title: 5-4_A2P036_ARV_CD8M

status: Public on May 10 2024

city: Bethesda

last: Brenchley

state: MD

address: 4 Center Drive

institute: NIAID

data_processing:
RNA-seq samples were sequenced as 101bp paired-end libraries on a Novaseq S4. All samples had over 109 million reads.
Reads were trimmed using Cutadapt (v1.18) and aligned to the Mmul_10/RheMac10 reference genome and Gencode (Ensembl release 108) using STAR (v2.7.6a) in 2-pass basic mode. Expression levels were quantified with RSEM (v1.3.3) before being converted into FPKM values.
Assembly: RheMac10
Supplementary files format and content: SIV.RawCountFile_rsemgenes.txt: tab-delimited raw counts for each sample
Supplementary files format and content: SIV.FPKM.all_samples.txt: tab-delimited FPKM values for each sample

organism: Macaca nemestrina

extract_protocol:
RNA was extracted from pelleted cells resuspended in Buffer RLT Plus (Qiagen) with 1% BME. RNA was extracted using RNeasy Micro kit (Qiagen).
SMART-Seq® v4 Ultra® Low Input RNA was used for mRNA library preparation.

value: peripheral blood

value: CD8 memory T cell

value: ARV


title: 5-2_A2P036_ARV_CD4M

type: SRA

first: Jason

country: USA

library_source: transcriptomic

molecule: polyA RNA

source_name: peripheral blood

tag: tissue

tag: cell type

value: CD4 memory T cell

tag: disease state


title: Osteoblast_trunk_biolRep3

status: Public on May 14 2024

city: Muenster

first: Kleio

last: Petratou-Busswinkel

address: Röntgenstraße 16

country: Germany

institute: Institute for Cardiovascular Organogenesis and Regeneration

description: GFP positive, mCherry negative cells

library_source: genomic

data_processing:
Details on all steps listed below can be found on github: https://github.com/KleioP/ATAC_RNAseq_analysis
QC of sequences, adapter trimming using fastp
Sequence alignment to genome using bowtie2, and samtools to sort and index aligned reads
removal of mitochondrial reads using bedtools intersect, and removing duplicate reads using sambamba
shifting all reads +4/-5 bps to account for transposome cutting during chromatin tagmentation using the alignmentSieve (deeptools)
significant peaks were called with macs2 using the parameters -g 1.412e9 --keep-dup all --nomodel --shift -100 --extsize 200
Assembly: danRer11
Supplementary files format and content: BED files. Columns 1-5: 1. Chromosome 2. Peak Start coordinate 3. Peak End coordinate 4. Peak name 5. Score

molecule: genomic DNA

organism: Danio rerio

source_name: trunk

extract_protocol:
ATAC-Seq was performed according to previously published protocols (Buenrostro et al., 2015), with the following modifications. Cells were incubated in lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween20, 0.1% NP40, 0.01% Digitonin) for 3min on ice. Lysis was stopped by resuspending in ice-cold wash buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween20) prior to centrifugation. The volume of enzyme added to the transposition reaction (1x Tagment DNA Buffer, 0.01% Digitonin, 0.1% Tween20, TDE1 enzyme) and the length of transposition were adjusted depending on the numbers of cells isolated in each sample. The Tagment DNA Buffer and TDE1 enzyme are both contained in the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina, 20034197). Following amplified DNA purification (Buenrostro et al., 2015), AMPure XP SPRI beads (Beckman Coulter, A63881) were used (1.4x sample volume) to remove primer dimers from the chromatin sample according to manufacturer's instructions
According to Illumina NextSeq System instructions (Standard Normalization Method, including Phix Control)

value: trunk

value: osteoblast (non-classical)

tag: genotype

tag: Stage

value: 15 days post fertilisation


title: 4-10_A2P036_SIV_CD4M

value: SIV


title: 4-12_A2P036_SIV_CD8M


title: 4-11_A2P036_SIV_CD8N

value: CD8 naiveT cell


title: 4-9_A2P036_SIV_CD4N

value: CD4 naiveT cell


title: 5-1_A2P036_ARV_CD4N


title: sh-R41, Male infected, 0 hour, replicate1

status: Public on May 15 2024

city: St Petersburg

first: Rui

last: Zhou

state: FL

address: REB 4130, 501 6th Ave S

institute: Johns Hopkins University

data_processing:
Adaptor sequences and low-quality reads (those with an average quality score < 20) were removed from the paired-end raw data using Trim-galore (version 0.4.4).
The resulting cleaned reads were aligned to the Drosophila melanogaster (dm6) reference genome using the STAR splice-aware aligner (version 2.6.0c) with default parameters.
Ambiguous reads mapping to multiple regions in the genome and reads with a MAPQ score less than 10 were discarded.
Subread featureCounts (version 2.0.1) was then utilized for gene quantification, employing the FlyBase r6.40 gene annotation.
Genes without read counts in all samples were excluded from subsequent analysis.
Assembly: dm6
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited text file include RPKM values for every gene and every sample

molecule: total RNA

organism: Drosophila melanogaster

source_name: whole fly

growth_protocol: Flies were maintained at room temperature with standard fly food (molasses formula).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
Total RNA samples were subjected to cDNA library construction using illumina kit.

treatment_protocol: Newly hatched male and female flies of appropriate genotypes were collected and kept in fresh food vials for 4-7 days prior to RNA extraction.

value: whole fly

tag: cell line

value: Male

value: w/Y; Actin-Gal4/+; UAS-sh-circ_ATP8B/+

tag: treatment

value: newly emerged flies that have been kept in molasses formulation food at room temperature for 4-7 days


title: 5-3_A2P036_ARV_CD8N


title: 4-4_A2P032_ARV_CD8M


title: 4-6_A2P036_Neg_CD4M

value: Neg


title: 4-5_A2P036_Neg_CD4N


title: 4-7_A2P036_Neg_CD8N


title: 4-3_A2P032_ARV_CD8N


title: 4-2_A2P032_ARV_CD4M


title: 3-12_A2P032_SIV_CD8M


title: 3-10_A2P032_SIV_CD4M


title: Osteoblast_trunk_biolRep1

description: GFP positive, mCherry negative cells. Due to loss of files, provided here is the BAM output file from read-shifting step (see protocol and github page)


title: 3-9_A2P032_SIV_CD4N


title: 4-1_A2P032_ARV_CD4N


title: 3-8_A2P032_Neg_CD8M


title: 3-6_A2P032_Neg_CD4M


title: 3-7_A2P032_Neg_CD8N


title: 3-5_A2P032_Neg_CD4N


title: 3-4_A0P031_SIV_CD8M


title: 3-3_A0P031_SIV_CD8N


title: 3-1_A0P031_SIV_CD4N


title: 3-2_A0P031_SIV_CD4M


title: 2-11_A0P031_ARV_CD8N


title: 2-7_A0P031_Neg_CD8N


title: 2-8_A0P031_Neg_CD8M


title: 4-8_A2P036_Neg_CD8M


title: 2-10_A0P031_ARV_CD4M


title: 2-6_A0P031_Neg_CD4M


title: 2-5_A0P031_Neg_CD4N


title: 2-4_A11263_Neg_CD8M


title: 3-11_A2P032_SIV_CD8N


title: 2-2_A11263_Neg_CD4M


title: 2-3_A11263_Neg_CD8N


title: 5_A11263_ARV_CD4N


title: 7_A11263_ARV_CD8N


title: 6_A11263_ARV_CD4M


title: 3_A11263_SIV_CD8N


title: 4_A11263_SIV_CD8M


title: 2_A11263_SIV_CD4M


title: 1_A11263_SIV_CD4N


title: 47_A2P036_ARV_CD8N ATAC

data_processing:
ATAC-seq samples were sequenced as 151bp paired-end libraries on a Novaseq S4. All samples had over ?? million reads.
Samples were trimmed for adapters using Cutadapt v 1.18 before alignment. The trimmed reads were aligned to the RheMac10 reference using Bowtie2 v2.3.4.1 with flag -k 10.
Assembly: RheMac10
Supplementary files format and content: The peaks were called using Genrich v0.6 with the following flags -j -y -r -v -d 150 -m 5 -e chrM,chrY.
Supplementary files format and content: Genrich-produced bedgraphs were normalized by library size (reads per million sequenced reads, RPM) for visualization.

extract_protocol:
Up to 10,000 sorted cells from each population were pelleted and resuspended in 2x Tagmentation Buffer (Illumina), 0.02% Digitonin, and 0.1% Tween-20, with Tagment DNA TDE1 Enzyme (Illumina) and incubating at 37°C for one hour.  The mix was then incubated with proteinase K for 30 minutes at 40°C.
High molecular weight DNA was removed with a 0.7x selection ratio of Agencourt AMPureXP beads (Beckman Coulter) and low molecular weight DNA was isolated from the remainder with a 1.2x selection ratio. Library amplification was performed with KAPA HiFi HotStart ReadyMix (KAPA) and i5 and i7 indexing primers (Nextera DNA CD Indexes) for 11-15 total cycles depending on the sample concentration reached after 5 cycles (KAPA Library Quantification kit). Library DNA was purified with a 1x selection ratio of AMPureXP beads. The final library was verified by High Sensitivity DNA Bioanalyzer (Agilent).


