title: SC9_72

description: total RNA


title: SC9_69

status: Public on Nov 17 2021

type: SRA

city: Macau

first: Heng

last: Sun

address: Avendia da Universidade, Taipa

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

description: total RNA

library_source: transcriptomic

data_processing:
sickle was used for data quality control.
trim_galore-v0.4.1 was used for data trimming.
STAR-2.5.3a was used for alignment with default parameter for pair-end sequencing.
subread-1.5.3 was used for generation of read_count.
Genome_build: mm10
Supplementary_files_format_and_content: Gene read_count value for each sample were summarized in text file.

molecule: total RNA

organism: Mus musculus

extract_protocol:
The sorted mammary luminal cells or tumor cells re-suspended in FACS buffer (300-500 cells/µL) were mixed (3:2 ratio) with C1 Cell Suspension Reagent (Fluidigm) before loading onto a  10 to 17-μm-diameter C1 Integrated Fluidic Circuit (IFC; Fluidigm). Each capture site was carefully examined and recorded under a ZEISS microscope in bright field channel for cell doublets. Cell lysing, reverse transcription and cDNA amplification were performed on the C1 Single-Cell Auto Prep IFC, as specified by the manufacturer (protocol 100-7168 E1). The SMARTer Ultra Low RNA Kit (Clontech) was used for cDNA synthesis from the single cells.
Illumina NGS library was constructed with Nextera XT DNA Sample Prep kit (Illumina), according to the manufacturer’s recommendations (protocol 100-7168 E1).

treatment_protocol: Three-to-four month-old female virgin or pregnant at day 12.5 mice were sacrificed to isolate the fourth pair of mammary glands for single-cell preparation as previously described. In brief, the mammary glands were minced, washed in PBS and digested in DMEM/F12 containing 300 U/ml collagenase Ⅲ (S4M7602S, Worthington, Lakewood, NJ), 100 U/ml hyaluronidase (H3506; Sigma-Aldrich), 5% FBS (Gibco), 5 µg/ml insulin (350-020; Biosource, Rockville, MD), 10 ng/ml EGF (13247-051, Invitrogen), and 500 ng/ml hydrocortisone (H0888; Sigma-Aldrich) for about 1 hour at 37℃, 5% CO2. The resultant organoid suspension was sequentially re-suspended in DMEM/F12 supplemented with 5 mg/ml dispase II (825-001; Roche Diagnostics, Indianapolis, IN) and 0.1 mg/ml DNase I (58C10349; Worthington) for 5 min at 37℃, and then digested with 0.25% trypsin-EDTA for 1–2 min, and treated with RBC lysis buffer (00433-57; eBioscience, San Diego, CA) for 3 min to remove the red blood cells before filtration through a 40-µm cell strainer (352340, BD Falcon) to obtain single-cell suspension. Enrichment of Lin- epithelial cells was achieved through selective depletion of hematopoietic and endothelial cells by using the EasySeq mouse epithelial cell enrichment kit according to the manufacturer (19758; Stemcell). When the mammary tumors grew to around 1 cm in diameter, they were removed from the Brca1-defeicient mice for single-cell preparation as per the same method. The enriched Lin- mouse mammary epithelial cells and tumor cells were stained at a concentration of 1x106 cells per 100 μl of FACS buffer (HBSS with 0.5% BSA and 2 mM EDTA). Antibodies against mouse CD24 (anti CD24-PE-Cy™7, 560536, BD), and CD29 (anti CD29-APC, 102216, Biolegend) were used to stain the cells. DAPI (1 µg/ml) was also used as an indicator for cell viability. Antibody incubations were performed at 4℃ for 30 min. Then the cells were washed with PBS for twice before sorting by using FACSAria III Cell Sorter (Becton Dickinson). DAPI-CD24HiCD29LomGFP+ mammary luminal cells and CD24+ tumor cells were sorted out for following single cell RNA sequencing.

tag: strain

value: C57BL/6 and 129/Sv mixed

tag: tissue

value: Mammary luminal

tag: Sex

value: female


title: SC9_71

description: total RNA


title: SC9_73

description: total RNA


title: SC9_66

description: total RNA


title: SC9_68

description: total RNA


title: SC9_67

description: total RNA


title: SC9_65

description: total RNA


title: SC9_61

description: total RNA


title: SC9_60

description: total RNA


title: SC9_59

description: total RNA


title: SC9_57

description: total RNA


title: SC9_50

description: total RNA


title: SC9_52

description: total RNA


title: SC9_58

description: total RNA


title: SC9_81

description: total RNA


title: SC9_51

description: total RNA


title: SC9_45

description: total RNA


title: SC9_47

description: total RNA


title: SC9_74

description: total RNA


title: SC9_43

description: total RNA


title: SC9_56

description: total RNA


title: SC9_36

description: total RNA


title: SC9_44

description: total RNA


title: SC9_53

description: total RNA


title: SC9_54

description: total RNA


title: SC9_48

description: total RNA


title: SC9_55

description: total RNA


title: SC9_42

description: total RNA


title: SC9_33

description: total RNA


title: SC9_30

description: total RNA


title: SC9_32

description: total RNA


title: SC9_40

description: total RNA


title: SC9_26

description: total RNA


title: SC9_25

description: total RNA


title: SC9_31

description: total RNA


title: SC9_34

description: total RNA


title: SC9_27

description: total RNA


title: SC9_28

description: total RNA


title: SC9_24

description: total RNA


title: SC9_29

description: total RNA


title: SC9_21

description: total RNA


title: SC9_22

description: total RNA


title: SC9_17

description: total RNA


title: SC9_16

description: total RNA


title: SC9_15

description: total RNA


title: SC9_13

description: total RNA


title: SC9_08

description: total RNA


title: SC9_04

description: total RNA


title: SC9_06

description: total RNA


title: SC9_09

description: total RNA


title: SC9_05

description: total RNA


title: SC9_01

description: total RNA


title: SC9_03

description: total RNA


title: SC7_95

description: total RNA


title: SC7_94

description: total RNA


title: Female environmental enrichment (EE) cortical neurons - nuclear RNAseq - rep6

city: Cambridge

first: Ravikiran

last: Raju

state: MA

address: 15A Maple Ave

department: Picower Institute

country: USA

institute: MIT

description:
nuclear RNA
nuclear RNAseq (introns and exons)
180821TsaA_Female_EEvsSH_RNAseq_CountMatrix.txt
180821TsaA_D18-8314

data_processing:
Illumina Casava1.7 software used for basecalling.
RNAseq processing from raw fastq: Star --runMode alignReads --outSAMtype BAM SortedByCoordinate --clip3pNbases 0 --clip5pNbases 3 (Star 2.5.4) --> DESeq2 dds[ rowSums(counts(dds)) > 1, ] (DESeq2 1.16.1) --> fdrtool statistic = "normal" method = "BH" (fdrtool 1.2.15)
ATACseq pocessing from raw fastq: samtools to remove duplicates and filter out mitochondrial reads (samtools 1.3.1) --> manual shifting of reads (bedtools bamtobed -bedpe -i ${out}.nsorted.rmdupNOS.noMt.bam 2>/dev/null | awk 'BEGIN {OFS="\t"}; {if($9 =="+") print $1,$2+4,$3+4,$4,$5-5,$6-5,$7,$8,$9,$10 ; else print $1,$2-5,$3-5,$4,$5+4,$6+4,$7,$8,$9,$10  }' > ${out}.shifted.rmdupNOS.noMt.bed) --> macs2 callpeak -f BAMPE -g mm -q 0.05 --nomodel --nolambda --keep-dup all (macs2 2.1.1) --> DiffBind for differenal peak analysis dba.analyze(contrastData, method=DBA_EDGER_CLASSIC) (DiffBind 3.2.2)
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq processed files are counts per gene. ATAC-seq processed files are counts per peaks, with peak universe defined as peaks present in at least two samples. Of note for both experiments, males and females were processed and analyzed seprately.

source_name: NeuN(+) Cortical neurons

growth_protocol: Wildtype Swiss Webster mice were housed in normal condition until weaning at Postnatal Day 25

extract_protocol:
Animals were euthanized by exposure to isoflurane, and frontal cortices were dissected. Mortar and pestle were used to break up tissue in Phosphate Buffered Saline (ph 7.4, PBS) with cOmplete protease inhibitor cocktail (Roche) and RNaseOUT Recombinant Ribonuclease Inhibitor (ThermoFisher). Protease and ribonuclease inhibitors were present in all downstream steps. Tissue was then fixed using 1% paraformaldehyde (Electron Microscopy Sciences) in PBS for 20 minutes. Fixation was quenched with 1M Tris base (ph 8.0) to a final concentration of 250 mM of Tris. Tissue was washed twice in NF1 buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 5 mM MgCl2, 0.1M sucrose, 0.5% Trixon X-100) to remove residual PFA and lyse cells for nuclear extraction. After washing, pellets were then resuspended in NF1 buffer for 30 rounds of dounce homogenization (Wheaton). After douncing, nuclear pellets were obtained by filtering sample through 70 micron mesh, and one more round of NF1 washing. Nuclear pellets were then resuspended in PBS with 1% Bovine Serum Albumin (BSA, ThermoFisher), and stained with Anti-NeuN antibody conjugated to Alexa Fluor 488 (clone A60, EMD Millipore) at a dilution of 1:2000 for 30 minutes. DAPI stain was also added at a concentration of 1:10,000 to aid in identification of nuclei when cell sorting.  After washing, nuclear suspension was subjected to fluorescence-activated cell sorting (FACS) on a BD FACS Aria II with 70 micron nozzle set to 70 PSI. Nuclei were identified via DAPI and neuronal nuclei were selected using the 488 channel. Sorted cells were immediately used for RNAseq or ATACseq library generation.
For RNAseq, Because tissues had been fixed prior to nuclear isolation, RNA was extracted from nuclei using the RecoverAll Total Nucleic Acid Isolation Kit for FFPE Tissue (ThermoFisher). Nuclear RNA was run on an Agilent 2100 BioAnalyzer for quality control (sample statsitics provided in Supplementary Table 10). RNA libraries were generated using the SMARTer Stranded Total RNA-seq for mammalian samples (Takara). Of note, libraries were amplified using random hexamer primers so not enriched for mature transcripts. For ATACseq, ATACseq libraries were generated from sorted neuronal nuclei using the Nextera DNA Library Preparation Kit (Illumina), as described previously{Buenrostro:2013bc}. Briefly, nuclear pellet was resuspended in transposase reaction mix buffer, and transposase. Transposition reaction was performed for 30 minutes at 37 ℃. As described previously{Chen:2016kb}, ATACseq libraries can be generated from fixed nuclei. After transposase reaction, defixation buffer (50 mM Tris-HCl ph8.0, 1 mM EDTA, 0.2 M NaCl, 1% SDS, 5 ng/mL proteinase K) was added to the mixture, which was then incubated at 65 ℃ overnight with agitation at 1000 rpm on a benchtop shaker/heater block. The next morning, the reaction was purified using a Qiagen MinElute kit. Following purification, library fragments were amplified using Nextera PCR primers with cycling and cycling number determination as described in the original ATACseq paper cited above.

treatment_protocol: Mice were then placed in either Environmental Enrichment (EE) or Standard Housing (SH) conditions. Standard cages consisted of a 7 1⁄2” x 11 1⁄2” x 5” plastic chamber containing a layer of wood chip bedding and a single pulped cotton fiber nestlet. Enrichment cages were larger (10 1⁄2” x 19” x 8”) and contained a layer of wood chip bedding, 2-3 nestlets, Crink-l’Nest, a running wheel, a plastic tube, and three additional rodent toys replaced every 3-4 days. Food and water were provided ad libitum.

