title: Donor 190514B_D21_SUV39H1 KO


title: Donor 190514B_D21_Mock

status: Public on Oct 30 2023

type: RNA

city: Paris

first: Sebastian

last: Amigorena

address: 26 rue d'Ulm

country: France

institute: Institut Curie

hyb_protocol: following manufacturer’s instructions

scan_protocol: following manufacturer’s instructions

data_processing: After passing internal quality control process, the calculated background was subtracted from raw gene expression data, then the data was normalized to the housekeeping genes with nSolver 4.0 software

label: not provided

molecule: total RNA

organism: Homo sapiens

source_name: CAR T cells

label_protocol: RNA was quantified using Nanodrop and quality controlled using an Agilent Bioanalyzer following manufacturer’s instructions. 300 ng of total RNA from all the samples were used as input for the NanoString nCounter® CAR-T Characterization

growth_protocol: CAR T cell production: To produce CAR T cells total CD8+ T cells (heterologous populations of naïve, memory, and effector cells) purified from peripheral blood mononuclear cells (PBMCs) were isolated from anonymous healthy donor leukapheresis ring (provided by EFS-Etablissement Francais du Sang) by density gradient centrifugation using Lymphoprep. T cells were plated at a concentration 106 cells /ml (5 x 10^5 cells in 24 well plate) using X-VIVO 15 media supplemented with 5% human serum (Sigma Aldrich) and 0.5 µM β–mercaptoethanol (referred to as complete X-VIVO), and stimulated with Dynabeads human T-Activator CD3/CD28 in a ratio of 1 bead per cell.   CAR transduction was achieved by lentiviral particles obtained from Flash Therapeutics and CARs were under the control of EF1a promoter. T cells were transduced approximately 24 hours after activation at a multiplicity of infection of 5. Viral vectors were added in 500 µl of complete X-VIVO with a final concentration of 4 µg/mL of Polybrene. After 16-18 hours the supernatant was almost completely discarded, and cell suspension was completed to a final volume of 2 mL with complete X-VIVO containing 100 IU/ml of rhIL-2. The following day, cells were subjected to CRISPR-Cas9 nucleofection (to invalidate SUV39H1): cells were harvested and activation beads were removed with magnets. crRNA targeting SUV39H1 and tracrRNA were first annealed at equimolar concentration to form the duplex at 95°C for 5 min. RNPs were then formed by combining precomplexed duplex (crRNA:tracrRNA) with Hifi Cas9 Nuclease V3 at a molar ratio of 3:1 and incubating them 10 min at room temperature. Nucleofection was done with P3 Primary Cell 4D-Nuleofector® X kit S adding between 1 to 2 x 10^6 cells with 10 µg of Cas9 in 5 µl of RNP and 20 µl of nucleofection solution. After electroporation using the EO-115 program (4D-Nucleofector Core Unit, Lonza), 200 µl of complete X-VIVO 15 with 500 IU/ml rhIL-2 was added to each reaction and cells were cultured at 32°C. After 16 h, cells were diluted in complete X-VIVO 15 with 500 IU/ml rhIL-2 at a concentration of 10^6 cells/ml. Cells were collected after 72 h (D0) and were also re-plated again in complete X-VIVO supplemented with 100 IU/ml of recombinant human rhIL-2 in a concentration 106 cells and re-activated with Dynabeads human T-Activator CD3/CD28 in a ratio of 1 bead per cell. Cells were diluted every 3-4 days to maintain the cell concentration and were re-plated and re-activated every 7 days.

extract_protocol: Total RNA was purified from CAR T cells at day 0 using RNeasy Mini Kit according to manufacturer’s instructions, and reverse transcription (RT) was done for cDNA synthesis from 200 ng of RNA using reverse transcriptase according to the manufacturer’s instructions.

tag: donor id

value: Donor 190514B

tag: timepoint

tag: genotype

value: Mock


title: Patient 54

status: Public on Oct 29 2023

city: Bialystok

first: Magdalena

last: Niemira

address: Kilinskiego 1

country: Poland

institute: Medical University of Bialystok

description: miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)

hyb_protocol: Standard nanostring nCounter miRNA Hybridization Protocol; The final hybridization reaction contained the following components: 10 μL Reporter CodeSet, 10 μL hybridization buffer, a 5 μL aliquot from the miRNA Sample Preparation Protocol, and 5 μL Capture ProbeSet.

scan_protocol: Raw count data were collected and captured by the nCounter Digital Analyzer for image capture (555 fields of view).

data_processing: The miRNA data analysis was performed using nSolver Analysis (version 4·0) software. Each miRNA count data was subtracted from the geometric mean of the negative controls. Profiling data were then normalized by the geometric mean of the positive controls and the geometric mean of the top 100 most highly-expressed microRNAs.

source_name: ovary

label_protocol: Standard nanostring miRNA protocols (nCounter Human v3 miRNA Expression Assays (NanoString Technologies,Seattle, USA))

extract_protocol: Total RNA was extracted from 400 mL of serum sample using miRNeasy Serum/Plasma Kit (Qiagen, Gaithersburg, MD, USA) according to the manufacturer’s protocol.

tag: tissue

value: ovary

tag: age


title: Patient 53


title: Patient 50


title: Patient 51


title: Patient 40


title: Patient 39


title: Patient 41


title: Patient 44


title: Patient 38


title: Patient 49


title: Patient 42


title: Patient 43


title: Patient 45


title: Patient 48


title: Patient 47


title: Patient 46


title: Patient 37


title: Patient 36

source_name: high-grade serous ovarian cancer

value: high-grade serous ovarian cancer


title: Patient 31


title: Patient 30


title: Patient 27


title: Patient 33


title: Patient 24


title: Patient 25


title: Patient 29


title: Patient 34


title: Patient 32


title: Patient 28


title: Patient 35


title: Patient 22


title: Patient 23


title: Patient 26


title: Patient 21


title: Patient 18


title: Patient 19


title: Patient 20


title: Patient 6


title: Patient 17


title: Patient 10


title: Patient 9


title: Patient 7


title: Patient 11


title: Patient 16


title: Patient 14


title: Patient 13


title: Patient 15


title: Patient 8


title: Patient 12


title: Patient 1


title: Patient 3


title: Patient 4


title: Patient 2


title: Patient 5


title: TCN+PD169316 10 µM_72h

city: Sendai-shi

first: Susumu

last: Suzuki

country: Japan

institute: Tohoku Medical and Pharmaceutical University

description: Affymetrix Clariom™ D Assay human

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: The data were analyzed using Transcriptome Analysis Console (TAC) Software (Thermo Fisher Scientific).

label: biotin

source_name: NB4 cell

label_protocol: Not provided

growth_protocol: RPMI containing 10% heat-inactivated fetal bovine serum (FBS) under 5% CO2 at 37°C in a humidified atmosphere.

extract_protocol: RNA extraction was performed using RNeasy Plus Kits (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Cells were seeded at a density of 2-3×10^5 cells/ml and treated with DMSO, 10 µM PD169316 and 10 µM TCN+10 µM PD169316 for 72h.

value: acute promyelocytic leukemia


title: PD169316 10 µM_72h

description: Affymetrix Clariom™ D Assay human


title: NSD2

type: SRA

city: Beijing

first: Lin

last: He

address: Xueyuan Road 38

country: China

institute: Peking University

library_source: genomic

data_processing:
Raw data were preprocessed by using fastp version0.19.6.
Filtered reads were aligned to the genome (GRCh38, hg38) assembly using Bowtie2.
Peaks were called using MACS version2.
Assembly: GRCh38, hg38
Supplementary files format and content: bigwig files were generated using deepTools.
Supplementary files format and content: peak txt files containing the specific binding region.

molecule: genomic DNA

source_name: LP-1 cells

growth_protocol: LP-1 cells were maintained according to the ATCC’s recommendation.

extract_protocol:
CUT&Tag was performed using NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (for Illumina) (Novoprotein) according to manufacturer’s instructions. In brief, LP-1 cells were collected and bounded to Concanavalin A–coated beads. Subsequently, cells were resuspended in antibody buffer and incubated with primary antibodies against PSMD14 or NSD2 and secondary antibodies in order. The samples were incubated with pA-Tn5 transposase. After transposon activation and tagmentation, DNA was isolated, amplified, and purified to construct library.
The library for sequencing was constructed and NovoNGS DNA Clean beads were used for purification steps. The library was quantified with NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (for Illumina) and sequenced on an Illumina novaseq 150PE.

treatment_protocol: Untreated

value: multiple myeloma

tag: chip antibody

tag: treatment

value: untreated


title: L363_ETV4KO_Ctrl2

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

country: USA

institute: Emory University

description:
L363.MACS2_q_0.01.noModel.union.annot.clean.cts
L363.MACS2_q_0.01.noModel.union.annot.clean.rppm.cov

data_processing:
ATAC-seq FASTQ files were quality and adapter trimmed using Trim Galore! (v0.6.4) and CutAdapt (v2.5) and mapped to the GRCh38 reference genome using bowtie2 (v2.3.5.1).
Aligned SAM files were converted to BAM files and putative PCR duplicates were marked with Samtools (v1.10) .
Regions of chromatin accessibility were identified in each sample using MACS2 (v2.1.1.20160309).
The union of all accessible regions was determined and reads mapping to these regions for each sample was assessed using the 'summarizeOverlaps' function of the GenomicAlignments package (v1.30.0) in R (v4.1.2).
Regions that overlapped ENCODE blacklisted regions were removed.
As a quality control metric the number of reads in peaks was determined and used to calculate a normalized accessibility score as reads per peak million (RPPM) according to the following formula: RPPM=reads×  〖10〗^6/(total reads in autosomal peaks)
Differential chromatin accessible regions were determined using edgeR (v3.36.0)
Assembly: GRCh38
Supplementary files format and content: L363.MACS2_q_0.01.noModel.union.annot.clean.cts: Raw read counts in peaks in L363 cells
Supplementary files format and content: L363.MACS2_q_0.01.noModel.union.annot.clean.rppm.cov: Reads per peak per million reads (RPPM) normalized data for L363 cells
Supplementary files format and content: RPMI8226.MACS2_q_0.01.noModel.union.annot.clean.cts: Raw read counts in peaks in RPMI8226 cells
Supplementary files format and content: RPMI8226.MACS2_q_0.01.noModel.union.annot.clean.rppm.cov: Reads per peak per million reads (RPPM) normalized data for RPMI8226 cells
Supplementary files format and content: Each sample has an individual bigWig file using the naming convention "[SAMPLENAME].union.rppm.bw", which includes RPPM normalized data.

source_name: cell line

growth_protocol: Cell lines were cultured in RPMI1640 medium (Corning) containing 10% fetal bovine serum, 100 U/mL penicillin, and 100 mg/mL streptomycin at 37°C under 5% CO2.

extract_protocol:
Nuclei from 50,000 cells were isolated by spinning at 500g for 10 minutes, all supernatant was pipet decanted, and pelleted cells were resuspended in 25 uL Tagmentation Reaction Mix composed of 12.5 uL Tagment DNA Buffer (Illumina), 0.02% Digitonin, 0.1% Tween-20, 2.5 uL TN5 enzyme (Illumina).
Tagmentation was performed for 1 hour at 37C. Tagmented DNA was isolated by adding Tagmentation Clean-up Buffer (326 mM NaCl, 109 mM EDTA, 0.63% SDS, 20 ug Proteinase K) and incubating at 40C for 1 hour and both a negative (0.7x) and positive (1.2x) SPRI bead (Kapa) selection. Libraries were amplified 12 times with Hifi polymerase (Kapa) and Nextera barcoded primers (Illumina) prior to 1x SPRI bead clean-up and sequencing on a Novaseq (Illumina).

treatment_protocol: Cells were treated with 10 uM lenalidomide for 72 hrs

value: cell line

tag: cell line

tag: cell type

value: ETV4 knock-out

value: control


title: L363_EV_Ctrl1

value: Empty Vector


title: RPMI8226_EV_Ctrl1

description:
RPMI8226.MACS2_q_0.01.noModel.union.annot.clean.cts
RPMI8226.MACS2_q_0.01.noModel.union.annot.clean.rppm.cov


title: L363_EV_Len1

value: lenalidomide (10 uM)


title: L363_ETV4KO_Len1


title: RPMI8226_ETV4KO_Len2


title: RPMI8226_ETV4KO_Len1


title: RPMI8226_EV_Len2


title: RPMI8226_EV_Len1


title: L363_ETV4KO_Ctrl1


title: RPMI8226_ETV4KO_Ctrl1


title: RPMI8226_EV_Ctrl2


title: L363_EV_Len2


title: RPMI8226_ETV4KO_Ctrl2


title: PSMD14


title: L363_ETV4KO_Len2


title: L363_EV_Ctrl2


title: H3K36me2_shPSMD14

growth_protocol: LP-1 control and PSMD14 knockdown cells were maintained according to the ATCC’s recommendation.

