title: LCR HS combination library, 0,3,10,20,50,100kb, HBG promoter rep3, bin3

city: St. Louis

first: Barak

last: Cohen

address: 4515 McKinley Ave

institute: Washington University in St. Louis

description: Library name: DLP1_HBG_6_distances_LCR_library_rep3_bin3

data_processing:
We parsed the enhancer barcode (eBC), distance barcode (dBC) and random barcode (rBC) from each read in the fastq files and counted the abundance of each eBC-dBC-rBC combination to generate the barcode_summary.txt files.
We filtered out eBC-dBC-rBC combinations with <= 20 reads to remove under-sequenced integrations or potential sequencing errors, and then only kept eBC-dBC pairs with >= 10 unique rBCs to make sure every enhancer at every distance was measured from at least 10 independent integration events.
After filtering, we collapsed all rBCs associated with certain eBC-dBC pairs. We normalized the read counts by the total reads in each bin and then renormalized each barcode across bins to get barcode distribution probability. We used the distribution probability and the median mScarlet fluorescence of each bin to calculate the weighted average mScarlet level of each eBC-dBC pair. To compare enhancer activities across different distances, we normalized the calculated mScarlet level by the mScarlet level of the basal promoter with no enhancer or with scrambled controls.
Assembly: hg38
Supplementary files format and content: barcode_summary.txt files: A tab-delimited txt file containing raw read counts of every unique eBC-dBC-rBC combination. 1st column: name of the enhancer; 2nd column: E-P distance; 3rd column: rBC sequence; 4th column: read count

extract_protocol:
Genomic DNA was extracted from each sorted population using Qiagen DNA mini kit (Qiagen, #51304).
For each of the genomic DNA sample, we performed 8 separate 50ul reactions with lr_P3:  GCATGCGAATGGCCTCGTAG and lr_P5: CACAGCCAGACCAACATTGCC using the following condition: 98 °C for 30 s; 20 cycles of 98 °C for 15 s, 69 °C for 15 s and 72 °C for 45 s. After PCR, we pooled eight PCRs for each sample, cleaned up DNA using 1.2x SPRIselect beads(Beckman Coulter, B23317) and quantified DNA concentration using Qubit (Invitrogen, Q33231). We added sequencing adapters and indices with two additional rounds of PCRs: for PCR2, we took 4ng PCR1 product as template and performed 8 cycles of PCR with primers lr_P4: CTTTCCCTACACGACGCTCTTCCGATCTGCATGCGAATGGCCTCGTAG and lr_P6: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCACAGCCAGACCAACATTGCC. For PCR3, we took 2ul PCR2 product as template and amplified another 8 cycles using primers IDT_10_i5: AATGATACGGCGACCACCGAGATCTACAC(10bp index)ACACTCTTTCCCTACACGACGCTC and IDT_10_i7: CAAGCAGAAGACGGCATACGAGAT(10bp index)GTGACTGGAGTTCAGACGTG. After PCR3, we cleaned up DNA using 1.2x SPRIselect beads and quantified DNA concentration using Qubit. (Invitrogen, Q33231).

tag: genotype

value: Pooled 0,3,10,20,50,100kb long-range landing pad cells with HBG promoter

value: integrated with LCR HS combination library


title: LCR HS combination library, 0,3,10,20,50,100kb, HBG promoter rep3, bin4

status: Public on Apr 15 2025

type: SRA

state: MO

department: Genetics

country: USA

description: Library name: DLP1_HBG_6_distances_LCR_library_rep3_bin4

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: K562 cells were grown in IMDM (Isocove's Modified Dulbecco's Medium) supplemented with 10% fetal bovine serum (FBS), 1% non-essential amino acids (NEAA) and 1% penicillin/streptomycin (pen/strep).

treatment_protocol: Pooled K562 long-range landing pad cells were transfected with Flpase recombinase along with the enhancer library. After 3 days, the transfected cells were treated with 2uM Ganciclovir for 7 days. The survived cells were allowed to grow for another 4 days and then FACS sorted on Day14 into four bins based on the mScarlet fluorescence levels. We collected 1.5 million cells from each sorted population.

tag: cell line

tag: treatment


title: Pachon_old_starved_3

city: Kansas City

first: Di

last: Wu

institute: Stowers Institute for Medical Research

description:
Library name: L66820
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_old_starved_3

library_source: transcriptomic

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl-convert 3.10.5 Reads were aligned to UCSC genome Astyanax_mexicanus-2.0 with STAR aligner (version 2.7.10b), using Ens_110 gene models. TPM values were generated using RSEM (version v1.3.1).
Assembly: Astyanax_mexicanus-2.0 (Annotation: Ensembl 110)
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample
Supplementary files format and content: tab-delimited txt file includes cpm for each sample

molecule: total RNA

organism: Astyanax mexicanus

source_name: Ovary

extract_protocol:
Total RNA was extracted using standard phenol/chloroform extraction. 1 ml of Trizol (15596026, Thermo Fisher Scientific) was used per 50 to 100 mg tissue. Samples were homogenized with Trizol and 3.0 mm TriplePure M-Bio Grade beads (D1132-30, Benchmark Scientific) on Beadbug 6 homogenizer (D1036, Benchmark Scientific). After a brief centrifugation, 200 µl of chloroform was added per 1 ml of Trizol, then vortex for 15 seconds and incubated at room temperature for 2 min. Samples were centrifuged at 12,000 g for 15 min at 4°C. Upper transparent aqueous phase was transferred carefully without disturbing the interphase into fresh tube and added with 500 µl of Isopropyl alcohol per 1 ml of Trizol used initially. 2 µl of GlycoBlue Coprecipitant (AM9515, Thermo Fisher Scientific) was added to visualize RNA pellets. Samples were incubated at room temperature for 10 min and centrifuged at 12,000 g for 10 min at 4°C. Supernatant was removed and RNA pellets were washed twice with 1 ml of 75% ethanol per 1 ml Trizol used initially. Samples were mixed by vortexing and centrifuged at 7400 g for 5 min at 4°C. RNA pellets were air dried for 15 min and dissolved in RNase free water. RNA solutions then went through on column purification and DNA digestion using RNeasy Mini Kit (74104, QIAGEN INC) and DNase kit (79254, QIAGEN INC).
Total RNA-Seq libraries were generated from 3.8-500 ng of high-quality total RNA, as assessed using the Bioanalyzer (Agilent), according to the manufacturer’s directions using a 200-5-fold dilution of the universal adaptor and 16-9 cycles of PCR per the respective input mass with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L, NEB), the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) (E7400L, NEB), and the NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) (E6440S, NEB) and purified using the SPRIselect bead-based reagent (B23318, Beckman Coulter). Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and Qubit Fluorometer (Life Technologies).  Equal molar libraries were pooled, quantified, and converted to process on the Singular Genomics G4 with the SG Library Compatibility Kit, following the “Adapting Libraries for the G4 – Retaining Original Indices” protocol.  The converted pools were sequenced to the required number of reads per library on F2 flow cells (700102) or F3 flow cells (700126) on the G4 instrument with the PP1 and PP2 custom index primers included in the SG Library Compatibility Kit (700141), using Instrument Control Software 23.08.1-1 with the following read lengths: 8 bp Index1, 100 bp Read1, 8 bp Index2, and 100 bp Read2. Following sequencing, sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.

tag: tissue

value: Ovary

value: WT

value: Starved


title: CPB_NoDrug_Liver_6

city: Aurora

first: Christopher

middle: Andrew

last: Mancuso

state: CO

address: 13001 East 17th Place

department: Department of Biostatistics and Informatics

institute: University of Colorado Anschutz Medical Campus

description:
Library name: Sample_61
CPB_Liver_6

data_processing:
Raw sequencing reads were de- multiplexed using bcl2fastq. The de-multiplexed fastq files were aligned using the Nextflow based nf-core rnaseq pipeline utilizing Singularity containers. Through this pipeline, Illumina adaptor sequences and low-quality sequencing bases were removed from the fastq files using the TrimGalore! implementation of cutadapt. The resulting reads were aligned to the Sus Scrofa genome using STAR and quantified using Salmon. Comprehensive quality control of every step of the pipeline was performed using MultiQC.
Assembly: Sscrofa11.1
Supplementary files format and content: Count file generated by the nf-core pipeline. Rows are genes and columns are samples.

molecule: polyA RNA

organism: Sus scrofa

source_name: Liver

growth_protocol: Infant swine between 5 – 10 kg

extract_protocol:
Kidney and terminal ileum were harvested en bloc immediately prior to euthanasia while liver, heart, and lungs were harvested immediately following euthanasia to allow circulation of the pentobarbital. All organs underwent passive venous drainage prior to processing and storage. Tissue samples were flash-frozen in liquid nitrogen and stored at −80◦C until homogenized and used for total RNA isolation from kidney (cortex), liver, heart (left ventricle), lungs (right lower lobe), and ileum with the RNeasy Plus Mini Kit (Qiagen, Santa Clarita, CA, USA) as described in the manufacturer’s protocol. RNA concentrations were quantified at 260 nm, and the purity and integrity were determined using NanoDrop (Thermo Fisher Scientific, Waltham, MA, USA).
Samples underwent whole transcriptome RNA sequencing at the University of Colorado Genomics Shared Resource (Aurora, CO, USA). RNA purity, quantity and integrity were determined with NanoDrop and TapeStation 4200 (Agilent Technologies, Santa Clara, CA, USA) analysis prior to RNA-seq library preparation. The Universal Plus mRNA-Seq library preparation kit with NuQuant was used (Tecan, Morrisville, NC, USA) with an input of 200 ng of total RNA to generate RNA-Seq libraries. Paired-end sequencing reads of 150 bp were generated on NovaSeq 6000 sequencer (Illumina, San Diego, CA, USA) at a target depth of 80 million paired-end reads per sample.

value: Liver

tag: intervention

value: CPB/DHCA

value: NoDrug

tag: Sex

value: F

tag: animal id

tag: batch


title: Ker_CD4+CLA+Th1_PAM108

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned by STAR1 2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: Processed data is in .csv format. Each row is a gene, each column is a sample.

source_name: Keratinocytes

extract_protocol:
High-quality total RNA was isolated from approximately 2 x 104 T cell supernatant-treated keratinocytes or fibroblasts using TRIzolTM Reagent (InvitrogenTM; 15596026). cDNA was prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara).
Library construction was performed using the NexteraXT DNA sample preparation kit (Illumina) using half the recommended volumes and reagents.
Libraries were pooled and quantified using a Qubit Fluorometer (Life Technologies).  Dual-index, single-read sequencing of the pooled libraries was carried out on a HiSeq 2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS Kits (Illumina) with a target depth of 5 million reads per sample.

