title: CNS P60 #2

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

data_processing:
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:3 TRAILING:10 MINLEN:25
single-end reads were aligned to the mm10 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05 i--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16  --quantMode GeneCounts
Assembly: mm10
Supplementary files format and content: tab-delimited txt file including read count per gene for each sample

source_name: CNS

extract_protocol:
For tissue dissection at E9.5, the embryonic heads were cut behind the 4th ventricle and above the forelegs and excessive non-neuroectodermal tissue was removed. At E14.5, brains were dissected and the meninges were removed. Directly after dissection, tissues were snap-frozen in liquid nitrogen. Adult brains (P60) were harvested after transcardial perfusion with 1xPBS. Mice were deeply anaesthetized with a 200 μl intraperitoneal injection of Ketamine (10 %, Essex Tierarznei) and Xylazin ((Rompun) 2 %, Bayer) (100 mg/kg Ketamine and 10 mg/kg Xylazin). Mice were transcardially perfused with 10 ml ice-cold PBS via the left ventricle until the liver was decolourized. Afterwards, the CNS was dissected from the skull and snap frozen in liquid nitrogen.
RNA extraction, library preparation and RNAseq were performed at the Genomics Core Facility “KFB - Center of Excellence for Fluorescent Bioanalytics” (University of Regensburg, Regensburg, Germany; www.kfb-regensburg.de). Total RNA was extracted from dissected brain tissue at E9.5, E14.5 and P60 stabilized in RLT buffer according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Micro Kit (QIAGEN, Hilden, Germany). In brief, cells were stored in buffer RLT containing 1% beta-mercaptoethanol and shipped on dry ice. After thawing, the samples were homogenized by vortexing for 1 min. Next, one volume of 70 % ethanol was added and the samples were applied to RNeasy MinElute spin columns, followed by an on-column DNase digestion and several wash steps. Finally, total RNA was eluted in 14 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA). The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from approximately 1 ng total-RNA. Double stranded cDNA was amplified by LD PCR (11 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). Thereby 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step, 1:5 dilutions of the unique dual indexing (i7 and I5) adapters were used. The libraries were quantified using the KAPA Library Quantification Kit - Illumina/ABI Prism User Guide (Roche Sequencing Solutions, Inc., Pleasanton, CA, USA). Equimolar amounts of each library were sequenced on an Illumina NextSeq 2000 instrument controlled by the NextSeq 2000 Control Software (NCS) v1.4.0.39521, using one 50 cycles P3 Flow Cell with the dual index, single-read (SR) run parameters. Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.9.2. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software.

value: CNS

tag: developmental stage

value: whole tissue

tag: strain


title: CNS E14.5 #3

status: Public on Aug 11 2025

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: treatment


title: 451LuR 18 h PUFA/Fe3+ 3

city: Leuven

first: Sahar

last: Motamedi

address: Herestraat 49, Nieuwstraat

department: Oncology

country: Belgium

institute: KU Leuven

description: Library name: Sample24

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads by CASAVA base recognition (Base Calling).
QC control: error rate (Phred score), GC content distribution, removing reads with adaptor contamination and with MAPQ<10  and with >5nt/100nt mismatches
Assembly: Assembly: mm10 using HISAT2
Supplementary files format and content: The files consists of the FPKM reads for all analyzed genes.

organism: Homo sapiens

source_name: Melanoma

extract_protocol:
RNA was isolated using the PureLink™ RNA Mini Kit (12183018A, Invitrogen).
standard library, poly-A enrichment

value: Melanoma

tag: cell line

value: 451Lu R


title: Normal dermal cells, with AA, rep 3

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

country: United Kingdom

institute: King's College London

description:
Library name: NDF_AA_3
column name in raw_FPKM_TPM_readcounts_allsamples.xlsx, GeneMappingSummary.xls, GenomeMappingSummary.xls : NDF_AA_3

data_processing:
The SOAPnuke software was used to filter out low-quality reads, with remaining clean reads aligned to the reference human genome (Homo Sapiens GRCh37) and using HISAT2 and Bowtie2 software. Transcripts per million (TPM) values were used for all analyses. The R script used to generate the figures in this manuscript is available as a Supplementary File provided with the original publication.
Assembly: Homo_sapiens.GRCh37
Supplementary files format and content: Excel file provides Raw FPKM, TPM and Read counts for all samples as separate tabs
Supplementary files format and content: Excel file provides genome mapping statistics for all samples
Supplementary files format and content: Excel file provides gene mapping statistics for all samples

source_name: Normal skin

extract_protocol:
Normal and keloid dermal fibroblasts (P8-9) were thawed and seeded in triplicate at a density of 26,300 cells/cm² (near confluency), and left overnight to adhere and spread. Cells were cultured in complete medium (high-glucose Dulbecco's Modified Eagle Medium (DMEM) with GlutaMAX and pyruvate (Gibco, #31966021) + 10% FBS and 1% penicillin/streptomycin (Sigma-Aldrich, #P0781)) with or without supplementation with 50μg/mL ascorbic acid for 5 days, with media changes every other day. After 5 days, triplicate wells were combined into 350μL RLT buffer (Qiagen, #74104), supplemented with 1% beta-mercaptoethanol (PanReac AppliChem, #A1108.0100) before being frozen at -80°C until downstream analysis. This experiment was repeated on serial passages, P8 & P9, which were used as technical replicates (N=4).   RNA was purified using the RNeasy Mini kit (Qiagen, #74104) following manufacturer’s instructions, and quantified using a Qubit high sensitivity RNA assay (Invitrogen, #Q32852). RNA quality was ascertained by Bioanalyzer 2100 (Agilent). RNA Integrity Number (RIN) values above 9 were used.
RNA from P8-9 normal and keloid fibroblasts cultured with and without ascorbic acid were shipped to BGI Genomics Co. Ltd., Hong Kong for library preparation and sequencing using the BGISEQ platform.

treatment_protocol: Experiment was conducted in 4 technical batches (rep 1-4). We processed all samples in the same library preparation and sequencing run.

value: Normal skin

tag: passage

value: Passage 9

value: With AA


title: CNS E14.5 #2


title: IP_DP1_FLAG_rep1

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

library_source: genomic

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a 16 h light/8 h dark photoperiod at 22°C for 12 d.

extract_protocol:
Arabidopsis seedlings were cross-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with antibody.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing).

value: seedlings

tag: genotype

value: wild type

tag: chip antibody

value: SIGMA, F1804


title: Keloid dermal cells, with AA, rep 3

description:
Library name: KDF_AA_3
column name in raw_FPKM_TPM_readcounts_allsamples.xlsx, GeneMappingSummary.xls, GenomeMappingSummary.xls : KDF_AA_3

source_name: Keloid scar

value: Keloid scar


title: BMDM treated with vehicle 2

city: Würzburg

first: Clement

last: Cochain

address: Josef Schneider Str.2 Haus D16

institute: University Hospital Würzburg

data_processing:
Demultiplexed FASTQ files were generated with bcl-convert v.4.0.3 (Illumina).
To assure high sequence quality, Illumina reads were quality- and adapter-trimmed via Cutadapt version 2.5 using a cutoff Phred score of 20 in NextSeq mode, and reads without any remaining bases were discarded (parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC).
Processed reads were subsequently mapped to the mouse genome (GCF_000001635.27/GRCm39) using STAR v2.7.2b with default parameters but including transcript annotations from RefSeq annotation version 109 for GRCm39.
This annotation was also used to generate read counts on exon level summarized for each gene via featureCounts v1.6.4 from the Subread package
Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (parameters: -s 2 -t exon -M -O --fraction).
Assembly: mm10
Supplementary files format and content: csv;raw read counts

source_name: bone marrow derived macrophage

growth_protocol: To obtain bone marrow derived macrophages, total bone marrow cells were obtained from the tibia and femur of C57BL6/J mice and cultured for 7 days (10ml at 2 million cells/ml in 10cm cell culture dishes) in RPMI containing 100 U/ml penicillin and streptomycin, 50µM of β-Mercaptoethanol, 10% fetal calf serum and 15% L929-cell conditioned medium as a source of M-CSF. Medium was refreshed on day 3 and 6 of the culture, and macrophages were detached with Accutase and harvested on Day 7. 400,000 macrophages were plated in wells of a 12-well plate and left to attach overnight in complete medium. Macrophages were then incubated in starvation medium (RPMI supplemented with 0.5%FCS) for 4 hours before initating treatment.

extract_protocol:
RNA extraction was performed with the Nucleo Spin RNA extraction kit (Macherey-Nagel, 740955.50) following the manufacturer’s instructions.
Libraries were prepared using TruSeq Stranded mRNA library prep kits (Illumina) according to the manufacturer's instructions

treatment_protocol: Macrophages were treated for 4 hours with vehicle (PBS), thrombin alone (0.01 U/mL), resting platelets, or thrombin-activated platelets (0.01 U/mL thrombin). Platelets had previously been purified from the blood of C57BL6/J mice.

value: bone marrow derived macrophage

value: Vehicle (PBS)


title: Keloid dermal cells, with AA, rep 2

description:
Library name: KDF_AA_2
column name in raw_FPKM_TPM_readcounts_allsamples.xlsx, GeneMappingSummary.xls, GenomeMappingSummary.xls : KDF_AA_2

value: Passage 8


title: Input_DP1_FLAG


title: 451LuR 18 h PUFA/Fe3+ 2

description: Library name: Sample23


title: CNS P60 #3


title: 451Lu 18 h PUFA/Fe3+ 3

description: Library name: Sample18


title: CNS E9.5 #3


title: Normal dermal cells, with AA, rep 2

description:
Library name: NDF_AA_2
column name in raw_FPKM_TPM_readcounts_allsamples.xlsx, GeneMappingSummary.xls, GenomeMappingSummary.xls : NDF_AA_2


title: CNS E9.5 #2


title: CNS P60 #1


title: 451LuR 18 h PUFA/Fe3+ 1

description: Library name: Sample22


title: IP_GTB1_FLAG_rep1


title: 451Lu 18 h PUFA/Fe3+ 1

description: Library name: Sample16


title: Normal dermal cells, with AA, rep 1

description:
Library name: NDF_AA_1
column name in raw_FPKM_TPM_readcounts_allsamples.xlsx, GeneMappingSummary.xls, GenomeMappingSummary.xls : NDF_AA_1


title: 451LuR 18 hCTRL3

description: Library name: Sample21


title: Input_1967_FLAG


title: IP_DP1_FLAG_rep2


title: Normal dermal cells, control without AA, rep 3

description:
Library name: NDF_C_3
column name in raw_FPKM_TPM_readcounts_allsamples.xlsx, GeneMappingSummary.xls, GenomeMappingSummary.xls : NDF_C_3

value: Control, without AA


title: Input_GTB1_FLAG


title: 451Lu 18 h CTRL2

description: Library name: Sample14


title: Keloid dermal cells, with AA, rep 4

description:
Library name: KDF_AA_4
column name in raw_FPKM_TPM_readcounts_allsamples.xlsx, GeneMappingSummary.xls, GenomeMappingSummary.xls : KDF_AA_4


title: CNS E14.5 #1


title: 451LuR 18 h CTRL2

description: Library name: Sample20


title: 451LuR 18 h CTRL1

description: Library name: Sample19


title: HG_C

city: Guangzhou

first: Junbiao

last: Zhang

state: Guangdong

address: No. 183, Zhongshan Avenue West

department: Ophthalmology

institute: The Third Affiliated Hospital of Southern Medical University

description:
Library name: SAMPLES 8
37.5 mM d-glucose for high glucose,48h,sample8

data_processing:
RNA was extracted using the Trizol method，500ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit  following manufacturer's protocols.
Homo_sapiens GRCh38.112
Raw data were processed using fastp v0.20.1 for adapter trimming and removal of low-quality sequences.
CleanData were aligned to Homo sapiens GRCh38.112,using HISAT2 (version 2.2.1)
Assembly: Homo_sapiens GRCh38.112
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

source_name: cell line

growth_protocol: ARPE-19l cells were maintained in DMEM supplemented with 10%fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

treatment_protocol: Cells were cultured for 48 hours in either control medium containing 5.5 mM D-glucose and 32 mM mannitol, or in high-glucose (HG) medium containing 37.5 mM D-glucose, followed by RNA extraction for sequencing.