extract_protocol:
CUT&Tag was performed using NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (for Illumina) (Novoprotein) according to manufacturer’s instructions. In brief, LP-1 control and PSMD14 knockdown cells were collected and bounded to Concanavalin A–coated beads. Subsequently, cells were resuspended in antibody buffer and incubated with primary antibodies against PSMD14 or NSD2 and secondary antibodies in order. The samples were incubated with pA-Tn5 transposase. After transposon activation and tagmentation, DNA was isolated, amplified, and purified to construct library.
The library for sequencing was constructed and NovoNGS DNA Clean beads were used for purification steps. The library was quantified with NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (for Illumina) and sequenced on an Illumina novaseq 150PE.

treatment_protocol: LP-1 cells were infected with lentiviruses carrying control shRNA or PSMD14 shRNA.

value: PSMD14 knockdown


title: H3K36me2_control


title: H2AK119ub_control


title: 46LCNEC_allo [321_S11]

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

library_source: transcriptomic

data_processing:
Reads were aligned to GRCm39 mouse genome with “Rbowtie2”
counts extracted with featureCounts function from “Rsubread” and gencode annotation release 27 (gencode.vM27.annotation.gtf)
DESeq2 was used to identify genes that were differentially expressed in the 46LCNEC_allo and 57SCLC_allo tumors versus non-tumor lung (Lung). Gene set enrichment analyses were conducted with GSEA (version 4.1.0) software 74, using the DESeq2 normalized count values.
Assembly: GRCm39
Supplementary files format and content: normalized counts

organism: Mus musculus

extract_protocol:
Tissues and cells were embedded in RNALater (Ambion Inc., Austin, TX, USA) and RNA was isolated and purified using miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s instructions. RNA yield and quality were determined using Agilent 2100 Bioanalyzer.
RNA sequencing was performed after poly-A selection using Illumina NovaSeq 2x150 bp sequencing.


title: Group1_DMSO

city: Sg

first: XIANG

last: GAO

country: Singapore

institute: GIS

description:
shapemap_group1_group1_circular_profile.txt
shapemap_group1_group1_circular.shape

library_source: other

data_processing:
The SHAPE reactivity is determined using the formula [(ModifiedMutR – UntreatedMutR)/DenaturedMutR], and subsequently normalized using a model-free box-plot methodology
The standard deviation (SD) of SHAPE reactivities is calculated, serving as an indicator of the methods' efficacy in distinguishing single- or double-stranded regions.
Assembly: Gaussia princeps
Supplementary files format and content: number of coverage and mutation at nucleotide positioin
Supplementary files format and content: SHAPE reativtiy output

molecule: other

organism: Gaussia princeps (in: crustaceans)

source_name: Synthetic

extract_protocol:
RNA was synthesized using NEB IVT kit and extracted using Monarch RNA Cleanup Kit (NEB, Cat.: T2040)
SHAPE-map protocol

value: Synthetic

value: DMSO


title: H2AK119ub_shPSMD14


title: Group1_NAI

value: NAI


title: Group2_NAI

description:
shapemap_group2_group2_circular_profile.txt
shapemap_group2_group2_circular.shape


title: Group2_DMSO


title: Group1_Denature

value: Denature


title: Heart, Tnnt2_2D2P_NIL, snRNAseq

city: Chongqing

first: Chunyu

last: Zeng

state: Chongqing

address: 10 Changjiangzhilu Road

institute: Third Military Medical University

data_processing:
The Cell Ranger Single-Cell Software Suit v6.1.2 (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/ what-is-cell-ranger) was used to perform sample demultiplexing, barcode processing and single-cell 3'gene counting.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Heart

extract_protocol:
Heart tissue samples were collected  and minced. Minced samples were resuspended in 5 mL Lysis Buffer (320 mM sucrose, 10 mM Tris-HCl, 5 mM CaCl2 , 5 mM Magnesium Acetate, 2 mM EDTA, 0.5 mM EGTA, 1 mM DTT, 1x complete protease inhibitor (Roche), 200U/mL RNase OUT Recombinant Ribonuclease Inhibitor (Invitrogen, 10777-019), pH=8) and homogenized with a dounce grinder for 15 strokes. The lysate was sequentially ﬁltered through 70 um and 40 um cell strainers (Falcon, 352350 and 352340) and centrifuged at 1,000 x g for 5 min at 4℃ to pellet nuclei. The nuclear pellet was subsequently resuspended in 2 mL Sucrose Buffer (1 M sucrose, 10 mM Tris-HCl, 5 mM magnesium acetate, 1mM DTT, 1x complete protease inhibitor, 200 U/mL RNase OUT Recombinant Ribonuclease Inhibitor, pH=8) and the suspension was cushioned on top of 4 mL Sucrose Buffer, followed by centrifugation at 1,000 x g for 5 min at 4℃ to pellet nuclei. The nuclear pellet was subsequently washed once in 1 mL of Nuclei Storage Buffer (NSB) (440 mM sucrose, 10 mM Tris-HCl, 70 mM KCl, 10 mM MgCl2 , 1.5 mM spermine, 1x complete protease inhibitor, 200 U/mL RNase OUT Recombinant Ribonuclease Inhibitor, pH=7.2).
Single nucleus RNA-seq libraries were generated using Single Cell 3'Reagent Kits v2 (10xGenomics) according to the manufacturer’s protocol. Brieﬂy, cells, reagents (10xGenomics, PN-120237), gel beads (10xGenomics, 220104), and partitioning oil (10xGenomics, 220088) were loaded into the Chromium Single Cell A Chip (10xGenomics, 2000019), targeting 2000、5000 nuclei to be recovered per channel. Chip was loaded to the Chromium Controller (10xGenomics) to generate Gel Bead-In-Emulsions (GEMs). After reverse transcription using GEM-RT incubation protocol, GEMs were broken with recovery reagent (10xGenomics, 220016), cDNA was puriﬁed with DynaBeads MyOne Silane beads (Thermo Scientiﬁc, 37002D), ampliﬁed with PCR for 14 cycles, and further puriﬁed with SPRIselect reagent (Beckman Coulter, B23318). Quality control of recovered PCR product was performed on a Tapestation (Agilent) with D5000 high sensitivity screentapes (Agilent, 5067-5592), and cDNA yield was measured by Qubit DNA high sensitivity assay (Invitrogen, Q32854). After fragmentation, end-repair, A-tailing and size selection puriﬁcation, cDNA was ligated with adaptor and subsequently puriﬁed with SPRIselect reagents. Libraries were ampliﬁed using PCR with sample indexes from Chromium i7 Multiplex kit (10xGenomics, PN-120262). Final PCR products were subjected to double-sided size selection with SPRIselect reagents. Library quality control was performed on the Agilent Tapestation with D1000 screentapes (Agilent, 5067-5582), and library yield was quantiﬁed by Qubit DNA high sensitivity assay. Sequencing was performed on an Illumina NovaSeq 6000 system.

value: Heart


title: Heart, Control_NIL, snRNAseq


title: 46LCNEC_allo [319_S10]


title: OPM2_Dox3

data_processing:
RNA-seq FASTQ reads were quality and adapter trimmed using Trim Galore (v0.6.4) and CutAdapt (v2.8)  and mapped to the GRCh38 reference genome using the STAR aligner (v2.5.3a) using the gencode (v22) transcript database.
Putative PCR duplicates were marked using Samtools (v1.13).
Gene read counts were summarized in R (v4.1.2) using the ‘summarizeOverlaps’ function in ‘IntersectionNotEmpty’ mode of the GenomicAlignments (v1.3.0) package relative to all exons from gencode (v22) retrieved using the makeTxDbFromGFF and exonsBy functions of the GenomicFeatures package (v1.46.5).
The reads were FPKM normalized based on the total number of autosomal and non-immunoglobulin reads.
Assembly: GRCh38
Supplementary files format and content: Len.geneCts.exon.csv: comma separated values of raw exonic read counts for MM1S and OPM2 cells with and without lenalidomide treatment
Supplementary files format and content: Len.geneFpkm.exon.csv: comma separated values of FPKM values for MM1S and OPM2 cells with and without lenalidomide treatment
Supplementary files format and content: shIKZF3.geneCts.exon.csv: comma separated values of raw exonic read counts for OPM2 cells with doxycycline inducible shIKZF3
Supplementary files format and content: shIKZF3.geneFpkm.exon.csv: comma separated values of FPKM values for OPM2 cells with doxycycline inducible shIKZF3

molecule: polyA RNA

growth_protocol: Cell lines were cultured in RPMI1640 medium (Life Technologies, Carlsbad, CA, USA) containing 10% fetal bovine serum (Life Technologies), 100 U/mL penicillin, and 100 mg/mL streptomycin (Life Technologies) at 37°C under 5% CO2.

extract_protocol:
Rneasy (Qiagen) following the manufacturer's recommendations
Ion RNA-seq Kit (Thermo Fisher)

treatment_protocol: Cells were treated with 10 uM lenalidomide for 12 hrs (MM1S) or 24 hrs (OPM2)

value: Doxycycline


title: OPM2_Dox1


title: Group2_Denature


title: HemECs, shMIR4435-2HG-2

city: Jinan

first: Zhiyu

last: Li

address: Jingwu Road

department: Department of Plastic and Aesthetic Surgery

institute: Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: hg38（GRCh38.104）
Supplementary files format and content: fpkm

source_name: infantile hemangiomas

growth_protocol: HemECs were cultured in an endothelial cell medium, containing 5% fetal bovine serum, 1% penicillin-streptomycin, and 1% endothelial cell growth factor, at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted using RNAiso Plus reagent (Takara, Tokyo, Japan). 2 μg of  total RNA was used for the construction of  sequencing labraries.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: infantile hemangiomas

value: HemECs

value: endothelial cells

value: MIR4435-2HG knock down


title: HemECs, shMIR4435-2HG-1


title: OPM2_3

value: multiple myeloma

value: Control


title: 46LCNEC_allo [312_S12]


title: OPM2_1

value: cell line


title: HemECs, shNC-2

value: WT


title: Granulosa cells,Control,rep2

city: Guangzhou

first: Ou

last: Xiang-Hong

address: Guangzhou

institute: Guangdong Second Provincial General Hospital

data_processing:
Illumina high-throughput sequencing results initially exist as raw image data files, which are converted to raw sequencing sequences after sequence base recognition.
Raw sequences were filtered to obtain high-quality Clean Reads for subsequent analysis. After filtering, a larger proportion of bases in the total sequence with a quality value greater than 30 (error rate less than 0.1%) indicates better sequencing quality.
Gene expression levels are estimated by the count of sequencing sequences (Reads) that map to genomic regions or exonic regions.
Assembly: ftp://ftp.ensembl.org/pub/release-90/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample.

source_name: Ovary

extract_protocol:
Granulosa cells were obtained by puncturing follicles in Milrinone-containing M2 solution. Subsequently, granulosa cells were cultured in DMEM/F12 medium supplemented with 10% FBS and 1% penicillin at 37℃ in a 5% CO2 atmosphere. After 24 hours of incubation, the cells were starved for 12 hours in serum-free medium, then treated with or without NR1D1 agonist GSK4112(10M/mL) for 24 hours, changing the medium every 12 hours. The cells were observed under the microscope and the growth status was determined to be good. The medium was discarded, an appropriate amount of TRIzol was added, and the lysed cell solution was transferred to a 1.5 mL EP tube for subsequent detection.
After the total RNA samples were qualified for detection, they were purified according to the characteristics of mRNA from different sources. To join in the mRNA of purified fragmentation bu _x0018_ ffer makes its fragments short clips. Then, the RNA fragment was used as a template for reverse transcription with random primers, and the target fragment was retrieved by magnetic bead screening and then amplified by PCR to complete the whole library preparation.

