title: A87r6

value: embryo6/right side


title: T-ALL Sample 315 [RNA-seq]

status: Public on Jan 29 2025

type: SRA

city: Umeå

first: Sofie

last: Degerman

state: Sweden

address: NUS, Blg 6M, 2nd floor

department: Medical Biosciensces

country: Sweden

institute: Umeå University

description:
TALL315
taken at diagnosis

library_source: transcriptomic

data_processing:
Data quality was controlled using FastQC followed by the removal of low-quality reads and adapter trimming with Atropos, sequences were aligned (GRCh38) using STAR, and post-alignment quality control was performed with MultiQC. Salmon was used for transcript quantification of protein-coding genes, expressed in variance stabilizing transformation (VST) counts. XY genes and low-expressed genes (with a mean count < 5) were filtered out of the processed data.
Assembly: GRCh38
Supplementary files format and content: Tab delimited *.txt with processed and filtered variance stabilizing transformation (VST) counts
Supplementary files format and content: Tab delimited *.txt with raw counts

molecule: total RNA

organism: Homo sapiens

source_name: T-ALL bone marrow/peripheral blood sample

growth_protocol: No growth; biobanked frozen samples.

extract_protocol:
The RNA was extracted using the AllPrep kit (Qiagen).
Pair ended 150 bp RNA sequencing libraries were prepared using the Illumina TruSeq RNA Library Prep Kit with RiboZero Gold treatment, and sequencing was performed using the Illumina NovaSeq 6000 system (Illumina, CA, USA).

tag: tissue

tag: tissue type

value: Tumor

tag: cimp subgroup

value: CIMP low

tag: disease

value: Pediatric T-cell acute lymphoblastic leukemia


title: F123 GAM library f123_1NP_GAM180123_A03_2_S113_R1_001

city: Berlin

first: Alexander

last: Kukalev

address: Hannoversche Str., 28

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max-Delbrueck Center for Molecular Medicine

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip

library_source: genomic

data_processing:
Sequenced reads from each GAM library were mapped to the mouse genome assembly GRCm38 (Dec. 2011, mm10) using bowtie2 with all default settings. All non-uniquely mapped reads, reads with mapping quality < 20 were filtered using the command “sed '/XS:/d' | samtools view -q 20 -F 4 -bS -”. PCR duplicates were removed with the “samtools rmdup” command. Samples were checked for contamination using fastq_screen. Number of nucleotides sequenced in each genomic bin was calculated using bedtools coverage command. Next, the optimal threshold between the sequencing noise and the signal to call positive windows was calculated as the lowest coverage per bin that gives the highest percent of clustered windows (windows that have a neighboring positive window on at-least one side) for each GAM sample in the dataset. Windows were called positive when the number of nucleotides covered by the reads is higher or equal to the optimal threshold. Each dataset was assessed for quality control by determining the percentage of orphan windows, number of uniquely mapped reads to the mouse genome, and cross-well contamination for every sample. 1NP samples that passed QC were merged into in-silico 3NPs at the level of positive windows. For good quality samples, we produced raw co-segregation, as well as normalized (NPMI) pair-wise chromatin contact matrices.
Assembly: mm10
Supplementary files format and content: Processed data files are raw GAM segregation tables, non-normalized pairwise cosegregation matrices and normalized NPMI matrices in tab-delimited format.
Library strategy: WGA

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Mouse F123 ESCs (a male, hybrid cell line, derived from S129/Jae and Cast) (Gribnau et al., 2003) were cultured in a layer of mitotically inactivated feeder murine embryonic fibroblasts under standard conditions (DMEM, supplemented with 15 % KSR, 1x Glutamax, 10 mM non-essential amino acids, 50 µM beta-mercaptoethanol , 1000 U / ml LIF). Before harvesting, mESCs were passaged onto feeder free 0.1% gelatin coated plates for at least 2 passages to remove feeder cells. As feeder-removal results in reduced levels of LIF in the culture, the LIF concentration in the media was doubled when the cells were in feeder-free culture conditions. Cells were harvested after ~ 48 h at 70 – 80 % confluency.

extract_protocol:
Fixation of F123 mESC was performed as described previously (Branco and Pombo, 2006). Briefly, cells were grown to 70 % confluency, media was removed, and cells were fixed in 4% and 8% paraformaldehyde in 250 mM HEPES-NaOH (pH 7.6; 10 min and 2 h, respectively), gently scrapped, and softly pelleted and embedded in saturated 2.1 M sucrose in PBS and frozen in liquid nitrogen on copper sample holders. Ultrathin cryosections were cut with a glass knife using an ultracryomicrotome (Leica Biosystems, EM UC7) at ~230 nm thickness, and transferred to PEN membrane steel frame slides 4.0 µm (Leica Microsystems, 11600289) for laser microdissection. Before laser microdissection, cryosections were washed in sterile-filtered 1x PBS (3 times, 5 min each), sterile-filtered H2O (3 times, 5 min each), and stained with sterile-filtered 1 % (w/v) cresyl violet (Sigma-Aldrich, C5042) in H2O for 10 min, followed by 2 washes with H2O (30 s each).  Individual NPs were isolated from the cryosection by laser microdissection using a laser microdissection microscope (Leica Microsystems, LMD7000). Cut NPs were collected in a PCR Cap Strip filled with opaque adhesive material (Carl Zeiss Microscopy, 415190-9161-000). For each collection day, 1 or 2 caps were left empty and taken through the whole genome amplification (WGA) and sequencing process as a negative control for quality control purposes.
Whole Genome Amplification (WGA) was performed as described previously (Winick-Ng et al, 2021) with minor modifications. Briefly, DNA was extracted from NPs at 60oC in the lysis buffer (20mM Tris-HCl pH 8.0, 1.4 mM EDTA, 560 mM guanidinium-HCl, 3.5% Tween-20, 0.35% Triton X-100) containing 0.75 units/ml Qiagen protease (Qiagen, 19155). After 24h of DNA extraction, the protease was heat inactivated at 75oC for 30 min and the extracted DNA was amplified via two rounds of PCR. At-first quasi-linear amplification was performed with random hexamer GAT-7N  primers with an adaptor sequence. The lysis buffer containing the extracted genomic DNA was mixed with 2x DeepVent mix buffer (2x Thermo polymerase buffer (10x), 400 µm dNTPs, 4 mM MgSO4 in ultrapure DNase free water), 0.5 µM GAT-7N primers (5′- GTG AGT GAT GGT TGA GGT AGT GTG GAG NNN NNN N) and 2 units/µl DeepVent® (exo-) DNA polymerase (New England Biolabs, M0259L) and incubated for 11 cycles in the BioRad thermocycler. The second exponential PCR amplification was performed in presence of 1x DeepVent mix, 10 mM dNTPs, 0.4 µM GAM-COM primers (5′-GTG AGT GAT GGT TGA GGT AGT GTG GAG) and 2 units/µl DeepVent (exo-) DNA polymerase in the programmable thermal cycler for 26 cycles.
After whole genome amplification, the DNA WGA product was purified withSPRI beads (1.7x) The DNA concentration of each sample was quantified using the Quant-iT® PicoGreen dsDNA assay kit (Invitrogen #P7589). Genomic sequencing library was prepared from 1ng of purified DNA using the Illumina Nextera XT library preparation kit (Illumina #FC-131-1096), following the manufacturer’s instructions or with reduce to 20% volume of reagents. After the library preparation, DNA was again purified with in-house SPRI beads (1.7x) and equal amounts of DNA from each sample was pooled together (up to 196 samples) for the sequencing. The final pool of libraries was additionally purified two more times with SPRI beads (1.7x) and analyzed using DNA High Sensitivity on-chip electrophoresis on an Agilent 2100 Bioanalyzer. The samples were sequenced on Illumina NextSeq500 machine as single-end 75 bp reads, according to manufacturer’s instructions.

tag: cell line

tag: cell type

value: mouse embryonic stem cells

tag: genotype

value: Hybrid F1 S129/Jae and Cast

tag: Sex

value: male


title: mESC, naive pluripotency, WT, IGG, rep2

city: San Francisco

first: Harold

last: Marin

state: CA

address: 555 Mission Bay Boulevard South

department: Smith Cardiovascular Institute

country: USA

institute: University of California San Francisco

description: Library name: WT_naive_IGG_2

data_processing:
Raw sequencing reads were mapped to the “soft masked” mm39 mouse genome using Bowtie2 version 2.3.5.1: -X 2000 -N 1 --local --dovetail.
SAMtools version 1.10 was used to keep properly paired, primary alignments and filter out unassembled contigs, read duplicates, and reads mapped to mitochondria.
RPKM signal coverage in 1kb and 10kb bins were calculated using the deepTools2 (version 3.4.3) function bamCoverage using the GENCODE M30 primary annotation file and the output was saved as bigwig files. Blacklist regions in the mm39 genome were obtained from a published dataset (PMID: 37067481) and excluded from the RPKM calculation.
Scale factors were calculated from the S. cerevisiae spike-in control to quantitatively compare RPKM signal between samples. Raw sequencing reads were mapped to the sacCer3 genome assembly. As was done for mm39, Bowtie2 and SAMtools were used for alignment and post-alignment processing, respectively. The SAMtools function flagstat was used to find the number of properly paired reads in sacCer3 alignments. These were used to calculate a scale factor that was defined by dividing an arbitrary constant number (7,000 for H3K9me3 CUT&RUN; 8,000 for LAP2B and IGG CUT&RUN) by the number of properly paired reads (Zheng Y et al (2020). Protocol.io). Using with the deepTools2 function bamCoverage, the scale factors for each library were used to generate 1kb- and 10kb-binned bigWig files containing spike-in normalized RPKM signal coverage tracks.
For transposable elements, spike-in controlled LAP2B RPKM signal coverage in 10kb bins were calculated with the deepTools2 function bamCoverage using a custom annotation file from the Hammell lab and including Blacklist regions where many transposable elements reside. For calculating modified z-scores of RPKM signal, RPKM values for each transposable element were first averaged across replicates of wildtype naive mESCs. Then, the median RPKM and median absolute deviation were calculated for all transposable elements. A modified z-score for each transposable element was calculated using the following formula: 0.6745 * (individual TE RPKM – median RPKM score) / (median absolute deviation RPKM).
Assembly: mm39
Supplementary files format and content: bigWig, RPKM values per 10kb bins.
Supplementary files format and content: bigWig, spike-in normalized RPKM values per 1kb bins.
Supplementary files format and content: bigWig, spike-in normalized RPKM values per 10kb bins.
Supplementary files format and content: csv file includes spike-in normalized signal from either LMNB1, LAP2B, or IGG CUT&RUN in gene bodies
Supplementary files format and content: csv file includes spike-in normalized signal from either LMNB1, LAP2B, or IGG CUT&RUN in transposable elements
Supplementary files format and content: csv file includes modified z-scores for LAP2B CUT&RUN signal in transposable elements in wildtype naive mESCs
Library strategy: CUT&Run

source_name: mESC

growth_protocol: Cells were cultured at 5% CO2 and 37°C. mESCs were grown in serum- and feeder-free 2i + LIF medium: N2B27 basal medium supplemented with the following compounds at a final concentration of 3 μM CHIR-99021 (Selleckchem S1263), 1 μM PD0325901 (Selleckchem S1036), 103 U/mL LIF (MilliporeSigma™ ESG1107), 55 μM β-mercaptoethanol (Gibco™ 21985023), and 1X PenStrep (GenClone 25-512). N2B27 medium was made by mixing equal parts of DMEM:F12 (GenClone 25-503) and Neurobasal medium (Gibco™ 21103049) then adding 1X N-2 (Gibco™ 17502001), 1X B-27 (Gibco™ 17504001) and 2 mM Glutamax (Gibco™ 35050061). mESCs were seeded at 2.11 x 104 cells/cm2 on dishes pre-coated with either Geltrex (Gibco™ A1413202) or Cultrex (Bio-Techne 3445-005-01). mESCs were replenished with fresh 2i + LIF medium after 24 hours then collected at 48 hours for CUT&RUN. EpiLCs were differentiated by seeding 2.11 x 104 cells/cm2 mESCs into either Geltrex or Cultrex coated dishes containing N2B27 media supplemented with 20 ng/mL FGF (Peprotech 100-18B) and 12 ng/mL Activin A (Peprotech 120-14E). EpiLCs were replenished with fresh differentiation medium after 24 hours then collected at 48 hours for CUT&RUN.

