title: LGG, mouse 5

city: Newark

state: NJ

address: 195 University Avenue

institute: Rutgers University

data_processing:
CLC Genomics Workbench v 20.0.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: Ileum

extract_protocol:
Total RNA was isolated from mouse ileum then purified with RNeasy Plus universal kit (Qiagen, Hilden, Germany) following manufacturer’s instructions.
Illumina-compatible RNA-seq libraries were constructed using the NEBNext Ultra II RNA library prep with sample purification beads (Cat. No. E7775) and NEB Next Multiplex Oligos for Illumina (dual index primers set 1; Cat. No. E7600) according to the manufacturer’s instructions.

treatment_protocol: GF mice were gavaged with either Lacticaseibacillus rhamnosus GG (108 CFU/ml, 200μl) or Ruminococus gnavus (108 CFU/ml, 200μl). Control GF mice received 200 μl sterile PBS. Colonization was confirmed by fecal DNA PCR. Mice were sacrificed 21 days after inoculation.

value: Ileum

value: tissue

value: LGG monocolonized


title: CRA_WB_155

status: Public on Oct 01 2023

type: SRA

city: Boston

first: Joanne

last: Sordillo

state: MA

address: 181 Longwood Avenue

department: Channing Division of Network Medicine

country: USA

institute: Mass General Brigham

library_source: transcriptomic

data_processing:
Alignment and QC was done using the COMPSRA (Li et al. 2020) pipeline, which is similar to BCBio.
miRNAs with less than five mapped reads in at least 50% of subjects were removed prior to analysis
Assembly: hg38
Supplementary files format and content: tab-delimited text file with log normalized counts of miRNA x Sample, including sample batch.

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
Total RNA was isolated from archival whole blood samples using the miRNeasy kit (Qiagen, Germantown, MD) according to the manufacturer's instructions
Blockers for miRs 451a, 486-5p, and 92a were added prior to library construction. Small RNA-seq libraries were prepared using the NEXTFLEX Small RNA-Seq Kit v3. First, adapters were ligated to the 3′ and 5′ ends of the RNA. Reverse transcription was then carried out to generate cDNA from the ligated RNA.
Detailed information is available in LaBelle et al, J Mol Diagnostics, 2021

tag: tissue

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: yes

tag: Sex

value: M


title: Human_235OSm_RGC

city: Seattle

first: Joshua

middle: William

last: Hahn

state: WA

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

description:
Human_count_mat_1.csv
Human_count_mat_2.csv
Human_count_mat_3.csv
Human_count_mat_4.csv

library_source: transcriptomic single cell

data_processing:
We used cellranger (v7.0, 10X Genomics) to align the sc- and snRNA-seq datasets, following manufacturer’s instructions. For each species, sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map (.bam) files.
Assembly: GRCh38.p13
Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample, regardless of cellular or nuclear origin, we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices (GEMs; genes x cells) for each sample, corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample.
Supplementary files format and content: GEMs from different sample runs were combined (column-wise concatenated) to yield a full species’ GEM. This GEM has been split into four separate csv files.

molecule: nuclear RNA

source_name: Retina

extract_protocol:
Frozen retinal tissues were homogenized in a Dounce homogenizer in 1ml Tris-based lysis buffer with 0.1% NP-40. Nuclei were stained with NEUN/RBFOX3 and/or CHX10/VSX2, washed once, pelleted at 500g for 5min, resuspended in PBS/BSA and stained with DAPI. NEUN+ and/or CHX10+ DAPI+ single nuclei were collected using a flow cytometer. The sorted nuclei were pelleted again, resuspended in PBS/BSA solution, and adjusted to a concentration of 1000 nuclei/µL. ~12µL of the nuclei suspension was loaded into a 10X Chromium Single Cell Chip (10X Genomics, Pleasanton, CA) with a targeted recovery of 8000 nuclei.
Single nuclei libraries were generated using the Chromium 3’ V3.1 platform (10X Genomics, Pleasanton, CA) according to the manufacturer’s protocol. Briefly, single nuclei were partitioned into Gel-beads-in-EMulsion (GEMs) where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full-length cDNA; this was followed by amplification, enzymatic fragmentation, and 5’ adaptor and sample index attachment to yield the final libraries.
Single nucleus RNA sequecning (10X Genomics)

value: Retina

tag: cell type

value: Retinal neurons


title: CRA_WB_159


title: LGG, mouse 3

last: Gao

organism: Mus musculus

tag: strain

tag: treatment


title: si_H_TGF_1

city: Mannheim

first: Joerg

last: Heineke

address: Ludolf-Krehlstr. 7-11 Tridomus B

department: Cardiovascular Physiology

country: Germany

institute: Medical Faculty of Mannheim Heidelberg University

data_processing:
Allignment, Hisat2
Mapping, feature counts
Diff analysis, Deseq2
Splicing, rMATs
Assembly: ensembl_mus_musculus_grcm38_p6_gca_000001635_8
Supplementary files format and content: Excel files from differentially expressed genes

molecule: polyA RNA

source_name: MCEC

extract_protocol:
RNA was extracted using a commertial RNA extraction kit
Novogene

treatment_protocol: NS vs. TGF-β

tag: cell line

value: MCEC

value: Endothelial Cells

tag: knockdown

value: sihnRNP H1

value: 10 ng/ml TGF-Beta


title: LGG, mouse 4


title: CRA_WB_154

value: no

value: F


title: si_H_NS_3

value: 0 ng/ml TGF-Beta


title: si_H_NS_2


title: Human_220OS_PeriRetina


title: Human_220OSm_RGC


title: LGG, mouse 2


title: si_H_NS_1


title: CRA_WB_152


title: Human_220235OSm_All


title: CRA_WB_151


title: Human_218OS_PeriRetina


title: siCtl_TGF_2

value: siControl


title: CRA_WB_150


title: CRA_WB_153


title: siCtl_TGF_3


title: CRA_WB_15


title: Human_218OSm_All


title: RG, mouse 4

value: R. gnavus monocolonized


title: RG, mouse 5

value: Ileum


title: Human_218OSm_RGC


title: RG, mouse 3

value: tissue


title: LGG, mouse 1

value: LGG monocolonized


title: CRA_WB_148

value: whole blood


title: RG, mouse 2


title: Human_088716OS_macula_NeuNPos


title: siCtl_NS_2


title: Human_105916OD_macula_NeuNPos


title: siCtl_NS_1


title: CRA_WB_147

value: yes


title: Human_086916OD_macula_NeuNPos


title: CRA_WB_149

value: M


title: RG, mouse 1


title: PBS, mouse 5

value: PBS


title: Csde1_TGF_3

data_processing:
Trimming, Skewer v. 0.1.126
QC, fastqc
rRNA removal, bowtie v. 2
Mapping, BWA v. 0.7.12
Peak calling, MACS2 v. 2.1.0
Motif predication, meme v. 4.10.2
Peak annotation, PeakAnnotator_Cpp v. 1.4
Diff analysis, diffbind
Assembly: ensembl_mus_musculus_grcm38_p6_gca_000001635_8
Supplementary files format and content: bw, Excel files from differentially expressed genes

extract_protocol:
RIP-IP
Novogene

tag: rip antibody


title: Human_082219_macular_All

value: Retina

value: Retinal neurons


title: siCtl_TGF_1

value: MCEC

value: Endothelial Cells


title: CRA_WB_146


title: siCtl_NS_3


title: PBS, mouse 4


title: Csde1_TGF_2

value: 10 ng/ml TGF-Beta


title: CRA_WB_145

value: no


title: Human_056416OS_macula_NeuNPos


title: Csde1_TGF_1


title: CRA_WB_144

value: F


title: PBS, mouse 3


title: CRA_WB_143


title: Human_035516OS_macula_NeuNPosS2


title: PBS, mouse 2


title: CRA_WB_142


title: PBS, mouse 1


title: Csde1_NS_1

value: 0 ng/ml TGF-Beta


title: CRA_WB_141


title: Human_035516OS_macula_NeuNPosS1


title: 03 naringin

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

country: Japan

institute: Graduate School of Medical Sciences, Kumamoto University

data_processing:
Making FASTQ were performed using Local Run Manager v2.4.0 for NextSeq 500 output
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim galore! v0.6.6
Trimmed sequence reads were mapped to UCSCmm10 using STAR v2.7.9a
Read count extraction and normalization were performed using RSEM v1.3.3
Assembly: UCSCmm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Lymph

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen). 10ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and Ultra II Directional RNA Library Prep Kit for Illumina

value: Lymph

value: myeloid

value: naringin


title: CRA_WB_140


title: 02 naringenin

value: naringenin


title: hnRNP_TGF_3

value: anti-hnRNP


title: 01 control

value: control


title: Csde1_NS_2


title: Human_032616OD_macula_NeuNPos


title: TBX3 KD (DsiRNA 13.8), biol rep 3, 24h

city: Bethesda

first: Dawn

last: Watkins-Chow

state: Maryland

address: 9000 Rockville Pike

institute: NIH

data_processing:
Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc.
Reads were trimmed using cutadapt
Quality scores were assessed using FastQC
Reads were aligned to the Homo sapiens genome build hg19 using STAR
Individual sample reads were quantified using Htseq and normalized via Relative Log Expression (RLE) using DESeq2 R library
Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC
DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction
Assembly: hg19
Supplementary files format and content: tab-delimited text file include raw counts for all samples

growth_protocol: 501mel cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and incubated in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
At 24h, cells were lysed with Trizol and processed for RNA collection with via Direct-zol RNA Miniprep.
Library construction was completed using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®.

treatment_protocol: Cells were treated at Day 0 with a diluted Lipofectamine and dsiRNAs (NC1 or dsiRNA TBX3) mix. 24h later samples were harvested for RNA extraction.

value: melanoma cells

tag: genotype

value: TBX3 knock-down


title: hnRNP_TGF_2


title: CRA_WB_14

value: whole blood

value: yes


title: i7F2_-_del_GFP_48

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

library_source: genomic

data_processing:
Libraries were sequenced on the Illumina Nextseq500 platform using the default RTA analysis software.
Alignment was performed in single-end non-directional mode followed by deduplication (deduplicate_bismark) and methylation calling (bismark_methylation_extractor) using Bismark (v0.18.2)
Libraries having a mapping efficiency <10%, fewer than 500,000 CpGs covered, or greater than 50% methylated CpGs were discarded
Assembly: GRCm38

molecule: genomic DNA

source_name: embryos

extract_protocol:
E13.5 embryos were dissected for gonad extraction, single cell primordial germ cells were FACS sorted
Single-cell BS-seq (scBS-seq) libraries were prepared as previously described (Smallwood et al., 2014), with minor changes. DNA purified from single cells was bisulphite converted using the EZ Methylation Direct kit (Zymo) according to the manufacturer’s instructions, but using half volumes. Five rounds of first-strand synthesis were carried out, starting by eluting bisulphite-converted DNA into 40 μl of first-strand synthesis mastermix (1 × Blue Buffer (Enzymatics), 0.4 mM dNTP mix (Roche), 0.4μM 6NF oligo (IDT)). The mixture was heated to 65 °C for 2 min and cooled on ice. 50U of Klenow exo- (Enzymatics) was added and the mixture incubated on a thermocycler at 37 °C for 30 min after slowly ramping from 4 °C. First-strand synthesis was repeated 4 more times with the addition of 2.5 μl of reaction mixture (1× blue buffer, 0.25 mM dNTPs, 10 mM 6NF oligo and 25U Klenow exo‑). In the final round, samples were incubated for 90 min at 37 °C. Exonuclease digestion was carried out by adding 20U of exonuclease I (NEB) to the reactions, diluting with water to a total volume of 100 μl, followed by incubation at 37 °C for 1 hour. Samples were purified with AMPure XP beads using a 0.75:1 ratio. Beads were resuspended in 50 μl second-strand master mix (1× Blue Buffer (Enzymatics), 0.4 mM dNTP mix (Roche), 0.4 μM 6NF oligo (IDT). Reactions were heated for 98 °C for 1 min, cooled on ice, before adding 50U of Klenow exo- (Enzymatics). The mixture was incubated on a thermocycler at 37 °C for 90 min after slowly ramping from 4 °C. Samples were purified using a 0.75:1 ratio of AMPure XP beads and libraries were amplified in 50 μl of PCR mastermix (1× KAPA HiFi Readymix, 0.2 μM PE1.0 primer, 0.2 μM iTAG index primer) using the following protocol: 2 min at 95 °C, 14 cycles of 80 sec at 94 °C, 30 sec at 65 °C, 30 sec at 72 °C and final extension for 3 min at 72 °C. Finally, scBS-seq libraries were purified using a 0.7:1 volumetric ratio of AMPure XP beads and eluted in 15 µl EB buffer before pooling and sequencing.

