title: SCC1.AID_IAA.RA_rep2_cnucRNAseq

description:
E14_Scc1mAID_nucRNAseq_iaa-ra-rep2
deseq2.Scc1_cnucRNASeq_summaryTable.csv

value: retinoic acid (RA) + auxin (IAA)

value: RA 4 hr, IAA 6 hr


title: Endometriosis13

status: Public on Oct 29 2024

type: SRA

city: Münster

first: Eberhard

last: Korsching

state: NRW

address: Niels-Stensen-Str. 14

department: Inst. of Bioinformatics

country: Germany

institute: University of Muenster

description:
E14
counts_mir_E_EH_raw.tsv

library_source: transcriptomic

data_processing:
Data pruning also according to Hagemann-Jensen M, et al. doi: 10.1038/s41596-018-0049-y
Alignment with STAR aligner version 2.7.10 using default values but transcriptome coordinates (for Salmon) according to protocol Dobin, A. and Gingeras, T.R. 2015 - section 7. Mapping RNA-seq reads with STAR. Curr. Protoc. Bioinform.51:11.14.1-11.14.19. doi: 10.1002/0471250953.bi1114s51.
Quantification with Salmon version 1.10 according to the manual and program defaults.
Further data handling, differential expression analysis [DESeq2], permutation controls, result visualization etc. with mathematical platform R version 3.6.1 to 4.0.5.
Assembly: Current builds of the Human genome reference GRCh38.p14 from EBI in England, mirBase release 22.1.
Supplementary files format and content: Tab separated table format, columns: miRNA-ID/result parameters/samples and expression counts (microRNAs)

molecule: polyA RNA

organism: Homo sapiens

source_name: Endometrium

extract_protocol:
RNeasy total RNA Kit (Qiagen, Hilden, Germany)
Hagemann-Jensen et al. Small-seq for single-cell small-RNA sequencing. Nature Protocols.2018;13(10):2407-24.
Small RNA sequencing, single end reads

tag: tissue

value: Endometrium

tag: subject status

value: Endometriosis


title: SCC1.AID_RA_rep1_cnucRNAseq

city: Heidelberg

first: Angelika

last: Feldmann

address: Im Neuenheimer Feld 581

institute: German Cancer Research Center

description:
E14_Scc1mAID_nucRNAseq_ra-rep1
deseq2.Scc1_cnucRNASeq_summaryTable.csv

data_processing:
RNA-Seq data were processed as previously described (Feldmann et al., 2020). Briefly, reads were aligned to mm10 genome (or mm10+dm6 genome for calibrated nuclear RNA-Seq) using STAR for gapped alignment (Dobin et al., 2013). Unaligned reads were then re-aligned using Bowtie2 (Langmead and Salzberg, 2012) and combined with STAR-aligned reads. Only uniquely aligned and correctly paired reads were retained for further analysis. High correlation between replicates (spearman coefficient > 0.9) was ensured for further analysis.
For visualization, downsampling factors (for calibrated nuclear RNA-Seq) were calculated based on the RNA reads aligning to mm10 (dm6) genome. Samples were downsampled using samtools –s (SAMtools (Li et al., 2009)). Read pile-ups were prepared using the coverage() function from the Bioconductor package GenomicFeatures (Lawrence et al., 2013). Heatmaps were plotted using the R package pheatmap.
For quantitative analysis, fragments aligning to RefSeq transcripts were quantified from non-downsampled BAM files using the summarizeOverlaps() function from GenomicFeatures with the options mode=‘Union’ and inter.feature=FALSE. For the global RA time-course reads were aligned to exons, for transient enhancer clones and SCC1-degron analysis reads were aligned to the whole gene body. Raw read counts were then analyzed using the DESeq2 Bioconductor package (Love et al., 2014). Scaling factors were generated using read count quantification over non-redundant mm10 transcriptome or dm6 mRNA counts in case of calibrated nuclear RNA-Seq. Shrunk log2 fold changes were extracted for each comparison and normalized read counts were extracted from DESeq2 objects. To compare across conditions with potentially varying numbers of replicates, mean read counts were calculated from these normalized reads from which mean FPKM was calculated. FPKM were log transformed for downstream analyses after addition of a pseudocount of 0.1.
Assembly: mm10
Supplementary files format and content: csv files contain DESEq2 normalized read counts for all samples and LFC/padj values for each comparison

molecule: nuclear RNA

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor.

extract_protocol:
(Nuclear) RNA sample preparation was performed using 10x106 ES or RA-treated cells (and 4x106 SG4 Drosophila cells for calibration) as described previously 18. Briefly, RNA was isolated using RNeasy RNA extraction kit (Qiagen) and gDNA contamination was depleted using TURBO DNA-free Kit (ThermoScientific). Quality of RNA was assessed using 2100 Bioanalyzer RNA 6000 Pico kit (Agilent).
Following this, ribosomal RNA was depleted with the NEBnext rRNA depletion kit and library preparation performed using the NEBNext Ultra II directional. Libraries were quantified by qPCR and samples were sequenced on NextSeq 500/550 so that paired 42bp reads were obtained.

treatment_protocol: To induce differentiation, ES cells were treated with 1uM retinoic acid (RA) for 2-72/74 hours. Cohesin was degraded by treatment with 500 μM auxin (IAA) for 2 hours prior to addition of RA for another 4 hours.

value: mouse embryonic stem cells

tag: cell line

tag: cell type

value: ESC

tag: genotype

tag: treatment

value: retinoic acid (RA)

tag: treatment duration

value: RA 4 hr


title: Endometriosis9

description:
E10
counts_mir_E_EH_raw.tsv


title: Endometriosis10

description:
E11
counts_mir_E_EH_raw.tsv


title: Endometriosis5

description:
E06
counts_mir_E_EH_raw.tsv


title: SCC1.AID_IAA_rep1_cnucRNAseq

description:
E14_Scc1mAID_nucRNAseq_iaa-rep1
deseq2.Scc1_cnucRNASeq_summaryTable.csv

value: auxin (IAA)

value: IAA 6 hr


title: SCC1.AID_IAA_rep2_cnucRNAseq

description:
E14_Scc1mAID_nucRNAseq_iaa-rep2
deseq2.Scc1_cnucRNASeq_summaryTable.csv


title: Endometriosis7

description:
E08
counts_mir_E_EH_raw.tsv


title: Endometriosis4

description:
E04
counts_mir_E_EH_raw.tsv


title: SCC1.AID_IAA.RA_rep1_cnucRNAseq

description:
E14_Scc1mAID_nucRNAseq_iaa-ra-rep1
deseq2.Scc1_cnucRNASeq_summaryTable.csv


title: SCC1.AID_IAA.RA_rep3_cnucRNAseq

description:
E14_Scc1mAID_nucRNAseq_iaa-ra-rep4
deseq2.Scc1_cnucRNASeq_summaryTable.csv


title: SCC1.AID_UNT_rep4_CapC_set2

description:
cd_unt_CapC23
ints_all_forGEO_CapC23.txt
DpnII.mm10_fromCapC1718.rmap

library_source: genomic

data_processing:
For CaptureC, paired-end reads were aligned and filtered for HiC artefacts using HiCUP (Wingett S, et al. (2015)) and Bowtie2 (Langmead and Salzberg, 2012) with fragment filter set to 100-800bp. Read counts of reads aligning to captured gene promoters and interaction scores (=significant interactions) were then called  by CHiCAGO (Cairns et al., 2016).
For visualisation of CaptureC data weighted pooled read counts from chicago data files were normalized to total read count aligning to captured gene promoters in the sample and further to the number of promoters in the respective capture experiment. Bigwig files were generated from these normalized read counts.
For comparative boxplot analysis normalized read counts and scores were quantified for interactions called by chicago (score >= 5) across all samples.
Assembly: mm10
Supplementary files format and content: cd_* files are chicago data objects that were generated using the R-package Chicago (Cairns et al., 2016). Ints files are summary tables of all significant interactions across a single Capture experiment with read counts and scores extracted from chicago data objects. .rmap files are corresponding .rmap files for a given experiment that is used to map the fragment IDs to a specific genomic location.
Library strategy: Capture-C

molecule: genomic DNA

extract_protocol:
CaptureC libraries were prepared as described previously (Hughes et al., Nature Genetics 2014). Briefly, 10 Million mouse ES cells were trypsinized, collected in 50ml falcon tubes in 9.3ml media and crosslinked with 1.25ml 16% formaldehyde for 10min at room temperature. Cells were quenched with 1.5M glycine, washed with PBS and lysed for 20 minutes at 4oC lysis buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40, supplemented with complete proteinase inhibitors) prior to snap freezing in 1ml lysis buffer per 10 Million cells at -80oC.
Lysates were then thawed on ice, pelleted and resuspended in 650µl 1x DpnII buffer (NEB). Three 1.5ml tubes with 200µl lysate each were treated in parallel with SDS (0.28% final concentration, 1hr, 37 oC, interval shaking 500rpm, 30sec on/30sec off), quenched with trypsin (1.67% final concentration, 1hr, 37 oC, interval shaking 500rpm, 30sec on/30sec off) and subjected to a 24 hour digestion with 3x10µl DpnII (homemade, 37 oC, interval shaking 500rpm, 30sec on/30sec off). For the DRE.H5.100 clones, 5 Million aliqots were collected and treated according to Downes et al., 2022 (Nature Protocols). Each chromatin aliquot was independently ligated with 8 µl T4 Ligase (240 U) in a volume of 1440µl (20 hours, 16oC). Following this, the nuclei containing ligated chromatin were pelleted to remove any non-nuclear chromatin, reverse-crosslinked and the ligated DNA was phenol-chloroform purified. The sample was resupended in 300µl water (200µl for DRE.H5.100 clones) and sonicated 13x (Pico Bioruptor, 30sec on, 30sec off) or until a fragment size of approximately 200bp was reached. Fragments were size selected using AmpureXP beads (Beckman Coulter: A63881, selection ratios: 0.85x / 0.4x). 2x 1-5µg of DNA were adaptor ligated and indexed using the NEBNext End Repair, dA-Tailing and Quick Ligation modules (NEB E6050, E6053, E6056) as well as NEBNext Multiplex Oligos for Illumina Primer sets 1 (New England: E7335S/L) and 2 (New England: E7500S/L). The libraries were amplified 7x using Herculase II Fusion Polymerase kit (Agilent: 600677). Libraries were hybridized in the following way: Probes were designed using the online tool by the Hughes lab (CapSequm: http://apps.molbiol.ox.ac.uk/CaptureC/cgi-bin/CapSequm.cgi) to be either 120bp (Sox2, Set6) or 70bp long each, two probes for each promoter of interest. The probes were pooled at a 2.9nM each and the samples were multiplexed by mass prior to hybridization. Hybridization was carried out using the Nimblegen SeqCap system (Roche, Nimblegen SeqCap EZ HE-oligo kit A # 06777287001, Nimblegen SeqCap EZ HE-oligo kit B # 06777317001, Nimblegen SeqCap EZ Accessory kit v2 # 07145594001, Nimblegen SeqCap EZ Hybridisation and wash kit # 05634261001) according to the Roche protocol for 72 hours followed by a 24 hours hybridization (double Capture). The captured libraries were sequenced on Illumina NextSeq to obtain 40-42bp paired-end reads.

treatment_protocol: To induce differentiation, ES cells were treated with 1uM retinoic acid (RA) for 2-72 hours. Cohesin was degraded by treatment with 500 μM auxin (IAA) for 2 hours prior to addition of RA for another 4 hours.

value: untreated

value: 0 hr


title: Hbx5_5hr_R2

city: London

first: Christopher

last: Thompson

address: Gower Street

country: United Kingdom

institute: University College London

data_processing:
galaxy
Assembly: Dictyostelium discoideum
Supplementary files format and content: excel spreadsheet, fkpm

molecule: total RNA

organism: Dictyostelium discoideum

extract_protocol:
Tri-reagent,  70% ethanol washes
Smarter RNA seq kit

tag: time point

value: 5 hours development.


title: Hbx5_8hr_R3

value: 8 hours development.


title: SCC1.AID_UNT_rep2_CapC_set2


title: Hbx5_5hr_R1


title: Hbx5_8hr_R2


title: SCC1.AID_UNT_rep1_CapC_set2


title: Hbx5_5hr_R3


title: Hbx5_8hr_R1


title: Endometriosis3

description:
E03
counts_mir_E_EH_raw.tsv


title: Hbx5_2hr_R2

value: 2 hours development.