extract_protocol:
CUT&RUN was performed as described in Skene et al. 2018. Live cells were harvested with accutase and washed once with PBS prior to starting the procedure. Three replicates containing 200,000 mESCs or EpiLCs each were used per condition, except for H3K9me3 CUT&RUN which only included two replicates of wildtype naïve mESCs. LAP2B antibody (Invitrogen PA5-52519, 1:100), H3K9me3 antibody (abcam 8898, 1:1000 dilution), and Lamin B1 antibody (sc56144, 1:500) were diluted in antibody buffer and incubated at 4°C overnight. Rabbit anti-mouse secondary antibody (abcam ab6709, 1:100 dilution) was used for as an IGG negative control in parallel with the LAP2B CUT&RUN. pA-MNase (batch #6 143µg/mL) generously gifted from the Hennikoff lab was used for the cleavage reaction. The 2X STOP buffer included genomic DNA from Saccharomyces cerevisiae such that each sample received 0.3pg of spike-in DNA as a spike-in control. The chromatin release step was carried out at 37°C for 1 hour. DNA was isolated by phenol-chloroform extraction. Purified DNA was resuspended with 40uL of 1mM Trish-HCl pH 8.0 and 0.1mM EDTA.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep with Sample Purification Beads (NEB E7103S) following the manufacturer’s protocol with 5ng of starting DNA input. Libraries were amplified using 8 cycles on the thermocycler. Each library was uniquely indexed with NEBNext Multiplex Oligos for Illumina (NEB E6440S), then pooled together in equimolar amounts. Library size was analyzed with the Agilent Bioanalyzer 2100 using the High sensitivity DNA kit.

value: mESC

value: wildtype


title: T-ALL Sample 309 [RNA-seq]

description:
TALL309
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample

value: CIMP high


title: A87r5

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
Reads were aligned to the Ciona genome using STAR (version 2.7.10a) with the ‘--quantMode GeneCounts’ option to quantify reads per gene (Dobin et al., 2013). Exon annotation was taken from the KH.KH.Gene2013.gff3 file reprocessed for compatibility with STAR gene/exon format. ReadsPerGene files were merged to a single gene by cell type raw count matrix.
Assembly: Ciona robusta sequences and annotation were taken from the GHOST database (http://ghost.zool.kyoto-u.ac.jp/download_kh.html)
Supplementary files format and content: raw_counts.txt : STAR reads per gene quantification matrix for all cells (Dobin et al., 2013)

organism: Ciona robusta

extract_protocol:
Embryos were dissected on a 1.5% agarose-coated dish with a fine glass ‘hair’ smeared with cellular debris. A single isolated cell was transferred in 0.5μl of seawater into a 0.2ml PCR tube containing 9μl RNase-free water. After visual inspection of the presence of the cell under stereomicroscope, 1μl of 10x Reaction buffer (SMARTer Ultra Low Input RNA Kit, Takara Bio) was added and the tube was vortexed immediately and stored at -80°C before being processed for library preparation.
Indexed Illumina libraries were prepared using Nextera XT kits (Illumina) from cDNAs generated with SMARTer Ultra low input RNA kit (Takara Bio) according to manufacturers’ instructions. Sequencing was conducted in the UCA GenomiX genomics platform (Sophia Antipolis, France) using Illumina NextSeq500 system. For each library, single end 75bp reads were obtained with sequencing depth of around 8 million reads.

tag: developmental stage

value: 112-cell stage

tag: lineage

value: A

tag: replicate

value: embryo5/right side


title: A87r3

value: embryo3/right side


title: mESC, primed pluripotency, LBRKO, LAP2B, rep3

description: Library name: LBRKO_epi_LAP2B_3

source_name: EpiLC

value: EpiLC

value: LBR knockout


title: mESC, naive pluripotency, LBRKO, LAP2B, rep3

description: Library name: LBRKO_naive_LAP2B_3


title: mESC, naive pluripotency, TKO, LAP2B, rep3

description: Library name: TKO_naive_LAP2B_3

value: Lamins triple knockout


title: A87r2

value: embryo2/right side


title: T-ALL Sample 307 [RNA-seq]

description:
TALL307
taken at diagnosis

value: Tumor


title: A87l7

value: embryo7/left side


title: mESC, primed pluripotency, WT, LAP2B, rep3

description: Library name: WT_epi_LAP2B_3


title: T-ALL Sample 306 [RNA-seq]

description:
TALL306
taken at diagnosis

value: CIMP low

value: Pediatric T-cell acute lymphoblastic leukemia


title: F123 GAM library f123_1NP_GAM180117_H08_2_S160_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

value: male


title: A87l2

value: embryo2/left side


title: F123 GAM library f123_1NP_GAM180117_H11_2_S184_R1_001


title: T-ALL Sample 308 [RNA-seq]

description:
TALL308
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample

value: CIMP high


title: T-ALL Sample 305 [RNA-seq]

description:
TALL305
taken at diagnosis


title: mESC, naive pluripotency, WT, LAP2B, rep3

description: Library name: WT_naive_LAP2B_3

value: mESC

value: wildtype


title: F123 GAM library f123_1NP_GAM180117_H07_2_S152_R1_001


title: T-ALL Sample 304 [RNA-seq]

description:
TALL304
taken at diagnosis


title: F123 GAM library f123_1NP_GAM180117_H10_2_S176_R1_001


title: T-ALL Sample 303 [RNA-seq]

description:
TALL303
taken at diagnosis


title: mESC, naive pluripotency, QKO, LAP2B, rep2

description: Library name: QKO_naive_LAP2B_2

value: Lamins and LBR quadruple knockout


title: mESC, primed pluripotency, QKO, LAP2B, rep2

description: Library name: QKO_epi_LAP2B_2

value: EpiLC


title: A85r7

value: 112-cell stage

value: A

value: embryo7/right side


title: A85r6

value: embryo6/right side


title: F123 GAM library f123_1NP_GAM180123_A01_2_S97_R1_001


title: F123 GAM library f123_1NP_GAM180117_H04_2_S128_R1_001


title: mESC, primed pluripotency, TKO, LAP2B, rep2

description: Library name: TKO_epi_LAP2B_2

value: Lamins triple knockout


title: A85r5

value: embryo5/right side


title: T-ALL Sample 302 [RNA-seq]

description:
TALL302
taken at diagnosis

value: Tumor

value: Pediatric T-cell acute lymphoblastic leukemia


title: F123 GAM library f123_1NP_GAM180117_G12_2_S191_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast


title: F123 GAM library f123_1NP_GAM180117_H09_2_S168_R1_001

value: male


title: mESC, naive pluripotency, TKO, LAP2B, rep2

description: Library name: TKO_naive_LAP2B_2


title: T-ALL Sample 301 [RNA-seq]

description:
TALL301
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample


title: A85r3

value: embryo3/right side


title: F123 GAM library f123_1NP_GAM180117_G11_2_S183_R1_001


title: mESC, primed pluripotency, LBRKO, LAP2B, rep2

description: Library name: LBRKO_epi_LAP2B_2

value: LBR knockout


title: T-ALL Sample 300 [RNA-seq]

description:
TALL300
taken at diagnosis

value: CIMP high


title: A85r2

value: embryo2/right side


title: T-ALL Sample 299 [RNA-seq]

description:
TALL299
taken at diagnosis

value: CIMP low


title: mESC, naive pluripotency, LBRKO, LAP2B, rep2

description: Library name: LBRKO_naive_LAP2B_2

value: mESC


title: F123 GAM library f123_1NP_GAM180117_G10_2_S175_R1_001


title: A85l7

value: 112-cell stage

value: A

value: embryo7/left side


title: F123 GAM library f123_1NP_GAM180117_G09_2_S167_R1_001


title: F123 GAM library f123_1NP_GAM180117_H05_2_S136_R1_001


title: mESC, naive pluripotency, WT, LAP2B, rep2

description: Library name: WT_naive_LAP2B_2

value: wildtype


title: a822r4

value: a

value: embryo4/right side


title: F123 GAM library f123_1NP_GAM180117_G07_2_S151_R1_001


title: A85l2

value: embryo2/left side


title: mESC, primed pluripotency, WT, LAP2B, rep2

description: Library name: WT_epi_LAP2B_2

value: EpiLC


title: T-ALL Sample 298 [RNA-seq]

description:
TALL298
taken at diagnosis

value: Tumor

value: Pediatric T-cell acute lymphoblastic leukemia


title: T-ALL Sample 296 [RNA-seq]

description:
TALL296
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample


title: T-ALL Sample 297 [RNA-seq]

description:
TALL297
taken at diagnosis


title: a822r3

value: embryo3/right side


title: mESC, naive pluripotency, QKO, LAP2B, rep1

description: Library name: QKO_naive_LAP2B_1

value: Lamins and LBR quadruple knockout


title: mESC, primed pluripotency, QKO, LAP2B, rep1

description: Library name: QKO_epi_LAP2B_1


title: a822r2


title: T-ALL Sample 294 [RNA-seq]

description:
TALL294
taken at diagnosis

value: CIMP high


title: a822r1

value: embryo1/right side


title: F123 GAM library f123_1NP_GAM180117_G05_2_S135_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

value: male


title: T-ALL Sample 295 [RNA-seq]

description:
TALL295
taken at diagnosis

value: CIMP low


title: T-ALL Sample 293 [RNA-seq]

description:
TALL293
taken at diagnosis


title: a822l3

value: 112-cell stage

value: embryo3/left side


title: mESC, primed pluripotency, TKO, LAP2B, rep1

description: Library name: TKO_epi_LAP2B_1

value: Lamins triple knockout


title: F123 GAM library f123_1NP_GAM180117_G04_2_S127_R1_001


title: mESC, naive pluripotency, TKO, LAP2B, rep1

description: Library name: TKO_naive_LAP2B_1

value: mESC


title: F123 GAM library f123_1NP_GAM180117_F12_2_S190_R1_001


title: F123 GAM library f123_1NP_GAM180117_G08_2_S159_R1_001


title: a822l2

value: a

value: embryo2/left side


title: T-ALL Sample 291 [RNA-seq]

description:
TALL291
taken at diagnosis

value: Tumor


title: mESC, primed pluripotency, LBRKO, LAP2B, rep1

description: Library name: LBRKO_epi_LAP2B_1

value: EpiLC

value: LBR knockout


title: F123 GAM library f123_1NP_GAM180117_G06_2_S143_R1_001


title: mESC, naive pluripotency, LBRKO, LAP2B, rep1

description: Library name: LBRKO_naive_LAP2B_1


title: F123 GAM library f123_1NP_GAM180117_F11_2_S182_R1_001


title: mESC, primed pluripotency, WT, LAP2B, rep1

description: Library name: WT_epi_LAP2B_1

value: wildtype


title: T-ALL Sample 290 [RNA-seq]

description:
TALL290
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample

value: Pediatric T-cell acute lymphoblastic leukemia


title: F123 GAM library f123_1NP_GAM180117_F10_2_S174_R1_001


title: mESC, naive pluripotency, WT, LAP2B, rep1

description: Library name: WT_naive_LAP2B_1


title: T-ALL Sample 288 [RNA-seq]

description:
TALL288
taken at diagnosis

value: CIMP high


title: T-ALL Sample 289 [RNA-seq]

description:
TALL289
taken at diagnosis


title: a822l1

value: embryo1/left side


title: T-ALL Sample 286 [RNA-seq]

description:
TALL286
taken at diagnosis


title: F123 GAM library f123_1NP_GAM180117_F08_2_S158_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast


title: a819r1

value: embryo1/right side


title: mESC, primed pluripotency, WT, LMNB1, rep3

description: Library name: WT_epi_LMNB1_3


title: F123 GAM library f123_1NP_GAM180117_F07_2_S150_R1_001

value: male


title: mESC, naive pluripotency, WT, LMNB1, rep3

description: Library name: WT_naive_LMNB1_3


title: T-ALL Sample 285 [RNA-seq]

description:
TALL285
taken at diagnosis


title: a819r3

value: 112-cell stage

value: embryo3/right side


title: F123 GAM library f123_1NP_GAM180117_F06_2_S142_R1_001


title: a819r4

value: embryo4/right side


title: T-ALL Sample 284 [RNA-seq]

description:
TALL284
taken at diagnosis

value: CIMP low


title: mESC, primed pluripotency, WT, LMNB1, rep2

description: Library name: WT_epi_LMNB1_2


title: F123 GAM library f123_1NP_GAM180117_F05_2_S134_R1_001


title: mESC, naive pluripotency, WT, LMNB1, rep2

description: Library name: WT_naive_LMNB1_2

value: mESC


title: F123 GAM library f123_1NP_GAM180117_F04_2_S126_R1_001


title: a819l2

value: a

value: embryo2/left side


title: T-ALL Sample 283 [RNA-seq]

description:
TALL283
taken at diagnosis

value: Tumor


title: F123 GAM library f123_1NP_GAM180117_F09_2_S166_R1_001


title: mESC, primed pluripotency, WT, LMNB1, rep1

description: Library name: WT_epi_LMNB1_1

value: EpiLC

value: wildtype


title: T-ALL Sample 282 [RNA-seq]

description:
TALL282
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample

value: Pediatric T-cell acute lymphoblastic leukemia


title: a819l1

value: embryo1/left side


title: mESC, naive pluripotency, WT, LMNB1, rep1

description: Library name: WT_naive_LMNB1_1


title: T-ALL Sample 281 [RNA-seq]

description:
TALL281
taken at diagnosis

value: CIMP high


title: A74r4

value: 64-cell stage

value: A


title: post-dissociation3

city: Minato-ku

first: Kenji

last: Matsui

state: Tokyo

address: Nishi-Shimbashi 3-25-8

country: Japan

institute: The Jikei University School of Medicine

data_processing:
Sequencing was performed using Novaseq X plus (Illumina). The obtained data were mapped to the mouse genome using GENCODE/GRCm39 (mm39) as a reference and normalized for each gene's expression to obtain TPM.
Assembly: GENCODE/GRCm39 (mm39)
Supplementary files format and content: A text file including raw counts and TPM values for each Sample

source_name: fetal kidney at embryonic day 14

extract_protocol:
For “pre-dissociation,” we collected 3 kidneys per sample, and for “post-dissociation,” we extracted over 1 × 10^6 cells with viability of over 80% from 8 kidneys per sample using the aforementioned treatment protocol. RNA extraction and DNA removal were then performed following the protocol with the RNeasy Plus Micro Kit (74034, QIAGEN). We confirmed that each sample yielded at least 66 ng of extracted RNA, which was stored at -80°C
Reverse transcription was carried out using the SMART-Seq v4 Ultra Low Input RNA kit (634892, Takara Bio), followed by library preparation using the Nextera XT DNA Library Prep Kit (FC131-1024 and FC-131-1096, Illumina).

