title: MB135_iDUX4ca_siKLF17_20hDOX_2

description: Library name: siKLF17_20hDOX_2


title: 25717-iNeuron-WT-20uM-Cisplatin-END-seq

status: Public on Jun 10 2026

type: SRA

city: Bethesda

first: Chuanyuan

last: Chen

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

country: USA

institute: National Institutes of Health

description: Library name: Sample4

library_source: genomic

data_processing:
Raw reads were trimmed by Trimmomatic or Trim Galore!.
Trimmed reads were mapped to reference genome using bowtie.
Bigwig were generated with bacmCoverage function from deepTools with -bs=1 -normalizeUsing BPM. The resulting BigWig files were then adjusted using spike-in normalization.
For spike-in normalization, a scaling factor was calculated by dividing the reads mapped to the mouse spike-in locus (TCRβ) by the total reads mapped to the human genome. The signal was then divided by this factor.
Assembly: hg19
Supplementary files format and content: bw files include spike-in normliazed value for each sample

molecule: genomic DNA

organism: Homo sapiens

source_name: WTC11 i3Neuron

growth_protocol: To differentiate iPSCs into neurons, iPSCs were grown on matrigel pre-coated plates in N2 medium. N2 medium was removed and changed daily for two additional days. 3 days post-plating, cells (“day3 neurons”) were dissociated in accutase and replated onto new plates freshly coated with poly-L-ornithine in BrainPhys medium to complete differentiation. For END-seq experiments, 10 million day3 neurons were plated onto 10-cm plates. Cells were treated on day 6 or 7 (3-4 days after plating on PLO-coated plates).

extract_protocol:
Cells were harvested by treatment with accutase for 20 minutes and gentle pipetting to reach approximate single-cell suspension. Neurons were counted and spike-in cells (G1-arrested Lig4-/- mouse pre-B cells expressing a site-specific zinc-finger endonuclease) were added at 10% of cell count. Cells were embedded in 1% agarose plugs and processed.
Agarose-embedded cells were lysed and digested using Proteinase K (50°C for 1 hour, then 37°C for 7 hours). Plugs were washed in TE buffer and treated with RNase A at 37°C for 1 hour. For S1-END-seq, plugs were then washed in EB and equilibrated in S1 nuclease buffer (40 mM sodium acetate pH 4.5, 300 mM NaCl, 2 mM ZnSO4) for 30 minutes. Plugs were added to 100 µL S1 nuclease buffer containing 1.8 U S1 nuclease and incubated for 15 minutes on ice to allow the enzyme to diffuse into the plug. Plugs were then incubated with the reaction mix at 37°C for 20 minutes before addition of EDTA (10 mM final concentration) to terminate the reaction. After this, the standard END-seq protocol was followed. Plugs were then washed first in TE buffer, then in ExoVII Buffer (NEB), before incubating with ExoVII (NEB, M0379S) in ExoVII buffer for 1 hour at 37°C. Plugs were washed twice in NEBuffer 4 and then incubated with ExoT (NEB, M0265S) in NEBuffer 4 for 1 hour at 24°C. After blunting, plugs were washed twice in NEBNext dA-Tailing Reaction Buffer (NEB, B6059S) and then incubated with Klenow exo- (NEB, M0212S) in dA-Tailing Reaction Buffer at 37°C for 30 minutes. Plugs were washed once in NEBuffer 2 and incubated with END-seq hairpin adapter 1 and NEB Quick Ligase in NEB Quick Ligation buffer for 20 minutes at 25°C. Agarose plugs were then melted and digested with β-Agarase I (NEB) and DNA was sonicated to approximately 200 bp using a Covaris S220 sonicator for 4 min at 10% duty cycle, peak incident power 175, 200 cycles per burst, 4°C. DNA was ethanol-precipitated and dissolved in 70 μL TE buffer. Biotin-containing DNA fragments were isolated using MyOne Streptavidin C1 Beads (Thermo Fisher, 650–01). 35 μL of beads were washed twice with 1 mL 1x wash and binding buffer (1x W&B; 10 mM Tris-HCl pH 7.5, 1 mM EDTA, 1 M NaCl, 0.1% Tween 20) on a DynaMag-2 magnetic separator (Invitrogen, 12321D) and resuspended in 70 µL of 2x W&B (10 mM Tris-HCl pH 7.5, 2 mM EDTA, 2 M NaCl, 0.2% Tween 20). This was added to the fragmented sample DNA and incubated at 24°C while in a ThermoMixer while shaking for 30 minutes. Dynabeads (now bound to DNA) were washed three times in 1 mL of 1x W&B, twice in 1 mL EB, and once in 1 mL 1x T4 DNA ligase buffer (NEB). Dynabeads were resuspended in 50 µL end-repair reaction mix (1x T4 DNA ligase buffer, 2.7 U T4 DNA polymerase (NEB), 9 U T4 Polynucleotide Kinase (NEB), 1 U Klenow fragment (NEB), and 0.4 mM dNTPs) and incubated with shaking at 24°C for 30 minutes. Beads were washed once in 1 mL 1x W&B, twice in 1 mL EB, once in 1 mL NEBuffer 2 (NEB), and resuspended in 50 µL A-tailing reaction mix (1x NEB dA-Tailing Buffer with 20 U Klenow fragment exo- (NEB)). Samples were incubated at 37°C with shaking for 30 minutes. Dynabeads were then washed in 1 mL NEBuffer 2 and resuspended in 115 µL ligation reaction mix (1x Quick Ligase Buffer (NEB), 6,000 U Quick Ligase (NEB), END-seq hairpin adaptor 2) and incubated with shaking at 25°C for 30 minutes. 50 mM EDTA was added to terminate the reaction. Hairpin adaptors were digested using USER enzyme (NEB, M5505S) for 30 minutes at 37°C. Dynabeads were then washed three times with 1 mL 1x W&B and three times with 1 mL EB. Beads were resuspended in 8 µL EB + 10 µL 2x Kapa HiFI HotStart Ready Mix (Kapa Biosciences). Primers (10 mM) 5′-CAAGCAGAAGACGGCATACGAGATxrefGTGACTGG AGTTCAGACGTGTGCTCTTCCGATC*T-3′ and 5′-AATGATACGGCGA CCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3′ (asterisk indicates a phosphothiorate bond and a NNNNNN TruSeq index sequence) were added to 37 µL PCR reaction mix (20 µL 2x Kapa HiFI HotStart Ready Mix added to 17 µL H2O) for a final volume of 60 µL. DNA was amplified using the following PCR parameters: 98°C (45 seconds); 15 cycles of 98°C (15 seconds), 63°C (30 seconds), 72°C (30 seconds); 72°C (5 minutes). The finished PCR reaction was cleaned using 1.8x volume AMPure Beads XP (Beckman Coulter), following the manufacturer’s instructions. Samples were then separated on a 2% agarose gel, with ≈200 bp DNA being excised and purified using a QIA-quick Gel Extraction Kit (Qiagen). Library concentrations were measured using a KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems) and then sequenced using Illumina NextSeq 550 or NextSeq 2000 instruments.

treatment_protocol: Day 6 or 7 iNs were incubated with 20 µM cisplatin for 24 hr

tag: cell line

value: WTC11 i3Neuron

tag: cell type

value: iPSC-derived neurons

tag: genotype

value: WT

tag: treatment

value: 20 µM cisplatin; 24 hours


title: XZ63068-XZ63069 Rat mammary tumor AAV-Nf1 immune 3

city: Houston

first: Tobie

middle: D

last: Lee

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
Library name: XZ63068-XZ63069_27702_imm
XZ63068-XZ63069, AAV-Nf1, rat Nf1-Indel edited immune (CD45-positive) cells

library_source: transcriptomic

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were performed with 10x Genomics Cell Ranger v8.0.0.
Assembly: mRatBN7.2
Supplementary files format and content: tab-separated value files for counts matrices, barcodes, and genes

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat mammary tumor

extract_protocol:
Mammary tumors were harvested from female Cas9-expressing rats, minced, and enzymatically digested with 1.5 mM collagenase I and 1 μg/mL DNase I at 37°C for 1 hour with rotation. Digested tissue was passed through a 70 μm strainer, washed with PBS containing 2% FBS, and live cells were sorted for downstream analysis.
Single-cell suspensions were processed using the 10x Genomics Chromium Single Cell 3′ Gene Expression platform (v3.1 chemistry) according to the manufacturer’s instructions. Libraries were prepared from sorted live cells, amplified, and sequenced on Illumina X platform at BCM RNA Profiling Core.

tag: tissue

value: Rat mammary tumor

tag: batch


title: XZ69317-XZ69318 background reads

description:
Library name: XZ69317-XZ69318_background
XZ69317-XZ69318 background reads


title: BeforePretreatment_rep2

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 2
g202

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
Supplementary files format and content: DEseq2

organism: Arabidopsis thaliana

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: MB135_iDUX4ca_siKLF17_20hDOX_1

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: siKLF17_20hDOX_1

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

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: MB135iDUX4 cells were treated with siRNAs targeting KLF17 (siKLF17), KLF18 (siKLF18), or non-targeting controls (siCTRL), ± 1 µg/mL doxycycline (DOX) for 20 hours

value: human myoblast with inducible DUX4 transgene

value: siKLF17, 20hr Dox treatment


title: iNeuron-CSB-XPC-20uM-Cisplatin-END-seq

description: Library name: Sample3

value: CSB KO, XPC KD


title: XZ63068-XZ63069 Rat mammary tumor AAV-Nf1 tumor 2

description:
Library name: XZ63068-XZ63069_27700_tumor
XZ63068-XZ63069, AAV-Nf1, rat Nf1-Indel edited tumor (CD45-negative) cells


title: BeforePretreatment_rep1

description:
Library name: Sample 1
g201


title: MB135_iDUX4ca_siKLF17_noDOX_3

description: Library name: siKLF17_noDOX_3

value: siKLF17, No Dox


title: XZ63068-XZ63069 Rat mammary tumor AAV-Nf1 immune 2

description:
Library name: XZ63068-XZ63069_27700_imm
XZ63068-XZ63069, AAV-Nf1, rat Nf1-Indel edited immune (CD45-positive) cells


title: iNeuron-WT-20uM-Cisplatin-END-seq

description: Library name: Sample2


title: EtOH_3d_4

description:
Library name: Sample 16
EtOH_3d_4

source_name: whole plant

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

treatment_protocol: Thirteen- or 11-day-old seedlings were treated with gaseous ethanol for 1 d or 3 d, respectively.

