title: DO mNPC Sample PB368.79

city: Bar Harbor

first: Selcan

last: Aydin

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

description: Library name: PB368.79

data_processing:
We aligned paired-end 75bp reads with bowtie v1.1.2 to a pooled “8-way” transcriptome containing strain-specific isoform sequences from all eight DO founder strains. For resolving multi-mapping reads and quantifying transcript- and gene- level expression counts, we utilized EMASE as implemented in GBRS v0.1.6.
Assembly: GRCm38/mm10
Supplementary files format and content: There are two kinds of procesed data files, one with the extension "expected_read_counts" and one with "tpm". The one with "expected_read_counts" contain the diploid gene counts for each gene and is used for downstream analysis. The one with "tpm" contains the transcripts per million value for each gene and is used for filtering genes with low expression.

source_name: Neural Progenitor Cells

growth_protocol: Neural progenitor cells were maintained in Neural Stem cell (NS) media as described in Pollard et al., 2006, PMID: 17141035. Total RNA was isolated from each of 186 DO mNPC lines and quantitated by paired-end RNA sequencing. Briefly, for each mNPC line, one 15cm dish of cells was grown to near confluence, washed 3x with PBS, and mechanically harvested to yield 10M cells. About 100k cells from each frozen cell pellet were used for RNA sequencing.

extract_protocol:
Total RNA was extracted using the Quick-RNA 96 well format kit (Zymo Research) with in-column DNase treatment.
Sequencing libraries were prepared by Akesogen using the TruSeq Stranded mRNA HT kit (Illumina, Cat no. 20020595) and included ribosomal RNA reduction and poly-A selection, enzymatic fragmentation, cDNA synthesis from random hexamer priming, adaptor ligation and PCR amplification steps to generate indexed, stranded mRNA-seq libraries. Libraries were checked for quality and quantitated with the Agilent Bioanalyzer, and samples that failed QC were repeated starting from the cryovial stage. Finally, pooled libraries were sequenced on the NextSeq platform (Illumina) using the NextSeq 500/550 High Output v2 150-cycle kits (Illumina, Cat no. FC-404-2002). To minimize technical variation, samples were randomly assigned to lanes prior to sample processing steps, barcoded, and multiplexed at 16 samples per flow cell, yielding 6M-55M 2x75bp paired-end (PE) reads per sample

value: Neural Progenitor Cells

value: Diversity Outbred

tag: Sex

value: Male


title: AccuTOX_25uM_n1_mouse

status: Public on Jan 24 2025

type: SRA

city: Montreal

first: Moutih

last: Rafei

address: Montreal

country: Canada

institute: Universite de Montreal

description:
Library name: Sample 4
ARMX mouse MSC
S4_S8

library_source: transcriptomic

data_processing:
Basecalls performed using Illumina RTA 2.4.11. followed by STAR v2.7 aligner Genecounts
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Assembly: Mouse mm10 and Human hg38
Supplementary files format and content: Files are tabular in tsv format (ensembl genes in row and samples in columns)

molecule: polyA RNA

organism: Mus musculus

source_name: Bone marrow

growth_protocol: Murine mesenchymal stromal cells (MSCs) were maintained in AMEM supplemented with 10% fetal bovine serum (FBS) and 50 U/mL Penicillin-Streptomycin in humidified atmosphere with 5% CO2 at 37C. Human MSCs were mainained in the RoosterBio media (RoosterKit-hBM-1M-XF) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

treatment_protocol: Treatment was added post confluency of 80%. AccuTOX condition consisted of 25uM of the compound diluted in AMEM supplemented with 10% fetal bovine serum (FBS) and 50 U/mL Penicillin-Streptomycin. AccuTOX+OVA/lysate condition consisted of 25uM of the compound, plus 1 mg/mL of Albumin from chicken egg white, diluted in AMEM supplemented with 10% fetal bovine serum (FBS) and 50 U/mL Penicillin-Streptomycin/ml insulin (Sigma). Cell were treated and incubated for 6h in humidified atmosphere with 5% CO2 at 37C. Similar treatments were done for the human cells except AccuTOX was used at 10uM.

tag: tissue

value: Bone marrow

tag: cell line

value: Primary cell

tag: cell type

value: Mesenchymal stromal cell

tag: genotype

value: WT

tag: treatment

value: 25 uM of AccuTOX


title: Negative_n3_mouse

description:
Library name: Sample 3
ARMX mouse MSC
S3_S7

value: Untreated


title: AccuTOX_25uM_n2_mouse

description:
Library name: Sample 5
ARMX mouse MSC
S5_S9


title: ChIP-seq-03_GFP_ARMC5-GFP-dB_SPT5-AID_H2O-90m_rep1

city: Chicago

first: Yuki

last: Aoi

state: IL

address: 303 E Superior St. SQBRC 7-300

department: Biochemistry & Molecular Genetics

country: USA

institute: Northwestern University

description: ChIP-seq

library_source: genomic

data_processing:
Following the quality-trimming using trimmomatic 0.39, the reads were aligned to the genome using bowtie 2.4.5 and convereted to genome coverage file in bigwig format using deepTools 3.5.1.
Assembly: hg38
Supplementary files format and content: bigwig files containing genome coverage data

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Cells were crosslinked in 1% formaldehyde/PBS and sonicated using Covaris to solubilize chromatin fraction. Following immunoprecipitation, elution fraction was reverse crosslinked and DNA was purified using PCR purification kit (QIAGEN).
Libraries were constructed using KAPA HyperPrep kit (Roche).

value: Colorectal adenocarcinoma


title: Negative_n2_mouse

description:
Library name: Sample 2
ARMX mouse MSC
S2_S6


title: DO mNPC Sample PB367.68

description: Library name: PB367.68

molecule: total RNA

tag: batch


title: RNA-seq_shNT_Rep3

description: polyA+ RNA-seq

data_processing:
Following the quality-trimming using cutadapt 4.2, the reads were applied to transcript quantification using salmon 1.9.0 with --gcBias option and summarization using tximeta.
Assembly: hg38
Supplementary files format and content: sf file containing transcript quantification from Salmon

extract_protocol:
Total RNA was extracted using RNeasy mini kit (QIAGEN).
Libraries were constructed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB# E7490) and NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770).

value: shNT


title: RNA-seq_shNT_Rep1

description: polyA+ RNA-seq


title: Neagtive_n1_mouse

description:
Library name: Sample 1
ARMX mouse MSC
S1_S5


title: RNA-seq_shNT_Rep2

description: polyA+ RNA-seq


title: DO mNPC Sample PB369.16

description: Library name: PB369.16


title: DO mNPC Sample PB369.29

description: Library name: PB369.29


title: Zebrafish, scRNAseq, shield-sibling-1

city: qingdao

first: yizhuang

last: zhang

state: shandong

address: No.72 Binhai Road  Jimo District

department: school of life sciences

country: China

institute: shandong university

description:
10X Genomics GemCode Single-cell
s97

library_source: transcriptomic single cell

data_processing:
To remove any remaining biochemical reagents and primers from the post GEM reaction mixture, silane magnetic beads were employed. The full-length, barcoded cDNAs were subsequently amplified by PCR to generate sufficient mass for library construction. During GEM incubation, the molecules had R1 (Read 1 primer sequence) added to them. P5, P7, a sample index, and R2 (Read 2 primer sequence) were added during library construction through processes such as End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers required for Illumina bridge amplification. The Single Cell 3' Protocol generated Illumina-ready sequencing libraries. Each Single Cell 3' Library consisted of standard Illumina paired-end constructs that began and ended with P5 and P7. The Single Cell 3' 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1, while Read 2 was utilized to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 corresponded to the standard Illumina® sequencing primer sites used in paired-end sequencing.
Assembly: GRCz10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C

extract_protocol:
For the preparation of single-cell suspensions, a total of thirty-three mutant embryos of Mrbm24a or wild-type embryos at the shield stage were collected. These cellular suspensions were then loaded onto a 10X Genomics GemCode Single-cell instrument, which generates single-cell Gel Bead-In-EMulsion (GEMs).
Libraries were generated and sequenced from the cDNAs using Chromium Next GEM Single Cell 3' Reagent Kits v3.1. Upon dissolution of the Gel Bead within a GEM, primers containing an Illumina® R1 sequence (Read 1 sequencing primer), a 16 nt 10x Barcode, a 10 nt Unique Molecular Identifier (UMI), and a poly-dT primer sequence were released. These primers were mixed with the cell lysate and Master Mix. Full-length, barcoded cDNAs were then reverse-transcribed from poly-adenylated mRNA

value: whole embryo

value: shield stage

value: embryonic cell

value: wild type


title: DO mNPC Sample PB367.55

description: Library name: PB367.55


title: AccuTOX_25uM_n3_mouse

description:
Library name: Sample 6
ARMX mouse MSC
S6_S10


title: DO mNPC Sample PB367.47

description: Library name: PB367.47


title: DO mNPC Sample PB366.44

description: Library name: PB366.44


title: DO mNPC Sample PB369.08

description: Library name: PB369.08


title: DO mNPC Sample PB366.21

description: Library name: PB366.21


title: DO mNPC Sample PB365.33

description: Library name: PB365.33


title: DO mNPC Sample PB369.07

description: Library name: PB369.07


title: DO mNPC Sample PB363.08

description: Library name: PB363.08


title: DO mNPC Sample PB363.07

description: Library name: PB363.07


title: DO mNPC Sample PB368.19

description: Library name: PB368.19


title: DO mNPC Sample PB368.24

description: Library name: PB368.24


title: DO mNPC Sample PB368.63

description: Library name: PB368.63


title: DO mNPC Sample PB366.43

description: Library name: PB366.43


title: DO mNPC Sample PB367.26

description: Library name: PB367.26


title: DO mNPC Sample PB365.33_B

description: Library name: PB365.33_B


title: DO mNPC Sample PB366.07

description: Library name: PB366.07


title: DO mNPC Sample PB362.40

description: Library name: PB362.40

value: Female


title: Drosophila,wingdisc,Input2_1

city: Beijing

first: Yao

last: Chen

state: Beijing

address: No.2 Yuanmingyuan western road

department: College of Plant Protection

institute: China Agricultural University

description: Library name: Input2_1

data_processing:
Quality control Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11, Chen et al., 2018) software. 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 of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
Fragment size estimation For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and present significant enrich. For single-end sequencing, the fragment size was estimated with MACS2 (Zhang et al., 2008) predicted method with default parameters. MACS2 scan all the genome with a specific window size and calculate the reads enrichment level. A particular number of windows were used as samples to build enrichment model and to predict fragment size. The following peak calling analysis was based on this predicted fragment size.
Peak detection After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Motif analysis The interaction between transcript factor or chromatin histone modification and DNA were not random, while they show some specific sequence preference. Homer (Heinz et al., 2010) was used to detect the denovo sequence motif and the matched known motifs.
Peak annotation The position of peak summit around transcript start sites of genes can predict the interaction sites between protein and gene. ChIPseeker (Yu et al., 2015) was used to retrieve the nearest genes around the peak and annotate genomic region of the peak. Peak-related genes can be confirmed by ChIPseeker, and then Gene Ontology (GO) enrichment analysis was performed to identify the function enrichment results. GO enrichment analysis was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P-value less than 0.05 were considered significantly enriched by peak-related genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical enrichment of peak related genes in KEGG pathways.
Different peak analysis Different peak analysis was based on the fold enrichment of peaks of different experiments. A peak was determined as different peak when the odds ratio between two groups was more than 2. Using the same method, genes associated with different peaks were identified and also do GO and KEGG enrichment analysis. s-Wheeler transform. Bioinformatics, 2
Assembly: D.melanogaster_r6.32
Supplementary files format and content: bigWig

