title: Bulk day 308 memory #4

city: Birmingham

first: Allan

last: Zajac

state: AL

address: 845 19th Street South

department: Microbiology

institute: University of Alabama at Birmingham

data_processing:
align to reference with tophat 2.0.10 with arguments "-r 150 --library-type fr-unstranded --keep-fasta-order "
reads per gene counted with summarizeOverlaps() from R/BioConductor's GenomicAlignments package, with mode=' Strict', ignore.strand=T and fragments=T
using the transcriptome from Illumina's iGenomes: Mus_musculus/UCSC/mm10/Annotation/Archives/archive-2015-07-17-14-33-26/Genes/genes.gtf from https://support.illumina.com/sequencing/sequencing_software/igenome.html
Genome_build: mm10
Supplementary_files_format_and_content: tab separated, per-gene raw read counts.

source_name: Splenic CD8+ T cells

growth_protocol: Splenocytes from P14 chimeric mice were harvested and either left untreated or stimulated with GP33 peptide for 5 hours

extract_protocol:
Cells were then sorted directly into TRIZOL-LS (Thermofisher). RNA was then isolated from the sorted fractions using a Direct-Zol RNA isolation kit (Zymo Research, Irvine CA)
Libraries were constructed using the TruSeq library generation kits as per the manufacturer's instructions (Illumina, San Diego, CA).

treatment_protocol: Stimulated and unstimulated splenocytes were then stained with anti-CD8 (53-6.7), anti-Thy1.1 (OX-7), anti-CD45.1 (A20), anti-CD45.2 (104) antibodies.

value: P14 IFN-g.Thy1.1 IL-2.GFP

value: Total donor memory

tag: dpi

tag: stimulated

value: no

value: Sorted CD45.2+CD8+


title: GPF pos/ IL-2 pos memory #4

status: Public on Jan 17 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: strain

tag: cell type

value: IL-2+ memory

value: yes

value: Sorted CD45.2+CD8+Thy1.1+GFP+


title: ANV5Enpp11

city: Pamplona

first: Fernando

last: Lecanda

address: Avda. Pio XII 55

country: Spain

institute: CIMA

description: Triple Negative cell line

data_processing:
The quality of the samples was verified using FastQC v0.11.5 software.
FASTQ files were mapped to GRCm38 mouse assembly using STAR v2.6.1c with default parameters.
featureCounts v1.6.0 software and Gencode vM25 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

molecule: total RNA

source_name: Enpp1 overexpresant cell line

growth_protocol: Cells lines were cultured in complete RPMI medium.

extract_protocol:
The RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit
RNA sequencing was performed by adapting the technology of SCRB-Seq (Bagnoli JW et al., Nat Comm, 2018) to allow for the high cost-efficient multiplexed transcriptome characterization. Briefly, cells were collected in cell lysis buffer and poly-(A)+ RNA were purified using the Dynabeads mRNA DIRECT Purification Kit (ThermoFisher Scientific). poly-(A)+ RNA were annealed to a custom primer containing a poly-(T) tract, a Unique Molecule Identifier (UMI), and a sample barcode. Retrotranscription using Template-switching oligonucleotides (TSO) was then used to synthetize and amplify 3’UTR enriched cDNA, resulting in barcoded cDNA fragments. Library preparation was performed using the Nextera XT library preparation protocol which introduces i5-P5 and i7-P7 structure for massive parallel sequencing. Quality control was performed following pre-amplification RT and library preparation to ensure quality and length accuracy, as well as to equilibrate sample pooling. Libraries were then circularized and sequenced using an DNBSeq-G400 sequencer (MGI), using the MGIEasy Circularization Kit (MGI). 5-10 million pair-end reads (100 bp) were sequenced for each sample. Raw sequences were called using Zebra caller (MGI) and demultiplexed using Cutadapt. RNAseq was carried out at the Genomics Unit of the Center for Applied Medical Research (CIMA, Universidad de Navarra).

treatment_protocol: Cells lines were washed twice with PBS at 4ºC prior RNA purification.

tag: cell line

value: FVB/n


title: Pneumonic patients (#1-3) PBMCs sampled at TP1 (GE) [20094_0001_A]

city: Munich

first: Markus

last: Joppich

state: Bavaria

address: Amalienstr. 17

department: Department of Informatics

country: Germany

institute: LMU Munich

description:
gene expression
20094_0001_A_B_raw_feature_bc_matrix.new.h5
20094-0001

data_processing:
Primary data analysis was performed using the bcl2fastq v2.19.1.403 software package.
The Illumina Sequence Analysis Viewer (SAV) 2.4.7 was used for imaging and evaluation of the sequencing run performance.
Sequenced reads were processed using cellranger version 4.0.0 with default settings and refdata-gex-GRCh38-2020-A reference
Genome_build: GRCh38
Supplementary_files_format_and_content: cellranger h5 raw feature-barcode matrices

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
Sample processing described in original article (Pekayvaz et al., Nature Communications 2022)
Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry) with Feature Barcoding technology for Cell Surface Protein, described in original article (TotalSeq™ anti-human Hashtag Antibodies B0251, A0252, A0253)

tag: tissue

value: blood

tag: disease state

value: SEVERE

value: PBMCs


title: Non-pneumonic patients (#4-6) PBMCs sampled at TP2 (GE) [20094_0005_A]

description:
gene expression
20094_0005_A_B_raw_feature_bc_matrix.new.h5
20094-0005

value: MILD


title: 4T1Mock3

description: Triple Negative cell line

source_name: 4T1 control cell line

value: Balb/c


title: GFP neg/ IL-2 neg memory #4

value: IL-2- memory

value: Sorted CD45.2+CD8+Thy1.1+GFP-


title: 136N

type: genomic

city: Cheras

first: Nurul Syakima

last: Ab Mutalib

state: Kuala Lumpur

address: Jalan Yaacob Latiff

department: UKM Medical Molecular Biology Institute

country: Malaysia

institute: Universiti Kebangsaan Malaysia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation 450K Beadchip using standard Illumina protocol

scan_protocol: Beadchip were scanned using iscan standard recommended Illumina scanner setting

data_processing: Genome studio v2011.1

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Normal tissue

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from CRC and normal tissues using Qiagen Dneasy kit according to manufacturer protocol

tag: gender

value: F

value: Normal


title: TSSC4 rep2

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

institute: Max-Planck-Institut für molekulare Genetik

data_processing:
Library strategy: FLASH
Basecalling carried out by NovaSeq 6000: 3.4.4 and bcl2fastq v2.20.0.422
Paired-end reads were merged, trimmed and filtered by size using bbmerge and bbduk, merged reads longer and 34 base-pairs were retained for analysis
umi_tools was used to separate UMI from reads with the following command: umi_tools extract --bc-pattern=NNNXXXXXXNNNNN -I {Input.fastq.gz} --3prime
flexbar was used to split biological replicates from each other with the command: flexbar -r {reads.fastq.gz} -b  new_flash_barcodes.fa --barcode-trim-end --barcode-error-rate 0.2 --zip-output GZ
Internal replicates were merged (taR3, taR6, taR8, taR13 for rep1 of TSSC4; taR5, taR11, taR12 and taR14 for rep2 of TSSC4 these files are provided)
Reads were mapped to the human genome (hg38) with bowtie2 and bbmap
umi_tools was used remove PCR duplicates: umi_tools dedup -I {in.bam} -S {out.bam} --spliced-is-unique --soft-clip-threshold 3
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage from deepTools2

source_name: Human Embryonic Kidney

growth_protocol: Flp-In T-REx HEK293 expression cell lines are maintained in DMEM with Glutamax, high glucose and Na-pyruvate (Thermo Fisher #31966), that is supplemented with 10% FBS and penicillin-streptomycin, and kept under blasticidin (15µg/ml) and hygromycin (150µg/ml) selection.

extract_protocol:
Cells were solubilized with 1X PBS with additional 0.3M NaCl 1% Triton™ X-100 and 0.2% TWEEN® 20
Flp-In™ T-REx™ 293 cells expressing either 3xFLAG-BIO tagged TSSC4 or 3xFLAG-BIO tagged GFP were induced with 0.1µg/mL doxycycline for ~16hrs and UV-crosslinked with 0.2mJ/cm2 UV-C light. Target proteins were purified using MyONE C1 streptavidin beads, after a partial RNase digestion using RNAse1 and end-repair with T4 PNK, uniquely barcoded s-oligos were ligated to each sample (2 biological replicates). After several stringent washes (up to 1% SDS), biological replicates are merged, and bead-bound RNA was released with proteinase K and purified with Oligo Clean and Concentrator columns. RNA was then reverse-transcribed and treated with RNaseH to phosphorylate 5’-ends of cDNA. The cDNA was then circularized with CircLigaseII, amplified with Q5 polymerase and sequenced on an Illumina platform (100bp, PE sequencing).
FLASH (Ilik et al., 2020)

treatment_protocol: Cells were UV-crosslinked with 200mJ/cm2 UV-C on 15 cm plates

value: Flp-In(TM) T-Rex(TM) 293

tag: treatment

value: 200mJ/cm2 UV-C


title: 56T

source_name: CRC tissue

value: Tumor


title: Bulk day 309 memory #3

value: P14 IFN-g.Thy1.1 IL-2.GFP

value: Total donor memory

value: no

value: Sorted CD45.2+CD8+


title: GPF pos/ IL-2 pos memory #3

value: IL-2+ memory

value: yes

value: Sorted CD45.2+CD8+Thy1.1+GFP+


title: 4T1Mock2

description: Triple Negative cell line


title: 4T1Mock1

description: Triple Negative cell line


title: ANV5Enpp12

description: Triple Negative cell line

value: FVB/n


title: 56N


title: 106N


title: 106T


title: 142T


title: day3_WT

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

description: single cell RNA-seq

data_processing:
scRNA data was processed using the 10x Genomics CellRanger pipeline
Seurat was used to call cluster and generate UMAPs
Monocle was used to perform pseudotime analysis
Genome_build: hg38
Supplementary_files_format_and_content: count matrix

source_name: H9 day3

growth_protocol: hESCs were maintained in Essential 8 plus supplement. Medium was changed to Essential 6 plus RA/BMP4 for 7 days to induce differentiation followed by an additional 43 days in keratinocyte media. cells were collected after 3 or 21 days using this differentiation procedure

extract_protocol:
Single cell suspensions were prepared with Accutase, and any large clumps were removed with 40μM cell strainers. Dead cells were eliminated with a dead cell removal kit (Miltenyi) per manufacturer instructions. 10,000 cells at a concentration of 1,000 cells per μL were resuspended in PBS with 0.04% BSA (Miltenyi).
Library prep was performed with a Chromium Single Cell 3’ Reagent Kit v3.1 (10x Genomics) per manufacturer instructions.

tag: genotype

value: WT


title: 4T1Enpp13

description: Triple Negative cell line

value: Balb/c


title: TSSC4 rep1


title: day21_WT

description: single cell RNA-seq

source_name: H9 day21


title: Bulk day 309 memory #2


title: Genomic DNA from hepatocellular carcinoma_L432

city: Shinjuku-ku

first: Yae

last: Kanai

state: Tokyo

address: 35 shinanomachi

department: Pathology

country: Japan

institute: Keio University School of Medicine

hyb_protocol: Standard Illumina Protocol.

scan_protocol: Standard Illumina iScan Protocol.

data_processing: GenomeStudio methylation software.

label_protocol: Standard Illumina Protocol.

extract_protocol: Phenol-chloroform extraction followed by dialysis.