value: cell line

value: Retinal pigment epithelial cell line

value: 37.5mM High glucose


title: Keloid dermal cells, control without AA, rep 3

description:
Library name: KDF_C_3
column name in raw_FPKM_TPM_readcounts_allsamples.xlsx, GeneMappingSummary.xls, GenomeMappingSummary.xls : KDF_C_3


title: Keloid dermal cells, with AA, rep 1

description:
Library name: KDF_AA_1
column name in raw_FPKM_TPM_readcounts_allsamples.xlsx, GeneMappingSummary.xls, GenomeMappingSummary.xls : KDF_AA_1


title: IP_GTE1_FLAG_rep2


title: M238 18 h PUFA/Fe3+ 2

description: Library name: Sample11


title: IP_GTB1_FLAG_rep2


title: Keloid dermal cells, control without AA, rep 2

description:
Library name: KDF_C_2
column name in raw_FPKM_TPM_readcounts_allsamples.xlsx, GeneMappingSummary.xls, GenomeMappingSummary.xls : KDF_C_2


title: Normal dermal cells, control without AA, rep 4

description:
Library name: NDF_C_4
column name in raw_FPKM_TPM_readcounts_allsamples.xlsx, GeneMappingSummary.xls, GenomeMappingSummary.xls : NDF_C_4


title: 451Lu 18 h PUFA/Fe3+ 2

description: Library name: Sample17


title: CNS E9.5 #1

value: CNS

value: whole tissue


title: HG_E

description:
Library name: SAMPLES 10
37.5 mM d-glucose for high glucose,48h,sample10

extract_protocol:
RNA was extracted using the Trizol method，500ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit  following manufacturer's protocols.


title: Input_GTE1_FLAG


title: 451Lu 18 hCTRL3

description: Library name: Sample15

value: Melanoma


title: Normal dermal cells, control without AA, rep 2

description:
Library name: NDF_C_2
column name in raw_FPKM_TPM_readcounts_allsamples.xlsx, GeneMappingSummary.xls, GenomeMappingSummary.xls : NDF_C_2

value: Normal skin


title: IP_CP2_FLAG_rep2


title: IP_GTE1_FLAG_rep1


title: Keloid dermal cells, control without AA, rep 1

description:
Library name: KDF_C_1
column name in raw_FPKM_TPM_readcounts_allsamples.xlsx, GeneMappingSummary.xls, GenomeMappingSummary.xls : KDF_C_1


title: HG_D

description:
Library name: SAMPLES 9
37.5 mM d-glucose for high glucose,48h,sample9


title: 451Lu 18 h CTRL1

description: Library name: Sample13


title: HG_B

description:
Library name: SAMPLES 7
37.5 mM d-glucose for high glucose,48h,sample7


title: IP_CP2_FLAG_rep1


title: IP_TRB4_FLAG_rep2


title: Input_CP2_FLAG


title: M238 18 h PUFA/Fe3+ 3

description: Library name: Sample12


title: HG_A

description:
Library name: SAMPLES 6
37.5 mM d-glucose for high glucose,48h,sample6


title: Normal dermal cells, control without AA, rep 1

description:
Library name: NDF_C_1
column name in raw_FPKM_TPM_readcounts_allsamples.xlsx, GeneMappingSummary.xls, GenomeMappingSummary.xls : NDF_C_1


title: Stem_PEG_180min_replicate2

city: Jinan

first: xiaoge

last: wang

state: Shandong province

address: 23788 Industrial North Road Avenue

department: Institute of Industrial Crops

institute: Shandong Academy of Agricultural  sciences

data_processing:
Illumina Casava2.19 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TM-1 UTX 2.1 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> } [-S <hit>]
Read count extraction and normalization were performed using featureCounts v1.5.0-p3 (featureCounts T 4 -F GTF -t exon -g gene_id -s 0 -Q 10 -C -B -p)
Assembly: TM-1 Genomics UTX v2.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

organism: Gossypium hirsutum

source_name: stem

growth_protocol: Cotton variety Hengmian HD008 was planted in the sterilized sand and cultivated at 25℃ with a 16 h/8 h light/dark photoperiod.

extract_protocol:
Total RNA was extracted using EASYspin Plus Complex Plant RNA Kit and 1μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer‘s protocols.

treatment_protocol: 10 % PEG 6000 was used for drought stree in three leaf stage of cotton seedlings

value: stem

tag: cultivar

value: Hengmian HD008

value: PEG treatment

tag: time

value: 180 min


title: M238 18 hCTRL3

description: Library name: Sample9


title: MG5

description:
Library name: SAMPLES 5
5.5 mM d-glucose and 32 mM mannitol concentration for control,48h,sample5

value: Normal glucose


title: MG2

description:
Library name: SAMPLES 2
5.5 mM d-glucose and 32 mM mannitol concentration for control,48h,sample2


title: M238 18 h PUFA/Fe3+ 1

description: Library name: Sample10


title: MG4

description:
Library name: SAMPLES 4
5.5 mM d-glucose and 32 mM mannitol concentration for control,48h,sample4


title: Keloid dermal cells, control without AA, rep 4

description:
Library name: KDF_C_4
column name in raw_FPKM_TPM_readcounts_allsamples.xlsx, GeneMappingSummary.xls, GenomeMappingSummary.xls : KDF_C_4

value: Keloid scar

value: Passage 9


title: M257 18 h PUFA/Fe3+ 2

description: Library name: Sample5


title: Stem_PEG_180min_replicate3


title: Stem_PEG_180min_replicate1


title: Stem_PEG_60min_replicate3

value: 60 min


title: MG1

description:
Library name: SAMPLES 1
5.5 mM d-glucose and 32 mM mannitol concentration for control,48h,sample1


title: IP_TRB4_FLAG_rep1

value: seedlings

value: wild type

value: SIGMA, F1804


title: M257 18 h PUFA/Fe3+ 1

description: Library name: Sample4


title: HeLa cells, shPOLDIP2, rep3

city: Yokohama

first: Chayanin

last: Wuttinontananchai

state: Kanagawa

address: 4259 Nagatsutacho, Midori Ward

country: Japan

institute: Institute of science tokyo

description: Library name: POLDIP2KD_3

data_processing:
A total of 212 million 150 bp paired-end reads were trimmed by using cutadapt and mapped to the Homo sapiens genome (hg38 by using HISAT2, version 2.0.2).
The genome and the transcript alignments were used to derive gene counts based on human Ensembl gene IDs by using htseq-count.
Differential expression analysis (DEA) was performed on the raw gene counts using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw and normalized counts for each sample

source_name: HeLa

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

extract_protocol:
Total RNA was extracted using Sepasol‐RNA I Super G (Nacalai Tesque) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina NR605 following manufacturer's protocols.

value: HeLa

value: cervical cancer cells

value: POLDIP2 knockdown


title: M238 18 h CTRL1

description: Library name: Sample7


title: HeLa cells, shPOLDIP2, rep2

description: Library name: POLDIP2KD_2


title: Input_TRB4_FLAG


title: IP_GTA1_FLAG_rep2


title: M257 18 h PUFA/Fe3+ 3

description: Library name: Sample6


title: Stem_PEG_60min_replicate1


title: IP_GTA1_FLAG_rep1


title: Stem_PEG_60min_replicate2


title: MG3

description:
Library name: SAMPLES 3
5.5 mM d-glucose and 32 mM mannitol concentration for control,48h,sample3

value: cell line

value: Retinal pigment epithelial cell line


title: M238 18 h CTRL2

description: Library name: Sample8

value: Melanoma


title: Input_GTA1_FLAG


title: Stem_PEG_30min_replicate2

value: stem

value: 30 min


title: Stem_PEG_30min_replicate3

value: Hengmian HD008

value: PEG treatment


title: M257 18 hCTRL3

description: Library name: Sample3


title: HeLa cells, shControl, rep3

description: Library name: CTRL_3

value: WT


title: IP_ZDP1_FLAG_rep2


title: HeLa cells, shPOLDIP2, rep1

description: Library name: POLDIP2KD_1


title: M257 18 h CTRL2

description: Library name: Sample2


title: IP_ZDP1_FLAG_rep1


title: M257 18 h CTRL1

description: Library name: Sample1


title: Stem_PEG_30min_replicate1


title: HeLa cells, shControl, rep2

description: Library name: CTRL_2


title: Stem_PEG_10min_replicate3

value: 10 min


title: Stem_PEG_10min_replicate2


title: ahp4 shoot ck treat sample 2

city: LOUGHBOROUGH

first: Anthony

last: Bishopp

state: Leicestershire

address: College Road

institute: University of Nottingham

data_processing:
Raw reads were mapped to genome
A cut-off value of < 1 was set to filter out the very lowly expressed genes.
Gene values that made the cut-off were expressed as the logarithm of 1.5-fold change (log2FC), and the threshold to define DE genes was set to 0.05 (p-value).
Assembly: Arabidopsis TAIR 10
Supplementary files format and content: Excel table of FPKM

molecule: polyA RNA

source_name: shoot

growth_protocol: Arabidopsis thaliana seeds were grown on half-strength Murashige and Skoog basal medium (½MS, 500mg/L MES, pH 7.8) supplemented with 0.8% w/v agar unless otherwise specified. Growth room conditions were set to a temperature of 22 0C with 16 16-hour light/ 8 hours cycle. Seeds were sterilised by submersion in 70% ethanol and 0.05% triton solution for 2 min, then washed with 95% ethanol and left to dry on filter papers before sowing on agar plates. Plates containing sterilised seed were stratified at 4 0C in the dark for at least 48 hours (and no more than seven days) before transfer in the growth rooms where they were grown vertically.

extract_protocol:
For expression studies with qRT-PCR, RNA extraction was done using the Qiagen Plant RNeasy Kit.
RNA integrity was assessed using the RNA Nano 6000 Assay Kit on a Bioanalyzer 2100 (Agilent Technologies, CA, USA). Total RNA was used as input. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, adaptors with hairpin loop structure were ligated to prepare for hybridization. In order to preferentially select cDNA fragments of 370~420 bp in length, library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to manufacturer’s instructions. After cluster generation, library preparations were sequenced on an Illumina Novaseq platform generating 150 bp paired-end reads

treatment_protocol: Seven-day-old seedlings were germinated and grown on ½ MS media for transcriptomics analysis. On the seventh day, the plants were removed from the plates and placed in ½ MS liquid solution for 2 hrs with either 100 nM 6-Benzylaminopurine (BA) diluted in 0.1% DMSO or 0.1% DMSO as the mock treatment.