value: whole plant

value: EtOH

tag: time point


title: 241218-iNeuron-WT-5uM-cisplatin-SAR-seq-rep2

description: Library name: Sample4

data_processing:
Reads were mapped to reference genome using bowtie with -n 2 -l 50 -m 1.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization
Assembly: hg19
Supplementary files format and content: bw files include normliazed value

growth_protocol: To differentiate iPSCs into neurons, iPSCs were grown on matrigel pre-coated plates in N2 medium. N2 medium was removed and changed daily for two additional days. 3 days post-plating, cells (“day3 neurons”) were dissociated in accutase and replated onto new plates freshly coated with poly-L-ornithine in BrainPhys medium to complete differentiation. For SAR-seq experiments, 10-15 million day3 neurons were plated onto 10-cm plates. Cells were treated on day 6 or 7 (3-4 days after plating on PLO-coated plates).

extract_protocol:
Cells were harvested as single cells by incubating with accutase for 15-20 minutes and resuspending by repeated pipetting. Cells were washed with PBS, resuspended in 1 mL PBS, and then fixed by dropwise addition of 4 mL ice cold methanol under mild vortexing. Fixed cells were washed with PBS, permeabilized with 0.2% Triton X-100/PBS for 10 minutes on ice, washed with PBS, and then resuspended in the Click-iT reaction mix for 2 hours shaking at room temperature to label EdU with biotin. Cells were then lysed with Proteinase K overnight at 37C. DNA was extracted with UltraPure Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) (Invitrogen) according to manufacturer’s instructions.
DNA was sonicated to 150-200 bp fragments using a Covaris S220 sonicator. Biotin-conjugated DNA fragments were isolated using MyOne Streptavidin C1 Beads added to the fragmented sample DNA and incubated at 24°C while in a ThermoMixer while shaking for 30 minutes. Dynabeads (now bound to DNA) were washed three times in 1 mL of 1x W&B, twice in 1 mL EB, and once in 1 mL 1x T4 DNA ligase buffer (NEB). Dynabeads were resuspended in 50 µL end-repair reaction mix (1x T4 DNA ligase buffer, 2.7 U T4 DNA polymerase (NEB), 9 U T4 Polynucleotide Kinase (NEB), 1 U Klenow fragment (NEB), and 0.4 mM dNTPs) and incubated with shaking at 24°C for 30 minutes. Beads were washed once in 1 mL 1x W&B, twice in 1 mL EB, once in 1 mL NEBuffer 2 (NEB), and resuspended in 50 µL A-tailing reaction mix (1x NEB dA-Tailing Buffer with 20 U Klenow fragment exo- (NEB)). Samples were incubated at 37°C with shaking for 30 minutes. Dynabeads were then washed in 1 mL NEBuffer 2 and resuspended in 115 µL ligation reaction mix (1x Quick Ligase Buffer (NEB), 6,000 U Quick Ligase (NEB), 5 nM annealed TruSeq truncated adapter) and incubated with shaking at 25°C for 20 minutes. 50 mM EDTA was added to terminate the reaction and Dynabeads were then washed three times with 1 mL 1x W&B and three times with 1 mL EB. Beads were resuspended in 8 µL EB + 10 µL 2x Kapa HiFI HotStart Ready Mix (Kapa Biosciences). Primers (10 mM) 5′-CAAGCAGAAGACGGCATACGAGATxrefGTGACTGG AGTTCAGACGTGTGCTCTTCCGATC*T-3′ and 5′-AATGATACGGCGA CCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3′ (asterisk indicates a phosphothiorate bond and a NNNNNN TruSeq index sequence) were added to 37 µL PCR reaction mix (20 µL 2x Kapa HiFI HotStart Ready Mix added to 17 µL H2O) for a final volume of 60 µL. DNA was amplified using the following PCR parameters: 98°C (45 seconds); 16 cycles of 98°C (15 seconds), 63°C (30 seconds), 72°C (30 seconds); 72°C (5 minutes). The finished PCR reaction was cleaned using 1.8x volume AMPure Beads XP (Beckman Coulter), following the manufacturer’s instructions. Samples were then separated on a 2% agarose gel, with 150-200 bp DNA being excised and purified using a QIA-quick Gel Extraction Kit (Qiagen). Library concentrations were measured using a KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems) and then sequenced using Illumina NextSeq 550 or NextSeq 2000 instruments.

treatment_protocol: Day 6 or 7 iNs were incubated with 20 μM EdU, 5-50 µM cisplatin, 1 µM THZ1, and/or 100 µM DRB for 24 hr

value: EdU (20 µM), 5 µM cisplatin; 24 hours


title: W6d_rep8

description:
Library name: Sample 16
g216


title: MB135_iDUX4ca_siKLF17_noDOX_2

description: Library name: siKLF17_noDOX_2


title: XZ71233-XZ71234 Rat mammary tumor AAV-rPT 2

description:
Library name: XZ71233-XZ71234_29604
XZ71233-XZ71234, AAV-rPT, rat Pik3caH1047R and Tp53-Indel edited tumor

value: Pik3caH1047R; Tp53-Indel


title: iNeuron-WT-NT-END-seq

description: Library name: Sample1

value: NT


title: W6d_rep7

description:
Library name: Sample 15
g215


title: MB135iDUX4ca_WT_PlusDox_2

description: Library name: MB135iDUX4ca_WT_PlusDox_2

treatment_protocol: MB135-iDUX4ca WT,  KLF18 Knockout clone 1, or clone 2 cells were treated with 1ug/mL Dox for 18 hours prior to harvest

value: Human Myoblast

value: iDUX4ca, WT KLF18

value: 18hr Plus Dox


title: XZ63068-XZ63069 Rat mammary tumor AAV-Nf1 tumor 1

description:
Library name: XZ63068-XZ63069_27698_tumor
XZ63068-XZ63069, AAV-Nf1, rat Nf1-Indel edited tumor (CD45-negative) cells


title: MB135iDUX4ca_WT_PlusDox_1

description: Library name: MB135iDUX4ca_WT_PlusDox_1


title: EtOH_3d_3

description:
Library name: Sample 15
EtOH_3d_3


title: MB135_iDUX4ca_siKLF17_noDOX_1

description: Library name: siKLF17_noDOX_1


title: 241218-iNeuron-WT-NT-SAR-seq-rep1

description: Library name: Sample1

value: WTC11 i3Neuron

value: iPSC-derived neurons

value: EdU (20 µM); 24 hours


title: In vitro synthesized CONCR lncRNA, DMSO-treated, rep3

city: Montpellier

first: Isabel

last: Chillón

address: 1919 Route de Mende

department: Institut de Génétique Moléculaire de Montpellier (IGMM)

country: France

institute: Centre National de la Recherche Scientifique (CNRS)

description: Library name: CONCR in vitro DMSO rep3

library_source: other

data_processing:
Mutations in sequencing reads were converted into reactivity profiles using ShapeMapper v2.1.3. RNA secondary structures were modeled using the folding pipeline Superfold ver. Alpha_22-Sept-2014 or the folding software package RNAstructure V62, with the 1M7 reactivity values obtained in ShapeMapper as constraints for minimum free energy calculations using default options.
ShapeMapper v2.1.3 was run using paired 1M7-treated and DMSO-control samples for each biological replicate. The DMSO channel was used as a background control to subtract mutation rates caused by reverse transcriptase errors and spontaneous RNA modifications. Processed output files (.map and _profile.txt) are therefore derived from both the 1M7 and DMSO raw.files of the same replicate and are listed in both sample rows accordingly.
Assembly: Human clone NT2RP7010109, Nucleotide accession number AK096360
Supplementary files format and content: .map files containing reactivity values at single-nucleotide resolution. Tab-delimited text. Four columns. First column is 1-based nucleotide position. Second is normalized reactivity, with excluded positions set to -999. Third column is stderr, fourth is nucleotide sequence.
Supplementary files format and content: Tab-delimited text columns. First line is column names. Content: Nucleotide number (1-based); Nucleotide (AUGCaugc); Mutation counts; Read depth; Effective read depth; Effective mutation rate calculated as (mutation count / effective read depth); Simple mapped read depths for reads not meeting --amplicon/--primer location requirements; Simple mapped read depths for reads not meeting --min-mapq; Simple mapped read depths for included reads, broken down by primer pair if applicable; Calculated reactivity profile; Standard error; Reactivity profile with high-background and low-depth positions excluded (set to nan); Standard error with high-background and low-depth positions excluded; Reactivity profile after normalization (scaling); Standard error after normalization.

molecule: other

source_name: missing

growth_protocol: Not applicable. RNA was produced by in vitro transcription.