title: 46_A2P036_ARV_CD4M ATAC


title: 48_A2P036_ARV_CD8M ATAC


title: 2-12_A0P031_ARV_CD8M


title: 45_A2P036_ARV_CD4N ATAC


title: 43_A2P036_SIV_CD8N ATAC


title: 44_A2P036_SIV_CD8M ATAC


title: 42_A2P036_SIV_CD4M ATAC


title: 39_A2P036_Neg_CD8N ATAC


title: 10-11_RhDFRi_ARV_CD8N

organism: Macaca mulatta


title: 10-9_RhDFRi_ARV_CD4N


title: 10-6_RhDFRi_SIV_CD4M


title: 35_A2P032_ARV_CD8N ATAC


title: 33_A2P032_ARV_CD4N ATAC


title: 31_A2P032_SIV_CD8N ATAC


title: 30_A2P032_SIV_CD4M ATAC


title: 10-2_RhDF86_ARV_CD4M


title: 29_A2P032_SIV_CD4N ATAC


title: 10-1_RhDF86_ARV_CD4N


title: 28_A2P032_Neg_CD8M ATAC


title: 26_A2P032_Neg_CD4M ATAC


title: 8-14_RhDF86_SIV_CD4M


title: 25_A2P032_Neg_CD4N ATAC


title: 8-12_RhDF86_Neg_CD8M


title: 23_A0P031_SIV_CD8N ATAC


title: 22_A0P031_SIV_CD4M ATAC


title: 21_A0P031_SIV_CD4N ATAC


title: 10-10_RhDFRi_ARV_CD4M


title: 37_A2P036_Neg_CD4N ATAC


title: 2-9_A0P031_ARV_CD4N


title: 40_A2P036_Neg_CD8M ATAC


title: 36_A2P032_ARV_CD8M ATAC


title: 8_A11263_ARV_CD8M


title: 38_A2P036_Neg_CD4M ATAC


title: 10-8_RhDFRi_SIV_CD8M


title: 10-12_RhDFRi_ARV_CD8M


title: 20_A0P031_ARV_CD8M ATAC


title: 34_A2P032_ARV_CD4M ATAC


title: 10-7_RhDFRi_SIV_CD8N


title: 2-1_A11263_Neg_CD4N


title: 10-5_RhDFRi_SIV_CD4N


title: 8-8_Rh4345_ARV_CD8M


title: 32_A2P032_SIV_CD8M ATAC


title: 10-4_RhDF86_ARV_CD8M


title: 10-3_RhDF86_ARV_CD8N


title: 41_A2P036_SIV_CD4N ATAC


title: 27_A2P032_Neg_CD8N ATAC


title: 8-13_RhDF86_SIV_CD4N


title: 8-15_RhDF86_SIV_CD8N


title: 8-11_RhDF86_Neg_CD8N


title: 8-10_RhDF86_Neg_CD4M


title: 8-5_Rh4345_ARV_CD4N


title: 8-4_Rh4345_SIV_CD8M


title: 8-16_RhDF86_SIV_CD8M


title: 15_A0P031_Neg_CD8N ATAC


title: 8-3_Rh4345_SIV_CD8N


title: 24_A0P031_SIV_CD8M ATAC


title: 7-16_Rh4345_Neg_CD8M


title: 8-9_RhDF86_Neg_CD4N


title: 8-2_Rh4345_SIV_CD4M


title: 17_A0P031_ARV_CD4N ATAC


title: 11_A11263_Neg_CD8N ATAC


title: 19_A0P031_ARV_CD8N ATAC


title: 12_A11263_Neg_CD8M ATAC


title: 7-15_Rh4345_Neg_CD8N


title: 10_A11263_Neg_CD4M ATAC


title: 7-14_Rh4345_Neg_CD4M


title: 18_A0P031_ARV_CD4M ATAC


title: 16_A0P031_Neg_CD8M ATAC


title: 8-6_Rh4345_ARV_CD4M


title: 8-7_Rh4345_ARV_CD8N


title: 13_A0P031_Neg_CD4N ATAC


title: 9_A11263_Neg_CD4N ATAC


title: 7-12_RhDF8d _ARV_CD8M


title: 7-11_RhDF8d _ARV_CD8N


title: 8_A11263_ARV_CD8M ATAC


title: 7-13_Rh4345_Neg_CD4N


title: 7_A11263_ARV_CD8N ATAC


title: 14_A0P031_Neg_CD4M ATAC


title: 6_A11263_ARV_CD4M ATAC


title: 7-10_RhDF8d _ARV_CD4M


title: 8-1_Rh4345_SIV_CD4N


title: 7-8_RhDF8d _SIV_CD8M


title: 4_A11263_SIV_CD8M ATAC


title: 5_A11263_ARV_CD4N ATAC


title: 7-9_RhDF8d _ARV_CD4N


title: 7-7_RhDF8d _SIV_CD8N


title: 2_A11263_SIV_CD4M ATAC


title: 3_A11263_SIV_CD8N ATAC


title: 7-6_RhDF8d _SIV_CD4M


title: 7-4_RhDF8d _Neg_CD8M


title: 7-3_RhDF8d _Neg_CD8N


title: 7-1_RhDF8d _Neg_CD4N


title: 7-5_RhDF8d _SIV_CD4N


title: 1_A11263_SIV_CD4N ATAC


title: 6-11_RhDFTF_ARV_CD8N


title: 6-8_RhDFTF_SIV_CD8M


title: 6-9_RhDFTF_ARV_CD4N


title: 6-7_RhDFTF_SIV_CD8N


title: 6-6_RhDFTF_SIV_CD4M


title: 6-5_RhDFTF_SIV_CD4N


title: 6-4_RhDFTF_Neg_CD8M


title: 6-2_RhDFTF_Neg_CD4M


title: 6-1_RhDFTF_Neg_CD4N


title: 5-15_GE34_ARV_CD8N


title: 5-13_GE34_ARV_CD4N


title: 5-9_GE34_SIV_CD4N


title: 5-10_GE34_SIV_CD4M


title: 5-11_GE34_SIV_CD8N


title: 7-2_RhDF8d _Neg_CD4M


title: 5-14_GE34_ARV_CD4M


title: 5-7_GE34_Neg_CD8N


title: 5-16_GE34_ARV_CD8M


title: 5-6_GE34_Neg_CD4M


title: 6-12_RhDFTF_ARV_CD8M


title: 5-5_GE34_Neg_CD4N


title: 6-10_RhDFTF_ARV_CD4M


title: 136_RhDFRi_ARV_CD8M ATAC


title: 134_RhDFRi_ARV_CD4M ATAC


title: 133_RhDFRi_ARV_CD4N ATAC


title: 5-8_GE34_Neg_CD8M


title: 132_RhDFRi_SIV_CD8M ATAC


title: 130_RhDFRi_SIV_CD4M ATAC


title: 129_RhDFRi_SIV_CD4N ATAC


title: 6-3_RhDFTF_Neg_CD8N


title: 127_RhDF86_ARV_CD8N ATAC


title: 5-12_GE34_SIV_CD8M


title: 108_RhDF86_SIV_CD8M ATAC


title: 126_RhDF86_ARV_CD4M ATAC


title: 107_RhDF86_SIV_CD8N ATAC


title: 105_RhDF86_SIV_CD4N ATAC


title: 135_RhDFRi_ARV_CD8N ATAC


title: 102_RhDF86_Neg_CD4M ATAC


title: 103_RhDF86_Neg_CD8N ATAC


title: 101_RhDF86_Neg_CD4N ATAC


title: 131_RhDFRi_SIV_CD8N ATAC


title: 99_Rh4345_ARV_CD8N ATAC


title: 97_Rh4345_ARV_CD4N ATAC


title: 98_Rh4345_ARV_CD4M ATAC


title: 100_Rh4345_ARV_CD8M ATAC


title: 104_RhDF86_Neg_CD8M ATAC


title: 128_RhDF86_ARV_CD8M ATAC


title: 95_Rh4345_SIV_CD8N ATAC


title: 93_Rh4345_SIV_CD4N ATAC


title: 92_Rh4345_Neg_CD8M ATAC


title: 91_Rh4345_Neg_CD8N ATAC


title: 94_Rh4345_SIV_CD4M ATAC


title: 90_Rh4345_Neg_CD4M ATAC


title: 96_Rh4345_SIV_CD8M ATAC


title: 87_RhDF8d _ARV_CD8N ATAC

description: 87_RhDF8d _ARV_CD8N


title: 125_RhDF86_ARV_CD4N ATAC


title: 86_RhDF8d _ARV_CD4M ATAC

description: 86_RhDF8d _ARV_CD4M


title: 88_RhDF8d _ARV_CD8M ATAC

description: 88_RhDF8d _ARV_CD8M


title: 106_RhDF86_SIV_CD4M ATAC


title: 89_Rh4345_Neg_CD4N ATAC


title: 85_RhDF8d _ARV_CD4N ATAC

description: 85_RhDF8d _ARV_CD4N


title: 83_RhDF8d _SIV_CD8N ATAC

description: 83_RhDF8d _SIV_CD8N


title: 82_RhDF8d _SIV_CD4M ATAC

description: 82_RhDF8d _SIV_CD4M


title: 79_RhDF8d _Neg_CD8N ATAC

description: 79_RhDF8d _Neg_CD8N


title: 84_RhDF8d _SIV_CD8M ATAC

description: 84_RhDF8d _SIV_CD8M


title: 81_RhDF8d _SIV_CD4N ATAC

description: 81_RhDF8d _SIV_CD4N


title: 78_RhDF8d _Neg_CD4M ATAC

description: 78_RhDF8d _Neg_CD4M


title: 75_RhDFTF_ARV_CD8N ATAC


title: 71_RhDFTF_SIV_CD8N ATAC


title: 76_RhDFTF_ARV_CD8M ATAC


title: 73_RhDFTF_ARV_CD4N ATAC


title: 80_RhDF8d _Neg_CD8M ATAC

description: 80_RhDF8d _Neg_CD8M


title: 67_RhDFTF_Neg_CD8N ATAC


title: 68_RhDFTF_Neg_CD8M ATAC


title: 69_RhDFTF_SIV_CD4N ATAC


title: 74_RhDFTF_ARV_CD4M ATAC


title: 72_RhDFTF_SIV_CD8M ATAC


title: 70_RhDFTF_SIV_CD4M ATAC


title: 77_RhDF8d _Neg_CD4N ATAC

description: 77_RhDF8d _Neg_CD4N


title: 64_RhDFRi_Neg_CD8M ATAC


title: 62_RhDFRi_Neg_CD4M ATAC


title: 61_RhDFRi_Neg_CD4N ATAC


title: 59_GE34_ARV_CD8N ATAC


title: 63_RhDFRi_Neg_CD8N ATAC


title: 65_RhDFTF_Neg_CD4N ATAC


title: 57_GE34_ARV_CD4N ATAC


title: 56_GE34_SIV_CD8M ATAC


title: 60_GE34_ARV_CD8M ATAC


title: 58_GE34_ARV_CD4M ATAC


title: 55_GE34_SIV_CD8N ATAC


title: 54_GE34_SIV_CD4M ATAC


title: 52_GE34_Neg_CD8M ATAC


title: 51_GE34_Neg_CD8N ATAC


title: 50_GE34_Neg_CD4M ATAC


title: 66_RhDFTF_Neg_CD4M ATAC


title: 53_GE34_SIV_CD4N ATAC


title: 49_GE34_Neg_CD4N ATAC


title: ndufa5 46, ZT2, rep1

status: Public on May 03 2024

city: Padova

first: Tomas

last: Morosinotto

address: Via Ugo Bassi 58b

department: Department of Biology

country: Italy

institute: University of Padova

data_processing:
The reference genome (Physcomitrium patens v3.3) from the JGI Plant Gene Atlas (Lang et al., 2018) was indexed using Bowtie 2 (v2.2.5) (Langmead & Salzberg, 2012). Reads were then aligned using Bowtie 2 and bam files were generated with SAMtools (v 1.6) (Danecek et al., 2021). HTSeq-count (v 2.0.2) (Putri et al., 2022) was used to align the mapped reads to the genes provided in the annotation file (Ppatens_318_v3.3.gene.gff).
Assembly: Physcomitrium patens v3.3 from the JGI Plant Gene Atlas
Supplementary files format and content: csv files contain counts per each sample

organism: Physcomitrium patens

source_name: Protonema and young gametophores

growth_protocol: Protonema grown for one week on solid PpNH4 medium under continuous illumination was disrupted using a T 25 UltraTurrax (IKA) and used for the inoculation of a 100 mL Erlenmeyer flask with 20 mL of liquid PpNH4. After one week of growth under continuous illumination, the plant was harvested, disrupted and used for the inoculation of a 250 mL Erlenmeyer flask with 50 mL of liquid PpNO3. After one week of growth under continuous illumination, the plant was harvested, disrupted and used for the inoculation of a 500 mL Erlenmeyer flask with 100 mL of liquid PpNO3. After one week of growth, the plant material was distributed into a layer of miracloth arranged on top of a plastic cylinder, inside of a Magenta™ box filled with fresh liquid PpNO3. The plant was in contact with the medium through the filter, allowing growth under this “hydroponics” system. Plants in closed Magenta™ boxes were grown for 15 days under a short day regime (light:dark 12h:12h). The day of harvesting, plants were immediately snap frozen at the corresponding zeitgeber time (ZT0, ZT2, ZT6). For plants harvested at ZT0, Magenta™ boxes were enclosed in aluminium foil at the beginning of the night period (ZT12) and samples were snap frozen at ZT0 in a dark room illuminated with dim, green light. For plants harvested at ZT2 or ZT6, plants were snap frozen directly in the growth chamber, avoiding shading the plant until it had been frozen. Frozen samples were kept at -80 ºC until used.

extract_protocol:
Frozen samples were powdered using a cold mortar and pestle, in presence of liquid nitrogen. Approximately 150 mg of powder were used for RNA extraction using the RNeasy Plant Mini Kit, ref. 74904 (Qiagen).
RNA was used to build cDNA libraries using the kit QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen), which exploits oligo-d(T) primers therefore enriching the cDNA library in cDNA representative of mRNA, but not ribosomal RNA or other types of RNA. Libraries were then sequenced with a depth of 5 million of reads using a NextSeq 500 System (Illumina).

value: Protonema and young gametophores

tag: plant line

value: NDUFA5 KO

tag: zeitgeber time


title: WT, ZT6, rep7

value: WT


title: cox11 150, ZT0, rep2

value: COX11 KO


title: ndufa5 48, ZT0, rep2


title: ndufa5 46, ZT2, rep3


title: cox11 150, ZT0, rep1


title: cox11 152, ZT0, rep2


title: cox11 150, ZT0, rep3


title: WT, ZT0, rep5


title: WT, ZT0, rep3


title: ndufa5 46, ZT2, rep2


title: WT, ZT0, rep6


title: WT, ZT6, rep8


title: cox11 152, ZT0, rep1


title: cox11 150, ZT6, rep2


title: WT, ZT0, rep4


title: cox11 150, ZT2, rep3


title: ndufa5 46, ZT0, rep2


title: ndufa5 48, ZT6, rep2


title: ndufa5 48, ZT6, rep1


title: ndufa5 46, ZT6, rep2


title: WT, ZT6, rep6


title: WT, ZT0, rep2


title: ndufa5 48, ZT0, rep1


title: ndufa5 46, ZT6, rep3


title: cox11 152, ZT6, rep3


title: WT, ZT6, rep5


title: cox11 152, ZT6, rep2


title: cox11 152, ZT6, rep1


title: WT, ZT0, rep1


title: ndufa5 48, ZT2, rep2


title: WT, ZT6, rep4


title: HCC-patient6-nonresponder

status: Public on Apr 29 2024

city: Baltimore

first: Luciane

middle: Tsukamoto

last: Kagohara

address: 1650 Orleans St - Rm 485

department: Oncology

data_processing:
Sequencing alignment and demultiplexing with Space Ranger (10x Genomics).
Quality check and filtering with Seurat.
Normalization using SCTransform in Seurat.
Dimensional reduction using PCA in Seurat.
Gene expression analysis using Seurat.
Assembly: GRCh38
Supplementary files format and content:
data_SME_<ID>_identity.csv: clustering information
barcodes.tsv: spatial barcodes
features.tsv: genes
matrix.mtx: sequencing counts
Library strategy: Spatial transcriptomics

organism: Homo sapiens

source_name: hepatocellular carcinoma

extract_protocol:
There was no extraction protocol used.
Libraries were constructed using the Visium Spatial Gene Expression Reagent Kits (10x Genomics).

value: hepatocellular carcinoma

tag: phenotype

value: non-responder

value: cabozantinib+nivolumab


title: WT, ZT2, rep2


title: ndufa5 48, ZT2, rep1


title: cox11 150, ZT2, rep2


title: WT, ZT2, rep4


title: ndufa5 46, ZT6, rep1


title: cox11 152, ZT2, rep1


title: HCC-patient7-nonresponder


title: ndufa5 46, ZT0, rep1


title: cox11 150, ZT6, rep1


title: WT, ZT2, rep1


title: cox11 150, ZT2, rep1


title: HCC-patient3-responder

value: responder


title: WT, ZT6, rep1


title: EoKO_rep2 (ATAC-seq)

status: Public on Apr 24 2024

city: Freiburg im Breisgau

first: Sebastian

last: Arnold

address: Albertstraße 25

department: Institute of Experimental and Clinical Pharmacology and Toxicology

institute: University Freiburg

data_processing:
For RNA-seq ESCs: Low-quality bases and adapter-containing reads were trimmed using Galaxy platform Trim Galore (Galaxy Version 0.4.3.1) and reads were aligned to the mouse reference genome mm10 (mm10_UCSC_07_15, RNA STAR Galaxy Version 2.7.2b) with default parameters. Duplicates were removed with RmDup (Galaxy version 2.0.1) and genomic features were counted using htseq-count (Galaxy Version 0.9.1) with following settings: mode-union, stranded-no, minimum alignment quality-10 and feature type-exon. Differential expression analysis was carried out using DESeq2 (Galaxy Version 2.11.40.6+galaxy1) with subsequent filtering for adjusted p-value<0.05 and log2FC as indicated in the figure legends.
For RNA-seq embryos: Reads were mapped to and annotated by using the mouse reference genome GRCm38/mm10 (iGenomes, Illumina; archive-2015-07-17-32-40 and archive-2015-07-17-33-26 for GRCM38 and mm10, respectively) containing the chromosomes 1-19, X, Y and M using Rsubread v1.28.1 package in R v3.4.3 (Liao et al., 2013). Genomic features were counted using the Rsubread::featureCounts function (Liao et al., 2013). Differential expression analysis was carried out using DESeq2 v1.18.1 in R (Love et al., 2014), which applies Negative Binomial GLM fitting and Wald statistics on the count data, with subsequent filtering for adjusted p-value<0.05 and log2FC as indicated in the figure legends. Prior to fitting and statistical analysis, counts were normalized by library size (DESeq2::estimateSizeFactors) and gene-wise dispersion (DESeq2::estimateDispersions) to normalize the gene counts by gene-wise geometric mean over samples.
For ChIP-seq: Low-quality bases and adapter-containing reads were trimmed using Galaxy platform Trim Galore (Galaxy Version 0.4.3.1). Reads were mapped to the mm10 genome using Galaxy platform Bowtie2 v2.3.4.3+galaxy0) (Langmead and Salzberg, 2012) with default settings and the duplicates removed with RmDup (Galaxy version 2.0.1). Peaks were detected using MACS2 (v2.1.1.20160309.6, Zhang et al., 2008) with BAMPE format of the input file, default settings for building the shifting model (confidence enrichment ratio against background 5-50; band width 300) and minimum q-value cut-off for detection of 0.01. Peaks were called for each individual replicate and for both replicates together. Intersection (minimal overlap of at least 1 bp) of the called peaks using bedtools intersect intervals (Galaxy Version 2.29.2) were defined as high confidence peaks and used for further analysis. Differential binding of EoGFP and BraGFP was analysed by using the Galaxy DiffBind tool (v2.10.0) with default settings and a minimal FDR threshold of 0.01 and subsequent filtering for minimal fold change (FC) of 2.5 (Galaxy version 1.1.1)
For ATAC-seq: Low-quality bases and adapter-containing reads were trimmed using Galaxy platform Trim Galore (Galaxy Version 0.4.3.1). Reads were mapped to the mm10 genome using Galaxy platform Bowtie2 v2.3.4.3+galaxy0) (Langmead and Salzberg, 2012) with default settings and the duplicates removed with RmDup (Galaxy version 2.0.1). Differential accessibility analyses were performed using DiffBind tool (Galaxy Version 2.10.0) with default settings and FDR threshold of 0.01 and subsequent filtering for minimal fold change (FC) of 2.5 (Galaxy version 1.1.1).
Coverage: For the generation of Coverage files for RNA-seq, ATAC-seq and ChIP-seq analysis corresponding bam files from biological replicates were merged using Merge BAM files (Galaxy version 1.2.0), the Coverage files were created using bamCoverage tool (Galaxy version 3.3.2.0.0) bin size 10 bases and normalization to RPKM.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Coverage files in BigWig format for RNA-seq, ChIP-seq and ATAC-seq reads are normalized to RPKM. Bed files for EoGFP and BraGFP ChIP-seq unique and common peaks contain coordinates of the peaks. Bedfiles for Diffbind analysis ATAC BraKO versus EoKO contain coordinates of the peaks with FDR threshold 0.01. Processed ESC RNA-seq results showing differential gene expression between WT and BraKO in tab-delimited txt format. Processed embryo RNA-seq results show raw count tables per replicate in tab-delimited txt format.

