title: NL03_2 [Pool #3]

description: Pool #3


title: NL03_3 [Pool #3]

status: Public on Jan 09 2023

type: SRA

city: Stanford

first: Myung Chang

last: Lee

state: CA

address: 265 Campus Drive, G2065

department: Pediatrics and Genetics

country: USA

institute: Stanford University

description: Pool #3

library_source: genomic

data_processing:
Library strategy: Tuba-seq
Illumina RTA software was used for basecalling, fastq files were generated by bcl2fastq software
Each read is expected to contain an 8-nucleotide sgID region followed by a 30-nucleotide barcode (BC) region (GCNNNNNTANNNNNGCNNNNNTANNNNNGC), and each of the 20 Ns represent random nucleotides with roughly equal representation of A, T, G and C.
We kept only the sgID-BC reads with perfect match between forward and reverese sequences, and we calculated the overall counts of sgID-BC to determine enrichment or depletion in the tumor samples.
Tumor size (number of neoplastic cells) is calculated by normalizing the number of reads to the three benchmark cell lines (1 * 10^5 cells for each) added to each sample.
Assembly: sgID-BC reference (8N followed by GCNNNNNTANNNNNGCNNNNNTANNNNNGC)

molecule: genomic DNA

organism: Mus musculus

source_name: Transformed lung epithelial cell

extract_protocol:
Genomic DNA isolation from tumor-bearing mouse lung was performed via phenol:chloroform isolation and ethanol precipitation. Three benchmark control cell lines (1 * 10^5 cells per control) were added to correlate sgID-BC reads with cell number. Q5 High-Fidelity 2X Master Mix (New England Biolabs M0494X) was used to amplify the sgID-BC region using unique dual-indexed primers.
For sgID-BC amplicon libraries, we performed PCR with dual-indexed primers and purified the amplicon using MinElute kit as well as two-sided bead purification with Sera-Mag Select beads or Ampure XP beads.

tag: tissue

value: Lung

tag: genotype

tag: treatment

value: Naphthalene (200 mg/kg) i.p. two days prior to intratracheal transduction with HIV-sgTSG_Pool/PGK-Cre


title: NL03_1 [Pool #3]

description: Pool #3


title: maize_leaf, D193T, 48hpi, rep2

city: Cologne

first: Gunther

last: Doehlemann

address: Zuelpicher Str. 47a

country: Germany

institute: University of Cologne

description: 48hpi, D193T treatment, rep2

library_source: transcriptomic

data_processing:
Trimmomatic (0.39) was used for quality filtering of the paired-end reads.
bowtie2 (2.3.5.1) was used for the mapping of the quality-filtered reads to the reference genome of maize.
samtools (1.9) were used to dort the BAM files.
Htseq-count (2.0.1) was used to count the mapped reads.
edgeR (3.36.0) was used for the differential gene expression analysis.
Assembly: Zea mays reference genome Zm-B73-REFERENCE-NAM-5.0
Supplementary files format and content: Gzipped text files containing transcript counts for each sample.

molecule: total RNA

organism: Zea mays

source_name: leaf

extract_protocol:
RNA was harvested from frozen and homogenized samples using TRIzol reagent (Invitrogen, Darmstadt, Germany). The Turbo DNA-Free Kit from Ambion (Ambion Life TechnologiesTM, Carlsbad, USA) was used to exclude DNA contamination.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: leaf

tag: time point


title: P21

city: San Diego

first: Diane

middle: M

last: Simeone

address: 3855 Health Sciences Drive

institute: UCSD Health

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Genomics Cell Ranger software, version 5.0.1.
Assembly: hg38/GRCh38
Supplementary files format and content: raw barcodes
Supplementary files format and content: raw genes
Supplementary files format and content: raw gene-barcode matrix

molecule: polyA RNA

organism: Homo sapiens

source_name: PDAC liver met

extract_protocol:
Within 4-6 h of tissue acquisition, the specimen was placed in ice-cold RPMI 1640 medium (Gibco, Cat. No. 11875101). Tissue samples were washed in ice-cold phosphate-buffered saline (PBS; Corning, Cat. No. 21- 040-CM) and grossly assessed for adequacy (solid tissue component, free of large hemorrhagic or necrotic areas). Next, the tissue was manually minced with a scalpel blade and filtered through a 40 μm mesh filter (Falcon; Cat. No. 352340) to remove any excess debris or blood. The tissue was then transferred to a sterile gentleMACS C tube (Miltenyi Biotec, Cat. No. 130096334), resuspended in 3-5 mL of Miltenyi Tumor Dissociation Kit buffer (Cat. No. 130-095-929), and mechanically minced to submillimeter particles. The suspension was then digested utilizing the gentleMACS Octo Dissociator (Miltenyi Biotec, Cat. No. 130-095-937) for 25-30 min using the “37C_h_TDK_3'' program for tumor tissue. Dissociated cells were then quenched with ice-cold RPMI 1640 containing 10% fetal bovine serum (FBS; Gibco, Cat. No. 10082147) and filtered through a 40 μm mesh filter. Red blood cells were removed by treatment with 3-5 mL of ACK lysis buffer (Gibco, Cat. No. A1049201) and a subsequent washing step in RPMI 1640 with 10% FBS. Final cell counts were established with 0.4% trypan blue solution and a Countess II Automated Cell Counter (Applied Biosystems, Cat. No. A27977). The final concentration was titrated to 300-500 viable cells/μL for further analysis.
Chromium Single Cell 3′ Reagent Kits (v3)—the Single Cell 3′ Library & Gel Bead Kit v3 (PN-1000075), the Chromium Next GEM Chip G Single Cell Kit (PN-100120), and the i7 Multiplex Kit (PN-120262) (10x Genomics)

value: PDAC liver met

value: Untreated

tag: procedure

value: Liver-Biopsy

tag: Stage

value: Metastatic


title: P27

description: 10x Genomics


title: BMDMs, SREBP1 ko, LPS, 4h, biol, rep1

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

data_processing:
Reads were aligned to the mm10 mouse genome using STAR.
Aligned read files were analyzed using HOMER. Batch effects were removed using ComBat-seq. Differentially expressed genes were analyzed using DESeq2.
Assembly: mm10
Supplementary files format and content: bedGraph

source_name: Srebf1-/- BMDMs treated with LPS for 4 h

extract_protocol:
Total RNA was isolated and purified using Rneasy columns and Rnase-free Dnase digestion according to the manufacturer’s instructions (QIAGEN).
Poly-A mRNA was extracted from total RNA using Oligo-dT beads in a NEBNext Poly (A) RNA Magnetic Isolation Module (New England Biolabs), after which RNA-seq libraries are prepared using a RNA-Seq library preparation kit for Illumina (New England Biolabs) according to the manufacturer’s protocols.

tag: cell type

value: Bone marrow-derived macrophage

value: LPS


title: NL03_24 [Pool #2]

description: Pool #2


title: P20

description: 10x Genomics

source_name: Primary PDAC

value: Primary PDAC

value: EUS-Biopsy


title: P22

description: 10x Genomics

value: Locally Advanced


title: BMDMs, Casp4 ko, LPS, 4h, biol, rep3

source_name: Casp4-/- BMDMs treated with LPS for 4 h


title: BMDMs, Casp4 ko, LPS, 4h, biol, rep2


title: NL03_5 [Pool #3]

description: Pool #3


title: maize_leaf, D193T, 48hpi, rep1

description: 48hpi, D193T treatment, rep1


title: P19

description: 10x Genomics

value: Resection

value: Resectable


title: NL03_23 [Pool #2]

description: Pool #2


title: maize_leaf, avrRxo1, 48hpi, rep3

description: 48hpi, avrRxo1 treatment, rep3


title: BMDMs, Casp4 ko, LPS, 4h, biol, rep1


title: maize_leaf, DMSO, 12hpi, rep2

description: 12hpi, control of FB1/SA, rep2

value: DMSO (control)


title: maize_leaf, avrRxo1, 48hpi, rep2

description: 48hpi, avrRxo1 treatment, rep2


title: maize_leaf, D193T, 48hpi, rep3

description: 48hpi, D193T treatment, rep3


title: BMDMs, WT, LPS, 4h, biol, rep3

source_name: wild-type BMDMs treated with LPS for 4 h

value: wild-type


title: maize_leaf, pHMI, 48hpi, rep3

description: 48hpi, control of avrRxo1/D193T, rep3

value: pHMI (empty vector)


title: maize_leaf, avrRxo1, 48hpi, rep1

description: 48hpi, avrRxo1 treatment, rep1


title: P18

description: 10x Genomics


title: BMDMs, WT, LPS, 4h, biol, rep2


title: P17

description: 10x Genomics

value: Treated


title: NL03_22 [Pool #2]

description: Pool #2

value: Lung

value: Naphthalene (200 mg/kg) i.p. two days prior to intratracheal transduction with HIV-sgTSG_Pool/PGK-Cre


title: NL03_21 [Pool #2]

description: Pool #2


title: NL03_20 [Pool #2]

description: Pool #2


title: BMDMs, WT, LPS, 0h, biol, rep3

source_name: untreated wild-type BMDMs

value: untreated


title: maize_leaf, pHMI, 48hpi, rep2

description: 48hpi, control of avrRxo1/D193T, rep2

value: leaf


title: P15

description: 10x Genomics

value: Untreated


title: P16

description: 10x Genomics

value: PDAC liver met

value: Liver-Biopsy

value: Metastatic


title: maize_leaf, pHMI, 48hpi, rep1

description: 48hpi, control of avrRxo1/D193T, rep1


title: BMDMs, WT, LPS, 4h, biol, rep1

value: Bone marrow-derived macrophage

value: LPS


title: P14

description: 10x Genomics

value: Primary PDAC


title: BMDMs, WT, LPS, 0h, biol, rep2


title: maize_leaf, D193T, 24hpi, rep3

description: 24hpi, D193T treatment, rep3


title: NL03_17 [Pool #2]

description: Pool #2


title: BMDMs, WT, LPS, 0h, biol, rep1


title: NL03_16 [Pool #2]

description: Pool #2


title: maize_leaf, D193T, 24hpi, rep2

description: 24hpi, D193T treatment, rep2


title: maize_leaf, D193T, 24hpi, rep1

description: 24hpi, D193T treatment, rep1


title: T

city: NEW DELHI

first: Anurag

middle: Singh

last: Rathore

state: DELHI

address: Lab no. 356, Block III

department: Chemical Engineering

country: India

institute: Indian Institute of Technology

data_processing:
The raw data generated was checked for the quality using FastQC. Reads were pre processed to remove the adapter sequences and removal of the low quality bases (<q30). Pre-processing of the data is done with Cutadapt. The pre-processed high quality data was aligned to reference genome using Bowtie2. Bowtie with  default parameter was run to identify the alignment percentage.
Genome_build: Escherichia coli_BL21(DE3), GCF_000022665.1 assembly was downloaded from NCBI
Supplementary_files_format_and_content: HTSeq was used to estimate and calculate gene abundance. Absolute counts for each genes were   identified ,which were used in differential expression calculations. DESeq was used to calculate the differentially expressed genes in test and control with and without ethanol supplemention. Genes were categorized into UP, Down and Neutrally regulated based on the log2fold change cutoff of 1 value.

organism: Escherichia coli

source_name: bacterial cell

growth_protocol: A complex medium is used for E. coli culture. Control (only Complex medium components) and Test (Complex medium components + 3% ethanol at the time of induction)  of  E. coli BL21(DE3) expressing recombinant protein was carried out. Sample at 2nd hour (post induction: control and test) was taken for RNA-seq analysis.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) using manufacturer’s instructions.
RNA sequencing libraries were prepared with Illumina-compatible NEBNext® UltraTM Directional RNA Library Prep Kit (New England BioLabs, MA, USA) at Genotypic Technology Pvt. Ltd., Bangalore, India. ~2.5μg of total RNA was taken for rRNA depletion using Ribo-Zero rRNA Removal Kit (Bacteria). ~50 ng of Qubit quantified ribodepleted RNA was taken for fragmentation and priming. The fragmented and primed mRNA was further subjected to first strand synthesis in the presence of Actinomycin D (Gibco, life technologies, CA, USA) followed by second strand synthesis. The double stranded cDNA was purified using HighPrep PCR magnetic beads (Magbio Genomics Inc, USA). The purified cDNA was end-repaired, adenylated and ligated to Illumina multiplex barcode adapters as per NEBNext® UltraTM Directional RNA Library Prep Kit protocol.