extract_protocol:
Not applicable. RNA was produced by in vitro transcription using the T7 system.
Sequencing libraries were created using the Nextera XT kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol:
The in vitro transcribed CONCR was purified with MOPS filtration buffer. Three pmol of purified CONCR were incubated with 150 mM KCl, 50 mM HEPES pH 7.4, and 5 mM MgCl2 at 37 ºC for 30 min. After the equilibration in the filtration solution, the RNA was chemically probed using 1-methyl-7-nitroisatoic anhydride (1M7) (Sigma) to a final concentration of 10 mM and maintained at 37 ºC for 6 min. RNA was precipitated with 100 % ethanol and washed both with 100 % and 70 % ethanol before resuspending it in 20 µl of water. Sites of chemical modifications in the RNA were converted into mutations using error-prone reverse transcription. Briefly, 1 pmol of CONCR chemically-modified RNA was incubated with 200 ng of random nonamers (Thermo) and 2 mM dNTPs at 65 ºC for 10 min followed by 4 °C for 2 min. Nine uL of 2.22X MaP buffer (6 mM MnCl2, 1 M betaine, 50 mM Tris pH 8, 75 mM KCl, 10 mM DTT) and 1 μL of SuperScript II Reverse Transcriptase (Invitrogen)  were added to the reaction and the combined solution incubated at 23 °C for 2 min followed by: 25 °C for 10 min, 42 °C for 90 min, 10 X [50 °C for 2 min, 42 °C for 2 min], and 72 °C for 10 min. The resulting cDNA was purified with the QIAquick PCR & Gel Cleanup Kitkit (Qiagen) and used as template for a PCR reaction. The PCR was performed using the primers 01_F_CONCR_T7_HindIII (GGGAGACCCAAGCTTGGTA) and 04_R_CONCR_XhoI (CGAGCTTATATTCAAGCTTTTATGTTGG), which produced a 793 bp amplicon. The PCR products were cleaned with the Monarch® PCR & DNA Cleanup Kit (5 μg).
The in vitro transcribed CONCR was purified with MOPS filtration buffer. Three pmol of purified CONCR were incubated with 150 mM KCl, 50 mM HEPES pH 7.4, and 5 mM MgCl2 at 37 ºC for 30 min. After the equilibration in the filtration solution, DMSO was added and maintained at 37 ºC for 6 min. RNA was precipitated with 100 % ethanol and washed both with 100 % and 70 % ethanol before resuspending it in 20 µl of water. Sites of chemical modifications in the RNA were converted into mutations using error-prone reverse transcription. Briefly, 1 pmol of CONCR chemically-modified RNA was incubated with 200 ng of random nonamers (Thermo) and 2 mM dNTPs at 65 ºC for 10 min followed by 4 °C for 2 min. Nine uL of 2.22X MaP buffer (6 mM MnCl2, 1 M betaine, 50 mM Tris pH 8, 75 mM KCl, 10 mM DTT) and 1 μL of SuperScript II Reverse Transcriptase (Invitrogen)  were added to the reaction and the combined solution incubated at 23 °C for 2 min followed by: 25 °C for 10 min, 42 °C for 90 min, 10 X [50 °C for 2 min, 42 °C for 2 min], and 72 °C for 10 min. The resulting cDNA was purified with the QIAquick PCR & Gel Cleanup Kitkit (Qiagen) and used as template for a PCR reaction. The PCR was performed using the primers 01_F_CONCR_T7_HindIII (GGGAGACCCAAGCTTGGTA) and 04_R_CONCR_XhoI (CGAGCTTATATTCAAGCTTTTATGTTGG), which produced a 793 bp amplicon. The PCR products were cleaned with the Monarch® PCR & DNA Cleanup Kit (5 μg).

value: missing

value: teratocarcinoma

value: WT

value: DMSO


title: XZ63068-XZ63069 Rat mammary tumor AAV-Nf1 immune 1

description:
Library name: XZ63068-XZ63069_27698_imm
XZ63068-XZ63069, AAV-Nf1, rat Nf1-Indel edited immune (CD45-positive) cells

value: Rat mammary tumor


title: EtOH_3d_2

description:
Library name: Sample 14
EtOH_3d_2


title: MB135_iDUX4ca_siCTRL_20hDOX_3

description: Library name: siCTRL_20hDOX_3

value: human myoblast with inducible DUX4 transgene

value: siControl, 20hr Dox treatment


title: XZ71702-XZ71703 Rat mammary tumor AAV-rPT 5

description:
Library name: XZ71702-XZ71703_29632
XZ71702-XZ71703, AAV-rPT, rat Pik3caH1047R and Tp53-Indel edited tumor


title: In vitro synthesized CONCR lncRNA, 1M7-treated, rep3

description: Library name: CONCR in vitro 1M7 rep3


title: EtOH_3d_1

description:
Library name: Sample 13
EtOH_3d_1

value: whole plant

value: EtOH


title: In vitro synthesized CONCR lncRNA, DMSO-treated, rep2

description: Library name: CONCR in vitro DMSO rep2


title: MB135_iDUX4ca_siCTRL_20hDOX_2

description: Library name: siCTRL_20hDOX_2


title: iNeuron-WT-20uM-cispt-dN-day14-RNA-seq-rep2

description: Library name: Sample5

data_processing:
Raw reads were trimmed by Trim Galore!.
Trimmed reads were mapped to reference genome using STAR.
Bigwig files were generated with bacmCoverage function from deepTools with -bs=1 -normalizeUsing BPM.
The gene expression raw counts were calculated using featureCounts function in Bioconductor Rsubread package.
Assembly: hg19
Supplementary files format and content: bw files include normliazed value
Supplementary files format and content: csv files include raw count expression matrix

growth_protocol: To differentiate iPSCs into neurons, iPSCs were grown on matrigel pre-coated plates in N2 medium. N2 medium was removed and changed daily for two additional days. 3 days post-plating, cells (“day3 neurons”) were dissociated in accutase and replated onto new plates freshly coated with poly-L-ornithine in BrainPhys medium to complete differentiation. For RNA-seq experiments, 3 million day3 neurons were plated onto each well of 6-well plates. Cells were treated on day 6 (4 days after plating on PLO-coated plates).

extract_protocol:
Total RNA was harvested using TRIzol reagent (Thermo Fisher, 15596018) following the manufacturer’s instructions. DNA was removed using DNAse and rRNA was removed using NEBNext rRNA Depletion kit v.2 (Human/Mouse/Rat) (NEB, E7400).
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB, E7760), using 1 µg of starting RNA material and following the manufacturer’s instructions. cDNA was amplified for 11 cycles. Libraries were sequenced on an Illumina NextSeq2000 with 100-bp single-end reads.

treatment_protocol: Day 6 iNs were either not treated or incubated with 20 µM cisplatin and 150 µM dN for 7 days

value: 20 µM cisplatin, 150 µM dN; 7 days


title: XZ71702-XZ71703 Rat mammary tumor AAV-rPT 4

description:
Library name: XZ71702-XZ71703_29629
XZ71702-XZ71703, AAV-rPT, rat Pik3caH1047R and Tp53-Indel edited tumor

value: Pik3caH1047R; Tp53-Indel


title: moc_3d_4

description:
Library name: Sample 12
moc_3d_4

value: moc


title: MB135_iDUX4ca_siCTRL_20hDOX_1

description: Library name: siCTRL_20hDOX_1


title: In vitro synthesized CONCR lncRNA, 1M7-treated, rep2

description: Library name: CONCR in vitro 1M7 rep2


title: XZ69803-XZ69804 Rat mammary tumor AAV-rPik3caH1047R 1

description:
Library name: XZ69803-XZ69804_29311
XZ69803-XZ69804, AAV-rPik3caH1047R, rat Pik3caH1047R edited tumor


title: moc_3d_3

description:
Library name: Sample 11
moc_3d_3


title: MB135_iDUX4ca_siCTRL_noDOX_3

description: Library name: siCTRL_noDOX_3

value: siControl, No Dox


title: In vitro synthesized CONCR lncRNA, DMSO-treated, rep1

description: Library name: CONCR in vitro DMSO rep1


title: Min Sham, biol rep 3

city: Baltimore

first: Franck

last: Housseau

address: 1651 E.Jefferson St

institute: Johns Hopkins University School of Medicine

description: Library name: Min Sham, biol rep 3

data_processing:
Raw data (raw reads) in FASTQ format were first processed using fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapters, reads containing poly-N, and low-quality reads from the raw data. At the same time, Q20, Q30, and GC content of the clean data were calculated. All downstream analyses were based on the high-quality clean data. Reference genome and gene model annotation files were downloaded directly from the genome website. An index of the reference genome was built using Hisat2 v2.0.5, and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. Hisat2 was selected as the mapping tool because it can generate a database of splice junctions based on the gene model annotation file, thereby producing better mapping results than other non-splice mapping tools. featureCounts v1.5.0-p3 was used to count the number of reads mapped to each gene, and FPKM for each gene was calculated based on gene length and the number of reads mapped to that gene. FPKM, or expected number of fragments per kilobase of transcript sequence per million base pairs sequenced, considers the effects of sequencing depth and gene length simultaneously and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCh38.p12
Supplementary files format and content: txt file containing FPKM values for all samples
Supplementary files format and content: txt file containing gene counts for all samples

organism: Mus musculus

source_name: colon

growth_protocol: primary epithelial cells

extract_protocol:
Cells (30,000 to 100,000 cells) were cell sorted directly in RLT buffer and Qiagen Micro Rneasy kit was used to extract RNA
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Min mice are infected by ETBF gavage or PBS gavage (ctrl). Epithelial cells from colons were isolated by enzymatic digestion and cell sorting

value: colon

value: epithelial cells

value: Min

value: Sham


title: moc_3d_2

description:
Library name: Sample 10
moc_3d_2


title: MB135_iDUX4ca_siCTRL_noDOX_2

description: Library name: siCTRL_noDOX_2


title: In vitro synthesized CONCR lncRNA, 1M7-treated, rep1

description: Library name: CONCR in vitro 1M7 rep1

value: missing


title: iNeuron-WT-20uM-cispt-dN-day14-RNA-seq-rep1

description: Library name: Sample4

value: WTC11 i3Neuron

value: iPSC-derived neurons


title: Min Sham, biol rep 2

description: Library name: Min Sham, biol rep 2


title: moc_3d_1

description:
Library name: Sample 9
moc_3d_1


title: MB135_iDUX4ca_siCTRL_noDOX_1

description: Library name: siCTRL_noDOX_1


title: EtOH_1d_4

description:
Library name: Sample 8
EtOH_1d_4


title: Min Sham, biol rep 1

description: Library name: Min Sham, biol rep 1


title: CAF66, H3K4me3 ChIP

city: Maebashi

first: Naoko

last: Hattori

state: Gunma

address: 3-39-15 Showa-mach

department: Institute for Molecular and Cellular Regulation

institute: Gunma University

description: Library name: CAF66_H3K4me3

data_processing:
Fastp (version 0.22.0) was used for sequencing QC and adapter trimming.
All reads were aligned to the human genome GRCh38/hg38 using the short-read aligner Bowtie 2 (version 2.5.1) with default parameters.
The resultant SAM file was converted into a BAM file and duplicates were removed using SAMtools (version 1.18).
Peak calling was performed with the input control using MACS2 (version 2.2.9.1) with a broad parameter for H3K4me1 data and a p-value threshold of 1E-5 for H3K4me3 data.
bedGraph files were converted to bigWig files using bedGraphToBigWig.
Assembly: hg38
Supplementary files format and content: bedGraph, bigWig, broadPeak for H3K4me1 data, narrowPeak for H3K4me3 (except for  Input samples)

source_name: Stomach

growth_protocol: CAFs or GIST fibroblasts were maintained in MF medium (Toyobo).

