title: Spinal cord, lamenectomy control (0 dpi)

city: Ann Arbor

first: Lonnie

last: Shea

address: 1600 Huron Pkwy

institute: University of Michigan- Ann Arbor

description:
Library name: 10340-SH-5
10x Chromium GEM-X Flex Gene Expression (Fix RNA Profiling)

data_processing:
This pool was subjected to 28x90bp of sequencing according to the manufacturer’s protocol (Illumina NovaSeqXPlus). BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files. Cell Ranger (v7.2.0) was used to align reads to mouse reference GRCm38 (mm10-2020-A).
per-sample-out .bam files were converted to fastq using Cell Ranger (v9.0.1) bamtofastq: bamtofastq --reads-per-fastq=500000000000 <input file> <output file>
Assembly: GRCm38 (mm10-2020-A)
Supplementary files format and content: tab-separated values files and matrix files

source_name: Spinal cord

extract_protocol:
naive, 2 and 7 days post-injury spinal cord segments C4-C6 were harvested from recipient mice in control and NP-treatment.Spinal cords were myelin depleted. Spinal cords were minced using spring scissors and incubated with 0.5 mg trypsin (Millipore Sigma) and 1 mg collagenase (Millipore Sigma) in 3 mL DMEM (Gibco) per sample for 20 minutes in a 37 C incubator. Samples were placed on a rotisserie rocker to prevent the tissue from aggregating. After the incubation, the trypsin and collagenase were neutralized with DMEM + 10% FBS. The samples were spun down and resuspended in 480 uL of MACS buffer. The samples were demyelinated using the Miltenyi Myelin Removal Beads II kit with 20 uL of beads/sample. Following myelin depletion,  spinal cords from 3-4 mice were pooled together. Cells were fixed using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics). Samples were fixed for 24 hours at 4C and stored at -80C in 50% glycerol solution. Samples were submitted to the University of Michigan Advanced Genomics Core for library preparation with 10X Single Cell Fixed RNA Hybridization and Library Kit (FlexSeq) and sequencing on NovaSeq X 10B flow cells (300 cycles) at approximately 30,000 reads per cell.
Chromium Fix RNA Profiling (10x Genomics) using the Chromium Mouse Transcriptome Probe Set v1.0.1.

treatment_protocol: 1 mg of NPs suspended in 0.1 mL DPBS were delivered within 2 hours and then every 24 hours following spinal cord injury. Saline controls were delivered PBS rather than NP.

value: Spinal cord

tag: Sex

value: female

value: 6-8 weeks

tag: model

value: C5 lateral hemisection spinal cord injury

value: PBS


title: Wide type mouse 6 (WT6)

status: Public on Aug 01 2026

type: SRA

city: Nanchang

first: Pan

last: Zheng

address: 17 of Yongwaizhengjie Street

country: China

institute: The Affiliated Hospital of Nanchang University

description: Library name: sample6

library_source: transcriptomic

data_processing:
Paired-end sequencing (150 bp) was performed on an Illumina NovaSeq 6000 platform (∼40 million reads/sample)
Raw reads were quality-trimmed (Fastp) and aligned to the mouse reference genome (GRCm38) using STAR
Gene-level counts were generated with featureCounts and normalized for differential expression analysis (DESeq2, FDR < 0.05).
Assembly: mm10
Supplementary files format and content: csv files including counts values for each sample

molecule: total RNA

organism: Mus musculus

source_name: pancreas

extract_protocol:
Total RNA of pancreas from Tnfr1-/- mice and wide type mice were depleted (NEBNext rRNA Depletion Kit)
Libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit.

tag: tissue

value: pancreas

tag: cell type

value: acinar cells, ductal cells, myeloid cells, neutrophil cells

tag: genotype

value: Wide type


title: Spinal cord and bridge implant, NP-treated 7 dpi

country: USA

description:
Library name: 10340-SH-4
10x Chromium GEM-X Flex Gene Expression (Fix RNA Profiling)

library_source: transcriptomic single cell

source_name: Spinal cord + PCL bridge implant

value: Spinal cord + PCL bridge implant

tag: strain

tag: age

tag: treatment

value: NP


title: bh11, intracellular to qs9

city: Waterville

first: Suegene

last: Noh

state: ME

address: 5717 Mayflower Hill

department: Biology

institute: Colby College

description:
Library name: b11_qs9
rRNA depleted

data_processing:
D. discoideum reads were aligned to the D. discoideum reference genome and GTF annotation file (downloaded Jan 2023 from dictybase). The segmental duplication in this reference genome (2: 3016083-3768654) was masked using bedtools v2.28.0 (Quinlan and Hall 2010). Paraburkholderia reads were aligned to draft genome assemblies (Noh et al 2022) and Prokka GFF annotation files. Host alignments were performed with STAR v2.7.5c and symbiont alignments were performed with Bowtie2 v2.4.2. Samtools v1.3.1 was used to sort and filter alignments, Picard v2.17.10 (downloaded from broadinstitute.github.io/picard) was used to assign read groups. Read counts were extracted from primary alignments with correct strand orientation using HTSeq v0.11.2 (Anders et al. 2015).
Assembly: The D. discdoideum reference genome was downloaded Jan 2023 from http://dictybase.org. Paraburkholderia draft genome assemblies are available from NCBI and https://github.com/noh-lab/clade_infection/tree/main/genome_files
Supplementary files format and content: Tab-delimited file of raw counts per gene for each sample

organism: Paraburkholderia hayleyella

source_name: whole organism

extract_protocol:
For uninfected host samples, cells were removed from RNAlater® and processed following a standard RNA extraction protocol using Qiagen RNeasy Mini kits. For free-living symbiont samples, cells were disrupted with a lysozyme treatment prior to RNeasy extraction, then treated with illumina Ribozero according to its product protocol. Symbiont-associated (infected) host samples were obtained by taking the supernatant of the first RLN buffer treatment of associated amoebas in the RNeasy protocol. Host-associated (intracellular) symbiont samples were obtained by taking the spun-down pellet of this same RLN buffer treatment step that contains amoeba nuclei as well as intracellular Paraburkholderia. This pellet was treated with lysozyme, then the RNeasy protocol and illumina Ribozero protocol as with the free-living symbiont samples.
All samples were then prepared with the illumina TruSeq Stranded mRNA library preparation protocol but only D. discoideum samples were subjected to the polyA enrichment step.

value: whole organism

value: intracellular

tag: batch


title: Wide type mouse 5 (WT5)

description: Library name: sample5


title: Bio Rep2_Wildtype1_ABA treat

city: Seoul

first: Zein Eddin

last: Bader

state: Seoul

address: 서울특별시 광진구 광나루로22나길 3

department: Biomedical Science and Engineering

country: South Korea

institute: Konkuk University

description: High Output, 75bp

data_processing:
Sequencing reads were trimmed for adaptor sequecning/low-quality sequence using bowtie2 with defautl-sensitive parameter
Trimmed sequence reads were mapped to TAIR10 genome reference using Salmon tool to calculate transcript level expression
Read counts and transcripts per million generated by Salmon is processed using Tximport (version 1.10.0 R package with lenghScaledTPM method
For the quality control, genes with low expression were filtered and batch effecs were estimated and corrected using RUVSeq (version 1.16.0)
The data of visualization performed using IGV on bigwig files generated from normalized bedgraph using bedools genomecov package with inputs from the aligned BAM files
DEG analysis si performed using LIMMA R package (version 3.56)
Assembly: TAIR10
Supplementary files format and content: tsv read counts

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Arabidopsis (Col-0) Wild type and hda9-1 plants were used in this study. All plants were grown in MS media contain 1% Sucrose under the condition (16 hr light/8hr dark, 20°C)

extract_protocol:
Total RNA was extracted from ABA-treated seedling including control sample (no ABA-treated) using Directzol RNA miniprep (Zymo Research, USA)
1µg of DNA-free total RNA for Isolate mRNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and followed the procedure by NEBNext UltraII Directional RNA library Prep Kit for Illumina (NEB, E7765) with slightly modified condition such diluted adaptor (1:5), extended incubation of ligation for 2 hours at room temperature, and 7 PCR cycles.

treatment_protocol: 2-3 week-old seedings (8 buds) were sprayed with 50 uM ABA for 4hr.

value: Seedling

tag: cell line

value: Wild Type

value: No


title: Spinal cord and bridge implant, saline control 7 dpi

description:
Library name: 10340-SH-3
10x Chromium GEM-X Flex Gene Expression (Fix RNA Profiling)


title: lateral septum of mice brain,CFA,day3-2

city: Hangzhou

first: Furui

last: Liu

address: Yuhangtang

institute: Hangzhou Normal University

description: Library name: Sample 8

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rat whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Bray N, Pimentel H, Melsted P, et al., Near-optimal RNA-Seq quantification, 2015. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: brain tissue

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 0.2 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Fast RNA-seq Lib Prep Kit V2 （Cat.No.RK20306） following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads (PE150) were generated.

value: brain tissue

value: WT

value: CFA


title: bh11, intracellular to qs864

description:
Library name: b11_864
rRNA depleted


title: Bio Rep1_Wildtype1_ABA treat

address: 서울특별시 광진구 광나루로22나길 3

description: High Output, 75bp


title: Wide type mouse 4 (WT4)

description: Library name: sample4


title: bh11, intracellular to qs18

description:
Library name: b11_qs18
rRNA depleted


title: Bio Rep3_Wildtype1_No ABA treat

address: 서울특별시 광진구 광나루로22나길 3

description: High Output, 75bp


title: bh11, freeliving, sample c

description:
Library name: b11_c
rRNA depleted

value: freeliving


title: Spinal cord and bridge implant, saline control 2 dpi

description:
Library name: 10340-SH-1
10x Chromium GEM-X Flex Gene Expression (Fix RNA Profiling)

value: female

value: 6-8 weeks


title: Bio Rep2_Wildtype1_No ABA treat

address: 서울특별시 광진구 광나루로22나길 3

description: High Output, 75bp


title: Spinal cord and bridge implant, NP-treated 2 dpi

description:
Library name: 10340-SH-2
10x Chromium GEM-X Flex Gene Expression (Fix RNA Profiling)

value: C5 lateral hemisection spinal cord injury


title: Wide type mouse 3 (WT3)

description: Library name: sample3

value: pancreas


title: bh11, freeliving, sample b

description:
Library name: b11_b
rRNA depleted


title: Sample 2 of wildtype mouse olfactory epithelial

city: Wuhan

first: Yang

address: No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province

institute: Institute of Hydrobiology, Chinese Academy of Sciences

description: Library name: Mouse 2

data_processing:
We initially generated raw reads, which were then processed and aligned to the mouse reference genomes (GRCm39) using BSTMatrix (http://www.bmkmanu.com/tools). Following this, we employed the STAR (Spliced Transcripts Alignment to a Reference) to map the expression matrices to the reference genomes. Gene expression counts were determined using unique molecular identifiers (UMIs) for each cell barcode-gene combination. After alignment, we filtered cell barcodes to identify those which contain cells using the approach implemented in Cell Ranger (version 7.0.0). Only these identified cell barcodes were included in the downstream analysis, which encompassed clustering and cell type identification.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Olfactory epithelium

extract_protocol:
We dissociated all tissues into single-cell suspensions using the following procedure. Mice were anesthetized and placed on a clean laboratory bench. Decapitation was quickly performed to extract the intact OE and washed 3 times at 4°C PBS on ice. Subsequently, these tissues were placed into 15 mL centrifuge tubes filled with PBS solution, where they were cut into small pieces. Tissues were incubated in a constant temperature water bath or shaker at 37℃ with the self-prepared hydrolysate or the hydrolysate kit (MACS Human Tumor Dissociation kit DS_130-095-929/ MACS Mouse Tumor Dissociation kit DS_130-096-730). After digestion, we used 40 µm cell sieve to filter and collected cell suspensions by centrifugation at 1500 r.p.m. for 5 minutes at 4°C. Then we discarded the supernatant and added 1mL of re-suspension and 3 mL of pre-cooled erythrocytes lysis liquid in tube, blowing and suction evenly at 4℃ for 10 minutes. Immediately, we put it at 1500 r.p.m. for 5 minutes at 4℃ after completion and added 1 mL of re-suspension (Precooled PBS) to fully re-suspend the cells. The number of single-cell suspensions were determined using a Luna fluorometer (Logos Biosystems), following Trypan blue staining, with the viability rate confirmed to be over 85%. Once the final cell activity were reached, these cells were placed on ice and BMKMANU C1000 Chip on-board experiment was carried out within 30 minutes.
We prepared mouse scRNA-seq sequencing libraries with BMKMANU DG1000 GEM Kits on the Droplet Generation Equipment (BMKMANU). Firstly, we suspended the prepared  single-cell suspensions in PBS containing 0.04% BSA. Then, we loaded the cell suspension onto the BMKMANU C1000 Chip and used the equipment to create GEMs according to the manufacturer's instructions. After that, we lysed the captured cells in the GEMs and reverse transcribed the released RNA to generate barcoded, full-length cDNA. Finally, we constructed the libraries following the given protocol. We sequenced all single-cell samples libraries on the Illumina NovaSeq TM X Plus system performed by Biomarker Technologies Co, LTD (Beijing, China).

