title: ABPC_EVs3

description:
Library name: ABPC_EVs3
blood.txt

value: Blood of ABPC_EVs treated old mice (rep3)


title: 4C_HS3_bWT_B1

status: Public on May 13 2025

type: SRA

city: Cambridge

first: Larry

last: Melidis

state: Not US or Canada

address: Robinson Way

department: CRUK-CI

country: United Kingdom

institute: University of Cambridge

library_source: genomic

data_processing:
library strategy: 4C
CUT&Tag and CUTAC read mapping and processing
Libraries were demultiplexed using demuxFQ (flags: -c -d -i -e -t 1 -r 0.01 -R -l 9). FASTQC- version 0.11.8 was used to assess the read quality and bases with a quality score below 20 were trimmed from both reads using cutadapt (cutadapt -q 20). For CUTAC libraries, reads greater than 120bp in length were removed alignment.  Reads were aligned to the hg38 reference genome using bwa mem with default parameters. Sorted bam files with duplicates removed were generated with SAMtools (version 1.15.1), and converted to bigwig using deepTools bamCoverage (parameters: --normalizeUsing CPM, --binSize 10, 5 or 3 with 12nt smoothing function). Statistical comparisons between WT and mutants were performed by two-sided t-test, using cpm signal summed over 1kb regions. Sample size for CUT&Tag;
4C-seq data was analysed using the pipe4C pipeline (https://github.com/deLaatLab/pipe4C) in R (version 4.3.0) Read 1 sequencing reads were used as input for the pipe4C pipeline and all reads mapped to the viewpoint chromosome were scaled to 1 million reads. An average running mean window size was set at 21 fragment ends. 4C plots were generated using peakC74 (https://github.com/deWitLab/peakC) where two biological replicates were used as input into the peakC program and subsequently plotted with ggplot2 in R. Biological replicates were processed on the same day and sequenced on the same flow cell. Samples for comparison were sequenced together in a single run.
Assembly: hg38
Supplementary files format and content: bigWig, counts

molecule: genomic DNA

organism: Homo sapiens

source_name: myelogenous leukemia

growth_protocol: K562 cells were cultured in RPMI1640 (Glutamine plus, Life Technologies) with 10% of fetal bovine serum (Life Technologies) at 37°C with 5% CO2. Cell cultures were routinely checked for mycoplasma infection.

extract_protocol:
First round PCR for specific enhancer sites was performed in four (for HS2 and HS3 viewpoints) or ten (for HS-40 viewpoint) parallel reactions per enhancer site using 25 uL NEBNext High-Fidelity 2X PCR Master Mix (M0541 New England Biolabs), 2 uL 10 mM 4C forward primer, 2 uL 10 mM 4C reverse primer and 200 ng of 4C template in total 50 uL volume, under the following conditions; 72 ºC for 3 min, 98 ºC for 1 min followed by 16 cycles of 98 ºC for 10 sec, primer specific Ta for 30 sec, 72 ºC for 1 min and final extension at 72 ºC for 2 min. Four reactions were pooled and purified with 1.3X Ampure XP Beads (A63882, Beckman Coulter Life Sciences) and eluted in 100 uL 10 mM Tris-HCl pH 8.0. For addition of Illumina adaptor sequences and dual indexes to amplified 4C template, DNA from round 1 PCR was divided in four 21 uL volumes to which 25 uL NEBNext High-Fidelity 2X PCR Master Mix, 2 uL 10mM forward adaptor primer, 2 uL 10mM reverse adaptor primer was added to each reaction and amplified under conditions; 98 ºC for 30 sec, followed by 12 cycles of 98 ºC for 10 sec, 63 ºC for 10 sec, 72 ºC for 30 sec and final extension at 72 ºC for 2 min. Reactions were pooled and purified with 1.3X Ampure XP Beads. Library size distribution was analysed on a Tapestation 2200 (Agilent Technologies) and library concentrations were quantified by NEBNext Library Quant Kit for Illumina (E7630, New England BioLabs). 4C libraries were multiplexed for next-generation sequencing on the NextSeq 500 or 2000 platform (single-end 76bp). Biological replicates were performed together and sequenced together in a single run.
30 million cells per sample were crosslinked in 2% formaldehyde for 10 min at room temperature and quenched with 0.125 M glycine for 5 min. Cells were washed once in 50 mL of ice-cold PBS and centrifuged at 1500 rpm for 10 min at 4 ºC. Nuclei were extracted by incubation in 50 mL cell lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% IGEPAL CA-630 (18896, Sigma-Aldrich), one tablet protease inhibitor (11873580001, Roche cOmplete, EDTA-free) for 30 min on ice and centrifuged at 1800 rpm for 5 min at 4 ºC. Nuclei were overlayed once with 500 uL of 1.25X NEBuffer r3.1 (B6003S, New England Biolabs), buffer was removed, pellet was resuspended in 1 uL of 1.25X NEBuffer r3.1, and aliquoted in 250 uL volumes. To each aliquot 108 uL of 1.25X NEBuffer r3.1 was added followed by 11 uL of 10% SDS (V6551, Promega) and incubated at 37 ºC for 1 hr in a thermomshaker (Eppendorf) at 950 rpm. 75 uL of 10% Triton X-100 (93443, Sigma-Aldrich) was added to each tube and incubated for 1 hr at 37 ºC at 950 rpm. 500 U of DpnII (R0543M, New England Biolabs) was added to each tube and incubated overnight at 37 ºC. After centrifugation at 2500 rpm at 4 ºC for 5 min, the pellet was resuspended in 950 uL of 1X ligation buffer (15224-025, Invitrogen), 50 uL of 1U/uL T4 DNA ligase (15224-025, Invitrogen) was added and incubated at 16 ºC for 4 hr, without shaking. Crosslinks were removed by addition of 60 uL 10 mg/mL Proteinase K (03115879001, Roche) and incubating overnight at 65 ºC with shaking at 800 rpm. Another 60 uL 10 mg/mL Proteinase K was adding the following day and incubated at 65 ºC at 800 rpm for 2 hr. 10 uL of 10 mg/mL Rnase A (10109142001, Roche) was then added followed by incubation at 37 ºC at 800 rpm for 1 hr. Reaction volumes were pooled and DNA was purified by phenol:chloroform extraction; equal volume of phenol pH 8.0 (P4557, Sigma-Aldrich) was added, vortexed for 1 min and centrifuged at 3500 rpm for 10 min at room temperature. Aqueous phase was transferred to a new tube and extraction repeated as above with equal volume of phenol:chloroform pH 8.0 (P3803, Sigma-Aldrich). DNA was precipitated in 1/10 volume 3M sodium acetate over 34 mL of ethanol overnight at -20 ºC. Precipitated DNA was centrifuged at 3900 rpm at 4 ºC for 30 min and resuspended in 400 uL of 1X TE buffer. DNA was purified again with an equal volume of phenol:chloroform as above, this was repeated twice in total and DNA was precipitated in 0.1X volume of 3M sodium acetate over 1 mL of ethanol overnight at -20 ºC. Precipitated DNA was centrifuged at 14000 rpm at 4 ºC for 30 min, washed three times with 1 mL of 70% ethanol and resuspended in 25 uL of 1X TE buffer. For the second restriction enzyme digestion, DNA was incubated with 500 U of DdeI (R0175L, New England Biolabs) in 1X NEBuffer r3.1 in 500 uL total volume overnight at 37 ºC at 500 rpm. Enzyme was heat inactivated by incubating for 20 min at 65 ºC. Ligation reaction was performed in 1X ligation buffer and 50 U 1U/mL T4 DNA ligase in total volume of 5 mL overnight at 16 ºC, without shaking. DNA was purified by phenol:chloroform following steps outlined above.

treatment_protocol: not applicable

tag: tissue

value: myelogenous leukemia

tag: cell line

tag: cell type

value: K562 bMut1


title: 4C_HS3_bWT_B2


title: P00296_3_2

city: Bursa

first: Ceyda

last: Colakoglu Bergel

address: Görükle Kampüsü, Nilüfer

country: Turkey

institute: Bursa Uludag University

description: Library name: Sample 8

library_source: transcriptomic

data_processing:
RPKM (reads per kilobase of exon per million reads mapped)-normalized count data from total RNA sequencing were used for analysis to identify differentially expressed genes and mature miRNAs via the R Bioconductor package “NOISeq”
Assembly: hg19
Supplementary files format and content: text files

molecule: total RNA

source_name: exosome

growth_protocol: Serum derived exosome, After clinical examinations, peripheral blood (10-12 mL) was collected in PAXgene® Blood RNA Tubes for exosome isolation,

extract_protocol:
Firstly, plasma isolation was performed from blood samples before and 1 week after treatment. For this purpose, samples taken in PAXgene® Blood RNA Tube were centrifuged at 4000 rpm for 15 minutes and plasma was stored at -80 o . Then, exo-RNA isolation was performed using QIAGEN exoRNeasy Midi kit (Qiagen, Hilden, Germany). For exo isolation, exo bound with XBP were collected by passing PBS through the column, and characterization experiments were carried out. 1 ml plasma samples were transferred to 15 ml conical tubes and RNA isolation was performed. The plasma sample was mixed with 2X binding buffer (XBP) at a ratio of 1:1 and added to the exoEasy membrane affinity column. Then, the washed samples were lysed by adding QIAzol. The lysate was collected after centrifugation at 500 g and after adding chloroform, the aqueous phase was recovered and mixed with ethanol. The samples were added to the RNeasy MinElute spin column, centrifuged and, eluted with 30 µl of RNase- free water after washing
To perform RNA sequencing, mRNA and small RNA libraries were generated using the NGS sequencing Illumina NextSeq 500 platform with the SMARTer smRNA-Seq Kit (Illumina, Takara Bio, Shiga, Japan) according to the manufacturer’s instructions. The libraries were gel-purified and assessed using the D1000 ScreenTape System (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: This cohort study enrolled 41 patients diagnosed with NAMD at Bursa Uludağ University Department of Ophthalmology. In current study, bevacizumab was administered as the anti- VEGF treatment in patients with NAMD. Before and after the anti-VEGF treatment, the patients were examined at the Bursa Uludağ University Department of Ophthalmology and the data were recorded. Clinical examinations of the patients were recorded at 1 week, 1 month and 3 months.

value: exosome

value: serum-derived

value: serum-derived exosome

tag: treatment

value: After treatment

tag: diagnosis

value: Neovascular Age-Related Macular Degeneration


title: ABPC_EVs2

city: Xi'an

first: Beibei

last: Yu

state: Shannxi

address: No. 157, Xiwu Road, Xincheng District, Xi'an City, Shaanxi Province

country: China

institute: Xijing hospital

description:
Library name: ABPC_EVs2
blood.txt

data_processing:
CLC Genomics Workbench w 11.0.1
Assembly: mm10
Supplementary files format and content: TPM

organism: Mus musculus

source_name: Blood

extract_protocol:
A NEBNext Ultra RNA library prep kit for Illumina (New England Biolabs, USA, Catalog #: E7530L) was used according to the manufacturer's guidelines to construct sequencing libraries and incorporate index codes for sample identification
he prepared libraries were sequenced on an Illumina platform using the paired-end 150 strategy at the Novogene Bioinformatics Technology Co. Ltd., Beijing, China. The sequencing process converted the original fluorescence images into raw data, which were then processed in FASTQ format, capturing both nucleotide sequences and their corresponding quality scores

value: Blood

tag: genotype

value: WT

value: Blood of ABPC_EVs treated old mice (rep2)


title: Pooled sample 11, backfat tissue, low protein diet, outdoor conditions

city: Ljubljana

first: Klavdija

last: Poklukar Žnidaršič

state: Ljubljana

address: Hacquetova ulica 17

department: Animal Science department

country: Slovenia

institute: Agricultural Institute of Slovenia

description: Library name: FAT11

data_processing:
Raw sequence data were converted into fastq files and de-multiplexed using Illumina bcl2fastq program (version 2.20).
The sequence reads were trimmed using Trimmomatic v.0.36
The trimmed reads were mapped to Sus scrofa 11.1 reference genome (release 108) using STAR aligner v.2.5.2b.
Unique gene hit counts were calculated using featureCounts (Subread package v.1.5.2.) and summarized using the gene_id feature in the annotation file. Unique reads that fell within the exon region were counted.
Assembly: Sus scrofa 11.1
Supplementary files format and content: text files includes raw counts for each sample

organism: Sus scrofa

source_name: Backfat tissue at the level of the last rib

extract_protocol:
RNeasy Lipid Tissue Mini Kit (Qiagen GmbH, Hilden, Germany)
NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA)

tag: breed

value: Krskopolje pig

value: low protein diet

value: outdoor system


title: Pooled sample 6, backfat tissue, standard protein diet, outdoor conditions

description: Library name: FAT6

value: Backfat tissue at the level of the last rib

value: standard protein diet


title: ABMC_EVs3

description:
Library name: ABMC_EVs3
blood.txt

value: Blood of ABMC_EVs treated old mice (rep3)


title: exo_2g

description: Library name: Sample 4

value: Before treatment


title: ABPC_EVs1

description:
Library name: ABPC_EVs1
blood.txt

value: Blood of ABPC_EVs treated old mice (rep1)