value: Ovary

value: control


title: Granulosa cells,GSK4112,rep2


title: Granulosa cells,Control,rep3


title: 46LCNEC_cell [B-46LCNEC-3P100-31-01-21_S14]


title: Granulosa cells,GSK4112,rep1


title: Granulosa cells,Control,rep1


title: Granulosa cells,GSK4112,rep3


title: OPM2_Len_2

description: Len.geneFpkm.exon.csv

value: wild type

value: Lenalidomide (10uM)


title: OPM2_ctrl_2

description: Len.geneFpkm.exon.csv


title: 46LCNEC_cell [C-46LCNEC-3P100-31-01-22_S15]


title: MM1S_Len_2

description: Len.geneFpkm.exon.csv


title: OPM2_Len_1

description: Len.geneFpkm.exon.csv


title: OPM2_ctrl_1

description: Len.geneFpkm.exon.csv


title: Post-RTX remission, donor 4, scRNAseq

city: Montreal

first: Tho-Alfakar

last: Al-Aubodah

state: Quebec

address: 1001 boulevard Decarie

country: Canada

institute: McGill University

description:
scRNAseq with 10X Genomics 5' v1.1
INS18remission

library_source: transcriptomic single cell

data_processing:
CellRanger (v3.0.1) was used to align reads to the GRCh38 reference genome assembly and generate the filtered UMI matrix.
Seurat (4.3.0) was used to further filter the UMI matrix to eliminate doublets and cells with poor viability. Seurat was then subsequently used to aggregate the data, run integrated clustering, and generate the processed data files.
Assembly: GRCh38
Supplementary files format and content: Processed data files include two GNU zipped tab-separated values (.tsv.gz) files, one file contains the filtered barcode UMIs (barcodes.tsv.gz) and the second file contains the filtered feature counts (features.tsv.gz), and one GNU zipped matrix (.mtx.gz) file containing the the filtered matrix of barcode UMIs and feature counts.
Supplementary files format and content: Supplementary processed data files include rtx_bcells_annotations.txt.gz (containing meta data for post-quality control total analyzed B cells), and rtx_bcells_umi.txt.gz (containing non-normalised UMI count data for post-quality control total analyzed B cells).

source_name: Blood

extract_protocol:
PBMC were isolated from fresh blood by Ficoll-paque density centrifugation and cryopreserved in FBS supplemented with 10% of DMSO. When all samples had been collected, PBMC were thawed at 37°C, treated with DNase I for 15 minutes, washed with RPMI containing 5% FBS and rested for 2 hours in a 37°C 5% CO2 incubator. Following rest, cells were washed twice with ice-cold PBS containing 2% FBS and stained with anti-human CD19 PerCp-Cy5.5 (BD Biosciences), anti-human CD4 Alexa Fluor 700 (BD Biosciences), and anti-human CD8α V500 (BD Biosciences) for 15 minutes on ice. Cell were washed again with ice-cold PBS containing 2% FBS, filtered through a 40 µm mesh, and a maximum of 50,000 live B cells were FACS isolated as CD19+ CD4- CD8- cells and on the basis of size and granularity. Sorted cells were then washed twice with ice-cold PBS containing 0.04% BSA (0.22 µm filtered) and brought to a concentration of 1,000 cells/µl. Samples were subsequently processed according to the 10x Genomics Single Cell 5’ v1.1 user guide to target 10,000 events. Briefly, single cell PBMC suspensions were loaded onto the 10x Single Cell Chip G along with 10x Genomics NextGem scRNA 5’ V1.1 reagents. Complementary DNA (cDNA) and 5’ gene expression libraries were generated using the standard 10x Genomics protocol.
5' gene expression libraries were constructed with 10X Genomics Chromium Single Cell 5' v1.1 Reagent Kits following the manufacturer's standard protocols.

value: Blood

value: B cells

value: Pediatric

tag: Sex

value: Male

tag: disease state

value: Remission


title: 46LCNEC_cell [A-46LCNEC-3P100-31-01-20_S13]


title: MM1S_Len_1

description: Len.geneFpkm.exon.csv


title: MM1S_ctrl_2

description: Len.geneFpkm.exon.csv


title: Post-RTX relapse, donor 4, scRNAseq

description:
scRNAseq with 10X Genomics 5' v1.1
INS18relapse

value: Relapse


title: 57SCLC_allo [317_S5]


title: MM1S_ctrl_1

description: Len.geneFpkm.exon.csv


title: Post-RTX remission, donor 3, scRNAseq

description:
scRNAseq with 10X Genomics 5' v1.1
INS17remission


title: HemECs, shNC-1

value: infantile hemangiomas

value: HemECs


title: 57SCLC_allo [275_S6]


title: 57SCLC_allo [316_S4]


title: Post-RTX relapse, donor 3, scRNAseq

description:
scRNAseq with 10X Genomics 5' v1.1
INS17relapse


title: 57SCLC_cell [C-RNA57SCLC-P11-28-07-23_S9]


title: Post-RTX relapse, donor 2, scRNAseq

description:
scRNAseq with 10X Genomics 5' v1.1
INS16relapse


title: 57SCLC_cell [B-RNA57SCLC-P11-28-07-22_S8]


title: Post-RTX remission, donor 1, scRNAseq

description:
scRNAseq with 10X Genomics 5' v1.1
INS15remission

value: Female


title: 57SCLC_cell [A-RNA57SCLC-P11-28-07-21_S7]


title: Post-RTX relapse, donor 1, scRNAseq

description:
scRNAseq with 10X Genomics 5' v1.1
INS15relapse


title: Lung [CT5_S3]

source_name: Lung

value: Lung


title: Post-RTX remission, donor 2, scRNAseq

description:
scRNAseq with 10X Genomics 5' v1.1
INS16remission


title: INS, donor 4, scRNAseq

description: scRNAseq with 10X Genomics 5' v1.1

data_processing:
CellRanger (v3.0.1) was used to align reads to the GRCh38 reference genome assembly and generate the filtered UMI matrix.
Seurat (4.3.0) was used to further filter the UMI matrix to eliminate doublets and cells with poor viability. Seurat was then subsequently used to aggregate the data, run integrated clustering, and generate the processed data file for total PBMC .
Seurat (4.3.0) was used to further subcluster B cells and generate the processed data file for total B cells.
Assembly: GRCh38
Supplementary files format and content: Processed data files include two GNU zipped tab-separated values (.tsv.gz) files, one file contains the filtered barcode UMIs (barcodes.tsv.gz) and the second file contains the filtered feature counts (features.tsv.gz), and one GNU zipped matrix (.mtx.gz) file containing the the filtered matrix of barcode UMIs and feature counts.
Supplementary files format and content: Supplementary processed data files include pbmc_annotations.txt.gz (containing meta data for post-quality control total PBMC), pbmc_umi.txt.gz (containing non-normalised UMI count data for post-quality control total PBMC), bcell_annotations.txt.gz (containing meta data for post-quality control total B cells), and bcell_umi.txt.gz (containing non-normalised UMI count data for post-quality control total B cells).

extract_protocol:
PBMC were isolated from fresh blood by Ficoll-paque density centrifugation and cryopreserved in FBS supplemented with 10% of DMSO. When all samples had been collected, PBMC were thawed at 37°C, treated with DNase I for 15 minutes, washed with RPMI containing 5% FBS and rested for 2 hours in a 37°C 5% CO2 incubator. Following rest, cells were washed twice with ice-cold PBS containing 2% FBS, filtered through a 40 µm mesh, and a maximum of 250,000 live lymphocytes were FACS isolated on the basis of size and granularity. Sorted cells were then washed twice with ice-cold PBS containing 0.04% BSA (0.22 µm filtered) and brought to a concentration of 1,000 cells/µl. Samples were subsequently processed according to the 10x Genomics Single Cell 5’ v1.1 user guide to target 10,000 events. Briefly, single cell PBMC suspensions were loaded onto the 10x Single Cell Chip G along with 10x Genomics NextGem scRNA 5’ V1.1 reagents. Complementary DNA (cDNA) and 5’ gene expression libraries were generated using the standard 10x Genomics protocol.
5' gene expression libraries were constructed with 10X Genomics Chromium Single Cell 5' v1.1 Reagent Kits following the manufacturer's standard protocols.

value: PBMC

value: Active INS


title: Ted3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

hyb_protocol: Labeled fragments were hybridized to Affymetrix Mouse Gene ST 1.0 arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

label_protocol: We used the Affymetrix Clariom S kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

extract_protocol: RNA was isolated using the miRNeasy Mini kit (Qiagen). RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent 141 Technologies). RNA samples with an RNA quality number (RQN) greater than 9 were further processed for Affymetrix microarrays.

treatment_protocol: Mice were treated with teduglutide or vehicle (injection water) twice a day for 13 days (three days beforeallogeneic hematopoietic stem cell transplantation and 10 dyas after)

tag: strain

value: BALB/c

value: 10 weeks

value: treated with teduglutide 0.2mg/kg/day

tag: tissues

value: small intestine; Ileum

value: mixture of:Enterocytes, Paneth cells, intestinal stem cells, goblet cells, enteroendocrine cells


title: RPMI8226 H3K27ac

data_processing:
ChIP-seq FASTQ reads were quality- and adapter-trimmed using Trim Galore (v0.6.4) and CutAdapt (v2.8).
ChIP-seq FASTQ files were then mapped to the GRCh38 reference genome using Bowtie2 (v2.3.5.1) with default parameters.
Bowtie2 SAM files were converted to BAM files using Samtools (v1.13). ChIP-seq reads per million (RPM) normalization used total autosomal reads.
ChIP-seq enrichment was determined using MACS (v2.2.7.1) with "-g hs -q 0.01" parameters relative to the input control for the same cell lines.
ChIP-seq signal was reads per million (RPM) normalized.
Assembly: GRCh38
Supplementary files format and content: Individual bigWig files depict the RPM signal

extract_protocol:
Cells were cross-linked for 10 min with 1% formaldehyde at 37C. This reaction was subsequently quenched with 125 mM glycine for 5 min and 5-10 million fixed cells were used for the ChIP experiments. Chromatin from fixed cells was fragmented by sonication with a Covaris E220, and the solubilized chromatin was incubated with the indicated antibody overnight at 4C. Antibody-chromatin complexes were pulled down by incubation with Protein G-Dynabeads (Thermo Fisher Scientific) for 3 hours at 4C, washed, and eluted. The samples then underwent crosslink reversal, RNase A (Roche) treatment, and proteinase K (Thermo Scientific) treatment before the captured DNA was extracted using AMP Pure beads (Beckman Coulter)
ChIP-seq libraries were made using the Ion Plus Fragment Library Kit (Thermo Fisher).

treatment_protocol: Cells were treated with 10 uM lenalidomide for 24 hrs or 48 hrs as defined in the accompanying paper

value: cell line

value: multiple myeloma

value: wild type

value: Control

value: Abcam (AB-4729)


title: RPMI8226 IKZF1 Len

value: Lenalidomide (10uM)

value: GeneTex (GTX129438)


title: RPMI8226 BRD4 1


title: RPMI8226 Input


title: RPMI8226 ETV4


title: RPMI8226 IKZF1


title: RPMI8226 H3K27ac Len


title: MM1S P300

value: Santa Cruz (SC-584)


title: Ted2


title: RPMI8226 BRD4 Len 1


title: RPMI8226 P300 Len


title: RPMI8226 ETV4 Len


title: RPMI8226 P300


title: Lung [CT4_S2]


title: INS, donor 3, scRNAseq

description: scRNAseq with 10X Genomics 5' v1.1

value: Blood

value: Pediatric

value: Female


title: Ctl1

source_name: Ileum_injection water

value: treated with injection water


title: MM1S Input


title: PdgfraLo_A_Rep2 (bulk RNA-seq)

city: Boston

first: RAMESH

last: SHIVDASANI

state: MASSACHUSETTS

address: 450 Brookline ave

institute: Dana-Farber Cancer Institute

data_processing:
RNA-seq samples were aligned to the mm10 genome and processed using the Viper pipeline (Cornwell et al.(2018). BMC Bioinformatics, 19. https://doi.org/10.1186/S12859-018-2139-9) with default parameters.
Assembly: mm10
Supplementary files format and content: bigwig files

source_name: Antrum

extract_protocol:
Adult murine tissue was harvested by dividing the stomach into antrum and corpus. Tissue was collected after perfusing adult PdgfraH2BeGFP with cold PBS. After manual muscle removal, epithelium was removed by shaking the tissue in pre-warmed chelation buffer (10 mM EDTA, 5% FBS, X DTT, HEPES in HBSS buffer) for 20 minutes at 37°C, 250rpm. The tissue was then washed with PBS and digested for 10 minutes at 37°C in 3mg/ml collagenase II (Worthington, LS004176) in HBSS complemented with 5% FBS and HEPES. Cells were harvested by centrifugation at 300g for 5 minutes. Cells were sorted on a BD FACSAria II cell sorter, gating on DAPI negative cells to identify live cells, and GFP high and GFP low to sort Pdgfra high or low expressing cells.
Samples with RNA-integrity number of >8.5 were processed with SMART-Seq v4 Ultra Low Input RNA library construction kit per manufacturer's recommendation; and sequenced on Illumina Novaseq platform by the molecular biology core facility at Dana-Farber.