title: Hbx5_2hr_R1


title: Hbx5_1hr_R2

value: 1 hours development.


title: Whole blood, control 18

city: St. Paul

first: Eva

last: Furrow

state: MN

address: 1352 Boyd Ave, C339 VMC

department: Veterinary Clinical Sciences

country: USA

institute: University of Minnesota

description: Ribosomal RNA removal during library preparation with SMARTer Stranded Total RNA-Seq Kit v2, Pico Input Mammalian

data_processing:
RNA-Seq data was processed using PURR, a pipeline housed within the Collection of Hierarchical UMII-RIS Pipelines (CHURP) at the University of Minnesota.
Raw reads were summarized using FastQC and trimmed to remove low quality sequences using Trimmomatic.
Reads were aligned to the Dog10K_Boxer_Tasha/canFam6 canine reference genome assembly using HISAT2.
Alignments were cleaned and name-sorted by feature. Features were only counted if both mates of a read pair mapped.
Raw read counts were used to perform differential expression analysis using the DESeq2 software package implemented in R.
Assembly: Dog10K_Boxer_Tasha/canFam6
Supplementary files format and content: tab-delimited text file with raw counts for each sample

organism: Canis lupus familiaris

source_name: whole blood

extract_protocol:
Peripheral blood RNA was extracted using the RNeasy Universal Kit
Library preparation was performed using the SMARTer Stranded Total RNA-Seq Kit v2, Pico Input Mammalian.

value: whole blood

tag: breed

value: Miniature Schnauzer

tag: Sex

value: male

tag: disorder

value: control


title: Endometriosis1

description:
E01
counts_mir_E_EH_raw.tsv

value: Endometrium

value: Endometriosis


title: SCC1.AID_RA_rep4_CapC_set2

description:
cd_ra_CapC23
ints_all_forGEO_CapC23.txt
DpnII.mm10_fromCapC1718.rmap

value: mouse embryonic stem cells

value: ESC

value: RA:4 hr


title: Hbx5_1hr_R3


title: SCC1.AID_RA_rep2_CapC_set2

value: retinoic acid (RA)


title: Endometriosis2

description:
E02
counts_mir_E_EH_raw.tsv


title: Whole blood, control 17


title: Hbx5_0hr_R1

value: 0 hours development.


title: Ax2_8hr_R3


title: Hbx5_0hr_R3


title: Hbx5_0hr_R2


title: SCC1.AID_RA_rep1_CapC_set2


title: Hbx5_2hr_R3


title: Whole blood, control 16

value: female


title: Ax2_5hr_R3


title: Ax2_8hr_R1


title: Whole blood, control 14


title: SCC1.AID_IAA_rep4_CapC_set2

description:
cd_iaa_CapC23
ints_all_forGEO_CapC23.txt
DpnII.mm10_fromCapC1718.rmap

value: auxin (IAA)

value: IAA:6 hr


title: Whole blood, control 13


title: Hbx5_1hr_R1


title: SCC1.AID_IAA_rep2_CapC_set2


title: Ax2_5hr_R2

value: 5 hours development.


title: Whole blood, control 12


title: SCC1.AID_IAA_rep1_CapC_set2


title: Ax2_5hr_R1


title: Ax2_2hr_R2

value: 2 hours development.


title: Ax2_2hr_R3


title: SCC1.AID_IAA.RA_rep2_CapC_set2

description:
cd_iaa-ra_CapC23
ints_all_forGEO_CapC23.txt
DpnII.mm10_fromCapC1718.rmap

value: retinoic acid (RA) + auxin (IAA)

value: RA:4 hr, IAA:6 hr


title: Whole blood, control 11

value: whole blood

value: Miniature Schnauzer


title: SCC1.AID_IAA.RA_rep1_CapC_set2


title: Ax2_1hr_R3

value: 1 hours development.


title: Ax2_2hr_R1


title: SCC1.AID_IAA.RA_rep4_CapC_set2


title: Whole blood, control 15

value: male

value: control


title: Ax2_8hr_R2

value: 8 hours development.


title: Ax2_1hr_R1


title: Ax2_0hr_R1


title: Ax2_1hr_R2


title: Ax2_0hr_R3


title: Whole blood, control 10


title: E14_ES_RA72h_rep4_CapC_set4

description:
cd_RA_72h_CapC1718
ints_all_forGEO_CapC1718.txt
DpnII.mm10_fromCapC1718.rmap

value: mouse embryonic stem cells

value: ESC

value: wildtype

value: 72 hr


title: Whole blood, control 09


title: E14_ES_RA72h_rep3_CapC_set4

value: retinoic acid (RA)


title: Whole blood, control 08

value: female


title: E14_ES_RA6h_rep4_CapC_set4

description:
cd_RA_6h_CapC1718
ints_all_forGEO_CapC1718.txt
DpnII.mm10_fromCapC1718.rmap

value: 6 hr


title: Whole blood, control 07


title: E14_ES_RA4h_rep4_CapC_set4

description:
cd_RA_4h_CapC1718
ints_all_forGEO_CapC1718.txt
DpnII.mm10_fromCapC1718.rmap

value: 4 hr


title: Whole blood, control 06


title: E14_ES_RA6h_rep3_CapC_set4


title: Whole blood, control 05


title: E14_ES_RA4h_rep3_CapC_set4


title: Myla cells, shControl, 1

city: Beijing

first: Kecen

last: Liu

address: Xishiku Street 8th

country: China

institute: Peking University First Hospital

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limt. 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters - mismath cost:2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Myla

growth_protocol: Myla cells were kept in RPMI 1640 culture media supplemented with 10% heat inactivated fetal bovine serum.The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2 before transduction.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat#74104, QIAGEN, GmBH, Germany) following the manufacturer's instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols.

treatment_protocol: 1X10^5 cells in 1mL culture media were treated with 10uL lentivirus media with lentivirus vector harboring shRNA against FOXM1. Media was changed after 24 hours and cells were kept in culture for additional 72 hours before RNA extraction. Cells transduced with lenti-vector harboring scrambled shRNA were used as controls.

value: Myla

value: mycosis fungoides cell line

value: WT


title: Whole blood, control 04

value: whole blood


title: Myla cells, shFOXM1, 1

value: FOXM1 knockdown


title: Metastatic prostate cancer sample D

city: Tampere

first: Matti

last: Nykter

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
10X Genomics software spaceranger was used to process the fastq-format sequencing data
Loupe browser was used to manually align and annotate tissue in the whole-slide scanned images
Fastq-files, manual alignment files, and the 20x zoom-level whole-slide images were given as input to spaceranger count v1.1.0
Sequences were aligned to the refdata-GRCh38-3.0.0 reference available on the 10X genomics website
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene Ids
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exhange format
Supplementary files format and content: scalefactors_json.json.gz: tissue image scale factors for correct display
Supplementary files format and content: tissue_hires_image.png.gz: high-resolution tissue image
Supplementary files format and content: tissue_lowres_image.png.gz: low-resolution tissue image
Supplementary files format and content: tissue_positions_list.csv.gz: table with rows that correspond to spots including tissue position information
Library strategy: Spatial Transcriptomics

source_name: Metastatic prostate cancer tumor, Pericardial metastasis, Patient sample

extract_protocol:
Fresh frozen tissue were cut into 10 μm sections using a cryostat
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's instructions


title: Metastatic prostate cancer sample C

source_name: Metastatic prostate cancer tumor, Pelvic paraaortic lymph node metastasis, Patient sample


title: E14_ES_RA48h_rep4.2_CapC_set4

description:
cd_RA_48h_CapC1718
ints_all_forGEO_CapC1718.txt
DpnII.mm10_fromCapC1718.rmap

value: 48 hr


title: Metastatic prostate cancer sample B

source_name: Metastatic prostate cancer tumor, Subdural metastasis, Patient sample


title: Ax2_0hr_R2

value: 0 hours development.


title: Myla cells, shFOXM1, 2


title: Whole blood, control 03

value: Miniature Schnauzer

value: male

value: control


title: S1D2,scATAC-seq

first: Jingxiao

last: Cao

state: Beijing

address: No.5 Yiheyuan Road, Yanyuan Street, Haidian District, Beijing

department: Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.

institute: Peking University

description: 10x Genomics

library_source: genomic single cell

data_processing:
The scATAC-seq data of all the samples were mapped to the human reference genome GRCh38 using Cell Ranger ATAC v.2.1.0. The output fragment files were loaded into R environment and performed preprocess using R package ArchR.
Performed arrow files creation, quality control
Performed iterative LSI dimensionality reduction, clustering and UMAP dimensionality reduction
Assembly: GRCh38
Supplementary files format and content: fragments files

source_name: induced from hADSC

extract_protocol:
Nuclei Isolation for Single-cell ATAC Sequencing (CG000169). After isolation, the nuclei were resuspended in the chilled diluted nuclei buffer (10x Genomics, 2000153). The amount of diluted nuclei buffer used for resuspension was determined based on the initial number of cells and the desired final concentration of nuclei. Nuclei counting was performed using Countstar (Rigel S2).
The processed nuclei were then rapidly utilized for the generation of scATAC-seq libraries. Following the 10x Genomics single-cell ATAC protocol, the Chromium Chip E Single Cell Kit (1000156) and the Chromium Single Cell ATAC Library & Gel Bead Kit (1000110) were employed to partition the nuclei from the bulk sample into nanoliter-scale GEMs. A pool of around 750,000 10x barcodes was sampled to separately and uniquely index the transposed DNA of each individual nucleus, and library construction was carried out by CapitalBio Technology.

value: induced from hADSC


title: hADSCs,scATAC-seq

description: 10x Genomics

source_name: adult human adipose derived mesenchymal stromal cells


title: S1D6,scATAC-seq

description: 10x Genomics


title: Metastatic prostate cancer sample A

source_name: Metastatic prostate cancer tumor, Liver metastasis, Patient sample


title: Castration-resistant prostate cancer sample 5

source_name: Primary prostate cancer tumor, Patient sample

value: LHRH


title: E14_ES_RA48h_rep4_CapC_set4

value: mouse embryonic stem cells

value: ESC

value: wildtype


title: Whole blood, control 02

value: female


title: Castration-resistant prostate cancer sample 4

value: Primary prostate cancer tumor, Patient sample

value: orchiectomy


title: E14_ES_RA48h_rep3_CapC_set4

value: retinoic acid (RA)


title: Castration-resistant prostate cancer sample 3

value: LHRH + bicalutamide


title: Castration-resistant prostate cancer sample 2


title: Myla cells, shControl, 2

value: Myla

value: mycosis fungoides cell line

value: WT


title: E14_ES_RA2h_rep4_CapC_set4

description:
cd_RA_2h_CapC1718
ints_all_forGEO_CapC1718.txt
DpnII.mm10_fromCapC1718.rmap

value: 2 hr


title: Castration-resistant prostate cancer sample 1


title: Whole blood, case 13

value: whole blood

value: Miniature Schnauzer

value: hypertriglyceridemia (HTG)


title: Neoadjuvant-treated prostate cancer sample 22

value: degarelix + apalutamide


title: Neoadjuvant-treated prostate cancer sample 21


title: Neoadjuvant-treated prostate cancer sample 20

value: degarelix


title: Whole blood, case 10

value: male


title: E14_ES_RA0h_rep4_CapC_set4

description:
cd_RA_0h_CapC1718
ints_all_forGEO_CapC1718.txt
DpnII.mm10_fromCapC1718.rmap

value: mouse embryonic stem cells

value: ESC

value: untreated


title: Neoadjuvant-treated prostate cancer sample 17

value: Primary prostate cancer tumor, Patient sample


title: Neoadjuvant-treated prostate cancer sample 19


title: Whole blood, case 09


title: Neoadjuvant-treated prostate cancer sample 16


title: Neoadjuvant-treated prostate cancer sample 15


title: E14_ES_RA0h_rep3_CapC_set4

value: wildtype


title: Whole blood, case 08

value: female


title: Neoadjuvant-treated prostate cancer sample 14


title: E14_ES_RA24h_rep3_CapC_set4

description:
cd_RA_24h_CapC1718
ints_all_forGEO_CapC1718.txt
DpnII.mm10_fromCapC1718.rmap

