title: Pol II Heart 3

value: Heart ECs


title: TargetSeq_Sample_63

status: Public on Feb 03 2022

type: SRA

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

library_source: genomic

data_processing:
Library strategy: TargetSeq
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh38/hg38 human reference genome using BWA-MEM v0.7.17.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Excel for base subtitutions

molecule: genomic DNA

organism: Homo sapiens

source_name: PE3-600ng+24h-4:hRNF2;PE3+_+53_nicking sgRNA-4:hSEC61B;PE3 del+_+46_nicking sgRNA-4:hLSP;

growth_protocol: 293FT cells from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and regularly tested to exclude mycoplasma contamination.

extract_protocol:
72 hours after transfection, the genomic DNA was extracted from the transfected cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre)
Target genomic sequences were PCR amplified by high-fidelity DNA polymerase PrimeSTAR HS (Clonetech) with primer sets flanking examined gRNA target sites. The gRNA target sequences and PCR primer sequences are listed in Supplementary Table 2. Indexed DNA libraries were prepared by using the NEBNext Ultra II FS DNA Library Prep Kit for Illumina. After quantitated with Qubit High-Sensitivity DNA kit (Invitrogen), PCR products with different tags were pooled together for deep sequencing by using the Illumina Hiseq X Ten (2×150) at Omics Core of Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Shanghai, China.

treatment_protocol: 293FT cells were seeded in a 24-well plate at a density of 1E+5 per well and transfected with 250 μl serum-free Opti-MEM that contained LIPOFECTAMINE LTX (Life, Invitrogen), LIPOFECTAMINE plus (Life, Invitrogen) and expression vector. After 24 hr, puromycin (ant-pr-1, InvivoGen) was added to the medium at the final concentration of 4 μg/ml. After another 48 hr, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre) for subsequent sequencing analysis

tag: cell line

value: 293FT cells

tag: treatment

value: 293FT-Apobec KO92-1-PE3-600ng+24h-4(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3+_+53_nicking sgRNA-4(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 del+_+46_nicking sgRNA-4(Target_gene:hLSP);


title: TargetSeq_Sample_62

source_name: PE3-600ng+24h-3:hRNF2;PE3+_+53_nicking sgRNA-3:hSEC61B;PE3 del+_+46_nicking sgRNA-3:hLSP;

value: 293FT-Apobec KO92-1-PE3-600ng+24h-3(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3+_+53_nicking sgRNA-3(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 del+_+46_nicking sgRNA-3(Target_gene:hLSP);


title: Pol II Heart 2

city: Cleveland

first: Mukesh

last: Jain

state: OH

address: 2103 Cornell Rd

country: USA

institute: Case Western Reserve University

data_processing:
Processed using TaRGET-II ATAC-Seq Pipeline
After initial quality checking with fastgc (0.11.90, we used TaRGET-II ATAC-Seq pipeline (https://github.com/Zhang-lab) for analysis. TaRGET-II includes quality trimming using cutadapt and trimmed reads (>36bp minimum alignment length) were mapped against the mm10 genome using BWA aligner. We used de-duplicated and uniquely mapped reads for peak calling analysis after excluding black-list regions defined by ENCODE. The candidate peaks were predicted by callpeak implemented in MACS2. We used predicted open chromatin peaks where at least two biological replicates were reproducible for the downstream analysis using an IDR cutoff of 0.05. We also applied limma based edgeR method to determine differentially accessible regions (DARs); cutoff: log2FC >1.0, CPM>2, p-value <0.01.
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 for peakcalling

organism: Mus musculus

source_name: Heart ECs

growth_protocol: Mouse heart and lungs were perfused, excised, minced,  digested with type I collagenase, and then were mechanically disrupted and filtered  through a 70 um cell strainer to get a single cell suspension. Cells were immediately  stained for FACS analysis. CD31+/CD45- cells were isolated as endothelial cells for  downstream analyses.

extract_protocol:
Flow-sorted endothelial cells were fixed using 1% formaldehyde. 200,000 cells were lysed and frozen in 100ul SDS lysis buffer (50mM Tris/HCl, 0.5% SDS, and 10mM EDTA) supplemented with 1x cOmplete EDTA-free protease inhibitor (Roche) (n=3 mice of each genotype, n=6 for heart H3K27ac). For ChIP-seq, anti-FLAG (Cell Signaling Technologies, #8146), anti-Pol II (Sigma, 05-623), anti-p300 (Cell Signaling Technologies, 54062), or anti-H3K27ac (Abcam, ab4729) antibodies were added to Protein A/G-coupled Dynabeads (Bimake, B23202) in PBS with 0.5% BSA and incubated with rotation for 4hr at 4 degrees. For 100,000-150,000 cells, 25 ul of beads were incubated with 5ug antibody per ChIP. Aliquots were diluted with SDS lysis buffer and 100 ul containing the appropriate number of cells were processed. Cells were sonicated for 12 cycles of 30s on/30s off on high power using a Bioruptor Pico (Diagenode). To neutralize the SDS, Triton-X-100 was added to a final concentration of 1% along with 50x cOmplete protease inhibitor (final concentration: 1x). Samples were incubated at room temperature for 10min and 5% aliquots were saved for preparation of input controls. Antibody-coated Dynabeads were washed with PBS and mixed with cell lysate and incubated overnight at 4 degrees with rotation. Immunoprecipitated chromatin was washed with 150ul low-salt buffer (50mM Tris/HCl, 150mM NaCl, 0.1% SDS, 0.1% NaDOC, 1% Triton-X-100, and 1mM EDTA), high-salt buffer (500mM NaCl), and LiCl buffer (10mM Tris/HCl, 250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% NaDOC, and 1mM EDTA), followed by two washes with TE buffer and two washes with ice cold Tris/HCl (pH 8, 10mM). For tagmentation, bead-bound chromatin was resuspended in 30ul of tagmentation buffer, 1ul of transposase (Nextera, Illumina) was added and samples were incubated at 37 degrees for 10min, followed by two washses with low-salt buffer. For standard reverse crosslinking, chromatin complexes were diluted with 200ul ChIP elution buffer (10mM Tris/HCl, 0.5% SDS, 300mM NaCL, and 5mM EDTA) and 2ul of 20ug/ml proteinase K (Thermo Scientific). Samples were vortexed and incubated overnight at 65 degrees. After reverse crosslinking, 1 ul 20ug/ml RNase (Sigma) was added and incubated at 37 degrees for 30min. DNA purification was carried out using Qiagen MinElute PCR Purification Kit.
15ul of PCR master mix and 5ul of primer mix (Nextera, Illumina) were added to 20ul of eluted DNA and libraries were amplified. After PCR amplification, library cleanup was done using Agencourt AmPureXP eads (Beckman Coulter) at a ratio of 1:1. DNA concentrations in purified samples were measured using the Qubit dsRNA HS Kit (Invitrogen). Libraries were pooled and single-end sequenced (50 cycles) using the NextSeq500 platform (Illumina). Analysis was performed as described in the ATAC-seq pipeline

tag: genotype

value: WT C57bl/6J

tag: age

value: 2 months

tag: cell type

tag: chip target

value: Pol II ChIP Seq


title: Fracture callus cells_wk12_Mg

city: St Louis

first: Nianye

last: Zheng

state: Missouri

address: 660 S Euclid Ave

department: Orthopedic Surgery

institute: Washington University

library_source: transcriptomic

data_processing:
Reads were aligned to the rats genome assembly using STAR
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: gene expression matrix with count number per gene and cell were genertaed and compressed into gz files.

molecule: total RNA

organism: Rattus norvegicus

source_name: Fracture callus cells

growth_protocol: Fracture callus cells were harvested from the fracture callus on week 4 and 12 post-fracture, cultured on patri dish for 24 hours before sent for RNA sequence

extract_protocol:
Callus tissues were digested with collagenase A for 4 hours to harvest cells
Libraries were prepared according to Illumina's instructions

treatment_protocol: Rats were treated with s.c. zoledroante at a dose of 0.3 mg/kg/week for 12 weeks before unilateral femoral closed fractures fixed with stainless steel IMN or Mg  containing IMN

value: Fracture callus cells

tag: strain

value: Sprague Dawley

value: zoledronate and Mg treated


title: TargetSeq_Sample_66

source_name: PE3-300ng+24h-3:hRNF2;PE3+_+103_nicking sgRNA-3:hSEC61B;PE3 del+_+104_nicking sgRNA-3:hLSP;

value: 293FT-Apobec KO92-1-PE3-300ng+24h-3(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3+_+103_nicking sgRNA-3(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 del+_+104_nicking sgRNA-3(Target_gene:hLSP);


title: TargetSeq_Sample_65

source_name: PE3-300ng+24h-2:hRNF2;PE3+_+103_nicking sgRNA-2:hSEC61B;PE3 del+_+104_nicking sgRNA-2:hLSP;

value: 293FT-Apobec KO92-1-PE3-300ng+24h-2(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3+_+103_nicking sgRNA-2(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 del+_+104_nicking sgRNA-2(Target_gene:hLSP);


title: NCI-H510A siSCRAMBLED UNTREATED rep1

city: Colmenar Viejo

first: Javier

middle: Díez

last: Pérez

state: Madrid

address: Avda. De los Reyes, 1

department: I+D

country: Spain

institute: Pharma Mar

data_processing:
Processed using nf-core RNA-Seq pipeline v1.3.3
Alingment with  HISAT 2.1.0
Read count with Subread featureCounts v1.6.4
DEG analisyed with Deseq2 from featurecounts matrix
FPKM calculated with Stringtie 1.3.5
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

growth_protocol: Cell lines were cultured in Waymouth’s medium (DMS‑53) or RPMI medium (NCI‑H82 and NCI‑H510A and supplemented with 10%FBS, 2nmol/L L-glutamine, and penicillin-streptomycin mix.

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen) according to the manufacturer’s recommendations.
Total RNA was extracted from cells using the RNeasy kit (Qiagen, Germantown, MD). On-column DNase treatment was given following the procedure provided by the manufacturer.  Strand-specific library was prepared using Illumina TruSeq stranded RNA library prep kit (Illumina, San Diego, CA) according to manufacturer’s protocols.

treatment_protocol: DMS-53, NCI-H82 and NCI-H510A cells were treated with 50 nM of lurbinectedin, 50nM of cisplatin or 20µM cisplatin for 4 hours.

tag: tissue

value: cell line

value: UNTREATED

tag: dose


title: Pol II Heart 1


title: p300 Lung 3

source_name: Lung ECs

value: Lung ECs

value: p300 ChIP Seq


title: Fracture callus cells_wk12_CGRP

value: zoledronate and CGRP treated


title: Fracture callus cells_wk4_Mg


title: TargetSeq_Sample_61

source_name: PE3-600ng+24h-2:hRNF2;PE3+_+53_nicking sgRNA-2:hSEC61B;PE3 del+_+46_nicking sgRNA-2:hLSP;

value: 293FT-Apobec KO92-1-PE3-600ng+24h-2(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3+_+53_nicking sgRNA-2(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 del+_+46_nicking sgRNA-2(Target_gene:hLSP);


title: Fracture callus cells_wk4_CGRP


title: TargetSeq_Sample_60

source_name: PE3-600ng+24h-1:hRNF2;PE3+_+53_nicking sgRNA-1:hSEC61B;PE3 del+_+46_nicking sgRNA-1:hLSP;

value: 293FT cells

value: 293FT-Apobec KO92-1-PE3-600ng+24h-1(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3+_+53_nicking sgRNA-1(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 del+_+46_nicking sgRNA-1(Target_gene:hLSP);


title: NCI-H82 siSCRAMBLED LURBI rep2

value: LURBINECTEDIN


title: NCI-H82 siSCRAMBLED UNTREATED


title: p300 Lung 2

value: WT C57bl/6J


title: Fracture callus cells_wk12_ZOL

value: zoledronate-treated


title: NCI-H82 siSCRAMBLED LURBI rep1


title: TargetSeq_Sample_59

source_name: PE3-900ng+24h-4:hRNF2;PE3+_-29_nicking sgRNA-4:hSEC61B;PE3 del+_-97_nicking sgRNA-4:hLSP;

value: 293FT-Apobec KO92-1-PE3-900ng+24h-4(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3+_-29_nicking sgRNA-4(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 del+_-97_nicking sgRNA-4(Target_gene:hLSP);


title: TargetSeq_Sample_58

source_name: PE3-900ng+24h-3:hRNF2;PE3+_-29_nicking sgRNA-3:hSEC61B;PE3 del+_-97_nicking sgRNA-3:hLSP;

