title: Human iPSCs, DM1, S118

city: Kodaira

first: Masayoshi

last: Kamon

state: Tokyo

address: 4-1-1 Ogawa-Higashi

department: Department of PNS Research

institute: National Center of Neurology and Psychiatry

description:
S118
Gene expression data from subclone 118 of human iPSCs from DM1 patient.

hyb_protocol: Following fragmentation, biotinylated cDNA were hybridized on GeneChip Clariom D Array, Human. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings and global scaling as normalization method (SST-RMA).

source_name: Subclone 118 of human iPSCs from DM1 patient

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA.

growth_protocol: Human iPSCs were cultured in Primate ES Cell medium supplemented with 8 ng/ml basic fibroblast growth factor on mitomycin C-treated SNL feeder cells.

extract_protocol: TRI Reagents extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 70–80% confluent iPSCs were harvested.

value: Human iPSCs

value: Peripheral blood

tag: disease state

value: Myotonic dystrophy type 1 (DM1)

tag: Sex

value: Male


title: DiFi_TC2_02d_1

status: Public on Dec 16 2024

type: SRA

city: Houston

first: exRNA

last: BRL

state: TX

address: One Baylor Plaza

department: Molecular & Human Genetics - Milosavljevic

country: USA

institute: Baylor College of Medicine

library_source: transcriptomic

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

molecule: total RNA

organism: Homo sapiens

source_name: cell culture

extract_protocol:
RNA Isolation method was "500uL of biofluid was incubated with 100uL warmed Slurry and 900uL warmed Lysis Buffer A (containing 2-Mercaptoethanol) for 10 min at 60C. To this 1.5 mL of 100% ethanol was added and centrifuged for 2min at 1000rpm. To the pellet 300uL Lysis Buffer A was added and incubated for 10 min at 60C. 300uL 100% Ethanol was added, loaded onto the filter column and centrifuged for 30sec at 1000xg followed by 1 min at 16000xg. The column was washed thrice with 400uL Wash Solution for 1 min at 16000 xg and then centrifuged once again for 3 min to dry the membrane. RNA was eluted in 14uL water with a slow spin for 2 mins at 300 xg followed by a spin for 3 min at 16000 xg.". RNA Isolation kit was Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek).
Library construction kit was NEBNext small RNA library prep (NEB). Samples were multiplexed. Type of Starting Material was total RNA.

tag: condition

value: Colorectal Carcinoma

tag: anatomical location

value: Colon structure

tag: rna source

value: other


title: C-2

city: Shanghai

first: Lei

last: Hou

state: Shanghai

address: 746 Zhongshan Middle Road

department: Department of Cardiology

country: China

institute: Songjiang Hospital and Songjiang Research Institute, School of Medicine, Shanghai Jiao Tong University

description:
Library name: Sample 2
C-2 in tpm_allsamples.txt

data_processing:
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters - mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Assembly: NCBI_GCF_000001635.27_GRCm39
Supplementary files format and content: tab-delimited text file includes TPM for each Sample

organism: Mus musculus

source_name: Primary ADSCs

extract_protocol:
RNA was harvested using Trizol (Takara). 800 ug of total RNA was used for the construction of sequencing libraries.
The extracted mRNA is enriched using mRNA Capture Beads. After purification with beads, the mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While synthesizing the second strand of cDNA, end repair and A-tailing are completed. Next, adapters are ligated, and Hieff NGS® DNA Selection Beads are used for purification to select target fragments.

tag: cell type

value: Primary ADSCs

tag: genotype

value: WT

tag: treatment

value: Ctrl

tag: batch

value: batch 2


title: DiFi_TC1_01w_3


title: Human iPSCs, DM1, S24

type: RNA

country: Japan

description:
S24
Gene expression data from subclone 24 of human iPSCs from DM1 patient.

label: biotin

source_name: Subclone 24 of human iPSCs from DM1 patient

tag: tissue


title: Human iPSCs, DM1, S16

description:
S16
Gene expression data from subclone 16 of human iPSCs from DM1 patient.

source_name: Subclone 16 of human iPSCs from DM1 patient


title: Human iPSCs, normal

description:
Normal
Gene expression data from human iPSCs, 409B2. Skin.

source_name: Human iPSC, 409B2, RIKEN

tag: cell line

value: Healthy


title: Ki67Cre_H1N1_tam07_sac366_rep1

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description: CellMetaData.csv

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, alignment and gene counting was performed using the STARSolo 2.7.9a
Ambineat RNAs were removed using SoupX
Clustering and dimesion reduction using Seurat V4
Assembly: GRCm39
Supplementary files format and content: SoupX processed H5 counts
Supplementary files format and content: CellMetaData.csv Cell annotation file

source_name: Lung

extract_protocol:
Cells were loaded onto the 10x Chromium (10X Genomics) aiming for 10,000 cells per sample.
Libraries were prepared according to the manufacturer’s protocol using Chromium Single Cell 3’ v2 chemistry.

treatment_protocol: Tamoxifen as noted; H1N1 PR8 influenza virus infection at "day 0"

value: Lung

tag: time


title: Human iPSCs, DM1, S1

description:
S1
Gene expression data from subclone 1 of human iPSCs from DM1 patient.

source_name: Subclone 1 of human iPSCs from DM1 patient


title: DiFi_TC2_02d_3


title: DiFi_TC1_04w_1


title: C-1

description:
Library name: Sample 1
C-1 in tpm_allsamples.txt

value: batch 1


title: DiFi_TC2_01d_1


title: Ki67Cre_H1N1_tam14_sac366_rep1

description: CellMetaData.csv


title: Human iPSCs, DM1, S45

description:
S45
Gene expression data from subclone 45 of human iPSCs from DM1 patient.

source_name: Subclone 45 of human iPSCs from DM1 patient


title: DiFi_250_HollowFiber2_3


title: DiFi_2500_HollowFiber2_3


title: Ki67Cre_H1N1_tam14_sac366_rep2

description: CellMetaData.csv


title: Human iPSCs, DM1, S14

description:
S14
Gene expression data from subclone 14 of human iPSCs from DM1 patient.

source_name: Subclone 14 of human iPSCs from DM1 patient


title: DiFiP2C2


title: DiFi_TC1_02w_1


title: HSES2M_BRM_1

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Affymetrix Clariom D Array one-color based hybridization protocol, cDNA samples were hybridized at 45°C for 16 h on separate Affymetrix Human Clariom D™ Arrays

scan_protocol: Affymetrix GeneChip 3000 Scanner

data_processing:
Raw data (.CEL files) were processed using the RMA (Robust Multi-array Average) normalization method implemented in the `oligo` package in R (version 4.0.3). Background correction and probe summarization were performed as described in the Affymetrix Clariom D Human array documentation. ProbeIDs were matched to Gene Symbols using the R package clariomdhumantranscriptcluster.db.
Clariom_D_Human.r1.pgf
Clariom_D_Human.r1.mps

source_name: Epithelioid Sarcoma cell line

label_protocol: Affymetrix GeneChip WT PLUS Reagent Kit, according to the manufacturer's protocol

growth_protocol: All cell lines were cultured in RPMI 1640 with stable glutamine (Gibco) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin (Sigma-Aldrich) at 37°C in a fully humidified 5% CO2 atmosphere. Cell lines were routinely tested for Mycoplasma contamination using a custom nested PCR protocol.

extract_protocol: For RNA extraction, the NucleoSpin RNA kit from Macherey-Nagel (Duren, Germany) was used following the manufacturer’s protocol.

treatment_protocol: 96h Dox or no Dox, BRM014 (1µM) or DMSO

tag: cell model type

value: isogenic SMARCB1 tetON

value: BRM


title: EdnrbCre_H1N1_tam-pre_sac19_rep3

description: CellMetaData.csv


title: HSES2M_DMSO_2

value: DMSO


title: DiFiP3C1


title: EdnrbCre_H1N1_tam-pre_sac19_rep1

description: CellMetaData.csv


title: Car4Cre_H1N1_tam-pre_sac19_rep2

description: CellMetaData.csv


title: Car4Cre_H1N1_tam-pre_sac19_rep1

description: CellMetaData.csv


title: DiFi_TC2_04d_2


title: DiFi_TC2_05d_2


title: DiFi_TC2_14d_1


title: DiFi_TC2_14d_2


title: HSES2R_DMSO_3


title: DiFi_TC2_21d_3


title: KitMCM_H1N1_tam-pre_sac19_rep3

description: CellMetaData.csv


title: KitMCM_H1N1_tam-pre_sac19_rep2

description: CellMetaData.csv


title: Ki67Cre_H1N1_tam14_sac90_rep1

description: CellMetaData.csv


title: DiFi_TC2_10d_1


title: DiFi_TC1_03w_1


title: DiFi_TC2_14d_3


title: Ki67Cre_H1N1_tam21_sac90_rep1

description: CellMetaData.csv


title: Ki67Cre_H1N1_tam02_sac90_rep1

description: CellMetaData.csv


title: Ki67Cre_H1N1_tam07_sac90_rep1

description: CellMetaData.csv


title: KitMCM_H1N1_tam-pre_sac19_rep1

description: CellMetaData.csv


title: DiFi_CD63_F2


title: Ki67Cre_H1N1_tam21_sac42_rep2

description: CellMetaData.csv


title: DiFi_CD81_B3


title: Ki67Cre_H1N1_tam07_sac42_rep2

description: CellMetaData.csv


title: DiFi_CD81_B2


title: EdnrbCre_H1N1_tam-pre_sac19_rep2

description: CellMetaData.csv


title: DiFi_CD63_F3


title: DiFi_IgG_B1


title: DiFi_TC1_03w_2


title: Ki67Cre_H1N1_tam02_sac42_rep2

description: CellMetaData.csv


title: Ki67Cre_H1N1_tam14_sac42_rep2

description: CellMetaData.csv


title: DiFi_CD9_F1


title: DiFi_CD9_F3


title: Ki67Cre_H1N1_tam14_sac19_rep2

description: CellMetaData.csv


title: DiFi_CD63_B3


title: Ki67Cre_H1N1_tam07_sac11_rep2

description: CellMetaData.csv


title: Ki67Cre_H1N1_homeostasis_d03_rep1

description: CellMetaData.csv

value: Tamoxifen


title: Ki67Cre_H1N1_tam02_sac06_rep2

description: CellMetaData.csv


title: DiFi_Input_2

value: total cell-free biofluid RNA


title: DiFi_CD81_B1


title: DiFi_CD9_B3


title: DiFi_CD9_F2


title: Ki67Cre_H1N1_tam14_sac42_rep1

description: CellMetaData.csv


title: DiFi_CD9_B1


title: DiFi_IgG_B3


title: Ki67Cre_H1N1_homeostasis_d42_rep1

description: CellMetaData.csv


title: DiFi_Input_3


title: DiFi_IgG_F2


title: Ki67Cre_H1N1_tam07_sac42_rep1

description: CellMetaData.csv


title: Ki67Cre_H1N1_tam07_sac11_rep1

description: CellMetaData.csv


title: Ki67Cre_H1N1_tam21_sac25_rep1

description: CellMetaData.csv


title: DiFi_Input_1


title: DiFi_CD63_F1


title: DiFi_CD63_B2


title: Ki67Cre_H1N1_tam02_sac06_rep1

description: CellMetaData.csv


title: Ki67Cre_H1N1_tam14_sac19_rep1

description: CellMetaData.csv


title: DiFi_2500_HollowFiber2_1


title: Ki67Cre_H1N1_tam21_sac25_rep2

description: CellMetaData.csv


title: DiFi_CD81_F3


title: Lung metastatic B16F10 cells with druggable library treatment by IgG

city: Beijing

first: Hu

last: Haitian

address: Haidian Beijing

institute: Tsinghua University

library_source: genomic

data_processing:
The read counts of each oligo in the sgRNA library were calculated with MAGeCK packages according to the protocol described in "Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute" (Nat Protoc, 2019).
Assembly: library
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: genomic DNA

source_name: lung

extract_protocol:
Metastatic tumors were harvested from lungs and then extract genomic DNA by TE buffer with proteinase K.
PCR of sgRNAs for Illumina sequencing

treatment_protocol: B16F10 cells were transfected with a druggable sgRNA library. Then, these cells will be injected mice through tail vein. Mice were treated by IgG or anti-Csf1R antibody before tumor cell injection.

