title: MCF10A_NIPBL KD_R4_HiC

data_processing:
Alignment of sequences to the reference human genome (hg19) was performed using ‘Bowtie2′  with --local --reorder flags.
To assess the reproducibility of the replicates, 5-kb raw matrices were summed to obtain 40-kb matrices and these were normalized first by coverage and then by KR algorithm.
Given the high correlation of the distribution of contacts as a function of genomic distance among replicates for each condition (control or KD), replicates were merged and analyzed at 5-kb resolution
Assembly: hg19
Supplementary files format and content: mcool

growth_protocol: MCF10A cells are grown in DMEM/F12 supplemented with 20ng/ml of EGF, 0.5mg/ml hydrocortisone, 100ng/ml of cholera toxin, 10mg/ml of insulin and 5% of horse serum.

extract_protocol:
MCF10A cells (3 mill cells per condition) were fixed with 2% formaldehyde (Sigma, #252549) in PBS with 10% FBS for 10 min. Formaldehyde was quenched with 300 mM of glycine at RT for 5 minutes. Hi-C experiments were performed with Arima-HiC Kit (A510008) following manufacturer’s instructions.
Libraries were prepared with Swift Biosciences Accel-NGS 2S Library Kit (Cat# 21024) and amplified with KAPA Library Amplification Kit (KAPA Cat# KK2620). For all the libraries, 8-9 PCR cycles were used for amplification and they were then sequenced on an Illumina NextSeq550 (82x43 bp).

value: breast

value: epithelial

value: NIPBL siRNA  (single oligont)


title: Patient99_Sample11

status: Public on Jan 30 2023

type: SRA

city: New York

first: Angelica

last: Galianese

state: New York

address: 615 W 164th Street, Apt 21C

country: USA

institute: Columbia University

description: COUNTS_TABLE_RAW13: P99_S11

library_source: transcriptomic

data_processing:
single end: For producing count tables: We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Human: NCBI/build37.2) using STAR(2.5.2b) and featureCounts(v1.5.0-p3).
paired end: For producing count tables: We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38) using kallisto (0.44.0).
For producing unmapped reads: Produced with Pandora (Abate et al., 2015; Wang et al). The Pandora workflow takes RNA-seq data as input and produces the annotated microbial reads present in the sample as outputs. The pipeline runs through five main modules: 1) mapping to the human host genome using STAR (Dobin et al., 2013) and bowtie2 (Langmead & Salzberg, 2012); 2) processing of the host-mapped reads with featureCounts (Liao et al., 2014)  to obtain the host gene expression profile; 3) de-novo assembly of host-subtracted short (2x100bp) reads using Trinity (Grabherr et al., 2011) to create long contiguous full-length transcripts (contigs); 4) contigs alignment to curated sets of NCBI sequences from viruses, bacteria, fungi and other eukaryotic parasites with BLAST (Altschul et al., 1990); and 5) filtering and parsing the BLAST results into a report specifying the detected microbial abundances in the sample.
Assembly: single end: NCBI/build37.2
Assembly: paired end: GRCh38
Raw counts provided for all samples

molecule: total RNA

organism: Homo sapiens

source_name: nasopharyngeal samples

extract_protocol:
Nasopharyngeal swabs were collected from each participant using a minitip flock swab (VWR catalog no. 10755-196; Copan Diagnostics) and immediately placed in a 15 mL tube containing 2 mL of DNA/RNA Shield (Product no. R1100-250; Zymo). Samples were separated into two 1 mL aliquots, and stored at −80°C. After thawing, RNA extraction was done using Zymo Quick-RNA™ Microprep Kit RNA extraction kit (ZYMO, R1050) including the recommended on column DNase I treatment step for 15 min. An Agilent Bioanalyzer was used for quality control prior to library creation
For single end samples: RNA RIBOZERO 30M SE100. For paired end samples: RNA RIBOZERO 20M PE100. Then proceed with library construction using Illumina TruSeq  chemistry.

tag: tissue

value: nasopharyngeal samples

tag: subject

tag: geographic location

tag: collection date


title: Patient99_Sample8

description: COUNTS_TABLE_RAW13: P99_S8


title: MCF10A_NIPBL KD_R2_HiC

city: Madrid

first: Daniel

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

library_source: genomic

molecule: genomic DNA

source_name: breast

treatment_protocol: MCF10A cells were transfected with 50 nM siRNAs using DharmaFECT reagent 1 and Gibco Opti-MEM I Reduced Serum Media and harvested 72h later.

tag: cell line

tag: cell type

tag: treatment


title: Tg(mitfa:dgat1a) Rep1

city: Manchester

first: Adam

last: Hurlstone

address: Michael Smith Building

country: United Kingdom

institute: University of Manchester

data_processing:
Adapters were trimmed from raw sequencing reads using Trimmomatics v0.32
Trimmed reads were aligned to the zebrafish genome (Ensembl, GRCz11) using STAR v2.5.3
Reads that mapped to chromosomes 1-25 were retained
Gene counts were determined using featureCounts v1.6.2 and differential expression analysis was performed using DESeq2 v1.14.1, using a adjusted p-value cut off of <0.05
DESeq2 was used to generate log2 normalised variance stabilising transformed (VST) counts
Genome_build: Ensembl, GRCz11
Supplementary_files_format_and_content: fpm_DGAT1_RNAseq_GEO
Supplementary_files_format_and_content: GFP_DGAT1_allresults_GEO
Supplementary_files_format_and_content: VST_DGAT1_RNAseq_GEO

organism: Danio rerio

source_name: Tumour

growth_protocol: Age matched tumours were harvested at 10-12 weeks

extract_protocol:
Tumours were removed and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: tp53m214K/m214k; mitfa-/-; nras G12D

value: Melanoma

tag: genotype


title: Patient99_Sample9

description: COUNTS_TABLE_RAW13: P99_S9


title: HJ7JJBGXH_1#146372_ATTCCT

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
fastQ quality assessment
cutadapt adater trimming
bowtie1 genome alignment
miRDeep2 miRNA quantification
edgeR differential expression
Supplementary files format and content: CSV with miRNA quantifications (raw and rpm)

organism: Equus caballus

source_name: chondrocytes

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Cat. 217004).
RealSeq Biofluids Plasma/Serum miRNA Library Kit

tag: biofluid

value: Synovial fluid

tag: breed

value: Dutch warmblood

tag: age

value: 5y 2m

tag: Sex

value: Male

tag: disease state

value: Mild OA

value: chondrocytes


title: MCF10A_Control_R3_HiC

value: mock transfection


title: HJ7JJBGXH_1#146373_CAAAAG

value: Belgian Warmblood


title: MCF10A_Control_R2_HiC


title: HJ7JJBGXH_1#146367_AGTTCC

value: Thoroughbred


title: Patient99_Sample6

description: COUNTS_TABLE_RAW13: P99_S6


title: M1uk SP1380 in THY broth bulk RNA-seq 3

city: Parkville

first: Magnus

middle: Ganer

last: Jespersen

state: Victoria

address: 792 Elizabeth street

country: Australia

institute: The University of Melbourne

description: Bulk RNA-seq from late-logarithmic phase from emm1 S. pyogenes M1uk

data_processing:
Size filtering using cutadapt verison 2.8, special parameters: -n 0 -U 0 --action none -m 45
rRNA read filtering using database comprised of rRNA from S. pyogenes SF370, 5448, and HKU488 and SortMeRNA version 4.3.4, special parameters: --fastx
Alignment of reads against 5448 (GCF_001021955.1) using BWA-mem, bwa version 0.7.17
Read counting using FeatureCounts, subreads version 2.0.0, special parameters: -s 1 --largestOverlap -B -t gene -g ID
Differential expression analysis using Deseq2 v.1.32.0 in R v. 4.0.0. Isolates compared to WT 5448
Assembly: GCF_001021955.1
Supplementary files format and content: M1uk_raw_read_counts.tsv - count file for m1uk and m1global files aligned to 5448 reference genome
Supplementary files format and content: HKU488_v_5448_DGE.tsv - Tab seperated file - Differential gene expression of HKU488 compared to 5448
Supplementary files format and content: SP1380_v_5448_DGE.tsv - Tab seperated file - Differential gene expression of SP1380 compared to 5448
Supplementary files format and content: SP1384_v_5448_DGE.tsv - Tab seperated file - Differential gene expression of SP1384 compared to 5448
Supplementary files format and content: SP1426_v_5448_DGE.tsv - Tab seperated file - Differential gene expression of SP1426 compared to 5448
Supplementary files format and content: SP1448_v_5448_DGE.tsv - Tab seperated file - Differential gene expression of SP1448compared to 5448

organism: Streptococcus pyogenes

source_name: Bacterial culture

growth_protocol: Bacteria were statically grown to late-logarithmic growth phase in Todd Hewitt broth supplemented with 1% yeast extract (THY) at 37˚C

extract_protocol:
RNA was isolated using the RNeasy Plus Kit (Qiagen). Briefly, bacteria were grown to late-logarithmic growth phase in THY. Two volumes of RNAprotect (Qiagen) were added to the cultures and the samples were then centrifuged at 5,000 x g for 25 min at 4°C to pellet cells. RNA was isolated from the dry pellet as per the manufacturer’s instructions with an additional mechanical lysis step using Lysing Matrix B tubes (MP Biomedicals) on the FastPrep-2 5G bead beating grinder and lysis system (MP Biomedicals). To ensure complete removal of DNA, the RNA was then further purified using the TURBO DNA-free kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
RNAseq analysis was performed at the Australian Centre for Ecogenomics (University of Queensland, Brisbane, Australia). cDNA libraries were prepared from total RNA using TruSeq Stranded Total RNA Library Prep with Ribo-Zero Plus rRNA Depletion kit (Illumina). Sequencing of the cDNA libraries was performed on the NovaSeq 6000 System (Illumina) on a 2x150 bp SP flowcell run generating an average of 20 million reads per sample.

treatment_protocol: No treatment

value: Bacterial culture

value: Bulk

tag: growth phase

value: Late logarithmic


title: Tg(mitfa:egfp) Rep3


title: MCF10A_CTCF_Control3_ChIP-seq

data_processing:
Alignment of reads to the reference human genome (hg19) was performed using ‘Bowtie2′ (version 2.4.2) under default settings
Duplicates were removed using GATK4 (version 4.1.9.0)
peak calling was carried out using MACS2 (version 2.2.7.1) after setting the q value (FDR) to 0.05 and using the ‘–extsize’ argument with the values obtained in the ‘macs2 predictd’ step
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: MCF10A cells are grown AT 37ºC at 5% CO2 in DMEM/F12 supplemented with 20ng/ml of EGF, 0.5mg/ml hydrocortisone, 100ng/ml of cholera toxin, 10mg/ml of insulin and 5% of horse serum.

extract_protocol:
Cells were fixed for 15 min in 1% formaldehyde and after quenchig and lysis, sonication with performed in Covaris instrument. Around 50 micrograms of antibody was added to immunoprecipitate chromatin from 10 million cells. 5% mouse ES cell chromatin was added for calibration.
At least 5 ng of DNA were processed through subsequent enzymatic treatments with "NEBNext Ultra II FS DNA Library Prep Kit for Illumina" from New England BioLabs (ref. E7805). Briefly, a short fragmentation of 10 min was followed by end-repair, dA-tailing, and ligation to adapters. Adapter-ligated libraries were completed by limited-cycle PCR (8-12 cycles). Resulting average fragment size is 300 bp from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on Illumina NextSeq 500 (with v2.5 reagent kits) following manufacturer's recommendations.

value: breast

value: epithelial

tag: chip antibody

value: Millipore Cat#07-729, RRID:AB_441965


title: Patient99_Sample7

description: COUNTS_TABLE_RAW13: P99_S7

value: nasopharyngeal samples


title: Patient99_Sample5

description: COUNTS_TABLE_RAW13: P99_S5


title: Tg(mitfa:egfp) Rep1

value: tp53m214K/m214k; mitfa-/-; nras G12D

value: Melanoma


title: MCF10A_NIPBL KD_R1_HiC

value: NIPBL siRNA  (smartpool)


title: MCF10A_CTCF_CTCF-KD2_ChIP-seq

value: CTCF siRNA


title: MCF10A_STAG1_CTCF-KD2_ChIP-seq

value: STAG1, custom made


title: Tg(mitfa:egfp) Rep2


title: MCF10A_STAG2_Control2_ChIP-seq

value: STAG2, custom made


title: MCF10A_STAG1_CTCF KD_ChIP-seq


title: MCF10A_Control_R1_HiC


title: Tg(mitfa:dgat1a) Rep4


title: Patient99_Sample1

description: COUNTS_TABLE_RAW13: P99_S1


title: Patient99_Sample4

description: COUNTS_TABLE_RAW13: P99_S4


title: MCF10A_STAG2_CTCF KD_ChIP-seq


title: MCF10A_Input_Control3_ChIP-seq


title: Patient98_Sample4

description: COUNTS_TABLE_RAW11: P98_S4


title: MCF10A_Input_Control2_ChIP-seq


title: MBD_input_PA_679

city: Seoul

first: Je-Yoel

last: Cho

address: 1, Gwanak-ro, Gwanak-gu

department: Biochemistry

country: South Korea

institute: Seoul National University

data_processing:
All of pre-processing steps including trimming, alignment, generation of signal track, peak calling and diverse type of QC were performed using ENCODE ChIP-seq processing pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2)
Fold-change in each 100bp bins were calculated using MEDIPS to identify methyl-CpG binding domain enriched sites compared to corresponding input samples in 11 differenct canine normal tissues
Assembly: canFam3.1
Supplementary files format and content: narrowPeak (except for Input sample)

organism: Canis lupus familiaris

source_name: Pancreas

growth_protocol: One male and two female beagles  were kindly donated by Dr. Jong-Gu Kang from the College of Veterinary Medicine at Chungbuk National University.

