title: PE-520_LNPs

city: Zurich

first: Tanja

last: Rothgangl

address: Winterthurerstrasse, 190

department: Pharmacology and Toxicology

country: Switzerland

institute: UZH Zurich

data_processing:
Library strategy: targeted amplicon sequencing
CHANGE-seq pipeline (https://github.com/tsailabSJ/changeseq)
Genome_build: mm10

organism: Mus musculus

source_name: primary hepatocytes

growth_protocol: DMEM growth medium supplemented with 10% FBS and 1% P/S for HEK293T and Hepa1-6 cells

extract_protocol:
Detachment with TryplE, wash with PBS, lysis and DNA isolation for cell lines and whole tissue or primary hepatocyte isolation for in vivo samples.
targeted amplicon sequencing; CHANGE-seq preparation

treatment_protocol: per 48 well plate: 1 ug total DNA with 1.5 ul Lipofectamine2000, cells were treated with the respective base-editor targeting the indicated locus.In vivo treatment was delivery by AAV or Ad5 mediated delivery via systemic injection.

value: systemic injection of LNP

value: Prime-editor with pegRNA

value: targeted amplicon sequencing

tag: genotype

value: prime-edited genomic locus


title: PKU-longTerm-84-Liver

status: Public on Dec 29 2021

type: SRA

library_source: genomic

molecule: genomic DNA

source_name: whole liver lysate

value: systemic injection of AdV5


title: PKU-longTerm-87-Tail

source_name: whole tissue lysate


title: PKU-longTerm-84-PrimHep


title: PKU-longTerm-91-Liver


title: PE-533_LNPs


title: PE-502_LNPs


title: PKU-longTerm-87-Liver


title: PE-483_LNPs


title: PE-535_LNPs


title: PE-529_LNPs


title: PKU-longTerm-84-Tail


title: PKU-longTerm-91-PrimHep


title: HNSC024T1_Tr_S22

city: San Francisco

first: Bushra

last: Samad

state: CA

address: 505 Parnassus Ave

country: USA

institute: USCF Immunoprofiler

library_source: transcriptomic

data_processing:
RNAseq reads were first aligned to reference of rRNA and mitochondrial rRNA using BWA-mem
The remaining reads were aligned to the Ensembl GRCh38.85 transcriptome build using STAR
Genome_build: GRCh38

molecule: total RNA

organism: Homo sapiens

source_name: Tumor assocaited CD4+ CD25+ Regulatory T cell sorted by flow cytometry from a primary tumor specimen located in the Head and Neck region

extract_protocol:
The mRNA was isolated via DinaBead Direct, then converted into amplified   cDNA using Tecan Ovation RNA-Seq System V2 kit, following the manufacturer protocol.
The dsDNA went through tagmentation, amplification and clean up with   AMPure XP beads steps, using the Illumina Nextera XT DNA Library Prep Kit. Quality control analysis was performed on the resulting pooled libraries with the Agilent Bioanalyzer HS DNA chip to assess fragment size distribution and concentration

tag: tissue

value: Head & Neck

tag: sorted compartment

value: treg

tag: disease

value: Head & Neck cancer


title: PE-480_LNPs


title: PE-479_LNPs


title: PKU-longTerm-87-PrimHep


title: PE-478_LNPs


title: MCF-10A expressed with EGFP-ARHGAP4

type: RNA

city: Toyonaka

first: Shinji

last: Degcuhi

state: Osaka

address: Machikaneyama 1-3

department: Mechanical Science and Bioengineering

country: Japan

institute: Osaka University

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

label: biotin

source_name: MCF-10A expressed with EGFP-ARHGAP4

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

extract_protocol: Tota RNAs were extracted using PureLink RNA mini kit (Thermo Fischer Scientific). cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer.

tag: cell line

tag: cell type

value: mammary epithelial cells

tag: genotype/variation


title: MCF-10A expressed with EGFP

source_name: MCF-10A expressed with EGFP

value: EGFP vector


title: IPIHEP021T1_rna_tregs_S14

source_name: Tumor assocaited CD4+ CD25+ Regulatory T cell sorted by flow cytometry from a primary Liver tumor specimen

value: Liver

value: Hepatobiliary cancer


title: PE-451_LNPs


title: V ckit+

city: Tianjin

first: Guo Guang

last: Zheng

state: Tianjin

address: Blood Hospital,288 Nanjing Road,Heping District

department: Institute of Hematology & Blood Hospital

country: China

institute: Chinese Academy of Medical Science& Peking Union  Medical College

description: Gene expression after transplanted leukemia cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting forAgilent-028005 SurePrint G3 Mouse GE 8x60K Microarrayand Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Leukemia Cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mouse AML was induced by expressing MLL-AF9 in mouse HSPCs. Sorted GFP+ AML BM cells were cultured within 12h prior to virus infection in Iscove's Modified Dulbecco's Medium (IMDM) with 10% fetal bovine serum (FBS) and 1% Streptomycin and penicillin (s/p).Then, cells were infected twice and sorted GFP+BFP+ leukemia cells were transplanted into 6-8 week-old C57BL/6J mice. BM and spleen cells were collected for further study after three transplantations.

extract_protocol: Exact total RNA by Trizol  following the manufacturer's protocol

treatment_protocol: Each group was sorted by FACS, then lysis in Trizol agent.

value: Bone Marrow

tag: strain

tag: age

tag: sample group

value: c-kit positive cells (V c-kit+)


title: wP2X7

value: overexpressed wide type P2X7 leukemia cells (wP2X7)


title: V ckit-

value: c-kit negative cells (V c-kit-)


title: HNSC024T1_Li_S50

source_name: Tumor infiltrating viable cells sorted by flow cytometry from a primary tumor specimen located in the head and neck region

value: live


title: V total

value: total cells (V total)


title: DNMT1-20-3-PrimHep

value: Prime-editor with pegRNA


title: HEP017T1_My_S56

source_name: Tumor assocaited HLA DR+ CD11b+ CD3-CD1920-CD56- myeloid cells  sorted by flow cytometry from a primary Liver tumor specimen

value: myeloid


title: HNSC021T1_Tr_S27


title: HEP017T1_Tr_S81


title: DNMT1-20-3-Liver

value: targeted amplicon sequencing

value: prime-edited genomic locus


title: DNMT1-20-2-Tail

value: systemic injection of AdV5


title: DNMT1-20-1-Tail


title: HEP017T1_Li_S86

source_name: Tumor infiltrating viable cells sorted by flow cytometry from a primary Liver tumor specimen


title: DNMT1-20-1-PrimHep


title: HEP015T1Li_S90_S34


title: HEP016T1Li_S15

source_name: Tumor infiltrating viable cells sorted by flow cytometry from a metastatic Liver tumor specimen


title: HEP013T1Tu_S10

source_name: CD45- CD90- CD44- Tumor cells sorted by flow cytometry from a primary liver tumor specimen

value: tumor


title: HEP016T1Tu_S29

source_name: CD45- CD90- CD44- Tumor cells sorted by flow cytometry from a metastatic liver tumor specimen


title: HEP013T1Tr_S46

value: treg


title: DNMT1-10-1-AdV-Liver


title: DNMT1-10-2-AdV-PrimHep


title: DNMT1-5-3-AdV-PrimHep


title: DNMT1-10-2-AdV-Liver


title: HEP013T1My_S30


title: DNMT1-5-3-AdV-Liver


title: DNMT1-5-2-AdV-PrimHep


title: IPIHEP016_T1_rna_treg_S25

source_name: Tumor assocaited CD4+ CD25+ Regulatory T cell sorted by flow cytometry from a metastatic Liver tumor specimen


title: DNMT1-20-1-Liver


title: HEP012T1St_S14

source_name: CD45- CD90+ CD44+ stromal cells  sorted by flow cytometry from a primary liver tumor specimen

value: stroma


title: HEP012T1Tc_S17

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary Liver tumor specimen

value: tcell


title: HEP013T1Li_S224

value: Liver


title: HEP012T1Tr_S16

value: Hepatobiliary cancer


title: DNMT1-5-1-AdV-PrimHep

source_name: primary hepatocytes


title: HEP012T1My_S13


title: DNMT1-1-2-AdV-PrimHep


title: DNMT1-5-1-AdV-Liver

source_name: whole liver lysate


title: DNMT1-1-2-AdV-Liver


title: DNMT1-10-1-AdV-PrimHep


title: HEP012T1Li_S9


title: DNMT1-1-1-AdV-Tail

source_name: whole tissue lysate


title: DNMT1-1-2-AdV-Tail


title: HEP003T1_My_S41


title: HEP003T1_Li_S3


title: HEP003T1_Tr_S70


title: HEP003T1_Tr_S14


title: PKU-tail-2

value: systemic injection of GLAdV


title: DNMT1-1-1-AdV-PrimHep


title: DNMT1-1-1-AdV-Liver


title: PKU-tail-1


title: IPIHEP002_T1_rna_treg_S28


title: HEP003T1_Ep_S42

source_name: CD45- CD90- CD44- EPCAM+ Tumor cells sorted by flow cytometry from a primary liver tumor specimen

value: epcam


title: PKU-tail-3


title: DNMT1-5-2-AdV-Liver


title: HEP001T1_Li_S71


title: PKU-PE2-35ul-PrimHep-4


title: PKU-PE2-35ul-PrimHep-3


title: PKU-PE2-35ul-Liver-4


title: PKU-PE2-35ul-PrimHep-1


title: PKU-PE2-35ul-PrimHep-2


title: IPIGYN125T1_rna_treg_S51

source_name: Tumor assocaited CD4+ CD25+ Regulatory T cell sorted by flow cytometry from a primary Gynecologic tumor specimen

value: Uterus & adnexa

value: Gynecologic cancer


title: IPIGYN125T1_rna_stroma_S59

source_name: CD45- CD90+ CD44+ stromal cells  sorted by flow cytometry from a primary Gynecologic tumor specimen


title: PKU-PE2-35ul-Liver-3


title: PKU-PE2-35ul-Liver-1


title: IPIGYN124T1_rna_tregs_S41


title: PKU-gutless-nb-PrimHep-5


title: PKU-gutless-nb-PrimHep-3


title: IPIGYN124T1_rna_epcam_S44

source_name: CD45- CD90- CD44- EPCAM+ Tumor cells sorted by flow cytometry from a primary Gynecologic tumor specimen


title: PKU-gutless-nb-PrimHep-2


title: IPIGYN116T1_rna_tregs_S31


title: PKU-gutless-nb-PrimHep-1


title: PKU-gutless-nb-Liver-5


title: HEP001T1_Tr_S33

source_name: Tumor assocaited CD4+ CD25+ Regulatory T cell sorted by flow cytometry from a primary Liver tumor specimen


title: PKU-gutless-nb-PrimHep-4


title: PKU-PE2-35ul-PrimHep-5


title: PKU-gutless-nb-Liver-3


title: PKU-gutless-nb-Liver-1


title: PKU-gutless-nb-Liver-2


title: PKU-gutless-nb-Liver-4


title: IPIGYN116T1_rna_epcam_S50


title: IPIGYN110_T1_rna_Treg_S29


title: IPIGYN109T1_rna_stroma_S11


title: IPIGYN110_T1_rna_EpCAM_S12


title: PKU-PE2-35ul-Liver-2


title: IPIGYN109T1_rna_tumor_S24

source_name: CD45- CD90- CD44- Tumor cells sorted by flow cytometry from a primary Gynecologic tumor specimen


