title: WT EV rep2

status: Public on Mar 31 2025

type: SRA

city: Los Angeles

first: ting

last: Xie

state: CA

address: 127 San Vicente Blvd

department: Pulmonary

country: USA

institute: Cedars-Sinai Medical Center

description:
C5
GEO EV

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control to filter out bad samples and reads
Alignment to mouse genome using Tophat 2
Read count quantification using HTSeq
Genome_build: mm9
Supplementary_files_format_and_content: Read Count Table

molecule: total RNA

organism: Mus musculus

source_name: lung mesenchymal cell EV

extract_protocol:
lung tissue were removed, flash frozen on dry ice. 48hr cultured cell suppernatant were collected, EVs were extracted. And RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: lung

tag: age

value: adult mouse

tag: genotype

value: wild type


title: WT EV rep4

description:
C7
GEO EV


title: ColcreER; Tbx4flox/flox EV rep2

description:
C3
GEO EV

value: ColcreER; Tbx4flox/flox


title: ColcreER; Tbx4flox/flox EV rep1

description:
C2
GEO EV


title: ColcreER; Tbx4flox/flox whole lung rep2

description:
C3
GEO whole lung

source_name: whole lung tissue


title: WT whole lung rep2

description:
C5
GEO whole lung


title: ColcreER; Tbx4flox/flox whole lung rep1

description:
C2
GEO whole lung


title: DU145, RIPK2 gRNA #10-2

city: Stony Brook

first: Wei

last: Yang

state: NY

address: Lauterbur Drive, MART 8M-0832

department: Pathology

institute: Stony Brook University

description: Library name: DURG10-2

data_processing:
Clean fastq files were generated by filtering out adaptors, contaminants, and low-quality reads (Phred+33 encoding).
Assembly: After quality control with FastQC, 150bp paired-end reads were aligned to the human reference genome (hg38) using STAR with parameters: -alignIntronMin 20 -alignIntronMax 1000000 -alignSJoverhangMin 8 -quantMode GeneCounts”. Data normalization was conducted using the TMM method in edgeR.
Supplementary files format and content: tab-delimited text file includes raw counts for each cell line.

organism: Homo sapiens

extract_protocol:
Total RNA was extracted from cells using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA, #74104).
RNA sequencing was performed by BGI Group (Shenzhen, China) using the DNBseq platform with a DNBSEQ Eukaryotic Strand-specific mRNA library and PE150 read length.

tag: cell line

tag: cell type

value: Prostate cancer cells

value: RIPK2 knockout


title: DU145, RIPK2 gRNA #10-3

description: Library name: DURG10-3


title: PC3, RIPK2 gRNA #2-1

description: Library name: PC3-r-g-2-1


title: DU145, RIPK2 gRNA #2-2

description: Library name: DURG2-3


title: PC3, RIPK2 gRNA #10-1

description: Library name: PC3-r-g-10-1


title: PC3, control gRNA #1-2

description: Library name: PC3-c-g-1-3

value: WT


title: PC3, RIPK2 gRNA #2-2

description: Library name: PC3-r-g-2-2


title: PC3, control gRNA #1-1

description: Library name: PC3-c-g-1-1


title: WT EV rep1

description:
C4
GEO EV


title: PC3, control gRNA #1-3

description: Library name: PC3-c-g-1-4


title: DU145, RIPK2 gRNA #10-1

description: Library name: DURG10-1


title: DU145, RIPK2 gRNA #2-1

description: Library name: DURG2-2


title: WT whole lung rep1

description:
C4
GEO whole lung


title: WT whole lung rep3

description:
C6
GEO whole lung


title: WT whole lung rep4

description:
C7
GEO whole lung


title: DU145, control gRNA #1-2

description: Library name: DUCG1-2


title: 22Rv1, RIPK2 gRNA #10-2

description: Library name: 22RG10-2


title: PC3, RIPK2 gRNA #10-3

description: Library name: PC3-r-g-10-3


title: PC3, RIPK2 gRNA #10-2

description: Library name: PC3-r-g-10-2


title: PC3, RIPK2 gRNA #2-3

description: Library name: PC3-r-g-2-4


title: 22Rv1, RIPK2 gRNA #1-3

description: Library name: 22RG1-4


title: 22Rv1, RIPK2 gRNA #1-1

description: Library name: 22RG1-2


title: DU145, RIPK2 gRNA #2-3

description: Library name: DURG2-4


title: 22Rv1, RIPK2 gRNA #1-2

description: Library name: 22RG1-3


title: 22Rv1, control gRNA #1-3

description: Library name: 22CG1-3


title: DU145, control gRNA #1-1

description: Library name: DUCG1-1


title: 22Rv1, RIPK2 gRNA #10-3

description: Library name: 22RG10-3


title: 22Rv1, control gRNA #1-1

description: Library name: 22CG1-1


title: 22Rv1, RIPK2 gRNA #10-1

description: Library name: 22RG10-1


title: nTSC_2

city: SEATTLE

first: Min

state: WA

address: 850 Republican ST

institute: University of Washington

data_processing:
Raw sequencing data was processed with SOAPnuke to remove low quality reads or reads with adaptor sequence. Clean sequencing reads were mapped to human reference genome (hg38) with Bowtie2 and gene expression quantification was performed with RSEM as read counts.
Assembly: hg38
Supplementary files format and content: raw and normalized read counts, TPM, FPKM for each sample

source_name: RUES2-derived TSC

extract_protocol:
Total RNA was harvested using the RNeasy mini Kit and RNase-free DNase (QIAGEN).
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit.

value: RUES2-derived TSC

value: trophoblast stem cell


title: nbTSC_1


title: nTSC_3


title: pdTSC_1


title: BAP_3

value: trophoblast cell


title: nTSC_4


title: ccTSC_1


title: nbTSC_4


title: nbTSC_3


title: BAP_2


title: BAP_1


title: ccTSC_4


title: WT EV rep3

description:
C6
GEO EV


title: pdTSC_2


title: ccTSC_2


title: BAP_4


title: ccTSC_3


title: nTSC_1


title: nRUES2_3

value: naive pluripotent stem cell


title: nRUES2_2


title: 22Rv1, control gRNA #1-2

description: Library name: 22CG1-2


title: pdTSC_4


title: pdTSC_3


title: DU145, control gRNA #1-3

description: Library name: DUCG1-3


title: nRUES2_1


title: RUES2_3

value: pluripotent stem cell


title: nbTSC_2


title: RUES2_2


title: RUES2_1


title: ArmiKD_KEErescue_Piwi-piRNA_rep3

city: Bunkyo-ku,

first: Yuica

last: Koga

state: Tokyo

address: Faculty of Science Bldg.3, Rm126, 2-11-16 Yayoi,

department: Biological Sciences

country: Japan

institute: The University of Tokyo

data_processing:
piRNAs were sequenced using MiSeq (Illumina) with MiSeq Reagent Kit v3 (Illumina). piRNA-seq analysis was performed as described previously (Hirakata et al., 2019) with some modifications. Adapter-trimmed reads of ≥ 18 nt in length were mapped against the Drosophila genome (BDGP Release 6 + ISO1 MT/dm6) with FlyBase gene model (Release 6.21) using STAR (Dobin et al., 2013). Uniquely mapped reads with up to one mismatch were used for the subsequent analysis.  After confirming high correlations between samples, reads were merged and used for subsequent analysis. For transposon annotation, the annotation file of repeat sequences was obtained from RepeatMasker (dm6-Apr 2006-RepeatMasker open-4.0.6-Dfam 2.0) and transposons were extracted without distinction between int and LTR. Reads mapped to transposons were counted using HTSeq (Anders et al., 2015). Reads mapped to exons of coding genes were counted with HTSeq using annotation file obtained from FlyBase.
Assembly: Drosophila melanogaster genome (BDGP Release 6 + ISO1 MT/dm6)
Supplementary files format and content: Piwi-piRNA_processed_gene_annotation.txt: Tab-separated text files include normalized count of reads mapped to each gene sequence.
Supplementary files format and content: Piwi-piRNA_processed_transposon_annotation.txt: Tab-separated text files include normalized count of reads mapped to each transposon and its mean length.

organism: Drosophila melanogaster

source_name: Ovarian Somatic Cells (OSC)

growth_protocol: OSCs were cultured at 26°C in Shields and Sang M3 medium (USBiological) supplemented with 10% fetal bovine serum (FBS, NICHIREI), 0.6 mg/mL glutathione, 10 mU/mL insulin, and 10% fly extract.

extract_protocol:
Cells were lysed in binding buffer C [20 mM HEPES-KOH (pH 7.3), 150 mM NaCl, 1mM EDTA, 1 mM DTT, 0.5% NP-40, 2 μg/mL leupeptin, 2 μg/mL pepstatin A, and 0.5% aprotinin] supplemented with 0.04 U/μL RNasin Plus RNase Inhibitor. Cell lysates were then incubated with anti-Piwi monoclonal antibodies (3G11) pre-bound to Dynabeads Protein G at 4°C for 2 h. The beads were washed with IP-wash buffer [20 mM HEPES-KOH (pH 7.3), 300 mM NaCl, 1 mM DTT, 0.05% NP-40, 2 μg/mL leupeptin, 2 μg/mL pepstatin A, and 0.5% aprotinin] and with high-salt IP-wash buffer [20 mM HEPES-KOH (pH 7.3), 500 mM NaCl, 1 mM DTT, 0.05% NP-40, 2 μg/mL leupeptin, 2 μg/mL pepstatin A, and 0.5% aprotinin]. RNAs were eluted from the beads with phenol-chloroform and precipitated with ethanol. RNAs were separated on denaturing polyacrylamide gels and 20–40-nt RNAs were eluted.
Eluted RNAs were cloned as described previously (Hirakata et al., 2019). QIAseq FastSelect-rRNA Fly Kit (QIAGEN) was used to remove rRNA from the library.

treatment_protocol: To initiate RNAi, 5.0 × 10^6 OSCs were mixed with 200 pmol of siRNAs in 20 μL of Solution SF of the Cell Line Nucleofector Kit SF (Lonza Bioscience) and electroporation was performed using a Nucleofector 96-well Shuttle device (Lonza Bioscience). For plasmid/siRNA co-transfection, 1.5 × 10^7 OSCs were mixed with 1.5–10 μg of plasmids with or without 600 pmol of siRNAs in 100 μL of transfection buffer [180 mM sodium phosphate buffer for Church and Gilbert hybridization (pH 7.2), 5 mM KCl, 15 mM MgCl2, and 50 mM D-mannitol], and electroporation was performed by a Nucleofector 2b device (Lonza Bioscience). For rescue assays, endogenous genes were depleted by RNAi and plasmids and siRNAs were introduced into the cells after 48 h of culture. Cells were harvested after another 48 h of culture.

value: Ovarian Somatic Cells (OSC)

value: Cultured cells derived from Drosophila melanogaster ovary

value: Armi KD + Armi KEE mutant-Flag overexpression

tag: treatment

value: RNAi and plasmid transfection


title: ArmiKD_KEErescue_Piwi-piRNA_rep1

description: Piwi-piRNA_processed_gene_annotation.txt


title: DaedKD_deltaSAMrescue_Piwi-piRNA_rep1

description:
Piwi-piRNA_processed_gene_annotation.txt
Piwi-piRNA_processed_transposon_annotation.txt

value: Daed KD + Flag-Daed deltaSAM mutant overexpression


title: ArmiKD_WTrescue_Piwi-piRNA_rep3

value: Armi KD + Armi WT-Flag overexpression


title: PA5525-2

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

library_source: genomic

data_processing:
Raw reads were trimmed by Trim Galore with default parameters.
ChIP-seq reads were mapped to the P. aeruginosa genomes (NC_002516) using Bowtie2 (Version 2.3.4.1). Only the uniquely mapped reads were kept for the subsequent analyses.
Binding peaks (q < 0.05) were identified using MACS2 software (version 2.1.1.20160309).
Assembly: P. aeruginosa genomes (NC_002516)
Supplementary files format and content: narrowPeak, please note that the processed data generated from replicates is linked to the corresponding rep1 sample records.

molecule: genomic DNA

organism: Pseudomonas aeruginosa

extract_protocol:
P. aeruginosa  was cultured in LB medium until mid-log phase (OD600 = 0.6), then treated with 1% formaldehyde for 10 min at 37℃. After quenching and lysis, cells were subjected to sonication to produce 100–300 bp DNA fragments.
ChIP-seq libraries were constructed using NEXTflex ChIP-Seq kit (Bio Scientific), and agarose gel was used to cut DNA fragments between 150 and 250 bp.