value: 293FT-Apobec KO92-1-PE3-900ng+24h-3(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3+_-29_nicking sgRNA-3(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 del+_-97_nicking sgRNA-3(Target_gene:hLSP);


title: DMS53 SiA+N CISPT 50nM rep2

value: CISPLATIN


title: TargetSeq_Sample_57

source_name: PE3-900ng+24h-2:hRNF2;PE3+_-29_nicking sgRNA-2:hSEC61B;PE3 del+_-97_nicking sgRNA-2:hLSP;

value: 293FT-Apobec KO92-1-PE3-900ng+24h-2(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3+_-29_nicking sgRNA-2(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 del+_-97_nicking sgRNA-2(Target_gene:hLSP);


title: p300 Lung 1

value: 2 months


title: DMS53 SiA+N CISPT 50nM rep1


title: Fracture callus cells_wk12_control

value: Fracture callus cells

value: Sprague Dawley

value: untreated


title: TargetSeq_Sample_56

source_name: PE3-900ng+24h-1:hRNF2;PE3+_-29_nicking sgRNA-1:hSEC61B;PE3 del+_-97_nicking sgRNA-1:hLSP;

value: 293FT-Apobec KO92-1-PE3-900ng+24h-1(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3+_-29_nicking sgRNA-1(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 del+_-97_nicking sgRNA-1(Target_gene:hLSP);


title: Fracture callus cells_wk4_ZOL


title: p300 Heart 3

value: Heart ECs

value: p300 ChIP Seq


title: p300 Heart 1


title: DMS53 SiA+N CISPT 20uM rep1

value: cell line


title: p300 Heart 2


title: TargetSeq_Sample_54

source_name: PE3-300ng+48h-3:hRNF2;PE3+_-73_nicking sgRNA-3:hSEC61B;PE3 ins+_+104_nicking sgRNA-3:hLSP;

value: 293FT cells

value: 293FT-Apobec KO92-1-PE3-300ng+48h-3(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3+_-73_nicking sgRNA-3(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 ins+_+104_nicking sgRNA-3(Target_gene:hLSP);


title: H3K27ac Lung 2

value: Lung ECs

value: H3K27ac ChIP Seq


title: DMS53 SiA+N LURBI rep2

value: LURBINECTEDIN


title: DMS53 SiA+N CISPT 20uM rep2


title: TargetSeq_Sample_55

source_name: PE3-300ng+48h-4:hRNF2;PE3+_-73_nicking sgRNA-4:hSEC61B;PE3 ins+_+104_nicking sgRNA-4:hLSP;

value: 293FT-Apobec KO92-1-PE3-300ng+48h-4(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3+_-73_nicking sgRNA-4(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 ins+_+104_nicking sgRNA-4(Target_gene:hLSP);


title: KO-testis longRNA rep1

city: Nanjing

first: Qin

last: RuiXin

state: Jiangsu

address: No. 101 Longmian Avenue, Jiangning District, Nanjing

institute: Nanjing Medical University

description: total cellular RNA

data_processing:
Raw read1 fastq of smRNA-seq(oocyte and embryo) was used to identify small RNAs, which were pre-processed using the fastx_toolkit. After quality filtering, sequencing reads were clipped from the 3' adaptor allowing a minimum match of 10 nt from the 5' end.
Reads unable to match the adaptor sequence or with lengths shorter than 17 bp were discarded, and the remaining reads were mapped to the golden hamster genome (MesAur2.0) by sports(version 1.1).The mapped genome sequences were further aligned to piRNAs, miRNAs, tRNAs, rRNAs, snoRNAs, and snRNAs.
The small RNAs were mapped in the following order: miRNA, rRNA, rRNA, piRNA, snoRNA, and snRNA. The reads in each library were normalized with sequencing depth or the count of exogenous spike-ins.
The raw fastq reads of RNA-seq were clipped off the adaptors and quality filtered by trim_galore with parameters --quality 20 --stringency=1 –length=35 --paired (http://tophat.cbcb.umd.edu/).
The remaining fastq reads were mapped to the genome by STAR (version 2.7.1a) with parameters --winAnchorMultimapNmax 10000 --outFilterMultimapNmax 10000. The reads uniquely and multiply mapped with genomic copies less than 10,000 were used for subsequent analysis. Gene abundance was retrieved by featurecounts with default parameters.
Genome_build: MesAur2.0
Supplementary_files_format_and_content: tab-delimited text files include useful reads count of smRNAs and each gene count.

organism: Mesocricetus auratus

source_name: Testis

extract_protocol:
The single oocytes or embryos were incubated at 72°C for 3 min to release and unfold the small RNAs.For testicular RNA seq, total RNA was extracted from 21 d.p.p. golden hasmters using the RNA isolater Total RNA Extraction Reagent(VAZYME,R401-01)according to the manufacturer’s protocol.
For single oocyte or embryos smRNA seq, after 3’adapter ligation, 5U of lambda exonuclease and 25U of 5’deadenylases, which performed better than the combination of RecJf and 5’deadenylases, were used to remove the excess 3’adaptor. Then, a 5’adapter was ligated and small RNAs were reverse transcribed. Pre-amplification was performed and then 1 μl of amplified product was used as a template for final amplification. The amplified libraries were separated on a 6% polyacrylamide gel and 130-160 bp DNA fragments were sliced to recover the library of small RNAs. Long RNA transcriptome libraries was performed following Smarter-seq2 method with some modifications.For every single oocyte or embryo, 0.125 μL 1/100,000 dilution of the ERCC RNA Spike-In Mix (Invitrogen, Cat# 4456740) was used. Following reverse transcription and PCR pre-amplification, cDNA libraries were purified by Agencourt Ampure XP beads (0.8:1 ratio) (Beckman Coulter, Cat#A63881) and 2 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase. Amplified libraries were purified by Agencourt Ampure XP beads (1:1 ratio).The small and long RNA libraries were sequenced on a HiSeq X Ten instrument (Illumina, USA) with 2 × 150 run cycles.For testicular long RNA seq,DNase I was used to digest double-stranded and single-stranded DNAin total RNA, then, magnetic beads were purified to recover the reaction products, RNase H or Ribo-Zero method(Illumina, USA) was used to remove the rRNA. Purified mRNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then,first-strand cDNA was generated in First Strand Reaction System by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to carry out end repair. The cDNA fragments with adapters were amplyfied by PCR, and the products were purified byAmpure XP Beads. Library was validating on the Agilent Technologies 2100 bioanalyzer for quality control.The double stranded PCR products above were heated denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGISEQ500 platform (BGI_x0002_Shenzhen, China).For testicular smRNA seq,library was prepared with 1 μg total RNA for each sample. Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to adenylated 3’ adapters annealed to unique molecular identifiers (UMI), followed by the ligation of 5’adapters. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 110~130 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA). The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The final ligation PCR products were sequenced using the BGISEQ-500 platform (BGI-Shenzhen, China).

tag: breed

value: Syrian

value: Pld6 KO

value: testis

value: 3 weeks

tag: molecule subtype

value: long RNA


title: Fracture callus cells_wk4_control

value: Fracture callus cells

value: Sprague Dawley


title: H3K27ac Lung 3

value: WT C57bl/6J

value: 2 months


title: KO-testis longRNA rep3

description: total cellular RNA


title: DMS53 SiA+N UNTREATED rep1

value: UNTREATED


title: DMS53 SiA+N LURBI rep1

value: cell line


title: H3K27ac Heart 6

value: Heart ECs


title: KO-testis longRNA rep2

description: total cellular RNA


title: TargetSeq_Sample_50

value: 293FT cells

value: 293FT-Apobec KO92-1-PE3-600ng+48h-3(Target_gene:hRNF2);293FT-Apobec KO92-1-NT-7(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 ins+_+46_nicking sgRNA-3(Target_gene:hLSP);


title: TargetSeq_Sample_53

source_name: PE3-300ng+48h-2:hRNF2;PE3+_-73_nicking sgRNA-2:hSEC61B;PE3 ins+_+104_nicking sgRNA-2:hLSP;

value: 293FT-Apobec KO92-1-PE3-300ng+48h-2(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3+_-73_nicking sgRNA-2(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 ins+_+104_nicking sgRNA-2(Target_gene:hLSP);


title: H3K27ac Heart 5

value: H3K27ac ChIP Seq


title: TargetSeq_Sample_52

source_name: PE3-300ng+48h-1:hRNF2;PE3+_-73_nicking sgRNA-1:hSEC61B;PE3 ins+_+104_nicking sgRNA-1:hLSP;

value: 293FT-Apobec KO92-1-PE3-300ng+48h-1(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3+_-73_nicking sgRNA-1(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 ins+_+104_nicking sgRNA-1(Target_gene:hLSP);


title: H3K27ac Heart 4

source_name: Heart ECs


title: DMS53 SiA+N UNTREATED rep2


title: H3K27ac Lung 1

value: Lung ECs


title: DMS53 SiNEUROD1 CISPT 50nM rep2

value: CISPLATIN


title: TargetSeq_Sample_51

value: 293FT-Apobec KO92-1-PE3-600ng+48h-4(Target_gene:hRNF2);293FT-Apobec KO92-1-NT-8(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 ins+_+46_nicking sgRNA-4(Target_gene:hLSP);


title: DMS53 SiNEUROD1 CISPT 50nM rep1


title: TargetSeq_Sample_49

value: 293FT-Apobec KO92-1-PE3-600ng+48h-2(Target_gene:hRNF2);293FT-Apobec KO92-1-NT-6(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 ins+_+46_nicking sgRNA-2(Target_gene:hLSP);


title: TargetSeq_Sample_47

value: 293FT-Apobec KO92-1-PE3-900ng+48h-4(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3 ins+_-97_nicking sgRNA-4(Target_gene:hLSP);


title: DMS53 SiNEUROD1 CISPT 20uM rep2


title: TargetSeq_Sample_48

value: 293FT-Apobec KO92-1-PE3-600ng+48h-1(Target_gene:hRNF2);293FT-Apobec KO92-1-NT-5(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 ins+_+46_nicking sgRNA-1(Target_gene:hLSP);


title: WT-testis longRNA rep1

description: total cellular RNA

value: Syrian

value: wild type

value: testis

value: 3 weeks

value: long RNA


title: H3K27ac Heart 3

value: WT C57bl/6J

value: 2 months

value: Heart ECs


title: TargetSeq_Sample_46

value: 293FT cells

value: 293FT-Apobec KO92-1-PE3-900ng+48h-3(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3 ins+_-97_nicking sgRNA-3(Target_gene:hLSP);


title: H3K27ac Heart 2

value: H3K27ac ChIP Seq


title: WT-testis longRNA rep2

description: total cellular RNA


title: KO-testis smRNA rep3

description: total cellular RNA

value: Pld6 KO

value: smRNA


title: KO-testis smRNA rep2

description: total cellular RNA


title: WT-testis longRNA rep3

description: total cellular RNA


title: DMS53 SiNEUROD1 LURBI rep2

value: cell line

value: LURBINECTEDIN


title: DMS53 SiNEUROD1 CISPT 20uM rep1

value: CISPLATIN


title: K4Tagged Lung 1

value: KLF4 Flag/Flag

value: Lung ECs

value: KLF4 ChIP Seq


title: KO-testis smRNA rep1

description: total cellular RNA

value: Syrian

value: testis


title: H3K27ac Heart 1


title: K4Tagged Lung 2


title: WT-testis smRNA rep2

description: total cellular RNA

value: wild type

value: 3 weeks


title: TargetSeq_Sample_43


title: TargetSeq_Sample_44

value: 293FT-Apobec KO92-1-PE3-900ng+48h-1(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3 ins+_-97_nicking sgRNA-1(Target_gene:hLSP);


title: DMS53 SiNEUROD1 LURBI rep1


title: WT-testis smRNA rep3

description: total cellular RNA


title: TargetSeq_Sample_42


title: DMS53 SiNEUROD1 UNTREATED rep2

value: UNTREATED


title: K2Tagged Lung 2

value: KLF2 Flag/Flag

value: 2 months

value: KLF2 ChIP Seq


title: K2Tagged Lung 1


title: DMS53 SiNEUROD1 UNTREATED rep1


title: WT-testis smRNA rep1

description: total cellular RNA


title: TargetSeq_Sample_41

value: 293FT cells


title: DMS53 SiASCL1 CISPT 50nM rep2


title: TargetSeq_Sample_45

value: 293FT-Apobec KO92-1-PE3-900ng+48h-2(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3 ins+_-97_nicking sgRNA-2(Target_gene:hLSP);


title: K4Tagged Heart 2

value: Heart ECs


title: DMS53 SiASCL1 CISPT 20uM rep1

value: cell line


title: DMS53 SiASCL1 CISPT 50nM rep1

value: CISPLATIN


title: TargetSeq_Sample_40


title: DMS53 SiASCL1 CISPT 20uM rep2


title: K2Tagged Heart 1


title: K4Tagged Heart 1

value: KLF4 Flag/Flag


title: Plastic5_Glass

city: Columbus

first: Erin

last: Gloag

state: Ohio

address: 460 W. 12th Ave

department: Microbial  Infection and Immunity

institute: The Ohio State Univerisity

description: Replicates denoted by A, B, C

data_processing:
HiSeq 4000 sequencing was performed, generating approximately 300 million total paired end 300 bp reads from the 15 total samples, with a mean quality score of 37.4.
Reads were aligned to the reference PAO1 genome using Rockhopper
Rockhopper: https://cs.wellesley.edu/~btjaden/Rockhopper/
Replicates denoted by A, B, C
Comparisons made to 5min attachment on Ibidi μ-Slide
Genome_build: PAO1 reference genome GenBank: AE004091.2
Supplementary_files_format_and_content: Comparison of 5min attachment on plastic to 30min attachment on silicone
Supplementary_files_format_and_content: Comparison of 5min attachment on plastic to 30min attachment on glass
Supplementary_files_format_and_content: Comparison of 5min attachment on plastic to 30min attachment on plastic

organism: Pseudomonas aeruginosa

source_name: Bacterial

growth_protocol: Coupons of silicone, glass, and polycarbonate plastic were purchased from Biosurfaces Technologies (Catalog numbers: RD128-Si, RD128-GL, RD128-PC). Coupons were placed into a 24-well plate and conditioned in LB for at least 10 min prior to bacterial addition. LB was removed and replaced with 2mL of logarithmic phase bacterial culture in LB (OD600 0.7).

