where greater than 20% of the 50-mers in either species were not uniquely mappable in their respective genomes, were removed from further analysis. In total, we retained ~17.6 million 100-bp high-quality windows for downstream analyses.
To examine patterns of activity near transcription start sites, we began by defining a set of highly orthologous meta-exons between human and chimpanzee, using Ensemblv75 (February 2014; code and documentation for meta-exon identification is available at [http://www.bitbucket.org/ee_reh_neh/orthoexon]). This data set contains at least 1 orthologous meta-exon associated with 40,075 human genes. We then defined the 5'-most position of the first meta-exon of each gene (adjusted for strand direction) as its orthologous transcription start site (orthologous TSS), and computed the number of high-quality orthologous 100bp windows (defined above) that fell within a 2kb window centred on the orthologous TSS. We retained only those regions with > 50% overlap, which yielded a set of 28,238 orthologous TSSs. As an additional filtering step, we discarded 7,493 orthologous TSSs that did not span the annotated human TSS for the relevant gene according to Ensembl 75 GENCODE Basic [74] annotations (when multiple GENCODE Basic transcripts were associated with a single gene, we used the average location of all TSS). In total, we retained 20,745 orthologous TSSs.
In parallel, we defined a set of randomly selected 2kb orthologous background regions matched to the orthologous TSSs for broad mappability, additionally requiring that they be at least 5kb away from any annotated orthologous TSS.
Genome_build: hg19/panTro3
Supplementary_files_format_and_content: ortho bg all_bg_regions.txt: log2 CPM at 20,745 orthologous background sites
Supplementary_files_format_and_content: all_oTSS_regions.txt: log2 CPM at 20,745 orthologous transcription start sites
Supplementary_files_format_and_content: overall_summary_stats.txt: PWM-level metrics for 306 PWMs associated with TFs expressed in iPSCs from at least one species
Supplementary_files_format_and_content: all_motifs_over_12.out: individual site-level binding predictions for all PWM sites with a PWM score >= 12 in at least one species

organism: Pan troglodytes

source_name: induced pluripotent stem cell line

growth_protocol: All lines were cultured under feeder free conditions on hESC-grade Matrigel and Essential 8 media

extract_protocol:
Tn5 transposition of nuclear DNA for 30 minutes followed by clean up with Qiagen Min Elute columns
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit, using 200,000 cells per pellet

value: induced pluripotent stem cell line

tag: Sex

value: F


title: C4955_atac_seq

description: Tn5-transposase treated nuclear DNA

value: M


title: C8861_atac_seq

description: Tn5-transposase treated nuclear DNA


title: 2016_DB_DF_09

description: processed data file: FibrInflRlog.txt


title: 2016_DB_DF_06

description: processed data file: FibrInflRlog.txt


title: C3649_atac_seq

description: Tn5-transposase treated nuclear DNA


title: C3651_atac_seq

description: Tn5-transposase treated nuclear DNA


title: C3647_atac_seq

description: Tn5-transposase treated nuclear DNA


title: 2016_DB_DF_07

description: processed data file: FibrInflRlog.txt


title: 2016_DB_DF_04

description: processed data file: FibrInflRlog.txt


title: 2016_DB_DF_05

description: processed data file: FibrInflRlog.txt


title: 2016_DB_DF_03

description: processed data file: FibrInflRlog.txt

value: Healthy

value: resting


title: Sumai3(SU) Rachis treated with 3ADON at 4 dpi replicate2

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

data_processing:
RNA-seq reads were preprocessed by trimming the adaptor sequences, filtering low-quality reads (Phred Score <=20 [Phred]) and eliminating short reads (length <= 20 bps) using software package from Stanford University (http://sfg.stanford.edu/)
RNA-seq reads were aligned to the pan-genome of Chinese Spring (IWGSC Survey genome 2.2) from Ensembl Plant (http://plants.ensembl.org/, Release 28) and Fusarium graminearum reference genome (Fusarium graminearum str. PH-1) from EnsemblFungi (http://fungi.ensembl.org/, Release 28) using STAR v2.5.3a
R package DESeq2 was used for data normalization and to generate differentially expressed gene (DEG)
Genome_build: IWGSC Survey genome 2.2; Fusarium graminearum str. PH-1
Supplementary_files_format_and_content: Raw read counts data; Normalized read counts data

organism: Triticum aestivum

source_name: Rachis

growth_protocol: Wheat plants were grown in controlled-environment growth chambers. Seeds were sown in peat pots (diameter, 12.7 cm) and maintained in a growth chamber with 16h light at 21°C and 8h dark at 19°C. Plants were fertilized weekly with 20-20-20 (N-P-K).

extract_protocol:
Total RNA from each sample was isolated using the Plant RNeasy Mini Kit (Qiagen, Mississauga, ON, Canada), according to the manufacturer’s instructions. All samples were treated with DNase I on column using the Qiagen RNase-Free DNase Set. The yield and RNA purity were determined spectrophotometrically with a Nanodrop 1100 (Thermo scientific, USA), and the quality of RNA was monitored by determining the RNA Integrity Number (RIN) with an Agilent 2100 bioanalyzer and RNA LabChip (Agilent Technologies, Santa Clara, CA, USA). Samples with a RIN value >= 7 were used to prepare cDNA libraries by using the TruSeq RNA Sample Preparation Kit v2 (Illumina).
Libraries were prepared according to Illumina's instructions, using the TruSeq RNA v2 LT kit and sequenced on the Genome Analyzer following the manufacturer's protocols (https://www.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf). Paired-end sequencing was conducted on the Illumina HiSeq2500, generating 101-nucleotide reads.

treatment_protocol: At mid-anthesis, 10 spikelets midway along the spike were point inoculated with 10 μl of the macroconidial suspension of F. graminearum, 3-ADON chemotype (M9-4-6) or with 10 μl ddH2O as a mock treatment.  Three spikes from each variety were pooled as one biological replicate and three biological replicates were harvested per time point. Each replicate was ground and divided into two parts for separate processing and analysis by RNA-seq and hormone profiling, respectively.

tag: genotype

value: Rachis

value: F. graminearum inoculation

tag: day sample taken (dpi)


title: Sumai3(SU) Rachis treated with water at 2 dpi replicate2

value: water (mock) inoculation


title: Sumai3(SU) Rachis treated with 3ADON at 4 dpi replicate3


title: 2016_DB_DF_02

description: processed data file: FibrInflRlog.txt


title: Sumai3(SU) Rachis treated with water at 2 dpi replicate3


title: Sumai3(SU) Rachis treated with 3ADON at 4 dpi replicate1


title: E. coli culture, DM, replicate 3

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

description:
processed data file : Ecoli K12_tRNA_Counts.xlsx
E. coli  culture, biological replicate 3, demethylase treated, which had tRNA subsequently isolated

data_processing:
We removed low-quality reads from the raw sequencing results using illumina-utils 17 (available from https://github.com/merenlab/illumina-utils). For the analysis of 16S rRNA gene amplicons data we used the program ‘iu-merge-pairs’ with default parameters, which merged partially overlapping paired-end Illumina reads while simultaneously removing any pair with more than 3 mismatches at the overlapped region. For pairs with three or less mismatches, we picked the base to be used in the final merged sequence from the read with the higher Q-score.
We used Minimum Entropy Decomposition 11 with default parameters to cluster high-quality 16S rRNA gene amplicons at 1-nt resolution, and GAST 18 to assign taxonomy to each read individually.
To recover tRNA sequences in this dataset we also used the program ‘iu-merge-pairs’, but with two additional flags and an additional parameter: --retain-only-overlap (to keep only the overlapping region while trimming tailing ends from both reads in a pair), --marker-gene-stringent (to align the reverse-complement of the second read even if the alignment occurs between the end of the second read and the beginning of the first read --which is a unique case for short inserts), and --max-num-mismatches 0 (to remove any pair if there was a disagreement between the aligned portions to increase the quality dramatically as described in 17).
We developed a new software tool to identify tRNA sequences in the raw sequencing results: tRNA-seq-tools (available from https://github.com/merenlab/tRNA-seq-tools). We used the tRNA-seq-tools program ‘trna-profile’ with default parameters to identify all sequences that matched our criteria for standard tRNA.
Supplementary_files_format_and_content: Bacterial tRNA counts in Excel file format

organism: Escherichia coli

source_name: bacterial culture

growth_protocol: We grew E. coli, B. subtilis, and S. aureus cultures at 37°C in Erlenmeyer flasks with a 10:1 flask medium ratio at 225rpm. We grew E. coli and B. subtilis in LB Lennox and S. aureus in tryptic soy broth. We grew B. viscericola in serum vials under strict anaerobic conditions at 37°C in chopped meat medium as previously described1. We harvested all cultures at midlog by centrifugation.

