title: stra8_homo_cap_tis_1

description:
dg2-cp-epi-1_S10
Supplemental_Table_S1_3.xlsx

value: Dgcr8+/fl; Stra8-iCre


title: ovarian cancer P0809

status: Public on Aug 31 2024

type: SRA

city: Kyoto

first: Shiro

last: Takamatsu

address: 54 Shogoin Kawahara, Sakyo, Kyoto

department: Gynecology and Obstetrics

country: Japan

institute: Kyoto University Graduate School of Medicine

library_source: transcriptomic

data_processing:
Raw fastq files were trimmed using Trim-Galore, then mapped to the human reference genome (GRCh38) with the gene annotation of Ensemble GRCh38.v99 using STAR (v2.7.8a). Subsequently, gene expression levels were normalised as TPM or FPKM values using RSEM (v1.3.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample
Supplementary files format and content: tab-delimited text file includes gene TPM values for each sample
Supplementary files format and content: tab-delimited text file includes gene FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: primary tumor

extract_protocol:
As per manufacturer protocol (SMART-Seq@Stranded Kit User Manual (022819), SMART-Seq@Stranded Kit, SMART-Seq@RNA Unique Dual Index Kit)
The cDNA was synthesized from the extracted total RNA using random primers, and a specific sequence was assigned to the end of the 1st strand cDNA by the SMART (Switching Mechanism At 5' End of RNA Template) method. The specific sequence was then amplified by PCR using primers with indexes having different tag sequences for each sample. The PCR product was purified by the magnetic bead method using AMPure XP (Beckman Coulter), and the ribosomal cDNA was cleaved using scZapR and scR-Probe. Finally, the uncut cDNA was PCR amplified using primers that recognize the adaptor, and a sequencing library was generated.
The quality of the generated sequence library was measured using an Agilent 2100 BioAnalyzer. The libraries were sequenced on Illumina NovaSeq6000. Depths of 180–350 million paired-end 150 bp reads were generated for each sample.

tag: disease state

value: ovarian cancer

tag: tissue

value: primary tumor

tag: histology cpr

value: HGSC

tag: histology iti

value: Serous carcinoma

tag: assigned cluster


title: stra8_het_cap_tis_7

city: Philadelphia

first: Natalie

middle: Alyce

last: Trigg

state: Pennsylvania

address: 421 Curie Blvd

country: USA

institute: Children's Hospital of Philadelphia

description:
hetCPepi-3_S21
Supplemental_Table_S1_3.xlsx

data_processing:
For each small RNA library, reads were mapped to rRNAs, miRbase, murine tRNAs, piRNA clusters, to Repeatmasker, and Refseq using Bowtie 2.
Supplementary files format and content: xlsx spreadsheet with one tab per tissue type/comparison

organism: Mus musculus

source_name: caput epididymis tissue

extract_protocol:
Total RNA was extracted from the tissues and subjected to gel electrophoresis to isolate small RNA (18-40nts).
Illumina Tru-seq Small RNA Library

value: caput epididymis tissue

tag: genotype

tag: genome build


title: ovarian cancer P0818


title: ovarian cancer P0808


title: EGCG treated replicate 1

city: Hyderabad

first: Divya Tej

last: Sowpati

state: Telangana

address: Habsiguda

country: India

institute: CSIR Centre for Cellular and Molecular biology

data_processing:
bcl2fastq v2.20 software used for basecalling
Read quality was checked for each sample using FastQC v0.11.9
Sequence reads were trimmed by cutadapt v2.8 and mapped to mm11 whole genome using STAR v2.7.1a with the following command:  STAR --runThreadN 16 --runMode alignReads --sjdbGTFfile ./Mus_musculus.GRCm39.105.gtf --limitBAMsortRAM 34000000000 --quantMode  GeneCounts --genomeDir  star_index/  --readFilesCommand zcat --outSAMstrandField intronMotif --readFilesIn file.1.fastq.gz  file.2.fastq.gz --outSAMtype BAM SortedByCoordinate  --outFileNamePrefix
Quantification of trancripts was done using RSEM v1.2.31
Assembly: mm11(GRCm39.105)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

extract_protocol:
Total RNA was extracted by RNeasy mini kit protocol.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Sample Library Prep Kit following manufacturer's protocols.

tag: cell line

value: TRT

tag: treatment

value: EGCG treated

tag: batch


title: stra8_het_cap_tis_6

description:
hetCPepi-2_S20
Supplemental_Table_S1_3.xlsx


title: Nr4a1 overexpressed replicate 3

value: OE

value: Nr4a1 overexpressed


title: ovarian cancer P0802


title: peripheral blood, colon polyps-r1 (PB1837)

type: RNA

city: Richmond

first: Adam

last: Dempsey

state: VA

address: 8751 Park Central Drive, Suite 200

institute: StageZero Life Sciences

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) v1.1.1 using Affymetrix default analysis settings and global scaling (MAS 5.0) as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

source_name: peripheral blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 701021 Rev. 4, Affymetrix).

extract_protocol: Trizol extraction of total RNA from the pelleted cells was performed according to the manufacturer's instructions.

treatment_protocol: Blood plasma was removed after centrifugation and a hypotonic buffer was added at a 3:1 volume ratio to lyse the red blood cells. The mixture was centrifuged to yield a pellet for subsequent total RNA isolation.

value: peripheral blood

tag: gender

value: M

tag: age

tag: cancer dx

value: colon polyps


title: stra8_het_cap_tis_5

description:
hetCPepi-1_S19
Supplemental_Table_S1_3.xlsx


title: Nr4a1 overexpressed replicate 2


title: peripheral blood, colon polyps-r1 (PB1856)

value: F


title: peripheral blood, colon polyps-r1 (PB1764)


title: peripheral blood, colon polyps-r1 (PB1747)


title: peripheral blood, colon polyps-r1 (PB1478)


title: ovarian cancer P0796


title: peripheral blood, colon polyps-r1 (PB1414)


title: Nr4a1 overexpressed replicate 1


title: stra8_het_cap_tis_4

description:
het2-cp-epi-4_S15
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (PB1836)


title: MIN6 CTRL replicate 3

value: CTRL

value: untransfected MIN6 cells


title: ovarian cancer P0791


title: stra8_het_cap_tis_3

description:
het2-cp-epi-3_S13
Supplemental_Table_S1_3.xlsx


title: MIN6 CTRL replicate 2


title: MIN6 CTRL replicate 1


title: ovarian cancer P0793


title: stra8_het_cap_tis_2

description:
het2-cp-epi-2_S12
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0781


title: peripheral blood, colon polyps-r1 (PB1341)


title: defb_homo_cau_tis_3

description:
sm_defb_homo_cau_tis_4_S36
Supplemental_Table_S1_3.xlsx

source_name: cauda epididymis tissue

value: cauda epididymis tissue

value: Dgcr8fl/fl; Defb41-iCre


title: ovarian cancer P0786

value: ovarian cancer


title: Liver 231/miR-9 KO_3

city: Wuhan

first: Li

last: Mei-Xin

address: College of Life Science, Wuhan University, Luojiashan Road, Wuchang District, Wuhan City, Hubei Province, China

country: China

institute: Wuhan University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep  and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.RSEM was used to quantify gene abundances.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: liver

growth_protocol: MDA-MB-231, MDA-MB-231/Rab27A KD and MDA-MB-231/miR-9 KO cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA-seq transcriptome library was prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA) using 1 μg of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: orthotopic injection 2 × 105  cells into the fourth pair of mammary fat pad in NSG mice.

value: liver

tag: cell type

value: Epithelial cell

value: orthotopic injection


title: defb_homo_cau_tis_2

description:
sm_defb_homo_cau_tis_3_S35
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (PB1317)


title: peripheral blood, colon polyps-r1 (PB1346)


title: peripheral blood, colon polyps-r1 (PB1307)


title: ovarian cancer P0775

value: primary tumor

value: HGSC

value: Serous carcinoma


title: peripheral blood, colon polyps-r1 (PB1265)


title: ovarian cancer P0777


title: Liver 231/miR-9 KO_2


title: peripheral blood, colon polyps-r1 (PB1237)


title: stra8_het_cap_tis_1

description:
het2-cp-epi-1_S9
Supplemental_Table_S1_3.xlsx

value: caput epididymis tissue

value: Dgcr8+/fl; Stra8-iCre


title: ovarian cancer P0774


title: Liver 231/miR-9 KO_1


title: peripheral blood, colon polyps-r1 (PB1224)

value: peripheral blood


title: defb_het_cau_tis_4

description:
sm_defb_het_cau_tis_4_S28
Supplemental_Table_S1_3.xlsx

value: Dgcr8+/fl; Defb41-iCre


title: Liver 231/Rab27A KD_3

value: 231/Rab27A KD


title: Liver 231/Rab27A KD_2


title: Liver 231/Rab27A KD_1


title: defb_het_cau_tis_2

description:
sm_defb_het_cau_tis_2_S26
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0773


title: ovarian cancer P0770


title: ovarian cancer P0771


title: defb_het_cau_tis_1

description:
sm_defb_het_cau_tis_1_S25
Supplemental_Table_S1_3.xlsx


title: Liver tumor bearing_3

value: WT


title: ovarian cancer P0766


title: defb_homo_cau_tis_1

description:
sm_defb_homo_cau_tis_1_S33
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (PB0759)

value: M

value: colon polyps


title: Liver tumor bearing_2


title: peripheral blood, colon polyps-r1 (PB0596)

value: F


title: peripheral blood, colon polyps-r1 (PB0537)


title: defb_het_cau_tis_3

description:
sm_defb_het_cau_tis_3_S27
Supplemental_Table_S1_3.xlsx

value: cauda epididymis tissue


title: Liver tumor free_3


title: Liver tumor bearing_1


title: ovarian cancer P0758

value: ovarian cancer


title: ovarian cancer P0756

value: Clear cell carcinoma


title: defb_homo_cap_tis_1

description:
sm_defb_homo_cap_tis_1_S29
Supplemental_Table_S1_3.xlsx

value: Dgcr8fl/fl; Defb41-iCre


title: peripheral blood, colon polyps-r1 (PB0511)


title: peripheral blood, colon polyps-r1 (PB0472)


title: ovarian cancer P0760


title: defb_het_cap_tis_3

description:
sm_defb_het_cap_tis_4_S24
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (PB0468)


title: defb_het_cap_tis_2

description:
sm_defb_het_cap_tis_3_S23
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0754

value: Endometrioid carcinoma


title: defb_homo_cap_tis_2

description:
sm_defb_homo_cap_tis_3_S31
Supplemental_Table_S1_3.xlsx


title: defb_het_cap_tis_1

description:
sm_defb_het_cap_tis_2_S22
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (PB0328)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.


title: defb_homo_cap_tis_3

description:
sm_defb_homo_cap_tis_4_S32
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0753

value: primary tumor


title: RAW264.7 25-HC_3

growth_protocol: RAW264.7 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

treatment_protocol: RAW264.7 cells were treated with vehicle or 25-HC for 24h.