tag: cell type

value: Keratinocytes

value: Blood T cell supernatant

tag: tcellsortforstimulation

tag: tcelldonorid

tag: tcellgmcsf

tag: tcellifngamma

tag: tcelltnfalpha


title: Control_NoDrug_Liver_4

description:
Library name: Sample_60
Control_F_Liver_4

value: Control


title: Pachon_old_starved_2

description:
Library name: L66819
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_old_starved_2


title: Ker_CD4+CLA+Th2_PAM108


title: Pachon_old_starved_1

description:
Library name: L66818
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_old_starved_1


title: CPB_NoDrug_Liver_2

description:
Library name: Sample_59
CPB_Liver_2

value: M


title: LCR HS combination library, 0,3,10,20,50,100kb, HBG promoter rep3, bin2

description: Library name: DLP1_HBG_6_distances_LCR_library_rep3_bin2


title: LCR HS combination library, 0,3,10,20,50,100kb, HBG promoter rep3, bin1

description: Library name: DLP1_HBG_6_distances_LCR_library_rep3_bin1


title: Surface_fish_old_starved_2

description:
Library name: L66816
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_old_starved_2


title: Ker_CD4+CLA+CD103+_PAM107


title: Control_NoDrug_Liver_1

description:
Library name: Sample_58
Control_M_Liver_1


title: Ker_CD4+CLA+Th22_PAM107


title: Surface_fish_old_starved_1

description:
Library name: L66815
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_old_starved_1


title: Control_NoDrug_Kidney_26

description:
Library name: Sample_57
Control_M_Kidney_26

source_name: Kidney

value: Kidney


title: Pachon_old_ctrl_4

description:
Library name: L66814
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_old_ctrl_4

value: Non-treated


title: LCR HS combination library, 0,3,10,20,50,100kb, HBG promoter rep2, bin4

description: Library name: DLP1_HBG_6_distances_LCR_library_rep2_bin4


title: Ker_CD4+CLA+Th17_PAM107


title: Ker_CD4+CLA+Th2_PAM107


title: LCR HS combination library, 0,3,10,20,50,100kb, HBG promoter rep2, bin2

description: Library name: DLP1_HBG_6_distances_LCR_library_rep2_bin2


title: Pachon_old_ctrl_3

description:
Library name: L66813
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_old_ctrl_3


title: LCR HS combination library, 0,3,10,20,50,100kb, HBG promoter rep2, bin1

description: Library name: DLP1_HBG_6_distances_LCR_library_rep2_bin1


title: CPB_Lind_Kidney_24

description:
Library name: Sample_55
CPB_Lind_Kidney_24

value: Linrodostat


title: LCR HS combination library, 0,3,10,20,50,100kb, HBG promoter rep1, bin4

description: Library name: DLP1_HBG_6_distances_LCR_library_rep1_bin4


title: Pachon_old_ctrl_1

description:
Library name: L66811
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_old_ctrl_1


title: CPB_NoDrug_Kidney_25

description:
Library name: Sample_56
CPB_Kidney_25


title: CPB_Lind_Kidney_20

description:
Library name: Sample_53
CPB_Lind_Kidney_20


title: Surface_fish_old_ctrl_4

description:
Library name: L66810
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_old_ctrl_4


title: LCR HS combination library, 0,3,10,20,50,100kb, HBG promoter rep1, bin3

description: Library name: DLP1_HBG_6_distances_LCR_library_rep1_bin3


title: CPB_NoDrug_Kidney_21

description:
Library name: Sample_54
CPB_Kidney_21


title: Ker_CD4+CLA+Th22_PAM106


title: LCR HS combination library, 0,3,10,20,50,100kb, HBG promoter rep1, bin2

description: Library name: DLP1_HBG_6_distances_LCR_library_rep1_bin2


title: CPB_Lind_Kidney_18

description:
Library name: Sample_51
CPB_Lind_Kidney_18


title: Surface_fish_old_ctrl_3

description:
Library name: L66809
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_old_ctrl_3


title: Ker_CD4+CLA+CD103+_PAM106


title: CPB_NoDrug_Kidney_19

description:
Library name: Sample_52
CPB_Kidney_19


title: Control_NoDrug_Kidney_15

description:
Library name: Sample_50
Control_F_Kidney_15


title: LCR HS combination library, 0,3,10,20,50,100kb, HBG promoter rep2, bin3

description: Library name: DLP1_HBG_6_distances_LCR_library_rep2_bin3


title: LCR HS combination library, 0,3,10,20,50,100kb, HBG promoter rep1, bin1

description: Library name: DLP1_HBG_6_distances_LCR_library_rep1_bin1


title: Ker_CD4+CLA+Th1/17_PAM106


title: Control_NoDrug_Kidney_14

description:
Library name: Sample_49
Control_F_Kidney_14


title: GATA1/non-GATA1 enhancer library, 0&100kb, HBG promoter, rep3, bin2

description: Library name: DLP1_HBG_0kb_100kb_GATA1_library_rep3_bin2

value: Pooled 0kb and 100kb long-range landing pad cells with HBE promoter

value: integrated with GATA1/non-GATA1 enhancer library


title: Ker_CD4+CLA+Th1/17_PAM107


title: Pachon_old_ctrl_2

description:
Library name: L66812
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_old_ctrl_2


title: Ker_CD4+CLA+Th1_PAM107


title: hum8h1C3 Placebo

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

data_processing:
Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.15
Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artefact reads (all but three bases in the read equal one base type) were filtered using FastX 0.0.14 and ShortRead 1.40.0
With Bowtie2 2.3.3.1 we identified and removed reads that aligned to phix_illumina
The pre-processed reads were aligned with STAR aligner v2.5.2b to the reference genome of Homo sapiens (GRCh38.88) or Mus musculus (GRCm38.82) . Default STAR aligner parameter settings were used, except for ‘--outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate’. Using Samtools 1.5, reads with a mapping quality smaller than 20 were removed from the alignments
The number of reads in the alignments that overlap with gene features were counted with featureCounts 1.5.3. Following parameters were chosen: -Q 0 -s 2 -t exon -g gene_id. We removed genes for which all samples had less than 1 count-per-million. Raw counts were further corrected within samples for GC-content and between samples using full quantile normalization, as implemented in the EDASeq package from Bioconductor
Assembly: Homo sapiens (GRCh38.88) or Mus musculus (GRCm38.82)
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample for each mapped genome.

source_name: human quadriceps muscle

growth_protocol: C2C12 myoblasts were cultured in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% foetal bovine serum, 100 units/mL penicillin, and 100 μg/mL streptomycin. For differentiation of the C2C12 myoblasts into myotubes, proliferation medium was replaced by differentiation medium when cells reached 80% confluence. Differentiation medium consisted of DMEM supplemented with 2% horse serum and 1% Pen/Strep. Human myoblasts were cultured in Skeletal Muscle Cell Media (PromoCell, no. C-23060), supplemented with 10% FBS and 1% Pen/Strep. For differentiation, proliferation medium was replaced by differentiation medium when cells reached 80% confluency (DMEM glutamax with 2% horse serum and 1% Pen/Strep).

extract_protocol:
Cells were scraped off from the well surface and resuspended in RLT lysis buffer (Qiagen). Total RNA was extracted from these lysed cells using RNeasy micro columns (Qiagen).
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-8000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyzer 2100 or Fragment Analyzer (Agilent). Per sample, an amount of 100 ng of total RNA was used as input. Using the Illumina TruSeq(r) Stranded mRNA Sample Prep Kit (protocol version: Part # 1000000040498 v00 October 2017) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Sequence-libraries of each sample were equimolarly pooled and sequenced on Illumina NovaSeq 6000 (S1 flowcell 100 cycles kit v1.5, 100 bp, Single Reads) at the VIB Nucleomics core (www.nucleomics.be).

treatment_protocol: Murine (C2C12) or human (AB678C53Q) myotubes were treated with quorum sensing peptide iAM373 or placebo for 8 hours or 24 hours.

value: Placebo

tag: incubation time


title: Surface_fish_old_ctrl_1

description:
Library name: L66807
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_old_ctrl_1

value: Ovary


title: Control_NoDrug_Kidney_13

description:
Library name: Sample_48
Control_F_Kidney_13


title: Ker_CD4+CLA+Th1_PAM106


title: GATA1/non-GATA1 enhancer library, 0&100kb, HBG promoter, rep3, bin3

description: Library name: DLP1_HBG_0kb_100kb_GATA1_library_rep3_bin3


title: Molino_oocytes_40um_2

description:
Library name: L66238
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Molino_oocytes_40um_2

value: WT


title: Surface_fish_old_ctrl_2

description:
Library name: L66808
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_old_ctrl_2


title: Ker_CD4+CLA+Th17_PAM106


title: CPB_NoDrug_Kidney_11

description:
Library name: Sample_46
CPB_Kidney_11


title: GATA1/non-GATA1 enhancer library, 0&100kb, HBG promoter, rep3, bin4

description: Library name: DLP1_HBG_0kb_100kb_GATA1_library_rep3_bin4


title: Pachon_oocytes_40um_3

description:
Library name: L66236
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_oocytes_40um_3


title: Molino_oocytes_40um_3

description:
Library name: L66239
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Molino_oocytes_40um_3


title: GATA1/non-GATA1 enhancer library, 0&100kb, HBG promoter, rep3, bin1

description: Library name: DLP1_HBG_0kb_100kb_GATA1_library_rep3_bin1


title: Pachon_oocytes_40um_2

description:
Library name: L66235
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_oocytes_40um_2


title: CPB_Lind_Kidney_12

description:
Library name: Sample_47
CPB_Lind_Kidney_12


title: GATA1/non-GATA1 enhancer library, 0&100kb, HBG promoter, rep2, bin2

description: Library name: DLP1_HBG_0kb_100kb_GATA1_library_rep2_bin2


title: Ker_CD4+CLA+CD103+_PAM105


title: Molino_oocytes_40um_1

description:
Library name: L66237
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Molino_oocytes_40um_1


title: Ker_CD4+CLA+Th2_PAM106


title: Ker_CD4+CLA+Th1/17_PAM105


title: Ker_CD4+CLA+Th22_PAM105


title: GATA1/non-GATA1 enhancer library, 0&100kb, HBG promoter, rep2, bin4

description: Library name: DLP1_HBG_0kb_100kb_GATA1_library_rep2_bin4


title: Control_NoDrug_Kidney_10

description:
Library name: Sample_45
Control_M_Kidney_10


title: GATA1/non-GATA1 enhancer library, 0&100kb, HBG promoter, rep2, bin1

description: Library name: DLP1_HBG_0kb_100kb_GATA1_library_rep2_bin1


title: Surface_fish_oocytes_40um_3

description:
Library name: L66233
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_oocytes_40um_3


title: Ker_CD4+CLA+Th1_PAM105


title: GATA1/non-GATA1 enhancer library, 0&100kb, HBG promoter, rep1, bin4

description: Library name: DLP1_HBG_0kb_100kb_GATA1_library_rep1_bin4


title: Ker_CD4+CLA+Th17_PAM105


title: Control_NoDrug_Kidney_7

description:
Library name: Sample_43
Control_M_Kidney_7


title: CPB_NoDrug_Kidney_9

description:
Library name: Sample_44
CPB_Kidney_9


title: GATA1/non-GATA1 enhancer library, 0&100kb, HBG promoter, rep1, bin3

description: Library name: DLP1_HBG_0kb_100kb_GATA1_library_rep1_bin3


title: Control_NoDrug_Kidney_4

description:
Library name: Sample_41
Control_F_Kidney_4


title: GATA1/non-GATA1 enhancer library, 0&100kb, HBG promoter, rep2, bin3

description: Library name: DLP1_HBG_0kb_100kb_GATA1_library_rep2_bin3


title: Surface_fish_oocytes_40um_1

description:
Library name: L66231
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_oocytes_40um_1


title: Molino_oocytes_40_100um_3

description:
Library name: L66070
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Molino_oocytes_40_100um_3


title: Ker_Control_1

value: Conditioned Media


title: CPB_NoDrug_Kidney_2

description:
Library name: Sample_40
CPB_Kidney_2


title: CPB_NoDrug_Kidney_6

description:
Library name: Sample_42
CPB_Kidney_6


title: Ker_CD4+CLA+Th2_PAM105


title: Ker_CD4+CLA+CD103+_PAM104


title: GATA1/non-GATA1 enhancer library, 0&100kb, HBG promoter, rep1, bin2

description: Library name: DLP1_HBG_0kb_100kb_GATA1_library_rep1_bin2


title: GATA1/non-GATA1 enhancer library, 0&100kb, HBG promoter, rep1, bin1

description: Library name: DLP1_HBG_0kb_100kb_GATA1_library_rep1_bin1


title: Ker_CD4+CLA+Th22_PAM104


title: Control_NoDrug_Ileum_26

description:
Library name: Sample_38
Control_M_Ileum_26

source_name: Ileum

value: Ileum


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBE promoter, rep3, bin4

description: Library name: DLP1_HBE_0kb_10kb_GATA1_library_rep3_bin4

value: Pooled 0kb and 10kb long-range landing pad cells with HBE promoter


title: Pachon_oocytes_40um_1

description:
Library name: L66234
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_oocytes_40um_1