value: Hepatocellular carcinoma

tag: sample type

value: Frozen tissue

value: Female

tag: age range


title: day21_AHDCKO

description: single cell RNA-seq

value: AHDC1 KO


title: GFP neg/ IL-2 neg memory #3

value: IL-2- memory

value: Sorted CD45.2+CD8+Thy1.1+GFP-


title: GFP neg/ IL-2 neg memory #2


title: Bulk day 308 memory #1


title: A375_sh3_input

city: Nanjing

first: Zhanghui

last: Yue

state: Jiangsu

address: 12 Jiangwangmiao Street, Xuanwu Area

country: China

institute: Hospital for Skin Diseases (Institute of Dermatology), Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Library strategy: m6A-seq
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genomeHomo sapiens (Version: v101). Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).
MEME (http://meme-suite.org) and HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: v101
Supplementary_files_format_and_content: xls include RPKM values for each Sample

source_name: cutaneous melanoma

growth_protocol: Corresponding lentivirus were transfected into A375 cells, the METTL3 knockdown efficiency was verified by qPCR and western blotting. A375 NC and shMETTL3 cells were inoculated in 10cm dish to a density of 90%.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. 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. Approximately more than 25 μg of total RNA representing a specific adipose type was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purification, the ribosomal-depleted RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was 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.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin derived melanoma cells

tag: lentivirus transfection


title: A375_sh2_input


title: Genomic DNA from hepatocellular carcinoma_L423

value: Male


title: Genomic DNA from hepatocellular carcinoma_L488


title: TIM-KD 60GG 2

type: RNA

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

hyb_protocol: Samples were then hybridized ON, washed, stained, and scanned using the GeneChip Hybridization Oven 640, Fluidic Station 450.

scan_protocol: Scanner 3000 7G (Thermo Fisher Scientific) were used to generate the raw data files (.CEL files) according to the manufacturer's instruction.

data_processing: Quality control and normalization of CEL files were performed using Transcriptome Analysis Console (TAC) software v4.0 (Thermo Fisher Scientific) by performing “Gene level SST-RMA” summarization method with human genome version hg38. The analyses were performed in two independent biological experiments and gene expression data were Log2 transformed before analyses.

label: biotin

label_protocol: RNA samples have been amplified, fragmented, and labeled for array hybridization according to the manufacturer’s instruction (GeneChip® Human Clarion S Array; ThermoFisher Scientific).

growth_protocol: cell lines were grown in RPMI 1640 (Gibco; Thermo Fisher Scientific), with 10% FBS and 1% penicillin/streptomycin. Cells were maintained at 37 °C and 5% CO2 in a humidified incubator.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany), treated with DNase-RNase free (Qiagen, Hilden, Germany) and quantified by Nanodrop (Thermo Fisher Scientific).

treatment_protocol: Lentiviral constructs functionally knocking-down TIM (p.LKO.1#1 - TRCN0000153760 and p.LKO.1#2 - TRCN0000153090, Sigma-Aldrich, S.Louis, MO, USA) and knocking-down ZEB1 (p.LKO.1#1 - TRCN0000369267 and p.LKO.1#2 - TRCN0000017565, Sigma-Aldrich), along with the corresponding control (p.LKO.1-puro (SHC002), Sigma-Aldrich) were transduced and packaged in 293T cells. Stable knock-down of TIM and/or ZEB1 in the different CRC cell lines were generated via lentiviral transduction in the presence of polybrene (8μg/ml) (Sigma-Aldrich, S.Louis, MO, USA), and selected with puromycin (Sigma, St Louis, MO, USA).

value: colon; derived from metastatic site:lymph node

value: TIM-KD

tag: time

value: 60-days post infection


title: GPF pos/ IL-2 pos memory #1

value: P14 IFN-g.Thy1.1 IL-2.GFP

value: IL-2+ memory


title: day3_AHDCKO

description: single cell RNA-seq


title: TIM-KD 60GG 1


title: 4T1Enpp12

description: Triple Negative cell line


title: GPF pos/ IL-2 pos memory #2

value: yes

value: Sorted CD45.2+CD8+Thy1.1+GFP+


title: 4T1Enpp11

description: Triple Negative cell line


title: A375_sh1_input


title: Genomic DNA from hepatocellular carcinoma_L360


title: Genomic DNA from hepatocellular carcinoma_L185


title: GFP neg/ IL-2 neg memory #1


title: Genomic DNA from hepatocellular carcinoma_L181


title: GFP pos/ IL-2 pos efectors #3

value: IL-2+ effector

value: Sorted  CD45.2+CD8+Thy1.1+GFP+


title: Genomic DNA from hepatocellular carcinoma_L191

value: Hepatocellular carcinoma


title: CTRL 60GG 1

value: CTRL


title: CTRL 60GG 2


title: A375_NC2_input

value: non-targeting control


title: Genomic DNA from hepatocellular carcinoma_L141

value: Frozen tissue


title: A375_NC1_input


title: ZEB1/TIM-KDs 15GG 2

value: 15-days post infection


title: Setd1b_WT_2_RNAseq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
bcl2fastq version 1.8.4 was used for demultiplexing
Genome_build: GRCm38
Alignment was done with 0.5.9-1.21009-MPI against a combination of the mm10 reference and a custom exon-exon junction reference was used as support to detect intron spanning reads. The custom reference was created with Ensembl Gene Version 69 mouse annotation
Genecounts were created with featureCounts v.1.4.4 and Ensembl Gene Version 69 mouse annotation was used. The counting was non strand-specific due to the library prep method
Supplementary_files_format_and_content: Tab-separated file (Annotated SeqMonk Probe report) where the first columns are information about the gene (name, strand, start, end, chromosome, …), and the remaining columns are the samples (log2RPM counts).

source_name: d21 GV oocytes

extract_protocol:
Ovaries were collection from 21-day-old females and digested with 2mg/mL collagenase (Sigma) and 0.02% trypsin solution, agitating at 37°C for 30 min.  GV oocytes were collected in KSOM medium (Sigma) and washed with PBS from females with an oocyte conditional deletion of Setd1b using Gdf9-cre (Setd1b cKO) and females carrying floxed Setd1b (Setd1b WT). Four GV oocytes for each genotype were collected for single cell RNA-seq (scRNA-seq).
Oocytes deposited in 2.5 µl lysis buffer and cDNA amplified exponentially with SMARTer Ultra Low RNA Kit for 12 cycles. Library construction was performed with NEBNext Ultra DNA Lib Prep Kit.

value: Germinal vesicle oocytes

value: Setd1b floxed/floxed, Gdf9-Cre negative

tag: age


title: Bulk Day 9 effectors#3

value: Total donor effector

value: no

value: Sorted CD45.2+CD8+


title: GFP pos/ IL-2 pos efectors #2


title: A375_sh3_IP

value: skin derived melanoma cells


title: Genomic DNA from hepatocellular carcinoma_L137

value: Male


title: GFP neg/ IL-2 neg effectors #2

value: P14 IFN-g.Thy1.1 IL-2.GFP

value: IL-2- effector

value: Sorted CD45.2+CD8+Thy1.1+GFP-


title: A375_sh2_IP


title: Genomic DNA from hepatocellular carcinoma_L253


title: ZEB1/TIM-KDs 15GG 1

value: colon; derived from metastatic site:lymph node


title: Genomic DNA from hepatocellular carcinoma_L244


title: GFP neg/ IL-2 neg effectors #3

value: yes

value: Sorted  CD45.2+CD8+Thy1.1+GFP-


title: A375_sh1_IP


title: Genomic DNA from hepatocellular carcinoma_L278

value: Hepatocellular carcinoma


title: Bulk Day 9 effectors #2


title: TIM-KD 15GG 2

value: TIM-KD


title: ZEB1-KD 15GG 2


title: GFP neg/ IL-2 neg effectors #1


title: A375_NC2_IP

value: non-targeting control


title: Genomic DNA from hepatocellular carcinoma_L265

value: Frozen tissue


title: A375_NC3_IP


title: Genomic DNA from hepatocellular carcinoma_L127


title: Genomic DNA from hepatocellular carcinoma_L134


title: Bulk Day 9 effectors #1


title: TIM-KD 15GG 1

value: 15-days post infection


title: CTRL 15GG 2

value: CTRL


title: CTRL 15GG 1


title: Naïve P14 donor CD8 T cells

value: naive donor

value: Immunomagnetic purification


title: Genomic DNA from hepatocellular carcinoma_L216


title: C_3

status: Public on Jan 16 2022

city: Changchun

first: Yanhong

last: Bao

state: jilin

address: jilin changchun

institute: Jilin Agricultural University

data_processing:
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome.generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). After the final transcriptome was generated, estimate the expression levels of all transcripts, and then lncRNA was screened. Transcripts overlapping with known mRNAs and transcripts shorter than 200 bp are discarded first. Then, Coding Potential Calculator (CPC) and Coding-Non-Coding Index (CNCI) were used to predict the transcripts with coding potential. All transcripts with CPC score < -1 and CNCI score < 0 were removed. The other types of transcripts with code names I, J, O, U, X are lncRNAs.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Bos taurus

source_name: cell

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the mRNA-Seq sample preparation kit for constructing sequencing library.
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.

value: Bovine peripheral blood mononuclear macrophages

value: untreated


title: MAP_1

value: Infecting bovine peripheral blood mononuclear macrophages with Mycobacterium avium subsp. paratuberculosis


title: MAP_3


title: MAP_2


title: A375_NC3_input

value: skin derived melanoma cells


title: A375_NC1_IP


title: C_2


title: C_1


title: Genomic DNA from hepatocellular carcinoma_L115

value: Male


title: ZEB1-KD 15GG 1


title: EPB02P1_Mouse_Endothelium_RCA_Veh_2wk_2wkV2R_70

city: Atlanta

first: Hanjoong

last: Jo

state: GA

address: 1760 Haygood Drive, Health Sciences Research Bldg E170

department: Coulter Department of Biomedical Engineering

institute: Georgia Tech and Emory Univ

description: sample_collection_overview: partial ligation surgery of LCA (left common carotid artery) was performed on all the mice. Endothelial RNAs were isolated at 2wk from LCA and the control RCA from each mouse.

hyb_protocol: Following fragmentation, biotin-labeled cRNA fragments were then hybridized to the probe array during 16 h at 450C of incubation before staining the array with streptavidin-phycoerythrin-conjugate and scanning it using the GeneChip® Scanner 3000, following the manufacturer’s recommendation

scan_protocol: Biotin-labeled cRNA was generated from cDNA and used to probe Affymetrix HT_MG-430_PM, comprising of ~43,000 probe sets and representing more than 20,000 mouse genes, using the Gene Titan MC instrument (Affymetrix, West Sacramento, CA). All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

data_processing: CEL files from the Affymetrix Array Station were processed and normalized by the Robust Multi-Array Average (RMA) algorithm

source_name: Endothelium

label_protocol: Total RNA was treated with DNase I and cleaned up with Qiagen RNeasy MiniElute Cleanup Kit (Cat. # 74204). The RNA concentrations were determined by NanoDrop and RNA quality was evaluated using Experion (Bio-Rad). All target labeling reagents were purchased from Affymetrix (West Sacramento CA). After cDNA synthesis, in vitro transcription in the presence of biotin-labeled ribonucleotides (biotin-11-CTPs and biotin-16-UTPs) was performed to yield biotin-labeled complementary RNA (cRNA) After cDNA synthesis, in vitro transcription in the presence of biotin-labeled ribonucleotides (biotin-11-CTPs and biotin-16-UTPs) was performed to yield biotin-labeled complementary RNA (cRNA)

extract_protocol: Total RNA was isolated from the endothelial flushing using the miRNEasy kit Qiagen (Cat # 217084).

treatment_protocol: Endothelial-enriched RNAs was flushed using 150uL of Qiazol and were stored at -80C until processing for RNA extraction. RNA extraction and Affy profiling were performed in four different batches, noted in the experiment design.

tag: therapeutic agent

value: vehicle

value: RCA

tag: time point


title: EPA05P1_Mouse_Endothelium_RCA_Veh_12h_12hV5R_15

description: sample_collection_overview: partial ligation surgery of LCA (left common carotid artery) was performed on all the mice. Endothelial RNAs were isolated at 12h from LCA and the control RCA from each mouse.


title: EPE09P1_Mouse_Endothelium_RCA_Veh_48h_48hV5R_54

description: sample_collection_overview: partial ligation surgery of LCA (left common carotid artery) was performed on all the mice. Endothelial RNAs were isolated at 48h from LCA and the control RCA from each mouse.