value: Mononuclear macrophage

tag: time


title: Liver tumor free_1

value: liver


title: peripheral blood, colon polyps-r1 (PB0305)


title: defb_homo_causp_8

description:
defb_homo_causp4_S8
Supplemental_Table_S1_3.xlsx

source_name: cauda sperm

value: cauda sperm

value: Dgcr8fl/fl; Defb-iCre


title: ovarian cancer P0750

value: HGSC

value: Serous carcinoma


title: peripheral blood, colon polyps-r1 (PB0310)

value: peripheral blood


title: RAW264.7 25-HC_2

value: WT


title: peripheral blood, colon polyps-r1 (PB0302)


title: ovarian cancer P0746


title: defb_homo_causp_7

description:
defb_homo_causp3_S7
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0740


title: ovarian cancer P0738


title: defb_homo_causp_6

description:
defb_homo_causp2_S6
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (PB0280)


title: peripheral blood, colon polyps-r1 (PB0289)


title: peripheral blood, colon polyps-r1 (PB0287)

value: M


title: defb_homo_causp_5

description:
defb_homo_causp1_S5
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0737


title: stra8_het_cau_tis_2

description:
het2-ca-epi-2_S4
Supplemental_Table_S1_3.xlsx

value: Dgcr8+/fl; Stra8-iCre


title: defb_homo_causp_4

description:
def_mut4_casp
Supplemental_Table_S1_3.xlsx


title: RAW264.7 vehicle_1

value: vehicle


title: defb_homo_causp_3

description:
def_mut3_casp
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0721


title: peripheral blood, colon polyps-r1 (PB0258)

value: colon polyps


title: RAW264.7 25-HC_1


title: ovarian cancer P0725

value: ovarian cancer


title: Liver MDA-MB-231EV_2

growth_protocol: MCF-10A and MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

treatment_protocol: MCF-10A and MDA-MB-231 cells derived EVs or PBS were injected into the tail vein  of NSG mice for 5 weeks.

value: Epithelial cell

value: i.v. EV injection


title: RAW264.7 vehicle_3


title: peripheral blood, colon polyps-r1 (PB0263)

value: F


title: defb_homo_causp_1

description:
def_mut1_casp
Supplemental_Table_S1_3.xlsx


title: RAW264.7 vehicle_2


title: ovarian cancer P0719

value: primary tumor


title: Liver MCF-10A EV_3


title: Liver MDA-MB-231EV_1


title: defb_het_causp_7

description:
defb_het_causp3_S3
Supplemental_Table_S1_3.xlsx

value: Dgcr8+/fl; Defb41-iCre


title: ovarian cancer P0713


title: Liver MDA-MB-231EV_3

value: liver


title: defb_homo_causp_2

description:
def_mut2_casp
Supplemental_Table_S1_3.xlsx

value: cauda sperm


title: peripheral blood, colon polyps-r1 (PB0214)


title: Liver MCF-10A EV_2


title: Liver MCF-10A EV_1


title: defb_het_causp_6

description:
defb_het_causp2_S2
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (PB0183)


title: peripheral blood, colon polyps-r1 (PB0196)


title: peripheral blood, colon polyps-r1 (PB0201)


title: ovarian cancer P0700

value: Clear cell carcinoma


title: peripheral blood, colon polyps-r1 (PB0255)


title: defb_het_causp_8

description:
defb_het_causp4_S4
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0698

value: HGSC


title: Liver PBS_3

value: i.v. PBS injection


title: ovarian cancer P0696

value: Serous carcinoma


title: defb_het_causp_5

description:
defb_het_causp1_S1
Supplemental_Table_S1_3.xlsx


title: Liver PBS_2

value: WT


title: ovarian cancer P0706


title: Liver PBS_1


title: ovarian cancer P0690


title: peripheral blood, colon polyps-r1 (PB0162)

value: peripheral blood

value: M


title: defb_het_causp_3

description:
def_het3_casp
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (PB0179)


title: ovarian cancer P0689


title: defb_het_causp_2

description:
def_het2_casp
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (PB0096)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.


title: ovarian cancer P0687


title: peripheral blood, colon polyps-r1 (PB0135)


title: KOAM-3

city: Xiamen

first: Bin

last: Xu

address: Room 112, Chengzhi building, School of Medicine, Xiamen University, Xiang'an South Road, Xiang'an District

institute: Xiamen University

data_processing:
In this project, we sequence 6 samples used DNBSEQ platform, averagely generating about 6.75GGb bases per sample. The average mapping ratio with reference genome is 98.64%, the averagemapping ratio with gene is 89.05%; 15824 genes were identified.
The raw data contains reads of low quality, reads with adaptor sequences and reads with highlevels of N base. Those reads need to be filtered before the data analysis for reliability analysisresults.
We used HISAT to align the clean reads to the reference genome. The alignment results are shownas follows.
We used Bowtie2 to align the clean reads to the reference genes.
The statistical results of significant DEGS are as follows.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Tab-delimited txt files includes fpkm, tpm, read counts, norm read counts and differential analysis of all genes between WT and KO samples

source_name: lung

extract_protocol:
WT and Men1 knockout(KO) alveolar macrophages were isolated from mice 8 weeks old by flow cytometry, and sent to BGI Center No.9, Yuanhua Road, Yantian District, Shenzhen 518081, China.
Sequencing libraries were generated using NEBNext® Ultra™ II DNA Library Prep Kit
polyA_selected

value: lung

value: alveolar macrophage

value: KO

value: flow cytometry


title: defb_het_causp_4

description:
def_het4_casp
Supplemental_Table_S1_3.xlsx


title: defb_het_causp_1

description:
def_het1_casp
Supplemental_Table_S1_3.xlsx


title: KOAM-2


title: defb_homo_tssp_4

description:
def_mut4_tsp
Supplemental_Table_S1_3.xlsx

source_name: testis sperm

value: testis sperm

value: Dgcr8fl/fl; Defb-iCre


title: peripheral blood, colon polyps-r1 (PB0092)

value: F

value: colon polyps


title: KOAM-1


title: ovarian cancer P0683

value: ovarian cancer

value: primary tumor


title: WTAM-3


title: peripheral blood, colon polyps-r1 (PB0090)


title: peripheral blood, colon polyps-r1 (PB0066)


title: ovarian cancer P0679


title: defb_homo_tssp_2

description:
def_mut2_tsp
Supplemental_Table_S1_3.xlsx


title: WTAM-2


title: defb_homo_tssp_1

description:
def_mut1_tsp
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0678


title: peripheral blood, colon polyps-r1 (PB0053)


title: WTAM-1


title: defb_het_tssp_4

description:
def_het4_testis
Supplemental_Table_S1_3.xlsx

value: Dgcr8+/fl; Defb41-iCre


title: ovarian cancer P0676

value: HGSC


title: ovarian cancer P0684


title: defb_het_tssp_3

description:
def_het3_tsp
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (PB0033)


title: 4T-1 cells, Lyplal1 KO, rep3

city: Xi'an

first: Yizeng

last: Fan

address: Yanta West Road

institute: Xi'an Jiaotong University

data_processing:
Clean sequence reads were mapped to GRCm38 using STAR(v2.7.8a) (parameter --outSAMtype BAM SortedByCoordinate)
Read count extraction were performed using featureCounts(v2.0.1) (parameters -d 36 -t exon -g gene_id)
Assembly: GRCm38
Supplementary files format and content: tab-delimited test file includes counts for each Sample
Supplementary files format and content: tab-delimited test file includes TPM values for each Sample

source_name: breast

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries for RNA-seq were prepared using DNBseq RNA-Seq Quantification library

value: breast

value: breast cancer cells

value: Lyplal1 knockout

value: no treatment


title: ovarian cancer P0675

value: Serous carcinoma


title: peripheral blood, colon polyps-r1 (PB0028)

value: peripheral blood


title: 4T-1 cells, Lyplal1 KO, rep2


title: defb_homo_tssp_3

description:
def_mut3_tsp
Supplemental_Table_S1_3.xlsx


title: 4T-1 cells, Lyplal1 KO, rep1


title: ovarian cancer P0670


title: peripheral blood, colon polyps-r1 (PB0005)


title: peripheral blood, colon polyps-r1 (PB0063)

value: M


title: defb_het_tssp_1

description:
def_het1_tsp
Supplemental_Table_S1_3.xlsx


title: defb_het_tssp_2

description:
def_het2_tsp
Supplemental_Table_S1_3.xlsx


title: 4T-1 cells, wild-type, rep3

value: wild type


title: 4T-1 cells, wild-type, rep2


title: ovarian cancer P0669


title: ovarian cancer P0661


title: stra8_homo_causp_4

description:
ca-sperm-dg-4_S8
Supplemental_Table_S1_3.xlsx

value: cauda sperm

value: Dgcr8fl/fl; Stra8-iCre


title: peripheral blood, colon polyps-r1 (MH0040)


title: 4T-1 cells, wild-type, rep1


title: peripheral blood, colon polyps-r1 (MH0055)


title: stra8_homo_causp_3

description:
ca-sperm-dg-3_S6
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (MH0052)


title: CLPTM1L_shRNA2_3

city: Kunming

first: Weipeng

last: Liu

state: Yunnan

address: Jiao ling road

department: Institute of Medical Biology

institute: Chinese Academy of Medical Sciences

description:
CLPTM1L knockdown
CLPTM1L_shRNA2_3.txt

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp  (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4  and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts  for each Sample

source_name: cervical tissue

growth_protocol: Cells were nurtured in Dulbecco's Modified Eagle medium (DMEM, Gibco), which was enriched with 10% fetal bovine serum (FBS, Gibco). All cell lines were maintained in an incubator set at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
The enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using the BGISEQ-500 platform (MGI Tech; China).

value: cervical tissue

value: HeLa

value: cervical cancer cell

value: CLPTM1L knockdown


title: ovarian cancer P0671

value: ovarian cancer

value: primary tumor


title: stra8_homo_causp_2

description:
ca-sperm-dg-2_S3
Supplemental_Table_S1_3.xlsx


title: stra8_homo_causp_1

description:
ca-sperm-dg-1_S2
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0652

value: HGSC


title: peripheral blood, colon polyps-r1 (MH0019)

value: F

value: colon polyps


title: ovarian cancer P0648


title: peripheral blood, colon polyps-r1 (HZ0083)


title: stra8_het_causp_4

description:
ca-sperm-het4_S7
Supplemental_Table_S1_3.xlsx

value: Dgcr8+/fl; Stra8-iCre


title: peripheral blood, colon polyps-r1 (MH0008)


title: ovarian cancer P0646


title: Liver tumor free_2

value: liver


title: CLPTM1L_shRNA2_1

description:
CLPTM1L knockdown
CLPTM1L_shRNA2_1.txt


title: stra8_het_causp_3

description:
ca-sperm-het3_S5
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0642

value: Serous carcinoma


title: ovarian cancer P0657


title: ovarian cancer P0641


title: CLPTM1L_shRNA1_2

description:
CLPTM1L knockdown
CLPTM1L_shRNA1_2.txt


title: stra8_het_causp_2

description:
ca-sperm-het2_S4
Supplemental_Table_S1_3.xlsx


title: CLPTM1L_shRNA1_3

description:
CLPTM1L knockdown
CLPTM1L_shRNA1_3.txt


title: stra8_het_causp_1

description:
ca-sperm-het1_S1
Supplemental_Table_S1_3.xlsx


title: CLPTM1L_shRNA1_1

description:
CLPTM1L knockdown
CLPTM1L_shRNA1_1.txt


title: CLPTM1L_shRNA2_2

description:
CLPTM1L knockdown
CLPTM1L_shRNA2_2.txt


title: ovarian cancer P0638


title: peripheral blood, colon polyps-r1 (HZ0042)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

value: peripheral blood


title: peripheral blood, colon polyps-r1 (HZ0075)

value: M


title: peripheral blood, colon polyps-r1 (HZ0034)


title: Ctrl_3

description:
Negative control
Ctrl_3.txt

value: Negative control


title: Ctrl_2

description:
Negative control
Ctrl_2.txt


title: stra8_homo_tssp_3

description:
t-sperm-dg-3_S22
Supplemental_Table_S1_3.xlsx

value: testis sperm


title: stra8_homo_tssp_4

description:
t-sperm-dg-4_S24
Supplemental_Table_S1_3.xlsx

value: Dgcr8fl/fl; Stra8-iCre


title: peripheral blood, colon polyps-r1 (HZ0019)


title: stra8_homo_tssp_2

description:
t-sperm-dg-2_S19
Supplemental_Table_S1_3.xlsx


title: peripheral blood, colon polyps-r1 (HZ0026)


title: Ctrl_1

description:
Negative control
Ctrl_1.txt

value: cervical tissue


title: peripheral blood, colon polyps-r1 (HZ0008)