organism: Drosophila melanogaster

source_name: wing disc

extract_protocol:
The ChIP experiments were performed following previous protocols with minor modifications. Wing imaginal discs were collected and transferred into a 1.5 ml loBind Eppendorf tube (022431021, Eppendorf).  Ice-cold buffer A1 was added and tissues were lysed for 5 min.  The samples were subjected for cross-linking in 1% formaldehyde for 15 min at RT, which were ended by adding of 160 ul 2.5 M glycine and rotating for 5 min. Chromatin fragmentation was performed with the Bioruptor sonicator (JY92II, Xinchen Biotech, Nanjing, China) using a high-power program (400W power, ON = 10 sec, OFF = 30 sec, 10 times). After sonication, the lysate was centrifuged and the supernatant was transferred into a new 1.5ml LoBind tube. The amount of DNA in each sample was quantified using the Equalbit 1× dsDNA HS Assay Kit (EQ121-00, Vazyme). The DNA samples were pre-cleared with 15 µl IgG and 15 µl protein A+G Dynabeads (10001D, Invitrogen) for 2 h at 4℃. Each sample was then incubated with 5 µg antibody for 4 h at 4℃, after which 30 µl Dynabeads were added and overnight incubation was done with rotating. After five washes in buffer A2 and a final wash in TE, the samples were eluted with 250µl elution buffer and de-crosslinked at 65°C for 6 h. Protease K was used to degrade proteins in the elution, after which the DNA was precipitated in -20 ℃ by adding 1/10 volume of 3M NaAc (pH5.5), 2 µl of 35 mg/ml glycogen and 2.5 volumes of 100% EtOH. DNA pellet was air dried and dissolved in the required volume of nuclease free H2O. For qPCR, we used 5 µl of Perfect Start Green qPCR Super Mix (AQ602, TransGen Biotech, Beijing, China), 0.1 µl of each primer (50 pmol/L), 2.8 µl of ddH2O and 2 µl of DNA sample. The real-time quantitative PCR experiments were conducted on ABI QuantStudio 6 Flex System (Thermo Fisher). Primer sequences for E(spl)-C genes were obtained from (Pillidge and Bray, 2019), and sequences of primers used in this study are listed in Supplementary Table 1. The value of % Input was calculated by the following formula: % Input = 100* 2^ (-(Ct [ChIP] - (Ct [Input] -Log2 (Input Dilution Factor)))). Antibodies used for ChIP include rabbit anti-H2Avac (ab232908, Abcam), mouse anti-H2Av (61751, Active Motif) and rabbit IgG (2729, Cell Signaling) for mock control. Buffer A1 contains 60 mM KCl, 15 mM NaCl, 4 mM MgCl2, 15 mM HEPES, 0.5% Triton X-100, 0.5 mM DTT and 10 mM sodium butyrate. Buffer A2 contains 140 mM NaCl, 15 mM HEPES, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.05% SDS, 0.1% sodium deoxycholate and 10 mM sodium butyrate. Elution buffer contains 10mM EDTA, 50mM Tris HCl, 1% SDS.
The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system

value: wing disc

value: input


title: Drosophila,wingdisc,Input1_1

description: Library name: Input1_1


title: DO mNPC Sample PB365.13

description: Library name: PB365.13

value: Neural Progenitor Cells

value: Diversity Outbred


title: DO mNPC Sample PB365.47

description: Library name: PB365.47

value: Male


title: DO mNPC Sample PB362.57

description: Library name: PB362.57


title: DO mNPC Sample PB362.13

description: Library name: PB362.13


title: Drosophila,wingdisc,H2Av_EGFP2_1(ChIP)

description: Library name: H2Av_EGFP2_1

value: ChIP


title: DO mNPC Sample PB361.78

description: Library name: PB361.78


title: IVAX, mouse 1

city: Irvine

first: Huw

last: Davies

state: CA

address: 812 Medical Plaza Drive, Med Surge II

department: Department of Physiology & Biophysics

institute: UC Irvine

description:
Library name: Sample 13
10X Genomics

data_processing:
Reads were aligned using CellRanger with defaults.
Assembly: mm10
Supplementary files format and content: The processed data are in .h5ad format.

source_name: Draining (inguinal) lymph node

extract_protocol:
Single-cell suspensions from draining lymph nodes were filtered through a 45-µm mesh, counted, and loaded at 2,000 cells per microliter, for a total of 20,000 cells per sequencing run following the 10X Geomics manufacturer's recommendations.
10× Genomics Chromium 3’ v3 kit

value: Draining (inguinal) lymph node

tag: strain

value: IVAX


title: DO mNPC Sample PB361.67

description: Library name: PB361.67


title: DO mNPC Sample PB361.47

description: Library name: PB361.47


title: DO mNPC Sample PB361.62

description: Library name: PB361.62


title: IVAX, mouse 2

description:
Library name: Sample 14
10X Genomics


title: DO mNPC Sample PB361.48

description: Library name: PB361.48


title: CpG+MPLA, mouse 3

description:
Library name: Sample 12
10X Genomics

value: CpG+MPLA


title: AddaVax, mouse 3

description:
Library name: Sample 9
10X Genomics

value: AddaVax


title: DO mNPC Sample PB361.37

description: Library name: PB361.37


title: CpG+MPLA, mouse 2

description:
Library name: Sample 11
10X Genomics


title: DO mNPC Sample PB361.44

description: Library name: PB361.44


title: Drosophila,wingdisc,H2Av_EGFP1_1(ChIP)

description: Library name: H2Av_EGFP1_1


title: PBS and antigen, mouse 3

description:
Library name: Sample 6
10X Genomics

value: PBS and antigen


title: DO mNPC Sample PB361.24

description: Library name: PB361.24


title: PBS and antigen, mouse 2

description:
Library name: Sample 5
10X Genomics


title: CpG+MPLA, mouse 1

description:
Library name: Sample 10
10X Genomics


title: DO mNPC Sample PB361.59

description: Library name: PB361.59


title: DO mNPC Sample PB361.33

description: Library name: PB361.33


title: AddaVax, mouse 2

description:
Library name: Sample 8
10X Genomics


title: WT-2.5min-S4-R2-spna

status: Public on Jan 25 2025

city: Worcester

first: Johan

middle: Harmen

last: Gibcus

state: MA

address: 368 Plantation Street, Dekker Lab HHMI, AS5.1015,

department: Department of Systems Biology

institute: UMass Chan Medical School

description: DT-40-CDK1 knockout , transfected with Xenops laevis CDK1as and TIR1

data_processing:
Fastq files were processed with the distiller pipeline (https://github.com/mirnylab/distiller-nf)
Reads were mapped to bGalGal1.mat.broiler.GRCg7b (GCA_016699485.1) using bwa mem with flags-SP.
To get pairs files, mapped reads were parsed and classified using  pairtools (https://github.com/mirnylab/pairtools).
PCR and optical duplicates were removed by matching the positions of aligned reads with 2bp flexibility.
Pairs were filtered using mapping quality scores (MAPQ > 30) on each side of aligned chimeric reads and binned into multiple resolutions before low coverage bins were removed.
Multiresolution cooler files were created with the cooler package (https://github.com/mirnylab/cooler.git)
Assembly: bGalGal1.mat.broiler.GRCg7b (GCA_016699485.1)
Supplementary files format and content: HDF5, Multiresolution cooler files (https://github.com/open2c/cooltools)
Supplementary files format and content: Mapping statistics for cooler files generated by pairtools (https://github.com/mirnylab/pairtools)
Supplementary files format and content: Compartment EV1 track (https://github.com/open2c/cooltools)
Supplementary files format and content: Eigen vectors (https://github.com/open2c/cooltools)
Supplementary files format and content: Insulation track (https://github.com/open2c/cooltools)
Supplementary files format and content: Insulation boundaries (https://github.com/open2c/cooltools)

organism: Gallus gallus

source_name: Bursa

growth_protocol: Chicken DT40 cells were cultured in RPMI 1640 medium supplemented with 10 % fetal bovine serum and 1% chicken serum at 39°C in 5% CO2 in air.

extract_protocol:
Following Hi-C 2.0 protocol steps 2.1 - 2.12 from supplemental material of Belaghzal et al., Methods 2017 Jul 1:123:56-65; PMID: 28435001
Following Hi-C 2.0 protocol steps 3.1 - 16.3 from supplemental material of Belaghzal et al., Methods 2017 Jul 1:123:56-65; PMID: 28435001

treatment_protocol: 1% formaldehyde for 10 minutes before glycine quenching (128 mM final) for 5 minutes at room temperature followed by 15 minutes on ice and wash with PBS before storing at -80°C

value: Bursa

value: lymphoblast

value: WT-CDK1as (Z11)

value: Cells were treated with 1NMPP1 for 10 h, release after 2.5 min


title: DO mNPC Sample PB361.28

description: Library name: PB361.28


title: DO mNPC Sample PB361.25

description: Library name: PB361.25


title: DO mNPC Sample PB361.16

description: Library name: PB361.16


title: PBS only, mouse 3

description:
Library name: Sample 3
10X Genomics

value: PBS only


title: DO mNPC Sample PB361.23

description: Library name: PB361.23


title: IVAX, mouse 3

description:
Library name: Sample 15
10X Genomics


title: PBS and antigen, mouse 1

description:
Library name: Sample 4
10X Genomics


title: PBS only, mouse 1

description:
Library name: Sample 1
10X Genomics


title: PBS only, mouse 2

description:
Library name: Sample 2
10X Genomics


title: DO mNPC Sample PB360.86

description: Library name: PB360.86

value: Female


title: DO mNPC Sample PB360.88

description: Library name: PB360.88


title: AddaVax, mouse 1

description:
Library name: Sample 7
10X Genomics


title: DO mNPC Sample PB361.14

description: Library name: PB361.14


title: DO mNPC Sample PB360.70

description: Library name: PB360.70


title: DO mNPC Sample PB360.75

description: Library name: PB360.75


title: DO mNPC Sample PB360.66

description: Library name: PB360.66


title: DO mNPC Sample PB360.71

description: Library name: PB360.71


title: DO mNPC Sample PB360.65

description: Library name: PB360.65


title: DO mNPC Sample PB360.59

description: Library name: PB360.59


title: DO mNPC Sample PB360.45

description: Library name: PB360.45


title: DO mNPC Sample PB360.42

description: Library name: PB360.42


title: Pat_13_T

type: genomic

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

hyb_protocol: Sodium bisulfite treated gDNA was amplified and enzymatically fragmented before hybridization to the microarray. After washing and staining, the microarray was scanned using the iScan device (Illumina).

scan_protocol: Infinium MethylationEPIC microarray platform

data_processing: Raw red/green channel *.idat files were imported into R using the RnBeads packages for initial quality  control, data normalization (SWAN) and extraction of β-values representing the percentage of  methylation for each CpG site on the microarray. SNP-enriched, cross-reactive, non-CpG  and sex chromosome specific probes were removed from further analyses. Unreliable  measurements were determined using the Greedycut algorithm implemented in RnBeads and  probes of highest impurity were iteratively removed from the dataset. Differential methylation  was calculated using limma and RnBead´s rank cutoff. The top 1000 differentially methylated  CpG sites were used for further analyses.

source_name: Tumor

label_protocol: 500ng of gDNA was sodium bisulfite converted using the EpiTect Fast DNA Bisulfite Kit (Qiagen, Germantown, MD, USA), processed using the Infinium HD FFPE DNA Restore Kit (Illumina, San Diego, CA, USA) and processed for microarray hybridization using Infinium MethylationEPIC Kit.

extract_protocol: Genomic DNA (gDNA) was extracted using the Maxwell FFPE Plus Kit (Promega, Madison, Wisconsin, USA).

