title: AMB_200630_9mo_2A_3A_1_P1-2-H14-J16


title: ZD_liver_input-2

status: Public on Dec 29 2025

type: SRA

city: Tokyo

first: Takao

last: Fujisawa

address: 7-3-1, Hongo, Bunkyo-ku

country: Japan

institute: The University of Tokyo

description: Library name: sample8

library_source: genomic

data_processing:
Sequence reads were trimmed for adaptor sequence/lowquality sequence using trim-galore (parameters: default, version 0.6.7).
Raw paired-end 150 bp reads were aligned to the reference genome (mm10) using HISAT2 (version 2.2.1).
Bigwig files were generated using deeptools(version 3.5.1)
Assembly: mm10
Supplementary files format and content: Bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: liver

extract_protocol:
Cells were fixed with 4% formaldehyde. Chromatin samples were prepared using a SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology, 9003).
DNA libraries for ChIP-seq were prepared using NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB, E6420) and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs Set 2) (NEB, E6446S).

tag: tissue

value: liver

tag: treatment

value: Zinc-deficient diet for two weeks


title: ZD_liver_input-1

description: Library name: sample7


title: RNA_Nodule_7wpi_3

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

country: USA

institute: University of California - Davis

description: Library name: 45

library_source: transcriptomic

data_processing:
We sent all sRNA and RNAseq libraries for sequencing to the University of Delaware Sequencing and Genotyping Center, where they were sequenced on a NovaSeq2000 instrument using 50-bp single-end reads for sRNA and 75-bp paired-end reads for RNAseq.
For sRNA libraries we first trimmed the adaptors using Cutadapt version 1.16 using a minimum insert size of 10 nt and no maximum. We assessed sequence quality using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/ fastqc/). We aligned clean reads to the Soybean W82 genome v4 and all subsequent analyses were performed using the software Bowtie2. For miRNA analyses, we used the latest version of miRBase (version 22).
For RNA-seq libraries were analyzed using HiSat2 and Stringtie pipeline, and the Soybean W82 genome v4 annotation file.
Assembly: Soybean W82 genome v4
Supplementary files format and content: small RNA seq.: microRNA count files
Supplementary files format and content: RNAseq.: gtf count files

molecule: total RNA

organism: Glycine max

source_name: Nodule

growth_protocol: All plants were cultivated in pots within the greenhouse facilities at the Donald Danforth Plant Science Center (St. Louis, Missouri, USA). They were subjected to a 14/10 hour light/dark cycle and maintained at temperatures of 25/20°C, respectively. Soybean seeds (Glycine max cv. Williams-82) were sown into 1-gallon pots (two seeds per pot) containing a pre-rinsed substrate, consisting of a three to one ratio of vermiculite:perlite (3:1). Plants were well-watered and fertilized regularly via Dosatron with reverse osmosis water and B&D nutrient solution for growing legumes (with the addition of minimal nitrogen - 0.5mM KNO3) (Broughton and Dilworth 1971). The lesser of the two plantlets was sacrificed following the seven-day germination period. Seven-day-old seedlings were then inoculated with 5ml of Bradyrhizobium diazoefficiens USDA110 diluted to 0.05 OD600nm. B. diazoefficiens USDA110 (USDA-ARS culture collection, NRRL B-4361) was grown aerobically at 28°C in HM liquid medium at 6.8 pH prior to inoculation (Tóth et al. 2016). Soybean (Glycine max cv. Williams-82) seed stocks used in this research were generated from seeds gifted by Doug Allen of the Donald Danforth Plant Science Center (St. Louis, Missouri, USA). Bradyrhizobium diazoefficiens USDA110 strain gifted by Gary Stacey of the University of Missouri – Columbia (Columbia, Missouri, USA)

extract_protocol:
Frozen nodules were manually ground using pre-chilled (liquid N2) mortar and pestles. Ground tissue was further pulverized using a MM400 tissuelyzer (Retsch, Germany): 2x 45 sec at 30 Hz. Total nodule RNA was extracted using TRIreagent (Ambion, USA), following manufacturer’s instructions plus additional isopropanol rinse to remove the remaining polysaccharides (Protocol 1: Soybean Nodule RNA Extraction).
sRNA libraries were constructed using the RealSeq-AC kit version 2 (Realseq Biosciences, Santa Cruz, CA, catalog no. 500-00048;) as per the manufacturer’s instructions. For RNAseq libraries, we used NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, catalog no. E7760L) protocol.

treatment_protocol: Soybean root nodules, aged 2 wpi to 10 wpi, were harvested weekly, typically between 9 and 10 am. Nodules were carefully collected in 2ml screw cap tubes, immersed in liquid nitrogen, and promptly stored at -80oC. Each technical replicate (TR) comprised of three nodules in close proximity to the root crown of a single plant. One biological replicate (BR) corresponded to one plant. For each BR, we collected four TRs to facilitate RNA and protein extractions.

value: Nodule

tag: weeks post_inoculation

tag: genotype

value: Williams 82

value: Inoculated with Bdi USDA110


title: ZD_liver_H3K14ac-2

description: Library name: sample6


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-J15

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq3
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
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. 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

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: age

value: 9 months

tag: brain region

value: FC

tag: gender

value: M


title: ND_liver_input-2

description: Library name: sample4

value: Normal diet for two weeks


title: RNA_Nodule_7wpi_2

description: Library name: 44


title: RNA_Nodule_7wpi_1

description: Library name: 43


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-I4


title: ND_liver_H3K14ac-2

description: Library name: sample2


title: ZD_H3K14ac-1

description: Library name: sample5

data_processing:
Sequence reads were trimmed for adaptor sequence/lowquality sequence using trim-galore (parameters: default, version 0.6.7).
Raw paired-end 150 bp reads were aligned to the reference genome (hg38  or mm10) using HISAT2 (version 2.2.1).
Bigwig files were generated using deeptools(version 3.5.1)
Assembly: hg38
Supplementary files format and content: Bigwig

organism: Homo sapiens

source_name: HeLa

extract_protocol:
Cells were fixed with 4% formaldehyde. Chromatin samples were prepared using a SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology, 9003).
DNS libraries for ChIP-seq were prepared using NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB, E6420) and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs Set 2) (NEB, E6446S).

tag: cell type

value: HeLa

value: Zinc-deficeint medium for 48 hours


title: ND_liver_H3K14ac-1

description: Library name: sample1


title: ZD-3

description: Library name: sample6

data_processing:
Sequence reads were trimmed for adaptor sequence/lowquality sequence using trim-galore (parameters: default, version 0.6.7).
Raw paired-end 150 bp reads were aligned to the reference genome (mm10) using HISAT2 (version 2.2.1).
The number of mapped reads to each gene was determined by featureCounts (version 2.0.6).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample.

extract_protocol:
RNA was harvested using ISOGEN (Wako). 20 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB, E6420) and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs Set 2) (NEB, E6446S).


title: RNA_Nodule_6wpi_3

description: Library name: 42


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-I3


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-I16


title: ZD-2

description: Library name: sample5


title: ZD-1

description: Library name: sample4


title: ND-3

description: Library name: sample3


title: RNA_Nodule_6wpi_2

description: Library name: 41


title: ND-2

description: Library name: sample2


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-I15


title: RNA_Nodule_6wpi_1

description: Library name: 40


title: ND-1

description: Library name: sample1


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-H4


title: RNA_Nodule_5wpi_3

description: Library name: 39


title: ZD_liver_H3K14ac-1

description: Library name: sample5


title: RNA_Nodule_5wpi_2

description: Library name: 38


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-H3


title: ND_liver_input-1

description: Library name: sample3


title: sc_dox free_human-3

city: Dallas

first: Leijie

last: Li

state: Texas

address: 5323 Harry Hines Blvd.

department: Molecular Biology

institute: UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER

description: Library name: h5_3

data_processing:
Trim Galore (Version 0.6.10) was utilized for quality control with quality score higher than Q30 and length larger than 20pb. Hisat2 (Version 2.1.0) and StringTie (Version 2.1.7) were used for sequence BLAST, assembly, and quantification. The GRCh38 and GRCm39 were downloaded from Ensembl database as the reference genomes for human and mouse, respectively. DESeq2 (Version 1.38.3) was applied to normalize gene expression in order to reduce the influence of batch effects and outlier genes in downstream analyses.
Assembly: GRCh38 and GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Primed H9

growth_protocol: Mouse EpiSCs derived from the C57BL/6 strain (B6 mEpiSCs) were cultured in NBFR medium atop a MEF feeder layer. Primed H9 human ESCs were maintained in mTeSR Plus medium on Matrigel-coated dishes during routine passaging and transfection, with 10 mM ROCKi for 24 hours after each passage.Cultured cells were treated with TrypLE for 3 minutes at 37℃ to detach them from the plate, then counted using a hemocytometer and passage into new plates at different dilution ratios depending on the cell line.

extract_protocol:
PSCs from different species were seeded onto MEF-coated plates either cultured separately or mixed at different ratios for co-cultures in NBFR medium. The seeding ratio and density were empirically tested and decided based on cell growth rate. For 4-days-co-culture assays between human-mouse, cells were seeded at a 4:1 ratio at a density of 1.25 × 10-4 cells cm−2. At each of the indicated time points, cell concentration was manually counted and calculated, and the percentages of each cell line were determined using FACS Calibur system (BD Bioscience). Total cell numbers (tN) for each species in co-cultures or separate cultures were determined by multiplying total cell volume (V) with cell concentration (CC) and percentage (P). tN = V × CC × P. Cell density (cells cm−2) was calculated by dividing the total cell number by the surface area.
by Novogene

tag: cell line

value: Primed H9


title: sc_dox free_human-2

description: Library name: h5_2


title: sc_dox free_human-1

description: Library name: h5_1


title: cc_dox free_human-2

description: Library name: h3_2


title: RNA_Nodule_5wpi_1

description: Library name: 37


title: cc_dox free_human-3

description: Library name: h3_3


title: cc_dox free_human-1

description: Library name: h3_1


title: cc_dox_human-2

description: Library name: h1_2


title: cc_dox_human-3

description: Library name: h1_3


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-H15


title: RNA_Nodule_4wpi_3

description: Library name: 36


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-G4


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-G3


title: cc_dox_human-1

description: Library name: h1_1


title: 5579

city: Asheville

first: Melissa

middle: Marie

last: Heintz

state: NC

address: 31 College Place, Suite B118

institute: ToxStrategies

data_processing:
Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing
fastqs were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches
Assembly: probe-based targeted sequencing
Supplementary files format and content: comma-separated text files include raw count values for each gene_probe

extract_protocol:
Mounted, unstained FFPE liver sections from HFPO-DA-exposed male and female mice (n = 4-5 per dose group per sex, total of 92 samples) were scraped from the slides and processed according to the TempO-Seq® protocol by BioSpyder Technologies
TempO-Seq® protocol by BioSpyder Technologies

treatment_protocol: Mice were administered 0, 0.05, 0.1, 0.5 or 5 mg/kg HFPO-DA by oral gavage once daily for a total of 9 or 18 months. Following the last treatment, mice were euthanized by CO2 anesthesia and exsanguination. Livers were fixed in 10% neutral-buffered formalin, embedded in paraffin (FFPE), and sections approximately 4 – 6 µm in thickness were mounted to glass slides.