title: 4C_HS3_bMut2_B2

value: myelogenous leukemia

value: K562 bMut2


title: 4C_HS3_bMut1_B1

value: K562 bMut1


title: 4C_HS3_bMut2_B1


title: Pooled sample 4, backfat tissue, standard protein diet, outdoor conditions

description: Library name: FAT4


title: 4C_HS3_bMut1_B2


title: Young1

description:
Library name: Young1
blood.txt

value: Blood of No treated young mice (rep1)


title: Pooled sample 3, backfat tissue, standard protein diet, outdoor conditions

description: Library name: FAT3


title: Pooled sample 1, backfat tissue, standard protein diet, outdoor conditions

description: Library name: FAT1


title: Pooled sample 2, backfat tissue, standard protein diet, outdoor conditions

description: Library name: FAT2


title: FBMC_EVs1

description:
Library name: FBMC_EVs1
blood.txt

value: Blood of FBMC_EVs treated old mice (rep1)


title: 4C_HS2_bWT_B1

value: K562 bWT


title: Pooled sample 7, backfat tissue, low protein diet, outdoor conditions

description: Library name: FAT7


title: 4C_HS2_bWT_B2


title: Mouse round spermatids, ATAC-seq, rep1

city: Nanjing

first: Peng

last: Hua

state: Jiangsu

address: 101 Longmiandadao

department: State Key Laboratory of Reproductive Medicine and Offspring Health

institute: Nanjing Medical University

description: Library name: ATACseq_Round_Spermatid_1

data_processing:
Fastp (0.20.0) were used to trim adapter and quality control for CUT&Tag, CUT&RUN reads. Trimmed sequencing reads were aligned to the mm10 reference genome using Bowtie2 (version 2.3.5.1). Reads with MAPQ score below 30 were excluded. PCR duplicates were removed using Sambamba(0.7.1). 6 algorithms (MACS2, HOMER, SEACR, SICER2, Genrich and GoPeaks) were used for peak calling. Peaks within mm10 blacklist were removed. For ATAC-seq, quality control and adapter trimming were performed by fastp (0.20.0) to remove replicated and low-quality reads (MAPQ<10). Trimmed reads were then aligned to mm10 reference genome. Peak calling for ATAC-seq were performed by Genrich (0.6.1) ATAC-seq mode with parament ‘-j –p 0.01’. Peaks within mm10 blacklist were removed.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Testis

extract_protocol:
Round Spermatids were separated from testis of adult C57B6J mice (8 weeks), using counterflow centrifugal elutriation (CCE) methods. For ATAC-seq, 1 × 10^4 Round spermatids were sorted and were incubated with 10 μl 5 × TTBL, 5 μl TTE Mix V50 in a 1.5 ml microtube at 55 °C for 10 min for fragmentation. The fragment products were purified using VAHTS DNA Clean Beads. CUT&Tag experiments were performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme Biotech, TD904). Briefly, 2 × 10^4 round spermatids were sorted and washed once in 0.5 ml wash buffer, and were incubated with 10 μl pre-activated concanavalin ConA beads in a 1.5 ml microtube at 25 °C for 10 min. H3K4me3 (07-473, Milipore), H3K27me3 (c36811, CST) or CTCF (07-729, Milipore) antibody buffer at 1:100 dilution was added and cultured with cells at 4°C overnight. Cell were washed with dig-wash buffer and incubated with secondary antibodies at 25°C for 1h. After washing thrice with dig-wash buffer, 100ul pA/G-Tnp in dig-300 buffer were added to samples and then rotated at 25 °C for 1 h. After washing, cells were resuspended in 40 μl dig-300 buffer with 10 ul 5 × TTBL and incubates at 37 °C for 1 h. 5 μl Proteinase K, 100 μl Buffer L/B and 20 μl DNA Extract Beads were added to samples and incubated at 55 °C for 10 min. CUT&RUN experiments were performed with Hyperactive pG-MNase CUT&RUN Assay Kit for Illumina (Vazyme Biotech, HD102). 2 × 10^4 Round spermatids were sorted and washed once in 0.5 ml wash buffer, and were incubated with 10 μl pre-activated concanavalin ConA beads Pro in a 1.5 ml microtube at 25 °C for 10 min. Cells were incubated with 1:100 dilution antibody buffer of H3K4me3 (07-473, Milipore), H3K27me3 (c36811, CST) or CTCF (07-729, Milipore) antibody buffer at 4°C overnight. After washing, 100ul pG-MNase Enzyme premix were added to samples at 4 °C for 1 h. After washing, 100ul CaCl2 premix were added to samples and then incubate on ice for 60-90 minutes. 100 μl Stop Buffer were added to samples and then incubate at 37 °C for 10-30 minutes and then extract DNA.
ATAC-seq libraries were constructed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501). CUT&Tag libraries were constructed using Hyperactive ® Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903). CUT&RUN libraries were constructed using Hyperactive pG-MNase CUT&RUN Assay Kit for Illumina (Vazyme, HD102). All libraries were sequenced on the Illumina NoveSeq 6000 platform to generate 150 bp pair-end reads.

value: Testis

value: Mouse round spermatid

tag: Sex

value: Male

tag: strain

value: Wild type

tag: antibody


title: Mouse round spermatids, ATAC-seq, rep2

description: Library name: ATACseq_Round_Spermatid_2


title: 4C_HS2_bMut2_B1


title: Mouse round spermatids, CTCF, CUTNRUN, rep2

description: Library name: CUTNRUN_Round_Spermatid_CTCF_2

data_processing:
Fastp (0.20.0) were used to trim adapter and quality control for CUT&Tag, CUT&RUN reads. Trimmed sequencing reads were aligned to the mm10 reference genome using Bowtie2 (version 2.3.5.1). Reads with MAPQ score below 30 were excluded. PCR duplicates were removed using Sambamba(0.7.1). 6 algorithms (MACS2, HOMER, SEACR, SICER2, Genrich and GoPeaks) were used for peak calling. Peaks within mm10 blacklist were removed. For ATAC-seq, quality control and adapter trimming were performed by fastp (0.20.0) to remove replicated and low-quality reads (MAPQ<10). Trimmed reads were then aligned to mm10 reference genome. Peak calling for ATAC-seq were performed by Genrich (0.6.1) ATAC-seq mode with parament ‘-j –p 0.01’. Peaks within mm10 blacklist were removed.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Run

value: CTCF (07-729, Milipore)


title: Atf4AKO iWAT, cold, biol rep 1

city: Cheonan-si, Chungcheongnam-do

first: Ahyeon

last: Son

address: 25 Bongjeong-ro, Dongnam-gu

country: South Korea

institute: Soonchunhyang Institute of Medi-bio Science

description: Library name: ko-ct-1

data_processing:
Raw data with adapter sequences or low-quality sequences was filtered using SOAPnuke with following filter parameters: "-n 0.01 -l 20 -q 0.4 --adaMR 0.25 --polyX 50 --minReadLen 150".
Clean reads were mapped to mm10 genome using STAR and the reads with unique alignments were counted using featureCounts (parameter: --largestOverlap -B -C).
Read counts of protein-coding transcripts were then normalized by pyDESeq2, which is a python implementation of the DESeq2 algorithm.
Assembly: mm10
Supplementary files format and content: csv file includes normalized counts for each sample

molecule: polyA RNA

source_name: Inguinal white adipose tissue

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) and mRNAs were purified using oligo clean and concentrator kits (Zymo Research).
RNA libraries for RNA-seq were prepared using DNBSEQ Eukaryotic Strand-specific mRNA library kit according to the manufacturer's protocols.

value: Inguinal white adipose tissue

value: Atf4 AKO

value: Cold for 24 hours


title: Atf4AKO iWAT, cold, biol rep 0

description: Library name: ko-ct-0


title: Young2

description:
Library name: Young2
blood.txt

value: Blood

value: WT

value: Blood of No treated young mice (rep2)


title: Pooled sample 5, backfat tissue, standard protein diet, outdoor conditions

description: Library name: FAT5

value: Backfat tissue at the level of the last rib

value: Krskopolje pig

value: standard protein diet

value: outdoor system


title: Mouse round spermatids, CTCF, CUTNRUN, rep1

description: Library name: CUTNRUN_Round_Spermatid_CTCF_1


title: 4C_HS2_bMut1_B2

value: myelogenous leukemia

value: K562 bMut1


title: 4C_HS2_bMut1_B1


title: Atf4WT iWAT, cold, biol rep 1

description: Library name: wt-ct-1


title: Mouse round spermatids, H3K27me3, CUTNRUN, rep2

description: Library name: CUTNRUN_Round_Spermatid_H3K27me3_2

value: Testis


title: Atf4AKO iWAT, cold, biol rep 2

description: Library name: ko-ct-2


title: 4C_HS2_bMut2_B2

value: K562 bMut2


title: Young3

description:
Library name: Young3
blood.txt

value: Blood of No treated young mice (rep3)


title: Atf4AKO iWAT, RT, biol rep 0

description: Library name: ko-rt-0

value: Room temperature


title: P300_bMut2_B1

data_processing:
library strategy: CUT&Tag
CUT&Tag and CUTAC read mapping and processing
Libraries were demultiplexed using demuxFQ (flags: -c -d -i -e -t 1 -r 0.01 -R -l 9). FASTQC- version 0.11.8 was used to assess the read quality and bases with a quality score below 20 were trimmed from both reads using cutadapt (cutadapt -q 20). For CUTAC libraries, reads greater than 120bp in length were removed alignment.  Reads were aligned to the hg38 reference genome using bwa mem with default parameters. Sorted bam files with duplicates removed were generated with SAMtools (version 1.15.1), and converted to bigwig using deepTools bamCoverage (parameters: --normalizeUsing CPM, --binSize 10, 5 or 3 with 12nt smoothing function). Statistical comparisons between WT and mutants were performed by two-sided t-test, using cpm signal summed over 1kb regions. Sample size for CUT&Tag;
4C-seq data was analysed using the pipe4C pipeline (https://github.com/deLaatLab/pipe4C) in R (version 4.3.0) Read 1 sequencing reads were used as input for the pipe4C pipeline and all reads mapped to the viewpoint chromosome were scaled to 1 million reads. An average running mean window size was set at 21 fragment ends. 4C plots were generated using peakC74 (https://github.com/deWitLab/peakC) where two biological replicates were used as input into the peakC program and subsequently plotted with ggplot2 in R. Biological replicates were processed on the same day and sequenced on the same flow cell. Samples for comparison were sequenced together in a single run.
Assembly: hg38
Supplementary files format and content: bigWig, counts

extract_protocol:
Sequencing libraries were generated by mixing 25 uL NEBNext High Fidelity 2X PCR Master Mix (M0541, New England Biolabs), 2 uL of P5 indexing primer (10 mM), 2 uL of P7 indexing primer (10 mM) with 21 uL of purified DNA in a PCR reaction under the following conditions: 72 ºC for 5 min, 98 ºC for 30 sec followed by n cycles of 98 ºC 10 sec, 63 ºC for 10 sec, and a final extension at 72 ºC for 1 min. For BG4 and SG4 libraries n=8 cycles were used, for all other CUT&Tag libraries n=10 was used. Libraries were purified using Ampure XP beads (A63882, Beckman Coulter Life Sciences) by incubation with 0.4X ratio of beads for 15 min, followed by supernatant incubation with 1.4X ratio of beads for 15 min. Beads were washed twice with 800 mL 80% ethanol and eluted in 25 uL of 10mM Tris-HCl pH 8.0. Library size distribution was analysed on a Tapestation 2200 (Agilent Technologies) and library concentrations were quantified by NEBNext Library Quant Kit for Illumina (E7630, New England BioLabs). Individual libraries were pooled for optimal read balancing and sequenced paired end with NextSeq 2000 P2 or P3 Reagents 100 Cycles v3 (20046811, 20040559, Illumina, Inc.) on the NextSeq 2000 platform (Illumina, Inc.).
Dynabeads MyOne Streptavidin T1 beads (65601, Thermo Fisher Scientific) were incubated with Concanavalin A (C2272, biotin conjugate, Sigma-Aldrich) in ratio of 10 mg/mL beads to 1.15 mg/mL Concanavalin A at 22 ºC for 30 min at 400 rpm on a thermoshaker (Eppendorf). Volume sufficient for 10 µL beads per reaction was prepared. Beads were washed with 1 mL of binding buffer (20mM HEPES pH 7.5, 10mM KCl, 1mM CaCl2, 1mM MnCl2) and resuspended in volume of binding buffer sufficient for 10 uL beads per reaction. Cells were fixed in 0.1% formaldehyde (28906, Thermo Fisher Scientific) in 1X PBS for 2 min at room temperature and quenched with 0.075M glycine. Cells were centrifuged at 1300xg 4 ºC for 4 min and resuspended in wash buffer (20mM HEPES pH 7.5, 150mM KCl, 0.5mM spermidine (S0266, Sigma-Aldrich), one tablet protease inhibitor (11873580001, Roche cOmplete, EDTA-free)) at 500 cells/mL. 10 uL beads were incubated with 100 uL of cell suspension at 25 ºC for 10 min at 600 rpm, washed twice with 100 uL wash buffer and resuspended in 50 uL of antibody buffer (2mM EDTA, 0.1% BSA (A8577, Sigma-Aldrich), 0.05% digitonin (300410, Merck Millipore) in wash buffer). Primary antibody was added and incubated at 4 ºC at 600rpm overnight. Primary antibodies used include; BG4 scFv (made in house) at 0.5 mM per reaction, SG4 (made in house) at 1 mM per reaction, anti-H3K4me1 antibody (710795, Thermo Fisher Scientific), anti-H3K27ac antibody (ab4729, Abcam), anti-Ser5 phosphorylated Rpb1 antibody (#13523, Cell Signaling Technology), anti-GATA1 antibody (ab181544, Abcam), anti-BRG1 antibody (ab110641, Abcam), anti-P300 antibody (sc-48343, Santa Cruz Biotechnology), Normal Rabbit IgG (2729, Cell Signaling Technology)). Cells were washed twice with 100 uL dig wash buffer (0.05% digitonin in wash buffer) and resuspended in 50 uL of dig-wash buffer. Secondary antibody was then added and incubated at 25 ºC at 600 rpm for 1 hr. For BG4 and SG4 samples, 2 uL of rabbit anti-FLAG antibody (#2368, Cell Signaling Technology) was added, for all other rabbit primary antibodies 0.5 uL of Guinea Pig anti-rabbit IgG antibody (ABIN101961, antibodies-online.com) was added, and for mouse primary antibodies 0.5 uL of Rabbit Anti-mouse IgG H&L (ab46540, Abcam) was added per reaction. Cells were then washed three times with 500 uL dig-wash buffer and resuspended in 50 uL dig-300 buffer (20mM 20mM HEPES pH 7.5, 300mM KCl, 0.5mM spermidine, 0.01% digitonin, one tablet protease inhibitor). pA-Tn5 (2 mM, made in house) was added in 1:250 dilution to each sample and incubated at 25 ºC at 600 rpm for 1 hr. Cells were washed three times with 500 uL dig-300 buffer and resuspended in 300 uL tagmentation buffer (10mM MgCl2 in dig-300 buffer) and incubated at 37 ºC at 600 rpm for 1 hr. Cells were then washed twice with 500 uL TAPS wash buffer (10 mM TAPS (J63268.AE, Thermo Fisher Scientific) and resuspended in 100 uL of proteinase K solution (0.5 mg/mL Proteinase K (EO0491, Thermo Fisher Scientific), 0.5% SDS in 10mM Tris-HCl pH 8.0). Samples were vortexed on full and incubated at 55 ºC for 1 hr at 800 rpm. DNA was extracted using DNA Clean & Concentrator 5 (D4013, Zymo Research) following the manufacturer’s instructions, DNA was eluted in 25 uL DNA elution buffer.