title: PKU-gutless-adult-PrimHep-3


title: PKU-gutless-adult-PrimHep-2


title: PKU-gutless-adult-Liver-4


title: PKU-gutless-adult-PrimHep-1


title: PKU-gutless-nb-PrimHep-6


title: IPIGYN125T1_rna_epcam_S62


title: IPIGYN109T1_rna_tregs_S13


title: PKU-gutless-adult-Liver-2


title: PKU-gutless-adult-Liver-3


title: PKU-gutless-adult-Liver-1


title: OTp5-DNMT1-neonate-AdV3

value: off-target site


title: OTp5-DNMT1-control1

value: untreated control


title: OTp5-DNMT1-neonate-AdV1


title: OTp5-DNMT1-control3


title: OTp4-DNMT1-neonate-AdV2


title: IPIGYN107_T1_rna_tumor_S16


title: OTp4-DNMT1-neonate-AdV3


title: OTp5-DNMT1-neonate-AdV2


title: OTp5-DNMT1-control2


title: IPIGYN106_T1_rna_Treg_S37


title: PKU-gutless-adult-PrimHep-4

value: Prime-editor with pegRNA


title: OTp4-DNMT1-neonate-AdV1


title: OTp3-DNMT1-neonate-AdV3


title: OTp4-DNMT1-control2


title: OTp3-DNMT1-neonate-AdV2


title: OTp2-DNMT1-neonate-AdV3


title: IPIGYN106_T1_rna_EpCAM_S6


title: OTp4-DNMT1-control3


title: OTp3-DNMT1-control1


title: OTp3-DNMT1-control3


title: OTp3-DNMT1-control2


title: IPIGYN105_T1_rna_EpCAM_S8


title: IPIGYN104_T1_rna_tumor_S57


title: OTp3-DNMT1-neonate-AdV1


title: OTp2-DNMT1-neonate-AdV2


title: IPIGYN104_T1_rna_treg_S48


title: IPIGYN105_T1_rna_Treg_S17


title: OTp2-DNMT1-control3


title: OTp2-DNMT1-control1


title: OTp1-DNMT1-neonate-AdV2


title: IPIGYN103_T1_rna_tumor_S4


title: OTp2-DNMT1-neonate-AdV1


title: OTp2-DNMT1-control2


title: OTp4-DNMT1-control1


title: IPIGYN103_T1_rna_treg_S43


title: OTp1-DNMT1-neonate-AdV3


title: OTp1-DNMT1-control2


title: OTp1-DNMT1-neonate-AdV1


title: OTp1-DNMT1-control3


title: OTp1-DNMT1-control1


title: DMNT1-Tail-81-adult-AdV-DMNT1intoPah


title: DMNT1-Tail-4-neonate-AdVandAAV


title: IPIGYN100_T1_rna_stroma_S11


title: DMNT1-Tail-2-neonate-AdV


title: DMNT1-PrimHep-4-adult-AdV


title: IPIGYN100_T1_rna_tumor_S13


title: DMNT1-Tail-1-neonate-AdV


title: IPIGYN099_T1_rna_Stroma_S51


title: DMNT1-PrimHep-3-adult-AdV


title: IPIGYN099_T1_rna_Treg_S49


title: DMNT1-PrimHep-2-neonate-AdV


title: IPIGYN103_T1_rna_Stroma_S41


title: DMNT1-PrimHep-1-adult-AdV


title: DMNT1-PrimHep-1-neonate-AdV


title: DMNT1-Liver-4-adult-AdV


title: DMNT1-Liver-3-adult-AdV


title: GYN098_T1_rna_stroma_S34


title: IPIGYN099_T1_rna_EpcAM_S19


title: DMNT1-Liver-1-neonate-AdV


title: DMNT1-Liver-2-neonate-AdV


title: GYN096T1_St_S61


title: DMNT1-Liver-1-adult-AdV


title: DMNT1-Liver-2-adult-AdV


title: DMNT1-PrimHep-2-adult-AdV


title: GYN096T1_Ep_S41


title: long-term-PKU-Tail1

data_processing:
Library strategy: targeted amplicon sequencing
CHANGE-seq pipeline (https://github.com/tsailabSJ/changeseq)
Genome_build: mm10
Supplementary_files_format_and_content: For CHANGE-seq_ text files containing identified off-target sites

source_name: tail

extract_protocol: Detachment with TryplE, wash with PBS, lysis and DNA isolation for cell lines and whole tissue or primary hepatocyte isolation for in vivo samples.

value: tail

value: systemic injection of AAV8


title: long-term-PKU-Tail2

value: targeted amplicon sequencing

value: prime-edited genomic locus


title: IPIGYN105_T1_rna_Stroma_S26


title: long-term-PKU-PE2nb-Liver3-92

value: whole liver lysate


title: GYN093T1_Tu_S37

value: tumor


title: GYN095T1_Li_S4

source_name: Tumor infiltrating viable cells sorted by flow cytometry from a primary Gynecologic tumor specimen

value: live


title: PKU-pup67-thymus

value: whole tissue lysate


title: PKU-pup67-testes


title: PKU-pup67-spleen


title: long-term-PKU-PE2n-PrimHep1-79

value: primary hepatocytes


title: long-term-PKU-PE2n-Liver2-80


title: PKU-pup67-tail


title: long-term-PKU-PE2n-Liver1-79


title: GYN091T1_Tu_S45


title: PKU-pup67-pancreas


title: PKU-pup67-skeletalMuscle


title: GYN089T1_Tr_S36

value: treg


title: PKU-pup67-diaphragm


title: PKU-pup67-kidney


title: GYN089T1_Ep_S59


title: long-term-PKU-PE2n-PrimHep3-92


title: GYN095T1_Tu_S8


title: GYN088T1_St_S35

value: stroma


title: PKU-pup67-brain


title: PKU-pup67-adrenal-gland


title: PKU-pup66-testes


title: PKU-pup66-thymus


title: GYN088T1_Ep_S57

value: epcam


title: PKU-pup66-tail


title: GYN089T1_St_S28

value: Uterus & adnexa


title: PKU-pup66-lung


title: PKU-pup66-kidney


title: GYN086T1_Tr_S15

value: Gynecologic cancer


title: PKU-pup66-intestine


title: PKU-pup66-pancreas


title: PKU-pup67-lung


title: PKU-pup66-heart


title: PKU-pup67-heart


title: GYN085T1_Tr_S39


title: PKU-pup67-colon


title: PKU-pup67-intestine


title: GYN085T1_Ep_S2


title: PKU-pup66-brain


title: PKU-pup66-diaphragm


title: PKU-pup62-thymus


title: PKU-pup66-adrenal-gland


title: GYN084T1_Li_S20


title: PKU-pup62-testes


title: GYN083T1Tu_S38


title: PKU-pup66-colon


title: GYN087T1_Ep_S15


title: PKU-pup66-skeletalMuscle


title: PKU-pup62-pancreas


title: GYN083T1My_S41

source_name: Tumor assocaited HLA DR+ CD11b+ CD3-CD1920-CD56- myeloid cells  sorted by flow cytometry from a primary Gynecologic tumor specimen

value: myeloid


title: PKU-pup62-spleen


title: PKU-pup62-skeletalMuscle


title: GYN086T1_Ep_S36


title: PKU-pup62-lung


title: GYN082T1Tr_S42


title: GYN082T1Tu_S36


title: PKU-pup62-brain


title: PKU-pup62-diaphragm


title: PKU-pup62-intestine


title: PKU-pup62-heart


title: GYN078T1Tr_S10


title: GYN078T1St_S25


title: PKU-pup62-colon


title: GYN078T1Tu_S44


title: PKU-pup62-kidney


title: PKU-pup62-adrenal-gland


title: PKUpup-PrimHep-41

value: systemic injection of AdV5


title: PKUpup-PrimHep-44

value: Prime-editor with pegRNA


title: IPIGYN069T1_rna_stroma_S49


title: IPIGYN069T1_rna_treg_S32


title: PKUpup-PrimHep-40


title: PKU-pup62-tail


title: PKUpup-PrimHep-38


title: PKUpup-PrimHep-37


title: PKUpup-PrimHep-36


title: PKUpup-PrimHep-33


title: PKUpup-PrimHep-34


title: PKUpup-PrimHep-43


title: GYN065T1St_S28


title: GYN066T1Tr_S8


title: GYN065T1Tr_S34


title: PKU-primHep-973-Ad5f-PE2n


title: PKU-pup66-spleen


title: PKU-tail-25L

value: untreated control


title: PKUpup-primHep-16R-PE2n-tv


title: GYN059T1Tu_S43


title: PKU-PE2-tv-Ad5-Liver


title: PKU-PE2-tv-Ad5-1-1


title: PKUpup-primHep-11R-PE2n-tv


title: GYN064_T1_rna_tregs_S6


title: PKU-Liver-16R-PE2n-tv


title: PKU-primHep-274-Ad5f-PE2n


title: PKU-6934adult


title: PKU-primHep-273-Ad5f-PE2n


title: PKU-Liver-25L


title: PKU-PE2-tv-Ad5-1-2


title: PKU-Liver-11R-PE2n-tv


title: GYN060T1Tr_S8


title: PKUpup-PrimHep-39


title: pHx-PKU-4

value: systemic injection of AAV8


title: mPKU-570adult

value: targeted amplicon sequencing


title: PKU-Liver-973-Ad5f-PE2n

value: prime-edited genomic locus


title: GYN043T1St_S12


title: pHx-PKU-2

value: whole liver lysate


title: PKU-Liver-274-Ad5f-PE2n


title: mPKU-558adult


title: PKU-6937adult


title: pHx-PKU-3


title: pHx-PKU-1


title: PKU-Liver-273-Ad5f-PE2n


title: mPKU-571adult


title: GYN045T1Ep_S4


title: GYN043T1Tr_S220


title: mPKU-555adult


title: PKU-573adult


title: PKUpup-Liver-41


title: PKUpup-Liver-40


title: PKUpup-Liver-38


title: PKUpup-Liver-44


title: PKUpup-Liver-39


title: GYN040_T1_rna_tregs_S5


title: PKUpup-Liver-45


title: PKUpup-Liver-43


title: GYN027T1Tr_S21


title: IPIGYN037T1_rna_tregs_S37


title: PKUpup-Liver-42


title: GYN025T1Tc_S209

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary Gynecologic tumor specimen

value: tcell


title: GYN025T1My_S12


title: PKUpup-Liver-37


title: PKUpup-Liver-36


title: GYN060T1Tu_S38

value: tumor


title: PKUpup-Liver-35


title: PKUpup-Liver-33


title: PKUpup-Liver-34


title: GYN025T1Li_S216

value: live


title: PKU-1913-Tail

value: tail


title: GYN021T1_Tr_S3

value: treg


title: GYN040_T1_rna_tumor_S30


title: GYN021T1_Li_S3_L001


title: PKU-1913-PrimHep

value: primary hepatocytes


title: GYN019T1_Tc_S41


title: PKU-1911-Tail


title: PKU-1911-Liver


title: GYN015T1_Li_S42


title: GYN019T1_Li2_S2


title: PKU-1658-PrimHep


title: GYN013T1_Tu_S35_L004


title: PKU-1911-caut-PrimHep


title: PKU-1016-Liver


title: PKU-1658-Tail


title: PKU-0123-PrimHep


title: PKU-1016-caut-PrimHep


title: GYN066T1St_S51

value: stroma


title: PKU-0123-Tail


title: GYN011T2_My_S12_L001

value: Uterus & adnexa


title: GYN011T2_Tc_S2_L001

value: Gynecologic cancer


title: GYN012T1_Tr_S9_L001


title: PKU-1658-Liver


title: GYN011T2_Tu_S14_L001


title: PKU-0123-Liver


title: PKU-0122-Tail


title: GYN011T2_Li_S33_L004


title: PKU-0122-PrimHep


title: GYN011T1_Tu_S38_L005


title: PKU-0122-Liver


title: PKU-1913-Liver


title: PKU-51-Tail


title: PKU-51-PrimHep


title: Krummel_0610_P7_GYN018T2Li2_S30


title: GYN007T1_Tr_S29_L004


title: PKU-31-Tail


title: PKU-31-PrimHep


title: PKU-31-Liver


title: Pahenu2-ctrl3adult


title: Pahenu2-ctrl2adult


title: Pahenu2-ctrl1adult


title: IPIGMB006T1_rna_tumor_S34

source_name: CD45- CD90- CD44- Tumor cells sorted by flow cytometry from a primary Brain tumor specimen

value: Brain

value: Glioblastoma


title: GALL001T1St_S28

source_name: CD45- CD90+ CD44+ stromal cells  sorted by flow cytometry from a primary Gallbladderl tumor specimen

value: Gallbladder

value: Gallbladder cancer


title: IPIGBM006T1_rna_live_S27

source_name: Tumor infiltrating viable cells sorted by flow cytometry from a primary Brain tumor specimen


title: Pahenu2-537adult

value: systemic injection of AAV8

value: Prime-editor with pegRNA


title: homozygous-ctrl-3

value: targeted amplicon sequencing

value: prime-edited genomic locus


title: homozygous-ctrl-2


title: homozygous-ctrl-1


title: GALL001T1Tr_S22

source_name: Tumor assocaited CD4+ CD25+ Regulatory T cell sorted by flow cytometry from a primary gallbladder tumor specimen


title: IPICRC093T1_rna_treg_S21

source_name: Tumor assocaited CD4+ CD25+ Regulatory T cell sorted by flow cytometry from a primary Colorectal tumor specimen

value: Colon & Rectum

value: Colorectal cancer


title: PKU-pup71-PrimHep

source_name: primary hepatocytes


title: IPICRC090T1_rna_treg_S27


title: PKU-pup70-PrimHep


title: Pahenu2-539adult

source_name: whole liver lysate

value: whole liver lysate


title: PKU-pup70-Liver


title: PKU-pup67-PrimHep


title: PKU-1016-Tail

value: tail

value: systemic injection of AdV5


title: PKU-pup71-Liver


title: PKU-pup67-Liver


title: Pahenu2-550adult


title: IPICRC089T1_rna_treg_S35

value: treg


title: IPICRC089T1_rna_tumor_S16

source_name: CD45- CD90- CD44- Tumor cells sorted by flow cytometry from a primary Colorectal tumor specimen