treatment_protocol:
The fetal kidneys were extracted from E14.5 B6 mice and collected into a 1.5-mL tube containing 1 mL of accutase (Innovative Cell Technologies), and vortexed for 30 sec.
They were incubated at 37°C for 15 min, with vortex after 5 min and gentle manual pipetting using a 200-μL pipette tip after 10 and 15 min, then centrifuged at 300 × g for 5 min. Pellets were resuspended in 1 mL MEM α supplemented with 20% FBS and 1% penicillin/streptomycin (168-23191, Wako) and dissociated by gentle manual pipetting.
Cell suspensions were passed through a 40-μm cell strainer (BD Falcon).

value: fetal kidney at embryonic day 14

tag: treatment

value: enzymatic dissociation


title: T-ALL Sample 280 [RNA-seq]

description:
TALL280
taken at diagnosis


title: A74l5

value: embryo5/left side


title: F123 GAM library f123_1NP_GAM180117_E10_2_S173_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

value: male


title: T-ALL Sample 279 [RNA-seq]

description:
TALL279
taken at diagnosis


title: a819l3

value: 112-cell stage

value: a

value: embryo3/left side


title: T-ALL Sample 278 [RNA-seq]

description:
TALL278
taken at diagnosis

value: Tumor

value: CIMP low


title: post-dissociation2


title: T-ALL Sample 277 [RNA-seq]

description:
TALL277
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample


title: post-dissociation1


title: pre-dissociation3


title: F123 GAM library f123_1NP_GAM180117_E08_2_S157_R1_001


title: A73r5

value: embryo5/right side


title: F123 GAM library f123_1NP_GAM180117_E09_2_S165_R1_001


title: F123 GAM library f123_1NP_GAM180117_E07_2_S149_R1_001


title: T-ALL Sample 276 [RNA-seq]

description:
TALL276
taken at diagnosis

value: Pediatric T-cell acute lymphoblastic leukemia


title: A73r4

value: embryo4/right side


title: T-ALL Sample 275 [RNA-seq]

description:
TALL275
taken at diagnosis

value: CIMP high


title: F123 GAM library f123_1NP_GAM180117_E06_2_S141_R1_001


title: A73l5

value: 64-cell stage

value: A


title: F123 GAM library f123_1NP_GAM180117_E11_2_S181_R1_001


title: A74r5


title: UW2.4_C_28

city: Göttingen

first: Victor

last: Chano

address: Buesgenweg 2

department: Forest Genetics and Forest Tree Breeding

institute: University of Göttingen

data_processing:
Initial quality control of sequencing reads (fastq files) was performed using FastQC v0.11.7 and MultiQC v.1.10.1. For detecting and removing Illumina adapters and filtering low-quality reads out, Trimmomatic v0.36 was used. The new genome version FRAX_001_PL version of F. excelsior was used for mapping by means of the software Hisat2 v.2.1.0. Sam/bam files were processed using samtools v.1.9, and the software HTSeq v.2.0.2 was then used to create counting tables.
Assembly: FRAX_001_PL
Supplementary files format and content: Matrix in txt format including the total counts for each gene (in rows) and samples (in columns). Column names (for samples) match with the library names in this metadata file.

organism: Fraxinus excelsior

source_name: Leaf petiole

growth_protocol: For this study, scions from the four selected genoytpes (ADB-tolerant FAR3 and FS36 and ADB-susceptible UW1 and UW2) were grafted in February 2021 onto rootstocks of two-year old ash trees (provenance F. excelsior 81101) and grown for one year in a greenhouse in 4 L plastic pots with commercially available substrate mixture (“Profi-Linie mineralisch” from Kleeschulte Erden GmbH & Co. KG, Rüthen, with pH (CaCl2) 6,0, Salinity 1,5 g/L, N 320 mg/L, P2O5 120 mg/L, K2O 350 mg/L, Mg: 120 mg/L). They were later repotted and fertilized with a universal plant fertilizer (Wuxal; Maag, concentration suggested by the manufacturer), and one month before inoculations trees were transferred to climate chambers with a 16 h photoperiod (light intensity of 80 ± 15 mmol m-2 s-1, constant temperature of 19° ± 3 °C and relative humidity at 65 ± 10%).

extract_protocol:
RNA was extracted using the E.Z.N.A. Plant RNA Kit (Omega Bio Tek, Norcross, USA, R6827-01) according to the manufacturer’s protocol for difficult samples. The concentration and purity of the RNA was assessed using a microvolume spectrophotometer (NanoDrop 2000, Thermo Fisher Scientific, Waltham, USA). Total RNA samples were treated with DNase I, RNase-free (Thermo Fisher Scientific).
cDNA libraries were obtained with the Stranded mRNA Prep kit (Illumina, San Diego, USA), which uses oligo(dT) magnetic beads for purifying and capturing polyA tail from mRNA molecules

treatment_protocol: Ash trees were inoculated with isolates from the highly-virulent H. fraxinueus strain 7 – RH03-T2-B1-1. Inoculations were performed in leaf petioles with round agar plugs (MYB medium) containing active mycelium after making one cm long superficial wound with a sterile scalpel. Control trees were mock-inoculated using sterile MYP medium. For both groups, the agar plug was kept in place by using parafilm, which was not removed until sampling.

value: Leaf petiole

value: Inoculation with sterile agar plugs (MYB medium)

tag: timepoint

value: Sample collected at 28 dpi


title: T-ALL Sample 274 [RNA-seq]

description:
TALL274
taken at diagnosis


title: F123 GAM library f123_1NP_GAM180117_E12_2_S189_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast


title: A73l4

value: embryo4/left side


title: A74l4


title: a819r2

value: 112-cell stage

value: a

value: embryo2/right side


title: pre-dissociation1

value: fetal kidney at embryonic day 14


title: UW2.3_C_28


title: T-ALL Sample 273 [RNA-seq]

description:
TALL273
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample

value: Tumor

value: CIMP low


title: A72r5

value: embryo5/right side


title: F123 GAM library f123_1NP_GAM180117_D12_2_S188_R1_001

value: male


title: A72r4

value: 64-cell stage

value: embryo4/right side


title: T-ALL Sample 272 [RNA-seq]

description:
TALL272
taken at diagnosis

value: CIMP high

value: Pediatric T-cell acute lymphoblastic leukemia


title: T-ALL Sample 271 [RNA-seq]

description:
TALL271
taken at diagnosis


title: UW2.3_I_28

value: Leaf petiole

value: Inoculation with agar plugs (MYB medium) containing active mycelium of H. fraxinueus strain 7 – RH03-T2-B1-1

value: Sample collected at 28 dpi


title: A72l5

value: A

value: embryo5/left side


title: F123 GAM library f123_1NP_GAM180117_D11_2_S180_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast


title: pre-dissociation2

value: fetal kidney at embryonic day 14


title: UW2.2_I_28


title: T-ALL Sample 270 [RNA-seq]

description:
TALL270
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample


title: A72l4

value: embryo4/left side


title: F123 GAM library f123_1NP_GAM180117_D09_2_S164_R1_001


title: UW2.1_I_28


title: T-ALL Sample 269 [RNA-seq]

description:
TALL269
taken at diagnosis

value: Tumor

value: CIMP low


title: A74r3

value: embryo3/right side


title: F123 GAM library f123_1NP_GAM180117_E05_2_S133_R1_001

value: male


title: F123 GAM library f123_1NP_GAM180117_D08_2_S156_R1_001


title: T-ALL Sample 268 [RNA-seq]

description:
TALL268
taken at diagnosis


title: UW2.3_C_21

value: Inoculation with sterile agar plugs (MYB medium)

value: Sample collected at 21 dpi


title: A74l3

value: 64-cell stage

value: embryo3/left side


title: F123 GAM library f123_1NP_GAM180117_E04_2_S125_R1_001


title: F123 GAM library f123_1NP_GAM180117_D07_2_S148_R1_001


title: T-ALL Sample 267 [RNA-seq]

description:
TALL267
taken at diagnosis

value: Pediatric T-cell acute lymphoblastic leukemia


title: UW2.2_C_21

value: Leaf petiole


title: A74l2

value: A

value: embryo2/left side


title: UW2.2_C_28

value: Sample collected at 28 dpi


title: UW2.1_C_21


title: F123 GAM library f123_1NP_GAM180117_D06_2_S140_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast


title: T-ALL Sample 266 [RNA-seq]

description:
TALL266
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample


title: T-ALL Sample 265 [RNA-seq]

description:
TALL265
taken at diagnosis

value: CIMP high


title: A73r3


title: F123 GAM library f123_1NP_GAM180117_D10_2_S172_R1_001


title: UW2.2_I_21

value: Inoculation with agar plugs (MYB medium) containing active mycelium of H. fraxinueus strain 7 – RH03-T2-B1-1


title: A73l2


title: UW2.3_I_21


title: F123 GAM library f123_1NP_GAM180117_D05_2_S132_R1_001


title: T-ALL Sample 263 [RNA-seq]

description:
TALL263
taken at diagnosis

value: Tumor

value: CIMP low


title: A73l3


title: T-ALL Sample 264 [RNA-seq]

description:
TALL264
taken at diagnosis


title: F123 GAM library f123_1NP_GAM180117_D04_2_S124_R1_001

value: male


title: UW2.3_C_14

value: Inoculation with sterile agar plugs (MYB medium)

value: Sample collected at 14 dpi


title: F123 GAM library f123_1NP_GAM180117_C12_2_S187_R1_001


title: T-ALL Sample 262 [RNA-seq]

description:
TALL262
taken at diagnosis


title: UW2.1_I_21

value: Sample collected at 21 dpi


title: A72r3

value: 64-cell stage

value: embryo3/right side


title: UW2.1_C_14

value: Leaf petiole


title: F123 GAM library f123_1NP_GAM180117_C11_2_S179_R1_001


title: F123 GAM library f123_1NP_GAM180117_C08_2_S155_R1_001


title: F123 GAM library f123_1NP_GAM180117_C09_2_S163_R1_001


title: A72l3

value: A

value: embryo3/left side


title: F123 GAM library f123_1NP_GAM180117_C07_2_S147_R1_001


title: T-ALL Sample 260 [RNA-seq]

description:
TALL260
taken at diagnosis

value: Pediatric T-cell acute lymphoblastic leukemia


title: UW2.2_C_14


title: A72l2

value: embryo2/left side


title: T-ALL Sample 261 [RNA-seq]

description:
TALL261
taken at diagnosis


title: a66r5

value: 32-cell stage

value: a

value: embryo5/right side


title: T-ALL Sample 258 [RNA-seq]

description:
TALL258
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample

value: CIMP high


title: F123 GAM library f123_1NP_GAM180117_C06_2_S139_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast


title: UW2.2_I_14

value: Inoculation with agar plugs (MYB medium) containing active mycelium of H. fraxinueus strain 7 – RH03-T2-B1-1


title: a66r2

value: embryo2/right side


title: T-ALL Sample 259 [RNA-seq]

description:
TALL259
taken at diagnosis

value: Tumor


title: a66l5

value: embryo5/left side


title: F123 GAM library f123_1NP_GAM180117_C05_2_S131_R1_001

value: male


title: F123 GAM library f123_1NP_GAM180117_C04_2_S123_R1_001


title: a66r1

value: embryo1/right side


title: T-ALL Sample 257 [RNA-seq]

description:
TALL257
taken at diagnosis


title: UW2.1_I_14

value: Leaf petiole

value: Sample collected at 14 dpi


title: F123 GAM library f123_1NP_GAM180117_B12_2_S186_R1_001


title: T-ALL Sample 256 [RNA-seq]

description:
TALL256
taken at diagnosis

value: CIMP low

value: Pediatric T-cell acute lymphoblastic leukemia


title: UW2.3_C_07

value: Inoculation with sterile agar plugs (MYB medium)