extract_protocol:
200μL of Trizol was added to the channel. Trizol was collected and stored at -80°C for RNA isolation. Following a 5 min incubation at room temperature, 0.2 mL of chloroform was added and the samples were shaken vigorously for 1 min. Phases were separated by centrifugation (12,000 g, 5 min, 4°C) and the aqueous phase was combined with 0.6 mL of 70% ethanol and transferred to an RNeasy mini column (Qiagen). RNA was purified as per manufactures protocols
Libraries were constructed using the ScriptSeq Complete Kit (Illumina) following the Bacteria-Low Input protocol.

tag: surface

value: Glass coupon (Biosurfaces Technologies; RD128-GL)

tag: adherance time


title: K2Tagged Heart 2


title: DKO Lung ATAC 2

description: ATAC Seq

data_processing:
ATAC Seq Processed through TaRGET-II pipeline
After initial quality checking with fastgc (0.11.90, we used TaRGET-II ATAC-Seq pipeline (https://github.com/Zhang-lab) for analysis. TaRGET-II includes quality trimming using cutadapt and trimmed reads (>36bp minimum alignment length) were mapped against the mm10 genome using BWA aligner. We used de-duplicated and uniquely mapped reads for peak calling analysis after excluding black-list regions defined by ENCODE. The candidate peaks were predicted by callpeak implemented in MACS2. We used predicted open chromatin peaks where at least two biological replicates were reproducible for the downstream analysis using an IDR cutoff of 0.05. We also applied limma based edgeR method to determine differentially accessible regions (DARs); cutoff: log2FC >1.0, CPM>2, p-value <0.01.
Genome_build: mm10
Supplementary_files_format_and_content: MAC2 for peakcalling

extract_protocol:
50-70,000 flow-sorted live endothelial cells were used to prepare the ATAC-seq library by preparing nuclei and applying a transposase reaction with 12 cycles of PCR amplification
The library was purified using SPRI beads (double-sided selection, 200-500bp fragment size). We utilized Illumina Hi-Seq system to sequence libraries

value: VE-Cad Cre KLF2F/F KLF4F/F + Tamox

value: Lung ECs


title: Plastic5_Silicon

description: Replicates denoted by A, B, C

value: Silicone coupon (Biosurfaces Technologies; RD128-Si)


title: TargetSeq_Sample_39


title: TargetSeq_Sample_36


title: Plastic5

description:
Ibidi μ-Slide
Replicates denoted by A, B, C

value: Ibidi mu-Slide


title: TargetSeq_Sample_38


title: TargetSeq_Sample_37


title: TargetSeq_Sample_35


title: plasma exosomes of CRT-sensitive patient 4

type: RNA

city: Chiba

first: Huan

last: Wang

state: Chiba

address: 1-8-1 Chuo-Ku

country: Japan

institute: Chiba University

description:
EQ0097_08
Control, exosomal miRNA

hyb_protocol: The hybridization and subsequent wash steps were performed, according to the miRCURYTM LNA array manual, in a Tecan HS 4800 ProTM hybridization station (Tecan, Austria).

scan_protocol: The miRCURYTM LNA array microarray slides were scanned by a ScanArrayTM 4000 XL scanner (Packard Biochip Technologies, USA) and the image analysis was carried out using the ImaGeneTM 6.1.0 software (BioDiscovery, Inc., USA).

data_processing: The quantified fluorescence intensities were normalized between the two channels on each array using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

label: SYBR® Green

source_name: plasma exosomes

label_protocol: The quality of the total RNAwas verified on an Agilent 2100 BioanalyzerTM profile immediately prior to the experiments. 2 µg total RNA per reaction were labeled with Hy3TM or Hy5TM fluorescent label using the miRCURYTM LNA Array labeling kit (Exiqon, Denmark) according to the manufacturers recommendations.

extract_protocol: Exosomes were isolated using an exosome isolation reagent (Total Exosome precipitation reagent from plasma; Invitrogen) according to the manufacturer's protocol.Total RNA was extracted from exosomes using the Total Exosome RNA and Protein Isolation Kit (Invitrogen, Carlsbad, Calif., United States) according to the manufacturer’s protocol.

tag: phenotype

value: CRT-sensitive

value: plasma

tag: fraction

value: exosome


title: Plastic5_Plastic30

description: Replicates denoted by A, B, C

value: Polycarbonate plastic coupon  (Biosurfaces Technologies; RD128-PC)


title: plasma exosomes of CRT-sensitive patient 1

description:
EQ0097_05
Control, exosomal miRNA


title: plasma exosomes of CRT-sensitive patient 3

description:
EQ0097_07
Control, exosomal miRNA


title: DMS53 SiASCL1 UNTREATED rep2

value: UNTREATED


title: DKO Heart ATAC 1

description: ATAC Seq

value: 2 months


title: DMS53 SiASCL1 LURBI rep1

value: LURBINECTEDIN


title: DMS53 SiASCL1 UNTREATED rep1


title: DKO Lung ATAC 1

description: ATAC Seq


title: DKO Heart ATAC 2

description: ATAC Seq


title: plasma exosomes of CRT-sensitive patient 2

description:
EQ0097_06
Control, exosomal miRNA


title: Cre Lung ATAC 2

description: ATAC Seq

value: VE-Cad Cre


title: DMS53 SiCONTROL CISPT 50nM rep2


title: TargetSeq_Sample_32

value: 293FT cells


title: TargetSeq_Sample_33


title: DMS53 SiASCL1 LURBI rep2

value: cell line


title: plasma exosomes of CRT-resistant patient 4

description:
EQ0097_04
Test, exosomal miRNA

value: CRT-resistant


title: DMS53 SiCONTROL CISPT 50nM rep1

value: CISPLATIN


title: Cre Lung ATAC 1

description: ATAC Seq


title: TargetSeq_Sample_30


title: Cre Heart ATAC 2

description: ATAC Seq

value: Heart ECs


title: TargetSeq_Sample_34


title: DMS53 SiCONTROL CISPT 20uM rep2


title: DMS53 SiCONTROL CISPT 20uM rep1


title: plasma exosomes of CRT-resistant patient 2

description:
EQ0097_02
Test, exosomal miRNA


title: TargetSeq_Sample_31


title: DMS53 SiCONTROL LURBI rep2


title: IP_Negative 3

city: Guangzhou

first: Qiqi

last: Zhao

address: 483 WUSHAN ROAD

institute: South China Agricultural University

data_processing:
Library strategy: MeRIP-seq
clean reads of input libraries were aligned to reference genome by STAR software.
circRNAs were identified by DCC software
clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4)
Methylated sites on RNAs (peaks) were identified by MACS software
Differentially methylated sites were identified by diffReps.
Genome_build: GCF_000002315.6_GRCg6a
Supplementary_files_format_and_content: excel format: Number of raw junction read

organism: Gallus gallus

source_name: liver

extract_protocol:
RNA extraction protocol
library construction protocol

value: Inoculated intraamdominally with the same volume of nutrient solution

value: liver


title: plasma exosomes of CRT-resistant patient 1

description:
EQ0097_01
Test, exosomal miRNA


title: IP_Negative 2


title: TargetSeq_Sample_29


title: IP_Negative 1


title: TargetSeq_Sample_26


title: plasma exosomes of CRT-resistant patient 3

description:
EQ0097_03
Test, exosomal miRNA


title: R-8

city: Shenzhen

first: Yan

address: No. 1088,Xueyuandadao

department: BIology

institute: Southern University of Science and Technology

description:
CRIPSR-iPAS with target sgRNA
gene.counts.tsv

data_processing:
Alignment was perfomed by using STAR (v2.7.9)
Counting the reads from gene and PAS was using featureCounts
The read counts of gene across different samples were normalized by DESeq2.
The read counts of PAS across different samples were normalized by DEXSeq
Genome_build: hg38
Supplementary_files_format_and_content: Raw count of PAS and gene in TSV format

molecule: polyA RNA

source_name: mRNA from HEK293T

growth_protocol: HEK293TAPA cells were cultured in DMEM with 10%FBS and 1% P/S at 37℃

extract_protocol:
Cells were harvested after 48-hour transfection and the total RNA was isolated by Trizol reagent.
The library for 3’ end mRNA sequencing was prepared using QuantSeq 3’mRNA-Seq Library Prep Kit REV for Illumina (Lexogen); The library for mRNA sequencing was generated using Hieff NGS MaxUp II Dual-mode mRNA Library Prep Kit for Illumina (Yeasen).

treatment_protocol: HEK293TAPA cell line was the HEK293T cells expressing APA repoter stably at the medium level. To perturb the inserted PAS usage, HEK293TAPA cells co-transfected with dPguCas13b and non-targeting control (gNT)  or gUSE respectively

tag: transfection

value: dPguCas13b gUSE


title: DMS53 SiCONTROL UNTREATED rep2

source_name: Lung


title: DMS53 SiCONTROL UNTREATED rep1


title: Cre Heart ATAC 1

description: ATAC Seq


title: IP_Positive 1

value: Inoculated intraamdominally with 10^3.7 TCID50/0.2 mL virulent ALV-J strain NX0101 at 1 day of age


title: IP_Positive 2


title: TargetSeq_Sample_25


title: pIUT [RMM2368]

city: SINGAPORE

first: Karthikeyan

last: Kandasamy

state: SINGAPORE

address: 10 Medical Drive

department: Obstetrics & Gynaecology

country: Singapore

institute: National University of Singapore

description: Total RNA extracted from magnetic and FACS sorted cells

data_processing:
Basecalls performed using bcl2fastq
For each samples with fastq files from different lanes were concatenated with unix cat command
Concatenated fastq were processed with nf-core rnaseq pipeline version 3.0 with following configuration 1) "stringtie_ignore_gtf" activated 2) genomic reference: GRCm39 (fasta) 3) gene annotation: GENCODE M26 (GTF)
Concatenated fastq were processed with MIXCR v2.1.10 with following configuration "mixcr analyze shotgun -s mmu --starting-material rna --contig-assembly --assemble-partial-rounds 4"
Genome_build: GRCm39
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table of gene count of immunoglobulins and T-cell receptor for a single sample

source_name: Fetal cells

growth_protocol: C57BL/6 (CD11c-DTR) females (shortly B6 females) and BALB/c males were time-mated to generate B6 pregnant dams. The day before in-utero transplantation (IUT) (E13), CD11c-DTR pregnant mothers (DT+) were given intraperitoneal DT injections (5ng/g body weight) for transient dendritic cell suppression. DT- dams received saline. IUT was performed on E14 and all fetuses received intrahepatic injection of 5E+6 donor inoculum of freshly prepared bone marrow mononuclear cells. Maternal donor cell IUT (mIUT) was performed using B6 BM-MNC (CD45.1, H-87 2Kb), BALB/c BM-MNC was administered in paternal donor cell IUT (pIUT). Uninjected controls were offspring of DT+ or DT- dams which did not undergo IUT. After littering, pups were nursed by their mothers and weaned at 4 weeks. Recipient (fetal) cells and trafficked  maternal cells were harvested from 1 week old F1 cross-bred hybrid pups.

