title: Non-pregnant, COVID severe, patient 213 (ADT)

library_source: other

data_processing:
Alignment with CellRanger (v6.0.1), genetic demultiplexing using Souporcell (v2.0), count matrices were aggregated using Pegasus (v1.7.1, python).
ADT count matrices were CLR normalized.
Assembly: GRCh38
Supplementary files format and content: ADT files contain sample info and n_counts wich is the total UMI counts per cell
Supplementary files format and content: B_Plasma_ADT.h5ad.tar.gz -  include ADT data of B cells from all samples. This object has clustering information (based on the GEX B cell data), PCs, UMAP and differential analysis info.
Supplementary files format and content: CD4T_ADT.h5ad.tar.gz - include ADT data of CD4 T cells from all samples. This object has clustering information (based on the GEX CD4 T cell data), PCs, UMAP and differential analysis info.
Supplementary files format and content: CD8T_ADT.h5ad.tar.gz - include ADT data of CD8 T cells from all samples. This object has clustering information (based on the GEX CD8 T cell data), PCs, UMAP and differential analysis info.
Supplementary files format and content: MNP_ADT.h5ad.tar.gz - include ADT data of MNP cells from all samples. This object has clustering information (based on the GEX MNP cell data), PCs, UMAP and differential analysis info.
Supplementary files format and content: TotalSeqC_Annotated.xlsx - includes information about the antibodies used for CITEseq.
Library strategy: CITE-seq

molecule: protein

tag: pregnancy status

value: NonPregnant

value: Positive


title: END [330-DD}

status: Public on Oct 30 2024

type: RNA

city: Brescia

first: Stefano

last: Calza

state: Brescia

address: Viale Europa 11

department: DMMT

country: Italy

institute: University of Brescia

description:
Test
330-DD

data_processing: Ct target values were normalized using reference genes values. FC were computed using a right-censored regression on (-Delta Ct) values to account for limit of detection. Results are reported as Fold Changes

molecule: total RNA

organism: Homo sapiens

source_name: serum

extract_protocol: Total RNA was extracted from 400 ul of serum with the miRNeasy Serum/Plasma advanced Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. RNA was eluted in 22 ul of H2O and quantified using the Qubit microRNA assay kit (Thermo Fisher Scientific, Waltham, MA, USA) by the Qubit 4 Fluorometer (Thermo Fisher Scientific). cDNA templates were prepared using the TaqMan Advanced miRNA cDNA Synthesis Kit (Thermo Fisher Scientific) according to the manufacturer's guidelines, starting from 10 ng of RNA.   The miR-Amp reaction products were thawed on ice and then diluted 1:20 in 0.1x TE buffer pH 8 (10 mM Tris, 1 mM EDTA, Thermo Fisher Scientific). Each RT-qPCR mix was prepared by combining equal quantities of 1:20 diluted sample and 2x TaqMan OpenArray Real-Time PCR Master Mix (Thermo Fisher Scientific) in a final volume of 60 μl. Each sample mix was transferred in 16 wells (6 μl/well) of an OpenArray 384-well Sample Plate (Thermo Fisher Scientific) and then automatically loaded in a Fixed-content TaqMan OpenArray Plate containing the Human Advanced miRNA panel (Cat. N. A32710, Thermo Fisher Scientific) by the QuantStudio 12K Flex Accufill System (Thermo Fisher Scientific). Each open array plate was loaded with three samples and run on the QuantStudio12K Flex Real-Time PCR System (Thermo Fisher Scientific). Quantification cycle (Cq) was automatically calculated using the ThermoFisher Cloud Software (Thermo Fisher Scientific Relative Quantification Analysis Module, available online at https://www.thermofisher.com/de/de/home/cloud.html). Only target values meeting all the following criteria were considered for subsequent analyses: Amplification Score >1, Cq confidence > 0.8, Cq ≥6. MiR-16-5p, spotted 16 times in each sub-array, was used as a quality control of the OpenArray procedure. Each serum sample was evaluated for the presence of hemolysis. The ratio between the expression levels of miR-451a (expressed in red blood cell) and miR-23a-3p (not affected by hemolysis) was calculated and samples with a delta Cq < 8 were considered acceptable. Samples with hemolysis were excluded from the study.

tag: disease

value: Deep Infiltrating Endometriosis


title: Non-pregnant, COVID severe, patient 223 (ADT)

type: SRA

city: Boston

first: Alexandra-Chloe

last: Villani

state: MA

country: USA

institute: MGH, Harvard

description: An AnnData object that contains both normalized counts and raw counts of this sample, in the raw layer.

source_name: PBMC

extract_protocol:
Cryopreserved PBMC samples. Full details are in the manuscript.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: PBMC

tag: covid infection_status

tag: covid severity_status

value: Severe

tag: Sex

value: Female


title: Non-pregnant, COVID severe, patient 1 (ADT)


title: END [329-MS}

description:
Test
329-MS


title: Non-pregnant, COVID severe, patient 191 (ADT)


title: CTR [365-CR}

description:
Control
365-CR

value: ovarian cystadenoma


title: CTR [314-SS}

description:
Control
314-SS

value: ovarian fibrothecoma


title: LPS_activated_THP-1_macrophages stimulated with_Fh-ES_rep6

city: Warsaw

first: Piotr

last: Bąska

state: Mazowieckie

address: Ciszewskiego 8

department: Department of Preclinical Sciences

country: Poland

institute: Warsaw University of Life Sciences WULS – SGGW

hyb_protocol: Each Cyanine-3-labeled RNA samples were hybridized onto microarray for 20h at 55°C in hybridization rotating oven (Agilent Technologies).

scan_protocol: Acquisition and analysis of hybridization intensities were performed using Agilent DNA Microarray Scanner G2505C. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: The scanned images were analyzed with Feature Extraction Software (version 10.10.1.1) using default parameters (protocol miRNA_1010_Sep10 and Grid: 046066_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: THP-1 cell line

label_protocol: One hundred ng of total RNA with miRNA Spike-In (microRNA Spike-In Kit, Agilent Technologies) added were taken for labeling reaction. miRNA was labeled with Cyanine 3-pCp using the Complete Labeling and Hyb Kit (Agilent Technologies) according to the manufacturer’s procedure. The labeled RNA samples were purified on Micro Bio-Spin 6 columns to remove DMSO and unbound Cyanine 3-pCp.

growth_protocol: The monocytes were cultured at 37°C with 5% CO2 in RPMI 1640 supplemented with 10% FBS, 100 U/ml penicillin, and 100 µg/ml streptomycin. Once the cells reached the appropriate number, they were seeded at 5E5 cells per a well in a 24-well cell culture plate and differentiated into macrophages for 48 hours using PMA (30 ng/ml).

extract_protocol: Total RNA, which also included miRNA, was isolated using miRNeasy Mini Kit (Qiagen) according to the manufacturer’s procedure. RNA quality was determined using Agilent 2100 Bioanalyzer (USA) and RNA 6000 Nano Kit (Agilent, Germany). All RNA samples taken for microarray analysis were of high quality (RIN was  between 9.5 and 10.0).

treatment_protocol: The cells were rinsed 3 × times using the medium followed by treatment with either LPS (100 ng/ml) for control cells or LPS (100 ng/ml) and Fh-ES (7 µg/ml) for experimental cells. Fh-ES concentration was used to stimulate THP-1 macrophages, resulting in an enrichment of the medium with endotoxin to a final concentration of 0.06 EU/ml, what fills the strict FDA recommendation for endotoxin level even for solutions that have a contact with cerebrospinal fluid

tag: cell type

value: acute monocytic leukemia

tag: treatment


title: LPS_activated_THP-1_macrophages stimulated with_Fh-ES_rep8


title: CD40KO-Control

city: Yokohama

first: Taishin

last: Akiyama

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were done using the Cell Ranger software v5.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Thymus

extract_protocol:
The thymus of 6-week-old mice was dissected and minced with a razor. Thymic fragments were pipetted up and down in 1 mL of Hepes-RPMI (Wako). The supernatant was used as lymphocytes, and the remaining fragments were digested by incubation in RPMI 1640 medium containing 0.05 U/mL Liberase (Roche) and 0.01% w/v DNase I (Sigma-Aldrich) at 37°C for 12 min x3 times after each incubation and Pipetting. Reactions were stopped by adding an equal volume of FACS buffer containing 1 mM ethylenediaminetetraacetic acid and washing with FACS buffer. Total cell count was calculated as the sum of lymphocytes and digested cells.
Single-cell emulsions were obtained using a 10x Genomics Controller and a v2 Library and Gel Bead kit (10X Genomics). RNA-sequencing libraries were prepared according to the 10x 3′ v2 kit protocol.

value: Thymus

value: Thymic epithelial cells

tag: strain

tag: age


title: LPS_activated_THP-1_macrophages stimulated with_Fh-ES_rep7


title: LPS_activated_THP-1_macrophages stimulated with_Fh-ES_rep5


title: LPS_activated_THP-1_macrophages stimulated with_Fh-ES_rep3


title: Organoids P53KO vs P53KO-Wnt-Independent

city: Berlin

first: Michael

last: Sigal

address: Augustenburger Platz 1

department: Dept. Hepatology and Gastroenterology

country: Germany

institute: Charité Universitätsmedizin

hyb_protocol: After precipitation, purification, and quantification, 0.75 g of each labeled cRNA was fragmented and hybridized to multipack microarrays (Agilent design 074809; SurePrint G3 Mouse GE v2 8x60K) according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed at 3-m resolution using a G2565CA high-resolution laser microarray scanner (Agilent Technologies). Microarray image data were processed with Image Analysis/Feature Extraction software G2567AA vA.11.5.1.1 (Agilent Technologies) using default settings and the GE2_1105_Oct12 extraction protocol.

data_processing: Data was processed in R using package limma.

source_name: KOWI rep1

label_protocol: Total RNA was amplified and labeled with a dual-color Quick-Amp labeling kit (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer and labeled with cyanine 3-CTP or cyanine 5-CTP.