value: embryos

value: facs-sorted PGCs


title: CRA_WB_139

value: M


title: Human_056316OD_macula_NeuNPos

value: Retina

value: Retinal neurons


title: Csde1_NS_3

value: MCEC

value: Endothelial Cells


title: TBX3 KD (DsiRNA 13.8), biol rep 1, 24h


title: hnRNP_NS_3

value: 0 ng/ml TGF-Beta


title: TBX3 KD (DsiRNA 13.6), biol rep 3, 24h


title: hnRNP_NS_2


title: i7F2_-_del_GFP_45


title: CRA_WB_136

value: no

value: F


title: TBX3 KD (DsiRNA 13.6), biol rep 2, 24h


title: hnRNP_NS_1


title: Input_TGF

value: 10 ng/ml TGF-Beta

value: none (input)


title: i7F2_-_del_GFP_42


title: i7F2_-_del_GFP_44


title: MS+2

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

organism: Rattus norvegicus

source_name: implanted fetal lung

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

value: mechanical strech+

value: implanted fetal lung


title: Control (NC1), biol rep 3, 24h

value: melanoma cells

value: Control


title: Input_NS


title: CRA_WB_134

value: whole blood


title: hnRNP_TGF_1

value: anti-hnRNP


title: i7F2_-_del_GFP_40

value: embryos

value: facs-sorted PGCs


title: CRA_WB_135

value: yes

value: M


title: Control (NC1), biol rep 2, 24h


title: i7F2_-_del_GFP_38


title: CRA_WB_133


title: Control (NC1), biol rep 1, 24h


title: CRA_WB_138


title: CRA_WB_132


title: i7F2_-_del_GFP_37


title: VS_OLD_WT_FEMALE_C3.5

city: Oxford

first: Peter

last: Kilfeather

address: Biochemistry Building Phase II, South Parks Road

department: Department of Physiology, Anatomy and Genetics

institute: University of Oxford

data_processing:
Reads were trimmed using trim galore with default settings
Alignment and quantification were performed using Salmon in mapping mode, using Gencode mm10 genome/transcriptome data as a reference
Read count extraction and normalization were performed using tximeta and DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts values for each sample

source_name: ventral midbrain

growth_protocol: C3H 10T1/2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: ventral midbrain

value: dopaminergic neurons

tag: region

value: VS

value: OLD

value: WT

value: FEMALE

tag: collection


title: i7F2_-_del_GFP_31


title: CRA_WB_137

value: F


title: MB_YOUNG_WT_MALE_C3.1

value: MB

value: YOUNG

value: MALE


title: VS_YOUNG_OVX_MALE_C3.9

value: OVX


title: TBX3 KD (DsiRNA 13.8), biol rep 2, 24h

value: melanoma cells

value: TBX3 knock-down


title: CRA_WB_131

value: whole blood


title: TBX3 KD (DsiRNA 13.6), biol rep 1, 24h


title: i7F2_-_del_GFP_28

value: embryos

value: facs-sorted PGCs


title: CRA_WB_13

value: yes

value: M


title: VS_OLD_WT_MALE_C3.TOTAL

value: ventral midbrain

value: dopaminergic neurons


title: VS_YOUNG_OVX_MALE_C3.6

value: VS


title: NETs treated-SAECs, 24 hours, 3

city: GuangZhou

first: Zhongji

last: Wu

address: No.151 Yanjiang West Road, Yuexiu District, Guangzhou City, Guangdong Province

department: Pediatrics

country: China

institute: the First Affiliated Hospital of Guangzhou Medical University

data_processing:
Solexa pipeline version 1.8 software used for basecalling.
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0)software
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.10.0)
Assembly: GRCh37
Supplementary files format and content: The xlsx format file contains the FPKM value of gene in every sample

source_name: human small airway epithelial cell line

growth_protocol: The human small airway epithelial cells (SAECs) were purchased from Procell Life Science & Technology Company (Wuhan, China) and were cultivated in DMEM high glucose supplemented with 10% of FBS, 1% of penicillin-streptomycin solution and 1% of L-glutamine (all purchased by Procell, Wuhan, China) at 37°C with 5% of CO2

extract_protocol:
Total RNA was extracted from cell using TaKaRa MiniBEST Universal RNA Extraction Kit (Takara, 9767).RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Libraries were prepared by using KAPA Stranded RNA-Seq Library Prep Kit(Illumina). Briefly,Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

treatment_protocol: SAECs were seeded in 24-well plates up to 90% confluency, washed once with PBS, and 20μg/mL DNA-NET in was added.The experimental group and the control group were supplemented with an appropriate amount of DMEM to achieve equal volumes.

value: human small airway epithelial cell line

value: human small airway epithelial cells

value: Treated with NETs

tag: time


title: MB_OLD_WT_MALE_C3.1

value: MB

value: OLD

value: WT


title: CRA_WB_129

value: no


title: i7F2_-_del_GFP_27


title: MB_OLD_WT_FEMALE_C3.7

value: FEMALE


title: NETs treated-SAECs, 24 hours, 2


title: i7F2_-_del_GFP_26


title: NETs treated-SAECs, 24 hours, 1


title: CRA_WB_128


title: untreated SAECs, 3

value: Untreated


title: VS_YOUNG_OVX_MALE_C3.10

value: YOUNG

value: OVX

value: MALE


title: CRA_WB_127

value: whole blood

value: yes

value: F


title: MB_OLD_WT_MALE_C3.TOTAL

value: ventral midbrain

value: dopaminergic neurons


title: CRA_WB_126

value: M


title: untreated SAECs, 2

value: human small airway epithelial cell line

value: human small airway epithelial cells


title: CRA_WB_125


title: untreated SAECs, 1


title: MB_OLD_OVX_MALE_C3.1

value: MB


title: i7F2_-_del_GFP_21

value: embryos

value: facs-sorted PGCs


title: i7F2_-_del_GFP_20


title: i7F2_-_del_GFP_22


title: MB_YOUNG_WT_FEMALE_C3.TOTAL

value: WT


title: i7F2_-_del_GFP_29


title: CRA_WB_130

value: no


title: sequenced matrices from cortices

first: Francesco

last: Limone

state: Massachusetts

address: 7 divinity avenue, Bauer Laboratory 008

institute: harvard university

description: 10x Genomics

data_processing:
Raw sequence data was demultiplexed and aligned following the standard Drop-Seq protocol (Macosko et al., 2015)
Human experiments were aligned to the GRCh18 reference . Sequencing reads were then filtered to reads that mapped at high quality (MQ>=10) to the human genome
Matrices were built from 10X Chromium Single Cell 3’ Reagents V2 as described above. Any barcode with less than 400 genes and combined UMI matrices were used for downstream analysis using Seurat (v3.0.2) (Stuart et al., 2019).
The matrix was then processed via the Seurat pipeline as described in publication methods
Assembly: GRCh18 reference

source_name: brain

extract_protocol:
RNA quality of brain samples was assessed by running bulk nuclear RNA on an Agilent TapeStation for RIN scores. Extraction of nuclei from frozen samples was performed as previously described85. Briefly, tissue was dissected and minced with a razor blade on ice and then placed in 4 ml ice-cold extraction buffer (Wash buffer (82 mM Na2SO4, 30 mM K2SO4, 5 mM MgCl2, 10 mM glucose, and 10 mM HEPES, pH adjusted to 7.4 with NaOH) containing 1% Triton X-100 and 5% Kollidon VA64). Tissue was homogenized with repeated pipetting, followed by passing the homogenized suspension twice through a 26 ½ gauge needle on a 3 ml syringe (pre-chilled), once through a 20 mm mesh filter, and once through a 5 mm filter using vacuum. The nuclei were then diluted in 50 ml ice-cold wash buffer, split across four 50 ml tubes, and centrifuged at 500xg for 10 minutes at 4°C. The supernatant was discarded, the nuclei pellet was resuspended in 1 ml cold wash buffer.
Nuclei were DAPI-stained with Hoechst, loaded onto a hemocytometer, and counted using brightfield and fluorescence microscopy. The solution was diluted to ~176 nuclei/ul before proceeding with Drop-seq as described in ref.1528. cDNA amplification was performed using around 6000 beads per reaction with 16 PCR cycles. The integrity of both the cDNA and tagmented libraries were assessed for quality control on the Agilent Bioanalyzer as in ref86. Libraries were sequenced on a Nova-seq S2, with a 60 bp genomic read. Reads were aligned to the human genome assembly (hg19). Digital Gene Expression files were generated with the Zamboni Drop-seq analysis pipeline, designed by the McCarroll group85,87.

value: brain


title: CRA_WB_124


title: MB_OLD_OVX_MALE_C3.TOTAL

value: OLD


title: i7F2_-_del_GFP_46


title: i7F2_-_del_GFP_17


title: IgG_BETi_OCI3_ChIPSeq

city: Mainz

first: Daniel

last: Sasca

address: Langenbeckstr 1

department: Department of Hematology and Oncology

institute: University Medical Center Mainz

data_processing:
Chip Seq pipeline: Adapter sequences were trimmed for all reads and mapped against hg19 reference genome using Bowtie2. Uniquely mapped, deduplicated reads were retained and peaks were called using MACS2.
RNA Seq pipeline: Rads were trimmed for adaptor sequence. Paired end reads were aligned to hg19 genome using STAR. Count files were generated count files HTSeq.
Assembly: hg19
Supplementary files format and content: Txt files with HTSeq count columns for RNA Seq, bedGraph files for ChIPSeq

source_name: Transformed hematopoiesis

growth_protocol: Cells were grown in standard media with addition 10-20% FCS

extract_protocol:
x-linking was performed with 1% Formaldehyde. Lysates were clarified from sonicated nuclei and chromatin proteins were isolated with antibodies.
ChIP-Seq libraries were prepared for sequencing using a TruSeq ChIP Sample Prep Kit (Illumina) and standard Illumina protocols