extract_protocol:
Beagle tissues (11 types, ~25mg each) were incubated in Buffer ATL (Qiagen, USA) and protease K at 56°C until the tissue was completely lysed. Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, USA), according to the manufacturer's protocol with modifications. The concentration and purity of isolated genomic DNA was assessed by NanoDrop. For each sample, 3 μg of DNA, normalized to 20 ng/μl, was subjected to shearing with the Bioruptor® Pico (Diagenode) and the size of fragmented DNA (~300 bp) was verified on an agarose gel. Finally, the concentration of sheared double-stranded DNA was measured using Qubit dsDNA HS Assay (ThermoFisher Scientific, USA).  For MBD-enrichment, 500 ng of fragmented double-stranded DNA was enrichedwith methylated CpGs using MethylMiner™ Kit (Invitrogen, cat# ME10025), according to the manufacturer's instructions. To counteract the possibility of increased unspecific binding, we used more stringent wash conditions. In more detail, for each capture reaction, prepared MBD-beads (10 μg beads and 350 ng MBD-biotin protein were used in the same reaction) were added to each 500 ng of fragmented DNA input. Prepared MBD-beads were diluted to 1x in Bind/Wash Buffer prior to addition of each DNA sample, to increase pipetting accuracy. Each capture reaction was brought up to 200 μl final volume in 1x Bind/Wash Buffer, and incubated on a rotator for 40 min at RT. Following incubation, each tube was placed on a magnet for 1 minute and the supernatant containing the non-captured (unmethylated) DNA fragments was removed. The beads with bound methylated DNA were then washed twice by incubation with 200 μl Bind/Wash Buffer. The beads were washed with Bind/Wash buffer, according to the protocol, and eluted in step-wise elution using 200 μl of serially diluted elution buffer (200, 300, 400, 600, and 800 mM).
Eluted methylated DNA fragments in the 600 and 800 mM elution buffers underwent cluster generation and 200 bp paired-end sequencing using TruSeq Nano DNA Kit on the Illumina HiSeq 4000 instrument (Illumina, San Diego, CA, USA).

treatment_protocol: Three dogs in healthy condition were euthanized by intravenous administration of alfaxalone and KCl. Eleven common tissues (cerebrum [CR], cerebellum [CL], colon [CO], kidney [KI], liver [LI], lung [LU], mammary gland [MG], ovary [OV], pancreas [PA], spleen [SP] and stomach [ST]) were isolated from the three beagles. All tissues were rinsed with ice-cold PBS before being minced. Immediately after mincing, tissues were divided into 4 tubes based on the types of analysis, and frozen with liquid nitrogen

value: Pancreas

value: Female

value: Beagle


title: MBD_input_SP_jj8

source_name: Spleen

value: Spleen


title: MCF10A_STAG2_NIPBL KD_ChIP-seq

value: NIPBL siRNA


title: MCF10A_STAG1_CTCF-NIPBL KD

value: CTCF & NIPBL siRNAs


title: MBD_input_ST_jj8

source_name: Stomach

value: Stomach


title: Patient99_Sample2

description: COUNTS_TABLE_RAW13: P99_S2


title: Patient98_Sample5

description: COUNTS_TABLE_RAW12: P98_S5


title: Patient98_Sample7

description: COUNTS_TABLE_RAW12: P98_S7


title: Patient99_Sample3

description: COUNTS_TABLE_RAW13: P99_S3


title: MCF10A_STAG2_CTCF-NIPBL KD_ChIP-seq

value: breast


title: MCF10A_STAG1_Control2_ChIP-seq

value: epithelial

value: mock transfection


title: MCF10A_Input_CTCF KD_ChIP-seq


title: MCF10A_Input_CTCF-NIPBL KD_ChIP-seq


title: MCF10A_STAG1_Control1_ChIP-seq


title: MCF10A_SMC1_NIPBL KD_ChIP-seq

value: SMC1A, custom made


title: MBD_input_LU_jj8

source_name: Lung

value: Lung


title: MCF10A_NIPBL KD_R3_HiC


title: Patient98_Sample3

description: COUNTS_TABLE_RAW11: P98_S3

value: nasopharyngeal samples


title: Patient97_Sample14

description: COUNTS_TABLE_RAW12: P97_S14


title: MCF10A_Input _NIPBL KD_ChIP-seq


title: Patient98_Sample6

description: COUNTS_TABLE_RAW12: P98_S6


title: MCF10A_STAG2_Control1_ChIP-seq


title: MCF10A_STAG1_NIPBL KD_ChIP-seq


title: MBD_input_CO_jj8

source_name: Colon

value: Colon


title: MCF10A_SMC1_Control1_ChIP-seq


title: Patient97_Sample11

description: COUNTS_TABLE_RAW11: P97_S11


title: MBD_input_OV_679

source_name: Ovary

value: Ovary


title: MCF10A_Control_R2_RNA-seq

data_processing:
Fastq files with 86-nt single-end sequenced reads were quality-checked with FastQC and aligned to the human genome (hg19) with Nextpresso,-2.0.0 using Bowtie 0.12.7 and Samtools 0.1.16 allowing two mismatches and five multi-hits
The reads were mapped to hg19 genes using HTSeq and the differencial expression was performed using the R package DESeq2
Supplementary files format and content: txt file with raw counts

extract_protocol:
Total RNA was extracted with total RNA (RNeasy Mini Kit, Qiagen) following manufacturer’s instructions and treated with DNaseI (Ambion).
Total RNA samples (500ng) were processed with the "NEBNext Single Cell/Low Input RNA Library Prep" kit (NEB #E6420) by following manufacturer instructions. RNA Quality scores were 9.9 on average (range 9.1-10) when assayed on a PerkinElmer LabChip analyzer.  Briefly, an oligo(dT) primed reverse transcription with a template switching reaction was followed by double stranded cDNA production by limited-cycle PCR.  {Non-directional}  sequencing libraries were completed with the "NEBNext Ultra II FS DNA Library Prep Kit for Illumina" (NEB #E7805) and subsequently analysed on an Illumina instrument (Illumina NextSeq 550 with v2.5 reagent kits) following manufacturer's protocols.


title: MBD_input_CR_jj8

source_name: Cerebrum

value: Cerebrum


title: Patient97_Sample10

description: COUNTS_TABLE_RAW11: P97_S10


title: MCF10A_Control_R1_RNA-seq


title: Patient97_Sample13

description: COUNTS_TABLE_RAW12: P97_S13


title: MCF10A_Input_Control1_ChIP-seq


title: MCF10A_NIPBL KD_R1_RNA-seq

value: NIPBL siRNA (single oligont)


title: Patient98_Sample1

description: COUNTS_TABLE_RAW12: P98_S1


title: P. falciparum ORC1 ChIPseq 30 hpi (input)

city: Cambridge

first: Catherine

last: Merrick

address: Tennis Court road

department: Pathology

institute: University of Cambridge

data_processing:
Sequencing reads were mapped against the PlasmoDB v26 P. falciparum genome utilizing the Burrows-Wheeler Alignment tool (v0.7.17)
Mapped reads were filtered to mapping quality ≥ 30 (SAMtools v1.7) and only uniquely mapped reads were used for further analysis.
ChIP log2ratios (bigwig files) were generated using deepTools 3.5.0 bamCompare by normalising reads against input/background reads, with a pseudocount of +1 and a bin size of 50 bp
MACS2 v2.1.1 was used for ChIP peak calling with p-value cut-off of 1e-3
Assembly: PlasmoDB v26 P. falciparum genome
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Plasmodium falciparum

source_name: whole parasite

growth_protocol: Custom made RPMI 1640 (with 2.3 g/L sodium bicarbonate, 4 g/L dextrose, 5.957 g/L HEPES, 0.05 g/L hypoxanthine, 5 g/L Albumax II, Invitrogen), 5% pooled human serum, 4% haematocrit O+ human red blood cells, 3% oxygen, 5% CO2 and 92% nitrogen gas mixture at 37C.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at 37C. After quenching with 0.125 M glycine and saponin lysis, chromatin was sonicated using a M220 focused-ultrasonicator (Covaris).
5 ng of α-HA ChIP or input DNA were end-repaired with T4 DNA polymerase (NEB), Klenow DNA polymerase (NEB), and T4 Polynucleotide Kinase (NEB). The 3’ends of end-repaired DNA were extended with an A- overhang with 3’ to 5’ exonuclease-deficient Klenow DNA polymerase (NEB). The resulting fragments were ligated to Nextflex adapters (Bio Scientific) with the use of T4 DNA ligase (Promega). The libraries were amplified using an AT-rich optimized KAPA protocol using KAPA HiFi HotStart ready mix (KAPA Biosystems), NextFlex primer mix (Bio Scientific) with the following PCR program: 98°C for 2 min; four cycles of 98°C for 20 sec, 62°C for 3 min; 62°C for 5 min. The fragments originating from mono-nucleosomes + 125 bp NextFlex adapter were selected using 2% E-Gel Size Select agarose gels (Invitrogen) and amplified by PCR for 8 cycles using the above conditions. Libraries were purified and adapter dimers removed with Agencourt AMPure XP beads purification using a 1:1 library:beads ratio (Beckman Coulter). ChIP-seq libraries were sequenced on the Illumina NextSeq 500 system with a 20% phiX spike-in (Illumina) to generate 75 bp single-end reads (NextSeq 500/550 High Output v2 kit).

treatment_protocol: P. falciparum orc1 (PF3D7_1203000) was C-terminally tagged with 3xHA using the selection linked integration (SLI) technique

value: whole parasite

value: 3D7 ORC1-HA + pTK-BSD

tag: time

value: 30 hpi


title: MBD_input_CL_jj8

source_name: Cerebellum

tag: tissue

value: Cerebellum

value: Female

value: Beagle


title: Patient97_Sample12

description: COUNTS_TABLE_RAW12: P97_S12

tag: subject


title: MBD_input_KI_679

source_name: Kidney

value: Kidney


title: P. falciparum ORC1 ChIPseq 24 hpi (anti-HA)

value: 24 hpi

value: Rat monoclonal anti-HA IgG1 antibody (clone 3F10) (Roche, catalog# 11867431001)


title: MBD_input_LI_jj8

source_name: Liver

value: Liver


title: Patient98_Sample2

description: COUNTS_TABLE_RAW12: P98_S2

tag: geographic location


title: MBD_input_MG_679

source_name: Mammary gland

value: Mammary gland


title: MCF10A_Control_R3_RNA-seq

value: breast

value: epithelial

value: mock transfection


title: MBD_ST_jj82

value: Stomach


title: MCF10A_NIPBL KD_R2_RNA-seq


title: P. falciparum ORC1 ChIPseq 24 hpi (input)


title: MCF10A_NIPBL KD_R3_RNA-seq

value: NIPBL siRNA  (single oligont)


title: Patient97_Sample8

description: COUNTS_TABLE_RAW11: P97_S8

source_name: nasopharyngeal samples

value: nasopharyngeal samples

tag: collection date


title: Patient97_Sample9

description: COUNTS_TABLE_RAW12: P97_S9


title: RNA_LU_679

data_processing:
Data were filtered and trimmed using Trimmomatic
The sequenced reads aligned to the canine reference genome (canFam3.1 assembly) using STAR
TIN values were calculated using RSeQC
Gene expression value were calculated usin RSEM
Assembly: canFam3.1
Supplementary files format and content: bigWig

extract_protocol:
Total RNA was extracted from each tissue using the RNeasy Mini plus kit (Qiagen, USA). Pulverization for sample homogenization was performed with liquid nitrogen prior to RNA isolation, according to the manufacturer's instruction. The RNA quality was assessed by analysis of 18S and 28S rRNA band integrity on a RNA 6000 Nano Kit (part # 5067-1511) using an Agilent Bioanalyzer (Agilent, USA).
Library was prepared using TruSeq Stranded Total RNA sample preparation kit (RS-122-9007) and sequenced using HiSeq 2500 or NovaSeq 6000 (Illumina) by Theragen Inc (Korea).