value: Sample collected at 7 dpi


title: T-ALL Sample 254 [RNA-seq]

description:
TALL254
taken at diagnosis


title: T-ALL Sample 253 [RNA-seq]

description:
TALL253
taken at diagnosis


title: UW2.4_I_07


title: UW2.2_C_07


title: a66l2

value: 32-cell stage

value: a

value: embryo2/left side


title: a66l3

value: embryo3/left side


title: UW2.3_I_14


title: T-ALL Sample 252 [RNA-seq]

description:
TALL252
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample

value: CIMP high


title: T-ALL Sample 251 [RNA-seq]

description:
TALL251
taken at diagnosis


title: UW2.2_I_07

value: Inoculation with agar plugs (MYB medium) containing active mycelium of H. fraxinueus strain 7 – RH03-T2-B1-1


title: F123 GAM library f123_1NP_GAM180117_B08_2_S154_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast


title: F123 GAM library f123_1NP_GAM180117_B10_2_S170_R1_001

value: male


title: UW2.1_C_07


title: a65r1

value: embryo1/right side


title: F123 GAM library f123_1NP_GAM180117_B11_2_S178_R1_001


title: T-ALL Sample 250 [RNA-seq]

description:
TALL250
taken at diagnosis

value: Tumor


title: T-ALL Sample 248 [RNA-seq]

description:
TALL248
taken at diagnosis


title: UW1.4_C_28

value: Leaf petiole

value: Sample collected at 28 dpi


title: UW2.3_I_07


title: UW1.2_C_28


title: F123 GAM library f123_1NP_GAM180117_B09_2_S162_R1_001


title: a65r2

value: embryo2/right side


title: F123 GAM library f123_1NP_GAM180117_B05_2_S130_R1_001


title: a66l4

value: embryo4/left side


title: a65l5

value: embryo5/left side


title: F123 GAM library f123_1NP_GAM180117_B06_2_S138_R1_001


title: a65l4

value: 32-cell stage


title: T-ALL Sample 243 [RNA-seq]

description:
TALL243
taken at diagnosis

value: CIMP low

value: Pediatric T-cell acute lymphoblastic leukemia


title: T-ALL Sample 244 [RNA-seq]

description:
TALL244
taken at diagnosis


title: UW1.1_C_28

value: Inoculation with sterile agar plugs (MYB medium)


title: F123 GAM library f123_1NP_GAM180117_A12_2_S185_R1_001


title: a65r5

value: a

value: embryo5/right side


title: UW1.3_I_28

value: Inoculation with agar plugs (MYB medium) containing active mycelium of H. fraxinueus strain 7 – RH03-T2-B1-1


title: a53r5

value: 16-cell stage


title: F123 GAM library f123_1NP_GAM180117_B04_2_S122_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast


title: UW1.2_I_28


title: T-ALL Sample 242 [RNA-seq]

description:
TALL242
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample

value: CIMP high


title: a53r6

value: embryo6/right side


title: T-ALL Sample 246 [RNA-seq]

description:
TALL246
taken at diagnosis

value: Tumor


title: T-ALL Sample 238 [RNA-seq]

description:
TALL238
taken at diagnosis


title: UW1.1_I_28

value: Leaf petiole

value: Sample collected at 28 dpi


title: F123 GAM library f123_1NP_GAM180117_A11_2_S177_R1_001

value: male


title: a53r3

value: embryo3/right side


title: T-ALL Sample 237 [RNA-seq]

description:
TALL237
taken at diagnosis


title: F123 GAM library f123_1NP_GAM180117_B07_2_S146_R1_001


title: T-ALL Sample 239 [RNA-seq]

description:
TALL239
taken at diagnosis


title: F123 GAM library f123_1NP_GAM180117_A08_2_S153_R1_001


title: F123 GAM library f123_1NP_GAM180117_A10_2_S169_R1_001


title: UW1.3_C_21

value: Sample collected at 21 dpi


title: UW1.2_C_21


title: F123 GAM library f123_1NP_GAM180117_A07_2_S145_R1_001


title: a53r1

value: embryo1/right side


title: T-ALL Sample 235 [RNA-seq]

description:
TALL235
taken at diagnosis

value: Pediatric T-cell acute lymphoblastic leukemia


title: a53r4

value: a

value: embryo4/right side


title: a65l2

value: 32-cell stage

value: embryo2/left side


title: UW1.4_I_21

value: Inoculation with agar plugs (MYB medium) containing active mycelium of H. fraxinueus strain 7 – RH03-T2-B1-1


title: UW1.1_C_21

value: Inoculation with sterile agar plugs (MYB medium)


title: T-ALL Sample 233 [RNA-seq]

description:
TALL233
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample

value: CIMP low


title: a65l3

value: embryo3/left side


title: F123 GAM library f123_1NP_GAM180117_A06_2_S137_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast


title: UW1.2_I_21

value: Leaf petiole


title: T-ALL Sample 232 [RNA-seq]

description:
TALL232
taken at diagnosis

value: Tumor

value: CIMP high


title: T-ALL Sample 231 [RNA-seq]

description:
TALL231
taken at diagnosis


title: F123 GAM library f123_1NP_GAM180117_A09_2_S161_R1_001

value: male


title: A51r6

value: 16-cell stage

value: A

value: embryo6/right side


title: UW1.1_C_14

value: Sample collected at 14 dpi


title: F123 GAM library f123_1NP_GAM180117_A04_2_S121_R1_001


title: A51r5

value: embryo5/right side


title: T-ALL Sample 230 [RNA-seq]

description:
TALL230
taken at diagnosis

value: Pediatric T-cell acute lymphoblastic leukemia


title: UW1.3_C_14


title: F123 GAM library f123_1NP_GAM180116_H12_1_S96_R1_001


title: A51r4

value: embryo4/right side


title: T-ALL Sample 229 [RNA-seq]

description:
TALL229
taken at diagnosis


title: F123 GAM library f123_1NP_GAM180116_H11_2_S184_R1_001


title: a53l6

value: a

value: embryo6/left side


title: UW1.2_C_14

value: Inoculation with sterile agar plugs (MYB medium)


title: T-ALL Sample 228 [RNA-seq]

description:
TALL228
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample


title: T-ALL Sample 227 [RNA-seq]

description:
TALL227
taken at diagnosis


title: A51l6


title: A51l5

value: embryo5/left side


title: a53l5


title: F123 GAM library f123_1NP_GAM180116_H10_2_S176_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast


title: T-ALL Sample 226 [RNA-seq]

description:
TALL226
taken at diagnosis

value: Tumor


title: F123 GAM library f123_1NP_GAM180116_H11_1_S88_R1_001


title: F123 GAM library f123_1NP_GAM180117_A05_2_S129_R1_001


title: UW1.1_I_21

value: Leaf petiole

value: Inoculation with agar plugs (MYB medium) containing active mycelium of H. fraxinueus strain 7 – RH03-T2-B1-1

value: Sample collected at 21 dpi


title: UW1.3_I_14


title: F123 GAM library f123_1NP_GAM180116_H10_1_S80_R1_001

value: male


title: A51l3

value: 16-cell stage

value: A

value: embryo3/left side


title: UW1.1_I_14

value: Sample collected at 14 dpi


title: F123 GAM library f123_1NP_GAM180116_H08_2_S160_R1_001


title: T-ALL Sample 225 [RNA-seq]

description:
TALL225
taken at diagnosis

value: CIMP high

value: Pediatric T-cell acute lymphoblastic leukemia


title: A62r3

value: 32-cell stage

value: embryo3/right side


title: T-ALL Sample 224 [RNA-seq]

description:
TALL224
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample

value: CIMP low


title: F123 GAM library f123_1NP_GAM180116_H07_2_S152_R1_001

value: mouse embryonic stem cells


title: UW1.2_C_07

value: Inoculation with sterile agar plugs (MYB medium)

value: Sample collected at 7 dpi


title: T-ALL Sample 223 [RNA-seq]

description:
TALL223
taken at diagnosis

value: Tumor


title: T-ALL Sample 222 [RNA-seq]

description:
TALL222
taken at diagnosis


title: A62r2

value: embryo2/right side


title: A51r1

value: embryo1/right side


title: UW1.4_I_14

value: Leaf petiole

value: Inoculation with agar plugs (MYB medium) containing active mycelium of H. fraxinueus strain 7 – RH03-T2-B1-1


title: UW1.1_C_07


title: A62r1

value: A


title: F123 GAM library f123_1NP_GAM180116_H05_2_S136_R1_001

value: Hybrid F1 S129/Jae and Cast

value: male


title: F123 GAM library f123_1NP_GAM180116_H04_2_S128_R1_001


title: A62l3

value: embryo3/left side


title: T-ALL Sample 221 [RNA-seq]

description:
TALL221
taken at diagnosis

value: CIMP high

value: Pediatric T-cell acute lymphoblastic leukemia


title: T-ALL Sample 220 [RNA-seq]

description:
TALL220
taken at diagnosis


title: UW1.3_I_07


title: A62l2

value: 32-cell stage

value: embryo2/left side


title: F123 GAM library f123_1NP_GAM180116_H02_2_S112_R1_001


title: UW1.1_I_07


title: UW1.2_I_07


title: T-ALL Sample 219 [RNA-seq]

description:
TALL219
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample


title: F123 GAM library f123_1NP_GAM180116_H01_2_S104_R1_001

value: mouse embryonic stem cells


title: A62l1

value: embryo1/left side


title: UW1.3_C_07

value: Inoculation with sterile agar plugs (MYB medium)

value: Sample collected at 7 dpi


title: FS36.4_C_28

value: Sample collected at 28 dpi


title: A61r3

value: embryo3/right side


title: T-ALL Sample 218 [RNA-seq]

description:
TALL218
taken at diagnosis

value: Tumor

value: CIMP low


title: FS36.3_C_28

value: Leaf petiole


title: A61r2

value: A

value: embryo2/right side


title: F123 GAM library f123_1NP_GAM180116_G12_1_S95_R1_001

value: Hybrid F1 S129/Jae and Cast

value: male


title: T-ALL Sample 217 [RNA-seq]

description:
TALL217
taken at diagnosis

value: CIMP high

value: Pediatric T-cell acute lymphoblastic leukemia


title: F123 GAM library f123_1NP_GAM180116_G11_2_S183_R1_001


title: T-ALL Sample 216 [RNA-seq]

description:
TALL216
taken at diagnosis


title: A61r1

value: 32-cell stage

value: embryo1/right side


title: F123 GAM library f123_1NP_GAM180116_G11_1_S87_R1_001

value: mouse embryonic stem cells


title: T-ALL Sample 215 [RNA-seq]

description:
TALL215
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample


title: FS36.4_I_28

value: Inoculation with agar plugs (MYB medium) containing active mycelium of H. fraxinueus strain 7 – RH03-T2-B1-1


title: F123 GAM library f123_1NP_GAM180116_G10_2_S175_R1_001


title: A61l3

value: embryo3/left side


title: F123 GAM library f123_1NP_GAM180116_H03_2_S120_R1_001


title: FS36.1_C_28

value: Inoculation with sterile agar plugs (MYB medium)

value: Sample collected at 28 dpi


title: FS36.2_I_28


title: T-ALL Sample 214 [RNA-seq]

description:
TALL214
taken at diagnosis

value: Tumor


title: A61l2

value: embryo2/left side


title: FS36.1_I_28

value: Leaf petiole


title: F123 GAM library f123_1NP_GAM180116_G10_1_S79_R1_001


title: T-ALL Sample 213 [RNA-seq]

description:
TALL213
taken at diagnosis

value: CIMP low


title: F123 GAM library f123_1NP_GAM180116_G09_2_S167_R1_001


title: A61l1

value: A

value: embryo1/left side


title: FS36.3_C_21

value: Sample collected at 21 dpi


title: T-ALL Sample 212 [RNA-seq]

description:
TALL212
taken at diagnosis

value: CIMP high


title: F123 GAM library f123_1NP_GAM180116_G08_2_S159_R1_001

value: Hybrid F1 S129/Jae and Cast

value: male


title: pad4_mock_2

city: shang hai

first: hua

last: yu

state: FengLin

country: China

institute: CAS Center for Excellence in Molecular Plant Sciences

data_processing:
CLC Genomics Workbench v11.0.1
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.The clean  reads were mapped to the  Arabidopsis thaliana genome using HISAT. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: TAIR10.1
Supplementary files format and content: tab-delimited text files include FPKM, count values for each Sample

organism: Arabidopsis thaliana

source_name: rosette leaf

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA). 1.3 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer's protocols

value: rosette leaf

value: PAD4 Knock out


title: T-ALL Sample 210 [RNA-seq]

description:
TALL210
taken at diagnosis

value: T-ALL bone marrow/peripheral blood sample

value: Pediatric T-cell acute lymphoblastic leukemia


title: FS36.2_C_21


title: pad4_mock_1


title: FS36.3_I_21

value: Inoculation with agar plugs (MYB medium) containing active mycelium of H. fraxinueus strain 7 – RH03-T2-B1-1


