title: 10_RNASE1_sg3_B

city: Bethesda

first: Ashish

last: Lal

state: MD

address: 37 Convent Drive, Bldg 3, Room 6134

department: Genetics Branch

institute: NCI, NIH

description: Library name: 10_RNASE1_sg3_B

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNASeq reads were aligned to Human Hg38 reference genome using TopHat2 version 2.0.8
Fusion detection was done using TopHat2 fusion version 2.0.8
fpkm was generated using Cufflink version 2.2.1
fastqc was done using fastqc version 0.11.2
Assembly: Hg38  for all samples
Supplementary files format and content: fpkm files are tab delimited text files for each sample. Fusion results are tab delimited text files of each sample. Fastqc results are for each sample in html format, zipped.

growth_protocol: all cell lines were cultured in DMEM with 10% FBS, at 37 degrees C, 5% CO2

extract_protocol:
RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
The Illumina mRNASeq protocol involves Oligo(dT) magnetic beads to capture and purify RNAs with polyA tails. The RNA is fragmented into small pieces and the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The resulting double-strand cDNA is used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification being performed to give you a library that is ready to go on the sequencer.

treatment_protocol: The cells were not treated with any drug.

value: colorectal cancer


title: Patient-11

status: Public on May 07 2025

type: SRA

city: Chandigarh

first: Priyanka

last: Srivastava

state: Chandigarh

address: PGIMER, Sector-12

department: Pediatrics

country: India

institute: PGIMER

description: Library name: RS-11

library_source: transcriptomic

data_processing:
The adapter sequences, low-quality bases, and reads shorter than 17 bp were removed using Trim-galore v0.6.6 and fastp program. The QC passed reads were mapped onto indexed human reference genome (GRCh38.p13) using mapper.pl script of miRDeep2 v2.0.1.2. Reads mapped to the reference genome were used to identify miRNAs with miRDeep2 using known and novel miRNA identification parameters. Human mature miRNAs from miRbase v22.1 were used for miRNA prediction. miRNAs with miRDeep score< 1 were excluded from the analysis resulting in total 1,569 novel and 679 known miRNAs. Expression levels of miRNAs were estimated using miRDeep2 quatifiler.pl script. Differential expression analysis was carried out using DESeq2 package after normalizing the data using relative log expression normalization method. miRNAs with absolute log2 fold change ≥ 1 and p-value ≤0.05 were considered significant.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
The total RNA was extracted from the EVs using Total Exosome RNA and Protein Isolation Kit (Cat. 4478545,Invitrogen, CA, USA) using the manufacturer’s protocol. The RNA was quantified using Tape Station System (Agilent Technologies, Santa Clara, USA).
These samples were then processed for sequencing. The miRNA sequencing library was constructed using the QIAseq miRNA Library Kit (Qiagen, Germany). Briefly, to prepare the miRNA library, total RNA of each sample was used. 3′-and 5′-adaptor ligations were followed by cDNA synthesis, PCR amplification, and gel purification. Quantification was done with Qubit (Thermo Fisher, USA), and quality assessment was done using Agilent D1000 ScreenTape System in a 4150 TapeStation System. The libraries were then sequenced using Illumina NovaSeq 6000 platform (Illumina, USA).

tag: tissue

value: blood


title: long-read sequencing of clone 2 of transgenic parasite, of which 7 subtelomeric regions  were deleted.

city: Suita

first: Shiroh

last: Iwanaga

state: Osaka

address: 3-1 Yamadaoka

department: Molecular protozoology

country: Japan

institute: RIMD, Osaka University

description: Library name: Uni7a2-2

library_source: genomic

data_processing:
The obtained long reads were mapped on the genomic sequence, of which version 62, deposited at PlasmoDB
The obtained long reads were mapped on the reference genome sequence of P. falcparum strain, which was downloaded from PlasmoDB62, using minimap2.
The generated sam files were converted to bam file using samtools.
The number of reads for gene at subtelomeric regions was tallied using featureCounts with generated bam files.
Assembly: PlasmoDB-62_Pfalciparum3D7
Supplementary files format and content: The bam formatted files of mapped read.

molecule: genomic DNA

organism: Plasmodium falciparum 3D7

source_name: Aseuxal blood stage

growth_protocol: P. falciparum was cultured with human RBCs (type O blood, hematocrit 2%) in complete medium (CM). This medium consisted of RPMI-1640 medium containing 10% human serum and 10% AlbuMAXI (Invitrogen), along with 25 mM HEPES, 0.225% sodium bicarbonate, and 0.38 mM hypoxanthine. Additionally, the medium was supplemented with 10 mg/ml gentamicin. Cultures were maintained under an atmosphere containing 90% N2, 5% CO2, and 5% O2.

extract_protocol:
PlasmoDB-62_Pfalciparum3D7
The libraries were made using SQK-LSK109 kit, which is provided by Oxford nanopore technolobies, according to the manufacture instruction.

treatment_protocol: Subtelomeric regions were deleted by combining AsCas12a-ultra with telomere helaing.

tag: strain

tag: cell type

value: Aseuxal blood stage

tag: batch


title: long-read sequencing of clone 1 of transgenic parasite, of which 7 subtelomeric regions  were deleted.

description: Library name: Uni7a2-1


title: long-read sequencing of P. falciparum 3D7 used as wild-type parasite

description: Library name: Wt_LD8


title: long-read sequencing of transgenic parasite, of which subtelomeric regions of chromosome 2 were deleted.

description: Library name: Sub-del-4-1-LD1


title: 9_RNASE1_sg2_B

country: USA

description: Library name: 9_RNASE1_sg2_B

tag: cell line


title: Patient-9

description: Library name: RS-9


title: Patient-8

description: Library name: RS-8


title: 8_RNASE1_sg1_B

description: Library name: 8_RNASE1_sg1_B


title: Patient-7

description: Library name: RS-7


title: 6_NTC1_B

description: Library name: 6_NTC1_B


title: 5_RNASE1_sg3_A

description: Library name: 5_RNASE1_sg3_A


title: Patient-6

description: Library name: RS-6


title: 7_NTC2_B

description: Library name: 7_NTC2_B


title: 4_RNASE1_sg2_A

description: Library name: 4_RNASE1_sg2_A


title: Patient-3

description: Library name: RS-3


title: Patient-2

description: Library name: RS-2


title: Control 05

description: Library name: C05


title: Control 04

description: Library name: C04


title: 3_RNASE1_sg1_A

description: Library name: 3_RNASE1_sg1_A


title: Patient-1

description: Library name: RS-1


title: Control 03

description: Library name: C03


title: 2_NTC2_A

description: Library name: 2_NTC2_A


title: 1_NTC1_A

description: Library name: 1_NTC1_A


title: Control 02

description: Library name: C02


title: Control 01

description: Library name: C01


title: CO3_effectorCD4

city: Chicago

first: Linghan

last: Mei

state: IL

address: 900 East 57th Street

institute: University of Chicago

description: Library name: CO3

data_processing:
Reads were demultiplexed using BCLconvert (v2.6.0).
Demultiplexed reads were aligned to mouse V/D/J segments and UMI were extracted with MiXCR (v4.3.2).
Assembly: mm10
Supplementary files format and content: .csv: aligned TCR-β chain clones in sample
Library strategy: TCR-Seq

molecule: polyA RNA

organism: Mus musculus

source_name: Colon

extract_protocol:
DAPI⁻, TCRβ⁺, CD8α⁻, CD4⁺, CD62L⁻, CD44⁺ activated CD4⁺ T cells were sorted using a MoFlo Astrios (Beckman) at the Flow Cytometry Core in the UIC Research Resources Center (RRC). Sorted cells were pelleted and lysed in RLT buffer (QIAGEN, 79216) supplemented with 1% β-mercaptoethanol (VWR Chemicals, M131) and immediately stored at -80 oC. Total RNA was extracted using Dynabeads MyOne Silane (Thermo Fisher Scientific, 37002D) with on-bead DNase I treatment (Thermo Fisher Scientific, AM2239) at 37 °C for 20 min to remove genomic DNA. After sequential washes with 80% ethanol, RNA was eluted. RNA quality was confirmed using a Tapestation 4200 (Agilent Technologies).
Reverse transcription, TCR amplification and library preparation were performed using the SMART-seq Mouse TCR kit w/ UMIs (Takara, 634815) according to the manufacturer’s instructions.

value: Colon

value: effector CD4 T cells

tag: genotype

tag: treatment

value: 16-weeks post-gavage with human stool from a healthy donor


title: CO1_effectorCD4

description: Library name: CO1


title: IL3_effectorCD4

description: Library name: IL3

source_name: Ileum

value: Ileum


title: IL4_effectorCD4

description: Library name: IL4


title: CO4_effectorCD4

description: Library name: CO4


title: CO2_effectorCD4

description: Library name: CO2


title: MjHKU4r-CoV-1 S transfected, rep4

city: Shanghai

first: Tianyu

last: Lu

address: No.130, Dongan Road

country: China

institute: Fudan University

description: Library name: Mj_rep4

data_processing:
Raw paired-end fastq reads were filtered by Fastp (0.23.4) discard the adapters and low quality bases. The clean reads obtained were then aligned to the hg19 genome using HISAT2 (2.2.1), followed by reference genome-guided transcriptome assembly and gene expression quantification using StringTie (2.2.3).
Assembly: hg19
Supplementary files format and content: the xlsx file containing raw counts for each sample

source_name: HEK-293T; Caco2

growth_protocol: All cells were grown in DMEM medium containing 10% fetal bovine serum at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424), which yielded > 2 μg of total RNA per sample. RNA quality was examined by 0.8% agarose gel electrophoresis and spectrophotometry. High-quality RNA with a 260/280 absorbance ratio of 1.8-2.2 was used for library construction and sequencing.
Poly (A) RNA is purified from 1 μg total RNA using Dynabeads Oligo (dT) . Then the poly(A) RNA was fragmented and reverse-transcribed to create the cDNA. Amplify cDNA for the synthesis of the second chain of cDNA. Purify cDNA products by AMPure XP system (Beckman Coulter, Beverly, USA). After library construction, library fragments were enriched by PCR amplification and selected according to a fragment size of 350-550 bp. The library was quality-assessed using an Agilent 4200 Bioanalyzer (Agilent, USA).

value: HEK-293T; Caco2

value: human embryonic kidney cells; human colorectal adenocarcinoma cells

value: 293T were transfected with MjHKU4r-CoV-1 S protein and fuse with Caco-2 cells


title: MjHKU4r-CoV-1 S transfected, rep2

description: Library name: Mj_rep2


title: MjHKU4r-CoV-1 S transfected, rep3

description: Library name: Mj_rep3


title: IL2_effectorCD4

description: Library name: IL2


title: MjHKU4r-CoV-1 S transfected, rep1

description: Library name: Mj_rep1


title: IL1_effectorCD4

description: Library name: IL1


title: Patient-4

description: Library name: RS-4


title: SARS-CoV-2 S transfected, the positive control, rep4

description: Library name: KP2_rep4

value: 293T were transfected with SARS-CoV-2 KP.2 variant S protein and fuse with Caco-2 cells


title: BR4_effectorCD4

description: Library name: BR4

source_name: Brain

value: Brain


title: SARS-CoV-2 S transfected, the positive control, rep3

description: Library name: KP2_rep3


title: SARS-CoV-2 S transfected, the positive control, rep2

description: Library name: KP2_rep2


title: BR3_effectorCD4

description: Library name: BR3


title: SARS-CoV-2 S transfected, the positive control, rep1

description: Library name: KP2_rep1


title: BR1_effectorCD4

description: Library name: BR1


title: BR2_effectorCD4

description: Library name: BR2


title: HKU4 S transfected, the negative control, rep4

description: Library name: H_rep4

value: 293T were transfected with HKU4 S protein and fuse with Caco-2 cells


title: HKU4 S transfected, the negative control, rep3

description: Library name: H_rep3


title: HKU4 S transfected, the negative control, rep2

description: Library name: H_rep2


title: JunctionalZone/Decidua, FCG_XXM_Control, Rep5

city: Burnaby

first: Julian

last: Christians

state: BC

address: 8888 University Drive

department: Biological Sciences

country: Canada

institute: Simon Fraser University

description:
Library name: F8B
RIN: 9.5
TranscriptPercent: 89.2
InputReads: 41485032
UniqueReads: 26445704
MappedReads: 40427737
TotalBases: 2425290877
MappedBases: 1182769529
Q30Bases: 2282419754

data_processing:
Read sequences were aligned to the Mus musculus (mm10) reference sequence using DRAGEN RNA app on Basespace Sequence Hub.
Assembly: mm10
Supplementary files format and content: Tab-delimited quant.sf files include TPM values for each sample.

source_name: placenta (junctional zone/decidua)

extract_protocol:
We homogenized placental tissue using zirconium oxide beads (0.5 mm, ZROB05, Next Advance) and a mechanical shaker (MM300, Retsch). Placental mRNA was extracted using the Qiagen RNeasy Plus kit, including gDNA Eliminator columns to remove genomic DNA, according to manufacturer instructions.
Samples were prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina). Sequencing was performed on the Illumina NextSeq2000 with Paired End 59bp × 59bp reads, with 20 million paired end reads per sample.