value: Female

tag: treatment

value: Environmental Enrichment

tag: age

value: 2 months


title: SC7_93

description: total RNA


title: SC9_23

description: total RNA


title: Female environmental enrichment (EE) cortical neurons - nuclear RNAseq - rep4

description:
nuclear RNA
nuclear RNAseq (introns and exons)
180821TsaA_Female_EEvsSH_RNAseq_CountMatrix.txt
180821TsaA_D18-8312


title: Female environmental enrichment (EE) cortical neurons - nuclear RNAseq - rep3

description:
nuclear RNA
nuclear RNAseq (introns and exons)
180821TsaA_Female_EEvsSH_RNAseq_CountMatrix.txt
180821TsaA_D18-8311


title: Female environmental enrichment (EE) cortical neurons - nuclear RNAseq - rep5

description:
nuclear RNA
nuclear RNAseq (introns and exons)
180821TsaA_Female_EEvsSH_RNAseq_CountMatrix.txt
180821TsaA_D18-8313


title: SC9_19

description: total RNA


title: Female environmental enrichment (EE) cortical neurons - nuclear RNAseq - rep2

description:
nuclear RNA
nuclear RNAseq (introns and exons)
180821TsaA_Female_EEvsSH_RNAseq_CountMatrix.txt
180821TsaA_D18-8310


title: SC7_90

description: total RNA


title: SC9_14

description: total RNA


title: Female standard housed (SH) cortical neurons - nuclear RNAseq - rep6

description:
nuclear RNA
nuclear RNAseq (introns and exons)
180821TsaA_Female_EEvsSH_RNAseq_CountMatrix.txt
180821TsaA_D18-8320

value: Standard Housing


title: SC9_07

description: total RNA


title: SC7_88

description: total RNA


title: Female standard housed (SH) cortical neurons - nuclear RNAseq - rep5

description:
nuclear RNA
nuclear RNAseq (introns and exons)
180821TsaA_Female_EEvsSH_RNAseq_CountMatrix.txt
180821TsaA_D18-8319


title: SC9_11

description: total RNA


title: SC7_89

description: total RNA


title: SC7_87

description: total RNA


title: Female standard housed (SH) cortical neurons - nuclear RNAseq - rep2

description:
nuclear RNA
nuclear RNAseq (introns and exons)
180821TsaA_Female_EEvsSH_RNAseq_CountMatrix.txt
180821TsaA_D18-8316


title: Female standard housed (SH) cortical neurons - nuclear RNAseq - rep4

description:
nuclear RNA
nuclear RNAseq (introns and exons)
180821TsaA_Female_EEvsSH_RNAseq_CountMatrix.txt
180821TsaA_D18-8318


title: SC7_85

description: total RNA


title: SC7_84

description: total RNA


title: Female standard housed (SH) cortical neurons - nuclear RNAseq - rep3

description:
nuclear RNA
nuclear RNAseq (introns and exons)
180821TsaA_Female_EEvsSH_RNAseq_CountMatrix.txt
180821TsaA_D18-8317


title: SC7_92

description: total RNA


title: Female standard housed (SH) cortical neurons - nuclear RNAseq - rep1

description:
nuclear RNA
nuclear RNAseq (introns and exons)
180821TsaA_Female_EEvsSH_RNAseq_CountMatrix.txt
180821TsaA_D18-8315


title: Male environmental enrichment (EE) cortical neurons - nuclear RNAseq - rep5

description:
nuclear RNA
nuclear RNAseq (introns and exons)
171107Tsa_Male_EEvsSH_RNAseq_countmatrix.txt
171107Tsa_D17-202005

value: Male


title: SC7_81

description: total RNA


title: Male environmental enrichment (EE) cortical neurons - nuclear RNAseq - rep4

description:
nuclear RNA
nuclear RNAseq (introns and exons)
171107Tsa_Male_EEvsSH_RNAseq_countmatrix.txt
171107Tsa_D17-202004


title: Female environmental enrichment (EE) cortical neurons - nuclear RNAseq - rep1

description:
nuclear RNA
nuclear RNAseq (introns and exons)
180821TsaA_Female_EEvsSH_RNAseq_CountMatrix.txt
180821TsaA_D18-8309


title: Male environmental enrichment (EE) cortical neurons - nuclear RNAseq - rep3

description:
nuclear RNA
nuclear RNAseq (introns and exons)
171107Tsa_Male_EEvsSH_RNAseq_countmatrix.txt
171107Tsa_D17-202003


title: SC7_80

description: total RNA


title: Male environmental enrichment (EE) cortical neurons - nuclear RNAseq - rep2

description:
nuclear RNA
nuclear RNAseq (introns and exons)
171107Tsa_Male_EEvsSH_RNAseq_countmatrix.txt
171107Tsa_D17-202002


title: SC7_78

description: total RNA


title: SC7_76

description: total RNA


title: Male environmental enrichment (EE) cortical neurons - nuclear RNAseq - rep1

description:
nuclear RNA
nuclear RNAseq (introns and exons)
171107Tsa_Male_EEvsSH_RNAseq_countmatrix.txt
171107Tsa_D17-202001


title: Male standard housed (SH) cortical neurons - nuclear RNAseq - rep5

description:
nuclear RNA
nuclear RNAseq (introns and exons)
171107Tsa_Male_EEvsSH_RNAseq_countmatrix.txt
171107Tsa_D17-202011


title: Male standard housed (SH) cortical neurons - nuclear RNAseq - rep6

description:
nuclear RNA
nuclear RNAseq (introns and exons)
171107Tsa_Male_EEvsSH_RNAseq_countmatrix.txt
171107Tsa_D17-202012


title: Male standard housed (SH) cortical neurons - nuclear RNAseq - rep4

description:
nuclear RNA
nuclear RNAseq (introns and exons)
171107Tsa_Male_EEvsSH_RNAseq_countmatrix.txt
171107Tsa_D17-202010


title: Male environmental enrichment (EE) cortical neurons - nuclear RNAseq - rep6

description:
nuclear RNA
nuclear RNAseq (introns and exons)
171107Tsa_Male_EEvsSH_RNAseq_countmatrix.txt
171107Tsa_D17-202006


title: SC7_86

description: total RNA


title: SC7_73

description: total RNA


title: Male standard housed (SH) cortical neurons - nuclear RNAseq - rep3

description:
nuclear RNA
nuclear RNAseq (introns and exons)
171107Tsa_Male_EEvsSH_RNAseq_countmatrix.txt
171107Tsa_D17-202009


title: SC7_91

description: total RNA


title: SC7_83

description: total RNA


title: SC7_82

description: total RNA


title: Male standard housed (SH) cortical neurons - nuclear RNAseq - rep2

description:
nuclear RNA
nuclear RNAseq (introns and exons)
171107Tsa_Male_EEvsSH_RNAseq_countmatrix.txt
171107Tsa_D17-202008


title: SC7_77

description: total RNA


title: Male standard housed (SH) cortical neurons - nuclear RNAseq - rep1

description:
nuclear RNA
nuclear RNAseq (introns and exons)
171107Tsa_Male_EEvsSH_RNAseq_countmatrix.txt
171107Tsa_D17-202007


title: SC7_71

description: total RNA


title: Tet1 WT mice brain 5hmC sample 1 input

city: Houston

first: Ziyi

last: Li

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

description:
5hmC sequencing
Tet1_5hmC_counts.csv

library_source: genomic

data_processing: The fastq files from each sample were aligned to mm9 using Bowtie2 v2.2.6. The peaks of 5hmC were called using MACS v2.

molecule: genomic DNA

source_name: Tet1 WT brain

extract_protocol: After purification, biotin-5-N3-gmC-containing DNA was used for library construction following the Illumina protocol for preparing samples for ChIP sequencing of DNA.

value: Tet1 WT


title: SC7_79

description: total RNA


title: SC7_72

description: total RNA


title: SC7_70

description: total RNA


title: SC7_69

description: total RNA


title: SC7_68

description: total RNA


title: Tet1 WT mice brain 5hmC sample 2

description:
5hmC sequencing
Tet1_5hmC_counts.csv


title: SC7_67

description: total RNA


title: Tet1 KO mice brain 5hmC sample 1 input

description:
5hmC sequencing
Tet1_5hmC_counts.csv

source_name: Tet1 KO brain

value: Tet1 KO


title: Tet1 KO mice brain 5hmC sample 2

description:
5hmC sequencing
Tet1_5hmC_counts.csv


title: SC7_66

description: total RNA


title: Tet1 WT mice brain 5hmC sample 1

description:
5hmC sequencing
Tet1_5hmC_counts.csv


title: SC7_75

description: total RNA


title: SC7_65

description: total RNA


title: SC7_64

description: total RNA


title: Neural progenitor cells - Activated input DNA

city: Providence

first: Ashley

middle: E

last: Webb

state: RI

address: 70 Ship St.

department: Molecular Biology, Cell Biology, and Biochemistry

institute: Brown University

data_processing:
Paired-end ATAC and ChIP-seq reads were trimmed with TrimGalore! (Version 0.4.0, Babraham Bioinformatics).
Reads were aligned to the mm10 genome assembly using Bowtie2 (Version 2.2.5).
PCR duplicate reads were marked with Picard (Version 1.88), and reads were filtered with SAMtools (Version 1.3.1). Reactivated ATAC-seq reads were downsampled to 40 million reads.
Peaks were called using MACS (Version 2.1.1).
ENCODE blacklist regions were filtered from peak files.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated using Homer "makeUCSCfile" function; narrowPeak (ATAC-seq) and broadPeak (ChIP-seq) files are formatted with default settings described by ENCODE.

source_name: Neural stem/progenitor cells

growth_protocol: Primary mouse neural stem/progenitor cells were isolated from postnatal day 5 brains. Cells were cultured in high growth factor signaling conditions: Neurobasal A (ThermoFisher), 2% B27 (ThermoFisher), and 20 ng/ml each of FGF2 (PeproTech) and EGF (PeproTech).

extract_protocol: For ATAC-seq, NSPCs were subjected to tagmentation reactions with 2.5 ul Tn5 Transposase (Illumina) for 30 min. For ChIP-seq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.

treatment_protocol: To induce quiescence, 50,000 cells were plated in poly-D-lysine coated (Sigma) plates with high growth factor signaling medium, and after 24 hours, fresh Neurobasal A medium with 2% B27, 20 ng/ml of FGF2, and 25 ng/ml of recombinant mouse BMP4 (R&D Systems) was added without EGF. Cells were kept in quiescent medium for 4 days. For reactivated condition, quiescent medium was removed, then switched to high growth factor signaling conditions for 9-12 days.

tag: cell type

value: Primary neural/progenitor cells

value: Proliferative condition


title: Tet1 KO mice brain 5hmC sample 1

description:
5hmC sequencing
Tet1_5hmC_counts.csv


title: SC7_63

description: total RNA


title: Neural progenitor cells - Quiescent input DNA


title: SC7_62

description: total RNA


title: SC7_61

description: total RNA


title: SC7_60

description: total RNA


title: Neural progenitor cells - Activated H3K4me3 ChIP-seq

tag: chip antibody

value: H3K4me3 antibody (Abcam, ab8580)


title: Neural progenitor cells - Reactivated ATAC-seq rep2

value: BMP4-treated, followed by proliferative condition


title: SC7_59

description: total RNA


title: SC7_58

description: total RNA


title: Neural progenitor cells - Reactivated ATAC-seq rep1


title: Neural progenitor cells - Activated ATAC-seq rep2


title: SC7_57

description: total RNA


title: Neural progenitor cells - Activated ATAC-seq rep1


title: Neural progenitor cells - Quiescent ATAC-seq rep2


title: SC7_56

description: total RNA


title: Neural progenitor cells - Quiescent ATAC-seq rep1


title: SC7_51

description: total RNA


title: SC7_53

description: total RNA


title: SC7_52

description: total RNA


title: SC7_54

description: total RNA


title: SC7_48

description: total RNA


title: SC7_47

description: total RNA


title: SC7_50

description: total RNA


title: SC7_49

description: total RNA


title: SC7_43

description: total RNA


title: SC7_44

description: total RNA


title: SC7_55

description: total RNA


title: SC7_42

description: total RNA


title: SC7_39

description: total RNA


title: SC7_37

description: total RNA


title: SC7_46

description: total RNA


title: SC7_35

description: total RNA


title: SC7_36

description: total RNA


title: SC7_34

description: total RNA


title: SC7_41

description: total RNA


title: Neural progenitor cells - Quiescent H3K4me3 ChIP-seq


title: SC7_27

description: total RNA


title: SC7_38

description: total RNA


title: SC7_45

description: total RNA


title: SC7_25

description: total RNA


title: SC7_40

description: total RNA


title: SC7_33

description: total RNA


title: SC7_31

description: total RNA


title: SC7_32

description: total RNA


title: SC7_30

description: total RNA


title: TKO_Sox9_1

city: Boston

first: Yuchen

last: Liu

state: Massachusetts

address: 188 Longwood Avenue, REB 514B

institute: Harvard school of dental medicine

description:
Liver
Ion GeneStudio S5 Plus
processed data file: processed_data_RPM.txt

data_processing:
Thermo Fisher Torrent Suite V5.10 used for basecalling.
Thermo Fisher Torrent Suite V5.10 used for alignment.
Thermo Fisher ampliSeqRNA V5.10 in Torrent Suite V5.10 used for reads counting.
sva 3.38.0 package for batch effect removal and data normalization.
Genome_build: AmpliSeq_Mouse_Transcriptome_v1.fasta
Supplementary_files_format_and_content: processed_data_log2CPM.txt: Tab-delimited text file includes normalized log2CPM values for each Sample.