growth_protocol: Axin2CreERT2 mice were crossed with Trp53 fl/fl mice and kept under SPF conditions with drinking water and standard chow ad libitum. Males were used for all experiments. For colon organoid preparation, the tissue cut into 5mm pieces was washed three times in cold phosphate-buffered saline (PBS) (Gibco), followed by incubation for 20 min in 10 mM EDTA (Invitrogen)/PBS supplemented with 0.5 mM dithiothreitol (DTT) (Sigma) at 37 °C. Buffer was changed to cold PBS, and the tube was vigorously shaken for 2 minutes to isolate crypts. After two times washing in PBS, the supernatant containing the crypts was collected and centrifuged at 400g for 5 min at 4 °C. The number of colonic crypts was counted, and 300 crypts per 10µl Cultrex (Cultrex Reduced Growth Factor Basement Membrane Extract, Type R1, R&D Systems) were resuspended and seeded in droplets. Cultrex was polymerized at 37 °C for 20 min and then colon medium was added: Advanced Dulbecco’s Modified Eagle’s Medium (DMEM)/F12 (Gibco) supplemented with 10 mM HEPES (Gibco), 2 mM GlutaMAX (Gibco), 100 U/ml penicillin/streptomycin (Gibco), 1.25 mM N-acetylcysteine (Sigma), 1x B-27 (Gibco), 1x N2 (Gibco), 50 ng/ml mouse epidermal growth factor (EGF) (Invitrogen), and 0.5 μM A83-01 (TGFβ–inhibitor, Sigma), 0.328 nM surrogate Wnt (sWnt, U-Protein Express), 3 μM CHIR-99021 (Chir, Selleckchem), 25% R-spondin 1 conditioned medium, and 100 ng/ml mouse noggin (PeproTech) for regeneration inducing +WM medium condition. For –WM medium, sWnt and Chir were not added. 10 μM Y-27632 (ROCK-inhibitor, Hoelzel) was added after the initial seeding and after passaging until the first medium change. Organoids were incubated at 37 °C, 5% CO2 in a humidified incubator. The medium was replaced every 2-3 days. Every 4-6 days, the organoids were passaged as single cells generated by a 7-min incubation in TryplE (Gibco) at 37 °C and shearing with a 100 Sterican 27G canulla (Braun) and syringe (Braun). 6000 single cells were seeded per 10 μl Cultrex. The organoids were cultured for at least one passage before conducting experiments.

extract_protocol: For tissue RNA analysis, mice were sacrificed 2 months after DSS. RNA from organoids or tissue was extracted with the Nucleospin RNA Kit (Machery Nagel). Quality control and quantification of total RNA was assessed using a 2100 bioanalyzer (Agilent Technologies) and a NanoDrop 1000 UV-Vis spectrophotometer (Kisker)

treatment_protocol: For knock-out induction in mice, Tamoxifen was injected intraperitoneally. 2% (w/v) dextran sodium sulfate (MP Biomedical, 36,000–50,000 MW) was dissolved in tap water and provided to mice for 5-7 days. For recovery experiments, DSS was replaced by normal drinking water. To generate Trp53 KO organoids, 800nM 4OH-tamoxifen (Sigma) was added to cultures from VillinCreERT2xTrp53fl/fl mice for 2 days before splitting. Trp53 KO organoids were selected by treating cultures with 10mM Nutlin-3A for several passages until like-wise treated WT organoids were depleted and genotyping confirmed pure KO.

tag: replicate

tag: genotype

value: KOWI

value: colon organoids

value: -Wnt-Chir medium

source_name: KO rep2

value: KO

value: Full medium


title: Organoids WT vs P53KO-Wnt-independent

source_name: wt rep2

value: WT


title: END [309-FM}

description:
Test
309-FM


title: Organoids P53KO-Wnt-Independent vs P53KO

source_name: KO rep1

source_name: KOWI rep2


title: LPS_activated_THP-1_macrophages stimulated with_Fh-ES_rep4


title: CTR [305-ON}

description:
Control
305-ON


title: Non-pregnant, COVID severe, patient 50 (ADT)

value: NonPregnant


title: Non-pregnant, COVID severe, patient 100 (ADT)

value: Positive


title: Non-pregnant, COVID severe, patient 77 (ADT)


title: Non-pregnant, COVID severe, patient 321 (ADT)


title: CTR [322-MV}

description:
Control
322-MV

value: no gynecological abnormality


title: END [300-GS}

description:
Test
300-GS

value: Deep Infiltrating Endometriosis


title: Organoids P53KO-Wnt-independent vs WT

source_name: wt rep1


title: LPS_activated_THP-1_macrophages stimulated with_Fh-ES_rep2


title: Non-pregnant, COVID severe, patient 382 (ADT)

value: PBMC

value: Severe


title: LPS_activated_THP-1_macrophages_rep8


title: END [299-BE}

description:
Test
299-BE

value: endometrioma


title: LPS_activated_THP-1_macrophages_rep6


title: LPS_activated_THP-1_macrophages_rep7


title: Non-pregnant, COVID severe, patient 182 (ADT)

value: Female


title: Organoids P53KO vs WT


title: Tissue WT_vs_KO_rep2, 2 month regeneration after DSS

source_name: P53 KO rep1

value: colon tissue

source_name: P53 WT rep 2


title: Organoids WT vs. P53KO


title: Tissue WT_vs_KO_rep1, 2 month regeneration after DSS

source_name: P53 KO rep 1

source_name: P53_WT rep 1


title: Non-pregnant, COVID asymptomatic, patient 47 (ADT)

value: Asymptomatic


title: W22, Fe resupply, shoots, biol rep 2

city: Amherst

first: Elsbeth

last: Walker

address: 611 North Pleasant Street

department: Biology

institute: University of Massachusetts Amherst

library_source: transcriptomic

data_processing:
The adapter sequences and low-quality reads were removed using Trim Galore
Trimmed reads were aligned to the maize W22v2 genome using the HISAT2 aligner
Transcript assembly and quantification was performed using StringTie
Differential gene expression analysis was performed using DESeq2
Assembly: Zm-W22-REFERENCE-NRGENE-2.0
Supplementary files format and content: raw counts, DESeq2 results

organism: Zea mays

source_name: Shoots

growth_protocol: Wild-type plants (W22) were grown in hydroponic culture for 12 days and then switched to +Fe or −Fe for 3 days to induce an iron deficiency environment. After the 3 days, one set of −Fe plants was resupplied with hydroponic solution containing 0.1mM FeSO4-EDTA (±Fe plants) while the +Fe and −Fe plants received new solution.  After 24 hours, the roots and shoots were sampled separately and immediately frozen in liquid nitrogen. Three biological replicates were used for each condition.

extract_protocol:
The total RNA from roots and shoots was isolated using the Direct-zol RNA MiniPrep Kit (Zymo Research) with DNase I treatment according to the manufacturer’s instructions.
Library preparation was performed by Novogene

value: Shoots

value: Fe resupply


title: CTR [287-TF}

description:
Control
287-TF

value: ovarian cystadenoma


title: W22, Fe resupply, shoots, biol rep 3


title: Non-pregnant, COVID severe, patient 325 (ADT)


title: LPS_activated_THP-1_macrophages_rep3

value: acute monocytic leukemia


title: CTR [295-ZM}

description:
Control
295-ZM

value: serous ovarian cyst


title: CTR [293-SL}

description:
Control
293-SL

value: ovarian fibrothecoma


title: LPS_activated_THP-1_macrophages_rep5


title: END [292-BM}

description:
Test
292-BM


title: W22, Fe resupply, shoots, biol rep 1


title: Non-pregnant, COVID asymptomatic, patient 103 (ADT)


title: END [283VM}

description:
Test
283VM


title: C. elegans, E. ulmoides extract, biol rep 5

first: Nadine

last: Saul

address: Philippstr. 13, House 22

department: Department of Biology

institute: Humboldt-Universitaet zu Berlin

data_processing:
Raw reads filtering: Raw reads are filtered to remove reads with adapter contamination or reads with low quality. Only clean reads were used in the downstream analyses.  The filtering process is as follows: (1) Discard reads with adaptor contamination. (2) Discard reads when uncertain nucleotides constitute more than 10% of either read (N > 10%). (3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50% of the read.
Mapping To Reference Genome Alignments were performed with HISAT2 to the reference.
The analysis of the read counts data was conducted with the R-based tool DEBrowser, using the Bioconductor package eEdgeR for the differential expression analysis with a trimmed mean of M-values (TMM) normalization and filtering out genes, whose counts per million (CPM) was lower than one. The genes/transcripts with a p-value (adjusted by DEBrowser with the Benjamini Hochberg procedure) below 0.05 and fold change higher than 1.5 or lower than 0.667 were considered differentially expressed genes (DEGs). The DEG data were further analyzed using the online tool DAVID (Database for Annotation, Visualization and Integrated Discovery), to create a list of Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways
Assembly: Genome assembly WBcel235
Supplementary files format and content: The excel file Matrix_FPKM.xlsx contains all FPKM values. The gene identifiers are listed one per row according to the genome assembly WBcel235 and were annotaded according to Wormbase. The samples are displayed in columns.

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: The wild-type N2 Bristol C. elegans strain was maintained and cultured on NGM agar plates seeded with the E. coli strain OP50 as a food source. Synchronized worms were regularly generated by treating young adults with a 3% sodium hypochlorite solution until eggs were isolated. The obtained eggs were incubated with overnight shaking in M9 buffer, and the hatched L1 larvae were transferred to new NGM plates the following day. Two days later, the nematodes reached the fourth larval stage (L4) and were transferred to the respective treatment plates.

extract_protocol:
On the 12th day of adulthood, the worms were collected and transferred to lysis tubes (around 3000-4000 worms per tube) with steel beads and stored at -80 °C. The RNA extraction proceeded according to the kit's manufacturer (innuSPEED Tissue RNA Kit by Analytik Jena Germany). The Turbo DNA-free kit from Thermo Fischer Scientific (Germany) was used at the end to degrade any possible DNA within the samples. The RNA content of each sample was measured with a Nanodrop and the condition of the RNA was checked with gel electrophoresis.
The preparation of RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Beijing, China). Briefly, a total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform, and paired-end reads were generated.

treatment_protocol: The dried TCM plants (20 g each) Cuscuta chinensis and Eucommia ulmoides were extracted with a mixture of t-butyl methyl ether, methanol (50:50, volume 75 mL) as well as with 100% methanol (volume 75 mL). The extracts were dissolved in Dimethyl sulfoxide (DMSO) at a stock concentration of 60 mg/mL and then added to the NGM agar plates as well as the feeding bacterial strains at a final concentration of 30 μg/mL; DMSO (0.05%) was used in the control feeding bacteria and NGM agar. Synchronized, untreated L4 larvae were transferred to the NGM agar plates that had been previously prepared with 2 mg/mL carbenicillin. Finally, 100 µM 5-fluorodeoxyuridine (FUdR) was added.  The nematodes were incubated at 22 °C until the 12th day of adulthood.