extract_protocol:
We lysed pelleted bacteria in 400μL of 0.3M NaOAc/HOAc, 10mM EDTA pH 4.8 with an equal volume acetate saturated phenol chloroform pH 4.8. We placed samples in a reciprocating bead beater for 45 seconds on  maximum intensity using FastPrep lysing matrix B. We centrifuged samples at 21,000rcf for 15  minutes at 4°C before re-extraction and ethanol precipitation of total RNA.Total tRNA was subsequently isolated using a denaturing 10% polyacrylamide gel followed by passive gel elution and ethanol precipitation.
Homemade protocol based on Illumina protocols. Deacylated RNAs with or without the demethylation were first treated with T4 Polynucleotide Kinase (Epicentre) at 37C° for 30 min to further warrant a free 3' hydroxyl group for template switching. Template-switching reactions were performed as described7. Briefly, we used an initial template-primer substrate consisting of a 41-nt RNA oligonucleotide (5’-AGA UCG GAA GAG CAC ACG UCU AGU UCU ACA GUC CGA CGA UC/3SpC3/-3’) that contains Illumina Read1 and Read2 primer-binding sites and a 3’ blocking group (three carbon spacer; IDT) annealed to a complementary 32P-labeled DNA primer with a single-nucleotide 3’ overhang, T, which facilitates the template switch to full-length tRNA that mostly contain a 3’ CCA end. For g2RT template-switching reactions, average 100 ng of demethylated tRNAs or 1 μg of demethylated total RNA were mixed with the initial template-primer substrate (100 nM) and g2RT (1 μM of TeI4cΔEn or 500 nM of GsI-IIC RT) in reaction medium containing 450 mM NaCl, 5 mM MgCl2, 20 mM Tris-HCl, pH 7.5, and DTT (1 mM for TeI4cΔEn or 5 mM for GsI-IIC RT). For template-switching with TeI4cΔEn RT, the reactions were pre-incubated at room temperature for 30 min, initiated by adding 25 mM dNTPs to a final concentration of 1 mM and incubating at 60°C for 30 min. For template-switching with GsI-IIC RT, the pre-incubation step is not required. The reactions were terminated by adding 5 M NaOH to a final concentration of 0.25 M, incubating at 95°C for 3 min, and neutralizing with 5M HCl. The cDNAs resulting from template switching were analyzed in a denaturing 6% polyacrylamide gel, electroeluted using a D-tube Dialyzer Maxi with MWCO of 6-8 kDa (EMD Millipore), and ethanol precipitated with 0.3 M sodium acetate in the presence of 25 µg of linear acrylamide (Life Technologies). The purified cDNAs were then circularized with CircLigase II (Epicentre) using manufacture’s protocol with extended incubation time of 5 hours at 60°C, phenol-CIA extracted, ethanol precipitated and amplified with Phusion-HF (Thermo Scientific) using Illumina multiplex (5’- AAT GAT ACG GCG ACC ACC GAG ATC TAC ACG TTC AGA GTT CTA CAG TCC GAC GAT C -3’) and barcode (5’- CAA GCA GAA GAC GGC ATA CGA GAT BARCODE GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T -3’) primers for 12 cycles of 98°C for 5 sec, 60°C for 10 sec and 72°C for 10 sec. The PCR products were sequenced on Illumina HiSeq 2000 system.

treatment_protocol: Sequenced tRNA was derived from bacterial pellets. DM refers to demethylase treatment. This is a cocktail of AlkB and AlkB engineered mutants that remove modifications from the tRNAs. This treatment was performed after isolation of tRNA from mouse cecum.

value: demethylase

value: bacterial culture

tag: molecule subtype

value: tRNA


title: 97-7_vector_1

type: RNA

city: Leeds

first: Erica

last: di Martino

address: Becket Street

department: Experimental Oncology

country: United Kingdom

institute: University of Leeds

description:
control cells transduced with empty vector
97-7_vector_1

hyb_protocol: Fragmented cRNA was hybridized at 45°C for 16 hrs on Human U133 Plus 2.0 expression arrays. Washing and staining were carried out in the Affymetrix GeneChip Fluidics Station according to the manufacturer's instructions.

scan_protocol: Scanning was carried out in the Affymetrix GeneChip Scanner 3000 system with Autoloader. Data collection and management was done in the Affymetrix GeneChip Operating Software (GCOS).

data_processing: Expression data were analyzed with Partek Genomic Suite 6.5. Raw values of intensity were normalized using RMA, and significant differences in expression levels between samples were identified using t-test, after correction for multiple testing

label: biotin

source_name: Empty Vector, bladder cancer cell line

label_protocol: 2ug of total RNA was used to prepare biotinylated target cRNA using the Affymetrix One Cycle Target Preparation Protocol

growth_protocol: Standard growth media

extract_protocol: Trizol extraction, DNAse treatment, RNeasy re-purification

treatment_protocol: Retroviral infection with relevant plasmid

tag: disease state

value: bladder cancer

value: bladder cancer cell line 97-7

value: Empty Vector

value: control


title: 97-7_sh155_1

description:
cells transduced with sh155 against ETV5
97-7_sh155_1

source_name: sh155, bladder cancer cell line

value: ETV5 silencing


title: 97-7_sh155_2

description:
cells transduced with sh155 against ETV5
97-7_sh155_2


title: 97-7_NS_2

description:
control cells transduced with scrambled shRNA
97-7_NS_2

source_name: Scrambled, bladder cancer cell line

value: Scrambled


title: 97-7_sh1189_3

description:
cells transduced with sh1189 against ETV5
97-7_sh1189_3

source_name: sh1189, bladder cancer cell line


title: 97-7_vector_3

description:
control cells transduced with empty vector
97-7_vector_3


title: E. coli culture, DM, replicate 2

description:
processed data file : Ecoli K12_tRNA_Counts.xlsx
E. coli  culture, biological replicate 2, demethylase treated, which had tRNA subsequently isolated


title: Sumai3(SU) Lemma treated with water at 2 dpi replicate1

source_name: Lemma

value: Lemma


title: Sumai3(SU) Lemma treated with water at 2 dpi replicate3


title: Sumai3(SU) Lemma treated with water at 2 dpi replicate2


title: 2016_DB_DF_01

description: processed data file: FibrInflRlog.txt

value: Dermal fibroblasts


title: 97-7_NS_3

description:
control cells transduced with scrambled shRNA
97-7_NS_3


title: E. coli culture, DM, replicate 1

description:
processed data file : Ecoli K12_tRNA_Counts.xlsx
E. coli  culture, biological replicate 1, demethylase treated, which had tRNA subsequently isolated


title: 97-7_sh1189_2

description:
cells transduced with sh1189 against ETV5
97-7_sh1189_2


title: 97-7_sh155_3

description:
cells transduced with sh155 against ETV5
97-7_sh155_3


title: 97-7_NS_1

description:
control cells transduced with scrambled shRNA
97-7_NS_1


title: Sumai3(SU) Rachis treated with 3ADON at 3 dpi replicate3


title: 97-7_sh1189_1

description:
cells transduced with sh1189 against ETV5
97-7_sh1189_1


title: 97-7_vector_2

description:
control cells transduced with empty vector
97-7_vector_2


title: E. coli culture, replicate 3

description:
processed data file : Ecoli K12_tRNA_Counts.xlsx
E. coli  culture, biological replicate 3, which had tRNA subsequently isolated

value: no demethylase


title: E. coli culture, replicate 2

description:
processed data file : Ecoli K12_tRNA_Counts.xlsx
E. coli  culture, biological replicate 2 which had tRNA subsequently isolated