value: placenta (junctional zone/decidua)

tag: group

value: XXM

value: Control


title: JunctionalZone/Decidua, FCG_XXF_Control, Rep5

description:
Library name: F9A
RIN: 9.5
TranscriptPercent: 90.8
InputReads: 60386468
UniqueReads: 31802984
MappedReads: 58380414
TotalBases: 3519521575
MappedBases: 1705512655
Q30Bases: 3289946448

value: XXF


title: HKU4 S transfected, the negative control, rep1

description: Library name: H_rep1


title: JunctionalZone/Decidua, FCG_XYF_FoodRest, Rep5

description:
Library name: F87A
RIN: 9.9
TranscriptPercent: 89
InputReads: 59046510
UniqueReads: 31078528
MappedReads: 57747728
TotalBases: 3451855392
MappedBases: 1689176718
Q30Bases: 3265720870

value: XYF

value: Food restriction


title: JunctionalZone/Decidua, WT_M_Control, Rep5

description:
Library name: F84A
RIN: 9.1
TranscriptPercent: 89.8
InputReads: 54792872
UniqueReads: 32019180
MappedReads: 53249135
TotalBases: 3197947972
MappedBases: 1556391185
Q30Bases: 2996576619

value: M


title: 786--O cell,Si-PARP1-2

city: Nanchang

first: Xiangpeng

last: Zhan

state: None Selected

institute: Department of Emergency, The First Affiliated Hospital of Nanchang University

description:
Library name: Sample 8
786-O cells transfected with PARP1 shRNA

data_processing:
Raw sequencing reads in FASTQ format were quality-checked using FastQC (v0.11.9). Adapter sequences and low-quality bases were trimmed using Trim Galore (v0.6.6). Cleaned reads were aligned to the Homo sapiens reference genome (GRCh38) using STAR aligner (v2.7.9a) with default parameters. Gene-level read counts were generated using featureCounts (v2.0.1) from the Subread package, based on GENCODE annotation release [e.g., v38]. Normalization and differential expression analysis were performed using DESeq2 (v1.30.0) in R (v4.0.3). Only genes with counts per million (CPM) >1 in at least two samples were retained for downstream analysis.Expression values are reported as raw counts and normalized counts FPKM as applicable.
Assembly: GRCh38 (Genome Reference Consortium Human Build 38)
Supplementary files format and content: The processed data file is provided in the directory 'GeneExpression' and contains one file: all.fpkm_anno.xls. This is a tab-delimited text file in XLS format, where each row represents a gene. The file includes gene identifiers (e.g., Ensembl IDs or gene symbols), annotation information, and FPKM values for each sample (Parental 786-O, TRIM28 knockdown, and PARP1 knockdown). Raw sequencing data in FASTQ format (compressed as .fq.gz) are provided separately in the 'Rawdata' directory.

source_name: kidney

extract_protocol:
Total RNA was extracted from Parental 786-O renal carcinoma cells, TRIM28 knockdown cells, and PARP1 knockdown cells using the  TRIzol Reagent (Invitrogen)] according to the manufacturer’s instructions. Briefly, cells were lysed directly in culture dishes with TRIzol reagent, followed by phase separation with chloroform. The aqueous phase was collected, and RNA was precipitated with isopropanol, washed with 75% ethanol, and dissolved in RNase-free water. RNA concentration and purity were assessed using a NanoDrop spectrophotometer, and RNA integrity was confirmed by agarose gel electrophoresis.
mRNA-seq libraries were prepared using the  NEBNext Ultra II Directional RNA Library Prep Kit for Illumina  following the manufacturer's protocol. Briefly, poly(A)+ RNA was enriched from total RNA using oligo(dT) magnetic beads. The mRNA was then fragmented and reverse-transcribed into first-strand cDNA using random primers and reverse transcriptase. Second-strand cDNA synthesis was performed to generate double-stranded cDNA. End repair, A-tailing, and adapter ligation were carried out, followed by PCR amplification to enrich the libraries. The final libraries were purified and quality-checked using Agilent Bioanalyzer 2100. Libraries were then quantified and pooled for sequencing on an Illumina NovaSeq 6000 platform.

value: kidney

value: epithelial cell

value: PARP1 knockdown

value: PARP1 siRNA


title: JunctionalZone/Decidua, FCG_XYM_FoodRest, Rep5

description:
Library name: F85A
RIN: 9.6
TranscriptPercent: 91
InputReads: 57164626
UniqueReads: 35572401
MappedReads: 54284996
TotalBases: 3342240478
MappedBases: 1588330522
Q30Bases: 3160844886

value: XYM


title: JunctionalZone/Decidua, FCG_XXF_Control, Rep4

description:
Library name: F8A
RIN: 9.6
TranscriptPercent: 86.9
InputReads: 56073680
UniqueReads: 33751694
MappedReads: 54731241
TotalBases: 3278145705
MappedBases: 1601381670
Q30Bases: 3069003815


title: JunctionalZone/Decidua, FCG_XXF_Control, Rep3

description:
Library name: F78B
RIN: 8.5
TranscriptPercent: 90.6
InputReads: 62388972
UniqueReads: 37002138
MappedReads: 60807126
TotalBases: 3644969375
MappedBases: 1778479606
Q30Bases: 3412427731


title: JunctionalZone/Decidua, FCG_XYM_Control, Rep5

description:
Library name: F78A
RIN: 9.6
TranscriptPercent: 88.8
InputReads: 54252780
UniqueReads: 31711496
MappedReads: 52856443
TotalBases: 3171468523
MappedBases: 1546208282
Q30Bases: 2972425522


title: 786--O cell,Si-TRIM28-3

address: The First Affiliated Hospital of Nanchang University

description:
Library name: Sample 6
786-O cells transfected with TRIM28 shRNA

value: TRIM28 knockdown

value: TRIM28 siRNA


title: 786--O cell,Si-TRIM28-1

description:
Library name: Sample 4
786-O cells transfected with TRIM28 shRNA


title: 786--O cell,Si-PARP1-1

description:
Library name: Sample 7
786-O cells transfected with PARP1 shRNA


title: JunctionalZone/Decidua, FCG_XXM_Control, Rep4

description:
Library name: F82A
RIN: 8.8
TranscriptPercent: 90.4
InputReads: 48507842
UniqueReads: 30100205
MappedReads: 46953628
TotalBases: 2833429513
MappedBases: 1373150861
Q30Bases: 2651466168


title: 786--O cell,Si-TRIM28-2

description:
Library name: Sample 5
786-O cells transfected with TRIM28 shRNA


title: JunctionalZone/Decidua, FCG_XXM_FoodRest, Rep5

description:
Library name: F74A
RIN: 8.6
TranscriptPercent: 90.3
InputReads: 51579028
UniqueReads: 31126104
MappedReads: 50442590
TotalBases: 3015908990
MappedBases: 1475843243
Q30Bases: 2847097865


title: 786--O cell,Si-PARP1-3

description:
Library name: Sample 9
786-O cells transfected with PARP1 shRNA


title: JunctionalZone/Decidua, WT_F_Control, Rep5

description:
Library name: F76A
RIN: 8.9
TranscriptPercent: 90.1
InputReads: 57101914
UniqueReads: 34449424
MappedReads: 55670787
TotalBases: 3339517361
MappedBases: 1628893387
Q30Bases: 3123086308

value: F


title: 786--O cell,Si-Control-3

description:
Library name: Sample 3
786-O cells transfected with negative control shRNA

value: wild type

value: negative control siRNA


title: JunctionalZone/Decidua, FCG_XXM_Control, Rep3

description:
Library name: F70B
RIN: 10
TranscriptPercent: 88.4
InputReads: 57654138
UniqueReads: 34165435
MappedReads: 55037095
TotalBases: 3369114380
MappedBases: 1610289534
Q30Bases: 3180676276

value: placenta (junctional zone/decidua)


title: JunctionalZone/Decidua, FCG_XYF_Control, Rep5

description:
Library name: F6A
RIN: 9.1
TranscriptPercent: 90.6
InputReads: 42899866
UniqueReads: 26116154
MappedReads: 41508712
TotalBases: 2506493699
MappedBases: 1214368071
Q30Bases: 2348440460


title: SW480 cells, WT4-3

city: Jining

first: Wenzhi

last: Shen

address: No. 133 Hehua Road

institute: Jining Medical University

description: Library name: Sample 6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Differential expression analysis of two conditions/groups was performed using the DESeq2.
Assembly: mm10
Supplementary files format and content: count, FPKM values for each Sample

source_name: SW480 cells

growth_protocol: SW480 cancer cancer cells were cultured in DMEM medium supplemented with 10% FBS and 1% L-Glutamine

extract_protocol:
The total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, 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 Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: DMSO and mitochondrial probe molecule 4 (WT4, named MPM-1 in the manuscript) treated the SW480 cells for 24h.

value: SW480 cells

value: Cancer cells

value: WT

value: WT4 (MPM-1)


title: 786--O cell, Si-Control-2

description:
Library name: Sample 2
786-O cells transfected with negative control shRNA


title: JunctionalZone/Decidua, FCG_XYF_Control, Rep4

description:
Library name: F66B
RIN: 7.9
TranscriptPercent: 91.8
InputReads: 44050684
UniqueReads: 27779892
MappedReads: 43049923
TotalBases: 2572749242
MappedBases: 1258978662
Q30Bases: 2409670137

value: XYF

value: Control


title: SW480 cells, WT4-2

description: Library name: Sample 5


title: JunctionalZone/Decidua, FCG_XYM_FoodRest, Rep4

description:
Library name: F64A
RIN: 9.7
TranscriptPercent: 92.2
InputReads: 54243424
UniqueReads: 27969152
MappedReads: 50177237
TotalBases: 3169716274
MappedBases: 1468218685
Q30Bases: 2993032501

value: Food restriction


title: SW480 cells, WT4-1

description: Library name: Sample 4


title: SW480 cells, DMSO3

description: Library name: Sample 3

value: DMSO


title: JunctionalZone/Decidua, WT_F_Control, Rep4

description:
Library name: F60A
RIN: 9.7
TranscriptPercent: 91.5
InputReads: 54724454
UniqueReads: 28521291
MappedReads: 51178262
TotalBases: 3198426125
MappedBases: 1497317090
Q30Bases: 3023512737


title: JunctionalZone/Decidua, FCG_XYM_FoodRest, Rep3

description:
Library name: F5B
RIN: 9.2
TranscriptPercent: 91.4
InputReads: 60170978
UniqueReads: 37123045
MappedReads: 57958696
TotalBases: 3515803008
MappedBases: 1695464633
Q30Bases: 3319830525


title: SW480 cells, DMSO2

description: Library name: Sample 2


title: SW480 cells, DMSO1

description: Library name: Sample 1


title: JunctionalZone/Decidua, FCG_XXF_FoodRest, Rep5

description:
Library name: F5A
RIN: 9.5
TranscriptPercent: 89.7
InputReads: 45880670
UniqueReads: 24529101
MappedReads: 44701834
TotalBases: 2680963783
MappedBases: 1307445953
Q30Bases: 2528544040

value: XXF


title: JunctionalZone/Decidua, FCG_XYM_Control, Rep4

description:
Library name: F59A
RIN: 9.1
TranscriptPercent: 89.1
InputReads: 56419618
UniqueReads: 35305499
MappedReads: 54935174
TotalBases: 3296269921
MappedBases: 1606421728
Q30Bases: 3089088871


title: JunctionalZone/Decidua, FCG_XXM_Control, Rep2

description:
Library name: F59B
RIN: 9.4
TranscriptPercent: 90.6
InputReads: 44696314
UniqueReads: 25433977
MappedReads: 43396155
TotalBases: 2610113171
MappedBases: 1268734407
Q30Bases: 2440782331

value: XXM


title: JunctionalZone/Decidua, WT_M_FoodRest, Rep5

description:
Library name: F58A
RIN: 9.6
TranscriptPercent: 90
InputReads: 47338984
UniqueReads: 28961847
MappedReads: 46288891
TotalBases: 2768073359
MappedBases: 1354212243
Q30Bases: 2591155947

value: M


title: NR8, Nonrecurrent 8

city: Birmingham

first: Kevin

middle: James

last: Maroney

state: Alabama

address: 1001 20th Street S, 1501, Ascend Apartments

institute: University of Alabama at Birmingham

description: Library name: NR8

data_processing:
Raw FASTQ sequences were first trimmed to remove adapter sequences to a minimum sequence length of 75 bp with a mean Phred score cutoff of 30 to ensure only high-quality reads were used for alignment and counting using Trim Galore as previously described
Input RNA-seq reads were aligned to the GRCh38 human reference genome using HISAT2 software
Transcript abundance was measured using featureCounts and the matrix of counts served as the unit for differentially expressed gene (DEG), which was conducted using EdgeR package offered through Bioconductor
Combination of negative binomial distribution, Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests were used to determine whether statistically significant differences exist between counts of one group of sequencing data to another through TMM normalized count matrices, controlling for sequencing depth between samples and datasets
Assembly: GRCh38 human reference genome
Supplementary files format and content: RPKM and EdgeR Analysis.xslx file contains processed reads per kilobase exon per million mapped reads (RPKM) expression value for each gene and sample, gene type, alongside EdgeR calculated Recurrent vs Nonrecurrent log fold change, log counts per million, p value significance change, and false discovery rate corrected p value (FDR) for each gene