tag: time

value: Day 12

value: whole animal

value: WT

value: 30 ug/mL E.ulmoides extract and DMSO(0.05%)


title: W22, -Fe, shoots, biol rep 2

value: Fe deficiency


title: LPS_activated_THP-1_macrophages stimulated with_Fh-ES_rep1


title: Tisseu KO_vs_WT_rep2, 2 month regeneration after DSS

source_name: P53_KO rep 2

value: KO


title: W22, -Fe, shoots, biol rep 1


title: Non-pregnant, COVID asymptomatic, patient 94 (ADT)

value: PBMC

value: NonPregnant

value: Positive


title: Non-pregnant, COVID asymptomatic, patient 31 (ADT)

value: Female


title: W22, -Fe, shoots, biol rep 3


title: END [272DM}

description:
Test
272DM

source_name: serum

value: endometrioma


title: Non-pregnant, COVID asymptomatic, patient 350 (ADT)

source_name: PBMC

value: Asymptomatic


title: END [275-SS}

description:
Test
275-SS

value: Deep Infiltrating Endometriosis


title: LPS_activated_THP-1_macrophages_rep2

source_name: THP-1 cell line


title: CTR [285-TR}

description:
Control
285-TR

value: leiomyoma


title: Pregnant, COVID severe, patient 101607-SEV (ADT)

value: Pregnant

value: Severe


title: C. elegans, E. ulmoides extract, biol rep 4


title: END [279PF}

description:
Test
279PF


title: LPS_activated_THP-1_macrophages_rep4

value: acute monocytic leukemia


title: Tissue KO_vs_WT_rep1, 2 month regeneration after DSS

value: colon tissue

source_name: P53_KO rep 1


title: LPS_activated_THP-1_macrophages_rep1


title: C. elegans, E. ulmoides extract, biol rep 1

value: Day 12

value: whole animal


title: END [267PM}

description:
Test
267PM


title: C. elegans, E. ulmoides extract, biol rep 2

value: WT

value: 30 ug/mL E.ulmoides extract and DMSO(0.05%)


title: W22, +Fe, shoots, biol rep 3

value: Shoots

value: Control


title: END [264FS}

description:
Test
264FS


title: C. elegans, E. ulmoides extract, biol rep 3


title: W22, +Fe, shoots, biol rep 1


title: W22, +Fe, shoots, biol rep 2


title: Pregnant, COVID asymptomatic, patient 105199-ASX (ADT)

value: PBMC


title: Pregnant, COVID negative, patient 729106-CTRL (ADT)

value: Negative


title: END [271-ZG}

description:
Test
271-ZG


title: Pregnant, COVID negative, patient 644394-CTRL (ADT)

value: Female


title: W22, Fe resupply, roots, biol rep 3

source_name: Roots

value: Roots

value: Fe resupply


title: Pregnant, COVID severe, patient 915348-SEV (ADT)

value: Positive


title: C. elegans, C.chinensis extract, biol rep 3

value: 30 ug/mL C.chinensis extract and DMSO(0.05%)


title: Pregnant, COVID asymptomatic, patient 803763-ASX (ADT)

value: Pregnant

value: Asymptomatic


title: C. elegans, C.chinensis extract, biol rep 2


title: Pregnant, COVID asymptomatic, patient 324058-ASX (ADT)


title: W22, Fe resupply, roots, biol rep 2


title: END [254-FM}

description:
Test
254-FM

value: Deep Infiltrating Endometriosis


title: W22, Fe resupply, roots, biol rep 1


title: W22, -Fe, roots, biol rep 3

value: Fe deficiency


title: END [229SC}

description:
Test
229SC


title: C. elegans, C.chinensis extract, biol rep 1

value: Day 12


title: END [220TP}

description:
Test
220TP

value: endometrioma


title: Pregnant, COVID severe, patient 705385-SEV (ADT)

value: Severe


title: C. elegans, DMSO(Control), biol rep 5

value: whole animal

value: WT


title: C. elegans, C.chinensis extract, biol rep 5


title: C. elegans, DMSO(Control), biol rep 4


title: CTR [213-CM}

description:
Control
213-CM

value: no gynecological abnormality


title: W22, -Fe, roots, biol rep 1


title: C. elegans, C.chinensis extract, biol rep 4


title: hPO1807

city: Milano

first: Alessandro

last: Cherubini

address: via F. Sforza 35

institute: IRCCS Ca' Granda Ospedale Maggiore Policlinico

data_processing:
Barcodes corresponding to real living cells were detected and extracted by counting the number of Unique Molecular Identifiers associated to each cell barcode (UMItool v.0.5.4)
Reads were aligned to the reference human genome hg38 (STAR version 2.5.3a)
Uniquely mapped reads were assigned to the annotated genomic features (Gencode genome version: GRCh38, basic annotation, release 28)
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: human pancreatic organoid (hPO)

growth_protocol: Theorganoids were cultured in complete composed of AdDMEM/F12 medium supplemented with 10 mM HEPES, 2 mM L-Glutamine, 1% B27 without vitamin A, 1% N2 supplement xeno-free, 1 mM N-acetyl-L-cysteine, 1μg/ml human recombinant protein RSPO1, 0.1μg/ml human Noggin recombinant protein, 50 ng/ml human EGF, 10 nM [Leu15]-Gastrin I Human, 100 ng/ml FGF10, 10 mM Nicotinamide, 10 μM Forskolin, 0.5 μM A83-01 and 3 μM Prostaglandin E2.

extract_protocol:
Organoids were dissociated using TrypLE Select. Then, cells were further dispersed by gentle pipetting, filtered through a 30 μm cell strainer, counted by hemocytometer and resuspended in PBS + 0.01% BSA. Single cell RNA-seq that was performed using Drop-seq technology as described in Macosko et al.
Libraries were prepared from 600 pg of of cDNA using the Nextera XT DNA sample prep kit according manufacturer’s instruction using a custom Read 1 primer (GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC, IDT) and were sequenced on a NovaSeq 6000 machine (Illumina).

tag: tissue source

value: healthy islet-depleted tissue

tag: tissue/cell type

value: pancreatic organoids


title: END [205FA}

description:
Test
205FA


title: C. elegans, DMSO(Control), biol rep 3


title: END [211RL}

description:
Test
211RL


title: CTR [239-MF}

description:
Control
239-MF

value: ovarian cystadenoma


title: W22, +Fe, roots, biol rep 2

value: Roots

value: Control


title: W22, +Fe, roots, biol rep 3


title: hPO1806


title: END [202BA}

description:
Test
202BA


title: C. elegans, DMSO(Control), biol rep 1


title: hPO1805


title: 7736_ADR_sh_Jun

status: Public on Oct 29 2024

first: Paulina

last: Richter-Pechanska

address: Augustenburgerplatz 1

institute: Charite

data_processing:
Bcl2fastq version: 2.20.0.422; Sequencing software: HCS HD 3.4.0.38; Basecall software: RTA 2.7.7
Raw reads trimming using trimgalore (v0.6.4_dev). Quality check of raw and trimmed reads with FastQC (v0.11.9).
Transcript quantification using salmon (v1.3.0) (Patro et al.).
Index used was built from Mus_musculus.GRCm38.cdna.all.fa.gz from Ensembl.
Transcript import using tximeta (v1.6.3) (Love et al.).
Differential expression analysis carried out by DESeq2 (v1.28.1).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample

source_name: primary lymphoma cells

growth_protocol: Primary Emu-myc lymphoma cells were cultivated in B-cell medium (DMEM and IMDM in 1:1 ratio, 10%FBS, 2mM L-glutamine, 25µM beta-mercaptoethanol, 100U/ml penicilin/streptamycin) on gamma-irradiated (24Gy) NIH 3T3 cells as feeder cells and transduced with a MSCV-bcl2 vector.

extract_protocol:
ADR treated lymphomas were purified from dead cells using a Dead Cell Removal Kit (Miltenyi). Total RNA from untreated or 5 days ADR treated Myc;Bcl2:shX lymphomas was prepared using an RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer's instruction.
RNA libraries for RNA-seq were prepared by DKFZ sequencing core facility (Heidelberg, Germany) according to Illumina's TruSeq Stranded RNA kit instructions.

treatment_protocol: Myc;Bcl2 cells were further retrovirally transduced by respective fluorescence-protein co-expressing shRNA vectors (shCtrl, shSpi1, shCebpb, shJun) and FACS sorted for GFP-positive cells. The resulting Myc;Bcl2;shX cells were either left untreated or treated in vitro with 0.05µg/ml Adriamycin for 5 days.

value: primary lymphoma cells

value: Emicro-myc

tag: modification

tag: lymphoma id

tag: short hairpin_rna

value: ADR day 5


title: W22, -Fe, roots, biol rep 2


title: W22, +Fe, roots, biol rep 1


title: 7736_ADR_sh_Cebpb


title: END [201DF}

description:
Test
201DF

tag: disease


title: 7736_UT_sh_Jun

value: untreated


title: Pregnant, COVID negative, patient OB7-CTRL (ADT)

tag: tissue

value: PBMC

tag: pregnancy status

value: Pregnant

value: Negative

value: Female


title: 7736_ADR_sh_Ctrl


title: 7736_UT_sh_Spi1


title: 7736_UT_sh_Ctrl


title: 4936_ADR_sh_Jun


title: 4936_ADR_sh_Cebpb


title: C. elegans, DMSO(Control), biol rep 2

value: Day 12


title: 4936_UT_sh_Jun


title: 4936_ADR_sh_Ctrl


title: 4936_ADR_sh_Spi1


title: 9458_ADR_sh_Cebpb

value: Suv39h1 WT


title: 4936_UT_sh_Cebpb


title: 4936_UT_sh_Spi1


title: 4936_UT_sh_Ctrl


title: 9458_ADR_sh_Spi1


title: 9458_UT_sh_Spi1


title: 7069_ADR_sh_Ctrl


title: 9458_ADR_sh_Ctrl


title: 7736_UT_sh_Cebpb


title: 9458_UT_sh_Cebpb


title: 7069_ADR_sh_Jun


title: 7736_ADR_sh_Spi1


title: 6614_ADR_sh_Cebpb


title: 6614_ADR_sh_Jun


title: 7069_UT_sh_Jun


title: 6614_ADR_sh_Spi1


title: 6614_ADR_sh_Ctrl


title: 7069_UT_sh_Ctrl


title: 6614_UT_sh_Cebpb


title: 6054_ADR_sh_Jun_biolrepl_2


title: 6614_UT_sh_Ctrl


title: 6054_ADR_sh_Ctrl_biolrepl_2


title: 6614_UT_sh_Jun


title: 6054_ADR_sh_Cebpb


title: 6054_ADR_sh_Spi1


title: 6054_ADR_sh_Ctrl


title: 9458_UT_sh_Ctrl


title: 6054_UT_sh_Jun


title: 6054_UT_sh_Cebpb


title: 6054_UT_sh_Spi1


title: 2801_ADR_sh_Jun


title: 6614_UT_sh_Spi1


title: 6054_UT_sh_Ctrl


title: 2801_ADR_sh_Cebpb


title: 2801_ADR_sh_Spi1


title: 2801_UT_sh_Jun


title: 2801_ADR_sh_Ctrl


title: vehicle, late, replicate 3

city: Heidelberg

first: Marc

last: Zapatka

state: Select State

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

data_processing:
Raw sequencing reads from RNA sequencing were aligned with STAR (2.5.3a) and reads were counted per gene using featurecounts (1.5.3).
Assembly: GRCm38
Supplementary files format and content: bam Aligned reads
Supplementary files format and content: counts*.txt Featurecounts

molecule: polyA RNA

source_name: spleen

extract_protocol:
Total ribonucleic acid (RNA) was extracted using the RNeasy® Micro kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol. RNA was eluted in RNase free water and stored at -80°C. RNA concentrations were determined using the NanoDrop spectrophotometer.  For simultaneous isolation of total RNA and genomic DNA (and protein) for submission to RNA  sequencing and whole exome sequencing of CD5+CD19+ FACS-sorted cell the AllPrep DNA/RNA/Protein Mini Kit was used according to manufacturer’s protocol.
Library preparation of RNA was performed according to the Illumina TruSeq Stranded protocol on a HiSeq 2000 v4 sequencer, paired-end 125 base pairs with five samples per lane.