value: lung

value: Mouse melanoma

value: IgG


title: DiFi_CD9_B2

value: Colorectal Carcinoma

value: Colon structure


title: Lung metastatic B16F10 cells with druggable library treatment by aCsf1R


title: B16F10 cells with druggable library in vitro


title: Lma-RANKL

data_processing:
Illumina adapter sequences have been trimmed off the reads, which weresubsequently mapped against the mm10 mouse reference using STAR (version2.6.0c). The counts for each gene were obtained by using featureCounts(version 1.6.2), and the minimum mapping quality score were set to 30.Assembly:mm10; hg19Supplementary files format and content: Processed data provided assupplementary file
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was harvested by RNeasy Plus Micro kit (QIAGEN). Total RNA was used for the construction of sequencing libraries
RNA libraries for sequencing were prepared using Smart-seq RNA kit. Library construction and sequencing were processed by GENEWIZ(Suzhou, CHINA)

value: Mo-macs

value: RANKL


title: DiFi_CD81_F1

value: other


title: DiFi_CD81_F2


title: Ki67Cre_H1N1_tam02_sac42_rep1

description: CellMetaData.csv


title: Lma-PBS

value: WT

value: PBS


title: DiFi_IgG_B2


title: D130

city: San Antonio

first: JINGRUO

last: ZHANG

state: TEXAS

address: 8403 Floyd Curl Dr

institute: UT HEALTH SAN ANTONIO

description: 10 X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger), and the downstream analysis was performed by Seurat package.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
Bone marrow cells were extracted using a syringe, and residual bone fragments were enzymatically digested with collagenase. Following red blood cell lysis, the bone marrow cells were suspended in flow buffer (DPBS+2% FBS), filtered using a cell strainer, stained with markers (CD31, CD45, Ter119, CD51, PDGFRα) at 4℃ for 1 hr, and subsequently sorted using a BD FACSAria.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: bone marrow

tag: strain

value: BM-MSCs

tag: age

value: 6-8 week


title: DiFi_CD63_B1


title: R76W

description: 10 X Genomics


title: DiFi_IgG_F1


title: WT

description: 10 X Genomics


title: DiFi_Miltenyi_CD9_FT1_1

tag: rna isolation kit

value: Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)


title: DiFi_IgG_F3


title: Wildtype lung - H1N1 day 14

city: Iowa City

first: Dakota

middle: L

last: Jones

state: IA

address: 51 Newton Road

department: Department of Anatomy and Cell Biology

institute: University of Iowa

description: 10x Genomics

data_processing:
The sequenced data was processed by aligning reads and obtaining unique molecular identifiers (UMIs) using STARsolo (v2.7.9a) (ref). For scRNA-seq from lineage-traced samples, libraries were aligned to a modified mm39 mouse genome to include the tdTomato reference sequence. The scRNA-seq data was further processed and analyzed using the Seurat v4 package (ref). Cells which had less than 200, or greater than 5000, detected genes were removed from the analysis. Cells were also removed if the percent mitochondrial reads were greater than 10%. Feature (gene) data was scaled in order to removed unwanted sources of variation using the Seurat SCTransform function based on percent mitochondrial reads, and the number of genes, and total reads. Integrated libraries were integrated using the RPCA method within Seurat. Non-linear dimension reduction was performed using uniform manifold approximation and projections (UMAPs) and Louvain graph-based clustering algorithms.
Assembly: mm39
Supplementary files format and content: h5

extract_protocol:
Lineage-traced cells were sorted by gating DAPI-, CD45-PeCy7-, CD31/326-APC-, tdTomato+ populations. The tdTomato+ cells were then loaded onto the 10x Chromium (10X Genomics). Epithelial and endothelial cells were sorted by gating DAPI-, CD45-PeCy7-, CD31/326-APC+. Immune cells were sorted by gating DAPI-, CD45-PeCy7+. Immune cells were then spiked back in with the epithelial and endothelial cells at a concentration of 25%. The resultant epithelial, endothelial, and immune cell mixture was then loaded onto the 10x Chromium (10x Genomics).  For the whole-lung scRNAseq presented in Figure 6, mouse lungs were digested and single cell suspensions were prepared as described above. Cell suspensions were then incubated with magnetic CD45 microbeads (Miltenyi Biotec, 130-052-301) for 30 minutes on ice. Cells were then passed through a magnetic column (LS column, Miltenyi Biotech) to deplete the cell suspension of CD45+ immune cells. CD45+ immune cells were then later recovered and spiked back into the CD45-depleted cell suspension at a concentration of 20%. The resultant cell mixture as then loaded onto the 10x Chromium controller.
All samples were loaded to aim for a recovery of 10,000 cells, and libraries were prepped according to the manufacturer’s protocol using the Chromium Single Cell 3’ v3 chemistry. Libraries were then sequenced on an Illumina Novaseq 6000 instrument.

value: whole lung

value: Pdgfra-CreERT2 x Rosa26-tdTomato

value: H1N1 influenza - day 14


title: Pdgfrb-lineage - bleomycin day 14

description: 10x Genomics

value: lung

value: Pdgfrb-lineage trace

value: Pdgfrb-CreERT2 x Rosa26-tdTomato

value: bleomycin - day 14


title: Pdgfra-Notch-KD - H1N1 day 14

description: 10x Genomics

value: Pdgfra-CreERT2 x Rosa26-dnMAML


title: DiFi_Miltenyi_CD63_B1_4

value: Colorectal Carcinoma

value: Colon structure


title: DiFi_Miltenyi_CD63_FT1_2

value: other


title: DiFi_Miltenyi_CD63_B1_6


title: DiFi_Miltenyi_IgG_B2_1

value: total cell-free biofluid RNA


title: DiFi_Miltenyi_CD81_FT2_2


title: Epithelial, endothelial, and immune cells - bleomycin day 14

description: 10x Genomics

value: epithelial, endothelial, and immune


title: DiFi_Miltenyi_IgG_B2_3


title: DiFi_Miltenyi_CD81_B1_5


title: Pdgfrb-lineage - bleomycin day 28

description: 10x Genomics

value: bleomycin - day 28


title: DiFi_Miltenyi_CD63_B1_5


title: Epithelial, endothelial, and immune cells - H1N1 influenza day 28

description: 10x Genomics

value: H1N1 influenza - day28


title: Pdgfra-lineage - bleomycin day 14

description: 10x Genomics

value: Pdgfra-lineage trace


title: Pdgfra-lineage - homeostasis

description: 10x Genomics

value: homeostasis


title: DiFi_Miltenyi_CD81_FT2_3

value: Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)


title: DiFi_Miltenyi_CD9_B1_5


title: Pdgfra-lineage - H1N1 influenza day 28

description: 10x Genomics

value: Pdgfra-CreERT2 x Rosa26-tdTomato


title: Pdgfrb-lineage - H1N1 influenza day 14

description: 10x Genomics

value: H1N1 influenza - day 14


title: DiFi_Miltenyi_CD63_FT2_3


title: Epithelial, endothelial, and immune cells - H1N1 influenza day 14

description: 10x Genomics

value: lung


title: Pdgfra-lineage - H1N1 influenza day 14

description: 10x Genomics


title: Pdgfrb-lineage - H1N1 influenza day 28

description: 10x Genomics

value: Pdgfrb-lineage trace


title: DiFi_Miltenyi_CD9_B1_4


title: DiFi_Miltenyi_CD9_B1_6


title: Epithelial, endothelial, and immune cells - bleomycin day 28

description: 10x Genomics


title: DiFi_Miltenyi_CD63_B2_3


title: Pdgfrb-lineage - homeostasis

description: 10x Genomics

value: Pdgfrb-CreERT2 x Rosa26-tdTomato


title: Epithelial, endothelial, and immune cells - homeostasis

description: 10x Genomics


title: Pdgfra-lineage - bleomycin day 28

description: 10x Genomics


title: DiFi_Miltenyi_CD63_FT2_2


title: bone marrow mix of wildtype and Ythdf2 cKO mice

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

data_processing:
Raw scRNA-seq data were processed demultiplexed and using 10 ×Genomics Cell Ranger (v7.1.0). Sequenced reads were aligned to mouse reference genome (GRCm38). Louvain clustering algorithm was used to group the cells into different clusters.
Assembly: GRCm38
Supplementary files format and content: gene expression in txt format

extract_protocol:
BM cells were collected and treated one time with 10 mL ammonium chloride (07850, StemCell technologies) followed by two times wash with 2% regular RPMI 1640 cell culture medium. Then, diluted 1 million cells of each BM sample in 49.5 µL of cell staining buffer (420201, Biolegend) in 12 x 75mm flow cytometry tubes and blocked cells with 0.5 µL anti-mouse CD16/CD32 antibody for 10 minutes on ice. Then diluted 1 µg TotalSeq type C antibody into cell staining buffer with a final volume of 50 µL and centrifuged at 14, 000 g at 4ºC for 10 minutes and subsequently added into 50 µL blocked cell suspension and incubated 30 minutes at 4ºC. Each antibody stained one mouse BM cells. After staining, a total wash of 3 times with 3 mL cell staining buffer by spinning down at 4ºC for 5 minutes at 600 g followed by filtering cells through a 40 µm Flowmi Cell strainer (BAH136800040-50EA, Sigma-Aldrich) with 500 mL cell staining buffer. Combined the 4 mice BM cells with featured antibodies with equal cell amounts. Then prepared a total number of exactly 10, 000 cells for 10×Genomics single cell platform to generate single cell by partitioning and recovery within the 10× Chromium chip and prepare the library.
Chromium Next GEM Single Cell 5’ Reagent Kits v2 with Feature Barcode technology for cell surface protein

value: bone marrow

value: wildtype and cKO

value: Poly I:C


title: DiFi_Miltenyi_CD81_FT2_1

value: Colorectal Carcinoma

value: Colon structure


title: DiFi_Miltenyi_CD81_B1_4

value: total cell-free biofluid RNA


title: DiFi_Miltenyi_CD81_B2_3


title: DiFi_Miltenyi_IgG_FT1_2

value: other


title: DiFi_Miltenyi_CD9_B2_3


title: DiFi_Miltenyi_CD9_FT2_2


title: DiFi_Miltenyi_CD63_B2_1


title: Week8_Tamoxifen_aKO_H4K20me2and3_Rep3

first: Sameer

middle: Subhash

last: Bajikar

address: 1250 Moursund St

department: Molecular and Human Genetics

data_processing:
Adapter sequences were removed from sequence reads using Trimmomatic version 0.36 (2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25) from the Truseq3.PE.fa adapter library and kseq
Confirmation of adapter removal and read quality was performed with fastqc (v0.11.8)
Alignment was performed with bowtie2-2.3.4.1 (--dovetail --phred33) to both mm10 (GRCm38 GCA_000001635.2) and the spike-in Ecoli K12 Genomes (GCF_000005845.2_ASM584v2)
Bedtools (v2.29.1) was used to process BAM files to BED files, remove blacklist (mm9 blacklist lifted over to mm10 and combined with mm10 blacklist downloaded with CUT&RUNTools (Zhu et al., 2019) and to generate bedgraphs
Each sample was normalized to internal Ecoli spike-in utilizing spike_in_calibration.sh as described previously (Meers et al., 2019)
Assembly: mm10 and E. coli
Supplementary files format and content: E. coli spike in normalized bigwig tracks
Library strategy: CUT&RUN

source_name: Hippocampus

extract_protocol:
Nuclei were purified from Mecp2_flox; CreER +/- Tamoxifen hippocampi according to Mo et al. at the indiciated timepoints post tamoixfen treatment. Purified nuclei were bound to concavalin A beads and incubated with the indicated antibody. Next, nuclei were incubated with pAG-MNase to cleave around antibody-bound DNA regions. Release fragments were collected and used for library prep.
CUT&RUN libraries were prepared using NEB Next II DNA Ultra Kit (NEB #E7645S) with NEB Illumina Unique Combinatorial Dual Index Kit (NEB # E6442S). 25 uL CUT&RUN fragments were used to prepare libraries for MeCP2 and IgG samples, 6 ng of input was used for histone samples. Libraries were amplified for 14 cycles and fragments. Post amplified libraries were selected for ~300bp in length using SPRI beads from Beckman Coulter. Libraries size distributions were measured using Agilent TapeStation HS DNA 1000 (Agilent #5067) and concentrations were determined using the KAPA library quantification kit (Roche #07960140001).

value: Hippocampus

value: Mecp2 Flox; CreER

value: Tamoxifen

tag: timepoint

value: Week 8

value: 24 weeks

value: male

tag: chip antibody

value: Mouse anti-Di and Tri-Methyl-Histone H4 Lysine 20 (H4K20me2/3) monoclonal 6F8-D9, abcam #ab78517, RRID:AB_1951279 ; 1:125 dilution


title: Week8_Tamoxifen_aKO_H4K20me2and3_Rep1

tag: Sex


title: Week8_Vehicle_H4K20me2and3_Rep1

value: Vehicle


title: Week8_Tamoxifen_aKO_H4K20me2and3_Rep2


title: Week8_Vehicle_H4K20me2and3_Rep2


title: Week8_Vehicle_H4K20me2and3_Rep3


title: DiFi_Miltenyi_IgG_FT1_1

tag: condition

value: Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)


title: Week4_Tamoxifen_aKO_H4K20me2and3_Rep2

value: Week 4

value: 20 weeks


title: DiFi_Miltenyi_IgG_B1_5

tag: anatomical location


title: DiFi_Miltenyi_CD81_B2_1

tag: rna source


title: DiFi_Miltenyi_CD9_FT2_3


title: DiFi_Miltenyi_CD9_FT1_3


title: DiFi_Miltenyi_IgG_B1_6


title: Week4_Vehicle_H4K20me2and3_Rep2


title: Week4_Vehicle_H4K20me2and3_Rep1


title: DiFi_Miltenyi_CD9_FT2_1


title: Week4_Vehicle_H4K20me2and3_Rep3


title: Week2_Tamoxifen_aKO_H4K20me2and3_Rep3

value: Week 2

value: 18 weeks


title: DiFi_Miltenyi_CD9_B2_2

value: Colorectal Carcinoma


title: Week2_Tamoxifen_aKO_H4K20me2and3_Rep1


title: Week4_Tamoxifen_aKO_H4K20me2and3_Rep3


title: DiFi_Miltenyi_CD81_FT1_3

value: Colon structure


title: DiFi_Miltenyi_IgG_FT1_3


title: Week2_Vehicle_H4K20me2and3_Rep2


title: Week2_Vehicle_H4K20me2and3_Rep3


title: DiFi_Miltenyi_IgG_FT2_2

value: total cell-free biofluid RNA


title: Week1_Tamoxifen_aKO_H4K20me2and3_Rep3

value: Week 1

value: 17 weeks


title: DiFi_Miltenyi_CD81_B2_2


title: DiFi_Miltenyi_CD81_FT1_1


title: DiFi_Miltenyi_CD9_B2_1

value: other


title: Week1_Tamoxifen_aKO_H4K20me2and3_Rep2

value: Hippocampus

value: Mecp2 Flox; CreER

value: Tamoxifen


title: DiFi_Miltenyi_CD63_FT2_1


title: Week1_Tamoxifen_aKO_H4K20me2and3_Rep1

value: male


title: DiFi_Miltenyi_CD63_FT1_1


title: DiFi_Miltenyi_CD63_FT1_3


title: Week4_Tamoxifen_aKO_H4K20me2and3_Rep1

value: Mouse anti-Di and Tri-Methyl-Histone H4 Lysine 20 (H4K20me2/3) monoclonal 6F8-D9, abcam #ab78517, RRID:AB_1951279 ; 1:125 dilution


