title: bone marrow, R12, 1st


title: ChIP_k9me3_ST_jj8

status: Public on Jan 30 2023

type: SRA

city: Seoul

first: Je-Yoel

last: Cho

address: 1, Gwanak-ro, Gwanak-gu

department: Biochemistry

country: South Korea

institute: Seoul National University

library_source: genomic

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

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: Stomach

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

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

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

tag: tissue

value: Stomach

tag: Sex

value: Male

tag: breed

value: Beagle

tag: chip antibody

value: H3K9me3 (Abcam, #ab8898)


title: ChIP_k9me3_OV_679

source_name: Ovary

value: Ovary

value: Female


title: AC_iMSCs3_D21

city: Atlanta

first: Mohd

middle: Nazir

last: Khan

state: GA

address: 21 Ortho Lane

department: Orthopaedics

country: USA

institute: Emory University

library_source: transcriptomic

data_processing:
NovaSeq 6000 Paired-end sequencing was used, PE150, Q30≥85%.
Raw data (FASTQ file) were imported in BioJupies for alignment to human reference sequence genome (hg19)
Read count extraction and normalization were performed BioJupies notebook work flow
Differentially gene expression analysis were perfromed the R package limma
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: AC-iMSCs and OA-iMSCs (mesenchymal cells derived from iPSCs) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 5ng/ml bFGF and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen). 250 ng of total RNA was used for the generation of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Chondrogenic differentiation was done in pellet culture in 15 ml conical tube using 0.5 million cells. Differentiation was induced by treating the pellet with chondrogenic media at 2-day post pellet culture (designated day 0, D0) until 21 days of culture. Media was every alternate days.
Chondrogenic media consist of DMEM-High Glucose media (Gibco), 1% ITS+ premix, 40 µg/ml L-proline, 1mM sodium pyruvate, 1X nonessential amino acids, 1X Glutamax, 50 µg/ml ascorbic acid 2-phosphate, and 0.1µM dexamethasone, 1X-penicillin/streptomycin and human recombinant BMP-2 (100 ng/ml, Peprotech)

tag: cell line

tag: cell type

value: MSCs derived from iPSC

tag: genotype

value: Healthy chondrocytes iPSC derived iMSC

tag: treatment

value: Chondrogenic differentiation

tag: time

value: Day 21


title: ChIP_k27me3_ST_jj8


title: bone marrow, NR3, 1st

city: Providence

first: Patrycja

middle: M

last: Dubielecka

state: RI

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

department: Division of Hematology/Oncology, Department of Medicine

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

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text files show raw hit counts for each Sample

source_name: bone marrow

extract_protocol:
RNA was isolated from patient FFPE core bone marrow biopsies using the Qiagen's Rneasy FFPE Kit (Catalog# 73504)
Library preparation, Illumina, RNA with rRNA depletion

value: M

value: bone marrow

tag: age

tag: treatment response

value: Non-Responder


title: bone marrow, NR2, 1st

value: F


title: ChIP_k27me3_SP_jj8

source_name: Spleen

value: Spleen


title: bone marrow, NR13, 1st


title: ChIP_k27me3_PA_679

source_name: Pancreas

value: Pancreas


title: ChIP_k27me3_OV_679


title: bone marrow, NR1, 2nd


title: ChIP_k27me3_MG_679

source_name: Mammary gland

value: Mammary gland


title: ChIP_k9me3_CR_jj8

source_name: Cerebrum

value: Cerebrum


title: bone marrow, NR13, 2nd


title: AC_iMSCs3_D0

value: Day 0


title: AC_iMSCs1_D21


title: AC_iMSCs2_D21


title: AC_iMSCs2_D0


title: bone marrow, NR1, 1st


title: bone marrow, NR2, 2nd


title: OA_iMSCs2_D21

value: OA chondrocytes iPSC derived iMSC


title: OA_iMSCs3_D21


title: AC_iMSCs1_D0


title: ChIP_k27me3_LI_jj8

source_name: Liver

value: Liver

value: Male

value: Beagle


title: OA_iMSCs1_D21

value: MSCs derived from iPSC


title: Experiment 1_SAOS2_pona_5

city: Singapore

first: Maya

last: Jeitany

address: 60 Nanyang Dr

country: Singapore

institute: Nanyang Technological University

data_processing:
Experiment 1: 100 bp paired-end reads were pseudo-aligned and quantified to Gencode  (hg38)  transcripts using the Kallisto program.
Experiment 2: Paired-end reads were aligned to the reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene and subsequently, FPKM values were calculated for every gene.
Supplementary_files_format_and_content: Expression abundances in terms of FPKM or TPM as measured by DESeq2 or Kallisto respectively.

source_name: SAOS2 cells

growth_protocol: SAOS2 and T1000 cells were cultured in DMEM and RPMI media, respectively, supplemented with 10% FBS and 1% PS

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit (experiment 1) or Promega Reliaprep RNA cell miniprep kit (experiment 2).
Poly-A mRNAs enrichment

treatment_protocol: Experiment 1: cells were treated with either DMSO or ponatinib (250 nM) for 24 hours before collection. Experiment 2: Cells were transduced with lentiviral particules containing desired plasmids, and then selected with puromycin for at least 7 days before collection.