value: Transformed hematopoiesis

value: AML cell line

value: 24h BETi treatment


title: CRA_WB_123

value: whole blood

value: yes


title: DS_OLD_WT_MALE_C3.TOTAL

value: ventral midbrain

value: DS

value: MALE


title: i7F2_-_del_GFP_24


title: i7F2_-_del_GFP_14


title: CRA_WB_122

value: M


title: IgG_DMSO_OCI3_ChIPSeq

value: 24h DMSO treatment


title: CRA_WB_121

value: F


title: VS_YOUNG_OVX_FEMALE_C3.TOTAL

value: dopaminergic neurons

value: VS

value: YOUNG

value: OVX

value: FEMALE


title: IgG_BETi_SKNO_ChIPSeq


title: i7F2_-_del_GFP_12

value: embryos

value: facs-sorted PGCs


title: MB_YOUNG_OVX_MALE_C3.9

value: MB


title: CRA_WB_120


title: IgG_DMSO_SKNO_ChIPSeq

value: Transformed hematopoiesis

value: AML cell line


title: VS_OLD_WT_FEMALE_C3.7

value: OLD

value: WT


title: p300_BETi_OCI3_ChIPSeq_1

value: 24h BETi treatment


title: CRA_WB_119

value: whole blood

value: no


title: i7F2_-_del_GFP_11


title: i7F2_-_del_GFP_4


title: CRA_WB_12

value: yes

value: M


title: i7F2_-_del_GFP_19


title: DS_OLD_OVX_FEMALE_C3.2

value: ventral midbrain

value: dopaminergic neurons

value: DS


title: i7F2_-_del_GFP_9


title: p300_BETi_OCI3_ChIPSeq_2


title: CRA_WB_117

value: F


title: p300_DMSO_OCI3_ChIPSeq_1

value: 24h DMSO treatment


title: MB_OLD_WT_FEMALE_C3.2

value: FEMALE


title: VS_YOUNG_WT_MALE_C3.10

value: VS

value: YOUNG

value: MALE


title: BRD4_BETi_OCI3_ChIPSeq_2

value: Transformed hematopoiesis

value: AML cell line


title: i7F2_-_del_GFP_2

value: embryos

value: facs-sorted PGCs


title: p300_DMSO_OCI3_ChIPSeq_2


title: i7F2_-_del_GFP_1


title: MB_YOUNG_OVX_MALE_C3.TOTAL

value: MB

value: OVX


title: CRA_WB_116

value: whole blood

value: no


title: CRA_WB_114

value: yes

value: M


title: i7F2_-_del_GFP_3


title: CRA_WB_115


title: BRD4_BETi_OCI3_ChIPSeq_1

value: 24h BETi treatment


title: i7F1_-_del_GFP_46


title: CRA_WB_113

value: F


title: DS_YOUNG_WT_MALE_C3.TOTAL

value: ventral midbrain

value: dopaminergic neurons

value: DS

value: WT


title: DS_YOUNG_WT_FEMALE_C3.5

value: YOUNG

value: FEMALE


title: i7F1_-_del_GFP_45


title: BRD4_DMSO_OCI3_ChIPSeq_2

value: Transformed hematopoiesis

value: AML cell line

value: 24h DMSO treatment


title: CRA_WB_112


title: VS_OLD_OVX_FEMALE_C3.2

value: VS

value: OLD


title: i7F1_-_del_GFP_44

value: embryos

value: facs-sorted PGCs


title: p300_BETi_SKNO_ChIPSeq_2


title: i7F1_-_del_GFP_43


title: MB_OLD_OVX_MALE_C3.10

value: MB

value: OVX

value: MALE


title: MB_OLD_OVX_FEMALE_C3.7


title: p300_BETi_SKNO_ChIPSeq_1

value: 24h BETi treatment


title: CRA_WB_110

value: whole blood

value: yes

value: F


title: i7F1_-_del_GFP_42


title: p300_DMSO_SKNO_ChIPSeq_2


title: CRA_WB_11

value: M


title: MB_OLD_OVX_MALE_C3.9

value: ventral midbrain

value: dopaminergic neurons


title: p300_DMSO_SKNO_ChIPSeq_1

value: Transformed hematopoiesis


title: VS_YOUNG_WT_MALE_C3.9

value: YOUNG

value: WT


title: i7F1_-_del_GFP_38


title: CRA_WB_109


title: CRA_WB_108

value: no


title: i7F1_-_del_GFP_37


title: BRD4_BETi_SKNO_ChIPSeq_2

value: AML cell line


title: BRD4_DMSO_OCI3_ChIPSeq_1

value: 24h DMSO treatment


title: CRA_WB_107


title: VS_OLD_OVX_FEMALE_C3.TOTAL

value: VS

value: OLD

value: FEMALE


title: BRD4_DMSO_SKNO_ChIPSeq_2


title: i7F1_-_del_GFP_34

value: embryos

value: facs-sorted PGCs


title: BRD4_BETi_SKNO_ChIPSeq_1

value: 24h BETi treatment


title: CRA_WB_106

value: whole blood

value: yes


title: VS_OLD_WT_FEMALE_C3.2


title: BRD4_DMSO_SKNO_ChIPSeq_1


title: i7F1_-_del_GFP_31


title: DS_OLD_OVX_MALE_C3.10

value: DS

value: OVX

value: MALE


title: i7F1_-_del_GFP_30


title: MB_YOUNG_WT_MALE_C3.TOTAL

value: ventral midbrain

value: dopaminergic neurons

value: MB


title: DS_YOUNG_WT_MALE_C3.9

value: YOUNG

value: WT


title: SKNO_p300i_3

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) as per manufacturer’s protocol
RNA-seq libraries were prepared for sequencing using standard Illumina protocols

value: Transformed hematopoiesis

value: AML cell line

value: p300i treatment 24h


title: i7F1_-_del_GFP_39


title: CRA_WB_104

value: M


title: i7F1_-_del_GFP_29

value: embryos


title: CRA_WB_103


title: DS_OLD_OVX_MALE_C3.6

value: OLD


title: SKNO_p300i_2


title: CRA_WB_102

value: F


title: DS_YOUNG_OVX_MALE_C3.10


title: CRA_WB_111

value: whole blood

value: no


title: SKNO_p300i_1


title: CRA_WB_105

value: yes


title: i7F1_-_del_GFP_22

value: facs-sorted PGCs


title: DS_OLD_WT_FEMALE_C3.2

value: DS

value: FEMALE


title: SKNO_DMSO_3

value: DMSO treatment 24h


title: i7F1_-_del_GFP_20


title: DS_OLD_OVX_FEMALE_C3.TOTAL

value: ventral midbrain

value: dopaminergic neurons

value: OVX


title: CRA_WB_100


title: SKNO_DMSO_2

value: Transformed hematopoiesis


title: CRA_WB_101


title: i7F1_-_del_GFP_19


title: SKNO_DMSO_1

value: AML cell line


title: i7F1_-_del_GFP_18


title: VS_OLD_OVX_MALE_C3.9

value: VS

value: MALE


title: SKNO_IC90r_p300_3

value: BETiIC90 resistant cells with 24h p300i treatment


title: DS_YOUNG_OVX_MALE_C3.TOTAL

value: YOUNG


title: i7F1_-_del_GFP_15

value: embryos


title: 616MV411TLR2

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
The quality of paired reads were checked using FASTQC (v0.11.7)
Reads were aligned against human GRCh37 genome using TopHat 2.9.13
Each gene-level raw counts were calculated using featureCounts (v1.5.2)
Genome_build: GRCh37
Supplementary_files_format_and_content: Gene list, sample metadata, rawcount matrix

growth_protocol: Cells were cultured in RPMI

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA Miniprep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with PBS or CU-T12-9 (1µg/mL) for 24 hours

tag: tumor stage

value: Acute Myeloid Leukemia

value: MV411 parental cells treated with CUT129

value: no applicable


title: 615MV411TLR1


title: DS_YOUNG_WT_MALE_C3.6

tag: tissue

value: WT


title: MB_YOUNG_OVX_MALE_C3.1

value: MB

tag: age


title: SKNO_IC90r_p300_1


title: i7F1_-_del_GFP_21

value: facs-sorted PGCs


title: 614MV411DMSO2

value: MV411 parental cells treated with DMSO


title: i7F1_-_del_GFP_13


title: i7F1_-_del_GFP_11


title: 613MV411DMSO1


title: MV411-R14-3

data_processing:
The quality of paired reads were checked using FASTQC (v0.11.7)
Reads were aligned against human GRCh38 genome using HISAT2 (v2.0.5)
Each gene-level raw counts were calculated using featureCounts (v1.5.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene list, sample metadata, rawcount matrix

value: MV411 cells with mutated MYC at K148R

value: no treatment


title: CRA_WB_1

value: whole blood

tag: height (cm)

value: yes

value: F


title: MV411-R14-2


title: SKNO_IC90r_1

value: Transformed hematopoiesis

value: AML cell line

value: BETiIC90 resistant cells with 24h DMSO treatment


title: MB_OLD_OVX_FEMALE_C3.4

value: ventral midbrain

value: dopaminergic neurons

value: OLD

value: OVX

value: FEMALE


title: i7F1_-_del_GFP_8

value: embryos


title: MV411-R14-1

value: Acute Myeloid Leukemia


title: MB_YOUNG_OVX_FEMALE_C3.TOTAL

value: MB

value: YOUNG


title: VS_YOUNG_OVX_FEMALE_C3.5

value: VS


title: SKNO_IC90r_p300_2

value: BETiIC90 resistant cells with 24h p300i treatment


title: i5F_del_GFP_48

value: facs-sorted PGCs


title: MV411-Q2-3

value: MV411 cells with mutated MYC at K148Q

value: no treatment


title: SKNO_IC50r_p300_3

value: Transformed hematopoiesis

value: BETiIC50 resistant cells with 24h p300i treatment


title: i5F_del_GFP_47


title: MV411-Q2-2


title: VS_OLD_OVX_MALE_C3.TOTAL

value: MALE


title: i7F1_-_del_GFP_14


title: SKNO_IC50r_p300_1

value: AML cell line


title: SKNO_IC90r_3

value: BETiIC90 resistant cells with 24h DMSO treatment


title: SKNO_IC50r_p300_2


title: MB_YOUNG_OVX_FEMALE_C3.2

value: ventral midbrain

value: dopaminergic neurons


title: MV411-Q2-1


title: VS_YOUNG_WT_FEMALE_C3.7

value: WT

value: FEMALE


title: DS_OLD_OVX_FEMALE_C3.5

value: DS

value: OLD

value: OVX


title: i5F_del_GFP_46

value: embryos


title: i5F_del_GFP_45


title: i7F1_-_del_GFP_10


title: SKNO_IC50r_2

value: BETiIC50 resistant cells with 24h DMSO treatment


title: DS_YOUNG_OVX_MALE_C3.9

value: YOUNG


title: i5F_del_GFP_44

value: facs-sorted PGCs


title: MV411-WT-2

value: Acute Myeloid Leukemia

value: Parental MV411 cells

value: no treatment


title: MB_OLD_WT_FEMALE_C3.5

value: MB


title: SKNO_IC50r_1

value: Transformed hematopoiesis

value: AML cell line


title: DS_OLD_WT_FEMALE_C3.5

value: ventral midbrain


title: MV411-WT-1


title: SKNO_IC90r_2

value: BETiIC90 resistant cells with 24h DMSO treatment


title: VS_YOUNG_OVX_FEMALE_C3.7

value: dopaminergic neurons

value: VS


title: i5F_del_GFP_43


title: i5F_del_GFP_42


title: SKNO_IC50r_3


title: SKNO_3d_3

value: 3dBETi and 24h DMSO treatment


title: SKNO_3d_p300i_3

value: 3dBETi and 24h p300i treatment


title: VS_OLD_OVX_FEMALE_C3.7

value: OLD

value: OVX

value: FEMALE


title: BETi2_MOLM13_RNASeq

description:
MOLM13_RNASeq_DMSO_vs_BETi_counts.txt
RNASeq

data_processing:
Chip Seq pipeline: Adapter sequences were trimmed for all reads and mapped against mm10 reference genome using Bowtie2. Uniquely mapped, deduplicated reads were retained and peaks were called using MACS2.
RNA Seq pipeline: Rads were trimmed for adaptor sequence. Paired end reads were aligned to mm10 genome STAR version 2.4.0. To generate the bigwig file, we first extended each read to 200 bp along 5' end and generated count files using HTSeq.
ATACSeq pipeline: Adapter sequences were trimmed for all reads and mapped against mm10 reference genome using Bowtie2. Uniquely mapped reads were retained without deduplication and peaks were called using MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: Txt files with HTSeq count columns for RNA Seq, bedGraph files for ChIP Seq and ATAC-Seq