value: Antrum

value: Pdgfra_low_mesenchymal cells

value: PdgfraH2BeGFP (JAX strain 007669)


title: Lung [CT3_S1]

value: Lung


title: PdgfraHi_A_Rep2 (bulk RNA-seq)

value: Pdgfra_high_mesenchymal cells


title: Ctl4

value: BALB/c

value: 10 weeks

value: small intestine; Ileum

value: mixture of:Enterocytes, Paneth cells, intestinal stem cells, goblet cells, enteroendocrine cells


title: MM1S P300 Len

value: cell line

value: multiple myeloma

value: wild type


title: INS, donor 2, scRNAseq

description: scRNAseq with 10X Genomics 5' v1.1

value: PBMC

value: Active INS


title: MM1S IKZF1 Len 2

value: Lenalidomide (10uM)

value: GeneTex (GTX129438)


title: Fgf7 KO whole epithelium 1month (scRNA-seq)

data_processing:
Samples were aligned to the mm10 genome using 10x Genomics Cell Ranger 3.0.2 using default parameters
Assembly: mm10
Supplementary files format and content: mtx and tsv

extract_protocol:
Adult murine tissue was harvested by dividing the stomach into antrum and corpus. Tissue was collected after perfusing adult PdgfraH2BeGFP with cold PBS. After manual muscle removal, epithelium was removed by shaking the tissue in pre-warmed chelation buffer (10 mM EDTA, 5% FBS, X DTT, HEPES in HBSS buffer) for 20 minutes at 37°C, 250rpm. The tissue was then washed with PBS and digested for 10 minutes at 37°C in 3mg/ml collagenase II (Worthington, LS004176) in HBSS complemented with 5% FBS and HEPES. Cells were harvested by centrifugation at 300g for 5 minutes. Cells were sorted on a BD FACSAria II cell sorter, gating on DAPI negative cells to identify live cells and all DAPI negative cells were sorted.
Single Cell 3′ V3.1 assay (10X Genomics).

value: epithelium


title: MM1S H3K27ac 1

value: Control

value: Abcam (AB-4729)


title: MM1S IKZF1 2


title: Fgf7 WT whole epithelium 1month (scRNA-seq)

value: Antrum

value: WT


title: PdgfraHi_C_Rep2 (bulk RNA-seq)

source_name: Corpus

value: Corpus

value: Pdgfra_high_mesenchymal cells

value: PdgfraH2BeGFP (JAX strain 007669)


title: HC, donor 4, scRNAseq

description: scRNAseq with 10X Genomics 5' v1.1

value: Blood

value: Pediatric

value: Female

value: Healthy


title: MM1S H3K27ac Len 1

value: cell line

value: multiple myeloma

value: wild type


title: PdgfraLo_C_Rep2 (bulk RNA-seq)

value: Pdgfra_low_mesenchymal cells


title: Corpus_whole_mesenchyme_rep1 (scRNA-seq)

value: mesenchymal cells


title: Corpus_whole_mesenchyme_rep2 (scRNA-seq)


title: Antrum_whole_mesenchyme_rep2 (scRNA-seq)


title: PdgfraLo_A_Rep1 (bulk RNA-seq)


title: INS, donor 1, scRNAseq

description: scRNAseq with 10X Genomics 5' v1.1

value: PBMC

value: Male

value: Active INS


title: HC, donor 2, scRNAseq

description: scRNAseq with 10X Genomics 5' v1.1


title: HC, donor 3, scRNAseq

description: scRNAseq with 10X Genomics 5' v1.1


title: HC, donor 1, scRNAseq

description: scRNAseq with 10X Genomics 5' v1.1


title: PdgfraLo_C_Rep1 (bulk RNA-seq)


title: MM1S BRD4 1

value: Control


title: Antrum_whole_mesenchyme_rep1 (scRNA-seq)

value: Antrum


title: PdgfraHi_C_Rep1 (bulk RNA-seq)

value: Corpus


title: PdgfraHi_A_Rep1 (bulk RNA-seq)

value: Pdgfra_high_mesenchymal cells


title: MM1S BRD4 Len 1

value: Lenalidomide (10uM)


title: Ted4

value: BALB/c

value: 10 weeks

value: treated with teduglutide 0.2mg/kg/day

value: small intestine; Ileum

value: mixture of:Enterocytes, Paneth cells, intestinal stem cells, goblet cells, enteroendocrine cells


title: Ctl3

value: treated with injection water


title: ATAC pESC rep2 (re-analysis)

status: Public on Oct 28 2023

city: Shanghai

first: Tu

middle: zhi

last: fen

address: Tongji University Siping Road Campus

department: life science and technology

institute: Tongji University

description:
re-analysis of GSM5327415
pES_RPKM.bw

data_processing:
All sequenced reads were checked for quality control by using FastQC (v0.11.9) with default parameters.
Sequenced reads was removed adapters and low-quality sequence by using trim_galore (v0.6.6 )with the default parameters.
The processed chip-Seq reads were mapped to hg38 genome using Bowtie2.
Assembly: hg38
Supplementary files format and content: peak files and FPKM values

source_name: ATAC pESC

extract_protocol:
the Nchip sequencing libraries were constructed by following the manufacturer’s instructions.
chip-seq libraries were prepared for sequencing using standard Illumina protocols

value: pluripotent stem cells

value: PtoN intermediate

tag: condition

value: PtoN transition

value: pESC

tag: library type

value: ATAC-seq


title: ATAC nESC rep2 (re-analysis)

description:
re-analysis of GSM5327412
nES_RPKM.bw

source_name: ATAC nESC

value: nESC


title: ATAC nESC rep3 (re-analysis)

description:
re-analysis of GSM5327413
nES_RPKM.bw


title: ATAC pESC rep3 (re-analysis)

description:
re-analysis of GSM5327416
pES_RPKM.bw


title: ATAC pESC rep1 (re-analysis)

description:
re-analysis of GSM5327414
pES_RPKM.bw


title: K562S1-1000 r3

city: Novosibirsk

first: Andrey

last: Popov

address: Academician Lavrentiev Avenue, 10

country: Russia

institute: Institute of Cytology and Genetics, SB RAS

description: K562S1-1000_repCombined_Offset1_bin1_noPCR.bigwig

data_processing:
Datasets were aligned to the hg38/hg19 human genome assembly using BWA v.0.7.17-r1188.
Bam file sorting and indexing was performed using samtools. PCR duplicates were removed by samtools markdup -r
BigWig files containing cut site coverage were generated using bamCoverage from deeptools with the options --OffSet 1 --binSize 1.
Merged_nodups were obtained using modified version of the Juicer 1.6 (https://github.com/genomech/juicer1.6_compact)
Assembly: hg38 and hg19 for iPSC and Fibroblasts
Supplementary files format and content: BigWig
Supplementary files format and content: Merged_nodups

source_name: lymphoblast cells isolated from the bone marrow

growth_protocol: Human K562 cells were grown in RPMI-1640 medium with 10% FBS and a penicillin/streptomycin mix. Fibroblasts were maintained in DMEM/F12 with 10% FBS and a penicillin/streptomycin mix

extract_protocol:
Extraction protocol was performed as described in (Gridina. et. al 2021).
Library construction protocol similar to the performed as described in (Gridina. et. al 2021) with some adaptions (see the paper for detailed protocol)


title: K562S1-10 r2

description: K562S1-10_repCombined_Offset1_bin1_noPCR.bigwig

value: lymphoblast cells isolated from the bone marrow


title: PBMC rep1

description:
patient confidential information
PBMCS1_repCombined_Offset1_bin1_noPCR.bigwig

source_name: blood

value: blood

tag: cell type PMBC


title: PBMC rep2


title: K562S1-500 r2

description: K562S1-500_repCombined_Offset1_bin1_noPCR.bigwig


title: K562S1-200 r2

description: K562S1-200_repCombined_Offset1_bin1_noPCR.bigwig


title: ATAC nESC rep1 (re-analysis)

description:
re-analysis of GSM5327411
nES_RPKM.bw


title: ATAC day8 RFP-GFP- rep3 (re-analysis)

description:
re-analysis of GSM5327410
8dRFP-GFP-_RPKM.bw

source_name: ATAC day8 RFP-GFP-


title: K562S1-500 r1


title: K562_S1Hi-C Repl1


title: K562S1-10 r1


title: iPSC_S1Hi-C

source_name: induced pluripotent stem cells

value: induced pluripotent stem cells

value: iPSC


title: K562S1-1000 r2


title: Fibroblasts_S1Hi-C

source_name: human skin fibroblasts

value: human skin fibroblasts


title: K562 DNase Hi-C Rep2


title: K562_S1Hi-C Rep2


title: K562S1-200 r1


title: ATAC day8 RFP-GFP- rep2 (re-analysis)

description:
re-analysis of GSM5327409
8dRFP-GFP-_RPKM.bw


title: ATAC day8 RFP+GFP- rep2 (re-analysis)

description:
re-analysis of GSM5327406
8dRFP+GFP-_RPKM.bw

source_name: ATAC day8 RFP+GFP-


title: ATAC day8 RFP+GFP- rep3 (re-analysis)

description:
re-analysis of GSM5327407
8dRFP+GFP-_RPKM.bw


title: ATAC day10 RFP+GFP+ rep2 (re-analysis)

description:
re-analysis of GSM5327375
10dRFP+GFP+_RPKM.bw

source_name: ATAC day10 RFP+GFP+


title: ATAC day8 RFP-GFP- rep1 (re-analysis)

description:
re-analysis of GSM5327408
8dRFP-GFP-_RPKM.bw


title: ATAC day10 RFP+GFP+ rep1 (re-analysis)

description:
re-analysis of GSM5327374
10dRFP+GFP+_RPKM.bw


title: ATAC day10 RFP+GFP- rep2 (re-analysis)

description:
re-analysis of GSM5327372
10dRFP+GFP-_RPKM.bw

source_name: ATAC day10 RFP+GFP-


title: ATAC day10 RFP+GFP- rep1 (re-analysis)

description:
re-analysis of GSM5327371
10dRFP+GFP-_RPKM.bw


title: pESC rep2 (re-analysis)

description:
re-analysis of GSM5327369
PtoN_counts.txt.gz, PtoN_FPKM.txt.gz

source_name: pESC

value: mRNA-seq


title: pESC rep3 (re-analysis)

description:
re-analysis of GSM5327370
PtoN_counts.txt.gz, PtoN_FPKM.txt.gz


title: pESC rep1 (re-analysis)

description:
re-analysis of GSM5327368
PtoN_counts.txt.gz, PtoN_FPKM.txt.gz


title: ATAC day8 RFP+GFP- rep1 (re-analysis)

description:
re-analysis of GSM5327405
8dRFP+GFP-_RPKM.bw


title: nESC rep3 (re-analysis)

description:
re-analysis of GSM5327367
PtoN_counts.txt.gz, PtoN_FPKM.txt.gz

source_name: nESC


title: day8 RFP-GFP- rep3 (re-analysis)

description:
re-analysis of GSM5327364
PtoN_counts.txt.gz, PtoN_FPKM.txt.gz

source_name: day8 RFP-GFP-


title: nESC rep1 (re-analysis)

description:
re-analysis of GSM5327365
PtoN_counts.txt.gz, PtoN_FPKM.txt.gz


title: ATAC day10 RFP+GFP- rep3 (re-analysis)

description:
re-analysis of GSM5327373
10dRFP+GFP-_RPKM.bw


title: nESC rep2 (re-analysis)

description:
re-analysis of GSM5327366
PtoN_counts.txt.gz, PtoN_FPKM.txt.gz


title: Xalb_totalRNASeq_Rep2

city: Würzburg

first: Chase

middle: Lawrence

last: Beisel

address: Josef-Schneider Straße 2

department: Helmholtz-Institute for RNA-based Infection Research (HIRI)

institute: Helmholtz Centre for Infection Research (HZI)

data_processing:
FastQC 0.11.8
Cutadapt 3.4
RNA STAR 2.7.8a
Htseq-count 0.9.1
Assembly: Chromosome: FP565176.1 with added locations of Acr_5, Acr_7, Acr_10, Acr_11 and Acr_14 (locations see manuscript); plasmI: FP340279.1; plasmIII: FP340277.1
Assembly: FP565176.1 for small RNRA-seq
Supplementary files format and content: text files with gene read counts; bed file

organism: Xanthomonas albilineans

source_name: bacteria

growth_protocol: X. albilineans CFBP7063 was grown in TSB medium to an OD of 1.0 and 2 mL were pelleted.