treatment_protocol: Not required

tag: strain

tag: age of culture

value: Post induction  (2nd Hour):Test


title: P12

description: 10x Genomics

value: EUS-Biopsy


title: P11

description: 10x Genomics


title: NL03_15 [Pool #2]

description: Pool #2


title: maize_leaf, avrRxo1, 24hpi, rep3

description: 24hpi, avrRxo1 treatment, rep3


title: Mab SPC 10mg/L Rep 2

city: Memphis

first: Richard

state: TN

address: 262 Danny Thomas Place

department: Department of Chemical Biology and Therapeutics

institute: St. Jude Children's Research Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
The resulting reads were saved in FASTQ format and data was processed through the High-Performance Computing Facility at St. Jude.
Adapter content and quality trimming was performed using Cutadapt. The quality of the raw and trimmed reads was assessed using FastQC and MultiQC.
The resulting processed reads were aligned to the reference Mycobacterium abscessus ATCC19977 genome (Genome accession: NC_010397) using STAR2.7.1 and aligned reads were counted using featureCounts.
Differential gene expression analysis was analyzed using DESeq2 in the R statistical computing environment.
Assembly: Mycobacterium abscessus ATCC19977 genome (Genome accession: NC_010397)
Supplementary files format and content: tab-delimited text file includes raw counts table used for differential expression analysis.

organism: Mycobacteroides abscessus ATCC 19977

source_name: Planktonic cells

growth_protocol: Mycobacteria abscessus ATCC 19977 was grown in 5mL of Mueller Hinton broth II (MHB II) to log phase O.D.600 0.4-0.8.

extract_protocol:
RNA was harvested through the addition of 2 volumes of RNA protect (Qiagen), then centrifuged for 4 minutes at 10,000xg at 4C. Supernatant was poured off and pellets stored at -80°C. Next day samples were thawed out and re-suspended in 500µL RLT + 1% betamercaptoethanol and transferred to Lysing Matrix B (VWR, Pittsburgh PA). Samples were placed into a Bead Mill 4 homogenizer (Fisher Scientific, Atlanta GA) and homogenized 4 times for 40 sec at 4.5m/s with 1 min of wet ice cooling between each round of homogenization. Lysate was spun down at 8000g for 2 minutes and supernatant removed to clean centrifuge tube. Subsequent extraction of RNA was performed according to the RNAeasy extraction kit (Qiagen). RNA was eluted in 40µL of elution buffer yielding a typical concentration of 400-500ng/µL. RNA samples were then DNase treated to remove residual genomic DNA from samples. This was performed using the Genomic DNA Clean and Concentrator Kit (Zymo Research, Irvine CA). Samples were eluted in 30-45µL of RNase free water, yields ranging from 100-250ng/µL.
Libraries were prepared from total RNA with the TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020595). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) and by low pass sequencing with a MiSeq nano kit (Illumina). Paired end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina) or HiSeq 2500 by the St. Jude Children's Research Hospital sequencing core at a depth of 100M reads/sample.

treatment_protocol: Samples were exposed to 1µg/mL or 10µg/mL  of spectinomycin or 2694, 1µg/mL of 2593, or equal volumes of vehicle control (DMSO) for 3 hours.

value: Planktonic cells

value: 10 mg/L SPC

tag: time

value: 3 hour


title: C

value: Post induction  (2nd Hour):Control


title: P10

description: 10x Genomics

value: Treated

value: Resection

value: Borderline


title: P09

description: 10x Genomics


title: Mab SPC 10mg/L Rep 3


title: maize_leaf, avrRxo1, 24hpi, rep1

description: 24hpi, avrRxo1 treatment, rep1

value: leaf


title: maize_leaf, avrRxo1, 24hpi, rep2

description: 24hpi, avrRxo1 treatment, rep2


title: P08

description: 10x Genomics


title: UCB3_DEL

city: Graz

first: Johannes

last: Foßelteder

address: Auenbruggerplatz 48

department: Blood Group Serology and Transfusion Medicine

country: Austria

institute: Medical University of Graz

data_processing:
Base calling was performed on-instrument using the Illumina Real-Time Analysis Software (RTA, 2.7.7).
NGS reads were mapped to the human reference genome hg38 using STAR and the Ensembl transcript annotation version e100 (April 2020).
Aligned NGS reads were counted with the GenomicAlignments (1.26.0) package via the summarizeOverlaps function in Union mode.
Differential expression analysis was performed with the DESeq2 (1.30.0) package on the basis of read counts from independent biological triplicates.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: Hematopoietic stem and progenitor cells

growth_protocol: Cord blood-derived CD34+ HSPCs were expanded for 3 days in SFEM II media (Stemcell Technologies, Vancouver, BC, Canada) supplemented with 100 ng/ml of SCF, FLT3L, TPO, IL-6, 750 nM of SR1 and 35 nM of UM171 (HSPC retention media) prior to CRISPR modification.

extract_protocol:
Total RNA was isolated using the Monarch Total RNA Miniprep Kit (NEB, Ipswich, MA, USA).
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) according to manufacturer's recommendations.

treatment_protocol: Calreticulin mutations were introduced via a CRISPR/Cas9 and AAV6-mediated knock-in. Modified cells were purified 48 h later using FACS and cultured for another 2 days in HSPC retention media prior to RNA isolation.

value: Umbilical cord blood

value: Hematopoietic stem and progenitor cells

value: CALR DEL/+


title: Mab SPC 10mg/L Rep 1


title: NL03_18 [Pool #2]

description: Pool #2

value: Lung

value: Naphthalene (200 mg/kg) i.p. two days prior to intratracheal transduction with HIV-sgTSG_Pool/PGK-Cre


title: P13

description: 10x Genomics

value: Untreated

value: Locally Advanced


title: UCB2_WT

value: CALR WT/+


title: maize_leaf, pHMI, 24hpi, rep3

description: 24hpi, control of avrRxo1/D193T, rep3

value: pHMI (empty vector)


title: P07

description: 10x Genomics

value: Primary PDAC

value: Resectable


title: maize_leaf, pHMI, 24hpi, rep2

description: 24hpi, control of avrRxo1/D193T, rep2


title: UCB2_INS

value: CALR INS/+


title: P06

description: 10x Genomics

value: EUS-Biopsy


title: Mab SPC 1mg/L Rep 2

value: Planktonic cells

value: 1 mg/L SPC

value: 3 hour


title: UCB2_DEL


title: maize_leaf, pHMI, 24hpi, rep1

description: 24hpi, control of avrRxo1/D193T, rep1

value: leaf


title: Mab SPC 1mg/L Rep 1


title: P05

description: 10x Genomics

value: Resection


title: UCB3_WT

value: Umbilical cord blood

value: Hematopoietic stem and progenitor cells


title: UCB3_INS


title: P04

description: 10x Genomics


title: maize_leaf, D193T, 12hpi, rep3

description: 12hpi, D193T treatment, rep3


title: maize_leaf, D193T, 12hpi, rep2

description: 12hpi, D193T treatment, rep2


title: Mab 2694 10mg/L Rep 3


title: UCB1_WT


title: P03

description: 10x Genomics

value: Treated


title: UCB1_INS


title: P02

description: 10x Genomics

value: PDAC liver met

value: Liver-BIopsy

value: Metastatic


title: maize_leaf, avrRxo1, 12hpi, rep3

description: 12hpi, avrRxo1 treatment, rep3


title: maize_leaf, D193T, 12hpi, rep1

description: 12hpi, D193T treatment, rep1


title: Mab 2694 10mg/L Rep 2


title: P01

description: 10x Genomics

value: Untreated

value: Liver-Biopsy


title: Mab SPC 1mg/L Rep 3


title: UCB1_DEL

value: CALR DEL/+


title: Mab 2694 10mg/L Rep 1


title: Mab 2694 1mg/L Rep 3


title: ko-4

city: Wuhan

first: Jing-Jing

last: Zhang

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

country: China

institute: Huazhong Agricultural University

data_processing:
All RNA-seq data were aligned to the mouse reference genome mm10 using STAR
Gene FPKM (Fragments per kilobase of transcript per million mapped reads) values were quantified using Stringtie (version 2.1.4)
Gene differential expression analysis using DESeq2 (version 1.30.1) based on the reads count file obtained by featureCounts (version 1.6.2)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene differential expression for each gene

source_name: cell

extract_protocol:
Two micrograms of total RNA were used for RNA sample preparation. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1 ng/μl. Library quality was assessed using the Agilent Bioanalyzer 2100 system.
cDNA was preamplification for 16-18 cycles by using KAPA HiFi HotStart ReadyMix (KK2601, Roche) and IS PCR primers, followed by PCR purification by AMPure XP beads (A63881, Beckman). Finally, amplified cDNA was fragmented and RNA-seq library was constructed by using TruePrep DNA Library Prep Kit (TD502, Vazyme) according to the manufacturer’s instructions. Paired-end 150-bp sequencing was performed on the Illumina HiSeq X-Ten or NovaSeq 6000 system.

treatment_protocol: Short hairpin RNAs (shRNAs) against mouse Atg5 were designed and transfected.

value: cumulus granulosa cells

value: Kun-Ming


title: ko-3


title: Mab 2694 1mg/L Rep 1


title: ko-2


title: maize_leaf, avrRxo1, 12hpi, rep1

description: 12hpi, avrRxo1 treatment, rep1


title: ctr-4

value: control


title: Mab 2593 1mg/L Rep 3

value: Planktonic cells


title: maize_leaf, pHMI, 12hpi, rep2

description: 12hpi, control of avrRxo1/D193T, rep2

value: pHMI (empty vector)


title: Mab 2593 1mg/L Rep 2

value: 3 hour


title: ctr-3


title: ctr-2


title: Mab 2593 1mg/L Rep 1


title: Syn7942/Δsps-ect, 300 mM NaCl, 4-day, rep2

status: Public on Jan 08 2023

city: Tianjin

first: Zhengxin

last: Dong

address: No. 135 Yaguan Road

institute: Tianjin University

description:
Syn7942/Δsps-ect 300 mM NaCl -2_Count
sps-ect-300-2

data_processing:
Cutadapt (version 1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1)
bowtie2 (v2.2.6)
HTSEQ (v0.6.0)
cufflinks (V2.2.1)
DESeq2 (V1.6.3)
Assembly: CP000100, CP000101 and NZ_KT751091
Supplementary files format and content: excel file includes count and FPKM values for each sample

organism: Synechococcus elongatus PCC 7942 = FACHB-805

growth_protocol: Grown at 37℃ in BG11 liquid medium

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent /RNeasy Mini Kit, 1μg total RNA was used for following library preparation.
Generation sequencing library preparations were constructed according to the manufacturer’s protocol.

