title: time point 0, complete medium, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R1C0


title: PCA4_Input

status: Public on Oct 09 2024

type: SRA

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

country: China

institute: Hunan University

library_source: transcriptomic

data_processing:
m6a-seq reads were filtered by fastp software with default parameters.
m6A-seq reads were aligned to the Ensembl hg38 genome using STAR software (version 2.5.3a) with default settings.
The exomePeak（Version 3.8）software was used for peak calling
Assembly: hg38
Supplementary files format and content: narrowPeak
Library strategy: m6a-seq

molecule: total RNA

organism: Homo sapiens

source_name: Human prostate cancer tissues

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

tag: tissue

value: Human prostate cancer tissues

tag: cell type

value: Human prostate cancer


title: Female_LPS rep5

city: Guangzhou

first: Wenjun

last: Yu

address: Nanfang Hospital, Southern Medical University

institute: Center for Genetics and Developmental Systems Biology, Department of Obstetrics and Gynecology

data_processing:
Quality control was performed by FastQC (v0.11.8) with passing all criteria.
Sequence reads were aligned to mouse genome MM10 (UCSC) using STAR (v2.7.1a) under the default parameters.
Aligned reads were quantified using HTSeq-counts (v0.11.2)
Low and un-expressed genes with < 3 reads in at least 5 samples in a group were omitted from the analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for all Samples

organism: Mus musculus

source_name: Whole brain

extract_protocol:
Total RNA was isolated using the RNeasy Plus Universal Mini Kit (Qiagen) according to the instruction.
RNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: The female mice (16th day of pregnancy) received an intraperitoneal injection with LPS (150ug/kg) or saline (150ug/kg). For each treatment group, 5 whole brain RNA samples of the female offspring (postnatal 56 days) were prepared.

value: Whole brain

tag: genotype

value: WT

tag: treatment

value: Maternal LPS injection

tag: time

value: 8 weeks


title: PCA4_IP

tag: rip antibody


title: KIRP8rep3

city: San Joan d'Alacant

first: Eloísa

last: Herrera

address: Av Ramon y Cajal s/n

department: Instituto Neurociencias Alicante

country: Spain

institute: CSIC-UMH

data_processing:
All sequenced datasets adapters were trimmed using cutadapt v1.18 (Martin, 2011) and aligned to mm10. Only reads with mapq > 10.
Data was processed with the extensive use of custom scripts, and Samtools (v1.9) (Li et al., 2009), bedtools v2.26.0 (Quinlan and Hall, 2010).
RNA-seq data: Reads were aligned with STAR (v2.5.0c) (Dobin et al., 2013). To retrieve differentially expressed genes (DEG), mapped reads were counted with HTSeq v0.6.1 (Anders et al., 2015) and processed by DESeq2 (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: bw files from whole genome alignments normalized to RPKM (read per kilobase per million sequenced reads).

source_name: Retinal Ganglion Cells

growth_protocol: Kir2.1eYFPFfl-Stop line was generated using human Kir2.1 cDNA (Benjumeda et al., 2013) and cloned in pEYFP-N1 plasmid to add the eYFP reporter protein at the C-terminal of Kir2.1. Subsequently, it was subcloned in A-102 with a CAG promoter and a fl-flanked STOP cassette upstream the transgene. The linearized and purified construct was injected in mice oocytes (CEBATEG, Barcelona).  Brn3b-cre line was obtained from Dr. George Vann Bennet’s laboratory in Duke University Medical Center. Sert-cre line (Tg(Slc6a4-cre)ET33Gsat) belongs to the GENSAT Project at Rockefeller University (Stock Number: MMRC. 031028-UCD). Mice were housed in a timed-pregnancy breeding colony at the Instituto de Neurociencias de Alicante, Spain. Conditions and procedures were approved by the IN Animal Care and Use Committee and met European (2013/63/UE) and Spanish regulations (RD 53/2013).

extract_protocol:
RNAseq: Retinas were dissected out from P4 or P11 Brn3b-Kir2.1 or Brn3b-cre mice. Isolated retinas were enzymatically dissociated in a mixture of collagenase/Trypsin and BSA for 20 minutes at 37.C followed by mechanical dissociation. Total RNA extraction was performed with Arcturus. Picopure. RNA isolation Kit (ThermoFisher Scientific). The samples were sequenced according to the manufacturer instructions in a HiSeq Sequencing v4 Chemistry (Illumina, Inc).
RNAseq samples were sent for library preparation and NGS service to Fasteris SA (Switzerland).

tag: strain

value: retina

tag: age

value: post natal day 8

tag: number of reads


title: KIRP8rep2


title: Female_LPS rep4


title: Female_LPS rep3


title: CUTandRUN_p53koKPC_DMSO_p53Epicypher

city: Cambridge

first: Dig

middle: B

last: Mahat

email: mahat@mit.edu, dbm222@cornell.edu

state: MA

address: Koch Institute, MIT, 500 Main St, Building 76, #417

department: Koch Institute for Integrative Cancer Research

country: USA

institute: Massachusetts Institute of Technology

library_source: genomic

data_processing:
We clipped adapters from CUT&RUN reads using Cutadapt. We discarded reads shorter than 15 bp as they map to multiple sites in the genome. We mapped the reads to the mouse genome mm10 in the --very-sensitive-local mode using bowtie2, requiring them to uniquely map to the genome. We then removed the PCR duplicates using the unique molecular identifiers (UMIs). We subsampled reads in the treatment group to match the reads in control (IgG) group and called peaks using SEACR_1.3.
Assembly: mm10
Supplementary files format and content: tab-delimited bedgraph files, which includes raw counts for each Sample
Library strategy: CUT&RUN

molecule: genomic DNA

growth_protocol: PDAC cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 4.5 g/L D-Glucose, L-Glutamine, 110 mg/L Sodium Pyruvate (Gibco, 11995) plus 10% heat inactivated fetal bovine serum (Tissue Culture Biologics cat.no. # 101HI, lot # 101226) on tissue culture-treated 10 cm plates (Corning, CLS430167). Cells were grown at 37°C and 5% CO2 and passed with 0.25% Trypsin-EDTA (Gibco, 25200) when 70% confluency was reached.

extract_protocol:
We purified the released DNA fragments after CUT with using SPRIselect reagent and eluted the DNA.
We purified the released DNA fragments using SPRIselect reagent. We quantified the eluted DNA using a Qubit fluorometer and prepared sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) according to the manufacturer's instructions. The resulting libraries were sequenced on an Illumina NextSeq 500.

treatment_protocol: Trp53R172H/- and Trp53-/- cells were treated with 5 um TPCA-1 for 24 hours.

tag: cell line

value: pancreatic ductal adenocarcinoma


title: KIRP8rep1


title: CUTandRUN_KPC_DMSO_p53Epicypher


title: WTP8rep3

value: wild type


title: CUTandRUN_KPC_5umTPCA1_p53Epicypher


title: NAT4_Input

source_name: Human paracancer tissues

value: Human paracancer tissues


title: Female_Saline rep2

value: Maternal Saline injection


title: PCA1_IP


title: CUTandRUN_p53koKPC_5umTPCA1_p53Epicypher


title: CUTandRUN_p53koKPC_5umTPCA1_NFkB


title: Bone marrow-derived MDSCs, mrWNT2 treated, Day6

city: Shenzhen

first: Albert

last: CUI

state: Guangdong

address: Xueyuan Avenue, Nanshan District, Shenzhen

institute: Shenzhen University

description:
gene_fpkm.txt
gene_count.txt

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: Bone marrow

growth_protocol: Cells were maintained in RPMI 1640 supplemented with 10% heat-treated FBS (fetal bovine serum) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Cells  were treated  at day 0 and day 3, respectively

value: Bone marrow

value: Bone marrow-derived MDSCs

value: Myeloid cells

value: mrWNT2 treatment


title: NAT4_IP


title: WTP8rep2


title: NAT1_Input


title: CUTandRUN_p53koKPC_DMSO_NFkB


title: Bone marrow-derived MDSCs, Control, Day6

description:
gene_fpkm.txt
gene_count.txt

value: Vehicle treatment


title: NAT1_IP


title: PCA1_Input

value: Human prostate cancer tissues


title: KIRP4rep3

value: post natal day 4


title: CUTandRUN_KPC_5umTPCA1_NFkB


title: KIRP4rep2


title: LNCAP_2_Input

data_processing:
RIP-seq reads were filtered by fastp software with default parameters.
RIP-seq reads were aligned to the Ensembl hg38 genome using STAR software (version 2.5.3a) with default settings.
The exomePeak（Version 3.8）software was used for peak calling
Peaks were annotated using bedtools（Version 2.25.0）. The deepTools（version 2.4.1）was used for peak distribution analysis.
The differentially binding peaks were identified by a python script，using fisher test.
Assembly: hg38
Supplementary files format and content: xls, peaks

source_name: LNCAP

growth_protocol: RPMI-1640, 20% (for LNCAP) or 10% (for PC3) fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RIP assay was performed on PC3 or LNCAP by SeqHealth (Wuhan, China). Tissue was collected and frozen in liquid nitrogen. The cells was treated with cell lysis buffer. The 10% lysis sample was stored and named “input”, and 80% was used in immunoprecipitation reactions with anti-METTL3 antibodyand named “IP”, and 10%  was incubated with rabbit IgG (Cell Signaling Technology) as a negative control and named “IgG”，respectively. The RNA of input and IP was extracted using TRIzol reagent (Invitrogen, Invitrogen, cat. NO 15596026)
The stranded RNA sequencing library was constructed by using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: LNCAP

value: Human prostate cancer


title: Female_LPS rep2

value: Whole brain

value: WT

value: Maternal LPS injection


title: Female_LPS rep1

value: 8 weeks


title: CUTandRUN_KPC_DMSO_NFkB

value: pancreatic ductal adenocarcinoma


title: KIRP4rep1

value: retina


title: CUTandRUN_p53koKPC_H3K4me3


title: CUTandRUN_KPC_H3K4me3


title: WTP8rep1

value: post natal day 8

value: wild type


title: LNCAP_1_Input


title: WTP4rep2


title: Cell, empty fruit bunch culture (ref4)

type: RNA

city: Tsukuba

first: Sirilak

last: Baramee

state: Ibaraki

address: 1-1 Ohwashi

country: Japan

institute: Japan International Research Center for Agricultural Sciences

description:
Cell at mid-log phase
SAMPLE 5

data_processing:
For the normalization, it uses Triosephosphate isomerase gene (Tpi) as the calibrator gene.
Fold Change worksheet reports the ratios between 2 carbon source.

label: SYBR Green

organism: Acetivibrio saccincola

source_name: Strain A7 cell, empty fruit bunch culture, 24 hours

label_protocol: The cDNA was synthesized from 40 ng of RNA using the QuantiTect Reverse Transcription Kit (QIAGEN). The cDNA was diluted ten times and stored at −20 °C until use.

growth_protocol: H. saccincola A7 was cultivated anaerobically at 55 oC in Basal medium (BMN) with the following composition per liter: 2.9 g K2HPO4, 1.5 g KH2PO4, 2.1 g urea, 6 g yeast extract, 0.01 g CaCl2·2H2O, 2.5 g Na2CO3, 0.5 g L-cysteine-HCl, 0.5 mg resazurin, and 200 µl mineral solution (25.0 g/L MgCl2·6H2O, 0.312 g/L FeSO4·7H2O, and 37.5 g/L CaCl2·2H2O).

extract_protocol: Bacterial cultures in each carbon source were harvested at mid-log phase, treated with RNA Protect Bacteria reagent immediately according to the manufacturer’s instructions and stored at −80 °C until extraction. Total RNA was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany), including on-column DNase treatment.

