title: x129_b1_p2_A05_1c_M_S129: Mouse embryonic stomach at E13.5 Batch1

value: embryonic day 13.5


title: S44T

status: Public on Sep 04 2020

type: genomic

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

hyb_protocol: BS-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing:
Data were processed using R studio
Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: CD4+ T cells isolated from PBMCs of SSc patient

label_protocol: Standard Illumina Protocol

growth_protocol: 15 ml of peripheral blood was collected from 16 healthy donors and 48 SSc patients in Lithium Heparin tubes

extract_protocol: DNA was extracted utilizing the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Hilden, Germany) according to manufacturers’ instructions.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were separated by laying on Lymphocytes Isolation Solution (Rafer, Zaragoza, Spain) and centrifuged without braking. PBMCs were stained with fluorochrom-conjugated antibody against CD4-APC (BD Pharmingen, New Jersey, USA) in staining buffer (PBS with 2 mM of EDTA and 4 % FBS) for 20 mins. Gating strategies were employed to eliminate doublets, cell debris and DAPI+ cells. Lymphocytes were separated by forward and side scatter, in which CD4+ cells were separated by positive selection.

tag: donor

value: Systemic sclerosis

tag: gender

value: F

tag: skin disease

value: dcSSc

tag: lung disease


title: S43T

value: lcSSc

value: PAH


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A6_ad008

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

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

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

value: SSp

tag: Sex

value: male

tag: age

tag: strain


title: ID36_VisitC_Input_Control

city: Toronto

first: Bharati

last: Bapat

state: Ontario

address: 60 Murray Street, Rm L6-304B

department: Lunenfeld-Tanenbaum Research Institute

country: Canada

institute: Sinai Health System

data_processing:
Fastq files were generated using Illumina bcl2fastq version 1.8.4.
Alignment to hg19 genome was performed using BWA mem version 0.7.6a
After read mapping quality filtering(QA>5),  duplicates were marked and collaped using Picard tools (version 1.52 ), and reads were directionally extended to 175bp.
Bigwig files were generated using the UCSC wigToBigwig tool (version 4).
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig

source_name: cfDNA

extract_protocol:
Plasma was separated from whole blood and cfDNA was extracted using the Qiagen circulating nucleic acids kit.
Libraries were prepared using a published protocol (PMID: 30429608). Briefly, end-repair, A-tailing and Illumina adapter ligation was performed using the KAPA hyper prep kit. Methylated cfDNA was immunoprecipated and purified using the Diagenode MagMeDIP and IPure kits. Prior to MeDIP, 10% of the adapter-ligated cfDNA sample was set aside as an input control. Both MeDIP and input control samples were then amplified using KAPA hyper prep kit protocols, followed by size selection.

tag: individual

value: patient ID36

tag: treatment visit

value: C

tag: sample type

value: Input Control

tag: tissue

value: Plasma

tag: medip antibody


title: x128_b2_p5_H04_1c_E_S128: Mouse embryonic stomach at E13.5 Batch2

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology, Mainz

library_source: transcriptomic

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4
Fastq files were mapped with STAR_2.5.2b onto Ensembl 88 GRCm38 reference
Secondary alignments were filtered with samtools 1.5
Counts for every gene were calculated with Subread’s FeatureCounts (version 1.5.1) using the gene model provided with Ensembl 88 GRCm38 reference
Genome_build: Ensembl 88 GRCm38
Supplementary_files_format_and_content: tab separated file containing counts per gene

molecule: total RNA

source_name: stomach cells

extract_protocol:
Single EpCAM+ and EpCAM- embryonic gastric cells were isolated by FACS directly in 96 well plates supplemented with buffer (Takara, Clontech). ERCC RNA Spike-In Mix (ThermoFisher) were added for quality and normalization controls. Plates were stored at -80°C.
50ng of total RNA was used for cDNA synthesis using Ovation v2.0 kit (NuGEN) according to manufacturer’s instructions. After cDNA fragmentation (Covaris), libraries were prepared using NEBNext v2.0 kit (NEB) according to manufacturer’s instructions.

treatment_protocol: Stomachs were dissected from mouse embryos at indicated stages, cut in pieces of 2 mm and incubated for 10 min with 0.15mg/ml collagenase (Sigma) in PBS at 37°C with shaking at 800 rpm. Single cell suspensions were collected by centrifugation at 200g for 3 min, washed twice and resuspended in PBS supplemented with 2% foetal calf serum. Cells were stained with APC–conjugated anti-EpCAM 1:1000 (eBioscience) for 30 min at room temperature. Living cells were gated by DAPI dye exclusion. Embryonic gastric epithelial cells were isolated as EpCAM+DAPI−, mesenchymal cells were EpCAM-DAPI-. Fluorescence-activated cell sorting was performed using BD FACS Aria III SORP cell sorter (100 μM nozzle)

value: mixed C57BL/6 CD1

value: stomach


title: ID36_VisitC_MeDIP-seq

value: MeDIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A6_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A5_ad012


title: S42T

value: ssSSc


title: S41T


title: x128_b1_p2_H04_1c_E_S128: Mouse embryonic stomach at E13.5 Batch1


title: ID36_VisitA_Input_Control

value: A


title: S40T

value: ILD


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A5_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A5_ad010


title: x127_b2_p5_G04_1c_E_S127: Mouse embryonic stomach at E13.5 Batch2

value: embryonic day 13.5


title: ID37_VisitA_MeDIP-seq

value: patient ID37


title: x127_b1_p2_G04_1c_E_S127: Mouse embryonic stomach at E13.5 Batch1


title: x126_b2_p5_F04_1c_E_S126: Mouse embryonic stomach at E13.5 Batch2


title: S39T

value: Systemic sclerosis

value: F


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A5_ad002


title: ID31_VisitC_Input_Control

value: patient ID31


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A5_ad006

value: SSp


title: x126_b1_p2_F04_1c_E_S126: Mouse embryonic stomach at E13.5 Batch1


title: ID31_VisitC_MeDIP-seq


title: S38T

value: dcSSc


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A5_ad008

value: male


title: H17T

source_name: CD4+ T cells isolated from PBMCs of healthy donor

value: Healthy donor

value: HD


title: ID31_VisitB_MeDIP-seq

value: B

value: Plasma


title: S36T

value: M


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A4_ad012


title: S35T

value: Initial


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A4_ad001


title: ID31_VisitB_Input_Control

value: Input Control


title: x125_b1_p2_E04_1c_E_S125: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1

value: stomach


title: ID31_VisitA_Input_Control

value: A


title: ID36_VisitA_MeDIP-seq

value: patient ID36

value: MeDIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A4_ad007


title: x124_b2_p5_D04_1c_E_S124: Mouse embryonic stomach at E13.5 Batch2

value: embryonic day 13.5


title: ID31_VisitA_MeDIP-seq

value: patient ID31


title: x124_b1_p2_D04_1c_E_S124: Mouse embryonic stomach at E13.5 Batch1


title: S34T

value: Systemic sclerosis

value: F

value: ssSSc

value: ILD


title: S33T

value: dcSSc


title: x123_b2_p5_C04_1c_E_S123: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A4_ad010

value: SSp

value: male


title: ID28_VisitC_Input_Control

value: patient ID28

value: C

value: Plasma


title: ID28_VisitC_MeDIP-seq


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A4_ad006


title: S32T


title: x123_b1_p2_C04_1c_E_S123: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1


title: S31T


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A4_ad004


title: x125_b2_p5_E04_1c_E_S125: Mouse embryonic stomach at E13.5 Batch2

value: stomach


title: x122_b2_p5_B04_1c_E_S122: Mouse embryonic stomach at E13.5 Batch2


title: ID28_VisitB_Input_Control

value: B

value: Input Control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A4_ad002


title: ID28_VisitB_MeDIP-seq

value: MeDIP


title: S30T


title: S29T


title: S28T

value: lcSSc

value: PAH


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A4_ad008


title: ID28_VisitA_MeDIP-seq

value: A


title: ID28_VisitA_Input_Control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A3_ad001


title: x121_b1_p2_A04_1c_E_S121: Mouse embryonic stomach at E13.5 Batch1

value: embryonic day 13.5


title: x121_b2_p5_A04_1c_E_S121: Mouse embryonic stomach at E13.5 Batch2


title: x122_b1_p2_B04_1c_E_S122: Mouse embryonic stomach at E13.5 Batch1


title: S27T

value: Systemic sclerosis

value: F


title: S26T

value: ssSSc


title: ID26_VisitB_Input_Control

value: patient ID26


title: x120_b2_p5_H03_1c_M_S120: Mouse embryonic stomach at E13.5 Batch2


title: S37T

value: Initial


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A3_ad007

value: SSp

value: male


title: x120_b1_p2_H03_1c_M_S120: Mouse embryonic stomach at E13.5 Batch1


title: ID26_VisitA_Input_Control

value: Plasma


title: S25T

value: dcSSc

value: ILD


title: ID26_VisitB_MeDIP-seq

value: B


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A3_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A3_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A3_ad004


title: x119_b1_p2_G03_1c_M_S119: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1

value: stomach


title: S24T

value: lcSSc


title: ID26_VisitA_MeDIP-seq

value: MeDIP


title: ID15_VisitC_Input_Control

value: patient ID15

value: C

value: Input Control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A3_ad012


title: S23T

value: Systemic sclerosis

value: F


title: x118_b2_p5_F03_1c_M_S118: Mouse embryonic stomach at E13.5 Batch2

value: embryonic day 13.5


title: ID15_VisitC_MeDIP-seq


title: S22T

value: PAH


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A3_ad008

value: SSp


title: x118_b1_p2_F03_1c_M_S118: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A2_ad012

value: male


title: S21T

value: M


title: ID15_VisitB_Input_Control

value: Plasma


title: ID15_VisitB_MeDIP-seq


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A2_ad001


title: x117_b1_p2_E03_1c_M_S117: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A2_ad007


title: x119_b2_p5_G03_1c_M_S119: Mouse embryonic stomach at E13.5 Batch2


title: x116_b2_p5_D03_1c_M_S116: Mouse embryonic stomach at E13.5 Batch2


title: S18T

value: Initial


title: ID15_VisitA_MeDIP-seq

value: A


title: S20T

value: dcSSc


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A2_ad006


title: S17T

value: ILD


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A2_ad010


title: S16T

value: lcSSc


title: x115_b2_p5_C03_1c_M_S115: Mouse embryonic stomach at E13.5 Batch2

value: mixed C57BL/6 CD1

value: stomach


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A2_ad004


title: x116_b1_p2_D03_1c_M_S116: Mouse embryonic stomach at E13.5 Batch1


title: ID12_VisitC_Input_Control

value: patient ID12

value: C


title: x115_b1_p2_C03_1c_M_S115: Mouse embryonic stomach at E13.5 Batch1


title: ID12_VisitB_Input_Control

value: B

value: Input Control


title: x117_b2_p5_E03_1c_M_S117: Mouse embryonic stomach at E13.5 Batch2

value: embryonic day 13.5


title: x114_b1_p2_B03_1c_M_S114: Mouse embryonic stomach at E13.5 Batch1


title: ID12_VisitB_MeDIP-seq

value: MeDIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A2_ad002

value: SSp


title: S14T

value: Systemic sclerosis

value: F


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A2_ad008

value: male


title: S13T


title: ID12_VisitA_Input_Control

value: Plasma


title: x114_b2_p5_B03_1c_M_S114: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A12_ad012


title: ID15_VisitA_Input_Control

value: patient ID15

value: A


title: S19T

value: dcSSc


title: S15T

value: ssSSc


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A12_ad010


title: ID12_VisitA_MeDIP-seq


title: S12T

value: ILD


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A12_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A12_ad002


title: ID12_VisitC_MeDIP-seq


title: ID9_VisitC_Input_Control

value: patient ID9


title: x112_b2_p5_H02_1c_E_S112: Mouse embryonic stomach at E13.5 Batch2

value: mixed C57BL/6 CD1

value: stomach


title: x113_b1_p2_A03_1c_M_S113: Mouse embryonic stomach at E13.5 Batch1


title: x112_b1_p2_H02_1c_E_S112: Mouse embryonic stomach at E13.5 Batch1


title: ID9_VisitC_MeDIP-seq

value: C


title: S10T

value: lcSSc


title: S9T


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A11_ad012


title: S8T


title: ID9_VisitB_MeDIP-seq

value: B


title: x111_b1_p2_G02_1c_E_S111: Mouse embryonic stomach at E13.5 Batch1

value: embryonic day 13.5


title: x110_b2_p5_F02_1c_E_S110: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A11_ad010

value: SSp


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A11_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A11_ad008


title: ID9_VisitA_Input_Control

value: Input Control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A11_ad007