title: EPF10P1_Mouse_Endothelium_RCA_Veh_48h_48hV3R_52


title: Genomic DNA from hepatocellular carcinoma_L109


title: EPH05P1_Mouse_Endothelium_RCA_Veh_24h_24hV5R_35

description: sample_collection_overview: partial ligation surgery of LCA (left common carotid artery) was performed on all the mice. Endothelial RNAs were isolated at 24h from LCA and the control RCA from each mouse.


title: EPG09P1_Mouse_Endothelium_RCA_Ator_24h_24hA8R_38

value: Atorvastatin


title: EPE01P1_Mouse_Endothelium_RCA_Veh_24h_24hV1R_31


title: EPE02P1_Mouse_Endothelium_RCA_Veh_24h_24hV4R_34


title: EPE08P1_Mouse_Endothelium_RCA_Ator_12h_12hA9R_19


title: EPF01P1_Mouse_Endothelium_RCA_Ator_48h_48hA9R_58


title: EPA03P1_Mouse_Endothelium_RCA_Veh_12h_12hV1R_11


title: EPE07P1_Mouse_Endothelium_RCA_Veh_12h_12hV4R_14


title: EPH07P1_Mouse_Endothelium_RCA_Ator_2wk_2wkA8R_76


title: EPH08P1_Mouse_Endothelium_RCA_Veh_2wk_2wkV4R_72


title: EPD03P1_Mouse_Endothelium_RCA_Veh_48h_48hV1R_50


title: EPC07P1_Mouse_Endothelium_RCA_Ator_2wk_2wkA10R_78


title: EPH04P1_Mouse_Endothelium_RCA_Ator_12h_12hA6R_16


title: EPH01P1_Mouse_Endothelium_RCA_Ator_24h_24hA6R_36


title: EPE06P1_Mouse_Endothelium_RCA_Veh_24h_24hV3R_33


title: Genomic DNA from hepatocellular carcinoma_L107


title: EPB07P1_Mouse_Endothelium_RCA_Veh_2wk_2wkV3R_71


title: EPD04P1_Mouse_Endothelium_RCA_Veh_12h_12hV3R_13


title: Genomic DNA from hepatocellular carcinoma_L092


title: EPC03P1_Mouse_Endothelium_RCA_Ator_48h_48hA7R_56


title: Genomic DNA from hepatocellular carcinoma_L054


title: HIPP_sc_Rep1_ONT

city: New York

first: Anoushka

last: Joglekar

state: NY

address: 413 E 69th St

department: Dept. of Neurogenetics

institute: Weill Cornell Medicine

data_processing:
Illumina basecaller
PacBio IsoSeq basecaller
Oxford Nanopore guppy basecaller
PacBio long-read mapping done with STARlong
ONT long-read mapping done with minimap2
Long read output processed with scisorseqr
Genome_build: hg38
Genome_build: mm10
Supplementary_files_format_and_content: processed gene count files for bulk RNA sequencing
Supplementary_files_format_and_content: gff files for ONT long-read sequencing
Supplementary_files_format_and_content: scisorseqr output for PacBio long-read gene counts by cell type

source_name: Brain

extract_protocol: 10x Chromium - single nuclei RNA-seq

value: Hippocampus

tag: Sex

value: Female

value: Control (healthy) sample


title: FCtx1_ONT

data_processing:
Illumina basecaller
PacBio IsoSeq basecaller
Oxford Nanopore Guppy basecaller
10X sequencing output processed with 10X cellranger v3
Cellranger output analyzed with Seurat v3
PacBio long read mapping done with STARlong
ONT long read mapping done with minimap2
Long read output processed with scisorseqr
Genome_build: hg38
Supplementary_files_format_and_content: cellranger output for single-cell expression data
Supplementary_files_format_and_content: scisorseqr output for long read gene counts by cell type

source_name: Frontal Cortex

extract_protocol:
As per recommendations of each individual platform
10x Chromium - single nuclei gene expression

value: Brain


title: FCtx2_ONT


title: EPF03P1_Mouse_Endothelium_RCA_Ator_24h_24hA10R_40


title: EPG05P1_Mouse_Endothelium_LCA_Ator_12h_12hA8L_8

value: LCA


title: EPG06P1_Mouse_Endothelium_RCA_Ator_2wk_2wkA9R_77


title: EPB08P1_Mouse_Endothelium_RCA_Veh_2wk_2wkV5R_73


title: EPG04P1_Mouse_Endothelium_RCA_Ator_2wk_2wkA7R_75


title: EPC09P1_Mouse_Endothelium_RCA_Ator_2wk_2wkA6R_74


title: EPG02P1_Mouse_Endothelium_RCA_Ator_24h_24hA7R_37


title: EPC01P1_Mouse_Endothelium_RCA_Veh_2wk_2wkV1R_69


title: EPD02P1_Mouse_Endothelium_RCA_Ator_24h_24hA9R_39


title: EPG01P1_Mouse_Endothelium_LCA_Ator_24h_24hA6L_26


title: EPD10P1_Mouse_Endothelium_RCA_Ator_48h_48hA6R_55


title: Myocarditis 2

city: Lincoln

first: Jay

last: Reddy

state: Nebraska

address: Room 202, East Campus

department: Veterinary and Biomedical Sciences

institute: University of Nebraska Lincoln

data_processing:
Basecalls were converted into FASTQs using the Illumina bcl2fastq software
10x Data was processed with the Cell Ranger pipeline, version 3.0.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited tsv files for genes and cell barcodes, mtx single-cell expression matrix

source_name: Heart

extract_protocol:
Annexin V-negative and propidium iodide-negative single cells
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart

value: Myocarditis


title: EPC05P1_Mouse_Endothelium_RCA_Ator_12h_12hA8R_18


title: Myocarditis 1


title: EPB04P1_Mouse_Endothelium_RCA_Veh_24h_24hV2R_32


title: EPB05P1_Mouse_Endothelium_RCA_Ator_12h_12hA7R_17


title: EPB10P1_Mouse_Endothelium_RCA_Veh_48h_48hV2R_51


title: EPG07P1_Mouse_Endothelium_LCA_Veh_2wk_2wkV3L_61


title: EPC06P1_Mouse_Endothelium_RCA_Ator_12h_12hA10R_20


title: EPH09P1_Mouse_Endothelium_LCA_Ator_24h_24hA8L_28


title: EPA06P1_Mouse_Endothelium_LCA_Veh_24h_24hV3L_23


title: EPF02P1_Mouse_Endothelium_LCA_Ator_24h_24hA7L_27


title: Healthy Controls 2

value: Healthy


title: EPB09P1_Mouse_Endothelium_RCA_Veh_12h_12hV2R_12


title: Healthy Controls 1


title: EPA10P1_Mouse_Endothelium_LCA_Ator_48h_48hA6L_46


title: EPD05P1_Mouse_Endothelium_LCA_Ator_12h_12hA7L_7


title: EPF08P1_Mouse_Endothelium_LCA_Ator_48h_48hA8L_48


title: EPG03P1_Mouse_Endothelium_LCA_Ator_48h_48hA7L_47


title: EPD08P1_Mouse_Endothelium_LCA_Veh_2wk_2wkV5L_63


title: EPG08P1_Mouse_Endothelium_LCA_Veh_2wk_2wkV4L_62


title: EPF09P1_Mouse_Endothelium_LCA_Ator_2wk_2wkA6L_64


title: EPH03P1_Mouse_Endothelium_LCA_Veh_12h_12hV1L_1


title: HLEB348h0.1

city: Harbin

first: lin

last: wang

address: 141 Yiman Street

institute: Eye Hospital, The First Aﬃliated Hospital of Harbin Medical University, Harbin, China

description: Gene expression after 48h in 0.1 μmol DEX treated  HLEB3

hyb_protocol: The labeled cRNAs were hybridized onto the microarray.

scan_protocol: The Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarray (Design ID: 072363) Chip experiment was used to analyze 20 samples. The total RNA of samples was quantified by Nanodrop nd-2000 (Thermo Fisher Scientific, Scotts Valley, CA, USA) and detected using an Agilent Bioanalyzer 2100 (Agilent). After RNA quality was determined, sample labeling, chip hybridization and elution referring to the chip standard were carried out. After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data.Genespring (version 14.8,Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “Detected” were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs. Finally, Hierarchical Clustering was performed to display the distinguishable genes' expression pattern among samples.

source_name: HLEB3 cells_48h_0.1 μmol

label_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies). The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol: After identifying the most significant exposure factors and cell types, total RNA was extracted from the cells and scanned by lncRNA and mRNA chips. RNA was extracted using an RNA extraction kit. The concentration of RNA was detected at 260 nm and 280 nm. The RNA in the experimental sample was matched with an Agilent expression microarray (Agilent, Santa Clara, CA, USA).

treatment_protocol: The HLEC line B-3 obtained from ATCC was cultured in Dulbecco’s Modiﬁed Eagle’s Medium (DMEM; Gibco) with 20% fetal calf serum, 100 U/mL penicillin, 0.1 mg/mL streptomycin and 2 mM L-glutamine in white six well plates with a transparent bottom (Corning) with approximately 105 cells per well to yield a conﬂuent monolayer. The treatments were the same for all assays. Three groups were used for each assay: the pc DNA3.1- HLECs group, the pc DNA3.1-αAC- HLECs group and the pc DNA3.1-αBC- HLECs group. In the Dex +pc DNA3.1- HLECs group, cells were treated with 0.1 μmol, 1 μmol, 10 μmol and 100 μmol Dex for 12 h, 24 h, 36 h, and 48 h. In the Dex + pc DNA3.1-αAC and αBC-HLECs groups, cells were treated with 0.1 μmol, 1 μmol, 10 μmol, and 100 μmol Dex for 12 h, 24 h, 36 h, and 48 h.

value: human lens epithelial cells (HLECs)

tag: treatment/time point

value: after 48h in 0.1 μmol DEX treated


title: EPF06P1_Mouse_Endothelium_LCA_Veh_48h_48hV4L_44


title: EPB01P1_Mouse_Endothelium_LCA_Veh_24h_24hV1L_21


title: HLEB336h1

description: Gene expression after 36h in 1 μmol DEX treated  HLEB3

source_name: HLEB3 cells_36h_1 μmol

value: after 36h in 1 μmol DEX treated


title: Genomic DNA from hepatocellular carcinoma_L102

value: Hepatocellular carcinoma

value: Frozen tissue


title: EPH02P1_Mouse_Endothelium_LCA_Veh_2wk_2wkV2L_60


title: HLEB336h100

description: Gene expression after 36h in 100 μmol DEX treated HLEB3

source_name: HLEB3 cells_36h_100 μmol

value: after 36h in 100 μmol DEX treated


title: HLEB348h100

description: Gene expression after 48h in 100 μmol DEX treated HLEB3

source_name: HLEB3 cells_48h,100 μmol

value: after 48h in 100 μmol DEX treated


title: EPA07P1_Mouse_Endothelium_LCA_Ator_2wk_2wkA8L_66


title: HLEB336h0.1

description: Gene expression after 36h in 0.1 μmol DEX treated HLEB3

source_name: HLEB3 cells_36h_0.1 μmol

value: after 36h in 0.1 μmol DEX treated


title: EPD09P1_Mouse_Endothelium_LCA_Veh_48h_48hV5L_45

value: vehicle


title: EPB03P1_Mouse_Endothelium_LCA_Veh_48h_48hV1L_41


title: HLEB348h10

description: Gene expression after 48h in 10 μmol DEX treated  HLEB3

source_name: HLEB3 cells_48h_10 μmol

value: after 48h in 10 μmol DEX treated


title: B48h100

description: Gene expression after 48h in 100 μmol DEX treated  αB-crystallin overexpressed HLEB3

