title: Subjected to one cycle drought stress, Leaf, bs-Seq, rep 3

description: Library name: M3_S1_L

value: One cycle drought stress

value: replicate 3


title: T47D_ERa_Y537S-hom_shGFP_2

status: Public on Jun 10 2026

type: SRA

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

country: USA

institute: University of Minnesota

description: Library name: T47D_ERa_Y537S-hom_shGFP_2

library_source: genomic

data_processing:
Initial quality control and peak calling was performed using Nf-core ChIPseq pipeline. DeepTools v.3.5.6 bamCompare function was used to generate fold enrichment bigWig tracks for each sample compared to the IgG control and to make enrichment plots.
DiffBind was used to identify regions of differential accessibility. HOMER was used for transcription factor motif analysis and peak annotation.
Assembly: Hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
T47D WT and Y537S ESR1 cells (shGFP and shPR) were hormone-starved for 48h and then treated with vehicle or R5020 (10 nM, 1h). 1 x 10e6 cells were harvested in ice-cold PBS. Cells were crosslinked in 1% formaldehyde in PBS. Crosslinking was quenched by adding glycine at a final concentration of 125 mM. Crosslinked cell pellets were snap-frozen and stored at -80°C. For each ChIP experimental replicate, 2 x 10e6 crosslinked cells (from 2 crosslinked aliquots) were lysed in lysis buffer with PICS III using sonication (high, 30 seconds on/off, for 5 intervals of 10 minutes). 5% of lysate was reserved for input control and snap frozen to store at -80°C. Lysates were diluted to 1 µg/µl protein based on Nanodrop A280 concentrations and divided into 1 ml aliquots. 5 µg of the appropriate antibodies (phospho-PR [S294] for phospho-PR ChIP, rabbit IgG for phospho-PR negative control) were added to the appropriate lysate aliquots and rotated at 4°C overnight.
Protein-chromatin was isolated and eluted using protein G beads (Cytiva Streptavidin Mag Sepharose Magnetic Beads, Thermo Fisher). Eluted ChIP samples were incubated with RNAse A and Proteinase K to reverse the crosslinked protein-chromatin. Input samples and ChIP-DNA were purified using a Qiagen QIAquick PCR Purification Kit, and purified DNA samples were eluted in 30 µl nuclease-free water. ChIP-DNA was quantitated by Qubit (Life Technologies), libraries were generated using the Illumina ChIP-SEQ kit and quality assessed using Bioanalyzer (Agilent). Sequencing was performed on the Illumina NovaSeq X by the University of Chicago Functional Genomics core. Samples were analyzed over 50M clusters per sample, which was variable due to the available library content.

tag: cell line

tag: cell type

value: breast cancer

tag: chip antibody

value: phosphoPR

tag: treatment

value: shGFP


title: Subjected to one cycle drought stress, Leaf, bs-Seq, rep 2

city: Beaucouze

first: Sandrine

last: Balzergue

address: 42 rue G. Morel

country: France

institute: INRAE

description: Library name: M2_S1_L

data_processing:
Paired-end sequencing (150 bp read length) was performed on the Illumina NovaSeq 6000 system. Adapter trimming and removal of low-quality reads were carried out using Trimmomatic (Bolger et al., 2014). Sequencing quality was assessed using MultiQC (Ewels et al., 2016), and alignments were performed with Bismark (Krueger and Andrews, 2011) using the M. domestica GDDH13 v1.1 genome.
Methylation levels were analysed using a sliding-window approach implemented in the methylKit R package (Akalin et al., 2012), with a window size of 1000 bp and a step size of 100 bp. Differentially methylated regions (DMRs) were defined as regions with at least 10× coverage, a minimum 25% difference in methylation levels, and a q-value < 0.01. All three methylation contexts (CG, CHG, and CHH) were examined. Genes located within 2 kb of each DMR were identified.
Assembly: M. domestica GDDH13 v1.1 genome
Supplementary files format and content: classical report.txt files for each sample

organism: Malus domestica

source_name: Leaf

growth_protocol: Apple seedlings were grown in the greenhouses of France's National Research Institute for Agriculture, Food and Environment (INRAe) in Angers, France (47° 28' 36.804'' N 0° 36' 41.4'' W). The seeds from ‘Golden Delicious’ double haploid 18 (GDDH18; Daccord et al., 2017) were stratified for 3 months in a 1:1 mixture of sand and vermiculite (humidity of 70%) and kept at 3 °C for 90 days. After the period of stratification, the seeds were sown in a soil mixture containing 50% peat moss, 40% perlite, 10% coco fibers, 7.5kg/ea carbonates and N-P-K mix 14-16-18. The sowing was performed in three blocks, interspersed by one week each, representing three biological replicates. The germination was carried out in a greenhouse (ambient light; 21 °C ± 5 °C; relative humidity 60 % ± 20). Four weeks after germination, the seedlings were transplanted into 0.4 L plastic pots using the same soil mixture and maintained under the same environmental conditions. At eight weeks of age, the seedlings were transferred to final 1 L pots and grown for an additional four weeks before the initiation of drought stress (DS) cycles.

extract_protocol:
All leaf and root samples were ground into a fine powder in liquid nitrogen and stored at -80 °C until nucleic acid extraction. Genomic DNA (gDNA) was extracted from 50 mg of freshly ground tissue powder, collected at the same time points as the RNA-seq samples, using the NucleoSpin™ Plant II kit (Macherey-Nagel, Germany).
Libraries were prepared using the NEBNext® Enzymatic Methyl-seq Library Prep Kit (New England Biolabs, USA) according to the manufacturer’s protocol.

treatment_protocol: Irrigation management was conducted by monitoring the soil water content (SWC) of all plants every two days using pot weighing. During well-watered (WW) periods, plants were maintained near field capacity (FC; 80% SWC), whereas during drought stress (DS) periods, irrigation was adjusted to maintain SWC at 45% of FC. The SWC corresponding to 100% FC was determined for the previously described soil mix by saturating pots with water and allowing free drainage for 24 hours. Two distinct irrigation regimes were established : (I) Control group (64 plants): maintained under WW conditions throughout the entire experiment. (II) Multiple-DS group (61 plants): subjected to three consecutive drought cycles, each consisting of three weeks under DS conditions followed by three weeks of recovery (as WW condition). To investigate long-term transcriptomic and epigenetic memory responses, in year n+1, roots and leaves from Control and Multiple-DS plants were also sampled prior to the application of a new stress (Before Stress – BS), after completing one winter cycle.

tag: tissue

value: Leaf

tag: genotype

value: Golden Delicious double haploid 18_ GDDH18

tag: batch

value: replicate 2


title: bESC.NBFRA.MF.LO2.E

city: Davis

first: Anna

last: Denicol

state: CA

address: 2251 Meyer Hall, One Shields Ave

department: Animal Science Department

institute: University of California Davis

description:
Library name: Sample 4
PE150

library_source: transcriptomic

data_processing:
Trimmomatic was used to trim adaptors with the following settings: SLIDINGWINDOW:4:15 MINLEAN: 36 LEADING:3 TRAILING:3.
Assembly: Alignment was performed using star/2.7.10a (default settings) and Bos taurus reference genome UCD2.0 NCBI.
Supplementary files format and content: Raw counts table was prepared using FeatureCounts (subread/1.6.2), using -p -O -g gene_id arguments. Raw data was processed removing low counts and normalization with edgeR, TMM function.

molecule: total RNA

organism: Bos taurus

source_name: embryonic stem cells

growth_protocol: Bovine ESCs were derived from early (eBL) or full (BL) blastocyst-staged embryos and maintained in NBFR medium on mouse embryonic fibroblast feeders (Guiltinan et al 2025; DOI: 10.1242/bio.061819). Then, those cells lines were adapted in low oxygen conditions (5%) on mouse embryonic fibroblasts (MEF) during 5 passages (samples 1-4). Then, bESCs were transitioned into feeder-free in low oxygen conditions (samples 5-8).

extract_protocol:
Total RNA was isolated using the Trizol method with DNAse treatment (12185010, Invitrogen).
Library preparation was performed using 1000 ng input with the NEBNext Ultra II kit.

value: embryonic stem cells

value: E

value: bovine ESC

value: XX

value: low O2, MEF


title: Spawning Female 3

city: West Lafayette

first: Harish

last: Kothandaraman

state: Indiana

address: 201S University St

department: Purdue Institute for Cancer Research

institute: Purdue University

description:
Library name: SF3
X3IIA

data_processing:
Reads were trimmed with fastp, assembled with Trinity.Contaminant sequences (non-fish transcripts) assembled were removed based on hits from Kaiju using a custom database containing proteins from various fishes. Nr+Euk run was performed using online Kaiju, and the results from the two were ranked to retain hits to fishes. For ncRNAs, we performed discontinous megablast and megablast were performed on the discarded transcript to recover fish related ncRNAs.
Evidential Gene was used to generate a non-redundant pool of transcripts. Reads were quantified to the non-redundant transcripts and contaminant transcripts with salmon exporting the resultant BAMs, and we use ngs_disambiguate to remove contaminant reads. Retained reads were used for requantification and binning transcripts to genes with Grouper.
Gene level counts are derived using Salmon, by passing the Grouper based transcript to gene assignments
Assembly: nr_final.fa.gz = transcript assembly; all_tx2clust.tsv = the transcripts -> cluster catalogue
Supplementary files format and content: txt

organism: Schizothorax plagiostomus

source_name: Ovaries

extract_protocol:
RNA was extracted using Trizol reagent and Total RNA quality and quantity was assessed using Agilent 4150 TapeStation system and Qubit 4 Fluorometer. The rRNA depleted using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat), Cat. No. #E6310X by following manufacturer’s protocol.
RNA-Seq libraries were prepared rRNA depleted sample using NEBNext® UltraTM II RNA Library Prep Kit for Illumina®, (E7770L), according to manufacturer’s protocols and quality and quantity was assessed using Agilent 4150 TapeStation system and Qubit 4 Fluorometer.

value: Ovaries

tag: maturational stage

value: Spawning

tag: Sex

value: female


title: Post Spawning Female 2

description:
Library name: PoSF2
X4IIIA

value: Post Spawning


title: Spawning Female 2

description:
Library name: SF2
X2_2A


title: Subjected to one cycle drought stress, Leaf, bs-Seq, rep 1

description: Library name: M1_S1_L

value: One cycle drought stress

value: replicate 1


title: NC2, healthy

city: Nanning

first: xiaoping

last: su

state: Guangxi

address: shuangyong road

country: China

institute: guangxi medical university

description: Library name: NC2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean data (clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw data were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself.
Summarizing all alignments and annotations obtained before. In the alignment and annotation before, some small RNA tags may be mapped to more than one category. To make every unique small RNA mapped to only one annotation, we follow the following priority rule: known miRNA > rRNA > tRNA > snRNA > snoRNA > repeat > gene > NAT-siRNA > gene > novel miRNA > ta-siRNA. The total rRNA proportion was used a marker as sample quality indicator. Usually, it should be less than 60% in plant samples and 40% in animal samples as high quality.
Assembly: ensembl_97_rattus_norvegicus_rnor_6_0_toplevel
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: gingiva

growth_protocol: The SDrats were maintained between 22 and 24℃ in standard ventilated cages holding 3 rats per cage and water ad libitum. The rats in the H and PH groups were fed a high-salt diet (containing 8% NaCl) for 7 weeks, while the rats in the NC and P groups were given standard maintenance feed, with all groups allowed free access to food and water.

extract_protocol:
The gingival tissues of the mandibular first molars were collected for RNA extraction.
Sequencing libraries were generated using NEB Next® Multiplex Small RNA Library Prep Set for Illumina® （NEB  E7300L）. Briefly, 3’ and 5’ adaptors were ligated to 3’ and 5’ end of small RNA, respectively. Then the first strand cDNA was synthesized after hybridazition with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between18~40 bp were ready for sequencing on Illumina sequencing with SE50. Subsequently, library quality was assessed on the Agilent 5400 system（Agilent，USA）and quantified by QPCR（1.5nM）. The Qualified libraries were pooled and sequenced on Illumina platforms with SE50 strategy in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to effective library concentration and data amount required.

