title: Low-50x

city: San Francisco

first: Alexander

last: Marson

state: CA

address: 1650 Owens St

institute: Gladstone-UCSF Institute of Genomic Immunology

data_processing:
A table of individual guide abundance in each sample was generated using the count command in MAGeCK version 0.5.8
Assembly: None
Supplementary files format and content: Count of guide RNAs, raw counts
Library strategy: CRISPR sequencing

source_name: CD4+CD25- T cells

growth_protocol: Cells were grown in RPMI (Sigma, Cat # R0883) with 10% FCS (Sigma, Cat # F0926), with 100U/mL Pen-Strep (Gibco, Cat # 15140-122), 2mM L-Glutamine (Sigma, Cat # G7513), 10mM HEPES (Sigma, Cat # H0887), 1X MEM Non-essential Amino Acids (Gibco, Cat # 11140-050), 1mM Sodium Pyruvate (Gibco, Cat # 11360-070), and 50 U/mL IL-2 (Amerisource Bergen, Cat #10101641) at a concentration of 1E6 cells/mL.

extract_protocol:
After sorting, cells were washed with PBS, counted, pelleted, and resuspending at up to 5E6 cells per 400 µl of lysis buffer (1% SDS, 50 mM Tris, pH 8, 10 mM EDTA). The remaining protocol reflects additives/procedures performed per each 400 µl of sample. 16µl of NaCl (5M) was added, and the sample was incubated on a heat block overnight at 66°C. The next morning, 8µl of RNAse A (10mg/ml, resuspended in ddH2O) (Zymo, Cat #E1008) was added, and the sample was vortexed briefly, and incubated at 37°C for 1 hour. Next, 8µl of Proteinase K (20mg/ml) (Zymo, Cat #D3001) was added, the sample was vortexed briefly, and incubated at 55°C for 1 hour. A phase lock tube (Quantabio, Cat #2302820) was prepared for each sample by spinning down the gel to the bottom of the tube at 20,000g for 1 minute and then 400µl of Phenol:Chloroform:Isoamyl Alcohol (25:24:1) was added to each tube. 400µl of the sample was then added to the phase lock tube and the tube was shaken vigorously. The sample was centrifuged at maximum speed at room temperature for 5 minutes. The aqueous phase was transferred to a low-binding eppendorf tube (Eppendorf, Cat #022431021) and then 40µl of Sodium Acetate (3M), 1µl GlycoBlue (Invitrogen, Cat # AM9515), and 600µl of room temperature isopropanol was added. The sample was then vortexed and stored at -80°C for 30 minutes or until the sample had frozen solid. Next the sample was centrifuged at maximum speed at 4°C for 30 minutes, the pellet was washed with fresh 70% room temperature Ethanol, and allowed to air dry for 15 minutes. Pellets were then resuspended in Zymo DNA elution buffer (Zymo, Cat No: D3004-4-10), and placed on the heat block at 65°C for 1 hour to completely dissolve the genomic DNA.
sgRNA was amplified and barcoded from the genomic DNA according to the protocol by Joung et al. (Joung et al. 2017). Up to 2.5 µg of genomic DNA were added to each 50 µL reaction, which included 25 µL of NEBNext Ultra II Q5 master mix (NEB, Cat #M0544L), 1.25 µL of the 10 µM forward primer and 1.25 µL of the 10 µM reverse primer, and H2O to 50 uL. The following PCR cycling conditions were used: 98°C for 3 minutes, followed by 23 cycles at 98°C for 10 seconds, 63°C for 10 seconds, and 72°C for 25 seconds, and ending with 2 minutes at 72°C. Samples were then cleaned and concentrated in Zymo Spin-V columns (Zymo, Cat #C1016-50) following Joung et al., and eluted in 150 uL of Zymo DNA elution buffer. Up to 2 µg of each library were loaded on a 2% agarose gel, and the band at ~250 base pairs was extracted using the Zymoclean Gel DNA recovery kit (Zymo, Cat #D4008). The concentration of each sample was then measured using the Qubit dsDNA high sensitivity assay kit (Thermo Fisher Scientific, Cat #Q32854). Samples were then sequenced on an Illumina HiSeq 4000 using 10-30% PhiX (Illumina, Cat #15017872), and a custom sequencing primer.

treatment_protocol: CD4+CD25- T cells were infected with lentivirus containing a 6000 guide RNA CRISPR library. Cas9 ribonucleoprotein complex was electroporated. 6 days after electroporation, FACS was performed to isolate CD25 high and low expressing cells.

value: CD4+CD25- T cells


title: mESC_diff_LBR_TMPO_KO_rep3

status: Public on Oct 01 2025

type: SRA

city: Zürich

first: Puneet

last: Sharma

state: Zürich

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH

library_source: transcriptomic

data_processing:
The paired-end reads from bulk RNA-seq datasets were processed to remove the Illumina universal adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) using Cutadapt (v4.4) with the parameters “-q 25 -m 25”. The resulting filtered reads were aligned to their respective reference genome using STAR aligner (v2.7.10b) with default parameters. Coordinate-sorted alignment files were indexed using SAMtools (v1.17). Exon mapped reads were counted using featureCounts from the subread package (v2.0.6). ATAC-seq datasets were processed to remove the Nextera adapter (CTGTCTCTTATACACATCT) using Cutadapt (v4.4) with the parameters “-q 25 -m 25”115. The resulting filtered reads were aligned to reference human genome using bowtie2 aligner (v2.5.1) with the parameter “--very-sensitive” (Bowtie2122). The alignment file was sorted by coordinate, indexed and filtered for mitochondrial reads using SAMtools (v1.17). The filtered alignment file was further processed to keep only uniquely mapped, non-duplicated reads using sambamba (v1.0.1). Reads were further processed using alignmentSieve from deepTools (v3.5.5) to account for transposon dimerization before insertion. Positive and negative strand alignments were shifted by +4 bp and −5 bp, respectively. Additionally, fragments of 100 bp, corresponding to nucleosome-free regions (NFRs), were retained with the parameters “--minMappingQuality 25 --maxFragmentLength 100 --ATACshift --BED”. Peaks were called on the resulting BEDPE files using MACS3 (v3.0.1) MACS3 with the parameters “--call-summits --bdg --nomodel --nolambda --gsize hs --keep-dup all --format BEDPE --qvalue 0.05”. The predicted peaks were filtered for ENCODE project blacklisted regions using BEDTools (v2.31.0) intersect.
Assembly: The reference genomes for human (GRCh38; annotation version 108) and mouse (GRCm39; annotation version 112) were obtained from ENSEMBL
Supplementary files format and content: HCT116_all_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr and nucleosomes.
Supplementary files format and content: HCT116_nfr_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr only.
Supplementary files format and content: HCT116_rna_seq_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.
Supplementary files format and content: HCT116_si11_all_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr and nucleosomes.
Supplementary files format and content: HCT116_si11_nfr_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr only.
Supplementary files format and content: HCT116_si11_rna_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.
Supplementary files format and content: mESC_all_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr and nucleosomes.
Supplementary files format and content: mESC_diff_rna_seq_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.
Supplementary files format and content: mESC_nfr_atac_raw_counts.tsv  is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr only.
Supplementary files format and content: mESC_rna_seq_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.

molecule: total RNA

organism: Mus musculus

source_name: Differentiated mESC

growth_protocol: HCT116 (CCL-247; ATCC), were grown in Dulbecco’s Modified Eagle’s medium (DMEM; Gibco), supplemented with 10% fetal calf serum (FCS; Eurobio Scientific) and 100 µg/mL penicillin/streptomycin (Corning) at 37°C, 5% CO2. ES-E14TG2a mESCs (CRL-1821; ATCC) were grown in Dulbecco’s Modified Eagle’s medium (DMEM; Sigma) supplemented with 13% fetal calf serum (FCS; Sigma), 0.32% 2-mercaptoethanol (Gibco), and 100 µg/mL penicillin/streptomycin (Corning). Media was freshly supplemented with 1000 units/mL recombinant mouse LIF protein (ESGRO®), 1 µM of the MEK/ERK inhibitor PD0325901 (Sigma), and 3 µM of the GSK inhibitor CHIR99021 (Sigma) (2i). Cells were plated at a density of 2.65 x 105 cells per cm2 on plates coated with 0.2% gelatin from porcine skin (Sigma). Cells were grown at 37°C, 8% CO2, and passaged every 48 hours using 0.05% Trypsin-EDTA for detachment (Gibco). Cells were frozen in fetal calf serum (FCS; Sigma) supplemented with 10% DMSO (Gibco).