title: F123 GAM library f123_1NP_GAM180116_G06_2_S143_R1_001

value: mouse embryonic stem cells


title: FS36.1_C_21

value: Inoculation with sterile agar plugs (MYB medium)


title: T-ALL Sample 209 [RNA-seq]

description:
TALL209
taken at diagnosis

value: Tumor


title: FS36.2_I_21


title: F123 GAM library f123_1NP_GAM180116_G05_2_S135_R1_001


title: F123 GAM library f123_1NP_GAM180116_G07_2_S151_R1_001


title: pad4_2_3


title: FS36.1_I_21


title: T-ALL Sample 207 [RNA-seq]

description:
TALL207
taken at diagnosis


title: T-ALL Sample 208 [RNA-seq]

description:
TALL208
taken at diagnosis


title: pad4_2_2


title: FS36.3_C_14

value: Sample collected at 14 dpi


title: F123 GAM library f123_1NP_GAM180116_G03_2_S119_R1_001


title: F123 GAM library f123_1NP_GAM180116_G04_2_S127_R1_001


title: pad4_mock_3


title: T-ALL Sample 206 [RNA-seq]

description:
TALL206
taken at diagnosis


title: T-ALL Sample 211 [RNA-seq]

description:
TALL211
taken at diagnosis


title: F123 GAM library f123_1NP_GAM180116_G01_2_S103_R1_001


title: WT_mock_3

value: Wild type


title: F123 GAM library f123_1NP_GAM180116_G02_2_S111_R1_001


title: WT_mock_2


title: FS36.2_C_14

value: Leaf petiole


title: T-ALL Sample 205 [RNA-seq]

description:
TALL205
taken at diagnosis

value: CIMP low


title: FS36.1_C_14


title: T-ALL Sample 204 [RNA-seq]

description:
TALL204
taken at diagnosis


title: WT_mock_1


title: T-ALL Sample 203 [RNA-seq]

description:
TALL203
taken at diagnosis


title: FS36.2_I_14


title: WT_2_3


title: F123 GAM library f123_1NP_GAM180116_F11_2_S182_R1_001


title: F123 GAM library f123_1NP_GAM180116_F12_1_S94_R1_001


title: FS36.4_I_14


title: T-ALL Sample 202 [RNA-seq]

description:
TALL202
taken at diagnosis


title: pad4_2_1


title: WT_2_2


title: T-ALL Sample 201 [RNA-seq]

description:
TALL201
taken at diagnosis


title: FS36.1_I_14


title: WT_2_1


title: FS36.3_C_07

value: Sample collected at 7 dpi


title: F123 GAM library f123_1NP_GAM180116_F11_1_S86_R1_001


title: COiMg_MSN9_B1_ctrl_biol rep 4

city: NEW YORK

first: Alice

last: Buonfiglioli

state: NY

address: 1468 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw fastq files were processed using then nextflow RAPiD pipeline.
Count files were processed in R.
Graphs were made with ggplot2.
Assembly: GRCh38.Gencode.v30
Supplementary files format and content: RData objects containing the raw counts of each sample.

source_name: cerebral organoids

growth_protocol: cerebral organoids mantained in Maturation Media (Stem Cell Technologies) in humified atmosphere with 5% CO2 at 37C.

extract_protocol:
mechanical dissociation of the tissue and RNA extraction by using the miRNeasy Micro kit (Qiagen).
Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit.

treatment_protocol: Treatment was done for 48h

value: cerebral organoids

tag: time

tag: condition

value: COiMg

value: ctrl


title: COiMg_MSN9_B1_LPS_biol rep 4

value: LPS


title: HCC-4 (RNA-seq 2)

city: Nanning

first: Xiaoke

last: Ran

address: Wuhe Avenue

institute: Guangxi University of Chinese Medicine

data_processing:
The quality and quantity of the constructed sequencing library were assessed using the Bio Analyzer 2100 system (Agilent Technologies, USA)
mRNA sequences were aligned to the reference genome using hisat2 software (v2.0.4).
HTSeq software (v0.9.1) was used to obtain gene-level raw counts, generating mRNA expression profiles.
The data was then standardized, and multiple changes and p-values between the two sample groups were calculated using edgeR software (v3.16.5) to identify differentially expressed mRNA.
The annotated differential genes were subjected to Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses.
Assembly: hg19
Supplementary files format and content: excel format

source_name: Blood

extract_protocol:
GenSeq®rRNA Removal Kit was used to eliminate ribosomal RNA (rRNA) from the sample in accordance with the instruction of the supplier.
After rRNA removal, GenSeq® LowInputRNA Library PrepKit was used to construct a sequencing library according to the provided instructions.

value: Blood

tag: disease state

value: HCC


title: F123 GAM library f123_1NP_GAM180116_F09_2_S166_R1_001

value: Hybrid F1 S129/Jae and Cast

value: male


title: HCC-5 (RNA-seq 2)


title: F123 GAM library f123_1NP_GAM180116_F08_2_S158_R1_001


title: FS36.1_C_07


title: FS36.2_C_07


title: HCC-3 (RNA-seq 2)


title: F123 GAM library f123_1NP_GAM180116_F07_2_S150_R1_001


title: FS36.3_I_07

value: Inoculation with agar plugs (MYB medium) containing active mycelium of H. fraxinueus strain 7 – RH03-T2-B1-1


title: CO_MSN9 B2_IFNg_biol rep 2

value: CO

value: IFng


title: F123 GAM library f123_1NP_GAM180116_F06_2_S142_R1_001

value: mouse embryonic stem cells


title: FS36.2_I_07


title: HCC-1 (RNA-seq 2)


title: CO_MSN9 B2_IFNg_biol rep 1

value: IFNg


title: HCC-2 (RNA-seq 2)


title: F123 GAM library f123_1NP_GAM180116_F04_2_S126_R1_001


title: LC-5 (RNA-seq 2)

value: LC


title: F123 GAM library f123_1NP_GAM180116_F05_2_S134_R1_001


title: CO_MSN9 B2_LPS_biol rep 2


title: LC-4 (RNA-seq 2)


title: FS36.1_I_07

value: Leaf petiole


title: F123 GAM library f123_1NP_GAM180116_F10_1_S78_R1_001


title: F123 GAM library f123_1NP_GAM180116_F03_2_S118_R1_001


title: FAR3.3_C_28

value: Inoculation with sterile agar plugs (MYB medium)

value: Sample collected at 28 dpi


title: CO_MSN9 B2_LPS_biol rep 3

value: cerebral organoids


title: CO_MSN9 B2_ctrl_biol rep 2


title: CO_MSN9 B2_IFNg_biol rep 3


title: FAR3.2_C_28


title: F123 GAM library f123_1NP_GAM180116_F02_2_S110_R1_001


title: COiMg_MSN9 B2_IFNg_biol rep 2

value: COiMg


title: FAR3.4_I_28


title: LC-2 (RNA-seq 2)


title: COiMg_MSN9 B2_IFNg_biol rep 1


title: LC-3 (RNA-seq 2)


title: LC-1 (RNA-seq 2)


title: F123 GAM library f123_1NP_GAM180116_F01_2_S102_R1_001


title: COiMg_MSN9 B2_LPS_biol rep 3


title: F123 GAM library f123_1NP_GAM180116_E12_1_S93_R1_001


title: FAR3.3_I_28


title: COiMg_MSN9 B2_LPS_biol rep 2


title: F123 GAM library f123_1NP_GAM180116_E11_2_S181_R1_001


title: FAR3.4_C_28


title: LC-4 (RNA-seq)


title: F123 GAM library f123_1NP_GAM180116_E11_1_S85_R1_001


title: FAR3.4_C_21

value: Sample collected at 21 dpi


title: LC-3 (RNA-seq)


title: F123 GAM library f123_1NP_GAM180116_E10_1_S77_R1_001


title: FAR3.2_C_21


title: COiMg_MSN9 B2_ctrl_biol rep 2

value: ctrl


title: F123 GAM library f123_1NP_GAM180116_E09_2_S165_R1_001


title: LC-2 (RNA-seq)

value: Blood


title: CO_MSN9_B1_LPS_biol rep 1

value: LPS


title: LC-1 (RNA-seq)


title: FAR3.1_C_21


title: F123 GAM library f123_1NP_GAM180116_E08_2_S157_R1_001

value: Hybrid F1 S129/Jae and Cast


title: CO_MSN9_B1_ctrl_biol rep 1


title: CHB-5 (RNA-seq)

value: CHB


title: FAR3.2_I_21

value: Inoculation with agar plugs (MYB medium) containing active mycelium of H. fraxinueus strain 7 – RH03-T2-B1-1


title: LC-5 (RNA-seq)


title: F123 GAM library f123_1NP_GAM180116_E06_2_S141_R1_001

value: male


title: COiMg_MSN9_B1_LPS_biol rep 1

value: CO


title: FAR3.2_I_28


title: FAR3.1_I_21


title: CHB-3 (RNA-seq)


title: COiMg_MSN9_B1_ctrl_biol rep 1


title: B9_COiMg_ LPS_biol rep 3


title: CHB-2 (RNA-seq)


title: COiMg_MSN9 B2_ctrl_biol rep 3


title: F123 GAM library f123_1NP_GAM180116_E04_2_S125_R1_001

value: mouse embryonic stem cells


title: FAR3.2_C_14

value: Sample collected at 14 dpi


title: CHB-1 (RNA-seq)


title: B5_CO_LPS_biol rep 3


title: FAR3.1_C_14


title: F123 GAM library f123_1NP_GAM180116_E03_2_S117_R1_001


title: FAR3.3_I_21


title: FAR3.3_I_14


title: SNU638 cell, YTHDF1, IFN-γ, biol rep 2

city: Seoul

first: Dongjun

last: Jang

address: 103 Daehak-ro (Yeongeon-dong), Jongno-gu

country: South Korea

institute: Seoul National University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic program
Trimmed sequence reads were mapped to GRCh38 using HISAT2 program.
Read count extraction and normalization were performed using String Tie program
Assembly: GRCh38
Supplementary files format and content: Tab-separated text files includes read counts for each sample

source_name: Stomach

growth_protocol: SNU638 cells were maintained in RPMI supplemented with 10 % fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5 % CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy Plus Mini Kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer’s protocols

treatment_protocol: SNU638 cells were preincubated in serum free medium for 24 hour and treated with 10 ng/ml IFN-γ for 8 h

value: Stomach

value: Gastric cancer cell

value: YTHDF1 overexpression

value: IFN-gamma


title: F123 GAM library f123_1NP_GAM180116_E07_2_S149_R1_001


title: F123 GAM library f123_1NP_GAM180116_E02_2_S109_R1_001


title: SNU638 cell, YTHDF1, IFN-γ, biol rep 1


title: F123 GAM library f123_1NP_GAM180116_E01_2_S101_R1_001


title: CHB-4 (RNA-seq)


title: B5_CO_ctrl_biol rep 3

value: cerebral organoids


title: SNU638 cell, Control, IFN-γ, biol rep 2

value: Control


title: FAR3.1_I_14

value: Leaf petiole


title: FAR3.2_I_14


title: F123 GAM library f123_1NP_GAM180116_E05_2_S133_R1_001


title: FAR3.3_C_14

value: Inoculation with sterile agar plugs (MYB medium)


title: B5_COiMg_IFNg_biol rep 3

value: COiMg

value: IFNg


title: F123 GAM library f123_1NP_GAM180116_D12_1_S92_R1_001

value: Hybrid F1 S129/Jae and Cast


title: F123 GAM library f123_1NP_GAM180116_D11_2_S180_R1_001


title: B5_COiMg_ctrl_biol rep 3

value: ctrl


title: FAR3.3_C_07

value: Sample collected at 7 dpi


title: B5_COiMg_LPS_biol rep 3

value: LPS


title: B5_CO_IFNg_biol rep 3

value: CO


title: MCF10CA1a cell, GPS

city: Shanghai

first: Baolong

last: Zhang

state: 上海市 — Shanghai Shi

address: 138 Yixueyuan Road, Xuhui District, Shanghai

institute: Fudan University

data_processing:
*library strategy: guide positioning sequencing (GPS)
The data quality was initially assessed using FastQC, followed by filtering and adapter sequence removal using the NGS QC Toolkit. To enhance genomic alignment efficiency, duplication was removed. Subsequently, bowtie2 and sw7.0 were employed for R2 single-end mapping and R1 positioning, respectively, using the hg19 (GRCh37) genome as a reference. To maintain the accuracy of GPS methylation levels, trim over-cut R1 and under-cut R2 resulting from T4 DNA polymerase digestion. For precious calculations of DNA methylation, only CpG sites with a coverage ≥ 5× were considered. The methylation level at each cytosine position was calculated by dividing the number of 'Cs' by the total count of 'Cs' and 'Ts' at the corresponding position in the reference genome, and then converted into a bedGraph matrix and reformatted into the bigWig file format.
Assembly: hg19
Supplementary files format and content: bedGraph, methylation level for each cytosine
Supplementary files format and content: bw,each cytosine methylation level

growth_protocol: MCF10A, MCF10AT, MCF10CA1h, and MCF10CA1a were maintained in DMEM/F-12 (1:1) medium supplemented with 5% horse serum, 100 ng/mL cholera toxin from Vibrio cholerae, 10 μg/mL insulin, 20 ng/mL human EGF, and 0.5 μg/mL hydrocortisone. All cells were cultured in a cell culture incubator maintained at 5% CO2 and 37 °C.