extract_protocol:
Trafficked maternal cells and fetal cells were magnetic and flow sorted from the pool of fetal mononuclear cells. Sorted cells were collected in RLT buffer (Rneasy micro kit, Qiagen) and total RNA was isolated with on-column Dnase digestion and extracted carrier-free. The quality of the total RNA was analysed by Agilent2100 Bioanalyzer, before cDNA library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mononuclear cells

value: F1 pups (C57BL/6 (CD11c-DTR) mom x BALB/c dad)

value: IUT with paternal donor cells


title: IP_Postive 3


title: R-7


title: DT+pIUT [RMM2372]

value: IUT with paternal donor cells following transient maternal dendritic cell depletion (DT+)


title: Control [RMM2370]

value: No IUT


title: mIUT [RMM2366]

value: IUT with maternal donor cells


title: TargetSeq_Sample_27


title: TargetSeq_Sample_24


title: DT+pIUT [RMM2371]

source_name: Trafficked maternal cells isolated from the fetal recipients

value: C57BL/6 (CD11c-DTR)


title: Input_Negative 2


title: Control [RMM2369]


title: R-5

description:
CRIPSR-iPAS with control sgRNA
gene.counts.tsv

value: dPguCas13b gNT


title: TargetSeq_Sample_23

source_name: hA3A-BE3-4:hRNF2;hA3A-BE3-4:hSEC61B;hA3A-BE3-4:hFANCF;PE3 ins-4:hLSP;PE3 ins-4:hHEK1;PE3 ins-4:hEMX1;

value: 293FT cells

value: 293FT-Apobec KO92-1-hA3A-BE3-4(Target_gene:hRNF2);293FT-Apobec KO92-1-hA3A-BE3-4(Target_gene:hSEC61B);293FT-Apobec KO92-1-hA3A-BE3-4(Target_gene:hFANCF);293FT-Apobec KO92-1-PE3 ins-4(Target_gene:hLSP);293FT-Apobec KO92-1-PE3 ins-4(Target_gene:hHEK1);293FT-Apobec KO92-1-PE3 ins-4(Target_gene:hEMX1);


title: TargetSeq_Sample_28


title: DMS53 SiCONTROL LURBI rep1

value: cell line

value: LURBINECTEDIN


title: R-6


title: pIUT [RMM2367]


title: SMAD-2-3

description:
CRIPSR-iPAS with control sgRNA
polyADB.PAS.count.tsv

source_name: 3'end of mRNA  from HEK293T


title: Input_Postive 3


title: SMAD-2-4

description:
CRIPSR-iPAS with target sgRNA
polyADB.PAS.count.tsv


title: Input_Negative 1


title: mIUT [RMM2365]


title: Input_Negative 3


title: TargetSeq_Sample_21

source_name: hA3A-BE3-2:hRNF2;hA3A-BE3-2:hSEC61B;hA3A-BE3-2:hFANCF;PE3 ins-2:hLSP;PE3 ins-2:hHEK1;PE3 ins-2:hEMX1;

value: 293FT-Apobec KO92-1-hA3A-BE3-2(Target_gene:hRNF2);293FT-Apobec KO92-1-hA3A-BE3-2(Target_gene:hSEC61B);293FT-Apobec KO92-1-hA3A-BE3-2(Target_gene:hFANCF);293FT-Apobec KO92-1-PE3 ins-2(Target_gene:hLSP);293FT-Apobec KO92-1-PE3 ins-2(Target_gene:hHEK1);293FT-Apobec KO92-1-PE3 ins-2(Target_gene:hEMX1);


title: Input_Positive 2


title: TargetSeq_Sample_20

source_name: hA3A-BE3-1:hRNF2;hA3A-BE3-1:hSEC61B;hA3A-BE3-1:hFANCF;PE3 ins-1:hLSP;PE3 ins-1:hHEK1;PE3 ins-1:hEMX1;

value: 293FT-Apobec KO92-1-hA3A-BE3-1(Target_gene:hRNF2);293FT-Apobec KO92-1-hA3A-BE3-1(Target_gene:hSEC61B);293FT-Apobec KO92-1-hA3A-BE3-1(Target_gene:hFANCF);293FT-Apobec KO92-1-PE3 ins-1(Target_gene:hLSP);293FT-Apobec KO92-1-PE3 ins-1(Target_gene:hHEK1);293FT-Apobec KO92-1-PE3 ins-1(Target_gene:hEMX1);


title: SMAD-1-4


title: D3 MTCH1 4

city: London

first: John

last: Labbadia

address: Darwin Building, Gower Street

department: GEE

country: United Kingdom

institute: UCL

data_processing:
Sequenced reads were trimmed for adaptor sequences and polyN and low quality reads were removed before mapping reads to the WBcel235 reference genome using  Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the number of reads mapped to each gene and FPKM for each gene was then calculated
DESeq2 was then used for differential expression analysis
Genome_build: WBcel235
Supplementary_files_format_and_content: Table with raw gene counts for every gene and every sample

organism: Caenorhabditis elegans

source_name: worms

growth_protocol: Worms were grown on NGM RNAi plates containing Ampicillin and 1 mM IPTG at 20degC. Plates were seeded with HT115 E.coli expressing L4440 empty vector or dsRNA against mtch-1 and induced for 3 hours at 37degC with 5 mM IPTG.

extract_protocol:
Worms were lysed in Trizol by vortexing at 4degC for 20 minutes. RNA was then purified using a Qiagen Rneasy Minelute kit as per manufacturers instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C. elegans were age-synchronised by egg-lay onto EV control (L4440) or mtch-1(RNAi) plates and grown to day 3 of adulthood before being collected and snap frozen in liquid N2.

tag: media


title: Input_Positive 1

value: liver


title: TargetSeq_Sample_18

source_name: PE3-3:hRNF2;PE3-3:hSEC61B;PE3-3:hFANCF;PE3 del-3:hLSP;PE3 del-3:hHEK1;PE3 del-3:hEMX1;

tag: cell line

value: 293FT-Apobec KO92-1-PE3-3(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3-3(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3-3(Target_gene:hFANCF);293FT-Apobec KO92-1-PE3 del-3(Target_gene:hLSP);293FT-Apobec KO92-1-PE3 del-3(Target_gene:hHEK1);293FT-Apobec KO92-1-PE3 del-3(Target_gene:hEMX1);


title: TargetSeq_Sample_22

source_name: hA3A-BE3-3:hRNF2;hA3A-BE3-3:hSEC61B;hA3A-BE3-3:hFANCF;PE3 ins-3:hLSP;PE3 ins-3:hHEK1;PE3 ins-3:hEMX1;

tag: treatment

value: 293FT-Apobec KO92-1-hA3A-BE3-3(Target_gene:hRNF2);293FT-Apobec KO92-1-hA3A-BE3-3(Target_gene:hSEC61B);293FT-Apobec KO92-1-hA3A-BE3-3(Target_gene:hFANCF);293FT-Apobec KO92-1-PE3 ins-3(Target_gene:hLSP);293FT-Apobec KO92-1-PE3 ins-3(Target_gene:hHEK1);293FT-Apobec KO92-1-PE3 ins-3(Target_gene:hEMX1);


title: KO-MII-D321 longRNA rep2

description: total cellular RNA mixed with exogenous spikein

source_name: Oocyte

value: Syrian

tag: genotype

value: Pld6 KO

value: MII stage oocyte

value: long RNA


title: KO-MII-D321 longRNA rep1


title: TargetSeq_Sample_19

source_name: PE3-4:hRNF2;PE3-4:hSEC61B;PE3-4:hFANCF;PE3 del-4:hLSP;PE3 del-4:hHEK1;PE3 del-4:hEMX1;

value: 293FT-Apobec KO92-1-PE3-4(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3-4(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3-4(Target_gene:hFANCF);293FT-Apobec KO92-1-PE3 del-4(Target_gene:hLSP);293FT-Apobec KO92-1-PE3 del-4(Target_gene:hHEK1);293FT-Apobec KO92-1-PE3 del-4(Target_gene:hEMX1);


title: KO-MII-D321 smRNA rep1

value: smRNA


title: D3 MTCH1 3


title: SMAD-1-3


title: KO-MII-D321 smRNA rep2


title: D3 MTCH1 2


title: KO-54PEA longRNA rep2

source_name: Embryo

value: embryo at 54PEA


title: D3 EV 4

value: EV control (L4440)


title: PROseq_auxin_4hr_N3

city: Nashville

first: Jing

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Peaks were called by MACS2 with a q-value of 1e-5.
Differential binding peaks were identified using DiffBind.
After adapter trimming and low quality sequence removal by cutadapt, PRO-seq reads longer than 15bp were reversed complemented using FastX tools.
Reverse complements of the trimmed reads were aligned to the human genome hg19 using Bowtie2.
Reads mapped to rRNA loci and reads with mapping quality less than 10 were removed.
Bam files were given to NRSA (http://bioinfo.vanderbilt.edu/NRSA/) to estimate RNA polymerase abundance in proximal-promoter and gene body regions of genes, to calculate pausing index and pausing index alterations, and to detect enhancers and quantify eRNA changes.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq: tab-delimited text file include raw counts for each Sample
Supplementary_files_format_and_content: ChIP-seq: one peak file per sample
Supplementary_files_format_and_content: PRO-seq: tab-delimited text file include raw counts for proximal-promoter and gene body region, and density for gene body

molecule: nuclear RNA

source_name: Ramos cell

growth_protocol: Ramos cells were obtained from ATCC (CRL-1596) and cultured with the recommended conditions (RPMI media supplemented with L-glutamine, 10% FBS, 100 IU/ml Penicillin, and 100 μg/ml streptomycin).

extract_protocol:
RNA-seq: 5 x 10^6 cells per sample were lysed using TRIZOL. The RNA was phase separated with chloroform, precipitated with isopropyl alcohol, and DNase treated .
ChIP-seq:ChIP-seq: Cells were resuspended in PBS at 4x106 cells/ml, and crosslinked with 1% methanol free formaldehyde for 10 min at room temperature before quenching with 125 mM Glycine. Cells were pelleted, washed twice with 1.5 ml PBS, and lysed in lysis buffer (50 mM Tris pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton, 0.1% SDS and protease inhibitor cocktail) at a concentration of 80x106 cells per ml. Aliquots of 300 ul were sonicated in a Bioruptor for 20 min and debris was removed by centrifugation. 100 ul of Chromatin was diluted to 1 ml using lysis buffer lacking SDS and incubated overnight at 4C with the appropriate antibody or control IgG. Antibodies were captured on 15 ul bed volume Protein A agarose beads and immune complexes were washed with 1 ml Low Salt Buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton), 1 ml Hi Salt Wash Buffer (20 mM Tris pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton), 1 ml LiCl Wash Buffer (10 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Triton) and twice with 1 ml of TE. Samples were decrosslinked overnight in 100 ul TE containing 20 ug of Proteinase K (PK) at 65C then brought up to 500 ul with water and incubated at 95C for 20 minutes to inactive PK.
PRO-seq: Nuclei from 30 x 10^6 Ramos cells per sample were isolated in buffer using dounce homogenization then flash frozen and kept at -80C until run on reaction. Primary transcripts were eluted using TRIZOL extractions and dynabeads, which isolate primary transcripts by binding the biotin incorperated during the run-on.
RNA-seq: Library preparation with rRNA depletion performed by Vanderbilt Technologies for Advanced Genomics (VANTAGE)
PRO-seq: RNA was used in a reverse transcriptase reaction to generate a cDNA library. Libraries were amplified based on the a PCR cycle number determined from a test analysis of a portion of sample. Library amplification was performed with Illumina-based index primers.
ChIP-seq: ChIP-seq: After de-crosslinking, samples were purified using the MinElute PCR Purification Kit (Qiagen). The NEBNext Ultra II DNA Library Prep Kit for Illumina was used to prepare unique dual indexed libraries from the entire eluate following the manufacture’s protocol.
RNA-seq, ChIP-seq, PRO-seq

treatment_protocol: Cells were treated with 100 uM IAA or 500 nM C16, and 0.1% DMSO for the times indicated.