title: x111_b2_p5_G02_1c_E_S111: Mouse embryonic stomach at E13.5 Batch2


title: S7T

value: Systemic sclerosis

value: M


title: S6T

value: F


title: S5T


title: ID9_VisitA_MeDIP-seq

value: MeDIP

value: Plasma


title: x110_b1_p2_F02_1c_E_S110: Mouse embryonic stomach at E13.5 Batch1


title: S4T


title: S11T


title: ID8_VisitB_Input_Control

value: patient ID8


title: x109_b1_p2_E02_1c_E_S109: Mouse embryonic stomach at E13.5 Batch1


title: ID8_VisitC_MeDIP-seq


title: x109_b2_p5_E02_1c_E_S109: Mouse embryonic stomach at E13.5 Batch2


title: ID9_VisitB_Input_Control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A11_ad001

value: male


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A11_ad002


title: ID8_VisitB_MeDIP-seq


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A11_ad004


title: S3T

value: dcSSc

value: ILD


title: x108_b1_p2_D02_1c_E_S108: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A10_ad012


title: ID8_VisitC_Input_Control


title: S1T


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A10_ad010


title: H13T

value: Healthy donor

value: HD


title: x107_b2_p5_C02_1c_E_S107: Mouse embryonic stomach at E13.5 Batch2

value: stomach


title: x107_b1_p2_C02_1c_E_S107: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A10_ad008


title: ID8_VisitA_MeDIP-seq

value: A


title: ID7_VisitC_Input_Control

value: patient ID7

value: C


title: x106_b2_p5_B02_1c_E_S106: Mouse embryonic stomach at E13.5 Batch2

value: embryonic day 13.5


title: H12T


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A10_ad007

value: SSp


title: ID8_VisitA_Input_Control

value: Input Control


title: x108_b2_p5_D02_1c_E_S108: Mouse embryonic stomach at E13.5 Batch2


title: ID7_VisitC_MeDIP-seq


title: H11T

value: F


title: H10T


title: x105_b2_p5_A02_1c_E_S105: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A10_ad004


title: S2T

value: Systemic sclerosis

value: lcSSc


title: H9T


title: ID7_VisitB_Input_Control

value: B

value: Plasma


title: x105_b1_p2_A02_1c_E_S105: Mouse embryonic stomach at E13.5 Batch1


title: ID7_VisitB_MeDIP-seq

value: MeDIP


title: H8T


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A10_ad002

value: male


title: x104_b2_p5_H01_1c_M_S104: Mouse embryonic stomach at E13.5 Batch2

value: mixed C57BL/6 CD1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A10_ad001


title: H7T

value: Healthy donor


title: x104_b1_p2_H01_1c_M_S104: Mouse embryonic stomach at E13.5 Batch1


title: H6T

value: HD


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A1_ad012


title: H5T


title: ID6_VisitC_Input_Control

value: patient ID6


title: x103_b2_p5_G01_1c_M_S103: Mouse embryonic stomach at E13.5 Batch2

value: stomach


title: x106_b1_p2_B02_1c_E_S106: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A10_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A1_ad001


title: H4T

value: M


title: x103_b1_p2_G01_1c_M_S103: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A1_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A1_ad010


title: ID7_VisitA_Input_Control

value: patient ID7

value: A


title: x102_b1_p2_F01_1c_M_S102: Mouse embryonic stomach at E13.5 Batch1

value: embryonic day 13.5


title: ID6_VisitB_MeDIP-seq


title: ID6_VisitA_Input_Control

value: Input Control


title: x101_b2_p5_E01_1c_M_S101: Mouse embryonic stomach at E13.5 Batch2


title: ID7_VisitA_MeDIP-seq


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A1_ad004

value: SSp


title: ID6_VisitA_MeDIP-seq


title: ID4_VisitC_Input_Control

description: Although Fastq file notation says B, it is  visit C

value: patient ID4

value: C


title: ID6_VisitC_MeDIP-seq


title: x101_b1_p2_E01_1c_M_S101: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A1_ad002


title: ID4_VisitC_MeDIP-seq


title: x102_b2_p5_F01_1c_M_S102: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A1_ad008


title: Runx3cKO_DZ3

city: Bunkyo-ku

first: Kosei

last: Nagata

state: Tokyo

department: Graduate School of Medicine

country: Japan

institute: the University of Tokyo

data_processing:
BGI
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Runx3_TMM.txt

source_name: DZ chondrocytes

extract_protocol:
SFZ/DZ cells were isolated as previously described (Lab Invest 2011;91(12):1739-52.).Total RNA was purified with an RNeasy Mini Kit (Qiagen, Hilden, Germany).
RNA libraries were prepared for sequencing using standard BGI protocols

tag: cell type

value: DZ chondrocytes

tag: genotype


title: ID4_VisitB_Input_Control

value: B

value: Plasma


title: x099_b2_p5_C01_1c_M_S99: Mouse embryonic stomach at E13.5 Batch2


title: Runx3cKO_DZ2


title: ID4_VisitB_MeDIP-seq

value: MeDIP


title: x099_b1_p2_C01_1c_M_S99: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1


title: Runx3cKO_DZ1


title: Cntl_DZ3

value: Cntl


title: x098_b2_p5_B01_1c_M_S98: Mouse embryonic stomach at E13.5 Batch2


title: x100_b2_p5_D01_1c_M_S100: Mouse embryonic stomach at E13.5 Batch2


title: Cntl_DZ2


title: ID4_VisitA_MeDIP-seq


title: ID3_VisitC_Input_Control

value: patient ID3


title: Cntl_DZ1


title: ID3_VisitC_MeDIP-seq


title: ID6_VisitB_Input_Control

value: patient ID6


title: Runx3cKO_SFZ3

source_name: SFZ chondrocytes

value: SFZ chondrocytes


title: x097_b1_p2_A01_1c_M_S97: Mouse embryonic stomach at E13.5 Batch1

value: stomach


title: x100_b1_p2_D01_1c_M_S100: Mouse embryonic stomach at E13.5 Batch1


title: ID4_VisitA_Input_Control


title: ID3_VisitB_Input_Control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A1_ad006

value: male


title: x098_b1_p2_B01_1c_M_S98: Mouse embryonic stomach at E13.5 Batch1


title: x096_b2_p4_H12_1c_E_S96: Mouse embryonic stomach at E13.5 Batch2


title: ID3_VisitB_MeDIP-seq


title: Runx3cKO_SFZ2


title: x097_b2_p5_A01_1c_M_S97: Mouse embryonic stomach at E13.5 Batch2


title: Runx3cKO_SFZ1


title: ID3_VisitA_Input_Control

value: A


title: x095_b2_p4_G12_1c_E_S95: Mouse embryonic stomach at E13.5 Batch2

value: embryonic day 13.5


title: Cntl_SFZ2


title: ID3_VisitA_MeDIP-seq


title: x095_b1_p1_G12_1c_E_S95: Mouse embryonic stomach at E13.5 Batch1


title: Cntl_SFZ3


title: x094_b2_p4_F12_1c_E_S94: Mouse embryonic stomach at E13.5 Batch2


title: ID2_VisitB_Input_Control

value: patient ID2

value: Input Control


title: Cntl_SFZ1


title: ID2_VisitB_MeDIP-seq


title: x094_b1_p1_F12_1c_E_S94: Mouse embryonic stomach at E13.5 Batch1


title: x096_b1_p1_H12_1c_E_S96: Mouse embryonic stomach at E13.5 Batch1


title: x113_b2_p5_A03_1c_M_S113: Mouse embryonic stomach at E13.5 Batch2


title: ID2_VisitA_Input_Control


title: ID2_VisitA_MeDIP-seq


title: x093_b2_p4_E12_1c_E_S93: Mouse embryonic stomach at E13.5 Batch2


title: ADR RNA-seq-R2

city: panjin

first: bo

middle: yu

last: liu

state: liaoning

address: Dagong Road 2

country: China

institute: Dalian University of Technology

data_processing:
base-calling: in-house BGISEQ-500 software
Bowtie2 (version: v2.2.5) was used to map clean reads to reference gene
peak-calling: MACS2 for ChIP-Seq; FPKM method was used in calculated RNA-seq expression level.
ChIPseeker for the annotation of peaks.
Genome_build: Genome_build: ChIP-Seq: hg19; RNA-Seq: hg19;
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigwig (bw): The signal intensity of binding.

source_name: human breast cancer cell MCF-7/ADR

extract_protocol:
MCF-7 and MCF-7/ADR cells were maintained in RPMI-1640 medium with 10% fetal calf serum. Approximately 2 x 10e7 cells were used for each COGC-seq, sWGA-seq or ChIP-seq assay. O-GlcNAz chromatin DNAs enriched by Streptavidin-magnetic beads were purified with the Qiagen PCR purification kit. For sWGA-seq, O-GlcNAc protein bound chromatin DNAs were enriched by sWGA-agarose beads. For NRF1, Flag-WT(wild type)-NRF1, or Flag-AA(Ser447/Ser450 → Ala)-NRF1 ChIP-seq, crosslinked chromatin complexes were immunoprecipitated with anti-NRF-1 antibody (protein A/G-magnetic beads) or anti-Flag-magnetic beads. For RNA-seq, total RNA was extracted from the MCF-7 and MCF-7/ADR cells using Trizol reagent (Invitrogen). RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, USA). RNA libraries were prepared for sequencing using standard BGI protocols.
DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptor. PCR amplification and size selection (usually 100-300bp, including adaptor sequence. Qualified library for sequencing. RNA-seq libraries were constructed using SMARTer cDNA library construction kit (Clontech, Takara Bio, CA, USA).
ChIP-Seq/RNA-Seq

treatment_protocol: MCF-7 and MCF-7/ADR cells were cultured in RPMI-1640 medium with 10% fetal calf serum. MCF-7/ADR cells were cultured in the presence of a low concentration of Dox (1 µg/ml) and passaged for 1 week in drug-free medium before the experiments. For labeling, media was aspirated and the cells were washed with PBS. DMSO stocks of GalNAz was added to achieve the final treatment conditions and incubated for 48 h, with vehicle-only controls always included. Full-length wild type (WT) human NRF1 and O-GlcNAc amino acid sites mutant (human NRF1, Ser447/Ser450 (conservative to mouse NRF1 Ser448/Ser451) → Ala) NRF1 were subcloned into pCMV-Puro64. Transfection of the MCF-7 and MCF-7/ADR cells was performed with Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. The stably transfected cells were then selected by the addition of puromycin to the medium. ~2x107 cells were used as a unit of cells for each experiment.

tag: morphology type

value: epithelial type of breast cancer cell

tag: chip antibody/selection

value: Total RNA


title: ChIP-seq_MCF-7_NRF-1_R2

source_name: human breast cancer cell MCF-7

growth_protocol: RPMI-1640 medium with 10% fetal calf serum.


title: methylation_Dis_02

city: Boston

first: JAE WON

last: CHO

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

description:
sample name:
201438350158_R03C01

hyb_protocol: Bisulphite coverted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850 Beadchip using standard Illumina protocol

scan_protocol: Imaging the BeadChip and data analysis: The iScan System has a two-color (532 nm/658 nm) confocal fluorescent scanner with 0.54-μm pixel resolution. The scanner excited the fluorophores generated during signal amplification/ staining of the allele-specific (one color) extension products on the BeadChips. The image intensities were extracted using Illumina’s GenomeStudio Software.

data_processing:
Cpgsite filtering: Rnbeads package
Additional filtering: SNP region from KOVA and KRGDB
Normalization: Functional normalization

label: Cy3, Cy5

source_name: NSCLC biopsies

label_protocol: Standard Illumina labelling protocol

extract_protocol:
Genomic DNA quantitation: DNA samples were checked for their quality using NanoDrop® ND-2000 UV-Vis Spectrophotometer. The samples were electrophoresed on agarose gels and those with intact genomic DNA, showing no smear upon agarose gel electrophoresis, were selected for subsequent experiment. Intact genomic DNA was diluted to 50 ng/㎕ based on Quant-iT PicoGreen (Invitrogen) quantitation. Concentrations were adjusted according to these results. All prepared samples were bisulfite-converted according to the EZ DNA methylation kit (Zymo Research) protocols.
Bisulfite conversion (Zymo EZ DNA methylation kit): For the bisulfite conversion, 600 ng of input gDNA was required. Conversion reagent was added, followed by subsequent incubation in a thermocycler to denature. CT-converted DNA was washed and de-sulfonated with de-sulfonation buffer, after which, the DNA was washed again and eluted with 12-ml elution buffer.
Sample amplification and hybridization for BeadChips: The whole-genome amplification process required 250 ng of input bisulfite-converted DNA, MA1, and created a sufficient quantity of DNA (1000× amplification) to be used on a single BeadChip in the Infinium methylation assay (Illumina RPM and MSM). After amplification, the product was fragmented using a proprietary reagent (FMS), precipitated with 2-propanol (plus precipitating reagent; PM1), and re-suspended in formamide-containing hybridization buffer (RA1). The DNA samples were denatured at 95 °C for 20 min, and placed in a humidified container for a minimum of 16 h at 48 °C, allowing CpG loci to hybridize with the 50-mer capture probes.