value: Lung


title: MBD_ST_679


title: RNA_SP_679

value: Spleen


title: MBD_SP_jj8

value: Male


title: Patient97_Sample7

description: COUNTS_TABLE_RAW12: P97_S7


title: RNA_CL_679

value: Cerebellum


title: Patient97_Sample5

description: COUNTS_TABLE_RAW11: P97_S5


title: ChIP_input_PA_244

data_processing:
All of pre-processing steps including trimming, alignment, generation of signal track, peak calling and diverse type of QC were performed using ENCODE ChIP-seq processing pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2)
Assembly: canFam3.1
Supplementary files format and content: narrowPeak (except for Input sample)

extract_protocol:
The 11 frozen tissues were thawed on ice and 10 mg of tissue per IP reaction was chopped into ~1 mm3 pieces with two razor blades on the ice. Chopped tissues were washed out with PBS buffer containing Protease K, 10mM PMSF, and 10mM Sodium Butyrate histone deacetylase inhibitor to remove blood from the tissue. Washed tissue was grinded using pestle and mortar. Then prepared cell mass was cross-linked in the PBS buffer with 1.5% Formaldehyde added at room temperature(RT) for 20 minutes. By adding 125 mM Glycine and placing the samples on the rotator for 5 min, cross-linking reactions were stopped. Fixed cell mass was washed twice with PBS buffer containing Protease K, 10mM PMSF, and 10mM Sodium Butyrate.  Fixed cell mass was lysed using buffer A (5 mM PIPES buffer, 85 mM KCl, and 0.5% NP 40). The supernatant was centrifuged out and added to buffer B (50 mM Tris-HCl, 0.5% SDS, and 2.5mM EDTA). All buffers contained Protease K, 10 mM PMSF, and 10 mM Sodium Butyrate histone deacetylase inhibitor. Sonication was then carried out to get 300-500 bp size fragments using Bioruptor Pico (Diagenode). Twenty to fifty cycles of 30 seconds, on and off, were performed at 4 ℃ depending on the tissue. Liver cells were sonicated for only 20 cycles. Chromatin solution was centrifuged to remove the debris and diluted with ChIP IP buffer (16.7 mM Tris-HCl, 0.05% SDS, 1.1% Triton X-100, 1.2 mM EDTA, and 167 mM NaCl). After adding 5 µg of sample to 10 µg of anti-H3K4me1 (ab8895), H3K27Ac (ab4729), H3K4me3 (ab8580), H3K27me3 (ab6002), H3K9me3 (ab8898), and IgG (Sc-2027) per IP reaction, the chromatin solution was incubated overnight at 4 ℃. The cross-linking was reversed and DNA was purified after treatment with protease K and RNase A. ChIPed DNA was quantified using the Qubit fluoro-spectrometer (ThermoFisher Scientific, Waltham, MA, USA) and the enrichment was validated by PCR.
The ChIP library was prepared using the TruSeq ChIP Library Preparation Kit and sequenced in ~500 bp fragments using HiSeq 2500 system (Illumina) by Macrogen (Macrogen, Korea).

value: Pancreas

value: Female


title: MBD_SP_679

value: Beagle


title: MBD_PA_jj8


title: ChIP_input_MG_244


title: ChIP_input_LU_679


title: Patient97_Sample3

description: COUNTS_TABLE_RAW11: P97_S3


title: ChIP_input_LI_679


title: ChIP_input_ST_679


title: RNA_CR_679

value: Cerebrum


title: P. falciparum ORC1 ChIPseq 30 hpi (anti-HA)

value: whole parasite

value: 3D7 ORC1-HA + pTK-BSD

value: 30 hpi

value: Rat monoclonal anti-HA IgG1 antibody (clone 3F10) (Roche, catalog# 11867431001)


title: Patient97_Sample4

description: COUNTS_TABLE_RAW12: P97_S4


title: ChIP_input_CO_679

value: Colon


title: MBD_PA_679


title: ChIP_input_CL_679


title: MBD_OV_679

value: Ovary


title: RNA_LI_679

value: Liver


title: Patient97_Sample6

description: COUNTS_TABLE_RAW12: P97_S6


title: MBD_OV_244


title: Patient97_Sample2

description: COUNTS_TABLE_RAW11: P97_S2


title: Patient97_Sample1

description: COUNTS_TABLE_RAW11: P97_S1


title: ChIP_input_CR_679


title: Patient96_Sample4

description: COUNTS_TABLE_RAW9: P96_S4


title: MBD_MG_244

value: Mammary gland


title: ChIP_k9me3_ST_679

value: Stomach

value: H3K9me3 (Abcam, #ab8898)


title: ChIP_k9me3_PA_244


title: ChIP_k9me3_SP_679

value: Spleen


title: Patient96_Sample2

description: COUNTS_TABLE_RAW9: P96_S2

value: nasopharyngeal samples


title: ChIP_k9me3_OV_244


title: ChIP_k9me3_LU_679

value: Lung


title: ChIP_input_OV_244


title: ChIP_k9me3_KI_jj8

value: Kidney

value: Male


title: MBD_LU_679

value: Female

value: Beagle


title: MBD_LI_jj8


title: ChIP_k9me3_MG_244


title: Patient95_Sample15

description: COUNTS_TABLE_RAW13: P95_S15


title: ChIP_k9me3_CR_679

value: Cerebrum


title: Patient95_Sample14

description: COUNTS_TABLE_RAW13: P95_S14


title: ChIP_input_KI_jj8


title: ChIP_k27me3_ST_679


title: MBD_CO_jj82


title: MBD_CO_679


title: MBD_LU_jj8


title: MBD_LI_679


title: Patient96_Sample1

description: COUNTS_TABLE_RAW9: P96_S1


title: MBD_MG_679


title: Patient96_Sample3

description: COUNTS_TABLE_RAW9: P96_S3


title: MBD_KI_jj8


title: MBD_CR_jj8


title: MBD_KI_679


title: ChIP_k27me3_SP_679


title: ChIP_k27me3_OV_244


title: MBD_CR_679


title: Patient95_Sample13

description: COUNTS_TABLE_RAW13: P95_S13


title: Patient95_Sample9

description: COUNTS_TABLE_RAW13: P95_S9


title: MBD_CL_jj8

value: Cerebellum


title: Patient95_Sample16

description: COUNTS_TABLE_RAW13: P95_S16

value: missing


title: ChIP_k9me3_CO_679


title: MBD_CL_679


title: Patient95_Sample12

description: COUNTS_TABLE_RAW13: P95_S12


title: Patient95_Sample8

description: COUNTS_TABLE_RAW13: P95_S8


title: ChIP_k27me3_LU_679


title: Patient95_Sample7

description: COUNTS_TABLE_RAW13: P95_S7


title: Patient95_Sample10

description: COUNTS_TABLE_RAW13: P95_S10


title: Patient95_Sample5

description: COUNTS_TABLE_RAW10: P95_S5


title: ChIP_k27me3_PA_244

value: Pancreas


title: ChIP_k27me3_MG_244


title: Patient95_Sample6

description: COUNTS_TABLE_RAW10: P95_S6


title: Patient95_Sample3

description: COUNTS_TABLE_RAW10: P95_S3


title: Patient95_Sample11

description: COUNTS_TABLE_RAW13: P95_S11


title: ChIP_k9me3_CL_679


title: ChIP_k27me3_KI_jj8


title: ChIP_k9me3_LI_679


title: Patient95_Sample4

description: COUNTS_TABLE_RAW10: P95_S4


title: ChIP_k27me3_CO_679

value: Colon


title: ChIP_k27me3_LI_679


title: ChIP_k27me3_CR_679


title: ChIP_k27ac_ST_679

value: H3K27ac (Abcam, #ab4729)


title: Patient95_Sample1

description: COUNTS_TABLE_RAW10: P95_S1


title: Patient95_Sample2

description: COUNTS_TABLE_RAW10: P95_S2


title: ChIP_k27me3_CL_679


title: CONTRA.TG.VEH

city: Edinburgh

first: Eoin

middle: D

last: O'Sullivan

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

data_processing:
Sequencing was performed on a NextSeq 550 High Output Kit v2 (Illumina) for 150 cycles at 400M PE reads comprising of 2x75bp and 8bp index reads for single cell and NextSeq® 500/550 High Output Kit v2 (300 cycles) (400M PE reads 2x150bp) for bulk
Using the Cell Ranger Single Cell software suite 2.1.0 by 10x Genomics the cellranger mkfastq wrapper demultiplexed the illumina output BCL files to library specific FASTQ files.  Subsequently, alignment was performed using the cellranger count function using STAR aligner 2.5.1b.1 The GRCm38 mouse reference genome, mm10 (Ensembl 93) was used. salmon 1.4 used for bulk
Genome_build: mm10
Supplementary_files_format_and_content: gene-cell matrixes are found in the .csv files

organism: Mus musculus

extract_protocol:
kidneys were removed , digested on ice and FACS sorted using DAPI as a live/dead gate. Libraries were constructed using the standard 10x single cell 3' V2 workflow
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For IRI: Unilateral renal artery ligation for 15 minutes performed under general anaesthesia to arrest renal blood flow.Mouse kidney was harvested 2 weeks following injury.

value: 8 week

tag: sample type

value: Kidney - contralateral to injury


title: ChIP_k27ac_SP_679


title: Patient94_Sample3

description: COUNTS_TABLE_RAW11: P94_S3


title: Patient94_Sample2

description: COUNTS_TABLE_RAW11: P94_S2


title: ChIP_k27ac_PA_244


title: CONTRA.WT.TAM

value: Kidney - contralateral to injury, mouse treated with tamoxifen


title: Patient94_Sample1

description: COUNTS_TABLE_RAW12: P94_S1


title: CONTRA.TG.TAM


title: Pig

city: xian

first: Cangang

last: Zhang

state: State...

address: Yanta district, xi 'an city, shaanxi province

country: China

institute: xian jiaotong university

data_processing:
The 10x Genomics Cell Ranger (3.0.1 version) pipeline was used to demultiplex raw files into FASTQ files, extract barcodes and UMI, filter, and map reads to the corresponding reference genome, and generate a matrix containing UMI counts.
A 10x Genomics Cell Ranger pipeline was used to identify clonotypes by alignment and annotation with the default settings.
Genome_build: Fish:GRCz11, Frog:Xenopus_laevis_v2, Mouse:GRCm38, Rat:Rnor_6.0, Pig:Sscrofa11, Monkey:Mmul_8, Human:GRCh38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: filtered_feature_bc_matrix.tar contains counts matrix (stored in the Market Exchange Format for sparse matrices).

organism: Sus scrofa

extract_protocol:
Spleen tissues were processed with the flat end of a syringe in a 100 mm culture dish containing 5 ml cold FACS buffer (2% FBS in PBS), then passed through a 70 μm cell strainer into a 15 ml tube. Cells were centrifuged to remove the supernatant. Cell pellets were treated with 1ml ACK (Ammonium-Chloride-Potassium) Lysing Buffer to remove the red blood cells. After washing with 10 ml cold FACS buffer, the remaining cells were stained with 7AAD (Part 76332; Lot B226294 Biolegend) for 30 min at 4 °C, then washed and resuspended in cold FACS buffer for flow cytometric sorting using FACS Aria II Cell Sorter (BD Biosciences). Sorted 7AAD- cells with a viability higher than 90% were used for 10X genomics scRNA-seq. Finally, libraries were sequenced on a NovaSeq 6000 system with NovaSeq 6000 S4 Reagent Kit (300 cycles).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Splenocytes were sorted from the spleens of  seven vertebrate species

tag: cell type

value: Splenocytes

value: Bama miniature pig


title: Patient93_Sample10

description: COUNTS_TABLE_RAW11: P93_S10

value: nasopharyngeal samples


title: CTRL

value: uninjured mouse


title: 6.52.NEPRECTOMY

value: Kidney

value: Kidney - contralateral to nephrecomy


title: ChIP_k27ac_LU_679

value: Lung

value: Female


title: FFPE bone marrow, Non-Responder Diagnosis, biological rep1

type: RNA

city: Providence

first: Patrycja

middle: M

last: Dubielecka

state: RI

address: 1 Hoppin St., Coro West, 5th Fl., Suite 5.36

department: Division of Hematology/Oncology, Department of Medicine

institute: Warren Alpert Medical School of Brown University and Rhode Island Hospital

description: 092519PD 13

scan_protocol: FS450_0001,  followed by scan on Affymetrix 3000 7 G scanner

data_processing: Data was analyzed using the default settings within the Applied Biosystem's Transcriptome Analysis Console (TAC) Software version 4.0.

label: biotin

source_name: bone marrow, Non-Responder #1, Diagnosis

label_protocol: Afffymetrix WT Pico expression protocol, 10 ng total RNA input

extract_protocol: RNA was isolated from patient FFPE core bone marrow biopsies using the Qiagen's Rneasy FFPE Kit (Catalog# 73504)

value: bone marrow

tag: diagnosis

value: AML

tag: treatment response

value: Non-Responder


title: FFPE bone marrow, Non-Responder Diagnosis, biological rep4

description: 092519PD 16

source_name: bone marrow, Non-Responder #4, Diagnosis


title: FFPE bone marrow, Non-Responder Diagnosis, biological rep2

description: 092519PD 18

source_name: bone marrow, Non-Responder #2, Diagnosis


title: FFPE bone marrow, Responder Diagnosis, biological rep6

source_name: bone marrow, Responder #6, Diagnosis

value: Responder


title: FFPE bone marrow, Non-Responder Diagnosis, biological rep5

description: 092519PD 14

source_name: bone marrow, Non-Responder #5, Diagnosis


title: Patient93_Sample8

description: COUNTS_TABLE_RAW12: P93_S8


title: FFPE bone marrow, Responder Diagnosis, biological rep3

source_name: bone marrow, Responder #3, Diagnosis


title: ChIP_k27ac_LI_679

value: Liver

value: Beagle


title: FFPE bone marrow, Non-Responder Diagnosis, biological rep3

description: 092519PD 17

source_name: bone marrow, Non-Responder #3, Diagnosis

value: Male


title: FFPE bone marrow, Responder Diagnosis, biological rep5

source_name: bone marrow, Responder #5, Diagnosis


title: IRI.TG.VEH

tag: strain

value: 8 week

value: Transgenic Ihh KO mouse not treated with Tamoxifen and post IRI


title: FFPE bone marrow, Responder Diagnosis, biological rep4

source_name: bone marrow, Responder #4, Diagnosis


title: ChIP_k27ac_OV_244

source_name: Ovary

value: Ovary

value: H3K27ac (Abcam, #ab4729)