value: spleen

tag: timepoint

value: late

value: vehicle


title: 2801_UT_sh_Cebpb


title: 2801_UT_sh_Spi1


title: vehicle, early, replicate 4

value: early


title: vehicle, early, replicate 3


title: vehicle, late, replicate 2


title: vehicle, late, replicate 4


title: ibrutinib, late, replicate 3

value: ibrutinib


title: vehicle, late, replicate 1


title: ibrutinib, late, replicate 2


title: vehicle, early, replicate 2


title: vehicle, early, replicate 1


title: ibrutinib, early, replicate 3


title: ibrutinib, late, replicate 1


title: ibrutinib, early, replicate 2


title: ibrutinib, early, replicate 4


title: SUDHL6_UT

data_processing:
Bcl2fastq version: 2.20.0.422; Sequencing software: HCS HD 3.4.0.38; Basecall software: RTA 2.7.7
Quality check of raw sequence reads with FastQC (v0.11.9).
Reads were quantified using Salmon (v1.5.2).
Import of gene-level estimates with tximport R package (v1.24.0).
Differential expression analysis was performed using DESeq2 package (v1.34.0).
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample.

growth_protocol: DLBCL cell lines were maintained in RPMI-1640, except for OCI-LY1 and OCI-LY7, which were maintained in IMDM media, supplemented with 10% FBS and 100 U/ml penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted from untreated-CellTrace-Low and ADR-CellTrace-High samples, using an RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer's instruction.
RNA libraries for RNA-seq were prepared by DKFZ sequencing core facility (Heidelberg, Germany) according to Illumina's TruSeq Stranded RNA kit instructions.

treatment_protocol:
On day 0 (d0) cell lines were seeded at 10^5 cells/ml, except for SU-DHL5 cells seeded at 2*10^5 cells/ml, and treated with cell line-specific concentrations of adriamycin (ADR) or left untreated. ADR concentrations chosen were the highest tolerable to achieve viabilities between 20-50% at the time of analysis and the lowest necessary to achieve a maximum senescence-associated beta-galactosidase readout.
On d1 all samples were labeled with the CellTrace Far Red (ThermoFisher) dye to track arrested and proliferating cells.
On d3 medium of ADR-treated samples was exchanged to fresh ADR-free medium.
On d5, except for RC-K8 cells on d7, samples were FACS sorted: ADR treated for CellTrace-High and untreated for CellTrace-Low cell fractions.

tag: cell line

value: Diffuse large B cell lymphoma

tag: senescence response

value: senescence-incompetent

value: Day 0


title: ibrutinib, early, replicate 1

tag: treatment


title: 2801_UT_sh_Ctrl

tag: cell type

value: primary lymphoma cells

tag: strain

value: Emicro-myc


title: SUDHL6_ADR

value: ADR (10 ng/ml)

value: Day 5


title: SUDHL5_ADR

value: ADR (5 ng/ml)


title: SUDHL5_UT

value: untreated


title: OCILY7_ADR

value: ADR (2.5 ng/ml)


title: NUDHL1_UT


title: NUDHL1_ADR


title: DOHH2_ADR


title: OCILY7_UT


title: DOHH2_UT


title: TOLEDO_ADR

source_name: Toledo

value: Toledo

value: ADR (15 ng/ml)

value: senescence-intermediate


title: CARNAVAL_UT

source_name: CARNAVAL

value: CARNAVAL


title: SUDHL4_ADR

value: ADR (7.5 ng/ml)


title: TOLEDO_UT


title: SUDHL2_ADR


title: SUDHL2_UT


title: SUDHL4_UT


title: OCILY18_UT


title: OCILY1_ADR


title: WSUDLCL2_ADR

value: ADR (8.5 ng/ml)

value: senescence-competent


title: OCILY18_ADR

value: Diffuse large B cell lymphoma


title: RI1_ADR


title: U2932_UT


title: OCILY1_UT


title: WSUDLCL2_UT


title: RCK8_ADR

value: Day 7


title: SUDHL10_ADR


title: U2932_ADR

value: ADR (22.5 ng/ml)


title: RI1_UT

value: Day 0


title: SUDHL10_UT


title: RCK8_UT


title: Karpas422_ADR


title: DB_ADR

source_name: DB

value: DB

value: ADR (25 ng/ml)


title: CARNAVAL_ADR

value: ADR (10 ng/ml)

value: senescence-incompetent

value: Day 5


title: Karpas422_UT

value: untreated


title: DB_UT


title: asap seedlings rep2

city: Bellaterra

first: Alvaro

middle: Santiago

last: Larran

state: Barcelona

address: C/ de la Vall Moronta s/n, Campus UAB

country: Spain

institute: CRAG

data_processing:
Gene expression (GE) quantification is performed using vast-tools. vast-tools maps the first 50 nucleotides of the forward read (if longer and paired end) to a library with one reference transcript per gene, the *.1 transcript according to the TAIR 10 nomenclature or else that with the lowest suffix (33,602 genes in total). GE levels are provided using the cRPKM metric (corrected [for mappability] Reads Per Kilobasepair and Million mapped reads), as detailed in Labbé et al., Stem Cells 2012. cRPKM can be converted to TPMs applying the following formula: TPM = 10^6 * cRPKM/sum_all(cRPKM).
Assembly: tair10
Supplementary files format and content: Tab-delimited text files include cRPKM values (as defined above), as well as the total read count for each gene's canonical transcript

organism: Arabidopsis thaliana

source_name: Whole seedling

growth_protocol: Seeds were stratified at 4 °C for 48 hours in MS media and plants were grown under 16:8 photoperiod at 22 °C for 11 days.

extract_protocol:
RNA was extracted from 100 mg of seedlings using RNeasy plant mini kit (Qiagen) following manufacturer’s instructions. 2 μg of RNA per sample was used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole seedling

tag: ecotype

value: asap


title: sap18sr45 seedlings rep1


title: F4_S4

city: NY

first: Emily

last: Birnbaum

state: NY

address: 200 West 93rd Street, 6J

institute: CUNY Graduate Center

description: Female, TgF-344AD transgenic rat, rodent chow

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.
The reads were mapped by STAR 2.7.9a [1] and read counts per gene were quantified using the rat genome rn6
In Partek Flow [2], read counts were normalized by median ratio.
All results of differential gene expression analysis utilized the statistical analysis tool, DESeq2
Assembly: rn6
Supplementary files format and content: Raw-Read-Counts_female.xlsx => excel file includes raw counts for each sample
Supplementary files format and content: Normalized-Read-Counts_female.xlsx =>excel file includes Normalized gene expression

organism: Rattus norvegicus

source_name: Left Hippocampus Brain

extract_protocol:
RNA was isolated by RNeasy Mini Kit from Qiagen
KAPA mRNA-Seq Hyper Prep Kit to generate strand-specific RNA-seq libraries
RNA-seq-Sequencing was performed on Illumina NovaSeq6000 for a PE 2x50 run

value: Left Hippocampus Brain

tag: Sex

value: Female

tag: genotype

value: Tg-AD

value: No Treatment


title: FBT1_S6

description: Female, TgF-344AD transgenic rat, BT-11 chow


title: sap18sr45 seedlings rep2


title: sr45 seedlings rep2


title: FBT4_S9


title: FBT5_S10


title: F3_S3


title: FBT2_S7


title: Col0 seedlings rep1


title: Col0 seedlings rep2


title: FBT3_S8


title: F2_S2


title: asap seedlings rep1


title: E14_ES_RA0h_rep4_xChIP.Ser5p

first: Angelika

last: Feldmann

address: Im Neuenheimer Feld 581

description:
SummaryTable_Ser5p_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra0h_SER5P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw

library_source: genomic

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. ResultTables contain the quantification of PolII ChIP-Seq reads at TSSs/gene bodies.

molecule: genomic DNA

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:
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 1µM retinoic acid (RA) for 2-72 hours.