source_name: hepatocytes

extract_protocol:
RNA was isolated from FACS sorted Hepatocytes using RNAqueousTM Micro Total RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
cDNA was synthesized using SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific). Libraries were prepared using Ion AmpliSeq Transcriptome Mouse Gene Expression Panel, Chef-Ready Kit on Ion Chef (Thermo Fisher Scientific) according to the manufacturer’s instructions.

treatment_protocol: AAV was injected into the mice at 3 weeks old by retro orbital injection. Hepatocytes were isolated, stained by a fluorescent antibody for the negative selection biliary marker Epcam and hematopoietic lineage marker CD45, GFP+ or TdTomato+; Lin- Hepatocytes were sorted by using BD FACS Aria II with 100μm nozzle.

value: Hepatocytes

tag: genotype

value: Mst1 fl/fl; Mst2 fl/fl;Sox9 fl/fl; ROSA26-lsl-TdTomato


title: TKO_Sox9_2


title: DKO_Sox9_het_2

value: Mst1 fl/fl; Mst2 fl/fl;Sox9 fl/+; ROSA26-lsl-TdTomato


title: SC7_29

description: total RNA

value: C57BL/6 and 129/Sv mixed


title: SC7_28

description: total RNA

value: Mammary luminal


title: SC7_18

description: total RNA

value: female


title: SC7_19

description: total RNA


title: SC7_23

description: total RNA


title: SC7_24

description: total RNA


title: SC7_22

description: total RNA


title: SC7_15

description: total RNA


title: SC7_21

description: total RNA


title: SC7_26

description: total RNA


title: Sox9_cko_1

value: Sox9 fl/fl


title: SC7_20

description: total RNA


title: SC7_17

description: total RNA


title: Mst1_2_fl_GFP_2

value: Mst1 fl/fl; Mst2 fl/fl; ROSA26-lsl-TdTomato


title: Mst1_2_fl_GFP_1


title: SC7_16

description: total RNA


title: Sox9_cko_2


title: SC7_07

description: total RNA


title: SC7_05

description: total RNA


title: SC7_06

description: total RNA


title: 28LP7

city: campinas

first: Marina

middle: Silva

last: Folguieri

state: são paulo

address: rua cinco de junho, 350

department: Fisiopatologia Médica

country: Brazil

institute: Universidade Estadual de Campinas, UNICAMP

data_processing:
Illumina Casava1.7 software used for basecalling.
All sequenced reads were aligned with the StarAligner 2.6 program (https://github.com/alexdobin/STAR, RRID:SCR_004463) with the Rattus norvegicus genome 3.1 (Rnor6 Ensembl release 6.0 - https://www.ensembl.org/Rattus_norvegicus/Info/Index).
DESeq2 package version 3.12(http://bioconductor.org/packages/release/bioc/html/DESeq2.html, RRID:SCR_015687) was used to calculate all differentially expressed genes(DEGs) between subfields and carry statistical analysis.
Genome_build: rnor6
Supplementary_files_format_and_content: comma-delimited text files include counts values for each pairwise comparison
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: left heart

extract_protocol:
Total RNA was extracted from left heart using the TRIzol reagent. Illumina TruSeq Stranded mRNA kit  was used with 50 ul of total RNA for the construction of sequencing libraries.
mRNA libraries were prepared for sequencing using standard IIllumina TruSeq Stranded mRNA protocols.

value: Wistar Rat

value: heart

value: 62-week old animals

tag: condition

value: gestational protein restricion (LP)


title: SC7_03

description: total RNA


title: 24NP1

value: normal protein (NP)


title: Sox9_het_1

value: Sox9 fl/+


title: SC7_14

description: total RNA


title: SC7_13

description: total RNA


title: SC7_12

description: total RNA


title: WT_GFP_2

value: Wild type


title: SC7_11

description: total RNA


title: SC6_96

description: total RNA

source_name: pBrL


title: 16LP6


title: SC7_10

description: total RNA


title: WT_GFP_1


title: DKO_Sox9_het_1


title: SC7_08

description: total RNA


title: 25NP5


title: 27NP1


title: 22LP5


title: SC6_93

description: total RNA


title: SC6_92

description: total RNA


title: PA14_FDH1_1h_Rep_1

city: Braunschweig

first: Alejandro

last: Arce Rodriguez

address: Inhoffenstraße 7

country: Germany

institute: Helmholtz-HZI

description:
PA14_FDH1_2h - PA14_SEVAF_2h.csv
rpg_table.csv (PA14_SEVAF_2h_R1)

data_processing:
Sequencing reads were mapped P. aeruginosa PA14 genome (NC_008463.1) with bowtie2
Reads per gene were extracted using featureCounts
Differential gene expression analysis between the strains harboring the empty vector and the bacteria expressing either of the enzymes was computed from the reads per gene edgeR
Genome_build: NC_008463.1
Supplementary_files_format_and_content: csv files showing the differential gene expression between overexpressing strain and its respective empty vector control (log2FC)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every sample

organism: Pseudomonas aeruginosa

source_name: P.aeruginosa culture

growth_protocol: Cells were grown in LB medium at 37°C until mid-exponential phase (OD600 = 0.4–0.5)

extract_protocol:
Samples for RNA isolation were collected in RNA protect after 1 h (in the case of the noxSp strain and its EV control) and 2 h (for FDH1Cb strain and its control) post-induction. The total RNA was isolated with a modified RNeasy mini kit protocol
cDNA libraries were generated with the ScriptSeq v2 kit (Illumina).

treatment_protocol: The cultures were amended with 1 mM IPTG and incubated at 37°C in an orbital shaker

value: Strain PA14

tag: plasmid

value: 1mM IPTG + 10 mM sodium formate

tag: induction time

value: 2 hours


title: SC6_91

description: total RNA


title: Sox9_het_2

value: Hepatocytes


title: 21NP2


title: 17LP1


title: SC7_04

description: total RNA


title: 14NP3


title: SC6_94

description: total RNA


title: SC7_09

description: total RNA


title: 04LP1


title: PA14_SEVA_1h_Rep_2

description:
PA14_nox_1h - PA14_SEVA_1h.csv
rpg_table.csv (PA14_FDH1_2h_R2)

value: 1mM IPTG

value: 1 hour


title: SC6_88

description: total RNA

value: C57BL/6 and 129/Sv mixed

value: Mammary luminal


title: PA14_SEVA_1h_Rep_1

description:
PA14_nox_1h - PA14_SEVA_1h.csv
rpg_table.csv (PA14_FDH1_2h_R1)


title: SC6_95

description: total RNA

value: female


title: SC6_85

description: total RNA


title: PA14_FDH1_1h_Rep_2

description:
PA14_FDH1_2h - PA14_SEVAF_2h.csv
rpg_table.csv (PA14_SEVAF_2h_R2)


title: SC6_84

description: total RNA


title: SC6_87

description: total RNA


title: SC6_89

description: total RNA


title: SC6_86

description: total RNA


title: PA14_Nox_1h_Rep_2

description:
PA14_nox_1h - PA14_SEVA_1h.csv
rpg_table.csv (PA14_nox_1h_R2)


title: PA14_SEVAF_2h_Rep_2

description:
PA14_FDH1_2h - PA14_SEVAF_2h.csv
rpg_table.csv (PA14_SEVA_1h_R2)


title: PA14_Nox_1h_Rep_1

description:
PA14_nox_1h - PA14_SEVA_1h.csv
rpg_table.csv (PA14_nox_1h_R1)


title: PA14_SEVAF_2h_Rep_1

description:
PA14_FDH1_2h - PA14_SEVAF_2h.csv
rpg_table.csv (PA14_SEVA_1h_R1)


title: SC6_82

description: total RNA


title: FJ_2M_1-MCP_R2

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

country: Italy

institute: University of Trento

data_processing:
Libraries were clustered on a cBot Cluster using the TrueSeq SR Cluster Kit v3 and sequenced with the Illumina HiSeq2000 using the TrueSeq SBS kit v3.
Genome_build: Reads were aligned to Malus domestica complete CDS sequences downloaded from the NCBI Nucleotide database using STAR 2.5.1a. Counts of unambiguously mapped reads were obtained using htseq-count.
Supplementary_files_format_and_content: excell file with FPKM values for each Sample. Each cultivar is reported in distinct sheet

organism: Malus domestica

source_name: FRUIT CORTEX

extract_protocol:
RNA extraction was performed, for each of the three biological replicates with the Spectrum Plant total RNA kit (Sigma-Aldrich Co., St. Luis, MO, USA). RNA was quantified using a NanoDrop ND-8000 spectrophotometer (Thermo Scientific, Waltham, MA, USA), while its purity and integrity was assessed with a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
For each replicate/sample, 3 mg of RNA was used for the construction of a non-directional Illumina RNA-seq library, using TrySeq RNA sample preparation kits, v2 (Illumina, San Diego, CA, USA). Libraries were quantified using quantitative PCR and quality control was performed with the DNA 1000 series II chip bioanalyzer (Agilent, Santa Clara, CA, USA). Sequencing of libraries was performed with an Illumina HiSeq 1000 Sequencer using TruSeq SBS v3-HS kit (100 cycles) and TruSeq SR Cluster v3-cBot-HS kits (Illumina, San Diego, CA, USA) generating 100-bp reads.

treatment_protocol: 1-MCP is a treatment with 1-methylcyclopropene operated on harvest fruit overnight in a sealed container according to the manufacturer instruction (AgroFresh)