value: Four Hour 100 uM Indole-3-Acetic Acid


title: PROseq_auxin_4hr_N2


title: PROseq_auxin_4hr_N1


title: D3 EV 3


title: TargetSeq_Sample_14

value: 293FT cells


title: TargetSeq_Sample_16

source_name: PE3-1:hRNF2;PE3-1:hSEC61B;PE3-1:hFANCF;PE3 del-1:hLSP;PE3 del-1:hHEK1;PE3 del-1:hEMX1;

value: 293FT-Apobec KO92-1-PE3-1(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3-1(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3-1(Target_gene:hFANCF);293FT-Apobec KO92-1-PE3 del-1(Target_gene:hLSP);293FT-Apobec KO92-1-PE3 del-1(Target_gene:hHEK1);293FT-Apobec KO92-1-PE3 del-1(Target_gene:hEMX1);


title: KO-54PEA longRNA rep1


title: WT-54PEA longRNA rep2

value: wild type


title: TargetSeq_Sample_15


title: TargetSeq_Sample_12


title: D3 MTCH1 1


title: D3 EV 1


title: TargetSeq_Sample_13


title: TargetSeq_Sample_17

source_name: PE3-2:hRNF2;PE3-2:hSEC61B;PE3-2:hFANCF;PE3 del-2:hLSP;PE3 del-2:hHEK1;PE3 del-2:hEMX1;

value: 293FT-Apobec KO92-1-PE3-2(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3-2(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3-2(Target_gene:hFANCF);293FT-Apobec KO92-1-PE3 del-2(Target_gene:hLSP);293FT-Apobec KO92-1-PE3 del-2(Target_gene:hHEK1);293FT-Apobec KO92-1-PE3 del-2(Target_gene:hEMX1);


title: TargetSeq_Sample_11


title: PROseq_auxin_2hr_N2

value: Two Hour 100 uM Indole-3-Acetic Acid


title: PROseq_auxin_2hr_N4


title: WT-54PEA longRNA rep1


title: PROseq_auxin_2hr_N3


title: D3 EV 2


title: TargetSeq_Sample_7


title: TargetSeq_Sample_6


title: KO-1C-20PEA longRNA rep2

value: 1C embryo at 20PEA


title: KO-33PEA longRNA rep1

value: embryo at 33PEA


title: KO-33PEA longRNA rep2


title: WT-33PEA longRNA rep2


title: Root cadmium treatment replicate 3

city: Catania

first: Angela Roberta

last: Lo Piero

state: CT

address: Via S. Sofia 98

country: Italy

institute: University of Catania

data_processing:
Base calling, base quality and Phred score relationship performed with the Illumina CASAVA v1.8 software
Raw reads are filtered to remove reads containing adapters or reads of low quality
In the absence of a reference genome clean reads have been assembled using Trinity software (minKmerCov= 3, min_glue=4). Corset software was used for hierarchical clustering (parameter -m 10)
Seven databases have been applied for gene functional annotation: Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG and GO.
CDS preduction using blast and EST-scan
De novo transcriptome filtered by Corset used as a reference for mapping reads back to transcriptome and quantify the expression level using RSEM.
DESeq2 used for gene expression difference analysis
Genome_build: FASTA assembled sequences
Supplementary_files_format_and_content: Microsoft excell file containing raw readcounts of all unigenes in each sample

organism: Arundo donax

source_name: Root

growth_protocol: The trial started on May 4th 2020, by filling each pot with 8 kg of clay soil and kept in open air. Afterwards, one litre of tap water was added to each pot to allow the element adsorption by soil colloids. Successively, in each pot a single A. donax stem node was transplanted and the irrigation was performed three times a week by adding one litre of tap water. The pots were arranged according to a randomized block factor scheme, considering three biological replicates for each treatment, with a total of six experimental units.

extract_protocol:
On July 28th both treated and control samples were collected after prolonged cadmium exposure. Leaves and roots were immediately frozen with liquid nitrogen and stored at -80°C until further uses. RNA isolation was carried out by using the Spectrum Plant Total RNA Extraction kit (Sigma-Aldrich, St. Louis, MO, USA) according to the manufacturer’s instructions.
All samples passed through three steps before library construction: Nanodrop for preliminary quantitation, agarose gel electrophoresis to tests RNA degradation and potential contamination, Agilent 2100 to checks RNA integrity and quantitation. After the QC procedures, mRNA from is enriched from total RNA using oligo(dT) beads. The mRNA is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added, with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation and AMPure XP beads is used to purify the cDNA. The final cDNA library is ready after a round of purification, terminal repair, Atailing, ligation of sequencing adapters, size selection and PCR enrichment. Libraries are fed into Illumina machines according standard Illumina protocol.

treatment_protocol: The contamination of each pots was achieved by using 4 ppm (4 mg/kg) of cadmium nitrate Cd(NO3)2 for treated plants and 5.774 grams/L of NH4NO3 for control plants, so as to equilibrate the N concentration between the two conditions.

value: Water + 4 ppm (4 mg/kg) of cadmium nitrate


title: Root control replicate 2

value: Water + 5.774 grams/L of ammonium nitrate


title: WT-33PEA longRNA rep1

value: Syrian


title: TargetSeq_Sample_10


title: TargetSeq_Sample_5


title: Root cadmium treatment replicate 2


title: TargetSeq_Sample_9


title: PROseq_auxin_2hr_N1


title: Root cadmium treatment replicate 1


title: TargetSeq_Sample_4


title: TargetSeq_Sample_8


title: Root control replicate 1


title: Root control replicate 3


title: WT-1C-20PEA longRNA rep1


title: KO-10PEA longRNA rep2

value: Pld6 KO

value: embryo at 10PEA


title: WT-1C-20PEA longRNA rep2

value: long RNA


title: Leaf cadmium treatment replciate 3

source_name: Leaf


title: Leaf control replciate 3


title: PROseq_NT_N3

value: No treatment


title: WT-10PEA longRNA rep1


title: KO-10PEA longRNA rep1


title: Leaf control replicate 2


title: ChIPseq_NT_H3K4me3_N3

value: No Treatment


title: hRNF2-PE3-3rd

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh38/hg38 human reference genome using BWA-MEM 0.7.17
Genome_build: hg38 for human samples
Supplementary_files_format_and_content: Number of off-target mutations in excel file

source_name: 293FT cells

extract_protocol:
Total RNAs were extracted from human 293FT cells and mouse livers tissues by using TransZol® Up Plus RNA Kit (ER501-01, TransGen)
For total RNA-seq, RNA libraries were prepared by using the TruSeq Stranded Total RNA with Ribo-Zero Globin. RNA-seq libraries were sequenced on an Illumina HiSeq X Ten (2×150) Omics core of Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China.

treatment_protocol: After 40hr after transfection, Cells in the first 15% of the fluorescence intensity were sorted by FACSAriaIII.


title: ChIPseq_IAA_IgG_N2

value: 18 Hour 100 uM Indole-3-Acetic Acid


title: PROseq_NT_N2


title: TargetSeq_Sample_3


title: KO-MII longRNA rep1

value: MII stage oocyte


title: PROseq_NT_N1


title: ChIPseq_IAA_H3K4me3_N3


title: ChIPseq_IAA_H3K4me3_N1


title: Leaf cadmium treatment replicate 2


title: ChIPseq_IAA_H3K4me3_N2


title: WT-10PEA longRNA rep2


title: ChIPseq_NT_H3K4me3_N1


title: KO-1C-20PEA longRNA rep1


title: ChIPseq_NT_H3K4me3_N2


title: hRNF2-PE3-1st

value: 293FT cells


title: ChIPseq_IAA_IgG_N3


title: Leaf cadmium treatment replicate 1


title: V4 CD8+TILs after vehicle treatment

city: Fuzhou

first: Zili

state: Fujian

address: 20th Chazhong Road

department: Oncology

institute: the First Affiliated Hospital, Fujian Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited txt files include TPM values for each Sample

source_name: B16F10 subcutaneous melanoma tumor tissue

growth_protocol: B16F10 cells were cultured with DMEM media containing 10% FBS, the cells were injected into C57BL/6 mice subcutaneously. 7-9 days later, the volume of subcutaneous tumor was about 50 mm3. Then the mice were treated with tacrolimus or vehicle.

extract_protocol:
RNA of CD8+ tumor-infiltrating lymphocytes were extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice were treated with tacrolimus at 3mg/kg every 5 days or vehicle every 5 days. 6 days post treatment onset, the subcutaneous tumors were harvested, digested and the CD8+ tumor-infiltrating lymphocytes were sorted by flow cytometry.

value: CD8+ tumor-infiltrating lymphocytes (TILs)

value: Vehicle was administered i.p. every 5 days


title: TargetSeq_Sample_1


title: KO-MII longRNA rep2


title: ChIPseq_NT_IgG_N1


title: hRNF2-NT-2nd

value: non-transfection


title: V2 CD8+TILs after vehicle treatment

value: B16F10 subcutaneous melanoma tumor tissue


title: hRNF2-NT-1st


title: RNAseq_C16_N4

value: 18 Hour 500 nM C16


title: Leaf control replicate 1


title: ChIPseq_IAA_IgG_N1


title: ChIPseq_NT_IgG_N3


title: hRNF2-PE3-2nd


title: WT-MII longRNA rep2

value: wild type


title: TargetSeq_Sample_2


title: ChIPseq_NT_IgG_N2


title: hRNF2-NT-3rd


title: WT-GV longRNA rep1

value: GV stage oocyte


title: V3 CD8+TILs after vehicle treatment


title: F3 CD8+TILs after tacrolimus (FK506) treatment

value: Tacrolimus was administered i.p. at 3mg/kg every 5 days


title: KO-54PEA smRNA rep2

value: Syrian

value: embryo at 54PEA

value: smRNA


title: KO-GV longRNA rep2

value: Pld6 KO

value: long RNA


title: KO-GV longRNA rep1


title: V1 CD8+TILs after vehicle treatment


title: WT-GV longRNA rep2


title: F2 CD8+TILs after tacrolimus (FK506) treatment


title: hRNF2-Cas9-3rd


title: hRNF2-Cas9-2nd


title: hRNF2-EGFP-2nd

value: EGFP


title: RNAseq_DMSO_N4

value: 18 Hour DMSO 0.1%


title: WT-MII longRNA rep1

value: MII stage oocyte


title: hRNF2-EGFP-1st

value: 293FT cells


title: RNAseq_C16_N3


title: old_ME

city: Beijing

first: Zhenhua

last: Chen

state: China

address: West Beichen Road, Olympic Village, Beijing

department: State Key Laboratory of Molecular Development Biology

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
CellRanger Mkfatsq/Count Analysis
Seurat R package (v3) was used for analysis. For quality control, we set the threshold and removed cells with more than15% (in young) and 20% (in aging) of reads mapping to mitochondrial genes (considered to aging cell exhibit extensive mitochondrial contamination), fewer than 600 genes (considered to be low-quality cells or empty droplets), more than 10,000 genes (considered likely to be cell doublets or multiplets), leaving residual cells for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: ME_integrate_re0.15_clean.rds. rds are serialized R objects of the Bioconductor class ExpressionSet that contains the final data used to generate the results. It can be imported into R with `readRDS(“ME_integrate_re0.15_clean.rds”)`. It contains the gene counts, sample metadata, and feature metadata for single cells that passed quality control.

source_name: Median eminence

extract_protocol:
3-month old and 12 month-old mice were breed and median eminence were dissociated for single-cell RNA-seq.
The libraries were prepared for sequencing following the manufacturer’s recommendations for the 10x Genomics 3’ Gene Expression v3 chemistry

value: Median eminence


title: hRNF2-EGFP-3rd


title: KO-54PEA smRNA rep1


title: F1 CD8+TILs after tacrolimus (FK506) treatment

value: CD8+ tumor-infiltrating lymphocytes (TILs)


title: F4 CD8+TILs after tacrolimus (FK506) treatment


title: young_ME_female


title: RNAseq_DMSO_N2


title: RNAseq_DMSO_N3


title: WT-54PEA smRNA rep1


title: WT-54PEA smRNA rep2


title: RNAseq_C16_N2


title: hRNF2-A3A-3rd


title: KO-33PEA smRNA rep2

value: embryo at 33PEA


title: RNAseq_DMSO_N1


title: hRNF2-Cas9-1st


title: ChIP_Th1_Stat4-1

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

data_processing:
ChIP-Seq and DNase-Seq reads (50 bp) were mapped to mm10 genome with Bowtie2 (Langmead and Salzberg, 2012). Only non-redundant reads with MAPQ >=10 were used for follow-up analysis. DNase-Seq peaks were called by MACS2 (Zhang et al., 2008) with settings of --nomodel--extsize 75.
Genome_build: mm10
Supplementary_files_format_and_content: Aligned unique high quality reads single end (BED files) and paired-end (BEDPE files). Peaks (narrowPeak files) were called for limited samples.