title: Control_NoDrug_Kidney_1

description:
Library name: Sample_39
Control_M_Kidney_1

value: NoDrug


title: Ker_CD4+CLA+Th17_PAM104


title: Molino_oocytes_40_100um_1

description:
Library name: L66068
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Molino_oocytes_40_100um_1


title: CPB_NoDrug_Ileum_25

description:
Library name: Sample_37
CPB_Ileum_25

value: CPB/DHCA


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBE promoter, rep3, bin3

description: Library name: DLP1_HBE_0kb_10kb_GATA1_library_rep3_bin3


title: Ker_CD4+CLA+Th2_PAM104

value: Keratinocytes


title: Surface_fish_oocytes_40um_2

description:
Library name: L66232
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_oocytes_40um_2


title: Pachon_oocytes_40_100um_3

description:
Library name: L66067
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_oocytes_40_100um_3


title: CPB_Lind_Ileum_24

description:
Library name: Sample_36
CPB_Lind_Ileum_24


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBE promoter, rep3, bin1

description: Library name: DLP1_HBE_0kb_10kb_GATA1_library_rep3_bin1


title: Pachon_oocytes_40_100um_1

description:
Library name: L66065
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_oocytes_40_100um_1


title: Ker_CD4+CLA+Th1_PAM104

value: Blood T cell supernatant


title: Pachon_oocytes_40_100um_2

description:
Library name: L66066
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_oocytes_40_100um_2


title: Ker_CD4+CLA+CD103+_PAM096


title: CPB_NoDrug_Ileum_19

description:
Library name: Sample_33
CPB_Ileum_19

value: F


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBE promoter, rep2, bin3

description: Library name: DLP1_HBE_0kb_10kb_GATA1_library_rep2_bin3


title: Surface_fish_oocytes_40_100um_3

description:
Library name: L66064
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_oocytes_40_100um_3


title: Molino_oocytes_40_100um_2

description:
Library name: L66069
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Molino_oocytes_40_100um_2


title: Ker_CD4+CLA+Th22_PAM096


title: Ker_CD4+CLA+Th17_PAM096


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBE promoter, rep3, bin2

description: Library name: DLP1_HBE_0kb_10kb_GATA1_library_rep3_bin2


title: Surface_fish_oocytes_40_100um_2

description:
Library name: L66063
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_oocytes_40_100um_2


title: Ker_Control_0

value: Control


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBE promoter, rep2, bin4

description: Library name: DLP1_HBE_0kb_10kb_GATA1_library_rep2_bin4


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBE promoter, rep2, bin1

description: Library name: DLP1_HBE_0kb_10kb_GATA1_library_rep2_bin1


title: Ker_CD4+CLA+Th2_PAM096


title: Control_NoDrug_Ileum_15

description:
Library name: Sample_31
Control_F_Ileum_15


title: Surface_fish_oocytes_40_100um_1

description:
Library name: L66062
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_oocytes_40_100um_1


title: CPB_Lind_Ileum_20

description:
Library name: Sample_34
CPB_Lind_Ileum_20


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBE promoter, rep2, bin2

description: Library name: DLP1_HBE_0kb_10kb_GATA1_library_rep2_bin2


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBE promoter, rep1, bin4

description: Library name: DLP1_HBE_0kb_10kb_GATA1_library_rep1_bin4


title: Control_NoDrug_Ileum_14

description:
Library name: Sample_30
Control_F_Ileum_14


title: Control_NoDrug_Ileum_13

description:
Library name: Sample_29
Control_F_Ileum_13


title: Molino_oocytes_100_300um_2

description:
Library name: L66060
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Molino_oocytes_100_300um_2


title: CPB_NoDrug_Ileum_21

description:
Library name: Sample_35
CPB_Ileum_21


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBE promoter, rep1, bin3

description: Library name: DLP1_HBE_0kb_10kb_GATA1_library_rep1_bin3


title: Ker_CD4+CLA+Th1_PAM096


title: CPB_Lind_Ileum_18

description:
Library name: Sample_32
CPB_Lind_Ileum_18


title: Pachon_oocytes_100_300um_3

description:
Library name: L66058
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_oocytes_100_300um_3


title: CPB_Lind_Ileum_12

description:
Library name: Sample_28
CPB_Lind_Ileum_12

value: M


title: CPB_NoDrug_Ileum_11

description:
Library name: Sample_27
CPB_Ileum_11


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBE promoter, rep1, bin1

description: Library name: DLP1_HBE_0kb_10kb_GATA1_library_rep1_bin1


title: Molino_oocytes_100_300um_1

description:
Library name: L66059
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Molino_oocytes_100_300um_1

value: Non-treated


title: GATA1/non-GATA1 enhancer library, 0&10kb, GAPDH promoter, rep3, bin4

description: Library name: DLP1_GAPDH_0kb_10kb_GATA1_library_rep3_bin4

value: Pooled 0kb and 10kb long-range landing pad cells with GAPDH promoter


title: CPB_NoDrug_Ileum_9

description:
Library name: Sample_25
CPB_Ileum_9


title: Pachon_oocytes_100_300um_2

description:
Library name: L66057
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_oocytes_100_300um_2


title: Pachon_oocytes_100_300um_1

description:
Library name: L66056
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_oocytes_100_300um_1


title: Control_NoDrug_Ileum_7

description:
Library name: Sample_24
Control_M_Ileum_7


title: Surface_fish_oocytes_100_300um_3

description:
Library name: L66055
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_oocytes_100_300um_3


title: Raji_DNase-seq_1

city: Montpellier

first: Amal

last: Makrini

address: 1919 route de mende

country: France

institute: IGMM

data_processing:
Mnase-seq , DNAse-seq and ChIP-seq samples were aligned to human genome (hg19, GRCh37) using Bowtie 2 aligner. Samples were then treated using PASHA pipeline to produce wig files (Fenouil et al. 2016). Uniquely aligned tags were elongated after estimating optimal elongation size in silico for single ended sequencing or between the pairs for paired end sequencing, enabling to use the original fragment length for further processing. Signals were scaled according to the mean signal. The number of tags covering each nucleotide of the genome was computed and averaged in bins of 10 or 50 nucleotides. For MNase-seq datasets, signals were smoothed on 5 bins.
RNA-seq samples were aligned to human genome (hg19, GRCh37)  and ERCC  reference using tophat2 aligner.
TT-seq samples were aligned to human genome (hg19, GRCh37)  and Drosophila melanogaster (DM6)  reference using tophat2 aligner.
Assembly: hg19
Supplementary files format and content: wig

source_name: Raji B cells

growth_protocol: Raji cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, penicillin/streptomycin (100 units/mL) and glutamin (2 mg/ml) at 37°C and 5% CO2.  NIH-3T3 cells were grown in DMEM supplemented with 10% fetal calf serum, penicillin/streptomycin (100 units/L) and glutamin (2.9 mg/L) at 37°C and 5% CO2.

