title: Bone-marrow aspirates, mRNA-derived cDNA 9

city: South San Francisco

first: Simon

middle: J

last: Hogg

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

data_processing:
FASTQ reads were processed using Cellranger v7.0.0 count workflow to generate gene expression and antibody capture data matrices; Cellranger multi pipeline was additionally executed to demultiplex hashed sequencing samples.
Resultant filtered sparse count matrices were loaded into R v4.0.0 as Seurat v4.0.6 objects.  Multiplets were tagged using scDblFinder v1.10.0 and removed.  Further filtering was applied to only retain: (1) RNA features detected in greater than 3 cells and (2) cells with greater than 200 and less than 2500 detected features.
Assembly: Human reference, GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: Raw count matrices:  RNA_counts.csv.gz, ADT_counts.csv.gz
Supplementary files format and content: Cell ID human sample assignments:  cell_sample_assign.csv.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: Bone Marrow

extract_protocol:
Human bone marrow samples were thawed using prewarmed RPMI + 10% FBS and washed twice with cold PBS prior to labeling with unique TotalSeq C compatible HashTags (Biolegend). Samples were subsequently incubated with Human Fc receptor blocking agent (Biolegend) and labeled with DAPI for live cell FACS sorting using an Aria cytometer (BD Bioscience).
Post sort, 150,000 cells were washed once with cold PBS prior to application of the TotalSeqC cocktail (Biolegend) and subsequently a custom ADT tagged U5 snRNP200 antibody (Biolegend).  Cells were washed three times with cold PBS and submitted to the Memorial Sloan Kettering Cancer Center Integrative Genomics Core for sequencing.

tag: tissue

value: Bone Marrow

tag: multiplexed

value: N

tag: antibodies/tags


title: undifferentiated hiPSC sample 1

status: Public on Dec 08 2022

type: SRA

city: Boston

first: Johan

last: Spetz

state: MA

address: HSPH2, Room 229, 655 Huntington Ave.

department: JBL Center for Radiation Sciences

country: USA

institute: Harvard School of Public Health

library_source: transcriptomic

data_processing:
Sequencing output was de-multiplexed, barcodes removed, trimmed for quality, and FastQC was run on all files for quality control.
Reads were aligned to human genome assembly GRCh38 using STAR76.
Genome_build: GRCh38
Supplementary_files_format_and_content: ipsc_rnaseq_processed.txt: Tab-delimited text file includes FPKM values for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: Human DiPS 1016 SeVA iPSC

growth_protocol: Human DiPS 1016 SeVA iPSC stocks (Harvard Stem Cell Institute iPS Core Facility, Harvard University) were thawed in complete StemFlex medium (Life Technologies) containing 10 µM Rho-associated, coiled-coil containing protein kinase (ROCK) inhibitor Y-27632 (Calbiochem). After 24 hours, medium was replaced with complete StemFlex free of ROCK inhibitor. Cells were detached using Accutase (StemCell Technologies) and split 1:5 to 1:10 prior to reaching confluence; cells were cultured in complete StemFlex media supplemented with ROCK inhibitor for the first 24 hours. hiPSC clones were split to 50% confluence and cultured overnight in StemFlex medium (Life Technologies) with 10 µM ROCK inhibitor. The next day (Day 1), differentiation was initiated by replacing the medium with N2B27, which consists of equal parts of Neurobasal medium and DMEM/F12 GlutaMAX (Life Technologies) supplemented with B-27 without vitamin A (Life Technologies) and N-2 supplement (Life Technologies). For the first three days 6 µM CHIR-99021 (Cayman Chemicals) and 25 ng/ml BMP4 (R&D Systems) was added daily. To generate VSMCs, media was replaced on day 4 by N2B27 supplemented with 10 ng/ml PDGF-BB (PeproTech) and 2 ng/ml Activin A (PeproTech). On Day 6, cells were split with trypsin-EDTA (Corning) into dishes coated with human fibronectin (Sigma-Aldrich) and maintained in Medium 231 (Life Technologies) supplemented with Smooth Muscle Growth Supplement (Life Technologies). To generate ECs, the same protocol was followed for the first 3 days to achieve the mesodermal lineage, but on Day 4 media was replaced with N2B27 supplemented with 200ng/ml VEGF (PeproTech) and 2µM forskolin (Sigma-Aldrich). On Day 6, cells were split and differentiated ECs were either MACS-separated using CD144 MicroBeads (Miltenyi Biotec) or flow cytometry sorted for CD144 positive cells to isolate the population expressing VE-cadherin. Endothelial lineage cells were maintained in EGM-2 Endothelial Cell Growth Medium (Lonza). Differentiation of hPSCs into adipocytes was performed as follows: hPSCs were passaged and grown in suspension culture to form embryoid bodies. After one week, the embryoid bodies were plated on tissue culture-treated plastic and grown in DMEM + 10% fetal bovine serum. The outgrowing mesenchymal progenitor cells (MPCs) were used from passage 4 through 8. For adipocyte differentiation MPCs were infected with previously described lentivirus to express the transactivator rtTA and inducible expression of PPARg2. MPCs were passaged and grown to confluence, and then exposed to 700ng/mL doxycycline for two weeks in previously established A2 medium, and then one week without doxycycline in A2 medium and used for assays. All culture media were supplemented with penicillin-streptomycin (Life Technologies) and Plasmocin (Invivogen) and changed every other day unless otherwise specified.

extract_protocol:
RNA was extracted from hiPSC-derived cells using the QIAcube and the RNeasy Plus Mini Kit (QIAGEN). RNA quality was ascertained with the TapeStation (Agilent), and only samples with a RIN>9.0 value were used for sequencing.
Sequencing libraries were made with the PrepX DNA library kit (Takara bio) using the Apollo system (Takara bio). Quality control for the libraries was performed using the KAPA library quantification kit (Roche) and the TapeStation (Agilent). Sequencing libraries were barcoded, pooled and sequenced on a HiSeq 2500 (Illumina) with single-end 150bp reads.

tag: cell type

value: undifferentiated human induced pluripotent stem cells


title: Bone-marrow aspirates, mRNA-derived cDNA 8

state: California

molecule: polyA RNA


title: Illumina.DMSO_3h.batch1

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

country: China

institute: Huaqiao University

data_processing:
(1) Only paired end raw reads where each read was ≥ 30 bases after adaptor trimming and each base had the Phred quality score ≥ 20 were selected.  (2) Such reads were then aligned to the GRCh38/hg38 assembly of the human genome by the Tophat software, and the uniquely mapping reads were used to calculate the FPKM for each transcript annotated in UCSC Genes database and vlincRNAs by the Cufflinks software with the default parameters.
Assembly: GRCh38/hg38

growth_protocol: Human CML leukemia cell line K562 was obtained from Cell Bank of Chinese Academy of Sciences. Cells were cultured in RPMI 1640 (Thermo Fisher Scientific) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (Thermo Fisher Scientific) and 1% (v/v) pen-strep (Thermo Fisher Scientific) at 37°C and 5% CO2.

extract_protocol:
Total RNA from the samples was extracted using TRNzol Universal (Tiangen, DP424) and Total RNA kit I (Omega, R6834-02) according to the manufacturer’s protocols.
The RNA samples were used for RNA-seq library construction using rRNA depletion and a strand-specific strategy. The library construction and sequencing using the Illumina NovaSeq 6000 platform with the PE150 strategy on the 10-GB scale were outsourced to Novogene Corporation (Beijing).

treatment_protocol: For drug treatments, 1.5 million cells were seeded in 3 ml of the medium without antibiotic per well in 6-well plates. After 16 hours, various drugs or DMSO/water controls were added and incubated for 3 or 6 hr. All drugs were obtained from Abmole Bioscience Inc and dissolved in DMSO (with the exception of YM-155 and cytarabine that were dissolved in water). The concentration of DMSO was kept at 0.1% in all treatments.

value: chronic myelogenous leukemia cell line

tag: treatment

value: treated with DMSO for 3 hours


title: Bone-marrow aspirates, mRNA-derived cDNA 7


title: Bone-marrow aspirates, ADT-derived/HTO-derived cDNA 8

library_source: other

molecule: other

value: Total-Seq C ADT Cocktail  with custom U5 snRNP200 antibody and Total-Seq C hashing oligos


title: Bone-marrow aspirates, ADT-derived/HTO-derived cDNA 9


title: undifferentiated hiPSC sample 2


title: Bone-marrow aspirates, ADT-derived/HTO-derived cDNA 5


title: Bone-marrow aspirates, ADT-derived/HTO-derived cDNA 6


title: microRNA counts from lower leg skin (ENCLB011WQD)

type: RNA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR798NKG/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human lower leg skin
experiment encode accession: ENCSR798NKG
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB011WQD
size range: <30

hyb_protocol: Nanostring protocol

scan_protocol: Nanostring protocol

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

source_name: Homo sapiens lower leg skin tissue male adult (54 years)

label_protocol: Nanostring protocol

value: lower leg skin

value: tissue

tag: description

value: Skin - Sun Exposed (Lower leg)

tag: biosample encode accession

tag: age

value: 54 year

tag: dev stage

value: adult

tag: Sex

value: male

tag: lab

value: Barbara Wold, Caltech

tag: link

value: ENCBS602BLH at ENCODE; https://www.encodeproject.org/ENCBS602BLH/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Bone-marrow aspirates, mRNA-derived cDNA 6


title: microRNA counts from myocyte (ENCLB329OFR)

description:
https://www.encodeproject.org/experiments/ENCSR782VMS/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human LHCN-M2 differentiated for 7 days
experiment encode accession: ENCSR782VMS
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-01-19
lab: Ali Mortazavi, UCI
library encode accession: ENCLB329OFR
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Homo sapiens LHCN-M2 in vitro differentiated cells male adult (41 year)

value: myocyte

value: in vitro differentiated cells

value: LHCN diff rep2

value: 41 year

value: ENCBS986HXG at ENCODE; https://www.encodeproject.org/ENCBS986HXG/

value: Derived from ENCODE donor ENCDO000ACW; https://www.encodeproject.org/ENCDO000ACW/


title: Bone-marrow aspirates, mRNA-derived cDNA 5

value: Bone Marrow

value: N


title: Tobacco GARP-G2-like TF Niben101Scf06721g00011 ChIP-seq replicate2

city: Hong Kong

first: Sibo

last: REN

address: Sha tin CUHK

institute: The Chinese University of Hong Kong

library_source: genomic

data_processing:
ChIP-seq reads 100 bp from 3’ end were trimmed with the bowtie2 parameter -3 100.
ChIP-seq reads were aligned to plant reference genomes (Arabidopsis thaliana TAIR10, Nicotiana benthamiana version 2.5.1, Solanum lycopersicum SL4.0, Oryza sativa MSU7.0 and Zea mays RefGen_v4) using Bowtie 2 (version 2.3.2).
The ENCODE2 ChIP-seq pipline with MACS2 (version 2.2.1) and IDR (version 2.0.4.2) were used for peak calling. Peak summit positions were retrieved by using the “--call-summits” function in MACS2. The regions +/- 75bp from the summit position with signal fold-change in NarrowPeak format were then supplied to IDR, and the regions passed the IDR 0.01 and summit signal foldchange cut-off were kept and resized back to 150bp.
BigWig files were generated using the samtools view with binsize 1bp.
Supplementary files format and content: bigWig, narrowPeak

molecule: genomic DNA

organism: Nicotiana benthamiana

source_name: Leaf

extract_protocol:
The nuclei were then isolated by filtration and centrifugation, and the chromatin was sonicated to sub-kb fragments using Bioruptor.
ChIP-seq libraries were prepared using the HiSeq X Ten.