tag: strain

tag: Sex

value: female

value: WT

tag: exposure duration

value: 18 months

value: 5 mg/kg HFPO-DA


title: RNA_Nodule_4wpi_1

description: Library name: 34


title: RNA_Nodule_4wpi_2

description: Library name: 35


title: 5572


title: 5573


title: 5571


title: 5567


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-G15


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-H16


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-G16


title: RNA_Nodule_3wpi_2

description: Library name: 32


title: 5543


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-F3


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-F4


title: 5541


title: 5551


title: 5542


title: RNA_Nodule_2wpi_3

description: Library name: 30


title: 5067

value: male


title: RNA_Nodule_3wpi_1

description: Library name: 31


title: 5045

value: liver


title: 5063


title: 5047


title: 5043


title: 5066


title: RNA_Nodule_2wpi_1

description: Library name: 28


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-E4


title: RNA_Nodule_3wpi_3

description: Library name: 33


title: 5042


title: sRNA_Nodule_10wpi_3

description: Library name: 27


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-F15


title: 5544


title: 5041


title: sRNA_Nodule_10wpi_2

description: Library name: 26


title: 4577

value: 0.5 mg/kg HFPO-DA


title: 4572


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-E16


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-E3


title: sRNA_Nodule_10wpi_1

description: Library name: 25

value: Nodule


title: 4561


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-D3


title: 4543


title: sRNA_Nodule_9wpi_1

description: Library name: 22

value: Williams 82


title: 4542


title: tx CD8+ OT-I T cells after crosspresentation by BMDCs, sample 08

city: Berlin

first: Benjamin

middle: N

last: Ostendorf

address: Augustenburger Platz 1

country: Germany

institute: Charité University Medicine

data_processing:
Adapter and polyA trimming with BBDuk (v38.9; options k=13, ktrim=r, forcetrimleft=11, useshortkmers=t, mink=5, qtrim=t, trimq=10, minlength=20)
Alignment and read counting with STAR aligner (v2.7.8a; default settings apart from --outFilterMismatchNoverLmax 0.1)
Library size normalization in R v4.1.0 with DESeq2 v1.4
Assembly: GRCm38
Supplementary files format and content: TSV-formatted table with raw gene counts for every gene and every sample

source_name: CD8+ OT-I cells

growth_protocol: CD8+ OT-I T cells were co-cultured with SIINFEKL-pulsed BMDCs in the presence of DMSO (ctrl) or 2µM RGX-104.

extract_protocol:
CD8+ OT-I T cells were purified by FACS and RNA was isolated using the Norgen total RNA isolation kit.
Lexogen 3' FWD kit

treatment_protocol: DMSO versus 2µM RGX-104.

value: CD8+ OT-I cells

value: OT-I


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-D15

value: 9 months

value: FC


title: 4068


title: tx CD8+ OT-I T cells after crosspresentation by BMDCs, sample 06


title: 4566


title: 4065


title: sRNA_Nodule_8wpi_1

description: Library name: 19

value: Inoculated with Bdi USDA110


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-C3

value: M


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-F16


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-E15


title: tx CD8+ OT-I T cells after crosspresentation by BMDCs, sample 05


title: 4544


title: 4563


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-D4


title: 4546


title: sRNA_Nodule_9wpi_2

description: Library name: 23


title: RNA_Nodule_2wpi_2

description: Library name: 29


title: 4064


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-D16


title: 4545


title: tx CD8+ OT-I T cells after crosspresentation by BMDCs, sample 07


title: sRNA_Nodule_8wpi_2

description: Library name: 20


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-C4


title: sRNA_Nodule_9wpi_3

description: Library name: 24


title: sRNA_Nodule_7wpi_3

description: Library name: 18


title: sRNA_Nodule_8wpi_3

description: Library name: 21


title: ctrl CD8+ OT-I T cells after crosspresentation by BMDCs, sample 03

value: control


title: 4062


title: ctrl CD8+ OT-I T cells after crosspresentation by BMDCs, sample 04


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-C15


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-B4


title: sRNA_Nodule_6wpi_3

description: Library name: 15


title: sRNA_Nodule_7wpi_1

description: Library name: 16


title: 4063


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-C16


title: sRNA_Nodule_7wpi_2

description: Library name: 17


title: ctrl CD8+ OT-I T cells after crosspresentation by BMDCs, sample 02


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-B3


title: ctrl CD8+ OT-I T cells after crosspresentation by BMDCs, sample 01


title: 4044


title: sRNA_Nodule_6wpi_2

description: Library name: 14


title: 4043


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-B15


title: 4048


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-B16


title: sRNA_Nodule_5wpi_3

description: Library name: 12


title: ATAC-seq of OT-I CD8+ T cells, sample 02

data_processing:
Adapter trimming with Cutadapt PE (v2.10) using `-g AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT`
Reference alignment with BWA (v0.7.17) at default settings.
Removal of PCR duplicates with Picard (v2.22.1)
Filtering of unstructured genomic regions as previously defined (Amemiya et al., Sci Rep, 2019) with the `intersect` function from bedtools (2.3)
Filtering of unmapped, low quality and duplicated reads using the `view` function form samtools (v1.10) with the settings ` -b -h -q 30 -F 0x004 -F 0x0400 -G 0x009 -f 0x001`
Generation of bigwig files usinge `bamCoverage` from Deeptools (v3.5.1) with the settings `--binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 –extendReads`
Generation of NarrowPeaks and bed files using Genrich (v0.6.1) with the parameters `-vjr -m 30`
Differential peak analysis using Diffbind (v3.10).
Assembly: GRCm38
Supplementary files format and content: A DBA object generated by Diffbind containing called peaks from control and treatment samples. Can be read into R and further processed using Diffbind.

source_name: OT-I CD8+ T cells

extract_protocol:
CD8+ OT-I T cells were purified by FACS and 60,000 cells were lysed before subjecting to transposase treatment and amplification.
Cells were lysed before treating with Tn5 transposase and subsequent amplification.

value: OT-I CD8+ T cells


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-A4


title: 4042


title: ATAC-seq of OT-I CD8+ T cells, sample 03


title: sRNA_Nodule_6wpi_1

description: Library name: 13


title: sRNA_Nodule_5wpi_2

description: Library name: 11


title: 4041


title: ATAC-seq of OT-I CD8+ T cells, sample 01


title: sRNA_Nodule_5wpi_1

description: Library name: 10


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-A3


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-A16


title: 3606

value: female

value: 0.1 mg/kg HFPO-DA


title: 3581

value: WT

value: 18 months


title: 3580


title: KO CD11c+, sample 12

data_processing:
Adapter and polyA trimming with BBDuk (v38.9; options k=13, ktrim=r, forcetrimleft=11, useshortkmers=t, mink=5, qtrim=t, trimq=10, minlength=20)
Alignment  with STAR aligner (v2.7.8a; default settings apart from --outFilterMultimapNmax 1)
Read counting with featureCounts (v1.5.1)
Library size normalization in R v4.1.0 with DESeq2 v1.4
Assembly: mm10
Supplementary files format and content: CSV-formatted table with raw gene counts for every gene and every sample

source_name: Lymph node

growth_protocol: E0771-cOC tumors were injected into C57BL6 or APOE-KO mice and tumor-draining lymph nodes were resected on day 9 post injection.

extract_protocol:
Resected lymph nodes were finely minced using scalpels before enzymatic digestion with collagenase I/IV and DNAse I. Cells were then strained and CD11c+ cells were enriched using the CD11c MicroBeads isolation kit (Miltenyi).
Lexogen 3' FWD kit

value: Lymph node

value: APOE-KO


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-A15


title: sRNA_Nodule_4wpi_3

description: Library name: 9


title: KO CD11c+, sample 10


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-P2


title: KO CD11c+, sample 11


title: ATAC-seq of OT-I CD8+ T cells, sample 04


title: 3579

value: liver


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-P14


title: sRNA_Nodule_4wpi_1

description: Library name: 7

value: Nodule


title: sRNA_Nodule_3wpi_3

description: Library name: 6

value: Williams 82


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-P13


title: 3578


title: sRNA_Nodule_3wpi_2

description: Library name: 5


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-P1


title: KO CD11c+, sample 08


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-O2


title: wt CD11c+, sample 06

value: wildtype


title: sRNA_Nodule_4wpi_2

description: Library name: 8


title: KO CD11c+, sample 07


title: 3546


title: 3544


title: sRNA_Nodule_2wpi_3

description: Library name: 3


title: 3543


title: wt CD11c+, sample 04


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-O13


title: sRNA_Nodule_2wpi_1

description: Library name: 1


title: KO CD11c+, sample 09


title: wt CD11c+, sample 05


title: sRNA_Nodule_2wpi_2

description: Library name: 2


title: wt CD11c+, sample 03


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-O1


title: 3542


title: 3545


title: Ovarian endometriotic cyst stromal cells treated without tucidinostat, rep4

city: Yufu-shi

first: Saki

last: Aso

address: 1-1 Hasamamachi Idaigaoka

institute: Oita University

description: Library name: C12_NC

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: hg38
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

source_name: Primary culture

growth_protocol: Endometriotic tissues were obtained from premenopausal patients who had undergone salpingo-oophorectomy or evisceration for ovarian endometriotic cysts (n=4). ECSCs were isolated from ovarian endometriotic tissues by enzymatic digestion with collagenase. Isolated ECSCs were cultured in DMEM supplemented with 100 IU/ml of penicillin, 50 mg/ml of streptomycin, and 10% heat-inactivated fetal bovine serum (FBS) (all obtained from Gibco-BRL) at 37ºC in 5% CO2 in air.

extract_protocol:
The total RNA was extracted with an RNeasy Mini kit (Qiagen, Valencia, CA, USA).
RNA libraries were prepared for sequencing using MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set  according protocols

value: Ovarian endometriotic cyst

value: Female

value: DMSO 10μM, 48h


title: wt CD11c+, sample 02


title: Ovarian endometriotic cyst stromal cells treated without tucidinostat, rep3

description: Library name: C11_NC


title: 3105

value: male


title: sRNA_Nodule_3wpi_1

description: Library name: 4

value: Inoculated with Bdi USDA110


title: 3063


title: Ovarian endometriotic cyst stromal cells treated without tucidinostat, rep2

description: Library name: C10_NC


title: wt CD11c+, sample 01


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-N13

value: 9 months

value: FC

value: M


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-N14


title: siPUM2_3

city: Urumqi City

first: Jie

address: No. 91, Tianchi Road

country: China

institute: People's Hospital of Xinjiang Uygur Autonomous Region

description: Library name: Sample6

data_processing:
Raw reads with more than 2-N bases were discarded, and adaptors and low-quality bases were trimmed using FASTX-Toolkit (Version 0.0.13). Additionally, reads shorter than 16nt were removed.
Clean reads were then aligned to the mRatBN7.2 genome using HISAT2, allowing for 4 mismatches. Uniquely mapped reads were utilized for gene read number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped).
The R Bioconductor package DESeq2 was employed to identify differentially expressed genes (DEGs), with a significance threshold set at a Pvalue < 0.01 and a fold change > 1.5 or < 0.67.
Alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between samples were defined and quantified using the ABLas pipeline as described previously[18]. Ten types of ASEs, including exon skipping (ES), alternative 5' splice site (A5SS), alternative 3' splice site (A3SS), mutually exclusive exons (MXE), mutually exclusive 5'UTRs (5pMXE), mutually exclusive 3'UTRs (3pMXE), cassette exon, A3SS&ES, and A5SS&ES, were detected based on splice junction reads. To assess lncRNA-regulated ASEs, Student’s t-test was applied, and events significant at a p-value cutoff corresponding to a false discovery rate cutoff of 5% were considered lncRNA-regulated ASEs.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes FPKM value for each Sample.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.