value: gingiva


title: T47D_ERa_Y537S-hom_Pooled_Input_2

description: Library name: T47D_ERa_Y537S-hom_Pooled_Input_2

value: breast cancer

value: rabbit Igg


title: NC1, healthy

description: Library name: NC1


title: Control (maintained under well-watered ) and sampling after the first drought stress , Leaf, bs-Seq, rep 3

description: Library name: C3_S1_L

value: Leaf

value: Control

value: replicate 3


title: T47D_ERa_WT_shPR_2

description: Library name: T47D_ERa_WT_shPR_2

value: phosphoPR

value: shPR


title: hTERT-HM cells day 6 rep1

city: St. Louis

first: Ritu

last: Dave

address: 425 S Euclid Ave

institute: Washington University School of Medicine

description:
Library name: sample8
column name in all.gene_counts.xlsx: sample.Day_6_A

data_processing:
Fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases.Basecalls and demultiplexing were performed with Illumina’s DRAGEN BCLconvert version 4.3.13.
RNA-seq reads were then aligned to the Ensembl GRCh38.113 primary assembly with STAR version 2.7.11b.
Gene counts were derived from the number of uniquely aligned unambiguous fragments by Subread:featureCount version 2.0.8. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.10.0.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 5.04.
Assembly: GRCh38.113
Supplementary files format and content: xlsx file includes raw counts for each Sample

source_name: myometrium

extract_protocol:
RNA was extracted using the Zymo Research RNA Miniprep kit. Library preperation was done with 1ug of total RNA.
Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (NEBNext Poly(A) mRNA Magnetic Isolation module, New England Biolabs). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

value: myometrium

value: hTERT-HM

value: myometrial cell

value: WT


title: TC1, differentiated 10 days, rep3

city: Oklahoma City

first: Jacob

middle: Gordon

last: Kirkland

state: OK

address: 825 NE 13th St

department: Cell Cycle and Cancer Biology

institute: Oklahoma Medical Research Foundation

description: Library name: CMd10_3

data_processing:
Kallisto V1
DEseq2
Assembly: V1 mouse_index_standard
Supplementary files format and content: .tsv files of pseudoaligned read counts
Supplementary files format and content: .xlsx file of DEseq2 results table

organism: Mus musculus

extract_protocol:
TRI Reagent (Sigma-Aldrich)
SMART-Seq Total RNA High Input (RiboGone Mammalian)

value: differentiated cells

value: wild-type

value: differentiated


title: PH3, periodontitis, hypertension

description: Library name: Sample9

data_processing:
Filtering of sequencing data: adapter reads were removed; reads with more than 10% N content (N means base information could not be determined) were removed; Low-quality reads(reads with a base number of Qphred<=5 accounting for more than 50% of the entire read length) were removed.
Hisat2 software was used to quickly and accurately align the clean reads with the reference genome to obtain the location information of the Reads on the reference genome.
Reads were spliced into transcripts and quantified using Stringtie software based on the results of alignment to the genome.
The Stringtie software merge parameter was used to merge the transcripts obtained from each sample splicing, and the transcripts with uncertain chain direction and the length of transcripts less than 200nt were removed. Then gffcompare software was used to compare the transcripts with the known database and filter out the known transcripts in the database. Finally, the coding potential of the selected new transcripts was predicted, and Novel_lncRNA and Novel_mRNA were finally obtained.
EdgeR software was used to analyze the significance of expression differences. pvalue or corrected pvalue (padj) was used to determine the significance level.
ClusterProfiler software was used to perform GO functional enrichment analysis and KEGG pathway enrichment analysis of the differential gene sets.
Assembly: ensembl_97_rattus_norvegicus_rnor_6_0_toplevel
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Trizol was used for RNA extraction from gingival tissues.
sequencing libraries were constructed with TruSeq RNA Sample Prepara-tion Kits v2 (Illumina) for mRNA/lncRNA. library quality was assessed on the Agilent 5400 system and quantified by QPCR. The Qualified libraries were pooled and sequenced on Illumina platforms with PE150 strategy.

treatment_protocol: The gingival tissues of the mandibular first molars were collected for RNA extraction.


title: Pre Spawning Female 2

description:
Library name: PrSF2
X2_1A

value: Ovaries

value: Pre Spawning

value: female


title: T47D_ERa_WT_shGFP_2_1_R5020

description: Library name: T47D_ERa_WT_shGFP_2_1_R5020

value: breast cancer


title: Control (maintained under well-watered ) and sampling after the first drought stress , Leaf, bs-Seq, rep 2

description: Library name: C2_S1_L

value: Golden Delicious double haploid 18_ GDDH18

value: replicate 2


title: Post Spawning Female 1

description:
Library name: PoSF1
X1_3A

value: Post Spawning


title: PH2, periodontitis, hypertension

description: Library name: Sample8

value: gingiva


title: T47D_ERa_WT_shGFP_2

description: Library name: T47D_ERa_WT_shGFP_2

value: phosphoPR

value: shGFP


title: Control (maintained under well-watered ) and sampling after the first drought stress , Leaf, bs-Seq, rep 1

description: Library name: C1_S1_L

value: Leaf

value: Control

value: replicate 1


title: Control (maintained under well-watered )  and sampling in year n+1  after one winter cycle, Leaf, bs-Seq, rept 1

description: Library name: C1_LTM_L

value: Control, Long Term Memory


title: Spawning Female 1

description:
Library name: SF1
X1_2A

value: Spawning


title: Subjected to three cycles drought stress and sampling in year n+1  after completing one winter cycle,Root, rept 3

description: Library name: M3_LTM_RO

data_processing:
Raw data quality was checked using FastQC (Andrews, 2010) and the estimation of transcript-level abundance was performed by Salmon tool (Patro et al., 2017) using default parameters. The reads were aligned against the Malus domestica GDDH13 genome v1.1 (Daccord et al., 2017).
The differential gene analysis was performed by the R package DESeq (Anders and Huber, 2010). The genes presenting a p-value lower than 0.05 were considered as differentially expressed in this study.
Assembly: Malus domestica GDDH13 genome v1.1 (Daccord et al., 2017).
Supplementary files format and content: for each comparison, txt file with at list logCPM_Ttmt_Drought, logCPM_Ctrl_Control, logFC,pval_DESeq2and BH_DESeq2

source_name: Root

extract_protocol:
For each tissue and condition, approximately 50 mg (fresh weight) were used for total RNA extraction using the NucleoSpin® RNA Plus kit (Macherey Nagel, Germany).
libraries were built using the NEB® mRNA stranded library preparation kit (New England Biolabs, USA). Sequencing was performed using Illumina NovaSeq S4 in a paired-end (PE) mode with read length 100 bp. A minimum of 25 million PE reads per sample were generated

treatment_protocol: Irrigation management was conducted by monitoring the soil water content (SWC) of all plants every two days using pot weighing. During well-watered (WW) periods, plants were maintained near field capacity (FC; 80% SWC), whereas during drought stress (DS) periods, irrigation was adjusted to maintain SWC at 45% of FC. The SWC corresponding to 100% FC was determined for the previously described soil mix by saturating pots with water and allowing free drainage for 24 hours. Two distinct irrigation regimes were established : (I) Control group (64 plants): maintained under WW conditions throughout the entire experiment. (II) Multiple-DS group (61 plants): subjected to three consecutive drought cycles, each consisting of three weeks under DS conditions followed by three weeks of recovery (as WW condition). To investigate long-term transcriptomic and epigenetic memory responses, in year n+1, roots and leaves from Control and Multiple-DS plants were also sampled prior to the application of a new stress (Before Stress – BS), after completing one winter cycle. For root samples only,  two biological replicates was performed due to the limited availability of root for this treatment.

value: Root

value: Golden Delicious double haploid 18 (GDDH18)

value: Three cycles drought stress, Long Term Memory

value: replicate 3


title: Pre Spawning Female 1

description:
Library name: PrSF1
X1_1A

value: Ovaries

value: Pre Spawning

value: female


title: P3, periodontitis

description: Library name: Sample6


title: P2, periodontitis

description: Library name: Sample5


title: T47D_ERa_Y537S-hom_shGFP_1_R5020

description: Library name: T47D_ERa_Y537S-hom_shGFP_1_R5020

value: breast cancer


title: T47D_ERa_Y537S-hom_shPR_1

description: Library name: T47D_ERa_Y537S-hom_shPR_1

value: shPR


title: Control (maintained under well-watered )  and sampling in year n+1  after completing one winter cycle, Root, rept 3

description: Library name: C3_LTM_RO


title: P1, periodontitis

description: Library name: Sample4

value: gingiva


title: E3dF2h_rep6

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

description:
Library name: Sample 30
g130

data_processing:
base-calling:RTA and bcl2fastq
adapter trim: trimmomatic
alignment: HISAT2
aligned reads count: featureCounts
normalize: DESeq2
Assembly: TAIR10
Supplementary files format and content: rawCounts

organism: Beta vulgaris subsp. vulgaris

source_name: shoot

growth_protocol: Arabidopsis seedlings were grown in pots containing horticultural cray granule soil at 22 °C with a 16 h light (110 to 140 µmol m-2 s-1 photon flux density) / 8 h dark cycle.

extract_protocol:
Total RNAs were extracted using purelink Plant RNA Reagent (Thermo Fisher Scientifc Inc., Waltham, MA, USA).
The sequencing library was prepared using the Lasy-Seq method (Kamitani et al. 2019). Specifically, 200 ng of total RNA was used per sample.

treatment_protocol: Fourteen-day-old plants grown in pots were used for ethanol pretreatment. The bottoms of the pots were dipped into 20 mM ethanol solution and kept for 6 days. After ethanol pretreatment, the pots were subjected to freezing temperature treatment at -4.0 °C onvernight by a low-temperature incubator. During the freezing temperature stress treatment, the pots were electrically rotated in the incubator to avoid the local effect. After the treatment, the pots were returned to the growth room and maintained for the indicated time periods.

value: shoot


title: T47D_ERa_Y537S-hom_shGFP_1

description: Library name: T47D_ERa_Y537S-hom_shGFP_1

value: phosphoPR

value: shGFP


title: E3dF2h_rep5

description:
Library name: Sample 29
g129


title: NC3, healthy, control

description: Library name: Sample3


title: Subjected to three cycles drought stress and sampling in year n+1  after completing one winter cycle, Leaf, rept 3

description: Library name: M3_LTM_LF

value: Leaf


title: E3dF2h_rep4

description:
Library name: Sample 28
g128


title: NC2, healthy, control

description: Library name: Sample2


title: T47D_ERa_WT_shPR_1

description: Library name: T47D_ERa_WT_shPR_1


title: Subjected to three cycles drought stress and sampling in year n+1  after completing one winter cycle, Leaf, rept 2

description: Library name: M2_LTM_LF

value: replicate 2


title: NC1, healthy, control

description: Library name: Sample1


title: Subjected to three cycles drought stress and sampling in year n+1  after completing one winter cycle, Leaf, rept 1

description: Library name: M1_LTM_LF

value: replicate 1


title: T47D_ERa_WT_shGFP_1_R5020

description: Library name: T47D_ERa_WT_shGFP_1_R5020


title: Control (maintained under well-watered )  and sampling in year n+1  after completing one winter cycle, Leaf, rept 3

description: Library name: C3_LTM_LF

value: Control, Long Term Memory


title: T47D_ERa_WT_shGFP_1

description: Library name: T47D_ERa_WT_shGFP_1


title: E3dF2h_rep1

description:
Library name: Sample 25
g125


title: Enriched uracil-DNA from 2.5 hpf Zebrafish embryos

city: Budapest

first: Angela

last: Bekesi

address: Műegyetem rakpart 3.