extract_protocol:
Fifty million cells were used to perform each Pol II ChIP-seq experiments. Cells were crosslinked for 10 min at 20°C with the crosslinking solution (10 mM NaCl, 0.1 mM EDTA pH 8, 0.05 mM EGTA pH 8, 5 mM HEPES pH 7.8 and 1% formaldehyde). The reaction was stopped by adding glycine at a final concentration of 250 mM. After 5 min of formaldehyde quenching, cells were washed twice with cold PBS and resuspended in cold 2.5L LB1 (50 mM HEPES pH 7.5, 140 mM NaCl,1 mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) at 4°C for 20 min on a rotating wheel. Nuclei were pelleted down by spinning at 1350 rcf in a refrigerated centrifuge and washed in 2.5L LB2 (200 mM NaCl, 1 mM EDTA pH 8, 0.5 mM EGTA pH 8, 10 mM Tris pH 8) for 10 min at 4°C on a rotating wheel followed by centrifugation to collect nuclei. Nuclei were then resuspended in 1L LB3 (1 mM EDTA pH 8, 0.5 mM EGTA pH8, 10 mM Tris pH8, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using Bioruptor Pico (Diagenode) in 15L tubes for 20 cycles of 30 s ON and 30 s OFF pulses in 4°C bath. All buffers (LB1, LB2 and LB3) were complemented with EDTA free Protease inhibitor cocktail (Roche), 0.2 mM PMSF and 1 µg/L Pepstatin just before use. After sonication, Triton X-100 was added to a final concentration of 1% followed by centrifugation at 20000 rcf and 4°C for 10 min to remove particulate matter. For sequencing of nucleosomal DNA in Raji cells, 35 million cells were resuspended in 350μl Solution I (150 mM sucrose, 80 mM KCl, 5 mM K2HPO4, 5 mM MgCl2, 0.5 mM CaCl2, 35 mM HEPES pH 7.4) and NP40 was added to a final concentration of 0.2%. Cell membranes were permeabilized for five min at 37°C. MNase was prepared at 50, 25, 12, 6 or 3 units in 0.5L of Solution II (150 mM sucrose, 50 mM Tris pH 8, 50 mM NaCl, 2 mM CaCl2) and incubated with 50 µL of cellular preparation, corresponding to 5. million cells, for exactly 10 min at 37°C. The reactions were stopped by adding of EDTA to a final concentration of 10 mM. The cells were lysed using 1.45L of SDS Lysis Buffer (1% SDS, 10 mM EDTA pH 8, 50 mM Tris pH 8), with 10 min incubation at 4°C. 200μl aliquots were taken for purification and the remaining extracts were stored at -80°C. An equal volume of TE (200ul) was added to the aliquots, followed by subsequent 2 hour treatments with each 0.2µg/L final concentrations of RNase A and Proteinase K at 37°C and 55°C, respectively. DNA was extracted by two subsequent phenol:chloroform:isoamylalcohol (25:24:1) extractions, further purified using QIAquick PCR purifications colums (Qiagen, Germany). Nucleosomal digestion was verified by running 500ng of DNA on a 1.5% agarose gel as well as on DNA high-sensitivity 2100 Bioanalyzer chips (Agilent, USA). Digestions showing 75% of mononucleomes (running at 150bp) were selected for library preparations. Chromatin RNA fraction was prepared from ∼20 million Raji cells. Cells were washed with ice-cold PBS twice. The cells were lysed with ice-cold 4 ml of HLB/NP40 buffer (10 mM Tris-Hcl, pH 7.5, 10 mM NaCl, 0.5% NP40, and 2.5 mM MgCl2) and incubated on ice for 5 min. After the incubation, 1 ml of ice-cold HLB/NP40/Sucrose buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.5% NP40, 2.5 mM MgCl2, and 10% Sucrose) was under-laid and then the nuclei were collected under 1,400 rcf centrifuge at 4°C for 5 min. Isolated nuclei were resuspended in 125 μl of NUN1 solution (20 mM Tri-HCl, pH 8.0, 75mM NaCl, 0.5 mM EDTA, 50% Glycerol) followed by 1.2 ml NUN2 buffer (20 mM HEPES-KOH pH 7.6, 7.5 mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1 M Urea, 1% NP40). Fifteen minutes incubation was carried out on ice with mixing by max speed vortex for 5 s every ∼4 min and then chromatin pellets were precipitatd under 15,000 rcf centrifuge at 4°C for 10 min. Chromatin pellet was resuspended in 500 μl NUN2 buffer. Chromatin were precipitated under 15,000 rcf centrifuge at 4°C for 10 min, then Chromatin RNAs were extracted by 500 μl of Trizol reagent (Life technologies). The RNA extraction steps were repeated three times with rigorous treatment with TurboDNase in beetween. For DNase I sensitivity mapping, nuclei were prepared from 5 millions Raji cells per sample and incubated for 10 min at 37 °C with limiting concentrations of the DNA endonuclease DNase I (Sigma) supplemented with Ca2+ and Mg2+. A dose response experiment of 16 samples was performed with 2X dilution of the DNaseI between samples in cascade. Digestion was stopped by the addition of EDTA, and the samples were treated with proteinase K. The small fragments (<500 bp in length) were recovered on agrose gel from the sample in which a smear just started to appear using Quiagen gel purification kit and librairies were prepared using illumina Truseq kit. G4access was performed in K562 and NIH3T3 cells. Cells were pelleted and rinsed twice in phosphate-buffered saline buffer (PBS). For each experiment, 5 millions cells per titration point were re-suspended in 50 μL of prewarmed permeabilization buffer (150 mM of sucrose, 80 mM KCl, 5 mM KH2PO4, 5 mM MgCl2, 0.5 mM CaCl2 and 35 mM HEPES pH 7.4) supplemented with 0.2% (v/v) NP40 and incubated for 5 minutes at 37ºC prior digestion. MNase digestions, were then performed by adding a volume of 500 μL of prewarmed MNase reaction buffer (150 mM sucrose, 50 mM Tris-HCl pH 8, 50 mM NaCl and 2 mM CaCl2) supplemented with either 3, 6, 12, 25 or 50U of MNase (Merck, 10107921001). Digestions were incubated at 37ºC for 10 min and stopped on ice and by adding 11 μL of 500 mM EDTA to each reaction. Samples were then incubated 10 minutes on ice with 550 μL of SDS lysis buffer (1% (v/v) SDS, 10 mM EDTA and 50 mM Tris.HCl pH 8). Before DNA purification, 1 mL of water was added to dilute the SDS and the samples were incubated with 5 µL of RNAse A (ThermoFisher, EN0531) at 37 ºC for 2 hours and with 8 µL of proteinase K (Euromedex, 09-0911) at 56 ºC for 2 hours to complete the lysis. To then quality control the MNase digestions: 125 μL of each sample were cleaned-up using QIAquick PCR Purification Kit (QIAGEN, 28106) and assessed by agarose gel and Bioanalyzer. At this step, for efficient G4access, samples should present ~30% (+/-5%) of mono-nucleosomes. Importantly, this assessment should be performed on purified DNA that does not contain the subnucleosomal fraction, using a bioanalyzer equipment. The remaining of the samples was then purified by phenol-chloroform and ethanol precipitation for subsequent steps. We recommend that, when implementing this method, a wide range of MNase concentrations shall be tested in a first round of preparative experiments to narrow down the condition in which the critical fraction of 30% of mononucleosome shall be obtained. Our experiences showed this fraction is on average optimal for best G4 sequence recovery. The 0-100 bp size-selected fragments from MNase digestions that have ~30% of mono-nucleosomes were subjected to DNA library preparation. In parallel, genomic DNA libraries were sonicated by Bioruptor® Pico sonicator (Diagenode) to obtain DNA fragments of ~150 bp to be used later as reference data sets for bioinformatic analyses. Paired-end libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645S) using a starting material of 50 ng. DNA fragments were treated with end-repair, A-tailing and ligation of Illumina-compatible adapters. Clean-up of adaptor-ligated DNA was performed by using CleanNGS beads (CNGS-0050) with a bead:DNA ratio of 2:1. The purified products were amplified with 8 cycles of PCR. Finally, samples were cleaned up with a bead:DNA ratio of 0.8:1 to remove the free sequencing adapters.  TT-seq experiments were performed in biological duplicates using 47 millions Raji cells treated with 10 μM pyridostatin (PDS; Sigma SML0678) or H2O (Control) for 10 minutes. Newly synthetised RNAs were labelled with 500µM 4-Thiouridine (4SU; Sigma T4509) for 10min at 37°C at the time of the treatment. In parallel, 60 x106 drosophila S2R+ cells were labelled for 10min with 500µM 4SU. Cells were then harvested by centrifugation and Total RNA was isolated with QIAzol reagent (QIAGEN) according to the manufacturer’s instructions. Drosophila RNA was used as spike-in and added to Raji TotRNAs (1:40 ratio). TotRNAs were fragmented (two-times 105µg in 120µL) using a Covaris sonicator M220 (7°C, Power 75W, Duty factor 1%, burst 200) to generate RNA fragments of 200bp to 10kb. 4SU-labeled RNA from 210µg of Fragmented RNA was biotinylated, pulled-down using streptavidin beads and eluted with freshly prepared 100mM DTT. 4sU-labeled RNA (TT-seq) were treated with RNase-free DNase I, purified with miRNeasy MinElute spin column and eluted in 15µL Nuclease-free water. Prior to library preparation, samples were quantified with Nanodrop and quality was assessed by Bioanalyzer Nano RNA ChIP. Ribosomal RNA were depleted from samples using NEBNext rRNA Depletion Kit V2 (NEB ; E7400) and sequencing libraries were prepared with NEBNext Ultra II Directional Kit (NEB, E7760) according to manufacturer’s instructions.
ChIP-seq, RNA-seq
Mnase-seq, DNase-seq and ChIP-seq librairies were prepared using Illumina's ChIP Sample Prep Kit according to standard protocol. ChrRNA-seq librairies were prepared using Illuminas's "TruSeq® Stranded Total RNA Library Prep Gold (ref. 20020599)" kit according to standard protocol. TT-seq librairies were prepared using NEBnext Utra II Directional Kit.

treatment_protocol: For the α-amanitin experiments, cells were treated with 2.5 µg/mL at the indicated times. For the Pyridostatin experiments, cells were treated with 10 µM pyridistatin. For Triptolide treatment,  Raji cells were treated for 2h with 1 µM. For serum stimulation, cells were starved overnight in DMEM/0.3% FCS before stimulation with 15%FCS for 15minutes.

value: B lymphocyte

tag: strain

value: Burkitt's lymphoma

value: Raji

tag: experiment

value: Dnase-seq

tag: chip antibody

tag: concentration

tag: duration


title: Surface_fish_oocytes_100_300um_2

description:
Library name: L66054
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_oocytes_100_300um_2

tag: tissue

value: Ovary

tag: genotype

value: WT

tag: treatment


title: GATA1/non-GATA1 enhancer library, 0&10kb, GAPDH promoter, rep3, bin2

description: Library name: DLP1_GAPDH_0kb_10kb_GATA1_library_rep3_bin2

tag: cell line

value: integrated with GATA1/non-GATA1 enhancer library


title: CPB_NoDrug_Ileum_6

description:
Library name: Sample_23
CPB_Ileum_6

value: Ileum

tag: intervention

tag: Sex

tag: animal id

tag: batch


title: Surface_fish_oocytes_100_300um_1

description:
Library name: L66053
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_oocytes_100_300um_1


title: GATA1/non-GATA1 enhancer library, 0&10kb, GAPDH promoter, rep3, bin1

description: Library name: DLP1_GAPDH_0kb_10kb_GATA1_library_rep3_bin1


title: Control_NoDrug_Ileum_4

description:
Library name: Sample_22
Control_F_Ileum_4

value: NoDrug


title: GATA1/non-GATA1 enhancer library, 0&10kb, GAPDH promoter, rep2, bin4

description: Library name: DLP1_GAPDH_0kb_10kb_GATA1_library_rep2_bin4


title: Raji_PolII_T30_PDS2

description: Treated with 10 µM Pyridostatin

data_processing:
All samples were aligned to human genome (hg19, GRCh37) using Bowtie 2 aligner. Samples were then treated using PASHA pipeline to produce wig files (Fenouil et al. 2016). Uniquely aligned tags were elongated after estimating optimal elongation size in silico for single ended sequencing or between the pairs for paired end sequencing, enabling to use the original fragment length for further processing. Signals were scaled according to the mean signal. The number of tags covering each nucleotide of the genome was computed and averaged in bins of 10 or 50 nucleotides. For MNase-seq datasets, signals were smoothed on 5 bins.
Genome_build: hg19
Supplementary_files_format_and_content: wig

growth_protocol: Raji cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, penicillin/streptomycin (100 units/mL) and glutamin (2 mg/ml) at 37°C and 5% CO2.

extract_protocol:
Fifty million cells were used to perform each Pol II ChIP-seq experiments. Cells were crosslinked for 10 min at 20°C with the crosslinking solution (10 mM NaCl, 0.1 mM EDTA pH 8, 0.05 mM EGTA pH 8, 5 mM HEPES pH 7.8 and 1% formaldehyde). The reaction was stopped by adding glycine at a final concentration of 250 mM. After 5 min of formaldehyde quenching, cells were washed twice with cold PBS and resuspended in cold 2.5L LB1 (50 mM HEPES pH 7.5, 140 mM NaCl,1 mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) at 4°C for 20 min on a rotating wheel. Nuclei were pelleted down by spinning at 1350 rcf in a refrigerated centrifuge and washed in 2.5L LB2 (200 mM NaCl, 1 mM EDTA pH 8, 0.5 mM EGTA pH 8, 10 mM Tris pH 8) for 10 min at 4°C on a rotating wheel followed by centrifugation to collect nuclei. Nuclei were then resuspended in 1L LB3 (1 mM EDTA pH 8, 0.5 mM EGTA pH8, 10 mM Tris pH8, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using Bioruptor Pico (Diagenode) in 15L tubes for 20 cycles of 30 s ON and 30 s OFF pulses in 4°C bath. All buffers (LB1, LB2 and LB3) were complemented with EDTA free Protease inhibitor cocktail (Roche), 0.2 mM PMSF and 1 µg/L Pepstatin just before use. After sonication, Triton X-100 was added to a final concentration of 1% followed by centrifugation at 20000 rcf and 4°C for 10 min to remove particulate matter. For sequencing of nucleosomal DNA in Raji cells, 35x106 cells were resuspended in 350μl Solution I (150 mM sucrose, 80 mM KCl, 5 mM K2HPO4, 5 mM MgCl2, 0.5 mM CaCl2, 35 mM HEPES pH 7.4) and NP40 was added to a final concentration of 0.2%. Cell membranes were permeabilized for five min at 37°C. MNase was prepared at 50, 25, 12, 6 or 3 units in 0.5L of Solution II (150 mM sucrose, 50 mM Tris pH 8, 50 mM NaCl, 2 mM CaCl2) and incubated with 50 µL of cellular preparation, corresponding to 5.106 cells, for exactly 10 min at 37°C. The reactions were stopped by adding of EDTA to a final concentration of 10 mM. The cells were lysed using 1.45L of SDS Lysis Buffer (1% SDS, 10 mM EDTA pH 8, 50 mM Tris pH 8), with 10 min incubation at 4°C. 200μl aliquots were taken for purification and the remaining extracts were stored at -80°C. An equal volume of TE (200ul) was added to the aliquots, followed by subsequent 2 hour treatments with each 0.2µg/L final concentrations of RNase A and Proteinase K at 37°C and 55°C, respectively. DNA was extracted by two subsequent phenol:chloroform:isoamylalcohol (25:24:1) extractions, further purified using QIAquick PCR purifications colums (Qiagen, Germany). Nucleosomal digestion was verified by running 500ng of DNA on a 1.5% agarose gel as well as on DNA high-sensitivity 2100 Bioanalyzer chips (Agilent, USA). Digestions showing 75% of mononucleomes (running at 150bp) were selected for library preparations.
ChIP-seq
Mnase-seq and ChIP-seq librairies were prepared using Illumina's ChIP Sample Prep Kit according to standard protocol.

