title: MYC T58I3002

description:
GRCm38_RAW_count_table.csv
t58i_14

value: 300 µg/ml


title: MYC T58I3001

status: Public on Nov 15 2021

type: SRA

city: Uppsala

first: Gustav

last: Arvidsson

state: Uppsala

address: Husargatan 3

department: Department of Medical Sciences

country: Sweden

institute: Uppsala Universitet

description:
GRCm38_RAW_count_table.csv
t58i_13

library_source: transcriptomic

data_processing:
The short reads were aligned to the mouse reference genome (build GRCm38.87, obtained from the Ensembl ftp repository with corresponding .gtf annotation file), concatenated with the plasmid vector sequence containing MYC and EGFP as well as the sequences for two other overexpressed human genes BMI1 and BCL2L1 using the splice-aware short read aligner STAR (v2.5.1b), with default options and –sjdbGTFfile pointing to the GRCm38.87 GTF file and --outFilterMultimapNmax set to 1.
Reads per feature (concatenated exons for one gene) were obtained using featurecounts (from the package Subread v1.5.1) with default options and -s set to 0
Normalization and tests for differential expression were conducted using the Bioconductor (v3.3) package EdgeR (v3.22.5) using the glmQLF workflow, features with CPM (counts per million) ≥ 0.95 for at least three samples were included in the analysis.
Genome_build: GRCm38.87
Supplementary_files_format_and_content: Read counts per gene for 49671 genes in GRCm38, plus three overexpressed human genes, MYC, BCL2L1 and BMI1, plus EGFP (comma separated table text file generated using featurecounts from the Subread package)

molecule: polyA RNA

organism: Mus musculus

source_name: Murine B cells from spleen

growth_protocol: Transduced B-cells expressing wild type or mutant cMyc (WtMyc, T58AMyc and T58IMyc) where cultured at 37¡C and 5% CO2 in GluMax-RPMI (Gibco-USA) supplemented with 10%FBS (0.01M of HEPES, 1x sodium pyruvate, 0.05mM 2-Beta mercaptoethanol (Gibco-USA) and 0.1 mg/ml Penicillin-streptomycin (Sigma,USA)) with addition of 2mg/ml Doxycycline.

extract_protocol:
Total RNA was isolated using a kit (QIAGEN,NL)
Libraries were constructed using Illumina Truseq 2.0 reagents according to manufacturers protocol, mRNA was purified by poly-T oligo-attached magnetic beads.

treatment_protocol: Cells (WtMyc, T58AMyc and T58IMyc) where cultured as described above for 48 hours, except that 7 different concentrations of doxycycline were used (0, 25, 50, 100, 300, 600, 1000 ug/ml).

tag: genotype

value: MYC T58I

tag: agent

value: doxycycline

tag: agent concentration

tag: cell type

value: B cells from spleen


title: MYC T58I3003

description:
GRCm38_RAW_count_table.csv
t58i_15


title: MYC T58I1001

description:
GRCm38_RAW_count_table.csv
t58i_10

value: 100 µg/ml


title: MYC T58I1002

description:
GRCm38_RAW_count_table.csv
t58i_11


title: Naive Nasal AWCTX_17

city: Toronto

first: Gengming

last: He

address: 27 King's College Circle

department: Biostatistics

country: Canada

institute: University of Toronto

data_processing:
TrimGalore was used to remove Illumina universal adaptors and bases with quality score under 20 from the raw reads data
After trimming, paired-end reads that have length > 40 bases were aligned to the hg19 genome reference using STAR
gene expression raw read was generated by Htseq-count based on UCSC hg19 annotation
transcripts per million reads (TPM) for each sample each gene was generated by RNA-SeQC based on gencode v19 annotation
Genome_build: hg19
Supplementary_files_format_and_content: Raw gene counts matrix (tab-delimited)
Supplementary_files_format_and_content: TPM matrix (tab-delimited)

molecule: total RNA

organism: Homo sapiens

source_name: Nasal

extract_protocol:
RNeasy Tissue (ThermoFisher) RNA extraction kit was used per manufacture's instruction
The New England Biolabs NEBNext Ultra II RNA Library Preparation kit was used for library preparation

tag: individual id

tag: tissue

value: Nasal

value: Naive

tag: rin


title: Culture Bronchial AWCTX_17

source_name: Bronchial

value: Bronchial

value: Culture


title: MYC T58I1003

description:
GRCm38_RAW_count_table.csv
t58i_12


title: MYC T58I502

description:
GRCm38_RAW_count_table.csv
t58i_8

value: 50 µg/ml


title: MYC T58I503

description:
GRCm38_RAW_count_table.csv
t58i_9


title: Naive Nasal AWCTX_18


title: 3_H22_3D_RtL

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Single-cell data were demultiplexed using bcl2fastq2 v2.20.
raw reads were pseudoaligned using Kallisto with default settings (v0.44.0)78. Based on the pseudo alignment estimated by Kallisto
reads mapped to each transcript against the mouse transcriptome GRCm38, Gencode vM16 primary assembly
Normalization using Seurat
Genome_build: transcriptome GRCm38, Gencode vM16
Supplementary_files_format_and_content: tab separated txt files; containing raw seurat input matrices

source_name: mESC

extract_protocol:
Rosette-to-Lumen stage embryoids and 2D mono-culturestem cells were harvested by washing with PBS and incubation in StemPro Accutase Cell Dissociation Reagent to create a single-cell solution
Cells lysed in Guanidine Hydrochloride (50 mM), dNTPs (17.4mM), 2.2µM SMART dT30VN primer lysis buffer
Nextera XT DNA Library Preparation Kit (Illumina)
NextSeq500 system SR 75bp with 2*8bp index reads

treatment_protocol: Cell lines with doxycycline-inducible transgenes were incubated with 2 µg/ml doxycycline

value: Rosette-to-Lumen stage embryoid stem cell


title: MYC T58I501

description:
GRCm38_RAW_count_table.csv
t58i_7


title: 3_H23_3D_RtL


title: Culture Nasal AWCTX_15


title: 3_H21_3D_RtL


title: Naive Nasal AWCTX_15


title: MYC T58I251

description:
GRCm38_RAW_count_table.csv
t58i_4

value: 25 µg/ml


title: MYC T58I252

description:
GRCm38_RAW_count_table.csv
t58i_5


title: Culture Bronchial AWCTX_15


title: MYC T58I253

description:
GRCm38_RAW_count_table.csv
t58i_6


title: MYC T58I03

description:
GRCm38_RAW_count_table.csv
t58i_3

value: control

value: 0 µg/ml


title: 3_H20_3D_RtL


title: 3_H2_3D_RtL


title: MYC T58I01

description:
GRCm38_RAW_count_table.csv
t58i_1


title: MYC T58A10003

description:
GRCm38_RAW_count_table.csv
t58a_21

value: MYC T58A


title: 3_H19_3D_RtL


title: MYC T58A10002

description:
GRCm38_RAW_count_table.csv
t58a_20


title: Culture Nasal AWCTX_13


title: Naive Nasal AWCTX_13


title: MYC T58A6003

description:
GRCm38_RAW_count_table.csv
t58a_18

value: 600 µg/ml


title: MYC T58A6002

description:
GRCm38_RAW_count_table.csv
t58a_17


title: 3_H17_3D_RtL


title: MYC T58A6001

description:
GRCm38_RAW_count_table.csv
t58a_16


title: Culture Bronchial AWCTX_13


title: 3_H18_3D_RtL


title: MYC T58A3003

description:
GRCm38_RAW_count_table.csv
t58a_15


title: 3_H16_3D_RtL


title: MYC T58A3002

description:
GRCm38_RAW_count_table.csv
t58a_14


title: Naive Bronchial AWCTX_13


title: MYC T58I02

description:
GRCm38_RAW_count_table.csv
t58i_2


title: Naive Nasal AWCTX-26


title: MYC T58A1003

description:
GRCm38_RAW_count_table.csv
t58a_12


title: Naive Bronchial AWCTX_15


title: 3_H14_3D_RtL


title: 3_H15_3D_RtL


title: MYC T58A1002

description:
GRCm38_RAW_count_table.csv
t58a_11


title: Naive Bronchial AWCTX-26


title: Culture Bronchial AWCTX-22


title: 3_H13_3D_RtL


title: MYC T58A501

description:
GRCm38_RAW_count_table.csv
t58a_7


title: MYC T58A502

description:
GRCm38_RAW_count_table.csv
t58a_8


title: MYC T58A503

description:
GRCm38_RAW_count_table.csv
t58a_9


title: MYC T58A253

description:
GRCm38_RAW_count_table.csv
t58a_6


title: 3_H12_3D_RtL


title: 3_H11_3D_RtL


title: MYC T58A251

description:
GRCm38_RAW_count_table.csv
t58a_4


title: MYC T58A252

description:
GRCm38_RAW_count_table.csv
t58a_5


title: Culture Nasal AWCTX-22


title: MYC T58A02

description:
GRCm38_RAW_count_table.csv
t58a_2


title: MYC T58A03

description:
GRCm38_RAW_count_table.csv
t58a_3


title: MYC T58A01

description:
GRCm38_RAW_count_table.csv
t58a_1


title: Culture Bronchial AWCTX-23


title: MYC T58A3001

description:
GRCm38_RAW_count_table.csv
t58a_13


title: 3_H10_3D_RtL


title: 3_H1_3D_RtL


title: MYC WT10002

description:
GRCm38_RAW_count_table.csv
wt_20

value: MYC WT


title: MYC WT10001

description:
GRCm38_RAW_count_table.csv
wt_19


title: Culture Bronchial AWCTX-24


title: Culture Nasal AWCTX-24


title: MYC WT6002

description:
GRCm38_RAW_count_table.csv
wt_17


title: MYC WT10003

description:
GRCm38_RAW_count_table.csv
wt_21


title: 3_G8_3D_RtL


title: MYC WT3003

description:
GRCm38_RAW_count_table.csv
wt_15

value: 300 µg/ml


title: Culture Nasal AWCTX-23


title: Naive Nasal AWCTX-22


title: MYC WT3002

description:
GRCm38_RAW_count_table.csv
wt_14


title: MYC T58A1001

description:
GRCm38_RAW_count_table.csv
t58a_10


title: 3_G6_3D_RtL


title: MYC WT3001

description:
GRCm38_RAW_count_table.csv
wt_13


title: Naive Nasal AWCTX-23


title: 3_G9_3D_RtL


title: Naive Bronchial AWCTX-24


title: MYC WT6003

description:
GRCm38_RAW_count_table.csv
wt_18


title: MYC WT503

description:
GRCm38_RAW_count_table.csv
wt_9


title: 3_G3_3D_RtL


title: MYC WT1003

description:
GRCm38_RAW_count_table.csv
wt_12


title: 3_G5_3D_RtL


title: MYC WT1002

description:
GRCm38_RAW_count_table.csv
wt_11


title: MYC WT1001

description:
GRCm38_RAW_count_table.csv
wt_10


title: MYC WT502

description:
GRCm38_RAW_count_table.csv
wt_8


title: 3_G7_3D_RtL


title: Naive Bronchial AWCTX-23


title: Naive Bronchial AWCTX_8


title: MYC WT253

description:
GRCm38_RAW_count_table.csv
wt_6


title: Naive Bronchial AWCTX-22


title: Naive Nasal AWCTX-14


title: Naive Nasal AWCTX-24


title: MYC WT252

description:
GRCm38_RAW_count_table.csv
wt_5


title: MYC WT6001

description:
GRCm38_RAW_count_table.csv
wt_16


title: 3_G24_3D_RtL


title: MYC WT501

description:
GRCm38_RAW_count_table.csv
wt_7


title: 3_G23_3D_RtL


title: 3_G4_3D_RtL


title: Naive Bronchial AWCTX-17


title: MYC WT02

description:
GRCm38_RAW_count_table.csv
wt_2


title: MYC WT03

description:
GRCm38_RAW_count_table.csv
wt_3


title: MYC WT01

description:
GRCm38_RAW_count_table.csv
wt_1


title: Naive Bronchial AWCTX-14


title: 3_G22_3D_RtL


title: 3_G21_3D_RtL


title: Right-sided CRC 3

city: jinan

first: Jingxin

last: Li

address: wenhuaxi road

country: China

institute: Shandong university

data_processing:
The protoplast suspension was loaded into Chromium microfluidic chips with 30 v3 chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit (10X Genomics) according to the manufacturer's instructions. Sequencing was performed with Illumina according to the manufacturer's instructions (Illumina).
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene_x0002_expression/software/pipelines/latest/what-is-cell-ranger) using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat (Macosko et al., 2015; Satija et al., 2015). In brief, for each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat: A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells.
Cellranger reanalyze takes feature-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using cellranger default parameter settings.
The Seurat package was used to normalise data, dimensionality reduction, clustering, differential expression. We used Seurat alignment method canonical correlation analysis (CCA) [Nat. Biotechnol. 36, 411–420 (2018).] for integrated analysis of datasets. For clustering, highly variable genes were selected and the principal components based on those genes used to build a graph, which was segmented with a resolution of 0.6.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: barcodes*.tsv: cell barcode files.
Supplementary_files_format_and_content: features*.tsv: gene files.
Supplementary_files_format_and_content: matrix*.mtx: gene-barcode counts files.