department: Department of Applied Biotechnology and Food Science

country: Hungary

institute: Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology

description:
Library name: U-DNA_enriched
DIP-seq

data_processing:
trimming using trimmomatic (ILLUMINACLIP:adapter.fa:2:15:5:2:keepBothReads LEADING:20 TRAILING:20 MINLEN:50)
alignment to the GRCz11 reference genome using BWA
filtering for uniquely mapped reads using samtools
calculate read coverage using the deeptools bamCoverage tool for 100 nt bins with 5000 nt smoothing and RPGC normalization
calculate log2(fold change) signal tracks using the deeptools bigWigCompare tool
extraction of U-DNA enriched regions from log2(fold change) signal tracks at three different thresholds (0.25, 0.5, and 1) using a custom script that includes bigWigToWig, awk, bigWigAverageOverBed.
Assembly: GRCz11
Supplementary files format and content: Read coverage tracks in bigwig format (*.bw)
Supplementary files format and content: log2 (fold change) signal track for enriched / input data in bigwig format (*log2.bw)
Supplementary files format and content: enriched intervals in BED format (*.bed)

organism: Danio rerio

source_name: embryo

growth_protocol: The wild-type (AB) zebrafish strain was maintained and bred in the animal facility of the Biology Institute of  Eötvös Loránd University, adhering to the standards of the field.

extract_protocol:
gDNA was isolated from 2.5 hpf embryos by lysis and proteinase K treatment, followed by ethanol precipitation and RNase treatment. As a final step of purification extraction with phenol:chloroform:isoamyl alcohol (25:24:1), and ethanol precipitation was performed. gDNA quality was checked by agarose gelelectrophoresis, the quantity was determined by Qubit assay. gDNA was sonicated to 300-500 bp fragments. Uracil-containing fragments were pull-down using flag-tagged U-DNA sensor and ANTI-FLAG(R) M2 Affinity Gel (Merck, Sigma). Input and enriched samples were sequenced.
Library preparation and sequencing were performed by iBioScience Ltd. (Pécs, Hungary). The libraries for Illumina sequencing were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, Ipswitch, MA, USA). The quality of the library was checked on 4200 TapeSation System using D1000 Screen Tape (Agilent Technologies, Palo Alto, CA, USA), and the quantity was measured on Qubit 3.0 (Thermo Fisher, Waltham, MA, USA). The sequencing was performed on a NovaSeq 6000 instrument (Illumina, San Diego, CA, USA) with 2x151 run configuration.

value: embryo

tag: developmental stage

value: 2.5 hpf

tag: strain

value: AB

value: wild-type


title: Isolated genomic DNA from 2.5 hpf Zebrafish embryos

description:
Library name: U-DNA_input
DIP-seq input


title: T47D_ERa_WT_Pooled_Input_1

description: Library name: T47D_ERa_WT_Pooled_Input_1

value: rabbit Igg


title: Control (maintained under well-watered )  and sampling in year n+1  after completing one winter cycle, Leaf, rept 2

description: Library name: C2_LTM_LF

value: Golden Delicious double haploid 18 (GDDH18)


title: ambpko-HFD

city: Zhan Jiang

first: Xiaoyu

last: Li

state: Guangdong

address: 57 People's Avenue

institute: Affiliated Hospital of Guangdong Medical University

description: Library name: Sample2

data_processing:
The clean data were mapped to the reference genome using Hisat2 software. Guiding by the Ensembl GTF gene annotation file, featureCounts was used to obtain the gene level FPKM as the expression profiles of mRNA, fold change and p-value were calculated based on FPKM.
Assembly: GRCz11
Supplementary files format and content: Excel format; expression matrix; count; FPKM

source_name: Liver

extract_protocol:
Total liver RNA was extracted using the TRIzol reagent.After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads,Then the enriched mRNA was fragmented into short fragments using fragmentation buffer.
mRNA was transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina

value: Liver

value: ambp ko

value: high-fat diet


title: JJN3 ka-kd rep2

city: Berlin

first: Stefan

last: Habringer

address: Hindenburgdamm 30

department: Hematology, Oncology and Cancer Immunology

country: Germany

institute: Charité - Universitaetsmedizin Berlin

description:
Library name: JJN3ka-kd_rep2
replicate 2 fastqs

data_processing:
The ATAC-seq data was then processed with a nf-core pipeline (v/2.1.2/).
Bowtie2 was used to map the reads to the human reference genome hg38. Then duplicated reads and reads mapped to the ENCODE blacklist regions v3 were removed from the bam files.
Peaks called by MACS2 (25) were then filtered to the consensus ones within each group of replicates. EdgeR (26) was used to detect the differentially accessible peaks in the JJN-3-KANSL2-KD vs. JJN-3 control samples
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: Two weeks post transduction of KANSL2-KD, bulk ATAC-seq was performed using 0.5 x 10^5 cells per sample.

extract_protocol:
Following centrifugation, cells were lysed and tagmented for 30 min in buffer (33 mM Tris-acetate, 66 mM Potassium acetate, 11 mM Magnesium acetate, 16% Dimethylformamide) containing in-house Tn5 transposase. DNA was then isolated using the Biozol Clean & Concentrator(™)-5 kit.
Tagmented DNA was amplified, and Illumina-compatible adapters were added during library preparation. Libraries were purified and sequenced on an Illumina NovaSeq X Plus system with a 25B flow cell in paired-end mode.

value: knockdown


title: Control (maintained under well-watered )  and sampling in year n+1  after completing one winter cycle, Leaf, rept 1

description: Library name: C1_LTM_LF


title: WT-HFD

description: Library name: Sample1

value: WT


title: Subjected to three cycles drought stress, Root, rep 3

description: Library name: M3_S3_RO

value: Root

value: Three cycles drought stress

value: replicate 3


title: JJN3 ka-kd rep1

description:
Library name: JJN3ka-kd_rep1
replicate 1 fastqs


title: JJN3 control rep2

description:
Library name: JJN3control_rep2
replicate 2 fastqs

value: control


title: W3dF2h_rep4

description:
Library name: Sample 22
g122

value: shoot


title: Subjected to three cycles drought stress, Root, rep 2

description: Library name: M2_S3_RO

value: replicate 2


title: JJN3 control rep1

description:
Library name: JJN3control_rep1
replicate 1 fastqs


title: Subjected to three cycles drought stress, Root, rep 1

description: Library name: M1_S3_RO

value: replicate 1


title: W3dF2h_rep2

description:
Library name: Sample 20
g120


title: Cortical neurons, shOpa1, Day 11, rep2 [6-OBD11]

city: Ottawa

first: Ruth

last: Slack

state: Ontario

address: 451 Smyth Road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

data_processing:
Indexed BAM files were aligned to mm10 genome using Hisat2.
Data normalization and differential gene expression was determined using DESeq2.
Assembly: mm10
Supplementary files format and content: Tab-limited text files include raw counts for 6 samples.

source_name: brain

growth_protocol: Primary cortical neurons were prepared from embryonic cortices at day E14.5-15 of CD1 mice and cultured in vitro for 11 days.

extract_protocol:
RNA was extracted using PureLink RNA mini Kit following the manufacture’s manual.
RNA from 3 biological replicates was sent to the Nation Research Council Canada (NRC). cDNA library was prepared using TruSeq Stranded mRNA kit

treatment_protocol:
Cells were seeded at a density of 1 million cells/ml. Neurons were cultured in neurobasal media containing 1X B27; 1X N2; 100 Units/mL Penicillin/Streptomycin, and 0.6 mM L-glutamine. Cells were treated with the mitotic inhibitor cytosine arabinoside at 2uM.
A 50 % Media change is performed every 3-4 days and a full media change 3 days following Ara-C treatment. Lentiviral transduction was performed at day 6 and cells were harvested for RNA extraction on day 11.

value: brain

value: primary cell

value: cortical neurons

value: Opa1 knock-down

value: neuron differentiation


title: Cortical neurons, shOpa1, Day 11, rep1 [4-OAD11]


title: W3dF2h_rep1

description:
Library name: Sample 19
g119


title: Cortical neurons, shControl, Day 11, rep3 [11-CCD11]


title: oml 28dpl, biological rep3

type: RNA

city: Frankfurt

first: Jessica

last: Schlaudraff

address: Heinrich-Hoffmann-Straße

institute: Klinische Neuroanatomie

description: gene expression data from tissue of the outer molecular layer 28 days postlesion

hyb_protocol: The Encore Biotin Module Kit (NuGEN) was then used for fragmentation and labeling of cDNA for analysis on Affymetrix Gene Chips. Samples were hybridized on a Mouse Gene 1.0 ST array  (Affymetrix)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Applied Biosystems)

data_processing: The data were checked with Expression console (Affymetrix) and analyzed with Partek-Software 6.5 (Partek) using default analysis settings.

label: biotin

source_name: 28 days postlesion

label_protocol: Total RNA was transcribed into cDNA and amplified with Single Primer Isothermal Amplification (SPIA) technology including in Ovation® Pico WTA System (NuGEN).

growth_protocol: 12 weeks old adult male Wildtype mice (C57Bl6/J@RJ ) were purchased from Janvier.

extract_protocol: Total RNA was isolated with RNeasy Plus Micro Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Experimental animals with transaction of the perforant path (n = 2-3 each time point) were allowed to survive 1, 3, 7, 14 or 28 days.

value: outer molecular layer


title: oml 28dpl, biological rep2

description:
gene expression data from tissue of the outer molecular layer 28 days postlesion
batch remover, other scan date


title: Control (maintained under well-watered ) and sampling after the third drought stress , Root, rep 2

description: Library name: C2_S3_RO

value: Golden Delicious double haploid 18 (GDDH18)

value: Control


title: E3d_rep6

description:
Library name: Sample 18
g118


title: Cortical neurons, shControl, Day 11, rep2 [5-CBD11]


title: Control (maintained under well-watered ) and sampling after the third drought stress , Root, rep 1

description: Library name: C1_S3_RO


title: E3d_rep5

description:
Library name: Sample 17
g117


title: Cortical neurons, shControl, Day 11, rep1 [3-CAD11]


title: oml 28dpl, biological rep1


title: Subjected to one cycle drought stress, Root, rep 3

description: Library name: M3_S1_RO

value: One cycle drought stress


title: E3d_rep4

description:
Library name: Sample 16
g116


title: oml 14dpl, biological rep3

description: gene expression data from tissue of the outer molecular layer 14 days postlesion

source_name: 14 days postlesion


title: Subjected to one cycle drought stress, Root, rep 2

description: Library name: M2_S1_RO


title: oml 14dpl, biological rep2


title: CBO, EB60, Rep 1

city: Gyeongsan

first: Byoung-San

last: Moon

state: Gyeongbuk

address: 280 Deahak-ro

department: Medical Biotechnology

country: South Korea

institute: Yeungnam University

description:
Library name: EB60_1
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw BCL files were demultiplexed to FASTQ files using Cell Ranger (v3.1.0) and aligned to the GRCh38 human reference transcriptome.
Filtered feature-barcode matrices were generated following barcode and UMI counting.
Low-quality cells were excluded based on the following thresholds: fewer than 500 UMIs, fewer than 250 detected genes, or mitochondrial transcript proportion exceeding 20%.
Each sample was normalized and scaled using SCTransform while regressing out mitochondrial transcript proportion (Seurat v4.1.1).
Samples within the same timepoint (EB60 or EB120) were integrated using canonical correlation analysis on 5,000 highly variable genes.
Assembly: GRCh38
Supplementary files format and content: Seurat object (.rds file)
Supplementary files format and content: Feature bc matrix (.h5 files)

molecule: nuclear RNA

source_name: Brain organoid

growth_protocol: CBOs were generated from hiPSCs following Pasca’s protocol with minor modifications (Paşca et al., 2015). hiPSC colonies at 60-70% confluence in Primaria dishes (Corning 100 mm ULA dish, Cat. 4615) were detached using 10% Dispase (STEMCELL Technologies Inc.) and transferred to ultra-low attachment plates to form embryoid bodies in mTeSR medium supplemented with 10 μM SB431542, 5 μM dorsomorphin, and 10 μM Y27632, with daily medium changes. On day 6, neuroectoderm induction was initiated in Neurobasal-A medium containing 1X B27 supplement without vitamin A, 1X penicillin/streptomycin, 1X GlutaMAX, 20 ng/ml bFGF, and 20 ng/ml EGF, with daily medium replenishment. From days 26 to 43, neural differentiation was promoted by supplementing the medium with 20 ng/ml NT3 or 20 ng/ml BDNF, with medium changes every other day. From day 44 onward, organoids were matured in Neurobasal-A medium supplemented with 1X B27, 1X penicillin/streptomycin, and 1X GlutaMAX, with medium replacement every other day.