value: osteosarcoma cells

value: ponatinib 24 hours (replicate 2)


title: Experiment 1_T1000_DMSO_1

source_name: T1000 cells

value: liposarcoma cells

value: DMSO (replicate 1)


title: ChIP_k27me3_CR_jj8


title: OA_iMSCs3_D0

value: Chondrogenic differentiation


title: ChIP_k27me3_LU_jj8

source_name: Lung

value: Lung


title: Experiment 1_T1000_pona_7


title: Experiment 1_T1000_pona_1

value: ponatinib 24 hours (replicate 1)


title: Experiment 1_T1000_DMSO_7

value: DMSO (replicate 2)


title: ChIP_k27me3_CL_jj8

source_name: Cerebellum

value: Cerebellum


title: OA_iMSCs2_D0


title: ChIP_k27me3_KI_679

source_name: Kidney

value: Kidney

value: Female


title: ChIP_k27ac_ST_jj8

value: Stomach

value: H3K27ac (Abcam, #ab4729)


title: Experiment 1_SAOS2_pona_4


title: Experiment 1_SAOS2_DMSO_5


title: OA_iMSCs1_D0

value: OA chondrocytes iPSC derived iMSC

value: Day 0


title: Experiment 1_SAOS2_DMSO_4


title: ChIP_k27ac_PA_679

value: Pancreas

value: Beagle


title: ChIP_k27ac_OV_679

value: Ovary


title: ChIP_k27me3_CO_jj8

source_name: Colon

value: Colon

value: Male


title: H2030,  input

city: New York

first: Jing

last: Hu

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

data_processing:
For mapping and visualization, paired-end (50/50 bp) FASTQ reads were mapped to human genome hg19 using Bowtie2 with default filtering criteria. Resulted SAM files were converted to BAM files though Samtools. BAM files were sorted and indexed with Samtools.
BAM files were normalized, converted to bigwig files using bamCoverage-deepTools and displayed with IGV browser.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: H2087-LCC and H2087-LCC-SO1 cells were cultured in RPMI 1640 media supplemented with 10% FBS, 2 mM glutamine, 100 IU/mL penicillin/streptomycin, 1 µg/mL amphotericin B, 0.5 mM sodium pyruvate, 10 mM HEPES, 50 nM hydrocortisone, 25 nM sodium selenite, 20 µg/mL insulin, 10 µg/mL transferrin, 0.5% bovine serum albumin (BSA), and 1 ng/mL recombinant human epidermal growth factor. H2030 cells were cultured in RPMI 1640 media supplemented with 10% FBS, 2 mM glutamine, 100 IU/mL penicillin/streptomycin, and 1 µg/mL amphotericin B. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min and quenched with 0.125 M glycine for 5 min at room temperature. ChIP was performed using the ChIP assay kit (Millipore Sigma, #17-295) according to the manufacturer’s instructions.
Illumina sequencing libraries were prepared using the KAPA HTP Library Preparation Kit (Kapa Biosystems KK8234) according to the manufacturer’s instructions with an undetectable mass to 10 ng input DNA and 10 cycles of PCR.

treatment_protocol: H2087-LCC cells were treated with TGF-β1 (100 nM, R&D Systems) for 4 days.

value: Human lung adenocarcinoma


title: MSC, TGF-b2, M8213 [M8213-1]

city: Raleigh

first: Alix

middle: Kay

last: Berglund

state: NC

address: 1060 William Moore Dr

department: Clinical Sciences

institute: North Carolina State University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36.
The trimmed reads were mapped to the EquCab 3.0 using the STAR aligner v.2.5.2b.
Unique hit counts were calculated using featureCounts from the Subread package v.1.5.2.
Read count extraction and normalization were performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-deliniated text file containing normalized gene expression

source_name: mesenchymal stem cell

growth_protocol: Primary human mesenchymal stem cells were maintatined in low glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
PolyA selection

treatment_protocol: Paired samples of cells from each donor were treated with 1 ng/ml human recombinant transforming growth factor-beta2 (TGF-b2) for 72 hours

value: mesenchymal stem cell


title: MSC, control, M8213 [M8213-0]

value: control


title: ChIP_k27ac_MG_679

value: Mammary gland


title: H2030, H3K4me1

value: H3K4me1 (Abcam, #ab8895)


title: MSC, TGF-b2, M7526 [M7526-1]


title: ChIP_k27ac_LU_jj8

value: Lung


title: H2030, H3K27ac

value: H3K27Ac (Active Motif, #39133)


title: ChIP_k27ac_KI_679

value: Kidney

value: Female


title: H2087-LCC-SO1, H3K4me3

value: H3K4me3 (Millipore Sigma, #05-745)


title: H2087-LCC-SO1, H3K4me1


title: ChIP_k27ac_LI_jj8

value: Liver

value: H3K27ac (Abcam, #ab4729)


title: ChIP_k27ac_CR_jj8

value: Cerebrum


title: MSC, control, F4245 [F4245-0]


title: MSC TGF-b2, F4170 [F4170-1]


title: MSC, TGF-b2, F4245 [F4245-1]


title: H2087-LCC-SO1, H3K27ac


title: H2030, H3K4me3


title: H2087-LCC-SO1, input


title: ChIP_k27ac_CO_jj8

value: Beagle


title: ChIP_k27ac_SP_jj8

value: Spleen


title: ChIP_k27ac_CL_jj8

value: Cerebellum


title: ChIP_k4me1_SP_jj8

value: Male


title: MSC, control, F4170 [F4170-0]


title: ChIP_k4me1_ST_jj8

value: Stomach


title: H2087-LCC-TGFb, H3K4me3

value: Human lung adenocarcinoma


title: H2087-LCC-TGFb, H3K4me1


title: H2087-LCC-TGFb, input


title: ChIP_k4me1_PA_679

value: Pancreas


title: MSC, control, M7526 [M7526-0]