source_name: Colorectal cancer

extract_protocol:
Rinse the tissue with PBS for 1-2 times. Cut the tissue and transfer to a 50 mL centrifuge tube, wash twice with PBS, remove the supernatant, and add 5 mL of digestion solution to the pellet. (Digestion solution formula: DMEM+10%FBS+ 1%PS+75 U/mL collagenase 4+ 125 U/mL separation enzyme.) Digest the tissue in a 37°C incubator for 1 hour, pipetting once every 5 minutes. Centrifuge at 500g for 5 minutes at 4 degrees, remove the supernatant, and add 20 mL PBS each time to wash 3-4 times, and collect the supernatant to 50 mL centrifuge tube. Centrifuge at 500g for 5 minutes at 4 degrees, remove the supernatant, and add the red blood cell lysate. Centrifuge at 500g for 5 minutes at 4 degrees, remove the supernatant, wash twice with PBS, and resuspend with 5 mL of PBS to form a single cell suspension.
RNA libraries were constructed with reagents from a Chromium Single Cell 3' Reagent v3 kit (10X Genomics) according to the manufacturer's instructions. Sequencing was performed with Illumina according to the manufacturer's instructions (Illumina).

value: Colorectal cancer

tag: age

tag: Sex

value: Male

tag: tumor location

value: Ascending


title: Naive Bronchial AWCTX-11


title: 3_G20_3D_RtL


title: Right-sided CRC 2

value: Female


title: Left-sided CRC 2

value: Sigmoid


title: Right-sided CRC 1


title: MYC WT251

description:
GRCm38_RAW_count_table.csv
wt_4

value: doxycycline

value: B cells from spleen


title: Left-sided CRC 3


title: Naive Nasal AWCTX-11

value: Nasal

value: Naive


title: Left-sided CRC 1


title: Naive Nasal AWCTC-16


title: RR057e_00887_SEQ014

city: San Francisco

first: Charles

last: Langelier

state: CA

address: HSE 401, 513 Parnassus Ave

department: Medicine

country: USA

institute: University of California San Francisco

data_processing:
Alignment against human genome- Kallisto v 0.46.1
Gene-level counts were generated from the transcript-level abundance estimates using the R package tximport
Fitering to retain samples with 400,000 gene counts
Differential expression with R package limma
Genome_build: HG-38, ENSEMBL v. 99
Supplementary_files_format_and_content: .csv file with genecounts

source_name: NP/OP swab

growth_protocol: Clinical naso/pharyngeal swab specimens

extract_protocol:
Zymo DNA/RNA magbead
NEBnext with Qiagen Fastselect rRNA depletion
Random hexamer RNAseq

treatment_protocol: DNAse

tag: gender

value: M

tag: sars-cov-2 pcr

value: NEG

tag: sars-cov-2 rpm

tag: infection

tag: sample type

value: Clinical naso/pharyngeal swab specimens


title: RR057e_00886_SEQ014


title: RR057e_00885_SEQ014

value: F


title: Culture Nasal AWCTX_19

value: Culture


title: Naive Bronchial AWCTC-16

value: Bronchial


title: 3_G2_3D_RtL

value: Rosette-to-Lumen stage embryoid stem cell


title: 3_G19_3D_RtL


title: RR057e_00883_SEQ014


title: 3_G17_3D_RtL


title: Naive Bronchial AWCTC-27


title: 3_G18_3D_RtL


title: RR057e_00882_SEQ014


title: Naive Nasal AWCTC-27


title: RR057e_00880_SEQ014


title: 3_G16_3D_RtL


title: RR057e_00879_SEQ014


title: 3_G15_3D_RtL


title: RR057e_00881_SEQ014


title: RR057e_00878_SEQ014


title: RR057e_00876_SEQ014


title: 3_G14_3D_RtL


title: RR057e_00874_SEQ014


title: 3_G13_3D_RtL


title: RR057e_00877_SEQ014


title: RR057e_00884_SEQ014


title: RR057e_00873_SEQ014


title: 3_G12_3D_RtL


title: 3_G11_3D_RtL


title: RR057e_00870_SEQ014


title: 3_G1_3D_RtL


title: RR057e_00868_SEQ014


title: RR057e_00865_SEQ014


title: MYC T58A10001

description:
GRCm38_RAW_count_table.csv
t58a_19

value: MYC T58A


title: 3_G10_3D_RtL


title: RR057e_00867_SEQ014


title: RR057e_00864_SEQ014


title: 3_F9_3D_RtL


title: RR057e_00862_SEQ014


title: RR057e_00875_SEQ014


title: RR057e_00860_SEQ014


title: 3_F7_3D_RtL


title: 3_F6_3D_RtL


title: RR057e_00872_SEQ014


title: RR057e_00869_SEQ014


title: RR057e_00855_SEQ014


title: 3_F5_3D_RtL


title: RR057e_00857_SEQ014


title: RR057e_00853_SEQ014


title: RR057e_00871_SEQ014


title: RR057e_00856_SEQ014


title: RR057e_00861_SEQ014


title: RR057e_00859_SEQ014


title: RR057e_00854_SEQ014


title: 3_F4_3D_RtL


title: 3_F3_3D_RtL


title: RR057e_00850_SEQ014


title: RR057e_00852_SEQ014


title: RR057e_00849_SEQ014


title: RR057e_00863_SEQ014


title: RR057e_00866_SEQ014


title: RR057e_00851_SEQ014


title: 3_F8_3D_RtL


title: 3_F23_3D_RtL


title: RR057e_00847_SEQ014


title: RR057e_00858_SEQ014


title: RR057e_00846_SEQ014


title: RR057e_00845_SEQ014


title: ChIP-Seq SETD2_mut_input

city: New York

first: Christina

middle: S

last: Leslie

state: NY

address: 417 E 68th St

department: Computational Biology Program

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
Reads were aligned to hg19 using BWA (v0.7.17-r1188) with parameters ‘-q 5 -l 32 -k 2’. Uniquely aligned paired reads were extracted using SAMtools. PCR duplicates were removed using Picard tools (v2.18.16).
Peak calling was performed for each individual and pooled replicates of each cell type using MACS2 v2.1.2 with parameters ‘-g hs -p 0.01 --keep-dup all --no-model -c $input_dna_control’
Genome_build: hg19
Supplementary_files_format_and_content: Normalized coverage track in bigWig format

molecule: genomic DNA

source_name: Clear cell renal cell carcinoma cells

growth_protocol: Cells were cultured in F10 medium (advanced DMEM/F12) with 10% FBS, 1× L-glutamine, 1× sodium pyruvate, 1× nonessential amino acid, and 1× penicillin/streptomycin).

extract_protocol:
2 x 10^6 JHRCC12 cells were cross-linked with 1% paraformaldehyde for 10 min at room temperature and quenched by glycine. Cells were washed with cold PBS, pelleted by centrifugation, and lysed. After sonication, samples were spun down and incubated with 1 μg primary antibody for each ChIP experiment at 4 °C overnight. Magnetic beads (Thermo Fisher Scientific) were added the next day and incubated at 4 °C for 2h. Samples were then washed and histone complexes were eluted. The eluted samples were treated with RNase A, proteinase K, reversed crosslink, and purified with Qiagen PCR purification kit.
Library preparation were performed by the Integrated Genomics Operation Core Facility at MSKCC.

tag: cell line

tag: chip antibody


title: RR057e_00844_SEQ014


title: 3_F21_3D_RtL


title: ChIP-Seq SETD2_rescue_H3K36me3_rep2

value: H3K36me3 (Abcam, ab9050)

tag: genotype


title: RR057e_00842_SEQ014


title: RR057e_00843_SEQ014


title: 3_F20_3D_RtL


title: ChIP-Seq SETD2_rescue_H3K36me3_rep1


title: RR057e_00841_SEQ014


title: 3_F2_3D_RtL


title: 3_F24_3D_RtL


title: 3_F22_3D_RtL


title: RR057e_00848_SEQ014


title: ChIP-Seq SETD2_mut_H3K36me3_rep2


title: ChIP-Seq SETD2_rescue_input


title: RR057e_00837_SEQ014


title: RR057e_00838_SEQ014


title: 3_F19_3D_RtL


title: ChIP-Seq SETD2_mut_H3K36me3_rep1


title: RR057e_00835_SEQ014


title: RR057e_00834_SEQ014


title: 3_F18_3D_RtL


title: RR057e_00833_SEQ014


title: ChIP-Seq SETD2_rescue_H3K27me3_rep2

value: H3K27me3 (Cell Signaling Technology, 9733)


title: 3_F17_3D_RtL


title: ChIP-Seq SETD2_rescue_H3K27me3_rep1


title: 3_F16_3D_RtL


title: RR057e_00831_SEQ014


title: RR057e_00832_SEQ014


title: ChIP-Seq SETD2_mut_H3K27me3_rep2


title: RR057e_00829_SEQ014


title: 3_F15_3D_RtL


title: RR057e_00830_SEQ014


title: RR057e_00840_SEQ014


title: ChIP-Seq SETD2_rescue_H3K56ac_rep2

value: H3K56ac (Millipore, 07-677)


title: 3_F14_3D_RtL


title: RR057e_00826_SEQ014


title: RR057e_00836_SEQ014


title: RR057e_00828_SEQ014


title: RR057e_00825_SEQ014


title: 3_F13_3D_RtL


title: 3_F12_3D_RtL


title: ChIP-Seq SETD2_mut_H3K56ac_rep2


title: ChIP-Seq SETD2_mut_H3K27me3_rep1


title: RR057e_00823_SEQ014


title: RR057e_00824_SEQ014


title: 3_F11_3D_RtL


title: ChIP-Seq SETD2_rescue_H3K56ac_rep1


title: RR057e_00821_SEQ014


title: ChIP-Seq SETD2_mut_H3K56ac_rep1


title: RR057e_00817_SEQ014


title: RR057e_00818_SEQ014


title: RR057e_00822_SEQ014


title: ChIP-Seq SETD2_rescue_H3K27ac_rep2

value: H3K27ac (Abcam, ab4729)


title: 3_F10_3D_RtL


title: RR057e_00816_SEQ014


title: 3_F1_3D_RtL


title: RR057e_00814_SEQ014


title: RR057e_00812_SEQ014


title: ChIP-Seq SETD2_rescue_H3K27ac_rep1


title: RR057e_00827_SEQ014


title: RR057e_00811_SEQ014


title: ChIP-Seq SETD2_mut_H3K27ac_rep2


title: RR057e_00809_SEQ014


title: 3_E8_3D_RtL


title: RR057e_00808_SEQ014


title: RR057e_00810_SEQ014


title: RR057e_00807_SEQ014


title: ChIP-Seq SETD2_mut_H3K27ac_rep1


title: 3_E7_3D_RtL


title: RR057e_00806_SEQ014


title: ChIP-Seq SETD2_rescue_H3K4me3_rep2

value: H3K4me3 (Abcam, ab8580)


title: ChIP-Seq SETD2_rescue_H3K4me3_rep1


title: 3_E9_3D_RtL


title: 3_E6_3D_RtL


title: RR057e_00799_SEQ014


title: RR057e_00803_SEQ014


title: RR057e_00804_SEQ014


title: RR057e_00802_SEQ014


title: ChIP-Seq SETD2_mut_H3K4me3_rep1


title: ChIP-Seq SETD2_rescue_H3K4me1_rep2

value: H3K4me1 (Abcam, ab8895)


title: RR057e_00798_SEQ014


title: ChIP-Seq SETD2_mut_H3K4me3_rep2


title: RR057e_00788_SEQ007


title: RR057i_00204_SEQ014

value: POS


title: RR057i_00189_SEQ014


title: 3_E22_3D_RtL


title: RR057e_00805_SEQ014


title: ChIP-Seq SETD2_mut_H3K4me1_rep1


title: ChIP-Seq SETD2_rescue_H3K4me1_rep1


title: 3_E5_3D_RtL


title: 3_E4_3D_RtL


title: RR057e_00953_SEQ014


title: 3_E3_3D_RtL


title: RR057e_00949_SEQ014


title: 3_E2_3D_RtL


title: RR057e_00801_SEQ014


title: 3_E21_3D_RtL


title: ATAC-Seq JHRCC12_SETD2_rescue_rep2

data_processing:
Raw reads were trimmed and filtered for quality using Trimmomatic (v0.38). Trimmed reads were mapped to the hg19 genome assembly using Bowtie2 (v2.3.4.3), and non-uniquely mapping reads were removed.
Peak calling was performed on each replicate using MACS2 (v2.1.2) with ‘-p 1e-2 --extsize 200 --shift -100 --nomodel’ parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized coverage track in bigWig format

extract_protocol: 50,000 JHRCC12 cells were used for the transposition reaction at 37 °C for 30 min. After purification of the DNA with the MinElute PCR purification kit (Qiagen), material was amplified for 5 cycles as described previously (Buenrostro et al., 2013). Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by AMPure Beads at a 1.5x ratio.