treatment_protocol: Treated with BG11 medium containing 300 mM NaCl for 4 days

value: bacterial cell

value: Synpcc7942_0808 locus knocked into ectABC

value: 300 mM NaCl


title: Syn7942/Δsps-ect, 300 mM NaCl, 4-day, rep3

description:
Syn7942/Δsps-ect 300 mM NaCl -3_Count
sps-ect-300-3


title: Syn7942/Δsps-ect, 0 mM NaCl, 4-day, rep3

description:
Syn7942/Δsps-ect 0 mM NaCl -3_Count
sps-ect-0-3

value: 0 mM NaCl


title: Syn7942/Δsps-ect, 0 mM NaCl, 4-day, rep1

description:
Syn7942/Δsps-ect 0 mM NaCl -1_Count
sps-ect-0-1


title: Syn7942/Δsps-ect, 0 mM NaCl, 4-day, rep2

description:
Syn7942/Δsps-ect 0 mM NaCl -2_Count
sps-ect-0-2


title: maize_leaf, pHMI, 12hpi, rep1

description: 12hpi, control of avrRxo1/D193T, rep1

value: leaf


title: maize_leaf, avrRxo1, 12hpi, rep2

description: 12hpi, avrRxo1 treatment, rep2


title: WT, 0 mM NaCl, 4-day, rep3

description:
WT 0 mM NaCl-3_Count
wt-0-3

value: WT


title: WT, 0 mM NaCl, 4-day, rep1

description:
WT 0 mM NaCl-1_Count
wt-0-1


title: Mab 2694 1mg/L Rep 2


title: WT, 300 mM NaCl, 4-day, rep1

description:
WT 300 mM NaCl-1_Count
wt-300-1


title: WT, 0 mM NaCl, 4-day, rep2

description:
WT 0 mM NaCl-2_Count
wt-0-2


title: WT, 300 mM NaCl, 4-day, rep3

description:
WT 300 mM NaCl-3_Count
wt-300-3


title: maize_leaf, pHMI, 12hpi, rep3

description: 12hpi, control of avrRxo1/D193T, rep3


title: Shengsimai, 96hour, rep3

city: Xianyang

first: Cheng

last: Kou

address: 3 Tai Cheng Road, Yangling District, Xianyang City, Shaanxi Province, China

institute: Northwest A&F University

data_processing:
Data process analysis was performed using BMKCloud (www.biocloud.net). Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped. The formula is shown as follow:  FPKM=cDNAFragments/(MappedFragments(Millions)∗TranscriptLength(kb))
Assembly: NCBI
Supplementary files format and content: txt

organism: Triticum aestivum

source_name: spike

extract_protocol:
The plant total RNA was extracted using the RNAprep Pure Plant Kit (Tiangen, Beijing, China) according the instructions provided by the manufacturer.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: cultivar

value: Shengsimai

value: spike

value: 96 hour


title: Zhoumai18, 96hour, rep1


title: Zhoumai18, 96hour, rep3


title: Zhoumai18, 96hour, rep2


title: Baipimai, 96hour, rep1

value: Baipimai


title: Baipimai, 96hour, rep2


title: Shengsimai, 96hour, rep1


title: Baipimai, 96hour, rep3


title: Zhoumai18, 48hour, rep3

value: 48 hour


title: Syn7942/Δsps-ect, 300 mM NaCl, 4-day, rep1

description:
Syn7942/Δsps-ect 300 mM NaCl -1_Count
sps-ect-300-1


title: Zhoumai18, 48hour, rep2


title: Zhoumai18, 48hour, rep1


title: WT, 300 mM NaCl, 4-day, rep2

description:
WT 300 mM NaCl-2_Count
wt-300-2


title: Shengsimai, 48hour, rep3


title: Shengsimai, 48hour, rep1


title: Baipimai, 48hour, rep3


title: Shengsimai, 48hour, rep2


title: Baipimai, 48hour, rep2


title: PlasmidPstI

city: Beijing

first: li

last: kuan

address: zhongguancun

institute: Tsinghua University

description: 3' end of DNA break

data_processing:
Illumina Casava1.7 software used for basecalling.
Duplicated reads which had same sequences for both forward and reverse reads were removed
Reads were aligned to the reference genome with Bowtie2 using --local settings
For visualization and split strand, we use bamCoverage from DeepTools (--binSize 1 --Offset 1 --samFlagInclude 128 --filterRNAstrand forward/reverse) to convert the aligned reads files (BAMs) including the second read in pairs to first single base bigWig files with 1bp bins. The option --filterRNAstrand forward means Crick strand and --filterRNAstrand reverse means Waston strand.
Genome_build: sacCer3

organism: synthetic construct

source_name: Plasmid digested by PstI

growth_protocol: The strains were grown for 24 hours in YPD medium (1% yeast extract, 2% peptone, and 2% glucose), diluted in liquid YPA medium (1% yeast extract, 2% peptone, and 2% potassium acetate) to OD600 = 0.3, and grown for 10 hours at 30°C.

extract_protocol: Each cell pellet was resuspended in 150 µl 50 mM EDTA pH 8.0 and allowed to thaw at 40°C. 498 µl LMP agarose (2% in 50 mM EDTA pH 8.0) was mixed with 102 µl Solution 1 (1 M sorbitol, 0.1 M sodium citrate, 60 mM EDTA pH 7.0, 5% β-mercaptoethanol and 1 mg/ml zymolyase 100T) and the mix was pre-warmed at 40°C before adding to the cells. The resuspended cells were pipetted into plug molds and chilled at 4°C for 30 min. Once solidified, the agarose plugs were cut into small pieces (one agarose plug to 16~24 pieces), and expressed into 1 ml of Solution 2 (0.45 M EDTA pH 8.0, 0.01 M Tris-HCl pH 7.5, 7.5% β-mercaptoethanol, 10 µg/ml RNase A) and incubated at 37°C for overnight. Plugs were quickly washed three times with 1 ml TE buffer, and then washed five times with TE buffer incubated at 37°C for 6min (total 30min). Then plugs were expressed into 1ml Solution 3 (0.25 M EDTA pH 8.0, 0.01 M Tris-HCl pH 7.5, 1% SDS, 1 mg/ml proteinase K) and incubated at 54°C overnight. Plugs were finally washed six times with TE buffer and stored in plug storage solution (0.05 M EDTA pH 8.0, 50% glycerol) at -20°C until all plugs were ready to be processed for library preparation.  The plugs were transferred to a PCR tube, and washed by 30 µl 1X Adaptase buffer (Swift, Accel-NGS, 10096) twice at room temperature, 10 min each time. Add 47 µl 1X Adaptase buffer and 3 µl Adaptase (Swift, Accel-NGS, 10096) to PCR tube, incubated with plugs at 37°C for 2 h. Removed buffer, and deactivated Adaptase in plugs by 98°C for 2 min. Purified DNA from plugs by Gel Extraction Kit (Qiagen, 28606). Sonicated DNA to 150~250 bp fragments by using Focused-ultrasonicator (Covaris, S220). The rest steps were following the manual of Accel-NGS 1S Plus DNA Library Kit (Swift, Accel-NGS, 10096). Briefly, denatured DNA fragments to ssDNA, and extended it to dsDNA. After purification, 2rd adaptor was ligated. After indexing PCR and purification, preparation of DEtail-seq library was finished. The DEtail-seq library was sequenced by NovaSeq 6000 (Illumina).

treatment_protocol: Cells were harvested, washed, resuspended in a sporulation medium (SPM, 2% potassium acetate) to OD600 = 1.9, and sporulated at 30°C for different durations.


title: PlasmidBmgBI

description: 3' end of DNA break

source_name: Plasmid digested by BmgBI


title: WT4h

description: 3' end of DNA break

organism: Saccharomyces cerevisiae

source_name: WT 4h


title: PlasmidEcoRI

description: 3' end of DNA break

source_name: Plasmid digested by EcoRI


title: WT0hAsiSI2

description: 3' end of DNA break

source_name: WT 0h digested by AsiSI


title: Shengsimai, 96hour, rep2


title: DEtail-seq ssDNA with 3N in 3' end

data_processing:
Illumina Casava1.7 software used for basecalling.
Duplicated reads which had same sequences for both forward and reverse reads were removed
Reads were aligned to the reference genome with Bowtie2 using --local settings
For visualization and spliting strand, the aligned reads files (BAM) including second read in pairs were converted to first single base bigWig file with 1bp bins using bamCoverage from deepTools with --binSize 1 --Offset 1 --samFlagInclude 128 --filterRNAstrand forward/reverse.The option --filterRNAstrand forward means Crick strand and --filterRNAstrand reverse means Waston strand.
Supplementary files format and content: bigWig

tag: sample type

value: 3' end of DNA break


title: Zhoumai18, 0hour, rep2

value: 0 hour


title: Zhoumai18, 0hour, rep3


title: Baipimai, 48hour, rep1


title: WT0hAsiSI1

description: 3' end of DNA break


title: Zhoumai18, 0hour, rep1


title: Shengsimai, 0hour, rep2


title: Shengsimai, 0hour, rep3


title: WT0h

description: 3' end of DNA break

source_name: WT 0h


title: DMC1KO4h

description: 3' end of DNA break

source_name: DMC1KO 4h

value: DMC1KO in SK1


title: Shengsimai, 0hour, rep1


title: SPO11KO4h

description: 3' end of DNA break

source_name: SPO11KO 4h

value: SPO11KO in SK1


title: Baipimai, 0hour, rep3


title: Small_RNA_C_18

city: London

first: Rachel

last: Wilson

address: Du Cane Road

country: United Kingdom

institute: Imperial College

description:
Generation 18
Alternate_Generation_Normalized_smallRNAsample_counts.txt

data_processing:
RNA
Alignment
Intersect with gene names
Assembly: cel_genomeWS252
Supplementary files format and content: data frame of normalised RNA counts for each generation by lineage
ATAC
Read trimming
Read pairing
Alignment
Assembly: cel_genomeWS252
intersect with coordinates of enhancers/promoters
Supplementary files format and content: data frame of normalised ATAC counts for each generation by lineage
small RNA
Read trimming
Read pairing
Alignment
Assembly: cel_genomeWS252
Supplementary files format and content: data frame of normalised small RNA counts for each generation by lineage

organism: Caenorhabditis elegans

source_name: embryo

growth_protocol: Bottlenecked lineage grown for 20 generations under controlled conditions at 20 degrees

extract_protocol:
Small RNA libraries produced from RNA using the Illumina TruSeq Small RNA Library Preparation Kit
embryos collected for ATAC and RNA protocols by bleaching of worms, embryos ground to release nuclei.

treatment_protocol: no treatment

value: embryo

tag: agent

value: untreated

tag: lineage

value: C

tag: generation


title: Baipimai, 0hour, rep2


title: Small_RNA_C_16

description:
Generation 16
Alternate_Generation_Normalized_smallRNAsample_counts.txt


title: Baipimai, 0hour, rep1


title: Small_RNA_C_10

description:
Generation 10
Alternate_Generation_Normalized_smallRNAsample_counts.txt


title: Small_RNA_C_8

description:
Generation 8
Alternate_Generation_Normalized_smallRNAsample_counts.txt


title: Small_RNA_C_4

description:
Generation 4
Alternate_Generation_Normalized_smallRNAsample_counts.txt


title: NL03_19 [Pool #2]

description: Pool #2

source_name: Transformed lung epithelial cell

value: Lung

value: Naphthalene (200 mg/kg) i.p. two days prior to intratracheal transduction with HIV-sgTSG_Pool/PGK-Cre


title: Small_RNA_C_2

description:
Generation 2
Alternate_Generation_Normalized_smallRNAsample_counts.txt


title: Small_RNA_C_6

description:
Generation 6
Alternate_Generation_Normalized_smallRNAsample_counts.txt


title: HEK293T WT Input-2

city: Shanghai

first: Gang

last: Wang

address: 2005 Songhu Rd

department: School of life sciences

institute: Fudan university

data_processing:
ChIP-seq raw reads were obtained from an Illumina X-10 sequence analyzer.
We utilized Fastqc (v0.1.0) for raw data quality summary. Cutadapt was used to remove sequencing adapters and poor-quality base trimming, retaining only reads with a quality score greater than 30 and discarding reads shorter than 50 bp or 75 bp for SE100 or PE150 reads, respectively.
Clean reads were aligned to the human reference genome hg19, and the mapping results were normalized to FPKM (counts per million mapped reads per kilobase) and converted to bigwig files for visualization and by bamCoverage.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Briefly, cells were crosslinked with 0.9% formaldehyde for 9 min at room temperature, and formaldehyde was quenched by glycine at a final concentration of 125 μM for 5 minutes. Cells were washed twice with ice-cold PBS and collected by a cell scraper. Cell pellets were lysed and sonicated in lysis buffer (1% SDS, 50 mM Tris-HCl (pH 7.4), 10 mM EDTA), and the chromatin was fragmented into 200-500 bp fragments using a COVARIS S220 sonicator.
ChIP-seq libraries were prepared using a commercial kit (Vazyme, Nanjing, China, ND607)  following manufacturer's protocols.