treatment_protocol: H. saccincola A7 was cultured in the BMN medium in which cellobiose, cellulose, xylan, cellulose-xylan mixture, or EFB at a concentration of 1% (w/v) was used as a sole carbon source.

tag: cultivation time

value: 24 hours


title: WTP4rep1


title: Cell, xylan culture (ref4)

description:
Cell at mid-log phase
SAMPLE 3

source_name: Strain A7 cell, xylan culture, 48 hours

value: 48 hours


title: LNCAP_2_IP


title: Cell, cellulose-xylan mixed culture (ref3)

description:
Cell at mid-log phase
SAMPLE 4

source_name: Strain A7 cell, cellulose-xylan mixed culture, 12 hours

value: 12 hours


title: LNCAP_1_IP


title: CUTandRUN_p53koKPC_H3K27Ac


title: PC3_2_Input


title: OO_L_4

city: East Lansing

first: Peter

last: Schall

state: MI

address: 474 S. Shaw Lane

department: CMIB ANS

institute: Michigan State University

data_processing:
Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1
Trimming was conducted utilizing Fastp (v0.20.0) with the following settings: reads begining with polyC nuceltoides were removed, minimum quality threshold of 20, minimum length of 20, removal of low complexity/poly-nucleotide reads.
The rhesus  cDNA genome (Mmul build v10.0, genome annotation release-100) was downloaded from Ensembl and indexed and transcript abundance quantified with Kallisto (v0.44.0), using standard settings.
Assembly: Mmul_v10.0
Supplementary files format and content: tab-delimited Kallisto output files for each sample

organism: Macaca mulatta

source_name: Rhesus oocytes

growth_protocol: The ovaries from adult females at necropsy for issues that would not affect reproduction (e.g. experimental surgery, trauma, etc…) were placed in PBS immediately after recovery and cell types were obtained from individual follicles.

extract_protocol:
PicoPure RNA extraction kit
Ovation RNA-Seq System v2

treatment_protocol: Cells were isolated from antral follicles of different sizes

value: Rhesus oocytes

tag: condition

value: Large follicle


title: Cell, cellobiose culture (rep4)

description:
Cell at mid-log phase
SAMPLE 1

source_name: Strain A7 cell, cellobiose culture, 15 hours

value: 15 hours


title: PC3_2_IP


title: NF54-gexp02-Tom, Sexualrings, IP, Rep1

city: Barcelona

first: SANDRA

last: NHIM

address: 153 Carrer del Rossello

institute: Isglobal

data_processing:
After a quality check using FastQC (v.0.11.9), reads were trimmed, and repetitive k-mers were removed using BBDUK (v.36.99) with the parameters ktrim = r, k = 22, and mink = 6.
Reads were aligned to the reference genome (P. falciparum 3D7 [PlasmoDB v28]) using Bowtie2 (v.2.3.0), and duplicate reads were excluded using the PICARD suite (v.4.1.9.0) with the RemoveDuplicates command.
Peak calling was performed using MACS2 (v.2.2.7.1) with the parameters -f BAMPE -B -g 2.41e7 –keep-dup all –fe-cutoff 1.5 -nomodel –extsize 150.
To calculate the normalized coverage of enrichment over the input (log2 transformed) at a 10-bp resolution, we used the DeepTools (v.3.5.0) BamCompare command with the parameters –normalizeUsing RPKM -bs 10 –smoothLength 200 –pseudocount 10.
Assembly: PlasmoDB v55
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Plasmodium falciparum

source_name: Cell line

growth_protocol: E5ind was maintained at 3% hematocrit with B+ RBCs in standard parasite culture medium with Albumax II and no human serum in an atmosphere containing 5% CO2 and 3% O2, balanced with N2.

extract_protocol:
After saponin lysis and formaldehyde-glycine treatment, chromatin was extracted with the MAGnify kit (Life technology), then sonicated with Covaris M220 to obtain 150bp-200bp DNA fragments
For library preparation, we used the NEBNext Multiplex Oligos for Illumina (New England BioLabs [NEB]), 8 to 10 cycles amplification with the KAPA HiFi PCR kit (Kapa Biosystems) and AMPure XP beads for purification steps

value: Cell line

value: Sexual rings

value: H3K9me3 (Diagenode, #A2217P)


title: OO_L_3


title: CUTandRUN_KPC_p300


title: NF54-gexp02-Tom, Asexualrings, IP, Rep1

value: Asexual rings


title: OO_L_2


title: OO_L_1


title: NF54-gexp02-Tom, Sexualrings, input, Rep1


title: CUTandRUN_KPC_IgG_runWithLeica


title: PC3_1_Input

value: Human prostate cancer


title: NF54-gexp02-Tom, Asexualrings, input, Rep1


title: Cell, cellulose culture (rep4)

description:
Cell at mid-log phase
SAMPLE 2

source_name: Strain A7 cell, cellulose culture, 24 hours


title: OO_M_4

value: Medium follicle


title: CUTandRUN_p53koKPC_p53Leica


title: E5ind, StageII-IIIgametocyte, IP, Rep2

value: StageII-IIIgametocyte


title: CUTandRUN_KPC_p53Leica

value: pancreatic ductal adenocarcinoma


title: PC3_sh812_rep2

data_processing:
RNA-seq reads were filtered by fastp software with default parameters.
RNA-seq reads were aligned to the Ensembl hg38 genome using STAR v2.7.1a with default settings.
The featurecounts software was utilized to quantify gene expression.
The DESeq2 package was utilized to identify differentially expressed genes.
Assembly: hg38
Supplementary files format and content: txt, gene count

growth_protocol: RPMI-1640, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Total RNA was extracted from cultured cells with Total RNA  KitI (Omega,USA) according to the manufacturer's protocol.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.


title: OO_M_3


title: CUTandRUN_KPC_H3K27Ac


title: E5ind, StageIgametocyte, IP, Rep2

value: StageIgametocyte


title: CUTandRUN_p53koKPC_p300


title: OO_M_2


title: PC3_shNC_rep2

value: shNC


title: PC3_shNC_rep1


title: OO_M_1


title: CUTandRUN_KPC_IgG_runWithEpicypher


title: PC3_1_IP


title: CUTandRUN_p53koKPC_p53Epicypher


title: E5ind, Asexualrings, IP, Rep2


title: E5ind, Sexualrings, IP, Rep2


title: OO_S_4

value: Small follicle


title: CUTandRUN_KPC_p53Epicypher


title: OO_S_3


title: E5ind, StageII-IIIgametocyte, input, Rep2


title: rpoC mutant host infected with phage K- 02 min time point (replicate D)

city: Silver Spring

first: Ramchander Rohit

last: Kongari

state: Maryland

address: 10903 New Hampshire Ave

department: Department of Bacterial, Parasitic and Allergenic products

institute: United States Food and Drug Administration

description:
Novaseq S2 100 bp paired end run
MR206_02_D

data_processing:
Initial quality check was done using FastQC and read mapping distribution was analyzed using MultiQC
Reads were mapped using Bowtie2 and visualized using IGV. For quantitative analysis, read counts were obtained using Kallisto and differntial expression analysis was done using EdgeR package on the Rstudio platform
Assembly: Reads were mapped to the full length genome of phage K (NC_005880.2) and NRS384 (CP027476.1) using Bowtie2 to check for transcriptional activity. No genome building/assembly was performed for our analysis purposes.
Supplementary files format and content: Transcripts per million (TPM) data for all the gene and tRNA features annotated in phage K (as calculated by Kallisto) from all the samples are provided as a separate file

organism: Staphylococcus aureus

growth_protocol: 25 ml TSB cultures were innoculated with 100 ul of overnight cultures and  grown at 30 °C

extract_protocol:
1 mL samples were collected at 2, 5, 10, 20, 30, 40 min after addition of phage, and total RNA was extracted from these samples using the QIAGEN RNEasy Mini Kit.
The samples were further treated with Turbo DNAse to degrade phage/bacterial DNA, and the RNA quality was measured using an Agilent 2100 Bioanalyzer. Ribosomal RNA was depleted using the Illumina Ribozero plus kit, and Illumina RNA-seq libraries were prepared without any enrichment.
A strand-specific RNA seq Novaseq S2 100-bp paired end run was performed on the samples using an Illumina Novaseq 6000 instrument

treatment_protocol: Phage K was added at an MOI of ~5 once the O.D. of the cultures reached 0.3

tag: time point

value: 02 min

value: bacterial cells

value: rpoC G17D

value: infected with phage K


title: PC3_sh812_rep1


title: E5ind, StageIgametocyte, input, Rep2


title: OO_S_1

value: Rhesus oocytes


title: OO_S_2


title: E5ind, Sexualrings, input, Rep2


title: 11wks_WT_4__SkMuscle

city: Seika-cho, Soraku-gun

first: Thomas

middle: N

last: Sato

state: Kyoto

address: 2-2-2 Hikaridai

institute: Karydo TherapeutiX, Inc.

description: 11wks_WT_4__raw-count-matrix.csv contains the raw count of the bulk RNA-seq.

data_processing:
Data mapping was performed by tophat2 (v2.1.1) and count data were generated by htseq-count (v0.9.1).
Assembly: mm10
Supplementary files format and content: The comma separated values file includes all raw count data.

source_name: Skeletal muscle (left)

extract_protocol:
Tissue preparation and RNA purification were as described in S. Kozawa et al. (doi: 10.1016/j.isci.2019.100791)
RNA libraries were constructed by using QuantSeq 3' mRNA-seq Library Prep Kit for Illumina.
QuantSeq 3' mRNA-seq

value: Skeletal muscle (left)

value: C57BL6/N Jcl

tag: Sex

value: Male

value: Wild type

value: 11 weeks


title: PMP-10_RNA-seq

city: Daejeon

first: sungghwan

last: park

address: Gwahak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Reference genome sequence data from Homo sapiens were obtained from the NCBI Genome database (assembly ID: GRCh38). The reference genome indexing and read mapping of tissue samples were performed using STAR software (ver. 2.5.4b).
Then, the read counts per million fragments mapped (CPM) of each sample were estimated and were log2-transformed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text format with log2 transformed CPM values of transcripts.

source_name: Pseudomyxoma Peritonei

extract_protocol:
Total RNA was extracted from tissues using TRIzol reagent (Invitrogen, Carlsbad, CA) and stored at -80°C. RNA quality and integrity were assessed using the RNA Integrity Number (RIN) and the DV200 metric, which were determined with an RNA 6000 Nano Kit and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
The sequencing library was prepared using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA). Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNA. Adapters were ligated to the cDNA, and the fragments were amplified by polymerase chain reaction (PCR). Paired-end sequencing reads (2 x 100 bp) were obtained using the Novaseq platform (Illumina, San Diego, CA).