organism: Mus musculus

source_name: embryoid bodies

growth_protocol: A2lox.Cre Mouse ESCs were grown in standard serum containing conditions (DMEM supplemented with 15% ESC-grade FBS, 2mM L-Glutamine, 50U/ml Penicillin/Streptomycin, 1xNEAA, 1mM sodium pyruvate, 100µM β-mercaptoethanol) with 1000 U/ml LIF, 3 mM CHIR99021 and 1 mM PD0325901 on amonolayer of mitotically inactivated STO feeder cells (SNL76/7). For embryoid body formation 1x10^5 feeder-depleted ESCs (WT and BraKO) were plated in 4 ml ESGRO Complete Basal medium in 60 mm non-adhesive dishes. Medium was changed on d2 and d5 using 4 ml ESGO Complete Basal medium supplemented with 30ng/ml human recombinant ActivinA (ActA, R&D systems).

extract_protocol: The protocol was modified from Kaestner Lab, 2020. In brief, EBs at day 5 of differentiation were trypsinised to single-cell suspension, washed with PBS and 50.000 cells were lysed in 50 µl ATAC-seq lysis buffer. Nuclei were mixed with 50 µl of transposition reaction mix containing Tagment DNA Enzyme 1 (Nextera DNA Library Preparation Kit, Illumina). The transposition reaction was carried out at 37°C and 600rpm for 30 min, purified using the Qiagen MinElute Kit and eluted in EB-buffer (Qiagen). DNA was amplified by PCR with an appropriate number of PCR cycles (5-8) using Custom Nextera PCR primer and the NEBNext High-Fidelity 2x PCR Master Mix (Nextera DNA Library Preparation Kit (New England BioLabs, E7530L) and purified with the Qiagen MinElute Kit (Qiagen, 28004). The libraries were size-selected using SPRI select beads (Beckman Coulter) to obtain fragments between <1000 bp of size. DNA concentration was measured with a Qubit Fluorometer (Thermo Fischer, Q32854) and fragment size determined with a Bioanalyzer (Agilent).

treatment_protocol: Embryoid bodies (EBs) were treated with 30ng/ml human recombinant Activin A from day 2 to 5.

value: embryoid bodies

value: EoKO


title: WT, ZT6, rep2


title: cox11 152, ZT2, rep2


title: HCC-patient2-responder


title: WT_rep1 (ATAC-seq)


title: HCC-patient4-responder


title: HCC-patient1-responder


title: EoKO_rep1 (ATAC-seq)


title: WT_rep2 (ATAC-seq)


title: WT,day1,rep3

status: Public on Apr 15 2024

city: philadelphia

first: Mustafa

last: Mir

state: PA

address: 3501 Civic Center Boulevard, CTRB 9030

institute: Children's Hospital of Philadelphia

data_processing:
To quantify transcript abundances from RNA-seq data we used the pseudoaligner Kallisto. Reads were aligned to the Drosophila melanogaster BDGP6.28 cDNA reference using a pre-built kallisto index (Bray et al., 2016). Data was normalized by eliminating transcripts with no reads in more than half of the samples from each condition and then using EdgeR to perform the ‘Trimmed Mean of M-values’ method to correct for compositional differences between libraries. Clear differences between the WT and ZF5 transcript abundances were observed via Principal Component Analysis (Fig S3). To determine differentially expressed genes, the ‘voom’ method from the ‘Limma’ package in R was applied to the log-transformed counts per million (CPM) data. After fitting linear models to the transformed gene expression data using the lmFit function, we applied the empirical Bayes (eBayes) method to the model fits. Subsequently, we extracted the top DEGs from the eBayes-fitted models. We adjusted for multiple testing to control the false discovery rate using the Benjamini-Hochberg (BH) method. Genes were classified as differentially expressed if they had logFC greater than 1.5 and an adj. p-value less than 0.05.
Assembly: DM6
Supplementary files format and content: .csv files have gene names and counts per million

extract_protocol:
Embryo was staged to proper NC13 to Nc14 before they were placed on 1.5mL microcentrifuge tube caps (3 embryos per sample). Embryos were macerated in 10ul TRIzol™ using sterile an 18 gauge needle. RNA was isolated using Chloroform and phasemaker tubes as described in Bogart, K. and Andrews, J.
RNA libraries were made using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® following manufacturer's recommended protocol.

value: sfGFP-ZLD


title: WT,day1,rep2


title: HCC-patient5-nonresponder


title: WT, ZT2, rep3


title: WT, ZT6, rep3


title: WT,day1,rep1


title: Zf5,day1,rep3

value: mNG-ZF5 GLC


title: Zf5,day2,rep6


title: Zf5,day1,rep1


title: WT,day2,rep2


title: Zf5,day2,rep4


title: Zf5,day2,rep5


title: Zf5,day1,rep2


title: Zf5,day2,rep2


title: Zf5,day2,rep1


title: WT,day2,rep5


title: WT,day2,rep3


title: WT,day2,rep1


title: PCL18-end stage-SITTH12

status: Public on Apr 04 2024

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

library_source: transcriptomic single cell

data_processing:
Quality control was peformed using fastQC ( v0.11.8) and multiQC (v 1.9)
Alignment, filtering and gene quantification was performed using 10x cellranger v5.0.0; the alignment was perfomed against the H Sapiens reference genome (GRCh38.p13)
Normalization of expression was levels was performed with SCTransform (Hafemeister and Satija, 2019)
Clustering was performed using SLM algorithm from the FindClusters function from Seurat (Satija, 2021)
Differential Expression was perfored using the Wilcoxon Rank Sum test  from FindMarkers function from Seurat (Satija, 2021)
Assembly: GRCh38.p13
Supplementary files format and content: Raw and norrmalised count matrices, in csv format.
Supplementary files format and content: Seurat object, rds format.

source_name: liver biopsy

extract_protocol:
Tissue lysis by dounce homogenisation and nuclei isolation by flow cytometry using scatter properties and DAPI staining to label nuclei.
Single-nuclei RNA-seq libraries were prepared using the following: Chromium Single Cell 3′ Library & Gel Bead Kit v3.1, Chromium Chip G Kit and Chromium Single Cell 3' Reagent Kits v3.1 User Guide (Manual Part CG000316 Rev A; 10X Genomics). For each sample 16k nuclei were loaded on the Chromium instrument with the expectation of collecting gel-beads emulsions containing nuclei cells. RNA from the barcoded nuclei for each sample was subsequently reverse-transcribed in a C1000 Touch Thermal cycler (Bio-Rad) and all subsequent steps to generate single-nuclei libraries were performed according to the manufacturer’s protocol with 19 PCR cycles in cDNA amplification step. cDNA quality and quantity was measured with Agilent TapeStation 4200 (High Sensitivity 5000 ScreenTape) after which 25% of material was used for gene expression library preparation. Library quality was confirmed with Agilent TapeStation 4200 (High Sensitivity D1000 ScreenTape to evaluate library sizes) and Qubit 4.0 Flourometer  (ThermoFisher Qubit™ dsDNA HS Assay Kit to evaluate dsDNA quantity). Each sample was normalized and pooled in equal molar concentration. To confirm concentration pool was qPCRed using KAPA Library Quantification Kit on QuantStudio 6 Flex before sequencing. Pool was sequenced on Illumina NovaSeq6000 sequencer with following parameters: 28 bp, read 1; 10 bp, i5 index; 10bp, i7 index; 90 bp, read 2

treatment_protocol: Biopsies were snap frozen in liquid nitrogen

value: liver

tag: disease status

value: end stage

tag: patient id

tag: liver lobe

value: Right

tag: gender

value: F

tag: saf score

tag: age


title: PCL17-end stage-SITTF11

value: M


title: Zf5,day2,rep3


title: P84-NAFLD-SITTG12

value: NAFLD


title: WT,day2,rep4


title: WT,day2,rep6


title: PHL1-Healthy control-SITTD1

value: Healthy control

value: Left

value: healthy control


title: P73-NASH w/o cirrhosis-SITTD3

value: NASH w/o cirrhosis


title: PHL1-Healthy control-SITTC1


title: PCL17-end stage-SITTG11

value: Caudate


title: P72-NASH w/o cirrhosis-SITTC3


title: P56-NAFLD-SITTB5


title: P55-NAFLD-SITTA5


title: PCL18-end stage-SITTA2


title: P3-NASH w/o cirrhosis-SIGAH3


title: P11-NASH w/o cirrhosis-SIGAH11


title: P57-NASH w/o cirrhosis-SIGAA4


title: PCL104-end stage-I-SITTF1


title: PCL104-end stage-I-SITTD1


title: PCL16-end stage-H-SITTB12


title: P98-Healthy control-G-SITTF7


title: PCL18-end stage-SITTC2


title: PHL2-Healthy control-E-SITTD9


title: P16-NASH w/o cirrhosis-E-SITTG5


title: PCL16-end stage-H-SITTC12


title: P19-NASH w/o cirrhosis-E-SITTB6


title: PCL103-end stage-E-SITTE9


title: PCL103-end stage-E-SITTF9


title: P7-NASH w/o cirrhosis-E-SITTB5


title: P9-NASH w/o cirrhosis-E-SITTD5


title: PCL103-end stage-F-SITTD3


title: P30-Healthy control-G-SITTB7


title: P8-NASH w/o cirrhosis-E-SITTC5


title: P20-NASH w/o cirrhosis-E-SITTC6


title: P21-NASH w/o cirrhosis-E-SITTD6


title: P50-NASH w/o cirrhosis-D-SITTB9


title: P49-NASH w/o cirrhosis-D-SITTA9


title: P75-NASH with cirrhosis-D-SITTE5

value: NASH with cirrhosis


title: P60-NAFLD-D-SITTG5


title: P68-NASH with cirrhosis-D-SITTD5


title: P51-NAFLD-D-SITTC9


title: P76-NASH w/o cirrhosis-D-SITTF5


title: P6-NAFLD-D-SITTA7


title: P64-NASH w/o cirrhosis-D-SITTA6


title: P54-NASH w/o cirrhosis-C-SITTF9


title: P71-NASH w/o cirrhosis-C-SITTG1


title: P53-NASH w/o cirrhosis-C-SITTE9


title: P67-NASH w/o cirrhosis-B-SITTF3


title: PCL16-end stage-H-SITTD12


title: P52-NASH w/o cirrhosis-C-SITTD9


title: P15-NASH w/o cirrhosis-E-SITTF5


title: PCL104-end stage-I-SITTE1


title: P22-NASH with cirrhosis-B-SITTE8


title: P83-NASH w/o cirrhosis-B-SITTF12


title: P62-NASH w/o cirrhosis-B-SITTD3


title: P12-NASH with cirrhosis-B-SITTD8


title: P48-NASH w/o cirrhosis-B-SITTA8


title: P70-NASH w/o cirrhosis-B-SITTA3


title: Heart, tt mice, RNA

status: Public on Mar 22 2024

city: Tucson

first: Sakthivel

last: Sadayappan

state: AZ

address: 1656 E Mabel Street, Medical Research Building, Rm 315, Cellular and Molecular Medicine

department: Cellular and Molecular Medicine

institute: University of Arizona College of Medicine

data_processing:
STAR aligner was used to align sample reads to Mus musculus genome build mm10.
HTSeq was used to generate counts.
Assembly: Genome_build: mm10
Supplementary files format and content: Supplementary_files_format_and_content: counts

source_name: 3 hearts combined

extract_protocol:
Isolated hearts from NTG and TG mice were homogenized in 1 mL of TriZol (Bio-Rad, Hercules, CA) using a bead homogenizer, and total RNA was extracted using the Aurum Total RNA Fatty and Fibrous Tissue Kit (Cat. No. 732-6820, Bio-Rad Laboratories, Hercules, CA), according to the manufacturer’s instructions.
mRNA in the total RNA was translated into a library of template molecules of known strand origin using the TruSeq® Stranded mRNA Library Prep kit (Cat. No. RS-122-2201, Illumina, Inc., San Diego, CA). Poly-T oligos attached to magnetic beads were used to isolate the mRNA, which was then fragmented and reverse transcribed. The resultant cDNA products were amplified, and cDNA libraries ready for sequencing were created using sequencing adapters and barcodes ligated onto the cDNA fragments for each respective sample.