value: Olfactory epithelium

value: male


title: Bio Rep1_Wildtype1_No ABA treat

address: 서울특별시 광진구 광나루로22나길 3

description: High Output, 75bp


title: Wide type mouse 2 (WT2)

description: Library name: sample2

value: acinar cells, ductal cells, myeloid cells, neutrophil cells

value: Wide type


title: Wide type mouse 1 (WT1)

description: Library name: sample1


title: Sample 1 of wildtype mouse olfactory epithelial

description: Library name: Mouse 1


title: bh11, freeliving, sample a

description:
Library name: b11_a
rRNA depleted

value: whole organism


title: Sk+PT-1LVAN (Sk_JF1O1_AR_Plate6)

status: Public on Jul 31 2026

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: Library name: Sk_and_PT-1LVAN_Sk_JF1O1_AR_Plate6

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)  The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.         The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates.      Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files. Tab-delimited files (HIC files) describing the chromatin contacts will be generated with in-house developing package using the filtered BAM files.
Assembly: hg38
Supplementary files format and content: An ALLC file contains 7 columns with DNA methylation information of a single cell at single base resolution. The columns are 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.   A contact file contains long range chromatin contacts of a single cell after removing the ones overlapping blacklists. The columns are 1. Strand1, 2. Chromosome1, 3. Position1, 4. place holder column, always be 0, 5. Strand2, 6. Chromosome2, 7. Position2, 8. place holder column, always be 1.
Library strategy: snm3C-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: Suprapubic Skin

extract_protocol:
Nuclei extraction protocol can be found at https://www.protocols.io/view/snm3c-seq3-kqdg3x6ezg25/v1
Library preparation protocol can be found at https://www.protocols.io/view/snm3c-seq3-kqdg3x6ezg25/v1

value: Suprapubic Skin


title: Sk+PT-1LVAN (Sk_JF1O1_AR_Plate5)

description: Library name: Sk_and_PT-1LVAN_Sk_JF1O1_AR_Plate5


title: Sk+PT-1LVAN (Sk_JF1O1_AR_Plate3)

description: Library name: Sk_and_PT-1LVAN_Sk_JF1O1_AR_Plate3


title: Sk+PT-1LVAN (Sk_JF1O1_AR_Plate4)

description: Library name: Sk_and_PT-1LVAN_Sk_JF1O1_AR_Plate4


title: Sk+PT-1LVAN (Sk_JF1O1_AR_Plate2)

description: Library name: Sk_and_PT-1LVAN_Sk_JF1O1_AR_Plate2


title: Sk+PT-1LGRB (Sk_IOBHT_AR_Plate7)

description: Library name: Sk_and_PT-1LGRB_Sk_IOBHT_AR_Plate7


title: Sk+PT-1LVAN (Sk_JF1O1_AR_Plate1)

description: Library name: Sk_and_PT-1LVAN_Sk_JF1O1_AR_Plate1


title: Sk+PT-1LGRB (Sk_IOBHT_AR_Plate6)

description: Library name: Sk_and_PT-1LGRB_Sk_IOBHT_AR_Plate6


title: Sk+PT-1LGRB (Sk_IOBHT_AR_Plate5)

description: Library name: Sk_and_PT-1LGRB_Sk_IOBHT_AR_Plate5


title: Sk+PT-1LGRB (Sk_IOBHT_AR_Plate3)

description: Library name: Sk_and_PT-1LGRB_Sk_IOBHT_AR_Plate3


title: Sk+PT-1LGRB (Sk_IOBHT_AR_Plate2)

description: Library name: Sk_and_PT-1LGRB_Sk_IOBHT_AR_Plate2


title: Sk+PT-1LGRB (Sk_IOBHT_AR_Plate4)

description: Library name: Sk_and_PT-1LGRB_Sk_IOBHT_AR_Plate4


title: Sk+PT-1LGRB (Sk_IOBHT_AR_Plate1)

description: Library name: Sk_and_PT-1LGRB_Sk_IOBHT_AR_Plate1


title: ST+PT-1LVAN (ST_JF1O3_Plate8)

description: Library name: ST_and_PT-1LVAN_ST_JF1O3_Plate8

source_name: Stomach

value: Stomach


title: ST+PT-1LVAN (ST_JF1O3_Plate6)

description: Library name: ST_and_PT-1LVAN_ST_JF1O3_Plate6


title: ST+PT-1LVAN (ST_JF1O3_Plate7)

description: Library name: ST_and_PT-1LVAN_ST_JF1O3_Plate7


title: ST+PT-1LVAN (ST_JF1O3_Plate5)

description: Library name: ST_and_PT-1LVAN_ST_JF1O3_Plate5


title: ST+PT-1LVAN (ST_JF1O3_Plate4)

description: Library name: ST_and_PT-1LVAN_ST_JF1O3_Plate4


title: ST+PT-1LVAN (ST_JF1O3_Plate2)

description: Library name: ST_and_PT-1LVAN_ST_JF1O3_Plate2


title: ST+PT-1LVAN (ST_JF1O3_Plate1)

description: Library name: ST_and_PT-1LVAN_ST_JF1O3_Plate1


title: ST+PT-1LVAN (ST_JF1O3_Plate3)

description: Library name: ST_and_PT-1LVAN_ST_JF1O3_Plate3


title: ST+PT-1LGRB (ST_IOBHV_Plate8)

description: Library name: ST_and_PT-1LGRB_ST_IOBHV_Plate8


title: ST+PT-1LGRB (ST_IOBHV_Plate7)

description: Library name: ST_and_PT-1LGRB_ST_IOBHV_Plate7


title: ST+PT-1LGRB (ST_IOBHV_Plate6)

description: Library name: ST_and_PT-1LGRB_ST_IOBHV_Plate6


title: ST+PT-1LGRB (ST_IOBHV_Plate4)

description: Library name: ST_and_PT-1LGRB_ST_IOBHV_Plate4


title: ST+PT-1LGRB (ST_IOBHV_Plate3)

description: Library name: ST_and_PT-1LGRB_ST_IOBHV_Plate3


title: ST+PT-1LGRB (ST_IOBHV_Plate5)

description: Library name: ST_and_PT-1LGRB_ST_IOBHV_Plate5


title: ST+PT-1LGRB (ST_IOBHV_Plate2)

description: Library name: ST_and_PT-1LGRB_ST_IOBHV_Plate2


title: SB+PT-1LVAN (SB_JF1O2_AR_Plate5)

description: Library name: SB_and_PT-1LVAN_SB_JF1O2_AR_Plate5

source_name: Ileum Peyer's Patch

value: Ileum Peyer's Patch


title: SB+PT-1LVAN (SB_JF1O2_AR_Plate4)

description: Library name: SB_and_PT-1LVAN_SB_JF1O2_AR_Plate4


title: SB+PT-1LVAN (SB_JF1O2_AR_Plate1)

description: Library name: SB_and_PT-1LVAN_SB_JF1O2_AR_Plate1


title: SB+PT-1LVAN (SB_JF1O2_AR_Plate2)

description: Library name: SB_and_PT-1LVAN_SB_JF1O2_AR_Plate2


title: SB+PT-1LVAN (SB_JF1O2_AR_Plate3)

description: Library name: SB_and_PT-1LVAN_SB_JF1O2_AR_Plate3


title: ST+PT-1LGRB (ST_IOBHV_Plate1)

description: Library name: ST_and_PT-1LGRB_ST_IOBHV_Plate1


title: SB+PT-1K2DA (SB_ADA5F_AR_Plate4)

description: Library name: SB_and_PT-1K2DA_SB_ADA5F_AR_Plate4


title: SB+PT-1K2DA (SB_ADA5F_AR_Plate3)

description: Library name: SB_and_PT-1K2DA_SB_ADA5F_AR_Plate3


title: SB+PT-1K2DA (SB_ADA5F_AR_Plate2)

description: Library name: SB_and_PT-1K2DA_SB_ADA5F_AR_Plate2


title: SB+PT-1K2DA (SB_ADA5F_AR_Plate1)

description: Library name: SB_and_PT-1K2DA_SB_ADA5F_AR_Plate1


title: RAA+STL003 (RAA_STL003_AR_Plate8)

description: Library name: RAA_and_STL003_RAA_STL003_AR_Plate8

source_name: Right Atrium Appendage

value: Right Atrium Appendage


title: RAA+STL003 (RAA_STL003_AR_Plate7)

description: Library name: RAA_and_STL003_RAA_STL003_AR_Plate7


title: RAA+STL003 (RAA_STL003_AR_Plate6)

description: Library name: RAA_and_STL003_RAA_STL003_AR_Plate6


title: RAA+STL003 (RAA_STL003_AR_Plate3)

description: Library name: RAA_and_STL003_RAA_STL003_AR_Plate3


title: RAA+STL003 (RAA_STL003_AR_Plate2)

description: Library name: RAA_and_STL003_RAA_STL003_AR_Plate2


title: RAA+STL003 (RAA_STL003_AR_Plate1)

description: Library name: RAA_and_STL003_RAA_STL003_AR_Plate1


title: RAA+STL003 (RAA_STL003_AR_Plate4)

description: Library name: RAA_and_STL003_RAA_STL003_AR_Plate4


title: RAA+PT-1LVAN (RAA_JF1NX_Tris_Plate4)

description: Library name: RAA_and_PT-1LVAN_RAA_JF1NX_Tris_Plate4


title: RAA+PT-1LVAN (RAA_JF1NX_Tris_Plate6)

description: Library name: RAA_and_PT-1LVAN_RAA_JF1NX_Tris_Plate6


title: RAA+PT-1LVAN (RAA_JF1NX_Tris_Plate5)

description: Library name: RAA_and_PT-1LVAN_RAA_JF1NX_Tris_Plate5


title: RAA+PT-1LVAN (RAA_JF1NX_Tris_Plate3)

description: Library name: RAA_and_PT-1LVAN_RAA_JF1NX_Tris_Plate3


title: RAA+PT-1LVAN (RAA_JF1NX_Tris_Plate1)

description: Library name: RAA_and_PT-1LVAN_RAA_JF1NX_Tris_Plate1


title: Tomato leaf, WT, rep2

city: nanjing

first: hai

last: zhu

address: xiaolingwei Street 50th

institute: nanjing agricultural university

description: Library name: WT-leaf_2

data_processing:
Illumina Casava1.7 software used for basecalling. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.The clean paired-end reads were mapped to the Solanum lycopersicum reference genome assembly SL3.1 using HISAT2 (version 2.1.0). Gene expression levels were also quantified as fragments per kilobase of transcript per million mapped reads (FPKM). FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: Solanum lycopersicum reference genome assembly SL3.1.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

organism: Solanum lycopersicum

source_name: Leaf

extract_protocol:
Total RNA was extracted using the TRlzol reagent (Invitrogen, CA, USA) according to themanufacturer' s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer's instructions.

value: Leaf


title: RAA+PT-1LVAN (RAA_JF1NX_Tris_Plate2)

description: Library name: RAA_and_PT-1LVAN_RAA_JF1NX_Tris_Plate2


title: PI+HP16134 (PI_HP16134_AR_Plate3)

description: Library name: PI_and_HP16134_PI_HP16134_AR_Plate3

source_name: Pancreatic Islet

value: Pancreatic Islet


title: PI+HP16134 (PI_HP16134_AR_Plate2)

description: Library name: PI_and_HP16134_PI_HP16134_AR_Plate2


title: PI+HP16134 (PI_HP16134_AR_Plate1)

description: Library name: PI_and_HP16134_PI_HP16134_AR_Plate1


title: RAA+STL003 (RAA_STL003_AR_Plate5)

description: Library name: RAA_and_STL003_RAA_STL003_AR_Plate5


title: PI+HP13049 (PI_HP13049_AR_Plate9)

description: Library name: PI_and_HP13049_PI_HP13049_AR_Plate9


title: PI+HP13049 (PI_HP13049_AR_Plate8)

description: Library name: PI_and_HP13049_PI_HP13049_AR_Plate8


title: PI+HP13049 (PI_HP13049_AR_Plate4)

description: Library name: PI_and_HP13049_PI_HP13049_AR_Plate4


title: PI+HP13049 (PI_HP13049_AR_Plate6)

description: Library name: PI_and_HP13049_PI_HP13049_AR_Plate6


title: PI+HP13049 (PI_HP13049_AR_Plate3)

description: Library name: PI_and_HP13049_PI_HP13049_AR_Plate3


title: PI+HP13049 (PI_HP13049_AR_Plate5)

description: Library name: PI_and_HP13049_PI_HP13049_AR_Plate5


title: PI+HP13049 (PI_HP13049_AR_Plate7)

description: Library name: PI_and_HP13049_PI_HP13049_AR_Plate7


title: PI+HP13049 (PI_HP13049_AR_Plate2)

description: Library name: PI_and_HP13049_PI_HP13049_AR_Plate2


title: PI+HP13049 (PI_HP13049_AR_Plate10)

description: Library name: PI_and_HP13049_PI_HP13049_AR_Plate10


title: PI+HP13049 (PI_HP13049_AR_Plate1)

description: Library name: PI_and_HP13049_PI_HP13049_AR_Plate1


title: Phase 3, Micro-C, Rep1

city: Cambridge

first: Varshini

last: Ramanathan

state: Massachusetts

address: Building 56 Room 787B, 32 Vassar Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

description:
Library name: Phase3, Rep1
Phase3.250.mcool is a merge of libraries Phase3, Rep1 and Phase3, Rep2