tag: histologic type

value: Pseudomyxoma Peritonei

tag: source of tumor tissue

value: Peritoneal implant


title: E5ind, Asexualrings, input, Rep2

value: Cell line

value: Asexual rings


title: 11wks_WT_4__Pancreas

source_name: Pancreas

value: Pancreas


title: PMP-12_RNA-seq


title: PMP-11_RNA-seq


title: PMP-9_RNA-seq


title: GC_L_3

source_name: Rhesus granulosa cells

value: Rhesus granulosa cells

value: Large follicle


title: E5ind, StageII-IIIgametocyte, IP, Rep1

value: StageII-IIIgametocyte

value: H3K9me3 (Diagenode, #A2217P)


title: PMP-8_RNA-seq


title: PMP-7_RNA-seq


title: PMP-6_RNA-seq


title: E5ind, StageIgametocyte, IP, Rep1

value: StageIgametocyte


title: GC_L_2


title: 11wks_WT_4__Lung

source_name: Lung (left lobe)

value: Lung (left lobe)


title: 11wks_WT_4__Liver

source_name: Liver

value: Liver


title: E5ind, Sexualrings, IP, Rep1

value: Sexual rings


title: 11wks_WT_4__Skin

source_name: Skin (dorsal)

value: Skin (dorsal)

value: C57BL6/N Jcl


title: 11wks_WT_4__Kidney

source_name: Kidney (left)

value: Kidney (left)

value: Male

value: Wild type


title: GC_L_1


title: E5ind, Asexualrings, IP, Rep1


title: PMP-5_RNA-seq

value: Pseudomyxoma Peritonei

value: Peritoneal implant


title: GC_M_4

value: Medium follicle


title: GC_L_4


title: E5ind, StageII-IIIgametocyte, input, Rep1

value: Cell line


title: PMP-4_RNA-seq


title: GC_M_3

value: Rhesus granulosa cells


title: E5ind, StageIgametocyte, input, Rep1


title: 11wks_WT_4__Fat

source_name: Fat (White adipose tissue)

value: Fat (White adipose tissue)

value: 11 weeks


title: PMP-2_RNA-seq


title: PMP-3_RNA-seq


title: 11wks_WT_4__Heart

source_name: Heart

value: Heart


title: 11wks_WT_4__Brain

source_name: Brain

value: Brain


title: GC_M_1


title: E5ind, Sexualrings, input, Rep1


title: PMP-1_RNA-seq


title: GC_M_2


title: 11wks_WT_3__SkMuscle

description: 11wks_WT_3__raw-count-matrix.csv contains the raw count of the bulk RNA-seq.

value: Skeletal muscle (left)


title: 11wks_WT_4__Spleen

source_name: Spleen

value: Spleen


title: GC_S_4

value: Small follicle


title: E5ind, Asexualrings, input, Rep1

value: Asexual rings


title: PMP-9N_RNA-seq

source_name: Normal

value: Normal

tag: source of healthy tissue

value: peritoneum


title: JS006 prm1 Musashi replica 2

city: Paterna

first: Guillermo

last: Rodrigo

address: Calle del Catedrático Agustín Escardino Benlloch, 9

institute: Agencia Estatal Consejo Superior de Investigaciones Científicas

data_processing:
The BioConductor R package DESeq2 was used to perform the differential gene expression analysis.
The statistical significance was evaluated by means of a Wald test in pair-wise data (i.e., two conditions) with a correction for multiple testing using the Benjamini-Hochberg’s FDR.
Assembly: NZ_CP009273.1 Escherichia coli BW25113 strain K-12 chromosome
Supplementary files format and content: tab-delimited text file includes counts for each gene in samples
Supplementary files format and content: tab-delimited text file includes fold change and p-values for each gene in samples

organism: Escherichia coli

source_name: bacteria

growth_protocol: E. coli JS006 cells transformed with pRM1+ or with a void plasmid (in duplicate) were grown in LB medium at 37 ºC to reach an OD600 around 0.4.

extract_protocol:
Total RNA was extracted from RNA-seq aliquots in TRIzol and ribosomal RNA (rRNA) was removed.
mRNAs were fractionated and converted into Illumina compatible cDNA libraries.

treatment_protocol: Cells were harvested from 200 mL of culture by rapid filtration through a Kontes 90 mm filtration apparatus with 0.45 μm nitrocellulose filters (Whatman).

value: bacteria

value: MG1655 [delta]araC [delta]lacI KanS

tag: plasmid

value: pRM1+ (MSI-1 coding)


title: PMP-7N_RNA-seq


title: GC_S_3

tag: cell type


title: 11wks_WT_3__Skin

tag: tissue

value: Skin (dorsal)

value: C57BL6/N Jcl

value: Male

tag: genotype

value: Wild type


title: 11wks_WT_3__Spleen


title: JS006 prm1 Musashi replica 1


title: GC_S_2

value: Rhesus granulosa cells


title: PMP-6N_RNA-seq


title: JS006 prm1 void replica 2

value: pRM1 void plasmid


title: 11wks_WT_3__Pancreas

value: Pancreas

value: 11 weeks


title: GC_S_1


title: PMP-5N_RNA-seq


title: JS006 prm1 void replica 1


title: 11wks_WT_3__Lung

value: Lung (left lobe)


title: 11wks_WT_3__Kidney

value: Kidney (left)


title: PMP-3N_RNA-seq


title: PMP-4N_RNA-seq


title: JS006 prm1 Musashi replica 2

library_source: other

data_processing:
The BioConductor R package DESeq2 was used to perform the differential gene expression analysis.
The statistical significance was evaluated by means of a Wald test in pair-wise data (i.e., two conditions) with a correction for multiple testing using the Benjamini-Hochberg’s FDR.
Assembly: NZ_CP009273.1 Escherichia coli BW25113 strain K-12 chromosome
Supplementary files format and content: tab-delimited text file includes counts for each gene in samples
Supplementary files format and content: tab-delimited text file includes fold change and p-values for each gene in samples
Library strategy: Ribo-seq

molecule: other

growth_protocol: E. coli JS006 cells transformed with pRM1+ or with a void plasmid (in duplicate) were grown in LB medium at 37 ºC to reach an OD600 around 0.4

extract_protocol:
Aliquots were lysed in Tris-based ice-cold polysome lysis buffer (Tris-based) by bead beating . Lysates were clarified by centrifugation and ribosomes were subsequently pelleted from lysates by ultracentrifugation. Samples were then digested with MNase, RNA was purified and ribosome-protected mRNA fragments ranging 20-40 nt in length were selected for size using 15% urea PAGE gels. rRNA was depleted from samples using custom biotinylated rRNA depletion oligos for E. coli.
mRNAs were fractionated and converted into Illumina compatible cDNA libraries

treatment_protocol: Cells were harvested from 200 mL of culture by rapid filtration through a Kontes 90 mm filtration apparatus with 0.45 μm nitrocellulose filters (Whatman)


title: CC_L_4

source_name: Rhesus cumulus cells

value: Rhesus cumulus cells

value: Large follicle


title: 11wks_WT_3__Liver

value: Liver


title: CC_L_3


title: CC_L_2


title: JS006 prm1 Musashi replica 1


title: PMP_FFPE_9_RNA-seq

extract_protocol:
Total RNA was extracted from FFPE tissuesusing RNeasy FFPE Kit(Qiagen, Valencia, CA)and stored at -80°C.RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) with an RNA Integrity Number (RIN) value greater than or equal to 7.
The sequencing library was prepared using the TruSeq RNA Access Library Prep Kit (Illumina, San Diego, CA). Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNA. Adapters were ligated to the cDNA, and the fragments were amplified by polymerase chain reaction (PCR). Paired-end sequencing reads (2 x 100 bp) were obtained using the Novaseq platform (Illumina, San Diego, CA).

value: Pseudomyxoma Peritonei

value: Peritoneal implant


title: 11wks_WT_3__Fat

value: Fat (White adipose tissue)


title: CC_L_1


title: JS006 prm1 void replica 2

value: bacteria

value: MG1655 [delta]araC [delta]lacI KanS


title: 11wks_WT_3__Heart

value: Heart

value: C57BL6/N Jcl


title: PMP-1N_RNA-seq

value: Normal

value: peritoneum


title: JS006 prm1 void replica 1

value: pRM1 void plasmid


title: CC_M_4

value: Medium follicle


title: CC_M_2


title: PMP_FFPE_8_RNA-seq


title: 11wks_WT_3__Brain

value: Brain

value: Male

value: Wild type

value: 11 weeks


title: 11wks_WT_2__Spleen

description: 11wks_WT_2__raw-count-matrix.csv contains the raw count of the bulk RNA-seq.

extract_protocol:
Tissue preparation and RNA purification were as described in S. Kozawa et al. (doi: 10.1016/j.isci.2019.100791)
RNA libraries were constructed by using QuantSeq 3' mRNA-seq Library Prep Kit for Illumina.

value: Spleen


title: PMP_FFPE_7_RNA-seq


title: CC_M_3

value: Rhesus cumulus cells


title: BC17166, scRNAseq

city: Seoul

first: SUMIN

last: CHA

address: 88, Olympic-ro 43-gil, Songpa-gu

institute: Asan Institute for Life Sciences, Asan Medical Center

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger 6.1.2
Assembly: hg38
Supplementary files format and content: tab-separated value files and matrix files

source_name: Breast cancer

extract_protocol:
Breast cancer tissues were placed in RPMI 1640 medium (11875093, Thermo Fisher Scientific, Waltham, MA, USA) and promptly transported to the laboratory within two hours post-resection. After washing with Dulbecco’s Phosphate Buffered Saline (DPBS, L0615, Biowest, Nuaillé, France) containing 1× ZellShield anticontaminant agent (Minerva Biolabs, Berlin, Germany), the tumour tissues were minced into 1-mm-diameter pieces. The minced breast cancer tissue was incubated for 1 h in digestion buffer (DMEM-F12 (11330032, Thermo Fisher Scientific), 2% FBS (Corning, VA, USA), 1% penicillin/streptomycin (15140-122, Thermo Fisher Scientific), 10 μg/mL insulin (51500056, Thermo Fisher Scientific), and 10 ng/mL epidermal growth factor (PHG0311, Thermo Fisher Scientific) supplemented with 1× collagenase/ hyaluronidase (CA094-002, Gendepot, Barker, TX, USA). The digested samples were centrifuged at 80 × g for 30 s, and the resultant supernatant was filtered through a 70-μm nylon mesh strainer (352350, Corning Life Sciences, Tewksbury, MA, USA). The pellets from the digested samples were resuspended in 0.25% trypsin/EDTA (25200072, Thermo Fisher Scientific) and incubated for 3–5 min to release single cells. Once a single cell suspension was obtained, cold Hank’s balanced salt solution (L0612, Biowest) containing 2% FBS was added, and cells were recovered through centrifugation at 300 × g for 5 min. Subsequently, the cells from the supernatants and the single cells from the pellet were combined, counted, and cryopreserved. CD45+ cells were isolated either through magnetic bead sorting or fluorescence-activated cell sorting (FACS). In the magnetic separation method, dead cells were initially removed using a dead cell removal kit (130-090-101, Miltenyi Biotec, Auburn, CA, USA), followed by cell labelling with CD45-microbeads (130-045-801, Miltenyi Biotec) and enriched using a magnetic-activated cell sorting (MACS) column (130-042-901, Miltenyi Biotec) and MACS separator (130-091-051, Miltenyi Biotec). For FACS sorting, single cells were stained with an anti-human CD45 antibody (304016, Biolegend, San Diego, CA, USA) and resuspended in 4',6-diamidino-2-phenylindole solution (D1306, Thermo Fisher Scientific). CD45+ live cells were sorted using FACSAria (BD bioscience, San Jose, CA, USA). The isolated cells were resuspended in CS10 freezing media (100-1061, Stemcell Technologies, Bothell, WA, USA) and stored in an NL2 tank until the next use or were immediately sequenced
scRNA-seq library preparation was conducted using the Chromium Single Cell 3′ Kit v2 and the Chromium Next GEM Single Cell 3′ Kit v3 platform (10x Genomics, Pleasanton, CA, USA)

value: Breast cancer

value: CD45+ cells

tag: subtype

value: TNBC

tag: til value_(%)