source_name: Squamous cellular carcinoma of the anus

extract_protocol:
RNA was purified from FFPE tissues with the Quick-DNA/RNA FFPE kit (R1009, Zymo Research). The concentration of RNA was assessed with a Nanodrop spectrophotometer.
A 20 uL volume of at least 400 ng RNA was used for library creation. Libraries were generated with the SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio USA)

value: Squamous cellular carcinoma of the anus

value: Mixed

value: Nonrecurrent


title: NR7, Nonrecurrent 7

description: Library name: NR7


title: JunctionalZone/Decidua, WT_F_FoodRest, Rep5

description:
Library name: F55A
RIN: 9.2
TranscriptPercent: 89.5
InputReads: 51753102
UniqueReads: 30473460
MappedReads: 49987873
TotalBases: 3025227171
MappedBases: 1462302474
Q30Bases: 2835299057

value: F


title: NR6, Nonrecurrent 6

description: Library name: NR6


title: JunctionalZone/Decidua, WT_M_Control, Rep4

description:
Library name: F57A
RIN: 9.7
TranscriptPercent: 90.8
InputReads: 57054358
UniqueReads: 28816163
MappedReads: 54009856
TotalBases: 3333624363
MappedBases: 1580523335
Q30Bases: 3135216155


title: NR5, Nonrecurrent 5

description: Library name: NR5


title: NR3, Nonrecurrent 3

description: Library name: NR3


title: 786-O cell, Si-Control-1

description:
Library name: Sample 1
786-O cells transfected with negative control shRNA

value: kidney

value: epithelial cell

value: wild type

value: negative control siRNA


title: NR4, Nonrecurrent 4

description: Library name: NR4


title: JunctionalZone/Decidua, FCG_XXF_Control, Rep2

description:
Library name: F52A
RIN: 9.4
TranscriptPercent: 90.6
InputReads: 49581604
UniqueReads: 27708927
MappedReads: 48141372
TotalBases: 2896877899
MappedBases: 1407756139
Q30Bases: 2709777931

value: placenta (junctional zone/decidua)


title: JunctionalZone/Decidua, FCG_XYM_FoodRest, Rep2

description:
Library name: F54A
RIN: 9.5
TranscriptPercent: 88
InputReads: 60612574
UniqueReads: 37083587
MappedReads: 58668700
TotalBases: 3545266000
MappedBases: 1717468778
Q30Bases: 3329303243

value: XYM


title: NR2, Nonrecurrent 2

description: Library name: NR2


title: JunctionalZone/Decidua, FCG_XYM_Control, Rep3

description:
Library name: F53B
RIN: 9.3
TranscriptPercent: 90.2
InputReads: 48132594
UniqueReads: 23976832
MappedReads: 46190067
TotalBases: 2811396987
MappedBases: 1350886996
Q30Bases: 2627572606


title: NR1, Nonrecurrent 1

description: Library name: NR1


title: JunctionalZone/Decidua, FCG_XYF_FoodRest, Rep4

description:
Library name: F51B
RIN: 9.8
TranscriptPercent: 90.4
InputReads: 62259648
UniqueReads: 35852103
MappedReads: 59881514
TotalBases: 3640535442
MappedBases: 1751707606
Q30Bases: 3441437392

value: XYF


title: JunctionalZone/Decidua, FCG_XYF_FoodRest, Rep3

description:
Library name: F48A
RIN: 8.5
TranscriptPercent: 90.3
InputReads: 49420978
UniqueReads: 28222554
MappedReads: 48027254
TotalBases: 2888846922
MappedBases: 1404890806
Q30Bases: 2726901314


title: JunctionalZone/Decidua, FCG_XXM_FoodRest, Rep4

description:
Library name: F50A
RIN: 9.4
TranscriptPercent: 88.1
InputReads: 48328174
UniqueReads: 28691314
MappedReads: 46982976
TotalBases: 2825960238
MappedBases: 1374816113
Q30Bases: 2666994980


title: NR9, Nonrecurrent 9

description: Library name: NR9


title: JunctionalZone/Decidua, FCG_XXM_Control, Rep1

description:
Library name: F49B
RIN: 9.3
TranscriptPercent: 87.6
InputReads: 52182872
UniqueReads: 32269114
MappedReads: 50923714
TotalBases: 3049650469
MappedBases: 1489939982
Q30Bases: 2852136904

value: Control


title: R1, Recurrent 1

description: Library name: R1

value: Recurrent


title: JunctionalZone/Decidua, WT_M_FoodRest, Rep4

description:
Library name: F42A
RIN: 9.3
TranscriptPercent: 89.8
InputReads: 52606538
UniqueReads: 30726692
MappedReads: 51117970
TotalBases: 3073076291
MappedBases: 1495152751
Q30Bases: 2873223241

value: Food restriction


title: JunctionalZone/Decidua, FCG_XYF_Control, Rep3

description:
Library name: F46B
RIN: 9.5
TranscriptPercent: 90.4
InputReads: 59620704
UniqueReads: 31373513
MappedReads: 57671519
TotalBases: 3482420606
MappedBases: 1686523840
Q30Bases: 3258729699


title: JunctionalZone/Decidua, FCG_XYF_FoodRest, Rep2

description:
Library name: F41B
RIN: 9.8
TranscriptPercent: 90.6
InputReads: 60731272
UniqueReads: 34395535
MappedReads: 57553354
TotalBases: 3551305765
MappedBases: 1684021886
Q30Bases: 3359719068


title: CAR-iNKT cells cocultured with tumor cells and iMRAS-TCR seq

city: Los Angeles

first: Youcheng

last: Yang

state: California

address: 430 Westwood Plaza, 5121 Engineering V, Box 951600, Attn (PI NAME): Li Lab

department: Bioengineering

institute: UCLA

description:
Library name: Sample_01_TCR
10X Genomics

data_processing:
For cell clustering and annotation, the merged digital expression matrix generated by Cellranger was analyzed using an R package Seurat (v.4.0.0) following the official website guidelines. Briefly, after filtering the low-quality cells, the expression matrix was normalized using NormalizeData function, followed by selecting top 2,000 most variable genes across datasets using FindVariableFeatures and SelectIntegrationFeatures functions. To correct the batch effect, FindIntegrrationAnchors and IntegrateData functions were used based on the selected feature genes. The corrected dataset was subjected to standard Seurat workflow for dimension reduction and clustering. In this study, clusters of therapeutic cells were manually merged and annotated based on gene signatures reported from Human Protein Atlas (proteinatlas.org) and previous studies, and clusters of mouse immune cells were merged and annotated based on the immune lineage markers. AddModuleScore was used to calculate module scores of each list of gene signatures, and FeaturePlot function was used to visualize the expression of each signature in the UMAP plots. For gene set enrichment analysis (GSEA), clusterProfiler packages were used to calculate the enrichment scores of each cluster in the signature gene list.
hg38
Assembly: matrix.mtx.gz: Matrix Market Format, with rows representing genes and columns representing cells. barcode.tsv.gz: Tab-separated values, where each row represents a unique identifier for a cell. features.tsv.gz: Tab-separated values, where each row represents a gene.
Supplementary files format and content: H5 files, filtered HDF5 file after alignment
Library strategy: TCR-Seq

source_name: CAR-iNKT

growth_protocol: Human iNKT and CAR-iNKT cells were generated from healthy donor-derived peripheral blood mononuclear cells (PBMCs), which were provided by the UCLA/CFAR Virology Core Laboratory without identifying information, in compliance with federal and state regulations. Healthy donor PBMCs were MACS-sorted using Anti-iNKT Microbead (Miltenyi Biotech; cat. no. 130-094-842) labeling to enrich human iNKT cells. A starting quantity of 5 x 108 PBMCs is typically used to isolate iNKT cells. Donor-matched PBMCs were loaded with αGC (by culturing 1 x 107 PBMCs in 5 ml C10 medium containing 5 mg/ml αGC for 1 hour), irradiated at 6,000 rads, then used to stimulate iNKT cells (denoted as αGC/PBMCs). The sorted iNKT cells were then stimulated with donor-matched irradiated αGC/PBMCs at a ratio of 1:1 and cultured in C10 medium supplemented with human IL-7 (10 ng/mL) and IL-15 (10 ng/mL) for 2–3 weeks. To generate iNKT-FG cells, Lenti/FG lentivector was used to transduce iNKT cells 2 days post αGC/PBMC stimulation. At 72 hours post-lentivector transduction, FG expression in engineered iNKT cells was confirmed by flow cytometry, identifying GFP+ cells. The resulting iNKT-FG cells were then further purified using FACS. To generate CD19-targeting CAR-iNKT cells, Lenti/CAR19 lentivector was used to transduce iNKT cells 2 days post αGC/PBMC stimulation. At 72 hours post-lentivector transduction, CAR expression in engineered iNKT cells was confirmed by flow cytometry, identifying CAR+ cells. The resulting CAR-iNKT cells were then further purified using FACS. To generate CAR-iNKT-FG cells, Lenti/FG and Lenti/CAR19 lentivectors were used to transduce iNKT cells 2 days post αGC/PBMC stimulation. At 72 hours post-lentivector transduction, CAR and FG expression were confirmed by flow cytometry, identifying CAR+GFP+ cells. The resulting CAR-iNKT-FG cells were then further purified using FACS.

extract_protocol:
Human CAR-iNKT cell samples were FACS sorted (identified as iNKT TCR+CD3+ cells) and delivered to the UCLA TCGB Core for library construction and scRNA-seq. Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics)
Libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies)

value: CAR-iNKT


title: CAR-iNKT cells cocultured with tumor cells-TCR seq

description:
Library name: Sample_02_TCR
10X Genomics


title: JunctionalZone/Decidua, FCG_XXM_FoodRest, Rep3

description:
Library name: F3A
RIN: 9.7
TranscriptPercent: 85.8
InputReads: 47310818
UniqueReads: 27644049
MappedReads: 46374001
TotalBases: 2766695940
MappedBases: 1356947966
Q30Bases: 2613236009

value: XXM


title: NCI-H2030, miR-494-3p AS

city: Aichi

first: Hisanori

last: Isomura

address: 1, Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya

institute: Nagoyacityuniversity

description: Library name: Sample2

data_processing:
RNA-seq data were analyzed using Salmon17.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes TPM for each samples

extract_protocol:
Total RNA was isolated following manufacturer’s instructions using RNeasy Mini Kit (Qiagen, 74104)
An RNA-seq library was prepared using the NEBNext UltraII Directional RNA Library Prep Kit for Illumina  (New England Biolabs, Ipswich, Massachusetts, USA) according to the manufacturer’s protocols.

value: lung adenocarcinoma

value: treated with miR-494-3p AS


title: JunctionalZone/Decidua, FCG_XYM_Control, Rep2

description:
Library name: F33B
RIN: 10
TranscriptPercent: 90.8
InputReads: 55427398
UniqueReads: 33540021
MappedReads: 52837776
TotalBases: 3240057195
MappedBases: 1545793352
Q30Bases: 3057521427


title: JunctionalZone/Decidua, WT_F_Control, Rep3

description:
Library name: F39A
RIN: 9.4
TranscriptPercent: 92
InputReads: 44986168
UniqueReads: 20092401
MappedReads: 42283306
TotalBases: 2617120091
MappedBases: 1237256338
Q30Bases: 2448562203


title: Hs578T, REPOP, RNA-seq, replicate 2

city: Budapest

first: Andras

last: Furedi

state: HU

address: Magyar tudosok krt 2

department: Molecular Life Sciences

country: Hungary

institute: HUN-REN RCNS

description: Library name: Hs578T-repop-2

data_processing:
The raw reads were preprocessed with Fastq Toolkit (v2.2.5) on Basespace Sequence Hub (Illumina), to remove low quality bases (<Q30) on 5' and 3' ends, trimming adapters (using sequences AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT), and filter reads with mean read quality less than Q30. Splice aware aligner STAR (v2.7.10) [BR ref 1] was used to map the filtered, trimmed reads to genome assembly hg38. Gene counts were obtained by Subread's (v2.0.3) Feature counts function [BR ref 2]. Post-processing on the count matrix was executed using the R language (v4.3.3).
Assembly: hg38
Supplementary files format and content: The count matrix file is a tab delimited txt file. The first column contains the Ensembl gene IDs, and the first row contains the sample IDs. The remaining cells contain the raw read counts for each gene in each sample.

