title: LFs tSAECs CoCu Control 1

description: Library name: LFs_tSAECs_CoCu_Control_1

value: airway epithelial cells, fibroblasts


title: WT_CD34_scRNAseq

status: Public on Jul 03 2025

type: SRA

city: Bochum

first: Holm

last: Zaehres

state: NRW

address: Universitaetsstr. 150

department: Institute of Anatomy

country: Germany

institute: Ruhr University Bochum

description:
10x Genomics
sample1_WT

library_source: transcriptomic

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
UMI-tools (v1.0.0) used for cell barcode and UMI counting
STAR (v2.7.1a) used for human reference genome (hg38) alignment
Subread featureCounts (v1.6.4) used for UMI quantification
Assembly: hg38
Supplementary files format and content: tsv files include UMI counts for each cell barcode and genes

molecule: total RNA

organism: Homo sapiens

source_name: iPSC-derived skeletal muscle organoid

extract_protocol:
Organoid 12 weeks post differentiation were dissociated into single cells upon incubation for 1hr with solution containing papain and EDTA. Upon dissociation, we estimated the cell number and viability; then cells were resuspended on solution containing 0.5% BSA in PBS to reach concentration of 390 cells per ul.
The cDNA library was prepared using the Chromium Single Cell 3′ Reagent Kits (v3): Single Cell 3′ Library & Gel Bead Kit v3 (PN-1000075), Single Cell B Chip Kit (PN-1000073) and i7 Multiplex Kit (PN-120262) (10x Genomics).

tag: tissue

value: iPSC-derived skeletal muscle organoid

tag: genotype

value: WT CB CD34 iPSC line

tag: treatment

value: 12 weeks


title: LFs tSAECs CoCu TGFb 5

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

institute: Boehringer Ingelheim

description: Library name: LFs_tSAECs_CoCu_TGFb_5

data_processing:
Demultiplexing was conducted using bcl2fastq2 v2.20.0.422 from Illumina. Other pre-processing was performed as previously described (PMID: 29231921).
Assembly: GRCh38.86
Supplementary files format and content: Tab-separated count matrix file containing combined raw counts of all 70 samples.

source_name: lung

growth_protocol: Primary healthy human lung airway epithelial cells (SAECs, Lonza) were used in passages 2-3. They were expanded in flasks on type I collagen (Corning) pre-coated cell culture flasks in PneumaCult-Ex Plus Medium (STEMCELL Technologie) until confluency of around 80%. For air-liquid-interface cultivation and differentiation, 30 000 cells/well SAECs were seeded on collagen-coated transwells and grown until confluency in PneumaCul-Ex Plus Medium. Airlift was conducted by changing medium to PneumaCul-ALI Medium (STEMCELL Technologies) and exposing cells apically to air. Healthy human lung fibroblasts (LF, Lonza) were used in passages 4-7. They were expanded in flasks in Fibroblast Basal Medium with FGM2- Fibroblast Growth Medium BulletKit (Lonza) until confluency of around 70%.

extract_protocol:
Chronically injured and acutely injured SAECs were cultivated as previously described and lysed in RLT plus buffer (Qiagen). Total RNA was isolated and purified using the MagMAXTM 96 Total RNA Isolation Kit (Thermo Fisher) following manufacturer’s instruction. Total RNA was assessed for quantity using the fluorescence-based Broad Range Quant-iT RNA Assay Kit (Thermo Fisher) and quality using the Standard Sensitivity RNA Analysis DNF-471 Kit (Agilent) on a 48-channel Fragment Analyzer (Agilent).
Samples were normalized on the MicroLab STAR automated liquid platform (Hamilton). A total of 200 ng RNA was used for library construction using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), together with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and NEBNext Multiplex Oligos for Illumina (New England Biolabs). RNA-seq libraries were processed on a Biomek i7 Hybrid instrument (Beckman Coulter) using 12 PCR cylces following manufacturer’s instruction instead of SRPIselect beads). Final RNA-seq libraries were then quantified by the High Sensitivity dsDNA Quanti- iT Assay Kit (Thermo Fisher) on a BioTek Synergy HTX (Agilent). And assessed for their size distribution and adapter dimer presence using the High Sensitivity Small Fragment DNF-477 Kit on a 48-channel Fragment Analyzer (Agilent). All sequencing libraries were then normalized on the MicroLab STAR and pooled. Additionally, PhiX Control v3 (Illumina) was spiked in. The pooled libraries were clustered on a Paired-End Flow Cell and sequenced on a HiSeq 4000 Sequencing System (Illumina) with dual index, paired-end reads at 75 bp length. Read parameters: Rd1: 76 bp, Rd2: 8 bp, Rd3: 8 bp, Rd4: 76 bp with an average sequencing depth of around 30 million pass-filter reads per sample.

treatment_protocol: SAECs were differentiated in air liquid interface on transwells for 10 days until differentiated cells were initially observed. Afterwards, ALI SAECs were treated for 14 days with 1 ng/ml TGF-β1 (Biotechne) to induce chronic injury on SAECs. For the acute injury model, ALI SAECs were cultivated for 14 days without any stimuli. After 14 days, both, SAECs for chronic and acute injury were transferred into cocultures with human lung fibroblasts +/- 1 ng/ml TGF-β1 and +/- PTX3 in the basolateral chamber for additional 3 days. Before setting up the coculture, both, SAECs and LFs were starved for 6-8 h in normal DMEM (GibcoTM).

value: lung

tag: cell line

tag: cell type

tag: injury model

value: chronic

value: TGFb

tag: culture format

value: co culture


title: From Severe CRKP pneumonia 1(scBCR seq)

city: Harbin

first: jiao

middle: ya

last: sun

state: Heilongjiang province

address: No. 246 Xuefu road, Nangang district

department: Respiratory and critical care department

country: China

institute: The second affiliated Hospital of Harbin Medical University

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific).
The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.
Reads were processed using the Cell Ranger 4.0 pipeline with default and recommended parameters.
Gene-Barcode matrices were generated for each sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts.
This output was then imported into the Seurat (v3.2.0) R toolkit for quality control and downstream analysis of our single-cell RNAseq data.
Assembly: GRCh38
Supplementary files format and content: tab-separated values and raw count

molecule: polyA RNA

source_name: PBMCs

extract_protocol:
Human blood were dissociated at 37 ℃ with a shaking speed of 50 r.p.m for about 40 min.We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield and viability. Cell suspensions were filtered using a 40 um nylon cell strainer and red blood cells were removed by 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. no. 00-4333-57) . Dissociated cells were washed with 1x DPBS containing 2% FBS. Cells were stained with 0.4% Trypan blue (Thermo Fisher, Cat. no. 14190144) to check the viability on Countess® II Automated Cell Counter (Thermo Fisher).
All the remaining procedures of single cell including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 5ʹ v2).

value: PBMCs

tag: disease

value: Severe CRKP pneumonia


title: From Severe CRKP pneumonia 1(scTCR seq)

description: 10x genomics


title: LFs nSAECs CoCu TGFb 5

description: Library name: LFs_nSAECs_CoCu_TGFb_5

value: acute


title: LFs nSAECs CoCu TGFb 4

description: Library name: LFs_nSAECs_CoCu_TGFb_4


title: LFs nSAECs CoCu TGFb 3

description: Library name: LFs_nSAECs_CoCu_TGFb_3


title: From Severe CRKP pneumonia 1(scRNA seq)

description: 10x genomics


title: LFs nSAECs CoCu TGFb 2

description: Library name: LFs_nSAECs_CoCu_TGFb_2


title: DMD1_scRNAseq

description:
10x Genomics
sample2_DMD1

value: DMD1 iPSC line


title: LFs nSAECs CoCu Control 5

description: Library name: LFs_nSAECs_CoCu_Control_5

value: control


title: LFs nSAECs CoCu Control 2

description: Library name: LFs_nSAECs_CoCu_Control_2


title: From Convalescent CRKP pneumonia1(scRNA seq)

description: 10x genomics

value: Convalescent CRKP pneumonia


title: LFs nSAECs CoCu Control 1

description: Library name: LFs_nSAECs_CoCu_Control_1


title: LFs MoCu TGFb 5

description: Library name: LFs_MoCu_TGFb_5

value: fibroblasts

value: mono culture


title: From Convalescent CRKP pneumonia 2(scBCR seq)

description: 10x genomics


title: LFs nSAECs CoCu Control 3

description: Library name: LFs_nSAECs_CoCu_Control_3


title: From Convalescent CRKP pneumonia 2(scTCR seq)

description: 10x genomics


title: LFs MoCu TGFb 3

description: Library name: LFs_MoCu_TGFb_3


title: LFs nSAECs CoCu TGFb 1

description: Library name: LFs_nSAECs_CoCu_TGFb_1


title: From Convalescent CRKP pneumonia 1(scBCR seq)

description: 10x genomics


title: LFs MoCu TGFb 1

description: Library name: LFs_MoCu_TGFb_1


title: LFs nSAECs CoCu Control 4

description: Library name: LFs_nSAECs_CoCu_Control_4


title: From Convalescent CRKP pneumonia 2 (scRNA seq)

description: 10x genomics


title: liver biopsy [GSM5774040 re-analysis]

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

source_name: liver biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol:
All human liver biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNAlater.
Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

tag: rejection archetype groups (nr,tcmr,nkrl,injury)

value: NR

value: liver biopsy


title: LFs MoCu TGFb 4

description: Library name: LFs_MoCu_TGFb_4


title: Pituitary_organoid_day15_success_rep4

city: Kyoto

first: Takuya

last: Yamamoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: CiRA

country: Japan

institute: Kyoto University

description: Library name: NKX_PITX1_60_15_s

data_processing:
Illumina RTA version 4.12.2 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Sequenced reads were mapped to the GRCh38 plus the reporter sequences using STAR v2.7.11a after trimming the adaptor sequences with cutadapt v4.6. The uniquely and properly mapped reads were used for further analysis.
GENCODE reference annotation (v44/ Ensembl 110) was used for gene annotation.
The raw counts were calculated using htseq-count ver. 2.0.5 with the GENCODE gtf file.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RawCounts values for each sample

source_name: hypothalamus-pituitary organoid

extract_protocol:
Total RNA was extracted with RNeasy mini kit (Qiagen).
The RNA-seq library construction was performed using an Illumina Stranded mRNA Prep Kit (Illumina) according to the manufacturer’s instructions.

