title: KELLY cells, dTAGv1 TADA2B, Input, 6 hours

data_processing:
ChIP-Seq data analysis was performed in alignment with the ENCODE Consortium standards (https://www.encodeproject.org/chip-seq/). Quality control tests for unmapped sequences were performed by using the FastQC v.0.11.9 software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The ChIP-sequences were aligned to the GRCh38/hg38 genome and to the spiked-in dm6 Drosophila melanogaster genome using bowtie2-2.3.5 (Langmead and Salzberg, 2012) with the standard options.  PCR duplicates were removed with the Picard Mark Duplicates method   implemented in the sambamba v0.7.1 tool (Tarasov et al., 2015). The alignments with MAPQ < 5 were skipped.
The mapped reads were normalized in units of reads per kilobase per million (RPKM or rpm/bp) and coverage tracks for the RPKM signal were created as bigwig files for bins of size 20 base pairs by using the bamCoverage tool available in deepTools v3.5.1 (Ramírez et al., 2016). The Active Motif Spike-in Normalization protocol was then applied to each hg38 sample. The dm6 genome-wide counts distribution on 200 bp size bins was computed with the multiBamSummary function available from the deepTools v3.5.1. The dm6 uniquely mapped reads were summed up from all the bins with at least 10 mapped dm6 reads. Each hg38 sample was normalized by multiplying the human tag counts with the scaling factor derived from the Drosophila reads as ratio between the average of the uniquely mapped dm6 counts across all samples vs. the dm6 uniquely mapped reads counts for that sample.
Peak calling was performed against the input control using the model-based MACS2 v2.1.1.20160309 software (Zhang et al., 2008), with the significance cut-off FDR ≤ 0.01. Area under the curve (AUC) RPKM normalized signal across genomic regions was computed with the bwtool software (Pohl and Beato, 2014). Each set of MACS2 peaks  was curated by removing the binding regions with low area under curve coverage (< 500 RPKM) and the regions overlapping with the  ENCODE black-listed regions for hg38 (available at https://www.encodeproject.org/annotations/ENCSR636HFF/). Quality control tests for the peaks were performed by using the ChIPQC library available from Bioconductor v3.9 (Carroll et al., 2014).
The peaks were annotated with the closest hg38 genes by using the annotatePeaks function implemented in the Homer v4.11 platform (Heinz et al., 2010) and the GREAT annotation platform (McLean et al., 2010).  Binding peaks and normalized binding signal were visualized on the Integrative Genomic Viewer (IGV) v2.12.3 platform (Thorvaldsdóttir et al., 2013).   Gene promoter regions were defined as the +/- 3.0 kb intervals around the hg38 gene transcription start site (TSS). Enhancer regions were defined as the H3K27ac binding regions outside TSS +/- 3.0 kb gene promoter regions. The samtools v1.9 (Li et al., 2009) and the BEDTools v2.29 suite (Quinlan and Hall, 2010) were used to perform various mapping and genomic region analyses (indexing, sorting, intersection, merging).
Per each antibody, the binding sites identified by MACS2 for treatment and control conditions across time points were merged into the antibody’s set of aggregated peaks.  A peak by sample counts matrix was created by counting the reads overlapping each aggregated peak with the multiBamSummary tool available from deepTools. The counts matrix was used to perform differential peak analysis. For a specific genomic region, the changes in signal between two conditions were classified as increase, decrease or not significant  based on the absolute cut-off 1.5 for the delta area under curve scores; the significance was quantified based on the cut-off p-value ≤ 0.10 for the differences in the mapped reads by using edgeR v3.36.0 with the  glmLRT model (Robinson et al., 2010).     Heatmaps of AUC ChIP-seq normalized signal occupancy on genomic regions were created using the computeMatrix and the plotHeatmap tools available in deepTools v3.5.1. The plotProfile tool from deepTools v3.5.1 was used to create metaplots based on the average normalized scores across genomic regions. Differences between metaplots were estimated based on the t-test with Welch correction (cutoff P-value ≤ 0.05) for the area under curve (AUC) RPKM normalized signal across the regions for the conditions.   Motif enrichment analysis was performed for genomic regions and gene promoters using the Homer v4.11 platform (Heinz et al., 2010) and the  MEME Suite v5.4.1 platform (FIMO method) (Bailey et al., 2015) with the adjusted p-value cutoff ≤ 0.01.
Assembly: hg38
Supplementary files format and content: bigWig RPKM binding signal

growth_protocol: Neuroblastoma cell lines were grown in 15 cm plates.

extract_protocol:
20 million cells were cross-linked with 1% formaldehyde in 22mL warm media for 10 minutes with rotation followed by quenching with the addition of 1.1mL of 2.5M glycine for 5 minutes. Cells were pelleted by centrifugation at 600xg and resuspended in 1mL cold PBS supplemented with protease inhibitors (Thermo Fisher cat.# 78430) and 1mM PMSF (Sigma Aldrich cat.# P7626). This wash was repeated twice for a total of three washes in PBS. Cells were resuspended in cytoplasmic and then nuclear lysis buffer, and cells were sheared on an E220 Covaris sonicator (Duty cycle: 5%; Peak power: 140W; Cycles per Burst:200; Temp: 4C; time 15 min). Sheared lysates were cleared by centrifugation at 15,000g for 10 minutes at 4C and incubated overnight with rotation at 4C with magnetic beads prebound with antibody, spike-in antibody (Active Motif cat.#61686), and spike-in chromatin (Active Motif cat.#53083). Following overnight incubation, beads were washed twice with low salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tri-HCl pH8.1, 150mM NaCl), twice with high salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tri-HCl pH8.1, 500mM NaCl), twice with LiCl wash buffer (0.25 M LiCl, 1% IGEPAL-CA 630, 1% deoxycholic acid, 10mM Tri-HCl ph8.1, 1mM EDTA), and once with TE. DNA was eluted in elution buffer (1% SDS, 0.1M NaHCO3). Cross linking was reversed overnight at 65C with 0.9% RNAse A, 0.9% Proteinase K, and 0.182M NaCl. DNA was isolated by adding Agencourt AMPure XP beads (Beckman Coulter cat.# A63880) at 1.2x volume, incubating 20 minutes, washing twice with 80% ethanol, and eluting into 10-20ul TE.
ChIP-seq libraries were prepared using Swift S2 Acel reagents on a Beckman Coulter Biomek i7 liquid handling platform from approximately 1ng of DNA according to manufacturer’s protocol and 14 cycles of PCR amplification. Finished sequencing libraries were quantified by Qubit fluorometer and Agilent TapeStation 2200.  Subsequently, libraries were paired end sequenced on Illumina NovaSeq 6000.

treatment_protocol: Antibodies used for ChIP were HA-tag (Cell Signaling Technologies, cat.# 3724), H3K9ac (Abcam cat.# ab4441), H3K27ac (Abcam cat.# ab4729), and MYCN (Abcam cat.# ab16898). For HA-tag ChIP in KELLY, 5ug of HA antibody was used for 100 million cells. For NGP and NB1 HA-tag ChIPs, 50ul of HA antibody was used for 20 million cells. For MYCN, 10ug of antibody was used per sample of 20 million cells. For H3K9ac, 5ug of antibody was used per sample of 5 million cells. For H3K9ac, 7.5ul of spike-in chromatin was used per sample. For MYCN, 3ul of spike-in chromatin was used per sample. For HA ChIP, 10ul of spike-in chromatin was used per sample of 20 million cells. For H3K27ac, 5ug antibody and 2ul of spike-in chromatin was used for 10 million cells.  For each sample, protein A or protein G beads (Life Technologies cat.#10003D) were prepared by washing thrice in BSA blocking solution, then resuspended in 250ul/sample BSA blocking solution with appropriate antibody and spike-in antibody. Beads were incubated overnight with rotation, washed four times with BSA blocking solution, and resuspended in 100ul/sample BSA blocking solution. Spike-in chromatin was added to the beads two hours before adding sheared human chromatin and incubated with rotation at 4C.

value: Neuroblastoma, MYCN amplified

tag: chip antibody

tag: spike-in antibody


title: RNAseq Clutch B Sample 3

status: Public on Apr 19 2024

type: SRA

city: Irvine

first: Kitt

middle: D.

last: Paraiso

state: CA

address: 4410 Nat Sci II, University of California, Irvine

department: Department of Developmental and Cell Biology

country: USA

institute: University of California, Irvine

library_source: transcriptomic

data_processing:
Paired-end reads were aligned using RSEM v.1.2.12 (Li and Dewey 2011) and Bowtie v2.2.7 (Langmead and Salzberg 2012) to the Xenopus tropicalis genome version 9.0 (Mitros et al., 2019; Karimi et al., 2018). Gene expression in transcripts per million were extracted from RSEM results output.
Genome_build: Xenopus tropicalis v9.0
Supplementary_files_format_and_content: RNA-Seq:The first column is populated by the gene models in the X. tropicalis v9.0 genome annotation. Each subsequent column is the expression of the gene from the 15 RNA-seq datasets.

molecule: polyA RNA

organism: Xenopus tropicalis

source_name: Early Embryo

growth_protocol: Xenopus tropicalis females were injected with 10 units of Chorulon (Merck and Co.) 1-3 nights before embryo collection and 100 units of Chorulon on the day of embryo collection. Eggs were collected in a dish coated with 0.1% BSA in 1/9x MMR. The eggs are in vitro fertilized with sperm suspension in 0.1% BSA in 1/9x MMR. The embryos are dejellied with 3% cysteine in 1/9x MMR, pH 7.8. After 10 minutes, embryos are washed with 1/9x MMR and transferred to 1/9x MMR.

extract_protocol:
Total RNA was extracted using the acid guanidinium thiocyanate method of Chomczynski and Sacchi (1987: Analytical Biochemistry 162:156-159). Final RNA pellets were resuspended in DEPC-treated water and then precipitated overnight at 4C in 2.5M LiCl to remove contaminating genomic DNA.
Library Construction Protocol: Smart-seq2 cDNA synthesis, Tagmentation

tag: tissue type

value: Whole Embryo

tag: developmental stage

value: Nieuwkoop Faber 10.25

tag: clock time (hours post-fertilization)

tag: agent

value: untreated


title: RNAseq Clutch B Sample 4


title: WBCminusNeu_ZT46

type: genomic

city: Vilnius

first: Karolis

last: Koncevičius

address: Saulėtekio al. 7

department: Institute of Biotechnology, Life Sciences Center

country: Lithuania

institute: Vilnius University

description: White blood cells left over after magnetically activated cell sorting isolation of neutrophils

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Infinium HD Methylation Assay protocol

scan_protocol: Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting

data_processing:
Processeing was done using the R “minfi” package. First, all samples having more than 3% of probes with poor detection p-values (detection p < 0.05) using an alternative detection p-value approach(Heiss and Just 2019) were removed as outliers. Then array normalization was performed using “noob” background correction followed by functional normalization, and signals from the methylated and unmethylated channels were combined to obtain the methylation beta values. Additional outliers were identified by measuring Pearson’s correlations among all the sample pairs and removing samples with an average inter-sample correlation value more than three standard deviations below the mean. Finally, for the datasets that contained technical replicates for every sample, all the samples with only a single replicate remaining after quality control were discarded.
R "minfi" package computed Average Beta values after "noob" background correction and "functional" normalization