value: Tumor


title: DO mNPC Sample PB360.24

description: Library name: PB360.24


title: DO mNPC Sample PB360.41

description: Library name: PB360.41


title: DO mNPC Sample PB360.13

description: Library name: PB360.13


title: DO mNPC Sample PB360.08

description: Library name: PB360.08


title: DO mNPC Sample PB360.40

description: Library name: PB360.40


title: DO mNPC Sample PB360.09

description: Library name: PB360.09


title: DO mNPC Sample PB360.15

description: Library name: PB360.15


title: DO mNPC Sample PB360.18

description: Library name: PB360.18


title: DO mNPC Sample PB359.86

description: Library name: PB359.86


title: DO mNPC Sample PB359.84

description: Library name: PB359.84


title: DO mNPC Sample PB359.83

description: Library name: PB359.83


title: DO mNPC Sample PB359.70

description: Library name: PB359.70


title: DO mNPC Sample PB359.66

description: Library name: PB359.66


title: DO mNPC Sample PB359.74

description: Library name: PB359.74


title: Pat_03_T


title: DO mNPC Sample PB359.73

description: Library name: PB359.73


title: Pat_07_S

source_name: Stroma

value: Stroma


title: Pat_12_T


title: DO mNPC Sample PB359.65

description: Library name: PB359.65

value: Neural Progenitor Cells


title: DO mNPC Sample PB360.07

description: Library name: PB360.07

value: Diversity Outbred


title: SMC3-AID-15min-S2-R2-SpnA

description: DT-40-CDK1 knockout , transfected with Xenops laevis CDK1as and TIR1, has a CRISPR derived mAID-clover knockin at SMC3. These cells will synchronize at mitotic entrance after addition of 1NM-PP1. Addition of auxin will deplete SMC3-clover via TIR1 proteasome degradation.

value: 1NMPP1 for 10 h + 3 h (auxin), washed (20 min), release for 15 min, after cross-linking, cells were GFP sorted (negative)


title: Pat_07_T


title: Pat_11_T


title: Pat_08_T


title: Normoxia_Control_N2

city: San Diego

first: Elana

middle: R

last: Elkin

address: 5500 Campanile Drive

department: School of Public Health

institute: San Diego State University

description: Library name: Normoxia_Control_N2

data_processing:
Reads were aligned to the human genome using STAR, with the options "outFilterMultimapNmax 10" and "sjdbScore 2".
Aligned reads were assigned to GRCh38 genes using featureCounts.
Genes with mean read counts-per-million less than four across all samples were filtered out and excluded from the analysis.
Data were normalized using the trimmed mean of M values (TMM) method
Differential gene expression testing was performed using the edgeR package (version 3.1) for R statistical computing. Quasi-likelihood general linear modeling was used for differential gene expression testing.
Assembly: hg38
Supplementary files format and content: tabular files

source_name: placenta

extract_protocol:
RNeasy Mini Kit
Stranded sequencing libraries for HTR-8/SVneo cells were prepared using the TruSeq Stranded mRNA Library Prep Kit with poly A enrichment (Illumina).

treatment_protocol: Cells were cultured between passages 78–84 in RPMI 1640 medium supplemented with 10% FBS and 1% P/S at 37°C in a 5% CO2 humidified incubator. Cells were grown to 70–90% confluence at least 24 h after plating prior to use in any experiments. Cells were seeded at a density of 800,000 cells per well in 6-well cell culture plates. Twenty-four hours later, cells were treated with RPMI 1640 complete medium alone (control) or complete medium plus DCVC diluted to a final concentration of 10 µM for 24 h.  Four independent biological replicate experiments were performed.Parallel experiments were performed under normoxic conidations or hypoxic conditions using a StemCell Hypoxia incubator chamber.

value: placenta

value: Extravillous trophoblast

tag: exposure time

value: 24 hours

tag: oxygen condition

value: normoxia


title: Normoxia_Control_N4

description: Library name: Normoxia_Control_N4

growth_protocol: Cells were cultured between passages 78–84 in RPMI 1640 medium supplemented with 10% FBS and 1% P/S at 37°C in a 5% CO2 humidified incubator.


title: Pat_12_S


title: DO mNPC Sample PB359.64

description: Library name: PB359.64

value: Male


title: Pat_09_S


title: Pat_10_S


title: DO mNPC Sample PB359.42

description: Library name: PB359.42


title: Pat_10_T


title: DO mNPC Sample PB359.57

description: Library name: PB359.57


title: Normoxia_Control_N1

description: Library name: Normoxia_Control_N1


title: DO mNPC Sample PB359.41

description: Library name: PB359.41


title: Pat_11_S


title: Normoxia_10umDCVC_N4

description: Library name: Normoxia_10umDCVC_N4


title: Normoxia_Control_N3

description: Library name: Normoxia_Control_N3


title: Pat_06_S


title: Normoxia_10umDCVC_N3

description: Library name: Normoxia_10umDCVC_N3


title: Pat_09_T


title: Pat_08_S


title: Normoxia_10umDCVC_N1

description: Library name: Normoxia_10umDCVC_N1


title: DO mNPC Sample PB359.25

description: Library name: PB359.25


title: DO mNPC Sample PB359.23

description: Library name: PB359.23


title: Hypoxia_Control_N4

description: Library name: Hypoxia_Control_N4

value: hypoxia


title: Normoxia_10umDCVC_N2

description: Library name: Normoxia_10umDCVC_N2


title: DO mNPC Sample PB359.19

description: Library name: PB359.19


title: Hypoxia_Control_N3

description: Library name: Hypoxia_Control_N3


title: DO mNPC Sample PB359.33

description: Library name: PB359.33


title: DO mNPC Sample PB358.39

description: Library name: PB358.39


title: Pat_05_T


title: Hypoxia_Control_N2

description: Library name: Hypoxia_Control_N2


title: DO mNPC Sample PB358.34

description: Library name: PB358.34


title: Pat_05_S


title: Pat_13_S


title: Pat_01_T


title: Hypoxia_Control_N1

description: Library name: Hypoxia_Control_N1


title: Pat_04_T


title: DO mNPC Sample PB359.29

description: Library name: PB359.29


title: Pat_03_S


title: Hypoxia_10umDCVC_N4

description: Library name: Hypoxia_10umDCVC_N4


title: DO mNPC Sample PB358.28

description: Library name: PB358.28


title: Hypoxia_10umDCVC_N3

description: Library name: Hypoxia_10umDCVC_N3


title: Hypoxia_10umDCVC_N1

description: Library name: Hypoxia_10umDCVC_N1


title: DO mNPC Sample PB358.25

description: Library name: PB358.25


title: Pat_01_S


title: Hypoxia_10umDCVC_N2

description: Library name: Hypoxia_10umDCVC_N2


title: HT144

city: Leipzig

first: Maciej

last: Rosolowski

address: Härtelstr. 16-18

country: Germany

institute: Institute for Medical Informatics, Statistics and Epidemiology (IMISE)

description: Library name: HT144

data_processing:
Preprocessing was done by Novogene (Cambridge, UK). Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Sequence reads were mapped to GRCh38 using Hisat2 v2.0.5
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: skin

extract_protocol:
Rneasy Mini Kit (Qiagen)
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library . For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, after size selection an additional USER enzyme digestion was performed.

value: skin

value: melanoma cells

value: NRAS

value: non


title: DO mNPC Sample PB358.33

description: Library name: PB358.33


title: Pat_06_T


title: Pat_02_T


title: DO mNPC Sample PB358.13

description: Library name: PB358.13


title: Z080423

description: Library name: Z080423


title: Z130515

description: Library name: Z130515


title: A375

description: Library name: A375


title: DO mNPC Sample PB358.12

description: Library name: PB358.12


title: DO mNPC Sample PB358.05

description: Library name: PB358.05


title: Pat_04_S


title: Multiplexed samples

city: Houston

first: Michael

middle: T

last: Lewis

state: TX

address: 1 Baylor Plaza N1210

department: Breast Center

institute: Baylor College of Medicine

description:
Library name: Multiplexed_Samples
10X Genomics

data_processing:
Demultiplexing, barcode processing, gene counting, and alignment were performed using the Cell Ranger Single Cell software v7.0.1 (10X Genomics). All steps were collectively handled by the "cellranger multi" utility.
Assembly: Hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Breast

extract_protocol:
Xenograft tumors were harvested, cut into small chunks and snap frozen using liquid nitrogren and stored at -80°C until sample preparation. Tissue processing and nuclei RNA fixation of the snap frozen PDX samples were performed using Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics). Fixation was then quenched and samples were stored at -80°C until sequencing.
Single nuclei RNAseq libraries were prepared according to Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics), similar to the cDNA synthesis and barcoding process for each single cell. Single-cell nuclei RNA libraries were sequenced using NovaSeq (read configuration: Paired End 28-10-10-90; 1% PhiX Spike-in; read depth 100M/sample).

value: Breast

value: Breast cancer patient-derived xenograft

value: SCID/beige


title: DO mNPC Sample PB358.18

description: Library name: PB358.18


title: DO mNPC Sample PB358.29

description: Library name: PB358.29


title: Z141208

description: Library name: Z141208

value: WT


title: DO mNPC Sample PB358.04

description: Library name: PB358.04

value: Neural Progenitor Cells

value: Female


title: DO mNPC Sample PB358.02

description: Library name: PB358.02

value: Diversity Outbred


title: DO mNPC Sample PB359.56

description: Library name: PB359.56


title: MaMel60

description: Library name: MaMel60


title: Z150548

description: Library name: Z150548


title: DO mNPC Sample PB357.22

description: Library name: PB357.22


title: Pat_02_S

value: Stroma


title: DO mNPC Sample PB357.14

description: Library name: PB357.14


title: SKM29

description: Library name: SKM29


title: Z130610

description: Library name: Z130610


title: MaMel62

description: Library name: MaMel62


title: DO mNPC Sample PB357.05

description: Library name: PB357.05


title: DO mNPC Sample PB357.07

description: Library name: PB357.07


title: DO mNPC Sample PB369.32

description: Library name: PB369.32


title: Z130604

description: Library name: Z130604


title: DO mNPC Sample PB369.17

description: Library name: PB369.17


title: Z101221

description: Library name: Z101221


title: DO mNPC Sample PB369.20

description: Library name: PB369.20


title: Z130820

description: Library name: Z130820


title: Z150536

description: Library name: Z150536


title: DO mNPC Sample PB368.65

description: Library name: PB368.65


title: Blood sample DNA from sepsis patient 72

city: Valencia

first: Jose Luis

last: Garcia-Gimenez

address: Avinguda Blasco Ibáñez, 15

department: Physiology

country: Spain

institute: University of Valencia

description:
207678520176_R07C01
SEP-0072-T1

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC v2.0 Beadchio arrays (Illumina) using standard Illumina Protocol.

scan_protocol: Arrays were read using an Illumina HiScan SQ.

data_processing:
.IDAT files were processed using minfi package in R environment. PreprocessQuantile function was used for normalization, and probes with potential interference were removed.
The 'MatrixProcessed_Betas.csv' contains Average Beta values.

label: Cy3 and Cy5

source_name: Blood

label_protocol: Standard Illumina Protocol.

extract_protocol: DNA was isolated from leukocytes in whole blood samples.