source_name: B cells_48h_100 μmol

tag: genotype/variation

value: αB-crystallin overexpressed HLEB3


title: HLEB336h10

description: Gene expression after 36h in10 μmol DEX treated HLEB3

source_name: HLEB3 cells_36h_10μmol

tag: cell type

value: after 36h in10 μmol DEX treated


title: EPH06P1_Mouse_Endothelium_RCA_Veh_48h_48hV4R_53

value: RCA


title: HLEB348h1

description: Gene expression after 48h in 1 μmol DEX treated HLEB3

source_name: HLEB3 cells_ 48h_1 μmol

value: after 48h in 1 μmol DEX treated


title: EPC04P1_Mouse_Endothelium_LCA_Ator_2wk_2wkA7L_65

value: Atorvastatin

value: LCA


title: B36h10

description: Gene expression after 36h in 10 μmol DEX treated  αB-crystallin overexpressed HLEB3

source_name: B cells_36h_10 μmol

value: after 36h in 10 μmol DEX treated


title: EPA01P1_Mouse_Endothelium_LCA_Veh_2wk_2wkV1L_59


title: B36h100

description: Gene expression after 36h in 100 μmol DEX treated  αB-crystallin overexpressed HLEB3

source_name: B cells_36h_100 μmol

value: human lens epithelial cells (HLECs)


title: A48h100

description: Gene expression after 48h in 100 μmol DEX treated  αA-crystallin overexpressed HLEB3

source_name: A cells_48h,100 μmol

value: αA-crystallin overexpressed HLEB3


title: MM1S_O4_rep2_RNAseq

city: London

first: Nikolaos

last: Trasanidis

address: Hammersmith Campus, Commonwealth Building, 4th Floor,, Du Cane Road, Imperial College London

department: Department of Immunology and Inflammation,

institute: Imperial College London

description:
processed data file:
RNAseq_MM1S_FOXM1_KD_genecounts.txt

data_processing:
Bcl2Fastq (v2.20) software used for basecalling.
ChIP-seq analysis: Alignment was performed with bowtie2 against the hg38/GRCh38 genome. The “samtools” package was used to convert sam to bam files. Duplicate reads were removed using the Picard “MarkDuplicates” package. Peak calling (ChIP versus Input)  was performed using MACS2. Genome browser tracks and heatmap enrichment plots were generated using the “deeptools”, with signal values  normalized as Fold  Change over Input. The MSPC package was used to obtain overlapping peaks between biological replicates.
RNA-seq analysis: Alignment was performed using STAR (2.5.3a) against hg38/GRCh3 genome. The “Rsubread” Bioconductor package was used to obtain gene-level read counts. The “DESeq2” Bioconductor package was used for data normalization and differential expression analysis across different conditions of knock-down experiments in each cell line.
Genome_build: GRCh38
Supplementary_files_format_and_content: peaks, counts

extract_protocol: NEBNext Ultra II RNA Library Prep kit for Illumina (NEB)

tag: cell line

value: Multiple myeloma cell line

value: anti-FOXM1 shRNA (O4)


title: MM1S_scrbl2_rep2_RNAseq


title: EPE04P1_Mouse_Endothelium_LCA_Veh_24h_24hV2L_22

tag: tissue


title: MM1S_O4_rep1_RNAseq


title: EPE03P1_Mouse_Endothelium_LCA_Ator_24h_24hA10L_30


title: EPA04P1_Mouse_Endothelium_LCA_Ator_12h_12hA6L_6


title: EPA09P1_Mouse_Endothelium_LCA_Veh_12h_12hV2L_2


title: A36h0.1

description: Gene expression after 36h in 0.1 μmol DEX treated  αA-crystallin overexpressed HLEB3

source_name: A cells_36h_0.1 μmol


title: Sa3_vs_Sa3_miR-30e-3p

city: Chiba city

first: Chikashi

last: MInemura

state: Chiba prefucture

address: 1-8-1 Inohana, chuo-ku

department: Oral science

institute: Chiba University

hyb_protocol: Agilent one-color Gene Expression Wash Pack (5188-5327 : Agilent) hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G4900DA Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were Images were quantified using Agilent Feature Extraction software version  12.1.1.1

source_name: Oral squamous cell carcinoma cell line Sa3

label_protocol: Agilent one-color Low Input Quick Amp Labeling Kit(5190-2305 :Agilent), protocol

growth_protocol: Normal cell culture medium DMEM.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

value: male

value: maxillary gingiva

value: Oral squamous cell carcinoma

value: control

value: miR-30e-3p transfected


title: EPF05P1_Mouse_Endothelium_LCA_Veh_12h_12hV5L_5

description: sample_collection_overview: partial ligation surgery of LCA (left common carotid artery) was performed on all the mice. Endothelial RNAs were isolated at 12h from LCA and the control RCA from each mouse.

source_name: Endothelium

value: vehicle


title: EPA02P1_Mouse_Endothelium_LCA_Veh_24h_24hV4L_24


title: EPF04P1_Mouse_Endothelium_LCA_Veh_12h_12hV3L_3


title: EPA08P1_Mouse_Endothelium_LCA_Ator_12h_12hA9L_9


title: EPD01P1_Mouse_Endothelium_LCA_Ator_48h_48hA9L_49

description: sample_collection_overview: partial ligation surgery of LCA (left common carotid artery) was performed on all the mice. Endothelial RNAs were isolated at 48h from LCA and the control RCA from each mouse.


title: B48h10

description: Gene expression after 48h in 10 μmol DEX treated  αB-crystallin overexpressed HLEB3

source_name: B cells_48h_10 μmol

value: αB-crystallin overexpressed HLEB3

value: after 48h in 10 μmol DEX treated


title: A36h100

description: Gene expression after 36h in 100 μmol DEX treated  αA-crystallin overexpressed HLEB3

source_name: A cells_36h_100 μmol

value: after 36h in 100 μmol DEX treated


title: A48h0.1

description: Gene expression after 48h in 0.1 μmol DEX treated  αA-crystallin overexpressed HLEB3

source_name: A cells_48h_0.1 μmol

value: after 48h in 0.1 μmol DEX treated


title: EPC08P1_Mouse_Endothelium_RCA_Ator_48h_48hA8R_57

value: Atorvastatin

value: RCA


title: A48h10

description: Gene expression after 48h in 10 μmol DEX treated  αA-crystallin overexpressed HLEB3

source_name: A cells_48h_10 μmol


title: EPD06P1_Mouse_Endothelium_LCA_Ator_12h_12hA10L_10

value: LCA


title: EPE05P1_Mouse_Endothelium_LCA_Veh_24h_24hV5L_25

description: sample_collection_overview: partial ligation surgery of LCA (left common carotid artery) was performed on all the mice. Endothelial RNAs were isolated at 24h from LCA and the control RCA from each mouse.


title: A48h1

description: Gene expression after 48h in 1 μmol DEX treated  αA-crystallin overexpressed HLEB3

source_name: A cells_48h_1 μmol

value: human lens epithelial cells (HLECs)

value: after 48h in 1 μmol DEX treated


title: A36h1

description: Gene expression after 36h in 1 μmol DEX treated  αA-crystallin overexpressed HLEB3

source_name: A cells_36h_1 μmol

value: αA-crystallin overexpressed HLEB3

value: after 36h in 1 μmol DEX treated


title: A36h10

description: Gene expression after 36h in10 μmol DEX treated  αA-crystallin overexpressed HLEB3

source_name: A cells_36h_10 μmol

value: after 36h in10 μmol DEX treated


title: MM1S_O1_rep2_RNAseq

value: Multiple myeloma cell line

value: anti-FOXM1 shRNA (O1)


title: MM1S_O1_rep1_RNAseq


title: MM1S_scrbl2_rep1_RNAseq


title: EPD07P1_Mouse_Endothelium_LCA_Ator_2wk_2wkA10L_68

description: sample_collection_overview: partial ligation surgery of LCA (left common carotid artery) was performed on all the mice. Endothelial RNAs were isolated at 2wk from LCA and the control RCA from each mouse.


title: U266_scrbl_rep2_RNAseq

description:
processed data file:
RNAseq_U266_PBX1_KD_genecounts.txt


title: EPF07P1_Mouse_Endothelium_LCA_Veh_12h_12hV4L_4


title: U266_P11_rep2_RNAseq

value: anti-PBX1 shRNA (P11)


title: U266_P31_rep2_RNAseq

value: anti-PBX1 shRNA (P31)


title: U266_P11_rep1_RNAseq


title: U266_scrbl_rep1_RNAseq


title: splotch ko rep2

city: Seattle

first: David

last: Beier

state: WA

address: 1900 9th Avenue

department: CDBRM

institute: Seattle Children's Research Institute

data_processing:
Sequnced read were aligned using STAR
Reads aligning to exons of a gene were counted using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

source_name: E12.5 embryo

growth_protocol: Timed matings were set up using intercrosses of heterozygous Carm1tm1Mtb or Pax3Sp2h and harvesting embryos at embryonic day 12.5 (E12.5).

extract_protocol:
RNA was isolated from homogenized whole embryos using the PureLink RNA Mini Kit (Invitrogen). RNA quality was assessed using a Agilent 4200 Tapestation and samples with a RNA Integrity Number equivalent (RINe) >9 were selected.
RNA library preparation with polyA enrichment and paired-end 150 bp sequencing was performed by the commercial provider Novogene Corporation, Inc. using the Illumina NovaSeq platform.

tag: strain

value: mixed

value: Pax3 null

value: embryonic day 12.5 (E12.5)

value: embryo


title: splotch wt rep3

value: Pax3 wild-type


title: splotch ko rep3


title: splotch wt rep2


title: splotch ko rep1


title: splotch wt rep1


title: carm1 wt rep3

value: Carm1 wild-type


title: MM1S_P11_rep2_RNAseq

description:
processed data file:
RNAseq_MM1S_PBX1_KD_genecounts.txt


title: EPB06P1_Mouse_Endothelium_LCA_Ator_2wk_2wkA9L_67

value: Atorvastatin


title: MM1S_P31_rep2_RNAseq


title: EPC10P1_Mouse_Endothelium_LCA_Veh_48h_48hV3L_43

value: vehicle

value: LCA


title: carm1 wt rep1


title: MM1S_P31_rep1_RNAseq


title: MM1S_P11_rep1_RNAseq


title: MM1S_scrbl_rep1_RNAseq


title: EPE10P1_Mouse_Endothelium_LCA_Veh_48h_48hV2L_42


title: carm1 wt rep2


title: carm1 ko rep3

value: Carm1 null


title: Input_rep2_ChIPseq_U266

description:
processed data file:
ChIPseq_U266_PBX1_rep1n2_regions.bed
ChIPseq_U266_PBX1_rep1n2_signal.bw

library_source: genomic

extract_protocol: NEBNext Ultra II ChIP-seq Library Prep Master Mix (NEB)

value: no treatment

tag: antibody


title: carm1 ko rep2


title: PBX1_rep2_ChIPseq_U266

tag: treatment

value: PBX1 (Abnova M01, clone 4A2)


title: Input_rep1_ChIPseq_U266


title: U266_P31_rep1_RNAseq


title: PBX1_rep1_ChIPseq_U266


title: Input_rep2_ChIPseq_MM1S

description:
processed data file:
ChIPseq_MM1S_PBX1_rep1n2_regions.bed
ChIPseq_MM1S_PBX1_rep1n2_signal.bw


title: PBX1_rep2_ChIPseq_MM1S


title: Input_rep1_ChIPseq_MM1S


title: PBX1_rep1_ChIPseq_MM1S


title: infected_Cacnes61_mouse_scRNAseq

city: La Jolla

first: Jason

middle: Samuel

last: Seidman

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

description: scRNA-Seq generated using 10x genomics Single Cell 3’ Reagent Kits. Data were aggregated using Cell Ranger software.