value: mouse embryonic stem cells (ESC)

value: wildtype

tag: treatment duration


title: E14_ES_RA2h_rep4_xChIP.NTD

description:
SummaryTable_Pol2NTD_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra2h_PolII_UniqMapped_sorted_rmdup_MERGED_no2hrep3_downsampled.bam.bw
SummaryTable_Pol2NTD_genebodies.deseq2.all.csv

value: retinoic acid (RA)

value: 2 hr


title: E14_ES_RA2h_rep4_xChIP.Ser2p

description:
SummaryTable_Ser2p_genebodies.deseq2.all.csv
E14_ra2h_SER2P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw


title: E14_ES_RA4h_rep4_xChIP.NTD

description:
SummaryTable_Pol2NTD_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra4h_PolII_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw
SummaryTable_Pol2NTD_genebodies.deseq2.all.csv

value: 4 hr


title: E14_ES_RA2h_rep4_xChIP.Ser5p

description:
SummaryTable_Ser5p_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra2h_SER5P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw


title: E14_ES_RA4h_rep4_xChIP.Ser2p

description:
SummaryTable_Ser2p_genebodies.deseq2.all.csv
E14_ra4h_SER2P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw


title: E14_ES_RA6h_rep4_xChIP.Ser5p

description:
SummaryTable_Ser5p_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra6h_SER5P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw

value: 6 hr


title: E14_ES_RA6h_rep4_xChIP.Ser2p

description:
SummaryTable_Ser2p_genebodies.deseq2.all.csv
E14_ra6h_SER2P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw


title: E14_ES_RA6h_rep4_xChIP.NTD

description:
SummaryTable_Pol2NTD_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra6h_PolII_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw
SummaryTable_Pol2NTD_genebodies.deseq2.all.csv


title: F5_S5


title: F1_S1


title: E14_ES_RA4h_rep4_xChIP.Ser5p

description:
SummaryTable_Ser5p_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra4h_SER5P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw


title: E14_ES_RA0h_rep4_xChIP.Ser2p

description:
SummaryTable_Ser2p_genebodies.deseq2.all.csv
E14_ra0h_SER2P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw


title: sr45 seedlings rep1


title: E14_ES_RA72h_rep3_xChIP.Ser5p

description:
SummaryTable_Ser5p_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra72h_SER5P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw

value: 72 hr


title: E14_ES_RA6h_rep3_xChIP.NTD


title: E14_ES_RA0h_rep4_xChIP.NTD

description:
SummaryTable_Pol2NTD_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra0h_PolII_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw
SummaryTable_Pol2NTD_genebodies.deseq2.all.csv


title: E14_ES_RA4h_rep3_xChIP.Ser2p


title: E14_ES_RA72h_rep3_xChIP.Ser2p

description:
SummaryTable_Ser2p_genebodies.deseq2.all.csv
E14_ra72h_SER2P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw


title: E14_ES_RA48h_rep3_xChIP.Ser5p

description:
SummaryTable_Ser5p_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra48h_SER5P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw

value: 48 hr


title: E14_ES_RA48h_rep3_xChIP.NTD

description:
SummaryTable_Pol2NTD_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra48h_PolII_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw
SummaryTable_Pol2NTD_genebodies.deseq2.all.csv


title: E14_ES_RA2h_rep3_xChIP.Ser5p


title: E14_ES_RA72h_rep3_xChIP.NTD

description:
SummaryTable_Pol2NTD_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra72h_PolII_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw
SummaryTable_Pol2NTD_genebodies.deseq2.all.csv


title: E14_ES_RA6h_rep3_xChIP.Ser2p


title: E14_ES_RA4h_rep3_xChIP.NTD


title: E14_ES_RA4h_rep3_xChIP.Ser5p


title: E14_ES_RA48h_rep3_xChIP.Ser2p

description:
SummaryTable_Ser2p_genebodies.deseq2.all.csv
E14_ra48h_SER2P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw


title: E14_ES_RA2h_rep3_xChIP.Ser2p


title: E14_ES_RA24h_rep3_xChIP.Ser5p

description:
SummaryTable_Ser5p_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra24h_SER5P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw

value: 24 hr


title: E14_ES_RA72h_rep1_xChIP.Ser2p


title: E14_ES_RA24h_rep3_xChIP.Ser2p

description:
SummaryTable_Ser2p_genebodies.deseq2.all.csv
E14_ra24h_SER2P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw


title: E14_ES_RA24h_rep2_xChIP.Ser2p


title: E14_ES_RA48h_rep2_xChIP.Ser5p


title: E14_ES_RA24h_rep3_xChIP.NTD

description:
SummaryTable_Pol2NTD_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra24h_PolII_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw
SummaryTable_Pol2NTD_genebodies.deseq2.all.csv


title: E14_ES_RA48h_rep2_xChIP.NTD


title: E14_ES_RA24h_rep2_xChIP.Ser5p


title: E14_ES_RA72h_rep1_xChIP.Ser5p


title: E14_ES_RA48h_rep2_xChIP.Ser2p


title: E14_ES_RA6h_rep3_xChIP.Ser5p


title: E14_ES_RA24h_rep2_xChIP.NTD


title: E14_ES_RA72h_rep1_xChIP.NTD


title: E14_ES_RA6h_rep1_xChIP.Ser2p


title: E14_ES_RA4h_rep1_xChIP.NTD

description:
SummaryTable_Pol2NTD_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra4h_PolII_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw
SummaryTable_Pol2NTD_genebodies.deseq2.all.csv


title: Somatic_differentiated_PGC_rep2

city: Midlothian

first: Kennosuke

last: Ichikawa

address: Easter Bush Campus

department: The Roslin Institute

country: United Kingdom

institute: The University of Edinburgh

data_processing:
The quality of the row sequence reads was assessed using FastQC (ver. 0.11.9).
The raw reads were trimmed and quality filtered using Trimmomatic (ver. 0.39) as well as Trim Galore (ver. 0.6.6) with Cutadapt (ver. 3.1) software then mapped to the chicken genome (GRCg6a) using STAR (ver. 2.7.3a).
Reads were counted using RSEM (ver.1.3.1).
Assembly: GRCg6a
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

organism: Gallus gallus

source_name: Primordial germ cells

growth_protocol: Chicken PGCs were isolated from blood of chicken embryos at Hamburger and Hamilton stage (HH) 16 to 16+. The PGCs were maintained in the KnockOut DMEM supplemented with 1% chicken serum, 1 × B-27, 2 mM GlutaMAX™, 1 × nucleosides, 1 × MEM Non-Essential Amino Acids Solution (NEAA), 1 × antibiotic–antimycotic mixed stock solution, 0.5 mM monothioglycerol, 1 mM sodium pyruvate, 1 unit/mL heparin, 10 ng/mL human FGF2, 0.2 μM H1152, and 0.2 μM Blebbistatin.

extract_protocol:
1 μg of total RNA was purified using FastGene™ RNA Premium kit (NIPPON Genetics Co. Ltd., Tokyo, Japan) from each PGC line.
mRNA was enriched from the total RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA), and cDNA libraries were constructed using SMARTer® Stranded RNA-Seq Kit (TaKaRa Bio, Kusatsu, Japan) and MGIEasy Universal Library Conversion Kit (MGI, Shenzhen, China).

treatment_protocol: The adherent (somatic differentiated) PGCs were enriched by removal of the suspension (undifferentiated) PGCs by aspiration and continued proliferation for an additional two–three weeks.

value: Primordial germ cells

value: Cultured


title: Undifferentiated_PGC_rep3


title: Undifferentiated_PGC_rep2


title: E14_ES_RA4h_rep1_xChIP.Ser5p


title: E14_ES_RA4h_rep1_xChIP.Ser2p

description:
SummaryTable_Ser2p_genebodies.deseq2.all.csv
E14_ra4h_SER2P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw


title: Somatic_differentiated_PGC_rep3


title: Undifferentiated_PGC_rep1


title: E14_ES_RA48h_rep1_xChIP.Ser5p


title: E14_ES_RA6h_rep1_xChIP.Ser5p

description:
SummaryTable_Ser5p_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra6h_SER5P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw


title: PMN, KO, biol. Rep 3, LPS

city: Mainz

first: Matthias

last: Bros

address: Langenbeckstrasse 1

department: Dermatology

institute: University Medical Center Mainz

data_processing:
RNA-Seq reads were aligned with STAR aligner (v2.7.3a) to the GRCm39 genome with the parameters --outStd SAM --outMultimapperOrder Random --outSAMattributes NH HI AS nM MD --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04.
Using the featureCounts program of subread software (v2.0.0) the primary alignments were assigned to exons with default parameters.
The GENCODE mouse annotation release M26 was used in all the steps.
Further, with only the uniquely mapped reads differential expression analysis was performed using the bioconductor release 3.14 and DESeq2 (v1.34.0) where genes showing a Benjamini-Hochberg adjusted FDR < 0.1 were considered differentially expressed.
Assembly: GRCm39 (v M26)
Supplementary files format and content: fastq.gz

source_name: bone marrow-derived neutrophils

growth_protocol: Polymorphonuclear neutrophils (PMN) were purified from bone marrow of WT and KSRP-/- mice using magnetic cell sorting using biotin-labeled Ly6G-specific antibodies and streptavidin-conjugated beads (both from Miltenyi Biotec, Bergisch Gladbach, Germany), following the manufacturer's protocol. PMN were either treated with 1 µg/µl LPS for 6 h or left untreated. 1x10^6 cells of each samples were lysed and total RNA was purified for sequencing.

extract_protocol:
RNA was purified with the RNeasy Plus Mini Kit according to the manufacturer’s protocol.
NGS library prep was performed with Illumina's Stranded mRNA Prep Ligation Kit following Stranded mRNA Prep Ligation ReferenceGuide (April 2021) (Document 1000000124518 v02). Libraries were prepared with a starting amount of 52.5 ng and amplified in 11 PCR cycles. Two post PCR purification steps were performed to exclude residual primer and adapter dimers. Libraries were profiled in a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 4.0 Fluorometer (Life technologies, Carlsbad, CA).
All 20 samples were pooled together in equimolar ratio aiming for at least 30M reads per sample and sequenced on a NextSeq 2000 P3 (100 cycles) FC, SR for 1x116 cycles plus 2x10 cycles for the dual index reads and 1 dark cycle upfront R1.

treatment_protocol: 1x106 BMDM of WT and KSRP-KO mice were cultured with LPS (1µg/ml) for 6h.

value: bone marrow-derived neutrophils

value: KSRP-/-

value: 1 µg/µl LPS

tag: time


title: PMN, KO, biol. Rep 2

value: KSRP+/-


title: PMN, KO, biol. Rep 2, LPS


title: Somatic_differentiated_PGC_rep1


title: E14_ES_RA48h_rep1_xChIP.NTD


title: E14_ES_RA6h_rep1_xChIP.NTD


title: PMN, WT, biol. Rep 3, LPS


title: PMN, KO, biol. Rep 1, LPS


title: PMN, KO, biol. Rep 1


title: E14_ES_RA48h_rep1_xChIP.Ser2p


title: E14_ES_RA0h_rep1_xChIP.Ser5p

description:
SummaryTable_Ser5p_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra0h_SER5P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw

value: untreated


title: PMN, WT, biol. Rep 3


title: PMN, WT, biol. Rep 2, LPS


title: E14_ES_RA2h_rep1_xChIP.Ser2p

description:
SummaryTable_Ser2p_genebodies.deseq2.all.csv
E14_ra2h_SER2P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw


title: E14_ES_RA2h_rep1_xChIP.NTD

description:
SummaryTable_Pol2NTD_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra2h_PolII_UniqMapped_sorted_rmdup_MERGED_no2hrep3_downsampled.bam.bw
SummaryTable_Pol2NTD_genebodies.deseq2.all.csv


title: PMN, KO, biol. Rep 3


title: PMN, WT, biol. Rep 2


title: PMN, WT, biol. Rep 1, LPS


title: PMN, WT, biol. Rep 1


title: E14_ES_RA0h_rep1_xChIP.NTD


title: E14_wtG4_ES_RA0h_rep2_CapC_set6

description:
cd_wt01_RA0 in set6_CHiCAGO_data_objects.tar
ints_all.txt
DpnII.mm10.rmap

data_processing:
*library strategy: CaptureC
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.