tag: cell line

value: Human embryonic kidney cells

tag: antibody


title: Small_RNA_B_20

description:
Generation 20
Alternate_Generation_Normalized_smallRNAsample_counts.txt

tag: tissue

value: B


title: Small_RNA_C_0

description:
Generation 0
Alternate_Generation_Normalized_smallRNAsample_counts.txt


title: HEK293T R617Q H3K27ac-1

tag: genotype


title: HEK293T R617Q PolII

value: PolII


title: HEK293T R617Q H3K27ac-2


title: HEK293T WT Input-1

value: WT


title: HEK293T R617Q Input-1


title: Small_RNA_B_16


title: Small_RNA_C_20


title: Small_RNA_B_18


title: HEK293T WT H3K27ac-2


title: HEK293T WT PolII


title: HEK293T WT H3K27ac-1


title: HEK293T R617Q H3K4me3-2


title: HEK293T R617Q H3K4me3-1


title: Small_RNA_B_14

description:
Generation 14
Alternate_Generation_Normalized_smallRNAsample_counts.txt


title: Small_RNA_B_10


title: Small_RNA_C_12

description:
Generation 12
Alternate_Generation_Normalized_smallRNAsample_counts.txt


title: HEK293T R617Q Input-2


title: HEK293T WT H3K4me3-2


title: Small_RNA_B_8


title: HEK293T WT H3K4me3-1


title: HEK293T R617Q H3K4me1-2


title: Small_RNA_B_2


title: HEK293T R617Q H3K4me1-1


title: Small_RNA_B_0


title: Small_RNA_A_18

value: A


title: Small_RNA_B_12


title: HEK293T WT H3K4me1-2


title: Small_RNA_A_16


title: Small_RNA_A_20


title: Small_RNA_A_12


title: Small_RNA_A_14


title: Small_RNA_A_8


title: Small_RNA_A_4


title: HEK293T cells, Hi-C, R617Q

data_processing:
Hi-C data analysis was performed with Hic-Pro (Servant et al., 2015), i.e., sequencing reads were separately aligned to the human reference genome hg19 with a two-step approach using Bowtie2.
We filtered out low mapping quality reads, PCR artifacts, multiple hits and singletons. The uniquely mapped reads were used to build the contact maps for a set of resolutions of 5, 10, 25, 50, 100, 250, 500, 1000 and 2500 kb.
Contact maps were converted into .hic files by the hicpro2juicebox.sh utility for visualization.
Assembly: hg19
Supplementary files format and content: hic

extract_protocol:
Cells were lysed in lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630) and digested in 100 U Mbo I restriction enzyme (NEB) at 37 °C overnight. The DNA ends were marked with biotin-labeled dATPs, and the 5' overhang was filled using the Klenow enzyme. The blunt ends were ligated with T4 DNA ligase for 4 h at RT.
Crude DNA was fragmented into ~400 bp fragments, and biotinylated DNA was pulled down with C1 streptavidin beads. For library preparation, approximately 500 ng of bead DNA was used as the initial material and amplified 5 cycles after adapter ligation.


title: Small_RNA_A_6


title: HEK293T cells, Hi-C, WT


title: Small_RNA_A_10


title: HEK293T cells, MED23/R617Q, 1

data_processing:
RNA-seq raw reads were obtained from an Illumina X-10 sequence analyzer.
Cutadapt was used to remove sequencing adapters and poor-quality base trimming, retaining only reads with a quality score greater than 30 and discarding reads shorter than 50 bp or 75 bp for SE100 or PE150 reads, respectively.
the filtered clean reads were mapped to the human reference genome hg19 with tophat2, and gene quantification and differential expression analysis were performed by cuffdiff with parameters -b -u.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using trizol. 1.3 ug of total RNA was used for the construction of sequencing libraries.
We used a commercial RNA library kit to prepare the RNA-seq library with the manufacturer’s specifications.


title: HEK293T cells, MED23/R617Q, 2


title: HEK293T cells, WT, 2


title: Small_RNA_A_2


title: HEK293T cells, WT, 3


title: HEK293T cells, WT, 1


title: HEK293T cells, MED23/R617Q, 3


title: Small_RNA_B_6


title: Small_RNA_A_0


title: ATAC_C_20

description:
Generation 20
Alternate_Generation_Normalized_ATAC_counts.txt

extract_protocol:
ATAC protocol after Buenrostro et al (2013) & Daugherty et al (2017)
embryos collected for ATAC and RNA protocols by bleaching of worms, embryos ground to release nuclei.


title: hits_23

city: Amsterdam

first: Sanne

last: Hoefnagel

state: Noord-Holland

address: Meibergdreef 9

department: Gastroenterology

country: Netherlands

institute: Academic Medical Centre Amsterdam

data_processing:
Quality control was performed with fastQC. Alignment program TopHat2 (version 2.1.1) (32) and alignment engine Bowtie2 (version 2.2.9) (33) with default parameters were used to map the reads to the Genome reference GRCh build 38 release7. FeatureCounts was used to quantify the reads.
Assembly: GRCh build 38 release7

extract_protocol:
RNA was extracted from biopsies with the AllPrep DNA/RNA/miRNA Universal kit (Qiagen, catalogue number 80224), according to manufacturer’s protocols.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: All patients were diagnosed with NDBE at baseline. Patients who received endoscopic treatment for early cancer or HGD in the past or who progressed within 6 months of follow up were excluded.

tag: disease status

value: Barrett’s esophagus (BE)


title: HEK293T WT H3K4me1-1


title: ATAC_C_18

description:
Generation 18
Alternate_Generation_Normalized_ATAC_counts.txt


title: hits_18


title: hits_26

source_name: Squamous

value: Squamous


title: ATAC_C_16

description:
Generation 16
Alternate_Generation_Normalized_ATAC_counts.txt


title: ATAC_C_14

description:
Gneration 14
Alternate_Generation_Normalized_ATAC_counts.txt


title: hits_28


title: ATAC_C_12

description:
Generation 12
Alternate_Generation_Normalized_ATAC_counts.txt


title: hits_24


title: ATAC_C_10

description:
Generation 10
Alternate_Generation_Normalized_ATAC_counts.txt


title: hits_21


title: hits_20


title: ATAC_C_0

description:
Generation 0
Alternate_Generation_Normalized_ATAC_counts.txt


title: ATAC_C_6

description:
Generation 6
Alternate_Generation_Normalized_ATAC_counts.txt


title: ATAC_C_4

description:
Generation 4
Alternate_Generation_Normalized_ATAC_counts.txt


title: hits_30


title: hits_25


title: hits_32


title: ATAC_C_2

description:
Gneration 2
Alternate_Generation_Normalized_ATAC_counts.txt


title: hits_29

source_name: Duodenum

value: Duodenum


title: hits_31


title: ATAC_B_20


title: ATAC_B_18


title: ATAC_B_14


title: hits_17


title: hits_22


title: hits_15


title: ATAC_B_12


title: ATAC_B_10


title: hits_8


title: hits_7


title: ATAC_B_8

description:
Gneration 8
Alternate_Generation_Normalized_ATAC_counts.txt


title: ATAC_B_6


title: hits_4


title: hits_19


title: ATAC_B_2


title: hits_33


title: hits_1


title: hits_12


title: ATAC_B_0


title: hits_6

source_name: Barrett

value: Barrett


title: ATAC_A_18


title: hits_2


title: hits_16


title: ATAC_B_16


title: ATAC_A_20


title: hits_27


title: ATAC_A_14


title: ATAC_A_12


title: ATAC_A_10


title: ATAC_A_16


title: hits_14


title: sample X103077.001.059

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17.
Reads were mapped to the current Genome Reference Consortium Human genome build 38 patch release 7 (GRCh38.p7) available via GenCode. Alignment was performed using Tophat2 with default parameters.
Based on the mapped read locations in the alignment file, the frequency of how often a read was mapped on a transcript was determined using featureCounts
Assembly: GRCh38.p7
Supplementary files format and content: countfile

source_name: healthy squamous cell tissue from patient with esophageal adenocarcinoma

extract_protocol:
RNeasy Universal Kit/RNeasy Plus Mini Kit/AllPrep DNA/RNA/miRNA Universal kit
NEB #E7420S/L

treatment_protocol: untreated endoscopic biopsies

tag: treatment


title: ATAC_A_8


title: ATAC_A_6


title: hits_10


title: ATAC_A_4


title: ATAC_A_2


title: sample X102842.001.046

value: healthy squamous cell tissue from patient with esophageal adenocarcinoma


title: sample X102842.001.045


title: sample X102842.001.043


title: RNA_C_18

description:
Generation 18
Alternate_Generation_Normalized_RNA_counts.txt

extract_protocol:
TRIzol-chloroform RNA extraction
embryos collected for ATAC and RNA protocols by bleaching of worms, embryos ground to release nuclei.


title: RNA_C_20

description:
Generation 20
Alternate_Generation_Normalized_RNA_counts.txt


title: sample X102842.001.047


title: sample X102842.001.039


title: RNA_C_10

description:
Generation 10
Alternate_Generation_Normalized_RNA_counts.txt


title: sample X102842.001.044


title: sample X102842.001.038


title: sample X103077.001.074

source_name: esophageal adenocarcinoma

value: esophageal adenocarcinoma


title: sample X102842.001.040


title: sample X102842.001.041


title: RNA_C_12

description:
Generation 12
Alternate_Generation_Normalized_RNA_counts.txt


title: RNA_C_2

description:
Gneration 2
Alternate_Generation_Normalized_RNA_counts.txt


title: hits_11


title: RNA_C_0

description:
Generation 0
Alternate_Generation_Normalized_RNA_counts.txt


title: sample X103077.001.070


title: sample X103077.001.065


title: RNA_C_4

description:
Generation 4
Alternate_Generation_Normalized_RNA_counts.txt


title: RNA_C_8

description:
Gneration 8
Alternate_Generation_Normalized_RNA_counts.txt


title: RNA_B_20


title: RNA_B_18


title: sample X103077.001.062


title: sample X103077.001.061


title: ATAC_A_0


title: sample X103077.001.056


title: RNA_B_16

description:
Generation 16
Alternate_Generation_Normalized_RNA_counts.txt


title: RNA_B_14

description:
Gneration 14
Alternate_Generation_Normalized_RNA_counts.txt


title: sample X103077.001.050


title: RNA_C_16


title: RNA_B_10


title: sample X103077.001.048


title: RNA_C_6

description:
Generation 6
Alternate_Generation_Normalized_RNA_counts.txt


title: RNA_B_6


title: sample X103077.001.044


title: sample X103077.001.037


title: sample X103077.001.042


title: sample X103077.001.046


title: sample X103077.001.045


title: sample X103077.001.036


title: sample X103077.001.047


title: RNA_A_20


title: RNA_A_12


title: sample X103077.001.035


title: RNA_B_0


title: sample X103077.001.040


title: sample X103077.001.051


title: RNA_A_14


title: RNA_A_18


title: sample X103077.001.034


title: RNA_A_10


title: RNA_A_8


title: sample X103077.001.030


title: RNA_A_6


title: RNA_B_12


title: sample X103077.001.032


title: RNA_B_8

description:
Generation 8
Alternate_Generation_Normalized_RNA_counts.txt


title: RNA_A_2


title: sample X103077.001.029


title: sample X103077.001.028


title: RNA_B_2

description:
Generation 2
Alternate_Generation_Normalized_RNA_counts.txt


title: RNA_A_16


title: sample X103077.001.026


title: RNA_A_0


title: sample X103077.001.024


title: sample X103077.001.017


title: sample X103077.001.019


title: sample X103077.001.022


title: sample X103077.001.020


title: sample X103077.001.012


title: sample X103077.001.011


title: sample X103077.001.021


title: M026.X1 replicate 2 [RNA-seq]

first: Kaspar

last: Bresser

address: Plesmanlaan 125

department: Hematopoeisis

institute: Sanquin

data_processing:
Obtained reads were aligned to the GRCh38 reference (gencode release 21) using STAR aligner (version 2.5.2b)
transcripts were quantified using Salmon (version 0.7.0)
Transcript counts belonging to a single consensus coding sequence were summed.
Assembly: GRCh38 reference (gencode release 21)
Supplementary files format and content: sf files: output files from salmon in tsv format, quantified reads per transcript
Supplementary files format and content: protein_data.tsv files: contain mRNA TPM values per swissprot identifier.

source_name: Cultured cells

growth_protocol: Patient-derived melanoma cell lines were cultured in RPMI (Gibco) supplemented with 8% fetal calf serum (FCS, Sigma), 100 U/ml penicillin (Gibco) and 100 µg/ml streptomycin (Gibco) at 37 °C and 5% CO2. For mRNA sequencing and ribosome profiling, cell lines were cultured to a density of 70-90% on 150mm Corning tissue-culture treated culture dishes (Merck).

extract_protocol:
Cells were cultured to an approximate density of 80%, and 10·106 cells were subsequently dissociated using a cell-scraper in cold (4 °C) PBS, centrifuged for 10 minutes at 300x g, and snap-frozen in liquid nitrogen. RNA was extracted from the frozen pellets using the RNeasy Mini Kit (Qiagen).
Whole transcriptome sequencing samples were prepared using the TruSeq Stranded mRNA Kit (Illumina). Single-end 65 bp sequencing was performed on a HiSeq 2500 System (Illumina).