title: ovarian cancer P0626

value: Other


title: ovarian cancer P0624


title: MEF cells AdORAI2-3

city: Yuzhong district

first: Xiang

last: Gao

state: Chongqing

address: No. 1 Yixueyuan Road, Yuzhong Chongqing, China 400016

institute: Chongqing Medical University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). expression level of gene was calculated by salmon (v1.4.0).
Assembly: GRCm39
Supplementary files format and content: text file includes COUNTs and TPMs for all samples

source_name: MEFs

extract_protocol:
RNA was harvested with TRIzol reagent following the manufacturer’s instructions.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library

value: MEFs

value: mesenchymal stem cells

value: ORAI2 Overexpression

value: osteogenic differentiation


title: stra8_het_tssp_4

description:
t-sperm-het4_S23
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0621

value: ovarian cancer

value: primary tumor

value: HGSC


title: stra8_homo_tssp_1

description:
t-sperm-dg-1_S18
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0620

value: Endometrioid carcinoma


title: stra8_het_tssp_3

description:
t-sperm-het3_S21
Supplemental_Table_S1_3.xlsx

value: Dgcr8+/fl; Stra8-iCre


title: MEF cells AdORAI2-2


title: ovarian cancer P0635

value: Serous carcinoma


title: peripheral blood, colon polyps-r1 (HZ0001)

value: peripheral blood

value: colon polyps


title: peripheral blood, colon polyps-r1 (HZ0007)

value: F


title: MEF cells AdGFP-3

value: WT


title: stra8_het_tssp_2

description:
t-sperm-het2_S20
Supplemental_Table_S1_3.xlsx

value: testis sperm


title: ovarian cancer P0619


title: ovarian cancer P0615


title: peripheral blood, colon polyps-r1 (CTL858)


title: peripheral blood, colon polyps-r1 (CTL383)

value: M


title: peripheral blood, colon polyps-r1 (CD1749)


title: MEF cells AdGFP-2


title: 4-5th instar larva of Galleria mellonella treated with Heterorhabditis indica after death

city: Bengaluru

first: Nagesh

last: Mandadi

state: Karnataka

address: Bellary Road, H.A. Farm Post, Hebbal, Bengaluru, Karnataka

department: Division of Genomics Resource

institute: ICAR-National Bureau of Agricultural Insect Resources

description:
4-5th instar larva of Galleria mellonella (snap frozen and stored at -80 degree Celsius)
SAMPLE 10

hyb_protocol: Organism Specific probes were designed for 19 genes (6 housekeeping and 13 endogenous) of (Spodoptera, Galleria, Nematode and Bacterial) and multiplexed assays were performed. Certain genes belongs to Drosophila melanogaster and are orthologous to the insects studied. Probes Stock solution was prepared as per nanoString recommendation. 250ng (in7ul) of total RNA was taken for hybridisation. nCounter® Elements™ TagSets chemistry was performed as per manufacturer protocol. Manual -  nCounter® Elements™ TagSets MAN-10057-03 (January 2020) TagSet Hybridization Setup

scan_protocol: Hybridized molecules are loaded to Nanostring sprint catridge and loaded onto nCounter SPRINT machine for scanning the barcodes. Raw counts data (.RCC) was retrieved from the machine after the scanning completes.

data_processing:
Raw data were normalized using nSolver 4.0 software. Normalization were carried out using Positive control probes and the house keeping gene, glutathione S-transferase (AF179869.1)
NSolver 4.0 software was used to compute Normalized log2 counts

organism: Galleria mellonella

label_protocol: NanoString uses combination of oligonucleotide based barcodes. Each probe hybridising the mRNAs will be unique with combination of color dye combination which are barcoded barcodes.

extract_protocol: The worms (snap frozen and stored at -80 degree Celsius) were crushed properly using plastic disposable pestle, in a microcentrifuge tube. Post initial crushing, Qiagen lysis buffer was added and crushed again for better lysis using plastic disposable pestle.  Intermittently vortexed vigorously for better homogenization. Once the worms were crushed it was proceeded with Qiagen miRNeasy mini kit protocol (catalogue no. 217004).

tag: developmental stage

value: 4-5th instar larva


title: ovarian cancer P0607


title: 4-5th instar larva of Galleria mellonella treated with Heterorhabditis indica

description:
4-5th instar larva of Galleria mellonella (snap frozen and stored at -80 degree Celsius)
SAMPLE 9


title: ovarian cancer P0606


title: peripheral blood, colon polyps-r1 (CD1553)


title: Untreated healthy 4-5th instar larva of Galleria mellonella

description:
4-5th instar larva of Galleria mellonella (snap frozen and stored at -80 degree Celsius)
SAMPLE 8


title: 4-5th instar larva of Spodoptera frugiperda treated with Steinernema carpocapsae after death

description:
4-5th instar larva of Spodoptera frugiperda (snap frozen and stored at -80 degree Celsius)
SAMPLE 7

organism: Spodoptera frugiperda


title: 4-5th instar larva of Spodoptera frugiperda treated with Steinernema carpocapsae

description:
4-5th instar larva of Spodoptera frugiperda (snap frozen and stored at -80 degree Celsius)
SAMPLE 6


title: peripheral blood, colon polyps-r1 (CD1535)


title: peripheral blood, colon polyps-r1 (CD1413)


title: stra8_het_tssp_1

description:
t-sperm-het1_S17
Supplemental_Table_S1_3.xlsx


title: ovarian cancer P0613


title: 4-5th instar larva of Spodoptera frugiperda treated with Steinernema riobrave after death

description:
4-5th instar larva of Spodoptera frugiperda (snap frozen and stored at -80 degree Celsius)
SAMPLE 5


title: peripheral blood, colon polyps-r1 (CD1412)


title: ovarian cancer P0594


title: 4-5th instar larva of Spodoptera frugiperda treated with Steinernema riobrave

description:
4-5th instar larva of Spodoptera frugiperda (snap frozen and stored at -80 degree Celsius)
SAMPLE 4


title: ovarian cancer P0593


title: MEF cells AdGFP-1

value: MEFs


title: ovarian cancer P0592


title: peripheral blood, colon polyps-r1 (CD1283)


title: peripheral blood, colon polyps-r1 (CD1258)


title: peripheral blood, colon polyps-r1 (CD1328)


title: 4-5th instar larva of Spodoptera frugiperda treated with Heterorhabditis indica after death

description:
4-5th instar larva of Spodoptera frugiperda (snap frozen and stored at -80 degree Celsius)
SAMPLE 3


title: ovarian cancer P0599


title: ovarian cancer P0602


title: 4-5th instar larva of Spodoptera frugiperda treated with Heterorhabditis indica

description:
4-5th instar larva of Spodoptera frugiperda (snap frozen and stored at -80 degree Celsius)
SAMPLE 2


title: Untreated healthy 4-5th instar larva of Spodoptera frugiperda

description:
4-5th instar larva of Spodoptera frugiperda (snap frozen and stored at -80 degree Celsius)
SAMPLE 1


title: ovarian cancer P0589


title: ovarian cancer P0587


title: peripheral blood, colon polyps-r1 (CD1143)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.


title: i9-control-24hr_S9

city: Oxford

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

description: samples were sequenced in a 41 bp paired-end configuration

data_processing:
Sequencing reads were pseudoaligned to the hg38 reference transcriptome using Kallisto. Differential gene expression analysis was conducted using the DESeq2 package, with genes considered differentially expressed if the adjusted p-value was < 0.01.
Assembly: hg38
Supplementary files format and content: tab delimited text file of counts from processing kallisto files

molecule: polyA RNA

source_name: MUG-Chor

growth_protocol: cells were cultured in 4:1 Iscove’s Modified Dulbecco’s Medium (IMDM) (Gibco): RPMI 1640 (Gibco) with 10% FBS (Life Technologies) and Penicillin Streptomycin (Life Technologies)

extract_protocol:
Total RNA was extracted from cell lines and tumour samples from treated mice using TRIzol reagent, followed by purification with the Direct-zol RNA Miniprep Kit (Zymo Research), which includes an on-column DNase I digestion step to remove genomic DNA
Poly(A) RNA was isolated from the total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). First-strand cDNA libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs)

treatment_protocol: cells were treated for 0, 6, 24 and 72 hours with either DMSO control, Halofuginone or Halofuginol

value: MUG-Chor

value: chordoma cell line

value: control


title: ovarian cancer P0581

value: ovarian cancer


title: peripheral blood, colon polyps-r1 (CD1153)


title: peripheral blood, colon polyps-r1 (CD1088)


title: i8-control-6hr_S8


title: ovarian cancer P0580

value: primary tumor


title: ovarian cancer P0577

value: HGSC


title: i7-control-6hr_S7


title: i6-control-6hr_S6


title: ovarian cancer P0588


title: i4-control-0hr_S4


title: ovarian cancer P0567


title: ovarian cancer P0573


title: i5-control-6hr_S5


title: peripheral blood, colon polyps-r1 (CD0919)


title: peripheral blood, colon polyps-r1 (CD0989)


title: ovarian cancer P0564


title: peripheral blood, colon polyps-r1 (CD0990)


title: i40-1805-72hr_S40

value: Halofuginol


title: ovarian cancer P0563


title: i3-control-0hr_S3


title: ovarian cancer P0560


title: i39-1805-72hr_S39


title: peripheral blood, colon polyps-r1 (CD0722)


title: peripheral blood, colon polyps-r1 (CD0874)


title: peripheral blood, colon polyps-r1 (CD0692)


title: peripheral blood, colon polyps-r1 (CD0899)


title: peripheral blood, colon polyps-r1 (CD0406)


title: i38-1805-72hr_S38


title: peripheral blood, colon polyps-r1 (CD0689)


title: peripheral blood, colon polyps-r1 (CD0099)


title: ovarian cancer P0553


title: peripheral blood, colon polyps-r1 (CD0139)


title: i36-1805-24hr_S36


title: ovarian cancer P0550


title: peripheral blood, breast cancer-r1 (SN0036)

value: breast cancer


title: i34-1805-24hr_S34


title: i37-1805-72hr_S37


title: ovarian cancer P0543

value: Serous carcinoma


title: ovarian cancer P0556


title: i33-1805-24hr_S33


title: ovarian cancer P0541


title: i35-1805-24hr_S35


title: ovarian cancer P0539


title: i31-1805-6hr_S31


title: ovarian cancer P0538


title: i32-1805-6hr_S32


title: ovarian cancer P0536


title: i30-1805-6hr_S30


title: ovarian cancer P0533


title: peripheral blood, breast cancer-r1 (SN0030)

value: peripheral blood


title: peripheral blood, breast cancer-r1 (SN0035)


title: peripheral blood, breast cancer-r1 (SN0031)


title: peripheral blood, breast cancer-r1 (SN0027)


title: peripheral blood, breast cancer-r1 (SN0033)


title: peripheral blood, breast cancer-r1 (SN0034)


title: i2-control-0hr_S2


title: peripheral blood, breast cancer-r1 (SN0029)


title: i29-1805-6hr_S29


title: ovarian cancer P0531


title: ovarian cancer P0525


title: MEF cells AdORAI2-1

value: mesenchymal stem cells

value: ORAI2 Overexpression

value: osteogenic differentiation


title: ovarian cancer P0528


title: i27-1392-72hr_S27

value: Halofuginone


title: i28-1392-72hr_S28


title: ovarian cancer P0527


title: ovarian cancer P0524


title: peripheral blood, breast cancer-r1 (SN0026)


title: i25-1392-72hr_S25


title: i26-1392-72hr_S26


title: ovarian cancer P0549


title: peripheral blood, breast cancer-r1 (SN0025)


title: ovarian cancer P0519


title: peripheral blood, breast cancer-r1 (SN0021)


title: peripheral blood, breast cancer-r1 (SN0022)


title: i24-1392-24hr_S24


title: peripheral blood, breast cancer-r1 (SN0020)


title: peripheral blood, breast cancer-r1 (SN0024)


title: peripheral blood, breast cancer-r1 (SN0019)