extract_protocol:
To prepare samples for RNA-seq, 3 individual batches of cells were plated on the same day and further processed in parallel. Freshly harvested cells were lysed with 500 µL of QIAzol lysis reagent (QIAGEN #79306) and mixed by gentle pipetting. Subsequently, 100 µL of chloroform (Sigma) was added, samples were vortexed for 10 s and spun at 12’000 x g for 15 s at 4°C. The upper phase was transferred into a new tube, 600 μL of isopropanol (Sigma) added and samples incubated O/N at -20°C. After centrifugation at 16’000 x g for 10 min at 4°C, the RNA pellet was washed in 75% ethanol and resuspended in RNase-free water (Invitrogen). DNase digestion of RNA was performed using RNase-Free DNase Set (QIAGEN) following the manufacturer’s instructions. RNA was then precipitated by adding sodium acetate (Sigma) to a final concentration of 0.3 M, and adding 3 volumes of 100% ethanol O/N at -20°C. RNA was recovered by centrifugation at 16’000 x g for 10 min and washed two times with 70% ethanol. RNA was dissolved in RNase-free water (Invitrogen). To prepare ATAC-seq samples, 3 individual batches of cells were plate on the same day in 6-wells (for si-11) or 10 cm plates (for KO cells). Cell batches were then further processed in parallel, during all subsequent steps. For harvest, cells were washed twice with 1x PBS and detached using 0.5 mM EDTA in 1x PBS. Cells were counted and 80’000 cells were pelleted. Pellets were resuspended in 200 µL of freezing medium (10% DMSO in FCS) and slowly frozen at -80°C. ATAC-seq was performed at QuickBiology (Monrovia, California). Here, cells were washed and lysed to generate a crude preparation of nuclei. This crude extract was then treated with Tn5 Transposase. Tn5 transposase tagmentation simultaneously fragments the genome and tags the resulting DNA with Illumina sequencing adapters. DNA fragments were PCR-amplified and subsequently purified using the MinElute PCR Purification Kit (Qiagen, Maryland, USA).
The ATAC-seq library was prepared as described in Corces, M.R. et al.Nat Methods, 2017. After quality control using an Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA) and Life Technologies Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA), the libraries were sequenced (150 bp paired-end reads) on an Illumina HiSeq Sequencer (Illumina Inc., San Diego, CA). For RNA-seq, the quality of the isolated RNA was determined using a Fragment Analyzer (Agilent, Santa Clara, California, USA). Only samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further used for library preparation. The Illumina Ribo Zero Plus (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (25-1000 ng) were depleted of ribosomal RNA and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired, and adenylated before ligation of an anchor. Fragments containing the anchor on both ends were selectively enriched with PCR at the same time adding the index with unique dual indexes (UDI). The quality and quantity of the enriched libraries were validated using the Fragment Analyzer (Agilent, Santa Clara, California, USA). The libraries were normalized to 10 nM in Tris-HCl 10 mM, pH8.5 with 0.1% Tween20.

tag: cell line

value: Differentiated mESC

tag: cell type

tag: genotype


title: mESC_diff_LBR_TMPO_LMNA_KO_rep1


title: Low-200x

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens


title: NK65-E_Day 13-1

city: Chengdu

first: chen

last: li

address: Renmin South Road

country: China

institute: Sichuan Univercity

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.32) (default parameters)
Trimmed sequence reads were mapped to Mus musculus genome (mm10) using STAR (v2.7.1a) with default parameters
Read count extraction were performed using GenomicAlignments (v1.24.0)
Read count extraction were normalization using DESeq2 (v1.24.0)
Assembly: mm10
Supplementary files format and content: Tab-delimited text file contains raw counts, with genes as rows and samples as columns

source_name: Lung

extract_protocol:
After samples thawed at 4°C, total RNA from purified cells was extracted using TRIzol (MiRNeasy Micro Kit, QIAGEN, #1071023) according to the manufacturer’s recommendation. All samples had high-quality RNA (Agilent 2100 Bioanalyzer RNA Integrity Number (RIN) >7). The RNA sequencing library was prepared using the Illumina TruSeq PE Cluster Kit V3-cBot-HS (Illumina) following the provided protocol
Sequencing was performed on the Illumina HiSeq platform (Illumina, San Diego, USA), generating standard 125 bp/150 bp paired-end reads.

tag: tissue

value: Lung

value: Total lung cells

value: Mixed lung cell types

value: WT

tag: treatment

value: Pb NK69-E infection


title: NK65-E_Day 11-4

value: Pb NK68-E infection


title: Low-100x


title: Low-1000x_seq2


title: Low-1000x_seq1


title: mESC_diff_LBR_TMPO_KO_rep2


title: mESC_diff_LBR_TMPO_KO_rep1


title: NK65-E_Day 11-2

value: Pb NK66-E infection


title: NK65-E_Day 11-3

value: Pb NK67-E infection


title: High-50x


title: Clone D-1

city: Nedlands

first: Kevin

middle: Guangxing

last: Chen

address: Hospital Avenue

country: Australia

institute: The Kids Research Institute Australia

description:
Library name: Run72_57_NS0104_MED12_clone_D_iPSC_ND1_conf gDNA
Molecule: PCR amplicon

library_source: other

data_processing:
Amplicon sequencing: reads were aligned to either WT or VUS amplicon using CRISPResso2
Assembly: WT and VUS amplicon
Supplementary files format and content: Run72_S57_Alleles_frequency_table_MED12_Clone_D_gDNA.txt shows all reads and alignments to the reference and genetic variant amplicons
Supplementary files format and content: Run72_S58_Alleles_frequency_table MED12_Clone_I_gDNA.txt shows all reads and alignments to the reference and genetic variant amplicons
Supplementary files format and content: Run73_S22_Alleles_frequency_table MED12_Clone_D_cDNA.txt shows all reads and alignments to the reference and genetic variant amplicons
Supplementary files format and content: Run73_S23_Alleles_frequency_table MED12_Clone_I_cDNA.txt shows all reads and alignments to the reference and genetic variant amplicons

molecule: other

source_name: Patient-derived, Day 0

growth_protocol: Patient-derived iPSCs were grown in Matrigel-coated plates in TeSR-E8 media. The STEMdiff SMADi Neural Induction Kit was used to stimulate differentiation of iPSCs into NPCs

extract_protocol:
cDNA for amplicon sequencing was prepared using SuperScript IV reverse transcriptase. Primers designed to bind across genetic variant region in gDNA and cDNA were used to prepare amplicons for sequencing.
PCR amplicon products corresponding to the SNV sites in WT and VUS MED12 were prepared from extracted gDNA with forward and reverse amplicon primers and Phusion High-Fidelity PCR Master Mix with HF Buffer (Thermo Scientific). Purified samples were barcoded with TruSeq primers (IDT) and MED12 sequences determined with paired-end, 250bp DNA amplicon sequencing with a MiniSeq Mid-Output Kit, 300 cycles.

value: induced pluripotent stem cell

tag: clone

value: D


title: 23_FH-Lp(a)_Low_50 mg/dL]

type: RNA

city: Barcelona

first: Lina

last: Badimon

state: BARCELONA

address: Carrer de Sant Antoni Maria Claret, 167

department: ICCC-Cardiovascular Program

country: Spain

institute: Research Institut- HSCSP

description:
Circualting miRNA data in absence of atherogenic Lp(a) concentration
Alternative to GSE178126

hyb_protocol: Hybridization was performed on Affymetrix miRNA 4.0 arrays and cartridges were incubated at 48°C with 60 rpm rotation for 48 h using Affymetrix Hybridization Oven 600. After, each array was washed and stained using the FS450_002 fluidics script in Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by using the GeneChip scanner 3000 7G System

data_processing: The data were explored using the Transcriptome Analysis Console software (TAC 4.0) for data summarization and normalization by RMA+DABG procedure (implemented in TAC 4.0 software).

label: Biotin

source_name: Familial hypercholesterolemia patients_FH-Lp(a)_Low_50 mg/dL]

label_protocol: We used Affymetrix FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, Rev3) to label 8 ul of total RNA isolated with miRNeasy Serum/Plasma Advanced Kit (Qiagen Inc) from each sample, according to manufacturers instructions. RNA quantitation was not considered due to low levels of total RNA isolated from plasma.

growth_protocol: Familial hypercholesterolemia patients plasma (200uL) was used for isolation of circulating miRNAs

extract_protocol: To isolate plasma miRNAs, we used plasma from familial hypercholesterolemia patients and miRNeasy Serum/Plasma Advanced Kit (Qiagen Inc), according to manufacturer’s instructions.

treatment_protocol: No treatment

value: Plasma

value: Patients carrying the heterozygous mutation in the LDLR gene

tag: lp(a) concentration

value: FH-Lp(a)_Low_50 mg/dL]

tag: Sex

value: Female

tag: age


title: PoxKu70_3

city: Nanning

first: Hao

last: Guo

state: Guangxi

address: No. 100 East University Road, Nanning

department: College of Life Science and Technology

institute: Guangxi University

data_processing:
The original file sequenced by the MGI high-throughput sequencer is an image file. After base calling and Bcl2Fastq conversion, the original sequenced reads in FASTQ (fq for short) format can be obtained, which is called raw data or raw reads.
The original sequencing data will contain linker information, low-quality bases, and undetected bases (represented by N). These information will cause great interference to subsequent information analysis. These interference information will be removed by fine filtering methods. The final data is valid data, we call it Clean data or Clean read.
Use SOAPnuke software (v2.1.0) to filter Raw reads to get Clean reads. The main parameters are: –lowQual=20, –nRate=0.005, –qualRate=0.5, other parameters are default. The steps of data processing are as follows: 1) Filter out the paired reads containing the linker sequence.2) Remove paired reads with a ratio of N (N means that the base information cannot be determined) greater than 0.5%.3) Remove low-quality paired reads (reads with Qphred<=20 bases accounting for more than 50% of the entire read length).
Image recognition, decontamination, and adapter removal of sequencing results. Statistical results include the number of sequencing reads, data yield, Q20 content, Q30 content, GC content, etc
Assembly: HISAT2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Penicillium oxalicum

source_name: Mycelium

growth_protocol: Penicillium oxalicum strains were cultured on PDA at 28°C for 4 days, and the spores were washed with 0.2% Tween-80 to obtain fresh spore fluid.