data_processing:
The 10X Genomics Cell Ranger version 3.0.1 software pipeline with default parameters was used to perform sample demultiplexing, barcode processing, alignment to the mm10 reference genome, and single-cell gene counting. Data was further filtered, processed and analyzed using the Seurat R toolkit version 3 (Butler et al, 2018 PMID: 29608179, Stuart et al, 2019 PMID: 31178118). Filtering of initial data involved selecting cells with > 100 features and < 10% mitochondrial genes. Data was normalized using the NormalizeData() function with parameters normalization.method = ‘LogNormalize’ and scale.factor = 10000. Variable genes were identified with the FindVariableFeatures() function with parameters with selection.method = 'vst'. Data was scaled with the ScaleData() function with default parameters. Principal components (PCs) were calculated from these variable genes using the function RunPCA() and the top 20 PCs were used for downstream analysis. Clusters were identified using the FindNeighbors() then FindClusters() function with arguments resolution = 0.5. Nonlinear dimensionality reduction and visualization was performed with tSNE using the RunTSNE(), and UMAP (Becht et al, 2019 PMID: 30531897) using the RunUMAP() function. Marker genes for each cluster were determined using the FindAllMarkers() function with parameters only.pos = TRUE, min.pct = 0.25, and thresh.use = 0.25. Clusters were assigned to cell types “Fibroblast”, “Keratinocyte”, “Myeloid”, “Lymphoid”, “Endothelial”, and “Melanocyte” based on marker genes. 6 out of the original 24 clusters were annotated as fibroblasts and underwent additional quality control. In brief, a new Seurat object was generated using only the cells in these clusters with their corresponding raw counts, followed by normalization, scaling, clustering and dimensionality reduction as described above, resulting in 15 fibroblast clusters. Clusters with high expression of leukocyte marker genes and cell cycle genes were excluded, and a final Seurat object was created from the remaining cells and their raw counts with a final iteration of normalization, scaling, clustering and dimensionality reduction. Cluster marker genes were identified on the finalized 10 clusters with FindAllMarkers() with parameter only.pos = TRUE and thresh.use = 0.4054651(corresponding to 1.5 fold change). Gene ontology analysis was performed on marker genes using the ‘clusterProfiler’ R package with default parameters (Yu et al, 2012 PMID: 22455463). Cell lineage and pseudotime inference was performed using the Slingshot R package (Street et al, 2018 PMID: 29914354). The Seurat object was transformed into a SingleCellExperiment object and Slingshot trajectory analysis was performed using Seurat clustering information and UMAP dimensionality reduction. We used the standard workflow of the recently developed package CellChat to perform cellular communication analysis and visualization our scRNAseq data (Jin et al, 2021 PMID: 33597522).
Genome_build: mm10
Supplementary_files_format_and_content: CSV file containing gene expression for each cell. Column names indicate sample_barcode for single cell

source_name: Skin biopsies from mice intradermally infected with C acnes

extract_protocol:
All animal experiments were approved by the University of California, San Diego (UCSD), Institutional Animal Care and Use Committee (#S09074). For single cell RNA-Seq analysis of mouse skin, the upper back skin of SKH-1 mice were intradermally infected with 1 x 107 CFU of C. acnes or RCM control for 3 days. Skin samples were collected from 6 mm punch biopsies and immediately placed on ice. In total, 3 biopsies were pooled per condition (infected or non-infected) for single cell generation. Single cell suspensions were generated by cutting skin into small pieces using a scalpel followed by digestion in Hanks Balanced Salt Solution (HBSS) (ThermoFisher, #14175095) supplemented with 20 mg/ml Bovine Serum Albumin (BSA), 1X Antibiotic-Antimycotic (ThermoFisher, #15240062), 50 U/ml DNAse I (Sigma, #04716728001), 0.1 mg/ml Liberase (Sigma, #05401020001), 20 mM HEPES (ThermoFisher, #15630080), 2 mM sodium pyruvate (ThermoFisher, #11360070) and 1 mg/ml Collagenase Type IV (ThermoFisher, 17104019). Tissue dissociation was carried out by a 2 h ice-cold incubation in the digestion buffer followed by 45 min incubation at 37°C shaking at 200 rpm. Enzymatic dissociation was terminated by addition of 5 mM EDTA and 10% Fetal Bovine Serum (FBS). Digests were filtered twice through a 40 μm filter, then incubated in red blood cell lysis buffer followed by removal of dead cell using MACS Dead Cell Removal Kit (Milteny Biotek) for downstream applications in 10X Genomics Chromium platform.
Single cell suspensions were loaded onto the 10X Genomics Chromium Controller instrument to generate single cell GEMs. GEM-RT and library construction were performed following the 10X Genomics Protocol.

tag: agent

value: C acnes


title: carm1 ko rep1

tag: genotype


title: RNA_WT_ML_rep2

city: Shanghai

first: Li

last: He

address: No. 3888 Chenhua Road

department: Shanghai Center for Plant Stress Biology

institute: CAS Center for Excellence in Molecular Plant Science (CEMPS)

data_processing:
For RNA-seq data processing, quality control was performed using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc). RNA-Seq reads were trimmed using cutadapt (Martin, 2011) and Trimmomatic (Bolger et al., 2014) before alignment. The trimmed reads were aligned to the Arabidposis TAIR10 genome using STAR (v2.5.3) (Dobin et al., 2013) with parameters “--outSAMmultNmax 1” and “--outSAMstrandField intronMotif” for running Cufflinks to assemble. The tool htseq-count of Python package HTSeq (Anders et al., 2015) was used to count the mapped fragments for each gene and TE with “--stranded=reverse” for differentially expressed genes analysis and “--stranded=yes” for differentially expressed antisense transcription of genes.
Genome_build: TAIR10
Supplementary_files_format_and_content: BW

organism: Arabidopsis thaliana

source_name: aerial part

growth_protocol: All plants were grown under long-day condition (16 h light/8 h dark). For seedling growth, Arabidopsis seeds were plated on 1/2 Murashige and Skoog (MS) medium with 0.6% agar, 0.7% agar, 1.0% or 1.2% agar and 1.5% sucrose and stratified for 7 days at 4℃ in darkness before being transferred to the growth chamber (16 h light/8 h dark, 22℃). For experiments with adult plants, 14-day-old seedlings were transplanted to soil in the growth chamber.

extract_protocol:
The RNeasy Plant Mini Kit (Qiagen) was used for RNA extraction.
Library construction and sequencing were performed at the PSC Genomics Core Facility.

tag: tag

value: wild type


title: RNA_WT_ML_rep3


title: control_RCM_mouse_scRNAseq

source_name: Skin biopsies from mice intradermally injected with reinforced clostridial media (RCM) control

value: clostridial media (RCM) control


title: MM1S_scrbl_rep2_RNAseq

value: Multiple myeloma cell line


title: RNA_WT_ML_rep1


title: DNA_mddcc_rep2

description: RL401-JKZ0363_3021DNA20200228_S20200318_BKDL202566393-1a-7UDI239-AK7214

data_processing:
For BS-seq, reads containing adapters and low-quality reads (q < 20) were trimmed using cutadapt (Martin, 2011) and Trimmomatic (Bolger et al., 2014), respectively, and clean reads that were shorter than 45nt were discarded. The remaining clean reads were mapped to the Arabidopsis TAIR 10 genome using BSMAP(2.90) (Xi and Li, 2009) with default parameters. In order to reduce the effect of RNA-DNA hybrids that interfere with bisulfite treatment, the reads were also mapped to the genome using bowtie2, and the reads with 0/1 mismatch both in BSAMP and bowite2 were filtered. Then methratio.py script was used to extract methylation ratio from filtered mapping results; the option -r was used to remove potential PCR duplicates. Cytosine positions with at least 4 reads coverage were retained for further analysis.
For RNA-seq data processing, quality control was performed using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc). RNA-Seq reads were trimmed using cutadapt (Martin, 2011) and Trimmomatic (Bolger et al., 2014) before alignment. The trimmed reads were aligned to the Arabidposis TAIR10 genome using STAR (v2.5.3) (Dobin et al., 2013) with parameters “--outSAMmultNmax 1” and “--outSAMstrandField intronMotif” for running Cufflinks to assemble. The tool htseq-count of Python package HTSeq (Anders et al., 2015) was used to count the mapped fragments for each gene and TE with “--stranded=reverse” for differentially expressed genes analysis and “--stranded=yes” for differentially expressed antisense transcription of genes.
Identification of non-reference TE insertions with TSDs (Target Site Duplications) was conducted using SPLITREADER with some modifications (Quadrana et al., 2016).
Genome_build: TAIR10
Supplementary_files_format_and_content: methylation wig files, RNA-seq coverage bedGraph, text files showing the TE insertion sites

source_name: DNA_mddcc_aeiral part

extract_protocol:
The DNeasy Plant Mini Kit (Qiagen) was used for DNA extraction; the RNeasy Plant Mini Kit (Qiagen) was used for RNA extraction.
Library construction and sequencing were performed at the PSC Genomics Core Facility.

tag: developmental stage

value: mutant

value: aerial part


title: DNA_mddcc_rep3

description: RL401-JKZ0363_3022DNA20200228_S20200318_BKDL202566393-1a-7UDI239-AK7215


title: DNA_mddcc_rep1

description: RL401-JKZ0363_3023DNA20200228_S20200318_BKDL202566393-1a-7UDI239-AK7216


title: DNA_met1-9_rep1

description: RL401-JKZ0363_3018DNA20200228_S20200318_BKDL202566393-1a-AK3404-AK7216

source_name: DNA_met1-9_aeiral part


title: DNA_ddcc_rep1

description: RL401-JKZ0363_3017DNA20200228_S20200318_BKDL202566393-1a-AK3404-AK7215

source_name: DNA_ddcc_aeiral part


title: RNA_mddcc_rep3

source_name: RNA_mddcc_aeiral part


title: DNA_WT_rep1

description: RL401-JKZ0363_3016DNA20200228_S20200318_BKDL202566393-1a-AK3404-AK7214

source_name: DNA_WT_aeiral part


title: FCtx1_PacBio_LAP_noCAP

source_name: Brain

value: Frontal Cortex

value: Male

value: Control (healthy) sample


title: RNA_mddcc_rep2


title: FCtx2_PacBio

source_name: Frontal Cortex

value: Brain

tag: disease state


title: RNA_mddcc_rep1


title: Arabidopsis_250mM sorbitol_rep 2

city: Observatory

first: Lara

middle: Elizabeth

last: Donaldson

state: Western Cape

address: Werner and Beit South, UCT Medical School, Anzio Road

country: South Africa

institute: International Centre for Genetic Engineering and Biotechnology

scan_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol, Scanned using Agilent Technologies Scanner G2505C US10123789

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software v. 10.7 with default protocol settings GE1_107_Sep09 to obtain processed signal intensities (raw data). For the final processed data, controls were removed and then the data was quantile normalized for each sample followed by z-score transformation of each gene. Logarithmic scaling of the absolute value of the data was then performed to stabilize variance.

source_name: whole seedlings, 2 week old

growth_protocol: Arabidopsis thaliana Col-0 seeds were sterlized and sown onto petri dishes containing ATS media (5 mM KNO3, 2 mM MgSO4.7H2O, 2 mM Ca(NO3)2.4H2O, 50 mM FeNaEDTA, 70 µM H3BO3, 14 µM MnSO4.H2O, 0.5 µM CuSO4.5H2O, 1 µM ZnSO4.6H2O, 0.2 µM Na2MoO4, 10 µM NaCl and 0.01 µM CoCl2.6H2O) with 6% (w/v) phytoagar (50 seeds per petri dish) and grown for 2 weeks under standard conditions (100 µM  photons.m-2.s-1, 16-hr light/8-hr dark, 22°C, 50 to 60% relative humidity)

extract_protocol: RNA was extracted from 100 mg tissue (whole seedlings including shoot and root tissue) using Trizol, Dnase treated using the Qiagen RNase-Free DNase kit and cleaned up using the Qiagen Rneasy Mini kit according to the manufacturers instructions

treatment_protocol: Arabidopsis plants grown under the same conditions on ATS media supplemented with either 50 mM NaCl, 75 mM NaCl, 100 mM NaCl, 125 mM NaCl, 100 mM sorbitol, 150 mM sorbitol, 200 mM sorbitol or 250 mM sorbitol

value: whole seedlings

tag: age

value: 2 week old

value: ATS media supplemented with 250mM sorbitol


title: Arabidopsis_200mM sorbitol_rep 1

hyb_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol

value: ATS media supplemented with 200mM sorbitol


title: Ectocervical 3D organoids_with HPV16 E6E7_5days post_Uninfected_Replicate3

city: Würzburg

first: Cindrilla

last: Chumduri

address: Am Hubland

department: Chair of Microbiology, Biozentrum

institute: Julius-Maximilians-Universität Würzburg

hyb_protocol: After precipitation, purification and quantification, 0.75µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted single-color raw data files were background corrected, quantile normalized, and further analyzed for differential gene expression using Rstudio (Rstudio. Inc.). Microarray data from three independent infection experiments were combined.