extract_protocol:
CBOs at EB60 and EB120 were dissociated using papain/DNase I at 37°C for 30 min and triturated into single-cell suspensions. Cells were pelleted and lysed for 3 min in cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Igepal CA-630, 0.01% digitonin, 1% BSA), then washed with chilled wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA), and nuclei were pelleted at 500 rcf for 5 min at 4°C
Single-cell libraries were constructed using the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics), targeting 10,000 cells per sample. GEM-based barcoding was followed by reverse transcription to generate 10X barcoded cDNA.

value: Brain organoid

value: brain cells

tag: developmental timepoint

value: embryoid body day 60 (EB60, immature)


title: Subjected to one cycle drought stress, Root, rep 1

description: Library name: M1_S1_RO

value: Root


title: oml 14dpl, biological rep1


title: E3d_rep2

description:
Library name: Sample 14
g114


title: CBO, EB120, Rep 2

description:
Library name: EB120_2
10x Genomics

value: embryoid body day 120 (EB120, mature)


title: E3d_rep1

description:
Library name: Sample 13
g113

value: shoot


title: CBO, EB120, Rep 1

description:
Library name: EB120_1
10x Genomics


title: W3d_rep6

description:
Library name: Sample 12
g112


title: oml 7dpl, biological rep1

description: gene expression data from tissue of the outer molecular layer 7 days postlesion

source_name: 7 days postlesion


title: Cortical neurons, shOpa1, Day 11, rep3 [12-OCD11]


title: Control (maintained under well-watered ) and sampling after the first drought stress , Root, rep 1

description: Library name: C1_S1_RO


title: oml 3dpl, biological rep3

description: gene expression data from tissue of the outer molecular layer 3 days postlesion

source_name: 3 days postlesion


title: 15Ai_C06-500nM_replicate-3

city: Reno

first: Peter

middle: L

last: Jones

state: NV

address: 1664 N. Virginia St.

department: Pharmacology

institute: University of Nevada, Reno School of Medicine

description: Library name: C03

data_processing:
Raw sequencing reads were processed using the standard RNA-seq analysis pipeline provided by GENEWIZ (Azenta Life Sciences).
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.  Only unique reads that fell within exon regions were counted.  If a strand-specific library preparation was performed, the reads were strand-specifically counted.
Assembly: GRCh38
Supplementary files format and content: csv files include raw counts for each Sample

growth_protocol: Immortalized FSHD1 myotubes (15Abic) were maintained in RoosterNourish MSC medium (RoosterBio) and cultutred on 0.1 % gelatin-coated dishes at 37°C with 5% CO2.

extract_protocol:
RNA was harvested using TRIzol Reagent (Ambion Life Technologies), followed by phenol-chloroform extraction and purification with RNeasy MinElute Cleanup Kit (QIAGEN), according to the manufacturer’s instructions.  2 µg of total RNAs were used for the construction of sequencing libraries.
RNA libraries and sequencing were performed by GENEWIZ (Azenta Life Sciences)

treatment_protocol: For C06 treatment, once the cells reached 70-80% confluence, differentiation was induced by replacing the medium with NbActiv4 (Brainbits/TransnetYX Tissue).  Compound CO6 was dissolved in DMSO and added at the indicated final concentrations at the onset of differentiation.  Cells treated with an equivalent volume of DMSO served as vehicle controls.  Differentiating myocytes were fed daily with fresh NbActiv4 medium with compounds re-administered at each feeding.  To enhance cell viability, horse serum was supplemented at a final concentration of 1% after the first 24 hours of differentiation.  After four days of differentiation and treatment, cells were harvested for RNA-seq analysis.

value: human immortalized myocytes


title: Subjected to three cycles drought stress, Leaf, rep 3

description: Library name: M3_S3_LF

value: Leaf

value: Three cycles drought stress

value: replicate 3


title: oml 3dpl, biological rep2


title: W3d_rep4

description:
Library name: Sample 10
g110


title: 15Ai_C06-500nM_replicate-2

description: Library name: C02


title: Subjected to three cycles drought stress, Leaf, rep 2

description: Library name: M2_S3_LF

value: replicate 2


title: oml 3dpl, biological rep1


title: W3d_rep3

description:
Library name: Sample 9
g109


title: 15Ai_C06-500nM_replicate-1

description: Library name: A01


title: Subjected to three cycles drought stress, Leaf, rep 1

description: Library name: M1_S3_LF

value: replicate 1


title: W3d_rep2

description:
Library name: Sample 8
g108


title: 15Ai_C06-500nM_replicate-4

description: Library name: F01


title: 15Ai_C06-100nM_replicate-4

description: Library name: F03


title: W3d_rep5

description:
Library name: Sample 11
g111


title: Control (maintained under well-watered ) and sampling after the third drought stress , Leaf, rep 3

description: Library name: C3_S3_LF


title: oml 1dpl, biological rep2

description: gene expression data from tissue of the outer molecular layer 1 day postlesion

source_name: 1 day postlesion


title: W3d_rep1

description:
Library name: Sample 7
g107


title: 15Ai_C06-100nM_replicate-3

description: Library name: F02


title: Control (maintained under well-watered ) and sampling after the third drought stress , Leaf, rep 2

description: Library name: C2_S3_LF


title: T47D_ERa_WT_Pooled_Input_2

description: Library name: T47D_ERa_WT_Pooled_Input_2

data_processing:
Initial quality control and peak calling was performed using Nf-core ChIPseq pipeline. DeepTools v.3.5.6 bamCompare function was used to generate fold enrichment bigWig tracks for each sample compared to the IgG control and to make enrichment plots.
DiffBind was used to identify regions of differential accessibility. HOMER was used for transcription factor motif analysis and peak annotation.
Assembly: Hg38
Supplementary files format and content: bigWig

extract_protocol:
T47D WT and Y537S ESR1 cells (shGFP and shPR) were hormone-starved for 48h and then treated with vehicle or R5020 (10 nM, 1h). 1 x 10e6 cells were harvested in ice-cold PBS. Cells were crosslinked in 1% formaldehyde in PBS. Crosslinking was quenched by adding glycine at a final concentration of 125 mM. Crosslinked cell pellets were snap-frozen and stored at -80°C. For each ChIP experimental replicate, 2 x 10e6 crosslinked cells (from 2 crosslinked aliquots) were lysed in lysis buffer with PICS III using sonication (high, 30 seconds on/off, for 5 intervals of 10 minutes). 5% of lysate was reserved for input control and snap frozen to store at -80°C. Lysates were diluted to 1 µg/µl protein based on Nanodrop A280 concentrations and divided into 1 ml aliquots. 5 µg of the appropriate antibodies (phospho-PR [S294] for phospho-PR ChIP, rabbit IgG for phospho-PR negative control) were added to the appropriate lysate aliquots and rotated at 4°C overnight.
Protein-chromatin was isolated and eluted using protein G beads (Cytiva Streptavidin Mag Sepharose Magnetic Beads, Thermo Fisher). Eluted ChIP samples were incubated with RNAse A and Proteinase K to reverse the crosslinked protein-chromatin. Input samples and ChIP-DNA were purified using a Qiagen QIAquick PCR Purification Kit, and purified DNA samples were eluted in 30 µl nuclease-free water. ChIP-DNA was quantitated by Qubit (Life Technologies), libraries were generated using the Illumina ChIP-SEQ kit and quality assessed using Bioanalyzer (Agilent). Sequencing was performed on the Illumina NovaSeq X by the University of Chicago Functional Genomics core. Samples were analyzed over 50M clusters per sample, which was variable due to the available library content.

value: breast cancer

value: rabbit Igg


title: PH1, periodontitis, hypertension

description: Library name: Sample7

value: gingiva


title: oml 1dpl, biological rep1

value: outer molecular layer


title: Subjected to three cycles drought stress and sampling in year n+1  after completing one winter cycle,Root, rept 1

description: Library name: M1_LTM_RO

value: Golden Delicious double haploid 18 (GDDH18)

value: Three cycles drought stress, Long Term Memory


title: Bacteria,fermentation,rep1

city: Guangzhou

first: Qin

last: Zhang

address: Wushan road

institute: College of Forestry and Landscape Architecture

description:
Library name: YLG372
MobiMicrobe

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation weremade using the Mobivison software
Assembly: Cellulomonas iranensis YLG372 (CP194061)
Supplementary files format and content: Tab-separated values file and matrix files

organism: Cellulomonas iranensis

source_name: Bacterial cell

extract_protocol:
Cellulomonas_iranensis were isolated from plant fermentations and made into single cell suspensions
Library was performed according to the manufacter's instructions (MobiCube® High-throughput 3' Single Cell Transcriptome Kit).We uses droplet microfluidic technology to combine single cell suspension, reverse transcription reagent and Medtronic microspheres, which are encapsulated by oil droplets to separate individual cells in a single water-in-oil droplet.Cells in water-in-oil droplets are lysed, and the released mRNA is captured by the sequence on the microspheres, which links the cell tag to the cDNA product by a reverse transcription reaction. Next, water in oil was broken again, and cDNA was used as template for PCR amplification, quality inspection, sequencing library construction, sequencing, and data analysis.

value: Bacterial cell


title: Control (maintained under well-watered )  and sampling in year n+1  after completing one winter cycle, Root, rept 2

description: Library name: C2_LTM_RO

value: Control, Long Term Memory


title: 15Ai_C06-100nM_replicate-2

description: Library name: C01


title: T47D_ERa_Y537S-hom_Pooled_Input_1

description: Library name: T47D_ERa_Y537S-hom_Pooled_Input_1


title: Control (maintained under well-watered ) and sampling after the third drought stress , Leaf, rep 1

description: Library name: C1_S3_LF

source_name: Leaf

value: Control


title: BeforePretreatment_rep5

description:
Library name: Sample 5
g105


title: 15Ai_C06-100nM_replicate-1

description: Library name: A02


title: BeforePretreatment_rep6

description:
Library name: Sample 6
g106


title: E3dF2h_rep3

description:
Library name: Sample 27
g127


title: oml control, biological rep3

description: gene expression data from tissue of the outer molecular layer without lesion

source_name: without lesion


title: Subjected to one cycle drought stress, Leaf, rep 3

description: Library name: M3_S1_LF

value: One cycle drought stress


title: E3dF2h_rep2

description:
Library name: Sample 26
g126

value: shoot


title: BeforePretreatment_rep4

description:
Library name: Sample 4
g104


title: oml control, biological rep2


title: 15Ai_DMSO_replicate-5

description: Library name: G03

value: human immortalized myocytes

value: DMSO


title: MB135_iDUX4ca_3xFLAG_KLF18_Long_Cl2_2

city: Seattle

first: Stephen

last: Tapscott

state: Washington

address: 1100 Fairview Ave N, Room C3-123

institute: Fred Hutchinson Cancer Research Center

description: Library name: KLF18_Long2_2

data_processing:
Reads trimmed using trim galore 0.6.7
Reads aligned using Rsubread 2.18.0 to GRCh38 p14
Gene features were called using featureCounts 2.18.0 against the Gencode R45 annotation release
Differential expression was analyzed using DESeq2 1.44.0
Assembly: GRCh38 p14
Supplementary files format and content: xlsx, DESeq2 differential expression output

molecule: polyA RNA

source_name: MB135-iDUX4ca 3xFLAG-KLF18_Long_2

growth_protocol: Grown in F10 media supplemented with 10% FBS, 1% P/S,

extract_protocol:
total RNA was extracted using Takara Nucleospin RNA extraction kit following mfr protocol
150bp paired end libraries were prepared using Illumina's TruSeq stranded mRNA kit following mfr protocol.