value: mesenchymal stem cell

value: control


title: H2087-LCC-TGFb, H3K27ac


title: H2087-LCC, input, bio rep 2


title: H2087-LCC, H3K4me3


title: 22Rv1, Liver metastase drived, rep3

city: Boston

first: Himisha

last: Beltran

state: MA

address: 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
RNA quantity and integrity were determined using the Qubit® Fluorometer and the Fragment Analyzer system with the PROSize 3.0 software (Agilent Technologies, Palo Alto, California, USA).
The RQN were ranging from 8.8 to 10 for all samples, which was considered sufficient. Illumina TruSEQ RNA library prep and sequencing reagents were used following the manufacturer’s recommendations using polyA-selected transcripts (Illumina, San Diego, CA, USA).
The samples were sequenced on the Illumina NovaSeq platform (2 x 150 bp, single index) and generated ~20 million paired-end reads for each sample.
Assembly: GRCh38
Supplementary files format and content: Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome.
Supplementary files format and content: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.

source_name: Cell line

growth_protocol: The medium for this cell lines is RPMI-1640 Medium supplumented with 10% fetal bovine serum.

extract_protocol:
 Total RNA was extracted from each tissue by using Qiagen's ‘RNeasy’ RNA extraction kit (Qiagen).
RNA-sequencing was performed by GENEWIZ (South Plainfield, NJ, USA). RNA quantity and integrity were determined using the Qubit® Fluorometer and the Fragment Analyzer system with the PROSize 3.0 software (Agilent Technologies, Palo Alto, California, USA). The RQN were ranging from 8.8 to 10 for all samples, which was considered sufficient. Illumina TruSEQ RNA library prep and sequencing reagents were used following the manufacturer’s recommendations using polyA-selected transcripts (Illumina, San Diego, CA, USA). The samples were sequenced on the Illumina NovaSeq platform (2 x 150 bp, single index) and generated ~20 million paired-end reads for each sample.

value: Cell line

value: Prostate cancer cell line

value: Liver metastase drived


title: ChIP_k4me1_OV_679

value: Ovary

value: Female

value: H3K4me1 (Abcam, #ab8895)


title: 22Rv1, Liver metastase drived, rep1


title: 22Rv1, Liver metastase drived, rep2


title: 22Rv1, Control, rep2

value: Wilde Type


title: ChIP_k4me1_MG_679

value: Mammary gland


title: H2087-LCC, input, bio rep 1


title: 22Rv1, Control, rep3


title: KiPS_RESET_Rep_4

city: Padua

first: Graziano

last: Martello

address: viale Colombo 3

department: Department of Biology

country: Italy

institute: University of Padua

data_processing:
trimming was performed using BBDuk from BBTools v38.87
alignment was performed with STAR 2.7.6a
quantification was performed with featureCounts 2.0.1
Genome_build: Human GRCh38.p13 Ensembl release 100
Supplementary_files_format_and_content: raw_counts_matrix.txt is a TSV containing EnsemblID, official gene symbols and raw counts for each condition

source_name: KiPS-chemical resetting

growth_protocol: Cells were cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs; DR4 ATCC) in PXGL medium3 or in RSeT medium (Stem Cell Technologies 05969 ). The PXGL medium was prepared as follows: N2B27 (DMEM/F12 [Gibco 11320-074], and Neurobasal in 1:1 ratio [Gibco 21103-049], with 1:200 N2 Supplement [Gibco 17502-048], and 1:100 B27 Supplement [Gibco 17504-044], 2 mM L-glutamine [Gibco 25030-024], 0.1 mM 2-mercaptoethanol [Sigma-Aldrich M3148]) supplemented with 1µM PD0325901 (Axon Medchem), 2 μM XAV939 (Axon Medchem), 2 μM Gö6983 (Axon Medchem) and 10 ng/ml human LIF (produced in-house). Human naive PSCs were passaged as single cells every 4 days at split ratio 1:3 or 1:4 following dissociation with TrypLE (Gibco 12563-029) for 10 minutes at room temperature (RT). The ROCK inhibitor (Y27632, Axon Medchem 1683) was added in the naïve medium only for 24h after passaging.

extract_protocol:
Total RNA was isolated using Total RNA Purification kit (Norgen Biotek), according to manufactorer's protocol.
Quant Seq 3' mRNA-seq Library Prep kit (Lexogen) is used for library construction.

treatment_protocol: Chemical resetting from primed to naive PSC. Cells were seeded at 10000 cells/cm2 on mitotically inactivated MEFs in E8 medium with 10µM ROCKi (added only for 24 hours). Two days after plating (day 0), medium was changed to PDL/HDACi (N2B27 with 1µM PD0325901, 10ng/ml human LIF and 1mM VPA (HDACi)). Following 3 days in PDL/HDACi, medium was changed to PXGL for a further 10-11 days before passing in PXGL medium on MEFs (see Fig. 1a). For the chemical resetting from primed to ccTSCs, KiPS were seeded at 10000 cells/cm2 on mitotically inactivated MEFs in E8 medium. Two days later (day 0) medium was changed to PDL/HDACi. Following 3 days in PDL/HDACi, medium was changed to PXGL.