treatment_protocol: For the α-amanitin experiments, cells were treated with 2.5 µg/mL at the indicated times. For the Pyridostatin experiments, cells were treated with 10 µM pyridistatin

tag: cell type

tag: spike-in reference organisme

value: Drosophila melanogaster

tag: spike-in cell line

value: Total PolII (N20 - sc899 - Santa Cruz Biotechnology)

value: Pyridostatin for 30 minutes

value: 10 µM Pyridostatin

value: 30 minutes


title: Molino_oocytes_300um_3

description:
Library name: L65725
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Molino_oocytes_300um_3


title: CPB_NoDrug_Ileum_2

description:
Library name: Sample_21
CPB_Ileum_2

value: CPB/DHCA

value: M


title: GATA1/non-GATA1 enhancer library, 0&10kb, GAPDH promoter, rep2, bin3

description: Library name: DLP1_GAPDH_0kb_10kb_GATA1_library_rep2_bin3

value: Pooled 0kb and 10kb long-range landing pad cells with GAPDH promoter


title: GATA1/non-GATA1 enhancer library, 0&10kb, HBE promoter, rep1, bin2

description: Library name: DLP1_HBE_0kb_10kb_GATA1_library_rep1_bin2

value: Pooled 0kb and 10kb long-range landing pad cells with HBE promoter


title: Control_NoDrug_Ileum_10

description:
Library name: Sample_26
Control_M_Ileum_10

value: Control


title: Raji_PolII_T30_PDS1

description: Treated with 10 µM Pyridostatin

value: B lymphocyte

value: Burkitt's lymphoma

value: Raji


title: Molino_oocytes_300um_2

description:
Library name: L65724
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Molino_oocytes_300um_2

value: Ovary

value: WT

value: Non-treated


title: Raji_PolII_T60_PDS2

description: Treated with 10 µM Pyridostatin

value: Pyridostatin for 60 minutes

value: 60 minutes


title: Control_NoDrug_Ileum_1

description:
Library name: Sample_20
Control_M_Ileum_1

value: Ileum

value: NoDrug


title: GATA1/non-GATA1 enhancer library, 0&10kb, GAPDH promoter, rep3, bin3

description: Library name: DLP1_GAPDH_0kb_10kb_GATA1_library_rep3_bin3

value: integrated with GATA1/non-GATA1 enhancer library


title: Raji_PolII_T10_PDS2

description: Treated with 10 µM Pyridostatin

value: Drosophila melanogaster

value: Total PolII (N20 - sc899 - Santa Cruz Biotechnology)

value: Pyridostatin for 10 minutes

value: 10 µM Pyridostatin

value: 10 minutes


title: Raji_PolII_T10_PDS1

description: Treated with 10 µM Pyridostatin


title: Pachon_oocytes_300um_3

description:
Library name: L65722
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_oocytes_300um_3


title: CPB_NoDrug_Heart_25

description:
Library name: Sample_18
X25_S27

source_name: Heart

value: Heart

value: CPB/DHCA

value: M


title: Control_NoDrug_Heart_26

description:
Library name: Sample_19
X26_S28

value: Control


title: GATA1/non-GATA1 enhancer library, 0&10kb, GAPDH promoter, rep2, bin1

description: Library name: DLP1_GAPDH_0kb_10kb_GATA1_library_rep2_bin1

value: Pooled 0kb and 10kb long-range landing pad cells with GAPDH promoter


title: Pachon_oocytes_300um_2

description:
Library name: L65721
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_oocytes_300um_2

value: Ovary

value: WT


title: Molino_oocytes_300um_1

description:
Library name: L65723
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Molino_oocytes_300um_1

value: Non-treated


title: Raji_PolII_T0_PDS2

description: untreated

value: B lymphocyte

value: Burkitt's lymphoma

value: Raji

value: untreated


title: GATA1/non-GATA1 enhancer library, 0&10kb, GAPDH promoter, rep1, bin4

description: Library name: DLP1_GAPDH_0kb_10kb_GATA1_library_rep1_bin4

value: integrated with GATA1/non-GATA1 enhancer library


title: GATA1/non-GATA1 enhancer library, 0&10kb, GAPDH promoter, rep1, bin3

description: Library name: DLP1_GAPDH_0kb_10kb_GATA1_library_rep1_bin3


title: Raji_PolII_T60_PDS1

description: Treated with 10 µM Pyridostatin

value: Drosophila melanogaster

value: Total PolII (N20 - sc899 - Santa Cruz Biotechnology)

value: Pyridostatin for 60 minutes

value: 60 minutes


title: GATA1/non-GATA1 enhancer library, 0&10kb, GAPDH promoter, rep2, bin2

description: Library name: DLP1_GAPDH_0kb_10kb_GATA1_library_rep2_bin2


title: Pachon_oocytes_300um_1

description:
Library name: L65720
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Pachon_oocytes_300um_1


title: CPB_Lind_Heart_24

description:
Library name: Sample_17
X24_S26

value: Heart

value: Linrodostat


title: Raji_Mnase-seq_T60_PDS2_2

description: Treated with 10 µM Pyridostatin

value: 10 µM Pyridostatin


title: CPB_NoDrug_Heart_21

description:
Library name: Sample_16
X21_S25

value: CPB/DHCA

value: NoDrug

value: F


title: GATA1/non-GATA1 enhancer library, 0&10kb, GAPDH promoter, rep1, bin2

description: Library name: DLP1_GAPDH_0kb_10kb_GATA1_library_rep1_bin2

value: Pooled 0kb and 10kb long-range landing pad cells with GAPDH promoter


title: CPB_Lind_Heart_20

description:
Library name: Sample_15
X20_S24


title: Surface_fish_oocytes_300um_3

description:
Library name: L65719
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_oocytes_300um_3

value: Ovary

value: WT

value: Non-treated


title: GATA1/non-GATA1 enhancer library, 0&10kb, GAPDH promoter, rep1, bin1

description: Library name: DLP1_GAPDH_0kb_10kb_GATA1_library_rep1_bin1


title: Raji_Mnase-seq_T60_PDS2_1

description: Treated with 10 µM Pyridostatin

value: B lymphocyte

value: Burkitt's lymphoma

value: Raji


title: Surface_fish_oocytes_300um_2

description:
Library name: L65718
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_oocytes_300um_2


title: CPB_NoDrug_Heart_19

description:
Library name: Sample_14
X19_S23


title: Surface_fish_oocytes_300um_1

description:
Library name: L65717
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_oocytes_300um_1


title: Raji_Mnase-seq_T60_PDS1_2

description: Treated with 10 µM Pyridostatin


title: CUT&Tag UM1_shPRMT5_H3K27ac

city: Cheng du

first: Yu cheng

last: Qi

state: Sichuan

address: No. 24, South Section of First Ring Road

country: China

institute: Sichuan University

description: Library name: CUT_Tag UM1_shPRMT5_H3K27ac

data_processing:
RNA-seq: Sequencing reads were mapped to reference human genome assembly GRCh37/hg19 using bowtie (maximum fragment size set to 2000 bp). Alignments with a MAPQ (mapping quality) score higher than 10 were considered for counting RefSeq (Reference Sequence) genes using featureCounts with its default parameters and continue to normalize the raw counts to transcripts per million (TPM) in R. CUT&Tag: FastQC software was utilized to perform an initial quality assessment of the raw data, followed by the removal of data that did not meet quality standards. Bowtie software was employed to align the quality-filtered data to the reference genome(GRCh37/hg19) with the parameters --end-to-end --very-sensitive --no-mixed --no-discordant.
Assembly: GRCh37
Supplementary files format and content: Differential gene expression analysis comparing control to p63 knockdown was carried out using DESeq2 v1.24.0. DEGs with Fold change > 1.5 and FDR value of ≤ 0.05 were considered statistically significant.
Library strategy: CUT&Tag

source_name: tongue

growth_protocol: No growth conditions

extract_protocol:
RNA-seq: Snap-frozen RNA samples were extracted using Mei5bio M5 HiPer Total RNA Extraction Reagent (MF034-01) including deoxyribonuclease digestion. CUT&Tag: Concanavalin A-coated magnetic beads (Novoprotein, N253-YH01) were introduced to the resuspended cells and incubated at room temperature to facilitate the binding of nuclei. The nonionic detergent digitonin was utilized to permeabilize the cell membrane. Then, ΔNp63α antibody (Cell Signaling Technology, 67825 S), H3K27ac antibody (Cell Signaling Technology, 4353), the secondary antibody and Hyperactive pA-Tn5 Transposase(The pA-Tn5 used in this study was kindly provided by Prof. Zhonghan Li, Sichuan University) were incubated with the cells that had been bound by ConA beads. Consequently, the highly active pA-Tn5 transposase can precisely cleave the DNA fragments that were bound with the target protein. Next, the cells were placed in fragmentation buffer and incubated at 37°C for one hour. Additionally, the cleaved DNA fragments can be ligated to P5 and P7 adaptors using Tn5 transposase.
RNA-seq: The reverse  transcription of RNA to cDNA and the construction of the sequencing library were carried out by Novogene. RNA-seq was performed at Novogene. CUT&Tag: The resulting libraries are then amplified through PCR with the P5 and P7 primers. The DNA fragments were then extracted, purified, and used to construct libraries with the kit's reagents. CUT&Tag sequencing was performed at Novogene, China using the Illumina HiSeq 2000 platform to generate approximately 12 Gb of 150 bp paired-end reads per sample.

value: tongue

value: Human tongue squamous cell carcinoma cell line.


title: Raji_PolII_T0_PDS1

description: untreated

value: Drosophila melanogaster

value: Total PolII (N20 - sc899 - Santa Cruz Biotechnology)

value: untreated


title: CPB_Lind_Heart_18

description:
Library name: Sample_13
X18_S22

value: Heart

value: Linrodostat


title: Tinaja_starved_3

description:
Library name: L66794
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Tinaja_starved_3

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl-convert 3.10.5 Reads were aligned to UCSC genome Astyanax_mexicanus-2.0 with STAR aligner (version 2.7.10b), using Ens_110 gene models. TPM values were generated using RSEM (version v1.3.1).
Assembly: Astyanax_mexicanus-2.0 (Annotation: Ensembl 110)
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample
Supplementary files format and content: tab-delimited txt file includes cpm for each sample
Library strategy: Ribo-Seq

value: Starved


title: CUT&Tag UM1_shPRMT5_DNp63a

description: Library name: CUT_Tag UM1_shPRMT5_DNp63a


title: Tinaja_starved_2

description:
Library name: L66793
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Tinaja_starved_2


title: CUT&Tag UM1_shGFP_H3K27ac

description: Library name: CUT_Tag UM1_shGFP_H3K27ac


title: Raji_Mnase-seq_T60_PDS1_1

description: Treated with 10 µM Pyridostatin

value: Pyridostatin for 60 minutes

value: 10 µM Pyridostatin

value: 60 minutes


title: Control_NoDrug_Heart_14

description:
Library name: Sample_11
X14_S20

value: Control

value: NoDrug

value: F


title: Control_NoDrug_Heart_13

description:
Library name: Sample_10
X13_S19


title: Raji_Mnase-seq_T30_PDS2_2

description: Treated with 10 µM Pyridostatin

value: B lymphocyte

value: Pyridostatin for 30 minutes

value: 30 minutes


title: Surface_fish_starved_3

description:
Library name: L66791
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_starved_3

value: Ovary

value: WT


title: Tinaja_starved_1

description:
Library name: L66792
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Tinaja_starved_1


title: Molino_oocytes_100_300um_3

description:
Library name: L66061
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Molino_oocytes_100_300um_3

value: Non-treated


title: Raji_Mnase-seq_T30_PDS2_1

description: Treated with 10 µM Pyridostatin

value: Burkitt's lymphoma

value: Raji


title: RNA-seq DNp63α（OE） biol rep3

description: Library name: RNA-seq UM1_DNp63α_rep3

data_processing:
RNA-seq: Sequencing reads were mapped to reference human genome assembly GRCh37/hg19 using bowtie (maximum fragment size set to 2000 bp). Alignments with a MAPQ (mapping quality) score higher than 10 were considered for counting RefSeq (Reference Sequence) genes using featureCounts with its default parameters and continue to normalize the raw counts to transcripts per million (TPM) in R. CUT&Tag: FastQC software was utilized to perform an initial quality assessment of the raw data, followed by the removal of data that did not meet quality standards. Bowtie software was employed to align the quality-filtered data to the reference genome(GRCh37/hg19) with the parameters --end-to-end --very-sensitive --no-mixed --no-discordant.
Assembly: GRCh37
Supplementary files format and content: Differential gene expression analysis comparing control to p63 knockdown was carried out using DESeq2 v1.24.0. DEGs with Fold change > 1.5 and FDR value of ≤ 0.05 were considered statistically significant.