title: IRI.WT.TAM

value: wild type as control, treated with tamoxifen and post IRI


title: Patient93_Sample9

description: COUNTS_TABLE_RAW11: P93_S9

value: nasopharyngeal samples


title: Patient93_Sample7

description: COUNTS_TABLE_RAW11: P93_S7


title: ChIP_k27ac_MG_244

value: Mammary gland


title: ChIP_k27ac_CO_679

source_name: Colon

value: Colon


title: IRI.TG.TAM

value: Kidney

value: Transgenic Ihh KO mouse treated with Tamoxifen and post IRI


title: FFPE bone marrow, Non-Responder Post-Treatment, biological rep1

description: 092519PD 19

source_name: bone marrow, Non-Responder #1, Post-Treatment

value: bone marrow

value: Female


title: ChIP_k27ac_KI_jj8


title: ChIP_k27ac_CR_679

source_name: Cerebrum

value: Cerebrum


title: FFPE bone marrow, Responder Diagnosis, biological rep1

source_name: bone marrow, Responder #1, Diagnosis

value: AML

value: Responder


title: FFPE bone marrow, Responder Diagnosis, biological rep2

source_name: bone marrow, Responder #2, Diagnosis


title: Patient93_Sample5

description: COUNTS_TABLE_RAW12: P93_S5


title: IRI_MOUSE_SC

source_name: Kidney

value: single cell post IRI


title: Patient93_Sample6

description: COUNTS_TABLE_RAW11: P93_S6

source_name: nasopharyngeal samples


title: UNINJURED_MOUSE_SC

value: single cell uninjured


title: FFPE bone marrow, Non-Responder Post-Treatment, biological rep4

description: 092519PD 22

source_name: bone marrow, Non-Responder #4, Post-Treatment

value: Non-Responder


title: ChIP_k27ac_CL_679

source_name: Cerebellum

value: Cerebellum

value: Beagle


title: ChIP_k4me1_PA_244

source_name: Pancreas

value: Pancreas

value: H3K4me1 (Abcam, #ab8895)


title: FFPE bone marrow, Non-Responder Post-Treatment, biological rep5

description: 092519PD 20

source_name: bone marrow, Non-Responder #5, Post-Treatment


title: Patient93_Sample2

description: COUNTS_TABLE_RAW11: P93_S2

value: nasopharyngeal samples


title: ChIP_k4me1_ST_679

source_name: Stomach

value: Stomach


title: Patient93_Sample1

description: COUNTS_TABLE_RAW12: P93_S1


title: Patient93_Sample4

description: COUNTS_TABLE_RAW11: P93_S4


title: Fish

value: Splenocytes


title: Patient92_Sample14

description: COUNTS_TABLE_RAW10: P92_S14


title: SH_ASF1A_set2_IP

city: Shanghai

first: Chuanwei

last: Yang

address: 2005 Songhu Road, Yangpu District

department: school of life sciences

institute: Fudan university

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT.
Quality filtered reads were then mapped to Tair10 using STAR.
Read counts were calculated by using htseq-count.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
Assembly: Tair 10
Supplementary files format and content: bigWig

organism: Arabidopsis thaliana

source_name: 6-day-white-light grown seedlings

growth_protocol: 6-day-white-light grown seedlings were treated 1 hr shade before harvesting for DNA extraction using GFP antibodies.

extract_protocol:
DNA was sonicated into fragments of 100-400 bp, followed by immuno-precipitation with anti-GFP.
DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: With 1 hr shade (white light as control) treatment.

value: whole seedlings

tag: genotype

value: 35S::ASF1A overexpression

tag: treatment

value: 1 hr shade

value: GFP antibodies (ab290)


title: ChIP_k4me1_LU_679

source_name: Lung

value: Lung

value: Female

tag: breed


title: Patient92_Sample12

description: COUNTS_TABLE_RAW10: P92_S12


title: SH_ASF1A_set1_IP


title: SH_ASF1A_set2_input


title: ChIP_k4me1_MG_244

source_name: Mammary gland

value: Mammary gland

tag: Sex


title: Patient92_Sample13

description: COUNTS_TABLE_RAW10: P92_S13


title: Patient93_Sample3

description: COUNTS_TABLE_RAW11: P93_S3


title: WL_ASF1A_set2_IP

value: 1 hr white light


title: ChIP_k4me1_SP_679

source_name: Spleen

value: Spleen


title: FFPE bone marrow, Non-Responder Post-Treatment, biological rep2

description: 092519PD 24

source_name: bone marrow, Non-Responder #2, Post-Treatment

value: bone marrow

value: AML

value: Non-Responder

tag: age


title: FFPE bone marrow, Responder Post-Treatment, biological rep6

source_name: bone marrow, Responder #6, Post-Treatment

value: Responder


title: FFPE bone marrow, Responder Post-Treatment, biological rep3

source_name: bone marrow, Responder #3, Post-Treatment

value: Male


title: FFPE bone marrow, Responder Post-Treatment, biological rep4

source_name: bone marrow, Responder #4, Post-Treatment


title: WL_ASF1A_set2_input


title: FFPE bone marrow, Responder Post-Treatment, biological rep1

source_name: bone marrow, Responder #1, Post-Treatment


title: proximal_rep6

city: Gainesville

first: William

middle: Bradley

last: Barbazuk

state: Florida

address: UF-CGRC Room 407 2033 Mowry Rd

department: Biology

institute: University of Florida

description: Full-thickness skin collected from the proximal end of the tail from a newborn Acomys cahirinus pup.

data_processing:
Base calls and quality scores produced by the Illumina NovaSeq6000 with onboard RTA3 software.
RNA-seq FASTQ-files were quality and adapter trimmed using Trimmomatic v0.39 with the parameters : LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 and ILLUMINACLIP with the TruSeq3-PE-2.fa adapter set (available on the Trimmomatic github page: https://github.com/timflutre/trimmomatic/tree/master/adapters) and values of 2, 30,10 for seed mismatches, palindrome clip threshold and simple clip threshold, respectively.
The preprocessed reads were aligned to the Acomys skin transcriptome (GEO Accession GSE113081) with HiSat2 (v2.2.1) using default parameters for paired-end reads.
Individual read set alignments representing the output from HiSat2 were assembled into transcripts with Stringtie using default settings. Counts per transcript for each RNA-Seq sample were determined with the featureCounts function from the Rsubreads package, which mapped the aligned reads to individual transcripts within the Acomys transcriptome assembly. Featurecounts was called with the following parameters: -s 2 -p -t exon -g gene_id -T 8. Counts to isoforms that are representatives of the same trinity loci were aggregated to enable gene level expression analysis.
The Acomys transcriptome has been annotated to define Mus – Acomys orthologous for a subset of the transcripts. These annotations were used in this analysis. Differentially expressed genes were discovered with the EdgeR package (v3.36) using the aggregated count matrix as input. Count data were TMM normalized, distal/proximal tail skin samples from the same individual were treated as paired samples, and genes differentially expressed between Acomys distal and proximal tail skin samples with pvalues <= 0.05 after Benjamini & Hochberg false discovery rate correction were reported as significant.
Assembly: Trinity assembled Acomys transcriptome (GSE113081).
Supplementary files format and content: featurecounts_Acomus_Distal_proximal.csv: Comma-separated file detailing the feature counts of each Acomys sample to the Acomus Trinity assembled transcript reference (GSE113081).
Supplementary files format and content: Trinity_gene_level_osteo_SAMPLE_ReadCounts.csv: Comma-separated file describing reads mapped to the Trinity based transcriptome assembly reduced from transcript ‘isoform’ level representation to ‘gene’ level representation. Thus, counts associated with isoforms from the same gene have been aggregated to represent counts/gene.
Supplementary files format and content: Trinity_gene_level_osteo_SAMPLES_RENAMED_AllSig-ANNOTATED.csv: Comma-separated file describing EdgeR results of genes identified to be differentially expressed between DISTAL and PROXIMAL samples after Benjamini & Hochberg false discovery rate correction (pval <= 0.05).

organism: Acomys cahirinus

source_name: proximal tail skin

extract_protocol:
Total RNA was extracted using a RNeasy Fibrous Tissue Mini Kit (QIAGEN 74704) according to the manufacturer’s protocol.
Strand-specific TruSeqTM (Illumina) cDNA libraries were prepared from 1 µg total RNA input with a 300 bp median insert length by HudsonAlpha Discovery in Huntsville, Alabama, USA.

value: proximal tail skin

value: WildType

value: newborn


title: FFPE bone marrow, Non-Responder Post-Treatment, biological rep3

description: 092519PD 23

source_name: bone marrow, Non-Responder #3, Post-Treatment


title: SH_ASF1A_set1_input

value: whole seedlings


title: ChIP_k4me1_LI_679

source_name: Liver

value: Liver

value: Beagle

value: H3K4me1 (Abcam, #ab8895)


title: proximal_rep4


title: proximal_rep5


title: WL_ASF1A_set1_IP

value: 35S::ASF1A overexpression

value: GFP antibodies (ab290)


title: ChIP_k4me1_OV_244

source_name: Ovary

value: Ovary

value: Female


title: Patient92_Sample10

description: COUNTS_TABLE_RAW10: P92_S10

source_name: nasopharyngeal samples

value: nasopharyngeal samples


title: Patient92_Sample9

description: COUNTS_TABLE_RAW10: P92_S9


title: ChIP_k4me1_CO_679

source_name: Colon

value: Colon


title: FFPE bone marrow, Responder Post-Treatment, biological rep2

source_name: bone marrow, Responder #2, Post-Treatment

value: bone marrow

value: AML


title: WL_ASF1A_set1_input

value: 1 hr white light


title: ChIP_k4me1_KI_jj8

source_name: Kidney

value: Kidney

value: Male


title: FFPE bone marrow, Responder Post-Treatment, biological rep5

source_name: bone marrow, Responder #5, Post-Treatment

value: Responder


title: Patient92_Sample11

description: COUNTS_TABLE_RAW10: P92_S11


title: ChIP_k4me1_CL_679

source_name: Cerebellum

value: Cerebellum


title: proximal_rep3

value: proximal tail skin

value: WildType

value: newborn


title: SH_HTR13_set2_IP

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to Tair10 using STAR
Read counts were calculated by using htseq-count
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
Assembly: Tair 10

source_name: whole seedlings

growth_protocol: 8-day-white-light grown seedlings were treated 1 hr shade before harvesting for pHTR13::HTR13-HA DNA extraction using HA antibodies.

extract_protocol:
DNA was sonicated into fragments of 100-400 bp, followed by immuno-precipitation with anti-HA.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: With 1 hr shade (white light as control) treatment

value: whole seedlings

value: Col-0 background

value: 8-day-old white light-grown seedlings with 1 hr shade treatment


title: Patient92_Sample7

description: COUNTS_TABLE_RAW10: P92_S7


title: SH_HTR13_set2_input


title: proximal_rep2


title: Patient92_Sample6

description: COUNTS_TABLE_RAW10: P92_S6


title: proximal_rep1


title: Patient92_Sample8

description: COUNTS_TABLE_RAW10: P92_S8


title: ChIP_k4me1_CR_679

source_name: Cerebrum

value: Cerebrum

value: Beagle

value: H3K4me1 (Abcam, #ab8895)


title: Patient92_Sample5

description: COUNTS_TABLE_RAW10: P92_S5

value: nasopharyngeal samples


title: distal_rep5

description: Full-thickness skin collected from the distal end of the tail from a newborn Acomys cahirinus pup.

source_name: distal tail skin

value: distal tail skin


title: distal_rep6


title: ChIP_k4me3_SP_679

source_name: Spleen

value: Spleen

value: Female

value: H3K4me3 (Abcam, #ab8580)


title: Patient92_Sample4

description: COUNTS_TABLE_RAW10: P92_S4


title: ChIP_k4me3_ST_679

source_name: Stomach

value: Stomach


title: ChIP_k4me3_PA_244

source_name: Pancreas

value: Pancreas


title: WL_HTR13_set2_input

value: 8-day-old white light-grown seedlings with 1 hr white light treatment


title: Patient92_Sample3

description: COUNTS_TABLE_RAW10: P92_S3


title: SH_HTR5_pif7_set2_IP

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to Tair10 using STAR
Read counts were calculated by using htseq-count
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
Assembly: Tair 10
Supplementary files format and content: BW

source_name: 8-day-old white light-grown pHTR5::HTR5-HA /pif7-1 seedlings

growth_protocol: 8-day-white-light grown seedlings were treated 1 hr shade before harvesting for pHTR5::HTR5-HA/pif7-1 DNA extraction using HA antibodies.