extract_protocol:
RNA was extracted with Trizol,  the purity of RNA (OD260/280) was detected by Nanodrop2000. The integrity of RNA were accurately detected by Agilent 2100,the detection indicators include: RIN value, 28S/18S, whether the map baseline is raised, 5S peak, and electrophoresis to detect whether the RNA sample is diffuse or has a genome DNA contamination.
After the sample is qualified, the library is constructed. The main process is as follows: 1) mRNA enrichment for total RNA by mRNA enrichment method: Enrich mRNA with polyA tail using magnetic beads with Oligo dT. 2) Fragment the RNA obtained by interrupting the buffer, perform reverse transcription with random N6 primers, and synthesize the double-stranded cDNA to form double-stranded DNA. 3) Fill in the end of the synthesized double-stranded DNA and phosphorylate the 5' end, form a sticky end with a protruding "A" at the 3' end, and then connect a bubbling linker with a protruding "T" at the 3' end. 4) The ligation product is amplified by PCR with specific primers. 5) The PCR product is thermally denatured into single-stranded DNA, and then a single-stranded circular DNA library is obtained by circularizing the single-stranded DNA with a bridge primer.

treatment_protocol: Fresh spore fluid was inoculated into the glucose medium for 24 hours and then transferred to the enzyme-producing medium containing raw starch as the only carbon source for 24 hours.

value: Mycelium

value: Culture in enzyme production medium with starch after transfer 24h


title: NK65-E_Day 11-1

value: Pb NK65-E infection


title: High-200x

value: CD4+CD25- T cells


title: 24_FH-Lp(a)_Low_50 mg/dL]

value: Male


title: High-100x


title: PoxKu70_2


title: mGcm1-3xHA_ChIP_input

city: Setagaya

first: Kazuhiko

last: Nakabayashi

country: Japan

institute: NCCHD

data_processing:
Single-read sequencing (101 bp x1) was performed on the HiSeq2500 system (illumina).
Basecalls were performed using the Real-Time Analysis software.
Sequencing reads (fastq.gz) were subjected to TrimGalore (version 0.6.6) to remove low-quality reads and to trim adapter sequences, and aligned to mm10 reference genome using hisat2 version 2.2.1. The resultant bam files were processed using samtools (version 1.6) to sort mapped reads, to mark PCR duplicate reads, and to generate bam files that do not contain PCR duplicate reads. Bigwig files were generated from the processed bam files using IGVTools (version 2.3.93). ChIP-seq peaks were detected for each sample using macs2 (version 2.1.2).
Assembly: mm10
Supplementary files format and content: wig files to visualize ChIP-seq peaks using a genomics data viewer such as IGV
Supplementary files format and content: ".narrowPeak" files contain information for detected peaks detected by macs2.

growth_protocol: Neuro2a cells were cultured in 10% FBS/DMEM media.

extract_protocol:
Trypsinised Neuro2a cells (1×10^6)  transfected with pCAG-Gcm1-3xHA expression plasmid or pCAG-3xHA control plasmid were collected and fixed with 1% formaldehyde at room temperature for 5  min. Crosslinking reaction was quenched with 200 mM glycine (ChIP Reagent, Nippon Gene Co., Ltd.) for 10 min. The cells were resuspended in SDS lysis buffer (ChIP Reagent, Nippon Gene Co., Ltd.), and the lysate was sonicated to fragment chromatin using a Covaris S220 (Covaris, Woburn, MA, USA). The sonicated lysate was subjected to immunoprecipitation with a mouse monoclonal antibody against HA (HA124) (Nacalai Tesque: 06340-54).
The immunoprecipitated and reverse-crosslinked DNA was purified using AMPure XP beads (Beckman Coulter, Inc., Pasadena, CA, USA) according to the manufacturer’s instructions. ChIP or input DNA (0.1 ~ 1 ng) was subjected to end repair, dA-tailing, and adaptor-ligation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645), and amplified by 6-13 cycles of PCR.

tag: chip antibody


title: PoxKu70_1


title: POX_a00954_3

value: POX_a00954 mutant


title: High-1000x_seq2


title: 3xHA_ChIP_HA_2

value: anti-HA antibody (Nacalai Tesque:06340-54)


title: 20_FH-Lp(a)_High_50 mg/dL

description:
Circualting miRNA data in presence of atherogenic Lp(a) concentration
Alternative to GSE178126

source_name: Familial hypercholesterolemia patients_FH-Lp(a)_High_50 mg/dL

value: FH-Lp(a)_High_50 mg/dL


title: POX_a00954_1


title: 22_2_FH-Lp(a)_High_50 mg/dL


title: 21_FH-Lp(a)_Low_50 mg/dL]


title: High-1000x_seq1


title: 3xHA_ChIP_HA_1


title: 17_FH-Lp(a)_Low_50 mg/dL]


title: NaAsO21

city: PRINCETON

first: Danyang

last: Wang

state: NJ

address: 307 Frick Chemistry Laboratory, Washington Road

institute: Princeton University

data_processing:
library strategy: icSHAPE/SHAPE-MaP
remove duplicete reads as icshape pipeline
trimmed reads adaptor as icshape pipeline
mapping reads to human hg38 reference genome with botie2 as default parameters
calculate rpkm as icshape pipeline
calulate reverse transcript stop sites as icshape pipeline
Assembly: calculate icSHAPE score as icshape pipeline
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files for icshape file

source_name: Kidney

growth_protocol: Human HEK293T cells were cultured in DMEM supplemented with 10% FBS at 37°C with 5% CO2 in 10-cm plates. Cells were cultured to 70~80% confluency, treated with 1 mM 2’-aminodeoxycytidine for 16 hrs

extract_protocol:
The  RNA or modified RNA was extracted by TRIazol
100 µg of total RNA from HEK293T cells was used for polyA enrichment  using the mouse/human ribominus kit (Invitrogen). IcSHAPE sequencing libraries were then constructed from these RNA samples as icSHAPE protocol. Libraries were sequenced on the Illumina NovaSeq to ~200 million reads per replicate.

treatment_protocol: For in cellular treatment, cells was incubated with isoS-N3 at 37°C for 15min. For in vitro treatment, RNA was extracted by TRIzol and treated with isoS-N3 for 15 minutes at 37°C.

value: Kidney

value: human embryonic kidney cells

value: Wide Type

value: 2’-aminodeoxycytidine+ isoSN3


title: 16_FH-Lp(a)_Low_50 mg/dL]


title: 15_FH-Lp(a)_High_50 mg/dL


title: mGcm1-3xHA_ChIP_HA_3


title: 3xHA_ChIP_input


title: 18_FH-Lp(a)_Low_50 mg/dL]


title: 19_FH-Lp(a)_Low_50 mg/dL]


title: 14_FH-Lp(a)_High_50 mg/dL


title: 3xHA_ChIP_HA_3


title: mGcm1-3xHA_ChIP_HA_1


title: Schiz_DLPFC_26

first: Sergi

last: Mas

address: Casanova 143, Unidad Farmacologia, Facultad de Medicina, Barcelona

department: Pharmacology Unit

institute: University of Barcelona

description: Gene expression data

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Microarray data preprocessing was performed using the Oligo package in R

label: biotin

source_name: DLPFC from schizophrenia patient

label_protocol: labeling and hybridization to the Clariom S Human Array (Affymetrix, Santa Clara, CA, USA), following the manufacturer’s protocols

extract_protocol: Total RNA was extracted from all human brain samples using a commercial RiboPure™ kit

tag: condition

value: Schizophrenia

value: DLPFC

value: M

value: no Clozapine


title: POX_a00954_2


title: NaAsO22


title: 42C2


title: 37C2


title: Schiz_DLPFC_25

description: Gene expression data

value: Clozapine


title: 12_FH-Lp(a)_High_50 mg/dL

value: Plasma

value: Patients carrying the heterozygous mutation in the LDLR gene


title: 11_FH-Lp(a)_Low_50 mg/dL]

value: FH-Lp(a)_Low_50 mg/dL]


title: 13_FH-Lp(a)_Low_50 mg/dL]

value: Female


title: chaetoc3

city: nanjing

first: kong

last: ming

address: 南京市江宁区龙眠大道639号

department: college of pharmacy

institute: China Pharmaceutical University

data_processing:
CLC Genomics Workbenchv11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic bendchwork (parameter-QQuality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10using CLC genomic benchwork (parame ters-mismath cost: 2 insertion cost: 3 deletion cos st 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested usina Rneasy mini plus kit(Qiagen)13 uaof total RNA was used for the construction of seauencina libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: RFB

value: Fibroblast

value: TGF-β+chaetocin


title: Schiz_DLPFC_23

description: Gene expression data


title: 10_FH-Lp(a)_Low_50 mg/dL]