value: tongue

value: Human tongue squamous cell carcinoma cell line.


title: Raji_Mnase-seq_T30_PDS1_2

description: Treated with 10 µM Pyridostatin


title: CPB_Lind_Heart_12

description:
Library name: Sample_9
X12_S18

value: Heart

value: CPB/DHCA

value: Linrodostat

value: M


title: Raji_Mnase-seq_T30_PDS1_1

description: Treated with 10 µM Pyridostatin

value: 10 µM Pyridostatin


title: RNA-seq DNp63α（OE） biol rep2

description: Library name: RNA-seq UM1_DNp63α_rep2


title: Surface_fish_starved_2

description:
Library name: L66790
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_starved_2

value: Starved


title: CPB_NoDrug_Heart_11

description:
Library name: Sample_8
X11_S17

value: NoDrug


title: RNA-seq DNp63α（OE） biol rep1

description: Library name: RNA-seq UM1_DNp63α_rep1


title: Raji_Mnase-seq_T10_PDS2_2

description: Treated with 10 µM Pyridostatin

value: B lymphocyte

value: Pyridostatin for 10 minutes

value: 10 minutes


title: Control_NoDrug_Heart_10

description:
Library name: Sample_7
X10_S16

value: Control


title: Surface_fish_starved_1

description:
Library name: L66789
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_starved_1

value: Ovary

value: WT


title: Control_NoDrug_Heart_15

description:
Library name: Sample_12
X15_S21

value: F


title: RNA-seq vector biol rep3

description: Library name: RNA-seq UM1_vector_rep3


title: Tinaja_ctrl_3

description:
Library name: L66788
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Tinaja_ctrl_3

value: Non-treated


title: CUT&Tag UM1_shGFP_DNp63a

description: Library name: CUT_Tag UM1_shGFP_DNp63a

value: tongue


title: CPB_NoDrug_Heart_9

description:
Library name: Sample_6
X9_S15


title: Tinaja_ctrl_2

description:
Library name: L66787
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Tinaja_ctrl_2


title: Raji_Mnase-seq_T10_PDS1_1

description: Treated with 10 µM Pyridostatin

value: Burkitt's lymphoma

value: Raji


title: RNA-seq vector biol rep1

description: Library name: RNA-seq UM1_vector_rep1

value: Human tongue squamous cell carcinoma cell line.


title: Raji_Mnase-seq_T10_PDS1_2

description: Treated with 10 µM Pyridostatin


title: Control_NoDrug_Heart_7

description:
Library name: Sample_5
X7_S14

value: Heart


title: Surface_fish_ctrl_3

description:
Library name: L66785
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_ctrl_3


title: RNA-seq vector biol rep2

description: Library name: RNA-seq UM1_vector_rep2


title: Tinaja_ctrl_1

description:
Library name: L66786
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Tinaja_ctrl_1


title: RNA-seq shPRMT5 biol rep1

description: Library name: RNA-seq UM1_shPRMT5_rep1


title: Raji_Mnase-seq_T0_PDS2_2

description: untreated

value: untreated


title: CPB_NoDrug_Heart_6

description:
Library name: Sample_4
X6_S13

value: CPB/DHCA


title: CPB_NoDrug_Heart_2

description:
Library name: Sample_2
X2_S11

value: M


title: Surface_fish_ctrl_2

description:
Library name: L66784
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_ctrl_2


title: Raji_Mnase-seq_T0_PDS2_1

description: untreated


title: Control_NoDrug_Heart_1

description:
Library name: Sample_1
X1_S10

value: NoDrug


title: Surface_fish_ctrl_1

description:
Library name: L66783
Instrument model: Singular Genomics G4; Column name in star_counts_all_samples.txt and cpm_all_samples.txt: Surface_fish_ctrl_1


title: RNA-seq shGFP biol rep1

description: Library name: RNA-seq UM1_shGFP_rep1


title: RNA-seq shGFP biol rep2

description: Library name: RNA-seq UM1_shGFP_rep2


title: Raji_Mnase-seq_T10_PDS2_1

description: Treated with 10 µM Pyridostatin

value: B lymphocyte

value: 10 µM Pyridostatin


title: Raji_Mnase-seq_T0_PDS1_1

description: untreated


title: RNA-seq shPRMT5 biol rep2

description: Library name: RNA-seq UM1_shPRMT5_rep2


title: Control_NoDrug_Heart_4

description:
Library name: Sample_3
X4_S12


title: Old mice treated with a Senolytic 35 days following BaCl injury, 3

status: Public on Apr 14 2025

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

description: Library name: Old Senolytic 35 DPI - 3

data_processing:
fastq reads were aligned to mm10 using HISAT2 aligner with default parameters
Assembly: mm10
Supplementary files format and content: tab-delimited count matrix

organism: Mus musculus

source_name: Skeletal Muscle

extract_protocol:
Total RNA was isolated using the Qiagen miRNeasy Mini Kit according to manufacturer’s instructions.
RNA was sent to Novogene Co. (Beijing, China) for library preparation and mRNA sequencing.

value: Skeletal Muscle

tag: group

value: Old

value: Senolytic


title: Old mice treated with a Senolytic 7 days following BaCl injury, 1

description: Library name: Old Senolytic 7 DPI - 1

tag: strain


title: Old mice treated with a Senolytic 7 days following BaCl injury, 4

description: Library name: Old Senolytic 7 DPI - 4


title: Old mice treated with a Senolytic 35 days following BaCl injury, 1

description: Library name: Old Senolytic 35 DPI - 1


title: Old mice treated with a Senolytic 7 days following BaCl injury, 2

description: Library name: Old Senolytic 7 DPI - 2


title: Old mice treated with a Senolytic 35 days following BaCl injury, 2

description: Library name: Old Senolytic 35 DPI - 2


title: Old mice treated with a vehicle 35 days following BaCl injury, 1

description: Library name: Old Vehicle 35 DPI - 1

value: Vehicle


title: Old mice treated with a Senolytic 7 days following BaCl injury, 3

description: Library name: Old Senolytic 7 DPI - 3


title: Old mice treated with a vehicle 7 days following BaCl injury, 4

description: Library name: Old Vehicle 7 DPI - 4


title: Old mice treated with a vehicle 7 days following BaCl injury, 2

description: Library name: Old Vehicle 7 DPI - 2


title: Old mice treated with a vehicle 7 days following BaCl injury, 1

description: Library name: Old Vehicle 7 DPI - 1


title: Old mice treated with a vehicle 35 days following BaCl injury, 4

description: Library name: Old Vehicle 35 DPI - 4


title: Raji_Mnase-seq_T0_PDS1_2

description: untreated


title: Old mice treated with a vehicle without injury, 3

description: Library name: Old Vehicle PBS - 3


title: Old mice treated with a vehicle without injury, 4

description: Library name: Old Vehicle PBS - 4


title: Old mice treated with a vehicle 7 days following BaCl injury, 3

description: Library name: Old Vehicle 7 DPI - 3


title: Old mice treated with a vehicle without injury, 2

description: Library name: Old Vehicle PBS - 2


title: Young mice treated with a vehicle 35 days following BaCl injury, 4

description: Library name: Young Vehicle 35 DPI - 4

value: Young


title: Old mice treated with a vehicle without injury, 1

description: Library name: Old Vehicle PBS - 1


title: Young mice treated with a vehicle 35 days following BaCl injury, 3

description: Library name: Young Vehicle 35 DPI - 3


title: Young mice treated with a vehicle 35 days following BaCl injury, 1

description: Library name: Young Vehicle 35 DPI - 1


title: Young mice treated with a vehicle 7 days following BaCl injury, 3

description: Library name: Young Vehicle 7 DPI - 3


title: Young mice treated with a vehicle 7 days following BaCl injury, 4

description: Library name: Young Vehicle 7 DPI - 4


title: Young mice treated with a vehicle 7 days following BaCl injury, 2

description: Library name: Young Vehicle 7 DPI - 2


title: Old mice treated with a Senolytic 35 days following BaCl injury, 4

description: Library name: Old Senolytic 35 DPI - 4


title: Old mice treated with a vehicle 35 days following BaCl injury, 2

description: Library name: Old Vehicle 35 DPI - 2


title: Old mice treated with a vehicle 35 days following BaCl injury, 3

description: Library name: Old Vehicle 35 DPI - 3


title: Young mice treated with a vehicle without injury, 4

description: Library name: Young Vehicle PBS - 4


title: Young mice treated with a vehicle without injury, 3

description: Library name: Young Vehicle PBS - 3


title: Young mice treated with a vehicle without injury, 2

description: Library name: Young Vehicle PBS - 2


title: Young mice treated with a vehicle without injury, 1

description: Library name: Young Vehicle PBS - 1


title: Young mice treated with a vehicle 35 days following BaCl injury, 2

description: Library name: Young Vehicle 35 DPI - 2


title: High-fat diet,RNA-seq,MII-3

city: Zhengzhou

first: Lin-Li

last: Yang

state: Henan

address: No. 1, Jianshe East Road, Erqi District

department: department of obstetrics and gynecology

institute: The First Affiliated Hospital of Zhengzhou University

description: Library name: HFD-MII-Seq-3

data_processing:
Quality Control and Adapter Removal: Raw sequencing data was processed using Trim Galore to perform quality control and remove adapter sequences, low-quality bases, and adapter sequences. The quality control parameters were set with a quality score threshold of 20 (Phred+33), requiring at least 3 bases to perfectly match the adapter sequence, a minimum retained sequence length of 50 bp, and allowing a 10% error rate.
Alignment to Reference Genome: After quality control, cleaned reads were aligned to the reference genome (mouse genome mm39) using Hisat2. The alignment process was performed using 8 threads for parallel computation, generating alignment reports and SAM files.
SAM to BAM Conversion and Sorting: The aligned SAM files were converted to BAM format using Samtools and were then sorted and indexed for further analysis.
Gene Expression Quantification: Gene expression was quantified using featureCounts, with exons as the counting unit. Overlapping and multi-mapping reads were allowed. To accurately calculate gene lengths, the latest version of the mouse genome annotation (GRCm39) was used, and exon annotation information was downloaded from the Gencode database (Mus_musculus.GRCm39.113.gtf.gz).
Exon Processing and Gene Length Calculation: Exon information from the gene annotation was extracted, including chromosome, start position, end position, gene ID, and gene name. These exonic regions were converted into GRanges objects using the GenomicRanges package. To remove overlapping or adjacent exonic regions within the same gene, exons were grouped by gene ID, and the reduce function was applied to merge overlapping regions. For each gene, the total exon length was calculated by merging all exon lengths.Gene Name Consistency: If multiple gene names were associated with a single gene, the most frequent name was retained to ensure consistency in gene naming.Export            Gene Length Information: Finally, the merged gene length information was exported as a CSV file for subsequent analysis.
Assembly: GRCm39
Supplementary files format and content: csv files include FPKM or TPM for each sample

source_name: oocytes

growth_protocol: Eight-week-old female C57BL/6J mice were randomly assigned to either normal diet (ND, 10% fat calories) or high-fat diet (HFD, 60% fat calories) groups and maintained on these diets for 12 weeks prior to oocyte collection. For superovulation, mice received an intraperitoneal injection of 10 IU pregnant mare serum gonadotropin (PMSG; Sigma-Aldrich), and germinal vesicle (GV)-stage oocytes were collected from antral follicles 44-48 hours post-injection. The collected oocytes were cultured in M2 medium (Sigma-Aldrich, MR-015-D) and M16 medium (Sigma-Aldrich, M7292) under mineral oil (Sigma-Aldrich, M8410) at 37°C with 5% CO₂, with cumulus-oocyte complexes (COCs) being dissected from antral follicles and denuded using hyaluronidase treatment (Sigma-Aldrich, H3506) to remove granulosa cells, leaving denuded oocytes for subsequent experiments, while in specified cases, 2.5 μM milrinone (MedChemExpress, HY-14252) was added to the culture medium to prevent spontaneous germinal vesicle breakdown (GVBD).