tag: antibody

value: HA


title: ChIP_k4me3_OV_244

value: Ovary

tag: chip antibody


title: distal_rep4

value: WildType

value: newborn


title: distal_rep3


title: SH_HTR5_pif7_set1_IP

value: whole seedlings


title: ChIP_k4me3_MG_244

source_name: Mammary gland

value: Mammary gland


title: SH_HTR5_pif7_set2_input


title: WL_HTR13_set2_IP

value: Col-0 background


title: distal_rep1


title: Patient92_Sample1

description: COUNTS_TABLE_RAW10: P92_S1

data_processing:
single end: For producing count tables: We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Human: NCBI/build37.2) using STAR(2.5.2b) and featureCounts(v1.5.0-p3).
paired end: For producing count tables: We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38) using kallisto (0.44.0).
For producing unmapped reads: Produced with Pandora (Abate et al., 2015; Wang et al). The Pandora workflow takes RNA-seq data as input and produces the annotated microbial reads present in the sample as outputs. The pipeline runs through five main modules: 1) mapping to the human host genome using STAR (Dobin et al., 2013) and bowtie2 (Langmead & Salzberg, 2012); 2) processing of the host-mapped reads with featureCounts (Liao et al., 2014)  to obtain the host gene expression profile; 3) de-novo assembly of host-subtracted short (2x100bp) reads using Trinity (Grabherr et al., 2011) to create long contiguous full-length transcripts (contigs); 4) contigs alignment to curated sets of NCBI sequences from viruses, bacteria, fungi and other eukaryotic parasites with BLAST (Altschul et al., 1990); and 5) filtering and parsing the BLAST results into a report specifying the detected microbial abundances in the sample.
Assembly: single end: NCBI/build37.2
Assembly: paired end: GRCh38
Raw counts provided for all samples


title: Patient91_Sample9

description: COUNTS_TABLE_RAW13: P91_S9


title: ChIP_k4me3_LU_679

source_name: Lung

value: Lung

value: Beagle


title: WL_HTR5_pif7_set2_IP


title: SH_HTR5_pif7_set1_input


title: ChIP_k4me3_KI_jj8

value: Kidney

value: Male


title: distal_rep2

value: distal tail skin


title: ChIP_k4me3_LI_679

source_name: Liver

value: Liver

value: Female


title: mnp-20-1586

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

source_name: CNS tumor tissue

label_protocol: Illumina

extract_protocol: DNA from FFPE tissue was extracted using a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: "material"

value: FFPE tissue

tag: "tumor type"

value: Schwannoma

tag: "patient age (years)"

tag: "patient gender"

value: female

tag: "tumor location"

value: spinal cord


title: WL_HTR5_pif7_set2_input

tag: tissue


title: Patient91_Sample6

description: COUNTS_TABLE_RAW13: P91_S6

source_name: nasopharyngeal samples

extract_protocol:
Nasopharyngeal swabs were collected from each participant using a minitip flock swab (VWR catalog no. 10755-196; Copan Diagnostics) and immediately placed in a 15 mL tube containing 2 mL of DNA/RNA Shield (Product no. R1100-250; Zymo). Samples were separated into two 1 mL aliquots, and stored at −80°C. After thawing, RNA extraction was done using Zymo Quick-RNA™ Microprep Kit RNA extraction kit (ZYMO, R1050) including the recommended on column DNase I treatment step for 15 min. An Agilent Bioanalyzer was used for quality control prior to library creation
For single end samples: RNA RIBOZERO 30M SE100. For paired end samples: RNA RIBOZERO 20M PE100. Then proceed with library construction using Illumina TruSeq  chemistry.

value: nasopharyngeal samples

tag: subject

tag: geographic location

tag: collection date


title: WL_HTR5_pif7_set1_input

tag: cell type


title: mnp-20-0918

value: Anaplastic astrocytoma

value: male

value: basal ganglia, thalamus


title: mnp-20-0296

value: Ganglioglioma

value: medulla oblongata


title: ChIP_k4me3_CR_679

value: Cerebrum

value: H3K4me3 (Abcam, #ab8580)


title: GRL18085-dscm3

city: Roanoke

first: Yuchin

middle: Albert

last: Pan

state: VA

address: 2 Riverside Circle

institute: Virginia Tech

data_processing:
Following sequencing, data was trimmed for both adaptor and quality using a combination of ea-utils and Btrim.
Sequencing reads were then aligned to the genome (Ensembl Danio_rerio.GRCz11.92 with and without unplaced contigs) using Tophat2/HiSat2 and counted via HTSeq.
Read counts for genes annotated on the unplaced contigs were added to the chromosome only count summary.  QC summary statistics were examined to identify any problematic samples (e.g. total read counts, quality and base composition profiles (+/- trimming)), raw fastq formatted data files, aligned files (bam and text file containing sample alignment statistics), and count files (HTSeq text files).
Assembly: Ensembl Danio_rerio.GRCz11.92

molecule: polyA RNA

source_name: Whole animal

growth_protocol: Zebrafish larvae were grown under standard rearing conditions (28.5 degrees, 14:10 light:dark cycle)

extract_protocol:
Tissue was dissociated with gentle pipetting and total RNA was prepared using the Zymo RNA miniprep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatments were applied.

value: Whole animal

tag: cell line

value: Sexually undifferentiated

tag: genotype

value: dscaml1 mutant


title: Patient92_Sample2

description: COUNTS_TABLE_RAW10: P92_S2


title: ChIP_k4me3_CO_679

source_name: Colon

value: Colon

tag: breed

value: Beagle


title: Patient91_Sample7

description: COUNTS_TABLE_RAW13: P91_S7


title: Patient91_Sample5

description: COUNTS_TABLE_RAW13: P91_S5


title: Patient91_Sample4

description: COUNTS_TABLE_RAW13: P91_S4


title: ChIP_k4me3_CL_679

value: Cerebellum

tag: Sex

value: Female


title: GRL18084-dscm2


title: WL_HTR5_set2_IP

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to Tair10 using STAR
Read counts were calculated by using htseq-count
The peak calling was used MACS2 software with cutoff qvalue < 0.05
Assembly: Tair 10
Supplementary files format and content: BW

source_name: 8-day-old white light-grown pHTR5::HTR5-HA seedlings

growth_protocol: 8-day-white-light grown seedlings were treated 1 hr shade before harvesting for pHTR5::HTR5-HA DNA extraction using HA antibodies.

tag: genotype/variation

value: whole seedlings


title: Patient91_Sample8

description: COUNTS_TABLE_RAW13: P91_S8


title: SH_HTR5_set2_IP

source_name: 8-day-old white light-grown pHTR5::HTR5-HA seedlings with 1hr shade treatment


title: GRL18083-dscm1


title: WL_HTR5_pif7_set1_IP

tag: antibody

value: HA


title: mnp-20-0345

value: FFPE tissue

value: Pilocytic Astrocytoma

value: female

value: spinal cord


title: mnp-20-1516

value: Anaplastic astrocytoma


title: SH_HTR5_set2_input


title: Patient91_Sample3

description: COUNTS_TABLE_RAW13: P91_S3

value: nasopharyngeal samples


title: Patient90_Sample7

description: COUNTS_TABLE_RAW12: P90_S7


title: SH, ASF1, input

source_name: 6-day-old white light-grown seedlings

extract_protocol:
DNA was sonicated into fragments of 100-400 bp, followed by immuno-precipitation with anti-HA and anti-H3K56ac.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: ASF1Aox transgenic

tag: age

tag: treatment

value: shade

tag: chip antibody


title: WL_HTR5_set2_input


title: SH, ASF1, IP

value: GFP


title: mnp-20-0636

tag: "material"

tag: "tumor type"

value: Medulloblastoma, NOS

tag: "patient age (years)"

value: male

value: fourth ventricle


title: GRL18081-dscmWT2

tag: tissue

value: Whole animal

value: Sexually undifferentiated

value: Wild type


title: WL, ASF1, IP

value: control


title: Patient90_Sample6

description: COUNTS_TABLE_RAW12: P90_S6

tag: subject


title: Cells from uninfected collagen gels, D14 [Mammalian_control3]

city: Bengaluru

first: Rachit

last: Agarwal

state: Karnataka

address: CV Raman road

department: Biosystems Science and Engineering

country: India

institute: Indian Institute of Science, Bangalore

description: Dual_mammalian vs Mammalian_control.txt

data_processing:
The data obtained from the sequencing run was de-multiplexed using Bcl2fastq software v2.20, and FastQ files were generated based on the unique dual barcode sequences.
The sequencing quality was assessed using FastQC v0.11.8 software. The adapter sequences were trimmed, bases above Q30 were considered, and low-quality bases were filtered off during read pre-processing and used for downstream analysis.
Supplementary files format and content: RPKM values for each Sample
Supplementary files format and content: log2fc of (average rpkm of Dual_mammalian (1,2,3)/mammalian_control (1,2))

source_name: Collagen hydrogels

growth_protocol: THP-1 cells were encapsulated in collagen gels with or without Mtb and cultured in RPMI1640 substituted with 10% FBS at 37 C in a humidified incubator supplemented with 5% CO2.

extract_protocol:
The mammalian RNA was isolated treating cells witj GTC buffer, followed by extraction using the choloroform-isopropanal method. The Mtb RNA was extracted by bead beating in a FastPrep instrument using the RNApro isolation kit.
RNA libraries for RNA-seq were prepared using mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Collagen hydrogels

value: mammalian

value: WT


title: GRL18080-dscmWT1


title: mnp-20-0430

value: FFPE tissue

value: Pilocytic Astrocytoma

tag: "patient gender"

value: female

tag: "tumor location"

value: temporal lobe


title: GRL18082-dscmWT3

tag: cell type


title: mnp-20-0731

value: primary visual cortex


title: mnp-20-0489

value: Medulloblastoma, non-WNT/SHH

value: cerebellum, fourth ventricle


title: WL, ASF1, input

value: ASF1Aox transgenic


title: Cells from uninfected collagen gels, D14 [Mammalian_control2]

description: Dual_mammalian vs Mammalian_control.txt

tag: cell line


title: Patient91_Sample1

description: COUNTS_TABLE_RAW13: P91_S1

value: nasopharyngeal samples

tag: geographic location

tag: collection date


title: Patient90_Sample5

description: COUNTS_TABLE_RAW11: P90_S5


title: SH_H3K56ac_1_IP

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to Tair10 using STAR
Read counts were calculated by using htseq-count
The peak calling was used MACS2 software with cutoff qvalue < 0.05
Genome_build: Tair 10
Supplementary_files_format_and_content: BW

source_name: 6-day-old white light-grown Col-0 seedlings with 1hr shade treatment

growth_protocol: 8-day-white-light grown seedlings were treated 1 hr shade before harvesting for pHTR13::HTR13-HA and pHTR5::HTR5-HA DNA extraction using HA antibodies. And 6-day-white-light grown seedlings were treated 1 hr shade before harvesting for Col-0 extraction using H3K56ac antibodies.

value: 1hr shade treatment

value: whole seedlings


title: Patient90_Sample4

description: COUNTS_TABLE_RAW11: P90_S4


title: mnp-20-1543

value: Glioblastoma, IDH-mutated

value: frontal lobe


title: Patient91_Sample2

description: COUNTS_TABLE_RAW13: P91_S2


title: Cells from infected collagen gels, D14 [Dual_mammalian3]

description: Dual_mammalian vs Mammalian_control.txt

tag: genotype

value: infection with Mtb


title: SH_H3K56ac_1_input

tag: genotype/variation


title: mnp-20-0921

value: Atypical meningioma, WHO grade II

value: male


title: Patient90_Sample3

description: COUNTS_TABLE_RAW11: P90_S3


title: Cells from infected collagen gels, D14 [Dual_mammalian2]

description: Dual_mammalian vs Mammalian_control.txt

value: Collagen hydrogels

value: mammalian

value: WT


title: Patient90_Sample2

description: COUNTS_TABLE_RAW11: P90_S2


title: Patient90_Sample1

description: COUNTS_TABLE_RAW11: P90_S1


title: Cells from infected collagen gels, D14 [Dual_mammalian1]

description: Dual_mammalian vs Mammalian_control.txt


title: mnp-20-1226

value: FFPE tissue

value: Pilocytic Astrocytoma

value: female

value: orbital frontal cortex


title: WL_H3K56ac_1_IP

source_name: 6-day-old white light-grown Col-0 seedlings


title: WL_H3K56ac_1_input


title: mnp-20-0253

value: Glioblastoma (GBM)

value: third ventricle


title: LTA4H_IP_2

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description: LTA4H bound RNA

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
After reads were aligned onto the genome with TopHat 2 (Kim et al. 2013), only uniquely mapped reads were used for the following analysis.
“ABLIRC” strategy was used to identify the binding regions of LTA4H on genome (Xia et al. 2017).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include peak information for each group.

source_name: Hela cells

growth_protocol: Human CC (Cervical Carcinoma) cell lines, HeLa (CCTCC@GDC0009) were obtained from CCTCC (China Center for Type Culture Collection, Wuhan, Hubei, China).  HeLa cells were cultured at 37℃ with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.  Plasmid transfection of HeLa cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol.  Transfected cells were harvested after 48h for RT-qPCR analysis and western blot.

extract_protocol:
The RBP-bound RNAs were isolated from the immunoprecipitation of anti-Flag using TRIzol (Invitrogen).
Complementary DNA (cDNA) libraries were prepared with the KAPA RNA Hyper RNA binding protein connects the future Prep Kit (KAPA, KK8541) according the manufacturer’s procedure and high-throughput sequencing of the cDNA libraries was performed on Illumina HiSeq X Ten platform for 150 bp paired-end sequencing.

treatment_protocol: HeLa cells were first lysed in ice-cold lysis buffer (1×PBS, 0.5% sodium deoxycholate, 0.1% SDS, 0.5% NP40) with RNase inhibitor (Takara, 2313) and a protease inhibitor (Solarbio, 329-98-6) on ice for 5 min. The mixture was then vibrated vigorously and centrifuged at 13,000 x g at 4℃ for 20 min to remove cell debris. The supernatant was incubated with DynaBeads protein A/G (Thermo, 26162) conjugated with anti-Flag antibody (Sigma, F1804) or normal IgG at 4℃ overnight. The beads were washed with Low-salt Wash buffer, High-salt Wash buffer and 1X PNK Buffer, respectively. Resuspend the beads in Elution Buffer for RNA isolation from RBP-RNA complexes.