extract_protocol:
Total RNA was extracted with Direct-zol RNA Miniprep Plus (Zymo Research) including the in-column DNase I treatment according to manufacturer's instructions. An additional DNase I treatment with TURBO DNA-free Kit (Thermo Fisher) was performed and the RNA was cleaned with RNA Clean & Concentrator (Zymo Research).
Ribosomal RNA was depleted and the cDNA library was prepared using NEBNext Ultra II Directional RNA Library Preparation Kit (NEB).

value: bacteria

value: WT


title: Xalb_smallRNASeq_Rep1

data_processing:
FastQC 0.11.8
Cutadapt 3.4
Bowtie2 2.4.2
Assembly: Chromosome: FP565176.1 with added locations of Acr_5, Acr_7, Acr_10, Acr_11 and Acr_14 (locations see manuscript); plasmI: FP340279.1; plasmIII: FP340277.1
Assembly: FP565176.1 for small RNRA-seq
Supplementary files format and content: text files with gene read counts; bed file

extract_protocol:
Total RNA was extracted with Direct-zol RNA Miniprep Plus (Zymo Research) including the in-column DNase I treatment according to manufacturer's instructions. An additional DNase I treatment with TURBO DNA-free Kit (Thermo Fisher) was performed and the RNA was cleaned with RNA Clean & Concentrator (Zymo Research).
RNA was treated with 2 U/µL T4 PNK (NEB) in 1x T4 DNA Ligase Reaction Buffer (NEB) and 1 U/µL SUPERase•In RNase Inhibitor (Thermo Fisher) for 40 min at 37°C. An additional clean up with RNA Clean & Concentrator (Zymo Research) was added. RNAs with a length of 15-100 nts were selected and the library was prepared using NEBNext Small RNA Library Preparation Kit (NEB).


title: Xalb_smallRNASeq_Rep2


title: Xalb_totalRNASeq_Rep1


title: Ted5

value: BALB/c

value: 10 weeks

value: wild type

value: treated with teduglutide 0.2mg/kg/day

value: small intestine; Ileum


title: day8 RFP- H3K27ac rep3

description:
PtoN transition day 8
8dAPRnegOCT4neg_H3K27ac_peaks.gappedPeak

source_name: day8 RFP- H3K27ac

value: pluripotent stem cells

value: PtoN intermediate

value: PtoN transition

value: ChIP-seq


title: day8 RFP+ input rep1

description: PtoN transition day 8

source_name: day8 RFP+ input


title: day8 RFP+ input rep2

description: PtoN transition day 8


title: day8 RFP- input rep1

description: PtoN transition day 8

source_name: day8 RFP- input


title: day8 RFP- H3K27ac rep2


title: day8 RFP- input rep2

description: PtoN transition day 8


title: day10 RFP+GFP+ rep1 (re-analysis)

description:
re-analysis of GSM5327340
PtoN_counts.txt.gz, PtoN_FPKM.txt.gz

source_name: day10 RFP+GFP+


title: day8 RFP-GFP- rep2 (re-analysis)

description:
re-analysis of GSM5327363
PtoN_counts.txt.gz, PtoN_FPKM.txt.gz


title: day8 RFP-GFP- rep1 (re-analysis)

description:
re-analysis of GSM5327362
PtoN_counts.txt.gz, PtoN_FPKM.txt.gz


title: day8 RFP+GFP- rep2 (re-analysis)

description:
re-analysis of GSM5327361
PtoN_counts.txt.gz, PtoN_FPKM.txt.gz

source_name: day8 RFP+GFP-


title: day10 RFP+GFP- rep1 (re-analysis)

description:
re-analysis of GSM5327338
PtoN_counts.txt.gz, PtoN_FPKM.txt.gz

source_name: day10 RFP+GFP-


title: day10 RFP+GFP+ rep2 (re-analysis)

description:
re-analysis of GSM5327341
PtoN_counts.txt.gz, PtoN_FPKM.txt.gz


title: day8 RFP+GFP- rep1 (re-analysis)

description:
re-analysis of GSM5327360
PtoN_counts.txt.gz, PtoN_FPKM.txt.gz


title: day10 RFP+GFP- rep2 (re-analysis)

description:
re-analysis of GSM5327339
PtoN_counts.txt.gz, PtoN_FPKM.txt.gz


title: day8 RFP- H3K27ac rep1


title: day8 RFP- H3K4me3 rep3

description:
PtoN transition day 8
8dAPRnegOCT4neg_H3K4me3_peaks.gappedPeak

source_name: day8 RFP- H3K4me3


title: Ctl5

source_name: Ileum_injection water

value: treated with injection water

value: mixture of:Enterocytes, Paneth cells, intestinal stem cells, goblet cells, enteroendocrine cells


title: TM3_2_13_3_Penicillin G [10 µg ml-1]

city: Dresden

first: Thorsten

last: Mascher

address: Zellescher Weg 20b

department: Institute of Microbiology

institute: Technische Universität Dresden

data_processing:
mapping was done with bowtie 2 (bowtie 2: 2.4.1)
unmapped reads were filtered with samtools (samtools: 1.10).
Mapped reads were sorted, and converted to bam with samtools (samtools: 1.10)
counting features with FeatureCounts on the opposite strand (subread: 2.0.1)
counts were normalized using DESeq2 and a differential gene expression was calculated (DESeq2: 1.28.0, r-base: 4.0.2)
The DESeq 2 comparisons were combined and enriched to an Excel sheet using in-house scripts(, which can be accessed on request). Condition TM3_2_05 was used as the reference point.
With bamCoverage from Deeptools, bam files were normalized and converted to BigWig files for forward and reverse strand (deeptools: 3.4.3)
Genome_build: Assembly ASM904v1 (RefSeq: GCF_000009045.1); Genome annotation (in GFF format) was gathered from BSGatlas (Version 1.0)
Supplementary_files_format_and_content: Counts and normalized counts in tab separated files. A differential gene expression xlsx sheet containing all genes with p-values, adjusted p-values, log2 fold-changes, and information extracted from the GFF file. BigWig files contain coverages for either forward or reverse strand

organism: Bacillus subtilis

source_name: whole cells

growth_protocol: Overnight culture of B. subtilis W168 was prepared in LB medium (Sigma L3522) at 37 °C, 220 rpm overnight. On the next day, 10 ml LB medium (Sigma L3522) was inoculated with overnight culture in a 100 ml flask 1:100 and grown at 37 °C, 220 rpm until OD600 = 0.4-0.5 as day culture 1. Subsequently, 200 ml LB (Sigma L3522) in a 2000 ml flask was inoculated with appropriate amount of day culture 1 to an OD600 of 0.01, and incubated at 37 °C, 220 rpm until OD600 reached to around 0.4 as day culture 2. Then, day culture 2 was split into 25 ml aliquots and either exposed to corresponding antibiotics or remained untreated for 10 min under shaking. After that, cells were immediately transferred into pre-cooled 50 ml falcon tubes in ice/NaCl bath (ice:NaCl=3:1) to stop induction and then centrifuged at 4 °C, 8000 rcf for 3 min. The falcons containing the cell pellets were then frozen in liquid nitrogen and kept at -80°C until further use.

extract_protocol:
B. subtilis cells were disrupted using a micro-dismembrator. Total RNA isolation was performed with a phenol-chloroform isoamyl-alcohol (25:24:1, pH 5.5) extraction method.
rRNA was subtracted from the samples with the Illumina Ribo-Zero rRNA removal Kit (Bacteria) according to manufacturer instructions. The cDNA library was prepared using the NEB Ultra directional RNA library prep kit for Illumina according to instructions and sequencing was performed on an Illumina HiSeq3000 system.

treatment_protocol: The B. subtilis W168 at exponential growth phase of OD600 = 0.4 were treated with bacitracin (50 µg ml-1), vancomycin (1 µg ml-1), tunicamycin (10 µg ml-1), phosphomycin (10 µg ml-1), penicillin G (10 µg ml-1), flavomycin (10 µg ml-1) and lysozyme (10 µg ml-1), respectively, for 10 min at 37°C, 220 rpm . Non-treated samples were used as control. Each of the treatments and control were prepared in triplicates.

value: Bacillus subtilis W168 (BaSysBio)

value: trp+

tag: growth phase

value: logarithmic phase

value: Penicillin G [10 µg ml-1]


title: TM3_2_14_1_Flavomycin [10 µg ml-1]

value: Flavomycin [10 µg ml-1]


title: TM3_2_19_2_Lysozyme [10 µg ml-1]

value: Lysozyme [10 µg ml-1]


title: TM3_2_19_1_Lysozyme [10 µg ml-1]


title: TM3_2_14_3_Flavomycin [10 µg ml-1]


title: TM3_2_14_2_Flavomycin [10 µg ml-1]


title: TM3_2_19_3_Lysozyme [10 µg ml-1]


title: day8 RFP+ H3K27ac rep2

description:
PtoN transition day 8
8dAPRposOCT4neg_H3K27ac_peaks.gappedPeak

source_name: day8 RFP+ H3K27ac


title: day8 RFP+ H3K27ac rep1


title: day8 RFP- H3K4me3 rep1


title: day8 RFP+ H3K27ac rep3


title: day8 RFP- H3K4me3 rep2


title: day8 RFP+ H3K4me3 rep3

description:
PtoN transition day 8
8dAPRposOCT4neg_H3K4me3_peaks.gappedPeak

source_name: day8 RFP+ H3K4me3


title: day8 RFP+ H3K4me3 rep2


title: TM3_2_13_1_Penicillin G [10 µg ml-1]


title: TM3_2_10_2_D-Cycloserine [30 µg ml-1]

value: D-Cycloserine [30 µg ml-1]


title: TM3_2_09_1_Vancomycin [1 µg ml-1]

value: Vancomycin [1 µg ml-1]


title: day8 RFP+ H3K4me3 rep1


title: TM3_2_09_2_Vancomycin [1 µg ml-1]


title: TM3_2_10_1_D-Cycloserine [30 µg ml-1]


title: TM3_2_09_3_Vancomycin [1 µg ml-1]


title: TM3_2_11_1_Tunicamycin [10 µg ml-1]

value: Tunicamycin [10 µg ml-1]


title: TM3_2_12_1_Phosphomycin [10 µg ml-1]

value: Phosphomycin [10 µg ml-1]


title: TM3_2_12_3_Phosphomycin [10 µg ml-1]


title: TM3_2_10_3_D-Cycloserine [30 µg ml-1]


title: TM3_2_08_3_Bacitracin [50 µg ml-1]

value: Bacitracin [50 µg ml-1]


title: TM3_2_12_2_Phosphomycin [10 µg ml-1]


title: TM3_2_11_3_Tunicamycin [10 µg ml-1]


title: TM3_2_13_2_Penicillin G [10 µg ml-1]


title: TM3_2_11_2_Tunicamycin [10 µg ml-1]


title: TM3_2_05_2_non-treatment

value: non-treatment


title: MIA40_PNS_3

city: Warsaw

first: Cecilia

middle: Lanny

last: Winata

state: Masovia

address: 4 Ks. Trojdena Street

department: Zebrafish Developmental Genomics Laboratory

institute: International Institute of Molecular and Cell Biology in Warsaw

data_processing:
Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10.
rRNA filtering was performed with SortMeRNA v4.2.0 with arguments: -fastx -other -num_alignments 1 -paired_in –out2
Mapped to zebrafish transcipt with Salmon v1.3.0 with arguments:  -l A -- validateMapping --gcBias -g
Differential Expression analysis with DESeq2 v1.28.1 and tximport v1.16.1
Genome_build: GRCz11
Supplementary_files_format_and_content: Tab deliminated text files including normalized counts in TPM for each samples
Supplementary_files_format_and_content: Comma deliminated text files including differential expression data produced by DESeq2.