growth_protocol: To prepare Th1 cells, naïve CD4 T cells are cultured in conditions: α-CD3, α-CD28, α-IL-4, IL-12 and IL-2. After 4 days, cells were harvested.

extract_protocol:
Detailed procedures for DNase-Seq (in duplicates) were reported previously (Jin et al., 2015).
Dnase and ChIP DNA were end-repaired using an End-It DNA End-Repair kit (Epicentre), universal adaptors were then ligated. The libraries were amplified using indexed primers with the PCR condition: 98°C, 10”; 67°C, 30”; 72°C, 30” for 16 cycles. The fragments between 180bp to 350bp were isolated on E-gel and subjected to sequencing on Illumina instruments.

value: Naive CD4 T cell

tag: cell culture condition

tag: markers

tag: chip antibody


title: RNAseq_C16_N1

value: 18 Hour 500 nM C16


title: WT-33PEA smRNA rep1

value: wild type


title: G11_Citrobacter_PAR5359_2_S87_L003

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

data_processing:
RNASeq data was processed using kallisto (version 0.45.0) and mouse genome GRCm38 Ensembl version 94 annotation (Mus_musculus.GRCm38.94.chr_patch_hapl_scaff.gtf). Gene-level TPM values and gene annotations were computed using tximport and biomaRt R package. Batch correction was performed using sva::ComBat_seq R function. Expression values were generated using log2(batch corrected counts + 1).
Genome_build: Genome assembly: GRCm38 Ensembl 94, Gene annotatiopn: Mus_musculus.GRCm38.94.chr_patch_hapl_scaff.gtf
Supplementary_files_format_and_content: tab-delimited text files include log2(batch corrected TPM+1).

source_name: Distal colon

growth_protocol: Adult C57BL/6 mice were acquired from Jackson Laboratories. All animals were maintained in an institutional animal care. Provided with standard light–dark cycle, fed with standard laboratory chow and clean drinking water.

extract_protocol:
All colon tissues were lysed using TRI-Reagent and RNA was isolated using Zymo Research: Direct-zol RNA MiniPrep Kit.
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: Mice were orally challenged with C. rodentium at 5 x 108 CFU in 0.1 ml of PBS. PPARa agonist (GW7647, 20 ug/kg body weight/day), PPARg agonist (Pioglitazone, 20mg/kg body weight/day), PPARa/g dual agonist (PAR5359, 1 mg/kg body weight/day) were administered via intraperitoneal route in 200 ul total volume (DMSO less than 4%).

tag: strain

tag: disease state

value: inflammatory bowel disease

value: distal colon

tag: time

value: day 18

tag: infection

value: Yes


title: G12_Citrobacter_PAR5359_3_S88_L003

tag: tissue


title: RNAseq_IAA_N4

value: 18 Hour 100 uM Indole-3-Acetic Acid


title: KO-33PEA smRNA rep1

tag: breed

value: Syrian

value: Pld6 KO

tag: molecule subtype

value: smRNA


title: hRNF2-A3A-2nd

city: Shanghai

first: Li

address: 131 Dong-An Road

institute: Fudan University


title: ChIP_Th1_Stat4-2

tag: cell type


title: WT-33PEA smRNA rep2


title: KO-1C-20PEA smRNA rep1

value: 1C embryo at 20PEA


title: G10_Citrobacter_PAR5359_1_S86_L003


title: RNAseq_IAA_N1


title: hRNF2-A3A-1st


title: RNAseq_IAA_N2


title: Citrobacter_7days_PAR5359_5_S15

value: day 7


title: young_ME_male


title: RNAseq_NT_N3

value: No treatment


title: RNAseq_NT_N4


title: Citrobacter_7days_PAR5359_4_S14


title: RNAseq_IAA_N3


title: RNAseq_NT_N2


title: S2502Nr15 [Rf_grain_3]

city: Vienna

first: Cátia

last: Pacífico

state: Vienna

address: Veterinaerplatz 1

country: Austria

institute: University of Veterinary Medicine Vienna

description: small RNA

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20).
Adapters were trimmed with Skewer (version 0.2.2) (Jiang et al. 2014).
Demultiplexed reads were analyzed using sRNAbench. Reads with an average PHRED score below 20 were discarded.
Genome_build: UMD3_1_mp
Supplementary_files_format_and_content: tab-delimited text file include counts of all samples (sRNAbench output)
Supplementary_files_format_and_content: tab-delimited text file include DESeq2-normalized counts of all samples

organism: Bos taurus

source_name: Rumen fluid

extract_protocol:
Total RNA was extracted using NucleoSpin miRNA kit (Macherey-Nagel, Germany).
Library preparation was prepared using the NETflex Small RNA-Seq Kit (Bioo Scientific).

value: Rumen fluid

tag: diet

value: Grain


title: S2502Nr13 [Rf_grain_1]

description: small RNA


title: S2502Nr14 [Rf_grain_2]

description: small RNA


title: S2502Nr16 [Rf_grain_4]

description: small RNA


title: S2502Nr12 [Rf_forage_4]

description: small RNA

value: Forage


title: KO-1C-20PEA smRNA rep2


title: WT-1C-20PEA smRNA rep1


title: S2502Nr11 [Rf_forage_3]

description: small RNA


title: KO-10PEA smRNA rep2

value: embryo at 10PEA


title: S2502Nr10 [Rf_forage_2]

description: small RNA


title: WT-1C-20PEA smRNA rep2


title: RNAseq_NT_N1


title: ATAC-Seq MM3038_72h

city: Pittsburgh

first: Timothy

last: Billiar

state: Pennsylvania

address: 200 Lothrop Street

department: Surgery

institute: University of Pittsburgh

description: All time points for the same patient were processed in the same batch.

data_processing:
The BCL files generated by Illumina sequencer were processed by Cell Ranger Atac pipeline (v1.2.0) for demultiplexing using cellranger-atac mkfastq and generated count matrix for peaks for each sample using cellranger-atac count (mapped to GRCh38 human reference genome). cellranger-atac aggr were used to aggregate the outputs from multiple samples.
The aggregated peak-barcode count matrix was processed using Signac R package (v1.0.0.9000) and Seurat R package (v3.2.0).
The peaks accessible in ≥ 10 cells and the cells with ≥ 200 peaks detected were retained. The cells with total number of fragments in peaks ≤ 3000 or ≥ 30000 were excluded to remove the cells with low sequencing depth or potential multiplets. The cells with fraction of fragments in peaks ≤ 15%, poor nucleosome banding pattern (nucleosome signal ≥ 4) or low TSS enrichment score (TSS ≤ 2) were excluded to remove potential low-quality cells. The cells with ratio of reads in genomic blacklist regions ≥ 0.05 were excluded to remove artifactual signals.
Genome_build: GRCh38
Supplementary_files_format_and_content: Peak-barcode cut site count matrix passing the above filtering step. Each sample was uploaded as a separated .txt.gz file.

source_name: PBMC

extract_protocol:
Ficoll centrifugation to isolate PBMC.
scATAC libraries were prepared for sequencing using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 (Cat#1000175, 10x Genomics), Chromium Next GEM Chip H Single Cell Kit (Cat#1000162, 10x Genomics) and Single Index Kit N Set A (Cat#1000212, 10x Genomics).
single-cell ATAC-seq

value: PBMC

tag: time point


title: ATAC-Seq MM3038_24h


title: Citrobacter_7days_PAR5359_2_S12


title: ATAC-Seq MM3038_Ctrl

value: Ctrl


title: ATAC-Seq MM3038_4h


title: KO-10PEA smRNA rep1

data_processing:
Raw read1 fastq of smRNA-seq(oocyte and embryo) was used to identify small RNAs, which were pre-processed using the fastx_toolkit. After quality filtering, sequencing reads were clipped from the 3' adaptor allowing a minimum match of 10 nt from the 5' end.
Reads unable to match the adaptor sequence or with lengths shorter than 17 bp were discarded, and the remaining reads were mapped to the golden hamster genome (MesAur2.0) by sports(version 1.1).The mapped genome sequences were further aligned to piRNAs, miRNAs, tRNAs, rRNAs, snoRNAs, and snRNAs.
The small RNAs were mapped in the following order: miRNA, rRNA, rRNA, piRNA, snoRNA, and snRNA. The reads in each library were normalized with sequencing depth or the count of exogenous spike-ins.
The raw fastq reads of RNA-seq were clipped off the adaptors and quality filtered by trim_galore with parameters --quality 20 --stringency=1 –length=35 --paired (http://tophat.cbcb.umd.edu/).
The remaining fastq reads were mapped to the genome by STAR (version 2.7.1a) with parameters --winAnchorMultimapNmax 10000 --outFilterMultimapNmax 10000. The reads uniquely and multiply mapped with genomic copies less than 10,000 were used for subsequent analysis. Gene abundance was retrieved by featurecounts with default parameters.
Genome_build: MesAur2.0
Supplementary_files_format_and_content: tab-delimited text files include useful reads count of smRNAs and each gene count.

extract_protocol:
The single oocytes or embryos were incubated at 72°C for 3 min to release and unfold the small RNAs.For testicular RNA seq, total RNA was extracted from 21 d.p.p. golden hasmters using the RNA isolater Total RNA Extraction Reagent(VAZYME,R401-01)according to the manufacturer’s protocol.
For single oocyte or embryos smRNA seq, after 3’adapter ligation, 5U of lambda exonuclease and 25U of 5’deadenylases, which performed better than the combination of RecJf and 5’deadenylases, were used to remove the excess 3’adaptor. Then, a 5’adapter was ligated and small RNAs were reverse transcribed. Pre-amplification was performed and then 1 μl of amplified product was used as a template for final amplification. The amplified libraries were separated on a 6% polyacrylamide gel and 130-160 bp DNA fragments were sliced to recover the library of small RNAs. Long RNA transcriptome libraries was performed following Smarter-seq2 method with some modifications.For every single oocyte or embryo, 0.125 μL 1/100,000 dilution of the ERCC RNA Spike-In Mix (Invitrogen, Cat# 4456740) was used. Following reverse transcription and PCR pre-amplification, cDNA libraries were purified by Agencourt Ampure XP beads (0.8:1 ratio) (Beckman Coulter, Cat#A63881) and 2 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase. Amplified libraries were purified by Agencourt Ampure XP beads (1:1 ratio).The small and long RNA libraries were sequenced on a HiSeq X Ten instrument (Illumina, USA) with 2 × 150 run cycles.For testicular long RNA seq,DNase I was used to digest double-stranded and single-stranded DNAin total RNA, then, magnetic beads were purified to recover the reaction products, RNase H or Ribo-Zero method(Illumina, USA) was used to remove the rRNA. Purified mRNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then,first-strand cDNA was generated in First Strand Reaction System by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to carry out end repair. The cDNA fragments with adapters were amplyfied by PCR, and the products were purified byAmpure XP Beads. Library was validating on the Agilent Technologies 2100 bioanalyzer for quality control.The double stranded PCR products above were heated denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGISEQ500 platform (BGI_x0002_Shenzhen, China).For testicular smRNA seq,library was prepared with 1 μg total RNA for each sample. Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to adenylated 3’ adapters annealed to unique molecular identifiers (UMI), followed by the ligation of 5’adapters. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 110~130 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA). The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The final ligation PCR products were sequenced using the BGISEQ-500 platform (BGI-Shenzhen, China).