title: RR057e_00947_SEQ014


title: RR057e_00782_SEQ007


title: 3_E20_3D_RtL


title: RR057e_00943_SEQ014


title: RR057e_00783_SEQ007


title: RR057e_00779_SEQ007


title: 3_E18_3D_RtL


title: RR057e_00776_SEQ007


title: RR057e_00775_SEQ007


title: 3_E17_3D_RtL


title: ATAC-Seq JHRCC12_SETD2_mut_rep2


title: RR057e_00797_SEQ007


title: RR057e_00773_SEQ007


title: 3_E19_3D_RtL


title: RR057e_00768_SEQ007


title: RR057i_00188_SEQ014


title: 3_E16_3D_RtL


title: ATAC-Seq JHRCC12_SETD2_rescue_rep3


title: RR057i_00187_SEQ006


title: 3Cb-T3

city: Chicago

first: Miriam

middle: S.

last: Domowicz

state: Illinois

address: 5841 S Maryland Ave MC5058

department: Pediatrics

institute: University of Chicago

data_processing:
Illumina Casava1.7 software used for basecalling.
All RNA-seq reads were used to align to the mm10 genome assembly using STAR v2.5.2b with default configurations.
Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM (Fragments Per Kilobase Million) tables.
Using 1.5 as the fold change cutoff, DEGs (Differentially expressed genes) were detected using both Tuxedo suite (FPKM-based method) and featureCounts-DESeq2 (v1.21.22), edgeR (v3.23.5), limma (v3.45.5) (read count-based method) with default configurations.
Genes detected by at least more than one method were collected to create a high-confidence DEG lists.
Genome_build: mm10
Supplementary_files_format_and_content: Count tables were generated using featureCount (v1.26.1) based on GENCODE annotation (vM18).

growth_protocol: The mouse model for cLINCL, in which Tpp1 is disrupted by gene targeting has been previously described (J. Neurosci. 2004, 24(41)9117). The line is being maintained by Tpp1 heterozygous crosses.  In all experiments  Tpp1-/- homozygous mice were compared to age matched non affected siblings.

extract_protocol:
Total RNA was obtained from the cerebellum (Cb) and forebrain/midbrain (F/M) of 1- 2- and 3-month-old  Tpp1-/- and control mice by TRIzol (Thermo Fisher Scientific) extraction followed by a QIAGEN RNeasy Kit®  clean-up procedure which included a DNAse digestion step.
For library making we used the Illumina TruSEQ stranded mRNA Library prep kit in combination with the Illumina provided protocol.

value: Cerebellum

tag: genotyping

value: Female


title: RR057i_00116_SEQ003


title: 3_E15_3D_RtL


title: RR057i_00175_SEQ003


title: ATAC-Seq JHRCC12_SETD2_rescue_rep1


title: 3Cb-T2

value: Male


title: RR057i_00117_SEQ003

value: NEG


title: 3_E14_3D_RtL


title: RR057i_00075_SEQ003

value: M

value: Clinical naso/pharyngeal swab specimens


title: 3Cb-T1


title: RR057i_00118_SEQ003


title: RR057i_00115_SEQ003


title: 3_E13_3D_RtL


title: RR057i_00120_SEQ003


title: 3Cb-Co3

value: wt


title: RR057i_00177_SEQ003


title: RR057e_00261_SEQ003


title: 3Cb-Co2


title: 3_E11_3D_RtL


title: RR057e_00203_SEQ003


title: 3_E12_3D_RtL


title: RR057e_00130_SEQ003


title: RR057e_00039_SEQ003


title: 3_E10_3D_RtL


title: RR057e_00504_SEQ005


title: 3_E1_3D_RtL


title: 3_E24_3D_RtL


title: 3Cb-Co1


title: RR057e_00058_SEQ003


title: RR057e_00488_SEQ005


title: 3_D9_3D_RtL


title: 3F/M-T2

value: Forebrain/Midbrain


title: RR057e_00456_SEQ003


title: RR057e_00431_SEQ005


title: 3F/M-T3


title: 3F/M-T1


title: RR057e_00534_SEQ005

value: F


title: 3_D8_3D_RtL

value: Rosette-to-Lumen stage embryoid stem cell


title: 3F/M-Co3


title: RR057e_00401_SEQ003


title: 3_D7_3D_RtL


title: RR057e_00761_SEQ003


title: RR057e_00512_SEQ005


title: 3_D6_3D_RtL


title: 3F/M-Co2


title: RR057e_00073_SEQ003


title: 3F/M-Co1


title: RR057e_00223_SEQ003


title: 2Cb-T3


title: 3_D4_3D_RtL


title: RR057i_00180_SEQ003


title: 2Cb-T2


title: RR057e_00260_SEQ003


title: RR057e_00586_SEQ005


title: 3_D3_3D_RtL


title: RR057e_00259_SEQ003


title: 2Cb-T1


title: RR057e_00800_SEQ014


title: RR057e_00168_SEQ003


title: RR057e_00161_SEQ005


title: RR057e_00540_SEQ005


title: 2Cb-Co3


title: RR057e_00093_SEQ003


title: RR057e_00173_SEQ003


title: RR057e_00133_SEQ005


title: 3_D5_3D_RtL


title: 2Cb-Co2


title: 3_D23_3D_RtL


title: RR057e_00102_SEQ003


title: 3_D22_3D_RtL


title: 2Cb-Co1


title: RR057e_00088_SEQ003


title: 3_D24_3D_RtL


title: RR057e_00416_SEQ003


title: 3_D21_3D_RtL


title: RR057e_00231_SEQ003


title: RR057e_00206_SEQ003


title: 2F/M-T2


title: 2F/M-T3


title: 2F/M-T1


title: 3_D2_3D_RtL


title: RR057e_00427_SEQ003


title: RR057e_00037_SEQ003


title: RR057i_00119_SEQ003


title: RR057e_00076_SEQ003


title: 3_D18_3D_RtL


title: RR057e_00449_SEQ005


title: RR057e_00187_SEQ005


title: 2F/M-Co3


title: 2F/M-Co2


title: 3_D17_3D_RtL


title: 3_D20_3D_RtL


title: RR057i_00190_SEQ014


title: RR057e_00066_SEQ005


title: RR057e_00250_SEQ005


title: RR057e_00403_SEQ003


title: 3_D15_3D_RtL


title: RR057e_00516_SEQ005


title: 1Cb-T3


title: 3_D16_3D_RtL


title: 3_D14_3D_RtL


title: 3_D19_3D_RtL


title: RR057e_00762_SEQ003


title: RR057e_00494_SEQ005


title: RR057e_00137_SEQ003


title: RR057e_00134_SEQ005


title: RR057e_00105_SEQ003


title: RR057i_00179_SEQ003


title: 1Cb-T2


title: 1Cb-Co3


title: 1Cb-T1


title: RR057e_00070_SEQ014


title: 3_D12_3D_RtL


title: 3_D13_3D_RtL


title: RR057e_00454_SEQ003


title: 2F/M-Co1


title: RR057e_00084_SEQ005


title: 3_E23_3D_RtL


title: RR057e_00116_SEQ003


title: 1Cb-Co1


title: 1Cb-Co2


title: RR057e_00052_SEQ005


title: 3_D11_3D_RtL


title: 1F/M-T3


title: ChIP-Seq SETD2_mut_H3K4me1_rep2


title: RR057e_00296_SEQ005


title: RR057e_00272_SEQ003


title: 3_D1_3D_RtL


title: 1F/M-T2

source_name: 1month- Forebrain/Midbrain-Tpp1-/-


title: 3_C9_3D_RtL


title: 1F/M-T1


title: 3_C8_3D_RtL


title: 3_C7_3D_RtL


title: RR057e_00549_SEQ005


title: RR057e_00237_SEQ005


title: ATAC-Seq JHRCC12_SETD2_mut_rep3


title: 1F/M-Co3


title: RR057e_00086_SEQ003


title: 1F/M-Co2


title: 3_D10_3D_RtL


title: ATAC-Seq JHRCC12_SETD2_mut_rep1


title: 3_C6_3D_RtL


title: RR057e_00290_SEQ005


title: 1F/M-Co1


title: RR057e_00442_SEQ003


title: RR057e_00232_SEQ005


title: RR057e_00318_SEQ005


title: RR057e_00246_SEQ005


title: 3_C4_3D_RtL


title: RR057e_00131_SEQ003


title: RR057e_00324_SEQ005


title: NOP2_WT_Input_Replicate2

city: Houston

first: Catherine

last: Denicourt

state: TX

address: 6431 Fannin St

department: Integrative Biology & Pharmacology

institute: The University of Texas HSC Houston

data_processing:
Raw sequencing data were adaptor trimmed using CutAdapt
Unique molecular identifier (UMI) was appended to the read name using fastp and Reads less than 18 nt were discarded.
Trimmed reads were aligned to human genome (hg38) and human repetitive elements using family-aware repetitive elements mapping pipeline described by Van Nostrand et al. (Genome Biol., 2020, 21, 90.)
miCLIP peak calling was performed on mapped reads from the above repetitive elements mapping pipeline using Peakachu (https://github.com/tbischler/PEAKachu) with parameter --paired_end --max_insert_size 220.
Genome_build: hg38
Supplementary_files_format_and_content: peak files in excel workbook

source_name: human embryonic kidney cells

growth_protocol: HEK293T cells were maintained in high glucose Dulbecco's modified Eagle's medium (DMEM) with 5% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 µg/ml streptomycin under 5% CO2 atmosphere at 37 C.

extract_protocol:
The eCLIP-sequencing protocol described by Van Nostrand et al (Methods Mol. Biol., 2017, 1648, 177-200.) was applied with minor modifications. Twenty million cells were lysed in CLIP buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, 1X Protease Inhibitor Cocktail) without UV crosslink on ice for 15 min, followed by sonication and digestion with RNase T1 and Turbo DNAse at 37 C for 5 min. Digested lysates were cleared by centrifugation and immunoprecipitated using 100 μl of protein G Dynabeads pre-bound with 10 μg of anti-FLAG antibody at 4 C overnight.  Samples were washed twice in high salt wash buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, 1 mM EDTA), once in wash buffer (20 mM Tris-HCl pH 7.4, 0.2% Tween-20) and RNA was dephosporylated, treated with T4 PNK and ligated to 3’ RNA adapter (/5Phos/rArGrArUrCrGrGrArArGrArGrCrArCrArCrGrUrC/3SpC3/) on beads. Samples (including SMinputs) were loaded on 8% SDS-PAGE gel for separation, transferred to a nitrocellulose membrane and RNA was isolated from membrane by cutting a region 75 kDa above NOP2/NSUN1.
CLIP and SMinput libraries were prepared into paired-end high-throughput libraries as described by Van Norstrand et al (Methods Mol. Biol., 2017, 1648, 177-200.) and sent for sequencing on Illumina Hi-Seq 4000 platform (Novogene).

treatment_protocol: Cells were transfected with FLAG tagged NOP2_WT or NOP2_C459A expressing plasmid and incubated for 40 hours.

tag: treatment

value: Transfected with FLAG tagged NOP2_WT expressing plasmid and incubated for 40 hours.

tag: miclip antibody


title: NOP2_WT_IP_Replicate2

value: FLAG (Sigma, F1804)


title: RR057e_00763_SEQ003


title: RR057e_00107_SEQ003


title: RR057e_00491_SEQ005


title: RR057e_00184_SEQ003


title: RR057e_00577_SEQ005


title: RR057e_00222_SEQ003


title: RR057e_00508_SEQ005


title: 3_C24_3D_RtL

tag: cell type


title: NOP2_WT_IP_Replicate1


title: NOP2_WT_Input_Replicate1


title: RR057e_00200_SEQ003


title: NOP2_C459A_IP_Replicate2

value: Transfected with FLAG tagged NOP2_C459A expressing plasmid and incubated for 40 hours.


title: NOP2_C459A_Input_Replicate2

value: Transfected with FLAG tagged NOP2_C459A expressing plasmid and incubated for 40  hours.


title: 3_C5_3D_RtL


title: 3_C23_3D_RtL


title: RR057e_00410_SEQ005


title: RR057e_00268_SEQ003


title: RR057e_00515_SEQ005


title: RR057e_00273_SEQ003


title: RR057e_00117_SEQ005


title: RR057e_00148_SEQ005


title: RR057e_00198_SEQ003


title: 3_C22_3D_RtL


title: RR057e_00581_SEQ005


title: NOP2_C459A_IP_Replicate1


title: 3_C21_3D_RtL


title: 3_C3_3D_RtL


title: RR057e_00140_SEQ003


title: RR057e_00423_SEQ003


title: NOP2_C459A_Input_Replicate1


title: ICA-negative for IHD (non-IHD) undergoing valvular surgery, 28-04-15-MES

city: Ankara

first: Arda

last: Eskin

state: Cankaya

address: Universiteler Mah.

