title: eyGAL_H3.3K27M_Vg_eye_H3K27me3_3_(20201027_KA_DmEc_1827_187)

description: CUT&Tag

source_name: CUT&Tag for H3K27me3 in 8 dissected eye portions of eye-antennal imaginal discs from eyGAL >H3.3K27M >Vg larvae

value: H3K27me3 Cell Signalling Technology cat#9733 lot# 14


title: mMB_YZ_A4

status: Public on Jun 15 2021

type: RNA

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

label: Biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from tumor specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

treatment_protocol: Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).

tag: tissue

value: glioma

tag: p53 status

tag: genetic specifics


city: Nanning

first: Aruo

state: Guangxi

address: Guangxi Medical University, Nanning 530021, Guangxi, China

country: China

institute: Guangxi Medical University

description: TUCR profile in human normal mucosal epithelial tissue of the colorectal

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA.

scan_protocol: 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed.

organism: Homo sapiens

label_protocol: Briefly, total RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442)). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen p/n 74104).

extract_protocol: Total RNA was isolated from all tissues using TRIzol reagent (Invitrogen, Grand Island, NY, USA) following the manufacturer's recommendations.

treatment_protocol: From April 2018 to December 2018, human colorectal cancer tissue and human normal mucosal epithelial tissue of the colorectal from the anorectal department of the First Affiliated Hospital of Wenzhou Medical University were surgically resected and pathologically confirmed CRC. All patients provided signed informed consent before surgery.


title: mMB_YZ2_A3

value: medulloblastoma


title: human colorectal cancer tissue

description: TUCR profile in human colorectal cancer tissue

source_name: human colorectal cancer tissue

value: human colorectal cancer tissue


title: eyGAL_H3.3K27M_Vg_eye_H3K27me3_1_(20201026_KA_DmEc_1806_187)

type: SRA

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

description: CUT&Tag

library_source: genomic

data_processing:
Genome_build: UCSC dm6
1. We used Bowtie2 2.4.1 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to dm6 Drosophila melanogaster genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> <strand> (Supplementary file dm6_fragments.bed.gz). 3. We used bedtools genomecov to make normalized count bedgraph files, which are the fraction of counts at each base pair scaled by the size of the reference sequence (137567484) so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

molecule: genomic DNA

organism: Drosophila melanogaster

extract_protocol:
cut-tag-with-drosophila-tissues-bnx5mfq6.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: 8 dissected eye portions of eye-antennal imaginal discs

tag: antibody

tag: genotype


title: CUT&Tag_Control-H3K4me3

city: Zibo

first: Dai

middle: Shang

last: Kun

state: Shandong

address: 266 Xincun West Road

department: School of Life Sciences and Medicine

institute: Shandong University of Technology

data_processing:
Library strategy: CUT&Tag
Genome_build: GRCm38
CUT&Tag reads were aligned to the mouse GRCm38 reference genome (vM23 from GENCODE) using Bowtie 2 (v.2.4.1) with parameters “--mm --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700”. Samtools (v1.10) was then used to convert files to bam format and filter reads mapped with parameters “-F 1804 -q 30”. After removing PCR duplicates using Mark Duplicates function in Picard (v2.22.0) and mitochondrial reads. MACS2 (v2.2.7.1) was used to call peaks with parameters “-g mm -q 0.05 -f BAMPE” relative to IgG samples.

source_name: E13.5 Forebrain

growth_protocol: NSPCs isolated from the E13.5 mice forebrain were cultured with DMEM/F12 medium (Invitrogen) supplemented with 20 ng/ml epidermal growth factor and 20 ng/ml fibroblast growth factor (EGF/FGF, PeproTech), 1% penicillin/streptomycin (Invitrogen), 0.5× B27 (Invitrogen), and 0.5× N2 (Invitrogen).

extract_protocol:
CUT&Tag assays were performed according the instructions of HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina (TD-901, Vazyme). Briefly, 1 × 105 NSPCs were washed with 500 μl Wash Buffer and entrifuged at 600 × g for 3 min at room temperature and then resuspend in 100 μL 1 × Wash Buffer. ConA beads were washed twice with Binding Buffer. Next, 10 μL of washed ConA beads were added into NSPCs and incubated at room temperature with slow rotation for 10 min. Bead-bound NSPCs were resuspended in 50 μL of Antibody Buffer. Then, 1 μg of primary antibody (H3K4me3 or H3K27me3) or normal rabbit IgG was added and incubated at room temperature with slow rotation for 2 h. The primary antibody was removed using a magnet stand. The secondary antibody (0.5 μL) (Goat anti-Rabbit IgG H&L (ab6702, abcam)) was diluted in 50 μL of Dig-wash Buffer and NSPCs were incubated at room temperature with slow rotation for 1 h. NSPCs were washed three times with Dig-wash Buffer to remove unbound antibodies. Next, NSPC were incubated with 0.44 μM The Hyperactive pG-Tn5 Transposon diluted in 100 uL Dig-300 Buffer at room temperature with slow rotation for 1 h, and subsequently washed three times with Dig-300 Buffer. NSPCs were then resuspended in 300 μl of Tagmentation Buffer at 37 °C without rotation for 1 h. To terminate tagmentation, 10 μL of 0.5 M EDTA, 3 μL of 10% SDS and 2.5 μL of 20 mg/mL Proteinase K were added to 300 μl of sample and incubated overnight at 50 °C without rotation. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. 1 × cOmpleteTM, EDTA-free Protease Inhibitor Cocktail (04693132001, Roche) was pre-added in all buffers mentioned above.
For library amplification, 24 μL of DNA was mixed with 1 μL of TAE of HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina (TD-901, Vazyme), 10 μL of 5 × TAB and 5 μL of ddH2O, as well as 5 μL of uniquely barcoded i5 and i7 primers from TruePrep® Index Kit V2 for Illumina (TD-202, Vazyme). A total volume of 50 μL of sample was placed in a Thermocycler using the following program: 72 °C for 3 min; 98 °C for 30 s; 16 cycles of 98 °C for 15 s, 60 °C for 30 s and 72 °C for 30 s; 72 °C for 5 min and hold at 4 °C. To purify the PCR products, 1.2× volumes of VAHTS® DNA Clean Beads (N411, Vazyme) were added and incubated at room temperature for 10 min. Libraries were washed twice with 80% ethanol and eluted in 22 μL of ddH2O, and were sequenced on an Illumina NovaSeq 6000 platform and 150-bp paired-end reads were generated.

treatment_protocol: Briefly, NSPCs (passage 2–3) were grown to 50–60% confluence in 10-cm plates, and were treated with water (control group) and 10 mM crotonate (crotonate group) for 24 h.

tag: cell type

value: Embryonic Neural Stem/Progenitor Cells (eNSPCs)

tag: treatment

value: Control

tag: chip antibody


title: eyGAL_H3.3K27M_Vg_eye_H3K27me3_2_(20201027_KA_DmEc_1826_187)

description: CUT&Tag


title: WT M9/rdm/glu, IPOD replicate 2

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

description:
wt_m9_rdm_glu_merged_truseqnano_nebnext_ipod_vs_inp_lograt.gr
wt_m9_rdm_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr

data_processing:
Adapter removal using the common Illumina Truseq adapter sequences with cutadapt 1.8.1
Read ends were trimmed using Trimmomatic 0.33 in paired end mode, with the trimming steps ‘TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10’
Reads were aligned using bowtie2 version 2.1.0 with ‘very sensitive’ end-to-end presets, and dovetailed alignments allowed
Surviving DNA reads with proper paired-end alignments were quantified using an in-house pipeline in which each read contributes a total signal of weight 1, divided over the length of the read. Further processing is described in detail in the accompanying paper
RNA reads were subject to quantitation using kallisto v0.43
Genome_build: E. coli U0006.3
Supplementary_files_format_and_content: Important: For all summary/processed files, note that we provide one file per experimental condition, which represents a consolidation of all replicates for that condition, as described in the accompanying manuscript.  Ipod_vs_inp.gr files – Raw IPOD occupancy traces prior to ChIP subtraction, given as a log_2 ratio of extracted to input. The .gr file extension refers to a simple graph type, where the first column indicates a genomic position and the second a corresponding signal    chip_vs_inp.gr files – RNA polymerase occupancy given as a log_2 ratio of extracted to input     V6rzlog10p.gr files – ChIP-subtracted IPODHR occupancy, z-scored and then used to calculate enrichment p values as described in the text    Abundance.tsv files – kallisto output giving (among other information) gene names and tpm estimates. See the kallisto documentation for details of the file format

organism: Escherichia coli

source_name: Cultured cells

growth_protocol: Cells were grown to exponential phase (OD600=0.2) in M9/rdm/glu rich defined medium

extract_protocol:
Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, the lysate was mixed with 1 volume of 100 mM Tris base and 2 volumes of 25:24:1 phenol:chloroform:isoamyl alcohol, vortexed, and then incubated for 10 minutes at room temperature. After incubation, the sample was spun at 21,130xg for two minutes at room temperature, allowing formation of a white disc at the aqueous-organic interface enriched for protein-DNA complexes. The complete aqueous phases were removed and discarded, and the remaining disc washed again with 350 microliters TE (10 mM Tris, pH 8.0; 1 mM EDTA), 350 microliters 100 mM Tris base, and 700 microliters 24:1 chloroform:isoamyl alcohol. The resulting mixture was vortexed vigorously, and again centrifuged for 2 minutes at 21,130xg. All liquid was again removed, and the wash was repeated using 700 microliters TE and 700 microliters 24:1 chloroform:isoamyl alcohol. After vortexing, centrifugation, and removal of the final wash (exactly as above), any residual liquid was removed by wicking with a laboratory wipe (if any substantial pools of liquid were present). Finally, the interface was resuspended in 500 microliters of elution buffer (described above), vortexed vigorously, and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA.
NEB Nebnext DNA kit, but with a spin column replacing the first bead cleanup

treatment_protocol: Cells were treated for 10 minutes with rifampicin, then crosslinked for 5 minutes with 1% formaldehyde, prior to quenching with excess glycine. The resulting pellets are washed with PBS and frozen

tag: condition

value: Exponential growth in M9/rdm/glu rich defined medium

value: WT


title: Dnmt1 CKO_2

city: Los Angeles

first: Brendan

middle: H

last: Grubbs

state: CA

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

description: 10X Chromium Single Cell 3' v3

library_source: transcriptomic

data_processing:
Basecalling with cellranger-3.1.0 mkfastq function and bcl2fastq2-v2.20 with cellranger default parameters.
Cell counting cellranger-3.1.0 count function with cellranger default parameters.
Genome_build: Gencode_M24-3.1.0 (GRCm38.p6)
Supplementary_files_format_and_content: A matrix of the filtered feature barcode data (matrix.mtx.gz) containing detected cellular barcodes in the Market Exchange Format (MEX) for sparse matrices. The corresponding outupt to the matrix file from the filtered feature barcode data,  features.tsv.gz and barcodes.tsv.gz, are tab seperated value text files which correspond to the gene features of Gencode M24 (rows) and cellular UMI barcodes (columns) respectively.  Commonly used with the Seurat software package.