value: retinoic acid (RA)

value: 24 hr


title: Whole blood, case 12


title: Neoadjuvant-treated prostate cancer sample 13


title: Neoadjuvant-treated prostate cancer sample 18


title: Whole blood, control 01

value: control


title: E14_ES_RA72h_rep4_CapC_set3

description:
cd_RA_72h_CapC15
ints_all_forGEO_CapC15.txt
DpnII.mm10_CapC101115.rmap

value: 72 hr


title: Neoadjuvant-treated prostate cancer sample 12


title: Neoadjuvant-treated prostate cancer sample 11

value: bicalutamide


title: Whole blood, case 07

value: whole blood


title: E14_ES_RA48h_rep4.2_CapC_set3

description:
cd_RA_48h_CapC15
ints_all_forGEO_CapC15.txt
DpnII.mm10_CapC101115.rmap

value: 48 hr


title: Neoadjuvant-treated prostate cancer sample 9


title: Neoadjuvant-treated prostate cancer sample 8

value: goserelin


title: E14_ES_RA2h_rep3_CapC_set4

value: 2 hr


title: Whole blood, case 11

value: Miniature Schnauzer

value: hypertriglyceridemia (HTG)


title: E14_ES_RA24h_rep4_CapC_set4

value: mouse embryonic stem cells


title: Neoadjuvant-treated prostate cancer sample 7


title: E14_ES_RA48h_rep4_CapC_set3

value: ESC


title: Whole blood, case 06

value: male


title: E14_ES_RA24h_rep4_CapC_set3

description:
cd_RA_24h_CapC15
ints_all_forGEO_CapC15.txt
DpnII.mm10_CapC101115.rmap


title: Neoadjuvant-treated prostate cancer sample 6

value: Primary prostate cancer tumor, Patient sample


title: Whole blood, case 05


title: Neoadjuvant-treated prostate cancer sample 5


title: Neoadjuvant-treated prostate cancer sample 3


title: Whole blood, case 04


title: Neoadjuvant-treated prostate cancer sample 10


title: Neoadjuvant-treated prostate cancer sample 4


title: Treatment-naïve prostate cancer sample 17


title: Whole blood, case 02


title: E14_ES_RA2h_rep4_CapC_set3

description:
cd_RA_2h_CapC15
ints_all_forGEO_CapC15.txt
DpnII.mm10_CapC101115.rmap

value: wildtype


title: E14_ES_RA6h_rep4_CapC_set3

description:
cd_RA_6h_CapC15
ints_all_forGEO_CapC15.txt
DpnII.mm10_CapC101115.rmap

value: 6 hr


title: Treatment-naïve prostate cancer sample 15


title: Neoadjuvant-treated prostate cancer sample 2


title: Whole blood, case 03

description: Ribosomal RNA removal during library preparation with SMARTer Stranded Total RNA-Seq Kit v2, Pico Input Mammalian


title: E14_ES_RA0h_rep4_CapC_set3

description:
cd_RA_0h_CapC15
ints_all_forGEO_CapC15.txt
DpnII.mm10_CapC101115.rmap

value: untreated


title: Treatment-naïve prostate cancer sample 14


title: Neoadjuvant-treated prostate cancer sample 1


title: Treatment-naïve prostate cancer sample 16


title: Plant tissue, 480 μM DNAN, rep5

city: York

first: Elizabeth

middle: L

last: Rylott

address: Wentworth Way

department: Department of Biology

institute: University of York

data_processing:
Pair-end fragments were mapped to the TAIR 10 Arabidopsis cDNA reference library using the Burrows-Wheeler Aligner (BWA) software.
Raw counts for each gene were prepared by inputing the BWA SAM files into HTSeq
Normalisation was carried out using the DESeq2 package in R
Assembly: TAIR10
Supplementary files format and content: tab delimited text file which includes the raw counts for each sample

organism: Arabidopsis thaliana

source_name: Whole plant shoot and root

growth_protocol: Sterile, stratified Arabidopsis seeds were germinated on 1/2 MS agar for 24 hours and then incubated in shake flasks containing 1/2 MS media for 14 days.

extract_protocol:
Plant root and shoot tissue from the shake flasks was ground up in liquid nitrogen and RNA extracted using the EasyPure plant RNA extraction kit (Transgen Biotech).
RNA libraries for RNAseq were constructed by poly(A) mRNA enrichment. 1 μg RNA was applied to the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs).

treatment_protocol: 14 day old plants in shake flasks were dosed with either 0, 60, 120, 240 or 480 μM DNAN for 6 hours.

value: Whole plant shoot and root

tag: ecotype

tag: plant growth

value: Shake flask

tag: plant age

value: 14 days

tag: treatment time

value: 6 hours

value: 480 μM DNAN


title: Treatment-naïve prostate cancer sample 11


title: Treatment-naïve prostate cancer sample 9


title: E14_ES_RA24h_rep3_CapC_set3

value: retinoic acid (RA)

value: 24 hr


title: E14_ES_RA6h_rep3_CapC_set3


title: E14_ES_RA72h_rep3_CapC_set3

value: 72 hr


title: Treatment-naïve prostate cancer sample 12


title: Treatment-naïve prostate cancer sample 10


title: E14_ES_RA4h_rep4_CapC_set3

description:
cd_RA_4h_CapC15
ints_all_forGEO_CapC15.txt
DpnII.mm10_CapC101115.rmap

value: 4 hr


title: E14_ES_RA48h_rep3_CapC_set3

value: 48 hr


title: Plant tissue, 480 μM DNAN, rep3


title: Whole blood, case 01

value: whole blood

value: Miniature Schnauzer

value: female

value: hypertriglyceridemia (HTG)


title: Treatment-naïve prostate cancer sample 13

value: Primary prostate cancer tumor, Patient sample


title: Plant tissue, 480 μM DNAN, rep2


title: Plant tissue, 240 μM DNAN, rep4

value: 240 μM DNAN


title: Treatment-naïve prostate cancer sample 4


title: Treatment-naïve prostate cancer sample 8


title: Plant tissue, 480 μM DNAN, rep1


title: Plant tissue, 480 μM DNAN, rep4


title: Treatment-naïve prostate cancer sample 7


title: Treatment-naïve prostate cancer sample 6


title: Plant tissue, 240 μM DNAN, rep3


title: E14_ES_RA4h_rep3_CapC_set3

value: mouse embryonic stem cells

value: ESC

value: wildtype


title: Plant tissue, 240 μM DNAN, rep5

value: Whole plant shoot and root

value: Shake flask

value: 14 days


title: E14_ES_RA2h_rep3_CapC_set3

value: retinoic acid (RA)

value: 2 hr


title: Treatment-naïve prostate cancer sample 3


title: Treatment-naïve prostate cancer sample 5


title: E14_ES_RA0h_rep3_CapC_set3

value: untreated


title: Plant tissue, 240 μM DNAN, rep1

value: 6 hours


title: Treatment-naïve prostate cancer sample 1


title: E14_ES_RA6h_rep4_CapC_set2

description:
cd_RA_6h_CapC11
ints_all_forGEO_CapC11.txt
DpnII.mm10_CapC101115.rmap

value: 6 hr


title: Plant tissue, 120 μM DNAN, rep5

value: 120 μM DNAN


title: E14_ES_RA72h_rep4_CapC_set2

description:
cd_RA_72h_CapC11
ints_all_forGEO_CapC11.txt
DpnII.mm10_CapC101115.rmap

value: 72 hr


title: Plant tissue, 240 μM DNAN, rep2


title: E14_ES_RA72h_rep3_CapC_set2


title: Benign prostatic hyperplasia sample 3

source_name: Benign primary prostate tumor, Patient sample


title: Treatment-naïve prostate cancer sample 2


title: Benign prostatic hyperplasia sample 4

value: Benign primary prostate tumor, Patient sample


title: E14_ES_RA6h_rep3_CapC_set2


title: Plant tissue, 120 μM DNAN, rep4


title: E14_ES_RA4h_rep4_CapC_set2

description:
cd_RA_4h_CapC11
ints_all_forGEO_CapC11.txt
DpnII.mm10_CapC101115.rmap

value: 4 hr


title: E14_ES_RA48h_rep4.2_CapC_set2

description:
cd_RA_48h_CapC11
ints_all_forGEO_CapC11.txt
DpnII.mm10_CapC101115.rmap

value: 48 hr


title: Plant tissue, 120 μM DNAN, rep3


title: Patient 6_vehicle (C1-CTRL)

type: RNA

city: Bologna

first: Dorian

last: Forte

address: Via Massarenti 9

department: Department of Medical and Surgical Sciences

country: Italy

institute: University of Bologna

hyb_protocol: Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol. Each reporter probe provided by the manufacturer was labeled with a propierty flourescent barcode system specific for each transcript.

scan_protocol: Scaning was conducted using the NanoString Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files. The data were normalized using 4 housekeeping genes with the lowest coefficient of variation among the ones included in the panel. Raw values are the number of copies of each molecular barcode representative of a specific transcript.
Mean count of negative controls plus two standard deviations was subtracted from each gene count to eliminate negative background. Then normalization on synthetic positive controls was conducted by multiplying the count of each gene for a correction factor. This factor was calculated for each sample as the ratio between the quadratic mean of positive controls counts and the mean of quadratic means in all samples. In order to performed CodeSet Content normalization on housekeeping genes, three reference genes were selected among the forty available in the panel based on the lowest coefficients of variation (CV= ratio between mean counts and standard deviations across all samples). Finally, CodeSet Content normalization was performed by multiplying genes counts for a further correction factor calculated on reference genes as described for positive technical controls. After completion of normalization processes, counts were log2 transformed.

label: Molecular barcode on reporter probe

source_name: CD34+ cells

label_protocol: RNA was not labeled, but it was pre-processed following the NanoString manufacturer's protocol.

extract_protocol: Total RNA was extracted by phenol-chloroform. RNA quantity and quality were assessed by NanoDrop2000 (Thermo Fisher Scientific). For samples that reached the quality standards (A260/A280 ≥ 1.7 and A260/A230 ≥ 1.8), we evaluated the expression profile of 768 genes by NanoString using the nCounter Human Metabolic Pathways Panel (NanoString Technologies).

treatment_protocol: CD34+ cells from AML patients at the diagnosis

tag: individual

value: Patient 6

value: CD34+ cells

tag: time

value: 24 hours

tag: condition

value: vehicle

tag: disease

value: AML

tag: diagnosis

value: yes


title: Patient 7_EV10 (V12-EV)

value: Patient 7

tag: cell type

value: treated with EV10


title: Patient 4_EV (V4-EV)

value: Patient 4

value: treated with EV6


title: Patient 4_vehicle (V9-CTRL)


title: Patient 7_vehicle (L3-CTRL)


title: Patient 5_vehicle (A1-CTRL)

value: Patient 5


title: Patient 7_EV9 (V10-EV)

value: treated with EV9


title: Patient 5_EV7 (F2-EV)

value: treated with EV7


title: Patient 6_EV8 (H2B-EV)

value: treated with EV8


title: E14_ES_RA48h_rep4_CapC_set2

tag: tissue

value: mouse embryonic stem cells

tag: cell line

value: ESC

tag: genotype

value: wildtype

value: retinoic acid (RA)


title: Comb03

city: Changsha

first: Lin

last: Qi

address: 139 Renmin Road

institute: The Second Xiangya Hospital, Central South University

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2
Differentially expression transcripts (DETs) were determined using the MA-plot-based method with Random Sampling (MARS) model in the DEGseq package between groups.
DETs were chosen for function and signaling pathway enrichment analysis using GO and KEGG database.
Assembly: Clean reads were aligned to the Human genome hg38 using STAR. StringTie.
Supplementary files format and content: The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per Million mapped reads) using Perl.

source_name: cell line

growth_protocol: 143B osteosarcoma cells were plated in 10-cm dishes at 2,000,000 cells per dish  in DMEM + 10% FBS + 1% penicillin/streptomycin the day prior to compound treatment.

extract_protocol:
Total RNA was isolated from each thymic sample using the RNAmini kit ( Qiagen, Germany). RNA quality was examined by gel electrophoresis and with Qubit (Thermo, Waltham, MA, USA).
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), and sequencing was carried out using the Illumina Novaseq 6000 instrument by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China).