value: shoot

value: 100 nM BA 2h


title: ahp4 shoot ck treat sample 1


title: Lunet_neoJFH_WT_SMI

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

description: Library name: Lunet_neoJFH_WT_SMI

data_processing:
Paired-end sequencing reads were adapter- and quality trimmed by cutadapt (v1.18) in two runs according to the ENCODE eCLIP-seq processing pipeline v. 2.2 (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016)). In the first run 5' and 3' adapters were clipped from both reads using the parameters: --match-read-wildcards --times 1 -e 0.1 -O 1 --quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT
In the second run 3' adapters of read 2 were clipped to control for double ligation events. Cutadapt clipping was performed with the parameters:  --match-read-wildcards --times 1 -e 0.1 -O 5 --quality-cutoff 6 -m 18 -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT
RNA-seq reads were aligned to the concatenated genomes of hg38 (ensembl) and Hepatitis C virus genome (pFK_i389neoNS3-3prime_JFH_dg) using STAR version 2.7.10a with parameters --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --outFilterType Normal --alignSoftClipAtReferenceEnds No --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNoverLmax 0.04 --scoreDelOpen -1 --alignIntronMin 20 --alignIntronMax 3000 --alignMatesGapMax 3000 --alignEndsType EndToEnd
Protein binding regions were predicted by using MACS2. For reads mapped to the positive strand of the replicon the parameters: --d-min 25 --scale-to small --nomodel --extsize 25 --max-gap 1 --shift 20 were applied and for reads mapping to the negative strand of the replicon the parameters --d-min 25 --scale-to small --nomodel --shift -10 --extsize 100 --max-gap 1 --min-length 5 were applied. The resulting peaks in wt and D1467G were combined and overlapping intervals were merged by extending to the respective outermost interval boundary. The identified and merged MACS2 peaks were further filtered by applying a one-sided Fisher's exact test. Statistically significant enrichment was determined by calculating the odds-ratio of mapped reads within each peak against all remaining mapped reads for each organism between IP and SMI. The Benjamini-Yekutieli procedure was applied to correct for multiple testing.
Assembly: hg38
Supplementary files format and content: bed files, containing statistically significant peaks in IP over SMI filtered only by adjusted p value < 0.05 and filtered by adjusted p value < 0.05 and log2 fold change greater than two

organism:
Homo sapiens
Hepacivirus hominis

extract_protocol:
Immunoprecipitation and cDNA library preparation was performed as described in the eCLIP method (PMID: 27018577), including the following modifications: immunoprecipitates were washed two times in 1 ml CLIP lysis buffer and two times in IP wash buffer (50 mM Tris-HCl pH 7.4, 300 mM NaCl, 1 mM EDTA, 1% [vol/vol] NP-40, 0.5% sodium deoxycholate, 0.25 mM TCEP), followed by two washes in 50 mM Tris-HCl pH 7.4, 1 mM EDTA, and 0.5% (vol/vol) NP-40. All other steps were carried out as described in the eCLIP method.
eCLIP-seq (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016))

value: Huh7-Lunet neoJFH1 wt

value: hepatoma cell line

value: HCV gt2a


title: Lunet_neoJFH_D1467G_IP

description: Library name: Lunet_neoJFH_D1467G_IP

value: Huh7-Lunet neoJFH1 D1467G


title: Lunet_neoJFH_WT_IP

description: Library name: Lunet_neoJFH_WT_IP


title: Input_ZDP1_FLAG

value: seedlings

value: wild type


title: ahp4 shoot ck treat sample 3


title: Stem_CK_replicate2

value: CK

value: 0 min


title: ahp4 root ck treat sample 3

source_name: root

value: root


title: Stem_PEG_10min_replicate1

value: stem


title: Stem_CK_replicate3


title: Root_PEG_180min_replicate2

value: 180 min


title: HeLa cells, shControl, rep1

description: Library name: CTRL_1

value: HeLa

value: cervical cancer cells


title: ahp4 Shoot mock sample 3

value: mock


title: ap4 root ck treat sample 2


title: Keloid dermal cells, passage-4

description:
Library name: KDF4
10X Genomics
processed.Robj
sct_v4.Robj
sct_v4_stromal.Robj
P4_only.Robj

library_source: transcriptomic single cell

data_processing:
The resulting fastq files were aligned to human (Homo.sapiens.GRCh38) in Google Colabs using kb-bustools (Melsted et al., 2021), with kallisto version 0.46.2 and bustools version 0.40.0. Count matrices were then imported into R and further analysed in Seurat (version 4.4). The R script used to generate the figures in this manuscript is available as a Supplementary File provided with the original publication.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: kb bustools unfiltered counts & Seurat objects

extract_protocol:
Cells were extracted from tissue as follows: Each tissue sample was washed successively in 10% w/w iodinated povidone (0.025g/10mL, Ecolab, #3030440), 70% ethanol (Sigma Aldrich, #32221) and twice in 0.05mg/mL gentamycin solution (Sigma Aldrich, #G1397), before being floated dermis side down in 10mg/mL dispase II solution (Gibco, #17105041) overnight at 4C. The epidermis was peeled and disposed of. The remaining dermis was dissociated using a Human Whole Skin Dissociation kit (Miltenyi Biotec, #130-101-540) as per manufacturer’s instructions. The resulting cell suspension (passage-zero) was frozen at -80C in complete media with 40% FBS and 10% DMSO (Sigma Aldrich, #D2650) before being moved to vapour-phase nitrogen for long term storage. Cells were thawed immediately prior to processing for sequencing.  To gain passage-4 cells, an aliquot of passage-zero cells were thawed and cultured in 2D adherent cultures in complete media (high-glucose Dulbecco's Modified Eagle Medium (DMEM) with GlutaMAX and pyruvate (Gibco, #31966021) supplemented with 10% fetal bovine serum (FBS; Cytiva, #SV30160.03) and 1% penicillin/streptomycin (Sigma-Aldrich, #P0781) until 80% confluent. Cells were detached each subpassage by incubation with trypsin-EDTA solution (Sigma-Aldrich, #T4174) for 5 mins at 37C. Cells were subsequently replated and allowed to further culture until the 4th passage, at which point the cells were subpassaged and collected as a single cell suspension.  All cell suspensions were purified for live cells using MACS Dead Cell removal kit (130-090-101) immediately prior to processing for sequencing.
Library preparation (Chromium 10X  single cell 3’ version 3)  proceeded following manufacturer's instructions and was carried out by specialists in the King's Genomics Centre  (Waterloo) at King’s College London. Sequencing was performed on an Illumina HiSeq system.

treatment_protocol: Experiment was conducted in 1 batch. We processed all samples in the same library preparation and sequencing run.

value: Keloid scar


title: ahp4 root ck treat sample 1


title: Keloid dermal cells, passage-zero

description:
Library name: KDF0
10X Genomics
processed.Robj
sct_v4.Robj
sct_v4_stromal.Robj

value: Passage-zero


title: Normal dermal cells, passage-4

description:
Library name: NDF4
10X Genomics
processed.Robj
sct_v4.Robj
sct_v4_stromal.Robj
P4_only.Robj

value: Normal skin


title: Root_PEG_180min_replicate3

value: Hengmian HD008

value: PEG treatment


title: Normal dermal cells, passage-zero

description:
Library name: NDF0
10X Genomics
processed.Robj
sct_v4.Robj
sct_v4_stromal.Robj


title: human, IPSCs, fraction 11, rep 3, total

city: Belo Horizonte

first: Izabela

last: Mamede

state: MG

address: Av. Pres. Antônio Carlos, 6627

department: Laboratory of Mucosal Immunology/Biochemistry And Immunology

country: Brazil

institute: Rockefeller University/Universidade federal de Minas gerais

description: Library name: hR3F11tot

data_processing:
Quality control, read mapping, and quantification was performed using nf-core/rnaseq v3.8.
Reads were mapped to GRCh38 (human) or mm10 (mouse) and quantified with Salmon v1.5.2 using the Gencode v38 (human) or M25 (mouse) annotation.
Softclip, position bias, sequence, bias GC bias, Gibbs sampling bootstrap of 100 and equivalence classes calling were arguments passed to Salmon during quantification.
Assembly: GRCh38 (human), GENCODE v38
Supplementary files format and content: All data files are on .rds format

source_name: IPSC

growth_protocol: Human Episomal iPSCs (Gibco, A18945) were cultured on Geltrex-coated (Gibco, A1413302) dishes using mTeSR Plus (Stem Cell Technologies, 100-0276). The medium was replaced following manufacturer’s instructions until cells were 70-80% confluent. Cells were maintained at 37°C and 5% CO2.

extract_protocol:
RNA was purified from sucrose fractions using Directzol RNA Miniprep kit (ZymoResearch, R2062), following the manufacturer’s instructions.
RNA-seq libraries were prepared using rRNA removal and sequenced paired-end (PE150) on the NovaSeq 6000 platform.

value: IPSC


title: human, IPSCs, fraction 10, rep 3, total

description: Library name: hR3F10tot


title: ahp4 Shoot mock sample 2

value: shoot


title: Lunet_neoJFH_D1467G_SMI

description: Library name: Lunet_neoJFH_D1467G_SMI

value: cell line

value: Huh7-Lunet neoJFH1 D1467G

value: hepatoma cell line

value: HCV gt2a


title: Root_PEG_60min_replicate3

value: root

value: 60 min


title: ahp4 shoot mock sample 1


title: Root_PEG_60min_replicate2


title: ahp4 root mock sample 4


title: human, IPSCs, fraction 8, rep 3, total

description: Library name: hR3F8tot


title: OVCAR3MJSO9

city: East Lansing

first: Sachi

last: Horibata

state: Michigan

address: 766 Service Rd

department: Pharmacology and Toxicology

country: USA

institute: Michigan State University

description: Library name: OVCAR3MJSO_3_24h

data_processing:
RNAseq data was aligned using STAR (v 2.7.2b) and quantified using RSEM (v 1.3.3).
Differential expression (DE) was performed using diffExp function in the OCTAD package with edgeR as the method for DE. The cutoff for significance was chosen as absolute value of log2FoldChange > 1 and padj < 0.05.
Assembly: Genome assembly GRCh38
Supplementary files format and content: fastq.gz, csv (tpm and raw counts in log2)

source_name: Epithelial  (progressive adenocarcinoma of the ovary)

growth_protocol: OVCAR3 cells were obtained from the National Cancer Institute (37 Convent Dr, Bethesda, MD 20814) and grown in Roswell Park Memorial Institute (RPMI)-1640 medium (GibcoTM, ThermoFisher Scientific, Cat# 11875-093) supplemented with 10% fetal bovine serum (FBS; GibcoTM, ThermoFisher Scientific, Cat# A52567-01) and 1 % Pen Strep (100 U/ml penicillin, 100 μg/mL streptomycin; GibcoTM, ThermoFisher Scientific, Cat# 15140-122) in a humidified incubator (Heracell VIOS 160i CO2 Incubator 165 L, Thermo Scientific, Cat# 51033557) containing 5% CO2 at 37 °C.

extract_protocol:
The RNA was isolated and purified using a RNeasy Mini Kit (Qiagen, Cat# 74104) according to the manufacturers instructions.
TruSeq RNA Library Prep Kit v2

treatment_protocol: Cells were plated in 6-well plates (avantor, Cat# 10062-892) with 500k cells per well and treated with 638 nM (500 ng/ml) MJS-O after 24 h. Durations of treatment were either 0 h, 4 h, or 24 h, and the DMSO concentration between samples was normalized.

value: High-grade serous ovarian cancer

tag: batch


title: ahp4 root ck treat sample 4

value: 100 nM BA 2h


title: Root_PEG_60min_replicate1


title: OVCAR3MJSO8

description: Library name: OVCAR3MJSO_3_4h

value: Epithelial  (progressive adenocarcinoma of the ovary)


title: human, IPSCs, fraction 6, rep 3, total

description: Library name: hR3F6tot


title: Cra galactose 1 (ChIP-exo)

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

data_processing:
ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using bowtie v1.0.0 with parameters -S.
MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity was used as background intensity.
For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
Assembly: ASM584v2
Supplementary files format and content: Tab-delimited text files in gff format which have 8 columns: sequence id, source (empty), feature (+/- strand), start position, end position, intensity score, strand (+/-), frame (.), attribute (.).