source_name: Embryonic E18.5 lung

extract_protocol:
Lung tissue was minced and digested with collagenase IV (1mg/ml, Sigma), DNase I (0.16 mg/ml, Sigma) and dispase II (2mb/ml, Roche) for 30 minutes at 37C. The raw tissue homogenate was filtered through a 70 um filter. Next, washed cells were resuspended in 1X red blood cell lysing buffer (Abcam) for 5 minutes to remove blood cells. Cells were counted with an automated cell counter to confirm absence of cell clumps.
10X Chromium Single Cell 3' v3

value: Embryonic lung

tag: developmentat stage


title: Dnmt1 CKO_1

description: 10X Chromium Single Cell 3' v3


title: Wildtype_2

description: 10X Chromium Single Cell 3' v3

value: Wild type


title: eyGAL_H3.3K27M_Vg_eye_H3K27M_2_(20201015_KA_DmEc_1769_D3B5T)

description: CUT&Tag

source_name: CUT&Tag for K27M in 6 dissected eye imaginal discs from eyGAL>H3.3K27M>Vg larvae

value: 6 dissected eye imaginal discs

value: H3K27M Cell Signaling Technology cat#74829


title: eyGAL_H3.3K27M_Vg_eye_H3K27M_1_(20201015_KA_DmEc_1768_D3B5T)

description: CUT&Tag


title: Wildtype_1

description: 10X Chromium Single Cell 3' v3


title: eyGAL_H3.3K27M_eye_H3K4me2_1_(20201015_KA_DmEc_1782_239)

description: CUT&Tag

source_name: CUT&Tag for H3K4me2 in 6 dissected eye imaginal discs from eyGAL>H3.3K27M larvae

value: H3K4me2 Epicypher cat#13-0027


title: Glycolytic mECs WT rep5

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

data_processing:
Expression values were computed using kallisto
Variance stabilizing transformation (VST) for negative binomial data with a dispersion-mean trend was used for exploratory analysis such as PCA and identification of highly variable genes.
Following DESeq2 analysis workflow, differential expression analysis were performed on the raw counts after estimation of size factors (controlling for differences in the sequencing depth of the samples), the estimation of dispersion values for each gene and fitting a generalized linear model.
Transcription factor motif enrichment analysis were performed using gProfiler online tool (https://biit.cs.ut.ee/gprofiler/gost) were an adjusted p-value ordered list of differentially expressed genes (log fold change > 1 and adjusted p-value < 0.05) were given as input.
Custom enrichment analysis (ATF4 dependent biological process) were performed using a kstest from hypeR package version 1.6.0 on the adjusted p-value ordered list of differentially expressed genes.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: text files holding kallisto expression estimates

source_name: Extensor digitorum longus muscle

extract_protocol:
ECs were directly sorted (70 μm nozzle) into 700 μl RNA lysis buffer, and RNA extraction was performed using RNeasy Plus Micro Kit (74034 QIAGEN).
The libraries were prepared following Illumina TruSeq stranded mRNA protocol. The quality of the RNA and final libraries was determined using an Agilent 4200 TapeStation System. The libraries were pooled equimolecularly and sequenced in an Illumina NovaSeq sequencer (single-end 100 bp) with a depth of around 20 Mio reads per sample.

treatment_protocol: Recombination was induced in 8-10 weeks old mice by daily intraperitoneal administration of 1mg tamoxifen (T5648, Sigma-Aldrich) dissolved in 1:10 ethanol: corn oil solution for 5 consecutive days. A wash out period of at least 7 days was allowed before starting the experiments. Tamoxifen-treated Cre-negative littermates were used as control for all experiments.

tag: celltype

value: Muscle endothelial cells

tag: strain


title: eyGAL_H3.3K27M_eye_H3K4me2_2_(20201015_KA_DmEc_1783_239)

description: CUT&Tag


title: Glycolytic mECs WT rep3


title: Glycolytic mECs WT rep2


title: ELST#4

type: genomic

city: Berlin

first: Felix

last: Thierfelder

address: Charitépl. 1

institute: Charite

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip and Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
using R (version 4.0.2) minfi_1.36.0 package
arrays from different plattforms were combined using combineArrays function; beta values were normalized using minfi PreprocessFunnorm function; detection p-values was calculated using detectionP function; for methylated and unmethylated signals preprocessIllumina function was used for normalization

label: Cy3, Cy5

source_name: endolymphatic sac tumors

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from FFPE tumor samples using Tissue DNA Purification Kit (Promega) according to the manufacturer´s protocol

tag: gender

value: f

tag: age

value: endolymphatic sac tumors

tag: group

value: sporadic


title: Glycolytic mECs WT rep1


title: eyGAL_H3.3K27M_eye_H3K27me3_4_(20201027_KA_DmEc_1829_187)

description: CUT&Tag

source_name: CUT&Tag for H3K27me3 in 8 dissected eye portions of eye-antennal imaginal discs from eyGAL >H3.3K27M larvae

value: H3K27me3 Cell Signalling Technology cat#9733 lot# 14


title: Glycolytic mECs WT rep4


title: eyGAL_H3.3K27M_eye_H3K27me3_2_(20201026_KA_DmEc_1801_187)

description: CUT&Tag


title: Oxidative mECs WT rep5

source_name: Soleus muscle


title: mMB_YZ2_B7

value: glioma

value: hGFAP-Cre::p53-/-; Rictor+/-


title: ELST#15

value: von Hippel-Lindau syndrome associated


title: mMBc_YZ2_Z2_b

value: normal brain

value: normal mice


title: eyGAL_H3.3K27M_eye_H3K27me3_1_(20201026_KA_DmEc_1800_187)

description: CUT&Tag

value: 8 dissected eye portions of eye-antennal imaginal discs


title: mMBc_YZ2_B7_b


title: eyGAL_H3.3K27M_Vg_eye_H3K27M_3_(20201026_KA_DmEc_1807_D3B5T)

description: CUT&Tag


title: mMBc_YZ2_C6_b

value: hGFAP-Cre::p53-/-; Rictor-/-


title: Oxidative mECs WT rep4


title: eyGAL_H3.3K27M_eye_H3K27M_2_(20201026_KA_DmEc_1803_D3B5T)

description: CUT&Tag

source_name: CUT&Tag for K27M in 6 dissected eye imaginal discs from eyGAL>H3.3K27M larvae


title: Oxidative mECs WT rep3


title: mMBc_YZ2_A6_b


title: mMBc_YZ2_B6_b


title: eyGAL_H3.3K27M_eye_H3K27M_1_(20201026_KA_DmEc_1802_D3B5T)

description: CUT&Tag


title: eyGAL_H3.3K27M_eye_H3K27me3_3_(20201027_KA_DmEc_1828_187)

description: CUT&Tag


title: mMBc_YZ2_C1_b


title: Oxidative mECs WT rep2


title: mMBc_YZ2_C2_b


title: mMB_YZ2_B6

value: medulloblastoma


title: mMBc_YZ2_G5_b

value: hGFAP-Cre::p53-/-; Pten+/-; Rictor-/-


title: Oxidative mECs WT rep1

value: Wild type


title: Glycolytic mECs Atf4-/- rep5

value: EC specific Atf4-/-


title: Glycolytic mECs Atf4-/- rep4


title: SAMPLE 9_Control 74 years

city: FORT WORTH

first: Tara

last: Tovar-Vidales

state: TX

address: 3500 Camp Bowie

department: Pharmacology & Neuroscience

institute: UNTHSC

description: Eye cells

data_processing: The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https//://dataanalysis.qiagen.com/mirna/arrayanalysis.php (accessed on June 24, 2020)

label: SYBR green

source_name: Control_lamina cribrosa cells

label_protocol: cDNA was synthesized using the HiSpec buffer and miScript II RT kit (Qiagen, Valencaia, CA, USA).miRNA profiling was performed by a SYBR green-based real-time PCR miRNA array. (MZ117; Qiagen).

growth_protocol: Lamina cribrosa cells were maintained in Ham's F10 medium (Sigma Aldrich, St. Louis, MO) supplemented with 10% fetal bovine serum. The medium was changed every 2-3 days and maintained at 37 degrees C with 5% CO2 within a humidified incubator.

extract_protocol: Total RNA

treatment_protocol: For TGFb2 treatment, lamina cribrosa were serum deprived for 24 hours, prior to treatment with 5ng/mL TGFb2 or with control for 24 hours.

tag: subject status/treatment

value: Control

tag: age (yrs)

value: human lamina cribrosa cells


title: SAMPLE 11_TGFB2 56 years

description: Eye cells

source_name: TGFB2_lamina cribrosa cells


title: mMB_YZ2_C6

tag: tissue


title: HBECs, pulse chase Nascent RNA-seq, rep_B_10min

city: Bethesda

first: Daniel

middle: R

last: Larson

address: 41 Medlar Dr.

institute: NIH

description: HBECs, pulse chase Nascent RNA seq_5

data_processing:
The Spliced Transcripts Alignment to a Reference (STAR) software (Dobin et al., 2013) was used to align trimmed reads to the reference genome hg19.  The splice junction output from STAR was then used for splice junction analysis.
Genome_build: hg19, hg38
Supplementary_files_format_and_content: Yihan_GEO_nascent_RNA_pulse_chase_processed_data.xlsx, Yihan_GEO_nascent_RNA_processed_data.xlsx, junction reads

source_name: Human Bronchial Epithelial Cells

extract_protocol:
Cells were trypsinized and washed with PBS. Nuclear fraction was collected with NE-PER nuclear and cytoplasmic extraction reagents (ThermoFisher, 78833). Nuclei pellet was resuspended in Trizol with 1 ml Dounce tissue grinder to homogenize the nuclei. Nascent RNA was purified as described above.
Ribosomal RNAs were depleted from the 4sU-selected nascent RNA samples and libraries were prepared with NEBNext RNA library prep kit for Illumina (NEB, E7770).