value: tumor


title: IPIGBM006T1_rna_myeloids_S29

source_name: Tumor assocaited HLA DR+ CD11b+ CD3-CD1920-CD56- myeloid cells  sorted by flow cytometry from a primary Brain tumor specimen

value: myeloid


title: IPICRC094T1_rna_tregs_S2


title: PKU-pup66-Liver


title: PKU-pup66-PrimHep

value: primary hepatocytes


title: PKU-pup62-Liver


title: PKU-pup61-PrimHep


title: PKU-pup62-PrimHep


title: long-term-DMNT1-low-Tail2


title: PKU-pup57-Liver


title: PKU-pup59-Liver


title: PKU-pup61-Liver


title: long-term-DMNT1-low-Tail1


title: PKU-pup57-PrimHep


title: PKU-pup59-PrimHep


title: PKU-51-Liver


title: IPICRC086T1_rna_treg_S34


title: long-term-DMNT1-low-PrimHep3


title: long-term-DMNT1-low-Liver3


title: long-term-DMNT1-low-PrimHep1


title: long-term-DMNT1-low-Liver2


title: IPICRC080T1_rna_epcam_S10

source_name: CD45- CD90- CD44- EPCAM+ Tumor cells sorted by flow cytometry from a primary Colorectal tumor specimen

value: epcam


title: IPICRC078_T2_rna_Tumor_S19

source_name: CD45- CD90- CD44- Tumor cells sorted by flow cytometry from a metastatic Colorectal tumor specimen


title: IPICRC088T1_rna_treg_S8


title: IPICRC078_T2_rna_Treg_S40

source_name: Tumor assocaited CD4+ CD25+ Regulatory T cell sorted by flow cytometry from a metastatic Colorectal tumor specimen


title: IPICRC078_T2_rna_Tcell_S46

description:
IPICRC078.T2
GSE179975

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a metastatic Colorectal tumor specimen

value: tcell


title: long-term-DMNT1-low-Liver1


title: long-term-DMNT1-high-PrimHep3


title: long-term-DMNT1-high-Tail2

source_name: tail


title: IPICRC088T1_rna_live_S4

source_name: Tumor infiltrating viable cells sorted by flow cytometry from a primary Colorectal tumor specimen

value: live


title: IPICRC078_T2_rna_Myeloid_S56

source_name: Tumor assocaited HLA DR+ CD3-CD1920-CD56- myeloid cells  sorted by flow cytometry from a metastatic Colorectal tumor specimen


title: IPICRC078_T2_rna_Live_S47

source_name: Tumor infiltrating viable cells sorted by flow cytometry from a metastastic Colorectal tumor specimen


title: long-term-DMNT1-high-PrimHep1


title: long-term-DMNT1-high-PrimHep2


title: IPICRC077_T1_rna_Treg_S4


title: long-term-DMNT1-high-Liver3


title: DMNT1-PE2nbl-Tail-1


title: IPICRC076_T1_rna_treg_S1


title: long-term-DMNT1-low-PrimHep2


title: long-term-DMNT1-high-Liver2


title: long-term-DMNT1-high-Liver1


title: DMNT1-PE2nbl-Tail-2


title: DMNT1-PE2nbl-PrimHep-3


title: DMNT1-PE2nbl-Liver-3


title: DMNT1-PE2nbl-PrimHep-2


title: IPICRC076_T1_rna_epcam_S18


title: DMNT1-PE2nbl-PrimHep-1


title: DMNT1-PE2nbl-Liver-1


title: IPICRC075_T1_rna_treg_S29


title: DMNT1-PE2s-Tail-1


title: DMNT1-PE2nbl-Liver-2


title: IPICRC075_T1_rna_epcam_S23


title: DMNT1-PE2s-PrimHep-3


title: IPICRC074_T1_rna_treg_S21


title: DMNT1-PE2s-Tail-2


title: DMNT1-PE2s-PrimHep-2


title: DMNT1-PE2s-PrimHep-1


title: DMNT1-PE2s-Liver-3


title: DMNT1-PE2s-Liver-2


title: IPICRC074_T1_rna_EpCAM_S32


title: IPICRC073_T1_rna_stroma_S22

source_name: CD45- CD90+ CD44+ stromal cells  sorted by flow cytometry from a primary Colorectal tumor specimen

value: stroma


title: DMNT1-PE2s-Liver-1

value: systemic injection of AAV8


title: DMNT1-dose4-PrimHep-3

value: Prime-editor with pegRNA


title: DMNT1-dose4-PrimHep-2

value: targeted amplicon sequencing


title: DMNT1-dose4-PrimHep-1

value: prime-edited genomic locus


title: DMNT1-dose4-Liver-2


title: DMNT1-dose4-Liver-3


title: IPICRC072_T1_rna_EpCAM_S12

value: Colon & Rectum


title: DMNT1-dose3-PrimHep-3


title: IPICRC072_T1_rna_treg_S60

value: Colorectal cancer


title: IPICRC073_T1_rna_epcam_S27


title: DMNT1-dose3-PrimHep-4


title: IPICRC071_T2_rna_Tumor_S29


title: DMNT1-dose3-Liver-2

value: whole liver lysate


title: DMNT1-dose3-PrimHep-2


title: DMNT1-dose3-PrimHep-1


title: IPICRC071_T2_rna_Tcell_S6

description:
IPICRC071.T2
GSE179975


title: DMNT1-dose3-Liver-4


title: DMNT1-dose2-PrimHep-1


title: DMNT1-dose3-Liver-1


title: DMNT1-dose2-PrimHep-2


title: CRC070_T1_rna_tregs_S7


title: DMNT1-dose2-Liver-2


title: CRC070_T1_rna_epcam_S52


title: IPICRC073_T1_rna_treg_S45


title: DMNT1-dose1-PrimHep-1


title: CRC067T1_St_S42


title: DMNT1-dose2-Liver-1


title: CRC067T1_Tr_S30


title: DMNT1-dose1-PrimHep-2


title: DMNT1-dose1-Liver-2


title: DMNT1-dose4-Liver-1


title: PE2n-38-sgRNA-005

value: off-target site


title: PE2n-38-sgRNA-004


title: DMNT1-dose3-Liver-3


title: CRC064T1_Tr_S54


title: PE2n-38-sgRNA-003


title: PE2n-38-sgRNA-002


title: PE2n-38-sgRNA-001


title: CRC064T1_Ep_S69


title: CRC063T1_St_S33


title: PE2n-38-pegRNA-005


title: PE2n-38-pegRNA-003


title: PE2n-38-pegRNA-002


title: PE2n-38-pegRNA-001


title: PE2n-38-pegRNA-004


title: CRC063T1_Tu_S44


title: PE2n-34-sgRNA-004


title: PE2n-34-sgRNA-005


title: IPICRC062_T1_rna_Ep_S34


title: PE2n-34-pegRNA-005


title: PE2n-34-sgRNA-001


title: CRC062T1_Tr_S5


title: PE2n-34-sgRNA-002


title: PE2n-34-pegRNA-004


title: PE2n-34-pegRNA-002


title: PE2n-34-pegRNA-003


title: CRC060T1_Li_S32_L001


title: PE2n-34-sgRNA-003


title: PE2n-34-pegRNA-001


title: DMNT1-dose1-Liver-1


title: PE2n-16-sgRNA-005


title: PE2n-16-sgRNA-004


title: CRC058T1_Tr_S45


title: PE2n-16-sgRNA-002


title: CRC063T1_Tr_S19


title: PE2n-16-pegRNA-005


title: PE2n-16-sgRNA-003


title: CRC058T1_Tu_S63


title: PE2n-16-sgRNA-001


title: PE2n-16-pegRNA-004


title: PE2n-16-pegRNA-003


title: CRC055T1St_S31


title: CRC055T1Tr_S19


title: ctrl923-sgRNA-005


title: PE2n-16-pegRNA-001


title: ctrl923-sgRNA-004


title: CRC054T1My_S33

source_name: Tumor assocaited HLA DR+ CD11b+ CD3-CD1920-CD56- myeloid cells  sorted by flow cytometry from a primary Colorectal tumor specimen


title: ctrl923-sgRNA-002


title: CRC054T1Li_S39


title: ctrl923-pegRNA-005


title: CRC053T1Tr_S15


title: CRC048T1Tu_S11


title: ctrl923-pegRNA-003


title: CRC057T1_Li_S49


title: ctrl923-pegRNA-004


title: CRC048T1Tr_S40


title: ctrl923-pegRNA-002


title: ctrl25-sgRNA-004


title: ctrl25-sgRNA-005


title: CRC039T1Tr_S49_S18


title: CRC040T2Tcb_S27_S43

description:
IPICRC040.T2
GSE179975


title: ctrl25-sgRNA-003


title: ctrl923-sgRNA-003


title: CRC054T1Tu_S12


title: ctrl25-pegRNA-004


title: ctrl25-sgRNA-001


title: CRC037T1Tr_S19


title: ctrl25-pegRNA-003


title: ctrl25-pegRNA-005


title: ctrl923-sgRNA-001


title: PE2n-16-pegRNA-002


title: CRC040T2Li_S35_S4


title: ctrl25-pegRNA-002


title: ctrl25-pegRNA-001


title: ctrl11-sgRNA-004


title: ctrl11-sgRNA-005


title: CRC054T1Tc_S54

description:
IPICRC054.T1
GSE179975

source_name: Tumor assocaited conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary Colorectal tumor specimen


title: CRC032T1_Tr_S55


title: ctrl11-sgRNA-003


title: IPIBLAD036T1_rna_live_S30

source_name: Tumor infiltrating viable cells sorted by flow cytometry from a primary Bladder tumor specimen

value: Bladder

value: Bladder cancer


title: ctrl923-pegRNA-001


title: ctrl11-sgRNA-002


title: ctrl25-sgRNA-002


title: IPIBLAD036T1_rna_tumor_S8

source_name: CD45- CD90- CD44- Tumor cells sorted by flow cytometry from a primary Bladder tumor specimen

value: tumor


title: ctrl11-sgRNA-001

source_name: primary hepatocytes


title: IPIBLAD036T1_rna_treg_S36

source_name: Tumor assocaited CD4+ CD25+ Regulatory T cell sorted by flow cytometry from a primary Bladder tumor specimen

value: treg


title: ctrl11-pegRNA-004

value: primary hepatocytes


title: ctrl11-pegRNA-003


title: IPIBLAD036T1_rna_myeloid_S29

source_name: Tumor assocaited HLA DR+ CD3-CD1920-CD56- myeloid cells  sorted by flow cytometry from a primary Bladder tumor specimen

value: myeloid


title: IPIBLAD034T1_rna_treg_S52


title: IPIBLAD034T1_rna_myeloids_S33


title: IPIBLAD034T1_rna_live_S32


title: IPIBLAD034T1_rna_epcam_S67

source_name: CD45- CD90- CD44- EPCAM+ Tumor cells sorted by flow cytometry from a primary Bladder tumor specimen

value: epcam


title: BLAD033T1_Tu_S13


title: ctrl11-pegRNA-001


title: DMNT1-primHep-tv4


title: ctrl1-pegRNA-005


title: DMNT1-wt-ctrl

source_name: whole liver lysate


title: BLAD033T1_Li_S58

value: live


title: DMNT1-tv-primHep


title: DMNT1-primHep-tv2


title: DMNT1-tv-Liver


title: BLAD030T1St_S20

source_name: CD45- CD90+ CD44+ stromal cells  sorted by flow cytometry from a primary Bladder tumor specimen

value: stroma


title: DMNT1-primHep-tv3

value: systemic injection of AAV8


title: DMNT1-pHx-2

value: Prime-editor with pegRNA


title: DMNT1-pHx-3

value: targeted amplicon sequencing


title: BLAD030T1Tu_S18


title: BLAD030T1Tr_S26


title: BLAD030T1My_S6

source_name: Tumor assocaited HLA DR+ CD11b+ CD3-CD1920-CD56- myeloid cells  sorted by flow cytometry from a primary Bladder tumor specimen


title: DMNT1-pHx-1

value: prime-edited genomic locus


title: ctrl11-pegRNA-002


title: BLAD032T1Li_S48


title: BLAD030T1Li_S12


title: BLAD029T1Tu_S68


title: DMNT1-Liver-tv4


title: DMNT1-Liver-tv2


title: DMNT1-iv-tail-2

value: tail


title: DMNT1-Liver-tv3


title: DMNT1-iv-primHep-4


title: BLAD029T1My_S49


title: BLAD029T1Li_S38


title: DMNT1-iv-tail-1


title: DMNT1-iv-primHep-3


title: BLAD028T1St_S37


title: BLAD028T1Tu_S47


title: DMNT1-iv-Liver-pHx-7


title: BLAD028T1My_S41


title: DMNT1-iv-pHx-primHep-5


title: BLAD028T1Li_S50


title: DMNT1-iv-pHx-primHep-6


title: DMNT1-iv-pHx-primHep-7


title: DMNT1-iv-Liver-pHx-6


title: RNAseq_S6_H

city: Milwaukee

first: Victor

last: Jin

state: WI

address: 8701 Watertown Plank Rd

department: IHE

institute: Medical college of Wisconsin

data_processing:
All raw reads were mapped to mm10 reference genome by using hisat2.
raw bam files were further processed by samtools and picard
Differentail genes were identified by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: xlsx;Differentiated expression genes

source_name: short day mice

growth_protocol: C57BL/6J breeder mice were purchased from the Jackson Laboratory (Stock No: 000664; RRID: IMSR_JAX:000664). Animals were housed in the animal facility at the University of Minnesota, Duluth with ad libitum access to mouse chow (LabDiet 5053) and tap water. Mouse colonies were maintained in the standard 12h/12h Light/Dark (LD) cycle. The room temperature was maintained at 22 ± 1℃ and humidity was at 35-45%.