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Whole blood depleted of neutrophils

label_protocol: Standard Infinium HD Methylation Assay protocol

extract_protocol: Neutrophils were isolated from whole blood by immunomagnetic negative selection with EasySep™ Direct Human Neutrophil Isolation Kit (STEMCELL) according to the manufacturer's protocol. The remaining fraction of white blood cells depleted of neutrophils were snap-frozen and stored in -80 °C before DNA extraction. DNA was extracted with NucleoSpin® Blood XL (Macherey-Nagel) using the standard protocol

tag: Sex

value: male

tag: age

tag: ct


title: WT bECs E15.5 JE6

city: Stanford

first: Kanako

last: Yuki

address: 265 CAMPUS DRIVE

institute: Stanford University

description: WT bECs E15.5

data_processing:
The sequencing libraries were multiplexed and clustered on a lane of a flowcell.
The samples were sequenced using a 2x150 Paired End (PE) configuration.
Image analysis and base calling were conducted by the HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
One mismatch was allowed for index sequence identification.
Assembly: mm10

molecule: total RNA

organism: Mus musculus

source_name: CD31+ brain endothelial cells

extract_protocol:
RNA was extracted using Arcturus PicoPure RNA Isolation Kit (Applied Biosystems)
RNA libraries for ultra-low input RNA-seq were prepared using SmartSeq V4 Ultra-Low RNA Library Prep following manufacturer's protocols.

tag: cell type

value: CD31+ brain endothelial cells

tag: genotype

value: WT

tag: time


title: WBCminusNeu_ZT43_replicate


title: KELLY cells, DMSO, Input, 6 hours

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

library_source: genomic

source_name: KELLY

tag: cell line

value: KELLY


title: WBCminusNeu_ZT43


title: WT bECs E15.5 JE1

description: WT bECs E15.5


title: V-1

city: Beijing

first: Yabing Nan

last: Yabing Nan

address: 17 Panjiayuan Nanli, Chaoyang Diistrict

country: China

institute: Cancer Hospital Chinese Academy of Medical Sciences

data_processing:
The paired-end libraries were prepared using a NEBNext UltraTM RNA Library Prep Kit for Illumina
Sequencing was performed using the Illumina NovaSeq 6000 platform.
A fold change of   >2 and P value of <0.05 were set as the criteria for identifying significantly differentially expressed genes
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Text file for rpkm values of each gene

extract_protocol:
TRIzol extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: Human ovarian cancer cell line

value: empty vector


title: RNAseq Clutch B Sample 2


title: KELLY cells, dTAGv1 TADA2B, MYCN antibody, 6 hours

value: MYCN (Abcam cat.# ab16898)

value: spike-in antibody (Active Motif cat.#61686)


title: RNAseq Clutch B Sample 1


title: SH-SY5Y cell line, shDDR2, 24h, 20kPa, bioreplicate 3

city: New York

first: Cong

last: Xiao

address: Hess 9th floor,1470 Madison AVE

institute: Icahn School of Medicine-Mt Sinai

data_processing:
Reads were sorted by the barcodes assigned to each library and adapter sequences were removed using Trimmomatic
The reads were then mapped to the human genome through STAR
The gene expressions count table was generated by Tetranscripts
DEGs were identified using a R package DeSeq2
GO analysis was performed using another R package clusterProfiler
Assembly: hg19
Supplementary files format and content: tex files includs raw counts for each sample

source_name: cell line

extract_protocol:
RNA was extracted using the RNeasy microKit (QIAGEN) combined with DNase (TurboDNase (ThermoFisher). The following RNA concentration and integrity were measured by the Qubit 4 Fluorometer (Thermo Fisher Scientific) and 2100 Bioanalyzer (Agilent), respectively.
We used the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® kit to make all RNA libraries without any modifications. For each library, the input of approximately 500 ng total RNA, and a total of nine PCR cycles were used for library amplification. The quality and concentration of libraries were measured by 2100 Bioanalyzer (Agilent) and Qubit 4 Fluorometer (Thermo Fisher Scientific), respectively. All libraries were normalized to 20 nM and pooled together, the final concentration of library pool was 5 nM, loaded onto the NextSeq500/550 High Output Kit v2.5(150 Cycles) chip (Illumina), and sequenced on the NextSeq550 (Illumina).

tag: tissue

value: cell line

value: neuroblastoma cell

tag: treatment

value: 20 pKa


title: WBCminusNeu_ZT40_replicate


title: WBCminusNeu_ZT40


title: RNAseq Clutch A Sample 5


title: KELLY cells, dTAGv1 TADA2B, H3K27ac antibody, 6 hours

value: H3K27ac (Abcam cat.# ab4729)


title: SH-SY5Y cell line, shDDR2, 24h, 20kPa, bioreplicate 2


title: WBCminusNeu_ZT37_replicate


title: RNAseq Clutch A Sample 4


title: WBCminusNeu_ZT37


title: RNAseq Clutch A Sample 3


title: WT bECs E15.5 KE8

description: WT bECs E15.5


title: SH-SY5Y cell line, shDDR2, 24h, 20kPa, bioreplicate 1


title: SH-SY5Y cell line, shCTRL, 24h, 20kPa, bioreplicate 3

value: shCTRL


title: KELLY cells, dTAGv1 TADA2B, H3K9ac antibody, 6 hours

value: Neuroblastoma, MYCN amplified

value: H3K9ac (Abcam cat.# ab4441)


title: KELLY cells, DMSO, H3K27ac antibody, 6 hours


title: KELLY cells, DMSO, H3K9ac antibody, 6 hours


title: WBCminusNeu_ZT34


title: SH-SY5Y cell line, shCTRL, 24h, 20kPa, bioreplicate 2


title: RNAseq Clutch A Sample 1

value: Whole Embryo

value: Nieuwkoop Faber 10.25


title: WBCminusNeu_ZT34_replicate

value: male


title: NGP-TADA2Bdeg cells, dTAGv1, Input, 6 hours

value: Neuroblastoma, MYCN amplified, with degraded TADA2B


title: RNAseq Clutch A Sample 2

value: untreated


title: ChIPKD H3K4me1 Mesoderm Wild Type

data_processing:
H3K4me1 ChIP-seq reads obtained from multiple sequencing lanes were concatenated and then aligned to the X. tropicalis genome v9.0 (Mitros et al., 2019; Karimi et al., 2018) using Bowtie v2.2.7 (Langmead and Salzberg 2012) with default options and peaks were called against stage 10 input DNA (Charney et al., 2017) using Macs v2.0.10 (Zhang et al., 2008) with the option –p 0.0000000001 but otherwise default options.
Genome_build: Xenopus tropicalis v9.0
Supplementary_files_format_and_content: ChIP-Seq: NarrowPeak (BED)

extract_protocol:
Samples were dissected from 100 fixed embryos and were then homogenized in RIPA buffer and incubated on ice for 10 minutes. Samples were then centrifuged at 14,000rpm for 10 minutes at 4C. Pellets were resuspended in RIPA buffer and sonicated on ice to an average size of 100-500bp. The resulting samples were centrifuged at 14,000 rpm for 30 minutes at 4C to remove insoluble cellular debris. The sheared chromatin was pre-cleared by incubating with 20 ¼L Protein G-coated Dynabeads (Invitrogen) for 2 hours at 4C with rotation. Meanwhile, another 20 ¼L Protein G Dynabeads were incubated in a tube rotator in 1 mg/mL torula RNA and 0.5% BSA in 1x PBS for 30 minutes at 4C to block non-specific binding. This second 20 ¼L Protein G Dynabeads were then pre-bound with 3 ug anti-H3K4me1 antibody at 4C for > 1 hour. The pre-cleared chromatin was added to antibody-bound Dynabeads, and incubated overnight at 4¡C on a tube rotator. The next day, the beads were washed, and DNA was eluted off the beads with TE buffer containing 1% SDS, and reverse-crosslinked at 65C overnight. Sonicated input control was diluted 3-fold with elution buffer and also incubated at 65C. All samples were treated with RNAse A, Proteinase K, phenol/chloroform extracted, and ethanol precipitated overnight. DNA pellets were resuspended in Qiagen EB solution.
Library Construction Protocol: Nextflex ChIP-seq kit (Bioo Scientific)

value: Marginal Zone (Mesoderm)

tag: antibody


title: SH-SY5Y cell line, shDDR2, 24h, 2kPa, bioreplicate 3

value: 2 pKa


title: WBCminusNeu_ZT31


title: WBCminusNeu_ZT31_replicate


title: KELLY cells, DMSO, MYCN antibody, 6 hours

value: KELLY


title: NGP-TADA2Bdeg cells, dTAGv1, HA antibody, 6 hours

value: HA-tag (Cell Signaling Technologies, cat.# 3724)


title: SH-SY5Y cell line, shCTRL, 24h, 20kPa, bioreplicate 1


title: SH-SY5Y cell line, shDDR2, 24h, 2kPa, bioreplicate 2


title: SH-SY5Y cell line, shDDR2, 24h, 2kPa, bioreplicate 1


title: NGP-TADA2Bdeg cells, DMSO, HA antibody, 6 hours

value: spike-in antibody (Active Motif cat.#61686)


title: WBCminusNeu_ZT25_replicate


title: NB1-TADA2Bdeg cells, dTAGv1, Input, 6 hours


title: SH-SY5Y cell line, shCTRL, 24h, 2kPa, bioreplicate 3

value: cell line


title: ChIPKD H3K4me1 Endoderm TF MO

value: Vegetal Mass (Endoderm)

value: Vegt/Otx1/Foxh1 MO injected


title: WBCminusNeu_ZT28


title: ChIPKD H3K4me1 Endoderm Alpha-amanitin

value: 5 pg Alpha-amanitin injected


title: SH-SY5Y cell line, shCTRL, 24h, 2kPa, bioreplicate 2

value: neuroblastoma cell

value: shCTRL


title: ChIPKD H3K4me1 Ectoderm Wild Type

value: Animal Cap (Ectoderm)


title: WBCminusNeu_ZT28_replicate


title: WBCminusNeu_ZT25


title: NB1-TADA2Bdeg cells, dTAGv1, HA antibody, 6 hours


title: NB1-TADA2Bdeg cells, DMSO, Input, 6 hours


title: WBCminusNeu_ZT22_replicate


title: SH-SY5Y cell line, shCTRL, 24h, 2kPa, bioreplicate 1


title: R3

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

library_source: transcriptomic single cell

data_processing:
Cell Ranger (version 6.1.2) was used for demultiplexing, aligning reads to the mouse genome.
Assembly: mm39 (version 110) supplemented with LCMV NC_004291 and NC_004294.
Supplementary files format and content: raw gene counts in H5 format

source_name: tumor

extract_protocol:
RNA was extracted following 10x Genomics 3’ protocol.
Library were constructed following 10x Genomics 3’ protocol.