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: E. coli K-12 MG1655 cra-8myc tagged strains was grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% galactose.

extract_protocol:
E. coli cells were crosslinked in 1% formaldehyde for 25 minutes at RT on a rocker, then washed 3 times with 50 ml of ice-cold TBS (Tris buffered saline) each time. Crosslinked cells were then resuspended in 500 ul of lysis buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl and 1 mM EDTA) with 40 ul of protease inhibitor cocktail (50 mg in 0.25 ml of DMSO and 0.75 ml of TDW). Cells were lyzed with 1 ul of lysozyme for 30 min at 37C on a rocker. 0.55 ml of 2X IP buffer (100 mM Tris-HCl (pH 7.5), 200 mM NaCl, 2% Triton X-100 and 1 mM EDTA) were added to the sample, and then was sonicated to fragmentize genomic DNA. 0.3 ml of Wash buffer I (50 mM Tris-HCl (pH 7.5), 140 mM NaCl, 1% Triton X-100 and 1mM EDTA) was added to make the volume up to 1.4 ml. Only 0.7 ml was taken and transferred to a new tube, and 15 ul of Anti-c-myc mouse antibody was added, and the sample was incubated overnight at 4C to make Antibody-TF complex. 50 ul of Dynabeads Pan mouse IgG were washed 3 times with bead washing solution (250 mg BSA in 50 ml of PBS), and were added to the sample. Cell lysate with beads were incubated for 6 hours or overnight at 4C to make Dynabead-antibody-TF complex. The beads were pulled down on a magnet stand, and washed 2 times with wash buffer I and with wash buffer II (50 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1% Triton X-100 and 1mM EDTA), wash buffer III (10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1% Triton X-100 and 1mM EDTA), and wash buffer IV (10 mM Tris-HCl (pH 8.0), 1mM EDTA). The bead-bound TF-DNA complex was then end-repaired, dA-tailed, and ligated to the first adapter. Adapter-ligated sample was then treated with nick-repair reagent, and was treated with lambda exonuclease and RecJ exonuclease. Then DNA was eluted away from Dynabeads by incubating in 200 ul of elution buffer (50 mM Tris-HCl (pH 8.0), 1% SDS and 1 mM EDTA) at 65C overnight. Protein was removed by treating 4 ul of protease K and being incubated at 55C for 2 hours, and by Phenol-Chloroform-IAA extraction. Purified DNA was used to build the second strand synthesis, followed by another dA-tailing, second strand ligation, and 3' overhang removal steps. Then the sequencing library was amplified with PCR enrichment.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype/variation

tag: culture medium

value: M9 minimal media with 0.2% galactose

tag: growth phase

value: mid-log

value: anti-myc, Santa Cruz Biotech, cat # sc-28207


title: ahp4 root mock sample 2

value: mock


title: OVCAR3MJSO7

description: Library name: OVCAR3MJSO_3_0h


title: Root_PEG_30min_replicate2

value: Hengmian HD008

value: 30 min


title: Root_PEG_30min_replicate3

value: PEG treatment


title: Root_PEG_30min_replicate1


title: Cra galactose 2 (ChIP-exo)


title: OVCAR3MJSO6

description: Library name: OVCAR3MJSO_2_24h


title: human, IPSCs, fraction 4, rep 3, total

description: Library name: hR3F4tot

value: IPSC


title: Col shoot ck treat sample 4

value: shoot


title: Root_PEG_10min_replicate3

value: 10 min


title: Col shoot ck treat sample 3


title: human, IPSCs, fraction 7, rep 3, total

description: Library name: hR3F7tot


title: Stem_CK_replicate1

value: stem

value: CK

value: 0 min


title: ahp4 root mock sample 1

value: root


title: OVCAR3MJSO4

description: Library name: OVCAR3MJSO_2_0h

value: High-grade serous ovarian cancer


title: human, IPSCs, fraction 9, rep 3, total

description: Library name: hR3F9tot


title: human, IPSCs, fraction 3, rep 3, total

description: Library name: hR3F3tot


title: OVCAR3MJSO5

description: Library name: OVCAR3MJSO_2_4h


title: Root_PEG_10min_replicate2


title: human, IPSCs, fraction 2, rep 3, total

description: Library name: hR3F2tot


title: ahp4 root mock sample 3


title: OVCAR3MJSO3

description: Library name: OVCAR3MJSO_1_24h


title: Root_PEG_10min_replicate1


title: Col shoot ck treat sample 1

value: 100 nM BA 2h


title: OVCAR3MJSO2

description: Library name: OVCAR3MJSO_1_4h

value: Epithelial  (progressive adenocarcinoma of the ovary)


title: human, IPSCs, fraction 5, rep 3, total

description: Library name: hR3F5tot


title: Root_CK_replicate3


title: human, IPSCs, fraction 1, rep 3, total

description: Library name: hR3F1tot


title: Col root ck treat sample 4


title: Col root ck treat sample 3


title: OVCAR3MJSO1

description: Library name: OVCAR3MJSO_1_0h


title: Root_CK_replicate2


title: human, IPSCs, fraction 10, rep 2, total

description: Library name: hR2F10tot


title: Root_CK_replicate1


title: human, IPSCs, fraction 9, rep 2, total

description: Library name: hR2F9tot


title: P. aeruginosa, biofilm growth, treated with midazolam 10 ug/ml, replica 3

city: Palma de Mallorca

first: Carlos

last: Juan

address: Crta. Valldemossa 79

country: Spain

institute: Health research Institute of the Balearic Islands

description: Library name: DKM3BF

data_processing:
Raw RNA-seq reads were quality-checked with FastQC v0.11.9 [1]. Adapter trimming and removal of low-quality (<Q30) bases were performed using Trimmomatic v0.39 [2]. Ribosomal RNA sequences were filtered out with SortMeRNA v4.3.6 [3] using default rRNA databases in paired-end mode. Filtered reads were aligned to the Pseudomonas aeruginosa PAO1 reference genome (NCBI RefSeq: NC_002516.2, assembly GCF_000006765.1) using STAR 2.7.10a [4], generating sorted BAM files and gene-level counts. The reference genome and annotation files were downloaded from NCBI (https://www.ncbi.nlm.nih.gov/nuccore/NC_002516). Read summarization was also performed with featureCounts v2.0.3 [5], using strand-specific settings and gene annotations from the corresponding GFF file. Quality reports from all steps were aggregated using MultiQC v1.26. Differential gene expression analysis was performed using DESeq2 v1.44.0 [6].  Differentially expressed genes (DEGs) were identified using the Benjamini–Hochberg method for controlling the false discovery rate (FDR), considering genes significant if FDR ≤ 0.05 and absolute log₂ fold change ≥ log₂(1.5). Functional enrichment analyses, including over-representation analysis (ORA) and gene set enrichment analysis (GSEA), were carried out using the clusterProfiler v4.12.6 [7] R package. Pathways with an adjusted p-value ≤ 0.05 were considered significantly enriched.
Assembly: GCF_000006765.1
Supplementary files format and content: counts_GEO.tsv:  5 597 gens × 72 samples; GEO_metadata.tsv

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa

growth_protocol: Growth of planktonic cells (PL): Briefly, 10 mL of LB containing the different treatments were inoculated with 500 μL of an overnight culture of the strain PAO1-DK, which was grown until OD600nm0.5-0.6 at 37ºC and 180 rpm. Growth of biofilms (BF): 5 ml cultures of PAO1-DK were grown overnight in LB broth at 37°C and 180 rpm, washed with PBS, pH 7.4 and normalised to an OD600nm= 0.1 prior to inoculation into RPMI-1640 without antibiotics and supplemented with the desired treatments (untreated control or treatment with Midazolam 10 µg/ml). A total of 1 mL of the normalised and treated culture was inoculated into a 24-well plate. After 24h at 37ºC, RPMI media was replaced by 1 mL of 0.9% NaCl and biofilm was thoroughly scratched from the well and transferred to a 1.5 mL tube. A bath sonicator was used to disaggregate the biofilm embedded cells prior RNA extraction.

extract_protocol:
RNA extraction from planktonic cells. Briefly, 10 mL of LB containing the different treatments (untreated control or treatment with Midazolam 10 µg/ml) were inoculated with 500 μL of an overnight PAO1 culture and grown until OD600nm0.5-0.6 at 37ºC and 180 rpm. One millilitre of the culture was mixed with 2 ml of RNA protect (QIAgen) and the RNA extraction was performed using the RNeasy kit (QIAgen). Contaminant DNA was removed using 2 U of the TURBO DNAse kit (Invitrogen) and incubated for 30 minutes at 37ºC. Bacterial RNA was extracted from three independent replicates for each experimental condition. RNA extraction from biofilms. Biofilms were prepared as previously explained except adding 1 mL of the normalised culture into a 24-well plate (untreated control or treatment with Midazolam 10 µg/ml). After 24h at 37ºC, RPMI media was replaced by 1 mL of 0.9% NaCl and biofilm was thoroughly scratched from the well and transferred to a 1.5 mL tube. A bath sonicator was used to disaggregate the biofilm embedded cells prior RNA extraction. RNA extraction was performed as previously explained but adding an extra DNA degradation step (RNase-Free DNase, QIAgen). The TURBO DNAse was also applied after RNA elution, doubling the enzyme amount used and increasing the incubation time up to 45 minutes. RNA was prepared from three independent biofilm cultures.
Library Construction, Quality Control and Sequencing. Firstly, ribosomal RNA was removed from total RNA using the Illumina Ribo-Zero Plus rRNA Depletion Kit followed by ethanol precipitation. For the library preparation, the Novogene NGS Stranded RNA Library Prep Set (PT044) was used.After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and 2 sequenced on an Illumina NovaSeq 6000 using the PE150 strategy, according to effective library concentration and data amount required. Data were unequally shared with 3G raw data (10 million paired reads) for each sample.