extract_protocol:
Total RNA was extracted by ZYMO Research Quick-RNA MiniPrep kit from lysed 10 million of cells and spheroids in RNA lysis buffer, then removed most of gDNA with the spin-away filter. After that, the mixture of RNA was transferred with ethanol to Zymo-Spin IIICG column to remove trace DNA by DNase I on the column, then washed twice with RNA wash buffer followed by elution with 50 μl DNase/RNase-free water.
RNA-seq library was prepared with NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). The Oligo dT Beads were washed with RNA binding buffer and incubated with a total 1 μg RNA to purify mRNA, followed with more washing by beads washing buffer. Then mRNA was eluted with elution buffer and reverse transcribed. After that, the first and the second strand cDNA were synthesized. After purification of Double-stranded DNA, an adaptor was added. Adaptor-ligated DNA was enriched by PCR followed by purification, then the DNA library was sequenced with Illumina HiSeq3000.

treatment_protocol: To create SD mice, six-week-old male and female breeders were transferred to the 8h/8h LD cycle (100 lux) and breeding pairs were set up. Breeding pairs were maintained in the 8h/8h LD cycle throughout gestation. Pups were also kept in the 8h/8h LD cycle until they became 42 days old

tag: treatment group

value: short day mice


title: RNAseq_C5_H

source_name: control mice

value: control mice


title: RNAseq_S2_H


title: RNAseq_S5_H


title: RNAseq_C1_H


title: DMNT1-iv-Liver-4

value: whole liver lysate


title: BLAD026T1Tu_S51

value: Bladder


title: DMNT1-iv-Liver-3


title: BLAD026T1My_S43

value: Bladder cancer


title: RNAseq_C2_H


title: DMNT1-iv-Liver-pHx-5


title: DNMT-without-2-3

description: gBlock-expressing human cell line

source_name: cell lysate_HEK293T

value: cell lysate_HEK293T


title: DMNT1-iv-Liver-2


title: DMNT1-iv-primHep-2


title: DNMT-without-2-1

description: gBlock-expressing human cell line


title: BLAD028T1Tr_S34

value: treg


title: DNMT-without-3-1

description: gBlock-expressing human cell line


title: BLAD026T1Li_S13


title: BLAD025T1Tr_S36


title: DMNT1-iv-Liver-1


title: DNMT-without-2-2

description: gBlock-expressing human cell line


title: CHANGE-seq  control

description: unbiased detection of sgRNA dependent off-target sites

data_processing:
Library strategy: CHANGE-seq
CHANGE-seq pipeline (https://github.com/tsailabSJ/changeseq)
Genome_build: mm10
Supplementary_files_format_and_content: For CHANGE-seq_ text files containing identified off-target sites

source_name: mus musculus gDNA

value: mus musculus gDNA

value: in situ gDNA digest

value: Cas9 digest with PKU pegRNA

value: CHANGE-seq

value: Cas9-KO PKU peg


title: DNMT-without-1-2

description: gBlock-expressing human cell line


title: DNMT-without-1-3

description: gBlock-expressing human cell line


title: BLAD024T1Tu_S22

value: tumor


title: DNMT-with-2-2

description: gBlock-expressing human cell line

value: Prime-editor with pegRNA


title: BLAD026T1Tr_S39


title: CHANGE-seq  pegRNA


title: DNMT-with-3-1

description: gBlock-expressing human cell line

value: targeted amplicon sequencing


title: DNMT-without-3-2

description: gBlock-expressing human cell line

value: prime-edited genomic locus


title: DNMT-with-2-3

description: gBlock-expressing human cell line


title: CHANGE-seq  nicking sgRNA

value: Cas9 digest with PKU nicking sgRNA

value: Cas9-KO PKU nick


title: BLAD024T1Li_S5

value: live


title: DNMT-with-2-1

description: gBlock-expressing human cell line


title: DNMT-with-1-1

description: gBlock-expressing human cell line


title: BLAD020T1Tu_S57


title: DNMT-with-1-2

description: gBlock-expressing human cell line


title: BLAD020T1Tr_S1


title: DNMT-untr-2

description: gBlock-expressing human cell line


title: DNMT-untr-1

description: gBlock-expressing human cell line


title: DNMT-with-1-3

description: gBlock-expressing human cell line


title: PKU-without-5-3

description: gBlock-expressing human cell line


title: DNMT-with-3-2

description: gBlock-expressing human cell line


title: PKU-without-5-2

description: gBlock-expressing human cell line


title: PKU-without-4-2

description: gBlock-expressing human cell line


title: PKU-without-4-3

description: gBlock-expressing human cell line


title: PKU-without-5-1

description: gBlock-expressing human cell line


title: PKU-without-4-1

description: gBlock-expressing human cell line


title: PKU-without-3-3

description: gBlock-expressing human cell line


title: PKU-without-3-2

description: gBlock-expressing human cell line


title: IPIBLAD019T1_rna_live_S50


title: BLAD019T1Tu_S4


title: PKU-without-3-1

description: gBlock-expressing human cell line


title: BLAD019T1Tr_S16


title: PKU-with-5-3

description: gBlock-expressing human cell line


title: PKU-with-5-2

description: gBlock-expressing human cell line


title: DNMT-without-1-1

description: gBlock-expressing human cell line


title: PKU-with-5-1

description: gBlock-expressing human cell line


title: PKU-with-4-3

description: gBlock-expressing human cell line


title: BLAD015T1Tr_S3


title: PKU-with-4-2

description: gBlock-expressing human cell line


title: BLAD020T1Li_S40


title: Wild type ventral mid brain rep2

city: Charleston

first: Michael

middle: C

last: Ostrowski

state: SC

address: 86 Jonathan Lucas street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

description: Wildtype

hyb_protocol: Following fragmentation, labeled cRNA was hybridized to the mouse chip MoGene-2_0-st. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: RMA method was applied to the primary data to correct the technical bias and summarize gene expression values over probe-sets

label: Biotin

source_name: Ventral mid brain

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

growth_protocol: Ventral midbrain of two month old male mice were dissected from age matched wild type or Bach1 Knockout mice

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by Qiagen clean up.

treatment_protocol: Not applicable

value: WT


title: PKU-with-3-3

description: gBlock-expressing human cell line


title: Bach1 KO ventral mid brain rep2

description: Bach1 Knockout

value: Bach1 KO


title: PKU-with-3-2

description: gBlock-expressing human cell line


title: Wild type ventral mid brain rep1

description: Wildtype


title: Bach1 KO ventral mid brain rep1

description: Bach1 Knockout


title: BLAD014T1My_S27

value: Bladder

value: myeloid

value: Bladder cancer


title: Wild type ventral mid brain rep3

description: Wildtype


title: PKU-with-3-1

description: gBlock-expressing human cell line

value: cell lysate_HEK293T


title: BLAD014T1Li_S21


title: DNMT1-without-5-2

description: gBlock-expressing human cell line


title: BLAD014T1Ep_S32

value: epcam


title: DNMT1-without-2-3

description: gBlock-expressing human cell line


title: PKU-with-4-1

description: gBlock-expressing human cell line


title: DNMT1-without-2-1

description: gBlock-expressing human cell line


title: DNMT1-without-2-2

description: gBlock-expressing human cell line


title: DNMT1-without-5-1

description: gBlock-expressing human cell line


title: DNMT1-without-1-3

description: gBlock-expressing human cell line


title: 3280.F1.C4.I9.R1

city: Sao Paulo

first: Augusto

middle: Lima

last: Diniz

state: SP

address: Av Lineu Prestes

department: Biochemistry

country: Brazil

institute: University of Sao Paulo

description: Internode 9 from 13-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B Scanner using Agilent Settings and image intensity data were extracted with Feature Extraction Software using Agilent Settings

data_processing: Raw and background corrected data

organism: Saccharum hybrid cultivar (mixed)

label_protocol: CyScribe Post-Labelling Kit Protocol - GE Healthcare

growth_protocol: Field in Araras

extract_protocol: Trizol, DNase treatment and Qiagen RNeasy purification

treatment_protocol: NO

value: internode 9

tag: variety

tag: collect

value: internodes


title: 3280.F1.C4.I9.R2

description: Internode 9 from 13-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages


title: BLAD013T1Tu_S17


title: 3280.F1.C3.I9.R1

description: Internode 9 from 11-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages


title: DNMT1-without-1-2

description: gBlock-expressing human cell line


title: 3280.F1.C4.I5.R2

description: Internode 5 from 13-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages

value: internode 5


title: 3280.F1.C3.I9.R2

description: Internode 9 from 11-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages


title: 3280.F1.C4.I5.R1

description: Internode 5 from 13-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages


title: 3280.F1.C3.I5.R2

description: Internode 5 from 11-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages


title: 3280.F1.C3.I5.R1

description: Internode 5 from 11-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages


title: BLAD013T1Tr_S37

value: treg


title: DNMT1-without-5-3

description: gBlock-expressing human cell line

value: Prime-editor with pegRNA


title: DNMT1-with-5-1

description: gBlock-expressing human cell line

value: targeted amplicon sequencing


title: Bach1 KO ventral mid brain rep3

description: Bach1 Knockout


title: BLAD013T1St_S3

value: stroma


title: BLAD013T1My_S218


title: DNMT1-with-5-3

description: gBlock-expressing human cell line

value: prime-edited genomic locus


title: 3280.F1.C2.I5.R2

description: Internode 5 from 8-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages

extract_protocol: Trizol, DNase treatmente and Qiagen RNeasy purification


title: DNMT1-with-2-3

description: gBlock-expressing human cell line


title: DNMT1-with-2-2

description: gBlock-expressing human cell line


title: DNMT1-with-2-1

description: gBlock-expressing human cell line


title: DNMT1-with-1-3

description: gBlock-expressing human cell line


title: DNMT1-with-5-2

description: gBlock-expressing human cell line


title: DNMT1-with-1-1

description: gBlock-expressing human cell line


title: DNMT1-with-1-2

description: gBlock-expressing human cell line


title: DNMT1-without-1-1

description: gBlock-expressing human cell line


title: BLAD011T1Tr_S15


title: 3280.F1.C4.I1.R2

description: Internode 1 from 13-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages

value: internode 1


title: BLAD013T1Li_S22

value: live


title: HEK4-2-011


title: BLAD006T1Tu_S14

value: tumor


title: 3280.F1.C2.I5.R1

description: Internode 5 from 8-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages


title: HEK4-2-008


title: HEK4-2-009


title: HEK4-2-010


title: BLAD006T1Li2_S8


title: HEK4-2-006


title: ADR002T1_St_S12

source_name: CD45- CD90- CD44- Tumor cells sorted by flow cytometry from a primary Adrenal tumor specimen

value: Adrenal

value: Adrenal cancer


title: HEK4-2-007


title: HEK4-2-005


title: 3280.F1.C3.I1.R2

description: Internode 1 from 11-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages


title: HEK4-2-004


title: 3280.F1.C3.I1.R1

description: Internode 1 from 11-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages


title: 3280.F1.C4.I1.R1

description: Internode 1 from 13-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages


title: 3280.F1.C4.L1.R2

description: Leaves +1 from 13-month-old plants T9 and T10 from Plot R2 compared with pool from leaves +1 from all developmental stages

value: Leaf +1


title: 3280.F1.C2.I1.R2

description: Internode 1 from 8-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages


title: HEK4-2-002


title: HEK4-2-003


title: 3280.F1.C4.L1.R1

description: Leaves +1 from 13-month-old plants T1 and T2 from Plot R1 compared with pool from leaves +1 from all developmental stages


title: HEK3-2-008


title: HEK3-2-010


title: HEK3-2-006_S6


title: HEK3-2-007


title: HEK4-2-001


title: 3280.F1.C3.L1.R2

description: Leaves +1 from 11-month-old plants T9 and T10 from Plot R2 compared with pool from leaves +1 from all developmental stages


title: 3280.F1.C2.I1.R1

description: Internode 1 from 8-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages


title: HEK3-2-005_S13


title: HEK3-2-006_S14


title: HEK3-2-004


title: HEK3-2-005_S5


title: HEK3-2-003_S11


title: HEK3-2-001_S9


title: HEK4-2_S72


title: HEK3-2-001_S1


title: A375K9Msort_2

city: New York

first: Yariv

last: Houvras

state: NY

address: 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Reads were then aligned to the human genome (hg19) using Star v2.3
The Ensemble transcriptome was used to identify genes
Differential gene expression was analyzed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 was used to normalize gene expression and to identify differentially regulated genes

growth_protocol: A375 cells were grown in DMEM supplemented with 10% FBS

extract_protocol:
Total RNA was isolated using Qiagen RNAeasy extraction kit
RNA-seq libraries were prepared according to the Illumina TruSeq RNA protocol. cDNA libraries were then run on the HiSeq platform to obtain 50 bp paired-end reads.