title: Week2_Tamoxifen_aKO_H4K20me2and3_Rep2


title: Week1_Vehicle_H4K20me2and3_Rep2

value: Vehicle


title: Week2_Vehicle_H4K20me2and3_Rep1


title: Week1_Vehicle_H4K20me2and3_Rep3


title: Week8_Tamoxifen_aKO_H3K9ac_Rep3

value: Week 8

value: 24 weeks

value: Rabbit anti-Acetyl Histone H3 (Lys9) monocloncal C5B11, Cell Signaling Technologies #9649, RRID:AB_823528; 1:125 dilution


title: DiFi_Miltenyi_IgG_FT2_1

value: Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)


title: DiFi_Miltenyi_IgG_FT2_3


title: DiFi_Miltenyi_CD63_B2_2


title: Week8_Tamoxifen_aKO_H3K9ac_Rep2


title: Week1_Vehicle_H4K20me2and3_Rep1


title: DiFi_Miltenyi_CD9_FT1_2


title: DiFi_Miltenyi_IgG_B1_4


title: Week8_Tamoxifen_aKO_H3K9ac_Rep1


title: DiFi_Miltenyi_CD81_B1_6


title: DiFi_Miltenyi_CD81_FT1_2


title: Week4_Tamoxifen_aKO_H3K9ac_Rep3

value: Week 4

value: 20 weeks


title: Week4_Tamoxifen_aKO_H3K9ac_Rep2


title: Week8_Vehicle_H3K9ac_Rep1


title: ORF2p_RIP, rep3

city: New york city

first: Siyu

last: Sun

state: NY

address: 321 61E street

institute: Memorial Sloan Kettering Cancer Center

data_processing:
STAR alignment
Assembly: hg38
Supplementary files format and content: tab-deliminated text file includs raw counts for each sample

source_name: N2102Ep clone 2/A6

extract_protocol:
RNA was harvest using RNAs were eluted from the affinity media after RIP with 250 μl of TRIzol Reagent followed by pheno-chloroform extraction
RNA-seq cDNA libraries were prepared using the Trio RNA-seq Library Prep kit (Tecan, #0357A01) with Any Deplete Probe MixHuman rRNA (Tecan, #S02305). DNase treatment preceded cDNA synthesis

value: N2102Ep clone 2/A6

tag: cell type

value: emrbynoal carcinomal cell line


title: Ki67Cre_H1N1_tam21_sac42_rep1

description: CellMetaData.csv

value: Lung

tag: genotype


title: Week8_Vehicle_H3K9ac_Rep2

tag: treatment


title: ORF2p_RIP, rep4


title: Week4_Tamoxifen_aKO_H3K9ac_Rep1


title: Week4_Vehicle_H3K9ac_Rep3


title: DiFi_Miltenyi_IgG_B2_2

value: Colorectal Carcinoma

value: Colon structure

value: total cell-free biofluid RNA


title: Week4_Vehicle_H3K9ac_Rep2

value: Hippocampus

value: Mecp2 Flox; CreER


title: Mock_IP, rep3


title: Week8_Vehicle_H3K9ac_Rep3

value: male


title: ORF2p_RIP, rep2


title: Week4_Vehicle_H3K9ac_Rep1


title: Mock_IP, rep2


title: Mock_IP, rep1


title: total RNA, rep5


title: ORF2p_RIP, rep1


title: total RNA, rep6


title: Week2_Tamoxifen_aKO_H3K9ac_Rep3

value: Tamoxifen

value: Week 2

value: 18 weeks


title: Week2_Vehicle_H3K9ac_Rep3

value: Vehicle


title: Week2_Tamoxifen_aKO_H3K9ac_Rep1

value: Rabbit anti-Acetyl Histone H3 (Lys9) monocloncal C5B11, Cell Signaling Technologies #9649, RRID:AB_823528; 1:125 dilution


title: total RNA, rep3


title: total RNA, rep2


title: Week1_Tamoxifen_aKO_H3K9ac_Rep3

value: Week 1

value: 17 weeks


title: Week2_Vehicle_H3K9ac_Rep1


title: total RNA, rep1


title: Week1_Vehicle_H3K9ac_Rep3


title: Week1_Tamoxifen_aKO_H3K9ac_Rep2


title: Week1_Tamoxifen_aKO_H3K9ac_Rep1


title: ORF1p_RIP, rep3

source_name: embryonal

value: embryonal


title: ORF1p_RIP, rep2


title: ORF1p_RIP, rep1


title: total RNA, rep4

value: N2102Ep clone 2/A6


title: Week1_Vehicle_H3K9ac_Rep1


title: Week8_Tamoxifen_aKO_H3K9me3_Rep2

value: Week 8

value: 24 weeks

value: Rabbit anti-Tri-Methyl Histone H3 (Lys9) polycloncal, abcam #ab8898, RRID:AB_306848; 1:100 dilution


title: Week8_Tamoxifen_aKO_H3K9me3_Rep3


title: Week1_Vehicle_H3K9ac_Rep2


title: Week2_Tamoxifen_aKO_H3K9ac_Rep2


title: Week8_Vehicle_H3K9me3_Rep3


title: Week4_Tamoxifen_aKO_H3K9me3_Rep3

value: Week 4

value: 20 weeks


title: Week8_Vehicle_H3K9me3_Rep2

value: Hippocampus


title: Week8_Tamoxifen_aKO_H3K9me3_Rep1

value: Mecp2 Flox; CreER


title: Week8_Vehicle_H3K9me3_Rep1

value: male


title: Week4_Tamoxifen_aKO_H3K9me3_Rep2

value: Tamoxifen


title: Week4_Tamoxifen_aKO_H3K9me3_Rep1


title: Week4_Vehicle_H3K9me3_Rep2


title: Week4_Vehicle_H3K9me3_Rep3


title: Week4_Vehicle_H3K9me3_Rep1


title: Week2_Vehicle_H3K9ac_Rep2

value: Week 2


title: ORF1p_RIP, rep4

value: emrbynoal carcinomal cell line


title: Week2_Tamoxifen_aKO_H3K9me3_Rep3

value: 18 weeks


title: Week2_Tamoxifen_aKO_H3K9me3_Rep2


title: Week2_Tamoxifen_aKO_H3K9me3_Rep1


title: Week2_Vehicle_H3K9me3_Rep3

value: Vehicle


title: Sbj25_OnT

city: Tokyo

first: Makito

last: Koga

address: 1-2-58 Hiromachi, Shinagawa-ku

institute: Daiichi Sankyo

data_processing:
The sequenced reads were aligned with STAR software (2.5.3a) to human genome references (hg38).
TPM, count and FPKM in each gene were estimated by RSEM software (1.3.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include expected counts, TPM and FPKM values for each Sample

source_name: Cancer cells derived from patients

extract_protocol:
Total RNA was extracted by AllPrep DNA/RNA FFPE Kit (Qiagen N.V.) according to the RNA extraction only protocol provided by the manufacturer. Total RNA was eluted with 30 μL RNase-free water.
cDNA library for RNA-seq was prepared for the directional sequencing method with the depletion of ribosomal cDNA and the unique-dual indexes using the following kits and reagents: Takara Bio Inc, SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio Inc.). In case that RNA concentration was ≥25 ng/μL, 25 ng of RNA was used for library preparation. In case that RNA concentration was <1.25 ng/μL, the RNA samples were concentrated by evaporation, and then all volume of RNA samples was used for library preparation. Otherwise, 10 ng of RNA was used for cDNA library preparation.

value: Cancer cells derived from patients


title: Sbj26_OnT


title: Sbj23_OnT


title: Sbj25_BL


title: Week2_Vehicle_H3K9me3_Rep1


title: Sbj28_BL


title: Sbj8_BL


title: Sbj24_BL


title: Sbj7_BL


title: Week1_Tamoxifen_aKO_H3K9me3_Rep2

value: Week 1

value: 17 weeks


title: Week1_Tamoxifen_aKO_H3K9me3_Rep3


title: Week1_Tamoxifen_aKO_H3K9me3_Rep1


title: Sbj3_BL


title: E15.5 limb muscle scRNAseq

city: Haifa

first: Peleg

last: Hasson

address: Efron 1

department: Medicine

country: Israel

institute: Technion

description: 10x Genomics

data_processing:
The RNAseq data was generated on Illumina NextSeq2000 (Illumina, cat no. 20040559)
P3 100 cycles (Read1-28; Read2-90; Index1-10; Index2-10)
Mouse datasets (fasta and gtf files, version mm10) were downloaded from the 10x genomics site.
Primary analysis was performed using 10X Genomics software - Cell Ranger-V4.0.0
Data was analyzed using Seurat R package (Seurat_4.3.0)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: limb skeletal muscles

extract_protocol:
Cells of the limb muscles were isolated mechanically and enzymaticaly using trypsin centrifuged and resuspended with BioAmf. Using a wide-bore pipette tip cells were thoroughly mixed to get single cells, centrifuged and resuspended with 1X PBS with 0.04% BSA.
Two RNA single cell libraries were prepared according to 10x manufacture protocol (Chromium Next GEM Single Cell 3’ Library & Gel Bead Kit v3.1, PN-1000121)  using 20,000 input cells per sample (10,000 target cells per sample).  Illumina NextSeq2000 (Illumina, cat no. 20040559)

value: limb skeletal muscles

value: WT


title: Week1_Vehicle_H3K9me3_Rep3


title: E12.5 limb muscle scRNAseq

description: 10x Genomics


title: Week1_Vehicle_H3K9me3_Rep2


title: Week2_Vehicle_H3K9me3_Rep2


title: Sbj26_BL


title: Sbj9_BL


title: Week8_Tamoxifen_aKO_H3K27ac_Rep3

value: Week 8

value: 24 weeks

value: Rabbit anti-acetyl Histone H3 (Lys27) monoclonal D5E4, Cell Signaling Technology #8173, RRID:AB_10949503; 1:125 dilution


title: Week8_Tamoxifen_aKO_H3K27ac_Rep2


title: Aft/atv/hp2 MR exocarp replicate 4

city: San Giuliano Terme

first: Silvia

last: Gonzali

state: Pisa

address: Via Guidiccioni n. 8/10

department: Institute of Plant Sciences

country: Italy

institute: Sant'Anna School of Advance Studies

description:
Test
SAMPLE 7.4

data_processing:
The Ct values were selected and exported to Excel worksheet according to the ABI Prism manufacturer's instructions.
For the normalization, two housekeeping genes (EF1A and ASR1) were used.
Target gene signals were normalized to housekeeping genes by using the datasheet of the geNorm geometric averaging method.
Each gene expression was explicited as ratio between quantity of target gene and quantity of the geometric averaging of the reference genes, calculated for each biological replicate of the eight groups of samples (SAMPLE 1-SAMPLE 8).
For each target gene, the average of the four biological replicates of each group of samples was calculated (excluding eventual outliners), to have a single value of gene exrpression for SAMPLE 1-SAMPLE 8 .
Fold changes were calculated as ratios between different pairs of averaged expression values.

label: SYBR Green

organism: Solanum lycopersicum

source_name: Fruit

label_protocol: DNAse treatment and retrotranscription were performed with the “Maxima First Strand cDNA Synthesis Kit for RT-qPCR, with dsDNase” by Thermo Fisher Scientific starting from 1 µg RNA. qPCR was performed with an ABI Prism 7300 Sequence Detection System (Thermo Fisher Scientific). Each qPCR was carried out using the “PowerUp™ SYBR® Green Master Mix” (Thermo Fisher Scientific), 15 ng of cDNA template, and 300 nM forward and reverse primers specific for each target gene, in a final reaction volume of 10 µl.

growth_protocol: Tomato plants were grown in pots containing a 70:30 soil/expanded clay mixture and placed in a growth chamber with 23°/20°C of day/night temperature, 12h photoperiod, 150 µmol photons m-2 s−1, and 40% relative humidity. Fruits were sampled at mature green (30 days after pollination) or mature red (50 days after pollination) stages with exocarp (containing also the cuticle layer) removed from the stem end and the inner parts, constituted by mesocarp and endocarp, collected without placenta and seeds.

extract_protocol: Total RNA extraction was carried out with the “SpectrumTM Plant Total RNA Kit” by Merck.