treatment_protocol: Cells were treated ± 0.25µg/mL doxycycline (DOX) for 18 hours.

value: MB135-iDUX4ca 3xFLAG-KLF18_Long_2

value: Human Myoblast

value: 3xFLAG-KLF18 Long 2

value: 0.25ug/mL Dox for 18hr


title: Mmac_vas lat_CALRES_4

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: Library name: Sample_19_G102

data_processing:
FastQC was used to check quality quality of reads.
Next, reads were trimmed using bbduk.
Cleaned FASTQ files were aligned to Mmul_10 using STAR.
Transcript data was generated using RSEM.
Finally, count data was generated by using featureCounts.
Assembly: Mmul_10
Supplementary files format and content: Count data

organism: Macaca mulatta

source_name: vastus lateralis skeletal muscle

extract_protocol:
RNeasy Fibrous Tissue Mini Kit  protocol (Qiagen, Cat. No. 74704) in QIAcube Connect (Qiagen, Cat. No. 9002864)
Library was prepared using Illumina Stranded Total RNA Prep. Ligation was performed with Rib-Zero Plus kit.

treatment_protocol: Caloric Restriction

value: vastus lateralis skeletal muscle

tag: age

value: CALRES


title: Mmac_vas lat_CALRES_5

description: Library name: Sample_2_9CF


title: MB135_iDUX4ca_3xFLAG_KLF18_Long_Cl2_1

description: Library name: KLF18_Long2_1


title: Subjected to one cycle drought stress, Leaf, rep 2

city: Beaucouze

first: Sandrine

last: Balzergue

address: 42 rue G. Morel

institute: INRAE

description: Library name: M2_S1_LF

value: Leaf

value: replicate 2


title: BeforePretreatment_rep3

description:
Library name: Sample 3
g103


title: 15Ai_DMSO_replicate-4

description: Library name: E02


title: oml 1dpl, biological rep3

value: outer molecular layer


title: W3dF2h_rep5

description:
Library name: Sample 23
g123


title: Subjected to one cycle drought stress, Leaf, rep 1

description: Library name: M1_S1_LF

value: Golden Delicious double haploid 18 (GDDH18)

value: replicate 1


title: BeforePretreatment_rep2

description:
Library name: Sample 2
g102


title: 15Ai_DMSO_replicate-3

description: Library name: E01


title: oml control, biological rep1


title: gcl 28dpl, biological rep3

description: gene expression data from tissue of the granule cell layer 28 days postlesion

value: granule cell layer


title: W3dF2h_rep6

description:
Library name: Sample 24
g124


title: Control (maintained under well-watered ) and sampling after the first drought stress , Leaf, rep 3

description: Library name: C3_S1_LF

value: Control

value: replicate 3


title: BeforePretreatment_rep1

description:
Library name: Sample 1
g101

value: shoot


title: gcl 28dpl, biological rep2


title: 15Ai_DMSO_replicate-2

description: Library name: D03

value: human immortalized myocytes


title: W3dF2h_rep3

description:
Library name: Sample 21
g121


title: Control (maintained under well-watered ) and sampling after the first drought stress , Leaf, rep 2

description: Library name: C2_S1_LF


title: 15Ai_DMSO_replicate-1

description: Library name: D02

value: DMSO


city: Chapel Hill

first: Joseph

middle: Mauro

last: Calabrese

state: NC

address: 120 Mason Farm Road

institute: UNC Chapel Hill

description: Library name: 293T_flagtagged_HNRNPU_RMCE_input_r2_rip_10

data_processing:
Wiggle tracks were generated using protocols and code from PMID: 39187382. Sequencing reads were aligned to the mm10 or Hg38 genome using STAR (v2.7.10a; 101). Replicates were downsampled and merged using SAMtools (v1.18; 95). Merged BAM files were filtered for MAPQ ≥ 30 and then split by strand with SAMtools and a custom script. Bam files were converted to BED12 format using Bedtools (v2.29; 98). Wiggle tracks were generated using a custom script which included normalizing wiggles to total aligned reads. WIG files were converted to BigWig format.
Assembly: mm10, hg36
Supplementary files format and content: bigwig files for mm10 alignment (hm_, m_) or hg38 alignment (hm_*hg38, h_). Replicated labels as "r1" or "r2". Merged files do not contain replicate information.

organism:
Homo sapiens
Mus musculus

source_name: HEK293T, B6/CAST F1-hybrid Rosa26-RMCE ESCs

extract_protocol:
Both input and immunoprecipitated RNA were purified with the Zymo Clean and Concentrator.
KAPA RNA Hyperprep Kit with RiboErase, 9uL of IP/input RNA + 1uL ERCC RNA spike-in

tag: antibody

value: FLAG (Sigma, F1804)

value: Human embryonic kidney cells, Mouse embryonic stem cells

value: 1:1 mix of human, mouse lysates


title: 15Ai_untreatment_replicate-5

description: Library name: G02

value: No treatment


description: Library name: 293T_flagtagged_HNRNPU_RMCE_flag_r2_rip_10

value: HEK293T, B6/CAST F1-hybrid Rosa26-RMCE ESCs


title: Ca + GBS repB

city: Aurora

first: Kelly

last: Doran

state: Colorado

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

description:
Library name: 6B
Column name in Ca_counts.tsv: Ca_GBS_B; Column name in GBS_counts.tsv: GBS_Ca_B

data_processing:
BCL convert v4.2.4 for demultiplexing, quality control, and adapter trimming
STAR v2.7.10b for read alignment
featureCounts v2.0.6 to assign counts
Assembly: GRCh38 (NCBI; human)
Assembly: Assembly 22 (CGD; C. albicans)
Assembly: NZ_HG939456.1 with sRNAs (S. agalactiae)
Supplementary files format and content: hVEC_counts.tsv is a tab-delimited text file of counts for human genes for each sample containing hVECs
Supplementary files format and content: Ca_counts.tsv is a tab-delimited text file of counts for C. albicans genes for each sample containing C. albicans
Supplementary files format and content: GBS_counts.tsv is a tab-delimited text file of counts for S. agalactiae genes for each sample containing S. agalactiae

organism:
Streptococcus agalactiae
Candida albicans

source_name: Bacteria

growth_protocol: S. agalactiae (strain COH1) was grown statically in Todd Hewitt Broth at 37°C. C. albicans (strain 529L) was grown shaking in Yeast Peptone Dextrose Broth at 30°C. Human vaginal epithelial cells (hVEC; cell line VK2-E6/E7) were grown in Keratinocyte Serum-Free Medium supplemented with 0.05 mg/mL bovine pituitary extract and 0.5 ng/mL epidermal growth factor (KSFM). hVECs were grown in 6-well transwell inserts at an air-liquid interface for 16 days.

extract_protocol:
RNA was isolated using the Qiagen RNeasy Mini Kit, then treated with Invitrogen Dnase.
Libraries were prepared with the Illumina Stranded Total RNA Prep ligation with Ribo-Zero Plus rRNA depletion kit.

treatment_protocol: 2x10^7 C. albicans yeast cells and/or 2x10^8 S. agalactiae CFU at mid-log were washed and resuspended in KSFM and added to hVEC air-liquid interface cultures in the apical compartment, then incubated at 37°C with 5% CO2 for six hours. Microbial mono- and co-cultures were grown in 6-well plates in KSFM at 37°C with 5% CO2 for six hours.

value: Fungus

value: Bacteria

value: C. albicans and S. agalactiae co-culture


title: 15Ai_untreatment_replicate-4

description: Library name: G01


title: gcl 28dpl, biological rep1


description: Library name: 293T_flagtagged_HNRNPU_RMCE_flag_r1_rip_9


title: Ca + GBS repA

description:
Library name: 6A
Column name in Ca_counts.tsv: Ca_GBS_A; Column name in GBS_counts.tsv: GBS_Ca_A


title: 15Ai_untreatment_replicate-3

description: Library name: E03


title: gcl 14dpl, biological rep1

description: gene expression data from tissue of the granule cell layer 14 days postlesion


title: GBS alone repC

description:
Library name: 5C
Column name in GBS_counts.tsv: GBS_C

organism: Streptococcus agalactiae

value: S. agalactiae mono-culture


title: 15Ai_untreatment_replicate-2

description: Library name: D01


title: GBS alone repB

description:
Library name: 5B
Column name in GBS_counts.tsv: GBS_B


title: Control (maintained under well-watered ) and sampling after the first drought stress , Leaf, rep 1

description: Library name: C1_S1_LF

value: Leaf

value: Golden Delicious double haploid 18 (GDDH18)


description: Library name: 293T_flagtagged_HNRNPK_RMCE_input_r1_rip_7


title: 15Ai_untreatment_replicate-1

description: Library name: B02


title: gcl 7dpl, biological rep1

description: gene expression data from tissue of the granule cell layer 7 days postlesion

value: granule cell layer


title: GBS alone repA

description:
Library name: 5A
Column name in GBS_counts.tsv: GBS_A


title: Msx2-KO, dorsal skin, epidermal progenitor cells, 6-month-old telogen, RNA-seq, rep 2

city: Los Angeles

first: Ya-Chen

last: Liang

address: 2011 Zonal Ave., HMR 304A

department: Department of Pathology

institute: University of Southern California

description:
Library name: Chuong-815
Column name in Msx2_EpdSC_DESeq2_cKO_vs_WT_counts.txt: Ch-815_S12

data_processing:
RNA-seq Data Processing and Analysis: RNA-seq analysis was conducted using the Partek® Flow® platform (Partek Inc.). Default parameters were applied unless otherwise specified.
Quality Control and Alignment: Pre-alignment quality control (QA/QC) steps were performed prior to read mapping. Reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR version 2.7.3a, followed by post-alignment QA/QC.
Quantification and Normalization: Aligned reads were quantified to the Ensembl release 103 annotation model using the Partek Expectation/Maximization (E/M) method. Gene expression values were normalized using Transcripts Per Million (TPM).
Differential Expression Analysis: Differential gene expression analysis was performed using Partek Gene-Specific Analysis (GSA). Genes with a false discovery rate (FDR) < 0.05 and an absolute fold change > 2 were considered significantly differentially expressed.
Assembly: Emsemble GRCm38/mm10 for all samples.
Supplementary files format and content: Tab-delimited text files include raw counts for each sample
Supplementary files format and content: Tab-delimited text files include GSA result for each sample

source_name: skin

growth_protocol: Mice were maintained under a 12 h light/dark cycle at 21–26 °C and 30–70 % relative humidity in the USC animal facility.

extract_protocol:
Total RNAs of indicated tissues were isolated using the standard AllPrep DNA/RNA Micro Kit protocol (Cat. 80284, Qiagen)
Library preparation using the SMARTer Stranded Total RNA-Seq Kit v3 was performed in Novogen company (CA, USA)

treatment_protocol: No treatment

value: skin

value: epidermal progenitor cell

value: Msx2 knockout


title: hVEC ALI + Ca + GBS repC

description:
Library name: 4C
Column name in hVEC_counts.tsv: hVEC_Ca_GBS_C; Column name in Ca_counts.tsv: Ca_GBS_hVEC_C; Column name in GBS_counts.tsv: GBS_Ca_hVEC_C

organism:
Streptococcus agalactiae
Candida albicans
Homo sapiens

value: Vaginal epithelial cells

value: Epithelial cells grown at air-liquid interface, inoculated with C. albicans and S. agalactiae


title: Stage 3 Day HNF1A-MODY + Purmorphamine 1

city: Bergen

first: Lucas

last: Unger

address: Haukelansbakken 15

country: Norway

institute: University of bergen

description: Library name: Sample 10

data_processing:
CLC Genomic Workbench version 24.0
Assembly: hg38 (Refseq)
Supplementary files format and content: Geneexpression Track for each sample als xlsx file

source_name: Differentiating cells

extract_protocol:
RNA was extracted using QIAGEN RNeasy mini
Performed by QIAGEN

treatment_protocol: Some of the conditions were treated with 10 µM purmorphamine instead of SANT1 on the first day of stage 3, for a duration of 24 hours.