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired-end reads were aligned with bwa-mem2 (v2.2.1) (flags: -SP) flag to the UCSC hg38 AnalysisSet genome and processed with pairtools (v1.1.2) parse2 (flags: --add-columns mapq --expand --report-position outer --min-mapq 30 --max-insert-size 150). Reads from the same replicate were merged then deduplicated with pairtools dedup (flags: --max-mismatch 1).
Replicate-wise .pairs files were  merged between sequencing runs (pairtools merge) and deduplicated once more (pairtools dedup). Due to sequencing read mismatch between phases, Phase 1, Rep 1 was downsampled using pairtools sample 0.65 to yield comparable read depth to the second replicate.
Final .pairs files were indexed with pairix (v0.3.8), and made into a .cool file with cooler (v0.10.3) cload pairs at 50bp bin size. Finally, .cool files were converted to .mcool files using cooler zoomify with the --balance flag up to 10Mb bin sizes.
Assembly: hg38
Supplementary files format and content: .mcool file contains all valid Micro-C pairs stored in HDF5 format with multiple binsizes

source_name: CD34+ HSPCs (donor-derived, peripheral blood), differentiated to day 13

growth_protocol: Human CD34+ hematopoietic stem and progenitor cells (HSPCs) isolated from mobilized peripheral blood of healthy adult donors were obtained from the Cooperative Center of Excellence in Hematology at the Fred Hutchinson Cancer Research Center. Cryopreserved HSPCs were thawed and cultured in maintenance medium consisting of StemSpan SFEM II (StemCell Technologies) supplemented with CC100 cytokine cocktail (StemCell Technologies), 50 ng/mL human thrombopoietin (TPO; PeproTech), 1% penicillin-streptomycin (Life Technologies), and 1% L-glutamine (Life Technologies). Following the maintenance phase, erythroid differentiation was performed as follows. A basal erythroid medium was prepared using IMDM (Gibco) supplemented with 2% human AB plasma (SeraCare), 3% human AB serum (Life Technologies), 3 U/mL heparin, 10 μg/mL insulin, 200 μg/mL holo-transferrin, and 1% penicillin-streptomycin. During phase I (days 1–7), the basal medium was supplemented with 3 U/mL erythropoietin (EPO), 10 ng/mL human stem cell factor (SCF), and 1 ng/mL interleukin-3 (IL-3). During phase II (days 7–12), cells were cultured in basal medium supplemented with 3 U/mL EPO and 10 ng/mL SCF. During phase III (day 12 onward), cells were cultured in basal medium supplemented with 3 U/mL EPO and 1 mg/mL holo-transferrin. Cells were collected on days 5, 9, and 13 from two independent healthy donors.

extract_protocol:
Cells were sequentially crosslinked with 3 mM  DSG for 35 min and 1% formaldehyde for 10 min at room temperature, followed by quenching with 0.375 M Tris-HCl (pH 7.5). Following quenching, nuclei were prepared from fixed cells. Chromatin was digested in situ using MNase, DNA 3' ends were chewed back and biotinylated, and then free DNA ends were proximity ligated. Unligated ends were digested, and chromatin crosslinks were reversed. DNA was purified by the DNA Clean and Concentrator kit (Zymo), and size selected for dinucleosomal fragments on an agarose gel. Following end polishing of DNA fragments, a streptavidin pulldown was used to enrich for ligated dinucleosomal fragments. Size selected DNA fragments bound to streptavidin coated beads were used to prepare Micro-C libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with 8-10 PCR cycles on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR and pooled. Following qPCR quantification, the library pool was submitted for sequencing.
Library preparation was performed with the NEBNext Ultra II kit (New England BioLabs #E7645).


title: Phase 3, Micro-C, Rep2

description:
Library name: Phase3, Rep2
Phase3.250.mcool is a merge of libraries Phase3, Rep1 and Phase3, Rep2

value: CD34+ HSPCs (donor-derived, peripheral blood), differentiated to day 13


title: Phase 2, Micro-C, Rep2

description:
Library name: Phase2, Rep2
Phase2.250.mcool is a merge of libraries Phase2, Rep1 and Phase2, Rep2

source_name: CD34+ HSPCs (donor-derived, peripheral blood), diffferentiated to day 9


title: Phase 2, Micro-C, Rep1

description:
Library name: Phase2, Rep1
Phase2.250.mcool is a merge of libraries Phase2, Rep1 and Phase2, Rep2

source_name: CD34+ HSPCs (donor-derived, peripheral blood), differentiated to day 9


title: Phase 1, Micro-C, Rep2

description:
Library name: Phase1, Rep2
Phase1.250.mcool is a merge of libraries Phase1, Rep1 and Phase1, Rep2

source_name: CD34+ HSPCs (donor-derived, peripheral blood), differentiated to day 5


title: Phase 1, Micro-C, Rep1

description:
Library name: Phase1, Rep1
Phase1.250.mcool is a merge of libraries Phase1, Rep1 and Phase1, Rep2

value: CD34+ HSPCs (donor-derived, peripheral blood), differentiated to day 5


title: AAVS1, Micro-C, Donor 3, Condition 2

description: Library name: AAVS1 Con2

source_name: CD34+ HSPCs (donor-derived, peripheral blood), differentiated to day 14

growth_protocol: Human CD34+ hematopoietic stem and progenitor cells (HSPCs) isolated from mobilized peripheral blood of healthy adult donors were obtained from the Cooperative Center of Excellence in Hematology at the Fred Hutchinson Cancer Research Center. Cryopreserved HSPCs were thawed and cultured in maintenance medium consisting of StemSpan SFEM II (StemCell Technologies) supplemented with CC100 cytokine cocktail (StemCell Technologies), 50 ng/mL human thrombopoietin (TPO; PeproTech), 1% penicillin-streptomycin (Life Technologies), and 1% L-glutamine (Life Technologies). Following the maintenance phase, erythroid differentiation was performed as follows. A basal erythroid medium was prepared using IMDM (Gibco) supplemented with 2% human AB plasma (SeraCare), 3% human AB serum (Life Technologies), 3 U/mL heparin, 10 μg/mL insulin, 200 μg/mL holo-transferrin, and 1% penicillin-streptomycin. During phase I (days 1–7), the basal medium was supplemented with 3 U/mL erythropoietin (EPO), 10 ng/mL human stem cell factor (SCF), and 1 ng/mL interleukin-3 (IL-3). During phase II (days 7–12), cells were cultured in basal medium supplemented with 3 U/mL EPO and 10 ng/mL SCF. During phase III (day 12 onward), cells were cultured in basal medium supplemented with 3 U/mL EPO and 1 mg/mL holo-transferrin. Cells were collected on day 13.

treatment_protocol: Genome editing was performed in primary human CD34⁺ hematopoietic stem and progenitor cells (HSPCs) using the 4D-Nucleofector system (Lonza) and the P3 Primary Cell 4D-Nucleofector X Kit S (Lonza). For NFE2 knockout, ribonucleoprotein (RNP) complexes were assembled by combining 100 pmol Cas9 protein (IDT) with 100 pmol chemically modified sgRNA (Synthego) and incubating at room temperature for 15 min. RNP complexes were delivered into CD34⁺ HSPCs using the P3 nucleofection reagent supplemented with Alt-R Cas9 Electroporation Enhancer (IDT) at a 20:1 molar ratio, using program DZ-100. For knockout of cohesin complex components (STAG1, STAG2, and NIPBL), two editing conditions were used to achieve different levels of gene disruption. In condition 1 (Con1), cells were edited using the same procedure described above. In condition 2 (Con2), cells underwent a second round of nucleofection 2 days after the initial editing using the same RNP delivery protocol. Following editing, cells were cultured under erythroid differentiation conditions beginning 3 days after the initial nucleofection. Knockout efficiency was assessed by western blot analysis of protein lysates or by genomic DNA extraction followed by ICE (Inference of CRISPR Edits) analysis.


title: AAVS1, Micro-C, Donor 3, Condition 1

description: Library name: AAVS1 Con1


title: NIPBL-KO, Micro-C, Donor 3, Condition 2

description: Library name: NIPBL-KO Con2


title: STAG2-KO, Micro-C, Donor 3, Condition 2

description: Library name: STAG2-KO Con2


title: NIPBL-KO, Micro-C, Donor 3, Condition 1

description: Library name: NIPBL-KO Con1


title: Muscle_Patient35_Post-RYGB

city: Ottawa

first: Mary-Ellen

last: Harper

state: ON

address: 451 Smyth Rd

country: Canada

institute: University of Ottawa

description: Library name: 70_L001

data_processing:
We quantified the expression of transcripts using RNA-seq data through Salmon.
Salmon’s transcript-level quantifications DESeq2 was applied for detection of differentially expressed genes (DEG).
Assembly: GENCODE GRCh38.p14
Supplementary files format and content: a csv file include TPM for all samples.

source_name: Skeletal Muscle, Vastus Lateralis

extract_protocol:
Tissues were homogenized and lysed in TRIzol reagent. After centrifuged, the supernatant (aqueous phase) was applied to the RNeasy kit (Qiagen, ID: 74106) for subsequent total RNA extraction and purification according to its protocols.
RNA libraries for RNA-seq were prepared using the NEBNext® Ultra™ II Directional RNA Library kit following manufacturer's protocols.

treatment_protocol: Skeletal muscle biospsies (m. vastus lateralis) were collected from 35 individuals before Roux-en-Y-Gastric Bypass (RYGB) bariatric surgery and one-year (52 weeks) after RYGB surgery.

