title: U87-RR_1

city: Nanjing

first: Xu

last: Qian

state: Jiangsu

address: 101 Longmian Ave

institute: Nanjing Medical University

description:
U87-RR_1
U87 gene_expression

data_processing:
Sequencing reads were mapped to the human genome (GRCh38) and transcripts per million (TPM) was used to normalize for sequencing depth and gene length for relative quantity.
The differential expression analysis was performed using DESeq2 according to the TPM values.
Gene set enrichment analysis (GSEA) was performed by selecting differentially expressed genes, generating a pre-ranked list, and weight by the inverse of the FDR multiplied by the sign of the log2(fold change) and inputting the list into the GSEA application
Gene set variation analysis (GSVA) was implemented by rank-normalizing and rank-ordering gene expression values, calculating the Empirical Cumulative Distribution Functions (ECDF) of the signature genes and the remaining genes, calculating a statistic by integration of the difference between the ECDFs and inputting into the GSVA package in R
Assembly: human genome (GRCh38)
Supplementary files format and content: excel files include FPKM, TPM and read count for each sample

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

extract_protocol:
Total RNA was extracted from GBM tissues or paired radioresistant and parental GBM cells using Trizol according to manual instruction.
The mRNA was purified by Oligo(dT)-attached magnetic beads and the cDNA fragments were amplified and circularized to get the final library. The library was amplified to make DNA nanoball which had more than 300 copies of one molecular. DNA nanoballs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China). The mRNA library construction, preparation, sequencing and quality control were provided by BGI.

treatment_protocol: Radioresistant cell lines were developed from their respective GBM cell lines (U87and U251) by weekly exposure to single 5 Gy of radiation. During the period, U87 cells received a total radiation dose of 100 Gy, while U251 cells received 60 Gy in total. The radioresistance of the established cell lines were validated in vitro through colony formation assay and DNA damage detection. Cells were subsequently maintained with further weekly doses of 5 Gy.

value: glioblastoma

value: radioresistant


title: U87-RR_2

status: Public on Jun 01 2023

type: SRA

country: China

description:
U87-RR_2
U87 gene_expression

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment


title: ATAC Il17eGFP_d3_npTh17_GFP_2

city: Cambridge

first: Pratiksha

middle: I

last: Thakore

state: MA

address: 415 Main St

country: USA

institute: Broad Institute

library_source: genomic

data_processing:
Base-calling was performed by RTA v2.4.11, and the BCL files were translated to fastqs using bcl2fastq2 v2.20.0.
ATAC-seq: Reads were aligned to reference mouse annotation mm10 using Bowtie2, and filtered for duplicated and mitochondrial reads. Peak-calling was performed using MACS2. Read counts per peak were computed using bedtools multicov tool for each sample and then column combined into a matrix.
Assembly: mm10
Supplementary files format and content: ATAC-seq: comma-separated values (CSV) files include count values for each gene in each sample.

molecule: genomic DNA

organism: Mus musculus

source_name: Sorted GFP+ cells polarized in npTh17 conditions for 72 hours

growth_protocol: For the in vitro differentiation of naive ATAC CD4+ T cells, naive ATAC CD4+ ATAC CD44- CD62L+ cells were activated with plate-bound anti-CD3 and anti-CD28 antibodies in the presence of cytokines. For the acquisition of ex vivo Th17 cells, mice were immunized subcutaneously into the flanks with an emulsion of the MOG35-55 peptide and M. tuberculosis H37Ra extract in CFA for the induction of ATAC EAE.

extract_protocol:
6,000 viable cells were sorted into PBS/2% FCS and were stored in BambankerTM cell freezing media at -80°C.
For bulk ATAC-seq, cells were thawed at 37°C. Subsequently, cells were lysed and tagmented in 1X TD Buffer, 0.2l TDE1 (Illumina), 0.01% digitonin, and 0.3X PBS at 37°C for 30 min at 300 rpm, as previously described [86]. DNA purification was performed with the MinElute PCR purification kit (QIAGEN). The complete eluate was pre-amplified with 5 PCR cycles using indexed primers with NEBNext High-Fidelity 2X PCR Master Mix (NEB) and the number of additional cycles was determined by SYBR Green quantitative PCR. After DNA purification, library quantification and quality control were performed with the Kapa Library Quantification Kit (Kapa Biosystems) and a Qubit dsDNA HS Assay kit (Invitrogen). Libraries were sequenced on an Illumina NextSeq 550 system with paired-end reads of 37 base pairs in length.

treatment_protocol: For the knockout of ATAC Bach2, we obtained naive T cells from Cas9 knock-in mice and in vitro differentiated them to npTh17 and pTh17 cells while simultaneously transducing them with retroviral vectors encoding a ATAC Bach2-targeting single guide RNA (ATAC Bach2 KO) or empty sgRNA as control. For the overexpression of ATAC Bach2, we polarized naive ATAC CD4+ T cells into pTh17 cells by simultaneous transduction of retroviral vectors with a constitutive ATAC Bach2 cDNA expression cassette (ATAC Bach2 OE) or an empty control.

tag: tissue

value: Spleen and lymph nodes


title: RNA-Seq Clone6_Plus

city: Boston

first: David

middle: T

last: Scadden

address: 185 Cambridge St

department: Center for Regenerative Medicine

institute: MGH

description: Gene expression data in ER-Hoxb8 cells

data_processing:
Illumina software used for basecalling.
Raw sequences of RNA-seq were mapped to the mouse reference genome mm9 using a Star aligner v2.7.3a
Read counts for individual genes were produced using the un-stranded count feature in HTSeq v.0.6.0
Genome_build: mm9
Supplementary_files_format_and_content: raw count

source_name: Mouse Bone Marrow ER-Hoxb8 GMP cells

growth_protocol: ER-HoxB8 cells were maintained in RPMI medium supplemented with 10% FBS, penicillin/streptomycin, and SCF. For primary monocytes, the mouse bone marrow cells were sorted from flow cytometry.

extract_protocol:
For RNA-seq, total RNAs were extracted using RNeasy mini kit (Qiagen).
RNA-sequencing libraries were generated using library prep kits (NEB) according to the manufacturer’s instructions.

value: ER-Hoxb8 cells


title: ATAC Il17eGFP_d3_pTh17_all_2

source_name: Sorted live cells polarized in pTh17 conditions for 72 hours


title: Kidney, KU0063794, rep 1

first: Alexander

last: Tyshkovskiy

state: Massachusetts

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital, Harvard Medical School

data_processing:
HiSeq Control Software v2.2 was used for system control and base calling through an integrated primary analysis software RTA (Real Time Analysis. v1.18). The BCL (base calls) binary was converted into FASTQ utilizing illumina package bcl2fastq (v1.8.4).
Quality filtering and adapter removal were performed using Trimmomatic version 0.32.
Reads were mapped to mm10 mouse genome using STAR (version 2.5.2b). Genes were counted via featureCounts (version 1.5).
Assembly: mm10
Supplementary files format and content: comma-separated values file includes gene counts for each sample

molecule: polyA RNA

source_name: Kidney

extract_protocol:
After sacrifice, liver and kidney were removed and frozen on dry ice. RNA was extracted from tissues with PureLink RNA Mini Kit and passed to CEL-seq.
Sequencing libraries were prepared as described in (Hashimshony et al., 2016).
CEL-seq

treatment_protocol: 3-month old male mice were kept on control diet (Purina 5LG6) or the same diet supplied with AS-703026, ascorbyl-palmitate, AZD8055, enzastaurin, GDC-0941 and KU0063794 for 1 month.

value: Kidney

tag: strain

tag: Sex

value: Male

tag: dose

value: 10 ppm

tag: age

value: 4 months


title: U87_3

description:
U87_3
U87 gene_expression

value: parental


title: ATAC Il17eGFP_d3_npTh17_GFP_1


title: U87_2

description:
U87_2
U87 gene_expression


title: ATAC Il17eGFP_d3_npTh17_all_3

source_name: Sorted live cells polarized in npTh17 conditions for 72 hours


title: Liver, AS-703026, rep 1

source_name: Liver

value: Liver

value: 30 ppm


title: Kidney, GDC-0941, rep 4

value: 50 ppm


title: U87_1

description:
U87_1
U87 gene_expression


title: U87-RR_3

description:
U87-RR_3
U87 gene_expression


title: ATAC Il17eGFP_d2_pTh17_GFP_3

source_name: Sorted GFP+ cells polarized in pTh17 conditions for 48 hours


title: ATAC Il17eGFP_d3_npTh17_all_2


title: Kidney, GDC-0941, rep 3


title: Kidney, GDC-0941, rep 1


title: RNA-Seq Clone4_Plus

description: Gene expression data in ER-Hoxb8 cells


title: RNA-Seq Clone7_Plus

description: Gene expression data in ER-Hoxb8 cells


title: RNA-Seq Clone3_Plus

description: Gene expression data in ER-Hoxb8 cells


title: Kidney, KU0063794, rep 2


title: RNA-Seq Clone1_Plus

description: Gene expression data in ER-Hoxb8 cells


title: Kidney, enzastaurin, rep 4

value: Enzastaurin

value: 75 ppm


title: Kidney, GDC-0941, rep 2


title: RNA-Seq Clone2_Plus

description: Gene expression data in ER-Hoxb8 cells


title: U251-RR_1

description:
U251-RR_1
U251 gene_expression


title: U251-RR_2

description:
U251-RR_2
U251 gene_expression


title: ATAC Il17eGFP_d2_pTh17_all_3

source_name: Sorted live cells polarized in pTh17 conditions for 48 hours


title: U251-RR_3

description:
U251-RR_3
U251 gene_expression


title: Kidney, enzastaurin, rep 2


title: U251_3

description:
U251_3
U251 gene_expression


title: ATAC Il17eGFP_d2_pTh17_all_1


title: ATAC Il17eGFP_d2_pTh17_GFP_1


title: RNA-Seq Clone5_Plus

description: Gene expression data in ER-Hoxb8 cells


title: ATAC-Seq Clone25_Minus

data_processing:
Illumina software used for basecalling.
Raw sequences of ATAC-seq data were mapped with a BWA mapper with a default setting to the mouse genome (mm9).
Genome_build: mm9
Supplementary_files_format_and_content: peaks.bed

source_name: Mouse Bone Marrow ER-Hoxb8 monocytic cells

growth_protocol: ER-HoxB8 cells were maintained in RPMI medium supplemented with 10% FBS, penicillin/streptomycin, and SCF.