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature. Lysates were clarified from sonicated nuclei and chromatins were isolated with antibodies against H3K4me1 and H3K4me3.
Sequencing libraries were prepared from 5 ng of DNA using the GenNext NGS Library Prep Kit (Toyobo, LPK-101). These libraries were sequenced using an Illumina NextSeq2000 to a final sequencing depth of 10 to 30 million reads per sample.

value: Stomach

value: gastric fibroblasts from cancerous tissues of scirrhous gastric cancer patient


title: 3D_Y537S_ER_shPR_003

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

institute: University of Minnesota

description: Library name: 3D_Y537S_ER_shPR_003

data_processing:
Quality scores across sequenced reads were assessed using FASTQC.
Illumina adapters were removed using Trim-Galore.
For alignment and transcript assembly, the sequencing reads were mapped to hg38 using STAR
Sorted reads were counted using HTseq
Assembly: Hg38
Supplementary files format and content: raw counts data for each sample as text files

growth_protocol: For 2D conditions, T47D WT and Y537S ESR1 cells (shGFP and shPR) were plated in triplicate. For 3D conditions, cells were plated in triplicate into tumorsphere media in ULA plates and allowed to form for 6 days.

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen).
Purity of the total RNA samples was assessed using BioAnalyzer (Agilent) and samples with an RNA integrity score >8 were used for library construction by the University of Minnesota Genomics Core. Libraries were built from individual samples with the TruSeq Stranded mRNA kit (Illumina).

treatment_protocol: Cells were hormone-starved for 24h, followed by treatment with E2 (1 nM, 48h) or R5020 (10 nM, 6h).

value: cancer

value: shPR


title: Min YAPKO Sham, biol rep 3

description: Library name: Min YAPKO Sham, biol rep 3

value: Min-YAPKO


title: 3D_Y537S_ER_shPR_002

description: Library name: 3D_Y537S_ER_shPR_002


title: CAF30, H3K4me3 ChIP

description: Library name: CAF30_H3K4me3

value: gastric fibroblasts from cancerous tissues of non-scirrhous gastric cancer patient


title: EtOH_1d_3

description:
Library name: Sample 7
EtOH_1d_3

value: whole plant

value: EtOH


title: CAF66, H3K4me1 ChIP

description: Library name: CAF66_H3K4me1


title: Min YAPKO Sham, biol rep 2

description: Library name: Min YAPKO Sham, biol rep 2


title: EtOH_1d_2

description:
Library name: Sample 6
EtOH_1d_2


title: 3D_Y537S_ER_shPR_001

description: Library name: 3D_Y537S_ER_shPR_001


title: Min YAPKO Sham, biol rep 1

description: Library name: Min YAPKO Sham, biol rep 1


title: CAF30, H3K4me1 ChIP

description: Library name: CAF30_H3K4me1


title: EtOH_1d_1

description:
Library name: Sample 5
EtOH_1d_1


title: XZ64126-XZ64127 Rat mammary tumor AAV-Tp53 immune 3

description:
Library name: XZ64126-XZ64127_27754_imm
XZ64126-XZ64127, AAV-Tp53, rat Tp53-Indel edited immune (CD45-positive) cells

value: Rat mammary tumor


title: 3D_Y537S_ER_shGFP_003

description: Library name: 3D_Y537S_ER_shGFP_003

value: shGFP


title: moc_1d_4

description:
Library name: Sample 4
moc_1d_4

value: moc


title: CAF66 Input

description: Library name: CAF66_Input


title: Min YAPKO ET, biol rep 3

description: Library name: Min YAPKO ET, biol rep 3

value: colon

value: epithelial cells

value: ETBF


title: 3D_Y537S_ER_shGFP_002

description: Library name: 3D_Y537S_ER_shGFP_002


title: CAF30 Input

description: Library name: CAF30_Input


title: Min YAPKO ET, biol rep 2

description: Library name: Min YAPKO ET, biol rep 2


title: 3D_Y537S_ER_shGFP_001

description: Library name: 3D_Y537S_ER_shGFP_001


title: moc_1d_3

description:
Library name: Sample 3
moc_1d_3


title: WTC11iCRISPRa_4C_sgDLX1_DLX1pe_rep3

city: London

first: Mikhail

last: Spivakov

address: Du Cane Road

country: United Kingdom

institute: MRC Laboratory of Medical Sciences (LMS)

description:
Library name: WTC11iCRISPRa_4C_sgDLX1_DLX1pe_rep3
4C-seq library amplified at the poised enhancer 280801 in the DLX1-DLX2 locus

data_processing:
Sequencing reads were trimmed with fastp v0.23.4 requiring a minimal length of 45 bp. Only read 1 from paired-end sequencing was used for downstream analysis. Processed reads were mapped and filtered with pipe4C (Krijger et al. 2020) (https://github.com/deLaatLab/pipe4C) using the following parameters: minimum mapping quality of 1, retention of uniquely mapped reads, and cis-only analysis. The genomic coordinate chr2:172,096,280 was used as the viewpoint position. Quality control of individual experiments was based on the diagnostic reports generated by pipe4C. Interaction profiles were exported as WIG files and visualised in the Integrative Genomics Viewer (IGV).
Assembly: GRCh38
Supplementary files format and content: Wig files per replicate presenting normalised 4C-seq signal (per-window contact intensity).
Library strategy: 4C-Seq

source_name: WTC11 iCRSPRa

growth_protocol: WTC11 iCRISPRa cells were grown at 37°C, 5% CO2 in mTeSR-E8 basal media using vitronectin XF (1:1000 dilution in D-PBS 1X) as a coating matrix.

extract_protocol:
10 million cells were crosslinked for 10 minutes with 2% formaldehyde.
Crosslinking was quenched with 0.13 M glycine, and nuclei were isolated in lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 0.5 % IGEPAL CA-630, 1 % TritonX-100, 5 mM EDTA, and protease inhibitors) for 20 min. Chromatin was digested overnight with 200 U DpnII (NEB), the primary restriction enzyme, then overnight ligated with 50 U of DNA ligase (Invitrogen) following published protocols (Krijger et al. 2020; Taylor et al. 2022; Ray-Jones et al. 2025). Crosslink were reversed with proteinase K, and 3C templates were purified with AMPure XP beads (Beckman Coulter). Up to 60 μg of template was diluted to 100 ng/μL, and digested overnight with NlaIII (NEB, 1 U/μg DNA template), the secondary restriction enzyme, followed by a second overnight ligation at a final DNA concentration of 5 ng/μL using 2 U/μg T4 DNA ligase (Invitrogen). DNA was purified by Phenol Chloroform Isoamyl Alcohol (P:C:I) extraction and AMPure XP beads, according to (Ray-Jones et al. 2025). 4C libraries were generated in two rounds of PCR, as described in (Krijger et al. 2020). Briefly, first-round PCRs (16 cycles) were performed with Expand Long Template polymerase (Roche) on four 200-ng reactions per sample, followed by pooling and 0.8 X AMPure XP beads cleanup to remove long primers. A second PCR (12 cycles) was performed with up to 100 ng of template per reaction to introduce Illumina sequencing adapters. Finally, libraries were purified as above and sequenced as 60-bp paired-end reads.

treatment_protocol: Single guide RNA (sgRNA) sequences targeting the poised enhancer located in the DLX1-DLX2 region (PE 280801), and a control region (Scramble) were used in this study. WTC11 iCRISPRa cells (1.6 x 10⁶) were seeded on vitronectin XF-coated (1:1000 in D-PBS) 10-cm dishes in mTeSR-E8 basal medium. Cells were transfected with 24 µg of plasmid DNA encoding either an equimolar pool of nine sgRNAs targeting the poised enhancer 280801 or a scrambled sgRNA control, using TransIT-LT1 reagent (Mirus Bio, MIR2300) at a ratio of 3 µl per 1 µg DNA, in mTeSR-E8 medium supplemented with 10 µM ROCK inhibitor (Y-27632). Twenty-four hours post-transfection, cells were selected with 1 µg/mL puromycin in mTeSR-E8 medium for 48 h. A parallel puromycin-only control (untransfected cells) was used to confirm selection efficiency. Following a 24 h recovery period in mTeSR-E8 medium, CRISPRa was induced by addition of 20 µM trimethoprim for exactly 24 h prior to harvesting for RT-qPCR (n = 4) and 4C-seq (n = 3) experiments.