organism: Danio rerio

source_name: whole larvae

growth_protocol: Zebrafish embryos were maintained according to standard protocol (Westerfield et al., 2000) and staged according to standard morphological criteria (Kimmel et al., 1995).

extract_protocol:
Around 250 zebrafish larve were pooled at 5dpf stage and homogenised in ribosome friendly buffer to obtain MARS and HSF by differential centrifugation. Larvae were anaesthetized using Tricaine in E3 medium, washed thrice with Ringer’s solution and incubated in cold isolation buffer (IB) composed of 220 mM mannitol, 70 mM sucrose, 20 mM HEPES (pH 7.6), for at least 30 min. The larvae were suspended in 4ml of the isolation buffer with magnesium (IB-M) composed of 20 mM HEPES (pH 7.6), 220 mM mannitol, 70mM sucrose, 5 mM MgCl2, supplemented freshly with 2 mM phenylmethylsulfonyl fluoride (PMSF), 2mg/ml bovine serum albumin (BSA), 200µg/ml cycloheximide (CHX) and 10U/ml RiboLock RNase inhibitor and then homogenized in a 5 ml Dounce glass homogenizer equipped with a tight-fitting glass pestle by giving 15 strokes. The homogenate was centrifuged twice at 1500 X g for 10 min to remove nuclei and debris to obtain the post-nuclear supernatant (PNS). The PNS was centrifuged at 14,000 X g for 15 min to pellet down crude MARS fraction. Subsequently, the ultra-centrifugation of the supernatant at 100,000 X g for 60 min was performed to obtain the high speed fraction (HSF).
Following poly(A) enrichment method, the libraries were  prepared using the KAPA Stranded mRNA-Seq kit according to manufacturer's protocol. The libraries were cleaned up using Ampure beads (1X bead-based). Library fragment size distribution was confirmed by electrophoresis in Tapestation (Agilent Technologies). Library concentration was determined by both Quantus and qPCR. Sequencing was performed on the NextSeq500 instrument (Illumina) using the v2 chemistry, resulting in an average of 100 M reads per library with 2 x 75 bp paired-end setup.

tag: developmental stage

value: 5 dpf

tag: fraction

value: post-nuclear supernatant


title: TM3_2_08_2_Bacitracin [50 µg ml-1]

tag: genotype


title: MIA40_PNS_2


title: TM3_2_05_3_non-treatment


title: TM3_2_05_1_non-treatment


title: U87-MG cells, Normoxia 24h, replicate 1

city: Lund

first: Mattias

last: Belting

state: Skåne

address: Barngatan

department: Clinical Sciences Lund

country: Sweden

institute: Lund University

description:
Sample_Probe_Summary.txt
Control_Probe_Summary.txt
200118400033_H

hyb_protocol: Standard Illumina hybridization with Illumina Whole-Genome Gene Expression with IntelliHyb Seal 11226030 Rev C protocol

scan_protocol: Standard Illumina scanning protocol with Illumina iScan

data_processing: Downstream background correction, normalization, and differential expression analysis were performed with limma r package followed by gene annotation with illuminaHumanv4.db r package. Detection pvalues were obtained with lumi r package (v2.52.0)

source_name: U87-MG GBM cells conditioned at 21% of O2 for 24h

label_protocol: RNA was labelled with Modified Illumina TotalPrep-96 RNA Amplification Kit (Cat #4393543)

growth_protocol: U87-MG (ATCC, RRID: CVCL_0022) human high-grade glioma cells, authenticated by ATCC via STR, karyotyping, morphology, and cytochrome C oxidase I (COI) analysis, were routinely cultured in high-glucose DMEM (HyClone, GE) medium supplemented with 2 mmol/L L-glutamine (Sigma Aldrich, G7513), 100 U/ml Penicillin, 100 µg/ml Streptomycin (PEST; Sigma Aldrich, P0781), and with 10% (v/v) FBS (Sigma Aldrich, F7524) (full medium)

extract_protocol: For profiling of U87-MG mRNA, cells were grown in serum-free DMEM and pre-conditioned to 24 h normoxia or hypoxia in triplicates. Total RNA was extracted with RNeasy mini kit (Qiagen).

treatment_protocol: For experiments requiring hypoxia, cells were incubated in a humidified SCI-TIVE N-N Hypoxia workstation (Baker Ruskinn Technology) set at 5% CO2, 1% O2, and 37 °C for 24 h. For normoxic controls, cells were kept in a humidified 21% O2 and 5% CO2 incubator at 37 °C for the 24h period.

tag: tissue

value: Brain

tag: tumor

value: Glioblastoma (GBM)


title: U87-MG cells, Normoxia 24h, replicate 3

description:
Sample_Probe_Summary.txt
Control_Probe_Summary.txt
200118400033_G


title: U87-MG cells, Hypoxia 24h, replicate 2

description:
Sample_Probe_Summary.txt
Control_Probe_Summary.txt
200118400035_H

source_name: U87-MG GBM cells conditioned at 1% of O2 for 24h


title: MIA40_PNS_1


title: U3047-MG cells, Hypoxia 24h, replicate 2 [P15252_1032_S32]

data_processing:
Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.6.0/RTA v3.4.4) with a 2x151 setup using 'NovaSeqXp' workflow in 'S4' mode flowcell
Raw sequencing data was demultiplexed and converted to FastQ. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used was Sanger / phred33 / Illumina 1.8+
Paired-end adapter trimming was performed with Trim Galore (version 0.6.4_dev), followed by alignment with Human reference genome (Homo sapiens, GRCh38) using STAR software (version 2.7.3a). Reads quality control checks were done with fastQC (version 0.11.9), and reads quantification as counts with featureCounts (version 2.0.0).
Output and quality control report was generated with multiQC, version 1.8. Background correction, normalization, and differential gene expression analysis of protein-coding genes were performed with the DESeq2 r package (version 1.38.6) followed by gene annotation performed with biomaRt r package.
Assembly: Homo sapiens, GRCh38
Supplementary files format and content: tab-delimited text file containing raw reads quantification as counts (output from featureCounts).
Supplementary files format and content: tab-delimited text file containing normalized log2 counts (output from rlog function of DESeq2 r package) with gene annotation from BiomaRt.

source_name: Brain - Glioblastoma (GBM)

growth_protocol: The cells were seeded on dishes pre-coated with 10 µg/mL poly-L-ornithine hydrobromide (PLO, Sigma Aldrich, P3655) and 10 µg/mL laminin from Engelbreth-Holm-Swarm murine sarcoma basement membrane (Sigma Aldrich, L2020). Cells were routinely cultured in a 1:1 mix of Neurobasal (Gibco, 21103-049) and Dulbeco’s modified Eagle medium (DMEM) /F12 (Gibco, 31331-028) media without serum, complemented with 1% (v/v) N2 supplement (Gibco, 17502-048), 2% (v/v) B27 (Gibco, 12587-010) supplement, 10 ng/mL human recombinant FGF2 (Peprotech, 100-18B), 10 ng/mL EGF (Peprotech, AF-100-15), 100 U/mL Penicillin and 100 µg/mL Streptomycin (PEST; Sigma Aldrich, P0781) (growth medium). All cells were grown in a humidified 21% O2 and 5% CO2 incubator at 37 °C

extract_protocol:
Primary cells seeded into T25 flasks (0.3 - 0.5 x 106 cells/flask) and left to attach overnight (O/N) were pre-conditioned to 24 h normoxia/hypoxia (in triplicate experiments), detached with Accutase (Gibco, A1110501), collected in medium, and centrifuged for 5 min at 300 x g. The pellets were resuspended in phosphate-buffered saline (PBS) (Cytiva, SH30028.02) for cell counting, centrifuged for 5 min at 300 x g and each sample was resuspended in 350 µL RLT lysis buffer provided by the AllPrep DNA/RNA Mini Kit (Qiagen) supplemented with 1% (v/v) β-mercaptoethanol. Total RNA/DNA was then extracted as per manufacturer’s instructions. Nucleotide concentration and purity were determined with NanoDrop (ND1000) and further confirmed with Agilent Bioanalyzer QC at the Bioinformatics and Expression Analysis (BEA) core facility (Karolinska Institute, Stockholm).
RNA libraries for RNA-seq were prepared using the Trueseq stranded mRNA seq library kit as per the manufacturer's recommendations.

value: Brain - Glioblastoma (GBM)

value: Proneural GBM

value: WT

value: 24h Hypoxia


title: U3047-MG cells, Hypoxia 24h, replicate 3 [P15252_1033_S33]


title: U3034-MG cells, Hypoxia 24h, replicate 3 [P15252_1027_S27]

value: Mesenchymal GBM


title: U3034-MG cells, Normoxia 24h, replicate 3 [P15252_1026_S26]

value: 24h Normoxia


title: U3047-MG cells, Normoxia 24h, replicate 1 [P15252_1028_S28]


title: U3047-MG cells, Normoxia 24h, replicate 2 [P15252_1029_S29]


title: U3047-MG cells, Normoxia 24h, replicate 3 [P15252_1030_S30]


title: U3047-MG cells, Hypoxia 24h, replicate 1 [P15252_1031_S31]


title: TM3_2_08_1_Bacitracin [50 µg ml-1]

value: Bacillus subtilis W168 (BaSysBio)

value: trp+

value: logarithmic phase


title: MIA40_HSF_3

value: fraction enriched with cytosolic polysomes and minor part ER


title: MIA40_HSF_2


title: OE_A20_2 TM3 cells O/E A20

city: Nanjing

first: Dong

last: Xing

state: Jiangsu

address: Dingjiaqiao street

institute: Southeast university

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

source_name: Testis

growth_protocol: They were cultured in DMEM/F12 medium supplemented with 2.5% FBS, 5% horse serum , and 1% penicillin/streptomycin in a 5% CO2 incubator at 37°C.

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

value: Testis

value: Leydig cells

value: A20 overexpression


title: U3034-MG cells, Hypoxia 24h, replicate 2 [P15252_1023_S23]


title: U3017-MG cells, Normoxia 24h, replicate 3 [P15252_1018_S18]

value: Classical GBM


title: U3017-MG cells, Hypoxia 24h, replicate 3 [P15252_1021_S21]


title: U3034-MG cells, Normoxia 24h, replicate 1 [P15252_1024_S24]


title: U3017-MG cells, Hypoxia 24h, replicate 1 [P15252_1019_S19]


title: U3017-MG cells, Normoxia 24h, replicate 2 [P15252_1017_S17]


title: U3017-MG cells, Hypoxia 24h, replicate 2 [P15252_1020_S20]


title: U3034-MG cells, Hypoxia 24h, replicate 1 [P15252_1022_S22]


title: U3034-MG cells, Normoxia 24h, replicate 2 [P15252_1025_S25]


title: OE_A20_1 TM3 cells O/E A20


title: control_3 TM3 cells O/E control


title: OE_A20_3 TM3 cells O/E A20


title: control_2 TM3 cells O/E control


title: U87-MG cells, Hypoxia 24h, replicate 3

description:
Sample_Probe_Summary.txt
Control_Probe_Summary.txt
200118400035_E


title: control_1 TM3 cells O/E control


title: U3017-MG cells, Normoxia 24h, replicate 1 [P15252_1016_S16]


title: Mmp3 positive Set2

city: Bronx

first: Kosaku

last: Shinoda

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

description: positive cells using VB1-19770-PF

data_processing:
Sequenced reads were mapped to Ensembl Mouse Transcriptomes using kallisto v0.45.0 with parameters kallisto quant -b 30 R1.fastq.gz R2.fastq.gz
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: Mmp3 positive cells from SVF of subcutaneous adipose tissue

extract_protocol:
RNeasy FFPE Kit - QIAGEN
Library preparation, Illumina, strand-specific RNA-seq with rRNA depletion

value: subcutaneous adipose tissue

value: stromal vascular fraction cells


title: Midbrain organoids

city: Esch-sur-Alzette

first: Jens

middle: Christian

last: Schwamborn

address: 6 Avenue du Swing

country: Luxembourg

institute: Univeristy of Luxembourg

data_processing:
Demultiplexing of reads was performed with Illumina’s BaseCloud, and the resulting fastq files were used to initiate the data analysis.
CeleScope ™ version 1.14.0. (www.github.com/singleron-RD/CeleScope; Singleron Biotechnologies) was used to process the Illumina reads (fastq files) into gene expression matrices.
Adapter sequences and poly-A tails were trimmed using Cutadapt (https://cutadapt.readthedocs.io/en/stable/installation.html).
The trimmed Read2 reads were then aligned to the GRCh38 version of the human genome with Ensembl version 92 gene annotations using STAR v. 2.6.1a_08-27 (https://github.com/alexdobin/STAR) and featureCounts 2.0. To calculate the number of UMIs per gene per cell, we grouped reads with the same cell barcode, UMI, and gene together. The resulting UMI count tables for each cellular barcode were used for further analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values file and count matrix

source_name: human organoids

growth_protocol: Assembloids of mdbrain and striatum organoids were generated using NESCs and iPSCs respectively and they were co-cultured in their optimised conditions for 30 days. Midbrain organoids and Striatum organoids were cultured in their specific medium for up to D20 and D35 respectively. After that, they were cultured for 30 more days in the same co-culture media as the assembloids, until reaching D50 and D65 respectively.