tag: chip antibody

value: Anti-vsv


title: DaedKD_WTrescue_Piwi-piRNA_rep3

value: Daed KD + Flag-Daed WT overexpression


title: DaedKD_WTrescue_Piwi-piRNA_rep2


title: ArmiKD_WTrescue_Piwi-piRNA_rep2


title: DaedKD_deltaSAMrescue_Piwi-piRNA_rep2


title: ArmiKD_WTrescue_Piwi-piRNA_rep1


title: PA5431-2


title: DaedKD_deltaSAMrescue_Piwi-piRNA_rep3


title: PA5525-1


title: PA5438-1


title: ArmiKD_KEErescue_Piwi-piRNA_rep2


title: PA5438-2


title: PA5428-2


title: PA5382-2


title: PA5428-1


title: PA5431-1


title: PA5389-2


title: PA5389-1


title: PA5374-2


title: PA5374-1


title: PA5382-1


title: PA5356-1


title: PA5356-2


title: PA5342-2


title: PA5550-1


title: DaedKD_WTrescue_Piwi-piRNA_rep1


title: PA5342-1


title: PA5218-2


title: PA5179-2


title: PA5218-1


title: PA5032-1


title: PA5032-2


title: PA5116-1


title: PA5179-1


title: PA5283-1


title: PA5255-1


title: PA5116-2


title: PA4885-1


title: PA5157-2


title: PA4914-1


title: PA5166-1


title: PA4885-2


title: PA4784-2


title: PA4806-1


title: PA5157-1


title: PA4493-2


title: PA4916-1


title: PA4916-2


title: PA4493-1


title: PA5029-1


title: PA5166-2


title: PA4784-1


title: PA4381-1


title: PA4381-2


title: PA4806-2


title: PA4914-2


title: PA4341-1


title: PA4296-2


title: PA4196-2


title: PA4296-1


title: PA4185-1


title: PA4174-1


title: PA4185-2


title: PA4196-1


title: PA4174-2


title: PA4165-1


title: PA4165-2


title: PA4157-2


title: PA4147-1


title: PA4145-1


title: PA4109-2


title: PA4147-2


title: PA4145-2


title: PA4109-1


title: PA4157-1


title: PA4094-2


title: PA4080-2


title: PA4074-2


title: PA4080-1


title: PA4074-1


title: PA3948-2


title: PA4094-1


title: PA4070-2


title: PA4070-1


title: PA3965-1


title: PA3948-1


title: PA3932-2


title: PA3932-1


title: PA3927-2


title: PA3927-1


title: PA3921-2


title: PA3845-2


title: PA3921-1


title: PA3776-2


title: PA3845-1


title: PA3714-1


title: PA3776-1


title: PA3714-2


title: PA3711-2


title: PA3711-1


title: PA3604-2


title: PA3604-1


title: PA3699-2


title: PA3599-2


title: PA3699-1


title: PA3587-2


title: PA3571-2


title: PA3599-1


title: PA3571-1


title: PA3433-1


title: PA3508-1


title: PA3587-1


title: PA3508-2


title: PA3420-1


title: PA3420-2


title: PA3433-2


title: PA3321-1


title: PA3321-2


title: PA3269-2


title: PA3269-1


title: PA3260-1


title: PA3174-2


title: PA3174-1


title: PA3124-2


title: PA3220-1


title: PA3124-1


title: PA3122-2


title: PA3122-1


title: PA3094-1


title: PA2917-2


title: PA2957-2


title: PA2930-2


title: PA2957-1


title: PA3045-1


title: PA2930-1


title: PA2899-2


title: PA2899-1


title: PA2917-1


title: PA2848-2


title: PA2718-2


title: PA2848-1


title: PA2766-2


title: PA2766-1


title: PA2704-2


title: PA2718-1


title: PA2696-1


title: PA2704-1


title: PA2692-2


title: PA2692-1


title: PA2696-2


title: PA2686-2


title: PA2601-2


title: PA2686-1


title: PA2601-1


title: PA2577-1


title: PA2556-2


title: PA2556-1


title: PA2577-2


title: PA2547-1


title: PA2523-2


title: PA2523-1


title: PA2488-2


title: PA2447-2


title: PA2449-1


title: PA2488-1


title: PA2417-1


title: PA2447-1


title: PA2299-1


title: PA2312-1


title: PA2417-2


title: PA2312-2


title: PA2281-2


title: PA2281-1


title: PA2270-2


title: PA2246-2


title: PA2123-2


title: PA2270-1


title: PA2299-2


title: PA2115-2


title: PA2276-1


title: PA2276-2


title: PA2115-1


title: PA2096-1


title: PA2246-1


title: PA2096-2


title: PA2196-2


title: PA2123-1


title: PA2196-1


title: PA2076-2


title: PA2076-1


title: PA2056-1


title: PA2054-2


title: PA2054-1


title: PA2047-1


title: PA2047-2


title: PA2032-2


title: PA2032-1


title: PA1998-2


title: PA1978-2


title: PA2010-1


title: PA1998-1


title: PA2010-2


title: PA1978-1


title: PA1961-2


title: PA1853-1


title: PA1859-1


title: PA1850-2


title: PA1859-2


title: PA1853-2


title: PA1850-1


title: PA1836-2


title: PA1836-1


title: PA1653-2


title: PA1484-2


title: PA1759-1


title: PA1759-2


title: PA1484-1


title: PA1403-1


title: PA1403-2


title: PA1380-2


title: PA1347-2


title: PA1380-1


title: PA1347-1


title: PA1312-1


title: PA1285-1


title: PA1309-2


title: PA1309-1


title: PA1283-2


title: PA1261-2


title: PA1283-1


title: PA1229-2


title: PA1184-2


title: PA1653-1


title: PA1261-1


title: PA1229-1


title: PA1184-1


title: PA1619-1


title: PA1182-2


title: PA1138-1


title: PA1136-2


title: PA1182-1


title: PA1136-1


title: PA1109-1


title: PA1312-2


title: PA1015-1


title: PA0942-2


title: PA0877-2


title: PA0876-2


title: PA0876-1


title: PA0831-1


title: PA0816-1


title: PA0815-2


title: PA0815-1


title: PA1138-2


title: PA0797-2


title: PA0780-1


title: PA0756-1


title: PA0707-2


title: PA0756-2


title: PA1961-1


title: PA0707-1


title: PA1015-2


title: PA0942-1


title: PA0475-1


title: PA0877-1


title: PA0448-1


title: PA0403-2


title: PA0831-2


title: PA0816-2


title: PA0367-2


title: PA0306-2


title: PA0797-1


title: PA0279-2


title: PA0701-2


title: PA0279-1


title: PA0272-1


title: PA0701-1


title: PA0601-1


title: PA0527-1


title: PA0475-2


title: PA0218-2


title: PA0233-1


title: PA0243-1


title: PA0218-1


title: PA0527-2


title: PA0217-2


title: PA0448-2


title: PA0207-2


title: PA0403-1


title: PA0167-1


title: PA0217-1


title: PA0367-1


title: PA0163-2


title: PA0306-1


title: PA0155-1


title: PA0243-2


title: PA0152-2


title: PA0233-2


title: PA0152-1


title: PA0272-2


title: PA0034-1


title: root, rep2

city: Poznań

first: Karolina

last: Kulak

address: Uniwersytetu Poznanskiego 6

department: Department of General Botany

country: Poland

institute: Adam Mickiewicz University

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using Cell Ranger v7.1.0 (10x Genomics).
Assembly: GCA_000002775.4
Supplementary files format and content: Matrix files

molecule: nuclear RNA

organism: Populus trichocarpa

source_name: root

growth_protocol: Experiments were conducted using black cottonwood (Populus trichocarpa Torr. & A. Gray ex Hook.) pioneer roots from plants germinated from seeds supplied by a seed bank. The initial cultivation phase occurred in a Conviron GR96 plant growth chamber, maintaining a 16/8-hour day/night photoperiod at temperatures of 18/14°C. Three-month-old plants were transferred to the experimental field site - a semi-open foil tunnel greenhouse, with the plants positioned in rhizotrons arranged vertically within an underground chamber

extract_protocol:
Single-nucleus RNA-sequencing (snRNA-Seq) was conducted on nuclei isolated from pioneer root fragments corresponding to the primary stages of vascular tissue development. The method for nuclei isolation was adapted from Dorrity et al. (2021) with minor modifications for Populus roots.
Single-nucleus transcriptomic libraries were prepared with the Chromium Controller and the Chromium Next GEM Single Cell 3′ Reagent Kit (10x Genomics, USA), following the manufacturer's instructions. Approximately 20,000 nuclei were combined with reverse transcription reagents and processed on the Chromium Next GEM Chip G to produce gel beads in emulsion (GEMs). This process released primers from the gel beads, facilitating the synthesis of barcoded cDNA from captured mRNA.

treatment_protocol: No treatment

value: root

value: wild type


title: Input-9


title: PA0207-1


title: root, rep1

description: 10x genomics


title: PA0034-2


title: Matar Ageta Heat Stress, Pea, rep2

city: Uttarakhand

first: Harsh

last: Chauhan

state: Haridwar

address: Roorkee-Haridwar Highway, Roorkee

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Roorkee

description: Library name: mahs

data_processing:
FASTQC toolkit used for QC.
Alignment and mapping of reads was performed using STAR (Dobin et al., 2013; https://github.com/alexdobin/STAR) and Trinity platform (genome-guided) (Bowtie2) (Hass et al., 2013; https://github.com/trinityrnaseq/trinityrnaseq).
Abundance estimation was calculated  using RSEM (RNA-Seq by Expectation-Maximization) method (Li and Dewey, 2011) and differential gene expression analysis was  performed using DESeq2 (Mi et al., 2014; https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Assembly: Pisum sativum cultivar ZW6 (Zhongwan 6); https://www.peagdb.com/download/
Supplementary files format and content: Text files having FPKM values for all samples.
Supplementary files format and content: Excel files in csv format having TMM expression values

organism: Lathyrus oleraceus

source_name: Flower

growth_protocol: AC and MA were grown in a greenhouse under controlled conditions with day/night temperatures of 22/16°C, a 16/8 h photoperiod, and an irradiance of 450-500 µmol photons m-2s-1 provided by cool fluorescent tubes.

extract_protocol:
Total RNA from unopened flower buds at pre-anthesis stage from under CON and HS conditions were extracted using TRIzol Reagent (Ambion, Life Technologies) and purified using RNAeasy MiniElute cleanup kit (Qiagen, Germany) followed by on-column DNase-I treatment. Total RNA quantification and quality control was checked photometrically using NanoDrop OneC Microvolume UV–Vis Spectrophotometer (Thermo Fisher Scientific, USA) for 260/280 and 260/230 ratios and stored in -80 °C until RNA-Seq.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: At the onset of small green buds at the pre-anthesis stage, prior to reproductive stage 1 (R1), pea plants were subjected directly to a short period of heat treatment of 35°C ± 0.5°C for 2 h with 450-500 µmol photons m-2s-1 supplemented light conditions in growth chamber (Conviron, USA). Meanwhile, control plants (CON) were kept in growth chamber at a constant temperature of 22/16°C.

value: Flower

value: Arka Chaitra

value: Heat stress at 35ºC for 2 hours

tag: batch

value: Genotype


title: Input-6

value: WT


title: Input-8


title: Matar Ageta Control, Pea, rep1

description: Library name: macon

value: Control


title: Arka Chaitra Heat Stress, Pea, rep2

description: Library name: achs

value: Matar Ageta


title: Input-4


title: Arka Chaitra Control, Pea, rep1

description: Library name: accon


title: PA0167-2


title: Input-5


title: PA0163-1


title: Input-7


title: Input-2


title: Input-10


title: PA0155-2


title: Input-3


title: Input-1


title: PA5550-2

data_processing:
Raw reads were trimmed by Trim Galore with default parameters.
ChIP-seq reads were mapped to the P. aeruginosa genomes (NC_002516) using Bowtie2 (Version 2.3.4.1). Only the uniquely mapped reads were kept for the subsequent analyses.
Binding peaks (q < 0.05) were identified using MACS2 software (version 2.1.1.20160309).
Assembly: P. aeruginosa genomes (NC_002516)
Supplementary files format and content: narrowPeak

organism: Pseudomonas aeruginosa PAO1

source_name: bacterial cell

value: bacterial cell


title: PA5550-1


title: MYC binding levels (40nM human MutSα + 100nM MYC)