value: WTC11 iCRSPRa

value: Expressing inducible dCas9, 4xVP48-P65-HSF1, and a sgRNA targeting the poised enhancer of interest


title: MB135_iDUX4ca_siKLF18_20hDOX_1

description: Library name: siKLF18_20hDOX_1

value: human myoblast with inducible DUX4 transgene

value: siKLF18, 20hr Dox treatment


title: Min YAPKO ET, biol rep 1

description: Library name: Min YAPKO ET, biol rep 1


title: moc_1d_2

description:
Library name: Sample 2
moc_1d_2


title: Min ET, biol rep 3

description: Library name: Min ET, biol rep 3

value: Min


title: moc_1d_1

description:
Library name: Sample 1
moc_1d_1


title: WTC11iCRISPRa_4C_sgDLX1_DLX1pe_rep2

description:
Library name: WTC11iCRISPRa_4C_sgDLX1_DLX1pe_rep2
4C-seq library amplified at the poised enhancer 280801 in the DLX1-DLX2 locus


title: XZ64126-XZ64127 Rat mammary tumor AAV-Tp53 tumor 2

description:
Library name: XZ64126-XZ64127_27751_nonimm
XZ64126-XZ64127, AAV-Tp53, rat Tp53-Indel edited tumor (CD45-negative) cells


title: 3D_WT_ER_shPR_003

description: Library name: 3D_WT_ER_shPR_003

value: cancer


title: WTC11iCRISPRa_4C_sgDLX1_DLX1pe_rep1

description:
Library name: WTC11iCRISPRa_4C_sgDLX1_DLX1pe_rep1
4C-seq library amplified at the poised enhancer 280801 in the DLX1-DLX2 locus


title: 3D_WT_ER_shPR_001

description: Library name: 3D_WT_ER_shPR_001

value: shPR


title: E6dF2h_rep8

description:
Library name: Sample 40
g240

value: shoot


title: Min ET, biol rep 2

description: Library name: Min ET, biol rep 2


title: 3D_WT_ER_shPR_002

description: Library name: 3D_WT_ER_shPR_002


description:
Library name: WTC11iCRISPRa_4C_scramblControl_DLX1pe_rep3
4C-seq library amplified at the poised enhancer 280801 in the DLX1-DLX2 locus

value: Expressing inducible dCas9, 4xVP48-P65-HSF1, and a non-targeting sgRNA


title: Min ET, biol rep 1

description: Library name: Min ET, biol rep 1


description:
Library name: WTC11iCRISPRa_4C_scramblControl_DLX1pe_rep2
4C-seq library amplified at the poised enhancer 280801 in the DLX1-DLX2 locus


title: Wild-type control mouse 4, 5 months, striatum

city: Shanghai

first: Yifei

last: He

email: crestedibistoki@gmail.com, 21301010016@m.fudan.edu.cn, yumei@fudan.edu.cn, 23211520033@m.fudan.edu.cn

address: 138 Yixueyuan Road

department: Institute of Brain Science

country: China

institute: Fudan University

description:
Library name: WT_5m_04
Column name in fpkm_counts_MitoPark_5m.csv: Control_4_count Control_4_FPKM

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
Assembly: Species: mus_musculus Origin: ensembl Version: GRCm39.107  Genome: http://ftp.ensembl.org/pub/release-107/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz Gff3: http://ftp.ensembl.org/pub/release-107/gff3/mus_musculus/Mus_musculus.GRCm39.107.chr.gff3.gz Transcript: http://ftp.ensembl.org/pub/release-107/fasta/mus_musculus/cdna/Mus_musculus.GRCm39.cdna.all.fa.gz
Supplementary files format and content: csv file includes the Sequencing Counts and FPKM values for A53T 12m Experiment and Control samples
Supplementary files format and content: csv file includes the Sequencing Counts and FPKM values for A53T 16m Experiment and Control samples
Supplementary files format and content: csv file includes the Sequencing Counts and FPKM values for MitoPark 5m Experiment and Control samples
Supplementary files format and content: csv file includes the Sequencing Counts and FPKM values for MPTP acute 3d Experiment and Control samples
Supplementary files format and content: csv file includes the Sequencing Counts and FPKM values for MPTP subacute 3d Experiment and Control samples

source_name: Striatum

growth_protocol: Male C57BL/6 mice (10-12 weeks old) and C57BL/6Smoc-Tfam(flox)Slc6a3(iCre)Smoc (MitoPark) were obtained from Shanghai Model Organisms Center, Inc. Human alpha-synuclein A53T (α-Syn A53T or A53T) transgenic mice (line G2-3) were acquired from the Jackson Laboratory. Animals were housed in individually ventilated cages with a 12-hour light/dark cycle, maintained at a suitable temperature and circadian rhythm. All experimental procedures were approved by the Institutional Animal Care and Use Committee of Shanghai Medical College, Fudan University (No. 20240712-010) and conducted in accordance with the National Research Council's Guide for the Care and Use of Laboratory Animals.

extract_protocol:
Total RNA from mouse striatum was extracted with Total RNA Isolation Reagent (YY101, epizyme, China) and its concentration was measured by BioTek Microplate Reader (USA).
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on the instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: For the acute MPTP model, C57BL/6J mice received four intraperitoneal injections of 15 mg/kg MPTP-HCl (Sigma-Aldrich, USA) at 2-hour intervals in a single day. For the subacute model, mice were injected with 20 mg/kg MPTP-HCl intraperitoneally once daily for five consecutive days. Control mice were administered an equivalent volume of normal saline (NS).

value: Striatum

value: WT


title: E6dF2h_rep7

description:
Library name: Sample 39
g239


title: 3D_WT_ER_shGFP_003

description: Library name: 3D_WT_ER_shGFP_003


title: 3D_WT_ER_shGFP_002

description: Library name: 3D_WT_ER_shGFP_002


description:
Library name: WTC11iCRISPRa_4C_scramblControl_DLX1pe_rep1
4C-seq library amplified at the poised enhancer 280801 in the DLX1-DLX2 locus


title: 3D_WT_ER_shGFP_001

description: Library name: 3D_WT_ER_shGFP_001


title: Wild-type control mouse 3, 5 months, striatum

description:
Library name: WT_5m_03
Column name in fpkm_counts_MitoPark_5m.csv: Control_3_count Control_3_FPKM


title: N70, H3K27ac ChIP

description: Library name: N70_K27ac

data_processing:
Fastp (version 0.23.4) was used for sequencing QC and adapter trimming.
All reads were aligned to the human genome GRCh38/hg38 using the short-read aligner Bowtie 2 (version 2.5.1) with default parameters.
The resultant SAM file was converted into a BAM file and duplicates were removed using SAMtools (version 1.18).
For identification of super-enhancers, peaks within a window ±2,000 bp around TSS were excluded, and then those within 12,500 bp were stitched into one region.  Read density of each stitched region was calculated by adding up the pileup signals for each bp and was normalized to reads per million per bp (rpm/bp). To draw the threshold between enhancers and super-enhancers, all stitched regions of H3K27ac were ranked along the x-axis by the background-subtracted ChIP-seq density in increasing order.  The threshold was defined as the intersection of the slope of 1 tangent to the curve produced by ranked stitched regions.  Regions below this threshold were defined as typical enhancers, and those above as super-enhancers.
Annotation of identified super-enhancers was performed using HOMER.
Assembly: hg38
Supplementary files format and content: bedGraph (except for  Input samples)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature. Lysates were clarified from sonicated nuclei and chromatins were isolated with an antibody against acetylated H3K27.
Sequencing libraries were prepared from 5 ng of DNA using the GenNext NGS Library Prep Kit (Toyobo, LPK-101).  These libraries were sequenced using an Illumina NextSeq2000 to a final sequencing depth of 20 to 170 million reads per sample.

value: Stomach

value: gastric fibroblasts derived from intact tissue of GIST patient without Helicobacter pylori infection


title: E6dF2h_rep5

description:
Library name: Sample 37
g237


title: Wild-type control mouse 2, 5 months, striatum

description:
Library name: WT_5m_02
Column name in fpkm_counts_MitoPark_5m.csv: Control_2_count Control_2_FPKM


title: 2D_YS_shPR_veh_veh_003

description: Library name: 2D_YS_shPR_veh_veh_003


title: E6dF2h_rep4

description:
Library name: Sample 36
g236


title: N54, H3K27ac ChIP

description: Library name: N54_K27ac


title: Wild-type control mouse 1, 5 months, striatum

description:
Library name: WT_5m_01
Column name in fpkm_counts_MitoPark_5m.csv: Control_1_count Control_1_FPKM


title: E6dF2h_rep3

description:
Library name: Sample 35
g235


title: 2D_YS_shPR_veh_veh_002

description: Library name: 2D_YS_shPR_veh_veh_002


title: N70, Input

description: Library name: N70_In


title: E6dF2h_rep2

description:
Library name: Sample 34
g234


title: 2D_YS_shPR_veh_veh_001

description: Library name: 2D_YS_shPR_veh_veh_001


title: N54, Input

description: Library name: N54_In


title: MitoPark mouse 4, 5 months, striatum

description:
Library name: MitoPark_5m_04
Column name in fpkm_counts_MitoPark_5m.csv: Experiment_4_count Experiment_4_FPKM

value: MitoPark


title: E6dF2h_rep6

description:
Library name: Sample 38
g238


title: 2D_YS_shPR_E2_veh_003

description: Library name: 2D_YS_shPR_E2_veh_003

value: shPR, E2


title: E6dF2h_rep1

description:
Library name: Sample 33
g233


title: CAF67, H3K27ac ChIP

description: Library name: CAF67_K27ac

value: gastric fibroblasts from cancerous tissues of scirrhous gastric cancer patient


title: 2D_YS_shPR_E2_veh_002

description: Library name: 2D_YS_shPR_E2_veh_002


title: MitoPark mouse 2, 5 months, striatum

description:
Library name: MitoPark_5m_02
Column name in fpkm_counts_MitoPark_5m.csv: Experiment_2_count Experiment_2_FPKM


title: MitoPark mouse 3, 5 months, striatum

description:
Library name: MitoPark_5m_03
Column name in fpkm_counts_MitoPark_5m.csv: Experiment_3_count Experiment_3_FPKM


title: W6dF2h_rep8

description:
Library name: Sample 32
g232


title: CAF66, H3K27ac ChIP

description: Library name: CAF66_K27ac


title: W6dF2h_rep7

description:
Library name: Sample 31
g231


title: 2D_YS_shPR_E2_veh_001

description: Library name: 2D_YS_shPR_E2_veh_001


title: MitoPark mouse 1, 5 months, striatum

description:
Library name: MitoPark_5m_01
Column name in fpkm_counts_MitoPark_5m.csv: Experiment_1_count Experiment_1_FPKM