treatment_protocol: 143B osteosarcoma cells were treated with DMSO,1.0 μM Ceritinib, 1.0 μM Crenolanib, and the combination of 1.0 μM Ceritinib and 1.0 μM Crenolanib for 48 hours. Three biological replicates of each sample were processed for next-generation sequencing (NGS).

value: cell line

value: osteosarcoma

value: wild-type

tag: treatment

value: the combination of 1.0 μM Crenolanib and 1.0 μM Ceritinib for 48 hours


title: E14_ES_RA4h_rep3_CapC_set2

tag: treatment duration

value: 4 hr


title: Benign prostatic hyperplasia sample 2

description: Fresh frozen Spatial transcriptome sequencing

value: Benign primary prostate tumor, Patient sample


title: Plant tissue, 120 μM DNAN, rep2

value: Whole plant shoot and root

value: Shake flask

value: 14 days

value: 6 hours

value: 120 μM DNAN


title: Plant tissue, 60 μM DNAN, rep5

value: 60 μM DNAN


title: Benign prostatic hyperplasia sample 1


title: Plant tissue, 60 μM DNAN, rep4


title: E14_ES_RA2h_rep4_CapC_set2

description:
cd_RA_2h_CapC11
ints_all_forGEO_CapC11.txt
DpnII.mm10_CapC101115.rmap

value: 2 hr


title: E14_ES_RA48h_rep3_CapC_set2

value: mouse embryonic stem cells

value: 48 hr


title: Plant tissue, 120 μM DNAN, rep1


title: Certi03

value: 1.0 μM Ceritinib for 48 hours


title: Comb01


title: Plant tissue, 60 μM DNAN, rep3


title: Patient 4_vehicle (V11-CTR)

value: Patient 4

value: CD34+ cells

value: 24 hours

value: vehicle

value: AML

value: yes


title: Patient 3_EV5 (G2-EV)

value: Patient 3

value: treated with EV5


title: Patient 1_EV4 (D2-EV)

value: Patient 1

value: treated with EV4


title: Patient 3_vehicle (H1A-CTRL)


title: Patient 3_vehicle (F1-CTRL)


title: Comb02

value: cell line

value: osteosarcoma

value: wild-type

value: the combination of 1.0 μM Crenolanib and 1.0 μM Ceritinib for 48 hours


title: Certi02


title: Plant tissue, 60 μM DNAN, rep1

value: Whole plant shoot and root

value: Shake flask

value: 14 days

value: 6 hours

value: 60 μM DNAN


title: Plant tissue, 60 μM DNAN, rep2


title: Plant tissue, 0 μM DNAN, rep5

value: 0 μM DNAN


title: E14_ES_RA24h_rep4_CapC_set2

description:
cd_RA_24h_CapC11
ints_all_forGEO_CapC11.txt
DpnII.mm10_CapC101115.rmap

value: mouse embryonic stem cells

value: ESC

value: wildtype

value: retinoic acid (RA)

value: 24 hr


title: Patient 4_vehicle (V5-CTRL)

value: Patient 4

value: CD34+ cells

value: 24 hours

value: vehicle

value: AML

value: yes


title: E14_ES_RA2h_rep3_CapC_set2

value: 2 hr


title: Plant tissue, 0 μM DNAN, rep4

value: Whole plant shoot and root

value: Shake flask


title: E14_ES_RA24h_rep3_CapC_set2


title: Certi01

value: cell line

value: osteosarcoma

value: wild-type

value: 1.0 μM Ceritinib for 48 hours


title: E14_ES_RA0h_rep4_CapC_set2

description:
cd_RA_0h_CapC11
ints_all_forGEO_CapC11.txt
DpnII.mm10_CapC101115.rmap

value: mouse embryonic stem cells

value: ESC

value: untreated


title: Patient 1_vehicle (D1-CTRL)

value: Patient 1


title: Patient 1_EV2 (BC9-EV)

value: treated with EV2


title: E14_ES_RA0h_rep3_CapC_set2

value: wildtype


title: Plant tissue, 0 μM DNAN, rep3

value: 14 days

value: 6 hours

value: 0 μM DNAN


title: Creno02

value: 1.0 μM Crenolanib for 48 hours


title: Creno01


title: Dexamethasone treatment 2

city: Rostock

first: Robert

last: Jaster

address: Ernst-Heydemann-Str. 6

department: Dept. of Medicine, Div. of Gastroenterology

institute: Rostock University Medical Center

data_processing:
Data processing was performed by Novogene (Cambridge, UK).
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions was performed using the DESeq2Rpackage (1.20.0). The resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts and fpkm for each sample
Supplementary files format and content: MS Excel file includes raw counts and fpkm for each sample

source_name: Pancreas

extract_protocol:
Total RNA was isolated from pancreatic tissue using the Tissue Lyser LT and the RNeasy Mini Kit (Qiagen, Hilden, Germany). Total RNA was quantified by spectrophotometry (NanoDrop 1000, Thermo Fisher Scientific, Waltham, MA, United States), and their integrity was checked using the Agilent Bioanalyzer 2100 with an RNA Nano chip kit (Agilent Technologies, Waldbronn, Germany). Afterwards, the samples were transferred to Novogene (Cambridge, UK) for further processing.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: Pancreas

tag: strain

value: MRL/MpJ

tag: Sex

value: male

tag: age

value: 3 months

value: Poly I:C + dexamethasone


title: Patient 4_EV3 (C2-EV)

value: Patient 4

value: CD34+ cells

value: 24 hours

value: treated with EV3

value: AML

value: yes


title: E14_ES_RA72h_rep4_CapC_set1

description:
cd_RA_72h_CapC10
ints_all_forGEO_CapC10.txt
DpnII.mm10_CapC101115.rmap

value: mouse embryonic stem cells

value: ESC

value: retinoic acid (RA)

value: 72 hr


title: Creno03

value: cell line

value: osteosarcoma

value: wild-type


title: Patient 1_EV1 (B2-EV)

value: Patient 1

value: treated with EV1


title: Plant tissue, 0 μM DNAN, rep2

value: Whole plant shoot and root

tag: ecotype

tag: plant growth

value: Shake flask

value: 14 days

value: 6 hours

value: 0 μM DNAN


title: E14_ES_RA48h_rep4.2_CapC_set1

description:
cd_RA_48h_CapC10
ints_all_forGEO_CapC10.txt
DpnII.mm10_CapC101115.rmap

value: wildtype

value: 48 hr


title: NC03

value: DMSO for 48 hours


title: Plant tissue, 0 μM DNAN, rep1

tag: plant age

tag: treatment time


title: Takinib treatment 3

value: Pancreas

value: MRL/MpJ

value: male

value: 3 months

value: Poly I:C + takinib


title: Takinib treatment 2


title: NC02

value: cell line

value: osteosarcoma


title: NC01

value: wild-type


title: E14_ES_RA24h_rep4_CapC_set1

description:
cd_RA_24h_CapC10
ints_all_forGEO_CapC10.txt
DpnII.mm10_CapC101115.rmap

value: mouse embryonic stem cells

value: ESC

value: retinoic acid (RA)

value: 24 hr


title: Takinib treatment 1


title: E14_ES_RA6h_rep4_CapC_set1

description:
cd_RA_6h_CapC10
ints_all_forGEO_CapC10.txt
DpnII.mm10_CapC101115.rmap

value: 6 hr


title: Dexamethasone treatment 1

value: Poly I:C + dexamethasone


title: Tofacitinib treatment 2

value: wildtype

value: Poly I:C + tofacitinib


title: MS23 macrophages stimulated with LPS+IFNg

city: Paris

first: violetta

last: zujovic

address: 47 boulevard de l'hôpital

country: France

institute: Paris brain institute

description: re-sequencing of sample for batch effect correction

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads with following parameters : cutoff: '20' leading: '10' minlen: '50' slidingwindow: '4' trailing: '10'
Star v2.5.3a has been used to align reads on  reference genome using standard options
Quantification of gene and isoform abundances has been done with rsem 1.2.28 on GENCODE v28 reference transcriptome
Assembly: HG38
Supplementary files format and content: tab-delimited text files including expecting counts, TPM and FPKM

source_name: blood derived macrophages

growth_protocol: Monocytes were isolated with anti-CD14 microbeads (Miltenyi) and plated in 12-well plates (500 000 cells/well) or in 24-well plates (200 000 cells/well) in RPMI 1640 + 10% FBS and granulocyte macrophage colony-stimulating factor (GM-CSF) (500 U/ml, ImmunoTools).

extract_protocol:
Nucleospin RNA extraction kit (Macherey-Nagel)
Truseq mRNA stranded ILLUMINA with UDI

treatment_protocol: After 72h, media was replaced with fresh media and one of the following: GM-CSF (500 U/ml); IL4 (1000 U/ml, ImmunoTools); or combined IFNγ (200 U/ml, ImmunoTools) and ultra-pure LPS (10 ng/ml, InvivoGen).

value: blood derived macrophages

value: MS patient

value: treated with LPS+IFNg for 24 hours

tag: batch

tag: re-sequencing


title: E14_ES_RA4h_rep4_CapC_set1

description:
cd_RA_4h_CapC10
ints_all_forGEO_CapC10.txt
DpnII.mm10_CapC101115.rmap

value: 4 hr


title: MS19 macrophages stimulated with LPS+IFNg


title: E14_ES_RA2h_rep4_CapC_set1

description:
cd_RA_2h_CapC10
ints_all_forGEO_CapC10.txt
DpnII.mm10_CapC101115.rmap

value: 2 hr


title: MS16 macrophages stimulated with LPS+IFNg


title: Tofacitinib treatment 1

value: Pancreas

value: MRL/MpJ

value: male

value: 3 months


title: E14_ES_RA48h_rep4_CapC_set1

value: mouse embryonic stem cells

value: 48 hr


title: MS23 macrophages stimulated with GMCSF

value: treated with GMCSF for 24 hours


title: E14_ES_RA0h_rep4_CapC_set1

description:
cd_RA_0h_CapC10
ints_all_forGEO_CapC10.txt
DpnII.mm10_CapC101115.rmap

value: ESC

value: untreated


title: ATAC,Zld294,rep4

city: philadelphia

first: Mustafa

last: Mir

state: PA

address: 3501 Civic Center Boulevard, CTRB 9030

institute: Children's Hospital of Philadelphia

data_processing:
For ATAC-seq and CUT&RUN, reads were aligned to the Berkeley Drosophila Genome Project (version six) reference genome using bowtie2 with the ‘--sensitive-local’ setting. Samtools was used to convert from .sam to .bam, index, sort, and remove duplicate, unmapped, and multi-mapped reads. For Cut and Run, peaks were called using macs2 using the ‘-f BAMPE’, ‘-g 129789873’, and ‘--bw 300’ settings using IgG as a control. For ATAC-seq, no IgG was used as a control and --nomodel --nolambda settings were used. Consensus peaks were called using the ‘diffbind’ package in R. Peaks were annotated using the CHIPseeker package and ‘TxDb.Dmelanogaster.UCSC.dm6.ensGene’ annotation. Bigwig files were generated using the Bamcoverage function from the deeptools package using the a ‘--binSize 20’, ‘--smoothLength 60’, ‘--centerReads’, ‘--normalizeUsing RPKM’, ‘--effectiveGenomeSize 142573017’.
Assembly: DM6
Supplementary files format and content: .bw files with averaged RPKM with a bine size of 20

organism: Drosophila melanogaster

extract_protocol:
Embryos were staged at NC12-NC13; placed on double-sided tape and rinsed before they were placed in 1.5 mL tube caps. Embryos were macerated with an 18-gauge needle in lysis buffer containing 10mM Tris-HCl pH7.5; 10mM NaCl, 3mM MgCl2; 0.1% Igepal-630.
ATAC libraries were prepared using Illumina Tagment DNA Enzyme and Buffer Small Kit with Nextera DNA CD indexes following manuafactor's protocol and previously described methods from Blythe, SA and Buenrostro JD.