tag: cultivar

value: MicroTom

value: exocarp

tag: developmental stage

value: mature red

tag: cell types

value: cuticle, epidermal and collenchymatous cells

value: 50 days after pollination

tag: activation agent 1

value: light (150 µmol photons m-2 s−1, 12 h photoperiod)

tag: activation agent 2

value: temperature:23°/20°C day/night


title: Aft/atv/hp2 MR mesocarp replicate 1

description:
Test
SAMPLE 8.1

treatment_protocol: 23°/20°C of day/night temperature, 12h photoperiod, 150 µmol photons m-2 s−1, and 40% relative humidity

tag: tissue

value: mesocarp + endocarp

value: parenchymatous cells and cells adjacent to locular cavities

tag: time


title: Aft/atv/hp2 MR exocarp replicate 3

description:
Test
SAMPLE 7.3


title: Aft/atv/hp2 MR exocarp replicate 1

description:
Test
SAMPLE 7.1


title: Week8_Tamoxifen_aKO_H3K27ac_Rep1

value: Hippocampus

value: Mecp2 Flox; CreER

value: Tamoxifen

tag: age

value: male

tag: strain


title: Week8_Vehicle_H3K27ac_Rep3

value: Vehicle

tag: timepoint

tag: chip antibody


title: Aft/atv/hp2 MR exocarp replicate 2

description:
Test
SAMPLE 7.2


title: Aft/atv MR mesocarp replicate 4

description:
Test
SAMPLE 6.4

value: Aft/atv


title: Aft/atv MR mesocarp replicate 2

description:
Test
SAMPLE 6.2


title: Aft/atv MR mesocarp replicate 3

description:
Test
SAMPLE 6.3


title: Week8_Vehicle_H3K27ac_Rep2

value: Week 8

value: 24 weeks

tag: Sex


title: Aft/atv MR exocarp replicate 4

description:
Test
SAMPLE 5.4

value: MicroTom


title: Week1_Vehicle_H3K9me3_Rep1

value: Week 1

value: 17 weeks

value: Rabbit anti-Tri-Methyl Histone H3 (Lys9) polycloncal, abcam #ab8898, RRID:AB_306848; 1:100 dilution


title: Aft/atv/hp2 MR mesocarp replicate 2

description:
Test
SAMPLE 8.2

value: mature red

value: 50 days after pollination


title: Week8_Vehicle_H3K27ac_Rep1

value: Rabbit anti-acetyl Histone H3 (Lys27) monoclonal D5E4, Cell Signaling Technology #8173, RRID:AB_10949503; 1:125 dilution


title: Aft/atv MR exocarp replicate 2

description:
Test
SAMPLE 5.2

value: exocarp

value: cuticle, epidermal and collenchymatous cells

value: light (150 µmol photons m-2 s−1, 12 h photoperiod)

value: temperature:23°/20°C day/night


title: Aft/atv MR exocarp replicate 3

description:
Test
SAMPLE 5.3


title: Aft/atv/hp2 MR mesocarp replicate 3

description:
Test
SAMPLE 8.3

value: mesocarp + endocarp

value: parenchymatous cells and cells adjacent to locular cavities


title: Aft/atv/hp2 MR mesocarp replicate 4

description:
Test
SAMPLE 8.4


title: Aft/atv MR exocarp replicate 1

description:
Test
SAMPLE 5.1


title: ER_96_1

city: Tucson

first: Jiawen

last: Yang

state: Arizona

address: 1515 N Campbell Ave

department: University of Arizona Cancer Center

institute: The University of Arizona

data_processing:
Ran fastqc to check the quality of raw data
Trimmed the adapter sequence from raw sequencing data by using trimmomatic-0.39
Performed data alignment by using STAR 2.7.10a with a hg38 reference genome (“GDC.h38.d1.vd1 STAR2 Index Files (v36)” downloaded from https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files)
The aligned data were mapped to the same reference genome and MCV reference genome by using Rsubread package.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts for individual sample

source_name: neonatoal normal human dermal fibroblast

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen）
Total RNA was sent to Novogene CO.for mRNA library preparation and sequencing.


title: ER_96_2

value: neonatoal normal human dermal fibroblast


title: ER_96_3


title: Aft/atv/hp2 MG mesocarp replicate 4

description:
Test
SAMPLE 4.4

value: mature green

value: 30 days after pollination


title: Week4_Tamoxifen_aKO_H3K27ac_Rep2

value: Hippocampus

value: Mecp2 Flox; CreER

value: Tamoxifen

value: Week 4

value: 20 weeks

value: male


title: Aft/atv/hp2 MG mesocarp replicate 2

description:
Test
SAMPLE 4.2

value: MicroTom


title: Aft/atv MR mesocarp replicate 1

description:
Test
SAMPLE 6.1

value: Aft/atv

value: mature red

value: 50 days after pollination


title: ER_48_3


title: Week4_Tamoxifen_aKO_H3K27ac_Rep1

value: Rabbit anti-acetyl Histone H3 (Lys27) monoclonal D5E4, Cell Signaling Technology #8173, RRID:AB_10949503; 1:125 dilution


title: Aft/atv/hp2 MG mesocarp replicate 3

description:
Test
SAMPLE 4.3

value: light (150 µmol photons m-2 s−1, 12 h photoperiod)

value: temperature:23°/20°C day/night


title: ER_48_2


title: Week4_Tamoxifen_aKO_H3K27ac_Rep3


title: Aft/atv/hp2 MG mesocarp replicate 1

description:
Test
SAMPLE 4.1

value: mesocarp + endocarp

value: parenchymatous cells and cells adjacent to locular cavities


title: Week4_Vehicle_H3K27ac_Rep3

value: Vehicle


title: ER_48_1

value: neonatoal normal human dermal fibroblast


title: Aft/atv/hp2 MG exocarp replicate 4

description:
Test
SAMPLE 3.4

value: exocarp

value: mature green

value: cuticle, epidermal and collenchymatous cells

value: 30 days after pollination


title: Week4_Vehicle_H3K27ac_Rep2

value: Hippocampus

value: Mecp2 Flox; CreER

value: Week 4

value: 20 weeks


title: Aft/atv/hp2 MG exocarp replicate 1

description:
Test
SAMPLE 3.1

value: MicroTom


title: ER_0_3


title: Aft/atv/hp2 MG exocarp replicate 2

description:
Test
SAMPLE 3.2


title: Aft/atv MG mesocarp replicate 4

description:
Test
SAMPLE 2.4

value: Aft/atv


title: ER_0_2


title: Week2_Tamoxifen_aKO_H3K27ac_Rep3

value: Tamoxifen

value: Week 2

value: 18 weeks

value: male

value: Rabbit anti-acetyl Histone H3 (Lys27) monoclonal D5E4, Cell Signaling Technology #8173, RRID:AB_10949503; 1:125 dilution


title: Week4_Vehicle_H3K27ac_Rep1

value: Vehicle


title: Aft/atv MG mesocarp replicate 2

description:
Test
SAMPLE 2.2

value: mesocarp + endocarp

value: parenchymatous cells and cells adjacent to locular cavities

value: light (150 µmol photons m-2 s−1, 12 h photoperiod)

value: temperature:23°/20°C day/night


title: Aft/atv MG mesocarp replicate 1

description:
Test
SAMPLE 2.1

value: mature green

value: 30 days after pollination


title: ER_0_1

value: neonatoal normal human dermal fibroblast


title: Aft/atv MG mesocarp replicate 3

description:
Test
SAMPLE 2.3


title: Week2_Tamoxifen_aKO_H3K27ac_Rep2

value: Hippocampus

value: Mecp2 Flox; CreER


title: CTRL_96_3


title: Aft/atv MG exocarp replicate 1

description:
Control
SAMPLE 1.1

value: MicroTom

value: exocarp

value: cuticle, epidermal and collenchymatous cells


title: Aft/atv MG exocarp replicate 3

description:
Control
SAMPLE 1.3

value: Aft/atv


title: Aft/atv MG exocarp replicate 4

description:
Control
SAMPLE 1.4


title: Aft/atv/hp2 MG exocarp replicate 3

description:
Test
SAMPLE 3.3


title: Aft/atv MG exocarp replicate 2

description:
Control
SAMPLE 1.2


title: Week2_Tamoxifen_aKO_H3K27ac_Rep1

value: Tamoxifen

value: Week 2

value: 18 weeks


title: 173 (VPCI 261/P/20)_rep2

city: Nutley

first: Neeraj

last: Chauhan

state: New Jersey

address: 111 ideation way

institute: Center for Discovery and Innovation, Hackensack Meridian Health

data_processing:
Quality control of raw sequencing reads was done using fastQC v0.11.8
Sequence reads were trimmed to remove the adapter sequences and nucleotides with poor quality using Trim Galore v0.4.5
The trimmed reads were mapped to the reference genome CBS573 strain using the HISAT2. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. The gene hit counts table was used for downstream differential expression analysis.
Using EdgeR, a comparison of gene expression between the two samples was performed. The Exact test was used to generate adj-P values and Log2 fold changes. Genes with p-values < 0.05 and absolute log2 fold changes ≥ 0.585 (1.5fold change) were called differentially expressed genes for each comparison.
Assembly: https://fungi.ensembl.org/Pichia_kudriavzevii_gca_002166775/Info/Index
Supplementary files format and content: csv file includes raw counts for each sample

organism: Pichia kudriavzevii

source_name: Whole fungal cell

growth_protocol: Both strains grown in YPD liquid medium at 30°C with 200 rpm shaking overnight. Next day, re-inoculated in fresh media and grown for log phase (4hours)

extract_protocol:
Total RNA was purified using the TRI reagent (Sigma). Quality of RNA was assessed on a Bioanalyzer using the RNA6000 Nanochip (Agilent).
mRNA was enriched using oligo(dT) beads (NEB) and subsequently, double-stranded cDNA libraries were generated by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

value: Whole fungal cell


title: 173 (VPCI 261/P/20)_rep1


title: Week2_Vehicle_H3K27ac_Rep3

value: Vehicle

value: male

value: Rabbit anti-acetyl Histone H3 (Lys27) monoclonal D5E4, Cell Signaling Technology #8173, RRID:AB_10949503; 1:125 dilution


title: CTRL_96_2


title: 172 (VPCI 218/P/20)_rep2


title: 172 (VPCI 218/P/20)_rep1


title: 171 (VPCI 06/P/16)_rep2


title: CTRL_96_1


title: 171 (VPCI 06/P/16)_rep1


title: Week2_Vehicle_H3K27ac_Rep2


title: Week2_Vehicle_H3K27ac_Rep1


title: Capan-1

data_processing:
reads trimmed and quality checked using skewer
aligned to hg38 and repeat elements using STAR
reads assigned to genes and repeats (Gencode and repeat masker) using featureCounts
unassigned reads remapped to Repbase consensus sequence
Assembly: GRCH38; REP
Supplementary files format and content: rawcounts in .tsv format

source_name: Pancreas

growth_protocol: Pancreatic cancer cell lines were cultured in DMEM (PDAC3, PDAC6. PDAC8, PDAC9, PANC-1, MiaPACA2), RPMI (YAPC, DAN-G, Bx-PC3) and IMDM (Capan-I, KP-4) supplemented with 10% (v/v) FBS and antibiotics (100 U/ml penicillin, 100 µg/ml streptomycin; Gibco, cat# 15140122) in a 37℃ incubator supplied with 5% CO2.

extract_protocol:
Total RNA extraction was performed using the miRNeasy Mini Kit (QIAGEN, cat# 217004). 7 ng of RNA was used for library construction.
Libraries were prepared for sequencing using the SMARTer Stranded Total RNA-seq Kit v2 (cat# 634413) – Pico Input Mammalian (Takara Bio USA). RNA samples were first converted into cDNA, then adaptors for Illumina sequencing were added through PCR. The PCR products are purified using AMPure Beads (Beckman Coulter, cat# A63881), then ribosomal cDNA was depleted. After depletion, the samples were further amplified using PCR, then purified again using AMPure Beads. Each sample was then qPCR quantified using a KAPA Library Quantification Kit (Roche, cat# 07960140001) and Phix Control Kit V3 (Illumina, cat# FC-110-3001). Samples were then pooled together and quantified again using the KAPA Library Quantification Kit. The Pooled library was then sequenced using the NextSeq 500 Sequencing Kit.

treatment_protocol: PDAC cells were grown in 3D (tumorsphere) for 7 days for RNA-sequencing.

value: Pancreas

tag: cell line

value: Pancreatic cancer cell lines

value: Wild type

value: 3D tumorsphere


title: KP-4


title: BxPC-3


title: Week1_Tamoxifen_aKO_H3K27ac_Rep3

value: Hippocampus

value: Week 1

value: 17 weeks


title: CTRL_48_2

value: neonatoal normal human dermal fibroblast


title: DAN-G

value: DAN-G


title: CTRL_48_1


title: Week1_Tamoxifen_aKO_H3K27ac_Rep2

value: Mecp2 Flox; CreER


title: PANC-1


title: YAPC

value: YAPC


title: CTRL_0_3


title: MiaPACA2


title: PDAC9


title: CTRL_0_2


title: PDAC8


title: Week1_Tamoxifen_aKO_H3K27ac_Rep1

value: Tamoxifen


title: Week1_Vehicle_H3K27ac_Rep3


title: HA48TI_inf

city: Dallas

first: Bingqing

last: Xie

state: Texas

address: 6001 Forest Park Rd

department: Internal medicine

institute: University of Texas Southwestern medical center

description: 10x RNA

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software (v7.0.1)
Extract high-quality cells with 200-6000 genes and greater than 1000 UMIs per cell and mitochondria percentage less than 50 using Seurat V4.3
Assembly: hg38
Supplementary files format and content: Each process sample contains the following files: barcodes.tsv.gz (cell barcodes),  features.tsv.gz (gene features), and  matrix.mtx.gz (sparse count matrix).