extract_protocol: ATAC-seq samples were performed as previously described (Buenrostro et al., 2015)


title: Kidney, enzastaurin, rep 3


title: ATAC Il17eGFP_d3_npTh17_all_1


title: ATAC-Seq Clone22_Minus


title: U251_2

description:
U251_2
U251 gene_expression


title: ATAC Il17eGFP_d2_npTh17_GFP_3

source_name: Sorted GFP+ cells polarized in npTh17 conditions for 48 hours


title: U251_1

description:
U251_1
U251 gene_expression


title: ATAC-Seq Clone21_Minus


title: ATAC Il17eGFP_d2_npTh17_GFP_2


title: Kidney, control for longevity compounds, rep 6

value: Control


title: ATAC-Seq Clone23_Minus


title: ATAC-Seq Clone24_Minus


title: ATAC-Seq Clone20_Minus


title: ATAC Il17eGFP_d2_pTh17_GFP_2


title: Kidney, enzastaurin, rep 1


title: Recurrent_2

description:
Recurrent_2
tissue gene_expression

source_name: glioblastoma

value: recurrent tumor


title: Primary_2

description:
Primary_2
tissue gene_expression

value: primary tumor


title: ATAC-Seq Clone19_Minus


title: C147

city: Shenzhen

first: Zheng

last: Zhang

state: Guangdong

address: No. 29, Bulan Road

institute: Shenzhen 3rd People's Hospital

description:
Single-cell RNAseq
MGI SEQ2000

data_processing:
The Cell Ranger Software Suite (Version 3.1.0) was used to perform sample de-multiplexing, barcode processing and single-cell UMI counting with human GRCh38 as the reference genome. Specifically, splicing-aware aligner STAR was used in FASTQs alignment. Cell barcodes were then determined based on distribution of UMI count automatically.
Genome_build: GRCh38
Supplementary_files_format_and_content: h5, raw count matrix generated by Cell Ranger count

source_name: BALF

extract_protocol: Total 11 µl of single cell suspension and 40 µl barcoded Gel Beads were loaded to Chromium Chip A to generate single-cell gel bead-in-emulsion (GEM). The poly-adenylated transcripts were reverse-transcribed later. The single-cell capturing and downstream library constructions were performed using the Chromium Single Cell 3’ V3 (liver biopsy) and Chromium Single Cell 5’ (BALF) library preparation kit according to the manufacturer’s protocol (10x Genomics). Full-length cDNA along with cell-barcode identifiers were PCR-amplified and sequencing libraries were prepared and normalized to 3 nM.

tag: organ

value: Lung

tag: diagnosis

value: male severe covid19 positive patient

tag: sars-ncov-2 status

value: positive

tag: cell subsets

value: Total cell


title: ATAC Il17eGFP_d2_pTh17_all_2

value: Spleen and lymph nodes


title: ATAC Il17eGFP_d2_npTh17_all_3

source_name: Sorted live cells polarized in npTh17 conditions for 48 hours


title: Kidney, control for longevity compounds, rep 5

value: Kidney

value: Male


title: Recurrent_1

description:
Recurrent_1
tissue gene_expression

value: glioblastoma


title: Kidney, control for longevity compounds, rep 2

value: 4 months


title: Kidney, control for longevity compounds, rep 4


title: Kidney, control for longevity compounds, rep 3


title: Primary_1

description:
Primary_1
tissue gene_expression


title: Kidney, control for longevity compounds, rep 1


title: ATAC-Seq Clone18_Minus

value: ER-Hoxb8 cells


title: ATAC-Seq Clone16_Minus


title: ATAC Il17eGFP_d2_npTh17_GFP_1


title: IL4_6_adipocyte_precursor_mRNAseq

city: Bongmyeongdong

first: Mihye

last: Lee

state: Cheonan

address: 25, Bongjeong-ro, Dongnam-gu, Cheonan-si, 31151, Korea

department: Department of Integrated Biomedical Science

country: South Korea

institute: Soonchunhyang Institute of Medi-bio Science (SIMS)

data_processing:
RNA-seq
From mRNA sequencing, low-quality raw sequence reads, reads with adapters, and reads with unknown bases were filtered by SOAPnuke software to yield clean reads.
Filtered clean reads were mapped into the reference mouse genome (mm10) using HISAT.
Novel genes predicted using StringTie and Cuffcompare to compare the reconstructed transcripts to the reference annotation and then used CPC tools to predict the novel transcripts.
Gene expression level for each sample was determined using the tools Bowtie2 and RSEM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
miRNA-seq
Small RNA raw sequencing reads are filtered based on their quality.
The readings are aligned to the reference mouse genome (mm10) and miRBase v21 precursor miRNAs to find known and novel miRNAs.
The miRDeep2 algorithm is then used to predict potential hairpin structures.
Unique cluster reads are then sequentially matched against the reference mouse genome, miRBase v21, and the non-coding RNA database, Rfam9.1 to classify known miRNAs.
Read counts for each miRNA are extracted from mapped miRNAs to report the abundance of each miRNA.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Subcutaneous white adipose tissue

extract_protocol:
The total RNA of the samples was extracted with the Trizol (Invitrogen) reagent and used for construction of sequencing libraries.
The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

value: Subcutaneous white adipose tissue

value: Adipocyte precursor

value: IL4 treatment


title: Kidney, AZD8055, rep 3

value: 20 ppm


title: ATAC-Seq Clone17_Minus


title: ATAC Il17eGFP_d2_npTh17_all_1


title: ATAC-Seq Clone13_Minus


title: ATAC Il17eGFP_d2_npTh17_all_2


title: IL4_4_adipocyte_precursor_mRNAseq


title: Kidney, AZD8055, rep 2


title: Kidney, AZD8055, rep 4


title: control_2_adipocyte_precursor_mRNAseq

value: control


title: ATAC-Seq Clone15_Minus


title: ATAC Il17eGFP_d1_pTh17_all_3

source_name: Sorted live cells polarized in pTh17 conditions for 24 hours


title: control_1_adipocyte_precursor_mRNAseq


title: ATAC Il17eGFP_d1_pTh17_all_1


title: ATAC Il17eGFP_d1_pTh17_all_2


title: ATAC-Seq Clone11_Minus


title: Kidney, AZD8055, rep 1


title: Liver, WT_rep12

city: Shantou

first: Xiu-Hui

last: Zhan

address: 22, Xinling Road

institute: Shantou University

data_processing:
Zebra software (developed for BGISEQ-500) used for base calling
We define "dirty" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads. Filtering steps are as follows: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).
Sequencing reads after filtering were mapped to reference genome using the HISAT software and to reference gene by Bowtie2 tool, followed by strict quality control for each sample from several aspects.
Gene expression was quantified by RSEM software and differentially-expressed genes between samples were analyzed by screening using the DEGSeq method.
Genome_build: GCF_000001635.25_GRCm38.p5
Supplementary_files_format_and_content: txt file includes FPKM values for each sample

extract_protocol:
Total RNA was directly extracted from liver tissue of using TRIzol reagent, and these samples were then prepared according to GBI's instructions.
RNA libraries were prepared for sequencing using standard BGISEQ-500 RNA-sequencing protocols.

value: Liver

tag: genotype

value: wild type


title: Kidney, ascorbyl-palmitate, rep 3

value: Ascorbyl-palmitate

value: 6.3 ppm


title: ATAC-Seq Clone10_Minus


title: Liver, WT_rep11


title: Kidney, ascorbyl-palmitate, rep 2


title: control_3_adipocyte_precursor_mRNAseq


title: ATAC-Seq Clone9_Minus


title: ATAC Il17eGFP_d1_npTh17_all_2

source_name: Sorted live cells polarized in npTh17 conditions for 24 hours


title: RNA EAE_CNS_5

data_processing:
Base-calling was performed by RTA v2.4.11, and the BCL files were translated to fastqs using bcl2fastq2 v2.20.0.
RNA-seq: Paired reads were mapped to mouse annotation mm10 using TopHat, and after duplicates were removed, counts tables were generaed using htseq counts. For more details, see Method section of paper, "Bulk RNA-seq pre-processing"
Assembly: mm10
Supplementary files format and content: RNA-seq: comma-separated values (CSV) files include read count values for each gene in each sample.

source_name: Sorted IL17+ cells harvested from the central nervous system at the peak of EAE

growth_protocol: For the in vitro differentiation of naïve CD4+ T cells, naïve CD4+ CD44- CD62L+ cells were activated with plate-bound anti-CD3 and anti-CD28 antibodies in the presence of cytokines. For the acquisition of ex vivo Th17 cells, mice were immunized subcutaneously into the flanks with an emulsion of the MOG35-55 peptide and M. tuberculosis H37Ra extract in CFA for the induction of EAE.

extract_protocol:
6,000 cells were sorted by FACS from the in vitro culture or draining lymph nodes and central nervous system of EAE mice into 5ul TCL buffer supplemented with 1% 2-mercaptoethanol and stored at -80°C until library preparation.
For bulk RNA-seq, full-length RNA-seq libraries were prepared following a modified SMART-Seq2 protocol as previously described. The cDNA concentration was measured using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) and normalized to 0.25ng/ul. The cDNA libraries were prepared using the Nextera XT DNA Library Preparation kit (Illumina). Final libraries were confirmed to have a size of 500 bp using a Bioanalyzer (Agilent). Prior to sequencing, the uniquely barcoded libraries were pooled, normalized to 2 nM, and denatured using 0.1 N NaOH. Flow cell cluster amplification and sequencing were performed according to the manufacturer’s protocols using the paired-end Illumina sequencing (38bp X 2) with 75 cycle Nextseq 500 high output V2 kit (Illumina).

value: CNS

value: Wildtype


title: ATAC Il17eGFP_d1_npTh17_all_1

value: Spleen and lymph nodes


title: ATAC-Seq Clone12_Minus


title: ATAC Il17eGFP_d1_npTh17_all_3


title: Liver, WT_rep9


title: ATAC-Seq Clone8_Minus


title: Kidney, ascorbyl-palmitate, rep 4

value: Kidney


title: Kidney, AS-703026, rep 4

value: Male

value: 30 ppm


title: ATAC-Seq Clone7_Minus


title: ATAC-Seq Clone6_Minus


title: Kidney, AS-703026, rep 3

value: 4 months


title: Liver, WT_rep7


title: IL4_5_adipocyte_precursor_mRNAseq


title: Liver, WT_rep10


title: RNA EAE_CNS_4


title: ATAC-Seq Clone5_Minus

value: ER-Hoxb8 cells


title: RNA EAE_CNS_1


title: ATAC-Seq Clone4_Minus


title: Liver, WT_rep8


title: Kidney, ascorbyl-palmitate, rep 1


title: Liver, WT_rep5


title: RNA Time_course_Th1_12hr_1

source_name: Sorted live cells polarized in Th1 conditions after 12hr


title: ATAC-Seq Clone3_Minus


title: RNA EAE_CNS_3


title: miR10b_inj_30

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

data_processing:
RNAseq raw data quality was checked using FastQC (v0.11.09) and adapter trimming on raw data was performed using Cutadapt (v3.5). Reads with low quality (quality score < 33, error rate > 10%) or reduced length after trimming (<25 bp) were removed before alignment
We used the reference genome downloaded from Ensembl GRCm38 release 101, and the reference index was built using Star (v2.7.9a). Paired end trimmed read alignment and raw read count calculation was performed using RSEM software (v1.3.1).
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (v1.36.0).
Assembly: GRCm38 release 101
Supplementary files format and content: tab-delimited text files include DESeq2 normalized count values for each sample

source_name: mammary tumor

growth_protocol: To induce super-ovulation, female mice (c57bl/6) received intra-peritoneal injections of 5 IU of pregnant mare’s serum gonadotropin (PMSG). About 48 hours after the PMSG injection, mice were injected with 5 IU of human chorionic gonadotropin (hCG). Super-ovulated females were mated with c57bl/6 male mice.