value: Leaf

tag: replicate

value: replicate 2

tag: genotype

tag: chip antibody

value: Rabbit monoclonal anti-HA (clone C29F4), Cell Signaling Technology, Cat# 3724


title: microRNA counts from right lobe of liver (ENCLB319WGX)

description:
https://www.encodeproject.org/experiments/ENCSR776XYQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human right lobe of liver
experiment encode accession: ENCSR776XYQ
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB319WGX
size range: <30

source_name: Homo sapiens right lobe of liver tissue female adult (53 years)

value: right lobe of liver

value: tissue

value: Liver

value: 53 year

value: female

value: ENCBS594VBH at ENCODE; https://www.encodeproject.org/ENCBS594VBH/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: Tobacco GARP-G2-like TF Niben101Scf06721g00011 ChIP-seq replicate1

value: replicate 1


title: Bone-marrow aspirates, ADT-derived/HTO-derived cDNA 4

value: Y

value: Total-Seq C ADT Cocktail  with custom U5 snRNP200 antibody and Total-Seq C hashing oligos


title: microRNA counts from right lobe of liver (ENCLB923HHV)

description:
https://www.encodeproject.org/experiments/ENCSR776XYQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human right lobe of liver
experiment encode accession: ENCSR776XYQ
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB923HHV
size range: <30

value: adult

value: Barbara Wold, Caltech

value: ENCBS688NPW at ENCODE; https://www.encodeproject.org/ENCBS688NPW/


title: Tobacco GARP-G2-like TF Niben101Scf09774g03004 ChIP-seq replicate2


title: Bone-marrow aspirates, ADT-derived/HTO-derived cDNA 3

value: Bone Marrow


title: Bone-marrow aspirates, ADT-derived/HTO-derived cDNA 7

value: N


title: microRNA counts from myocyte (ENCLB406PCP)

description:
https://www.encodeproject.org/experiments/ENCSR782VMS/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human LHCN-M2 differentiated for 7 days
experiment encode accession: ENCSR782VMS
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-01-19
lab: Ali Mortazavi, UCI
library encode accession: ENCLB406PCP
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: myocyte

value: in vitro differentiated cells

value: LHCN diff rep1

value: 41 year

value: male

value: ENCBS575BSN at ENCODE; https://www.encodeproject.org/ENCBS575BSN/

value: Derived from ENCODE donor ENCDO000ACW; https://www.encodeproject.org/ENCDO000ACW/


title: microRNA counts from bipolar neuron (ENCLB267ROE)

description:
https://www.encodeproject.org/experiments/ENCSR765ZSI/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on PGP human bipolar spindle neuron
experiment encode accession: ENCSR765ZSI
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-01-19
lab: Ali Mortazavi, UCI
library encode accession: ENCLB267ROE
size range: <30

source_name: Homo sapiens bipolar spindle neuron in vitro differentiated cells male adult (53 years) derived from induced pluripotent stem cell

value: bipolar neuron

value: These are bipolar neurons created from iPSC from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: Thomas Gingeras, CSHL

value: ENCBS369AAA at ENCODE; https://www.encodeproject.org/ENCBS369AAA/

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


title: Tobacco GARP-G2-like TF Niben101Scf09774g03004 ChIP-seq replicate1

value: Leaf

value: replicate 1

value: Rabbit monoclonal anti-HA (clone C29F4), Cell Signaling Technology, Cat# 3724


title: Bone-marrow aspirates, mRNA-derived cDNA 3

value: Bone Marrow

value: Y


title: microRNA counts from gastrocnemius medialis (ENCLB533RPX)

description:
https://www.encodeproject.org/experiments/ENCSR655NLY/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human skeletal muscle tissue
experiment encode accession: ENCSR655NLY
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB533RPX
size range: <30

source_name: Homo sapiens gastrocnemius medialis tissue male adult (54 years)

value: gastrocnemius medialis

value: tissue

value: Muscle - Skeletal

value: 54 year

value: adult

value: Barbara Wold, Caltech

value: ENCBS178APY at ENCODE; https://www.encodeproject.org/ENCBS178APY/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: WGBS data of DMS3-ZF line 204

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Whole genome bisulfite sequencing data of cassava DMS3-ZF line 204.

data_processing:
For WGS, paired-end reads were mapped to transgene construct sequence by BWA (v0.7.15-r1140) with default parameters (Li H. and Durbin R., 2009). Completely unmapped or mapped reads were filtered, and only partially mapped reads were retained. Partially mapped reads were subjected to sequence assembling with Velvet (v1.2.10, > 3 folds coverage) (Zerbino, Daniel R., and Ewan Birney, 2008). Assembled sequences were searched against plasmid and TME7 genome with blastn (v2.6.0+, E value < 1E-10) (Altschul, S.F., 1990). Sequences that have hit on both transgenic plasmid and TME7 were obtained. Accuracy of the insertion site prediction was validated by 1) mapping WGS reads back to the sequences that have hit on both transgenic plasmid and TME7 sequence, 2) Reads coverage over insertion region in TME7.
For WGBS, WGBS reads were mapped to TME7 phase0 genome with BSMAP (v2.90) allowing 1 mismatch and 1 best hit (-v 1 -w 1) (Xi, Y., 2009; Ben N. Mansfeld, 2021). Duplicated reads were removed with SAMtools (v1.3.1). Reads with three or more consecutive methylated CHH sites were considered as unconverted reads and removed in the following analysis. Conversion rate was estimated by calculating methylation level of the chloroplast genome. DNA methylation level at each cytosine was calculated by number of methylated C vs. total C and T account. Methylation levels of each chromosome were determined by calculating CG, CHG, and CHH level of 100 kb bins. Methylation track files were visualized with Integrative Genomics Viewer (IGV, v3.0) (James T. Robinson, 2011).
Genome_build: TME7
Supplementary_files_format_and_content: bigWig

organism: Manihot esculenta

source_name: Cassava leaf tissue

growth_protocol: Cassava plants of the TME419 ecotype were used in this study. All plants were grown under green house condition. Leaf tissues were collected from 7-8 week plants.

extract_protocol:
Leaf tissues from 7-8 week-old plant were used for DNA extraction.
For WGS, libraries were prepared from genomic DNA by using Kapa HyperPrep kit (Roche) with DNA UD indexes (IDT for Illumina) and sequenced on NovaSeq 6000 sequencer (Illumina).
For WGBS, genomic DNA from samples were end-repaired and ligated with TruSeq LT DNA single adapters (Illumina) using Kapa DNA HyperPrep kit (Roche). Adapter-ligated DNA was converted with EpiTect Bisulfite Kit (Qiagen). Converted DNA was PCR-amplified by MyTaq polymerase (Bioline) for 12 cycles. Library quality and size were determined by D1000 ScreenTape (Agilent) and libraries were subsequently purified by AMPure XP beads (Beckman Coulter). Library concentrations were measured with Qubit dsDNA Broad-Range Assay kit (ThermoFisher). Libraries were sequenced on NovaSeq 6000 sequencer (Illumina).

value: leaf tissue

tag: developmental stage

value: 7-8 weeks

tag: ecotype

value: DMS3-ZF line 204


title: microRNA counts from bipolar neuron (ENCLB350YBL)

description:
https://www.encodeproject.org/experiments/ENCSR765ZSI/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on PGP human bipolar spindle neuron
experiment encode accession: ENCSR765ZSI
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-01-19
lab: Ali Mortazavi, UCI
library encode accession: ENCLB350YBL
size range: <30

value: bipolar neuron

value: in vitro differentiated cells

value: These are bipolar neurons created from iPSC from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS374AAA at ENCODE; https://www.encodeproject.org/ENCBS374AAA/

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


title: WGBS data of DMS3-ZF line 133

description: Whole genome bisulfite sequencing data of cassava DMS3-ZF line 133.

tag: tissue

value: DMS3-ZF line 133


title: Bone-marrow aspirates, ADT-derived/HTO-derived cDNA 2

value: Bone Marrow

tag: multiplexed

value: Y

value: Total-Seq C ADT Cocktail  with custom U5 snRNP200 antibody and Total-Seq C hashing oligos


title: microRNA counts from gastrocnemius medialis (ENCLB914FLX)

description:
https://www.encodeproject.org/experiments/ENCSR655NLY/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human skeletal muscle tissue
experiment encode accession: ENCSR655NLY
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB914FLX
size range: <30

value: gastrocnemius medialis

value: tissue

value: Muscle - Skeletal

value: 54 year

value: adult

value: Barbara Wold, Caltech

value: ENCBS689LIY at ENCODE; https://www.encodeproject.org/ENCBS689LIY/


title: WGBS data of wild type TME419

description: Whole genome bisulfite sequencing data of cassava wild type TME419.

value: leaf tissue

value: 7-8 weeks

value: Wild type


title: microRNA counts from prostate gland (ENCLB943SVW)

description:
https://www.encodeproject.org/experiments/ENCSR630JWA/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human prostate
experiment encode accession: ENCSR630JWA
assay title: microRNA counts
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB943SVW
size range: <30

source_name: Homo sapiens prostate gland tissue male adult (37 years)

value: prostate gland

value: Prostate

value: 37 year

value: male

value: ENCBS553XGK at ENCODE; https://www.encodeproject.org/ENCBS553XGK/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Bone-marrow aspirates, mRNA-derived cDNA 4

value: Bone Marrow

value: Y

tag: antibodies/tags


title: Bone-marrow aspirates, ADT-derived/HTO-derived cDNA 1

value: Total-Seq C ADT Cocktail  with custom U5 snRNP200 antibody and Total-Seq C hashing oligos


title: NHBE + IFNL3 NHBE_26

city: Munich

first: Anna

last: Erb

address: Biedersteinerstr 29

department: Zentrum für Allergie und Umwelt

country: Germany

institute: Klinikum Rechts der Isar

description:
NHBE + IFNL3
NHBE + IFNL3

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and 20 bit Tiff.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Agilent.SingleColor.28004 microarray, Software GeneSpring 14.5; Threshold: 1.0, Logbase: 2; Normalization: Quantile; Baseline Transformation: None; Filtered on Expression (20.0-100.0); Filtered on Flags (Detected, Not Detected); T test unpaired , P<=:0.05, FC>=1.5

source_name: NHBE

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 25 ng RNA using the One-Color Agilent Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, GER). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: NHBEs were directly transferred into RNAcell protect reagent (Qiagen) and stored at -80°C until RNA extraction. Total RNA was extracted using RNeasy Mini Kit (Cat.-No. 74104, Qiagen, Hilden, Germany) with on-column DNase digestion (Cat.-No. 79254, DNase-Free DNase Set, Qiagen) for avoiding DNA contaminations (Zissler UM, 2016 Mucosal Immunology). RNA quantification was performed by ultraviolet–visible spectrophotometry (Nanodrop Technologies, Wilmington, DE, USA), for assessment of the RNA integrity by the RNA 6000 Nano Chip Kit with the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

tag: donor no.