value: Blood

tag: disease state

value: Septic patient hospitalized for an infection


title: DO mNPC Sample PB368.41

description: Library name: PB368.41


title: DO mNPC Sample PB358.19

description: Library name: PB358.19


title: DO mNPC Sample PB368.15

description: Library name: PB368.15


title: Z000921

description: Library name: Z000921


title: DO mNPC Sample PB368.12

description: Library name: PB368.12


title: Blood sample DNA from sepsis patient 69

description:
207678520176_R05C01
SEP-0069-T1


title: DO mNPC Sample PB367.67

description: Library name: PB367.67


title: DO mNPC Sample PB367.49

description: Library name: PB367.49


title: Z140905

description: Library name: Z140905


title: Z111031

description: Library name: Z111031


title: DO mNPC Sample PB357.04

description: Library name: PB357.04


title: Blood sample DNA from control 76

description:
207678520176_R06C01
SEP-0076-T1

value: Control patient hospitalized for an infection


title: DO mNPC Sample PB368.78

description: Library name: PB368.78

value: Male


title: DO mNPC Sample PB367.45

description: Library name: PB367.45


title: Z980513

description: Library name: Z980513


title: Z130427

description: Library name: Z130427


title: DO mNPC Sample PB367.20

description: Library name: PB367.20


title: Blood sample DNA from control 77

description:
207678520176_R08C01
SEP-0077-T1


title: DO mNPC Sample PB367.19

description: Library name: PB367.19


title: Blood sample DNA from sepsis patient 48

description:
207678520176_R03C01
SEP-0048-T1


title: DO mNPC Sample PB367.06

description: Library name: PB367.06


title: DO mNPC Sample PB366.78

description: Library name: PB366.78


title: LR0118

description: Library name: LR0118


title: Blood sample DNA from control 20

description:
207678520176_R02C01
SEP-0020-T1


title: DO mNPC Sample PB366.49

description: Library name: PB366.49


title: Z150831

description: Library name: Z150831


title: DO mNPC Sample PB366.41

description: Library name: PB366.41


title: DO mNPC Sample PB368.06

description: Library name: PB368.06


title: DO mNPC Sample PB366.12

description: Library name: PB366.12


title: Z130425

description: Library name: Z130425


title: DO mNPC Sample PB366.03

description: Library name: PB366.03


title: Blood sample DNA from control 47

description:
207678520165_R08C01
SEP-0047-T1


title: DO mNPC Sample PB366.02

description: Library name: PB366.02


title: Blood sample DNA from sepsis patient 41

description:
207678520165_R07C01
SEP-0041-T1


title: Blood sample DNA from control 46

description:
207678520165_R06C01
SEP-0046-T1


title: Z150414

description: Library name: Z150414


title: Blood sample DNA from control 7

description:
207678520176_R04C01
SEP-0007-T1


title: 19468X82,esophogeal biopsy

city: Holladay

first: Jeffery

middle: C

last: Stevens

state: UT

address: 2004 East Lincoln Circ

department: Epidemiology

institute: Univristy of Utah

data_processing:
DESeq2
Assembly: HG38
Supplementary files format and content: EOE.counts.txt contains raw counts for each sample
Supplementary files format and content: EOE_DESeq.xlsx, Processed counts via DESeq2, https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

source_name: Esophagus

extract_protocol:
2-to-5 10-micron-thick FFPET sampleswere deparaffinized with NeoClear, rinsed in ethanol, dried, and applied to the High Pure FFPET RNA isolation kit (Roche Diagnostics #06650775001) with the manufacturer’s recommended on-column DNase treatment.
Libray prep was perfprormed using the IDT xgen-exome-hyb-panel-v2-targets-hg38 capture kit.

value: Esophagus

value: Normal


title: DO mNPC Sample PB365.57

description: Library name: PB365.57


title: DO mNPC Sample PB365.56

description: Library name: PB365.56


title: Blood sample DNA from sepsis patient 40

description:
207678520165_R05C01
SEP-0040-T1


title: LH0319

description: Library name: LH0319

value: skin

value: melanoma cells


title: Z150607

description: Library name: Z150607

value: non


title: 19468X77,esophogeal biopsy

value: EoE


title: Blood sample DNA from control 66

description:
207678520165_R04C01
SEP-0066-T1


title: 19468X8,esophogeal biopsy


title: DO mNPC Sample PB364.86

description: Library name: PB364.86


title: DO mNPC Sample PB365.46

description: Library name: PB365.46


title: Z130421

description: Library name: Z130421

value: NRAS


title: 19468X73,esophogeal biopsy


title: Blood sample DNA from sepsis patient 43

description:
207678520176_R01C01
SEP-0043-T1


title: DO mNPC Sample PB364.80

description: Library name: PB364.80


title: Blood sample DNA from sepsis patient 37

description:
207678520165_R03C01
SEP-0037-T1


title: 19468X72,esophogeal biopsy


title: Blood sample DNA from control 38

description:
207678520165_R02C01
SEP-0038-T1


title: DO mNPC Sample PB364.74

description: Library name: PB364.74


title: Z140625

description: Library name: Z140625


title: DTB_06-T

city: Chongqing

first: Zhen

last: Gong

address: Tian Sheng road

institute: Southwest University

description: Library name: DTB_06-T

data_processing:
The single-cell RNA-seq data were processed using the Cell Ranger 3.0.1 pipeline. FASTQs generated from Illumina sequencing output were aligned to the human genome, version GRCh38, using the STAR algorithm.Next, Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-Seq

source_name: blood

extract_protocol:
Whole blood samples were collected from patients diagnosed with 7 disseminated tuberculosis (DTB)
Cells were stained with 0.4% Trypan blue (Thermo Fisher, Cat. no. 14190144) to check the viability on Countess® II Automated Cell Counter (Thermo Fisher). 10× library preparation and sequencing Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in emulsion (GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 RevD). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.

value: blood

value: Immune Cell


title: 19468X81,esophogeal biopsy


title: DO mNPC Sample PB364.73

description: Library name: PB364.73

value: Neural Progenitor Cells


title: 19468X7,esophogeal biopsy


title: Blood sample DNA from sepsis patient 36

description:
207678520165_R01C01
SEP-0036-T1

value: Female


title: Blood sample DNA from control 59

description:
207678520164_R08C01
SEP-0059-T1


title: DTB_05-T

description: Library name: DTB_05-T


title: DO mNPC Sample PB364.66

description: Library name: PB364.66

value: Diversity Outbred


title: 19468X69,esophogeal biopsy


title: DTB_04-T

description: Library name: DTB_04-T


title: Blood sample DNA from sepsis patient 31

description:
207678520164_R07C01
SEP-0031-T1


title: 19468X68,esophogeal biopsy


title: 19468X67,esophogeal biopsy


title: DTB_03-T

description: Library name: DTB_03-T


title: DO mNPC Sample PB364.19

description: Library name: PB364.19


title: Blood sample DNA from control 5

description:
207678520164_R06C01
SEP-0005-T1


title: 19468X66,esophogeal biopsy


title: DTB_01-T

description: Library name: DTB_01-T


title: DTB_02-T

description: Library name: DTB_02-T


title: Blood sample DNA from sepsis patient 30

description:
207678520164_R05C01
SEP-0030-T1


title: Blood sample DNA from control 50

description:
207678520164_R04C01
SEP-0050-T1


title: DTB_07-T

description: Library name: DTB_07-T


title: DO mNPC Sample PB363.33

description: Library name: PB363.33


title: DO mNPC Sample PB364.51

description: Library name: PB364.51


title: 19468X64,esophogeal biopsy

value: UNAFFECTED


title: 19468X65,esophogeal biopsy


title: DO mNPC Sample PB363.01

description: Library name: PB363.01


title: DTB_07

description: Library name: DTB_07

data_processing:
The single-cell RNA-seq data were processed using the Cell Ranger 3.0.1 pipeline. FASTQs generated from Illumina sequencing output were aligned to the human genome, version GRCh38, using the STAR algorithm.Next, Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files


title: 19468X63,esophogeal biopsy


title: DTB_06

description: Library name: DTB_06


title: DO mNPC Sample PB363.02

description: Library name: PB363.02


title: Blood sample DNA from sepsis patient 29

description:
207678520164_R03C01
SEP-0029-T1

value: Blood


title: DTB_05

description: Library name: DTB_05


title: 19468X60,esophogeal biopsy


title: Blood sample DNA from sepsis patient 27

description:
207678520164_R01C01
SEP-0027-T1

value: Septic patient hospitalized for an infection


title: Blood sample DNA from control 65

description:
207678520164_R02C01
SEP-0065-T1

value: Control patient hospitalized for an infection


title: DO mNPC Sample PB362.73

description: Library name: PB362.73

value: Male


title: Blood sample DNA from control 18

description:
207678520120_R08C01
SEP-0018-T1


title: 19468X6,esophogeal biopsy

value: Esophagus


title: DTB_04

description: Library name: DTB_04


title: DO mNPC Sample PB362.56

description: Library name: PB362.56


title: Blood sample DNA from sepsis patient 25

description:
207678520120_R07C01
SEP-0025-T1


title: 19468X59,esophogeal biopsy


title: DTB_03

description: Library name: DTB_03


title: DTB_02

description: Library name: DTB_02


title: DO mNPC Sample PB362.11

description: Library name: PB362.11


title: Blood sample DNA from sepsis patient 23

description:
207678520120_R05C01
SEP-0023-T1


title: 19468X58,esophogeal biopsy


title: DO mNPC Sample PB362.06

description: Library name: PB362.06


title: 19468X57,esophogeal biopsy


title: DTB_01

description: Library name: DTB_01


title: NC3

city: taiyuan

first: qianqian

state: shanxi

address: 99 Longcheng Street, Xiaodian District

department: Department of Obstetrics and Gynecology

institute: Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital,

description: control group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes gene counts for each sample

source_name: SiHa

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

value: SiHa

value: WT


title: Blood sample DNA from control 22

description:
207678520120_R04C01
SEP-0022-T1


title: Blood sample DNA from sepsis patient 10

description:
207678520120_R03C01
SEP-0010-T1


title: 19468X56,esophogeal biopsy


title: NC2

description: control group, replicate biosample 2


title: DO mNPC Sample PB362.03

description: Library name: PB362.03

data_processing:
We aligned paired-end 75bp reads with bowtie v1.1.2 to a pooled “8-way” transcriptome containing strain-specific isoform sequences from all eight DO founder strains. For resolving multi-mapping reads and quantifying transcript- and gene- level expression counts, we utilized EMASE as implemented in GBRS v0.1.6.
Assembly: GRCm38/mm10
Supplementary files format and content: There are two kinds of procesed data files, one with the extension "expected_read_counts" and one with "tpm". The one with "expected_read_counts" contain the diploid gene counts for each gene and is used for downstream analysis. The one with "tpm" contains the transcripts per million value for each gene and is used for filtering genes with low expression.


title: Blood sample DNA from control 57

description:
207678520120_R02C01
SEP-0057-T1


title: 19468X54,esophogeal biopsy


title: DO mNPC Sample PB362.01

description: Library name: PB362.01


title: DO mNPC Sample PB362.55

description: Library name: PB362.55


title: KD3

description: KD group, replicate biosample 3

value: KD


title: Blood sample DNA from sepsis patient 1

description:
207678520120_R01C01
SEP-0001-T1


title: 19468X53,esophogeal biopsy


title: DO mNPC Sample PB361.91

description: Library name: PB361.91


title: KD2

description: KD group, replicate biosample 2


title: DO mNPC Sample PB361.90

description: Library name: PB361.90


title: Scaffold cells, Day 9, MOG

city: Ann Arbor

first: Lonnie

middle: D

last: Shea

state: MI

address: 1600 Huron Parkway

department: Biomedical Engineering

institute: University of Michigan

description:
Library name: 4831_2
10x Genomics

data_processing:
Cellranger v6.1.0 was used for sample demultiplexing, barcode processing, and gene counting.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PCL scaffold

growth_protocol: Spleens and lymph nodes (inguinal, axillary, and brachial) from donor mice were harvested, processed to a single cell suspension and cultured in RPMI with 10% FBS, 2 mM L-glutamine, 100 IU/mL penicillin, 0.1 mg/mL streptomycin, 1x non-essential amino acids solution, 1 mM sodium pyruvate, 10 mM HEPES, 50 µg/mL peptide antigen, and 25 ng/mL rmIL-12 p70. After 72 hrs in culture at 37°C and 5% CO2, non-adherent cells were harvested.