extract_protocol:
Single nuclei suspension was obtained using the Minute Single Nucleus Isolation Kit for Neuronal tissues/cells (Invent Biotechnologies, INC.). To homogenize the frozen organoids, a pellet was first formed and then placed in an Eppendorf tube. 200μl of cold buffer A were added, and the mixture was pipetted up and down with a P200 pipette for 30 seconds. After that, 500μl of Buffer A were added, and the suspension was incubated on ice for 20 minutes. Every 5 minutes during incubation, pipetting up and down with a P200 for 30 seconds was performed to fully dissociate the organoids. The level of dissociation was observed under a light microscope at 5-minute intervals. After homogenization and dissociation, the suspension was transferred to a filter in a collection tube and then directly centrifuged at 13,000 X g for 30 seconds. The filter was discarded, and the resulting pellet was gently resuspended by pipetting up and down for 10-20 times and then centrifuged at 600xg for 5 minutes. The pellet containing nuclei was then resuspended in 500 μl of cold nuclei suspension buffer. Trypan Blue staining (0.4% w/v, Gibco) staining was used to assess the quality of the nuclei under a light microscope, propidium iodine with a Luna FX7 automated cell counter (Logos Biosystems, Villeneuve d’Ascq, France) was used to count the nuclei.
The reverse transcription to cDNA and the library were prepared with the GEXSCOPE® Single Nucleus RNA Library Kit V2 (Singleron Biotechnologies). A total of 30,000 nuclei were utilized and loaded onto a microfluidic chip (Singleron GEXSCOPE® Single Nucleus RNA Library Kit V2) to achieve a minimum capture of 6,000 nuclei. In a brief overview of the process, barcoded beads containing unique Cell Barcodes were loaded onto the chip, and then the nuclei were lysed. Following the nuclei lysis, Barcode Beads using poly (dT) sequences captured the polyadenylated RNA. The Barcode Beads, now containing captured mRNA molecules, were collected and subjected to a reverse transcription reaction. Subsequently, the cDNA was amplified and subjected to quality control (QC) procedures.

value: human organoids


title: Mmp3 positive Set1

description: positive cells using VB1-19770-PF


title: Assembloids


title: WT_PNS_3

value: 5 dpf

value: WT(AB)

value: post-nuclear supernatant


title: WT_PNS_2


title: MIA40_WHOLE_2

value: whole, unfractionated cell lysate


title: MIA40_MARS_3

value: fraction enriched with mitochondria with associated ribosomes


title: MIA40_HSF_1


title: MIA40_WHOLE_1


title: WT_HSF_2


title: MIA40_MARS_1


title: MIA40_WHOLE_3


title: MIA40_MARS_2


title: WT_HSF_3


title: Mmp3 negative Set2

description: negative cells using VB1-19770-PF

source_name: Mmp3 negative cells from SVF of subcutaneous adipose tissue

value: WT


title: WT_PNS_1


title: HCT-SIN3B-/-_SIN3A-siRNA#2

city: Santa Cruz

first: Gerd

middle: Armin

last: Mueller

state: CA

address: 1156 High Street

department: Chemistry and Biochemistry

institute: University of California, Santa Cruz

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
Reads were trimmed with trimgalore (version 0.6.10, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using cutadapt version 4.2 and fastqc v0.12.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) for quality control. After trimming, 0.5 % to 0.7% of reads were too short to be considered mappable (<20 nt).
Trimmed reads were mapped to the hg38 genome using segemehl (version 0.3.4), using standard parameters and the -S option to be able to map spliced reads. 42 to 53 million reads were mapped per sample (93 % to 96 % of all reads). Between 86 % and 91 % of all reads were mapped uniquely.
The mapped reads were annotated using featureCounts version 2.0.3 against the gencode v.27 annotation, using the following parameters:  -p -t exon -g gene_id.
Assembly: hg38
Supplementary files format and content: txt file read counts per gene

source_name: HCT116-SIN3B-/- ; SIN3A knockdown

growth_protocol: DMEM supplemented with 10% FBS; 5% CO2, 37°C

extract_protocol:
Total RNA was isolated with the Direct-zol RNA MiniPrep Kit (Zymo Research, #R2053).
RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). RNA samples were treated with TURBO DNase (ThermoFisher Scientific, Waltham, MA, USA) to remove DNA following manufacturer’s protocol. rRNA depletion sequencing library was prepared by using QIAGEN FastSelect rRNA HMR Kit (Qiagen, Hilden, Germany). RNA sequencing library preparation uses NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered on one flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration.

treatment_protocol: 20nM siRNA transfected with Lipofectamine RNAiMax for 48 h; 5µM Idasanutlin or DMSO for the final 24 h.

value: colon carcinoma

value: CTRL SIN3A siRNA #2 / Idasanulin


title: HCT-SIN3B-/-_SIN3A-siRNA#1

value: CTRL SIN3A siRNA #1 / Idasanulin


title: U87-MG cells, Normoxia 24h, replicate 2

description:
Sample_Probe_Summary.txt
Control_Probe_Summary.txt
200118400035_L

value: Brain

value: Glioblastoma (GBM)


title: U87-MG cells, Hypoxia 24h, replicate 1

description:
Sample_Probe_Summary.txt
Control_Probe_Summary.txt
200118400033_I


title: Striatum organoids


title: HCT-SIN3B-/-_SIN3A-siRNA#4

value: CTRL SIN3A siRNA #4 / Idasanulin


title: HCT-SIN3B-/-_CTRLsiRNA-3

value: CTRL siRNA / Idasanulin


title: Mmp3 negative Set1

description: negative cells using VB1-19770-PF


title: HCT-SIN3B-/-_CTRLsiRNA-2


title: HCT-SIN3B-/-_CTRLsiRNA-1


title: HCT-WT-SIN3A-siRNA#4

source_name: HCT116-SIN3A knockdown


title: HCT-WT-SIN3A-siRNA#1


title: WT_WHOLE_2


title: HCT-WT-SIN3A-siRNA#2


title: HCT-WT_CTRLsiRNA-2


title: WT_WHOLE_1


title: HCT-WT_CTRLsiRNA-1


title: WT_MARS_1


title: WT_HSF_1

value: fraction enriched with cytosolic polysomes and minor part ER


title: WT_MARS_2


title: WT_MARS_3


title: WT_WHOLE_3


title: CD34 negative cells rep4

city: New Haven

first: Rolando

last: Garcia-Milian

state: CT

address: 333 Cedar St

department: CWML

institute: Yale University

data_processing:
RNA libraries were prepared according to the Illumina kit protocol after poly-A selection and sequenced on the HiSeq 2500 platform in a stranded paired-end manner.
The generated fastq files were trimmed using custom Perl scripts. The trimmed reads were aligned to the mm10 genome using TopHat2 (C. Trapnell, L. Pachter, S. L. Salzberg, TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009). The transcript abundance estimation and differential gene expression was done using cuffdiff (C. Trapnell, D. G. Hendrickson, M. Sauvageau, L. Goff, J. L. Rinn, L. Pachter, Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol. 31, 46–53 (2013))
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: Erythroid-Myeloid-Lymphoid cells

extract_protocol:
After fresh bone marrow cells , 14.5 day C57BL/6 fetal liver cells or EML cells were isolated, the apoptotic cells were excluded using Annexin V Apoptosis Detection Kit eFluor® 450 (ebioscience), and only Annexin V negative cells were used to sort pure live cell populations for further analysis
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

tag: age

value: post natal day 14.7

value: CD43 negative


title: CD34 positive cells rep3

value: CD34 positive


title: CD34 positive cells rep2


title: B11_390_UNTR

data_processing:
fastp software was used first to obtain the clean reads
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was usend to count the reads
DESeq2 was used for differential expression analysis
Assembly: hg38
Supplementary files format and content: tab-delimited txt file (gene_count.txt) includes raw counts for each sample
Supplementary files format and content: tab-delimited txt file (gene_fpkm.txt) includes FPKM values for each sample
Supplementary files format and content: tab-delimited txt file (gene_fpkm_group.txt) includes FPKM values for each group of sample

growth_protocol: Assembloids of mdbrain and striatum organoids were generated using NESCs and iPSCs respectively and they were co-cultured in their optimised conditions for 60 days.

extract_protocol:
RNA was extracted from the assembloids using the RNeasy Mini Kit (Qiagen, 74106).
Poly-T oligo-attached magnetic beads were used to purify the messeger RNA from the total RNA. After fragmentation, random hexamer primers were used to synthesise the first cDNA strand. The second cDNA strand was synthesised using dUTP for the creation of directional library.

treatment_protocol: Assembloids from the DOX conditions, were treated with 4 ng/μl doxycycline (Sigma-Aldrich, D9891), disolved in water.

value: human organoids

value: PROG

tag: treatment

value: untreated


title: B11_390_DOX

value: doxycycline


title: CD34 positive cells rep1


title: B11_389_DOX

value: WT


title: B11_389_UNTR


title: Torin1-treated sample, 1h, whole-cell lysate (unfractionated)

city: Baltimore

first: James

last: Saba

state: MD

address: 725 N Wolfe St, 714 PCTB

department: Molecular Biology and Genetics

institute: Johns Hopkins

data_processing:
Sequencing was basecalled in real-time using the on-device Guppy basecaller (v4.2.3) in the MinKNOW software (v20.10.6) using the “high-accuracy” basecalling model. Multiplexed samples were demultiplexed in real-time, also using the on-device Guppy basecaller with the following key settings: “barcoding_kits=["SQKPCB109"], trim_barcodes="off", require_barcodes_both_ends="off", detect_mid_strand_barcodes="off", min_score=60.”
Each library was mapped to the transcriptome (using minimap2 with the -ax splice option), non-primary alignments excluded (using samtools view with the -F 256 option), and sorted (using samtools sort)
Raw counts were quantified directly from the SAM file using the uniq -c command and output to a raw counts file (processed data file 1)
Individual raw counts files were combined into a large data frame, filtered for transcripts with at least 80 reads across all fractions. Raw counts were then normalized to the raw counts value for the eGFP spike-in and raw counts for multiple transcripts for each gene were collapsed to the a single ENSEMBL canonical transcript (processed data file 2)
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file contains a transcript ID and raw counts associated with each transcript from each library
Supplementary files format and content: comma-delimited text file contains normalized counts for all transcripts in all libraries combined into a large data frame

growth_protocol: U266B1 cells were seeded at a density of 7.5 x 105 cells/mL in 55mL of media (RPMI supplemented with 20% FBS, 1 mM sodium pyruvate, and 5 ng/µL IL-6) in a T225 flask (CytoOne CC7682-4822) for 24h.

extract_protocol:
1h after treatment, cells were spun at 1000 x g for 1 min at room temperature, the media aspirated, and the cell pellet directly lysed in 150 µL of sucrose gradient lysis buffer. Lysates were gently pipetted to homogenize, transferred to ice for 10 min, and clarified by centrifuging at 8000 x g at 4°C for 5 min. 120 µg of RNA was sedimented along 10-50% sucrose gradients for 75 min and subsequently fractionated to 8 fractions. Thirty pg of eGFP mRNA was spiked into each fraction and RNA was extracted using TRIzol according to the manufacturer's instructions. Five µg of extracted RNA from each fraction was subjected to polyA-enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) according to the manufacturer’s instructions.
One ng of polyA-enriched RNA from each sample was subjected to the Nanopore PCR-cDNA Barcoding kit (ONT SQK-PCB109) according to the manufacturer’s instructions.