growth_protocol: No growth

extract_protocol:
Tissues were incubated in buffered EGTA at 37 Celsius for 15 minutes to separate epithelium from lamina propria. Epithelium was digested in TrypLE express at 37 Celsius for 5 minutes. Lamina propria was digested in liberase TM at 37 Celsius for 20 minutes.
Amplication product of cDNA was processed with Dnase fragmentation, A tailling, ligation of adaptors and index PCR per 10x Genomics 3'RNA v3.1 library construction protocol.

treatment_protocol: No treatment

tag: patient

tag: condition

value: CD

tag: race

value: caucasian

tag: history

tag: treatment (biological)

tag: sample region

value: inf


title: Week1_Vehicle_H3K27ac_Rep2

tag: genotype

tag: treatment

value: Vehicle

value: male


title: CTRL_48_3

tag: cell type


title: PDAC6

tag: tissue

value: Pancreas


title: Parental HCT116 cells, Dox-treated, Rep 3

city: Liverpool

first: Claire

last: Wilson

address: Ashton Street

country: United Kingdom

institute: University of Liverpool

data_processing:
Quality assessed using FastQC(v0.11.9).
Sequence reads were trimmed for adapters and low-quality reads using TrimGalore (v0.6.6).
Genome mapping was performed with STAR (v2.7.10b) against the human reference genome (hg38 assembly).
Reads were counted using FeatureCounts (subread v2.0.3).
Differential analysis was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

extract_protocol:
Cells were harvested in TRI Reagent® (Zymo Research) and RNA extraction was performed using the Direct-zol RNA Miniprep Kit (Zymo Research), including DNase I treatment, according to the manufacturer’s instructions. RNA quality and concentration was determined using the 4200 tapestation system.
Novokit Novogene NGS Stranded RNA Library Prep Set

value: Human colorectal carcinoma cells


title: HA48TI_ad

description: 10x RNA

value: adjacent


title: PDAC3

value: Pancreatic cancer cell lines

value: Wild type

value: 3D tumorsphere


title: HA41TI

description: 10x RNA

value: control

value: african

value: no


title: Week8_Tamoxifen_aKO_H3K27me3_Rep3

value: Hippocampus

value: Mecp2 Flox; CreER

value: Week 8

value: 24 weeks

value: Rabbit anti-Tri-Methyl Histone H3 (Lys27) monocloncal C36B11, Cell Signaling Technology #9733, RRID:AB_2616029; 1:125 dilution


title: Parental HCT116 cells, Dox-treated, Rep 1


title: Parental HCT116 cells, Dox-treated, Rep 2


title: Sbj33_OnT

value: Cancer cells derived from patients


title: HA41AC

description: 10x RNA


title: Sbj22_OnT


title: Week8_Tamoxifen_aKO_H3K27me3_Rep2

value: Tamoxifen


title: Sbj32_OnT


title: Week1_Vehicle_H3K27ac_Rep1

value: Vehicle

value: Week 1

value: 17 weeks

value: male

value: Rabbit anti-acetyl Histone H3 (Lys27) monoclonal D5E4, Cell Signaling Technology #8173, RRID:AB_10949503; 1:125 dilution


title: Sbj32_BL


title: Parental HCT116 cells, Control, Rep 2

value: Human colorectal carcinoma cells


title: Week8_Tamoxifen_aKO_H3K27me3_Rep1


title: CTRL_0_1

value: neonatoal normal human dermal fibroblast


title: Parental HCT116 cells, Control, Rep 3


title: Sbj33_BL


title: Week8_Vehicle_H3K27me3_Rep3


title: Parental HCT116 cells, Control, Rep 1


title: Week8_Vehicle_H3K27me3_Rep2


title: HCT116-RH2B cells, Dox-induced RH2B expression, Rep 3


title: Sbj20_BL


title: Sbj19_BL


title: Week8_Vehicle_H3K27me3_Rep1


title: Sbj16_BL


title: HCT116-RH2B cells, Dox-induced RH2B expression, Rep 2


title: Week4_Tamoxifen_aKO_H3K27me3_Rep3

value: Week 4

value: 20 weeks


title: Sbj14_BL


title: HCT116-RH2B cells, Dox-induced RH2B expression, Rep 1


title: Shoot, drought, wild type, R1

city: Northfield

first: Heather

middle: Elizabeth

last: Driscoll

state: VT

address: 158 Harmon Drive

department: Biology

institute: Norwich University

description:
HS95s
Bdist_raw_counts.txt
Bdist_median_ratio_norm_annot.txt

data_processing:
Partek® Flow® software v.10.0, build 10.0.22.0729, FastQC v0.11.9
Reads were demultiplexed and then assessed for quality using the FastQC v0.11.9 and Partek Flow® pre-alignment QAQC tools, followed by quality trimming and filtering according to quality score (Q30) at the 3' end and a fixed-length trimming (12) of bases at the 5' end using the Flow® trimbases tool (25 bp minimum length).
Curated reads were aligned to the B. distachyon v3.0 genome obtained from the NCBI (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/505/) with HISAT2 (Kim et al., 2019).
Aligned reads were quantified at the gene level based on the B. distachyon v3.0 annotation model in gff format from the same URL above using a modified full expectation-maximization (EM) algorithm (Xing et al., 2006), as implemented in Flow® with default values and strand specificity set to autodetect.
Differential expression analyses were conducted at the gene-level using unfiltered raw read counts in DESeq2 (Love et al., 2014), and genes with very low read counts were excluded from the false discovery rate (FDR) calculation using the default parameter independentFiltering=true.
Reads were median ratio normalized as part of the DESeq2 analysis.
Assembly: B. distachyon v3.0 genome from the NCBI (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/505/)
Supplementary files format and content: Tab-delimited text file includes raw gene counts for each sample
Supplementary files format and content: Tab-delimited text file includes median ratio normalized gene counts for each sample

organism: Brachypodium distachyon

source_name: 5 leaf stage shoot

growth_protocol: Plants were grown for 18 days at 20°C with 14 h light and 18°C for 10 h dark.

extract_protocol:
Total RNA was extracted using TriReagent (Ambion) according to the manufacturer's instructions. Contaminating DNA was removed with a TURBO DNase treatment and RNA was stabilized with addition of RNaseInhibitor.
Libraries were constructed using the protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490)

treatment_protocol: After their intiial growth, plants were subjected to 16 h light and 8 h dark conditions with 15 days no water.

tag: cultivar

value: 5 leaf stage shoot

value: Wildtype

value: 15 day drought


title: Shoot, drought, CR:hdac19-2b, R3

description:
HJ183s
Bdist_raw_counts.txt
Bdist_median_ratio_norm_annot.txt

value: Mutant hdac19-2b


title: Shoot, drought, CR:hdac19-2b, R2

description:
HJ172s
Bdist_raw_counts.txt
Bdist_median_ratio_norm_annot.txt


title: HCT116-RH2B cells, Control, Rep 3


title: Week4_Tamoxifen_aKO_H3K27me3_Rep1

city: Houston

institute: Baylor College of Medicine

value: Hippocampus

value: Mecp2 Flox; CreER

tag: age


title: Sbj23_BL

value: Cancer cells derived from patients


title: Shoot, drought, CR:hdac19-2b, R1

description:
HJ170s
Bdist_raw_counts.txt
Bdist_median_ratio_norm_annot.txt


title: Shoot, drought, wild type, R3

description:
HJ154s
Bdist_raw_counts.txt
Bdist_median_ratio_norm_annot.txt


title: HCT116-RH2B cells, Control, Rep 1


title: Week4_Vehicle_H3K27me3_Rep3

tag: strain

value: Rabbit anti-Tri-Methyl Histone H3 (Lys27) monocloncal C36B11, Cell Signaling Technology #9733, RRID:AB_2616029; 1:125 dilution


title: Shoot, drought, CR:gf14h-1, R3

description:
HJ35
Bdist_raw_counts.txt
Bdist_median_ratio_norm_annot.txt

value: Mutant gf14h-1


title: Week4_Tamoxifen_aKO_H3K27me3_Rep2

value: Tamoxifen

tag: timepoint


title: Shoot, drought, wild type, R2

description:
HJ100s
Bdist_raw_counts.txt
Bdist_median_ratio_norm_annot.txt


title: Week4_Vehicle_H3K27me3_Rep2

value: Vehicle

tag: chip antibody


title: Shoot, drought, CR:gf14h-1, R2

description:
HJ28s
Bdist_raw_counts.txt
Bdist_median_ratio_norm_annot.txt


title: Sbj17_BL


title: scATAC_P2-TI-CDnonInf

city: Chicago

first: Yu

last: Zhao

state: IL

address: 5841 S. Maryland Ave

department: Section of Genetic Medicine, Department of Medicine

institute: The University of Chicago

library_source: genomic single cell

data_processing:
scATAC-seq raw sequencing data were processed using the Cell Ranger ATAC 2.0.0, and the 10X human transcriptome GRCh38-2020-A-2.0.0 as the reference. Further filtering was conducted using ArchR(v.1.0.3). Only high quality individual cells are kept for downstream analysis (doublet filter ratio = 2.0, minimum fragments per cell = 5000, minimum TSS enrichment score = 6).
Assembly: hg38
Supplementary files format and content: Fragments files and tabix index of fragments files

source_name: terminal ileum

extract_protocol:
Intact mucosal tissues were rinsed in 1.5 ml ice-cold PBS [Thermo Fisher 10010023] six times. Mucosal tissues from the same regions were combined and minced by iris scissors. Minced tissues were transferred to 2 ml fresh chelator solution (HBSS Ca/Mg-Free [Thermo Fisher 14175095], 10 mM EGTA [Fisher Scientific 50-255-956], 10 mM HEPES [Thermo Fisher 15630080], and 10% FBS [Gemini Bio 100-106]). The tissues were incubated at 37°C for 15 minutes with end-over-end rotation, then cooled on ice for 10 minutes. The epithelium was separated from lamina propria by mechanical agitation (shaking 20 times). Visualizing epithelial sheets in the solution, the supernatant was collected and spun down at 300g for 5 minutes at 4°C. The remnant tissue chunks were rinsed in ice-cold PBS and incubated in 2 ml enzyme solution (HBSS Ca/Mg-Free [Thermo Fisher 14175095], 10 mM HEPES [Thermo Fisher 15630080], 200 μg/ml Liberase TM [Millipore Sigma 5401127001] and DNase I [Gold Bio D-301-100]) at 37°C for 20 minutes. The spun-down epithelium was resuspended and incubated in 2 ml TrypLE express [Thermo Fisher 12605010], at 37°C for 5 minutes. Both incubations were applied with end-over-end rotation. Tissues were gently triturated with a P1000 pipette after incubations and no visible tissue chunks remained after trituration. Cells were filtered through a 40 μM cell strainer [Falcon/VWR 21008–949]. After filtration, epithelial cells and cells from lamina propria were combined and spun down at 300 g for 5 minutes at 4°C. Cell pellet from each region were resuspended in 200 μl cold wash buffer (HBSS Ca/Mg-Free [Thermo Fisher 14175095] and 10% FBS [Gemini Bio 100-106]). Cell suspension was then diluted by 2 ml lysis buffer [Miltenyi Biotec 130-094-183] and sat for 3 minutes at room temperature to eliminate red blood cells. Cells in suspensions were spun at 300g for 5 minutes at 4°C. Cell pellets were resuspended in 200 μl suspension buffer (PBS and 0.04% BSA [Miltenyi Biotec 130-091-376]) and assessed for density and viability with Trypan Blue [Thermo Fisher 15250061]. Only cell suspensions with >85% viability were used for downstream single cell assays.
Single nuclei were isolated from single cell suspensions following the manufacturer’s protocol for the Chromium Single cell ATAC (v 1.1). Briefly, single nuclei were transposed before loading to chip H. Transposed nuclei were partitioned into GEMS in Chromium controller. GEMs were incubated for barcoding, followed by fragment indexing. Approximately 8,000 single nuclei were transposed and loaded to a channel with a target recovery for 5,000 nuclei. Libraries were sequenced on Illumina NovaSeq 6000 platforms.

value: terminal ileum

tag: Sex

value: Male

tag: disease

value: Crohn's Disease

tag: inflammation

value: CD non-inflamed


title: Sbj4_BL


title: Week4_Vehicle_H3K27me3_Rep1

value: Week 4

value: male


title: scATAC_P27-TI-CDadjInf

value: CD adjacent-inflamed


title: Shoot, drought, CR:gf14h-1, R1

description:
HJ8s
Bdist_raw_counts.txt
Bdist_median_ratio_norm_annot.txt

value: 5 leaf stage shoot


title: Week2_Tamoxifen_aKO_H3K27me3_Rep3

value: Week 2

value: 18 weeks


title: Clark five-foliate 2 (total RNA)

city: Urbana

first: Lila

middle: O.

last: Vodkin

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

data_processing:
75 bp reads were aligned to soybean reference genome cv. Williams 82 phytozome v.4, using BOWTIE (Langmead et al., 2009) with up to 3 mismatches and 25 alignments allowed.
RNA-Seq data was normalized in reads per kilobase of gene model per million mapped reads (RPKM) (Mortazavi et al., Nat Met 5:621-628, 2008).
Genome_build: Glycine max cv. Williams 82 (http://www.phytozome.net/soybean.php)
Supplementary_files_format_and_content: RPKM

organism: Glycine max

source_name: vegetative bud

growth_protocol: Soybean plants (Clark standard and Clark five-foliate) were grown in the green house and the young shoot tips & the vegetative bud were harvested from 4-week-old-multiple plants to represent biological replications. All tissues were lyophillized and stored at -70C till further use.