department: Informatics Institute

country: Turkey

institute: Middle East Technical University

data_processing:
Fastq files were trimmed using Trimmomatic v0.32 (1) applying the following parameters: ILLUMINACLIP:<fasta with adapters>:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to the reference genome (EnsEMBL gene collection v82 ) using STAR v2.3.0  with the following parameters: --genomeLoad NoSharedMemory --readFilesCommand zcat --outSAMattributes All --outSAMunmapped Within.
For read quantification, we used featureCounts (4) with the following parameters: "-F" "GTF" "-t" "exon" "-g" "gene_id" "-O" "-T" "16" "-a".
Genome_build: Ensembl gene collection v82 (GRCh38.p3)
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt (Matrix table with raw gene counts for every gene and every sample)

source_name: Heart (Atrial Appendage)

extract_protocol:
During cardiac surgery, a biopsy sample of the RAA was collected from each patient. Tissue samples were collected at the cannulation site, the insertion site of the venous line for the heart–lung machine. Dissected biopsies were briefly washed in ice-cold sterile saline, cut into 0.5 cm thick tissue pieces, and immersed into 3 ml of RNAlater (Sigma Aldrich, Merck KGaA, Darmstadt, Germany) to inactivate RNAses and stabilize RNA. Samples were let to stabilize at +4°C for one day and stored at under -70°C until processing. Total RNA was isolated from RAA biopsies via initial ice-cold tissue homogenization using a Precellys 24 tissue homogenizer equipped with the Cryolys cooling option (Bertin Technologies SAS, Montigny-le-Bretonneux, France) followed by RNA isolation using combined QIAzol / chloroform extraction and Qiagen RNeasy mini spin column purification  according to the manufacturer’s instructions (Qiagen, Venlo, Netherlands). The sample RNA integrity number (RIN; mean 7.95 ± 0.55; range 7.1–9.0) and total quantity (mean 3069.55 ± 1141.08 ng; range 867.8–6855.0 ng) was evaluated in the Functional Genomics Unit (FuGU, University of Helsinki, Helsinki, Finland). Isolated total RNA was stored at under -70oC until sequencing. Ribosomal RNA was removed using the Ribo-ZeroTM Magnetic kit (Illumina Inc, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Heart (Atrial Appendage)

tag: disease state

value: ICA-negative


title: RR057e_00418_SEQ005

tag: age


title: RR057e_00119_SEQ005


title: ICA-negative for IHD (non-IHD) undergoing valvular surgery, 26-02-15-OAP


title: RR057e_00765_SEQ003


title: RR057e_00291_SEQ005


title: ICA-negative for IHD (non-IHD) undergoing valvular surgery, 12-03-15-VKM


title: RR057e_00485_SEQ005


title: 3_C17_3D_RtL


title: 3_C19_3D_RtL


title: ICA-negative for IHD (non-IHD) undergoing valvular surgery, 10-03-15-MJK


title: 3_C18_3D_RtL


title: 3_C20_3D_RtL


title: RR057i_00176_SEQ003


title: ICA-negative for IHD (non-IHD) undergoing valvular surgery, 06-03-15-HKR


title: 3_C16_3D_RtL


title: ICA-negative for IHD (non-IHD) undergoing valvular surgery, 10-03-15-JVL


title: 3_C2_3D_RtL


title: RR057e_00079_SEQ003


title: RR057e_00042_SEQ005


title: RR057e_00169_SEQ005


title: RR057e_00145_SEQ005


title: RR057e_00051_SEQ005


title: 3_C13_3D_RtL


title: ICA-negative for IHD (non-IHD) undergoing valvular surgery, 04-03-15-VHF


title: RR057e_00340_SEQ005


title: 3_C15_3D_RtL


title: RR057e_00171_SEQ003


title: 3_C12_3D_RtL


title: RR057e_00049_SEQ003


title: RR057e_00216_SEQ003


title: RR057e_00590_SEQ005


title: 3_C11_3D_RtL


title: ICA-negative for IHD (non-IHD) undergoing valvular surgery, 03-03-15-THH


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 31-03-15-EN

value: (ICA)-positive


title: RR057e_00138_SEQ005


title: RR057e_00295_SEQ005


title: RR057e_00567_SEQ005


title: 3_C10_3D_RtL


title: RR057e_00143_SEQ003


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 30-12-14-KJ


title: 3_C14_3D_RtL


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 29-12-14-JK


title: RR057i_00173_SEQ003


title: RR057e_00224_SEQ005


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 28-01-15-EM


title: RR057e_00074_SEQ003


title: RR057e_00280_SEQ005


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 25-02-15-JV


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 28-01-15-AP


title: 3_B7_3D_RtL


title: RR057e_00142_SEQ003


title: RR057e_00239_SEQ005


title: RR057e_00309_SEQ005


title: 3_B6_3D_RtL


title: 3_B8_3D_RtL


title: RR057e_00489_SEQ005


title: RR057e_00302_SEQ003


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 24-03-15-RM


title: 3_B5_3D_RtL


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 23-02-15-MO


title: RR057e_00460_SEQ005


title: RR057e_00414_SEQ003


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 23-01-15-RV


title: RR057e_00412_SEQ003


title: 3_B4_3D_RtL


title: 3_B9_3D_RtL


title: RR057e_00436_SEQ003


title: RR057e_00047_SEQ005


title: 3_B3_3D_RtL


title: RR057e_00475_SEQ005


title: RR057e_00440_SEQ005


title: RR057e_00253_SEQ003


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 24-04-15-LA


title: 3_B24_3D_RtL


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 22-04-15-HTJ


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 20-02-15-PA


title: RR057e_00294_SEQ005


title: RR057e_00165_SEQ005


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 19-08-15-AL


title: RR057e_00399_SEQ003


title: 3_B23_3D_RtL


title: 3_B22_3D_RtL


title: RR057e_00437_SEQ003


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 19-03-15-TA


title: RR057e_00560_SEQ005


title: 3_B21_3D_RtL


title: RR057e_00060_SEQ005


title: RR057e_00285_SEQ005


title: 3_B20_3D_RtL


title: RR057e_00451_SEQ003


title: RR057e_00254_SEQ005


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 18-09-15-AM


title: RR057e_00764_SEQ003


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 13-03-15-ML


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 16-04-15-SB


title: RR057i_00083_SEQ003


title: 3_B2_3D_RtL


title: RR057e_00520_SEQ005


title: RR057e_00505_SEQ005


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 13-02-15-JR


title: 3_B19_3D_RtL


title: RR057e_00287_SEQ005


title: RR057e_00080_SEQ003


title: 3_B18_3D_RtL


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 12-03-15-HSN


title: RR057e_00202_SEQ005


title: 3_B17_3D_RtL


title: RR057i_00067_SEQ003

value: POS


title: RR057e_00728_SEQ003


title: 3_B16_3D_RtL


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 11-03-15-EOS


title: 3_B15_3D_RtL


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 11-02-15-SJ


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 11-03-15-JJT


title: RR057e_00721_SEQ003


title: RR057e_00731_SEQ003


title: 3_B14_3D_RtL


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 11-02-15-AV


title: RR057e_00719_SEQ003


title: 3_B13_3D_RtL


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 10-04-15-SR


title: RR057i_00158_SEQ003


title: 3_B12_3D_RtL


title: RR057i_00156_SEQ003


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 10-04-15-JP


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 09-03-15-EJH


title: RR057i_00137_SEQ003


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 10-02-15-RL


title: 3_B10_3D_RtL


title: 3_B11_3D_RtL


title: 3_B1_3D_RtL


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 09-01-15-ES


title: RR057i_00138_SEQ003


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 06-03-15-HYJM


title: RR057i_00136_SEQ003


title: 3_A9_3D_RtL


title: 3_A8_3D_RtL


title: RR057i_00108_SEQ003


title: colon, GR iKO_DSS Replicate 4

type: RNA

city: Durham

first: Jian-Liang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description: Colon from DSS treated  GR iKO mice

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNA was fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2505C using one color scan setting

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent, version 12.0.0.7) using default parameters (protocol GE1_1200_Jun14 and Grid: 014868_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities. The log2-transformed Processed Signal intensities were imported to Partek Genomics Suite (version 6.6) for quantile normalization and subsequent analysis.

source_name: GR iKO DSS, colon

label_protocol: Starting with 500ng of total RNA, sample labeling was performed based on the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

growth_protocol: Mice were maintained on normal chow diet

extract_protocol: TRIzol reagent, followed by RNA clean up using the Qiagen RNA easy mini kit with on-column DNAseI treatment

treatment_protocol: 4-6 month old Flox and GR iKO female mice were treated with regular water (control) or 2.5% DSS water for 7 days. Colon tissues were harvested after the treatment.

tag: strain

value: female

value: 4-6 months

value: colon

tag: diet

value: chow diet

value: GR iKO

value: DSS-treated


title: 3_A7_3D_RtL


title: colon, GR iKO_DSS Replicate 1

description: Colon from DSS treated  GR iKO mice

tag: gender


title: RR057i_00109_SEQ003

value: M

tag: sars-cov-2 pcr

value: Clinical naso/pharyngeal swab specimens


title: 3_A6_3D_RtL

value: Rosette-to-Lumen stage embryoid stem cell


title: colon, GR iKO_ctrl Replicate 3

description: Colon from control  GR iKO mice

source_name: GR iKO control, colon

value: control


title: RR057i_00110_SEQ003

value: F

tag: sars-cov-2 rpm


title: 3_A5_3D_RtL


title: colon, GR iKO_DSS Replicate 3

description: Colon from DSS treated  GR iKO mice


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 05-03-15-JK


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 05-03-15-JRS


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 06-02-15-MH


title: colon, GR iKO_ctrl Replicate 2

description: Colon from control  GR iKO mice


title: RR057i_00112_SEQ003

tag: infection


title: colon, GR iKO_ctrl Replicate 1

description: Colon from control  GR iKO mice


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 04-03-15-LI


title: 3_A4_3D_RtL


title: RR057i_00114_SEQ003

tag: sample type


title: colon, GR iKO_ctrl Replicate 4

description: Colon from control  GR iKO mice


title: colon, Flox_DSS Replicate 2

description: Colon from DSS treated  Flox mice

source_name: Flox DSS, colon


title: 3_A3_3D_RtL


title: HCT116_3R

city: Orlando

first: Deborah

last: Altomare

state: FLORIDA

address: 6900 Lake Nona Blvd.

department: Cancer Research

institute: University of Central Florida

data_processing:
Basecalling performed by NovaSeq 6000 software RTA3
Cutadept and Perl scripts were used remove Poly(A) tails and adapter sequences, as well as low quality and undetermined bases
HISAT2 was used to align and map reads to the GRCm38 (Mus musculus) reference genome
StringTie was used to assemble mapped reads to transcripts
Gene count matrix was generated by merging transcript profiles using gffcompare and Perl scripts
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with FPKM expression values for every gene and every sample

source_name: Liver

extract_protocol:
Livers were removed and placed into RNALater. Total RNA was then extracted frm homogenized liver tissue using TRIzol reagent.
RNA libraries were prepared for sequencing using Illumina’s TruSeq-stranded-mRNA protocol.

value: NOD Scid Gamma (NSG)

value: Female

tag: cell line

value: Liver

tag: protocol

value: Subcutaneous xenografts were established using the indicated cell line


title: colon, Flox_DSS Replicate 1

description: Colon from DSS treated  Flox mice

tag: genotype


title: colon, Flox_DSS Replicate 4

description: Colon from DSS treated  Flox mice


title: RR057i_00141_SEQ003


title: colon, Flox_ctrl Replicate 4

description: Colon from control  Flox mice

source_name: Flox control, colon


title: HCT116_3L


title: colon, Flox_ctrl Replicate 3

description: Colon from control  Flox mice


title: colon, Flox_ctrl Replicate 2

description: Colon from control  Flox mice


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 04-03-15-HEK

value: Heart (Atrial Appendage)

value: (ICA)-positive


title: 3_A24_3D_RtL


title: RR057i_00134_SEQ003

value: POS


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 03-12-14-OL


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 01-09-15-ES


title: RR057i_00145_SEQ003


title: HCT116_1L

value: Male


title: 3_A23_3D_RtL


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 04-03-15-IO


title: RR057i_00133_SEQ003


title: 3_A22_3D_RtL


title: Colo201_4R


title: HCT116_1R


title: (ICA)-positive IHD undergoing coronary artery bypass surgery, 01-03-15-RTL


title: Colo201_4L


title: RR057i_00070_SEQ003


title: 3_A20_3D_RtL


title: RR057i_00071_SEQ003


title: RNA-Seq JHRCC12_SETD2_rescue_rep3

description:
All_gene_counts.txt.gz
2210_3

data_processing:
Raw reads were trimmed and filtered for quality using Trimmomatic (v0.38). Trimmed reads were then aligned against the hg19 genome using STAR (v2.7.1a).
For each RefSeq annotated gene, reads overlapping with exon regions were counted using HTSeq (v0.11.2).
Genome_build: hg19
Supplementary_files_format_and_content: Gene quantification count in txt format

extract_protocol:
Total RNA was extracted and cleaned up using RNeasy Mini Kit (Qiagen).
After RiboGreen quantification and quality control of Agilent BioAnalyzer, 6-15 ng of total RNA underwent amplification (12 cycles) using the SMART-seq V4 (Clontech) Ultra Low Input RNA kit for sequencing. 10 ng of amplified cDNA was used to prepare Illumina HiSeq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR.