tag: tissue source

value: Skin

tag: time point

value: 80% confluency

value: Melanoma cell line


title: NKIRTIL006 replicate 2 [RNA-seq]

tag: cell type


title: SK-MEL-95 replicate 2 [RNA-seq]


title: NKIRTIL006 replicate 2

data_processing:
library strategy: ribosome profiling
Obtained reads were aligned to the GRCh38 reference (gencode release 21) using  the Ribomap pipeline
Transcript counts belonging to a single consensus coding sequence were summed.
Assembly: GRCh38 reference (gencode release 21)
Supplementary files format and content: txt files: Ribsome occupancy values per trancript
Supplementary files format and content: protein_data.tsv files: contain mRNA TPM values per swissprot identifier.

growth_protocol: Cells were cultured to an approximate density of 80%

extract_protocol:
Frozen pellets were resuspended in lysis buffer (20 mM Tris–HCl, pH 7.8, 100 mM KCl, 10 mM MgCl2, 1% Triton X-100, 2 mM DTT, 100 μg/ml cycloheximide, 1× Complete protease inhibitor), and incubated on ice for 20 minutes. Lysates were sheared using a 26G needle, centrifuged for 10 minutes at 1,300x g, and supernatants were transferred to a clean tube. Supernatants were treated with 2 U/μl of RNase I (Ambion) for 45 min at room temperature, with rotation. Next, lysates were fractionated on a linear sucrose gradient (7–47%) using the SW-41Ti rotor (Beckman Coulter) at 221,633x g for 2 hours at 4 °C, without brake. Obtained sucrose gradients were then divided in 14 fractions, and fractions 7–10 (cytosolic ribosomes) were pooled and treated with PCR grade proteinase K (Roche) in 1% SDS to release ribosome protected fragments. The resulting fragments were subsequently purified using Trizol reagent (Invitrogen) and precipitated in the presence of glycogen, following the manufacturer’s instructions.
For library preparation, RNA was gel-purified on a denaturing 10% polyacrylamide urea (7 M) gel. A section corresponding to 25 to 36 nucleotides—the region that comprises the majority of the ribosome-protected RNA fragments—was excised, and purified through ethanol precipitation. RNA fragments were then 3′-dephosphorylated using T4 polynucleotide kinase (New England Biolabs) for 6 hours at 37°C in 2-(N-morpholino)ethanesulfonic acid (MES) buffer (100 mM MES-NaOH pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol, 300 mM NaCl). The 3′ adaptor was added using T4 RNA ligase 1 (New England Biolabs) for 2.5 hours at 37°C. Ligation products were 5′-phosphorylated with T4 polynucleotide kinase for 30 minutes at 37 °C, and the 5′ adaptor was added using T4 RNA ligase 1 for 2 hours at 37 °C.

treatment_protocol: 50·106 cells were subsequently treated with 100 μg/ml cycloheximide for 5 minutes at 37 °C. Cells were then washed once in cold (4 °C) PBS containing 100 μg/ml cycloheximide, dissociated using a cell-scraper in cold (4 °C) PBS supplemented with 100 μg/ml cycloheximide, centrifuged for 10 minutes at 300x g, and snap-frozen in liquid nitrogen.

value: Melanoma


title: NKIRTIL006 replicate 1 [RNA-seq]


title: M026.X1 replicate 1 [RNA-seq]


title: M026.X1 replicate 2


title: SK-MEL-95 replicate 1 [RNA-seq]


title: M026.X1 replicate 1


title: sample X103077.001.009

value: untreated


title: RNA_A_4

value: embryo


title: SK-MEL-95 replicate 2


title: SK-MEL-95 replicate 1


title: sample X103077.001.006


title: sample X103077.001.008


title: NKIRTIL006 replicate 1


title: sample X103077.001.013


title: sample X103077.001.010


title: sample X103077.001.005


title: SRR10203575_H1

city: Fort Worth

first: Kejin

last: Hu

state: TX

address: 3400 Camp Bowie Boulevard

department: Microbiology, Immunology and Genetics

institute: UNT Health Science Center

description:
GSM4101209
reuse of SRA item of SRR10203575
BET_normalizedCount27samples.xlsx
H1

data_processing:
Original image data file from high-throughput sequencing (Illumina) is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
The human refernce genome (assembly GRCH38, release 105) was indexed  using STAR (STAR version 2.7.3a) (runMode  genomeGenerate) on Cheaha supercomputer, and the read fragments of each FASTQ file was aligned to human reference genome using the STAR aligner (version 2.7.3a).
The BAM files were sorted and indexed using SAMtools (version 1.12), and the counting was achieved using HTSeq tools (Htseq-count).
The statistics and normalization of the RNA-seq were conducted using the DESeq2 software (version 1.30.1) on the Cheaha Rstudio server.
Assembly: GRCH38, release 105

growth_protocol: Human iPS cells were cultured in standard feeder-free and serum-free chemically defined E8 media. Human fibroblast BJ cells were cultured in fibroblast media: DMEM: F12 media supplemented with 10% FBS and 5 ng/mL human bFGF

extract_protocol:
BJ fibroblast cells (ATCC, CRL-2522, foreskin fibroblasts) were cultured in six well plates at a density of 2 ´ 105 cells per well. At 24 hrs post seeding, the medium was removed and 2 mL fresh medium containing polybrene (final concentration=5 µg/mL) was added to the wells. The viruse preparations were then added into respective wells (day 0). At 18 hrs after virus addition, the virus-containing spent media were removed and fresh fibroblast medium was added. At 72 hrs after virus removal (on Day 4), the spent medium was removed and 1 mL of TRIzol (Invitrogen; Cat no. 15596018) was added directly to the each well. RNA was extracted following manufacturer’s protocol. After extraction, the RNA was further purified using Quick RNA Miniprep kit (Zymo Research; Cat. no. R1055) using manufacturer’s protocol.
Human mRNAs are captured via oligo(dT) beads. Non-stranded protocol was used. The purified mRNAs are fragmented randomly in fragmentation buffer and the first-strand cDNA is synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). The second strand is subsequently generated by dNTPs, DNA polymerase I and RNase H. Double-stranded cDNA molecules are purified by AMPure XP beads and overhanging ends are repaired to blunt ends by exonuclease/polymerase. After 5’ phosphorylation and 3’ adenylation, the cDNAs are ligated with P5/P7 sequencing adapters to prepare for hybridization. In order to select the insert fragment of preferentially 150~200 bp in length, the modified libraries are purified with AMPure XP system (Beckman Coulter, Beverly, USA). The final library is ready after PCR amplification and products purification by AMPure XP beads.
The following samples were sequenced using DNA nanoball (DNB) technology, BJ48hS1, BJ48hS2, BJ48HS3, hESH1, hESH9, H1P43, H9P69S2.  mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. The obtained mRNA molecules were fragmented into small pieces using fragmentation reagent. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments. The cDNA fragments were amplified  with adapters from previous step. PCR products were purified with Ampure XP Beads (AGENCOURT), and dissolved in EB solution. Library was validated on the Agilent Technologies 2100 bioanalyzer. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and paired end 100 bases reads were generated in the way of sequenced by synthesis.

treatment_protocol: Human fibroblasts BJ were transduced with lentiviral preparation of the indicated genes or BET mutants (MOI, OCT4, 8; SOX2, 5, KLF4, 5; and all others are 3). At 18 hours post transduction, virus-containing spent media were removed and RNAs were extracted 72 hours after virus removal using extraction protocols described.

value: human embryonic stem cells

value: no treatment


title: SRR10203574_H9

description:
GSM4101208
reuse of SRA item of SRR10203574
BET_normalizedCount27samples.xlsx
H9


title: sample X103077.001.004


title: sample X102842.001.037


title: sample X103077.001.003


title: sample X103077.001.001


title: SRR10203573_H1_2

description:
GSM4101207
reuse of SRA item of SRR10203573
BET_normalizedCount27samples.xlsx
H1_2


title: sample X102842.001.034


title: sample X102842.001.031


title: sample X102842.001.032


title: SRR10203571_BJ

description:
GSM4101205
reuse of SRA item: SRR10203571
BET_normalizedCount42samples.xlsx
BET_normalizedCount27samples.xlsx
BJ_3

source_name: BJ

value: BJ

value: foreskin fibroblasts


title: SRR10203572_BJ

description:
GSM4101206
reuse of SRA item: SRR10203572
BET_normalizedCount42samples.xlsx
BET_normalizedCount27samples.xlsx
BJ_4

value: WT


title: SRR10203569_BJ

description:
GSM4101203
reuse of SRA item: SRR10203569
BET_normalizedCount42samples.xlsx
BET_normalizedCount27samples.xlsx
BJ_2


title: SRR10203570_BJ

description:
GSM4101204
reuse of SRA item: SRR10203570
BET_normalizedCount42samples.xlsx
BET_normalizedCount27samples.xlsx
BJ_1


title: sample X102842.001.028


title: sample X102842.001.025


title: sample X102842.001.026


title: sample X102842.001.027


title: sample X102842.001.024


title: sample X102842.001.023


title: primary FBGC MONO_NUCLEATED GC1001318

city: Singapore

first: Harry

last: Park

address: 8 College Rd

country: Singapore

institute: Duke-NUS Medical School

description: primary FBGC MONO_NUCLEATED

data_processing:
Sequencing adapters were removed using Trimmomatic (v.0.36) and the reads quality was checked using FastQC (v.0.11.2) before and after trimming
Reads were aligned to the human genome (GRCh38.primary_assembly.genome.fa; annotation: gencode.v26.annotation.gtf) using HISAT2 package (v.2.1.0)
Reads mapping to multiple loci in the reference genome were discarded. Mapping quality, read distribution, gene body coverage, GC content and rRNA contamination, were checked using picard (v.2.6.0) software
Gene level read counts were computed using HT-Seq-count (v2.7.14, annotation: gencode.v26.annotation.gtf).
Genes with less than 10 aligned reads across all samples were filtered out as lowly expressed genes. Differential gene expression analysis between groups was performed using DESeq2 (v.1.14.1) and significantly differentially expressed genes were reported using fold-change at 1.5 times and below 5 % Benjamini-Hochberg (BH) adjusted p-value
Assembly: GRCh38
Supplementary files format and content: Excel files include baseMean, log2FoldChange, p-value and adjusted p-value

source_name: Primary (donor-derived)

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were re-suspended in RPMI for osteoclasts (Life Technologies) and MEM-REGA 3 (1X) + 10% FBS (Life Technologies) for LGCs and FBGCs.

extract_protocol:
Total RNA was extracted from sorted mononuclear and multinucleated LGCs, FBGCs and osteoclasts using Trizol (Invitrogen) and RNeasy mini kit (Qiagen) according to manufacturer's instructions
Sequencing libraries for osteoclasts were prepared using NEBNext Ultra II Directional RNA Library Prep kit (Illumina). Sequencing libraries for LGCs and FBGCs were prepared with the Lexogen QuantSeq 3' mRNA-Seq Library prep kit according to the manufacturer's instructions.