treatment_protocol: CD45+ enrichment

value: tumor

value: day 4


title: WBCminusNeu_ZT22

value: male


title: ChIPKD H3K4me1 Mesoderm Alpha-amanitin

value: Nieuwkoop Faber 10.25


title: NB1-TADA2Bdeg cells, DMSO, HA antibody, 6 hours

value: Neuroblastoma, MYCN amplified, with degraded TADA2B


title: WBCminusNeu_ZT19_replicate


title: NGP-TADA2Bdeg cells, DMSO, Input, 6 hours


title: ChIPKD H3K4me1 Endoderm Wild Type

value: untreated


title: PBS

value: PBS


title: KELLY-TADA2Bdeg cells, dTAGv1, HA antibody, 6 hours


title: Ala3 BM cells

city: Tianjin

first: junli

last: mou

address: Nanjing Road 288

institute: Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

description: Ala3 in Processed data

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

organism: Mus

source_name: BM

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: BM

value: Bone marrow cells

value: CCND2 mutation


title: Ala2 BM cells

description: Ala2 in Processed data


title: E14.5 whole lung Input ChIP-seq rep2

city: Houston

first: Dalia

last: Hassan

state: TX

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

data_processing:
Fastqc was run on the raw Fastq files to determine initial quality of reads.
Trimmomatic was performed to remove barcodes and poor quality bases.
Fastqc was run for quality control.
Bowtie alignment to the mm10 genomic with -m1 -k1 -v1 parameters and filtered for unmapped reads with sam file output
After alignment, sam files were converted to bam files and filtered for unmapped reads, chimeric alignments, low quality alignments, and PCR duplicates using Picard59 MarkDuplicates and samtools60 settings: -b -h -F 4 -F 1024 -F 2048 -q 30.
Assembly: mm10
Supplementary files format and content: .bw files can be opened with igv

source_name: lung

extract_protocol:
Whole lung ChIP-seq were performed as described in the associated paper and cell type specific ChIp-seqs were performed on chromatin from sorted nulcei based on a SunGFP reporter induced by recombination undercontrol of cell type specific Cre or CreERs.
ChIP DNA quantity was measured using the Qubit dsDNA HS Assay Kit (Invitrogen, Q32851). 2-5ng of sample DNA was used to generate sequencing libraries using the NEB Next Ultra II DNA Library Prep Kit for Illumina (NEB, E7645). Step 3.1 in the NEB protocol was skipped to improve sample retention per manufacturer’s recommendation. Samples were PCR amplified for 12 cycles and barcoded using indexing primers (New England BioLabs, E7335s or E7500S) followed by a final (.65 x -1 x bead volume) size selection and purification step using a SPRIselect reagent (Beckman Coulter, B23318). Samples were then verified for library size by gel electrophoresis and concentration measured using the Qubit HS dsDNA assay. Samples were then sequenced on the Illumina NextSeq500.

treatment_protocol: GFP labeling of AT2 cells was carried out by 250ug of Tamoxifen at P0 and 3mg of Tamoxifen 3 days before harvesting adults . CEBPA mutant were induced with Tamoxifen at the indicated timepoints

value: lung

value: whole lung

value: wild type

value: no treatment


title: WBCminusNeu_ZT19


title: Ala1 BM cells

description: Ala1 in Processed data


title: E14.5 whole lung Input ChIP-seq rep1


title: KELLY-TADA2Bdeg cells, DMSO, Input, 6 hours


title: WBCminusNeu_ZT16


title: wt3  BM cells

description: wt3 in Processed data

value: CCND2 wildtype


title: 6-wk AT2 Input rep2

value: 3mg Tamoxifen started at 5-wk every other day


title: WBCminusNeu_ZT16_replicate


title: 6-wk AT2 Input rep1


title: KELLY-TADA2Bdeg cells, DMSO, HA antibody, 6 hours

value: HA-tag (Cell Signaling Technologies, cat.# 3724)

value: spike-in antibody (Active Motif cat.#61686)


title: ChIPKD H3K4me1 Ectoderm Alpha-amanitin

value: Animal Cap (Ectoderm)

value: 5 pg Alpha-amanitin injected


title: WBCminusNeu_ZT13_replicate

value: male


title: wt2  BM cells

description: wt2 in Processed data


title: KELLY-TADA2Bdeg cells, dTAGv1, Input, 6 hours

value: Neuroblastoma, MYCN amplified, with degraded TADA2B


title: vec4 BM cells

description: vec4 in Processed data

value: Vec


title: P2 ctrl AT2 input rep2

value: 250ug Tamoxifen at P0


title: KELLY cells, CRISPR sg4 TADA2B, 7 days, replicate 2

data_processing:
RNA-Seq data analysis was performed in alignment with the ENCODE Consortium standards (https://www.encodeproject.org/chip-seq/). Quality control tests for unmapped reads were performed based on the FastQC v.0.11.9 software (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and summarized with multiQC v1.9 PMID: 27312411.  All samples except the CRISPR KO and sg LacZ at 12 days were spiked-in with the ERCC RNA Spike-In Mix1 (ThermoFisher Cat. No.: 4456740, https://tools.thermofisher.com/content/sfs/manuals/ERCC92.zip). The spiked human reads were mapped to hg38/gencode v30 and to the ERCC genome  using STAR v2.7.2b  PMID: 23104886
Quality control for the mapped reads and for replicate reproducibility were performed using SARTools v1.7.3 PMID: 27280887.
Gene level reads were summarized by counting the reads that overlapped the hg38/gencode v30 gene exons and separately the ERCC annotated genes, by using the featureCounts v1.6.3 method implemented in the Subread v2.0.0 package (http://subread.sourceforge.net) PMID: 24227677. The erccdashboard R package PMID: 25254650 available from Bioconductor v3.9  was used to estimate the ERCC spiked-in variability in transcriptional performance.
Gene counts were normalized and used to quantify the differential genes between the experimental and control conditions using DESeq2 v1.32.0 PMID: 25516281. Gene expression was estimated based on the log2(TPM+1) scores for normalized reads PMID: 34158060. The expressed genes were identified as the genes with  maximum log2(TPM+1)  expression ≥ 1 across all conditions.
The gene differentiability was assessed with DESeq2 based on the robust shrunken log2 fold change scores  and  the approximate posterior estimation for GLM coefficients (apeglm v1.6)  method for effect size PMID: 25516281. The cutoffs for gene differentiability were |fold change expression| ≥ 1.5 and adj P-value ≤ 0.10.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts and log2(TPM+1) values for each sample.

extract_protocol:
RNeasy PLUS Mini Kit from Qiagen (cat #74134)
Illumina TruSeq Stranded Total RNA Library Prep. Preparation of RNA library followed by 2x150 nt paired sequencing was performed by Novogene Co., LTD for all samples, except the day 12 samples.  For the day 12 samples the preparation of RNA library followed by 2x75 nt paired sequencing was performed at the  MD Anderson Science Park Next-Generation Sequencing Facility.

value: KELLY

value: neuroblastoma cell line

value: TADA2B knocked out

value: Day 7


title: P2 ctrl AT2 input rep1

value: lung


title: vec2 BM cells

description: vec2 in Processed data

value: BM

value: Bone marrow cells


title: KELLY cells, CRISPR sg4 TADA2B, 7 days, replicate 1


title: P8 mutant AT2 input rep2

value: CebpaCKO/CKO; SftpcCreER/+;Sun1GFP/+

value: 250ug Tamoxifen at P2


title: KELLY cells, CRISPR sg2 TADA2B, 7 days, replicate 3


title: P8 mutant AT2 input rep1


title: WBCminusNeu_ZT13


title: vec1 BM cells

description: vec1 in Processed data


title: KELLY cells, CRISPR sg4 TADA2B, 7 days, replicate 3


title: KELLY cells, CRISPR sg2 TADA2B, 7 days, replicate 2


title: KELLY cells, CRISPR sg2 TADA2B, 7 days, replicate 1


title: P8 ctrl AT2 input rep2

value: CebpaCKO/+; SftpcCreER/+;Sun1GFP/+


title: P8 ctrl AT2 input rep1


title: wt4  BM cells

description: wt4 in Processed data

value: CCND2 wildtype


title: KELLY cells, CRISPR LACZ, 7 days, replicate 3

value: WT


title: KELLY cells, CRISPR LACZ, 7 days, replicate 2


title: Daphnia_magna_7bodyparts_barcoded_rep4

city: Johnson City

first: Lev

middle: Y

last: Yampolsky

state: Tennessee

address: 811 Lazywood Dr

department: Biological sciences

institute: East Tennessee State University

description: barcodes: bc01=Hemocytes; bc02=Eggs; bc03=Gut; bc04=Antenna; bc05=Head; bc06=Carapace; bc07=Carcass (Body)

data_processing:
basecalling: guppy basecaller
demultiplexing: guppy barcoder
alignment: guppy alighner
bam indexing and read count extraction: samtools
downstream analysis: DESeq2
Assembly: Daphnia magana Xinb3, BioProject ID: PRJNA624896
Supplementary files format and content: xlsx
Supplementary files format and content: Columns: replicate, barcode ID, anatomical feature, transcript ID, reads count, RPKM

organism: Daphnia magna

source_name: whole body

growth_protocol: Daphnia were grown in ADaM medium (20 mL per adult Daphnia) at 20C and fed daily with Scendesmus acutus cultures at the concentration of 1E5 cells/mL

extract_protocol:
Zymo Research Miniprep kit
ONT Ligation cDNA seq protocol

treatment_protocol: standard Daphnia lab protocol

value: whole body

value: 7bodyparts, barcoded


title: Daphnia_magna_7bodyparts_barcoded_rep7


title: Daphnia_magna_7bodyparts_barcoded_rep3


title: KELLY cells, CRISPR LACZ, 7 days, replicate 1


title: 7-wk mutAT2 input rep2

value: 3mg Tamoxifen started at 5-wk every other day


title: KELLY cells, dTAG v1 TADA2B, 72 hours, replicate 3

value: TADA2B degraded

value: 72 hours


title: 7-wk ctrl AT2 input rep1


title: E14.5 whole lung NKX2-1 ChIP-seq rep2

value: whole lung

value: wild type

value: no treatment


title: SS_3M_WT_AD_E1

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

description: Fresh frozen Stereo-seq spatial transcriptome sequencing

data_processing:
The Stereo-seq raw data processing was performed as described using the publicly available SAW pipeline (https://github.com/BGIResearch/SAW). In brief, fastq files were generated using a MGI DNBSEQ-Tx sequencer. CID sequences (1-25 bp) on the first reads were first mapped to the designed coordinates of the in situ captured chip, allowing 1 base mismatch. Low quality reads were filtered out, and retained reads were aligned to the mm10 reference genome using STAR. Mapped reads with MAPQ > 10 were counted and annotated to their corresponding genes. UMIs with the same CID and the same gene locus were collapsed, again allowing 1 base mismatch, resulting in a CID-containing expression profile matrix. Gem files specifying the X/Y coordinates and MID count for every DNB were read in using stereopy’s read_gem() (https://github.com/BGIResearch/stereopy) to generate both a bin20 expression matrix (with argument bin_size = 20) and a cell_bin expression matrix (argument bin_type = ‘cell_bins’).
Assembly: mm10
Supplementary files format and content: bin1_max.gem: GEM formatted counts file including X/Y coordinates
Supplementary files format and content: aligned_ssDNA.tif: ssDNA staining image aligned to transcriptomics coordinate space
Supplementary files format and content: PlaqueSegmentation_Binary_Aligned.png: segmented amyloid plaque staining on adjacent section, aligned to transcriptomic space
Supplementary files format and content: barcodeToPos.h5: Stereo-seq mask file
Supplementary files format and content: StereoSeq_mouse_combined.h5ad: filtered and annotation count matrices (.X: normalized, .layers['counts']: raw) for all cells passing QC