source_name: t(9;11) MLL-AF9 AML

treatment_protocol: BETi treatment 24h

value: MOLM-13 cell line


title: DS_YOUNG_WT_MALE_C3.10

value: DS

value: YOUNG

value: WT

value: MALE


title: BETi1_MOLM13_RNASeq


title: i5F_del_GFP_37

value: embryos

value: facs-sorted PGCs


title: MV411-WT-3

value: Acute Myeloid Leukemia

value: Parental MV411 cells

value: no treatment


title: DMSO2_MOLM13_RNASeq

treatment_protocol: DMSO treatment 24h


title: SKNO_3d_p300i_2

value: Transformed hematopoiesis

value: AML cell line


title: MB_OLD_OVX_FEMALE_C3.5

value: ventral midbrain

value: dopaminergic neurons

value: MB


title: i5F_del_GFP_36


title: BRD4_BETi_KASUMI_ChIPSeq

description:
BRD4_BETi_KASUMI_ChIPSeq.bdg
ChIP-Seq

source_name: t(8;21) RUNX1-ETO AML

value: KASUMI-1 cell line

tag: chip antibody


title: VS_YOUNG_WT_FEMALE_C3.TOTAL

value: VS

value: FEMALE


title: i5F_del_GFP_35


title: SKNO_3d_1

value: 3dBETi and 24h DMSO treatment


title: i5F_del_GFP_39


title: VS_OLD_OVX_MALE_C3.10

value: OLD

value: OVX


title: SKNO_3d_2


title: BRD4_DMSO_KASUMI_ChIPSeq

description:
BRD4_DMSO_KASUMI_ChIPSeq.bdg
ChIP-Seq


title: SKNO_3d_p300i_1

value: 3dBETi and 24h p300i treatment


title: i5F_del_GFP_41

value: embryos


title: MB_OLD_WT_MALE_C3.9

value: WT

value: MALE


title: THP1-derived macrophages, siPTX3-6

city: Shanghai

first: Xiao

last: Han

state: Select state...

address: 399 Wanyuan Rd, Minhang, Shanghai, China

institute: Children’s Hospital of Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Differentially expressed genes were identified using Cuffdiff. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR). The fold-changes were also estimated according to the FPKM in each sample.
Genome_build: GRCh38.91
Supplementary_files_format_and_content: Excel file includes FPKM values for each Sample .

source_name: THP1-derived macrophages, siPTX3

growth_protocol: Human THP1 cell lines (purchased from the American Type Culture Collection (ATCC), USA) were maintained in RPMI-1640 medium, 10% heat-inactivated FBS. To generate macrophage-like cells, THP-1 cell were seeded along with 200 nM PMA for 48 h. Cells were incubated at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat#74004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide

treatment_protocol: THP1-derived macrophages were transfected with PTX3 siRNA pools or control siRNA for 48 h. Then, macrophages were stimulated with  IL-4 (20 ng/ml)  for 24 h.

value: peripheral blood

value: THP1 monocyte cell line -derived macrophages

value: transfected with PTX3 siRNA pools for 48 h

value: PTX3 depletion


title: i5F_del_GFP_34

value: facs-sorted PGCs


title: i5F_del_GFP_33


title: CDK9_BETi_KASUMI_ChIPSeq

description:
CDK9_BETi_KASUMI_ChIPSeq.bdg
ChIP-Seq

value: CDK9 (Bethyl, A303-493A)


title: DMSO1_MOLM13_RNASeq

value: MOLM-13 cell line


title: THP1-derived macrophages, siPTX3-5


title: CDK9_DMSO_KASUMI_ChIPSeq

description:
CDK9_DMSO_KASUMI_ChIPSeq.bdg
ChIP-Seq

value: KASUMI-1 cell line


title: THP1-derived macrophages, siPTX3-4


title: THP1-derived macrophages, siNC-3

source_name: THP1-derived macrophages, siNC

value: transfected with  control siRNA for 48 h

value: control


title: i5F_del_GFP_31


title: MB_OLD_WT_FEMALE_C3.TOTAL

value: ventral midbrain

value: dopaminergic neurons

value: MB

value: FEMALE


title: THP1-derived macrophages, siNC-2


title: ERG_DMSO_KASUMI_ChIPSeq

description:
ERG_DMSO_KASUMI_ChIPSeq.bdg
ChIP-Seq


title: i5F_del_GFP_28

value: embryos


title: i5F_del_GFP_27


title: MB_YOUNG_WT_MALE_C3.6

value: YOUNG

value: WT


title: ERG_BETi_KASUMI_ChIPSeq

description:
ERG_BETi_KASUMI_ChIPSeq.bdg
ChIP-Seq


title: DS_YOUNG_WT_FEMALE_C3.7

value: DS


title: THP1-derived macrophages, siNC-1

value: peripheral blood

value: THP1 monocyte cell line -derived macrophages


title: FLI1_BETi_KASUMI_ChIPSeq

description:
FLI1_BETi_KASUMI_ChIPSeq.bdg
ChIP-Seq

value: FLI1 (Abcam, ab15289)


title: VS_YOUNG_WT_MALE_C3.6

value: VS

value: MALE


title: FLI1_DMSO_KASUMI_ChIPSeq

description:
FLI1_DMSO_KASUMI_ChIPSeq.bdg
ChIP-Seq


title: i5F_del_GFP_24

value: facs-sorted PGCs


title: i5F_del_GFP_25


title: NAT_3

city: Kaifeng

first: Xiong

last: Jin

state: Henan

address: Jin Ming Avenue

department: School of Pharmacy

institute: Henan University

data_processing:
Clean data (clean reads) were obtained from raw data (raw reads) of fastq format by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
Paired-end clean reads were aligned to the reference genome (GRCh38.p12 assembly) by using Hisat2 software (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
For quantification purposes, the relative abundance of the transcript/gene was measured by a normalized method, Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM).
Differential expression analysis of two groups was performed using the DESeq2 R package (v1.16.1).
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: raw_count
Supplementary_files_format_and_content: FPKM

source_name: Normal tissues adjacent to tumors

extract_protocol:
RNA was extracted from tissues by using TRIzol reagent kit (Ambion, Invitrogen, USA) according to the reagent protocols.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Normal tissues adjacent to tumors


title: MB_OLD_OVX_FEMALE_C3.2

value: OLD

value: OVX


title: NAT_2


title: i5F_del_GFP_23


title: DS_YOUNG_WT_FEMALE_C3.TOTAL

value: ventral midbrain


title: VS_OLD_WT_FEMALE_C3.TOTAL

value: dopaminergic neurons


title: H3K27ac_BETi_KASUMI_ChIPSeq

description:
H3K27ac_BETi_KASUMI_ChIPSeq.bdg
ChIP-Seq

value: KASUMI-1 cell line

value: H3K27ac (Abcam, ab4729)


title: NAT_1


title: MB_YOUNG_WT_FEMALE_C3.4

value: MB

value: FEMALE


title: Input_BETi_KASUMI_ChIPSeq

description:
Input_BETi_KASUMI_ChIPSeq.bdg
ChIP-Seq


title: GBM_4

source_name: GBM tissue

value: GBM tissue


title: i5F_del_GFP_20

value: embryos


title: LMO2_BETi_KASUMI_ChIPSeq

description:
LMO2_BETi_KASUMI_ChIPSeq.bdg
ChIP-Seq


title: DS_OLD_WT_FEMALE_C3.TOTAL

value: DS

value: WT


title: DS_YOUNG_OVX_FEMALE_C3.TOTAL

value: YOUNG


title: GBM_3


title: i5F_del_GFP_22


title: GBM_2


title: Input_DMSO_KASUMI_ChIPSeq

description:
Input_DMSO_KASUMI_ChIPSeq.bdg
ChIP-Seq


title: i5F_del_GFP_19


title: LMO2_DMSO_KASUMI_ChIPSeq

description:
LMO2_DMSO_KASUMI_ChIPSeq.bdg
ChIP-Seq


title: MB_YOUNG_OVX_MALE_C3.10


title: i5F_del_GFP_18


title: MB_YOUNG_WT_FEMALE_C3.5


title: i5F_del_GFP_17


title: p300_BETi_KASUMI_ChIPSeq

description:
p300_BETi_KASUMI_ChIPSeq.bdg
ChIP-Seq


title: LOVO-Fn-replicate 2

first: Yile

last: Xie

address: 145 Middle Shandong Road

institute: Renji Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
The raw data was checked by FastQC v
Clean reads were aligned to the human genome using STAR 2.5
The expression of the transcript was calculated by FPKM using Cuffnorm
Differentially expression transcripts were determined using DESeq v1.22.1
Function and signaling pathway enrichment analysis using GO and KEGG database
Genome_build: hg18
Supplementary_files_format_and_content: FPKM_with_isoform_exp_significant_mRNA_with_GO_KEGG

source_name: Human colorectal cancer cell line

growth_protocol: Lovo cells were cultured with RMPI 1640 with 10%FBS and 1%  penicillin and streptomycin.

extract_protocol:
RNA was isolated using the standard TRIzol protocol.
Stand-specific libraries were constructed using the TruSeq RNA sample prepartion kit (Illumina).

treatment_protocol: Sample 1,2,3 were treated as PBS control. Sample 4,5,6 were cocultured with F. nucleatum for 2 hours.

value: LOVO

value: Human colorectal cancer cell line

value: F. nucleatum cocultured


title: LOVO-Fn-replicate 3


title: i5F_del_GFP_16

value: facs-sorted PGCs


title: MB_OLD_WT_FEMALE_C3.4

value: OLD


title: H3K27ac_DMSO_KASUMI_ChIPSeq

description:
H3K27ac_DMSO_KASUMI_ChIPSeq.bdg
ChIP-Seq


title: p300_DMSO_KASUMI_ChIPSeq

description:
p300_DMSO_KASUMI_ChIPSeq.bdg
ChIP-Seq


title: PU.1_BETi_KASUMI_ChIPSeq

description:
PU.1_BETi_KASUMI_ChIPSeq.bdg
ChIP-Seq


title: VS_OLD_WT_FEMALE_C3.4

value: VS


title: LOVO-NC-replicate 3

value: PBS


title: LOVO-Fn-replicate 1


title: i5F_del_GFP_13


title: i5F_del_GFP_11


title: PU.1_DMSO_KASUMI_ChIPSeq

description:
PU.1_DMSO_KASUMI_ChIPSeq.bdg
ChIP-Seq


title: RUNX1_BETi_KASUMI_ChIPSeq

description:
RUNX1_BETi_KASUMI_ChIPSeq.bdg
ChIP-Seq

value: RUNX1 (Abcam, ab23980)


title: MB_YOUNG_WT_FEMALE_C3.2

value: ventral midbrain

value: dopaminergic neurons


title: LOVO-NC-replicate 1


title: RUNX1_DMSO_KASUMI_ChIPSeq

description:
RUNX1_DMSO_KASUMI_ChIPSeq.bdg
ChIP-Seq

value: KASUMI-1 cell line


title: i5F_del_GFP_10


title: DS_OLD_WT_MALE_C3.9

value: MALE


title: DS_OLD_OVX_FEMALE_C3.7

value: OVX

value: FEMALE


title: OCI3_p300i_2

description:
Readcounts_all_DMSO_vs_p300i_RNASeq_comparisons.txt
RNASeq

source_name: NPM1mut AML

treatment_protocol: p300i treatment 24h

value: OCI-AML3 cell line


title: OCI3_p300i_3


title: RUNX1-ETO_BETi_KASUMI_ChIPSeq

description:
RUNX1-ETO_BETi_KASUMI_ChIPSeq.bdg
ChIP-Seq

value: AML1-ETO (Diagenode, C15310197)