title: Bone-marrow aspirates, mRNA-derived cDNA 1


title: Tasmanian_devil_H3K4me3_IP

city: Cerdanyola del Valles

first: Lucía

last: Alvarez-Gonzalez

state: Barcelona

address: Campus de la UAB, Bellaterra

department: Dept. Biologia Cel.lular, Fisiologia i Immunologia

country: Spain

institute: Universitat Autonoma de Barcelona

data_processing:
HiC: BBDuk (version 09/2019) was used for quality check and trimming of the raw fastq sequences. HiC data processing was conducted using TADbit
ChIP-seq: Reads were trimmed using Trimmomatic (version 0.39).  Trimmed fastq files were then aligned to the reference genome using bwa-mem (version 0.7.17). Alignments with a MAPQ > 30 were extracted and used as input for MACS2 (version 2.2.7.1).
RNA-seq: BBDuk (version 09/2019) was used for quality check and trimming of the raw. Then, reads were mapped with STAR (version 2.7.10a ) using the end-to-end alignment mode and gene expression quantification was performed with featureCounts.
Assembly: Elephant (this paper); Aardvark (OryAfe1.0_HiC); Tasmanian devil (mSarHar1.11); Tammar wallaby (me-1k)
Supplementary files format and content: HiC: Mapped reads files; ChIP-seq: BedGraph coverage files;RNA-seq: tab-delimited text files include raw counts

organism: Sarcophilus harrisii

source_name: Fibroblasts

growth_protocol: Fibroblasts cell cultures were incubated at 37°C in 10% CO2. A cell fraction of each cell line was kept for immunofluorescence analysis and quality controls (see below) and the rest were fixated with 1% formaldehyde for 10’ at RT for Hi-C and ChIP-seq

extract_protocol:
For HiC:  Fibroblasts were processed following the in situ Hi-C protocol described by Vara et. Al 2019; For CTCF ChIP-seq: Lysates were clarified from Mnase I digested nuclei and CTCF-DNA complexes were isolated with CTCF antibody (Millipore, #07-729); For H3K4me ChIP-seq: Lysates were clarified from Mnase I digested nuclei and H3K4me3-DNA complexes were isolated with H3K4me3 antibody (Abcam, #ab8580); For RNA-seq: RNA was TRIzol (Invitrogen) extracted from Tasmanian devil cultured fibroblasts according to manufactures instructions.
Libraries were prepared for sequencing using standard Illumina protocols
Hi-C
ChIP-seq
RNA-seq

tag: cell type

value: Fibroblasts


title: microRNA counts from prostate gland (ENCLB247MZQ)

description:
https://www.encodeproject.org/experiments/ENCSR630JWA/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human prostate
experiment encode accession: ENCSR630JWA
assay title: microRNA counts
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB247MZQ
size range: <30

value: tissue

tag: description

value: ENCBS886OHA at ENCODE; https://www.encodeproject.org/ENCBS886OHA/


title: RNAseq_Tasmanian_devil


title: NHBE + IFNL1 NHBE_24

description:
NHBE + IFNL1
NHBE + IFNL1

tag: treatment


title: NHBE + IFNL3 NHBE_25

description:
NHBE + IFNL3
NHBE + IFNL3


title: NHBE + IFNL1 NHBE_23

description:
NHBE + IFNL1
NHBE + IFNL1


title: NHBE + IFNL3 NHBE_27

description:
NHBE + IFNL3
NHBE + IFNL3


title: NHBE + IFNL1 NHBE_22

description:
NHBE + IFNL1
NHBE + IFNL1


title: Tasmanian_devil_H3K4me3_Input


title: NHBE + IFNL1 NHBE_21

description:
NHBE + IFNL1
NHBE + IFNL1


title: LNCaP cells with pcDNA3.1 vector rep3

city: Xi'an

first: Shengjia

last: Shi

address: No.169 Changle Road

department: Department of Immunology

institute: Air Force Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38 using Hisat2 software (default)
Reads  Per Kilobase of exon per Megabase of library size (RPKM) were calculated using using featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and evry sample

source_name: human prostate cancer

extract_protocol:
RNA was havested using Trizol reagent.  1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: human prostate cancer

tag: cell line

value: LNCaP

value: prostate cancer cells

value: WT

value: transfected with pcDNA3.1 vector


title: NHBE + IFNg NHBE_19

description:
NHBE + IFNg
NHBE + IFNg

value: IFNg


title: microRNA counts from smooth muscle cell (ENCLB941AUY)

description:
https://www.encodeproject.org/experiments/ENCSR625DUG/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on SESCC human H9 derived smooth muscle
experiment encode accession: ENCSR625DUG
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-01-19
lab: Ali Mortazavi, UCI
library encode accession: ENCLB941AUY
size range: <30

source_name: Homo sapiens smooth muscle in vitro differentiated cells female embryo (5 days) derived from H9

value: smooth muscle cell

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated smooth muscle cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

tag: biosample encode accession

tag: age

value: 5 day

tag: dev stage

value: embryonic

value: female

tag: health state

value: healthy

value: Richard Myers, HAIB

value: ENCBS899TTJ at ENCODE; https://www.encodeproject.org/ENCBS899TTJ/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: Aardvark_CTCF_IP

organism: Orycteropus afer

value: Fibroblasts


title: Bone-marrow aspirates, mRNA-derived cDNA 2

value: Bone Marrow

value: Y


title: LNCaP cells with pcDNA3.1 vector rep2

value: human prostate cancer

value: LNCaP

value: prostate cancer cells


title: microRNA counts from neural progenitor cell (ENCLB864MSF)

description:
https://www.encodeproject.org/experiments/ENCSR624LFP/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human neural progenitor cell
experiment encode accession: ENCSR624LFP
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-01-19
lab: Ali Mortazavi, UCI
library encode accession: ENCLB864MSF
size range: <30

source_name: Homo sapiens neural progenitor in vitro differentiated cells female embryo (5 days) derived from H9

value: neural progenitor cell

value: Frozen or fixed, in vitro differentiated neural progenitor cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

tag: Sex

tag: lab

tag: link

value: ENCBS044KWE at ENCODE; https://www.encodeproject.org/ENCBS044KWE/


title: Aardvark_CTCF_Input


title: LNCaP cells transfected with VIM-AS1 overexpression vector rep3

tag: genotype

value: VIM-AS1 overexpressed


title: microRNA counts from neural progenitor cell (ENCLB927GTU)

description:
https://www.encodeproject.org/experiments/ENCSR624LFP/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human neural progenitor cell
experiment encode accession: ENCSR624LFP
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-01-19
lab: Ali Mortazavi, UCI
library encode accession: ENCLB927GTU
size range: <30

value: in vitro differentiated cells

value: Frozen or fixed, in vitro specified neural progenitor cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: ENCBS018TPT at ENCODE; https://www.encodeproject.org/ENCBS018TPT/


title: NHBE + IFNg NHBE_17

description:
NHBE + IFNg
NHBE + IFNg

value: IFNg


title: microRNA counts from vagina (ENCLB399NPP)

description:
https://www.encodeproject.org/experiments/ENCSR591LEQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human vagina
experiment encode accession: ENCSR591LEQ
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB399NPP
size range: <30

source_name: Homo sapiens vagina tissue female adult (53 years)

value: vagina

value: tissue

value: Vagina 3-2

value: female

value: Barbara Wold, Caltech

value: 53 year

value: adult

value: ENCBS156MDB at ENCODE; https://www.encodeproject.org/ENCBS156MDB/

value: derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: LNCaP cells transfected with VIM-AS1 overexpression vector rep2

value: human prostate cancer

value: LNCaP

value: prostate cancer cells


title: NHBE + IFNg NHBE_20

description:
NHBE + IFNg
NHBE + IFNg


title: microRNA counts from smooth muscle cell (ENCLB239NJU)

description:
https://www.encodeproject.org/experiments/ENCSR625DUG/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on SESCC human H9 derived smooth muscle
experiment encode accession: ENCSR625DUG
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-01-19
lab: Ali Mortazavi, UCI
library encode accession: ENCLB239NJU
size range: <30

value: smooth muscle cell

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated smooth muscle cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: embryonic

value: healthy

value: Richard Myers, HAIB

value: ENCBS780PCJ at ENCODE; https://www.encodeproject.org/ENCBS780PCJ/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: Aardvark_H3K4me3_Input

value: Fibroblasts


title: microRNA counts from vagina (ENCLB946XIP)

description:
https://www.encodeproject.org/experiments/ENCSR591LEQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human vagina
experiment encode accession: ENCSR591LEQ
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB946XIP
size range: <30

value: vagina

value: tissue

value: Vagina 3-1

value: female

value: Barbara Wold, Caltech

value: ENCBS464ZLQ at ENCODE; https://www.encodeproject.org/ENCBS464ZLQ/


title: LNCaP cells with pcDNA3.1 vector rep1

value: human prostate cancer

value: LNCaP

value: WT

value: transfected with pcDNA3.1 vector


title: LNCaP cells transfected with VIM-AS1 overexpression vector rep1

value: prostate cancer cells

value: VIM-AS1 overexpressed


title: microRNA counts from thyroid gland (ENCLB338UEV)

description:
https://www.encodeproject.org/experiments/ENCSR567SVD/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human thyroid gland
experiment encode accession: ENCSR567SVD
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB338UEV
size range: <30

source_name: Homo sapiens thyroid gland tissue male adult (54 years)

value: thyroid gland

value: Thyroid

value: 54 year

value: adult

value: male

value: ENCBS182ITA at ENCODE; https://www.encodeproject.org/ENCBS182ITA/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: TL-Om1, Mock, Replicate3

city: Farmington

first: Yuqi

last: Zhao

state: CT

address: 273 Main Street A4

institute: City Of Hope

data_processing:
Raw sequencing reads were filtered using the fastp (https://github.com/OpenGene/fastp) and aligned against a reference genome with HTLV sequence in chromosome 1 into the hg38 genome using HISAT2 V2.1.0 aligner with its very-sensitive default parameters.
Aligned reads with a mapping quality less than 20 along with PCR duplicates were filtered out using samtools v1.6.
Detection of open chromatin areas was performed with the MACS2 v2.2.5 peak calling tool using the paired-end alignment information setup (–BAMPE parameter), after which the peaks detected within the promoter regions of protein coding genes defined as 3 kb upstream from the Transcription Start Site (TSS) were selected for analysis.
The peaks are annotated using ChIPseeker (https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html) and UCSC genome hg38 with default settings. The pathway enrichments were done using ReactomePA package (https://bioconductor.org/packages/release/bioc/html/ReactomePA.html), including 3 canonical pathway databases, KEGG (https://www.genome.jp/kegg/), Reactome (https://reactome.org/), and Biocarta (https://maayanlab.cloud/Harmonizome/resource/Biocarta).
The R/Bioconductor package csaw was used to detect differential accessibility among groups.
Assembly: hg38
Supplementary files format and content: narrowPeak

growth_protocol: RPMI, 10% fetal bovine serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
A previously published OMNI ATAC-Seq protocol (Corces et al, 2017) was used for cell lysis, tagmentation, and DNA purification.
The Tn5 treated DNA was amplified with 10 cycles of PCR in 50 μl reaction volumes. 1.8X AmpurXP beads purification was used for the PCR product clean-up. The libraries were validated with Agilent Bioanalyzer DNA High Sensitivity Kit, and quantified with qPCR. ATAC-seq libraries were sequenced on Illumina NovaSeq6000 with S4 Reagent v1.5 kit (Illumina, Cat 20028312) at Tgen with the sequencing length of 2x101. Real-time analysis (RTA) 3.4.4 software was used to process the image analysis.