value: hypothalamus-pituitary organoid

value: induced pluripotent stem cell-derived hypothalamus-pituitary organoid

value: non


title: liver biopsy [GSM5774038 re-analysis]

value: Injury


title: LFs MoCu TGFb 2

description: Library name: LFs_MoCu_TGFb_2

value: lung


title: From Moderate CRKP pneumonia 2(scBCR seq)

description: 10x genomics

value: Moderate CRKP pneumonia


title: LFs MoCu Control 4

description: Library name: LFs_MoCu_Control_4


title: Pituitary_organoid_day15_success_rep3

description: Library name: NKX_PITX1_59_15_s


title: nSAECs MoCu TGFb 4

description: Library name: nSAECs_MoCu_TGFb_4

value: airway epithelial cells

value: TGFb


title: liver biopsy [GSM5774034 re-analysis]


title: From Moderate CRKP pneumonia 2(scTCR seq)

description: 10x genomics

value: PBMCs


title: LFs MoCu Control 3

description: Library name: LFs_MoCu_Control_3


title: Pituitary_organoid_day15_success_rep2

description: Library name: NKX_PITX1_58_15_s


title: From Moderate CRKP pneumonia 2(scRNA seq)

description: 10x genomics


title: liver biopsy [GSM5774037 re-analysis]


title: LFs MoCu Control 5

description: Library name: LFs_MoCu_Control_5


title: liver biopsy [GSM5774036 re-analysis]


title: liver biopsy [GSM5774030 re-analysis]


title: liver biopsy [GSM5774031 re-analysis]

value: TCMR


title: liver biopsy [GSM5774035 re-analysis]


title: Pituitary_organoid_day15_success_rep1

description: Library name: NKX_PITX1_57_15_s


title: liver biopsy [GSM5774032 re-analysis]

value: NKRL


title: liver biopsy [GSM5774033 re-analysis]


title: liver biopsy [GSM5774028 re-analysis]


title: liver biopsy [GSM5774027 re-analysis]


title: liver biopsy [GSM5774029 re-analysis]


title: LFs MoCu Control 1

description: Library name: LFs_MoCu_Control_1

value: control


title: From Moderate CRKP pneumonia 1(scBCR seq)

description: 10x genomics


title: liver biopsy [GSM5774025 re-analysis]


title: liver biopsy [GSM5774024 re-analysis]


title: LFs MoCu Control 2

description: Library name: LFs_MoCu_Control_2


title: From Moderate CRKP pneumonia 1(scRNA seq)

description: 10x genomics


title: Pituitary_organoid_day15_fail_rep3

description: Library name: NKX_PITX1_59_15_f


title: bZIP1-GFP leaves, 3-4 week old, rep3, Input

city: Berlin

first: Cezary

last: Smaczniak

address: Philippstr. 13

department: Institute for Biology

institute: Humboldt-Universität zu Berlin

description: Library name: bZIP1-GFP rep3 Input

library_source: genomic

data_processing:
Adapter sequences were removed from the sequencing reads using Trimmomatic v0.39 and the quality of sequencing data was evaluated by FastQC v0.12.1. Sequences of the re-sequenced libraries, if available, were merged at this point. Trimmed reads were mapped to the Arabidopsis TAIR10 genome using Bowtie2 v2.5.1. Unmapped reads, not primary aligned reads, reads that failed platform/vendor quality checks, PCR or optical duplicate reads and reads with MAPQ score lower than 40 were removed using Picard MarkDuplicates v2.27.5 and Samtools v1.16.1. For data visualization, RPGC (reads per genomic content, 1x normalization) normalized genome alignment tracks (BigWig files) were generated using deepTools bamCoverage v3.5.5. Peak calling was performed using MACS2 v2.2.7.1 against the Input control samples.
Assembly: TAIR10
Supplementary files format and content: .bw bigWig genome track data
Supplementary files format and content: _peaks.narrowPeak MACS2 output
Supplementary files format and content: _peaks.xls MACS2 output
Supplementary files format and content: _summits.bed MACS2 output

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Plants were grown for 3-4 weeks under 12h day/12h night regime. On the day of harvest the night period was extended for 6 hours and two grams of leaves were collected.

extract_protocol:
Leaves were fixed in 1% formaldehyde, 2 times for 15 min at room temperature in vacuum. Fixed tissue was ground to a fine powder in liquid nitrogen and nuclei were isolated. The crude nuclei were sonicated using Covaris S220 and centrifuged. The input sample was collected at this step. The rest of the supernatant was incubated with the GFP antibodies (#ab290, Abcam) followed by a capture with magnetic protein A beads (Dynabeads, Thermo) for immunoprecipitation. Bound chromatin was eluted from the beads. ChIP and Input samples were de-crosslinked and purified.
The DNA sequencing libraries for both ChIP and Input samples were prepared using ThruPLEX DNA-Seq Kit (Takara Bio) and SMARTer DNA Unique Dual Index Kit (Takara Bio) following manufacturer’s instructions. DNA double size selection 100-700 bp was performed using SPRIselect beads (Beckman Coulter).

value: leaf

value: pbZIP1:bZIP1-GFP bzip1


title: Pituitary_organoid_day15_fail_rep4

description: Library name: NKX_PITX1_60_15_f


title: liver biopsy [GSM5774026 re-analysis]


title: bZIP1-GFP leaves, 3-4 week old, rep2, Input

description: Library name: bZIP1-GFP rep2 Input


title: Pituitary_organoid_day15_fail_rep2

description: Library name: NKX_PITX1_58_15_f


title: bZIP1-GFP leaves, 3-4 week old, rep1, Input

description: Library name: bZIP1-GFP rep1 Input


title: UMI‑4C ΔCTRL2 latent rep2

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

country: USA

institute: University of Vermont

description:
Library name: SK9_DCRTL2_2
Viewpoint counts for LAT, CTRL2, ICP4, VP16

data_processing:
Sequencing reads were demultiplexed and trimmed for adapters and low-quality bases using custom scripts. Reads with Phred scores <20 were discarded.
Trimmed reads were aligned to the HSV-1 reference genome (NC_001806.2) using Bowtie2. Alignments with MAPQ <10 were excluded.
4C-seq interactions were analyzed using peakC. Cis-interactions from each viewpoint were determined and visualized using Circos plots. Comparisons between wild-type and ΔCTRL2 strains were performed using statistical tests on peak count profiles.
UMI-4C reads were processed with the UMI4Cats pipeline. Unique molecular identifiers were used to collapse PCR duplicates. Profiles were normalized across samples, and domainograms were plotted. Differential interactions were analyzed with DESeq2 and Fisher’s exact test.
Assembly: NC_001806.2 (HSV-1 reference genome)
Supplementary files format and content: Tab-delimited files containing UMI-collapsed interaction counts per genomic fragment for each viewpoint (UMI-4C); BED files listing statistically significant interaction regions identified from 4C-seq experiments.

source_name: neurons

growth_protocol: LUHMES cells (ATCC CRL-2927) were cultured in DMEM/F12 supplemented with 1× N2 supplement, 1% penicillin-streptomycin-glutamine, and 40 ng/mL FGF-basic at 10% CO2. Differentiation was induced at 60–70% confluence by switching to medium containing 1 μg/mL tetracycline hydrochloride, 1 mM dibutyryl-cAMP, and 2 ng/mL GDNF for 5 days on poly-L-ornithine/fibronectin-coated plates.

extract_protocol:
Cells were crosslinked with 2% formaldehyde for 10 min and quenched with 0.125 M glycine. After washing with PBS, cell pellets were lysed in buffer with Tris-HCl, NaCl, NP-40, Triton X-100, EDTA, PMSF, and protease inhibitors. Nuclei were isolated for chromatin digestion and ligation.
For 4C-seq, chromatin was first digested with HindIII, heat inactivated, and ligated with T4 DNA ligase overnight. Crosslinks were reversed, and a second digestion was performed using DpnII followed by a second ligation to generate circular DNA. Inverse PCR using bait-specific primers amplified 4C fragments. Barcodes were added in a second PCR round. For UMI-4C, chromatin was digested with DpnII, ligated, purified, and then sonicated to 450–550 bp. Illumina adapters were ligated, and bait-specific nested PCR was performed to generate 500 bp libraries. Dual-index barcodes were added before sequencing.

treatment_protocol: Cells were infected with either wild-type HSV-1 strain 17Syn+ or ΔCTRL2 recombinant virus at MOI 3 in the presence of 50 μM acyclovir for 48 h. Medium was then replaced with differentiation medium lacking acyclovir. Cells were harvested 8 days post-infection to establish latent infection for downstream 4C-seq or UMI-4C analysis.

value: neurons

value: LUHMES

value: latent

tag: batch


title: Pituitary_organoid_day15_fail_rep1

description: Library name: NKX_PITX1_57_15_f

value: hypothalamus-pituitary organoid


title: bZIP1-GFP leaves, 3-4 week old, rep3, ChIP

description: Library name: bZIP1-GFP rep3 ChIP

value: GFPab (Abcam, #ab290)


title: From Moderate CRKP pneumonia 1(scTCR seq)

description: 10x genomics


title: UMI‑4C ΔCTRL2 latent rep1

description:
Library name: SK10_DCRTL2_1
Viewpoint counts for LAT, CTRL2, ICP4, VP16


title: liver biopsy [GSM5774022 re-analysis]

value: NR

value: liver biopsy


title: Pituitary_organoid_day9_success_rep4

description: Library name: ML_61_9_s

value: induced pluripotent stem cell-derived hypothalamus-pituitary organoid

value: non


title: liver biopsy [GSM5774021 re-analysis]


title: UMI‑4C WT latent rep2

description:
Library name: SK6V_LAT_2
Viewpoint counts for LAT, CTRL2, ICP4, VP16

value: WT


title: liver biopsy [GSM5774023 re-analysis]

value: Injury


title: bZIP1-GFP leaves, 3-4 week old, rep2, ChIP

description: Library name: bZIP1-GFP rep2 ChIP


title: bZIP1-GFP leaves, 3-4 week old, rep1, ChIP

description: Library name: bZIP1-GFP rep1 ChIP


title: liver biopsy [GSM5774020 re-analysis]


title: Pituitary_organoid_day9_success_rep3

description: Library name: ML_60_9_s


title: Pituitary_organoid_day9_success_rep2

description: Library name: ML_59_9_s


title: 4C-seq ΔCTRL2 viewpoint 1 replicate 3

description:
Library name: HSV1_E_1
deltaCTRL2 rep3, VP1

data_processing:
Sequencing reads were demultiplexed and trimmed for adapters and low-quality bases using custom scripts. Reads with Phred scores <20 were discarded.
Trimmed reads were aligned to the HSV-1 reference genome (NC_001806.2) using Bowtie2. Alignments with MAPQ <10 were excluded.
4C-seq interactions were analyzed using peakC. Cis-interactions from each viewpoint were determined and visualized using Circos plots. Comparisons between wild-type and ΔCTRL2 strains were performed using statistical tests on peak count profiles.
UMI-4C reads were processed with the UMI4Cats pipeline. Unique molecular identifiers were used to collapse PCR duplicates. Profiles were normalized across samples, and domainograms were plotted. Differential interactions were analyzed with DESeq2 and Fisher’s exact test.
Assembly: NC_001806.2 (HSV-1 reference genome)
Supplementary files format and content: Tab-delimited files containing UMI-collapsed interaction counts per genomic fragment for each viewpoint (UMI-4C); BED files listing statistically significant interaction regions identified from 4C-seq experiments.
Library strategy: 4C-Seq