tag: time and treatment

value: 2 months after harvest treated with 1-MCP

value: FRUIT CORTEX

tag: cultivar

value: Fuji


title: FJ_2M_CTRL_R2

value: 2 months after harvest control


title: FJ_2M_CTRL_R3


title: FJ_2M_CTRL_R1


title: SC6_83

description: total RNA


title: FJ_21DAH_CTRL_R2

value: 21 days after harvest control


title: SC6_79

description: total RNA


title: FJ_2M_1-MCP_R3


title: SC6_80

description: total RNA


title: FJ_2M_1-MCP_R1


title: SC6_76

description: total RNA


title: SC6_77

description: total RNA


title: FJ_21DAH_1-MCP_R3

value: 21 days after harvest treated with 1-MCP


title: SC6_81

description: total RNA


title: FJ_21DAH_CTRL_R3


title: SC6_90

description: total RNA


title: SC6_74

description: total RNA


title: FJ_21DAH_1-MCP_R2


title: SC6_75

description: total RNA


title: SC6_73

description: total RNA


title: FJ_14DAH_CTRL_R3

value: 14 days after harvest control


title: SC6_72

description: total RNA


title: SC6_78

description: total RNA


title: FJ_21DAH_CTRL_R1


title: FJ_21DAH_1-MCP_R1


title: SC6_71

description: total RNA


title: FJ_14DAH_CTRL_R1


title: FJ_14DAH_CTRL_R2


title: FJ_14DAH_1-MCP_R3

value: 14 days after harvest treated with 1-MCP


title: SC6_67

description: total RNA


title: SC6_70

description: total RNA


title: SC6_69

description: total RNA


title: SC6_65

description: total RNA


title: FJ_7DAH_CTRL_R2

value: 7 days after harvest control


title: SC6_64

description: total RNA


title: FJ_7DAH_CTRL_R1


title: FJ_14DAH_1-MCP_R1


title: FJ_14DAH_1-MCP_R2


title: SC6_63

description: total RNA


title: SC6_61

description: total RNA


title: SC6_59

description: total RNA


title: FJ_1DAH_CTRL_R3

value: 1 day after harvest control


title: FJ_7DAH_1-MCP_R3

value: 7 days after harvest treated with 1-MCP


title: FJ_7DAH_1-MCP_R2

value: 7 day after harvest treated with 1-MCP


title: FJ_7DAH_CTRL_R3


title: SC6_60

description: total RNA


title: FJ_1DAH_CTRL_R2


title: SC6_62

description: total RNA


title: SC6_56

description: total RNA

value: Mammary tumor


title: FJ_7DAH_1-MCP_R1


title: SC6_57

description: total RNA


title: FJ_1DAH_1-MCP_R3

value: 1 day after harvest treated with 1-MCP


title: SC6_68

description: total RNA

value: C57BL/6 and 129/Sv mixed


title: FJ_1DAH_CTRL_R1


title: FJ_1DAH_1-MCP_R1


title: FJ_1DAH_1-MCP_R2


title: SC6_55

description: total RNA


title: SC6_53

description: total RNA


title: FJ_H_R2

value: harvest


title: SC6_52

description: total RNA

value: female


title: FJ_H_R1


title: SC6_51

description: total RNA


title: SC6_50

description: total RNA


title: SC6_58

description: total RNA

value: Mammary luminal


title: SC6_49

description: total RNA


title: GS_2M_CTRL_R1

value: FRUIT CORTEX

value: Granny Smith


title: SC6_48

description: total RNA


title: GS_2M_1-MCP_R1

value: 2 months after harvest treated with 1-MCP


title: SC6_46

description: total RNA


title: SC6_43

description: total RNA


title: GS_21DAH_CTRL_R2

value: 21 days after harvest control


title: SC6_42

description: total RNA


title: GS_21DAH_1-MCP_R3

value: 21 days after harvest treated with 1-MCP


title: GS_2M_1-MCP_R2


title: GS_21DAH_CTRL_R3


title: FJ_H_R3

value: Fuji


title: SC6_41

description: total RNA


title: GS_2M_1-MCP_R3


title: SC6_47

description: total RNA


title: GS_21DAH_CTRL_R1


title: SC6_45

description: total RNA


title: SC6_44

description: total RNA


title: SC6_54

description: total RNA


title: GS_21DAH_1-MCP_R1


title: GS_2M_CTRL_R3

value: 2 months after harvest control


title: GS_2M_CTRL_R2


title: GS_14DAH_CTRL_R3

value: 14 days after harvest control


title: SC6_38

description: total RNA


title: GS_21DAH_1-MCP_R2


title: SC6_40

description: total RNA


title: GS_14DAH_CTRL_R2


title: SC6_39

description: total RNA


title: SC6_37

description: total RNA


title: GS_14DAH_CTRL_R1


title: SC6_36

description: total RNA


title: GS_14DAH_1-MCP_R3

value: 14 days after harvest treated with 1-MCP


title: SC6_34

description: total RNA


title: GS_14DAH_1-MCP_R2


title: GS_14DAH_1-MCP_R1


title: SC6_31

description: total RNA


title: SC6_35

description: total RNA


title: SC6_32

description: total RNA


title: SC6_33

description: total RNA


title: SC6_30

description: total RNA


title: SC6_28

description: total RNA


title: SC6_29

description: total RNA


title: SC6_27

description: total RNA


title: SC6_25

description: total RNA


title: SC6_26

description: total RNA


title: SC6_24

description: total RNA


title: GS_7DAH_CTRL_R2

value: 7 days after harvest control


title: GS_7DAH_1-MCP_R1

value: 7 day after harvest treated with 1-MCP


title: GS_7DAH_1-MCP_R2


title: GS_1DAH_CTRL_R2

value: 1 day after harvest control


title: SC6_23

description: total RNA

value: Mammary tumor


title: GS_7DAH_CTRL_R3


title: GS_7DAH_CTRL_R1


title: GS_1DAH_CTRL_R3


title: GS_1DAH_1-MCP_R2

value: 1 day after harvest treated with 1-MCP


title: SC6_22

description: total RNA

value: C57BL/6 and 129/Sv mixed


title: GS_1DAH_1-MCP_R1


title: SC6_21

description: total RNA

value: female


title: GS_7DAH_1-MCP_R3

value: 7 days after harvest treated with 1-MCP


title: SC6_20

description: total RNA


title: GS_H_R3

value: harvest

value: FRUIT CORTEX


title: GS_H_R2

value: Granny Smith


title: SC6_19

description: total RNA


title: SC6_18

description: total RNA


title: GS_H_R1


title: GD_2M_CTRL_R3

value: Golden Delicious


title: SC6_16

description: total RNA


title: GD_2M_CTRL_R1


title: SC6_17

description: total RNA


title: GS_1DAH_CTRL_R1


title: SC6_15

description: total RNA


title: GS_1DAH_1-MCP_R3


title: SC6_14

description: total RNA


title: GD_2M_1-MCP_R2

value: 2 months after harvest treated with 1-MCP


title: GD_21DAH_CTRL_R3

value: 21 days after harvest control


title: GD_21DAH_CTRL_R2


title: SC6_12

description: total RNA


title: SC6_08

description: total RNA


title: SC6_09

description: total RNA


title: SC6_11

description: total RNA


title: SC6_10

description: total RNA


title: GD_2M_1-MCP_R1


title: SC6_07

description: total RNA


title: GD_21DAH_1-MCP_R3

value: 21 days after harvest treated with 1-MCP


title: GD_21DAH_1-MCP_R2


title: GD_21DAH_CTRL_R1


title: SC5_96

description: total RNA

value: Mammary luminal


title: SC6_06

description: total RNA


title: SC5_95

description: total RNA


title: GD_2M_CTRL_R2

value: 2 months after harvest control


title: GD_14DAH_CTRL_R2

value: 14 days after harvest control


title: SC5_93

description: total RNA


title: GD_14DAH_CTRL_R1


title: GD_2M_1-MCP_R3


title: SC5_91

description: total RNA


title: SC5_90

description: total RNA


title: GD_14DAH_1-MCP_R2

value: 14 days after harvest treated with 1-MCP


title: SC5_89

description: total RNA


title: GD_14DAH_1-MCP_R1


title: GD_7DAH_CTRL_R3

value: 7 days after harvest control


title: SC5_87

description: total RNA


title: SC5_88

description: total RNA


title: GD_7DAH_CTRL_R2


title: SC5_85

description: total RNA


title: GD_7DAH_CTRL_R1


title: SC5_86

description: total RNA


title: GD_7DAH_1-MCP_R2

value: 7 day after harvest treated with 1-MCP


title: SC5_83

description: total RNA


title: SC5_84

description: total RNA


title: GD_14DAH_CTRL_R3


title: GD_21DAH_1-MCP_R1


title: SC5_94

description: total RNA


title: GD_1DAH_CTRL_R3

value: 1 day after harvest control


title: GD_1DAH_CTRL_R1


title: GD_1DAH_CTRL_R2


title: GD_14DAH_1-MCP_R3


title: GD_1DAH_1-MCP_R3

value: 1 day after harvest treated with 1-MCP


title: GD_1DAH_1-MCP_R2


title: SC5_79

description: total RNA

value: C57BL/6 and 129/Sv mixed

value: female


title: GD_1DAH_1-MCP_R1


title: SC5_78

description: total RNA


title: SC5_76

description: total RNA


title: SC5_77

description: total RNA


title: SC5_75

description: total RNA


title: GD_H_R3

value: harvest


title: GD_7DAH_1-MCP_R3

value: 7 days after harvest treated with 1-MCP

value: FRUIT CORTEX


title: GD_7DAH_1-MCP_R1

value: Golden Delicious


title: GD_H_R1


title: SC5_72

description: total RNA


title: SC5_81

description: total RNA


title: GD_H_R2


title: SC5_73

description: total RNA


title: SC5_74

description: total RNA


title: SC5_71

description: total RNA


title: SC5_80

description: total RNA


title: HeLa siRNA NDP52 3

city: Sheffield

first: Chris

last: Toseland

address: Medical School

country: United Kingdom

institute: University of Sheffield

description: siRNA NDP52 3

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Genome_build: GRch38
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each sample.

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: Full DMEM medium with 10%FBS and Pen/Strep

extract_protocol:
Total RNA was extracted from three replicates of NDP52 KD (using CALCOCO2 siRNA, Ambion, 4392420) and scrambled siRNA (using control siRNA, Qiagen, 1027280) in  HeLa cells. Ice cold TRIzol reagent was added to each cell culture dish and homogenised. The mixture was incubated at room temperature for 10 minutes. Chloroform was then added to the mixture and incubated at room temperature for 5 minutes. The samples were centrifuged at 8,000 xg. The top, aqueous layer was collected and isopropanol was added. The mixture was then centrifuged at 12, 000 xg for 30 minutes and the supernatant discarded. The pellet was washed in 75% (v/v) ethanol and centrifuged at 7, 500 xg for 5 minutes. The pellet was air dried and resuspended in RNAse-free H2O. RNA concentration and quality was then assessed by measuring absorbance at 260 nm and A260/A280 ratio. RNA samples were stored at -80°C. The following procedures were performed by  GENEWIZ. The RNA-seq libraries were prepared using Poly-A selection. Resulting libraries concentration, size distribution and quality were assessed on a Qubit fluorometer and on an Agilent 2100 bioanalyzer. Paired-end sequencing (2x150 bp) was then performed on an Illumina NovaSeq next generation sequencer for HeLa cells (GENEWIZ) .
The following procedures were performed by GENEWIZ. The RNA-seq libraries were prepared using Poly-A selection. Resulting libraries concentration, size distribution and quality were assessed on a Qubit fluorometer and on an Agilent 2100 bioanalyzer.

treatment_protocol: For NDP52 KD experiments, HeLa cell monolayers were seeded at 50% confluency and then transfected with NDP52 KD (using CALCOCO2 siRNA, Ambion, 4392420) or scrambled siRNA (using control siRNA, Qiagen, 1027280) using lipofectamine 2000. Cells were harvested at 48hrs.

tag: cell line

value: HeLa

value: cervical cancer cell line


title: SC5_68

description: total RNA


title: HeLa siRNA NDP52 1

description: siRNA NDP52 1


title: SC5_66

description: total RNA


title: SC5_67

description: total RNA


title: HeLa siRNA NDP52 2

description: siRNA NDP52 2


title: SC5_69

description: total RNA


title: RNA-seq of PLC-8024-CTR cells.

city: Guangzhou

first: Wei

last: Cheng

state: Guangdong

address: Xinzao, Panyu District

country: China

institute: Guangzhou Medical University

data_processing:
Library quality was assessed on the Agilent Bioanalyzer 2100 system. The libraries were then quantified and pooled. Paired-end sequencing of the library was performed on the HiSeq XTen sequencers (Illumina, CA).
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36), then the remaining clean data was used for further analysis. These highquality reads were aligned against the human genome assembly (National Center for Biotechnology Information build 37.1/hg19) using HISAT2 (version 2.1.0) with the RefSeq refGene annotation, which was downloaded from the University of California, Santa Cruz (UCSC) Genome Browser.
RSeQC (version 2.6.1) was used for statistics of the alignment results and analysis of the redundancy sequences and the distribution of insert fragments. Qualimap (version 2.2.1) was used to check the homogeneity distribution and analysis of the genome structure. BEDTools (version 2.26.0) was used for statistical analysis of the gene coverage ratio and the distribution of sequenced sequence on chromosome. Transcripts abundances were quantified by StringTie (version 1.3.3b), which was used to calculate Transcripts Per Million (TPM) of both protein-coding genes and lncRNAs in each sample. For the samples without biological repetition, TMM was used to standardize the read count data, and then DEGseq (version 1.26.0) was used for differential gene expression analysis.
In order to obtain the significant differential genes, the screening conditions were set as follows: q-value <0.05 and difference multiple log2FoldChange >1.
Genome_build: National Center for Biotechnology Information build 37.1/hg19
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample .

source_name: HCC cell line

extract_protocol:
RNA samples were analyzed by RNA sequencing based on the manufacturer’s protocols. Briefly, Illumina HiSeq platform was used to sequence the RNA samples for the subsequent generation of raw data.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Control

value: liver


title: HeLa WT control 3

description: WT control 3


title: HeLa WT control 2

description: WT Control 2


title: SC5_65

description: total RNA

value: Mammary luminal


title: HeLa WT control 1

description: WT Control 1


title: SC5_64

description: total RNA


title: RNA-seq of PLC-8024-GDF1 cells.