treatment_protocol: For pulse-chase nascent RNA sequencing, ~10^8 cells were used for each experimental condition. Cells were treated with 100 uM DRB for 3hr, wash with PBS 3X, release in 4sU (500 uM) for 10, 20 or 40 min. 5ug/ml actinomycin D was added to stop elongation but allow splicing for another 20 min.

value: Human Bronchial Epithelial Cells

tag: time

tag: fraction

value: Nascent RNA


title: SAMPLE 7_Control 82 years

description: Eye cells


title: SAMPLE 8_Control 56 years

description: Eye cells


title: HBECs, pulse chase Nascent RNA-seq, rep_B_20min

description: HBECs, pulse chase Nascent RNA seq_6


title: Glycolytic mECs Atf4-/- rep2

value: Muscle endothelial cells


title: SAMPLE 12_TGFB2 74 years

description: Eye cells


title: SAMPLE 6_Glaucoma 97 years

description: Eye cells

source_name: Glaucoma_lamina cribrosa cells

value: Glaucoma


title: Glycolytic mECs Atf4-/- rep1


title: Glycolytic mECs Atf4-/- rep3


title: HBECs, pulse chase Nascent RNA-seq, rep_A_40min

description: HBECs, pulse chase Nascent RNA seq_3


title: mMB_YZ2_F2

tag: p53 status

tag: genetic specifics

value: hGFAP-Cre::p53-/-; Pten+/-; Rictor+/fl


title: mMBc_YZ2_F4_b


title: mMB_YZ2_D2

value: hGFAP-Cre::p53-/-; Pten+/-


title: Oxidative mECs ATf4-/- rep5

tag: genotype


title: SAMPLE 5_Glaucoma 73 years

description: Eye cells

tag: cell type


title: mMB_YZ2_C2


title: HBECs, pulse chase Nascent RNA-seq, rep_A_20min

description: HBECs, pulse chase Nascent RNA seq_2


title: mMB_YZ2_F4


title: HBECs, pulse chase Nascent RNA-seq, rep_A_10min

description: HBECs, pulse chase Nascent RNA seq_1


title: Oxidative mECs ATf4-/- rep4


title: Control Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB422YQF)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR034MTZ/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR034MTZ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB422YQF
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens naive thymus-derived CD8-positive, alpha-beta T primary cell with multiple sclerosis, preserved by cryopreservation

value: primary cell

tag: description

value: CD8+ naive CD3+ CD4- CD8+ CD45RA+ CD45RO-

tag: biosample encode accession

tag: Sex

value: not collected

tag: health state

value: multiple sclerosis

tag: dev stage

value: unknown

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: David Hafler

tag: link

value: ENCBS512HTQ at ENCODE; https://www.encodeproject.org/ENCBS512HTQ/

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


title: SAMPLE 4_Glaucoma 66 years

description: Eye cells

tag: subject status/treatment


title: Hearts, homo_2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Trimmomatic version 0.39 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides . Only reads between 30 and 150 nucleotides were used in subsequent analyses.
Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 (GRCz11.92) using STAR 2.6.1d with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package (Liao et al., 2014).  Only reads mapping at least partially inside exons were admitted and aggregated per gene, while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses.
Differentially expressed genes were identified using DESeq2 version 1.18.1. The Ensembl annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers
Genome_build: DanRer11
Supplementary_files_format_and_content: library size normalized counts

organism: Danio rerio

source_name: Heart

extract_protocol:
48 hpf Tg(myl7:BFP-CAAX) snai1b+/+ and snai1b-/- hearts were manually dissected using forceps.  Approximately 20 hearts per replicate were pooled, and total RNA was isolated using the miRNeasy micro kit, combined with on-column DNase digestion.
Approximately 10 ng of total RNA was used as input for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Clontech) for cDNA pre-amplification.  Obtained full length cDNA was checked on LabChip GX Touch 24 and fragmented by Ultrasonication by E220 machine (Covaris).  Final Library Preparation was performed by Low Input Library Prep Kit v2 (Takara Clontech).

tag: developmental stage

value: 48 hpf

value: Heart


title: SAMPLE 2_Normal 70 years

description: Eye cells

source_name: Normal_lamina cribrosa cells

value: Normal

tag: age (yrs)

value: human lamina cribrosa cells


title: Hearts, wt_2

tag: tissue

value: wild type


title: HBECs, pulse chase Nascent RNA-seq, rep_B_5min

description: HBECs, pulse chase Nascent RNA seq_4

value: Human Bronchial Epithelial Cells

tag: time

tag: fraction

value: Nascent RNA


title: Oxidative mECs ATf4-/- rep1

tag: celltype

value: Muscle endothelial cells

tag: strain

value: EC specific Atf4-/-


title: CR5_C5_24h

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

data_processing:
The software BCL2FASTQ version 2.18 was used to convert raw data into fastq format
Raw sequences were quality checked using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Sequences were filtered using Trimmomatic v.0.36 to remove adapters and low-quality reads, using the following parameters:ILLUMINACLIP:/bioinf/progs/Trimmomatic-0.32/adapters/TruSeq2-PE.fa:2:30:10:8:true SLIDINGWINDOW:4:15 MINLEN:50
Reads were also analyzed using SortmeRNA v. 2.0 to remove rRNA reads
QC reads were mapped to the reference genome of S. passalidarum available at JGI (https://genome.jgi.doe.gov/spathaspora/) using the Hisat2 algorithm
Counting data was estimated using the featureCounts function from the Rsubread package
Differential expression analysis was performed based on the Walt test implemented in the Bioconductor DESeq2 package (Love, 2014), using p-ajusted < 0.05 and | Log2 Fold Change| ≥ 1, as thresholds.
Genome_build: Spathaspora passalidarum NRRL Y-27907 v2.0
Genome_build: https://mycocosm.jgi.doe.gov/Spapa3/Spapa3.home.html
Supplementary_files_format_and_content: Matrix tab-delimited file with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix tab-delimited file include TPM values for each Sample
Supplementary_files_format_and_content: Matrix tab-delimited file include DESeq2 results

organism: Spathaspora passalidarum

source_name: Yeast cells

growth_protocol: Yeast cells were grown in YPX medium for 24h and propagated in bioreactor for 24h in sugarcane molasses. Fermentations were carried out in synthetic medium composed of: xylose, glucose, urea, yest extract and heptahydrate sulphate magnesium

extract_protocol:
For cell lysis, the tubes containing the cell suspension samples in TRIzol™, 200 µL of 0.5 mm GlassBeads (Sigma-Aldrich, Darmstadt, Germany) was added. The Eppendorf tubes were shaken in 05 cycles lasting 60 s alternating with ice cooling for 60 s at a speed of 5 m.s-1 per cycle in a FastPrep 24 bench homogenizer (MP Biomedicals, Irvine, CA, USA).  Total RNAs were extracted from the cells of each sample, using the Direct-zol ™ RNA MiniPrep Plus extraction kit (Zymo Research, Irvine, CA, USA), according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples were collected, centrifuged, ressuspended in TriZol and stored at -80ºC

value: NRRL Y-2790

tag: group


title: RNA_WT_rep2

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

data_processing:
Sequencing reads adaptor and low-quality bases were removed by Trim Galore (version 0.6.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Filtered RNA-seq reads were mapped to the mouse reference genome mm9, which excluded mitochondria and random chromosomes, by STAR (version 2.5.4b)(Dobin et al., 2013)
Trimmed epigenomic sequencing data were then mapped to the mouse reference genome mm9 using Bowtie2(Langmead and Salzberg, 2012).PCR duplicates were removed by GATK4 (version 4.1.4.0) (https://github.com/broadinstitute/gatk) with the parameter ‘--REMOVE_DUPLICATES =true’.
Expression matrixes were counted by featureCounts(Liao et al., 2014) (version 2.0.0)
Bedtools(Quinlan, 2014) (version 2.92.2) and bedGraphToBigWig (https://www.encodeproject.org/software/bedgraphtobigwig/) (version 4) were used to normalize mapped reads and calculate the coverage of features among the genome with the following parameters ‘genomecov --scaleFactor 10,000,000/mapped_reads_number’.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample of RNA-seq

source_name: Embryonic stem cells

growth_protocol: All J1 mESCs were cultured in DMEM supplemented with 15% fetal bovine serum (FBS), 1% antibiotic solution (penicillin/streptomycin), 1% Glutamax, 1% MEM nonessential amino acids, 1% sodium pyruvate, 0.1 mM β-Mercaptoethanol, and 1,000 U/ml recombinant leukemia inhibitory factor (LIF). Cells were cultured on 0.1% gelatin coated plates with fresh medium.

extract_protocol:
RNA-seq: Total RNA from 10^6 cells was purified by RNeasy plus mini kit (Qiagen, Cat.# 74134). ATAC-seq: 10^6 mESCs were collected and lysed by lysis buffer (10 mM Tris pH7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40) and separated into 50 µl with 50,000 cells. CUT&RUN/CUT&Tag: mESCs were harvested and washed with Wash buffer (20 mM HEPES pH7.5, 150 mM NaCl, 0.5 mM Spermidine, and 1X Roche Complete Protease Inhibitor EDTA-Free tablet), 10 μl pre-washed Concanavalin A coated beads in binding buffer (20 mM HEPES pH7.9, 10 mM KCl, 1 mM CaCl2, and 1 mM MnCl2) were added per sample.
RNA-seq and ATAC-seq libraries were prepared for sequencing using standard Illumina protocols. Other libraries preparation was described previously(Kaya-Okur et al., 2019a).