source_name: brain

extract_protocol:
Brains were dissected and immediately snap-frozen in isopentane chilled with liquid nitrogen and stored at -80°C. 10μm coronal sections were cut using a cryostat, adhered to the Stereo-seq chip, and incubated at 37°C for 3 minutes. Immediately adjacent slides were collected for staining. The sections were fixed in methanol for 30 minutes at -20°C. The middle sections were then stained for ssDNA and imaged to obtain nuclei location information.  Tissue optimization was performed using the Stereo-seq Permeabilization kit according to the manufacturer’s protocol. Tissue sections were  permeabilized for 12 minutes and reverse transcription was performed overnight at 42°C.
The recovered cDNA was amplified and a total of 20ng was fragmented for library construction. PCR products were purified and sequenced on a MGI DNBSEQ-Rx sequencer.
Stereo-seq Spatial Transcriptomics
Adjacent slides from the Stereo-seq experiments were stained using a standard IHC protocol to visualize reactive astrocytes and amyloid-β plaques. In brief, after fixation with 4% paraformaldehyde for 10 minutes and 90 minutes incubation with a blocking solution (5% donkey serum and 0.5% Triton X, in PBS) at room temperature, the tissue sections were incubated with GFAP antibody and anti-amyloid-β 3-8 (6E10) antibody conjugated with fluorophore Alexa 488 overnight at 4°C. The following day, sections were incubated with appropriate secondary antibodies (Goat anti-Guinea Pig Alexa 568) for 90 minutes at room temperature. After five wash steps, autofluorescence was quenched by treating sections for 30 seconds. with 1x TrueBlack solution diluted in 70% ethanol. Afterwards, the sections were rinsed by dipping the slides 20x in PBS. Nuclei were visualized by incubating the sections with DAPI staining for 15 minutes at room temperature. Sections were rinsed in SSC buffer, before 100 µl glycerol was added and a coverslip was applied. 16-bit fluorescent images of DAPI, 6E10, and GFAP were acquired on a Zeiss Axioscan.Z1 slidescanner, with a 20x/0.8 NA air objective using the ZEN blue software (version 3.1, Carl Zeiss Microscopy GmbH). Different FOV were stitched together using the online stitching configuration in the software.

value: brain

value: APP-NLGF &  C57BL/6J


title: SS_WT18_F5


title: E14.5 whole lung NKX2-1 ChIP-seq rep1

value: lung


title: KELLY cells, dTAG v1 TADA2B, 72 hours, replicate 2

value: KELLY

value: neuroblastoma cell line


title: PANC-1 cell - ShCTRL - Rep4

type: RNA

city: Toulouse

first: jerome

last: torrisani

address: 2 avenue Hubert Curien

country: France

institute: inserm

description: Biological replicate 4 of 4.PANC-1 ShControl

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE v2 microarray (8X60K, Design 039494) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 039494_D_F_20120628). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 7 out of 8 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 34483 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 28273 rows each corresponding to a unique ProbeName.

source_name: Pancreatic cancer-derived PANC-1 cell line

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: PANC-1 cells were grown in DMEM (1g/L Glucose) medium  supplemented with 10% Fetal calf serum, L-Glutamine and antibiotics

extract_protocol: Total RNAs were extracted using Trizol following manufacturer's instructions

treatment_protocol: No treatment. cells were harvested in exponential growth phase

value: PANC-1 ATCC CRL-1469

tag: shRNA

value: ShCTRL


title: PANC-1 cell - ShTRIP12 - Rep4

description: Biological replicate 4 of 4. PANC-1 ShTRIP12


title: PANC-1 cell - ShTRIP12 - Rep3

description: Biological replicate 3 of 4. PANC-1 ShTRIP12


title: SS_AD18_E4

value: APP-NLGF


title: PANC-1 cell - ShTRIP12 - Rep1

description: Biological replicate 1 of 4. PANC-1 ShTRIP12


title: P8 mutant  AT2 cell NKX2-1 ChIP-seq rep2

value: CebpaCKO/CKO; SftpcCreER/+;Sun1GFP/+

value: 250ug Tamoxifen at P2

tag: chip antibody


title: KELLY cells, DMSO, 72 hours, replicate 3

value: WT


title: P8 mutant  AT2 cell NKX2-1 ChIP-seq rep1


title: PANC-1 cell - ShTRIP12 - Rep2

description: Biological replicate 2 of 4. PANC-1 ShTRIP12


title: PANC-1 cell - ShCTRL - Rep3

description: Biological replicate 3 of 4. PANC-1 ShControl


title: HRP2-KO44

first: Zhiqiang

last: Liu

address: 22 Qixiangtai Rd

department: Pathophysiology

institute: Tianjin Medical University

data_processing:
Basecalls performed using DNBSEQ-G400
Mapping clean reads to Mus_musculus whole genome using BWA.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include fpkm values for each Sample

source_name: bone marrow

growth_protocol: BMSCs were cultured in αMEM medium with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard BGI protocols

value: bone marrow

value: BMSC


title: PANC-1 cell - ShCTRL - Rep2

description: Biological replicate 2 of 4.PANC-1 ShControl


title: SS_3M_WT_AD_E2


title: P8 control AT2 cell NKX2-1 ChIP-seq rep2

value: CebpaCKO/+; SftpcCreER/+;Sun1GFP/+


title: PANC-1 cell - ShCTRL - Re1

description: Biological replicate 1 of 4.PANC-1 ShControl


title: KELLY cells, DMSO, 72 hours, replicate 2

value: 72 hours


title: KELLY cells, dTAG v1 TADA2B, 72 hours, replicate 1

value: TADA2B degraded


title: 7-wk mutant AT2 cell NKX2-1 ChIP-seq rep2

value: 3mg Tamoxifen started at 5-wk every other day


title: HRP2-KO7


title: MiaPACA-2 cell - ShCTRL - Rep1

description: Biological replicate 1 of 4. MiaPACA-2 ShControl

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 039494_D_F_20120628). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 7 out of 8 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 33001 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 27158 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Pancreatic cancer-derived MiaPACA-2 cell line

growth_protocol: MiaPACA-2 cells were grown in DMEM (4.5g/L Glucose) medium  supplemented with 10% Fetal calf serum, L-Glutamine and antibiotics

value: MiaPACA-2 ATCC® CRL-1420


title: P8 control AT2 cell NKX2-1 ChIP-seq rep1


title: KELLY cells, DMSO, 72 hours, replicate 1


title: MiaPACA-2 cell - ShTRIP12 - Rep4

description: Biological replicate 4 of 4. MiaPACA-2 ShTRIP12


title: HRP2-KO6


title: KELLY cells, dTAG v1 TADA2B, 24 hours, replicate 2

value: 24 hours


title: WT12


title: SS_AD18_E3

value: brain


title: 7-wk mutant AT2 cell NKX2-1 ChIP-seq rep1

value: lung


title: MiaPACA-2 cell - ShTRIP12 - Rep3

description: Biological replicate 3 of 4. MiaPACA-2 ShTRIP12


title: 7-wk control AT2 cell NKX2-1 ChIP-seq rep2


title: KELLY cells, dTAG v1 TADA2B, 24 hours, replicate 1

value: KELLY

value: neuroblastoma cell line


title: WT10


title: 7-wk control AT2 cell NKX2-1 ChIP-seq rep1


title: KELLY cells, dTAG v1 TADA2B, 24 hours, replicate 3


title: MiaPACA-2 cell - ShCTRL - Rep2

description: Biological replicate 2 of 4. MiaPACA-2 ShControl

value: ShCTRL


title: KELLY cells, CRISPR sg5 TADA2B, 12 days, replicate 3

value: TADA2B knocked out

value: Day 12


title: WT BMDM,induced, batch3

city: Los Angeles

first: Kai

last: Li

address: 8700 Beverly Boulevard

institute: Cedar-Sinai Medical Center

data_processing:
Sequencing data were analyzed using nf-core/rnaseq bioinformatics pipeline (v3.11.1) under default parameters with STAR-Salmon alignment and quantification
Low abunance genes were filtered out (ensure at least 3 samples with a count of 10 or more)
DESeq2(v1.34.0) was used to conduct differential gene expression analysis
Assembly: mm10
Supplementary files format and content: TSV files containing the normalized gene counts exported from the DESeq2 analysis

source_name: Bone marrow-derived macrophage

extract_protocol:
RNA was extracted using the RNeasy plus mini kit (Qiagen) following the manufacturer’s protocol.
Library construction on the DNBseq platform includes fragmentation, size selection, end repair and A-tailing, adaptor ligation, PCR amplification, and splint circularization

treatment_protocol: BMDM were treated with w/oIAA (RPL20B-sufficient) or induced (RPL20B-depleted) yeast at MOI=5 for 4h.