title: CAF63, H3K27ac ChIP

description: Library name: CAF63_K27ac


title: W6dF2h_rep6

description:
Library name: Sample 30
g230


title: Wild-type control mouse 4, 16 months, striatum

description:
Library name: WT_16m_04
Column name in fpkm_counts_A53T_16m.csv: Control_4_count Control_4_FPKM


title: 2D_YS_shGFP_veh_veh_003

description: Library name: 2D_YS_shGFP_veh_veh_003

value: shGFP


title: CAF42, H3K27ac ChIP

description: Library name: CAF42_K27ac

value: gastric fibroblasts from cancerous tissues of non-scirrhous gastric cancer patient


title: 2D_YS_shGFP_veh_veh_002

description: Library name: 2D_YS_shGFP_veh_veh_002


title: Wild-type control mouse 3, 16 months, striatum

description:
Library name: WT_16m_03
Column name in fpkm_counts_A53T_16m.csv: Control_3_count Control_3_FPKM


title: CAF30, H3K27ac ChIP

description: Library name: CAF30_K27ac


title: W6dF2h_rep5

description:
Library name: Sample 29
g229


title: Wild-type control mouse 1, 16 months, striatum

description:
Library name: WT_16m_01
Column name in fpkm_counts_A53T_16m.csv: Control_1_count Control_1_FPKM


title: CAF19, H3K27ac ChIP

description: Library name: CAF19_K27ac


title: W6dF2h_rep4

description:
Library name: Sample 28
g228


title: W6dF2h_rep3

description:
Library name: Sample 27
g227


title: Wild-type control mouse 2, 16 months, striatum

description:
Library name: WT_16m_02
Column name in fpkm_counts_A53T_16m.csv: Control_2_count Control_2_FPKM


title: 2D_YS_shGFP_veh_R50_003

description: Library name: 2D_YS_shGFP_veh_R50_003

value: shGGP, R5020


title: W6dF2h_rep2

description:
Library name: Sample 26
g226


title: 2D_YS_shGFP_veh_veh_001

description: Library name: 2D_YS_shGFP_veh_veh_001


title: Alpha-synuclein A53T transgenic mouse 4 (line G2-3), 16 months, striatum

description:
Library name: A53T_16m_04
Column name in fpkm_counts_A53T_16m.csv: Experiment_4_count Experiment_4_FPKM

value: Transgenic, expressing human alpha-synuclein with A53T mutation (line G2-3)


title: 2D_YS_shGFP_veh_R50_002

description: Library name: 2D_YS_shGFP_veh_R50_002


title: Alpha-synuclein A53T transgenic mouse 3 (line G2-3), 16 months, striatum

description:
Library name: A53T_16m_03
Column name in fpkm_counts_A53T_16m.csv: Experiment_3_count Experiment_3_FPKM


title: CAF66, Input

description: Library name: CAF66_Input


title: W6dF2h_rep1

description:
Library name: Sample 25
g225


title: 2D_YS_shGFP_veh_R50_001

description: Library name: 2D_YS_shGFP_veh_R50_001


title: CAF67, Input

description: Library name: CAF67_Input


title: Alpha-synuclein A53T transgenic mouse 2 (line G2-3), 16 months, striatum

description:
Library name: A53T_16m_02
Column name in fpkm_counts_A53T_16m.csv: Experiment_2_count Experiment_2_FPKM


title: CAF63, Input

description: Library name: CAF63_Input


title: 2D_YS_shGFP_E2_veh_003

description: Library name: 2D_YS_shGFP_E2_veh_003

value: shGGP, E2


title: 2D_YS_shGFP_E2_veh_002

description: Library name: 2D_YS_shGFP_E2_veh_002


title: Alpha-synuclein A53T transgenic mouse 1 (line G2-3), 16 months, striatum

description:
Library name: A53T_16m_01
Column name in fpkm_counts_A53T_16m.csv: Experiment_1_count Experiment_1_FPKM


title: E6d_rep8

description:
Library name: Sample 24
g224


title: CAF42, Input

description: Library name: CAF42_Input


title: CAF30, Input

description: Library name: CAF30_Input


title: E6d_rep7

description:
Library name: Sample 23
g223


title: CAF19, Input

description: Library name: CAF19_Input


title: 2D_YS_shGFP_E2_veh_001

description: Library name: 2D_YS_shGFP_E2_veh_001


title: flu_3_DC

city: wuhan

first: shan-jie

last: Rong

address: wuxian road tongji hospital research buliding

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology,

description: Library name: sample6

data_processing:
RNA sequencing was performed on the NovaSeq X Plus platform using the Illumina NovaSeq Reagent Kit. Raw sequencing reads were first subjected to quality control using FastQC, to ensure data integrity. Clean reads were then aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) aligner. Transcript abundance was quantified using feature Counts, which provides read counts for each gene. The read counts were normalized to account for library size and other technical variations using the DESeq2 package. Differential expression analysis was then performed to identify genes with statistically significant changes in expression between conditions. Among the six samples, a minimum of a one-fold difference in log 2 expression and FDR adjusted P value < 0.05 were considered as expression differences.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: BMDC

extract_protocol:
The bone marrow-derived dendritic cells (DCs) were prepared by inducing bone marrow from the hind leg femurs of mice using conventional methods. On the fifth day of the differentiation induction process, the cells were treated with fludarabine/solvent control. After DC maturation, total RNA was extracted.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BMDC

value: Dendritic cells

value: DC

value: flu


title: Aorta, WT, pooled

city: New Haven

first: Kathryn

last: Citrin

address: 10 Amistad St

institute: Yale University

description:
Library name: WT
10X Genomics

library_source: transcriptomic single cell

data_processing:
Reads from all three samples were aligned to mm10 with cellranger count and the subsequently generated filtered matrix, barcodes, and feature files were imported into R for further analysis with Seurat
Assembly: mm10
Supplementary files format and content: Tab separated values and matrix files

source_name: Aorta

extract_protocol:
After euthanasia, the thoracic aorta and arch were harvested and perivascular fat removed. The aorta was then minced and digested for 45 min at 37˚C in digestion media (DMEM with 1.5 mg/mL Collagenase A, 0.5 mg/mL elastase, 125 U/mL DNAseI, and 10% FBS) with gentle agitation. The digestion was then stopped with additional FBS, washed, and samples were stained with eBioscience Fixable Viability Dye eFluor 780 (Invitrogen) and TotalSeqB Hashtag Oligos (BioLegend) prior to pooling samples from different mice. Single cell suspensions were then generated by FACS sorting: viable tdTom negative and tdTom positive cells were sorted separately and then recombined to enrich tdTom positive cells to ~20%
Library prep was performed according to the manufacturer's protocol (10X Genomics Single Cell 3p v4).

value: Aorta

value: cdh5CreERT2; lsl-tdTomato

value: PCSK9-AAV8, 8 weeks WD


title: E6d_rep5

description:
Library name: Sample 21
g221

value: shoot


title: 2D_YS_shGFP_E2_R50_003

description: Library name: 2D_YS_shGFP_E2_R50_003

value: cancer

value: shGGP, E2, R5020


title: flu_2_DC

description: Library name: sample5


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

city: Beaucouze

first: Sandrine

last: Balzergue

address: 42 rue G. Morel

institute: INRAE

description: Library name: M3_LTM_R

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: Root

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.

value: Root

value: Golden Delicious double haploid 18_ GDDH18

value: Three cycles drought stress, Long Term Memory

value: replicate 3


title: E6d_rep4

description:
Library name: Sample 20
g220


title: 2D_YS_shGFP_E2_R50_002

description: Library name: 2D_YS_shGFP_E2_R50_002


title: Subjected to three cycles drought stress and sampling in year n+1  after one winter cycle,Root, bs-Seq, rept 2

description: Library name: M2_LTM_R

value: replicate 2


title: flu_1_DC

description: Library name: sample4


title: Porcine intestinal organoid 5 day

city: Sangju-si

first: Tae

middle: Hong

last: Kang

state: Gyeongsangbuk-do

address: Sangju-si 37224, Gyeongsangbuk-do, Republic of Korea

department: Department of Animal Science and Biotechnology

country: South Korea

institute: Kyungpook National University

description:
Library name: Smaple 3
10x Genomics

data_processing:
Sequencing reads were processed with the Cell Ranger version 9.0.0 (10X Genomics, CA) using the Procine reference transcriptome Sscrofa11.1 from ensembl. From the gene expression matrix, the downstream analysis was carried out with R version 4.2.2.
Assembly: Sscrofa11.1
Supplementary files format and content: Tab-seperated values files and matrix files

organism: Sus scrofa

source_name: small intestinal organoid

extract_protocol:
After organoid cells culture for 1, 3, and 5 days, treated with TrypLE (Thermo Fisher Scientific, Wilmington, DE, USA) containing 10 μM Y-27632 for 20 min, with pipetting every 5 min to obtain single-cell form. Dead cells were removed from a Dead cell removal kit (Miltenyl Biotec, Bergisch Gladbach, Germany). Single cells were washed in PBS containing 0.04% BSA and counted using a Countness II (Thermo Fisher, Waltham, MA, USA) to determine their cell number.
To obtain single cell RNA-sequencing libraries, Chromium Next GEM Single Cell 3’ reagent kit v3.1 (10X Genomics, Pleasanton, CA, USA) was used according to the manufacturer’s protocol. the cells were diluted into the Chromium Next GEM Chip G as to yield a recovery of ~ 5,000 single-cell and then the cell libraries were sequenced using a multiplex on the Novaseq 6000 sequencer (Illumina, San Diego, CA) to produce on average a minimum of 60,000 reads per single cell.

value: small intestinal organoid

value: Small intestinal epithelium


title: 2D_WT_shPR_veh_veh_003

description: Library name: 2D_WT_shPR_veh_veh_003

value: shPR


title: 2D_YS_shGFP_E2_R50_001

description: Library name: 2D_YS_shGFP_E2_R50_001


title: ctr_2_DC

description: Library name: sample2

value: BMDC

value: Dendritic cells

value: ctrl


title: Porcine intestinal organoid 3 day

description:
Library name: Sample 2
10x Genomics


title: Porcine intestinal organoid 1 day

description:
Library name: Sample 1
10x Genomics


title: 2D_WT_shPR_veh_veh_002

description: Library name: 2D_WT_shPR_veh_veh_002


title: ctr_1_DC

description: Library name: sample1

value: DC


title: TC1, day 0 mESC, rep4

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: TC1_4

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

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

value: mESCs

value: wild-type

value: control


title: 2D_WT_shPR_veh_veh_001

description: Library name: 2D_WT_shPR_veh_veh_001

value: cancer


title: TC1, day 0 mESC, rep3

description: Library name: TC1_3


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

description: Library name: C1_LTM_R

value: Control, Long Term Memory

value: replicate 1


title: 2D_WT_shPR_E2_veh_003

description: Library name: 2D_WT_shPR_E2_veh_003

value: shPR, E2


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

description: Library name: M3_LTM_L

source_name: Leaf

value: Leaf

value: Golden Delicious double haploid 18_ GDDH18

value: Three cycles drought stress, Long Term Memory


title: bESC.NBFRA.FF.LO2.C

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 7
PE150

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.