treatment_protocol: For LGCs and FBGCs, monocytes were purified using a CD14 positive selection kit (StemCell Technologies, Cat # 17858). Monocytes were seeded in 1 well Labtek chamber slides (ThermoFisher Scientific, Cat # 177372) and stimulated with 20 ng/ml M-CSF (PeproTech) for 3 days. At day 3, cells were differentiated with M-CSF (20 ng/ml, PeproTech) and IFN-γ (25 ng/ml, PeproTech, LGC differentiation) or IL-4 (10 ng/ml, PeproTech, FBGC differentiation) for further 4 days with the cell culture media changed every 2 days. For osteoclast generation, monocytes were purified by adherence for 1h at 37 °C, 5% CO2. The monolayer was washed 3 times with HBSS to remove non-adherent cells and monocytes were differentiated into macrophages for 3 days in RPMI media + 10% FBS containing 30 ng/ml M-CSF (PeproTech) and for further 4 days in media containing 30 ng/ml RANKL (PeproTech) and M-CSF

value: Primary (donor-derived)

value: FBGC

value: IL4 FBGC differentiation


title: primary FBGC MULTI_NUCLEATED GC1001321

description: primary FBGC MULTI_NUCLEATED


title: primary FBGC MULTI_NUCLEATED GC1001325

description: primary FBGC MULTI_NUCLEATED


title: primary FBGC MONO_NUCLEATED GC1001324

description: primary FBGC MONO_NUCLEATED


title: primary FBGC MONO_NUCLEATED GC1001322

description: primary FBGC MONO_NUCLEATED


title: primary FBGC MULTI_NUCLEATED GC1001323

description: primary FBGC MULTI_NUCLEATED


title: primary FBGC MULTI_NUCLEATED GC1001319

description: primary FBGC MULTI_NUCLEATED


title: sample X102842.001.035


title: sample X102842.001.036


title: primary FBGC MULTI_NUCLEATED GC1001327

description: primary FBGC MULTI_NUCLEATED


title: sample X102842.001.022


title: sample X102842.001.020


title: primary FBGC MULTI_NUCLEATED GC1001317

description: primary FBGC MULTI_NUCLEATED


title: primary FBGC MONO_NUCLEATED GC1001316

description: primary FBGC MONO_NUCLEATED


title: sample X102842.001.013


title: sample X102842.001.019


title: primary FBGC MONO_NUCLEATED GC1001314

description: primary FBGC MONO_NUCLEATED


title: sample X102842.001.014


title: primary FBGC MULTI_NUCLEATED GC1001315

description: primary FBGC MULTI_NUCLEATED


title: primary LGC MULTI_NUCLEATED GC1001313

description: primary LGC MULTI_NUCLEATED

value: LGC

value: IFNG LGC differentiation


title: sample X102842.001.011

value: esophageal adenocarcinoma


title: primary LGC MONO_NUCLEATED GC1001312

description: primary LGC MONO_NUCLEATED


title: primary FBGC MONO_NUCLEATED GC1001320

description: primary FBGC MONO_NUCLEATED


title: sample X102697.001.075


title: sample X102697.001.074


title: primary LGC MONO_NUCLEATED GC1001310

description: primary LGC MONO_NUCLEATED


title: primary LGC MULTI_NUCLEATED GC1001309

description: primary LGC MULTI_NUCLEATED


title: sample X102697.001.072


title: sample X102697.001.073


title: sample X102697.001.071


title: sample X102697.001.070


title: sample X102697.001.069


title: primary LGC MULTI_NUCLEATED GC1001307

description: primary LGC MULTI_NUCLEATED


title: primary LGC MONO_NUCLEATED GC1001306

description: primary LGC MONO_NUCLEATED


title: primary LGC MONO_NUCLEATED GC1001304

description: primary LGC MONO_NUCLEATED


title: primary LGC MULTI_NUCLEATED GC1001305

description: primary LGC MULTI_NUCLEATED


title: primary LGC MONO_NUCLEATED GC1001308

description: primary LGC MONO_NUCLEATED


title: primary LGC MULTI_NUCLEATED GC1001303

description: primary LGC MULTI_NUCLEATED


title: sample X102697.001.067


title: sample X102697.001.065


title: primary LGC MULTI_NUCLEATED GC1001311

description: primary LGC MULTI_NUCLEATED


title: primary LGC MONO_NUCLEATED GC1001302

description: primary LGC MONO_NUCLEATED


title: sample X102842.001.009


title: HF

city: Hangzhou

first: Qingbo

last: Xu

state: Zhejiang

address: 79 Qingchun Road

department: Department of Cardiology

institute: First Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
Data were processed following standard protocols using Cell Ranger version 5.0.0.
Cellranger mkfastq was used to demultiplex raw base call files into fastq files.
Cellranger count was used to perform alignment, filtering, barcode counting, UMI counting, and to generate feature-barcode matices.
Assembly: mm10
Supplementary files format and content: TSV data for genes and barcodes; MTX data for gene expression matrix

source_name: heart

extract_protocol:
After collecting the human heart, the tissue was minced into fine pieces using a scalpel and transferred into a glass vial with 1.5 ml of cold digestion buffer (Liberase, Roche). The tissues were digested by either using a shaking (100 rpm) 37°C waterbath for 15 min. The obtained cell suspension was gently pipetted up and down (10 x) and transferred onto a 70μm cell strainer placed on top of a 50ml Falcon tube. The tissue was gently rubbed through the strainer using the plunger of a 1ml syringe, after which the strainer was rinsed with 8.5ml of DMEM to obtain a total volume of 10 ml, which was centrifuged for 6 min at 4°C at 300 xg. After the supernatant was removed, non-cardiomyocytes samples pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. After washing with PBS, cells were filtered with 40 μm filter and then centrifuged at 300xg for 5 minutes. Cells resuspended in PBS were stained with LIVE/DEAD Fixable Near-IR (APC/Cy7 channel) Dead Cell Stain Kit (Invitrogen; L34975, 1:1000) and Hoechst 33342 (Invitrogen; H3570, 1:1000) for 20 minutes. Unstained cells and cells staining with only 1 fluorochrome prepared concomitantly served as control. After 1 wash in PBS for 5 minutes, cells were resuspended in PBS and then sorted by Flow Cytometer. Nucleated live cells (Hoechst+/APC/Cy7− population) were sorted into PBS with 0.04% BSA for subsequent scRNA-seq.
RNA libraries were prepared with Chromium™ Single Cell 3′ Reagent Kit v3 chemistry (10× Genomics) according to the manufacturer's protocol.

value: heart

tag: condition

value: heart failure heart with the history of hypertension

value: Total non-cardiomyocytes isolated from the human heart


title: scATAC-seq_RCC120

city: Nanning

first: Zhenyuan

last: Yu

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

library_source: genomic single cell

data_processing:
Preliminary sequencing results (bcl files) were converted to FASTQ files with Cell Ranger V3.0 and CellRanger ATAC V1.2.0
The CellRanger (10X Genomics) secondary analysis pipeline was used to generate a digital gene expression matrix
Normalization and additional analysis by Seurat and Signac R package
Assembly: GRCh38 for human data
Supplementary files format and content: The barcodes, genes, expression matrix files for scRNA-seq. The peaks.bed, singlecell.csv and fragments.tsv.gz files for scATAC-seq.

source_name: scATAC-seq of ccRCC

extract_protocol:
We used 10x Genomics Chromium Single Cell 3′ Reagents Kit v3 user guide   to perform single cell suspension which were prepared before. Briefly, the single-cell samples were passed through a 40μm cells strainer and counted using  a hemocytometer with trypan blue. Subsequently, the appropriate volume for each sample was calculated to  recover 10,000 cells. With the 10x protocol, we added the single cells, the Gel Beads and the  oils onto the 10x Genomics single-cell-A chip and run this machine. After droplet generation, samples were transferred onto a PCR tube and reverse  transcription was performed using T100 Thermal Cycler (BIO-RAD). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x genomics followed by a Silane DynaBead clean-up as outlined in the user guide. Purified cDNA was amplified for 10 cycles before being cleaned up by using SPRIselect beads. The samples were detected by Qubit2.0 Fluorometer (invitrogen) to determine cDNA concentration.
Suitable nuclei concentrations were adjusted from the above experiment. As mentioned in the previous study (avoiding potential cell duplets), the number of target nucleus captured in each sample was 6,000. We adopted 10x Genomics ‘Chromium Single Cell ATAC Reagent Kits User Guide’ for library preparation (https://support.10xgenomics.com/single-cell-atac/library-prep/doc/technical-note-chromium-next-gem-single-cell-atac-v11-reagent-workflow-and-software-updates). Briefly, the ATAC Buffer (10x Genomics, 200122) and ATAC Enzyme (10x Genomics, 200123) were added to the 5 µL nuclei, which was incubated for 60 min at 37 °C. We prepared ‘Master Mix’, including 56.5 µL of Barcoding Reagent B (10x Genomics, 2000194), 1.5 µL of Reducing Agent B (10x Genomics, 2000087) and 2 µL of Barcoding Enzyme (10x Genomics, 2000125). After mixing the nuclei with the Master Mix, we added it to the Chromium Chip E (10x Genomics, 2000121). At the same time, we added Partitioning Oil (10x Genomics, 220088) and Chromium Single Cell ATAC Gel Beads (10x Genomics, 2000132) to the Chromium Chip E. The Chromium Chip E was placed into a Chromium Single Cell Controller instrument (10x Genomics) before attaching a 10x Gasket (10x Genomics, 3000072). Then, the Chromium Single Cell Controller Instrument could be run.  The gel bead in emulsions (GEMs) were generated after the above steps. Subsequently, GEMs were incubated and cleaned by using Dynabeads (10x Genomics, 2000048) and SPRIselect (Beckman Coulter, B23318). scATAC-seq library construction eliminates the process of reverse transcription compared with scRNA-seq. PCR was performed after ‘Sample Index PCR Mix’ and Single Index Kit N Set A (10x Genomics, 1000212) were added into the samples. The details of PCR parameters could be referred to Chromium Single Cell ATAC Reagent Kits User Guide. DNA libraries were sequenced by NovaSeq 6000 (Illumina, San Diego, CA). Consistent with previous studies, we followed the 2 × 50 paired-end sequencing scheme: 50 bp read 1N, 8 bp i7 index, 16 bp i5 index and 50 bp read 2N.
10X Genomics Single Cell 3' v3 Reagent Kit and Chromium Single Cell ATAC Reagent Kits V1

value: Total clear cell renal cell carcinoma Homogenate


title: Control

value: donor heart


title: primary osteoclasts MULTI_NUCLEATED osteoclast_16

description: primary osteoclasts MULTI_NUCLEATED

value: osteoclasts

value: RANKL osteoclast differentiation


title: sample X102697.001.062

value: untreated


title: scRNA-seq_RCC119

source_name: scRNA-seq of ccRCC


title: sample X102697.001.061


title: scRNA-seq_RCC120


title: scATAC-seq_RCC116


title: scRNA-seq_RCC115


title: scATAC-seq_RCC115


title: sample X102697.001.068


title: primary osteoclasts MULTI_NUCLEATED osteoclast_14

description: primary osteoclasts MULTI_NUCLEATED


title: sample X102697.001.060


title: scATAC-seq_RCC114


title: scRNA-seq_RCC116


title: sample X102697.001.064


title: primary osteoclasts MONO_NUCLEATED osteoclast_15

description: primary osteoclasts MONO_NUCLEATED


title: primary osteoclasts MONO_NUCLEATED osteoclast_12

description: primary osteoclasts MONO_NUCLEATED


title: sample X102697.001.059


title: primary osteoclasts MULTI_NUCLEATED osteoclast_20

description: primary osteoclasts MULTI_NUCLEATED


title: scATAC-seq_RCC113


title: scRNA-seq_RCC114


title: primary osteoclasts MULTI_NUCLEATED osteoclast_11

description: primary osteoclasts MULTI_NUCLEATED


title: primary osteoclasts MONO_NUCLEATED osteoclast_18

description: primary osteoclasts MONO_NUCLEATED


title: sample X102697.001.057


title: scRNA-seq_RCC113


title: primary osteoclasts MULTI_NUCLEATED osteoclast_9

description: primary osteoclasts MULTI_NUCLEATED


title: scATAC-seq_RCC112


title: sample X102697.001.058


title: scATAC-seq_RCC106


title: sample X102697.001.056


title: scATAC-seq_RCC119


title: scRNA-seq_RCC112


title: scRNA-seq_RCC106


title: primary osteoclasts MONO_NUCLEATED osteoclast_7

description: primary osteoclasts MONO_NUCLEATED


title: sample X102697.001.055


title: scATAC-seq_RCC104


title: scRNA-seq_RCC104


title: sample X102697.001.054


title: scATAC-seq_RCC103


title: scATAC-seq_RCC101


title: primary osteoclasts MULTI_NUCLEATED osteoclast_6

description: primary osteoclasts MULTI_NUCLEATED


title: scRNA-seq_RCC103


title: primary osteoclasts MONO_NUCLEATED osteoclast_5

description: primary osteoclasts MONO_NUCLEATED


title: scRNA-seq_RCC101


title: sample X102697.001.052


title: sample X102697.001.051


title: scATAC-seq_RCC100


title: scATAC-seq_RCC99


title: primary osteoclasts MONO_NUCLEATED osteoclast_1

description: primary osteoclasts MONO_NUCLEATED


title: sample X102697.001.050


title: primary osteoclasts MULTI_NUCLEATED osteoclast_3

description: primary osteoclasts MULTI_NUCLEATED


title: primary FBGC MONO_NUCLEATED GC1001326

description: primary FBGC MONO_NUCLEATED


title: scATAC-seq_RCC94


title: scRNA-seq_RCC99


title: MA1748

city: Bloomington

first: Ellen

middle: D

last: Ketterson

state: IN

address: 1001 E. Third Street

institute: Indiana University

data_processing:
Read sequences were de-multiplexed using bcl2fastq (software versions v2.20.0.422).
Sequencing reads were trimmed for quality and adapters using Trimmomatic (v0.33 for all samples) with the following parameters: ILLUMINACLIP:adapters.fa:3:20:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:25
Reads were mapped to the Junco genome using STAR (v2.7.2b) with the following parameters: --outSAMattributes All --outSAMunmapped Within --outReadsUnmapped Fastx --outFilterMultimapNmax 1 --seedSearchStartLmax 16 --quantMode GeneCounts --twopassMode Basic --outWigType wiggle --outWigStrand Unstranded --outWigNorm None --outSAMtype BAM SortedByCoordinate
Read counts for genes were generated with featureCounts from the subread package (v1.6.0) with the following parameters: -F SAF --fracOverlap 0.51 --primary -p -O -s 2 -Q 30 -T 30
Genome_build: dark_eyed_junco genome equivalent to genome on Ensemble and accessible here: ftp://ftp.ebi.ac.uk/pub/databases/ena/wgs/public/qzw/QZWM01.fasta.gz
Supplementary_files_format_and_content: Processed data files are tab-delimited files indicating the number of reads from a given sample (column) associated with a given gene (row)

organism: Junco hyemalis

source_name: feather

growth_protocol: We plucked the 6th, 4th, and 2nd rectrices from both left and right side of the tail (6 feathers total) from 6 Dark-eyed junco individuals to induce feather development. Developing feathers were collected 14 days later, by which time the length of the developing pin was approximately 1cm, and 1-1.5 cm long plumes were erupting from the tip of the pin. Feathers were collected by grabbing and pulling the developing pin at the base of the feather with curved forceps. The two 4th rectrices, which show incomplete pigmentation along the long axis were dissected on sterile culture dishes to separate the apigmented and the pigmented feather regions. The dissected samples were then immediately placed in a sterile 1.5ml centrifuge tube and flash-frozen on pulverized dry ice. The 6th and 2nd rectrices were flash-frozen without dissection as these feathers are either completely pigmented or apigmented. Feathers were then transferred to a -80C freezer until RNA extraction.