title: Mouse round spermatids, H3K4me3, CUTNRUN, rep1

description: Library name: CUTNRUN_Round_Spermatid_H3K4me3_1

value: Mouse round spermatid

value: Male

value: Wild type

value: H3K4me3 (07-473, Milipore)


title: Mouse round spermatids, CTCF, CUTNTag, rep1

description: Library name: CUTNTag_Round_Spermatid_CTCF_1

data_processing:
Fastp (0.20.0) were used to trim adapter and quality control for CUT&Tag, CUT&RUN reads. Trimmed sequencing reads were aligned to the mm10 reference genome using Bowtie2 (version 2.3.5.1). Reads with MAPQ score below 30 were excluded. PCR duplicates were removed using Sambamba(0.7.1). 6 algorithms (MACS2, HOMER, SEACR, SICER2, Genrich and GoPeaks) were used for peak calling. Peaks within mm10 blacklist were removed. For ATAC-seq, quality control and adapter trimming were performed by fastp (0.20.0) to remove replicated and low-quality reads (MAPQ<10). Trimmed reads were then aligned to mm10 reference genome. Peak calling for ATAC-seq were performed by Genrich (0.6.1) ATAC-seq mode with parament ‘-j –p 0.01’. Peaks within mm10 blacklist were removed.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

value: CTCF (07-729, Milipore)


title: Atf4WT iWAT, cold, biol rep 0

description: Library name: wt-ct-0

value: Inguinal white adipose tissue

value: WT

value: Cold for 24 hours


title: Atf4AKO iWAT, RT, biol rep 2

description: Library name: ko-rt-2

value: Atf4 AKO


title: P300_bWT_B2

value: K562 bWT


title: Atf4WT iWAT, RT, biol rep 2

description: Library name: wt-rt-2


title: Atf4AKO iWAT, RT, biol rep 1

description: Library name: ko-rt-1


title: P300_bMut2_B2


title: Mouse round spermatids, H3K27me3, CUTNTag, rep2

description: Library name: CUTNTag_Round_Spermatid_H3K27me3_2


title: Mouse round spermatids, CTCF, CUTNTag, rep2

description: Library name: CUTNTag_Round_Spermatid_CTCF_2


title: Mouse round spermatids, H3K4me3, CUTNRUN,rep2

description: Library name: CUTNRUN_Round_Spermatid_H3K4me3_2


title: P300_bMut1_B2


title: Atf4WT iWAT, cold, biol rep 2

description: Library name: wt-ct-2


title: P300_bMut1_B1


title: Mouse round spermatids, H3K27me3, CUTNRUN, rep1

description: Library name: CUTNRUN_Round_Spermatid_H3K27me3_1


title: Atf4WT iWAT, RT, biol rep 1

description: Library name: wt-rt-1


title: P300_bWT_B1


title: Atf4WT iWAT, RT, biol rep 0

description: Library name: wt-rt-0


title: Mouse round spermatids, H3K27me3, CUTNTag, rep1

description: Library name: CUTNTag_Round_Spermatid_H3K27me3_1


title: Mouse round spermatids, H3K4me3, CUTNTag,rep2

description: Library name: CUTNTag_Round_Spermatid_H3K4me3_2


title: GATA1_bWT_B2


title: GATA1_bWT_B1


title: SHP_iHO_Veh_3

city: bunkyo-ku

first: Masato

last: Miyoshi

address: yushima

department: Gastroenterology

country: Japan

institute: Tokyo Medical and Dental University

data_processing:
The TruSeq Stranded mRNA protocol was used for the preparation of RNA-seq libraries and sequenced on a Illumina NovaSeq 6000, as paired-end, 101 base paires reads.
The sequencing reads were trimmed using Trimmomatic 0.38.
Trimmed  reads were aligned to the GRCh38 genome assembly using HISAT2 version 2.1.0.
Read count extraction and normalization were performed by StringTie version 2.1.3b.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts

extract_protocol:
Total RNA was extracted by RNeasy Micro (QIAGEN, Venlo, Netherlands).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: iPSC

value: Veh


title: Mouse round spermatids, H3K4me3, CUTNTag, rep1

description: Library name: CUTNTag_Round_Spermatid_H3K4me3_1


title: SHP_iHO_Veh_2


title: GATA1_bMut2_B2

value: myelogenous leukemia


title: GATA1_bMut2_B1


title: intestinal organoids, fibroblast coculture, LPS_Indoles_CH223191, rep3

city: Shanghai

first: Yihuang

last: Huang

address: No.399, Wanyuan Road, Minhang District

institute: Children's Hospital of Fudan University

data_processing:
Raw reads underwent quality control using FastQC, and adapters and low-quality bases were trimmed using Trimmomatic.
The high-quality reads were aligned to the mouse genome (GRCm38/mm10).
Base-calling was performed using Illumina CASAVA (version 1.8.2).
Adapter sequences were removed and low-quality bases were trimmed using Trimmomatic (version 0.39). Quality control of reads was done using FastQC (version 0.11.9).
Reads were aligned to the reference genome (GRCm39) using STAR (version 2.7.5c). Gene expression was quantified using HTSeq-count (version 0.11.2) with default settings.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Intestinal organoid

growth_protocol: Organoids were passaged and seeded into 24-well plates. Concurrently, fibroblasts were passaged and seeded into 0.4 µm pore-size transwell inserts, which were then placed into the wells containing organoids. Each well was supplemented with 750 µL of complete medium (DMEM with 10% FBS and 1% PS).

extract_protocol:
RNA was extracted using the TRIzol method according to the manufacturer’s instructions.
Total RNA was extracted using TRIzol, and libraries were prepared for Illumina following polyA enrichment and sequenced on an Illumina NovaSeq 6000 platform using paired-end 150 bp reads

treatment_protocol: The co-cultures were treated with lipopolysaccharide (LPS, 100 µg/mL), ILA or IAA (each at 6 µM), and/or CH223191 (1 µM), based on the experimental conditions.

value: Intestinal organoid

value: Fibroblast coculture and LPS and Indoles and CH223191 intervention


title: intestinal organoids, fibroblast coculture, LPS_Indoles_CH223191, rep1


title: GATA1_bMut1_B1

value: K562 bMut1


title: SHP_iHO_Dox_2

value: Dox


title: SHP_iHO_Dox_3


title: intestinal organoids, fibroblast coculture, LPS_Indoles, rep3

value: Fibroblast coculture and LPS and indoles intervention


title: BRG1_bWT_B2


title: SHP_iHO_Dox_1


title: intestinal organoids, fibroblast coculture, LPS_Indoles_CH223191, rep2


title: intestinal organoids, fibroblast coculture, LPS_Indoles, rep2


title: Bladder Cancer cells (SUP)

type: RNA

city: Guangzhou

first: Ying

last: Xiaoling

address: 250 Changgang east road, Guangzhou

institute: The second affiliated Hospital of Guangzhou Medical University

hyb_protocol: The labeled RNAs were combined together and hybridized onto Arraystar Human small RNA Microarray (8x15K, Arraystar)

scan_protocol: After washing the slides, the arrays were scanned in two-color channels by an Agilent Scanner G2505C

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images.

source_name: Bladder Cancer cells

label_protocol: The “IP” and “Sup” RNAs were enzymatically labeled with Cy5 and Cy3 respectively

growth_protocol: cells were kept in 10% FBS 1640

extract_protocol: The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions, 1-5 μg of each total RNA sample was immunoprecipitated by 6 μg anti-m5C antibody

tag: tag

value: Bladder cancer cells


title: SC1, Input

first: Jianfeng

last: Chen

address: 651East Dongfeng Road

institute: SYSUCC

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by bowtie2 and STAR instruction
MACS2 were used for the binding profile
IGV and R were used for visualization
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: SC1 cellls were cultured in RPMI1640 medium supplemented with 10% FBS and 1% P/S.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared according to NEB ChIP-Seq Library Prep Kit (E6240).

value: DLBCL

tag: chip antibody

value: no antibody


title: intestinal organoids, fibroblast coculture, LPS_Indoles, rep1


title: BRG1_bMut2_B2

value: K562 bMut2


title: BRG1_bWT_B1


title: CdCl2 inducted SV-HUC-1 cells (IP)

description: RNA sample was immunoprecipitated by 6 μg anti-m5C antibody

source_name: Malignant transformed cells of bladder epithelium

value: Bladder epithelial cells


title: Bladder Cancer cells (IP)


title: GATA1_bMut1_B2


title: CdCl2 inducted SV-HUC-1 cells (SUP)


title: SC1, H3K27ac

value: H3K27ac(Abcam, ab4729)


title: intestinal organoids, fibroblast coculture, LPS, rep3

value: WT

value: Fibroblast coculture and LPS stimulation


title: BRG1_bMut2_B1


title: SC1, CREBBP

value: CREBBP (Santacruz, sc-7300X)


title: SHP_iHO_Veh_1

value: iPSC


title: SV-HUC-1 cells (SUP)

source_name: Bladder epithelial cells


title: BRG1_bMut1_B2


title: NKS1-S+A1

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by bowtie2 and STAR instruction
MACS2 were used for the binding profile
RSEM were used for counting
IGV and R were used for visualization
Assembly: GRCh38
Supplementary files format and content: TXT file contains counts for each sample

growth_protocol: YT cells were cultured in IMDM medium supplemented with 20% fetal bovine serum, 1% penicillin-streptomycin; NK-S1 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum, 10% horse serum, 1% penicillin-streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: YT  treated with DMSO or selinexor for 48h; while NK-S1 treated with DMSO, selinexor, abemaciclib or combination for 48h.

value: Nature killer/T-cell lymphoma

value: combination (S+A1)


title: BRG1_bMut1_B1

value: myelogenous leukemia


title: mGB1-KD 3

type: genomic

city: Heidelberg

first: Anna-Sophie

last: Spreng

address: INF 280

country: Germany

institute: DKFZ

hyb_protocol: Cells were profiled using Infinium MouseMethylation285k BeadChip arrays.