tag: til level

value: Low


title: PMP_FFPE_6_RNA-seq

value: Pseudomyxoma Peritonei

value: Peritoneal implant


title: pericardial cells, female, larvae, rep3

city: Kiel

first: Judith

last: Bossen

address: Am Botanischen Garten 3-9

department: Molecular Physiology

country: Germany

institute: CAU Kiel, Zoological Institute

description: DEGs female 1w PNCs vs. larval PNCs.xlsx

data_processing:
CLC Genomics Workbench 9.5.2
Imported using Illumina Single Read import (FastQ); Quality Score = NCBI/Sanger or Illumina Pipeline 1.8 and later; failed reads were removed
Sequence reads were mapped to gene regions only using the Drosophila melanogaster genome (assembly Release 6 plus ISO1 MT)  (parameters: mismatch cost = 2, insertion cost = 2, deletion cost = 2, length fraction = 0.8, similarity fraction = 0.85, global alignment = no, strand specific = both, maximum number of hits for a read = 10, count paired reads as two = no, expression value = RPKM, calculate RPKM for genes without transcripts = no, use EM estimation = yes)
Differential expression for RNA-Seq was perfomed compairing to a control group (complete animals, GNCs/PNCs from 1 week old animals )
Assembly: Drosophila melanogaster Release 6 plus ISO1 MT
Supplementary files format and content: RPKM-value xlsx files include RPKM values for each sample
Supplementary files format and content: DEGs xlsx files include differentially expressed genes based on comparison to a control group

organism: Drosophila melanogaster

source_name: pericardial cells

growth_protocol: handC-GFP animals where raised at 25 °C until use for RNA isolation or dissection of the nephrocytes

extract_protocol:
Animals were opened in PBS and exposed nephrocytes were treated with 1 mg/ml collagenase for 15 min at 37 °C. Afterwards, individual nephrocytes were extracted using a microinjector (CellTram®4rOil, Eppendorf, Hamburg, Germany) equipped with glass capillaries and transfered inRoti®Zol (Roth, Karlsruhe, Germany).
RNA was extracted using RNAmagic after manufacturer's protocol (Bio-Budget Technologies GmbH, Germany). cDNA synthesis was performed after Hagemann-Jensen et al. 2020 with minor modifications. Due to low cDNA amount whole length cDNA was amplified via PCR by controlling cycle number to avoid overamplification with LA Taq polymerase (TAKARA BIO INC., Japan).
Library preparation was done  adopted to Picelli et al. 2014. The samples were equimolar pooled and quantified (with Agilent Bioanalyzer, DNA 7500). Sequencing was done on the NextSeq 500 (Illumina) using the High Output Kit v2.5 (75 cycles)

value: pericardial cells

value: handC-GFP

tag: developmental stage

value: larvae


title: pericardial cells, female, larvae, rep2


title: 11wks_WT_2__SkMuscle

source_name: Skeletal muscle (left)

value: Skeletal muscle (left)

tag: strain

value: C57BL6/N Jcl

tag: age


title: CC_M_1

value: Medium follicle


title: pericardial cells, female, larvae, rep1


title: pericardial cells, female, 5 week, rep3

description: DEGs female 5w PNCs vs 1w PNCs.xlsx

value: adult (5 week)


title: 11wks_WT_2__Skin

value: Skin (dorsal)

value: Male

value: Wild type


title: 11wks_WT_2__Pancreas

value: Pancreas

value: 11 weeks


title: PMP_FFPE_46_RNA-seq

source_name: Pseudomyxoma Peritonei


title: PMP_FFPE_42_RNA-seq


title: PMP_FFPE_43_RNA-seq


title: pericardial cells, female, 5 week, rep1

description: DEGs female 5w PNCs vs 1w PNCs.xlsx


title: 11wks_WT_2__Liver

value: Liver


title: pericardial cells, female, 3 week, rep3

description: DEGs female 3w PNCs vs 1w PNCs.xlsx

value: adult (3 week)


title: PMP_FFPE_45_RNA-seq


title: CC_S_2

value: Rhesus cumulus cells

value: Small follicle


title: CC_S_1


title: 293T, Mock, fraction 13 to 14, 48 hpi

city: New York

first: Chuan-Tien

last: Hung

state: New York

address: 1468 Madison Avenue

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Trimming, alignment, and quantification were all performed in Partek Flow v10.0. The reference genome was generated by concatenating the hg38 (release 110) using STAR (v2.7.11a). Counts were generated with Homo sapiens annotation (Partek E/M). Normalization was performed by transcripts per kilobase million. Unaligned reads were then aligned to rHPIV3-JS-G.luc-EGFP (Genbank: KY295925) using BWA-MEM (BWA v0.7.17). Transcriptional gradient analyses was performed using IGVtools on samples with >100 aligned reads.
Assembly: hg38 and rHPIV3-JS-G.luc-EGFP (KY295925)
Supplementary files format and content: The processed data file includes normalized gene counts (shown by TPM values) for each sample.

source_name: HEK 293T

growth_protocol: HEK 293T cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted and on-column DNase I treated using Direct-zol RNA Miniprep kit.
RNA libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina.

tag: cell line

value: HEK 293T

value: human embryonic kidney cell

tag: treatment

value: Mock infected


title: 11wks_WT_2__Heart

value: Heart


title: PMP_FFPE_41_RNA-seq

value: Pseudomyxoma Peritonei

value: Peritoneal implant


title: 293T, Mock, fraction 11 to 12, 48 hpi


title: pericardial cells, female, 3 week, rep2

description: DEGs female 3w PNCs vs 1w PNCs.xlsx

value: pericardial cells

value: handC-GFP


title: 11wks_WT_2__Kidney

value: Kidney (left)

value: C57BL6/N Jcl


title: CC_S_3

tag: condition


title: 293T, Mock, fraction 9 to 10, 48 hpi


title: 293T, Mock, fraction 7 to 8, 48 hpi


title: 11wks_WT_2__Lung

value: Lung (left lobe)

tag: Sex

value: Male

value: Wild type


title: 11wks_WT_2__Brain

value: Brain

value: 11 weeks


title: PMP_FFPE_4_RNA-seq

tag: histologic type


title: Spontaneous tumor, 756OFF

city: Newark

first: Pingping

last: Hou

state: New Jersey

address: 205 South Orange Ave

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.
Assembly: GRCm38
Supplementary files format and content: DEGs csv files
Supplementary files format and content: Cell Ranger output files: barcodes.tsv, features.tsv, matrix.mtx

source_name: bulk pancreatic tumor

extract_protocol:
Tumors were dissociated into single cells using the Tumor Dissociation Kit from Miltenyi Biotec, followed by the removal of dead cells using the Dead Cell Removal Kit (Miltenyi Biotec). Cells were resuspended in PBS + 0.05% BSA at a concentration of 500-600 cells/μL for library preparation (10x Genomics).
Library was constructed according to manufacturer's protocol.

value: bulk pancreatic tumor

value: mixed cells

value: p48-Cre, tetO_LKrasG12D, ROSA_rtTA, Trp53Lox/+ (iKPC)

value: Doxycycline withdrawal


title: PMP_FFPE_38_RNA-seq

tag: source of tumor tissue


title: 11wks_WT_2__Fat

value: Fat (White adipose tissue)


title: pericardial cells, female, 5 week, rep2

description: DEGs female 5w PNCs vs 1w PNCs.xlsx

value: adult (5 week)


title: 293T, Mock, fraction 5 to 6, 48 hpi

value: HEK 293T

value: human embryonic kidney cell

value: Mock infected


title: garland cells, female, larvae, rep3

description: DEGs female 1w GNCs vs larval GCs.xlsx

source_name: garland cells

value: garland cells

value: handC-GFP

value: larvae


title: PMP_FFPE_37_RNA-seq

value: Pseudomyxoma Peritonei

value: Peritoneal implant


title: pericardial cells, female, 1 week, rep3

description:
DEGs female 1w PNCs vs 1w total.xlsx
DEGs female 1w PNCs vs. 1w GNCs.xlsx
DEGs female 1w PNCs vs. larval PNCs.xlsx
DEGs female 3w PNCs vs 1w PNCs.xlsx
DEGs female 5w PNCs vs 1w PNCs.xlsx

value: pericardial cells

value: adult (1 week)


title: 293T, Mock, fraction 15 to 16, 48 hpi


title: pericardial cells, female, 1 week, rep2


title: Spontaneous tumor, 183_Ki

description: 10X Genomics

value: p48-Cre, lox-stop-lox KrasG12D, Trp53lox/+ (KPC)


title: garland cells, female, larvae, rep1

description: DEGs female 1w GNCs vs larval GCs.xlsx


title: Zymosan + vehicle, 12h, mouse 4

city: Boston

last: Chiang

address: 60 Fenwood Rd. 3016Q

institute: Brigham and Women's Hospital

data_processing:
RNA-seq were performed and anlyzed by Azenta, who provided the following bioinformatics analysis workflow: Evaluate Sequence Quality, Trim reads, Map reads to Genome, Generate hit counts for genes/exons, Compare exon hit counts, Compare gene hit counts, Analyze Gene Ontology
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 ERCC reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with a p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison. Below are the results of the number of significantly differentially expressed genes for all comparisons provided.
A gene ontology analysis was performed on the statistically significant set of genes by implementing the software GeneSCF v.1.1-p2. The mgi GO list was used to cluster the set of genes based on their biological processes and determine their statistical significance. A list of genes clustered based on their gene ontologies was generated.
Assembly: Mus musculus C57BL/6 WT Genome assembly: GRCm39 (GCA_000001635.9)
Supplementary files format and content: txt files with raw counts and TPM values

molecule: polyA RNA

source_name: peritoneal exudate

extract_protocol:
mRNA were extracted for RNA-seq
Pre-made library – no library preparation performed

value: peritoneal exudate

value: mixed leukocytes

value: WT

value: Vechicle control


title: pericardial cells, female, 1 week, rep1


title: PMP_FFPE_34_RNA-seq


title: 293T, Mock, fraction 3 to 4, 48 hpi


title: PMP_FFPE_3_RNA-seq


title: Spontaneous tumor, 69

description: 10X Genomics

value: bulk pancreatic tumor

value: mixed cells

value: solvent


title: garland cells, female, larvae, rep2

description: DEGs female 1w GNCs vs larval GCs.xlsx


title: PMP_FFPE_30_RNA-seq


title: Zymosan + vehicle, 12h, mouse 3


title: pericardial cells, female, 3 week, rep1

description: DEGs female 3w PNCs vs 1w PNCs.xlsx

value: adult (3 week)


title: Zymosan + vehicle, 12h, mouse 1


title: PMP_FFPE_21_RNA-seq


title: PMP_FFPE_35_RNA-seq


title: Zymosan + vehicle, 12h, mouse 2


title: garland cells, female, 1 week, rep3

description:
DEGs female 1w GNCs vs 1w total.xlsx
DEGs female 1w GNCs vs larval GCs.xlsx
DEGs female 1w PNCs vs. 1w GNCs.xlsx


title: Spontaneous tumor, 752OFF

description: 10X Genomics

value: p48-Cre, tetO_LKrasG12D, ROSA_rtTA, Trp53Lox/+ (iKPC)

value: Doxycycline withdrawal


title: Grhl3-null replicate 1

city: Melbourne

first: Zihao

last: Deng

state: VIC

address: L6, The Alfred Centre, 99 Commercial Rd

department: Medicine (Alfred Hospital)

country: Australia

institute: Monash University

description: 10X Genomics

data_processing:
The raw sequencing data were processed using Cell Ranger (10X Genomics, version 3.0.0, https://www.10xgenomics.com/support/software/cell-ranger).
Assembly: mm10