treatment_protocol: Treatment: Untreated control (C) or treatment with Midazolam 10 µg/ml (M)

value: Pseudomonas aeruginosa


title: Leaf_PEG_180min_replicate3

source_name: leaf

value: leaf

value: 180 min


title: Col root ck treat sample 1


title: Col root ck treat sample 2


title: P. aeruginosa, biofilm growth, treated with midazolam 10 ug/ml, replica 2

description: Library name: DKM2BF


title: Col shoot ck treat sample 2


title: human, IPSCs, fraction 8, rep 2, total

description: Library name: hR2F8tot


title: P. aeruginosa, biofilm growth, treated with midazolam 10 ug/ml, replica 1

description: Library name: DKM1BF


title: Root_PEG_180min_replicate1


title: P. aeruginosa, biofilm growth, untreated control, replica 3

description: Library name: DKC3BF


title: Leaf_PEG_180min_replicate2


title: Col Shoot mock sample 3

value: mock


title: human, IPSCs, fraction 7, rep 2, total

description: Library name: hR2F7tot


title: Leaf_PEG_180min_replicate1

value: Hengmian HD008


title: Col shoot mock sample 4


title: human, IPSCs, fraction 11, rep 2, total

description: Library name: hR2F11tot


title: human, IPSCs, fraction 6, rep 2, total

description: Library name: hR2F6tot


title: Col Shoot mock sample 2


title: P. aeruginosa, biofilm growth, untreated control, replica 2

description: Library name: DKC2BF


title: P. aeruginosa, biofilm growth, untreated control, replica 1

description: Library name: DKC1BF


title: Col shoot mock sample 1


title: P. aeruginosa, planktonic growth, treated with midazolam 10 ug/ml, replica 3

description: Library name: DKM3PL


title: Leaf_PEG_60min_replicate1

value: 60 min


title: human, IPSCs, fraction 4, rep 2, total

description: Library name: hR2F4tot


title: Leaf_PEG_30min_replicate3

value: PEG treatment

value: 30 min


title: P. aeruginosa, planktonic growth, treated with midazolam 10 ug/ml, replica 2

description: Library name: DKM2PL


title: Leaf_PEG_60min_replicate2


title: Col root mock sample 4


title: human, IPSCs, fraction 5, rep 2, total

description: Library name: hR2F5tot

value: IPSC


title: Col root mock sample 3


title: human, IPSCs, fraction 3, rep 2, total

description: Library name: hR2F3tot


title: human, IPSCs, fraction 2, rep 2, total

description: Library name: hR2F2tot


title: P. aeruginosa, planktonic growth, treated with midazolam 10 ug/ml, replica 1

description: Library name: DKM1PL


title: Leaf_PEG_30min_replicate2


title: Col root mock sample 2


title: human, IPSCs, fraction 1, rep 2, total

description: Library name: hR2F1tot


title: P. aeruginosa, planktonic growth, untreated control, replica 3

description: Library name: DKC3PL


title: Leaf_PEG_30min_replicate1


title: Leaf_PEG_60min_replicate3


title: human, IPSCs, fraction 11, rep 1, total

description: Library name: hR1F11tot


title: P. aeruginosa, planktonic growth, untreated control, replica 2

description: Library name: DKC2PL


title: P. aeruginosa, planktonic growth, untreated control, replica 1

description: Library name: DKC1PL


title: Leaf_PEG_10min_replicate3

value: 10 min


title: human, IPSCs, fraction 10, rep 1, total

description: Library name: hR1F10tot


title: human, IPSCs, fraction 9, rep 1, total

description: Library name: hR1F9tot


title: Leaf_PEG_10min_replicate2


title: human, IPSCs, fraction 8, rep 1, total

description: Library name: hR1F8tot


title: Mouse uterus aged group2 rep3 Input

city: Cambridge

first: Sarah

last: Inglesfield

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

description:
Library name: Input_48wk_MH236(3Di)
ChIP-seq input sample. No associated processed data file.

data_processing:
Reads were aligned to the mouse genome assembly GRCm38 using bowtie2. We assessed the data quality using ChIPQC (v1.34.0). Peaks were identified using MACS2 (v2.2.9.1) with q < 0.01. The DiffBind R package (v3.8.0) was used to find consensus peaks in different sample groups and perform differential binding analysis [Stark & Brown, 2011]. Consensus peaks were defined as those present in more than 66% of samples within each group. A binding matrix was generated using read counts from consensus peaks overlapping within each group (summit width = 200 bp), followed by normalization. This matrix was then used to identify differentially accessible regions between age groups using DESeq2 (as implemented by default in DiffBind), applying a false discovery rate (FDR) threshold of ≤ 0.05. Peaks were assigned to genes or nearby genes using ChIPpeakAnno (v3.32.0). In addition to gene assignment, peaks were annotated for genomic feature overlap—whether located in TSS, exon, 5′ UTR, 3′ UTR, intronic, or intergenic regions using ChIPseeker (v1.34.1). deepTools (v3.5.1) was used to visualize the average profiles of histone modifications across gene regions ±5 kb in different groups.
To identify super-enhancers, H3K27ac peaks called with MACS2 (with parameter --- broad) and used as input for the ROSE (Rank Ordering of Super-Enhancers) software, which stitches together enhancer peaks located within 12.5 kb of each other (Whyte et al., 2013).
Assembly: Grcm38
Supplementary files format and content: Processed data files are in .txt format. Data contained are Log2RPKM quantitation of 1. consensus H3K4me3 peaks for H3K4me3 ChIp-seq samples (H3K4me3_AllPeaks_Log2RPKM.txt) and 2. consensus H3K27ac peaks for H3K27ac ChIP-seq samples (H3K27ac_AllPeaks_Log2RPKM.txt).

source_name: uterus

extract_protocol:
Ultra-low input native ChIP-seq was performed on pieces of snap frozen endometrial tissue as previously described [ref]. Briefly, tissue was thawed on ice in 100μL nuclear isolation buffer (NIB, Sigma) and diced using a blade. An aliquot of 20,000 nuclei in 10μL NIB was then taken forward for Mnase (NEB) digestion at 21 °C for 7.5 minutes. Digested chromatin was then suspended in Complete IP buffer (20mM Tris-HCl (pH8), 2mM EDTA, 150mM NaCl, 0.1%Triton-X100, 1x Protease inhibitor cocktail,1mM PMSF). Following pre-clearing the chromatin on a mix of protein A/protein G beads (Thermo Fisher Scientific), and after 10% was set aside for input, the chromatin was divided for immunioprecipitation overnight rotating at 30 rpm, at 4 °C. IP was performed using 250ng antibodies for H3K4me3 (Diagenode, C15410003) and H3K27ac (Abcam, ab4729). DNA was washed in low then high salt washes, before eluting in ChIP elution buffer (100mM NaHCO3, 1% SDS). DNA was then SPRI purified before continuing to library preparation
Libraries were prepred using the MicroPlex Library Preparation kit (Diagenode, C05010001). Libraries were quantitated using the Agilent Bioanalyzer High Sensitivity DNA assay before pooling for sequencing. Libraries were sequenced on the Illumina NextSeq500, 75 bp paired end.

value: uterus


title: Leaf_CK_replicate3

value: CK


title: Mouse uterus young rep1 Input

description:
Library name: Input_10wk_MH60(2Ci)
ChIP-seq input sample. No associated processed data file.


title: Seedlings, WT-control

city: Taipei

first: Jeng-Shane

last: Lin

address: No. 1, Sec. 4, Roosevelt Road

department: Plant Biology

country: Taiwan

institute: National Taiwan University

description: WT-C

data_processing:
Raw sequences were obtained from the Illumina Pipeline software bcl2fastq v2.1.7 and expected to generate 6 G per sample.
Trimmomatics was implemented to trim or remove the reads according to the quality score.
Qualified reads after filtering low-quality data were analyzed using TopHat/Cufflinks for gene expression estimation.
For differential expression analysis, CummeRbund was employed to perform statistical analyses of gene expression profiles.
The reference genome and gene annotations were retrieved from Ensembl database.
Genome_build: TAIR10
Supplementary_files_format_and_content: WT-164OE_FPKM file includes FPKM values for each Sample

source_name: Seedlings

growth_protocol: Arabidopsis thaliana (Col-0) was grown in a controlled environment at 22°C under 16 h light/8 h dark with cool fluorescent light at 100 μmolm-2 s-1.

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual.
Library construction of all samples were used by Agilent's SureSelect Strand Specific RNA Library Preparation Kit

treatment_protocol: The 5-day-old seedlings were treated with heat stress at 35oC for 5 days.

value: Seedlings

tag: ecotype

value: Wild-type

tag: stress

value: control


title: human, IPSCs, fraction 7, rep 1, total

description: Library name: hR1F7tot


title: Col root mock sample 1

value: root


title: MEF, H3K9me3, Rep2

city: Rochester

first: Patrick

middle: J

last: Murphy

state: New York

address: 601 Elmwood Avenue

department: Biomedical Genetics and Genomics

institute: University of Rochester

description: Library name: H3K9me3_rep2

data_processing:
cutAdapt was used on all raw fastq files, and then each was mapped with bowtie2 using mm10.
PICARD MergeSamFiles was used to convert files to BAM files, and PICARD MarkDuplicates was used to remove duplicate reads.
bigWig files were made with deeptools BAMcoverage  --normalizeUsing RPKM --binSize 10 --extendReads 100.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: mouse embyronic fibroblast

growth_protocol: Primary MEFs were obtained from embryonic day 13.5 mouse embryos and grown in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin.  Cells were cultured at 37°C.

extract_protocol:
Nuclei were extracted from MEFs using the standard CUT&Tag (Kaya-Okur et al. Nat. Comm. 2019. and https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3) protocol (Nuclear Extraction Buffer).
Libraries were prepared for sequencing using standard CUT&Tag (Kaya-Okur et al. Nat. Comm. 2019. and https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3) protocols. i5 and i7 sequencing adaptors were added to isolated DNA via PCR.
CUT&Tag with H2A.Z, H3K27ac, H3K27me3 and H3K9me3 antibodies

value: mouse embyronic fibroblast

value: WT


title: human, IPSCs, fraction 6, rep 1, total

description: Library name: hR1F6tot


title: Leaf_CK_replicate2

value: leaf

value: 0 min


title: Mouse uterus aged group1 rep1 Input

description:
Library name: Input_28wk_MH223(1Di)
ChIP-seq input sample. No associated processed data file.


title: Leaf_CK_replicate1


title: Mouse uterus aged group3 rep2 Input

description:
Library name: Input_64wk_MH34(2Ai)
ChIP-seq input sample. No associated processed data file.


title: Seedlings, 164OE-Heat

value: miR164 ovexpression transgenic

value: Heat


title: MEF, H3K9me3, Rep1

description: Library name: H3K9me3_rep1


title: human, IPSCs, fraction 5, rep 1, total

description: Library name: hR1F5tot


title: human, IPSCs, fraction 4, rep 1, total

description: Library name: hR1F4tot


title: P1_ferret_subpallium, scRNAseq

city: San Francisco

first: Alex

last: Pollen

state: CA

institute: University of California San Francisco

data_processing:
Genes were quantified using CellRanger v7.0.1, ambient RNA was removed using Cellbender v0.2.1, inhibitory neurons were isolated used conserved markers (DLX1/2/5/6, GAD1/2)
Assembly: Sscrofa11.1 (pig), MusPutFur1.0 (ferret), mm10 (mouse)
Supplementary files format and content: barcodes.csv contains cell metadata
Supplementary files format and content: genes.csv contains gene metadata
Supplementary files format and content: matrix.mtx contains raw cells by genes CellRanger and Cellbender matrix

organism: Mustela putorius furo

source_name: subpallium

extract_protocol:
Regions of interest were dissected and tissue was dissociated in papain. Whole cells  from pig and ferret were resuspended in PBS supplemented with 0.04% BSA for Chromium 10X processing, mouse cells were resuspended in PBS supplemented with 0.1% BSA and sorted for Nkx2.1-cre;Ai14 expression using BD FACSAria Fusion for Chromium 10X processing.
Library was constructed according to manufacturer's instructions (10X Genomics Chromimum Next GEM single Cell 3' HT  v3.1)

value: subpallium

value: WT, P1

value: developing brain


title: Osimertinib single compound treatment replicate 2

city: New York

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

description: Library name: Osimertinib-B

data_processing:
Raw data was first processed using DMS_tools2 to get codon counts and enriched sites. Sites with spurisous mutations based on codon table were manually removed from further consideration.
Supplementary files format and content: CSV files contain codon counts of all sites.

growth_protocol: Parental Ba/F3 cells were cultured in RPMI 1640 medium (Gibco #11875085) supplemented with 1% Penicillin-Streptomycin (Gibco #15140-122), 5% Foundation™ fetal bovine serum (Gemini Bio-Products), and 10 ng/mL recombinant mouse interleukin-3 (IL-3) (BioLegend #575504). Deep mutational scanning library expressing cells will not require IL-3 for culture.