organism: Rattus norvegicus

source_name: H9C2 cardiomyocytes

extract_protocol:
Total RNA was extracted using TRIzol Reagent and then treated with RQ1 DNase to remove DNA, followed by assessing its quality and quantity using a smartspec plus spectrophotometer (BioRad) and confirming integrity through 1.5% agarose gel electrophoresis. Each sample underwent mRNA capture using VAHTS mRNA capture Beads (Vazyme, N401), with an additional round of RQ1 DNase treatment.
Directional library preparation with the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (NR605) involved purifying, fragmenting, and converting polyadenylated mRNAs into double-stranded cDNA. This was followed by end repair, A tailing, and adaptor ligation (N323), with subsequent purification and size fractionation (300 - 500bps). Ligated products were then amplified, purified, quantified, and stored at -80℃ prior to sequencing, with strand-specific sequencing achieved by excluding amplification of the dUTP-marked strand. High-throughput sequencing was performed on an Illumina Novaseq 6000 system using 150nt paired-end sequencing, as per the manufacturer's instructions.

value: H9C2 cardiomyocytes

value: Inhibition of PUM2 expression in H9C2 cardiomyocytes was achieved through siRNA transfection.


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-O14


title: 3052

value: WT

value: 0.1 mg/kg HFPO-DA


title: Ovarian endometriotic cyst stromal cells treated without tucidinostat, rep1

description: Library name: C9_NC


title: Ovarian endometriotic cyst stromal cells treated with tucidinostat (10 μM), rep4

description: Library name: C12_Tucidi_10

value: Tucidinostat 10μM and DMSO 10μM, 48h


title: siPUM2_2

description: Library name: Sample5


title: 3047

value: liver


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-M2


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-M14


title: 3046


title: Ovarian endometriotic cyst stromal cells treated with tucidinostat (10 μM), rep2

description: Library name: C10_Tucidi_10


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-M13


title: 3044


title: 3041


title: Ovarian endometriotic cyst stromal cells treated with tucidinostat (10 μM), rep1

description: Library name: C9_Tucidi_10


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-M1


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-N2


title: NC_1

description: Library name: Sample1

value: Inhibition control with empty vector transfection.


title: 3061

value: 18 months


title: 2584

value: female

value: 0.05 mg/kg HFPO-DA


title: A549 dncHSF1 DOX 6

city: Cambridge

first: Vincent

last: Butty

state: MA

address: 77 Massachusetts Avenue 68-317A

department: Biology

institute: MIT

description:
Library name: D25-197024
Singular Genomics G4 instrument was used to produce the reads.

data_processing:
Base calling was performed on the instrument using Singular Genomics's  basecalling pipeline v. 24.06.0.
Reads were aligned against hg19 (Feb., 2009) using bwa mem v. 0.7.12-r1039 with flags –t 16 –f, and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5´ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using bedtools v. 2.25.0. In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against hg19, and read density across genomic features were estimated for RNA-Seq-specific quality control metrics
Fastq files were processed using the nf-core/rnaseq v 3.11.1 pipeline [https://zenodo.org/records/10171269] in the Nextflow 22.10.4 environment, using the GRCh38 reference genome and GENCODE v43 murine annotation.
Gene-level expression tables of counts and transcript-per-million (TPM) generated by STAR/Salmon processing were retrieved [Dobin2013, Soneson2015, Patro2017] .
Assembly: GRCh38 / Gencode v43
Supplementary files format and content: Raw counts per sample (merged salmon quant.sf output), comma-separated file.
Supplementary files format and content: log2Tpm values per sample (merged salmon quant.sf output), comma-separated file.

molecule: polyA RNA

source_name: Lung basal adenocarcinoma with dox-inducible HSF1

growth_protocol: All cell lines were seeded at 100,000 cells/ well in a 12-well plate in DMEM media.

extract_protocol:
Cellular RNA was harvested using the RNeasy Plus Mini Kit with QIAshredder homogenization columns (Qiagen). RNA samples were quantified using an Advanced Analytical Fragment Analyzer.
Two microliters were taken from each RNA sample and incubated with NEB polyA-selection beads. 1.2ul of the reaction mix was used to generate cDNA, and left on beads overnight at 4C. RNA Sequencing libraries were generated with  the NEB Ultra II kit using half of the volumes of cDNA and reagents (as defined in the standard protocol) and adapaters diluted 1:50. Singular Truseq primers were added and the samples were amplified with a n6 iconPCR instrument, where well-specific thermal cycling was performed until until each individual well/sample had reached a set amount of library product (as determined through real-time monitoring of PCR product accumulation), after which the well was maintained at 4C. Library sizes and concentrations were checked using a Fragment Analyzer instrument and submitted for paired-end, 50bp sequencing on a Singular Genomics G4 instrument.

treatment_protocol: 24 hours after plating, cells were treated with 0.01% DMSO or 1μg/mL dox for 24 h.

value: Lung alveolar adenocarcinoma

value: Dox

tag: batch


title: 2565


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-L14


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-N1


title: 2564


title: siPUM2_1

description: Library name: Sample4


title: Untreated zebrafish melanoma

city: Boston

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description:
Library name: Puck_220827_08_Original
Fresh frozen Spatial transcriptomics sequencing

data_processing:
Raw sequencing data (bcl) was processed with bcl-convert v4.0.3 to generate fastq files.
For Slide-seq assay, whole zebrafish bearing melanoma tumors were frozen in OCT on dry ice and placed at -80oC. Slide-seq arrays were prepared and spatial bead barcodes sequenced following Slide-seqV2 (Stickels et al. https://doi.org/10.1038/s41587-020-0739-1) protocol using arrays created with custom synthesized barcoded beads (5’-TTT_PC_GCCGGTAATACGACTCACTATAGGGCTACACGACGCTCTTCCGATCTJJJJJJJJTCTTCAGCG TTCCCGAGAJJJJJJNNNNNNNVVT30-3’) with a photocleavable linker (PC), a bead barcode sequence (J, 14 bp), a UMI sequence (NNNNNNNVV, 9 bp), and a poly dT tail. OCT-embedded frozen tissue samples were warmed to -20◦C in a cryostat (Leica, CM3050S) and serially sectioned at a 10 μm thickness (2-3 Slide-seq array replicates per sample), with consecutive sections used for hematoxylin and eosin staining and immunofluorescence staining. Each tissue section was affixed to an array and moved into a 1.5 mL Eppendorf tube for downstream processing. The sample library was prepared as previously described (Stickels et al. https://doi.org/10.1038/s41587-020-0739-1). Libraries were sequenced using the following read structure on a NovaSeq (S2; Illumina): Read1: 42 bp; Read2: 41 bp; Index1: 8 bp, and sequences were processed as previously described (Stickels et al. https://doi.org/10.1038/s41587-020-0739-1) using the pipeline available at https://github.com/MacoskoLab/ slideseq-tools. For CRATER vs non-CRATER analysis, RCTD was applied as described73 to identify cell types. We marked CRATER and non CRATER areas (shown in Figure 2A, circles) on the expression map and applied C-SIDE to perform differential expression analysis as described (Cable et al. https://doi.org/10.1038/s41592-022-01575-3).
Assembly: GRCz11
Supplementary files format and content: R rds file
Supplementary files format and content: h5ad file
Library strategy: Spatial Transcriptomics

organism: Danio rerio

source_name: Melanoma

growth_protocol: Extracted tumor

extract_protocol:
Surgical extraction
Raw sequencing data (bcl) was processed with bcl-convert v4.0.3 to generate fastq files.

treatment_protocol: Frozen section- 100% Ethanol on dry ice

value: Melanoma

value: Mixed

value: BRAF(V600E), p53 mitfa specific null, Tyrosinase mitfa specific null, mitfa:tagBFP

value: Untreated


title: Whole brain from 6 stage47 tadpoles, ap3b2 mosaic F0 CRISPant, replicate 3

city: Dunedin

first: Caroline

last: Beck

state: Otago

address: 340 Great King Street, North Dunedin

department: Zoology

country: New Zealand

institute: University of Otago

description: Library name: Ap3b2_3

data_processing:
FastQ files were demultiplexed and downloaded from Illumina Base Space.
Trimming and mapping to X. laevis v10.1 genome (Xenbase) was done using STAR.
Sorted BAM files were used to generate a read count matrix in Galaxy.eu, using FeatureCounts  with settings stranded_reverse, gene_id, paired count as 1
Using the scrambled guide samples (n=5) as controls, differentially expressed genes were identified from normalised read counts for ap3b2 and for eef1a2 edited brain using EdgeR, filtering out gene IDs with CPM<1 in 4 or more samples.
Principal component analysis identified one strong outlier ap3b2 sample which was removed from the analysis. This sample had a much lower RIN reported by our sequencing provider and was likley degraded.
Assembly: X.laevis v10.1 downloaded 30/05/2025
Supplementary files format and content: Processed data file 1(readcountmatrix.csv) is raw read counts with Gene_id in the left column, generated by FeatureCounts.
Supplementary files format and content: Processed data file 2 (NormalisedReadCounts_log2CPM.csv) is normalised log2CPM readcounts generated by EdgeR after removal of the outlier sample.

organism: Xenopus laevis

source_name: Brain

growth_protocol: Fertilised embryos from two female X.laevis frogs grown to stage 47 in 0.1 x MMR (Marc's modified Ringers)

extract_protocol:
Whole brains were dissected from groups of 6 tadpoles at stage 47 onto 2 mL eppendorf tube  caps, removing as much liquid as possible, and spun breifly to collect the tissue into 2 mL tubes placed on dry ice. Samples were mechanically homogenised and total RNA was purified using Qiagen mini RNeasy kit with on column DNase.
1 ug of total RNA was used to make TruSeq stranded (reverse) mRNA libraries (Otago Genomics) which were sequenced using an Illumina Nextseq 2000 P3-200 XLEAP kit generating 2 x 100bp paired end reads.

treatment_protocol: Fertilised embryos from two female X.laevis frogs were injected with Spy-Cas9-NLS bound to one of three sgRNAs targeting ap3b2, eef1a2 (both generating truncated LOF edits) or a scrambled guide with no targets (control).

value: Brain

value: Stage 47 tadpole

value: Bulk

value: ap3b2-/- (mosiac)


title: Whole brain from 6 stage47 tadpoles, ap3b2 mosaic F0 CRISPant, replicate 2

description: Library name: Ap3b2_2


title: Whole brain from 6 stage47 tadpoles, ap3b2 mosaic F0 CRISPant, replicate 1

description: Library name: Ap3b2_1


title: NC_2

description: Library name: Sample2

value: H9C2 cardiomyocytes


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-L1

value: 9 months

value: FC

value: M


title: Whole brain from 6 stage47 tadpoles, ap3b2 mosaic F0 CRISPant, replicate 4

description: Library name: Ap3b2_4


title: NC_3

description: Library name: Sample3

value: Inhibition control with empty vector transfection.


title: 2556

value: liver

value: female

value: WT


title: A549 dncHSF1 DOX 3

description:
Library name: D25-197021
Singular Genomics G4 instrument was used to produce the reads.

value: Lung basal adenocarcinoma with dox-inducible HSF1

value: Lung alveolar adenocarcinoma

value: Dox


title: 2563

value: 18 months

value: 0.05 mg/kg HFPO-DA


title: 2553


title: Whole brain from 6 stage47 tadpoles,eef1a2 mosaic F0 CRISPant, replicate 4

description: Library name: Eef1a2_4

value: Brain


title: Whole brain from 6 stage47 tadpoles,eef1a2 mosaic F0 CRISPant, replicate 5

description: Library name: Eef1a2_5

value: Stage 47 tadpole


title: A549 dncHSF1 DOX 2

description:
Library name: D25-197020
Singular Genomics G4 instrument was used to produce the reads.