extract_protocol:
Total RNA was isolated from snap frozen mouse tissues (mammary tumors and embryos at the blastocyst stage) using Qiagen’s RNeasy extraction kit, according to the manufacturer’s instructions. RNA purity, integrity and quality was examined by Bioanalyzer 2100 (Agilent Technologies) and Qubit (Thermo Fisher Scientific)
Transcript libraries were constructed using the TruSeq mRNA Library Prep Kit (Illumina)

treatment_protocol: About 16 hours later, fertilized eggs were harvested. Zygotes were injected with the RNA load from sperm of CO and DDT-exposed males (sperm RNA isolated from 5 mice per group was pooled prior to injection ). Each zygote received 10 pL injection of the sperm RNA load (the amount of sperm RNA are the equivalent to RNA from 10 sperm cells or approximately ~2-10ng/µL). Injected zygotes were transferred into recipient female mice to produce offspring. Another subset of zygotes was injected with synthetic miRNA-10b or scramble miR (at 2ng/µL; mirVana®, ThermoFisher) diluted in TE solution (10mM Tris-HCl, pH7.4, 0.25 EDTA) or TE solution only (to control for microinjection).  Synthetic miRNAs are double- stranded RNA oligonucleotides that mimic a specific endogenous mature miRNA. Injected zygotes were transferred into recipient female mice as described above for term delivery. A subset of the of zygotes injected with synthetic miRNA-10b or controls were cultured and harvested at the blastocyst stage (E3.5)

value: mammary tumor

value: zygote stage injected with synthetic miRNA-10b


title: miR10b_inj_29


title: RNA CD4diff_Th0_4

source_name: Sorted live cells polarized in Th0 conditions for 72 hours


title: ATAC-Seq Clone1_Minus


title: Liver, WT_rep3


title: RNA CD4diff_Th0_3


title: miR10b_inj_28


title: RNA CD4diff_Th0_2


title: Liver, WT_rep6


title: ATAC-Seq Clone2_Minus


title: Liver, WT_rep2


title: CO_inj_27

value: zygote stage injected with vehicle solution


title: ATAC-Seq Clone25_Plus

source_name: Mouse Bone Marrow ER-Hoxb8 GMP cells


title: Liver, WT_rep1


title: Liver, WT_rep4


title: ATAC-Seq Clone24_Plus


title: CO_inj_26


title: Liver, L2 13_rep12


title: CO_inj_25


title: ATAC-Seq Clone23_Plus


title: RNA CD4diff_Th0_1


title: Kidney, AS-703026, rep 1

source_name: Kidney


title: ATAC-Seq Clone22_Plus


title: scATAC_Th1_2

library_source: genomic single cell

data_processing:
Basecalls performed by RTA v2.4.11.
RNA-seq: Fastq files were generated from bcl with CellRanger v2.2.0 with default parameters. ATAC-seq: Fastq files were generated from bcl with CellRanger-ATAC v1.0.1 with default parameters.
RNA-seq: Reads were mapped to mm10 and UMI count matrices were computed by CellRanger v2.2.0 with default parameters. ATAC-seq: Reads were mapped to mm10 and UMI count matrices were computed by CellRanger-ATAC v1.0.1.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (scRNA-seq) and barcodes.tsv, peaks.bed, and matrix.mtx (scATAC-seq) files together define a matrix of raw UMI counts

source_name: Sorted live cells polarized in Th1 conditions for 48 hours

growth_protocol: For the in vitro differentiation of naïve CD4+ T cells, naïve CD4+ CD44- CD62L+ cells were activated with plate-bound anti-CD3 and anti-CD28 antibodies in the presence of cytokines.

extract_protocol:
After 48h, live cells were sorted into PBS/2%FCS and were encapsulated into droplets and libraries were prepared using the Chromium Single Cell 5’ Library & Gel Bead Kit (10x Genomics) following the manufacturer’s instructions.
ScRNA-seq library preparations were performed according to manufacturer’s instructions (10X Genomics, Chromium Single Cell 5’ Library & Gel Bead Kit). scATAC-seq library preparations were performed according to manufacturer's instructions (10X Genomics, Chromium Single Cell ATAC Library & Gel Bead Kit).

value: spleen and lymph nodes


title: scATAC_Th1_1


title: scATAC_pTh17_2


title: ATAC-Seq Clone21_Plus


title: ATAC-Seq Clone20_Plus


title: Liver, L2 13_rep11

source_name: Liver


title: scATAC_pTh17_1

source_name: Sorted live cells polarized in pTh17 conditions for 48 hours


title: Liver, L2 13_rep10


title: DDT_2ng_22

description: These are the samples injected with scramble miR (at 2ng/µL; mirVana®, ThermoFisher) diluted in TE solution (10mM Tris-HCl, pH7.4, 0.25 EDTA). They were used to validate the functional importance of miRNA-10b.

value: DDT injected with 2ng/uL scramble miR


title: scATAC_npTh17_2


title: Liver, L2 13_rep8

value: Liver


title: Liver, L2 13_rep9


title: DDT_2ng_23


title: Liver, L2 13_rep6


title: ATAC-Seq Clone18_Plus


title: CO_2ng_21

value: CO injected with 2ng/uL scramble miR


title: CO_2ng_20


title: ATAC-Seq Clone17_Plus


title: NCI-H23-R (AMG 510) treated with AMG510 [SAM24390915]

city: South San Francisco

first: Marc

last: Hafner

state: CA

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

data_processing:
RNA-Seq reads were first aligned to ribosomal RNA sequences to remove ribosomal reads
remaining reads were aligned to the human reference genome (GRCh38) using GSNAP version 2013-10-10, allowing a maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 —pairmax-rna=200000—clip-overlap)
To quantify gene expression levels, the number of reads mapped to the exons of each RefSeq gene was calculated.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file that include gene counts for each sample

source_name: Lung

extract_protocol:
Total RNA
TrueSeq Stranded Total RNA Dual index

value: Lung

value: Carcinoma Non-Small Cell


title: NCI-H23-R (AMG 510) treated with AMG510 [SAM24390914]


title: Liver, L2 13_rep5


title: DDT_2ng_24


title: ATAC-Seq Clone16_Plus


title: DDT_6

value: zygote stage injected with DDT-exposed male sperm


title: CO_2ng_19


title: NCI-H23 treated with AMG510 [SAM24390913]


title: ATAC-Seq Clone15_Plus


title: Liver, L2 13_rep3


title: DDT_5


title: NCI-H23 treated with AMG510 [SAM24390912]


title: Liver, L2 13_rep7


title: ATAC-Seq Clone13_Plus


title: NCI-H23 treated with DMSO [SAM24390911]

value: DMSO


title: Liver, L2 13_rep2


title: Liver, L2 13_rep1


title: DDT_4


title: NCI-H23 treated with DMSO [SAM24390910]


title: ATAC-Seq Clone11_Plus


title: CO_2

value: zygote stage injected with control male sperm


title: CO_3


title: NCI-H358-R (AMG 510) treated with AMG510 [SAM24385476]


title: ATAC-Seq Clone19_Plus


title: CO_1


title: Wild type + DP - sample 3 (OMA - DP 6-6)

city: Richmond

first: Janina

middle: P

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

description:
WT iron deplete
Pi - OMA14 vs. Pi - OMA14 + DP

data_processing:
Base calls were done using CLC Genomic Workbench
Reads were aligned to the genomes of Prevotella intermedia OMA14 NZ_AP014597 and NZ_AP014598 using Genomic Workbench
Reads per gene were determined using Genomic Workbench
Statistical analysis was done using Genomic Workbench
Genome_build: Prevotella intermedia OMA14 two genomes: NZ_AP014597 and NZ_AP014598

organism: Prevotella intermedia

source_name: Bacterial cell

growth_protocol: Samples of wildtype Prevotella intermedia OMA14 were grown in an overnight culture of BHI media. The overnight cultures served to inoculate cultures of BHI media starting at an OD660 of approximately 0.05. Cultures were grown with and without dipyridyl to mid-log phase, centrifuged, and stored at -20 °C.

extract_protocol:
RNA isolation was carried out using the RNeasy mini-kit (Qiagen) following manufacturers protocol. Residual DNA was removed using the DNA-free DNase kit (Ambion) following manufacturers protocol.
For RNA-seq library generation, the Ovation complete Prokaryotic RNA-Seq DR multiplex kit (Nugen) was used. The library was generated following the manufacturers protocol and fragment sizes from sonication during library generation was confirmed using a bioanalyzer (Agilent Technologies). Libraries were sequenced by VCU nucleic acid sequencing core using Miseq Illumina sequencing.

treatment_protocol: Dipyridyl (Fe Chelator) - 150uM

tag: phase of growth

value: logarithmic phase of growth

tag: dp treatment

value: iron deplete


title: NCI-H358-R (AMG 510) treated with AMG510 [SAM24385475]


title: ATAC-Seq Clone10_Plus


title: ATAC-Seq Clone9_Plus


title: Wild type + DP - sample 4 (OMA - DP 6-8)


title: Wild type + DP - sample 2 (QG20)


title: NCI-H358-R (AMG 510) treated with AMG510 [SAM24385474]


title: ATAC-Seq Clone8_Plus


title: ZT22-KO3-WAT

city: Guangzhou

first: Min

last: Chen

address: No. 232, East Waihuan Street/Road

institute: Guangzhou university of Chinese medicine

data_processing:
Clean reads were obtained by removing those containing an adapter and ploy-N using FASTQ program, and aligned to mouse GRCm38/mm10 genome using HISAT2 v2.0.4 with default parameters.
Read counts were normalized to FPKM values using DESeq2 (v.1.16.1).
FeatureCounts v1.5.0-p3 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.
Assembly: GRCm38/mm10 genome
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: White adipose tissue

growth_protocol: 8- to 12-week-old male mice were used , and were maintained on a 12 h light/dark cycle (lights on at 7:00 AM, lights off at 7:00 PM) with free access to water and food.

extract_protocol:
RNA was isolated using Trizol (Invitrogen, Carlsbad, CA) and its quality was checked using an Agilent 2100 Bioanalyzer (Santa Clara, CA).
Sequencing libraries were prepared using NEBNext Ultra RNA library Prep Kit for Illumina (Ipswich, MA). Sequencing was performed on an Illumina HiSeq X Ten for 150 bp length reads.

treatment_protocol: Not application.