extract_protocol:
PCL implants were processed for scRNAseq by pooling 2-3 mice for each condition at each time point. Briefly, scaffolds were minced and incubated in RPMI containing 0.2 U/mL Liberase TL (Roche) at 37 ℃ for 20 minutes and then passed through a 70 µm filter to make a single cell suspension. ACK buffer (Gibco) was used to lyse RBCs in suspension, and cells were washed in PBS before being resuspended to 1 million cells/mL in PBS containing 0.04% w/v BSA
10x Genomics single cell 5' kit

treatment_protocol: Donor mice were subcutaneously immunized with150 µL of an emulsion containing 1:1 complete Freund’s adjuvant (incomplete Freund’s adjuvant with 4 mg/mL heat killed M. tuberculosis H37 Ra) : PBS with 4 mg/mL peptide (MOG or OVA. Chronic EAE was induced by adoptive transfer of T cells reactive to myelin oligodendrocyte glycoprotein peptide 35-55 and control animals received an adoptive transfer of T cells reactive to Ovalbumin peptide 323-339. 40 million cells were administered by i.p. injection.

value: PCL scaffold

tag: age

value: 8-9 weeks old

value: female

tag: disease model

value: AT MOG-reactive splenocytes

tag: time

value: Day 9

value: symptomatic


title: Blood sample DNA from control 8

description:
207678520120_R06C01
SEP-0008-T1

value: Female


title: KD1

description: KD group, replicate biosample 1


title: DO mNPC Sample PB362.09

description: Library name: PB362.09

extract_protocol:
Total RNA was extracted using the Quick-RNA 96 well format kit (Zymo Research) with in-column DNase treatment.
Sequencing libraries were prepared by Akesogen using the TruSeq Stranded mRNA HT kit (Illumina, Cat no. 20020595) and included ribosomal RNA reduction and poly-A selection, enzymatic fragmentation, cDNA synthesis from random hexamer priming, adaptor ligation and PCR amplification steps to generate indexed, stranded mRNA-seq libraries. Libraries were checked for quality and quantitated with the Agilent Bioanalyzer, and samples that failed QC were repeated starting from the cryovial stage. Finally, pooled libraries were sequenced on the NextSeq platform (Illumina) using the NextSeq 500/550 High Output v2 150-cycle kits (Illumina, Cat no. FC-404-2002). To minimize technical variation, samples were randomly assigned to lanes prior to sample processing steps, barcoded, and multiplexed at 16 samples per flow cell, yielding 6M-55M 2x75bp paired-end (PE) reads per sample

value: Neural Progenitor Cells

value: Diversity Outbred


title: 19468X5,esophogeal biopsy

value: EoE


title: DO mNPC Sample PB361.88

description: Library name: PB361.88


title: DO mNPC Sample PB361.84

description: Library name: PB361.84


title: Scaffold cells, Day 9, OVA

description:
Library name: 4831_1
10x Genomics

value: AT OVA-reactive splenocytes

value: control


title: Add DMSO to MCF7 cells as a negative control rep3

city: Shen yang

first: siyu

last: jiang

state: Liaoning

address: 77 Puhe Road

department: School of Basic Medicine

institute: CHINA Medical University

description:
S3
Group.Res_vs_Sen.degene_all.annot.txt

data_processing:
Data filtering: The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification: Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis: Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation: To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
1.1.1Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107).
1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min.
1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column.
1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification.
1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification.
1.2 DNA Purification
1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate.
1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate.
1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube.
1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min.
1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA.
1.3 RNA Purification
1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting.
1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow.
1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.
1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.
1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.
1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube.
1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min.
1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.


title: Scaffold cells, Day 7, MOG

description:
Library name: 4809_2
10x Genomics

value: Day 7

value: pre-symptomatic


title: 19468X49,esophogeal biopsy

value: Esophagus


title: 19468X55,esophogeal biopsy


title: 19468X48,esophogeal biopsy


title: Scaffold cells, Day 7, OVA

description:
Library name: 4809_1
10x Genomics


title: DO mNPC Sample PB361.74

city: Bar Harbor

first: Selcan

address: 600 Main Street

institute: The Jackson Laboratory

description: Library name: PB361.74


title: DO mNPC Sample PB361.81

description: Library name: PB361.81

value: Male


title: 19468X50,esophogeal biopsy


title: Add Adriamycin to MCF-7 cells to induce Adriamycin resistant cells rep3

description:
R3
Group.Res_vs_Sen.degene_all.annot.txt


title: NC1

description: control group, replicate biosample 1

value: SiHa

value: WT


title: Add DMSO to MCF7 cells as a negative control rep2

description:
S2
Group.Res_vs_Sen.degene_all.annot.txt


title: 19468X45,esophogeal biopsy


title: Add Adriamycin to MCF-7 cells to induce Adriamycin resistant cells rep2

description:
R2
Group.Res_vs_Sen.degene_all.annot.txt


title: DO mNPC Sample PB361.69

description: Library name: PB361.69


title: 19468X44,esophogeal biopsy


title: CD248_pos_2

city: Hangzhou

first: Mo

last: Li

address: Jiefang road 88

department: Department of Cardiology of The Second Affiliated Hospital, School of Medicine

institute: Zhejiang University

description: Library name: Sample6

data_processing:
Sequencing was performed on an Illumina Novaseq 6000 platform. Around 50 million RNA-seq clean mapping reads were obtained per sample using HISAT2 (v 2.1.0). Transcripts were assembled and raw gene read counts were calculated using StringTie (v2.2.0).
Assembly: mm39
Supplementary files format and content: FPKM values for all Samples

source_name: Heart tissue

extract_protocol:
Total RNA from FACs sorted CD248+ and CD248- fibroblasts was isolated using the RNeasy Mini Kit (Qiagen), and RNA purity and quantification were assessed using the Qubit 2.0 fluorometer (Life Technologies). RNA integrity was evaluated using the 2100 Bioanalyzer (Agilent Technologies).
Libraries were prepared with the TruSeq Stranded Total RNA Sample Preparation kit (Illumina)

value: Heart tissue

value: Cardiac fibroblasts

value: FACS-sorted CD248+ PDGFR-α+ cardiac fibroblasts


title: CD248_pos_1

description: Library name: Sample5


title: Add Adriamycin to MCF-7 cells to induce Adriamycin resistant cells rep1

description:
R1
Group.Res_vs_Sen.degene_all.annot.txt


title: DO mNPC Sample PB361.21

last: Aydin

description: Library name: PB361.21

source_name: Neural Progenitor Cells


title: 19468X43,esophogeal biopsy


title: Negative control plasmid overexpressing C12orf43 rep3  in MCF-7

description:
NC43-3
C12orf43_vs_Con.degene.txt


title: 19468X42,esophogeal biopsy


title: Negative control plasmid overexpressing C12orf43 rep2    in MCF-7

description:
NC43-2
C12orf43_vs_Con.degene.txt


title: DO mNPC Sample PB361.15

description: Library name: PB361.15


title: CD248_neg_3

description: Library name: Sample3

value: FACS-sorted CD248- PDGFR-α+ cardiac fibroblasts


title: Add DMSO to MCF7 cells as a negative control rep1

description:
S1
Group.Res_vs_Sen.degene_all.annot.txt


title: CD248_pos_4

description: Library name: Sample8


title: 19468X47,esophogeal biopsy


title: 19468X41,esophogeal biopsy


title: CD248_pos_3

description: Library name: Sample7


title: Negative control plasmid overexpressing C12orf43 rep1  in MCF-7

description:
NC43-1
C12orf43_vs_Con.degene.txt


title: DO mNPC Sample PB361.73

description: Library name: PB361.73


title: Overexpression of C12orf43 rep3  plasmid in MCF-7

description:
C43-3
C12orf43_vs_Con.degene.txt


title: CD248_neg_1

description: Library name: Sample1


title: CD248_neg_2

description: Library name: Sample2


title: DO mNPC Sample PB361.01

description: Library name: PB361.01


title: 19468X39,esophogeal biopsy


title: Overexpression of C12orf43 rep2  plasmid in MCF-7

description:
C43-2
C12orf43_vs_Con.degene.txt


title: ECKO Nogo high fat diet (HFD) replicate 4

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

description: RNAseq

data_processing:
Fastq files were processed using STAR and Cuffinks
Assembly: mm10
Supplementary files format and content: count files contain normalized data

source_name: Heart

extract_protocol:
FACS sorted ECs were isolated from hearts of ApoE-/- and Nogo-A/B(ECKO)ApoE-/- mice after 8 weeks post-TAC and were then processed for bulk RNAseq
Libraries were prepared as per the manufacturer's protocol (Trueseq v2 protocol)