extract_protocol:
We collected GV and MII stage oocytes (n=4 per sample) from ND and HFD groups, lysing them in 10 µL ice-cold sample buffer (Vazyme N711 containing 0.2 µL 1:2500 ERCC spike-in [Invitrogen 4456740] and RNase inhibitor) for 10 minutes, then divided each lysate into 2.0 µL for transcriptomics and 8.0 µL for proteomics. For ribosome profiling, we functionalized RiboLace beads (Immagina RL001), resuspended them in the 8 µL lysate supplemented with binding buffer (100 µg/mL cycloheximide, 1 mM DTT, 5 mM MgCl₂, 150 mM NaCl, 20 mM Tris-HCl pH 8.0) and RNase inhibitor, then incubated at 4°C for 1 hour with 3 rpm rotation. After magnetic rack washing with W-buffer, we eluted ribosome-bound RNA in 12 µL RLT buffer (Qiagen 74004) containing β-mercaptoethanol and GlycoBlue, then purified using VAHTS RNA Clean Beads (Vazyme N411) with 2M LiCl precipitation following manufacturer protocols.
For ultra-sensitive T&T-seq library construction, total RNA (2 µL lysate) and ribosome-bound full-length RNA were reverse transcribed into cDNA and amplified for 18 PCR cycles using the Single Cell Full Length mRNA-Amplification Kit (Vazyme N711), followed by purification with VAHTS DNA Clean Beads (Vazyme N411), with cDNA concentration measured by Qubit (Invitrogen) and size distribution (~2000 bp) analyzed using Bioanalyzer 2100 (Agilent), then index libraries were prepared using TruePrep DNA Library Prep Kit V2 (Vazyme TD502) and size-selected (250-450 bp) with VAHTS DNA Clean Beads before quantification and paired-end sequencing (PE150) on Illumina Novaseq 6000 (Azenta Life Sciences). For RNA-seq library preparation, GV and MII stage oocytes (n=4/sample) from ND/HFD groups were lysed in sample buffer (Vazyme N711) containing 0.2 µL 1:2500 ERCC spike-in (Invitrogen 4456740), followed by cDNA synthesis using Oligo dT primers and Discover-sc reverse transcriptase for template switching adapter addition, PCR amplification of full-length cDNA, magnetic bead purification (Vazyme N411), library construction using TruePrep Kit V2 (Vazyme TD503) with 15 PCR cycles, size selection (250-450 bp), Qubit quantification, Bioanalyzer quality assessment, and PE150 sequencing on Illumina Novaseq 6000 (Azenta Life Sciences).

treatment_protocol: Fully matured oocytes were collected and maintained in M2 medium (Sigma-Aldrich, MR-015-D) containing 2.5 μM milrinone (MedChemExpress, HY-14252) to prevent spontaneous germinal vesicle breakdown (GVBD), followed by microinjection using an NTX-N4 micromanipulator system (Nikon) to deliver 5-10 picoliters (pl) of either 500 μg/ml mRNA or 20 μM siRNA per oocyte. After injection, oocytes were washed and cultured in M16 medium (Sigma-Aldrich, M7292) supplemented with 2.5 μM milrinone at 37°C under 5% CO₂ atmosphere to enable either translation of injected mRNA or target transcript knockdown by siRNA. Subsequently, oocytes were transferred to milrinone-free M16 medium (Sigma-Aldrich, M7292) for 14 hours before being processed for either confocal microscopy imaging or transcriptomic and proteomic library construction.

value: oocytes

value: MII oocytes

value: Obese

value: Oocyte maturation


title: High-fat diet,RNA-seq,GV-1

description: Library name: HFD-GV-Seq-1

value: GV oocytes


title: Normal diet,RNA-seq,MII-1

description: Library name: ND-MII-Seq-1

value: WT


title: Eif2b1 knockdown,RNA-seq,GV-1

description: Library name: Eif2b1-GV-Seq-1

value: FIF2B1 knocldown


title: Normal diet,RNA-seq,GV-2

description: Library name: ND-GV-Seq-2


title: Normal diet,RNA-seq,MII-2

description: Library name: ND-MII-Seq-2


title: Eif2b1 knockdown,RNA-seq,GV-2

description: Library name: Eif2b1-GV-Seq-2


title: Normal diet,RNA-seq,MII-4

description: Library name: ND-MII-Seq-4


title: Normal diet,RNA-seq,GV-1

description: Library name: ND-GV-Seq-1


title: High-fat diet,RNA-seq,GV-3

description: Library name: HFD-GV-Seq-3


title: High-fat diet,RNA-seq,MII-2

description: Library name: HFD-MII-Seq-2


title: Negtive control,RNA-seq,GV-2

description: Library name: NC-GV-Seq-2


title: High-fat diet,RNA-seq,GV-2

description: Library name: HFD-GV-Seq-2


title: Normal diet,RNA-seq,MII-3

description: Library name: ND-MII-Seq-3


title: Negtive control,RNA-seq,GV-3

description: Library name: NC-GV-Seq-3


title: Young mice treated with a vehicle 7 days following BaCl injury, 1

description: Library name: Young Vehicle 7 DPI - 1


title: Eif2b1 knockdown,RNA-seq,GV-3

description: Library name: Eif2b1-GV-Seq-3


title: High-fat diet,RNA-seq,MII-1

description: Library name: HFD-MII-Seq-1


title: High-fat diet,Transcriptomics,MII-1

description: Library name: HFD-MII-RNA-1

data_processing:
library strategy: T&T seq(Transcriptomics)
Quality Control and Adapter Removal: Raw sequencing data was processed using Trim Galore to perform quality control and remove adapter sequences, low-quality bases, and adapter sequences. The quality control parameters were set with a quality score threshold of 20 (Phred+33), requiring at least 3 bases to perfectly match the adapter sequence, a minimum retained sequence length of 50 bp, and allowing a 10% error rate.
Alignment to Reference Genome: After quality control, cleaned reads were aligned to the reference genome (mouse genome mm39) using Hisat2. The alignment process was performed using 8 threads for parallel computation, generating alignment reports and SAM files.
SAM to BAM Conversion and Sorting: The aligned SAM files were converted to BAM format using Samtools and were then sorted and indexed for further analysis.
Gene Expression Quantification: Gene expression was quantified using featureCounts, with exons as the counting unit. Overlapping and multi-mapping reads were allowed. To accurately calculate gene lengths, the latest version of the mouse genome annotation (GRCm39) was used, and exon annotation information was downloaded from the Gencode database (Mus_musculus.GRCm39.113.gtf.gz).
Exon Processing and Gene Length Calculation: Exon information from the gene annotation was extracted, including chromosome, start position, end position, gene ID, and gene name. These exonic regions were converted into GRanges objects using the GenomicRanges package. To remove overlapping or adjacent exonic regions within the same gene, exons were grouped by gene ID, and the reduce function was applied to merge overlapping regions. For each gene, the total exon length was calculated by merging all exon lengths.Gene Name Consistency: If multiple gene names were associated with a single gene, the most frequent name was retained to ensure consistency in gene naming.Export            Gene Length Information: Finally, the merged gene length information was exported as a CSV file for subsequent analysis.
Assembly: GRCm39
Supplementary files format and content: csv files include FPKM or TPM for each sample


title: High-fat diet,Transcriptomics,GV-1

description: Library name: HFD-GV-RNA-1


title: High-fat diet,Transcriptomics,GV-3

description: Library name: HFD-GV-RNA-3


title: 2_RpgrEx3d8_18mths

city: Edinburgh

first: Roly

last: Megaw

address: Crewe Road

country: United Kingdom

institute: University of Edinburgh

description:
Library name: Sample 4
8bp deletion mutation in Rpgr exon 3. Protein null.

library_source: transcriptomic single cell

data_processing:
fastq files were aligned to version 98 of mouse reference genome GRCm38 using Kallisto
The unfiltered count matrices produced by Kallisto were converted to SingleCellExperiment (SCE) objects and empty droplets were removed with EmptyDrops using the default parameters. After removing all genes with counts of zero for all barcodes, the remaining genes were annotated with relevant features from Ensembl. Cell-level QC was performed with Scater 70, excluding cells with high amount of reads coming from mitochondrial genes (nmads >3)
Using Seurat we further filtered the count matrices to contain only protein-coding genes with non-zero counts in at least 10 cells and cells expressing at least 500 protein-coding genes. Mutant and wild-type cells were then merged for each experiment.
Clustering of the cells for the two experiments was done with Seurat, by performing log-normalisation, centring and scaling, clustering based on the identified variable features using shared nearest neighbour graph and the Louvain algorithm with multilevel refinement with resolution = 0.5 to produce the UMAP plots
Cluster annotation was initiated by identification of each cluster markers against the remaining clusters using Seurat’s FindMarkers function (with min.pct = 0.25, logfc.threshold = 0.25) and selecting only upregulated genes with p_val_adj < 0.05, followed by manual curation based on existing literature.
Assembly: Version 98 of reference genome GRCm38
Supplementary files format and content: Unfiltered count matrices stored as SingleCellExperiment objects (https://bioconductor.org/packages/devel/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html) for the 4 samples used in this study.

source_name: Mouse retina, C57BL/6

extract_protocol:
Retinas dissected and dissociated into single cells using the NeuroCult Enzymatic Dissociation Kit for Adult CNS Tissue (Stem Cell Technologies cat. 05715) according to the manufacturer’s instructions. Live cells were sorted into singlets by FACS and then processed using Chromium Single Cell 3’ Reagent kits v3 (10X Genomics) according to the manufacturer’s instructions.
Chromium Single Cell 3’ Reagent kits v3 (10X Genomics), according to the manufacturer's instructions.

value: Mouse retina, C57BL/6

value: untreated


title: 1_RpgrORFd5_18mths

description:
Library name: Sample 2
5bp deletion mutation in RpgrORFd5 (retina specific isoform). Protein null.


title: Normal diet,Transcriptomics,MII-3

description: Library name: ND-MII-RNA-3


title: High-fat diet,Transcriptomics,MII-2

description: Library name: HFD-MII-RNA-2


title: Normal diet,RNA-seq,GV-3

description: Library name: ND-GV-Seq-3


title: High-fat diet,Transcriptomics,GV-2

description: Library name: HFD-GV-RNA-2


title: Normal diet,Transcriptomics,MII-2

description: Library name: ND-MII-RNA-2


title: 2_WT_18mths

description:
Library name: Sample 3
wild-type littermate control for RpgrEx3d8

value: wild-type


title: Normal diet,Transcriptomics,GV-3

description: Library name: ND-GV-RNA-3


title: WT-Total-C

city: Philadelphia

first: Gregory

last: Chen

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
Mouse_LCMV_Tcell_ATAC-Seq_ReadCounts.tsv
Mouse_LCMV_Tcell_ATAC-Seq_CPM.tsv

data_processing:
RNA-Seq alignment with STAR v 2.7.10a
RNA quantification with cufflinks v2.2.1
Read count quantification with Rsubread in R v4.0.2
ATAC-Seq alignment with bwa-mem
ATAC-Seq peak calling with MACS2
Assembly: mm39
Supplementary files format and content: Tab-delimited text file. First column is MGI Gene Symbol or Peak coordinate. Subsequent columns are sample names. The first row is a header. Subsequent rows represent a gene or peak

source_name: Total

growth_protocol: Recipient mice were intravenously infected with 4 × 10^6 PFU of LCMV clone 13

extract_protocol:
RNA was isolated using the Qiagen rNeasy Micro Kit
cDNA libraries were generated following the manufacturer’s instructions with the SMART-Seq v4 Ultra Low Input RNA Kit and Nextera XT DNA library kit

treatment_protocol: WT and TET2KO P14 cells were mixed at a 1:1 ratio, and a total of 500 P14 cells (250 WT and 250 TET2KO) were adoptively transferred intravenously into recipient mice of a third congenic background.