source_name: breast

growth_protocol: Cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and 5 mmol/L glutamine, and 50 units/mL penicillin and streptomycin at 37 °C with 5% CO2

extract_protocol:
MCF7, T47D, MDA-MB-231 and Hs578T TIS cells were harvested at day 12, HFF TIS cells were harvested at day 24. CTR and REPOP cells were harvested at ~80% confluency. Cells were homogenized in TRIzol™ Reagent (Thermo Fisher Scientific). Total RNA was extracted from samples using Direct-zol® MiniPrep kit (Zymo Research) following the manufacturer's instructions. To prevent DNA contamination, an in-column DNAse I treatment was performed.  The RNA concentration was determined by using the Qubit RNA HS Assay Kit on the Qubit 3.0 Fluorometer (Thermo Fisher Scientific). Quality CTR was assessed by Labchip GX Touch HT instrument on DNA 5K/RNA/CZE Chip (Perkin Elmer) with RNA Pico Sensitivity Assay Reagents (Perkin Elmer).
NextFlex PolyA beads 2.0 kit and NextFlex Rapid Directional RNA-seq Kit 2.0 with UDIs (Perkin Elmer) were used for mRNA capture and strand-specific library preparation. The library quantities were measured by Quant-iT 1x dsDNA HS Assay kit (Thermo Fisher Scientific) with Fluostar Omega (BMG Labtech). The fragment size distribution of the libraries was determined by capillary electrophoresis on Labchip GX Touch Nucleic Acid Analyzer on XMark HT chip by using DNA NGS 3k Assay kit (Perkin Elmer). Pooled libraries were sequenced with 50M 150 bp paired-end reads on NovaSeq 6000 platform (Illumina).

treatment_protocol: For TIS induction cells were treated with 120 nM (MCF7), 70 nM (T47D), 150 nM (MDA-MB-231), 200 nM (Hs578T), 210 nM (HFF) DOX and incubated for 5 days. After five days of incubation, treated cells were washed with pre-warmed PBS and the medium was renewed. MCF7, T47D, MDA-MB-231 and Hs578T plates remained in the incubator for seven days to ensure that the cells had become senescent. HFF plates remained in the incubator for 19 days with medium change every week.

value: breast

tag: sample group

value: REPOP


title: JunctionalZone/Decidua, WT_M_Control, Rep3

description:
Library name: F37A
RIN: 9.5
TranscriptPercent: 87.5
InputReads: 50221146
UniqueReads: 29064587
MappedReads: 49888915
TotalBases: 2935749555
MappedBases: 1459796561
Q30Bases: 2769144291

value: M


title: NCI-H2030, SC

description: Library name: Sample 1

value: treated with SC


title: R3, Recurrent 3

description: Library name: R3

value: Squamous cellular carcinoma of the anus

value: Mixed


title: R2, Recurrent 2

description: Library name: R2


title: MDA-MB-231, REPOP, RNA-seq, replicate 4

description: Library name: MDA-MB-231-repop-4

value: triple-negative breast cancer


title: JunctionalZone/Decidua, WT_F_FoodRest, Rep4

description:
Library name: F36A
RIN: 8.7
TranscriptPercent: 90.2
InputReads: 55148194
UniqueReads: 33025757
MappedReads: 54035763
TotalBases: 3224207912
MappedBases: 1580881621
Q30Bases: 3023903106

value: placenta (junctional zone/decidua)

value: F


title: JunctionalZone/Decidua, WT_F_FoodRest, Rep3

description:
Library name: F31A
RIN: 9.6
TranscriptPercent: 91.6
InputReads: 49669234
UniqueReads: 31036284
MappedReads: 48534830
TotalBases: 2901772819
MappedBases: 1419341794
Q30Bases: 2718111302


title: Hs578T, REPOP, RNA-seq, replicate 3

description: Library name: Hs578T-repop-3

value: epithelial cell


title: Hs578T, REPOP, RNA-seq, replicate 1

description: Library name: Hs578T-repop-1


title: JunctionalZone/Decidua, WT_M_FoodRest, Rep3

description:
Library name: F32A
RIN: 9.7
TranscriptPercent: 89.9
InputReads: 51271680
UniqueReads: 27394820
MappedReads: 49653235
TotalBases: 2996174327
MappedBases: 1452032807
Q30Bases: 2803495957


title: JunctionalZone/Decidua, FCG_XXM_FoodRest, Rep2

description:
Library name: F29B
RIN: 9.3
TranscriptPercent: 89.8
InputReads: 50960056
UniqueReads: 30606034
MappedReads: 50236373
TotalBases: 2979738896
MappedBases: 1469733517
Q30Bases: 2815687583


title: JunctionalZone/Decidua, FCG_XXF_FoodRest, Rep3

description:
Library name: F29A
RIN: 9.4
TranscriptPercent: 88.7
InputReads: 58516934
UniqueReads: 35834002
MappedReads: 57193137
TotalBases: 3421283215
MappedBases: 1673299109
Q30Bases: 3204440626

value: XXF


title: CAR-iNKT cells cocultured with tumor cells

description:
Library name: Sample_02
10X Genomics

library_source: transcriptomic single cell

data_processing:
For cell clustering and annotation, the merged digital expression matrix generated by Cellranger was analyzed using an R package Seurat (v.4.0.0) following the official website guidelines. Briefly, after filtering the low-quality cells, the expression matrix was normalized using NormalizeData function, followed by selecting top 2,000 most variable genes across datasets using FindVariableFeatures and SelectIntegrationFeatures functions. To correct the batch effect, FindIntegrrationAnchors and IntegrateData functions were used based on the selected feature genes. The corrected dataset was subjected to standard Seurat workflow for dimension reduction and clustering. In this study, clusters of therapeutic cells were manually merged and annotated based on gene signatures reported from Human Protein Atlas (proteinatlas.org) and previous studies, and clusters of mouse immune cells were merged and annotated based on the immune lineage markers. AddModuleScore was used to calculate module scores of each list of gene signatures, and FeaturePlot function was used to visualize the expression of each signature in the UMAP plots. For gene set enrichment analysis (GSEA), clusterProfiler packages were used to calculate the enrichment scores of each cluster in the signature gene list.
hg38
Assembly: matrix.mtx.gz: Matrix Market Format, with rows representing genes and columns representing cells. barcode.tsv.gz: Tab-separated values, where each row represents a unique identifier for a cell. features.tsv.gz: Tab-separated values, where each row represents a gene.
Supplementary files format and content: H5 files, filtered HDF5 file after alignment


title: T47D, REPOP, RNA-seq, replicate 2

description: Library name: T47D-repop-2


title: CAR-iNKT cells cocultured with tumor cells and iMRAS

description:
Library name: Sample_01
10X Genomics


title: JunctionalZone/Decidua, FCG_XYF_FoodRest, Rep1

description:
Library name: F28A
RIN: 9.5
TranscriptPercent: 88.5
InputReads: 47362120
UniqueReads: 28234727
MappedReads: 46515241
TotalBases: 2769080854
MappedBases: 1360994239
Q30Bases: 2602424111

value: XYF


title: T47D, REPOP, RNA-seq, replicate 3

description: Library name: T47D-repop-3


title: T47D, REPOP, RNA-seq, replicate 1

description: Library name: T47D-repop-1


title: MDA-MB-231, REPOP, RNA-seq, replicate 1

description: Library name: MDA-MB-231-repop-1


title: JunctionalZone/Decidua, WT_M_FoodRest, Rep2

description:
Library name: F27A
RIN: 9.9
TranscriptPercent: 87.3
InputReads: 61540540
UniqueReads: 32975008
MappedReads: 59793453
TotalBases: 3597818375
MappedBases: 1749274894
Q30Bases: 3368342395

value: Food restriction


title: MCF7, REPOP, RNA-seq, replicate 3

description: Library name: MCF7-repop-3

value: human adenocarcinoma cells


title: JunctionalZone/Decidua, WT_F_Control, Rep2

description:
Library name: F34A
RIN: 8.9
TranscriptPercent: 89
InputReads: 54787460
UniqueReads: 34747697
MappedReads: 53627006
TotalBases: 3204069496
MappedBases: 1569185936
Q30Bases: 2997447803

value: Control


title: JunctionalZone/Decidua, FCG_XYM_Control, Rep1

description:
Library name: F26B
RIN: 8.6
TranscriptPercent: 88.3
InputReads: 52649692
UniqueReads: 33676365
MappedReads: 51442637
TotalBases: 3076724004
MappedBases: 1505117443
Q30Bases: 2878324040

value: XYM


title: JunctionalZone/Decidua, FCG_XYF_Control, Rep2

description:
Library name: F26A
RIN: 9.2
TranscriptPercent: 90.1
InputReads: 53839508
UniqueReads: 32123283
MappedReads: 52134751
TotalBases: 3144399011
MappedBases: 1524984746
Q30Bases: 2940653166


title: MCF7, REPOP, RNA-seq, replicate 2

description: Library name: MCF7-repop-2


title: JunctionalZone/Decidua, FCG_XYM_FoodRest, Rep1

description:
Library name: F24A
RIN: 8.7
TranscriptPercent: 91.4
InputReads: 61771746
UniqueReads: 37244859
MappedReads: 58920306
TotalBases: 3611100347
MappedBases: 1723662162
Q30Bases: 3410332757


title: HFF, TIS, RNA-seq, replicate 3

description: Library name: HFF-tis-3

source_name: foreskin

value: foreskin

value: HFF

value: fibroblast cell

value: TIS


title: JunctionalZone/Decidua, FCG_XXF_Control, Rep1

description:
Library name: F25B
RIN: 9
TranscriptPercent: 88.8
InputReads: 58551124
UniqueReads: 36654851
MappedReads: 57248663
TotalBases: 3423197162
MappedBases: 1674725162
Q30Bases: 3213079651


title: MCF7, REPOP, RNA-seq, replicate 1

description: Library name: MCF7-repop-1

value: breast

value: REPOP


title: JunctionalZone/Decidua, WT_M_FoodRest, Rep1

description:
Library name: F23A
RIN: 9.1
TranscriptPercent: 89.8
InputReads: 53757848
UniqueReads: 31481570
MappedReads: 52455822
TotalBases: 3142581663
MappedBases: 1534443745
Q30Bases: 2947785395

value: M


title: MDA-MB-231, REPOP, RNA-seq, replicate 3

description: Library name: MDA-MB-231-repop-3

value: triple-negative breast cancer


title: MDA-MB-231, REPOP, RNA-seq, replicate 2

description: Library name: MDA-MB-231-repop-2


title: Hs578T, TIS, RNA-seq, replicate 2

description: Library name: Hs578T-tis-2


title: HFF, TIS, RNA-seq, replicate 2

description: Library name: HFF-tis-2


title: JunctionalZone/Decidua, WT_M_Control, Rep1

description:
Library name: F18B
RIN: 9.4
TranscriptPercent: 91
InputReads: 57229860
UniqueReads: 33517197
MappedReads: 55687701
TotalBases: 3345635169
MappedBases: 1628782769
Q30Bases: 3133817488

value: placenta (junctional zone/decidua)


title: JunctionalZone/Decidua, FCG_XYF_Control, Rep1

description:
Library name: F16A
RIN: 9.5
TranscriptPercent: 89.2
InputReads: 48503558
UniqueReads: 29377723
MappedReads: 46848215
TotalBases: 2835107359
MappedBases: 1370245631
Q30Bases: 2662122052


title: MDA-MB-231, TIS, RNA-seq, replicate 4

description: Library name: MDA-MB-231-tis-4


title: MDA-MB-231, TIS, RNA-seq, replicate 2

description: Library name: MDA-MB-231-tis-2


title: JunctionalZone/Decidua, WT_F_Control, Rep1

description:
Library name: F13B
RIN: 9.5
TranscriptPercent: 89.7
InputReads: 53392412
UniqueReads: 33936839
MappedReads: 52147620
TotalBases: 3122510919
MappedBases: 1525851561
Q30Bases: 2921152971

value: F


title: JunctionalZone/Decidua, WT_F_FoodRest, Rep1

description:
Library name: F11A
RIN: 9.9
TranscriptPercent: 90.8
InputReads: 52497096
UniqueReads: 31259049
MappedReads: 48675454
TotalBases: 3067763348
MappedBases: 1424006379
Q30Bases: 2898430170


title: JunctionalZone/Decidua, WT_F_FoodRest, Rep2

description:
Library name: F15A
RIN: 9.4
TranscriptPercent: 91.3
InputReads: 55541734
UniqueReads: 33269517
MappedReads: 53564955
TotalBases: 3245852702
MappedBases: 1566712532
Q30Bases: 3030543975


title: MDA-MB-231, TIS, RNA-seq, replicate 3

description: Library name: MDA-MB-231-tis-3


title: MDA-MB-231, TIS, RNA-seq, replicate 1

description: Library name: MDA-MB-231-tis-1


title: T47D, TIS, RNA-seq, replicate 3

description: Library name: T47D-tis-3

value: epithelial cell


title: JunctionalZone/Decidua, FCG_XXF_FoodRest, Rep4

description:
Library name: F2B
RIN: 9.1
TranscriptPercent: 93.2
InputReads: 57315958
UniqueReads: 34533064
MappedReads: 55360074
TotalBases: 3344124006
MappedBases: 1618754164
Q30Bases: 3160281902

value: XXF


title: JunctionalZone/Decidua, WT_M_Control, Rep2

description:
Library name: F20A
RIN: 9
TranscriptPercent: 89.2
InputReads: 52588488
UniqueReads: 33539953
MappedReads: 51563010
TotalBases: 3072731306
MappedBases: 1508240201
Q30Bases: 2875752619


title: HFF, TIS, RNA-seq, replicate 1

description: Library name: HFF-tis-1


title: JunctionalZone/Decidua, FCG_XXM_FoodRest, Rep1

description:
Library name: F22A
RIN: 8.9
TranscriptPercent: 92.6
InputReads: 55015792
UniqueReads: 31276360
MappedReads: 52343497
TotalBases: 3210725310
MappedBases: 1530760292
Q30Bases: 3028833653

value: XXM


title: T47D, TIS, RNA-seq, replicate 2

description: Library name: T47D-tis-2


title: JunctionalZone/Decidua, FCG_XXF_FoodRest, Rep2

description:
Library name: F1B
RIN: 9
TranscriptPercent: 93.4
InputReads: 59858156
UniqueReads: 39532680
MappedReads: 58853466
TotalBases: 3501316108
MappedBases: 1735333276
Q30Bases: 3152825595

value: Food restriction


title: T47D, TIS, RNA-seq, replicate 1

description: Library name: T47D-tis-1


title: MCF7, TIS, RNA-seq, replicate 2

description: Library name: MCF7-tis-2

value: human adenocarcinoma cells


title: Stim_mouse4

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

institute: University of Pittsburgh

description:
Library name: 4_stim
ILC2 were cultured in complete RPMI with 20ng/mL IL-33 for 24 hours.