extract_protocol:
The methods of phenol-chloroform was employed for the extraction of DNA. Approximately 460 μL of nuclear lysis buffer was added to 1.5 mL tubes containing up to 107 cells. The cell suspension was mixed with 20 μL of proteinase K and 20 μL of SDS (10%) and incubated at 58 °C overnight for digestion. The following day, 5 μL of RNAse A was added, and the mixture was incubated at 37 °C for 2 h. Subsequently, 500 μL of phenol-chloroform (pH > 7.8) was used for phase separation, and the upper aqueous phase was extracted. DNA precipitation was achieved by adding an equal volume of isopropanol and 1/10 volume of sodium acetate (3M; pH 5.2). After washing and air-drying, the DNA pellet was dissolved in preheated ddH2O.
For GPS libraries construction, 0.5–1 μg of input DNA was taken, and 0.1% (wt/wt) unmethylated lambda DNA was added as an internal spike-in for calculating bisulfite treatment efficiency. Genomic DNA was sonicated using a sonicator to generate fragments with a peak range of 300–350 bp. The fragmented DNA underwent end repair, proteinase K digestion, removal of dNTPs in the 3'→5' direction at 12 °C, and incorporation of 5-methyl-dCTP at 37 °C using T4 DNA polymerase. Subsequently, A-tailing, ligation of pre-prepared methylated adapters, and bisulfite conversion were performed, followed by a 12-cycle library pre-amplification using KAPA HiFi HotStart Uracil+ ReadyMix. The final library was double size-selected for an average size of 400–500 bp using 0.55/0.2 ratio of VAHTS DNA Clean Beads. The elution was performed in 22.5 μL nuclease-free water.

value: High-grade metastatic breast cancer cells

value: Poor differentiation

value: DMEM/F-12 (1:1) medium with 5% horse serum, 100 ng/mL cholera toxin from Vibrio cholerae, 10 μg/mL insulin, 20 ng/mL human EGF, and 0.5 μg/mL hydrocortisone

tag: library type

value: guide positioning sequencing (GPS)


title: SNU638 cell, Control, IFN-γ, biol rep 1

tag: tissue

value: Stomach

value: Gastric cancer cell


title: F123 GAM library f123_1NP_GAM180116_D11_1_S84_R1_001

value: mouse embryonic stem cells

value: male


title: FAR3.2_C_07

value: Leaf petiole


title: B4_CO_IFNg_biol rep 2

value: cerebral organoids


title: F123 GAM library f123_1NP_GAM180116_D10_1_S76_R1_001


title: MCF10CA1h cell, GPS

value: Low-grade metastatic breast cancer cells

value: Well differentiation


title: FAR3.1_C_07

value: Inoculation with sterile agar plugs (MYB medium)


title: B4_CO_LPS_biol rep 2


title: MCF10AT cell, GPS

value: Premalignant breast cells

value: Precancerous Lesion


title: F123 GAM library f123_1NP_GAM180116_D09_2_S164_R1_001

value: Hybrid F1 S129/Jae and Cast


title: FAR3.3_I_07

value: Inoculation with agar plugs (MYB medium) containing active mycelium of H. fraxinueus strain 7 – RH03-T2-B1-1

value: Sample collected at 7 dpi


title: B4_CO_ctrl_biol rep 2

value: CO

value: ctrl


title: F123 GAM library f123_1NP_GAM180116_D08_2_S156_R1_001


title: B4_COiMg_IFNg_biol rep 2

value: COiMg

value: IFNg


title: ENZR-C4-2B-2

city: Xuzhou

first: Xiannan

last: Meng

address: Tongshan Road

institute: Xuzhou Medical University

data_processing:
The Clean Data is abotained after filtering, and statistics analyses are performed on its quantity and quality, including Q30 statistics, data quantity statistics, base content statistics, etc.
And Clean Data were mapped to the reference genome using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml).
Read Count for each gene in each sample is counted by HTSeq, and FPKM (Fragments Per Kilobase Millon Mapped Reads) were then calculated to represent the expression level of genes in each sample.
Assembly: hg38
Supplementary files format and content: cut adaptor
Supplementary files format and content: cut adaptor

extract_protocol:
Total RNA extraction were used TRIzol reagent, total RNAs underwent treatment with a ribo-zero kit and RNase R to eliminate ribosomal RNA and linear RNA, respectively.
cDNA library was constructed, validated using an Agilent 2100 Bioanalyzer

value: Epithelioid cells

value: Enzalutamide Resistant C4-2B


title: F123 GAM library f123_1NP_GAM180116_D07_2_S148_R1_001

value: mouse embryonic stem cells

value: male


title: FAR3.1_I_07

value: Leaf petiole


title: FAR3.2_I_07


title: F123 GAM library f123_1NP_GAM180116_D06_2_S140_R1_001


title: MCF10A cell, GPS

value: Normal breast epithelial cells

value: Normal

value: DMEM/F-12 (1:1) medium with 5% horse serum, 100 ng/mL cholera toxin from Vibrio cholerae, 10 μg/mL insulin, 20 ng/mL human EGF, and 0.5 μg/mL hydrocortisone

value: guide positioning sequencing (GPS)


title: ENZR-C4-2B-1


title: B4_COiMg_ctrl_biol rep 2

value: cerebral organoids


title: Trichophyton mentagrophytes (XM109), control, biological replicates 3

city: Nanchang

first: Suqing

last: Yang

address: Nanchang

institute: Jiangxi Provincial People's Hospital (the First Affiliated Hospital of Nanchang Medical College)

description: Library name: XM109-KB3

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by StringTie (v2.1.2).
Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: GCA_003118255.1
Supplementary files format and content: tab-delimited txt file includes fpkm values for each sample
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

organism: Trichophyton mentagrophytes

source_name: spores

growth_protocol: The fungal strain of T. mentagrophytes used for RNA isolation was cultured on SDA for 2 weeks, and then spores were harvested from sporulating colonies and suspended in sterile 0.85% NaCl solution containing 1% Tween-20. The concentrations of spores of the final working suspension were determined and adjusted to the inoculum of 5×103 CFU/mL with RPMI-1640 medium using a hemocytometer.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
After the total RNA passed quality inspection, the magnetic beads connected to Oligo (dT) were used to enrich the eukaryotic messenger RNA (mRNA). The extracted mRNA was randomly interrupted into short fragments by RNA fragmentation buffer. Using fragmented mRNA as a template, a single-stranded complementary DNA (cDNA) was synthesized using random hexamers with 6 bases. Then buffer, dNTPs, RNaseH, and DNA polymerase I (Pol I) were added for double-strand cDNA synthesis. Hieff NGS®DNA Selection Beads were used to purify double-strand products and perform fragment selection. Finally, PCR amplification was performed to obtain the final sequencing library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on DNBSEQ-T7 platform at Tsingke Biotechnology Co., Ltd..

treatment_protocol: The experimental samples were divided into 2 groups: (1) the HQD-treatment group (three biological replicated samples: XM109-HQD1, XM109-HQD2, XM109-HQD3) fed with HQD at a concentration of MIC (3.13 mg/mL) ; (2) the control group (three biological replicated samples: XM109-KB1, XM109-KB2, XM109-KB3) treated with blank SDB without drugs. After 5 days of treatment and incubation at 28°C, the seeds were filtered with gauze and frozen for RNA isolation and further analysis.

value: spores

value: blank SDB without drugs


title: Trichophyton mentagrophytes (XM109), control, biological replicates 2

description: Library name: XM109-KB2


title: B2_CO_IFNg_biol rep 1


title: C4-2B-1

value: WT


title: Trichophyton mentagrophytes (XM109), control, biological replicates 1

description: Library name: XM109-KB1


title: F123 GAM library f123_1NP_GAM180116_D04_2_S124_R1_001

value: Hybrid F1 S129/Jae and Cast


title: B2_CO_LPS_biol rep 1

value: CO

value: LPS


title: C4-2B-2


title: F123 GAM library f123_1NP_GAM180116_D05_2_S132_R1_001


title: HeLa, Vehicle

city: Taipei

first: Zih-Syuan

last: Wu

address: No.161, Minquan E. Road 6th Sec., Neihu dist.

department: Biochemistry

country: Taiwan

institute: National Defense Medical Center

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data. Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1). In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

molecule: polyA RNA

source_name: Uterus; Cervix

extract_protocol:
RNA was extracted using RNeasy Mini Kit_QIAGEN.
Libraries for polyA+ RNA-Sequencing were prepared from 1 μg RNA per sample using NovaSeq 6000 (Illumina)

value: Uterus; Cervix

value: HeLa

value: epithelial cell


title: F123 GAM library f123_1NP_GAM180116_D03_2_S116_R1_001

value: mouse embryonic stem cells


title: Trichophyton mentagrophytes (XM109), HQD-treatment, biological replicates 3

description: Library name: XM109-HQD3

value: HQD


title: B2_CO_ctrl_biol rep 1

value: ctrl


title: HeLa, Formo


title: Trichophyton mentagrophytes (XM109), HQD-treatment, biological replicates 2

description: Library name: XM109-HQD2


title: B2_COiMg_IFNg_biol rep 1

value: COiMg

value: IFNg


title: F123 GAM library f123_1NP_GAM180116_D02_2_S108_R1_001

value: male


title: HeLa, Formo-Caf


title: F123 GAM library f123_1NP_GAM180116_D01_2_S100_R1_001


title: Trichophyton mentagrophytes (XM109), HQD-treatment, biological replicates 1

description: Library name: XM109-HQD1


title: B4_COiMg_LPS_biol rep 2


title: B2_COiMg_LPS_biol rep 1


title: F123 GAM library f123_1NP_GAM180116_C12_1_S91_R1_001


title: PBMC from BatchD (9 hashed donors, chip2 lane8) during ART, HTO

city: Silver Spring

first: Rasmi

last: Thomas

state: MD

address: 503 Robert Grant Avenue

department: MHRP

institute: Walter Reed Army Institute of Research

description:
HTO library: R1 contains cell barcode and UMI; R2 contains Hashtag Antibody Derived Tag reads
BatchD_Lane8_barcodes.tsv.gz
BatchD_Lane8_features.tsv.gz
BatchD_Lane8_matrix.mtx.gz

library_source: other

data_processing:
Sequencing reads were generated from bcl files using cellranger mkfastq
Matched gene expression and HTO libraries for each chip well from both sequencing runs at a time were aligned to the Homo sapiens genome (GRCh38; Ensembl annotation 93) using cellranger count v3.1.0
Gene expression and HTO counts per cell barcode were quantified using cellranger count v3.1.0
Assembly: GRCh38
Supplementary files format and content: Processed files are gzipped barcode/features/matrix files that include raw gene expression and HTO counts
Library strategy: CITE-seq

molecule: protein

source_name: PBMC

extract_protocol:
PBMC from 38 participants were washed then individually hashed with TotalSeq-C anti-human hashtag antibodies (BioLegend). Uniquely-hashed participant PBMC were pooled into 4 batches of 9 or 10 participants and cells from each batch were loaded into 4 different wells of a Chromium chip (10x Genomics), with targeted recoveries of 16,000 cells/well, for subsequent library construction.
Library constructions were processed for CITE-seq using the Chromium Next GEM 5’ Single Cell V(D)J Reagent Kit with Feature Barcode v1.1 (10x Genomics) per manufacturer’s instructions.

value: PBMC

value: HTO

tag: hto

value: TotalSeq-C0251 anti-human Hashtag 1, TotalSeq-C0252 anti-human Hashtag 2, TotalSeq-C0253 anti-human Hashtag 3, TotalSeq-C0254 anti-human Hashtag 4, TotalSeq-C0255 anti-human Hashtag 5, TotalSeq-C0256 anti-human Hashtag 6, TotalSeq-C0257 anti-human Hashtag 7, TotalSeq-C0258 anti-human Hashtag 8, TotalSeq-C0259 anti-human Hashtag 9


title: RNA-seq of D. radiodurans dr_0199 deletion mutant -Replicate 3

city: Wuhan

first: binguang

last: ma

address: No.1,Shizishan Street, Hongshan

institute: Huazhong Agricultural University

description:
dr0199C
gene_count_matrix.csv
gene_fpkm_matrix.csv

data_processing:
Raw data (raw reads) of fastq format were firstly processed through Trimmomatic v0.39 software. Clean data (clean reads) were obtained by removing reads containing low quality reads from raw data.
Reference genome and gene annotation files were downloaded from genome website directly (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000008565.1/). Both building index of reference genome and aligning clean reads to reference genome were used Hisat2-2.2.1.
StringTie v2.1.7 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DEGSeq R package.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented on the website (http://geneontology.org/). Clusterprofiler R package was used to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: Deinococcus radioduransR1. NCBI RefSeq assembly: GCF_000008565.1
Supplementary files format and content: comma-delimited csv file including raw counts for each sample
Supplementary files format and content: comma-delimited csv file including FPKM values for each sample

organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

source_name: bacterial cell

growth_protocol: D. radiodurans cells were grown at 30°C in tryptone glucose yeast extract (TGY) liquid media (0.5% tryptone, 0.1% glucose, and 0.3% yeast extract).