value: T cells

value: Total

value: T cells in LCMV mouse experiment


title: Normal diet,Transcriptomics,GV-1

description: Library name: ND-GV-RNA-1


title: High-fat diet,Translatomics,MII-3

description: Library name: HFD-MII-Ribo-3

library_source: other

data_processing:
library strategy: T&T seq(Translatomics)
Quality Control and Adapter Removal: Raw sequencing data was processed using Trim Galore to perform quality control and remove adapter sequences, low-quality bases, and adapter sequences. The quality control parameters were set with a quality score threshold of 20 (Phred+33), requiring at least 3 bases to perfectly match the adapter sequence, a minimum retained sequence length of 50 bp, and allowing a 10% error rate.
Alignment to Reference Genome: After quality control, cleaned reads were aligned to the reference genome (mouse genome mm39) using Hisat2. The alignment process was performed using 8 threads for parallel computation, generating alignment reports and SAM files.
SAM to BAM Conversion and Sorting: The aligned SAM files were converted to BAM format using Samtools and were then sorted and indexed for further analysis.
Gene Expression Quantification: Gene expression was quantified using featureCounts, with exons as the counting unit. Overlapping and multi-mapping reads were allowed. To accurately calculate gene lengths, the latest version of the mouse genome annotation (GRCm39) was used, and exon annotation information was downloaded from the Gencode database (Mus_musculus.GRCm39.113.gtf.gz).
Exon Processing and Gene Length Calculation: Exon information from the gene annotation was extracted, including chromosome, start position, end position, gene ID, and gene name. These exonic regions were converted into GRanges objects using the GenomicRanges package. To remove overlapping or adjacent exonic regions within the same gene, exons were grouped by gene ID, and the reduce function was applied to merge overlapping regions. For each gene, the total exon length was calculated by merging all exon lengths.Gene Name Consistency: If multiple gene names were associated with a single gene, the most frequent name was retained to ensure consistency in gene naming.Export            Gene Length Information: Finally, the merged gene length information was exported as a CSV file for subsequent analysis.
Assembly: GRCm39
Supplementary files format and content: csv files include FPKM or TPM for each sample

molecule: other


title: WT-Total-B


title: WT-Ly108_neg-C


title: Normal diet,Transcriptomics,MII-1

description: Library name: ND-MII-RNA-1


title: 1_WT_18mths

description:
Library name: Sample 1
wild-type littermate control for RpgrORFd5


title: WT-Ly108_neg-A


title: WT-Total-A


title: Normal diet,Transcriptomics,GV-2

description: Library name: ND-GV-RNA-2


title: High-fat diet,Translatomics,GV-3

description: Library name: HFD-GV-Ribo-3


title: WT-Naive-B

source_name: Naive

value: Naive


title: WT-Naive-C


title: High-fat diet,Translatomics,MII-1

description: Library name: HFD-MII-Ribo-1


title: High-fat diet,Translatomics,GV-2

description: Library name: HFD-GV-Ribo-2


title: Normal diet,Translatomics,GV-3

description: Library name: ND-GV-Ribo-3


title: WT-Ly108_pos-A


title: High-fat diet,Translatomics,GV-1

description: Library name: HFD-GV-Ribo-1


title: Normal diet,Translatomics,MII-3

description: Library name: ND-MII-Ribo-3


title: WT-Ly108_pos-C


title: TET2KO-Total-A


title: TET2KO-Total-B


title: TET2KO-Total-C


title: Normal diet,Translatomics,MII-1

description: Library name: ND-MII-Ribo-1


title: Normal diet,Translatomics,MII-2

description: Library name: ND-MII-Ribo-2


title: Normal diet,Translatomics,GV-2

description: Library name: ND-GV-Ribo-2


title: WT-Naive-A


title: High-fat diet,Translatomics,MII-2

description: Library name: HFD-MII-Ribo-2


title: TET2KO-Ly108_neg-A


title: TET2KO-Naive-A


title: TET2KO-Naive-B


title: Normal diet,Translatomics,GV-1

description: Library name: ND-GV-Ribo-1


title: TET2KO-Naive-C


title: TET2KO-Ly108_pos-C


title: FW75109

city: CLICHY

first: Camille

last: PIGNOLET

address: 100 Bd du Général Leclerc

department: CRI U1149

institute: INSERM

description: Library name: FW75109

data_processing:
Reads were aligned using STAR and gene expression counts obtained with FeatureCount
Assembly: GRCm38.75
Supplementary files format and content: tab_delimited text file includes raw counts for each Sample

source_name: cd4 T cells

extract_protocol:
Five µm-thick sections were cut from FFPE blocks. Total RNAs were further isolated using the Qiagen FFPE RNA extraction kit (RNeasy FFPE kit, Qiagen)
Gene expression was analysed using SMARTer Stranded Total RNA-Seq Kit.

value: cd4 T cells

value: wildtype


title: SlowBKK, control, body, rep3

city: Planegg-Martinsried

first: Vera

middle: Miyase

last: Yilmaz Bachmaier

state: Bavaria

address: Grosshaderner St. 2

department: Evolutionary Biology

country: Germany

institute: LMU Munich

description:
pooled 4 iso-female lines, 10 individuals
S_RT_W_3

data_processing:
quality control: FastQC (version 0.11.9)
mapping: NextGenMap (version 0.5.2)
Assembly: dana_r1.05_FB2016_01
Supplementary files format and content: tab-delimited text file includes counts for each sample

organism: Drosophila ananassae

source_name: body

growth_protocol: Fly lines were kept on standard corn-molasses medium. The day after eclosure, treatment started.

extract_protocol:
Total RNA was extracted from the body samples using MasterPureTM RNA Purification Kit (Epicentre), from hindgut and malpighian tubules using RNeasy Mini Kit (Qiagen).
The libraries were constructed by Novogene using poly-A enrichment method.

treatment_protocol: The cold acclimation treatment started the day after eclosure (from pupa). Adult flies were kept at 10˚C for 4 days (96 hours), which was followed by 90-minute recovery. The control samples were kept at rearing temperature (22 ˚C ±1˚C) for 4 days.

value: body

tag: population

value: Bangkok

tag: phenotype

value: sensitive

value: male

value: control


title: FK75113

description: Library name: FK75113


title: FW75107

description: Library name: FW75107


title: FW75106

description: Library name: FW75106


title: FW33335

description: Library name: FW33335


title: SlowBKK, control, body, rep4

description:
pooled 4 iso-female lines, 10 individuals
S_RT_W_4


title: FK75112

description: Library name: FK75112


title: TET2KO-Ly108_pos-A


title: FK75111

description: Library name: FK75111


title: SlowBKK, control, body, rep2

description:
pooled 4 iso-female lines, 10 individuals
S_RT_W_2


title: SlowBKK, control, malpighiantubule, rep5

description:
pooled 4 iso-female lines, 60 individuals
S_RT_Mt_5

source_name: malpighian tubule

value: malpighian tubule


title: TET2_KO_Negative_C_S24

description:
Mouse_LCMV_Tcell_RNA-Seq_ReadCounts_MGI.tsv
Mouse_LCMV_Tcell_RNA-Seq_TPM_MGI.tsv


title: FW75262

description: Library name: FW75262


title: DR_MG_2022 FBC library - Mammary Gland- Hash Reads for all samples

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description:
Library name: DR_MG_2022_FBC
DR_MG_2022_barcodes.tsv.gz (lined to the DR_MG_2022 GEX library sample records)

data_processing:
The demultiplexing, barcode process and GEX/ GTO counts were generated using Cellranger software v6.1.0.
Assembly: mm10
Supplementary files format and content: Cellranger output files: DR_MG_2021_GEX_barcodes.tsv, DR_MG_2021_GEX_features.tsv, DR_MG_2021_GEX_matrix.mtx - Barcodes, features and counts for GEX.
Supplementary files format and content: Cellranger output files: DR_MG_2021_FBC_barcodes.tsv, DR_MG_2021_FBC_features.tsv, DR_MG_2021_FBC_matrix.mtx - Barcodes, features and counts for HTO.
Supplementary files format and content: Cellranger output files: DR_MG_2022_barcodes.tsv, DR_MG_2022_GEX_features.tsv, DR_MG_2022_GEX_matrix.mtx - Barcodes, features and counts for GEX.
Supplementary files format and content: Cellranger output files: DR_MG_2022_barcodes.tsv, DR_MG_2022_FBC_features.tsv, DR_MG_2022_FBC_matrix.mtx - Barcodes, features and counts for HTO.
Library strategy: CITE-seq

molecule: protein

source_name: Mammary gland

extract_protocol:
Mammary glands were isolated in 2% FBS DMEM, minced, treated with collagenase type 2 and digested at 37 degrees in a shaking water bath. The small intestines and colons were collected in 2% FBS RPMI and treated with 1mM DTT and 20mM EDTA at 37 degrees for 15 mins then minced and dissociated in collagenase type 2 with constant stirring at 37 for 40 minutes. Spleen and thymus were collected in 2% FBS RPMI and mechanically disrupted. All samples were filtered and washed in 2% FBS DMEM. All organs, other than spleen, underwent red blood cell lysis and additional washing to obtain a single cell suspension.
Libraries were prepared according to the 10x Genomics 3'v3.1 protocol for GEX and FBC

value: Mammary gland

value: CD45+ cells


title: FK75108

description: Library name: FK75108


title: TET2KO-Ly108_neg-C


title: DR_MG_2022 GEX library - Mammary Gland- Nulliparous; Pregnant; Lactation; Involution;  Regression; Balb; GF

description: Library name: DR_MG_2022_GEX


title: SlowBKK, control, malpighiantubule, rep2

description:
pooled 4 iso-female lines, 60 individuals
S_RT_Mt_2


title: TET2_KO_Total_C_S22


title: DR_MG_2021 FBC library - Mammary Gland- Hash reads for all samples

description: Library name: DR_MG_2021_FBC


title: SlowBKK, control, malpighiantubule, rep1

description:
pooled 4 iso-female lines, 60 individuals
S_RT_Mt_1


title: TET2_KO_Naive_C_S21


title: SlowBKK, control, hindgut, rep5

description:
pooled 4 iso-female lines, 60 individuals
S_RT_Hg_5

source_name: hindgut

value: hindgut


title: FK75264

description: Library name: FK75264


title: DR_MG_2021 GEX library - Mammary Gland- Nulliparous; Pregnant; Lactation; Involution

description: Library name: DR_MG_2021_GEX


title: WT Liver, MASLD, 16weeks, rep4

city: Eonyang-eup, Ulju-gun

first: Bukyung

last: Baik

state: Ulsan

department: Department of Biological Science

country: South Korea

institute: Ulsan National Institute of Science and Technology

data_processing:
Read trimming and quality filtering were performed using Cutadapt (version 4.2).
Trimmed fastq files were aligned to the mm39 mouse genome using STAR (version 2.7.10a) software.
Read count extraction was performed using GeneCounts options to quantMode parameter of STAR (version 2.7.10a) software.
Raw read counts of each sample are combined to generate a raw count matrix.
Assembly: mm39
Supplementary files format and content: Tab-delimited text files include gene read counts for each sample

source_name: Liver

extract_protocol:
Total mRNAs were isolated using TRIzol reagent purchased from Thermo Fisher Scientific. Reverse-transcription of the RNA (total RNA 1ug) was performed with ABI Reverse Transcription Kit
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Liver

value: Wild-type

value: Diet:High fat-high fructose