source_name: Caudal half of the embryo

extract_protocol:
To generate animals for scRNA-seq, Grhl3+/- mice were intercrossed through timed mating. E8.5 embryos were harvested at 3 p.m. on the eighth day post-fertilisation. Embryos were dissected in DEPC-PBS and the yolk sac samples were utilised for genotyping as described above. The caudal half of five wild-type and three Grhl3-null embryos was separated using tungsten needles in 0.04% BSA (Sigma-Aldrich) in DEPC-PBS and then pelleted through centrifugation at 300 rcf for 3 mins at 4℃. The supernatant was removed, and the caudal half of the embryo was then incubated with 50 μL 0.25% (v/v) trypsin (Gibco) in DEPC-PBS for 5 mins at 37℃ and triturated with a 200 μL pipette tip to dissociate tissues. The digestion reaction was then inactivated by adding 100 μL 10% (v/v) FBS (Bovogen Biologicals) in DMEM (Gibco). Cells from five wild-type embryos and from three Grhl3-null embryos were pooled and filtered through Flowmi Cell Strainers (40 μm). Cells were then pelleted through centrifugation at 300 rcf for 3 mins at 4℃ and resuspended in 15 μL 10% (v/v) FBS (Bovogen Biologicals) in DMEM (Gibco) per embryo. Cell number and viability were assessed using a hemocytometer by mixing 8 μl cell suspension with 8 μl 0.4% (v/v) Trypan Blue Solution (Sigma-Aldrich) and a ~95% cell viability was observed in both wild-type and Grhl3-null samples. Cells were then diluted in 10% (v/v) FBS (Bovogen Biologicals) in DMEM (Gibco) to a final concentration of 1,000 cells/μL for single cell droplet generation and library preparation.
A Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 and a Chromium Controller from 10X Genomics were used to generate single cell droplets as per manufacturer’s instructions. Two wild-type and two Grhl3-null reactions were performed. Briefly, cell suspension with a master mix, gel beads and partitioning oil were loaded onto a Chromium Chip B to generate Gel Beads-in-emulsion. After this, samples were transferred into PCR tube strips and proceeded for reverse transcription and template switching using a T100 Thermal Cycler (Bio-Rad Laboratories). Synthesised full-length cDNA was then purified and amplified, followed by a clean-up reaction. The quality and quantity of amplified cDNA were assessed using an Agilent 4200 TapeStation with a High Sensitivity D5000 ScreenTape. Two wild-type and two Grhl3-null 3’ gene expression libraries were then constructed for sequencing as outlined in the manufacturer’s user guide. In short, cDNA amplicon from the previous reaction was fragmented and ligated with adaptors, and then subjected for a sample index PCR and a size selection with SPRIselect reagent. The quality and quantity of the libraries were again assessed again using an Agilent 4200 TapeStation with a High Sensitivity D5000 ScreenTape. Finally, the libraries were sequenced on an Illumina NextSeq 500 System with the NextSeq 500/550 High Output Kit v2.5 at a targeted sequencing depth of 400 million reads per library.

value: Caudal half of the embryo


title: Zymosan +  SPMs, 12h, mouse 4

value: SPMs


title: PMP_FFPE_20_RNA-seq

value: Pseudomyxoma Peritonei


title: PMP_FFPE_31_RNA-seq

value: Peritoneal implant


title: garland cells, female, 1 week, rep2

value: garland cells

value: handC-GFP


title: Grhl3-null replicate 2

description: 10X Genomics


title: PMP_FFPE_1_RNA-seq


title: PMP_FFPE_24_RNA-seq


title: whole animal, female, 1 week, rep3

description:
DEGs female 1w GNCs vs 1w total.xlsx
DEGs female 1w PNCs vs 1w total.xlsx

source_name: whole animal

value: whole animal

value: adult (1 week)


title: Wild-type replicate 2

description: 10X Genomics

value: Wild-type


title: Zymosan +  SPMs, 12h, mouse 2

value: peritoneal exudate

value: mixed leukocytes

value: WT


title: garland cells, female, 1 week, rep1


title: Zymosan +  SPMs, 12h, mouse 3


title: Spontaneous tumor, 713_Ki

description: 10X Genomics

value: bulk pancreatic tumor

value: mixed cells

value: p48-Cre, lox-stop-lox KrasG12D, Trp53lox/+ (KPC)


title: PMP_FFPE_13_RNA-seq


title: Zymosan +  SPMs, 12h, mouse 1


title: PMP_FFPE_12_RNA-seq


title: MC38 WT_rep1

first: Jane

last: Oliaro

state: Victoria

address: 305 Grattan St

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were trimed using cutadapt (v1.9) to remove adapter sequences.
trimmed reads were aligned using HISAT2 (v2.1.0) to the mouse reference genome (mm10)
Aligned reads were counted using featurecounts (v2.0.1)
Assembly: mm10
Supplementary files format and content: csv file include normalized (CPM) values for each sample

extract_protocol:
Cells were lysed and total RNA was isolated as per the manufacturer’s instructions (NucleoSpin RNA Extraction kit, Macherey-Nagel, Bethlehem, PA)
RNA was analyzed on a TapeStation (Agilent TapeStation 2200), and only RNA with RNA integrity number values greater than 9 were used for downstream library preparation. The QuantSeq 3′ mRNA Library Prep Kit (Lexogen) was used to prepare libraries.

treatment_protocol: At least 1 week after electroporation with Cas9-sgRNA (non-targeting or Cbfb-targeting), approximately 1 million WT and CbfbKO cells were collected for RNA extraction and sequencing

value: Colorectal Cancer


title: PMP_FFPE_46N_RNA-seq

value: Normal

tag: source of healthy tissue

value: colon


title: CbfbKO_rep3

treatment_protocol: At least 1 week after electroporation with Cas9-sgRNA (non-targeting or Cbfb-targeting), approximately 1 million WT and CbfbKO cells were collected for RNA extraction and sequencing.

value: Breast Cancer

value: CbfbKO


title: MC38 CbfbKO_rep2


title: whole animal, female, 1 week, rep2


title: Wild-type replicate 1

description: 10X Genomics

value: Caudal half of the embryo


title: whole animal, female, 1 week, rep1


title: PMP_FFPE_17_RNA-seq

value: Pseudomyxoma Peritonei

value: Peritoneal implant


title: MC38 CbfbKO_rep1


title: SMA fibroblast-derived iPSC_replicate 1 [CS77iSMA-nxx(1)]

city: Subang Jaya

first: Wendy

middle: Wai Yeng

last: Yeo

state: Selangor

address: Jalan Lagoon Selatan, 47500 Bandar Sunway,

department: Pharmacy

country: Malaysia

hyb_protocol: After incubation at 100°C, samples are then immediately hybridized to Agilent SurePrint G3 Human miRNA Microarray 8x60K (Design ID: 070156) for 20 hours at 55 °C in a rotating Agilent microarray hybridization oven.

scan_protocol: After hybridization, microarrays were washed for 5 min at room temperature with GE Wash Buffer 1 (Agilent) and 5 min with 37 °C GE Wash buffer 2 (Agilent). Slides were immediately scanned using Agilent SureScan Microarray Scanner (G4900DA) with 3 μm resolution at wavelengths of 532 nm using the extended dynamic range (10–100 %) setting.

data_processing: Normalized intensities were extracted using the Agilent Feature Extraction Software with protocol miRNA_1200_Jun14 and all the 24 data (in .txt format) files were obtained. Analysis were performed using Agilent Genespring Analysis Software version 14.9.1.

source_name: fibroblast-derived iPSC

label_protocol: Cyanine 3-pCp labeled using the miRNA Complete Labeling and Hyb Kit (Agilent, Valencia, Ca) according to manufacturer’s instructions. Labeled miRNA was then purified by drying it using vacuum concentrator with heat. The labeled miRNA was then mix with 10X Agilent blocking agent, 2× Hi-RPM Hybridization buffer and Hybridization spike-in solution following the manufacturers’ instructions.

growth_protocol: Fibroblasts cells (GM05400, GM09677 and GM00232) were grown Eagle’s Minimum Essential Medium (EMEM, Gibco, California, USA) according to manufacturer’s instruction. The complete media was prepared by adding 15% fetal bovine serum (FBS) (Gibco, USA), 1% Glutamax (Gibco, USA) and 1% 10,000 U/mL penicillin streptomycin (Gibco, USA). The NHDF cell line was maintained in FGM-2-Fibroblast Growth Media 2 (Lonza, Switzerland). The complete media was prepared with the provided fetal bovine serum (FBS), insulin, human Fibroblast Growth Factor-Beta (hFGF-β) and Gentamicin/Amphotericin (GA, Lonza, Switzerland). As for the iPSCs, (CS77SMA-nxx and CS32SMA-nxx) iPSCs were maintained with mTeSR1 (STEMCELL Technologies, Vancouver, Canada) with Matrigel coating (Corning, USA). The NHDF iPSC was maintained in Essential 8 Flex Medium (Gibco, USA) with Vitronectin coating (Gibco, USA). The growth condition is 37 °C with 5 % CO2 in the cell culture incubator.

extract_protocol: Total RNA was extracted using Hybrid-R (GeneAll, Korea) following the manufacturer's instruction. The protocol includes homogenization, phase separation, RNA bind and RNA wash and finally elution. RNA was quantified using a Nanodrop (PCRmax Lambda, Staffordshire, United Kingdom) and quality was determined with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: No treatments were applied in this study.

value: fibroblast-derived iPSC

value: 2 years

tag: gender

value: male

tag: subject status

value: SMA disease


title: CbfbKO_rep2

tag: cell type


title: SMA fibroblast-derived iPSC_replicate 4 [CS32iSMA-nxx(4)]

value: 7 months


title: PMP_FFPE_42N_RNA-seq

value: uterine


title: MC38 WT_rep2

value: WT


title: Keap1C226SC613Shomo::Trspfl/fl::AlbCre_4

city: Sendai

first: Takafumi

last: Suzuki

state: Miyagi

address: 2-1 Seiryo-machi, Tohoku University

institute: Tohoku University

data_processing:
Transcript per million (TPM) normalized read counts were generated using Salmon quant script (Galaxy version 1.5.1+galaxy0) with mouse reference transcript sequences (version 30)
Assembly: transcript sequences (version 30)
Supplementary files format and content: tab-delimited text file inculde raw counts for each Sample

source_name: Liver

extract_protocol:
Total RNA was extracted from livers of male mice using Sepasol®-RNA I Super G (09379-97; Nacalai Tesque).
Double-stranded DNA (dsDNA) libraries were created from the rRNA-depleted eluate using an MGIEasy RNA directional library prep kit (MGI).

tag: tissue

value: Liver

value: Male

value: 20 days old


title: PMP_FFPE_38N_RNA-seq

value: Normal

value: small intestine


title: WT_rep3

value: Breast Cancer


title: Keap1C226SC613Shomo::Trspfl/fl::AlbCre_3


title: PMP_FFPE_11_RNA-seq


title: Keap1C226SC613Shomo::Trspfl/fl::AlbCre_1


title: SMA fibroblast-derived iPSC_replicate 3 [CS77iSMA-nxx(3)]


title: Keap1C226SC613Shomo::Trspfl/fl_2


title: SMA fibroblast-derived iPSC_replicate 2 [CS77iSMA-nxx(2)]


title: PMP_FFPE_35N_RNA-seq

value: colon


title: SMA fibroblast-derived iPSC_replicate 2 [CS32iSMA-nxx(2)]


title: WT_rep2


title: WT_rep1


title: PMP_FFPE_43N_RNA-seq


title: SMA fibroblast-derived iPSC_replicate 1 [CS32iSMA-nxx(1)]


title: Trspfl/fl::AlbCre_4


title: Keap1C226SC613Shomo::Trspfl/fl_4


title: SMA fibroblast-derived iPSC_replicate 3 [CS32iSMA-nxx(3)]


title: Keap1C226SC613Shomo::Trspfl/fl::AlbCre_2


title: PMP_FFPE_28N_RNA-seq


title: Keap1C226SC613Shomo::Trspfl/fl_3


title: CbfbKO_rep1

value: CbfbKO


title: PMP_FFPE_27N_RNA-seq


title: PMP_FFPE_20N_RNA-seq


title: Control fibroblast-derived iPSC_replicate 3 [NHDF-iPSC(3)]

value: 45 years

value: female

value: Healthy control


title: Trspfl/fl_4


title: Control fibroblast-derived iPSC_replicate 2 [NHDF-iPSC(2)]

value: fibroblast-derived iPSC


title: PMP-3

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software cellranger v2.20.0.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
The Chromium Single Cell 3' Protocol enables to profile 3' digital gene expression of 500 - 10,000 individual cells per sample. Single cells, reagents and a single Gel Bead containing barcoded oligonucleotides are encapsulated into nanoliter-sized GEMs (Gel Bead in emulsion) using the GemCode Technology. GemCode Technology samples a pool of about 3,500,000 10x Barcodes to separately index each cell's transcriptome and cell surface protein.
It does so by partitioning thousands of cells into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated DNA molecules share a common 10x Barcode. The poly(dT) primer captures poly-adenylated mRNA and barcoded, full-length cDNA is produced. The Single Cell 3' v3 Gel Beads include two additional primer sequences, that facilitate capture and priming of targets containing interested feature.