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: C

value: bovine ESC

value: XX

value: low O2, Feeder Free


title: TC1, day 0 mESC, rep1

description: Library name: TC1_1


title: bESC.NBFRA.FF.LO2.D

description:
Library name: Sample 6
PE150

value: D


title: 2D_WT_shPR_E2_veh_001

description: Library name: 2D_WT_shPR_E2_veh_001


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

description: Library name: M1_LTM_L


title: bESC.NBFRA.FF.LO2.A

description:
Library name: Sample 5
PE150

value: A


title: TC1, differentiated 10 days, rep4

description: Library name: CMd10_4

value: differentiated cells

value: differentiated


title: 2D_WT_shGFP_veh_veh_003

description: Library name: 2D_WT_shGFP_veh_veh_003

value: shGFP


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

description: Library name: C3_LTM_L

value: replicate 3


title: 2D_WT_shGFP_veh_veh_002

description: Library name: 2D_WT_shGFP_veh_veh_002

value: cancer


title: bESC.NBFRA.MF.LO2.C

description:
Library name: Sample 3
PE150

value: low O2, MEF


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

description: Library name: C2_LTM_L

value: Control, Long Term Memory

value: replicate 2


title: TC1, differentiated 10 days, rep2

description: Library name: CMd10_2

value: wild-type


title: JJN3 cells, nontargeting control, rep 1

city: Berlin

first: Stefan

last: Habringer

address: Hindenburgdamm 30

department: Hematology, Oncology and Cancer Immunology

country: Germany

institute: Charité - Universitaetsmedizin Berlin

description:
Library name: Sample 10
JJN3_nt_1

data_processing:
Analysis with usegalaxy.org
Trim Galore
Bowtie 2
htseq-count
DESeq2
Assembly: hg38
Supplementary files format and content: rLog normalized counts

extract_protocol:
Rneasy mini prep kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification (Source: Novogene).

value: plasma cell

value: nontargeting sgRNA control

value: untreated


title: 2D_WT_shGFP_veh_veh_001

description: Library name: 2D_WT_shGFP_veh_veh_001


title: bESC.NBFRA.MF.LO2.D

description:
Library name: Sample 2
PE150

value: embryonic stem cells

value: bovine ESC


title: TC1, differentiated 10 days, rep1

description: Library name: CMd10_1


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

description: Library name: M3_S3_R

value: Root

value: Golden Delicious double haploid 18_ GDDH18

value: Three cycles drought stress


title: 2D_WT_shGFP_veh_R50_003

description: Library name: 2D_WT_shGFP_veh_R50_003

value: shGGP, R5020


title: bESC.NBFRA.MF.LO2.A

description:
Library name: Sample 1
PE150

value: A

value: XX


title: 2D_WT_shGFP_veh_R50_002

description: Library name: 2D_WT_shGFP_veh_R50_002


title: JJN3 cells, KANSL2 knockdown, rep 3

description:
Library name: Sample 9
JJN3_KANSL2KD_3

value: KANSL2 knockdown


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

description: Library name: M2_S3_R


title: igg_hek293t_rip_2

city: Chapel Hill

first: Joseph

middle: Mauro

last: Calabrese

state: NC

address: 120 Mason Farm Road

institute: UNC Chapel Hill

description: Library name: igg_hek293t_rip_2

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.

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: Rabbit IgG(Invitrogen #02-6102)

value: Human embryonic kidney cells


title: Tn 4T1 cells-bearing tumor 5

city: Sao Paulo

first: Alexis Germán

last: Murillo Carrasco

email: agmurilloc@gmail.com, agmurilloc@usp.br

state: Sao Paulo

address: Av. Dr. Arnaldo 251, Sao Paulo

country: Brazil

institute: ICESP

description: Library name: T4

data_processing:
Raw paired-end RNA sequencing reads obtained from the tumor samples were initially subjected to quality assessment using FastQC to evaluate sequencing quality metrics, including per-base sequence quality, GC content distribution, sequence duplication levels, and adapter contamination. Subsequently, read preprocessing and filtering were performed using fastp (v0.23.x). During this step, Illumina adapter sequences were automatically detected and removed, low-quality bases were trimmed from both read ends, sequencing errors in paired-end reads were corrected when possible, and short or low-quality reads (PHRED<20) were excluded from downstream analyses. Only reads meeting predefined quality and length criteria were retained for transcriptomic processing. Quality control analyses were repeated after trimming to confirm improvements in read quality and overall dataset integrity.
Processed reads were aligned to the Mus musculus reference genome (GRCm39) using STAR version 2.7.11a. A two-pass alignment strategy was employed to improve splice junction detection sensitivity and mapping accuracy. Gene-level expression quantification was subsequently performed using featureCounts from the Subread package version 2.1.1. Reads were assigned to annotated exonic regions and summarized at the gene level based on the reference annotation file. Only properly paired reads mapping to exonic regions were considered for transcript abundance estimation.
Assembly: Mus musculus reference genome (GRCm39)
Supplementary files format and content: count matrix file with all samples

source_name: breast

extract_protocol:
Tumor tissues were processed for total RNA extraction using the miRNeasy Tissue/Cells Advanced Mini Kit (Qiagen) following mechanical homogenization in RLT buffer supplemented with β-mercaptoethanol.
Transcriptomic libraries were prepared using the Illumina Stranded mRNA Prep protocol with Illumina DNA/RNA UD Indexes Set B, including poly(A) mRNA enrichment, fragmentation, cDNA synthesis, adapter ligation, and PCR amplification.

treatment_protocol: murine 4T1 breast cancer cells carrying CRISPR/Cas9-mediated silencing of the Cosmc gene (Tn+) compared with parental wild-type 4T1 cells (WT)

value: breast

value: Tn


title: 2D_WT_shGFP_veh_R50_001

description: Library name: 2D_WT_shGFP_veh_R50_001

value: cancer


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

description: Library name: M1_S3_R

value: replicate 1


title: igg_hek293t_rip_1

description: Library name: igg_hek293t_rip_1


title: Tn 4T1 cells-bearing tumor 4

description: Library name: T12


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

description: Library name: C3_S3_R

value: Control

value: replicate 3


title: hnrnpk_hek293t_rip_2

description: Library name: hnrnpk_hek293t_rip_2

value: HNRNPK(Santa Cruz, sc-28380)


title: Tn 4T1 cells-bearing tumor 3

description: Library name: T3


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

description: Library name: C2_S3_R

value: replicate 2


title: Tn 4T1 cells-bearing tumor 2

description: Library name: T11


title: hnrnpk_hek293t_rip_1

description: Library name: hnrnpk_hek293t_rip_1


title: 2D_WT_shGFP_E2_veh_001

description: Library name: 2D_WT_shGFP_E2_veh_001

value: shGGP, E2


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

description: Library name: C1_S3_R

value: Root

value: Golden Delicious double haploid 18_ GDDH18


title: 293T_hnrnpu_r2_rip_2

description: Library name: 293T_hnrnpu_r2_rip_2

value: HNRNPU(Santa Cruz, sc-32315)


title: Tn 4T1 cells-bearing tumor 1

description: Library name: T5


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

description: Library name: M3_S1_R

value: One cycle drought stress


title: 293T_hnrnpu_r1_rip_1

description: Library name: 293T_hnrnpu_r1_rip_1


title: 2D_WT_shGFP_E2_R50_002

description: Library name: 2D_WT_shGFP_E2_R50_002

value: shGGP, E2, R5020


title: WT 4T1 cells-bearing tumor 6

description: Library name: T23

value: WT


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

description: Library name: M2_S1_R


title: Pre Spawning Male 1

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: PrSM1
Y6IA

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: Testes

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: Testes

tag: maturational stage

value: Pre Spawning

tag: Sex

value: male


title: WT 4T1 cells-bearing tumor 5

description: Library name: T18

value: breast


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

description: Library name: M1_S1_R


title: 2D_WT_shGFP_E2_R50_001

description: Library name: 2D_WT_shGFP_E2_R50_001

value: cancer


title: WT 4T1 cells-bearing tumor 4

description: Library name: T17


title: T47D_ERa_Y537S-hom_shPR_3

description: Library name: T47D_ERa_Y537S-hom_shPR_3

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

tag: chip antibody

value: phosphoPR

value: shPR


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

description: Library name: C3_S1_R

value: Control

value: replicate 3


title: Spawning Male 2

description:
Library name: SM2
Y3IIA

value: Spawning


title: WT 4T1 cells-bearing tumor 3

description: Library name: T22


title: T47D_ERa_Y537S-hom_shGFP_3_1_R5020

description: Library name: T47D_ERa_Y537S-hom_shGFP_3_1_R5020


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

description: Library name: C2_S1_R

value: Root

value: replicate 2


title: WT 4T1 cells-bearing tumor 2

description: Library name: T24


title: T47D_ERa_Y537S-hom_shGFP_3

description: Library name: T47D_ERa_Y537S-hom_shGFP_3

value: shGFP


title: Post Spawning Male 2

description:
Library name: PoSM2
Y1_IIIB_2

value: Post Spawning


title: WT 4T1 cells-bearing tumor 1

description: Library name: T20


title: 2D_WT_shGFP_E2_R50_003

description: Library name: 2D_WT_shGFP_E2_R50_003

value: shGGP, E2, R5020


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

description: Library name: M3_S3_L

value: Leaf

value: Golden Delicious double haploid 18_ GDDH18

value: Three cycles drought stress


title: T47D_ERa_Y537S-hom_Pooled_Input_3

description: Library name: T47D_ERa_Y537S-hom_Pooled_Input_3

value: rabbit Igg


title: Pre Spawning Male 2

description:
Library name: PrSM2
Y1_1A

value: Testes

value: Pre Spawning

value: male


title: Spawning Male 3

description:
Library name: SM3
Y4IIA


title: E6d_rep6

city: Yokohama

first: motoaki

last: seki

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

institute: RIKEN

description:
Library name: Sample 22
g222

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
Supplementary files format and content: DEseq2