value: latent HSV-1 infection


title: Col-0 leaves, 3-4 week old, rep1, ChIP

description: Library name: Col-0 rep1 ChIP

value: Col-0 wild type


title: Col-0 leaves, 3-4 week old, rep2, ChIP

description: Library name: Col-0 rep2 ChIP


title: Pituitary_organoid_day9_fail_rep4

description: Library name: ML_61_9_f


title: Pituitary_organoid_day9_success_rep1

description: Library name: ML_58_9_s


title: 4C-seq ΔCTRL2 viewpoint 2 replicate 2

description:
Library name: HSV1_D_2
deltaCTRL2 rep2, VP2


title: 4C-seq ΔCTRL2 viewpoint 2 replicate 3

description:
Library name: HSV1_E_2
deltaCTRL2 rep3, VP2


title: liver biopsy [GSM5774018 re-analysis]


title: liver biopsy [GSM5774019 re-analysis]

value: NKRL


title: Pituitary_organoid_day9_fail_rep3

description: Library name: ML_60_9_f


title: 4C-seq ΔCTRL2 viewpoint 1 replicate 2

description:
Library name: HSV1_D_1
deltaCTRL2 rep2, VP1


title: liver biopsy [GSM5774016 re-analysis]


title: Pituitary_organoid_day9_fail_rep2

description: Library name: ML_59_9_f


title: UMI‑4C WT latent rep1

description:
Library name: SK5V_LAT_1
Viewpoint counts for LAT, CTRL2, ICP4, VP16


title: liver biopsy [GSM5774017 re-analysis]


title: 4C-seq ΔCTRL2 viewpoint 2 replicate 1

description:
Library name: HSV1_B_2
deltaCTRL2 rep1, VP2


title: Pituitary_organoid_day9_fail_rep1

description: Library name: ML_58_9_f


title: liver biopsy [GSM5774015 re-analysis]


title: 4C-seq ΔCTRL2 viewpoint 1 replicate 1

description:
Library name: HSV1_B_1
deltaCTRL2 rep1, VP1


title: liver biopsy [GSM5774014 re-analysis]


title: Pulvinar-projecting

city: Charlottesville

first: Yuanming

last: Liu

state: Virginia

address: Gilmer Hall

department: Biology Department

institute: University of Virginia

description:
Library name: Sample 3
10x Genomics

data_processing:
the 10X Cell Ranger pipeline (version 7.2.0) was used to demultiplex
Assembly: a custom “pre-mRNA” reference genome created from the published tree shrew database (http://www.treeshrewdb.org/)
Supplementary files format and content: H5 file; feature-barcode matrices

organism: Mus musculus

source_name: Superficial superior colliculus

extract_protocol:
Brains were rapidly dissected, cooled in ice-cold Hibernate-A for 1.5 minutes, transferred to PBS, and prepared under a dissecting microscope. The cortex and cerebellum were removed to expose the superior colliculus (SC). The sSC was visualized coronally, micro-dissected by knife cuts along its visually approximated anatomical borders, and processed into a single-nucleus suspension using a published detergent-mechanical lysis protocol (Matson et al., 2018). Briefly, the sSC was homogenized in a lysis buffer, and cell nuclei were purified by density gradient centrifugation. After resuspension, nuclei were labeled with propidium iodide (Propidium Iodide Ready Flow™ Reagent, Invitrogen, catalog # R37169) and then counted with a CellDrop automated cell counter (DeNovix, Delaware, USA).
We used the 10X Genomics Chromium Next GEM 3’ kit v3.1 according to the manufacturer’s protocol (user guide revision D) to encapsulate each nucleus’s poly-adenylated RNA and then process the poly-adenylated RNA into cDNA sequencing libraries. We then sequenced the cDNA libraries by Illumina Next-Seq 2000 to an average of 29,857 mean reads per cell.

value: Superficial superior colliculus

tag: Sex

value: pooled male and female

value: Neural cells

tag: age

value: 2-4 months


title: 4C-seq WT viewpoint 2 replicate 3

description:
Library name: HSV1_G_2
WT rep3, VP2

value: neurons

value: LUHMES


title: 4C-seq WT viewpoint 2 replicate 2

description:
Library name: HSV1_F_2
WT rep2, VP2


title: liver biopsy [GSM5774045 re-analysis]


title: liver biopsy [GSM5774013 re-analysis]


title: R1, +Met 12 hr, 3

city: Irvine

first: Fiona

last: Law

state: CA

address: 839 Health Sciences Road

institute: UCI

description: Library name: Met_R1_3

data_processing:
kallisto v0.48.0
Assembly: GRCh38
Supplementary files format and content: csv file containing gene counts of all samples

extract_protocol:
Qiagen
Novogene Corporation Inc

treatment_protocol: Cells were cultured in either +Met or -Met+Hcy media for 12 hours

value: +Met 12hr


title: 6 weeks Post-Spinal Cord Injury Sup Replicate 3

city: Shanghai

first: Liming

last: Cheng

address: Siping Road No.1239

institute: Tongji University

description:
6w-3.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

hyb_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μL 10x Blocking Agent and 1 μL of 25x Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2x Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-mRNA&lncRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. The probe signals passing P or M QC flags in at least 3 samples were retained for further analysis.
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 24 samples were retained as “All Targets Value” in the Excel sheet for further “m6A methylation level”, “m6A quantity” and “expression level” analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. “expression level” was calculated based on the total of IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities of RNA. Differentially m6A-methylated RNAs or differentially expressed RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. Hierarchical Clustering was performed to show the distinguishable m6A-methylation or expression pattern among samples.

source_name: 6 weeks Post-Spinal Cord Injury Spinal Cord

label_protocol: The “IP” RNA and “Sup” RNAs were added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labling Kit. The synthesized cRNAs were purified by RNeasy Mini Kit. The concentration and specific actitity (pmol dye/μg cRNA) were measured with NanoDrop ND-1000.

extract_protocol: 1-3 μg total RNA and m6A spike-in control mixture were added to 300 μL 1IP buffer (50mM Tris-HCl, pH7.4, 150mM NaCl, 0.1% NP40, 40U/μL RNase Inhibitor) containing 2 μg anti-m6A rabbit polyclonal antibody (Synaptic Systems). The reaction was incubated with head-over-tail rotation at 4°C for 2 hours. 20 L Dynabeads™ M-280 Sheep Anti-Rabbit IgG suspension per sample was blocked with freshly prepared 0.5% BSA at 4°C for 2 hours, washed three times with 300 μL 1IP buffer, and resuspended in the total RNA-antibody mixture prepared above. The RNA binding to the m6A-antibody beads was carried out with head-over-tail rotation at 4°C for 2 hours. The beads were then washed three times with 500 μL 1IP buffer and twice with 500 μL Wash buffer (50 mM Tris-HCl, pH7.4, 50 mM NaCl, 0.1% NP40, 40 U/μL RNase Inhibitor). The enriched RNA was eluted with 200 μL Elution buffer (10 mM Tris-HCl, pH7.4, 1 mM EDTA, 0.05% SDS, 40U Proteinase K) at 50°C for 1 hour. The RNA was extracted by acid phenol-chloroform and ethanol precipitated.

value: spinal cord

tag: fraction

value: unmodified RNAs


title: 4C-seq WT viewpoint 1 replicate 2

description:
Library name: HSV1_F_1
WT rep2, VP1


title: R1, +Met 12 hr, 2

description: Library name: Met_R1_2


title: 6 weeks Post-Spinal Cord Injury Sup Replicate 1

description:
6w-1.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: 293T, +Met 12 hr, 2

description: Library name: Met_293T_2


title: 293T, +Met 12 hr, 3

description: Library name: Met_293T_3


title: 4C-seq WT viewpoint 1 replicate 1

description:
Library name: HSV1_A_1
WT rep1, VP1


title: 4C-seq WT viewpoint 1 replicate 3

description:
Library name: HSV1_G_1
WT rep3, VP1


title: liver biopsy [GSM5774009 re-analysis]

value: liver biopsy


title: 4 weeks Post-Spinal Cord Injury Sup Replicate 3

description:
4w-3.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

source_name: 4 weeks Post-Spinal Cord Injury Spinal Cord


title: 4C-seq WT viewpoint 2 replicate 1

description:
Library name: HSV1_A_2
WT rep1, VP2


title: 6 weeks Post-Spinal Cord Injury Sup Replicate 2

description:
6w-2.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: liver biopsy [GSM5774010 re-analysis]

value: NR


title: liver biopsy [GSM5774011 re-analysis]


title: 4 weeks Post-Spinal Cord Injury Sup Replicate 1

description:
4w-1.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: 293T, +Met 12 hr, 1

description: Library name: Met_293T_1


title: knockout 3

city: Noda

first: HAIYANG

last: SUN

state: Chiba

address: Yamazaki

institute: Research Institute for Biomedical Sciences,  Tokyo University of Science

data_processing:
library strategy: 16S rDNA sequencing
By Qiime2 version: 2021.4, first quality_check of data
relative_abundance
rep-seqs.qzv: Represents a representative array. You can also search directly on BLAST.
taxonomy.qzv: This is a summary of which microorganisms in the database the base sequence of rep-seqs corresponds to.
relative-frequency-table.qzv: The result of converting an absolute value to a relative value.
Assembly: mm10
Supplementary files format and content: Relative frequency of typical phyla in excle file

source_name: BALB/c

extract_protocol:
WT and KO mice co-housed at least 4 weeks, then take fecal from these mice, extracted DNA from fecal, the 16s rDNA sequencing
Amplification of target sequence Amplification of 16SrDNA V3-V4 region (1st_PCR) The target region was amplified with the following primers. After confirming amplification, purify using AmpureXP and purify.