title: ovarian cancer P0518


title: ovarian cancer P0517


title: i23-1392-24hr_S23


title: i21-1392-24hr_S21


title: ovarian cancer P0513


title: ovarian cancer P0516


title: ovarian cancer P0514


title: i1-control-0hr_S1


title: ovarian cancer P0504


title: i20-1392-6hr_S20


title: i18-1392-6hr_S18


title: i19-1392-6hr_S19


title: ovarian cancer P0510


title: ovarian cancer P0488


title: peripheral blood, breast cancer-r1 (SN0018)


title: i17-1392-6hr_S17


title: peripheral blood, breast cancer-r1 (SN0015)


title: peripheral blood, breast cancer-r1 (SN0013)


title: peripheral blood, breast cancer-r1 (SN0016)


title: peripheral blood, breast cancer-r1 (SN0017)


title: peripheral blood, breast cancer-r1 (SN0012)


title: peripheral blood, breast cancer-r1 (SN0014)


title: ovarian cancer P0480


title: i16-control-72hr_S16


title: i15-control-72hr_S15


title: i22-1392-24hr_S22


title: ovarian cancer P0466


title: ovarian cancer P0456


title: ovarian cancer P0468


title: i14-control-72hr_S14


title: i12-control-24hr_S12


title: i13-control-72hr_S13


title: peripheral blood, breast cancer-r1 (SN0011)


title: ovarian cancer P0447


title: ovarian cancer P0451

value: Endometrioid carcinoma


title: i11-control-24hr_S11


title: ovarian cancer P0446


title: i10-control-24hr_S10


title: ovarian cancer P0445


title: ovarian cancer P0438


title: pooled whole embryos 210 ng/L repE

city: Saskatoon

first: Natacha

last: Hogan

state: SK

address: 51 Campus Drive

country: Canada

institute: University of Saskatchewan

description:
SigGene_Medium_vs_Control_Hisat2
XL_lead_II_nitrate_HiSat2.tabular
XE3-MEP5-WT4

data_processing:
The fastq files were trimmed using TrimGalore to remove adapter contamination and carry out quality control steps. This was carried out in galaxy.ecotoxxplorer.ca
The trimmed sequencing reads were aligned to the reference Xenopus laevis genome (GenBank assembly accession: GCA_001663975.1) using HiSat2 to obtain the raw count files. This was carried out in galaxy.ecotoxxplorer.ca
Low variance and low abundance features were filtered out and normalized using ecotoxxplorer.ca
The differentially expressed genes were identified using EdgeR, genes with adjusted p value <0.05 and log2 fold change value > 1 were considered significantly dysregulated. This was done in ecotoxxplorer.ca
Genome_build: Xenopus laevis genome (GenBank assembly accession: GCA_001663975.1)
Supplementary_files_format_and_content: csv - results of differentially expressed genes analysis using HiSat2
Supplementary_files_format_and_content: tabular - results of raw counts using Kallisto

organism: Xenopus laevis

source_name: whole body tissue

growth_protocol: Embryos were obtained by breeding adult Xenopus laevis from an established colony. Adults were maintained at 18 ± 1°C water temperature and a 12 h light:12 h dark photoperiod. Males and female pairs were selected for breeding, and gradually acclimated to 21 ± 1°C. Mating was induced by injecting human chorionic gonadotropin (hCG, Sigma-Aldrich, St. Louis, MN) dissolved in sterilized phosphate buffered saline (PBS). Males and females were randomly paired for breeding, placed into aquaria with water temperature maintained at 21 ± 1 °C, and left to spawn overnight. After collection the following day, selection and preparation of embryos closely followed protocols outlined in “Standard guide for conducting the Frog Embryo Teratogenesis Assay-Xenopus (FETAX)” (ASTM, 2019)  with some modifications. Up to 30 selected embryos were placed in each egg cup in an aquarium to incubate in facility water maintained at 21 ± 1 °C for 48 h. Animals used in this study were handled in accordance with the University of Saskatchewan’s Animal Research Ethics Board (protocol #20160090) and the Canadian Council on Animal Care guidelines for humane animal use.

extract_protocol:
Tissue was homogenized and RNA was extracted using the RNeasy Plus Universal Mini kit (QIAGEN) according to the manufacturer’s instructions.
Libraries were generated from 250 ng of total RNA as following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GXII (PerkinElmer) instrument.

treatment_protocol: Embryos at approximately Nieuwkoop and Faber (NF) stage 29 (~48 h post-fertilization) were used for treatment and exposed for 96h. Embryos were placed in 50 mL plastic petri dishes containing one of the folllowing solutions of lead nitrate 0, 210 or 630 μg/L. During the exposure, animals were kept in an environmental chamber with ambient temperature of 21°C and a 16 h light: 8 h dark photoperiod.

value: 6 days post fertilization

tag: exposure compound

value: lead (II) nitrate

value: 210 ng/L lead (II) nitrate


title: pooled whole embryos 210 ng/L repC

description:
SigGene_Medium_vs_Control_Hisat2
XL_lead_II_nitrate_HiSat2.tabular
XE3-MCP3-WT4


title: ovarian cancer P0431

tag: disease state


title: ovarian cancer P0434

tag: tissue


title: peripheral blood, breast cancer-r1 (SN0008)


title: peripheral blood, breast cancer-r1 (SN0009)


title: peripheral blood, breast cancer-r1 (SN0004)


title: peripheral blood, breast cancer-r1 (SN0010)


title: peripheral blood, breast cancer-r1 (SN0007)


title: pooled whole embryos 630 ng/L repE

description:
SigGene_High_vs_Control_hisat2
XL_lead_II_nitrate_HiSat2.tabular
XE3-HEP5-WT4

value: 630 ng/L lead (II) nitrate


title: pooled whole embryos 210 ng/L repB

description:
SigGene_Medium_vs_Control_Hisat2
XL_lead_II_nitrate_HiSat2.tabular
XE3-MBP2-WT4


title: ovarian cancer P0429

tag: histology cpr


title: pooled whole embryos 210 ng/L repA

description:
SigGene_Medium_vs_Control_Hisat2
XL_lead_II_nitrate_HiSat2.tabular
XE3-MAP1-WT4


title: peripheral blood, breast cancer-r1 (SN0003)


title: ovarian cancer P0414

tag: histology iti


title: ovarian cancer P0415

tag: assigned cluster


title: peripheral blood, breast cancer-r1 (SN0001)


title: pooled whole embryos 630 ng/L repD

description:
SigGene_High_vs_Control_hisat2
XL_lead_II_nitrate_HiSat2.tabular
XE3-HDP4-WT4


title: peripheral blood, breast cancer-r1 (PN0428)

value: F


title: peripheral blood, breast cancer-r1 (SN0006)


title: peripheral blood, breast cancer-r1 (PN0418)


title: pooled whole embryos 210 ng/L repD

description:
SigGene_Medium_vs_Control_Hisat2
XL_lead_II_nitrate_HiSat2.tabular
XE3-MDP4-WT4


title: pooled whole embryos 630 ng/L repC

description:
SigGene_High_vs_Control_hisat2
XL_lead_II_nitrate_HiSat2.tabular
XE3-HCP3-WT4


title: ovarian cancer P0422

value: ovarian cancer


title: pooled whole embryos 630 ng/L repA

description:
SigGene_High_vs_Control_hisat2
XL_lead_II_nitrate_HiSat2.tabular
XE3-HAP1-WT4


title: peripheral blood, breast cancer-r1 (PN0416)


title: ovarian cancer P0411

value: primary tumor


title: pooled whole embryos 630 ng/L repB

description:
SigGene_High_vs_Control_hisat2
XL_lead_II_nitrate_HiSat2.tabular
XE3-HBP2-WT4


title: peripheral blood, breast cancer-r1 (PN0409)


title: peripheral blood, breast cancer-r1 (SN0002)


title: peripheral blood, breast cancer-r1 (PN0443)


title: ovarian cancer P0406

value: HGSC


title: pooled whole embryos 0 ng/L repD

description:
XL_lead_II_nitrate_HiSat2.tabular
XE3-CDP4-WT4

value: water control

value: 0 ng/L lead (II) nitrate


title: ovarian cancer P0407

value: Serous carcinoma


title: ovarian cancer P0413


title: ovarian cancer P0404


title: peripheral blood, breast cancer-r1 (PN0354)

value: peripheral blood

value: breast cancer


title: pooled whole embryos 0 ng/L repA

description:
XL_lead_II_nitrate_HiSat2.tabular
XE3-CAP1-WT4


title: ovarian cancer P0400


title: ovarian cancer P0401


title: ovarian cancer P0398


title: peripheral blood, breast cancer-r1 (PN0406)


title: pooled whole embryos 0 ng/L repE

description:
XL_lead_II_nitrate_HiSat2.tabular
XE3-CEP5-WT4


title: Pancreatic Islets from CCR2-DTR+/- 1 month time point

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

department: Medicine

institute: University of Washington

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v5.0.1  and 10X prebuilt mouse reference refdata-gex-mm10-2020-A (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Assembly: mm10

source_name: CCR2-DTR+/- Females on C57b6/J bkg

growth_protocol: Newborn CCR2-DTR+/-mice and wild type littermates were injected with diphteria toxin every 48 hours starting at P2 for a total of 4 injections.

extract_protocol:
Pancreatic islets were freshly isolated by collagenase digestion, Ficoll gradient and hand picking
Three hundred freshly isolated islets, pooled from 2-3 DT-treated CCR2DTR/+ and WT female at each time point, were then processed for library preparation using the 10X Genomics Chromium platform following the manufacturer’s instructions.

treatment_protocol: Injected female mice were weaned at 21 days to regular chow diet, and mantained up to either 1 month or 6 months of age

value: Pancreatic Islets

value: islet cells

tag: genotype

value: DT-treated


title: Pancreatic Islets from CCR2-DTR+/-  6 months time point

description: 10x Genomics


title: ovarian cancer P0395


title: ovarian cancer P0394


title: Pancreatic Islets from WT 1 month time point

description: 10x Genomics

source_name: WT Females on C57b6/J bkg

value: WT CCR2-DTR-/-


title: ovarian cancer P0385


title: Pancreatic Islets from WT 6 months time point

description: 10x Genomics


title: ovarian cancer P0383

value: Endometrioid carcinoma


title: ovarian cancer P0387


title: NIL-WT-72 Drought Rep 2 [WTD2]

city: Cerdanyola del Vallès

first: Veredas

last: Coleto-Alcudia

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Molecular Genetics

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

data_processing:
Raw reads were quality-checked using FastQC tool (v0.11.2), trimmed 13bp at the 3’ end quality-trimmed and filtered at a minimum quality score of 28 (Phred+33, minimum read length of 75bp) using trimmomatic software (v0.38).
Filtered reads were mapped to the Sorghum bicolor v3.0.1 genome (Phytozome) release using HISAT2 2.1.0 aligner and quantified at a gene level using FeatureCount software v1.6.2 on the Sorghum bicolor v3.1.1 annotation file (Phytozome).
Assembly: Sorghum bicolor v3.0.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Sorghum bicolor

source_name: Root

extract_protocol:
Sorghum roots in control conditions and drought stress conditions (30% FC) were detached from mature plants and freeze in liquid nitrogen. RNA was extracted with Maxwell® 16 LEV Plant RNA Kit (Promega) and quality checked using Bioanalyzer.
Stranded cDNA libraries were prepared with TrueSeq Stranded mRNA KIT (Illumina). Paired-end sequencing, with 100-bp reads, was performed in Illumina NextSeq2000 sequencer, with 33M of minimum sequencing depth.