value: Skeletal Muscle, Vastus Lateralis

tag: time point

value: Female


title: STAG2-KO, Micro-C, Donor 3, Condition 1

description: Library name: STAG2-KO Con1


title: STAG1-KO, Micro-C, Donor 3, Condition 2

description: Library name: STAG1-KO Con2


title: Muscle_Patient34_Post-RYGB

description: Library name: 68_L001


title: Muscle_Patient34_Pre-RYGB

description: Library name: 67_L001

value: Pre-RYGB


title: STAG1-KO, Micro-C, Donor 3, Condition 1

description: Library name: STAG1-KO Con1


title: NFE2-KO, Micro-C, Donor 2

description: Library name: NFE2-KO Don2


title: Muscle_Patient35_Pre-RYGB

description: Library name: 69_L001


title: Muscle_Patient33_Post-RYGB

description: Library name: 66_L001


title: NFE2-KO, Micro-C, Donor 1

description: Library name: NFE2-KO Don1


title: Muscle_Patient33_Pre-RYGB

description: Library name: 65_L001


title: Muscle_Patient32_Post-RYGB

description: Library name: 64_L001


title: AAVS1, Micro-C, Donor 2

description: Library name: AAVS1 Don2


title: AAVS1, Micro-C, Donor 1

description: Library name: AAVS1 Don1


title: Muscle_Patient31_Post-RYGB

description: Library name: 62_L001


title: Muscle_Patient31_Pre-RYGB

description: Library name: 61_L001


title: Muscle_Patient32_Pre-RYGB

description: Library name: 63_L001


title: Muscle_Patient30_Post-RYGB

description: Library name: 60_L001


title: Muscle_Patient30_Pre-RYGB

description: Library name: 59_L001


title: Muscle_Patient29_Post-RYGB

description: Library name: 58_L001


title: Muscle_Patient29_Pre-RYGB

description: Library name: 57_L001


title: Muscle_Patient28_Post-RYGB

description: Library name: 56_L001


title: Muscle_Patient28_Pre-RYGB

description: Library name: 55_L001


title: Muscle_Patient27_Post-RYGB

description: Library name: 54_L001


title: Muscle_Patient27_Pre-RYGB

description: Library name: 53_L001


title: Muscle_Patient26_Post-RYGB

description: Library name: 52_L001


title: Muscle_Patient26_Pre-RYGB

description: Library name: 51_L001


title: Muscle_Patient24_Post-RYGB

description: Library name: 48_L001


title: Muscle_Patient25_Post-RYGB

description: Library name: 50_L001


title: Muscle_Patient24_Pre-RYGB

description: Library name: 47_L001


title: Muscle_Patient23_Pre-RYGB

description: Library name: 45_L001


title: Muscle_Patient23_Post-RYGB

description: Library name: 46_L001


title: Muscle_Patient22_Pre-RYGB

description: Library name: 43_L001


title: Muscle_Patient25_Pre-RYGB

description: Library name: 49_L001


title: Muscle_Patient21_Post-RYGB

description: Library name: 42_L001


title: Muscle_Patient21_Pre-RYGB

description: Library name: 41_L001


title: Muscle_Patient20_Post-RYGB

description: Library name: 40_L001


title: Muscle_Patient20_Pre-RYGB

description: Library name: 39_L001


title: Muscle_Patient22_Post-RYGB

description: Library name: 44_L001


title: Muscle_Patient19_Post-RYGB

description: Library name: 38_L001


title: Muscle_Patient19_Pre-RYGB

description: Library name: 37_L001


title: Muscle_Patient18_Post-RYGB

description: Library name: 36_L001


title: Human macrophages, Donor H2, IFNy stimulated

city: Greifswald - Insel Riems

first: Björn

last: Corleis

state: Mecklenburg-Western Pomerania

address: Südufer 10

department: Institute of immunology

country: Germany

institute: Friedrich-Loeffler-Institut

description: Library name: H2_IFNy

data_processing:
STAR (version 2.7.9a) read alignment
Subread featureCounts (version 2.0.3) read counting
Assembly: GRCh38.p14, GRCm39
Supplementary files format and content: tab delimeted .txt file containing raw read counts for each gene

source_name: monocyte derived macrophages

growth_protocol: For transcriptomic analysis, macrophages were differentiated in 48-well plates at a density of 1 × 10⁶ cells per well in RPMI 1640 supplemented with 10% FCS, 2 mM L-glutamine, and 1 mM sodium pyruvate.

extract_protocol:
RNA was extracted from 1 ml Trizol™ using PhaseMaker tubes and chloroform. After phase separation by centrifugation (12,000 × g, 15 min, 4°C), the aqueous phase was precipitated with glycogen and isopropanol (–20°C, 60 min), pelleted, washed with 75% ethanol, and air-dried. RNA was resuspended in 20 µl nuclease-free water and incubated at 60°C for 15 min.
TotTotal RNA was purified with RNA-SPRI beads and ethanol washes. Whole-transcriptome amplification was performed using Smart-seq2. cDNA was synthesized, amplified, and purified with DNA-SPRI beads. Quality was assessed via Qubit and Bioanalyzer. Libraries were prepared using Nextera XT for tagmentation and adapter ligation, PCR-amplified, bead-purified, and stored at –20 °C

treatment_protocol: Cells were pre-treated with 500 ng/ml recombinant IFNγ for 24 hours, followed by infection with M. tuberculosis (Mtb) at a multiplicity of infection (MOI) of 1 for an additional 24 hours

value: monocyte derived macrophages

value: IFNy stimulated


title: Muscle_Patient17_Post-RYGB

description: Library name: 34_L001


title: Muscle_Patient17_Pre-RYGB

description: Library name: 33_L001


title: Muscle_Patient18_Pre-RYGB

description: Library name: 35_L001


title: Muscle_Patient16_Post-RYGB

description: Library name: 32_L001


title: Muscle_Patient16_Pre-RYGB

description: Library name: 31_L001


title: Muscle_Patient14_Post-RYGB

description: Library name: 28_L001


title: Muscle_Patient15_Post-RYGB

description: Library name: 30_L001


title: Muscle_Patient15_Pre-RYGB

description: Library name: 29_L001


title: Muscle_Patient14_Pre-RYGB

description: Library name: 27_L001


title: Muscle_Patient13_Post-RYGB

description: Library name: 26_L001


title: Muscle_Patient12_Post-RYGB

description: Library name: 24_L001


title: Muscle_Patient13_Pre-RYGB

description: Library name: 25_L001


title: Muscle_Patient12_Pre-RYGB

description: Library name: 23_L001


title: Muscle_Patient11_Post-RYGB

description: Library name: 22_L001


title: Muscle_Patient10_Pre-RYGB

description: Library name: 19_L001


title: Muscle_Patient10_Post-RYGB

description: Library name: 20_L001


title: Muscle_Patient9_Pre-RYGB

description: Library name: 17_L001


title: Muscle_Patient11_Pre-RYGB

description: Library name: 21_L001


title: Muscle_Patient9_Post-RYGB

description: Library name: 18_L001


title: Muscle_Patient8_Pre-RYGB

description: Library name: 15_L001


title: Muscle_Patient8_Post-RYGB

description: Library name: 16_L001


title: Muscle_Patient7_Pre-RYGB

description: Library name: 13_L001


title: Muscle_Patient6_Post-RYGB

description: Library name: 12_L001


title: Muscle_Patient7_Post-RYGB

description: Library name: 14_L001


title: Muscle_Patient6_Pre-RYGB

description: Library name: 11_L001


title: Muscle_Patient5_Post-RYGB

description: Library name: 10_L001


title: Muscle_Patient5_Pre-RYGB

description: Library name: 9_L001


title: Muscle_Patient4_Pre-RYGB

description: Library name: 7_L001


title: Muscle_Patient4_Post-RYGB

description: Library name: 8_L001


title: Muscle_Patient3_Post-RYGB

description: Library name: 6_L001


title: Muscle_Patient3_Pre-RYGB

description: Library name: 5_L001


title: Muscle_Patient1_Post-RYGB

description: Library name: 2_L001


title: Muscle_Patient1_Pre-RYGB

description: Library name: 1_L001


title: Muscle_Patient2_Pre-RYGB

description: Library name: 3_L001


title: Muscle_Patient2_Post-RYGB

description: Library name: 4_L001


title: human iPSC-derived neurospheres_P8

status: Public on Jul 23 2026

city: Tokorozawa-si

first: Noriko

last: Mizota

state: Saitama

address: 2-579-15 Mikajima

department: Faculty of Human Sciences

country: Japan

institute: Waseda University

description: Library name: human_sample1

data_processing:
CAGE libraries were sequenced using paired-end reads of 150 nt on a NextSeq 2000 instrument (Illumina). Obtained reads (CAGE tags) were mapped to the human hg38 genome using STAR (version 2.7.9a).
CAGE tag clustering was performed using the RECLU pipeline (Ohmiya et al., BMC Genetics 2014, 15:269). Tag count data were clustered using the modified Paraclu program (Frith et al., Genome Research 2007 18:1-12), and clusters with a count per million (CPM) < 0.1 were discarded. Regions with ≥90% overlap between replicates were extracted using BEDtools (version 2.12.0). Clusters with an irreproducible discovery rate (IDR) ≥ 0.1 or a length exceeding 200 bp were discarded.
Assembly: hg38
Supplementary files format and content: BigWig files are track objects generated by splitting normalized CAGE tag counts into positive and negative strands. These files can be uploaded to a genome browser for visualization in a genomic context.

extract_protocol:
Total RNA was isolated using an RNA purification column.
The cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5' cap structures of RNAs were oxidized and biotinylated, followed by selection of biotinylated RNA/cDNA using streptavidin beads via cap-trapping. After RNA digestion with RNaseONE/H and adapter ligation at both ends, double-stranded cDNA libraries (CAGE libraries) were constructed.

value: neurosphere


title: U937, 3-HF-3

status: Public on Jul 21 2026

city: Guangzhou

first: Yage

last: Nie

address: No.74 Zhongshan Rd.2, Guangzhou

institute: Sun Yat-sen University

description: Library name: Sample 18

data_processing:
The quality of the RNA-seq data was assessed using FastQC. Subsequently, the reads were aligned to the human genome (hg19) using Hisat2 (version 2.1.0). The resulting alignment files were sorted using SAMtools (version 1.9). HTSeq (version 0.11.2) was employed for read assignment and gene-level count summarization.
Assembly: hg19
Supplementary files format and content: csv

source_name: Pleural effusion

growth_protocol: MOLM13, MV411 and U937 cells were maintained in in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIZOL (740404.2, MACHEREY-NAGEL) reagent . 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Kit following manufacturer's protocols.

treatment_protocol: DMSO (Sigma), and 10μM 3-hydroxyflavone (Topscience)

value: Pleural effusion

value: WT

value: 3-HF 10μM

value: total RNA


title: U937, 3-HF-1

description: Library name: Sample 16


title: U937, DMSO-3

description: Library name: Sample 15

value: DMSO


title: U937, DMSO-2

description: Library name: Sample 14


title: U937, DMSO-1

description: Library name: Sample 13


title: MV411, 3-HF-3

description: Library name: Sample 12

source_name: Peripheral blood

value: Peripheral blood


title: U937, 3-HF-2

description: Library name: Sample 17


title: MV411, 3-HF-2

description: Library name: Sample 11


title: MV411, 3-HF-1

description: Library name: Sample 10


title: MV411, DMSO-3

description: Library name: Sample 9


title: MV411, DMSO-2

description: Library name: Sample 8


title: MV411, DMSO-1

description: Library name: Sample 7


title: MOLM13, 3-HF-2

description: Library name: Sample 5


title: MOLM13, 3-HF-1

description: Library name: Sample 4


title: MOLM13, DMSO-2

description: Library name: Sample 2


title: MOLM13, DMSO-3

description: Library name: Sample 3


title: MOLM13, 3-HF-3

description: Library name: Sample 6


title: MOLM13, DMSO-1

description: Library name: Sample 1


title: HCI-011, DMSO, MN93, RREMS

status: Public on Jul 13 2026

city: Salt Lake City

first: Katherine

middle: E

last: Varley

state: UT

address: 2000 Circle of Hope, Room 3719

department: Department of Oncological Sciences

institute: Huntsman Cancer Institute University of Utah

description:
Library name: HCI-011_DMSO_MN93_RREMS
HCI-011_DMSO_MN93

data_processing:
Single cell multiome fastq files (mRNA and ATAC) were aligned, filtered, peaks called, and counted using Cell Ranger ARC Count v2.1.0 with parameters createBam: true, gexExcludeIntrons: false, skipCellAnnotation: false, noSecondaryAnalysis: false, checkLibraryCompatibility: true, and aligning to human reference (GHCh38) - 2024 - A.
Sincle cell mRNA and ATAC counts and ATAC fragments were aggregated using Cell Ranger ARC Aggr v2.1.0 with parameters noSecondaryAnalysis: false and normalizationModeArc: depth.
ATAC bigWig files were generated from the all_samples_atac_fragments.tsv.gz file using bedtools genomecov v2.28.0 followed by UCSC bedGraphToBigWig v2.10 with hg38 chromosome sizes from UCSC (https://hgdownload.soe.ucsc.edu/goldenpath/hg38/bigZips/hg38.chrom.sizes).
RREMS fastq files were trimmed, aligned, counted, and aggregated using the rrems v0.1.2 pipeline (https://github.com/jadonwagstaff/rrems). Breifly, the rrems pipeline consists of trimming adapters using Trim Galore v0.6.7 and options --rrbs and --fastqc, alignments are done with Bismark v0.22.3 with options --bowtie2, --non_bs_mm, -N 1, and aligning to UCSC hg38 reference genome (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz), CpG methylation are quantified using Bismark Methylation Extractor v0.22.3 with default options, and CpG's with less than 10 reads are removed and a color bed file for each sample is created with rounded cg percent methylation as the "score" values.
Sample DNA methylation results were combined into a matrix using the full_join function of dplyr v 1.2.1 in R v4.4.2
RREMS color bed files were converted to bigBed files using UCSC bedToBigBed v2.7 and UCSC hg38 chromosome sizes (https://hgdownload.soe.ucsc.edu/goldenpath/hg38/bigZips/hg38.chrom.sizes).
Assembly: hg38
Supplementary files format and content: Cell Ranger output files: all_samples_filtered_feature_bc_matrix.h5, all_samples_filtered_feature_bc_barcodes.tsv.gz, all_samples_filtered_feature_bc_features.tsv.gz, all_samples_filtered_feature_bc_matrix.mtx.gz, all_samples_atac_fragments.tsv.gz.
Supplementary files format and content: CSV file assigning barcodes to sample names: all_samples_libraryids.csv.
Supplementary files format and content: BigWig files for visualizing atac fragments: sample specific .bw files.
Supplementary files format and content: Matrix of proportion (0 to 1) CpG methylation: all_samples_cg_methylation.tsv.
Supplementary files format and content: BigBed files for visualizing DNA methylation: sample specific .bb files.