value: White adipose tissue

value: male

value: 8-12 weeks

tag: time


title: ZT22-KO2-WAT


title: Wild type + DP - sample 1 (QG3)


title: Liver, L2 13_rep4


title: NCI-H358 treated with AMG510 [SAM24385473]


title: scATAC_npTh17_1


title: ATAC-Seq Clone7_Plus

value: ER-Hoxb8 cells


title: NCI-H358 treated with AMG510 [SAM24385472]


title: ATAC-Seq Clone6_Plus


title: ATAC-Seq Clone12_Plus


title: ZT18-KO3-WAT


title: ZT22-KO1-WAT


title: Wild type - sample 3 (OMA 6-6)

description:
WT iron replete
Pi - OMA14 vs. Pi - OMA14 + DP

value: iron replete


title: Wild type - sample 4 (OMA 6-8)


title: NCI-H358 treated with AMG510 [SAM24385471]


title: Wild type - sample 2 (QG10)


title: ATAC-Seq Clone5_Plus


title: Wild type - sample 1 (QG1)


title: NCI-H358 treated with DMSO [SAM24385470]


title: ATAC-Seq Clone4_Plus


title: ZT18-KO1-WAT


title: NCI-H358 treated with DMSO [SAM24385469]


title: ZT14-KO3-WAT


title: ATAC-Seq Clone3_Plus


title: A1762-3-3: Mutant4, replicate 3

city: Qingdao

first: Yanhai

last: Gong

address: No.189 Songling Road

department: single cell center

institute: qibebt, cas

data_processing:
This dataset was processed using nfcore/rnaseq:1.5dev pipeline, with minor modifications.
Genome_build: NoIMET1v2
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: matrix table with TPM values for every gene and every sample

organism: Nannochloropsis oceanica strain IMET1

source_name: Nannochloropsis, NO06G02500 knockout mutant

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: NO06G02500 knockout mutant


title: ATAC-Seq Clone2_Plus


title: ZT14-KO2-WAT


title: NCI-H358 treated with DMSO [SAM24385468]


title: HEK293T, pcDNA_ISG20_M1, rep4

city: Lyon

first: Andrea

last: CIMARELLI

address: 46 Allée d'Italie

country: France

institute: CIRI-ENS-L

description:
15_HTSeq_count_stats.df
DE_ISG_pcDNA_vs_ISG20M1.txt
DE_ISG_ISG20M1_vs_ISG20WT.txt

data_processing:
Used a custom perl pipeline
RNA, phiX174 and GFP reads were filtered out using Bowtie2
Reads were mapped on the hg38 genome using HISAT2
duplicates with identical UMI, same position of Read1 an read2 mapping and a correct orientation were removed
tRNA and small-ncRNA reads were filtered out using HISAT2
reads mapped on exons were counted using HTSeq-count and GRC-Genecode.GRCh38.v37.primary_assembly.annotation.gtf
differential expression between all pairs of conditions were analysed using DESeq2
Assembly: hg38
Supplementary files format and content: .df tab-delimited text files include HTSeq-count raw count for all samples
Supplementary files format and content: .bw binary files include bigWig overage data for each samples
Supplementary files format and content: .txt tab-delimited text files include results of DESeq2 analyses

growth_protocol: HEK293T cells were grown in DMEM medium (Gibco, cat.  61965-026) supplemented with 10% Fetal bovine serum (Sigma, cat. F7524) and 100U/mL of penicillin-streptomycin (Gibco, cat.11548876)

extract_protocol:
Cells were lysed directly in the 10cm plate using 1mL of Trizol to extract total RNA. Total RNA was then depleted from ribosomal RNA using antisense DNA oligonucleotides and RNaseH treatment. Resulting rRNA-depleted RNAs were used as input for library preparation.
Libraries were prepared following the protocol described in: DOI: 10.1093/nar/gku1235
Ligation of a 3’ preadenylated adaptor(5’ AppAGATCGGAAGAGCACACGTCTGAACTCCAddC 3’), followed by Reverse-transcription using a custom oligonucleotide (3’ TTCTCGTGTGCAGACTTGAGGTCAGTG-SP18-TAGATGTGAGAAAGGGATGTGCTGCGAGAAGGCTAGA-NNNNNNNNATCACGGp–5’), circularisation of the obtained ssDNA and PCR amplification using a multiplexing forward PCR primer (5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3') and a multiplexing reverse primer containing an illumina index (5'- CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCG-3').

treatment_protocol: Cells were grown in 10cm cell culture treated plates and co-transfected with 10µg of a pcDNA3.1 plasmid either empty or coding for a wild-type version of ISG20 (ISG20_WT) or a mutant version of ISG20 (ISG20_M1) and 0.5µg of a GFP encoding plasmid. 24 hours after transfection, cells were lysed directly in Trizol to extract total RNA.

value: ISG20_M1 Ectopic Expression


title: ZT14-KO1-WAT


title: A1762-3-2: Mutant4, replicate 2


title: HEK293T, pcDNA_ISG20_M1, rep3


title: Replicate 4, scRNAseq

city: Shanghai

first: Qiang

last: Fu

address: No.100 Haining Road

institute: Department of Spine Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was processed by Cell Ranger (10xGenomics, version cellranger-6.0.0) pipeline and aligned to the human reference genome (GRCh38) to generate Gene-Barcode matrices of gene expression. The Gene-Barcode matrices containing the barcoded cells and gene expression counts were imported into the Seurat R toolkit (R version 4.0.3 (2020-10-10)). Cells with gene number (<300 & > 6000) or high mitochondrial transcript ratio (<25%), and genes expressed in less than 3 cells were all excluded. After removing unwanted cells from the dataset, all samples were combined with function "merge". Next, we employed a global-scaling normalization method "LogNormalize" to normalize the feature expression measurements (UMI counts) for each cell by the total expression and the canonical correlation analysis (CCA) method to remove the batch effect.
Highly variable genes (top 4000) were extracted to perform the principal component analysis (PCA) and top 30 of significant principal components were used for cluster analysis. Clusters were visualized using the Uniform Manifold Approximation and Projection (UMAP) and t-Distributed Stochastic Neighbor Embedding (t-SNE). Marker genes for each cluster, cell type and subgroup were identified by contrasting gene expression of cells from certain cluster, cell type or subgroup to that of others using the Seurat FindMarkers function. The types of cell clusters were annotated by specific marker genes of published cell types.
GO enrichment, KEGG enrichment of markers from cluster or cell type were performed using clusterProfiler software with Benjamini-Hochberg multiple testing adjustment, using marker genes from Seurat software with wilcox test and log-scale foldchange (logfc.threshold >= 0.25). The results were visualized using R package.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Herniated nucleus pulposus

extract_protocol:
NP samples were obtained from patients with a diagnosis of IDD during surgery. NP samples from four patients in lumbar discectomy surgery were collected and minced with a razor blade into 1 mm3 fragments on a dish under aseptic conditions. NP fragments were suspended in 10 ml of 1×TrypLE Express and incubated in 37℃ water bath with shaking for 30 min. Centrifuge the tissue at 500g for 5 minutes at room temperature and wash twice by adding 25 ml PBS. Discard the supernatant and add 10 mL of digestion buffer consisting of 2 mg/mL Collagenase type II (Sigma, c6885), 0.1mg/ml DNase I (Roche, 4716728001) in RPMI medium (Coring, 10-040-CV), and incubated in 37℃ water bath with shaking for 4-6 hours. Terminate the enzymatic digestion when the tissue pieces have entirely disintegrated.  The suspension was passed through a 100 μm filter (Falcon, 3523260) and centrifuged (400g, 10 min, 4℃). Pelleted cells were resuspended in red blood cell lysis buffer (Solarbio, R1010) for 5 min at room temperature, followed by an additional filter step through a 40 μm filter (Falcon,3523240). Cells were collected by centrifugation (400g, 10 min, 4℃) and resuspended in PBS (BI, 02-024-1ACS) containing 0.04% BSA (Sigma, B2064).Cells were manually counted by Trypan blue (Thermo, T10282) and AO-PI (LUNA, D23001) after each centrifugation (400g, 10 min, 4℃) and resuspended.
By using Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics, 1000268) and Chromium Next GEM Chip G Single Cell Kit (10xGenomics, 1000120), we performed single cell 3ʹ gene expression profiling. The cell suspension was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Cell-barcoded 3ʹ gene expression libraries were sequenced on an Illumina NovaSeq6000 system by Shanghai Biochip Co., Ltd., Shanghai, China.

value: nucleus pulposus cells

value: Herniated nucleus pulposus

tag: surgery

value: lumbar discectomy surgery

value: 28 years old


title: ZT10-KO3-WAT


title: A1762-3-1: Mutant4, replicate 1


title: ZT18-KO2-WAT


title: ZT10-KO2-WAT


title: Replicate 3, scRNAseq

description: 10x Genomics

value: 23  years old


title: HEK293T, pcDNA_ISG20_M1, rep1

tag: cell line


title: HEK293T, pcDNA_ISG20_M1, rep2


title: ZT10-KO1-WAT


title: ZT6-KO3-WAT


title: A1761-1-1: Mutant3, replicate 1


title: A1763-5-2: Mutant2, replicate 2

source_name: Nannochloropsis, NO08G00280 knockout mutant

value: NO08G00280 knockout mutant


title: A1761-1-2: Mutant3, replicate 2


title: HEK293T, pcDNA_ISG20_WT, rep4

description:
15_HTSeq_count_stats.df
DE_ISG_ISG20M1_vs_ISG20WT.txt
DE_ISG_pcDNA_vs_ISG20WT.txt

value: ISG20_WT Ectopic Expression


title: A1761-1-3: Mutant3, replicate 3


title: HEK293T, pcDNA_ISG20_WT, rep2


title: Replicate 1, scRNAseq

description: 10x Genomics

tag: cell type

value: 20 years old


title: ZT6-KO2-WAT


title: HEK293T, pcDNA_ISG20_WT, rep3

tag: treatment


title: hiPSCs, myogenic_diff, Healthy, Day10

city: Nantes

first: Jean-Baptiste

last: Dupont

address: 22 boulevard Benoni Goullin

department: INSERM

institute: Nantes Université

description: scRNA-Seq by split-pool barcoding

data_processing:
Demultiplexing, quality control, alignment to the human genome and gene counting were carried out using the custom analysis suite provided by Parse Biosciences
Assembly: hg19
Supplementary files format and content: expression values aggregated in a matrix (.mtx) file
Supplementary files format and content: cell and feature (gene) informations providede as csv files

source_name: hiPSCs

growth_protocol: Commercial myogenic differentiation protocol provided by amsbio

extract_protocol:
Cells were detached with Trypsin-EDTA and resuspended in DPBS prior to fixation and permeabilization with the Cell Fixation kit from Parse Biosciences
Evercode Whole Transcriptome Mini Kit provided by Parse Biosciences, according to manufacturer's instructions

tag: tissue

value: hiPSCs

value: somite progenitors


title: Kidney, AS-703026, rep 2

value: Kidney

tag: strain

value: Male

value: 30 ppm

value: 4 months


title: Noness, Hi-C

city: La Jolla

first: Peiyao

last: Wu

address: 9500 Gilman Dr

department: Chemistry

institute: University of California, San Diego

description: Arima

data_processing:
fastq files were aligned to hg19 (modified with ABL1-BCR translocation) with Juicer (v1.6) with the default settings
VC normalization was performed with Juicer (v1.6) with the default settings
Assembly: hg19
Supplementary files format and content: Hi-C contact counts in .hic format

source_name: blood

growth_protocol: K562 cells that stably express Cas9-mCherry were infected with lentivirus expressing a hub-targeting pgRNA and EGFP. The cells were then cultured for 10 days and sorted for mCherry/GFP dual positivity.

extract_protocol:
According to Arima Hi-C kit for Mammalian cell lines manual (A160134 v01). In brief, the crosslinked cells were lysed, and then underwent restriction enzymatic digestion, biotin integration, and proximal ligation. The ligated DNA was finally captured with AMPure XP beads.
According to NEBNext Ultra II DNA Library Prep (Arima, A160141 v01). In brief, the proximally-ligated genomic DNA was sheared to 200-600 bp (average 400 bp) on a Covaris Ultrasonicator, and then biotin enrichment was performed using streptavidin beads, followed by end repair, dA-tailing, and adapter ligation.
Arima Hi-C

treatment_protocol: The sorted cells were washed in PBS, crosslinked with 2% formaldehyde for 10 min at room temperature, followed by adding stop solution I (Arima) for 5 min. The fixed cells were then snap-frozen for Hi-C library preparation.