data_processing:
trimmed high quality reads were aligned to genome  using bowtie2
Raw count values generated with Subread
Gene expression values were nromalized to transcripts per million
Differential peak analysis determined using DESeq2 with cutoffs of 2 fold and p value<0.05
Assembly: mm10
Supplementary files format and content: csv file contains transcripts per million (TPM)

source_name: Lung

growth_protocol: ILC2s were sorted from mouse lung by the following markers: live, lineage-, CD90.2+, CD3-.

extract_protocol:
SMART-seq v4 Ultra Low Input RNA Kit for Sequencing
Nextera XT DNA Library Preparation kit (Illumina)

treatment_protocol: Specific treatment are described in the description tab

value: Lung


title: Stim_mouse3

description:
Library name: 3_stim
ILC2 were cultured in complete RPMI with 20ng/mL IL-33 for 24 hours.


title: Stim_mouse1

description:
Library name: 1_stim
ILC2 were cultured in complete RPMI with 20ng/mL IL-33 for 24 hours.


title: Unstim_mouse4

description:
Library name: 4_unstim
ILC2 were cultured in complete RPMI and left unstimulated.


title: Hs578T, TIS, RNA-seq, replicate 1

description: Library name: Hs578T-tis-1


title: MCF7, TIS, RNA-seq, replicate 1

description: Library name: MCF7-tis-1


title: HFF, CTR, RNA-seq, replicate 3

description: Library name: HFF-ctr-3

value: CTR


title: Stim_mouse2

description:
Library name: 2_stim
ILC2 were cultured in complete RPMI with 20ng/mL IL-33 for 24 hours.


title: Hs578T, TIS, RNA-seq, replicate 3

description: Library name: Hs578T-tis-3


title: Unstim_mouse2

description:
Library name: 2_unstim
ILC2 were cultured in complete RPMI and left unstimulated.


title: JunctionalZone/Decidua, FCG_XXF_FoodRest, Rep1

description:
Library name: F10B
RIN: 9.3
TranscriptPercent: 88.9
InputReads: 56014378
UniqueReads: 34032010
MappedReads: 55089154
TotalBases: 3275145965
MappedBases: 1611822622
Q30Bases: 3092304438


title: HFF, CTR, RNA-seq, replicate 2

description: Library name: HFF-ctr-2

value: foreskin


title: HFF, CTR, RNA-seq, replicate 1

description: Library name: HFF-ctr-1

value: HFF


title: Blimp1_KO, mouse3

description:
Library name: KO_3
ILC2 were cultured in complete RPMI with 20ng/mL IL-33 and 20ng/mL IL-25 for 72 hours.


title: Hs578T, CTR, RNA-seq, replicate 3

description: Library name: Hs578T-ctr-3


title: Hs578T, CTR, RNA-seq, replicate 2

description: Library name: Hs578T-ctr-2


title: Blimp1_KO, mouse1

description:
Library name: KO_1
ILC2 were cultured in complete RPMI with 20ng/mL IL-33 and 20ng/mL IL-25 for 72 hours.


title: Blimp1_KO, mouse2

description:
Library name: KO_2
ILC2 were cultured in complete RPMI with 20ng/mL IL-33 and 20ng/mL IL-25 for 72 hours.


title: Hs578T, CTR, RNA-seq, replicate 1

description: Library name: Hs578T-ctr-1


title: Blimp1_WT, mouse3

description:
Library name: WT_3
ILC2 were cultured in complete RPMI with 20ng/mL IL-33 and 20ng/mL IL-25 for 72 hours.


title: MDA-MB-231, CTR, RNA-seq, replicate 4

description: Library name: MDA-MB-231-ctr-4


title: Blimp1_WT, mouse2

description:
Library name: WT_2
ILC2 were cultured in complete RPMI with 20ng/mL IL-33 and 20ng/mL IL-25 for 72 hours.


title: MDA-MB-231, CTR, RNA-seq, replicate 3

description: Library name: MDA-MB-231-ctr-3


title: MDA-MB-231, CTR, RNA-seq, replicate 2

description: Library name: MDA-MB-231-ctr-2


title: Unstim_mouse3

description:
Library name: 3_unstim
ILC2 were cultured in complete RPMI and left unstimulated.


title: Blimp1_WT, mouse1

description:
Library name: WT_1
ILC2 were cultured in complete RPMI with 20ng/mL IL-33 and 20ng/mL IL-25 for 72 hours.


title: MCF7, TIS, RNA-seq, replicate 3

description: Library name: MCF7-tis-3


title: Blimp1_WT_mouse2

description:
Library name: Blimp1_WT2
ILC2s were cultured in complete RPMI with 20ng/mL IL-33 and 20ng/mL IL-25 for 72 hours.

data_processing:
trimmed high quality reads were aligned to genome  using bowtie2
Sam files are convereted to BAM files and duplicate reads and blacklist regions are removed
Files are converetd to bedgraphs and then converted to bigwig files
Assembly: mm10
Supplementary files format and content: bigwig file contaning open chromatin regions

growth_protocol: ILC2s were sorted from mouse lung by the following markers: live, lineage-, CD90.2+, CD3-

extract_protocol:
OMNI-ATAC protocol (Corces et al, Nat.Meth. 2017)
Nextera XT DNA Library Preparation kit


title: T47D, CTR, RNA-seq, replicate 3

description: Library name: T47D-ctr-3


title: Blimp1_KO_mouse2

description:
Library name: Blimp1_KO2
ILC2s were cultured in complete RPMI with 20ng/mL IL-33 and 20ng/mL IL-25 for 72 hours.


title: T47D, CTR, RNA-seq, replicate 2

description: Library name: T47D-ctr-2


title: Blimp1_WT_mouse1

description:
Library name: Blimp1_WT1
ILC2s were cultured in complete RPMI with 20ng/mL IL-33 and 20ng/mL IL-25 for 72 hours.


title: T47D, CTR, RNA-seq, replicate 1

description: Library name: T47D-ctr-1


title: MDA-MB-231, CTR, RNA-seq, replicate 1

description: Library name: MDA-MB-231-ctr-1


title: Labyrinth, FCG_XXF_Control, Rep5

description: Library name: F9A

data_processing:
Read sequences were aligned to the Mus musculus (mm10) reference sequence using DRAGEN RNA app on Basespace Sequence Hub.
Assembly: mm10
Supplementary files format and content: tab-delimited quant.sf files include TPM values for each sample

source_name: placenta

value: placenta

value: Control

tag: number of_viable_conceptuses

tag: female age

tag: rin

tag: transcriptpercent

tag: inputreads

tag: uniquereads

tag: mappedreads

tag: totalbases

tag: mappedbases


title: Blimp1_KO_mouse1

description:
Library name: Blimp1_KO1
ILC2s were cultured in complete RPMI with 20ng/mL IL-33 and 20ng/mL IL-25 for 72 hours.

tag: tissue


title: MCF7, CTR, RNA-seq, replicate 3

description: Library name: MCF7-ctr-3

value: breast

tag: cell type


title: Labyrinth, FCG_XXM_Control, Rep5

description: Library name: F8B

tag: strain


title: Unstim_mouse1

description:
Library name: 1_unstim
ILC2 were cultured in complete RPMI and left unstimulated.


title: Labyrinth, FCG_XXF_Control, Rep4

description: Library name: F8A


title: MCF7, CTR, RNA-seq, replicate 1

description: Library name: MCF7-ctr-1

tag: cell line


title: Labyrinth, FCG_XYM_FoodRest, Rep5

description: Library name: F85A

value: XYM


title: siPDL1-2-IFN2

city: Boston

first: Marco

last: Mineo

state: MA

address: 60 Fenwood Rd, BTM 8016N

institute: Brigham and Women's Hospital

description: Library name: Sample 12

data_processing:
CLC genomics workbench version 22.0.2
Raw data were trimmed and mapped using CLC genomics workbench version 22.0.2. Quality trimming was set at quality limit = 0.05, maximum number of ambiguities = 2.
Trimmed reads were aligned to the human genome from the Ensembl release GRCh38. The mapping options were set as mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, auto-detect paired distances, maximum number of hits for a read = 10.
Assembly: Ensembl release GRCh38
Supplementary files format and content: tab-delimited text file contains CPM for each sample

growth_protocol: U251 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested from cells using RNeasy Mini Kit (Qiagen Cat#74104). 1 ug total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA kit following manufacturer's protocol.

treatment_protocol: Cells were treated with 100U/ml interferon-gamma for 24 hours.

value: Brain

value: glioblastoma

tag: genotype

value: PD-L1 knockdown

value: interferon-gamma


title: Labyrinth, FCG_XYF_FoodRest, Rep5

description: Library name: F87A

value: XYF

tag: treatment


title: siPDL1-2-C2

description: Library name: Sample 10


title: Labyrinth, FCG_XXM_Control, Rep4

description: Library name: F82A

tag: group


title: Labyrinth, WT_M_Control, Rep5

description: Library name: F84A

value: M


title: siPDL1-2-C1

description: Library name: Sample 9


title: siPDL1-1-IFN2

description: Library name: Sample 8


title: siPDL1-1-IFN1

description: Library name: Sample 7


title: Labyrinth, FCG_XYM_Control, Rep5

description: Library name: F78A


title: Labyrinth, WT_F_Control, Rep5

description: Library name: F76A

value: F


title: Labyrinth, FCG_XXF_Control, Rep3

description: Library name: F78B

value: XXF


title: MCF7, CTR, RNA-seq, replicate 2

description: Library name: MCF7-ctr-2

value: human adenocarcinoma cells

tag: sample group


title: Labyrinth, FCG_XXM_FoodRest, Rep5

description: Library name: F74A

value: XXM

value: Food restriction

tag: number of_viable_conceptuses


title: Labyrinth, FCG_XXM_Control, Rep3

description: Library name: F70B

tag: female age


title: siNC-IFN1

description: Library name: Sample 3

value: WT


title: siNC-IFN2

description: Library name: Sample 4


title: Labyrinth, FCG_XYF_Control, Rep4

description: Library name: F66B

tag: rin


title: Labyrinth, FCG_XYF_Control, Rep5

description: Library name: F6A

tag: transcriptpercent


title: Labyrinth, FCG_XYM_FoodRest, Rep4

description: Library name: F64A

tag: inputreads


title: siNC-C2

description: Library name: Sample 2


title: siNC-C1

description: Library name: Sample 1


title: siPDL1-1-C1

description: Library name: Sample 5


title: Labyrinth, FCG_XYM_FoodRest, Rep3

description: Library name: F5B

tag: uniquereads


title: SH-SY5Y, replicate2

city: Bloomington

first: Hui-Chen

state: Indiana

address: 702 N Walnut Grove Ave, Multidisciplinary Science Building II

department: Psychological and Brain Sciences

institute: Indiana University Bloomington

data_processing:
The single-end FASTQ raw data were analyzed using w4CSeq (github.com/WGLab/w4CSeq). The raw reads were trimmed free of the viewpoint primer sequences, and then mapped to the reference genome hg19. In w4CSeq, the binomial model was used to call out statistically significant regions that pass p<0.05. For counting the number of ligated sites to define interchromosomal interactions, a window size of 500 was used. To define intrachromosomal interactions, a window size of 100 with a background window size of 3,000 was used. FDR of 0.05 was used to remove most random chromosomal interactions.
Assembly: human reference genome hg19
Supplementary files format and content: bed file wiith bedGraph tracks including 4C interacting sites and read counts
Library strategy: 4C-seq

growth_protocol: SH-SY5Y cells were cultured in the culture medium consisting of 45% eagle's minimum essential medium (Sigma), 45% nutrient mixture F-12 Ham (Sigma), 10% heat-inactivated fetal bovine serum (FBS)(ATCC), 1% non-essential amino acids (Sigma), and 2 mM GlutaMax (Gibco).