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-K2


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-L2


title: A549 dncHSF1 DOX 1

description:
Library name: D25-197019
Singular Genomics G4 instrument was used to produce the reads.


title: 2552


title: Ovarian endometriotic cyst stromal cells treated with tucidinostat (10 μM), rep3

description: Library name: C11_Tucidi_10

value: Ovarian endometriotic cyst

value: Female

value: Tucidinostat 10μM and DMSO 10μM, 48h


title: A549 dncHSF1 DOX 5

description:
Library name: D25-197023
Singular Genomics G4 instrument was used to produce the reads.


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-K13

value: 9 months


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-K14

value: FC


title: Whole brain from 6 stage47 tadpoles,eef1a2 mosaic F0 CRISPant, replicate 3

description: Library name: Eef1a2_3

value: Bulk


title: 2551


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-L13

value: M


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-K1


title: Whole brain from 6 stage47 tadpoles,eef1a2 mosaic F0 CRISPant, replicate 2

description: Library name: Eef1a2_2


title: A549 cHSF1 DOX 6

description:
Library name: D25-197018
Singular Genomics G4 instrument was used to produce the reads.


title: A549 cHSF1 DOX 5

description:
Library name: D25-197017
Singular Genomics G4 instrument was used to produce the reads.


title: 2069

value: liver

value: male


title: Whole brain from 6 stage47 tadpoles,eef1a2 mosaic F0 CRISPant, replicate 1

description: Library name: Eef1a2_1


title: A549 dncHSF1 DOX 4

description:
Library name: D25-197022
Singular Genomics G4 instrument was used to produce the reads.


title: Whole brain from 6 stage47 tadpoles, unedited, replicate 5

description: Library name: Control_5

value: WT


title: A549 cHSF1 DOX 4

description:
Library name: D25-197016
Singular Genomics G4 instrument was used to produce the reads.

value: Lung basal adenocarcinoma with dox-inducible HSF1


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-J2


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-J14


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-J13


title: A549 cHSF1 DOX 3

description:
Library name: D25-197015
Singular Genomics G4 instrument was used to produce the reads.

value: Lung alveolar adenocarcinoma


title: 2066


title: A549 cHSF1 DOX 2

description:
Library name: D25-197014
Singular Genomics G4 instrument was used to produce the reads.

value: Dox


title: Whole brain from 6 stage47 tadpoles, unedited, replicate 4

description: Library name: Control_4


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-J1


title: 2056


title: Whole brain from 6 stage47 tadpoles, unedited, replicate 2

description: Library name: Control_2


title: A549 cHSF1 DOX 1

description:
Library name: D25-197013
Singular Genomics G4 instrument was used to produce the reads.


title: A549 parental DOX 6

description:
Library name: D25-197012
Singular Genomics G4 instrument was used to produce the reads.


title: 2055


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-I14


title: Whole brain from 6 stage47 tadpoles, unedited, replicate 1

description: Library name: Control_1


title: 2054


title: 2052


title: A549 parental DOX 5

description:
Library name: D25-197011
Singular Genomics G4 instrument was used to produce the reads.


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-I13


title: 2067

value: 18 months


title: 2051

value: 0.05 mg/kg HFPO-DA


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-H14


title: A549 parental DOX 2

description:
Library name: D25-197008
Singular Genomics G4 instrument was used to produce the reads.


title: A549 parental DOX 4

description:
Library name: D25-197010
Singular Genomics G4 instrument was used to produce the reads.


title: A549 parental DOX 3

description:
Library name: D25-197009
Singular Genomics G4 instrument was used to produce the reads.


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-I1


title: Whole brain from 6 stage47 tadpoles, unedited, replicate 3

description: Library name: Control_3

value: Brain


title: 2065


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-H2


title: A549 parental DOX 1

description:
Library name: D25-197007
Singular Genomics G4 instrument was used to produce the reads.


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-I2


title: 1564

value: female

value: 0 mg/kg HFPO-DA


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-H13


title: 1566


title: 8026C (-)

city: Ann Arbor

first: Justin

last: Colacino

state: MI

address: 6651 SPH1, 1415 Washington Heights

department: Environmental Health Sciences

institute: University of Michigan

description: Library name: Sample_3613-ED-8

data_processing:
The reads were trimmed using Cutadapt v2.3 (Martin, 2011). FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010). Fastq Screen v0.13.0 was used to screen for various types of contamination (Wingett and Andrews, 2018). Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Assembly: GRCm38
Supplementary files format and content: Reads counts generated by RSEM

source_name: primary gastric organoid culture

growth_protocol: Organoids were established by plating isolated gastric glands in Matrigel, and overlayed with culture media containing 50% L-WRN conditioned media, 20% (corpus) or 10% (antrum) fetal bovine serum, 2mM L-glutamine, 1X Pen-Strep, 1X fungizone, 50 mg/mL gentamycin, 10mM Y-27632  in Advanced DMEM/F12. This growth medium without Y-27632 was subsequently used for feeding and passaging of organoid cultures

extract_protocol:
24 hours post-Wnt inhibition organoids were lysed in Buffer RLT and 1% b-mercaptoethanol, and RNA was isolated using the Qiagen RNeasy kit. On-column DNase I digestion was performed according to the manufacturer’s instructions.
RNA libraries for RNAseq were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext UltraExpress RNA Library Prep Kit following manufacturer instructions

treatment_protocol: Established wild-type mouse organoids passaged at least three times. On day 4 post-passage, 3 independent gastric organoid lines were treated with the Wnt inhibitor XAV939 (1 mM) with removal of exogenous Wnt/Rspondin and supplementation with Noggin-1 (100 ng/mL), or with vehicle (DMSO) in normal culture media.

value: primary gastric organoid culture

value: corpus epithelial cells

value: Wnt Inhibition


title: 8028A

description: Library name: Sample_3613-ED-6

value: antral epithelial cells


title: 8025C (-)

description: Library name: Sample_3613-ED-7


title: 8026A

description: Library name: Sample_3613-ED-5


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-H1

value: 9 months

value: FC


title: 8025A

description: Library name: Sample_3613-ED-4


title: A549 parental DMSO 5

description:
Library name: D25-197005
Singular Genomics G4 instrument was used to produce the reads.

value: DMSO


title: 8028C (-)

description: Library name: Sample_3613-ED-9


title: 1563

value: liver


title: A549 parental DMSO 6

description:
Library name: D25-197006
Singular Genomics G4 instrument was used to produce the reads.


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-G2

value: M


title: A549 parental DMSO 4

description:
Library name: D25-197004
Singular Genomics G4 instrument was used to produce the reads.

value: Lung basal adenocarcinoma with dox-inducible HSF1


title: 1571

value: WT


title: 8028C

description: Library name: Sample_3613-ED-3


title: 1562


title: 8026C

description: Library name: Sample_3613-ED-2


title: 1554


title: A549 parental DMSO 3

description:
Library name: D25-197003
Singular Genomics G4 instrument was used to produce the reads.

value: Lung alveolar adenocarcinoma


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-G13


title: 8028A (-)

description: Library name: Sample_3613-ED-12


title: 1545


title: A549 parental DMSO 2

description:
Library name: D25-197002
Singular Genomics G4 instrument was used to produce the reads.


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-G1


title: A549 parental DMSO 1

description:
Library name: D25-197001
Singular Genomics G4 instrument was used to produce the reads.


title: 1544


title: NCI-H2122_RMC-6291+RMC-6236_8hour_rep3

city: Redwood City

first: Ximo

last: Pechuan-Jorge

address: 700 Saginaw Drive

institute: Revolution Medicines

description: Library name: N23_G11_8_3

data_processing:
Sequence reads aligned using salmon v1.10
CDX models were demoused by mapping to bother human and mouse, and subsequently removing mouse reads.
Human mapped to reference hg38
Mouse mapped to reference mm39
Read count and normalization performed using edgeR limma-voom.
Assembly: hg38, mm39
Supplementary files format and content: Table of raw counts formatted as a .csv file

source_name: CDX

extract_protocol:
NCI-H2122 CDX samples had RNA was extracted using RNeasy Mini Kit (Qiagen, 74106). Mouse 3LL NRAS KO #86 samples had RNA extracted using Qiagen miRNeasy mini.
NCI-H2122 CDX samples were prepared using directional mRNA library preparation (poly A enrichment). Mouse 3LL NRAS KO #86 samples were prepared using Illumina TruSeq Stranded mRNA, 50M, 100bp PE.