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to desired concentrations in a 95-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. For measuring binding intensity of Cbf1, microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Penta·His Alexa Fluor 647 Conjugate antibody (Qiagen) or Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-532-conjugated protein, Alexa-647 conjugated antibody, or Alexa-488 conjugated antibody using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices).

data_processing: For each unique sequence represented on the array, we calculated the median over 10 or 5 replicate spots.

label: Alexa 647

molecule: protein

source_name: human MYC

label_protocol: Yeast Msh2-Msh6 eluted from the size exclusion column was labeled with Alexa Fluor 555 C2 maleimide (ThermoFisher). The dye was resuspended in DMSO and added to protein samples at 20-fold molar excess (with DMSO final concentration below 0.5% vol/vol) . The dye-protein mixture was incubated at 20 °C for 15 minutes in the dark, and then passed over a desalting column (PD10, GE Biosciences) to remove unbound dye. The labeled sample was concentrated with a centrifugal spin concentrator (Amicon Ultra-4, 50 kDa cutoff, Millipore). Notably, extensive washing by diluting with additional buffer C followed by spin concentration confirmed free dye was removed from the samples. Final labeling efficiency was estimated by UV-VIS spectroscopy. Maintaining precise molar ratios and incubation times during labeling resulted in repeatable outcomes. 4 independent attempts at expression, purification and labeling yielded estimated maleimide labeling efficiencies of 3.3, 3.2, 2.3 and 3.1 dyes per Msh2-Msh6 dimer. Purity was monitored using SDS-PAGE. Human MutSα was kindly provided by Susanne Bruekner and Titia Sixma in 10 ul aliquots in buffer containing 25 mM HEPES pH 7.5, 400 mM KCl, 20 % Glycerol, 5 mM MgCl2, 1 mM DTT, 1 mM ADP and 10 mM Biotin. Labeling manipulations used 2 buffers we call: 1) Hepes-KCL buffer = 25 mM Hepes-KOH pH 7.5, 400 mM KCl, 5 mM MgCl2; 2) Hepes-KCL-glycerol buffer = Hepes-KCL buffer + 20 % glycerol. When fluorescently labeling human MutSα, we pursued 2 approaches to remove unreacted dye: dialysis or gel filtration. For the gel filtration approach, 0.05 mg of dry Alexa Fluor 555 NHS ester was resuspended in 3 ul water. A 10 ul aliquot of MutSα was mixed with 20 ul of Hepes-KCL buffer and then mixed with 1 ul of the dye-water solution. The dye-MutSα mixture was reacted 13 minutes at 20 C and then at 4C for another 45 minutes, both in the dark. The unreacted dye was then removed by passing the sample over a Sephadx G-25 column (NAP-5, Cytiva) equilibrated in Hepes-KCL buffer. For the dialysis approach, 0.05 mg of dry Alexa Fluor 555 NHS ester was resuspended in 0.2 microliters of DMSO followed by addition of 30 ul of Hepes-KCL buffer. A 10 ul aliquot of MutSα was mixed with this dye solution. The mixture was incubated at room temperature in the dark for 25 minutes, and then placed in a 3.5K MWCO Slide-A-Lyzer MINI Dialysis Device (Thermo Scientific). Free dye was removed from the sample by dialyzing against 140 ml of Hepes-KCL-glycerol buffer at 4C with stirring. The dialysis buffer was changed after 4 hours, changed again after 17 more hours, and then the sample was recovered after 5 more hours in dialysis. In both methods, to determine protein and dye concentrations (combined for fluorescence labeling efficiency) we measured absorbance at 550 nm and 280 nm. The dye concentration was determined using the 550 nm measurement and extinction coefficient of 150,000/Mole-cm for Alexa 555. Protein concentration was determined by subtracting 7.4% of the Alexa 555 peak absorbance at 550 nm from the 280 nm absorbance and using 204,000/Mole-cm as the extinction coefficient for Human MutSα. The gel filtration approach resulted in labeling efficiencies of 2-3 dyes per MutSα dimer. The dialysis approach did not remove unreacted dye sufficiently for accurate labeling efficiency determination with this method.

growth_protocol: S. cerevisiae Msh2-Msh6 (yeast MutSα) was expressed in E. coli using plasmids (pET-11a-Msh2-Msh6 and pLANT-2/RIL-Msh6) as described in (Antony E, Hingorani MM. Mismatch recognition-coupled stabilization of Msh2-Msh6 in an ATP-bound state at the initiation of DNA repair. Biochemistry. 2003 Jul 1;42(25):7682-93. doi: 10.1021/bi034602h. PMID: 12820877; PMCID: PMC2839877.) The plasmids yield un-tagged, wild-type versions of Msh2 and Msh6. pET-11a-Msh2-Msh6 and pLANT-2/RIL-Msh6 were cotransformed into BL21(DE3) cells and plated on agar selection media containing both kanamycin and ampicillin.  A single colony was transferred to LB liquid media + kanamycin + ampicillin for overnight shaking incubation at 37 °C. The overnight was added at 1:100 to 1 L flasks of LB media + kanamycin + ampicillin and incubated while shaking at 37 °C. When OD reached 1.0, 0.5 mM IPTG was added. Cells were collected after 4 hours additional shaking incubation at 37 °C, washed in PBS buffer (50 mM Sodium Phosphate–NaOH pH 7.4, 300 mM NaCl), and stored at -80 °C.

extract_protocol: Cells were resuspended in buffer A (25 mM Sodium Phosphate–NaOH pH 7.4, 1 mM DTT, 1 mM EDTA) augmented with 25 mM NaCl, 1 mM PMSF (phenylmethylsulfonyl fluoride), and a cocktail of protease inhibitors (2 µg/m antipain, 1 µg/ml leupeptin, 10 µg/ml benzamidine, aprotinin 2 µg/ml, all from Sigma-Aldrich). Resuspended cells were lysed by sonication. The lysate was clarified by centrifugation at 40,000 RPM for 35 minutes (MLA-80 rotor, Beckman). The supernatant was collected and loaded onto a HiTRAP SP HP column (Cytiva) equilibrated in buffer A augmented with 50 mM NaCl. After washing in Buffer A + 50 mM NaCl, the SP column was eluted in buffer A with a gradient of NaCl from 50 mM to 1 M (Msh2-Msh6 eluted around 330 mM NaCl). Elution fractions from the SP column containing Msh2-Msh6 were pooled and diluted with buffer A to a final NaCl concentration around 100 mM and loaded on a HiTRAP Heparin HP column (Cytiva) equilibrated in buffer A + 50 mM NaCl. After washing in Buffer A + 50 mM NaCl, the Heparin column was eluted in buffer A with a gradient of NaCl from 50 mM to 1 M (Msh2-Msh6 eluted around 420 mM NaCl). Elution fractions from the heparin column containing Msh2-Msh6 were pooled and diluted with buffer B (20 mM Tris-HCl pH 7.8, 1 mM EDTA, 1 mM DTT) to a final NaCl concentration around 75 mM and loaded on a HiTRAP Q HP column (Cytiva) equilibrated in buffer B + 50 mM NaCl. After washing in Buffer B + 50 mM NaCl, the Q column was eluted in buffer B with a gradient of NaCl from 50 mM to 1 M (Msh2-Msh6 eluted around 350 mM NaCl). Elution fractions from the Q column containing Msh2-Msh6 were pooled, concentrated to 300 microliters using a centrifugal spin concentrator (Amicon Ultra-4, 50 kDa cutoff, Millipore) and injected onto a size exclusion column (Superdex200, 10/300 GL ,Cytiva) running in buffer C (25 mM Sodium Phosphate–NaOH pH 7.4, 200 mM NaCl).  Superdex200 elution fractions containing Msh2-Msh6 were pooled and concentration was determined by UV-VIS spectroscopy. The samples were immediately used in dye labeling reactions. All purification steps before dye labeling were performed at 4 °C.

tag: observed protein

value: human MYC

tag: observed protein concentration

tag: competitor tf - concentration

value: MYC - 100nM


title: AF555 dye signal (1.5uM AF555 dye+100nM-MYC)

type: other

label: Alexa 532

molecule: other

organism: synthetic construct


title: PA5374-1


title: PA5374-2


title: PA5255-1


title: PA5255-2


title: PA4806-1


title: MYC binding levels (1.5uM AF555 dye+100nM-MYC)


title: Human MutSα binding levels (40nM human MutSα, dialysis-purified)

source_name: human MutS⍺

value: human MutS⍺


title: AF555/Human MutSα binding levels (40nM human MutSα + 100nM MYC)


title: Yeast MutSα binding levels (20nM yeast MutSα)

organism: Saccharomyces cerevisiae

source_name: yeast MutS⍺

value: yeast MutS⍺


title: PA4493-1


title: PA4493-2


title: PA4165-1


title: PA4165-2


title: PA4070-2


title: AF555/Human MutSα binding levels (40nM human MutSα alone)


title: PA4070-1


title: PA3921-2


title: PA4806-2


title: PA3921-1


title: PA3711-2


title: Cbf1 binding levels (100nM Cbf1)

source_name: yeast Cbf1

label_protocol: Msh2-Msh6 eluted from the size exclusion column was labeled with Alexa Fluor 555 C2 maleimide (ThermoFisher). The dye was resuspended in DMSO and added to protein samples at 20-fold molar excess (with DMSO final concentration below 0.5% vol/vol) . The dye-protein mixture was incubated at 20 °C for 15 minutes in the dark, and then passed over a desalting column (PD10, GE Biosciences) to remove unbound dye. The labeled sample was concentrated with a centrifugal spin concentrator (Amicon Ultra-4, 50 kDa cutoff, Millipore). Notably, extensive washing by diluting with additional buffer C followed by spin concentration confirmed free dye was removed from the samples. Final labeling efficiency was estimated by UV-VIS spectroscopy. Maintaining precise molar ratios and incubation times during labeling resulted in repeatable outcomes. 4 independent attempts at expression, purification and labeling yielded estimated maleimide labeling efficiencies of 3.3, 3.2, 2.3 and 3.1 dyes per Msh2-Msh6 dimer. Purity was monitored using SDS-PAGE.


title: MutSα binding levels (50nM MutSα + 100nM Cbf1) rep 1

value: MutS⍺

value: Cbf1 - 100nM


title: MutSα binding levels (50nM MutSα) rep 2


title: Human MutSalpha binding levels (0.04uM MutSalpha, gel filtration-purified)

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to desired concentrations in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-532-conjugated protein or Alexa-647 conjugated antibody using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices)

data_processing: For each unique sequence represented on the array, we calculated the median over 10 replicate spots.