value: 3 hearts combined

value: FvB/N

value: 12 weeks old


title: P78-NAFLD-B-SITTC8


title: P77-NASH w/o cirrhosis-B-SITTB8


title: Heart, 25bp variant MYBPC3 transgenic mice, RNA


title: Heart, Control mice, RNA


title: Heart, Nontransgenic mice, RNA,


title: Healthy mouse liver-4

status: Public on Mar 06 2024

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+120-base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Raw sequencing data for each sample were converted to matrices of expression using Space Ranger (version spaceranger-1.0.0, 10X Genomics).
Assembly: refdata-cellranger-mm10-3.0.0
Supplementary files format and content: filtered_barcodes.tsv.gz: list of spatial barcode. This file was in the "filtered_feature_bc_matrix" output folder of Space Ranger software.
Supplementary files format and content: filtered_features.tsv.gz: list of gene name and Ensembl ID. This file was in the "filtered_feature_bc_matrix" output folder of Space Ranger software.
Supplementary files format and content: filtered_matrix.mtx.gz: non-zero gene expresion count data in Matrix Market Exchange Formats. This file was in the "filtered_feature_bc_matrix" output folder of Space Ranger software.
Supplementary files format and content: raw_barcodes.tsv.gz: list of spatial barcode. This file was in the "raw_feature_bc_matrix" output folder of Space Ranger software.
Supplementary files format and content: raw_features.tsv.gz: list of gene name and Ensembl ID. This file was in the "raw_feature_bc_matrix" output folder of Space Ranger software.
Supplementary files format and content: raw_matrix.mtx.gz: non-zero gene expresion count data in Matrix Market Exchange Formats. This file was in the "raw_feature_bc_matrix" output folder of Space Ranger software.
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcode and the cordinate specifying spot
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: tissue_hires_image.png: image of tissue

source_name: liver

extract_protocol:
Mouse liver slide gene expression were detected by 10x Visium Spatial Gene Expression Slide & Reagents Kit.
RNA libraries were prepared for sequencing using 10x Visium spatial protocols and standard Illumina protocols.

value: Wild type


title: Healthy mouse liver-2


title: Healthy mouse liver-3


title: Healthy mouse liver-1


title: N1800110-KTP-00377_08

status: Public on Feb 26 2024

type: RNA

city: Santa Monica

first: Simone

last: Filosto

state: California

address: 2400 Broadway

institute: Kite Pharma

hyb_protocol: After hybridization, samples are transferred to an nCounter instrument which removes excess probes. Purified target-probe complexes are bound, immobilized and aligned on the imaging surface of the nCounter cartridge

scan_protocol: Sample cartridges are scanned by an automated fluorescence microscope. Barcodes are counted for each target molecule and the data are exported as a simple CSV file

data_processing: Raw data qualification and normalisation using internal Negative control, positive control and house keeping gene set.

label: Nanostring

source_name: DLBCL tumor

label_protocol: RNA hybridization with nCounter codeset chemistry (Capture probe & Reporter probe). The Reporter Probe carries the fluorescent barcode and the Capture Probe contains a biotin moiety that immobilizes the hybridized complex for data collection. Use of PanCancer IO360 Panel and Lymphoma Subtyping Panel

extract_protocol: RNA extracted from 5 sections/ 4µm thickness - FFPE blocks. Region of interest identifed by pathologist expert based on H&E images.

tag: visit

value: Screening

tag: treatment arm

value: Axicabtagene Ciloleucel

tag: baseline tumor burden (spd)

tag: cell of origin

value: GCB

value: Ongoing

value: Ongoing Response

value: DLBCL+Others

value: N


title: N1800110-KTP-00370_03

value: Others

value: Nonresponders

value: Y


title: N1800110-KTP-00368_01

value: Standard of Care Chemotherapy

value: Unclassified


title: N1800110-KTP-00373_02


title: N1800110-KTP-00375_06


title: N1800110-KTP-00366_04


title: N1800110-KTP-00364_11

value: Relapsed


title: N1800110-KTP-00363_09

value: Missing


title: N1800110-KTP-00352_08


title: N1800110-KTP-00362_06


title: N1800110-KTP-00360_05


title: N1800110-KTP-00353_09


title: N1800110-KTP-00355_03

value: HGBL


title: N1800110-KTP-00359_04


title: N1800110-KTP-00351_07


title: N1800110-KTP-00349_05


title: N1800110-KTP-00350_06


title: NB34_Bone

status: Public on Mar 03 2024

city: Boston

first: Shenglin

last: Mei

state: MA

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

data_processing:
FASTQ files were processed with the CellRanger software (10x Genomics, Inc., version 5.0.0). Human genome hg19 was used as the reference genome (10x Genomics, Inc.) to generate the matrix files containing cell barcodes and transcript counts. Quality control metrics were used to select cells with total UMI more than 700.
Assembly: GRCh38/hg38
Supplementary files format and content: count matrix in csv

source_name: bone marrow

extract_protocol:
10X Genomics Single cell 3' gene expression V2
Single cells from neuroblastoma bone metastatic and non-metastatic  samples subjected to RBC lysis were surface stained with anti-CD235-PE (Biolegend) for 30 min at 4°C. Cells were washed once with 2% FBS-PBS (v/v) followed by DAPI staining (1 ug/ml). Flow sorting for live and non-erythroid cells (DAPI-neg/CD235-neg) was performed on a BD FACS Aria III equipped with a 100um nozzle (BD Biosciences, San Jose, CA) instrument. All flow cytometry data were analyzed using FlowJo software (Treestar, San Carlos, CA).

value: neuroblastoma

value: yes

tag: metastatic

value: metastatic


title: N1800110-KTP-00346_04

value: Screening


title: N1800110-KTP-00345_03

value: GCB


title: N1800110-KTP-00342_12

value: Axicabtagene Ciloleucel


title: N1800110-KTP-00344_02


title: N1800110-KTP-00343_08

value: ABC


title: V5-DDX39A

status: Public on Mar 11 2024

type: protein

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

description: Array ID: 0000088678

hyb_protocol: The protein microrrays (ProtoArray v5.1, Invitrogen) were incubated for 1 h at 4 °C in Blocking Buffer I (PBS, 0.1 % Tween-20, 1 % BSA). The arrays were washed three times at 4 °C in Blocking Buffer II (TBS supplemented with 0.5 % Triton X-100, 1 mM β-mercaptoethanol, 5 % Glycerol, 2 mM MgCl2, 1 % BSA), placed at room temperature and incubated for 1 h with 600 µl of ~ 0.5 µM of immunopurified V5-DDX39A, V5-DDX56 or V5-GFP. The arrays were then washed twice in Blocking Buffer II at 4 °C and incubated with 1:1000 α-V5 tag monoclonal antibody (Thermo Fisher, R960-25) for 2 h at 4 °C. After three additional washes in Blocking Buffer II, the microarrays were incubated with anti-mouse secondary antibody Alexa Fluor 680 (Thermo Fisher) for 1 h at 4 °C and washed again three times. Finally, the arrays were rinsed 3 times in water and dried by spinning at 300 g for 5 min.

scan_protocol: The microarrays were scanned in an Odyssey scanner (LI-COR) using the following parameters: Channel 700, Grid = 8x3, 21.17, Intensity = 5, Offset = 0.

data_processing: ProtoArray signal data was determined with GenePix Pro v5.0.0.49 (Molecular Devices) and then processed following the manufacturer's recommendations using ProtoArray Prospector v5.2 (Invitrogen) with default settings.

label: Alexa Fluor 680

molecule: protein

source_name: V5-tagged DDX39A protein purified from HEK293T cells

label_protocol: Anti-mouse secondary antibody Alexa Fluor 680 (Thermo Fisher).

growth_protocol: HEK293T cells were grown in 15 cm2 dishes at 37°C with 5% CO2 in DMEM medium supplemented with 10% fetal calf serum, 2 mM L-Glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: Cells were lysed in 50 mM HEPES-KOH, pH 7.7, 1 mM MgCl2, 300 mM NaCl, 0.8 % Triton X-100, 5 mM NaF, 0.1 % Sodium deoxycholate, 2 mM β-mercaptoethanol, 1x protease inhibitor mixture tablet (Roche). Cleared lysates were immunoprecipitated using anti-V5 agarose beads (Roche) at 4 °C for 3 h. Beads were washed in TBS-T supplemented with 1 mM MgCl2, 2 mM β-mercaptoethanol and 1x protease inhibitor mixture tablet (Roche), followed by elution in the same buffer using 200 µg/ml V5 peptide.

treatment_protocol: HEK293T cells were transfected with 15 µg of the respective expression constructs using Calcium phosphate.