value: Bone marrow-derived macrophage

value: wild-type

value: GM-CSF-primed


title: WT BMDM,induced, batch2


title: KELLY cells, CRISPR sg5 TADA2B, 12 days, replicate 2


title: P2 AT2 cell NKX2-1 ChIP-seq rep1

value: 250ug Tamoxifen at P0


title: MiaPACA-2 cell - ShTRIP12 - Rep1

description: Biological replicate 1 of 4. MiaPACA-2 ShTRIP12


title: MiaPACA-2 cell - ShTRIP12 - Rep2

description: Biological replicate 2 of 4. MiaPACA-2 ShTRIP12


title: KELLY cells, DMSO, 24 hours, replicate 1

value: WT


title: WT BMDM,induced, batch1


title: MiaPACA-2 cell - ShCTRL - Rep4

description: Biological replicate 4 of 4. MiaPACA-2 ShControl


title: KELLY cells, CRISPR sg5 TADA2B, 12 days, replicate 1


title: 6-wk AT2 cell CEBPA ChIP-seq rep3

value: 3mg Tamoxifen at 5-wk

value: CEBPA(D56F10XP, Cell Signalling)


title: KELLY cells, dTAG v1 TADA2B, 6 hours, replicate 3

value: TADA2B degraded

value: 6 hours


title: WT11

value: bone marrow

value: BMSC


title: KELLY cells, DMSO, 24 hours, replicate 3

value: 24 hours


title: KELLY cells, CRISPR sg4 TADA2B, 12 days, replicate 3

value: KELLY


title: WT BMDM,w/oIAA, batch2


title: 6-wk AT2 cell CEBPA ChIP-seq rep2

value: lung


title: P2 AT2 cell NKX2-1 ChIP-seq rep2


title: 6-wk AT2 cell CEBPA ChIP-seq rep1


title: KELLY cells, CRISPR sg4 TADA2B, 12 days, replicate 2

value: neuroblastoma cell line


title: KELLY cells, dTAG v1 TADA2B, 6 hours, replicate 2


title: KELLY cells, dTAG v1 TADA2B, 6 hours, replicate 1


title: WT BMDM,w/oIAA, batch1


title: KELLY cells, CRISPR sg4 TADA2B, 12 days, replicate 1

value: TADA2B knocked out


title: WT BMDM,unstimulated, batch3


title: KELLY cells, DMSO, 6 hours, replicate 3


title: P2 AT2 cell CEBPA ChIP-seq rep3


title: KELLY cells, DMSO, 24 hours, replicate 2


title: KELLY cells, CRISPR LACZ, 12 days, replicate 3

value: Day 12


title: WT BMDM,unstimulated, batch2

value: Bone marrow-derived macrophage


title: P2 AT2 cell CEBPA ChIP-seq rep2


title: KELLY cells, CRISPR LACZ, 12 days, replicate 2


title: WT BMDM,w/oIAA, batch3

value: wild-type


title: KELLY cells, DMSO, 6 hours, replicate 1


title: P2 AT2 cell CEBPA ChIP-seq rep1


title: KELLY cells, CRISPR LACZ, 12 days, replicate 1


title: WT BMDM,unstimulated, batch1

value: GM-CSF-primed


title: OFE 6

status: Public on Apr 18 2024

city: Pamplona

first: SERGIO

last: ROA

address: Irunlarrea, 1

department: Biochemistry and Genetics

country: Spain

institute: University of Navarra

data_processing:
After 24 h, a total of 398,221 nanopore reads in two pooled runs were obtained for the 11 individual samples of this study, with a median long-read length of 1.59 kb, consistent with the expected 16S rRNA size. Data acquisition, real-time analysis, base-calling, and data transmission of FASTQ files was operated using the MinKNOW (v22.10.7) operating software on the MinION-Mk1C sequencing device. The cloud-based EPI2ME Fastq 16S (v2023.04.21) algorithm was used for analytical workflow of 16S rRNA FASTQ files, including alignment and classification of reads into operational taxonomic units (OUT) to the species level, according to the NCBI 16S rRNA reference sequence database (containing over 26,000 curated type strain sequences of 16S rRNA from bacteria and archaea).
Assembly: 16S RefSeq
Supplementary files format and content: EPI2ME output files 16S: classification_16s_barcode.csv
Library strategy: long-read sequencing of 16S rRNA gene

organism: mouse gut metagenome

source_name: murine feces

extract_protocol:
Murine fecal samples were collected for bacterial genomic DNA extraction using the centrifugal affinity column system in the PureLink Microbiome DNA Purificaction Kit (Invitrogen), according to the manufacturer's instructions. Quantity and purity of the extracted genomic DNA were evaluated with a Thermo Scientific NanoDrop and stored at -20ºC until used.
For long-read sequencing of 16S rRNA gene, 10ng of total genomic DNA were subjected to library construction using the 16S barcoding kit (SQK-16S024) according to Oxford Nanopore Technologies (ONT) protocol. Specifically, bacterial DNA was amplified using barcoded universal 16S primers (27F and 1492R) supplied by ONT with 5’-tags that facilitate the ligase-free attachment of rapid sequencing adapters required during nanopore library preparation. The barcoded libraries were loaded and sequenced on MinION flow cells (FLO-MIN106D R9.4.1; ONT) using the MinION-Mk1C instrument (ONT)

treatment_protocol: Fecal pellets were collected from 52 weeks-old female mice were pooled, mixed and homogenized in PBS at concentration at 1 g feces/10mL PBS (Day 0). Mixture was centrifuged at 500 rpm for 5 min at 4◦C and supernatants were collected and used for fecal microbiota transplantation (FMT). Fifty-two weeks-old male mice were treated with a high-dose of an antibiotics cocktail (ABx) before FMT (Day 1). ABx was prepared in sterile H2O at the following concentration: ampicillin (1 mg/ml), vancomycin (5 mg/ml), streptomycin (10 mg/ml), and metronidazole (10 mg/ml). This antibiotics cocktail combines b-lactam (ampicillin), glycopeptide (vancomycin), aminoglycoside (streptomycin) and nitroimidazole (metronidazole) antibiotics and was proved sufficient to decrease mouse gut microbial load within hours targeting against the full spectrum of bacteria including both gram positive (ampicillin and vancomycin) and gram negative (ampicillin and neomycin) strains. Each 52 weeks-old male mice received 150 μL of the supernatant by oral gavage once a day continuously for 3 days (Days 2–4). Acute intoxication with ethanol was performed 15 days after the FMT (Day 19) across all groups (female/OFE, male/OME and male+FMT/OME+FMT). Specifically, mice were fasted at night for 12 hours before they were fed in the morning with one oral dose of 30% EtOH (gavage 6 g/kg body weight) with a gavage needle (Kent Scientific, Torrington CT). Feces were collected 8 hours after EtOH challenge and submitted to microbiota analysis.

tag: mouse strain

value: 52-week old

value: female

value: EtOH

value: murine feces

tag: run id

tag: barcode


title: OME 17 + FMT

value: male

value: FMT + EtOH


title: OFE 7


title: OME 16 + FMT


title: Pat 91-FU

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data) .
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 104) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner) .
Aligned reads were filtered to remove: duplicates with Picard 2.27.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads .
Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features) .
The raw count matrix was normalized with DESeq2 version 1.30.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2) .
Contrasts were created with DESeq2 based on the raw count matrix .
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

source_name: myocardial interventricular septum biopsy

extract_protocol:
RNA isolation was performed with Qiagen miRNeasy micro Kit and Covaris Cryo-Prep homogenization.
100ng-1µg total RNA was used for Hi-Mammalian whole transcriptome preparation (Takara Bio). Sequencing was performed on Nextseq2000 with 1x72bp single-end setup.

tag: disease state

value: CTEPH

tag: individual

value: Male

value: postPEA


title: Pat 72-FU

value: myocardial interventricular septum biopsy

tag: Sex


title: OFE 5

tag: age


title: Pat 75-FU


title: OFE 4


title: Pat 33-FU


title: Pat 89-FU


title: Pat 100-FU


title: Pat 88-FU

value: Female


title: Pat 95-FU


title: OME 15


title: OME 14


title: Pat 86-FU


title: Pat 83-FU


title: OME 11 + FMT


title: Pat 15-FU


title: Pat 77-FU


title: KELLY cells, DMSO, 6 hours, replicate 2

value: KELLY

value: neuroblastoma cell line

value: WT

value: 6 hours


title: Pat 3-FU


title: Pat 56-FU


title: Pat 65-FU


title: OME 12


title: Pat 42-FU


title: Pat 14-FU


title: Pat 49-FU


title: Pat 1-FU


title: OME 13


title: Pat 94-BL

source_name: Right ventricular myocardial free wall biopsy

tag: esc risk group

value: Moderate

value: prePEA


title: Pat 37-BL

value: Right ventricular myocardial free wall biopsy


title: Pat 9-FU


title: Pat 96-FU


title: Pat 70-BL


title: Pat 91-BL

value: Intermediate


title: Pat 72-BL

value: Severe


title: Pat 75-BL


title: MiaPACA-2 cell - ShCTRL - Rep3

description: Biological replicate 3 of 4. MiaPACA-2 ShControl

value: MiaPACA-2 ATCC® CRL-1420

value: ShCTRL


title: Pat 50-FU


title: Pat 20-BL


title: Pat 17-BL


title: Pat 65-BL


title: Pat 31-BL


title: Pat 31-FU


title: Pat 100-BL


title: Pat 54-FU


title: Pat 36-BL


title: Pat 88-BL


title: Pat 95-BL


title: Pat 23-BL


title: Pat 87-BL


title: Pat 86-BL


title: Pat 89-BL


title: Pat 73-BL


title: Pat 33-BL


title: Pat 53-BL


title: Pat 68-BL


title: Pat 15-BL


title: Pat 64-BL


title: Pat 77-BL


title: Pat 30-BL


title: Pat 7-BL


title: Pat 28-BL


title: Pat 63-BL


title: Pat 85-BL


title: Pat 56-BL


title: Pat 3-BL


title: Pat 47-BL


title: Pat 59-BL


title: Pat 49-BL


title: Pat 18-BL


title: Pat 8-BL


title: Pat 1-BL


title: Pat 41-BL


title: Pat 61-BL


title: Pat 60-BL


title: Pat 50-BL


title: Pat 6-BL


title: Pat 48-BL


title: Pat 2-BL


title: Pat 34-BL


title: FACS Astrocytes, LPS Injected, KO, rep3

city: Suita

first: Koki

last: Sakurai

state: Osaka

address: Yamadaoka 3-2

department: Institute for Protein Research

country: Japan

institute: Osaka University

description:
198_LPS_Ast
Ast_STAR_genes_count_matrix.tsv
198_KO_AST
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio)

data_processing:
Sequenced reads were mapped to the mouse reference genome (NCBI-RefSeq - GCF_000001635.27_GRCm39) using STAR 2.7.10b. RSEM-1.3.3 was used to calculate gene counts for each gene based on number of reads. Differential expression analysis of each gene was performed on the TCC-GUI platform using TMM-Voom for calculation of differentially expressed genes .
Assembly: NCBI-RefSeq - GCF_000001635.27_GRCm39
Supplementary files format and content: tsv file of raw count values generated by STAR

source_name: Astrocytes sorted from whole brain

extract_protocol:
Total RNA was extracted from cells with an miRNeasy Mini kit (Qiagen) according to the manufacturer’s instructions.
Library preparation and sequencing was performed at the NGS core facility at the Research Institute for Microbial Diseases of Osaka University. Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina) according to SMARTer kit instructions.

treatment_protocol: Adult mouse whole brain was minced, digested, and processed into cell suspensions using an Adult Brain Dissociation Kit and gentleMACS™ Octo Dissociator with Heaters (both Miltenyi Biotec). Glial cell populations (Microglia, Astrocytes) were sorted from cell suspension by  FACS (used for RNAseq).

value: Astrocytes sorted from whole brain

tag: cell type

value: Astrocytes

value: KPNA4 KO

value: LPS i.p.