value: NSCLC

tag: treatment status

value: pre-treatment

tag: patient response

value: responder


title: MC98 (MC98)

city: Bologna

first: Luca

last: Morandi

address: via Altura 3

department: DIBINEM

country: Italy

institute: University of Bologna

data_processing:
Reads were mapped by BWAmeth generating the .bam file which was processed by MethylDackel using hg38 for human samples, Felis_catus_9.0 for feline samples as a reference;
EPIC-TABSAT web-tool
Methylation Plotter Webtool
ClustVis webtool
EasyROC
Genome_build: hg38
Supplementary_files_format_and_content: Table 1: Clinical details of mammalian species other than human included in this study:
Supplementary_files_format_and_content: Table 2: genomic regions investigated in this study (reference genome: hg38; gene annotations were retrieved from UCNE database[2] and from Bajerano database[1]):
Supplementary_files_format_and_content: Table 3: Best and worst AUC values for all the seven UCNEs; the number indicates the position on the genome taking into account hg38 as a reference:
Supplementary_files_format_and_content: Table S1: Summary Table with the mean, the standard deviation, the minimum, the maximum and p value of the Kruskal-Wallis test for each position and group of samples comparing all SCC from all the species together vs normal samples and feline stomatitis
Supplementary_files_format_and_content: Table S2: Summary Table comparing human normal donors vs SCC
Supplementary_files_format_and_content: Table S3: Summary Table with the mean, the standard deviation, the minimum, the maximum and p value of the Kruskal-Wallis test for feline SCC vs feline normal samples and feline stomatitis
Supplementary_files_format_and_content: TUCRDataFinalJuly2020: methylation level of each CpG for all cases

source_name: oral mucosa

extract_protocol:
MasterPure DNA purification kit or QuickExtract FFPE DNA Extraction kit
Locus-specific amplicon libraries were generated with tagged primers in two steps: a first PCR amplification for target enrichment, and a second shorter amplification session (8 cycles) to allow the barcoding of the template-specific amplicons obtained from the first amplification step using the Nextera™ Index Kit (Illumina, San Diego, CA, USA)

treatment_protocol: Formali Fixed Paraffin Embedded Tissue or oral brushing specimens

tag: disease state

value: SCC

value: oral brush

tag: tnm

value: Oral Squamous Cell Carcinoma


title: x093_b1_p1_E12_1c_E_S93: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1


title: methylation_Dis_07

description:
sample name:
201959750223_R04C01

value: non-responder


title: ID1_VisitC_Input_Control

value: patient ID1

value: C

value: Plasma


title: ChIP-seq_MCF-7_NRF-1_R1


title: ID1_VisitC_MeDIP-seq

value: MeDIP


title: x092_b2_p4_D12_1c_E_S92: Mouse embryonic stomach at E13.5 Batch2

value: stomach

value: embryonic day 13.5


title: methylation_Dis_09

description:
sample name:
201414140083_R02C01


title: methylation_Dis_10

description:
sample name:
201959750064_R06C01


title: methylation_Dis_04

description:
sample name:
201414140121_R07C01


title: MC68 (MC68)

value: Normal

value: Normal oral mucosa


title: x092_b1_p1_D12_1c_E_S92: Mouse embryonic stomach at E13.5 Batch1


title: ChIP-seq_MCF-7_input_NRF-1_R2

value: epithelial type of breast cancer cell


title: methylation_Dis_06

description:
sample name:
201414140121_R01C01

value: NSCLC


title: x091_b2_p4_C12_1c_E_S91: Mouse embryonic stomach at E13.5 Batch2


title: MCF7 RNA-seq-R2

value: Total RNA


title: MC62 (MC62)


title: ChIP-seq_MCF-7_input_NRF-1_R1


title: methylation_Dis_03

description:
sample name:
201959750039_R01C01

value: pre-treatment


title: ID1_VisitB_MeDIP-seq

value: B


title: MC106 (MC106)

value: SCC

value: oral brush


title: ChIP-seq_MCF-7_input_Flag-WT-NRF-1_R2


title: MC121 (MC121)


title: MC100 (MC100)


title: methylation_Dis_11

description:
sample name:
201105900048_R01C01


title: ChIP-seq_MCF-7_input_Flag-AA-NRF-1_R2


title: ChIP-seq_MCF-7_input_Flag-AA-NRF-1_R1


title: MC77 (MC77)


title: methylation_Dis_01

description:
sample name:
201959750020_R08C01


title: methylation_Dis_17

description:
sample name:
201105980019_R03C01

value: responder


title: ChIP-seq_MCF-7_input_Flag-WT-NRF-1_R1


title: x090_b1_p1_B12_1c_E_S90: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1


title: methylation_Dis_08

description:
sample name:
201414140121_R05C01

value: non-responder


title: x089_b2_p4_A12_1c_E_S89: Mouse embryonic stomach at E13.5 Batch2


title: BT549-PTEN-Rep2 (control)

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

description:
Re-analysis of GSM3538844
SRR8393506 (same as SRR12025831)
SRR8393507 (same as SRR12025832)

data_processing:
Base calling and generation of FASTQ files performed using standard CASAVA pipeline
RNA-seq sequencing quality was checked by running FastQC and TrimGalore was used for dapter and quality trimming. RNA-seq reads were mapped against hg38 using STAR aligner.
Differential gene expression analysis was performed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: csv files of normalized abundance measurements include baseMean, lfcSE, stat etc.

source_name: Breast cancer cell line

growth_protocol: Cells were cultured in DMEM/F-12 medium (Life Technologies, Grand Island, NY) supplemented with 10% FBS (Thermo Scientific Gibco, Waltham, MA) at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using the RNeasy kit (Qiagen, Germantown, MD). On-column DNase treatment was given following the procedure provided by the manufacturer.
Strand-specific library was prepared using Illumina TruSeq stranded RNA library prep kit (Illumina, San Diego, CA) according to manufacturer’s protocols.

treatment_protocol: Three hours of glucose deprivation

tag: cell line

value: PTEN over-expressed

tag: treatment

value: control


title: methylation_Dis_05

description:
sample name:
201414140083_R03C01


title: methylation_Dis_13

description:
sample name:
200863770047_R04C01


title: methylation_Dis_14

description:
sample name:
201105980019_R01C01


title: methylation_Dis_16

description:
sample name:
201105980019_R05C01


title: x089_b1_p1_A12_1c_E_S89: Mouse embryonic stomach at E13.5 Batch1

tag: age


title: SB300P (SB300P)


title: ChIP-seq_MCF-7_Flag-WT-NRF-1_R2

value: Flag


title: x090_b2_p4_B12_1c_E_S90: Mouse embryonic stomach at E13.5 Batch2

tag: strain

value: stomach


title: BT549-Vector-Rep2 (control)

description:
Re-analysis of GSM3538842
SRR8393502 (same as SRR12025827)
SRR8393503 (same as SRR12025828)

value: WT


title: x088_b2_p4_H11_1c_M_S88: Mouse embryonic stomach at E13.5 Batch2

value: embryonic day 13.5


title: ChIP-seq_MCF-7_Flag-WT-NRF-1_R1


title: RS-309T (RS-309T)

value: Oral Squamous Cell Carcinoma


title: methylation_Dis_18

description:
sample name:
201105980019_R06C01


title: methylation_Dis_12

description:
sample name:
201105900048_R05C01


title: BT549-Vector-Rep1 (control)

description:
Re-analysis of GSM3538841
SRR8393500 (same as SRR12025825)
SRR8393501 (same as SRR12025826)


title: x088_b1_p1_H11_1c_M_S88: Mouse embryonic stomach at E13.5 Batch1


title: ChIP-seq_MCF-7_Flag-AA-NRF-1_R2

value: epithelial type of breast cancer cell


title: methylation_Dis_15

description:
sample name:
201105900048_R07C01

value: NSCLC


title: BT-549-PTEN_2 (woGlc)

value: 3 hrs Glucose deprivation


title: OF-276T (OF-276T)


title: ML-279T (ML-279T)


title: ID1_VisitA_Input_Control

tag: individual

value: patient ID1

value: A

value: Input Control

value: Plasma


title: x091_b1_p1_C12_1c_E_S91: Mouse embryonic stomach at E13.5 Batch1


title: BT-549-PTEN_1 (woGlc)


title: ChIP-seq_MCF-7_Flag-AA-NRF-1_R1


title: x087_b1_p1_G11_1c_M_S87: Mouse embryonic stomach at E13.5 Batch1


title: MC52 (MC52)

value: Normal

value: oral brush

value: Normal oral mucosa


title: ChIP-seq_ADR_NRF-1_R2


title: ChIP-seq_ADR_NRF-1_R1


title: ID1_VisitB_Input_Control

tag: treatment visit

value: B


title: MC36 (MC36)


title: x086_b2_p4_F11_1c_M_S86: Mouse embryonic stomach at E13.5 Batch2

value: mixed C57BL/6 CD1


title: x086_b1_p1_F11_1c_M_S86: Mouse embryonic stomach at E13.5 Batch1


title: ChIP-seq_ADR_input_NRF-1_R2


title: IL1T-561 (IL1T-561)

value: SCC


title: x085_b2_p4_E11_1c_M_S85: Mouse embryonic stomach at E13.5 Batch2

value: stomach


title: BT-549-PTEN_Pol-II_2 (woGlc)

data_processing:
Base calling and generation of FASTQ files performed using standard CASAVA pipeline
Reads were aligned against hg38 by using Bowtie2.
BAM files were normalized by depth after removal of PCR duplicates and blacklisted regions.
For generating heatmap and metagene plots, ngs.plot program was used.
Genome_build: hg38
Supplementary_files_format_and_content: Library normalized bigWig files were provided.

extract_protocol:
Chromatin was immunoprecipitated using RNA Pol II antibody, washed, reverse-crosslinked, and DNA isolated using the phenol-chloroform method. Input DNA isolated using the phenol-chloroform method
10ng precipitated DNA was used to prepare library using Illumina TruSeq ChIP library preparation kit.

value: PTEN over-expressed

tag: chip antibody

value: RNA Pol II antibody


title: GV-261T (GV-261T)

tag: tissue

value: Oral Squamous Cell Carcinoma


title: BT-549-PTEN_Pol-II_1 (woGlc)


title: ID1_VisitA_MeDIP-seq

tag: sample type

value: MeDIP

tag: medip antibody


title: BT-549-Vector_2 (woGlc)

tag: genotype

value: WT


title: ChIP-seq_ADR_input_Flag-WT-NRF-1_R2

tag: morphology type

value: epithelial type of breast cancer cell


title: x085_b1_p1_E11_1c_M_S85: Mouse embryonic stomach at E13.5 Batch1

value: embryonic day 13.5


title: ChIP-seq_ADR_input_NRF-1_R1

tag: chip antibody/selection


title: BT-549-PTEN_Input_2 (woGlc)

value: 3 hrs Glucose deprivation


title: BE-403T (BE-403T)

tag: cell type


title: SM2-581 (SM2-581)


title: BT-549-PTEN_Input_1 (woGlc)


title: x084_b2_p4_D11_1c_M_S84: Mouse embryonic stomach at E13.5 Batch2


title: SC-548 (SC-548)


title: BT-549-Vector_1 (woGlc)


title: BT-549-Vector_Pol-II_2 (woGlc)


title: x084_b1_p1_D11_1c_M_S84: Mouse embryonic stomach at E13.5 Batch1


title: LA2-582 (LA2-582)


title: ChIP-seq_ADR_input_Flag-AA-NRF-1_R2


title: x083_b2_p4_C11_1c_M_S83: Mouse embryonic stomach at E13.5 Batch2


title: x087_b2_p4_G11_1c_M_S87: Mouse embryonic stomach at E13.5 Batch2


title: NS2-580 (NS2-580)


title: ChIP-seq_ADR_input_Flag-AA-NRF-1_R1


title: x083_b1_p1_C11_1c_M_S83: Mouse embryonic stomach at E13.5 Batch1


title: BT-549-Vector_Input_2 (woGlc)


title: x082_b2_p4_B11_1c_M_S82: Mouse embryonic stomach at E13.5 Batch2


title: BT-549-Vector_Pol-II_1 (woGlc)


title: x082_b1_p1_B11_1c_M_S82: Mouse embryonic stomach at E13.5 Batch1


title: GB-546 (GB-546)