treatment_protocol: 1 day after seeding, cells were treated with either 300 nM Torin1 or an equivalent volume of DMSO (vehicle) for 1h

tag: cell line

value: Multiple myeloma


title: Torin1-treated sample, 1h, Fraction 3

tag: cell type


title: Torin1-treated sample, 1h, Fraction 5


title: Torin1-treated sample, 1h, Fraction 2


title: DMSO-treated sample, 1h, whole-cell lysate (un-fractionated)

value: DMSO


title: Torin1-treated sample, 1h, Fraction 4


title: Torin1-treated sample, 1h, Fraction 7


title: Torin1-treated sample, 1h, Fraction 1


title: Torin1-treated sample, 1h, Fraction 6


title: Torin1-treated sample, 1h, Fraction 8


title: Plasma EVPs Aged 11

city: Washington

first: Laura

last: Reck Cechinel

state: District of Columbia

address: 7144 13th Pl NW

institute: Children's National Medical Center

description:
Circulating plasma Extracellular vesicles and particles_Aged
miRNA expression data

hyb_protocol: Following labeling RNA was hybridized to affymetrix miRNA 4.0 GeneChips for 16 hours and washed and stained on the GeneChip Fluidics Station 450 using protocol FS450_0002.

scan_protocol: GeneChips were scanned on the Affymetrix GeneChip Scanner 3000

data_processing: Resulting data were normalized in Affymetrix Expression Console software using RMA-DABG and exported into Partek Genomics Suite version 6.6 for analysis.

organism: Rattus norvegicus

label_protocol: 1,000 ng of RNA was labeled using Affymetrix FlashTag Biotin HSR RNA labeling kit.

extract_protocol: extracellular vesicles and particles were isolated from plasm using Exoquick precipitation reagent. Total RNA was extracted using mirVana RNA isolation kits. Total RNA was amplified with the complete Seramir Exosome RNA amplification kit.

value: plasma extracellular vesicles and particles

tag: Sex

value: Male


title: Plasma EVPs Young-adult 9

description:
Circulating plasma Extracellular vesicles and particles_Young adult
miRNA expression data


title: Plasma EVPs Young-adult 10


title: CD34 negative cells rep3


title: Plasma EVPs Young-adult 21


title: Plasma EVPs Aged 20


title: Plasma EVPs Aged 13


title: Plasma EVPs Aged 12


title: Plasma EVPs Aged 14


title: Plasma EVPs Young-adult 18


title: Plasma EVPs Young-adult 15


title: Plasma EVPs Young-adult 17


title: Plasma EVPs Young-adult 16


title: CD34 negative cells rep2


title: DMSO-treated sample, 1h, Fraction 8


title: B10_390_DOX


title: CD34 negative cells rep1


title: DMSO-treated sample, 1h, Fraction 7


title: B10_389_DOX


title: B10_390_UNTR


title: DMSO-treated sample, 1h, Fraction 5


title: DMSO-treated sample, 1h, Fraction 6


title: B10_389_UNTR


title: B6_390_DOX


title: DMSO-treated sample, 1h, Fraction 3


title: DMSO-treated sample, 1h, Fraction 2


title: B6_389_DOX


title: B6_389_UNTR


title: DMSO-treated sample, 1h, Fraction 1


title: DMSO-treated sample, 1h, Fraction 4


title: B6_390_UNTR


title: Plasma EVPs Aged 19


title: Plasma EVPs Aged 1


title: Plasma EVPs Young-adult 2


title: Plasma EVPs Aged 4


title: Plasma EVPs Aged 3


title: B2-3W

city: Seongbuk-gu

first: Gyu-Bum

last: Yeon

state: Seoul

address: 145, Anam-ro

department: Department of Biodtechnology

country: South Korea

institute: Korea University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw FASTQ files were trimmed for adapters using BBDuk, and quntified their transcripts with Salmon using the reference transcript GENCODEV32 (GRCh38.p13)
Normalized abundance measurements was conducted with DESeq2 (1.27.12)
Assembly: GENCODEV32

source_name: Astrocyte

extract_protocol:
The total RNAs were extracted using TRIzol® (Thermo Fisher Scientific) according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using QuantSeq 3' mRNA-Seq Library Prep Kit FWD

value: H1 (hESC)

tag: regional character

value: Control (3week culture)


title: B3-3W


title: B2-6W

value: Senescent cell (6week culture)


title: B3-6W


title: R10 ecm 1-1

status: Public on Oct 27 2023

city: Richmond

first: Jonathan

middle: Michael

last: Plett

state: NSW

address: Bourke St. Entrance, Building L9

department: Hawkesbury Institute for the Environment

country: Australia

institute: Western Sydney University

description: Biological Replicate 1

data_processing:
Raw reads were trimmed and mapped to either the P. microcarpus (Plett et al., 2023) or E. grandis (Myberg et al., 2014) genomes in CLC Workbench (v22).
Normalisation of raw count data and analysis of differential gene regulation was performed using the DESeq2 package in R (version 1.30.1; Love et al., 2014).
Genes having less than an average of 5 counts per sample for all conditions were considered to be unexpressed and removed prior to the analysis. Genes were considered to be significantly differentially expressed when the padj < 0.05 (calculated from DESeq2 based on a Benjamini-Hochberg method) and the log2(fold change) was above 1 (over-expressed) or below 1 (under-expressed) for fungal genes or above 2.23 (over-expressed) or below 2.23 (under-expressed) for plant genes (equivalent to 2x and 5x differentially expressed, respectively).
Assembly: https://phytozome-next.jgi.doe.gov/info/Egrandis_v2_0; https://mycocosm.jgi.doe.gov/Pismi2/Pismi2.home.html
Supplementary files format and content: Raw read counts of all genes across all samples for E. grandis
Supplementary files format and content: Raw read counts of all genes across all samples for Pisolithus microcarpus

organism:
Eucalyptus grandis
Pisolithus microcarpus

source_name: Ectomycorrhizal root tip (fungus + lateral root)

growth_protocol: Plants and fungus were grown on half-strength MMN medium ((pH 5.5; 0.1 g l−1 glucose) at 22–30°C night/day temperature with a 16 h light cycle.

extract_protocol:
Spectrum Plant Total RNA (Sigma-Aldrich
Poly-A RNA libraries were prepared and sequenced using Illumina HiSeq platform with a 150bp paired-end configuration

treatment_protocol: Once the E. grandis seedlings were two months old and the fungal cultures had grown for 2 weeks, the plants and fungi were separated into one of two treatment categories: (1) fungal-free controls whereby the seedlings were transferred onto new half-strength MMN medium; (2) ‘physical contact’ seedlings were transferred onto new half-strength MMN medium and then placed into direct contact with the active growing edge of a fungal colony and then samples were harvested at 2 week post-contact. These plates were then closed using micropore tape to allow for gas exchange with the external environment.

value: Root + Hyphae

value: 2 week colonisation


title: MD06 ecm 1-1

description: Biological Replicate 1

value: Ectomycorrhizal root tip (fungus + lateral root)


title: R10 ecm 1-3

description: Biological Replicate 3


title: R10 ecm 1-2

description: Biological Replicate 2


title: R10 ecm 1-4

description: Biological Replicate 4


title: B1-3W


title: B1-6W


title: MD06 ecm 1-4

description: Biological Replicate 4


title: E. grandis Root (1/2 MMN) GA-28

description: Biological Replicate 1

organism: Eucalyptus grandis

source_name: Root tissue (axenic control)

value: Root tissue (axenic control)

value: Root

value: Axenic Control


title: MD06 ecm 1-2

description: Biological Replicate 2


title: Plasma EVPs Aged 5


title: Plasma EVPs Young-adult 8


title: Plasma EVPs Young-adult 7


title: Plasma EVPs Aged 6


title: MD06 ecm 1-3

description: Biological Replicate 3


title: si14 ecm 1-1

description: Biological Replicate 3


title: E. grandis Root (1/2 MMN) GA-30

description: Biological Replicate 3


title: E. grandis Root (1/2 MMN) GA-29

description: Biological Replicate 2


title: Mh615 ecm 1-3

description: Biological Replicate 3


title: Mh615 ecm 1-2

description: Biological Replicate 2


title: Md06 flm 1-2

description: Biological Replicate 2

organism: Pisolithus microcarpus

source_name: Free living mycelium (axenic control)

value: Free living mycelium (axenic control)

value: Hyphae


title: mw3 ecm 1-1

description: Biological Replicate 1


title: mw3 ecm 1-4

description: Biological Replicate 4


title: si14 ecm 1-3

description: Biological Replicate 1


title: si14 ecm 1-4

description: Biological Replicate 2


title: Wil3 ecm 1-4

description: Biological Replicate 4


title: Wil3 ecm 1-3

description: Biological Replicate 3


title: mw3 ecm 1-2

description: Biological Replicate 2


title: Wil3 ecm 1-2

description: Biological Replicate 2


title: Wil3 ecm 1-1

description: Biological Replicate 1


title: R10 flm 1-1

description: Biological Replicate 3


title: MD06 flm 1-1

description: Biological Replicate 1


title: MD06 Flm 1-3

description: Biological Replicate 3


title: R10 flm 1-3

description: Biological Replicate 2


title: Splenic NK cells, WT, Rep1

city: Zwijnaarde

first: Sophie

last: Janssens

address: Technologiepark 71

department: Inflammation Research Center

country: Belgium

institute: VIB/UGhent

data_processing:
Illumina software was used for basecalling.
Sequenced reads were inspected with FastQC v0.11.8, trimmed for adaptor sequences with Trimmomatic v0.39, then mapped to mm10 whole genome using STAR v2.7.3a, converted to BAM-files with Samtools v1.9 and finally counted with HTSeqCount v0.11.2
Limma v3.42.2 was used to normalize the count data.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with log-CPM values for all biologically meaningfully expressed genes for each sample

source_name: Spleen

extract_protocol:
NK cells were enriched from the spleens of NK-XBP1, NK-DKO and corresponding littermate controls with an NK cell-specific magnisort negative selection kit. Enriched fractions were stained in 150 µl FACS antibody mix containing Fc block. For each biological replicate a total of 50 000 NK cells were directly sorted into an eppendorf containing 450 µl RLT plus buffer (supplemented with 1/100 beta-mercapto) and snap-frozen on dry ice. Samples were stored at -80°C until further processing by the VIB Nucleomics Core.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Spleen

value: mRNA

value: NK cells

value: Steady-state


title: Splenic NK cells, WT, Rep5

value: WT


title: Splenic NK cells, XBP1-KO, Rep1


title: Splenic NK cells, WT, Rep6


title: Splenic NK cells, WT, Rep4


title: Splenic NK cells, DKO, Rep4

value: DKO


title: Splenic NK cells, XBP1-KO, Rep2


title: Splenic NK cells, WT, Rep3


title: mw3 ecm 1-3

description: Biological Replicate 3


title: Splenic NK cells, XBP1-KO, Rep3


title: Mh615 ecm 1-1

description: Biological Replicate 1


title: Splenic NK cells, DKO, Rep3


title: R10 flm 1-2

description: Biological Replicate 1


title: Splenic NK cells, WT, Rep2


title: Splenic NK cells, DKO, Rep5


title: Splenic NK cells, DKO, Rep2


title: si14 flm 1-2

description: Biological Replicate 2


title: Splenic NK cells, DKO, Rep1


title: mw3 flm 1-3

description: Biological Replicate 3


title: si14 flm 1-3

description: Biological Replicate 3


title: si14 flm 1-1

description: Biological Replicate 1


title: mw3 flm 1-2

description: Biological Replicate 2


title: wil3 flm 1-3

description: Biological Replicate 3


title: wil3 flm 1-2

description: Biological Replicate 2


title: Splenic NK cells, XBP1-KO, Rep4


title: MH615 flm 1-3

description: Biological Replicate 3

value: Fungal hyphae


title: wil3 flm 1-1

description: Biological Replicate 1


title: MH615 flm 1-1

description: Biological Replicate 1


title: Mw3 flm 1-1

description: Biological Replicate 1