tag: treatment

value: untreated

tag: chip antibody

tag: genotype


title: Hearts, homo_1


title: CR5_C5_12h


title: SAMPLE 3_Normal 82 years

description: Eye cells

tag: cell type


title: Oxidative mECs ATf4-/- rep3


title: Hearts, wt_1


title: RNA_WT_rep1


title: CR5_C3_24h


title: CR5_C5_0h


title: RNA_NSD1KO2_rep2


title: Oxidative mECs ATf4-/- rep2


title: RNA_NSD1KO2_rep1


title: CR5_C3_12h


title: RNA_NSD1KO1_rep2


title: RNA_NSD1KO1_rep1


title: CR5_C3_0h


title: CR5_C1_24h


title: HDAC1_WT_rep2

data_processing:
Library strategy: CUT&Tag
Sequencing reads adaptor and low-quality bases were removed by Trim Galore (version 0.6.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Filtered RNA-seq reads were mapped to the mouse reference genome mm9, which excluded mitochondria and random chromosomes, by STAR (version 2.5.4b)(Dobin et al., 2013)
Trimmed epigenomic sequencing data were then mapped to the mouse reference genome mm9 using Bowtie2(Langmead and Salzberg, 2012).PCR duplicates were removed by GATK4 (version 4.1.4.0) (https://github.com/broadinstitute/gatk) with the parameter ‘--REMOVE_DUPLICATES =true’.
Expression matrixes were counted by featureCounts(Liao et al., 2014) (version 2.0.0)
Bedtools(Quinlan, 2014) (version 2.92.2) and bedGraphToBigWig (https://www.encodeproject.org/software/bedgraphtobigwig/) (version 4) were used to normalize mapped reads and calculate the coverage of features among the genome with the following parameters ‘genomecov --scaleFactor 10,000,000/mapped_reads_number’.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample of RNA-seq

value: HDAC1 (Cell Signaling Technology, Cat.# 34589)


title: HDAC1_WT_rep1


title: CR5_C1_12h


title: HDAC1_NSD1_KO2_rep2


title: SAMPLE 1_Normal 56 years

description: Eye cells


title: Mint-ChIP-seq from GM23338 (ENCLB770EWE)

description:
https://www.encodeproject.org/experiments/ENCSR212MTU/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR212MTU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB770EWE
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

source_name: Homo sapiens GM23338 cell line

tag: antibody

tag: line

value: cell line

tag: description

value: PGP-1 iPSCs provided by the George Church lab at HMS. purity 100%

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 53 year

value: Paola Arlotta

value: ENCBS299FWQ at ENCODE; https://www.encodeproject.org/ENCBS299FWQ/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: HDAC1_NSD1_KO2_rep1


title: CR5_C1_0h


title: CR4_C5_24h


title: Mint-ChIP-seq from GM23338 (ENCLB151GSG)

description:
https://www.encodeproject.org/experiments/ENCSR212MTU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR212MTU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB151GSG
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

tag: lab

value: Bradley Bernstein, Broad

tag: source

tag: link


title: Mint-ChIP-seq from GM23338 (ENCLB576KBL)

description:
https://www.encodeproject.org/experiments/ENCSR212MTU/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR212MTU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB576KBL
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: ENCBS695QJS at ENCODE; https://www.encodeproject.org/ENCBS695QJS/


title: HDAC1_NSD1_KO1_rep2


title: GAN-KP_2

city: Chiyoda-ku

first: Shogo

last: Okazaki

state: Tokyo

address: 1-8-13 Kanda-Surugadai

department: School of Dentistry

country: Japan

institute: Nihon University

description: Gene expression data from GAN-KP

hyb_protocol: The Agilent array were hybridized and washed using the manufacturer's protocol.

scan_protocol: Agilent arrays were scanned using the Agilent Technologies Scanner G2505C.

data_processing: The data were normalized with 75 Percentile method

label_protocol: Cy3 labeled cRNA were prepared according to the standard Agilent protocol.

growth_protocol: GAN-WT, GAN-p53KO, GAN-KP organoids ware maintained in Advanved DMEM F12 containing Noggin (100 ng/mL), FGF10 (100 ng/mL), EGF (50 ng/mL), NAC (2.5 mM), GlutaMAX (x 100), B27 (x 50), HEPES (x 100), Penisilin/Streptmycin (x 100) and y-27632 (10 nM) in 5% CO2.

extract_protocol: RNA was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.

tag: genotype/variation

value: GAN-KP


title: HDAC1_NSD1_KO1_rep1

tag: strain


title: CR4_C5_12h

tag: group


title: GAN-KP_1

description: Gene expression data from GAN-KP


title: CR4_C5_0h


title: mMB_YZ2_B4

tag: tissue

value: medulloblastoma

tag: p53 status

tag: genetic specifics

value: hGFAP-Cre::p53-/-; Rictor+/-


title: HDAC1_HDAC1_KO2_rep2

tag: treatment

tag: chip antibody

tag: genotype


title: GAN-p53KO_4

description: Gene expression data from GAN-p53KO


title: GAN-p53KO_2

description: Gene expression data from GAN-p53KO


title: GAN-KP_3

description: Gene expression data from GAN-KP


title: Mint-ChIP-seq from GM23338 (ENCLB164XIV)

description:
https://www.encodeproject.org/experiments/ENCSR212MTU/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR212MTU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB164XIV
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

tag: antibody

tag: line

tag: description


title: GAN-KP_4

description: Gene expression data from GAN-KP


title: HDAC1_HDAC1_KO2_rep1


title: GAN-p53KO_1

description: Gene expression data from GAN-p53KO


title: GAN-p53KO_3

description: Gene expression data from GAN-p53KO


title: CR4_C3_24h


title: GAN-WT_4

description: Gene expression data from GAN-WT

value: GAN-WT


title: GAN-WT_3

description: Gene expression data from GAN-WT


title: CR4_C3_12h

value: NRRL Y-2790


title: HEK_siDBR1_A

data_processing:
Lariats were detected using in-house scripts. Briefly reads that failed to align to the genome using Bowtie and to the known transcriptome using TopHat where split in pieces of various lengths and were aligned again using bowtie. Longest uniquely aligned reads from each end that meet the following criteria where kept. The 3’ end of the read should align upstream of the 5’ withing the same intron.
Genome_build: hg38
Supplementary_files_format_and_content: Yihan_GEO_lariat_DBR1_all_combined_09292020.xlsx (lariats detected by sequencing; bed12 format)

source_name: HEK293 Cells

growth_protocol: HEK293 were grown in DMEM with 1% penicillin-streptomycin (ThermoFisher, 15140122).

extract_protocol:
To enrich for lariats, poly(A)- and rRNA depleted RNA was prepared as follows. Total RNA was purified from HEK293 cells (10 cm plates) using the Direct-zol RNA Miniprep Kit (Zymo Research) and poly(A)+ RNA was depleted using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) following the manufacturer’s instructions with some modifications. Briefly, unbound RNA (supernatant) was further purified using the RNA Clean & Concentrator Kit (Zymo Research). Poly(A)+ RNA depletion was performed twice followed by rRNA depletion using NEBNext® rRNA Depletion Kit (NEB E6310).
RNA libraries were constructed using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB, E7760) with the following modification. Reverse transcription was performed using Superscript IV at 57 oC for 30 minutes that showed higher efficiency to reverse transcribe branch points FigureS14). Similar library construction approach was followed to detect lariats in nascent RNA obtained by 4SU pulse chase. 150 bp paired end sequencing was performed on the Ilumina NextSeq 500 or HiSeq X Ten platforms

treatment_protocol: DBR1 knockdown

tag: cell line

tag: sirna

tag: fraction

value: lariats


title: CR4_C3_0h


title: GAN-WT_2

description: Gene expression data from GAN-WT


title: GAN-WT_1

description: Gene expression data from GAN-WT


title: HEK_siCtrl_A

value: control


title: CR4_C1_24h


title: HDAC1_HDAC1_KO1_rep1

value: untreated

value: HDAC1 (Cell Signaling Technology, Cat.# 34589)


title: CR4_C1_12h


title: Mint-ChIP-seq from excitatory neuron (ENCLB292WTA)

description:
https://www.encodeproject.org/experiments/ENCSR212HWF/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human PGP1 derived excitatory neuron
experiment encode accession: ENCSR212HWF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR508IYL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB292WTA
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

source_name: Homo sapiens male adult (53 years) excitatory neuron in vitro differentiated cells, preserved by cryopreservation

value: excitatory neuron

value: in vitro differentiated cells

value: PGP1 derived excitatory cortical neurons

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

tag: age

tag: lab

tag: source

value: George Church

value: ENCBS932EVS at ENCODE; https://www.encodeproject.org/ENCBS932EVS/


title: Mint-ChIP-seq from excitatory neuron (ENCLB527HJW)

description:
https://www.encodeproject.org/experiments/ENCSR212HWF/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human PGP1 derived excitatory neuron
experiment encode accession: ENCSR212HWF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR508IYL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB527HJW
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: adult

value: 53 year

value: Bradley Bernstein, Broad

tag: link

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: HEK_siDBR1_B


title: HEK_siCtrl_B


title: HDAC1_HDAC1_KO1_rep2

tag: strain


title: CR3_C5_24h

tag: group


title: CR4_C1_0h


title: H3K27ac_HDAC1_KO2_rep1

tag: treatment

tag: chip antibody

value: H3K27ac (Abcam, Cat.# ab4729)


title: H3K27ac_HDAC1_WT_rep1

tag: genotype

value: wild type


title: Ex3_10_Non-cycling

city: Cambridge

first: Yaara

last: Oren

state: Massachusetts

address: 415 Main street cambridge

institute: Broad institute

data_processing:
Reads were aligned ,samples were aggregated and expression quantified using the 10x pipeline cell ranger-2.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma-separated values file. Each column is a cell Id and each row is a gene. For cell IDs, the number after the dash refers to sample type where 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 map to samples "0","3_rep1","3_rep2","7_rep1", "7_rep2", "14_rep1_high", "14_rep1_med", "14_rep1_low","14_rep2_high", "14_rep2_med", "14_rep2_low", respectively.
Supplementary_files_format_and_content: pooled_watermelon.count.matrix.csv, pooled_watermelon.metadata.matrix.csv, pooled_watermelon.data.matrix.csv.  In the pooled*csv files, the cell IDs are formatted barcode-n, where n is 1 through 8 (1=Ex1_0_A, 2=Ex1_0_B, 3=Ex2_0 , 4=Ex2_10_Cycling, 5=Ex2_10_Non-cycling, 6=Ex3_0, 7=Ex3_10_Cycling, 8=Ex3_10_Non-cycling).

extract_protocol:
Dissociated Cells were washed, trypsinized, passed through a 40μM cell strainer, centrifuged at 400g, and resuspended at a concentration of 1,000 cells/μL in PBS + 0.5% BSA.
Single cells were processed through the Chromium Single Cell 3′ Solution platform using the Chromium Single Cell 3’ Gel Bead, Chip and Library Kits (10X Genomics), as per the manufacturer’s protocol.