title: ChIP-seq_ADR_input_Flag-WT-NRF-1_R1


title: ChIP-seq_ADR_Flag-WT-NRF-1_R2

value: Flag


title: ChIP-seq_ADR_Flag-WT-NRF-1_R1


title: x081_b2_p4_A11_1c_M_S81: Mouse embryonic stomach at E13.5 Batch2


title: CE-413T (CE-413T)


title: BT-549-Vector_Input_1 (woGlc)


title: ChIP-seq_ADR_Flag-AA-NRF-1_R1


title: ChIP-seq_ADR_Flag-AA-NRF-1_R2


title: FB-547 (FB-547)


title: SR1-565 (SR1-565)


title: CE-412T (CE-412T)


title: x080_b2_p4_H10_1c_E_S80: Mouse embryonic stomach at E13.5 Batch2


title: CE-411T (CE-411T)


title: GF-550 (GF-550)


title: x080_b1_p1_H10_1c_E_S80: Mouse embryonic stomach at E13.5 Batch1


title: x079_b2_p4_G10_1c_E_S79: Mouse embryonic stomach at E13.5 Batch2


title: ADM2-579 (ADM2-579)


title: RR74-569 (RR74-569)


title: SP2-572 (SP2-572)


title: x079_b1_p1_G10_1c_E_S79: Mouse embryonic stomach at E13.5 Batch1


title: x078_b2_p4_F10_1c_E_S78: Mouse embryonic stomach at E13.5 Batch2


title: ADP-549 (ADP-549)


title: x078_b1_p1_F10_1c_E_S78: Mouse embryonic stomach at E13.5 Batch1


title: x077_b2_p4_E10_1c_E_S77: Mouse embryonic stomach at E13.5 Batch2


title: KRG102219_Aag2_mIgG_Exp8A

city: New York

first: Kathryn

last: Rozen-Gagnon

state: NY

address: 1230 York Avenue, Box 64

institute: The Rockefeller University

description: Ago-CLIP RNA

data_processing:
All raw files provided are not quality filtered and uncollapsed, provided as fastq files.  Standard samples are split by index but are not processed further; they still contain the 5'index/linker/UMI (27nt total) and the 3'linker (GTGTCAGTCACTTCCAGCGG). BrdU samples have the 7nt UMI stripped and appended to the read name in order to de-multiplex, but otherwise contain the 5'  index + 3 Ds (9nt) and the 3' linker (GTGTCAGTCACTTCCAGCGG).
Sequenced reads were collapsed to remove exact duplicates, adaptors, indices, and UMIs were removed, and reads were mapped to the Aedes aegypti AaegL5  genome assembly using Rbowtie2 v1.4.0  (--threads 4 -f -N 1 -L 18).
Peaks were called in all samples using HOMER v4.8.1 makeTagDirectory (-single -format bed) and findPeaks ( -o auto -style factor -L 2 -localSize 10000 -strand separate -minDist 50 -size 10 -fragLength  25 -gsize 1278731969).
Overlapping peak genomic ranges were reduced to yield unique ranges and reads at each peak were counted in the peak matrix by sample.
Genome_build: AaegL5
Supplementary_files_format_and_content: all_samples_raw_count_peak_matrix.txt

organism: Aedes aegypti

source_name: cell line

extract_protocol: CLIP libraries were prepared using custom Ago1, Drosophila Ago2 (9D6; a kind gift from M. Siomi), or paired irrelevant IgG control antibodies, from Aag2 cells or whole homogenized female Aedes aegypti mosquitoes.

value: UV 254 nm

tag: clip antibody

value: mIgG (control antibody for Ago2)

tag: cloning strategy

value: standard linker ligation (not processed, de-multiplexed)


title: KRG102219_Aag2_rIgG_Exp8A

description: Ago-CLIP RNA

value: rIgG (control antibody for Ago1)


title: KRG102219_Aag2_Ago1_Exp8A

description: Ago-CLIP RNA


title: KRG102219_Aag2_Ago1_Exp8B

description: Ago-CLIP RNA


title: KRG102219_Aag2_Ago2_Exp8A

description: Ago-CLIP RNA


title: KRG102219_Aag2_rIgG_Exp8B

description: Ago-CLIP RNA


title: KRG102219_Aag2_mIgG_Exp8B

description: Ago-CLIP RNA


title: x081_b1_p1_A11_1c_M_S81: Mouse embryonic stomach at E13.5 Batch1


title: PS2-573 (PS2-573)

tag: disease state

value: Normal

value: oral brush

tag: tnm

value: Normal oral mucosa


title: KRG102219_aegypti_rIgG_Exp8B

description: Ago-CLIP RNA

source_name: whole organism

value: Orlando

tag: treatment


title: MC2-577 (MC2-577)

tag: age


title: x077_b1_p1_E10_1c_E_S77: Mouse embryonic stomach at E13.5 Batch1

tag: strain

value: mixed C57BL/6 CD1

value: stomach


title: x076_b1_p1_D10_1c_E_S76: Mouse embryonic stomach at E13.5 Batch1


title: KRG102219_aegypti_mIgG_Exp8B

description: Ago-CLIP RNA


title: KRG102219_aegypti_rIgG_Exp8A

description: Ago-CLIP RNA


title: x076_b2_p4_D10_1c_E_S76: Mouse embryonic stomach at E13.5 Batch2


title: LcMOld (LcMOld)


title: MW4

city: Cincinnati

first: Shailendra

last: Patel

address: 231 Albet Sabin Way

department: Endorcrinology

institute: University of Cincinnati

data_processing:
Fastq files were trimmed to remove adapter and low quality sequences using Trimmomatic V 0.33
Trimmed reads were mapped to the reference (mm10) using hisat2 V 2.0.5
After trimming the reads were quantified using Kallisto V 0.43.1, this gives us TPM and Counts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM and COUNTS for all samples

source_name: Adrenal

growth_protocol: All animals were group housed with 4 animals per cage in climate controlled facility with 12hr light/dark cycle, and allowed to feed ad libitum on standard rodent chow.

extract_protocol:
Livers were stored in RNA later at -80 degrees until RNA extraction according to manufacturer protocol with Qiagen RNeasy RNA extraction kit.
RNA libraries were prepared for sequencing using TruSeq RNA Library Prep Kit v2  and NEBNext Ultra Directional RNA Library Prep kit

treatment_protocol: No other treatment, only difference between groups is the genetics

value: Dhcr24lx/flx, Alb-Cre-

tag: Sex

value: Female

tag: library prep kit


title: x075_b2_p4_C10_1c_E_S75: Mouse embryonic stomach at E13.5 Batch2


title: x075_b1_p1_C10_1c_E_S75: Mouse embryonic stomach at E13.5 Batch1


title: LcM603 (LcM603)


title: MM2-574 (MM2-574)


title: KRG102219_aegypti_Ago2_Exp8B

description: Ago-CLIP RNA


title: MW2

source_name: Liver

value: Dhcr24flx/flx, Alb-Cre-

value: NEBNext Ultra Directional RNA Library Prep kit


title: KS78-567 (KS78-567)


title: x074_b2_p4_B10_1c_E_S74: Mouse embryonic stomach at E13.5 Batch2

value: embryonic day 13.5


title: KRG102219_aegypti_Ago2_Exp8A

description: Ago-CLIP RNA


title: GS73-568 (GS73-568)


title: KRG102219_aegypti_Ago1_Exp8A

description: Ago-CLIP RNA


title: KRG102219_aegypti_Ago1_Exp8B

description: Ago-CLIP RNA


title: GM2-578 (GM2-578)


title: x073_b2_p4_A10_1c_E_S73: Mouse embryonic stomach at E13.5 Batch2


title: MW1

value: Dhcr24flx/flx, Alb-Cre+


title: x074_b1_p1_B10_1c_E_S74: Mouse embryonic stomach at E13.5 Batch1


title: YueLab-Input-embryonic-Brain-rep2

city: CHICAGO

first: Yu

last: Luan

state: Illinois

address: 303 E. Superior Simpson Querrey 7-518

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
RNA-seq reads were aligned to zv10 genome assembly using STAR;
ChIP-seq and ATAC-seq reads were aligned to zv10 genome assembly using BWA
HiC reads were aligned to zv10 genome assembly using Bowtie2
The TPM value of gene expression was caculated using RSEM
ChIP-seq and ATAC-seq peaks were called using MACS2 with the following  setting: ChIP-seq q-value <10e-2, p-value<10e-5, Change>1,FC>2. ATAC-seq: q-value<10e-2 and p-value<10e-5
HiC matrix was generated using HiC-Pro
Genome_build: zv10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi-C for each Sample.**All replicates were merged

organism: Danio rerio

source_name: Tissue

growth_protocol: Embryonic  Tuebingen zebrafish were raised under standard laboratory conditions

extract_protocol:
Zebrafish embryonic tissue ChIP-seq was performed similarly to the adult tissue with a few modifications. For embryonic trunk, 50 trunks of 1 dpf embryos were dissected and digested in 500 µL of 0.25% trypsin at room temperature for 20 min. The reaction was then neutralized with FBS.  Trunk cells were washed once with cold 1X PBS and cross-linked with 1% formaldehyde at room temperature for 12 min. For embryonic neuronal cells, Tg(Huc:Kaede) transgenic fish were crossed with wildtype Tuebingen fish. At 1 dpf, embryos were checked under the fluorescence microscope and green positive embryos were selected, dechorionated and pipetted in calcium free Ringer's solution to remove yolk. Supernatant was removed and 500 µL of 0.25% trypsin was added to digeste embryos at room temperature for 20 min. Neutralized with 500 µL of FBS and washed once with cold 1X PBS, digested cells were then cross-linked with 1% formaldehyde at room temperature for 12 min. Cells were then sorted and only green fluoresced cells, which corresponded to embryonic neuronal cells, were collected .
To prepare the library, eluted chromatin was reverse crosslinked and purified by phenol-chloroform extraction. Then DNA was end-repaired by END-IT DNA end-repair kit (Epicentre, ER81050) according to kit’s protocol, added A using Klenow  fragment (3’->5’ exo-) (NEB, M0212S), ligated with Illumina TruSeq adaptor (Illumina, FC-121-3001) and subsequently amplified by PCR (Roche, kk2601). The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit (Agilent). The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp.

value: Tuebingen

value: embryonic-Brain


title: LcM17-5 (LcM17-5)


title: YueLab-Input-embryonic-Brain-rep1


title: x073_b1_p1_A10_1c_E_S73: Mouse embryonic stomach at E13.5 Batch1


title: KRG102219_Aag2_Ago2_Exp8B

description: Ago-CLIP RNA

tag: cell line

value: UV 254 nm


title: KRG092419_aegypti_mIgG_Exp7D

description: Ago-CLIP RNA

value: mIgG (control antibody for Ago2)

value: standard linker ligation (not processed, de-multiplexed)


title: KRG102219_aegypti_mIgG_Exp8A

description: Ago-CLIP RNA


title: MW3


title: KRG092419_aegypti_mIgG_Exp7C

description: Ago-CLIP RNA


title: YueLab-Input-embryonic-Trunk-rep2

tag: tissue

value: embryonic-Trunk


title: ZM366TTUCR (ZM366T)

value: SCC

value: oral brush

value: Oral Squamous Cell Carcinoma


title: x072_b2_p4_H09_1c_M_S72: Mouse embryonic stomach at E13.5 Batch2

value: mixed C57BL/6 CD1


title: MC195TUCR (MC195)


title: YueLab-Input-embryonic-Trunk-rep1


title: x072_b1_p1_H09_1c_M_S72: Mouse embryonic stomach at E13.5 Batch1

value: stomach


title: KRG092419_aegypti_mIgG_Exp7B

description: Ago-CLIP RNA

value: Orlando


title: YueLab-Input-Testis-rep1

growth_protocol: Ault Tuebingen zebrafish were raised under standard laboratory conditions

extract_protocol:
All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP-seq lysis buffer (20 mM Tris-HCl, pH 8.0, 1% SDS, 50 mM EDTA, 1X proteinase inhibitor cocktail). Next, 900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W, duty factor 5, 200 per burst. Sonication time is variable, depending on tissue types. To check the chromatin fragmentation size, 20 µL of input chromatin was reverse crosslinked in elution buffer (20 mM Tris-HCl, pH 8.0, 1% SDS, 1 mM EDTA) at 65 °C overnight, treated with Rnase A and proteinase K and purified by phenol-chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100-300 bp. To prepare antibody-beads complex, 3 µg of histone H3K27ac antibody (Active Motif, 39133) or H3K4me3 antibody (EMD Millipore, 07-473) was mix with 12 µL M-280 sheep anti-rabbit IgG Dynabeads (ThermoFisher, 11203D) in 150 µL of 5 mg/mL BSA/1X PBS buffer, with rotation at 4 °C for 3 h. After incubation, antibody-beads complex was washed once with BSA/1X PBS buffer. About 200 µg chromatin was used per IP. Equal volume of master mix (1X TE, 2% Triton X-100, 0.2% sodium deoxycholate, 2X proteinase inhibitor cocktail) was mixed with 200 µg chromatin and then incubated with antibody-beads complex overnight with rotation. The next morning, the beads were washed 5 times with cold RIPA wash buffer (20 mM Tris-HCl, pH 8.0, 1% NP-40, 0.7% sodium deoxycholate, 500 mM LiCl, 1 mM EDTA, 1X proteinase inhibitor cocktail). Then the chromatin bound on the beads was eluted by 150 µL of elution buffer at 65 °C for 30 min.
To prepare the library, eluted chromatin was reverse crosslinked and purified by phenol-chloroform extraction. Then DNA was end-repaired by END-IT DNA end-repair kit (Epicentre, ER81050) according to kit’s protocol, added A using Klenow  fragment (3’->5’ exo-) (NEB, M0212S), ligated with Illumina TruSeq adaptor (Illumina, FC-121-3001) and subsequently amplified by PCR (Roche, kk2601). The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit (Agilent). The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp.