treatment_protocol: Electroperated with Neon system with mRNA

value: ATL

value: cell line

value: TL-Om1 Mock


title: PBMC

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

description:
erythrocytes were removed with ammonium-chlorate-potassium lysis buffer
Sample_5619-RG-14
Peripheral_Blood.RDS

library_source: transcriptomic single cell

data_processing:
NovaSeq control software 1.6.0, RTA v3.4.4
Cellranger version 3.1.0 used with mm10 genome to align and count reads and generate filtered_feature_bc_matrix with default settings
filtered_feature_bc_matrix imported with R 4.1.2 and Seurat 4.0.5; cells with more than 7500 features, fewer than 500 features, more than 15% mitochondrial removed
Seurat SCTransform + CCA used to normalize and integrate datasets
PCA dimension reduction
UMAP visualization
Assembly: mm10
Supplementary files format and content: Seurat Objects in R data format. Read into R using the command readRDS()

organism: Mus musculus

source_name: Peripheral blood mononuclear cells

extract_protocol:
0.5 ml of cardiac blood was collected from naive mice and lysed in Ammonium-Chloride-Potassium (ACK) buffer.
The Chromium Next GEM Single Cell 3’ Reagent kit v3.1 (Dual Index) was used. Barcoding and library preparation was performed following the manufacturer’s protocols. Briefly, to generate single-cell gel-bead-in-emulsion (GEMs) solution, approximately 15,000 cells, in a final volume of 43 µl, were loaded on a Next GEM Chip G (10x Genomics) and processed with the 10x Genomics Chromium Controller

tag: strain

tag: sampletype

value: PBMC collected by cardiac puncture of naïve mice


title: PBMC_2

description:
erythrocytes were removed with ammonium-chlorate-potassium lysis buffer
Peripheral_Blood.RDS
Sample_6421-RG-03


title: Aardvark_H3K4me3_IP

value: Fibroblasts


title: microRNA counts from thyroid gland (ENCLB957TEU)

description:
https://www.encodeproject.org/experiments/ENCSR567SVD/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human thyroid gland
experiment encode accession: ENCSR567SVD
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB957TEU
size range: <30

value: tissue

value: Barbara Wold, Caltech

value: ENCBS504VQX at ENCODE; https://www.encodeproject.org/ENCBS504VQX/


title: TL-Om1, Mock, Replicate2

tag: tissue


title: microRNA counts from body of pancreas (ENCLB184WZO)

description:
https://www.encodeproject.org/experiments/ENCSR538MBL/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human pancreas
experiment encode accession: ENCSR538MBL
assay title: microRNA counts
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB184WZO
size range: <30

source_name: Homo sapiens body of pancreas tissue male adult (37 years)

value: body of pancreas

value: Pancreas

value: 37 year

value: ENCBS953BPT at ENCODE; https://www.encodeproject.org/ENCBS953BPT/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: TL-Om1, Mock, Replicate1


title: Pooled Input

city: New Brunswick

first: Daniel

last: Herranz

state: New Jersey

address: 195 Little Albany Street

institute: Rutgers Cancer Institute of New Jersey

data_processing:
Basecalls were performed using bcl2fastq v2.20 for Novaseq output.
ChIP-seq reads were aligned to the UCSC mm10 genome using bwa version 0.7.12. Only uniquely mapping reads with at most two mismatches were retained. n addition, duplicate reads (“PCR duplicates”) are removed
The tags (5' ends of aligned reads) were extended in silico (using Active Motif software) at their 3 ́- ends to a length of 200 bp, which corresponds to the average fragment length in the size-selected library.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using wigToBigWig (v4).
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Spleen

growth_protocol: Sirt1 conditional knockout T-ALLs were injected intravenously in sub-lethally Irradiated mice.

extract_protocol:
Leukemic spleens were removed, single-cell suspensions were obtained by pressing them through a 40mm filter, and subsequently subjected to red blood cell lysis. Pellets of 25 million cells were formaldehyde-crosslinked and frozen prior to shipment to Active Motif.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were trated with vehicle only (control: corn oil, C8267, Sigma-Aldrich) or tamoxifen (T5648, Sigma-Aldrich; 3 mg per mouse in corn oil) administered by intraperitoneal injection.

value: Spleen

value: delta_E-NOTCH1-induced Sirt1 conditional knockout leukemia

value: Leukemic splenocytes

tag: chip antibody

value: none (input)


title: NHBE + IFNb NHBE_16

description:
NHBE + IFNb
NHBE + IFNb

value: IFNb

tag: donor no.


title: NHBE + IFNb NHBE_15

description:
NHBE + IFNb
NHBE + IFNb


title: TL-Om1, ZFP-HIV-ZFP362, Replicate3

value: ATL

tag: cell type

value: cell line

value: TL-Om1 treated withZFP-HIV-ZFP362


title: TMX8, H4K12Ac

value: Active Motif #39165


title: NHBE + IFNg NHBE_18

description:
NHBE + IFNg
NHBE + IFNg

value: IFNg


title: microRNA counts from gastrocnemius medialis (ENCLB784TIW)

description:
https://www.encodeproject.org/experiments/ENCSR505IZZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human skeletal muscle tissue
experiment encode accession: ENCSR505IZZ
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB784TIW
size range: <30

source_name: Homo sapiens gastrocnemius medialis tissue male adult (37 years)

value: gastrocnemius medialis

value: tissue

tag: description

value: Muscle - Skeletal

value: adult

value: male

value: Barbara Wold, Caltech

value: ENCBS661PVF at ENCODE; https://www.encodeproject.org/ENCBS661PVF/


title: Veh3, H4K12Ac

value: Spleen


title: NHBE+IFNa NHBE_13

description:
NHBE+IFNa
NHBE+IFNa

tag: treatment

value: IFNa


title: NHBE + IFNb NHBE_14

description:
NHBE + IFNb
NHBE + IFNb


title: NHBE+IFNa NHBE_12

description:
NHBE+IFNa
NHBE+IFNa


title: NHBE+IFNa NHBE_11

description:
NHBE+IFNa
NHBE+IFNa


title: NHBE+IFNa NHBE_10

description:
NHBE+IFNa
NHBE+IFNa


title: NHBE+IFNa NHBE_09

description:
NHBE+IFNa
NHBE+IFNa


title: TL-Om1, ZFP-HIV-ZFP362, Replicate2

tag: cell line


title: microRNA counts from gastrocnemius medialis (ENCLB943BEK)

description:
https://www.encodeproject.org/experiments/ENCSR505IZZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human skeletal muscle tissue
experiment encode accession: ENCSR505IZZ
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB943BEK
size range: <30

tag: biosample encode accession

value: 37 year

value: ENCBS884FWU at ENCODE; https://www.encodeproject.org/ENCBS884FWU/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: TL-Om1, ZFP-HIV-ZFP362, Replicate1

value: ATL


title: PML KO-H3K27ac rep2

city: Beijing

first: Hongyao

last: Sun

address: Tsinghua street

institute: Tsinghua university

data_processing:
ChIP-seq reads were quality checked with FastQC v0.11.5 and mapped to the mouse (mm10) genome with Bowtie2 v2.3.3 using standard settings for paired reads. The .sam and .bam files were manipulate with samtools v1.9. Peaks were called using macs2 2.1.4 with default settings. The visualizations of detected peaks were performed using deeptools 3.4.3, and downstream analyses were performed using DiffBind 3.2.4.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: Mouse ESCs E14Tg2a.IV, CCE lines were cultured and maintained in feeder free leukemia inhibitory factor (LIF) -supplemented medium (Keller, 1995), which 15% FBS, 100 U of Penicillin-Streptomycin, β-me, NEAA, and sodium pyruvate were also added in.Media was changed daily.

extract_protocol:
For GFP-TRIM33-chip experiment, GFP-TRIM33 mESCs were cross-linked with 1% formaldehyde at 37 °C for 10 min and quenched with 0.125 M glycine for 5 min at room temperature. Then cells were scraped and GFP-trap-beads assisted ChIP was performed and DNA were extracted using a ChIP assay kit (Millipore) as described. For SMAD2/3, PML or H3K27ac chip, 20 million mESCs were collected for cut&tag experiment followed manuals (Yeason) using anti-SMAD2/3, PML or H3K27ac antibody  to got enriched DNA.
For library construction and sequencing, ChIP DNA samples were quantified and quality assessed by Qubit 2.0 and Agilent 2100. DNA fragments range from 200-600bp were selected constructed for ChIP-Seq library with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions. After scraped from plate, embryonic stem cells were washed with PBS and incubated in lysis buffer.

treatment_protocol: mESCs with treatment of activin A (50ng/ml) or SB431542 (10μM) for 2 hr

value: mouse embryonic stem cell

value: untreated


title: microRNA counts from testis (ENCLB219QLL)

description:
https://www.encodeproject.org/experiments/ENCSR494FIS/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human testis
experiment encode accession: ENCSR494FIS
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB219QLL
size range: <30

source_name: Homo sapiens testis tissue male adult (54 years)

value: testis

value: Testis 2-2

tag: age

value: 54 year

value: ENCBS238DLV at ENCODE; https://www.encodeproject.org/ENCBS238DLV/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: PML KO-H3K27ac rep1


title: TL-Om1, ZFP5-meCP2, Replicate3

value: cell line

value: TL-Om1 treated with ZFP5-meCP2


title: microRNA counts from uterus (ENCLB623BTJ)

description:
https://www.encodeproject.org/experiments/ENCSR486QHW/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human uterus
experiment encode accession: ENCSR486QHW
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB623BTJ
size range: <30

source_name: Homo sapiens uterus tissue female adult (51 year)

value: uterus

value: tissue

value: Uterus

value: 51 year

tag: dev stage

value: adult

value: female

value: Barbara Wold, Caltech

value: ENCBS133MAA at ENCODE; https://www.encodeproject.org/ENCBS133MAA/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: microRNA counts from testis (ENCLB011SBP)

description:
https://www.encodeproject.org/experiments/ENCSR494FIS/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human testis
experiment encode accession: ENCSR494FIS
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB011SBP
size range: <30

value: Testis 2-1

value: male

value: ENCBS288YWQ at ENCODE; https://www.encodeproject.org/ENCBS288YWQ/


title: NHBE+IFNa NHBE_08

description:
NHBE+IFNa
NHBE+IFNa

value: IFNa


title: PML WT-H3K27ac rep2

value: mouse embryonic stem cell

value: untreated


title: TL-Om1, ZFP5-meCP2, Replicate2

value: ATL

value: cell line


title: NHBE+IFNa NHBE_07

description:
NHBE+IFNa
NHBE+IFNa


title: microRNA counts from uterus (ENCLB370ZYO)