tag: cell lines

value: A375_SKIN, BT474_BREAST, COLO829_SKIN, COLO829_SKIN, EFM192A_BREAST, HCC827_LUNG, HT29_LARGE_INTESTINE, MMACSF_SKIN, PC9_LUNG

tag: kinase inhibitor treatment

value: Osimertinib/dabrafenib/lapatinib

tag: cherry expression

value: low


title: Ex3_10_Cycling

value: A375_SKIN, HCC827_LUNG, HT29_LARGE_INTESTINE, PC9_LUNG

value: high


title: Ex3_0

value: A375_SKIN, BT474_BREAST, COLO829_SKIN, EFM192A_BREAST, HT29_LARGE_INTESTINE, MMACSF_SKIN, PC9_LUNG

value: untreated


title: Ex2_10_Cycling

value: A375_SKIN, COLO829_SKIN, HT29_LARGE_INTESTINE, MMACSF_SKIN


title: H3K27ac_HDAC1_KO1_rep1


title: H3K27ac_HDAC1_KO2_rep2


title: CR3_C3_24h

value: NRRL Y-2790


title: H3K27ac_HDAC1_KO1_rep2


title: Ex2_0

value: A375_SKIN, COLO829_SKIN, HT29_LARGE_INTESTINE, MMACSF_SKIN, PC9_LUNG


title: NSrp70 Conditional KO DP thymocytes 3

city: Gwangju

first: Chang-Hyun

last: Kim

address: 123, Cheomdangwagi-ro, Buk-gu

department: School of Life Sciences

country: South Korea

institute: Gwangju Institute of Science and Technology (GIST)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
FPKM calculation using Cufflink
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: thymocytes

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

tag: tag

value: thymus

value: 6 weeks

tag: genotype/variation


title: CR3_C3_12h


title: CR3_C3_0h


title: Ex1_0_B

value: PC9_LUNG, COLO829_SKIN


title: Control Mint-ChIP-seq from naive B cell (ENCLB898BUS)

description:
https://www.encodeproject.org/experiments/ENCSR111MNI/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR111MNI
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB898BUS
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

source_name: Homo sapiens naive B primary cell with multiple sclerosis, preserved by cryopreservation

value: naive B cell

value: primary cell

tag: description

value: B naive CD3- CD14- CD19+ CD27- IgD+

tag: biosample encode accession

value: not collected

tag: health state

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS743ZAV at ENCODE; https://www.encodeproject.org/ENCBS743ZAV/

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


title: NSrp70 Conditional KO DP thymocytes 1


title: CR3_C1_24h


title: NSrp70 Conditional KO DP thymocytes 2


title: Ex1_0_A

value: untreated


title: WGS from Caki2 (ENCLB502MNH)

description:
https://www.encodeproject.org/experiments/ENCSR969YUG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR969YUG
assay title: WGS
encode release date: 2019-08-23
lab: Feng Yue, PSU
library encode accession: ENCLB502MNH
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cell-equivalent

source_name: Homo sapiens Caki2 cell line

tag: line

value: cell line

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 69 year

value: Feng Yue, PSU

value: ATCC

tag: passage number

value: ENCBS787YGO at ENCODE; https://www.encodeproject.org/ENCBS787YGO/

value: Derived from ENCODE donor ENCDO140IFG; https://www.encodeproject.org/ENCDO140IFG/


title: Control ChIP-seq from HCT116 (ENCLB913OTJ)

description:
https://www.encodeproject.org/experiments/ENCSR012LAX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR012LAX
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-06
lab: Yijun Ruan, JAX
library encode accession: ENCLB913OTJ

source_name: Homo sapiens HCT116 cell line

value: colorectal carcinoma

value: 48 year

tag: lab

value: Yijun Ruan, JAX

tag: source

tag: link

value: ENCBS576BOA at ENCODE; https://www.encodeproject.org/ENCBS576BOA/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: CR3_C5_12h

tag: strain

value: NRRL Y-2790

tag: group


title: WT DP thymocytes 3

value: thymus

value: 6 weeks


title: CR3_C5_0h


title: CR3_C1_12h


title: CR3_C1_0h


title: WGS from Panc1 (ENCLB728FUC)

description:
https://www.encodeproject.org/experiments/ENCSR696BCR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR696BCR
assay title: WGS
encode release date: 2019-08-23
lab: Feng Yue, PSU
library encode accession: ENCLB728FUC
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cell-equivalent

source_name: Homo sapiens Panc1 cell line

value: pancreatic carcinoma

value: 56 year

value: ENCBS808TSD at ENCODE; https://www.encodeproject.org/ENCBS808TSD/

value: Derived from ENCODE donor ENCDO000ABB; https://www.encodeproject.org/ENCDO000ABB/


title: WT DP thymocytes 1


title: Ex2_10_Non-cycling

tag: cell lines

value: A375_SKIN, COLO829_SKIN, HT29_LARGE_INTESTINE, MMACSF_SKIN, PC9_LUNG

tag: kinase inhibitor treatment

value: Osimertinib/dabrafenib/lapatinib

value: low


title: WT DP thymocytes 2

tag: tag


title: ABUW_1103-112:T26_Rep3

city: North Ryde

first: Ian

last: Paulsen

state: New South Wales

address: 14 Eastern Road

department: Molecular Sciences

country: Australia

institute: Macquarie University

data_processing:
Basecalling and adaptor sequence trimming were processed by commercial sequencing provider
The sequence reads from the 6 RNA-Seq samples were aligned to the A. baumannii AB5075_UW reference genome and counted using EDGE-pro (Estimated Degree of Gene Expression in Prokaryotic Genomes)
Differential gene expression between the parental and mutant samples were analysed using the DEseq2 R package
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCA_000963815.1
Supplementary_files_format_and_content: Differential gene expression

organism: Acinetobacter baumannii

growth_protocol: Three independent A. baumannii parental AB5075_UW and ABUW_1103-112:T26 mutant cultures were grown overnight in 5ml Müller Hinton broth at 37°C, with shaking. The overnight cultures were diluted 1:100 in MH and grown to mid-exponential phase cultures (15 mL, OD600 ~ 0.6) at 37°C, with shaking.

extract_protocol:
Total RNA was extracted using the miRNeasy mini kit (Qiagen) and DNA digestion was performed on the total RNA using DNaseI (TURBO DNA-freeTM kit, Invitrogen).
Ribosomal RNA was depleted using Ribozero magnetic kit (Bacteria) (Illumina, Inc., USA) and the cDNA library was generated using TruSeq® stranded RNA preparation kit (Illumina, Inc., USA). The samples were then sequenced on Illumina NextSeq_500 (2x75bp high output flowcell) platform.

tag: genotype

value: Tn mutant

tag: condition

value: Bacterial planktonic cells grown in Müller Hinton broth


title: WGS from K562 (ENCLB544CFT)

description:
https://www.encodeproject.org/experiments/ENCSR711UNY/
***************
biological replicate number: 1
technical replicate number: 1
description: These data correspond to shotgun PE151 Illumina sequencing done on short insert fragmented gDNA from the K562 cell line
experiment encode accession: ENCSR711UNY
assay title: WGS
assembly: hg19
possible controls: ENCSR025GPQ
encode release date: 2017-12-19
lab: Alexander Urban, Stanford
library encode accession: ENCLB544CFT
fragmentation methods: shearing (Covaris generic)
size range: 373-373
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens K562 cell line

extract_protocol:
pipeline protocol: https://www.encodeproject.org/documents/0a14f50a-5674-4f33-9b5d-2d169750c8aa/@@download/attachment/Supplementary%20Figure%201_duplicate.pdf
pipeline protocol: https://www.encodeproject.org/documents/2f406601-9c9f-4c47-94cd-d0814ac30eb6/@@download/attachment/Experiment%20accession%20ENCSR711UNY.pdf
standards document: https://www.encodeproject.org/documents/7a4411d3-04a8-4198-856b-9f8fd5c160d4/@@download/attachment/ENCSR711UNY_variant_call_file_details.pdf
extraction method: QIAGEN DNeasy Blood & Tissue Kit

value: cell line

tag: biosample encode accession

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Alexander Urban, Stanford

value: Michael Snyder

value: ENCBS806UYV at ENCODE; https://www.encodeproject.org/ENCBS806UYV/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: WGS from NCI-H460 (ENCLB506POB)

description:
https://www.encodeproject.org/experiments/ENCSR654YMF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR654YMF
assay title: WGS
encode release date: 2019-08-23
lab: Feng Yue, PSU
library encode accession: ENCLB506POB
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cell-equivalent

source_name: Homo sapiens NCI-H460 cell line

value: male

tag: health state

value: carcinoma; large cell lung cancer

value: unknown

value: not collected

value: Feng Yue, PSU

value: ATCC

value: ENCBS657CEJ at ENCODE; https://www.encodeproject.org/ENCBS657CEJ/

value: Derived from ENCODE donor ENCDO267PTG; https://www.encodeproject.org/ENCDO267PTG/


title: WGS from A549 (ENCLB091ZMP)

description:
https://www.encodeproject.org/experiments/ENCSR521ELB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR521ELB
assay title: WGS
encode release date: 2019-08-23
lab: Feng Yue, PSU
library encode accession: ENCLB091ZMP
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cell-equivalent

source_name: Homo sapiens A549 cell line

tag: line

value: cell line

value: 58 year

value: ENCBS551POM at ENCODE; https://www.encodeproject.org/ENCBS551POM/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ABUW_1103-112:T26_Rep2

value: Tn mutant

value: Bacterial planktonic cells grown in Müller Hinton broth


title: LysMcre/+ Zeb1floxed rep 3

city: Freiburg

first: Sebastian

last: Baasch

address: Breisacher Str.

department: Institute for Immunodeficiency; Center for Chronic Immunodeficiency

institute: University Medical Center

data_processing:
De-multiplexing: Illumina bcl2fastq
Trimming: Skewer
Read count: STAR (V2.5.2b)
Quality control reads: FASTQC
Alignment: STAR (V2.5.2b)
Differentially expressed genes: DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tabular files of differentially expressed genes CMV-infected alveolar macrophages (Zeb1wt vs Zeb1floxed)

source_name: infected macrophages

extract_protocol:
Total RNA, obtained with QIAGEN microkit, was subjected to library synthesis.
After the QC procedures, total RNA was subjected to the KAPA RNA HperPrep Kit with RiboErase (HMR) (Roche)

treatment_protocol: Mice were intranasally infected with a murine cytomegalovirus strain, which expresses a GFP cassette preceeded by a loxP sequence flanked STOP codon. 3 days after infection the mice were sacrificed and infected alveolar macrophages were sorted from lung homogenates. Subsequently the alveolar macrophages were washed and lysed in RNA lysis buffer.