value: chemical reset induced pluripotent stem cells


title: H2087-LCC, H3K4me1


title: 22Rv1, Primary Prostate, A03 22rv1-PT-m2

description: 22Rv1, Primary Prostate, A03

source_name: Primary Prostate

value: Primary Prostate


title: KiPS_RESET_Rep_3


title: 22Rv1, Primary Prostate, A01 22rv1-PT-m3

description: 22Rv1, Primary Prostate, A01


title: H2087-LCC, H3K27ac, bio rep 1

value: H3K27Ac (Active Motif, #39133)


title: ChIP_k4me1_LU_jj8

value: Lung

value: Male

value: Beagle


title: KiPS_RESET_Rep_2


title: 22Rv1, Primary Prostate, A01 22rv1-PT-m1

description: 22Rv1, Primary Prostate, A01


title: H2087-LCC, H3K27ac, bio rep 2

value: Human lung adenocarcinoma


title: ChIP_k4me1_LI_jj8

value: Liver


title: ChIP_k4me1_KI_679

value: Kidney


title: 22Rv1, Lymph node metastase, A01 22rv1-mLN-m3

description: 22Rv1, Lymph node metastase, A01

source_name: Lymph node metastase

value: Lymph node metastase


title: HK-2 cells, Lactoferrin and PM2.5, t24h, rep3

city: Taipei

first: Yung-Li

last: Wang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Graduate Institute of Clinical Medicine, Taipei Medical University

data_processing:
The original data obtained by high-throughput sequencing (Illumina NovaSeq 6000 platform) were transformed into raw sequenced reads by CASAVA base calling and stored in FASTQ format. FastQC and MultiQC were used to check fastq files for quality.
The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
The obtained high-quality data (clean reads) was used for subsequent analysis. Read pairs from each sample were aligned to the reference genome (e.g., H. sapiens, GRCh38) by the HISAT2 software (v2.1.0).
FeatureCounts (v1.6.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed DEGseq (v1.36.1) without biological duplicate and the “Relative Log Expression” normalization (RLE) was performed using DESeq2 (v1.22.1) with biological duplicate.
Assembly: GRCh38
Supplementary files format and content: *.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: human kidney

growth_protocol: HK-2 cells were maintained in Keratinocyte-serum-free medium (K-SFM) with bovine pituitary extract and human recombinant EGF (Invitrogen, CA), cultured at 37 °C/5% CO2.

extract_protocol:
Total RNA was isolated using the EasyPrep Total RNA Kit (Cat:TB-DPT-BD19).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were seeded 24 hours before treatment on 6-cm dish at a density of 6x10^5 cells per well with 4 ml of medium per dish. Cells were treated at ~90% confluency with the required doses for the required timepoints. Control cells were exposed to an appropriate concentration of the control vehicle.

value: immortalized human renal proximal tubular epithelial cells

value: pretreated with lactoferrin for 6 hours and then treated PM2.5 for 18 hours


title: ChIP_k4me1_CL_jj8

value: Cerebellum


title: HK-2 cells, Lactoferrin and PM2.5, t24h, rep2


title: 22Rv1, Control, rep1

value: Cell line

value: Prostate cancer cell line


title: ChIP_k4me1_CR_jj8

value: Cerebrum

value: H3K4me1 (Abcam, #ab8895)


title: KiPS_RESET_Rep_1

value: chemical reset induced pluripotent stem cells


title: 22Rv1, Liver metastase drived, A04 22rv1-Lv-m4

description: 22Rv1, Liver metastase drived, A04

source_name: Liver metastase

value: Liver metastase


title: 22Rv1, Lymph node metastase, A02 22rv1-mLN-m1

description: 22Rv1, Lymph node metastase, A02


title: KiPS_PRIMED_Rep_4

source_name: KiPS primed-iPSCs

growth_protocol: Cells were cultured in Feeder-free on pre-coated plates with 0.5% growth factor-reduced Matrigel (CORNING 356231) (in PBS with MgCl2/CaCl2, Sigma-Aldrich D8662) in E8 medium (made in-house according to12) at 37°C, 5% CO2, 5% O2. Cells were passaged every 3-4 days at a split ratio of 1:8 following dissociation with 0.5 mM EDTA (Invitrogen AM99260G) in PBS without MgCl2/CaCl2 (Sigma-Aldrich D8662), pH8.

value: primed induced pluripotent stem cells


title: ChIP_k4me3_ST_jj8

source_name: Stomach

value: Stomach

value: H3K4me3 (Abcam, #ab8580)