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.

value: shoot


title: T47D_ERa_WT_shPR_3

description: Library name: T47D_ERa_WT_shPR_3

value: breast cancer

value: phosphoPR

value: shPR


title: PH3, periodontitis, hypertension

city: Nanning

first: xiaoping

last: su

state: Guangxi

address: shuangyong road

institute: guangxi medical university

description: Library name: PH3

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

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: Subjected to three cycles drought stress, Leaf, bs-Seq, rep 2

description: Library name: M2_S3_L


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

description: Library name: M1_LTM_R

value: Root

value: Three cycles drought stress, Long Term Memory

value: replicate 1


title: Biological replicate 1, technical replicate 1, naive SW620s

city: San Francisco

first: Balyn

last: Zaro

address: 555 Mission Bay Blvd S, Rm 484

institute: UCSF

description:
Library name: Sample 5
B1T1_SW620_S5_L001.counts

data_processing:
RNA-seq reads were trimmed to remove sequencing adapters using Trimmomatic (v0.39) with the TruSeq3-PE-2 adapter sequences. Low-quality bases and short reads were filtered using the parameters LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:36. Trimmed reads were aligned to the human reference genome (hg38) using STAR (v2.7.11b). Gene expression levels were quantified using HTSeq-count, where aligned reads were counted against gene features defined in the Gencode v45 GTF annotation.
Assembly: human reference genome (hg38) using STAR (v2.7.11b)
Supplementary files format and content: Processed data file for all samples is: RNA_seq_raw_reads_count_all and contains columns with raw counts for each individua sample outlined above. Rows represent ensembl gene ids.

extract_protocol:
Cells were sorted via FACS following co-incubation as indicated. Following PBS washing steps to remove excess FBS, samples were lysed into TRI Reagent (Zymo Research, R2071) and then snap frozen and stored at -80°C until RNA extraction was performed. RNA extraction was performed using Direct-zol RNA MiniPrep Plus (Zymo Research, R2071) following manufacturer’s instructions.
Two biological replicates of each cell type (Eaters, Non-eaters, Uneaten, SW620, and Naive macrophages) were used for RNA sequencing, with each biological replicate consisting of two technical replicates. RNA-seq libraries were prepared using the Single Cell/Low Input RNA Library Prep Kit (NEB, E6420), following the manufacturer's protocol. In brief, 200 ng of total RNA was used as input. First, reverse transcription was performed, followed by 7 cycles of cDNA amplification and clean-up. The cDNA was then fragmented, repaired, ligated with NEBNext adaptors, and enriched using 4-5 cycles of PCR. Libraries were sequenced on a NovaSeq X 10B platform using paired-end 150 bp (PE150) reads.

value: Human colorectal cancer cells


title: hTERT-HM cells day 6 rep4

city: St. Louis

first: Ritu

last: Dave

address: 425 S Euclid Ave

institute: Washington University School of Medicine

description:
Library name: sample11
column name in all.gene_counts.xlsx: sample.Day_6_D

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: Post Spawning Male 3

description:
Library name: PoSM3
Y1IIIC

value: Post Spawning


title: cortical brain tissue, B6M1

city: Copenhagen

first: Shohreh

last: Issazadeh-Navikas

address: Ole Maaløes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

data_processing:
Raw data were demultiplexed, aligned, and quantified using Cell Ranger version (v)3.1.0. To allow for counting of unspliced pre-mRNA, a custom version of the mm10-3.0.0 mouse reference genome provided by 10x Genomics was used, where the feature ‘type of transcripts’ was changed from ‘transcript’ to ‘exon’.
Data analysis was performed in R using Seurat v3.1.5 and Conos v1.2.1. The -barcode matrices were filtered to include cells meeting the following criteria: 200<nFeature_RNA<6000, nCount_RNA>1000, and percent_MT<10. Doublets were filtered out using the Scrublet package
Data were log-normalized, and individual samples were integrated using the fast mutual nearest neighbors (fastMNN) method based on the top 3,000 variable features. Clustering and UMAP visualization were performed using the first 40 dimensions of the MNN reduction.
The integrated dataset was annotated using canonical correlation analysis (CCA) based label transfer in Seurat with the Allen Brain Map Mouse Whole Cortex and Hippocampus SMART-seq dataset [https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-smart-seq] as the reference
Assembly: mm10-3.0.0
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

molecule: nuclear RNA

source_name: Cortex (brain)

extract_protocol:
16,000 nuclei per sample were loaded on the 10x Chromium chip for library preparation using the Single Cell 3’ v3 chemistry according to manufacturer instructions. For cDNA amplification, 12 PCR cycles were applied. For each sample, 230 ng of purified cDNA was used for library construction.
The libraries were diluted to a concentration of 10 nM and pooled for sequencing. After denaturation, the library pool was diluted to a loading concentration of 300 pM and sequenced on a Novaseq6000 in paired-end mode (2x100) (read 1:28 cycles, read 2:91 cycles, and i7 index: 8 cycles) at an average depth of 50,000 reads per nucleus.
single nuclei (sn)RNA-seq

value: Cortex (brain)

value: Cortical cells

tag: age

value: 6 week old

tag: gender

value: Male

tag: strain

value: naive


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

description: Library name: M1_S3_L

value: Leaf

value: Golden Delicious double haploid 18_ GDDH18

value: Three cycles drought stress


title: PH2, periodontitis, hypertension

description: Library name: PH2

value: gingiva


title: T47D_ERa_WT_shGFP_3_1_R5020

city: Minneapolis

first: Nuri

last: Temiz

address: 2231 6th St SE

institute: University of Minnesota

description: Library name: T47D_ERa_WT_shGFP_3_1_R5020

value: breast cancer

value: phosphoPR


title: ctr_3_DC

description: Library name: sample3

value: BMDC

value: Dendritic cells

value: DC

value: ctrl


title: Post Spawning Male 1

description:
Library name: PoSM1
Y1IIIB

value: Testes

value: male


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

description: Library name: C3_LTM_R

value: Root

value: Control, Long Term Memory

value: replicate 3


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

description: Library name: C2_LTM_R

value: replicate 2


title: Pre Spawning Male 3

description:
Library name: PrSM3
Y2_1A

value: Pre Spawning


title: bESC.NBFRA.FF.LO2.E

description:
Library name: Sample 8
PE150

value: embryonic stem cells

value: E

value: bovine ESC

value: XX

value: low O2, Feeder Free


title: PH1, periodontitis, hypertension

description: Library name: PH1

value: gingiva


title: T47D_ERa_WT_shGFP_3

description: Library name: T47D_ERa_WT_shGFP_3

value: breast cancer

value: phosphoPR

value: shGFP


title: Spawning Male 1

description:
Library name: SM1
Y1IIA

value: Spawning


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

description: Library name: C3_S3_L

value: Leaf

value: Golden Delicious double haploid 18_ GDDH18

value: Control


title: T47D_ERa_WT_Pooled_Input_3

description: Library name: T47D_ERa_WT_Pooled_Input_3

value: rabbit Igg


title: P3, periodontitis

description: Library name: P3


title: TC1, day 0 mESC, rep2

description: Library name: TC1_2

value: mESCs

value: wild-type

value: control


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

description: Library name: C2_S3_L

value: replicate 2


title: 2D_WT_shPR_E2_veh_002

description: Library name: 2D_WT_shPR_E2_veh_002

data_processing:
Quality scores across sequenced reads were assessed using FASTQC.
Illumina adapters were removed using Trim-Galore.
For alignment and transcript assembly, the sequencing reads were mapped to hg38 using STAR
Sorted reads were counted using HTseq
Assembly: Hg38
Supplementary files format and content: raw counts data for each sample as text files

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen).
Purity of the total RNA samples was assessed using BioAnalyzer (Agilent) and samples with an RNA integrity score >8 were used for library construction by the University of Minnesota Genomics Core. Libraries were built from individual samples with the TruSeq Stranded mRNA kit (Illumina).

value: cancer

value: shPR, E2


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

description: Library name: C1_S1_R

value: Root

value: replicate 1


title: Post Spawning Female 3

description:
Library name: PoSF3
X4_IIIA_2

source_name: Ovaries

value: Ovaries

value: Post Spawning

value: female


title: T47D_ERa_Y537S-hom_shPR_2

description: Library name: T47D_ERa_Y537S-hom_shPR_2

value: breast cancer

value: phosphoPR

value: shPR


title: P2, periodontitis

description: Library name: P2

value: gingiva


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

description: Library name: C1_S3_L

value: Leaf

value: Golden Delicious double haploid 18_ GDDH18

value: Control


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

description: Library name: M2_LTM_L

value: Three cycles drought stress, Long Term Memory


title: Pre Spawning Female 3

description:
Library name: PrSF3
X4_1A

value: Pre Spawning


title: P1, periodontitis

description: Library name: P1


title: T47D_ERa_Y537S-hom_shGFP_2_1_R5020

description: Library name: T47D_ERa_Y537S-hom_shGFP_2_1_R5020


title: NC3, healthy

description: Library name: NC3