description:
https://www.encodeproject.org/experiments/ENCSR486QHW/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human uterus
experiment encode accession: ENCSR486QHW
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB370ZYO
size range: <30

value: uterus

value: ENCBS171SNZ at ENCODE; https://www.encodeproject.org/ENCBS171SNZ/


title: PML WT-H3K27ac rep1


title: TL-Om1, ZFP5-meCP2, Replicate1

value: TL-Om1 treated with ZFP5-meCP2


title: NHBE Medium NHBE_06

description:
NHBE Medium
NHBE Medium

value: no


title: PML KO-SMAD2/3 rep2

value: SMAD2/3(CST, D7G7)


title: TL-Om1, ZFP5, Replicate3

value: TL-Om1 treated with ZFP5


title: microRNA counts from hepatocyte (ENCLB880LRI)

description:
https://www.encodeproject.org/experiments/ENCSR448MNV/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA array on human hepatocyte derived from H9
experiment encode accession: ENCSR448MNV
assay title: microRNA counts
assembly: GRCh38
encode release date: 2017-02-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB880LRI
size range: <30

source_name: Homo sapiens hepatocyte in vitro differentiated cells female embryo (5 days) derived from H9

value: hepatocyte

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated hepatocyte-like cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: female

tag: health state

value: healthy

value: Richard Myers, HAIB

value: ENCBS077RUJ at ENCODE; https://www.encodeproject.org/ENCBS077RUJ/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: PML KO-SMAD2/3 rep1

value: mouse embryonic stem cell

value: untreated


title: microRNA counts from hepatocyte (ENCLB723MGC)

description:
https://www.encodeproject.org/experiments/ENCSR448MNV/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA array on human hepatocyte derived from H9
experiment encode accession: ENCSR448MNV
assay title: microRNA counts
assembly: GRCh38
encode release date: 2017-02-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB723MGC
size range: <30

tag: Sex

value: ENCBS520VFV at ENCODE; https://www.encodeproject.org/ENCBS520VFV/


title: NHBE Medium NHBE_04

description:
NHBE Medium
NHBE Medium


title: NHBE Medium NHBE_03

description:
NHBE Medium
NHBE Medium


title: NHBE Medium NHBE_05

description:
NHBE Medium
NHBE Medium


title: NHBE Medium NHBE_02

description:
NHBE Medium
NHBE Medium


title: PML WT-SMAD2/3 rep2


title: microRNA counts from heart left ventricle (ENCLB108CMO)

description:
https://www.encodeproject.org/experiments/ENCSR425ZMS/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human heart left ventricle
experiment encode accession: ENCSR425ZMS
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB108CMO
size range: <30

source_name: Homo sapiens heart left ventricle tissue female adult (53 years)

value: heart left ventricle

value: tissue

value: Heart - Left Ventricle

value: 53 year

value: adult

tag: lab

value: Barbara Wold, Caltech

value: ENCBS504IQD at ENCODE; https://www.encodeproject.org/ENCBS504IQD/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: TL-Om1, ZFP5, Replicate1

value: ATL

value: cell line

value: TL-Om1 treated with ZFP5


title: microRNA counts from heart left ventricle (ENCLB870WXC)

description:
https://www.encodeproject.org/experiments/ENCSR425ZMS/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human heart left ventricle
experiment encode accession: ENCSR425ZMS
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB870WXC
size range: <30

value: female

tag: link

value: ENCBS156VIV at ENCODE; https://www.encodeproject.org/ENCBS156VIV/


title: SCAF8 EMCAP rep3

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

description: small RNAPII protected RNAs

data_processing:
Illumina bcl2fastq v1.8 software used for basecalling.
Reads were adapter trimmed using TrimGalore v0.4.4 (Martin, 2011). Reads < 10bp in length and those with a maximum error rate > 0.05 were discarded.
HISAT2 v2.0.4 was used to align remaining reads against the GRCh38 genome build in a strand-specific manner, allowing for at most 5 distinct primary alignments for each read (Kim et al., 2015).
Reads were sorted and indexed using SAMtools and multi-mapping reads were removed.
Picard were used to remove duplicate reads and those not mapping in proper pairs (for the paired end mNET-seq data).
The 3' ends of reads were extracted from the BAM files and used to generate strand-specific bigwig files at single bp resolution using bedtools and bedGraphToBigWig.
Assembly: GRCh38
Supplementary files format and content: Strand-specific (i.e. forward and reverse), single-nucleotide resolution bigwig files representing the combined coverage of the 3' most bp of each read.

source_name: HEK293 Flp-In TREX

growth_protocol: DMEM (Thermo Fisher Scientific, 11965118) supplemented with 10% v/v FBS (Clontech, 631106), 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine, 100 μg/ml hygromycin, 15 μg/ml blasticidin.

extract_protocol:
Chromatin extracts were harvested as previously described (Gregersen et al. 2019 Cell) and used for IP of RNAPII (4H8 antibody coupled to ProteinG dynabead) or double FLAG IP (M2 agarose beads followed by 3x FLAG peptide elution for SCAF4 and SCAF8 samples) followed by a RNAPII 4H8 IP, RNA was extracted directed from beads using Zymo Quick-RNA microPrep.
NEBNext small RNA library prep protocol followed by gel purification of 140-230bp PCR products

treatment_protocol: FLAG4-SCAF4 or FLAG-SCAF8 expression was induced by overnight treatment with 100ng/uL doxycycline overnight

value: HEK293 Flp-In TREX

value: Human embryonic kidney cell line

value: 100ng/uL doxycycline ON

tag: expression

value: stably expressing FLAG-tagged SCAF8 (N-terminal) from the Flp-In locus

tag: ip reagent

value: anti-FLAG (M2 agarose beads), FLAG peptide elution followed by anti-RNAPII (4H8) coupled to Protein G dynabeads


title: PML WT-SMAD2/3 rep1

value: mouse embryonic stem cell

tag: strain

value: SMAD2/3(CST, D7G7)

value: untreated


title: SCAF4 EMCAP rep3

description: small RNAPII protected RNAs

value: stably expressing FLAG-tagged SCAF4 (C-terminal) from the Flp-In locus


title: Diff-PML rep2


title: Diff-PML rep1


title: H2BK15ac_rep2

city: Warszawa

middle: Maria

last: Stroynowska-Czerwińska

address: Trojdena 4

department: Laboratory of Structural Biology

country: Poland

institute: International Institute of Molecular and Cell Biology

data_processing:
Trimming was perfromed using TrimGalore! And FastQ Trimmer on Galaxy server.
CUT&RUN reads were aligned to hg38 genome using Bowtie2 with default parameters on Galaxy server.
Aligned reads were filtered out from blacklist reads, reads <20MAPQ and deduplicated
For peak calling MACS2 on Galaxy server was used.
Assembly: hg38
Supplementary files format and content: bigwig files were generated on filtered aligned reads
Supplementary files format and content: bed files were generated with MACS2
Library strategy: CUT&RUN

source_name: Cervix cancer cells

growth_protocol: HeLa S3 cells and HeLa S3-derived stable cell lines were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Biowest) supplemented with 10% fetal bovine serum (FBS, Biowest) and penicillin-streptomycin solution (Biowest) at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
DNA was extracted from chromatin-DNA complexes released to supernatant by Mnase activity in HeLa S3 cells
Libraries were prepared using NEBNext Ultra II DNA Library Prep kit (NEB #E7103), according to protocol of Nan Liu, published on protocols.io dx.doi.org/10.17504/protocols.io.bagaibse. The libraries were paired-end sequenced on Illumina NovaSeq 6000.

value: HeLa S3 cell line

tag: experiment

value: CUT&RUN

tag: c&r antibody

value: anti-H2BK15ac (Diagenode, #C15410220)

tag: control sample


title: H3K56ac_rep2

tag: cell type

value: anti-H3K56ac (Diagenode, #C15410213)


title: microRNA counts from adrenal gland (ENCLB258WUR)

description:
https://www.encodeproject.org/experiments/ENCSR381ADE/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human adrenal gland
experiment encode accession: ENCSR381ADE
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB258WUR
size range: <30

source_name: Homo sapiens adrenal gland tissue male adult (37 years)

value: adrenal gland

value: tissue

tag: description

value: Adrenal Gland

value: male

value: Barbara Wold, Caltech

value: 37 year

value: adult

value: ENCBS156HYA at ENCODE; https://www.encodeproject.org/ENCBS156HYA/

value: derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: RNAPII EMCAP rep3

description: small RNAPII protected RNAs

value: female

value: HEK293 Flp-In TREX

value: Human embryonic kidney cell line

tag: treatment

value: control

value: anti-RNAPII (4H8) coupled to Protein G dynabeads


title: SCAF8 EMCAP rep2

description: small RNAPII protected RNAs

tag: cell line

value: 100ng/uL doxycycline ON

value: stably expressing FLAG-tagged SCAF8 (N-terminal) from the Flp-In locus

value: anti-FLAG (M2 agarose beads), FLAG peptide elution followed by anti-RNAPII (4H8) coupled to Protein G dynabeads


title: H2BK15ac_rep1

value: HeLa S3 cell line

value: CUT&RUN

value: anti-H2BK15ac (Diagenode, #C15410220)


title: SCAF4 EMCAP rep2

description: small RNAPII protected RNAs

value: stably expressing FLAG-tagged SCAF4 (C-terminal) from the Flp-In locus


title: microRNA counts from right atrium auricular region (ENCLB178UFL)

description:
https://www.encodeproject.org/experiments/ENCSR326JQW/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human right cardiac atrium
experiment encode accession: ENCSR326JQW
assay title: microRNA counts
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB178UFL
size range: <30

source_name: Homo sapiens female adult (53 years) right atrium auricular region tissue

value: right atrium auricular region

value: tissue

value: Heart - Atrial Appendage

tag: biosample encode accession

tag: organism

value: Homo sapiens

value: 53 year

value: Barbara Wold, Caltech

tag: source

value: Kristin Ardlie

value: ENCBS903KZP at ENCODE; https://www.encodeproject.org/ENCBS903KZP/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: microRNA counts from adrenal gland (ENCLB072EOZ)

description:
https://www.encodeproject.org/experiments/ENCSR381ADE/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human adrenal gland
experiment encode accession: ENCSR381ADE
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB072EOZ
size range: <30

value: adrenal gland

value: Adrenal Gland

value: male

tag: age

value: 37 year

tag: dev stage

value: adult

value: ENCBS636AEJ at ENCODE; https://www.encodeproject.org/ENCBS636AEJ/

value: derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: TL-Om1, ZFP5, Replicate2

tag: tissue

value: ATL

value: cell line

value: TL-Om1 treated with ZFP5


title: H3K56ac_rep1

value: HeLa S3 cell line

value: CUT&RUN

value: anti-H3K56ac (Diagenode, #C15410213)