value: Differentiating cells

value: induced pluripotent stem cells

value: Differentiation towards pancreatic endocrine progenitors treated with Purmorphamine


description: Library name: 293T_flagtagged_HNRNPK_RMCE_flag_r1_rip_7

value: FLAG (Sigma, F1804)

value: Human embryonic kidney cells, Mouse embryonic stem cells

value: 1:1 mix of human, mouse lysates


title: Msx2-KO, dorsal skin, epidermal progenitor cells, 6-month-old telogen, RNA-seq, rep 1

description:
Library name: Chuong-814
Column name in Msx2_EpdSC_DESeq2_cKO_vs_WT_counts.txt: Ch-814_S11


title: gcl 3dpl, biological rep1

description: gene expression data from tissue of the granule cell layer 3 days postlesion


title: hVEC ALI + Ca + GBS repB

description:
Library name: 4B
Column name in hVEC_counts.tsv: hVEC_Ca_GBS_B; Column name in Ca_counts.tsv: Ca_GBS_hVEC_B; Column name in GBS_counts.tsv: GBS_Ca_hVEC_B

value: Fungus

value: Bacteria


title: gcl 1dpl, biological rep3

description: gene expression data from tissue of the granule cell layer 1 day postlesion


title: WT, dorsal skin, hair follicle stem cells, 2-month-old telogen, RNA-seq, rep 2

description:
Library name: Chuong-673
Column name in Msx2_HFSC_DESeq2_cKO_vs_WT_counts.txt: YC-673

value: hair follicle stem cell

value: wild-type


title: 293T_flagtagged_GFP_RMCE_input_r2_rip_6

description: Library name: 293T_flagtagged_GFP_RMCE_input_r2_rip_6

value: HEK293T, B6/CAST F1-hybrid Rosa26-RMCE ESCs


title: WT, dorsal skin, hair follicle stem cells, 2-month-old telogen, RNA-seq, rep 1

description:
Library name: Chuong-631
Column name in Msx2_HFSC_DESeq2_cKO_vs_WT_counts.txt: YC-631


title: XRE mutant set 4

city: New Orleans

first: Zezhang

middle: T

last: Wen

state: Louisiana

address: 1100 FLORIDA AVE, Clinical Bldg Room 619

institute: LSU Health In New Orleans

description: Library name: XRE_4

data_processing:
Sequencing was done on an Illumina NovaSeq X Plus platform, producing paired end 150 bp reads.
Demultiplexing, quality control, and adapter trimming were performed with bcl-convert (v4.2.4).
Processed/cleaned reads were mapped to the S. mutans UA159 genome (GCF_000007465.2/) with  HISAT2 (v2.2.1) using default parameters + “very sensitive” 25.
Read mapping was performed with HISAT22. Read quantification was performed using Subread’s featureCounts3 functionality.
Read counts loaded into R4 were normalized using edgeR’s5 Trimmed Mean of M values (TMM) algorithm. Subsequent values were then converted to counts per million (CPM).
Assembly: Differential expression analysis was performed using edgeR’s glmQLFTest with those with a log2(fold change)> 1 and a P <0.05. Selected genes were further analyzed using RealTime-PCR 6, 24.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Streptococcus mutans

source_name: genotype

growth_protocol: The allelic exchange xre mutant and its parent strain UA159 were grown in regular BHI broth at 37C in a aerobic chamber with 5% CO2.

extract_protocol:
Total RNAs were extracted from mid-exponential (OD600nm ~0.4) phase cultures treated with RNAProtect prior to RNA extraction using a ZymoBIOMICS Quick-bacteria RNA extraction kit.
The RNA samples were depleted of ribosomal RNA; and libraries were generated using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit.

treatment_protocol: The xre mutant was created via allelci excange with a non-polar erythromycin-resistence marker to replace nucleotides 47 to 214 of its coding region (408 bp).

value: genotype

value: xre mutant


title: gcl 1dpl, biological rep1

description:
gene expression data from tissue of the granule cell layer 1 day postlesion
batch remover, other scan date

value: granule cell layer


title: Ovarian cancer cell line with shRNA for RelB, spheroid growth condition, replicate 4

city: San Diego

first: Mikella

last: Robinson

address: 5500 Campanile Drive

institute: San Diego State University

description: Library name: Spheroid4_shRelB

data_processing:
Adapter trimming: Cutadapt
Alignment: STAR
Normalization: RSEM - CPM - TMM
Assembly: Genome_build: hg38 (GRCh38)
Supplementary files format and content: RSEM counts for each sample
Supplementary files format and content: Tab-delimited normalized RSEM-CPM-TMM counts matrix with all samples

source_name: ovarian serous carcinoma

growth_protocol: Adherent OV90 cells were grown in RPMI 1640 medium supplemented with Tetracycline-free Fetal Calf Serum (10%) and 1% penicillin/streptomycin. Spheroids were grown in ultra-low attachment plates or flasks in DMEM-F12 media supplemented with 1% KnockOut serum replacement, 1% penicillin/streptomycin, 0.1% insulin-transferrin-selenium, and 0.4% bovine serum albumin and growth factors EGF 20 ng/mL and FGF 10 ng/mL.

extract_protocol:
Total RNA was collected from cells according to the manufacturer's instructions using the RNeasy Mini Kit (Qiagen 74104).
Libraries were prepared according to the manufacturer's instructions using TruSeq Stranded mRNA library kit (Illumina 20020594).

treatment_protocol: 6 days growth in each condition, fresh medium was supplemented after 72 hours.

value: ovarian serous carcinoma

value: ovarian cancer cell line

value: shRelB

tag: growth condition

value: Spheroid


title: XRE mutant set 3

description: Library name: XRE_3


title: XRE mutant set 2

description: Library name: XRE-2


title: GSH, 6

city: Madison

first: Anna

last: Gregory

state: WI

address: 1550 Linden Dr., MSB Rm3435

department: Department of Gastroenterology and Department of Medical Microbiology and Immunology

institute: University of Wisconsin-Madison

description: Library name: GSH_6

data_processing:
RNA-seq was performed by SeqCenter, LLC on high-quality rRNA-depleted RNA extracts (12M RNA reads). Quality control and adapter trimming was performed with bcl-convert (v 4.1.5). Read mapping was performed with HISAT2 (v 2.2.0), while read quantification was performed using Subread’s featureCounts3 (v 2.0.1) functionality. Read counts were loaded into R (v 4.0.2) and normalized using edgeR’s (version 1.14.5) Trimmed Mean of M values (TMM) algorithm. Subsequent values were then converted to counts per million (CPM). Differential expression analysis was performed using edgeR’s glmQLFTest. Transcript level quantification, count normalization, and differential expression analysis were provided using C. difficile 630Δerm (GCA_002080065.1) as the reference genome.
Assembly: GCA_002080065.1
Supplementary files format and content: Text file includes raw counts and fold change

organism: Clostridioides difficile

extract_protocol:
At indicated timepoints, 5 mL aliquots were diluted 1:1 in chilled 1:1 ethanol:acetone and stored at -20° to preserve RNA. RNA was extracted by centrifuging samples at 3,000 xg for 5 minutes at 4°C. Pellets were washed with 5 mL cold, nuclease free PBS, and centrifuged at 3,000 xg for 5 minutes at 4°C. The supernatant was removed, and remaining pellets were resuspended in 1 mL TRIzol and processed using a TRIzol Plus RNA Purification Kit (Thermo) with on-column DNase treatment. Purified RNA integrity was confirmed via 2100 Agilent BioAnalyzer and frozen at -80°C.
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.

value: perR corrected (perRWT)

value: 25 mM GSH


title: Ovarian cancer cell line with shRNA for RelB, spheroid growth condition, replicate 2

description: Library name: Spheroid2_shRelB


title: Wild-type set 4

description: Library name: UA159_4


title: GSH, 4

description: Library name: GSH_4


title: gcl control, biological rep1

description:
gene expression data from tissue of the granule cell layer without lesion
batch remover, other scan date


title: 293T_flagtagged_GFP_RMCE_input_r1_rip_5

description: Library name: 293T_flagtagged_GFP_RMCE_input_r1_rip_5

value: FLAG (Sigma, F1804)


title: WGBS SetDB1 KO serum-to-2i mouse ESCs, day4

city: Nijmegen

first: Nick

last: Bovee

state: Gelderland

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: RIMLS

description:
Library name: Serum-2i_SetDB1O_d4
day4

data_processing:
All WGBS analyses were performed using the Mus musculus NCBI GRCm39 genome assembly (mm39). The WGBS data, including FASTQ and BED, have been deposited in this entry. Paired-end reads from the FASTQ files were trimmed using Trim Galore with the flags --paired --trim1. The trimmed reads were then aligned to the reference genome using the Bismark package in combination with Bowtie 2 (Krueger, F., & Andrews, S. R. (2011). Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. bioinformatics, 27(11), 1571-1572.) with the flag -n 1 --bowtie2. BAM files were deduplicated using Deduplicate Bismark with the flag -p. Cytosine methylation levels were calculated using the Bismark Methylation Extractor with the flags -p --no_overlap and applying a minimum read coverage threshold of ≥5. Methylation levels of genomic features were determined by intersecting them with genomic coordinates of the mm39 reference genome.
Assembly: NCBI GRCm39 genome assembly (mm39)
Supplementary files format and content: BED

source_name: SetDB1 CKO mouse ESCs, Matsui et al. (2010)

growth_protocol: ESCs were maintained at 37 °C, 5% CO2 and routinely tested negative for mycoplasma. Serum ESCs were cultured on 0.1% gelatin-coated culture plates in DMEM-Glutamax basal medium (Gibco) supplemented with 0.1mM non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco), 0.1mM 2-mercaptoethanol, 5·105U leukemia inhibitory factor (LIF) (home-made), 10% fetal bovine serum and 25U/ml Penstrep (Gibco). 2i ESCs were maintained on 0.2% gelatin-coated culture plates in Ndiff 227 medium (Takara) supplemented with 1uM MEK inhibitor PD0325901, 3uM GSK3 inhibitor CHIR99021, together known as ‘2i’, 5·105U leukemia inhibitory factor (LIF) (home-made) and 25U/ml Penstrep (Gibco).

extract_protocol:
DNA from ESCs was isolated using either (i) a Cell Culture DNA Midi Kit (Qiagen), following the manufacturer’s instructions, or (ii) a standard protocol for phenol/chloroform extraction with ethanol precipitation. WGBS on isolated DNA was conducted as previously described: Kulis, M., Heath, S., Bibikova, M., Queirós, A. C., Navarro, A., Clot, G., ... & Martín-Subero, J. I. (2012). Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nature genetics, 44(11), 1236-1242.
Libraries were sequenced on an Illumina HiSeq 2000 platform in paired-end mode (2x100 nucleotides).