title: ChIP_k4me3_PA_679

source_name: Pancreas

value: Pancreas

value: Female

value: Beagle


title: ChIP_k4me1_CO_jj8

value: Colon

value: Male


title: KiPS_PRIMED_Rep_2


title: KiPS_PRIMED_Rep_3


title: HK-2 cells, Lactoferrin and PM2.5, t24h, rep1

value: immortalized human renal proximal tubular epithelial cells


title: ChIP_k4me3_OV_679

source_name: Ovary

value: Ovary


title: HK-2 cells, Lactoferrin and PM2.5, t24h, control sample, rep3

value: untreated


title: KiPS_PRIMED_Rep_1


title: 22Rv1, Lymph node metastase, A03 22rv1-mLN-m2

description: 22Rv1, Lymph node metastase, A03

value: Lymph node metastase


title: 22Rv1, Liver metastase drived, A01 22rv1-Lv-m3-2

description: 22Rv1, Liver metastase drived, A01


title: 22Rv1, Liver metastase drived, A01 22rv1-Lv-m3-3

description: 22Rv1, Liver metastase drived, A01


title: HK-2 cells, PM2.5, t24h, rep3

value: treated with PM2.5 for 24 hours


title: ChIP_k4me3_MG_679

source_name: Mammary gland

value: Mammary gland


title: HK-2 cells, PM2.5, t24h, rep1


title: HK-2 cells, PM2.5, t24h, rep2


title: HPD06_Rep_2

source_name: HPD06 naive-iPSCs

value: naive induced pluripotent stem cells


title: HK-2 cells, Lactoferrin and PM2.5, t24h, control sample, rep2


title: 22Rv1, Liver metastase drived, A01 22rv1-Lv-m3-4

description: 22Rv1, Liver metastase drived, A01


title: HPD06_Rep_1


title: ChIP_k4me3_LU_jj8

source_name: Lung

value: Lung


title: HPD06_Rep_3


title: ChIP_k4me3_SP_jj8

source_name: Spleen

value: Spleen


title: 22Rv1, Liver metastase drived, A02 22rv1-Lv-m1

description: 22Rv1, Liver metastase drived, A02

value: Liver metastase


title: HPD01_Rep_3

source_name: HPD01 naive-iPSCs


title: ssDNA_rep1

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

country: China

institute: Zhejiang University

description: H3.1 DNA

data_processing:
Sequencing reads adaptor and low-quality bases were removed by Trim Galore (version 0.6.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Bowtie2 (version 2.3.5.1) was used to map trimmed reads to the mouse reference genome mm9 and Tsin-H3.1-flag plasmid construct reference. PCR duplicates were removed by GATK4 (version 4.1.4.0) (https://github.com/broadinstitute/gatk) with the parameter ‘--REMOVE_DUPLICATES = true’ in cDNA data.
Expression matrixes were counted by featureCounts(Liao et al., 2014) (version 2.0.0)
BEDtools (version 2.92.2) and bedGraphToBigWig (version 4) (https://www.encodeproject.org/software/bedgraphtobigwig/) were used with the following parameters ‘genomecov --scaleFactor 10,000,00/(the number of reads mapped to mm9 or Tsin-H3.1-flag plasmid construct reference)’. Normalized signals were visualized in Integrative Genomics Viewer (IGV)  (version 2.6.3).
Assembly: mm9
Assembly: Tsin-H3.1-flag plasmid construct reference
Supplementary files format and content: BigWig files
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample of TABLE-seq

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured on 0.1% gelatin-coated dishes in DMEM supplemented with 15% fetal bovine serum (FBS), 1% antibiotic solution (penicillin/streptomycin), 1% glutamax, 1% MEM nonessential amino acids, 1% sodium pyruvate, 0.1 mM beta-mercaptoethanol and 1000 U/ml recombinant leukemia inhibitory factor (LIF). HEK293T cells were cultured in DMEM supplemented with 10% FBS and 1% antibiotic solution (penicillin/streptomycin). All cells were grown at 37 C and 5% CO2.

extract_protocol:
RNA extraction was performed by RNeasy Plus Mini Kit (Qiagen, Cat. #74134).
2 μl 100 μM 5ph_Tn5a and 2 μl 100 μM Tn5a_N6_invert_dT were added to 16 μl H2O. Samples were annealed by 95 C for 5 min and ramped to 25 C at 5 C/min. 1 μl Exo I, 3 μl 10X Exo I reaction buffer, and 6 μl H2O were added and incubated at 37 C for 30 min, followed by 80 C for 15 min. The annealed adaptors were purified by 2X of VAHTS DNA clean beads, eluted into 20 μl H2O, and stored at -20 C until usage.    10 μl tagmented ssDNA or cDNA was mixed with 2 μl annealed adaptors, 0.5 μl T4 DNA ligase (Takara, Cat. #2011A), 2 μl 10X ligation buffer, 2.5 μl 40% PEG6000, 3 μl H2O, and incubated at 20 C for 1 hour. The ligated DNA was purified by 0.8X VAHTS DNA clean beads and eluted into 10 μl H2O. The purified DNA was amplified by primers with sequencing indexes. 1 μl 10 μM forward primer, 1 μl 10 μM reverse primer, 8 μl DNA, and 10 μl 2X HIFI PCR Master Mix (NEB, Cat. #M0541L) were mixed and amplified at 72 C for 5 min, 98 C for 30 sec, 20 cycles of 98 C for 10 sec and 63 C for 10 sec, then 72 C for 1 min, 16 C to hold. PCR products were purified by 0.9X VAHTS DNA clean beads and eluted into 20 μl H2O. The concentrations of DNA were detected by Equalbit 1X dsDNA HS Working Solution (Vazyme, Cat. #121-01-AA). The libraries were sequenced on an Illumina NovaSeq platform with pair-end reads of 150 bp.
TABLE-seq

value: WT


title: HPD00_Rep_3

source_name: HPD00 primed-iPSCs

value: primed induced pluripotent stem cells


title: Experiment 2_JUN_3

source_name: SAOS2 cells

value: osteosarcoma cells

value: cells overexpressing JUN  (replicate 3)


title: 22Rv1, Liver metastase drived, A02 22rv1-Lv-m3-1

description: 22Rv1, Liver metastase drived, A02


title: ChIP_k4me3_CR_jj8

source_name: Cerebrum

value: Cerebrum

value: Beagle

value: H3K4me3 (Abcam, #ab8580)


title: ChIP_k4me3_CO_jj8

source_name: Colon

value: Colon

value: Male


title: B111, IL-13

city: Davos Wolfgang

first: Milena

last: Sokolowska

state: Graubünden

country: Switzerland

institute: Swiss Institute of Allergy and Asthma Research (SIAF)