title: MB_OLD_OVX_FEMALE_C3.TOTAL

value: MB


title: i5F_del_GFP_9

value: embryos


title: RUNX1-ETO_DMSO_KASUMI_ChIPSeq

description:
RUNX1-ETO_DMSO_KASUMI_ChIPSeq.bdg
ChIP-Seq


title: i5F_del_GFP_7


title: BETi2_KASUMI_ATACSeq

description:
BETi_2_KASUMI_ATACSeq.bdg
ATAC-Seq

extract_protocol:
Nuclei were isolated with lysis buffer for tagmentation
ATACSeq libraries were prepared using the Nextera DNA Sample Preparation Kit (Illumina)


title: OCI3_p300i_1


title: MB_YOUNG_WT_MALE_C3.10

value: YOUNG

value: WT


title: BETi1_KASUMI_ATACSeq

description:
BETi_1_KASUMI_ATACSeq.bdg
ATAC-Seq


title: i5F_del_GFP_12

value: facs-sorted PGCs


title: i5F_del_GFP_6


title: OCI3_DMSO_3


title: DS_YOUNG_OVX_MALE_C3.6

value: DS


title: LOVO-NC-replicate 2

value: LOVO

value: Human colorectal cancer cell line


title: i5F_del_GFP_5


title: OCI3_DMSO_2


title: DS_OLD_WT_FEMALE_C3.7

value: OLD


title: DMSO1_KASUMI_ATACSeq

description:
DMSO_1_KASUMI_ATACSeq.bdg
ATAC-Seq


title: i5F_del_GFP_4


title: OCI3_DMSO_1


title: OCI3_IC90r_p300_3

treatment_protocol: BETiIC90 resistant cells with 24h p300i treatment


title: DMSO2_KASUMI_ATACSeq

description:
DMSO_2_KASUMI_ATACSeq.bdg
ATAC-Seq


title: i5F_del_GFP_8


title: BETi2_KASUMI_nucRNASeq

description:
BETi2_KASUMI_nucRNASeq.bdg
nuclear RNASeq

extract_protocol:
Nuclei were isolated with lysis buffer for tagmentation, then RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) as per manufacturer’s protocol
RNA-seq libraries were prepared for sequencing using standard Illumina protocols


title: OCI3_IC90r_p300_2


title: DS_OLD_OVX_MALE_C3.9

value: ventral midbrain


title: i5F_del_GFP_3


title: i5F_del_GFP_2


title: MB_YOUNG_OVX_FEMALE_C3.7

value: dopaminergic neurons


title: BETi1_KASUMI_nucRNASeq

description:
BETi1_KASUMI_nucRNASeq.bdg
nuclear RNASeq

value: KASUMI-1 cell line


title: DS_YOUNG_OVX_FEMALE_C3.5


title: i5F_del_GFP_1


title: DMSO2_KASUMI_nucRNASeq

description:
DMSO2_KASUMI_nucRNASeq.bdg
nuclear RNASeq


title: VS_OLD_OVX_MALE_C3.6

value: VS

value: MALE


title: VS_YOUNG_WT_FEMALE_C3.5

value: FEMALE


title: OCI3_IC90r_3

treatment_protocol: BETiIC90 resistant cells with 24h DMSO treatment

value: OCI-AML3 cell line


title: CowNeuN2

description:
Nuclei enriched for NEUN
Cow_count_mat.csv

data_processing:
We used cellranger (v7.0, 10X Genomics) to align the sc- and snRNA-seq datasets, following manufacturer’s instructions. For each species, sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map (.bam) files.
To include both exonic and intronic reads in the quantification of gene expression for each sample, regardless of cellular or nuclear origin, we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices (GEMs; genes x cells) for each sample, corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample.
Assembly: ARS-UCD1.2
Supplementary files format and content: GEMs from different sample runs were combined (column-wise concatenated) to yield a full species’ GEM.

organism: Bos taurus

source_name: Retina

extract_protocol:
Frozen retinal tissues were homogenized in a Dounce homogenizer in 1ml Tris-based lysis buffer with 0.1% NP-40. Nuclei were stained with NEUN/RBFOX3 and/or CHX10/VSX2, washed once, pelleted at 500g for 5min, resuspended in PBS/BSA and stained with DAPI. NEUN+ and/or CHX10+ DAPI+ single nuclei were collected using a flow cytometer. The sorted nuclei were pelleted again, resuspended in PBS/BSA solution, and adjusted to a concentration of 1000 nuclei/µL. ~12µL of the nuclei suspension was loaded into a 10X Chromium Single Cell Chip (10X Genomics, Pleasanton, CA) with a targeted recovery of 8000 nuclei.
Single nuclei libraries were generated using the Chromium 3’ V3.1 platform (10X Genomics, Pleasanton, CA) according to the manufacturer’s protocol. Briefly, single nuclei were partitioned into Gel-beads-in-EMulsion (GEMs) where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full-length cDNA; this was followed by amplification, enzymatic fragmentation, and 5’ adaptor and sample index attachment to yield the final libraries.
Single nucleus RNA sequecning (10X Genomics)

value: Retina

value: Retinal neurons

value: Control


title: OCI3_IC90r_2


title: CowNeuN1


title: MB_YOUNG_WT_FEMALE_C3.7

value: MB

value: YOUNG


title: CowNEUN


title: OCI3_IC90r_1


title: BETi1_KASUMI_RNASeq

description:
KASUMI_RNASeq_DMSO_vs_BETi_counts.txt
RNASeq


title: OCI3_IC50r_p300_3

treatment_protocol: BETiIC50 resistant cells with 24h p300i treatment


title: DMSO1_KASUMI_nucRNASeq

description:
DMSO1_KASUMI_nucRNASeq.bdg
nuclear RNASeq


title: DS_OLD_OVX_MALE_C3.TOTAL

value: OVX


title: VS_YOUNG_OVX_MALE_C3.TOTAL


title: OCI3_IC50r_p300_2


title: DMSO2_KASUMI_RNASeq


title: OCI3_IC90r_p300_1


title: DMSO1_KASUMI_RNASeq


title: MB_OLD_OVX_MALE_C3.6


title: OCI3_IC50r_p300_1


title: VS_YOUNG_WT_MALE_C3.TOTAL

value: WT


title: DS_OLD_OVX_FEMALE_C3.4

value: DS


title: BETi2_KASUMI_RNASeq


title: OCI3_IC50r_2

treatment_protocol: BETiIC50 resistant cells with 24h DMSO treatment


title: OCI3_IC50r_3


title: CowCHx10_r2

description:
Nuclei enriched for CHX12
Cow_count_mat.csv


title: cowchx10 2

description:
Nuclei enriched for CHX11
Cow_count_mat.csv


title: MB_YOUNG_OVX_FEMALE_C3.5


title: cowneun 1


title: OCI3_IC50r_1


title: CowCHx10 1

description:
Nuclei enriched for CHX10
Cow_count_mat.csv


title: DS_OLD_WT_FEMALE_C3.4


title: CowAll

description:
All nuclei
Cow_count_mat.csv


title: CowNeuN 2


title: VS_OLD_WT_MALE_C3.9


title: OCI3_3d_p300i_3

treatment_protocol: 3dBETi and 24h p300i treatment


title: MB_OLD_WT_MALE_C3.6


title: OCI3_3d_p300i_2


title: MB_YOUNG_WT_MALE_C3.10_ONT


title: MB_YOUNG_OVX_MALE_C3.6


title: OCI3_3d_p300i_1


title: MB_YOUNG_OVX_FEMALE_C3.4


title: ppsR_dark_3

city: Braunschweig

first: Elisabeth

last: Haertig

state: Lower Saxony

address: Spielmannstr. 7

department: Microbiology

institute: TU Braunschweig

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppsR::Tn under dark conditions cultivated, replicate 3

hyb_protocol: 300 ng of labeled RNA were pooled, fragmented and hybridized according to the “one-color microarray” protocol from Agilent.

scan_protocol: The DNA microarrays were scanned using a Agilent C scanner and the Agilents scan control 8.4.1 software as well as the feature extraction 10.7.3.1 software.

data_processing: Data processing was performed in the R environment (http://www.cran.r-project.org/) using the limma package (Smyth, 2005), BioBASE package (Miller, 1996.) and the GPLOTS package (Warnes, 2012) of the BioConductor project (http:// www.bioconductor.org/). For analyses only genes with an absolute 2 fold logarithmic change (FC) >0.8 expression and a P-value <0.05 were considered in subsequent analyses.

organism: Dinoroseobacter shibae

source_name: D. shibae, transposonmutant ppsR::Tn, dark, replicate 3

label_protocol: 1 µg of isolated total cellular RNA was labeled with Cy3, using the ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech, Amsterdam, The Netherlands) according to the manufacturers manual.

growth_protocol: For the  experiment Dinoroseobacter shibae DFL12T wild type and transposonmutant strains Dshi_1135::Tn, D. shibae ppaA::Tn and D. shibae ppsR::Tn were grown in artificial saltwater minimal medium (SWM). For cultivation 100 ml of cell culture was inoculated with a grown pre-culture to an OD578 nM of 0.05 in a baffled flasks shaking at 180 rpm at 30°C under light, dark or bluelight conditions. After reaching an OD578 nM of 0.5 cells were harvested.

extract_protocol: A 2 ml volume of a D. shibae culture was used for RNA isolation using RNA protect and RNeasy mini Kit (Qiagen, Hilden, Germany) according to the manufactures manual. Thereby, 1 µl of isolated RNA was analyzed using the Agilent RNA 6000 Nano Kit and the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).

treatment_protocol: Growth under light, dark or bluelight conditions.

value: exponential phase

tag: light

value: dark


title: ppsR_dark_1

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppsR::Tn under dark conditions cultivated, replicate 1

source_name: D. shibae, transposonmutant ppsR::Tn, dark, replicate 1


title: MB_YOUNG_WT_MALE_C3.9_ONT

value: ventral midbrain

tag: Sex


title: MB_YOUNG_WT_MALE_C3.9

tag: cell type

value: dopaminergic neurons


title: cow_neunpos_B1


title: ppsR_dark_4

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppsR::Tn under dark conditions cultivated, replicate 4

source_name: D. shibae, transposonmutant ppsR::Tn, dark, replicate 4

tag: strain


title: MB_YOUNG_OVX_MALE_C3.9_ONT


title: OCI3_3d_2

treatment_protocol: 3dBETi and 24h DMSO treatment


title: ppsR_blue_3

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppsR::Tn under bluelight conditions cultivated, replicate 3

value: blue


title: MB_YOUNG_OVX_MALE_C3.10_ONT


title: ppsR_blue_4

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppsR::Tn under bluelight conditions cultivated, replicate 4


title: OCI3_3d_1

description:
Readcounts_all_DMSO_vs_p300i_RNASeq_comparisons.txt
RNASeq


title: VS_OLD_OVX_FEMALE_C3.5

value: VS

value: OLD


title: DS_YOUNG_OVX_FEMALE_C3.7

value: FEMALE


title: ppsR_blue_2

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppsR::Tn under bluelight conditions cultivated, replicate 2

source_name: D. shibae, transposonmutant ppsR::Tn, dark, replicate 2


title: ppsR_dark_2

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppsR::Tn under dark conditions cultivated, replicate 2


title: MOLM13_p300i_3

value: MOLM-13 cell line


title: VS_OLD_OVX_FEMALE_C3.4

source_name: ventral midbrain


title: MB_YOUNG_WT_FEMALE_C3.7_ONT


title: MOLM13_p300i_2


title: ppaA_dark_4

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppaA::Tn under dark conditions cultivated, replicate 4

source_name: D. shibae, transposonmutant ppaA::Tn, dark, replicate 4


title: OCI3_3d_3

value: OCI-AML3 cell line


title: ppsR_blue_1

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppsR::Tn under bluelight conditions cultivated, replicate 1