title: ATAC,Zld294,rep6


title: ATAC,Zld294,rep5


title: Tofacitinib treatment 3


title: Poly I:C-treated control 2

value: Poly I:C + solvent


title: Poly I:C-treated control 3

value: wildtype


title: Zld294,day3,rep8

data_processing:
To quantify transcript abundances from RNA-seq data we used the pseudoaligner Kallisto. Reads were aligned to the Drosophila melanogaster BDGP6.28 cDNA reference using a pre-built kallisto index (Bray et al., 2016). Data was normalized by eliminating transcripts with no reads in more than half of the samples from each condition and then using EdgeR to perform the ‘Trimmed Mean of M-values’ method to correct for compositional differences between libraries. Clear differences between the WT and ZF5 transcript abundances were observed via Principal Component Analysis (Fig S3). To determine differentially expressed genes, the ‘voom’ method from the ‘Limma’ package in R was applied to the log-transformed counts per million (CPM) data. After fitting linear models to the transformed gene expression data using the lmFit function, we applied the empirical Bayes (eBayes) method to the model fits. Subsequently, we extracted the top DEGs from the eBayes-fitted models. We adjusted for multiple testing to control the false discovery rate using the Benjamini-Hochberg (BH) method. Genes were classified as differentially expressed if they had logFC greater than 1.5 and an adj. p-value less than 0.05.
Assembly: DM6
Supplementary files format and content: .csv files have gene names and counts per million

extract_protocol:
Embryo was staged to proper NC13 to Nc14 before they were placed on 1.5mL microcentrifuge tube caps (3 embryos per sample). Embryos were macerated in 10ul TRIzol™ using sterile an 18 gauge needle. RNA was isolated using Chloroform and phasemaker tubes as described in Bogart, K. and Andrews, J.
RNA libraries were made using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® following manufacturer's recommended protocol.


title: ATAC,Zld294,rep3


title: ATAC,Zld294,rep2


title: MS16 macrophages stimulated with GMCSF


title: E14_ES_RA48h_rep3_CapC_set1

value: retinoic acid (RA)


title: Zld294,day3,rep7


title: MS23 macrophages stimulated with IL4

value: blood derived macrophages

value: treated with IL4 for 24hours


title: Untreated control 3


title: MS19 macrophages stimulated with GMCSF

value: MS patient


title: ATAC,Zld294,rep1


title: E14_ES_RA6h_rep3_CapC_set1

value: 6 hr


title: MS16 macrophages stimulated with IL4


title: Zld294,day3,rep5


title: E14_ES_RA4h_rep3_CapC_set1

value: 4 hr


title: Zld294,day3,rep6


title: Untreated control 1

value: Pancreas


title: Zld294,day3,rep4


title: MS19 macrophages stimulated with IL4


title: E14_ES_RA72h_rep3_CapC_set1

value: 72 hr


title: Poly I:C-treated control 1

value: MRL/MpJ

value: male


title: E14_ES_RA2h_rep3_CapC_set1

value: mouse embryonic stem cells

value: 2 hr


title: HC17 macrophages stimulated with LPS+IFNg

value: healthy control

value: treated with LPS+IFNg for 24 hours


title: HC18 macrophages stimulated with LPS+IFNg


title: E14_ES_RA24h_rep3_CapC_set1

value: ESC

value: 24 hr


title: Untreated control 2

value: 3 months

value: wildtype

value: untreated


title: Zld294,day3,rep2


title: E14_ES_RA0h_rep3_CapC_set1


title: Zld294,day3,rep3


title: E14_ES_RA72h_rep7_nChIP.Input

data_processing:
Paired-end reads were aligned to the genome sequence of concatenated mouse and spike-in genomes (mm10+dm6 for native ChIP-seq) using Bowtie 2 with the “--no-mixed” and “--no-discordant” options specified. Reads that were mapped more than once were discarded, followed by removal of PCR duplicates with SAMTools and Sambamba.
For annotation data visualisation, mm10 reads were randomly subsampled using factors that reflected the total number of reads in each sample.
Upon assessing sample correlation, for each condition, biological replicates were merged for downstream applications. Genome coverage tracks were generated using the pileup function from MACS2 (Zhang et al. 2008).
Peaks were called using the macs2 callpeak function from MACS2, with native ChIP input samples as control and non-downsampled native ChIP reads as input and the option --scale-to small and --broad. Following parameters were used: H3K27ac: -q 0.1, --broad-cutoff 0.05 H3K4me1: -q 0.01, --broad-cutoff 0.1, peaks were merged at 1kb, H3K27me3: -q 0.1, --broad-cutoff 0.1. The peaks were called individually for each replicate, following which the peaks from different replicates were merged using the reduce() function from GenomicRanges to generate peak intervals. Depending on the number of replicates in a sample, only those peak intervals were retained that were identified in at least 2/3, 3/4 or 2/2 biological replicates. Final peak sets were obtained by combining these filtered peak intervals called for individual samples using reduce().
For quantitative analysis, fragments overlapping peaks were quantified from non-downsampled bam files using the summarizeOverlaps() function from the R package GenomicFeatures, with the parameters mode=’Union’ and paired=TRUE. The resulting count tables were then processed by DESeq2. Normalized read counts were extracted from the DESeq2 results tables and mean normalized counts across replicates for each sample calculated. Mean FPKM were calculated from these mean normalized counts and log-transformed using a pseudocount of 0.1.
Assembly: mm10
Supplementary files format and content: bigWig files representing genome coverage for merged replicates of normalised ChIP-seq profiles. .rds files contain all final high-confidence peak intervals and their normalized read counts extracted from DESeq2.

extract_protocol:
For native ChIP-seq, 5 x 10^7 mouse ESCs (both untreated and following RA treatment) were pelleted and nuclei were released by resuspending in ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 5 mM N-ethylmaleimide). Nuclei were then washed, and resuspended in 1ml of MNase digestion buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.25M sucrose, 3mM CaCl2, 10 mM N-ethylmaleimide, 1x cOmplete protease inhibitor cocktail (Roche)). Each sample was then incubated with 200 units of MNase (ThermoFisher Scientific) at 37°C for 5 min, followed by the addition of 4 mM EDTA to halt MNase digestion. Following centrifugation at 1500 g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300 µl of nucleosome release buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 1x protease inhibitors, 10 mM N-ethylmaleimide) at 4°C for 1 h, passed five times through a 27G needle using a 1 ml syringe, and spun at 1500 g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 sample from above. A small amount of S1/S2 DNA was purified and visualized on a 1.5% agarose gel to confirm digestion to mostly mono-nucleosomes. For a given ChIP, purified nuclease-digested chromatin from 5 × 10^6 ES cells was 10-fold diluted in native ChIP incubation buffer (10mM Tris-HCl pH 7.5, 70mM NaCl, 2mM MgCl2, 0.1% Triton X-100, 2mM EDTA, 5mM Sodium butyrate, 1× cOmplete protease inhibitor cocktail (Roche)) before being pre-cleared for 2h with Protein A Dynabeads (Life Technologies #10001D) blocked with 0.05mg/ml tRNA and 0.2mg/ml BSA. The pre-cleared chromatin was further incubated overnight at 4 °C with the appropriate antibody: anti-H3K27ac (CST, #8173, 5µg), anti-H3K27me3 (Millipore, #07-449, 5µg), anti-H3K4me1 (CST, #5326, 5µg). Antibody-bound chromatin was captured using blocked Dynabeads for 1h at 4 °C and isolated through magnetizing on ice. After four washes with ice-cold native ChIP wash buffer (20mM Tris-HCl pH 7.5, 125mM NaCl, 0.1% Triton X-100, 2mM EDTA) and one wash with ice-cold 1x TE buffer, the ChIP DNA was eluted in fresh elution buffer (1% SDS, 0.1 M NaHCO3) and incubated with shaking at 25 °C for 30min. In parallel, a matched 10% input sample was identically processed. Both ChIP and input DNA were purified using ChIP DNA Clean and Concentrator Kit (Zymo Research # D5205) following manufacturer protocol.
Crosslinked ChIP-seq was performed to profile RNAP2 binding (NTD, Ser2p, Ser5p). Briefly, 5 × 10^7 ES cells were washed with 1× PBS and crosslinked with 1% formaldehyde. After 15 min incubation at RT with rotation, the fixation reaction was quenched with 0.15M glycine solution and washed again with 1x PBS. The pellet was stored at -80°C. For the nuclei isolation and sonication, the pellet was thawed on ice and then resuspended in 10mL LB1-solution (10% glycerol, 50mM HEPES-KOH (pH 7.9), 0.14 M NaCl, 1mM EDTA, 0.5 % NP-40 (IGEPAL), 0,25% Triton X100, 1x cOmplete protease inhibitor cocktail (Roche)) and rotated at 4°C for 10min. After centrifugation (5 min, 1000xg, 4°C), the supernatant was removed and the cells were resuspended in 10 mL LB2 solution (10mM Tris-HCl (pH 8.0), 0.2M NaCl, 1mM EDTA, 0.5mM EGTA, 1x cOmplete protease inhibitor cocktail (Roche)), rotated at 4°C for 5min and centrifuged (5 min, 1000xg, 4°C). The cell pellet was resuspended in 1mL LB3 (10mM Tris-HCl (pH 8.0), 0.1M NaCl, 1mM EDTA, 0.5mM EGTA, 1x cOmplete protease inhibitor cocktail (Roche)) and transferred to a sonication tube containing sonication beads (Diagenode). Sonication was performed using the Bioruptor® Pico sonicator (Diagenode) for 20 cycles, 30 sec on / off. The sonicated cell solution was transferred to 1.5 mL collection tubes and 100 µL of 10% Triton X100 in LB3 was added and mixed by inversion. After centrifugation at 20,000 xg for 10 min at 4°C, the supernatant was aliquoted into dry ice-cooled tubes (150µg chromatin/tube). Sonication was confirmed with a 1.5 % agarose gel. For each ChIP, either 150 µg (NTD polymerase) or 300 µg (Ser2p, Ser5p) chromatin were diluted 10-fold in ChIP dilution buffer (10% Triton X100, 1mM EDTA, 20mM Tris-HCl (pH 8.0), 0.15M NaCl) and then pre-cleared for 2h with Protein A Dynabeads (Life Technologies #10001D) blocked with 0.05mg/ml tRNA and 0.2mg/ml BSA. Prior to the addition of the antibody, 2% input was taken from the pre-cleared chromatin. The pre-cleared chromatin was further incubated overnight at 4 °C with the appropriate antibody: anti-Rpb1 NTD (CST, #14958, 7.5µg/150µg chromatin), anti-phospho-Rpb1 CTD (Ser2p) (CST, #13499, 6.25µg/150µg chromatin), anti-phospho-Rpb1 CTD (Ser5p) (CST, #13523, 6.25µg/150µg chromatin). Antibody-bound chromatin was captured with blocked Dynabeads for 1h at 4 °C and isolated by magnetisation on ice. Dynabeads were washed with low salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl (pH 8.0), 0.15M NaCl), high salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl (pH 8.0), 0.5M NaCl), LiCl buffer (0.25M LiCl, 0.1% NP40, 0.1% sodium deoxycholate, 1mM EDTA, 10mM Tris-HCl (pH 8.0)) and twice with TE buffer (10mM Tris-HCl (pH 8.0), 0.1mM EDTA). The chromatin-bound beads were eluted with 100µl/150µg chromatin elution buffer (1% SDS, 0.1M NaHCO3) and incubated at 25 °C for 30min with shaking. The input sample was topped up to the same volume as the ChIP sample and 4µL 4M NaCl and 2µL RNaseA (Qiagen #19101, 20mg/mL) were added. Samples were incubated overnight at 65°C with slow shaking. Then 1µL of Proteinase K was added and the samples were incubated at 55°C for 1 hour with slow shaking. Both ChIP and input DNA were purified using the ChIP DNA Clean and Concentrator Kit (Zymo Research # D5205) following manufacturer protocol.
Libraries for both ChIP and Input samples were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size of all libraries was analysed using either the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent, nChIP) or the TapeStation (xChIP). Library concentration was further determined either by using qPCR with SensiMix SYBR (Bioline, UK)  and KAPA Illumina DNA standards (Roche) for nChIP or by quantification via Qubit for xChIP. Libraries were sequenced as 40-42 bp paired-end reads on Illumina NextSeq 500 platform in biological triplicates or quadruplicates.

treatment_protocol: To induce differentiation, ES cells were treated with 1uM retinoic acid (RA) for 2-72 hours.