scan_protocol: BeadArray Reader

data_processing:
minfi (1.24.0) and conumee (1.3.0)
Average Beta

label: Cy3 and Cy5

label_protocol: Standard Infinium protocol

extract_protocol: QIAgen DNA prep

value: KD


title: intestinal organoids, fibroblast coculture, LPS, rep1

value: Intestinal organoid


title: intestinal organoids, fibroblast coculture, rep3

value: Fibroblast coculture


title: SV-HUC-1 cells (IP)


title: BG4_bWT_B3_t3

value: K562 bWT


title: NKS1-S+A2


title: Cd-SV-HUC-1 cells (IP)


title: NSUN6-knockout Cd-SV-HUC-1 cells (IP)

source_name: NSUN6-knockout Malignant transformed cells of bladder epithelium


title: NKS1-A2

value: abemaciclib


title: NSUN6-knockout Cd-SV-HUC-1 cells (SUP)


title: intestinal organoids, fibroblast coculture, rep2


title: BG4_bWT_B3_t2


title: NKS1-A1


title: mGB1-KD 1


title: intestinal organoids, fibroblast coculture, rep1


title: Cd-SV-HUC-1 cells (SUP)


title: NKS1-S2

value: selinexor


title: BG4_bWT_B3_t1


title: intestinal organoids, fibroblast coculture, LPS, rep2


title: mGB1-Ctrl 3

value: control


title: intestinal organoids, control, rep3

value: Control


title: BG4_bWT_B2_t3


title: intestinal organoids, control, rep2


title: NKS1-S1


title: mGB1-Ctrl 2


title: BG4_bWT_B2_t2


title: NKS1-C2


title: Fibroblast, LPS_Indoles_CH223191, rep2

source_name: Intestinal fibroblast

growth_protocol: Cells were cultured in a prewarmed complete medium consisting of DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (PS) at 37°C in a humidified incubator with 5% CO2.

value: Intestinal fibroblast

value: LPS and indoles and CH223191 intervention


title: mGB1-KD 2


title: Fibroblast, LPS_Indoles_CH223191, rep3

value: WT


title: mGB1-Ctrl 1


title: EPC_Med12KO_M_4

city: Fort Collins

first: Michelle

middle: M

last: Halstead

state: CO

address: 200 West Lake Street

department: Biomedical Sciences

country: USA

institute: Colorado State University

data_processing:
Raw reads were trimmed with Trim_Galore (v0.6.7) and aligned to the GRCm39 assembly with STAR (v2.7.10b). Low quality alignments (q < 5) were removed with SAMtools (v1.16) and raw counts for genes in the Ensembl (v108) annotation were calculated with HTSeq (v2.0.2) in mode “intersection-nonempty”.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw gene counts for each sample

source_name: Ectoplacental cone

growth_protocol: Ovaries from 12 day old females were incubated in digestion media (1x DPBS, 2 mg/mL collagenase type 1, 2 mg/mL BSA) at 37°C for 1 hr, then supplemented with 40 mM EDTA (pH 8.0) and incubated at 37°C for 10 min. Digested ovaries were centrifuged at 1000 rpm for 5 min, and cell pellets resuspended in pick-up media (1x MEM-Alpha, 25 mM NaHCO3, 2 mg/mL BSA). Oocytes were transferred to wash buffer (1x MEM-Alpha, 25 mM NaHCO3, 1 mg/mL BSA), then to 1x DPBS, and stored in media at -80°C. For GV and MII oocyte collection, female mice older than 6 weeks were synchronized by 5 IU PMSG. For GV oocytes, ovaries were collected 48 h after PMSG administration and transferred to collection media (1X Hepes-MEM, 6 mM NaHCO3, 0.23 mM sodium pyruvate, 3 mg/mL BSA) with 1/1000 cilostamide. Follicles were mechanically disrupted using two needles and oocytes were selected based on size and morphology. Oocytes were washed in maturation media (1X MEM-Alpha, 6 mM NaHCO3, 3 mg/mL BSA) with 1/1000 cilostamide, then in 1X DPBS, and stored in Trizol solution at -80°C. For MII oocytes, female mice were injected with 5 IU hCG 48 h after PMSG, and oocytes were collected 12-15 h after hCG. Ovaries were transferred to collection media. After follicle disruption, cumulus complexes were transferred to maturation media and denuded with 0.3 mg/mL hyaluronidase for 1 min. Denuded oocytes were washed in maturation media, then 1X DBPS, and stored in Trizol at -80°C. For E7,5 embryo collection, female mice older than 6 weeks were synchronized by 5 IU PMSG for 48 h, then injected with 5 IU hCG and mated with wild-type stud males of proven fertility. Uteri were collected from euthanized females 8 days post conception and transferred to HEPES-buffered DMEM supplemented with 10% FBS. Each embryo was carefully separated from the maternal decidua and dissected into the ectoplacental cone, extraembryonic ectoderm, and epiblast. Tissues were stored in Trizol solution at -80°C prior to RNA extraction.

extract_protocol:
For samples stored in Trizol solution at -80°C (GV and MII oocytes, E7.5 embryonic tissues), total RNA was extracted by phenol-chloroform extraction. The aqueous phase was subjected to column purification using the PicoPure RNA Isolation kit (ThermoFisher, KIT0204) and treated with DNase I (Qiagen, 79254) to remove genomic DNA. For samples stored in collection media at -80°C, total RNA was extracted using the Extraction Buffer provided in the PicoPure RNA Isolation kit.
For RNA extracted from oocytes, libraries were constructed with the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio). For RNA extracted from E7.5 embryonic tissues, libraries were constructed with the Tecan Universal Plus Total RNA library preparation kit (Tecan Life Sciences).

value: Ectoplacental cone

value: Maternal Med12 knockout

tag: developmental stage

tag: embryo sex

value: Male

tag: embryo id


title: BG4_bWT_B2_t1


title: BG4_bWT_B1_t3


title: NKS1-C1

value: Nature killer/T-cell lymphoma


title: EPC_Med12KO_M_3


title: YT_S2

source_name: YT

value: YT


title: YT_S1


title: YT_C2


title: BG4_bWT_B1_t2

value: myelogenous leukemia


title: Fibroblast, LPS_Indoles_CH223191, rep1


title: EPC_Med12KO_M_2


title: BG4_bWT_B1_t1


title: Fibroblast, LPS_Indoles, rep3

value: LPS and indoles intervention


title: EPI_Med12KO_M_3

source_name: Epiblast

value: Epiblast


title: YT_C1


title: Fibroblast, LPS_Indoles, rep2


title: BG4_bMut2_B3_t3

value: K562 bMut2


title: BG4_bMut2_B3_t2


title: Fibroblast, LPS_Indoles, rep1


title: EPI_Med12KO_M_2


title: Combo_2

state: Shanghai

address: 270 Dong'an Road

institute: Fudan University Shanghai Cancer Center

data_processing:
Raw reads were filtered and cleaned by fastp software.
adpators were removed by trim_galore
Aliments were performed followed by hisat2 instruction
featureCounts were used for counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

growth_protocol: SC1 are cultured in RPMI1640 medium supplemented with 20% fetal bovine serum, 1% penicillin-streptomycin.

treatment_protocol: SC1 were treated with DMSO,100 nM alisertib, 10 µM SGC-CBP30 or the combination for 24 hours.

value: diffuse large B-cell lymphoma

value: 100 nM alisertib + 10 µM SGC-CBP30


title: intestinal organoids, control, rep1

value: Intestinal organoid


title: BG4_bMut2_B3_t1


title: Fibroblast, LPS, rep3

value: LPS stimulation


title: Combo_1


title: EPI_Med12KO_M_1


title: ExE_Med12KO_M_2

source_name: Extraembryonic ectoderm

value: Extraembryonic ectoderm


title: Fibroblast, LPS, rep2

value: Intestinal fibroblast


title: SGC_2

value: 10 µM SGC-CBP30


title: BG4_bMut2_B2_t2


title: BG4_bMut2_B2_t3


title: EPC_Med12KO_M_1


title: SGC_1


title: BG4_bMut2_B2_t1


title: ExE_Med12KO_M_1


title: Fibroblast, LPS, rep1

value: WT


title: Alis_2

value: 100 nM alisertib


title: EPC_Med12KO_F_4

value: Ectoplacental cone

value: Maternal Med12 knockout

value: Female


title: Alis_1


title: Fibroblast, control, rep2

value: Control


title: Fibroblast, control, rep3


title: EPC_Med12KO_F_3


title: CTRL_2

value: DMSO


title: BG4_bMut2_B1_t3

value: myelogenous leukemia


title: BG4_bMut2_B1_t2


title: EPC_Med12KO_F_2


title: BG4_bMut2_B1_t1


title: Fibroblast, control, rep1


title: CTRL_1


title: EPC_Med12KO_F_1


title: RAW264.7 cells, fibroblast coculture, LPS_Indoles_CH223191, rep3

data_processing:
Raw reads underwent quality control using FastQC, and adapters and low-quality bases were trimmed using Trimmomatic.
The high-quality reads were aligned to the mouse genome (GRCm38/mm10).
Base-calling was performed using Illumina CASAVA (version 1.8.2).
Adapter sequences were removed and low-quality bases were trimmed using Trimmomatic (version 0.39). Quality control of reads was done using FastQC (version 0.11.9).
Reads were aligned to the reference genome (GRCm39) using STAR (version 2.7.5c). Gene expression was quantified using HTSeq-count (version 0.11.2) with default settings.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized data for each sample

source_name: RAW264.7 cells

value: RAW264.7 cells

value: Macrophage

value: Fibroblast coculture and LPS and  indoles and CH223191 intervention


title: BG4_bMut1_B2_t3

source_name: myelogenous leukemia

value: K562 bMut1


title: EPI_Med12KO_F_4

value: Epiblast


title: RAW264.7 cells, fibroblast coculture, LPS_Indoles_CH223191, rep2


title: BG4_bMut1_B2_t2


title: BG4_bMut1_B2_t1


title: RAW264.7 cells, fibroblast coculture, LPS_Indoles_CH223191, rep1


title: EPI_Med12KO_F_3


title: HC 5

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Main Building, 3-1 Yamadaoka,

department: Immunology Frontier Research Center

institute: Osaka University

description: Library name: 240112_231204_135

data_processing:
Following DNBelab C Series Single-Cell RNA Analysis Software instructions available in https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_scRNA-analysis-software.
Assembly: hg38
Supplementary files format and content: Filtered matrix and cell barcode files in tar.gz

source_name: Normal colon

extract_protocol:
Intestinal mucosa was washed in phosphate-buffered saline (PBS) to remove feces and intestinal mucosa was replaced in RPMI 1640 containing 2.5 mM EDTA and incubated for 15 minutes in a 37℃ shaking water bath. After washing in PBS, the mucosa was cut into small pieces and incubated in RPMI 1640 containing 10% fetal bovine serum, 2 mg/mL collagenase D, 1 mg/mL dispase, and 15 mg/mL DNase I for 45 minutes in a 37℃ shaking water bath. The digested tissues were suspended with RPMI 1640 containing 2.5 mM EDTA, and passed through a 40μm cell strainer. The isolated LPMCs were washed in PBS. Freshly collected LPMCs from normal sites of colorectal cancer were sorted by FCM. Freshly collected from inflamed sites of UC were stored at −80 ℃ and sorted by FCM after 1–2 weeks.
Following DNBelab C4 Pocket Single-Cell Lab instructions.

value: Normal colon

value: stromal cells


title: RAW264.7 cells, fibroblast coculture, LPS_Indoles, rep3

value: Fibroblast coculture and LPS and indoles intervention


title: BG4_bMut1_B1_t3


title: HC 3

description: Library name: 231215_231108_128


title: EPI_Med12KO_F_2


title: HC 6

description: Library name: 240112_231213_136


title: UC 1

description: Library name: 240216_231214_137M

source_name: UC colon

value: UC colon


title: RAW264.7 cells, fibroblast coculture, LPS_Indoles, rep2

value: WT


title: RAW264.7 cells, fibroblast coculture, LPS_Indoles, rep1


title: BG4_bMut1_B1_t1


title: ExE_Med12KO_F_3

value: Extraembryonic ectoderm


title: ExE_Med12KO_F_2


title: RAW264.7 cells, fibroblast coculture, LPS, rep3

value: Fibroblast coculture and LPS stimulation


title: HCT116 TP53 -/- cells, 6h, rep3

city: BALTIMORE

first: Marikki

last: Laiho

state: Maryland

address: 1550 Orleans St

department: Department of Radiation Oncology and Molecular Radiation Sciences

institute: Johns Hopkins University

data_processing:
Reads were analyzed using Tophat 2 and Cuffdiff 2.0, respectively for alignment to reference genome
Assembly: GRCh37
Supplementary files format and content: xlsx, gene expression(FPKM) table

source_name: colon

growth_protocol: McCoy's5a Medium +10%FBS

extract_protocol:
Trizol extraction protocol
RNA-seq library for Illumina platform sequencing was prepared using Illumina TruSeq stranded total RNA Sample kit

treatment_protocol: Cells were treated with DMSO (control) or treated with BMH-21, 1 microM for 6 hours.