value: Hela cells


title: mnp-20-1536

value: Ependymoma, WHO grade III

value: cerebellum, fourth ventricle, pons


title: LTA4H_IP_1

description: LTA4H bound RNA


title: Patient89_Sample9

description: COUNTS_TABLE_RAW11: P89_S9

value: nasopharyngeal samples


title: Patient89_Sample8

description: COUNTS_TABLE_RAW12: P89_S8


title: SH_HTR5_1_input

value: 1hr shade treatment

value: whole seedlings


title: WL_HTR5_1_IP

value: anti-HA


title: mnp-20-1196

value: Anaplastic astrocytoma

value: male

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: Patient89_Sample6

description: COUNTS_TABLE_RAW11: P89_S6


title: Patient89_Sample7

description: COUNTS_TABLE_RAW11: P89_S7


title: mnp-20-0989

value: Medulloblastoma, WNT

value: fourth ventricle


title: SH_HTR13_1_IP

source_name: 8-day-old white light-grown pHTR13::HTR13-HA seedlings with 1hr shade treatment


title: Patient89_Sample5

description: COUNTS_TABLE_RAW12: P89_S5


title: WL_HTR5_1_input


title: SH_HTR13_1_input


title: LTA4H_input_1

description: LTA4H bound RNA


title: mnp-20-0399

value: FFPE tissue

value: Low-grade astrocytoma, NOS

value: pons, medulla oblongata


title: Patient89_Sample4

description: COUNTS_TABLE_RAW11: P89_S4


title: Patient89_Sample3

description: COUNTS_TABLE_RAW12: P89_S3


title: mnp-20-0109

value: Diffuse midline glioma, H3 K27-mutated

value: thalamus, basal ganglia


title: C2C12 cell line, 7 day

city: Debrecen

first: Endre

last: Barta

state: Hungary

address: Egyetem tér 1.

department: Institute of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

data_processing:
Reads were aligned to the reference genome using BWA mem
Any further steps were done using the utilities included in the Homer tools (http://homer.ucsd.edu/homer/)
Assembly: mm10
Supplementary files format and content: bed, all called peaks
Supplementary files format and content: table, Homer annotatePeaks.pl
Supplementary files format and content: bedgraph

extract_protocol:
Proliferating myoblasts and myotubes from late differentiation stage (»20 million cells/reaction) were cross-linked using 2 mM disuccinimidyl glutarate (DSG, Sigma) for 45 min followed by cross-linking using 1% methanol-free ultrapure formaldehyde (Thermo Scientific) for 10 min. Cross-linking was stopped by the addition of glycine to a final concentration of 125 mM for 10 min, followed by washing steps (2x) with PBS. Cells were harvested in ChIP lysis buffer
libraries were prepared from  ChIP-DNA using a TruSeq ChIP Sample Preparation Kit (Illumina) according to manufacturer's instructions

treatment_protocol: myotube differentiation induced by reduced serum in media

tag: antibody


title: SH_HTR5_1_IP


title: LTA4H_input_2

description: LTA4H bound RNA

value: Hela cells


title: mnp-20-0997

value: Meningioma, WHO grade I


title: WL_HTR13_1_IP

source_name: 8-day-old white light-grown pHTR13::HTR13-HA seedlings


title: WL_HTR13_1_input


title: mnp-20-0040

value: Descriptive diagnosis

value: parietal lobe, occipital lobe, temporal lobe


title: Patient89_Sample2

city: New York

first: Angelica

last: Galianese

address: 615 W 164th Street, Apt 21C

institute: Columbia University

description: COUNTS_TABLE_RAW11: P89_S2

value: nasopharyngeal samples


title: Patient89_Sample1

description: COUNTS_TABLE_RAW12: P89_S1


title: Rat

organism: Rattus norvegicus

value: Splenocytes


title: CD8 C269 6c

city: Novara

first: Giorgia

last: Colombo

state: NO

address: Via Bovio 6, Presso Fondazione Novara Sviluppo

department: Department of Pharmaceutical Sciences

country: Italy

institute: UNIUPO

description: CD8 C269

data_processing:
Quality check of RNA-seq reads was performed using fastQC
RNA-seq reads were mapped against the murine genome (mm9) using ContextMap version 2.7.9
Number of read counts per gene and exon were determined from the mapped RNA-seq reads in a strand-specific manner using featureCounts gene annotations from GENCODE version 27.
Differential gene expression analysis was performed using DESeq2
Assembly: mm9
Supplementary files format and content: The data are processed as base mean and log2fold change

source_name: Tumour

extract_protocol:
RNA was extracted using SPLIT RNA Extraction Kit (Lexogen, Vienna, Austria).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
4T1-GFP cells were sorted, while CD4+ and CD8+ T cells were isolated using magnetic beads
Mice were treated wih control IgG1 or C269 (anti-eNAMPT, 2.5mg/kg) twice a week for 1 months

value: Tumour

value: Isolated CD8+ T cells

value: wild-type

value: C269-treated (anti-eNAMPT)


title: CD8 C269 6d

description: CD8 C269


title: CD8 C269 6e

description: CD8 C269


title: CD8 CTRL 5d

description: CD8 CTRL

value: CTRL


title: Patient88_Sample8

description: COUNTS_TABLE_RAW12: P88_S8


title: mnp-20-1419

value: Pilocytic Astrocytoma

value: male

value: hypothalamus, third ventricle


title: Patient88_Sample6

description: COUNTS_TABLE_RAW12: P88_S6


title: CD8 CTRL 5e

description: CD8 CTRL


title: mnp-20-1043

value: FFPE tissue

value: Medulloblastoma, non-WNT/SHH

value: female

value: cerebellum


title: CD8 C269 6b

description: CD8 C269


title: Patient82_Sample1

description: COUNTS_TABLE_RAW2: P82_S1


title: Patient88_Sample7

description: COUNTS_TABLE_RAW11: P88_S7


title: CD8 C269 6a

description: CD8 C269


title: Patient88_Sample3

description: COUNTS_TABLE_RAW11: P88_S3


title: CD8 CTRL 5a

description: CD8 CTRL


title: Patient82_Sample2

description: COUNTS_TABLE_RAW2: P82_S2


title: Patient81_Sample1

description: COUNTS_TABLE_RAW2: P81_S1


title: CD8 CTRL 5c

description: CD8 CTRL


title: Patient88_Sample5

description: COUNTS_TABLE_RAW11: P88_S5


title: mnp-20-0160

value: angular gyrus


title: CD8 CTRL 5b

description: CD8 CTRL


title: CD4 C269 4c

description: CD4 C269

value: Isolated CD4+ T cells


title: mnp-20-0309

value: Anaplastic oligoastrocytoma

value: temporal lobe


title: mnp-20-0806

value: Medulloblastoma, WNT


title: Patient81_Sample3

description: COUNTS_TABLE_RAW2: P81_S3

value: nasopharyngeal samples


title: Patient81_Sample4

description: COUNTS_TABLE_RAW2: P81_S4


title: Patient88_Sample2

description: COUNTS_TABLE_RAW11: P88_S2


title: Patient87_Sample5

description: COUNTS_TABLE_RAW12: P87_S5


title: mnp-20-0910

value: cerebellum, fourth ventricle


title: Patient81_Sample2

description: COUNTS_TABLE_RAW2: P81_S2


title: Patient87_Sample4

description: COUNTS_TABLE_RAW11: P87_S4


title: Patient80_Sample4

description: COUNTS_TABLE_RAW3: P80_S4


title: Patient80_Sample3

description: COUNTS_TABLE_RAW3: P80_S3


title: Patient80_Sample6

description: COUNTS_TABLE_RAW3: P80_S6


title: CD4 C269 4d

description: CD4 C269

value: Tumour

value: wild-type


title: CD4 C269 4e

description: CD4 C269

value: C269-treated (anti-eNAMPT)


title: CD4 C269 4a

description: CD4 C269


title: Patient81_Sample5

description: COUNTS_TABLE_RAW2: P81_S5


title: mnp-20-1322

value: Germinoma

value: hypothalamus


title: Patient80_Sample5

description: COUNTS_TABLE_RAW3: P80_S5


title: Patient86_Sample4

description: COUNTS_TABLE_RAW13: P86_S4


title: Patient79_Sample2

description: COUNTS_TABLE_RAW5: P79_S2


title: CD4 CTRL 3e

description: CD4 CTRL

value: CTRL


title: Patient88_Sample1

description: COUNTS_TABLE_RAW11: P88_S1


title: mnp-20-1209

value: FFPE tissue

value: Ganglioglioma

value: male


title: mnp-20-1247

value: Medulloblastoma, non-WNT/SHH

value: fourth ventricle


title: mnp-20-0591

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-0798

value: CNS tumor with BCOR internal tandem duplication

value: parietal lobe


title: CD4 CTRL 3a

description: CD4 CTRL

value: Isolated CD4+ T cells


title: Patient87_Sample3

description: COUNTS_TABLE_RAW11: P87_S3

value: nasopharyngeal samples


title: mnp-20-0961

value: cerebellum, fourth ventricle


title: CD4 C269 4b

description: CD4 C269

value: Tumour

value: wild-type


title: mnp-20-1302

value: Anaplastic oligodendroglioma

value: thalamus


title: Patient87_Sample2

description: COUNTS_TABLE_RAW11: P87_S2


title: Patient88_Sample4

description: COUNTS_TABLE_RAW11: P88_S4


title: mnp-20-1358

value: Pilocytic Astrocytoma

value: hypothalamus


title: Patient79_Sample3

description: COUNTS_TABLE_RAW5: P79_S3


title: CD4 CTRL 3d

description: CD4 CTRL

value: CTRL


title: Patient80_Sample1

description: COUNTS_TABLE_RAW3: P80_S1


title: CD4 CTRL 3c

description: CD4 CTRL


title: Patient86_Sample1

description: COUNTS_TABLE_RAW13: P86_S1


title: Patient79_Sample1

description: COUNTS_TABLE_RAW5: P79_S1


title: Patient80_Sample2

description: COUNTS_TABLE_RAW3: P80_S2


title: Patient86_Sample5

description: COUNTS_TABLE_RAW13: P86_S5


title: 4T1 C269 2e

description: 4T1 C269

value: Sorted Tumoral cells

value: C269-treated (anti-eNAMPT)


title: mnp-20-0717

value: FFPE tissue

value: male

value: hypothalamus, third ventricle


title: Patient77_Sample1

description: COUNTS_TABLE_RAW2: P77_S1


title: Patient86_Sample3

description: COUNTS_TABLE_RAW13: P86_S3


title: mnp-20-0501

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: temporal lobe, hippocampus


title: mnp-20-1018

value: Diffuse midline glioma, H3 K27-mutated

value: female

value: brain stem


title: 4T1 C269 2a

description: 4T1 C269

value: Tumour


title: Patient86_Sample2

description: COUNTS_TABLE_RAW13: P86_S2

value: nasopharyngeal samples


title: CD4 CTRL 3b

description: CD4 CTRL

value: Isolated CD4+ T cells

value: wild-type


title: Patient77_Sample3

description: COUNTS_TABLE_RAW2: P77_S3


title: mnp-20-0094

value: Meningioma, WHO grade I

value: orbital frontal cortex


title: Patient74_Sample5

description: COUNTS_TABLE_RAW3: P74_S5


title: 4T1 C269 2d

description: 4T1 C269


title: Patient74_Sample6

description: COUNTS_TABLE_RAW3: P74_S6


title: Patient85_Sample5

description: COUNTS_TABLE_RAW10: P85_S5


title: 4T1 C269 2b

description: 4T1 C269


title: 4T1 CTRL 1c

description: 4T1 CTRL

value: CTRL


title: 4T1 CTRL 1e

description: 4T1 CTRL

value: Sorted Tumoral cells


title: Patient85_Sample4

description: COUNTS_TABLE_RAW10: P85_S4


title: Patient84_Sample7

description: COUNTS_TABLE_RAW13: P84_S7


title: Patient77_Sample2

description: COUNTS_TABLE_RAW2: P77_S2


title: mnp-20-0270

value: Medulloblastoma, non-WNT/SHH

value: cerebellum, fourth ventricle


title: Patient85_Sample2

description: COUNTS_TABLE_RAW10: P85_S2


title: Patient74_Sample4

description: COUNTS_TABLE_RAW3: P74_S4


title: Patient85_Sample3

description: COUNTS_TABLE_RAW10: P85_S3


title: Patient74_Sample3

description: COUNTS_TABLE_RAW3: P74_S3


title: 4T1 CTRL 1b

description: 4T1 CTRL


title: 4T1 C269 2c

description: 4T1 C269

value: C269-treated (anti-eNAMPT)