value: Peritoneal implant


title: PMP_FFPE_34N_RNA-seq


title: Control fibroblast-derived iPSC_replicate 4 [NHDF-iPSC(4)]


title: SMA fibroblast_replicate 3 [GM09677(3)]

source_name: fibroblast

value: fibroblast

value: 2 years

value: male

value: SMA disease


title: SMA fibroblast_replicate 2 [GM09677(2)]


title: PMP-2


title: Trspfl/fl::AlbCre_3

value: Liver


title: Trspfl/fl::AlbCre_2

value: Male


title: Trspfl/fl_1

value: 20 days old


title: AAA sample1

city: Iowa City

first: Long-Sheng

last: Song

state: IA

address: 285 Newton Rd

department: Internal Medicine

institute: University of Iowa

data_processing:
Raw files were uploaded into Illumina's BaseSpace hub (basespace.illumina.com) and quality assessed with the FastQC Version 1.0.0 App.
Sequences were trimmed to 125bp by cutting 10bp from the 5'-end and 16bp from the 3'end using the FASTQ Toolkit Version 2.2.5 App.
The BaseSpace RNA Express app (v1.1.0) was used to align reads to the homo sapiens hg19 genome, determine read counts, and perform pairwise differential gene expression analysis.
Assembly: hg19
Supplementary files format and content: comma separated file containing sequence reads counts for each sample

source_name: aorta

extract_protocol:
Aorta tissues were collected from patients, flash frozen in liquid nitrogen and stored at -80C until processed.
Total RNA was isoated using the Arturus PicoPure RNA Isolateion Kit (Applied Biosystems). cDNA was generated with the Ovation Pico WTA System V2 kit (NuGEN)
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II for DNA Library Prep Kit following manufacturer's protocols.

value: aorta

tag: disease state

value: Abdominal aortic aneurysm


title: Control fibroblast-derived iPSC_replicate 1 [NHDF-iPSC(1)]


title: PMP-5


title: AAA sample4


title: PMP-4


title: SMA fibroblast_replicate 3 [GM00232(3)]

value: 7 months


title: Progesterone rep3

city: Urbana

first: Camila

last: Braz

state: IL

address: 1207 W. Gregory Dr.

department: Animal Sciences

institute: University of Illinois Urbana-Champaign

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq Conversion Software (version 2.20, Illumina). Adaptors were trimmed from the 3'-end of the reads.
Salmon version 1.4.0, was used to quasi-map reads to the transcriptome of the bovine reference genome (ARS-UCD1.2, NCBI) and quantify the abundance of each transcript.
Then quasi-mapping was performed with the additional arguments --seqBias and --gcBias to correct sequence-specific and GC content biases, --numBootstraps=30 to compute bootstrap transcript abundance estimates, and --validateMappings to help improve the accuracy of mappings. Gene-level counts were then estimated based on transcript-level counts using the "bias corrected counts without an offset" method from the "tximport" R package.
Assembly: ARS-UCD1.2
Supplementary files format and content: Matrix table with the length normalized gene counts for every gene and every sample

organism: Bos taurus

source_name: uterine epithelium

growth_protocol: BUTE cells were generated from a Holstein dairy cow and validated. BUTE cells were maintained in α-Minimum Essential Media (αMEM) media containing 5.55 mM glucose supplemented with 10% FBS, 2 mM L-glutamine, 10 mg/ml ITS, 1.8 ng/ml EGF, and 18.2 ng/ml estradiol-17β. BUTE cells were maintained at 37°C in a humidified incubator with 5% CO2 and were passed every 3-4 days. BUTE cells were plated and allowed to grow until 80% confluent. Then the media was removed, rinsed twice with PBS, and the cells were serum and steroid starved in media without phenol red and treated with insulin-like growth factor 1 for 24 hours to stimulate glycogenesis. The media was removed and replaced with serum and steroid-free media containing 50 ng/ml of IGF1 and appropriate treatments for indicated times.

extract_protocol:
Total RNA was extracted from BUTE cells using the Quick-RNA MiniPrep Plus Kit (R1058, Zymo Research) per the manufacturer's instructions
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit'

treatment_protocol: Controls were treated with a vehicle (DMSO) for all experiments (n=4). BUTE cells were plated in a 10 cm dish and treated with progesterone for 24 hours (n=4).

value: uterine epithelium

value: BUTE

value: epithelial

tag: genotype

value: widltype

value: progesterone


title: Keap1C226SC613Shomo::Trspfl/fl_1


title: Trspfl/fl_3


title: SMA fibroblast_replicate 2 [GM00232(2)]


title: AAA sample2


title: Trspfl/fl_2


title: SMA fibroblast_replicate 1 [GM09677(1)]


title: Progesterone rep2


title: SMA fibroblast_replicate 4 [GM00232(4)]


title: PMP-1


title: TAA sample4

value: Thoracic aortic aneurysm


title: Progesterone rep1


title: Trspfl/fl::AlbCre_1


title: Myh6-CreER; Rosa-Runx1 Sample 1

city: Milwaukee

first: Michaela

last: Patterson

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

data_processing:
Sequencing was performed using a DNBSEQ platform at >20M, 150bp pair-end reads per sample.
Trimmed reads were then aligned to the mouse genome (mm9) using Hisat2
Transcripts were assembled from RNA-seq alignments using Stringtie2
Expression was quantified by fragments per kilobase of transcript per million reads mapped (FPKM).
Assembly: mm9 - genome assembly MGSCv37
Supplementary files format and content: File of defferentially expressed genes (adj P value < 0.05) with FPKM values for each sample, average expression among groups, and log2 fold gene expression changes in the Runx1 over expression group.

source_name: neonatal heart ventricles

growth_protocol: Postnatal day 10 hearts

extract_protocol:
Left ventricles were harvested from P10 neoental mice and placed in TRIzol. RNA was subsequently collected and purified by phenol/chloroform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared by BGI Americas
Prepared by BGI Americas

treatment_protocol: Tamoxifen injections at P0 and P1

value: neonatal heart ventricles

value: Myh6-CreER; Rosa-Runx1 OE

value: tamoxifen at P0 & P1


title: AAA sample3


title: TAA sample3


title: DMSO rep4

value: control


title: Control fibroblast_replicate 2 [NHDF(2)]

value: fibroblast

value: 45 years

value: female

value: Healthy control


title: Control sample3

value: aorta

value: normal


title: TAA sample2


title: Myh6-CreER; Rosa-Runx1 Sample 3


title: DMSO rep3


title: Myh6-CreER; Rosa-Runx1 Sample 2


title: Control sample2


title: SMA fibroblast_replicate 1 [GM00232(1)]

value: 7 months

value: male

value: SMA disease


title: TAA sample1


title: Progesterone rep4

value: uterine epithelium

value: BUTE

value: epithelial


title: Control sample1


title: Myh6-CreER; Rosa-Runx1 Sample 4


title: Control sample4


title: Control fibroblast_replicate 3 [NHDF(3)]


title: shNC2

city: Fukuoka

first: Chikanori

last: Tsutsumi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Surgery and Oncology, Graduate School of Medical Sciences

institute: Kyushu University

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v7.1.0 (10x Genomics)
Output files were analyzed with the R v4.2.1 package "Seurat v4.3.0".
To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.
Assembly: mouse reference, mm10
Supplementary files format and content: rds file

source_name: pancreatic cancer

extract_protocol:
Single-cell library preparation was performed according to the manual of the Chromium Next GEM Single-cell 5' Reagent Kits v2 (Dual index). The cell suspensions were loaded on the Single-cell G Chip for gel bead-in-emulsion (GEM) generation and barcoding. cDNA library thus was generated with a droplet-based sequencing platform (10X Genomics). Next, reverse transcription, RT cleanup cDNA amplification, and quantification was performed to construct a 5’ gene library.
The libraries were sequenced on  DNBSEQ-G400 (MGI Tech).

value: pancreatic cancer

value: KrasG12D/+; Trp53R172H/+; Pdx-1-Cre

value: Female

value: no


title: Myh6-CreER Sample 2

value: neonatal heart ventricles

value: Myh6-CreER control

value: tamoxifen at P0 & P1


title: Myh6-CreER Sample 1


title: spinal cord, control3

status: Public on Oct 08 2024

city: Shinjuku-ku

first: Keitaro

last: Ito

state: Tokyo

institute: Keio university

data_processing:
Raw reads were trimmed for quality and read length using Trimmomatic 0.38.
Transcript counts were obtained using StringTie version 2.1.3b.
Assembly: rn6
Supplementary files format and content: raw counts for each sample
Supplementary files format and content: TPM values for each sample

organism: Rattus norvegicus

source_name: spinal cord

extract_protocol:
The total RNA was extracted using the RNeasy Mini Kit (Qiagen)
 The RNA from each sample was purified, and the mRNA libraries were prepared following the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, United States) protocol

value: spinal cord

value: no treatment

tag: time

value: 7weeks after SCI


title: spinal cord, control2


title: spinal cord, control1


title: Control fibroblast_replicate 1 [NHDF(1)]

value: fibroblast

value: 45 years

value: female

value: Healthy control


title: DMSO rep2

value: uterine epithelium

value: widltype

value: control


title: spinal cord, scar resection + scaffold3

value: Scar resection + scaffold


title: spinal cord, scar resection + scaffold1


title: spinal cord, scar resection4

value: Scar resection + PBS


title: Control fibroblast_replicate 2 [GM05400(2)]

value: 6 years

value: male


title: spinal cord, scar resection1


title: Control fibroblast_replicate 3 [GM05400(3)]


title: shLDHA1

value: pancreatic cancer

value: KrasG12D/+; Trp53R172H/+; Pdx-1-Cre

value: Female

value: no


title: Control fibroblast_replicate 1 [GM05400(1)]


title: DMSO rep1

value: BUTE

value: epithelial


title: cropseq_hek293T_library1_grna

city: Durham

first: Charles

last: Gersbach

state: NC

address: 2127 Campus Drive

institute: Duke University

data_processing:
fastqs were trimmed using FASTX-toolkit
trimmed fastqs were aligned using bowtie2
Assembly: gRNA library
Supplementary files format and content: text file containing gRNA counts
Library strategy: CRISPR library

growth_protocol: All cells were grown at 37°C. HEK293T/17 cells were cultured in DMEM + 10% FBS and NIH3T3 cells were cultured in DMEM + 10% CBS.