label_protocol: Msh2-Msh6 eluted from the size exclusion column was labeled with either Alexa Fluor 555 NHS Ester or Alexa Fluor 555 C2 maleimide (ThermoFisher). For either reactive group variant, dye was resuspended in DMSO and added to protein samples at 20-fold molar excess (with DMSO final concentration below 0.5% vol/vol) . The dye-protein mixture was incubated at 20 °C for 15 minutes in the dark, and then passed over a desalting column (PD10, GE Biosciences) to remove unbound dye. The labeled sample was concentrated with a centrifugal spin concentrator (Amicon Ultra-4, 50 kDa cutoff, Millipore). Notably, extensive washing by diluting with additional buffer C followed by spin concentration confirmed free dye was removed from the samples. Final labeling efficiency was estimated by UV-VIS spectroscopy. Maintaining precise molar ratios and incubation times during labeling resulted in repeatable outcomes. 4 independent attempts at expression, purification and labeling yielded estimated maleimide labeling efficiencies of 3.3, 3.2, 2.3 and 3.1 dyes per Msh2-Msh6 dimer. For the experiment comparing the different reactive groups on the dyes, the estimated labeling efficiencies were 3.4 (NHS) and 3.3 (maleimide) dyes per Msh2-Msh6 dimer. Purity was monitored using SDS-PAGE. Human MutSα was kindly provided by Susanne Bruekner and Titia Sixma in 10 ul aliquots in buffer containing 25 mM HEPES pH 7.5, 400 mM KCl, 20 % Glycerol, 5 mM MgCl2, 1 mM DTT, 1 mM ADP and 10 mM Biotin. Labeling manipulations used 2 buffers we call: 1) Hepes-KCL buffer = 25 mM Hepes-KOH pH 7.5, 400 mM KCl, 5 mM MgCl2; 2) Hepes-KCL-glycerol buffer = Hepes-KCL buffer + 20 % glycerol. When fluorescently labeling human MutSα, we pursued 2 approaches to remove unreacted dye: dialysis or gel filtration. For the gel filtration approach, 0.05 mg of dry Alexa Fluor 555 NHS ester was resuspended in 3 ul water. A 10 ul aliquot of MutSα was mixed with 20 ul of Hepes-KCL buffer and then mixed with 1 ul of the dye-water solution. The dye-MutSα mixture was reacted 13 minutes at 20 C and then at 4C for another 45 minutes, both in the dark. The unreacted dye was then removed by passing the sample over a Sephadx G-25 column (NAP-5, Cytiva) equilibrated in Hepes-KCL buffer. For the dialysis approach, 0.05 mg of dry Alexa Fluor 555 NHS ester was resuspended in 0.2 microliters of DMSO followed by addition of 30 ul of Hepes-KCL buffer. A 10 ul aliquot of MutSα was mixed with this dye solution. The mixture was incubated at room temperature in the dark for 25 minutes, and then placed in a 3.5K MWCO Slide-A-Lyzer MINI Dialysis Device (Thermo Scientific). Free dye was removed from the sample by dialyzing against 140 ml of Hepes-KCL-glycerol buffer at 4C with stirring. The dialysis buffer was changed after 4 hours, changed again after 17 more hours, and then the sample was recovered after 5 more hours in dialysis. In both methods, to determine protein and dye concentrations (combined for fluorescence labeling efficiency) we measured absorbance at 550 nm and 280 nm. The dye concentration was determined using the 550 nm measurement and extinction coefficient of 150,000/Mole-cm for Alexa 555. Protein concentration was determined by subtracting 7.4% of the Alexa 555 peak absorbance at 550 nm from the 280 nm absorbance and using 204,000/Mole-cm as the extinction coefficient for Human MutSα. The gel filtration approach resulted in labeling efficiencies of 2-3 dyes per MutSα dimer. The dialysis approach did not remove unreacted dye sufficiently for accurate labeling efficiency determination with this method.

growth_protocol: S. cerevisiae Msh2-Msh6 (yeast MutSα) was expressed in E. coli using plasmids (pET-11a-Msh2-Msh6 and pLANT-2/RIL-Msh6) as described in (Antony E, Hingorani MM. Mismatch recognition-coupled stabilization of Msh2-Msh6 in an ATP-bound state at the initiation of DNA repair. Biochemistry. 2003 Jul 1;42(25):7682-93. doi: 10.1021/bi034602h. PMID: 12820877; PMCID: PMC2839877.) The plasmids yield un-tagged, wild-type versions of Msh2 and Msh6. pET-11a-Msh2-Msh6 and pLANT-2/RIL-Msh6 were cotransformed into BL21(DE3) cells and plated on agar selection media containing both kanamycin and ampicillin. A single colony was transferred to LB liquid media + kanamycin + ampicillin for overnight shaking incubation at 37 °C. The overnight was added at 1:100 to 1 L flasks of LB media + kanamycin + ampicillin and incubated while shaking at 37 °C. When OD reached 1.0, 0.5 mM IPTG was added. Cells were collected after 4 hours additional shaking incubation at 37 °C, washed in PBS buffer (50 mM Sodium Phosphate–NaOH pH 7.4, 300 mM NaCl), and stored at -80 °C.

extract_protocol: Cells were resuspended in buffer A (25 mM Sodium Phosphate–NaOH pH 7.4, 1 mM DTT, 1 mM EDTA) augmented with 25 mM NaCl, 1 mM PMSF (phenylmethylsulfonyl fluoride), and a cocktail of protease inhibitors (2 µg/m antipain, 1 µg/ml leupeptin, 10 µg/ml benzamidine, aprotinin 2 µg/ml, all from Sigma-Aldrich). Resuspended cells were lysed by sonication. The lysate was clarified by centrifugation at 40,000 RPM for 35 minutes (MLA-80 rotor, Beckman). The supernatant was collected and loaded onto a HiTRAP SP HP column (Cytiva) equilibrated in buffer A augmented with 50 mM NaCl. After washing in Buffer A + 50 mM NaCl, the SP column was eluted in buffer A with a gradient of NaCl from 50 mM to 1 M (Msh2-Msh6 eluted around 330 mM NaCl). Elution fractions from the SP column containing Msh2-Msh6 were pooled and diluted with buffer A to a final NaCl concentration around 100 mM and loaded on a HiTRAP Heparin HP column (Cytiva) equilibrated in buffer A + 50 mM NaCl. After washing in Buffer A + 50 mM NaCl, the Heparin column was eluted in buffer A with a gradient of NaCl from 50 mM to 1 M (Msh2-Msh6 eluted around 420 mM NaCl). Elution fractions from the heparin column containing Msh2-Msh6 were pooled and diluted with buffer B (20 mM Tris-HCl pH 7.8, 1 mM EDTA, 1 mM DTT) to a final NaCl concentration around 75 mM and loaded on a HiTRAP Q HP column (Cytiva) equilibrated in buffer B + 50 mM NaCl. After washing in Buffer B + 50 mM NaCl, the Q column was eluted in buffer B with a gradient of NaCl from 50 mM to 1 M (Msh2-Msh6 eluted around 350 mM NaCl). Elution fractions from the Q column containing Msh2-Msh6 were pooled, concentrated to 300 microliters using a centrifugal spin concentrator (Amicon Ultra-4, 50 kDa cutoff, Millipore) and injected onto a size exclusion column (Superdex200, 10/300 GL ,Cytiva) running in buffer C (25 mM Sodium Phosphate–NaOH pH 7.4, 200 mM NaCl). Superdex200 elution fractions containing Msh2-Msh6 were pooled and concentration was determined by UV-VIS spectroscopy. The samples were immediately used in dye labeling reactions. All purification steps before dye labeling were performed at 4 °C.

value: Human MutS⍺

tag: muts⍺ concentration


title: MYC binding levels (0.02uM MutSalpha + 0.1uM MYC)

value: MYC

value: MYC - 0.1uM


title: MAX binding levels (0.02uM MutSalpha + 0.1uM MAX)

source_name: human MAX

value: MAX

value: MAX - 0.1uM


title: MutSα binding levels (50nM MutSα + 100nM Cbf1) rep 2


title: MutSα binding levels (50nM MutSα) rep 1


title: Human MutSalpha binding levels (0.04uM MutSalpha + 0.4uM EGR1)

value: EGR1 - 0.4uM


title: EGR1 binding levels (0.02uM MutSalpha + 0.2uM EGR1)

source_name: human EGR1

value: EGR1 - 0.2uM


title: MutSalpha binding levels (0.02uM MutSalpha + 0.1uM MYC)


title: CREB1 binding levels (0.02uM MutSalpha + 0.2uM CREB1)

source_name: human CREB1

value: CREB1 - 0.2uM


title: PA3711-1

value: Anti-vsv

value: WT


title: PA3508-2

value: bacterial cell


title: EGR1 binding levels (0.4uM EGR1)

label: Alexa 488


title: MutSalpha binding levels (0.02uM MutSalpha + 0.1uM MAX)


title: MutSalpha binding levels (0.02uM MutSalpha + 0.2uM CREB1)


title: PA3321-2


title: PA3321-1


title: PA3420-1


title: 3P_Hep3B_rep2

city: New Haven

first: Michael

last: Mak

state: CT

address: 55 Prospect St

institute: Yale University

description: Library name: SAMPLE 10

data_processing:
The raw reads were aligned by a read aligner STAR to the human GRCh38 release-86 transcriptome (https:// www.ensembl.org/). Data normalization and differential expression analysis were conducted with the R-package DESEQ2.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file with raw counts for all samples

source_name: Liver

extract_protocol:
Total RNA was extracted with an RNeasy mini kit (QIAGEN), following the manufacturer’s protocol.
The library was prepared and sequenced on the Illumina HiSeq or NovaSeq platforms (paired-end 100bp reads per sample) by Yale Center for Genome Analysis (YCGA).

value: Liver

value: Hepatocellular carcinoma


title: 3P_Hep3B_rep1

description: Library name: SAMPLE 9


title: MutSalpha binding levels (0.02uM MutSalpha) rep 2


title: PA3420-2


title: MutSalpha binding levels (0.02uM MutSalpha + 0.2uM EGR1)


title: PA3508-1


title: Mech_compressed_Hep3B_rep2

description: Library name: SAMPLE 8


title: PA3269-2


title: Mech_compressed_Hep3B_rep1

description: Library name: SAMPLE 7


title: Non_compressed_Hep3B_rep2

description: Library name: SAMPLE 6


title: PA3269-1


title: PA3220-1


title: Mech_compressed_HepG2_rep2

description: Library name: SAMPLE 4

value: Hepatoblastoma


title: PA3220-2


title: PA2957-2


title: Non_compressed_Hep3B_rep1

description: Library name: SAMPLE 5


title: Non_compressed_HepG2_rep2

description: Library name: SAMPLE 2


title: Mech_compressed_HepG2_rep1

description: Library name: SAMPLE 3


title: PA2766-2


title: Non_compressed_HepG2_rep1

description: Library name: SAMPLE 1


title: PA2766-1


title: PA2704-2


title: PA2957-1


title: HBEC-Vector Twist1wt-Vector HRasG12V-EGFP #2

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Homo sapiens.GRCh38 reference using the Hisat2 (Version 2.1.0) aligner
Reads counts were calculated for each sample.
Differential expression of genes were computed between groups using DEseq2
Assembly: Homo sapiens(GRCh38)
Supplementary files format and content: tab-delimited text files include raw count for each sample

growth_protocol: HBEC cells were grown in Gibco Keratinocyte-SFM media (#17005042, Gibco). Routine passages were done before reaching 80% confluence, and cultures were maintained in 37C, 5% CO2.

extract_protocol:
Total RNA was isolated using TRIzol™ RNA Isolation Reagent (#15596018, ThermoFisher Sci.) protocol and cleaned with RNeasy mini kit (#74104, Qiagen) according to the manufacturer’s protocol. RNA sequencing was performed by Genewiz-Azenta (https://www.genewiz.com/, (RRID: SCR_003177)) from total RNA isolated from HBEC
RNA sequencing was performed by Genewiz-Azenta (https://www.genewiz.com/): Library preparation, Illumina, RNA with PolyA selection with ERCC spike-in. Library preparation: NEBNext Ultra II RNA Library Prep kit. Briefly, RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles.

treatment_protocol: HBEC cells (HBEC-Vector Control (HC); HBEC-Vector Twist1wt (HT); HBEC-Vector Twist1F187G (HF)) were seeded at 1500-2000cells/cm2 and infected with an adenoviral vector for HRasG12V-EGFP (#VB150925-10024, VectorBuilder) (HCH/HTH/HFH) or an adenoviral vector for Control-EGFP (#VB200812-4494afw, VectorBuilder) (HCE/HTE/HFE), optimized at MOI25. Media was changed after 24h post-infection. The positivity for HRasG12V-EGFP or Control-EGFP expression were validated starting at 24h by fluorescence microscopy (magnification x10, Life Technologies EVOS® FL Auto Imaging System, ThermoFisher Sci. (RRID: SCR_008452)) for EGFP and was optimal starting at 48h post-infection. Analyses were then performed at 72h post-infection and positivity for HRasG12V expression was confirmed by Western-Blot.

value: Human Bronchial Epithelial Cell

value: Twist1wt + Adenovector HRasG12V-EGFP


title: HBEC-Vector Twist1wt-Vector HRasG12V-EGFP #3


title: PA2704-1


title: HBEC-Vector Twist1F187G-Vector HRasG12V-EGFP #3

value: Twist1F187G + Adenovector HRasG12V-EGFP


title: PA2692-2


title: HBEC-Vector Twist1wt-Vector HRasG12V-EGFP #1


title: PA2692-1


title: HBEC-Vector Twist1F187G-Vector HRasG12V-EGFP #2


title: PA2276-2


title: HBEC-Vector Twist1F187G-Vector HRasG12V-EGFP #1


title: HBEC-Vector control-Vector HRasG12V-EGFP #3

value: Control + Adenovector HRasG12V-EGFP


title: PA2246-2


title: MutSalpha binding levels (0.02uM MutSalpha) rep 1

value: MutS⍺


title: PA2276-1


title: PA2246-1


title: HBEC-Vector control-Vector HRasG12V-EGFP #2


title: HBEC-Vector control-Vector HRasG12V-EGFP #1


title: HBEC-Vector control-Vector EGFP #3

value: Control + Adenovector EGFP


title: HBEC-Vector control-Vector EGFP #2


title: PA2196-2


title: HBEC-Vector control-Vector EGFP #1


title: PA2196-1


title: PA1850-1


title: PA1850-2


title: PA1283-2


title: PA1283-1


title: PA1619-1


title: PA1619-2


title: RNA library from IVF F2 female E18.5 Placenta 6

city: Philadelphia

first: Eric

middle: Alejandro

last: Rhon Calderon

state: Pennsylvania

address: 3400 Civic Center Blvd, Bldg 421, Floor 9-175

department: Cell and Developmental Biology

institute: University of Pennsylvania

description: Library name: IVF_F2_E185_Placenta_Female_6

data_processing:
RNA-seq reads were trimmed for quality using Trimmomatic (version 0.32). Illumina TruSeq3-PE primers, leading and trailing low-quality (below quality 3) and N base calls were trimmed, and reads were scanned using a 4-bp sliding window and trimmed when the average quality per base dropped below 15. Reads of at least 30-bp in length following this quality control process were retained and used for subsequent analyses.
The resulting reads were then aligned to mm10 reference genome assembly using STAR (version 2.3.0e), allowing read pairs to align no farther than 2000-bp apart and keeping alignments with a mapping quality score (MAPQ) greater than 1 for genome-wide transcript counting.
FeatureCounts (version 1.5.0) was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Analysis for differential gene expression was performed using DESeq2 with the cutoff of FDR < 0.05. Clustering and heatmaps of differentially expressed genes were generated using heatmaply R package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: E18.5 Placenta

growth_protocol: All animals were housed in polysulfone cages containing drinking water and chow (Laboratory Irradiated Rodent Diet 5LG4, LabDiet) ad libitum.