extract_protocol:
Total RNA was extracted using standard phenol chloroform method with lithium chloride precipitation, based on the procedure from McCarty DR from 1986.
Library construction and high-throughput sequencing was carried out using RNA-Seq technology with Illumina GA II instrument at the W. M. Keck Center for Comparative and Functional Genomics at the University of Illinois, Urbana-Champaign.

treatment_protocol: optimal green house growth conditions

value: Clark

value: five foliate mutant

value: vegetative bud


title: Clark standard 2 (total RNA)

value: wild type


title: Sbj22_BL

value: Cancer cells derived from patients


title: CX19A3

city: Rio de Janeiro

first: Mariana

last: Boroni

state: RJ

address: Rua André Cavalcanti 37

country: Brazil

institute: Instituto Nacional de Câncer

description: Library name: CX19A3

data_processing:
Raw reads were trimmed using Trimmomatic with parameters 2:30:10, SLIDINGWINDOW:4:20, TRAILING:20, and MINLEN:50. Filtered paired-end reads were aligned against the Mouse reference genome m38 using the tool Star inside the RSEM package to generate an expression matrix of Transcripts per Million (TPM). To increase robustness in the analysis, genes were categorized according to their expression in 1) genes with TPM >=1 in all control and treated samples; 2) genes with TPM >=1 in both treated replicates and TPM < 1 in both control replicates; 3) genes with TPM >=1 in both control replicates and TPM < 1 in both treated samples; Finally, mean TPM for each condition was calculated and only genes with TPM >=1 in at least one condition were kept to exclude noise associated with low expression levels. Log Fold changes (LFC) were calculated using log2(TPM mean of treated/TPM mean of control).
Assembly: GRCm38
Supplementary files format and content: compressed tab-delimited text files for each sample
Supplementary files format and content: tsv contains: gene_id, transcript_id(s), length, effective_length, expected_count, TPM and FPKM

source_name: mouse atrial

extract_protocol:
Samples were treated with RNALater (Ambion) and preserved at -80º until the RNA extraction procedure. Total RNA was isolated with the RNeasy Kit (Qiagen) following the manufacturer’s instructions. The integrity of RNA was assessed with an RNA 6000 Nano chip with a Bioanalyzer platform (Agilent), and samples with RNA integrity number (RIN) ≥7 were included.
RNA samples were quantified using Qubit (Thermo) and 1000 ng were used for constructing cDNA libraries with TruSeq Stranded mRNA Library Preparation Kit (Illumina) following the manufacturer’s protocol. Libraries were quantified in Quibit and sequenced in the Illumina HiSeq 2500 platform to produce 2×100 bp reads.

value: mouse atrial


title: Week2_Tamoxifen_aKO_H3K27me3_Rep2

value: Hippocampus

value: Mecp2 Flox; CreER

value: Tamoxifen

value: Rabbit anti-Tri-Methyl Histone H3 (Lys27) monocloncal C36B11, Cell Signaling Technology #9733, RRID:AB_2616029; 1:125 dilution


title: Clark five-foliate 1 (total RNA)

source_name: shoot tip

value: shoot tip


title: scATAC_P27-TI-CDinf

value: terminal ileum

value: Male

value: Crohn's Disease

value: CD inflamed


title: scATAC_P26-TI-CDadjInf

value: CD adjacent-inflamed


title: CX18A5

description: Library name: CX18A5

value: control


title: HCT116-RH2B cells, Control, Rep 2

tag: cell line

value: Human colorectal carcinoma cells


title: scATAC_P26-TI-CDinf


title: CX18A2

description: Library name: CX18A2


title: scATAC_C16-TI-Control

value: Female

value: Control


title: Week2_Vehicle_H3K27me3_Rep3

value: Vehicle

value: Week 2

value: 18 weeks

value: male


title: Cortex, Mecp2 G118E Replicate 6

description:
G118E-6
Mecp2_G118E_raw_counts.txt
Mecp2_G118E_normalized_counts.txt

data_processing:
Raw reads were trimmed before mapping by Trimmomatic-0.39 using default parameters
STAR v2.7.2d was used to align trimmed reads to the Mus musculus genome (GRCm38.p6, https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26) and to obtain read counts with default parameters except -sjdbOverhang149
Differential gene expression analysis using DESeq2 package v1.34.0
Assembly: mm10
Supplementary files format and content: tab delimited table of raw counts per sample
Supplementary files format and content: tab delimited table of normalized expression of detected genes per sample

molecule: polyA RNA

source_name: Cortex

extract_protocol:
Qiagen miRNeasy with DNase digestion
RNA libraries were prepared by Genewiz using polyA selection and standard Illumina protocols

value: Cortex

value: Mecp2 G118E


title: Week2_Vehicle_H3K27me3_Rep2

value: Hippocampus

value: Mecp2 Flox; CreER

value: Rabbit anti-Tri-Methyl Histone H3 (Lys27) monocloncal C36B11, Cell Signaling Technology #9733, RRID:AB_2616029; 1:125 dilution


title: Clark standard (Small RNA)

data_processing:
The raw sRNA sequencing reads obtained from Illumina HiSeq2000 machine were processed for 5’ and 3’adapter trimming using Illumina’s binary run_trimmer software.
Sequences with lengths of 16- to 24- nt were retained in a dataset for further analysis and rest of the sequences falling outside of the criteria were removed.
The adapter-trimmed sequences were subjected to a Python script that added up identical sequences to produce a merged FASTA format file containing the total counts for each unique sequence from each library.
Small RNA unique sequences were mapped to the soybean reference genome from cv Williams 82 (downloaded from http://www.phytozome.net/soybean.php) and miRBase (http://www.mirbase.org/) for Glyma and miRNA annotations, respectively using Bowtie (Langmead et al., 2009) with up to 2 mismatches.
Genome_build: Glycine max cv. Williams 82 (http://www.phytozome.net/soybean.php)
Supplementary_files_format_and_content: small RNA abundance

growth_protocol: Soybean plants (Clark standard and Clark five-foliate) were grown in the green house and the young shoot tips were harvested from 4-week-old-multiple plants to represent biological replications. All tissues were lyophillized and stored at -70C till further use.

extract_protocol:
Total RNA was extracted using standard phenol chloroform method without lithium chloride precipitation, based on the procedure from McCarty DR from 1986.
Library construction and high-throughput sequencing were carried out using Illumina small RNA kits (catalog number RS-200-0012) and sequenced on the Illumina HiSeq2000 instrument at the W. M. Keck Center for Comparative and Functional Genomics at the University of Illinois, Urbana-Champaign.

value: Clark standard trifoliate line (PI 547402, L58-231, abbreviated as CS)

value: wild type, trifoliate leaves

value: shoot tip


title: scATAC_C15-TI-Control

value: terminal ileum


title: Cortex, Mecp2 G118E Replicate 5

description:
G118E-5
Mecp2_G118E_raw_counts.txt
Mecp2_G118E_normalized_counts.txt


title: Week1_Tamoxifen_aKO_H3K27me3_Rep3

value: Tamoxifen

value: Week 1

value: 17 weeks


title: Cortex, Mecp2 G118E Replicate 4

description:
G118E-4
Mecp2_G118E_raw_counts.txt
Mecp2_G118E_normalized_counts.txt


title: Cortex, Mecp2 G118E Replicate 3

description:
G118E-3
Mecp2_G118E_raw_counts.txt
Mecp2_G118E_normalized_counts.txt


title: Clark standard 1 (total RNA)

value: Clark

value: wild type


title: Jaw joint cells, 70 dpjr, Pooled

city: New York

first: Joanna

last: Smeeton

address: 650 W 168TH ST, ROOM 1103A, William Black Building

department: Rehabilitation and Regenerative Medicine

institute: Columbia University Irving Medical Center

description:
Library name: Sample 14
10X Genomics

data_processing:
CellRanger v6.1.2 (10X Genomics)  with default parameters was used to generate cell-by-gene count matrices.
Assembly: Danio rerio GRCz11
Supplementary files format and content: matrix, features, barcode files

organism: Danio rerio

source_name: Jaw joint

extract_protocol:
Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells.
scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10X Genomics), following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1, 10 bp sequencing for Index1, and 101 bp sequencing for Read2, and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86,000 reads per cell.

treatment_protocol: Whole-joint resection surgery was performed on adult zebrafish and collected at 1, 3, 7, 14, 28, and 70 days-post-joint-resection. Controls consisted of uninjured samples.

value: Jaw joint

value: 3-6 mpf

value: 70 dpjr

tag: batch


title: Week1_Tamoxifen_aKO_H3K27me3_Rep2

data_processing:
Adapter sequences were removed from sequence reads using Trimmomatic version 0.36 (2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25) from the Truseq3.PE.fa adapter library and kseq
Confirmation of adapter removal and read quality was performed with fastqc (v0.11.8)
Alignment was performed with bowtie2-2.3.4.1 (--dovetail --phred33) to both mm10 (GRCm38 GCA_000001635.2) and the spike-in Ecoli K12 Genomes (GCF_000005845.2_ASM584v2)
Bedtools (v2.29.1) was used to process BAM files to BED files, remove blacklist (mm9 blacklist lifted over to mm10 and combined with mm10 blacklist downloaded with CUT&RUNTools (Zhu et al., 2019) and to generate bedgraphs
Each sample was normalized to internal Ecoli spike-in utilizing spike_in_calibration.sh as described previously (Meers et al., 2019)
Assembly: mm10 and E. coli
Supplementary files format and content: E. coli spike in normalized bigwig tracks
Library strategy: CUT&RUN

extract_protocol:
Nuclei were purified from Mecp2_flox; CreER +/- Tamoxifen hippocampi according to Mo et al. at the indiciated timepoints post tamoixfen treatment. Purified nuclei were bound to concavalin A beads and incubated with the indicated antibody. Next, nuclei were incubated with pAG-MNase to cleave around antibody-bound DNA regions. Release fragments were collected and used for library prep.
CUT&RUN libraries were prepared using NEB Next II DNA Ultra Kit (NEB #E7645S) with NEB Illumina Unique Combinatorial Dual Index Kit (NEB # E6442S). 25 uL CUT&RUN fragments were used to prepare libraries for MeCP2 and IgG samples, 6 ng of input was used for histone samples. Libraries were amplified for 14 cycles and fragments. Post amplified libraries were selected for ~300bp in length using SPRI beads from Beckman Coulter. Libraries size distributions were measured using Agilent TapeStation HS DNA 1000 (Agilent #5067) and concentrations were determined using the KAPA library quantification kit (Roche #07960140001).

value: male


title: Jaw joint cells, 70 dpjr, Single

description:
Library name: Sample 15
10X Genomics


title: CX20A2

description: Library name: CX20A2

value: mouse atrial


title: Week2_Tamoxifen_aKO_H3K27me3_Rep1

value: Hippocampus

value: Week 2

value: 18 weeks


title: Cortex, Mecp2 G118E Replicate 2

description:
G118E-2
Mecp2_G118E_raw_counts.txt
Mecp2_G118E_normalized_counts.txt

value: Cortex

value: Mecp2 G118E


title: scATAC_P20-TI-CDadjInf

value: Female

value: Crohn's Disease

value: CD adjacent-inflamed


title: Jaw joint cells, 28 dpjr, Pooled

description:
Library name: Sample 12
10X Genomics

value: 28 dpjr


title: scATAC_P21-TI-CDinf

value: terminal ileum

value: Male

value: CD inflamed


title: Cortex, Mecp2 G118E Replicate 1

description:
G118E-1
Mecp2_G118E_raw_counts.txt
Mecp2_G118E_normalized_counts.txt


title: scATAC_P20-TI-CDinf


title: Jaw joint cells, 14 dpjr, Single Animal

description:
Library name: Sample 11
10X Genomics

value: Jaw joint

value: 14 dpjr


title: Cortex, Wild-type Replicate 4

description:
WT-4
Mecp2_G118E_raw_counts.txt
Mecp2_G118E_normalized_counts.txt

value: Wild-type


title: Week1_Vehicle_H3K27me3_Rep2

value: Mecp2 Flox; CreER

value: Vehicle

value: Week 1

value: 17 weeks

value: male

value: Rabbit anti-Tri-Methyl Histone H3 (Lys27) monocloncal C36B11, Cell Signaling Technology #9733, RRID:AB_2616029; 1:125 dilution


title: scATAC_P18-TI-CDadjInf


title: Week2_Vehicle_H3K27me3_Rep1

value: Hippocampus

value: Week 2

value: 18 weeks


title: Jaw joint cells, 14 dpjr, Pooled

description:
Library name: Sample 10
10X Genomics

value: 3-6 mpf


title: Cortex, Wild-type Replicate 3

description:
WT-3
Mecp2_G118E_raw_counts.txt
Mecp2_G118E_normalized_counts.txt

value: Cortex


title: Week1_Vehicle_H3K27me3_Rep1


title: scATAC_P21-TI-CDadjInf

value: terminal ileum

value: Crohn's Disease

value: CD adjacent-inflamed


title: scATAC_C14-TI-Control

value: Male

value: Control


title: Week8_Tamoxifen_aKO_MeCP2_Rep3

value: Tamoxifen

value: Week 8

value: 24 weeks

value: Rabbit anti-MeCP2 monoclonal D443 Cell Signaling Technology #3456, clone D4F3, RRID:AB_2143894; 1:125 dilution


title: Clark five-foliate (Small RNA)

data_processing:
The raw sRNA sequencing reads obtained from Illumina HiSeq2000 machine were processed for 5’ and 3’adapter trimming using Illumina’s binary run_trimmer software.
Sequences with at least 8 counts with lengths of 16- to 24- nt were retained in a dataset for further analysis and rest of the sequences falling outside of the criteria were removed.
sRNA unique sequences were mapped to the soybean reference genome from cv Williams 82 (downloaded from http://www.phytozome.net/soybean.php) and miRBase (http://www.mirbase.org/) for Glyma and miRNA annotations, respectively using Bowtie (Langmead et al., 2009) with up to 2 mismatches.
Genome_build: Glycine max cv. Williams 82 (http://www.phytozome.net/soybean.php)
Supplementary_files_format_and_content: small RNA abundance

extract_protocol:
Total RNA was extracted using standard phenol chloroform method without lithium chloride precipitation, based on the procedure from McCarty DR from 1986.
Library construction and high-throughput sequencing was carried out using small RNA technology with Illumina HiSeq2000 instrument at the W. M. Keck Center for Comparative and Functional Genomics at the University of Illinois, Urbana-Champaign.