value: CDX

value: NSCLC


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-F2


title: 8025A (-)

description: Library name: Sample_3613-ED-10


title: 8025C

description: Library name: Sample_3613-ED-1


title: 1541


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-F13


title: NCI-H2122_RMC-6291+RMC-6236_8hour_rep2

description: Library name: N23_G11_8_2


title: NCI-H2122_RMC-6291+RMC-6236_8hour_rep1

description: Library name: N23_G11_8_1


title: 1069

value: male

value: 18 months


title: 1542

value: female

value: 0 mg/kg HFPO-DA


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-F14


title: Input-Keto_4

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Library name: Input-Keto_4

data_processing:
Bioinformatic analysis of ChIP-seq data was performed following the ENCODE consortium pipeline. Briefly, paired-end sequencing reads were aligned to the Mus musculus reference genome (mm10) using Bowtie2 (version 2.3.4.3) with a maximum fragment length of 2000 bp. PCR duplicates were identified and marked using Picard (version 2.20.7).
MACS2 (version 2.2.9) was used for peak calling with default parameters. For visualization, bigWig files representing fold enrichment of histone mark signals over their corresponding input controls were generated.
Promoter regions (−1000 bp to +100 bp relative to the transcription start site) and gene body regions of differentially expressed genes (DEGs) were defined according to the latest Mus musculus NCBI RefSeq annotation (mm10).
ChIP-seq signal intensities over the defined genomic regions were quantified using deepTools multiBigwigSummary (version 3.5.5). Statistical comparisons between groups were performed using the Wilcoxon rank-sum test.
Assembly: mm10
Supplementary files format and content: bigWig except for Input samples

source_name: Hippocampus

extract_protocol:
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was carried out using established protocols1. Briefly, fresh frozen hippocampal tissue (both hemispheres) from each mouse (n=4 for each chow and keto diet) was finely minced on cold plate, crosslinked in 1% formaldehyde in PBS for 10 min at RT, then the reaction was quenched using 125 mM glycine for 5 min at RT. Crosslinked tissues were washed with ice-cold PBS. The pelleted tissue was suspended in Sucrose/ TKM buffer (0.25 M sucrose, 50 mM Tris-HCl (pH 7.5), 25 mM potassium chloride, 5 mM magnesium chloride, 1X Protease Inhibitors, 10 mM sodium butyrate) and subjected to dounce homogenization to isolate nuclei. The sample is centrifuged for 5 min at 5,000 g at 4C and the pelleted nuclei are resuspended in nuclei lysis buffer (10 mM Tris-HCl, pH 8, 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 0.1 % sodium deoxycholate, 0.5% N-lauroylsarcosine). Chromatin was fragmented to approximately 250 bp using a Covaris E220 sonicator (used the following sonication settings: 150 Watts peak incident power, 13% duty factor, 200 cycles/burst, 20 min/sample (1200 sec/sample)). 0.1X volume of 10% Triton-X was added to the sonicated lysate to stabilize proteins. Equivalent quantities of sheared chromatin were incubated with Dynabeads-antibody complex and input control overnight at 4 °C with gentle rotation. For each sample, H3K4me antibody (Abcam, Cat. No. 8895) Dynabead complex was prepared.  Next day, the immunoprecipitated samples were washed with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM sodium chloride), high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM sodium chloride), lithium chloride wash buffer (0.25 M lithium chloride, 1% CA-630, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0) and 1X TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). DNA was eluted from beads, crosslinks reversed, and DNA purified (QIAquick PCR Purification Kit Qiagen, Cat. No. 28106) together with input samples. The DNA was quantified using Qubit dsDNA high sensitivity assay kit (Cat. No. Q32851) and size distribution of DNA was assessed using an Agilent Bioanalyzer.
10ng of DNA was used for the library preperation. The enzymes and buffers used are from Qiagen Beverley, adapters & indexing primers are from IDT. DNA fragments were end-repaired to generate blunt ends, followed by the addition of a single adenosine (A) residue to the 3′ ends. Illumina sequencing adapters were then ligated to the DNA fragments. Size selection was performed using AMPure XP beads to enrich for fragments between 150 and 700 bp. Adapter-ligated fragments were amplified by PCR for 15 cycles using primers containing unique dual index sequences. The resulting libraries were sequenced on an Illumina NovaSeq X Plus platform using paired-end 150 bp reads.

treatment_protocol: 4 week-old C57BL6/NJ mice were placed on a 4-week ketogenic diet or chow diet

value: Hippocampus

tag: diet

value: Keto

tag: chip antibody


title: NCI-H2122_RMC-6291+RMC-6236_24hour_rep3

description: Library name: N23_G11_24_3


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-G14


title: Input-Keto_2

description: Library name: Input-Keto_2


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-E2


title: 1064


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-F1


title: Input-Keto_3

description: Library name: Input-Keto_3


title: NCI-H2122_RMC-6291+RMC-6236_24hour_rep2

description: Library name: N23_G11_24_2


title: 8026A (-)

description: Library name: Sample_3613-ED-11

value: primary gastric organoid culture

value: antral epithelial cells

value: Wnt Inhibition


title: NCI-H2122_RMC-6291+RMC-6236_24hour_rep1

description: Library name: N23_G11_24_1


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-E13

value: 9 months

value: FC


title: 1062

value: liver


title: Input-Keto_1

description: Library name: Input-Keto_1


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-E14

value: M


title: Input-Chow_4

description: Library name: Input-Chow_4

value: Chow


title: 1061

value: WT


title: NCI-H2122_RMC-6236_8hour_rep2

description: Library name: N23_G7_8_2

value: CDX


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-E1


title: NCI-H2122_RMC-6236_8hour_rep3

description: Library name: N23_G7_8_3

value: NSCLC


title: Input-Chow_3

description: Library name: Input-Chow_3


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-D2


title: Input-Chow_2

description: Library name: Input-Chow_2


title: 1044

value: male


title: Input-Chow_1

description: Library name: Input-Chow_1


title: NCI-H2122_RMC-6236_24hour_rep3

description: Library name: N23_G7_24_3


title: 1043


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-D13


title: NCI-H2122_RMC-6236_8hour_rep1

description: Library name: N23_G7_8_1


title: NCI-H2122_RMC-6236_24hour_rep2

description: Library name: N23_G7_24_2


title: H3k4me-Keto_4

description: Library name: H3k4me-Keto_4


title: 1041


title: NCI-H2122_RMC-6236_24hour_rep1

description: Library name: N23_G7_24_1


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-D1


title: 1063

value: 18 months


title: par-cHSF1_37_dox_6

data_processing:
Base calling was performed using the Illumina Offline Base Caller, Illumina RTA v. 2.11.3.
Forward reads containing barcode information (Read 1) were extracted and split into well barcode and unique molecular identifier (UMI) sequences and added to the header of the corresponding reverse read (Read 2), which was then treated as a single-end read.
Reads were aligned against hg19 (Feb., 2009) using bwa mem v. 0.7.12-r1039 with flags –t 16 –f, and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5´ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using bedtools v. 2.25.0. In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against hg19, and read density across genomic features were estimated for RNA-Seq-specific quality control metrics.
For mapping and quantitation, reads were scored against GRCh38/ENSEMBL 101 annotation using Salmon v.1.3 with flags quant -p 8 -l ISR –validateMappings. The resulting quant.sf files were imported into the R statistical environment using the tximport library (tximport function, option “salmon”), and gene-level counts and transcript per-milllion (TPM) estimates were calculated for all genes.
Assembly: GRCh38/ENSEMBL 101
Supplementary files format and content: Raw counts per sample (merged salmon quant.sf output), comma-separated file.
Supplementary files format and content: log2Tpm values per sample (merged salmon quant.sf output), comma-separated file.

source_name: Lung basal adenocarcinoma with dox-inducible HSF1, WT p53

growth_protocol: A549cHSF1 cells were seeded at 7.5 x 104 cells/well in a 12-well plate in DMEM media.

extract_protocol:
Cellular RNA was harvested using the RNeasy Plus Mini Kit with QIAshredder homogenization columns (Qiagen). RNA samples were quantified using an Advanced Analytical Fragment Analyzer.
High throughput three prime digital gene expression (HT-3'DGE) was adapted from the Soumillon et al. protocol (Soumillon et al. BioRxiv https://www.biorxiv.org/content/10.1101/003236v1) to perform reverse-transcription reactions using a dedicated RT primer containing sample and unique molecular identifier (UMI) sequences, to generate four subpools of 24 samples each. After second strand synthesis, Illumina adapters were added using the Nextera Flex tagmentation protocol substituting the normal P500 primer with an ad-hoc primer. Final libraries were cleaned using SPRI beads at 0.7X and quantified using the Fragment Analyzer and qPCR before being loaded for paired-end sequencing using the Illumina NextSeq500 in high-output paired-end mode (20/57 nt reads).

treatment_protocol: Cells were then treated with either 0.01 % DMSO or 1 μg/mL dox for 24 h.

value: Lung alveolar adenocarcinoma

tag: temperature

value: dox

tag: biological replicate

tag: included


title: H3k4me-Keto_3

description: Library name: H3k4me-Keto_3

tag: tissue

value: Hippocampus


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-C2

data_processing:
Library strategy: snmC-seq3
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
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. 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

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: NCI-H2122_RMC-6291_8hour_rep3

description: Library name: N23_G4_8_3

tag: treatment


title: H3k4me-Keto_2

description: Library name: H3k4me-Keto_2

value: Keto


title: par-cHSF1_37_dox_5

value: Lung basal adenocarcinoma with dox-inducible HSF1, WT p53

tag: genotype


title: H3k4me-Keto_1

description: Library name: H3k4me-Keto_1


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-C14

tag: age


title: 1045

value: 0 mg/kg HFPO-DA


title: NCI-H2122_RMC-6291_8hour_rep2

description: Library name: N23_G4_8_2


title: par-cHSF1_37_dox_4


title: H3k4me-Chow_4

description: Library name: H3k4me-Chow_4


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-D14

tag: brain region


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-C13

tag: gender


title: NCI-H2122_RMC-6291_8hour_rep1

description: Library name: N23_G4_8_1

tag: cell type


title: NCI-H2122_RMC-6291_24hour_rep3

description: Library name: N23_G4_24_3

tag: cell line


title: H3k4me-Chow_3

description: Library name: H3k4me-Chow_3


title: par-cHSF1_37_dox_2


title: par-cHSF1_37_dox_3


title: H3k4me-Chow_2

description: Library name: H3k4me-Chow_2


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-C1


title: NCI-H2122_RMC-6291_24hour_rep2

description: Library name: N23_G4_24_2


title: par-cHSF1_37_dox_1


title: par-cHSF1_37_DMSO_6

value: DMSO


title: NCI-H2122_RMC-6291_24hour_rep1

description: Library name: N23_G4_24_1


title: ATAC-seq of naive CD8+ T cells, sample 06

description: Library name: tx_03

source_name: Naive CD8+ T cells

growth_protocol: Naïve CD8+ T cells cultured n the presence of DMSO (ctrl) or 2µM RGX-104 for 24 hours.

extract_protocol:
CD8+ T cells were isolated using the MojoSort Mouse CD8 Naïve T Cell Isolation Kit (Biolegend, 480044) and 60,000 cells were used as input for the ATAC-Seq kit (Active Motif, 53150)
ATAC-Seq kit (Active Motif, 53150)

value: Naive CD8+ T cells


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-B14

value: 9 months

value: FC


title: NCI-H2122_vehicle_8hour_rep3

description: Library name: N23_G1_8_3

value: Vehicle


title: H3k4me-Chow_1

description: Library name: H3k4me-Chow_1

value: Chow


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-B1

value: M


title: par-cHSF1_37_DMSO_4


title: NCI-H2122_vehicle_8hour_rep2

description: Library name: N23_G1_8_2

value: CDX


title: ATAC-seq of naive CD8+ T cells, sample 05

description: Library name: tx_02


title: par-cHSF1_37_DMSO_3


title: NCI-H2122_vehicle_8hour_rep1

description: Library name: N23_G1_8_1

value: NSCLC


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-A14


title: NCI-H2122_vehicle_24hour_rep3

description: Library name: N23_G1_24_3


title: par-cHSF1_37_DMSO_2

value: male


title: ATAC-seq of naive CD8+ T cells, sample 04

description: Library name: tx_01


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-B2


title: ATAC-seq of naive CD8+ T cells, sample 02

description: Library name: ctrl_02

value: control


title: par-cHSF1_37_DMSO_1

value: Lung alveolar adenocarcinoma


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-B13


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-A1


title: ATAC-seq of naive CD8+ T cells, sample 01

description: Library name: ctrl_01


title: NCI-H2122_vehicle_24hour_rep1

description: Library name: N23_G1_24_1


title: Dhaka Birth Cohort year-1 serum S_3286

status: Public on Dec 28 2025

type: protein

city: Charlottesville

first: Jennifer

last: Hendrick

state: VA

address: 345 Crispell Drive

department: Medicine, Division of Infectious Diseases

institute: University of Virginia

description: Serum diluted 1:100; bound IgG detected by DyLight650-conjugated secondary antibody; scanned with InnoScan 910AL.