value: Testis


title: x071_b2_p4_G09_1c_M_S71: Mouse embryonic stomach at E13.5 Batch2


title: MC193TUCR (MC193)


title: KRG092419_aegypti_Ago2_Exp7B

description: Ago-CLIP RNA


title: YueLab-Input-Spleen-rep1

value: Spleen


title: x071_b1_p1_G09_1c_M_S71: Mouse embryonic stomach at E13.5 Batch1


title: MCPR5TUCR (MCPR5)


title: KRG092419_aegypti_mIgG_Exp7A

description: Ago-CLIP RNA


title: YueLab-Input-Spleen-rep2


title: MCPR4TUCR (MCPR4)


title: KRG092419_Aag2_rIgG_Exp7B

description: Ago-CLIP RNA

value: rIgG (control antibody for Ago1)


title: MC194TUCR (MC194)


title: KRG092419_aegypti_Ago2_Exp7A

description: Ago-CLIP RNA


title: YueLab-Input-Skin-rep1

value: Skin


title: YueLab-Input-Skin-rep2


title: x070_b1_p1_F09_1c_M_S70: Mouse embryonic stomach at E13.5 Batch1

value: embryonic day 13.5


title: x069_b2_p4_E09_1c_M_S69: Mouse embryonic stomach at E13.5 Batch2


title: KRG092419_Aag2_rIgG_Exp7A

description: Ago-CLIP RNA


title: x070_b2_p4_F09_1c_M_S70: Mouse embryonic stomach at E13.5 Batch2


title: MCPR3TUCR (MCPR3)


title: MCPR2TUCR (MCPR2)


title: YueLab-Input-Muscle-rep2

value: Tuebingen

value: Muscle


title: YueLab-Input-Muscle-rep1


title: MCPR1TUCR (MCPR1)


title: x068_b2_p4_D09_1c_M_S68: Mouse embryonic stomach at E13.5 Batch2


title: KRG092419_Aag2_mIgG_Exp7B

description: Ago-CLIP RNA

value: UV 254 nm


title: KRG092419_Aag2_mIgG_Exp7A

description: Ago-CLIP RNA

value: mIgG (control antibody for Ago2)


title: YueLab-Input-Liver-rep2

value: Liver


title: KRG092419_Aag2_Ago2_Exp7B

description: Ago-CLIP RNA

value: standard linker ligation (not processed, de-multiplexed)


title: MC192TUCR (MC192)

value: Normal

value: Normal oral mucosa


title: x068_b1_p1_D09_1c_M_S68: Mouse embryonic stomach at E13.5 Batch1


title: YueLab-Input-Liver-rep1


title: MC191TUCR (MC191)

value: oral brush


title: KRG092419_Aag2_Ago1_Exp7A

description: Ago-CLIP RNA


title: x069_b1_p1_E09_1c_M_S69: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1


title: YueLab-Input-Kidney-rep1

value: Kidney


title: MC190TUCR (MC190)


title: x067_b1_p1_C09_1c_M_S67: Mouse embryonic stomach at E13.5 Batch1

value: stomach


title: x066_b2_p4_B09_1c_M_S66: Mouse embryonic stomach at E13.5 Batch2


title: MC188TUCR (MC188)


title: MC189TUCR (MC189)


title: KRG092419_Aag2_Ago1_Exp7B

description: Ago-CLIP RNA


title: YueLab-Input-Intestine-rep2

value: Intestine


title: MC187TUCR (MC187)


title: KRG091218_aegypti_rIgG_Exp4B

description: Ago-CLIP RNA

value: Orlando


title: KRG091218_aegypti_rIgG_Exp4A

description: Ago-CLIP RNA

value: rIgG (control antibody for Ago1)


title: x065_b2_p4_A09_1c_M_S65: Mouse embryonic stomach at E13.5 Batch2


title: MC186TUCR (MC186)

value: SCC

value: Oral Squamous Cell Carcinoma


title: YueLab-Input-Heart-rep1

value: Tuebingen

value: Heart


title: YueLab-Input-Intestine-rep1


title: KRG091218_aegypti_Ago1_Exp4F

description: Ago-CLIP RNA

value: UV 254 nm


title: YueLab-Input-Kidney-rep2


title: YueLab-Input-Colon-rep2

value: Colon


title: MC185TUCR (MC185)


title: KRG092419_Aag2_Ago2_Exp7A

description: Ago-CLIP RNA


title: KRG091218_aegypti_Ago1_Exp4E

description: Ago-CLIP RNA


title: x064_b2_p4_H08_1c_E_S64: Mouse embryonic stomach at E13.5 Batch2

value: embryonic day 13.5


title: x067_b2_p4_C09_1c_M_S67: Mouse embryonic stomach at E13.5 Batch2


title: x065_b1_p1_A09_1c_M_S65: Mouse embryonic stomach at E13.5 Batch1


title: YueLab-Input-Colon-rep1


title: MC182TUCR (MC182)


title: KRG091218_aegypti_Ago1_Exp4D

description: Ago-CLIP RNA

value: standard linker ligation (not processed, de-multiplexed)


title: x064_b1_p1_H08_1c_E_S64: Mouse embryonic stomach at E13.5 Batch1


title: MC180TUCR (MC180)

value: Normal


title: KRG091218_aegypti_Ago1_Exp4C

description: Ago-CLIP RNA


title: x066_b1_p1_B09_1c_M_S66: Mouse embryonic stomach at E13.5 Batch1


title: x063_b2_p4_G08_1c_E_S63: Mouse embryonic stomach at E13.5 Batch2


title: RL77-570 (RL77-570)

value: Normal oral mucosa


title: MC179TUCR (MC179)

value: oral brush


title: x063_b1_p1_G08_1c_E_S63: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1


title: YueLab-H3K4me3-embryonic-Brain-rep1

description: YueLab-ChIP-seq-embryonic-Brain_H3K4me3_merged.narrowPeak

value: embryonic-Brain

tag: chip-seq antibody

value: H3K4me3 antibody (EMD Millipore, 07-495)


title: YueLab-H3K4me3-embryonic-Brain-rep2

value: H3K4me3 antibody (EMD Millipore, 07-496)


title: KRG091218_aegypti_Ago1_Exp4A

description: Ago-CLIP RNA

value: Orlando


title: KRG091218_aegypti_Ago1_Exp4B

description: Ago-CLIP RNA


title: KRG091218_Aag2_rIgG_Exp4B

description: Ago-CLIP RNA

value: rIgG (control antibody for Ago1)


title: KRG091218_Aag2_rIgG_Exp4A

description: Ago-CLIP RNA


title: brain_scATAC-seq_rep1

data_processing:
RNA-seq reads were aligned to zv10 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM
ChIP-seq and ATAC-seq reads were aligned to zv10 genome assembly using Bowtie2;H3K27ac, H3K4me3 ChIP-seq were called using MACS2 with the following  setting: ChIP-seq q-value <10e-2, p-value<10e-5, Change>1,FC>2. ATAC-seq: q-value<10e-2 and p-value<10e-5.For the ATAC-seq, the peak length were fixed to 500 bp. We only selected the peak with the most significant signal if several peaks overlap with each other in each tissue.Since the H3K9me3 and H3K9me2 makers are broad domain, we called the peak using Homer with the parameter “-region -size 1000”, and peaks within 5 kb were merged together.
HiC matrix was generated using HiC-Pro
WGBS data were mapped to in silico bisulfite-converted zebrafish genome reference by using Bismark
For the scATAC-seq, the BCL files generated from sequencing were used as inputs to the 10X Genomics Cell Ranger ATAC-seq pipeline; then the FASTQ files were aligned to the GRCz10 genome using BWA and the fragments with MAPQ>30 were kept for further analysis and each fragment is associated with a single cell barcode.
Genome_build: zv10(GRCz10)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi-C for each Sample.**All replicates were merged

growth_protocol:
RNA-seq: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions
ChIP-seq, ATAC-seq, Hi-C and WGBS: Ault Tuebingen zebrafish were raised under standard laboratory conditions

extract_protocol:
RNA-seq: For each RNA-seq experiment, the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk, ten 1-dpf fish were dechorionated with pronase and trunk were cut off for RNA-seq. For embryonic neuron, green cells from Tg(Huc:Kaede) cells were sorted by FACS and approxinately 20,000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol (Invitrogen).
RNA-seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit (Agilent) according to the manufacturer’s protocol. Briefly, polyA RNA was purified from 1000 ng of total RNA using oligo (dT) beads (Invitrogen). Extracted RNA was first fragmented, then followed by reverse transcription, end repair, adenylation, adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent) and Kapa Library Quantification Kit (Kapa Biosystems) and then followed by pair-end 2X 50 bp high-throughput sequencing using HiSeq 2500 (Illumina).
ChIP-seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP-seq lysis buffer (20 mM Tris-HCl, pH 8.0, 1% SDS, 50 mM EDTA, 1X proteinase inhibitor cocktail). Next, 900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W, duty factor 5, 200 per burst. Sonication time is variable, depending on tissue types. To check the chromatin fragmentation size, 20 µL of input chromatin was reverse crosslinked in elution buffer (20 mM Tris-HCl, pH 8.0, 1% SDS, 1 mM EDTA) at 65 °C overnight, treated with Rnase A and proteinase K and purified by phenol-chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100-300 bp. To prepare antibody-beads complex, 3 µg of histone H3K27ac antibody (Active Motif, 39133) or H3K4me3 antibody (EMD Millipore, 07-473) was mix with 12 µL M-280 sheep anti-rabbit IgG Dynabeads (ThermoFisher, 11203D) in 150 µL of 5 mg/mL BSA/1X PBS buffer, with rotation at 4 °C for 3 h. After incubation, antibody-beads complex was washed once with BSA/1X PBS buffer. About 200 µg chromatin was used per IP. Equal volume of master mix (1X TE, 2% Triton X-100, 0.2% sodium deoxycholate, 2X proteinase inhibitor cocktail) was mixed with 200 µg chromatin and then incubated with antibody-beads complex overnight with rotation. The next morning, the beads were washed 5 times with cold RIPA wash buffer (20 mM Tris-HCl, pH 8.0, 1% NP-40, 0.7% sodium deoxycholate, 500 mM LiCl, 1 mM EDTA, 1X proteinase inhibitor cocktail). Then the chromatin bound on the beads was eluted by 150 µL of elution buffer at 65 °C for 30 min.
ChIP-seq: To prepare the library, eluted chromatin was reverse crosslinked and purified by phenol-chloroform extraction. Then DNA was end-repaired by END-IT DNA end-repair kit (Epicentre, ER81050) according to kit’s protocol, added A using Klenow  fragment (3’->5’ exo-) (NEB, M0212S), ligated with Illumina TruSeq adaptor (Illumina, FC-121-3001) and subsequently amplified by PCR (Roche, kk2601). The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit (Agilent). The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp.
ATAC-seq: Tuebingen adult tissues were ground in liquid nitrogen,resuspended in 1 mL of lysis buffer (1X PBS, 0.2% NP-40, 5% BSA, 1 mM DTT, protease inhibitors), followed by incubation at  4 °C for 10 min on an overhead shaker. After that, lysate was filtered through 40 m cell strainer and nuclei were collected at 1000X g for 5 min.
ATAC-seq: Tagmentation was performed immediately according to ATAC-seq protocol reported previously(Buenrostro et al., 2013)
Hi-C: For brain tissue, two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer (20 mM Tris-HCl, pH 8.0, 10 mM NaCl, 20 mM EDTA). Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue, 60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. After neutralization with FBS, muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation.
Hi-C: Hi-C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocol(Rao et al., 2014). The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent) and Kapa Library Quantification Kit (Kapa Biosystems) and then followed by pair-end 2X 100 bp high-throughput sequencing using HiSeq 2500  or HiSeq 4000(Illumina).
WGBS: Tübingen adult tissues were dissected, and the genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen, 69504). Then 1 µg of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation-Gold Kits
WGBS: The final libraries were prepared using the Accel-NGS® Methyl-Seq DNA Library Kit.
scATAC-seq: Single-cell ATAC-seq (scATAC-seq) was performed in one female brain and one male brain, respectively, on the 10X Genomics platform. To isolate nuclei, freshly dissected single brain was transferred to 1 mL NbActiv1 medium (BrainBits, NbActiv1 500) with a wide-bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular-bore pipette tips followed by filtering through a 30 µm cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 °C and then lysed in 100 µL chilled 0.1X Lysis Buffer (10 mM Tris HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 1% BSA,0.01% Tween-20, 0.01% NP40 and 0.001% digitonin) on ice for 5 min. Then 1 mL chilled Wash Buffer (10 mM Tris HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20) was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 °C. At last, 300 µL chilled Diluted Nuclei Buffer (10x Genomics, PN 2000153/2000207) was added to resuspend the nuclei. The nuclei were filtered again using a 30 µm cell strainer before cell counting
scATAC-seq: Around 12,000 nuclei were used for one Tn5 tagmentation reaction, and the scATAC-seq library was prepared and sequenced exactly according to the company’s user guide.