value: Root

value: Drought


title: ovarian cancer P0380


title: ovarian cancer P0378


title: NIL-WT-72 Drought Rep 1 [WTD1]


title: NIL-WT-72 Control Rep 3 [WTC3]

value: Water


title: NIL-WT-72 Control Rep 2 [WTC2]


title: ovarian cancer P0375

value: Other


title: NIL-WT-72 Drought Rep 3 [WTD3]


title: NIL-WT-72 Control Rep 1 [WTC1]


title: ovarian cancer P0371

value: ovarian cancer


title: pooled whole embryos 0 ng/L repC

description:
XL_lead_II_nitrate_HiSat2.tabular
XE3-CCP3-WT4

value: 6 days post fertilization


title: ovarian cancer P0372

value: primary tumor

value: HGSC


title: ovarian cancer P0369


title: pooled whole embryos 0 ng/L repB

description:
XL_lead_II_nitrate_HiSat2.tabular
XE3-CBP2-WT4

value: water control

value: 0 ng/L lead (II) nitrate


title: NIL-bri1-72 Drought Rep 1 [bri1D1]


title: NIL-bri1-72 Drought Rep 2 [bri1D2]


title: ovarian cancer P0361

value: Serous carcinoma


title: NIL-bri1-72 Drought Rep 3 [bri1D3]


title: ovarian cancer P0363


title: NIL-bri1-72 Control Rep 1 [bri1C1]


title: NIL-bri1-72 Control Rep 3 [bri1C3]


title: peripheral blood, breast cancer-r1 (PN0211)

description:
Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.

value: peripheral blood

value: F

value: breast cancer


title: peripheral blood, breast cancer-r1 (PN0161)


title: peripheral blood, breast cancer-r1 (PN0091)


title: peripheral blood, breast cancer-r1 (PN0123)


title: peripheral blood, breast cancer-r1 (PN0149)


title: peripheral blood, breast cancer-r1 (PN0101)


title: peripheral blood, breast cancer-r1 (PN0098)


title: peripheral blood, breast cancer-r1 (PN0377)


title: NIL-bri1-72 Control Rep 2 [bri1C2]


title: peripheral blood, breast cancer-r1 (PN0162)


title: peripheral blood, breast cancer-r1 (PN0105)


title: peripheral blood, breast cancer-r1 (PN0165)


title: peripheral blood, breast cancer-r1 (PN0079)


title: peripheral blood, breast cancer-r1 (PN0203)


title: peripheral blood, breast cancer-r1 (PN0191)


title: peripheral blood, breast cancer-r1 (PN0116)


title: peripheral blood, breast cancer-r1 (PN0142)

value: M


title: peripheral blood, breast cancer-r1 (PN0112)


title: peripheral blood, breast cancer-r1 (PN0111)


title: peripheral blood, breast cancer-r1 (PN0097)


title: peripheral blood, breast cancer-r1 (PN0199)


title: peripheral blood, breast cancer-r1 (PN0185)


title: peripheral blood, breast cancer-r1 (PN0221)


title: peripheral blood, breast cancer-r1 (PN0093)


title: ovarian cancer P0347


title: ovarian cancer P0349


title: ovarian cancer P0332


title: peripheral blood, breast cancer-r1 (PN0075)


title: Sample1-WT-3

city: Zhe jiang

first: Shenghong

last: Ge

address: No. 2318, Yuhangtang Road, Hangzhou, Zhejiang, China

institute: Hangzhou Normal University

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Samples

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
Using a RNeasy Plant Mini Kit to eetracted total RNA (Qiagen, R415102).
Total RNAs were extracted from 8-day-old seedlings under HP or LP conditions using a RNeasy Plant Mini Kit (Qiagen, R415102) according to the instruction manual. 1.3μg of total RNA was used for the construction of sequencing libraries

value: seedlings

value: WT


title: Sample1-WT-1


title: ovarian cancer P0339

source_name: primary tumor


title: Sample1-phod2-3


title: Mite-infested, 15 d, rep 4

city: Madrid

first: Alejandro

last: García

address: Parque Científico y Tecnológico, UPM Campus de Montegancedo, Ctra, M-40, km 38

institute: Universidad Politécnica de Madrid

data_processing:
Raw data (reads) obtained as FASTQ files were processed to remove adapters, poly-N sequences and reads with low quality from raw data using fastp. Quality of the resulting data was assessed by the evaluation of Q20, Q30 and GC content. Paired-end clean reads were mapped against the TAIR10 reference genome of A. thaliana using HISAT2 software. Quality of the mapping was also checked. FeatureCounts was used for the generation of the count data files from sorted BAM files
Differential expression analysis comparing treated against control samples at each time point was performed using DESeq2 R package. P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Differentially expressed genes (DEGs) were considered when p-value adjusted < 0.05 and log2FC > |1| were present. Fold change data can be accessed directly from the publication.
Assembly: TAIR 10 reference genome
Supplementary files format and content: tab delimited tsv file containing raw counts for each Sample

source_name: aerial plant tissue from four plants pooled

growth_protocol: Sterilized seeds were planted in a mixture of peat moss and vermiculite (3:2 v/v) and incubated in the dark for 5 days at 4°C. Plants were then transferred to growth chambers (Aralab D1200PLH) under controlled conditions (23°C ± 1°C, >70% RH and a 16 h/8 h day/night photoperiod).

extract_protocol:
Frozen material was thoroughly grinded on liquid nitrogen and total RNA was extracted by means of the RNeasy plant mini kit (Qiagen), and a DNase treatment (Qiagen) following manufacturer´s instructions.
RNA libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina according to manufacturer’s instructions. Libraries were sequenced on an Illumina platform generating paired-end reads fragments of 150 bp.

treatment_protocol: Three-week-old Arabidopsis plants were infested with twenty T. urticae female adults per plant. Plant aerial material was sampled at specific ontological stages of the plant development, coinciding with 30 min, 24 h, 4 d, 7 d, 12 d and 15 d post-mite infestation. Plant material was introduced in liquid nitrogen and stored at -80ºC until used for RNA extraction.

tag: ecotype

value: Columbia (col-0)

value: Mites

tag: treatment time


title: Sample1-phod2-2


title: ovarian cancer P0337


title: peripheral blood, breast cancer-r1 (PN0110)

source_name: peripheral blood


title: ovarian cancer P0327


title: peripheral blood, breast cancer-r1 (PN0065)


title: peripheral blood, breast cancer-r1 (PN0074)


title: Sample1-WT-2


title: ovarian cancer P0320


title: ovarian cancer P0324


title: ovarian cancer P0356


title: ovarian cancer P0318


title: ovarian cancer P0357


title: Mite-infested, 15 d, rep 3

value: aerial plant tissue from four plants pooled

tag: treatment


title: ovarian cancer P0322


title: Mite-infested, 15 d, rep 2


title: Mite-infested, 12 d, rep 4


title: Mite-infested, 15 d, rep 1


title: ovarian cancer P0326


title: MIA PaCa-2 treated with AMG510

city: Shanghai

first: yafang

last: Wang

address: 393 Middle Huaxia Road

institute: Shanghaitech University

data_processing:
The python toolkit bcbio: (https://bcbio-nextgen.readthedocs.io/en/latest/) was used to implement the RNA-seq analysis pipeline using human hg38 reference genome and hg38 Ensembl transcripts (Ensembl version 79).
FASTQ files were aligned to the human reference genome
Clean reads were separately aligned to the reference genome in orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software and converted into binary alignment map (BAM) files.
The value of the exon model per kilobase base fragment per million gene location fragments (FPKM) for each identified gene was calculated using Stringtie’s default parameters.
Subsequently, DESeq2 was used to identify significantly differentially expressed genes (DEGs) based on the following criteria: multiple variations and corrected p value were >2 and <0.05, respectively.
Assembly: hg38 (GRCh38) & hg38 Ensembl transcripts
Supplementary files format and content: gene.count.matrix.annot.xls
Supplementary files format and content: gene.tpm.matrix.annot.xls

source_name: pancreas

growth_protocol: MIA PaCa-2 cells were cultured in Dulbecco's modified Eagle medium (DMEM) with 10% FBS, 2.5% horse serum and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted from MIA PaCa-2 parental and resistant treated with DMSO or AMG510 for 24 hr using TRIzol® Reagent (Invitrogen)
An RNA-seq transcriptome library was generated with a TruSeqTM RNA sample preparation kit from Illumina (San Diego, CA) using 1 μg of total RNA and sequenced by Majorbio Company (Shanghai, China)

treatment_protocol: MIA PaCa-2 parental and resistant cells were treated with DMSO or 100nM AMG510 for 24h.

value: pancreas

tag: cell line

value: MIA PaCa-2

value: Cancer cell line


title: peripheral blood, breast cancer-r1 (PN0056)

tag: gender


title: peripheral blood, breast cancer-r1 (PN0051)

tag: age


title: peripheral blood, breast cancer-r1 (PN0069)

tag: cancer dx


title: ovarian cancer P0313

city: Kyoto

last: Takamatsu

address: 54 Shogoin Kawahara, Sakyo, Kyoto

institute: Kyoto University Graduate School of Medicine

data_processing:
Raw fastq files were trimmed using Trim-Galore, then mapped to the human reference genome (GRCh38) with the gene annotation of Ensemble GRCh38.v99 using STAR (v2.7.8a). Subsequently, gene expression levels were normalised as TPM or FPKM values using RSEM (v1.3.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample
Supplementary files format and content: tab-delimited text file includes gene TPM values for each sample
Supplementary files format and content: tab-delimited text file includes gene FPKM values for each sample

extract_protocol:
As per manufacturer protocol (SMART-Seq@Stranded Kit User Manual (022819), SMART-Seq@Stranded Kit, SMART-Seq@RNA Unique Dual Index Kit)
The cDNA was synthesized from the extracted total RNA using random primers, and a specific sequence was assigned to the end of the 1st strand cDNA by the SMART (Switching Mechanism At 5' End of RNA Template) method. The specific sequence was then amplified by PCR using primers with indexes having different tag sequences for each sample. The PCR product was purified by the magnetic bead method using AMPure XP (Beckman Coulter), and the ribosomal cDNA was cleaved using scZapR and scR-Probe. Finally, the uncut cDNA was PCR amplified using primers that recognize the adaptor, and a sequencing library was generated.
The quality of the generated sequence library was measured using an Agilent 2100 BioAnalyzer. The libraries were sequenced on Illumina NovaSeq6000. Depths of 180–350 million paired-end 150 bp reads were generated for each sample.

value: ovarian cancer

value: primary tumor


title: peripheral blood, breast cancer-r1 (PN0055)


title: peripheral blood, breast cancer-r1 (PN0054)


title: peripheral blood, breast cancer-r1 (PN0050)


title: Mite-infested, 12 d, rep 3


title: ovarian cancer P0299

value: HGSC


title: ovarian cancer P0300


title: Mite-infested, 12 d, rep 1


title: peripheral blood, breast cancer-r1 (PN0053)


title: Mite-infested, 7 d, rep 3

value: 7 d


title: peripheral blood, breast cancer-r1 (LE0013)


title: Mite-infested, 12 d, rep 2


title: peripheral blood, breast cancer-r1 (PN0046)


title: ovarian cancer P0294

value: Serous carcinoma


title: ovarian cancer P0284


title: peripheral blood, breast cancer-r1 (LE0012)

value: peripheral blood


title: Mite-infested, 7 d, rep 1


title: ovarian cancer P0286

value: Other


title: ovarian cancer P0283


title: Mite-infested, 7 d, rep 2


title: ovarian cancer P0314


title: peripheral blood, breast cancer-r1 (LE0011)

value: F

value: breast cancer


title: Mite-infested, 4 d, rep 4

value: 4 d


title: ovarian cancer P0298


title: ovarian cancer P0279


title: Mite-infested, 7 d, rep 4


title: ovarian cancer P0278


title: Mite-infested, 4 d, rep 2


title: peripheral blood, breast cancer-r1 (LE0008)


title: Mite-infested, 24 h, rep 4


title: ovarian cancer P0264


title: peripheral blood, breast cancer-r1 (LE0002)


title: peripheral blood, breast cancer-r1 (LE0010)


title: peripheral blood, breast cancer-r1 (LE0005)


title: peripheral blood, breast cancer-r1 (LE0007)


title: Mite-infested, 4 d, rep 1


title: peripheral blood, breast cancer-r1 (LE0001)