title: MB_OLD_WT_MALE_C3.10

value: MALE


title: MB_OLD_OVX_MALE_C3.10_ONT


title: MOLM13_p300i_1


title: MB_OLD_WT_MALE_C3.10_ONT


title: ppaA_dark_2

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppaA::Tn under dark conditions cultivated, replicate 2

source_name: D. shibae, transposonmutant ppaA::Tn, dark, replicate 2


title: MB_YOUNG_OVX_FEMALE_C3.7_ONT


title: ppaA_dark_3

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppaA::Tn under dark conditions cultivated, replicate 3

source_name: D. shibae, transposonmutant ppaA::Tn, dark, replicate 3


title: MOLM13_DMSO_3

source_name: t(9;11) MLL-AF9 AML


title: MB_OLD_OVX_MALE_C3.9_ONT


title: WT-STAT5-MSC

city: Atlanta

first: Peng

last: Qiu

state: GA

address: 950 Atlantic Dr. NW

institute: Georgia Institute of Technology

data_processing:
Raw sequencing reads were processed by Cell Ranger (10x Genomics) to generate gene expression count matrices for every sample (wild type and knockout samples for KLS and MSC respectively). After sequence alignment to GRCm38/mm10 mouse reference genome, UMI (Unique Molecular Identifiers) counts for each gene per cell formed the gene expression count matrices.
Assembly: GRCm38/mm10
Supplementary files format and content: Cell Ranger output files of barcodes, genes and count matrix

source_name: bone marrow

extract_protocol:
Bone marrow cells were harvested from the femurs and tibias of 4 Vav1-Cre/+ or Vav1-Cre/+/STAT5abflox/flox (8-12 weeks). The cells were lineage depleted using a mouse lineage cell depletion kit (Miltenyi Biotech, Auburn, CA) and stained with FITC-labeled lineage antibodies (Gr-1, Mac-1, B220, Ter119, CD3, CD4, CD8a), anti-c-Kit-APC, anti-Sca-1-PE-Cy7 (Thermo Fisher Scientific, Norcross, GA), and dead cells were excluded by staining with propidium iodide dye. KLS cells were sorted using BD FACSAria III Cell Sorter. For sorting bone marrow stromal cells, cells were isolated as described [reference: Houlihan, D.D.; Mabuchi, Y.; Morikawa, S.; Niibe, K.; Araki, D.; Suzuki, S.; Okano, H.; Matsuzaki, Y. Isolation of mouse mesenchymal stem cells on the basis of expression of Sca-1 and PDGFR-alpha. Nature protocols 2012, 7, 2103-2111, doi:10.1038/nprot.2012.125]. Briefly, mouse bones (tibia and femur) were isolated and cleaned from 6-8 weeks old mice, then were crushed and cut into tiny pieces with sterile scissors, incubated them in 20 ml of preheated DMEM plus 0.2% (wt/vol; 40 mg) collagenase at 110 rpm at 37°C for 1 hour ). The cell suspension was filtered through a 70-μm cell strainer and bone fragment was further crushed and washed to liberate cells out of the bone into solution. CD45+ cells were depleted with mouse CD45 microbeads from Miltenyi Biotech( Auburn, CA) and stained with anti-Ter119-PE  (BD Biosciences, San Jose, CA), anti-CD45-FITC, Anti-CD71-Alexa 700, Anti-Sca-1-PE-Cy7 and Anti-CD140a-APC (Thermo Fisher Scientific, Norcross, GA). CD45negTer119-/lowCD71-Sca-1+CD140a+  cells were sorted using BD FACSAria III Cell Sorter. Sorted cells were immediately processed for single cells RNA sequencing.
Tissue derived single cells were loaded onto the 10X Chromium Controller targeting 3000-6000 cells/sample. Single cell capture, barcoding, GEM-RT, clean-up, cDNA amplification and library construction were performed according to the manufacturers’ instructions for v3 chemistry using 10x Genomics Single Cell 5’ Chromium Chip B kit (PN-1000074) and Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (PN 1000092).  Final gene expression library pools were sent to Genewiz (South Plainfield, NJ) and sequenced on an Illumina’s Novaseq6000 instrument with a targeted sequencing depth of 150,000 reads/cell.

value: bone marrow

value: stromal


title: WT-STAT5-KLS

value: hematopoietic


title: MB_OLD_WT_MALE_C3.9_ONT

value: MB


title: ppaA_dark_1

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppaA::Tn under dark conditions cultivated, replicate 1

source_name: D. shibae, transposonmutant ppaA::Tn, dark, replicate 1


title: MOLM13_DMSO_1


title: MB_OLD_OVX_FEMALE_C3.7_ONT

value: OVX


title: KO-STAT5-KLS


title: KO-STAT5-MSC


title: MOLM13_DMSO_2


title: KASUMI_p300i_3

source_name: t(8;21) RUNX1-ETO AML

value: KASUMI-1 cell line


title: KASUMI_p300i_2


title: MB_OLD_WT_FEMALE_C3.7_ONT

value: WT


title: GSDMD-CKO-DOX-3

city: Hangzhou

first: Rifeng

state: Zhejiang

address: No. 88 Jiefang Road

institute: Zhejiang University

data_processing:
Data Analysis: 1. Data quality control Use fastp v 0.19.3 to filter the original data, mainly to remove reads with adapters; when the N content in any sequencing reads exceeds 10% of the base number of the reads, remove the paired reads; when any sequencing reads When the number of low quality (Q<=20) bases contained in reads exceeds 50% of the bases of the reads, this paired reads will be removed. All subsequent analyses are based on clean reads. 2. Reads mapping to the reference genome Download the reference genome and its annotation files from the designated website, use HISAT v2.1.0 to construct the index, and compare clean reads to the reference genome. 3. New transcript prediction Use StringTie v1.3.4d for new gene prediction. StringTie applies network streaming algorithms and optional de novo to splice transcripts. Compared with Cufflinks and other software, StringTie can splice a more complete and accurate transcript, and the splicing speed is faster. 4. Quantification of gene expression levels Use featureCounts v1.6.2 to calculate the gene alignment, and then calculate the FPKM of each gene based on the gene length. FPKM is currently the most commonly used method to estimate gene expression levels. 5. Difference analysis DESeq2 v1.22.1 was used to analyze the differential expression between the two groups, and the P value was corrected using the Benjamini & Hochberg method. The corrected P value and |log2foldchange| are used as the threshold for significant difference expression. 6. Differential gene enrichment analysis The enrichment analysis is performed based on the hypergeometric test. For KEGG, the hypergeometric distribution test is performed with the unit of pathway; for GO, it is performed based on the GO term. 7. Differential AS analysis Use rMATS v3.1.0 to analyze variable splicing events, including five alternative splicing events: SE, RI, MXE, A5SS, and A3SS. 8. SNP analysis Use GATK v4.0.11.0 to analyze the variant sites, and use annovar to annotate the variant sites. 9. Differential gene protein interaction analysis The protein interaction analysis of differentially expressed genes is based on the STRING database of known and predicted protein--protein interactions. For the species existing in the database, we construct the network by extracting the target gene list from the database; otherwise, use blast v2.7.1+ to compare the target gene sequence with the selected reference protein sequence, and then according to the selected reference species Know the interaction to build a network. 10. GSEA Use gsea--3.0.jar for gene set enrichment analysis. 11. WGCNA Use WGCNA v1.69 for weighted gene co--expression network analysis.
genome_build: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Heart

growth_protocol: GSDMD (flox/flox) and GSDMD-myocardial specific knockout (GSDMD-CKO) mice were kept under a 12:12-h light/dark cycle at consistent temperature and humidity and were given access to food and water ad libitum.

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Then the libraries were constructed using TruSeq Stranded mRNALTSample Prep Kit(Ilumina,San Diego, CA, USA) .

treatment_protocol:
Intraperitoneal injections (IP) of doxorubicin(DOX) (20 mg/kg; Sigma, 25316-40-9) were administered to the 6–8-week-old mice.
Select myocardial tissue 3 days after DOX treatment for RNA-seq

value: Heart

value: GSDMD knockout

tag: treatment

value: Doxorubicin


title: ppaA_blue_1

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppaA::Tn under bluelight conditions cultivated, replicate 1

source_name: D. shibae, transposonmutant ppaA::Tn, bluelight, replicate 1

value: exponential phase

value: blue


title: GSDMD-CKO-DOX-2


title: ppaA_blue_2

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppaA::Tn under bluelight conditions cultivated, replicate 2

source_name: D. shibae, transposonmutant ppaA::Tn, bluelight, replicate 2


title: ppaA_blue_3

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppaA::Tn under bluelight conditions cultivated, replicate 3

source_name: D. shibae, transposonmutant ppaA::Tn, bluelight, replicate 3


title: KASUMI_p300i_1

tag: cell line


title: t32lps5 (miRNA-seq)

city: Bodø

first: Jorge

last: Fernandes

address: Universitetsalleen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

data_processing:
Used bcl2fastq for demultiplexing
cutadapt (v1.12) for trimming adapters
FASTX-Toolkit for filtering low-quality reads
FastQC (v0.11.5) for quality control
Clean reads were sequentially mapped to the mature miRNA of zebrafish, another 15 teleost species (Astatotilapia burtoni, Cyprinus carpio, Electrophorus electricus, Fugu rubripes, Gadus morhua, Hippoglossus hippoglossus, Ictalurus punctatus, Metrizclima zebra, Neolamprologus brichardi, Oryzias latipes, Oreochromis niloticus, Pundamilia nyererei, Paralichthys olivaceus, Salmo salar, Tetraodon nigroviridis) and three model species (Drosophila melanogaster, Mus musculus, Homo sapiens) in miRBase (Release 22). Other non-coding RNAs (tRNA, rRNA, snRNA, snoRNA) were filterred out, and remaining reads were used for identifying novel miRNAs by miRDeep2.
All mapped reads were combined and subjected to DESeq2 (v1.11.1) for differential miRNA expression analysis
Target genes of DEmiRs were predicted by miRanda (v3.3a)
Genome_build: miRBase (release 22)
Supplementary_files_format_and_content: tab-delimited matrix containing read counts of each library

organism: Danio rerio

source_name: spleen

growth_protocol: Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue (Sigma-Aldrich, USA) until first feeding. One-third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C, 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS (Special Diets Services, SDS, UK) 100, 200, 300, and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.

extract_protocol:
Total RNA was isolated from spleen using the PicoPure RNA Isolation kit (ThermoFisher Scientific, USA) with some changes. In brief, spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip, and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min, centrifuged at 3,000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube, mixed thoroughly with 100 μl 70% Ethanol, and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially, and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 (Agilent Technologies, USA).
Libraries were built following the manual of NEXTflex Small RNA-Seq Kit v3 (Bioo Scientific, USA). Fifty ng of total RNAs from each replicate were ligated with 3' 4N and 5' 4N adenylated adapters sequentially, and reverse transcribed into first-strand complement DNAs (cDNAs). Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min, 1 cycle; 95 °C for 20 s, 60 °C for 30 s, 72 °C for 15 s, 22 cycles; 72 °C for 2 min, 1 cycle. The size selection (~150 bp) was based on a 10% TBE-PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 (Agilent Technologies, USA).

treatment_protocol: Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate (MS-222; Sigma-Aldrich, USA) and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 (Sigma-Aldrich, USA), and kept for 12 h. Then, fish were euthanized by immersing in 300 mg/L MS-222. The spleen was dissected immediately, snap-frozen in liquid nitrogen, and stored at -80 °C.