value: Brain


title: YueLab-H3K4me3-embryonic-Trunk-rep1

description: YueLab-ChIP-seq-embryonic-Trunk_H3K4me3_merged.narrowPeak

value: embryonic-Trunk

value: H3K4me3 antibody (EMD Millipore, 07-493)


title: x061_b1_p1_E08_10c_E_S61: Mouse embryonic stomach at E13.5 Batch1

value: stomach


title: YueLab-H3K4me3-Testis-rep2

description: YueLab-ChIP-seq-Testis_H3K4me3_merged.narrowPeak

value: Tuebingen

value: Testis

value: H3K4me3 antibody (EMD Millipore, 07-492)


title: YueLab-Input-Brain-rep1


title: x061_b2_p4_E08_10c_E_S61: Mouse embryonic stomach at E13.5 Batch2

value: embryonic day 13.5


title: YueLab-H3K4me3-Testis-rep1

value: H3K4me3 antibody (EMD Millipore, 07-491)


title: KRG091218_Aag2_Ago1_Exp4C

description: Ago-CLIP RNA

value: UV 254 nm

value: standard linker ligation (not processed, de-multiplexed)


title: KRG091218_Aag2_Ago1_Exp4B

description: Ago-CLIP RNA


title: x060_b1_p1_D08_1c_E_S60: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1


title: x060_b2_p4_D08_1c_E_S60: Mouse embryonic stomach at E13.5 Batch2


title: x062_b2_p4_F08_0c_E_S62: Mouse embryonic stomach at E13.5 Batch2


title: YueLab-H3K4me3-Spleen-rep2

description: YueLab-ChIP-seq-Spleen_H3K4me3_merged.narrowPeak

value: Spleen

value: H3K4me3 antibody (EMD Millipore, 07-490)


title: MC175TUCR (MC175)

value: Normal

value: oral brush

value: Normal oral mucosa


title: brain_scATAC-seq_rep2

value: Brain


title: x059_b2_p4_C08_1c_E_S59: Mouse embryonic stomach at E13.5 Batch2


title: YueLab-H3K4me3-Spleen-rep1

value: H3K4me3 antibody (EMD Millipore, 07-489)


title: KRG091218_Aag2_Ago1_Exp4A

description: Ago-CLIP RNA


title: YueLab-H3K4me3-embryonic-Trunk-rep2

value: embryonic-Trunk

value: H3K4me3 antibody (EMD Millipore, 07-494)


title: BT549-PTEN-Rep1 (control)

description:
Re-analysis of GSM3538843
SRR8393504 (same as SRR12025829)
SRR8393505 (same as SRR12025830)

value: PTEN over-expressed

value: control


title: fatty acid

type: RNA

city: Torrance

first: Robert

middle: Allen

last: Gelfand

address: 1124 W Carson St

department: surgery/urology

institute: los angeles biomedical research institute

description: extracted RNA

hyb_protocol: as per Affymetrix

scan_protocol: as per Affymetrix

data_processing: RNA levels were presented as rma. The numerical values represent an arbitrary scale based on relative expression level.

label: biotin

organism: Rattus norvegicus

source_name: skeletal muscle derived stem cells

label_protocol: RNA was analyzed by the Affymetrix gene chip procedure at UCLA core lab by the Affymetrix protocol.

growth_protocol: Muscle derived stem cells were isolated from rat by the plating method and were carried in 25 sq cm flasks or in 6 well plates

extract_protocol: Cells were washed once with phosphate buffered saline and RNA was extracted using the Qiagen RNeasy Plus Micro kit.

treatment_protocol: In a six well plate, cells were subjected to 100 mg/dl cholesterol in the presence of carrier cyclodextrin; alternatively, sodium palmitate was added.

value: skeletal muscle derived stem cells

value: male


title: x059_b1_p1_C08_1c_E_S59: Mouse embryonic stomach at E13.5 Batch1

value: stomach

value: embryonic day 13.5


title: high glucose control

description: extracted RNA


title: KRG091819_Aag2_rIgG_Exp6B

description: Ago-CLIP RNA

value: UV 254 nm

value: rIgG (control antibody for Ago1)

value: BrdU (UMI is already appended to read name in order to  de-multiplex; no other processing)


title: x062_b1_p1_F08_0c_E_S62: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1


title: YueLab-H3K4me3-Skin-rep2

description: YueLab-ChIP-seq-Skin_H3K4me3_merged.narrowPeak

value: Tuebingen

value: Skin

value: H3K4me3 antibody (EMD Millipore, 07-488)


title: x058_b2_p4_B08_1c_E_S58: Mouse embryonic stomach at E13.5 Batch2


title: KRG091819_Aag2_rIgG_Exp6A

description: Ago-CLIP RNA


title: low glucose control

description: extracted RNA


title: YueLab-H3K4me3-Muscle-rep2

description: YueLab-ChIP-seq-Muscle_H3K4me3_merged.narrowPeak

value: Muscle

value: H3K4me3 antibody (EMD Millipore, 07-486)


title: YueLab-H3K4me3-Skin-rep1

value: H3K4me3 antibody (EMD Millipore, 07-487)


title: KRG121817B_Aag2_rIgG_Exp2B

description: Ago-CLIP RNA

value: standard linker ligation (not processed, de-multiplexed)


title: x058_b1_p1_B08_1c_E_S58: Mouse embryonic stomach at E13.5 Batch1


title: x057_b2_p4_A08_1c_E_S57: Mouse embryonic stomach at E13.5 Batch2


title: KRG091819_Aag2_mIgG_Exp6B

description: Ago-CLIP RNA

value: mIgG (control antibody for Ago2)


title: KRG121817B_Aag2_rIgG_Exp2A

description: Ago-CLIP RNA


title: YueLab-H3K4me3-Muscle-rep1

value: H3K4me3 antibody (EMD Millipore, 07-485)


title: KRG091819_Aag2_Ago2_Exp6B

description: Ago-CLIP RNA


title: cholesterol

description: extracted RNA

value: skeletal muscle derived stem cells


title: YueLab-H3K4me3-Liver-rep2

description: YueLab-ChIP-seq-Liver_H3K4me3_merged.narrowPeak

value: Liver

value: H3K4me3 antibody (EMD Millipore, 07-484)


title: x057_b1_p1_A08_1c_E_S57: Mouse embryonic stomach at E13.5 Batch1

value: stomach

value: embryonic day 13.5


title: KRG091819_Aag2_Ago2_Exp6A

description: Ago-CLIP RNA

value: UV 254 nm


title: KRG121817A_Aag2_rIgG_Exp1B

description: Ago-CLIP RNA

value: rIgG (control antibody for Ago1)


title: KRG121817A_Aag2_rIgG_Exp1A

description: Ago-CLIP RNA


title: YueLab-H3K4me3-Liver-rep1

value: H3K4me3 antibody (EMD Millipore, 07-483)


title: KRG091819_Aag2_Ago1_Exp6B

description: Ago-CLIP RNA

value: BrdU (UMI is already appended to read name in order to  de-multiplex; no other processing)


title: x056_b2_p4_H07_1c_M_S56: Mouse embryonic stomach at E13.5 Batch2

value: mixed C57BL/6 CD1


title: LZ serum

description: extracted RNA

value: male


title: KRG121817B_Aag2_mIgG_Exp2B

description: Ago-CLIP RNA


title: OZ serum

description: extracted RNA


title: KRG091819_Aag2_Ago1_Exp6A

description: Ago-CLIP RNA


title: KRG091819_Aag2_mIgG_Exp6A

description: Ago-CLIP RNA


title: x056_b1_p1_H07_1c_M_S56: Mouse embryonic stomach at E13.5 Batch1


title: YueLab-H3K4me3-Kidney-rep2

description: YueLab-ChIP-seq-Kidney_H3K4me3_merged.narrowPeak

value: Tuebingen

value: Kidney

value: H3K4me3 antibody (EMD Millipore, 07-482)


title: x055_b2_p4_G07_1c_M_S55: Mouse embryonic stomach at E13.5 Batch2


title: KRG121817B_Aag2_mIgG_Exp2A

description: Ago-CLIP RNA

value: standard linker ligation (not processed, de-multiplexed)


title: KRG091819_aegypti_rIgG_Exp6B

description: Ago-CLIP RNA

value: Orlando


title: KRG091819_aegypti_rIgG_Exp6A

description: Ago-CLIP RNA


title: YueLab-H3K4me3-Kidney-rep1

value: H3K4me3 antibody (EMD Millipore, 07-481)


title: KRG121817A_Aag2_mIgG_Exp1B

description: Ago-CLIP RNA

value: mIgG (control antibody for Ago2)


title: KRG121817A_Aag2_mIgG_Exp1A

description: Ago-CLIP RNA


title: YueLab-H3K4me3-Intestine-rep1

description: YueLab-ChIP-seq-Intestine_H3K4me3_merged.narrowPeak

value: Intestine

value: H3K4me3 antibody (EMD Millipore, 07-479)


title: YueLab-H3K4me3-Intestine-rep2

value: H3K4me3 antibody (EMD Millipore, 07-480)


title: KRG121817B_Aag2_Ago2_Exp2B

description: Ago-CLIP RNA


title: KRG091819_aegypti_mIgG_Exp6B

description: Ago-CLIP RNA


title: x054_b1_p1_F07_1c_M_S54: Mouse embryonic stomach at E13.5 Batch1

value: stomach

value: embryonic day 13.5


title: KRG121817B_Aag2_Ago2_Exp2A

description: Ago-CLIP RNA

value: UV 254 nm


title: x053_b2_p4_E07_1c_M_S53: Mouse embryonic stomach at E13.5 Batch2


title: YueLab-H3K4me3-Heart-rep1

description: YueLab-ChIP-seq-Heart_H3K4me3_merged.narrowPeak

value: Heart

value: H3K4me3 antibody (EMD Millipore, 07-477)


title: KRG121817A_Aag2_Ago2_Exp1B

description: Ago-CLIP RNA


title: x053_b1_p1_E07_1c_M_S53: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1


title: YueLab-H3K4me3-Colon-rep2

description: YueLab-ChIP-seq-Colon_H3K4me3_merged.narrowPeak

value: Colon

value: H3K4me3 antibody (EMD Millipore, 07-476)


title: YueLab-H3K4me3-Colon-rep1

value: Tuebingen

value: H3K4me3 antibody (EMD Millipore, 07-475)


title: KRG121817A_Aag2_Ago2_Exp1A

description: Ago-CLIP RNA

value: standard linker ligation (not processed, de-multiplexed)


title: x052_b2_p4_D07_1c_M_S52: Mouse embryonic stomach at E13.5 Batch2


title: x055_b1_p1_G07_1c_M_S55: Mouse embryonic stomach at E13.5 Batch1


title: YueLab-H3K4me3-Brain-rep2

description: YueLab-ChIP-seq-Brain_H3K4me3_merged.narrowPeak

value: Brain

value: H3K4me3 antibody (EMD Millipore, 07-474)


title: KRG121817B_Aag2_Ago1_Exp2B

description: Ago-CLIP RNA


title: KRG091819_aegypti_Ago1_Exp6A

description: Ago-CLIP RNA

value: Orlando

value: BrdU (UMI is already appended to read name in order to  de-multiplex; no other processing)


title: KRG091819_aegypti_Ago1_Exp6B

description: Ago-CLIP RNA


title: x054_b2_p4_F07_1c_M_S54: Mouse embryonic stomach at E13.5 Batch2


title: x052_b1_p1_D07_1c_M_S52: Mouse embryonic stomach at E13.5 Batch1


title: KRG091819_aegypti_mIgG_Exp6A

description: Ago-CLIP RNA

value: mIgG (control antibody for Ago2)