tag: chip antibody


title: Zld294,day3,rep1


title: HC14 macrophages stimulated with LPS+IFNg

value: blood derived macrophages


title: HC18 macrophages stimulated with GMCSF

value: treated with GMCSF for 24 hours


title: E14_ES_RA72h_rep7_nChIP.H3K27ac

description:
K27ac_peaks_InBothReplicates.rds
E14_ra72h_H3K27ac_rmdup_MERGED_reps5to8_downsampled.bam.bw


title: Tumor sample with Toll pathway activation, biol rep 3

city: Zurich

first: Fabienne

last: Brutscher

address: Winterthurerstrasse 190

department: Department of Molecular Life Sciences

country: Switzerland

institute: University of Zurich

data_processing:
The mapping and counting was performed using a snakemake pipeline (https://doi.org/10.1093/bioinformatics/btz436) with default parameters:  Reads were aligned to the Drosophila melanogaster genome, assembly dm6 using HISAT2. Gene level quantification was performed using featureCounts.  Count matrices were analysed in R.
Assembly: Drosophila melanogaster genome, dm6 assembly
Supplementary files format and content: A tab-delimited (.tsv) featureCounts table contains raw counts of all four samples (LacZ, Dorsal, RasLacZ; RasDorsal) in biological triplicates

source_name: eye-antennal imaginal disc

extract_protocol:
RNA was isolated from dissected eye-antennal discs at 96h AED (after egg deposition) using the RNeasy Micro Kit (Qiagen) following the manufacturer's protocol.
RNA-seq libraries were generated from total RNA according to the TruSeq Stranded mRNA library preparation protocol (Ilumina).

value: eye-antennal imaginal disc

tag: group


title: HC17 macrophages stimulated with GMCSF

tag: cell type


title: E14_ES_RA48h_rep7_nChIP.Input

source_name: mouse embryonic stem cells


title: MGC Exp2 NT Rep 1

city: Baltimore

first: Matthew

middle: D

last: Smith

state: MD

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University

data_processing:
Raw sequencing data were processed with fastp to remove reads with adapter, poly-N, or low quality sequences. High quality reads were mapped to mouse genome with Spliced Transcripts Alignment to a Reference (STAR) software. FeatureCounts was used to count read numbers for each gene and Fragments per kilobase of transcript sequence per Millions base pairs sequenced (FPKM) for each gene was calculated.
Assembly: mm10
Supplementary files format and content: readcount_genename: raw counts for reach gene and each sample along with Ensembl  gene ID, gene_name, gene_chr, gene_start, gene_end, gene_strand, gene_length, gene_biotype, gene_description, and tf_family
Supplementary files format and content: fpkm_genename: Fragments per kilobase of transcript sequence per Millions base pairs sequenced for each gene and each sample along with gene_name, gene_chr, gene_start, gene_end, gene_strand, gene_length, gene_biotype, gene_description, and tf_family

source_name: Mixed glia culture

growth_protocol: Mixed Glia Cultures (MGCs) were prepared from P3-P6 C57BL6 mice. Cortices were isolated and dissociated with trypsin (1mL of 0.05%) with 10mL serological pipet and incubated for 15-20 minutes at 37C in water bath. Trypsin was neutralized with equal volume of Dulbecco's Modified Eagle Media (DMEM)/F12 containing 1% antibiotics and 10% fetal bovine serum. Dissociated cortices were then triturated in 6mL HBSS with serological pipet and filtered twice through 100μm cell strainer and centrifuged for 1,000rpm for 10 minutes. Cells were resuspended in in DMEM/F12 media and plated on 6-well plates (250k cells/mL) pre-coated with 100mg/ml poly-D-lyse (PDL). Media was replaced every three days until confluency on 14 days in vitro (DIV).

extract_protocol:
RNA was isolated using Qiagen RNeasy Mini Plus Kit.
Unstranded polyA-mRNA libraries were prepared and sequenced by Novogene. 1μg RNA was used as input into NEBNext Ultra RNA Library Prep Kit.

treatment_protocol: MGC were treated for 24 hours with with 50nM bryostatin, LPS (100ng/mL), 20ng/mL IFNγ, 20ng/mL IL-4, or a combination of these treatments prior to RNA isolation.

tag: tissue

value: Mixed glia culture

value: No Treatment

tag: replicate


title: MGC Exp1 NT Rep 2


title: MGC Exp2 NT Rep 2


title: MGC Exp1 NT Rep3


title: MGC Exp2 NT Rep3


title: HC14 macrophages stimulated with GMCSF


title: E14_ES_RA48h_rep7_nChIP.H3K27ac

description:
K27ac_peaks_InBothReplicates.rds
E14_ra48h_H3K27ac_rmdup_MERGED_reps5to8_downsampled.bam.bw

tag: cell line


title: MGC Exp1 NT Rep 1

tag: treatment


title: Tumor sample with Toll pathway activation, biol rep 2


title: Tumor sample with Toll pathway activation, biol rep 1


title: HC18 macrophages stimulated with IL4

value: treated with IL4 for 24hours


title: E14_ES_RA24h_rep7_nChIP.Input


title: Tumor sample, biol rep 3

value: Tumor sample


title: MGC Exp1 LPS+IFNγ Rep 3

value: LPS+IFNγ


title: E14_ES_RA24h_rep7_nChIP.H3K27ac

description:
K27ac_peaks_InBothReplicates.rds
E14_ra24h_H3K27ac_rmdup_MERGED_reps5to8_downsampled.bam.bw


title: Tumor sample, biol rep 2


title: E14_ES_RA0h_rep7_nChIP.Input


title: E14_ES_RA0h_rep7_nChIP.H3K27ac

description:
K27ac_peaks_InBothReplicates.rds
E14_ra0h_H3K27ac_rmdup_MERGED_reps5to8_downsampled.bam.bw


title: MGC Exp1 LPS+Bryo Rep 3

value: LPS+Bryo


title: Tumor sample, biol rep 1


title: MGC Exp1 LPS+IFNγ Rep 2


title: HC17 macrophages stimulated with IL4


title: MGC Exp1 LPS+IFNγ Rep 1


title: HC14 macrophages stimulated with IL4


title: MS44 macrophages stimulated with GMCSF

value: MS patient


title: Control sample with Toll pathway activation, biol rep 3


title: MGC Exp1 LPS+Bryo Rep 1


title: MS44 macrophages stimulated with IL4


title: MS44 macrophages stimulated with LPS+IFNg


title: E14_ES_RA72h_rep6_nChIP.Input


title: MS43 macrophages stimulated with LPS+IFNg


title: Control sample with Toll pathway activation, biol rep 2


title: MGC Exp1 LPS+Bryo Rep 2


title: Control sample with Toll pathway activation, biol rep 1


title: E14_ES_RA72h_rep6_nChIP.H3K27ac


title: MGC Exp1 LPS Rep 3

value: LPS


title: E14_ES_RA48h_rep6_nChIP.Input


title: MGC Exp1 LPS Rep 2


title: Control sample, biol rep 3

value: Control sample


title: Control sample, biol rep 2


title: E14_ES_RA24h_rep6_nChIP.Input

value: ESC


title: MGC Exp1 LPS Rep 1


title: MS43 macrophages stimulated with IL4


title: Control sample, biol rep 1


title: E14_ES_RA24h_rep6_nChIP.H3K27ac


title: MGC Exp1 LPS+IFNγ+Bryo Rep 3

value: LPS+IFNγ+Bryo


title: MS42 macrophages stimulated with LPS+IFNg

value: treated with LPS+IFNg for 24 hours


title: MS42 macrophages stimulated with GMCSF


title: control MKN45 cells 3

city: Wu Han

first: Gongcai

last: Tao

state: Hu Bei Province

address: No. 9, Zhangzhidong Road, Wuchang District

department: Department of Gastrointestinal Surgery

institute: Renmin Hospital of Wuhan University

data_processing:
Quality control and mapping
Gene-level quantification, analysis of differentially expressed genes (DEGs), cluster analysis, GGene-level quantification, analysis of differentially expressed genes (DEGs), cluster analysis, GO and KEGG enrichment (parameter- Quality limit: 0.05)
Transcript-level quantification, analysis of differentially expressed transcript (DEGs), cluster analysis, GO and KEGG enrichment.(P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.)
Gene structure extension and novel transcripts identification
Assembly: human genome (GRCh38)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: MKN45 gastric cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using mirVana™ miRNA ISOlation Kit（Ambion-1561）. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LTSample Prep Kit following manufacturer's protocols.

value: tumor cells

tag: genotype

value: WT

tag: disease state

value: malignant tumor

tag: time

value: Day 0


title: E14_ES_RA0h_rep6_nChIP.Input


title: MGC Exp1 LPS+IFNγ+Bryo Rep 2


title: MS43 macrophages stimulated with GMCSF

value: blood derived macrophages

value: treated with GMCSF for 24 hours


title: MGC Exp2 IL4 Rep 3

value: Mixed glia culture


title: MS41 macrophages stimulated with GMCSF


title: control MKN45 cells 2


title: control MKN45 cells 1


title: E14_ES_RA72h_rep5_nChIP.Input


title: E14_ES_RA72h_rep5_nChIP.H3K27ac


title: E14_ES_RA48h_rep6_nChIP.H3K27ac


title: MGC Exp1 LPS+IFNγ+Bryo Rep 1


title: MS41 macrophages stimulated with LPS+IFNg


title: E14_ES_RA48h_rep5_nChIP.Input


title: MS41 macrophages stimulated with IL4

value: treated with IL4 for 24hours


title: MGC Exp2 IL4 Rep 2


title: GBP5 -overexpressed MKN45 cells 3


title: MGC Exp2 IL4 Rep 1


title: GBP5 -overexpressed MKN45 cells 2


title: E14_ES_RA48h_rep5_nChIP.H3K27ac


title: MS40 macrophages stimulated with LPS+IFNg


title: MS42 macrophages stimulated with IL4


title: E14_ES_RA0h_rep6_nChIP.H3K27ac


title: E14_ES_RA24h_rep5_nChIP.Input


title: MGC Exp2 IL4+Bryo Rep 3


title: MGC Exp2 IL4+Bryo Rep 2


title: MGC Exp2 IL4+Bryo Rep 1


title: E14_ES_RA24h_rep5_nChIP.H3K27ac


title: MS40 macrophages stimulated with IL4


title: H3f3a_WTA_H3f3b_AA_CUTRUN_NoAb

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

data_processing:
Paired-end fastq files were trimmed to 25 bp and mapped to the mm10 genome with bowtie2 (options -q -N 1 -X 1000).
Mapped reads were duplicate-filtered reads and with insufficient mapping quality (MAPQ ≥ 10) were removed using samtools. Samples were size class filtered for nucleosome size class (150-500bp).
Indexed, sorted BAMs were converted to bigWig files using deepTools with normalization RPGC (options -bs 10 --normalizeUsing RPGC, --effectiveGenomeSize 2862010578). Heatmaps and metaplots were generated using deeptools.
Peaks were called from CUT&RUN samples using MACS2 with no antibody samples as input. For each target, peaks from all samples were combined to create a consensus peak set.
Assembly: mm10
Supplementary files format and content: bigwigs
Library strategy: CUT&RUN

source_name: Cell line

growth_protocol: ES-E14TG2a (E14) mES cells from male Mus musculus origin (RRID:CVCL9108361) were cultured at 37°C and 5% CO2 in DMEM base medium (Sigma Aldrich) supplemented with 10% FBS(Sigma Aldrich), 1X nonessential amino acids (Corning), 2mM L-glutamine (Corning), β-mercaptoethanol (Acros Organics) and LIF on 10cm plates precoated with 0.2% gelatin. For LIF+2i media, LIF media was further supplemented with 3 µM CHIR99021 GSK inhibitor (p212121), and 1 µM PD0325091 MEK inhibitor (p212121). Cells were passaged every ~48 h using trypsin and split at a ratio of ~1:8 with fresh medium. Routine anti-mycoplasma TC hood cleaning was conducted (LookOut DNA Erase spray, Sigma Aldrich) and cell lines were screened to confirm no mycoplasma presence. While generating clones, cells were grown in media with the addition of 1X penicillin/streptomycin (Corning) to prevent bacterial contamination.