extract_protocol:
RNA was extracted using the Maxwell RSC automated nucleic acid extraction system (Promega, Madison, WI, USE; product number AS4500), using the Maxwell RSC simplyRNA Tissue kit (Promega, AS1340), following the manufacturer’s instructions. RNA was eluted in double-distilled water, and frozen at -80C.
RNA integrity was analyzed with Agilent Technologies 2200 Tape Station (Agilent Technologies). Input was quantified by using Qubit RNA BR Assay Kit. Samples were prepared using TruSeq Stranded mRNA HT Sample Prep Kit (Illumina). Sequencing was performed using an Illumina NextSeq 500/550 Kits v2 reagents with 75 bp sequencing module.

tag: side

value: right

tag: position

value: 6th rectrix

tag: pigmentation

value: apigmented

tag: individual animal id

tag: rna extraction batch


title: sample X102697.001.048


title: scRNA-seq_RCC94


title: MA1747

value: 4th rectrix


title: scATAC-seq_RCC96


title: scRNA-seq_RCC96


title: sample X102697.001.044


title: scATAC-seq_RCC87


title: scATAC-seq_RCC86


title: scRNA-seq_RCC87


title: scATAC-seq_RCC84


title: scRNA-seq_RCC100


title: sample X102697.001.042


title: scRNA-seq_RCC84


title: MA1743

value: left


title: MA1742

value: pigmented


title: MA1744

value: 2nd rectrix


title: scATAC-seq_RCC81


title: sample X102697.001.043


title: scRNA-seq_RCC86


title: sample X102697.001.039


title: sample X102697.001.041


title: MA1746


title: scRNA-seq_RCC81


title: sample X102697.001.046


title: iPSC, BRD3RDBD1, P16

value: human induced pluripotent stem cells

value: WT

value: no treatment


title: hESC, H9, passage 69, sample 2

description:
BET_normalizedCount27samples.xlsx
BET_normalizedCount27samples.xlsx
H9P69S2

value: human embryonic stem cells


title: sample X102697.001.036

value: esophageal adenocarcinoma


title: BJ, OSK, BRD4SDBD1DET, replicate b

description:
BET_normalizedCount42samples.xlsx
BET_normalizedCount27samples.xlsx
OSK335b

value: BJ

value: foreskin fibroblasts

value: OCT4, SOX2, KLF4, BRD4SDBD1DET

value: lentiviral OSK + BRD4SDBD1DET


title: BJ, OSK, BRD4SDBD1DET, replicate a

description:
BET_normalizedCount42samples.xlsx
BET_normalizedCount27samples.xlsx
OSK335a


title: MA1745


title: hESC, H1, passage 43, 2022

description:
BET_normalizedCount27samples.xlsx
BET_normalizedCount27samples.xlsx
H1P43


title: MA1739


title: sample X102697.001.035

value: untreated


title: hESC, H9, 2022

description:
BET_normalizedCount27samples.xlsx
BET_normalizedCount27samples.xlsx
hESH9


title: MA1738

value: right


title: BJ, OSK, BRD2DBD1DET, replicate b

description:
BET_normalizedCount42samples.xlsx
BET_normalizedCount27samples.xlsx
OSK357b

value: OCT4, SOX2, KLF4, BRD2DBD1DET

value: lentiviral OSK + BRD2DBD1DET


title: sample X102697.001.032


title: BJ, 72 hours, sample 3

description:
BET_normalizedCount27samples.xlsx
BET_normalizedCount27samples.xlsx
BJ72HS3


title: sample X102697.001.030


title: BJ, OSK, BRD2DBD1DET, replicate a

description:
BET_normalizedCount42samples.xlsx
BET_normalizedCount27samples.xlsx
OSK357a


title: hESC, H1, 2022

description:
BET_normalizedCount27samples.xlsx
BET_normalizedCount27samples.xlsx
hESH1


title: BJ, 48 hours, sample 3

description:
BET_normalizedCount27samples.xlsx
BET_normalizedCount27samples.xlsx
BJ48HS3


title: BJ, OSK, BRD3RDBD1, replicate b

description:
BET_normalizedCount42samples.xlsx
BET_normalizedCount27samples.xlsx
OSK251b

value: OCT4, SOX2, KLF4, BRD3RDBD1

value: lentiviral OSK + BRD3RDBD1


title: MA1737

value: left

value: pigmented


title: MA1736

value: 4th rectrix

value: apigmented


title: MA1735


title: BJ, 48 hours, sample 2

description:
BET_normalizedCount27samples.xlsx
BET_normalizedCount27samples.xlsx
BJ48hS2

value: WT

value: no treatment


title: BJ, OSK, BRD3RDBD1, replicate a

description:
BET_normalizedCount42samples.xlsx
BET_normalizedCount27samples.xlsx
OSK251a


title: sample X102697.001.029

value: esophageal adenocarcinoma


title: sample X102697.001.028


title: BJ, 48 hours, sample 1

description:
BET_normalizedCount27samples.xlsx
BET_normalizedCount27samples.xlsx
BJ48hS1

value: BJ


title: MA1734

value: 6th rectrix


title: BJ, OSK, BRD4S, replicate b

description:
BET_normalizedCount42samples.xlsx
OSK333b

value: foreskin fibroblasts

value: OCT4, SOX2, KLF4, BRD4S

value: lentiviral OSK + BRD4S


title: sample X102697.001.026

value: untreated


title: MA1741


title: MA1740

value: right


title: BJ, OSK, BRD4S, replicate a

description:
BET_normalizedCount42samples.xlsx
OSK333a


title: sample X102697.001.033


title: sample X102697.001.025


title: BJ, OSK, BRD3, replicate b

description:
BET_normalizedCount42samples.xlsx
OSK232b

value: OCT4, SOX2, KLF4, BRD3

value: lentiviral OSK + BRD3


title: MA1733


title: DEtail-seq K12 ICeuI

source_name: bacteria

value: bacteria

tag: sample type

value: 3' end of DNA break

value: I-CeuI digestion


title: Glioma 4704

city: chengdu

first: huang

last: liang

address: No.24, South First Section, First Ring Road, Wuhou District, Chengdu City

institute: sicuan university

description: CD45+ cells from glioma

data_processing:
Alignment and quality control of sequencing data: The Cell Ranger Software Suite (version 3.0.2; 10x Genomics) was used to perform sample de-multiplexing, alignment, barcode processing and unique molecular identifier (UMI) counting. Briefly, sequencing reads were aligned against the GRCh38 human reference genome with STAR[PMID: 23104886], and count matrices were built from the resulting BAM files.     Quality of cells were then assessed based on three metrics step by step: (1) The number of total UMI counts per cell (library size); (2) The number of detected genes per cell; (3) The proportion of mitochondrial gene counts. The following criteria were then applied to filter low-quality cells:UMI number > 1000, gene number < 200, ribosomal gene proportion > 0.4 or mitochondrial gene proportion > 0.3.
Integration of cell from different samples: Gene-cell matrix of all samples was integrated with Seurat to remove batch effects across different samples. In parameter settings, the first 30 dimensions of canonical correlation analysis (CCA) and principal-component analysis (PCA) were used.
Dimensionality reduction and visualization: The filtered gene-cell matrix was first normalized using ‘LogNormalize’ methods in Seurat v.3 with default parameters. The top 2,000 variable genes were then identified using the ‘vst’ method in Seurat FindVariableFeatures function. PCA was performed using the top 2,000 variable genes. Then UMAP was performed on the top 30 principal components for visualizing the cells.
Clustering of cells: Graph-based clustering was performed on the PCA-reduced data for clustering analysis with Seurat v.3. The resolution was set to 0.5 to obtain a finer result. Briefly, the first 50 PCs of the integrated gene-cell matrix were used to construct a shared nearest-neighbor graph (SNN; FindNeighbors() in Seurat) and this SNN was used to cluster the dataset (FindClusters()) using a graph-based modularity-optimization algorithm of the Louvain method for community detection.
Cluster-specific biomarker analysis: Wilcoxon rank sum test in FindAllMarkers() in Seurat was used to perform differential gene expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: None

source_name: CD45+ cells isolated from tumor of glioma-bearing mice brain by magnetic cell sorting 4704

extract_protocol:
Chromium Single cell 3’ Reagent v2 (or v3) Kits according to the manufacturer’s protocol.
The libraries were constructed by Oebiotech (China) and sequenced on the Illumina sequencing platform (HiSeq X Ten) and 150 bp paired-end reads were generated (Oebiotech, China).

value: tumor

tag: cell marker


title: sample X102697.001.024


title: MA1731

value: left

value: apigmented


title: sample X102697.001.023


title: BJ, OSK, BRD3, replicate a

description:
BET_normalizedCount42samples.xlsx
OSK232a

tag: cell line


title: Glioma 4703

description: CD45+ cells from glioma

source_name: CD45+ cells isolated from tumor of glioma-bearing mice brain by magnetic cell sorting 4703


title: BJ, OSK, BRD2, replicate b

description:
BET_normalizedCount42samples.xlsx
OSK353b

value: OCT4, SOX2, KLF4, BRD2

value: lentiviral OSK + BRD2


title: BJ, OSK, BRD2, replicate a

description:
BET_normalizedCount42samples.xlsx
OSK353a

value: BJ


title: MA1729

value: 4th rectrix


title: MA1730

value: 6th rectrix


title: sample X102697.001.018

value: esophageal adenocarcinoma


title: Control 4711

description: CD45+ cells from brain

source_name: CD45+ cells isolated from normal mice brain by magnetic cell sorting 4711

value: brain


title: Glioma 1450

description: CD45+ cells from glioma

source_name: CD45+ cells isolated from tumor of glioma-bearing mice brain by magnetic cell sorting 1450


title: Glioma 4702

description: CD45+ cells from glioma

source_name: CD45+ cells isolated from tumor of glioma-bearing mice brain by magnetic cell sorting 4702


title: sample X102697.001.020

value: untreated


title: BJ, OSK, replicate c

description:
BET_normalizedCount42samples.xlsx
BET_normalizedCount27samples.xlsx
OSKc

value: foreskin fibroblasts

value: OCT4, SOX2, KLF4, GFP

value: lentiviral OSK + GFP


title: sample X102697.001.017


title: MA1728

value: right

value: pigmented


title: sample X102697.001.016


title: BJ, OSK, replicate a

description:
BET_normalizedCount42samples.xlsx
BET_normalizedCount27samples.xlsx
OSKa


title: MA1732


title: Control 4709

description: CD45+ cells from brain

source_name: CD45+ cells isolated from normal mice brain by magnetic cell sorting 4709