title: x051_b2_p4_C07_1c_M_S51: Mouse embryonic stomach at E13.5 Batch2


title: YueLab-H3K4me3-Brain-rep1

value: H3K4me3 antibody (EMD Millipore, 07-473)


title: YueLab-H3K4me3-Heart-rep2

value: H3K4me3 antibody (EMD Millipore, 07-478)


title: KRG121817B_Aag2_Ago1_Exp2A

description: Ago-CLIP RNA


title: KRG090619_Aag2_rIgG_Exp5A

description: Ago-CLIP RNA

value: rIgG (control antibody for Ago1)


title: KRG090619_Aag2_rIgG_Exp5B

description: Ago-CLIP RNA

value: UV 254 nm


title: YueLab-H3K27ac-embryonic-Brain-rep2

description: YueLab-ChIP-seq-embryonic-Brain_H3K27ac_merged.narrowPeak

value: embryonic-Brain

value: H3K27ac antibody (Active Motif, 39156)


title: KRG121817A_Aag2_Ago1_Exp1B

description: Ago-CLIP RNA


title: KRG091819_aegypti_Ago2_Exp6B

description: Ago-CLIP RNA


title: YueLab-H3K27ac-embryonic-Brain-rep1

value: H3K27ac antibody (Active Motif, 39155)


title: x050_b2_p4_B07_1c_M_S50: Mouse embryonic stomach at E13.5 Batch2

value: mixed C57BL/6 CD1

value: stomach

value: embryonic day 13.5


title: KRG090619_Aag2_mIgG_Exp5B

description: Ago-CLIP RNA


title: KRG121817A_Aag2_Ago1_Exp1A

description: Ago-CLIP RNA


title: YueLab-H3K27ac-embryonic-Trunk-rep2

description: YueLab-ChIP-seq-embryonic-Trunk_H3K27ac_merged.narrowPeak

value: Tuebingen

value: embryonic-Trunk

value: H3K27ac antibody (Active Motif, 39154)


title: KRG081018_Aag2_Ago1_Exp3B

description: Ago-CLIP RNA

value: standard linker ligation (not processed, de-multiplexed)


title: KRG091819_aegypti_Ago2_Exp6A

description: Ago-CLIP RNA

value: Orlando


title: KRG090619_Aag2_mIgG_Exp5A

description: Ago-CLIP RNA

value: BrdU (UMI is already appended to read name in order to  de-multiplex; no other processing)


title: x050_b1_p1_B07_1c_M_S50: Mouse embryonic stomach at E13.5 Batch1


title: YueLab-H3K27ac-embryonic-Trunk-rep1

value: H3K27ac antibody (Active Motif, 39153)


title: KRG081018_Aag2_rIgG_Exp3

description: Ago-CLIP RNA


title: KRG090619_Aag2_Ago2_Exp5A

description: Ago-CLIP RNA


title: KRG090619_Aag2_Ago1_Exp5B

description: Ago-CLIP RNA


title: YueLab-H3K27ac-Testis-rep2

description: YueLab-ChIP-seq-Testis_H3K27ac_merged.narrowPeak

value: Testis

value: H3K27ac antibody (Active Motif, 39152)


title: x048_b2_p4_H06_1c_E_S48: Mouse embryonic stomach at E13.5 Batch2


title: KRG081018_Aag2_Ago1_Exp3A

description: Ago-CLIP RNA


title: KRG090619_Aag2_Ago2_Exp5B

description: Ago-CLIP RNA


title: x051_b1_p1_C07_1c_M_S51: Mouse embryonic stomach at E13.5 Batch1


title: YueLab-H3K27ac-Testis-rep1

value: H3K27ac antibody (Active Motif, 39151)


title: KRG081018_aegypti_Ago1_Exp3C

description: Ago-CLIP RNA

value: UV 254 nm


title: KRG081018_aegypti_Ago1_Exp3A

description: Ago-CLIP RNA


title: YueLab-H3K27ac-Spleen-rep1

description: YueLab-ChIP-seq-Spleen_H3K27ac_merged.narrowPeak

value: Spleen

value: H3K27ac antibody (Active Motif, 39149)


title: KRG081018_aegypti_Ago1_Exp3B

description: Ago-CLIP RNA


title: BOV2 (BOV2)

organism: Bos taurus

value: Normal

value: oral brush

value: Normal oral mucosa


title: x048_b1_p1_H06_1c_E_S48: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1

value: stomach

value: embryonic day 13.5


title: KRG090619_Aag2_Ago1_Exp5A

description: Ago-CLIP RNA


title: x047_b1_p1_G06_1c_E_S47: Mouse embryonic stomach at E13.5 Batch1


title: YueLab-H3K27ac-Spleen-rep2

value: Tuebingen

value: H3K27ac antibody (Active Motif, 39150)


title: KRG090619_aegypti_rIgG_Exp5B

description: Ago-CLIP RNA

value: Orlando

value: rIgG (control antibody for Ago1)


title: KRG090619_aegypti_rIgG_Exp5A

description: Ago-CLIP RNA

value: BrdU (UMI is already appended to read name in order to  de-multiplex; no other processing)


title: BOV1 (BOV1)


title: YueLab-H3K27ac-Skin-rep2

description: YueLab-ChIP-seq-Skin_H3K27ac_merged.narrowPeak

value: Skin

value: H3K27ac antibody (Active Motif, 39148)


title: x049_b1_p1_A07_1c_M_S49: Mouse embryonic stomach at E13.5 Batch1


title: YueLab-H3K27ac-Skin-rep1

value: H3K27ac antibody (Active Motif, 39147)


title: x046_b2_p4_F06_1c_E_S46: Mouse embryonic stomach at E13.5 Batch2


title: x046_b1_p1_F06_1c_E_S46: Mouse embryonic stomach at E13.5 Batch1


title: KRG090619_aegypti_mIgG_Exp5A

description: Ago-CLIP RNA

value: UV 254 nm

value: mIgG (control antibody for Ago2)


title: x045_b2_p4_E06_1c_E_S45: Mouse embryonic stomach at E13.5 Batch2


title: YueLab-H3K27ac-Muscle-rep2

description: YueLab-ChIP-seq-Muscle_H3K27ac_merged.narrowPeak

value: Muscle

value: H3K27ac antibody (Active Motif, 39146)


title: KRG090619_aegypti_Ago2_Exp5B

description: Ago-CLIP RNA


title: AP12812TUCR (AP12812)

value: SCC

value: FFPE

value: Squamous Cell Carcinoma


title: x049_b2_p4_A07_1c_M_S49: Mouse embryonic stomach at E13.5 Batch2

value: mixed C57BL/6 CD1

value: stomach


title: x047_b2_p4_G06_1c_E_S47: Mouse embryonic stomach at E13.5 Batch2

value: embryonic day 13.5


title: KRG090619_aegypti_mIgG_Exp5B

description: Ago-CLIP RNA


title: YueLab-H3K27ac-Liver-rep1

description: YueLab-ChIP-seq-Liver_H3K27ac_merged.narrowPeak

value: Tuebingen

value: Liver

value: H3K27ac antibody (Active Motif, 39143)


title: YueLab-H3K27ac-Muscle-rep1

value: H3K27ac antibody (Active Motif, 39145)


title: YueLab-H3K27ac-Liver-rep2

value: H3K27ac antibody (Active Motif, 39144)


title: YueLab-H3K27ac-Kidney-rep1

description: YueLab-ChIP-seq-Kidney_H3K27ac_merged.narrowPeak

value: Kidney

value: H3K27ac antibody (Active Motif, 39141)


title: x044_b1_p1_D06_1c_E_S44: Mouse embryonic stomach at E13.5 Batch1


title: Induced - HeLa GCN10xp300gCol1 rep. 2

city: Newark

first: Ryan

last: Dikdan

state: NJ

address: 225 Warren St

department: Dept. of Medicine

institute: NJMS

data_processing:
Base calling was done with bcl2fastq2 v2.20.0.422
Fastq files were merged across lanes and trimmed with trimmomatic v0.39
The trimmed files were aligned to the human genome using bowtie2 v2.4.1 with the following command, for use in peak calling: bowtie2 --very-sensitive -k 20 -x GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index -1 sample1_R1.fastq -2 sample1_R2.fastq -S output.sam
Peak calling was done using Genrich with the following command: Genrich v0.6 -t sample1_aligned.sortedbyname.bam -o sample_1_peaks.narrowPeak -e chrM -E ENCFF356LFX.bed -r -v -j
BigWig coverage files were generate using deeptools v3.4.3 bamCoverage function: bamCoverage --normalizeUsing CPM -p 32 -bs 1 -b sample1_aligned.dedup.single.sortedbycoord.bam -o sample1_coverage.bw
Genome_build: GCA_000001405.15_GRCh38_no_alt_analysis_set
Supplementary_files_format_and_content: Called peaks in narrowPeak format and genomic coverage data in bigWig format for each sample, all details in supplementary file

source_name: cervical adenocarcinoma

growth_protocol: HeLa (American Type Culture Collection, Manassas, MA) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Sigma-Aldrich), supplemented with 2x Penicillin-Streptomycin (Corning, NY), 4 mM L-Glutamine (Sigma-Aldrich), and 10 % Fetal Bovine Serum (Gemini Bio-products, West Sacramento, CA) at 37 °C under the cover of 5 % CO2.

extract_protocol:
Active Motif ATAC-seq kit was used to tagment accessible DNA after nuclei purification
The aforementioned Active Motif ATAC-seq kit supplied i5 and i7 primers and Q5 polymerase for library generation

treatment_protocol: Steady state cell were cultured in the medium mentioned above, serum starved cells were cultured for 24 hr in the medium above but without any serum, and serum induced cells were induced from the serum starved state by addition of serum containing medium above supplemented with 200 nM phorbol 12-myristate 13-acetate (PMA) for four hours.  All three categories were cultured at 37 °C under the cover of 5 % CO2.

value: HeLa

tag: genotype/variation

value: HeLa GCN10xp300gCol1

tag: induction

value: treated with serum and PMA


title: Steady - HeLa GCN10xp300gControl

value: HeLa GCN10xp300gControl


title: KRG090619_aegypti_Ago2_Exp5A

description: Ago-CLIP RNA

value: Orlando

value: UV 254 nm

value: BrdU (UMI is already appended to read name in order to  de-multiplex; no other processing)


title: Induced - HeLa GCN10xp300gControl


title: YueLab-H3K27ac-Intestine-rep2

description: YueLab-ChIP-seq-Intestine_H3K27ac_merged.narrowPeak

value: Intestine

value: H3K27ac antibody (Active Motif, 39140)


title: x045_b1_p1_E06_1c_E_S45: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1

value: stomach

value: embryonic day 13.5


title: KRG090619_aegypti_Ago1_Exp5A

description: Ago-CLIP RNA


title: x043_b2_p4_C06_1c_E_S43: Mouse embryonic stomach at E13.5 Batch2


title: x044_b2_p4_D06_1c_E_S44: Mouse embryonic stomach at E13.5 Batch2


title: Steady - HeLa GCN10xp300gCol1


title: Induced - HeLa GCN10xp300gCol1 rep. 1


title: YueLab-H3K27ac-Intestine-rep1

value: Tuebingen

value: H3K27ac antibody (Active Motif, 39139)


title: Induced - HeLa p300gCol1

value: HeLa p300gCol1


title: x043_b1_p1_C06_1c_E_S43: Mouse embryonic stomach at E13.5 Batch1


title: x042_b1_p1_B06_1c_E_S42: Mouse embryonic stomach at E13.5 Batch1


title: Steady - HeLa p300gCol1


title: x042_b2_p4_B06_1c_E_S42: Mouse embryonic stomach at E13.5 Batch2


title: Induced - HeLa p300gCox2 rep. 2

value: HeLa p300gCox2


title: KRG090619_aegypti_Ago1_Exp5B

description: Ago-CLIP RNA


title: YueLab-H3K27ac-Colon-rep1

description: YueLab-ChIP-seq-Colon_H3K27ac_merged.narrowPeak

value: Colon

value: H3K27ac antibody (Active Motif, 39135)


title: YueLab-H3K27ac-Heart-rep1

description: YueLab-ChIP-seq-Heart_H3K27ac_merged.narrowPeak

value: Heart

value: H3K27ac antibody (Active Motif, 39137)


title: YueLab-H3K27ac-Colon-rep2

value: H3K27ac antibody (Active Motif, 39136)


title: Steady - HeLa p300gCox2 rep. 2

value: HeLa


title: x041_b2_p4_A06_1c_E_S41: Mouse embryonic stomach at E13.5 Batch2


title: Induced - HeLa p300gCox2 rep. 1

value: treated with serum and PMA


title: YueLab-H3K27ac-Brain-rep1

description: YueLab-ChIP-seq-Brain_H3K27ac_merged.narrowPeak

value: Brain

value: H3K27ac antibody (Active Motif, 39133)


title: YueLab-H3K27ac-Heart-rep2

value: H3K27ac antibody (Active Motif, 39138)


title: x041_b1_p1_A06_1c_E_S41: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1


title: YueLab-H3K27ac-Brain-rep2

value: H3K27ac antibody (Active Motif, 39134)


title: Steady - HeLa p300gCox2 rep. 1


title: x040_b1_p1_H05_1c_M_S40: Mouse embryonic stomach at E13.5 Batch1

value: stomach

value: embryonic day 13.5


title: Starved - HeLa p300gCox2

value: serum starved


title: Induced - HeLa rep. 2


title: YueLab-RNA-Seq-embryonic-Brain-rep2

molecule: polyA RNA

growth_protocol: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions

extract_protocol:
For each RNA-seq experiment, the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk, ten 1-dpf fish were dechorionated with pronase and trunk were cut off for RNA-seq. For embryonic neuron, green cells from Tg(Huc:Kaede) cells were sorted by FACS and approxinately 20,000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol (Invitrogen).
The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit (Agilent) according to the manufacturer’s protocol. Briefly, polyA RNA was purified from 1000 ng of total RNA using oligo (dT) beads (Invitrogen). Extracted RNA was first fragmented, then followed by reverse transcription, end repair, adenylation, adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent) and Kapa Library Quantification Kit (Kapa Biosystems) and then followed by pair-end 2X 50 bp high-throughput sequencing using HiSeq 2500 (Illumina).