title: 2018_PU_DF_07

description: processed data file: PU1oexpRlog.txt

value: Healthy

tag: genotype/variation

value: PU.1 overexpression


title: Sumai3(SU) Rachis treated with 3ADON at 3 dpi replicate1

value: Rachis


title: Sumai3(SU) Rachis treated with 3ADON at 3 dpi replicate2

value: F. graminearum inoculation


title: Sumai3(SU) Rachis treated with water at 2 dpi replicate1

value: water (mock) inoculation


title: E. coli culture, replicate 1

description:
processed data file : Ecoli K12_tRNA_Counts.xlsx
E. coli  culture, biological replicate 1, which had tRNA subsequently isolated


title: 2018_PU_DF_08

description: processed data file: PU1oexpRlog.txt

value: resting


title: Sumai3(SU) Lemma treated with 3ADON at 3 dpi replicate2


title: 2018_PU_DF_05

description: processed data file: PU1oexpRlog.txt

value: scr transfection


title: 2018_PU_DF_04

description: processed data file: PU1oexpRlog.txt


title: UTI8 6mACEseq

city: Shenzhen

first: Wee Siong Sho

last: Goh

state: Guangdong

address: Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District

department: Institute of Molecular Physiology

country: China

institute: Shenzhen Bay Laboratory

data_processing:
Library strategy: 6mACE-seq
Basecalls performed using FASTQ Generation v1.0.0
Sequenced reads were trimmed of adapter sequence using Cutadapt v1.8.1 then mapped to the corresponding genome using Bowtie2 v2.2.6 with parameters -q -p 30 -N 1 --no-mixed --no-discordant
The coordinates for the first nucleotide and the total number of associated mapped reads were consolidated (bedgraph file) and used for 6mA site/peak-calling: A potential site was under consideration only if it possessed at least 1 read in all replicates. For each potential site, the probability of reads beginning at that site was calculated using the maximum-likelihood estimates of the parameters of a negative binomial distribution using the counts of read-starts in a 1,000nt window centered around the site. Probabilities at each candidate site across replicates were then combined via Fisher’s method for combining p-values. Multiple-testing correction using the Benjamini-Hochberg procedure was implemented and sites where the false discovery rate <0.01 were deemed significant (bed file).
Genome_build: UTI89 (Escherichia), 14028S (Salmonella), hg38 (human)
Supplementary_files_format_and_content: Bedgraph files of first nucleotide coordinates of mapped reads. Bed files of significantly called 6mA sites.

source_name: Bacteria

growth_protocol: Bacteria were cultivated overnight at 37oC in L-Broth.

extract_protocol:
Bacteria were lysed overnight in SNET lysis buffer (400mM NaCl, 1% SDS, 20mM Tris pH 8, 5mM EDTA, 200µg/ml Proteinase K) at 56oC with shaking at 1,000rpm. Genomic DNA was purified from cell lysate using Phenol-chloroform-Isoamyalcohol (25:24:1), precipitated with 50% isopropanol. The DNA pellet was washed once with 100% ethanol and once with 70% ethanol before being reconstituted in IDTE (10mM Tris pH 8, 0.1mM EDTA).
Genomic DNA was first sonicated to ~150bp and treated with RNAseA/T1 (Ambion AM2286) for 1hr at 37oC then purified using 1.8X volume Agencourt AMpure XP beads (Beckman A63880). 5µg of sonicated and RNA-free genomic DNA was then incubated with 4µg anti-6mA antibody (Synaptic Systems 202003) in 1X IP buffer (150mM NaCl, 10mM Tris pH 7.4, 0.1% IGEPAL) overnight at 4oC. This antibody-genomic DNA mixture was then crosslinked with 0.15J 254nm UV radiation six times before being mixed with 40µl BSA-blocked Protein-A-dynabeads (Life Technologies 10002). Beads bound with crosslinked genomic DNA were then washed with 500µl of the following buffers in this order: Wash buffer 1 (1M NaCl, 50mM HEPES-KOH pH 7.4, 1% Triton X-100, 0.1% Sodium Deoxycholate, 2mM EDTA), Wash buffer 2 (0.5M NaCl, 50mM HEPES-KOH pH 7.4, 1% IGEPAL, 0.1% Sodium Deoxycholate, 2mM EDTA), Wash buffer 3 (1% Sodium Deoxycholate, 25mM LiCl, 10mM Tris pH 8, 1% Triton X-100, 2mM EDTA), TE (10mM Tris pH 8, 1mM EDTA) and finally 10mM Tris pH 8. Genomic DNA was then subjected to progressive on-bead reactions as follows: End-repair with 6U T4 DNA polymerase (NEB M0203) at 12oC for 30min, end-phosphorylation with 30U T4 PNK (NEB M0201) and T4 DNA ligase buffer (NEB B0202) at 37oC for 30min, first adapter ligation with 1500U T4 DNA ligase (NEB M0202) and 202.5pmol first adapter at 25oC for 2hr, fill-in DNA synthesis with 20U Phi29 DNA polymerase (NEB M0269), a second round of end-phosphorylation using the same conditions, Lamda exonuclease digestion with 20U Lambda exonuclease (NEB M0262) at 37oC for 30min and finally RecJf exonuclease digestion with 90U RecJf (NEB M0264) at 37oC for 30min. The same bead-wash steps were carried out between each reaction. DNA was then eluted off beads with elution buffer (0.5% SDS, 0.2M NaCl, 25mM Tris pH 8, 2mM EDTA) and treated with 8,000U of proteinase K  (Thermo Scientific EO0491) overnight at 65oC with shaking at 1,000rpm. The eluted ssDNA was ethanol-precipitated before undergoing the following reactions as follows: Annealing of PG162 primer to the reverse adapter and primer extension with 20U Phi29 polymerase, second adapter ligation with 1000U T4 DNA ligase and 30.15pmol forward adapter, dsDNA purification with 1.7x volume Ampure XP beads, 18 cycles amplification with Phusion High-fidelity PCR mastermix (NEB M0530) and finally, primer-dimer removal with 0.8X volume AMpure XP beads before undergoing sequencing on the Illumina Miseq or Nextseq single-end platforms.

tag: 6ma antibody

value: Synaptic systems 202003

tag: passage number

value: Dam+


title: Sumai3(SU) Lemma treated with 3ADON at 3 dpi replicate1


title: Sumai3(SU) Rachis treated with 3ADON at 2 dpi replicate1


title: Sumai3(SU) Rachis treated with 3ADON at 2 dpi replicate3


title: Sumai3(SU) Rachis treated with 3ADON at 2 dpi replicate2


title: ATF7-Overexpressing-beige-rep2

city: Tsukuba

first: Yang

last: LIU

state: Ibaraki.

address: 3-1-1 Koyadai, Tsukuba, Ibaraki

country: Japan

institute: Riken

description: With rosiglitazone treatment

data_processing:
Sequences were mapped to mouse mm10 with CLC.
Expression values were quantified as FPKM.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values and gene annotations for each sample.

source_name: Beige adipocytes

extract_protocol:
Total RNA was isolated from differentiated cells using TRIZOL reagent (Thermo Fisher Scientific, Waltham, MA). RNA quality was evaluated using an RNA 6000 Pico kit (Agilent, Santa Clara, CA). Fifty nanograms of total RNA was used for RNA sequencing (RNA-seq) library preparation with a NEBNext rRNA Depletion Kit and a NEBNext Ultra Directional RNA Library Preparation Kit (New England Biolabs, Ipswich, MA), then 2 × 36 base pair-end sequencing was performed using NextSeq500 (Illumina, San Diego, CA) by Tsukuba i-Laboratory LLP (Tsukuba, Ibaraki, Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Beige adipocytes derived from C3H10t1/2