title: Control1 for RNA-seq

first: Yue

last: Zhu

address: No. 56, Lingyuan West Road

institute: Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University

description: total RNA

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For RNA-seq, MeRIP-seq, RIP-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
For RNA-seq: The reads mapped the genome were calculated using featureCounts (v1.6.3). For MeRIP-seq: The m6A peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”. Identified m6A peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 6 -rna”.
Genome_build: hg38

source_name: oral squamous cell carcinoma cells

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
For RNA-seq: VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina v2 was used for library construction. For MeRIP-seq: Briefly, the concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). Total RNA was fragmented into 100-200 nt RNA fragments using ZnCl2. Subsequently, the purified RNA was incubated with anti-m6A polyclonal antibody (Sigma-Aldrich, ABE572) for 3 h at 4℃ and then with protein A/G magnetic beads (Thermo Fisher Scientific, 88802) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The m6A-enriched RNA was eluted from the beads in RLT buffer supplied in RNeasy Mini Kit (QIAGEN, 74106). The RNA-seq library was prepared by NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, E7775).
RNA-seq; MeRIP-seq;

value: control


title: Control2 for RNA-seq

description: total RNA


title: autophagy2 for RNA-seq

description: total RNA


title: SC5_63

description: total RNA


title: SC5_62

description: total RNA


title: SC5_70

description: total RNA


title: human cavernous hemangioma scRNA-seq

city: Tianjin

first: Shan

last: Gao

address: No 94, weijin road

institute: Nankai University

description: one sample from human cavernous hemangioma

data_processing:
Cell Ranger v4.0.0 was used to map reads and generate an UMI-count matrix
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: tumour tissue from a 6-year-old patient

extract_protocol:
The single-cell suspensions were filtered with a 40-μm-diameter cell strainer (FALCON, USA), then washed twice times with RPMI1640 wash buffer at 4 temperature. Cell viability was determined by trypan blue staining with TC20 automated cell counter (BioRad, USA). The ratio of viable cells in single-cell suspension was more than 85%. The concentration of single-cell suspension was adjusted to 700–1200 cells/μL.
The cells of each sample were then processed to generate 10x libraries with the Chromium Single Cell 3’ Reagent Kits v3 CG000183 (10x Genomics, USA) following the manufacturer’s instruction.

tag: diagnosis

value: cavernous hemangioma

value: tumour


title: SC5_61

description: total RNA


title: autophagy1 for RNA-seq

description: total RNA


title: SC5_58

description: total RNA


title: SC5_59

description: total RNA


title: SC5_60

description: total RNA


title: Control1-IP for meRIP-seq

description: IP RNA


title: Control1-input for meRIP-seq

description: total RNA


title: SC5_57

description: total RNA


title: Control2-input for meRIP-seq

description: total RNA


title: Control2-IP for meRIP-seq

description: IP RNA


title: Autophagy2-IP for meRIP-seq

description: IP RNA


title: Autophagy2-input for meRIP-seq

description: total RNA


title: SC5_54

description: total RNA


title: Autophagy1-IP for meRIP-seq

description: IP RNA


title: SC5_53

description: total RNA


title: SC5_56

description: total RNA


title: Autophagy1-input for meRIP-seq

description: total RNA


title: SC5_51

description: total RNA


title: SC5_52

description: total RNA


title: SC5_50

description: total RNA


title: SC5_49

description: total RNA


title: CWR22_shCTL_RT_Q30 [CWR22 xenograft]

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Base-calling was performed using Illumina Real Time Analysis RTA.2.7.7.0 with default parameters.
Quasi-alignment of raw sequence reads to the human transcriptome and subsequent transcript abundance estimation was performed via Salmon.
Genome_build: GRCh37
Supplementary_files_format_and_content: Processed data (raw counts) is in supplementary file (CWR22_RawCounts_PerGene.csv), which is a comma-separated file containing a matrix of read counts for each gene symbol and sample.

source_name: CWR22 xenograft

growth_protocol: Male Athymic Nude Balb/c mice were allowed to reach approximately 3 months of age at which point they were surgically castrated and implanted with silastic tubing containing 12.5 mg of testosterone for sustained release 2 weeks prior to xenograft implantation. 1x10^6 CWR22 cells in a 1:1 mix of media to matrigel were injected subcutaneously on the right flank. Once tumors reached 0.3 cm3 in size, androgen withdrawal was achieved by removal of the silastic tubing and tumor volumes were followed for a maximum of 336 days.

extract_protocol:
RNA was isolated from tumors using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) as per manufacturer’s protocols.
Sequencing was performed at the Roswell Park Genomics Shared Resource core facility, and sequencing libraries prepared with the TruSeq Stranded Total RNA kit (Illumina Inc), from 1ug total RNA.

value: CWR22 xenograft

tag: shRNA

value: shCTL

tag: gender

value: male

tag: disease stage

value: RT


title: SC5_48

description: total RNA

tag: strain

value: C57BL/6 and 129/Sv mixed

tag: tissue

value: female


title: CWR22_shCTL_RT_N10 [CWR22 xenograft]


title: SC5_47

description: total RNA

tag: Sex


title: CWR22_shCTL_RT_D10 [CWR22 xenograft]


title: CWR22_shCTL_RT_C3 [CWR22 xenograft]


title: CWR22_shCTL_POST_I1 [CWR22 xenograft]


title: SC5_42

description: total RNA


title: SC5_44

description: total RNA


title: CWR22_shNCOR2_PRE_PN1 [CWR22 xenograft]

value: PRE-ADT


title: CWR22_shNCOR2_POST_CC3 [CWR22 xenograft]


title: CWR22_shNCOR2_PRE_DD1 [CWR22 xenograft]


title: SC5_41

description: total RNA


title: SC5_39

description: total RNA


title: CWR22_shCTL_PRE_PC1 [CWR22 xenograft]


title: CWR22_shCTL_RT_H10 [CWR22 xenograft]


title: SC5_38

description: total RNA


title: CWR22_shNCOR2_POST_HH10 [CWR22 xenograft]


title: SC5_46

description: total RNA


title: SC5_40

description: total RNA


title: SC5_37

description: total RNA


title: CWR22_shNCOR2_RT_T3 [CWR22 xenograft]


title: CWR22_shNCOR2_RT_X1 [CWR22 xenograft]


title: SC5_35

description: total RNA


title: SC5_32

description: total RNA


title: DH24:TLI treated wild type Balb/C mice - pool/set 4: CD8lo CD172hi DC: DC2

city: Stanford

first: Pingping

last: Zheng

state: CA

address: 269 Campus Drive, CCSR

department: BMT

institute: Stanford University

data_processing:
Data was exported from the HisSeq 4000 instrument as FastQ files
Fastq files were trimmed with trimmomatic
hisat2 was used to align fastq data to premade index reference (grcm38_tran )
stringtie were used to generate the gene_count_matrix.csv with Mus_musculus.GRCm38.84.gtf
Deseq2 in R was used for differential expression analysis
Genome_build: GRCm38
Supplementary_files_format_and_content: a gene count matrix csv file is with column names from sample names, and rownames are ensemble id

source_name: sorted spleen cells

extract_protocol:
Cells were sorted directly into RT-PCR reaction buffer and cDNA was synthesized using a SMARTseq v4  UltraLow Input RNA kit (Takara Inc.).
KAPA HyperPlus library kit (Roche Inc.) to prep libraries

value: Balb/C

tag: treatment

value: TLI

value: spleen

value: CD8lo CD172hi DC


title: SC5_36

description: total RNA


title: CWR22_shCTL_POST_O3 [CWR22 xenograft]


title: SC5_45

description: total RNA


title: CWR22_shNCOR2_RT_BB3 [CWR22 xenograft]


title: SC5_31

description: total RNA


title: DH23:TLI treated wild type Balb/C mice - pool/set 4: CD8- CD172lo DC: DC3

value: CD8- CD172lo DC


title: SC5_30

description: total RNA


title: CWR22_shNCOR2_RT_KK10 [CWR22 xenograft]


title: CWR22_shNCOR2_POST_EE10 [CWR22 xenograft]


title: CWR22_shNCOR2_RT_BB1 [CWR22 xenograft]


title: CWR22_shNCOR2_POST_CC10 [CWR22 xenograft]


title: DH22:TLI treated wild type Balb/C mice - pool/set 4: CD8Int CD172+ DC: DC1b

value: CD8Int CD172+ DC


title: SC5_29

description: total RNA

value: Mammary luminal


title: SC5_43

description: total RNA


title: CWR22_shCTL_POST_A10 [CWR22 xenograft]


title: DH21:TLI treated wild type Balb/C mice - pool/set 4: CD8hi CD172- DC: DC1a

value: CD8hi CD172- DC


title: CWR22_shCTL_POST_A1 [CWR22 xenograft]


title: SC5_28

description: total RNA


title: CWR22_shNCOR2_POST_U10 [CWR22 xenograft]


title: CWR22_shNCOR2_POST_HH3 [CWR22 xenograft]


title: CWR22_shNCOR2_PRE_FF10 [CWR22 xenograft]


title: CWR22_shNCOR2_PRE_PN3 [CWR22 xenograft]


title: CWR22_shNCOR2_PRE_PN2 [CWR22 xenograft]


title: CWR22_shCTL_PRE_PC2 [CWR22 xenograft]


title: SC5_27

description: total RNA


title: SC5_25

description: total RNA


title: CWR22_shNCOR2_POST_U30 [CWR22 xenograft]


title: SC5_23

description: total RNA


title: CWR22_shCTL_POST_A30 [CWR22 xenograft]


title: CWR22_shCTL_POST_F1 [CWR22 xenograft]


title: DH17:TLI treated wild type Balb/C mice - pool/set 3: CD8hi CD172- DC: DC1a


title: DH19:TLI treated wild type Balb/C mice - pool/set 3: CD8- CD172lo DC: DC3


title: CWR22_shCTL_PRE_PC3 [CWR22 xenograft]


title: DH18:TLI treated wild type Balb/C mice - pool/set 3: CD8Int CD172+ DC: DC1b


title: CWR22_shCTL_PRE_L3 [CWR22 xenograft]


title: MDA-MB-468 SMARCA4-KO rep3

city: GOYANG

first: JIHYUN

last: KIM

address: 323 ILSAN-RO

country: South Korea

institute: National cancer center

data_processing:
STAR (version. 2.5.2a) in two-pass mapping mode was used to align reads
Quantification for gene expression profilng was performed using RSEM vv1.1.13
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values

source_name: MDA-MB-468 cell line

extract_protocol:
The short guide RNA (sgRNA) targeting exon 4 of the human SMARCA4 gene (NM_001128849) was designed by CRISPR design website (https://design.synthego.com). In brief, the 25bp DNA oligos containing the 20 bp target sequence and BsmbI sticky end were annealed and inserted into the lentiCRISPR-v2 plasmid digested with BsmbI (NEB Cat# 0580S). The sgRNA sequence for generating is as follows: Exon 4 SMARCA4 forward: 5’- ATGGTCCCTCTCGCAGCCCA -3’ and reverse: 5’- TGGGCTGCGAGAGGGACCAT -3’. To prepare lentivirus particles, cloned lentiCRISPR-v2 plasmid were co-transfected with lentiviral packaging vector pCMV-VSV-G and pCMV-dR8.2 into HEK293FT cells. The viral supernatants were harvested 48h after transfection and filtered through a 0.45-μm pore size filter. Cells were infected for 48h and selected for at least 2 days with puromycin (2ug/ml). For KO validation, genomic DNA from SMARCA4 sgRNA transduced cells was extracted using the DNA Mini Kit (Qiagen) according to manufacturer’s instructions and amplified using primers the sgRNA target site. The PCR products were analyzed using TIDE (Tracking of Indels by Sequence Decomposition).
TruSeq Stranded mRNA sample Preparation Guide, Part #15031047 Rev. E

tag: cell type

value: Breast cancer cell line

value: SMARCA4 knock-out


title: MDA-MB-468 SMARCA4-KO rep2


title: MDA-MB-468 SMARCA4-KO rep1


title: SC5_22

description: total RNA


title: MDA-MB-231 SMARCA4-KO rep2

source_name: MDA-MB-231 cell line


title: DH16:Untreated wild type Balb/C mice - pool/set 2: CD8lo CD172hi DC: DC2

value: Untreated


title: DH20:TLI treated wild type Balb/C mice - pool/set 3: CD8lo CD172hi DC: DC2