treatment_protocol: fecal DNA from cohoused mice

tag: strain

value: BALB/c

value: DCIR KO

value: co-housed

tag: molecule type

value: fecal DNA

tag: time

value: 4 weeks after co-housed


title: liver biopsy [GSM5774007 re-analysis]

value: TCMR


title: liver biopsy [GSM5774012 re-analysis]


title: 2 weeks Post-Spinal Cord Injury Sup Replicate 2

description:
2w-2.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

source_name: 2 weeks Post-Spinal Cord Injury Spinal Cord


title: liver biopsy [GSM5774008 re-analysis]

value: Injury


title: 4 weeks Post-Spinal Cord Injury Sup Replicate 2

description:
4w-2.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: R1, +Met 12 hr, 1

description: Library name: Met_R1_1


title: knockout 1


title: 2 weeks Post-Spinal Cord Injury Sup Replicate 3

description:
2w-3.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: From Convalescent CRKP pneumonia 1(scTCR seq)

description: 10x genomics

value: PBMCs

value: Convalescent CRKP pneumonia


title: 2 weeks Post-Spinal Cord Injury Sup Replicate 1

description:
2w-1.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: R1, -Met+Hcy 12 hr, 3

description: Library name: Hcy_R1_3

value: -Met+Hcy 12hr


title: knockout 2


title: 293T, -Met+Hcy 12 hr, 3

description: Library name: Hcy_293T_3


title: 1 week Post-Spinal Cord Injury Sup Replicate 3

description:
1w-3.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

source_name: 1 week Post-Spinal Cord Injury Spinal Cord


title: R1, -Met+Hcy 12 hr, 2

description: Library name: Hcy_R1_2


title: wild type 3

value: WT


title: 1 week Post-Spinal Cord Injury Sup Replicate 2

description:
1w-2.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: liver biopsy [GSM5774005 re-analysis]


title: 1 week Post-Spinal Cord Injury Sup Replicate 1

description:
1w-1.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: wild type 1


title: 293T, -Met+Hcy 12 hr, 2

description: Library name: Hcy_293T_2


title: ChIP for H3K27ac in RpA70-EGFP (wt) embryos staged at NC14L replicate ID= rep2

city: Evanston

first: Shelby

middle: A

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

description:
Library name: wt_ChIP-H3K27ac_NC14L_rep2
H3K27ac ChIP at NC14 late

data_processing:
Barcode-split fastq files were trimmed of adapter sequences using TrimGalore
Adapter-trimmed fastq files were mapped to the dm6 Drosophila reference genome using Bowtie2, with option -X 2000.
Mapped reads were sorted using Samtools
Suspected PCR and optical duplicate mapped reads were marked using Picard MarkDuplicates
Duplicate-marked mapped reads were imported into R, discarding duplicates, and keeping only reads with map-quality scores of 10 or greater. Wiggle files were generated by calculating the average number of mapped reads within 10 bp windows, and normalizing to millions of reads in the overall sample. Peaks were called using MACS2. Broad polycomb domains were called using STAN.
Assembly: Drosophila melanogaster dm6
Supplementary files format and content: wiggle files for merged replicates are provided . Data represents counts per million normalized average reads per 10 bp genomic bin
Supplementary files format and content: Coverage files for merged replicates for all ChIP experiments are provided in bigwig format. Peak calls for Cg, GAF, Pho, and E(z) are provided in .bed format. Broad polycomb domains are provided in .bed format.

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: Adult flies were placed in a cage with yeasted apple juice plates and embryos were collected prior to treatment and/or processing for ChIP.

extract_protocol:
For ChIP experiments, embryos were crosslinked (Heptane/PBS/formaldehyde, 15 minutes) and sorted by stage prior to homogenization in RIPA buffer and sonication. Sonicated chromatin samples were subjected to immunoprecipiation with the indicated antibodies.
ChIP libraries: following IP but prior to washes, antibody-chromatin complexes were tagmented by incubation with Illumina Tn5 (Nextera) reagent for 40 minutes at 37 degrees C. Following tagmentation, beads were washed and subjected to PCR with barcoding primers (Buenrostro, 2013).

value: embryo

tag: chip antibody

tag: developmental stage


title: wild type 2

tag: genotype


title: R1, -Met+Hcy 12 hr, 1

description: Library name: Hcy_R1_1

tag: treatment


title: 293T, -Met+Hcy 12 hr, 1

description: Library name: Hcy_293T_1

tag: cell line

value: -Met+Hcy 12 hr


title: ChIP for H3K27ac in RpA70-EGFP (wt) embryos staged at NC14L replicate ID= rep1

description:
Library name: wt_ChIP-H3K27ac_NC14L_rep1
H3K27ac ChIP at NC14 late

tag: tissue


title: liver biopsy [GSM5774004 re-analysis]

value: NKRL


title: liver biopsy [GSM5774002 re-analysis]


title: 3 Days Post-Spinal Cord Injury Sup Replicate 3

description:
3d-4.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

source_name: 3 Days Post-Spinal Cord Injury Spinal Cord

value: spinal cord

value: unmodified RNAs


title: liver biopsy [GSM5774003 re-analysis]

value: liver biopsy


title: liver biopsy [GSM5773999 re-analysis]


title: ChIP for GFP in His2Av-RFP zld; EGFP-Ez/+ (zld_EGFP-Ez) embryos staged at NC14M replicate ID= rep3

description:
Library name: zld_EGFP-Ez_ChIP-GFP_NC14M_rep3
E(z) binding in zelda mutants at NC14

value: His2Av-RFP zld; EGFP-Ez/+

value: GFP


title: liver biopsy [GSM5773998 re-analysis]


title: Flex_C_07

city: Memphis

first: Jasmine

last: Plummer

state: TN

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description: Library name: Sample_2

data_processing:
The Flex datasets were aligned to probe set reference from 10x Genomics using cellRanger v8.0 with the filter-probes argument set to false. Filtered feature-barcode matrices were loaded into R (v4.4.1) as a SingleCellExperiment object using the read10XCounts function from the DropletUtils  package (v. 1.24.0). Quality control metrics were computed for each cell using the addPerCellQC function from the scater package (v1.32.0). Outliers in the number of counts and detected features were identified and removed using the isOutlier function from scater with parameters type = "lower", log = TRUE, and nmads = 2 for counts and nmads = 2.5 for detected features, respectively. Cells with a high percentage of mitochondrial gene expression were filtered out by applying isOutlier with type = "higher", log = FALSE, and nmads = 5. The count data were log-normalized using the logNormCounts function from scater. Feature selection was performed by modeling the mean-variance relationship with the modelGeneVar function from the scran package (v1.32.0). Highly variable genes were selected using getTopHVGs with an FDR threshold of 0.7. Principal Component Analysis (PCA) was conducted using the fixedPCA function from scran, specifying the subset.row argument to include the selected highly variable genes. The first 25 PCs were selected for downstream analyses based on the variance explained. UMAP dimensionality reduction was then applied using the runUMAP function from scater on these components. Cells were clustered using the clusterCells function from scran, specifying dimred = "PCA" and BLUSPARAM = NNGraphParam(k = 50, cluster.fun = "louvain"). Potential doublets were identified using the scDblFinder function from the scDblFinder package  (v1.16.0), incorporating cluster information via the clusters = colLabels(sce) argument, and subsequently removed by looking at the scDblFinder.score metrics together with canonical markers exclusive of specific populations.
Assembly: Chromium Human Transcriptome Probe Set v1.0
Supplementary files format and content: format: qs; content: SingleCellExperiment object

source_name: BMP4 treated hEST H1, Differentiated iPSC 32F, iPSC 32F parental

growth_protocol: All cultures were grown at 37 °C, 5% CO₂. Human embryonic stem cells (hESCs, WA01, WiCell) were cultured in vessels coated with growth factor-reduced Matrigel (Corning, 354230) and maintained in mTeSR+ growth media (STEMCELL Technologies, 85850). Cultures were passaged by removing the medium, washing with DPBS (Sigma-Aldrich, D8537), and treating with Gentle Cell Dissociation Reagent (STEMCELL Technologies, 100-0485,) at sufficient volume to cover cells for 3 min at 37 °C. The dissociation reagent was aspirated, growth media was added, and cells were lifted by scraping with a cell lifter to produce small cell clumps. One-sixth volume of lifted cells was added to a new culture vessel and topped up with mTeSR+ growth media. Induced Pluripotent Stem Cells (iPSCs, 32F) were generated via Sendai virus reprogramming and maintained in E8 media (ThermoFisher Scientific, A2656101) on Matrigel-coated plates (Corning, 354277). MCF-7 cells were cultured in DMEM (Gibco, 11965-092) + 10% FBS (Gibco, 16000-044), 2 mM L-Glutamine (Gibco, 25030-081). SK-BR-3 cells were cultured in McCoy (modified) 5A medium (ThermoFisher Scientific, 16600082),10% FBS (Gibco, 16000-044).LNCaP cells were cultured in RPMI 1640 (Gibco, 11875-093), 10% FBS (Gibco, 16000-044).

extract_protocol: Singleplex or multiplex gene expression libraries generated from Chromium fixed RNA profiling of cancer cell lines and hESC were prepared according to the user guides CG000691 (RevB) and CG000527 (RevF), respectively.

treatment_protocol: hESCs were seeded as colonies into 6-well trays by passaging as described for differentiation. The following day, hESCs were treated with 50 ng/mL human recombinant BMP4 (STEMCELL Technologies, 78211) in mTeSR+ media for 0, 6, 12, 24, 48, 72, 96, or 120 h, with daily media replacement. For mesodermal differentiation, iPSCs were seeded at 90% confluency in E8 medium. On day 1, cells were switched to RPMI (ThermoFisher Scientific, 12633012) supplemented with 0.5% B27 without insulin (ThermoFisher Scientific, A1895601) and 40 ng/mL BMP4 (PeproTech, 120-05ET-500UG). On day 2, the medium was replaced with the same medium plus 6 µM CHIR99021 (STEMCELL Technologies, 72052). On day 3, 5 µM IWR1 (STEMCELL Technologies, 72562) was added, removed the next day, and replaced with RPMI + 0.5% B27 without insulin. For ectodermal differentiation, iPSCs were plated in E8 medium until 80% confluency. On day 1, the medium was replaced with neural induction medium (NIM) composed of DMEM/F12 (ThermoFisher Scietific, 11320033) + 1x NEAA (ThermoFisher Scientific, MEM Non-Essential Amino Acids, 11140050) + 0.5% B27 (ThermoFisher Scientific, 17504044), 5 uM SB431542 (STEMCELL Technologies, 100-1051), and 0.1 uM LDN193189 (Sigma Aldrich, SML0559) for 5 days, after which cells were harvested. For endodermal differentiation, iPSCs at 50% confluency were switched to RPMI supplemented with 0.5% B27 without insulin, 100 ng/mL Activin A (PeproTech, 120-14E), 10 ng/mL BMP4, and 20 ng/mL FGF2 (PeproTech, 100-18B). On day 3, cells were switched to RPMI supplemented with 0.5% B27 without insulin and 100 ng/mL Activin A until harvest on day 5. PBMCs were then cultured in a 6 well plate at 4 million cells/mL in complete RPMI media at 37ºC + 5% CO2 under three different culture conditions: (1) Dynabeads™ Human T-Activator CD3/CD28 for T Cell Expansion and Activation (PN 11132D, Thermo Fisher Scientific) following manufacturer’s protocol, (2) lipopolysaccharide (LPS) at 100 ng/mL (PN L2630-25MG, InvivoGen); and (3) complete medium only as control. After 4 and 24 h in culture, cells in each condition were harvested, washed with filtered 1X PBS with 0,05% BSA and STAMPed


title: Flex_C_02

description: Library name: Sample_1

source_name: Breast and prostate cancer cell lines

value: Breast and prostate cancer cell lines


title: Day 90 MGEO

city: Ann Arbor

first: Jeyoon

last: Bok

state: MI

address: 2350 Hayward Street

department: Mechanical Engineering Department

institute: University of Michigan

description: Library name: Sample2

data_processing:
Illumina NovaSeqXPlus for basecalling
Assembly: GRCh38-2020-A
Supplementary files format and content: TSV and MTX files are generated by Cell Ranger pipeline, including barcodes, features and matrix.