tag: recombinant protein expression


title: N1800110-KTP-00365_09


title: N1800110-KTP-00358_03

value: Ongoing

value: Ongoing Response

value: DLBCL+Others


title: N1800110-KTP-00341_11

value: N


title: N1800110-KTP-00339_09


title: N1800110-KTP-00338_09


title: N1800110-KTP-00335_07

value: Others


title: N1800110-KTP-00330_05

value: Standard of Care Chemotherapy

value: Nonresponders


title: N1800110-KTP-00327_04


title: N1800110-KTP-00323_02


title: N1800110-KTP-00326_03

value: Relapsed


title: N1800110-KTP-00322_06

value: Unclassified


title: N1800110-KTP-00337_02


title: N1800110-KTP-00321_07


title: N1800110-KTP-00320_12

value: Missing


title: N1800110-KTP-00334_08


title: N1800110-KTP-00319_11


title: N1800110-KTP-00318_10


title: N1800110-KTP-00311_04


title: N1800110-KTP-00314_06


title: N1800110-KTP-00317_09


title: N1800110-KTP-00313_05


title: N1800110-KTP-00309_10


title: N1800110-KTP-00310_03


title: N1800110-KTP-00308_02


title: N1800110-KTP-00307_01

value: HGBL


title: N1800110-KTP-00286_05


title: N1800110-KTP-00300_08


title: N1800110-KTP-00301_11


title: N1800110-KTP-00283_06


title: N1800110-KTP-00284_04


title: N1800110-KTP-00297_09


title: N1800110-KTP-00281_12


title: N1800110-KTP-00279_05


title: N1800110-KTP-00296_10


title: N1800110-KTP-00295_04


title: N1800110-KTP-00268_03


title: N1800110-KTP-00266_06


title: N1800110-KTP-00282_07


title: N1800110-KTP-00264_08


title: N1800110-KTP-00315_07

value: Y


title: N1800110-KTP-00265_09


title: N1800110-KTP-00263_12


title: N1800110-KTP-00304_12


title: N1800110-KTP-00278_11


title: N1800110-KTP-00257_12


title: N1800110-KTP-00251_09


title: N1800110-KTP-00253_11


title: N1800110-KTP-00254_04


title: N1800110-KTP-00249_12


title: N1800110-KTP-00260_01


title: N1800110-KTP-00256_01


title: N1800110-KTP-00247_11


title: N1800110-KTP-00248_07


title: N1800110-KTP-00255_10


title: N1800110-KTP-00245_05


title: N1800110-KTP-00243_04


title: N1800110-KTP-00262_05


title: N1800110-KTP-00244_05


title: N1800110-KTP-00240_01


title: N1800110-KTP-00239_12


title: N1800110-KTP-00261_01


title: N1800110-KTP-00242_03


title: N1800110-KTP-00252_10


title: N1800110-KTP-00238_11


title: N1800110-KTP-00237_10


title: N1800110-KTP-00235_08


title: N1800110-KTP-00233_01


title: N1800110-KTP-00232_06


title: N1800110-KTP-00234_07


title: N1800110-KTP-00228_04


title: N1800110-KTP-00227_03


title: N1800110-KTP-00231_05


title: N1800110-KTP-00241_02


title: N1800110-KTP-00225_01


title: N1800110-KTP-00223_11


title: N1800110-KTP-00222_10


title: N1800110-KTP-00214_03


title: N1800110-KTP-00213_02


title: N1800110-KTP-00208_09


title: N1800110-KTP-00207_08


title: N1800110-KTP-00209_10


title: N1800110-KTP-00211_12


title: N1800110-KTP-00212_01


title: N1800110-KTP-00205_06


title: N1800110-KTP-00206_07


title: N1800110-KTP-00203_04


title: N1800110-KTP-00204_05


title: N1800110-KTP-00202_03


title: N1800110-KTP-00201_02


title: N1800110-KTP-00216_05


title: N1800110-KTP-00226_02


title: N1800110-KTP-00197_10


title: N1800110-KTP-00199_12


title: N1800110-KTP-00195_08


title: N1800110-KTP-00194_07


title: N1800110-KTP-00210_11


title: N1800110-KTP-00220_08


title: N1800110-KTP-00196_09


title: N1800110-KTP-00189_02


title: N1800110-KTP-00192_05


title: N1800110-KTP-00191_04


title: N1800110-KTP-00185_10


title: N1800110-KTP-00181_06


title: N1800110-KTP-00198_11


title: N1800110-KTP-00187_12


title: N1800110-KTP-00193_06


title: N1800110-KTP-00179_04


title: N1800110-KTP-00180_05


title: N1800110-KTP-00176_01


title: N1800110-KTP-00178_03


title: N1800110-KTP-00174_11


title: N1800110-KTP-00173_10


title: N1800110-KTP-00171_08


title: N1800110-KTP-00170_07


title: N1800110-KTP-00168_05


title: N1800110-KTP-00167_04


title: N1800110-KTP-00162_12


title: N1800110-KTP-00161_11


title: N1800110-KTP-00160_10


title: N1800110-KTP-00169_06


title: N1800110-KTP-00166_03


title: N1800110-KTP-00188_01


title: N1800110-KTP-00175_12


title: N1800110-KTP-00158_08


title: N1800110-KTP-00155_05


title: N1800110-KTP-00156_06


title: N1800110-KTP-00164_01


title: N1800110-KTP-00177_02


title: N1800110-KTP-00151_01


title: N1800110-KTP-00154_04


title: N1800110-KTP-00153_03


title: N1800110-KTP-00152_02


title: N1800110-KTP-00157_07


title: N1800110-KTP-00148_10


title: N1800110-KTP-00146_08


title: N1800110-KTP-00150_12


title: N1800110-KTP-00144_06


title: N1800110-KTP-00137_01


title: N1800110-KTP-00138_02


title: N1800110-KTP-00143_05


title: N1800110-KTP-00140_04


title: N1800110-KTP-00130_01


title: N1800110-KTP-00124_07


title: N1800110-KTP-00125_08


title: N1800110-KTP-00127_10


title: N1800110-KTP-00128_11


title: N1800110-KTP-00139_03


title: N1800110-KTP-00123_06


title: N1800110-KTP-00134_05


title: N1800110-KTP-00149_11


title: N1800110-KTP-00129_12


title: N1800110-KTP-00122_05


title: N1800110-KTP-00121_04


title: N1800110-KTP-00120_03


title: N1800110-KTP-00131_02


title: N1800110-KTP-00115_06


title: N1800110-KTP-00112_10


title: N1800110-KTP-00117_08


title: N1800110-KTP-00118_01


title: N1800110-KTP-00113_11


title: N1800110-KTP-00109_07


title: N1800110-KTP-00108_06


title: N1800110-KTP-00106_04


title: N1800110-KTP-00100_12


title: N1800110-KTP-00097_09


title: N1800110-KTP-00098_10


title: N1800110-KTP-00095_11


title: N1800110-KTP-00093_09


title: N1800110-KTP-00096_12


title: N1800110-KTP-00090_06


title: N1800110-KTP-00089_05


title: N1800110-KTP-00087_04


title: N1800110-KTP-00091_07


title: N1800110-KTP-00081_11


title: N1800110-KTP-00078_08


title: N1800110-KTP-00077_07


title: N1800110-KTP-00080_10


title: N1800110-KTP-00084_01


title: N1800110-KTP-00073_03


title: N1800110-KTP-00075_05


title: N1800110-KTP-00085_02


title: N1800110-KTP-00076_06


title: N1800110-KTP-00082_12


title: N1800110-KTP-00099_11


title: N1800110-KTP-00074_04


title: N1800110-KTP-00086_03


title: N1800110-KTP-00070_12


title: N1800110-KTP-00071_01


title: N1800110-KTP-00072_02


title: N1800110-KTP-00061_03


title: N1800110-KTP-00060_02


title: N1800110-KTP-00067_09


title: N1800110-KTP-00068_10


title: N1800110-KTP-00066_08


title: N1800110-KTP-00069_11


title: N1800110-KTP-00065_07


title: N1800110-KTP-00056_10


title: N1800110-KTP-00053_08


title: N1800110-KTP-00052_07


title: N1800110-KTP-00049_04


title: N1800110-KTP-00051_06


title: N1800110-KTP-00050_05


title: N1800110-KTP-00047_02


title: N1800110-KTP-00048_03


title: N1800110-KTP-00046_01


title: N1800110-KTP-00029_05


title: N1800110-KTP-00027_03


title: N1800110-KTP-00059_01


title: N1800110-KTP-00025_01


title: N1800110-KTP-00028_04


title: N1800110-KTP-00026_02


title: N1800110-KTP-00058_12


title: N1800110-KTP-00024_12


title: N1800110-KTP-00022_10


title: N1800110-KTP-00023_11


title: N1800110-KTP-00021_09


title: N1800110-KTP-00016_04


title: N1800110-KTP-00017_05


title: N1800110-KTP-00018_06


title: N1800110-KTP-00020_08


title: N1800110-KTP-00019_07


title: N1800110-KTP-00013_01


title: N1800110-KTP-00015_03


title: N1800110-KTP-00030_06


title: N1800110-KTP-00012_12


title: N1800110-KTP-00006_06


title: N1800110-KTP-00010_10


title: N1800110-KTP-00008_08


title: N1800110-KTP-00014_02


title: N1800110-KTP-00004_04


title: N1800110-KTP-00007_07


title: Mx1-Cre OSM 6

status: Public on Feb 18 2024

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description:
CNT_LTHSC_5_OSM_GT22
WT_CNT_OSM_22_5_cpm
150bp paired-end
re-analysis of GSM7569887
21NGS_002_and_22SEQ_002_merge_WT.CNT.OSM_vs_WT.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.OSM_vs_WT.CNT.OSM.txt

data_processing:
For 2021 the samples were run twice and the fastq's were concatenated
FASTQ files were adapter trimmed, and had leading and trailing low quality (below 3) or N bases and reads below 36 bases removed using Trimmomatic v0.35.
Trimmed FASTQ files were used to generate read counts using RSEMv1.3.3.
Expected read counts per gene produced by RSEM were rounded to integer values, filtered to include only genes that had at least two samples within a sample group having a counts per million reads >1, and passed to R (v4.1.3)and edgeR (v3.36.0) for differential expression analysis.A negative binomial generalized log-linear model was fit to the read counts for each gene.The dispersion trend was estimated by Cox-Reid approximate profile likelihood followed by empirical Bayes estimate of the negative binomial dispersion parameter for each tag, with expression levels specified by a log-linear model.
Likelihood ratio tests for coefficient contrasts in the linear model were evaluated producing a p-value per contrast. The Benjamini and Hochberg's algorithm (P value adjustment) was used to control the false discovery rate (FDR). Features with FDR-adjusted P < 0.05 were declared significantly differentially expressed.
mm10
Assembly: tab-delimited text file

source_name: Bone Marrow

growth_protocol: whole bone marrow was collect from adult mice and sorted for HSCs based on cell surface markers (Lin- Sca-1+ c-Kit+ Flt3- CD150+ CD48-) 2000 per sample

extract_protocol:
Total RNA was isolated from cells using the RNeasy Micro kit (Qiagen), according to manufacturers’ protocols, including the optional DNase digest step. RNA concentration and quality were assessed using the RNA 6000 Pico Assay (Agilent Technologies).
Libraries were constructed using the SMARTer Stranded Total RNA-Seq Kit v2-Pico (Takara), according to the manufacturer’s protocol.  Briefly, the protocol entails RNA fragmentation and cDNA synthesis, addition of Illumina-specific adapters containing a unique barcode sequence for each library, cleavage of ribosomal cDNA with Takara’s ZapR v2 and R-Probes v2, and PCR amplification of uncleaved fragments.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.
2021:Libraries were sequenced 75 bp paired-end on an Illumina NextSeq 500 using the High Output Reagent Kit v2.5. 2022: Libraries were sequenced 150 bp paired-end on an Illumina NovaSeq 6000 using the S4 Reagent Kit v1.5.

treatment_protocol: HSCs were stimulated for 1hour with PBS (vehicle) or OSM (500ng/ml) following stimulation cells were flash frozen in liquid nitrogen

tag: tissue

value: Bone Marrow

tag: cell number

value: 2000 cells

tag: cell type

value: HSCs

tag: genotype

value: OSM


title: N1800110-KTP-00001_01

value: Screening

value: Axicabtagene Ciloleucel

value: GCB


title: Mx1-Cre OSM 5

description:
CNT_LTHSC_3_OSM_GT22
WT_CNT_OSM_22_3_cpm
150bp paired-end
re-analysis of GSM7569886
21NGS_002_and_22SEQ_002_merge_WT.CNT.OSM_vs_WT.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.OSM_vs_WT.CNT.OSM.txt

tag: treatment


title: Mx1-Cre OSM 4

description:
CNT_LTHSC_1_OSM_GT22
WT_CNT_OSM_22_1_cpm
150bp paired-end
re-analysis of GSM7569884
21NGS_002_and_22SEQ_002_merge_WT.CNT.OSM_vs_WT.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.OSM_vs_WT.CNT.OSM.txt


title: Mx1-Cre Veh 4

description:
CNT_LTHSC_1_vehicle_GT22
WT_CNT_v_22_1_cpm
150bp paired-end
re-analysis of GSM7569877
21NGS_002_and_22SEQ_002_merge_WT.CNT.OSM_vs_WT.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.v_vs_WT.CNT.v.txt

value: Vehicle


title: Osmrfl/fl Mx1-Cre OSM 3

description:
OSMR_CNT_LTHSC_5_OSM_GT22
OSMR_CNT_OSM_22_5_cpm
150bp paired-end
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.OSM_vs_OSMR.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.OSM_vs_WT.CNT.OSM.txt

value: Osmrfl/fl Mx1-Cre


title: Mx1-Cre Veh 5

description:
CNT_LTHSC_3_vehicle_GT22
WT_CNT_v_22_3_cpm
150bp paired-end
re-analysis of GSM7569878
21NGS_002_and_22SEQ_002_merge_WT.CNT.OSM_vs_WT.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.v_vs_WT.CNT.v.txt


title: N1800110-KTP-00002_02

value: Others

value: DLBCL+Others

value: N


title: Osmrfl/fl Mx1-Cre OSM 2

description:
OSMR_CNT_LTHSC_3_OSM_GT22
OSMR_CNT_OSM_22_3_cpm
150bp paired-end
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.OSM_vs_OSMR.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.OSM_vs_WT.CNT.OSM.txt


title: N1800110-KTP-00003_03

value: Relapsed


title: Mx1-Cre Veh 6

description:
CNT_LTHSC_5_vehicle_GT22
WT_CNT_v_22_5_cpm
150bp paired-end
re-analysis of GSM7569880
21NGS_002_and_22SEQ_002_merge_WT.CNT.OSM_vs_WT.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.v_vs_WT.CNT.v.txt


title: Osmrfl/fl Mx1-Cre OSM 1

description:
OSMR_CNT_LTHSC_1_OSM_GT22
OSMR_CNT_OSM_22_1_cpm
150bp paired-end
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.OSM_vs_OSMR.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.OSM_vs_WT.CNT.OSM.txt


title: Osmrfl/fl Mx1-Cre Veh 1

description:
OSMR_CNT_LTHSC_1_vehicle_GT22
OSMR_CNT_v_22_1_cpm
150bp paired-end
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.OSM_vs_OSMR.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.v_vs_WT.CNT.v.txt


title: Osmrfl/fl Mx1-Cre Veh 2

description:
OSMR_CNT_LTHSC_3_vehicle_GT22
OSMR_CNT_v_22_3_cpm
150bp paired-end
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.OSM_vs_OSMR.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.v_vs_WT.CNT.v.txt


title: Mx1-Cre Veh 2

description:
CNT_LTHSC_3_vehicle_GT21
WT_CNT_v_21_3_cpm
76bp-paired end
re-analysis of GSM7569875
21NGS_002_and_22SEQ_002_merge_WT.CNT.OSM_vs_WT.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.v_vs_WT.CNT.v.txt


title: Osmrfl/fl Mx1-Cre Veh 3

description:
OSMR_CNT_LTHSC_5_vehicle_GT22
OSMR_CNT_v_22_5_cpm
150bp paired-end
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.OSM_vs_OSMR.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.v_vs_WT.CNT.v.txt


title: Mx1-Cre OSM 2

description:
CNT_LTHSC_3_OSM_GT21
WT_CNT_OSM_21_3_cpm
76bp-paired end
re-analysis of GSM7569882
21NGS_002_and_22SEQ_002_merge_WT.CNT.OSM_vs_WT.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.OSM_vs_WT.CNT.OSM.txt


title: Mx1-Cre OSM 1

description:
CNT_LTHSC_1_OSM_GT21
WT_CNT_OSM_21_1_cpm
76bp-paired end
re-analysis of GSM7569881
21NGS_002_and_22SEQ_002_merge_WT.CNT.OSM_vs_WT.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.OSM_vs_WT.CNT.OSM.txt


title: Mx1-Cre OSM 3

description:
CNT_LTHSC_5_OSM_GT21
WT_CNT_OSM_21_5_cpm
76bp-paired end
re-analysis of GSM7569883
21NGS_002_and_22SEQ_002_merge_WT.CNT.OSM_vs_WT.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.OSM_vs_WT.CNT.OSM.txt


title: Mx1-Cre Veh 1

description:
CNT_LTHSC_1_vehicle_GT21
WT_CNT_v_21_1_cpm
76bp-paired end
re-analysis of GSM7569874
21NGS_002_and_22SEQ_002_merge_WT.CNT.OSM_vs_WT.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.v_vs_WT.CNT.v.txt


title: HSPCs, barcode-derived cDNA, 7

status: Public on Feb 09 2024

city: San Francisco

first: Catherine

last: Smith

address: 513 Parnassus Avenue

department: Medicine

institute: University of California, San Francisco

description:
Mission Bio Tapestri
Experiment 7

data_processing:
*library strategy: Dabseq
FASTQ files from single-cell DAbseq samples were processed via an open-source pipeline. This analysis pipeline trims adaptor sequences, demultiplexes DNA panel amplicons and antibody tags into single cells, and aligns panel reads to the hg19 reference genome. Valid cell barcodes were called using the inflection point of the cell-rank plot in addition to the requirement that 60% of DNA intervals were covered by at least eight reads. Variants were called using GATK (v 4.1.3.0) according to GATK best practices. ITDseek was used to detect FLT3 internal tandem duplication (ITD) from amplicon sequencing reads. For each valid cell barcode, variants were filtered according to quality and sequence depth reported by GATK, with low quality variants and cells excluded based on the cutoffs of quality score < 30, read depth < 10, and alternate allele frequency < 20%. Cell-surface protein reads were normalized using centered log ratio transformation.
To de-multiplex individual patients combined into a single sample, we used a novel computational approach incorporating both patient-specific anti-CD45 oligo-conjugated “hash” antibody tags as well as single nucleotide polymorphisms (SNPs) covered by the SC DNA panel. Individual samples were multiplexed together into groups of 3 and all SNPs were treated as binary (mutated or wildtype). For each multiplexed run, to identify SNPs that maximally differ between samples we filtered all SNPs mutated in <10% or >80% of cells. We performed a series of hierarchical clustering steps to further refine antibody hash data.
Assembly: hg19
Supplementary files format and content: hdf5 files
Supplementary files format and content: h5ad files

source_name: Bone Marrow/Peripheral Blood

extract_protocol:
We performed DAbseq on unsorted mononuclear cells using a microfluidic approach with molecular barcode technology using the Tapestri platform (MissionBio) as previously described .
Briefly, cryopreserved cells were blocked and stained with unique anti-CD45 oligo-conjugated antibodies to provide sample-level identifiers, and groups of 2-3 individual patients were pooled together for multiplexed runs. Pooled samples were run through Mission Bio Tapestri platform as previously described. DNA from barcoded cells was amplified via PCR using a targeted panel that included 288 amplicons associated with acute leukemia. DNA PCR products were isolated and purified with standard library preparation protocol. Protein PCR products were isolated from the supernatant from AmpureXP bead purification via incubation with a 5’ Biotin Oligo (ITD), and purified using Streptavidin C1 beads.