extract_protocol:
cells were washed three times, trypsinized, and strained through a 40 µm cell strainer
Up to 20 μg of genomic DNA per sample was used to amplify the U6-3’ to gRNA hairpin region. PCR2 was performed to add full-length Illumina sequencing adapters using internally ordered primers with equivalent sequences to NEBNext Index Primer Sets 1 and 2 (New England Biolabs). All PCRs were performed using Q5UltraII polymerase (NEB). Pooled samples were sequenced using MiSeq (Illumina), using 50-nt reads and collecting greater than 100 reads per gRNA in the library.  The library prep primers were as follows: PCR1: U6_BcA_r1seq_halftail  5' ACTCTTTCCCTACACGACGCTCTTCCGATCTACTAGGGAAAGGACGAAACACCG 3' gRNAFE_r2seq_halftail 5' GACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCCTTATTTAAACTTGCTATGCTGT 3' PCR2: r1seq_fulltail 5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTC 3’ r2seq_fulltail (Two distinct indexed versions of this primer were used to allow for pooling) 5' CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCT 3'


title: spinal cord, scar resection + scaffold4

value: spinal cord

value: 7weeks after SCI


title: spinal cord, scar resection3


title: spinal cord, scar resection2


title: RNA-Seq MP rep1

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

description: Replica 1

data_processing:
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control.
Sequenced reads were trimmed from low quality and/or short sequences by trimmomatic v. 0.39 using the following options:  LEADING:22 TRAILING:22 SLIDINGWINDOW:4:26 MINLEN:20
Trimmed reads were mapped to H.sapiens genome (hg38/GRCh38 Ensembl v.106) by STAR aligner 2.7.5c with hg38 Ensembl genome map v.106 http://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.gtf.gz. Alignment options were the following:  --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --quantMode TranscriptomeSAM
Alignment files were separated by samtools 1.15 view -F 0x10 to get forward strand alignments and by samtools 1.15 view -f 0x10 to get reverse strand alignments. Then bamCoverage (deepTools 3.5.1) tool was used to obtain normalized expression profiles. The bamCoverage options list is the following: --binSize 10 --effectiveGenomeSize 2913022398 --skipNAs --normalizeUsing RPKM --exactScaling. The obtained profiles were averaged between replicates by WiggleTools v1.2.11 and converted to bigWig format by bedGraphToBigWig tool from UCSC genome tools.
Trimmed reads were quantified to H. sapiens hg38 GRCh38 Ensembl v.106 genome with Ensembl genome map v.106 by RSEM 1.3.1 using the following options: --fragment-length-mean 255 --star --calc-ci --ci-memory 30720. This operation was performed for both replicates separately. The results were averaged by in-house R script.
Assembly: Homo sapiens hg38/GRCh38 Ensembl release 106 genome build. Homo sapiens hg38/GRCh38 Ensembl annotation v106 in GTF format.
Supplementary files format and content: bigWig files contain normalized (RPKM, reads per kilobase million) expression signal genomewide for each strand. Results files contain quantified expression values in TPM (Transcripts Per Million) and FPKM (Fragments Per Kilobase Million) for each gene averaged between replicates.

source_name: melanoma cells

growth_protocol: The Mel Z melanoma cells initially were propagated on plastic surface in RPMI-1640 medium supplemented with 10% fetal calf serum, 2 mM glutamine and 0.1% gentamicin sulphate at 37°C under a humidified atmosphere containing 5% CO2 up to 10 million of cells with 70–75% confluency. Then the cells were divided into three equal samples and seeded either on plastic, or on Matrigel, or on Matrigel in the presence of non-cytotoxic concentration of inhibitor (LCS1269, 10-6 M) in the same medium. The growth was performed under the same conditions for 20 h, and then the cells were used for RNA isolation. This sample corresponds to cells grown for 20 h on plactic (MP).

extract_protocol:
Total RNA was extracted from cell lysed with Trisol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA Quality was checked with  BioAnalyser and  RNA 6000 Nano Kit(Agilent). Poly(A)+ RNA was isolated with Dynabeads® mRNA Purification Kit (Ambion).
Poly(A)+ RNA was isolated with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length.

value: Mel Z melanoma cells

value: skin

value: melanocytes


title: RNA-Seq MP rep2

description: Replica 2


title: HEK293, NTSR1

city: Salt Lake City

first: Justin

last: English

state: UT

address: 15 N Medical Drive East, Rm 4100

department: Biochemistry

institute: University of Utah

data_processing:
Barcodes were obtained by collecting the first 24 nucleotides of each read from demultiplexed fastq files.
Paired-end reads were trimmed using TrimGalore and joined using FastQ-Join.
Barcodes were clustered within each sample via Starcode using a Levenshtein distance of one.
Assembly: Custom barcode dictionary.
Supplementary files format and content: finalBarcodeMap.csv contains the barcode sequences and associated candidate transcriptional response elements
Supplementary files format and content: rpms.csv contains the barcode reads per million for each treatment and plasmid library

source_name: Kidney

growth_protocol: Cell lines were maintained in maintenance media (typically DMEM supplemented with 10% FBS and antibiotics) in a 37C humidified incubator with 5% carbon dioxide.

extract_protocol:
RNA was isolated from cell pellets using the AllPrep DNA/RNA Mini Kit (Qiagen) with QIAshredder columns (Qiagen).
RNA libraries were prepared using the Superscript IV One-Step RT-PCR System (Invitrogen) with custom primers. DNA libraries from plasmid inputs were prepared using the Platinum SuperFI II Green PCR Master Mix (Invitrogen) with custom primers.

treatment_protocol: Cells on 10 cm dishes were transfected with 10 micrograms of the TRE-MPRA plasmid library when subconfluent.Six hours after transfection, the maintenance media was replaced with serum-free media. The following day, cells were treated for six hours. Cells were then trypsinied and pellets were frozen at -80 C until processing.

value: Kidney

value: Epithelial

value: fetal


title: HEK293, NTSR1 and neurotensin and Gq inhibitor

value: 100 nM neurotensin 8-13 and 50 nM FR900359


title: HEK293, NTSR1 and neurotensin

value: 100 nM neurotensin 8-13


title: HNSCC P5 TIL ADT

city: Portland

first: Wesley

last: Rosales

state: OR

address: 4805 NE Glisan St

institute: Earle A. Chiles Research Institute

data_processing:
CellRanger v7.0.1 (v6.1.2 for CRC P1-P4 samples) count  with "include_introns=false" parameter and vdj
Assembly: GRCh38-2020-A
Supplementary files format and content: CRC_CD8TIL_SeuratObject.rds.gz, HNSCC_CD8TILSeuratObject.rds.gz: Seurat objects containing normalized count data, dimension reductions, clustering, and TCR information
Supplementary files format and content: CRC_CD8TIL_metadata.csv, HNSCC_CD8TIL_metadata.csv: Metadata for each cell present in seurat object including cluster, patient ID, etc.
Supplementary files format and content: CRC_CD8TIL_AData.h5ad.gz, HNSCC_CD8TIL_AData.h5ad.gz: Anndata object containing spliced and unspliced gene counts of CD8 T cells.
Supplementary files format and content: CRC_CD8TIL_RNACounts.rds.gz, HNSCC_CD8TIL_RNACounts.rds.gz: Raw mRNA count data of CD8 T cells
Supplementary files format and content: CRC_CD8TIL_ADTCounts.rds.gz, HNSCC_CD8TIL_ADTCounts.rds.gz: Raw ADT count data of CD8 T cells
Library strategy: CITE-seq

molecule: protein

source_name: HNSCC Cancer Tissue

extract_protocol:
Tumor digests from patients with CRC or HNSCC were stained for CD45 and CD3, and live (PI-) CD45+CD3+ T cells were FACS sorted into a 1.5 ml eppendorf containing 100 ul of MACS buffer.
Library was performed according to manufacturer's instructions (Chromium Next GEM Single Cell 5’ kit protocol, 10X genomics)

value: HNSCC Cancer Tissue

tag: library type

value: ADT

tag: adt

value: TotalSeq-C antibodies (CD4, cat #344651 401 clone SK3; CD8, cat #344753 clone SK1; CD39, cat #328237 clone A1; CD103, cat #350233 402 clone Ber-ACT8; CD127, cat#351356 clone A019D5; CD25, cat#302649 clone BC96; PD-1, 403 cat#329963, clone EH12.2H7; ICOS, cat#313553 clone C398.4A)


title: spinal cord, scar resection + scaffold2

value: Scar resection + scaffold


title: HNSCC P5 TIL GEX

value: mRNA


title: HNSCC P6 TIL ADT


title: KOPN8_Combo_PU.1

city: Sydney

first: Dominik

last: Beck

state: NSW

address: Level 10, UTS Building 11 (CB11 81-113, Broadway, Ultimo)

department: School of Biomedical Engineering

institute: University of Technology Sydney

description: PU.1 ChIP-seq of DB2313&Dex combo-treated KOPN8 cells

data_processing:
Raw fastq data was trimmed to remove sequencing adapters, followed by removal of low quality reads and N reads using SOAPnuke developed by BGI Genomics
Clean demultiplexed data was aligned to UCSC genome assembly hg19 using the software package BWA with standard parameters.
Peak calling for PU.1 was performed using the software packages HOMER, SPP and MACS2, with peaks detected by at least 2 algorithms considered real peaks.
Assembly: hg19
Supplementary files format and content: bam
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak

growth_protocol: KOPN8 cells cultured in RPMI media supplemented with 10% fetal bovine serum, 2mM L-glutamine, cultured at 37ºC with 5% CO2

extract_protocol:
After 16hrs of treatment, cells were washed once in PBS, and fixed with 1%formaldehyde for 10 minutes at room temperature. After quenching and nucleus extraction, chromatin was released by nuclear lysis and sonicated using Bioruptor Pico sonicator for 10 cycles (30sec on/30sec off). Protein/DNA complex was immunoprecipitated using 0.2µg PU.1 antibody or equivalent amount of Rabbit IgG, and ChIP DNA was released by reverse crosslinking at 67ºC overnight, followed by column-based DNA purification.
ChIP-seq library preparation was performed by BGI Genomics using the following steps: ChIP DNA was end repaired for 3'-dA overhang and adapters ligated. PCR amplification was then performed, amplified library DNA purified, and subjected to sequencing on DNBSEQ platform for 20 million reads per sample using single-end 50bp strategy.

treatment_protocol: Cells were seeded at 1x10^6/mL in growth media, 10mL per treatment condition. Cells were treated with 1µM DB2313, 1µM Dexamethasone, 1µM DB2313+1µM Dexamethasone, or equivalent concentration of DMSO (vehicle control) at 37ºC with 5%CO2 for 16hrs

tag: chip antibody


title: KOPN8_Dex_PU.1

description: PU.1 ChIP-seq of Dexamethasone-treated KOPN8 cells

tag: cell line


title: HNSCC P6 TIL GEX


title: HNSCC P3 TIL ADT


title: HNSCC P4 TIL ADT


title: ExVivoCell_72Hr_20μM_circRNA_rep3

city: Zhengzhou

first: Panpan

last: Wang

address: 郑州市高新区科学大道100号郑州大学

department: College of Public Health

institute: 郑州大学

description: Gene expression after 72 h of exposure to 20 μM of CdCl2 in L-02 cell

hyb_protocol: Array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.).1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction.

source_name: L-02 cells,72hr, 20μM

label_protocol: Sample labeling were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: The total RNA of the cells was extracted by the TRIzol assay. The RNA purified was according to RNasey Mini Kit (Qiagen 74104, USA). The quantity of the total RNA from each sample was measured by NanoDrop® ND-1000 (Thermo-Fisher Scientific, USA) and the integrity of the total RNA and gDNA contamination were measured by agarose gel electrophoresis.

treatment_protocol: L-02 cells in logarithmic phase were divided into control and CdCl2 exposure group with the concentrations of 20 μM for 72 h in the RPMI 1640 medium containing 10% fetal bovine serum (Gibco, No. 10099-141) at 37℃ in 5% CO2., respectively. There were three replicate samples in each group.