value: Clark

value: five foliate mutant

value: shoot tip


title: Jaw joint cells, 7 dpjr, Pooled

description:
Library name: Sample 8
10X Genomics

value: Jaw joint

value: 7 dpjr


title: Week1_Tamoxifen_aKO_H3K27me3_Rep1

value: Hippocampus

value: Mecp2 Flox; CreER

value: Week 1

value: 17 weeks

value: male

value: Rabbit anti-Tri-Methyl Histone H3 (Lys27) monocloncal C36B11, Cell Signaling Technology #9733, RRID:AB_2616029; 1:125 dilution


title: Week8_Tamoxifen_aKO_MeCP2_Rep2


title: Jaw joint cells, 28 dpjr, Single Animal

description:
Library name: Sample 13
10X Genomics

value: 3-6 mpf

value: 28 dpjr


title: Jaw joint cells, 3 dpjr, Single Animal

description:
Library name: Sample 7
10X Genomics

value: 3 dpjr


title: scATAC_C13-TI-Control

value: terminal ileum

value: Female

value: Control


title: CreER + TMX Week 8 Replicate 4 [Sample_144]

treatment_protocol: 16-week old mice were treated with tamoxifen (100 mg/kg) or vehicle for 3 injections every other day. Whole hippocampal tissue was dissected at the indicated timepoint after first injection.

value: CreER

value: Tamoxifen

value: Week 8

value: 24 weeks


title: Week8_Tamoxifen_aKO_MeCP2_Rep1

value: Rabbit anti-MeCP2 monoclonal D443 Cell Signaling Technology #3456, clone D4F3, RRID:AB_2143894; 1:125 dilution


title: Cortex, Wild-type Replicate 1

description:
WT-1
Mecp2_G118E_raw_counts.txt
Mecp2_G118E_normalized_counts.txt

value: Cortex

value: Wild-type


title: scATAC_P18-TI-CDinf

value: Crohn's Disease

value: CD inflamed


title: scATAC_C11-TI-Control


title: Week8_Vehicle_MeCP2_Rep3

value: Hippocampus

value: Mecp2 Flox; CreER

value: Vehicle

value: male


title: scATAC_C10-TI-Control

value: Male


title: Jaw joint cells, 3 dpjr, Pooled

description:
Library name: Sample 6
10X Genomics

value: Jaw joint

value: 3-6 mpf

value: 3 dpjr


title: CreER + TMX Week 8 Replicate 2 [Sample_142]

value: CreER


title: scATAC_C9-TI-Control

value: terminal ileum

value: Female

value: Control


title: Jaw joint cells, 1 dpjr, Single Animal

description:
Library name: Sample 5
10X Genomics

value: 1 dpjr


title: Jaw joint cells, 7 dpjr, Single Animal

description:
Library name: Sample 9
10X Genomics

value: 7 dpjr


title: Jaw joint cells, 1 dpjr, Pooled

description:
Library name: Sample 4
10X Genomics


title: Week8_Vehicle_MeCP2_Rep2

value: Week 8

value: 24 weeks

value: Rabbit anti-MeCP2 monoclonal D443 Cell Signaling Technology #3456, clone D4F3, RRID:AB_2143894; 1:125 dilution


title: Cortex, Wild-type Replicate 2

description:
WT-2
Mecp2_G118E_raw_counts.txt
Mecp2_G118E_normalized_counts.txt

value: Cortex

value: Wild-type


title: CreER + TMX Week 8 Replicate 1 [Sample_141]

value: Hippocampus

value: Tamoxifen


title: Week8_Vehicle_MeCP2_Rep1

value: Mecp2 Flox; CreER

value: Vehicle

value: male


title: Jaw joint cells, Uninjured, Single Animal 2

description:
Library name: Sample 3
10X Genomics

value: Jaw joint

value: 3-6 mpf

value: Uninjured


title: scATAC_P15-TI-CDadjInf

value: terminal ileum

value: Male

value: Crohn's Disease

value: CD adjacent-inflamed


title: Week4_Tamoxifen_aKO_MeCP2_Rep3

value: Week 4

value: 20 weeks


title: Mecp2_flox + TMX Week 8 Replicate 4 [Sample_140]

value: Mecp2 Flox

value: Week 8

value: 24 weeks


title: Jaw joint cells, Uninjured, Single Animal 1

description:
Library name: Sample 2
10X Genomics


title: CreER + TMX Week 8 Replicate 3 [Sample_143]

value: Hippocampus

value: CreER


title: Week4_Tamoxifen_aKO_MeCP2_Rep2

value: Mecp2 Flox; CreER

value: Tamoxifen

value: Rabbit anti-MeCP2 monoclonal D443 Cell Signaling Technology #3456, clone D4F3, RRID:AB_2143894; 1:125 dilution


title: Jaw joint cells, Uninjured, Pooled

description:
Library name: Sample 1
10X Genomics

value: Jaw joint


title: Mecp2_flox + TMX Week 8 Replicate 3 [Sample_139]

value: male


title: Mecp2_flox + TMX Week 8 Replicate 1 [Sample_137]


title: ddx4E4Δ_ovary_rep3

city: Wuhan

first: Fei

last: Liu

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

institute: Institute of Hydrobiology, Chinese Academy of Sciences

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters. Then clean reads were separately aligned to zebrafish reference genome (GRCz11) with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software. The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/index.shtml) in a reference-based approach.
To identify DEGs (differential expression genes) between the ovaries of WT and ddx4-E4Δ zebrafish, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes.
Functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ≤0.05 compared with the whole-transcriptome background.
Assembly: GRCz11
Supplementary files format and content: read_count.txt is a tab-delimited text file for read count numbers of each gene in all six samples.

source_name: Ovary

extract_protocol:
Ovaries were dissected from WT and ddx4-E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol.
RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 spectrophotometer (NanoDrop Technologies). RNA-seq libraries were constructed using the TruSeqTM RNA sample preparation Kit (Illumina, San Diego, CA). About 1μg of high-quality total RNA samples (OD260/280=1.8~2.2, RIN≥6.5) was used for each RNA-seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. The final sequencing libraries were quantified by TBS-380 Mini-Fluorometer (Promega).

value: Ovary


title: Mecp2_flox + TMX Week 8 Replicate 2 [Sample_138]

source_name: Hippocampus


title: Week4_Tamoxifen_aKO_MeCP2_Rep1


title: scATAC_P13-TI-CDnonInf

value: terminal ileum

value: CD non-inflamed


title: ddx4E4Δ_ovary_rep2


title: scATAC_P12-TI-CDnonInf

value: Female

value: Crohn's Disease


title: scATAC_P15-TI-CDinf

value: Male

value: CD inflamed


title: ddx4E4Δ_ovary_rep1


title: WT_ovary_rep3

value: WT


title: WT + TMX Week 8 Replicate 3 [Sample_135]

value: Wild-type

value: Week 8


title: scATAC_P11-TI-CDnonInf


title: Week4_Vehicle_MeCP2_Rep1

value: Hippocampus

value: Vehicle

value: Week 4

value: 20 weeks


title: WT + TMX Week 8 Replicate 2 [Sample_134]

value: Tamoxifen

value: 24 weeks


title: scATAC_P10-TI-CDnonInf


title: scATAC_P14-TI-CDinf


title: scATAC_P14-TI-CDadjInf

value: CD adjacent-inflamed


title: Week2_Tamoxifen_aKO_MeCP2_Rep3

value: Mecp2 Flox; CreER

value: Week 2

value: 18 weeks

value: male

value: Rabbit anti-MeCP2 monoclonal D443 Cell Signaling Technology #3456, clone D4F3, RRID:AB_2143894; 1:125 dilution


title: Week4_Vehicle_MeCP2_Rep3


title: scATAC_P8-TI-CDnonInf

value: terminal ileum

value: Female

value: Crohn's Disease

value: CD non-inflamed


title: WT + TMX Week 8 Replicate 1 [Sample_133]

value: Wild-type

value: Week 8


title: scATAC_P8-TI-CDinf

value: CD inflamed


title: WT + TMX Week 8 Replicate 4 [Sample_136]

value: Hippocampus


title: Week2_Tamoxifen_aKO_MeCP2_Rep2


title: Week2_Tamoxifen_aKO_MeCP2_Rep1


title: WT_ovary_rep1

value: Ovary

value: WT


title: Mecp2_flox; CreER + Vehicle Week 8 Replicate 6 [Sample_132]

value: Vehicle

value: 24 weeks


title: U_SR_C

first: Amrit

last: Koirala

address: 1 Baylor Plaza

description: Replicate C

data_processing:
Sequenced reads were trimmed for adaptor sequence using TrimGalore
Reads were mapped to the UCSC zebrafish reference genome danRer11 using STAR
featureCounts was used to evaluate gene expression level as read counts
Assembly: Danio rerio GRCz11 (Ensembl Release 98)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Zebrafish embryo explants

growth_protocol: Explants were cultured in explant media from their time of isolation from the embryo at approximately 3 hours post until collection

extract_protocol:
Total RNA was isolated using Trizol reagent, then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Explants of N and T conditions were isolated from embryos injected at the 1-cell stage with 10 pg ndr2 or 0.5 pg CA-acvr1b* mRNA, respectively

tag: condition

value: uninjected (U) controls

tag: developmental stage

value: sphere (SR)

tag: approx time (hours post fertilization)

tag: stage index


title: Week4_Vehicle_MeCP2_Rep2

tag: genotype

value: Mecp2 Flox; CreER

tag: treatment

value: Week 4

value: 20 weeks


title: Week2_Vehicle_MeCP2_Rep3

tag: tissue

value: Week 2

value: 18 weeks

value: male

value: Rabbit anti-MeCP2 monoclonal D443 Cell Signaling Technology #3456, clone D4F3, RRID:AB_2143894; 1:125 dilution


title: Mecp2_flox; CreER + Vehicle Week 8 Replicate 5 [Sample_131]


title: scATAC_P8-TI-CDadjInf

value: terminal ileum

value: Female

value: Crohn's Disease

value: CD adjacent-inflamed


title: U_SR_B

description: Replicate B


title: scATAC_P7-TI-CDnonInf

value: CD non-inflamed


title: Week2_Vehicle_MeCP2_Rep2

value: Hippocampus


title: U_SR_A

description: Replicate A


title: Mecp2_flox; CreER + Vehicle Week 8 Replicate 4 [Sample_130]

value: Vehicle

value: Week 8


title: WT_ovary_rep2

value: Ovary

value: WT


title: Mecp2_flox; CreER + Vehicle Week 8 Replicate 3 [Sample_129]

value: Mecp2 Flox; CreER

value: 24 weeks


title: Week2_Vehicle_MeCP2_Rep1


title: scATAC_P5-TI-CDinf

value: CD inflamed


title: Mecp2_flox; CreER + Vehicle Week 8 Replicate 2 [Sample_128]


title: scATAC_P5-TI-CDnonInf


title: Week1_Tamoxifen_aKO_MeCP2_Rep3

value: Tamoxifen

value: Week 1

value: 17 weeks


title: U_SH_C

description: Replicate C

value: uninjected (U) controls

value: shield (SH)


title: U_SH_B

description: Replicate B


title: scATAC_P5-TI-CDadjInf

value: terminal ileum

value: Female


title: Week1_Tamoxifen_aKO_MeCP2_Rep2

value: male

value: Rabbit anti-MeCP2 monoclonal D443 Cell Signaling Technology #3456, clone D4F3, RRID:AB_2143894; 1:125 dilution


title: Mecp2_flox; CreER + Vehicle Week 8 Replicate 1 [Sample_127]

value: Hippocampus


title: U_SH_A

description: Replicate A


title: scATAC_C7-TI-Control

value: Control


title: U_90_C

description: Replicate C

value: 90% epiboly (90)


title: Mecp2_flox; CreER + TMX Week 8 Replicate 5 [Sample_125]

value: Week 8


title: Week1_Tamoxifen_aKO_MeCP2_Rep1


title: Mecp2_flox; CreER + TMX Week 8 Replicate 6 [Sample_126]


title: Week1_Vehicle_MeCP2_Rep3

value: Vehicle


title: U_90_B

description: Replicate B


title: Mecp2_flox; CreER + TMX Week 8 Replicate 4 [Sample_124]

value: Mecp2 Flox; CreER


title: scATAC_C4-TI-Control

value: Male


title: Mecp2_flox; CreER + TMX Week 8 Replicate 3 [Sample_123]

value: 24 weeks


title: Week1_Vehicle_MeCP2_Rep1


title: Mecp2_flox; CreER + TMX Week 8 Replicate 2 [Sample_122]