title: MA1726

value: 2nd rectrix


title: MA1727


title: sample X102697.001.014


title: Control 4187

description: CD45+ cells from brain

source_name: CD45+ cells isolated from normal mice brain by magnetic cell sorting 4187


title: BJ, BRD4SDBD1DET, replicate c

description:
BET_normalizedCount42samples.xlsx
KH335c

value: lentiviral BRD4SDBD1DET


title: MA1725

value: left


title: BJ, BRD4SDBD1DET, replicate b

description:
BET_normalizedCount42samples.xlsx
KH335b


title: sample X102697.001.013


title: MA1724


title: sample X102697.001.011


title: BJ, BRD4SDBD1DET, replicate a

description:
BET_normalizedCount42samples.xlsx
KH335a


title: Control 4710

description: CD45+ cells from brain

source_name: CD45+ cells isolated from normal mice brain by magnetic cell sorting 4710


title: BJ, OSK, replicate b

description:
BET_normalizedCount42samples.xlsx
BET_normalizedCount27samples.xlsx
OSKb


title: sample X102697.001.005

source_name: esophageal adenocarcinoma


title: P12WT3

city: San Francisco

first: Yan

address: 513 Parnassus Avenue

department: Orofacial Sciences

institute: UCSF

data_processing:
Basecalls performed using CASAVA
the details of Illumina Sequencing identifier are as follows: (1) HWI-ST1276:71 HWI-ST1276, Instrument - unique identifier of the sequencer; 71, run number - Run number on instrument; (2) C1162ACXX:1:1101:1208:2458 means the coordinate of read on C1162ACXX (Flowcell ID) flowcell, line 1, 1101 tile is(x=1208, y=2458); (3) 1:N:0:CGATGT the first number is 1 or 2, 1 refers to single reads or the first read of paired ends, 2 refers to the second of paired ends; the second letter means whether reads is adjusted(Y means yes, N means no); the third number represent the number of Control Bits in sequence; six bases on the fourth place is Illumina index sequence. The sequencing reads/raw reads often contain low quality reads or reads with adaptors, which will affect the quality of downstream analysis. To avoid this, it is necessary to filter the raw reads and obtain the clean reads. Mapping clean reads to the reference genome or the transcriptome is the basis for the next following analysis. For human and mice, the species with completed annotation, when only differential expression gene(quantification) analysis is needed, the raw data can map reads to the transcriptome directly. However, in studies on transcript structural variation, such as alternative splicing, variation, the fusion gene, the alignment should be carried out at the genomic level.
Mapped regions can be classified as exons, introns, or intergenic regions. Exon-mapped reads should be the most abundant type of read when the reference genome is well-annotated. Intron-reads may be derived from pre-mRNA contamination or intron-retention from alternative splicing. Reads mapped to intergenic regions are mainly attributed to weak annotation of the reference genome. The distribution of sequencing reads of all samples in the genomic region is shown in the figure below.
Assembly: mm39
Supplementary files format and content: txt format--a standard file format that contains mapping results–indicate the information of the corresponding referenced genome and gene annotations for some species.

source_name: first molar enamel organ cells

growth_protocol: C57BL/6  mouse colony was purchased from JAX Laboratory. The mice have been maintained in UCSF Laboratory Animal Rsource Center (LARC)

extract_protocol:
P5 and P12 pups were euthanized and the first molars were microdissected from those wild type pups. After the first molars were obtained, the pup tissues were removed from molars.
The remaining molars were placed into TRIzol solution and homogenized, the total RNA from the enamel organ cells were purified by using Zymo quick RNA purification kit.
Total RNA went through polyA caputure to remove rRNA removal), RNA was fragmented, and reverse transcription was performed to generate cDNA library.

treatment_protocol: No specific treatment has been applied to these animals.

tag: strain

value: first molar enamel organ cells

tag: cell source

value: epithelially derived cells

value: wt

tag: age


title: sample X102697.001.002

tag: tissue


title: MA1723

value: apigmented


title: MA1722


title: MA1721

value: 4th rectrix


title: BJ, BRD4S, replicate a

description:
BET_normalizedCount42samples.xlsx
KH333a

source_name: BJ

value: BJ

tag: genotype

tag: treatment

value: lentiviral BRD4S


title: BJ, BRD4S, replicate b

description:
BET_normalizedCount42samples.xlsx
KH333b


title: CRC1707

first: Vinay

last: Tergaonkar

address: 61 Biopolis Drive,  Proteos

institute: Institute of Molecular and Cell Biology

data_processing:
FASTQ files of ATAC-seq data were processed by cutadapt for adapter removal. Trimmed reads were mapped against human genome (hg19) using bowtie2 aligner
Alignment files were filtered by sambamba tool for duplicates
Filtered mapping files were processed by MACS2 for peaks calling
DiffBind was used to identify the deferentially bound peaks between samples.
ATAC-seq profiles were generated using UCSC genome browser (hg19)
Genome_build: hg19

source_name: Colon

growth_protocol: Primary colorectal cancer cell lines were grown in 6-well tissue-culture treated plates (Falcon) precoated with Coating Matrix Kit (Gibco), and were maintained in DMEM/F12 medium (Gibco) supplemented with penicillin streptomycin (Gibco), B27 (without vitamin A, Gibco), 20ng/mL EGF (Gibco), and 10ng/mL bFGF (Gibco).

extract_protocol:
omni-ATAC-seq
ATAC seq library was prepared as described previously in PMID: 28846090. 50,000 cells were lysed for nuclei isolation. Transposition reaction was performed using Nextera DNA library preparation kit (NEB). Samples were amplified by eight PCR cycles for library preparation. Primer dimers and long DNA fragments were cleaned by AMPure XP beads purification step. DNA concentration was measured by Qubit fluorometric assay and library quality was determined by Bioanalyzer.

tag: cancer type

value: colon cancer


title: MA1719


title: P12WT2

tag: cell type


title: CRC1391

value: untreated


title: P5WT5


title: MA1720


title: P12WT1


title: AsiSI_mmSC2

data_processing:
Illumina Casava1.7 software used for basecalling.
Duplicated reads which had same sequences for both forward and reverse reads were removed
Reads were aligned to the reference genome with Bowtie2 using --local settings
For visualization and spliting strand, the aligned reads files (BAM) including second read in pairs were converted to first single base bigWig file with 1bp bins using bamCoverage from deepTools with --binSize 1 --Offset 1 --samFlagInclude 128 --filterRNAstrand forward/reverse.The option --filterRNAstrand forward means Crick strand and --filterRNAstrand reverse means Waston strand.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: Detail-seq

source_name: sertoli cells (SC)

extract_protocol:
Testes from adult C57BL/6 mice were removed and decapsulated. The seminiferous tubules were tore into small pieces and incubated in 8 ml PBS containing 1 mg/ml collagenase (Sigma, C5138, St. Louis, MO, USA) and 1 mg/ml hyaluronidase (Sigma, H3506, St. Louis, MO) at 37°C for 6 min with gentle shaking. After pipetting, the dispersed seminiferous tubules and cells were incubated at 37°C for 5 min with gentle shaking. Then, the cells were collected by centrifugation at 200 × g for 5 min at 4°C, washed once with PBS, resuspended in 15 ml PBS containing 0.25% Trypsin and 1 mg/ml DNase I, and incubated at 37°C for 5 min with gentle shaking. Thereafter, the cells were collected and washed with PBS containing 0.5% BSA. After filtration through a 40 μm Nylon Cell Strainer, the cells were separated by sedimentation velocity at unit gravity at 4°C, using a 2–4% BSA gradient in PBS. The cell fractions were bottom-loaded in a volume of 300 ml. An aliquot of each fraction was examined by light microscope to assess cellular purity and cell type identity.
Each cell pellet was resuspended in 150 µl 50 mM EDTA pH 8.0 and allowed to thaw at 40°C. 498 µl LMP agarose (2% in 50 mM EDTA pH 8.0) was mixed with 102 µl Solution 1 (1 M sorbitol, 0.1 M sodium citrate, 60 mM EDTA pH 7.0, 5% β-mercaptoethanol and 1 mg/ml zymolyase 100T) and the mix was pre-warmed at 40°C before adding to the cells. The resuspended cells were pipetted into plug molds and chilled at 4°C for 30 min. Once solidified, the agarose plugs were cut into small pieces (one agarose plug to 16~24 pieces), and expressed into 1 ml of Solution 2 (0.45 M EDTA pH 8.0, 0.01 M Tris-HCl pH 7.5, 7.5% β-mercaptoethanol, 10 µg/ml RNase A) and incubated at 37°C for overnight. Plugs were quickly washed three times with 1 ml TE buffer, and then washed five times with TE buffer incubated at 37°C for 6min (total 30min). Then plugs were expressed into 1ml Solution 3 (0.25 M EDTA pH 8.0, 0.01 M Tris-HCl pH 7.5, 1% SDS, 1 mg/ml proteinase K) and incubated at 54°C overnight. Plugs were finally washed six times with TE buffer and stored in plug storage solution (0.05 M EDTA pH 8.0, 50% glycerol) at -20°C until all plugs were ready to be processed for library preparation.  The plugs were transferred to a PCR tube, and washed by 30 µl 1X Adaptase buffer (Swift, Accel-NGS, 10096) twice at room temperature, 10 min each time. Add 47 µl 1X Adaptase buffer and 3 µl Adaptase (Swift, Accel-NGS, 10096) to PCR tube, incubated with plugs at 37°C for 2 h. Removed buffer, and deactivated Adaptase in plugs by 98°C for 2 min. Purified DNA from plugs by Gel Extraction Kit (Qiagen, 28606). Sonicated DNA to 150~250 bp fragments by using Focused-ultrasonicator (Covaris, S220). The rest steps were following the manual of Accel-NGS 1S Plus DNA Library Kit (Swift, Accel-NGS, 10096). Briefly, denatured DNA fragments to ssDNA, and extended it to dsDNA. After purification, 2rd adaptor was ligated. After indexing PCR and purification, preparation of DEtail-seq library was finished. The DEtail-seq library was sequenced by NovaSeq 6000 (Illumina).

value: sertoli cells (SC)

value: AsiSI


title: BJ, BRD2DBD1DET, replicate a

description:
BET_normalizedCount42samples.xlsx
KH357a

value: foreskin fibroblasts

value: lentiviral BRD2DBD1DET


title: AsiSI_mmSC1


title: BJ, BRD2DBD1DET, replicate c

description:
BET_normalizedCount42samples.xlsx
KH357c


title: BJ, BRD2DBD1DET, replicate b

description:
BET_normalizedCount42samples.xlsx
KH357b


title: MA1718

value: pigmented


title: CRC1489


title: P12WT4


title: CRC1846


title: BJ, BRD2, replicate b

description:
BET_normalizedCount42samples.xlsx
KH353b

value: lentiviral BRD2


title: MA1716

value: right

value: 6th rectrix


title: MA1717

value: left


title: BJ, BRD2, replicate a

description:
BET_normalizedCount42samples.xlsx
KH353a


title: P5WT3

value: first molar enamel organ cells

value: epithelially derived cells


title: P5WT4

value: wt


title: CRC948


title: MA1715

value: 4th rectrix

value: apigmented


title: BJ, BRD3RDBD2, replicate c

description:
BET_normalizedCount42samples.xlsx
KH256c

value: BJ

value: lentiviral BRD3RDBD2


title: P5WT1


title: HCT116_TinT2_SP1_KO_2_rep2

source_name: Cell Line

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS (Gibco), penicillin and streptomycin (Gibco).

treatment_protocol: No treatment

value: colon cancer

value: untreated

value: KO HCT116


title: HCT116_TinT2_SP1_KO_2_rep1


title: BJ, BRD3RDBD2, replicate b

description:
BET_normalizedCount42samples.xlsx
KH256b

value: foreskin fibroblasts


title: BJ, BRD3RDBD2, replicate a

description:
BET_normalizedCount42samples.xlsx
KH256a


title: MA1713

value: 2nd rectrix


title: MA1712

value: pigmented


title: MA1714


title: HCT116_TinT2_SP1_KO_1_rep2


title: BJ, WT BRD3, replicate a

description:
BET_normalizedCount42samples.xlsx
KH232a

value: WT BRD3

value: lentiviral BRD3


title: MA1711


title: BJ, WT BRD3, replicate b

description:
BET_normalizedCount42samples.xlsx
KH232b


title: CRC1258


title: BJ, BRD3RDBD1DBD2, replicate b

description:
BET_normalizedCount42samples.xlsx
KH273b

value: lentiviral BRD3RDBD1DBD2