value: colon

value: Human colorectal carcinoma cell line

value: BMH-21 1 uM 6 hours


title: UC 2

description: Library name: 240226_231221_141M


title: UC 7

description: Library name: 240425_240125_163


title: ExE_Med12KO_F_1

value: Maternal Med12 knockout

value: Female


title: RAW264.7 cells, fibroblast coculture, LPS, rep2

value: RAW264.7 cells


title: HCT116 TP53 -/- cells, 6h, rep2


title: UC 5

description: Library name: 240425_240117_155


title: EPC_WT_M_4

value: Ectoplacental cone

value: Male


title: EPI_Med12KO_F_1


title: RAW264.7 cells, fibroblast coculture, LPS, rep1

value: Macrophage


title: UC 4

description: Library name: 240226_240111_148M


title: HCT116 TP53 -/- cells, 6h, rep1


title: EPC_WT_M_3


title: BG4_bMut1_B1_t2

value: myelogenous leukemia

value: K562 bMut1


title: HCT116 TP53 -/- cells, 0h, rep3

value: control


title: HC 2

description: Library name: 230927_90

value: Normal colon

value: stromal cells


title: RAW264.7 cells, fibroblast coculture, rep2

value: WT

value: Fibroblast coculture


title: HC 4

description: Library name: 231215_231129_134


title: UC 6

description: Library name: 240425_240122_156

value: UC colon


title: EPC_WT_M_1


title: HCT116 TP53 -/- cells, 0h, rep2

value: colon


title: RAW264.7 cells, fibroblast coculture, rep3


title: EPI_WT_M_4

value: Epiblast


title: HCT116 TP53 +/+ cells, 6h, rep3

data_processing:
Reads were analyzed using Tophat 2 and Cuffdiff 2.0, respectively for alignment to reference genome
Assembly: GRCh37
Supplementary files format and content: xlsx, gene expression (FPKM) table

value: Human colorectal carcinoma cell line

value: BMH-21 1 uM 6 hours


title: HCT116 TP53 -/- cells, 0h, rep1


title: RAW264.7 cells, LPS_Indoles_CH223191, rep3

value: LPS and indoles and CH223191 intervention


title: UC 3

description: Library name: 240226_240110_146M


title: EPI_WT_M_3


title: RAW264.7 cells, LPS_Indoles_CH223191, rep2

value: RAW264.7 cells


title: HC 1

description: Library name: 230913_88


title: HCT116 TP53 +/+ cells, 6h, rep2


title: EPI_WT_M_2


title: C18_iHO_P4

description: Library name: C18_iHO_P4

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v8.0.1
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
iPSC-derived organoids (under iHO and FOcondition) embedded in Matrigel were washed by ice-cold PBS and dissociated into single cells by using trypsin/EDTA(0.05%) for 10-20 minutes. Cell viability was confirmed to be over 80 % by staining trypan blue. Viable cells (over 5000) underwent scRNA-seq library preparation and were sequenced using the 10x Genomics Chromium platform, according to the manufacturer’s protocols.
Libraries were prepared using Single Cell 3' v2 Reagent Kit(10X Genomics)

value: iPSC


title: RAW264.7 cells, fibroblast coculture, rep1


title: RAW264.7 cells, LPS_Indoles_CH223191, rep1


title: HCT116 TP53 +/+ cells, 6h, rep1


title: C18_FO_P0

description: Library name: C18_FO_P0


title: EPI_WT_M_1

value: Male


title: RAW264.7 cells, LPS_Indoles, rep3

value: Macrophage

value: LPS and indoles intervention


title: EPC_WT_M_2

value: Ectoplacental cone


title: HCT116 TP53 +/+ cells, 0h, rep3

value: control


title: RAW264.7 cells, LPS_Indoles, rep2


title: ExE_WT_M_3

value: Extraembryonic ectoderm


title: HCT116 TP53 +/+ cells, 0h, rep2


title: Old_MDSC_3

city: Ulm

first: Emma

last: Keltsch

address: Eythstr. 24

department: Department of Pediatrics and Adolescent Medicine

institute: University Medical Center Ulm

data_processing:
Raw reads were filtered using SOAPnuke (v1.5.2), and clean reads were aligned to the reference genome (Homo_sapiens, NCBI, GCF_000001405.39_GRCh38.p13) with HISAT2 (v2.0.4). Bowtie2 (2.2.5) was used for gene set mapping.
Assembly: Homo_sapiens, NCBI, GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: Peripheral blood

growth_protocol: CD14+ cells were isolated from peripheral blood by negative depletion and density gradient separation. CD14+ cells from each donor were used for both RNA extraction and in vitro differentiation into MDSCs. MDSCs were differentiated in the presence of IL-6 and GM-CSF for 5 days.

extract_protocol:
Total RNA was isolated using the Direct-zol™ RNA Mini Prep Kit (Zymo Research) according to the manufacturer's protocol.
RNA samples were forwarded to the Beijing Genomics Institute (BGI, Beijing, China) for paired-end RNA-Seq. Quality control was initially performed using a fragment analyzer. For RNA library construction, mRNA was enriched using oligo(dT) beads. The mRNA was then fragmented, and cDNA was synthesized with dUTP incorporated into the second strand. After end-repair, adenylation, and adaptor ligation, the dUTP-labeled strand was degraded by Uracil-DNA-Glycosylase (UDG), and the remaining strand was amplified by PCR. The PCR product was denatured, cyclized, and used to generate DNA nanoballs, which were sequenced on the DNBSEQ platform.
Raw reads were filtered using SOAPnuke (v1.5.2), and clean reads were aligned to the reference genome (Homo_sapiens, NCBI, GCF_000001405.39_GRCh38.p13) with HISAT2 (v2.0.4). Bowtie2 (2.2.5) was used for gene set mapping.

value: Peripheral blood

value: CD14+-derived MDSCs

value: IL-6 and GM-CSF

tag: age


title: HCT116 TP53 +/+ cells, 0h, rep1


title: Old_MDSC_4


title: RAW264.7 cells, LPS_Indoles, rep1

value: WT


title: ExE_WT_M_1


title: RAW264.7 cells, LPS, rep3

value: LPS stimulation


title: Old_MDSC_2


title: EPC_WT_F_4

value: Female


title: Old_MDSC_1


title: A375_6h_rep2

source_name: skin

value: skin

value: melanoma


title: A375_6h_rep1

value: BMH-21 1 uM 6 hours


title: RAW264.7 cells, LPS, rep1

value: RAW264.7 cells


title: EPC_WT_F_3


title: RAW264.7 cells, LPS, rep2


title: EPC_WT_F_2


title: Young_MDSC_5


title: RAW264.7 cells, control, rep3

value: Control


title: A375_0h_rep3


title: Young_MDSC_4


title: EPC_WT_F_1


title: C18_iHO_P0

description: Library name: C18_iHO_P0

value: iPSC


title: RAW264.7 cells, control, rep2

value: Macrophage


title: A375_0h_rep2


title: EPI_WT_F_3

value: Epiblast


title: Young_MDSC_3


title: RAW264.7 cells, control, rep1


title: ExE_WT_M_2

value: Male


title: Young_MDSC_2


title: SVI cells, unstretched, experiment 2, 3

city: Hamburg

first: Olga

last: Tsoy

state: Hamburg

address: Alber-Einstein Ring 8-10

institute: Universität Hamburg

data_processing:
RNA-Seq raw reads were aligned to the mouse reference genome mm39 with the genome annotation from Ensembl version 104 using STAR version 2.7.5c (2-pass mode)
Gene read counts were obtained by the featureCounts tool included in the Subread 2.0.0 with default parameters
Read counts were further normalized and used for differential gene expression by DESeq2 version 1.38.3
Transcript counts were obtained using salmon version 1.9.0 with the transcript annotation based on Ensembl version 104
Assembly: mm39
Supplementary files format and content: whitespace-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes transcript TPM counts for each Sample

source_name: Kidney

extract_protocol:
Cells were processed in Tri-Reagent (Sigma-Aldrich) according to manufacturer's instructions, followed by DNA-digestion steps  using the RNAase-Free DNase I Kit and RNA Clean-Up and Concentration kit according to manufacturer’s instructions (both Norgen Biotek Corp., Thorold, ON, Canada).
Briefly, after quality assessment using Tape Station 4200 (Agilent, Santa Clara, CA, USA), a PolyA library was prepared based on 500ng total RNA per sample using the TruSeq stranded mRNA kit (Illumina, San Diego, CA, USA).  Subsequently, for sequencing 200pM of the final library were loaded on the NovaSeq 6000 System, S1 FlowCell (2 x 100 bp pair-end reads). A sequencing depth of ~ 200 Mio Cluster per sample was obtained, recorded at the Competence Centre for Genomic analysis in Kiel.

value: Kidney

value: SVI

value: Podocytes

value: unstretched


title: EPI_WT_F_2


title: Young_MDSC_1

value: Peripheral blood

value: CD14+-derived MDSCs

value: IL-6 and GM-CSF


title: EPI_WT_F_1

value: WT

value: Female


title: MCF7 Parental RNAseq Replicate 3

city: Bethesda

first: Pedro

middle: J

last: Batista

state: MD

address: 37 Convent Street Bldg 37

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
FastQC Read Quality Analysis
Cutadapt Trimming
hg38 alignment using Spliced Transcripts Alignment
Htseq-count read-mapping
Differential Expression with DESeq2
Assembly: hg38
Supplementary files format and content: count matrix

extract_protocol:
Rneasy kit
TruSeq Stranded mRNA library prep kit

value: Breast Cancer


title: A375_6h_rep3

value: skin

value: melanoma

value: BMH-21 1 uM 6 hours


title: SVI cells, high-stretch, experiment 2, 3


title: MCF7 Parental RNAseq Replicate 2


title: SVI cells, unstretched, experiment 2, 2


title: Old_CD14_2

value: CD14+ monocytes

value: no treatment


title: MCF7 Parental RNAseq Replicate 1


title: ExE_WT_F_4

value: Extraembryonic ectoderm


title: ExE_WT_F_3


title: Old_CD14_3


title: SVI cells, high-stretch, experiment 2, 2


title: Old_CD14_1


title: Young_CD14_4


title: MCF7 DpVp RNAseq Replicate 2

source_name: MCF7 DPVP

value: MCF7 DPVP

value: Romidepsin Resistant


title: MCF7 DpVp RNAseq Replicate 3


title: A375_0h_rep1

value: control


title: ExE_WT_F_1


title: MCF7 DpVp RNAseq Replicate 1


title: SVI cells, high-stretch, experiment 2, 1

value: Kidney

value: SVI

value: Podocytes


title: Young_CD14_3

value: Peripheral blood


title: MII_WT_3

source_name: Metaphase II oocytes

value: Metaphase II oocytes

value: Adult


title: SVI cells, unstretched, experiment 1, 3

value: unstretched


title: SVI cells, unstretched, experiment 2, 1


title: Young_CD14_2


title: HuT78 Parental RNAseq Replicate 3

value: T-lymphocyte

value: WT


title: SVI cells, low-stretch, experiment 1, 5


title: HuT78 Parental RNAseq Replicate 2


title: MII_WT_1


title: MII_WT_2


title: SVI cells, low-stretch, experiment 1, 6


title: HuT78 Parental RNAseq Replicate 1


title: ExE_WT_F_2

value: Female


title: iPSC_1

data_processing:
Salmon v1.2.1
Read count extraction and normalization were performed using salmon
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts

extract_protocol:
Total RNA was extracted by RNeasy Micro (QIAGEN, Venlo, Netherlands).
RNA libraries for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Set following manufacturer's protocols.

value: iPSC

tag: sample type

value: 2D cultured cell


title: BR2DM25T0B_RNAseq_0 hours_DM25

city: Houston

first: Brittney

last: Lozzi

state: TX

address: 1 Baylor Plaza

department: Cell & Gene Therapy

institute: Baylor College of Medicine

description:
Library name: BR2DM25T0B
BR2DM25T0B

data_processing:
The NASA GeneLab RNA-Seq pipeline was utilized to perform a STAR alignment of reads to the REL606 (NCBI Reference Sequence: NC_012967.1) genome for transcriptomic analysis
Feature counts (v2.0.6) was used to generate a counts table of reads per gene for each sample.
DESeq2 (v1.40.2) was used for read count normalization and differential gene expression analysis.
Assembly: REL606 (NCBI Reference Sequence: NC_012967.1)
Supplementary files format and content: Comma separated file includes normalized counts per million values for each sample

organism: Escherichia coli

growth_protocol: cultures were grown at 25C for 24 hours

extract_protocol:
Samples were collected at 4.5 or 6.5 or 24 hours depending on culture media. Cultures were concentrated with CP SELECT (0.20 µm) device. Frozen cell pellets were sent on dry ice to Azenta GeneWiz for RNA extraction, ribosomal depletion, library preparation and 2x150 base pair, paired-end sequencing.
Ribosomal RNA-depleted libraries were constructed at Azenta GeneWiz

treatment_protocol: Cuttures were rotataed at 20rpm vertically, horizontially, or  static with no rotation. Cultures were grown in Davis Minimal media with 25mg/L glucose or in 2000mg/L glucose.