tag: cell type

value: alveolar macrophage

value: LysMcre/+ Zeb1flox/flox

tag: tissue

value: lung

value: infected


title: Parental AB5075_Rep3

source_name: Parental AB5075

value: Parental


title: WGS from K562 (ENCLB557IGA)

description:
https://www.encodeproject.org/experiments/ENCSR053AXS/
***************
biological replicate number: 1
technical replicate number: 1
description: The data contained in this Experiment come from 10X Chromium Genomics WGS of K562 cell line using the Chromium™ Genome v2 Library Kit & Gel Bead Kit
experiment encode accession: ENCSR053AXS
assay title: WGS
assembly: hg19
encode release date: 2018-01-25
lab: Alexander Urban, Stanford
library encode accession: ENCLB557IGA

tag: Sex

value: female

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: age

value: 53 year

value: Alexander Urban, Stanford

value: Michael Snyder

value: ENCBS806UYV at ENCODE; https://www.encodeproject.org/ENCBS806UYV/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: WGS from HepG2 (ENCLB553KIK)

description:
https://www.encodeproject.org/experiments/ENCSR276ECO/
***************
biological replicate number: 1
technical replicate number: 1
description: These data correspond to shotgun PE151 Illumina sequencing done on short insert fragmented gDNA from the HepG2 cell line.
experiment encode accession: ENCSR276ECO
assay title: WGS
assembly: hg19
possible controls: ENCSR350RUO
encode release date: 2019-02-26
lab: Alexander Urban, Stanford
library encode accession: ENCLB553KIK
fragmentation methods: shearing (Covaris generic)
size range: 442-442
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens HepG2 cell line

extract_protocol:
pipeline protocol: https://www.encodeproject.org/documents/0a14f50a-5674-4f33-9b5d-2d169750c8aa/@@download/attachment/Supplementary%20Figure%201_duplicate.pdf
general protocol: https://www.encodeproject.org/documents/eb874284-780f-486e-859c-2c69aaef982a/@@download/attachment/updated2_Experiment%20accession%20ENCSR276ECO.pdf
general protocol: https://www.encodeproject.org/documents/9378ee19-5223-48c8-82e7-06af34e0bf3b/@@download/attachment/ENCSR276ECO_file_details.pdf
extraction method: QIAGEN DNeasy Blood & Tissue Kit

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

tag: lab

tag: source

tag: passage number

value: ENCBS760ISV at ENCODE; https://www.encodeproject.org/ENCBS760ISV/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: LysMcre/+ Zeb1floxed rep 2

value: alveolar macrophage

tag: strain

value: LysMcre/+ Zeb1flox/flox

value: lung

value: infected


title: Parental AB5075_Rep2

value: Parental

value: Bacterial planktonic cells grown in Müller Hinton broth


title: LysMcre/+ Zeb1floxed rep 1


title: WGS from SK-N-MC (ENCLB653PBO)

description:
https://www.encodeproject.org/experiments/ENCSR236KYS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR236KYS
assay title: WGS
encode release date: 2019-08-23
lab: Feng Yue, PSU
library encode accession: ENCLB653PBO
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cell-equivalent

source_name: Homo sapiens SK-N-MC cell line

value: SK-N-MC

value: female

value: Ewing's sarcoma

value: 14 year

value: Feng Yue, PSU

value: ATCC

tag: link

value: ENCBS423QPB at ENCODE; https://www.encodeproject.org/ENCBS423QPB/

value: Derived from ENCODE donor ENCDO000ABC; https://www.encodeproject.org/ENCDO000ABC/


title: LysMcre/+ Zeb1wt rep 3

value: LysMcre/+ Zeb1+/+


title: LysMcre/+ Zeb1wt rep 2


title: WGS from T47D (ENCLB926USO)

description:
https://www.encodeproject.org/experiments/ENCSR121TMQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR121TMQ
assay title: WGS
encode release date: 2019-08-23
lab: Feng Yue, PSU
library encode accession: ENCLB926USO
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cell-equivalent

source_name: Homo sapiens T47D cell line

value: cell line

value: mammary ductal carcinoma

value: adult

value: 54 year

value: ENCBS754KLC at ENCODE; https://www.encodeproject.org/ENCBS754KLC/

value: Derived from ENCODE donor ENCDO000ABA; https://www.encodeproject.org/ENCDO000ABA/


title: ABUW_1103-112:T26_Rep1

value: Tn mutant


title: Cpt2L-/- Ppara KO rep4

city: Baltimore

first: Michael

middle: J

last: Wolfgang

state: Maryland

address: 820 N Wolfe St, Rangos Building, 480.14

institute: Johns Hopkins School of Medicine

data_processing:
NovaSeq S4 6000 platform was used
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and our wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts and fpkm values for every gene and every sample

source_name: Liver tissue

extract_protocol:
Liver tissues are removed. Small pieces of livers from samples subjected to RNA extraction using Trizol. RNA quality was checked by nanodrop and by independent company.
RNA quality was assessed, and Illumina TruSeq stranded mRNA library was prepared for sequencing single 75bp reads using an Illumina NextSeq 500 sequencing platform.

value: liver

value: 8-10 weeks old male

value: Cpt2L-/- Ppara KO

tag: treatment

value: 24 hours fasting


title: Mint-ChIP-seq from excitatory neuron (ENCLB379TBD)

description:
https://www.encodeproject.org/experiments/ENCSR201NXK/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human PGP1 derived excitatory neuron
experiment encode accession: ENCSR201NXK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR508IYL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB379TBD
fragmentation methods: none

tag: antibody

value: excitatory neuron

value: in vitro differentiated cells

tag: description

value: PGP1 derived excitatory cortical neurons

value: male

value: 53 year

value: Bradley Bernstein, Broad

value: George Church

value: ENCBS932EVS at ENCODE; https://www.encodeproject.org/ENCBS932EVS/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: MCF7 treated with RG7388 biological rep 1

city: Toyoake

first: Akila

last: Mayeda

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Institute for Comprehensive Medical Science

institute: Fujita Health University

description: Gene expression data from human MCF-7 cells treated with MDM2 inhibitor RG7388 for 12 h

hyb_protocol: Following fragmentation, ss-cDNA were hybridized for 16 h at 45oC on Clariom_S_Human Array.  Clariom Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Data were collected using GeneChip Scanner 3000 7G.

data_processing: The data were normalized using SST-RMA algorithm and analyzed with Transcriptome Analysis Console (TAC; version 4.0.0.25; Thermo Fisher Scientific).

source_name: MCF7 treated with MDM2 inhibitor RG7388

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: MCF-7 cells were culltured in DMEM supplemented with 10% FBS.

extract_protocol: Total RNA was prepared with RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: MCF-7 cells were treated with 30 nM RG7388, or DMSO as the control, for 12 h.

value: Breast cancer cell line

tag: cell line

value: MDM2 inhibitor RG7388 for 12 h


title: P14

city: Shanghai

first: Shengwei

last: Zhang

state: Shanghai

address: Songhu street

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2-2.1.0 with default parameters.
Unmapped reads with hg19 were extracted by samtools view v1.9 with parameters -b -f 4, then were mapped to the reference genome of all viruses with human as host in GenBank using hisat2-2.1.0 with default parameters.  The URL of the reference genome of all viruses with human as host is: https://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=10239&host=human.
TPM were calculated using salmon v0.13.1 with  parameters quant --validateMappings -l A -r.
Genome_build: hg19
Supplementary_files_format_and_content: The TPM .txt files report the abundance of viral genome sequences in human samples.

source_name: patient donor diseased tissue

extract_protocol:
Total RNA was extracted from normal and pathological tissues by using TRIzol reagent (Invitrogenfrom patients of normal and pathological group). RNAs were then reverse-transcribed with oligo(dT) primer.
RNA-seq libraries for expression analysis were constructed using KAPA RNA HyperPrep Kit KR1350 v1.16 according to the vendor’s protocol and paired-end 2 × 150 bp reads were sequenced using Illumina HiSeq platform.

tag: individual

value: patient donor 14

value: vulva, diseased tissue


title: C18

source_name: patient donor normal tissue

value: patient donor 18

value: vulva, normal tissue


title: 190717_Gata1_e8-5_tomNEG

first: Melania

last: Barile

address: Puddicombe Way

department: Haematology

country: United Kingdom

institute: Cambridge University

description:
chimeric embryos (host cells: WT tdTom- ; injected cells: Gata1-/- tdTom+)
gata1_count_matrix_spliced.csv
gata1_count_matrix_unspliced.csv
metadata.csv
metadata2.csv

data_processing:
Raw files were processed with Cell Ranger 3.0.2 using default mapping arguments.
Reads were mapped to the mm10 genome and counted with GRCm38.92 annotation, including tdTomato sequence for chimera cells.
Cell barcodes with expression profiles significantly different to the ambient mRNA expression profile were identified using emptyDrops (Lun et al., 2019), and cell barcodes with low complexity, i.e. low total mRNA counts and/or high mitochondrial proportion, were identified by fitting four-component bivariate mixture models to the log10 transformed total mRNA counts and percentage of mitochondrial counts, and selecting the components with high total mRNA and low mitochondrial percentage.
Gene expression normalization, selection of highly variable genes (HVGs), and doublet cell barcodes were identified using the approach taken by Pijuan-Sala et al. (2019).
Chimeric cells were assigned a cell type by mapping each sample to the reference atlas data in Pijuan-Sala et al. (2019). using `fastMNN`, applied to the first 50 principal components among HVGs identified with the chimeric sample and atlas data combined, and identifying the majority cell type among the closest (Euclidean distance) 10 atlas cells within the batch-corrected principal component space.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are tab separated tables containing gene expression counts for filtered cells, normalised gene expression logcounts, cell metadata including cell type prediction and sample status, and genes metadata

molecule: polyA RNA

source_name: Gata1 chimaera

growth_protocol: TdTomato-expressing mouse PSCs were generated as previously described (Pijuan-Sala et al., 2019), and maintained in Lif/2i conditions (Ying et al., 2008). Two guides were cloned into the pX458 plasmid (Addgene, #48138) as previously described (Ran et al., 2013). The obtained plasmids were then used to transfect the cells and single transfected clones were expanded and assessed for Cas9-induced mutations. Genomic DNA was isolated, and Cas9 targeting was assessed by next-generation sequencing.