extract_protocol:
Cells were fixed with 2% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was digested with restriction enzyme DpnII (NEB) and CviAII (NEB).
Krijger et al 2020 protocol was ued to prepare the 4C-seq libraries

treatment_protocol: For differentiation, SH-SY5Y cells were treated with 10 mM all-trans-retinoic acid (RA) (Tocris) the next day. After 5 days of RA incubation, cells were washed with the serum-free culture medium and subsequently treated with 50 ng/ml brain-derived neurotrophic factor (BDNF) (alomone labs) in the serum-free culture medium for 7 days.

value: No differentiation


title: SH-SY5Y, replicate3


title: siPDL1-2-IFN1

description: Library name: Sample 11


title: Labyrinth, FCG_XXF_FoodRest, Rep5

description: Library name: F5A

value: placenta

tag: mappedreads


title: Labyrinth, WT_F_Control, Rep4

description: Library name: F60A

value: Control

tag: totalbases


title: SH-SY5Y, replicate1


title: Labyrinth, FCG_XXM_Control, Rep2

description: Library name: F59B

tag: mappedbases


title: Differentiated SH-SY5Y, replicate3

value: RA/BDNF differentiation


title: Labyrinth, FCG_XYM_Control, Rep4

description: Library name: F59A

tag: tissue

value: XYM


title: Differentiated SH-SY5Y, replicate2


title: Differentiated SH-SY5Y, replicate1


title: siPDL1-1-C2

description: Library name: Sample 6

value: Brain

tag: cell type


title: Labyrinth, WT_M_Control, Rep4

description: Library name: F57A

tag: strain


title: SH-SY5Y, replicate3

data_processing:
The sequence data were mapped to the human reference genome hg19 with STAR-2.7.10a
FeatureCounts (subread-2.0.3) was used to quantify gene expression (parameters applied: "“-s 2 –p –Q 10")
Differential expression analysis was performed using edgeR
Assembly: human reference genome hg19
Supplementary files format and content: excel file including raw counts, log2 fold change, p-values and FDR

extract_protocol:
RNA was harvested using RNeasy Plus Universal Mini kit (Qiagen). 200 ng of total RNA was used for the library construction.
KAPA mRNA Hyperprep Kit (KK8581) was ued to prepare the RNA-seq libraries

tag: cell line


title: SH-SY5Y, replicate2


title: Labyrinth, WT_F_FoodRest, Rep5

description: Library name: F55A


title: Labyrinth, FCG_XYM_FoodRest, Rep2

description: Library name: F54A


title: Labyrinth, FCG_XYM_Control, Rep3

description: Library name: F53B


title: SH-SY5Y, replicate1


title: Differentiated SH-SY5Y, replicate3


title: Differentiated SH-SY5Y, replicate2


title: Labyrinth, FCG_XXM_FoodRest, Rep4

description: Library name: F50A


title: Labyrinth, FCG_XXF_Control, Rep2

description: Library name: F52A


title: T47D, REPOP, replicate 2

data_processing:
The demultiplexing, barcodes processing, gene countig were made using the Cytonaut web-based platform v2.1.0
Assembly: hg38
Supplementary files format and content: Count matrix in TSV format.

extract_protocol:
MCF7 and T47D CTR, TIS (at day 12) and REPOP cells were collected by trypsinization, and 15.000 cells/samples were used. Two biological replicates of single-cell suspensions were prepared using Scipio Bioscience’s reversible hydrogel technology RevGel-seq™ with the instrument-free 3’ scRNA-seq benchtop kit Asteria™, allowing for coupling of solid polymer-barcoded beads and cells in a homogenous phase. Cell capture was followed by cell lysis, mRNA capture on barcoded beads, reverse transcription, PCR amplification and cDNA sequencing. The samples were sequenced to yield approx. 35.000 raw reads per analyzed cell.
Library was constructed by NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs) with some adaptations according to the instruction of Asteria kit and were then sequenced on the Illumina NovaSeq 6000 sequencer with a medium of 35.000 raw reads per sample.

treatment_protocol: For TIS induction cells were treated with 120 nM (MCF7) and 70 nM (T47D) DOX and incubated for 5 days. After five days of incubation, treated cells were washed with pre-warmed PBS and the medium was renewed. MCF7 and T47D flasks remained in the incubator for seven days to ensure that the cells had become senescent (day 12). For REPOP induction flasks remained in the incubator with medium change every week.

value: breast

value: epithelial cell


title: T47D, REPOP, replicate 1


title: Differentiated SH-SY5Y, replicate1


title: Labyrinth, FCG_XYF_FoodRest, Rep4

description: Library name: F51B


title: T47D, TIS, replicate 2


title: Labyrinth, FCG_XYF_FoodRest, Rep3

description: Library name: F48A


title: Labyrinth, WT_M_FoodRest, Rep5

description: Library name: F58A


title: Labyrinth, WT_M_FoodRest, Rep4

description: Library name: F42A


title: Labyrinth, FCG_XYF_FoodRest, Rep2

description: Library name: F41B


title: T47D, CTR, replicate 1


title: Labyrinth, FCG_XYF_Control, Rep3

description: Library name: F46B


title: T47D, TIS, replicate 1


title: MCF7, REPOP, replicate 2


title: Labyrinth, WT_F_Control, Rep3

description: Library name: F39A


title: MCF7, TIS, replicate 2


title: Labyrinth, WT_M_Control, Rep3

description: Library name: F37A


title: Labyrinth, WT_F_FoodRest, Rep4

description: Library name: F36A


title: MCF7, REPOP, replicate 1


title: MCF7, TIS, replicate 1


title: Labyrinth, FCG_XYM_Control, Rep2

description: Library name: F33B


title: Labyrinth, FCG_XXM_Control, Rep1

description: Library name: F49B


title: MCF7, CTR, replicate 2


title: MCF7, CTR, replicate 1


title: Labyrinth, WT_M_FoodRest, Rep3

description: Library name: F32A


title: Labyrinth, WT_F_FoodRest, Rep3

description: Library name: F31A


title: Labyrinth, WT_F_Control, Rep2

description: Library name: F34A


title: Spatial RNA seq of Homo sapiens : P53 tumor ROI19

city: Seongnam City

first: Doo Hyun

last: Koh

address: Yatap-ro 64

country: South Korea

institute: CHA university

data_processing:
After sequencing, the reads were aligned to reveal the unique ID of the probe. PCR duplicate reads were removed using the unique identifier region of each read and then the reads were converted to digital counts.
The presence or absence of a gene was defined by the limit of quantitation (LOQ) which is the geometric mean of the negative probes
For normalization, we used Q3 normalization.
Assembly: Genome assembly was not used.
Supplementary files format and content: Q3_BC.TargetCountMatrix_norm.txt : normalized expression data using Q3 normalization from count expression data
Library strategy: Spatial Transcriptomics

source_name: ovarian high grade serous carcinomas fresh frozen

extract_protocol:
For nanoString GeoMx digital spatial profiling, tissue microarray (TMA) construction was constructed. For each case, one representative core of 5mm diameter was obtained from FFPE block. For 11 cases, two rectangular shaped regions of interests (ROI) per each core were annotated. For P12, one ROI was annotated.
Each ROI consisted of 3 areas of interests (AOI) of morphologic markers. PanCK was for epithelial tumor area, SMA was for stroma, and CD45 was for pan-immune cells. Oligonucleotides from the selected ROI were released upon localized exposure to UV light. Collected oligos from each area of illumination (AOI) were amplified in PCR machine

value: platinum-based chemotherapy


title: Spatial RNA seq of Homo sapiens : P53 CD45 ROI19

value: ovarian high grade serous carcinomas fresh frozen


title: Labyrinth, FCG_XXM_FoodRest, Rep2

description: Library name: F29B


title: Spatial RNA seq of Homo sapiens : P53 SMA ROI18


title: Labyrinth, FCG_XXF_FoodRest, Rep3

description: Library name: F29A


title: T47D, CTR, replicate 2


title: Labyrinth, FCG_XXF_FoodRest, Rep4

description: Library name: F2B


title: Labyrinth, FCG_XYF_FoodRest, Rep1

description: Library name: F28A

value: XYF


title: Spatial RNA seq of Homo sapiens : P53 CD45 ROI18


title: Labyrinth, FCG_XXM_FoodRest, Rep3

description: Library name: F3A


title: Spatial RNA seq of Homo sapiens : P53 tumor ROI18


title: Labyrinth, FCG_XYM_Control, Rep1

description: Library name: F26B


title: Labyrinth, FCG_XYF_Control, Rep2

description: Library name: F26A


title: Spatial RNA seq of Homo sapiens : P42 CD45 ROI16


title: Spatial RNA seq of Homo sapiens : P42 tumor ROI16


title: Labyrinth, FCG_XXF_Control, Rep1

description: Library name: F25B


title: Labyrinth, FCG_XYM_FoodRest, Rep1

description: Library name: F24A


title: Spatial RNA seq of Homo sapiens : P42 SMA ROI15


title: Spatial RNA seq of Homo sapiens : P53 SMA ROI19


title: Spatial RNA seq of Homo sapiens : P42 tumor ROI15


title: Spatial RNA seq of Homo sapiens : P05 SMA ROI19

source_name: ovarian high grade serous carcinomas FFPE (formalin fixed paraffin embedded)


title: Labyrinth, WT_M_FoodRest, Rep1

description: Library name: F23A

value: M


title: Spatial RNA seq of Homo sapiens : P42 CD45 ROI15


title: Spatial RNA seq of Homo sapiens : P05 tumor ROI19

value: ovarian high grade serous carcinomas FFPE (formalin fixed paraffin embedded)


title: Labyrinth, FCG_XXF_FoodRest, Rep2

description: Library name: F1B

value: XXF


title: Labyrinth, WT_M_Control, Rep2

description: Library name: F20A


title: Labyrinth, FCG_XXM_FoodRest, Rep1

description: Library name: F22A

value: XXM


title: Spatial RNA seq of Homo sapiens : P05 tumor ROI18


title: Labyrinth, WT_F_FoodRest, Rep2

description: Library name: F15A

value: F

value: Food restriction


title: Labyrinth, WT_M_Control, Rep1

description: Library name: F18B


title: Spatial RNA seq of Homo sapiens : P05 CD45 ROI18


title: Spatial RNA seq of Homo sapiens : P05 SMA ROI18


title: Spatial RNA seq of Homo sapiens : P42 SMA ROI16


title: Spatial RNA seq of Homo sapiens : P05 CD45 ROI19


title: Labyrinth, WT_F_FoodRest, Rep1

description: Library name: F11A


title: Labyrinth, FCG_XYF_Control, Rep1

description: Library name: F16A


title: Spatial RNA seq of Homo sapiens : P09 tumor ROI17


title: Spatial RNA seq of Homo sapiens : P09 CD45 ROI17


title: Smad3 KO LPS Replicate 4

first: Thierry

last: Gauthier

address: 30 convent drive (NIH)

institute: NIH/NIDCR

description: Library name: Smad3 KO LPS 4

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to a customized GRCm38 vM23 genome supplemented with ERCCs and commom mouse transgenes using STAR v2.7.3a in  single-pass mode with –outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.7.3a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM23 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: mm10
Supplementary files format and content: RawCountFile.txt, Raw counts expression matrix.
Supplementary files format and content: RawCountFile_filtered.txt, Filtered counts expression matrix. Genes with less than 5 counts in at least one sample were removed.
Supplementary files format and content: CPM_TMM_counts.txt, TMM-normalized Counts Per Million expression matrix.

source_name: Peritoneum

extract_protocol:
Bulk RNA was extracted from cultured macrophages using Qiagen Rnesay mini kit
Library preparation was performed according to the manufacturer’s instructions for the Nextera XT unstranded library kit. The libraries were then pooled and sequenced on a NextSeq 2000 sequencer (Illumina) in paired-end mode, 100nt read length.