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.


title: E14_wtG4_ES_RA24h_rep2_CapC_set6

description:
cd_wt01_RA24 in set6_CHiCAGO_data_objects.tar
ints_all.txt
DpnII.mm10.rmap


title: H3f3a_WTA_H3f3b_AA_TTseq

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

description: 4sU-labelled RNA

data_processing:
Reads mapped to mm10 genome using STAR, with options options --outSAMtype SAM, --outFilterMismatchNoverReadLmax 0.02, and --outFilterMultimapNmax 1, and quality filtered using samtools view with options -q 7, -f 2, -bS to create indexed, sorted BAMs
Feature counts were generated using featurecounts options -B -t "exon" -g "gene_name" -F GTF -p -s 2 with the mm10 (GRCm38.p6, vM23) genome annotation (GTF format)
Raw count files were imported into the R/Bioconductor and differential gene expression analysis was conducted using DEseq2 with cutoff as |log2(FC)|≥0.75 and FDR ≤0.05.
Aligned reads were processed to generate strand specific bigwigs using deeptools bamCoverage with binsize 1 and DEseq2-derived scaling factors
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: DEseq2 analysis results of each comparison

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:
The media was aspirated from cell plates and replaced with 10 mL of 500 nM 4-thiouridine (4sU, Carbosynth T4509) containing ES cell media and the plates incubated at 37°C with 5% CO2 for 5 min. After 5 min, the 4sU-containing media was aspirated and the cells were washed with 1xPBS, and 2 mL TRIzol (Invitrogen) was added directly to the plate. Cell lysate were collected, and RNA was extracted according to ThermoFisher’s recommendations. RNA concentration was determined by Qubit with the Qubit RNA broad range quantification kit (ThermoFisher). 100 µg of total RNA was diluted to a concentration of 240 ng/µL at a volume of 416.67 µL in 1XTE and then fragmented with a Diagenode Bioruptor Pico on high power for one 30 second cycle. The fragmented RNA was then combined with 283.33 µL 1XTE, 100 µL 10X Biotinylation buffer (100 mM Tris pH 7.4 and 10 mM EDTA), and 200 µL of 1 mg/mL biotin-HPDP (ThermoFisher) in dimethylformamide (DMF; freshly prepared). Samples were vortexed, then incubated in a thermomixer at 37°C shaking at 1000 RPM in the dark for 2 hours. Samples were then chloroform extracted, isopropanol/salt precipitated, and resuspended in 22 µL of nuclease-free water. 60 uL of Streptavidin C1 beads (Invitrogen) were prepared for RNA separation as by washes with 1 mL of 1 M NaOH and 50 mM NaCl and resuspended in 60 µL of TT-seq Binding buffer (10 nM Tris pH 7.4, 300 mM NaCl, 0.1% Triton). Then, 60 µL of prepared streptavidin C1 beads were added to each sample and rotated at room temperature for 20 min. Following incubation, the samples were magnetized for 1 min and the supernatant (containing the unlabeled RNA) was placed in a separate 1.5 mL tube and put on ice. The unlabeled RNA from supernatant was Phenol:Chroloform:Isopropanol(PCI)/chloroform extracted, isopropanol/salt precipitated, and resuspended in 100 µL of nuclease-free water. The bead-bound labeled nascent RNA was washed twice with 500 µL of High Salt buffer (50 mM Tris pH 7.4, 2M NaCl, 0.5% Triton), twice with 500 µL of TT-seq Binding buffer, and once with 500 µL of Low Salt buffer (5 mM Tris pH 7.4, 0.1% Triton), rotating for 1 min at room temperature, re-magnetized and resuspending the beads during each wash. The nascent RNA was recovered from the beads through two rounds of 100 µL of freshly prepared 100 mM DTT and incubating in a thermomixer at 65°C and 1000 RPM shaking for 5 min. Eluted nascent RNA recovered with a PCI extraction and an isopropanol/salt/glycogen precipitation. RNA pellets were resuspended in 25 µL of nuclease-free water.
Strand-specific nascent RNA library building was performed using the NEBNext Ultra II Directional Library kit according to the manufacturer's protocol with the following changes: The rRNA depleted RNA was fragmented at 94°C for fifteen minutes following the manufacturer’s instructions for intact RNA, the fragmentation, first strand cDNA synthesis, and second strand cDNA synthesis were performed at double the reaction volume in the manufacturer’s instructions, the adaptors were diluted 1:5 in Adaptor Dilution Buffer, the primers were diluted 1:5 in nuclease-free water, and 7 cycles of PCR were used to amplify the libraries. Finished libraries were quantified by Quibit with the dsDNA High Sensitivity kit and run on a Fragment Analyzer to confirm high quality of each library prior to sequencing. Libraries were sequenced paired-end on an Illumina NextSeq500 to ~40 million mapped reads.

treatment_protocol: All cell lines were treated with 4sU-containing media

value: Cell line

value: embryonic stem cells

value: H3f3a WT/A H3f3b A/A


title: E14_wtG4_ES_RA72h_rep1_CapC_set6

description:
cd_wt01_RA72 in set6_CHiCAGO_data_objects.tar
ints_all.txt
DpnII.mm10.rmap

value: mouse embryonic stem cells (ESC)

value: retinoic acid (RA)


title: E14_wtG4_ES_RA0h_rep1_CapC_set6


title: E14_ES_RA2h_rep1_xChIP.Ser5p

description:
SummaryTable_Ser5p_TSS.plmin1kb_tss.deseq2.all.csv
E14_ra2h_SER5P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw

value: wildtype

value: 2 hr


title: H3f3a_AA_H3f3b_WTA_clone2_TTseq

description: 4sU-labelled RNA

value: H3f3a A/A H3f3b WT/A


title: H3f3a_WTWT_H3f3b_AA_TTseq

description: 4sU-labelled RNA

value: H3f3a WT/WT H3f3b A/A


title: H3f3a_AA_H3f3b_WTA_clone1_TTseq

description: 4sU-labelled RNA


title: E14_koH12_ES_RA24h_rep2_CapC_set6

description:
cd_ko02_RA24 in set6_CHiCAGO_data_objects.tar
ints_all.txt
DpnII.mm10.rmap

value: 24 hr


title: E14_koH12_ES_RA72h_rep2_CapC_set6

description:
cd_ko02_RA72 in set6_CHiCAGO_data_objects.tar
ints_all.txt
DpnII.mm10.rmap

value: 72 hr


title: H3f3a_AA_H3f3b_WTWT_TTseq

description: 4sU-labelled RNA

value: H3f3a A/A H3f3b WT/WT


title: E14_koH12_ES_RA72h_rep1_CapC_set6


title: WT2_TTseq

description: 4sU-labelled RNA

value: Wildtype


title: WT3_TTseq

description: 4sU-labelled RNA


title: E14_koH12_ES_RA24h_rep1_CapC_set6


title: E14_ES_RA0h_rep1_xChIP.Ser2p

description:
SummaryTable_Ser2p_genebodies.deseq2.all.csv
E14_ra0h_SER2P_UniqMapped_sorted_rmdup_MERGED_downsampled.bam.bw


title: E14_koH12_ES_RA0h_rep2_CapC_set6

description:
cd_ko02_RA0 in set6_CHiCAGO_data_objects.tar
ints_all.txt
DpnII.mm10.rmap


title: WT1_TTseq

description: 4sU-labelled RNA


title: E14_koH12_ES_RA0h_rep1_CapC_set6


title: Spleen, CD3 T cell, stimulated,Ring1b, biol rep 2

city: Philadelphia

first: Montserrat

middle: C

last: Anguera

address: Rosenthal Building- 3800 Spruce St, Room 304

department: Department of Biomedical Sciences

institute: University of Pennyslvania School of Veterinary Medicine

data_processing:
Adaptors were removed using Trimmomatic (V 0.32)
N-masked mm10 genome was created using SNPsplit (C57Bl/6j N-masked Castaneus) and reads were mapped using Bowtie2 (v 2.3.4.1)
Duplicates were removed using Picard MarkDuplicates
Reads mapped to regions from the ENCODE blacklist were removed
CPM normalized bigwig files were generated using deepTools bamCoverage with options [--effectiveGenomeSize 2652783500 --normalizeUsing CPM --ignoreForNormalization chrX]
Assembly: mm10
Supplementary files format and content: CPM normalized bigwig files separated by allele for each Sample
Library strategy: CUT&RUN

source_name: Spleen

growth_protocol: Splenic CD3+ T cells were isolated using CD3+ T cell enrichment columns (R&D Systems, MTCC25).

extract_protocol:
3:50 of Ring1b antibody (Cat # 5694, Cell Signaling) was added and incubated for 5 hours with rotation.
Libraries were constructed with 5ng CUT&RUN DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturor's protocol

value: Spleen

value: Female

value: CD3+ T cell

value: F1 mus x cast

tag: antibody

value: stimulated with anti-CD3/anti-CD28 for 48 hours


title: E14_koE3_ES_RA24h_rep2_CapC_set6

description:
cd_ko01_RA24 in set6_CHiCAGO_data_objects.tar
ints_all.txt
DpnII.mm10.rmap


title: E14_koE3_ES_RA72h_rep2_CapC_set6

description:
cd_ko01_RA72 in set6_CHiCAGO_data_objects.tar
ints_all.txt
DpnII.mm10.rmap


title: E14_koE3_ES_RA0h_rep2_CapC_set6

description:
cd_ko01_RA0 in set6_CHiCAGO_data_objects.tar
ints_all.txt
DpnII.mm10.rmap

value: untreated


title: Spleen, CD3 T cell, stimulated,Ring1b, biol rep 3


title: Spleen, CD3 T cell, unstimulated, Ring1b, biol rep 3

value: unstimulated


title: Spleen, CD3 T cell, unstimulated, Ring1b, biol rep 2


title: E14_koE3_ES_RA72h_rep1_CapC_set6

value: mouse embryonic stem cells (ESC)


title: E14_koE3_ES_RA24h_rep1_CapC_set6

value: retinoic acid (RA)


title: E14_koE3_ES_RA0h_rep1_CapC_set6


title: Spleen, CD3 T cell, stimulated+NFkB inhibition, biolrep 3

data_processing:
N-masked mm10 genome was created using SNPsplit (C57Bl/6j N-masked Castaneus) and used to generated STAR indexes
Reads were aligned using STAR (v2.7.1a) with quantMode GeneCounts
Reads were quantified using FeatureCounts
Assembly: mm10
Supplementary files format and content: tab delimited text file includes count values for all Samples

extract_protocol:
RNA was harvested using phenol/chloroform extraction
RNA libraries were prepared with Illumina TruSeq Stranded Total RNA Stranded Ligation Ribo-Zero+ kit according to manufacturor's protocol.