label_protocol: RNA was labeled with the single-color Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: Ectocervical 2D stem cells and 3D organoids were grown in defined media using the protocol described in the accompanying manuscript (Materials and Methods)

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.

treatment_protocol: Ectocervical 2D stem cells and 3D organoids with or with out HPV16 E6E7 expression were either uninfected or infected with Chlamydia trachomatis for 2days and 5days.

tag: tissue type

value: Ectocervical squamous

tag: infection

value: HPV E6E7

tag: cells culture type

tag: time


title: Arabidopsis_200mM sorbitol_rep 3

label_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol


title: RNA_met1-9_rep3

source_name: RNA_met1-9_aeiral part


title: Arabidopsis_250mM sorbitol_rep 1


title: Arabidopsis_250mM sorbitol_rep 3


title: Arabidopsis_150mM sorbitol_rep 3

value: ATS media supplemented with 150mM sorbitol


title: Ectocervical 3D organoids_with HPV16 E6E7_5days post_Chlamydia trachomatis_Infection_Replicate3


title: Arabidopsis_150mM sorbitol_rep 1


title: FCtx1_PacBio

tag: Sex


title: Ectocervical 3D organoids_5days post_Chlamydia trachomatis_Infection_Replicate3

value: no


title: Arabidopsis_200mM sorbitol_rep 2


title: Ectocervical 3D organoids_48hours post_Uninfected_Replicate3


title: Arabidopsis_100mM sorbitol_rep 2

value: ATS media supplemented with 100mM sorbitol


title: Arabidopsis_100mM sorbitol_rep 1


title: Arabidopsis_100mM sorbitol_rep 3


title: Ectocervical 3D organoids_with HPV16 E6E7_5days post_Uninfected_Replicate2


title: Ectocervical 3D organoids_with HPV16 E6E7_5days post_Chlamydia trachomatis_Infection_Replicate2


title: Ectocervical 3D organoids_5days post_Chlamydia trachomatis_Infection_Replicate2


title: RNA_met1-9_rep2


title: FCtx2_PacBio_preCAP


title: RNA_met1-9_rep1


title: FCtx1_PacBio_preCAP


title: RNA_ddcc_rep3

source_name: RNA_ddcc_aeiral part


title: Arabidopsis_150mM sorbitol_rep 2


title: RNA_ddcc_rep2


title: RNA_WT_rep2

source_name: RNA_WT_aeiral part

value: wild type


title: RNA_WT_rep3


title: Arabidopsis_125mM NaCl_rep 3

value: ATS media supplemented with 125mM NaCl


title: JT_683_gata6RFPline1_0h_FLAG_chip1_Nanog_chip2_rep1

city: Bethesda

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health

data_processing:
mapping to genome using bowtie2 with the following options (-N 1 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -x). Reads that mapped to ENCODE mm10 blacklist regions were removed using Samtools (Li et al., 2009). Piccard (broadinstitute.github.io/picard/) was then used to identify non-duplicated reads. Duplicate reads were removed for libraries generated from blastocysts but kept for all others.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Embryonic stem cell line

growth_protocol: Cells were maintained at a density of 1 million cells per 10cm gelatinized plates at 37ºC x% O2, x% CO2 in 2i media (50% DMEM/F12, 50% Neurobasal, Penicillin-Streptomycin, GlutaMAX, 2-Mercaptoethanol, N2, B27, 0.3nM PD0325901, 0.1nM CHIR9902, and 2x105units/mL LIF).

extract_protocol:
30 million cells were fixed by resuspending them in 1% formaldehyde in HBSS (1ml/million cells). Cells were incubated for 10 mins at room temperature, protected from light, on a nutator. After 10 mins, 1.42M glycine (100µl/ml of fixative) was added and cells were mixed by inversion and incubated for 5 mins at room temperature to quench PFA. Cells were then pelleted at 2000g, at 40C for 5 mins and washed twice in 1X TBS (50 mM Tris-Cl, pH 7.5, 150 mM NaCl). Cell pellets were then flash frozen and stored at -800C. For the first round of ChIP, fixed pellets of undifferentiated cells and cells induced with Dox for 2 hours were thawed on ice for 10 mins. For each time point 6 replicates of 10 million cells each, were used. Nuclei were extracted and lysed from thawed cell pellets using the Covaris truChIP® Chromatin Shearing Kit, following recommendations for high cell numbers (1ml lysis buffer/ 20million cells). Lysed nuclei were sonicated in Covaris 1 ml AFA Fiber milliTUBE (Duration: 2100Secs, peak power-75W, duty factor 15%) to fragment chromatin to an average size of 200bp. Sonication chromatin was centrifuged at 20800g for 15mins to separate residual debris and the cleared lysate was transferred to a fresh pre-chilled tube. 25µl was aliquoted separately to confirm sonication efficiency and estimate chromatin concentration while the rest was frozen and stored at -80C. To the 25µl, 1 µl of RNase A (10 mg/mL) was added and incubated at 37C for 30 min after which 1 µl of Proteinase K (10 mg/mL) was added and chromatin was reverse cross-linked overnight at 65C in a PCR cycler with a heated lid. The following day, after performing 2X SPRI bead clean fragment size was confirmed by running 1ng on a tape station, and concentration was estimated using Qubit 1X dsDNA high sensitivity kit. Frozen chromatin was thawed and NaCl (final concentration of 150mM), Triton-x-100 (final concentration of 1%) and Na-deoxycholate (final concentration of 0.1%) were added. 10µg chromatin was used per replicate and a total of six replicates for each time point were subjected to immunoprecipitation with anti-FLAG M2 conjugated to protein A/G beads. For each sample, 30 µl of Protein A/G beads preconjugated to 2 µg antibody (by incubation of antibody with washed beads resuspended in 500µl RIPA for 3h) was added to the reaction and chromatin was capture by overnight incubation at 40C, on a rotating platform. The next day, captured chromatin was washed successively as follows: once in low-salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), twice in high-salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), twice in lithium chloride wash buffer (250mM LiCl, 1% NP-40, 1% Sodium Deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0), and twice in 1X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). To elute FLAG-bound chromatin, beads were resuspended in 60µl of freshly made Direct Elution Buffer (10mM Tris-HCl pH8, 0.3M NaCl, 5mM EDTA pH8, 0.5% SDS) supplemented with 10mM DTT and incubated at 370C, 500rpm, 15mins. Eluted material was collected in a fresh tube and the process was repeated once more and pooled with the first elution. Finally, eluates from three replicates were pooled together to give two replicates per timepoint. 100µl was subjected to reverse crosslinking and library preparation to map FLAG-bound regions, and 100µl was added to 900µl RIPA and used for immunoprecipitation with anti-Nanog conjugated to protein A/G beads and the protocol described above was followed. 20 amplification cycles were used to prepare libraries.
DNA was using the Zymo DNA Clean and Concentrator kit. For each sample, double stranded DNA (10µl), Template Preparation D Buffer (2µl), and Template Preparation D Enzyme (1µl) were combined and End Repair and A-tailing was performed in a Thermocycler with a heated lid (22ºC, 25 min; 55ºC, 20 min). Library Synthesis D Buffer (1µl) and Library Synthesis D Enzyme (1µl) were subsequently added, and library synthesis was performed (22ºC, 40min). Immediately after, Library Amplification D Buffer (25µl), Library Amplification D Enzyme (1µl), Nuclease-free water (4µl), and a unique Illumina-compatible indexed primer (5µl) were added. Library amplification was performed using the following cycling conditions: 72ºC for 3 min; 85ºC for 2 min; 98ºC for 2 min (denaturation); 4 cycles of 98ºC for 20 s, 67ºC for 20 s, 72ºC for 10 s (addition of indexes); 14 cycles of 98ºC for 20 s, 72ºC for 10 s (library amplification). Post-PCR clean-up was performed on amplified libraries with a SPRIselect bead 0.6X left/1x right double size selection then washed twice gently in 80% ethanol and eluted in 10-12µl 10 mM Tris pH 8.0.

treatment_protocol: Differentiation into primitive endoderm was induced in serum containing ESS media (Knockout DMEM, 15% FBS,1% GlutaMAX, 1% Penicillin-Streptomycin, 1% 2-Mercaptoethanol, 1% Sodium Pyruvate, 1% MEM NEAA, 2x105units/mL LIF) containing doxycycline (1ug/mL) for 2 to 12 hours. For time points greater than 12 hours, mES cells were induced in serum media containing doxycycline for 12 hours and switched to serum media in the absence of doxycycline for the remaining time.

tag: time point

value: 0 hour no doxycycline

tag: trangene

value: Stem cells have TRE:GATA6-DSREd2

value: NANOG


title: JT_682_gata6RFPline1_2h_FLAG_chip1_rep2

value: 2 hour post doxycycline

value: FLAG


title: JT_684_gata6RFPline1_0h_FLAG_chip1_Nanog_chip2_rep2


title: Ectocervical 3D organoids_with HPV16 E6E7_5days post_Chlamydia trachomatis_Infection_Replicate1


title: RNA_WT_rep1

tag: tissue

value: aerial part


title: Ectocervical 3D organoids_with HPV16 E6E7_5days post_Uninfected_Replicate1


title: Ectocervical 3D organoids_48hours post_Uninfected_Replicate2


title: Arabidopsis_125mM NaCl_rep 2

value: whole seedlings


title: Arabidopsis_100mM NaCl_rep 2

value: 2 week old

value: ATS media supplemented with 100mM NaCl


title: Arabidopsis_100mM NaCl_rep 1


title: Ectocervical 3D organoids_5days post_Uninfected_Replicate1


title: Ectocervical 2D stem cells_with HPV16 E6E7_48hours post_Chlamydia trachomatis_Infection_Replicate3


title: BS_mddcc_rep3

source_name: BS_mddcc_aeiral part

value: mutant


title: Arabidopsis_75mM NaCl_rep 3

value: ATS media supplemented with 75mM NaCl


title: JT_686_gata6RFPline1_2h_FLAG_chip1_Nanog_chip2_rep2

tag: strain


title: Arabidopsis_75mM NaCl_rep 2


title: Ectocervical 2D stem cells_48hours post_Chlamydia trachomatis_Infection_Replicate3

value: Ectocervical squamous


title: Arabidopsis_100mM NaCl_rep 3


title: Ectocervical 2D stem cells_with HPV16 E6E7_48hours post_Uninfected_Replicate3

value: HPV E6E7


title: JT_685_gata6RFPline1_2h_FLAG_chip1_Nanog_chip2_rep1

tag: antibody


title: Arabidopsis_125mM NaCl_rep 1

tag: treatment


title: BS_mddcc_rep2

description:
RL166-JKZ0269-7687BSDNA16052018-S12112018_TKR181100868-31_HTGCLCCXY_L8
JKZ0269_5900_BS051618_S051818


title: Ectocervical 3D organoids_5days post_Chlamydia trachomatis_Infection_Replicate1

value: no


title: EPC02P1_Mouse_Endothelium_LCA_Ator_24h_24hA9L_29

description: sample_collection_overview: partial ligation surgery of LCA (left common carotid artery) was performed on all the mice. Endothelial RNAs were isolated at 24h from LCA and the control RCA from each mouse.