description:
High Output v4
Asthma_IL13_over_unst.txt
Asthma_IL13_over_Control_IL13.txt

data_processing:
Data was processed with the workflow available at https://github.com/uzh/ezRun
Significant treshold was set to FDR > 0.05 calculated using the edgeR R package
Normalized abundance measurements was performed by edgeR
Assembly: GRCh38.p10
Supplementary files format and content: tab-delimited text files include FPKM values and normalized counts for each Sample, including fdr and p-value

source_name: primary bronchial epithelial cells

growth_protocol: bronchial epithelial cells were maintained in BEGM medium (Lonza), diluted 1:1 with DMEM containing 10% fetal bovine serum (FBS)  in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted with RNeasy Plus Micro Kit (Qiagen, Hilden, Germany), according to manufacturers protocol.
Samples with RNA integrity greater than 9.0 were chosen for library preparation with the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, California), according to manufacturers protocol.

treatment_protocol: Upon full differentiation (4 weeks), cells have been treated with IL-13 (50ng/ml) and harvested 24h post stimulation

tag: disease state

value: Asthma

tag: gender

value: female

value: primary bronchial epithelial cells


title: HK-2 cells, Lactoferrin and PM2.5, t24h, control sample, rep1

value: immortalized human renal proximal tubular epithelial cells

value: untreated


title: HPD01_Rep_2

value: naive induced pluripotent stem cells


title: HPD00_Rep_1


title: ChIP_k4me3_KI_679

source_name: Kidney

value: Kidney

value: Female


title: ssDNA_rep2

description: H3.1 DNA

source_name: Tsin-H3.1-flag plasmid construct reference

value: WT


title: ChIP_k4me3_LI_jj8

source_name: Liver

value: Liver


title: B121, IL-13

value: male


title: B99, unstimulated

description:
High Output v4
Asthma_IL13_over_unst.txt


title: B99, IL-13


title: HPD00_Rep_2

value: primed induced pluripotent stem cells


title: ChIP_k4me3_CL_jj8

source_name: Cerebellum

value: Cerebellum


title: Experiment 2_CTRL_2

value: osteosarcoma cells

value: cells overexpressing GFP as a control (CTRL) (replicate 2)


title: Experiment 2_JUN_2

value: cells overexpressing JUN  (replicate 2)


title: B111, unstimulated


title: B121, unstimulated


title: Experiment 2_CTRL_3

value: cells overexpressing GFP as a control (CTRL) (replicate 3)


title: HPD01_Rep_1


title: B116, IL-13

value: Asthma


title: Experiment 2_JUN_1

value: cells overexpressing JUN  (replicate 1)


title: B116, unstimulated

value: female

value: primary bronchial epithelial cells


title: H9_Rep_2

source_name: H9 primed-ESCs

value: human embryonic stem cells


title: B117, unstimulated

value: untreated


title: H9_Rep_3


title: Experiment 2_cjunsg_3

value: cells transduced with CRISPR-Cas9 and jun sg (replicate 3)


title: B117, IL-13


title: Experiment 2_cjunsg_2

value: cells transduced with CRISPR-Cas9 and jun sg (replicate 2)


title: AA_CD8_unstim_D2_KT_02

city: Molndal

first: Elisabeth

last: Israelsson

address: Pepparedsleden 1

department: Translational Biology

country: Sweden

institute: AstraZeneca, IMED RIA

description:
AA_CD8_unstim_D2_KT_02_S5
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

data_processing:
Base calling was done by bcl2fastq from Illumina.
Reads were mapped with HiSat2 (2.0.4).
Counts were generated with featurecounts (1.4.4).
TPMs were generated using Sailfish (0.10.1).
All processing was wrapped together with bcbio 0.9.9.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: combined.counts.txt: Tab-delimited text file includes counts.
Supplementary_files_format_and_content: combined.gene.sf.tpm.txt: Tab-delimited text file includes TPMs.

source_name: peripheral blood CD8+ T-cells, Unstimulated

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMCs) were isolated by Sepmate technique (Stemcell Technologies) from heparinized venous blood from healthy volunteers. Primary human CD8+ T-cells were further isolated using a negative selection kit according to protocol (Miltenyi Biotech).

extract_protocol:
RNeasy Mini kit with on-column DNA digestion (QIAGEN, Hilden, Germany) and eluted in 50 ul RNase-free water.
RNA was diluted to 5ng/ul and used as input to create RNA libraries using TruSeq Stranded mRNA kit (Illumina, CA, USA) following standard instructions. Libraries were validated on the BioAnalyzer (Agilent, CA, USA) using DNA1000 chip and the concentration was determined using Quant-iT dsDNA High Sensitivity assay kit on the Qubit fluorometer (Thermo Fisher, MA, USA). Sample libraries were pooled in equimolar concentrations and diluted and denatured according to Illumina guidelines. The pool was then sequenced using a High Output 2 x 76 bp kit on an Illumina NextSeq500.

treatment_protocol: CD8+ T-cells were stimulated in vitro with plate bound anti-CD3 (OKT3) in complete media in the presence or absence of different JAK inhibitors; tofacitinib, ruxolitinib and a selective JAK1 inhibitor at 300 nM. Soluble anti-CD28 were added to the CD8+ cultures to facilitate co-stimulation. After 40h, supernatants were harvested for mediator analysis and the cells were washed and resuspended in RLT buffer (Qiagen) for RNA isolation.

value: healthy

value: CD8+ T-cells

value: Unstimulated

tag: timepoint

tag: donor


title: B87, IL-13

description:
High Output v4
Control_IL13_over_unst.txt
Asthma_IL13_over_Control_IL13.txt

value: Control


title: AA_CD8_unstim_D4_KT_04

description:
AA_CD8_unstim_D4_KT_04_S13
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: AA_CD8_unstim_D3_KT_03

description:
AA_CD8_unstim_D3_KT_03_S9
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: H9_Rep_1


title: Metaplastic breast cancer 4

type: RNA

city: London

first: Ernesto

last: Yague

address: Du Cane Road

department: Division of Cancer

country: United Kingdom

institute: Imperial College London

hyb_protocol: GeneChip® Cartridge Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix).