title: Pat 97-BL

value: CTEPH

value: Male


title: Pat 66-BL


title: Pat 44-BL


title: P17OIR_2

city: Fukui

first: Kengo

last: Nakanishi

address: 3-9-1 Bunkyo,Fukui

department: Applied Chemistry & Biotechnology

institute: University of Fukui

description: SAMPLE 6

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. • Transfer 130μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm • Fluidics washing is FS450_0002

scan_protocol: Gene ChIP Scanner 3000 7G System

data_processing: Data were processed using R. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

label: Biotin

source_name: retina, oxygen-induced retinopathy(OIR)

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: oxygen-induced retinopathy(OIR) Seven-day-old mice were grown in 75% oxygen for 5 days and then housed in air.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Vitreous injection was performed immediately after the end of hyperoxia.

value: retina

tag: strain

tag: condition

value: oxygen-induced retinopathy(OIR)


title: FACS Astrocytes, LPS Injected, KO, rep1

description:
194_LPS_Ast
Ast_STAR_genes_count_matrix.tsv
194_KO_AST
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio)

tag: genotype


title: Pat 57-BL

tag: tissue

value: Female


title: AGS HP+, biological rep3

city: Chongqing

first: yuan

last: zhuang

address: Gaotanyan Street

institute: Third Military Medical University

description: Gene expression data from WT H. pylori-infected AGS cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: WT H. pylori-infected AGS cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: AGS cells were cultured in complete RPMI 1640 medium supplemented with 10% FBS in a humidified environment containing 5% CO2 at 37 °C.

treatment_protocol: AGS cells were infected with WT H. pylori at a multiplicity of infection (MOI) of 100 for 6 h.

value: AGS cells

tag: treatment

value: H. pylori-infected


title: AGS HP+, biological rep1


title: P7Control_2

description: SAMPLE 8

source_name: retina, untreated

value: untreated


title: P17OIR+ISOX DUAL_2

description: SAMPLE 2

source_name: retina, oxygen-induced retinopathy(OIR), Inhibitor (ISOX DUAL)


title: P17OIR+ISOX DUAL_1

description: SAMPLE 1

value: oxygen-induced retinopathy(OIR), Inhibitor (ISOX DUAL)


title: FACS Astrocytes, LPS Injected, WT, rep3

description:
204_LPS_Ast
Ast_STAR_genes_count_matrix.tsv
204_WT_AST
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio)

value: WT


title: P17Control_2

description: SAMPLE 5


title: P17OIR+PBS_1

description: SAMPLE 9

source_name: retina, oxygen-induced retinopathy(OIR), PBS (Intravitreal administration)


title: Pat 92-BL

value: Right ventricular myocardial free wall biopsy

value: Severe

value: prePEA


title: P17OIR+PBS_2

description: SAMPLE X

value: oxygen-induced retinopathy(OIR), PBS (Intravitreal administration)


title: FACS Astrocytes, LPS Injected, WT, rep2

description:
197_LPS_Ast
Ast_STAR_genes_count_matrix.tsv
197_WT_AST
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio)

value: Astrocytes sorted from whole brain

value: Astrocytes


title: Pat 79-BL

value: Moderate


title: AGS HP+, biological rep2


title: Pat 62-BL

value: CTEPH

value: Intermediate


title: Pat 43-BL


title: P17OIR_1

description: SAMPLE 4

value: retina


title: FACS Astrocytes, LPS Injected, WT, rep1

description:
195_LPS_Ast
Ast_STAR_genes_count_matrix.tsv
195_WT_AST
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio)

value: LPS i.p.


title: AGS HP N, biological rep2

description: Gene expression data from uninfected AGS cells

source_name: Uninfected AGS cells

value: uninfected


title: P17Control_1

description: SAMPLE 3


title: Pat 5-BL

value: Male


title: P7Control_1

description: SAMPLE 7


title: AGS HP N, biological rep1

value: AGS cells


title: Pat 25-BL


title: FACS Microglia, LPS Injected, KO, rep3

description:
198_LPS_MG
MG_STAR_genes_count_matrix.tsv
198_KO_MG
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio)

source_name: Microglia sorted from whole brain

value: Microglia sorted from whole brain

value: Microglia

value: KPNA4 KO


title: UVS1_3

city: Zhanjiang

first: Wei

last: Feng

address: 236 Yuanzhu Road

institute: Central People's Hospital of Zhanjiang

data_processing:
Raw data (raw reads) of fastq format were processed with Fastp (v 0.23.0), an ultra-fast FASTQ preprocessor with useful quality.
The clean reads were mapped to the mus musculus genome (mm10) using the HISAT2 software (v 2.1.0).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript.
The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: skull

growth_protocol: The mouse brain, meninges and skullcap samples were harvested 0.5 h and 24 h after irradiating the mouse interparietal bone of skullcap with UVB (311 nm, 2 mW) was done.

extract_protocol:
TRIzol Reagent (Thermo Fisher Scientific Inc.) was used to extract total RNA of the samples. NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA) was used to isolate the mRNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The skullcap was wished with the cold PBS to clean the blood. The meninges were scraped from the skullcap in cold RNAlater (AM7020, Thermo Scientific), and the samples were snap frozen immediately at -80 °C, until further use.

value: skull

value: 24 h after photobiomodulation of the skull


title: UVS1_2


title: Pat 96-BL

value: Right ventricular myocardial free wall biopsy

value: Female

value: prePEA


title: Pat 78-BL


title: Pat 14-BL


title: Pat 46-BL


title: FACS Microglia, LPS Injected, KO, rep2

description:
196_LPS_MG
MG_STAR_genes_count_matrix.tsv
196_KO_MG
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio)


title: FACS Microglia, LPS Injected, KO, rep1

description:
194_LPS_MG
MG_STAR_genes_count_matrix.tsv
194_KO_MG
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio)


title: UVS1_1


title: Pat 74-BL


title: UVM1_3

source_name: meninges

value: meninges


title: FACS Microglia, LPS Injected, WT, rep3

description:
204_LPS_MG
MG_STAR_genes_count_matrix.tsv
204_WT_MG
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio)

value: WT


title: Pat 27-BL

value: CTEPH

value: Severe


title: Pat 24-BL

value: Intermediate


title: UVM1_2


title: FACS Microglia, LPS Injected, WT, rep2

description:
197_LPS_MG
MG_STAR_genes_count_matrix.tsv
197_WT_MG
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio)

value: LPS i.p.


title: Pat 38-BL


title: Pat 35-BL

value: Moderate


title: UVM1_1


title: FACS Astrocytes, LPS Injected, KO, rep2

description:
196_LPS_Ast
Ast_STAR_genes_count_matrix.tsv
196_KO_AST
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio)

value: Astrocytes sorted from whole brain

value: Astrocytes


title: FACS Microglia, LPS Injected, WT, rep1

description:
195_LPS_MG
MG_STAR_genes_count_matrix.tsv
195_WT_MG
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio)

value: Microglia sorted from whole brain


title: Pat 22-BL


title: UVB1_3

source_name: brain

value: brain


title: Pat 42-BL


title: Pat-33-FU

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 104) with STAR 2.7.9a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.25.5 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows raw gene counts.

extract_protocol:
RNA was isolated using the miRNeasy micro Kit (Qiagen) and Covaris Cryo-Prep homogenization. To avoid contamination by genomic DNA samples were treated by on-column DNase digestion (RNase-Free DNase Set, Qiagen). Total RNA and library integrity were verified on LabChip Gx Touch 24 (Perkin Elmer).
Approximately 100ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry with 1x75bp single end setup or NextSeq2000 using P2 flowcell with v3 chemistry with 1x72bp single-end setup.

value: myocardial interventricular septum biopsy

value: Male

value: postPEA


title: Pat-91-FU


title: Pat-72-FU


title: UVB1_2

value: 24 h after photobiomodulation of the skull


title: Pat-72-preBL

value: pre-septal-PEA


title: UVS0_3

value: skull

value: 0.5 h after photobiomodulation of the skull


title: Pat-33-preBL


title: UVS0_2


title: SCAF3092_Fezf2_fl_B5t_iCre

city: Bethesda

first: Michael

middle: C

last: Kelly

state: MD

address: 41 Center Drive

department: Center for Cancer Research

institute: NCI

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10

source_name: Thymic epithelial cells

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains a partial Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Thymic epithelial cells

value: Floxed Fezf2; B5t-iCre-positive


title: Patient_6

first: Guillermo

last: Serrano

state: Navarra

address: Av. de Pío XII, 55

institute: CIMA - Universidad de Navarra

description: Treated with Lenalidomide, Complete Cytogenetic Response with 0% del(5q)

data_processing:
Demultiplexing, alignment to the hg38 genome and quantification was carried out with Cellranger (v3.1)
Posterior analysis (quality control, clustering, integration and differential expression) was performed with Seurat v4.2
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files, containing the name of genes, barcodes and raw counts.
Supplementary files format and content: Tab-separated values files, containing the annotation of the cells having passed the QC and the presence or absence of the deletion of the 5q region.

source_name: Bone Marrow

extract_protocol:
Cells were sorted by FACS based on the presence of CD34 from bone marrow aspirates.
Single cell 3’ RNA sequencing libraries were prepared using the chromiun controller from 10X Genomics. NEXTGEM Single Cell 3' Reagent Kits v3 and v3.1  were used

value: Bone Marrow

tag: cell line

value: Tissue


title: UVM0_3

value: meninges


title: UVS0_1


title: Patient_5

description: Treated with Lenalidomide, Partial Cytogenetic Response with 50% del(5q)


title: SCAF3091_Fezf2_fl_B5t_wt

description: 10x Genomics

value: Floxed Fezf2; Cre-negative


title: Patient_7

description: Treated with Lenalidomide, Non responder with 100% del(5q)


title: SCAF3090_Fezf2_fl_FoxN1_Cre

description: 10x Genomics

value: Floxed Fezf2; FoxN1-Cre-positive


title: Patient_4

description: Diagnosed with 30% del(5q)

value: Diagnosed with 30% del(5q)


title: AGS HP N, biological rep3

value: AGS cells

value: uninfected


title: UVB1_1

value: brain


title: UVM0_2


title: Pat 54-BL

value: Right ventricular myocardial free wall biopsy

value: CTEPH

value: Intermediate

value: Female

value: prePEA


title: Pat-91-preBL

value: myocardial interventricular septum biopsy

value: Male

value: pre-septal-PEA


title: UVM0_1

value: 0.5 h after photobiomodulation of the skull


title: Pat 32-BL


title: UVB0_3


title: Pat 40-BL

value: Moderate


title: Group B SCC

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description:
A total of 2 micro gram of extracted total RNA from the pooled samples in each disease category was prepared and 250 ng of this was labelled with a 3D-Gene miRNA labelling kit (Toray) followed by hybridizing onto 3D-Gene Human miRNA Oligo chips (Toray).
SCC

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

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

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

source_name: Serum collected from the patient

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

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

value: Pooled serum from 13 patients with SCC


title: Pat 67-BL


title: Antibody_2 treated

city: Minneapolis

first: Jesse

middle: W

last: Williams

state: MN

address: 2101 6th St. SE

department: Dept. Integrative Biology & Physiology

institute: University of Minnesota

description: GEX

data_processing:
10x formated output files for GEX were generated using cellranger
Further analysis was performed using Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz.gz, features.tsv.gz.gz, matrix.mtx.gz.gz

source_name: Aorta

extract_protocol:
Whole aorta was dissociated for scRNAseq.
Library was generated according to Chromium Single Cell 3ʹ v3 protocol (10x Genomics).