source_name: Endothelium

tag: therapeutic agent

value: Atorvastatin

value: LCA


title: JT_680_gata6RFPline1_0h_FLAG_chip1_rep2


title: JT_679_gata6RFPline1_0h_FLAG_chip1_rep1


title: BS_mddcc_rep1

tag: genotype


title: Arabidopsis_75mM NaCl_rep 1


title: JT_681_gata6RFPline1_2h_FLAG_chip1_rep1


title: BS_met1-9_rep2

description: RL304JKZ0341_1410BSDNA20190725_S20190729

source_name: BS_met1-9_aeiral part


title: JT_678_gata6RFPline1_2h_1%input_rechip

value: Input


title: Ectocervical 2D stem cells_with HPV16 E6E7_48hours post_Chlamydia trachomatis_Infection_Replicate2


title: Ectocervical 2D stem cells_with HPV16 E6E7_48hours post_Uninfected_Replicate2


title: BS_met1-9_rep1

description: RL303JKZ0341_1409BSDNA20190725_S20190729


title: BS_ddcc_rep1

description:
RL130-JKZ0276-6170-BS070518-S071318_TKR180700741-28
RL166-JKZ0276-7686BSDNA05072018-S12112018_TKR181100868-28_HTGCLCCXY_L8

source_name: BS_ddcc_aeiral part


title: JT_671_Bl6SpOv_E3.5Blastocysts130x_CR_0.1perPFA_Nanog

data_processing:
Library strategy: CUT&RUN
mapping to genome using bowtie2 with the following options (-N 1 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -x). Reads that mapped to ENCODE mm10 blacklist regions were removed using Samtools (Li et al., 2009). Piccard (broadinstitute.github.io/picard/) was then used to identify non-duplicated reads. Duplicate reads were removed for libraries generated from blastocysts but kept for all others.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Blastocysts

extract_protocol:
Cells were harvested using accutase and 100,000 cells per replicate, per time point, were subjected to CUT&TAG and CUT&RUN. Blastocysts were fixed in 0.1% PFA and subjected to CUT&RUN by physically transferring the embryos into different CUT&RUN buffers under a dissection microscope.
DNA was issolated using phenol-chloroform extraction. For each sample, double stranded DNA (10µl), Template Preparation D Buffer (2µl), and Template Preparation D Enzyme (1µl) were combined and End Repair and A-tailing was performed in a Thermocycler with a heated lid (22ºC, 25 min; 55ºC, 20 min). Library Synthesis D Buffer (1µl) and Library Synthesis D Enzyme (1µl) were subsequently added, and library synthesis was performed (22ºC, 40min). Immediately after, Library Amplification D Buffer (25µl), Library Amplification D Enzyme (1µl), Nuclease-free water (4µl), and a unique Illumina-compatible indexed primer (5µl) were added. Library amplification was performed using the following cycling conditions: 72ºC for 3 min; 85ºC for 2 min; 98ºC for 2 min (denaturation); 4 cycles of 98ºC for 20 s, 67ºC for 20 s, 72ºC for 10 s (addition of indexes); 14 cycles of 98ºC for 20 s, 72ºC for 10 s (library amplification). Post-PCR clean-up was performed on amplified libraries with a SPRIselect bead 0.6X left/1x right double size selection then washed twice gently in 80% ethanol and eluted in 10-12µl 10 mM Tris pH 8.0. For CUT&TAG, DNA (20µl) was mixed with 5X Q5 reaction buffer (10µl), Q5 polymerase (0.5µl), dNTPs (1µl), nuclease free water (16µl), and an equimolar mixture of an universal i5 and a uniquely barcoded i7 primer (2.5µl) , using different barcodes for each sample. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C.

treatment_protocol: Differentiation into primitive endoderm was induced in serum containing ESS media (Knockout DMEM, 15% FBS,1% GlutaMAX, 1% Penicillin-Streptomycin, 1% 2-Mercaptoethanol, 1% Sodium Pyruvate, 1% MEM NEAA, 2x105units/mL LIF) containing doxycycline (1ug/mL) for 2 to 12 hours. For time points greater than 12 hours, mES cells were induced in serum media containing doxycycline for 12 hours and switched to serum media in the absence of doxycycline for the remaining time. Blastocysts were collected from 4-5 weeks old C57BL/6N females six days after PMSG/HCG injections. Blastocysts were used right away to profile E3.5 embryos, after removing the zona pellucida using acid tyrode’s solution. E4.5 embryos were isolated seven days after PMSG/HCG injections, and only blastocysts without any zona pellucida were used. Embryos were manipulated in 1% agar-coated 4-well dishes (ThermoFisher scientific, Nunc 4-Well Dishes for IVF) throughout the protocol.

tag: assay

value: CUT&RUN

value: Mouse embryos


title: JT_672_Bl6SpOv_E4.5Blastocysts55x_CR_0.1perPFA_Gata6


title: PFC_S2

value: Prefrontal Cortex

value: Male

value: Control (healthy) sample


title: RNA_ddcc_rep1

tag: developmental stage

value: aerial part


title: BS_WT_rep2

source_name: BS_WT_aeiral part

value: wild type


title: Arabidopsis_50mM NaCl_rep 1

value: whole seedlings

value: 2 week old

value: ATS media supplemented with 50mM NaCl


title: PFC_S1

value: Female


title: Ectocervical 2D stem cells_48hours post_Uninfected_Replicate3

value: Ectocervical squamous


title: BS_WT_rep1

description:
RL166-JKZ0276-7684BSDNA05072018-S12112018_TKR181100868-24_HTGCLCCXY_L8
RL129-JKZ0276-6168-BS070518-S071318_TKR180700740-24


title: Ectocervical 2D stem cells_48hours post_Uninfected_Replicate2


title: FCtx1_10X_sc

value: Brain

tag: disease state


title: Arabidopsis_ATS media_rep 3

tag: age

value: ATS media


title: Arabidopsis_ATS media_rep 2


title: Ectocervical 2D stem cells_with HPV16 E6E7_48hours post_Chlamydia trachomatis_Infection_Replicate1

tag: tissue type

value: HPV E6E7


title: Arabidopsis_50mM NaCl_rep 3


title: RMY2_7 DPI_young_Lung

status: Public on Jan 15 2022

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

description: 10X Genomics single-cell RNA Sequencing

data_processing:
reads demultiplexed and bcl to fastq conversion using cellranger mkfastq v3.0.2
reads aligned and counted using cellranger count v3.0.2
Genome_build: GCA_003339765.3 & NC_045512.2
Supplementary_files_format_and_content: features.tsv, barcodes.tsv, and matrix.mtx (set of 3 files)

organism: Macaca mulatta

source_name: Lung

extract_protocol: 10X Genomics version 3.1 reagents were used to construct libraries

treatment_protocol: SARS-CoV-2 inoculated Rhesus macaques. Each animal received 2.6e6 TCID15 of total virus through a combined inoculation route of intranasal, intratracheal, oral, and oculated routes.

value: Lung

value: young

tag: days post infection

value: 7 DPI


title: RMY3_7 DPI_young_Lung

description: 10X Genomics single-cell RNA Sequencing


title: RMY4_7 DPI_young_Lung

description: 10X Genomics single-cell RNA Sequencing


title: JT_677_gata6RFPline1_0h_1%input_rechip

value: 0 hour no doxycycline

value: Stem cells have TRE:GATA6-DSREd2

value: Input


title: BS_ddcc_rep2

value: mutant


title: RMO4_7 DPI_old_Lung

description: 10X Genomics single-cell RNA Sequencing

value: old


title: RMO3_7 DPI_old_Lung

description: 10X Genomics single-cell RNA Sequencing


title: RMO1_7 DPI_old_Lung

description: 10X Genomics single-cell RNA Sequencing


title: RMO2_7 DPI_old_Lung

description: 10X Genomics single-cell RNA Sequencing


title: Arabidopsis_ATS media_rep 1


title: Arabidopsis_50mM NaCl_rep 2


title: RMY4_7 DPI_young_BALF

description: 10X Genomics single-cell RNA Sequencing

source_name: Bronchoalveolar lavage

value: Bronchoalveolar lavage


title: Ectocervical 2D stem cells_48hours post_Chlamydia trachomatis_Infection_Replicate1

tag: infection

value: no

tag: cells culture type


title: RMY3_7 DPI_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY2_7 DPI_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: FCtx2_10X_sc

tag: Sex

value: Male

value: Control (healthy) sample


title: RMO3_7 DPI_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: Ectocervical 2D stem cells_with HPV16 E6E7_48hours post_Uninfected_Replicate1

tag: time


title: Ectocervical 2D stem cells_48hours post_Chlamydia trachomatis_Infection_Replicate2


title: RMO4_7 DPI_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY4_3 DPI_young_BALF

description: 10X Genomics single-cell RNA Sequencing

value: 3 DPI


title: RMY1_7 DPI_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY1_7 DPI_young_Lung

description: 10X Genomics single-cell RNA Sequencing


title: RMO3_3 DPI_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: Ectocervical 2D stem cells_48hours post_Uninfected_Replicate1

value: Ectocervical squamous


title: RMO4_3 DPI_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY2_3 DPI_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMO1_3 DPI_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMO2_3 DPI_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY4_PRE_young_BALF

description: 10X Genomics single-cell RNA Sequencing

value: PRE


title: RMY3_3 DPI_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY2_PRE_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY3_PRE_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMO4_PRE_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMO3_PRE_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY8_7 DPI_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMO1_PRE_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMO8_7 DPI_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY6_7 DPI_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY5_7 DPI_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMO7_7 DPI_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMO6_7 DPI_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMO2_7 DPI_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMO5_7 DPI_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY1_3 DPI_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY8_3 DPI_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY5_3 DPI_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMO7_3 DPI_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMO5_3 DPI_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMO6_3 DPI_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMO8_3 DPI_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY6_3 DPI_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY1_PRE_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMO2_PRE_old_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY7_7 DPI_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: RMY7_3 DPI_young_BALF

description: 10X Genomics single-cell RNA Sequencing


title: murine MPS I fibroblast 120 µM genistein and kaempferol 1:1 mixture, biological rep1

city: Gdańsk

first: Marta

middle: Magdalena

last: Moskot

address: Kładki 24

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description:
16
Gene expression data upon genistein and kaempferol treatment.

hyb_protocol: 6 μg of the fragmented and labeled cDNA was hybridized to Mouse Clariom S array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin in an Affymetrix Fluidics Station 450 according to Affymetrix GeneChip Pico Reagent Kit guide (Thermo Fisher).