title: Sumai3(SU) Lemma treated with 3ADON at 2 dpi replicate3


title: Sumai3(SU) Lemma treated with 3ADON at 2 dpi replicate2


title: Sumai3(SU) Lemma treated with 3ADON at 2 dpi replicate1


title: Sumai3(SU) Lemma treated with 3ADON at 1 dpi replicate3


title: 2018_PU_DF_02

description: processed data file: PU1oexpRlog.txt


title: Sumai3(SU) Lemma treated with 3ADON at 1 dpi replicate2


title: Control-beige-rep2

description: With rosiglitazone treatment

value: Control


title: Sumai3(SU) Lemma treated with 3ADON at 1 dpi replicate1


title: ATF7-Overexpressing-beige-rep1

description: With rosiglitazone treatment


title: 2018_PU_DF_06

description: processed data file: PU1oexpRlog.txt


title: Control-beige-rep1

description: With rosiglitazone treatment


title: 2018_PU_DF_01

description: processed data file: PU1oexpRlog.txt


title: Stettler(ST) Rachis treated with water at 2 dpi replicate3

value: Stettler


title: ATF7KO-white-rep2

description: Without rosiglitazone treatment

source_name: White adipocytes

tag: strain/background

value: White adipocytes derived from inguinal WAT preadipocytes


title: Sumai3(SU) Lemma treated with 3ADON at 3 dpi replicate3

tag: tissue


title: HUtt60_atac_seq

description: Tn5-transposase treated nuclear DNA

value: induced pluripotent stem cell line

value: F


title: H19114_atac_seq

description: Tn5-transposase treated nuclear DNA


title: ATF7KO-white-rep1

description: Without rosiglitazone treatment


title: Stettler(ST) Rachis treated with water at 2 dpi replicate2


title: Stettler(ST) Rachis treated with water at 2 dpi replicate1


title: Stettler(ST) Lemma treated with water at 2 dpi replicate3

value: Lemma


title: Stettler(ST) Lemma treated with water at 2 dpi replicate2


title: HUtt45_atac_seq

description: Tn5-transposase treated nuclear DNA

value: M


title: Stettler(ST) Lemma treated with water at 2 dpi replicate1


title: 2018_PU_DF_03

description: processed data file: PU1oexpRlog.txt

value: Healthy

value: Dermal fibroblasts


title: WT-white-rep2

description: Without rosiglitazone treatment

value: WT


title: H28834_atac_seq

description: Tn5-transposase treated nuclear DNA


title: Stettler(ST) Rachis treated with 3ADON at 3 dpi replicate3

value: Rachis

value: F. graminearum inoculation


title: Stettler(ST) Lemma treated with 3ADON at 3 dpi replicate3


title: H20961_atac_seq

description: Tn5-transposase treated nuclear DNA


title: Stettler(ST) Rachis treated with 3ADON at 3 dpi replicate2


title: Stettler(ST) Rachis treated with 3ADON at 3 dpi replicate1


title: WT-white-rep1

description: Without rosiglitazone treatment


title: H19101_atac_seq

description: Tn5-transposase treated nuclear DNA


title: ATF7KO-beige-rep2

description: With rosiglitazone treatment

value: Beige adipocytes derived from inguinal WAT preadipocytes


title: Stettler(ST) Rachis treated with 3ADON at 2 dpi replicate3


title: Stettler(ST) Lemma treated with 3ADON at 3 dpi replicate2


title: Stettler(ST) Rachis treated with 3ADON at 2 dpi replicate2


title: Stettler(ST) Lemma treated with 3ADON at 3 dpi replicate1


title: ATF7KO-beige-rep1

description: With rosiglitazone treatment


title: Salt m6A Supernatant Rep 2

city: Philadelphia

first: Stephen

middle: James

last: Anderson

state: PA

address: 433 South University Avenue

department: Biology

institute: University of Pennsylvania

description: polyA+ RNA, m6A- fraction

data_processing:
In order to call m6A peaks reads from all samples were aligned to the Col-0 reference genome/annotation file TAIR10 using STAR (v2.4.0). All non-unique reads were discarded from downstream analysis. Mapped read coverage was split into + and minus strand fractions and macs2 callpeak was then used to call m6A peaks on each strand, respectively, using parameters --nomodel --extsize 50 genome size was set to ½ the transcriptome using -g 32542107 and with an FDR cutoff of < 0.05. m6A peaks are provided in bedgraph format.
Genome_build: TAIR10
Supplementary_files_format_and_content: m6A peaks are presented in bed format with respect to treatment.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: 4 week old rosette leaves

growth_protocol: Plants were grown in soil under 16 hour light/8 hour dark cycle at 22°C

extract_protocol:
Following control or salt treatment, rosette leaves were collected 4 hrs after first light. Leaves were immediately placed on liquid N2 and ground using a mortar and pestle. RNA was extracted using Qiazol (Qiagen) according to manufacturers instructions. 2 rounds of PolyA+ selection was performed using the Dynabeads mRNADirect kit (Thermo). miCLIP-seq was performed using 3 μg of polyA+ selected mRNA per replicate. Samples were placed at 75 degrees Celsius for 5 minutes and snap cooled on ice for 2 minutes. Samples were brought to 686 uxL with nuclease free water. Next, 10 uxL RNaseOUT, 200 uxL 5X IP buffer (250 mM tris HCl, 750 mM NaCl, 0.5% vol/vol Igepal[CA-6300]), and 3 uxL of m6A antibody (Abcam ab151230) were added to samples which were rotated at 4 °C for 2 hours. While rotating, Protein A bead slurry was washed twice with 1mL 1X IP buffer and resuspended in 1 mL 1X IP buffer, which was supplemented with 0.5 mg/mL BSA and rotated for 2 hours at 4 °C. After 2 hours, RNA was transferred into 3 cm cell culture dish and cross linked twice with 0.15 J/cm2 UV light in an agilent stratalinker. Protein A beads were then pelleted using magnetic strand and washed twice using 1 mL 1X IP buffer. 250 uxL of bead mixture and RNA samples were placed into a 2 mL tube and rotated for 2 hours at 4 °C. After 2 hours, beads were pelleted using a magnetic stand, supernatant was removed and stored at -80 °C as unbound supernatant. Bead bound samples were removed from beads by adding 95 uxL proteinase K buffer, 5 uxL of proteinase K, and treated for 45 minutes at 50 °C, agitating every ten minutes. Supernatant was removed and stored at -80 °C as the m6A+ sample. Beads were washed twice using 300 uxL 1X IP buffer. Supernatant from both washes were also stored as m6A+ samples. All samples were kept at -80°C overnight and precipitated using NaOAc. m6A+ samples were then pooled after resuspension in nuclease free water. m6A+ and – were then prepared into libraries using the strand-specific sequencing library preparation as previously described (Silverman et al, 2014).
Strand specific libraries were constructed as previously described (Silverman et al, 2014).

treatment_protocol: Two weeks after sowing, plants were treated with Hoaglands solution with or without 50mM NaCl added. Three days later they were watered again with Hoaglands solution with or without 100mM NaCl. They were watered with or without 100mM NaCl every three days for a total of 3 waterings.

tag: background ecotype

value: rosette leaves

tag: age

value: 4 weeks


title: WT-beige-rep2

description: With rosiglitazone treatment

tag: cell type


title: Stettler(ST) Lemma treated with 3ADON at 2 dpi replicate2


title: Stettler(ST) Lemma treated with 3ADON at 2 dpi replicate3


title: Stettler(ST) Rachis treated with 3ADON at 2 dpi replicate1


title: Stettler(ST) Lemma treated with 3ADON at 2 dpi replicate1


title: WT-beige-rep1

description: With rosiglitazone treatment


title: Salt m6A Supernatant Rep 1

description: polyA+ RNA, m6A- fraction


title: HEK293T 6mACEseq rep3

source_name: Human embryonic kidney cells

growth_protocol: ATCC HEK293T CRL-3216 cells were cultivated in a sterile 5% CO2 incubator at 37oC, and in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin, and used within passage number 3-15.