tag: time

value: 0 hours

tag: media


title: BR2DM25T0A_RNAseq_0 hours_DM25

description:
Library name: BR2DM25T0A
BR2DM25T0A

tag: cell line


title: SVI cells, unstretched, experiment 1, 2

tag: tissue

tag: cell type

tag: treatment


title: HuT78 DpVp RNAseq Replicate 2

source_name: HuT78 DpVp

value: HuT78 DpVp

tag: genotype


title: HuT78 DpVp RNAseq Replicate 3


title: BR2DM2000T2SuGA_RNAseq_24 hours_DM2000

description:
Library name: BR2DM2KT24uGA
BR2DM2000T2SuGA

value: 24 hours

value: simulated microgravity


title: iPSHPC_1


title: BR5DM2000T1SuGA_RNAseq_6.5 hours_DM2000

description:
Library name: BR5DM2000T65SuGA
BR5DM2000T1SuGA

value: 6.5 hours


title: HuT78 DpVp RNAseq Replicate 1

value: Romidepsin Resistant


title: Patient 3, atopic dermatitis, lesional, sample 1, scATAC-seq [P3_AD_ATAC_L1]

city: Cambridge

first: Evgenij

last: Fiskin

state: MA

address: 415 Main St

institute: Broad Institute of MIT and Harvard, Massachusetts General Hospital

description: 10x Genomics

data_processing:
Raw sequencing data were demultiplexed using CellRanger-ATAC mkfastq and aligned to a mtDNA blacklist-modified (Lareau et al., 2020) hg19 human reference genome using CellRanger-ATAC count v1.1. Fragment files from this pre-processing were used as input to ArchR (Granja et al., 2021).
Assembly: hg19
Supplementary files format and content: ArchR Version 1.0.1 file in RDS format

extract_protocol:
Whole skin punch biopsies (3-4mm) or mouse dorsal skin was cut into two pieces, such that each piece contains all skin layers and storage medium was removed. Enzymatic dissociation was performed using Whole Skin Dissociation kit (Miltenyi Biotec, #130-101-540) with a modified protocol. Cut biopsies were transferred into a gentleMACS C-tube containing 435µl Buffer L, 12.5µl Enzyme P, 50µl Enzyme D and 2.5µl Enzyme A. Enzymatic dissociation was performed for 3.5h at 37°C. After incubation, 500µl of cold DMEM containing 10% FBS and 2 mM L-glutamine were added. The tissue was mechanically dissociated using a gentleMACS dissociator run on program h_skin_01. The resulting cellular suspension was filtered through a 70µm cell strainer (Falcon, #352350) and 4.5ml cold DMEM containing 10% FBS and 2 mM L-glutamine were added. Cells were spun down at 300g for 10min at 4°C. The supernatant was then aspirated and cells were resuspended in 1.2ml ACK buffer (A10492-01). Suspensions were transferred to 1.5ml tubes and incubated for 2min for red blood cell lysis and spun at 350g for 4min at 4°C. Supernatants were aspirated and cells were resuspended in 50-100µl 0.4% BSA in PBS. Cell viability and cell counts were determined and cells were processed for scRNA-seq.
Library was performed according to the manufacter’s instructions (single cell ATAC v1.1 protocol, 10x Genomics). Single cells were processed through the 10x Genomics Chromium Platform according to manufacturer’s instructions (10x Genomics). Briefly, cells were lysed and transposed using Tn5 transposase, then encapsulated into Gel Beads in Emulsion (GEMs) droplets using the Chromium instrument. After encapsulation, ATAC fragment libraries were generated following the manufacturer’s protocol, including barcoded linear amplification and sample indexing steps.

value: skin

tag: disease

value: Atopic dermatitis


title: BR5DM2000T1SA_RNAseq_6.5 hours_DM2000

description:
Library name: BR5DM2000T65SA
BR5DM2000T1SA

value: static


title: Patient 9, atopic dermatitis, lesional, sample 1, 5' scRNA-seq, VDJ [P9_AD_5_L1]

description: 10x Genomics

data_processing:
library strategy: 5' scRNA-seq and VDJ
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger v2.0.2 V(D)J pipeline
Assembly: GRCh38
Supplementary files format and content: h5ad files

extract_protocol:
Whole skin punch biopsies (3-4mm) or mouse dorsal skin was cut into two pieces, such that each piece contains all skin layers and storage medium was removed. Enzymatic dissociation was performed using Whole Skin Dissociation kit (Miltenyi Biotec, #130-101-540) with a modified protocol. Cut biopsies were transferred into a gentleMACS C-tube containing 435µl Buffer L, 12.5µl Enzyme P, 50µl Enzyme D and 2.5µl Enzyme A. Enzymatic dissociation was performed for 3.5h at 37°C. After incubation, 500µl of cold DMEM containing 10% FBS and 2 mM L-glutamine were added. The tissue was mechanically dissociated using a gentleMACS dissociator run on program h_skin_01. The resulting cellular suspension was filtered through a 70µm cell strainer (Falcon, #352350) and 4.5ml cold DMEM containing 10% FBS and 2 mM L-glutamine were added. Cells were spun down at 300g for 10min at 4°C. The supernatant was then aspirated and cells were resuspended in 1.2ml ACK buffer (A10492-01). Suspensions were transferred to 1.5ml tubes and incubated for 2min for red blood cell lysis and spun at 350g for 4min at 4°C. Supernatants were aspirated and cells were resuspended in 50-100µl 0.4% BSA in PBS. Cell viability and cell counts were determined and cells were processed for scRNA-seq.
Library was performed according to the manufacter’s instructions (single cell 5’ v1.1 protocol, 10x Genomics). 5’- v1.1 chemistry for single-cell TCR-enriched V(D)J profiling. Single cells were processed through the 10x Genomics Chromium Platform according to manufacturer’s instructions (10x Genomics). Briefly, cells were encapsulated into Gel Beads in Emulsion (GEMs) droplets using the Chromium instrument. After encapsulation and cell lysis, cDNA expression libraries were generated following the manufacturer’s protocol, including barcoded reverse transcription, cDNA amplification, enzymatic fragmentation, adapter ligation and sample indexing steps.


title: SVI cells, low-stretch, experiment 1, 2

value: Kidney

value: SVI

value: Podocytes


title: iPSHep_1


title: BR5DM2000T1RA_RNAseq_6.5 hours_DM2000

description:
Library name: BR5DM2000T65RA
BR5DM2000T1RA

value: rotating


title: Young_CD14_1

value: Peripheral blood

value: CD14+ monocytes

value: no treatment


title: iPSC_2

value: iPSC

value: 2D cultured cell


title: Patient 8, atopic dermatitis, lesional, sample 1, 5' scRNA-seq, VDJ [P8_AD_5_L1]

description: 10x Genomics


title: SVI cells, low-stretch, experiment 1, 1


title: iHO3_P3_2

value: organoid

tag: passage


title: BR5DM2000T2SuGA_RNAseq_24 hours_DM2000

description:
Library name: BR5DM2000T24SuGA
BR5DM2000T2SuGA

value: 24 hours


title: WT3-IgG

first: Yue

last: Lu

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
library strategy: CUT&RUN
Adapter sequences were removed from the 3' ends of reads using Trim Galore! (version 0.6.5) and cutadapt (version 2.8).
The reads were then mapped to the mouse genome (mm10) using Bowtie (version 1.1.2) with the following parameters: "-v 2 -m 1 --best --strata".
To avoid PCR bias, only one copy of multiple fragments mapped to the same genomic position was retained for further analysis. Moreover, fragments longer than 800 bp (less than 1% of the total) were excluded from subsequent analysis.
To generate the signal landscape, each fragment was resized to a length of 151 bp, spanning from -75 bp to +75 bp around its midpoint. The count of fragments covering each genomic position was multiplied by 10M divided by the number of total fragments. These values were then averaged over a 10 bp resolution and stored in bigwig format.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: embronic liver

growth_protocol: Mouse fetal liver cells were collected and treated with 10 ng/mL thrombopoietin for 4 days. Megakaryocytes were separated by sedimentation for 1 hour at 37C.

extract_protocol:
Genomic DNA were extracted using the CUTANA™ CUT&RUN Library Prep Kit, following the manufacture's protocol.
CUT&RUN libraries were prepared with the CUTANA™ CUT&RUN Library Prep Kit, following the manufacture's instructions.

value: embronic liver

value: primary cells

value: megakaryocytes

value: IgG


title: Patient 13, scleroderma, non-lesional and lesional, sample 1, 3' scRNA-seq [P13_SC]

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0
Assembly: GRCh38 (human samples) and mm10 (murine samples)
Supplementary files format and content: h5ad files

extract_protocol:
Whole skin punch biopsies (3-4mm) or mouse dorsal skin was cut into two pieces, such that each piece contains all skin layers and storage medium was removed. Enzymatic dissociation was performed using Whole Skin Dissociation kit (Miltenyi Biotec, #130-101-540) with a modified protocol. Cut biopsies were transferred into a gentleMACS C-tube containing 435µl Buffer L, 12.5µl Enzyme P, 50µl Enzyme D and 2.5µl Enzyme A. Enzymatic dissociation was performed for 3.5h at 37°C. After incubation, 500µl of cold DMEM containing 10% FBS and 2 mM L-glutamine were added. The tissue was mechanically dissociated using a gentleMACS dissociator run on program h_skin_01. The resulting cellular suspension was filtered through a 70µm cell strainer (Falcon, #352350) and 4.5ml cold DMEM containing 10% FBS and 2 mM L-glutamine were added. Cells were spun down at 300g for 10min at 4°C. The supernatant was then aspirated and cells were resuspended in 1.2ml ACK buffer (A10492-01). Suspensions were transferred to 1.5ml tubes and incubated for 2min for red blood cell lysis and spun at 350g for 4min at 4°C. Supernatants were aspirated and cells were resuspended in 50-100µl 0.4% BSA in PBS. Cell viability and cell counts were determined and cells were processed for scRNA-seq.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, single cell supsension from whole skin biopsies were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: skin

value: Scleroderma


title: iHO3_P3_1


title: WT3-H3K4me3


title: iPSHPC_2


title: iHO2_P3_2


title: SVI cells, low-stretch, experiment 1, 3

value: Kidney


title: BR5DM2000T2SA_RNAseq_24 hours_DM2000

description:
Library name: BR5DM2000T24SA
BR5DM2000T2SA

value: static


title: SVI cells, low-stretch, experiment 1, 4

value: SVI

value: Podocytes


title: WT3-H3K4me1


title: iPSHep_2


title: Normal skin 6, sample 1, 3' scRNA-seq [Normal6_1]

description: 10x Genomics

value: Healthy


title: iHO2_P3_1


title: BR5DM2000T2RA_RNAseq_24 hours_DM2000

description:
Library name: BR5DM2000T24RA
BR5DM2000T2RA

value: rotating


title: WT3-H3K27ac


title: iHOwoBA2_P3_2


title: Normal skin 5, sample 1, 3' scRNA-seq [Normal5_1]

description: 10x Genomics


title: SVI cells, unstretched, experiment 1, 1

value: unstretched


title: WT2-IgG


title: BR5DM2000T0A_RNAseq_0 hours_DM2000

description:
Library name: BR5DM2000T0A
BR5DM2000T0A

value: 0 hours


title: iHOwoBA2_P3_1

value: iPSC


title: BR5DM2000T0B_RNAseq_0 hours_DM2000

description:
Library name: BR5DM2000T0B
BR5DM2000T0B


title: Normal skin 3, sample 2, 3' scRNA-seq [Normal3_2]

description: 10x Genomics


title: BR5DM25T1SuGA_RNAseq_4.5 hours_DM25

description:
Library name: BR5DM25T45SuGA
BR5DM25T1SuGA

value: 4.5 hours

value: simulated microgravity


title: FO2_P3_2

value: organoid


title: WT2-H3K4me1

value: embronic liver

value: primary cells


title: FO2_P3_1


title: WT2-H3K4me3

value: megakaryocytes


title: BR2DM2000T2SA_RNAseq_24 hours_DM2000

description:
Library name: BR2DM2KT24SA
BR2DM2000T2SA

value: 24 hours


title: Patient 12, scleroderma, non-lesional and lesional, sample 1, 3' scRNA-seq [P12_SC]

description: 10x Genomics

value: skin

value: Scleroderma


title: Normal skin 2, sample 1, 3' scRNA-seq [Normal2_1]

description: 10x Genomics


title: BR5DM25T1SA_RNAseq_4.5 hours_DM25

description:
Library name: BR5DM25T45SA
BR5DM25T1SA

value: static


title: WT2-H3K27ac


title: BR5DM25T1RA_RNAseq_4.5 hours_DM25

description:
Library name: BR5DM25T45RA
BR5DM25T1RA


title: Normal skin 1, sample 1, 3' scRNA-seq [Normal1_1]

description: 10x Genomics


title: iHO1_P3_1


title: BR5DM25T2SuGA_RNAseq_24 hours_DM25

description:
Library name: BR5DM25T24SuGA
BR5DM25T2SuGA


title: Normal skin 4, sample 1, 3' scRNA-seq [Normal4_1]

description: 10x Genomics


title: BR5DM25T2SA_RNAseq_24 hours_DM25

description:
Library name: BR5DM25T24SA
BR5DM25T2SA


title: iHOTCA1_P3_2


title: iHOTCA1_P3_1


title: WT1-H3K4me1


title: Patient 11, atopic dermatitis, lesional, sample 1, 3' scRNA-seq [P11_AD_L1]

description: 10x Genomics

value: Atopic dermatitis


title: Patient 10, atopic dermatitis, lesional, sample 2, 3' scRNA-seq [P10_AD_L2]

description: 10x Genomics


title: WT1-H3K27ac


title: iHOwoBA1_P3_2


title: Normal skin 3, sample 1, 3' scRNA-seq [Normal3_1]

description: 10x Genomics


title: Patient 11, atopic dermatitis, non-lesional, sample 1, 3' scRNA-seq [P11_AD_NL1]

description: 10x Genomics


title: BR2DM2000T2RA_RNAseq_24 hours_DM2000

description:
Library name: BR2DM2KT24RA
BR2DM2000T2RA


title: Patient 10, atopic dermatitis, lesional, sample 1, 3' scRNA-seq [P10_AD_L1]