value: EC

value: Heart

value: C57BL/6 ApoE-/-

value: Nogo-B KO


title: 19468X40,esophogeal biopsy

value: EoE


title: DO mNPC Sample PB360.87

description: Library name: PB360.87

value: Neural Progenitor Cells

value: Diversity Outbred

value: Female


title: DO mNPC Sample PB360.94

description: Library name: PB360.94


title: CD248_neg_4

description: Library name: Sample4


title: DO mNPC Sample PB361.02

description: Library name: PB361.02


title: Overexpression of C12orf43 rep1  plasmid in MCF-7

description:
C43-1
C12orf43_vs_Con.degene.txt


title: ECKO Nogo high fat diet (HFD) replicate 3

description: RNAseq


title: 19468X37,esophogeal biopsy


title: Negative control plasmid overexpressing C12orf43 rep3 in MCF-7

description:
NC-3-R-Input
C12orf43VSNC.All.fpkm.anno.txt


title: ECKO Nogo high fat diet (HFD) replicate 2

description: RNAseq


title: DO mNPC Sample PB360.82

description: Library name: PB360.82


title: 19468X38,esophogeal biopsy


title: Negative control plasmid overexpressing C12orf43 rep2  in MCF-7

description:
NC-2-R-Input
C12orf43VSNC.All.fpkm.anno.txt


title: 19468X35,esophogeal biopsy


title: Negative control plasmid overexpressing C12orf43 rep1 in MCF-7

description:
NC-1-R-Input
C12orf43VSNC.All.fpkm.anno.txt


title: ECKO Nogo high fat diet (HFD) replicate 1

description: RNAseq


title: DO mNPC Sample PB360.76

description: Library name: PB360.76


title: DO mNPC Sample PB360.72

description: Library name: PB360.72


title: WT mice on high fat diet (HFD) replicate 4

description: RNAseq

value: Nogo-B WT


title: 19468X34,esophogeal biopsy

value: Esophagus


title: Overexpression of C12orf43 rep2 plasmid in MCF-7

description:
C12orf43-2-Input
C12orf43VSNC.All.fpkm.anno.txt


title: Overexpression of C12orf43 rep3 plasmid in MCF-7

description:
C12orf43-3-Input
C12orf43VSNC.All.fpkm.anno.txt


title: 19468X32,esophogeal biopsy


title: 19468X33,esophogeal biopsy


title: WT mice on high fat diet (HFD) replicate 3

description: RNAseq


title: 19468X31,esophogeal biopsy


title: DO mNPC Sample PB360.69_B

description: Library name: PB360.69_B

value: Male


title: Overexpression of C12orf43 rep1 plasmid in MCF-7

description:
C12orf43-1-Input
C12orf43VSNC.All.fpkm.anno.txt


title: WT mice on high fat diet (HFD) replicate 2

description: RNAseq


title: DO mNPC Sample PB360.69

description: Library name: PB360.69


title: WT mice on high fat diet (HFD) replicate 1

description: RNAseq


title: DO mNPC Sample PB360.84

description: Library name: PB360.84


title: DO mNPC Sample PB360.63

description: Library name: PB360.63


title: 19468X36,esophogeal biopsy


title: WT mice on chow diet (CD) replicate 4

description: RNAseq


title: 19468X30,esophogeal biopsy


title: Negative control plasmid overexpressing C12orf43 rep3 in ZR-75-1

description:
NC-3
C12orf43VSNC.All.fpkm-RNA.anno.txt


title: DO mNPC Sample PB360.57

description: Library name: PB360.57


title: 19468X3,esophogeal biopsy

value: Normal


title: WT mice on chow diet (CD) replicate 3

description: RNAseq


title: DO mNPC Sample PB360.53

description: Library name: PB360.53


title: 19468X29,esophogeal biopsy


title: DO mNPC Sample PB360.52

description: Library name: PB360.52


title: Overexpression of C12orf43 rep3 plasmid in ZR-75-1

description:
C12orf43-3
C12orf43VSNC.All.fpkm-RNA.anno.txt


title: WT mice on chow diet (CD) replicate 1

description: RNAseq


title: WT mice on chow diet (CD) replicate 2

description: RNAseq


title: Negative control plasmid overexpressing C12orf43 rep1 in ZR-75-1

description:
NC-1
C12orf43VSNC.All.fpkm-RNA.anno.txt


title: DO mNPC Sample PB360.50

description: Library name: PB360.50


title: 19468X27,esophogeal biopsy


title: Overexpression of C12orf43 rep2 plasmid in ZR-75-1

description:
C12orf43-2
C12orf43VSNC.All.fpkm-RNA.anno.txt


title: 19468X26,esophogeal biopsy


title: Overexpression of C12orf43 rep1 plasmid in ZR-75-1

description:
C12orf43-1
C12orf43VSNC.All.fpkm-RNA.anno.txt


title: DO mNPC Sample PB360.49

description: Library name: PB360.49


title: wt_6_r

city: London

first: Jeremie

last: Subrini

address: 1 Midland road

country: United Kingdom

institute: The Francis Crick Intitute

description:
batch 5
SUB4754A88

data_processing:
Raw RNA-seq reads were processed using the RNA-seq nf-core pipeline (v3.2), star_rsem was used to generate raw reads counts.  The read counts were processed in R using the DESeq2 (v1.34) package. Very lowly expressed genes were filtered out by applying a rowSums filter of >=5 to the raw counts table. Principal component analysis (PCA) plots were generated using the top 500 most variable genes, applying the vst()  function and limma::removeBatchEffect() to remove batch effects for PCA visualisation. Raw counts were batch corrected and normalised using the DESeq() function, specifying “~batch + Sample_Genotype” in the design formula.  Log2 fold change (log2FC) and adjusted p-values between KO and WT were calculated using the results() function in DESeq2, specifying the “BH” (Benjamini-Hochberg p-value adjustment). Log2FCs were shrunk using the lfcShrink(type=”apeglm”) function.
Assembly: mm39
Supplementary files format and content: tab-deliminted file containing raw counts for each sample

source_name: testis

extract_protocol:
About 20mg of frozen testis pieces were placed in Precellys Homogenizer tubes 2.8 mm ceramic reinforced (Precellys 50722019, Bertin Technologies, France) on dry ice. 500μl of Trizol reagent (Sigma-Aldrich, USA) was added to the tubes and the samples placed in a Bertin Precellys 24-Dual High-throughput Tissue Homogenizer (Bertin Technologies, France). The machine was then run with the factory programme 5: 6,500 rpm for 20 seconds, automatic 25 seconds of pause and a repeat of 6500 rpm for 20 seconds. The lysate was then centrifuged for 5 minutes at 12,000 x g at 4°C and the clear supernatant transferred to a MaXtract High Density phase lock tube (Qiagen, UK). After 5 minutes of incubation at room temperature, 100μl of chloroform was added and tubes shaken vigorously for 2-3 minutes. Tubes were spun down for 15 minutes at 12,000 x g at 4°C. The upper aqueous phase was transferred to a new tube and 250μl of isopropanol added and mixed by pipetting. After 10 minutes of incubation at room temperature samples were spun down for 10 minutes at 12,000 x g at 4°C. The supernatant was discarded, the RNA pellet washed with 1ml of 75% ethanol and the samples spun down for 5 minutes at 7,500 x g at 4°C. Finally, the pellet was air-dried for 5-10 minutes and resuspended in 40μl of nuclease-free water.
Libraries were prepared using the NEBNext Ultra II Directional PolyA mRNA kits according to manufacturer instructions.

value: testis

value: control


title: wt_5_r

description:
batch 5
SUB4754A87


title: DO mNPC Sample PB360.48

description: Library name: PB360.48


title: 19468X25,esophogeal biopsy


title: ChIP-seq-01_Input_SPT5AID_shNT_H2O-3h

city: Chicago

first: Yuki

last: Aoi

address: 303 E Superior St. SQBRC 7-300

institute: Northwestern University

description: ChIP-seq

data_processing:
Following the quality-trimming using trimmomatic 0.39, the reads were aligned to the genome using bowtie 2.4.5 and convereted to genome coverage file in bigwig format using deepTools 3.5.1.
Assembly: hg38
Supplementary files format and content: bigwig files containing genome coverage data

extract_protocol:
Cells were crosslinked in 1% formaldehyde/PBS and sonicated using Covaris to solubilize chromatin fraction. Following immunoprecipitation, elution fraction was reverse crosslinked and DNA was purified using PCR purification kit (QIAGEN).
Libraries were constructed using KAPA HyperPrep kit (Roche).

value: Colorectal adenocarcinoma


title: Uty_2_r

description:
batch 5
SUB4754A86


title: ChIP-seq-01_Pol2_SPT5AID_shARMC5-2_Aux-3h

description: ChIP-seq


title: 19468X24,esophogeal biopsy


title: Negative control plasmid overexpressing C12orf43 rep2 in ZR-75-1

description:
NC-2
C12orf43VSNC.All.fpkm-RNA.anno.txt


title: DO mNPC Sample PB360.21

description: Library name: PB360.21


title: DO mNPC Sample PB360.32

description: Library name: PB360.32


title: 19468X28,esophogeal biopsy


title: DO mNPC Sample PB360.20

description: Library name: PB360.20


title: ChIP-seq-01_Pol2_SPT5AID_shARMC5-1_Aux-3h

description: ChIP-seq


title: Eif2s3y_3

description:
batch 5
SUB4754A83


title: 19468X20,esophogeal biopsy


title: DO mNPC Sample PB360.02

description: Library name: PB360.02


title: ChIP-seq-01_Pol2_SPT5AID_shARMC5-1_H2O-3h

description: ChIP-seq


title: 19468X2,esophogeal biopsy


title: Eif2s3y_1

description:
batch 5
SUB4754A81


title: ChIP-seq-01_Pol2_SPT5AID_shNT_Aux-3h

description: ChIP-seq


title: Eif2s3y_2

description:
batch 5
SUB4754A82


title: DO mNPC Sample PB359.78

description: Library name: PB359.78


title: Uty_1_r

description:
batch 5
SUB4754A85


title: 19468X17,esophogeal biopsy


title: AZFa_4

description:
batch 5
SUB4754A80


title: DO mNPC Sample PB359.48

description: Library name: PB359.48


title: DO mNPC Sample PB359.77

description: Library name: PB359.77


title: ChIP-seq-01_Pol2_SPT5AID_shARMC5-2_H2O-3h

description: ChIP-seq


title: scATAC-seq of ccRCC for RCC76

city: Nanning

first: Zhenyuan

last: Yu

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

data_processing:
Preliminary sequencing results (bcl files) were converted to FASTQ files with CellRanger ATAC V1.2.0
The CellRanger (10X Genomics) secondary analysis pipeline was used to generate a digital gene expression matrix
Normalization and additional analysis by Seurat and Signac R package
Assembly: GRCh38 for human data
Supplementary files format and content: The peaks.bed, singlecell.csv and fragments.tsv.gz files for scATAC-seq.

source_name: Clear cell renal cell carcinoma

extract_protocol:
Suitable nuclei concentrations were adjusted from the above experiment. As mentioned in the previous study (avoiding potential cell duplets), the number of target nucleus captured in each sample was 7,000. We adopted 10x Genomics ‘Chromium Single Cell ATAC Reagent Kits User Guide’ for library preparation (https://support.10xgenomics.com/single-cell-atac/library-prep/doc/technical-note-chromium-next-gem-single-cell-atac-v11-reagent-workflow-and-software-updates). Briefly, the ATAC Buffer (10x Genomics, 200122) and ATAC Enzyme (10x Genomics, 200123) were added to the 5 µL nuclei, which was incubated for 60 min at 37 °C. We prepared ‘Master Mix’, including 56.5 µL of Barcoding Reagent B (10x Genomics, 2000194), 1.5 µL of Reducing Agent B (10x Genomics, 2000087) and 2 µL of Barcoding Enzyme (10x Genomics, 2000125). After mixing the nuclei with the Master Mix, we added it to the Chromium Chip E (10x Genomics, 2000121). At the same time, we added Partitioning Oil (10x Genomics, 220088) and Chromium Single Cell ATAC Gel Beads (10x Genomics, 2000132) to the Chromium Chip E. The Chromium Chip E was placed into a Chromium Single Cell Controller instrument (10x Genomics) before attaching a 10x Gasket (10x Genomics, 3000072). Then, the Chromium Single Cell Controller Instrument could be run. The gel bead in emulsions (GEMs) were generated after the above steps. Subsequently, GEMs were incubated and cleaned by using Dynabeads (10x Genomics, 2000048) and SPRIselect (Beckman Coulter, B23318). scATAC-seq library construction eliminates the process of reverse transcription compared with scRNA-seq. PCR was performed after ‘Sample Index PCR Mix’ and Single Index Kit N Set A (10x Genomics, 1000212) were added into the samples. The details of PCR parameters could be referred to Chromium Single Cell ATAC Reagent Kits User Guide. DNA libraries were sequenced by NovaSeq 6000 (Illumina, San Diego, CA). Consistent with previous studies, we followed the 2 × 50 paired-end sequencing scheme: 50 bp read 1N, 8 bp i7 index, 16 bp i5 index and 50 bp read 2N.
10X Genomics Chromium Single Cell ATAC Reagent Kits V1

value: Total clear cell renal cell carcinoma Homogenate


title: AZFa_3

description:
batch 5
SUB4754A79


title: 19468X14,esophogeal biopsy


title: 19468X12,esophogeal biopsy


title: AZFa_2

description:
batch 5
SUB4754A78


title: scATAC-seq of ccRCC for RCC61


title: DO mNPC Sample PB359.34

description: Library name: PB359.34


title: 19468X23,esophogeal biopsy

value: UNAFFECTED


title: Eif2s3y_4

description:
batch 5
SUB4754A84


title: AZFa_1

description:
batch 5
SUB4754A77


title: 19468X11,esophogeal biopsy


title: scATAC-seq of ccRCC for RCC30


title: DO mNPC Sample PB358.57

description: Library name: PB358.57


title: DO mNPC Sample PB359.90

description: Library name: PB359.90


title: 3516_2_AML_CITE

first: Cameron

last: Park

institute: Columbia University

library_source: other

data_processing:
10x genomics pipeline
CellRanger 5.0.0
Assembly: GRCh38-2020-A
Supplementary files format and content: zipped csv file for counts and metadata
Library strategy: CITE-seq

molecule: protein

source_name: bone  marrow

extract_protocol:
CML data were obtained from previously described sequencing runs and all cells were analyzed for the current study, whereas we previously reported only the subset of data originating from T cells. For preparation of AML samples, cryopreserved primary bone marrow mononuclear cells (BMMCs) or peripheral blood mononuclear cells (PBMCs, for the matched sample from R 3501) were thawed on the day of sequencing at 37°C and dispensed into a warmed solution of 10% FBS, 10% DNaseI (StemCell Technologies, cat. No. 07900) in PBS. The cell suspension was centrifuged at 200g for 10 minutes at room temperature. Viable cells were negatively selected using MACS Dead Cell Removal Kit (Miltenyi Biotec, cat. No. 130-090-101). Collected live cells were resuspended in warmed Cell Staining Buffer (BioLegend). Cells were stained with TotalSeq C hashtag antibodies as well as CITE-seq antibodies according to manufacturer instructions. For batch AML1, after washing three times, cells from four samples were combined into one pool with approximately 20,000 cells from each sample and diluted to a final concentration of 1000 cells/ μl in 0.04% UltraPure BSA (ThermoFisher). Seven total pools were processed in this way. Subsequent samples (i.e. those in batch AML2, DLI products, and controls samples) were run individually.
Approximately 50,000 cells from each of the pooled samples or 10,000 cells from each of the individual samples were loaded into one lane of a 10x Genomics ChromiumTM instrument (10x Genomics) according to the manufacturer’s instructions. The scRNA-seq libraries were processed using Chromium Single Cell 5’ Library & Gel Bead v2 Kit (10x Genomics), and coupled scCITE-seq libraries were obtained using ChromiumTM single cell Feature Barcode kit. Quality control for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent).