title: MDA-MB-231 SMARCA4-KO rep3


title: DH15:Untreated wild type Balb/C mice - pool/set 2: CD8- CD172lo DC: DC3


title: MDA-MB-231 SMARCA4-KO rep1


title: SC5_24

description: total RNA


title: MDA-MB-468 WT rep3

value: wild type


title: MDA-MB-468 WT rep2


title: DH14:Untreated wild type Balb/C mice - pool/set 2: CD8Int CD172+ DC: DC1b


title: SC4_37

description: total RNA

value: Mammary tumor


title: DH13:Untreated wild type Balb/C mice - pool/set 2: CD8hi CD172- DC: DC1a


title: MDA-MB-231 WT rep3


title: SC4_36

description: total RNA


title: MDA-MB-231 WT rep2


title: SC4_35

description: total RNA


title: DH12:Untreated wild type Balb/C mice - pool/set 1: CD8lo CD172hi DC: DC2


title: merged Samples [Hashtag]

first: Ivan

last: Zanoni

address: 300 Longwood Ave

institute: Boston Children's Hospital

data_processing:
10X CellRanger v5.0 mkFastq was used to generate fastqs from bcl files for both RNA and HT data, using default parameters
10X CellRanger v5.0 Count and Aggr was used to align data and collapse samples into one file. Hashtag reads were also aligned and aggregated, using default parameters
Data was uploaded to R and filtered and normalized using Seurat. Data was filtered to remove cells with <200 genes and >25% Mitochondrial RNA
Hashtagged samples were demultiplexed using R (v and Seurat's (v4.0) HTODemux function, a positive hashtag signal was in the >99% percentile of the specific hashtag signal
Genome_build: GRCh38
Supplementary_files_format_and_content:
20210605_EECorgo_Raw10x.tar.gz: Outputted 10X folder from Cellranger Count
210606_EECorgo_filtered_RNA.txt.gz: Matrix of all cells from the 9 different conditions and filtered to remove cells that contained less than 200 features and cells that were deemed to be doublets by hashtag detection, contains normalized RNA counts
210606_EECorgo_filtered_HTO.txt.gz: Matrix of all cells from the 9 different conditions and filtered to remove cells that contained less than 200 features and cells that were deemed to be doublets by hashtag detection, contains normalized hashtag feature barcode counts
210606_EECorgo_filtered_meta.txt.gz: Meta data from processed seurat object. Contains Hashtag identity and cell cluster identity from original study

source_name: Enteroid

growth_protocol: Isolated crypts in Matrigel were grown in specific growth media (GM) based on the tissue of origin. The resulting enteroids were passaged every 6-8 days as needed, with media changes occurring every two days.

extract_protocol:
Enteroids were isolated and then a single cell suspension was made.  Dead cells were removed using MACS separation (Dead Cell Removal Kit) and then cells were labeled with Totalseq-B hashtag antibodies. Samples were then combined and RNA libraries prepared using 10X across 4  ge Chromium 3' Library and Gel bead Kit v3.1 with dual index barcodes.
RNA libraries were prepared for sequencing using standard 10X Chromium protocols

treatment_protocol: For differentiation, enteroids were passaged and grown in GM for two days, to allow for ISC expansion, after which the enteroids were transitioned to tissue-specific differentiation media (DM) with additional small molecules (ie AS and RSP) added. Media was changed every two days, with Tubastatin A being removed after the second day of differentiation. Enteroids were taken for analysis after 14 days.

tag: enteroid line

tag: source tissue

value: Duodenum

tag: culture treatment

value: Merged

tag: molecule

value: total RNA +HT oligo


title: DH11:Untreated wild type Balb/C mice - pool/set 1: CD8- CD172lo DC: DC3


title: DH10:Untreated wild type Balb/C mice - pool/set 1: CD8Int CD172+ DC: DC1b


title: MDA-MB-231 WT rep1

tag: genotype


title: SC4_34

description: total RNA

value: C57BL/6 and 129/Sv mixed

value: female


title: merged Samples [RNA]


title: DH09:Untreated wild type Balb/C mice - pool/set 1: CD8hi CD172- DC: DC1a

value: Balb/C


title: SC4_33

description: total RNA


title: NB4-NC-2

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: NB4 sample with CEBPG presence

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treat

value: CEBPG presence


title: SC4_32

first: Heng

last: Sun

address: Avendia da Universidade, Taipa

institute: University of Macau

description: total RNA

data_processing:
sickle was used for data quality control.
trim_galore-v0.4.1 was used for data trimming.
STAR-2.5.3a was used for alignment with default parameter for pair-end sequencing.
subread-1.5.3 was used for generation of read_count.
Genome_build: mm10
Supplementary_files_format_and_content: Gene read_count value for each sample were summarized in text file.

extract_protocol:
The sorted mammary luminal cells or tumor cells re-suspended in FACS buffer (300-500 cells/µL) were mixed (3:2 ratio) with C1 Cell Suspension Reagent (Fluidigm) before loading onto a  10 to 17-μm-diameter C1 Integrated Fluidic Circuit (IFC; Fluidigm). Each capture site was carefully examined and recorded under a ZEISS microscope in bright field channel for cell doublets. Cell lysing, reverse transcription and cDNA amplification were performed on the C1 Single-Cell Auto Prep IFC, as specified by the manufacturer (protocol 100-7168 E1). The SMARTer Ultra Low RNA Kit (Clontech) was used for cDNA synthesis from the single cells.
Illumina NGS library was constructed with Nextera XT DNA Sample Prep kit (Illumina), according to the manufacturer’s recommendations (protocol 100-7168 E1).


title: NB4-CEBPG3-1

source_name: NB4 sample with CEBPG knockdown

value: CEBPG knockdown


title: NB4-NC-1


title: DH07:TLI treated wild type Balb/C mice - pool/set 2: CD8- CD172lo DC: DC3

value: TLI

value: spleen

value: CD8- CD172lo DC


title: MDA-MB-468 WT rep1


title: DH06:TLI treated wild type Balb/C mice - pool/set 2: CD8Int CD172+ DC: DC1b

value: CD8Int CD172+ DC


title: MV4-CEBPG3-1

source_name: MV4-11 sample with CEBPG knockdown


title: MV4-NC-2

source_name: MV4-11 sample with CEBPG presence


title: MV4-CEBPG3-2


title: SC4_31

description: total RNA


title: SC4_30

description: total RNA


title: SC5_21

description: total RNA

value: Mammary luminal


title: BRCA11

city: IRVINE

first: Kevin

last: Nee

address: 839 Health Science Road, Sprague Hall 114

department: Biological Chemistry

institute: University of California, Irvine

data_processing:
Alignment of scRNAseq analyses were completd utilizing 10x Genomics Cell ranger pipeline (version2.1.0) Each library was aligned to an indexed GRCh38 genome using Cell Ranger Count.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed Data files are tab-delimited .txt files of counts expression matrices corresponding to each sample of this study

molecule: polyA RNA

source_name: patient breast surgical sample

extract_protocol:
Human breast surgical samples were mechanically dissociated with scalpels, diged with 2mg/ml collagenease I in DMEM overnight with 20U/ml DNaseI, these created human organoids that were viably cryoperserved. Thawed human organoids were then digested with 0.05% trypsin for 6 mins before they were stained for FACS.
Library generation for four 10x genomics v1 chemistry, and twenty-four 10x genomics v2 chemistry was performed following the Chromim Singel Cell 3' Reagents Kits v2 User Guide: CFG00052 Rev B. Libraries were sequenced on the Illumina NovaSeq6000 platform targeting approximately 50,000 reads per cell.

tag: tissue source

value: Prophylatic Mastectomy

tag: brca1 status

tag: cell types

value: Epithelial/Stromal


title: MV4-NC-1

tag: cell line


title: BRCA10


title: BRCA9


title: DH05:TLI treated wild type Balb/C mice - pool/set 2: CD8hi CD172- DC: DC1a

value: CD8hi CD172- DC


title: DH03:TLI treated wild type Balb/C mice - pool/set 1: CD8- CD172lo DC: DC3


title: DH04:TLI treated wild type Balb/C mice - pool/set 1: CD8lo CD172hi DC: DC2

value: CD8lo CD172hi DC


title: SC4_29

description: total RNA

value: Mammary tumor


title: NB4-CEBPG3-2


title: SC4_28

description: total RNA


title: BRCA8


title: BRCA7


title: BRCA6


title: SC4_26

description: total RNA


title: DH02:TLI treated wild type Balb/C mice - pool/set 1: CD8Int CD172+ DC: DC1b


title: BRCA3

value: Epithelial


title: SC4_25

description: total RNA


title: DH01:TLI treated wild type Balb/C mice - pool/set 1: CD8hi CD172- DC: DC1a


title: SC4_24

description: total RNA


title: BRCA4


title: BRCA5


title: Telogen rep2

city: Bronx

first: Deyou

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: Hair_Cycle_HFSC_P29_vs_P52_DESeq2_result.xls

data_processing:
The paired-end RNA-seq reads were aligned to the mouse transcriptome corresponding to the Gencode annotation (vM20) using the software Kallisto (v0.42.5). The counts for protein-coding genes were collapsed and used for DESeq2 (v3.11) for differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: The text tables were DESeq2 results with normalized counts from DESeq2.

source_name: Skin epidermis

extract_protocol:
FACS isolation of HFSCs from the back skin of control and PRC2 iKO mice was performed as following. The back skin from adult mice was collected. The adipose layer from the dorsal side was scraped off and the scraped skin sample was washed with 1x PBS prior to incubation with 0.25% Trypsin/EDTA (Corning Cellgro) at 37C for 1 hour. After incubation, the epidermal cells, including the HFSCs, was scraped off from the trypsinized skin into the plate. 25 mLs of E-media was added to the cell suspension and was strained through 40µm filters and was washed twice with 1x DPBS. The cells were stained with 1:200 PerCP-Cy5.5-Sca1 (Thermo Fisher Scientific), 1:200 FITC-α6-integrin (Thermo Fisher Scientific), 1:100 APC-EpCAM (Biolegend) and 1:20 Alexa700-CD34 (Biolegend) in staining buffer (HBSS + 2% Fetal Bovine Serum) for 30 minutes on ice and then washed twice with 1x DPBS before cell sorting. HFSCs, was sorted as EpCAM(+), Sca1(-), α6-integrin(high) and CD34(+).FACS-purified cells were collected directly into RLT Plus buffer (QIAGEN), and total RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN).
10ng of total RNA were reverse transcribed and amplified using the Ovation RNA-seq System V2 (NuGEN). Libraries were constructed from 100ng of sonicated cDNA (Covaris) using the Ovation Ultralow system V2 (NuGEN).  The concentration and quality of the libraries were determined using Qubit (Invitrogen) and Bioanalyzer (Agilent). Constructed RNA-seq libraries were sequenced at GENEWIZ on the Illumina HiSeq platform, obtaining 150 nucleotide paired-end reads.

treatment_protocol: For RU-486 (Cayman Chemicals) topical treatment to induce Eed ablation, RU-486 was dissolved in 100% ethanol (Sigma-Aldrich) to a final concentration of 10 mg/ml. 100l of RU-486 was topically applied on shaved dorsal skin of postnatal day 19 (P19) or P50 mice once per day for 7 days

value: Hair Follicle Stem cells

tag: growth cycle

value: Telogen

value: Epidermis

tag: age

value: Postnatal day 50-52

value: wildtype


title: Telogen rep3

tag: strain


title: Control11

value: Contralateral to Tumor

value: No Mutation


title: BRCA2


title: Control10

value: Contralateral to DCIS


title: Control9


title: BRCA1


title: SC4_27

city: Macau

description: total RNA

value: C57BL/6 and 129/Sv mixed

tag: tissue

value: female


title: Telogen rep1


title: Control7


title: Control8


title: Control6


title: Anagen rep3

value: Anagen

value: Postnatal day 28-30


title: SC4_21

description: total RNA

tag: Sex


title: SC4_22

description: total RNA


title: Anagen rep2


title: SC4_20

description: total RNA


title: Anagen rep1


title: Control3

value: Reduction Mammoplasty


title: Control1


title: SC4_23

description: total RNA


title: HFSC_Eed KO rep3

description: EedKO_HFSC_RNA_seq_analysis_deseq2_results.xls

value: Postnatal day 70

value: Eed -/-


title: SC4_19

description: total RNA

value: Mammary tumor


title: HFSC_Eed KO rep2


title: SC4_17

description: total RNA


title: B2_D2_Uninfected Enriched

city: Oxford

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

data_processing:
Reads were quality trimmed and adapters were removed using Cutadapt software
Reads were aligned to joint Salmonella-Human reference genome using STAR and cross-species multi-mappers were filtered out
Expression was quantified using Subread featureCounts, with multi-mappers counted as fractions
Data normalisation and differential expression analyses were performed using DESeq2
Genome_build: hg38, NC_003197.2, NC_016854.1 and NC_004631.1
Supplementary_files_format_and_content: Raw expression counts matrices per sample

source_name: Monocyte-derived dendritic cells

growth_protocol: Leukocyte Reduction System cones were obtained from the UK National Blood Centre with informed consent following local ethical guidelines. Blood was diluted in Phosphate-Buffered Saline (PBS) and layered on a standard density gradient (LymphoprepTM). Peripheral Blood Mononuclear Cells (PBMC) were collected from the interface and washed in PBS at 4 C. Monocytes were obtained by magnetic positive selection, using the human anti-CD14+ MicroBeads (Miltenyi Biotec, Germany) according to the manufacturer’s protocol.  Freshly isolated monocytes were differentiated into Dendritic Cells (MoDCs)  in the presence of 40 ng/mL of recombinant human (rh) Granulocyte Macrophage-Colony-Stimulating Factor (GM-CSF; Peprotech) and 40 ng/mL rh Interleukin-4 (IL-4; Peprotech).