description: 10x Genomics


title: BR5DM25T0B_RNAseq_0 hours_DM25

description:
Library name: BR5DM25T0B
BR5DM25T0B


title: PKO3-IgG

value: IgG


title: WT1-H3K4me3


title: iHOwoBA1_P3_1


title: Patient 10, atopic dermatitis, non-lesional, sample 2, 3' scRNA-seq [P10_AD_NL2]

description: 10x Genomics


title: PKO3-H3K4me3


title: BR5DM25T2RA_RNAseq_24 hours_DM25

description:
Library name: BR5DM25T24RA
BR5DM25T2RA


title: iHO1_P3_2


title: Patient 10, atopic dermatitis, non-lesional, sample 1, 3' scRNA-seq [P10_AD_NL1]

description: 10x Genomics


title: PKO3-H3K4me1


title: BR5DM25T0A_RNAseq_0 hours_DM25

description:
Library name: BR5DM25T0A
BR5DM25T0A


title: FO1_P3_1


title: FO1_P3_2


title: WT1-IgG


title: PKO3-H3K27ac


title: BR4DM2000T1SuGA_RNAseq_6.5 hours_DM2000

description:
Library name: BR4DM2000T65SuGA
BR4DM2000T1SuGA

value: 6.5 hours


title: Patient 9, atopic dermatitis, lesional, sample 1, 3' scRNA-seq [P9_AD_L1]

description: 10x Genomics


title: iHO1_P1_2


title: Patient 9, atopic dermatitis, lesional, sample 2, 3' scRNA-seq [P9_AD_L2]

description: 10x Genomics


title: PKO2-IgG


title: iHO1_P1_1


title: BR4DM2000T1RA_RNAseq_6.5 hours_DM2000

description:
Library name: BR4DM2000T65RA
BR4DM2000T1RA

value: rotating


title: PKO2-H3K4me3


title: Patient 9, atopic dermatitis, non-lesional, sample 1, 3' scRNA-seq [P9_AD_NL1]

description: 10x Genomics


title: PKO2-H3K4me1


title: Patient 9, atopic dermatitis, non-lesional, sample 2, 3' scRNA-seq [P9_AD_NL2]

description: 10x Genomics


title: BR4DM2000T2SuGA_RNAseq_24 hours_DM2000

description:
Library name: BR4DM2000T24SuGA
BR4DM2000T2SuGA


title: Patient 8, atopic dermatitis, lesional, sample 1, 3' scRNA-seq [P8_AD_L1]

description: 10x Genomics


title: iHOTCA1_P1_1


title: PKO2-H3K27ac


title: PKO1-IgG


title: iHOwoBA1_P1_2


title: Patient 7, atopic dermatitis, lesional, sample 2, 3' scRNA-seq [P7_AD_L2]

description: 10x Genomics


title: BR4DM2000T2RA_RNAseq_24 hours_DM2000

description:
Library name: BR4DM2000T24RA
BR4DM2000T2RA


title: iHOwoBA1_P1_1


title: PKO1-H3K4me3


title: PKO1-H3K4me1


title: BR4DM2000T0A_RNAseq_0 hours_DM2000

description:
Library name: BR4DM2000T0A
BR4DM2000T0A


title: Patient 7, atopic dermatitis, non-lesional, sample 1, 3' scRNA-seq [P7_AD_NL1]

description: 10x Genomics


title: Patient 7, atopic dermatitis, lesional, sample 1, 3' scRNA-seq [P7_AD_L1]

description: 10x Genomics


title: BR4DM2000T1SA_RNAseq_6.5 hours_DM2000

description:
Library name: BR4DM2000T65SA
BR4DM2000T1SA


title: FO1_P1_2


title: FO1_P1_1


title: Patient 6, atopic dermatitis, lesional, sample 2, 3' scRNA-seq [P6_AD_L2]

description: 10x Genomics


title: BR2DM2000T1SuGA_RNAseq_6.5 hours_DM2000

description:
Library name: BR2DM2KT16uGA
BR2DM2000T1SuGA


title: BR4DM25T1SuGA_RNAseq_4.5 hours_DM25

description:
Library name: BR4DM25T45SuGA
BR4DM25T1SuGA


title: PKO1-H3K27ac


title: iPS-Hepatocyte-Organoid

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v2.1.1
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Organoids (under iHO condition and passage 1) embedded in Matrigel were washed by ice-cold PBS and dissociated into single cells by using trypsin/EDTA(0.05%) for 10-20 minutes. Cell viability was confirmed to be over 80 % by staining trypan blue. The viable 5000 cells underwent the scRNA-seq library preps and sequenced with 10x Genomics Chronium platform, according to the manufacturer’s protocols.
Libraries were prepared using Single Cell 3' v2 Reagent Kit(10X Genomics)


title: iHOTCA1_P1_2


title: Patient 6, atopic dermatitis, lesional, sample 1, 3' scRNA-seq [P6_AD_L1]

description: 10x Genomics


title: DKO3-IgG


title: Patient 6, atopic dermatitis, non-lesional, sample 2, 3' scRNA-seq [P6_AD_NL2]

description: 10x Genomics


title: BR4DM25T1SA_RNAseq_4.5 hours_DM25

description:
Library name: BR4DM25T45SA
BR4DM25T1SA


title: DKO3-H3K4me3


title: C16_day3_rep2

city: Athens

first: Romanos

last: Siaperas

address: 9 Iroon Polytechniou str.

department: School of Chemical Engineering

country: Greece

institute: National Technical University of Athens

description: Library name: C16_D3C

data_processing:
Analysis was done with the nf-core rnaseq v3.10.1 pipeline
Mapping with STAR 2.7.9a and options "--alignIntronMin 10 --alignIntronMax 3000”
Quantification with Salmon 1.9.0
Counts were imported in edgeR v3.43.4 and normalized with TMM.
Differential expression with the edgeR-exact test. The p- value was adjusted with the Benjamini-Hochberg correction and corresponds to an FDR of 5 %
Assembly: GCA_037075405.1
Supplementary files format and content: tab delimited text files include raw counts for each sample
Supplementary files format and content: tab delimited text file includes log2 rpkm values after TMM normalization for each sample

organism: Aspergillus parasiticus

source_name: fungal

growth_protocol: Aspergillus parasiticus MM36 was grown in liquid cultures using mineral medium either supplemented with hexadecane (C16) or a mixture of long-chain alkanes (lcAlk) dissolved in hexadecane. Cultures were incubated at 27 °C, under continuous stirring at 120 rpm.

extract_protocol:
Total RNA was extracted by Novogene and the polyA+ fraction was purified.
Libraries were constructed with the Novogene NGS RNA Library Prep Set (PT042)* kit

treatment_protocol: The fungal biomass was harvested under vacuum and washed with ultrapure water under aseptic conditions and immediately flash-frozen using liquid nitrogen.

value: fungal

value: WT

value: Hexadecane 3 days

value: Day 3


title: BR4DM2000T2SA_RNAseq_24 hours_DM2000

description:
Library name: BR4DM2000T24SA
BR4DM2000T2SA


title: BR4DM25T1RA_RNAseq_4.5 hours_DM25

description:
Library name: BR4DM25T45RA
BR4DM25T1RA

value: 4.5 hours


title: Patient 6, atopic dermatitis, non-lesional, sample 1, 3' scRNA-seq [P6_AD_NL1]

description: 10x Genomics


title: BR4DM2000T0B_RNAseq_0 hours_DM2000

description:
Library name: BR4DM2000T0B
BR4DM2000T0B

value: 0 hours


title: C16_day3_rep1

description: Library name: C16_D3B


title: Patient 5, atopic dermatitis, lesional, sample 1, 3' scRNA-seq [P5_AD_L1]

description: 10x Genomics


title: BR4DM25T2SuGA_RNAseq_24 hours_DM25

description:
Library name: BR4DM25T24SuGA
BR4DM25T2SuGA

value: simulated microgravity


title: DKO3-H3K27ac

value: embronic liver

value: primary cells


title: DKO3-H3K4me1

value: megakaryocytes


title: Patient 5, atopic dermatitis, non-lesional, sample 1, 3' scRNA-seq [P5_AD_NL1]

description: 10x Genomics

value: skin


title: lcAlk_day3_rep2

description: Library name: Alkanes_D3B

value: Long-chain alkanes 3 days


title: BR4DM25T2SA_RNAseq_24 hours_DM25

description:
Library name: BR4DM25T24SA
BR4DM25T2SA

value: 24 hours

value: static


title: lcAlk_day3_rep1

description: Library name: Alkanes_D3A


title: DKO2-IgG

value: IgG


title: Patient 4, atopic dermatitis, lesional, sample 1, 3' scRNA-seq [P4_AD_L1]

description: 10x Genomics

value: Atopic dermatitis


title: BR4DM25T2RA_RNAseq_24 hours_DM25

description:
Library name: BR4DM25T24RA
BR4DM25T2RA

value: rotating


title: DKO2-H3K4me3


title: lcAlk_day2_rep3

description: Library name: Alkanes_D2C

value: fungal

value: Long-chain alkanes 2 days

value: Day 2


title: BR4DM25T0B_RNAseq_0 hours_DM25

description:
Library name: BR4DM25T0B
BR4DM25T0B


title: Patient 4, atopic dermatitis, non-lesional, sample 1, 3' scRNA-seq [P4_AD_NL1]

description: 10x Genomics


title: DKO2-H3K4me1


title: lcAlk_day2_rep2

description: Library name: Alkanes_D2B

value: WT


title: DKO2-H3K27ac


title: BR4DM25T0A_RNAseq_0 hours_DM25

description:
Library name: BR4DM25T0A
BR4DM25T0A


title: Patient 3, atopic dermatitis, lesional, sample 1, 3' scRNA-seq [P3_AD_L1]

description: 10x Genomics


title: lcAlk_day2_rep1

description: Library name: Alkanes_D2A


title: BR3DM25T2SuGA_RNAseq_24 hours_DM25

description:
Library name: BR3DM25T24uGA
BR3DM25T2SuGA


title: Patient 3, atopic dermatitis, non-lesional, sample 1, 3' scRNA-seq [P3_AD_NL1]

description: 10x Genomics


title: DKO1-IgG


title: sTO04, single cell

city: Durham

first: Cole

last: McCutcheon

state: North Carolina

address: 3 Genome Court

department: Department of Integrative Immunobiology

institute: Duke University

description: Library name: sTO04_sc

data_processing:
Cellranger v7.1.0
genome build/assembly: Sus scrofa genome v11.2
processed data files format and content: filtered feature matrices h5 file exported from Cellranger

source_name: swine tropoblast organoids

extract_protocol:
10X Genomics standard extraction protocol (see below for full methods)
Libraries were prepared following standard 10x Genomics Single Cell Gene Expression 3’ protocols. Samples containing highly viable cells (80% viability or higher), were washed and filtered through 40µm filter and resuspended in a 1x PBS / 0.04% BSA buffer, at a concentration of 1000 cells/µL. A Cellometer K2 instrument (Nexcelom - Lawrence, MA) was then used to determine the concentration of the single cell suspension. Cells were then suspended in master mix containing reverse transcription (RT) reagents using a volume equivalent to the target capture number of 10,000 cells (plus approximately 60% overage to account for capture efficiency of the assay). This master mix was loaded onto the 10x microfluidics chip, together with gel beads carrying the Illumina TruSeq Read 1 sequencing primer, a 16bp 10x barcode, a 12bp unique molecular identifier (UMI) and a poly-dT primer, and oil for the emulsion reaction. The Chromium X instrument was then used to generate gel beads in emulsion (GEMS) for the RT and barcoding of single cells. After the RT reaction, the GEMs were broken, full length cDNAs were cleaned with Silane Dynabeads, and then amplified via PCR. Following purification using SPRI bead size selection the cDNAs were assayed on a 4200 TapeStation 4200 High Sensitivity D5000 ScreenTape (Agilent - Santa Clara, CA) for qualitative and quantitative analysis. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size for the sequencing library preparation in which Illumina P5 and P7 sequences (San Diego, CA), a sample index, and TruSeq read 2 primer sequence are added via end repair, A-tailing, adaptor ligation, and PCR. The final libraries contained P5 and P7 primers used in Illumina bridge amplification. Following additional purification libraries were assayed for quality, using a TapeStation HSD1000 ScreenTape, then quantitated and checked for successful adapter ligation with the KAPA Library Quantification Kit (Roche-Indianapolis, IN). Sequences were generated using paired end sequencing on an NovaSeq X Plus, at ~62k reads/cell.