title: RNA-Seq JHRCC12_SETD2_rescue_rep2

description:
All_gene_counts.txt.gz
2210_2


title: RR057i_00069_SEQ003


title: colon, Flox_ctrl Replicate 1

description: Colon from control  Flox mice

value: female

value: 4-6 months

value: colon


title: 3_A2_3D_RtL


title: RNA-Seq JHRCC12_SETD2_rescue_rep1

description:
All_gene_counts.txt.gz
2210_1


title: 3_A19_3D_RtL


title: RR057i_00122_SEQ003


title: 3_C1_3D_RtL


title: RNA-Seq JHRCC12_SETD2_mut_rep3

description:
All_gene_counts.txt.gz
1633_3


title: RR057i_00088_SEQ003


title: 3_A18_3D_RtL


title: 3_A21_3D_RtL


title: RR057i_00090_SEQ003


title: ID6_230

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

data_processing:
RSEM v1.3.1 for quantification of expressed genes annotated by Mus_musculus.GRCm38.89.chr.gtf
Genome_build: GRCm38
Supplementary_files_format_and_content: gene expression TPM in txt file

source_name: Flash frozen liver

extract_protocol:
Total RNA was extracted and isolated from ~0.3g flash frozen murine liver using the Direct-zol RNA MiniPrep kit (Zymo Research #R2051).
An input of 100ng of RNA was used for library preparation. Library construction was performed by Novogene using a NEBNext® Ultra RNA Library Prep Kit for Illumina.
Libraries were quantified using a Qubit 2.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA) and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

value: Balbc

tag: reproductive stage

value: involution day 6

tag: Sex

value: 12 weeks


title: ID6_232


title: RNA-Seq JHRCC12_SETD2_mut_rep1

description:
All_gene_counts.txt.gz
1633_1


title: RR057i_00089_SEQ003

value: M

value: Clinical naso/pharyngeal swab specimens


title: ID6_216


title: ID6_218


title: 3_A17_3D_RtL

value: Rosette-to-Lumen stage embryoid stem cell


title: 3_A16_3D_RtL


title: 3_A15_3D_RtL


title: Colo201_2R

value: NOD Scid Gamma (NSG)


title: ribo_72_rcas9_f

city: Berkeley

first: Nicholas

middle: T

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
Library strategy: ribosome profiling
Adapter trimming with fastx_clipper v0.0.14 -Q33 -a AGATCGGAAGAGCACACGTCTGAA -n -v
Alignment with hisat2 v2.1.0 using GRCh38
Footprint counting using custom fp-count script and Gencode v22 APPRIS principal splice isoforms
Genome_build: GRCh38
Supplementary_files_format_and_content: qexpr.txt files are tab-delimited text files with three columns: transcript id, CDS length, and read count

source_name: HEK293 cell line

growth_protocol: HEK 293 (ATCC) cell lines were cultured in DMEM, high glucose, GlutaMAX (Gibco) with 10% FBS (VWR) in a 37°C incubator with 5.0% CO2 and 20% O2. HEK cells were passaged 2 days before nucleofection and trypsinized at 60-90% confluency.

extract_protocol:
RNase I footprinting, ultracentrifugation, denaturing RNA extraction, dephosphorylation, preadenylated inker ligation, reverse transcription, cDNA circularization, PCR amplification
Total RNA was prepared by detergent lysis.

treatment_protocol: Cas9, dCas9, and D10A Cas9 ribonucleoproteins (RNPs) targeting intron 12 of JAK2 were prepared as detailed in (Lingeman et al., 2017). 300 pmol Cas9 and 300 pmol guideRNA were added to 1 x 106 cells suspended in 100 μl SF Solution (Lonza). HEK cells were nucleofected using program CM-130 in the X Unit of a Lonza 4D-Nucleofector (AAF-1002X, AAF-1002B) and pre-warmed media was immediately added to the cuvettes to increase cell viability.

value: HEK293 cell line

tag: treatment

value: Cas9 RNP nucleofection

tag: timepoint

value: 72 hours


title: ribo_72_rcas9_e

tag: tissue


title: 3_A14_3D_RtL

tag: cell type


title: Colo201_2L

value: Liver

value: Subcutaneous xenografts were established using the indicated cell line


title: ID6_201

tag: age


title: RR057i_00082_SEQ003

value: F

value: POS


title: ribo_72_dcas9_f

value: dCas9 RNP nucleofection


title: RR057i_00080_SEQ003


title: ribo_72_dcas9_e


title: RNA-Seq JHRCC12_SETD2_mut_rep2

description:
All_gene_counts.txt.gz
1633_2


title: RR057i_00078_SEQ003


title: LAC_36

tag: strain

value: lactation day 10

value: female


title: 3_A12_3D_RtL


title: LAC_240

value: Balbc


title: RR057i_00081_SEQ003


title: 3_A11_3D_RtL


title: LAC_213


title: ribo_36_dcas9_e

value: 36 hours


title: RR057i_00074_SEQ003


title: LAC_200

value: 12 weeks


title: RR057i_00077_SEQ003

value: M


title: ID6_209

value: involution day 6


title: RR057e_00746_SEQ003

value: Clinical naso/pharyngeal swab specimens


title: LAC_133


title: 3_A10_3D_RtL

value: Rosette-to-Lumen stage embryoid stem cell


title: ribo_36_dcas9_d

value: HEK293 cell line


title: 3_A1_3D_RtL


title: mrna_72_dcas9_rna_b

data_processing:
Adapter trimming with fastx_clipper v0.0.14 -Q33 -a AGATCGGAAGAGCACACGTCTGAA -n -v
Alignment with hisat2 v2.1.0 using GRCh38
Footprint counting using custom fp-count script and Gencode v22 APPRIS principal splice isoforms
Genome_build: GRCh38
Supplementary_files_format_and_content: qexpr.txt files are tab-delimited text files with three columns: transcript id, CDS length, and read count

extract_protocol:
Denaturing RNA extraction, rRNA depletion, stranded RNA-Seq library generation
Total RNA was prepared by detergent lysis.


title: ribo_36_cas9_a

value: Cas9 RNP nucleofection


title: RR057i_00062_SEQ003


title: 3_A13_3D_RtL


title: mrna_72_dcas9_rna_a

value: 72 hours


title: NUL_4

value: nulliparous


title: RR057i_00098_SEQ003


title: E14_ADNP-dHD-HA_ADNP

city: Philadelphia

first: Phillip

last: Wulfridge

state: Pennsylvania

address: 3601 Spruce St

institute: The Wistar Institute

data_processing:
Library strategy: CUT&RUN
Alignment (CUT&RUN, MapR)
Bowtie2
Alignment (RNA-Seq)
STAR
RNA expected counts were generated with RSEM.
Bigwig files were made from .bam files using "deepTools bamCoverage --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and RPM normalization. Normalized MapR bigwigs were generated by subtracting MapR-GST-MNase tracks from MapR tracks using deepTools bigwigCompare.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: bigwig files compatible with UCSC genome browser and IGV, TPM output in .counts tab-delimited for RNA-Seq alignment

growth_protocol: Mouse embryonic stem cells were grown in DMEM medium with 15% FBS, 25mM HEPES, 1x GlutaMAX, 1x non-essential amino acids, 100 U/mL penicillin-steptomycin, LIF, 3µM GSK inhibitor, 1µM MEK1/2 inhibitor at 37 ˚C. Human induced pluripotent stem cell lines were grown on Geltrex (ThermoFisher A1413302) coated plates in Essential 8 media (Gibco A1517001).

extract_protocol:
CUT&RUN for CTCF, ADNP, and HA was performed on cells as previously described (Skene and Henikoff, eLife 2017).
R-loop containing DNA was collected using MapR protocol as previously described (Yan et al., Cell Reports 2019).
Total RNA was collected using Trizol (Invitrogen) and digested with Turbo Dnase (Ambion). rRNA was selectively depleted using FastSelect (Qiagen).
rRNA-depleted RNA was converted to cDNA using the Ultra II Directional RNA kit for Illumina (NEB #E7760).
DNA samples were end-repaired using End-Repair Mix (Enzymatics), A-tailed using Klenow exonuclease minus (Enzymatics), purified with MinElute columns (Qiagen), and ligated to Illumina adapters (NEB E7600) with T4 DNA ligase (Enzymatics).  Size selection for fragments >150 bp was performed with AMPure XP (Beckman Coulter).  Libraries were PCR amplified with dual index barcode primers for Illumina sequencing (NEB E7600) using Q5 DNA polymerase (NEB M0491) and purified with MinElute.

value: ADNP HA-Tag Knock-in + Homeodomain Deletion

value: CUT&RUN

tag: antibody

value: ADNP


title: E14_ADNP-HA_HA_Rep2

data_processing:
Alignment (CUT&RUN, MapR): Bowtie2
Alignment (RNA-Seq): STAR
RNA expected counts were generated with RSEM.
Bigwig files were made from .bam files using "deepTools bamCoverage --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and RPM normalization. Normalized MapR bigwigs were generated by subtracting MapR-GST-MNase tracks from MapR tracks using deepTools bigwigCompare.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: bigwig files compatible with UCSC genome browser and IGV, TPM output in .counts tab-delimited for RNA-Seq alignment

value: ADNP HA-Tag Knock-in

value: HA


title: RR057i_00101_SEQ003

tag: gender

value: POS


title: LAC_102

value: Balbc

value: lactation day 10

value: female


title: E14_ADNP-dHD-HA_HA_Rep2


title: ribo_36_cas9_c

value: 36 hours


title: E14_ADNP-dHD-HA_RNA-Seq_Rep3

data_processing:
Alignment (CUT&RUN, MapR)
Bowtie2
Alignment (RNA-Seq)
STAR
RNA expected counts were generated with RSEM.
Bigwig files were made from .bam files using "deepTools bamCoverage --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and RPM normalization. Normalized MapR bigwigs were generated by subtracting MapR-GST-MNase tracks from MapR tracks using deepTools bigwigCompare.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: bigwig files compatible with UCSC genome browser and IGV, TPM output in .counts tab-delimited for RNA-Seq alignment

value: ADNP Knockout

value: RNA-Seq


title: mrna_72_cas9_rna_b


title: NUL_226

value: 12 weeks


title: mrna_72_cas9_rna_a

value: HEK293 cell line


title: RR057i_00106_SEQ003

value: M

tag: sars-cov-2 pcr

value: Clinical naso/pharyngeal swab specimens


title: E14_ADNP-dHD-HA_RNA-Seq_Rep2


title: mrna_36_dcas9_e

value: dCas9 RNP nucleofection


title: RR057i_00104_SEQ003

tag: sars-cov-2 rpm


title: E14_ADNP-dHD-HA_RNA-Seq_Rep1


title: NUL_220

value: nulliparous


title: E14_ADNP-dHD-HA_MapR_GST-MNase_Rep2

value: ADNP HA-Tag Knock-in + Homeodomain Deletion

value: MapR

tag: fusion protein

value: GST-MNase


title: NUL_221


title: mrna_36_dcas9_d


title: RR057i_00095_SEQ003

tag: infection

tag: sample type


title: E14_ADNP-dHD-HA_MapR_GST-MNase_Rep1

tag: protocol


title: mrna_36_cas9_b

value: Cas9 RNP nucleofection


title: NUL_227


title: NUL_1


title: RR057i_00100_SEQ003

value: F

value: POS


title: RR057i_00103_SEQ003


title: E14_ADNP-dHD-HA_MapR_Rep2

tag: genotype

value: GST-RHΔ-Mnase


title: RR057i_00096_SEQ003


title: E14_ADNP-dHD-HA_MapR_Rep1


title: snRNAseq_JW18_iris_control_RP3_

city: Baltimore

first: Amir

last: Rattner

state: MD - Maryland

address: 725 North Wolfe St.