value: Tamoxifen


title: scATAC_C3-TI-Control


title: scATAC_C5-TI-Control


title: U_90_A

description: Replicate A


title: U_75_B

description: Replicate B

value: 75% epiboly (75)


title: Mecp2_flox; CreER + TMX Week 8 Replicate 1 [Sample_121]


title: Week8_Tamoxifen_aKO_IgG_Rep2

value: Normal Rabbit IgG Millipore #12-370, RRID:AB_145841; 1:125 dilution


title: Week8_Tamoxifen_aKO_IgG_Rep3


title: scATAC_C1-TI-Control


title: CreER + TMX Week 6 Replicate 4 [Sample_120]

value: CreER

value: Week 6

value: 22 weeks


title: scATAC_C6-TI-Control

value: terminal ileum

value: Female


title: Week8_Tamoxifen_aKO_IgG_Rep1

value: male


title: CreER + TMX Week 6 Replicate 3 [Sample_119]

value: Hippocampus


title: Week8_Vehicle_IgG_Rep3


title: scATAC_P31-AC-CDinf

source_name: ascending colon

value: ascending colon

value: Crohn's Disease

value: CD inflamed


title: scATAC_P31-AC-CDadjInf

value: CD adjacent-inflamed


title: CreER + TMX Week 6 Replicate 2 [Sample_118]


title: U_50_B

description: Replicate B

value: uninjected (U) controls

value: 50% epiboly (50)


title: U_50_C

description: Replicate C


title: CreER + TMX Week 6 Replicate 1 [Sample_117]


title: U_50_A

description: Replicate A


title: U_75_C

description: Replicate C


title: Week8_Vehicle_IgG_Rep1

value: Mecp2 Flox; CreER

value: Vehicle

value: Week 8

value: 24 weeks


title: U_30_C

description: Replicate C

value: 30% epiboly (30)


title: scATAC_C2-TI-Control

value: Control


title: Mecp2_flox + TMX Week 6 Replicate 4 [Sample_116]

value: Mecp2 Flox

value: Tamoxifen

value: Week 6

value: 22 weeks


title: scATAC_P30-AC-CDadjInf

value: Male


title: Week4_Tamoxifen_aKO_IgG_Rep2

value: Hippocampus

value: Week 4

value: 20 weeks

value: male

value: Normal Rabbit IgG Millipore #12-370, RRID:AB_145841; 1:125 dilution


title: Mecp2_flox + TMX Week 6 Replicate 3 [Sample_115]


title: U_30_A

description: Replicate A

value: uninjected (U) controls


title: Week4_Tamoxifen_aKO_IgG_Rep3

value: Mecp2 Flox; CreER


title: Week8_Vehicle_IgG_Rep2

value: Vehicle


title: scATAC_P29-AC-CDadjInf

value: ascending colon

value: Crohn's Disease

value: CD adjacent-inflamed


title: scATAC_P30-AC-CDinf

value: CD inflamed


title: U_75_A

description: Replicate A

value: 75% epiboly (75)


title: Mecp2_flox + TMX Week 6 Replicate 2 [Sample_114]

value: Mecp2 Flox

value: Tamoxifen


title: U_2S_C

description: Replicate C

value: 2-somite (2S)


title: Week4_Tamoxifen_aKO_IgG_Rep1


title: scATAC_P29-AC-CDinf

value: Male


title: Week4_Vehicle_IgG_Rep3

value: Hippocampus


title: scATAC_C17-AC-Control

value: Control


title: scATAC_C15-AC-Control

value: Female


title: WT + TMX Week 6 Replicate 4 [Sample_112]

value: Wild-type

value: Week 6

value: 22 weeks

value: male


title: Week4_Vehicle_IgG_Rep1

value: Mecp2 Flox; CreER

value: Vehicle

value: Week 4

value: 20 weeks

value: Normal Rabbit IgG Millipore #12-370, RRID:AB_145841; 1:125 dilution


title: T_SR_C

description: Replicate C

value: constitutively active Nodal receptor CA-acvr1b* (T)

value: sphere (SR)


title: WT + TMX Week 6 Replicate 3 [Sample_111]

value: Tamoxifen


title: scATAC_P19-AC-CDadjInf

value: ascending colon

value: Crohn's Disease

value: CD adjacent-inflamed


title: scATAC_P19-AC-CDinf

value: CD inflamed


title: WT + TMX Week 6 Replicate 2 [Sample_110]

value: Hippocampus


title: Week4_Vehicle_IgG_Rep2


title: Week2_Tamoxifen_aKO_IgG_Rep3

value: Week 2

value: 18 weeks


title: WT + TMX Week 6 Replicate 1 [Sample_109]

value: Wild-type

value: Week 6

value: 22 weeks


title: T_SR_B

description: Replicate B


title: T_SR_A

description: Replicate A


title: Mecp2_flox + TMX Week 6 Replicate 1 [Sample_113]

value: Mecp2 Flox

value: male


title: T_SH_C

description: Replicate C

value: shield (SH)


title: Week1_Vehicle_H3K27me3_Rep3

value: Mecp2 Flox; CreER

value: Vehicle

value: Week 1

value: 17 weeks

value: Rabbit anti-Tri-Methyl Histone H3 (Lys27) monocloncal C36B11, Cell Signaling Technology #9733, RRID:AB_2616029; 1:125 dilution


title: scATAC_C13-AC-Control

value: ascending colon

value: Female

value: Control


title: Mecp2_flox; CreER + Vehicle Week 6 Replicate 6 [Sample_108]

value: Hippocampus


title: U_2S_A

description: Replicate A

value: uninjected (U) controls

value: 2-somite (2S)


title: Week2_Tamoxifen_aKO_IgG_Rep1

value: Tamoxifen

value: Week 2

value: 18 weeks

value: Normal Rabbit IgG Millipore #12-370, RRID:AB_145841; 1:125 dilution


title: Week2_Vehicle_IgG_Rep3

value: male


title: scATAC_C14-AC-Control

value: Male


title: Mecp2_flox; CreER + Vehicle Week 6 Replicate 4 [Sample_106]

value: Mecp2 Flox; CreER

value: Week 6

value: 22 weeks


title: scATAC_C11-AC-Control


title: Week2_Vehicle_IgG_Rep2

value: Vehicle


title: Week2_Tamoxifen_aKO_IgG_Rep2


title: U_2S_B

description: Replicate B


title: T_SH_A

description: Replicate A

value: constitutively active Nodal receptor CA-acvr1b* (T)

value: shield (SH)


title: Mecp2_flox; CreER + Vehicle Week 6 Replicate 3 [Sample_105]


title: Mecp2_flox; CreER + Vehicle Week 6 Replicate 2 [Sample_104]


title: Week1_Tamoxifen_aKO_IgG_Rep3

value: Week 1

value: 17 weeks


title: T_90_C

description: Replicate C

value: 90% epiboly (90)


title: scATAC_C9-AC-Control

value: ascending colon

value: Female

value: Control


title: scATAC_C10-AC-Control


title: T_90_B

description: Replicate B


title: Mecp2_flox; CreER + Vehicle Week 6 Replicate 1 [Sample_103]

value: Hippocampus


title: scATAC_C12-AC-Control


title: scATAC_P13-AC-CDnonInf

value: Crohn's Disease

value: CD non-inflamed


title: Week1_Tamoxifen_aKO_IgG_Rep2

value: Tamoxifen

value: male

value: Normal Rabbit IgG Millipore #12-370, RRID:AB_145841; 1:125 dilution


title: T_75_C

description: Replicate C

value: 75% epiboly (75)


title: Week1_Tamoxifen_aKO_IgG_Rep1

value: Mecp2 Flox; CreER


title: scATAC_P12-AC-CDnonInf


title: Mecp2_flox; CreER + TMX Week 6 Replicate 5 [Sample_101]

value: Week 6

value: 22 weeks


title: scATAC_P10-AC-CDnonInf

value: Male


title: Week1_Vehicle_MeCP2_Rep2

value: Vehicle

value: Week 1

value: Rabbit anti-MeCP2 monoclonal D443 Cell Signaling Technology #3456, clone D4F3, RRID:AB_2143894; 1:125 dilution


title: T_90_A

description: Replicate A

value: constitutively active Nodal receptor CA-acvr1b* (T)

value: 90% epiboly (90)


title: T_SH_B

description: Replicate B

value: shield (SH)


title: Mecp2_flox; CreER + TMX Week 6 Replicate 6 [Sample_102]

value: Hippocampus


title: T_75_B

description: Replicate B


title: Mecp2_flox; CreER + TMX Week 6 Replicate 4 [Sample_100]


title: Week1_Vehicle_IgG_Rep3

value: 17 weeks


title: Week1_Vehicle_IgG_Rep2


title: scATAC_P9-AC-CDnonInf

value: ascending colon

value: Female

value: Crohn's Disease

value: CD non-inflamed


title: T_75_A

description: Replicate A

value: 75% epiboly (75)


title: Mecp2_flox; CreER + TMX Week 6 Replicate 3 [Sample_99]

value: Mecp2 Flox; CreER

value: Tamoxifen

value: male


title: Week1_Vehicle_IgG_Rep1

value: Normal Rabbit IgG Millipore #12-370, RRID:AB_145841; 1:125 dilution


title: T_50_C

description: Replicate C

value: 50% epiboly (50)


title: Mecp2_flox; CreER + TMX Week 6 Replicate 2 [Sample_98]

value: Week 6

value: 22 weeks


title: scATAC_P6-AC-CDnonInf


title: scATAC_P8-AC-CDnonInf


title: T_50_B

description: Replicate B

value: constitutively active Nodal receptor CA-acvr1b* (T)


title: PabWT_48h_4_FPKM

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

institute: Tel Aviv University

data_processing:
rRNA reads, low quality reads, adaptors and reads with unknown bases (N>5%) were filtered using SOAPnuke software (version：v1.5.2, parameters: -n 0.001 -l 20 -q 0.4 -A0.25, website: https://github.com/BGI-flexlab/SOAPnuke). After reads filtering, mapping was performed to reference genome using HISAT2 (Version: v2.0.4 Parameters: --phred33 --sensitive --no-discordant --no-mixed -I 1 -X1000 --rna-strandness RF Website: http://www.ccb.jhu.edu/software/hisat) (Kim, Langmead and Salzberg, 2015). On average 85.62% of the reads are mapped. StringTie (Version: v1.0.4, Parameters: -f 0.3 -j 3 -c 5 -g 100 -s 10000 -p 8 –rf, Website: http://ccb.jhu.edu/software/stringtie) (Pertea et al., 2015) was used to reconstruct transcripts, and with genome annotation information we identify novel transcripts by using Cuffcompare (Version: v2.2.1, Parameters: -p 12, Website: http://cole-trapnell-lab.github.io/cufflinks) (Trapnell et al., 2012) and predict the coding ability of those new transcripts using CPC (Version: v0.9-r2, Parameters: Default, Website: http://cpc.cbi.pku.edu.cn) (Kong et al., 2007)
Assembly: GCF_002917755.1_EL10_1.0_NCBI)
Supplementary files format and content: FASTQ
Supplementary files format and content: FPKM expression data, excel file

organism: Beta vulgaris

growth_protocol: Seeds of Beta vulgaris cv. Red Egyptian were germinated for 10 days. The seedlings were then transferred into pots and grown in a growth chamber at 21 °C with a photoperiod of 12 h.

extract_protocol:
Total RNA was isolated with the RNeasy Plant Mini Kit (QIAGEN) from mock, PabhrcC-, and PabWT inoculated leaves at 12 hpi and 48 hpi (three biological replicates for each treatment, in total 18 samples were collected).
Oligo dT beads were used to enrich mRNA with poly A tail. RNA fragmentation and first strand cDNAs were generated using random N6-primed reverse transcription, followed by the second strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3' adenylated.

treatment_protocol: Mature leaves from 1.5-month old beet plants were infiltrated with mock (ddH2O), suspension of PabhrcC- (108 CFU/mL), and PabWT (108 CFU/mL).

value: wild-type Pab


title: Mecp2_flox; CreER + TMX Week 6 Replicate 1 [Sample_97]

first: Sameer

last: Bajikar

address: 1250 Moursund St


title: T_50_A

description: Replicate A


title: PabWT_48h_3_FPKM

source_name: Mature leaves from 1.5-month old beet plants


title: scATAC_P3-AC-CDnonInf


title: scATAC_P4-AC-CDnonInf

value: Male


title: T_30_C

description: Replicate C

value: 30% epiboly (30)


title: T_30_B

description: Replicate B


title: CreER + TMX Week 4 Replicate 4 [Sample_96]

value: Hippocampus

value: CreER

value: Week 4

value: 20 weeks


title: scATAC_C7-AC-Control

value: ascending colon

value: Female

value: Control


title: CreER + TMX Week 4 Replicate 2 [Sample_94]

value: Tamoxifen


title: PabWT_12h_3_FPKM

value: Mature leaves from 1.5-month old beet plants


title: scATAC_C5-AC-Control


title: scATAC_C6-AC-Control


title: PabWT_48h_2_FPKM


title: CreER + TMX Week 4 Replicate 1 [Sample_93]

value: male


title: T_30_A

description: Replicate A


title: PabWT_12h_1_FPKM


title: Mecp2_flox + TMX Week 4 Replicate 4 [Sample_92]

value: Mecp2 Flox


title: scATAC_C4-AC-Control


title: Pab_hrcC_48h_4_FPKM

value: PabhrcC- (inactive mutant)


title: T_2S_B

description: Replicate B

value: 2-somite (2S)