title: RNAPII EMCAP rep2

description: small RNAPII protected RNAs

tag: Sex

value: female

value: HEK293 Flp-In TREX

value: Human embryonic kidney cell line

value: control

value: anti-RNAPII (4H8) coupled to Protein G dynabeads


title: ES AS-PML rep2

value: mouse embryonic stem cell

tag: chip antibody

value: sodium arsenite treated


title: microRNA counts from right atrium auricular region (ENCLB669LMV)

description:
https://www.encodeproject.org/experiments/ENCSR258UGT/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human right cardiac atrium
experiment encode accession: ENCSR258UGT
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB669LMV
size range: <30

source_name: Homo sapiens right atrium auricular region tissue female adult (51 year)

value: right atrium auricular region

value: tissue

value: Heart - Atrial Appendage

value: 51 year

tag: lab

value: Barbara Wold, Caltech

tag: link

value: ENCBS827YEF at ENCODE; https://www.encodeproject.org/ENCBS827YEF/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: H3K27ac_rep2

value: HeLa S3 cell line

tag: experiment

value: anti-H3K27ac (Diagenode, #C15410196)


title: ES N-PML rep2

tag: strain

value: untreated


title: SCAF8 EMCAP rep1

description: small RNAPII protected RNAs

value: female

value: 100ng/uL doxycycline ON

tag: expression

value: stably expressing FLAG-tagged SCAF8 (N-terminal) from the Flp-In locus

tag: ip reagent

value: anti-FLAG (M2 agarose beads), FLAG peptide elution followed by anti-RNAPII (4H8) coupled to Protein G dynabeads


title: ES N-PML rep1

tag: cell type


title: microRNA counts from right atrium auricular region (ENCLB406MXB)

description:
https://www.encodeproject.org/experiments/ENCSR258UGT/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human right cardiac atrium
experiment encode accession: ENCSR258UGT
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB406MXB
size range: <30

tag: description

value: adult

value: ENCBS168GTY at ENCODE; https://www.encodeproject.org/ENCBS168GTY/


title: H3K27ac_rep1

value: CUT&RUN

tag: c&r antibody

tag: control sample


title: microRNA counts from prostate gland (ENCLB590ZWB)

description:
https://www.encodeproject.org/experiments/ENCSR227VCK/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human prostate
experiment encode accession: ENCSR227VCK
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB590ZWB
size range: <30

source_name: Homo sapiens prostate gland tissue male adult (54 years)

value: prostate gland

value: Prostate

tag: biosample encode accession

value: 54 year

value: male

value: ENCBS845PWD at ENCODE; https://www.encodeproject.org/ENCBS845PWD/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: H3K23ac_rep2

value: anti-H3K23ac (Diagenode, #C15410344)


title: NHBE Medium NHBE_01

description:
NHBE Medium
NHBE Medium

source_name: NHBE

tag: treatment

value: no

tag: donor no.


title: ES AS SB-TRIM33 input

value: mouse embryonic stem cell

value: GFP-trap

value: SB431542 treated

tag: cell line


title: RNAPII EMCAP rep1

description: small RNAPII protected RNAs

value: female

value: HEK293 Flp-In TREX

value: Human embryonic kidney cell line

value: control

value: anti-RNAPII (4H8) coupled to Protein G dynabeads


title: H3K23ac_rep1

value: HeLa S3 cell line

value: CUT&RUN


title: microRNA counts from prostate gland (ENCLB976LQC)

description:
https://www.encodeproject.org/experiments/ENCSR227VCK/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human prostate
experiment encode accession: ENCSR227VCK
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB976LQC
size range: <30

value: prostate gland

value: tissue

value: Prostate

tag: dev stage

value: adult

tag: age

value: Barbara Wold, Caltech

value: ENCBS940OCV at ENCODE; https://www.encodeproject.org/ENCBS940OCV/


title: ES AS AC-TRIM33 input

tag: chip antibody

value: activin A treated


title: ES N SB-TRIM33 input

value: mouse embryonic stem cell


title: H3K9ac_rep2

value: anti-H3K9ac (Diagenode, #C15410004)


title: H3K9ac_rep1


title: ES AS-PML rep1

value: sodium arsenite treated


title: microRNA counts from uterus (ENCLB928FPB)

description:
https://www.encodeproject.org/experiments/ENCSR101DVP/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human uterus
experiment encode accession: ENCSR101DVP
assay title: microRNA counts
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB928FPB
size range: <30

source_name: Homo sapiens uterus tissue female adult (53 years)

value: uterus

value: Uterus

value: 53 year

tag: Sex

value: female

tag: lab

value: ENCBS057LPE at ENCODE; https://www.encodeproject.org/ENCBS057LPE/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: microRNA counts from uterus (ENCLB614GFV)

description:
https://www.encodeproject.org/experiments/ENCSR101DVP/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human uterus
experiment encode accession: ENCSR101DVP
assay title: microRNA counts
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB614GFV
size range: <30

tag: link

value: ENCBS084QBB at ENCODE; https://www.encodeproject.org/ENCBS084QBB/


title: ES N AC-TRIM33 input

tag: strain

value: GFP-trap


title: IgG7

value: HeLa S3 cell line

tag: experiment

value: CUT&RUN

value: normal rabbit IgG (Sigma, #I8140)


title: ES AS SB-TRIM33 rep2

value: SB431542 treated


title: microRNA counts from vagina (ENCLB337YGP)

description:
https://www.encodeproject.org/experiments/ENCSR065OIA/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human vagina
experiment encode accession: ENCSR065OIA
assay title: microRNA counts
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB337YGP
size range: <30

source_name: Homo sapiens vagina tissue female adult (51 year)

value: vagina

value: tissue

value: Vagina 4-1

value: Barbara Wold, Caltech

value: 51 year

value: adult

value: ENCBS402XXG at ENCODE; https://www.encodeproject.org/ENCBS402XXG/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Lyz2Cre Control 3

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to reference genome using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Assembly: mm10
Supplementary files format and content: matrix.txt (tab delimited file containing FPKM values for each gene/sample)

source_name: BMDMs

extract_protocol:
Total RNA was isolated from indicated samples using the High Pure RNA Isolation Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: BMDMs

value: Macrophages

tag: developmental stage

value: Postnatal week 10


title: IgG6

tag: cell type


title: Lyz2Cre Cited2 Fl Fl Control 1


title: SCAF4 EMCAP rep1

description: small RNAPII protected RNAs

value: female

value: HEK293 Flp-In TREX

value: Human embryonic kidney cell line

value: 100ng/uL doxycycline ON

tag: expression

value: stably expressing FLAG-tagged SCAF4 (C-terminal) from the Flp-In locus

tag: ip reagent

value: anti-FLAG (M2 agarose beads), FLAG peptide elution followed by anti-RNAPII (4H8) coupled to Protein G dynabeads


title: ES AS SB-TRIM33 rep1

value: mouse embryonic stem cell

value: GFP-trap

value: SB431542 treated


title: Lyz2Cre Control 2


title: Lyz2Cre Cited2 Fl Fl Control 3


title: 2D46mut

value: stable HeLa S3 cell line expressing NLS-EYFP-2D46mut

value: CUT&RUN

tag: c&r antibody

value: anti-GFP-Mnase (Marc Timmers)

tag: control sample


title: Lyz2Cre Cited2 Fl Fl Control 2


title: microRNA counts from lower leg skin (ENCLB811GWZ)

description:
https://www.encodeproject.org/experiments/ENCSR021JTM/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human lower leg skin
experiment encode accession: ENCSR021JTM
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB811GWZ
size range: <30

source_name: Homo sapiens lower leg skin tissue male adult (37 years)

value: lower leg skin

value: tissue

tag: description

value: Skin - Sun Exposed (Lower leg)

tag: biosample encode accession

value: 37 year

value: adult

value: male

value: Barbara Wold, Caltech

value: ENCBS617UGR at ENCODE; https://www.encodeproject.org/ENCBS617UGR/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: ES AS AC-TRIM33 rep2

tag: treatment

value: activin A treated

tag: cell line


title: 2A13mut

value: stable HeLa S3 cell line expressing NLS-EYFP-2A13mut


title: Lyz2Cre Control 1

value: BMDMs

value: Macrophages

value: Postnatal week 10


title: microRNA counts from lower leg skin (ENCLB107EEX)

description:
https://www.encodeproject.org/experiments/ENCSR021JTM/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human lower leg skin
experiment encode accession: ENCSR021JTM
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB107EEX
size range: <30

tag: dev stage

tag: age

value: ENCBS926XRV at ENCODE; https://www.encodeproject.org/ENCBS926XRV/


title: ES AS AC-TRIM33 rep1

value: mouse embryonic stem cell

tag: chip antibody

value: GFP-trap


title: Maize ChIP-Seq GLK_TF172 Zm00001d039260 replicate 2

organism: Zea mays

source_name: Leaf

value: Leaf

tag: replicate

value: replicate 2

tag: genotype

value: Dynabeads™ MyOne™ Streptavidin T1


title: ES N SB-TRIM33 rep2

tag: strain

value: SB431542 treated


title: PT+circSCMH1 IP

city: Nanjing

first: bin

last: li

address: No.87 of Dingjiaqiao

institute: Southeast University

data_processing:
Off-Line Basecaller software (OLB V1.8) software used for basecalling.
Sequencing quality was examined by FastQC software and trimmed reads (pass Illumina quality filter,trimmed adaptor bases by cutadapt) were aligned to genome sequences from Ensembl using HISAT2 software (v2.1.0).
Aligned reads were used for peak calling by exomePeak, statistically significant MeRIP enriched regions (peaks) were also identified for each compare by exomePeak.
The MeRIP enriched regions (peaks)were annotated by the overlapped gene using the newest Ensembl database.
Then the statistic of peak in each transcript region was done.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: The read Numbers at each position of chromosomes in the comparison results were calculated, and the results were saved as UCSCbedGraph format after being standardized（RPM）

source_name: peri-infarct cortex

growth_protocol: C57BL/6J mice were subjected to PT stroke model surgery.

extract_protocol:
Total RNA samples are qualified by agarose gel electrophoresis and quantified using Nanodrop
mRNA was isolated and then fragmented to 100-nucleotide-long fragments. m6A methylated mRNAs were enriched with anti-N6-methyadenosine(m6A) antibody. We use commercial kit for RNA-seq library preparation of m6A mRNA and input samples.
Completed libraries were qualified and then sequenced on Hiseq 4000 platform.