extract_protocol:
100,000 nuclei were isolated from cell populations using a hypotonic buffer (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.5mM spermidine, 0.1% Triton X-100, 20% glycerol, freshly added protease inhibitors) and flash frozen. Nuclei were thawed and bound to lectin-coated concanavalin A magnetic beads (50 µL bead slurry per 100,000 nuclei; Polysciences). Immobilized nuclei were pre-blocked with blocking buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5mM spermidine, 0.1% BSA, 2 mM EDTA, fresh protease inhibitors) and washed in wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5mM spermidine, 0.1% BSA, fresh protease inhibitors). Nuclei were incubated in wash buffer containing primary antibody (H3.3, K122ac, K27ac) overnight at 4°C with rotation. Nuclei were incubated in wash buffer containing primary antibody for 1 hour at room temperature with rotation. Next, samples were washed twice with wash buffer and incubated in wash buffer containing recombinant pA-MN (for K122ac, K27ac) or pA/G-MN (for H3.3) for 30 minutes at room temperature with rotation. Controls lacking a primary antibody were subjected to the same conditions but incubated in wash buffer without any primary antibody prior to incubation with pA-MN/pA/G-MN. After incubation, samples were washed twice with was buffer and equilibrated to 0°C in an ice/water bath. MNase cleavage was activated upon addition of 3 mM CaCl2. Digestion was chelated for samples containing primary antibodies K27ac, after 30 mins on the ice water bath, using 20 mM EDTA, 4 mM EGTA, 200 mM NaCl, and 1.5 pg MNase-digested S. cerevisiae mononucleosomes were added as a spike-in control. Genomic fragments were released after an RNase A treatment. Released fragments were separated through centrifugation. Digestion was chelated for samples containing primary antibodies K122ac and H3.3 after 30 mins on the ice water bath, using a low-salt treatment: 10 mM EDTA, 2 mM EGTA, 150 nM NaCl, 5 mM TritonX, and 1.5 pg MNase-digested S. cerevisiae mononucleosomes were added as a spike-in control. Genomic fragments were released after being incubated for 1 hour at 4°C and released fragments were separated from beads. The salt concentration of low-salt treated samples were increased to 500 mM and additional RNase A.
Isolated fragments from all samples were used as input for a library build consisting of end repair and adenylation, adapter ligation, and subsequent purification with AMPure XP beads (Agencourt). Barcoded fragments were then amplified by 15 cycles of high-fidelity PCR and purified using agarose gel extraction. Libraries were pooled and sequenced on an Illumina NextSeq500 to a depth of ~10 million mapped reads.

value: Cell line

value: embryonic stem cells


title: MS39 macrophages stimulated with LPS+IFNg


title: H3f3a_WTA_H3f3b_AA_CUTRUN_H33


title: MGC Exp2-Bryo Rep 3

value: Bryostatin


title: H3f3a_WTA_H3f3b_AA_CUTRUN_K27ac


title: E14_ES_RA0h_rep5_nChIP.H3K27ac


title: H3f3a_WTA_H3f3b_AA_CUTRUN_K122ac


title: MGC Exp2-Bryo Rep 2


title: MS39 macrophages stimulated with IL4

value: MS patient


title: H3f3a_AA_H3f3b_WTA_clone2_CUTRUN_NoAb


title: E14_ES_RA72h_rep4_nChIP.Input


title: E14_ES_RA0h_rep5_nChIP.Input


title: MS39 macrophages stimulated with GMCSF


title: E14_ES_RA72h_rep4_nChIP.H3K27ac


title: H3f3a_AA_H3f3b_WTA_clone2_CUTRUN_H33


title: MS37 macrophages stimulated with LPS+IFNg


title: GBP5 -overexpressed MKN45 cells 1


title: MGC Exp2-Bryo Rep 1


title: CNS-Myeloid Vehicle Rep3

data_processing:
Raw fastq files were quantified using Salmon (1.4.0) against a decoy aware RefSeq GRCm39 transcriptome generated by concatenating the GRCm39 genome to the GRCm39 transcriptome.
Transcripts were then summarized to gene level counts using tximport
Assembly: GRCm39
Supplementary files format and content: Quant files generated by salmon for each sample including name of transcript, length, effective length, transcripts per million (tpm), and numreads (estimated count of reads that map to that transcript)

source_name: Mouse CNS

growth_protocol: C57BL/6J female mice were purchased from the Jackson Laboratory (000664). Mice were immunized at 8-12 weeks with 100μL sub-cutaneous emulsion and 250ng pertussis toxin IP on Day 0. Emulsion was prepared by mixing MOG35-55 peptide (2mg/ml) and CFA (8mg/ml heat-killed Mycobacterium tuberculosis H37 Ra in Incomplete Freund's Adjuvant). Mice were given another 250ng pertussis toxin IP on Day 2.

extract_protocol:
On day 35 mice were euthanized by isoflurane overdose and perfused with chilled PBS containing 5μg/mL actinomycin and 10μM triptolide. Brains and spinal cord were extracted and mechanically dissociated through a 16G needle five times in PBS with actinomycin and triptolide. Dissociated samples were spun 2 minutes at 200g and resuspended in papain digestion buffer with actinomycin and triptolide. Samples were enzymatically dissociated in papain for 10 minutes at 37c with slow rotation then triturated and passed over a 100μM filter. Samples were spun for 10 minutes then resuspended in PBS and Miltenyi Debris Removal Solution to remove myelin following manufacturer's protocol. Samples were then incubated with TruStain Fc Blocker (1:200) and Live/Dead Aqua (1:2000) for 20 minutes at RT. Cells were washed and stained in 0.5% BSA, 1mM EDTA with Ly6G eFluor 450 (1:250), CD11b PerCP-Cy5.5 (1:250), CD45 APCFire750 (1:250), and stained for 30 minutes at RT, then washed in 1mL and resuspended in 200μL of 0.5% BSA, 1mM EDTA and filtered. Cells were then sorted on Viable,CD45+,CD11b+,Ly6G- into RLT lysis buffer. RNA was then isolated using Qiagen RNEasy Plus Mini Kit
Unstranded poly-A mRNA Seq libraries were prepared from RNA isolated from sorted cells

treatment_protocol: Starting on Day 19 post immunization, mice were treated three days per week via IP injection with 35 nmol/kg bryo-1 or vehicle control (20% ethanol in PBS).

value: Mouse CNS

value: CD11b+ Sorted

value: Vehicle


title: MS40 macrophages stimulated with GMCSF


title: MS37 macrophages stimulated with GMCSF


title: E14_ES_RA48h_rep4_nChIP.Input

value: ESC


title: H3f3a_AA_H3f3b_WTA_clone2_CUTRUN_K122ac


title: CNS-Myeloid Vehicle Rep2


title: H3f3a_AA_H3f3b_WTA_clone2_CUTRUN_K27ac


title: MS37 macrophages stimulated with IL4


title: E14_ES_RA48h_rep4_nChIP.H3K27ac


title: MS35 macrophages stimulated with LPS+IFNg

value: treated with LPS+IFNg for 24 hours


title: CNS-Myeloid Vehicle Rep1


title: E14_ES_RA24h_rep4_nChIP.Input


title: MS35 macrophages stimulated with GMCSF


title: H3f3a_AA_H3f3b_WTA_clone1_CUTRUN_H33


title: MS35 macrophages stimulated with IL4


title: CNS-Myeloid Bryo Rep2


title: E14_ES_RA24h_rep4_nChIP.H3K27ac


title: MS34 macrophages stimulated with LPS+IFNg


title: E14_ES_RA0h_rep4_nChIP.Input


title: H3f3a_AA_H3f3b_WTA_clone1_CUTRUN_K122ac


title: MS34 macrophages stimulated with GMCSF


title: H3f3a_AA_H3f3b_WTA_clone1_CUTRUN_K27ac


title: E14_ES_RA72h_rep3_nChIP.H3K4me1

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
E14TC_ChIPK4me1_ra72h_merged.bw


title: H3f3a_WTWT_H3f3b_AA_CUTRUN_NoAb


title: E14_ES_RA72h_rep3_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra72h_H3K27me3_rmdup_MERGED_downsampled.bam.bw


title: LPS+TMP-1

city: Shanghai

first: janghong

last: bin

address: 507 Zhengmin Road, Yangpu District, Shanghai

institute: Department of Emergency Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The single-cell RNA-seq data were processed using the Cell Ranger 3.0.1 pipeline. FASTQs generated from Illumina sequencing output were aligned to the mouse genome, version mm10, using the STAR algorithm.Next, Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts.
This output was then imported into the Seurat (v3.0.2) R toolkit for quality control and downstream analysis of our single cell RNA-seq data. All functions were run with default parameters, unless specified otherwise. We excluded cells with fewer than 200 or more than 5000 detected genes, which each gene had to have at least one UMI aligned in at least three cells. The expression of mitochondria genes was calculated using PercentageFeatureSet function of the seurat package. To remove low activity cells, cells with more than 10 percent expression of mitochondria genes were excluded. The normalized data (NormalizeData function in Seurat package) was performed for extracting a subset of variable genes. Variable genes were identified while controlling for the strong relationship between variability and average expression. Next, we integrated data from different samples after identifying ‘anchors’ between datasets using FindIntegrationAnchors and IntegrateData in the Seurat package
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
Fresh lung tissues were resected from mice and stored in tissue preservation solution (Shanghai Biotechnology Corporation, 21903-10). Take the tissue into a sterile culture dish, add 5 mL of 1 X DPBS precooled at 4 ℃ for rinsing, repeat 1-2 times to remove residual tissue protective solution. Place the moistened tissue in a new 1.5 mL EP tube, add a small amount of digestive solution (500 μL), and use clean scissors to cut the tissue as much as possible. Transfer the shredded tissue to a 50 mL centrifuge tube containing 5 mL of digestive solution, and place it in a 37 ℃ water bath for shaking digestion. Gently shake the digestive solution well, do not shake vigorously. Collect the first sample after about 15 minutes of digestion, add enzyme solution again and digest for 20 minutes before collecting for the second time (if there are fewer cells and residual tissue after the first digestion, second digestion can be used). Pass the cell suspension collected twice through prewetted 40 μm filter membrane. Collect the filtrate into a new 50 mL centrifuge tube through M-cell sieve. Centrifuge all collected cell suspensions at 2000 rpm and room temperature for 10 minutes, then discard the supernatant. If there is a red color in the cell precipitate, it indicates that there are red blood cells in the precipitate. Add 2 mL of precooled 1 X red blood cell lysis solution to the cell precipitate, gently blow and mix, do not vortex, and incubate at room temperature for 3 minutes. After the red blood cell split time, centrifuge at 1500 rpm for 5 minutes at room temperature, discard the supernatant, add an appropriate amount of 1 X DPBS (including 2% FBS) to resuspend the cells, mix well, count, and observe the cell state and debris under a microscope
Dissociated cells were washed with 1 X DPBS containing 2% FBS. Cells were stained with 0.4% Trypan blue (Thermo Fisher, Cat. no. 14190144) to check the viability on Countess® II Automated Cell Counter (Thermo Fisher). 10× library preparation and sequencing Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in emulsion (GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 RevD). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.