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) and KAPA Single-Indexed adapter kit following manufacturer's protocols.

treatment_protocol: E18.5 placentas from F2 females and males were collected, snap frozen in liquid nitrogen and stored at -80C for RNA extraction.

value: E18.5 Placenta

value: Female

tag: group

value: IVF


title: RNA library from IVF F2 female E18.5 Placenta 4

description: Library name: IVF_F2_E185_Placenta_Female_4


title: RNA library from IVF F2 female E18.5 Placenta 5

description: Library name: IVF_F2_E185_Placenta_Female_5


title: RNA library from IVF F2 female E18.5 Placenta 3

description: Library name: IVF_F2_E185_Placenta_Female_3


title: RNA library from IVF F2 female E18.5 Placenta 2

description: Library name: IVF_F2_E185_Placenta_Female_2


title: PA1261-1


title: PA1261-2


title: RNA library from IVF F2 female E18.5 Placenta 1

description: Library name: IVF_F2_E185_Placenta_Female_1


title: RNA library from Natural F2 female E18.5 Placenta 4

description: Library name: Natural_F2_E185_Placenta_Female_4

value: Natural


title: PA1184-2


title: RNA library from Natural F2 female E18.5 Placenta 3

description: Library name: Natural_F2_E185_Placenta_Female_3


title: PA1157-2


title: PA1184-1


title: RNA library from Natural F2 female E18.5 Placenta 2

description: Library name: Natural_F2_E185_Placenta_Female_2


title: PA1157-1


title: RNA library from Natural F2 female E18.5 Placenta 1

description: Library name: Natural_F2_E185_Placenta_Female_1


title: RNA library from IVF F2 male E18.5 Placenta 6

description: Library name: IVF_F2_E185_Placenta_Male_6

value: Male


title: PA1136-2

value: Anti-vsv


title: RNA library from IVF F2 male E18.5 Placenta 5

description: Library name: IVF_F2_E185_Placenta_Male_5


title: PA1136-1

value: WT


title: RNA library from IVF F2 male E18.5 Placenta 4

description: Library name: IVF_F2_E185_Placenta_Male_4


title: PA1109-1

value: bacterial cell


title: PA1109-2


title: RNA library from IVF F2 male E18.5 Placenta 3

description: Library name: IVF_F2_E185_Placenta_Male_3


title: RNA library from IVF F2 male E18.5 Placenta 2

description: Library name: IVF_F2_E185_Placenta_Male_2


title: PA0942-2


title: PA0876-1


title: RNA library from IVF F2 male E18.5 Placenta 1

description: Library name: IVF_F2_E185_Placenta_Male_1


title: RNA library from Natural F2 male E18.5 Placenta 5

description: Library name: Natural_F2_E185_Placenta_Male_5


title: RNA library from Natural F2 male E18.5 Placenta 4

description: Library name: Natural_F2_E185_Placenta_Male_4


title: PA0816-2


title: PA0876-2


title: RNA library from Natural F2 male E18.5 Placenta 6

description: Library name: Natural_F2_E185_Placenta_Male_6


title: PA0942-1


title: RNA library from Natural F2 male E18.5 Placenta 2

description: Library name: Natural_F2_E185_Placenta_Male_2


title: RNA library from Natural F2 male E18.5 Placenta 3

description: Library name: Natural_F2_E185_Placenta_Male_3


title: PA0306-1


title: PA0816-1


title: PA0306-2


title: RNA library from F2 12 weeks IVF Ovary Female 5

source_name: F2 12 weeks Ovary

treatment_protocol: E18.5 testis, 12 weeks testis, 39 weeks testis, F2 12 weeks testis, F2 12 weeks male livers, F2 12 weeks ovaries, F2 weeks female livers awere collected, snap frozen in liquid nitrogen and stored at -80C for RNA extraction.

value: F2 12 weeks Ovary

value: F2 Female


title: RNA library from F2 12 weeks IVF Ovary Female 4


title: PA5525-1


title: PA5525-2


title: RNA library from Natural F2 male E18.5 Placenta 1

description: Library name: Natural_F2_E185_Placenta_Male_1


title: RNA library from F2 12 weeks IVF Ovary Female 3


title: PA5342-1


title: PA5342-2


title: RNA library from F2 12 weeks IVF Ovary Female 2


title: RNA library from F2 12 weeks Natural Ovary Female 4


title: PA2899-2


title: RNA library from F2 12 weeks IVF Ovary Female 1


title: RNA library from F2 12 weeks Natural Ovary Female 3


title: PA2899-1


title: PA2123-2


title: PA2123-1


title: RNA library from F2 12 weeks Natural Ovary Female 2


title: RNA library from F2 12 weeks Natural Ovary Female 1


title: RNA library from F2 12 weeks IVF Liver Female 6

source_name: F2 12 weeks Liver

value: F2 12 weeks Liver


title: PA2096-1


title: RNA library from F2 12 weeks IVF Liver Female 5


title: PA2096-2


title: PA2076-2


title: RNA library from F2 12 weeks IVF Liver Female 4


title: PA2076-1


title: PA2054-2


title: RNA library from F2 12 weeks IVF Liver Female 2


title: PA2054-1


title: RNA library from F2 12 weeks IVF Liver Female 3


title: RNA library from F2 12 weeks Natural Liver Female 5


title: PA2047-1


title: RNA library from F2 12 weeks IVF Liver Female 1


title: RNA library from F2 12 weeks Natural Liver Female 4


title: PA2032-2


title: PA2047-2


title: RNA library from F2 12 weeks Natural Liver Female 3


title: PA2032-1


title: RNA library from F2 12 weeks Natural Liver Female 2


title: PA1998-1


title: RNA library from F2 12 weeks Natural Liver Female 1


title: PA1015-2


title: RNA library from F2 12 weeks IVF Liver Male 5

value: F2 Male


title: PA1015-1


title: RNA library from F2 12 weeks IVF Liver Male 4


title: PA1998-2


title: RNA library from F2 12 weeks IVF Liver Male 3


title: PA0893-2


title: RNA library from F2 12 weeks IVF Liver Male 2


title: RNA library from F2 12 weeks IVF Liver Male 1


title: ChIP-Seq_TBP_Brains_NHS_rep2

city: Moscow

first: Nadezhda

middle: E

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
ChIP-seq, FAIRE-Seq and RNA-Seq reads were aligned to the dm6 genome by HISAT2 (using UseGalaxy.eu online tools)
Assembly: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT)
Supplementary files format and content: Aligned reads were sorted to have MAPQ>5. BigWig files were generated using  bamCoverage 3.0.2. Scores represent number of reads normalized by the size of the library. Final BigWIgs were generated The final bigwig files (representing the protein binding profiles) were obtained using bigwigcompare tool by computing a ratio between the ChIP signal and the Input (all Inputs were preliminary smoothed over a 1 kb window). For the H3K27Ac ChIP-Seqs the Input was substracted from the signal. FAIRE-Seq data were not normalized by Input and presented as a number of reads. The final bigwig files (representing the protein binding profiles) were obtained using bigwigcompare tool by computing a ratio between the ChIP signal and the Input (all Inputs were preliminary smoothed over a 1 kb window). For the H3K27Ac ChIP-Seqs the Input was substracted from the signal. FAIRE-Seq data were not normalized by Input and presented as a number of reads.

source_name: Brains/eye-antennal discs were dissected from hsp-e23 wandering larvae 4-6 hours before puparium formation

growth_protocol: The Drosophila melanogaster of hsp-GAL4 7-1,CyO/IF;10UAS-3xFLAG-E23,w+  stock (=hsp-e23; capable of expressing E23 after treatment with the heat shock) and Oregon-R-modENCODE (corresponds to Bloomington stock 25211) stock were used. All flies were raised at 25°C on standard agar medium.

extract_protocol:
ChIP protocol: crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine. After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 500-bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 5 ug of antibodies and 8 uL of MabSelect sepharose (GE healthcare) were taken. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 uL per 500 uL sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 uL of proteinase K and 5 uL of 0.5M EDTA per 500 uL sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation. Total RNA was extracted with the TRI reagent (Ambion). PolyA comprising RNA fraction was isolated with the NEBNext UltraTM II Directional RNA Library Prep Kit. FAIRE-Seq protocol was perfomed exactly as previously described in Simon et al (2012) Nat protocols, 7:256-267.
DNA and RNA-Seq libraries were prepared for sequencing using standard Illumina NEBNext protocols

treatment_protocol:
no treatment
For the RNA-Seq and ChIP-Seq experiments, hsp-e23 larvae (or Oregon-R larvae) of L3 stage 20-22h before puparium formation were subjected to double 1-hour heat shocks at 37°C with a 1-hour rest period between at RT. For dissection, wandering larvae were used approximately 4-6 hours before the puparium formation. Dissections were performed manually in PBS/0.1% NP-40. Tissues targeted for RNA-Seqs were collected directly into TRI-reagent. Dissected salivary glands and brains (brains were taken with eye/antennal discs) aimed for ChIP-Seqs and FAIRE-Seqs were accumulated in tubes containing PBS/0.1% NP-40 and placed on ice. Dissected tissues were stored on ice not more than 1 hour. After the dissection, tissues were warmed to room temperature and fixated by addition of FA up to 1% for 10 min. The fixation was stopped by addition of 1/20V 2.5M Gly to the reaction for 5 min. After the fixation, the Sonication buffer (ChIP lysis buffer) containing 0.1% SDS and PIC (Roche) was added to the tissues and they were stored at -70°C. The sonication step was performed after the thawing.

value: hsp-GAL4 7-1,CyO/IF;10UAS-3xFLAG-E23,w+  stock (described in a current study)

tag: chip antibodies

value: anti-TBP (1–55 aa) antibodies (Vorobyeva et al (2009) Proc Natl Acad Sci USA 106:11049–11054 )

value: no treatment


title: ChIP-Seq_TBP_Brains_NHS_rep1

value: Brains/eye-antennal discs were dissected from hsp-e23 wandering larvae 4-6 hours before puparium formation


title: PA0893-1


title: RNA library from F2 12 weeks Natural Liver Male 4


title: RNA library from F2 12 weeks Natural Liver Male 5


title: PA0815-2


title: ChIP-Seq_TBP_Salivary_glands_HS_rep2

source_name: Salivary glands were dissected from hsp-e23 wandering larvae 4-6 hours before puparium formation

treatment_protocol:
hsp-e23 larvae of L3 stage 20-22h before puparium formation were subjected to double 1-hour heat shocks at 37°C with a 1-hour rest period between at RT. For dissection, wandering larvae were used approximately 4-6 hours before the puparium formation.
For the RNA-Seq and ChIP-Seq experiments, hsp-e23 larvae (or Oregon-R larvae) of L3 stage 20-22h before puparium formation were subjected to double 1-hour heat shocks at 37°C with a 1-hour rest period between at RT. For dissection, wandering larvae were used approximately 4-6 hours before the puparium formation. Dissections were performed manually in PBS/0.1% NP-40. Tissues targeted for RNA-Seqs were collected directly into TRI-reagent. Dissected salivary glands and brains (brains were taken with eye/antennal discs) aimed for ChIP-Seqs and FAIRE-Seqs were accumulated in tubes containing PBS/0.1% NP-40 and placed on ice. Dissected tissues were stored on ice not more than 1 hour. After the dissection, tissues were warmed to room temperature and fixated by addition of FA up to 1% for 10 min. The fixation was stopped by addition of 1/20V 2.5M Gly to the reaction for 5 min. After the fixation, the Sonication buffer (ChIP lysis buffer) containing 0.1% SDS and PIC (Roche) was added to the tissues and they were stored at -70°C. The sonication step was performed after the thawing.