treatment_protocol: The circSCMH1 by extracellular vesicle was delivered to brain at day 1 after PT stroke

tag: tissue

value: brain

tag: time point

value: post stroke day 14

tag: genotype/variation

tag: antibody

value: anti-N6-methyadenosine(m6A) antibody


title: ES N SB-TRIM33 rep1

tag: cell type


title: HeLa-3

value: HeLa S3 cell line

tag: experiment

value: CUT&RUN

tag: c&r antibody

value: anti-GFP-Mnase (Marc Timmers)


title: PT+circCon IP

value: EV-vector


title: Maize ChIP-Seq GLK_TF172 Zm00001d039260 replicate 1

value: replicate 1


title: ES N AC-TRIM33 rep2

value: activin A treated


title: 2DS

value: stable HeLa S3 cell line expressing NLS-EYFP-2DS

tag: control sample


title: Maize ChIP-Seq GLK_TF5 Zm00001d044785 replicate 2


title: microRNA counts from vagina (ENCLB889ZRH)

description:
https://www.encodeproject.org/experiments/ENCSR065OIA/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human vagina
experiment encode accession: ENCSR065OIA
assay title: microRNA counts
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB889ZRH
size range: <30

value: vagina

value: tissue

tag: description

value: Vagina 4-2

tag: biosample encode accession

tag: Sex

value: female

tag: lab

value: Barbara Wold, Caltech

value: 51 year

value: adult

tag: link

value: ENCBS738IGW at ENCODE; https://www.encodeproject.org/ENCBS738IGW/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Maize ChIP-Seq GLK_TF5 Zm00001d044785 replicate 1

value: Leaf

tag: chip antibody

value: Dynabeads™ MyOne™ Streptavidin T1


title: sham IP

value: brain

value: post stroke day 14

value: sham

value: anti-N6-methyadenosine(m6A) antibody


title: 2CS

value: stable HeLa S3 cell line expressing NLS-EYFP-2CS

value: CUT&RUN

value: anti-GFP-Mnase (Marc Timmers)


title: PT+circCon input

value: EV-vector


title: PML KO SB-TRIM33 input

value: mouse embryonic stem cell

value: GFP-trap

tag: treatment

value: SB431542 treated

tag: cell line


title: 2D2P

value: stable HeLa S3 cell line expressing NLS-EYFP-2D2P


title: ES N AC-TRIM33 rep1

tag: strain

value: activin A treated


title: Hippocampus, Slm2 KO, size‐matched input, rep2

city: Basel

first: Peter

last: Scheiffele

state: Basel-Stadt

address: Spitalstrasse 41

country: Switzerland

institute: University of Basel

description: The SLM2 KO eCLIP experiment was used as a negative control, those raw fastq files were included in the GEO submission for the sake of completeness.  No conclusions were made from those samples, and there are no processed tables with eCLIP peaks for that condition.

data_processing:
Only read2 were used for analysis.
For adapter trimming and low quality reads elimination, we used cutadapt 3.4 (-e 0.1 -O 1  --quality-cutoff 6 -m 18 -a AATAGCANNNNNAGATCGGAAGAGC -a ATATAGGNNNNNAGATCGGAAGAGC).
Trimmed and filtered reads were aligned to mm10 genome using STAR 2.7.9 (--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 -- outFilterScoreMin 10).
Aligned reads were deduplicated using dedup from UMI-tools 1.1.1
Peaks were called from aligned and deduplicated reads using clipper3.
Peaks were input-normalized and compressed using scripts from https://github.com/YeoLab/eclip
Peaks from replicates were merged using IDR software (https://github.com/nboley/idr), and further filtered with thresholds -Log10(IDR) >= 2 and Log2FC >= 2.
Assembly: mm10
Supplementary files format and content: Processed data files are in ENCODE broadPeak (http://www.genome.ucsc.edu/FAQ/FAQformat.html#format13).

source_name: Hippocampus

growth_protocol: Whole brain or hippocampus were obtained from 30 days old mice.

extract_protocol:
The CLIP experiments were performed according to the eCLIP protocol from Nostrand et al. (Van Nostrand et al., 2016) with some modifications. After IP, beads were washed 2x with the high salt wash buffer (50mM Tris-HCl pH7.5, 1M NaCl, 1mM EDTA, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate), 2x CLIP-lysis buffer, 2x with low salt wash buffer (20mM Tris-HCl pH7.5, 10mM MgCl2, 0.2% Tween-20) and 1x with PNK buffer 70mM Tris-HCl pH6.5, 10mM MgCl2). Beads were re-suspended in 100µl PNK-mix (70mM Tris-HCl pH6.5, 10mM MgCl2, 1mM DTT, 100U RNasin, 1U TurboDNase, 25U Polynucleotide-Kinase (NEB)) and incubated for 20min at 37°C in a thermomixer with shaking (1200 x rpm). After RNA dephosphorylation beads were washed as before with 2x high salt, 2x lysis and 2x low salt buffers and additionally with 1x Ligase buffer (50mM Tris-HCl pH7.5, 10mM MgCl2). Beads were re-suspended in 50µl ligase mix (50mM Tris-HCl pH7.5, 10mM MgCl2, 1mM ATP, 3 % DMSO, 15% PEG8000, 30U RNasin, 75U T4 RNA-ligase (NEB)). 10µl of the beads / ligase mix were transferred to a new tube and 1µl of pCp-Biotin (Jena Bioscience) were added to validate IP of the RNA-protein-complexes by western blot. To the rest (40µl) 4µl of the RNA-adaptor mix containing 40µM of each RNA_X1A & RNA_X1B (IDT) were added and samples were incubated for 2h at RT. After adaptor ligation samples were washed 2x with high salt, 2x with lysis and 1x with low salt buffers. Beads were re-suspended in 1x LDS sample buffer (Thermofisher) supplemented with 10 uM DTT and incubated at 65°C for 10min with shaking at 1200 x rpm. Eluates or inputs were loaded on 4-12% Bis-Tris, 10-well, 1.5mm gel (Thermofisher) and separated at 130V for ca. 1.5h. Proteins were transferred to the nitrocellulose membrane (Amersham) overnight at 30V. After transfer the membranes were placed in a 15cm Petri dish on ice and an area between 55 and 145kDa was cut out in small pieces and transferred to 2ml tube. For CLIP samples RNA extraction, reverse transcription using AR17 primer, cDNA clean-up using silane beads (Thermofisher), second adaptor ligation (rand103Tr3) and final cDNA purification were performed as previously described (Van Nostrand et al., 2016). For sized matched input samples (SMIn) isolated RNA was dephosphorylated. The sequencing libraries were amplified using Q5-DNA polymerase (NEB) and i50X/i70X Illumina indexing primers (IDT). The amplified libraries were purified and concentrated first with ProNEX size selective purification system (Promega) using sample/beads ratio of 1/2.4. The purified libraries were loaded on a 2% agarose gel, the area corresponding to the size between 175bp and 350bp was cut and the libraries were extracted from the gel using gel extraction kit (Machery&Nagel) and eluted with 16µl. Concentrations and size distributions of the libraries were determined on Fragment analyzer system (Agilent). 75bp paired-end sequencing was performed on the NextSeq500 platform using Mid Output Kit v2.5 (150 cycles).
Eric L. Van Nostrand et al. 2016
eCLIP-Seq

treatment_protocol: Tissue was dissected on ice, flash frozen in liquid nitrogen, and ground on dry ice. Frozen powder was UV-crosslinked 3x with 400mJ/cm2 on dry ice with a UV-crosslinker.

tag: age

value: 30 days old

tag: tissue

value: Hippocampus

tag: genotype

value: Slm2 KO

tag: fraction

value: SMI


title: 2C2P

tag: cell type

value: stable HeLa S3 cell line expressing NLS-EYFP-2C2P


title: PML KO AC-TRIM33 input


title: Hippocampus, Slm2 KO, size‐matched input, rep1


title: NLS-EYFP-3

value: stable HeLa S3 cell line expressing NLS-EYFP

tag: experiment


title: PML WT SB-TRIM33 input


title: 2ACP

value: stable HeLa S3 cell line expressing NLS-EYFP-2ACP

tag: c&r antibody


title: PT+circSCMH1 input

value: brain

tag: time point

value: post stroke day 14

tag: genotype/variation

tag: antibody


title: Hippocampus, Slm2 KO, eCLIP, rep2

value: eCLIP


title: TD007_Env_after

city: 上海

first: Zhu

last: YouWei

state: Shanghai

address: 130 Dong'an Road

department: Institutes of Biomedical Sciences

institute: Fudan university

data_processing:
Raw data statistics: Perform statistical analysis on subreads to obtain information such as the number, average length and GC content of subreads sequence.
CCS analysis:Perform Circular Consensus Calling on subreads to obtain high-quality CCS reads by using pbccs software (version 3.3.0), and perform statistical analysis on CCS sequences.
barcode split: Split CCS reads according to barcode by using lima software (version 1.9.0), and statistics the split results.
Statistics of target sequences abundance:If the target area is specified, the target sequence is captured according to the 10nt of upstream and downstream of the target sequence, otherwise, the target sequence refs to the full-length sequences.
Statistics of base distribution: The CCS reads are aligned to the reference sequence by using BWA software, and the section on the alignment is extracted and mutation abundance information is counted.
Assembly: HIV-1, complete genome (GenBank: AF033819.3)
Supplementary files format and content: The target sequence is captured according to the 10nt of upstream and downstream of the HIV protease/ reverse transcriptase (PR/RT) region sequences (headers represent the date of sequencing and the sequencing number of the ccs reads)
Supplementary files format and content: The CCS reads are aligned to the reference sequence by using BWA software, and the section on the alignment is preserved to bam files

organism: Human immunodeficiency virus 1

source_name: peripheral blood

extract_protocol:
PacBio Sequel instrument (Pacific Biosciences of California, Inc., California, USA)
For each sample, >2ug purified PCR fragments (1kb~10kb) was used for library preparation. Fragmented DNAs were treated with End Prep Enzyme Mix for end repairing, 5’Phosphorylation and 3’dA-tailing in one reaction, followed by a T-A ligation to add universal hairpin adapters to both ends. Then the SMRTbell libraries were validated by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 3.0 Fluorometer. The final SMRTbell libraries were loaded on PacBio Sequel instrument according to manufacturer’s instructions (Pacific Biosciences of California, Inc., California, USA).

value: peripheral blood

value: Primary cell

value: PBMC

value: M10 CAR-T cells

value: 57 years old

tag: gender

value: male


title: NLS-EYFP-2

value: CUT&RUN

value: anti-GFP-Mnase (Marc Timmers)

tag: control sample


title: Hippocampus, Slm2 KO, eCLIP, rep1

value: 30 days old

value: Hippocampus


title: PFB007_after

value: protease/ reverse transcriptase (PR/RT) region sequences

value: 22 years old


title: HeLa-2

value: HeLa S3 cell line


title: PFB007_before


title: Hippocampus, WT, size‐matched input, rep1

description: SLM2_hippocampus_merged_peaks_broadpeak.bed

value: WT

value: SMI


title: sham input

value: brain

value: post stroke day 14

value: sham


title: Hippocampus, WT, size‐matched input, rep2


title: PML KO SB-TRIM33 rep2

value: mouse embryonic stem cell

value: GFP-trap

value: SB431542 treated


title: PFB004_after

value: peripheral blood

value: Primary cell

value: PBMC

value: M10 CAR-T cells

value: 30 years old


title: PML KO SB-TRIM33 rep1


title: NHEK 3D culture Air

city: Chikusa-ku

first: Hirofumi

last: Teshima

state: Aichi

address: furo-chou

country: Japan

institute: Nagoya university

data_processing:
Analysis of RNA-seq data was provided by Novogene. To remove reads containing adapters or reads of low quality, raw data of fastq format were firstly processed through in-house perl scripts. Reads were discarded when uncertain nucleaotides constitute more than 10 percents of eihter read and low quality nucleotides constitute more than 50 percents of the read. RNA 5' Adapter (RA5), part # 15013205: 5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3', RNA 3' Adapter (RA3), part # 15013207: 5'-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC(6-nucleotide index)ATCTCGTATGCCGTCTTCTGCTTG-3'
Paired-end clean reads were aligned to the reference genome(GRCh38.82) using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCh38.82
Supplementary files format and content: Cleaned raw data (raw reads) by Novogene in-house perl scripts.
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.