value: blood

value: Lymphoblast

tag: restriction enzyme

value: Arima (multi-enzyme)


title: ZT6-KO1-WAT

value: White adipose tissue

tag: Sex

value: male

value: 8-12 weeks


title: A1763-5-3: Mutant2, replicate 3


title: Ess, Hi-C

description: Arima


title: ATAC-Seq Clone1_Plus

value: ER-Hoxb8 cells


title: ZT2-KO3-WAT

tag: age


title: A1763-2-3: Mutant1, replicate 3


title: HEK293T, pcDNA_ISG20_WT, rep1


title: HEK293T, pcDNA Control, rep4

description:
15_HTSeq_count_stats.df
DE_ISG_pcDNA_vs_ISG20M1.txt
DE_ISG_pcDNA_vs_ISG20WT.txt

value: mock transfected


title: Noness, scATAC-seq

description: 10x Genomics

data_processing:
Barcode processing was performed using the 10x Genomics Cellranger (v7.0.0)
low-quality single cells were filtered out if they did not satisfy: (peak_region_fragments > 3000) & (peak_region_fragments < 20000) & (pct_reads_in_peaks > 15) & (nucleosome_signal < 4) & (TSS.enrichment > 2), performed with Seurat (v4.1.0) and Signac (v1.8.0)
Gene activities were predicted using the top 2000 variable peaks, and each single cell was anchor-transferred to scRNA pseudobulk clusters
Assembly: GRCh38
Supplementary files format and content: HDF5 files containing the peak barcode matrix
Supplementary files format and content: bed files indicating the ATAC fragments
Supplementary files format and content: comma-separated values files containing the metadata of the single cells (barcodes)

extract_protocol:
According to the 10x Genomics Chromium Next GEM Single Cell ATAC Reagent Kits (v1.1) User Guide. The isolated nuclei were subjected to transposition to add adapter sequences to the genomic fragments, preferentially in the open regions. Gel-beads in emulsions (GEMs) were created on the Chromium Next GEM Chip H, and oligos containing P5 adapter, 10x Barcode, and Read 1N sequence were added.
According to the 10x Genomics Chromium Next GEM Single Cell ATAC Reagent Kits (v1.1) User Guide. The GEMs were cleaned-up with SPRI beads, then PCRs were performed to build the library.

treatment_protocol: The sorted cells underwent nuclei-isolation steps according to Chromium Nuclei Isolation Kit_UG_RevA from 10x Genomics Chromium.


title: A1763-5-1: Mutant2, replicate 1

value: NO08G00280 knockout mutant


title: A1763-2-2: Mutant1, replicate 2


title: ZT2-KO2-WAT


title: Replicate 2, scRNAseq

description: 10x Genomics

value: nucleus pulposus cells

value: Herniated nucleus pulposus

value: lumbar discectomy surgery

value: 69  years old


title: HEK293T, pcDNA Control, rep3


title: ZT2-KO1-WAT


title: RNA EAE_CNS_2

source_name: Sorted IL17+ cells harvested from the central nervous system at the peak of EAE

value: CNS

value: Wildtype


title: Ess, scATAC-seq

description: 10x Genomics


title: A1763-2-1: Mutant1, replicate 1


title: HEK293T, pcDNA Control, rep2


title: SW1417_LTX_Rep1

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: wild type cells treatd with lometrexol

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using bowtie/1.1.2.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg38 using STAR/2.5.2.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were nonstranded, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: mm9, hg38
Supplementary files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

source_name: SW1417 colorectal cancer cell line

growth_protocol: Mouse ES cells were maintained serum free neurobasal+DMEM/F12 media supplemented with 2i+LIF; for colorectal cancer cells, RKO, HCT116, SW1417 were cultured in DMEM+10%FBS, DLD1 were cultured in RPM-1640 + 10% FBS, HT55 and Caco2 were cultured in DMEM+20% FBS

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Cells were treated with DMSO or 1 uM LTX for 24 hours.

value: SW1417 colorectal cancer cell line

tag: passages

value: Low passages (6-10)

value: WT

value: wild type


title: HEK293T, pcDNA Control, rep1


title: ZT22-WT3-WAT


title: ZT22-WT2-WAT


title: WT-2: wild-type, replicate 2

source_name: Nannochloropsis, wild-type

value: wild-type


title: WT-1: wild-type, replicate 1


title: SW1417_DMSO_Rep1

description: wild type cells treatd with DMSO


title: SW1417_DMSO_Rep2

description: wild type cells treatd with DMSO


title: ZT18-WT3-WAT

value: White adipose tissue


title: WT-3: wild-type, replicate 3


title: mocktotal

city: Yangzhou

first: Liao

last: Tianxing

state: Jiangsu province

address: 48 Wenhui East Road, Hanjiang District, Yangzhou City, Jiangsu Province

department: College of Veterinary Medicine

institute: Yangzhou University

data_processing:
The raw sequencing data was filtered using the software SOAPnuke (v1.5.2) to remove any unwanted artifacts or low-quality reads.
The obtained clean data was aligned to the reference gene sequences using the Bowtie2 software (v2.2.5). Subsequently, the RESM software package (v1.2.8) was employed to calculate the gene expression levels of each sample.
Differential gene analysis within the group was performed using DESeq with the criteria of Fold Change ≥ 2 and Adjusted Pvalue ≤ 0.001. Inter-group differential analysis was conducted using PossionDis with the criteria of Fold Change ≥ 2 and FDR ≤ 0.001.
Supplementary files format and content: tab-delimited text file contains FPKM value of each sample
Supplementary files format and content: tab-delimited text file contains read counts of each sample

source_name: HeLa

growth_protocol: Cells were seeded into 10 cm dishes and incubated in a 6%-CO2 incubator at 37°C for 18 hours.

extract_protocol:
Ribosome-bound RNA and total RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-Seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were incubated with 100 μg/mL cycloheximide (CHX) at 37°C for 15 min, washed, and lysed for polysome fractionation via sucrose density gradient ultracentrifugation.

value: HeLa

value: human epithelial carcinoma cell line

value: mock HeLa cells

value: mock


title: S25_M_3

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

country: Australia

institute: The University of Queensland

data_processing:
The CLC Genomics Workbench version 12.1.1 was used for bioinformatics analyses in this study. RNA-Seq analysis was done by mapping next-generation sequencing reads, distributing and counting the reads across genes and transcripts. The latest assembly of P. xylostella genome (GCF_000330985.1) was used as reference. All libraries were trimmed from sequencing primers, adapter sequences and low-quality reads. Low quality reads (quality score below 0.05) and reads with more than 2 ambiguous nucleotides were discarded. We applied the quality score of 0.05 as cut off for trimming. The Phred quality scores (Q), defined as: Q= -10log10(P), where P is the base-calling error probability, can then be used to calculate the error probabilities, which in turn can be used to set the limit for which bases should be trimmed. Clean reads were subjected to RNA-Seq analysis toolbox for mapping reads to the reference genome with mismatch, insertion and deletion cost of 2, 3 and 3, respectively. Mapping was performed with stringent criteria and allowed a length fraction of 0.8 in mapping parameter, which encounter at least 80% of nucleotides in a read must be aligned to the reference genome. The minimum similarity between the aligned region of the read and the reference sequence was set at 80%.
The relative expression levels were produced as RPKM (Reads Per Kilobase of exon model per Million mapped reads) values, which consider the relative size of the transcripts and only uses the mapped-read datasets to determine relative transcript abundance. To explore genes with differential expression profile between two samples, CLC Genomic Workbench uses multi-factorial statistics based on a negative binomial Generalized Linear Model (GLM). Each gene is modelled by a separate GLM and this approach allows us to fit curves to expression values without assuming that the error on the values is normally distributed. TMM (Trimmed mean of M values) normalization method was applied on all data sets to calculate effective library sizes, which were then used as part of the per-sample normalization (Robinson & Oshlack, 2010). The Wald Test was also used to compare each sample against its control group to test whether a given coefficient is non-zero. We considered genes with more than 2-fold change and false discovery rate (FDR) of less than 0.05 as statistically significantly modulated genes.
All differentially expressed genes were uploaded to Blast2GO server for functional annotation and GO analysis. We used BLAST and InterProScan algorithms to reveal the GO terms of differentially expressed sequences. More abundant terms were computed for each category of molecular function, biological process and cellular components. Blast2GO has integrated the FatiGO package for statistical assessment and this package uses the Fisher’s Exact Test.
Genome_build: GCF_000330985.1
Supplementary_files_format_and_content: TPM, RPKM values

organism: Plutella xylostella

source_name: Male_25 C_larval body

growth_protocol: The laboratory population of P. xylostella was first collected from cabbage field in Gatton, Queenland, Australia in 2014, and it has been maintained with common cabbages (Brassica oleracea var. sugarloaf) at 25 ± 1°C for generations. To examine the reproductive response such as fecundity and fertility to cold stress, P. xylostella were reared at 10°C with fresh and young common cabbage leaves from egg to adult eclosion. The control group P. xylostella were reared at 25°C from egg to adult eclosion. To study the impact of drastic change in ambient temperature on P. xylostella global gene expression, P. xylostella in two treatments were firstly all reared with fresh and young common cabbage leaves at 25 °C from the egg to the early third instar. The early third instar larvae were then placed in incubator set at 10°C (treatment) and 25°C (control) and reared with fresh and young common cabbage leaves until the mid-fourth instars.

extract_protocol:
To determine P. xylostella gene expression responses to cold stress in male and female larvae, total RNA samples were collected from mid-fourth instar larvae treated with 10C and 25C (control) regime. This included 12 samples includes three biological replicates for each temperature and sex. Each biological replicate consists eight P. xylostella larvae. Total RNA of whole bodies of samples in each replicate was extracted using Qiazol lysis reagent according to manufacture instruction (QIAGEN; Cat No.: 79306). The RNA samples were treated with DNase I for 1 h at 37°C and then their concentrations were measured using a spectrophotometer and integrity was ensured through analysis of RNA on a 1% (w/v) agarose gel. The quality of the RNA samples was examined by using Agilent RNA 6000 pico kit with Agilent 2100 bioanalyzer (Agilent Technologies Inc.). After checking the RNA quality, total RNA samples were submitted to the Novogene Genomics Singapore Pte Ltd for RNA deep sequencing (RNA-seq).
The NEBNext Ultra II RNA library kit (New England Biolabs) was used for RNA-Seq library construction. Fragmented poly A+ RNA samples were converted to cDNA by random primed synthesis using ProtoScript II reverse transcriptase (New England Biolabs). After second strand synthesis, the double-stranded DNAs were treated with T4 DNA polymerase, 5’ phosphorylated and then an adenine residue was added to the 3’ ends of the DNA. Adapters were then ligated to the ends of these target template DNAs.  After ligation, the template DNAs were amplified (5-9 cycles) using primers specific to each of the non-complimentary sequences in the adapters. This created a library of DNA templates that have non-homologous 5’ and 3’ ends.  A qPCR analysis was performed to determine the template concentration of each library. The PCR-based cDNA libraries were sequenced using Illumina NovaSeq 6000 (PE150) technology with the insert size between 250-300 bp.