extract_protocol:
Strains were harvested, frozen using liquid nitrogen, and RNA was isolated using Trizol reagent.
RNA libraries were prepared for sequencing using standard BGI protocols.

treatment_protocol: The cultures were grown to OD600 ~= 3.0 (middle exponential).

tag: strain

value: bacterial cell

value: dr_0199 deletion mutant


title: PBMC from BatchD (9 hashed donors, chip2 lane8) during ART, GEX

description:
GEX (5' mRNA) library: R1 contains cell barcode and UMI; R2 contains transcript
BatchD_Lane8_barcodes.tsv.gz
BatchD_Lane8_features.tsv.gz
BatchD_Lane8_matrix.mtx.gz

value: mRNA


title: F123 GAM library f123_1NP_GAM180116_C11_2_S179_R1_001

value: Hybrid F1 S129/Jae and Cast


title: RNA-seq of D. radiodurans dr_0199 deletion mutant -Replicate 2

description:
dr0199B
gene_count_matrix.csv
gene_fpkm_matrix.csv


title: PBMC from BatchD (9 hashed donors, chip2 lane6) during ART, HTO

description:
HTO library: R1 contains cell barcode and UMI; R2 contains Hashtag Antibody Derived Tag reads
BatchD_Lane6_barcodes.tsv.gz
BatchD_Lane6_features.tsv.gz
BatchD_Lane6_matrix.mtx.gz


title: F123 GAM library f123_1NP_GAM180116_C11_1_S83_R1_001


title: RNA-seq of D. radiodurans dr_0199 deletion mutant -Replicate 1

description:
dr0199A
gene_count_matrix.csv
gene_fpkm_matrix.csv


title: PBMC from BatchD (9 hashed donors, chip2 lane6) during ART, GEX

description:
GEX (5' mRNA) library: R1 contains cell barcode and UMI; R2 contains transcript
BatchD_Lane6_barcodes.tsv.gz
BatchD_Lane6_features.tsv.gz
BatchD_Lane6_matrix.mtx.gz


title: B11_CO_IFNg_biol rep 2

value: cerebral organoids

value: CO


title: PBMC from BatchD (9 hashed donors, chip2 lane4) during ART, HTO

description:
HTO library: R1 contains cell barcode and UMI; R2 contains Hashtag Antibody Derived Tag reads
BatchD_Lane4_barcodes.tsv.gz
BatchD_Lane4_features.tsv.gz
BatchD_Lane4_matrix.mtx.gz


title: F123 GAM library f123_1NP_GAM180116_C09_2_S163_R1_001


title: RNA-seq of D. radiodurans wt cells -Replicate 2

description:
DRB
gene_count_matrix.csv
gene_fpkm_matrix.csv

value: WT


title: RNA-seq of D. radiodurans wt cells -Replicate 3

description:
DRC
gene_count_matrix.csv
gene_fpkm_matrix.csv


title: B8_CO_IFNg_biol rep 1


title: B9_COiMg_ IFNg_biol rep 3


title: RNA-seq of D. radiodurans wt cells -Replicate 1

description:
DRA
gene_count_matrix.csv
gene_fpkm_matrix.csv


title: 3C-seq of D. radiodurans dr_0199 deletion mutant -Replicate 2

data_processing:
3C-seq libraries were proccessed using the 3C-seq pipeline available at (https://github.com/koszullab/).
Iterative alignment, Min-leght=20, step=5, bowtie2 --very-sensitive
Filtering, Mapping quality=30, no ambiguous reads. Assignment to restriction fragment.
Removal of un-informative events (uncuts, loops etc) as described in Lioy et al. Cell 2018.
Binning at 5kb.
Assembly: Deinococcus radioduransR1. NCBI RefSeq assembly: GCF_000008565.1
Supplementary files format and content: raw contact matrices (2D array of 659 5kb-bins x 659 5kb-bins).
Supplementary files format and content: normalized contact matrices through the sequential component normalization procedure
Library strategy: 3C-seq

organism: Deinococcus radiodurans

source_name: bacteria

growth_protocol: D. radiodurans cells were grown at 30°C in tryptone glucose yeast extract (TGY) liquid media or on agar plates (0.5% tryptone, 0.1% glucose, and 0.3% yeast extract). The cultures were grown to OD600 ~= 3.0 (middle exponential).

extract_protocol:
To fix DNA-DNA contacts, 1-2 x 109 cell culture were collected by centrifugation and mixed with fresh formaldehyde for 30 minutes at 25C (7% final concentration) followed by 30 minutes at 4°C. Formaldehyde was then quenched with a final concentration of 0.25 M glycine for 20 minutes at 4°C. Fixed cells were collected by centrifugation and washed once with double distilled water. The cell pellets by liquid nitrogen flash freezer were stored at −80°C until use. Frozen pellets were thawed in the ice box, resuspended and lysed by incubation with lysozyme at 37°C for 30 min. The reaction was quenched by adding 10% SDS and incubating for 5 min at 65°C. 50 μL of lysed cells were then transferred in one EP tube containing 450 μL of digestion mix (355 μL of double distilled water, 50 μL of 10 × rCutSmart™ Buffer, 25 μL of 25% Triton X-100, and 20 μL of 10 U/μL HpaII enzyme). DNA was digested for 10 hours at 37°C with shaking at 200 rpm/min. For ligation, the reaction was mixed with 7945 μL of double distilled water, 1000 μL of 10 × T4 DNA Ligase Reaction Buffer (NEB), 50 μL of 20 mg/mL BSA (TaKaRa), 500 μL of 20% Triton X-100, and 5 μL of 400 U/μl T4 DNA ligase (NEB). The ligation reaction was incubated for 4 h at 16°C with occasional inversion of the tube (every 1 h). After the ligation was completed, the reaction was mixed with 100 μL of 0.5 M EDTA and 50 μL of 20 mg/ml proteinase K (TransGen) and incubated at 58°C for 4 h. Precipitation of DNA was performed by standing overnight at 4°C in presence of 3 M Na-Acetate (pH 5.2) and iso-propanol. The following day, the DNA was extracted through using DNA Extraction Reagent (SOLARBIO). The obtained DNA was washed with 500 μL 75% cold ethanol, dissolved in 40 μl 1 × TE buffer containing 0.1 mg/ml RNase A and incubated for 30 min at 37°C. Successful proximity ligation was confirmed by running 5 μL of the DNA on a gel.
The resulting DNA was andomly fragmented, followed by end repair and addition of an 'A' base at the 3' end. After ligating the adapters, PCR amplification was performed for each library. The PCR products were then purified, circularized into single-stranded templates, and subjected to paired-end sequencing on the BGI DNBSEQ platform.

treatment_protocol: For ultraviolet irradiation, the bacterial solution under normal culture condition was irradiated with 2.5J/(m2·s) UV (254 nm) for 5 min (namely, irradiation dose of 750J/m2) and sampled 10 min later.

value: bacteria

value: normal


title: PBMC from BatchD (9 hashed donors, chip2 lane2) during ART, HTO

description:
HTO library: R1 contains cell barcode and UMI; R2 contains Hashtag Antibody Derived Tag reads
BatchD_Lane2_barcodes.tsv.gz
BatchD_Lane2_features.tsv.gz
BatchD_Lane2_matrix.mtx.gz


title: F123 GAM library f123_1NP_GAM180116_C07_2_S147_R1_001

value: mouse embryonic stem cells


title: F123 GAM library f123_1NP_GAM180116_C08_2_S155_R1_001


title: B2_COiMg_ctrl_biol rep 1

value: ctrl


title: B8_COiMg_IFNg_biol rep 2

value: COiMg


title: B7_COiMg_IFNg_biol rep 1

value: IFNg


title: F123 GAM library f123_1NP_GAM180116_C06_2_S139_R1_001

value: male


title: 3C-seq of D. radiodurans dr_0199 deletion mutant -Replicate 1


title: 3C-seq of D. radiodurans cells after ultraviolet irradiation -Replicate 2

value: ultraviolet irradiation


title: F123 GAM library f123_1NP_GAM180116_C05_2_S131_R1_001


title: B11_CO_IFNg_biol rep 3


title: B8_CO_LPS_biol rep 3

value: LPS


title: PBMC from BatchD (9 hashed donors, chip2 lane2) during ART, GEX

description:
GEX (5' mRNA) library: R1 contains cell barcode and UMI; R2 contains transcript
BatchD_Lane2_barcodes.tsv.gz
BatchD_Lane2_features.tsv.gz
BatchD_Lane2_matrix.mtx.gz

value: PBMC


title: B7_CO_LPS_biol rep 2


title: F123 GAM library f123_1NP_GAM180116_C04_2_S123_R1_001


title: PBMC from BatchC (10 hashed donors, chip2 lane7) during ART, GEX

description:
GEX (5' mRNA) library: R1 contains cell barcode and UMI; R2 contains transcript
BatchC_Lane7_barcodes.tsv.gz
BatchC_Lane7_features.tsv.gz
BatchC_Lane7_matrix.mtx.gz


title: B6_CO_LPS_biol rep 1


title: PBMC from BatchC (10 hashed donors, chip2 lane5) during ART, HTO

description:
HTO library: R1 contains cell barcode and UMI; R2 contains Hashtag Antibody Derived Tag reads
BatchC_Lane5_barcodes.tsv.gz
BatchC_Lane5_features.tsv.gz
BatchC_Lane5_matrix.mtx.gz

value: HTO

value: TotalSeq-C0251 anti-human Hashtag 1, TotalSeq-C0252 anti-human Hashtag 2, TotalSeq-C0253 anti-human Hashtag 3, TotalSeq-C0254 anti-human Hashtag 4, TotalSeq-C0255 anti-human Hashtag 5, TotalSeq-C0256 anti-human Hashtag 6, TotalSeq-C0257 anti-human Hashtag 7, TotalSeq-C0258 anti-human Hashtag 8, TotalSeq-C0259 anti-human Hashtag 9, TotalSeq-C0260 anti-human Hashtag 10


title: F123 GAM library f123_1NP_GAM180116_C10_1_S75_R1_001


title: PBMC from BatchD (9 hashed donors, chip2 lane4) during ART, GEX

description:
GEX (5' mRNA) library: R1 contains cell barcode and UMI; R2 contains transcript
BatchD_Lane4_barcodes.tsv.gz
BatchD_Lane4_features.tsv.gz
BatchD_Lane4_matrix.mtx.gz

value: mRNA


title: 3C-seq of D. radiodurans cells after ultraviolet irradiation -Replicate 1


title: B6_COiMg_LPS_biol rep 2


title: F123 GAM library f123_1NP_GAM180116_C03_2_S115_R1_001

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip

value: Hybrid F1 S129/Jae and Cast


title: 3C-seq of D. radiodurans wt cells -Replicate 2


title: PBMC from BatchC (10 hashed donors, chip2 lane5) during ART, GEX

description:
GEX (5' mRNA) library: R1 contains cell barcode and UMI; R2 contains transcript
BatchC_Lane5_barcodes.tsv.gz
BatchC_Lane5_features.tsv.gz
BatchC_Lane5_matrix.mtx.gz


title: B6_COiMg_LPS_biol rep 1

value: cerebral organoids


title: F123 GAM library f123_1NP_GAM180116_C02_2_S107_R1_001


title: patient16_day100

city: Oslo

first: Maria

middle: Dehli

last: Vigeland

address: Kirkeveien 166

country: Norway

institute: Oslo University Hospital

description:
Library name: sample_122
Column name in counts.csv: sample_122

data_processing:
The reads were mapped to the human genome (GRCh38.p10) using HISAT2 v2.1.0 and counted with featureCounts from Subread v1.6.3, using gene coordinates from Ensembl 88.
Assembly: GRCh38.p10 and Ensembl 88
Supplementary files format and content: Csv file "counts.csv" includes gene counts for each sample

source_name: whole blood

extract_protocol:
Total RNA was isolated from the blood using the Preserved Blood RNA Purification Kit I (Norgen Biotek, Thorold, Canada) according to the manufacturer’s instructions. DNAse treatment was included as recommended.
RNA was prepared for sequencing using TruSeq RNA library prep kits (Illumina) and sequenced with 2×75 bp paired-end configuration on the HiSeq3000 platform (Illumina)