title: Mite-infested, 4 d, rep 3


title: ovarian cancer P0262


title: ovarian cancer P0256


title: Mite-infested, 24 h, rep 3


title: peripheral blood, breast cancer-r1 (CTL386)


title: ovarian cancer P0252


title: Sample1-phod2-1

value: seedlings


title: ovarian cancer P0230


title: Mite-infested, 24 h, rep 1

value: Columbia (col-0)


title: ovarian cancer P0250


title: Mite-infested, 24 h, rep 2

value: Mites


title: peripheral blood, breast cancer-r1 (CTL253)


title: ovarian cancer P0242


title: Mite-infested, 30 min, rep 1

value: aerial plant tissue from four plants pooled

value: 30 min


title: Mite-infested, 30 min, rep 2


title: Mite-infested, 30 min, rep 4


title: ovarian cancer P0215


title: peripheral blood, breast cancer-r1 (CTL231)


title: ovarian cancer P0220


title: peripheral blood, breast cancer-r1 (CTL0724)


title: peripheral blood, breast cancer-r1 (CTL0912)


title: Control, 15 d, rep 4

value: Control


title: peripheral blood, breast cancer-r1 (LE0003)


title: Mite-infested, 30 min, rep 3


title: ovarian cancer P0211


title: Control, 15 d, rep 3


title: peripheral blood, breast cancer-r1 (BT0007)


title: peripheral blood, breast cancer-r1 (BT0004)


title: peripheral blood, breast cancer-r1 (BT0014)


title: Control, 12 d, rep 4


title: Control, 15 d, rep 2


title: peripheral blood, breast cancer-r1 (BT0005)


title: ovarian cancer P0205


title: peripheral blood, breast cancer-r1 (BT0001)


title: Control, 15 d, rep 1


title: ovarian cancer P0197

value: Endometrioid carcinoma


title: ovarian cancer P0196

value: ovarian cancer


title: peripheral blood, bladder cancer-r1 (PN0446)

value: M

value: bladder cancer


title: Control, 12 d, rep 2


title: ovarian cancer P0194

value: primary tumor

value: HGSC


title: ovarian cancer P0210

value: Serous carcinoma


title: peripheral blood, bladder cancer-r1 (PN0437)

value: peripheral blood


title: peripheral blood, bladder cancer-r1 (PN0431)


title: Control, 12 d, rep 3


title: peripheral blood, bladder cancer-r1 (PN0420)

value: F


title: Control, 12 d, rep 1


title: Control, 7 d, rep 3

value: 7 d


title: ovarian cancer P0184


title: Control, 7 d, rep 4


title: ovarian cancer P0193


title: ovarian cancer P0179


title: ovarian cancer P0183


title: peripheral blood, bladder cancer-r1 (PN0309)


title: Control, 7 d, rep 1


title: peripheral blood, bladder cancer-r1 (PN0321)


title: ovarian cancer P0174


title: peripheral blood, bladder cancer-r1 (PN0293)


title: Control, 7 d, rep 2


title: ovarian cancer P0177


title: peripheral blood, bladder cancer-r1 (PN0288)


title: peripheral blood, bladder cancer-r1 (PN0284)


title: ovarian cancer P0166


title: Control, 4 d, rep 3

value: 4 d


title: ovarian cancer P0189


title: ovarian cancer P0164


title: Control, 4 d, rep 2


title: ovarian cancer P0163


title: Control, 4 d, rep 1


title: Control, 24 h, rep 3


title: ovarian cancer P0159


title: ovarian cancer P0160


title: Control, 24 h, rep 4


title: Control, 24 h, rep 2


title: ovarian cancer P0154


title: Control, 4 d, rep 4


title: Control, 24 h, rep 1


title: ovarian cancer P0151


title: ovarian cancer P0152


title: Control, 30 min, rep 4


title: Control, 30 min, rep 3


title: ovarian cancer P0147


title: ovarian cancer P0144


title: Control, 30 min, rep 2


title: ovarian cancer P0142


title: ovarian cancer P0133


title: ovarian cancer P0127


title: AsV_24h_root_rep1

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

institute: Centro Nacinal de Biotecnologia-CSIC

data_processing:
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Raw reads were aligned to the Arabidopsis Information resource (TAIR10) genome using STAR (v2.5.4) with default parameters
Mapped reads were counted by HTSeq (v0.6.0)
Normalization and differential expression analysis with EdgeR
Assembly: TAIR10
Supplementary files format and content: Text format with two columns: geneID and FPKM per gene

source_name: Roots

growth_protocol: Plants were grown on horizontal plates with Johnson’s medium (1 mM Pi) for 7 days and transferred to J-P plates for 2 days. Then, they were treated with liquid J-P supplemented with 30 µM As(V) for the indicated times. Each sample consisted on 60 seedlings

extract_protocol:
Total RNA was isolated using High Pure RNA Isolation kit (Roche)
Stranded mRNA-seq libraries were generated using the Illumina TruSeq Stranded mRNA Library Prep Kit following the manufacturer’s instructions.
Libraries were  sequenced at single-end 50 bp in the Illumina Hi-Seq 2500 System at the Salk In stitute’s Next Generation Sequencing Core Facility

treatment_protocol: Liquid J-P media supplemented with 30 µM As(V) for the indicated times

value: Roots

value: AsV

tag: time point

value: 24 hours


title: ovarian cancer P0124

first: Shiro


title: AsV_6_root_rep2

value: 6 hours


title: ovarian cancer P0114


title: AsV_6_root_rep1


title: ovarian cancer P0112


title: Control, 30 min, rep 1

value: aerial plant tissue from four plants pooled

value: Columbia (col-0)

value: 30 min


title: AsV_15_root_rep2

value: 1.5 hours


title: ovarian cancer P0111

value: ovarian cancer


title: AsV_15_root_rep1


title: ovarian cancer P0110


title: control_24h_root_rep2

value: mock


title: ovarian cancer P0107

value: primary tumor

value: Endometrioid carcinoma


title: ovarian cancer P0105

value: HGSC

value: Serous carcinoma


title: AsV_24h_root_rep2


title: peripheral blood, bladder cancer-r1 (PN0269)

value: peripheral blood

value: M

value: bladder cancer


title: peripheral blood, bladder cancer-r1 (PN0159)


title: peripheral blood, bladder cancer-r1 (PN0183)


title: peripheral blood, bladder cancer-r1 (PN0271)


title: peripheral blood, bladder cancer-r1 (PN0278)


title: peripheral blood, bladder cancer-r1 (PN0188)

value: F


title: peripheral blood, bladder cancer-r1 (PN0198)


title: peripheral blood, bladder cancer-r1 (PN0255)


title: peripheral blood, bladder cancer-r1 (PN0192)


title: control_6_root_rep2

value: Roots


title: peripheral blood, bladder cancer-r1 (PN0125)


title: peripheral blood, bladder cancer-r1 (IO050p)


title: peripheral blood, bladder cancer-r1 (PN0174)


title: peripheral blood, bladder cancer-r1 (IO052Bp)


title: peripheral blood, bladder cancer-r1 (PN0238)


title: peripheral blood, bladder cancer-r1 (IO049p)


title: ovarian cancer P0102


title: control_6_root_rep1


title: peripheral blood, bladder cancer-r1 (PN0057)


title: peripheral blood, bladder cancer-r1 (PN0144)


title: peripheral blood, bladder cancer-r1 (PN0084)


title: peripheral blood, bladder cancer-r1 (IO048p)


title: peripheral blood, bladder cancer-r1 (IO047)


title: peripheral blood, bladder cancer-r1 (IO051p)


title: peripheral blood, bladder cancer-r1 (IO053Bp)


title: peripheral blood, bladder cancer-r1 (IO045p)


title: ovarian cancer P0085


title: ovarian cancer P0094


title: ovarian cancer P0099


title: ovarian cancer P0080


title: ovarian cancer P0076


title: control_15_root_rep1


title: control_15_root_rep2


title: ovarian cancer P0079


title: ovarian cancer P0074


title: peripheral blood, bladder cancer-r1 (IO046p)


title: control_24h_root_rep1

value: 24 hours


title: peripheral blood, bladder cancer-r1 (PN0073)


title: ovarian cancer P0065


title: peripheral blood, bladder cancer-r1 (IO0142)


title: peripheral blood, bladder cancer-r1 (IO015)


title: CD4 T cells_Ctrl-4

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

description: Gene expression data

hyb_protocol: The labelled products were hybridized using GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix Inc.) for 48 hours at 45°C and 60rpm.

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G (Affymetrix Inc.).

data_processing: The expression signals were acquired using the Affymetrix GeneChip Command Console Software (AGCC). The system was used to generate the numerical values of the probe intensity (Signal). The differentially expressed mRNAs were defined using Partek Genomics Suite software (Partek Incorporated, Missouri, USA) and and RMA normalization.

source_name: healthy control

label_protocol: Biotinylated mRNAs were prepared according to the GeneChip® Human Transcriptome Pico Assay 2.0  protocol (Affymetrix Inc.) using 50ng total RNA.

extract_protocol:
CD4+ T cells were FACS-purified from BM of newly diagnosed AML patients and also control subjects.
Total RNA was extracted using RNeasiy micro kit (QIAGEN AG) according to the manufacturer's instructions.

tag: patient id

tag: disease

value: healthy control

tag: cell type

value: CD4 T cells


title: CD4 T cells_Ctrl-6

description: Gene expression data


title: CD4 T cells_Ctrl-1

description: Gene expression data


title: ovarian cancer P0070

tag: disease state


title: ovarian cancer P0073

tag: tissue


title: peripheral blood, bladder cancer-r1 (IO044p)

last: Dempsey

address: 8751 Park Central Drive, Suite 200

institute: StageZero Life Sciences

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) v1.1.1 using Affymetrix default analysis settings and global scaling (MAS 5.0) as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

extract_protocol: Trizol extraction of total RNA from the pelleted cells was performed according to the manufacturer's instructions.


title: CD4 T cells_Ctrl-3

description: Gene expression data


title: CD4 T cells_Ctrl-7

description: Gene expression data


title: CD4 T cells_Ctrl-2

description: Gene expression data


title: peripheral blood, bladder cancer-r1 (IO0143)


title: peripheral blood, bladder cancer-r1 (IO0135)


title: ovarian cancer P0068

tag: histology cpr


title: CD4 T cells_Ctrl-5

description: Gene expression data


title: peripheral blood, bladder cancer-r1 (IO014)


title: peripheral blood, bladder cancer-r1 (IO0130)


title: peripheral blood, bladder cancer-r1 (IO0136)


title: peripheral blood, bladder cancer-r1 (IO0129)


title: ovarian cancer P0075

tag: histology iti


title: ovarian cancer P0053

tag: assigned cluster


title: ovarian cancer P0063


title: CD4 T cells_AML-30

description: Gene expression data

source_name: acute myeloid leukemia

value: acute myeloid leukemia


title: ovarian cancer P0057


title: ovarian cancer P0055


title: ovarian cancer P0044


title: peripheral blood, bladder cancer-r1 (IO0127)


title: ovarian cancer P0046


title: ovarian cancer P0050


title: peripheral blood, bladder cancer-r1 (IO0132)


title: CD4 T cells_AML-29

description: Gene expression data


title: peripheral blood, bladder cancer-r1 (IO0123)


title: peripheral blood, bladder cancer-r1 (IO0134)


title: peripheral blood, bladder cancer-r1 (IO0122)


title: ovarian cancer P0037


title: CD4 T cells_AML-27

description: Gene expression data


title: CD4 T cells_AML-25

description: Gene expression data


title: CD4 T cells_AML-26

description: Gene expression data


title: CD4 T cells_AML-28

description: Gene expression data


title: CD4 T cells_AML-23

description: Gene expression data


title: CD4 T cells_AML-24

description: Gene expression data


title: ovarian cancer P0033

value: Other


title: CD4 T cells_AML-22

description: Gene expression data


title: peripheral blood, bladder cancer-r1 (IO012)