source_name: Breast cancer PDXO

growth_protocol: PDxO were grown on 6 well plate in Matrigel dome. For the experiments, organoids were trypsinized with TrypLE as single cells, counted and 200.000 cells per well were seeded in a 6 well ULA plate.

extract_protocol:
After 3 weeks, organoids were dissociated with TrypLE for 10 minutes until reached a single-cell suspension. Single cell suspension was counted and between 400.000 and 1.000.000 cells were frozen in PDxO medium (70%) plus FBS (20%) and DMSO (10%).
Single cell nuclei were isolated using the Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics, PN-1000494), Chromium Nuclei Isolation Reagents Kit (10x Genomics, PN-1000447) and Chromium Nuclei Isolation Consumables Kit (10x Genomics, PN-1000448). Cryopreserved PDxO were transferred to 2 mL tubes, centrifuged (4°C /2 min/1200g) and washed one time with 1.7 ml PBS then spun again (4°C /2min/1200g). All supernatant was removed, preserving the pellet and samples were kept samples on ice. Lysis buffer was prepared by 1:10 diluting the lysis buffer from 10x Genomics Nuclei isolation kit (freshly prepared as in 10x Genomics manual CG000505, Rev B, 1X+10%: Lysis Reagent, 550 µl, Reducing Agent B, 0.55 µl and Surfactant A 5.5 µl). The diluent was buffer containing 10mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2. Samples were lysed using 200 µl lysis buffer for 4-10 min. depending on the input cell number (400K-2M cells). 1 ml Wash Buffer (1% BSA in PBS with RNase inhibitor (10x Genomics)) was added to stop the lysis, and samples were centrifuge at 4°C /7 min/600g, supernatant removed preserving the pellet. The nuclei pellet was resuspended in 1X Nuclei Buffer (10x Genomics). The volume varied from 50-200 µl/sample depending on the size of the nuclei pellet to achieve a target concentration of 3500 nuclei/µl.
For RREMS, genomic DNA was extracted from leftover nuclei pellets sent for multiome using the DNeasy Blood & Tissue Kit (Qiagen, Cat no. 69504).
Single-nucleus chromatin accessibility and gene expression libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression platform (10x Genomics, Pleasanton, CA, USA) following the manufacturer’s protocol (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide, CG000338 Rev. G).
For RREMS, 100ng of genomic DNA is digested with MspI (NEB) to enrich for CG rich regions of the genome. DNA fragment overhangs are filled with Klenow Fragment (3’-5’ exo-) (NEB) to leave an A-overhang. Next, we ligated the NEBNext® EM-seq™ Adaptor (NEB, E7165) and then samples were purified using AmpureXP beads (1:2X). To convert unmethylated cytosine to uracil we followed the NEB protocol for the NEBNext® Enzymatic Methyl-seq v2 Conversion Module (E8020L) using formamide at the step 1.7 (Denaturation of DNA). The converted libraries were then PCR amplified using Epimark HS Taq DNA Polymerase (NEB, M0490L) and the barcoded primers NEBNext® Multiplex Oligos for Enzymatic Methyl-seq (Unique Dual Index Primer Pairs Plate, E7166). PCR cycling conditions were 95°C for 30 sec, (94°C for 30 sec, 60°C for 3 mins, for 14 cycles). Libraries were purified using AmpureXP beads (1:1.2X). Equimolar quantities of barcoded libraries were pooled and sequenced using the Illumina NovaSeq X instrument. PhiX genome control library (Illumina) was included at 20% in each sequencing lane to improve cluster identification and base-balancing during sequencing.

treatment_protocol: CDK4/6i: Final concentration 250nM (Stock 100uM) with fresh media replaced every 2 to 3 days.

value: Breast cancer PDXO

tag: model source

tag: experimental replicate

tag: library type

value: RREMS


title: HCI-011, DMSO, MN93, ATAC

description:
Library name: HCI-011_DMSO_MN93_ATAC
HCI-011_DMSO_MN93

library_source: genomic single cell

value: ATAC


title: HCI-011, CDKi, MN93, RREMS

description:
Library name: HCI-011_CDKi_MN93_RREMS
HCI-011_CDKi_MN93

value: CDKi


title: HCI-011, CDKi, MN93, ATAC

description:
Library name: HCI-011_CDKi_MN93_ATAC
HCI-011_CDKi_MN93


title: HCI-011, DMSO, MN93, mRNA

description:
Library name: HCI-011_DMSO_MN93_mRNA
HCI-011_DMSO_MN93

molecule: nuclear RNA

value: mRNA


title: HCI-011, DMSO, MN87, RREMS

description:
Library name: HCI-011_DMSO_MN87_RREMS
HCI-011_DMSO_MN87


title: HCI-011, CDKi, MN93, mRNA

description:
Library name: HCI-011_CDKi_MN93_mRNA
HCI-011_CDKi_MN93


title: HCI-011, DMSO, MN87, ATAC

description:
Library name: HCI-011_DMSO_MN87_ATAC
HCI-011_DMSO_MN87


title: HCI-011, DMSO, MN87, mRNA

description:
Library name: HCI-011_DMSO_MN87_mRNA
HCI-011_DMSO_MN87


title: HCI-011, CDKi, MN87, RREMS

description:
Library name: HCI-011_CDKi_MN87_RREMS
HCI-011_CDKi_MN87


title: HCI-011, CDKi, MN87, mRNA

description:
Library name: HCI-011_CDKi_MN87_mRNA
HCI-011_CDKi_MN87


title: HCI-011, CDKi, MN87, ATAC

description:
Library name: HCI-011_CDKi_MN87_ATAC
HCI-011_CDKi_MN87


title: HCI-005, DMSO, MN94, RREMS

description:
Library name: HCI-005_DMSO_MN94_RREMS
HCI-005_DMSO_MN94


title: HCI-005, DMSO, MN94, ATAC

description:
Library name: HCI-005_DMSO_MN94_ATAC
HCI-005_DMSO_MN94


title: HCI-005, DMSO, MN94, mRNA

description:
Library name: HCI-005_DMSO_MN94_mRNA
HCI-005_DMSO_MN94


title: HCI-005, CDKi, MN94, ATAC

description:
Library name: HCI-005_CDKi_MN94_ATAC
HCI-005_CDKi_MN94


title: HCI-005, CDKi, MN94, RREMS

description:
Library name: HCI-005_CDKi_MN94_RREMS
HCI-005_CDKi_MN94


title: HCI-005, DMSO, MN93, RREMS

description:
Library name: HCI-005_DMSO_MN93_RREMS
HCI-005_DMSO_MN93


title: HCI-005, CDKi, MN94, mRNA

description:
Library name: HCI-005_CDKi_MN94_mRNA
HCI-005_CDKi_MN94


title: HCI-005, DMSO, MN93, ATAC

description:
Library name: HCI-005_DMSO_MN93_ATAC
HCI-005_DMSO_MN93


title: HCI-005, DMSO, MN93, mRNA

description:
Library name: HCI-005_DMSO_MN93_mRNA
HCI-005_DMSO_MN93


title: HCI-005, CDKi, MN93, RREMS

description:
Library name: HCI-005_CDKi_MN93_RREMS
HCI-005_CDKi_MN93


title: HCI-005, CDKi, MN93, ATAC

description:
Library name: HCI-005_CDKi_MN93_ATAC
HCI-005_CDKi_MN93


title: HCI-005, CDKi, MN93, mRNA

description:
Library name: HCI-005_CDKi_MN93_mRNA
HCI-005_CDKi_MN93


title: HCI-003, DMSO, MN93, RREMS

description:
Library name: HCI-003_DMSO_MN93_RREMS
HCI-003_DMSO_MN93


title: HCI-003, CDKi, MN93, RREMS

description:
Library name: HCI-003_CDKi_MN93_RREMS
HCI-003_CDKi_MN93


title: HCI-003, CDKi, MN93, ATAC

description:
Library name: HCI-003_CDKi_MN93_ATAC
HCI-003_CDKi_MN93


title: HCI-003, DMSO, MN93, ATAC

description:
Library name: HCI-003_DMSO_MN93_ATAC
HCI-003_DMSO_MN93


title: HCI-003, CDKi, MN93, mRNA

description:
Library name: HCI-003_CDKi_MN93_mRNA
HCI-003_CDKi_MN93


title: HCI-003, DMSO, MN87, RREMS

description:
Library name: HCI−003_DMSO_MN87_RREMS
HCI−003_DMSO_MN87


title: HCI-003, DMSO, MN87, ATAC

description:
Library name: HCI−003_DMSO_MN87_ATAC
HCI−003_DMSO_MN87


title: HCI-003, DMSO, MN87, mRNA

description:
Library name: HCI−003_DMSO_MN87_mRNA
HCI−003_DMSO_MN87


title: HCI-003, DMSO, MN93, mRNA

description:
Library name: HCI-003_DMSO_MN93_mRNA
HCI-003_DMSO_MN93


title: HCI-003, CDKi, MN87, RREMS

description:
Library name: HCI−003_CDKi_MN87_RREMS
HCI−003_CDKi_MN87


title: HCI-003, CDKi, MN87, ATAC

description:
Library name: HCI−003_CDKi_MN87_ATAC
HCI−003_CDKi_MN87


title: HCI-003, CDKi, MN87, mRNA

description:
Library name: HCI−003_CDKi_MN87_mRNA
HCI−003_CDKi_MN87


title: Mouse kidney single nuclei, cKOt genotype, ZT16, rep 2

status: Public on Jul 08 2026

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

country: Switzerland

institute: Swiss Institute of Bioinformatics

description:
Library name: ZT16_KO2
10X Genomics; column name in data files:cKOt_ZT16_02

data_processing:
Base calling and demultiplexing were conducted using bcl2fastq2 (v2.20).
Gene expression matrices were generated using Cell Ranger (v7.1.0).
Downstream analysis was performed using th R package Seurat (v5)
Assembly: refdata-gex-GRCm39-2024-A (provided by 10X Genomics)
Supplementary files format and content: tab-separated barcodes, features, and matrix files generated by Cell Ranger (filtered_feature_bc_matrix)
Supplementary files format and content: Seurat R object (.rds) containing read counts, PCA and UMAP reductions based on 1000 PCs,  and cell type labels from manual, cluster-based cell-type assignment

source_name: Kidney

growth_protocol: All experiments were performed on male mice housed under 12-hours light/12-hours dark cycles with ad libitum access to drinking water and a standard laboratory chow diet (KLIBA NAFAG diet 3800). A Bmal1lox/lox/Pax8-rtTA/LC-1 Cre mouse strain was bred on the genetic background of the C57BL/6J mouse from The Jackson Laboratory. Eight weeks old Bmal1lox/lox/Pax8-rtTA/LC1 mice (referred as cKOt mice) and their Bmal1lox/lox littermates (referred as CTRL or control mice) were treated for 2 weeks with Doxycycline (DOX; 2 mg/ml in drinking water along with 20mg/ml sucrose) to induce the Cre recombinase inactivation of the Bmal1 (Arntl) gene.

extract_protocol:
Frozen mouse kidney tissue was used for nuclei isolation. Samples were immersed in ice-cold lysis buffer (Sigma-Aldrich, NUC-101) supplemented with RNase inhibitors (RNasin, 100 U/mL; RiboLock, 50 U/mL) and protease inhibitors. Tissue was mechanically homogenized at −20 °C using a TissueLyser (Qiagen) with stainless-steel beads. The lysate was filtered through a 40 µm cell strainer and centrifuged at 500 × g for 5 min at 4 °C. The pellet was washed with lysis buffer, incubated on ice, and centrifuged again. Nuclei were resuspended in PBS containing 2% BSA and RNase inhibitors and purified by sequential filtration through 20 µm strainers. Nuclei were stained with DAPI and sorted on a MoFlo Astios EQ cell sorter (Beckman Coulter) to isolate intact nuclei. Sorted nuclei were collected in ice-cold resuspension buffer and counted prior to downstream processing.
Single-nucleus RNA-seq libraries were generated using the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (Dual Index, 10x Genomics) according to the manufacturer’s instructions.  . The Chromium Next GEM Chip G (10X genomics, ref 2000177) was loaded with 20’000 nuclei per sample. Following GEM generation, reverse transcription and cDNA amplification were performed (12 cycles). Amplified cDNA was purified (SPRI beads), quantified (Qubit), and quality-checked (Fragment Analyzer). Libraries were constructed from 6.7–32 ng cDNA and amplified (15 cycles), followed by SPRI purification and quality control. Sequencing was performed on an Illumina NovaSeq 6000 using a 28-10-10-90 bp paired-end configuration with 1% PhiX spike-in.