value: Male


title: isoSN3 ctrl3

value: Kidney


title: chaetoc1

address: 南京市江宁区龙眠大道639号


title: isoSN3 ctrl4

value: human embryonic kidney cells


title: Schiz_DLPFC_22

description: Gene expression data


title: V4

address: 南京市江宁区龙眠大道639号

value: TGF-β


title: 37C1

value: Wide Type

value: 2’-aminodeoxycytidine+ isoSN3


title: 6hour chase2


title: chaetoc2

address: 南京市江宁区龙眠大道639号


title: 42C1


title: V3

address: 南京市江宁区龙眠大道639号


title: 6hour chase1


title: chaetoc4

address: 南京市江宁区龙眠大道639号


title: Schiz_DLPFC_21

description: Gene expression data

value: Schizophrenia

value: DLPFC


title: Schiz_DLPFC_24

description: Gene expression data

value: M

value: no Clozapine


title: V2

address: 南京市江宁区龙眠大道639号


title: 1hour2


title: Schiz_DLPFC_20

description: Gene expression data


title: mGcm1-3xHA_ChIP_HA_2

value: anti-HA antibody (Nacalai Tesque:06340-54)


title: V1

address: 南京市江宁区龙眠大道639号


title: 7_FH-Lp(a)_High_50 mg/dL

value: Plasma

value: Patients carrying the heterozygous mutation in the LDLR gene

value: FH-Lp(a)_High_50 mg/dL


title: CRE4

address: 南京市江宁区龙眠大道639号

value: RFB

value: TGF-β ad-CRE


title: 9_FH-Lp(a)_Low_50 mg/dL]

value: FH-Lp(a)_Low_50 mg/dL]


title: 1hour1


title: 6_FH-Lp(a)_High_50 mg/dL

value: Male


title: 8_FH-Lp(a)_High_50 mg/dL

value: Female


title: 5_FH-Lp(a)_Low_50 mg/dL]


title: isoSN3 ctrl1

value: Kidney

value: human embryonic kidney cells


title: CRE3

address: 南京市江宁区龙眠大道639号

value: Fibroblast


title: Schiz_DLPFC_18

description: Gene expression data


title: RNA-seq_ko2_cl13

city: Beijing

first: Ruifeng

last: Li

address: haidian

institute: Tsinghua University

description: Library name: RNA-seq_ko2_cl13

data_processing:
1) Raw data processing. Raw sequencing reads were first adapter-trimmed by Trim Galore v0.4.4 with the “--paired” option, and aligned to mm10 reference genome with HISAT2 (version 2.2.1) with “-X 600 --rg-id --rg --known-splicesite-infile --novel-splicesite-outfile -p 25 --reorder” options. StringTie (v2.1.4) was used for transcript quantification with GENCODE vM12 annotation and “-e -B -p 10 -G -o” options. “prepDE.py” script was used to extract the read count information directly from the gtf files generated by StringTie with “-i -g -t” options. The reads count per gene was regarded as the gene expression. 2) Differential Genes Analysis. The gene expression matrix was normalized and analyzed by DESeq2 as the software recommended.
Assembly: mm10
Supplementary files format and content: CSV  file includes normalized counts for each Sample

molecule: polyA RNA

source_name: spleens and lymph nodes

extract_protocol:
Total RNA from CD8+ T cells was extracted by TRIzol (Invitrogen) according to manufacturer’s instruction.
total RNA was sent to BGI Genomics for cDNA library preparation and sequencing. Every sample has two replicates.

value: spleens and lymph nodes

value: cd8+ T cell

value: Irf8 knockout


title: Schiz_DLPFC_17

description: Gene expression data

value: Schizophrenia

value: DLPFC

value: M

value: Clozapine


title: aminoC ctrl2

value: Wide Type


title: CRE2

address: 南京市江宁区龙眠大道639号


title: aminoC ctrl1


title: RNA-seq_ko1_cl13

description: Library name: RNA-seq_ko1_cl13


title: CRE1

address: 南京市江宁区龙眠大道639号


title: RNA-seq_wt2_cl13

description: Library name: RNA-seq_wt2_cl13

value: WT


title: Col-0, D45, FT, SD, EM-seq

city: Berkeley

first: Dawei

last: Dai

address: 2151 Berkeley Way

institute: University of California, Berkeley

description:
Library name: Col-0_D45_FT_SD
150x 150

data_processing:
Reads were preprocessed with TrimGalore 0.6.6 (Babraham Bioinformatics) to remove adaptors
Bismark 0.22.3 (2) was used to map filtered reads to the A. thaliana TAIR10 genome, allowing for 0 mismatch per read in the seed region and removing PCR duplicates.
Methylation values for each cytosine were calculated as #C/(#C+#T) using the Bismark methylation extractor function.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited bed files includes methylation level at single base resolution in CHH, CHG, and CG context for each sample.
Library strategy: EM-seq

organism: Arabidopsis thaliana

source_name: First true leaves

extract_protocol:
DNA was isolated using the CTAB method.
EM-seq libraries were constructed following the NEBNext® Enzymatic Methyl-seq Kit protocol with 50 ng initial DNA (25 ng for all embryo samples). Library quality was verified with a KAPA Library Quant Kit and fragment analyzer. Libraries were pooled and sequenced using an Illumina NextSeq 2000 (150 bp, paired-end reads) or an NovaSeq X (150 bp, paired-end reads).

value: First true leaves

tag: seed stock

tag: background

tag: developmental stage

value: grown under short day conditions (8 h light/ 16 h dark)


title: 2_FH-Lp(a)_Low_50 mg/dL]

value: Plasma

value: Patients carrying the heterozygous mutation in the LDLR gene

value: FH-Lp(a)_Low_50 mg/dL]


title: 4_FH-Lp(a)_High_50 mg/dL

value: FH-Lp(a)_High_50 mg/dL

value: Female


title: Schiz_DLPFC_16

description: Gene expression data

value: no Clozapine


title: isoSN3 ctrl2

value: Kidney

value: human embryonic kidney cells


title: Schiz_DLPFC_14

description: Gene expression data


title: Ctcf_KO_rep1

description: Library name: Ctcf_KO_rep1

data_processing:
We performed read mapping and filtering of the Hi-C data following previous methods. All Hi-C sequencing reads were mapped to the mouse reference genome (mm10) using HiC-Pro (v2.11.4). We used the iterative correction and eigenvector decomposition (ICE) method to normalize raw interaction matrices.
Assembly: mm10
Supplementary files format and content: .hic files

source_name: E.G7 tumor

extract_protocol:
The Hi-C experiment was performed following the in situ Hi-C protocol
a total of 100000 cells were isolated and crosslinked with 1% formaldehyde for 10 min at room temperature, and next, 2.5 M glycine solution was added at a final concentration of 0.2 M. Then, the cells were collected, flash-frozen in liquid nitrogen and stored at -80°C. The fixed cells were then lysed on ice-cold Hi-C lysis buffer for 30 minutes on ice, followed by Mbo I (NEB, R0147) digestion overnight. The next day, treat sample at 62 ° C for 10 min to inactivate Mbo I, and then biotin-14-dATP (Life Technologies, 19524-016) was added to label the digested ends. Then, add ligation master mix (NEB, B0202 & M0202) and connect overnight. On the third day, use Covaris LE220 (Covaris) to break the end-ligated DNA fragments to a suitable length, followed by size selection with AMPure XP beads (Beckman Coulter, A63881). Dynabeads MyOne Streptavidin T1 beads (Life Technologies, 65602) pull down the biotin-labeled fragments, and these fragments are the fragments that truly represent chromatin interactions.

value: E.G7 tumor

value: cd8+ T cell

value: Ctcf knockout


title: Schiz_DLPFC_15

description: Gene expression data

value: Schizophrenia

value: DLPFC

value: M


title: Schiz_DLPFC_13

description: Gene expression data

value: Clozapine


title: Schiz_DLPFC_19

description: Gene expression data


title: RNA-seq_wt1_cl13

description: Library name: RNA-seq_wt1_cl13

value: spleens and lymph nodes

value: WT


title: Col-0, D30, FT, SD, EM-seq

description:
Library name: Col-0_D30_FT_SD
150x 150

value: First true leaves

value: grown under short day conditions (8 h light/ 16 h dark)


title: Ctcf_KO_rep2

description: Library name: Ctcf_KO_rep2


title: GFP3

address: 南京市江宁区龙眠大道639号

value: RFB

value: Fibroblast

value: TGF-β ad-GFP


title: 1_FH-Lp(a)_Low_50 mg/dL]

value: Plasma

value: Patients carrying the heterozygous mutation in the LDLR gene

value: FH-Lp(a)_Low_50 mg/dL]

value: Female


title: Col-0, D23, FT, SD, EM-seq

description:
Library name: Col-0_D23_FT_SD
150x 150


title: 3_FH-Lp(a)_Low_50 mg/dL]


title: GFP2

address: 南京市江宁区龙眠大道639号

value: Kidney


title: WT_rep2

description: Library name: Empty_rep2

value: E.G7 tumor

value: cd8+ T cell


title: Schiz_DLPFC_11

description: Gene expression data

value: Schizophrenia

value: DLPFC

value: F


title: Schiz_DLPFC_10

description: Gene expression data

value: M

value: no Clozapine


title: Col-0, D13, FT, SD, EM-seq

description:
Library name: Col-0_D13_FT_SD
150x 150

value: First true leaves


title: GFP1

address: 南京市江宁区龙眠大道639号


title: Schiz_DLPFC_8

description: Gene expression data


title: Schiz_DLPFC_12

description: Gene expression data


title: Col-0, D18, FT, SD, EM-seq

description:
Library name: Col-0_D18_FT_SD
150x 150

value: grown under short day conditions (8 h light/ 16 h dark)


title: Irf8_KO_rep2

extract_protocol:
The Hi-C experiment was performed following the in situ Hi-C protocol
a total of 1 x 106 cells were isolated and crosslinked with 1% formaldehyde for 10 min at room temperature, and next, 2.5 M glycine solution was added at a final concentration of 0.2 M. Then, the cells were collected, flash-frozen in liquid nitrogen and stored at -80°C. The fixed cells were then lysed on ice-cold Hi-C lysis buffer for 30 minutes on ice, followed by Mbo I (NEB, R0147) digestion overnight. The next day, treat sample at 62 ° C for 10 min to inactivate Mbo I, and then biotin-14-dATP (Life Technologies, 19524-016) was added to label the digested ends. Then, add ligation master mix (NEB, B0202 & M0202) and connect overnight. On the third day, use Covaris LE220 (Covaris) to break the end-ligated DNA fragments to a suitable length, followed by size selection with AMPure XP beads (Beckman Coulter, A63881). Dynabeads MyOne Streptavidin T1 beads (Life Technologies, 65602) pull down the biotin-labeled fragments, and these fragments are the fragments that truly represent chromatin interactions.