institute: Johns Hopkins University

data_processing:
Reads were aligned to a mm10 pre-mRNA index using Cellranger version 3.1.0.  Libraries were merged using Cellranger and data was analyzed using the Seurat R package.
Genome_build: mm10
Supplementary_files_format_and_content: expression_data.mtx
Supplementary_files_format_and_content: cell_metadata

source_name: Adult iris

extract_protocol: Five or six irise  a femalemice were rapidly dissected in ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH).  The tissue was minced with a razor blade and Dounce homogenized using a loose-fitting pestle in 5 ml of homogenization buffer supplemented with 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, and EDTA-free protease inhibitor (Roche 11 836 170 001), and 60 U/mL RNasin Plus RNase Inhibitor (Promega N2611).  A 5% IGEPAL-630 solution was added to bring the homogenate to 0.3% IGEPAL-630, and the homogenate was further homogenized with five strokes of a tight-fitting pestle.  The sample was filtered through a 50 μm filter (CellTrix, Sysmex, 04-004-2327), underlayed with solutions of 30% and 40% iodixanol in homogenization buffer (Sigma D1556), and centrifuged at 10,000 x g for 18 minutes in a swinging bucket centrifuge at 4°C.  Nuclei were collected at the 30%-40% interface, diluted with 2 volumes of homogenization buffer and concentrated by centrifugation for 10 min at 0.5 x g at 4°C.  snRNA-seq sequencing libraries were constructed using the 10X Genomics Chromium single cell 3’ v3 kit.

value: iris

value: WT

value: contol


title: sheep line 13 p12

city: Exeter

first: Daniel

last: Spindlow

state: Devon

address: Stocker Road

department: Living Systems Institute

country: United Kingdom

institute: University of Exeter

description:
Sheep_EDSC_raw_counts.txt
sheep line 13 p12

data_processing:
Trim-Galore!
STAR
FeatureCounts
Supplementary_files_format_and_content: raw counts text file

organism: Ovis aries

source_name: sheep line 13 p12

growth_protocol: EDSCs were cultured in AFX medium on Laminin/Fibronectin coated dish.

extract_protocol:
Cells were lysed in Trizol and total RNAs are prepared by PureLink RNA Mini Kit
Libraries were prepared by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

value: EDSCs

tag: passage


title: snRNAseq_JW17_iris_control_RP2


title: E14_ADNP-dHD-HA_IgG

value: CUT&RUN

value: IgG


title: RR057i_00068_SEQ003

data_processing:
Alignment against human genome- Kallisto v 0.46.1
Gene-level counts were generated from the transcript-level abundance estimates using the R package tximport
Fitering to retain samples with 400,000 gene counts
Differential expression with R package limma
Genome_build: HG-38, ENSEMBL v. 99
Supplementary_files_format_and_content: .csv file with genecounts


title: E14_ADNP-dHD-HA_HA

value: HA


title: snRNAseq_JW16_iris_dilated_RP2_

value: dilated


title: mrna_36_cas9_c

value: HEK293 cell line

value: 36 hours


title: snRNAseq_JW15_iris_constricted_RP3

value: constricted


title: Sheep line1 p11

description:
Sheep_EDSC_raw_counts.txt
Sheep line1 p11

source_name: Sheep line1 p11


title: RR057i_00099_SEQ003

value: M

value: Clinical naso/pharyngeal swab specimens


title: NUL_13

value: Balbc

tag: reproductive stage

value: nulliparous

tag: Sex

value: female

value: 12 weeks


title: sheep line 13 p10

description:
Sheep_EDSC_raw_counts.txt
sheep line 13 p10

source_name: sheep line 13 p10


title: sheep line 13 p11

description:
Sheep_EDSC_raw_counts.txt
sheep line 13 p11

source_name: sheep line 13 p11


title: RR057e_00759_SEQ005

source_name: NP/OP swab

value: POS


title: snRNAseq_JW13_iris_constricted_RP2

value: iris

value: WT


title: mrna_36_cas9_a

tag: treatment

value: Cas9 RNP nucleofection

tag: timepoint


title: E14_ADNP-HA_MapR_GST-MNase_Rep1

value: ADNP HA-Tag Knock-in

value: MapR

value: GST-MNase


title: snRNAseq_JW04_iris_dilated_RP1

tag: tissue

value: dilated


title: E14_ADNP-HA_MapR_Rep2

value: GST-RHΔ-Mnase


title: RR057i_00072_SEQ003

value: F

tag: age


title: Sheep line1 p9

description:
Sheep_EDSC_raw_counts.txt
Sheep line1 p9

source_name: Sheep line1 p9

tag: cell type

value: EDSCs


title: RR057e_00748_SEQ003

value: M


title: AFX23p9

description:
Sheep_EDSC_raw_counts.txt
AFX23p9


title: snRNAseq_JW03_iris_constricted_RP1

value: constricted


title: RR057i_00147_SEQ003

value: Clinical naso/pharyngeal swab specimens


title: E14_ADNP-HA_MapR_Rep1


title: RR057e_00756_SEQ005


title: E14_ADNP-HA_IgG

value: CUT&RUN

tag: antibody

value: IgG


title: snRNAseq_JW02_iris_control_RP1

value: contol


title: E14_ADNP-HA_MapR_GST-MNase_Rep2


title: E14_ADNP-HA_HA

value: HA


title: mCherry-M2

city: La Jolla

first: Dario

last: Meluzzi

address: 9500 Gilman Drive #0648

department: School of Medicine

institute: UC San Diego

description: AAVs injected via retro-orbital injections and mouse harvested 2 weeks post injections. This mouse serves as an AAV control.

data_processing:
Basecalls were performed using Illumina RTA3, and fastq files were then generated using Illumina bcl2fastq2 v2.20. Both tasks were carried out by the UCSD IGM Genomics Center.
Sequence read pairs from stranded RNA-seq libraries were mapped to the reference mouse genome mm39 by running STAR aligner version 2.7.7a with the following command line options: --clip3pAdapterSeq AGATCGGAAGAGCACACGTCTGAACTCCAGTCA AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (to trim Illumina adapter sequences from the 3′ ends of the reads in each pair), --quantMode GeneCounts (to collect read counts for each gene), --alignSJDBoverhangMin 1 (following ENCODE standard practice), --peOverlapNbasesMin=10 --peOverlapMMp=0.05 (to correctly align pairs of overlapping reads), --outSAMmultNmax 1 (to limit output of multimapping reads), --alignEndsType EndToEnd (to avoid soft-clipping of reads), --outFilterMismatchNmax -1 --outFilterMismatchNoverReadLmax 0.2 --outFilterMultimapNmax 1 (to increase the likelihood of successful alignment for reads containing A-to-I editing events). The genome index for STAR aligner was built using transcript annotations from Gencode release M27 for the mouse genome assembly GRCm39. Each aligned read was retained for downstream analysis even when the corresponding mate in the pair could not be successfully aligned.
Samtools version 1.11 was used to sort the aligned reads by genomic coordinate and to mark duplicated single or paired reads.
The uniquely aligned reads for each sample were down-sampled using samtools view with option -s. Down-sampling fractions were calculated by dividing the smallest number of uniquely aligned reads among all samples by the number of uniquely aligned reads available for the sample being down-sampled. Down-sampling was not performed on the reads of the control samples. To handle transcripts oriented as the forward reference strand, base counts were collected at reference A-sites using the second (first) read in a pair, if that read was mapped to the forward (reverse) reference strand. Conversely, to handle transcripts oriented as the reverse reference strand, base counts were collected at reference T-sites using the first (second) read in a pair, if that read was mapped to the forward (reverse) reference strand. The C library htslib (github.com/samtools/htslib), version 1.12, was used to enumerate the aligned reads that overlapped each base position in the reference genome, while avoiding double-counts of bases in regions covered by both reads in a pair. Reference sites covered by less than ten reads were ignored. The value of the SAM tag MD, “String for mismatching positions”, recorded by samtools calmd version 1.11 in each alignment record, was used to determine the reference base at each position of an aligned sequence read. Base deletions and insertions relative to the reference genome were ignored. Sequenced bases with a Phred quality score less than 13 were ignored. For each sample, an initial list of base counts from reads overlapping each selected reference A- and T-site was generated. The initial lists of base counts from all samples were then used to generate a final list of reference A- and T-sites where such base counts were available for all samples, and where at least one sample had a non-zero count of G (C) at reference A-sites (T-sites).
At each selected reference site in the final list, a pairwise comparison between the base counts for each treatment sample and those for the control sample was carried out using Fisher’s exact test, as implemented in R function fisher.test, with a 2-by-2 contingency table containing the counts of G (C) at reference A-sites (T-sites) in the first row, the counts of all other bases at those sites in the second row, the base counts for the control sample in the first column, and the base counts for the compared treatment sample in the second column. The resulting p-values were adjusted for multiple comparisons using the method of Benjamini and Hochberg, as implemented in R function p.adjust. The proportion of the number of G (C) bases relative to the number all bases was also calculated at each A-site (T-site). Reference A-sites (T-sites) with a significant change in such base proportion for at least one comparison between a treatment sample and the control sample were selected by requiring an adjusted p-value less than 0.01 and a fold change greater than 1.1 in either direction.
RNA-seq libraries from mice were analyzed for differential gene expression using the Bioconductor package DESeq2 version 1.28.1. The per-gene counts of aligned read for each of four samples were collected by STAR aligner version 2.7.7a into a corresponding ReadsPerGene.out.tab file (submitted with name pattern pm_adar_rnas_011-eadcgm_seq_rna_rc_mapr_*_res-rpg-0.tsv.gz). The read counts corresponding to “the 2nd read strand aligned with RNA” were loaded for all samples into a DESeq2::DESeqDataSet object. Genes with less than 10 read counts in all samples were discarded. The counts for the remaining genes were processed using R function DESeq2::DESeq with default parameters. The comparison between untreated and treated mice was carried out using R function DESeq2::results with default parameters, except that the significance cutoff for independent filtering optimization was set to 0.01. Shrinkage of effect sizes was carried out using R function DESeq2::lfcShrink with default parameters.
Genome_build: mm39
Supplementary_files_format_and_content: The measured base proportions for each off-target site (row) and sample (column) are reported in processed data file pm_adar_rned_011-eadcgm_seq_rna_ed_bfscr_0-0_res-bpr-0.tsv.gz (tab separated values, compressed with gzip). The adjusted p-values for the comparison (column) of base proportion between each sample and the control sample at each off-target site (row) are reported in processed data file pm_adar_rned_011-eadcgm_seq_rna_ed_bfscr_0-0_res-pad-0.tsv.gz. Processed data files with name pattern pm_adar_rnas_011-eadcgm_seq_rna_rc_mapr_*_res-rpg-0.tsv.gz contain per-gene read counts generated by the STAR aligner software.

source_name: Liver from C57BL6/J mouse

growth_protocol: All experiments were carried out in 6 week old C57BL6/J mice. These mice were litter mates and obtained from Jackson Labs.

extract_protocol:
RNA extraction from mice livers was carried out using QIAzol Lysis Reagent and purified using RNeasy Plus Universal Mini Kit (Qiagen), according to the manufacturer’s protocol.
RNA-seq libraries were prepared from 500ng RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: AAV injection via retro-orbital route.

value: Liver

value: Mouse injected with AAV8-mCherry


title: AFXKp7

description:
Sheep_EDSC_raw_counts.txt
AFXKp7

source_name: SheepK


title: AFX23p6

description:
Sheep_EDSC_raw_counts.txt
AFX23p6


title: RR057e_00747_SEQ003

tag: gender

value: POS


title: E14_ADNPKO_RNA-Seq_Rep3

value: ADNP Knockout

value: RNA-Seq


title: RR057i_00151_SEQ003

tag: sars-cov-2 pcr


title: E14_ADNPKO_RNA-Seq_Rep2


title: Sheep line1 p10

description:
Sheep_EDSC_raw_counts.txt
Sheep line1 p10

source_name: Sheep line1 p10


title: RR057i_00171_SEQ003

tag: sars-cov-2 rpm


title: mCherry-M1


title: AFXKp6

description:
Sheep_EDSC_raw_counts.txt
AFXKp6


title: Circular.200.100(PCSK9)-M2

description: AAVs injected via retro-orbital injections and mouse harvested 2 weeks post injections. This mouse is injected with AAV8 carrying a ribozyme flanked antisense RNA (targeting the PCSK9 transcript) and results in the formation of a circular guide in vivo.