value: Aorta

value: Isotype Control


title: UVB0_2


title: Antibody_1 treated

description: GEX

value: Anti-Trem2 (AL002a)


title: UVB_skull

data_processing:
Downstream analysis was performed with R-package Seurat v4.3.0 using R v4.3.1. Low-quality cells and cell doublets were removed by filtering cells with few genes (<200), high number of genes (>5000) and high mitochondrial percentages (>20%) for each sample separately. After quality control the total remaining cell numbers used for further analysis were 27,018 brain cells, 27,353 meninges cells and on 22,937 skull bone marrow cells. (Supplementary Table 1). Filtered data were subjected to a recently described approach with reference-based mapping pipeline called Azimuth with default parameters. Azimuth provides well-curated cell reference map that input a count matrix and performs normalization, visualization, cell annotation and differential expression. For the mouse brain cell annotation, we used Azimuth provided mouse brain cell reference. For the mouse meninge and skull bone marrow cell annotation which Azimuth did not curate cell map reference, we built cell reference map by Azimuth-reference using Mazzitelli et al. mouse skull bone marrow scRNA-seq data for skull cell reference and Hove et al. dura scRNA-seq data for meninge cell reference. The brain, meninges and skull bone marrow cells were aligned between different treatment by using Harmony, a tool for batch correction that project cells into a shared embedding to cluster cell type across multiple conditions. The Harmony embeddings were used as input for t-distributed stochastic neighbor embedding (tSNE). The clusters were identified by the “FindNeighbors” and “FindClusters” functions in Seurat. To solve the automate Azimuth cell annotation inconsistence with clusters, we used “FindAllMarkers” from Seurat to identify marker genes to manually annotate clusters (Fig. 4h, i, j). To identify the differentially expressed genes (DEGs) across different conditions from merged dataset of brain, meninges and skull bone marrow, we used “FindMarker” function in Seurat to identify DEGs of tMCAO vs. Sham and tMCAO+UVB vs. tMCAO. The genes with |avg_log2FC| > 0.5 and p_val_adj < 0.05 were considered as significant differentially expressed genes.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
A total of 33 male C57BL/6J mice from sham, tMCAO and tMCAO+UVB groups were used for library preparation to perform scRNA-seq. After 1 day ischemia-reperfusion, mice were anesthetized, fixed and perfused with cooling PBS to remove the blood. The ischemic hemisphere (tMCAO ipsilateral brain) was immediately dissected. Meanwhile, the skullcap and meninges were harvested, respectively. The skullcap and meninges samples were minced using a scalpel for digestion with 2 mg/mL collagenase (Shanghai Life iLab Biotech Co., Ltd. China) for 1 h and 35 min, respectively, and red blood cells were lysed with 2 mL blood red cell lysing reagent (Biosharp, Labgic Technology Co., Ltd.). The brain tissue was digested with 10U/mL papain (Worthington Biochemical Corporation, USA) for 30 minutes. And, red blood cells were lysed with 4 mL blood red cell lysing reagent (Biosharp, Labgic Technology Co., Ltd.). Debris Removal Solution（130-109-398, Miltenyi Biotec）was used to remove fragments. After the single-cell suspension was obtained, automated cell counters (Countstar Rigel S2, Shanghai Ruiyu Biotechnology Co., LTD, China) was employed for cell number count (cell viability >80%). Single-cell suspensions from all tissues (10 μl each) were counted and the cell concentration was adjusted to achieve a cell recovery of approximately 10,000 cells.Single-cell suspensions were loaded onto the Chromium Controller using the Chromium Single Cell 3′ Library & Gel Bead Kit (10x Genomics, PN-1000268).
The 3′ scRNA-seq libraries was established mainly following Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry). Briefly, the gel bead emulsion was generated from the mixture of single cell suspension, gel beads and oils using the 10x Genomics chromium controller. Following droplet formation, the samples were transferred into PCR tubes. Reverse transcription was carried out using a T100 Thermal Cycler (Bio-Rad) according to the following protocol: incubation at 53℃ for 45 minutes, 85℃ for 5 minutes and finally held at 4℃. The resulting cDNA was then amplified and subjected to quality assessment using an Agilent Bioanalyzer 2100. The library was constructed by adding the P5 primer, Read 2 (primer site for sequencing read 2), Sample Index and P7 primer, respectively. Subsequently, the constructed library underwent quality control measures before being subjected to sequencing using the Illumina Novaseq 6000 platform (NovaSeq 6000 S4 Reagent Kit v1.5 with a 151-8-8-151 read setup). Details regarding sequencing depth and cell recovery are provided in Supplementary Table 2. Processing of scRNA-seq data was performed with the cellranger pipeline (v6.0.1, 10X Genomics) according to the manufacturer’s instructions. Briefly, raw bcl files were de-multiplex using the cellranger mkfastq pipeline. Subequent read alignments and transcript counting were performed individually for each sample using cellranger count pipeline with default parameters.

value: skull

value: tMCAO+UVB (UVB treatment was performed after tMCAO)


title: Group B Normal

description:
A total of 2 micro gram of extracted total RNA from the pooled samples in each disease category was prepared and 250 ng of this was labelled with a 3D-Gene miRNA labelling kit (Toray) followed by hybridizing onto 3D-Gene Human miRNA Oligo chips (Toray).
Normal

value: Pooled serum from 20 patients with normal  confirmed by histology


title: Group A SCC

description:
A total of 2 micro gram of extracted total RNA from the pooled samples in each disease category was prepared and 250 ng of this was labelled with a 3D-Gene miRNA labelling kit (Toray) followed by hybridizing onto 3D-Gene Human miRNA Oligo chips (Toray).
4 SCC

value: Pooled serum from 18 patients with SCC


title: NS_3

value: untreatment with UVB


title: UVB_meninges

value: meninges


title: Group A CIN3

description:
A total of 2 micro gram of extracted total RNA from the pooled samples in each disease category was prepared and 250 ng of this was labelled with a 3D-Gene miRNA labelling kit (Toray) followed by hybridizing onto 3D-Gene Human miRNA Oligo chips (Toray).
3 CIN3

value: Pooled serum from 23 patients with CIN3


title: UVB_brain

value: brain


title: Set7KO_Sal_9-C-438

first: Yao Wei

last: Lu

address: 2011 Zonal Ave

department: Department of Medicine

institute: University of Southern California

data_processing:
The gene expression levels were measured by HISAT2 (ref: Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019). using the mouse reference transcriptome from GENCODE (GRCm38 Ensembl release 102; https://www.gencodegenes.org/).
Transcript assembly and quantification was performed using the StringTie (ref:. Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT & Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads Nature Biotechnology 2015, doi:10.1038/nbt.3122)
The gene expression matrix generated was used as the input to perform differential expression analysis using edgeR (ref: McCarthy DJ, Chen Y, Smyth GK (2012). “Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.” Nucleic Acids Research, 40(10), 4288-4297. Doi: 10.1093/nar/gks042.)
Assembly: GRCm38 Ensembl release 102
Supplementary files format and content: raw count

source_name: Heart

extract_protocol:
Total RNA from the heart was isolated (TRIzol® Reagent, Invitrogen)
The sequencing libraries were obtained by the TruSeq Stranded mRNA Library Prep (Illumina).
The libraries were sequenced in the Illumina Nextseq platform using NextSeq 500 High Output Kit v2.5, 1x75 cycles, following the manufacturer’s instructions.

value: Heart

value: saline


title: Group A Normal

description:
A total of 2 micro gram of extracted total RNA from the pooled samples in each disease category was prepared and 250 ng of this was labelled with a 3D-Gene miRNA labelling kit (Toray) followed by hybridizing onto 3D-Gene Human miRNA Oligo chips (Toray).
1 nomal

value: Pooled serum from 12 patients with normal  confirmed by histology


title: Group A AD

description:
A total of 2 micro gram of extracted total RNA from the pooled samples in each disease category was prepared and 250 ng of this was labelled with a 3D-Gene miRNA labelling kit (Toray) followed by hybridizing onto 3D-Gene Human miRNA Oligo chips (Toray).
5 AD

value: Pooled serum from 10 patients with AD


title: SCAF3089_Fezf2_fl_FoxN1_wt

description: 10x Genomics

value: Thymic epithelial cells

value: Floxed Fezf2; Cre-negative


title: WT, repeat2, SCRNAseq

city: Manhasset

first: Hai

last: Huang

state: NY

address: 350 community drive

department: Institute of Molecular Medicine

institute: Feinstein Institutes for Medical Research

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software v3.0.0(https://support.10xgenomics.com/single-cell-gene-expression/sotware/pipelines/lateset/what-is-cell-ranger)
Assembly: mouse genome mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peritoneal adipose tissues

extract_protocol:
Omentum and mesentery adipose tissue were minced in RPMI 1640 Medium (Gibco) containing 2% FBS (Biotechne), 60 μg/ml Liberase TL (millpore sigma), 250 μg/ml DNase I (millpore sigma). Minced adipose tissue was placed at 37°C for 25 minutes, shaking.
Library was performed according to the manufacter's instructions. The final libraries were sequenced with pair-end on Illumina platform with at least 50,000 reads per cell.

value: peritoneal adipose tissues

value: FALC cells

value: Wild-type


title: WT, repeat1, SCRNAseq

description: 10x Genomics


title: WT_Sal_7-C-341

value: WT


title: Set7KO_Sal_6-B-123


title: tMCAO_skull

value: skull

value: tMCAO


title: NS_1


title: Set7KO_ISO_3-A-177

value: isoproterenol (60mg/kg )


title: tMCAO_meninges


title: NM_3

value: untreatment with UVB


title: WT_ISO_10-D-173


title: Sham_skull

value: Sham


title: Set7KO_ISO_2-A-161


title: WT_ISO_11-D-178


title: UVB0_1

value: 0.5 h after photobiomodulation of the skull


title: E9.5 WT3 Heart RNA

city: Chapel Hill

last: Shi

state: NC

address: 221 Fordham Hall

department: Biology

institute: UNC-Chapel Hill

data_processing:
Libraries were run on a HiSeq2500 (Illumina) with 2×150 bp paired end reads.
The sequence reads were aligned to the mm10 reference genome using STAR via the bcbio-nextgen RNA-sequencing pipeline. Differential gene expression was determined by DEseq2.
Assembly: mm10
Supplementary files format and content: Raw and normalized FPKM values for each sample.