treatment_protocol: A375 cells were transfected with constructs expressing mScarlet-H3.3 (wildtype) or mScarlet(H3.3(K9M))

value: Melanoma


title: A375H33sort_3


title: A375K9Msort_1


title: A375K9Msort_3


title: HEK4-2_S71

value: cell lysate_HEK293T


title: 3280.F1.C2.L1.R2

description: Leaves +1 from 8-month-old plants T9 and T10 from Plot R2 compared with pool from leaves +1 from all developmental stages


title: HEK4-2-ctrl2


title: HEK3-2-003_S3


title: HEK4-2_S68


title: 3280.F1.C3.L1.R1

description: Leaves +1 from 11-month-old plants T1 and T2 from Plot R1 compared with pool from leaves +1 from all developmental stages


title: A375H33sort_2


title: HEK4-2-ctrl1


title: 3280.F1.C2.L1.R1

description: Leaves +1 from 8-month-old plants T1 and T2 from Plot R1 compared with pool from leaves +1 from all developmental stages


title: 3280.F1.C1.L1.R2

description: Leaves +1 from 3-month-old plants T17 and T18 from Plot R2 compared with pool from leaves +1 from all developmental stages


title: 3280.F1.C1.L1.R1

description: Leaves +1 from 3-month-old plants T1 and T2 from Plot R1 compared with pool from leaves +1 from all developmental stages


title: AAVS1-4-004


title: A375H33sort_1


title: AAVS1-4-002


title: AAVS1-4-003


title: HEK3-2-002


title: PANC-1 small RNA si-MYEOV-3

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

description: expressed small RNA after MYEOV siRNA transfection

data_processing:
Basecalling based on Illumina Casava1.7 software
After RNA sequencing reads quality checking, 3' adaptor was trimmed and the resulting data were mapped to the human genome (hg19) using bowtie by allowing no mismatch
The miRNA expression abundance was estimated by counting number of reads mapped to the cognate annotated miRNA in miRBase
Genome_build: hg19 (human)
Supplementary_files_format_and_content: tab-delimited text files include miRNA ID and expression level in reads count for each sample

growth_protocol: AsPC-1 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 Medium supplemented with 10% fetal bovine serum (FBS) in a humidified incubator at 37°C with 5% CO2. PANC-1 cells were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
small RNAs was prepared 48 hours after siRNA transfection
A small RNA library was generated according to the Illumina small RNA sequencing protocol. The sequencing library was sequenced on an Illumina Hiseq4000 by a 1x50 bp run.

treatment_protocol: siRNAs against human MYEOV (Stealth RNAi, siMYEOV-1: HSS120166, siMYEOV-2: HSS120167) and the negative control (Stealth RNAi, siNC: #12935-300) were purchased from Life Technologies. Transfection was performed using lipfectamine 3000 (Invitrogen) according to the manufacturer’s protocol. In brief, AsPC-1 and PANC-1 cells were plated in six-well plate to 50-60% confluence. For each well, 5μL siRNA (20μM) was added into 250 μL Opti-MEM medium (GIBCO BRL), 5μL lipofectamine 3000 into 250 μL Opti-MEM medium, and then mixed siRNA with lipofectamine 3000. The mixture was added to cells and incubated for 6 hours before replacing the medium.

value: human pancreatic cancer cell line


title: PANC-1 small RNA si-MYEOV-2


title: AAVS1-1-004


title: AAVS1-4-001


title: AAVS1-1-006


title: AAVS1-1-005


title: PANC-1 small RNA si-MYEOV-1


title: PANC-1 small RNA WT3

description: expressed small RNA without treatment


title: AAVS1-1-003


title: AAVS-014


title: AAVS-011


title: PANC-1 small RNA WT2

description: expressed small RNA without treatment


title: AAVS1-1-001


title: HEK-PKU-x2-13-19-001


title: HEK-PKU-x2-13-16n002


title: AAVS-004


title: AsPC-1 small RNA si-MYEOV-3


title: HEK-PKU-x2-13-19n001


title: HEK-PKU-x2-13-16n001


title: HEK-PKU-x2-13-19n002


title: AsPC-1 small RNA si-MYEOV-2


title: AAVS-009


title: AsPC-1 small RNA si-MYEOV-1


title: HEK-PKU-x1-13-19n002


title: AsPC-1 small RNA WT3

description: expressed small RNA without treatment


title: PANC-1 small RNA WT1

description: expressed small RNA without treatment


title: HEK-PKU-x2-13-16-001


title: Shield_dnmt1_mKD_H3K4me1_rep2

city: Beijing

first: Wei

last: Xie

address: Zhongguancun street, Haidian

department: THU-PKU Center for Life Sciences

institute: Tsinghua University

data_processing:
Library strategy: CUT&RUN
All STEM-seq datasets were mapped to the danRer7 reference genome by Bismark (Krueger and Andrews, 2011). Reads were trimmed with cutadaptor (Martin, 2011) using parameters: --minimum-length 20 --pair-filter=any. Alignments were performed with the following parameters: -N 1 -X 600 --score_min L,0,-0.6. Multi-mapped reads and PCR duplicates were removed. bismark_methylation_extractor was used to calculate the DNA methylation level.
Total RNA-seq data were firstly processed using Trim Galore! with default parameters to trim the adapter-containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome (danRer7) by STAR (version: STAR_2.5.3a_modified) (Dobin et al., 2013) with the following parameters: --outSAMstrandField intronMotif --outSAMattributes All --outSAMunmapped Within --outSAMattrIHstart 0 --outWigStrand Stranded --outFilterMultimapNmax 20 --twopassMode Basic. The gene expression level was normalized to fragments per kilobase of transcript per million mapped (FPKM) values using Cufflinks (version 2.2.1) (Trapnell et al., 2012).
The scRNA-seq data were processed with Cell Ranger 3.1 for genome alignment (danRer10), transcript counting, and gene-cell-barcode matrix generation. Before the downstream analysis, cells with unique detected genes lower than <2,000 and higher than 6,000 genes were discarded, and cells with high percentage of mitochondrial genes (>5%) were removed too. Subtypes of cells were identified with Seurat 3.0 through the integrating of control and mKD embryos at dome and shield stages with setting control embryos as reference. To make the data comparable samples, we performed SCTransform normalization separately for each dataset. To further reduce the bais caused by sequencing depth of scRNA-seq and percentage of mitochondrial genes, UMI variance and percent.mt were regressed out from SCTransform normalized data matrix by linear model with negative binomial distribution.
All ChIP-seq reads were aligned to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM). To visualize the STAR ChIP-seq signal in the UCSC genome browser, each read was extended by 250 bp and the coverage for each base was counted. Replicates of STAR ChIP-seq were pooled for the downstream analysis.
The ATAC-seq data were mapped to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM). To minimize the batch and cell type variation, RPKM values across whole genome were further Z-score normalized. To visualize the CUT&RUN signals in the UCSC genome browser, each read was extended by 250 bp and the coverage for each base was counted.
Genome_build: danRer7
Supplementary_files_format_and_content: Matrix for scRNA-seq data, gene expression table for total RNA-seq data, Bigwig and narrowPeak for ChIP-seq and ATAC-seq data

organism: Danio rerio

source_name: embryo

growth_protocol: The wild-type AB strain was used in the experiments. The females after OMIS were fed with live adult brine shrimp thrice a day. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously (Kimmel et al., 2001).

extract_protocol:
CUT&RUN was conducted based on previously published protocol (Xia et al., 2019) with modifications in cell permeation to adapt it for zebrafish embryos. Embryos were deyolked by tweezers manually and transferred into 1.5 mL conventional, non-low-binding tube (Axygen). Then tubes were flicked several times to disperse cells in embryos, and resuspended by 60 ul washing buffer (20 mM HEPES-KOH, pH = 7.5; 150 mM NaCl; 0.5 mM Spermidine and Roche complete protease inhibitor). 10 µl Concanavalin-coated magnetic beads (Polyscience, Cat 86057) for each sample were gently washed twice, resuspended by binding buffer (20 mM HEPES-KOH, pH = 7.5; 10 mM KCl; 1 mM CaCl2; 1 mM MnCl32), and added carefully to the cells.
The cells with beads were incubated at 23C for 30 min on Thermomixer (Eppendorf) at 400 rpm, then held at magnetic stand to exclude buffer, and resuspended by 75 µl antibody buffer (washing buffer supplied with 0.02% digitonin and 2 mM EDTA, freshly made) with H3K4me3 (validated homemade) (Zhang et al., 2016) antibody, or H3K27me3 antibody (Active Motif, Cat 61017), or H2AK119ub antibody (CST, Cat 8240s) diluted at ratio of 1:100. Then the samples were incubated at 4℃ on Thermomixer overnight at 400 rpm. On the second day, the samples were washed by digitonin-washing buffer several times on magnetic stand, and resuspended with 50 µl digitonin-washing buffer supplied with 700 ng/ml pA-MNase, which is kindly provided by Dr. Steven Henikoff, and incubated at 4℃ on Thermomixer for 3hrs at 400 rpm. After that, the cells were washed by digitonin-washing buffer on magnetic stand, and resuspended by 100 µl digitonin-washing buffer on ice for at least 2 min. Targeted region digestion was activated by adding 2 µl 100 mM CaCl2 for 30 min in ice, then stopped by 100 µl 2 X stop buffer (340 mM NaCl; 20 mM EDTA, pH = 8.0; 4 mM EGTA, pH = 8.0; 50 µg/ml RNase; 100 µg/ml glycogen; 0.02% digitonin suppled with spike-in DNA) and fully vortexed. To release fragments, the samples were incubated at 37℃ on Thermomixer at 400 rpm for 20 min. Then the supernatants were purified by phenol chloroform and ethanol purification, and subjected to Tru-seq library construction using NEBNext Ultra II DNA Library Prep kit (NEB, Cat E7645S) as standard protocols. The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2508 or XTen platform according to manufacturer’s instruction.

treatment_protocol: Briefly, on the first day of OMIS (Wu et al., 2018b), adult females at 5-12 month old were anesthetized in 550 µg/ml tricaine (Sigma, Cat A5040) in a petri dish. Then the fish was placed on a damp sponge with specific buffer (5.4 mM KCl, 136.8 mM NaCl, 4.2 mM NaHCO3, 0.44 mM KH2PO4, 0.25 mM Na2HPO4, and 0.5% (wt/vol) BSA). A cut was made on one side of belly to expose the ovary. The diluted MOs were microinjected into each oocyte. Rhodamine B (Sigma, Cat R8881) was co-injected with MOs as a dye. After injection, the wound on the belly was sewed with a surgical sewing needle carefully and quickly. Once the operation was done, the female was transferred into fish water supplemented with 32 µg/ml tricaine, 10 unit/ml penicillin and 10 µg/ml streptomycin (HyClone, Cat SV30010). Then the fish was transferred to fish water containing gradually reduced concentrations of tricaine. In the evening of the second day, the female was paired with a wild type male. In the morning of the third day, the pair started to chase and lay fertilized eggs naturally. The injected oocyte-derived embryos were identified by co-injected dye (rhodamine B) at very early developmental stages. The injection doses of dnmt1 MO were 5 ng per oocyte in the same assay. MOs were dissolved in RNase-free water, and heated to 65°C for 11 min before microinjection.

value: AB

value: WT

tag: treatment

value: Oocyte microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage (GV)


title: AsPC-1 small RNA WT1

description: expressed small RNA without treatment


title: AAVS-001


title: AAVS-006


title: HEK-PKU-x1-13-19-002


title: HEK-PKU-x1-13-19-001


title: AsPC-1 small RNA WT2

description: expressed small RNA without treatment


title: HEK-PKU-x1-13-16n001


title: Shield_ctrl_H3K4me1_rep2

growth_protocol: The wild-type AB strain was used in the experiments. The females after OMIS were fed with live adult brine shrimp thrice a day. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously (Kimmel et al., 1999).