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL intensity files were generated by Affymetrix GeneChip Command Console Software (AGCC, Thermo Fisher).

data_processing:
The Affymetrix Clariom S microarrays were further analyzed using Affymetrix Expression Console with the SST-RMA procedure. The gene-level differential expression was performed using the Affymetrix Transcriptome Analysis Console (TAC) Software using default parameters. The significant genes were ranked by fold-change with a cutoff of 2 and the ANOVA p-value less than 0.05 according to Affymetrix.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Clariom_S_Mouse
program-name = Expression Console
program-version = 1.4.1.46

source_name: Murine MPS I fibroblasts

label_protocol: Microarray was prepared at Genomics Core, University of Chicago. The RNA integrity was examined on a bioanalyzer (Agilent). High-quality RNA (RNA integrity number >8.5) was used for expression microarray analysis. 10 ng of total RNA was used to generate double strand cDNA. 6 μg of ds cDNA were fragmented and labeled with biotin according to Affymetrix GeneChip Pico Reagent Kit manual (Thermo Fisher).

growth_protocol: Murine MPS I fibroblasts were cultivated in DMEM, 37°C, 5% CO2.

extract_protocol: RNA was extracted with High Pure RNA isolation kit according to manufacturer's protocol.

treatment_protocol: Murine MPS fibroblasts were 24 hours cultured with 60 and 120 µM genistein, 60 and 120 µM kaempferol and 60 and 120 µM genistein and kaempferol 1:1 mixture in 0.05% DMSO.

tag: cell type

value: MPS I fibroblasts

value: 120 uM genistein and kaempferol 1:1 mixture


title: murine MPS I fibroblast 120 µM genistein, biological rep2

description:
5
Gene expression data upon genistein treatment.

value: 120 uM genistein


title: murine MPS I fibroblast 120 µM genistein and kaempferol 1:1 mixture, biological rep2

description:
17
Gene expression data upon genistein and kaempferol treatment.


title: murine MPS I fibroblast 60 µM kaempferol, biological rep2

description:
8
Gene expression data upon kaempferol treatment.

value: 60 uM kaempferol


title: murine MPS I fibroblast 0.1% DMSO, biological rep1

description:
22
Gene expression data_DMSO treated control cells.

value: 0.1% DMSO


title: murine MPS I fibroblast 60 µM genistein and kaempferol 1:1 mixture, biological rep1

description:
13
Gene expression data upon genistein and kaempferol treatment.

value: 60 uM genistein and kaempferol 1:1 mixture


title: murine MPS I fibroblast 60 µM genistein and kaempferol 1:1 mixture, biological rep2

description:
14
Gene expression data upon genistein and kaempferol treatment.


title: murine MPS I fibroblast 0.05% DMSO, biological rep1

description:
19
Gene expression data_DMSO treated control cells.


title: cerebellum KO animal 2

city: Düsseldorf

first: Boris

last: Goerg

address: Moorenstrasse 5

department: Clinic for Gastroenterology, Hepatology and Infectiology

institute: Heinrich-Heine Universität Düsseldorf

hyb_protocol: The labeled and fragmented ss cDNA was spiked with cDNA hybridization controls. The spiked cDNA samples were hybridized at 45°C for 16 h on separate Affymetrix Clariom™ S Arrays. After hybridization, microarrays were stained in two binding cycles using anti-Biotin antibodies and a Streptavidin-phycoerythrin conjugate. Subsequently, the microarrays were washed with increasing stringency and conserved in holding buffer using the Affymetrix GeneChip® 3000 Fluidics Station in combination with the Affymetrix GeneChip® Command Console (AGCC) – Fluidics Control Software v4.0.0.1567.

scan_protocol: Fluorescent signal intensities were detected with the Affymetrix GeneChip® 3000 Scanner and AGCC Scan Control Software v4.0.0.1567. Automatic grid was arranged and raw data (*.DAT files) were processed to generate image and intensity files (*.CEL) by the AGCC software.

data_processing:
Automatic grid was arranged and raw data (*.DAT files) were processed to generate image and intensity files (*.CEL) by the AGCC software.
Summarized and quantile normalized log2 transformed intensities (SST-RMA (Signal Space Transformation  Robust Multi-Array Analysis) algorithm)

source_name: cerebellum KO

label_protocol: 200 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. The quality of second cycle cDNA and fragmented single-stranded (ss) cDNA were analyzed on the 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: The RNA was isolated by using the RNeasy Lipid Tissue Kit (Qiagen) according to the manufacturer's instructions including on-column DNase digestion. Total RNA was eluted in 30 µl RNase-free water. RNA concentration and purity were measuered on the NanoDrop ND-1000 spectral photometer (peqlab) and on the 2100 Bioanalyzer (Agilent Technologies) using the RNA 6000 Nano LabChip Kit (Agilent Technologies).

tag: sample source

value: KO

tag: tissue

value: brain tissue

tag: tissue region

value: cerebellum


title: murine MPS I fibroblast 120 µM kaempferol, biological rep1

description:
10
Gene expression data upon kaempferol treatment.

tag: treatment

value: 120 uM kaempferol


title: murine MPS I fibroblast 60 µM genistein, biological rep2

description:
2
Gene expression data upon genistein treatment.

value: 60 uM genistein


title: cerebellum KO animal 3


title: cerebellum wildtype animal 4

source_name: cerebellum wildtype

value: WT


title: murine MPS I fibroblast 60 µM kaempferol, biological rep1

description:
7
Gene expression data upon kaempferol treatment.


title: cerebellum KO animal 1


title: murine MPS I fibroblast 0.1% DMSO, biological rep2

description:
23
Gene expression data_DMSO treated control cells.


title: murine MPS I fibroblast 0.05% DMSO, biological rep2

description:
20
Gene expression data_DMSO treated control cells.


title: cerebellum wildtype animal 3


title: cerebellum KO animal 4


title: cerebellum wildtype animal 1


title: hippocampus KO animal 2

source_name: hippocampus KO

value: hippocampus


title: murine MPS I fibroblast 120 µM genistein, biological rep1

description:
4
Gene expression data upon genistein treatment.


title: hippocampus wildtype animal 4

source_name: hippocampus wildtype


title: hippocampus KO animal 1


title: murine MPS I fibroblast 60 µM genistein, biological rep1

description:
1
Gene expression data upon genistein treatment.


title: hippocampus KO animal 3


title: hippocampus KO animal 4


title: hippocampus wildtype animal 3


title: murine MPS I fibroblast 120 µM kaempferol, biological rep2

description:
12
Gene expression data upon kaempferol treatment.


title: cerebral cortex KO animal 3

source_name: cerebral cortex KO

value: cerebral cortex


title: cerebral cortex KO animal 4


title: BMM_AM_3

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

country: Switzerland

institute: ETH Zürich

description:
Bone Marrow Macrophages transferred into lungs of neonal Csf2Rb KO mice
CSF2.cFLiMo_AM--over--BMM_AM.csv
CSF2-cFLiMo_AM_3

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped and annotated to GRCm38.p5 STAR with cmdOptions --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
the read counts were scaled with the use of the trimmed mean of M-values (TMM) method
Genome_build: GRCm38.p5 Release_91-2018-02-26
Supplementary_files_format_and_content: tab-delimited text files, the processed data file includes Gene Identifier, gene name, description, log2 Ratio, pValue, fdr, normalized count (between-sample-normalization)

source_name: Bone Marrow Macrophages

growth_protocol: Sorted cells were then seeded at a density of 1 × 105 cells/mL in untreated 24-well plates (Sarstedt, 83.3922.500) or 12-well plates (Sarstedt, 83.3921.500) and maintained in GlutaMAX supplement RPMI 1640 (Gibco, 61870036), containing 10% FCS, 10 mM Hepes, 50uM 2-mercaptoethanol, 100 U/ml penicillin, 100 U/ml streptomycin, in the presence of 30 ng/mL murine GM-CSF (PeproTech, 315-03) in vitro. Cells were sub-cultured when cell density reached 5 × 105 cells/mL, normally every 3-4 days. After 2 weeks culter cells were either sequenced or transferred into Csf2Ra deficinet neonates. 8 weeks later cells were isolated from bronchoalveolar lavage and sequenced

extract_protocol:
RNeasy kit was used for RNA isolation (Qiagen)
RNA libraries were prepared for sequencing using standard NextSeq protocols

treatment_protocol: In vitro cells were treated with 30 ng/mL murine GM-CSF (PeproTech, 315-03)

tag: strain

value: Bone Marrow Macrophages


title: B7P2KD_EtOH 3

city: Ithaca

first: Scott

last: Coonrod

state: New York

address: 235 Hungerford Hill Road

department: Baker Institute for Animal Health

institute: Cornell University

description:
D3_34
Nascent RNA

data_processing:
Library strategy: PRO-seq
Paired end sequencing data were preprocessed to remove the adapter sequences and trim based on base quality, and deduplicating the reads based on unique molecular identifiers in RNA adapters.
Sequencing reads were mapped into a human genome assembly (hg19) using the Burrows-Wheeler Aligner software package.
Aligned BAM files were converted into bigWig format.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: BigWig files were generated from aligned BAM files by proseq 2.0 pipeline (https://github.com/Danko-Lab/proseq2.0).

source_name: B7_PADI2 KD

growth_protocol: MCF7 cells were routinely grown in 10% Bovine Calf Serum in DMEM. 5x 10^6 cells were plated in 15 cm dish prior to the treatment.

extract_protocol:
Cells were washed with ice-cold PBS and lysed with NP-40 lysis buffer (Horibata S, et al., 2016). Nuclei were isolated and snap-frozen.
Precision run-on sequencing libraries were prepared following PRO-seq protocol (Mahat DB et al., Nat Protoc. 2016).

treatment_protocol: Cells in 15 cm dish were pre-treated in charcoal stripped serum media for 3 days. On the day of experiment, charcoal stripped serum pre-treated cells were treated with control (EtOH), E2 (100 nM estradiol), Tam (1 micro M Tamoxifen) for 40 min.

tag: cell line

value: ER+ breast cancer cell line

value: EtOH

tag: tamoxifen sensitivity

value: Sensitive

tag: shRNA knockdown

value: PADI2 shRNA


title: BMM_AM_1

description:
Bone Marrow Macrophages transferred into lungs of neonal Csf2Rb KO mice
CSF2.cFLiMo_AM--over--BMM_AM.csv
CSF2-cFLiMo_AM_1


title: BMM_AM_2

description:
Bone Marrow Macrophages transferred into lungs of neonal Csf2Rb KO mice
CSF2.cFLiMo_AM--over--BMM_AM.csv
CSF2-cFLiMo_AM_2


title: CSF2-cFliMo_AM_3

description:
CSF2 KO cultured fetal liver Monocytes transferred into lungs of neonal Csf2Rb KO mice
CSF2.cFLiMo_AM--over--BMM_AM.csv
BMM_AM_3

source_name: Alveolar Macrophages

value: CSF2 KO cultured fetal liver Monocytes


title: B7P2KD_E2 3

description:
D3_35
Nascent RNA

value: Estradiol


title: hippocampus wildtype animal 1

tag: genotype


title: CSF2-cFliMo_AM_1

description:
CSF2 KO cultured fetal liver Monocytes transferred into lungs of neonal Csf2Rb KO mice
CSF2.cFLiMo_AM--over--BMM_AM.csv
BMM_AM_1


title: G11_Tam 3

description:
D3_27
Nascent RNA

source_name: G11 (Tam Res MCF7)

value: Tamoxifen

value: Resistant


title: B7_EtOH 3

description:
D3_31
Nascent RNA

source_name: B7 (Tam Sen MCF7)


title: G11P2KD_E2 3

description:
D3_29
Nascent RNA

source_name: G11_PADI2 KD


title: B7_E2 3

description:
D3_32
Nascent RNA


title: CSF2-cFliMo_AM_2

description:
CSF2 KO cultured fetal liver Monocytes transferred into lungs of neonal Csf2Rb KO mice
CSF2.cFLiMo_AM--over--BMM_AM.csv
BMM_AM_2


title: G11P2KD_EtOH 3

description:
D3_28
Nascent RNA


title: B7_Tam 3

description:
D3_33
Nascent RNA


title: G11P2KD_Tam 3

description:
D3_30
Nascent RNA


title: hippocampus wildtype animal 2


title: cerebral cortex wildtype animal 1

source_name: cerebral cortex wildtype


title: cerebral cortex wildtype animal 2


title: cerebral cortex KO animal 1

value: KO


title: cerebral cortex wildtype animal 4

value: brain tissue


title: cerebral cortex wildtype animal 3


title: cerebral cortex KO animal 2


title: B7P2KD_Tam 3

description:
D3_36
Nascent RNA


title: G11_Tam 2

description:
D3_25
Nascent RNA


title: G11_E2 2

description:
D2_23
Nascent RNA


title: G11_EtOH 2

description:
D2_22
Nascent RNA


title: B7P2KD_E2 2

description:
D2_20
Nascent RNA


title: B7P2KD_Tam 2

description:
D2_21
Nascent RNA


title: cerebellum wildtype animal 2

value: cerebellum


title: B7P2KD_EtOH 2

description:
D2_19
Nascent RNA


title: B7_E2 2

description:
D2_17
Nascent RNA


title: B7_EtOH 2

description:
D2_16
Nascent RNA


title: B7_Tam 2

description:
D2_18
Nascent RNA


title: G11P2KD_E2 2

description:
D2_14
Nascent RNA


title: G11P2KD_EtOH 2

description:
D2_13
Nascent RNA