extract_protocol:
Genomic DNA (gDNA) was extracted from ~1.5 × 10⁷ cells using salt precipitation56. Cells were resuspended in 200 µL of DPBS in a 15 mL tube. Lysis was achieved by adding 3 mL of lysis buffer (10 mM Tris, 100 mM EDTA, 2% SDS, pH 8.0) containing RNase A (10 mg/mL), followed by vortexing and incubation at 37°C for 5 minutes, then cooling on ice for 3 minutes. Protein contaminants were removed by adding 1 mL of protein precipitation solution (7.5 M ammonium acetate), vortexing, and centrifuging at 2,000 × g for 10 minutes. The supernatant was transferred to a new tube containing 3 mL of isopropanol to precipitate DNA, and the mixture was gently inverted 50 times. DNA was pelleted by centrifugation at 2,000 × g for 3 minutes, washed with 3 mL of 70% ethanol, and air-dried for 5–10 minutes. The pellet was resuspended in 400 µL of hydration buffer (10 mM Tris, pH 8.0), incubated at 65°C for 1 hour, and hydrated overnight at room temperature with shaking at 600 rpm.
cDNA were sequenced using a two-step barcoded subamplicon PCR strategy. In the first step, the EGFR kianse domain was divided into two equal subamplicons, and each half was amplifed in a separate reeation. Approximately 5 µg of the DMS library DNA was split between these two reactions, each containing primers encoding 8 degenerate nucleotides to introduce unique molecular identifiers (UMIs). Following amplification, PCR1 products were purified by isopropanol precipitation to remove residual primers and short fragments, and the concentration of each purified product was determined using the PicoGreen method (Invitrogen #P11496). For the second PCR step (PCR2), 500 fg of the purified PCR1 product was used as the template for each subamplicon. This PCR step incorporated Illumina sequencing adapters and sample-specific indexes for multiplexed sequencing. The resulting indexed libraries were then purified using SPRI beads. Libraries were pooled at equimolar concentrations and sequenced on an Illumina NovaSeq SP (500 cycles) platform using paired end reads configured to capture the UMI, barcode, and subamplicon regions.

treatment_protocol: The established Ba/F3 cell pool expressing DMS library was cultured for 14 days wiith 100nM inhibitor or DMSO replenished every two days to maintain consistant drug pressure.

value: Osimertinib single compound treatment


title: Seedlings, 164OE-control


title: Mouse uterus aged group3 rep10 H3K27ac

description: Library name: H3K27ac_60wk_MH245(7A2)


title: Osimertinib single compound treatment replicate 1

description: Library name: Osimertinib-A


title: P1_ferret_cortex, scRNAseq

source_name: cortex

value: cortex


title: Mouse uterus aged group3 rep5 Input

description:
Library name: Input_64wk_MH249(5Ai)
ChIP-seq input sample. No associated processed data file.

value: uterus


title: Seedlings, WT-Heat

description: WT-H


title: Mouse uterus aged group3 rep9 H3K27ac

description: Library name: H3K27ac_60wk_MH242(6D2)


title: gnotobiotic_Candida-albicans_13

first: Haley

middle: Elizabeth

last: Gause

institute: UCSF

description: Library name: Sample08_21CF4_gnoto_Candida-albicans

data_processing:
trimming/filtering: fastp (ver: 0.20.1), parameters: "--adapter_sequence='AGATCGGAAGAGCACACGTCTGAACTCCAGTCA' -x"
alignment: star (ver: 2.7.9a), parameters: "--outSAMmultNmax 10,  --alignIntronMax 4000 --alignIntronMin 4"
filter out reads less than 30bp in length:  samtools (ver:1.14), parameters: "view --expr 'length(seq)>30'  -O {outputfolder} -o {outputfilename} {inputfilename}"
extract gene counts: subread (ver: 2.0.1)
Assembly: CGD Candida albicans Assembly 22 (C_albicans_SC5314_version_A22-s07-m01-r105_chromosomes.fasta)
Assembly: Enterococcus_faecalis_og1rf.ASM17257v2.dna.chromosome.Chromosome.fa
Supplementary files format and content: CaSTAR_mRNA_counts_above30bp.txt, , EfSTAR_gene_counts_above30bp.txt: counts matrix with raw counts per gene. Columns are sample names, genes are column names
Supplementary files format and content: *_normcounts.csv: normalized count per gene using DESeq2 count normalization
Supplementary files format and content: *.bam: BAM files of alignment of reads to genome generated by STAR, then filtered to contain only reads that were greater than 30bp in length. These BAM files were used to generate the count files

organism:
Candida albicans
Mus musculus

source_name: cecum contents

growth_protocol: gnotobiotic mice were gavaged with 100µL cells in PBS. Cecum was harvested 10 days post-gavage and contents were harvested into RNA-later stabilization solution

extract_protocol:
RNA extracted following the protocol found at: dx.doi.org/10.17504/protocols.io.5jyl8jjx7g2w/v1
rRNA depletion using siTOOLS riboPOOL probes: filamentous fungi, pan-bacteria, and Mus musculus (probes used when species is present). Followed manufacturer protocol for one-step depletion followed by NEB Monarch RNA Clean Up 10ug kit (NEB #T2030) per provided protocol. 5 ng of rRNA depleted RNA was used to prepare libraries using CORALL Total RNA-seq kit according to provided protocols.
RNA extracted following the protocol found at: dx.doi.org/10.17504/protocols.io.5jyl8jjx7g2w/v1

value: cecum contents

tag: strain 1

tag: genotype 1

tag: genotype 3

value: BALB/c

tag: sex 3

value: female


title: Leaf_PEG_10min_replicate1

tag: tissue

value: Hengmian HD008

tag: treatment

value: PEG treatment

value: 10 min


title: human, IPSCs, fraction 2, rep 1, total

description: Library name: hR1F2tot

tag: cell line

value: IPSC


title: gnotobiotic_Candida-albicans_12

description: Library name: Sample07_21CF3_gnoto_Candida-albicans

value: WT


title: human, IPSCs, fraction 1, rep 1, total

description: Library name: hR1F1tot


title: Mouse uterus aged group3 rep8 H3K27ac

description: Library name: H3K27ac_65wk_MH260(6C2)

tag: strain


title: Mouse uterus aged group3 rep7 H3K27ac

description: Library name: H3K27ac_60wk_MH241(6B2)


title: human, IPSCs, fraction 10, rep 3, extract

description: Library name: hR3F10ext


title: Mouse uterus aged group3 rep5 H3K27ac

description: Library name: H3K27ac_64wk_MH249(5A2)


title: human, IPSCs, fraction 8, rep 3, extract

description: Library name: hR3F8ext


title: Osimertinib+BLU-945 combo replicate 2

description: Library name: BLU945plusOsi-B

value: Osimertinib+BLU-945 combo


title: Mouse uterus aged group3 rep6 H3K27ac

description: Library name: H3K27ac_60wk_MH246(5D2)


title: gnotobiotic_Candida-albicans_10

description: Library name: Sample05_21CF1_gnoto_Candida-albicans


title: BLU-945 single compound treatment replicate 2

description: Library name: BLU945-B

value: BLU-945 single compound treatment


title: Osimertinib+BLU-945 combo replicate 1

description: Library name: BLU945plusOsi-A


title: Mouse uterus aged group3 rep3 H3K27ac

description: Library name: H3K27ac_63wk_MH253(3C2)


title: gnotobiotic_Candida-albicans_8

description: Library name: Sample04_21BM4_gnoto_Candida-albicans

value: male


title: human, IPSCs, fraction 9, rep 3, extract

description: Library name: hR3F9ext


title: human, IPSCs, fraction 3, rep 1, total

description: Library name: hR1F3tot


title: Mouse uterus aged group3 rep4 H3K27ac

description: Library name: H3K27ac_54wk_MH51(4B2)


title: gnotobiotic_Candida-albicans_7

description: Library name: Sample04_13CF2_gnoto_Candida-albicans


title: DMSO control replicate 2

description: Library name: DMSO-control-B

value: DMSO control


title: bone,Zin,10weeks

city: Shenyang

first: Fangming

last: Cao

state: Liaoning

address: 155 Nanjing Street

institute: First Hospital of China Medical University/Department of Orthopedics

description:
Library name: A6
treatment（Zin）

data_processing:
Raw reads were processed to remove adaptor sequences and low-quality bases using Trimmomatic (quality threshold: 0.05). FastQC was used to assess the quality of the reads before and after trimming.
Trimmed reads were aligned to the mm10 (mouse genome assembly version 10) using STAR aligner with default parameters for mapping quality.
Gene expression was quantified by counting the number of mapped reads for each gene using featureCounts. Gene annotations were obtained from the mm10 genome assembly.
Gene expression data was normalized to RPKM (Reads Per Kilobase of transcript per Million mapped reads) to account for differences in sequencing depth across samples.
Assembly: mm10
Supplementary files format and content: Processed data is stored in tab-delimited text files, which include RPKM (Reads Per Kilobase of transcript per Million mapped reads) values for each sample.

source_name: bone

growth_protocol: Culture conditions: RAW264.7 cells are cultured in DMEM supplemented with 10% fetal bovine serum and maintained in a humidified incubator at 37°C with 5% CO₂.

extract_protocol:
RNA extraction: At the end of the experiment, femoral tissue from mice is collected, immediately frozen in liquid nitrogen, ground into bone powder, and RNA is extracted.
RNA-seq library construction: Total RNA extracted from femoral tissue is used for library construction, and RNA-seq sequencing is performed by Novogene (Beijing, China).

treatment_protocol: Control group: Saline is used as the solvent control. Treatment group: In vivo, zingerone is administered orally at a dose of 100 mg/kg body weight per day for 8 weeks.

value: bone

tag: cell type

value: Osteoclast precursor cells

tag: genotype

value: zingerone


title: gnotobiotic_Candida-albicans_9

description: Library name: Sample05_13CF3_gnoto_Candida-albicans


title: gnotobiotic_Candida-albicans_6

description: Library name: Sample03_21AM3_gnoto_Candida-albicans


title: human, IPSCs, fraction 7, rep 3, extract

description: Library name: hR3F7ext


title: Mouse uterus aged group3 rep2 H3K27ac

description: Library name: H3K27ac_64wk_MH34(2A2)


title: gnotobiotic_Candida-albicans_11

description: Library name: Sample06_21CF2_gnoto_Candida-albicans


title: human, IPSCs, fraction 11, rep 3, extract

description: Library name: hR3F11ext


title: Mouse uterus aged group3 rep1 H3K27ac

description: Library name: H3K27ac_64wk_MH44(1C2)


title: human, IPSCs, fraction 6, rep 3, extract

description: Library name: hR3F6ext


title: bone,Zin,8weeks

description:
Library name: A4
treatment（Zin）


title: DMSO control replicate 1

description: Library name: DMSO-control-A


title: human, IPSCs, fraction 5, rep 3, extract

description: Library name: hR3F5ext


title: BLU-945 single compound treatment replicate 1

description: Library name: BLU945-A


title: gnotobiotic_Candida-albicans_5

description: Library name: Sample03_13BM3_gnoto_Candida-albicans


title: Mouse uterus aged group2 rep6 H3K27ac

description: Library name: H3K27ac_48wk_MH237(6A2)


title: human, IPSCs, fraction 4, rep 3, extract

description: Library name: hR3F4ext


title: bone,OVX,10week

description:
Library name: A3
OVX

value: Saline solution


title: Mouse uterus aged group2 rep5 H3K27ac

description: Library name: H3K27ac_42wk_MH233(5B2)

value: uterus


title: bone,Zin,9weeks

description:
Library name: A5
treatment（Zin）


title: gnotobiotic_Candida-albicans_4

description: Library name: Sample02_21AM2_gnoto_Candida-albicans

value: cecum contents


title: human, IPSCs, fraction 2, rep 3, extract

description: Library name: hR3F2ext


title: gnotobiotic_Candida-albicans_2

description: Library name: Sample01_21AM1_gnoto_Candida-albicans

value: BALB/c


title: Mouse uterus aged group2 rep4 H3K27ac

description: Library name: H3K27ac_42wk_MH234(4A2)


title: gnotobiotic_Candida-albicans_1

description: Library name: Sample01_13AM1_gnoto_Candida-albicans


title: human, IPSCs, fraction 3, rep 3, extract

description: Library name: hR3F3ext


title: human, IPSCs, fraction 11, rep 2, extract

description: Library name: hR2F11ext


title: TCR-LN-IL12

first: K.