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

data_processing: RMA-normalised expression was calculated using the R tool ‘oligo’ (Carvalho BS, Irizarry RA. “A Framework for Oligonucleotide Microarray Preprocessing” Bioinformatics (2010) 26(19), 2363-7).

label: biotin

source_name: RNA isolated from FFPE sections

label_protocol: Affymetrix FlashTag Biotin HSR RNA Labeling Kit

extract_protocol: 2-3 10 micrometer FFPE pathological slides were used to isolate RNA using a Qiagen miRNeasy FFPE kit

value: breast

tag: disease

value: Breast cancer

tag: pathology

value: Metaplastic

tag: further pathological characteristics

value: IHC showed spindle-lke type with regions with chondroid elements


title: Metaplastic breast cancer 2

tag: tissue

value: IHC indicates zones E-cadherin positive; some chondroid and osteoid zones; some foci IDC


title: Metaplastic breast cancer 5

value: IHC showed homogeneous spindle-lke type


title: Experiment 2_LacZsg_1

value: osteosarcoma cells

value: cells transduced with CRISPR-Cas9 and LacZ sg (replicate 1)


title: Invasive lobular carcinoma 5

value: Invasive lobular carcinomar

value: IHC showed homogeneous IDC


title: AA_CD8_unstim_D1_KT_01

description:
AA_CD8_unstim_D1_KT_01_S1
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: AA_CD8_Tofa_300nM_D3_KT_19

description:
AA_CD8_Tofa_300nM_D3_KT_19_S11
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

source_name: peripheral blood CD8+ T-cells, Tofacitinib

value: Tofacitinib

tag: concentration


title: B87, unstimulated

description:
High Output v4
Control_IL13_over_unst.txt

value: female

value: primary bronchial epithelial cells

value: untreated


title: Metaplastic breast cancer 1


title: Experiment 2_cjunsg_1

value: cells transduced with CRISPR-Cas9 and jun sg (replicate 1)


title: AA_CD8_Tofa_300nM_D4_KT_20

description:
AA_CD8_Tofa_300nM_D4_KT_20_S15
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

value: healthy

value: CD8+ T-cells


title: Metaplastic breast cancer 3

value: breast


title: Invasive lobular carcinoma 4

value: Breast cancer


title: Experiment 2_CTRL_1

value: cells overexpressing GFP as a control (CTRL) (replicate 1)


title: AML_Patients_8

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

description:
P-8_FRAS202431939-1r
processed data file:
AML_VS_Normal_count_and_DESeq2Normalised_anno.csv,AML_VS_Normal_rMATS_results.csv

data_processing:
Sequenced reads were mapped to hg19 whole genome using STAR_2.6.0a
Counts were normalized by Transcript per million (TPM) and differentially expressed genes identified by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: txt files with gene TPM

molecule: polyA RNA

source_name: WBC

extract_protocol:
WBC Preparation: Blood samples of newly diagnosed patients with a higher leukemia cells number and normal samples are collected in tubes containing EDTA, Collect 4 ml of each person. Centrifuge samples at 800 g for 5 min at room temperature, remove the upper plasma layer with a transfer pipet, being careful not to disturb the cells layer, and add 10mL 1XACK lysis buffer to resuspend cells on ice for 5 min, and then centrifuge at 400g at room temperature for 3min. Discard the supernatant and wash cells twice with PBS then centrifuge at 400g at RT for 3min, add 2%FBS(PBS) buffer to resuspend WBCs ,and count with a manual counter. 2 million WBCs was used to extract RNA with 1ml Trizol.
RNA-seq libraries were constructed by Illumina Stranded mRNA Sample Preparation Kit (NEB, Cat#E7770) according to the manufacturer’s protocol,

tag: tissue type

value: AML patient

value: WBC

tag: strategy


title: Human

city: xian

first: Cangang

last: Zhang

state: State...

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

institute: xian jiaotong university

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

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

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

tag: cell type

value: Splenocytes


title: Experiment 2_LacZsg_2

value: osteosarcoma cells

value: cells transduced with CRISPR-Cas9 and LacZ sg (replicate 2)

tag: cell line


title: B129, IL-13

value: Control

value: male

tag: treatment


title: Invasive lobular carcinoma 3

value: Invasive lobular carcinomar

value: IHC showed homogeneous IDC


title: B90, IL-13

value: primary bronchial epithelial cells

tag: time


title: Invasive ductal carcinoma 5

value: Invasive ductal carcinoma

value: IHC showed heterogeneous ILC with other types


title: AML_Patients_5

description:
P-5_FRAS202431936-1r
processed data file:
AML_VS_Normal_count_and_DESeq2Normalised_anno.csv,AML_VS_Normal_rMATS_results.csv


title: B113, IL-13


title: B129, unstimulated

value: untreated


title: AA_CD8_Tofa_300nM_D2_KT_18

description:
AA_CD8_Tofa_300nM_D2_KT_18_S7
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