value: Tuebingen

value: embryonic-Brain


title: x040_b2_p4_H05_1c_M_S40: Mouse embryonic stomach at E13.5 Batch2


title: x039_b2_p4_G05_1c_M_S39: Mouse embryonic stomach at E13.5 Batch2


title: gall bladder epithelium_non infected_replicate 1_vs_ΔcdtB infected_replicate 1

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

institute: Max Planck Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted dual-color raw data txt files were further analyzed using R and the associated BioConductor package limma. Agilent FE software processed green and red signals were extracted and within-array normalized using method LOESS followed by averaging of duplicated probes was applied.

source_name: ΔcdtB infected, replicate 1

label_protocol: RNA was labeled with the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: Human gall bladder epithelial cells were derived from patients that underwent cholecystectomy, stored in ice-cold PBS for up to 2 hours and the tissue was washed with PBS from the residual bile and mucus and it was incubated at 37°C with the mucosal side facing a solution of 0.2% collagenase type IV.  The mucosa was abraded thoroughly with the end of a glass microscope slide held at an angle of 45°every 5 minutes, for 4 times. The isolated cells were passed through a cell strainer with 70μm pores, spun down and 1 to 3 million cells were resuspended in a drop of 50μl matrigel. The polymerized matrigel drop was then supplemented with a medium based on Advanced/DMEM F12 (Invitrogen). The medium was changed twice a week. Every 7 to 10 days the organoids were spit with a ratio 1 to 3-4 by treating with Trypsin, then passing them 10 times through a heat-narrowed Pasteur pipet.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany).

treatment_protocol: Organoids were harvested 4 or 14 days (for early and differentiated organoids, respectively) after seeding. For infection experiments, 2D primary cells infected with /Salmonella/ paratyphi A were harvested 5 days post infection, FACS sorted based on the /Salmonella/ mCherry fluorescence to get 3x10^5 infected cells for RNA extraction.

value: gall bladder

value: epithelium

value: infected

value: S. paratyphi A, ΔcdtB

tag: culture type

tag: replicate

source_name: non infected, replicate 1

value: not infected


title: MRC5_24hr_R1_HiC

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee,Knoxville

data_processing:
Sequenced reads were mapped to the hg19 genome using bowtie2
Filtering was carried out using the dekkerlab-cMapping pipeline available on github
Iterative correction was performed using method described by Imakaev et al.
All processed Hi-C contact maps were scaled to a sum of 1 million
Genome_build: hg19
Supplementary_files_format_and_content: each .tar file contains the iteratively corrected and raw matrix.gz files for 40 kb, 250 kb, and 2.5 Mb in their respective directories

growth_protocol: Fibroblast lines were grown to confluency prior to X-ray exposure. For the GM12878 suspension cell line, cells were passaged at a density around 500,000 cells per 1 mL of medium. For irradiation experiments, GM12878 cells were grown to a density of 1 million cells per 1 mL of medium prior to X-ray exposure.

extract_protocol:
Briefly, 5-20 million cells were fixed with 1% formaldehyde, suspended in cell lysis buffer for permeabilization, and homogenized by douncing. Crosslinked chromatin was digested overnight with HindIII. Sticky ends were filled in with biotin-dCTP, and the blunt ends of interacting fragments were ligated together. DNA was purified by two phenol-chloroform extractions and ethanol precipitation. Biotin-dCTP at unligated ends was removed, and the DNA was sheared to a target size of 200-400 bp by a Covaris sonicator
Biotinylated DNA was pulled down using streptavidin coated magnetic beads and prepared for multiplex sequencing on an Illumina platform using the NEBNext Ultra II kit (NEB). All end preparation, adaptor ligation, and PCR amplification steps were carried out on bead bound DNA libraries.

treatment_protocol: Treated cells were X-rayed using 5 Gy X-rays and fixed for Hi-C after 30 mins, 24 hours, or split after 24 hours and allowed to recover for 5 days. The treated cells and their control counterparts were then fixed for Hi-C. ATM inhibitor treated cells were subjected to 10um KU-55933 for 1 hour before experiment began. ATMiC was subjected to KU-55933, but not IR.

tag: cell type

value: Lung fibroblast

tag: condition

tag: media


title: gall bladder epithelium_ΔcdtB infected_replicate 2_vs_non infected_replicate 2

source_name: non infected, replicate 2

source_name: ΔcdtB infected, replicate 2


title: gall bladder epithelium_early organoids P4_vs_differentiated organoids P4

source_name: differentiated organoids P4

value: not infected, harvested day 14

value: organoids

source_name: early organoids P4

value: not infected, harvested day 4


title: gall bladder epithelium_differentiated organoids P3_vs_early organoids P3

source_name: early organoids P3

source_name: differentiated organoids P3


title: Induced - HeLa rep. 1

value: HeLa

value: treated with serum and PMA


title: gall bladder epithelium_ΔcdtB infected_replicate 1_vs_WT infected_replicate 1

source_name: WT infected, replicate 1

value: S. paratyphi A, WT


title: gall bladder epithelium_WT infected_replicate 2_vs_ΔcdtB infected_replicate 2

source_name: WT infected, replicate 2


title: YueLab-RNA-Seq-embryonic-Brain-rep1


title: x039_b1_p1_G05_1c_M_S39: Mouse embryonic stomach at E13.5 Batch1

source_name: stomach cells

extract_protocol:
Single EpCAM+ and EpCAM- embryonic gastric cells were isolated by FACS directly in 96 well plates supplemented with buffer (Takara, Clontech). ERCC RNA Spike-In Mix (ThermoFisher) were added for quality and normalization controls. Plates were stored at -80°C.
50ng of total RNA was used for cDNA synthesis using Ovation v2.0 kit (NuGEN) according to manufacturer’s instructions. After cDNA fragmentation (Covaris), libraries were prepared using NEBNext v2.0 kit (NEB) according to manufacturer’s instructions.

value: mixed C57BL/6 CD1

value: stomach


title: YueLab-RNA-Seq-embryonic-Trunk-rep1

value: embryonic-Trunk


title: YueLab-RNA-Seq-embryonic-Trunk-rep2

value: Tuebingen


title: Steady - HeLa


title: MRC5_Control_R1_HiC

value: Control


title: Starved - HeLa

value: serum starved


title: HEK293 EHMT1_Ter H3 cells [RNA-seq]

city: North Coogee

first: Denise

last: Anderson

state: WA

address: 71 Caledonia Loop

country: Australia

institute: INSiGENe Pty Ltd

description: C1_HEKEHMT1_KO_H3_HJK3MDRXX_ACTAAGAT-AACCGCGG

data_processing:
TagDust2 was used to extract unique molecular identifiers which were appended to read names
Reads were mapped to the human reference genome GRCh38 using Hisat2 (v. 2.1.0), including SNP and transcript annotations
Duplicated reads were removed using umitools depup command (options: --paired --unpaired-reads=discard --chimeric-pairs=discard)
Known genes and transcripts were quantified from the corrected BAM alignment files using StringTie2 (options -eB -G)
The script prepDE.py from StringTie2 was used to construct gene expression tables
Genome_build: GRCh38
Supplementary_files_format_and_content: Both are csv files containing gene counts

source_name: HEK293 EHMT1_Ter

growth_protocol: DMEM/10%FCS/ penstrep

extract_protocol:
RNeasy Plus Mini Kit with gDNA eliminator (Qiagen)
TrueSeq stranded mRNA sample preparation on the Illumina NovaSeq 6000, 20 million 100bp single reads

treatment_protocol: grown to log phase

value: Human embryonic kidney cell line


title: x038_b1_p1_F05_0c_M_S38: Mouse embryonic stomach at E13.5 Batch1

value: embryonic day 13.5


title: x038_b2_p4_F05_0c_M_S38: Mouse embryonic stomach at E13.5 Batch2


title: HEK293 EHMT1_WT F8 cells [RNA-seq]

description: C4_HEKEHMT1_WT_F8_HJK3MDRXX_TCCAACGC-TTGGACTT

source_name: HEK293 EHMT1_WT


title: x036_b2_p4_D05_1c_M_S36: Mouse embryonic stomach at E13.5 Batch2


title: x037_b2_p4_E05_10c_M_S37: Mouse embryonic stomach at E13.5 Batch2


title: x037_b1_p1_E05_10c_M_S37: Mouse embryonic stomach at E13.5 Batch1


title: HEK293 EHMT1_Ter G3 cells [RNA-seq]

description: C6_HEKEHMT1_KO_G3_HJK3MDRXX_TTACAGGA-TGACAAGC


title: YueLab-RNA-Seq-Testis-rep1

value: Testis


title: YueLab-RNA-Seq-Testis-rep2


title: YueLab-RNA-Seq-Spleen-rep2

value: Spleen


title: gall bladder epithelium_WT infected_replicate 1_vs_non infected_replicate 1

value: gall bladder

value: epithelium

value: not infected

value: infected


title: BJ1_24hr_R1_HiC

value: Foreskin fibroblast

value: 4:1DMEM:Medium199,10%FBS, 0.01mgHygroB


title: gall bladder epithelium_non infected_replicate 2_vs_WT infected_replicate 2

value: S. paratyphi A, WT


title: HEK293 EHMT1_WT E9 cells [RNA-seq]

description: C8_HEKEHMT1_WT_E9_HJK3MDRXX_AATGCCTC-TCGATCCA


title: x035_b2_p4_C05_1c_M_S35: Mouse embryonic stomach at E13.5 Batch2

value: mixed C57BL/6 CD1


title: YueLab-RNA-Seq-Skin-rep1

value: Skin


title: x036_b1_p1_D05_1c_M_S36: Mouse embryonic stomach at E13.5 Batch1

value: stomach


title: HEK293 EHMT1_Ter E1 cells [RNA-seq]

description: C3_HEKEHMT1_KO_E1_HJK3MDRXX_CTTGGTAT-CCAAGTCC


title: BJ1_30min_R1_HiC


title: x035_b1_p1_C05_1c_M_S35: Mouse embryonic stomach at E13.5 Batch1


title: HEK293 EHMT1_WT E8 cells [RNA-seq]

description: C2_HEKEHMT1_WT_E8_HJK3MDRXX_GTCGGAGC-GGTTATAA


title: x034_b2_p4_B05_1c_M_S34: Mouse embryonic stomach at E13.5 Batch2


title: ATMhTERT_Control_R2_HiC

value: ATMhTERT

value: Skin fibroblast


title: YueLab-RNA-Seq-Muscle-rep1

value: Tuebingen

value: Muscle


title: x033_b2_p4_A05_1c_M_S33: Mouse embryonic stomach at E13.5 Batch2

value: embryonic day 13.5


title: YueLab-RNA-Seq-Spleen-rep1


title: YueLab-RNA-Seq-Skin-rep2


title: YueLab-RNA-Seq-Liver-rep2

value: Liver


title: YueLab-RNA-Seq-Muscle-rep2


title: YueLab-RNA-Seq-Liver-rep1


title: YueLab-RNA-Seq-Kidney-rep2

value: Kidney


title: ATMhTERT_24hr_R1_HiC