extract_protocol: 10X genomics Chromium, v3 chemistry

treatment_protocol: An ESC clone showing a 38 base-pair frameshift mutation in exon 4 resulting in the functional inactivation of Gata1 were selected for injection into C57BL/6 E3.5 blastocysts. A total of 6 chimaeric embryos were harvested at E8.5, dissected, and single-cell suspensions were generated by TrypLE Express dissociation reagent (Thermo Fisher Scientific) incubation for 7-10 minutes at 37°C under agitation. Single-cell suspensions were sorted into tdTom+ and tdTom- samples using a BD Influx sorter with DAPI at 1µg/ml (Sigma) as a viability stain for subsequent 10X scRNA-seq library preparation.

tag: tdtomato status

value: Negative

tag: embryo portion

value: whole

tag: barcode


title: Parental AB5075_Rep1

tag: genotype

value: Parental

tag: condition

value: Bacterial planktonic cells grown in Müller Hinton broth


title: C14

tag: tissue


title: Cpt2L-/- Ppara KO rep3

value: liver

tag: age

value: 8-10 weeks old male

value: Cpt2L-/- Ppara KO

value: 24 hours fasting


title: 190717_Gata1_e8-5_tomPOS

value: Positive


title: MCF7 treated with RG7388 biological rep 2


title: SAMPLE 10_TGFB2 82 years

description: Eye cells

data_processing: The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https//://dataanalysis.qiagen.com/mirna/arrayanalysis.php (accessed on June 24, 2020)

source_name: TGFB2_lamina cribrosa cells

extract_protocol: Total RNA

tag: subject status/treatment

tag: age (yrs)

tag: cell type

value: human lamina cribrosa cells


title: P12

value: patient donor 12


title: Mint-ChIP-seq from excitatory neuron (ENCLB015UEF)

description:
https://www.encodeproject.org/experiments/ENCSR201NXK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human PGP1 derived excitatory neuron
experiment encode accession: ENCSR201NXK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR508IYL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB015UEF
fragmentation methods: none

source_name: Homo sapiens male adult (53 years) excitatory neuron in vitro differentiated cells, preserved by cryopreservation

value: excitatory neuron

value: in vitro differentiated cells

value: PGP1 derived excitatory cortical neurons

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

value: 53 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: George Church

value: ENCBS932EVS at ENCODE; https://www.encodeproject.org/ENCBS932EVS/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: Cpt2L-/- Ppara KO rep1

tag: strain

value: liver

tag: treatment


title: C12

tag: individual

value: vulva, normal tissue


title: MCF7 treated with RG7388 biological rep 3

value: Breast cancer cell line

tag: cell line

value: MDM2 inhibitor RG7388 for 12 h


title: WGS from K562 (ENCLB932PRR)

description:
https://www.encodeproject.org/experiments/ENCSR045NDZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR045NDZ
assay title: WGS
encode release date: 2019-08-23
lab: Feng Yue, PSU
library encode accession: ENCLB932PRR
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cell-equivalent

tag: line

value: cell line

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: Feng Yue, PSU

value: ATCC

tag: passage number

tag: link

value: ENCBS701BIM at ENCODE; https://www.encodeproject.org/ENCBS701BIM/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: LN4-R_42

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

data_processing:
data filtering: Prior to mapping, adaptors were removed using Cutadapt (Martin 2011) and default parameters. Reads were further trimmed and filtered using Sickle (https://github.com/najoshi/sickle) with a 40 bp minimum remaining sequence length, Sanger quality of 20, and no 5’ end trimming.
Mapping: Each intestinal RNAseq library was mapped individually to the labrus genome assembly (European Nucleotide Archive accession number: PRJEB13687, http://www.ebi.ac.uk/ena/data/view/PRJEB13687) using the Tophat2 short read aligner (Langmead et al. 2009). Transcript abundances were estimated using the FeatureCounts (Liao et al. 2014) software of the Subread package (http://subread.sourceforge.net/). The Bioconductor - DESeq2 analysis package (Love et al. 2014) was used for differential expression analysis

organism: Labrus bergylta

source_name: hindgut

growth_protocol: fish were distributed to 10 cylindrical flat-bottomed black tanks with a volume of 350 l, equipped with separate light sources and artificial kelp. The tank water temperature during the experiment was 14.5-17 °C. The fish was acclimatized for four weeks prior to the experiment and fed the reference diet (Control diet) containing 61% protein, 16% lipid, 7% carbohydrate and 16% ash (of dry matter). Fish densities were adjusted to 20 kg/m3 before start of the experiment.

extract_protocol:
Total RNA was extracted from distal intestinal samples (IN4) using a BioRobot® EZ1 and RNA Tissue Mini Kit (Qiagen, Hilden, Germany) including a DNase treatment step according to the manufactures instructions. RNA quantity and quality were assessed using a NanoDrop ND-1000 UV–vis Spectrophotometer (NanoDrop Technologies, Wilmington, USA). All samples had 260/230 and 260/280 ratios above 2.0 and 2.2 respectively, indicating high RNA purity. Agilent 2100 Bioanalyzer and RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, USA) was used for assessment of RNA integrity for the individual samples. The average RNA integrity number (RIN) of all samples was 7.8 ± 0.5.. RNA sequencing was performed by the Norwegian Sequencing Centre (www.sequencing.uio.no). Sequencing libraries were prepared with an automated NeoPrep platform (Illumina) using 90 ng total RNA input to the TruSeq Stranded mRNA Library Prep Kit (Illumina) and standard Illumina adaptors included in the kit. The libraries were sequenced using HiSeq4000 according to manufacturer instructions, generating paired end libraries with an average library size of 14.2 ± 1.4 million reads.   Filtering of raw reads? Data deposition to Genbank?
RNA sequencing was performed by the Norwegian Sequencing Centre (www.sequencing.uio.no). Sequencing libraries were prepared with an automated NeoPrep platform (Illumina) using 90 ng total RNA input to the TruSeq Stranded mRNA Library Prep Kit (Illumina) and standard Illumina adaptors included in the kit. The libraries were sequenced using HiSeq4000 according to manufacturer instructions, generating paired end libraries with an average library size of 14.2 ± 1.4 million reads.

treatment_protocol: In addition to the reference diet, three experimental diets were made by supplementing the reference diet with either soyasaponin (0.7%), a commercial prebiotic (Aquate™ SG, 0.4%) or the combination of soyasaponin and prebiotics. Ref, Sap, Pre and P+S are used to refer to the respective diets in this paper hereafter. Feed was distributed to duplicate tanks per diet every 10 min using automatic belt feeders for the duration of the experiment. The each tank was fed 80 g feed/kg fish per day. Before loading to each belt automat, the 80 g of feed was soaked in 10 ml of water for 4-5 minutes to soften the feed. The fish was fed the experimental feed for five weeks before termination and sampling

tag: tissue

value: hindgut

value: Control+Saponi+Prebiotic


title: P18

value: patient donor 18

value: vulva, diseased tissue


title: LysMcre/+ Zeb1wt rep 1

value: alveolar macrophage

tag: genotype

value: LysMcre/+ Zeb1+/+

value: lung

tag: condition

value: infected


title: PPAR alpha knockout rep4

value: liver

tag: age

value: 8-10 weeks old male

value: PPAR-a KO

value: 24 hours fasting


title: P11

value: patient donor 11


title: PPAR alpha knockout rep3


title: MCF7 treated with DMSO biological rep 3

description: Gene expression data from human MCF-7 cells treated with DMSO for 12 h

source_name: MCF7 treated with DMSO

value: Breast cancer cell line

value: DMSO for 12 h


title: LN4-R_40


title: MCF7 treated with DMSO biological rep 1


title: MCF7 treated with DMSO biological rep 2


title: Cpt2L-/- Ppara KO rep2

value: Cpt2L-/- Ppara KO


title: LN4-R_39


title: C11

value: vulva, normal tissue


title: WGBS PXGGY/A

city: St Louis

first: Thorold

last: Theunissen

state: MO

address: 4515 McKinley Ave, Room 3313

department: Developmental Biology

institute: Washington Unversity School of Medicine

data_processing:
MethylC-Seq data were trimmed of adapters using Cutadapt version 1.2.1 (Martin, 2011), and aligned to the human genome hg38 with Bismark version 0.22.3 (https://academic.oup.com/bioinformatics/article/27/11/1571/216956).
The aligned reads were further processed with MethPipe (Song Q, Decato B, Hong E, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J, Smith AD (2013) A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics), and % DNA methylation levels of CpGs on imprinted regions were compiled with the roimethstats function from MethPipe.
The genome-wide average % DNA methylation of CpGs was compiled on 1 kB sliding windows (offset 500 bp).
Genome_build: hg38
Supplementary_files_format_and_content: .meth

source_name: Naïve hESC

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA). Whole Genome Bisulfite conversions were performed with 200 ng of gDNA using the EZ DNA Methylation-Gold, 50rxn (Fisher-part#50444294) kit.
WGBS Libraries were created using the Accel-NGS Methyl-Seq DNA Library Kit - 24 rxns (Swift Biosciences-part#30024) and Accel-NGS Methyl-Seq Dual Indexing Kit - 96rxns (Swift Biosciences-part#38096). The libraries were pooled and sequenced on 0.240 of an NovaSeq S4 flow cell (300 XP; targeting 30x wgbs coverage/120Gb per sample) at the Genome Technology Access Center at Washington University School of Medicine in St. Louis.