value: Bone Marrow/Peripheral Blood

tag: subject status

value: adult patients with acute myeloid leukemia

tag: subject id

value: Patient A, B, C, D


title: HSPCs, barcode-derived cDNA, 6

description:
Mission Bio Tapestri
Experiment 6

value: Patient B, C, D


title: HSPCs, barcode-derived cDNA, 3

description:
Mission Bio Tapestri
Experiment 3

value: Patient C


title: HSPCs, barcode-derived cDNA, 4

description:
Mission Bio Tapestri
Experiment 4

value: Patient D


title: HSPCs, barcode-derived cDNA, 5

description:
Mission Bio Tapestri
Experiment 5

value: Patient A, B


title: HSPCs, barcode-derived cDNA, 2

description:
Mission Bio Tapestri
Experiment 2

value: Patient B


title: HSPCs, barcode-derived cDNA, 1

description:
Mission Bio Tapestri
Experiment 1

value: Patient A


title: KO-UUO2-cr

status: Public on Feb 08 2024

city: chengdu

first: Ting

last: Xiang

address: chengdu

country: China

institute: West China Hospital of Medicine: Sichuan Universit

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Clean reads were mapped to the reference genome using Bowtie2 software. And reads from organelle, mapping quality smaller then 30, PCR duplicated reads all removed. Those high quality mapping reads were subjected to further peak calling.
Macs2 software was used to call peaks with qvalue < 0.05.
Peaks were annotated by ChIPseeker package.
Assembly: mm10
Supplementary files format and content: bigWig,narrowPeak(except for Input sample)

source_name: kidney

extract_protocol:
Briefly, tissues were harvested and crosslinker with 1% formaldehyde for 10 min at room temperature. After sonication, immunoprecipitation was performed with anti-H3K9ac and H3K9cr. The immunoprecipitated complex was washed, and DNA was extracted and purified by Universal DNA Purification Kit (TIANGEN, #DP214).
The ChIP-Seq library was prepared using original Ultra II DNA Library Kits (NEB, #E7645) according to the manufacturer's instructions. For ChIP-seq, extracted DNA was ligated to specific adaptors followed by deep sequencing in the Illumina Novaseq 6000 using 150bp paired-end.

value: kidney

tag: chip antibody

value: UUO+ACSS2 knockout


title: KO-UUO2-ac

value: H3K9ac(Motif Active,39020)


title: KO-UUO1-cr


title: WT-UUO2-ac

value: H3K9ac(Motif Active,39019)

value: UUO


title: WT-UUO1-cr


title: KO-C2-ac

value: H3K9ac(Motif Active,39018)

value: ACSS2 knockout


title: KO-C1-cr


title: KO-UUO1-ac


title: WT-UUO2-cr


title: WT-UUO1-ac


title: KO-C2-cr


title: KO-C1-ac


title: WT-C2-cr

value: WT


title: WT-C1-ac

value: H3K9ac(Motif Active,39017)


title: Mx1-Cre Veh 3

description:
CNT_LTHSC_5_vehicle_GT21
WT_CNT_v_21_5_cpm
76bp-paired end
re-analysis of GSM7569876
21NGS_002_and_22SEQ_002_merge_WT.CNT.OSM_vs_WT.CNT.v.txt
21NGS_002_and_22SEQ_002_merge_OSMR.CNT.v_vs_WT.CNT.v.txt

value: Bone Marrow

value: 2000 cells

value: HSCs

value: Vehicle


title: WT-C2-ac


title: BM32 CD34+CD271+ (HTO)

status: Public on Jan 26 2024

city: Cincinnati

first: Xuan

last: Zhang

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's hospital

description:
CD271_4_antibody_features.csv
single indexed HTO
CD271-4_filtered_feature_bc_matrix.h5

library_source: other

data_processing:
CellRanger version 6.1.2 was applied to the combined scRNA-Seq, HTO and ADT FASTQ files, alinged to both the hg38 and hg19 genomes. Example: cellranger count --id=$INPUTFILE --libraries=library.csv --transcriptome=/database/cellranger/$SPECIESDATABASE --feature-ref=$ADT-feature.csv --localmem 132 --chemistry SC3Pv3HT (for HT experiment)
SoupX ambient RNA removal was perfomred using an estimated contamination fraction of 15% on all samples.
Cells HTO associations destinguishing both donor and ADT concentration were de-multiplexed using the HTO processing module of AltAnalyze. Cell barcodes with > 30% of normalized reads assigned to multiple HTOs were annotated as doublets, with confident singlet assigned to cells with >40% of normalized reads assigned to a single HTO. Cells were further filtered based on the 7 mouse/rat isotype control antibodies counts (custom code), and nFeature_RNA>500 & nCount_RNA >1000 & percent.mt<25. This QC step filtered 393,748 cells to 315,792 high-quality single cells in the initial titration dataset and 90,889 to 72,198 cells in the final titrated CITE-Seq dataset.
Ambient corrected transcriptome counts and associated ADTs counts were supplied as input to the software TotalVI to obtain normalized and denoised ADT counts. To derive clusters from the initial titration CITE-Seq datasets, the software Azimuth or cellHarmony was used to transfer labels from counts per ten thousand (CPTT) normalized expression centroids computed in author provided labels from three prior published reference bone marrow atlases. Projected labels and unsupervised clusters were integrated in the software scTriangulate, using either RNA data alone or RNA+ADTs.
Assembly: hg38
Supplementary files format and content: CellRanger filtered HDF5 sparse count matrix
Supplementary files format and content: ADT/HTO feature files
Supplementary files format and content: CD34_1_antibody_features.csv
Supplementary files format and content: CD34_2_antibody_features.csv
Supplementary files format and content: CD34_3_antibody_features.csv
Supplementary files format and content: CD34_4_antibody_features.csv
Supplementary files format and content: CD271_1_antibody_features.csv
Supplementary files format and content: CD271_2_antibody_features.csv
Supplementary files format and content: CD271_3_antibody_features.csv
Supplementary files format and content: CD271_4_antibody_features.csv
Supplementary files format and content: TNC_12_antibody_features.csv
Supplementary files format and content: TNC_34_antibody_features.csv
Supplementary files format and content: titrated_mix_human.csv
Supplementary files format and content: Cell annotation files
Supplementary files format and content: Level3R-Titrated-Titration-Annotation.txt
Supplementary files format and content: Level3M-titrated-cell-annotation.txt
Library strategy: CITE-Seq

source_name: Bone marrow

extract_protocol:
Cells were isolated from fresh bone marrow. Total nucleated cells were live and dead sorted on Sony MA900. ficoled and enriched for CD34+ cells with double column setup on AutoMACS.
The CITE-Seq library construction protocol followed the Biolegend 10X 3' V3.1 single index ADT protocol and 10X 3' V3.1 dual index protocol, with additional modifications.

value: Bone marrow

tag: self reported ethnicity

value: Black

tag: Sex

value: Male

value: 32 yrs

tag: library type

value: HTO

tag: hto


title: BF32 CD34+CD271+ (HTO)

description:
CD271_3_antibody_features.csv
single indexed HTO
CD271-3_filtered_feature_bc_matrix.h5

value: Female

tag: age


title: BM32 CD34+CD271+ (ADT)

description:
CD271_4_antibody_features.csv
TotalSeq-A single indexed ADT, 266-antibodie
CD271-4_filtered_feature_bc_matrix.h5

value: ADT

tag: adt


title: BM32 CD34+ (HTO)

description:
CD34_4_antibody_features.csv
single indexed HTO
CD34-4_filtered_feature_bc_matrix.h5


title: BM32 CD34+ (ADT)

description:
CD34_4_antibody_features.csv
TotalSeq-A single indexed ADT, 266-antibodie
CD34-4_filtered_feature_bc_matrix.h5


title: BF32 CD34+ (ADT)

description:
CD34_3_antibody_features.csv
TotalSeq-A single indexed ADT, 266-antibodie
CD34-3_filtered_feature_bc_matrix.h5


title: BF32 CD34+CD271+ (GEX)

description:
10X 3' V3.1 HT dual indexed GEX
CD271-3_filtered_feature_bc_matrix.h5

value: 10x Chromium 3' V3.1 GEX


title: BM32 CD34+CD271+ (GEX)

description:
10X 3' V3.1 HT dual indexed GEX
CD271-4_filtered_feature_bc_matrix.h5


title: BM32 CD34+ (GEX)

description:
10X 3' V3.1 HT dual indexed GEX
CD34-4_filtered_feature_bc_matrix.h5


title: BF32 CD34+ (GEX)

description:
10X 3' V3.1 HT dual indexed GEX
CD34-3_filtered_feature_bc_matrix.h5


title: gastric cancer-Chemotherapy [G57T]

status: Public on Jan 19 2024

city: Fukuoka

first: Chikanori

last: Tsutsumi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Surgery and Oncology, Graduate School of Medical Sciences

institute: Kyushu University

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v5.0.0 (10x Genomics)
Output files were analyzed with the R v3.6.3 package "Seurat v3.1.5".
Supplementary files format and content: To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.

extract_protocol:
Single-cell library preparation was performed according to the manual of the Chromium Next GEM Single-cell 3' Reagent Kits v3.1. The cell suspensions were loaded on the Single-cell G Chip for gel bead-in-emulsion (GEM) generation and barcoding. cDNA library thus was generated with a droplet-based sequencing platform (10X Genomics). Next, reverse transcription, RT cleanup cDNA amplification, and quantification was performed to construct a 3’ gene library.
The libraries were sequenced on NovaSeq6000 (Illumina) or DNBSEQ-G400 (MGI Tech).

value: stomach

tag: disease state

value: gastric cancer-Chemotherapy


title: gastric cancer-Chemotherapy [G54T]


title: gastric cancer-Chemotherapy+Anti-PD1 [G60T]

value: gastric cancer-Chemotherapy+Anti-PD1


title: non-malignant gastric mucosa [G51N]

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v5.0.0 (10x Genomics)
Output files were analyzed with the R v3.6.3 package "Seurat v3.1.5".
Assembly: GRCh38
Supplementary files format and content: To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.

extract_protocol:
Single-cell library preparation was performed according to the manual of the Chromium Next GEM Single-cell 3' Reagent Kits v3.1. The cell suspensions were loaded on the Single-cell G Chip for gel bead-in-emulsion (GEM) generation and barcoding, aiming to recover 10,000 cells per sample. cDNA library thus was generated with a droplet-based sequencing platform (10X Genomics). Next, reverse transcription, RT cleanup cDNA amplification, and quantification was performed to construct a 3’ gene library.
The libraries were sequenced on NovaSeq6000 (Illumina) or DNBSEQ-G400 (MGI Tech).

tag: organ

tag: gender

value: non-malignant gastric mucosa


title: non-malignant gastric mucosa [G50N]

tag: tissue


title: non-malignant gastric mucosa [G52N]


title: non-malignant gastric mucosa [G49N]


title: gastric cancer [G55T]

value: gastric cancer


title: gastric cancer [G51T]


title: gastric cancer [G52T]


title: gastric cancer [G49T]


title: gastric cancer [G45T]


title: gastric cancer [G44T]


title: BF32 CD34+CD271+ (ADT)

description:
CD271_3_antibody_features.csv
TotalSeq-A single indexed ADT, 266-antibodie
CD271-3_filtered_feature_bc_matrix.h5


title: gastric cancer [G48T]


title: WT-C1-cr

value: kidney

value: WT


title: BF32 CD34+ (HTO)

description:
CD34_3_antibody_features.csv
single indexed HTO
CD34-3_filtered_feature_bc_matrix.h5


title: gastric cancer [G50T]


title: gastric cancer [G43T]


title: non-malignant gastric mucosa [G43N]


title: CPM,MEF2A,CUT&Tag,bio_rep2

status: Public on Dec 05 2023

city: Chengdu

first: Xinglong

last: Wang

state: Sichuan

address: Wangjiang

department: College of Life Sciences

institute: sichuan university

data_processing:
Raw sequencing reads were pre-processed using Trim Galore software (version 0.6.7) with the following parameters: -q20, --phred33, --length35, --stringency3, --paired. Subsequently, BWA-MEM (version 0.7.17-r1188) with default parameters was used to align the reads to the gal6 and E. coli reference genome. Later, duplicated reads were eliminated using Picard tools (version 2.7.3). All aligned reads were normalized using bedtools with a scaling factor based on the number of reads aligned to the E. coli genome, known as spike-in calibration. A scaling factor S was calculated using the following formula: S = C / (fragments mapped to E. coli genome), where C was set at 1,000,000. The generated bam files were converted to bigwig files using bamCoverage in order to visualize them using IGV software (version 2.16.0). The detection of peaks was performed using SEACR software (version 1.3) with parameter non (non-normalized) and stringent (stringent threshold). Merging of peaks from the two biological replicate samples was carried out by employing Bedtools intersect (version 2.30.0) with the parameter -f 0.80.
Assembly: gal6
Supplementary files format and content: bigwig,bed (peak file),bedgraph
Library strategy: CUT&Tag

organism: Gallus gallus

source_name: muscle

growth_protocol: The cell pellet was resuspended in DMEM supplemented with high glucose, 20% (vol/vol) fetal bovine serum (HyClone), 100 U/ml penicillin G, 100 g/ml streptomycin (Life Technologies, Inc., Grand Island, NY).

extract_protocol:
We utilized the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (TD904-1) from Vazyme. The Anti-MEF2A Rabbit pAb (GB11965) from Servicebio was chosen to detect the MEF2A-bound DNA fragments. By overexpressing MEF2A in primary myoblasts and harvesting them with ConA beads, the sufficient amount and purity of starting material for the CUT&Tag assay were prepared. Subsequently, the cells were incubated with the primary antibody overnight, followed by a secondary antibody and pA-Tn5 transposase, which allowed for precise fragmentation and tagging of DNA segments.
Library construction was performed using the TruePrep Index Kit V2 for Illumina (TD202) from Vazyme.