value: Kidney

value: cKOt

tag: circadian time

value: male


title: Mouse kidney single nuclei, cKOt genotype, ZT16, rep 1

description:
Library name: ZT16_KO1
10X Genomics; column name in data files:cKOt_ZT16_01


title: Mouse kidney single nuclei, control genotype, ZT16 rep 2

description:
Library name: ZT16_C2
10X Genomics; column name in data files:CTRL_ZT16_02

value: Ctrl


title: Mouse kidney single nuclei, cKOt genotype, ZT04, rep 2

description:
Library name: ZT04_KO2
10X Genomics; column name in data files:cKOt_ZT4_02


title: Mouse kidney single nuclei, control genotype, ZT16, rep 1

description:
Library name: ZT16_C1
10X Genomics; column name in data files:CTRL_ZT16_01


title: Mouse kidney single nuclei, cKOt genotype, ZT04, rep 1

description:
Library name: ZT04_KO1
10X Genomics; column name in data files:cKOt_ZT4_01


title: Mouse kidney single nuclei, control genotype, ZT04, rep 2

description:
Library name: ZT04_C2
10X Genomics; column name in data files:CTRL_ZT4_02


title: Mouse kidney single nuclei, control genotype, ZT04, rep 1

description:
Library name: ZT04_C1
10X Genomics; column name in data files: CTRL_ZT4_01


title: HEPM cells, ARHGAP29 siRNA, biological replicate 3

status: Public on Jul 03 2026

city: Yinchuan

first: Zhumin

last: wang

state: ningxia

address: Shengli Street

department: School of Stomatology

institute: ningxia medical university

description: Library name: Si3

data_processing:
Raw sequencing reads were assessed with FastQC v0.11.8.
Adapter-contaminated and low-quality reads were filtered using fastp v0.19.5. Terminal bases with quality scores below Q15 were removed, and reads shorter than 40 bp after filtering were discarded.
Clean reads were aligned to the human reference genome GRCh38/hg38 using STAR v2.7.10b.
Gene- and transcript-level expression was quantified using StringTie v1.3.5. Gene-level raw read counts and normalized fragments per kilobase of transcript per million mapped reads (FPKM) were generated.
Differential expression analysis between ARHGAP29-knockdown and negative-control samples was performed using DESeq2 v1.10.1. Genes with an absolute log2 fold change greater than 0.585 and P < 0.05 were considered differentially expressed in the associated manuscript.
Assembly: GRCh38/hg38
Supplementary files format and content: Comma-separated values file containing gene-level raw read counts for all six samples. The first column contains gene symbols and the remaining columns contain the NC1, NC2, NC3, Si1, Si2 and Si3 raw counts.
Supplementary files format and content: Comma-separated values file containing gene-level FPKM expression values for all six samples. The first column contains gene symbols and the remaining columns contain the NC1, NC2, NC3, Si1, Si2 and Si3 FPKM values.

source_name: HEPM

growth_protocol: HEPM cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37 degrees C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from HEPM cells using the E.Z.N.A. Total RNA Kit (Omega Bio-tek). RNA quantity and purity were assessed before library preparation, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer.
Ribosomal RNA was depleted from total RNA. Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit. RNA was fragmented, reverse-transcribed using random primers, converted to dUTP-containing double-stranded cDNA, adapter-ligated, size-selected and PCR-amplified. Qualified libraries were sequenced on an Illumina platform using a 2 x 150-bp paired-end strategy.

treatment_protocol: Cells were seeded in six-well plates and transfected at approximately 60% confluence. Knockdown samples received ARHGAP29-targeting siRNA, whereas control samples received a non-targeting negative-control siRNA. siRNAs and lipid-based transfection reagents were obtained from GenePharma, and transfection was performed according to the manufacturer's protocol.

value: HEPM

value: human embryonic palatal mesenchymal cells

value: wild type

value: ARHGAP29-targeting siRNA


title: HEPM cells, ARHGAP29 siRNA, biological replicate 2

description: Library name: Si2


title: HEPM cells, negative-control siRNA, biological replicate 3

description: Library name: NC3

value: non-targeting negative-control siRNA


title: HEPM cells, ARHGAP29 siRNA, biological replicate 1

description: Library name: Si1


title: HEPM cells, negative-control siRNA, biological replicate 2

description: Library name: NC2


title: HEPM cells, negative-control siRNA, biological replicate 1

description: Library name: NC1


title: 30 minutes estradiol, INPUT

status: Public on Jul 01 2026

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

country: United Kingdom

institute: Newcastle University

description: Library name: 30_INPUT

data_processing:
Reads were trimmed using  Trimmomatic version 0.39
Reads were aligned to the T2T-CHM13v2.0 genome assembly using BWA version 0.7.18
Reads aligning to centromere/satellite  locations were counted using htseq-count from HTSeq version 2.0.7
Assembly: T2T-CHM13v2.0 genome assembly from the Telomere-to-telomere consortium CHM13 project.
Supplementary files format and content: Tab-delimted text file containing counts of reads aligning to centromere/satellite  locations, based on comprehensive centromere/satellite repeat annoation file provided by the Telomere-to-telomere consortium CHM13 project.

source_name: breast

growth_protocol: MCF7 cells were cultured in Minimum Essential Medium Eagle (MEME) (Sigma-Aldrich, M2279) supplemented with 10% (v/v) foetal bovine serum (PAA, A15-151), 1% (v/v) penicillin and streptomycin (PAA, P11-010) and 1% (v/v) glutamine (200 mM) (GIBCO, 25030-032), 1% NEAA (Sigma-Aldrich, M7145) in a 37°C incubator with 5% CO2. Estradiol (E2) was dissolved in the above medium at a stock concentration of 20 µg/ml and for E2 treatment was added to cells to a final concentration of 10 nM for 30 min.

extract_protocol:
ChIP was performed using the kits and the protocol from Millipore (Magna ChIP A, 17-610/EZ-Magna ChIP A, 17-408). Briefly, MCF7 cells were grown to ∼80% confluency and treated with 17β-estradiol (10 nM, 30 min) (Sigma-Aldrich). E2-treated and untreated (control) cells were fixed with formaldehyde (1% (v/v), Sigma-Aldrich), neutralised with glycine, washed with 1× PBS and trypsinised (0.05% trypsin in 0.53 mM EDTA (Invitrogen, 25300-054). Cells were collected and lysed with cell lysis buffer containing protease inhibitors, collected and resuspended in nuclear lysis buffer containing protease inhibitors. Chromatin was sonicated to between 500-1000bp, 14×15 s cycles, and 5% was removed as ‘input’. 3.6µg anti-TOP2B (3535), 7µg anti-TOP2B (30400), or7ug anti- TOP2A (3116)   or 1µg anti-GFP (Santa Cruz Biotechnology, sc-8334) or 5µg anti-AcH3 (Millipore, 06-599B) were added to protein A magnetic beads (Invitrogen, 100.02D). Chromatin was diluted, incubated with the beads and rotated for 4.5 h at 4°C. Immunoprecipitated protein-DNA complexes were washed sequentially in Low Salt Buffer, High Salt Buffer, LiCl Buffer and TE Buffer and then resuspended in ChIP Elution Buffer+Proteinase K, rotated at 65°C for 2 h followed by incubation at 95°C for 10min. DNA was then purified using spin columns (Binding Reagent ‘A’, Wash Buffer ‘B’, Elution reagent ‘C’).
Libraries were generated with chromatin immunoprecipitated from MCF7 cells±E2 (10 nM for 30 min). Multiple immunoprecipitates were pooled for each antibody (3535, 30400 and anti-GFP) to obtain between 400 and 800 ng DNA, at a concentration of 6-21 ng/µl for library preparation for Illumina ChIP Sequencing on an Illumina Genome Analyser II. Each library was sequenced 3 or 4 times for input libraries and for TOP2B libraries

value: breast

value: breast cancer epithelial cells

value: 30 minutes estradiol


title: 30 minutes estradiol, GFP antibody control

description: Library name: 30_GFP

treatment_protocol: Estradiol (E2) was dissolved in the above medium at a stock concentration of 20 µg/ml and for E2 treatment was added to cells to a final concentration of 10 nM for 30 min.


title: 30 minutes estradiol,  TOP2A antisera 3116 raised to CTD of TOP2A

description: Library name: 30_3116


title: 30 minutes estradiol,TOP2B antisera 3535 raised to last 116 amino acids of TOP2B

description: Library name: 30_3535


title: No estradiol, INPUT

description: Library name: 0_INPUT


title: 30 minutes estradiol,  TOP2B antisera 30400 raised to CTD of TOP2B

description: Library name: 30_30400


title: No estradiol, GFP antibody control

description: Library name: 0_GFP


title: No estradiol, TOP2B antisera 3535 raised to last 116 amino acids of TOP2B

description: Library name: 0_3535


title: No estradiol, TOP2A antisera 3116 raised to CTD of TOP2A

description: Library name: 0_3116


title: No estradiol, TOP2B antisera 30400 raised to CTD of TOP2B

description: Library name: 0_30400


title: Hi-C in post-mortal NeuN- rep2

status: Public on Jun 17 2026

city: Moscow

first: Anna

last: Kononkova

address: Nobel st., Building 1

department: Skoltech Center of Life Sciences

country: Russia

institute: Skolkovo Institute of Science and Technology

description: Library name: Sample6

data_processing:
Raw reads of each Hi-C library were preprocessed with trimmomatic and then processed  with distiller-nf pipeline. The hg38 genome assembly was provided for the mapping step. Filters  'mapq_30 (mapq1>=30 and mapq2>=30)' and '--walk-policy all'  were applied.
Assembly: hg38
Supplementary files format and content: Processed data files have mcool format. The files contain Hi-C matrices of intra- and interchromosomal contacts at multiple resolutions.

source_name: Left posterior superior temporal gyrus (Wernicke's area - BA22p)

growth_protocol: IPSCs Cultivation IPSCs were maintained in mTeSR1 or GibriS-8 media according to the manufacturer’s instructions. Matrigel was used for coating culture plates. Preparation of Matrigel-coated culture dishes and plates was performed according to the manufacturer’s instructions. Cells were passaged using 0.05% trypsin. ROCK inhibitor (Y27632) was added to the culture medium for 1 day after seeding at a concentration of 5 μ IPSCs Differentiation to  Neurons IPSCs were detached with trypsin and plated at a density of 40,000 cells/cm2  in mTeSR1 or GibriS-8 medium with presence of 5 μM of ROCK inhibitor. At a density of 100%, the mTeSR1 (GibriS-8) medium was replaced by the neural differentiation medium. Cells were cultured for 14 days with the medium change every other day. The resulting neural progenitors were detached with Versene solution by incubating the cells for 10 min in a CO2  incubator at 37 ∘ . After that, cells were centrifuged for 5 min at 250× g. The cells were washed with DMEM/F12 medium. Cells were plated at a density of 250,000–400,000 cells/cm2 in cell culture-treated dishes coated with Matrigel and cultured for 10 days in neuronal progenitor medium. The medium was changed every other day. The resulting neuronal progenitors were detached with Versene solution as described above. Cells were plated at a density of 250,000–400,000 cells/cm2 in cell culture-treated dishes coated with Matrigel and cultured for 7 days in NB maturation medium. The medium was changed every other day. After this stage, the cells could no longer be reseeded. The cells were cultured in NBA maturation medium for at least 2 weeks.