title: Patient74_Sample1

description: COUNTS_TABLE_RAW3: P74_S1


title: mnp-20-1404

value: FFPE tissue

value: Medulloblastoma, SHH

value: cerebellum


title: mnp-20-1245

value: Ganglioglioma

value: parietal lobe


title: Patient85_Sample1

description: COUNTS_TABLE_RAW10: P85_S1


title: Patient84_Sample6

description: COUNTS_TABLE_RAW13: P84_S6


title: mnp-20-1219

value: male

value: brain stem, cerebellum


title: mnp-20-0123

value: Medulloblastoma, WNT

value: female


title: Patient87_Sample1

description: COUNTS_TABLE_RAW12: P87_S1

value: nasopharyngeal samples


title: mnp-20-0115

value: Germ cell tumor


title: Patient84_Sample3

description: COUNTS_TABLE_RAW13: P84_S3


title: mnp-20-0386

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: occipital lobe


title: Patient74_Sample2

description: COUNTS_TABLE_RAW3: P74_S2


title: Patient84_Sample4

description: COUNTS_TABLE_RAW13: P84_S4


title: Patient73_Sample9

description: COUNTS_TABLE_RAW4: P73_S9


title: 4T1 CTRL 1a

description: 4T1 CTRL

value: Tumour

value: Sorted Tumoral cells

value: wild-type

value: CTRL


title: 4T1 CTRL 1d

description: 4T1 CTRL


title: Patient73_Sample10

description: COUNTS_TABLE_RAW4: P73_S10


title: Patient73_Sample6

description: COUNTS_TABLE_RAW4: P73_S6


title: mnp-20-1034

value: FFPE tissue

value: Atypical choroid plexus papilloma

value: third ventricle


title: Patient83_Sample14

description: COUNTS_TABLE_RAW10: P83_S14


title: Patient84_Sample2

description: COUNTS_TABLE_RAW13: P84_S2


title: Tumor draining lymph node, Tx + anti-CD4 treated, D3, bio rep 4 [LN3TxDep28]

first: Joseph

middle: R

last: Palmeri

state: MA

address: 500 Main St., Attn: 76-291: Joseph Palmeri

department: Chemical Engineering

institute: Massachusetts Institute of Technology

description: 75-nt kit

data_processing:
Data preprocessing and count matrix construction were performed using the Smart-seq2 Multi-Sample v2.2.0 Pipeline (RRID:SCR_018920) on Terra
.
Assembly: GENCODE mouse (M21) reference genome
Supplementary files format and content: Seurat object containing count matrices and sample metadata
Supplementary files format and content: Metadata spreadsheet containing sample information
Supplementary files format and content: Count matrix containing counts each sample
Supplementary files format and content: Gene metadata spreadsheet

source_name: Inguinal (tumor draining) lymph node

extract_protocol:
Total RNA was extracted using RNAeasy plus mini kit
RNA-sequencing was performed by the BioMicro Center at MIT using a modified version of the SCRB-seq protocol (https://www.biorxiv.org/content/10.1101/003236v1)

treatment_protocol: C57Bl/6 mice were inoculated with 1e6 B16F10 cells subcutaneously on their flank. Mice were then subseqently treated with either PBS, Tx, Tx + anti-CD4, or anti-CD4. Tx is defined as 200µg or TA99 given intraperitoneally on day 7 post tumor inoculation and 36.1 µg of anti-4-1BB-LAIR given intratumorally on day 8 post tumor inoculation. Anti-CD4 treatment (clone GK1.5) was given at a dose of 400 µg intraperitoneally on days 6, 9, and 12. Tumors and tumor draining lymph nodes were harvested on days 11 or day 14 (denoted as D3 and D6, defined relative to anti-4-1BB-LAIR treatment day). Samples were enriched for CD45+ cells using a magnetic bead postiive isolation step prior to RNA extratction.

tag: strain

value: Inguinal (tumor draining) lymph node

value: Primary CD45+ cells

value: CD45+ Immune cells

value: Tx (TA99 + anti-4-1BB-LAIR) + anti-CD4

tag: timepoint


title: Tumor draining lymph node, anti-CD4 treated, D3, bio rep 2 [LN3Dep30]

description: 75-nt kit

tag: treatment


title: Tumor draining lymph node, Tx + anti-CD4 treated, D3, bio rep 3 [LN3TxDep27]

description: 75-nt kit


title: mnp-20-0402

tag: "material"

value: Pilocytic Astrocytoma

value: cerebellum


title: Patient73_Sample5

description: COUNTS_TABLE_RAW4: P73_S5

value: nasopharyngeal samples


title: Patient73_Sample2

description: COUNTS_TABLE_RAW4: P73_S2


title: Patient84_Sample5

description: COUNTS_TABLE_RAW13: P84_S5


title: Tumor draining lymph node, anti-CD4 treated, D3, bio rep 4 [LN3Dep32]

description: 75-nt kit


title: mnp-20-1116

tag: "tumor type"

value: Medulloblastoma, non-WNT/SHH

value: male


title: Tumor draining lymph node, anti-CD4 treated, D3, bio rep 1 [LN3Dep29]

description: 75-nt kit


title: mnp-20-1318

tag: "patient age (years)"

value: hypothalamus


title: Patient73_Sample4

description: COUNTS_TABLE_RAW4: P73_S4

tag: tissue


title: mnp-20-1189

value: Germinoma

value: female


title: Patient73_Sample1

description: COUNTS_TABLE_RAW4: P73_S1

tag: subject


title: Tumor draining lymph node, Tx treated, D3, bio rep 4 [LN3Tx24]

description: 75-nt kit

value: Tx (TA99 + anti-4-1BB-LAIR)


title: Patient83_Sample9

description: COUNTS_TABLE_RAW10: P83_S9


title: mnp-20-0178

tag: "patient gender"

value: fourth ventricle


title: Patient73_Sample8

description: COUNTS_TABLE_RAW4: P73_S8


title: Patient73_Sample3

description: COUNTS_TABLE_RAW4: P73_S3


title: mnp-20-0794

value: FFPE tissue

value: Embryonal tumor with multilayered rosettes (ETMR)

tag: "tumor location"

value: parietal lobe, occipital lobe


title: Tumor draining lymph node, Tx + anti-CD4 treated, D3, bio rep 1 [LN3TxDep25]

description: 75-nt kit

value: Inguinal (tumor draining) lymph node

tag: cell type


title: Patient83_Sample6

description: COUNTS_TABLE_RAW13: P83_S6


title: Tumor draining lymph node, anti-CD4 treated, D3, bio rep 3 [LN3Dep31]

description: 75-nt kit

tag: cell line

value: Primary CD45+ cells


title: Tumor draining lymph node, Tx treated, D3, bio rep 3 [LN3Tx23]

description: 75-nt kit

value: CD45+ Immune cells


title: Patient83_Sample12

description: COUNTS_TABLE_RAW10: P83_S12

tag: geographic location


title: Patient84_Sample1

description: COUNTS_TABLE_RAW13: P84_S1

tag: collection date


title: Patient83_Sample4

description: COUNTS_TABLE_RAW13: P83_S4


title: Patient83_Sample13

description: COUNTS_TABLE_RAW10: P83_S13


title: Patient71_Sample6

description: COUNTS_TABLE_RAW4: P71_S6


title: Patient83_Sample3

description: COUNTS_TABLE_RAW13: P83_S3


title: Patient73_Sample7

description: COUNTS_TABLE_RAW4: P73_S7


title: Patient83_Sample10

description: COUNTS_TABLE_RAW10: P83_S10


title: Patient71_Sample5

description: COUNTS_TABLE_RAW4: P71_S5


title: Tumor draining lymph node, Tx + anti-CD4 treated, D3, bio rep 2 [LN3TxDep26]

description: 75-nt kit

value: Tx (TA99 + anti-4-1BB-LAIR) + anti-CD4


title: Patient83_Sample5

description: COUNTS_TABLE_RAW13: P83_S5


title: Patient83_Sample7

description: COUNTS_TABLE_RAW10: P83_S7


title: Tumor draining lymph node, Tx treated, D3, bio rep 2 [LN3Tx22]

description: 75-nt kit


title: Patient71_Sample10

description: COUNTS_TABLE_RAW4: P71_S10


title: Patient71_Sample4

description: COUNTS_TABLE_RAW4: P71_S4


title: mnp-20-0594

value: Pilocytic Astrocytoma

value: cerebellum, fourth ventricle


title: Patient83_Sample11

description: COUNTS_TABLE_RAW10: P83_S11

value: nasopharyngeal samples


title: mnp-20-1433

value: Ganglioglioma

value: temporal lobe


title: Tumor draining lymph node, Tx treated, D3, bio rep 1 [LN3Tx21]

description: 75-nt kit


title: Patient71_Sample8

description: COUNTS_TABLE_RAW4: P71_S8


title: Patient71_Sample11

description: COUNTS_TABLE_RAW4: P71_S11


title: Patient71_Sample9

description: COUNTS_TABLE_RAW4: P71_S9


title: mnp-20-0756

value: Descriptive diagnosis

value: male


title: Tumor draining lymph node, PBS treated, D3, bio rep 3 [LN3PBS19]

description: 75-nt kit

value: PBS


title: Patient83_Sample8

description: COUNTS_TABLE_RAW10: P83_S8


title: Tumor draining lymph node, PBS treated, D3, bio rep 2 [LN3PBS18]

description: 75-nt kit


title: Tumor draining lymph node, PBS treated, D3, bio rep 1 [LN3PBS17]

description: 75-nt kit


title: mnp-20-0887

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: female


title: Tumor draining lymph node, PBS treated, D3, bio rep 4 [LN3PBS20]

description: 75-nt kit


title: Patient71_Sample7

description: COUNTS_TABLE_RAW4: P71_S7


title: Tumor draining lymph node, anti-CD4 treated, D6, bio rep 2 [LN6Dep14]

description: 75-nt kit


title: Patient71_Sample2

description: COUNTS_TABLE_RAW4: P71_S2


title: mnp-20-0925

value: FFPE tissue

value: Pleomorphic xanthoastrocytoma (PXA)

value: parietal lobe


title: mnp-20-1446

value: Chordoma


title: Tumor draining lymph node, anti-CD4 treated, D6, bio rep 1 [LN6Dep13]

description: 75-nt kit

value: Inguinal (tumor draining) lymph node

value: Primary CD45+ cells


title: Patient83_Sample2

description: COUNTS_TABLE_RAW13: P83_S2


title: Patient71_Sample3

description: COUNTS_TABLE_RAW4: P71_S3


title: Tumor draining lymph node, Tx + anti-CD4 treated, D6, bio rep 4 [LN6TxDep12]

description: 75-nt kit

value: CD45+ Immune cells

value: Tx (TA99 + anti-4-1BB-LAIR) + anti-CD4


title: mnp-20-0761

value: Pilocytic Astrocytoma

value: cerebellum


title: Tumor draining lymph node, anti-CD4 treated, D6, bio rep 3 [LN6Dep15]

description: 75-nt kit


title: Patient80_Sample14

description: COUNTS_TABLE_RAW10: P80_S14

value: nasopharyngeal samples


title: Patient70_Sample9

description: COUNTS_TABLE_RAW4: P70_S9


title: Patient71_Sample1

description: COUNTS_TABLE_RAW4: P71_S1


title: Patient83_Sample1

description: COUNTS_TABLE_RAW10: P83_S1


title: Tumor draining lymph node, Tx + anti-CD4 treated, D6, bio rep 3 [LN6TxDep11]

description: 75-nt kit


title: Tumor draining lymph node, anti-CD4 treated, D6, bio rep 4 [LN6Dep16]

description: 75-nt kit


title: mnp-20-1567

value: Medulloblastoma, SHH

value: cerebellum, fourth ventricle, pons


title: mnp-20-0726

value: male


title: Tumor draining lymph node, Tx + anti-CD4 treated, D6, bio rep 2 [LN6TxDep10]

description: 75-nt kit


title: Patient80_Sample15

description: COUNTS_TABLE_RAW10: P80_S15


title: Patient80_Sample13

description: COUNTS_TABLE_RAW10: P80_S13


title: mnp-20-1599

value: Diffuse midline glioma, H3 K27-mutated

value: pons


title: mnp-20-0157


title: mnp-20-0941

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: female

value: frontal lobe


title: Patient70_Sample7

description: COUNTS_TABLE_RAW4: P70_S7


title: Patient80_Sample11

description: COUNTS_TABLE_RAW10: P80_S11


title: Tumor draining lymph node, Tx treated, D6, bio rep 4 [LN6Tx8]

description: 75-nt kit

value: Tx (TA99 + anti-4-1BB-LAIR)


title: Patient70_Sample4

description: COUNTS_TABLE_RAW4: P70_S4


title: Patient80_Sample10

description: COUNTS_TABLE_RAW10: P80_S10


title: Tumor draining lymph node, Tx + anti-CD4 treated, D6, bio rep 1 [LN6TxDep9]

description: 75-nt kit


title: Patient70_Sample5

description: COUNTS_TABLE_RAW4: P70_S5


title: mnp-20-1203

value: FFPE tissue

value: Atypical teratoid/rhabdoid tumor (AT/RT)

value: fourth ventricle


title: Tumor draining lymph node, Tx treated, D6, bio rep 3 [LN6Tx7]

description: 75-nt kit

value: Inguinal (tumor draining) lymph node

value: Primary CD45+ cells

value: CD45+ Immune cells


title: mnp-20-1505

value: Medulloblastoma, WNT


title: Tumor draining lymph node, Tx treated, D6, bio rep 2 [LN6Tx6]

description: 75-nt kit


title: Patient80_Sample12

description: COUNTS_TABLE_RAW10: P80_S12

value: nasopharyngeal samples


title: Tumor draining lymph node, Tx treated, D6, bio rep 1 [LN6Tx5]

description: 75-nt kit


title: Patient70_Sample2

description: COUNTS_TABLE_RAW4: P70_S2


title: Patient70_Sample6

description: COUNTS_TABLE_RAW4: P70_S6


title: Patient80_Sample8

description: COUNTS_TABLE_RAW10: P80_S8


title: Patient70_Sample3

description: COUNTS_TABLE_RAW4: P70_S3


title: mnp-20-0541

value: Pilocytic Astrocytoma

value: cerebellum, fourth ventricle


title: Patient80_Sample7

description: COUNTS_TABLE_RAW10: P80_S7


title: Patient70_Sample1

description: COUNTS_TABLE_RAW4: P70_S1


title: Tumor draining lymph node, PBS treated, D6, bio rep 4 [LN6PBS4]