value: IRF8 knockout


title: Schiz_DLPFC_7

description: Gene expression data

value: Clozapine


title: Schiz_DLPFC_9

description: Gene expression data


title: GFP4

address: 南京市江宁区龙眠大道639号

value: RFB

value: Fibroblast

value: TGF-β ad-GFP


title: CXCL10-5ul-1

address: 南京市江宁区龙眠大道639号

data_processing:
CLC Genomics Workbenchv11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using C
Trimmed sequence reads were mapped to GrCM38/mm10using CLC genomic benchwork (parame ters-mismath cost: 2 insertion cost: 3 deletion cos st 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample


title: CXCL10-5ul-2

address: 南京市江宁区龙眠大道639号


title: Irf8_KO_rep1


title: Col-0, D23, FT, LD, EM-seq

description:
Library name: Col-0_D23_FT_LD
150x 150

value: grown under long day conditions (16h light/ 8 h dark)


title: Col-0, D45, FT, LD, EM-seq

description:
Library name: Col-0_D45_FT_LD
150x 150


title: WT_rep1

description: Library name: Empty_rep1

value: WT


title: CXCL10-5ul-3

address: 南京市江宁区龙眠大道639号

value: Kidney


title: NC3

address: 南京市江宁区龙眠大道639号

value: TGF-β


title: Col-0, D13, FT, LD, EM-seq

description:
Library name: Col-0_D13_FT_LD
150x 150


title: NC1

address: 南京市江宁区龙眠大道639号


title: NC2

address: 南京市江宁区龙眠大道639号


title: Col-0, D60, FT, LD, EM-seq

description:
Library name: Col-0_D60_FT_LD
150x 150


title: ter_cl13_rep2

value: spleens and lymph nodes

value: cd8+ T cell


title: WT_rep1

value: E.G7 tumor


title: Schiz_DLPFC_6

description: Gene expression data

value: Schizophrenia

value: DLPFC


title: ter_cl13_rep1


title: R3_9

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

institute: IRB Barcelona

description: sequencing of PCR amplicons encompasing the sgRNA region

data_processing:
Reads were preprocessed by removing adapters using cutadapt [1] with parameters "-e 0.2 -a  GTTTTAGAGCTAGAAATAGCAAGTTAAAATA -m 18". Processed reads were aligned to the sgRNA probe sequences using bowtie (v.0.12.9) [2] with parameters "-n 1 -l 19". The number of reads aligning to each probe and sample were computed in R [3].  References  [1] Martin, Marcel. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, [S.l.], v. 17, n. 1, p. pp. 10-12, may 2011. ISSN 2226-6089 [2] Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. [3] R Development Core Team (2008). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org
Assembly: mm10/hg19
Supplementary files format and content: Microsoft Excel XLSX file with raw counts for all samples and sgRNAs.
Supplementary files format and content: FASTA file contains the siRNA guide sequences for each gene.
Library strategy: amplicon-seq

source_name: mouse embryonic stem cells

growth_protocol: mES cells were grown on a feeder layer of inactivated mouse embryonic fibroblasts (MEFs) with ES medium (EM): Dulbecco's modified Eagle's medium (DMEM, high glucose, Life Technologies) supplemented with 15% foetal bovine serum (FBS) (Gibco), penicillin/streptomycin (100 U/mL), LIF (1000 U/ml), 0.1 mM non-essential amino acids, 1% glutamax, and 55 mM β-mercaptoethanol.

extract_protocol:
genomic DNA was extracting using QIAGEN Blood & Cell Culture DNA Midi Kit according to manufacturer's instructions.
The sequencing library preparation method is a two-step PCR protocol. The first round of PCR amplifies the region of 250-300 bp containing the sgRNA from the genomic DNA with custom primers. The PCR1 forward primer has only the part needed to bind to the flow cell (P5) and vector-specific sequence upstream of the sgRNA insert (about 40nt in length). The primer lacks the Illumina sequencing primer binding site. The PCR1 reverse primer contains the partial adaptor sequence of the NEBNext Multiplex Oligo for single indexing for Illumina (the 3' region after the index) plus vector-specific sequence downstream of the sgRNA insert (about 25 nt in length). The second round of PCR adds at 3’ unique single indexes to each library. A 5ul aliquot of PCR1 is taken to perform the PCR2. The PCR2 forward primer is the P5 sequence and the PCR2 reverse primer is a NEBNext Multiplex Oligo for single indexing for Illumina. PCR2 amplicons are purified with magnetic beads. Libraries are sequenced as a pool with a custom sequencing primer to increase complexity in the first 20 nucleotides of the libraries. The sequencing primer are the 44 nt of the vector sequence immediatly upstream of the first nucleotide of the sgRNA where the sequence read begins.

treatment_protocol: Differentiation was induced by switching into differentiation medium (DM): EM without LIF and supplemented with 0.1μM retinoic acid (RA). Senescence was induced by irradiation (5 Gy) or Palbociclib (5 μM, Sellekchem).

value: mouse embryonic stem cells

value: R26:rtTA | Col1a1:tetO-Cas9

value: PD doxy


title: Col-0, D18, FT, LD, EM-seq

description:
Library name: Col-0_D18_FT_LD
150x 150

value: First true leaves


title: 03_Dmel_IgG_male

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

country: Germany

institute: Institute of Molecular Biology (IMB)

description:
Library name: sample_03
03_Dmel_IgG_male

data_processing:
Reads were trimmed with cutadapt (v.4.0).
Trimmed reads were mapped to reference genome with bowtie2 (2.4.5).
Coverage signal tracks (bigWigs) of alignments were generated using the bamCoverage tool from deepTools software suite (v.3.5.1).
Assembly: Bacillus rossius redtenbacheri (Brsri_v3, GCF_032445375.1) and Drosophila melanogaster (dm6, GCA_000001215.4), respectively.
Supplementary files format and content: bigWig files, containing CPM normalized coverage signals of primary alignments
Library strategy: CUT&Tag

organism: Drosophila melanogaster

source_name: head

growth_protocol: Bacillus grandii stock cultures were maintained on field-collected bramble cuttings (Rubus ssp) at 25°C, 60% humidity and 12:12 hours light-dark cycle. Drosophila melanogaster were raised on a standard molasses-based food at 25°C, 55% humidity and 12:12 hours light-dark cycle.

extract_protocol:
heads of D.melanogaster and B.grandii were dissected and homogenized  in 100 µl wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1x protease inhibitor (Sigma P8340) in nuclease-free H2O) using a handheld pestle.
CUT&Tag libraries were amplified using NEBNext Ultra II Q5 Master Mix with standard protocols. Libraries were cleaned up using Ampure XP beads and were pooled together for paired-end sequencing.

value: head

value: adult

value: male

tag: antibody

value: IgG (abcam, AB37415)


title: P+5 endometrium tissue in RIF patient88

city: GuangZhou

first: Yameng

last: Xu

address: 6 Chenggui Road, East District

institute: Boai Hospital of Zhongshan Affiliated to Southern Medical University

data_processing:
The raw data were filtered to exclude low-quality reads.
The reads were alternative alignment with RNASeQC.
Qualified reads were mapped to the human reference genome (GRCh37) by using STAR.
Calculate the count of each gene.
Estimate the RNA expression level by FPKM.
Assembly: Ensembl primary assembly, version GRCh37
Supplementary files format and content: Tab-delimited text files include raw counts for each Sample.
Supplementary files format and content: Comma-separated text file includes FPKM values for each Sample.

source_name: endometrium

growth_protocol: The tip of the endometrial sampler was placed into the uterine fundus, and 5–10 mm3 of endometrial tissues were aspirated into the sampler.

extract_protocol:
Total RNA extraction was performed using the RNeasy Micro Kit (74004; Qiagen, Germantown, MD, USA) and followed by quantification with a Qubit HS RNA Kit.
RNA reverse transcription was conducted using the MALBAC® Platinum Single Cell RNA Amplification Kit. Library construction was accomplished using a gene sequencing and library preparation kit (XY045; Yikon Genomics, Suzhou, Jiangsu, China).