extract_protocol:
Cell nuclei from adult donor brain tissue were isolated and sorted as previously described (Nott et al., 2021; Pletenev et al., 2024), with modifications. Briefly, the tissue pieces were homogenized with an automated pestle homogenizer in 100 ul of fixative solution (1x PBS, 2% formaldehyde). The homogenate was rocked for 10 minutes at room temperature in a total volume of fixative solution of 10 ml, followed by the addition of 2 M glycine to a final concentration of 125 mM to quench the cross-linking reaction. The homogenate was then centrifuged at 1100g for 5 min at 4°C. The pellet was washed twice with NF1 buffer (Tris–HCl 10 mM, pH 8.0; EDTA 1 mM; MgCl2 5 mM; sucrose 100 mM; Triton X100 0.5%) and incubated in NF1 buffer for 30 min. The mixture was homogenized on ice using a Dounce homogenizer and filtered through a 70 um cell strainer. A sucrose cushion (10 mM Tris-HCl, pH 8.0; 1.6 M sucrose, 3 mM MgCl2; 1 mM DTT) was placed under the homogenate and the mixture was centrifuged at 3200g for 30 min at 4°C with brakes on ‘low’ to separate nuclei from debris. The nuclei pellet was washed sequentially with NF1 buffer and PBS, and resuspended in PBST with 5% BSA and 3% bovine serum. The nuclei were incubated with fluorescent antibodies (Abcam, ab196184) for the neuronal nuclear marker NeuN (at 100 ul per 1 million nuclei, dilution 1:500) overnight at 4°C in the dark. The next day, nuclei were washed and resuspended in 1x PBS, and DAPI dye was added to a final concentration of 2 ug/ml. The nuclei were passed through a 35 μm cell strainer followed by fluorescence-activated nuclei sorting (FANS). The sorted NeuN-positive and NeuN-negative nuclei were collected in FANS buffer (1x PBS, 0.1% Tween-20, 5% BSA), spun at 2,300g for 10 min at 4°C, and washed in PBS. The collected nuclei were either snap-frozen for storage at −80 °C, or used immediately for Hi-C library preparation.
Hi-C experiments were conducted on cultured iPSC-derived neurons (whole cells) and adult neuronal and non-neuronal FANS-sorted nuclei. In each case, two biological replicates were performed. Approximately 1 million cells or nuclei per sample were used. The previously described protocol (Lieberman-Aiden, van Berkum, et al., 2009; Pletenev et al., 2024) was followed for downstream steps. Hi-C libraries were sequenced on Illumina Novaseq 6000 by Skoltech Genomics Core Facility and Evrogen Joint Stock Company.

value: post-mortal non-neurons


title: Hi-C in post-mortal NeuN- rep1

description: Library name: Sample5

value: Left posterior superior temporal gyrus (Wernicke's area - BA22p)

value: female


title: Hi-C in iPSC-derived neurons rep1

description: Library name: Sample3

source_name: neurons differentiated from iPSC

value: neurons differentiated from iPSC


title: Hi-C in post-mortal NeuN+ rep2

description: Library name: Sample2

value: post-mortal neurons


title: Hi-C in post-mortal NeuN+ rep1

description: Library name: Sample1


title: Hi-C in iPSC-derived neurons rep2

description: Library name: Sample4


title: Y. lipolytica strain E122-EdU labeling without hydroxyurea for 60 minutes #2

status: Public on May 31 2026

city: Cold Spring Harbor

first: Bruce

last: Stillman

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: Library name: S06_S6

data_processing:
Paired-end reads were trimmed using Fastp v.0.23.2 90 default settings and automatic adapter detection. Quality assessment was performed using FastQC v0.12.1. Trimmed reads were aligned to the Yarrowia lipolytica strain E122 (MATA) reference genome using Bowtie2 v.2.5.4 with the default options. The output SAM alignment files were converted to BAM format, sorted, and indexed using SAMtools v.1.22.1. Additionally, BAM files were filtered for proper pairs and minimum quality scores of q30; multiple mappings, unmapped queries, and duplicate reads were dropped. BAM coverages were normalized using counts per million mapped reads (CPM) then converted to bigWig (.bw) format to produce illustrated genome coverage tracks.
A total of 75 EdU-seq libraries were prepared across 11 time points (15–210 minutes), with biological and technical replicates ensuring data reproducibility (Supplement Table 1). Fifty high-quality libraries were selected for downstream analysis. Temporal replication patterns were consistent across replicates, demonstrating the robustness of the protocol.
Trimmed reads were aligned to the Yarrowia lipolytica strain E122 (MATA) reference genome using Bowtie2 v.2.5.4 with the default options.
SAM alignment files were converted to BAM format, sorted, and indexed using SAMtools v.1.22.1. Additionally, BAM files were filtered for proper pairs and minimum quality scores of q30; multiple mappings, unmapped queries, and duplicate reads were dropped. BAM coverages were normalized using counts per million mapped reads (CPM) then converted to bigWig (.bw) format to produce illustrated genome coverage tracks.
For peak calling, we employed MACS3 v3.0.1 on BAM files for each EdU+HU timepoint up to 180 minutes using a q-value filter of 0.05 (0.01 for the 30-minute timepoint) and a minimum length of 400 bp, with a maximum gap of 1800 bp and optimization of background calculation parameters (--slocal 500 –llocal 30000) to prevent duplicate peak calling or peaks called due to the noisiness of the BAM files at later time points (--slocal and llocal parameter optimization was done with the assistance of Claude Science). Reproducible and consistent calls across time points were then aggregated, with the median peak summit used for anchoring. From there, BAM files for early (30, 45, 60 min), medium (60, 75, 90 min), and late (90, 120, 180 min) time points were normalized, pooled, and underwent a round of peak calling (max gap reduced to 1250 bp). This allowed for stricter quality control for the calling of additional late origins that did not reach the signal threshold in individual timepoints, adjusting the position of the anchors with pooled early and medium peak calls when the signal amplitude was stronger in pooled peaks than in the anchor, the splitting of nearby peaks that converged in later timepoints, and for manual review of anchors that were not called in any pooled segment. The final peak set was then centered on the summit of each peak. The final peak set was annotated using annotatePeaks.pl from HOMER v5.1 (http://homer.ucsd.edu/homer), which also provides the annotation class (Promoter-TSS/TTS/Gene/Intergenic) enrichment analysis.
Assembly: Y. lipolytica strain E122
Supplementary files format and content: Genome coverage tracks in Bigwig format

organism: Yarrowia lipolytica

growth_protocol: To synchronize cells in G0/G1, YlB0002 was grown in YPD for 72 hours when they reached stationary phase and then diluted 1:10 into fresh medium to re-enter the cell cycle. EdU (500 µM for sequencing, 100 µM for imaging) (Thermo Fisher, E10187) and HU (5 mM) (Sigma, H8627) were added as needed. Samples were collected at multiple time points for EdU imaging, flow cytometry, and sequencing.

extract_protocol:
To identify early- and late-firing origins, stationary phase cells were transferred into fresh YPD containing either EdU+HU or EdU alone. A mock (no EdU) control was included. At each time point, replication was halted with sodium azide (0.1%), and cells were collected for flow cytometry and DNA extraction. DNA was purified using a Qiagen Genomic-tip after Zymolyase-20T (Sunrise Science Products, N0766391) digestion and lysis. Purified genomic DNA was fragmented using the Bioruptor Pico and checked on a Bioanalyzer (100–550 bp fragments).
Biotinylated DNA was ligated to adapters and PCR-amplified using the Illumina TruSeq kit. The resulting libraries were sequenced to profile replication timing at high resolution.

treatment_protocol: To track DNA replication dynamics, Y. lipolytica cells were synchronized in G0/G1 by 72-hour culture in YPD. Cells were then released into fresh YPD containing 500 µM EdU (± 5 mM HU), and samples were collected over a 210-minute time course. Flow cytometry confirmed synchronization.

value: MATA, leu2-270, ura3-302, xpr2-322, axp1-2,Int1::HSVTK,hENT1

value: without hydroxyurea for 60 minutes


title: Y. lipolytica strain E122-EdU labeling with hydroxyurea for 90 minutes #2

description: Library name: S08_S8

value: with hydroxyurea for 90 minutes


title: Y. lipolytica strain E122-EdU labeling without hydroxyurea for 45 minutes #2

description: Library name: 2818_S06_S6

value: without hydroxyurea for 45 minutes


title: Y. lipolytica strain E122-EdU labeling with hydroxyurea for 210 minutes #1

description: Library name: S12_S12

value: with hydroxyurea for 210 minutes


title: Y. lipolytica strain E122-EdU labeling with hydroxyurea for 60 minutes #2

description: Library name: 2770_S04_S4

value: with hydroxyurea for 60 minutes


title: Y. lipolytica strain E122-EdU labeling with hydroxyurea for 30 minutes #1

description: Library name: 9-30min-eh5_S3

value: with hydroxyurea for 30 minutes


title: Y. lipolytica strain E122-EdU labeling without hydroxyurea for 45 minutes #1

description: Library name: 45min_S5


title: Y. lipolytica strain E122-EdU labeling with hydroxyurea for 180 minutes #1

description: Library name: S11_S11

value: with hydroxyurea for 180 minutes


title: Y. lipolytica strain E122-EdU labeling with hydroxyurea for 75 minutes #1

description: Library name: S09_S9

value: with hydroxyurea for 75 minutes


title: Y. lipolytica strain E122-EdU labeling with hydroxyurea for 45 minutes #3

description: Library name: NZ2770_S07_S7

value: with hydroxyurea for 45 minutes


title: Y. lipolytica strain E122-EdU labeling without hydroxyurea for 60 minutes #1

description: Library name: S04_S4


title: Y. lipolytica strain E122-EdU labeling with hydroxyurea for 45 minutes #2

description: Library name: 72-45-eh-5_S3


title: Y. lipolytica strain E122-EdU labeling with hydroxyurea for 120 minutes #1

description: Library name: S14_S14

value: with hydroxyurea for 120 minutes


title: Y. lipolytica strain E122-EdU labeling with hydroxyurea for 90 minutes #1

description: Library name: S07_S7


title: Y. lipolytica strain E122-EdU labeling with hydroxyurea for 45 minutes #1

description: Library name: S03_S3


title: Y. lipolytica strain E122-EdU labeling without hydroxyurea for 30 minutes #1

description: Library name: 30min_S4

value: without hydroxyurea for 30 minutes


title: Benign_97_1

status: Public on May 26 2026

city: Turku

first: Matti

last: Poutanen

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

description:
Library name: 97_1
1

data_processing:
The reads were base-called using Illumina Bcl2fastq version 1.8.4 base-calling software.
The reads were aligned against the human hg19 reference genome using STAR version 2.4.2a.
Then, reads were assigned to known genes, and the number of reads per gene was counted using the subreads package
Assembly: Illumina iGenome hg19
Supplementary files format and content: Text file containing genewise raw read counts
Supplementary files format and content: csv file containing the anonymized clinical data of the patients

source_name: prostate

extract_protocol:
RNA-sequencing was carried out on fresh-frozen samples, alongside validation samples containing at least 50% Gleason score (GS) ≥6 carcinoma (malignant sample) or morphologically benign prostatic tissue (benign control sample) from the same patient. Samples were homogenized using an Ultra Turrax homogenizer, and total RNA was extracted using NucleoSpin® RNA kit and NucleoSpin® RNA/DNA buffer set (Macherey-Nagel, Düren, Germany). Proper RNA quality was detected using a Fragment Analyzer™ (Advanced Analytical Technologies, Ankeny, IA).
The samples were prepared for sequencing using the Illumina TruSeq Stranded mRNA Sample Preparation Kit and sequenced on the HiSeq 3000 instrument with paired-end chemistry and 100 bp read length.

value: prostate

tag: group

value: Benign

tag: biochemical recurrance

value: Yes

tag: ggg

tag: pn

value: Unknown


title: Cancer_95_2

description:
Library name: 95_2
2

tag: tissue

value: Cancer

value: No


title: Benign_95_1

description:
Library name: 95_1
1


title: Cancer_87_2

description:
Library name: 87_2
2


title: Cancer_82_4

description:
Library name: 82_4
4


title: Cancer_59_1

description:
Library name: 59_1
1


title: Benign_56_1

description:
Library name: 56_1
1


title: Cancer_40_1

description:
Library name: 40_1
1


title: Benign_50_2

description:
Library name: 50_2
2


title: Cancer_97_2

description:
Library name: 97_2
2


title: Benign_55_2

description:
Library name: 55_2
2


title: Benign_40_2

description:
Library name: 40_2
2


title: Cancer_35_2

description:
Library name: 35_2
2


title: Benign_82_3

description:
Library name: 82_3
3


title: Cancer_50_1

description:
Library name: 50_1
1


title: Cancer_55_1

description:
Library name: 55_1
1


title: Cancer_34_2

description:
Library name: 34_2
2


title: Benign_87_1

description:
Library name: 87_1
1


title: Cancer_258_2

description:
Library name: 258_2
2


title: Benign_59_2

description:
Library name: 59_2
2


title: Benign_34_1

description:
Library name: 34_1
1


title: Benign_35_1

description:
Library name: 35_1
1


title: Cancer_56_2

description:
Library name: 56_2
2


title: A549 cells, EV, rep3

city: Beijing

first: Chu

last: Xiao

state: Beijing

address: Nanli panjiayuan, Chaoyang District, Beijing

department: Thoracic Surgery

institute: Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

description:
Library name: Control A549 cells of OE, rep3
column name in raw_counts_RAD21OE_EV_samples.xls: A549_Ctrl_3

data_processing:
Raw data of fastq format was processed by fastp to remove low quality reads and adaptor reads. The clean data was mapped to the hg38 reference genome by HISAT2 (v2.0.5). Then the read counts of genes were obtained by featureCounts (v1.5.0-p3).
Assembly: hg38
Supplementary files format and content: xls files include raw count values for each sample

growth_protocol: A549 and H358 lung adenocarcinoma cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 ℃.