title: Citrobacter_7days_PAR5359_1_S11

value: inflammatory bowel disease


title: Citrobacter_7days_PAR5359_3_S13

value: distal colon


title: AntpII1_2

city: Princeton

first: Mike

last: Levine

state: NJ

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

data_processing:
Library strategy: Micro-C
Micro-C data was analyzed using the 4D Nucleome Hi-C analysis pipeline [Reference]. Briefly, paired-end reads were mapped to the dm6 reference genome using BWA v0.7.17 [Li and Durbin, 2009], and alignments were filtered using pairtools v0.2.2 to retain only uniquely-mapping reads with alignment quality ≥3. Reads were assigned to 100bp genomic bins, and “inward”/”outward” reads assigned to adjacent bins (separated by less than 50bp) were removed. Matrix aggregation and normalization were performed using Cooler v0.8.3 [Abdennur and Mirny 2019], using the built-in ICE balancing method. Matrices were visualized using HiGlass [Kerpedjiev et al. 2018]. Visual inspection of contact matrices showed high concordance between biological duplicates, which were therefore pooled to generate final high-coverage contact matrices for each genotype.
Boundaries were identified with FAN-C v0.9.9 [Kruse et al. 2020 Gen. Biol], using the combined wild-type Micro-C datasets at 400bp resolution. Insulation scores were calculated with a window size of 10kb, and boundaries were called using the following parameters: -d 3 -s 0.7. We required a boundary score of ?1.25 for our final set (n=2,034 boundaries). Focal contacts (?loops?) were identified genome-wide using SIP v1.6.1 [Rowley et al. 2020 Gen. Res]. We combined the two wild-type (yw) Micro-C datasets, and called loops using the following parameters: -isDroso false -res 400 -factor 2 -t 2000 -fdr 0.1 -d 15 -mat 5000 -nbZero 6 -del true -cpu 1 -g 3 -min 2 -max 2. We used the Cooler ?Marginals? file to identify genomic regions with low Micro-C data coverage (marginals < 500), and filtered out any loop call with an anchor within 3.2 kb (8 bins) of a low-coverage region. We required a loop score of ?4.25 for our final set (n=331 loops, corresponding to 620 non-redundant anchors).
Genome_build: dm6
Supplementary_files_format_and_content: cool,validpairs

organism: Drosophila melanogaster

source_name: nc14 embryo

growth_protocol: Embryos were collected on yeasted apple juice plates at 25˚C. Following two 1-hour pre-lays, embryos were collected for 45 mins and subsequently incubated at 25˚C for 2 hours to enrich for nc14 embryos.

extract_protocol:
Chromatin was digested with a pre-determined amount of Micrococcal Nuclease (Worthington Biochem) to yield a 90% mononucleosome / 10% dinucleosome ratio given the appropriate number of embryos.
Micro-C libraries were constructed as previously described [Hsieh et al. 2020], with the following modifications.
Libraries were barcoded, pooled and subjected to paired-end sequencing on an Illumina Novaseq S1 100nt Flowcell (read length 50 bases per mate, 6-base index read).

treatment_protocol: Embryos were collected in nylon mesh sieves, dechorionated for 3 mins in 3% sodium hypochlorite, rinsed with deionized water, and transferred to glass scintillation vials containing 6 mL PBST (0.1% Triton-X in PBS), 7.5 mL N-heptane, and 1.5 mL fresh 16% formaldehyde. Crosslinking was carried out at room temperature for exactly 15 mins on an orbital shaker at 250rpm, followed by addition of 5.5 mL 2M Tris-HCl pH7.5 and shaking for 5 mins to quench the reaction. Embryos were washed twice with >15mL PBST and stored at 4˚C while an additional 2-3 collection rounds were carried out (45 mins each). Pooled embryos were subjected to a secondary crosslinking in 15 mL DSG+EGS (ThermoFisher, 3 mM each) at room temperature for 45 mins on a rotating mixer. Following quenching by addition of 5.5 mL 2M Tris-HCl pH7.5 and rotation for 5 mins, the embryos were washed twice with PBST and stored at 4˚C overnight. Samples were hand-sorted the following day under a dissection microscope to remove inappropriately staged embryos, snap-frozen in liquid nitrogen and stored at -80˚C.

tag: developmental stage

value: embryo


title: WT-10PEA smRNA rep1

city: Nanjing

first: Qin

address: No. 101 Longmian Avenue, Jiangning District, Nanjing

institute: Nanjing Medical University

value: wild type


title: ScrEE2

data_processing:
Micro-C data was analyzed using the 4D Nucleome Hi-C analysis pipeline [Reference]. Briefly, paired-end reads were mapped to the dm6 reference genome using BWA v0.7.17 [Li and Durbin, 2009], and alignments were filtered using pairtools v0.2.2 to retain only uniquely-mapping reads with alignment quality ≥3. Reads were assigned to 100bp genomic bins, and “inward”/”outward” reads assigned to adjacent bins (separated by less than 50bp) were removed. Matrix aggregation and normalization were performed using Cooler v0.8.3 [Abdennur and Mirny 2019], using the built-in ICE balancing method. Matrices were visualized using HiGlass [Kerpedjiev et al. 2018]. Visual inspection of contact matrices showed high concordance between biological duplicates, which were therefore pooled to generate final high-coverage contact matrices for each genotype.
Boundaries were identified with FAN-C v0.9.9 [Kruse et al. 2020 Gen. Biol], using the combined wild-type Micro-C datasets at 400bp resolution. Insulation scores were calculated with a window size of 10kb, and boundaries were called using the following parameters: -d 3 -s 0.7. We required a boundary score of ?1.25 for our final set (n=2,034 boundaries). Focal contacts (?loops?) were identified genome-wide using SIP v1.6.1 [Rowley et al. 2020 Gen. Res]. We combined the two wild-type (yw) Micro-C datasets, and called loops using the following parameters: -isDroso false -res 400 -factor 2 -t 2000 -fdr 0.1 -d 15 -mat 5000 -nbZero 6 -del true -cpu 1 -g 3 -min 2 -max 2. We used the Cooler ?Marginals? file to identify genomic regions with low Micro-C data coverage (marginals < 500), and filtered out any loop call with an anchor within 3.2 kb (8 bins) of a low-coverage region. We required a loop score of ?4.25 for our final set (n=331 loops, corresponding to 620 non-redundant anchors).
Genome_build: dm6
Supplementary_files_format_and_content: cool,validpairs


title: G9_Citrobacter_Pioglitazone_3_S85_L003

value: day 18

value: Pioglitazone

value: Yes


title: ScrEE1


title: S2502Nr9 [Rf_forage_1]

description: small RNA


title: WT-10PEA smRNA rep2

value: Syrian

value: smRNA


title: ATAC-Seq MM3016_72h


title: WT-MII smRNA rep2

value: MII stage oocyte


title: KO-MII smRNA rep1

value: Pld6 KO


title: ATAC-Seq MM3016_24h


title: WT-MII smRNA rep1


title: AntpII1_1


title: ATAC-Seq MM3016_Ctrl


title: G7_Citrobacter_Pioglitazone_1_S83_L003


title: Citrobacter_7days_Pioglitazone_3_S18

value: day 7


title: AntpDTE1_2


title: Citrobacter_7days_Pioglitazone_4_S19


title: Citrobacter_7days_Pioglitazone_2_S17


title: KO-GV smRNA rep2

value: GV stage oocyte


title: Scr_DTE_2


title: ATAC-Seq MM3008_72h


title: AntpDTE1_1


title: WT-GV smRNA rep1


title: ATAC-Seq MM3008_Ctrl


title: ATAC-Seq MM3008_24h


title: Dfd_3Ins_2


title: Citrobacter_7days_Pioglitazone_1_S16


title: Vegfr2 knockout

city: Tokyo

first: Yoshiaki

last: Kubota

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Anatomy

institute: Keio University School of Medicine

data_processing:
A DNBSEQ-G400 platform (MGI, Shenzhen, China) was used to sequence 28 and 91 base paired-end reads. Sequenced reads were aligned to the reference genome (mm10) using cell ranger v6.0.1 software (10×Genomics).
Genome_build: mm10
Supplementary_files_format_and_content: Filtered raw counts output by Cell Ranger count

source_name: PI- cells from dental pulp at P12

growth_protocol: Mice care was performed according to the standard method.

extract_protocol:
Dental pulps were collected, and incubated for 30 mins at 37°C in DMEM containing 1% collagenase D (from Clostridium histolyticum; Sigma-Aldrich, Saint Louis, MO; C5138-1G), 1 U/ml dispase (ThermoFisher; 17105-041), and 1 U/ml DNase (Invitrogen, Carlsbad, CA) before cells were dissociated by trituration. The cells were dissociated to a single-cell suspension by filtering thorough 40μm nylon mesh. Cells are stained Propidium Iodide (PI) (BioLegend, San Diego, CA, USA, 421301; 1:500). PI- cells were sorted with Cell Sorter SH800Z (SONY, Tokyo, Japan).
Libraries were constructed using a commercial microdroplet-based platform, Chromium Single Cell 3’ v3.1 (10×Genomics) according to the manufacturer’s instructions.

treatment_protocol: No special treatment has been conducted.

value: Vegfr2 knockout


title: ATAC-Seq MM3016_4h


title: G5_Citrobacter_GW7647_2_S81_L003


title: Scr_DTE_1


title: ATAC-Seq MM3008_4h


title: Dfd_3Ins_1


title: ATAC-Seq MM3001_Ctrl


title: control

value: control


title: KO-GV smRNA rep1


title: Citrobacter_7days_GW7647_5_S10


title: WT-GV smRNA rep2


title: ATAC-Seq MM3001_72h

value: PBMC


title: G6_Citrobacter_GW7647_3_S82_L003


title: SF2_del1


title: Citrobacter_7days_GW7647_4_S9


title: G4_Citrobacter_GW7647_1_S80_L003


title: SF2_del2


title: ATAC-Seq MM3001_24h


title: ATAC-Seq MM3001_4h


title: SF1_del2


title: SF1_del1


title: Citrobacter_7days_GW7647_1_S6


title: Citrobacter_7days_GW7647_2_S7


title: S9_2: iPS XXXXY,49 KS Whole exome sequencing

city: Jeddah

first: Antonio

last: Adamo

state: Not in US

address: 4700 KAUST, Thuwal

department: Biological and Environmental Science and Engineering Division, BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology, KAUST

description:
Whole exome sequencing
S9_2_BKDN192007987-1A_HTMGNDSXX_L3

data_processing:
Library strategy: Whole Exome Sequencing
Bulk RNA-Seq data validation, pairing and FastQC quality control was followed by trimming using BBDuk by setting a minimum read length of 35 bp and a minimum Phred-quality score of 25. After trimming quality control, high quality reads were mapped against the reference genome (GrCh38 release 91) using the STAR end-to-end alignment method and gene expression quantification performed with featureCounts. Data normalization was performed with the Trimmed Mean of M-values (TMM) method
The pre-processing of single cell RNA-Seq data that includes the identification of cell barcodes and the steps of UMI detection, extraction and processing was performed using UMI-tools 1.0.1. Read quality control (QC) analyses and filtering of high-quality reads, were executed using FastQC and BBDuk with default options of minimum size 35 bp and minimum quality score 25 to perform adapter and quality trimming. To align the filtered reads to a human genome reference (GrCh38 release 91) STAR 2.7.3a was used, while FeatureCounts 1.6.3 package was used to assign reads to genes.
Data from single cell RNA-sequencing were then analyzed using the R packages: SC3 for clustering methods, differential expression analysis and gene marker detection algorithm and Scater 1.16.0 was used for expression data pre-processing, quality control, normalization and visualization through the t-distributed stochastic neighbor embedding (t-SNE) analysis. The package scImpute 0.0.9 was used to correct dropout values.
Genome_build: GrCh38 release 91 was used fo bulk and scRNA-SEQ analysis
Supplementary_files_format_and_content: File including FPKM values for each Sample
Supplementary_files_format_and_content: Rdata file includes single cell experiment objects

source_name: iPS

growth_protocol: hiPSC lines were adapted to feeder-free conditions on matrigel-coated plates in E8 medium

extract_protocol:
For bulk RNA-Seq libraries the RNA has been extracted using the Qiagen RNeasy Mini Kit according to manufacturer’s instructions
Bulk RNA libraries were generated using the human mRNA TruSeq Stranded library preparation KIT from Illumina, and profiled using a HiSeq4000 system with 150 bp paired-end sequencing method

treatment_protocol: Before RNA extraction hiPSCs were adapted to Vitronectin (VTN-N) coated plates  in presence of E8 medium and passaged with Versene.

value: human induced pluripotent stem cell

tag: karyotype

value: XXXXY,49 KS

tag: name in the manuscript

value: KS7 #B


title: yw2

value: embryo

tag: genotype

value: WT


title: S9_1: iPS XXXY,48 KS Whole exome sequencing

description:
Whole exome sequencing
S9_1_BKDN192007986-1A_HTLWVDSXX_L3

value: XXXY,48 KS

value: KS7 #A


title: yw1


title: Cbx2 WT mouse HSPCs H3K4me3 replicate 2

city: Boston

first: Grant

last: Rowe

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
Bowtie2 alignment (human specimens)
FastQC and CUT&RUNTools (Bowtie2, Trimmomatic, Picard, Samtools)
E. coli spike-in normalization with Bowtie2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

source_name: HSPCs

growth_protocol: Mouse HSPCs were purified from fresh tissue and processed immediately.