value: human normal liver cell

value: female

tag: treatment


title: KOPN8_IgG

description: IgG ChIP-seq of wild type untreated KOPN8 cells

value: IgG


title: KOPN8_DB2313_PU.1

description: PU.1 ChIP-seq of DB2313-treated KOPN8 cells


title: direct_capture_hek293T_library1_grna


title: HNSCC P2 TIL GEX


title: HNSCC P4 TIL GEX


title: HNSCC P2 TIL ADT


title: KOPN8_Ctrl_PU.1

description: PU.1 ChIP-seq of DMSO-treated KOPN8 cells


title: ExVivoCell_72Hr_20μM_circRNA_rep2

address: 郑州市高新区科学大道100号郑州大学

value: after 72 h of exposure to 20 μM of CdCl2


title: hearts, AAV9-CTRL, rep2

city: Wuhan

first: Xin

last: Zhang

state: Hubei

address: 238 Jiefang Road

department: Geriatrics

institute: Renmin Hospital of Wuhan University

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads
The clean reads were mapped to the GRCm38/mm10 mouse genome using HISAT2
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples
Differential expression analysis was performed using the DESeq2
Assembly: GRCm38/mm10
Supplementary files format and content: tab delimited text file includes raw counts for each Sample
Supplementary files format and content: tab delimited text files includes FPKM values for each Sample

source_name: heart

extract_protocol:
RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
Libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: heart

value: Control

value: I/R


title: hearts, AAV9-CTRL, rep3


title: HNSCC P3 TIL GEX


title: ExVivoCell_72Hr_0μM_circRNA_rep3

address: 郑州市高新区科学大道100号郑州大学

description: Gene expression in L-02 cells were cultured normally after 72h

source_name: L-02 cells,72hr, 0μM

value: cultured normally after 72h


title: HNSCC P1 TIL ADT


title: HNSCC P1 TIL GEX


title: ExVivoCell_72Hr_0μM_circRNA_rep2

address: 郑州市高新区科学大道100号郑州大学


title: hearts, AAV9-hFNDC4, rep2

value: FNDC4 overexpression


title: hearts, AAV9-hFNDC4, rep3


title: CRC P5 TIL ADT

source_name: Colorectal Cancer Tissue

value: Colorectal Cancer Tissue


title: ExVivoCell_72Hr_20μM_circRNA_rep1

address: 郑州市高新区科学大道100号郑州大学


title: CRC P4 TIL GEX


title: CRC P4 TIL ADT


title: hearts, AAV9-hFNDC4, rep1


title: CRC P5 TIL GEX


title: ExVivoCell_72Hr_0μM_circRNA_rep1

address: 郑州市高新区科学大道100号郑州大学


title: e10_5_ant

city: San Francisco, CA

first: Rebecca

middle: Garrett

last: Jaszczak

state: California

address: 35 Medical Center Way, Room 913D

institute: UCSF

data_processing:
Initial processing of the v2 10x libraries was done through CellRanger v3.1.1. Libraries for all timepoints were aligned to the mouse genome (10× Genomics prebuilt mm10 version 3.0.0 reference genome) with all cellranger default parameters for demultiplexing and aligning. Our libraries were sequenced at a depth of 125,100 mean reads per cell for the E9.5 Anterior sample and 111,258 mean reads per cell for the E9.5 posterior sample. At E10.5, our anterior technical replicates 1 and 2 were 493,803 and 399,673, and our posterior replicates 3 and 4 492,512 and 556,014. At E11.5, our first biologic replicate was 15,542 mean reads per cell, and the second biologic replicate 20,967. Data was processed through SoupX (version 1.5.2) to remove ambient RNA contamination, as follows: E9.5 Anterior, 12%; E9.5 Posterior, autoEstCont; E10.5 Anterior, 19%, E10.5 Posterior, autoEstCont. The resulting gene by cell matrices were analyzed with the python package ScanPy v1.9.3 95. Cells were filtered to retain only high quality cells with a minimum of 2000 transcripts per cell barcode, a maximum of 10% mitochondrial transcripts, and a doublet score of 0.15 computed with Scrublet v0.2.3 96. Further downstream, any remaining cell populations lacking unique marker genes or with a high density of doublet scores near the 0.15 doublet score cutoff were also removed.
Assembly: mm10
Supplementary files format and content: h5ad with all somatic and germ cell populations
Supplementary files format and content: h5ad with only germ cell populations

source_name: E10.5 anterior PGC migratory niche

extract_protocol:
Pou5f1-ΔPE-eGFP embryos were somite counted and age-matched. After microdissecting out the migratory region, samples were dissociated. After dissociation, cells were submitted for FACS to concentrate GFP+ migratory germ cells. Samples were reecombined with Oct4-GFP- somatic cells. These cell populations were used to create two 10X Chromium Single Cell 3' (v2 Chemistry) single cell RNA sequencing libraries.
10X ChromiumTM Single Cell 3' Reagent Kits v2 User Guide Rev A. Briefly, we used Single-Cell 3′ Reagent Version 2 Kit (10X Genomics) and used fluidics to create individual cells in gel bead-in-emulsions (GEMS). Samples were prepared directly according to the protocol, with the following steps tailored to maximize library yield: at the cDNA amplification step, we used 14 cycles, and at the sample index PCR step, we used 14 cycles. Samples were tested for quality on an Agilent Bioanalyzer High Sensitivity chip before sequencing. E9.5 and E11.5 libraries were sequenced on HiSeq 4000 (Illumina) with paired-end sequencing parameters: Read1, 98 cycles; Index1, 14 cycles; Index2, 8 cycles; and Read2, 10 cycles. E10.5 libraries were sequenced on Novaseq (Illumina) with paired-end sequencing parameters: Read1, 150 cycles; i7 Index, 8 cycles; i5 index, 0 cycles; and Read2, 150 cycles.

value: E10.5 anterior PGC migratory niche

value: CD1 dams crossed to sires homozygous for Pou5f1-deltaPE-eGFP (MGI:3057158)


title: e10_5_post

source_name: E10.5 posterior PGC migratory niche

value: E10.5 posterior PGC migratory niche


title: direct_capture_nih3t3_library2_grna

description:
NIH3T3_MCH2_NTlib2_barcodes.tsv.gz
NIH3T3_MCH2_NTlib2_features.tsv.gz
NIH3T3_MCH2_NTlib2_matrix.mtx.gz

data_processing:
Each lane of cells was processed using cellranger (version 6.0.1) count using default parameters and mapping to the GRCh38-and-mm10-2020 reference genome from 10x Genomics
Assembly: GRCh38-and-mm10-2020
Supplementary files format and content: Sparse matrices in Market Exchange (MEX) format for UMI counts for each barcode/gene or barcode/gRNA pair. Files are barcodes.tsv: This file contains the barcodes represented in the mtx file. genes.tsv: This file contains all annotated genes and gRNAs. matrix.mtx:  contained the "gene id" index, "cell id" index, and the total UMI count per cell and gene/gRNA combination.
Supplementary files format and content: R1/R2/I1/I2 .fastq files for lane 1 and 2 of the sequencing run. Read 1 contains UMI and cell barcode information. Read 2 contains the RNA transcript sequence.

extract_protocol:
cells were washed three times, trypsinized, and strained through a 40 µm cell strainer
Approximately 10,000 cells were captured per lane of a 10x Chromium chip (Next GEM Chip G) using Chromium Next GEM Single Cell 3ʹ HT Reagent Kits v3.1 with Feature Barcoding technology for CRISPR Screening (10x Genomics, Inc, Document number CG000418, Rev D). CROP-seq protospacer sequences were amplified from barcoded cDNA.


title: CRC P3 TIL ADT

value: ADT


title: CRC P2 TIL ADT

value: TotalSeq-C antibodies (CD4, cat #344651 401 clone SK3; CD8, cat #344753 clone SK1; CD39, cat #328237 clone A1; CD103, cat #350233 402 clone Ber-ACT8; CD127, cat#351356 clone A019D5; CD25, cat#302649 clone BC96; PD-1, 403 cat#329963, clone EH12.2H7; ICOS, cat#313553 clone C398.4A)


title: CRC P3 TIL GEX


title: CRC P2 TIL GEX


title: cropseq_nih3t3_library2_grna

description:
NIH3T3_LRB100_NTlib2_barcodes.tsv.gz
NIH3T3_LRB100_NTlib2_features.tsv.gz
NIH3T3_LRB100_NTlib2_matrix.mtx.gz


title: direct_capture_nih3t3_library2_gene_exp


title: cropseq_nih3t3_library2_gene_exp


title: hearts, AAV9-CTRL, rep1


title: WT, BAY 24HR, Rep4

city: Oslo

first: Jason

last: Matthews

address: Sognsvannsveien 9

department: Nutrition

country: Norway

institute: University of Oslo

data_processing:
The raw RNA seq paired end fastq files were quantified using the Salmon tool (v1.10.1) with “libtype” flag as automatic and mm10 version of the Salmon index file. The index was generated using the salmon “index” flag with the mm10 transcripts fasta file supplied.
The “tximport” import function from the tximport package was used to import the Salmon quantification data for further processing including differential expression analysis using DeSeq2.
Assembly: mm10
Supplementary files format and content: There are three files including txi_length_data.txt, txi_abundance_data.txt and txi_counts_data.txt. These are generated by tximport function of R package tximport (v1.26.1)

source_name: PyMT

growth_protocol: The PyMT cell line was isolated from a spontaneous mammary tumour that developed in mouse mammary tumour virus-Polyoma virus middle T-antigen (MMTV-PyMT) female mice on a C57BL/6 background. PyMT cells were cultured in Dulbecco’s Modified Eagle Media (Sigma-Aldrich), supplemented with 10% v/v fetal bovine serum (FBS; Sigma-Aldrich), 1% v/v penicillin-streptomycin (Sigma-Aldrich), and 1% v/v L-glutamine (Sigma-Aldrich). Cells were incubated at 37℃ and 5% CO2, in a 100% humidified environment and sub-cultured when they reached 80% confluency.

extract_protocol:
PyMT WT, AhrKO and LT-BAY cells were plated in a 12-well plate at a density of 1×105 cells/well in quadruplicates. Total RNA was isolated with the Aurum™ Total RNA isolation kit (BioRad), following manufacturer’s protocol.
Total RNA was isolated with the Aurum™ Total RNA isolation kit (BioRad), following manufacturer’s protocol.

treatment_protocol: PyMT AhrKO cells were generated using CRISPR/Cas9. Briefly, the guide oligos forward 5´‑CCTACGCCAGTCGCAAGCGG-3´ and reverse 5´‑CCGCTTGCGACTGGCGTAGG-3´ were annealed and ligated into the pSpCas9(BB)-2A-Puro (PX459) plasmid (Addgene, Watertown, MA, USA; plasmid #62988). PyMT cells were transfected with 4 µg of PX459 containing AHR gRNA. Forty-eight hours after transfection, cells were selected with 4 µg/ml puromycin for 5 days. PyMT PX459 cells which represent a pooled cell population were expanded. For the PyMT cells transfected with PX459 AHR gRNA we did single cell dilution cloning and isolated independent clones as previously described {Rasmussen, 2023 #3456}. After screening the clones for AHR activity, DNA was isolated, and the region surrounding the target site of the Ahr gene was amplified using forward: 5´- TGTTTCGTCGGTAGAGCAGT-3´ and reverse 5´-AGTCCTAGCCCCAATCAGTCT-3´. The presence of indels resulting in frame shift mutations was confirmed by DNA sequencing. PyMT cells transfected with PX459 vector with no gRNA and exposed to puromycin as described for AhrKO cells, were used as control cells in further experiments and will be referred to as WT cells. In addition, we generated long-term-BAY2416964 (LT-BAY) cells by supplementing the media of WT cells with 1 µM of BAY2416964 when the cells were sub-cultured for at least 6 weeks.

value: PyMT

value: breast cancer cell

value: WT


title: WT, BAY 24HR, Rep3


title: WT, BAY 24HR, Rep2