description: 75-nt kit

value: PBS


title: Patient68_Sample10

description: COUNTS_TABLE_RAW4: P68_S10


title: mnp-20-0090

value: male

value: third ventricle


title: Patient68_Sample11

description: COUNTS_TABLE_RAW4: P68_S11


title: mnp-20-1115

value: cerebellum


title: Tumor draining lymph node, PBS treated, D6, bio rep 2 [LN6PBS2]

description: 75-nt kit


title: Patient80_Sample9

description: COUNTS_TABLE_RAW10: P80_S9


title: Tumor draining lymph node, PBS treated, D6, bio rep 3 [LN6PBS3]

description: 75-nt kit


title: Patient78_Sample6

description: COUNTS_TABLE_RAW12: P78_S6


title: mnp-20-0159

value: Diffuse midline glioma, H3 K27-mutated

value: thalamus, pineal region


title: mnp-20-1584


title: Patient78_Sample7

description: COUNTS_TABLE_RAW11: P78_S7


title: Tumor draining lymph node, PBS treated, D6, bio rep 1 [LN6PBS1]

description: 75-nt kit


title: Patient78_Sample4

description: COUNTS_TABLE_RAW11: P78_S4


title: Patient68_Sample7

description: COUNTS_TABLE_RAW4: P68_S7


title: Patient78_Sample8

description: COUNTS_TABLE_RAW12: P78_S8


title: Patient78_Sample3

description: COUNTS_TABLE_RAW12: P78_S3


title: B16F10 tumor, anti-CD4 treated, D3, bio rep 4 [T3Dep32]

description: 75-nt kit

source_name: B16F10 tumor

value: B16F10 tumor


title: Patient68_Sample6

description: COUNTS_TABLE_RAW4: P68_S6


title: mnp-20-1298

value: FFPE tissue

value: Medulloblastoma, non-WNT/SHH


title: B16F10 tumor, anti-CD4 treated, D3, bio rep 3 [T3Dep31]

description: 75-nt kit


title: Patient68_Sample9

description: COUNTS_TABLE_RAW4: P68_S9


title: Patient68_Sample8

description: COUNTS_TABLE_RAW4: P68_S8


title: B16F10 tumor, anti-CD4 treated, D3, bio rep 2 [T3Dep30]

description: 75-nt kit


title: Patient78_Sample9

description: COUNTS_TABLE_RAW12: P78_S9


title: Patient68_Sample5

description: COUNTS_TABLE_RAW4: P68_S5


title: mnp-20-0945


title: Patient78_Sample5

description: COUNTS_TABLE_RAW11: P78_S5


title: Patient78_Sample2

description: COUNTS_TABLE_RAW11: P78_S2


title: Patient68_Sample4

description: COUNTS_TABLE_RAW4: P68_S4


title: mnp-20-1264

value: Meningioma, WHO grade I


title: mnp-20-0027

value: female

value: orbital frontal cortex


title: B16F10 tumor, anti-CD4 treated, D3, bio rep 1 [T3Dep29]

description: 75-nt kit

value: Primary CD45+ cells

value: CD45+ Immune cells


title: Patient68_Sample3

description: COUNTS_TABLE_RAW4: P68_S3

value: nasopharyngeal samples


title: Patient78_Sample1

description: COUNTS_TABLE_RAW11: P78_S1


title: mnp-20-1158

value: Ependymoma, WHO grade II


title: Patient76_Sample11

description: COUNTS_TABLE_RAW10: P76_S11


title: mnp-20-1361

value: temporal lobe, occipital lobe


title: Patient76_Sample10

description: COUNTS_TABLE_RAW10: P76_S10


title: Patient68_Sample2

description: COUNTS_TABLE_RAW4: P68_S2


title: Patient76_Sample9

description: COUNTS_TABLE_RAW10: P76_S9


title: B16F10 tumor, Tx + anti-CD4 treated, D3, bio rep 3 [T3TxDep27]

description: 75-nt kit

value: Tx (TA99 + anti-4-1BB-LAIR) + anti-CD4


title: B16F10 tumor, Tx + anti-CD4 treated, D3, bio rep 4 [T3TxDep28]

description: 75-nt kit


title: B16F10 tumor, Tx + anti-CD4 treated, D3, bio rep 2 [T3TxDep26]

description: 75-nt kit


title: mnp-20-0374

value: male

value: fourth ventricle


title: mnp-20-0816

value: Medulloblastoma, NOS


title: Patient76_Sample7

description: COUNTS_TABLE_RAW13: P76_S7


title: Patient76_Sample8

description: COUNTS_TABLE_RAW13: P76_S8


title: B16F10 tumor, Tx + anti-CD4 treated, D3, bio rep 1 [T3TxDep25]

description: 75-nt kit


title: B16F10 tumor, Tx treated, D3, bio rep 4 [T3Tx24]

description: 75-nt kit

value: Tx (TA99 + anti-4-1BB-LAIR)


title: mnp-20-1379

value: Ganglioglioma

value: temporal lobe


title: B16F10 tumor, Tx treated, D3, bio rep 2 [T3Tx22]

description: 75-nt kit

value: B16F10 tumor


title: Patient76_Sample6

description: COUNTS_TABLE_RAW13: P76_S6


title: B16F10 tumor, Tx treated, D3, bio rep 3 [T3Tx23]

description: 75-nt kit


title: Patient76_Sample5

description: COUNTS_TABLE_RAW11: P76_S5


title: B16F10 tumor, Tx treated, D3, bio rep 1 [T3Tx21]

description: 75-nt kit


title: Patient67_Sample5

description: COUNTS_TABLE_RAW2: P67_S5


title: Patient76_Sample4

description: COUNTS_TABLE_RAW11: P76_S4


title: Patient67_Sample3

description: COUNTS_TABLE_RAW2: P67_S3


title: mnp-20-1575

value: FFPE tissue

value: Anaplastic astrocytoma

value: pons


title: Patient67_Sample4

description: COUNTS_TABLE_RAW2: P67_S4


title: mnp-20-0493

value: Anaplastic pilocytic astrocytoma

value: cerebellum


title: Patient67_Sample2

description: COUNTS_TABLE_RAW2: P67_S2


title: mnp-20-1484

value: Glioblastoma (GBM)

value: female

value: parietal lobe, occipital lobe


title: Patient67_Sample1

description: COUNTS_TABLE_RAW2: P67_S1

value: nasopharyngeal samples


title: B16F10 tumor, PBS treated, D3, bio rep 4 [T3PBS20]

description: 75-nt kit

value: Primary CD45+ cells

value: CD45+ Immune cells

value: PBS


title: B16F10 tumor, PBS treated, D3, bio rep 3 [T3PBS19]

description: 75-nt kit


title: Patient68_Sample1

description: COUNTS_TABLE_RAW4: P68_S1


title: Patient76_Sample3

description: COUNTS_TABLE_RAW12: P76_S3


title: Patient76_Sample2

description: COUNTS_TABLE_RAW12: P76_S2


title: mnp-20-0017

value: Neurofibroma


title: Patient66_Sample4

description: COUNTS_TABLE_RAW2: P66_S4


title: Patient66_Sample3

description: COUNTS_TABLE_RAW2: P66_S3


title: mnp-20-1083

value: Pilocytic Astrocytoma

value: medulla oblongata


title: Patient75_Sample3

description: COUNTS_TABLE_RAW9: P75_S3


title: B16F10 tumor, PBS treated, D3, bio rep 1 [T3PBS17]

description: 75-nt kit


title: B16F10 tumor, PBS treated, D3, bio rep 2 [T3PBS18]

description: 75-nt kit


title: Patient76_Sample1

description: COUNTS_TABLE_RAW11: P76_S1


title: Patient66_Sample2

description: COUNTS_TABLE_RAW2: P66_S2


title: Patient66_Sample1

description: COUNTS_TABLE_RAW2: P66_S1


title: Patient75_Sample2

description: COUNTS_TABLE_RAW9: P75_S2


title: Patient66_Sample5

description: COUNTS_TABLE_RAW2: P66_S5


title: Patient65_Sample6

description: COUNTS_TABLE_RAW2: P65_S6


title: B16F10 tumor, anti-CD4 treated, D6, bio rep 4 [T6Dep16]

description: 75-nt kit


title: Patient75_Sample1

description: COUNTS_TABLE_RAW9: P75_S1


title: B16F10 tumor, anti-CD4 treated, D6, bio rep 2 [T6Dep14]

description: 75-nt kit


title: B16F10 tumor, anti-CD4 treated, D6, bio rep 3 [T6Dep15]

description: 75-nt kit


title: Patient65_Sample7

description: COUNTS_TABLE_RAW2: P65_S7


title: B16F10 tumor, anti-CD4 treated, D6, bio rep 1 [T6Dep13]

description: 75-nt kit


title: mnp-20-0277

value: Adamantinomatous craniopharyngioma

value: male

value: pituitary gland


title: B16F10 tumor, Tx + anti-CD4 treated, D6, bio rep 4 [T6TxDep12]

description: 75-nt kit

value: B16F10 tumor

value: Tx (TA99 + anti-4-1BB-LAIR) + anti-CD4


title: mnp-20-0080

value: FFPE tissue

value: fourth ventricle


title: Patient73_Sample14

description: COUNTS_TABLE_RAW13: P73_S14


title: mnp-20-0574

value: Low-grade astrocytoma, NOS

value: thalamus, hypothalamus, basal ganglia


title: Patient65_Sample5

description: COUNTS_TABLE_RAW2: P65_S5


title: Patient73_Sample13

description: COUNTS_TABLE_RAW13: P73_S13


title: Patient65_Sample4

description: COUNTS_TABLE_RAW2: P65_S4


title: mnp-20-0053

value: female


title: B16F10 tumor, Tx + anti-CD4 treated, D6, bio rep 3 [T6TxDep11]

description: 75-nt kit


title: Patient73_Sample12

description: COUNTS_TABLE_RAW13: P73_S12

value: nasopharyngeal samples


title: mnp-20-1273

value: Embryonal rhabdomyosarcoma (ERMS)

value: pons


title: mnp-20-0131

value: Glioblastoma (GBM)

value: inferior temporal cortex


title: B16F10 tumor, Tx + anti-CD4 treated, D6, bio rep 2 [T6TxDep10]

description: 75-nt kit

value: Primary CD45+ cells

value: CD45+ Immune cells


title: Patient65_Sample3

description: COUNTS_TABLE_RAW2: P65_S3


title: Patient73_Sample15

description: COUNTS_TABLE_RAW13: P73_S15


title: B16F10 tumor, Tx + anti-CD4 treated, D6, bio rep 1 [T6TxDep9]

description: 75-nt kit


title: mnp-20-0237

value: Pilocytic Astrocytoma


title: Patient65_Sample2

description: COUNTS_TABLE_RAW2: P65_S2


title: Patient72_Sample6

description: COUNTS_TABLE_RAW9: P72_S6


title: mnp-20-1192

value: male

value: spinal cord


title: Patient65_Sample1

description: COUNTS_TABLE_RAW2: P65_S1


title: B16F10 tumor, Tx treated, D6, bio rep 4 [T6Tx8]

description: 75-nt kit

value: B16F10 tumor

value: Tx (TA99 + anti-4-1BB-LAIR)


title: mnp-20-1434

value: FFPE tissue

value: frontal lobe, temporal lobe


title: Patient62_Sample2

description: COUNTS_TABLE_RAW4: P62_S2


title: Patient72_Sample5

description: COUNTS_TABLE_RAW9: P72_S5


title: B16F10 tumor, Tx treated, D6, bio rep 2 [T6Tx6]

description: 75-nt kit


title: Patient62_Sample1

description: COUNTS_TABLE_RAW4: P62_S1


title: Patient72_Sample3

description: COUNTS_TABLE_RAW9: P72_S3


title: Patient72_Sample2

description: COUNTS_TABLE_RAW9: P72_S2


title: B16F10 tumor, Tx treated, D6, bio rep 1 [T6Tx5]

description: 75-nt kit


title: B16F10 tumor, Tx treated, D6, bio rep 3 [T6Tx7]

description: 75-nt kit


title: mnp-20-0802

value: parietal lobe


title: mnp-20-1200

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: orbital frontal cortex


title: B16F10 tumor, PBS treated, D6, bio rep 4 [T6PBS4]

description: 75-nt kit

value: PBS


title: Patient73_Sample11

description: COUNTS_TABLE_RAW13: P73_S11

value: nasopharyngeal samples


title: Patient61_Sample9

description: COUNTS_TABLE_RAW4: P61_S9


title: Patient61_Sample10

description: COUNTS_TABLE_RAW4: P61_S10


title: mnp-20-0553

value: Descriptive diagnosis

value: female

value: frontal lobe


title: B16F10 tumor, PBS treated, D6, bio rep 3 [T6PBS3]

description: 75-nt kit

value: Primary CD45+ cells


title: mnp-20-0978

value: thalamus


title: Patient72_Sample1

description: COUNTS_TABLE_RAW9: P72_S1


title: mnp-20-0478

value: Medulloblastoma, non-WNT/SHH

value: cerebellum, fourth ventricle


title: B16F10 tumor, PBS treated, D6, bio rep 2 [T6PBS2]

description: 75-nt kit

value: CD45+ Immune cells