value: heat shock


title: PA0815-1


title: RNA library from F2 12 weeks Natural Liver Male 1


title: RNA library from F2 12 weeks Natural Liver Male 2


title: ChIP-Seq_TBP_Salivary_glands_HS_rep1

value: Salivary glands were dissected from hsp-e23 wandering larvae 4-6 hours before puparium formation


title: RNA library from F2 12 weeks IVF Testis Male 7

source_name: F2 12 weeks Testis

value: F2 12 weeks Testis


title: RNA library from F2 12 weeks IVF Testis Male 6

value: IVF


title: RNA library from F2 12 weeks Natural Liver Male 3

value: Natural


title: ChIP-Seq_TBP_Salivary_glands_NHS_rep2


title: PA0797-1


title: PA0797-2


title: RNA library from F2 12 weeks IVF Testis Male 5


title: PA0780-2


title: RNA library from F2 12 weeks IVF Testis Male 4


title: RNA library from F2 12 weeks IVF Testis Male 3


title: RNA library from F2 12 weeks IVF Testis Male 2


title: PA0780-1


title: ChIP-Seq_TBP_Salivary_glands_NHS_rep1


title: RNA library from F2 12 weeks IVF Testis Male 1


title: FoxA(RNAi), rep1, scRNA-seq

city: ITHACA

first: Carolyn

last: Adler

address: 930 Campus road

institute: Cornell University

description:
Library name: FoxA(RNAi)
10x Genomics

data_processing:
CellRanger v7 is used for generating processed files.
Assembly: mapped to Smed_chr_ref_v1
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Schmidtea mediterranea

source_name: Cells from trunk region

extract_protocol:
For each biological replicate, tunks of 50 animals from each condition were dissected. The tissues were dissociated into single-cell suspension by dicing in CMFB buffer [calcium-magnesium-free solution with 1% BSA (400 mg/L NaH2PO4, 800 mg/L NaCl, 1200 mg/L KCl, 800 mg/L NaHCO3, 240 mg/L glucose, 1% BSA, 15 mM HEPES, pH7.3)] and rocking for 2 hours at room temperature. The cells were washed by centrifugation at 500g for 5 min, resuspended, and filtered through a 30µm cell strainer (BD Biosciences, cat.no 340628) to remove debris. The concentration of filtered cells was calculated with a TC20 automated cell counter (Bio-Rad). After centrifugation, cell concentration was adjusted to 100,000 cells/mL with staining buffer [CMFB containing DRAQ5 (5 µM) and Calcein-AM (0.4 µM)] and nutated at room temperature for 5 min. Nucleated Calcein-AM+ cells were collected on a Sony MA900 Cell Sorter. 100,000 cells were sorted and diluted to a concentration of 1000 cells/µL for subsequent library preparation.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics) with DASH treatment. The cDNA prior to fragmentation was treated with CRISPR, which 30 sgRNAs targeting 16S ribosomal sequences. Digested cDNA were PCR-clean up by Ampure beads, and followed by 10 cycles of PCR using R1 and TSO primers. The subsequent library preparation were according to manufacter’s instructions for end repair and indexing.

value: Cells from trunk region

value: FoxA RNAi


title: Ctrl, rep1, scRNA-seq

description:
Library name: Ctrl(RNAi)
10x Genomics

value: Control RNAi


title: RNA library from F2 12 weeks Natural Testis Male 5


title: RNA library from F2 12 weeks Natural Testis Male 4


title: PA0756-2

value: bacterial cell

value: Anti-vsv

value: WT


title: RNA library from F2 12 weeks Natural Testis Male 3


title: RNA library from F2 12 weeks Natural Testis Male 2


title: RNA library from F2 12 weeks Natural Testis Male 1


title: PA0756-1


title: Fpr2_V3

city: Shanghai

first: shuting

last: Yu

address: 320 Yueyang Road, Xuhui District

country: China

institute: Shanghai Institute of Nutrition and Health

description:
Library name: sample6
MobiNova-100

data_processing:
Raw sequencing data were processed and aligned to the mm10 mouse reference genome using MobiVision software (version 2.1), with unique molecular identifier (UMI) counts summarized for each barcode.
The UMI count matrix was then analyzed using the R package Seurat (version 4.0.0), and cells with low quality or doublets were removed based on UMI or using the R package DoubletFinder (version 2.0.3)
Normalization, top variable gene identification, and batch effect removal of scRNAseq-seq were performed using the NormalizeData and FindVariableGenes functions in Seurat (version 4.0) and the R batchelor package (version 1.6.3).
Graph-based clusters were identified according to the gene expression profile of cells using the FindClusters function in Seurat and visualized using a t-distributed Stochastic Neighbor Embedding (t-SNE) algorithm.
FindAllMarkers function was used to identify marker genes of each cluster, and cell clusters were assigned based on known markers of each intestinal epithelial cell type. The Differentially expressed genes (DEGs) were identified using the FindMarkers function. P-value < 0.05 and |foldchange| > 1.2 were used as thresholds for significant differential expression.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Small intestinnal crypts

extract_protocol:
Crypts were isolated from mouse ileum and dissociated into single cells by incubation with TrypLE Express (Thermo Fisher Scientific). The cells were then stained with APC anti-Ep-CAM (118213, 1:200, BioLegend), and intestinal epithelial cells were sorted using an ultra-high speed flow cytometry sorter (MoFlo AstriosEQ, Beckman Coulter).
The scRNA-seq libraries were constructed and sequenced using the MobiNova-100 microfluidic platform at OE Biotech Co. Ltd, Shanghai, China.

value: Small intestinnal crypts

value: Intestinal epithelia cells

value: intestinal epithelil Fpr2 knockout


title: RNA library from 39 weeks IVF Testis 6

source_name: 39 weeks Testis

value: 39 weeks Testis

value: Male


title: RNA library from 39 weeks IVF Testis 5


title: RNA library from 39 weeks IVF Testis 4


title: Fpr2_V2

description:
Library name: sample5
MobiNova-100


title: PA0611-2

source_name: bacterial cell


title: Fpr2_V1

description:
Library name: sample4
MobiNova-100


title: RNA library from 39 weeks IVF Testis 3


title: PA0601-2


title: RNA library from 39 weeks IVF Testis 1


title: RNA library from 39 weeks IVF Testis 2


title: Fpr2_F2

description:
Library name: sample2
MobiNova-100


title: RNA library from 39 weeks Natural Testis 4


title: RNA library from 39 weeks Natural Testis 3


title: PA0601-1


title: PA0475-2


title: RNA library from 39 weeks Natural Testis 1


title: RNA library from 12 weeks IVF Testis 5

source_name: 12 weeks Testis

value: 12 weeks Testis


title: RNA library from 12 weeks IVF Testis 4


title: PA0475-1


title: RNA library from 12 weeks IVF Testis 3


title: RNA library from 12 weeks IVF Testis 2


title: CTCF_diffdtag_hic_rep2

city: San Diego

first: Melodi

last: Tastemel

address: 9500, Gilman drive

department: CMME

institute: UCSD

description: Library name: CTCF_diffdtag_hic_rep2

data_processing:
ChIP-seq sequencing data was trimmed and aligned to mm10 by bowtie2. Unmapped, multimapped and PCR duplicates were removed.
Relevant comparisons were made by using "test" function within the MaGeCK tools
The RNA-Seq alignment and quantification pipeline is available at https://github.com/ren-lab/rnaseq-pipeline. Briefly, reads were aligned to mm10 (GRCm38) and GENCODE GTF version M25 with rnaSTAR77. PCR duplicates were removed using Picard. Raw reads for each gene were quantified using featureCounts. RPKM values were calculated for each gene Particularly, we created two extra chromosomes for the two tagged Sox2 alleles. Reads uniquely mapped to egfp and mCherry sequences were counted using samtools. Expression level of Sox2 gene from CAST and 129 allele was calculated by RPKM values of the egfp and mCherry gene, respectively.
Hi-C reads were aligned to mm10 using bwa-mem for each read separately and then paired. For chimeric reads, only 5′ end-mapped locations were kept. Duplicated read pairs mapped to the same location were removed to leave only one unique read pair. The output bam files were transformed into juicer file format for visualization in Juicebox. Contact matrices were normalized using the Knight–Ruiz matrix balancing method
Assembly: mm10
Supplementary files format and content: Signal tracks were generated by bamCoverage with parameters "--normalizeUsingRPKM -bs 50 --smoothLength 150" (deepTools)
Supplementary files format and content: Gene comparison summary files in "txt" format
Supplementary files format and content: tab-delimited text files include raw counts matrix for each sample
Supplementary files format and content: juicer hic files that can be visualized in Juicebox

source_name: F123 ESC

growth_protocol: Cells were cultured on feeder-free, serum free 2i condition (Serum free mouse ES medium supplemented with 1uM PD03259010, 3uM CHIR99021, 2mM glutamine, 0.15uM Monothioglycerol, 1000U/ml LIF). The growth medium was changed every day. Cells were dissociated by Accutase (AT104) and passaged to onto 0.2% gelatin-coated plates every 2-3 days.

extract_protocol:
Crosslinked cells were processed by Covaris truChIP Chromatin Shearing kit and chromatin were sonicated to 300-500bp by Covaris M220.
After cell harvesting genomic DNA was isolated as described before (Sanjana et al., 2014 and Shalem et al., 2014).
Total RNA from cells was extracted using the TRIzol Plus RNA purification kit (Thermo Fisher Scientific, Catlog: 12183555).
Hi-C experiments were performed in biological replicates using MboI, following the protocol described by Rao et al., Cell 2014 (PMID: 25497547)
ChIP DNA and Input DNA were constucted into illumina Tru-seq libraries using VAHTS Universal DNA Prep Kit for Illumina V4 (ND610-01)
CRISPR libraries were prepared on sorted populations according to previously described protocol mainly consisting of two-step PCRs (Sanjana et al., 2014 and Shalem et al., 2014)
RNA-Seq libraries were prepared from 4 µg total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit Set A (RS-122-2101; Illumina) or Set B (RS-122-2102; Illumina). RNA-seq libraries were sequenced on illumina Next-seq 2000  (100-bp paired ends).
Hi-C libraries were prepared following the protocol described by Rao et al., Cell 2014 (PMID: 25497547)

value: F123 ESC

value: F1 hybrid (castaneus x S129/SvJae)

value: 4CBS insertion, CTCF-FKBP36V

value: 24h 2uM dtag13 + diff media


title: Kat6bKO_hic_rep2

description: Library name: Kat6bKO_hic_rep2

value: 4CBS insertion, Kat6b KO


title: CTCF_diffdtag_hic_rep1

description: Library name: CTCF_diffdtag__hic_rep1


title: PA0611-1


title: Fpr2_F3

description:
Library name: sample3
MobiNova-100


title: RNA library from 12 weeks Natural Testis 5

value: Natural


title: PA0448-1


title: PA0272-2


title: CTCF_diff_hic_rep2

description: Library name: CTCF_diff_hic_rep2

value: 24h diff media


title: RNA library from 12 weeks IVF Testis 1

value: IVF


title: RNA library from 12 weeks Natural Testis 3


title: CTCF_diff_hic_rep1

description: Library name: CTCF_diff_hic_rep1


title: RNA library from 12 weeks Natural Testis 4


title: RNA library from 39 weeks Natural Testis 2


title: PA0272-1

value: bacterial cell


title: RNA library from 12 weeks Natural Testis 1


title: STARR-seq_EE_output_rep3

city: Marseille

first: Benoit

last: Ballester

address: 162 Avenue de Luminy

country: France

institute: INSERM

description:
Library name: AVO9ExonhcDNA5
cDNA output replicate 3

library_source: other

data_processing:
FastQ paired-end files were mapped to the input library using bowtie2 with the « very-sensitive » parameter.
Sam files were converted using samtools to BAM files. BAM files were processed to remove unmapped reads and any reads aligned to the reverse strand (using samtools view -F 20).
The filtered reads were then sorted and indexed, and unique identifiers in the library were quantified to produce raw read counts for each sample.
Counts were normalized to counts per million (CPM).
Fragments with a standard deviation above 20 for the three CPM input of the isolated DNA were removed. Fragments with a raw Maxiprep library input count less than 500 were also removed.
Activity of each fragments (= reads) is computed using the log2(average cDNA CPM / Maxiprep input library CPM).
Assembly: hg38 (custom library)
Supplementary files format and content: tsv

source_name: K-562 Cell line

growth_protocol: K-562 cells were maintained in RPMI 1640 medium (Thermo Fisher) at 37 °C, subcultured according to ATCC recommendations, and verified to have 97% viability at the time of transfection (passage +10).