value: Mouse injected with AAV8-circular.200.100(PCSK9)-mCherry


title: E14_ADNPKO_RNA-Seq_Rep1


title: Circular.200.100(PCSK9)-M1


title: RR057i_00086_SEQ003


title: AFXKp4

description:
Sheep_EDSC_raw_counts.txt
AFXKp4


title: NPC_WT_RNA-Seq_Rep3

value: Wildtype NPC Differentiated


title: RR057i_00084_SEQ003


title: KO_ADT

city: Indianapolis

first: Yongyao

last: Fu

state: IN

address: 635 Barnhill Drive, MS 218

department: Microbiology and Immunology

institute: Indiana University

description:
CD64+MerTK+ total lung macrophages and blood monocytes were sorted from HDM challenged mice, and further labelled by HTO (hashtag oligonucleotides) antibodies separately. Lung macrophages were stained with ADT (Antibody Derived Tag) antibodies against CD11c and SiglecF. Lung macrophages and blood monocytes were pooled and then loaded onto the 10X Genomics Chromium platform.
KO_filtered_feature_bc_matrix.h5

data_processing:
CellRanger 3.0.2 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices (including the ADT and HTO tag counts) generated by CellRanger were used for further analysis.
Seurat 3.1.0 was used for hashtag demultiplexing, data normalization, data scaling, graph-based clustering, cluster marker genes idenfification, and integrative analysis.
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 file of filtered gene-barcode matrices, including ADT and HTO tag counts

source_name: lung macrophage and blood monocyte

extract_protocol:
Lung total macrophages (CD64+MerTK+) and blood monocytes (CD115+)  were isolated by FACS sorting.
CITE-seq and cell hashtagging were carried out according to the CITE-seq and cell Hashing in parallel protocol (cite-seq.com).  Twenty thousand targeted cell recovery per sample pool were super-loaded on a multiple-channel micro-fluidics chip of the Chromium Single Cell Instrument (10x Genomics). Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated with the v3 single cell reagent kit (10X Genomics). Following cell capture and cell lysis, cDNA was synthesized and amplified; and cDNA was separated into ADT-derived, HTO-derived and mRNA-derived cDNA. Illumina sequencing libraries were prepared for each type with Illumina TruSeq Small RNA adapter, Illumina TruSeq adapter and 10x Chromium adapter respectively.
CITE-seq and cell Hashing in parallel, 10X genomics 3' RNA-seq V3 single cell reagent kit

treatment_protocol: Cells are from house dust mite induced allergic lung inflammation mice

tag: strain

value: lung macrophage and blood monocyte


title: AFX23p8

description:
Sheep_EDSC_raw_counts.txt
AFX23p8


title: RR057e_00752_SEQ005

extract_protocol:
Zymo DNA/RNA magbead
NEBnext with Qiagen Fastselect rRNA depletion
Random hexamer RNAseq

tag: infection


title: RR057e_00750_SEQ003

value: F

tag: sample type


title: AFXBp7

description:
Sheep_EDSC_raw_counts.txt
AFXBp7

source_name: SheepB

value: EDSCs


title: NPC_WT_RNA-Seq_Rep2

tag: protocol


title: WT_HTO

description:
CD64+MerTK+ total lung macrophages and blood monocytes were sorted from HDM challenged mice, and further labelled by HTO (hashtag oligonucleotides) antibodies separately. Lung macrophages were stained with ADT (Antibody Derived Tag) antibodies against CD11c and SiglecF. Lung macrophages and blood monocytes were pooled and then loaded onto the 10X Genomics Chromium platform.
WT_filtered_feature_bc_matrix.h5

tag: genotype

value: WT


title: RR057e_00736_SEQ003


title: AFXBp5

description:
Sheep_EDSC_raw_counts.txt
AFXBp5

tag: passage


title: WT_ADT


title: KO


title: Pig4 p10

description:
Pig_EDSC_raw_counts.txt
2128

organism: Sus scrofa


title: RR057i_00139_SEQ003

value: M


title: E14_ADNPKO_MapR_GST-MNase_Rep2

value: MapR

tag: fusion protein

value: GST-MNase


title: Pig4 p8

description:
Pig_EDSC_raw_counts.txt
2124


title: E14_ADNPKO_MapR_Rep2

value: GST-RHΔ-Mnase


title: RR057i_00154_SEQ003

value: Clinical naso/pharyngeal swab specimens


title: Pig4 p6

description:
Pig_EDSC_raw_counts.txt
2120


title: RR057e_00741_SEQ003


title: KO_HTO


title: E14_ADNPKO_MapR_GST-MNase_Rep1


title: WT


title: AFXBp8

description:
Sheep_EDSC_raw_counts.txt
AFXBp8


title: E14_ADNPKO_MapR_Rep1


title: Pig2 p10

description:
Pig_EDSC_raw_counts.txt
2126


title: RR057e_00729_SEQ003


title: E14_ADNP-HA_ADNP

value: Wildtype

value: CUT&RUN

value: ADNP


title: Maize leaf tissue control_KT2

city: Bhavnagar

first: Khanjan

last: Trivedi

state: Gujarat

address: GB Marg

department: AP&BD

country: India

institute: CSIR-Central Salt & Marine Chemical Research Institute

data_processing:
The Illumina HiSeq 2500 was used to generate paired end reads
Cutadapt tool (version 1.8.1) was used in the pre-processing step for adapter sequence removal.
Unwanted sequences like non-polyA tailed RNAs, ribosomal RNAs, transfer RNAs, adapter sequences and others were removed by using bowtie2 (version 2.2.6), perl scripts and picard tools (version 1.115).
The aligned reads were used for estimating expression of the genes and transcripts using cufflinks program (version 2.2.1) after its aligning with reference gene model.
The differential expression analysis for the sample comparison is performed using cuffdiff program of cufflinks package (Trapnell et al. 2009, 2010).
The pathway of differentially expressed genes were plotted by MapMan (Thimm et al. 2004). Different samples comparison were annotated for biochemical pathway analysis with Plant MetGenMAP (Joung et al. 2009).
Genome_build: Zea mays genome and gene model downloaded from MaizeSequence.org (http://ftp.maizesequence.org/release-5b/assembly/ZmB73_RefGen_v2.tar.gz) was used to align pre-processed reads by Tophat program (version 2.1.0).

organism: Zea mays

source_name: Maize leaf tissue

extract_protocol:
Leaf tissue was collected from control and seaweed treated plants of V5 stage and stored at -80 °C for further RNA isolation procedure. Total RNA was isolated from leaves by using NucleoSpin RNA Plant kit following the manufacturer’s protocol. The quantity and integrity of total RNA was assessed by Epoch microplate reader (BioTek, USA) and Agilent 2100 Bioanalyzer (USA), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sugar 75

value: Leaf

tag: developmental stage


title: Pig2 p8

description:
Pig_EDSC_raw_counts.txt
2122


title: RR057e_00737_SEQ003

value: POS


title: NPC_WT_RNA-Seq_Rep1

value: RNA-Seq


title: Maize leaf tissue sample_KT6


title: RR057e_00757_SEQ005


title: Pig2 p6

description:
Pig_EDSC_raw_counts.txt
2118


title: CY706-2

city: Shenzhen

first: Conghui

last: You

state: Guangdong

address: 1068 Xueyuan Rd., Nanshan District

institute: Shenzhen University

description:
2nd-round RNA-Seq Assays
CY706.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, poly-N and low-quality sequence, then mapped to NCM3722 whole genome using bowtie2 v2.2.3 with parameters -q --phred33 --sensitive -I 100 -X 500 --end-to-end --no-unal -p 4.
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. To avoid counting reads from the neighbor genes, we use TMM to normalize the read count.
Genome_build: NCM3722 (NZ_CP011495.1 and NZ_CP011496.1)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with raw gene counts and RPKM values for every gene and every sample.

organism: Escherichia coli

source_name: E. coli CY706

growth_protocol: In N-C- minimal medium supplemented with 22 mM glucose, 20 mM NH4Cl, and 0.2% (w/v) Casamino acid aerobically at 37°C water bath, 250rpm.

extract_protocol:
All samples were quick freezed in liquid nitrogen and stored at -80 °C for RNA extraction. Total RNA was extracted by RNAiso plus (Takara) and PureLink RNA Mini Kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: No treatment.

value: clpX-V78F (spontaneous)

tag: culture conditions

value: Batch culture at 37oC, OD600~0.4


title: CY706-3

description:
2nd-round RNA-Seq Assays
CY706.txt


title: RR057e_00727_SEQ003

value: F


title: Ronin_ChIP_1

city: Cambridge

first: Matthew

middle: C

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

description:
ChIP-seq on Brain tissue
RONIN_Brain_ChIPseq_all_peaks.txt

data_processing:
Reads were mapped to the mm9 assembly (NCBI Build 37) using bowtie2 (version 2.3.4.2) (cite = https://doi.org/10.1038/nmeth.1923). The ChIP-Seq signal was normalized to a 10 million read total and visualized in the UCSC genome browser after tag directories were generated using HOMER (version v4.10.3) (cite. = PMID: 20513432)3. ChIP enriched peaks were identified using Homer 3 with default transcription factor settings (findPeaks -style factor). All Ronin ChIP-seq peaks were called using input ChIP-seq data as background, generating 33,394 peaks with a peak score greater than 1.95. The nearest genes associated to the enriched peaks were annotated using the annotatePeaks function and de novo motif discovery was performed using the findMotifsGenome function in Homer. Genes associated to ChIP-Seq peaks were overlaid with differentially expressed genes in the RoninF80L/F80L versus wild type RNA-seq dataset. The overlaid gene list was analyzed with Metascape for enriched gene ontology terms.
Genome_build: mm9
Supplementary_files_format_and_content:  peak file and bedgraph

source_name: Embryonic Brain tissue

extract_protocol: Freshly harvested E16.5 brains from CD-1 mice were cut into small pieces and the tissue cross-linked for 15 min. and chromatin isolated using the ChIP-IT High-Sensitivity Kit (Active Motif, No. 53040). We thank the Duke University School of Medicine for the use of the Sequencing and Genomic Technologies Shared Resource, which provided ChIP-seq library generation and sequencing services. All libraries were sequenced on an Illumina Hiseq 2500.

value: brain

tag: mouse strain


title: RR057e_00735_SEQ003

city: San Francisco

first: Charles

address: HSE 401, 513 Parnassus Ave

institute: University of California San Francisco


title: Brain_ChIP_input

tag: tissue


title: CY598-6

description:
2nd-round RNA-Seq Assays
CY598-round2.txt

source_name: E. coli CY598

value: Wild Type


title: RR057e_00754_SEQ005

value: M

tag: age


title: Ronin_F80L/F80L_3

description:
RNA-seq on E16.5 brain tissue
RONIN_F80L_RNAseq_raw_counts.txt

data_processing:
Alignment of RNA-Seq data was performed using STAR (version 2.7.3a ) (cite = doi: 10.1093/bioinformatics/bts635). All reads were mapped to the mm9 genome. Genes differentially expressed between the Control and mutant samples were detected using ‘DESeq’ version 2.13. Significantly differentially expressed genes were defined using cutoffs of p-value ≤ 0.05; fold change ≥ 1.5 and FDR ≤ 0.10. A total of 980 genes that were up-regulated and 1,301  that were down-regulated in RoninF80L/F80L brains relative to control. All GO aalysis was perfomred with Metascape (cite. = doi: 10.1038/s41467-019-09234-6).
Genome_build: mm9
Supplementary_files_format_and_content:  raw counts

extract_protocol: Three independent E16.5 brains per genotype were disected in ice cold 1X PBS and total RNA was extracted using the RNeasy Mini Kit (Qiagen). Next, 1 µg of total RNA was incubated with oligo(dT) magnetic beads (SeraMag) in order to enrich for mRNA with poly-A tails. The eluted RNA was incubated at 94°C in Tris buffer with potassium acetate and magnesium acetate resulting in fractionated RNA (200-500 nucleotide range). This poly-A-selected RNA was ethanol precipitated with sodium acetate, then resuspended in water. cDNA was generated using the Invitrogen SuperScript III reverse transcription kit containing random oligonucleotide hexamers. Next, the RNA was degraded by addition of RNase and DNA polymerase was added to generate a second strand. The resulting DNA was then used for standard Illumina adaptor ligation for sequencing as described in previously 1. To generate blunt-ended DNA molecules, the 5´ and 3´ overhangs were filled-in by T4 polymerase and T4 polynucleotide kinase. Next, the Klenow fragment (exo-) was used to add a deoxyadenosine (dA) 5´ tail to the DNA strands. Using T4 ligase, double stranded DNA adapters with 3´ thymidine overhangs were ligated to the dA-tailed library as previously described 2.