extract_protocol:
The total RNA of cells was extracted with TRIzol regent (Invitrogen) and the qualities of RNA were evaluated with Qubit3.0 and Agilent 2100 bioanalyzer.
RNA libraries for RNA-seq were constructed using a VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme) following manufacturer's protocols.

tag: cell type

value: lung adenocarcinoma cells

value: wild type


title: Benign_237_2

description:
Library name: 237_2
2


title: P. promelas larvae, MHW, biological replicate MHW_B1, lane 1, time step = NA, analyzed on 20160804

city: Durham

first: Steven

middle: Thomas

last: Purucker

state: NC

address: 109 TW Alexander Dr

institute: US EPA

description: Library name: 20160804_ 15-08_B1_ACTGAT_L001_R1_001

data_processing:
Raw read quality assessment with FastQC 0.11.9 & MultiQC 1.12
Reads were processed with fastp 0.23.2 trimming with quality, length, and adapter trimming all enabled by default, and polyX trimming (flag: -x) enabled manually
Alignment with STAR 2.7.10a (--outSAMattributes NH HI AS NM MD --outSAMtype BAM SortedByCoordinate --outSAMheaderHD @HD VN 1.4 SO:sorted --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outSAMunmapped Within --outFilterType BySJout)
Quantification with STAR 2.7.10a (--quantMode GeneCounts TranscriptomeSAM)
Assembly: P. promelas, GCF_016745375.1_EPA_FHM_2.0
Supplementary files format and content: Tab delimited text file with gene counts: all_counts_20220629.txt uploaded separately.

organism: Pimephales promelas

source_name: whole larvae

growth_protocol: Lab-reared individual fathead minnow larvae (Pimephales promelas) 2 days post-fertilization.

extract_protocol:
Total RNA was isolated from individual FHM using the MagMAX-96 Total RNA Isolation Kit (ThermoFisher Scientific) following manufacturer's protocols. RNA was quantified by spectrophotometric analysis with a Synergy HTX multi-mode plate reader (BioTek).
Neoprep Library Prep System (Illumina) and the TruSeq Stranded mRNA Library Prep for NeoPrep (Illumina). Library concentrations were determined using either the KAPA Library Quantification Kit (Kapa Biosystems) or Qubit dsDNA HS Assay (ThermoFisher Scientific), normalized to equimolar amounts, and then combined into pools of eight samples each. Sequencing was performed at Michigan State University’s RTSF Genomics Core on the Illumina HiSeq 2500 Rapid Run flow cell (v2) for 1x50 bp single-end reads with Rapid SBS reagents.

treatment_protocol: 48 hour lab exposures to moderately hard reconstituted water or river water grab samples collected in August 15 for 6 locations in the vicinity of a wastewater treatment plant (WWTP): upstream of WWTP, WWTP effluent discharging point, proximal location downstream WWTP outfall, distal location downstream of WWTP outfall, a downstream drinking water intake, and treated drinking water collected prior to discharge to the distribution system. Other exposures included 48 hour field fish deployments in exposure vessels secured to a minnow trap at 2 locations (upstream of a WWTP, WWTP effluent discharging point).

value: whole larvae

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

tag: treatment-location

value: MHW


title: Benign_258_1

description:
Library name: 258_1
1


title: liver/anterior intestine/gill, Day 0, 12 ppt, rep c

city: Fort Pierce

first: David

last: Bradshaw

state: FL

department: Aquaculture & Stock Enhancement

institute: Florida Atlantic University at Harbor Branch Oceanographic Institute

data_processing:
Qiagen CLC Genomics Step - The resulting paired-end reads were processed through Qiagen’s CLC Genomics Workbench for adapter trimming and elimination of low-quality reads (Qiagen, 2021). The filtered reads were then merged and mapped to a reference genome of a related species, the greater amberjack (Seriola dumerili; RefSeq: GCF_002206705.1), with > 75% mapping success. Gene expression values were calculated as transcripts per million (TPM) and identification of differentially expressed genes (DEGs) were conducted in the CLC Genomics Workbench.  DEGs were defined as biologically significant with an absolute fold change ≥2 and statistically significant with an FDR p-value ≤0.05 when compared to expression under control conditions (Day 0 or 28 ppt).
R Data Processing and Statistical Analysis -  Abundance tables and DEGs from CLC Genomics were uploaded into RStudio. Gene and transcript counts were variance stabilizing transformed for beta diversity analysis. These tables were converted into a Bray-Curtis dissimilarity matrix which was analyzed with principal coordinates of analysis (PCoA) and permutational analysis of variance (PERMANOVA). PRIMER7/PERMANOVA+ was used to conduct PERMANOVA analysis with Monte Carlo (MC) p-value. In order to discover general functional trends, DEGs underwent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses via clusterProfiler.
Assembly: Seriola dumerili; RefSeq: GCF_002206705.1
Supplementary files format and content: VST_TX_Table.csv is the DESeq2 variance stabilizing transformed counts for transcripts
Supplementary files format and content: VST_GN_Table.csv is the DESeq2 variance stabilizing transformed counts for genes

organism: Trachinotus carolinus

source_name: Florida pompano

growth_protocol: Prior to initiation of the experiment, a total of 300 juvenile pompano (~5g) were transferred from their larviculture facility (Proaquatix, Vero Beach, FL) to a recirculating aquaculture system (RAS) tanks at 28 ppt at FAU-HBOI facilities. Salinity treatments included marine control (28 ppt), estuarine (20 ppt), isosmotic (12 ppt), and hypoosmotic (8 ppt) treatments. Each treatment was run in triplicate (n= 3, total 12 tanks) in a 300 L RAS tanks. In each tank, 25 fish were stocked to replicate production stocking densities. In order to avoid undue stress on the fish, salinities in the estuarine, isosmotic, and hypoosmotic tanks were lowered from marine (28 ppt) to their target salinities over the course of 4 days at the rate of -2 ppt, -4 ppt, and -5 ppt per day in estuarine, isosmotic, and hypoosmotic tanks, respectively. During this time, the 28 ppt marine control tanks underwent partial water changes to mimic water exchanges occurring in the estuarine, isosmotic, and hypoosmotic tanks. Target salinities were achieved and maintained through a combination of treated marine water and dechlorinated freshwater. Fish were fed commercially available fish pellets (provided by Proaquatix) at a rate of approximately 2% body weight per day.

extract_protocol:
In order to ensure sufficient RNA yields for transcriptomic analysis, the liver, anterior intestine, and gill lamellae (removed from three gill arches on the left side of the fish) were dissected and pooled in 1 mL cryovials, then flash frozen at -80oC. All samples were stored at -80oC until RNA extraction. RNA extractions were conducted on pooled gill lamellae, immune organs, and liver samples using Qiagen RNeasy kits (Qiagen, Hilden, Germany) according to manufacturer protocols. RNA quality and concentrations were determined using a Qubit Fluorometer 3 (Thermo Fisher Scientific, Waltham, MA) and a ThermoFisher NanoDrop Spectrophotometer 2000 (Thermo Fisher Scientific Inc., Waltham, MA). Extracted RNA for transcriptomics was flash frozen and shipped overnight on dry ice to Novogene (Sacramento, CA) for high throughput RNA sequencing.
Total RNA was used to create 21 poly-A enriched libraries that were then sequenced on an Illumina NovaSeq to generate 2 x 150 bp paired-ends sequencing reads.

treatment_protocol: In order to avoid undue stress on the fish, salinities in the estuarine, isosmotic, and hypoosmotic tanks were lowered from marine (28 ppt) to their target salinities over the course of 4 days at the rate of -2 ppt, -4 ppt, and -5 ppt per day in estuarine (20 ppt), isosmotic (12 ppt), and hypoosmotic (8 ppt) tanks, respectively. During this time, the 28 ppt marine control tanks underwent partial water changes to mimic water exchanges occurring in the estuarine, isosmotic, and hypoosmotic tanks. Target salinities were achieved and maintained through a combination of treated marine water and dechlorinated freshwater.

value: liver/anterior intestine/gill

tag: treatment

value: Day 0, 12 ppt


title: LDH mutant, molasses + yeast, repl LM2

city: Bloomington

first: Jason

middle: M

last: Tennessen

email: tennessenlab@gmail.com, tennlab@iu.edu, jtenness@iu.edu, tourigny@iu.edu

state: IN

address: 1001 E 3rd St

institute: Indiana University

description:
Library name: GSF3528-MR08-mut-molasses-repl-LM2
GSF3528_MR08_mut_molasses_repl_LM2

data_processing:
Quantification via Salmon pseudoaligner
Normalization and differential expression via DESeq2
Assembly: BDGP6.32
Supplementary files format and content: tab-separated, transformed log counts from DESeq2

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: whole animal

growth_protocol: Control (Impl317/+) and Ldh (Impl317/16) mutant eggs were collected on M+Y food. After 40-44hrs, 50 larvae were transferred to each M+Y food plate and BDSC-F Cubes plate, kept at 25ºC.

extract_protocol:
Three biological replicates containing 25 mid-L2 (~60 hours AEL after egg-laying) larvae were collected from both plates and washed twice with ice-cold 1X PBS. Total RNA was extracted from homogenized samples using a RNeasy kit (Qiagen; 74104).
Illumina TruSeq Stranded mRNA Library Kit

value: whole animal

tag: genotype

value: LDH mutant (Impl3 17/16)

value: molasses + yeast

tag: replicate


title: LDH mutant, molasses + yeast, repl LM1

description:
Library name: GSF3528-MR07-mut-molasses-repl-LM1
GSF3528_MR07_mut_molasses_repl_LM1


title: Cancer_237_1

description:
Library name: 237_1
1


title: Cancer_235_2

description:
Library name: 235_2
2


title: Benign_235_1

description:
Library name: 235_1
1


title: Cancer_210_2

description:
Library name: 210_2
2


title: Cancer_209_1

description:
Library name: 209_1
1


title: Benign_194_1

description:
Library name: 194_1
1


title: Cancer_194_2

description:
Library name: 194_2
2


title: Cancer_178_3

description:
Library name: 178_3
3


title: Cancer_180_1

description:
Library name: 180_1
1


title: Benign_180_2

description:
Library name: 180_2
2


title: Benign_178_2

description:
Library name: 178_2
2


title: Cancer_174_2

description:
Library name: 174_2
2


title: Benign_209_2

description:
Library name: 209_2
2


title: Benign_174_1

description:
Library name: 174_1
1


title: Cancer_158_2

description:
Library name: 158_2
2


title: Benign_171_2

description:
Library name: 171_2
2


title: Cancer_171_1

description:
Library name: 171_1
1


title: Benign_210_1

description:
Library name: 210_1
1


title: Benign_158_1

description:
Library name: 158_1
1


title: Benign_154_2

description:
Library name: 154_2
2


title: Cancer_154_1

description:
Library name: 154_1
1


title: Cancer_152_4

description:
Library name: 152_4
4


title: Cancer_151_4

description:
Library name: 151_4
4


title: Benign_152_3

description:
Library name: 152_3
3


title: Benign_151_3

description:
Library name: 151_3
3


title: Cancer_137_1

description:
Library name: 137_1
1


title: Benign_138_1

description:
Library name: 138_1
1


title: Benign_137_2

description:
Library name: 137_2
2


title: Benign_136_2

description:
Library name: 136_2
2


title: Benign_126_2

description:
Library name: 126_2
2


title: Cancer_116_2

description:
Library name: 116_2
2


title: Benign_125_1

description:
Library name: 125_1
1


title: Benign_114_2

description:
Library name: 114_2
2


title: Cancer_114_1

description:
Library name: 114_1
1


title: Cancer_125_2

description:
Library name: 125_2
2


title: Cancer_126_1

description:
Library name: 126_1
1


title: Benign_0294_1

description:
Library name: 0294_1
1


title: Cancer_0294_2

description:
Library name: 0294_2
2


title: Cancer_104_1

description:
Library name: 104_1
1


title: Cancer_0274_1

description:
Library name: 0274_1
1


title: Benign_0274_2

description:
Library name: 0274_2
2


title: Cancer_0275_2

description:
Library name: 0275_2
2


title: Cancer_0272_1

description:
Library name: 0272_1
1


title: Benign_0266_1

description:
Library name: 0266_1
1


title: Cancer_0263_2

description:
Library name: 0263_2
2


title: Benign_0259_2

description:
Library name: 0259_2
2


title: Cancer_0259_1

description:
Library name: 0259_1
1


title: Benign_0263_1

description:
Library name: 0263_1
1


title: Cancer_0266_2

description:
Library name: 0266_2
2