title: peripheral blood, bladder cancer-r1 (IO0118)


title: peripheral blood, bladder cancer-r1 (IO0116)


title: CD4 T cells_AML-19

description: Gene expression data


title: CD4 T cells_AML-18

description: Gene expression data


title: CD4 T cells_AML-21

description: Gene expression data


title: CD4 T cells_AML-20

description: Gene expression data


title: ovarian cancer P0038


title: ovarian cancer P0042


title: ovarian cancer P0029


title: peripheral blood, bladder cancer-r1 (IO0112)


title: peripheral blood, bladder cancer-r1 (IO0117)


title: ovarian cancer P0030


title: ovarian cancer P0019


title: ovarian cancer P0016


title: ovarian cancer P0013


title: ovarian cancer P0007


title: peripheral blood, bladder cancer-r1 (IO011)


title: ovarian cancer P0006


title: ovarian cancer P0023


title: peripheral blood, bladder cancer-r1 (IO0105)


title: CD4 T cells_AML-13

description: Gene expression data


title: peripheral blood, bladder cancer-r1 (IO0107)


title: CD4 T cells_AML-16

description: Gene expression data


title: peripheral blood, bladder cancer-r1 (IO0103)


title: peripheral blood, bladder cancer-r1 (IO0106)


title: CD4 T cells_AML-15

description: Gene expression data


title: CD4 T cells_AML-11

description: Gene expression data


title: peripheral blood, bladder cancer-r1 (IO0110)


title: hES scATAC

city: New York City

first: Christina

last: Leslie

state: NY

address: 417 East 68th Street

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic single cell

data_processing:
scATAC-seq FASTQ files were aligned to hg38, hg19 or mm10 and counted by Cell Ranger ATAC v1.2.0 with default parameters.
For peak calling of the scATAC-seq data, filtered fragments for cells in each dataset/cell population were aggregated and used as input to the MACS2 peak caller (parameters -f BED, -g 2.7e9, -no-model, -shift -75, -extsize 150, -q 0.05). Peaks were filtered using an IDR cutoff of 0.05. Peaks within 500bp of each other were merged. A peak-by-cell count matrix was then created by ArchR.
Hi-C FASTQ files were aligned to mm10 genomes and reads that are duplicates or invalid ligation products were filtered out using the HiC-Pro pipeline (v3.1.0) with default settings.
Assembly: hg38/mm10
Supplementary files format and content: fragment files were generated by cellranger

molecule: genomic DNA

source_name: hES

extract_protocol:
10x Genomics single cell multiome protocol for nuclei preparation for scATAC samples. Arima HiC+ kit (Arima Genomics, San Diego, CA) was used for Hi-C samples.
Single-cell Multiome libraries were generated with the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit following the manufacturer’s guidelines. The libraries were sequenced on the NovaSeq 6000 platform following the manufacturer’s guidelines. Hi-C library preparation follows Arima protocol modifications for Accel-NGS 2S DNA plus library kit (IDT, Coralville, IA). After end repair and ligation, libraries were quantified using the KAPA library quantification kit (Roche, Indianapolis, IN) and PCR amplified for the number of cycles required to generate >4nM per library. Hi-C libraries were sequenced on an Illumina NovaSeq and raw sequencing data in the Fastq format were obtained.

value: hES


title: peripheral blood, bladder cancer-r1 (IO0104)

city: Richmond

first: Adam


title: ovarian cancer P0005

value: ovarian cancer


title: CD4 T cells_AML-14

description: Gene expression data


title: peripheral blood, bladder cancer-r1 (IO0102)


title: CD4 T cells_AML-12

description: Gene expression data


title: PBMCs, Control, sample6

city: Changzhou

first: Shusu

address: No 185，Juqian Road

department: Department of Nephrology

institute: The Third Affiliated Hospital of Soochow University

description: 10x Genomics

data_processing:
Cell Ranger (version 5.0.0) from 10×Genomics was applied to process raw gene expression matrices from each sample’s sequencing data. The R package Seurat (version 4.0.0) was used to process the unique molecular identifier (UMI) counting matrix, which was then used for quality control, normalization, dimensional reduction, batch effect removal, clustering, and visualization. DecontX, a novel Bayesian approach, was applied to eliminate the contamination in individual cells. To exclude low-quality captures and eliminate the possibility of multiple captures, cells were filtered out according to the following criteria: (1) gene numbers less than 400, (2) gene numbers more than 6000, (3) UMI larger than 50000, (4) percentage of mitochondrial RNA UMIs more than 10%, (5) percentage of ribosome RNA UMIs more than 40%, and (6) percentage of contamination in each cell more than 20%. Subsequently, use the “Normalize Data” function in Seurat to normalize and count the library size. Elimination of batch effects between individuals was achieved by identifying anchors between individuals and passing them to the “IntegrateData” function.
Assembly: GRCH38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: PBMC

extract_protocol:
Patients' blood  was collected on the first day of each hospitalization. Blood samples from the participates were collected into the EDTA anticoagulant tube for later management. Then PBMCs were separated on the day of blood collection, and Ficoll-Paque density gradient centrifugation was used to isolate PBMCs. Cell viability was assessed by microscopic examination using Taipan blue staining. Finally, samples with more than 85% viability can be used to conduct single-cell RNA-seq libraries.
Single-cell RNA-seq libraries were generated using Chromium Single-Cell 3’ Library and Gel Bead Kit v2 (10×Genomics, Pleasanton, CA) according to the manufacturer’s instructions. Then, the libraries were read on  Illumina NovaSeq 6000 system.

tag: condition

value: control

value: PBMC


title: CD4 T cells_AML-8

description: Gene expression data


title: peripheral blood, bladder cancer-r1 (IO010)


title: PBMCs, Control, sample5

description: 10x Genomics


title: CD4 T cells_AML-10

description: Gene expression data


title: peripheral blood, bladder cancer-r1 (IO0100)


title: PBMCs, Control, sample4

description: 10x Genomics


title: peripheral blood, bladder cancer-r1 (IO0101)


title: CD4 T cells_AML-9

description: Gene expression data


title: CD4 T cells_AML-7

description: Gene expression data


title: CD4 T cells_AML-17

description: Gene expression data


title: peripheral blood, bladder cancer-r1 (IO0099)


title: peripheral blood, bladder cancer-r1 (IO0098)


title: CD4 T cells_AML-6

description: Gene expression data


title: PBMCs, Renal irAEs, sample2

description: 10x Genomics

value: renal irAEs


title: PBMCs, Renal irAEs, sample1

description: 10x Genomics


title: peripheral blood, bladder cancer-r1 (IO0097)


title: PBMCs, Renal irAEs, sample3

description: 10x Genomics


title: p53_WT_1

city: New York

first: Zhe

last: Ying

address: 1428 Madison Avenue

department: Department of Cell, Developmental and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

description:
ChIP-seq library
Combined_Peaks_WT.bed.gz

library_source: genomic

data_processing:
Short reads were mapped via BWA; ChIP peaks were called using MACS2
Assembly: MM10
Supplementary files format and content: BED, peaks called from combined reads of 3 replicates.

source_name: basal progenitor cells of epidermis

growth_protocol: 8 weeks old mice

extract_protocol:
Cells were fixed and processed for ChIP using Pierce Magnetic ChIP Kit (Thermo Fisher)
Purified ChIP DNA was prepped into library with NEBNext Ultra II DNA Library Prep Kit (NEB)

treatment_protocol: isolate basal progenitor using FACS (a6 intergrin high, EpCAM+)

value: basal progenitor cells of epidermis

tag: genotype


title: p53_WT_3


title: CD4 T cells_AML-5

description: Gene expression data


title: CD4 T cells_AML-4

description: Gene expression data


title: p53_3KR_3

description:
ChIP-seq library
Combined_Peaks_3KR.bed.gz


title: p53_3KR_2


title: peripheral blood, bladder cancer-r1 (IO0093)


title: peripheral blood, bladder cancer-r1 (IO0095)


title: peripheral blood, bladder cancer-r1 (IO0094)


title: peripheral blood, bladder cancer-r1 (IO0096)


title: TGF_b1

first: laimeng

last: song

address: 五角镇街道佳木斯路2号复旦大学科技园2号楼216

institute: University of Shanghai for Science and Technology

description: replicate biosample 1

data_processing:
Rstudio was used to analyze the gene expression differences between the two groups based on the sequenced data, select miR-with significant expression, and search for targeted mRNA for functional enrichment analysis.
Assembly: mm9
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TGF-beta


title: peripheral blood, bladder cancer-r1 (IO0092)

value: peripheral blood


title: p53_WT_2


title: TGF_b3

address: 五角镇街道佳木斯路2号复旦大学科技园2号楼216

description: replicate biosample 3


title: CD4 T cells_AML-3

description: Gene expression data


title: NC_2

address: 五角镇街道佳木斯路2号复旦大学科技园2号楼216

description: replicate biosample 2


title: NC_3

address: 五角镇街道佳木斯路2号复旦大学科技园2号楼216

description: replicate biosample 3


title: CD4 T cells_AML-1

description: Gene expression data


title: p53_3KR_1


title: NC_1

address: 五角镇街道佳木斯路2号复旦大学科技园2号楼216

description: replicate biosample 1


title: peripheral blood, bladder cancer-r1 (IO0090)

value: M


title: peripheral blood, bladder cancer-r1 (IO0091)

value: bladder cancer


title: peripheral blood, bladder cancer-r1 (IO0089)


title: peripheral blood, bladder cancer-r1 (IO0086)


title: peripheral blood, bladder cancer-r1 (IO0085)


title: peripheral blood, bladder cancer-r1 (IO0088)


title: TGF_b2

address: 五角镇街道佳木斯路2号复旦大学科技园2号楼216

description: replicate biosample 2


title: CXCR4 BBZ+antigen rep2

first: RUIXIN

last: SUN

address: No.25/Ln2200, XieTu Road Shanghai 200032, P.R.China

institute: Shanghai Cancer Institute

description: Sample 8

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data were processed through Seqtk. In this step, the raw data were cleaned by removing reads containing adaptors, contaminants, and low-quality reads. Additionally, the Q30, and GC content were calculated to estimate the quality of clean reads. Next, the clean reads were aligned to the reference genome ( GRCm38) using HISAT2.
The Read Counts of transcripts were calculated by Stringtie（version:1.3.0）. And the expression of mRNA was normalized to FPKM. FPKM refers to the number of fragments per kilobase length from a gene per million fragments mapped. It considers the effect of both sequencing depth and gene length on fragments count.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: CXCR4 CAR-T cells

extract_protocol:
Different T cells were cocultured with antigen-positive tumor cells for four hours and then sorted for RNA-sequencing. Total RNA was extracted from T cells using TRIzolTM Reagent (Invitrogen) and the RNA quality was checked using an Agilent Bioanalyzer 4200 (Agilent technologies). Then, the total RNA was purified with the RNA Clean XP Kit (A63987, Beckman Coulter) and DNase set (79254, QIAGEN).
Sequencing libraries were generated using VAHTS® mRNA-seq V2 Library Prep Kit for Illumina (NR603, Vazyme) according to the manufacturer’s instructions.