extract_protocol:
HEK293T cells were lysed overnight in SNET lysis buffer (400mM NaCl, 1% SDS, 20mM Tris pH 8, 5mM EDTA, 200µg/ml Proteinase K) at 56oC with shaking at 1,000rpm. Genomic DNA was purified from cell lysate using Phenol-chloroform-Isoamyalcohol (25:24:1), precipitated with 50% isopropanol. The DNA pellet was washed once with 100% ethanol and once with 70% ethanol before being reconstituted in IDTE (10mM Tris pH 8, 0.1mM EDTA).
Genomic DNA was first sonicated to ~150bp and treated with RNAseA/T1 (Ambion AM2286) for 1hr at 37oC then purified using 1.8X volume Agencourt AMpure XP beads (Beckman A63880). 5µg of sonicated and RNA-free genomic DNA was then incubated with 4µg anti-6mA antibody (Synaptic Systems 202003) in 1X IP buffer (150mM NaCl, 10mM Tris pH 7.4, 0.1% IGEPAL) overnight at 4oC. This antibody-genomic DNA mixture was then crosslinked with 0.15J 254nm UV radiation six times before being mixed with 40µl BSA-blocked Protein-A-dynabeads (Life Technologies 10002). Beads bound with crosslinked genomic DNA were then washed with 500µl of the following buffers in this order: Wash buffer 1 (1M NaCl, 50mM HEPES-KOH pH 7.4, 1% Triton X-100, 0.1% Sodium Deoxycholate, 2mM EDTA), Wash buffer 2 (0.5M NaCl, 50mM HEPES-KOH pH 7.4, 1% IGEPAL, 0.1% Sodium Deoxycholate, 2mM EDTA), Wash buffer 3 (1% Sodium Deoxycholate, 25mM LiCl, 10mM Tris pH 8, 1% Triton X-100, 2mM EDTA), TE (10mM Tris pH 8, 1mM EDTA) and finally 10mM Tris pH 8. Genomic DNA was then subjected to progressive on-bead reactions as follows: End-repair with 6U T4 DNA polymerase (NEB M0203) at 12oC for 30min, end-phosphorylation with 30U T4 PNK (NEB M0201) and T4 DNA ligase buffer (NEB B0202) at 37oC for 30min, first adapter ligation with 1500U T4 DNA ligase (NEB M0202) and 202.5pmol first adapter at 25oC for 2hr, fill-in DNA synthesis with 20U Phi29 DNA polymerase (NEB M0269), a second round of end-phosphorylation using the same conditions, Lamda exonuclease digestion with 20U Lambda exonuclease (NEB M0262) at 37oC for 30min and finally RecJf exonuclease digestion with 90U RecJf (NEB M0264) at 37oC for 30min. The same bead-wash steps were carried out between each reaction. DNA was then eluted off beads with elution buffer (0.5% SDS, 0.2M NaCl, 25mM Tris pH 8, 2mM EDTA) and treated with 8,000U of proteinase K  (Thermo Scientific EO0491) overnight at 65oC with shaking at 1,000rpm. The eluted ssDNA was ethanol-precipitated before undergoing the following reactions as follows: Annealing of PG162 primer to the reverse adapter and primer extension with 20U Phi29 polymerase, second adapter ligation with 1000U T4 DNA ligase and 30.15pmol forward adapter, dsDNA purification with 1.7x volume Ampure XP beads, 18 cycles amplification with Phusion High-fidelity PCR mastermix (NEB M0530) and finally, primer-dimer removal with 0.8X volume AMpure XP beads before undergoing sequencing on the Illumina Miseq or Nextseq single-end platforms.

value: Synaptic systems 202003

value: Wild type


title: Stettler(ST) Lemma treated with 3ADON at 1 dpi replicate3


title: Control m6A Supernatant Rep 1

description: polyA+ RNA, m6A- fraction


title: Muchmore(MM) Rachis treated with 3ADON at 4 dpi replicate3

value: Muchmore


title: Salt m6A IP Rep 2

description: polyA+ RNA, m6A+ fraction


title: HEK293T 6mACEseq rep1


title: Stettler(ST) Lemma treated with 3ADON at 1 dpi replicate1

value: Stettler


title: HEK293T 6mACEseq rep2


title: Muchmore(MM) Rachis treated with 3ADON at 4 dpi replicate1


title: Salt m6A IP Rep 1

description: polyA+ RNA, m6A+ fraction


title: Muchmore(MM) Rachis treated with 3ADON at 4 dpi replicate2


title: Muchmore(MM) Rachis treated with water at 2 dpi replicate3

value: water (mock) inoculation


title: Muchmore(MM) Rachis treated with water at 2 dpi replicate2


title: Control m6A IP Rep 1

description: polyA+ RNA, m6A+ fraction


title: Control m6A Supernatant Rep 2

description: polyA+ RNA, m6A- fraction


title: Muchmore(MM) Lemma treated with water at 2 dpi replicate2


title: Muchmore(MM) Rachis treated with water at 2 dpi replicate1


title: MCF7_NoRx_input

city: Vancouver

first: Sunny

middle: Y

last: Yang

state: British Columbia

address: 2405 Wesbrook Mall

department: Faculty of Pharmaceutical Sciences

institute: University of British Columbia

description:
processed data file:
MCF7_NoRx_BioTASQ_vs_Input.tabular.txt

data_processing:
Paired-end sequenced reads were mapped to human reference genome hg19 using HISAT2 with default settings
Exon feature count and annotation to genes were performed using HTSeq-count
Normalization of counts and differential gene expression analyses were performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include normalized read counts for all annotated genes (from hg19 human reference genome) for all samples; tabular files include BioTASQ vs input for each condition

growth_protocol: MCF-7 cells were seeded at 350000 per 10-cm dish

extract_protocol:
G4 targets from cellular sonicate were extracted using BioTASQ and streptavidin beads. BioTASQ-enriched RNA or Input RNA was isolated using TRIZOL. RNA was ribo-depleted before library construction.
cDNA library was generated using Illumina TruSeq RNA library prep kit.

treatment_protocol: MCF-7 cells were treated with either vehicle (untreated control), BRACO-19 5 µg/mL or RHPS4 1.5 µM for 72h

tag: cell line

value: breast cancer cells

value: Untreated

tag: probe

value: Input


title: MCF7_RHPS4_BioTASQ_rep2

description:
processed data file:
MCF7_RHPS4_BioTASQ_vs_Input.tabular.txt

value: BioTASQ


title: Salt GMUCT Rep2

data_processing:
Reads from all samples were aligned to the Col-0 reference genome/annotation file TAIR10 using STAR (v2.4.0) using default parameters.
Read counts in mapped bam files were assessed using Htseq (v0.6.0) with parameters --format=bam --stranded=reverse --mode=intersection-strict.
Proportion uncapping was calculated for all transcripts detectable in all replicates of our mRNA sequencing experiment by dividing the average per genotype GMUCT HTseq read counts (per million reads) over the average per genotyp mRNA seq HTseq read counts (per million reads).
Cleavage sites were determined by finding the highest coverage of 5' read ends within the window of interest
Genome_build: TAIR10
Supplementary_files_format_and_content: bed12 +1 was generated using genomeCoverageBed with the -5 option. The files were scaled by the inverse of number of reads *1000000 in each respective library

extract_protocol:
Control and salt treated plants were collected 4 hrs after first light. Leaves were immediately placed on liquid N2 and ground using a mortar and pestle. RNA was extracted using miRNeasy mini kit (Qiagen) according to manufacturers instructions. 2 rounds of PolyA+ selection was performed using the Dynabeads mRNADirect kit (Thermo) according to manufacturers instructions. 5' adapters were ligated directly this polyA+ selected mRNA as previously described (Willman et al, 2016).
GMUCT libraries were generated as previously described (M. R. Willmann et al, 2016) where 5' adapters were ligated directly to polyA+ selected mRNA and downstream library preparation was also performed as previously described (M. R. Willmann et al, 2016).