extract_protocol:
CUT&RUN was conducted based on previously published protocol (Xia et al., 2019) with modifications in cell permeation to adapt it for zebrafish embryos. Embryos were deyolked by tweezers manually and transferred into 1.5 mL conventional, non-low-binding tube (Axygen). Then tubes were flicked several times to disperse cells in embryos, and resuspended by 60 ul washing buffer (20 mM HEPES-KOH, pH = 7.5; 150 mM NaCl; 0.5 mM Spermidine and Roche complete protease inhibitor). 10 µl Concanavalin-coated magnetic beads (Polyscience, Cat 86057) for each sample were gently washed twice, resuspended by binding buffer (20 mM HEPES-KOH, pH = 7.5; 10 mM KCl; 1 mM CaCl2; 1 mM MnCl30), and added carefully to the cells.
The cells with beads were incubated at 23C for 30 min on Thermomixer (Eppendorf) at 400 rpm, then held at magnetic stand to exclude buffer, and resuspended by 75 µl antibody buffer (washing buffer supplied with 0.02% digitonin and 2 mM EDTA, freshly made) with H3K4me3 (validated homemade) (Zhang et al., 2016) antibody, or H3K27me3 antibody (Active Motif, Cat 61017), or H2AK119ub antibody (CST, Cat 8240s) diluted at ratio of 1:100. Then the samples were incubated at 4℃ on Thermomixer overnight at 400 rpm. On the second day, the samples were washed by digitonin-washing buffer several times on magnetic stand, and resuspended with 50 µl digitonin-washing buffer supplied with 700 ng/ml pA-MNase, which is kindly provided by Dr. Steven Henikoff, and incubated at 4℃ on Thermomixer for 3hrs at 400 rpm. After that, the cells were washed by digitonin-washing buffer on magnetic stand, and resuspended by 100 µl digitonin-washing buffer on ice for at least 2 min. Targeted region digestion was activated by adding 2 µl 100 mM CaCl2 for 30 min in ice, then stopped by 100 µl 2 X stop buffer (340 mM NaCl; 20 mM EDTA, pH = 8.0; 4 mM EGTA, pH = 8.0; 50 µg/ml RNase; 100 µg/ml glycogen; 0.02% digitonin suppled with spike-in DNA) and fully vortexed. To release fragments, the samples were incubated at 37℃ on Thermomixer at 400 rpm for 20 min. Then the supernatants were purified by phenol chloroform and ethanol purification, and subjected to Tru-seq library construction using NEBNext Ultra II DNA Library Prep kit (NEB, Cat E7645S) as standard protocols. The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2508 or XTen platform according to manufacturer’s instruction.

treatment_protocol: Briefly, on the first day of OMIS (Wu et al., 2018b), adult females at 5-12 month old were anesthetized in 550 µg/ml tricaine (Sigma, Cat A5040) in a petri dish. Then the fish was placed on a damp sponge with specific buffer (5.4 mM KCl, 136.8 mM NaCl, 4.2 mM NaHCO3, 0.44 mM KH2PO4, 0.25 mM Na2HPO4, and 0.5% (wt/vol) BSA). A cut was made on one side of belly to expose the ovary. The diluted MOs were microinjected into each oocyte. Rhodamine B (Sigma, Cat R8881) was co-injected with MOs as a dye. After injection, the wound on the belly was sewed with a surgical sewing needle carefully and quickly. Once the operation was done, the female was transferred into fish water supplemented with 32 µg/ml tricaine, 10 unit/ml penicillin and 10 µg/ml streptomycin (HyClone, Cat SV30010). Then the fish was transferred to fish water containing gradually reduced concentrations of tricaine. In the evening of the second day, the female was paired with a wild type male. In the morning of the third day, the pair started to chase and lay fertilized eggs naturally. The injected oocyte-derived embryos were identified by co-injected dye (rhodamine B) at very early developmental stages. The injection doses of standard control MO (cMO) were 5 ng per oocyte in the same assay. MOs were dissolved in RNase-free water, and heated to 65°C for 10 min before microinjection.

value: Oocyte microinjection with Rhodamine B and control MO at oogenesis III stage (GV)


title: HEK-PKU-x2-13-19-002

value: Prime-editor with pegRNA


title: HEK-PKU-x2-13-16-002

value: targeted amplicon sequencing


title: AAVS1-1-002


title: WT_Input_2

city: Stanford

first: Ashby

middle: J

last: Morrison

address: 371 Serra Mall Gilbert Bldg, Room 326

department: Biology

institute: Stanford University

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using BWA
Reads were filttered by mapping quality and deduplicated.
Signal tracks were generated from reads by calculating ChIP fold-enrichment over input.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file was generated using ENCODE pipeline; score represents log2 fold change (IP/Input)

source_name: Human fetal lung fibroblast

growth_protocol: Cells were grown in 37°C and 5% CO2 in DMEM with high glucose, 15%(v/v) FBS and 1% Pen/Strep.

extract_protocol:
Approximately 2 x 106 confluent cells were fixed with 1% formaldehyde for 5 minutes at room temperature under gentle agitation. Formaldehyde was then quenched with the final concentration of 0.125M glycine. Cells were then washed with ice-cold PBS twice, and washed twice in micrococcal nuclease (MNase) buffer (50mM Tris-HCl pH 8.0, 250mM sucrose, 25mM KCI, 1mM MgCl2, 1mM CaCl2, 0.5mM 2-mercaptoethanol, 0.1% NP-40). Nuclei were isolated and DNA was digested with 400 gel units of MNase (NEB cat no. M0247S) for 16 minutes on ice, and digestion was terminated with MNase stop buffer (1% SDS, 50mM Tris-HCl pH 8.0, 20mM EGTA). Nuclei were then sonicated for 2 minutes on low with a bioruptor (30s ON/OFF, Diagenode). Cell debris was removed by centrifugation at 20000g for 15 minutes at 4°C. DNA fragments size was verified via bioanalyzer and most fragments (~90%) were the size of mono or di-nucleosomes (<500 bp). The supernatant was diluted with RIPA buffer without SDS, and 5% of the sample was used as the input for the experiment.
Library preparation was performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB cat no. E7645S) and NEBNext Multiplex Oligos for Illumina (NEB cat no. 6440S) as instructed by the manufacturer

treatment_protocol: RB1 was knocked out with CRISPR-Cas9.

value: wild type

tag: histone modification

value: Input


title: HEK-PKU-x1-13-19n001

value: prime-edited genomic locus


title: Dome_ctrl_H3K4me1_rep2

growth_protocol: The wild-type AB strain was used in the experiments. The females after OMIS were fed with live adult brine shrimp thrice a day. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously (Kimmel et al., 1995).

extract_protocol:
CUT&RUN was conducted based on previously published protocol (Xia et al., 2019) with modifications in cell permeation to adapt it for zebrafish embryos. Embryos were deyolked by tweezers manually and transferred into 1.5 mL conventional, non-low-binding tube (Axygen). Then tubes were flicked several times to disperse cells in embryos, and resuspended by 60 ul washing buffer (20 mM HEPES-KOH, pH = 7.5; 150 mM NaCl; 0.5 mM Spermidine and Roche complete protease inhibitor). 10 µl Concanavalin-coated magnetic beads (Polyscience, Cat 86057) for each sample were gently washed twice, resuspended by binding buffer (20 mM HEPES-KOH, pH = 7.5; 10 mM KCl; 1 mM CaCl2; 1 mM MnCl26), and added carefully to the cells.
The cells with beads were incubated at 23C for 30 min on Thermomixer (Eppendorf) at 400 rpm, then held at magnetic stand to exclude buffer, and resuspended by 75 µl antibody buffer (washing buffer supplied with 0.02% digitonin and 2 mM EDTA, freshly made) with H3K4me3 (validated homemade) (Zhang et al., 2016) antibody, or H3K27me3 antibody (Active Motif, Cat 61017), or H2AK119ub antibody (CST, Cat 8240s) diluted at ratio of 1:100. Then the samples were incubated at 4℃ on Thermomixer overnight at 400 rpm. On the second day, the samples were washed by digitonin-washing buffer several times on magnetic stand, and resuspended with 50 µl digitonin-washing buffer supplied with 700 ng/ml pA-MNase, which is kindly provided by Dr. Steven Henikoff, and incubated at 4℃ on Thermomixer for 3hrs at 400 rpm. After that, the cells were washed by digitonin-washing buffer on magnetic stand, and resuspended by 100 µl digitonin-washing buffer on ice for at least 2 min. Targeted region digestion was activated by adding 2 µl 100 mM CaCl2 for 30 min in ice, then stopped by 100 µl 2 X stop buffer (340 mM NaCl; 20 mM EDTA, pH = 8.0; 4 mM EGTA, pH = 8.0; 50 µg/ml RNase; 100 µg/ml glycogen; 0.02% digitonin suppled with spike-in DNA) and fully vortexed. To release fragments, the samples were incubated at 37℃ on Thermomixer at 400 rpm for 20 min. Then the supernatants were purified by phenol chloroform and ethanol purification, and subjected to Tru-seq library construction using NEBNext Ultra II DNA Library Prep kit (NEB, Cat E7645S) as standard protocols. The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2508 or XTen platform according to manufacturer’s instruction.


title: HEK-PKU-x1-13-16n002


title: HEK-PKU-split-16-001


title: Dome_dnmt1_mKD_H2AK119ub_rep2

growth_protocol: The wild-type AB strain was used in the experiments. The females after OMIS were fed with live adult brine shrimp thrice a day. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously (Kimmel et al., 1997).

extract_protocol:
CUT&RUN was conducted based on previously published protocol (Xia et al., 2019) with modifications in cell permeation to adapt it for zebrafish embryos. Embryos were deyolked by tweezers manually and transferred into 1.5 mL conventional, non-low-binding tube (Axygen). Then tubes were flicked several times to disperse cells in embryos, and resuspended by 60 ul washing buffer (20 mM HEPES-KOH, pH = 7.5; 150 mM NaCl; 0.5 mM Spermidine and Roche complete protease inhibitor). 10 µl Concanavalin-coated magnetic beads (Polyscience, Cat 86057) for each sample were gently washed twice, resuspended by binding buffer (20 mM HEPES-KOH, pH = 7.5; 10 mM KCl; 1 mM CaCl2; 1 mM MnCl12), and added carefully to the cells.
The cells with beads were incubated at 23C for 30 min on Thermomixer (Eppendorf) at 400 rpm, then held at magnetic stand to exclude buffer, and resuspended by 75 µl antibody buffer (washing buffer supplied with 0.02% digitonin and 2 mM EDTA, freshly made) with H3K4me3 (validated homemade) (Zhang et al., 2016) antibody, or H3K27me3 antibody (Active Motif, Cat 61017), or H2AK119ub antibody (CST, Cat 8240s) diluted at ratio of 1:100. Then the samples were incubated at 4℃ on Thermomixer overnight at 400 rpm. On the second day, the samples were washed by digitonin-washing buffer several times on magnetic stand, and resuspended with 50 µl digitonin-washing buffer supplied with 700 ng/ml pA-MNase, which is kindly provided by Dr. Steven Henikoff, and incubated at 4℃ on Thermomixer for 3hrs at 400 rpm. After that, the cells were washed by digitonin-washing buffer on magnetic stand, and resuspended by 100 µl digitonin-washing buffer on ice for at least 2 min. Targeted region digestion was activated by adding 2 µl 100 mM CaCl2 for 30 min in ice, then stopped by 100 µl 2 X stop buffer (340 mM NaCl; 20 mM EDTA, pH = 8.0; 4 mM EGTA, pH = 8.0; 50 µg/ml RNase; 100 µg/ml glycogen; 0.02% digitonin suppled with spike-in DNA) and fully vortexed. To release fragments, the samples were incubated at 37℃ on Thermomixer at 400 rpm for 20 min. Then the supernatants were purified by phenol chloroform and ethanol purification, and subjected to Tru-seq library construction using NEBNext Ultra II DNA Library Prep kit (NEB, Cat E7645S) as standard protocols. The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2508 or XTen platform according to manufacturer’s instruction.