value: whole blood

value: placebo sugar pills


title: 3C-seq of D. radiodurans wt cells -Replicate 1

value: bacteria

value: WT


title: F123 GAM library f123_1NP_GAM180116_C01_2_S99_R1_001

data_processing:
Sequenced reads from each GAM library were mapped to the mouse genome assembly GRCm38 (Dec. 2011, mm10) using bowtie2 with all default settings. All non-uniquely mapped reads, reads with mapping quality < 20 were filtered using the command “sed '/XS:/d' | samtools view -q 20 -F 4 -bS -”. PCR duplicates were removed with the “samtools rmdup” command. Samples were checked for contamination using fastq_screen. Number of nucleotides sequenced in each genomic bin was calculated using bedtools coverage command. Next, the optimal threshold between the sequencing noise and the signal to call positive windows was calculated as the lowest coverage per bin that gives the highest percent of clustered windows (windows that have a neighboring positive window on at-least one side) for each GAM sample in the dataset. Windows were called positive when the number of nucleotides covered by the reads is higher or equal to the optimal threshold. Each dataset was assessed for quality control by determining the percentage of orphan windows, number of uniquely mapped reads to the mouse genome, and cross-well contamination for every sample. 1NP samples that passed QC were merged into in-silico 3NPs at the level of positive windows. For good quality samples, we produced raw co-segregation, as well as normalized (NPMI) pair-wise chromatin contact matrices.
Assembly: mm10
Supplementary files format and content: Processed data files are raw GAM segregation tables, non-normalized pairwise cosegregation matrices and normalized NPMI matrices in tab-delimited format.
Library strategy: WGA

extract_protocol:
Fixation of F123 mESC was performed as described previously (Branco and Pombo, 2006). Briefly, cells were grown to 70 % confluency, media was removed, and cells were fixed in 4% and 8% paraformaldehyde in 250 mM HEPES-NaOH (pH 7.6; 10 min and 2 h, respectively), gently scrapped, and softly pelleted and embedded in saturated 2.1 M sucrose in PBS and frozen in liquid nitrogen on copper sample holders. Ultrathin cryosections were cut with a glass knife using an ultracryomicrotome (Leica Biosystems, EM UC7) at ~230 nm thickness, and transferred to PEN membrane steel frame slides 4.0 µm (Leica Microsystems, 11600289) for laser microdissection. Before laser microdissection, cryosections were washed in sterile-filtered 1x PBS (3 times, 5 min each), sterile-filtered H2O (3 times, 5 min each), and stained with sterile-filtered 1 % (w/v) cresyl violet (Sigma-Aldrich, C5042) in H2O for 10 min, followed by 2 washes with H2O (30 s each).  Individual NPs were isolated from the cryosection by laser microdissection using a laser microdissection microscope (Leica Microsystems, LMD7000). Cut NPs were collected in a PCR Cap Strip filled with opaque adhesive material (Carl Zeiss Microscopy, 415190-9161-000). For each collection day, 1 or 2 caps were left empty and taken through the whole genome amplification (WGA) and sequencing process as a negative control for quality control purposes.
Whole Genome Amplification (WGA) was performed as described previously (Winick-Ng et al, 2021) with minor modifications. Briefly, DNA was extracted from NPs at 60oC in the lysis buffer (20mM Tris-HCl pH 8.0, 1.4 mM EDTA, 560 mM guanidinium-HCl, 3.5% Tween-20, 0.35% Triton X-100) containing 0.75 units/ml Qiagen protease (Qiagen, 19155). After 24h of DNA extraction, the protease was heat inactivated at 75oC for 30 min and the extracted DNA was amplified via two rounds of PCR. At-first quasi-linear amplification was performed with random hexamer GAT-7N  primers with an adaptor sequence. The lysis buffer containing the extracted genomic DNA was mixed with 2x DeepVent mix buffer (2x Thermo polymerase buffer (10x), 400 µm dNTPs, 4 mM MgSO4 in ultrapure DNase free water), 0.5 µM GAT-7N primers (5′- GTG AGT GAT GGT TGA GGT AGT GTG GAG NNN NNN N) and 2 units/µl DeepVent® (exo-) DNA polymerase (New England Biolabs, M0259L) and incubated for 11 cycles in the BioRad thermocycler. The second exponential PCR amplification was performed in presence of 1x DeepVent mix, 10 mM dNTPs, 0.4 µM GAM-COM primers (5′-GTG AGT GAT GGT TGA GGT AGT GTG GAG) and 2 units/µl DeepVent (exo-) DNA polymerase in the programmable thermal cycler for 26 cycles.
After whole genome amplification, the DNA WGA product was purified withSPRI beads (1.7x) The DNA concentration of each sample was quantified using the Quant-iT® PicoGreen dsDNA assay kit (Invitrogen #P7589). Genomic sequencing library was prepared from 1ng of purified DNA using the Illumina Nextera XT library preparation kit (Illumina #FC-131-1096), following the manufacturer’s instructions or with reduce to 20% volume of reagents. After the library preparation, DNA was again purified with in-house SPRI beads (1.7x) and equal amounts of DNA from each sample was pooled together (up to 196 samples) for the sequencing. The final pool of libraries was additionally purified two more times with SPRI beads (1.7x) and analyzed using DNA High Sensitivity on-chip electrophoresis on an Agilent 2100 Bioanalyzer. The samples were sequenced on Illumina NextSeq500 machine as single-end 75 bp reads, according to manufacturer’s instructions.

value: mouse embryonic stem cells


title: PBMC from BatchC (10 hashed donors, chip2 lane3) during ART, GEX

description:
GEX (5' mRNA) library: R1 contains cell barcode and UMI; R2 contains transcript
BatchC_Lane3_barcodes.tsv.gz
BatchC_Lane3_features.tsv.gz
BatchC_Lane3_matrix.mtx.gz


title: patient33_day100

description:
Library name: sample_121
Column name in counts.csv: sample_121


title: PBMC from BatchC (10 hashed donors, chip2 lane3) during ART, HTO

description:
HTO library: R1 contains cell barcode and UMI; R2 contains Hashtag Antibody Derived Tag reads
BatchC_Lane3_barcodes.tsv.gz
BatchC_Lane3_features.tsv.gz
BatchC_Lane3_matrix.mtx.gz


title: PBMC from BatchC (10 hashed donors, chip2 lane7) during ART, HTO

description:
HTO library: R1 contains cell barcode and UMI; R2 contains Hashtag Antibody Derived Tag reads
BatchC_Lane7_barcodes.tsv.gz
BatchC_Lane7_features.tsv.gz
BatchC_Lane7_matrix.mtx.gz


title: F123 GAM library f123_1NP_GAM180116_B12_2_S186_R1_001


title: PBMC from BatchC (10 hashed donors, chip2 lane1) during ART, HTO

description:
HTO library: R1 contains cell barcode and UMI; R2 contains Hashtag Antibody Derived Tag reads
BatchC_Lane1_barcodes.tsv.gz
BatchC_Lane1_features.tsv.gz
BatchC_Lane1_matrix.mtx.gz


title: B6_CO_ctrl_biol rep 1

value: CO

value: ctrl


title: B7_CO_ctrl_biol rep 2


title: B8_CO_ ctrl_biol rep 3


title: patient1_day100

description:
Library name: sample_119
Column name in counts.csv: sample_119


title: F123 GAM library f123_1NP_GAM180116_B11_2_S178_R1_001


title: patient1_1y

description:
Library name: sample_120
Column name in counts.csv: sample_120


title: PBMC from BatchB (9 hashed donors, chip1 lane8) during ART, HTO

description:
HTO library: R1 contains cell barcode and UMI; R2 contains Hashtag Antibody Derived Tag reads
BatchB_Lane8_barcodes.tsv.gz
BatchB_Lane8_features.tsv.gz
BatchB_Lane8_matrix.mtx.gz

value: TotalSeq-C0251 anti-human Hashtag 1, TotalSeq-C0252 anti-human Hashtag 2, TotalSeq-C0253 anti-human Hashtag 3, TotalSeq-C0254 anti-human Hashtag 4, TotalSeq-C0255 anti-human Hashtag 5, TotalSeq-C0256 anti-human Hashtag 6, TotalSeq-C0257 anti-human Hashtag 7, TotalSeq-C0258 anti-human Hashtag 8, TotalSeq-C0259 anti-human Hashtag 9


title: B6_COiMg_ctrl_biol rep 2

value: COiMg


title: PBMC from BatchB (9 hashed donors, chip1 lane8) during ART, GEX

description:
GEX (5' mRNA) library: R1 contains cell barcode and UMI; R2 contains transcript
BatchB_Lane8_barcodes.tsv.gz
BatchB_Lane8_features.tsv.gz
BatchB_Lane8_matrix.mtx.gz


title: patient1_day0

description:
Library name: sample_118
Column name in counts.csv: sample_118


title: PBMC from BatchB (9 hashed donors, chip1 lane6) during ART, HTO

description:
HTO library: R1 contains cell barcode and UMI; R2 contains Hashtag Antibody Derived Tag reads
BatchB_Lane6_barcodes.tsv.gz
BatchB_Lane6_features.tsv.gz
BatchB_Lane6_matrix.mtx.gz


title: B6_COiMg_ctrl_biol rep 1


title: patient3_day0

description:
Library name: sample_115
Column name in counts.csv: sample_115


title: F123 GAM library f123_1NP_GAM180116_B10_1_S74_R1_001

value: male


title: F123 GAM library f123_1NP_GAM180116_B09_2_S162_R1_001


title: PBMC from BatchB (9 hashed donors, chip1 lane4) during ART, HTO

description:
HTO library: R1 contains cell barcode and UMI; R2 contains Hashtag Antibody Derived Tag reads
BatchB_Lane4_barcodes.tsv.gz
BatchB_Lane4_features.tsv.gz
BatchB_Lane4_matrix.mtx.gz


title: B8_COiMg_ ctrl_biol rep 3


title: patient41_1y

description:
Library name: sample_114
Column name in counts.csv: sample_114


title: PDSD-1

city: Luzhou

first: Fengtian

last: Li

address: Zhongshan Road

institute: Southwest Medical University

data_processing:
Filtering of Clean Reads Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp(version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Alignment with Ribosome RNA (rRNA) Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
Alignment with reference genome An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 (version 2.1.0) with “-rna-strandness RF” and other parameters set as a default.
Transcripts Reconstruction The reconstruction of transcripts was carried out with software Stringtie (version 1.3.4), which together with HISAT2, allow biologists to identify new genes and new splice variants of known ones.
Novel Transcripts Identification and Annotation To identify the new transcripts, all of the reconstructed transcripts were aligned to reference genome and were divided into twelve categories by using Cuffcompare. Transcripts with one of the classcodes “u,i,j,x,c,e,o” were defined as novel transcripts. We used the following parameters to identify reliable novel genes: the length of transcript was longer than 200bp and the exon number was more than 2 (plants more than 1). Novel transcripts were then aligned to the Nr, KEGG, and GO database to obtain protein functional annotation.
lncRNA Prediction Two softwares CNCI (version 2) and CPC (version 0.9-r2) ( http://cpc.cbi.pku.edu.cn/) were used to assess the protein-coding potential of novel transcripts by default parameters. The intersection of both non protein-coding potential results were chosen as long non-coding RNAs.
lncRNA type classification lncRNAs were classified into five classes according to their location relative to protein-coding genes: intergenic lncRNAs, bidirectional lncRNAs, intronic lncRNAs, antisense lncRNAs, and sense overlapping lncRNAs. Different types of lncRNAs may have different biological functions.
Quantification of Transcripts Abundance Transcripts abundances were quantified by software StringTie in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using StringTie software.
Assembly: Ensembl_release104
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Colorectal tumor

extract_protocol:
Tumor samples stored in RNA-later buffer were used for RNA extraction. Total RNA was extracted using RNAiso Plus (9109, TaKaRa, Japan) following the manufacturer's protocol.
The RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and confirmed through RNase-free agarose gel electrophoresis. Following RNA extraction, rRNAs were depleted to enrich mRNAs and ncRNAs. The enriched mRNAs and ncRNAs were fragmented into short segments using a fragmentation buffer and then reverse transcribed into cDNA with random primers. Subsequently, second-strand cDNA synthesis was carried out using DNA polymerase I, RNase H, dNTPs (with dUTP substituted for dTTP), and buffer. The resulting cDNA fragments were purified with the QiaQuick PCR extraction kit (Qiagen, Venlo, The Netherlands), subjected to end repair, poly(A) tail addition, and ligation to Illumina sequencing adapters. Subsequently, Uracil-N-Glycosylase (UNG) was employed to degrade the second-strand cDNA. The digested products underwent size selection via agarose gel electrophoresis, PCR amplification, and sequencing on the Illumina HiSeq TM 4000 platform by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: Colorectal tumor

value: Neoadjuvant therapy


title: PBMC from BatchB (9 hashed donors, chip1 lane6) during ART, GEX

description:
GEX (5' mRNA) library: R1 contains cell barcode and UMI; R2 contains transcript
BatchB_Lane6_barcodes.tsv.gz
BatchB_Lane6_features.tsv.gz
BatchB_Lane6_matrix.mtx.gz

value: PBMC