value: Male

tag: rearing temparture

value: larval body


title: Caco2_LTX_Rep1

description: wild type cells treatd with lometrexol

source_name: Caco2 colorectal cancer cell line

value: Caco2 colorectal cancer cell line


title: INPtotal

value: HeLa cells expressing INP

value: HNP means NP from NDV strain I4


title: ZT18-WT2-WAT

value: male

value: 8-12 weeks


title: ZT22-WT1-WAT


title: ZT18-WT1-WAT


title: HNPtotal

value: HeLa cells expressing HNP

value: HNP means NP from NDV strain Herts/33


title: S25_M_2


title: mockRibosome

description: Ribosome-bound mRNA


title: ZT14-WT3-WAT


title: SW1417_LTX_Rep2

description: wild type cells treatd with lometrexol

value: SW1417 colorectal cancer cell line

value: Low passages (6-10)

value: WT


title: INPRibosome

description: Ribosome-bound mRNA


title: S25_M_1


title: S25_F_4

source_name: Female_25 C_larval body

value: Female


title: Caco2_LTX_Rep2

description: wild type cells treatd with lometrexol

value: wild type


title: S25_F_2


title: Caco2_DMSO_Rep1

description: wild type cells treatd with DMSO


title: ZT14-WT1-WAT

value: White adipose tissue


title: S25_F_1


title: ZT10-WT2-WAT


title: HT55_LTX_Rep1

description: wild type cells treatd with lometrexol

source_name: HT55 colorectal cancer cell line

value: HT55 colorectal cancer cell line


title: T47D AAV_DMSO2

city: Heidelberg

first: massimo

last: petretich

address: Meyerhofstrasse 1

country: Germany

institute: Cellzome

data_processing:
Reads were aligned with STAR,
Sequence reads were trimmed for adaptor sequence/low-quality sequence, aligned with STAR on Hg38 genome.
Read count extraction was done using FeatureCounts R package
Supplementary files format and content: Hg38
Supplementary files format and content: tab-delimited text files. Count column: "STDIN"

source_name: T47D AAV

growth_protocol: T47D cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 500ng of total RNA was used for the construction of sequencing libraries.
NEB Next ultra II kit

treatment_protocol: Cells were treated with 10uM of inhibitor (or corresponding amount of DMSO for the control samples) for 48h under the same culturing condition mentioned above.

value: T47D AAV

value: DMSO


title: T47D AAV_DMSO1


title: T47D AAV_DMSO3


title: ZT10-WT3-WAT


title: HT55_DMSO_Rep1

description: wild type cells treatd with DMSO


title: S10_M_3

source_name: Male_10 C_larval body

value: Male

value: larval body


title: HT55_DMSO_Rep2

description: wild type cells treatd with DMSO


title: S10_F_3

source_name: Female_10 C_larval body


title: ZT10-WT1-WAT

source_name: White adipose tissue


title: S10_M_2


title: S10_M_1


title: T47D AAV_Nira2

value: Niraparib 10uM


title: DLD1_LTX_Rep2

description: wild type cells treatd with lometrexol

source_name: DLD1 colorectal cancer cell line

value: DLD1 colorectal cancer cell line


title: ZT6-WT3-WAT

value: male


title: T47D AAV_Nira3


title: ZT14-WT2-WAT

value: 8-12 weeks


title: T47D AAV_Nira1


title: S10_F_2


title: ZT6-WT2-WAT


title: HT55_LTX_Rep2

description: wild type cells treatd with lometrexol


title: HNPRibosome

description: Ribosome-bound mRNA

value: HeLa

value: human epithelial carcinoma cell line

value: HeLa cells expressing HNP


title: DLD1_DMSO_Rep2

description: wild type cells treatd with DMSO

value: Low passages (6-10)


title: ZT6-WT1-WAT


title: S10_F_1


title: DLD1_DMSO_Rep1

description: wild type cells treatd with DMSO

value: WT


title: T47D AAV_Ola2

value: Olaparib 10uM


title: DLD1_LTX_Rep1

description: wild type cells treatd with lometrexol

value: wild type


title: HCT116_LTX_Rep2

description: wild type cells treatd with lometrexol

source_name: HCT116 colorectal cancer cell line

value: HCT116 colorectal cancer cell line


title: ZT2-WT3-WAT

value: White adipose tissue


title: ZT2-WT2-WAT


title: ZT22-KO3-KN

source_name: Kidney

value: Kidney


title: ARF36

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: DNA Affinity Purification and sequencing

data_processing:
Library strategy: DAP-seq
Reads are trimmed by filtering out adaptor-only nucleotides with the following parameters ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50, using Trimmomatic (ver 0.36; (Bolger, et al., 2014)).
Trimmed reads were aligned to the reference genome (Gmax505 v4.0) using bowtie2 v2.2.853 (Langmead and Salzberg, 2012).
Mapped reads with >MAPQ30 were removed to use the reads that are not mapped into multiple locations.
Genome_build: Reference genome Gmax505 v4.0.
Supplementary_files_format_and_content: *.bw: bigWig; Genome coverage of each sample.
Supplementary_files_format_and_content: *.narrowPeak: Peak text files.

organism: Glycine max

source_name: leaf tissue

extract_protocol:
Genomic DNA (gDNA) was extracted from leaf tissue using phenol:chloroform:IAA extraction.
Libraries were prepared based on Illumina instruction.

tag: treatment - transcription factor binding

value: Maize ARF36 binding sequences

value: leaf


title: ZT22-KO2-KN


title: T47D JL_DMSO3

source_name: T47D JL

value: T47D JL

value: PARP1 KO

value: DMSO


title: T47D AAV_Ola3

value: T47D AAV


title: HCT116_LTX_Rep1

description: wild type cells treatd with lometrexol


title: ARF14

value: Maize ARF14 binding sequences


title: HCT116_DMSO_Rep1

description: wild type cells treatd with DMSO


title: ARF25

value: Maize ARF25 binding sequences


title: ZT22-KO1-KN

value: male

value: 8-12 weeks


title: HCT116_DMSO_Rep2

description: wild type cells treatd with DMSO

value: Low passages (6-10)


title: T47D JL_DMSO1


title: ARF10

value: Maize ARF10 binding sequences


title: T47D JL_Nira2

value: Niraparib 10uM


title: RKO_LTX_Rep2

description: wild type cells treatd with lometrexol

source_name: RKO colorectal cancer cell line

value: RKO colorectal cancer cell line

value: WT

value: wild type


title: RKO_LTX_Rep1

description: wild type cells treatd with lometrexol


title: ZT18-KO3-KN

value: Kidney


title: ARF7

value: Maize ARF7 binding sequences


title: T47D AAV_Ola1

value: Olaparib 10uM


title: negative control GST-HALO

description:
DNA Affinity Purification and sequencing
Control

value: Negative control GST-HALO

value: leaf


title: T47D JL_Nira1

value: T47D JL

value: PARP1 KO


title: ARF39

value: Maize ARF39 binding sequences


title: ZT2-WT1-WAT

value: White adipose tissue


title: T47D JL_DMSO2

value: DMSO


title: ARF34

value: Maize ARF34 binding sequences


title: RKO_DMSO_Rep2

description: wild type cells treatd with DMSO

value: Low passages (6-10)


title: ZT18-KO2-KN

value: male

value: 8-12 weeks


title: T47D JL_Ola3


title: T47D JL_Nira3

value: Niraparib 10uM


title: ZT18-KO1-KN


title: T47D JL_Ola2


title: ZT14-KO3-KN


title: T47D JL_Ola1


title: ARF29

value: Maize ARF29 binding sequences


title: ZT14-KO2-KN


title: ZT14-KO1-KN


title: ARF18

value: Maize ARF18 binding sequences


title: ARF16

value: Maize ARF16 binding sequences


title: ZT10-KO3-KN

value: Kidney


title: stat-bmp9_rep2

city: Berlin

first: Paul-Lennard

last: Mendez

address: Thielallee 63

department: Institute for Chemistry and Biochemistry

institute: Freie Universität Berlin

data_processing:
ATAC-seq data were processedvia the standard ENCODE (Dunham et al. 2012) ATAC-seq pipeline, using Caper with Conda (v1.10.0, https://github.com/ENCODE-DCC/atac-seq-pipeline/releases/tag/v1.10.0). Briefly, reads were aligned with Bowtie2 (v2.3.4.3) (Langmead and Salzberg 2012) to hg38 reference genome and filtered for unmapped, duplicates and mitochondrial reads. Peaks calling was performed using MACS2 (v2.2.4) (Zhang et al. 2008) for each individual replicate.
We generated bigWig files for visualization purposes using bamCoverage (v3.5.1) module from deepTools (Ramírez et al. 2016) with parameters --normalizeUsing RPGC --effectiveGenomeSize 2913022398. We further used deepTools computeMatrix (v3.5.1) module with parameters –referencePoint center -a 1500 -b 1500 and plotHeatmap (v3.5.1) module with default parameters to generate heatmaps.
We performed differential accessibility analysis for each condition using DiffBind R package (v3.0) (Ross-Innes et al. 2012; Stark and Brown 2011)after sequencing depth normalization and by using DESeq2 as the underlying method. We identified significantly differential accessible regions by filtering for FDR <= 0.05 and fold change > 1.5.
Assembly: hg38
Supplementary files format and content: bam, NarrowPeak, bigWig

source_name: Umbilical artery

growth_protocol: 3*105 cells were seeded in EBM-2 full medium (Basal Medium 2 and Supplement Pack (PromoCell, no.C-22111) supplemented with 1% P/S) to gelatin coated 0.4 ibidi µ-Slides (ibidi, no.80176). For static conditions, cells were seeded to an equal area in a 10 cm dish, restricted by a silicone barrier during gelatin coating and cell seeding. Cells were kept under culture conditions (37°C, 5% CO2, 95% RH) for 48 h with daily medium exchanges.

extract_protocol:
For each sample 50.000 cells were transferred to a reaction tube and spun down (500×g, 4°C, 5 min). Samples were kept on ice from now on. ATAC-seq (Buenrostro et al. 2013; Buenrostro, Wu, Chang, et al. 2015) was performed as described in the section transposition reaction and buffers from Omni ATAC protocol (Corces et al. 2017), followed by DNA purification with the MinElute Reaction Cleanup Kit (Qiagen, no. 28206). For clean-up, the manufacturers protocol was followed with two exceptions: Elution was done in 11 µl to get full 10 µl residual volume. Also, longer elution time (3-5 min) was used for higher yield of DNA fragments. DNA concentration was measured with a Qubit fluorometer. Libraries were stored at ‑20°C until further processing.
Library amplification and purification was conducted as in Buenrostro2015 (Buenrostro, Wu, Chang, et al. 2015), including the qPCR step to estimate the appropriate number of additional PCR cycles. Double barcoding with indexing primers v2_Ad1.2/3 and v2_Ad2.3/4/5/6 from Buenrostro2015a (Buenrostro, Wu, Litzenburger, et al. 2015) was used. After that, two-sided size selection with magnetic AMPure XP Beads (Beckmann Coulter, no. A63881; 0.55× and 0.9× sample volume of bead solution added) was used to remove primer-dimers and large DNA fragments > 1kb. Library quality was assessed with a HS DNA Bioanalyzer chip (Agilent, no. 5067-4626) before 2×100 paired end Illumina high output sequencing.