value: Peritoneum

value: Macrophages

tag: genotype

value: Smad3 KO

tag: Sex

value: female

value: LPS


title: Spatial RNA seq of Homo sapiens : P09 SMA ROI17

tag: treatment


title: Labyrinth, FCG_XXF_FoodRest, Rep1

description: Library name: F10B

value: placenta

tag: group


title: Labyrinth, WT_F_Control, Rep1

description: Library name: F13B

value: Control

tag: number of_viable_conceptuses


title: Spatial RNA seq of Homo sapiens : P09 SMA ROI16


title: Spatial RNA seq of Homo sapiens : P09 tumor ROI16


title: Smad3 KO Replicate 4

description: Library name: Smad3 KO 4

value: Ctrl


title: WT LPS Replicate 4

description: Library name: WT LPS 4

value: WT


title: Spatial RNA seq of Homo sapiens : P10 SMA ROI15

value: platinum-based chemotherapy


title: WT Replicate 4

description: Library name: WT 4


title: Spatial RNA seq of Homo sapiens : P09 CD45 ROI16


title: Smad3 KO LPS Replicate 3

description: Library name: Smad3 KO LPS 3


title: Smad3 KO Replicate 3

description: Library name: Smad3 KO 3


title: Spatial RNA seq of Homo sapiens : P10 tumor ROI15


title: WT LPS Replicate 3

description: Library name: WT LPS 3


title: WT Replicate 3

description: Library name: WT 3


title: Spatial RNA seq of Homo sapiens : P10 SMA ROI14


title: Smad3 KO Replicate 2

description: Library name: Smad3 KO 2


title: Smad3 KO LPS Replicate 2

description: Library name: Smad3 KO LPS 2


title: Spatial RNA seq of Homo sapiens : P10 tumor ROI14


title: Spatial RNA seq of Homo sapiens : P11 SMA ROI13


title: WT Replicate 2

description: Library name: WT 2


title: Spatial RNA seq of Homo sapiens : P11 CD45 ROI13


title: Smad3 KO LPS Replicate 1

description: Library name: Smad3 KO LPS 1


title: Spatial RNA seq of Homo sapiens : P11 tumor ROI13


title: Spatial RNA seq of Homo sapiens : P10 CD45 ROI14


title: Smad3 KO Replicate 1

description: Library name: Smad3 KO 1


title: WT LPS Replicate 1

description: Library name: WT LPS 1


title: Spatial RNA seq of Homo sapiens : P11 tumor ROI12


title: WT LPS Replicate 2

description: Library name: WT LPS 2


title: WT Replicate 1

description: Library name: WT 1


title: Spatial RNA seq of Homo sapiens : P11 CD45 ROI12


title: MEF_RXMM_siTICAM_siRIPK1_AP1_3

city: Seattle

first: Sigal

middle: B

last: Kofman

email: sigalk@uw.edu, Kofmansb@gmail.com

state: Washington

address: 750 Republican St

department: Immunology

institute: University of Washington

data_processing:
Raw reads mapped to Mus_musculus.GRCm39.cdna.all.fa.gz using Kallisto. Quality of reads checked on FASTqc and Multiqc
Transcripts annotated using Ensembl database Mus musculus v 79.
Samples were filtered to exlude genes with counts per million = in 3 or more samples and log2 counts per million were subsequently normalized in EdgeR.
Assembly: Mus_musculus.GRCm39.cdna.all.fa.gz
Supplementary files format and content: Data provided are log2 counts per million, filtered and normalized in a TSV file

source_name: immortalized MEFs

extract_protocol:
Total RNA from cell cultures was isolated uisng a Macherey-Nagel Nucleospin RNA kit
Libraries were prepared using a Nextera XT library preparation kit

value: immortalized MEFs

value: recombined RXMM

value: qVD and BB homodimerizer


title: Spatial RNA seq of Homo sapiens : P12 tumor ROI11

value: ovarian high grade serous carcinomas FFPE (formalin fixed paraffin embedded)


title: Spatial RNA seq of Homo sapiens : P12 SMA ROI11


title: Spatial RNA seq of Homo sapiens : P10 CD45 ROI15


title: Spatial RNA seq of Homo sapiens : P12 CD45 ROI11


title: MEF_RXMM_siTICAM_siRIPK1_AP1_2


title: MEF_RXMM_siSCR_AP1_3


title: Labyrinth, WT_M_FoodRest, Rep2

description: Library name: F27A

value: M

tag: female age


title: CSF1R inhibitor treated Rag2 KO transferred with GM-CSF deficient (CD4cre/+ TdTomato) CD4 naïve T cells

first: Margarette

middle: Helen

last: Clevenger

address: 900 E 57th St

department: Pritzker School of Molecular Engineering

description:
Library name: Sample 5
10X Genomics

data_processing:
The GRCm38 transcriptome was used as a reference for alignment and feature counting using Cell Ranger (V9.0.0, 10X Genomics).
Feature-barcode matrices were processed as Seurat objects in the Seurat R package 5.0.0 and filtered to retain genes exhibiting expression in ≥ 5 cells and cells with >500 detected transcripts. Each dataset was independently normalized, scaled, processed to identify variable features.
Assembly: The GRCm38 transcriptome
Supplementary files format and content: tab-separated value files and matrix files

source_name: thalamus, cerebrum, and brainstem

extract_protocol:
Brains were isolated following perfusion with DPBS. The brainstem, thalamus, and hypothalamus—regions characterized by robust CD4⁺ T cell infiltration and activated microglia—were dissected and dissociated for 30 minutes at 37°C using the Adult Brain Dissociation Kit (Miltenyi Biotec) and gentle MACSTM Octo Dissociator with Heaters (Miltenyi Biotec) followed by the protocol provided in the kit. The resulting cell suspension was passed through a 70-µm strainer, and debris and red blood cells were removed according to the kit protocol. The pellet was sequentially depleted of myelin using Myelin Removal Beads v2 (Miltenyi Biotec) and dead cells using the Dead Cell Removal Kit serum albumin.
After the cell viability was confirmed more than 80%, Single-cell 3' cDNA libraries were prepared at the DNA Services laboratory of the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign. Cells were processed into individually barcoded cDNA libraries using the 5' GEM-X scRNA library platform from 10X Genomics (Pleasanton, CA, USA) following the manufacturer’s protocol, with a target of 10,000 cells per library. The 10X Chromium instrument encapsulated single cells into Gel Bead Emulsions (GEMs) to barcode mRNA from individual cells. Following double-stranded cDNA synthesis, barcoded libraries compatible with Illumina sequencing chemistry were constructed. Each library was quantified using Qubit, and the average fragment size was assessed with an AATI Fragment Analyzer (Advanced Analytics, Ames, IA, USA).

treatment_protocol: The sorted 1.0 x 10e5 cells of CD4-TdTomato+ Csf-2- (GM-CSF)-sufficient or -deficient TCR7B8 naïve CD4 T cells were retro-orbitally injected into adult SFB-colonizing Rag2-/- (6 weeks-old) mice. Four days following the naïve CD4 T cell transfer, PLX5622-formulated AIN-67A or AIN-67A as a control were provided. Fresh diets were provided every week for 6 weeks. At 6 weeks following the naïve T cell transfer, the brainstem, thalamus, and hypothalamus—regions characterized by robust CD4⁺ T cell infiltration and activated microglia—were dissected and cells in the indicated tissues were collected for single cell transcriptomic analysis.

value: thalamus, cerebrum, and brainstem

value: Rag2 KO

value: CSF1R inhibitor + adoptive transfer of GM-CSF KO (CD4cre/+ TdTomato) CD4 naïve T cells


title: MEF_RXMM_siSCR_AP1_2


title: Spatial RNA seq of Homo sapiens : P13 SMA ROI10


title: MEF_RXMM_siTICAM_siRIPK1_AP1_1


title: Spatial RNA seq of Homo sapiens : P13 tumor ROI10


title: CSF1R inhibitor treated Rag2 KO transferred with GM-CSF sufficient (CD4cre/+ TdTomato) CD4 naïve T cells

description:
Library name: Sample 4
10X Genomics

value: CSF1R inhibitor + adoptive transfer of GM-CSF Het (CD4cre/+ TdTomato) CD4 naïve T cells


title: MEF_RXMM_siSCR_AP1_1


title: MEF_RXMM_siTICAM_siRIPK1_Mock_3

value: qVD only


title: Rag2 KO transferred with GM-CSF deficient (CD4cre/+ TdTomato) CD4 naïve T cells

description:
Library name: Sample 3
10X Genomics

value: Adoptive transfer of GM-CSF KO (CD4cre/+ TdTomato) CD4 naïve T cells


title: MEF_RXMM_siTICAM_siRIPK1_Mock_2


title: Spatial RNA seq of Homo sapiens : P11 SMA ROI12


title: Spatial RNA seq of Homo sapiens : P13 CD45 ROI10


title: MEF_RXMM_siTICAM_siRIPK1_Mock_1


title: MEF_RXMM_siSCR_Mock_3


title: Rag2 KO transferred with GM-CSF sufficient (CD4cre/+ TdTomato) CD4 naïve T cells

description:
Library name: Sample 2
10X Genomics

value: Adoptive transfer of GM-CSF Het (CD4cre/+ TdTomato) CD4 naïve T cells


title: Spatial RNA seq of Homo sapiens : P13 SMA ROI9


title: MEF_RXMM_siSCR_Mock_1


title: Rag2 KO without transfer

description:
Library name: Sample 1
10X Genomics


title: Spatial RNA seq of Homo sapiens : P13 tumor ROI9


title: RHIM_RHIM_siScr_ZIKV_4

source_name: Primary cortical neurons

value: Primary cortical neurons

value: Zika virus


title: RHIM_RHIM_siScr_ZIKV_3


title: Spatial RNA seq of Homo sapiens : P13 CD45 ROI9


title: Col1a1+/-  female 12 week old tibia sample 3

city: Houston

first: Ellen

last: Busschers

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: Library name: 1907

data_processing:
Trimmomatic (Version 0.39) to remove low quality reads and adapter sequences.
All reads were aligned to the mouse genome version GRCm39 using Hisat2 (Version 2.2.1)
The Samtools package (Version 1.20) was used to convert, sort and index the reads.
Featurecounts from the subred package (Version 2.0.3) was used to generate counts of all mapped reads.
Assembly: GRCm39
Supplementary files format and content: featurecounts

source_name: Tibia

growth_protocol: mice were housed in groups with unlimited access to food and water. They were euthanized at 12-weeks old

extract_protocol:
bone marrow was flushed from tibia and tibia were flash frozen. Tibia were disrupted using tissuelyser by Quiagen and RNA was extracted using Direct-Zol kit by Zymo research.
poly-A selection

value: Tibia


title: RHIM_RHIM_siScr_ZIKV_1


title: WT  female 12 week old tibia sample 3

description: Library name: 1906

value: wt


title: Spatial RNA seq of Homo sapiens : P15 SMA ROI8

value: platinum-based chemotherapy


title: RHIM_RHIM_siScr_Mock_4

value: Mock


title: RHIM_RHIM_siScr_ZIKV_2


title: WT  female 12 week old tibia sample 2

description: Library name: 1905


title: RHIM_RHIM_siScr_Mock_3


title: Col1a1+/-  female 12 week old tibia sample 2

description: Library name: 1904


title: Spatial RNA seq of Homo sapiens : P15 tumor ROI8


title: RHIM_RHIM_siScr_Mock_2


title: RHIM_RHIM_siScr_Mock_1


title: Spatial RNA seq of Homo sapiens : P15 CD45 ROI8


title: WT_RHIM_siScr_ZIKV_4


title: WT  female 12 week old tibia sample 1

description: Library name: 1903


title: Col1a1+/-  female 12 week old tibia sample 1

description: Library name: 1902


title: WT_RHIM_siScr_ZIKV_2


title: WT_RHIM_siScr_ZIKV_3


title: WT_RHIM_siScr_ZIKV_1


title: Spatial RNA seq of Homo sapiens : P15 tumor ROI7


title: WT_RHIM_siScr_Mock_4


title: Spatial RNA seq of Homo sapiens : P15 CD45 ROI7


title: WT_RHIM_siScr_Mock_3


title: WT_RHIM_siScr_Mock_2


title: Sepsis young adult male 4

city: Gainesville

first: Philip

middle: A

last: Efron

state: FL

address: 1600 SW Archer Road

department: Departament of Surgery

institute: University of Florida

data_processing:
Cell Ranger Single-Cell Software v 7.0.1 (10x Genomics) was used to obtain FASTQ files from the Illumina base call files, align the sequencing reads to the mm10 mouse transcriptome reference using “intronic reads included” mode, and further quantify the expression level of transcripts in single-cells.
Assembly: mm10-2020-A
Supplementary files format and content: Output of Cell Ranger from the filtered_feature_bc_matrix folder

source_name: spleen

growth_protocol: All studies were approved by the Institutional Animal Care and Use Committee at the University of Florida. Wild-type (C57BL/6j; B6) mice were purchased from Jackson Laboratories (Bar Harbor, ME) and were kept at the University of Florida’s rodent facility, where they received standard care, ad libitum feeding and 12-hour light-dark cycle schedule.  Mice were kept in harem-breeding schemes.  Once a pregnant female was identified, it was separated and monitored daily to accurately record the date of birth of the pups.  Mixed-gender litters were used for all experiments.

extract_protocol:
Splenocytes from naïve, BCG-vaccinated, septic (18 hours post-CS) and BCG plus sepsis (18 hours post-CS) neonatal mice, were obtained after mechanical dissociation using 70 mm strainers.  After centrifugation at 300 x g for 10 min, RBC were lysed with ACK lysing buffer (Thermo Fisher Scientific, Waltham, MA) for five minutes at room temperature.  Total splenocytes were washed in PBS supplemented with 2% FBS, quantified (Cellometer Auto 2000 Cell Viability Counter; Nexcelom Bioscience, Lawrence, MA) and diluted to 106 cells/ml before single-cell library preparation.
Libraries were prepared with Chromium Next GEM Single Cell 5’ v2 kit targeting 10,000 cells/lane on the 10x Chromium microfluidics device (10x Genomics, Pleasanton, CA).  Libraries were sequenced at a minimum depth of 20,000 read pairs per cell on an Illumina Novaseq X plus Platform (Illumina, San Diego, CA).