value: bone  marrow

value: DLI


title: 19468X15,esophogeal biopsy


title: 19468X10,esophogeal biopsy


title: Zfy1_3r_2

description:
batch 4
SUB4754A76_2


title: 3516_1_AML_CITE


title: DO mNPC Sample PB358.37

description: Library name: PB358.37


title: 3514_product_DLI_CITE

source_name: peripheral blood

value: peripheral blood


title: 19456X17,esophogeal biopsy


title: Zfy1_3r

description:
batch 4
SUB4754A76


title: Uba1y_1r_2

description:
batch 4
SUB4754A75_2


title: 3514_2_AML_CITE


title: DO mNPC Sample PB358.32

description: Library name: PB358.32


title: 19456X19,esophogeal biopsy


title: 3514_1_AML_CITE


title: 18483X24,esophogeal biopsy


title: Uba1y_1r

description:
batch 4
SUB4754A75


title: 18483X23,esophogeal biopsy


title: Ddx3y_4r_2

description:
batch 4
SUB4754A74_2


title: DO mNPC Sample PB358.24

description: Library name: PB358.24


title: 3512_3_AML_CITE


title: DO mNPC Sample PB358.14

description: Library name: PB358.14


title: 18483X22,esophogeal biopsy


title: Ddx3y_4r

description:
batch 4
SUB4754A74


title: DO mNPC Sample PB358.08

description: Library name: PB358.08


title: 3512_2_AML_CITE


title: Ddx3y_3r_2

description:
batch 4
SUB4754A73_2


title: 3512_1_AML_CITE


title: 18483X21,esophogeal biopsy


title: DO mNPC Sample PB358.44

description: Library name: PB358.44


title: DO mNPC Sample PB358.01

description: Library name: PB358.01


title: Ddx3y_3r

description:
batch 4
SUB4754A73


title: 18483X19,esophogeal biopsy


title: 3510_3_AML_CITE


title: 3510_2_AML_CITE


title: DO mNPC Sample PB357.29

description: Library name: PB357.29


title: Kdm5d_4r_2

description:
batch 4
SUB4754A72_2


title: 18483X17,esophogeal biopsy


title: Zfy1_and_2_DKO_4

data_processing:
Replicates from the P10 and adult 10x nuclei datasets were aligned to the mm39 genome using STARsolo (v2.7.9), specifying the parameters –soloMultiMappers EM –outFilterScoreMin 30 --soloFeatures Gene GeneFull --soloType CB_UMI_Simple --soloFeatures Gene GeneFull --soloUMIlen 12 --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIdedup 1MM_CR. Empty droplets were separated from nuclei using the proportion of reads mapping to intronic reads. Replicates were then processed in the Seurat R package (v4.3.0). Cells were retained if they had <5% reads aligning to mitochondrial and rRNA genes, if the total number of molecules within a cell was between 1000 and 50000 and the number of genes detected per cell was between 500 and 10000. The data was normalised using NormalizeData, then FindVariableFeatures. The dataset was scaled using ScaleData. Principle Component Analysis was applied using RunPCA followed by FindNeighbours and FindClusters. Uniform Manifold Approximation and Projection was estimated for the integrated dataset using RunUMAP. Doublets were identified using the DoubletFinder R package (v2.0.3). Replicates from each KO were integrated together, then the integrated KOs from their respective P10 and adult datasets were integrated with each other using SelectIntegrationFeatures, FindIntegrationAnchors and IntegrateData, generating one integrated dataset for the P10 10x data, and another for the adult 10x data. Each dataset was processed using ScaleData, then RunPCA and RunUMAP. Clusters were identified using a 0.5 resolution for both the adult and P10 datasets. In the adult dataset, ambient RNA clusters were identified using the FindAllMarkers function, and subsequently removed.
Assembly: mm39
Supplementary files format and content: tab-separated matrix files

molecule: nuclear RNA

extract_protocol:
On ice, around 10mg of frozen testis was homogenised in 1ml of lysis buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8, 1% BSA, 0.1% IGEPAL and freshly added 1 µM DTT, 0.4 U µl−1 RNase Inhibitor (New England BioLabs), 0.2 U µl−1 SUPERasIn (ThermoFischer Scientific)) and incubated on ice for 4 minutes. The lysate was filtered through a 30µm filter and then centrifuged at 500g for 5 minutes at 4C. The supernatant was removed, and the pellet resuspended in 1ml of wash buffer 1 (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8, 1% BSA, and freshly added 1 µM DTT, 0.4 U µl−1 RNase Inhibitor, 0.2 U µl−1 SUPERasIn). This was spun down at 500g for 5 minutes at 4°C and washing step repeated. Next the pellet was resuspended in 670 µl of freshly diluted dithio-bis (succinimidyl propionate) (DSP) (1mg/ml in PBS) and incubated at room temperature for 30 minutes. Fixation was quenched by adding 14.07µl Tris-HCL, pH8. Nuclei were spined down at 500g for 5 minutes at 4C and resuspended in 1ml of wash buffer 2 (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10mM Tris-HCL, pH8, 1% BSA, and freshly added 1 µM DTT, 0.4 U µl−1 RNase Inhibitor, 0.2 U µl−1 SUPERasIn). The sample were spun down one more time at 500g for 4 minutes at 4°C and the pellet resuspended in 0.04% BSA in PBS.  Testis nuclei isolation was adapted from a previously published protocol36. On ice, around 10mg of frozen testis was homogenised in 1ml of lysis buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8, 1% BSA, 0.1% IGEPAL and freshly added 1 µM DTT, 0.4 U µl−1 RNase Inhibitor (New England BioLabs), 0.2 U µl−1 SUPERasIn (ThermoFischer Scientific)) and incubated on ice for 4 minutes. The lysate was filtered through a 30µm filter and then centrifuged at 500g for 5 minutes at 4C. The supernatant was removed, and the pellet resuspended in 1ml of wash buffer 1 (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8, 1% BSA, and freshly added 1 µM DTT, 0.4 U µl−1 RNase Inhibitor, 0.2 U µl−1 SUPERasIn). This was spun down at 500g for 5 minutes at 4°C and washing step repeated. Next the pellet was resuspended in 670 µl of freshly diluted dithio-bis (succinimidyl propionate) (DSP) (1mg/ml in PBS) and incubated at room temperature for 30 minutes. Fixation was quenched by adding 14.07µl Tris-HCL, pH8. Nuclei were spined down at 500g for 5 minutes at 4C and resuspended in 1ml of wash buffer 2 (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10mM Tris-HCL, pH8, 1% BSA, and freshly added 1 µM DTT, 0.4 U µl−1 RNase Inhibitor, 0.2 U µl−1 SUPERasIn). The sample were spun down one more time at 500g for 4 minutes at 4°C and the pellet resuspended in 0.04% BSA in PBS.
Libraries were prepared according to the manufacturers protocol from 10X Genomics for 10X_3prime_mRNA


title: Kdm5d_4r

description:
batch 4
SUB4754A72


title: 3509_product_DLI_CITE


title: Kdm5d_3r_2

description:
batch 4
SUB4754A71_2


title: Zfy1_and_2_DKO_3


title: DO mNPC Sample PB357.25

description: Library name: PB357.25


title: DO mNPC Sample PB357.12

description: Library name: PB357.12


title: 3510_1_AML_CITE


title: DO mNPC Sample PB357.26

description: Library name: PB357.26


title: Ctrl_3


title: 3507_product_DLI_CITE


title: mPFC, WT, m, K, 2339, biol rep 4

city: Münster

first: Christa

last: Hohoff

address: Albert-Schweitzer-Campus 1, A9

department: Department of Psychiatry

institute: University of Muenster

description:
WT_m_K_2339 _P
39__33_RNA_r_mPFC_2339_m

data_processing:
Demultiplexing and conversion of samples to fastq data (bcl2fastq2 conversion software v. 2.20; Illumina) and quality control (FastQC v. 0.11.9; Babraham Bioinformatics)
Adapter trimming and read filtering (Trimmomatic v. 0.38)
Alignment of resulting reads (HISAT2 v. 2.1.0) to reference genome (Ensembl GRCm38)
Sorting (SAMtools v. 1.9) and counting of reads into genomic features (htseq-count v .0.11.1)
Assembly: Ensembl GRCm38
Supplementary files format and content: .xlsx file includes raw read counts aligned to Ensembl GRCm38 genome

source_name: medial prefrontal cortex

growth_protocol: Controlled housing conditions (1 same-sex KO-WT-littermate pair per cage), filtertops, 22±2°C, 55±10% humidity,12h:12h light-dark cycle, sawdust as bedding plus nesting material, tab water and standard diet ad libitum

extract_protocol:
RNA was harvested using Direct-zol RNA Micro- or Mini-Prep Kit (Zymo Research) resulting in total RNA of good quality (RIN > 7.5) and sufficient amount (110-250ng for hippocampus samples, 200-500ng for prefrontal cortex samples) to be used for library construction
RNA libraries for mRNA-seq were prepared using the NEBNext Ultra II RNA directional kit (BioLabs) following manufacturer protocols

treatment_protocol: Four weeks of non-stress control condition or chronic stress paradigm (unpredictably applied different mild stressors) followed by sacrificing (5% isoflurane, 50 sec.; decapitation 10 sec. later) to dissect hippocampi and prefrontal cortices (stored in RNAlater 6 to 8 min. after decapitation)

tag: brain part

value: right hemisphere

value: medial prefrontal cortex

value: wildtype (WT)

value: male

value: non-stress (K)


title: Kdm5d_3r

description:
batch 4
SUB4754A71


title: Zfy2_2


title: Zfy12_4r_2

description:
batch 4
SUB4754A70_2


title: mPFC, WT, m, K, 2411, biol rep 3

description:
WT_m_K_2411 _P
35__37_RNA_r_mPFC_2411_m


title: 3507_4_AML_CITE


title: Zfy12_4r

description:
batch 4
SUB4754A70


title: Ctrl_2


title: mPFC, WT, m, K, 2302, biol rep 2

description:
WT_m_K_2302 _P
31__31_RNA_r_mPFC_2302_m


title: 3507_3_AML_CITE


title: mPFC, WT, m, K, 2244, biol rep 1

description:
WT_m_K_2244 _P
25__25_RNA_r_mPFC_2244_m


title: Zfy12_3r_2

description:
batch 4
SUB4754A69_2


title: Zfy2_1


title: DO mNPC Sample PB361.63

description: Library name: PB361.63

value: Neural Progenitor Cells

value: Diversity Outbred

value: Female


title: 3507_2_AML_CITE


title: mPFC, WT, m, CS, 2434, biol rep 4

description:
WT_m_CS_2434 _P
38__40_RNA_r_mPFC_2434_m

value: chronic stress (CS)


title: Zfy1_1

value: testis


title: 3507_1_AML_CITE


title: mPFC, WT, m, CS, 2395, biol rep 3

description:
WT_m_CS_2395 _P
34__36_RNA_r_mPFC_2395_m


title: UTY_KO_P10_1


title: Zfy2_4r_2

description:
batch 4
SUB4754A68_2


title: 3505_product_DLI_CITE


title: mPFC, WT, m, CS, 2257, biol rep 2

description:
WT_m_CS_2257 _P
30__30_RNA_r_mPFC_2257_m


title: Zfy2_4r

description:
batch 4
SUB4754A68


title: Eif2s3y_KO_P10_2


title: Eif2s3y_KO_P10_1


title: Zfy2_3r_2

description:
batch 4
SUB4754A67_2


title: mPFC, WT, m, CS, 2271, biol rep 1

description:
WT_m_CS_2271 _P
28__28_RNA_r_mPFC_2271_m


title: WT_Ctrl_P10_1


title: Zfy2_3r

description:
batch 4
SUB4754A67


title: 3505_2_AML_CITE


title: mPFC, WT, f, K, 2429, biol rep 6

description:
WT_f_K_2429 _P
23__23_RNA_r_mPFC_2429_f

value: female


title: mPFC, WT, f, K, 2408, biol rep 5

description:
WT_f_K_2408 _P
18__18_RNA_r_mPFC_2408_f


title: 3505_1_AML_CITE


title: 3503_product_DLI_CITE


title: Usp9y_2r_2

description:
batch 4
SUB4754A66_2


title: Zfy12_3r

description:
batch 4
SUB4754A69


title: Whole blood_Placebo_Before_No28

type: RNA

city: Kawasaki

first: Fumika

last: SHINOZAKI

address: 3-25-13 Tonomachi, Kawasaki-ku

country: Japan

institute: Kanagawa Institute of Industrial Science and Technology

hyb_protocol: Following fragmentation, 2.3 microgram of ss-cDNA were hybridized for 16 hr at 45C on Clariom S Array, human. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G.