extract_protocol:
gDNA: After 24 h, cells from each replicate were pelleted, and gDNA was extracted using the Flexigene protocol (Qiagen) in a final volume of 50 µL. RNA: Total RNA was isolated using the RNeasy kit (Qiagen), followed by mRNA enrichment with Dynabeads (Invitrogen). cDNA was synthesized with Superscript III (Thermo Fisher) and a reverse-transcription primer, treated with RNase H, purified, and quantified. cDNA was then PCR-amplified (KAPA HiFi) prior to library indexing.
A custom oligo pool of 11,999 sequences (Twist Bioscience) was synthesized with short 15 bp adapters corresponding to TruSeq indices. These oligos were PCR-amplified to add homology arms, then cloned into a STARR-seq vector (digested with AgeI-HF, SalI-HF, NotI-HF) via Gibson Assembly. The assembly was transformed into MegaX DH10B T1R cells (Thermo Fisher), and colonies were expanded in Terrific Broth. The resulting plasmid library (Exonhancer) was purified using midiprep kits, yielding ~1.75 mg of DNA.

treatment_protocol: Fifty million K-562 cells were pelleted, washed in PBS, and resuspended in Neon transfection buffer. A total of 250 µg of the STARR-seq plasmid library (Exonhancer) was introduced by electroporation (1450 V, 10 ms, 3 pulses). Cells were then incubated for 24 h at 37 °C prior to downstream analyses. As a control, one replicate was transfected with the STARR-seq empty vector using the same settings.

value: K-562 Cell line


title: STARR-seq_EE_output_rep2

description:
Library name: AVO8ExonhcDNA4
cDNA output replicate 2


title: PA0218-2

value: Anti-vsv

value: WT


title: Fpr2_F1

description:
Library name: sample1
MobiNova-100

value: Small intestinnal crypts

value: Intestinal epithelia cells


title: CTCF_2ildtag24h_hic_rep1

description: Library name: CTCF_2ildtag24h_hic_rep1

value: 24h 2uM dtag13


title: PA0448-2


title: PA0218-1


title: STARR-seq_EE_input_Maxiprep

description:
Library name: AVO4Exonhmaxi4
gDNA input Maxiprep


title: CTCF_2il_hic_rep2

description: Library name: CTCF_2il_hic_rep2


title: STARR-seq_EE_input_rep3

description:
Library name: AVO1ExonhDNA3
gDNA input replicate 3


title: STARR-seq_EE_input_rep2

description:
Library name: AVO1ExonhDNA2
gDNA input replicate 2


title: PA0163-1


title: 19SD00840_005

city: LYON

first: Julie

last: CARAMEL

address: 28 Rue Laennec

institute: Cancer Research Center of Lyon

hyb_protocol: not provided

scan_protocol: not provided

data_processing: The nCounter digital barcode counts for each antibody and ROI sample were first normalized using internal spike-in controls, then using the mean expression of house-keeping proteins

source_name: melanoma

label_protocol: not provided

extract_protocol: NanoString GeoMx Digital Spatial Profiler (Human Immuno-Oncology Protein Assay) was used on FFPE tissues. Tissue sections were incubated with a cocktail of 32 unique oligonucleotide-conjugated antibodies and counterstained with a nuclear stain .

value: melanoma

tag: tissue preparaation

value: FFPE


title: 19SD00840_004


title: RNA library from 12 weeks Natural Testis 2

value: 12 weeks Testis

value: Male


title: PF-07220060-resistant, Mouse-9-8, Replicate B

first: Lars

last: Anders

address: 10555 Science Center Dr

institute: Pfizer

description: Library name: PF0060.M9.8.B

data_processing:
The reference genomes and the corresponding annotation files (gtf files) for Homo sapiens (GRCh38.77) and Mus musculus (GRCm38.96) were downloaded from the Ensembl database.
BBMap was used for adapter trimming and FastQC was used for quality control checks on raw sequence data coming from high throughput sequencing pipelines. Xenome (version 1.0.1-r) was used for classifying reads into human and mouse reads.
Classified reads were then aligned to the reference genome using STAR.
The aligned reads were then sorted and counted in features using HTSeq.
RSEM (RNA-Seq by Expectation Maximization) was used for estimating gene and isoform expression levels from RNA-Seq data.
Assembly: GRCh38.77, GRCm38.96
Supplementary files format and content: tab-delimited text file includes tpm for each Sample

source_name: Breast

growth_protocol: In vivo xenograft study.

extract_protocol:
Tumors were powderized and mRNA extraction performed by Genewiz (Azenta) according to their internal process.
Libraries were prepared by Genewiz (Agenta) according to their internal procedure.

treatment_protocol: ZR751 tumor bearing mice were treated for 3 days with vehicle or atirmociclib, PO, 60 mg/kg BID (7 hr apart). In a separate study, ZR751 tumor bearing mice were treated for 84-91 days with atirmociclib, PO, 60 mg/kg BID (7 hr apart).

value: Breast

value: breast cancer cells

tag: replicate

value: B

tag: treatment time_(hours)


title: PF-07220060-resistant, Mouse-9-8, Replicate A

description: Library name: PF0060.M9.8.A

tag: tissue

value: A


title: CTCF_2ildtag24h_hic_rep2

description: Library name: CTCF_2ildtag24h_hic_rep2

value: F123 ESC

value: F1 hybrid (castaneus x S129/SvJae)

value: 4CBS insertion, CTCF-FKBP36V


title: PF-07220060-resistant, Mouse-9-9, Replicate B

description: Library name: PF0060.M9.9.B


title: 19SD00840_007


title: 19SD00840_003


title: STARR-seq_EE_output_rep1

description:
Library name: AVO7ExonhcDNA3
cDNA output replicate 1

value: K-562 Cell line


title: PA5166-1

tag: strain

value: bacterial cell

value: Anti-vsv


title: PF-07220060-resistant, Mouse-9-7, Replicate A

description: Library name: PF0060.M9.7.A


title: CTCF_2il_hic_rep1

description: Library name: CTCF_2il_hic_rep1

tag: genotype


title: STARR-seq_EE_input_rep1

description:
Library name: AVO1ExonhDNA1
gDNA input replicate 1

tag: cell line


title: 19SD00840_002


title: PF-07220060-resistant, Mouse-9-9, Replicate A

description: Library name: PF0060.M9.9.A

tag: cell type


title: PA0163-2

value: WT


title: PA0056-2


title: PA0056-1


title: PA4914-1


title: PF-07220060-resistant, Mouse-9-7, Replicate B

description: Library name: PF0060.M9.7.B

tag: treatment


title: 19SD00840_006


title: PF-07220060-sensitive, Mouse-6-5, Replicate A

description: Library name: PF0060.M6.5.A


title: PF-07220060-resistant, Mouse-9-6, Replicate B

description: Library name: PF0060.M9.6.B


title: PF-07220060-resistant, Mouse-9-6, Replicate A

description: Library name: PF0060.M9.6.A


title: PA5166-2

tag: chip antibody


title: PF-07220060-sensitive, Mouse-6-4, Replicate B

description: Library name: PF0060.M6.4.B

tag: batch


title: PF-07220060-sensitive, Mouse-6-4, Replicate A

description: Library name: PF0060.M6.4.A


title: PA4784-1


title: Control, Mouse-1-9, Replicate B

description: Library name: DMSO.M1.9.B

value: DMSO


title: 16SD03279_001


title: Control, Mouse-1-9, Replicate A

description: Library name: DMSO.M1.9.A


title: 19SD00840_001


title: PF-07220060-sensitive, Mouse-6-6, Replicate B

description: Library name: PF0060.M6.6.B


title: PF-07220060-resistant, Mouse-9-3, Replicate A

description: Library name: PF0060.M9.3.A


title: PF-07220060-resistant, Mouse-9-3, Replicate B

description: Library name: PF0060.M9.3.B


title: PA4145-2


title: PA4914-2


title: 16SD03279_007


title: Control, Mouse-1-6, Replicate A

description: Library name: DMSO.M1.6.A


title: Control, Mouse-1-6, Replicate B

description: Library name: DMSO.M1.6.B


title: 16SD03279_003


title: 19SD00840_008


title: PF-07220060-sensitive, Mouse-6-5, Replicate B

description: Library name: PF0060.M6.5.B


title: PF-07220060-sensitive, Mouse-6-6, Replicate A

description: Library name: PF0060.M6.6.A


title: Control, Mouse-1-5, Replicate B

description: Library name: DMSO.M1.5.B


title: PA3845-2


title: PA4145-1


title: PA4784-2


title: Control, Mouse-1-5, Replicate A

description: Library name: DMSO.M1.5.A


title: 16SD03279_005


title: Control, Mouse-1-4, Replicate A

description: Library name: DMSO.M1.4.A


title: 16SD03279_004


title: Control, Mouse-1-2, Replicate B

description: Library name: DMSO.M1.2.B


title: PA3845-1


title: Control, Mouse-1-4, Replicate B

description: Library name: DMSO.M1.4.B


title: PA3830-2


title: THP-1 cells, Uninfected, biol rep 3

city: Clayton

first: Kathleen

last: McCaffrey

state: VIC

address: 25-31 Wright Street

country: Australia

institute: Hudson Institute of Medical Research

description: Library name: Sample 12

data_processing:
Image analysis was performed in real time by the NextSeq 2000 Control Software and the Illumina pipeline was used to generate the sequence data.
Trimmed reads were mapped to GRCh38.90 using STAR
Read counts were generated using featureCounts
Assembly: Homo sapiens genome (GRCh38.90)
Supplementary files format and content: tabular files of feature counts

growth_protocol: THP-1 monocytes [Homo sapiens, male] (ATCC Cat#TIB-202) were cultured in RPMI 1640 supplemented with Glutamax (Gibco Cat#61870036) and 10 % foetal bovine serum (FBS) (Bovagen Cat#SFBS-AU) at 37C and 5 % CO2. THP-1 monocytes were seeded at 2.5x105 cells/cm2 in tissue-culture dishes and differentiated for 48 h prior to infection using 50 ng/mL phorbol 12-myristate 13-acetate (PMA) (Sigma Aldrich Cat#P8139).

extract_protocol:
At 5 h post-infection, RNA was extracted from cell monolayers using the ISOLATE II RNA Mini Kit (Bioline Cat# BIO-52073) according to the manufacturer’s instructions and analysed using a 2100 Bioanalyzer (Agilent).
cDNA was generated using first-strand synthesis with custom indexed primers and amplified for multiplexed library preparation.

treatment_protocol: THP-1 cell monolayers were infected with either L. pneumophila 130b or the mutant strains at a MOI of 10. At 2 h post-infection, cell monolayers were incubated with gentamicin at 100 g/mL (Gibco Cat#15750060) for 1 h to kill any remaining extracellular bacteria followed by washing and the addition of fresh media.