source_name: H9 (hESC), 79B (hiPSC), 2E (hiPSC)

extract_protocol:
MGEOs from different cell lines were fixed, permeabilized, dissociated, and barcoded separately with 10x Chromium Controller Instrument (10x Genomics).
cDNA library was constructed according to the standard 10x Genomics scRNA-seq library construction protocol (Fixed RNA Profiling). Different samples in the same library were barcoded with different probes.

value: H9 (hESC), 79B (hiPSC), 2E (hiPSC)


title: liver biopsy [GSM5774001 re-analysis]

value: NR


title: 3 Days Post-Spinal Cord Injury Sup Replicate 1

description:
3d-2.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: 3 Days Post-Spinal Cord Injury Sup Replicate 2

description:
3d-3.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: 1 Day Post-Spinal Cord Injury Sup Replicate 3

description:
1d-3.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

source_name: 1 Day Post-Spinal Cord Injury Spinal Cord


title: ChIP for GFP in His2Av-RFP zld; EGFP-Ez/+ (zld_EGFP-Ez) embryos staged at NC14M replicate ID= rep1

description:
Library name: zld_EGFP-Ez_ChIP-GFP_NC14M_rep1
E(z) binding in zelda mutants at NC14


title: liver biopsy [GSM5774000 re-analysis]


title: Day 30 MGEO

description: Library name: Sample1


title: 1 Day Post-Spinal Cord Injury Sup Replicate 1

description:
1d-1.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: liver biopsy [GSM5773997 re-analysis]

value: TCMR


title: 1 Day Post-Spinal Cord Injury Sup Replicate 2

description:
1d-2.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: ChIP for H2Aub in zld; RpA70GFP/+ (zld) embryos staged at NC14M replicate ID= rep2

description:
Library name: zld_ChIP-H2Aub_NC14M_rep2
H2Aub ChIP in zelda mutants at NC14 mid

value: zld; RpA70GFP/+


title: RAB7A U7smOPT snRNA biol rep 1

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

description: Library name: RAB7A_U7_rep1

data_processing:
Reads were mapped using STAR 2.7.6a
Read count extraction was performed using featureCounts from the Subread package, with results sorted into counts matrices
Differential gene expression analysis was performed on the counts matrices using DESeq2
Assembly: GRCh38
Supplementary files format and content: Supplementary files format and content: tab-delimited text files include gene expression analysis for each transfection condition relative to pUC19 (empty vector)

extract_protocol:
RNA was harvested using RNeasy Plus Mini kit (Qiagen)
RNA libraries for RNA-seq were prepared using Stranded mRNA Prep, Ligation kit (Illumina) following manufacturer's protocols.

treatment_protocol: Human HEK 293T cells were transfected with plasmids: pUC19 (empty vector), U7 promoter-driven U7smOPT snRNA (targeting DMD and RAB7A) in pUC19, and U6 promoter-driven cadRNA (targeting DMD and RAB7A) in pUC19


title: RAB7A cadRNA biol rep 2

description: Library name: RAB7A_cad_rep2


title: ChIP for H2Aub in zld; RpA70GFP/+ (zld) embryos staged at NC14M replicate ID= rep1

description:
Library name: zld_ChIP-H2Aub_NC14M_rep1
H2Aub ChIP in zelda mutants at NC14 mid


title: RAB7A U7smOPT snRNA biol rep 2

description: Library name: RAB7A_U7_rep2


title: RAB7A cadRNA biol rep 1

description: Library name: RAB7A_cad_rep1


title: ChIP for H3K27me3 in zld; RpA70GFP/+ (zld) embryos staged at NC14M replicate ID= rep4

description:
Library name: zld_ChIP-H3K27me3_NC14M_rep4
H3K27me3 ChIP in zelda mutants at NC14 mid


title: DMD U7smOPT snRNA biol rep 2

description: Library name: DMD_U7_rep2


title: ChIP for H3K27me3 in zld; RpA70GFP/+ (zld) embryos staged at NC14M replicate ID= rep2

description:
Library name: zld_ChIP-H3K27me3_NC14M_rep2
H3K27me3 ChIP in zelda mutants at NC14 mid


title: 0 Day Post-Spinal Cord Injury Sup Replicate 2

description:
0d-2.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

source_name: 0 Day Post-Spinal Cord Injury Spinal Cord


title: 0 Day Post-Spinal Cord Injury Sup Replicate 3

description:
0d-3.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: Sham Control Sup Replicate 3

description:
sham-3.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

source_name: Sham Control Spinal Cord


title: DMD U7smOPT snRNA biol rep 1

description: Library name: DMD_U7_rep1


title: ChIP for H3K27me3 in zld; RpA70GFP/+ (zld) embryos staged at NC14M replicate ID= rep1

description:
Library name: zld_ChIP-H3K27me3_NC14M_rep1
H3K27me3 ChIP in zelda mutants at NC14 mid


title: liver biopsy [GSM5773996 re-analysis]

source_name: liver biopsy


title: 0 Day Post-Spinal Cord Injury Sup Replicate 1

description:
0d-1.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: liver biopsy [GSM5773995 re-analysis]


title: ChIP for H3K27me3 in zld; RpA70GFP/+ (zld) embryos staged at NC14M replicate ID= rep3

description:
Library name: zld_ChIP-H3K27me3_NC14M_rep3
H3K27me3 ChIP in zelda mutants at NC14 mid


title: liver biopsy [GSM5773992 re-analysis]


title: DMD cadRNA biol rep 2

description: Library name: DMD_cad_rep_2


title: liver biopsy [GSM5773993 re-analysis]


title: ChIP for H3K27me3 in JT/+; EGFP-GAF (JT-GAF) embryos staged at NC14M replicate ID= rep3

description:
Library name: JT-GAF_ChIP-H3K27me3_NC14M_rep3
H3K27me3 ChIP in Jabba-Trap-EGFP-GAF background at NC14

value: JT/+; EGFP-GAF


title: DMD cadRNA biol rep 1

description: Library name: DMD_cad_rep_1


title: Sham Control Sup Replicate 2

description:
sham-2.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: Sham Control Sup Replicate 1

description:
sham-1.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: ChIP for H3K27me3 in JT/+; EGFP-GAF (JT-GAF) embryos staged at NC14M replicate ID= rep2

description:
Library name: JT-GAF_ChIP-H3K27me3_NC14M_rep2
H3K27me3 ChIP in Jabba-Trap-EGFP-GAF background at NC14


title: liver biopsy [GSM5773994 re-analysis]


title: 6 weeks Post-Spinal Cord Injury IP Replicate 3

description:
6w-3.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

value: m6A methylated RNAs


title: liver biopsy [GSM5773990 re-analysis]


title: ChIP for H3K27me3 in JT/+; EGFP-GAF (JT-GAF) embryos staged at NC14M replicate ID= rep1

description:
Library name: JT-GAF_ChIP-H3K27me3_NC14M_rep1
H3K27me3 ChIP in Jabba-Trap-EGFP-GAF background at NC14


title: 6 weeks Post-Spinal Cord Injury IP Replicate 1

description:
6w-1.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: liver biopsy [GSM5773991 re-analysis]


title: pUC19 biol rep 1

description: Library name: pUC19_rep1


title: 6 weeks Post-Spinal Cord Injury IP Replicate 2

description:
6w-2.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: ChIP for H3K27me3 in EGFP-GAF (EGFP-GAF) embryos staged at NC14M replicate ID= rep3

description:
Library name: EGFP-GAF_ChIP-H3K27me3_NC14M_rep3
H3K27me3 ChIP in EGFP-GAF background at NC14

value: EGFP-GAF


title: liver biopsy [GSM5773988 re-analysis]


title: liver biopsy [GSM5773987 re-analysis]


title: liver biopsy [GSM5773989 re-analysis]


title: 4 weeks Post-Spinal Cord Injury IP Replicate 2

description:
4w-2.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: liver biopsy [GSM5773986 re-analysis]


title: ChIP for H3K27me3 in EGFP-GAF (EGFP-GAF) embryos staged at NC14M replicate ID= rep2

description:
Library name: EGFP-GAF_ChIP-H3K27me3_NC14M_rep2
H3K27me3 ChIP in EGFP-GAF background at NC14


title: U2AF1_mutant-3

city: Beijing

first: Zhaoqi

address: NO.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomic Chinese Academy of Sciences

description: Library name: Sample 6

data_processing:
Raw data were aligned to hg19 using the STAR alignment package
Unique junction counts as determined by STAR are output to a tabular file
Assembly: hg19 for human samples
Supplementary files format and content: Raw junction counts for each sample as output by STAR

extract_protocol:
Total RNA
Total RNA was isolated using the miRNeasy Mini Kit (Qiagen). Poly(A)+ RNAs were selected and Illumina libraries were prepared using TruSeq RNA Sample Prep Kit. Libraries were then sequenced using Illumina HiSeq2000.
60 million paired-end reads performed at Columbia University Genome Center

value: U2AF1 S34F


title: pUC19 biol rep 2

description: Library name: pUC19_rep2


title: liver biopsy [GSM5773985 re-analysis]


title: U2AF1_mutant-2

description: Library name: Sample 5


title: ChIP for H3K27me3 in EGFP-GAF (EGFP-GAF) embryos staged at NC14M replicate ID= rep1

description:
Library name: EGFP-GAF_ChIP-H3K27me3_NC14M_rep1
H3K27me3 ChIP in EGFP-GAF background at NC14