value: AB

tag: developmental stage

value: adult

value: 100 d post-fertilization

value: LPS

tag: temperature

value: spleen


title: GSDMD-CKO-DOX-1

last: Gao

tag: genotype


title: ppaA_light_3

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppaA::Tn under light conditions cultivated, replicate 3

source_name: D. shibae, transposonmutant ppaA::Tn, light, replicate 3

value: light


title: ppaA_light_4

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppaA::Tn under light conditions cultivated, replicate 4

source_name: D. shibae, transposonmutant ppaA::Tn, light, replicate 4


title: t32lps7 (miRNA-seq)


title: KASUMI_DMSO_3


title: KASUMI_DMSO_2


title: GSDMD-FLOX/FLOX-DOX-3

value: GSDMD-FLOX


title: t32lps2 (miRNA-seq)


title: GSDMD-FLOX/FLOX-DOX-2


title: ppaA_light_2

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppaA::Tn under light conditions cultivated, replicate 2

source_name: D. shibae, transposonmutant ppaA::Tn, light, replicate 2


title: t32lps3 (miRNA-seq)


title: ppaA_light_1

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppaA::Tn under light conditions cultivated, replicate 1

source_name: D. shibae, transposonmutant ppaA::Tn, light, replicate 1


title: GSDMD-FLOX/FLOX-DOX-1


title: t32lps1 (miRNA-seq)


title: KASUMI_DMSO_1


title: Dshi_1135_dark_4

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae Dshi_1135::Tn under dark conditions cultivated, replicate 4

source_name: D. shibae, transposonmutant Dshi_1135::Tn, dark, replicate 4

value: dark


title: hPSC-AO

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v3.0.2)
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built human reference genome (GRCh38 v3.0.0) and to extract gene expression UMI counts matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

source_name: hPSC-derived airway organoids

growth_protocol: Airway organoid differentiation   hPSC-AOs were derived using a protocol slightly modified from previous studies (15, 18). For definitive endoderm (DE) differentiation, cells were passaged with Accutase (Innovative Cell Technology) at 1:2-1:3 for the first day. When achieving 80-90% confluency, hESCs were treated with 3 μM CHIR99021 (CHIR, Sigma) and 100 ng/ml Activin A (R&D systems) in basal medium RPMI1640 (Cellgro) supplemented with 1X Pen-Strep (Gibco) for 1 day, and changed to the basal medium containing 100 ng/ml Activin A and 2% FBS for the next 48 hours. To induce anterior foregut endoderm, the endoderm cells were cultured in completed serum free differentiation (cSFD) medium supplemented with 1.5 μM dorsomorphin dihydrochloride (R&D Systems) and 10 μM SB431542 (R&D Systems) for 24 hours, and then switched to 10 μM SB431542 and 1 μM IWP2 (R&D Systems) treatment for 24 hours. For induction of early stage lung progenitor cells (day 15), the anterior foregut endoderm was treated with 3 μM CHIR99021, 10 ng/ml human BMP4 (peprotech) and 50 nM all-trans retinoic acid (ATRA) in cSFD medium. At day 15, the lung progenitor cells detached from 2D culture by trypsinization, mixed with matrigel, and replated to form 70 μL domes on 24-well plate. The 3D culture was maintained in cSFD containing 100 ng/ml human FGF10, 250 ng/ml human FGF2, 50 nM dexamethasone, 0.1 mM 8-bromo-cAMP (Sigma Aldrich) and 0.1 mM IBMX (Sigma Aldrich).

extract_protocol: Library was constructed according to the user manual of Chromium Single Cell 3’ Library & Gel Bead Kit v3, and were sequenced on the Illumina NovaSeq6000 sequencer with pair-end reads (28 bp for read 1 and 91 bp for read 2).

treatment_protocol: The organoids were dissociated using into single cells using accutase.

value: hPSC-derived airway organoids


title: hPSC_CO_SARS-CoV-2_GW_3

description:
colon_gw_3
processed data file:
raw_counts.hPSC_CO.txt

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome plus SARS-CoV-2 genome using STAR v2.5.2b.
Raw read counts were quantified using HTSeq-count v0.11.2.
Genome_build: hg19
Supplementary_files_format_and_content: txt files storing raw read counts per gene per sample

extract_protocol:
Total RNA was extracted in TRIzol (Invitrogen) and DNase I treated using Directzol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions.
RNAseq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. cDNA libraries were sequenced with pair-end 51 bps using an Illumina NovaSeq6000 platform.

treatment_protocol: hPSC-AOs or hPSC-COs were fragmented into small cell clusters and plated on  10% matrigel-coated plates. The infection was performed in the culture media at the indicated MOIs at 37°C. For pre-infection treatment experiments, hPSC-AOs or hPSC-COs were pretreated with DMSO (control), 10 µM GW6471, 10 µM Xanthohumol or 1 µM Chemotin for 4 hours prior to infection.

value: hPSC-derived colon organoids

value: SARS-CoV-2 infect


title: t32ct8 (miRNA-seq)

value: control


title: Exosc3_mESC_cKO_TTseq_Rep2

first: Robert

last: Sebra

state: New York

address: 1 Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Adapters were trimmed from reads using Trim Galore (v0.5.0) (Martin, 2011). Reads were aligned to the GRCm38/mm10 reference genome using STAR (v2.7.5b) (Dobin et al., 2013) with the following custom parameters: --outFilterMultimapNmax 100 –winAnchorMultimapNmax 100. BAM files were filtered using sambamba (v.0.5.6), removing reads that are duplicated, unmapped, and removing all secondary alignments (i.e. keeping the best genomic alignment location for multimapping reads). BigWigs were generated on the filtered BAM files using deepTools (v3.5.0) (Ramirez et al., 2016) with RPKM normalization.
Assembly: mm10
Supplementary files format and content: TT-Seq coverage in bigWig format
Library strategy: TT-seq

source_name: mESC

extract_protocol:
For RNA extraction, cells were washed 3x with DPBS and lysed directly on the plate with 1mL of TRIzol reagent (Invitrogen, 15596026). Subsequently, RNA was purified using Direct-zol RNA Miniprep Plus Kits (Zymo, R2072) following manufacturer instructions. In brief, lysed cells in TRIzol were mixed 1:1 with 100% ethanol. Mixed lysates were added to the Zymo-spin columns, treated with DNase I, and washed with provided buffers. RNA was eluted with UltraPure DNase/RNase-Free Distilled Water (Invitrogen, 10977015).
250 ng of enriched RNA was used for library construction with the Illumina TruSeq stranded total RNA kit and Illumina CD index plate. After 5 cycles of PCR, samples were removed from the thermal cycler and a test PCR was performed to determine the optimal number of final cycles.


title: hPSC_CO_SARS-CoV-2_GW_2

description:
colon_gw_2
processed data file:
raw_counts.hPSC_CO.txt


title: Dshi_1135_dark_3

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae Dshi_1135::Tn under dark conditions cultivated, replicate 3

source_name: D. shibae, transposonmutant Dshi_1135::Tn, dark, replicate 3


title: Exosc3_mESC_CTRL_TTseq_Rep2

value: CTRL


title: t32ct6 (miRNA-seq)


title: t32ct7 (miRNA-seq)


title: hPSC_CO_SARS-CoV-2_GW_1

description:
colon_gw_1
processed data file:
raw_counts.hPSC_CO.txt


title: hPSC_CO_SARS-CoV-2_Control_3

description:
colon_d_3
processed data file:
raw_counts.hPSC_CO.txt


title: Exosc3_mESC_CTRL_TTseq_Rep1


title: t32ct3 (miRNA-seq)


title: ppaA_blue_4

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae ppaA::Tn under bluelight conditions cultivated, replicate 4

source_name: D. shibae, transposonmutant ppaA::Tn, bluelight, replicate 4


title: Dshi_1135_blue_3

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae Dshi_1135::Tn under bluelight conditions cultivated, replicate 3

source_name: D. shibae, transposonmutant Dshi_1135::Tn, bluelight, replicate 3


title: Dshi_1135_dark_1

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae Dshi_1135::Tn under dark conditions cultivated, replicate 1

source_name: D. shibae, transposonmutant Dshi_1135::Tn, dark, replicate 1


title: Dshi_1135_blue_4

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae Dshi_1135::Tn under bluelight conditions cultivated, replicate 4

source_name: D. shibae, transposonmutant Dshi_1135::Tn, bluelight, replicate 4


title: t28lps8 (miRNA-seq)


title: Exosc3_EpiLC_cKO_bulkRNA_Rep1

data_processing:
Illumina adapters were trimmed from reads using Trim Galore (v0.5.0). Reads were aligned to the GRCm38/mm10 reference genome using STAR (v2.7.5b) with the following custom parameters: --outFilterMultimapNmax 100 –winAnchorMultimapNmax 100. Gene and TE-level counts were calculated using TEcount (v2.2.1) using the Ensembl GRCm38 v102 transcript annotation and the GRCm38 RepeatMasker annotation downloaded from UCSC table browser.
Assembly: mm10
Supplementary files format and content: TSV file containing gene counts

source_name: EpiLC

extract_protocol:
For RNA extraction, cells were washed 3x with DPBS and lysed directly on the plate with 1mL of TRIzol reagent (Invitrogen, 15596026). Subsequently, RNA was purified using Direct-zol RNA Miniprep Plus Kits (Zymo, R2072) following manufacturer instructions. In brief, lysed cells in TRIzol were mixed 1:1 with 100% ethanol. Mixed lysates were added to the Zymo-spin columns, treated with DNase I, and washed with provided buffers. RNA was eluted with UltraPure DNase/RNase-Free Distilled Water (Invitrogen, 10977015). For DNA extraction, PureLink™ Genomic DNA Mini Kit (Invitrogen, K1820-00) was used followed manufacturer instructions. In brief, cells were washed 3x with DPBS and lysed directly on the plates using supplied Lysis/Binding buffer. Lysates were subsequently applied to the column and washed with buffers provided. DNA was eluted in PureLink Genomic Elution Buffer provided in the kit.
For complementary DNA synthesis, 100-200 µg of DNase I treated RNA was reverse transcribed using High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, 4368814). Random hexamers were used to capture total RNA. For metabolic RNA labeling, cDNA synthesis was carried out while RNA was bound to beads using SuperScript VILO cDNA synthesis kit (Invitrogen, 11754-050).


title: hPSC_CO_SARS-CoV-2_Control_1

description:
colon_d_1
processed data file:
raw_counts.hPSC_CO.txt


title: t32ct9 (miRNA-seq)


title: Exosc3_EpiLC_CTRL_bulkRNA_Rep2


title: t28lps5 (miRNA-seq)


title: Dshi_1135_blue_2

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae Dshi_1135::Tn under bluelight conditions cultivated, replicate 2

source_name: D. shibae, transposonmutant Dshi_1135::Tn, bluelight, replicate 2


title: Exosc3_mESC_cKO_TTseq_Rep1


title: Dshi_1135_blue_1

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae Dshi_1135::Tn under bluelight conditions cultivated, replicate 1

source_name: D. shibae, transposonmutant Dshi_1135::Tn, bluelight, replicate 1


title: hPSC_AO_SARS-CoV-2_GW_3

description:
airway_gw_3
processed data file:
raw_counts.hPSC_AO.txt
raw_counts.hPSC_AO.downsample.txt


title: t28lps4 (miRNA-seq)


title: Dshi_1135_dark_2

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae Dshi_1135::Tn under dark conditions cultivated, replicate 2

source_name: D. shibae, transposonmutant Dshi_1135::Tn, dark, replicate 2


title: t28lps2 (miRNA-seq)

source_name: spleen


title: hPSC_AO_SARS-CoV-2_GW_2

description:
airway_gw_2
processed data file:
raw_counts.hPSC_AO.txt
raw_counts.hPSC_AO.downsample.txt


title: Dshi_1135_light_3

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae Dshi_1135::Tn under light conditions cultivated, replicate 3

source_name: D. shibae, transposonmutant Dshi_1135::Tn, light, replicate 3


title: Exosc3_EpiLC_cKO_bulkRNA_Rep2


title: Dshi_1135_light_4

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae Dshi_1135::Tn under light conditions cultivated, replicate 4

source_name: D. shibae, transposonmutant Dshi_1135::Tn, light, replicate 4


title: hPSC_AO_SARS-CoV-2_GW_1

description:
airway_gw_1
processed data file:
raw_counts.hPSC_AO.txt
raw_counts.hPSC_AO.downsample.txt


title: t28lps1 (miRNA-seq)


title: Exosc3_mESC_cKO_bulkRNA_Rep1


title: hPSC_CO_SARS-CoV-2_Control_2

description:
colon_d_2
processed data file:
raw_counts.hPSC_CO.txt


title: Dshi_1135_light_2

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae Dshi_1135::Tn under light conditions cultivated, replicate 2

source_name: D. shibae, transposonmutant Dshi_1135::Tn, light, replicate 2


title: Exosc3_mESC_CTRL_bulkRNA_Rep2


title: hPSC_AO_SARS-CoV-2_Control_2

description:
airway_d_2
processed data file:
raw_counts.hPSC_AO.txt
raw_counts.hPSC_AO.downsample.txt


title: t28ct3 (miRNA-seq)


title: Dshi_1135_light_1

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae Dshi_1135::Tn under light conditions cultivated, replicate 1

source_name: D. shibae, transposonmutant Dshi_1135::Tn, light, replicate 1


title: KO3

first: zhou

last: hui

address: no

data_processing:
Clustering and sequencing (Novogene Experimental Department) The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Quality control Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mmp9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Mouse BMDMs

growth_protocol: To generate bone marrow-derived macrophages (BMDMs), the bone marrow was flushed from tibias and femurs, then the bone marrow cells were plated in RPMI 1640 medium (Gibco) supplemented with 10% heat-inactivated FBS (Gibco) and GM-CSF (10ng/ml) for 6 days.