value: swine tropoblast organoids


title: Patient 2, atopic dermatitis, lesional, sample 2, 3' scRNA-seq [P2_AD_L2]

description: 10x Genomics


title: BR3DM25T2SA_RNAseq_24 hours_DM25

description:
Library name: BR3DM25T24SA
BR3DM25T2SA


title: DKO1-H3K4me3


title: BR2DM2000T1SA_RNAseq_6.5 hours_DM2000

description:
Library name: BR2DM2KT16SA
BR2DM2000T1SA

value: 6.5 hours


title: Patient 2, atopic dermatitis, lesional, sample 1, 3' scRNA-seq [P2_AD_L1]

description: 10x Genomics


title: lcAlk_day3_rep3

description: Library name: Alkanes_D3C

value: Day 3


title: DKO1-H3K4me1

value: embronic liver


title: BR3DM25T2RA_RNAseq_24 hours_DM25

description:
Library name: BR3DM25T24RA
BR3DM25T2RA


title: DKO1-H3K27ac

value: primary cells


title: Patient 2, atopic dermatitis, non-lesional, sample 2, 3' scRNA-seq [P2_AD_NL2]

description: 10x Genomics


title: A375_24h_rep3

data_processing:
Reads were analyzed using STAR aligner and Salmon, respectively for alignment to reference genome and quantification at the gene level
Assembly: GRCh38
Supplementary files format and content: xlsx, gene expression (TPM) table

extract_protocol:
Trizol extraction protocol
rRNA was removed using the Ribo-Zero kit. mRNA was fragmented randomly using fragmentation buffer, and cDNA was synthesized using random hexamer primers, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to initiate the second strand synthesis. Double-stranded cDNA library construction was completed by size selection and PCR enrichment.

treatment_protocol: Cells were treated with DMSO (control) or treated with BMH-21, 1 microM for 24 hours.

value: melanoma

value: BMH-21 1 uM 24 hours


title: BR3DM25T1SuGA_RNAseq_4.5 hours_DM25

description:
Library name: BR3DM25T7uGA
BR3DM25T1SuGA

value: 4.5 hours

value: simulated microgravity


title: Patient 2, atopic dermatitis, non-lesional, sample 1, 3' scRNA-seq [P2_AD_NL1]

description: 10x Genomics

value: skin


title: BR3DM25T1SA_RNAseq_4.5 hours_DM25

description:
Library name: BR3DM25T7SA
BR3DM25T1SA

value: static


title: A375_24h_rep2


title: WT-2 [RNA-seq]

data_processing:
Adapter sequences were removed from the 3' ends of reads using Trim Galore! (version 0.6.5) and cutadapt (version 2.8).
The reads were then aligned to the mouse genome (mm10) using TopHat (version 2.0.10).
The number of fragments for each known gene from GENCODE Release M25 was quantified using htseq-count from the HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the normalized fragment count for each gene was calculated by R/Bioconductor package DESeq (version 1.18.0).
Assembly: mm10
Supplementary files format and content: The first column is Ensembl gene id. The last column is gene symbol. The other columns are normalized expression values (estimated by DESeq) for all the samples.

extract_protocol:
Total RNA were extracted using the RNeasy Mini Kit, following the manufacture's protocol.
cDNA libraries libraries were prepared with the KAPA HyperPrep Kit, following the manufacture's instructions.

value: megakaryocytes


title: WT-3 [RNA-seq]


title: Patient 1, atopic dermatitis, lesional, sample 2, 3' scRNA-seq [P1_AD_L2]

description: 10x Genomics

value: Atopic dermatitis


title: BR3DM25T1RA_RNAseq_4.5 hours_DM25

description:
Library name: BR3DM25T7RA
BR3DM25T1RA

value: rotating


title: A375_24h_rep1


title: Patient 1, atopic dermatitis, lesional, sample 1, 3' scRNA-seq [P1_AD_L1]

description: 10x Genomics


title: WT-1 [RNA-seq]


title: A375_0h_rep3

value: control


title: PKO-3 [RNA-seq]


title: Patient 1, atopic dermatitis, non-lesional, sample 2, 3' scRNA-seq [P1_AD_NL2]

description: 10x Genomics


title: A375_0h_rep2


title: BR3DM25T0B_RNAseq_0 hours_DM25

description:
Library name: BR3DM25T0C
BR3DM25T0B

value: 0 hours


title: BR3DM25T0A_RNAseq_0 hours_DM25

description:
Library name: BR3DM25T0A
BR3DM25T0A


title: Patient 1, atopic dermatitis, non-lesional, sample 1, 3' scRNA-seq [P1_AD_NL1]

description: 10x Genomics


title: PKO-2 [RNA-seq]


title: sTO02, single cell

description: Library name: sTO02_sc


title: A375_0h_rep1


title: PKO-1 [RNA-seq]


title: sTO01, single cell

description: Library name: sTO01_sc


title: HCT116_siRRN3_rep3

growth_protocol: McCoy's 5a Medium + 10% FBS

treatment_protocol: Cells were transfected with control siRNA or with siRRN3 siRNA

value: colon

value: Human colorectal carcinoma cell line


title: BR3DM2000T2SuGA_RNAseq_24 hours_DM2000

description:
Library name: BR3DM2KT24uGA
BR3DM2000T2SuGA

value: 24 hours


title: DKO-3 [RNA-seq]


title: BR3DM2000T1uGA_RNAseq_6.5 hours_DM2000

description:
Library name: BR3DM2KT17uGA
BR3DM2000T1SuGA

value: 6.5 hours


title: DKO-2 [RNA-seq]

value: embronic liver


title: HCT116_siRRN3_rep2


title: BR3DM2000T1SA_RNAseq_6.5 hours_DM2000

description:
Library name: BR3DM2KT17SA
BR3DM2000T1SA


title: HCT116_siRRN3_rep1


title: DKO-1 [RNA-seq]

value: primary cells


title: HCT116_ctrl_rep3


title: BR2DM2000T1RA_RNAseq_6.5 hours_DM2000

description:
Library name: BR2DM2KT16RA
BR2DM2000T1RA


title: EVsABPC

city: Xi'an

first: Beibei

last: Yu

address: No. 157, Xiwu Road, Xincheng District, Xi'an City, Shaanxi Province

institute: Xijing hospital

description: Library name: EVsABPC

data_processing:
Cell Ranger software (version 7.0.1) (10x Genomics), using default parameters, was utilized to align and quantify the dataset. The sample-specific FASTQ file was evaluated by the cell ranger count function, aligning it with the Macaca mulatta reference genome (Mmul_10) to produce the gene expression matrix.
Assembly: Mmul_10
Supplementary files format and content: Rdata

organism: Macaca mulatta

source_name: Bone marrow

extract_protocol:
For single-cell RNA sequencing (scRNA-seq), bone marrow samples from aged rhesus macaques were collected from each group (vehicle, EVsF-BMSCs and EVsABPCs) at 20 weeks post treatment. Specifically, one rhesus macaque per group was selected for bone marrow aspiration under anesthesia. A 10x Chromium Controller (10x Genomics) was utilized to capture individual cells within droplet emulsions, targeting an output of 10,000 cells for each sample.
Following the manufacturer's protocol, a scRNA-seq library was constructed using a Chromium single-cell 3' gel bead and library V3 kit in accordance with the manufacturer’s guidelines. The libraries were pooled and sequenced using a NovaSeq 6000 sequencing system (Illumina), strictly adhering to the manufacturer's instructions.

value: Bone marrow

value: Global cells

value: WT

value: Evs-ABPC


title: HCT116_ctrl_rep2


title: BR3DM2000T2SA_RNAseq_24 hours_DM2000

description:
Library name: BR3DM2KT2SA
BR3DM2000T2SA


title: HCT116_ctrl_rep1


title: Vehicle

description: Library name: Vehicle

value: PBS injection


title: BR3DM2000T0B_RNAseq_0 hours_DM2000

description:
Library name: BR3DM2KT0B
BR3DM2000T0B


title: HCT116_24h_rep3

value: BMH-21 1 uM 24 hours


title: BR3DM2000T2RA_RNAseq_24 hours_DM2000

description:
Library name: BR3DM2KT24RA
BR3DM2000T2RA


title: Evs-ABPC3

institute: The Second Affiliated Hospital, Xi’an Jiaotong University

data_processing:
CLC Genomics Workbench w 11.0.1
Assembly: Mmul_10
Supplementary files format and content: TPM

source_name: whole blood

extract_protocol:
A NEBNext Ultra RNA library prep kit for Illumina (New England Biolabs, USA, Catalog #: E7530L) was used according to the manufacturer's guidelines to construct sequencing libraries and incorporate index codes for sample identification
he prepared libraries were sequenced on an Illumina platform using the paired-end 150 strategy at the Novogene Bioinformatics Technology Co. Ltd., Beijing, China. The sequencing process converted the original fluorescence images into raw data, which were then processed in FASTQ format, capturing both nucleotide sequences and their corresponding quality scores

value: whole blood


title: BR3DM2000T0A_RNAseq_0 hours_DM2000

description:
Library name: BR3DM2KT0A
BR3DM2000T0A


title: SKOV3 cells, hypoxia-mitomycinC, biological rep4

city: Warsaw

first: Aleksandra

last: Gawrylak

email: aklemba@gmail.com, agawrylak@wim.mil.pl

address: Szaserów 128

country: Poland

institute: Military Institute of Medicine – National Research Institute

description: Gene expression data from SKOV3 ovarian cancer cells treated with mitomycin C in hypoxia.

hyb_protocol: GeneChip Hybridization Oven was used for HTA 2.0 microarrays hybridization at 45°C for 16h. Then chips were washed and stained in the Affymetrix fluidics Station 450.

scan_protocol: The microarrays were scanned with GeneChip Scanner 3000 7G (Affymetrix) according to WT labeling protocol.

data_processing: HTA 2.0 microarray scans were visually inspected with the Affymetrix GeneChip Command Console (AGCC) version 4.0, generating CEL files with processed pixel intensity values for each probe on the arrays. The CEL files (n=16, 1 GB of data) were then imported to the Transcriptome Analysis Console 4.0 software (Affymetrix) for probe set summarization with the robust multi-array average (RMA) algorithm including background adjustment, quantile normalization, and a log2 transformation of the data, that was later used in the gene-level and the exon-level analysis.

label: biotin

label_protocol: Briefly, the first step of the WT (Whole-Transcript) Sense Target Labelling protocol was incorporation of T7 promoter tags to all RNA strands with (N63’ ends) to enable DNA strand synthesis. Once RNA molecules were replaced, cRNA (non-labeled antisense RNA) was synthesized by in vitro transcription (IVT) overnight. 3’ bias was prevented by linear transcription of all RNA strands. Purified cRNA was used as a template to produce single-stranded sense strand DNA (ss-DNA) by reverse transcription reaction with random primers and dNTP mix (with dUTP included).  The cRNA was eliminated with RNaseH digestion.  The resulting ss-DNA with unnatural dUTP (uracil residues) was fragmented with uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1. The 3’ ends of ss-DNA fragments were biotin-coupled using the DNA labeling reagent (Biotin-11-dXTP) by deoxynucleotidyl transferase.

growth_protocol: Human ovarian cancer cell line SKOV3 was cultured in RPMI-1640 GlutaMaxTM medium supplemented with 10% Fetal Bovine Serum (FBS). SKOV3 cells seeded in T-25 flask in 5ml medium were incubated for 24h in normoxic conditions.

extract_protocol: Total RNA was extracted from the SKOV3 cells incubated with or without MMC under normoxia or hypoxia using Direct-zol TM RNA Miniprep Kit. Genomic DNA was removed with TURBO DNA-free kit.

treatment_protocol: After 24h medium was changed to preconditioned medium (incubated in normoxia or hypoxia for 24h before the experiment), with or without mitomycin C (MMC) and the flasks were incubated for the following 72h before material RNA collection.

value: Ovary; Ascites

value: mitomycin C

tag: stress

value: hypoxia


title: Evs-ABPC2


title: HCT116_24h_rep1


title: BR2DM25T2uGA_RNAseq_24 hours_DM25

description:
Library name: BR2DM25T24uGA
BR2DM25T2uGA

value: simulated microgravity


title: Evs-ABPC1


title: SKOV3 cells, hypoxia-mitomycinC, biological rep1

source_name: SKOV3 ovarian cancer cells treated with mitomycin C in hypoxia


title: BR2DM25T2SA_RNAseq_24 hours_DM25

description:
Library name: BR2DM25T24SA
BR2DM25T2SA

value: static


title: HCT116_0h_rep3

value: colon

value: Human colorectal carcinoma cell line

value: control


title: SKOV3 cells, hypoxia-control, biological rep2

description: Gene expression data from SKOV3 ovarian cancer control cells cultured in hypoxia.


title: SKOV3 cells, hypoxia-control, biological rep1

source_name: SKOV3 ovarian cancer control cells cultured in hypoxia


title: SKOV3 cells, hypoxia-control, biological rep4


title: SKOV3 cells, hypoxia-mitomycinC, biological rep2


title: SKOV3 cells, hypoxia-control, biological rep3


title: SKOV3 cells, hypoxia-mitomycinC, biological rep3


title: SKOV3 cells, normoxia-mitomycinC, biological rep4

description: Gene expression data from SKOV3 ovarian cancer cells treated with mitomycin C in normoxia.

value: normoxia


title: EVsFBMSC

description: Library name: EVsFBMSC

value: Evs-FBMSC


title: BR3DM2000T1RA_RNAseq_6.5 hours_DM2000

description:
Library name: BR3DM2KT17RA
BR3DM2000T1RA

value: 6.5 hours

value: rotating


title: BR2DM25T2RA_RNAseq_24 hours_DM25

description:
Library name: BR2DM25T24RA
BR2DM25T2RA

value: 24 hours


title: Evs-FBMSC2

value: WT


title: HCT116_0h_rep2