treatment_protocol: On the day of stimulation, medium was exchanged by pre-warmed EBM-2 starvation medium (Basal Medium 2 and Supplement Pack (PromoCell, no.C-22211) supplemented with 1% P/S and 2% FCS) and unidirectional laminar flow of 30 dyn/cm2 was applied for 2 h (subsequent to a 5 h ramp phase to allow call adaption to increasing shear stress). Shear stress was applied using the ibidi pump system (ibidi GmbH) with the associated software (v 1.4.2). BMP9 in PBS was added to pump reservoirs and static controls dishes at a final concentration of 0.3 nM. Same volumes of PBS were added to control cells.

value: Umbilical artery

value: HUAEC

value: Endothelial

value: WT


title: ARF4

value: Maize ARF4 binding sequences

value: leaf


title: stat-bmp9_rep1


title: stat-cont_rep2

value: without


title: MCF-7_ZNF652_ChIPSeq

city: beijing

first: cheng

middle: yun

last: liu

address: 北京市海淀区学院路38号

institute: peking university

data_processing:
Base calling through Illumina BCL2fastq
Data filtering through NGS QC Toolkit
Alignment through Bowtie version1
Peak-calling through MACS version14
Assembly: GRGH37/hg19
Supplementary files format and content: bigwig file contained binding signal

growth_protocol: MCF-7 cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Lysates were clarified from sonicated nuclei and ZNF652-DNA complexes were isolated with antibody. All DNA samples were processed as Illumina ChIP-seq sample processing methods. 10 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments, followed by the Qiaquick column clean up.After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were electively isolated from the 1% agarose gel and eluted by the Qiagen gel extraction kit. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.  Lysates were clarified from sonicated nuclei and ZNF652-DNA complexes were isolated with antibody. All DNA samples were processed as Illumina ChIP-seq sample processing methods. 10 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments, followed by the Qiaquick column clean up.After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were electively isolated from the 1% agarose gel and eluted by the Qiagen gel extraction kit. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: mammary adenocarcinoma cells

tag: chip antibody


title: MCF-7_Input_ChIPSeq

address: 北京市海淀区学院路38号


title: flow-bmp9_rep2

tag: genotype

value: flow + BMP9


title: ZT10-KO2-KN


title: stat-cont_rep1


title: ZT10-KO1-KN


title: RKO_DMSO_Rep1

description: wild type cells treatd with DMSO

value: RKO colorectal cancer cell line

value: Low passages (6-10)

value: wild type


title: flow-bmp9_rep1


title: flow-cont_rep2

value: flow only


title: Control Sheep Thymus

city: Winston Salem

first: Maria Graça

last: Almeida-Porada

state: NC

address: 391 Technology Way

institute: Wake Forest Institute for Regnerative Medicine

description:
ovis aries thymus
Control Sheep thymus-specific transcripts

data_processing:
FASTQ files were uploaded to QIAGEN RNA-seq Analysis Portal (https://geneglobe.qiagen.com/us/analyze/) and aligned to Homo sapiens (GRCh38.noalt.103) with analysis workflow version: 1.0.
Assembly: GRCh38.noalt.103
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Ovis aries

source_name: control, untransplanted sheep thymus

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
total RNA was subjected to ribosomal RNA (rRNA) suppression using QIAseq FastSelect rRNA removal kits HMR and then reverse transcribed into cDNA using random hexamers and oligo-dt primers for 90 minutes at 42C.   During cDNA synthesis each sample receives a unique sample ID that allows for cDNA pooling and all subsequent library construction steps of pooled samples was done in a single tube to minimize batch affects. Following cDNA pooling, 2 rounds of bead selection / reaction clean-up was done with QIAseq beads.  The cDNA was then amplified with unique-dual sample indexes using the (331801) QIAseq UX 12 Index Kit IL UDI.    Completed libraries were then purified using 2 rounds of bead-based cleanup with QIAseq beads.  Final libraries were quality controlled using an Agilent Bioanalyzer and quantitated by real-time qPCR using the (333314) QIAseq Library Quant Assay Kit and sequenced using an illumina Next-Seq 500 using 75 base paired end sequencing using NextSeq 500/550 Mid Output Kit (150 Cycles)

value: ovis aries thymus

value: control, untransplanted sheep thymus


title: ARF27

value: Maize ARF27 binding sequences


title: Control sheep Ovary

description:
ovis aries ovary
Control sheep Ovary-specific transcripts

source_name: control, untransplanted sheep ovary

value: ovis aries ovary

value: control, untransplanted sheep ovary


title: ZT6-KO3-KN

value: Kidney

value: male

value: 8-12 weeks


title: Control sheep Lung

description:
ovis aries lung
Control sheep Lung transcripts

source_name: control, untransplanted sheep lung

value: ovis aries lung

value: control, untransplanted sheep lung


title: flow-cont_rep1

value: Umbilical artery

value: HUAEC

value: Endothelial

value: WT


title: ZT6-KO2-KN


title: 57794: Colon_31_GOS_maternal

type: RNA

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

country: Netherlands

institute: Wageningen UR

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
705_705_2607_1

hyb_protocol: Hybridization was performed at 65°C for 17 h with head-over-head rotation. Microarrays were washed as recommended by the manufacturer.

scan_protocol: Microarrays were scanned using the Surescan high resolution scanner (Agilent Technologies) at a resolution of 3 µm, 20 bits and PMT of 100%. Feature extraction was performed using protocol 10.7.3.1 (v10.7) for 1 color gene expression.

data_processing: The data were analyzed using R (v3.0.2) by executing different packages, including LIMMA and arrayQualityMetrics. The R package LIMMA from Bioconductor was used to correct for background (method=normexp and offset=1). Quantile normalization of the data was done between arrays. The duplicate probes mapping to the same gene were averaged (‘avereps’) and subsequently the lower percentile of probes were removed in a three-step procedure: 1) select the highest of the dark spots to acquire a base value, 2) multiply by 1.1, 3) the gene/probe had to be expressed in each of the samples in the experimental condition.

organism: Sus scrofa

source_name: Colon; 31; GOS; maternal

label_protocol: Labelling of RNA was done as recommended by Agilent Technologies using the One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labelling. 200 ng of total RNA was used as input, 600 ng of labelled cRNA was used to hybridize the porcine microarray (Agilent Technologies).

extract_protocol: Total RNA was extracted from 50 to 100 mg of mucosal scraping of jejunum, ileum, or colon tissue. Samples were homogenized using the TissuePrep Homogenizer Omni TP TH220P in 5 ml TRIzol reagent (Life Technologies). The homogenate was centrifuged for 5 min at 21,000 x g. 350 μl of supernatant was used to isolate RNA using the Direct-zol kit (Zymo Research) according to instructions of the manufacturer. Quality control was performed on the BioAnalyzer (Agilent Technologies), quantity of RNA was determined using the TapeStation (Agilent 2200 TapeStation, Agilent technologies).

value: Colon

tag: gender

value: Male

tag: day

value: GOS

tag: route

value: maternal

tag: animalid


title: 57681: Colon_31_GOS_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
708_708_2561_2


title: ExPEC cells, none [Neg4]

city: Guelph

first: Dion

last: Lepp

address: 93 Stone Rd W

country: Canada

institute: Agriculture and Agri-Food Canada

data_processing:
NextFlow nf-core RNASeq pipeline
Quality assessment and mapping of filtered reads the E. coli O7:H18 (ST38) genome and read counting was performed with the NextFlow nf-core RNASeq pipeline v 3.0 using the STAR 2.6.1d for alignment and Salmon v1.4.0 for read counting
Supplementary files format and content: tab-delimited text file includes TPM values scaled to gene-length for all Samples

organism: Escherichia coli

source_name: E. coli O7:H18 (ST38)

extract_protocol:
Total RNA was extracted using the PureLink RNA Mini Kit (Ambion, Invitrogen Fisher Scientific, Carlsbad, CA, USA) according to the manufacturer’s instructions
Bacterial stranded mRNA sequencing libraries were constructed with the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-9004DOC) according to the manufacturer’s instructions

tag: agent


title: 57979: Colon_31_GOS_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
704_704_2565_2

value: betaglucans


title: Control sheep Liver

description:
ovis aries liver
Control sheep Liver transcripts

source_name: control, untransplanted sheep liver

tag: cell type

value: ovis aries liver

value: control, untransplanted sheep liver

tag: time


title: MIC_III-3, severe deformity of  auricular cartilage, rep1

city: Beijing

first: Qiao-li

last: Shang

state: Beijing

address: 33 Badachu Road, Shijingshan District

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

data_processing:
Bioinformatic analysis was performed using the OECloud tools at https://cloud.oebiotech.com.
The libraries were sequenced on an llumina Novaseq 6000 platformand 150 bppaired-endreadswere generated. About 7.0 G raw reads for each sample were generated. Rawreads of fastqformatwere firstly processed using fastp and the low quality reads were removed to obtainthecleanreads. Then about 1.145-1.208 G clean reads for each sample were retained for subsequent analyses. The cleanreads were mapped to the reference genome using HISAT2. FPKM of each gene was calculatedandthe read counts of each gene were obtained by HTSeq-count. PCA analysis were performed usingR (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. Qvalue<0.05 and foldchange > 1 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples.
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagramandbubblediagram of the significant enrichment term.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: auricular cartilage

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) accordingtothemanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop2000spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed usingtheAgilent2100Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
n the libraries were constructedusingVAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

tag: tissue

value: auricular cartilage

value: chondrocyte


title: ZT2-KO3-KN

city: Guangzhou

first: Min

last: Chen

institute: Guangzhou university of Chinese medicine

data_processing:
Clean reads were obtained by removing those containing an adapter and ploy-N using FASTQ program, and aligned to mouse GRCm38/mm10 genome using HISAT2 v2.0.4 with default parameters.
Read counts were normalized to FPKM values using DESeq2 (v.1.16.1).
FeatureCounts v1.5.0-p3 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.
Assembly: GRCm38/mm10 genome
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was isolated using Trizol (Invitrogen, Carlsbad, CA) and its quality was checked using an Agilent 2100 Bioanalyzer (Santa Clara, CA).
Sequencing libraries were prepared using NEBNext Ultra RNA library Prep Kit for Illumina (Ipswich, MA). Sequencing was performed on an Illumina HiSeq X Ten for 150 bp length reads.