title: Salt GMUCT Rep1


title: Muchmore(MM) Rachis treated with 3ADON at 3 dpi replicate3


title: MCF7_RHPS4_BioTASQ_rep1


title: Stettler(ST) Lemma treated with 3ADON at 1 dpi replicate2

value: Lemma


title: Muchmore(MM) Rachis treated with 3ADON at 3 dpi replicate2


title: Muchmore(MM) Rachis treated with 3ADON at 3 dpi replicate1


title: MCF7_RHPS4_input


title: Control GMUCT Rep1


title: Muchmore(MM) Lemma treated with 3ADON at 3 dpi replicate2


title: MCF7_BRACO_BioTASQ_rep2

description:
processed data file:
MCF7_BRACO19_BioTASQ_vs_Input.tabular.txt


title: Muchmore(MM) Lemma treated with 3ADON at 3 dpi replicate3


title: Muchmore(MM) Lemma treated with 3ADON at 3 dpi replicate1


title: Control GMUCT Rep2


title: MCF7_BRACO_BioTASQ_rep1


title: Muchmore(MM) Rachis treated with 3ADON at 2 dpi replicate3


title: Control m6A IP Rep 2

description: polyA+ RNA, m6A+ fraction


title: Muchmore(MM) Lemma treated with water at 2 dpi replicate3


title: MCF7_BRACO_input


title: Muchmore(MM) Rachis treated with 3ADON at 2 dpi replicate1


title: MCF7_NoRx_BioTASQ_rep2


title: Muchmore(MM) Rachis treated with 3ADON at 2 dpi replicate2


title: Muchmore(MM) Lemma treated with water at 2 dpi replicate1


title: MCF7_NoRx_BioTASQ_rep1


title: Muchmore(MM) Lemma treated with 3ADON at 2 dpi replicate1


title: Muchmore(MM) Lemma treated with 3ADON at 2 dpi replicate2


title: Muchmore(MM) Lemma treated with 3ADON at 2 dpi replicate3


title: Muchmore(MM) Lemma treated with 3ADON at 1 dpi replicate3


title: Muchmore(MM) Lemma treated with 3ADON at 1 dpi replicate2


title: Salt mRNA-seq rep1

data_processing:
Reads from all samples were aligned to the Col-0 reference genome/annotation file TAIR10 using STAR (v2.4.0) using default parameters.
Read counts in mapped bam files were assessed using HTSeq with parameters --format=bam --stranded=reverse --mode=intersection-strict.
DESeq2 was run on HTSeq count files using default parameters and a cutoff of  FDR < 0.05 for assigning significantly differentially abundant transcripts.
Genome_build: TAIR10
Supplementary_files_format_and_content: text file containing read counts

extract_protocol:
Following control or salt treatment, rosette leaves were collected 4 hrs after first light. Leaves were immediately placed on liquid N2 and ground using a mortar and pestle. RNA was extracted using Qiazol (Qiagen) according to manufacturers instructions. 2 rounds of PolyA+ selection was performed using the Dynabeads mRNADirect kit (Thermo). polyA+ mRNA was then prepared into libraries using the strand-specific sequencing library preparation as previously described (Silverman et al, 2014).
Strand specific libraries were constructed as previously described (Silverman, et al, 2014)


title: Control mRNA-seq rep1


title: FL62R1(FL) Rachis treated with 3ADON at 4 dpi replicate3


title: Muchmore(MM) Lemma treated with 3ADON at 1 dpi replicate1


title: FL62R1(FL) Rachis treated with 3ADON at 4 dpi replicate2


title: mta rep2 dsRNase protein-bound

description:
processed data file:
mta_rep2_merged_merged.CSAR_PPS_FDR05.bed

data_processing:
Reads from all samples were aligned to the Col-0 reference genome/annotation file TAIR10 using STAR (v2.4.0) using default parameters. Read counts in mapped bam files were assessed using HTseq with parameters --format=bam --stranded=reverse --mode=intersection-strict. Proportion uncapping was calculated for all transcripts detectable in all replicates of our mRNA sequencing experiment by dividing the average per genotype GMUCT HTseq read counts (per million reads) over the average per genotyp mRNA seq HTseq read counts (per million reads). Cleavage sites were calculated by calculating the position with the highest coverage of 5' read ends.
Reads from PIP-seq were trimmed to remove 3’ sequencing adapters with cutadapt (version 1.2.1 using parameters -e 0.06 -O 6 -m 14). The resulting trimmed sequences were collapsed to unique reads and aligned to the TAIR10 Arabidopsis genome sequence using TopHat (version 2.0.10 with parameters –library-type fr-secondstrand –read-mismatches 2 –read-edit-dist 2 –max-multihits 10 –b2-very-sensitive –transcriptome-max-hits 10 –no-coverage-search –no-novel-juncs). Exact duplicate reads were collapsed for subsequent analyses.
A modified version of the CSAR software package was used to call PPSs. Read coverage was calculated for each nucleotide position. Enrichment scores for footprint versus structure only libraries were assigned using a poisson test. PPSs were called with an FDR of 5% as described previously (Gosai et al., 2015; Silverman et al., 2014).
We calculated the sense-mapping dsRNA-seq and ssRNA-seq coverages for each base in detectable transcripts from structure only samples in each replicate,then calculated the structure score as described previously (Gosai et al., 2015).
Genome_build: TAIR10
Supplementary_files_format_and_content:
*_structScore_TAIR10_At_MTA_filtered_spliced.bed12.scaled = The normalized merged secondary structure score for each genotype resulting from our structure only PIP-seq treatments, in bed12 + 1 format with column 13 representing a per-nucleotide structure score of spliced transcripts.
col0_*_merged_merged.CSAR_PPS_FDR05.bed = Bed files of significant PPSs occurring in each replicate of Col-0 leaves.
mta_*_merged_merged.CSAR_PPS_FDR05.bed = Bed files of significant PPSs occurring in each replicate of mta leaves.

source_name: mta dsRNase protein-bound

growth_protocol: Plants were grown in soil under 12 hour light/12 hour dark cycle at 22°C

extract_protocol:
Leaves 5-9 were collected 4 hrs after first light. For each replicate in each genotype, ~12 cross linked leaves were homogenized to a fine powder in mortar and pestle pre-cooled with liquid N2. ~1 mL of powdered tissue was then placed in 2 mL tube containing 850μl of RIP buffer (25 mM Tris-HCl, pH = 7.4; 150 mM KCl, 5 mM EDTA, pH = 7.5; 0.5% NP40; 10 μM DTT; 1 tablet protease inhbitors and 0.5μl/ml RNaseOUT (Life Technologies; Carlsbad, CA, USA)).Homogenized samples were divided into 2 subsamples one for interrogation of protein binding, the other for interrogation of secondary structure. For protein binding samples, each subsample  were then was further divided and half was incubated in either 100 U/ml of a single-stranded RNase (ssRNase) (RNaseONE (Promega; Madison, WI, USA)) with 200 μg/ml BSA in 1X RNaseONE buffer for 1 hour at room temperature (RT), or 2.5 U/ml of a double-stranded RNase (dsRNase) (RNaseV1 (Ambion; Austin, TX, USA)) 1X RNA structure buffer for 1 hour at 37°C as previously described (Anderson et al., 2016). Following RNAse treatment, proteins were denatured and digested by treatment with 1% SDS and 0.1 mg/ml Proteinase K (Roche; Basel, Switzerland) for 15 minutes at RT. Finally, RNAse crosslinks were reversed by incubation at 65°C for 2 hours. For structure only samples,  we performed the identical treat-ments as described for protein bound samples, except that the cross-linked homogenate was treated with 1% SDS and 0.1 mg/ml Proteinase K (Roche;Basel,Switzerland)and ethanol precipitated before treatment with the structure specific RNAses. Post digestion, RNA was then isolated using Qiagen miRNeasy RNA isolation kit as described in the manual.
Strand specific libraries were constructed as previously described (Silverman et al, 2014).

tag: ecotype background

value: ABI3:MTA (mta)

value: 4 week old leaves 5-9


title: FL62R1(FL) Rachis treated with 3ADON at 4 dpi replicate1

value: Rachis

tag: treatment


title: FL62R1(FL) Rachis treated with water at 2 dpi replicate3


title: FL62R1(FL) Rachis treated with water at 2 dpi replicate2


title: mta rep2 ssRNase protein-bound

source_name: mta ssRNase protein-bound


title: Salt mRNA-seq rep2


title: mta rep2 ssRNase structure-only

description:
processed data file:
MTA_structScore_TAIR10_At_MTA_filtered_spliced.bed12.scaled.txt