extract_protocol:
Per Epicypher CUTANA kit instructions
Per Epicypher CUTANA kit and New England Biolabs next generation library instructions

treatment_protocol: No treatments

value: Lineage- CD117+ HSPCs

tag: cut&run antibody

value: Epicypher anti-H3K4me3 positive control antibody

value: CUT&RUN DNA


title: S8_2: iPS XXY,47 KS Whole exome sequencing

description:
Whole exome sequencing
S8_2_BKDN192007985-1A_HTLWVDSXX_L1

value: XXY,47 KS

value: KS6 #B


title: S8_1: iPS XY,46 Whole exome sequencing

description:
Whole exome sequencing
S8_1_BKDN192007984-1A_HTMGNDSXX_L3

value: KS6 #A


title: Cbx2 WT mouse cells IgG replicate 3

value: Epicypher control IgG


title: Citrobacter_7days_GW7647_3_S8

value: inflammatory bowel disease

value: distal colon

value: day 7

tag: treatment

value: Yes


title: S7_1: iPS XXY,47 KS Whole exome sequencing

description:
Whole exome sequencing
S7_1_BKDN192007982-1A_HTMGNDSXX_L3

value: human induced pluripotent stem cell

value: KS5 #A


title: G2_Citrobacter_DMSO_2_S78_L003

value: day 18

value: DMSO


title: Cbx2 WT mouse cells IgG replicate 2


title: Citrobacter_7days_DMSO_5_S5


title: G3_Citrobacter_DMSO_3_S79_L003


title: Cbx2 WT mouse cells H2AK119Ub replicate 3

value: Cell Signal rabbit anti-H2AK199Ub (8240S)


title: S5_2: iPS XXY,47 KS Whole exome sequencing

description:
Whole exome sequencing
S5_2_BKDN192007979-1A_HTLWVDSXX_L2

value: KS4 #D


title: Citrobacter_7days_DMSO_4_S4


title: Cbx2 WT mouse cells H2AK119Ub replicate 2

value: Lineage- CD117+ HSPCs


title: Citrobacter_7days_DMSO_3_S3


title: S5_1: iPS XXY,47 KS Whole exome sequencing

description:
Whole exome sequencing
S5_1_BKDN192007978-1A_HTMGNDSXX_L3

value: KS4 #C


title: PA_2h

city: Seeland

first: Anja

last: Hartmann

state: Saxony-Anhalt

address: Corrensstraße 3

department: PZB

country: Germany

institute: IPK Gatersleben

description: Gene expression after 2 h incubation in 1% glucose and 0.5 % protocatechuic acid

hyb_protocol: The microarrays were hybridized according to the Agilent Technologies “One-Color Microarray-Based Gene Expression Analysis (v6.5)” instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner G2505C using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 (Read Only) and Grid: 035454_D_F_20110711) to obtain background subtracted and spatially detrended Processed Signal intensities. The R package limma was used for microarray data analysis (Smyth, 2005). The background of raw expression data was corrected by “normexp” and normalized between arrays using “quantile”.

organism: Blastobotrys raffinosifermentans

source_name: treatment, protocatechuic acid, 2 h

label_protocol: The samples were labeled according to the Agilent Technologies “One-Color Microarray-Based Gene Expression Analysis (v6.5)” instructions.

growth_protocol: Blastobotrys raffinosifermentans LS3 was cultivated overnight in YMM-glucose-NaNO3.

extract_protocol: Cells were harvested and total RNA was isolated using RNeasy Mini Kit (Qiagen, Germany)

treatment_protocol: Cells were then pelleted (3,220 × g at 20°C), and shifted to YMM-NaNO3 containing a mixture of 1% glucose and 0.5% protocatechuic acid or 1% glucose only. Cells were   harvested after 15 min, 30 min, 2 h and 5 h of incubation in shaking flasks at 30 °C  and 180 rpm.

value: 1% glucose and 0.5% protocatechuic acid

tag: harvest time

value: 2 h


title: Glc_30min

description: Gene expression after 30 min incubation in 1% glucose

source_name: control, glucose, 30 min

tag: strain

value: 1% glucose

value: 30 min


title: Glc_5h

description: Gene expression after 5 h incubation in 1% glucose

source_name: control, glucose, 5 h

value: 5 h


title: Citrobacter_7days_DMSO_2_S2

tag: disease state

value: inflammatory bowel disease


title: Cbx2 KO mouse HSPCs IgG replicate 2

value: Epicypher control IgG

value: CUT&RUN DNA


title: Glc_2h

description: Gene expression after 2 h incubation in 1% glucose

source_name: control, glucose, 2 h


title: PA_15min

description: Gene expression after 15 min incubation in 1% glucose and 0.5 % protocatechuic acid

source_name: treatment, protocatechuic acid, 15 min

value: 15 min


title: Glc_15min

description: Gene expression after 15 min incubation in 1% glucose

source_name: control, glucose, 15 min


title: PA_5h

description: Gene expression after 5 h incubation in 1% glucose and 0.5 % protocatechuic acid

source_name: treatment, protocatechuic acid, 5 h


title: PA_30min

description: Gene expression after 30 min incubation in 1% glucose and 0.5 % protocatechuic acid

source_name: treatment, protocatechuic acid, 30 min


title: S4_2: iPS XXY,47 KS Whole exome sequencing

description:
Whole exome sequencing
S4_2_BKDN192007977-1A_HTLWVDSXX_L2

value: human induced pluripotent stem cell

value: XXY,47 KS

value: KS2 #B


title: S4_1: iPS XXY,47 KS Whole exome sequencing

description:
Whole exome sequencing
S4_1_BKDN192007976-1A_HTLWVDSXX_L3

value: KS2 #A


title: Cbx2 KO mouse HSPCs H3K4me3 replicate 2

value: Epicypher anti-H3K4me3 positive control antibody


title: Cbx2 KO mouse cells H2AK119Ub replicate 3

value: Cell Signal rabbit anti-H2AK199Ub (8240S)


title: G15_Uninfected_3_S91_L003

value: distal colon

tag: time

value: day 18

value: No

value: Yes


title: S3_3: iPS XXXXY,49 KS Whole exome sequencing

description:
Whole exome sequencing
S3_3_BKDN192007975-1A_HTLWVDSXX_L2

value: XXXXY,49 KS

value: KS1 #D


title: GA 5h

description: Gene expression after 5 h incubation in 1% glucose and 0.5 % gallic acid

source_name: treatment, gallic acid, 5 h

treatment_protocol: Cells were then pelleted (3,220 × g at 20°C), and shifted to YMM-NaNO3 containing a mixture of 1% glucose and  0.5% gallic acid or 1% glucose only. Cells were   harvested after 15 min, 30 min, 2 h and 5 h of incubation in shaking flasks at 30 °C  and 180 rpm.

value: 1% glucose and 0.5% gallic acid

value: 5 h


title: S6_1: iPS XXY,47 KS Whole exome sequencing

description:
Whole exome sequencing
S6_1_BKDN192007980-1A_HTLWVDSXX_L3

value: KS3 #A


title: Citrobacter_7days_DMSO_1_S1

value: inflammatory bowel disease

value: day 7

value: DMSO

tag: infection


title: GA 2h

description: Gene expression after 2 h incubation in 1% glucose and 0.5 % gallic acid

source_name: treatment, gallic acid, 2 h

value: 2 h


title: Cbx2 KO mouse cells H2AK119Ub replicate 2

value: Lineage- CD117+ HSPCs

value: CUT&RUN DNA


title: S3_2: iPS XXY,47 KS Whole exome sequencing

description:
Whole exome sequencing
S3_2_BKDN192007974-1A_HTLWVDSXX_L1

value: human induced pluripotent stem cell

value: XXY,47 KS

value: KS4 #F


title: GA 30min

description: Gene expression after 30 min incubation in 1% glucose and 0.5 % gallic acid

source_name: treatment, gallic acid, 30 min

value: 30 min


title: G13_Uninfected_1_S89_L003

source_name: Distal colon

tag: tissue

value: distal colon

value: day 18

value: No


title: S3_1: iPS XXY,47 KS Whole exome sequencing

description:
Whole exome sequencing
S3_1_BKDN192007973-1A_HTLWVDSXX_L1

value: KS4 #E


title: GA 15min

description: Gene expression after 15 min incubation in 1% glucose and 0.5 % gallic acid

source_name: treatment, gallic acid, 15 min

value: 1% glucose and 0.5% gallic acid

value: 15 min


title: S2_2: iPS XX,46 Whole exome sequencing

description:
Whole exome sequencing
S2_2_BKDN192007971-1A_HTLWVDSXX_L1

value: HM #B


title: Cbx2 WT mouse cells IgG

data_processing:
library strategy: CUT&RUN
Bowtie2 alignment (human specimens)
FastQC and CUT&RUNTools (Bowtie2, Trimmomatic, Picard, Samtools)
E. coli spike-in normalization with Bowtie2
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: bigwig files

growth_protocol: HUDEP1 were cultured in StemSpan SFEM with SCF, EPO, dexamethasone, and doxycycline prior to processing.  Mouse HSPCs were purified from fresh tissue and processed immediately.

value: Epicypher control IgG


title: Citrobacter_7days_Uninf_5_S24

value: inflammatory bowel disease

value: day 7


title: Citrobacter_7days_Uninf_4_S23


title: Cbx2 WT mouse cells H3K4me3

value: Epicypher anti-H3K4me3 positive control antibody


title: Cbx2 WT mouse cells H2AK119Ub

value: Lineage- CD117+ HSPCs

value: Cell Signal rabbit anti-H2AK199Ub (8240S)


title: Citrobacter_7days_Uninf_3_S22


title: S2_1: iPS XX,46 Whole exome sequencing

description:
Whole exome sequencing
S2_1_BKDN192007970-1A_HTLWVDSXX_L1

value: human induced pluripotent stem cell

value: HM #A


title: G14_Uninfected_2_S90_L003

value: Yes


title: SAS cells, shCCT2_3

city: guangzhou

first: Lu

last: Lin

address: 74 zhongshaner road

institute: sun yat-sen university

description:
gene expression_2.txt
The fastq files are no longer available.

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using STAR (v1.5.1)
The read counts were extracted using HTSeq-count （v0.11.3）
Matrix table with raw gene counts for every gene and every sample was generated.
Clean reads after quality control were compared to the reference genome using sequence alignment software, allowing quantification of gene/transcript expression in the sample. At the same time, the whole transcriptome sequencing was analyzed, including the randomness of transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.  ReadsRandom.txt.

source_name: SAS cell line

extract_protocol:
RNA was extracted using Trizol reagent. mRNA was enriched with oligo(dT)-attach magnetic beads and fragmented into small pieces, cDNA library was generated using random hexamer-primed reverse transcription followed by second-strand cDNA synthesis and sequenced on an MGI 2000 platform (BGI, Shenzhen, China).
RNA libraries were prepared for sequencing using standard BGI 2000 protocols
instrument model: MGI 2000

value: tongue

tag: cell line

value: SAS

value: Head and neck squamous cell carcinoma (HNSCC)

value: CCT2 knockdown


title: SAS cells, shCCT2_2

description: gene expression_1.txt


title: SAS cells, shCCT2_1

description: gene expression_1.txt


title: Cbx2 KO mouse HSPCs H3K4me3

tag: molecule subtype

value: CUT&RUN DNA


title: S1_2: iPS XY,46 Whole exome sequencing

description:
Whole exome sequencing
S1_2_BKDN192007969-1A_HTLWVDSXX_L1

tag: cell type

value: HB #B


title: Glc 30min

description: Gene expression after 30 min incubation in 1% glucose

value: 1% glucose

value: 30 min


title: Glc 2h

description: Gene expression after 2 h incubation in 1% glucose

value: 2 h


title: Citrobacter_7days_Uninf_2_S21

value: inflammatory bowel disease

value: distal colon

value: No


title: Citrobacter_7days_Uninf_1_S20

value: day 7


title: Cbx2 KO mouse HSPCs IgG

value: Lineage- CD117+ HSPCs

value: Epicypher control IgG


title: SAS cells, shCtrl_2

value: Control


title: Glc 5h

description: Gene expression after 5 h incubation in 1% glucose

value: 5 h


title: G8_Citrobacter_Pioglitazone_2_S84_L003

value: day 18

value: Pioglitazone

value: Yes


title: SAS cells, shCtrl_1

description: gene expression_1.txt

value: tongue

value: SAS

value: Head and neck squamous cell carcinoma (HNSCC)


title: KO-MII smRNA rep2

last: RuiXin

description: total cellular RNA mixed with exogenous spikein

source_name: Oocyte

tag: breed

value: Syrian

value: Pld6 KO

value: MII stage oocyte

value: smRNA


title: Cbx2 KO mouse cells H2AK119Ub

value: Cell Signal rabbit anti-H2AK199Ub (8240S)

value: CUT&RUN DNA