treatment_protocol: The collected endometrial tissues were immediately placed into 1.5 mL RNA-later buffer for RNA stabilization, sealed, and cryopreserved at -20 °C.

value: endometrium

value: repeated implantation failure

tag: group

value: rsERT

tag: receptive/non-receptive

value: non-receptive


title: 02_Dmel_H4K16ac_female

description:
Library name: sample_02
02_Dmel_H4K16ac_female

value: female

value: H4K16ac (Millipore, 07-329)


title: Schiz_DLPFC_2

description: Gene expression data

value: F

value: no Clozapine


title: Schiz_DLPFC_3

description: Gene expression data

value: Schizophrenia

value: DLPFC

value: Clozapine


title: R3_8

value: mouse embryonic stem cells

value: R26:rtTA | Col1a1:tetO-Cas9

value: IR doxy


title: WT_rep2

value: E.G7 tumor

value: cd8+ T cell

value: WT


title: pro_cl13_rep1

value: spleens and lymph nodes


title: R3_7

value: doxo doxy


title: Schiz_DLPFC_4

description: Gene expression data


title: P+5 endometrium tissue in RIF patient86

value: endometrium

value: repeated implantation failure

value: rsERT


title: Aeromonas hydrophila resistant to 200ppm oxytetracycline, replicate 3

city: Hong Kong

first: Sophie

middle: Natasha

last: ST-HILAIRE

address: Kowloon Tong, Hong Kong SAR, PR China

institute: City University of Hong Kong

description:
Library name: R200_3_0601
column name in gene_count.csv: R200_3_0601

data_processing:
Raw data in FASTQ format was firstly processed through fastp. In this step, clean data was obtained by trimming reads containing adapter and removing poly-N sequences and reads with low quality. Q20 and Q30 values (proportion of nucleotides with quality values larger than 20 and 30, respectively) were then calculated to quantify gene expression levels. The genome of A. hydrophila ATCC 7966 from the National Center for Biotechnology Information (NCBI) GCA_000014805.1 was selected as the reference genome. Gene function annotation was performed using Prokka (Seemann 2014) (v1.14.6), which employs a hierarchical annotation approach. The pipeline primarily relies on UniProtKB/Swiss-Prot for high-confidence annotations, followed by complementary annotation using the following databases: Pfam (protein domain identification via HMMER), COG/KOG (Clusters of Orthologous Groups for functional classification), and Prokka's curated bacterial annotation database.
Assembly: Both building index of reference genome and aligning clean reads to reference genome were used Hisat2. The GeneMarkS software (http://topaz.gatech.edu) was used to identify novel genes, operon and transcription start sites. FeatureCounts was used to count the reads numbers mapped to each gene. The levels of gene expression were calculated using the reads per kb transcriptome per million (FPKM) mapped reads method for each sample.
Supplementary files format and content: csv format. gene_count; gene_fpkm; gene_fpkm_group

organism: Aeromonas hydrophila

growth_protocol: A stock solution of OTC (20,000 ppm) was made by dissolving 40 mg of OTC into 2 mL of DMSO (20688, Thermo Fisher, USA). Different amounts of this stock solution were added to TSA after the agar had cooled to 50 ℃ to make the following concentrations of OTC: 5 ppm, 20 ppm, 50 ppm, 100 ppm and 200 ppm. To create plates with different concentrations of OTC, we placed a small sterile petri dish (height = 1.3 cm, diameter = 5 cm) in the center of a larger petri dish (height = 2.4 cm, diameter = 14 cm) (BKMAN company of China). We then added 30ml of the lower concentration of OTC to the inner small plate, and 190 mL of the next highest concentration of OTC TSA agar to the outer petri dish. This created antibiotic-resistant gradient plates with two incremental concentrations of OTC: 0-5 ppm (G5), 5-20 ppm (G20), 20-50 ppm (G50), 50-100 ppm (G100), and 100-200 ppm (G200).After the antibiotic agar (base layer) solidified, we poured 31 mL of a semi-liquid 0.5% TSA to create a “swimming layer” over the entire plate to permit the bacteria to cross over the inner petri dish wall to the outer petri dish, which had the higher OTC concentration. To suppress fungal contamination in the semi-liquid layer, 100 μg/mL Ketoconazole (R41400, MedChemExpress, USA) was added to the media before it was poured on the plates.  High-performance liquid chromatography with diode-array detection (HPLC-DAD) was used to assess the concentration of OTC in the semi-liquid layer of antibiotic-resistant gradient plates over time. In brief, we collected 2mL of semi-liquid agar from either the center of small petri dish with the lower OTC concentration, as well as the middle area of the large petri dish with the higher OTC concentration at day 1 and day 4 in G5, G20, G50, and G100 (Supplemental Figure 1) from 3 replicate plates. Samples for HPLC-DAD in the plates with 100ppm in the center base layer and 200 ppm in the outer base layer were collected on day 1 and day 3. Samples were analyzed at the Hong Kong Baptist University (HKBU) Chemistry laboratory for analysis.

extract_protocol:
The RNA were extracted using HiPure Bacterial RNA Kit (R4181, Magen Biotech, China), respectively, as per manual instructions. Further, the RNA quality and quantity were determined by NanoDrop™ One/OneC Microvolume UV-Vis Spectrophotometer (Thermo Fisher, USA). Samples with concentration of RNA greater than 50 ng/uL, respectively were submitted to Novogene (China) for whole genome sequencing and RNA-seq.
Extracted RNA were submitted to Novogen company (China) to conduct the RNA-seq. Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina NovaSeq 6000 (2 × 150 bp read length).

tag: cell line

value: bacteria trained to be resistant to 200 ppm oxytetracycline


title: 01_Dmel_H4K16ac_male

description:
Library name: sample_01
01_Dmel_H4K16ac_male

value: head

value: adult

value: male

value: H4K16ac (Millipore, 07-329)


title: Schiz_DLPFC_5

description: Gene expression data

value: Schizophrenia

value: DLPFC

value: M

value: Clozapine


title: Schiz_DLPFC_1

description: Gene expression data

value: F


title: P+5 endometrium tissue in RIF patient87

value: non-receptive


title: R3_6

tag: cell type

value: mouse embryonic stem cells

value: R26:rtTA | Col1a1:tetO-Cas9

value: PD


title: R3_5

tag: genotype

value: IR


title: Aeromonas hydrophila resistant to 200ppm oxytetracycline, replicate 2

description:
Library name: R200_2_0518
column name in gene_count.csv: R200_2_0518


title: ter_tumor_rep2

tag: tissue

value: E.G7 tumor

value: cd8+ T cell

value: WT


title: P+5 endometrium tissue in RIF patient83

value: endometrium

value: repeated implantation failure

value: rsERT

value: receptive


title: pro_tumor_rep2


title: Aeromonas hydrophila resistant to 100ppm oxytetracycline, replicate 3

description:
Library name: R100_3_0328
column name in gene_count.csv: R100_3_0328

tag: treatment

value: bacteria trained to be resistant to 100 ppm oxytetracycline


title: P+5 endometrium tissue in RIF patient65


title: Aeromonas hydrophila resistant to 200ppm oxytetracycline, replicate 1

description:
Library name: R200_1_0518
column name in gene_count.csv: R200_1_0518

value: bacteria trained to be resistant to 200 ppm oxytetracycline


title: P+5 endometrium tissue in RIF patient66


title: Aeromonas hydrophila resistant to 100ppm oxytetracycline, replicate 2

description:
Library name: R100_2_0328
column name in gene_count.csv: R100_2_0328


title: R3_2

value: diff


title: ter_tumor_rep1


title: memory_rep2

value: spleens and lymph nodes


title: R3_3

value: doxy


title: pro_cl13_rep2


title: Aeromonas hydrophila resistant to 100ppm oxytetracycline, replicate 1

description:
Library name: R100_1_0328
column name in gene_count.csv: R100_1_0328


title: memory_rep1


title: 12wkCPZ_3

city: Riverside

first: Seema

last: Tiwari-Woodruff

address: 900 University Avenue

department: Biomedical Sciences

institute: University of California-Riverside School of Medicine

hyb_protocol: 50 ng of unamplified RNA was hybridized with the Hybridization Master Mix (composed of the reporter code set and hybridization buffer) and 2µl of the Capture ProbeSet at 65°C for 18 hours.

data_processing: Normalized linear counts for all genes were generated by dividing individual gene counts by the average raw data counts for the gene in the normal control group.

label: Capture and Report probes

source_name: homogenized hippocampus

extract_protocol: Dissected hippocampus was immersed in 100µl RIPA buffer and homgenized with zirconium oxide microbeads.RLT Plus solution from Qiagen RNeasy Plus Micro Kit (Qiagen, Hilden, Germany) was added and the mixture re-homogenized two more times. Immediately after, RNA isolation was performed using the Qiagen RNeasy Plus Micro Kit according to manufacturer’s protocol

treatment_protocol: Except normals, 6-8 week old mice were fed 0.2% Cuprizone-milled chow (Harlan Teklad, Madison, WI) ad libitum for 6 and 12 weeks (Crawford et al.,2009).