title: HEK-PKU-PE2-16-002


title: HEK-PKU-x1-13-16-001


title: HEK-PKU-x1-13-16-002


title: WT_Input_1


title: HEK-PKU-split-16-002


title: HEK-PKU-PAM4-14-19-T-n2T-2


title: HEK-PKU-PE2-16-001


title: WT_H3K27me3_rep2


title: HEK-PKU-PAM4-14-19-T-n2T-1


title: HEK-PKU-PAM4-14-19-T-n1T-2


title: WT_H3K9me3_rep2


title: HEK-PKU-PAM4-14-19-T-n1T-1


title: HEK-PKU-PAM4-14-19-T-1


title: HEK-PKU-PAM4-14-19-T-2


title: HEK-PKU-PAM4-13-10-TT-n2T-2


title: WT_H3K9me3_rep1


title: Dome_dnmt1_mKD_H3K4me1_rep2

extract_protocol:
CUT&RUN was conducted based on previously published protocol (Xia et al., 2019) with modifications in cell permeation to adapt it for zebrafish embryos. Embryos were deyolked by tweezers manually and transferred into 1.5 mL conventional, non-low-binding tube (Axygen). Then tubes were flicked several times to disperse cells in embryos, and resuspended by 60 ul washing buffer (20 mM HEPES-KOH, pH = 7.5; 150 mM NaCl; 0.5 mM Spermidine and Roche complete protease inhibitor). 10 µl Concanavalin-coated magnetic beads (Polyscience, Cat 86057) for each sample were gently washed twice, resuspended by binding buffer (20 mM HEPES-KOH, pH = 7.5; 10 mM KCl; 1 mM CaCl2; 1 mM MnCl28), and added carefully to the cells.
The cells with beads were incubated at 23C for 30 min on Thermomixer (Eppendorf) at 400 rpm, then held at magnetic stand to exclude buffer, and resuspended by 75 µl antibody buffer (washing buffer supplied with 0.02% digitonin and 2 mM EDTA, freshly made) with H3K4me3 (validated homemade) (Zhang et al., 2016) antibody, or H3K27me3 antibody (Active Motif, Cat 61017), or H2AK119ub antibody (CST, Cat 8240s) diluted at ratio of 1:100. Then the samples were incubated at 4℃ on Thermomixer overnight at 400 rpm. On the second day, the samples were washed by digitonin-washing buffer several times on magnetic stand, and resuspended with 50 µl digitonin-washing buffer supplied with 700 ng/ml pA-MNase, which is kindly provided by Dr. Steven Henikoff, and incubated at 4℃ on Thermomixer for 3hrs at 400 rpm. After that, the cells were washed by digitonin-washing buffer on magnetic stand, and resuspended by 100 µl digitonin-washing buffer on ice for at least 2 min. Targeted region digestion was activated by adding 2 µl 100 mM CaCl2 for 30 min in ice, then stopped by 100 µl 2 X stop buffer (340 mM NaCl; 20 mM EDTA, pH = 8.0; 4 mM EGTA, pH = 8.0; 50 µg/ml RNase; 100 µg/ml glycogen; 0.02% digitonin suppled with spike-in DNA) and fully vortexed. To release fragments, the samples were incubated at 37℃ on Thermomixer at 400 rpm for 20 min. Then the supernatants were purified by phenol chloroform and ethanol purification, and subjected to Tru-seq library construction using NEBNext Ultra II DNA Library Prep kit (NEB, Cat E7645S) as standard protocols. The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2508 or XTen platform according to manufacturer’s instruction.


title: HEK-PKU-PAM4-13-10-TT-n2T-1


title: HEK-PKU-PAM4-13-10-TT-2


title: Shield_dnmt1_mKD_Sox2_rep1

data_processing:
genome build: danRer7
no additional details provided by the submitter

extract_protocol: none provided by the submitter

tag: chip antibody


title: RBKO_Input_2

value: RB1 knockout


title: Dome_ctrl_H2AK119ub_rep2

extract_protocol:
CUT&RUN was conducted based on previously published protocol (Xia et al., 2019) with modifications in cell permeation to adapt it for zebrafish embryos. Embryos were deyolked by tweezers manually and transferred into 1.5 mL conventional, non-low-binding tube (Axygen). Then tubes were flicked several times to disperse cells in embryos, and resuspended by 60 ul washing buffer (20 mM HEPES-KOH, pH = 7.5; 150 mM NaCl; 0.5 mM Spermidine and Roche complete protease inhibitor). 10 µl Concanavalin-coated magnetic beads (Polyscience, Cat 86057) for each sample were gently washed twice, resuspended by binding buffer (20 mM HEPES-KOH, pH = 7.5; 10 mM KCl; 1 mM CaCl2; 1 mM MnCl10), and added carefully to the cells.
The cells with beads were incubated at 23C for 30 min on Thermomixer (Eppendorf) at 400 rpm, then held at magnetic stand to exclude buffer, and resuspended by 75 µl antibody buffer (washing buffer supplied with 0.02% digitonin and 2 mM EDTA, freshly made) with H3K4me3 (validated homemade) (Zhang et al., 2016) antibody, or H3K27me3 antibody (Active Motif, Cat 61017), or H2AK119ub antibody (CST, Cat 8240s) diluted at ratio of 1:100. Then the samples were incubated at 4℃ on Thermomixer overnight at 400 rpm. On the second day, the samples were washed by digitonin-washing buffer several times on magnetic stand, and resuspended with 50 µl digitonin-washing buffer supplied with 700 ng/ml pA-MNase, which is kindly provided by Dr. Steven Henikoff, and incubated at 4℃ on Thermomixer for 3hrs at 400 rpm. After that, the cells were washed by digitonin-washing buffer on magnetic stand, and resuspended by 100 µl digitonin-washing buffer on ice for at least 2 min. Targeted region digestion was activated by adding 2 µl 100 mM CaCl2 for 30 min in ice, then stopped by 100 µl 2 X stop buffer (340 mM NaCl; 20 mM EDTA, pH = 8.0; 4 mM EGTA, pH = 8.0; 50 µg/ml RNase; 100 µg/ml glycogen; 0.02% digitonin suppled with spike-in DNA) and fully vortexed. To release fragments, the samples were incubated at 37℃ on Thermomixer at 400 rpm for 20 min. Then the supernatants were purified by phenol chloroform and ethanol purification, and subjected to Tru-seq library construction using NEBNext Ultra II DNA Library Prep kit (NEB, Cat E7645S) as standard protocols. The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2508 or XTen platform according to manufacturer’s instruction.


title: RBKO_H3K27me3_rep2


title: HEK-PKU-PAM4-13-10-TT-n1T-2


title: Shield_ctrl_Sox2_rep2


title: HEK3-2-009


title: Shield_ctrl_Sox2_rep1


title: WT_H3K27me3_rep1


title: Shield_dnmt1_mKD_ATAC_seq_rep2

growth_protocol: The wild-type AB strain was used in the experiments. The females after OMIS were fed with live adult brine shrimp thrice a day. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously (Kimmel et al., 2002).

extract_protocol:
The miniATAC-seq procedure was performed as previously described (Wu et al., 2018a) with modifications to adapt it for zebrafish embryos. Briefly, dispersed cells from deyolked zebrafish embryos were transferred into 6 µl lysis buffer (10 mM Tris-HCl, pH = 7.4; 10 mM NaCl; 3 mM MgCl2; and 0.02% digitonin) in ice for 17 min.
The ATAC reaction was performed by adding 4 µl ddH2O, 4 µl 5 X TTBL, and 5 µl TTE mix V5 (Vazyme, Cat TD502) at 37℃ for 30 min, then stopped by adding 5 µl 5 X TS stop buffer at room temperature for 5 min. The DNA was extracted by phenol chloroform and ethanol purification after adding 40 ng carrier RNA and 103 µl Tris-EDTA. Then the DNA was PCR amplified with 10 µl index (Vayzme, Cat TD202), 10 µl 5 X TAB and 1 µl TAE (Vayzme, Cat TD502), with the program of 72℃ for 3 min, 98℃ for 30s, (98℃ for 15s, 60℃ for 30s, and 72℃ for 3min) with 18 cycles, and 72℃ for 5 min. The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2507 or XTen platform according to manufacturer’s instruction.


title: HEK-PKU-PAM2-posctrl-2


title: RBKO_H3K27me3_rep1


title: HEK-PKU-PAM4-13-10-TT-n1T-1


title: HEK-PKU-PAM2-posctrl-1


title: HEK-PKU-PAM4-13-10-TT-1


title: RBKO_Input_1


title: Shield_ctrl_ATAC_seq_rep2

growth_protocol: The wild-type AB strain was used in the experiments. The females after OMIS were fed with live adult brine shrimp thrice a day. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously (Kimmel et al., 2000).

extract_protocol:
The miniATAC-seq procedure was performed as previously described (Wu et al., 2018a) with modifications to adapt it for zebrafish embryos. Briefly, dispersed cells from deyolked zebrafish embryos were transferred into 6 µl lysis buffer (10 mM Tris-HCl, pH = 7.4; 10 mM NaCl; 3 mM MgCl2; and 0.02% digitonin) in ice for 15 min.
The ATAC reaction was performed by adding 4 µl ddH2O, 4 µl 5 X TTBL, and 5 µl TTE mix V5 (Vazyme, Cat TD502) at 37℃ for 30 min, then stopped by adding 5 µl 5 X TS stop buffer at room temperature for 5 min. The DNA was extracted by phenol chloroform and ethanol purification after adding 40 ng carrier RNA and 103 µl Tris-EDTA. Then the DNA was PCR amplified with 10 µl index (Vayzme, Cat TD202), 10 µl 5 X TAB and 1 µl TAE (Vayzme, Cat TD502), with the program of 72℃ for 3 min, 98℃ for 30s, (98℃ for 15s, 60℃ for 30s, and 72℃ for 3min) with 18 cycles, and 72℃ for 5 min. The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2505 or XTen platform according to manufacturer’s instruction.


title: Shield_dnmt1_mKD_Sox2_rep2


title: HEK-PKU-ctrl3

extract_protocol: Detachment with TryplE, wash with PBS, lysis and DNA isolation for cell lines and whole tissue or primary hepatocyte isolation for in vivo samples.


title: Shield_dnmt1_mKD_ATAC_seq_rep1

extract_protocol:
The miniATAC-seq procedure was performed as previously described (Wu et al., 2018a) with modifications to adapt it for zebrafish embryos. Briefly, dispersed cells from deyolked zebrafish embryos were transferred into 6 µl lysis buffer (10 mM Tris-HCl, pH = 7.4; 10 mM NaCl; 3 mM MgCl2; and 0.02% digitonin) in ice for 16 min.
The ATAC reaction was performed by adding 4 µl ddH2O, 4 µl 5 X TTBL, and 5 µl TTE mix V5 (Vazyme, Cat TD502) at 37℃ for 30 min, then stopped by adding 5 µl 5 X TS stop buffer at room temperature for 5 min. The DNA was extracted by phenol chloroform and ethanol purification after adding 40 ng carrier RNA and 103 µl Tris-EDTA. Then the DNA was PCR amplified with 10 µl index (Vayzme, Cat TD202), 10 µl 5 X TAB and 1 µl TAE (Vayzme, Cat TD502), with the program of 72℃ for 3 min, 98℃ for 30s, (98℃ for 15s, 60℃ for 30s, and 72℃ for 3min) with 18 cycles, and 72℃ for 5 min. The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2506 or XTen platform according to manufacturer’s instruction.


title: HEK-PKU-ctrl2


title: HEK-PKU-ctrl1


title: P244L-008


title: RBKO_H3K9me3_rep1


title: P244L-007


title: otc004-ctrl


title: Dome_ctrl_ATAC_seq_rep1

data_processing:
All STEM-seq datasets were mapped to the danRer7 reference genome by Bismark (Krueger and Andrews, 2011). Reads were trimmed with cutadaptor (Martin, 2011) using parameters: --minimum-length 20 --pair-filter=any. Alignments were performed with the following parameters: -N 1 -X 600 --score_min L,0,-0.6. Multi-mapped reads and PCR duplicates were removed. bismark_methylation_extractor was used to calculate the DNA methylation level.
Total RNA-seq data were firstly processed using Trim Galore! with default parameters to trim the adapter-containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome (danRer7) by STAR (version: STAR_2.5.3a_modified) (Dobin et al., 2013) with the following parameters: --outSAMstrandField intronMotif --outSAMattributes All --outSAMunmapped Within --outSAMattrIHstart 0 --outWigStrand Stranded --outFilterMultimapNmax 20 --twopassMode Basic. The gene expression level was normalized to fragments per kilobase of transcript per million mapped (FPKM) values using Cufflinks (version 2.2.1) (Trapnell et al., 2012).
The scRNA-seq data were processed with Cell Ranger 3.1 for genome alignment (danRer10), transcript counting, and gene-cell-barcode matrix generation. Before the downstream analysis, cells with unique detected genes lower than <2,000 and higher than 6,000 genes were discarded, and cells with high percentage of mitochondrial genes (>5%) were removed too. Subtypes of cells were identified with Seurat 3.0 through the integrating of control and mKD embryos at dome and shield stages with setting control embryos as reference. To make the data comparable samples, we performed SCTransform normalization separately for each dataset. To further reduce the bais caused by sequencing depth of scRNA-seq and percentage of mitochondrial genes, UMI variance and percent.mt were regressed out from SCTransform normalized data matrix by linear model with negative binomial distribution.
All ChIP-seq reads were aligned to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM). To visualize the STAR ChIP-seq signal in the UCSC genome browser, each read was extended by 250 bp and the coverage for each base was counted. Replicates of STAR ChIP-seq were pooled for the downstream analysis.
The ATAC-seq data were mapped to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM). To minimize the batch and cell type variation, RPKM values across whole genome were further Z-score normalized. To visualize the CUT&RUN signals in the UCSC genome browser, each read was extended by 250 bp and the coverage for each base was counted.
Genome_build: danRer7
Supplementary_files_format_and_content: Matrix for scRNA-seq data, gene expression table for total RNA-seq data, Bigwig and narrowPeak for ChIP-seq and ATAC-seq data

extract_protocol:
The miniATAC-seq procedure was performed as previously described (Wu et al., 2018a) with modifications to adapt it for zebrafish embryos. Briefly, dispersed cells from deyolked zebrafish embryos were transferred into 6 µl lysis buffer (10 mM Tris-HCl, pH = 7.4; 10 mM NaCl; 3 mM MgCl2; and 0.02% digitonin) in ice for 10 min.
The ATAC reaction was performed by adding 4 µl ddH2O, 4 µl 5 X TTBL, and 5 µl TTE mix V5 (Vazyme, Cat TD502) at 37℃ for 30 min, then stopped by adding 5 µl 5 X TS stop buffer at room temperature for 5 min. The DNA was extracted by phenol chloroform and ethanol purification after adding 40 ng carrier RNA and 103 µl Tris-EDTA. Then the DNA was PCR amplified with 10 µl index (Vayzme, Cat TD202), 10 µl 5 X TAB and 1 µl TAE (Vayzme, Cat TD502), with the program of 72℃ for 3 min, 98℃ for 30s, (98℃ for 15s, 60℃ for 30s, and 72℃ for 3min) with 18 cycles, and 72℃ for 5 min. The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.