tag: culture condition

value: Alternative naive conversion condition:PXGGY/A

tag: passage


title: PPAR alpha knockout rep1


title: LN4-R_15

value: hindgut

value: Control+Saponi+Prebiotic


title: Tsc1Cpt2 L -/- Cre rep4

value: Tsc1Cpt2 L-/-


title: P9

value: patient donor 9

value: vulva, diseased tissue


title: LN4-R_13


title: WGBS PXGGY

value: Alternative naive conversion condition:PXGGY


title: LN4-R_16


title: LN4-R_36

value: Control+Saponin


title: PPAR alpha knockout rep2

value: liver


title: C9


title: Tsc1Cpt2 L -/- Cre rep2

value: 8-10 weeks old male


title: WGBS GXGY

value: Alternative naive maintenance condition:GXGY


title: P7

value: patient donor 7


title: C7


title: tissue_6

value: patient donor 6


title: WGBS AXGY

value: Alternative naive maintenance condition:AXGY


title: H3K27ac_HDAC1_WT_rep2

source_name: Embryonic stem cells

value: untreated

tag: chip antibody

value: H3K27ac (Abcam, Cat.# ab4729)

value: wild type


title: LN4-R_35


title: Tsc1Cpt2 L -/- Cre rep1

value: 24 hours fasting


title: LN4-R_32

value: hindgut


title: WGBS PXGY

value: Alternative naive maintenance condition:PXGY


title: tissue_6C

value: vulva, normal tissue


title: Cpt2 L -/- Cre rep4

value: Cpt2 L-/-


title: WGBS FXGY

value: Alternative naive maintenance condition:FXGY


title: LN4-R_29


title: tissue_5

value: patient donor 5

value: vulva, diseased tissue


title: Cpt2 L -/- Cre rep3

value: liver


title: LN4-R_28

value: Control+Saponin


title: Tsc1Cpt2 L -/- Cre rep3

value: 8-10 weeks old male

value: Tsc1Cpt2 L-/-


title: LN4-R_27


title: WGBS 5i/L/A


title: Cpt2 L -/- Cre rep2


title: tissue_4

value: patient donor 4


title: tissue_5C


title: LN4-R_7

value: Control+Prebio


title: Tsc1 L -/- Cre rep2

value: Tsc1 L-/-


title: LN4-R_9


title: LN4-R_21


title: RNA-seq PXGGY (P2), rep2

data_processing:
RNA-seq reads were aligned to the human genome hg38 with HISAT2 version 2.2.0 (ref: https://www.nature.com/articles/s41587-019-0201-4).
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount (Liao et al., 2013), version 1.4.6, with hg38 annotation gencodeV31 (Harrow et al., 2012).
All gene-level transcript counts were then imported into the R/Bioconductor package DESeq2 (Love et al., 2014).
Transcripts with CPM >1.0 were converted into a DESeq2 dataset and then regularized log transformed using the rlog function from the DESeq2 package.
Adjusted p-values for DGE were determined by DESeq2 using the R stats function p.adjust using the Benjamini and Hochberg correction to determine the false discovery rate with a 1.5- fold expression change and FDR < 0.05 required to consider a gene differentially expressed.
Genome_build: hg38
Supplementary_files_format_and_content: counts

extract_protocol:
Total RNA was isolated using the E.Z.N.A. total RNA kit I.
Library construction was performed using the SMARTer Directional cDNA Library Construction Kit
Libraries were sequenced on an Illumina HiSeq3000 1X50 or NovaSeq S4 2x150 (4 lanes) platform

value: Alternative naive conversion conditions:PXGGY

value: H9 hESC


title: Cpt2 L -/- Cre rep1

value: 24 hours fasting


title: tissue_4C


title: RNA-seq PXGGY/A (P2), rep1

value: Alternative naive conversion conditions:PXGGY/A


title: RNA-seq PXGGY (P2), rep1


title: N2

source_name: normal donor control

value: normal donor 2


title: Tsc1 L -/- Cre rep4


title: LN4-R_20

value: hindgut


title: RNA-seq PXGGY (P8)


title: Tsc1 L -/- Cre rep3


title: LN4-R_24


title: LN4-R_11


title: Tsc1 L -/- Cre rep1


title: RNA-seq PXGGY (P1)


title: N3

value: normal donor 3

value: vulva, normal tissue


title: N1

value: normal donor 1


title: RNA-seq PXGGY/A (P2), rep2


title: RNA-seq GXGY

value: Alternative naive maintenance conditions:GXGY


title: Wt rep4

value: liver

value: Wild type


title: N4

value: normal donor 4


title: Wt rep3

value: 8-10 weeks old male


title: LN4-R_78

value: Control


title: RNA-seq AXGY

value: Alternative naive maintenance conditions:AXGY


title: SH82K33 AZD-PC9 Exo-RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: Osimertinib-resistant PC9 (AZD-PC9) cells were established using a stepwise method.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: primary lung cancer cell line

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: Exosomes were obtained from the culture supernatant of these cells by a centrifugal ultrafiltration-based method. Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, USA) from  isolated exosomes.

value: primary lung cancer cell line


title: RNA-seq FXGY

value: Alternative naive maintenance conditions:FXGY


title: Wt rep1


title: Wt rep2


title: RNA-seq PXGY

value: Alternative naive maintenance conditions:PXGY

value: H9 hESC


title: LN4-R_75


title: NORMAL2

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

institute: Tongji University

data_processing:
Cutadapt software was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software.
StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM
Genome_build: mm9
Supplementary_files_format_and_content: processed data file is a xls file contains the fpkm

source_name: skin

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

treatment_protocol: Bleomycin (BLM, Thermo Fisher Scientific, USA) was diluted in phosphate buffered saline (PBS, Sangon Biotech, China) at a concentration of 1 mg/mL and sterilized by filtration. To establish the murine fibrosis model, 100µL BLM solution were subcutaneously injected into the shaved backs (1 cm2) of mice for 28 days using a 27-gauge needle.BLM-induced SSc mice were randomly divided into 2 groups treated with PBS (100µL) or BMSC derived exosome. (15μg/100μL).

value: PBS


title: LN4-R_64


title: RNA-seq mTeSR1_2

source_name: Primed hESC


title: NORMAL


title: LN4-R_77


title: LN4-R_62


title: EXO1

value: exosome


title: BLM2


title: HBECs_1 (Nanopore)

first: Daniel

last: Larson

address: 41 Medlar Dr.

institute: NIH

description:
Nanopore direct Nascent RNA long read sequencing
direct RNA long read sequencing
run1
larson.corrected_collapse.min.3.fa.isoforms.gtf

data_processing:
Raw direct rna fastq reads were align to reference genome hg19 using minmap2 v2-2.16 with “-ax splice -uf -k14” options.
Raw direct rna fastq reads were align to reference genome hg19 using minmap2 v2-2.16 with "-ax splice -uf -k14" options.
Mapped data were analyzed by Sqanti2 https://github.com/Magdoll/SQANTI2. (larson.sqanti2.flair.min.3.classification.txt)
Also high-confidence isoforms are defined by Flair. https://github.com/BrooksLabUCSC/flair#collapse  (larson.corrected_collapse.min.3.fa.isoforms.gtf)
Genome_build: hg38
Supplementary_files_format_and_content: larson.corrected_collapse.min.3.fa.isoforms.gtf
Supplementary_files_format_and_content: larson.sqanti2.flair.min.3.classification.txt

source_name: Human Bronchial Epithelial Cells

growth_protocol: Human bronchial epithelial cells (HBECs) were grown in Keratinocyte-SFM medium (Gibco, 17005-042) with 1% penicillin-streptomycin (ThermoFisher, 15140122).

extract_protocol:
After media removal, cells were trypsinized and washed with PBS. We preformed nuclei fractionation before nascent RNA purification. Briefly, cells were lysed for 2 min with 400 μl cytoplasmic lysis buffer (0.15% (vol/vol) NP-40 (Thermo Fisher Scientific, 28324), 10 mM Tris-HCl (pH 7.0), and 150 mM NaCl), layered over 1000 μl of a sucrose cushion (10 mM Tris-HCl (pH 7.0), 150 mM NaCl, 25% (wt/vol) sucrose), and nuclei were collected by centrifugation at 16,000 g for 10 minutes. The nuclei pellet was resuspended in 800 μl wash buffer (0.1% (vol/vol) Triton X-100, 1 mM EDTA, in 1X PBS) and collected by centrifugation at 1,150 g for 1 minute. All steps were performed at 4 °C and all buffers were prepared with 0.05U/μl SUPERase.In (ThermoFisher Scientific, AM2694) and protease inhibitor mix (Roche, 11873580001). extract the RNA from nucleus with Trizol. 1ml douncer was used to homogenize the nuclei. 4sU labeled nascent RNA was purified from the nucleus RNA (methods described in session: 4sU metabolic labeling and nascent RNA sequencing). polyA tailing was done with 5 unit Ecoli polyA polymerase in 20ml volume, incubated at 37°C for 30min. 0.5 ml RNase inhibitor was added to prevent RNA degradation.
Two RNA sequencing libraries were prepared from 500 ng polyadenylated nascent RNA using the Nanopore Direct RNA Sequencing kit (SQK-RNA002, Oxford Nanopore Technologies) according to manufacturer’s instructions. Briefly, the poly(T) adapter was ligated to the RNA using T4 DNA ligase (New England Biolabs, M0202) in the Quick Ligase reaction buffer (New England Biolabs, B6058) for 10 min at room temperature. SuperScript III Reverse Transcriptase (Thermo Fisher Scientific, 18080044) was used to synthesize the first-strand cDNA. The RNA–cDNA hybrid was then purified using 1.8X Agencourt RNAClean XP magnetic beads (Beckman Coulter, A66514). Finally, the RNA sequencing adapter was ligated onto the RNA-cDNA hybrid using T4 DNA ligase in the Quick Ligase reaction buffer for 10 min at room temperature, and the final library was purified using 1X Agencourt RNAClean XP magnetic beads.
Each library was loaded onto a flow cell (FLO-MIN106, R9.4.1) and sequenced using a MinION sequencer (Oxford Nanopore Technologies) during 20 – 23 hour long runs. The direct RNA sequencing raw data was processed using Guppy version 4.0. The sequencing reads were mapped to human reference genome hg19 using minimap2 version 2.17. The aligned read bam files were indexed and visually inspected using IGV.

treatment_protocol: 4X T225 flask (~10^8) of HBEC Cells were metabolic labeled with 4sU (500uM) for 20 min.

tag: cell type

value: Human Bronchial Epithelial Cells

tag: fraction

value: polyadenylated nascent RNA


title: EXO2


title: HBECs_2 (Nanopore)

description:
Nanopore direct Nascent RNA long read sequencing
direct RNA long read sequencing
run2
larson.corrected_collapse.min.3.fa.isoforms.gtf


title: LN4-R_65

value: hindgut


title: EXO


title: BLM


title: BLM1