tag: strain

value: Male


title: R2_9

value: mouse embryonic stem cells

value: PD doxy


title: Aeromonas hydrophila resistant to 50ppm oxytetracycline, replicate 3

description:
Library name: R50_3_0518
column name in gene_count.csv: R50_3_0518

value: bacteria trained to be resistant to 50 ppm oxytetracycline


title: Aeromonas hydrophila resistant to 50ppm oxytetracycline, replicate 2

description:
Library name: R50_2_0328
column name in gene_count.csv: R50_2_0328


title: R3_4

value: R26:rtTA | Col1a1:tetO-Cas9

value: doxo


title: 6wkCPZ_3


title: R2_8

value: IR doxy


title: effector_rep2

value: cd8+ T cell

value: WT


title: effector_rep1


title: 12wkCPZ_2


title: Aeromonas hydrophila resistant to 50ppm oxytetracycline, replicate 1

description:
Library name: R50_1_0328
column name in gene_count.csv: R50_1_0328


title: R2_7

value: doxo doxy


title: pro_tumor_rep1

value: E.G7 tumor


title: Aeromonas hydrophila resistant to 20ppm oxytetracycline, replicate 3

description:
Library name: R20_3_0328
column name in gene_count.csv: R20_3_0328

value: bacteria trained to be resistant to 20 ppm oxytetracycline


title: 12wkCPZ_1


title: R2_6

value: PD


title: RACK1 kncokdown group

first: Junjie

last: Du

state: Beijing

address: Dongdajie Street 8

institute: The Fifth Medical Center of Chinese PLA General Hospital

library_source: transcriptomic single cell

data_processing:
The raw data were aligned to the Mmul_10 reference genome using cellranger count (Version 6.1.2).
Assembly: mm10
Supplementary files format and content: mtx

source_name: scRNA-seq profiling from RACK1 knockdown mice bone marrow Lin-cKit+ cells sampling at 12 days after single intraperitoneal injection of poly(I:C)

extract_protocol:
Bone marrow cells were stained with PE-conjugated antibody against c-Kit in PBS containing 2% FBS for 30 min on ice in the dark. Samples were washed once in staining buffer. Then, the cells were incubated with anti-PE microbeads, and all c-Kit+ cells were enriched using an MS column. The purity of c-Kit+ cells was > 95% as confirmed by flow cytometry.
Libraries were produced with a Chromium system (10X Genomics, PN120263) following the manufacture’s instruction (https://support.10xgenomics.com/single-cell-gene-expression/library-prep/doc/technical-note-assay-scheme-and-configuration-of-chromium-single-cell-3-v2-libraries)

value: Bone marrow

value: Lin-cKit+ hematopoetic cells

value: Rack1F/F; Mx1-Cre

value: Single intraperitoneal injection of poly(I:C)


title: Aeromonas hydrophila resistant to 20ppm oxytetracycline, replicate 1

description:
Library name: R20_1_0328
column name in gene_count.csv: R20_1_0328


title: R2_5

value: IR


title: R3_1

value: mouse embryonic stem cells

value: ESC


title: Normal_6

value: Male


title: Aeromonas hydrophila resistant to 20ppm oxytetracycline, replicate 2

description:
Library name: R20_2_0328
column name in gene_count.csv: R20_2_0328


title: R2_4

value: R26:rtTA | Col1a1:tetO-Cas9


title: Aeromonas hydrophila resistant to 5ppm oxytetracycline, replicate 3

description:
Library name: R5_3_0328
column name in gene_count.csv: R5_3_0328

value: bacteria trained to be resistant to 5 ppm oxytetracycline


title: Control group

source_name: scRNA-seq profiling from wild type mice bone marrow Lin-cKit+ cells sampling at 12 days after single intraperitoneal injection of poly(I:C)


title: R2_3

description: sequencing of PCR amplicons encompasing the sgRNA region

value: doxy


title: R2_2

value: diff


title: naive_rep2

value: spleens and lymph nodes

value: cd8+ T cell

value: WT


title: 6wkCPZ_2


title: E. coli TRIC-seq, stationary - Replicate 11

city: Amsterdam

first: Gaurav

last: Dugar

address: Science Park 904

department: Bacterial Cell Biology

country: Netherlands

institute: University of Amsterdam

description: Library name: R14S3

data_processing:
*library strategy: TRIC-seq
paired-end FASTQ files were pre-processed using fastp (version 1.0.1) for adapter trimming, quality filtering, PCR duplicate removal, and merging of overlapping read pairs
STAR mapper 2.7.11a was used for mapping and extract chimeric reads (RNA-RNA interactions).
Custom scripts used to analyse and visualize RNA-RNA interactions in TRIC-seq can be found at - https://github.com/gdx7/TRIC-seq and https://github.com/gdx7/TRICweb
Assembly: NC_000913.3 (E. coli)
Assembly: CP003725.1 (S. stutzeri)
Assembly: NC_008095.1 (M. xanthus)
Assembly: NC_007795.1 (S. aureus)
Supplementary files format and content: .csv file with mapping statistics and extraction of chimeric reads

organism: Escherichia coli

extract_protocol:
Cells were pelleted, and crosslinks were reversed by incubation with Proteinase K at 65°C for 3 hours. Total RNA was extracted using PCI (Phenol:Chloroform:Isoamyl alcohol for RNA, Carl Roth, #X985.3). The biotinylated chimeric RNAs were captured using MyOne Streptavidin C1 beads (Thermo Fisher, #65002)
The construction of TRIC-seq libraries includes a multi-step in situ protocol involving cell fixation, permeabilization, RNA fragmentation, 3'-end biotin labelling, proximity ligation, followed by RNA purification, enrichment of chimeric junctions, and strand-specific library preparation for sequencing.
directional sequencing library was prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, #E7760), which employs a dUTP-based method with random hexamers for reverse transcription


title: E. coli TRIC-seq, stationary - Replicate 12

description: Library name: R14S7


title: Aeromonas hydrophila resistant to 5ppm oxytetracycline, replicate 1

description:
Library name: R5_1_0601
column name in gene_count.csv: R5_1_0601


title: R2_1


title: Normal_5


title: E. coli TRIC-seq, stationary - Replicate 10

description: Library name: R14S2


title: naive_rep1


title: Normal_4


title: R1_9

value: PD doxy


title: original Aeromonas hydrophila ATCC9766, replicate 3

description:
Library name: R0_3_0328
column name in gene_count.csv: R0_3_0328

value: the original bacteria


title: Normal_3


title: E. coli TRIC-seq, stationary - Replicate 9

description: Library name: R14S1


title: Aeromonas hydrophila resistant to 5ppm oxytetracycline, replicate 2

description:
Library name: R5_2_0328
column name in gene_count.csv: R5_2_0328


title: 6wkCPZ_1


title: Normal_1


title: original Aeromonas hydrophila ATCC9766, replicate 2

description:
Library name: R0_2_0328
column name in gene_count.csv: R0_2_0328


title: AB43 galE knockout mutant biol rep 3

city: Yangzhou

first: JIngchen

last: Hao

address: No. 136, Jiangyang Middle Road

institute: Yangzhou University

description:
Library name: SAMPLE 6
Gram-negative coccobacillus
ABG3

data_processing:
featureCounts (2.0.6) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GCF_019997865.1
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

organism: Acinetobacter baumannii

source_name: Bacterial cell

extract_protocol:
Total bacterial RNA was extracted using the RNAprep Pure Cell/Bacteria Kit (TIANGEN, China) in accordance with the manufacturer's instructions.
Ribosomal RNA was removed from the total RNA and then precipitated with ethanol.   After fragmentation, the first strand cDNA was synthesized using random hexamer primers.   During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer.   The directional library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection

value: Bacterial cell

value: AB43 galE knockout mutant


title: E. coli TRIC-seq, stationary - Replicate 8

description: Library name: R20S21


title: AB43 galE knockout mutant biol rep 1

description:
Library name: SAMPLE 4
Gram-negative coccobacillus
ABG1


title: E. coli TRIC-seq, stationary - Replicate 7

description: Library name: R20S4


title: original Aeromonas hydrophila ATCC9766, replicate 1

description:
Library name: R0_1_0328
column name in gene_count.csv: R0_1_0328


title: S. stutzeri TRIC-seq, stationary

description: Library name: R20S9

organism: Stutzerimonas stutzeri


title: AB43 biol rep 3

description:
Library name: SAMPLE 3
Gram-negative coccobacillus
AB433


title: Normal_2


title: E. coli TRIC-seq, stationary - Replicate 6

description: Library name: R20S3


title: AB43 galE knockout mutant biol rep 2

description:
Library name: SAMPLE 5
Gram-negative coccobacillus
ABG2


title: R1_5


title: 08_Bacillus_IgG_male_Rep12

description:
Library name: sample_08
08_Bacillus_IgG_male_Rep12

organism: Bacillus grandii

value: head

value: adult

value: male

value: IgG (abcam, AB37415)


title: 07_Bacillus_RNAPol2_male_Rep2

description:
Library name: sample_07
07_Bacillus_RNAPol2_male_Rep2


title: R1_4

value: mouse embryonic stem cells

value: doxo


title: E. coli TRIC-seq, stationary - Replicate 5

description: Library name: R20S2


title: 06_Bacillus_RNAPol2_male_Rep1

description:
Library name: sample_06
06_Bacillus_RNAPol2_male_Rep1


title: AB43 biol rep 1

description:
Library name: SAMPLE 1
Gram-negative coccobacillus
AB431


title: AB43 biol rep 2

description:
Library name: SAMPLE 2
Gram-negative coccobacillus
AB432


title: R1_3

value: R26:rtTA | Col1a1:tetO-Cas9


title: hap5_NoUV

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description:
Library name: hap5_NoUV
Replicate 1

data_processing:
Base calling by Azenta and separated based on barcoded adapters
Read1 Fastq files were trimmed using either Trimmomatic v0.39 (BOLGER et al. 2014) or BBDuk version 38.95, with the parameters “ILLUMINACLIP:[XR-seq_adapter_file]:2:30:10”
Read1 fastq files were aligned to the Saccharomyces cerevisiae genome (saccer3) using bowtie2 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl scripts
Only reads mapping to dipyrimidine sequences (i.e., TT, TC, CT, CC), corresponding to CPD lesions were retained in BED files using a custom perl script.
BED files were converted to WIG file using COUNT function of IGVTools or custom perl script
Assembly: saccer3
Supplementary files format and content: WIG files containing counts of DNA CPD lesion reads in dipyrimidine-mapping sequences and their position coordinates are included.