treatment_protocol: Addition of 4-OHT (4-hydroxytamoxifen) for 4 days, or DMSO (control)

value: Mouse pluripotency stem cells

value: SetDB1 CKO


title: Wild-type set 3

description: Library name: UA159_3


title: GSH, 3

description: Library name: GSH_3


title: Ovarian cancer cell line with shRNA for RelA, spheroid growth condition, replicate 4

description: Library name: Spheroid4_shRelA

value: shRelA


title: Wild-type set 2

description: Library name: UA159_2


title: GSH, 1

description: Library name: GSH_1


title: Ovarian cancer cell line with shRNA for RelA, spheroid growth condition, replicate 3

description: Library name: Spheroid3_shRelA


title: WGBS SetDB1 KO serum-to-2i mouse ESCs, day2

description:
Library name: Serum-2i_SetDB1O_d2
day2

value: SetDB1 CKO mouse ESCs, Matsui et al. (2010)


title: Ca alone repC

description:
Library name: 7C
Column name in Ca_counts.tsv: Ca_C

organism: Candida albicans

source_name: Fungus

value: Fungus

value: C. albicans mono-culture


title: Media Control 6

description: Library name: Contr_6

value: Media Control


title: Ovarian cancer cell line with shRNA for RelA, spheroid growth condition, replicate 2

description: Library name: Spheroid2_shRelA

organism: Homo sapiens


title: WGBS SetDB1 KO serum-to-2i mouse ESCs, day1

description:
Library name: Serum-2i_SetDB1O_d1
day1


title: Ca alone repB

description:
Library name: 7B
Column name in Ca_counts.tsv: Ca_B


title: Media Control 4

description: Library name: Contr_4


title: Ovarian cancer cell line with shRNA for RelA, spheroid growth condition, replicate 1

description: Library name: Spheroid1_shRelA


title: Media Control 3

description: Library name: Contr_3


title: Ovarian cancer cell line with shRNA for RelB, adherent growth condition, replicate 4

description: Library name: AD4_shRelB

value: Adherent


title: E13.5 heart 9 Littermate control

city: Oxford

first: Sophie

last: Payne

address: Old Road Campus

department: Department of Physiology, Anatomy & Genetics

country: United Kingdom

institute: University of Oxford (UK, Oxford)

description:
Library name: E13_10-9_Con
10X Genomics

data_processing:
The raw read data was downloaded from Illumina BaseSpace and the standard Cell Ranger pipelines used to demultiplex the raw base call (BCL) files, align reads to the mouse mm10 reference genome, generate feature-barcode matrices and aggregate the samples. This dataset was used to create a SeuratObject in R for further processing and analysis: following normalisation across samples, cells were excluded if they had fewer than 200 or more than 7000 genes, contained more than 10% mitochondrial RNA, or were assessed as doublets using DoubletFinder.
Assembly: Mouse mm10
Supplementary files format and content: A Seurat Object of the processed data is provided as an Rds file, which can be loaded in R.

source_name: Heart

extract_protocol:
The embryonic hearts were dissociated using the Neonatal Heart Dissociation Kit (Miltenyi Biotec, 130-098-373) according to manufacturer’s instructions in combination with the gentleMACSTM Octo Dissociator with Heaters (Miltenyi Biotec), including the red blood cell lysis steps. The resulting cell pellets were resuspended in 100µl of 3% FBS in PBS containing 1:100 anti-mouse-CD31 conjugated to FITC (BioLegend, 102406) and incubated on ice for 25 minutes. 100µl of 1µg/ml DAPI solution was then added to each sample and incubated on ice for a further 5 minutes before cell suspensions were centrifuged at 600x g for 5 minutes at 10°C. Cell pellets were then resuspended in 500µl of 2% FBS in PBS, transferred to FACS tubes and sorted using a Sony MA900 FACS Sorter. CD31-positive endothelial cells from each sample were sorted into 100µl 3% FBS in PBS, centrifuged at 600x g for 5 minutes at 10°C and the cell pellets resuspended in 30µl 0.04% BSA in PBS.
Samples were processed for sequencing using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 from 10X Genomics according to manufacturer’s instructions. Each sample was processed in separate GEM well, and then samples were pooled to a single flow cell and run on a NextSeq2000 sequencer.

value: Heart

value: Endothelial cell


title: Media Control 1

description: Library name: Contr_1


title: Ovarian cancer cell line with shRNA for RelB, adherent growth condition, replicate 3

description: Library name: AD3_shRelB

value: ovarian serous carcinoma


title: WGBS SetDB1 KO 2i mouse ESCs, day1

description:
Library name: 2i_SetDB1KO_d1
day1


title: E13.5 heart 8 Littermate control

description:
Library name: E13_10-8_Con
10X Genomics


title: TSC, SP6, BL3h_rep3

first: yulong

last: zhong

state: Guangdong Province

address: 1838 Guangzhou Avenue North

department: physiology

institute: Southern Medical University

data_processing:
Sequencing reads were trimmed by cutadapt (v 4.3) to get high quality reads. High quality reads were aligned to the human reference genome hg19 using Bowtie2 (v 2.2.5) with the parameter of "-X 2000". The mapped reads were sorted using Samtools (v 1.13), retaining any reads with a MAPQ less than 30. Duplicated reads were removed by Picard (v 2.7). Peaks were called by MACS2 (v 2.2.7.1).  Bigwig files were generated from bam files using deeptools (v 3.5.1) bamCoverage. All samples were normalized to 10 million reads with binsize as 50-bp by "--scaleFactor --binSize 50" parameters.
Assembly: hg19
Supplementary files format and content: The processed files were bigwig files and bed files.

growth_protocol: TSCsSP6-3HA are cultured in TS medium according to the Hiroaki Okae's protocol and maintained in a humidified 5% CO2 incubator at 37°C.

extract_protocol:
In summary, the fixed cells underwent three times washing with 0.1% BSA/PBS. The cells were then resuspended in 80 µl of Antibody Buffer (a mixture of 4 µl 0.5 M EDTA and 1 ml 0.01% Digitonin-Wash Buffer (Dig-Wash Buffer), supplemented with cocktail, 10 mM sodium butyrate, and 0.05% Triton X-100) that contained 1.6 µg of the primary antibody. This mixture was incubated at 4°C for 4 hours on a rotator with 16 rpm. The cells were subsequently washed twice with 180 µl of Dig-Wash Buffer. The secondary antibody (used at a 1:500 ratio) was incubated under the same conditions, except for a shorter duration of 10 minutes. After two times washing with Dig-Wash Buffer, the cells were suspended in 80 µl of Dig-Wash Buffer (containing 0.05% Triton-X, cocktail, and 10 mM sodium butyrate) that also contained 0.83 µM PAT-MEA/B. This was done at 4°C for 1 hour. The free PAT-MEA/B were then dislodged with 180 µl Dig-Wash Buffer containing 0.05% Triton X-100 three times at 5 min each time. The reaction was activated by suspending the cells with 10 µl Reaction Buffer (10 mM TAPS-NaOH pH 8.3, 5 mM MgCl2, 10% DMF, 300 mM NaCl, 0.05% Triton-X, 0.01% Digtonin and supplemented with cocktail, 10 mM sodium butyrate), followed by gently flicking and incubating at 37°C for 1 h in an Eppendorf ThermoMixer with 300 rpm. The reaction was gently mixed once after 30 min incubation and was halted by adding 10 µl of 40 mM EDTA, followed by further incubation at 4°C for 10 min. The samples were then washed with 0.1% BSA/PBS and finally resuspended in 5 µl of Lysis Buffer (0.1 mg/ml Proteinase K, 10 mM Tris-HCl pH 8.5, and 0.05% SDS), and lysed at 55°C for 3 hours in a PCR cycler. Finally, 1.8% Triton X-100 with 5 mM PMSF was added to the cell lysate and incubated at room temperature for 10 minutes to inactivate the proteinase K. This was followed by a 5-minute incubation at 55°C to quench the SDS in the reaction.
After PCR enrichment using 2x KAPA master mix,fragments larger than 1 kb were first eliminated using 0.4x AMPure beads, after which the library was purified using the Zymo DNA Clean and Concentrator-5 Kit.

treatment_protocol: The TSCsSP6-3HA were treated with  or without bleomycin (BL) for 1 hour,and then replaced with fresh culture medium to repair 3 hours. and then in situ ChIP-seq was performed.

value: HA (Invitrogen #71-5500)

value: cell line

value: BL treated 1 hour


title: Ca alone repA

description:
Library name: 7A
Column name in Ca_counts.tsv: Ca_A


title: Ovarian cancer cell line with shRNA for RelB, adherent growth condition, replicate 2

description: Library name: AD2_shRelB

value: ovarian cancer cell line

value: shRelB


title: WGBS WT 2i mouse ESCs, day0

description:
Library name: 2i_WT_d0
day0


title: E13.5 heart 7 Littermate control

description:
Library name: E13_10-7_Con
10X Genomics


title: WGBS SetDB1 KO 2i mouse ESCs, day4

description:
Library name: 2i_SetDB1KO_d4
day4


title: TSC, SP6, BL3h_rep2


title: Ovarian cancer cell line with shRNA for RelB, adherent growth condition, replicate 1

description: Library name: AD1_shRelB


title: WGBS SetDB1 KO serum mouse ESCs, day10

description:
Library name: Serum_SetDB1KO_d10
day10


title: WGBS SetDB1 KO 2i mouse ESCs, day2

description:
Library name: 2i_SetDB1KO_d2
day2


title: E13.5 heart 5 Hypoxia mimic

description:
Library name: E13_10-5_Cre
10X Genomics


title: TSC, SP6, BL3h_rep1


title: Ovarian cancer cell line with shRNA for RelA, adherent growth condition, replicate 4

description: Library name: AD4_shRelA


title: E13.5 heart 4 Hypoxia mimic

description:
Library name: E13_10-4_Cre
10X Genomics


title: WGBS SetDB1 KO serum mouse ESCs, day8

description:
Library name: Serum_SetDB1KO_d8
day8


title: TSC, SP6, noBL_rep2

value: NO BL treated


title: Ovarian cancer cell line with shRNA for RelA, adherent growth condition, replicate 3

description: Library name: AD3_shRelA


title: WGBS SetDB1 KO serum mouse ESCs, day6

description:
Library name: Serum_SetDB1KO_d6
day6

value: Mouse pluripotency stem cells


title: TSC, SP6, noBL_rep1


title: E13.5 heart 3 Littermate control

description:
Library name: E13_10-3_Con
10X Genomics


title: gcl 14dpl, biological rep3

first: Jessica

last: Schlaudraff

institute: Klinische Neuroanatomie

description: gene expression data from tissue of the granule cell layer 14 days postlesion

data_processing: The data were checked with Expression console (Affymetrix) and analyzed with Partek-Software 6.5 (Partek) using default analysis settings.

source_name: 14 days postlesion

extract_protocol: Total RNA was isolated with RNeasy Plus Micro Kit (Qiagen) according to the manufacturer's instructions.

value: granule cell layer


description: Library name: 293T_flagtagged_HNRNPU_RMCE_input_r1_rip_9

value: FLAG (Sigma, F1804)

value: HEK293T, B6/CAST F1-hybrid Rosa26-RMCE ESCs

value: Human embryonic kidney cells, Mouse embryonic stem cells

value: 1:1 mix of human, mouse lysates


title: Ovarian cancer cell line with shRNA for RelA, adherent growth condition, replicate 2

description: Library name: AD2_shRelA

value: shRelA


title: gcl 14dpl, biological rep2


title: WGBS SetDB1 KO serum mouse ESCs, day4

description:
Library name: Serum_SetDB1KO_d4
day4

value: SetDB1 CKO mouse ESCs, Matsui et al. (2010)

value: SetDB1 CKO


title: E13.5 heart 2 Hypoxia mimic

description:
Library name: E13_10-2_Cre
10X Genomics

value: Heart

value: Endothelial cell


description: Library name: 293T_flagtagged_HNRNPK_RMCE_input_r2_rip_8


title: Ovarian cancer cell line with shRNA for RelA, adherent growth condition, replicate 1

description: Library name: AD1_shRelA

value: ovarian serous carcinoma

value: Adherent


title: All patients all timepoints PBMC scRNA-seq

city: Houston

first: Ziyi

last: Li

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

data_processing:
Processing of raw reads was performed using the Cell Ranger software provided by 10X genomics and the hg38 human reference genome (GRCm38 v86 and corresponding GENCODE annotation file). During read alignment, PCR duplicates were removed. The UMI (unique molecular identifier) for each gene is counted to measure the gene expression levels. The cell doublet status is inferred by the software DoubletFinder. A number of quality-control metrics are evaluated to control the data quality, including the total UMI count, the total number of genes detected, the mitochondrial gene ratio, log10(gene number) per UMI, and the inferred status of cell doublet.  Low-quality cells with a total UMI count smaller than 500, a total number of genes smaller than 200, and a mitochondrial gene ratio greater than 50% are excluded for further analysis.
Assembly: GRCm38 v86
Supplementary files format and content: Filtered bc matrix from CellRanger and Parse pipelines.