source_name: mta ssRNase structure-only


title: FL62R1(FL) Lemma treated with water at 2 dpi replicate2


title: FL62R1(FL) Lemma treated with water at 2 dpi replicate3


title: FL62R1(FL) Rachis treated with water at 2 dpi replicate1


title: FL62R1(FL) Lemma treated with water at 2 dpi replicate1


title: mta rep1 dsRNase protein-bound

description:
processed data file:
mta_rep1_merged_merged.CSAR_PPS_FDR05.bed


title: FL62R1(FL) Rachis treated with 3ADON at 3 dpi replicate3

value: F. graminearum inoculation


title: FL62R1(FL) Rachis treated with 3ADON at 3 dpi replicate2


title: FL62R1(FL) Rachis treated with 3ADON at 3 dpi replicate1


title: mta rep1 ssRNase protein-bound


title: mta rep1 dsRNase structure-only

source_name: mta dsRNase structure-only


title: Control mRNA-seq rep2


title: FL62R1(FL) Lemma treated with 3ADON at 3 dpi replicate2


title: FL62R1(FL) Lemma treated with 3ADON at 3 dpi replicate3


title: FL62R1(FL) Lemma treated with 3ADON at 3 dpi replicate1


title: mta rep1 ssRNase structure-only


title: FL62R1(FL) Rachis treated with 3ADON at 2 dpi replicate2


title: Col0 rep2 dsRNase protein-bound

description:
processed data file:
col0_rep2_merged_merged.CSAR_PPS_FDR05.bed

source_name: Col0 dsRNase protein-bound

value: wild-type (WT)


title: FL62R1(FL) Lemma treated with 3ADON at 2 dpi replicate3


title: FL62R1(FL) Lemma treated with 3ADON at 2 dpi replicate2


title: mta rep2 dsRNase structure-only


title: Col0 rep2 dsRNase structure-only

description:
processed data file:
Col0_structScore_TAIR10_At_MTA_filtered_spliced.bed12.scaled.txt

source_name: Col0 dsRNase structure-only


title: FL62R1(FL) Lemma treated with 3ADON at 2 dpi replicate1


title: FL62R1(FL) Lemma treated with 3ADON at 1 dpi replicate2


title: ski2; asc1; PGK-SL

city: St Louis

first: Hani

last: Zaher

state: MO

address: 1 Brookings Drive

institute: Washington University in St Louis

description:
5-11_processed.xlsx
processed (sheet 11: (asc1-SL))

data_processing:
Fastx-toolkit V0.0.13 used to trim terminal nt from barcode reads
Reads were processed with Cutadapt 1.12 to prep for Novoalign (no trimming)
Reads were demultiplexed with novobarcode V3.03.00 with Distance 1 and Format N 5
Trim Illumina adapter sequence with cutadapt 1.12 (ATTGATGGTGCCTACAG) with max 10% errors, single end mode
Align reads to custom reference seqeunce (reporter gene seqeunce) using nonoalign V3.03.00
Filter reads, convert sam to bam, sort and index bam file with samtools-1.13
Convert bam files to bed files with bedtools
Genome_build: N/A
Supplementary_files_format_and_content: Processed data is in an excel file, one sheet per dataset, with position of read relative to the reference seqeunce ATG and number of reads at that position.

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: Cells were grown in defined media (-ura) containing 2%galactose and 2%raffinose to OD~0.8.

extract_protocol:
RNA was extracted using hot phenol followed by chloroform extraction and ethanol precipitation.
An adenylated DNA oligo was ligated to extracted RNA. cDNA was amplified using primers designed for the Illumina HiSeq platform that contain sequence complementary to the adaptor and to position 585 of PGK1.

tag: strain

value: expressing a PGK-stall sequence reporter gene

tag: stalling reporter type

value: SL

tag: barcode

value: ACTTGA


title: FL62R1(FL) Lemma treated with 3ADON at 1 dpi replicate1

tag: genotype

tag: day sample taken (dpi)


title: FL62R1(FL) Lemma treated with 3ADON at 1 dpi replicate3


title: Col0 rep1 ssRNase protein-bound

description:
processed data file:
col0_rep1_merged_merged.CSAR_PPS_FDR05.bed

source_name: Col0 ssRNase protein-bound

tag: genotype/variation


title: Col0 rep1 dsRNase protein-bound


title: ski2; rps3; PGK-CGA

description:
5-11_processed.xlsx
processed (sheet 9: (rps3-CGA))

value: GCCAAT


title: Col0 rep1 dsRNase structure-only


title: ski2; dom34; PGK-CGA

description:
5-11_processed.xlsx
processed (sheet 6: (dom34-CGA))

value: BY4741; ski2D; dom34D

value: TACGAT


title: ski2; rps3; PGK-SL

description:
5-11_processed.xlsx
processed (sheet 8: (rps3-SL))

value: ACAGTG


title: ski2; dom34; PGK-AAA

description:
5-11_processed.xlsx
processed (sheet 7: (dom34-AAA))

value: TGACCA


title: ski2; dom34; PGK-SL

description:
5-11_processed.xlsx
processed (sheet 5: (dom34-SL))

value: GCAGCT


title: Col0 rep2 ssRNase protein-bound


title: FL62R1(FL) Rachis treated with 3ADON at 2 dpi replicate3

source_name: Rachis


title: FL62R1(FL) Rachis treated with 3ADON at 2 dpi replicate1


title: mta GMUCT rep2

data_processing:
Reads from all samples were aligned to the Col-0 reference genome/annotation file TAIR10 using STAR (v2.4.0) using default parameters.
Read counts in mapped bam files were assessed using Htseq (v0.6.0) with parameters --format=bam --stranded=reverse --mode=intersection-strict.
Cleavage sites were determined by finding the highest coverage of 5' read ends within the window of interest
Genome_build: TAIR10
Supplementary_files_format_and_content: MTA_DMSO_merged_GMUCT.5primeend.bed12 = Bed12 + 1 file with the 13th column showing the per nucleotide average coverage of 5' read ends along the unspliced transcript, representing sites of cleavage, in mta leaves.

source_name: mta GMUCT

extract_protocol:
Leaves 5-9 were collected 4 hrs after first light. Leaves were immediately placed on liquid N2 and ground using a mortar and pestle. RNA was extracted using miRNeasy mini kit (Qiagen) according to manufacturers instructions. 2 rounds of PolyA+ selection was performed using the Dynabeads mRNADirect kit (Thermo) according to manufacturers instructions. 5' adapters were ligated directly this polyA+ selected mRNA as previously described.
GMUCT libraries were generated as previously described (M. R. Willmann et al, 2016) where 5' adapters were ligated directly to polyA+ selected mRNA and downstream library preparation was also performed as previously described (M. R. Willmann et al, 2016).


title: mta GMUCT rep1


title: mta  rep2 m6A IP m6A+ fraction

data_processing:
In order to call m6A peaks reads from all samples were aligned to the Col-0 reference genome/annotation file TAIR10 using STAR (v2.4.0). All non-unique reads were discarded from downstream analysis. Mapped read coverage was split into + and minus strand fractions and macs2 callpeak was then used to call m6A peaks on each strand, respectively, using parameters --nomodel --extsize 50 genome size was set to ½ the transcriptome using -g 32542107 and with an FDR cutoff of < 0.05. m6A peaks are provided in bedgraph format in supplementary excel file.
In order to call cross-linking induced mutations (CIMS) , m6A+ library fastqs were trimmed adapters using and subsequently converted to fasta. PCR duplicates were collapsed and aligned using novalign with parameters -l 15 -s 1. Mismatch files were generated using novoalign2bed.pl with parameters -v –mismatch-file. Peaks were called with respect to strand using tag2profile with parameters -v -ss -exact. Mutations were extracted to unique CIMS tags using the tool joinWrapper. CIMS were then filtered into candidate A or C's that were mutated and that had a frequency score of > 30.
Genome_build: TAIR10
Supplementary_files_format_and_content: m6A peak and CIMS are presented in bed format with respect to genotype.