extract_protocol:
WT and Smyd1-KO hearts at E9.5, n=3 for each genotype, were dissected in cold PBS and immediately stored in RNAlater (Thermo, AM7020) solution, and were kept in -20C until use. RNA from individual embryonic hearts was extracted using the RNAqueous-Micro total RNA isolation kit (Thermo, AM1931).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: NM_2

value: meninges


title: Sham_meninges


title: E9.5 WT1 Heart RNA

value: Heart


title: E9.5 WT2 Heart RNA


title: E9.5 Smyd1 KO3 Heart RNA


title: NB_3

value: brain


title: NM_1


title: NS_2


title: E9.5 Smyd1 KO1 Heart RNA


title: WT_Sal_8-C-189

value: saline


title: E9.5 Smyd1 KO2 Heart RNA


title: E9.5 WT2 heart ATAC

data_processing:
Libraries were run on a HiSeq2500 (Illumina) with 2×150 bp paired end reads.
Pooled libraries were then sequenced (Illumina Next-seq) to a depth of 100 million reads per sample. Reads were aligned to the mm10 reference genomes using BWA-MEM and peaks were called using HOMERv4.10.3. Annotation and analysis were performed using ChIP-Seeker v1.20.0.
Assembly: mm10
Supplementary files format and content: BigWig
Supplementary files format and content: Bed files of differential peaks

extract_protocol:
Four hearts at E9.5 were pooled per genotype per replicate, and were then dissociated into single cells. 40,000 viable cells were taken for were lysed to isolate nuclei, which were treated with Tn5 transposase (Nextera DNA Sample Prep Kit, Illumina) to isolate DNA. Fragmented DNA was then amplified using bar-coded PCR primers and libraries were seuqenced.
Dissociated embryonic cardiac cells were lysed to isolate nuclei, which were treated with Tn5 transposase (Nextera DNA Sample Prep Kit, Illumina) to isolate DNA Fragmented DNA was then amplified using bar-coded PCR primers and libraries were pooled.


title: E9.5 Smyd1 KO2 heart ATAC


title: NB_1


title: E9.5 Smyd1 KO1 heart ATAC


title: Donor.D1173_Untransduced_CD8_media alone_CD33+ MV4-11 AML target cells_24h

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

institute: Regeneron

description:
Two technical replicates of 150bp PE
D12

data_processing:
Reads were filtered for quality and aligned to the Genome Resource Consortium hg38 human genome reference using STAR (2.6.1d).
Gene expression was quantified as transcripts per million (TPM) using RSEM (1.3.1).
Assembly: hg38
Supplementary files format and content: comma-delimited text file contains RSEM TPMs for each sample.
Supplementary files format and content: comma-delimited text file contains RSEM expected counts for each sample.

source_name: CD8+ T cells

growth_protocol: To generate research scale DARIC cell products, PBMCs were thawed (recorded as day 0 of culture) and resuspended in TCGM supplemented with 250 IU/ml recombinant human IL-2 (Stemcell, catalog 78220.3) prior to activation with 50ng/ml anti-CD3 (clone OKT3) and anti-CD28 (clone 15E8) antibodies (Miltenyi Biotec). Lentivirus supernatants were directly added to PBMC cultures 24 hours later (multiplicity of infection [MOI] = 10). On day 3 of culture (72 hours after activation), transduced PBMC were collected, washed, and resuspended in complete TCGM with human IL-2 at 0.5 x 10^6 cells/ml and transferred to gas permeable culture vessels (G-REX, WilsonWolf). PBMC cultures were expanded in vitro at cell density of 0.5-2 x 10^6 cells/ml maintained by the addition of fresh media every 2-3 days for a total of 10-11 days until cryopreservation.

extract_protocol:
Total RNA was isolated using the Qiagen 96-well RNeasy Prep Kit.
Libraries were generated using KAPA 148 Hyperprep Kit with RiboErase and KAPA Unique Dual-Indexed Adapter Kit (Roche).
The sequencing strategy was two technical replicates of 150bp paired-end reads.  Samples were sequenced on a NextSeq500 instrument.

treatment_protocol: DARIC33 T cells and untransduced T cells generated from four donor PBMC samples were cultured with media or media supplemented with 1 nM rapamycin for 24 hours, washed and then stimulated with MV4-11 tumor cells or left unstimulated for an additional 24 hours. Cells were then sorted into CD4+ and CD8+ populations using a FACSAria (BD Biosciences).  In addition, transcriptomes were assesed at the 168hr timepoint for CD4+ and CD8+ DARIC33 transduced T cells derived from 3 donors and incubated with 1nM rapamycin and activated by CD33+ MV4-11 AML target cells.

value: CD8+ T cells

tag: transgene

value: Untransduced

tag: donor

value: media alone

tag: stimulation

value: CD33+ MV4-11 AML target cells

tag: time


title: Donor.D2172_DARIC33_CD4_1nM rapamycin_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
E12

source_name: CD4+ T cells

value: CD4+ T cells

value: 1nM rapamycin


title: Donor.D1173_DARIC33_CD4_1nM rapamycin_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
C12


title: Donor.D732_DARIC33_CD4_media alone_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
B12


title: Term-UC-Muse#2

city: Sendai

first: Yoshihiro

last: Kushida

address: 2-1 Seiryo-machi, Aoba-ku

institute: Tohoku University

data_processing:
Quality control and adapter trimming of sequencing data were performed using fastp version 0.20.0.
DNA reads were mapped to the human reference genome DNA (build GRCh38.94) by HISAT2 version 2.2.1 with the default setting.
Gene counts from the mapped HISAT2 output for downstream expression analysis were generated by featureCounts version 2.0.1.
Read counts for each gene were normalized to transcripts per million.
Assembly: GRCh38.94
Supplementary files format and content: tab-delimited text file includes TPM value for each Sample

source_name: Term-UC-Muse

extract_protocol:
Total RNA was isolated using the NucleoSpin RNA (Macherey-Nagel, Duren, Germany, 740902.50).
The library was constructed by NEB Next Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Hitchin, UK, E7490) and NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, E7530).

value: Term-UC-Muse

value: pluripotent-like cells


title: Term-UC-Muse#1


title: Term-UC-Muse#3


title: Donor.D732_Untransduced_CD4_1nM rapamycin_Unstimulated_24h

description:
Two technical replicates of 150bp PE
E11

value: Unstimulated


title: Donor.D1173_Untransduced_CD4_media alone_Unstimulated_24h

description:
Two technical replicates of 150bp PE
A12


title: Preterm-UC-Muse#3

source_name: Preterm-UC-Muse

value: Preterm-UC-Muse


title: Donor.D1173_Untransduced_CD8_1nM rapamycin_Unstimulated_24h

description:
Two technical replicates of 150bp PE
C11


title: Donor.D732_Untransduced_CD8_1nM rapamycin_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
D11


title: Preterm-UC-Muse#2


title: E9.5 WT1 heart ATAC

value: WT


title: NB_2

value: untreatment with UVB


title: Donor.D732_Untransduced_CD8_1nM rapamycin_Unstimulated_24h

description:
Two technical replicates of 150bp PE
B11


title: Preterm-UC-Muse#1


title: Macrophages, 7 Hypoxia Edicotinib

city: La Tronche

first: arnaud

last: MILLET

address: Allée des Alpes

institute: Institute for Advanced Studies

data_processing:
Gene expression was performed using the STAR software
Assembly: hg38
Supplementary files format and content: tab delimited-text files includes raw counts for each samples

source_name: Monocytes derived macrophages

extract_protocol:
RNA extraction was performed using the Nucleospin RNA kit (Macherey Nagel)
RNA library for RNAseq was prepared using the kit NEBNext Ultra II mRNAseq

tag: group

value: Monocytes derived macrophages

tag: stress

value: Hypoxia

value: Edicotinib


title: Macrophages, 7 Hypoxia Vehicle

value: Vehicle


title: Donor.D732_DARIC33_CD4_1nM rapamycin_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
F10


title: RGFP966-2

city: Shanghai

first: ZHU

middle: JIA

last: YAN

address: 197 Ruijin Er Rd

institute: Department of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava software used for basecalling.
Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted );Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality);Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample …

growth_protocol: EL4 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)  with 10% HBS, 2 mM L-glutamine, and antibiotics  in a humidified atmosphere containing 5% CO2 at 37°C

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNALibrary Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’srecommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 10μM RGFP966 (Abmole) or vehicle were added to the cell culture medium 24 hr in advance

value: T lymphocyte cells


title: RGFP966-3


title: Donor.D932_DARIC33_CD8_media alone_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
A11

value: CD8+ T cells


title: BM-Muse#2

source_name: BM-Muse

value: BM-Muse


title: BM-Muse#3


title: Macrophages, 7 Normoxia Edicotinib

value: Normoxia


title: BM-Muse#1


title: Donor.D1173_DARIC33_CD4_media alone_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
E10

value: media alone

value: CD33+ MV4-11 AML target cells


title: Macrophages, 7 Normoxia Vehicle


title: Donor.D732_DARIC33_CD8_1nM rapamycin_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
D10

value: 1nM rapamycin


title: ctrl-3

value: vehicle


title: Macrophages, 3 Hypoxia Edicotinib


title: Donor.D932_DARIC33_CD8_1nM rapamycin_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
C10


title: Macrophages, 3 Hypoxia Vehicle


title: Flag_MBD2c_input

city: Hefei

first: Yijie

last: Hao

address: Huangshan Road 443

institute: USTC

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.
Quality control is applied to guarantee the meaningful downstream analysis, and  fastp (version 0.23.1) is used to perform basic statistics on the quality of the raw reads.
Sequenced reads were mapped to the hg19 ChM only using software Bowtie2 (version 2.2.6). Aligned reads were used for subsequent generation of bindingprofiles, peak callings, motif analyses and traveling ratio analyses.
Assembly: hg19 ChM
Supplementary files format and content: bw for ChIP-seq data

source_name: human breast cancer

growth_protocol: DMEM supplemented with 10% FBS and 1% Pen/Strep. Cells were maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde and subsequently quenched with 0.125 M glycine. The cells were sonicated using a Scientz JY99-IIDN device. Anti-Flag antibody (Sigma-Aldrich) were used.
The DNA fragments were end-repaired and A-tailed, which were further ligated with sequencing adaptors. The final DNA library was obtained after size selection and PCR amplification. Libraries were analyzed for size distribution by Agilent 5400 system(Agilent, USA) and quantified by qPCR (1.5 nM).

treatment_protocol: shRNAs targeting TFAM were commercially purchased (Sigma-Aldrich). Flag- MBD2c were cloned into pSin-3xFlag  vectors.

value: human breast cancer

value: MDA-MB-468 genomic DNA


title: Flag_MBD2c+shTFAM

value: MDA-MB-468 infected with viruses expressing  Flag-MBD2c and shTFAM using Flag antibody (Sigma-Aldrich, Cat#F1804) to IP genomic DNA.


title: Donor.D2172_Untransduced_CD8_1nM rapamycin_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
B10

value: Untransduced


title: ctrl-1

value: WT


title: Macrophages, 3 Normoxia Edicotinib

value: Monocytes derived macrophages


title: Donor.D1173_DARIC33_CD8_media alone_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
A10


title: RGFP966-1


title: Macrophages, 3 Normoxia Vehicle