value: embryo


title: U2AF1_mutant-1

description: Library name: Sample 4


title: ChIP for GFP in w (wt) embryos staged at NC14M replicate ID= rep3

description:
Library name: wt_ChIP-GFP_NC14M_rep3
negative control ChIP

value: w


title: 4 weeks Post-Spinal Cord Injury IP Replicate 3

description:
4w-3.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: WT-3

description: Library name: Sample 3

value: U2AF1 wild type knock-in


title: ChIP for GFP in w (wt) embryos staged at NC14M replicate ID= rep2

description:
Library name: wt_ChIP-GFP_NC14M_rep2
negative control ChIP


title: WT-2

description: Library name: Sample 2


title: ChIP for GFP in w (wt) embryos staged at NC14M replicate ID= rep1

description:
Library name: wt_ChIP-GFP_NC14M_rep1
negative control ChIP


title: liver biopsy [GSM5773983 re-analysis]


title: ChIP for GFP in His2Av-RFP zld; EGFP-Ez/+ (zld_EGFP-Ez) embryos staged at NC14M replicate ID= rep2

description:
Library name: zld_EGFP-Ez_ChIP-GFP_NC14M_rep2
E(z) binding in zelda mutants at NC14


title: ChIP for GFP in JT/+; EGFP-GAF (JT-GAF) embryos staged at NC14M replicate ID= rep3

description:
Library name: JT-GAF_ChIP-GFP_NC14M_rep3
GAF binding in Jabba-Trap EGFP-GAF background at NC14


title: 2 weeks Post-Spinal Cord Injury IP Replicate 3

description:
2w-3.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

value: spinal cord


title: 2 weeks Post-Spinal Cord Injury IP Replicate 1

description:
2w-1.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: ChIP for GFP in JT/+; EGFP-GAF (JT-GAF) embryos staged at NC14M replicate ID= rep2

description:
Library name: JT-GAF_ChIP-GFP_NC14M_rep2
GAF binding in Jabba-Trap EGFP-GAF background at NC14


title: liver biopsy [GSM5773982 re-analysis]

value: NKRL


title: SU-DIPG-IV Day 5 24 Gy

city: London

first: Scott

last: Haston

address: 30 Guilford Street

department: Developmental Biology and Cancer

country: United Kingdom

institute: Institute of Child Health, University College London

description: Library name: NM8669_r

data_processing:
Differential Expression Analysis with DESeq2 DESeq2 was employed for differential expression (DE) analysis, applying normalisation factors based on a negative binomial model. Independent filtering was used to include only genes with sufficient reads for differential expression detection. Gene ontology enrichment analysis considered the heteroskedastic nature of RNA sequencing data, utilizing the GOSeq package in R. Visualization of results was done using R. Gene Set Enrichment Analysis GSEA assessed ranked DESeq2 results using the Wald Statistic. Pre-ranked gene lists were obtained from MSigDB, and GSEA was performed with version 4.2.3 from the Broad Institute. The False Discovery Rate (FDR) was used to estimate the probability of false positive findings.
Assembly: hg18
Supplementary files format and content: Processed data file named, "vldallsamples.csv" and contained normalised read counts for transcripts across all of the samples and treatment conditions.

source_name: SU-DIPG-IV

growth_protocol: Grown in TSM-Complete media in standard conditions

extract_protocol:
Cells were stored in RLT with beta mercaptoethanol snap frozen at -80. Gentle thawing, and RNA extraction was carried out as per instructions, RNA was extracted from both non-irradiated (proliferative) and irradiated (senescent) human DMG cells using the Rneasy Micro kit (Qiagen).
Total RNA integrity was validated using Agilent’s 4200 Tapestation, with all samples having RIN values >9.4. UCL genomics core facility prepared cDNA libraries using 250ng of total RNA and the KAPA mRNA HyperPrep Kit. High-quality libraries were confirmed on the Agilent TapeStation 4200. Samples were pooled, normalized to 4nM using the Normalase assay, and sequenced on the NextSeq 500 instrument with a 75bp paired-end run.

treatment_protocol: Cells were exposed to 0, 6 or 24 Gy of caesium source radiation

value: SU-DIPG-IV

tag: cell type

value: Diffuse Midline Glioma Tumour Cell

value: Day 5 24 Gy


title: 2 weeks Post-Spinal Cord Injury IP Replicate 2

description:
2w-2.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: 1 week Post-Spinal Cord Injury IP Replicate 3

description:
1w-3.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: liver biopsy [GSM5773984 re-analysis]

value: liver biopsy


title: SU-DIPG-IV Day 5 6 Gy

description: Library name: NM8668_q

value: Day 5 6 Gy


title: 4 weeks Post-Spinal Cord Injury IP Replicate 1

description:
4w-1.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: SU-DIPG-IV Day 5 0 Gy

description: Library name: NM8667_p

value: Day 5 0 Gy


title: liver biopsy [GSM5773981 re-analysis]

value: TCMR


title: liver biopsy [GSM5773980 re-analysis]

value: NR


title: 3 Days Post-Spinal Cord Injury IP Replicate 3

description:
3d-4.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: ChIP for H3K27me1 in RpA70-EGFP (wt) embryos staged at NC14L replicate ID= rep2

description:
Library name: wt_ChIP-H3K27me1_NC14L_rep2
H3K27me1 timecourse NC14 late


title: 1 week Post-Spinal Cord Injury IP Replicate 2

description:
1w-2.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: liver biopsy [GSM5773978 re-analysis]


title: ChIP for H3K27me1 in RpA70-EGFP (wt) embryos staged at NC14L replicate ID= rep1

description:
Library name: wt_ChIP-H3K27me1_NC14L_rep1
H3K27me1 timecourse NC14 late


title: SU-DIPG-IV Day 1 24 Gy

description: Library name: NM8666_o

value: Day 1 24 Gy


title: 3 Days Post-Spinal Cord Injury IP Replicate 1

description:
3d-2.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

value: m6A methylated RNAs


title: liver biopsy [GSM5773979 re-analysis]


title: SU-DIPG-IV Day 1 6 Gy

description: Library name: NM8665_n

value: Day 1 6 Gy


title: ChIP for H3K27me1 in RpA70-EGFP (wt) embryos staged at NC14M replicate ID= rep3

description:
Library name: wt_ChIP-H3K27me1_NC14M_rep3
H3K27me1 timecourse NC14 mid


title: liver biopsy [GSM5774006 re-analysis]


title: SU-DIPG-IV Day 1 0 Gy

description: Library name: NM8664_m

value: Day 1 0 Gy


title: ChIP for H3K27me1 in RpA70-EGFP (wt) embryos staged at NC14M replicate ID= rep2

description:
Library name: wt_ChIP-H3K27me1_NC14M_rep2
H3K27me1 timecourse NC14 mid

value: embryo


title: ChIP for GFP in JT/+; EGFP-GAF (JT-GAF) embryos staged at NC14M replicate ID= rep1

description:
Library name: JT-GAF_ChIP-GFP_NC14M_rep1
GAF binding in Jabba-Trap EGFP-GAF background at NC14

value: JT/+; EGFP-GAF

value: GFP


title: 1 Day Post-Spinal Cord Injury IP Replicate 3

description:
1d-3.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

value: spinal cord


title: liver biopsy [GSM5773977 re-analysis]


title: liver biopsy [GSM5773976 re-analysis]

value: NKRL


title: HSJD-DIPG-007 Day 5 24 Gy

description: Library name: NM8663_l


title: ChIP for H3K27me1 in RpA70-EGFP (wt) embryos staged at NC14M replicate ID= rep1

description:
Library name: wt_ChIP-H3K27me1_NC14M_rep1
H3K27me1 timecourse NC14 mid


title: 1 week Post-Spinal Cord Injury IP Replicate 1

description:
1w-1.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: liver biopsy [GSM5773974 re-analysis]


title: liver biopsy [GSM5773975 re-analysis]


title: 3 Days Post-Spinal Cord Injury IP Replicate 2

description:
3d-3.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: HSJD-DIPG-007 Day 5 0 Gy

description: Library name: NM8661_j


title: ChIP for H3K27me1 in RpA70-EGFP (wt) embryos staged at NC14E replicate ID= rep1

description:
Library name: wt_ChIP-H3K27me1_NC14E_rep1
H3K27me1 timecourse NC14 early


title: liver biopsy [GSM5773973 re-analysis]


title: WT-1

description: Library name: Sample 1

value: U2AF1 wild type knock-in


title: HSJD-DIPG-007 Day 1 24 Gy

description: Library name: NM8660_i

value: Diffuse Midline Glioma Tumour Cell


title: HSJD-DIPG-007 Day 5 6 Gy

description: Library name: NM8662_k


title: liver biopsy [GSM5773972 re-analysis]


title: ChIP for H3K27me1 in RpA70-EGFP (wt) embryos staged at NC13 replicate ID= rep1

description:
Library name: wt_ChIP-H3K27me1_NC13_rep1
H3K27me1 timecourse NC13


title: ChIP for H3K27me1 in RpA70-EGFP (wt) embryos staged at NC14E replicate ID= rep2

description:
Library name: wt_ChIP-H3K27me1_NC14E_rep2
H3K27me1 timecourse NC14 early


title: 1 Day Post-Spinal Cord Injury IP Replicate 1

description:
1d-1.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: HSJD-DIPG-007 Day 1 6 Gy

description: Library name: NM8659_h


title: 0 Day Post-Spinal Cord Injury IP Replicate 3

description:
0d-3.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: 1 Day Post-Spinal Cord Injury IP Replicate 2

description:
1d-2.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: ChIP for H3K27me3 in RpA70-EGFP (wt) embryos staged at NC14M replicate ID= rep4

description:
Library name: wt_ChIP-H3K27me3_NC14M_rep4
H3K27me3 timecourse NC14 mid


title: liver biopsy [GSM5773970 re-analysis]


title: Sham Control IP Replicate 3

description:
sham-3.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: ChIP for H3K27me3 in RpA70-EGFP (wt) embryos staged at NC14M replicate ID= rep3

description:
Library name: wt_ChIP-H3K27me3_NC14M_rep3
H3K27me3 timecourse NC14 mid


title: liver biopsy [GSM5773971 re-analysis]


title: Endometrial tissues, LER+LIG, rep2

city: Zhengzhou

first: Aiwu

last: Wei

address: No. 19, Renmin Road, Jinshui District

institute: The First Affiliated Hospital of Henan University of Chinese Medicine

description: Library name: Sample 8

data_processing:
The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQ format, which contains sequence information and corresponding sequencing quality information.
Fastp (version 0.23.1) was used to perform basic statistics on the quality of the raw reads.
Assembly: Rnor_6
Supplementary files format and content: diff_gene_of_all_groups.xlsx

organism: Rattus norvegicus

source_name: Uterus

growth_protocol: Female and male Sprague-Dawley (SD) rats (age 10 weeks) had free access to food and water. The rats were kept under temperature (23 ± 1°C), humidity (45%–55%), and 12 h light-dark cycle conditions.