hyb_protocol: Serum probed on array at 1:100 dilution; overnight incubation; washed per manufacturer protocol.

scan_protocol: Arrays scanned and quantified using an InnoScan 910AL microarray scanner (Innopsys).

data_processing:
Raw spot intensities were log2-transformed. For each sample, the median log2 signal intensity of IVTT control spots was subtracted to normalize and remove systematic effects. Normalized signal intensity (SI) values were used for downstream analyses and to define seropositivity thresholds.
Processed matrix values are normalized signal intensities (SI) on the log2 scale after subtraction of the median log2 IVTT control signal for each sample. Raw matrix contains log2-transformed feature-extraction intensities prior to IVTT normalization.

label: DyLight 650 (goat anti-human IgG-Fc; Bethyl/Fortis Life Sciences, Cat#A80-104D5)

molecule: protein

source_name: Year-1 infant serum (Dhaka Birth Cohort)

label_protocol: Bound IgG detected with DyLight 650-conjugated goat anti-human IgG-Fc (Bethyl/Fortis Life Sciences, Cat#A80-104D5).

growth_protocol: Not applicable (human serum).

extract_protocol: No extraction performed; archived infant serum was diluted 1:100 prior to probing.

treatment_protocol: Not applicable.

value: Mirpur

value: Male

value: Yes

value: Some Primary

value: Textile Industry

value: No


title: Dhaka Birth Cohort year-1 serum S_3213

value: Female

value: Home Caretaker


title: Dhaka Birth Cohort year-1 serum S_3346

value: Some Secondary


title: Dhaka Birth Cohort year-1 serum S_3249


title: Dhaka Birth Cohort year-1 serum S_3162


title: Dhaka Birth Cohort year-1 serum S_3050

value: H.S.C. Passed


title: par-cHSF1_37_DMSO_5

value: Lung basal adenocarcinoma with dox-inducible HSF1, WT p53

value: DMSO


title: Dhaka Birth Cohort year-1 serum S_3131

value: Above H.S.C.


title: Dhaka Birth Cohort year-1 serum S_3374


title: Dhaka Birth Cohort year-1 serum S_3149


title: Dhaka Birth Cohort year-1 serum S_3290


title: ATAC-seq of naive CD8+ T cells, sample 03

description: Library name: ctrl_03

value: Naive CD8+ T cells


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-A2

value: 9 months

value: FC

value: M


title: Dhaka Birth Cohort year-1 serum S_3062

value: Mirpur


title: Dhaka Birth Cohort year-1 serum S_3200

value: Male


title: AMB_200630_9mo_2A_3A_1_P1-1-C6-A13


title: Dhaka Birth Cohort year-1 serum S_3371

value: Yes


title: Dhaka Birth Cohort year-1 serum S_3139


title: Dhaka Birth Cohort year-1 serum S_3012


title: Dhaka Birth Cohort year-1 serum S_3187

value: Some Primary


title: Dhaka Birth Cohort year-1 serum S_3245

value: Textile Industry


title: Dhaka Birth Cohort year-1 serum S_3097

value: No


title: Dhaka Birth Cohort year-1 serum S_3059

value: Female

value: Student


title: NCI-H2122_vehicle_24hour_rep2

description: Library name: N23_G1_24_2

value: CDX

value: NSCLC

value: Vehicle


title: Dhaka Birth Cohort year-1 serum S_3179

value: Home Caretaker


title: Dhaka Birth Cohort year-1 serum S_3031

value: Some Secondary

value: Business Owner


title: Dhaka Birth Cohort year-1 serum S_3228


title: Dhaka Birth Cohort year-1 serum S_3336


title: Dhaka Birth Cohort year-1 serum S_3171

value: S.S.C. Passed


title: Dhaka Birth Cohort year-1 serum S_3108


title: Dhaka Birth Cohort year-1 serum S_3196


title: Dhaka Birth Cohort year-1 serum S_3001


title: Dhaka Birth Cohort year-1 serum S_3124

value: Above H.S.C.


title: Dhaka Birth Cohort year-1 serum S_3279


title: Dhaka Birth Cohort year-1 serum S_3284

value: H.S.C. Passed


title: Dhaka Birth Cohort year-1 serum S_3016

value: Mirpur


title: Dhaka Birth Cohort year-1 serum S_3024

value: Teacher


title: Dhaka Birth Cohort year-1 serum S_3154

value: Male

value: Yes


title: Dhaka Birth Cohort year-1 serum S_3307


title: Dhaka Birth Cohort year-1 serum S_3138


title: Dhaka Birth Cohort year-1 serum S_3255

value: Some Primary


title: Dhaka Birth Cohort year-1 serum S_3259

value: No


title: Dhaka Birth Cohort year-1 serum S_3194

value: Female


title: Dhaka Birth Cohort year-1 serum S_3101


title: Dhaka Birth Cohort year-1 serum S_3172


title: Dhaka Birth Cohort year-1 serum S_3262


title: Dhaka Birth Cohort year-1 serum S_3157


title: Dhaka Birth Cohort year-1 serum S_3301


title: Dhaka Birth Cohort year-1 serum S_3084


title: Dhaka Birth Cohort year-1 serum S_3281


title: Dhaka Birth Cohort year-1 serum S_3242


title: Dhaka Birth Cohort year-1 serum S_3076


title: Dhaka Birth Cohort year-1 serum S_3091


title: Dhaka Birth Cohort year-1 serum S_3115


title: Dhaka Birth Cohort year-1 serum S_3351


title: Dhaka Birth Cohort year-1 serum S_3288


title: Dhaka Birth Cohort year-1 serum S_3114


title: Dhaka Birth Cohort year-1 serum S_3119


title: Dhaka Birth Cohort year-1 serum S_3093

value: Textile Industry


title: Dhaka Birth Cohort year-1 serum S_3127


title: Dhaka Birth Cohort year-1 serum S_3088


title: Dhaka Birth Cohort year-1 serum S_3092


title: Dhaka Birth Cohort year-1 serum S_3116


title: Dhaka Birth Cohort year-1 serum S_3163


title: Dhaka Birth Cohort year-1 serum S_3161


title: Dhaka Birth Cohort year-1 serum S_3267


title: Dhaka Birth Cohort year-1 serum S_3234


title: Dhaka Birth Cohort year-1 serum S_3086


title: Dhaka Birth Cohort year-1 serum S_3075


title: Dhaka Birth Cohort year-1 serum S_3205


title: Dhaka Birth Cohort year-1 serum S_3400


title: Dhaka Birth Cohort year-1 serum S_3327


title: Dhaka Birth Cohort year-1 serum S_3070


title: Dhaka Birth Cohort year-1 serum S_3355


title: Dhaka Birth Cohort year-1 serum S_3347


title: Dhaka Birth Cohort year-1 serum S_3002


title: Dhaka Birth Cohort year-1 serum S_3214


title: Dhaka Birth Cohort year-1 serum S_3270


title: Dhaka Birth Cohort year-1 serum S_3322


title: Dhaka Birth Cohort year-1 serum S_3121


title: Dhaka Birth Cohort year-1 serum S_3021


title: Dhaka Birth Cohort year-1 serum S_3229


title: Dhaka Birth Cohort year-1 serum S_3173


title: Dhaka Birth Cohort year-1 serum S_3330


title: Dhaka Birth Cohort year-1 serum S_3221


title: Dhaka Birth Cohort year-1 serum S_3240


title: Dhaka Birth Cohort year-1 serum S_3226


title: Dhaka Birth Cohort year-1 serum S_3049


title: Dhaka Birth Cohort year-1 serum S_3029


title: Dhaka Birth Cohort year-1 serum S_3113


title: Dhaka Birth Cohort year-1 serum S_3170


title: Dhaka Birth Cohort year-1 serum S_3256


title: Dhaka Birth Cohort year-1 serum S_3359


title: Dhaka Birth Cohort year-1 serum S_3180

value: Student


title: Dhaka Birth Cohort year-1 serum S_3251


title: Dhaka Birth Cohort year-1 serum S_3040


title: Dhaka Birth Cohort year-1 serum S_3189


title: Dhaka Birth Cohort year-1 serum S_3028


title: Dhaka Birth Cohort year-1 serum S_3125


title: Dhaka Birth Cohort year-1 serum S_3342


title: Dhaka Birth Cohort year-1 serum S_3069


title: Dhaka Birth Cohort year-1 serum S_3182


title: Dhaka Birth Cohort year-1 serum S_3306


title: Dhaka Birth Cohort year-1 serum S_3077


title: Dhaka Birth Cohort year-1 serum S_3126


title: Dhaka Birth Cohort year-1 serum S_3073


title: Dhaka Birth Cohort year-1 serum S_3222


title: Dhaka Birth Cohort year-1 serum S_3155


title: Dhaka Birth Cohort year-1 serum S_3165


title: Dhaka Birth Cohort year-1 serum S_3201

value: Other


title: Dhaka Birth Cohort year-1 serum S_3148


title: Dhaka Birth Cohort year-1 serum S_3134


title: Dhaka Birth Cohort year-1 serum S_3027


title: Dhaka Birth Cohort year-1 serum S_3348


title: Dhaka Birth Cohort year-1 serum S_3329


title: Dhaka Birth Cohort year-1 serum S_3197


title: Dhaka Birth Cohort year-1 serum S_3150


title: Dhaka Birth Cohort year-1 serum S_3074


title: Dhaka Birth Cohort year-1 serum S_3293


title: Group: CAR19/CXCR4S338X with CXCL12 (related to Figure 5, shown as sample b)

city: Changchun

first: Yushu

last: Mao

address: Xinzhu Road

institute: Jinlin university

description: Library name: DBW_SB

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Assembly: hg38
Supplementary files format and content: FPKM values for each sample; two files generated from independent analyses

source_name: peripheral blood

extract_protocol:
Cell samples were lysed in 1 mL TRIzol reagent and extraced according to manufacturer's protocol.
mRNA was enriched from total RNA using oligo(dT) magnetic beads. After fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. The resulting cDNA underwent end repair, A-tailing, adapter ligation, size selection, amplification, and purification to generate the final sequencing library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: 1×10^6 T cells were resuspended with 100 IU IL-2 in 600 μL T Cell Expansion Medium, and 100 ng/mL CXCL12 or the same volume of PBS was added into the culture system, RNA of the cells were extracted 6 hours later.