extract_protocol:
RNA were extracted 24 h after CD47 Stimulation
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: ~8 x 105 streptavidin beads were washed three times with PBS, mixed within PBS plus 0.4% BSA, and incubated with biotinylated mouse CD47 at room temperature for 0.5 h with end-over-end mixing to allow for protein coupling. Beads were then washed three times to remove excess protein. Biotinylated mouse CD47 (ACRObiosystem) was added at 50 nm for target particle experiments.

value: Mouse bone marrow


title: hPSC_AO_SARS-CoV-2_Control_1

description:
airway_d_1
processed data file:
raw_counts.hPSC_AO.txt
raw_counts.hPSC_AO.downsample.txt


title: t28ct7 (miRNA-seq)


title: hPSC_AO_Mock_3

description:
airway_m_3
processed data file:
raw_counts.hPSC_AO.txt
raw_counts.hPSC_AO.downsample.txt

value: Mock


title: wt_dark_3

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae wildtype under dark conditions cultivated, replicate 3

source_name: D. shibae, wildtype, dark, replicate 3

value: WT

value: exponential phase


title: Exosc3_mESC_CTRL_bulkRNA_Rep1

source_name: mESC


title: wt_dark_4

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae wildtype under dark conditions cultivated, replicate 4

source_name: D. shibae, wildtype, dark, replicate 4


title: Exosc3_EpiLC_CTRL_bulkRNA_Rep1


title: Exosc3_mESC_cKO_bulkRNA_Rep2


title: hPSC_AO_Mock_2

description:
airway_m_2
processed data file:
raw_counts.hPSC_AO.txt
raw_counts.hPSC_AO.downsample.txt


title: wt_dark_2

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae wildtype under dark conditions cultivated, replicate 2

source_name: D. shibae, wildtype, dark, replicate 2


title: t28ct1 (miRNA-seq)

value: AB


title: KO1


title: hPSC_AO_Mock_1

description:
airway_m_1
processed data file:
raw_counts.hPSC_AO.txt
raw_counts.hPSC_AO.downsample.txt


title: wt_dark_1

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae wildtype under dark conditions cultivated, replicate 1

source_name: D. shibae, wildtype, dark, replicate 1


title: t24lps8 (miRNA-seq)

value: adult


title: hPSC_AO_SARS-CoV-2_Control_3

description:
airway_d_3
processed data file:
raw_counts.hPSC_AO.txt
raw_counts.hPSC_AO.downsample.txt


title: Rhabdomys_NeunPos2b1

city: Seattle

first: Joshua

last: Hahn

address: 3747 W Stevens Wy NE

institute: University of Washington

data_processing:
We used cellranger (v7.0, 10X Genomics) to align the sc- and snRNA-seq datasets, following manufacturer’s instructions. For each species, sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map (.bam) files.
Assembly: Rhabdomys_pumilio_2.0
Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample, regardless of cellular or nuclear origin, we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices (GEMs; genes x cells) for each sample, corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample.
Supplementary files format and content: GEMs from different sample runs were combined (column-wise concatenated) to yield a full species’ GEM.

organism: Rhabdomys pumilio

source_name: Retina

value: Retina

value: Retinal neurons


title: t24lps6 (miRNA-seq)

value: 100 d post-fertilization

value: LPS

value: spleen


title: wt_blue_4

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae wildtype under bluelight conditions cultivated, replicate 4

source_name: D. shibae, wildtype, bluelight, replicate 4

value: blue


title: t28ct5 (miRNA-seq)


title: WT2

value: wild type


title: Rhabdomys_NeunPos1b2


title: t24lps3 (miRNA-seq)


title: t28ct2 (miRNA-seq)


title: Rhabdomys_NeunPos1b1


title: KO2


title: wt_blue_2

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae wildtype under bluelight conditions cultivated, replicate 2

source_name: D. shibae, wildtype, bluelight, replicate 2


title: WT1


title: PCOS_A145

city: shijiazhuang

first: zhiming

last: zhao

state: hebei

address: 215 heping west road

institute: The second hospital of hebei medical university

data_processing:
Illumina Casava1.7 software used for basecalling
The raw reads generated by RNA-seq were processed by removing the Illumina adapters with Trimmomatic and then low-quality regions at the 5' and 3' ends were deleted.
Counculat Counts and TPM with alignment-free software, kallisto, Genome index were build form HUMAN reference genome GRCh38.p13, downloaded from GENCODE (https://www.gencodegenes.org/human/release_36.html).The GTF annotation were also from GENCODE Release 36
Assembly: GENCODE GRCh38.p13
Supplementary files format and content: tab-delimited text files include counts and TPM values for each Sample

source_name: Cumulus granule cells

extract_protocol:
testis were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
These libraries were constructed based on the recommendations of the NEBNext®Ultra™ Directed RNA Library Preparation Kit. RNA fragments and short-stranded RNA were carried using NEBNext First Strand Synthesis Reaction Buffer (5×). First strand cDNA was synthesized using a random hexamer primer and M-MuLV reverse transcriptase. Subsequently, second strand cDNA was synthesized using DNA polymerase I and RNase h, the purified second strand cDNA ends were repaired, and then poly(A) and A adapters were added. A fragment of approximately 300 base pairs (bp) was selected using the UNG enzyme.

value: Cumulus granule cells

value: manual sorting

tag: disease state

value: polycystic ovary syndrome (PCOS)

value: female


title: t24lps2 (miRNA-seq)


title: PCOS_A129


title: wt_blue_1

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae wildtype under bluelight conditions cultivated, replicate 1

source_name: D. shibae, wildtype, bluelight, replicate 1


title: t24lps1 (miRNA-seq)


title: Rhabdomys_NeunNeg1b2


title: WT3

value: Mouse bone marrow


title: PCOS_A146


title: Rhabdomys_AllnoStnoSob2


title: wt_light_3

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae wildtype under light conditions cultivated, replicate 3

source_name: D. shibae, wildtype, light, replicate 3

value: light


title: t24ct8 (miRNA-seq)

source_name: spleen

value: control


title: Control_B17


title: Rhabdomys_AllnoStb2


title: wt_light_2

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae wildtype under light conditions cultivated, replicate 2

source_name: D. shibae, wildtype, light, replicate 2

value: WT

value: exponential phase


title: t24ct9 (miRNA-seq)

value: AB

value: adult


title: t24ct5 (miRNA-seq)


title: Rhabdomys_NeunNegb1

value: Retina

value: Retinal neurons


title: wt_light_4

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae wildtype under light conditions cultivated, replicate 4

source_name: D. shibae, wildtype, light, replicate 4


title: Control_B16


title: wt_blue_3

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae wildtype under bluelight conditions cultivated, replicate 3

source_name: D. shibae, wildtype, bluelight, replicate 3


title: Opossum_neun_S2

data_processing:
We used cellranger (v7.0, 10X Genomics) to align the sc- and snRNA-seq datasets, following manufacturer’s instructions. For each species, sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map (.bam) files.
Assembly: ASM229v1
Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample, regardless of cellular or nuclear origin, we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices (GEMs; genes x cells) for each sample, corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample.
Supplementary files format and content: GEMs from different sample runs were combined (column-wise concatenated) to yield a full species’ GEM.

organism: Didelphis marsupialis

extract_protocol:
Frozen retinal tissues were homogenized in a Dounce homogenizer in 1ml Tris-based lysis buffer with 0.1% NP-40. Nuclei were stained with NEUN/RBFOX3 and/or CHX10/VSX2, washed once, pelleted at 500g for 5min, resuspended in PBS/BSA and stained with DAPI. NEUN+ and/or CHX10+ DAPI+ single nuclei were collected using a flow cytometer. The sorted nuclei were pelleted again, resuspended in PBS/BSA solution, and adjusted to a concentration of 1000 nuclei/µL. ~12µL of the nuclei suspension was loaded into a 10X Chromium Single Cell Chip (10X Genomics, Pleasanton, CA) with a targeted recovery of 8000 nuclei.
Single nuclei libraries were generated using the Chromium 3’ V3.1 platform (10X Genomics, Pleasanton, CA) according to the manufacturer’s protocol. Briefly, single nuclei were partitioned into Gel-beads-in-EMulsion (GEMs) where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full-length cDNA; this was followed by amplification, enzymatic fragmentation, and 5’ adaptor and sample index attachment to yield the final libraries.
Single cell RNA sequecning (10X Genomics)


title: t24ct3 (miRNA-seq)

value: 100 d post-fertilization


title: Control_B23


title: wt_light_1

description:
Dinoroseobacter shibae DFL12T DSM 16496T
Gene expression of D. shibae wildtype under light conditions cultivated, replicate 1

source_name: D. shibae, wildtype, light, replicate 1


title: t24ct1 (miRNA-seq)

value: spleen


title: Opossum2_neun_neg_2


title: t32lps5 (RNA-seq)

data_processing:
Used bcl2fastq for demultiplexing
cutadapt (v1.12) for trimming adapters
FASTX-Toolkit for filtering low-quality reads
FastQC (v0.11.5) for quality control
Clean reads were mapped to zebrafish transcriptome (GRCz11.92) and genome (GRCz11) by STAR (version 020201)
Read counts were extracted from mapping result of STAR, and merged into one matrix
DESeq2 (v1.11.1) was used for differential gene expression analysis
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited matrix containing read counts of each library

extract_protocol:
Total RNA was isolated from spleen using the PicoPure RNA Isolation kit (ThermoFisher Scientific, USA) with some modifications. In brief, spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip, and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min, centrifuged at 3,000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube, mixed thoroughly with 100 μl 70% Ethanol, and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially, and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 (Agilent Technologies, USA).
Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, USA). Fifty ng total RNAs from each replicate were purified with Oligo(dT) beads, fragmented to ~200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs (cDNAs) were synthesized sequentially. The double-stranded cDNAs were repaired ends, ligated with universal adaptors on the 5' end and indexed adaptors on the 3' end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s, 1 cycle; 98 °C for 10 s, 65 °C for 75 s, 14 cycles; 65 °C for 5 min, 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads, and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 (Agilent Technologies, USA).

value: LPS


title: Opossum_neun_S1