treatment_protocol: Neonatal mice from the same litter were randomized in order to reduce variation from differences in maternal care and virulence of different lots of cecal slurry (CS).  Pups received either 106 CFU of the BCG vaccine (TICE® strain, Merck, Rahway, NJ), 100 g of the heat-inactivated BCG vaccine or saline, subcutaneously (s.c.) either at birth (P1) or day 4 of life (P4).  Polymicrobial intra-abdominal sepsis was induced in neonatal mice at day 7 of life (P7) using the CS model as described previously.  Briefly, cecal contents were harvested from a wild-type female adult mouse and an 80 mg/ml of fresh CS solution was prepared using 5% dextrose.  CS (1.1 – 1.3 mg/g BW) was administered intraperitoneally (i.p.) to achieve the desire lethality (LD30-70).  After sepsis-induction, mice were monitored every six hours for the first 48 hours, then every 12 hours thereafter, for any signs of morbidity (absence of milk spot, hypothermia).  Survival was assessed for seven days following sepsis induction.  Moribund animals were euthanized following approved IACUC guidelines and were deemed to be non-survivors.  Additional neonatal mice were used to collect blood and spleen immediately prior to induction of sepsis and six- and 18-hours following sepsis induction.

value: spleen

value: splenocytes

value: Male

tag: age group

value: Young adult

tag: sepsis condition

value: Sepsis

value: No


title: WT_RHIM_siScr_Mock_1


title: Spatial RNA seq of Homo sapiens : P16 SMA ROI6

value: ovarian high grade serous carcinomas FFPE (formalin fixed paraffin embedded)


title: siRipk1_ZIKV_3

source_name: Primary cortical neuron

value: Primary cortical neuron

value: B6J (WT)


title: Sepsis young adult male 3


title: Spatial RNA seq of Homo sapiens : P16 tumor ROI6


title: siRipk1_ZIKV_2


title: Sepsis young adult male 1


title: MEF_RXMM_siSCR_Mock_2

value: immortalized MEFs

value: recombined RXMM

value: qVD only


title: siRipk1_Mock_4


title: siRipk1_ZIKV_1

value: Zika virus


title: Spatial RNA seq of Homo sapiens : P16 CD45 ROI6


title: siRipk1_Mock_2


title: Spatial RNA seq of Homo sapiens : P15 SMA ROI7


title: siRipk1_Mock_3


title: Spatial RNA seq of Homo sapiens : P16 SMA ROI5


title: Sepsis young adult female 3

value: Female


title: siRipk1_Mock_1


title: siTicam1_ZIKV_4


title: siTicam1_ZIKV_3


title: Spatial RNA seq of Homo sapiens : P16 CD45 ROI5


title: siTicam1_ZIKV_1


title: siTicam1_ZIKV_2


title: Sepsis young adult female 2


title: siTicam1_Mock_4


title: Sepsis young adult female 1


title: Sepsis young adult male 2


title: Spatial RNA seq of Homo sapiens : P20 SMA ROI4


title: siTicam1_Mock_3


title: siZbp1_ZIKV_4


title: Sepsis young adult male 080923 1


title: Sepsis young adult female 0705 3


title: siTicam1_Mock_2


title: Spatial RNA seq of Homo sapiens : P20 CD45 ROI4


title: siZbp1_ZIKV_3


title: Spatial RNA seq of Homo sapiens : P20 SMA ROI3


title: Sepsis young adult female 4


title: siZbp1_ZIKV_2


title: siZbp1_ZIKV_1


title: Naive young adult male 3


title: Spatial RNA seq of Homo sapiens : P16 tumor ROI5


title: Naive young adult male 4


title: siZbp1_Mock_4


title: Spatial RNA seq of Homo sapiens : P20 tumor ROI3


title: siZbp1_Mock_2


title: Spatial RNA seq of Homo sapiens : P20 CD45 ROI3


title: siZbp1_Mock_3


title: Naive young adult male 2


title: siZbp1_Mock_1


title: Naive young adult male 1


title: siRipk3_ZIKV_3


title: Naive young adult female 4


title: siRipk3_ZIKV_2


title: Spatial RNA seq of Homo sapiens : P21 tumor ROI2


title: Spatial RNA seq of Homo sapiens : P20 tumor ROI4


title: siTicam1_Mock_1


title: siRipk3_ZIKV_1


title: siRipk3_Mock_4


title: Naive young adult female 3


title: siRipk3_Mock_1


title: siScr_ZIKV_2


title: Spatial RNA seq of Homo sapiens : P21 tumor ROI1


title: Naive young adult female 1


title: siScr_ZIKV_3


title: Naive neonatal 8

value: Neonatal


title: siScr_ZIKV_4


title: Spatial RNA seq of Homo sapiens : P21 SMA ROI2

value: platinum-based chemotherapy


title: siRipk3_ZIKV_4


title: siScr_Mock_4

value: Mock


title: 23

city: Kunming

first: Yanjiao

last: Li

address: Puxin Road 2

institute: Kunming University

data_processing:
Illumina Casava software used for basecalling
(1) Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted) (2) Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality). (3) Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
Hisat2 v2.2.1 was used for building the genome index, and Clean Data was mapped to the reference genome(GRCh38.109) using Hisat2 v2.2.1.
Stringtie v 2.1.7 was used for transcriptome expression estimation. Reads Count for each gene in each sample was counted by python scripts.
Assembly: human NCBI genome build 38 (hg38)
Supplementary files format and content: "counts.csv" containes gene counts;"TPM.csv" contains gene TPM values.

source_name: bone

growth_protocol: Human fibroblast cells and  fibroblast-derived cells till 18 days were routinely maintained in high glucose DMEM (Gibco) with 10% fetal bovine serum(Excell),  bone mesenchymal stem cells  were cultured in MSC medium including low glucose DMEM(Gibco) with 8% fetal bovine serum(Excell).

extract_protocol:
A total amount of 1μg RNA per sample was used as input material for the RNA sample preparations. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Fibroblasts were treated by small molecule cocktail for 18 days,  and on day 18 denoted as induced osteoblast.

value: bone

value: bone mesenchymal stem cell


title: Naive neonatal 6

value: spleen

value: splenocytes


title: Spatial RNA seq of Homo sapiens : P21 CD45 ROI1


title: siScr_Mock_2


title: Naive neonatal 7


title: 21


title: siScr_Mock_1


title: 15


title: RXMM_siZBP1_AP1_3

value: qVD and BB


title: Naive neonatal 4

value: No


title: Spatial RNA seq of Homo sapiens : P21 CD45 ROI2

value: ovarian high grade serous carcinomas FFPE (formalin fixed paraffin embedded)


title: Naive young adult female 2

value: Young adult


title: siRipk3_Mock_2

value: Primary cortical neuron

value: B6J (WT)


title: siRipk3_Mock_3


title: Spatial RNA seq of Homo sapiens : P21 SMA ROI1


title: RXMM_siZBP1_AP1_1

value: immortalized MEFs

value: recombined RXMM


title: Naive neonatal 3


title: 13


title: RXMM_siRIPK1_AP1_3


title: Naive neonatal 2


title: 9


title: RXMM_siRIPK1_AP1_1


title: siScr_Mock_3


title: siScr_ZIKV_1

value: Zika virus


title: RXMM_siTICAM_AP1_2


title: 27

source_name: skin

value: skin

value: induced osteoblasts


title: RXMM_siTICAM_AP1_3


title: RXMM_siTICAM_AP1_1


title: RXMM_siSCR_AP1_3


title: 25


title: CS18h neonatal 5

value: Neonatal


title: RXMM_siZBP1_AP1_2


title: CS18h neonatal 6


title: 22


title: RXMM_siZBP1_Mock_3

value: qVD only


title: 19


title: CS18h neonatal 4


title: RXMM_siSCR_AP1_1


title: RXMM_siZBP1_Mock_2


title: 16


title: CS18h neonatal 3


title: RXMM_siZBP1_Mock_1


title: CS18h neonatal 2


title: RXMM_siRIPK1_Mock_3


title: RXMM_siRIPK1_AP1_2


title: RXMM_siRIPK1_Mock_2


title: RXMM_siRIPK1_Mock_1


title: Naive neonatal 1


title: RXMM_siTICAM_Mock_3


title: BCG neonatal 7

value: BCG


title: W08F

value: fibroblast


title: RXMM_siTICAM_Mock_2


title: RXMM_siSCR_AP1_2


title: RXMM_siTICAM_Mock_1


title: RXMM_siSCR_Mock_3


title: 12


title: BCG neonatal 5

value: spleen


title: RXMM_siSCR_Mock_2


title: RXMM_siSCR_Mock_1


title: 24F


title: RXMM_AP1_qVD_24hrs5

source_name: Immortalized MEFs

value: Immortalized MEFs

value: BB homodimerizer and qVD


title: RXMM_AP1_qVD_24hrs6


title: 23F


title: U74F


title: 6F


title: BCG neonatal 4

value: splenocytes

value: No


title: BCG neonatal 3


title: RXMM_AP1_qVD_24hrs4


title: RXMM_AP1_qVD_24hrs3


title: RXMM_AP1_qVD_24hrs2


title: BCG neonatal 2


title: RXMM_AP1_qVD_24hrs1


title: BCG neonatal 1


title: RXMM_AP1_qVD_4hrs6


title: RXMM_AP1_qVD_4hrs5


title: MDA-MB-231 treated 24 h with RBCs from metastatic breast cancer patient 3

city: Santiago de Compostela

first: Clotilde

last: Costa

address: Travesia da Choupana sn

country: Spain

institute: FIDIS

data_processing:
nbinomWaldTest using DESeq2
Assembly: transcripts were assembled with StringTie
Supplementary files format and content: excel files each column includes data fro each sample

extract_protocol:
RNA was harvested using AllPrep DNA/RNA Mini kit (Qiagen, Hilden, Germany).
Truseq stranded total RNA Library with Ribo-Zero Globin

value: trile negative breast cancer

value: primed with RBCs from metastatic breast cancer patient 3


title: BCG neonatal 6


title: BCG CS18h neonatal 7


title: MDA-MB-231 treated 24 h with RBCs from metastatic breast cancer patient 2

value: primed with RBCs from metastatic breast cancer patient 2


title: RXMM_AP1_qVD_4hrs3


title: RXMM_AP1_qVD_4hrs4


title: BCG CS18h neonatal 6


title: RXMM_AP1_qVD_4hrs2


title: MDA-MB-231 treated 24 h with RBCs from metastatic breast cancer patient 1

value: primed with RBCs from metastatic breast cancer patient 1


title: RXMM_Mock_qVD3

value: recombined RXMM


title: MDA-MB-231 treated 24 h with liposomes, replicate 3

value: primed with liposomes


title: RXMM_Mock_qVD2


title: MDA-MB-231 treated 24 h with liposomes, replicate 2


title: RXMM_Mock_qVD1


title: RXMM_AP1_24hrs6

value: BB homodimerizer


title: BCG CS18h neonatal 3


title: RXMM_AP1_24hrs4


title: BCG CS18h neonatal 4


title: 2F

value: skin


title: MDA-MB-231 treated 24 h with liposomes, replicate 1


title: BCG CS18h neonatal 2

value: Neonatal


title: RXMM_AP1_24hrs5


title: RXMM_AP1_24hrs3


title: RXMM_AP1_24hrs1


title: Healthy control 10

type: genomic

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

hyb_protocol: DNA was bisulfite converted, amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChips (Illumina)  according to the standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan)

data_processing: pOOBAH using sesame

label: Cy5 and Cy3

source_name: PBMC

label_protocol: Standard Illumina protocol

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifucation (Ficoll) of 28 patients diagnosed with PMF, 2 patients diagnosed with ET and 10 healthy donors.

extract_protocol: Genomic DNA was isolated using the QIAamp DNA Mini Kit.

value: Male

tag: age

tag: mutation

value: CTRL

value: PBMC


title: Healthy control 9


title: MDA-MB-231, treated 24 h with RBCs from healthy donor 3

value: primed with RBCs from healthy donor 3


title: RXMM_AP1_4hrs5

value: Immortalized MEFs


title: RXMM_AP1_qVD_4hrs1

value: BB homodimerizer and qVD


title: MDA-MB-231, treated 24 h with RBCs from healthy donor 1

value: primed with RBCs from healthy donor 1


title: BCG CS18h neonatal 5

value: spleen

value: splenocytes

value: BCG


title: Healthy control 8


title: MDA-MB-231 non treated, replicate 3

value: trile negative breast cancer

value: non-primed


title: RXMM_AP1_4hrs4

value: recombined RXMM


title: RXMM_AP1_4hrs3


title: RXMM_AP1_4hrs1


title: RXMM_AP1_4hrs6


title: MDA-MB-231 non treated, replicate 2


title: Healthy control 5

value: Female


title: RXMM_AP1_24hrs2

value: BB homodimerizer


title: MDA-MB-231 non treated, replicate 1


title: RXMM_Mock5

value: Mock


title: RXMM_Mock4


title: RXMM_Mock2