value: peripheral blood

value: primary T cells

value: Group:CAR19/CXCR4S338X with CXCL12


title: Group: CAR19/CXCR4S338X with CXCL12 (related to Figure 5, shown as sample a)

description: Library name: DQH_SB


title: Dhaka Birth Cohort year-1 serum S_3141

value: Home Caretaker


title: Group: CAR19/CXCR4S338X without CXCL12 (related to Figure 5, shown as sample c)

description: Library name: HL_SA

value: Group:CAR19/CXCR4S338X without CXCL12


title: Group: CAR19/CXCR4S338X without CXCL12 (related to Figure 5, shown as sample b)

description: Library name: DBW_SA


title: Group: CAR19/CXCR4S338X without CXCL12 (related to Figure 5, shown as sample a)

description: Library name: DQH_SA


title: Dhaka Birth Cohort year-1 serum S_3319


title: Dhaka Birth Cohort year-1 serum S_3341

value: Some Secondary


title: Dhaka Birth Cohort year-1 serum S_3111


title: Dhaka Birth Cohort year-1 serum S_3271


title: Group: CAR19/CXCR4S338X with CXCL12 (related to Figure 4G, not shown 12)

description: Library name: MYS_28SB


title: Group: CAR19/CXCR4S338X with CXCL12 (related to Fig 4G, not shown 11; related to Fig 5, shown as sample a)

description: Library name: DQH_28SB


title: Group: CAR19/CXCR4S338X without CXCL12 (related to Fig 4G, representative; related to Fig 5, shown as sample c)

description: Library name: HL_28SA


title: Group: CAR19/CXCR4S338X without CXCL12 (related to Figure 4G, not shown 10)

description: Library name: MYS_28SA


title: Group: CAR19/CXCR4S338X without CXCL12 (related to Fig 4G, not shown 9; related to Fig 5, shown as sample a)

description: Library name: DQH_28SA


title: Group: CAR19/CXCR4WT with CXCL12 (related to Figure 4G, not shown 8)

description: Library name: MYS_28CB

value: Group:CAR19/CXCR4WT with CXCL12


title: Group: CAR19/CXCR4WT with CXCL12 (related to Figure 4G, representative)

description: Library name: HL_28CB


title: Group: CAR19/CXCR4WT without CXCL12 (related to Figure 4G, representative)

description: Library name: HL_28CA

value: Group:CAR19/CXCR4WT without CXCL12


title: Group: CAR19/CXCR4WT with CXCL12 (related to Figure 4G, not shown 7)

description: Library name: DQH_28CB


title: Group: CAR19 without CXCL12 (related to Figure 4G, representative)

description: Library name: HL_28ZA

value: Group:CAR19 without CXCL12


title: PDX, vehicle_2

city: Beijing

first: Xin

last: Xu

state: Undefined

address: Panjiayuannanli 17

institute: National Cancer Center/Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC)

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
Assembly: Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: pancreatic cancer

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: pancreatic cancer

value: KRAS G12D

value: vehicle


title: Group: CAR19/CXCR4WT without CXCL12 (related to Figure 4G, not shown 5)

description: Library name: DQH_28CA


title: CFPAC-1, BI-2865_3

value: pancreatic cancer cells

value: KRAS G12V


title: CFPAC-1, BI-2865_2


title: Group: CAR19/CXCR4S338X with CXCL12 (related to Figure 5, shown as sample c)

description: Library name: HL_SB


title: CFPAC-1, BI-2865_1


title: Group: CAR19 with CXCL12 (related to Figure 4G, not shown 3)

description: Library name: DQH_28ZB

value: Group:CAR19 with CXCL12


title: Group: CAR19 with CXCL12 (related to Figure 4G, representative)

description: Library name: HL_28ZB


title: Group: CAR19 without CXCL12 (related to Figure 4G, not shown 2)

description: Library name: MYS_28ZA


title: Group: CAR19 with CXCL12 (related to Figure 4G, not shown 4)

description: Library name: MYS_28ZB


title: Group: CAR19 without CXCL12 (related to Figure 4G, not shown 1)

description: Library name: DQH_28ZA


title: SW1990, MRTX1133_3


title: PDX, MRTX1133_2


title: PDX, MRTX1133_1


title: SW1990, MRTX1133_2


title: PDX, vehicle_3


title: PANC-1, MRTX1133_3


title: PANC-1, MRTX1133_1


title: PDX, vehicle_1


title: CFPAC-1, vehicle_3


title: SW1990, vehicle_1


title: PANC-1, MRTX1133_2


title: CAR19/CXCR4S338X with CXCL12 (related to Fig 4G, representative; related to Fig 5, shown as sample c)

description: Library name: HL_28SB


title: Group: CAR19/CXCR4WT without CXCL12 (related to Figure 4G, not shown 6)

description: Library name: MYS_28CA


title: AsPC-1, MRTX1133_3


title: PANC-1, vehicle_3


title: CFPAC-1, vehicle_2


title: PDX, MRTX1133_3


title: CFPAC-1, vehicle_1


title: AsPC-1, MRTX1133_1


title: iALG11_ATc1

city: Wenzhou

first: Ya-Ni

last: Mou

state: China

address: Chashan University Town, Ouhai District, Wenzhou City, Zhejiang Province

institute: Wenzhou Medical University

description: Library name: Sample 4

data_processing:
1. Data quality control. Rawdata (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
2. Reads mapping to the reference genome. Reference genome and gene model annotation files were downloaded from genome website. Use HISAT2 (2.2.1) to build the index of the reference genome, and use HISAT2 to align paired-end clean reads to the reference genome. HISAT2 can use the gene model annotation file to create splice-aware alignments, providing better alignment accuracy compared to other non-splice alignment tools.
3. Novel transcripts prediction. The mapped reads of each sample were assembled by StringTie (v2.2.3) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
4. Quantification of gene expression level feature. Counts (2.0.6) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
5. Differential expression analysis. For DESeq2 with biological replicates: Differential expression analysis for two conditions/groups was performed using the DESeq2 R package (1.42.0). DESeq2 provides statistical programs for determining differential expression in digital gene expression data using models based on negative binomial distribution. The resulting P-value is adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate. The threshold of significant differential expression：|log2fc|>=1 & q<0.05.
Assembly: ToxoDB_68_TgondiiGT1_Genome
Supplementary files format and content: Transcriptomic dataset.xlsx(including Gene_id、log2 FC、p-value、Annotation…

organism: Toxoplasma gondii

source_name: Tachyzoites

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure.  RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Non strand specific library Messenger RNAwaspurified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Strand specific library Messenger RNAwaspurified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Clustering and sequencing After library quality control, different libraries were pooled based on the effective concentration and targeted data amount, then subjected to Illumina sequencing. The basic principle of sequencing is "Sequencing by Synthesis", where fluorescently labeled dNTPs, DNA polymerase, and adapter primers are added to the sequencing flow cell for amplification. As each sequencing cluster extends its complementary strand, the addition of each fluorescently labeled dNTP releases a corresponding fluorescence signal. The sequencer captures these fluorescence signals and converts them into sequencing peaks through computer software, thereby obtaining the sequence information of the target fragment.

value: Tachyzoites

value: ATc


title: iALG11_ATc2

description: Library name: Sample 5


title: iALG11_ATc3

description: Library name: Sample 6


title: SW1990, MRTX1133_1


title: SW1990, vehicle_2


title: SW1990, vehicle_3


title: AsPC-1, vehicle_1


title: PANC-1, vehicle_2


title: AsPC-1, vehicle_3


title: AsPC-1, MRTX1133_2


title: AsPC-1, vehicle_2


title: iALG11_1

description: Library name: Sample 1

value: DMSO


title: iALG11_3

description: Library name: Sample 3


title: KPC1199, ola_3

description: Library name: Sample9

library_source: transcriptomic single cell

data_processing:
Sequence alignment of single cell data to the mm10 genome using Cell Ranger software (version 9.0.0) from 10x Genomics, with unique molecular identifier (UMI) counts summarized for each barcode.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

extract_protocol:
Under sterile conditions, freshly collected KPC1199 mouse tumor tissues were washed twice with pre-chilled RPMI 1640 medium supplemented with 0.04% BSA. The tissues were thoroughly minced into small pieces using surgical scissors and subsequently placed in a freshly prepared enzymatic digestion solution. Digestion was carried out for 30-60 minutes in a 37°C incubator, with the mixture being inverted every 5-10 minutes to ensure uniform dissociation.The digestion solution consisted of RPMI 1640 (Corning, cat. no. 10-040-CVR), 0.04% BSA (MACS, cat. no. 1000076), and 0.2% Collagenase II (Gibco, cat. no. 17101015).Following digestion, the resulting cell suspension was filtered once or twice through a 40 μm cell strainer (BD Falcon, cat. no. 352340) and centrifuged at 300 x g for 5 minutes at 4°C. The cell pellet was resuspended in a suitable volume of medium, and an equal volume of Red Blood Cell Lysis Buffer (Miltenyi, cat. no. 130-094-183) was added. The mixture was incubated at 4°C for 10 minutes. The cell suspension was then centrifuged at 300 x g for 5 minutes, and the supernatant was discarded. The pellet was washed once more with medium by centrifuging at 300 x g for 5 minutes and discarding the supernatant. Finally, the cells were resuspended in 100 μl of RPMI 1640 medium (Corning, cat. no. 10-040-CVR) containing 0.04% BSA. The concentration and viability of the single-cell suspension were determined using a Luna-FL™ Automated Fluorescence Cell Counter (Logos Biosystems, Korea) or by manual counting with trypan blue staining.
KPC1199 tumors were processed to single cell suspension and the directly used for library extraction. Library was constructed using Chromium Next GEM Single Cell 3' Reagent Kits version3.1 (10x Genomics)

value: Olaparib


title: iALG11_2

description: Library name: Sample 2


title: KPC1199, ola_1

description: Library name: Sample7


title: KPC1199, 1133_2

description: Library name: Sample12


title: KPC1199, Combination_2

description: Library name: Sample5

value: Combination


title: Sample 160, 12 months EGCG treatment (t12)

city: Barcelona

first: Anna

last: Ramos-Triguero

address: C/ del Rosselló, 149

country: Spain

institute: FRCB-IDIBAPS

description: Library name: Sample_160_t12

data_processing:
RNA was analyzed at Microomics Systems S.L. using an Illumina TruSeq Stranded mRNA, yielding 2x125bp sequences. Quality-control was evaluated using FastQC.
Pre-processing with Trimmomatic, alignment to GRCh38 with STAR, and alignment quality-control with FastQC and MultiQC.
Reads were counted with featureCounts.
Assembly: GRCh38
Supplementary files format and content: tab-delimeted csv file includes counts for each sample

source_name: Blood

extract_protocol:
Two 5 mL tubes of blood were collected in BD Vacutainer® K3E 15% Aprotinin 250KIU (SGSH;BD361017). Peripheral blood mononuclear cells were isolated by centrifugation in Blood Collection tube BD Vacutainer®, BD CPT™ (Avantor, BDAM362781). RNA was isolated using QIAshredder (Qiagen,79654) and RNAsy Mini-Kit (Qiagen, 74104) protocols.
RNA libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit following the manufacturer’s instructions. Poly-A mRNA was purified using poly-T oligo-attached magnetic beads, fragmented, and converted to cDNA with random primers. Libraries were size-selected and sequenced on an Illumina HiSeq 2500 platform to generate 2×125 bp paired-end reads.

treatment_protocol: Participants received 9 mg/kg/day of EGCG via FontUp, a cocoa-flavored nutritional powder dissolved in 200 mL of semi-skimmed milk. FontUp was purchased from Grand Fontaine Laboratories (Barcelona, Spain).