extract_protocol:
Total RNA was extracted and RNA quality was assessed by agarose electrophoresis, Nanodrop and Agilent 5400.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: The rats in the LER and LIG groups were given hydroxyurea solution (450 mg/kg/d) by gavage for 10 d and adrenaline (0.3 mg/kg/d) by subcutaneous injection from the 4th day to the 10th day.   The control group received intragastric administration of equal saline for 10 d and subcutaneous injection of equal saline from the 4th day to the 10th day. After model generation, the female rats in each group were mated with male rats at a ratio of 2:1 at 5 pm every day.    The following morning, the presence or absence of vaginal plugs was observed at 9 am.    The day on which a vaginal plug appeared was considered as the day 0.5 of gestation (GD 0.5).    For the LIG group,  40 mg/kg LIG was given daily by gavage to each rat starting at GD 0.5.    And the control and LER group received intragastric administration of equal olive oil

value: Uterus

value: LIG


title: Endometrial tissues, LER+LIG, rep3

description: Library name: Sample 9


title: ChIP for H3K27me1 in RpA70-EGFP (wt) embryos staged at NC13 replicate ID= rep2

description:
Library name: wt_ChIP-H3K27me1_NC13_rep2
H3K27me1 timecourse NC13


title: ICR-B117 Day 5 6 Gy

description: Library name: NM8656_e

value: Day 5 6 Gy


title: 0 Day Post-Spinal Cord Injury IP Replicate 2

description:
0d-2.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: liver biopsy [GSM5773967 re-analysis]

value: liver biopsy


title: HSJD-DIPG-007 Day 1 0 Gy

description: Library name: NM8658_g


title: Sham Control IP Replicate 1

description:
sham-1.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: liver biopsy [GSM5773966 re-analysis]


title: ICR-B117 Day 5 0 Gy

description: Library name: NM8655_d

value: Day 5 0 Gy


title: liver biopsy [GSM5773969 re-analysis]


title: ChIP for H3K27me3 in RpA70-EGFP (wt) embryos staged at NC14M replicate ID= rep1

description:
Library name: wt_ChIP-H3K27me3_NC14M_rep1
H3K27me3 timecourse NC14 mid


title: Sham Control IP Replicate 2

description:
sham-2.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.


title: Endometrial tissues, LER, rep3

description: Library name: Sample 6

value: olive oil


title: liver biopsy [GSM5773968 re-analysis]

value: NR


title: liver biopsy [GSM5773965 re-analysis]

value: Injury


title: ICR-B117 Day 1 24 Gy

description: Library name: NM8654_c

value: Day 1 24 Gy


title: Endometrial tissues, LER, rep2

description: Library name: Sample 5


title: ICR-B117 Day 5 24 Gy

description: Library name: NM8657_f

value: Day 5 24 Gy


title: liver biopsy [GSM5773964 re-analysis]


title: ICR-B117 Day 1 6 Gy

description: Library name: NM8653_b

value: Day 1 6 Gy


title: ChIP for H3K27me3 in RpA70-EGFP (wt) embryos staged at NC14E replicate ID= rep1

description:
Library name: wt_ChIP-H3K27me3_NC14E_rep1
H3K27me3 timecourse NC14 early

value: embryo


title: Endometrial tissues, LER+LIG, rep1

description: Library name: Sample 7


title: ChIP for H3K27me3 in RpA70-EGFP (wt) embryos staged at NC14E replicate ID= rep2

description:
Library name: wt_ChIP-H3K27me3_NC14E_rep2
H3K27me3 timecourse NC14 early


title: ChIP for H3K27me3 in RpA70-EGFP (wt) embryos staged at NC14M replicate ID= rep2

description:
Library name: wt_ChIP-H3K27me3_NC14M_rep2
H3K27me3 timecourse NC14 mid


title: Endometrial tissues, NER, rep3

description: Library name: Sample 3


title: ChIP for H3K27me3 in RpA70-EGFP (wt) embryos staged at NC13 replicate ID= rep2

description:
Library name: wt_ChIP-H3K27me3_NC13_rep2
H3K27me3 timecourse NC13


title: Endometrial tissues, LER, rep1

description: Library name: Sample 4


title: liver biopsy [GSM5773963 re-analysis]


title: liver biopsy [GSM5773962 re-analysis]


title: ChIP for H2Aub in RpA70-EGFP (wt) embryos staged at NC14L replicate ID= rep2

description:
Library name: wt_ChIP-H2Aub_NC14L_rep2
H2Aub timecourse NC14 late


title: liver biopsy [GSM5773961 re-analysis]


title: Endometrial tissues, NER, rep1

description: Library name: Sample 1


title: ICR-B117 Day 1 0 Gy

description: Library name: NM8652_a

value: Day 1 0 Gy


title: 16S-seq, Flagellin, 4, sample number 76

city: Geneva

first: Aleksander

last: Czauderna

address: Rue Michel-Servet 1

department: PATIM

country: Switzerland

institute: University of Geneva

description: Library name: 76

data_processing:
Raw sequence reads were filtered using Trimmomatic (Bolger et al., 2014), sequentially aligned to the mouse genome to remove mouse-derived sequences and then to each of the 4 CBBP genomes using bowtie2 (Langmead and Salzberg, 2012). BAM files obtained were analyzed using R. Reads were assigned to genes using featureCounts (Liao et al., 2014), and analyzed using ‘DeSeq2’ (Love et al., 2014).
Assembly: mm10
Supplementary files format and content: processed files are counts tables of the host (mouse) and microbes (4mix members) (.txt)
Library strategy: 16S rRNA-seq

organism: mouse gut metagenome

source_name: microbial consortium, mainly B. thetaiotaomicron, P. distasonis, B. producta, E. bolteae

extract_protocol:
microbial DNA for 16S-seq was extracted with PureLink Microbiome DNA kit (Invitrogen), microbial RNA extracted with RNeasy PowerMIcrobiome kit (Qiagen), host RNA extracted with trizol (Invitrogen)
16S-seq - custom library preparation protocol, dual RNA-seq libraries were prepared using Illumina Stranded Total RNA Prep kit with the Ribo-zero Plus, and they were sequenced using the Illumina NovaSeq 6000 with single read 100bp.

treatment_protocol: ip injection (Flagellin) or oral gavage (oleic acid, linoleic acid)

value: cecal pouch contents

value: bacterial cells

value: Flagellin


title: ChIP for H2Aub in RpA70-EGFP (wt) embryos staged at NC14L replicate ID= rep1

description:
Library name: wt_ChIP-H2Aub_NC14L_rep1
H2Aub timecourse NC14 late


title: liver biopsy [GSM5773960 re-analysis]

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.


title: ChIP for H2Aub in RpA70-EGFP (wt) embryos staged at NC14M replicate ID= rep2

description:
Library name: wt_ChIP-H2Aub_NC14M_rep2
H2Aub timecourse NC14 mid


title: 16S-seq, Flagellin, 3, sample number 75

description: Library name: 75


title: ChIP for H2Aub in RpA70-EGFP (wt) embryos staged at NC14M replicate ID= rep1

description:
Library name: wt_ChIP-H2Aub_NC14M_rep1
H2Aub timecourse NC14 mid


title: 16S-seq, Flagellin, 2, sample number 74

description: Library name: 74


title: 16S-seq, Flagellin, 1, sample number 73

description: Library name: 73


title: milk somatic cells Polish Fawn Improved goat_4

city: Warszawa

first: Alicja

last: Majewska

address: Nowoursynowska 159

department: Department of Physiology Sciences

country: Poland

institute: Warsaw University of Life Sciences-SGGW Faculty of Veterinary Medicine

description: MSC_F_goat4  SRLV-seropositive goats (SRLV-SP)

hyb_protocol: according to the manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Capra hircus

source_name: milk somatic cells (MSC)

growth_protocol: not applicable

extract_protocol: isolation of total RNA from goat MSC  the RNeasy Lipid Tissue Mini Kit (Qiagen, USA); the RNA isolationfrom goat PNCB was conducted by using Total RNA mini Kit (A & A Biotechnology, POLAND)

treatment_protocol: MSC was protected with Qiazol reagent from the RNeasy Lipid Tissue Mini Kit Qiagen (Qiagen, USA); Blood from vein was mixed with erythrocyte lysis buffer RBCL and protected with fenozol from Total RNA mini Kit (A & A Biotechnology,POLAND)

value: milk somatic cells (MSC)

tag: breed

value: female goat breed Polish Fawn Improved the peak of 1st lactation

source_name: peripheral nuclear cells blood

value: peripheral nuclear cells

tag: sample type

value: common reference sample compsed of total RNAs isolated from peripheral nuclear cells blood  of  7 healthy goats in 4th lactation from both Polish breeds (PWI=4 & PFI=3) after the lactation cycle


title: ChIP for H2Aub in RpA70-EGFP (wt) embryos staged at NC13 replicate ID= rep2

description:
Library name: wt_ChIP-H2Aub_NC13_rep2
H2Aub timecourse NC13


title: ChIP for H3K27me3 in RpA70-EGFP (wt) embryos staged at NC13 replicate ID= rep1

description:
Library name: wt_ChIP-H3K27me3_NC13_rep1
H3K27me3 timecourse NC13


title: ChIP for H2Aub in RpA70-EGFP (wt) embryos staged at NC13 replicate ID= rep1

description:
Library name: wt_ChIP-H2Aub_NC13_rep1
H2Aub timecourse NC13


title: 16S-seq, PBS, 4, sample number 83

description: Library name: 83

value: PBS


title: ChIP for H3K27me3 in RpA70-EGFP (wt) embryos staged at NC14L replicate ID= rep3

description:
Library name: wt_ChIP-H3K27me3_NC14L_rep3
H3K27me3 timecourse NC14 late


title: 16S-seq, PBS, 3, sample number 82

description: Library name: 82


title: milk somatic cells Polish Fawn Improved goat_2

description: MSC_F_goat2  SRLV-seropositive goats (SRLV-SP)

label_protocol: according to the manufacturer's protocol


title: liver biopsy [GSM5773957 re-analysis]

city: Edmonton

first: Jessica

address: 250 Heritage Medical Research Centre

institute: University of Alberta

extract_protocol:
All human liver biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNAlater.
Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

tag: rejection archetype groups (nr,tcmr,nkrl,injury)