tag: developmental stage

value: Dome

value: embryo


title: P244-001-ctrl

tag: genotype


title: Dome_ctrl_ATAC_seq_rep2

tag: tissue


title: otc2-2-PedRnase-r1


title: P244-003-ctrl


title: otc2-2Pe-r1


title: otc2-2-PedRnase-r2


title: otc001-ctrl


title: Shield_dnmt1_mKD_H3K27ac_rep1

description: STAR ChIP-seq

extract_protocol:
The ChIP procedure was based on a previously described method (Zhang et al., 2018a). Embryos were deyolked by repeatedly blowing with a 200 µl pipette and cell pellets were collected by spinning down at 5000 rpm for 5 min at 4℃. After centrifuge, cell pellet was lysed in 40 µl lysis buffer (0.5% NP-40, 0.5% Tween, 0.1% SDS and proteinase inhibitor) with pipetting up and down several times.
0.1 unit of MNase (Sigma, Cat N3755) was added for chromatin digestion at 37℃ for 5 min. The reaction was then terminated by adding 1 µl 0.5 M EGTA. IP sample was incubated with 1 µg H3K4me3 antibody (Homemade) (Zhang et al., 2016) and 2 µg H3K27me3 antibody (Active Motif, Cat 61017) overnight with rotation at 4℃. In the next day, the sample was incubated with 300 µg protein A or protein G dynabeads (Life technologies, Cat 10001D or 10003D) for 2hrs with rotation at 4℃. The beads were washed 5 times in 150 µl RIPA buffer and once in 150 µl LiCl buffer. After washing, spin tubes briefly and remove the supernatant. For each IP sample, resuspend beads with 27 µl ddH2O and 1 µl 10x Ex-Taq buffer (TaKaRa). 1 µl proteinase K (Roche, Cat 10910000) was then added and the mix was incubated at 55℃ for 90 min to elute DNA from beads. The supernatant was then transferred to a new tube and the proteinase K was inactivated at 72℃ for 40 min. 1 µl rSAP (NEB, Cat M0371) was then added to dephosphorylate 3’ end of DNA at 37℃ for 1hr. rSAP was inactivated at 65℃ for 10 min. The resulting sample was subjected to TELP library preparation as previously described (Peng et al., 2015). The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.

value: Shield


title: Shield_ctrl_H3K27ac_rep1

description: STAR ChIP-seq


title: Shield_dnmt1_mKD_H3K4me1_rep1

extract_protocol:
CUT&RUN was conducted based on previously published protocol (Xia et al., 2019) with modifications in cell permeation to adapt it for zebrafish embryos. Embryos were deyolked by tweezers manually and transferred into 1.5 mL conventional, non-low-binding tube (Axygen). Then tubes were flicked several times to disperse cells in embryos, and resuspended by 60 ul washing buffer (20 mM HEPES-KOH, pH = 7.5; 150 mM NaCl; 0.5 mM Spermidine and Roche complete protease inhibitor). 10 µl Concanavalin-coated magnetic beads (Polyscience, Cat 86057) for each sample were gently washed twice, resuspended by binding buffer (20 mM HEPES-KOH, pH = 7.5; 10 mM KCl; 1 mM CaCl2; 1 mM MnCl2), and added carefully to the cells.
The cells with beads were incubated at 23℃ for 30 min on Thermomixer (Eppendorf) at 400 rpm, then held at magnetic stand to exclude buffer, and resuspended by 75 µl antibody buffer (washing buffer supplied with 0.02% digitonin and 2 mM EDTA, freshly made) with H3K4me3 (validated homemade) (Zhang et al., 2016) antibody, or H3K27me3 antibody (Active Motif, Cat 61017), or H2AK119ub antibody (CST, Cat 8240s) diluted at ratio of 1:100. Then the samples were incubated at 4℃ on Thermomixer overnight at 400 rpm. On the second day, the samples were washed by digitonin-washing buffer several times on magnetic stand, and resuspended with 50 µl digitonin-washing buffer supplied with 700 ng/ml pA-MNase, which is kindly provided by Dr. Steven Henikoff, and incubated at 4℃ on Thermomixer for 3hrs at 400 rpm. After that, the cells were washed by digitonin-washing buffer on magnetic stand, and resuspended by 100 µl digitonin-washing buffer on ice for at least 2 min. Targeted region digestion was activated by adding 2 µl 100 mM CaCl2 for 30 min in ice, then stopped by 100 µl 2 X stop buffer (340 mM NaCl; 20 mM EDTA, pH = 8.0; 4 mM EGTA, pH = 8.0; 50 µg/ml RNase; 100 µg/ml glycogen; 0.02% digitonin suppled with spike-in DNA) and fully vortexed. To release fragments, the samples were incubated at 37℃ on Thermomixer at 400 rpm for 20 min. Then the supernatants were purified by phenol chloroform and ethanol purification, and subjected to Tru-seq library construction using NEBNext Ultra II DNA Library Prep kit (NEB, Cat E7645S) as standard protocols. The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.


title: gaba1-5PedRnase-r2


title: Shield_ctrl_ATAC_seq_rep1

extract_protocol:
The miniATAC-seq procedure was performed as previously described (Wu et al., 2018a) with modifications to adapt it for zebrafish embryos. Briefly, dispersed cells from deyolked zebrafish embryos were transferred into 6 µl lysis buffer (10 mM Tris-HCl, pH = 7.4; 10 mM NaCl; 3 mM MgCl2; and 0.02% digitonin) in ice for 14 min.
The ATAC reaction was performed by adding 4 µl ddH2O, 4 µl 5 X TTBL, and 5 µl TTE mix V5 (Vazyme, Cat TD502) at 37℃ for 30 min, then stopped by adding 5 µl 5 X TS stop buffer at room temperature for 5 min. The DNA was extracted by phenol chloroform and ethanol purification after adding 40 ng carrier RNA and 103 µl Tris-EDTA. Then the DNA was PCR amplified with 10 µl index (Vayzme, Cat TD202), 10 µl 5 X TAB and 1 µl TAE (Vayzme, Cat TD502), with the program of 72℃ for 3 min, 98℃ for 30s, (98℃ for 15s, 60℃ for 30s, and 72℃ for 3min) with 18 cycles, and 72℃ for 5 min. The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2504 or XTen platform according to manufacturer’s instruction.


title: M328P_miR145_B

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

hyb_protocol: Agilent : 200.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and paired differential analysis in R / Bioconductor.

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Qiagen - miRNeasy

value: BRAFV600E mutant human melanoma

value: miR145 overexpression

tag: amount in (µg)

tag: rin number


title: Shield_ctrl_H3K4me1_rep1


title: M328P_miR143_B

value: miR143 overexpression


title: M328P_miR143_A


title: gaba1-5Pe-r1

value: cell lysate_HEK293T


title: LJCN2 Degradome-seq

city: Nanjing

first: Anburaj

last: Jeyaraj

state: Jiangsu

address: No. 1 Weigang

institute: Nanjing Agricultural University

data_processing:
Library strategy: Degradome-Seq
Degradome-Seq: Raw sequencing reads were obtained using Illumina’s software to remove adaptors and low quality reads.
Degradome-Seq: The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline.
Degradome-Seq: The degradome reads were mapped to the mRNA database. Only the perfect matching alignment(s) for the given read would be kept for degradation analysis.
Degradome-Seq: All resulting reads (t-signature) were reverse- complemented and aligned to the miRNA identified in our study. No more than four alignment scores were allowed. Alignments where the degradome sequence position coincident with the tenth or eleventh nucleotide of miRNA were retained and scored. The target was selected and categorized as 0, 1, 2，3，or 4. category 0—over one raw read at the position, abundance at the position is equal to the maximum on the transcript, and there is only one maximum on the transcript; category 1—over one raw read at theposition, abundance at the position is equal to the maximum on the transcript, and there is more than one maximum position on the transcript; category 2—over one raw read at the position, abundance at position is less than the maximum but higher than the median for the transcript; category 3—over one raw read at the position, abundance at the position is equal to or less than the median for the transcript; and category 4—only one raw read at the position.
Genome_build: http://tpia.teaplant.org/web/Download/Genomic_data/Teaplant_CSS_Genome.fas.gz
Supplementary_files_format_and_content: excel,expression profiles

organism: Camellia sinensis

source_name: Tea leaves

growth_protocol: Two-year-old tea plants [Camellia sinensis (L.) O. Kuntze, susceptible cultivar Longjing43 (LJ43) and the resistant cultivar Zhongcha108 (ZC108)] with different levels of resistance to anthracnose were pre-incubated in an artificial climate chamber at 25 ± 1 °C with 85 ± 5 % relative humidity, 14/10 h (day/night) photoperiod and photosynthetic photo flux density (300 μmol m-2 s-1) for 2 weeks.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
The libraries were sequenced by Illumina Hiseq 2500/Hiseq 4000 at the LC-BIO following the vendor’s recommended protocol.

treatment_protocol: After 2 weeks of acclimation, tea plants were subjected to inoculation with C. gloeosporioides and exogenous treatment of caffeine for the identification of miRNA regulatory networks in response to C. gloeosporioides stress. Tea plants were also mock-inoculated with sterile distilled water. All experimental plants were watered duly and fertilized with Hoagland’s solution once a week.

value: Leaves collected at 7dpi

value: Zhongcha

tag: fungal pathogen

value: Colletotrichum gloeosporioides and exogenous caffeine-inoculated


title: RBKO_H3K9me3_rep2

tag: cell line


title: gaba1-5Pe-r2


title: otc2-2Pe-r2


title: Shield_dnmt1_mKD_H3K27ac_rep2

description: STAR ChIP-seq

value: AB

value: WT

value: Oocyte microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage (GV)


title: Gaba001-ctrl

value: Prime-editor with pegRNA

value: targeted amplicon sequencing


title: LJCN1 Degradome-seq

value: exogenous caffeine-inoculated


title: Dome_ctrl_H3K4me1_rep1

value: Oocyte microinjection with Rhodamine B and control MO at oogenesis III stage (GV)


title: eIF2B5002-ctrl

value: prime-edited genomic locus


title: LJCg3 Degradome-seq


title: eIF2B5001-ctrl


title: Gaba002-ctrl


title: Shield_dnmt1_mKD_H3K4me3_rep1

value: embryo


title: eIF2B4002-ctrl


title: gaba1-5PedRnase-r1


title: eIF2B5-6PedRnase-r2


title: eIF2B4001-ctrl


title: Shield_dnmt1_mKD_H3K4me3_rep2

value: Shield


title: M328P_miR145_A

tag: cell type

value: BRAFV600E mutant human melanoma

tag: genotype/variation


title: Pahenu2-548adult

value: whole liver lysate

value: systemic injection of AAV8


title: Shield_ctrl_H3K4me3_rep2

tag: strain


title: eIF2B5-6PedRnase-r1

value: cell lysate_HEK293T


title: M328P_miRNeg_B

value: miR-Neg overexpression


title: eIF2B5-6Pe-r2


title: LJCg1 Degradome-seq

value: Leaves collected at 7dpi

value: Longjing


title: eIF2B5-6Pe-r1


title: eIF2B4P244L005


title: eIF2B4-4PedRnase-r2


title: LJCK2 Degradome-seq


title: Dome_ctrl_H3K4me3_rep2

value: AB

value: Dome


title: LJCg2 Degradome-seq

value: Zhongcha

value: Mock-inoculated


title: Shield_dnmt1_mKD_H2AK119ub_rep2

value: WT

value: Oocyte microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage (GV)