middle: Dane

last: Wittrup

state: MA

address: 500 Main St

institute: MIT

description:
Library name: TCR-LN-IL12
10x Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were done using the 10x Genomics Clound Analysis with the Cell Ranger Count v9.0.1
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: TCR-Seq

source_name: Lymph node

extract_protocol:
FACS + 10x Genomics Chromium
10x Genomics 5` v3

value: Lymph node

value: T-cell


title: TCR-LN-Both

description:
Library name: TCR-LN-Both
10x Genomics

value: Both


title: Mouse uterus aged group2 rep3 H3K27ac

description: Library name: H3K27ac_48wk_MH236(3D2)


title: TCR-LN-PBS

description:
Library name: TCR-LN-PBS
10x Genomics

value: PBS


title: hypoxic_Enterococcus_faecalis_1

description: Library name: Enterococcus_faecalis_hypoxic_1

organism: Enterococcus faecalis

source_name: whole cell

growth_protocol: All cell growth was done at 0.2% O2, 5% CO2, and 37C. For each strain, mid-log cells were backdiluted to OD=0.2 in BHI broth and at shaken at 800RPM for 4 hours. Cells were harvested via centrifugation (3500 RPM for 5 min) and flash frozen in liquid nitrogen before placed at -80C.

extract_protocol:
RNA extracted following the protocol found at dx.doi.org/10.17504/protocols.io.5jyl8jjx7g2w/v1, with the following modifications: only 1 phenol/chloroform precipitation.
rRNA depletion using siTOOLS riboPOOL probes: filamentous fungi, pan-bacteria, and Mus musculus (probes used when species is present). Followed manufacturer protocol for one-step depletion followed by NEB Monarch RNA Clean Up 10ug kit (NEB #T2030) per provided protocol. 5 ng of rRNA depleted RNA was used to prepare libraries using CORALL Total RNA-seq kit according to provided protocols.
RNA extracted following the protocol found at: dx.doi.org/10.17504/protocols.io.5jyl8jjx7g2w/v1

value: whole cell


title: human, IPSCs, fraction 9, rep 2, extract

description: Library name: hR2F9ext

value: IPSC


title: Mouse uterus aged group1 rep4 H3K27ac

description: Library name: H3K27ac_36wk_MH228(4D2)


title: Mouse uterus aged group2 rep1 H3K27ac

description: Library name: H3K27ac_48wk_MH240(1B2)


title: FB-LN-Both

description:
Library name: FB-LN-Both
10x Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were done using the 10x Genomics Clound Analysis with the Cell Ranger Count v9.0.1
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq


title: hypoxic_Enterococcus_faecalis_3

description: Library name: Enterococcus_faecalis_hypoxic_3

value: WT


title: Mouse uterus aged group1 rep3 H3K27ac

description: Library name: H3K27ac_36wk_MH227(3A2)


title: C57BL/6J mouse ovary, hypobaric hypoxia (6500m) 3

city: Lanzhou

first: mengwen

last: Jiao

state: Gansu

address: No. 333, Nanbinhe Road, Qilihe District

department: Department of Reproductive Center

institute: The 940th Hospital of Joint Logistic Support Force of Chinese People's Liberation Army

description:
Library name: Hypoxia（PU）3
Fifteen female C57BL/6J mice (6-8 weeks old) were hormonally synchronized via oral gavage administration of levonorgestrel (0.1 mg/kg) and ethinylestradiol (0.02 mg/kg), then exposed to hypobaric hypoxia (simulated 5000 m altitude) for 15 consecutive days.Ovarian tissues were harvested for RNA sequencing to investigate the circRNA-mediated competitive endogenous RNA (ceRNA) regulatory network in hypoxia-induced ovarian injury.

data_processing:
Raw reads were filtered using SOAPnuke (v1.5.6) to remove low-quality reads, adaptor contamination, and reads with >1% unknown bases. Clean reads were aligned to the reference genome using BWA-MEM and Bowtie2. Circular RNAs were identified using CIRI (v2.0.5) and find_circ (v1.2). Expression levels were quantified using back-spliced read counts normalized as RPM. Differential expression analysis was performed using DEGseq. Functional annotation was conducted with GO and KEGG. Coding potential was predicted using cORF_pipeline and IRESfinder. miRNA binding prediction was performed using miRanda and RNAhybrid.
Assembly: Mus musculus GRCm38
Supplementary files format and content: csv files include RPM of each sample

source_name: Ovary

extract_protocol:
Total RNA was extracted using TRIzol reagent, treated with DNase I, rRNA was removed by Ribo-off kit, and linear RNA was digested with RNase R for circRNA enrichment.
Total RNA was depleted of rRNA using Ribo-off, digested with RNase R, and converted into cDNA. Libraries were constructed using strand-specific protocols and sequenced on the DNBSEQ-G400 platform.

value: Ovary

value: Ovarian cell

value: ypobaric hypoxia (simulated 6500m altitude, 8.1kPa O₂, 21 - 24℃, 50% humidity, 24h continuous hypoxia except 0.5h/2d for feeding, 12h/12h light - dark)


title: human, IPSCs, fraction 8, rep 2, extract

description: Library name: hR2F8ext


title: bone,OVX,8week

description:
Library name: A1
OVX

value: bone


title: FB-LN-IL12

description:
Library name: FB-LN-IL12
10x Genomics


title: gnotobiotic_Candida-albicans_3

description: Library name: Sample02_13AM2_gnoto_Candida-albicans

value: male


title: bone,OVX,9week

description:
Library name: A2
OVX

value: Osteoclast precursor cells


title: C57BL/6J mouse ovary, hypobaric hypoxia (6500m) 2

description:
Library name: Hypoxia（PU）2
Fifteen female C57BL/6J mice (6-8 weeks old) were hormonally synchronized via oral gavage administration of levonorgestrel (0.1 mg/kg) and ethinylestradiol (0.02 mg/kg), then exposed to hypobaric hypoxia (simulated 5000 m altitude) for 15 consecutive days.Ovarian tissues were harvested for RNA sequencing to investigate the circRNA-mediated competitive endogenous RNA (ceRNA) regulatory network in hypoxia-induced ovarian injury.


title: FB-LN-PBS

description:
Library name: FB-LN-PBS
10x Genomics


title: Mouse uterus aged group1 rep1 H3K27ac

description: Library name: H3K27ac_28wk_MH223(1D2)


title: human, IPSCs, fraction 7, rep 2, extract

description: Library name: hR2F7ext


title: C57BL/6J mouse ovary, hypobaric hypoxia (6500m) 1

description:
Library name: Hypoxia（PU）1
Fifteen female C57BL/6J mice (6-8 weeks old) were hormonally synchronized via oral gavage administration of levonorgestrel (0.1 mg/kg) and ethinylestradiol (0.02 mg/kg), then exposed to hypobaric hypoxia (simulated 5000 m altitude) for 15 consecutive days.Ovarian tissues were harvested for RNA sequencing to investigate the circRNA-mediated competitive endogenous RNA (ceRNA) regulatory network in hypoxia-induced ovarian injury.


title: Mouse uterus aged group1 rep2 H3K27ac

description: Library name: H3K27ac_28wk_MH225(2B2)


title: GEX-LN-Both

description:
Library name: GEX-LN-Both
10x Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were done using the 10x Genomics Clound Analysis with the Cell Ranger Count v9.0.1
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files


title: C57BL/6J mouse ovary, normal pressure (1500m) 3

description:
Library name: Control（MP）3
Fifteen female C57BL/6J mice (6-8 weeks old) were synchronized by oral gavage administration of levonorgestrel and ethinylestradiol, then maintained under normoxic conditions in Lanzhou, China.All mice were housed continuously for 15 days.Ovarian tissues were collected for RNA-seq as the control group to analyze the circular RNA (circRNA)-mediated competitive endogenous RNA (ceRNA) network in hypoxia-induced ovarian injury.

value: Normal pressure (Lanzhou local, ~1500m altitude, 17.8kPa O₂, 20 - 23℃, 12h/12h light - dark)


title: human, IPSCs, fraction 6, rep 2, extract

description: Library name: hR2F6ext


title: Mouse uterus aged group2 rep2 H3K27ac

description: Library name: H3K27ac_42wk_MH231(2D2)

value: uterus


title: Mouse uterus young rep7 H3K27ac

description: Library name: H3K27ac_11wk_MH55(7D2)


title: human, IPSCs, fraction 10, rep 2, extract

description: Library name: hR2F10ext


title: human, IPSCs, fraction 4, rep 2, extract

description: Library name: hR2F4ext


title: C57BL/6J mouse ovary, normal pressure (1500m) 2

description:
Library name: Control（MP）2
Fifteen female C57BL/6J mice (6-8 weeks old) were synchronized by oral gavage administration of levonorgestrel and ethinylestradiol, then maintained under normoxic conditions in Lanzhou, China.All mice were housed continuously for 15 days.Ovarian tissues were collected for RNA-seq as the control group to analyze the circular RNA (circRNA)-mediated competitive endogenous RNA (ceRNA) network in hypoxia-induced ovarian injury.


title: GEX-LN-IL12

description:
Library name: GEX-LN-IL12
10x Genomics


title: Mouse uterus young rep6 H3K27ac

description: Library name: H3K27ac_11wk_MH59(7C2)


title: C57BL/6J mouse ovary, normal pressure (1500m) 1

description:
Library name: Control（MP）1
Fifteen female C57BL/6J mice (6-8 weeks old) were synchronized by oral gavage administration of levonorgestrel and ethinylestradiol, then maintained under normoxic conditions in Lanzhou, China.All mice were housed continuously for 15 days.Ovarian tissues were collected for RNA-seq as the control group to analyze the circular RNA (circRNA)-mediated competitive endogenous RNA (ceRNA) network in hypoxia-induced ovarian injury.


title: GEX-LN-PBS

description:
Library name: GEX-LN-PBS
10x Genomics


title: 9750_Total_Kidney

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

description: Library name: Sample_32

data_processing:
Sequencing adapters and low-quality bases were trimmed using Trim Galore (v0.6.10). Reads were aligned to the human genome (hg38) using STAR (v2.7.10a). Gene-level counts were quantified with featureCounts (Subread v2.0.3). Differential expression was analyzed using the limma-voom pipeline in R (v4.3.2), with genes filtered by CPM >1 in at least 3 samples and adjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files log read counts values for each Sample

source_name: kidney

extract_protocol:
Trizol and Rneasy columns
RNA-seq libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), including polyA enrichment for mRNA. Libraries were barcoded, quantified by qPCR, and sequenced on an Illumina NovaSeq 6000 using 150 bp paired-end reads.

value: kidney

value: endothelial cells

value: wt

value: lps


title: Glucose 2 (RNA-seq)

data_processing:
RNA-seq reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters -S
Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity was used as background intensity.
DESeq2 was used to calculate transcripts per million (TPM) value for each gene and investigate the differential expression of the genes (threshold: log2 fold change≥1.0 and q-value ≤0.05)
Assembly: ASM584v2
Supplementary files format and content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

growth_protocol: E. coli K-12 MG1655 wild type strains was grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% galactose and glucose.