value: liver biopsy


title: single-embryo Library 4

city: Grand Rapids

first: Adelheid

last: Lempradl

state: Michigan

address: 333 Bostwick Ave NE

department: Metabolism and Nutritional Programing

institute: Van Andel Institute

data_processing:
Reads were trimmed using TrimGalore v0.6.10 with the parameters, ‘--length 15 --hardtrim5 200 --paired’. Trimmed reads were processed using a custom Snakemake workflow (https://github.com/vari-bbc/scRNAseq; commit 834077) that calls variants using a process partly adapted from GATK’s standard RNA-seq workflow (https://github.com/gatk-workflows/gatk4-rnaseq-germline-snps-indels).
BAM files were split by the cell barcode tag (CB) using ‘bamtools split’ from BamTools v2.5.234; the sample tag (SM) in each split BAM file was made unique by appending the CB tag via ‘samtools reheader’ from SAMtools v1.17. Duplicate reads were identified based on UMIs using MarkDuplicates from PicardTools v3.0.0 (http://broadinstitute.github.io/picard/) with the parameters, ‘--BARCODE_TAG “UB” --VALIDATION_STRINGENCY SILENT’. Variants were called using the joint genotyping workflow in GATK v4.4.0.0 as suggested in Brouard et al., 2019. Reads with Ns in the CIGAR string were split using ‘SplitNCigarReads’. Base qualities were recalibrated using ‘BaseRecalibrator’ and ‘ApplyBQSR’ using the DGRP2 variants (dm6 liftover downloaded from https://www.hgsc.bcm.edu/arthropods/drosophila-genetic-reference-panel on Mar 30, 2021) for the set of known variants. ‘HaplotypeCaller’ was run with the parameters, ‘-ERC GVCF -dont-use-soft-clipped-bases --standard-min-confidence-threshold-for-calling 20’, on each embryo (cell barcode), for each chromosome separately to reduce runtime. Joint genotyping was conducted on each chromosome separately, by running ‘GenomicsDBImport’ then ‘GenotypeGVCFs’. Per-chromosome VCF files were sorted using ‘SortVcf’ then merged into a single VCF using ‘MergeVcfs’. Variants were filtered by running ‘VariantFiltration’ with the parameters, ‘--window 35 --cluster 3 --filter-name "FS" --filter "FS > 30.0" --filter-name "QD" --filter "QD < 2.0" --genotype-filter-name "GQ" --genotype-filter-expression "GQ < 15.0" --genotype-filter-name "DP" --genotype-filter-expression "DP < 10.0"’, followed by ‘SelectVariants’ with the parameters, ‘--exclude-filtered --set-filtered-gt-to-nocall’. Genic variants were annotated using ‘eff’ from SNPEff v5.1, with the parameters, ‘-no-downstream -no-intergenic -no-upstream’, and the pre-configured ‘BDGP6.32.105’ database. A table containing variant coordinates, variant information and allelic depth was extracted from the VCF file using ‘VariantsToTable’ from GATK v4.4.0.0 using the parameters, ‘-F CHROM -F POS -F REF -F ALT -F TYPE -F ANN -GF AD’.  Downstream analyses were conducted in R v4.2.1 and the script can be found at https://github.com/vari-bbc/scRNAseq/blob/main/scripts/ASE_example.Rmd. The allelic depth table was imported as a GenomicRanges object (v1.50.2). Only variants on standard chromosomes or “mitochondrion_genome” were retained. Only biallelic SNPs annotated to a single gene were retained. A SummarizedExperiment object was created to store the variant coordinates, the sample metadata, and the REF and ALT allelic depths as separate assays. Variants were further filtered to retain only those with at least 5 samples with > 5 read counts for each of REF and ALT (not necessarily the same samples); for mitochondrial variants, if either REF or ALT allelic depths passed the above filter, the variant was retained. The DGRP2 VCF file was imported and processed using the VariantAnnotation v1.44.1 package, retaining only variants polymorphic between line_737 and line_352. DGRP2 variant information was merged with the SummarizedExperiment based on matching chromosomal coordinates, and reference and alternate alleles. Where there was a matching entry, parental origins for alleles were determined based on the parental genotypes identified in DGRP2 and used to derive maternal and paternal counts, which were stored as additional assays in the SummarizedExperiment object. Variants annotated to the same gene were ranked in descending order based on the number of samples expressing both alleles (> 0 counts), and the total counts (reference or alternate) across samples. Diagnostic plots of the maternal and paternal counts were created by coercing the SummarizedExperiment object into a SingleCellExperiment object (v1.20.1) and utilizing functions from scater v1.26.1 on only the top-ranked variant of each gene.
Raw gene counts were combined by columns into a single data frame using R in the following order: Library1[,1:96], Library2[,97:192], Library3[,1:96], Library4 [,97:192]. Sample names were assigned and gene names updated using gene_map_table_fb_2023_06.tsv from FlyBase.
The gene counts were analyzed using the RaceID3/StemID2/FateID workflow (Herman et al. 2018) as described step-by-step in Pérez-Mojica et al., 2023. DOI:10.1016/j.xpro.2023.102535 Embryos with less than 150,000 reads or transcripts with < 5 read counts on < 5 samples were filtered out from the analysis. Embryos older than 3h were removed, leaving a total of 245 embryos and 22 unfertilized eggs in the final dataset.
Raw gene counts were normalized using RUVg in both non-allele and allele-specific data. For non-allele-specific data 40 genes were used as controls: Act5C, Hsc70-4, Cam, fs(2)ltoPP43, SmD2, Eb1, wal, CG9302, CG1103, Pex2, CG31715, Mettl14, vito, eEF1alpha1, mt:lrRNA, mt:ATPase6, mt:Cyt-b, mt:CoI, mt:CoIII, mt:CoII, Rpt4, CG15237, CG31195, zf30C, Sap47, baf, SkpA, cnk, Hcf, Srp54k, PlexA, anne, Myb, kuz, sl, HP1c, RpLP0-like, ttv, SmE, Nup205. For allele-specific data only the first 13 genes were used as the others were not present in the dataset.
Assembly: BDGP6.28/dm6
Supplementary files format and content: *raw_counts.txt, non-allele-specific gene counts matrix with barcodes converted to barcode numbers (1-192)
Supplementary files format and content: non_allele_pseudotime_normalized_reads.csv, non-allele-specific normalized gene counts by pseudo-temporal (developmental) order with sampleID
Supplementary files format and content: allele_specific_pseudotime_normalized_reads.csv, allele-specific normalized gene counts by pseudo-temporal (developmental) order with sampleID
Supplementary files format and content: barcode2sampleID.csv, List of barcode numbers use for each sample in each library
Library strategy: CEL-Seq2

source_name: Embryo

growth_protocol: DGRP_737 and DGRP_352 lines from Bloomington Stock Center (#83729 and #83728, respectively) were kept in incubators at 25 °C with 60% humidity with a 12-hour light-dark cycle. All flies were raised at constant densities on standardized cornmeal food (Bloomington recipe), Fly food M (LabExpress, Michigan, USA), and DGRP_737 virgin females and DGRP_352 males transferred into mating cages 3-4 days after eclosion.

extract_protocol:
Frozen embryos or unfertilized eggs were homogenized in 1 mL 80% methanol (v/v) (Optima™ LC/MS Grade, Fisher Chemical™) by bead-beating at 6 m/s for 30 seconds at 4°C using a Bead Ruptor Elite homogenizer coupled with Bead Ruptor Cryo Cooling Unit (OMNI international, USA). After metabolite extraction, the pellet, ceramic beads, and remaining metabolite soluble fraction (~200 µL) of each sample was dried (~1 h) in a Genevac EZ-2 series evaporator using low-BP lamp-off settings. RNA was then isolated following a miniaturized version of the TRIzol protocol. Briefly, 500 µL TRIzol™ (Invitrogen, USA) and 50 µL Gibco™ phosphate buffered saline pH 7.4 (Thermo Fisher Scientific, USA) were added to each sample mixing thoroughly. After 5 min incubation at room temperature, 100 µL chloroform (Sigma-Aldrich, USA) were added, samples mixed by vortex, incubated 2 min at room temperature, centrifuged for 15 minutes at 12,000 × g at 4 °C, and RNA-containing aqueous phase pipetted into a new 1.5 mL tube. RNA was precipitated by adding 250 µL ice-cold isopropanol (Sigma-Aldrich, USA) and 2 µL GlycoBlue™ (Thermo Fisher, USA), samples mixed by hand, incubated for 10 min at RT, and centrifuged for 10 minutes at 12,000 × g at 4°C. After discarding the supernatant, RNA pellets were washed with 1 ml 75% (v/v) ethanol (Pharmco, USA), air-dried, and stored at -80 °C until library preparation for RNA-seq.
RNA-seq was carried out following a miniaturized version of the sensitive highly-multiplexed single-cell RNA-seq (CEL-Seq2) protocol (Hashimshony et al. 2016) using the I.DOT liquid handler (Dispendix). Dried RNA was resuspended in 8 µL nuclease-free water (Invitrogen, USA) and 120 nL dispensed into a 384-well plate holding 240 nL of primer-mix including 192 different cell barcodes with unique molecular identifiers (UMI). Subsequent steps and reagents are detailed in Pérez-Mojica et al., 2023. DOI:10.1016/j.xpro.2023.102535, except that libraries were diluted 1:10 (cDNA:H2O) before an 11-cycle amplification. Each library includes 96 single-embryos.
Modified CelSeq2 protocol

value: Embryo


title: milk somatic cells Polish White Improved goat_4

description: MSC_W_goat4  SRLV-seronegative goats (SRLV-SN)

value: female goat breed Polish White Improved the peak of 1st lactation


title: ChIP for H3K27me3 in RpA70-EGFP (wt) embryos staged at NC14L replicate ID= rep2

description:
Library name: wt_ChIP-H3K27me3_NC14L_rep2
H3K27me3 timecourse NC14 late


title: 16S-seq, PBS, 2, sample number 81

description: Library name: 81


title: ChIP for H3K27me3 in RpA70-EGFP (wt) embryos staged at NC14L replicate ID= rep1

description:
Library name: wt_ChIP-H3K27me3_NC14L_rep1
H3K27me3 timecourse NC14 late


title: single-embryo Library 3


title: single-embryo Library 2


title: liver biopsy [GSM5773954 re-analysis]

last: Chang

value: NR


title: liver biopsy [GSM5773958 re-analysis]


title: milk somatic cells Polish White Improved goat_2

description: MSC_W_goat2  SRLV-seronegative goats (SRLV-SN)


title: 16S-seq, PBS, 1, sample number 80

description: Library name: 80


title: liver biopsy [GSM5773959 re-analysis]

value: Injury


title: milk somatic cells Polish Fawn Improved goat_3

description: MSC_F_goat3  SRLV-seropositive goats (SRLV-SP)


title: liver biopsy [GSM5773955 re-analysis]


title: single-embryo Library 1


title: milk somatic cells Polish Fawn Improved goat_1

description: MSC_F_goat1  SRLV-seropositive goats (SRLV-SP)


title: liver biopsy [GSM5773953 re-analysis]


title: liver biopsy [GSM5773951 re-analysis]


title: milk somatic cells Polish White Improved goat_3

description: MSC_W_goat3  SRLV-seronegative goats (SRLV-SN)