value: muscle

tag: cell line

value: CPM

value: chicken primary myoblasts

tag: antibody


title: gastric cancer [G41T]


title: gastric cancer [G42T]


title: CPM,IgG,CUT&Tag

tag: cell type

value: IgG


title: CPM,MEF2A,CUT&Tag,bio_rep1


title: wTRHC82_2

status: Public on Sep 21 2023

first: Sylvan

middle: C

last: Baca

address: 450 Brookline Ave

department: Center for Functional Cancer Epigenetics

institute: Dana Farber Cancer Institute

data_processing:
cfChIP-seq / cfMeDIP-seq reads were aligned to the hg19 human genome build using the Burrows-Wheeler Aligner (BWA) version 0.7.1740
Non-uniquely mapping and redundant reads were discarded.
MACS v2.1.1.2014061641 was used for ChIP-seq peak calling with a q-value (FDR) threshold of 0.01.
Fragment locations were converted to bed files using bedtools (v2.29.2) bamtobed with the -bedpe flag set.
Assembly: GRCh37 - hg19
Library strategy: Low-pass whole genome sequencing (lpWGS)

source_name: Hepatocellular

growth_protocol: All plasma extracted from whole blood by centrifugation for 10 min at 1500g at 4°

extract_protocol:
Library was prepped by KAPA Hyper Prep Kit (KAPA Biosystems, cat# KK8500) according to the manufacturer’s protocol.
cell-free DNA (cfDNA) was extracted from plasma supernatant after cfCHIP by QIAmp Circulating Nucleic Acid kit (Qiagen, cat# 55114)

value: Hepatocellular

value: LPWGS


title: wTRHC68_2


title: wTRHC66_2


title: wTRHC47_1


title: wTRHC33_2


title: wTRHC25_2


title: wTRHC103_2


title: wTRHC128_2


title: wTRHC101_2


title: wTRC78_1

source_name: Prostate

value: Prostate


title: wTRC84_2


title: wTRC53_1


title: wTRC61_2


title: wTRC40_1


title: wTRC42_1


title: wTRC30_1


title: wTRC25_1


title: gastric cancer [G40T]

value: Male


title: wTRC23_1


title: wSMAC5_2

source_name: Ovarian

value: Ovarian


title: wSMAC23_2


title: wSMAC16_2


title: WRC38

source_name: Renal

value: Renal


title: wTRHC88_2


title: wPS96_2

source_name: NSCLC

value: NSCLC


title: wSMAC11_2


title: wPS75_2


title: wPS245_2


title: wPS248_2


title: wTRHC54_2


title: wPS219_2


title: wPS197_2


title: wPS173_2


title: wPS122_2


title: wTRC67_2


title: wPS12_2


title: wPCmlf080

source_name: Colorectal

value: Colorectal


title: wPCmlf081

source_name: SCLC

value: SCLC


title: WPCmlf37


title: WPC38


title: WPC40


title: wPCmlf066

source_name: NEPC

value: NEPC


title: wPCmlf049

source_name: Thymic

value: Thymic


title: wPCmlf052

source_name: Merkel cell

value: Merkel cell


title: WPC32


title: WPC39


title: WPC31


title: wPS55_2


title: wNIH_TRHC_14_2


title: wNIH_TRHC_7_2


title: wNIH_TRC_7_1


title: wNIH_PS_7_1


title: WP2627


title: wNIH_PS_36_2


title: wNIH_AMP_8_2


title: wNEmlf021


title: wPS154_2


title: wNEmlf019


title: wNEmlf020


title: wNEmlf017


title: wPCmlf074


title: wNEmlf016


title: wNEmlf015


title: wNEmlf013


title: WNE2273


title: WMPC54


title: WMPC53


title: WML05

source_name: Melanoma

value: Melanoma


title: WML01


title: WML03


title: WML04


title: WML02


title: wMGI942_1


title: wNEmlf022


title: wMGI933_1


title: wMGI940_2


title: wMGI938_1


title: wNIH_TRC_4_2


title: wMerk229


title: wMerk212


title: wMerk197


title: wMerk168


title: wMCC323


title: wNEmlf014


title: wMCC316


title: wMCC324


title: wMCC279


title: wMCC274


title: wMCC270


title: wMCC266


title: wMCC260


title: wMCC253


title: WML06


title: wMCC245


title: wMCC241


title: wMCC240


title: wMCC228


title: wLCmlf0013


title: wLXE8W_TF

source_name: Breast

value: Breast


title: wLCmlf0014


title: WLC34


title: WLC31


title: WLC29


title: WLC32


title: WLC26


title: WLC33


title: WLC23


title: wMCC306


title: WLC17


title: WLC21


title: wMCC284


title: WLC16


title: WLC20


title: WLC10


title: WLC09


title: WLC08


title: WLC07


title: WLC36


title: WLC01


title: wISIS21_2


title: WLC04


title: wISIS90_1


title: wISIS32_1


title: wLC25


title: wISIS13_1


title: wISIS109_1


title: wHU30E_TF


title: WHPC54


title: wIGFSE_TF


title: WLC12


title: WHPC53


title: WLC11


title: WHP140197

source_name: Healthy

value: Healthy


title: wH5UBF_TF


title: WH34881


title: WH56703


title: WH98228


title: WGPC54


title: WH30642


title: wEZJFG_TF


title: WLC05


title: WCRpt436


title: WLC02


title: WCRpr749


title: wL8WWS_TF


title: WCRpr436


title: WCRpr987


title: wBMS7_2


title: WCRpr070


title: WCRpr257b


title: wBMS4_2


title: wBELI82_2


title: wBELI74_2


title: wBELI68_2


title: wBELI70_2


title: wBELI64_2


title: wBELI56_2


title: wAMP28_2


title: wAMP31_2


title: wBELC83_2


title: wAMP20_2


title: wAMP11_2


title: wAMP16_2


title: wAMP13_2


title: tPC40K4

data_processing:
cfChIP-seq / cfMeDIP-seq reads were aligned to the hg19 human genome build using the Burrows-Wheeler Aligner (BWA) version 0.7.1740
Non-uniquely mapping and redundant reads were discarded.
MACS v2.1.1.2014061641 was used for ChIP-seq peak calling with a q-value (FDR) threshold of 0.01.
Fragment locations were converted to bed files using bedtools (v2.29.2) bamtobed with the -bedpe flag set.
Assembly: GRCh37 - hg19

extract_protocol:
ChIP-seq libraries were prepped with ThruPLEX DNA-Seq Kit (Takara Bio, cat# R400675) following the manufacturer's instructions. After library amplification, the DNA was purified by AMPure XP (Beckman coulter, cat# A63880).
DNA was purified through Phenol extraction (Invitrogen, cat# 15593031) and the subsequent Ethanol precipitation with 3M NaOAc (Ambion, cat# AM9740) and glycogen (Ambion, cat# AM9510).


title: WCRpt070


title: tNG0065_JS8584_S138


title: tPC40Ac


title: tNG0083_JS8584_S139


title: tNG0050_JS8584_S141


title: tNG0065


title: tM1K4


title: tNG0083


title: tM2K4


title: tNG0050


title: tLC29K4


title: tLC21K4


title: tLC21Ac


title: tHP098228K4


title: TherF_metPC_33_JS8753_S107


title: TherF_metPC_35_JS8753_S109


title: TherF_metPC_34_JS8753_S108


title: TherF_metPC_32_JS8753_S106


title: TherF_metPC_28_JS8753_S103


title: TherF_metPC_31_JS8753_S105


title: TherF_metPC_27_JS8753_S102


title: TherF_metPC_29_JS8753_S104


title: TherF_metPC_26_JS8753_S101


title: TherF_metPC_24_JS8753_S100


title: TherF_metPC_22_JS8753_S98


title: TfM9mP29


title: tFMCG189_JS8585_S85


title: tFMCG106_JS8585_S84


title: tFMNG181


title: tFMCG181


title: tFMNG0181_JS8584_S137


title: TfM7mP27


title: TfM5mP24


title: TfM4mP23


title: TfM3mP35


title: TfM3mP32


title: TfM3mP22


title: TfM6mP26


title: TEZ_PC_45_JS9177_S41


title: TfM3mP33


title: TEZ_PC_46_JS9177_S42


title: TEZ_PC_43_JS9177_S39


title: TEZ_PC_42_JS9177_S38


title: TfM10mP31


title: TEZ_PC_44_JS9177_S40


title: TEZ_PC_40_JS9177_S36


title: TEZ_PC_41_JS9177_S37


title: TherF_metPC_23_JS8753_S99


title: TEZ_PC_39_JS9177_S35


title: TfM8mP28


title: TEZ_PC_33_Sample2_JS8960_S98


title: TEZ_PC_33_Sample1_JS8960_S97


title: TfM3mP34


title: rPC31Me3R1


title: tCG0046_JS8584_S135


title: rLC29Me3R1


title: tCG0046


title: tCG0011_JS8584_S134


title: tCG0028


title: rLC09Me3R1


title: rGL09828K4R2

source_name: Glioma

value: Glioma


title: rGL10261K4R2


title: reS_K4_TRHC82_2


title: reS_K4_TRC42_1


title: reS_K4_MGI940_1


title: reS_K4_BELI83_2


title: reS_K4_MGI942_1


title: reS_K27_TRHC82_2


title: reS_K4_SMAC23_2


title: reS_K4_ISIS21_1


title: reS_K4_AMP28_2


title: tCG0011


title: reS_K27_MGI942_1


title: TEZ_PC_38_JS9177_S34


title: reS_K27_PS245_2


title: reS_K27_AMP28_2


title: reS_K27_PS55_2


title: rePR2777Me3R1


title: RCh1331Me3R1


title: RCcC702Me3R1


title: RC170Me3R1


title: RC170PanR3


title: PRAD3260_JS8584_S130


title: PR2777PanR2


title: RCcC702PanR2


title: PRAD3260


title: PR3294Me3R1


title: PR2777Me3R1


title: PCmlf041


title: PR2514PanR2


title: PCmlf038


title: PCmlf040


title: PCmlf022PanAC_AbC1ug_JS9371_S43


title: PR3294PanR2


title: PCmlf021


title: PCmlf039PanAC_AcM1ug_JS9371_S51


title: PCmlf0059M3R2


title: PCmlf022PanAC_AcM1ug_JS9371_S50


title: PCmlf022


title: PC53K4me3


title: PC53K27ac


title: PC48pAcR2


title: PC48Me3R1


title: PC40K4me3


title: PC40K27ac


title: PC36r1Me3R1


title: PC36r2Me3R1


title: PC32nMe3R1


title: PC07v043


title: PC07v046


title: PC07v041


title: PC32oMe3R1


title: PC31K4me3


title: PC07v038


title: PC07v039


title: PC07v030


title: PC32npAcR2


title: NEPC9PanAR2


title: NG0013_JS8585_S91


title: PC31K27ac


title: PC05v040


title: NEPC8K4R2


title: NEPC8PanAR2


title: NEPC9K27R1


title: NEPC8K4R1


title: reS_K27_MGI940_1


title: NEPC8K27R1


title: NEPC7PanAR2


title: NEPC7K4R2


title: NEPC7K4R1


title: NEPC7K27R1


title: NEPC6PanAR2


title: NEPC6K4R2


title: reCRpt257Me3R1


title: NEPC6K4R1


title: NEPC9K4R2


title: PC31Me3R1


title: NEPC5K4R1


title: NEPC5K4R2


title: NEPC6K27R1


title: PC07v032


title: NEPC5PanAR2


title: NEPC4PanAR2


title: NEPC4K27R1


title: NEPC5K27R1


title: NEPC4K4R1


title: NEPC3K4R2

source_name: Small cell bladder

value: Small cell bladder


title: NEPC3K4R1


title: NEPC9K4R1


title: NEPC4K4R2


title: NEPC3K27R1


title: NEPC12PanAR2


title: NEPC12K4R2


title: NEPC3PanAR2


title: NEPC12K27R1


title: NEPC12K4R1


title: NEPC11K4R1


title: NEPC11K27R1


title: NEPC11PanAR2


title: NEPC10K4R2


title: NEPC10K4R1


title: NEPC10K27R1


title: mTRHC68_2

extract_protocol:
Performed end-repair, A-tailing, and ligation of NEBNext adaptors (NEBNext Multiplex Oligos for Illumina kit, New England BioLabs. Cat# E7645L). Libraries were digested using the USER enzyme (New England BioLabs, cat# M5505S). Then library was amplified cusing the KAPA HyperPrep Kit according to the manufacturer’s protocol.
cell-free DNA (cfDNA) was extracted from plasma supernatant after cfCHIP by QIAmp Circulating Nucleic Acid kit (Qiagen, cat# 55114) and, MeDIP ip was purified using the iPure Kit v2 (Diagenode, cat# C0301001)