extract_protocol:
20'000 cells were sorted in PBS and spun down and the pellet resuspended in Monarch RNA lysis buffer supplemented with 2mg/mL of Lysozime (thermoFisher). Total RNA extraction was performed with the Monarch® Total RNA Miniprep Kit (New England BioLabs) according to the manufacturers.
Libraries were prepared by using the SMARTer® stranded total RNA seq v2 pico input Mammalian (Takara) with minor technical adaptations. PCR1 was carried on for 5 cycles and PCR2 for 11 cycles (for the bacterial libraries) or 12 cycles (for the host-pathogen libraries). After cDNA synthesis, the human ribosomal cDNA was removed by using probes specific to mammalian rRNA.

treatment_protocol: DCs were infected with S. Tyhpimurium strain LT2 or D23580 or S. Typhi strain Ty2 at a MOI of 10 or left uninfected for 6h before sorting.

tag: infection

value: Mock

tag: status

value: Uninfected

tag: bacterial probe enrichment

value: Enriched


title: D3_D4_uninfected Enriched


title: Control5

value: Epithelial/Stromal


title: SC4_16

description: total RNA


title: HFSC_Control rep3

tag: cell type

value: Hair Follicle Stem cells

value: Epidermis


title: H2_LT2 Enriched

description:
Enriched_LT2.txt
WTCHG_774525_73125288

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: Bacteria

value: Bacterial liquid culture

value: Bacterial liquid culture + DFO


title: F2_LT2_2 Enriched

description:
Enriched_LT2.txt
WTCHG_774525_73105286


title: HFSC_Eed KO rep1


title: C2_LT2 Enriched

description:
Enriched_LT2.txt
WTCHG_774525_73075283


title: A2_D3_uninfected Enriched


title: SC4_15

description: total RNA


title: HFSC_Control rep2

value: wildtype


title: A1_D1_Uninfected Enriched


title: SC4_14

description: total RNA

value: C57BL/6 and 129/Sv mixed


title: Control2

value: No Mutation

value: Stromal


title: HFSC_Control rep1


title: D1_LT2 Enriched

description:
Enriched_LT2.txt
WTCHG_774525_73005276


title: A3_LT2_3 Enriched

description:
Enriched_LT2.txt
WTCHG_774525_72905266


title: SC4_13

description: total RNA

value: female


title: A1_LT2_1 Enriched

description:
Enriched_LT2.txt
WTCHG_774525_72915267


title: D3_D4_uninfected Unenriched

value: Unenriched


title: SC4_18

description: total RNA


title: B2_D2_Uninfected Unenriched


title: SC4_12

description: total RNA


title: mIMCD3 DOX 6D replicate 4

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

data_processing:
Four technical repliates of each experimental group were prepared for further downstream data processing.
Counts and abundance of transcripts were generated by quantifying sequence reads on transcripts from Gencode GRCm38.p6 using salmon (0.14.10).
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: mouse inner medullary collecting duct cell line

growth_protocol: mIMCD3 cells were grown on a permeable filter membrane for 10 days in the RenaLife Epithelial Basal Medium (LM-0010, LIFELINE CELL TECHNOLOGY) supplemented with a RenaLife LifeFactors Kit (LS-1048, LIFELINE CELL TECHNOLOGY) and 5% FBS.

extract_protocol:
Cells were lyzed in Trizol. Total RNA was extracted using Direct-zol RNA Miniprep kit (ZYMO RESEARCH).
To enrich mRNA, 1-3 ug of total RNA was applied to oligo dT-based mRNA isolation using NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490, NEW ENGLAND BioLabs Inc.) as a manufacturer’s instruction. mRNA (20-30 ng) was sequentially used for the further sequencing library preparation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, NEW ENGLAND BioLabs Inc.) and NEBNext® Multiplex Oligos (E7335; E7500, NEW ENGLAND BioLabs Inc.). cDNA libraries were sequenced on Illumina HiSeq 4000 platform. Sequence reads (2 × 75 bp, paired-end) were aligned on Ensembl genome GRCm38p6 using STAR (2.6.0c).

treatment_protocol: Cells were grown on the permeable filters of a transwell system (6-well) for 10 days and treated with doxycycline (2 ug/mL) or vehicle (DMSO) for 3 days or 6 days. Media containing doxycycline or vehicle were daily changed.

value: kidney

value: wild type

tag: treatment

value: DOX

tag: time

value: 6 days


title: LT2_H2 Unenriched

description:
Unenriched_LT2.txt
WTCHG_790509_73125288


title: Control4

value: Contralateral to Tumor


title: mIMCD3 DOX 6D replicate 3

tag: genotype

value: mouse inner medullary collecting duct cell line


title: A2_D3_uninfected Unenriched

value: Mock

value: Uninfected


title: SC4_11

description: total RNA

value: Mammary tumor


title: LT2_C2 Unenriched

description:
Unenriched_LT2.txt
WTCHG_790509_73075283

value: Bacterial liquid culture


title: mIMCD3 DOX 6D replicate 2


title: mIMCD3 DMSO 6D replicate 4

value: DMSO


title: LT2_D1 Unenriched

description:
Unenriched_LT2.txt
WTCHG_790509_73005276

value: Bacterial liquid culture + DFO


title: A3_LT2_3 Unenriched

description:
Unenriched_LT2.txt
WTCHG_790509_72905266


title: mIMCD3 DOX 6D replicate 1


title: SC5_55

description: total RNA

source_name: pBrL

value: C57BL/6 and 129/Sv mixed

value: Mammary luminal


title: SC4_09

description: total RNA


title: mIMCD3 DMSO 6D replicate 3


title: F2_LT2_2 Unenriched

description:
Unenriched_LT2.txt
WTCHG_790509_73105286


title: SC4_08

description: total RNA


title: SC4_10

description: total RNA


title: A1_LT2_1 Unenriched

description:
Unenriched_LT2.txt
WTCHG_790509_72975273


title: STM-LT2 Unenriched

description:
Unenriched_LT2.txt
WTCHG_545174_269147


title: SC4_05

description: total RNA


title: B1_D23_2 Unenriched

description:
Unenriched_LT2.txt
WTCHG_790509_72985274


title: mIMCD3 DMSO 6D replicate 1


title: mIMCD3 DOX 3D replicate 4

value: 3 days


title: A1_D1_Uninfected Unenriched


title: SC4_04

description: total RNA

value: female


title: mIMCD3 DOX 3D replicate 3


title: D2_Ty2_infected Unenriched

description:
intracellular_unenriched_TY2.txt
WTCHG_531625_264112

organism:
Homo sapiens
Salmonella enterica

source_name: Monocyte-derived dendritic cells + Bacteria

value: Infected

value: Unenriched


title: D2_D23580_infected Unenriched

description:
intracellular_unenriched_D23580.txt
WTCHG_531625_263124


title: SC4_03

description: total RNA


title: CWR22_shCTL_PRE_L1 [CWR22 xenograft]

value: CWR22 xenograft

tag: shRNA

value: shCTL

tag: gender

value: male

tag: disease stage

value: PRE-ADT


title: SC4_07

description: total RNA


title: D2_LT2_infected Unenriched

description:
intracellular_unenriched_LT2.txt
WTCHG_531625_262136


title: D1_Ty2_infected Unenriched

description:
intracellular_unenriched_TY2.txt
WTCHG_531625_260160


title: SC4_06

description: total RNA


title: SC4_02

description: total RNA


title: D1_LT2_infected Unenriched

description:
intracellular_unenriched_LT2.txt
WTCHG_531625_258184


title: D1_D23580_infected Unenriched

description:
intracellular_unenriched_D23580.txt
WTCHG_531625_259172


title: SC4_01

description: total RNA


title: mIMCD3 DMSO 6D replicate 2

value: kidney

value: wild type

value: mouse inner medullary collecting duct cell line

value: 6 days


title: SC2_28

description: total RNA

value: Mammary tumor


title: mIMCD3 DMSO 3D replicate 1

value: DMSO


title: mIMCD3 DMSO 3D replicate 3


title: mIMCD3 DMSO 3D replicate 4


title: mIMCD3 DOX 3D replicate 1

value: DOX


title: SC2_30

description: total RNA

value: C57BL/6 and 129/Sv mixed


title: OVX+EX YH5-3

city: Ji’nan

first: Li

address: No. 10600 Century Avenue, Licheng District

institute: SHANDONG SPORT UNIVERSITY

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.
Genome_build: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: the peripheral blood mononuclear cells (PBMCs)

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®UltraTM RNA Library Prep Kit for Illumina®(NEB, USA) following manufacturer’ s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3 ’ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 200-250 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: three-month-old female Sprague–Dawley rats


title: SC2_29

description: total RNA


title: mIMCD3 DMSO 3D replicate 2

value: 3 days


title: OVX+EX YH3-2

value: the peripheral blood mononuclear cells (PBMCs)


title: mIMCD3 DOX 3D replicate 2


title: MCY-IRRA

city: Hangzhou

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

description: scRNA-seq (2 females)

data_processing:
scRNA-seq data were demultiplexed, aligned to the mouse genome, version mm10, and UMI-collapsed with the Cellranger toolkit (version 3.0.1, 10X Genomics). We excluded cells with fewer than 500 detected genes (where each gene had to have at least one UMI aligned). Gene expression was represented as the fraction of its UMI count with respect to total UMI in the cell and then multiplied by 10,000. For bulk RNA-seq, adaptor sequences were cut using CutAdapt and trimmed reads shorter than 30bp were discarded. Trimmed data were aligned to mouse reference genome mm10 using STAR (79), with uniquely mapping rates greater than 80%. HTseq-count  was used to count the number of reads mapped to each gene. Then data were loaded into the R platform where further statistical analyses occurred. Counts of genes were normalized and differentially expressed genes (p-value < 0.05, fold-change > 1.35) was determined in the DESeq2 package . Relationship among samples was assessed by principal component analysis (PCA) of DESeq2 normalized counts.
Genome_build: mm10
Supplementary_files_format_and_content: gene-barcode matrices

source_name: Long bones

growth_protocol: All mice were kept in an SPF facility operated in a 12-hour light/dark cycle.

extract_protocol: For scRNA-seq, 10X Genomics Single Cell 3’ v3 kit was used.

treatment_protocol: Normal feeding

value: Bone marrows and bone fragments

value: CD45-Ter119-Tie2-Lepr-Cre+ cells

value: Sub-lethally irradiated (5 Gy) at 7 weeks old, analyzed after one week


title: OVX+EX YH4-2


title: SC2_25

description: total RNA

value: female


title: SC2_26

description: total RNA


title: SC2_24

description: total RNA


title: SC2_27

description: total RNA


title: CWR22_shNCOR2_RT_BB3

type: genomic

hyb_protocol: DNA methylation profiles were obtained using the Infinium MethylationEPIC BeadChip (EPIC array) platform, performed in the RP Genomics Shared Resource.

data_processing: Data Importing and subsequent processing was accomplished using ChAMP. Detectible beta values for all probed CpG sites were initially compiled and filtered to remove those associated with multiple alignments and known SNPs. To adjust for probe design bias (Infinium Type-I, Type-II), a beta-mixture quantile normalization method (BMIQ) was employed. Additionally, cross-array batch effect was corrected using ComBat.

label: Cy5 and Cy3

source_name: genomic DNA from xenograft tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from all samples using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen), following manufacturer’s protocol.