value: Ronin F80L/F80L


title: RR057i_00076_SEQ003


title: CY598-4


title: CY598-5


title: Pig1 p8

description:
Pig_EDSC_raw_counts.txt
2121

tag: cell type

value: EDSCs


title: CY706-1

description:
2nd-round RNA-Seq Assays
CY706.txt


title: RR057e_00749_SEQ003


title: Ronin_F80L/F80L_2


title: CY570-1

data_processing:
bcl2fastq v2.17.1.14 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, poly-N and low-quality sequence, then mapped to MG1655 whole genome using FANSe3 with parameters -E 5% -I 0 -S 14
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: E. coli K-12 MG1655 (NC_000913.3)
Supplementary_files_format_and_content: Tab-delimited text files with raw gene counts and RPKM values for every gene and every sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli_CY570

growth_protocol: in N-C- minimal medium supplemented with 22 mM glucose and 20 mM NH4Cl aerobically at 37°C water bath, 250rpm

extract_protocol:
All samples were quick freezed in liquid nitrogen and stored at -80 °C for RNA extraction. Total RNA was extract by RNAiso plus (Takara) and PureLink RNA Mini Kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: no treatment

tag: culture

value: Batch culture at 37°C, OD600≈0.4

value: IS-element (IS5 family) insertion at -298 to -1496 of flhD


title: CY570-2


title: Ronin_F80L/F80L_1


title: Ronin_ChIP_2


title: Control_RNAseq3


title: CY1179-3

description:
1st-round RNA-Seq Assays
CY1179.txt
∆clpX

source_name: E. coli CY1179

value: <delta>clpX


title: RR057i_00167_SEQ003

tag: gender

value: Clinical naso/pharyngeal swab specimens


title: CY1179-2


title: CY562-2

source_name: E. coli_CY562

value: No IS-element insertion at the upstream of flhD


title: Control_RNAseq1


title: CY562-1


title: Pig1 p10

description:
Pig_EDSC_raw_counts.txt
2125


title: RR057i_00157_SEQ003

tag: sars-cov-2 pcr


title: Pig1 p6

description:
Pig_EDSC_raw_counts.txt
2117


title: Control_RNAseq2


title: CY1166-3

description:
1st-round RNA-Seq Assays
CY1166.txt

source_name: E. coli CY1166

value: clpX-wild type (manipulated)


title: CY1179-1


title: RR057e_00751_SEQ005

tag: sars-cov-2 rpm


title: CY1166-2

description:
1st-round RNA-Seq Assays
CY1166.txt

tag: strain


title: RNA-Seq RTE_SETD2_KO_rep2

city: New York

first: Christina

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Raw reads were trimmed and filtered for quality using Trimmomatic (v0.38). Trimmed reads were then aligned against the mm10 genome using STAR (v2.7.1a).
For each RefSeq annotated gene, reads overlapping with exon regions were counted using HTSeq (v0.11.2).
Genome_build: mm10
Supplementary_files_format_and_content: Gene quantification count in txt format

source_name: Murine renal tubular epithelial cells

growth_protocol: Kidneys were dissected from Setd2(F/F)Ksp-Cre+ and Setd2(F/F) mice at 4-5 weeks of age. Kidney cortices were minced and digested in advanced DMEM/F12 (Thermo Fisher Scientific) containing liberase (Sigma) for 1h at 37 °C. Digested samples were filtered through 40 μm strainers (BD Biosciences) and washed with cold Hank's Balanced Salt Solution (HBSS, Thermo Fisher Scientific) twice. Finally, samples were resuspended in advanced DMEM/F12 supplemented with penicillin/streptomycin (Thermo Fisher Scientific), non-essential amino acids (NEAA, Thermo Fisher Scientific), glutamine (Thermo Fisher Scientific), 10 mM HEPES (Thermo Fisher Scientific), Insulin-transferrin-selenium (Thermo Fisher Scientific), 20 ng/ml EGF (R & D Systems), and 100 nM hydrocortisone (Sigma), and plated in dishes.

extract_protocol:
Total RNA was extracted and cleaned up using RNeasy Mini Kit (Qiagen).
The isolated RNA samples were then processed using the TruSeq RNA Sample Prep kit (Illumina).

value: primary renal tubular epithelial (RTE) cells


title: RR057e_00753_SEQ005

value: POS

tag: infection


title: RNA-Seq RTE_SETD2_KO_rep1


title: CY1166-1

description:
1st-round RNA-Seq Assays
CY1166.txt


title: Circular 200,100

data_processing:
Basecalls were performed using Illumina RTA3, and fastq files were then generated using Illumina bcl2fastq2 v2.20. Both tasks were carried out by the UCSD IGM Genomics Center.
Sequence read pairs from stranded RNA-seq libraries were mapped to the reference human genome hg38 by running STAR aligner version 2.7.3a with the following command line options: --clip3pAdapterSeq AGATCGGAAGAGCACACGTCTGAACTCCAGTCA AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (to trim Illumina adapter sequences from the 3′ ends of the reads in each pair), --quantMode GeneCounts (to collect read counts for each gene), --alignSJDBoverhangMin 1 (following ENCODE standard practice), --peOverlapNbasesMin=10 --peOverlapMMp=0.05 (to correctly align pairs of overlapping reads), --outSAMmultNmax 1 (to limit output of multimapping reads), --alignEndsType EndToEnd (to avoid soft-clipping of reads), --outFilterMismatchNmax -1 --outFilterMismatchNoverReadLmax 0.2 --outFilterMultimapNmax 1 (to increase the likelihood of successful alignment for reads containing A-to-I editing events). The genome index for STAR aligner was built using transcript annotations from Gencode release 32. Each aligned read was retained for downstream analysis even when the corresponding mate in the pair could not be successfully aligned.
Samtools version 1.10 was used to sort the aligned reads by genomic coordinate and to mark duplicated single or paired reads.
The uniquely aligned reads for each sample were down-sampled using samtools view with option -s. Down-sampling fractions were calculated by dividing the smallest number of uniquely aligned reads among all samples by the number of uniquely aligned reads available for the sample being down-sampled. Down-sampling was not performed on the reads of the control samples. To handle transcripts oriented as the forward reference strand, base counts were collected at reference A-sites using the second (first) read in a pair, if that read was mapped to the forward (reverse) reference strand. Conversely, to handle transcripts oriented as the reverse reference strand, base counts were collected at reference T-sites using the first (second) read in a pair, if that read was mapped to the forward (reverse) reference strand. The C library htslib (github.com/samtools/htslib) was used to enumerate the aligned reads that overlapped each base position in the reference genome, while avoiding double-counts of bases in regions covered by both reads in a pair. Reference sites covered by less than ten reads were ignored. The value of the SAM tag MD, “String for mismatching positions”, recorded by STAR aligner in each alignment record, was used to determine the reference base at each position of an aligned sequence read. Base deletions and insertions relative to the reference genome were ignored. Sequenced bases with a Phred quality score less than 13 were ignored. For each sample, an initial list of base counts from reads overlapping each selected reference A- and T-site was generated. The initial lists of base counts from all samples were then used to generate a final list of reference A- and T-sites where such base counts were available for all samples, and where at least one sample had a non-zero count of G (C) at reference A-sites (T-sites).
At each selected reference site in the final list, a pairwise comparison between the base counts for each treatment sample and those for the control sample was carried out using Fisher’s exact test, as implemented in R function fisher.test, with a 2-by-2 contingency table containing the counts of G (C) at reference A-sites (T-sites) in the first row, the counts of all other bases at those sites in the second row, the base counts for the control sample in the first column, and the base counts for the compared treatment sample in the second column. The resulting p-values were adjusted for multiple comparisons using the method of Benjamini and Hochberg, as implemented in R function p.adjust. The proportion of the number of G (C) bases relative to the number all bases was also calculated at each A-site (T-site). Reference A-sites (T-sites) with a significant change in such base proportion for at least one comparison between a treatment sample and the control sample were selected by requiring an adjusted p-value less than 0.01 and a fold change greater than 1.1 in either direction.
Genome_build: hg38
Supplementary_files_format_and_content: The measured base proportions for each site (row) and sample (column) are reported in processed data file pm_adar_rned_010-eadcgs_seq_rna_ed_bfscr_0_0_res-bpr-0.tsv.gz (tab separated values, compressed with gzip). The adjusted p-values for the comparison (column) of base proportion between each sample and the control sample at each site (row) are reported in processed data file pm_adar_rned_010-eadcgs_seq_rna_ed_bfscr_0_0_res-pad-0.tsv.gz (tab separated values, compressed with gzip).

source_name: Cell line

growth_protocol: All experiments were carried out in HEK293FT cells which were  grown in DMEM supplemented with 10% FBS and 1% Antibiotic-Antimycotic (Thermo Fisher) in an incubator at 37 °C and 5% CO2 atmosphere.

extract_protocol:
RNA was extracted using the RNeasy mini kit.
RNA-seq libraries were prepared from 250ng RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: Plasmid transfection according to standard protocols.

tag: cell line

tag: treatment

value: Plasmid transfection


title: CY1102-3

description:
1st-round RNA-Seq Assays
CY1102.txt

source_name: E. coli CY1102

tag: genotype

value: clpX-V78F (manipulated)


title: RNA-Seq RTE_SETD2_wt_rep3


title: Internode explant on callus-inducing medium for 34D, biological replicate 3

city: Hautcharage

first: Gea

last: Guerriero

state: Luxembourg

address: 5, rue Bommel, Z.A.E. Robert Steichen, L-4940

department: Environmental Research and Innovation Department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology (LIST)

description: Advanced stage of callogenesis

data_processing:
Sequences >35 bps were retained, the sequence quality score was by default 0.05, the maximum number of ambiguities was set to 0.
Adaptor trimming was performed using the Illumina adaptor sequences, then a hard trim of 15 bps at the 5′ end and 3 bps at the 3′ end was additionally carried out, resulting in a final sequence average length of 57 bps.
Mapping was performed against the previously published de novo transcriptome of nettle clone 13 with the following parameters: maximum hit per read=3, similarity and length fraction=0.95, mismatch/insertion/deletion cost=3.
The expression values were calculated using the RPKM method. An ANOVA one-way statistical test with four groups (0-1-10-34 days) was applied, each composed of 3 biological replicates and a false discovery rate (FDR) correction was thereafter applied.
Only those genes showing a corrected p-value <0.05 were retained for the bioinformatics analysis. The data were filtered by removing the genes showing a maximum value of the means <1 RPKM and a maximum FC>|4|.
Genome_build: Mapping using the de novo transcriptome assembly of Urtica dioica clone 13.
Supplementary_files_format_and_content: Tab-delimited text file includes: contig number, FDR p-value, TAIR ID,  contig size, gene annotation; unique gene reads, RPKM values for each sample, average of the three biological replicates.

organism: Urtica dioica

source_name: Internode explant

growth_protocol: Terminal shoots containing several nodes were collected from healthy vigorous nettle plants (i.e., the fibre clone 13) growing in the incubators under a cycle of 16 h light at 25° C and 8 h dark at 20° C, as previously reported. The shoots were first washed with detergent (i.e., water with a few drops of soap) for 10 min, then submerged in 50% (v/v) commercial bleach for 10 min, followed by three rinses with sterilized distilled water. Segments bearing a single node of the surface sterilized shoots were put vertically onto Murashige and Skoog (MS) basal medium containing vitamins (Duchefa Biochemie, Haarlem, The Netherlands), 3% (w/v) sucrose and 0.8% (w/v) agar and grown in a culture room under light-emitting diode (LED) lights (Philips GreenPower LED production module DeepRed/Blue) with 16/8 h light/dark cycle at constant 22° C. The obtained in vitro plantlets were sub-cultured by transferring terminal shoots to the same fresh media. The internode explants of 1 cm length were excised from 4-weeks old plantlets and used for subsequent experiments.

extract_protocol:
Total RNA extraction was performed using the RNeasy Plant Mini kit (Qiagen, Leusden, The Netherlands) according to the manufacturer’s instructions. RNA quan-tity was measured using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Villebon-sur-Yvette, France). RNA quality was assessed with a 2100 bioana-lyzer (Agilent, Santa Clara, CA, USA). Libraries were prepared from 3µg of total RNA using the SMARTer Stranded RNA-Seq kit (Clontech). The isolation of mRNAs was performed using the Illumina beads and the TruSeq protocol (Illumina).The final elution of the mRNAs was performed using the Illumina elution buffer (19.5 µl).  The isolated mRNAs were quantified using a Qubit fluorometer.
Libraries were pooled and sequenced to generate 75 bp paired-end reads using an Illumina NextSeq500 instrument with NextSeq500/550 Mid Output Kit v2.5 (150 cycles; Illumina, San Diego, CA, USA).

treatment_protocol: The internode explants were cultured on the medium supplemented with 3 mg/L NAA and 0.01 mg/L BAP in the dark and collected at 0, 1, 10 and 34 days. Ten explants from the same plate were pooled to generate one biological replicate for each time point and three biological replicates were collected.

tag: clone

value: clone 13

tag: biological replicate

value: Callogenesis 34D repl 3

tag: stage of de-differentiation

value: Callogenesis 34d


title: CY1102-2

description:
1st-round RNA-Seq Assays
CY1102.txt

tag: culture conditions

value: Batch culture at 37oC, OD600~0.4


title: Circular 100,50


title: Internode explant on callus-inducing medium for 10D, biological replicate 3

description: Intermediate stage of callogenesis

value: Callogenesis 10D repl 3

value: Callogenesis 10d


title: Internode explant on callus-inducing medium for 10D, biological replicate 2

description: Intermediate stage of callogenesis

value: Callogenesis 10D repl 2


title: RNA-Seq RTE_SETD2_wt_rep2


title: CY1102-1

description:
1st-round RNA-Seq Assays
CY1102.txt


title: 293FT


title: Internode explant on callus-inducing medium for 10D, biological replicate 1

description: Intermediate stage of callogenesis

value: Callogenesis 10D repl 1


title: RNA-Seq RTE_SETD2_wt_rep1


title: Internode explant on callus-inducing medium for 1D, biological replicate 3

description: Early stage of callogenesis

value: Callogenesis 1D repl 3

value: Callogenesis 1d


title: CY708-3

description:
1st-round RNA-Seq Assays
CY708.txt

source_name: E. coli CY708

value: clpX-V78F (spontaneous)