value: lung

value: epithelial cells


title: H3f3a_WTWT_H3f3b_AA_CUTRUN_K122ac


title: LPS+TMP-3

description: 10x Genomics


title: MS34 macrophages stimulated with IL4


title: CNS-Myeloid Bryo Rep1


title: H3f3a_AA_H3f3b_WTA_clone1_CUTRUN_NoAb


title: E14_ES_RA6h_rep3_nChIP.H3K4me1

first: Angelika

last: Feldmann

address: Im Neuenheimer Feld 581

institute: German Cancer Research Center

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
E14TC_ChIPK4me1_ra6h_merged.bw


title: MS33 macrophages stimulated with LPS+IFNg


title: H3f3a_WTWT_H3f3b_AA_CUTRUN_K27ac


title: LPS+Dex-3

description: 10x Genomics


title: MS33 macrophages stimulated with GMCSF


title: E14_ES_RA0h_rep4_nChIP.H3K27ac


title: MS33 macrophages stimulated with IL4


title: MS32 macrophages stimulated with LPS+IFNg


title: E14_ES_RA4h_rep3_nChIP.H3K4me1

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
E14TC_ChIPK4me1_ra4h_merged.bw


title: H3f3a_AA_H3f3b_WTWT_CUTRUN_NoAb


title: H3f3a_WTWT_H3f3b_AA_CUTRUN_H33


title: E14_ES_RA6h_rep3_nChIP.H3K27ac

description:
K27ac_peaks_InBothReplicates.rds
E14_ra6h_H3K27ac_rmdup_MERGED_reps1to3_downsampled.bam.bw


title: LPS+Dex-1

description: 10x Genomics


title: LPS+Dex-2

description: 10x Genomics


title: LPS-3

description: 10x Genomics


title: LPS+TMP-2

description: 10x Genomics


title: H3f3a_AA_H3f3b_WTWT_CUTRUN_K27ac


title: E14_ES_RA6h_rep3_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra6h_H3K27me3_rmdup_MERGED_downsampled.bam.bw


title: H3f3a_AA_H3f3b_WTWT_CUTRUN_K122ac


title: LPS-1

description: 10x Genomics


title: WT2_CUTRUN_NoAb

value: Wildtype


title: MS32 macrophages stimulated with GMCSF


title: WT2_CUTRUN_H33


title: E14_ES_RA4h_rep3_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra4h_H3K27me3_rmdup_MERGED_downsampled.bam.bw


title: MS31  macrophages stimulated with GMCSF


title: MS32 macrophages stimulated with IL4


title: E14_ES_RA4h_rep3_nChIP.H3K27ac

description:
K27ac_peaks_InBothReplicates.rds
E14_ra4h_H3K27ac_rmdup_MERGED_reps1to3_downsampled.bam.bw


title: MS31  macrophages stimulated with LPS+IFNg


title: E14_ES_RA48h_rep3_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra48h_H3K27me3_rmdup_MERGED_downsampled.bam.bw


title: E14_ES_RA48h_rep3_nChIP.H3K4me1

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
E14TC_ChIPK4me1_ra48h_merged.bw


title: H3f3a_AA_H3f3b_WTWT_CUTRUN_H33


title: Con-3

description: 10x Genomics


title: Con-2

description: 10x Genomics


title: WT2_CUTRUN_K122ac


title: E14_ES_RA2h_rep3_nChIP.H3K4me1

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
E14TC_ChIPK4me1_ra2h_merged.bw


title: Con-1

description: 10x Genomics


title: E14_ES_RA2h_rep3_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra2h_H3K27me3_rmdup_MERGED_downsampled.bam.bw


title: WT1_CUTRUN_NoAb


title: MS30 macrophages stimulated with LPS+IFNg


title: MS30 macrophages stimulated with GMCSF


title: E14_ES_RA24h_rep3_nChIP.H3K4me1

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
E14TC_ChIPK4me1_ra24h_merged.bw


title: LPS-2

description: 10x Genomics


title: E14_ES_RA24h_rep3_nChIP.H3K27me3

description:
K27me3_peaks_reduced_all.rds
E14_ra24h_H3K27me3_rmdup_MERGED_downsampled.bam.bw


title: MS31 macrophages stimulated with IL4


title: MS30 macrophages stimulated with IL4


title: control E13.5, scRNA-seq

city: Vestec

first: Lukas

last: Valihrach

address: Prumyslova 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science

description:
10x Genomics
WT_E13

data_processing:
Reads were mapped against mouse genome GRCm38 and counted against annotation gencode_vM8 using STARSolo (v 2.7.3a). Nonfiltered UMI deduplicated count matrix loaded into R. Probable empty droplets were filtered out using DropletUtils package (v1.14.1) with parameter “lower = 1000” and all droplets with FDR lower than 0.001 were considered as cell containing. About 8,000-11,000 cells per sample were obtained.
Conversion of matrix into Seurat was done using Seurat package (v4.1.0) Data were normalized using SC Transformation including glmGamPoi method. UMAP plots were done with FindNeighbors using the first 41 PCs and FindClusters using resolution 0.3. Clusters were annotated manually using known markers and merged into broader cell types. This primary FACS sorted object contained 37,559 cells.
Assembly: mouse genome GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: craniofacial tissue

extract_protocol:
Embryos were harvested at stages E12.5 and E13.5 and genotyped. Brains were separated from dissected heads and craniofacial tissues were homogenized to single-cell suspension using TrypLE Express (Gibco). The highest efficiency was achieved by 3 rounds of incubation at 37 0C for 3 minutes, which was stopped in D-MEM with 10% FCS, followed by centrifugation at 1000 g for three minutes. Cells were resuspended in HBSS with 3% FCS before FACS. A total of 61% of cells were GFP-positive during FACS sorting. After cell sorting, 98.3% of cells were GFP-positive with the cell viability 99% .  For each condition, samples from 3 control embryonic heads (Wnt1-Cre2; Meis2 +/+; R26R-EYFPfl/+) and three conditional knockouts (Wnt1-Cre2; Meis2 fl/fl; R26R-EYFPfl/+) were pooled for scRNA-seq.
Single-cell libraries were prepared using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 according to the manufacturer’s protocol targeting 10,000 cells per sample. Briefly, GEM droplets with oligo-dT primers containing cell-barcode and UMI sequence were encapsulated together with cells. Cells were lysed inside droplets and RNA were transcribed into cDNA. The droplets were broken, and cDNA was amplified and fragmented. Adaptors were ligated to fragmented cDNA and amplified using Illumina specific adaptors with unique dual indices. Libraries were equimolarly pooled and sequenced using NovaSeq 6000 instrument with SP flow-cell in mode: read1 – 28 cycles, index1 – 10 cycles, index2 – 10 cycles, read2 – 90 cycles. About 250M reads per sample were obtained.

value: craniofacial tissue

value: cranial neural crest

value: Wnt1-Cre2; Meis2fl/+; R26R-EYFPfl/+

tag: developmental stage


title: WT1_CUTRUN_H33


title: Meis2 cKO E12.5, scRNA-seq

description:
10x Genomics
MUT_E12

value: Wnt1-Cre2; Meis2fl/fl; R26R-EYFPfl/+


title: WT1_CUTRUN_K122ac


title: WT1_CUTRUN_K27ac


title: E14_ES_RA0h_rep3_nChIP.H3K27me3

city: Heidelberg

description:
K27me3_peaks_reduced_all.rds
E14_ra0h_H3K27me3_rmdup_MERGED_downsampled.bam.bw


title: control E12.5, scRNA-seq

description:
10x Genomics
WT_E12


title: MS29 macrophages stimulated with LPS+IFNg

value: blood derived macrophages


title: E14_ES_RA0h_rep3_nChIP.H3K4me1

description:
K4me1_peaks_gap1kb_q0.01_b0.1_InBothReplicates_gap500.rds
E14TC_ChIPK4me1_ra0h_merged.bw


title: 3-month-old male bone marrow sorted SP cells

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the human genome hg19 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: bone marrow

extract_protocol:
For each age group, bone marrow (BM) was harvested from 2 to 4 mice of the same age group. BM cell side population (SP) staining with the PE-conjugated lineage antibody cocktail, the cells were washed twice with PBS-BSA buffer and resuspended in 500µl PBS. SP cells were immediately sorted into 400 µl DMEM containing 0.04%  BSA with an Aria SORP cell sorter, and at least 5000 SP cells were collected for each sample. The cell numbers and viability were confirmed by both automated cell counter and manual counting. The cells viability of all samples we processed were greater than 80%.
The libraries were prepared with SMART-Seq® Ultra Low Input RNA Kit for Sequencing – v4 (TaKaRa, Cat. 634888) according to the manufacturer's protocol. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit.  Sequencing was performed on Illumina HiSeq 2500 with the single read mode of 51cycle.

value: bone marrow

value: 3 month males


title: MS29 macrophages stimulated with IL4

value: treated with IL4 for 24hours


title: HBMEC cells, siControl (siCont 3)

city: Pessac

first: Claire

last: Peghaire

address: 1 avenue de Magellan

institute: University of Bordeaux-INSERM 1034

data_processing:
Quality of raw data was evaluated with FastQC.
Poor quality sequences were trimmed or removed with fastp tool, with default parameters, to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on hg38 reference genome and quantification with gencode v37 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with tpm gene counts for every gene and every sample

source_name: HBMEC

growth_protocol: HBMEC were maintained in complete Endothelial Cell Growth Medium-2 media (EGM-2) (Lonza) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA from HBMEC were isolated by using the Direct-zol™ RNA MicroPrep kit (R2062, Zymo Research).
1 ug of total RNA was used for the construction of sequencing libraries.(kit?)

treatment_protocol: Cells were transfected with a pool of two siRNA against TRIM47 (siTRIM47#1 and #2, denoted as siTRIM47) (15nM for each TRIM47 siRNA) using INTERFERin® transfection reagent (Polyplus). Negative control siRNA (Eurogentec) was used, which is denoted as siCont.

value: HBMEC

value: primary endothelial cells

value: WT

value: 72h after siRNA treatment


title: HBMEC cells, siControl (siCont 2)


title: Meis2 cKO E13.5, scRNA-seq

description:
10x Genomics
MUT_E13


title: MS28 macrophages stimulated with LPS+IFNg

value: MS patient


title: 3-month-old female bone marrow sorted SP cells

value: 3 month females


title: E14_ES_RA0h_rep3_nChIP.H3K27ac

description:
K27ac_peaks_InBothReplicates.rds
E14_ra0h_H3K27ac_rmdup_MERGED_reps1to3_downsampled.bam.bw

value: ESC


title: E14_ES_RA72h_rep2_nChIP.H3K27me3


title: HBMEC cells, siControl (siCont 1)


title: MS28 macrophages stimulated with GMCSF

value: treated with GMCSF for 24 hours


title: E14_ES_RA6h_rep2_nChIP.H3K4me1


title: 28-month-old female bone marrow sorted SP cells

data_processing:
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the mouse genome mm10 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

value: 28 month females


title: MS28 macrophages stimulated with IL4


title: 28-month females

data_processing:
bcl2fastq v2.20 (loaded by cellranger mkfastq (3.0.1)) software used for basecalling.
reads were aligned to refdata-cellranger-mm10-1.2.0 genome assembly using cellranger v5.0.0
Counting data of reference gene expression levels were generated by cellranger v5.0.0 (automatic identification of chemistry properties)
Assembly: mm10
Supplementary files format and content: Tab separated values; MatrixMarket

extract_protocol:
For each age group, bone marrow (BM) was harvested from 2 to 4 mice of the same age group. BM cell side population (SP) were stained with the PE-conjugated lineage antibody cocktail, the cells were washed twice with PBS-BSA buffer and resuspended in 500µl PBS. SP cells were immediately sorted into 400 µl DMEM containing 0.04%  BSA with an Aria SORP cell sorter, and at least 5000 SP cells were collected for each sample. The cell numbers and viability were confirmed by both automated cell counter and manual counting. The cells viability of all samples we processed were greater than 80%.
About 1000 cells were captured per sample on a 10xGenomics Chromium controller using a 10X V3.1 Single Cell 3’ Solution kit (10xGenomics, Chromium Next GEM Single Cell 3’ Regent kits V3.1, Cat. PN-1000268). All protocols were performed following the manufacture’s instruction. Final sequencing libraries were analyzed on a High Sensitivity DNA Chip (Agilent, Cat 5067-4626) to determine the library size. The library concentration was determined with a Qubit high Sensitivity DNA assay Kit (Thermo, Cat. Q32854). The libraries were sequenced with the paired end setting of 28 cycles of read1, 101 cycles of R2, 8 cycles of index i7 and 8 cycles of index i5 read on Illumina NovaSeq 6000 platform with S4 Reagent kit v1.5 (Illumina, Cat 20028313) at TGEN with a depth of 100K - 135K reads per cell.


title: HBMEC cells, siTRIM47 (siTRIM47 3)

value: TRIM47 knockdown


title: HBMEC cells, siTRIM47 (siTRIM47 2)


title: CNS-Myeloid Bryo Rep3

value: Mouse CNS

value: CD11b+ Sorted

value: Bryostatin


title: E14_ES_RA6h_rep2_nChIP.H3K27ac


title: MS27 macrophages stimulated with LPS+IFNg

value: blood derived macrophages

value: treated with LPS+IFNg for 24 hours


title: 3-month females

value: bone marrow


title: E14_ES_RA4h_rep2_nChIP.H3K4me1


title: MS27 macrophages stimulated with GMCSF


title: HBMEC cells, siTRIM47 (siTRIM47 1)