value: Monocyte

value: PMA differentiated, 48 h


title: PA3830-1


title: THP-1 cells, Uninfected, biol rep 2

description: Library name: Sample 11


title: 16SD03279_012

value: melanoma

value: FFPE


title: THP-1 cells, deltadotA Legionella infection, 18h post-infection, biol rep 3

description: Library name: Sample 9


title: THP-1 cells, Uninfected, biol rep 1

description: Library name: Sample 10


title: PA3776-2


title: 16SD03279_011


title: THP-1 cells, deltadotA Legionella infection, 18h post-infection, biol rep 1

description: Library name: Sample 7


title: 16SD03279_010


title: THP-1 cells, delta4 Legionella infection, 18h post-infection, biol rep 3

description: Library name: Sample 6


title: 16SD03279_009


title: THP-1 cells, delta4 Legionella infection, 18 h post-infection, biol rep 1

description: Library name: Sample 4


title: PA3587-2


title: THP-1 cells, delta4 Legionella infection, 18 h post-infection, biol rep 2

description: Library name: Sample 5


title: Control, Mouse-1-2, Replicate A

description: Library name: DMSO.M1.2.A


title: THP-1 cells, WT Legionella infection, 18 h post-infection, biol rep 3

description: Library name: Sample 3


title: 16SD03279_008


title: 16SD03279_006


title: PA3587-1


title: 16SD03279_002


title: THP-1 cells, WT Legionella infection, 18 h post-infection, biol rep 1

description: Library name: Sample 1


title: PA3565-2


title: THP-1 cells, WT Legionella infection, 18 h post-infection, biol rep 2

description: Library name: Sample 2


title: SBC5CPr-1

city: Toyoake

first: Juntaro

last: Yamasaki

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake-cho

institute: Fujita Health University

data_processing:
Sequenced reads were processed by GLC Genomics Workbench 24.1 (Qiagen).
Assembly: GRCh38.107
Supplementary files format and content: The processed data file consists of gene name, TPM, gene ID, ENSEMBLE ID, Biotype, Transcripts annotated Uniquely identified transcripts, Exon length, Unique exon reads, Total exon reads.

growth_protocol: Both cell lines were maintained under 5% CO2 at 37°C in RPMI 1640 medium (Nacalai) supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted and purified with the use of RNeasy Mini Kit (Qiagen).
Total RNA was treated with NEBNext Poly(A) Magnetic Isolation Module (NEB) to eliminate rRNA molecules and used for cDNA library preparation. cDNA synthesis followed by transcriptome library preparation were conducted by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB), where dUTP were incorporated in the process of the 2nd strand cDNA synthesis, instead of dTTP, that block PCR amplification against the 2nd strand templates, enabling strand-specific transcriptome profiling. A 12-cycle PCR amplification was performed to increase library yield. Resulting transcriptome sequencing libraries were quantified by Qubit dsDNA HS Assay (Thermofisher) and their fragment size distribution was confirmed by TapeStation D5000 ScreenTape (Agilent).

treatment_protocol: Cisplatin-resistant (CPr) DMS273 and SBC5 cells were generated by exposure of the parental cell lines to stepwise increases in cisplatin concentration (1, 2, 4, and 20 μg/ml).

value: SCLC cells


title: SBC5CPr-2


title: 15SD06183_006


title: SBC5CPr-3


title: PA3565-1

extract_protocol:
P. aeruginosa  was cultured in LB medium until mid-log phase (OD600 = 0.6), then treated with 1% formaldehyde for 10 min at 37℃. After quenching and lysis, cells were subjected to sonication to produce 100–300 bp DNA fragments.
ChIP-seq libraries were constructed using NEXTflex ChIP-Seq kit (Bio Scientific), and agarose gel was used to cut DNA fragments between 150 and 250 bp.


title: SBC5P-3


title: THP-1 cells, deltadotA Legionella infection, 18h post-infection, biol rep 2

description: Library name: Sample 8


title: PA3433-2


title: SBC5P-1


title: 15SD06183_005


title: SBC5P-2


title: 273CPr-3


title: PA3776-1


title: 15SD06183_004


title: PA3433-1


title: PA3260-2


title: 273CPr-2


title: 15SD06183_003


title: 273CPr-1


title: 15SD06183_002


title: PA3260-1


title: 273P-2


title: 15SD06183_001


title: 273P-3


title: 273P-1


title: Airway_Influenza_Top_3

city: Nishkyo ward

first: Ryuji

last: Yokokawa

state: Kyoto

address: Kyotodaigaku-katsura, Nishikyo-ku, c2N06, C cluster, Micro Biosystems Laboratory

department: Department of Microengineering

institute: Kyoto University

data_processing:
FASTQ files were generated using bcl2fastq-2.20
Adapter sequences and low-quality bases were trimmed from the raw reads using Cutadapt ver v4.1
Mapping of the trimmed reads to human reference genome sequences (hg38) was conducted using STAR version 2.7.10a with a GENCODE (release 32, GRCh38.p13) GTF file
The raw counts were calculated using the htseq-count ver. 0.13.5 10 with the GENCODE GTF file
Assembly: hg38
Supplementary files format and content: text delimited file that conatins raw count for each sample

source_name: Human lung airway

extract_protocol:
RNA was extracted from each cell lysate using a Qiagen miniprep kit. The RNA was analyzed using the 2100 Bioanalyzer (Agilent Technologies).
Library was prepared using the TruSeq Stranded mRNA Sample Prep Kit, according to the manufacturer's instructions.

value: Human lung airway

value: SFTPC-GFP knockin reporter iPSCs (B2-3)

value: hiPSC-derived lung airway cells

value: SFTPC-GFP knockin

value: IAV


title: Airway_Influenza_Top_1


title: Airway_Influenza_Top_2


title: PA3215-2

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

institute: City University of Hong Kong


title: 15SD06183_010


title: Airway_SARS_Top_2


title: PA3094-2


title: PA3215-1


title: Airway_SARS_Top_3


title: 15SD06183_009


title: Airway_Control_Top_3

value: Mock


title: Airway_SARS_Top_1


title: Airway_Control_Top_2


title: PA3094-1


title: Airway_Control_Top_1


title: 15SD06183_008


title: 15SD06183_007


title: PA3027-2


title: PA3027-1


title: Alveolus_Influenza_Top_3

source_name: Human lung alveoli

value: Human lung alveoli

value: hiPSC-derived lung alveoli cells


title: 17SD09568_013


title: Alveolus_Influenza_Top_2


title: Alveolus_Influenza_Top_1


title: 17SD09568_014


title: Alveolus_SARS_Top_3


title: PA2917-2

value: bacterial cell


title: Alveolus_SARS_Top_2


title: Alveolus_SARS_Top_1


title: 17SD09568_015


title: PA2917-1

value: Anti-vsv


title: 17SD09568_016


title: Alveoli_Control_Top_2

value: WT


title: Alveoli_Control_Top_3


title: Alveoli_Control_Top_1


title: 17SD09568_017


title: PA2577-2


title: Alveolus_Influenza_Bottom_3

source_name: Vasculature

value: Vasculature

value: Human Umbilical Vein Endothelial Cells

value: Endothelial cells


title: Alveolus_Influenza_Bottom_1


title: 17SD09568_005

value: melanoma


title: PA2556-2


title: PA2556-1


title: Alveolus_SARS_Bottom_3


title: Alveolus_Influenza_Bottom_2


title: PA2577-1


title: Alveolus_SARS_Bottom_1


title: Alveolus_SARS_Bottom_2


title: 17SD09568_004

value: FFPE


title: PA2551-2


title: Alveoli_Control_Bottom_3


title: Alveoli_Control_Bottom_2


title: PA2551-1


title: Alveoli_Control_Bottom_1


title: 17SD09568_003


title: PA2299-2


title: Airway_Influenza_Bottom_3


title: Airway_Influenza_Bottom_2


title: Airway_Influenza_Bottom_1


title: PA2299-1


title: 17SD09568_018


title: 17SD09568_002


title: Airway_SARS_Bottom_3


title: 17SD09568_001


title: Airway_SARS_Bottom_2


title: PA1859-2


title: Airway_SARS_Bottom_1


title: 17SD09568_007


title: PA1859-1


title: Airway_Control_Bottom_2


title: Airway_Control_Bottom_3


title: PA1759-2


title: Airway_Control_Bottom_1


title: PA1759-1


title: 17SD09568_008


title: 17SD09568_009


title: 29T,Empty vector ,48hr

city: Houston

first: Yi-Lan

last: Weng

state: Texas

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

description:
Library name: YG010
rRNA depletion

data_processing:
Sequence read were trimmed using Trimmomatic.
The sequence reads were aligned to the human genome (hg38) using the STAR aligner.
pileup2var was used to count reads and identify editing events from RNA-seq data.
Editing events with at least 5-read coverage and a minimum of 1% base conversion (A to G or T to C) were retained for downstream analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited excel file includes editing rate and read coverage for each sample

source_name: Kidney

extract_protocol:
Total RNA was extracted using the Trizol reagent, followed by purification with Zymo RNA Clean and Concentrator.
Ribosomal RNA (rRNA) was depleted from 100 ng of total RNA, followed by library construction using the Smart-seq2 protocol that utilizes random primers and Tn5 tagmentation.

value: Kidney

value: Embryonic kidney cells

value: Empty vector


title: 29T,Y1112F,48hr

description:
Library name: YG008
rRNA depletion

value: Y1112F OE


title: 29T,G1007R,48hr

description:
Library name: YG007
rRNA depletion

value: G1007R OE


title: 29T,D1113H,48hr

description:
Library name: YG009
rRNA depletion

value: D1113H OE


title: 17SD09568_010


title: 29T,K999N,48hr

description:
Library name: YG006
rRNA depletion

value: K999N OE


title: PA1504-2

city: Hong Kong

data_processing:
Raw reads were trimmed by Trim Galore with default parameters.
ChIP-seq reads were mapped to the P. aeruginosa genomes (NC_002516) using Bowtie2 (Version 2.3.4.1). Only the uniquely mapped reads were kept for the subsequent analyses.
Binding peaks (q < 0.05) were identified using MACS2 software (version 2.1.1.20160309).
Assembly: P. aeruginosa genomes (NC_002516)
Supplementary files format and content: narrowPeak


title: 29T,R892H,48hr

description:
Library name: YG005
rRNA depletion

value: R892H OE


title: 29T,I872T,48hr

description:
Library name: YG004
rRNA depletion

value: I872T OE


title: PA1504-1

value: bacterial cell


title: 17SD09568_011


title: 17SD09568_012


title: PA1484-2

value: Anti-vsv


title: 29T,P193A,48hr

description:
Library name: YG002
rRNA depletion

value: WT

value: P193A OE


title: 17SD09568_006


title: 17SD06149_001


title: 29T,WT,48hr

description:
Library name: YG001
rRNA depletion

value: ADAR WT OE


title: PA1484-1


title: Ctrl_screen_high_rep2

description:
Library name: Ctrl_screen_high_rep2
Control_low_vs_high.gene_summary.txt

data_processing:
ChIP-seq sequencing data was trimmed and aligned to mm10 by bowtie2. Unmapped, multimapped and PCR duplicates were removed.
Relevant comparisons were made by using "test" function within the MaGeCK tools
The RNA-Seq alignment and quantification pipeline is available at https://github.com/ren-lab/rnaseq-pipeline. Briefly, reads were aligned to mm10 (GRCm38) and GENCODE GTF version M25 with rnaSTAR77. PCR duplicates were removed using Picard. Raw reads for each gene were quantified using featureCounts. RPKM values were calculated for each gene Particularly, we created two extra chromosomes for the two tagged Sox2 alleles. Reads uniquely mapped to egfp and mCherry sequences were counted using samtools. Expression level of Sox2 gene from CAST and 129 allele was calculated by RPKM values of the egfp and mCherry gene, respectively.
Hi-C reads were aligned to mm10 using bwa-mem for each read separately and then paired. For chimeric reads, only 5′ end-mapped locations were kept. Duplicated read pairs mapped to the same location were removed to leave only one unique read pair. The output bam files were transformed into juicer file format for visualization in Juicebox. Contact matrices were normalized using the Knight–Ruiz matrix balancing method
Assembly: mm10
Supplementary files format and content: Signal tracks were generated by bamCoverage with parameters "--normalizeUsingRPKM -bs 50 --smoothLength 150" (deepTools)
Supplementary files format and content: Gene comparison summary files in "txt" format
Supplementary files format and content: tab-delimited text files include raw counts matrix for each sample
Supplementary files format and content: juicer hic files that can be visualized in Juicebox
Library strategy: CRISPR Screen

value: F123 ESC

value: F1 hybrid (castaneus x S129/SvJae)

value: 4CBS insertion outside Sox2 locus


title: 29T,A870T,48hr

description:
Library name: YG003
rRNA depletion

value: Kidney

value: A870T OE


title: Ctrl_screen_low_rep2

description:
Library name: Ctrl_screen_low_rep2
Control_low_vs_high.gene_summary.txt


title: PA1380-2