source_name: Peripheral Blood Mononuclear Cells (PBMC)

extract_protocol:
The sample was incubated at 37 °C for 5 min. After dissociation, 2ml of advanced DMEM+10%FBS media was added to the sample and filtered through a 70 μm cell strainer (Fisher Scientific, cat.43-10070-40) into Eppendorf tubes
The filtrate was centrifuged at 500g for 5 min, and the supernatant was removed. If the pellet was bloody, red blood cell (RBC) removal was performed using RBC Lysis Solution (1x) (Miltenyi Biotec, cat. No. 130-094-183) for 10 min at RT. Sample was then centrifuged at 500g for 5 min and pellet was resuspended in 1ml of advanced DMEM, to be combined into one Eppendorf tube.
The single-cell suspension was visualized, counted, and stored at nitrogen until 10x Genomics Single-Cell sequencing was performed.

value: All - mulitplexed


title: WGBS WT serum mouse ESCs, day0

description:
Library name: Serum_WT_d0
day0


title: E13.5 heart 1 Hypoxia mimic

description:
Library name: E13_10-1_Cre
10X Genomics


title: NC4

status: Public on Jun 09 2026

city: Guilin

first: Nianying

last: Qin

address: No. 2 Lingui Road, Xiangshan District, Guilin, Guangxi Zhuang Autonomous Region

department: Department of Emergency

institute: Guilin Municipal Hospital of Traditional Chinese Medicine

description: Library name: NC4

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene count and TPM value for each Sample

source_name: Skin

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, tissue were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

value: Skin

value: Mice received intradermal injection of PBS vehicle (50 μL) on the right side of the dorsal midline. Skin tissue from the injection site was collected on 2025-06-28 at 10:00.


title: gcl 7dpl, biological rep2

city: Frankfurt

address: Heinrich-Hoffmann-Straße

description: gene expression data from tissue of the granule cell layer 7 days postlesion

source_name: 7 days postlesion


title: NC3

description: Library name: NC3


description: Library name: 293T_flagtagged_HNRNPK_RMCE_flag_r2_rip_8


title: NC2

description: Library name: NC2


title: gcl 3dpl, biological rep2

description: gene expression data from tissue of the granule cell layer 3 days postlesion

source_name: 3 days postlesion


title: NC1

description: Library name: NC1


title: C64

description: Library name: C64

value: Mice received intradermal injection of CTX (120 μg/50 μL) on the right side of the dorsal midline. Skin tissue from the injection site was collected on 2025-06-25 at 16:00 (6 hours post-injection).


title: C63

description: Library name: C63


title: C62

description: Library name: C62


title: hVEC ALI + Ca + GBS repA

description:
Library name: 4A
Column name in hVEC_counts.tsv: hVEC_Ca_GBS_A; Column name in Ca_counts.tsv: Ca_GBS_hVEC_A; Column name in GBS_counts.tsv: GBS_Ca_hVEC_A

value: Vaginal epithelial cells

value: Fungus

value: Bacteria

value: Epithelial cells grown at air-liquid interface, inoculated with C. albicans and S. agalactiae


title: C61

description: Library name: C61


title: C244

description: Library name: C244

value: Mice received intradermal injection of CTX (120 μg/50 μL) on the right side of the dorsal midline. Skin tissue from the injection site was collected on 2025-06-26 at 10:00 (24 hours post-injection).


title: C243

description: Library name: C243


title: C242

description: Library name: C242


title: gcl 1dpl, biological rep2

description: gene expression data from tissue of the granule cell layer 1 day postlesion

source_name: 1 day postlesion

value: granule cell layer


title: C241

description: Library name: C241


title: 293T_flagtagged_GFP_RMCE_flag_r2_rip_6

description: Library name: 293T_flagtagged_GFP_RMCE_flag_r2_rip_6

value: FLAG (Sigma, F1804)

value: HEK293T, B6/CAST F1-hybrid Rosa26-RMCE ESCs

value: Human embryonic kidney cells, Mouse embryonic stem cells

value: 1:1 mix of human, mouse lysates


title: C124

description: Library name: C124

value: Mice received intradermal injection of CTX (120 μg/50 μL) on the right side of the dorsal midline. Skin tissue from the injection site was collected on 2025-06-25 at 22:00 (12 hours post-injection).


title: C123

description: Library name: C123


title: 293T_flagtagged_GFP_RMCE_flag_r1_rip_5

description: Library name: 293T_flagtagged_GFP_RMCE_flag_r1_rip_5


title: C122

description: Library name: C122


title: C121

description: Library name: C121


title: E14.5 kidney mutant 4

city: Cincinnati

first: Cristina

last: Cebrian

state: Ohio

address: 240 Albert Sabin Way

department: Division of Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

description: Library name: m816_1

data_processing:
Raw data was processed with fastp (version 0.23.2) for initial trimming and quality control.
Pseudoalignment was performed with kallisto (version 0.46.0) against the mm10 transcriptome.
DESeq2 (version 1.40.2) was used for differential expression and visualization
Assembly: mm10
Supplementary files format and content: Raw counts and TPM in CSV format

source_name: E14.5 Kidney

extract_protocol:
Both kidneys from Etv4/5 mutant embryos and control littermates were isolated at E14.5 and snap frozen using dry ice. RNA was extracted from 4 controls and 4 experimental kidney pairs using the Nucleospin RNA prep kit (Takara Bio, 740984.50)
Library preparation and sequencing was performed by Novogene. Library was prepared by polyA enrichment of submitted RNA. Sequencing was performed using Illumina NovaSeq PE150

value: E14.5 Kidney

value: Six2-GFPcre tg/+; Etv4-/-; Etv5fl/fl


title: E14.5 kidney mutant 2

description: Library name: m755_10


title: E14.5 kidney mutant 1

description: Library name: m755_7


title: E14.5 kidney mutant 3

description: Library name: m759_1


title: E14.5 kidney control 4

description: Library name: c816_2

value: Six2-GFPcre tg/+; Etv4+/-; Etv5fl/fl


title: E14.5 kidney control 3

description: Library name: c775_3


title: E14.5 kidney control 2

description: Library name: c755_8


title: p53_VEGF-PARPi-OCDC_M7_ROI-050_TMA5B

city: Lausanne

first: Aspram

last: Minasyan

address: Bugnon 25A

country: Switzerland

institute: Ludwig Institute for Cancer Research / CHUV

description: Library name: TMA5B__050

data_processing:
Raw sequencing data were processed with the bcl2fastq program from Illumina to generate FASTQ files.
FASTQ files were converted into Digital Count Conversion (DCC) format through Nanotring's GeoMx DnD pipeline v2.0.0.16.
QC was performed using the R package GeoMxTools v3.4.0.
Batch effect correction was done by substracting  background and then minimum value was added per batch.
Q3 normalization were performed on the merged corrected experiment.
Assembly: probe-based quantification, Mm_R_NGS_WTA_v1.0.pkc
Supplementary files format and content: DCC files are count files converted from FASTQ files
Supplementary files format and content: data_matrix.csv contains corrected and Q3-normalized read counts from all QC-passed AOIs and filtered genes.
Library strategy: Spatial Transcriptomics

source_name: tumor

extract_protocol:
Tissue microarrays were prepared by extracting 2 mm punches from FFPE blocks to prepare nine slides, each containing up to 30 tumor sections. 5µm FFPE tissue microarrays were baked at 60°C for 1hour, then deparaffinized and underwent antigen retrieval at 100°C for 15 minutes, followed by 1µg/mL proteinase K at 37°C for 15 min. The slides were incubated overnight with the RNA probe mix (Whole Transcriptome Atlas).Tissues were stained with visualization markers panCK-AF647, CD68-AF594 and CD3-AF488 along with the nuclear marker Syto83. Tissue slides were then loaded into the GeoMx DSP instrument for scanning. Probe barcodes from each ROI were UV-photocleaved, collected into a 96-well plate, followed by library preparation and sequencing.
GeoMx DSP Whole Transcriptomic Atlas (WTA) library construction involving probe hybridization, ligation and PCR amplification were done according to Nanostring's protocol (GeoMx DSP NGS readout User Manual Library Preparation & GeoMx NGS Pipeline, MAN-10153-01).

treatment_protocol: Treatment of mice carrying ID8 tumors started 10 days after tumor graft and continued for 3 weeks. Mice were vaccinated intradermally with 1 x 106 OCDC every week. Anti-VEGF (40 µg, together with OCDC, Absolute Antibody) and anti-PD1 (200 µg, every 3 days, BioXcell) were given intraperitoneally (i.p.). Olaparib (PARPi) was administered orally at 40 mg/kg/day. As treatment controls, tumor-bearing mice were treated with PBS or isotype controls.

value: tumor

tag: mouse id

tag: slide id

tag: region of_interest

tag: model

tag: ck

value: low

value: B


title: BRAC1_OCDC_M38_ROI-049_TMA5B

description: Library name: TMA5B__049

tag: treatment

value: OCDC

value: high


title: BRAC2_OCDC_M57_ROI-045_TMA5B

description: Library name: TMA5B__045

tag: tissue

value: medium


title: BRAC2_OCDC_M57_ROI-044_TMA5B

description: Library name: TMA5B__044


title: BRAC2_OCDC_M57_ROI-043_TMA5B

description: Library name: TMA5B__043


title: BRAC2_VEGF_M54_ROI-041_TMA5B

description: Library name: TMA5B__041

value: VEGF


title: BRAC2_VEGF_M54_ROI-040_TMA5B

description: Library name: TMA5B__040


title: BRAC2_PBS_M51_ROI-039_TMA5B

description: Library name: TMA5B__039

value: PBS


title: BRAC2_PBS_M51_ROI-038_TMA5B

description: Library name: TMA5B__038


title: BRAC2_PBS_M51_ROI-037_TMA5B

description: Library name: TMA5B__037


title: BRAC1_OCDC_M38_ROI-034_TMA5B

description: Library name: TMA5B__034


title: BRAC1_OCDC_M38_ROI-035_TMA5B

description: Library name: TMA5B__035


title: BRAC1_OCDC_M38_ROI-033_TMA5B

description: Library name: TMA5B__033


title: BRAC1_OCDC_M37_ROI-032_TMA5B

description: Library name: TMA5B__032


title: BRAC1_PARPi_M33_ROI-029_TMA5B

description: Library name: TMA5B__029

value: PARPi


title: BRAC1_PARPi_M33_ROI-028_TMA5B

description: Library name: TMA5B__028


title: BRAC1_PARPi_M33_ROI-027_TMA5B

description: Library name: TMA5B__027


title: BRAC1_PBS_M27_ROI-026_TMA5B

description: Library name: TMA5B__026


title: BRAC1_PBS_M27_ROI-025_TMA5B

description: Library name: TMA5B__025


title: BRAC1_PBS_M27_ROI-024_TMA5B

description: Library name: TMA5B__024


title: p53_PARPi_M13_ROI-022_TMA5B

description: Library name: TMA5B__022


title: p53_PARPi_M12_ROI-021_TMA5B

description: Library name: TMA5B__021


title: p53_PARPi_M12_ROI-020_TMA5B

description: Library name: TMA5B__020


title: p53_PARPi_M12_ROI-019_TMA5B

description: Library name: TMA5B__019