treatment_protocol: Unstimulated samples were immediately collected into TRIzol reagent. Stimulated samples were cultured in RPMI-1640 containing 0.1% β-mercaptoethanol, 1% nonessential amino acids, 1% sodium pyruvate, and 1% penicillin- streptomycin in the presene of 1 μg/ml plate-bound anti-CD3 (Bio X cell), 10 μg/ml soluble anti-CD28 (Bio X cell) for 48 hours. Stimulated+nfkb were also cultured in the presence of 2.5uM IMD-0354 (Cayman chemical)

value: stimulated with anti-CD3/anti-CD28 for 48 hours in the presence of 2.5uM IMD-0354


title: Spleen, CD3 T cell, stimulated+NFkB inhibition, biolrep 2


title: Spleen, CD3 T cell, stimulated+NFkB inhibition, biolrep 1


title: Spleen, CD3 T cell, stimulated,Ring1b, biol rep 1


title: Spleen, CD3 T cell, stimulated, biolrep 2


title: E14_ES_RA48h_rep4_RNAseq

description:
RA48h_rep4_RNAseq
deseq2.RAtimecourse.RNAseq_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

source_name: mouse embryonic stem cells

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

value: ESC

value: wildtype

value: 48 hr


title: E14_ES_RA72h_rep3_RNAseq

description:
RA72h_rep3_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv

value: 74 hr


title: E14_ES_RA72h_rep4_RNAseq

description:
RA72h_rep4_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv


title: E14_ES_RA72h_rep1_RNAseq

description:
RA72h_rep1_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv


title: Spleen, CD3 T cell, stimulated, biolrep 1


title: Spleen, CD3 T cell, unstimulated, biolrep 2


title: E14_ES_RA72h_rep2_RNAseq

description:
RA72h_rep2_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv


title: Spleen, CD3 T cell, unstimulated, biolrep 3


title: E14_ES_RA48h_rep2_RNAseq

description:
RA48h_rep2_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv


title: E14_ES_RA24h_rep3_RNAseq

description:
RA24h_rep3_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv

value: 24 hr


title: Spleen, CD3 T cell, stimulated, biol rep 2

data_processing:
N-masked mm10 genome was created using SNPsplit (C57Bl/6j N-masked Castaneus) and used to generated STAR indexes
Reads were aligned using STAR (v2.7.1a) with alignEndsType set to EndToEnd, and outSAMattributes set to NH HI NM MD
STAR-aligned files were passed to SNPsplit for allele-specific sorting of reads
Reads were quantified using FeatureCounts on both the diploid N-masked aligned and the haploid allele-specific aligned reads.
Assembly: mm10
Supplementary files format and content: tab delimited text file includes RPKM diploid values for all Samples
Supplementary files format and content: tab delimited text file includes counts for each allele for all Samples

treatment_protocol: Unstimulated samples were immediately collected into TRIzol reagent. Stimulated samples were cultured in RPMI-1640 containing 0.1% β-mercaptoethanol, 1% nonessential amino acids, 1% sodium pyruvate, and 1% penicillin- streptomycin in the presene of 1 μg/ml plate-bound anti-CD3 (Bio X cell), 10 μg/ml soluble anti-CD28 (Bio X cell) for 48 hours.


title: Spleen, CD3 T cell, stimulated, biol rep 1


title: Spleen, CD3 T cell, unstimulated, Ring1b, biol rep 1


title: Spleen, CD3 T cell, stimulated, biolrep 3


title: Spleen, CD3 T cell, unstimulated, biolrep 1


title: E14_ES_RA24h_rep4_RNAseq

description:
RA24h_rep4_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv


title: E14_ES_RA6h_rep3_RNAseq

description:
RA6h_rep3_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv

value: 6 hr


title: Spleen, CD3 T cell, stimulated, biol rep 3

value: Spleen


title: E14_ES_RA48h_rep3_RNAseq

description:
RA48h_rep3_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv


title: E14_ES_RA6h_rep4_RNAseq

description:
RA6h_rep4_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv


title: Spleen, CD3 T cell, unstimulated, biol rep 3

value: Female


title: E14_ES_RA48h_rep1_RNAseq

description:
RA48h_rep1_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv


title: E14_ES_RA6h_rep1_RNAseq

description:
RA6h_rep1_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv


title: Spleen, CD3 T cell, stimulated+NFkB inhibtion, biol rep 4

value: CD3+ T cell


title: E14_ES_RA6h_rep2_RNAseq

description:
RA6h_rep2_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv


title: Spleen, CD3 T cell, stimulated+NFkB inhibtion, biol rep 3

value: F1 mus x cast


title: E14_ES_RA4h_rep4_RNAseq

description:
RA4h_rep4_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv

value: 4 hr


title: Spleen, CD3 T cell, stimulated+NFkB inhibtion, biol rep 2


title: Spleen, CD3 T cell, unstimulated, biol rep 1


title: E14_ES_RA4h_rep1_RNAseq

description:
RA4h_rep1_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv


title: Spleen, CD3 T cell, unstimulated, IgG

extract_protocol:
3ug of appropriate antibody was added and incubated for 5 hours with rotation.
Libraries were constructed with 5ng CUT&RUN DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturor's protocol

value: IgG


title: E14_ES_RA4h_rep2_RNAseq

description:
RA4h_rep2_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv


title: E14_ES_RA4h_rep3_RNAseq

description:
RA4h_rep3_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv


title: E14_ES_RA2h_rep4_RNAseq

description:
RA2h_rep4_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv

value: 2 hr


title: E14_ES_RA24h_rep1_RNAseq

description:
RA24h_rep1_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv


title: Spleen, CD3 T cell, stimulated, IgG

value: stimulated with anti-CD3/anti-CD28 for 48 hours


title: E14_ES_RA2h_rep3_RNAseq

description:
RA2h_rep3_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv

value: retinoic acid (RA)


title: Spleen, CD3 T cell, stimulated, H3K27me3, biol rep 3


title: E14_ES_RA0h_rep4_RNAseq

description:
RA0h_rep4_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv

value: untreated


title: Spleen, CD3 T cell, unstimulated, H3K27me3, biol rep 3

value: unstimulated


title: E14_ES_RA0h_rep3_RNAseq

description:
RA0h_rep3_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv

value: mouse embryonic stem cells

value: ESC


title: E14_ES_RA2h_rep2_RNAseq

description:
RA2h_rep2_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv

value: wildtype


title: Spleen, CD3 T cell, unstimulated, H3K27me3, biol rep 2


title: HoxTransE_KO_CH12_RA74h_rep2_nucRNAseq

description:
ch12_ko02-rep2-ra74_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv

molecule: nuclear RNA

value: 74 hr


title: Spleen, CD3 T cell, unstimulated, biol rep 2


title: Spleen, CD3 T cell, stimulated, H3K27me3, biol rep 1


title: E14_ES_RA2h_rep1_RNAseq

description:
RA2h_rep1_RNAseq
deseq2.RAtimecourse.RNAseq_summaryTable.csv


title: Spleen, CD3 T cell, stimulated, H3K27me3, biol rep 2


title: Spleen, CD3 T cell, stimulated, H2AK119Ub, biol rep 3


title: Spleen, CD3 T cell, stimulated+NFkB inhibtion, biol rep 1

value: stimulated with anti-CD3/anti-CD28 for 48 hours in the presence of 2.5uM IMD-0354


title: HoxTransE_KO_CH12_RA24h_rep2_nucRNAseq

description:
ch12_ko02-rep2-ra24_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv

value: 24 hr


title: HoxTransE_KO_CH12_RA2h_rep2_nucRNAseq

description:
ch12_ko02-rep2-ra2_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_KO_CH12_RA6h_rep2_nucRNAseq

description:
ch12_ko02-rep2-ra6_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv

value: 6 hr


title: HoxTransE_KO_CH12_RA4h_rep2_nucRNAseq

description:
ch12_ko02-rep2-ra4_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: Spleen, CD3 T cell, stimulated, H2AK119Ub, biol rep 1

value: Spleen

value: Female


title: Spleen, CD3 T cell, unstimulated, H2AK119Ub, biol rep 3

value: CD3+ T cell

value: F1 mus x cast


title: HoxTransE_KO_CH12_RA48h_rep1_nucRNAseq

description:
ch12_ko02-rep1-ra48_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv

value: 48 hr


title: Spleen, CD3 T cell, unstimulated, H2AK119Ub, biol rep 1


title: Gm137 noninfected RNA bio rep 3

city: Knoxville

first: Tarek

last: Hewezi

state: TN

address: 2431 Joe Johnson Drive

department: Plant Sciences

institute: University of Tennessee

data_processing:
Trimmomatic - fastq trimming and pairing
STAR - mapping the reads to a reference genome
Htseq - counting the reads mapped
DEseq2 - the differential expression analysis
Assembly: Gmax_508_v4.0

organism: Glycine max

source_name: Root

extract_protocol:
Hot Phenol RNA extraction from soybean root tissue
mRNA library preperation (polyA enrichment) - NoaSeq PE150 (12G raw data per sample)

value: Root


title: Spleen, CD3 T cell, unstimulated, H2AK119Ub, biol rep 2


title: Gm137 noninfected RNA bio rep 2


title: HoxTransE_KO_CH12_RA6h_rep1_nucRNAseq

description:
ch12_ko02-rep1-ra6_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: Spleen, CD3 T cell, unstimulated, H3K27me3, biol rep 1


title: HoxTransE_KO_CH12_RA48h_rep2_nucRNAseq

description:
ch12_ko02-rep2-ra48_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_KO_CH12_RA4h_rep1_nucRNAseq

description:
ch12_ko02-rep1-ra4_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv

value: 4 hr


title: HoxTransE_KO_CH12_RA2h_rep1_nucRNAseq

description:
ch12_ko02-rep1-ra2_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv

value: retinoic acid (RA)

value: 2 hr


title: Gm137 H. glycines Race 2 infected RNA bio rep 1

value: Heterodera glycines


title: HoxTransE_KO_CH12_RA0h_rep2_nucRNAseq

description:
ch12_ko02-rep2-ra0_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv

value: mouse embryonic stem cells

value: untreated


title: Spleen, CD3 T cell, stimulated, H2AK119Ub, biol rep 2

value: stimulated with anti-CD3/anti-CD28 for 48 hours


title: Gm137 H. glycines Race 3 infected RNA bio rep 2


title: Gm137 noninfected RNA bio rep 1


title: Gm137 H. glycines Race 2 infected RNA bio rep 3


title: HoxTransE_KO_CH12_RA0h_rep1_nucRNAseq

description:
ch12_ko02-rep1-ra0_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv

value: ESC


title: Gm137 H. glycines Race 2 infected RNA bio rep 2


title: Gm137 H. glycines Race 3 infected RNA bio rep 3


title: HoxTransE_KO_CH12_RA74h_rep1_nucRNAseq

description:
ch12_ko02-rep1-ra74_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv

value: 74 hr


title: HoxTransE_WT_CG4_RA48h_rep2_nucRNAseq

description:
cg4_wt02-rep2-ra48_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_WT_CG4_RA74h_rep2_nucRNAseq

description:
cg4_wt02-rep2-ra74_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_WT_CG4_RA2h_rep2_nucRNAseq

description:
cg4_wt02-rep2-ra2_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_KO_CH12_RA24h_rep1_nucRNAseq

description:
ch12_ko02-rep1-ra24_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv

value: 24 hr


title: HoxTransE_WT_CG4_RA24h_rep2_nucRNAseq

description:
cg4_wt02-rep2-ra24_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: Gm137 H. glycines Race 3 infected RNA bio rep 1


title: Gm072 noninfected RNA bio rep 2


title: Gm072 noninfected RNA bio rep 3


title: HoxTransE_WT_CG4_RA4h_rep2_nucRNAseq

description:
cg4_wt02-rep2-ra4_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: Gm072 noninfected RNA bio rep 1


title: Gm072 H. glycines Race 2 infected RNA bio rep 3


title: HoxTransE_WT_CG4_RA0h_rep2_nucRNAseq

description:
cg4_wt02-rep2-ra0_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_WT_CG4_RA0h_rep1_nucRNAseq

description:
cg4_wt02-rep1-ra0_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: Healthy15

city: Münster

first: Eberhard

last: Korsching

state: NRW

address: Niels-Stensen-Str. 14

department: Inst. of Bioinformatics

institute: University of Muenster

description:
EH15
counts_mir_E_EH_raw.tsv

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)

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

value: Endometrium

tag: subject status

value: healthy


title: Healthy14

description:
EH14
counts_mir_E_EH_raw.tsv


title: HoxTransE_WT_CG4_RA48h_rep1_nucRNAseq

description:
cg4_wt02-rep1-ra48_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_KO_CE3_RA24h_rep2_nucRNAseq

description:
ce3_ko01-rep2-ra24_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: Gm072 H. glycines Race 2 infected RNA bio rep 1


title: HoxTransE_WT_CG4_RA74h_rep1_nucRNAseq

description:
cg4_wt02-rep1-ra74_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_WT_CG4_RA24h_rep1_nucRNAseq

description:
cg4_wt02-rep1-ra24_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_KO_CE3_RA6h_rep2_nucRNAseq

description:
ce3_ko01-rep2-ra6_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv

value: 6 hr


title: HoxTransE_KO_CE3_RA48h_rep2_nucRNAseq

description:
ce3_ko01-rep2-ra48_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: Healthy12

description:
EH12
counts_mir_E_EH_raw.tsv


title: Gm072 H. glycines Race 3 infected RNA bio rep 3


title: Healthy10

description:
EH10
counts_mir_E_EH_raw.tsv


title: Gm072 H. glycines Race 3 infected RNA bio rep 2


title: HoxTransE_WT_CG4_RA6h_rep2_nucRNAseq

description:
cg4_wt02-rep2-ra6_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_WT_CG4_RA4h_rep1_nucRNAseq

description:
cg4_wt02-rep1-ra4_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_WT_CG4_RA6h_rep1_nucRNAseq

description:
cg4_wt02-rep1-ra6_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: CTR [ME233}

first: Stefano

last: Calza

address: Viale Europa 11

institute: University of Brescia

description:
Control
ME233

data_processing: Ct target values were normalized using reference genes values. FC were computed using a right-censored regression on (-Delta Ct) values to account for limit of detection. Results are reported as Fold Changes

source_name: serum

extract_protocol: Total RNA was extracted from 400 ul of serum with the miRNeasy Serum/Plasma advanced Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. RNA was eluted in 22 ul of H2O and quantified using the Qubit microRNA assay kit (Thermo Fisher Scientific, Waltham, MA, USA) by the Qubit 4 Fluorometer (Thermo Fisher Scientific). cDNA templates were prepared using the TaqMan Advanced miRNA cDNA Synthesis Kit (Thermo Fisher Scientific) according to the manufacturer's guidelines, starting from 10 ng of RNA.   The miR-Amp reaction products were thawed on ice and then diluted 1:20 in 0.1x TE buffer pH 8 (10 mM Tris, 1 mM EDTA, Thermo Fisher Scientific). Each RT-qPCR mix was prepared by combining equal quantities of 1:20 diluted sample and 2x TaqMan OpenArray Real-Time PCR Master Mix (Thermo Fisher Scientific) in a final volume of 60 μl. Each sample mix was transferred in 16 wells (6 μl/well) of an OpenArray 384-well Sample Plate (Thermo Fisher Scientific) and then automatically loaded in a Fixed-content TaqMan OpenArray Plate containing the Human Advanced miRNA panel (Cat. N. A32710, Thermo Fisher Scientific) by the QuantStudio 12K Flex Accufill System (Thermo Fisher Scientific). Each open array plate was loaded with three samples and run on the QuantStudio12K Flex Real-Time PCR System (Thermo Fisher Scientific). Quantification cycle (Cq) was automatically calculated using the ThermoFisher Cloud Software (Thermo Fisher Scientific Relative Quantification Analysis Module, available online at https://www.thermofisher.com/de/de/home/cloud.html). Only target values meeting all the following criteria were considered for subsequent analyses: Amplification Score >1, Cq confidence > 0.8, Cq ≥6. MiR-16-5p, spotted 16 times in each sub-array, was used as a quality control of the OpenArray procedure. Each serum sample was evaluated for the presence of hemolysis. The ratio between the expression levels of miR-451a (expressed in red blood cell) and miR-23a-3p (not affected by hemolysis) was calculated and samples with a delta Cq < 8 were considered acceptable. Samples with hemolysis were excluded from the study.

value: ovarian cystadenoma


title: HoxTransE_KO_CE3_RA2h_rep2_nucRNAseq

description:
ce3_ko01-rep2-ra2_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: Gm072 H. glycines Race 3 infected RNA bio rep 1


title: Healthy17

description:
EH17
counts_mir_E_EH_raw.tsv


title: HoxTransE_WT_CG4_RA2h_rep1_nucRNAseq

description:
cg4_wt02-rep1-ra2_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: Healthy16

description:
EH16
counts_mir_E_EH_raw.tsv


title: Healthy13

description:
EH13
counts_mir_E_EH_raw.tsv


title: Healthy8

description:
EH08
counts_mir_E_EH_raw.tsv


title: HoxTransE_KO_CE3_RA0h_rep2_nucRNAseq

description:
ce3_ko01-rep2-ra0_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_KO_CE3_RA74h_rep2_nucRNAseq

description:
ce3_ko01-rep2-ra74_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: Healthy9

description:
EH09
counts_mir_E_EH_raw.tsv


title: Healthy11

description:
EH11
counts_mir_E_EH_raw.tsv


title: Healthy7

description:
EH07
counts_mir_E_EH_raw.tsv


title: Gm072 H. glycines Race 2 infected RNA bio rep 2


title: HoxTransE_KO_CE3_RA48h_rep1_nucRNAseq

description:
ce3_ko01-rep1-ra48_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_KO_CE3_RA24h_rep1_nucRNAseq

description:
ce3_ko01-rep1-ra24_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: Healthy5

description:
EH05
counts_mir_E_EH_raw.tsv


title: Healthy4

description:
EH04
counts_mir_E_EH_raw.tsv


title: HoxTransE_KO_CE3_RA4h_rep1_nucRNAseq

description:
ce3_ko01-rep1-ra4_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_KO_CE3_RA6h_rep1_nucRNAseq

description:
ce3_ko01-rep1-ra6_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_KO_CE3_RA2h_rep1_nucRNAseq

description:
ce3_ko01-rep1-ra2_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_KO_CE3_RA0h_rep1_nucRNAseq

description:
ce3_ko01-rep1-ra0_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: Healthy1

description:
EH01
counts_mir_E_EH_raw.tsv


title: Endometriosis15

description:
E16
counts_mir_E_EH_raw.tsv

value: Endometriosis


title: HoxTransE_KO_CE3_RA4h_rep2_nucRNAseq

description:
ce3_ko01-rep2-ra4_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: HoxTransE_KO_CE3_RA74h_rep1_nucRNAseq

description:
ce3_ko01-rep1-ra74_cnRNAseq
deseq2.HoxB_transE_summaryTable.csv


title: SCC1.AID_UNT_rep3_cnucRNAseq

description:
E14_Scc1mAID_nucRNAseq_unt-rep4
deseq2.Scc1_cnucRNASeq_summaryTable.csv

value: 0 hr


title: Endometriosis14

description:
E15
counts_mir_E_EH_raw.tsv


title: SCC1.AID_UNT_rep2_cnucRNAseq

description:
E14_Scc1mAID_nucRNAseq_unt-rep2
deseq2.Scc1_cnucRNASeq_summaryTable.csv


title: Healthy6

description:
EH06
counts_mir_E_EH_raw.tsv


title: SCC1.AID_RA_rep3_cnucRNAseq

description:
E14_Scc1mAID_nucRNAseq_ra-rep4
deseq2.Scc1_cnucRNASeq_summaryTable.csv

value: RA 4 hr


title: Healthy3

description:
EH03
counts_mir_E_EH_raw.tsv


title: SCC1.AID_IAA_rep3_cnucRNAseq

description:
E14_Scc1mAID_nucRNAseq_iaa-rep4
deseq2.Scc1_cnucRNASeq_summaryTable.csv

value: auxin (IAA)

value: IAA 6 hr


title: Healthy2

description:
EH02
counts_mir_E_EH_raw.tsv


title: Endometriosis8

description:
E09
counts_mir_E_EH_raw.tsv


title: SCC1.AID_UNT_rep1_cnucRNAseq

description:
E14_Scc1mAID_nucRNAseq_unt-rep1
deseq2.Scc1_cnucRNASeq_summaryTable.csv


title: Endometriosis11

description:
E12
counts_mir_E_EH_raw.tsv


title: SCC1.AID_RA_rep2_cnucRNAseq

description:
E14_Scc1mAID_nucRNAseq_ra-rep2
deseq2.Scc1_cnucRNASeq_summaryTable.csv

value: retinoic acid (RA)


title: Endometriosis6

description:
E07
counts_mir_E_EH_raw.tsv


title: Endometriosis12

description:
E13
counts_mir_E_EH_raw.tsv