source_name: mta m6A IP m6A+ fraction

extract_protocol:
Leaves 5-9 were collected 4 hrs after first light. Leaves were immediately placed on liquid N2 and ground using a mortar and pestle. RNA was extracted using miRNeasy mini kit (Qiagen) according to manufacturers instructions. 2 rounds of PolyA+ selection was performed using the Dynabeads mRNADirect kit (Thermo). miCLIP-seq was performed using 7 μg of polyA+ selected mRNA per replicate. Samples were placed at 75 degrees Celsius for 5 minutes and snap cooled on ice for 2 minutes. Samples were brought to 686 uxL with nuclease free water. Next, 10 uxL RNaseOUT, 200 uxL 5X IP buffer (250 mM tris HCl, 750 mM NaCl, 0.5% vol/vol Igepal[CA-6300]), and 3 uxL of m6A antibody (Abcam ab151230) were added to samples which were rotated at 4 °C for 2 hours. While rotating, Protein A bead slurry was washed twice with 1mL 1X IP buffer and resuspended in 1 mL 1X IP buffer, which was supplemented with 0.5 mg/mL BSA and rotated for 2 hours at 4 °C. After 2 hours, RNA was transferred into 3 cm cell culture dish and cross linked twice with 0.15 J/cm2 UV light in an agilent stratalinker. Protein A beads were then pelleted using magnetic strand and washed twice using 1 mL 1X IP buffer. 250 uxL of bead mixture and RNA samples were placed into a 2 mL tube and rotated for 2 hours at 4 °C. After 2 hours, beads were pelleted using a magnetic stand, supernatant was removed and stored at -80 °C as unbound supernatant. Bead bound samples were removed from beads by adding 95 uxL proteinase K buffer, 5 uxL of proteinase K, and treated for 45 minutes at 50 °C, agitating every ten minutes. Supernatant was removed and stored at -80 °C as the m6A+ sample. Beads were washed twice using 300 uxL 1X IP buffer. Supernatant from both washes were also stored as m6A+ samples. All samples were kept at -80°C overnight and precipitated using NaOAc. m6A+ samples were then pooled after resuspension in nuclease free water. m6A+ and – were then prepared into libraries using the strand-specific sequencing library preparation as previously described (Silverman et al, 2014).
Strand specific libraries were constructed as previously described (Silverman et al, 2014).

tag: molecule subtype

value: polyA+ RNA, m6A+ fraction


title: mta  rep2 m6A IP supernatant

source_name: mta m6A IP supernatant

value: polyA+ RNA, m6A- fraction


title: ski2; rps3; PGK-AAA

description:
5-11_processed.xlsx
processed (sheet 10: (rps3-AAA))

value: CAGATC


title: Col0 rep2 ssRNase structure-only

source_name: Col0 ssRNase structure-only


title: mta  rep1 m6A IP m6A+ fraction

value: ABI3:MTA (mta)


title: Staphylococcus aureus, DM, replicate 2

description:
processed data file : StaphAureusCount.xlsx
Staphylococcus aureus, biological replicate 2, demethylase treated, which had tRNA subsequently isolated

organism: Staphylococcus aureus

source_name: bacterial culture

value: demethylase

value: bacterial culture

value: tRNA


title: Staphylococcus aureus, DM, replicate 3

description:
processed data file : StaphAureusCount.xlsx
Staphylococcus aureus, biological replicate 3, demethylase treated, which had tRNA subsequently isolated


title: mta rep1 m6A IP supernatant

value: 4 week old leaves 5-9


title: Col0 rep1 ssRNase structure-only

value: wild-type (WT)


title: WT  rep2 m6A IP m6A+ fraction

source_name: WT m6A IP m6A+ fraction


title: Staphylococcus aureus, replicate 3

description:
processed data file : StaphAureusCount.xlsx
Staphylococcus aureus, biological replicate 3, which had tRNA subsequently isolated

value: no demethylase


title: WT  rep2 m6A IP supernatant

source_name: WT m6A IP supernatant


title: PEAR2_DEX_2h_rep3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Arabidopsis Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.42.0).

source_name: 4-day-old seedlings, transfered to MS for 2h, harvested root tips

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: All seeds were surface sterilized, sown on solid MS plates and vernalized for two days before growing at a constant temperature of 22°C in a growth room.

extract_protocol: Total RNA was isolated using Trizol-Chlorophorm extraction followed by clean-up using the RNeasy Plant Mini kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: 4-day-old seedlings were transferred to MS medium supplemented with the indicated compound for the indicated time. Next, roots were harvested and used for total RNA extraction.

tag: treatment time

value: DEX

value: root

tag: genetic background (ecotype)

tag: introduced construct

tag: arraying batch


title: WT  rep1 m6A IP m6A+ fraction

tag: tissue


title: PEAR2_DEX_2h_rep2


title: PEAR1_DMSO_CHX_2h_rep3

value: DMSO+CHX


title: PEAR1_DMSO_CHX_2h_rep1


title: PEAR1_DMSO_CHX_2h_rep2


title: PEAR2_DMSO_CHX_2h_rep3


title: PEAR2_DMSO_rep3

source_name: 4-day-old seedlings, transfered to MS for 1h, harvested root tips

value: DMSO


title: PEAR2_DEX_2h_rep1


title: PEAR2_DEX_CHX_2h_rep2

value: DEX+CHX


title: PEAR2_DMSO_rep2


title: PEAR2_DEX_CHX_2h_rep3


title: PEAR1_DEX_2h_rep2


title: WT  rep1 m6A IP supernatant


title: PEAR2_DMSO_CHX_2h_rep2


title: mta mRNA-seq rep4

data_processing:
Reads from all samples were aligned to the Col-0 reference genome/annotation file TAIR10 using STAR (v2.4.0) using default parameters.
Read counts in mapped bam files were assessed using HTSeq with parameters --format=bam --stranded=reverse --mode=intersection-strict.
DESeq2 was run on HTSeq count files using default parameters and a cutoff of  FDR < 0.05 for assigning significantly differentially abundant transcripts.
Genome_build: TAIR10
Supplementary_files_format_and_content: HTSeq count file

extract_protocol:
Leaves 5-9 were collected 4 hrs after first light. Leaves were immediately placed on liquid N2 and ground using a mortar and pestle. RNA was extracted using miRNeasy mini kit (Qiagen) according to manufacturers instructions.
Strand specific libraries were constructed using the TruSeq mRNA sample library preparation (Truseq) as described in the manual.


title: PEAR2_DEX_CHX_2h_rep1


title: Staphylococcus aureus, replicate 2

description:
processed data file : StaphAureusCount.xlsx
Staphylococcus aureus, biological replicate 2, which had tRNA subsequently isolated


title: Staphylococcus aureus, replicate 1

description:
processed data file : StaphAureusCount.xlsx
Staphylococcus aureus, biological replicate 1, which had tRNA subsequently isolated


title: PEAR2_DMSO_CHX_2h_rep1


title: PEAR2_DMSO_rep1


title: PEAR1_DEX_2h_rep3


title: PEAR1_DMSO_rep1


title: PEAR1_DMSO_rep2


title: PEAR1_DEX_2h_rep1


title: PEAR1_DMSO_rep3


title: mta mRNA-seq rep1


title: mta mRNA-seq rep2


title: WT mRNA-seq rep1


title: WT mRNA-seq rep4


title: WT mRNA-seq rep2


title: HEK293T 6mACEseq rep1 Ab151230

data_processing:
Library strategy: 6mACEseq
Basecalls performed using FASTQ Generation v1.0.0
Sequenced reads were trimmed of adapter sequence using Cutadapt v1.8.1 then mapped to the corresponding genome using Bowtie2 v2.2.6 with parameters -q -p 30 -N 1 --no-mixed --no-discordant
The coordinates for the first nucleotide and the total number of associated mapped reads were consolidated (bedgraph file) and used for 6mA site/peak-calling: A potential site was under consideration only if it possessed at least 1 read in all replicates. For each potential site, the probability of reads beginning at that site was calculated using the maximum-likelihood estimates of the parameters of a negative binomial distribution using the counts of read-starts in a 1,000nt window centered around the site. Probabilities at each candidate site across replicates were then combined via Fisher’s method for combining p-values. Multiple-testing correction using the Benjamini-Hochberg procedure was implemented and sites where the false discovery rate <0.01 were deemed significant. Significant 6mA sites were then filtered for only those that possess an A at the actual 6mA site to output the 6mA bed files.
Genome_build: hg38
Supplementary_files_format_and_content: Bedgraph files of first nucleotide coordinates of mapped reads. Bed files of significantly called 6mA sites.

source_name: Human embryonic kidney cells

tag: 6ma antibody

tag: passage number

value: Wild type


title: HEK293T 6mACEseq rep2 Ab151230


title: mta mRNA-seq rep3


title: HEK293T 6mACEseq rep3 Ab151230


title: PEAR1_DEX_CHX_2h_rep4


title: PEAR1_DEX_CHX_2h_rep1


title: PEAR1_DEX_CHX_2h_rep3


title: WT mRNA-seq rep3


title: PEAR1_DEX_CHX_2h_rep2