value: Male

tag: sample type

value: PCa xenograft

value: RT


title: 24w-D1-5

city: Nashville

first: Yinqiu

last: Wang

state: TN

address: 313 Harpeth view circle

department: medicine

institute: vumc

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v1.16
GENCODE vM16 gene annotations were provided to STAR to improve the accuracy of mapping
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC
Feature Counts v1.15.2 was used to count the number of mapped reads to each gene
Fragments per kilobase of transcript per million mapped reads (FPKM) values for all genes in each sample were calculated based on gene length in GENCODE vM16 gene annotations.
Genome_build: mm9
Supplementary_files_format_and_content: Fragments per kilobase of transcript per million mapped reads (FPKM)
Supplementary_files_format_and_content: raw counts

source_name: Kidney

extract_protocol:
TRAP RNA isolation
Ovation RNA-Seq Systems 1-16 for Model Organisms – Mouse (NuGEN Technologies, Redwood City, CA).
Library preparation was performed according to the manufacturer’s instructions. RNA underwent DNase treatment and cDNA was fragmented (200bp) on a Covaris LE220.

value: podocyte

tag: disease

value: Type 1 Diabetes

tag: treatment stz

value: 8 months

tag: molecule subtype

value: TRAP RNA


title: 24w-D1-3

tag: strain

tag: age


title: OVX+EX YH2-1


title: SC2_22

description: total RNA

tag: tissue

value: Mammary tumor

tag: Sex


title: OVX+EX YH1-1


title: CWR22_shNCOR2_RT_KK10

scan_protocol: DNA methylation profiles were obtained using the Infinium MethylationEPIC BeadChip (EPIC array) platform, performed in the RP Genomics Shared Resource.


title: OVX MH5-2


title: 24w-D1-1


title: OVX MH4-2


title: CWR22_shNCOR2_RT_BB1


title: SC2_21

description: total RNA


title: 24w-CT-4

value: normal

value: no STZ


title: CWR22_shNCOR2_POST_HH3


title: 24w-CT-5


title: SC2_19

description: total RNA

value: C57BL/6 and 129/Sv mixed


title: CWR22_shNCOR2_POST_EE10


title: OVX MH3-2

value: three-month-old female Sprague–Dawley rats


title: 24w-CT-3


title: CWR22_shNCOR2_POST_CC10


title: SC2_23

description: total RNA


title: 24w-D1-2


title: SC2_18

description: total RNA


title: 24w-CT-2


title: OVX MH2-2

value: the peripheral blood mononuclear cells (PBMCs)


title: CWR22_shNCOR2_RT_T3


title: CWR22_shNCOR2_POST_CC3


title: OVX MH1-2


title: CWR22_shNCOR2_POST_U30


title: 24w-CT-1


title: SHAM DH5-3


title: CWR22_shNCOR2_POST_U10


title: SC2_16

description: total RNA


title: SC2_20

description: total RNA


title: 3w-D1-4

value: 3 months


title: SC2_17

description: total RNA


title: SHAM DH4-1


title: CWR22_shNCOR2_PRE_PN3

value: PRE-ADT


title: 3w-D1-3


title: SHAM DH3-3


title: SC2_15

description: total RNA


title: SC2_14

description: total RNA


title: CWR22_shNCOR2_PRE_PN2


title: SHAM DH2-3


title: CWR22_shNCOR2_PRE_PN1


title: 3w-D1-5


title: SHAM DH1-1


title: SC2_13

description: total RNA


title: 3w-D1-1


title: 3w-CT-3


title: SC2_10

description: total RNA


title: SC2_12

description: total RNA


title: SC2_11

description: total RNA


title: CWR22_shNCOR2_PRE_DD1


title: 3w-CT-4


title: S1NLP-P71-12-13-19-S1-Empty-NLP

city: Livermore

first: Claire

last: Robertson

address: 7000 East Ave.

institute: Lawrence Livermore National Lab

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
Genome_build: The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Supplementary_files_format_and_content: Hit counts

source_name: Cultured breast epithelial cells

growth_protocol: Human immortalized breast cells (S1) from the HMT3522 progression series (kind gift of Mina Bissell) 44 were maintained in DMEM/F12 (11330, ThermoFisher) supplemented with 250ng/ml insulin (I6634, Sigma Aldrich), 10μg/ml Apo-transferrin (T2252, Sigma Aldrich), 2.6ng/ml sodium selenite (Corning, 47743-618), 10-10 M beta-estradiol (E2785, Sigma Aldrich), 1.4x10-6 M hydrocortisone (H0888, Sigma Aldrich), 5μg/ml ovine prolactin (LA Biomedical Research Institute),  and for S1 only, 10ng/ml EGF (11376454001, Roche). S1 were seeded in uncoated T75 flasks (corning) at 2e4/cm2, refed every 2 days, and passed every 7 days and T4-2 were seeded in collagen coated flasks (corning) at 1e4/cm2, refed every 2 days and passed every 5 and 3 days respectively. Cells were kept in humidified incubators at 37C and 5% CO2 supplementation, and CO2 calibrations were performed biweekly with a test kit (Fyrite, Bacharach). Cells were screened for mycoplasma contamination every 2 months (Mycoalert, Lonza).

extract_protocol:
After 10 days of culture, cells were harvested from lrECM by incubation with 5mM EDTA in PBS on ice for 30 minutes with gentle agitation and spun down to collect structures.  Cell pellets were then snap frozen on dry ice for shipping,
RNA-seq (HiSeq 2x150 PE HO).   Cell pellets underwent RNA extraction, poly-A capture, strand specific cDNA synthesis, end repair and adaptor ligation.  RNA-seq library preparation and sequencing were performed by Genewiz's service.

treatment_protocol: HMT-3522-S1 were passaged, counted, and resuspended in 100% lrECM (354230, growth factor reduced Matrigel, Corning) at 800k cells/ml or 600k/ml respectively on ice.  Cells in lrECM were transferred to dishes, allowed to gel for 20 minutes at 37C, then covered with complete culture media ± 5μg/ml Her2-NLPs or empty NLPs.  Media containing fresh NLPs was replaced every 2-3 days for 10 days.

tag: cell line

value: nonmalignant breast epithelial acinar cultures

value: 5ug/ml Empty NLP

tag: passage number


title: CWR22_shCTL_RT_Q30

value: Male

value: shCTL


title: 3w-CT-2

tag: cell type


title: S1NLP-P71-12-13-19-S1-Her2NLP

tag: treatment

value: 5ug/ml Her2-NLP


title: CWR22_shNCOR2_RT_X1

value: PCa xenograft

value: RT


title: S1NLP-P71-12-13-19-S1-0

value: Control/no stimulus


title: S1NLP-p66-12-11-19-S1-Her2-NLP


title: SC2_09

description: total RNA

value: female


title: CWR22_shCTL_RT_N10


title: 3w-CT-1

value: podocyte

value: TRAP RNA


title: CWR22_shCTL_RT_H10


title: SC2_08

description: total RNA

value: Mammary tumor


title: 3w-D1-2

value: Type 1 Diabetes


title: CWR22_shNCOR2_PRE_FF10


title: S1NLP-p66-12-11-19-S1-Empty-NLP


title: 6m-D2-3

value: Type 2 Diabetes

value: eNOS-/- db/db

value: 6 months


title: SC2_07

description: total RNA

value: C57BL/6 and 129/Sv mixed


title: CWR22_shCTL_RT_D10


title: CWR22_shCTL_RT_C3


title: S1NLP-p66-12-11-19-S1-0

value: nonmalignant breast epithelial acinar cultures


title: 6m-D2-2


title: 6m-D2-1


title: SC2_05

description: total RNA


title: CWR22_shCTL_POST_O3


title: SC2_04

description: total RNA


title: 6m-CT-3

value: normal

value: eNOS-/-


title: SC2_03

description: total RNA


title: WDR45-3

city: Chuncheon

first: Sehyun

last: Chae

address: 1 Kangwondaehakgil

department: Division of Chemical Engineering and Bioengineering

institute: Kangwon National University

data_processing:
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Illumina adapter sequences were removed using the cutadapt software (version 2.7), and the remaining reads sequences were aligned to the Homo sapiens reference genome (GRCh38) using Tophat2 software (version 2.1.1) with the default parameters.
After the alignment, the numbers of reads mapped to the gene features (GTF file of GRCh38.89) were counted using HTseq sofrware. The read counts for the samples in each condition were then normalized using the TMM (trimmed mean of M-values) normalization of the edgeR package.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TMM-normalized read counts for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: WDR45 mutant fibroblasts

extract_protocol:
Total RNAs were obtained from fibroblasts using Trizol reagent (Invitrogen Life Technologies, Grand Island, NY). Poly(A) mRNA isolation from the total RNA and subsequent fragmentation were performed using TruSeq RNA Sample Prep Kits v2 (Illumina, San Diego, CA, USA), according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols. The adaptor ligated libraries were sequenced using an Illumina NovaSeq 6000.

value: fibroblasts


title: NHDF-3

source_name: Normal fibroblasts

value: WDR45 wild-type


title: WDR45-2


title: WDR45-1


title: CWR22_shCTL_POST_I1

value: Male

value: PCa xenograft

value: shCTL


title: CWR22_shCTL_POST_A30


title: 6m-CT-2


title: SC2_02

description: total RNA

value: female


title: 6m-CT-1

value: podocyte


title: CWR22_shCTL_POST_A10


title: 3m-D2-5

value: 3 months

value: TRAP RNA


title: SC2_01

description: total RNA

value: Mammary tumor


title: NHDF-1


title: CWR22_shCTL_POST_A1


title: SC2_06

description: total RNA


title: SC10_44

description: total RNA

source_name: vBrL

value: Mammary luminal


title: CWR22_shCTL_POST_F1


title: 3m-D2-4

value: Type 2 Diabetes

value: eNOS-/- db/db


title: SC10_43

description: total RNA

value: C57BL/6 and 129/Sv mixed


title: C42_shNCOR2_B_DHT_C [RNA-seq]

data_processing:
Base-calling was performed using Illumina Real Time Analysis RTA.2.7.7.0 with default parameters
Raw sequencing reads were aligned to the human genome using the splice junction aligner TopHat2.
Gene expression counts per gene were extracted from aligned reads using featureCounts.
Genome_build: GRCh37
Supplementary_files_format_and_content: processed data is in supplementary file, which is a comma-separated text file containing a matrix of read counts for each gene accession number and sample

source_name: PCa cell line

growth_protocol: Cells were maintained at 37oC and 5.0% CO2 using a cell culture incubator with UV contamination control. LNCaP and LNCaP-C4-2 cells were regularly maintained in RPMI 1640 Medium containing 10% FBS. All media was supplemented with 100 U/mL Penicillin-Streptomycin.

extract_protocol:
Total RNA was extracted from all samples using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen), following manufacturer’s protocol.
Sequencing was performed at the Roswell Park Genomics Shared Resource core facility, and sequencing libraries prepared with the TruSeq Stranded Total RNA kit (Illumina Inc), from 1ug total RNA

treatment_protocol: Cells were treated with indicated concentration of DHT or EtOH for 6 hr.

value: PCa cell line

tag: cell line source gender

value: male

value: 10nm DHT


title: C42_shNCOR2_B_DHT_B [RNA-seq]


title: 3m-D2-3

tag: genotype


title: 6m-CT-4

value: normal

value: eNOS-/-

value: 6 months


title: CWR22_shCTL_PRE_PC2

value: Male

value: PCa xenograft

value: PRE-ADT

tag: shRNA


title: SC10_42

description: total RNA

value: female


title: CWR22_shCTL_PRE_PC3

tag: gender

value: shCTL


title: C42_shNCOR2_B_DHT_A [RNA-seq]


title: CWR22_shCTL_PRE_L3

tag: disease stage


title: C42_shNCOR2_B_ETOH_C [RNA-seq]

value: EtOH


title: SC10_40

description: total RNA


title: NHDF-2

value: fibroblasts

value: WDR45 wild-type


title: SC10_37

description: total RNA

value: Mammary luminal


title: CWR22_shCTL_PRE_L1

tag: sample type


title: C42_shNCOR2_B_ETOH_A [RNA-seq]


title: 3m-CT-4

value: podocyte

tag: disease

value: 3 months

value: TRAP RNA


title: SC10_36

description: total RNA

value: C57BL/6 and 129/Sv mixed


title: LNCaP_shNCOR2_B_DHT_C

source_name: genomic DNA from cell line

value: Cell line

value: LNCaP


title: 3m-CT-5

value: normal

value: eNOS-/-