value: Kidney

value: male

tag: strain


title: 57963: Colon_31_GOS_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
709_709_2407_4

tag: treatment


title: ExPEC cells, none [Neg3]


title: ExPEC cells, none [Neg1]


title: MIC_II-3, mild deformity of  auricular cartilage, rep1


title: ZT6-KO1-KN

tag: Sex

value: 8-12 weeks


title: ZT2-KO1-KN

tag: age


title: ExPEC cells, cranberry pomace [Cr5]

value: cranberry pomace


title: MIC_II-2, mild deformity of  auricular cartilage, rep1


title: ZT2-KO2-KN


title: ZT22-WT3-KN


title: MIC_II-1, mild deformity of  auricular cartilage, rep1


title: ExPEC cells, cranberry pomace [Cr3]


title: MIC_III-2, severe deformity of  auricular cartilage, rep1


title: MIC_III-1, severe deformity of  auricular cartilage, rep1


title: ExPEC cells, cranberry pomace [Cr1]


title: ZT22-WT2-KN


title: 58144: Ileum_31_betaglucans_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
702_702_2562_2

source_name: Ileum; 31; betaglucans; maternal

value: Ileum

value: Female


title: NOR-3, normal auricular cartilage, rep1


title: NOR-2, normal auricular cartilage, rep1


title: ZT22-WT1-KN


title: ZT18-WT3-KN


title: NOR-1, normal auricular cartilage, rep1


title: ExPEC cells, cranberry pomace and ceftriaxone [CC1]

value: cranberry pomace and ceftriaxone


title: 58203: Ileum_31_betaglucans_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
703_703_2464_3


title: parental NCI-H460 DMSO biol_rep_3

city: Freiburg im Breisgau

first: Sven

last: Diederichs

state: Baden Württemberg

address: Breisacherstrasse 115

department: ZTZ

institute: Universitätsklinikum Freiburg

description:
featureCounts on data 115 and data 188: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(DMSO_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(DMSO_level).xlsx

data_processing:
RNA-seq data analysis was executed on the European Galaxy platform (https://usegalaxy.eu)
RNA-seq reads quality was assessed with FastQC and MultiQC. Reads were aligned to the GRCh38/hg38 human reference genome with STAR.
Aligned reads were counted using featureCounts and differentially expressed genes were identified using DESeq2.
Gene-set enrochment analysis was carried out using the DESeq2 normalized counts as the expression dataset examining the hallmark gene set collection (MSigDB, UC San Diego and Broad Institute) in the GSEA software (v4.2.3, Broad Institute).
Assembly: GRCh38/hg38
Supplementary files format and content: txt files with normalized counts
Supplementary files format and content: excel files containing DESeq2 differential gene expression analysis results of NCI-H460 resistant #1 and #2 cells compared to parental NCI-H460 cells (ATRA+DAChigh treated level or DMSO control level)

growth_protocol: NCI-H460 cells (both parental and resistant #1 and #2) were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
At 72 hours, cells were lysed and RNA was isolated using the RNeasy Mini kit (Qiagen) following the manufacturer’s quick-start protocol with the optional in-column DNase I (Qiagen) digestion step
RNA libraries for RNA-seq were prepared by the DKFZ Genomics and Proteomics Core Facility using TruSeq stranded mRNA sample prep kit (Illumina).

treatment_protocol: At the 0-hour time point, 1.5 x 105 NCI-H460 cells per well were seeded in 6-well plates (Greiner Bio-One). At 24 hours, cells were treated with 2 μM ATRA and 50 μM DAC or DMSO as control.

tag: cell line

value: epithelial, adherent, large cell lung cancer cells

value: WT

tag: cell population

value: parental NCI-H460

value: DMSO control (0.7% v/v in  RPMI-1640)

value: 72 hours


title: ZT18-WT1-KN

address: No. 232, East Waihuan Street/Road


title: ZT18-WT2-KN


title: 58040: Ileum_31_betaglucans_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
608_608_2495_3

value: Male

value: MCFA

value: maternal


title: 58212: Ileum_31_betaglucans_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
701_701_2611_1

value: betaglucans


title: 57929: Ileum_31_betaglucans_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
610_610_2365_5


title: ZT14-WT3-KN


title: parental NCI-H460 DMSO biol_rep_1

description:
featureCounts on data 115 and data 140: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(DMSO_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(DMSO_level).xlsx


title: ExPEC cells, cranberry pomace and ceftriaxone [CC3]


title: ExPEC cells, ceftriaxone [AXO3]

value: ceftriaxone


title: ZT14-WT2-KN

value: Kidney


title: 57741: Jejunum_31_MCFA_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
604_604_2563_2

source_name: Jejunum; 31; MCFA; maternal

value: Jejunum

value: CONTROL

value: neonatal


title: 57941: Jejunum_31_MCFA_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
603_603_2303_7


title: parental NCI-H460 ATRA+DAChigh biol_rep_3

description:
featureCounts on data 115 and data 184: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level)

value: decitabine 50 μM and all-trans retinoic acid 2 μM in RPMI-1640


title: ExPEC cells, ceftriaxone [AXO1]


title: parental NCI-H460 ATRA+DAChigh biol_rep_2

description:
featureCounts on data 115 and data 160: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level)


title: ZT14-WT1-KN

value: male

value: 8-12 weeks


title: 58169: Jejunum_31_MCFA_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
606_606_2510_3


title: Liver, long-tailed macaque, rep 6

city: Boston

first: Alexander

last: Tyshkovskiy

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital, Harvard Medical School

data_processing:
To generate reference sequences and identify species-specific ortholog gene sets, pipeline from (Ma et al., 2016) was utilized. Published annotated genomes in Ensembl or NCBI were used if available. Otherwise, de novo transcriptomes were assembled with Trinity.
Reads were mapped to the species-specific ortholog sets using STAR (Dobin et al., 2013).Read counting was performed by featureCounts (Liao et al., 2014).
Supplementary files format and content: comma-separated values file includes gene counts for each sample

organism: Macaca fascicularis

source_name: Liver

extract_protocol:
After sacrifice, organs were removed and frozen on dry ice. RNA was extracted from tissues with PureLink RNA Mini Kit and passed to sequencing.
Sequencing libraries were prepared as described in (Fushan et al., 2015)

treatment_protocol: The 39 organ samples for young adults of baboon (Papio anubis), beaver (Castor canadensis), and long-tailed macaque (Macaca fascicularis) were collected from the Southwest National Primate Research Center (SNPRC). The 9 organ samples for young adults of chipmunk (Tamias sibiricus), American black bear (Ursus americanus), sugar glider (Petaurus breviceps), tube-nosed bat (Murina leucogaster), and white-footed mouse (Peromyscus leucopus) were collected as previously described (Fushan et al., 2015).

value: Liver

value: adult

value: wild type


title: 58181: Jejunum_31_MCFA_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
605_605_2615_1


title: parental NCI-H460 DMSO biol_rep_2

description:
featureCounts on data 115 and data 164: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(DMSO_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(DMSO_level).xlsx

value: epithelial, adherent, large cell lung cancer cells

value: WT

value: parental NCI-H460

value: DMSO control (0.7% v/v in  RPMI-1640)


title: ExPEC cells, ceftriaxone [AXO5]


title: Kidney, long-tailed macaque, rep 6


title: 58005: Ileum_31_betaglucans_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
609_609_2606_1

value: Ileum

value: Male

value: maternal


title: ZT10-WT3-KN

value: Kidney


title: parental NCI-H460 ATRA+DAChigh biol_rep_1

description:
featureCounts on data 115 and data 136: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level)

value: 72 hours


title: ZT10-WT2-KN


title: ExPEC cells, cranberry pomace and ceftriaxone [CC5]

value: cranberry pomace and ceftriaxone


title: Cerebellum, long-tailed macaque, rep 6

source_name: Cerebellum

value: Cerebellum


title: Liver, long-tailed macaque, rep 5


title: 57809: Jejunum_31_MCFA_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
602_602_2608_1

value: Jejunum

value: CONTROL


title: ZT10-WT1-KN

value: male

value: 8-12 weeks


title: ZT6-WT3-KN


title: NCI-H460 resistant #2 DMSO biol_rep_1

description:
featureCounts on data 115 and data 132: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(DMSO_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(DMSO_level).xlsx

value: NCI-H460 resistant #2


title: NCI-H460 resistant #2 DMSO biol_rep_3

description:
featureCounts on data 115 and data 180: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(DMSO_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(DMSO_level).xlsx


title: NCI-H460 resistant #2 DMSO biol_rep_2

description:
featureCounts on data 115 and data 156: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(DMSO_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(DMSO_level).xlsx


title: 58231: Colon_31_GOS_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
206_206_2610_1

source_name: Colon; 31; GOS; neonatal

value: Colon

value: GOS


title: Cerebellum, long-tailed macaque, rep 5

value: adult

value: wild type


title: Kidney, long-tailed macaque, rep 5

source_name: Kidney


title: 57914: Jejunum_31_MCFA_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
601_601_2395_4

value: neonatal


title: NCI-H460 resistant #2 ATRA+DAChigh biol_rep_3

description:
featureCounts on data 115 and data 176: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level)

value: epithelial, adherent, large cell lung cancer cells

value: WT

value: decitabine 50 μM and all-trans retinoic acid 2 μM in RPMI-1640


title: ZT6-WT1-KN

value: Kidney


title: 58020: Ileum_31_betaglucans_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
607_607_2346_6

value: Ileum

value: Male

value: betaglucans

value: maternal


title: NCI-H460 resistant #2 ATRA+DAChigh biol_rep_2

description:
featureCounts on data 115 and data 152: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level)

value: 72 hours


title: Liver, long-tailed macaque, rep 4

value: Liver

value: male


title: NCI-H460 resistant #2 ATRA+DAChigh biol_rep_1

description:
featureCounts on data 115 and data 128: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level)

value: NCI-H460 resistant #2


title: ZT2-WT2-KN

value: 8-12 weeks


title: Liver, long-tailed macaque, rep 3


title: Cerebellum, long-tailed macaque, rep 4

value: Cerebellum


title: ZT2-WT3-KN


title: NCI-H460 resistant #1 DMSO biol_rep_3

description:
featureCounts on data 115 and data 172: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(DMSO_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(DMSO_level).xlsx

value: NCI-H460 resistant #1

value: DMSO control (0.7% v/v in  RPMI-1640)


title: Kidney, long-tailed macaque, rep 3

value: adult

value: wild type


title: ZT2-WT1-KN


title: ZT6-WT2-KN


title: NCI-H460 resistant #1 DMSO biol_rep_2

description:
featureCounts on data 115 and data 148: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(DMSO_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(DMSO_level).xlsx

value: epithelial, adherent, large cell lung cancer cells

value: WT


title: Cerebellum, long-tailed macaque, rep 3


title: 58156: Colon_31_GOS_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
110_110_2405_4

value: Colon


title: ZT22-KO2-LI


title: 58148: Colon_31_GOS_neonatal

value: Female

value: GOS


title: 57892: Colon_31_GOS_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
205_205_2567_2


title: 57904: Colon_31_GOS_neonatal

value: Male


title: 58108: Colon_31_GOS_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
109_109_2476_3

value: MCFA

value: maternal


title: ZT22-KO3-LI

value: Liver


title: 57732: Ileum_31_betaglucans_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
208_208_2483_3

source_name: Ileum; 31; betaglucans; neonatal

value: Ileum


title: 58224: Colon_31_GOS_neonatal


title: 58099: Colon_31_GOS_neonatal


title: NCI-H460 resistant #1 ATRA+DAChigh biol_rep_3

description:
featureCounts on data 115 and data 168: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level)

value: decitabine 50 μM and all-trans retinoic acid 2 μM in RPMI-1640

value: 72 hours


title: 57723: Ileum_31_betaglucans_neonatal

value: neonatal


title: NCI-H460 resistant #1 ATRA+DAChigh biol_rep_2

description:
featureCounts on data 115 and data 144: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level)

value: NCI-H460 resistant #1


title: 58083: Ileum_31_betaglucans_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
207_207_2394_4


title: ZT22-KO1-LI

value: male

value: 8-12 weeks


title: Kidney, long-tailed macaque, rep 2

value: Kidney

value: adult

value: wild type


title: NCI-H460 resistant #1 ATRA+DAChigh biol_rep_1

description:
featureCounts on data 115 and data 120: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(ATRA+DAChigh_level)

value: epithelial, adherent, large cell lung cancer cells

value: WT


title: ZT18-KO2-LI


title: ZT18-KO3-LI


title: Cerebellum, long-tailed macaque, rep 2

value: Cerebellum


title: Kidney, long-tailed macaque, rep 1