value: CXCR4 CAR-T cells

value: mouse T cells

value: CXCR4 CAR

value: antigen-positive stimuli for 4h


title: peripheral blood, bladder cancer-r1 (IO0084)


title: CXCR4 BBZ+antigen rep1

description: Sample 7


title: CXCR4 BBZ rep2

description: Sample 6

value: antigen-negative stimuli for 4h


title: CXCR4 BBZ rep1

description: Sample 5


title: cfh1_mutant_Rep3

city: New Haven

first: Chun Chung

last: Leung

state: CT

address: YSB 424, 260 Whitney Avenue

department: MCDB

institute: Yale University

data_processing:
Adaptor sequence and low-quality sequence were removed with Trimmomatic (v.0.39) with the parameters -phred33 ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:8 TRUE SLIDINGWINDOW:4:20 LEADING:5 TRAILING:5 MINLEN:36
The trimmed sequences were aligned to the TAIR10 genome (version 47) with HISAT2 (v.2.1.0) using the parameters: --rna-strandness FR --no-mixed -I 100 -X 800 -x -p 10
Mapped reads were annotated with stringtie (v.2.1.2) using -v -e -B -G
Assembly: TAIR10 EnsemblPlants release 47
Supplementary files format and content: comma-delimited text files include gene count values for each sample

source_name: Whole seedling

extract_protocol:
Total RNA was extracted using TRIzol reagent (ThermoFisher) according to manufacturer's instructions.
Library was prepared at the Yale Center for Genome Analysis using Illumina's mRNA Sample preparation Kit (Part# 1004814) following manufactuer's protocol with the modification that 5 - 20 nanograms of total RNA was used as starting material

value: Whole seedling

tag: ecotype

value: Columbia 0

value: cfh1 mutant


title: cfh1_mutant_Rep2


title: CD4 T cells_AML-2

description: Gene expression data

value: acute myeloid leukemia

value: CD4 T cells


title: 8E5 BBZ+antigen rep2

description: Sample 4

source_name: mBBZ CAR-T cells

value: mBBZ CAR-T cells

value: mBBZ CAR

tag: treatment


title: peripheral blood, bladder cancer-r1 (IO0087)


title: peripheral blood, bladder cancer-r1 (IO0121)

value: F


title: peripheral blood, bladder cancer-r1 (IO0111)


title: peripheral blood, bladder cancer-r1 (BT0012)


title: peripheral blood, bladder cancer-r1 (IO008)


title: S1393Nr71_PANC1_K2

city: Warszawa

first: AKANKSHA

last: JAISWAR

address: ul. Adolfa Pawińskiego 5

country: Poland

institute: Mossakowski Medical Research Institute

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.19).
Quality check of the reads has been performed by FastQC and adapters were trimmed with trimmomatic toolkit,then trimmed raw reads were aligned to the human reference genome (hg38) using HISAT2.
Read count extraction and normalization were performed using R packages
Differential Gene Expression Analysis were performed with DESeq2 also we calculate exon gene sizes with the GenomicFeatures Package in R and FeaturesCount which are required to calculate FPKM values in DESeq2.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Pancreatic Cancer

growth_protocol: Standard, ATCC-derived protocls for 2D in vitro growth for each cell line.

extract_protocol: RNA libraries were prepared for sequencing using TruSeq Stranded TotalRNA (Illumina) protocols

treatment_protocol: Cell lines indicated in the file names were 48h post knock-out of the oncogenes with CRISPR/Cas9 techniques in biological triplicates (numbers 1-3). Total RNA was exracted from cells and subjected to mRNA sequencing.

value: Pancreatic Cancer

tag: cell line

value: epithelial cells

value: KRAS


title: peripheral blood, bladder cancer-r1 (BT0009)

value: peripheral blood

tag: gender

value: bladder cancer


title: 8E5 BBZ rep2

description: Sample 2

value: mouse T cells


title: S1393Nr70_PANC1_K1


title: S1393Nr69_PANC1_M3

value: hyperactive CMYC


title: S1393Nr68_PANC1_M2


title: 8E5 BBZ rep1

description: Sample 1


title: pif3_mutant_Rep3

value: PIF3 over-expression


title: CFH1_decoy_Rep3

value: CFH1 decoy


title: 8E5 BBZ+antigen rep1

description: Sample 3

value: antigen-positive stimuli for 4h


title: peripheral blood, bladder cancer-r1 (BT0017)

tag: age


title: pif3_mutant_Rep2

value: Whole seedling

value: Columbia 0


title: CFH1_decoy_Rep2


title: S1393Nr67_PANC1_M1


title: S1393Nr72_PANC1_K3


title: pif3_mutant_Rep1


title: S1393Nr66_PANC1_P3

value: mut. TP53


title: cfh1_mutant_Rep1

value: cfh1 mutant


title: CFH1_decoy_Rep1


title: hTERT-HM_S118Emutantcells -Rln_Replicate2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
Rep_S118E_1_h_Rln.sorted_strandSp.Forward.bw
Rep_S118E_1_h_Rln.sorted_strandSp.Reverse.bw

data_processing:
The RNA-seq reads were aligned to the hg38 human reference genome using star aligner.
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig - Browser Tracks showing normalized count for visualization on IGV or UCSC geneome browser

source_name: myometrium

growth_protocol: hTERT-HM cells with Dox-inducible expression of ER⍺(WT,S118E) were generated by lentivirus-mediated transduction.  The lentiviral ER⍺ expression constructs or the empty vector were co-transfected with additional virus constructs (pRSV-Rev, pMDLg, pCMV-VSV-G) into HEK-293 FT cells using Polyjet reagent (SignaGen Laboratories).  The medium containing the transfection reagent was replaced with fresh medium (DMEM) 7 hours post-transfection.  The lentivirus containing supernatant was collected and filtered for transduction.  hTERT-HM cells were infected with recombinant lentivirus at a multiplicity of infection (MOI) or approximately 1.  One day after infection, the cells were allowed to recover in fresh medium for 24 hours and were then subjected to drug selection using G418.  The expression of ER⍺ under Dox induction was confirmed by Western blotting.

extract_protocol:
Total RNA was isolated from myometrial tissue or cultured hTERT-HM-ER⍺ cells using an RNeasy Plus Mini Kit (Qiagen), according to manufacturer’s instructions.  Myometrial tissue was homogenized in RLT buffer with a cooled blade homogenizer (Power Gen25; Fisher).  hTERT-HM-ER⍺ cells were collected and lysed in RLT buffer.  The samples were centrifuged to remove debris and passed through a gDNA eliminator column, followed by RNA binding column.  After multiple washes, total RNA was eluted with RNase-free water.  The eluted RNA was assayed for quality by electrophoresis (Agilent Technologies, Santa Clara, CA, USA).  Only samples with RIN values greater than 8 were included in subsequent analyses.
RNA-seq libraries from myometrial tissue were prepared as follows. Polyadenylated RNA was isolated from total RNA using Oligo(dT)25 Dynabeads (Invitrogen) and reverse transcribed using SuperScript III Reverse Transcriptase (Invitrogen).  Second strand synthesis was performed using DNA polymerase I.  Complementary DNA ends were repaired, tailed with dATP, and ligated with barcode adapters for Illumina sequencing platform.  Ligated libraries were selected for average size 270 bp, PCR amplified for 9 cycles, and sequenced on an Illumina NextSeq 500 in a 75 bp single-end format in the McDermott Center Next Generation Sequencing Core at UT Southwestern Medical Center to a total read count of ~40 M per condition.
RNA-seq experiment was performed in two biological replicates of wild-type and S118E mutant hTERT-HM cells treated with Veh, E2, Rln and E+R at 1h. 0h treatment is taken as the control samples.

value: myometrium

value: hTERT


title: hTERT-HM_S118Emutantcells E+R_Replicate2

description:
Rep_S118E_1_h_E_plus_R.sorted_strandSp.Forward.bw
Rep_S118E_1_h_E_plus_R.sorted_strandSp.Reverse.bw


title: hTERT-HM_S118Emutantcells -Rln_Replicate1


title: hTERT-HM_S118Emutantcells E+R_Replicate1


title: Columbia0_Rep_3

value: wildtype


title: S1393Nr64_PANC1_P1

value: Pancreatic Cancer


title: hTERT-HM_S118Emutantcells -E2_Replicate2

description:
Rep_S118E_1_h_E2.sorted_strandSp.Forward.bw
Rep_S118E_1_h_E2.sorted_strandSp.Reverse.bw


title: S1393Nr63_PANC1_C3

value: epithelial cells

value: non-specific gRNA control


title: Columbia0_Rep_2


title: hTERT-HM_S118Emutantcells -E2_Replicate1


title: Columbia0_Rep_1


title: hTERT-HM_S118Emutantcells -Vehicle_Replicate1

description:
Rep_0h_S118E.sorted_strandSp.Forward.bw
Rep_0h_S118E.sorted_strandSp.Reverse.bw


title: S1393Nr65_PANC1_P2


title: hTERT-HM cells -E+R_Replicate2

description:
Rep_WT_1_h_E_plus_R.sorted_strandSp.Forward.bw
Rep_WT_1_h_E_plus_R.sorted_strandSp.Reverse.bw


title: CON9_1

city: Beijing

first: Shen

last: Wu

state: - 选择州/省 -

address: No.17 hougou hutong, Dongcheng district，Beijing

institute: institute of ophthalmology

data_processing:
barcodes.tsv.gz:list of spatial barcodes
features.tsv.gz:list of gene IDs
matrix.mtx.gz:gene expression count data in matrix market exchange format
Assembly: Rattus_norvegicus.Rnor_6.0
Library strategy: spatial transcriptomics

organism: Rattus norvegicus

source_name: eye

extract_protocol:
fresh frozen tissue were OCT embedded, and 10um frozen sections were cut with cryostat
spatial transcriptome sequencing libraries were prepared with 10x Genomics visium spatial gene expression slides and reagent kit according to manufacturer's construction

value: eye

value: PBS injection


title: S1393Nr61_PANC1_C1


title: CON7_2


title: hTERT-HM cells -E+R_Replicate1


title: S1393Nr62_PANC1_C2


title: CON9_2


title: S1393Nr60_HT29_P3

source_name: Colon Cancer

value: Colon Cancer


title: hTERT-HM cells -Rln_Replicate2

description:
Rep_WT_1_h_Rln.sorted_strandSp.Forward.bw
Rep_WT_1_h_Rln.sorted_strandSp.Reverse.bw


title: CON7_1


title: S1393Nr59_HT29_P2


title: 7dIOP3S_2

value: hydrogel injection


title: S1393Nr57_HT29_C3


title: hTERT-HM cells -Rln_Replicate1


title: 7dIOP3S_1


title: S1393Nr58_HT29_P1


title: S1393Nr56_HT29_C2


title: S1393Nr55_HT29_C1


title: hTERT-HM cells -E2_Replicate1

description:
Rep_WT_1_h_E2.sorted_strandSp.Forward.bw
Rep_WT_1_h_E2.sorted_strandSp.Reverse.bw


title: 7dIOP3_1


title: S1393Nr54_LoVo_K3

value: LoVo

value: KRAS


title: EpOME_11 (t=week9)

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute

description: 16S rRNA

data_processing:
For all sequencing data, the raw reads were subject to quality check using FastQC.
The sequencing data was further trimmed and analyzed by QIIME software qiime2-2020.11.
Sequences were then clustered into operational taxonomic unites (OTUs) using a public dataset (SILVA release 132) with 99% similarity threshold.
QIIME2 output were imported to R to build a phyloseq project.
Differential  abundance analysis in the polysome fraction was determine using AVONA.
Supplementary files format and content: tab-delimited text files include differential  abundance analysis results

organism: mouse gut metagenome

source_name: colon

growth_protocol: C57BL/6 mice were stimulated with AOM/DSS to induce colon tumorigenesis,

extract_protocol:
DNA was extracted from mouse fecal samples using DNeasy PowerSoil Kit (Qiagen) following instructions from the manufacturer with an additional bead-beating step.
The quantity of the extracted DNA was measured using a NanoDrop Spectrophotometer (Thermo Fisher Scientific). The DNA was then subjected to 16S rRNA sequencing analysis that was conducted by Novogene

treatment_protocol: then treated with 12,13-EpOME.

value: colon

value: EpOME (t=week9)


title: hTERT-HM cells -Vehicle_Replicate2

description:
Rep_0h_WT.sorted_strandSp.Forward.bw
Rep_0h_WT.sorted_strandSp.Reverse.bw


title: S1393Nr53_LoVo_K2


title: hTERT-HM cells -Vehicle_Replicate1


title: hTERT-HM cells -E2_Replicate2


title: hTERT-HM_S118Emutantcells -Vehicle_Replicate2