source_name: keratinocyte

growth_protocol: Neonatal human epidermal keratinocytes were seeded on cell culture inserts and grown for 3 days to reach confluency in CnT-PR (cellntec) growth medium. After confluency of the cells, the medium was changed to CnT-PR-3D (cellntec) differentiation medium and cells were maintained overnight.

extract_protocol:
Total RNA was harvested using Favorprep RNA mini kit (Favorgen). 3 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Air-liquid interface culture was started by removing media on the apical side from the next day of the exchange to the differentiation medium.

value: keratinocyte

tag: condition

value: air-liquid interface


title: H3K4me3_rep1

data_processing:
library strategy: CUT&RUN
Trimming was perfromed using TrimGalore! And FastQ Trimmer on Galaxy server.
CUT&RUN reads were aligned to hg38 genome using Bowtie2 with default parameters on Galaxy server.
Aligned reads were filtered out from blacklist reads, reads <20MAPQ and deduplicated
For peak calling MACS2 on Galaxy server was used.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated on filtered aligned reads
Supplementary_files_format_and_content: bed files were generated with MACS2

value: CUT&RUN

value: anti-H3K4me3 (Cell Signaling Technology, #9751)


title: PML KO AC-TRIM33 rep2

tag: chip antibody

value: activin A treated


title: PFB003_after

value: protease/ reverse transcriptase (PR/RT) region sequences

tag: treatment

value: 28 years old

value: male


title: Hippocampus, WT, eCLIP, rep1

value: 30 days old

value: Hippocampus

value: WT

value: eCLIP


title: Hippocampus, WT, eCLIP, rep2


title: TD007_Env_before

value: peripheral blood

tag: cell line

value: 57 years old


title: H3K4me1_rep1

value: HeLa S3 cell line

value: anti-H3K4me1 (Cell Signaling Technology, #5326)


title: H4K16ac_rep2

value: anti-KH4K16ac (ActiveMotif, #39168)


title: PFB003_before

value: Primary cell

value: PBMC

value: M10 CAR-T cells


title: PML WT SB-TRIM33 rep2

value: mouse embryonic stem cell

tag: strain

value: GFP-trap

value: SB431542 treated


title: PML WT AC-TRIM33 input

value: activin A treated


title: TD011_after

value: protease/ reverse transcriptase (PR/RT) region sequences

tag: age

value: 32 years olf

value: male


title: Whole brain, WT, size‐matched input, rep1

description: SLM2_whole_brain_merged_peaks_broadpeak.bed

source_name: Brain

value: 30 days old

tag: tissue

value: Brain

value: WT

value: SMI


title: H4K16ac_rep1

value: HeLa S3 cell line

value: CUT&RUN


title: NHEK 3D culture Liq

value: keratinocyte

value: submerged


title: Whole brain, WT, eCLIP, rep2

tag: genotype

value: eCLIP


title: PML WT AC-TRIM33 rep2


title: TD011_before

value: peripheral blood

value: Primary cell

value: PBMC

value: M10 CAR-T cells


title: Whole brain, WT, eCLIP, rep1

tag: fraction


title: H4K5acK8acK12acK16ac_rep2

tag: cell type


title: PML WT AC-TRIM33 rep1

value: mouse embryonic stem cell

value: GFP-trap

value: activin A treated


title: PFB004_before

value: protease/ reverse transcriptase (PR/RT) region sequences

value: 30 years old

value: male


title: PML KO AC-TRIM33 rep1


title: CAGE-seq SCC HP e2

city: Schlieren

first: Ramona

last: Weber

address: Wagistrasse 12

department: Institute for Regenerative Medicine

institute: University of Zurich

data_processing:
Quality check by FastQC
Filtering rRNA, mtRNA and tRNA by Bowtie2 v2.4.1 (Langmead et al., 2019) (Ribosome profiling only)
Read mapping by STAR v2.6.1 (Dobin et al., 2013)
Assembly: GRCm38
Supplementary files format and content: bigWig files with the identified TSS

source_name: Primary keratinocytes from P0 back skin

extract_protocol:
In vivo: CHX treatment, followed by dispase/CHX treatment to separate epidermis from dermis, trypsin/CHX to obtain single cell suspension.
The cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5’ cap structures of RNAs were oxidized, and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNA, double-stranded cDNA libraries (CAGE libraries) were constructed.

value: HrasG12V; Tgfbr2 fl/fl KO

value: Passage 10-15


title: TD007_after

value: 57 years old


title: CAGE-seq SCC HP e1


title: H4K5acK8acK12acK16ac_rep1

source_name: Cervix cancer cells

value: HeLa S3 cell line

tag: experiment

value: CUT&RUN


title: TD007_before


title: Day3_SNC_Distal_rep2

description: Myeloid_Subset_3Day_Distal_Injury_Site.RDS

source_name: Distal

extract_protocol:
mice were perfused with ice-cold saline solution, sciatic nerve trunks harvested and kept on ice. On ice, nerves were minced and subsequentily digested in collagenase at 37°C for 45-60 min. To block gene transcription, actinomycin D was added to the digestion step.  Cell suspensions were loaded on a Percoll gradient, cells collected, and myelin depleted using a myelin depletion column. To enrich for immune cells, some samples were run over an anti-CD45 or anti-CD11b column (Miltenyi, 130-052-301).
The Chromium Next GEM Single Cell 3’ Reagent kit v3.1 (Dual Index) was used. Barcoding and library preparation was performed following the manufacturer’s protocols. Briefly, to generate single-cell gel-bead-in-emulsion (GEMs) solution, approximately 15,000 cells, in a final volume of 43 µl, were loaded on a Next GEM Chip G (10x Genomics) and processed with the 10x Genomics Chromium Controller

treatment_protocol: mid-thigh sciatic nerve crush


title: Whole brain, WT, size‐matched input, rep2

value: 30 days old

value: Brain

value: WT

value: SMI


title: TD005_after

value: peripheral blood

value: Primary cell

value: PBMC

value: 48 years old


title: CAGE-seq SCC LP e2


title: H4K5acK8acK12ac_rep2

tag: c&r antibody


title: H4K5acK8acK12ac_rep1


title: PML WT SB-TRIM33 rep1

value: mouse embryonic stem cell

value: GFP-trap

value: SB431542 treated


title: TD005_before

value: protease/ reverse transcriptase (PR/RT) region sequences

value: M10 CAR-T cells

value: male


title: H2A.Zac_rep2

value: anti-H2A.Zac (Diagenode, #C15410173)


title: Day3_SNC_Injured_rep1

source_name: Injury Site


title: Day3_SNC_Injured_rep2


title: TD004_after

value: 38 years old

value: female


title: H2A.Zac_rep1

value: HeLa S3 cell line

value: CUT&RUN


title: CAGE-seq SCC LP e1

value: HrasG12V; Tgfbr2 fl/fl KO

value: Passage 10-15


title: Day7_SNC_rep8

source_name: sciatic nerve trunk


title: TD004_before

value: peripheral blood


title: CAGE-seq WT HP e2

value: R26-Sox2-IRES-eGFP fl/+


title: Day7_SNC_rep7


title: CAGE-seq WT LP e2


title: TD003_after

value: Primary cell

value: PBMC

value: 30 years old


title: CAGE-seq WT HP e1


title: RbBP5_rep2

value: anti-RbBP5 (ActiveMotif, #61406)


title: RbBP5_rep1


title: Day3_SNC_Distal_rep1


title: TD003_before


title: Day7_SNC_rep6


title: CAGE-seq HrasG12V; Tgfbr2 KO (SCC)


title: WDR5_rep1

value: anti-WDR5 (Diagenode, #C15410027)

value: IgG


title: Day7_SNC_rep5


title: WDR5_rep2


title: KMT2A_rep2

value: anti-KMT2A (Diagenode, #C15310264)


title: GW002_after

value: protease/ reverse transcriptase (PR/RT) region sequences

value: M10 CAR-T cells

value: male


title: GW002_before

value: 38 years old


title: control2_after

value: HAART only

value: 53 years old

value: female


title: CAGE-seq WT

value: Passage 10-15


title: CAGE-seq P60 EpSC

source_name: Mouse back skins

tag: marker

value: SCA-1+ EpSCs


title: KMT2A_rep1

value: HeLa S3 cell line

value: CUT&RUN


title: Day7_SNC_rep2


title: Day7_SNC_rep3


title: IgG5

value: normal rabbit IgG (Sigma, #I8140)


title: control2_before

value: peripheral blood

value: Primary cell

value: PBMC


title: Day7_SNC_rep1


title: EL004

city: New York

first: Edmund

last: Au

address: 630 West 168th Street, room P&S14-401

institute: Columbia University Irving Medical Center

data_processing:
Genome alignment on Cellranger version 5.0.1 (10X Genomics).
Quantification with Cellranger.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix.mtx.gz: Mtx containing UMI counts associated with a gene (row) and barcode (column), in a gzipped Market Exchange Format sparse matrix; Features.tsv.gz: Gzipped TSV containing metadata about each gene in the matrix; Barcodes.tsv.gz: Gzipped TSV containing metadata about each barcode in the matrix.

source_name: medial ganglionic eminence

extract_protocol:
E14.5 embryos generated from a cross of St18 (-/+) heterozygous breeders were collected and MGE was microdissected into chilled Hibernate A solution. During the dissection, embryo DNA was genotyped using a rapid PCR digest. St18 null and WT MGE were pooled and dissociated separately. Samples were submitted to the Sulzberger Genome Center Single Cell Core at the Columbia University Medical Center.
10X genomics chemistry

treatment_protocol: St18 whole animal null (-/-) and WT (+/+) E14.5 embryos from St18 (-/+) heterozygous parental mice.

tag: developmental stage

value: e14.5 mouse embryo

value: wildtype

value: C57/BL6 ICR mix

value: MGE


title: IgG4


title: EL003


title: Day3_SNC_rep6


title: control1_before

value: protease/ reverse transcriptase (PR/RT) region sequences

value: 23 years old

value: male


title: IgG3


title: Day7_SNC_rep4


title: Elephant_CTCF_IP

organism: Loxodonta africana

source_name: Fibroblasts

value: Fibroblasts


title: CAGE-seq WT LP e1

value: R26-Sox2-IRES-eGFP fl/+


title: EL002


title: IgG2


title: Day3_SNC_rep5


title: Day3_SNC_rep4


title: EL001


title: Elephant_CTCF_Input


title: Day3_SNC_rep3

description:
Reprocess of GSM4653878
post_injury_day_3.RDS


title: IgG


title: Elephant_H3K4me3_IP


title: 2D46_rep2

value: stable HeLa S3 cell line expressing NLS-EYFP-2D46

value: greenCUT&RUN

value: anti-GFP-Mnase (Marc Timmers)


title: Elephant_H3K4me3_Input