value: Blood

value: PBMCs

value: 12 months EGCG treatment


title: KPC1199, 1133_3

description: Library name: Sample13


title: PANC-1, vehicle_1


title: KPC1199, 1133_1

description: Library name: Sample10


title: KPC1199, ola_2

description: Library name: Sample8


title: Sample 146, 12 months EGCG treatment (t12)

description: Library name: Sample_146_t12


title: KPC1199, vehicle_3

description: Library name: Sample3

value: Vehicle


title: Sample 174, 12 months EGCG treatment (t12)

description: Library name: Sample_174_t12


title: VMCUB1, p63, rep2 (ChIP)

city: Gif-sur-Yvette

first: Lilia

last: Estrada Virrueta

address: 1, Avenue de la Terrasse

country: France

description: Library name: VMCUB1_p63_2, ChIP

data_processing:
Sequencing adapters were trimmed using TrimGalore (v0.6.6).
Resulting reads were mapped to the UCSC hg19 genome using bowtie2 (v2.4.2), reporting at most one hit for each read.
Peaks were called using MACS2 (v2.2.7.1).
Bigwig files were generated after using samtools (v1.21) before applying RPKM normalization using deeptools (3.5.6).
Assembly: hg19
Supplementary files format and content: broadPeaks, BigWig

source_name: bladder cancer

growth_protocol: Cells were cultured in DMEM (MGHU3, VMCUB1) or RPMI (RT112) supplemented with 10% fetal bovine serum at 37°C under a 5% CO2 atmosphere.

extract_protocol:
Cells were crosslinked in 1% formaldehyde for 10 min at room temperature before reaction was stopped with glycine (125mM) for 5min. ChIP were carried out using the ChIP-IT High Sensitivity Kit (Actif Motif, 53040).
Library were prepared by GenomEast platform of the IGBMC Strasbourg, a member of the ‘France Génomique’ consortium (ANR-10-INBS-0009).

value: bladder cancer


title: VMCUB1, p63, rep1 (Input)

description: Library name: VMCUB1_p63_1, INPUT


title: VMCUB1, p63, rep1 (ChIP)

description: Library name: VMCUB1_p63_1, ChIP


title: VMCUB1, p63, rep2 (Input)

description: Library name: VMCUB1_p63_2, INPUT


title: KPC1199, vehicle_2

description: Library name: Sample2


title: KPC1199, Combination_3

description: Library name: Sample6


title: KPC1199, vehicle_1

description: Library name: Sample1


title: RT112, p63, rep1 (Input)

description: Library name: RT112_p63_1, INPUT


title: KPC1199, Combination_1

description: Library name: Sample4


title: Sample 164, 12 months EGCG treatment (t12)

description: Library name: Sample_164_t12


title: RT112, p63, rep1 (ChIP)

description: Library name: RT112_p63_1, ChIP


title: Sample 161, 12 months EGCG treatment (t12)

description: Library name: Sample_161_t12


title: Setdb1 8c control single embryo replicate 7

city: Grand Rapids

first: Piroska

last: Szabó

address: 333 Bostwick Ave NE

department: Department of Epigenetics

institute: Van Andel Insitute

data_processing:
Base calling was done by Illumina RTA3, and the output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0. We obtained an average of 25 M reads/library.
Adaptor sequences and low-quality reads of RNA-seq reads were trimmed using Trim Galore. Trimmed reads were aligned to mm10 reference genome using STAR with parameter “--quantMode GeneCounts”.
Bigwig tracks of alignment was generated using bamCoverage from deepTools with normalization method “CPM” (counts per million); reverse and forward strand aligment were separated
Assembly: mm10
Supplementary files format and content: bigwig files of each samples, with alignment to top and bottom strands of genome separated.

source_name: C57Bl/6N X JF1Ms F1

growth_protocol: The Setdb1 conditional knockout mouse line (Setdb1f/f) was derived from the line Setdb1tm1a(EUCOMM)Wtsi (European Mouse Mutant Archive). We removed the Pgk-neo positive selection cassette by crossing with an Flpe recombinase expressing transgenic mouse B6.Cg-Tg(Pgk1-flpo)10Sykr/J from the Jackson Laboratory (JAX#011065). Zp3-cre transgenic mice C57BL/6-Tg(Zp3-cre)93Knw/J, from the Jackson Laboratory (JAX#003651), were used to excise the SET-domain–encoding exons from Setdb1 in growing oocytes. Setdb1f/f; Zp3-CreTg+ female mice were used as the experimental group. Setdb1f/f female mice without the Zp3-Cre transgene were used as the control group. Setdb1f/f and Zp3-Cre mice were maintained on a C57BL/6N and C57BL/6J genetic background, respectively.

extract_protocol:
Total RNA was isolated from single 2c and 8c embryos using RNA-Bee extraction followed by ethanol precipitation according to the manufacturer's instructions. Briefly, the tubes containing single embryos in 100 µL RNA-Bee were thawed and vortexed and 20 µL of chloroform was added. After vortexing rigorously for 15-30 seconds, the tubes were placed on ice for 5 min and then centrifuged at 12,000 g for 15 min at 4°C. The aqueous phase was transferred into a new 1.5 mL tube containing 3 µL of 0.25% linear polyacrylamide which was used as a carrier. 50 µL of isopropanol was added and vortexed for 15 sec, and the samples were kept on ice for 30 minutes to precipitate the RNA. After centrifugation at 10,000g for 15 min at 4°C the pellet of RNA was washed with 0.4 mL of cold 75% ethanol. After re-spinning and brief air drying, the total RNA was dissolved in 22.3 µL of 10 mM Tris-HCl buffer pH 8.5 containing 0.2 U/µL RNasin® ribonuclease inhibitor (Promega, Cat. N2515). Potential genomic DNA contamination was removed from the total RNA using 0.2 µL of rDNase I from the DNA-free Kit (Ambion, Cat. AM1906). After the DNase Inactivation Reagent (0.1 volume) was added and centrifuged, the RNA was transferred into a new tube containing 3 µL of 0.25% linear polyacrylamide and recovered by ethanol precipitation.  The single embryo total RNA samples were eluted in 7 µL of 10 mM Tris-HCl buffer pH 8.5 containing 0.2 U/µL RNasin® ribonuclease inhibitor.
Libraries were prepared by the Van Andel Genomics Core (RRID: SCR_022913) using the Takara SMART-Seq Stranded Kit (Cat. No. 634444, Takara Biosciences USA, Mountain View CA) with the following specifics. Samples were randomized before beginning processing to avoid batch effects. Fragmentation for embryo RNA and Takara control RNA was performed for 10 min or 6 min, respectively, at 85°C to obtain an average insert size of 250 bp. 10 cycles were used for PCR1, during which unique dual indexes were added to each sample, then 8 samples were pooled for subsequent steps. PCR2 used 12 cycles. Library pools were assessed for quality using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems).

treatment_protocol: To collect WT and Setdb1mat-/+ embryos at 2c stage, female mice at 6~8 weeks of age were superovulated by intraperitoneally injecting 5 IU of human chorionic gonadotropin (hCG) 46~48 hours after injecting 5 IU of pregnant mare serum gonadotropin (PMSG) and then mated with wild-type male mice. To collect WT and Setdb1mat-/+ embryos at 8c stage, we used CARD HyperOva (Cosmo Bio, Catalog No: KYD-010-EX) on 26~30 days old female mice.  2-cell and 8-cell embryos were harvested from the oviduct in M2 medium at 1.5 dpc and 2.5 dpc, respectively. The embryos were washed three times in PBS. Individual embryo was manually picked into 1.5 mL tubes, added 100 µL RNA-Bee (Tel-Test or Amsbio, Cat. CS-105B), snap frozen on dry ice and kept at -80 °C until RNA isolation.

tag: age days_post_coitum

tag: collection time

tag: embryo stage

value: 8 cell

tag: strain

value: C57Bl/6N X JF1Ms F1


title: Sample 149, 12 months EGCG treatment (t12)

description: Library name: Sample_149_t12


title: Setdb1 8c control single embryo replicate 5


title: MGHU3, p63, rep1 (Input)

description: Library name: MGHU3_p63_1, INPUT


title: Setdb1 8c control single embryo replicate 6


title: Setdb1 8c control single embryo replicate 4


title: Sample 143, 12 months EGCG treatment (t12)

description: Library name: Sample_143_t12


title: Sample 135, 12 months EGCG treatment (t12)

description: Library name: Sample_135_t12


title: Setdb1 8c control single embryo replicate 2


title: Setdb1 8c control single embryo replicate 3


title: MGHU3, p63, rep1 (ChIP)

description: Library name: MGHU3_p63_1, ChIP


title: MGHU3, p63, rep2 (ChIP)

description: Library name: MGHU3_p63_2, ChIP


title: Sample 146, baseline (t0)

description: Library name: Sample_146_t0

value: baseline


title: Setdb1 2c control single embryo replicate 7

value: 2 cell


title: Sample 174, baseline (t0)

description: Library name: Sample_174_t0


title: Setdb1 2c control single embryo replicate 6


title: MDCK cells IAV infection 24h-2

city: Tianjin

first: Shu-Lin

last: Liu

address: No.94 of Weijin Road

institute: Nankai University

description: Library name: 24h-2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Assembly: canFam4
Supplementary files format and content: CSV(.list) files include FPKM value for each sample

organism: Canis lupus familiaris

source_name: MDCK cells

extract_protocol:
RNA was purified using the Takara RNA Extraction Kit. 1 μg of total RNA was used for library construction.
The extracted and purified mRNA is subjected to quality control. Samples that pass the quality control are then used for library construction with a kit.

value: MDCK cells

value: Epithelial cell


title: Setdb1 2c control single embryo replicate 4


title: Setdb1 2c control single embryo replicate 5


title: Setdb1 8c control single embryo replicate 8


title: Setdb1 2c control single embryo replicate 2


title: Sample 160, baseline (t0)

description: Library name: Sample_160_t0


title: MDCK cells IAV infection 24h-3

description: Library name: 24h-3


title: Setdb1 2c control single embryo replicate 3


title: Setdb1 8c matKO single embryo replicate 8


title: Setdb1 8c matKO single embryo replicate 7


title: Sample 164, baseline (t0)

description: Library name: Sample_164_t0


title: MGHU3, p63, rep2 (Input)

description: Library name: MGHU3_p63_2, INPUT


title: MDCK cells control-3

description: Library name: non-3


title: Setdb1 8c matKO single embryo replicate 6


title: Sample 161, baseline (t0)

description: Library name: Sample_161_t0


title: Setdb1 8c matKO single embryo replicate 5


title: MDCK cells control-2

description: Library name: non-2


title: Setdb1 8c control single embryo replicate 1


title: Setdb1 8c matKO single embryo replicate 4


title: Sample 149, baseline (t0)

description: Library name: Sample_149_t0


title: MDCK cells control-1

description: Library name: non-1


title: Setdb1 8c matKO single embryo replicate 3


title: Sample 143, baseline (t0)

description: Library name: Sample_143_t0


title: Setdb1 8c matKO single embryo replicate 1


title: Setdb1 8c matKO single embryo replicate 2