value: Hepatocellular

value: MeDIP


title: mTRHC82_2


title: mTRHC88_2


title: NE3784Me3R1


title: mTRHC66_2


title: mTRHC33_2


title: mTRHC128_2


title: mTRHC25_2


title: NEPC11K4R2

value: Prostate


title: mTRHC47_1


title: mTRC67_2


title: mTRHC103_2


title: mTRHC101_2


title: mTRC61_2


title: mTRC78_1


title: mTRC30_1


title: mTRC23_1


title: NEPC10PanAR2


title: mTRC53_1


title: mTRC11_1


title: mTRC84_2


title: mTRC40_1


title: mTRC25_1


title: mSMAC5_2


title: mSMAC23_2


title: mTRHC54_2


title: mSMAC11_2


title: mPS248_2


title: mPS245_2


title: mPS219_2


title: mPS96_2


title: mPS197_2


title: mPS173_2


title: mPS154_2


title: mTRC42_1


title: mPCmlf081


title: mPS122_2


title: mPCmlf074


title: mPCmlf052


title: mPCmlf049


title: mPCmlf080


title: mPC39K4


title: mPS12_2


title: mPCmlf066


title: mPC31_K4_3hr


title: mPC32_K4_3hr


title: mSMAC16_2


title: mNIH_TRHC_7_2


title: MPAcLC31


title: mPC31_K27ON


title: MPAcmel4


title: mPS75_2


title: mNIH_TRHC_14_2


title: mNIH_TRC_7_1


title: mNIH_PS_7_1


title: mNIH_PS_36_2


title: MNEPC9a


title: mNIH_AMP_8_2


title: MNEPC8a


title: MNEPC9b


title: MNEPC6a


title: MNEPC5b


title: MNEPC3a


title: MNEPC6b


title: MNEPC4b


title: mPC39Ac


title: MNEPC12b


title: MNEPC3b


title: MNEPC4a


title: MNEPC5a


title: MNEPC12a


title: MNEPC11b


title: MPAcmel3


title: MNEPC10b


title: MNEPC10a


title: MNEPC11a


title: mNIH_TRC_4_2


title: mNEmlf019


title: mNEmlf020


title: mNEmlf017


title: mNEmlf015


title: mNEmlf021


title: mNEmlf016


title: mNEmlf014


title: mNEmlf013


title: mmPS55_2


title: mMGI942_1


title: mMGI938_1


title: mMGI940_2


title: mMGI933_1


title: mMerk212


title: mMerk168


title: mMerk197


title: mMerk229


title: mMCC284


title: mNEmlf022


title: mMCC279


title: mMCC324


title: mMCC274


title: mMCC270


title: mMCC266


title: mMCC260


title: mMCC245


title: mMCC240


title: mMCC253


title: mMCC241


title: mMCC228


title: mLCmlf046


title: mLCmlf0015


title: MmPC15r3


title: mLCmlf0014


title: mLCmlf0013


title: mLC9_K27ON


title: mMCC323


title: mMCC306


title: mLC34_K4_3hr


title: mMCC316


title: mLC34_K27ON


title: mLC33


title: mLC25


title: mLC33_K4_3hr


title: mLC12Ac


title: mLC12K4


title: mLC20K4


title: mLC11Ac


title: mLC11K4


title: mLC10K4


title: mLXE8W_TF


title: MK4mel4


title: Mk4Pc60


title: MK4mel3


title: mL8WWS_TF


title: MK4Lc45


title: MK4LC31


title: MK4Lc40


title: mK4_PC62a


title: mLC9_K4_3hr


title: mK4_PC59_2


title: mK4_PC59a


title: mK27_PC62b


title: MJH9


title: mLC34


title: mK4_PC59_1


title: mLC33_K27ON


title: mK27_PC59b


title: MJH8


title: mLC19K4


title: MJH5


title: MJH6


title: MJH4


title: MJH7


title: MJH2


title: mLC10Ac


title: MJH10


title: mISIS32_1


title: mISIS90_1


title: mISIS21_2


title: MJH1


title: mISIS13_1


title: mISIS109_1


title: mIGFSE_TF


title: mH5UBF_TF


title: mHU30E_TF


title: mHP034881Ac


title: mEZJFG_TF


title: mHP034881K4


title: MESG9920


title: MESG4348

source_name: Esophageal

value: Esophageal


title: MESG3845


title: MESG4325


title: MESG4275


title: MESG4300


title: MESG3794


title: MESG3726


title: MESG3801


title: MESG3906


title: MESG3789


title: Merk324_K27


title: Merk324_K4


title: Merk323_K4


title: Merk323_K27


title: Merk316_K27


title: MESG4206


title: Merk316_K4


title: Merk306_K4


title: MJH3


title: Merk284_K27


title: Merk284_K4


title: Merk279_K4


title: Merk274_K4


title: Merk274_K27


title: Merk270_K4


title: Merk270_K27


title: Merk266_K27


title: Merk266_K4


title: Merk245_K4


title: Merk253_K27


title: Merk260_K4


title: Merk245_K27


title: Merk240_K4


title: Merk241_K4


title: Merk241_K27


title: MEGS4488


title: Merk240_K27


title: Merk238_K27


title: MeDptP42


title: MeDprP40


title: MeDptP41


title: MeDptP40


title: MeDptP39


title: MeDptP38


title: Merk306_K27


title: Me3_LC021AC_JS8952_S177


title: Me3_LC012AC_JS8952_S175


title: MdRCcC973


title: MdRCcC944


title: MdRCh1331


title: MdPR2778


title: MdPR3294


title: MdPR2777


title: MdPR8665


title: MdRC38


title: MdPC48


title: Merk253_K4


title: MdPC39


title: MdPC40


title: MdP2627


title: MdNE3838


title: MdPC32


title: MdPC31


title: MdPC38


title: MdPR2514


title: MdNE2273


title: MdNE3784


title: MdMP54


title: MdMel02


title: Me3_LC020AC_JS8952_S176


title: MdMP53


title: MdMel06


title: MdMel05


title: MdPR3424


title: MdMel04


title: MdMel01


title: MdMel03


title: MdLC45


title: MdLC36


title: MdLC46


title: MdLC32


title: MdLC31


title: MdLC33


title: MdLC34


title: MdLC29


title: MdLC26


title: MdLC23


title: MdLC20


title: MdLC21


title: MdLC17


title: MdLC12


title: MdLC16


title: MdLC19


title: MdLC11


title: MdLC08


title: MdLC09


title: MdLC07


title: MdLC05


title: MdLC02


title: MdHP53


title: MdLC04


title: MdHP140197


title: MdHP10135963


title: MdHP10133405


title: MdHP10132279


title: MdLC10


title: MdHP10116305


title: MdHP54


title: MdHP10123027


title: MdLC28


title: MdHP10111016


title: MdLC01


title: MdHP10102703


title: MdHP10095999


title: MdHP10095178


title: MdHP10097407


title: MdHP10077180


title: MdHP10069519


title: MdHP10058173


title: MdHP10075732


title: MdHP10053744


title: MdHP10059620


title: MdHP10047328


title: MdHP10045456


title: MdHP10031645


title: MdHP10033740


title: MdHP10028203


title: MdHP10041556


title: MdHP10111717


title: MdHP10111616


title: MdH34881


title: MdHP10038748


title: MdHP10035094_2


title: MdHP10036348


title: MdHP10035094


title: MdCRpt987


title: MdH30642


title: MdGP54


title: MdH56703


title: MdGP53


title: MdCRpt436


title: MdCRpt257b


title: MdCRpt547


title: MdCRpt575


title: MdHP10059091


title: MdCRpr436


title: MdCRpr749


title: MdCRpr907


title: MdCRpt257


title: MdCRpr257


title: MdH98228


title: MCOL9962


title: MdCRpr575


title: MCOL9602


title: MCOL9517


title: MCOL9629


title: MCOL9614RF


title: MCOL10387


title: MCOL9587


title: MCOL10380


title: MCOL10250


title: MCOL10241


title: MCOL10191


title: MCOL10375


title: MCOL10279


title: MdCRpr987


title: mBMS7_2


title: MCOL10160


title: mBMS4_2


title: MCOL10194


title: mBELI82_2


title: mBELI74_2


title: mBELI68_2


title: mBELC83_2


title: mBELI56_2


title: MCOL9647


title: mBELI64_2


title: MBC548b


title: MBC541b


title: MBC729a


title: MCOL10221


title: MBC541a


title: MBC509a


title: MBC509b


title: MBC287b


title: MBC320b


title: MBC287a


title: MBC320a


title: MBC103b


title: MBC225b


title: MBC225a


title: MBC033a


title: MATT_PC_46_JS9177_S33


title: MBC103a


title: MBC088b


title: MBC088a


title: MATT_PC_45_JS9177_S32


title: MBC729b


title: MATT_PC_44_JS9177_S31


title: MATT_PC_42_JS9177_S29


title: MATT_PC_40_JS9177_S27


title: MATT_PC_41_JS9177_S28


title: MATT_PC_39_JS9177_S26


title: MBC548a


title: mAMP31_2


title: mAMP28_2


title: MATT_PC_38_JS9177_S25


title: mAMP20_2


title: mAMP13_2


title: mAcS_PC59


title: MBC033b


title: mAMP11_2

extract_protocol:
MeDIP-seq
cell-free DNA (cfDNA) was extracted from plasma supernatant after cfCHIP by QIAmp Circulating Nucleic Acid kit (Qiagen, cat# 55114) and, MeDIP ip was purified using the iPure Kit v2 (Diagenode, cat# C0301001)


title: mAMP16_2


title: MAcPc60


title: MAc2H912


title: MAc2H740


title: MAc1H645


title: MAc1H740


title: MAc1H094


title: MAc1H091


title: MAc2H094


title: MATT_PC_43_JS9177_S30


title: Lung2


title: Lung22


title: Lung14


title: Lung13


title: Lung11


title: LNEPC7a

value: LPWGS


title: LNEPC9a


title: LNEPC9b


title: LNEPC8b


title: LNEPC6a


title: LNEPC5b


title: LNEPC4b


title: LNEPC4a


title: LNEPC5a


title: LNEPC3b


title: MAc2Lc45


title: LNEPC12b


title: LNEPC11b


title: LNEPC12a


title: LNEPC11a


title: Lung9


title: LJH9


title: LNEPC3a


title: LNEPC10a


title: LJH4


title: LJH6


title: LJH3


title: LJH5


title: LJH8


title: LJH2


title: LJH10


title: LJH1


title: LESG9920


title: LESG4488


title: LESG4275


title: LESG4300


title: LESG4348


title: LESG4206


title: LESG3906


title: LESG3845


title: LESG3808


title: LNEPC10b


title: LESG3789


title: LESG3794


title: LJH7


title: LESG3801


title: LESG3726


title: LCOL9962


title: LCOL9629


title: LCOL9647


title: LCOL9614RF


title: LCOL9602


title: LCOL9752


title: LCOL9587


title: LCOL10375


title: LCOL10387


title: LESG4325


title: LESG4352


title: LCOL10279


title: LCOL10241


title: LCOL10221


title: LESG3867


title: LCOL10194


title: LCOL10191


title: LCmlf006


title: LCmlf010


title: LCmlf007


title: LCmlf005


title: LCmlf004


title: LCm025


title: LCm024


title: LCm018


title: LC9K4me3


title: LCm003


title: LCm005


title: LCOL10380


title: LC9K27ac


title: LCOL9517


title: LCOL10250


title: LC17PanR2


title: LC33pAcR2


title: LC05v021


title: LC09Me3R1


title: LC05v020


title: LC09pAcR2


title: LCOL10160


title: LC05v017


title: LCmlf011


title: LC05v019


title: LC05v007


title: LC05v016


title: LC05v010


title: LC05v006


title: LC021AC2


title: LC05f012


title: LC021AC_JS8935_S143


title: LC019MT_JS8935_S115


title: LC020AC2


title: LC020AC_JS8935_S116


title: LC020AC_JS8935_S142


title: LC021AC_JS8935_S117


title: LC017MT2


title: LC017MT_JS8935_S140


title: LC017MT_JS8935_S114


title: LC019MT_JS8935_S141


title: LC33Me3R1


title: LC016SQ_JS8935_S113


title: LC012AC2


title: LC012AC_JS8935_S138


title: LC016SQ_JS8935_S139


title: LC012AC_JS8935_S112


title: LC010MT_JS8935_S137


title: LC012AC


title: LC010MT_JS8935_S111


title: LC007AC_JS8935_S136


title: LC007AC2


title: LC007AC_JS8935_S110


title: LC010MT


title: LC007AC


title: LC006AC2


title: LC006AC_JS8935_S135


title: LC006AC_JS8935_S109


title: LC006AC


title: LC001SQ


title: LBC729a


title: LBC729b


title: LBC548b


title: LBC509b


title: LBC548a


title: LBC541b


title: LBC509a


title: LBC287b


title: LBC320a


title: LBC287a


title: LBC225b


title: LBC103b


title: LC010MT2


title: LBC088b


title: LBC225a


title: LBC033b


title: LBC033a


title: L36_H3ac


title: L26_H3ac


title: L30_K4


title: K4me3_TRHC2


title: K4TRHC66_2


title: K4me3_TRHC1


title: K4me3_TRC2


title: K4me3_TRC1


title: K4me3_PS2


title: LBC541a


title: K4me3_BELI2


title: K4me3_BELI1


title: K4me3_AMP1


title: K4L8WWS_TF


title: K4H5UBF_TF


title: K4EZJFG_TF


title: K4_TRHC68_2


title: K4me3_AMP2


title: K4_TRHC53_2


title: K4_TRHC33_2


title: LBC088a


title: K4IGFSE_TF


title: K4_TRHC25_2


title: K4_TRHC82_2


title: K4_TRHC66_2


title: K4_TRHC225_2


title: K4_TRHC47_1


title: K4HU30E_TF


title: K4_TRHC216_2


title: K4_TRHC192_1


title: K4_TRHC208_2


title: K4_TRHC169_2


title: K4me3_PS1


title: K4_TRHC88_2


title: K4_TRHC161_2


title: K4_TRHC229_1


title: K4_TRHC238_2


title: K4_TRHC160_2


title: K4LXE8W_TF


title: k4_TRHC145_2


title: K4_TRHC148_2


title: K4_TRHC123_2


title: K4_TRHC101_2


title: K4_TRC97_1


title: K4_TRC94_1


title: K4_TRHC103_2


title: K4_TRC78_2


title: K4_TRC67_1


title: K4_TRC84_1


title: K4_TRC42_1


title: K4_TRC40_1


title: K4_TRC53_1


title: K4_TRC148_2


title: K4_TRC121_2


title: K4_TRC133_2


title: K4_TRC61_2


title: K4_TRC25_1


title: K4_SMAC78_2

value: Ovarian


title: K4_TRC11_1


title: K4_TRC30_1


title: K4_TRC113_1


title: K4_SMAC57_2


title: K4_TRC23_1


title: K4_SMAC70_2


title: K4_TRC134_1


title: K4_SMAC41_2


title: K4_SMAC64_2


title: K4_SMAC35_2


title: K4_SMAC26_2


title: K4_SMAC23_2


title: K4_SMAC05_2


title: K4_PS96_2

value: NSCLC


title: K4_PS75_2


title: K4_PS55_2


title: K4_PS475_2


title: K4_PS466_2


title: K4_PS410_2


title: K4_PS438_2


title: K4_PS353_2


title: K4_PS325_2


title: K4_PS381_2


title: K4_PS248_2


title: K4_PS245_2


title: K4_PS197_2


title: K4_PS123_2


title: K4_SMAC49_2


title: K4_NEPC20


title: K4_PS154_1


title: k4_PS296_2


title: K4_NEPC19


title: K4_SMAC11_2


title: K4_NEPC16


title: K4_NEPC18


title: K4_PS_122_2


title: k4_PS278_2


title: K4_NEPC22


title: K4_PS173_1


title: K4_NEPC14


title: K4_NEPC15


title: K4_NEPC13


title: k4_MMYE1


title: K4_SATR1_2


title: K4_PS219_2


title: K4_MGI958_1


title: K4_MGI954_1


title: K4_MGI952_2


title: K4_NEPC21


title: K4_MGI946_1


title: K4_MGI948_1


title: K4_MGI944_1


title: K4_MGI942_1


title: K4_MGI940_1


title: K4_Merk212


title: k4_LYCQK


title: K4_MGI_933_1


title: K4_Merk165


title: k4_LWZIR


title: K4_MGI938_1


title: K4_Merk229


title: K4_LC46_Tak


title: K4_Merk168


title: K4_LC46_IDT


title: K4_LC46_CD


title: k4_LC33g


title: k4_KN7SQ


title: K4_MGI956_2


title: k4_JR6BR


title: k4_LC34


title: K4_ISIS21_1

value: Colorectal


title: K4_ISIS90_1


title: k4_LC25


title: k4_KOL1X


title: K4_ISIS363_1


title: k4_LC33m

value: SCLC


title: k4_KVFUI


title: K4_ISIS184_1


title: k4_ISIS151_1


title: K4_Merk197


title: K4_HPC81_1


title: K4_HPC81_2