extract_protocol:
E. coli cells were mixed with RNAprotect Bacteria Reagent (Qiagen) via vertexing for 5 seconds and incubated for 5 minutes at room temperature and then centrifuged at 5000 x g for 10 minutes. Then total RNA samples were isolated with RNAeasy Plus Mini kit (Qiagen).   Crosslinked cells were then resuspended in 500 ul of lysis buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl and 1 mM EDTA) with 40 ul of protease inhibitor cocktail (50 mg in 0.25 ml of DMSO and 0.75 ml of TDW). Cells were lyzed with 1 ul of lysozyme for 30 min at 37C on a rocker. 0.55 ml of 2X IP buffer (100 mM Tris-HCl (pH 7.5), 200 mM NaCl, 2% Triton X-100 and 1 mM EDTA) were added to the sample, and then was sonicated to fragmentize genomic DNA. 0.3 ml of Wash buffer I (50 mM Tris-HCl (pH 7.5), 140 mM NaCl, 1% Triton X-100 and 1mM EDTA) was added to make the volume up to 1.4 ml. Only 0.7 ml was taken and transfered to a new tube, and 15 ul of Anti-c-myc mouse antibody was added, and the sample was incubated overnight at 4C to make Antibody-TF complex. 50 ul of Dynabeads Pan mouse IgG were washed 3 times with bead washing solution (250 mg BSA in 50 ml of PBS), and were added to the sample. Cell lysate with beads were incubated for 6 hours or overnight at 4C to make Dynabead-antibody-TF complex. The beads were pulled down on a magnet stand, and washed 2 times with wash buffer I and with wash buffer II (50 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1% Triton X-100 and 1mM EDTA), wash buffer III (10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1% Triton X-100 and 1mM EDTA), and wash buffer IV (10 mM Tris-HCl (pH 8.0), 1mM EDTA). The bead-bound TF-DNA complex was then end-repaired, dA-tailed, and ligated to the first adapter. Adapter-ligated sample was then treated with nick-repair reagent, and was treated with lambda exonuclease and RecJ exonuclease. Then DNA was eluted away from Dynabeads by incubating in 200 ul of elution buffer (50 mM Tris-HCl (pH 8.0), 1% SDS and 1 mM EDTA) at 65C overnight. Protein was removed by treating 4 ul of protease K and being incubated at 55C for 2 hours, and by Phenol-Chloroform-IAA extraction. Purified DNA was used to bulid the second strand synthesis, followed by another dA-tailing, second strand ligation, and 3' overhang removal stpes. Then the sequencing library was amplified with PCR enrichment.
Paired-end, strand-specific RNA-seq was performed using the dUTP method with the following modifications. The ribosomal RNAs were removed from isolated total RNA using riboPooL Probes (Pan-prokaryote) siTOOLS BIOTECH and Dynabeads™ MyOne™ Streptavidin C1 (Invitrogen #65001). Following RNA purification was performed using RNA clean & concentrator (Zymoresearch #R1013). The final purified RNA samples were used to construct RNA-seq library through KAPA stranded RNA-seq kit (Roche KK8400).

value: wild type

value: M9 minimal media with 0.2% glucose

value: mid-log


title: human, IPSCs, fraction 3, rep 2, extract

description: Library name: hR2F3ext

data_processing:
Quality control, read mapping, and quantification was performed using nf-core/rnaseq v3.8.
Reads were mapped to GRCh38 (human) or mm10 (mouse) and quantified with Salmon v1.5.2 using the Gencode v38 (human) or M25 (mouse) annotation.
Softclip, position bias, sequence, bias GC bias, Gibbs sampling bootstrap of 100 and equivalence classes calling were arguments passed to Salmon during quantification.
Assembly: GRCh38 (human), GENCODE v38
Supplementary files format and content: All data files are on .rds format

value: IPSC


title: human, IPSCs, fraction 2, rep 2, extract

description: Library name: hR2F2ext


title: Mouse uterus young rep5 H3K27ac

description: Library name: H3K27ac_10wk_MH54(7B2)


title: 9750_Kidney_Endo

description: Library name: Sample_31


title: Glucose 1 (RNA-seq)


title: human, IPSCs, fraction 11, rep 1, extract

description: Library name: hR1F11ext


title: Mouse uterus young rep3 H3K27ac

description: Library name: H3K27ac_10wk_MH52(4C2)


title: Galactose 2 (RNA-seq)

value: M9 minimal media with 0.2% galactose


title: human, IPSCs, fraction 10, rep 1, extract

description: Library name: hR1F10ext


title: human, IPSCs, fraction 5, rep 2, extract

description: Library name: hR2F5ext


title: 9734_Kidney_Endo

description: Library name: Sample_29


title: Mouse uterus young rep2 H3K27ac

description: Library name: H3K27ac_9wk_MH270(3B2)


title: Galactose 1 (RNA-seq)


title: human, IPSCs, fraction 9, rep 1, extract

description: Library name: hR1F9ext


title: hypoxic_Candida-albicans_3

description: Library name: Candida-albicans_hypoxic_3

organism: Candida albicans

value: whole cell

value: WT


title: 9733_Total_Kidney

description: Library name: Sample_28


title: Mouse uterus aged group3 rep10 H3K4me3

description: Library name: H3K4me3_60wk_MH245(7A1)


title: human, IPSCs, fraction 7, rep 1, extract

description: Library name: hR1F7ext


title: human, IPSCs, fraction 8, rep 1, extract

description: Library name: hR1F8ext


title: Mouse uterus young rep1 H3K27ac

description: Library name: H3K27ac_10wk_MH60(2C2)


title: 9732_Total_Kidney

description: Library name: Sample_26

value: saline


title: 9733_Kidney_Endo

description: Library name: Sample_27


title: hypoxic_Candida-albicans_2

description: Library name: Candida-albicans_hypoxic_2


title: human, IPSCs, fraction 6, rep 1, extract

description: Library name: hR1F6ext


title: Mouse uterus young rep4 H3K27ac

description: Library name: H3K27ac_10wk_MH53(5C2)


title: 9732_Kidney_Endo

description: Library name: Sample_25


title: Mouse uterus aged group3 rep9 H3K4me3

description: Library name: H3K4me3_60wk_MH242(6D1)


title: 9731_Total_Kidney

description: Library name: Sample_24


title: Mouse uterus aged group3 rep8 H3K4me3

description: Library name: H3K4me3_65wk_MH260(6C1)


title: Mouse uterus aged group3 rep7 H3K4me3

description: Library name: H3K4me3_60wk_MH241(6B1)


title: Mouse uterus aged group3 rep6 H3K4me3

description: Library name: H3K4me3_60wk_MH246(5D1)


title: human, IPSCs, fraction 4, rep 1, extract

description: Library name: hR1F4ext


title: 9731_Kidney_Endo

description: Library name: Sample_23


title: human, IPSCs, fraction 3, rep 1, extract

description: Library name: hR1F3ext


title: Mouse uterus aged group3 rep5 H3K4me3

description: Library name: H3K4me3_64wk_MH249(5A1)


title: Mouse uterus aged group3 rep4 H3K4me3

description: Library name: H3K4me3_54wk_MH51(4B1)


title: 9730_Total_Kidney

description: Library name: Sample_22


title: human, IPSCs, fraction 2, rep 1, extract

description: Library name: hR1F2ext


title: RPE1 cell,sg53BP1-2

city: wuhan

first: wu

last: wei

address: Shuiguohu Subdistrict

institute: Wuhan University

data_processing:
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq was used for differential gene expression analysis between two samples with non biological replicates.
Assembly: hg19
Supplementary files format and content: 53BP1 KO RNA-seq.xlsx

growth_protocol: hTERT-RPE1 cells was cultured at 37°C under 5% CO2 in DMEM supplemented with 10% FBS, 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol:
RNA was extracted by phenol/chloroform method. A total amount of 2 μg RNA per sample was used as input material for the construction of sequecing libraries.
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.

value: retinal pigment epithelium

value: 53BP1 knockout

value: no


title: Mouse uterus aged group3 rep3 H3K4me3

description: Library name: H3K4me3_63wk_MH253(3C1)


title: 9730_Kidney_Endo

description: Library name: Sample_21


title: Mouse uterus aged group3 rep2 H3K4me3

description: Library name: H3K4me3_64wk_MH34(2A1)


title: 9729_Kidney_Endo

description: Library name: Sample_19


title: RPE1 cell,sg53BP1-1


title: hypoxic_Enterococcus_faecalis_2

description: Library name: Enterococcus_faecalis_hypoxic_2


title: 9729_Total_Kidney

description: Library name: Sample_20


title: human, IPSCs, fraction 5, rep 1, extract

description: Library name: hR1F5ext

extract_protocol:
RNA was purified from sucrose fractions using Directzol RNA Miniprep kit (ZymoResearch, R2062), following the manufacturer’s instructions.
RNA-seq libraries were prepared using rRNA removal and sequenced paired-end (PE150) on the NovaSeq 6000 platform.


title: hypoxic_Candida-albicans_1

description: Library name: Candida-albicans_hypoxic_1


title: RPE1 cell,sgControl-2


title: Mouse uterus aged group3 rep1 H3K4me3

description: Library name: H3K4me3_64wk_MH44(1C1)


title: RPE1 cell,sgControl-1


title: 9728_Total_Kidney

description: Library name: Sample_18


title: WTE068-21TALLREM3

type: RNA

city: Perugia

first: Roberta

last: La Starza

address: Piazzale Menghini 9

department: Department of Medicine and Surgery

country: Italy

institute: University of Perugia

description: Remission sample for WTE037-21TALL

hyb_protocol: Hybridization of the microarrays was performed in a GeneChip® Hybridization Oven 645 (Affymetrix/Thermo Fisher Scientific). GeneChips were washed and stained

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 (Affymetrix Applied Biosystem Microarray, Thermo Fisher, Milan, Italy)

data_processing: Primary data analysis was performed with Transcriptome Analysis Console software version 4.0 (TAC 4.0.2.15). Differentially expressed RNA were estimated by fold-change filtering combined with Student’s t-test. Transcripts with fold change in expression > ±2.0 and FDR<0.05 were considered significantly differentially expressed. Hierarchical clustering was performed to show the distinguishing genes expression pattern among samples

label: biotin

source_name: BONE MARROW

label_protocol: GeneChip® WT PLUS Reagent Kit (Affymetrix Applied Biosystem Microarray, Thermo Fisher, Milan, Italy) was used to generates amplified and biotinylated sense-strand DNA targets from total RNA; it uses a reverse transcription priming method that primes the entire length of RNA. Amplified cDNA was quantified, fragmented, marked, and prepared for hybridization from the GeneChip® Clariom S Human Array (Thermo Fisher Scientific) for expression level measurement

extract_protocol: RNA was extracted from bone marrow or peripheral blood samples using a QIAamp RNA Blood Mini Kit (Qiagen) at a QIAcube automated station

value: BONE MARROW


title: WTE008-22TALLREM4

description: Remission sample for WTE037-21TALL


title: Mouse uterus aged group2 rep6 H3K4me3

description: Library name: H3K4me3_48wk_MH237(6A1)

value: uterus


title: WTE013-21TALL

source_name: PERIPHERAL BLOOD

value: PERIPHERAL BLOOD


title: 9728_Kidney_Endo

description: Library name: Sample_17

value: kidney

value: endothelial cells


title: WTE063-21TALLREM1

description: Remission sample for WTE037-21TALL


title: 9734_Total_Kidney

description: Library name: Sample_30

value: lps


title: WTE067-21TALLREM2

description: Remission sample for WTE037-21TALL


title: Mouse uterus aged group2 rep5 H3K4me3

description: Library name: H3K4me3_42wk_MH233(5B1)


title: WTE100-20TALL