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Wild-type (WT) and hap5 yeast were grown overnight in rich (YPD) medium at normal growth temperature (30C), subcultured in YPD to midlog phase to an OD600 ~0.8, and harvested for UV exposure.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with approximately equal volumes of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 7.5-8.0, 1 mM EDTA) and PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and approximately 0.5 volumes of acid-washed glass beads. Beads were vortexed vigorously for about 4 min. After adding TE (10mM Tris-HCl, pH 7.5-8.0, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 2.5-3 volumes of 100% ethanol and stored at -20C to precipitate the DNA.  DNA pellets were washed with 75-80% ethanol, dissolved in mixture of 1xTE (pH7.5) and 0.2 μg/μl RNase A, and incubated at 37C for approximately 1 hr. The purified genomic DNA was then used for each sequencing library preparation.
The CPD-seq method was employed as previously described (Mao et al., PNAS 2016, 113 (32) 9057-9062). Briefly, approximately 50ug of yeast genomic DNA (gDNA; as measured by NanoDrop spectrophotometry) was extracted from UV-exposed cells via the phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation method. Genomic DNA was then sonicated (30s ON/OFF; 25 cycles; Diagenode Biorupter 300) to generate ~200-600bp fragments and ethanol precipitated. Fragmented DNA was converted to blunt-ended DNA with 5' phosphates and 3' hydroxyls with the NEBNext End Repair Module (NEB) and dA-tailed for ligation with the NEBNext dA-Tailing Module (NEB). A first double-stranded i7 Illumina adapter was ligated onto blunted 3' hydroxyls. Any remaining free 3' hydroxyls were blocked via incubation with terminal transferase (NEB) and either dideoxy ATP or GTP.  T4 endonuclease V (NEB) and APE1 were used to cleave at sites of CPDs and generate new ligatable 3' hydroxyl ends. A second double-stranded, biotinylated i7 Illumina adapter was ligated to these free 3' hydroxyls. Streptavidin beads were used to capture fragments containing the biotinylated second adapter, a wash with 1X SSC (saline sodium citrate) buffer removed non-specific binding, and 0.15M NaOH was used to elute the DNA prior to ethanol precipitation. The complementary strand was synthesized with EconoTaq (Lucigen) and the resulting libraries were amplified with 5 cycles of PCR containing unique barcoded primers for each sample. Libraries were pooled and submitted to Azenta for either Illumina HiSeq 4000 or Illumina NovaSeq X Plus sequencing. Cytiva SeraMag Select beads were used to purify DNA between enzyme incubation steps.

treatment_protocol: Cells were washed with water and exposed to either 90 or 125 J/m^2 UVC radiation (naked DNA vs cells, respectively). Cells were then spun down to obtain cell pellets for the 0h timepoint.

value: Yeast cells

value: No UV

tag: repair time

value: 0 min


title: 05_Bacillus_H4K16ac_male_Rep2

description:
Library name: sample_05
05_Bacillus_H4K16ac_male_Rep2

tag: Sex

value: H4K16ac (Millipore, 07-329)


title: E. coli TRIC-seq, stationary - Replicate 3

description: Library name: R17S4


title: E. coli TRIC-seq, stationary - Replicate 4

description: Library name: R20S1


title: E. coli TRIC-seq, stationary - Replicate 2

description: Library name: R17S2


title: R1_7

value: doxo doxy


title: 04_Bacillus_H4K16ac_male_Rep1

description:
Library name: sample_04
04_Bacillus_H4K16ac_male_Rep1


title: R1_8

description: sequencing of PCR amplicons encompasing the sgRNA region

value: IR doxy


title: hap5_UV_0hr_cellular_replicate2

description:
Library name: hap5_UV_0hr_cellular_replicate2
Replicate 2

value: UV irradiated 125 J/m2


title: R1_2

value: diff


title: R1_1

value: ESC


title: R1_6

value: PD


title: ATAC_PABPN1L_rep2

status: Public on Sep 30 2025

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

data_processing:
After sequencing, the ATAC-seq reads were treated with trim_galore to remove the adapters.  Bowtie2 was used to align the sequences to the mm10 reference genome using the following arguments: bowtie2  -p 10-very sensitive -X 2000. Macs2 was used to call the peaks and visualization was performed using deep tools.
Assembly: mm10
Supplementary files format and content: bw files

source_name: Zygote

extract_protocol:
Each sample contained 50 zygotes collected from mated female mice 28 h after the hCG injection.
The lysis buffer was added directly after sample collection. Tn5 enzyme in Chromatin Profile Kit for Illumina (Novoprotein; N248) was used to fragment chromatin at 37 ℃ on Thermo Mixer (TS100) with 1000 rpm for 30 min and stopped using stop buffer. After extraction with DNA extract beads, DNA fragments were amplified for 15 cycles using the following PCR conditions: 72 ℃ for 3 min; 98 ℃ for 30 s; and thermocycling at 98 ℃ for 15 s, 60 ℃ for 15 s and 72 ℃ for 8 s; following by 72 ℃ 2 min. After the PCR, libraries were purified with 1.2 × DNA clean beads, followed by fragment selection with 0.5×/0.7× beads.

value: Zygote


title: hap5_UV_0hr_cellular_replicate1

description:
Library name: hap5_UV_0hr_cellular_replicate1
Replicate 1


title: E. coli TRIC-seq, stationary - Replicate 1

description: Library name: R17S1


title: ATAC_WT_rep2

value: WT


title: ATAC_PABPN1L_rep1


title: Intestinal epithelial cells from the duodenum Vipr1fl mouse 6

status: Public on Sep 29 2025

city: Lisbon

first: Eric

last: de Sousa

address: Champalimaud Centre for the Unknown, Avenida Brasília

department: Champalimaud Research

country: Portugal

institute: Champalimaud Foundation

description:
Library name: D6
10x Genomics

data_processing:
Ranger version 7.1.0 was used to align reads to the genome and to generate feature barcode matrices
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Duodenum

extract_protocol:
Intestinal segments (duodenum and ileum; ~50mg) from Vipr1fl and Vipr1∆Villin mice were snap frozen and pulverised on dry ice. Tissues were resuspended in fixation buffer and fixed overnight according to 10x Genomics Demonstrated protocol for tissue fixation and dissociation (CG000553). Samples were quenched, dissociated on GentleMACS Octo dissociator, stained with AO/PI and counted on Luna Fx7 following the same manual.
Cells were then hybridised overnight with 10x Genomics Mouse probes for Flex protocols, according to the 10x Genomics Flex protocol for Multiplexed samples (CG000527). The rest of the steps in the protocol included hybridisation, counting on Luna Fx7 and pooling the samples into one reaction which was loaded onto 10x Genomics chip. Libraries were also constructed according to the manufacturers protocol.

value: Duodenum

value: Intestinal epithelial cells

tag: age

value: 8-10 weeks


title: Intestinal epithelial cells from the ileum Vipr1fl mouse 5

description:
Library name: I5
10x Genomics

source_name: Ileum

value: Ileum


title: Intestinal epithelial cells from the ileum Vipr1fl mouse 6

description:
Library name: I6
10x Genomics


title: Intestinal epithelial cells from the duodenum Vipr1fl mouse 5

description:
Library name: D5
10x Genomics


title: ATAC_WT_rep1


title: Intestinal epithelial cells from the duodenum Vipr1∆Villin mouse 1

description:
Library name: D1
10x Genomics


title: Intestinal epithelial cells from the ileum C57BL/6J mouse 8

description:
Library name: I8
10x Genomics


title: Intestinal epithelial cells from the duodenum Vipr1∆Villin mouse 2

description:
Library name: D2
10x Genomics


title: Intestinal epithelial cells from the ileum C57BL/6J mouse 7

description:
Library name: I7
10x Genomics


title: Intestinal epithelial cells from the ileum Vipr1∆Villin mouse 2

description:
Library name: I2
10x Genomics


title: Intestinal epithelial cells from the ileum Vipr1∆Villin mouse 1

description:
Library name: I1
10x Genomics


title: Intestinal epithelial cells from the duodenum C57BL/6J mouse 8

description:
Library name: D8
10x Genomics


title: Intestinal epithelial cells from the duodenum C57BL/6J mouse 7

description:
Library name: D7
10x Genomics