data_processing: CEL files were quantified with the qFARMs, using the statistical language R (R-4.0.3) and Bioconductor 3.12

label: biotin

source_name: Human whole blood before placebo ingestion and cognitive measure test

label_protocol: Biotinylated ss-cDNA were prepared according to the Thermo Fisher Scientific (Affymetrix) protocol from 50ng total RNA (Manual Target Preparation for GeneChip Whole Transctipt Expression Arrays, Publication Number MAN0018137, Revision B.0, 2020, Thermo Fisher Scientific).

extract_protocol: Total RNA from whole blood was extracted using PAXgene Blood miRNA Kit according to the manufacturer's instructions.

treatment_protocol: Blood was collected using a PAX gene Blood RNA tube.

value: Male


title: mPFC, WT, f, K, 2342, biol rep 4

description:
WT_f_K_2342 _P
13__13_RNA_r_mPFC_2342_f


title: Usp9y_2r

description:
batch 4
SUB4754A66


title: Usp9y_1r_2

description:
batch 4
SUB4754A65_2


title: 3503_6_AML_CITE


title: mPFC, WT, f, K, 2337, biol rep 3

description:
WT_f_K_2337 _P
12__12_RNAf_r_mPFC_2337_f


title: Whole blood_Placebo_Before_No27


title: mPFC, WT, f, K, 2253, biol rep 2

description:
WT_f_K_2253 _P
06__6_RNA_r_mPFC_2253_f


title: Usp9y_1r

description:
batch 4
SUB4754A65


title: 3505_4_AML_CITE


title: Whole blood_Placebo_Before_No26


title: 3505_3_AML_CITE


title: wt_4r_2

description:
batch 4
SUB4754A64_2

value: control


title: 3503_3_AML_CITE


title: mPFC, WT, f, K, 2278, biol rep 1

description:
WT_f_K_2278 _P
02__2_RNA_r_mPFC_2278_f


title: mPFC, WT, f, CS, 2417, biol rep 6

description:
WT_f_CS_2417 _P
22__22_RNA_r_mPFC_2417_f


title: wt_4r

description:
batch 4
SUB4754A64


title: wt_3r_2

description:
batch 4
SUB4754A63_2


title: Whole blood_Placebo_Before_No24


title: Whole blood_Placebo_Before_No23


title: Whole blood_Placebo_Before_No25


title: mPFC, WT, f, CS, 2409, biol rep 5

description:
WT_f_CS_2409 _P
20__20_RNA_r_mPFC_2409_f


title: 3503_1_AML_CITE


title: wt_3r

description:
batch 4
SUB4754A63


title: Whole blood_Placebo_Before_No22


title: mPFC, WT, f, CS, 2397, biol rep 4

description:
WT_f_CS_2397 _P
15__15_RNA_r_mPFC_2397_f


title: 3501_product_DLI_CITE


title: 3503_4_AML_CITE


title: Whole blood_Placebo_Before_No21


title: mPFC, WT, f, CS, 2315, biol rep 3

description:
WT_f_CS_2315 _P
09__9_RNA_r_mPFC_2315_f


title: wt_6_2

description:
batch 4
SUB4754A62_2


title: 3501_4_AML_CITE


title: wt_6

description:
batch 4
SUB4754A62


title: mPFC, WT, f, CS, 2285, biol rep 2

description:
WT_f_CS_2285 _P
08__8_RNA_r_mPFC_2285_f


title: mPFC, WT, f, CS, 2274, biol rep 1

description:
WT_f_CS_2274 _P
03__3_RNA_r_mPFC_2274_f


title: 3503_2_AML_CITE


title: 3501_2_AML_CITE


title: 3501_3_AML_CITE


title: 3501_1_AML_CITE


title: Whole blood_Placebo_Before_No20


title: Prssly_4_2

description:
batch 4
SUB4754A60_2


title: wt_5

description:
batch 4
SUB4754A61


title: Whole blood_Placebo_Before_No18


title: Whole blood_Placebo_Before_No17


title: KM2__CML_RNA

data_processing:
10x genomics pipeline
CellRanger 5.0.0
Assembly: GRCh38-2020-A
Supplementary files format and content: zipped csv file for counts and metadata


title: mPFC, KO, m, K, 2412, biol rep 3

description:
KO_m_K_2412 _P
36__38_RNA_r_mPFC_2412_m

value: knockout (KO)


title: mPFC, KO, m, K, 2341, biol rep 4

description:
KO_m_K_2341 _P
63__34_RNA_r_mPFC_2341_m


title: Whole blood_Placebo_Before_No19


title: Prssly_4

description:
batch 4
SUB4754A60


title: wt_5_2

description:
batch 4
SUB4754A61_2


title: mPFC, KO, m, K, 2303, biol rep 2

description:
KO_m_K_2303 _P
32__32_RNA_r_mPFC_2303_m


title: KM1__CML_RNA

value: bone  marrow


title: Whole blood_Placebo_Before_No16


title: mPFC, KO, m, K, 2246, biol rep 1

description:
KO_m_K_2246 _P
26__26_RNA_r_mPFC_2246_m


title: Prssly_3_2

description:
batch 4
SUB4754A59_2


title: Whole blood_Placebo_Before_No15


title: Prssly_3

description:
batch 4
SUB4754A59


title: E8__CML_RNA

value: DLI


title: mPFC, KO, m, CS, 2433, biol rep 4

description:
KO_m_CS_2433 _P
37__39_RNA_r_mPFC_2433_m


title: E7__CML_RNA


title: Whole blood_Placebo_Before_No14


title: Whole blood_Placebo_Before_No13


title: Prssly_2_2

description:
batch 4
SUB4754A58_2


title: E6__CML_RNA


title: mPFC, KO, m, CS, 2393, biol rep 3

description:
KO_m_CS_2393 _P
33__35_RNA_r_mPFC_2393_m


title: Whole blood_Placebo_Before_No12


title: mPFC, KO, m, CS, 2256, biol rep 2

description:
KO_m_CS_2256 _P
29__29_RNA_r_mPFC_2256_m


title: Prssly_2

description:
batch 4
SUB4754A58


title: Prssly_1_2

description:
batch 4
SUB4754A57_2


title: Prssly_1

description:
batch 4
SUB4754A57


title: mPFC, KO, m, CS, 2269, biol rep 1

description:
KO_m_CS_2269 _P
27__27_RNA_r_mPFC_2269_m


title: Whole blood_Placebo_Before_No11


title: E4__CML_RNA


title: Teyorf_4_2

description:
batch 4
SUB4754A56_2


title: mPFC, KO, f, K, 2406, biol rep 5

description:
KO_f_K_2406 _P
17__17_RNA_r_mPFC_2406_f


title: E3__CML_RNA


title: Whole blood_Placebo_Before_No10


title: Whole blood_Placebo_Before_No9


title: Teyorf_4

description:
batch 4
SUB4754A56


title: E1__CML_RNA


title: mPFC, KO, f, K, 2343, biol rep 4

description:
KO_f_K_2343 _P
14__14_RNA_r_mPFC_2343_f


title: Whole blood_Placebo_Before_No7


title: B9__CML_RNA


title: mPFC, KO, f, K, 2336, biol rep 3

description:
KO_f_K_2336 _P
11__11_RNA_r_mPFC_2336_f


title: Teyorf_3_2

description:
batch 4
SUB4754A55_2


title: ChIP-seq-01_Pol2_SPT5AID_shNT_H2O-3h

description: ChIP-seq

value: Colorectal adenocarcinoma


title: Teyorf_3

description:
batch 4
SUB4754A55


title: E5__CML_RNA


title: mPFC, KO, f, K, 2252, biol rep 2

description:
KO_f_K_2252 _P
05__5_RNA_r_mPFC_2252_f

value: right hemisphere


title: B8__CML_RNA


title: Whole blood_Placebo_Before_No6


title: mPFC, KO, f, K, 2430, biol rep 6

description:
KO_f_K_2430 _P
24__24_RNA_r_mPFC_2430_f

value: medial prefrontal cortex


title: Teyorf_2_2

description:
batch 4
SUB4754A54_2


title: mPFC, KO, f, K, 2273, biol rep 1

description:
KO_f_K_2273 _P
01__1_RNA_r_mPFC_2273_f


title: B7__CML_RNA


title: Whole blood_Placebo_Before_No4


title: E2__CML_RNA


title: Teyorf_2

description:
batch 4
SUB4754A54


title: B6__CML_RNA


title: Whole blood_Placebo_Before_No8


title: mPFC, KO, f, CS, 2416, biol rep 6

description:
KO_f_CS_2416 _P
21__21_RNA_r_mPFC_2416_f


title: Teyorf_1_2

description:
batch 4
SUB4754A53_2


title: B4__CML_RNA


title: Whole blood_Placebo_Before_No2


title: mPFC, KO, f, CS, 2317, biol rep 3

description:
KO_f_CS_2317 _P
10__10_RNA_r_mPFC_2317_f


title: B46__CML_CONTROL_RNA


title: H2al2y_4_2

description:
batch 4
SUB4754A52_2


title: mPFC, KO, f, CS, 2284, biol rep 2

description:
KO_f_CS_2284 _P
07__7_RNA_r_mPFC_2284_f


title: H2al2y_4

description:
batch 4
SUB4754A52


title: Whole blood_Placebo_Before_No5


title: Whole blood_Placebo_Before_No1


title: Whole blood_Placebo_After_No28

source_name: Human whole blood after placebo ingestion and cognitive measure test


title: Whole blood_Placebo_After_No27


title: mPFC, KO, f, CS, 2277, biol rep 1

description:
KO_f_CS_2277 _P
04__4_RNA_r_mPFC_2277_f


title: H2al2y_3_2

description:
batch 4
SUB4754A51_2


title: mPFC, KO, f, CS, 2407, biol rep 5

description:
KO_f_CS_2407 _P
19__19_RNA_r_mPFC_2407_f


title: H2al2y_3

description:
batch 4
SUB4754A51


title: Whole blood_Placebo_After_No26


title: Hippocampus, WT, m, K, 2411, biol rep 4

description:
WT_m_K_2411_H
80__77_RNA_r_v_Hip_2411_m

source_name: hippocampus (ventral)

value: hippocampus (ventral)

value: wildtype (WT)