value: healthy

value: CD8+ T-cells

value: Tofacitinib


title: Experiment 2_LacZsg_3

value: cells transduced with CRISPR-Cas9 and LacZ sg (replicate 3)


title: B90, unstimulated


title: AML_Patients_4

description:
P-4_FRAS202431935-1r
processed data file:
AML_VS_Normal_count_and_DESeq2Normalised_anno.csv,AML_VS_Normal_rMATS_results.csv

value: AML patient


title: Invasive lobular carcinoma 1

value: breast

value: Breast cancer

value: IHC showed heterogeneous IDC with other types


title: AML_Patients_6

description:
P-6_FRAS202431937-1r
processed data file:
AML_VS_Normal_count_and_DESeq2Normalised_anno.csv,AML_VS_Normal_rMATS_results.csv

value: WBC


title: AA_CD8_Tofa_300nM_D1_KT_17

description:
AA_CD8_Tofa_300nM_D1_KT_17_S3
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: AML_Patients_7

description:
P-7_FRAS202431938-1r
processed data file:
AML_VS_Normal_count_and_DESeq2Normalised_anno.csv,AML_VS_Normal_rMATS_results.csv


title: B113, unstimulated

value: Control


title: AA_CD8_Ruxo_300nM_D2_KT_14

description:
AA_CD8_Ruxo_300nM_D2_KT_14_S21
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

source_name: peripheral blood CD8+ T-cells, Ruxolitinib

value: Ruxolitinib


title: Invasive lobular carcinoma 2

value: Invasive lobular carcinomar


title: Invasive ductal carcinoma 1

value: IHC showed homogeneous IDC


title: Invasive ductal carcinoma 4


title: B86, unstimulated

value: male

value: primary bronchial epithelial cells


title: B86, IL-13


title: AA_CD8_Ruxo_300nM_D1_KT_13

description:
AA_CD8_Ruxo_300nM_D1_KT_13_S18
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: AA_CD8_Ruxo_300nM_D3_KT_15

description:
AA_CD8_Ruxo_300nM_D3_KT_15_S24
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: AA_CD8_DMSO_D3_KT_07

description:
AA_CD8_DMSO_D3_KT_07_S23
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

source_name: peripheral blood CD8+ T-cells, DMSO

value: DMSO


title: AA_CD8_DMSO_D4_KT_08

description:
AA_CD8_DMSO_D4_KT_08_S26
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: AML_Patients_3

description:
P-3_FRAS202431934-1r
processed data file:
AML_VS_Normal_count_and_DESeq2Normalised_anno.csv,AML_VS_Normal_rMATS_results.csv


title: Planktonic H37Rv [Mtb_control2]

city: Bengaluru

first: Rachit

last: Agarwal

state: Karnataka

address: CV Raman road

department: Biosystems Science and Engineering

country: India

institute: Indian Institute of Science, Bangalore

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

organism: Mycobacterium tuberculosis H37Rv

source_name: Mtb

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

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

value: Mtb

tag: genotype

value: WT

value: planktonic Mtb


title: AA_CD8_DMSO_D1_KT_05

description:
AA_CD8_DMSO_D1_KT_05_S17
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

value: healthy

value: CD8+ T-cells


title: AA_CD8_DMSO_D2_KT_06

description:
AA_CD8_DMSO_D2_KT_06_S20
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: AML_Patients_1

description:
P-1_FRAS202431932-1r
processed data file:
AML_VS_Normal_count_and_DESeq2Normalised_anno.csv,AML_VS_Normal_rMATS_results.csv

value: AML patient


title: Frog

organism: Xenopus tropicalis

value: Splenocytes


title: Planktonic H37Rv [Mtb_control3]


title: Normal_3

description:
N-3_FRAS202431942-1r
processed data file:
AML_VS_Normal_count_and_DESeq2Normalised_anno.csv,AML_VS_Normal_rMATS_results.csv

value: normal


title: Planktonic H37Rv [Mtb_control1]


title: AA_CD8_AZ8709_300nM_D4_KT_12

description:
AA_CD8_AZ8709_300nM_D4_KT_12_S14
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

source_name: peripheral blood CD8+ T-cells, AZ8709


title: Invasive ductal carcinoma 3

value: breast

value: Breast cancer

value: Invasive ductal carcinoma


title: AA_CD8_Ruxo_300nM_D4_KT_16

description:
AA_CD8_Ruxo_300nM_D4_KT_16_S27
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

value: Ruxolitinib


title: AML_Patients_2

description:
P-2_FRAS202431933-1r
processed data file:
AML_VS_Normal_count_and_DESeq2Normalised_anno.csv,AML_VS_Normal_rMATS_results.csv

value: WBC


title: bening tumor 2

value: Bening tumour

value: Fibroadenoma


title: Normal_2

description:
N-2_FRAS202431941-1r
processed data file:
AML_VS_Normal_count_and_DESeq2Normalised_anno.csv,AML_VS_Normal_rMATS_results.csv


title: Mtb from infected collagen gels, D14 [Dual_Mtb3]

source_name: Collagen hydrogels

value: Collagen hydrogels

value: Mtb RNA from infected collagen gels


title: bening tumor 1

value: Tubular adenoma


title: Mtb from infected collagen gels, D14 [Dual_Mtb2]

value: Mtb

value: WT


title: cosmetic reduction mammoplasty 2

value: Normal

value: cosmetic reduction mammoplasty


title: bening tumor 3


title: cosmetic reduction mammoplasty 3


title: AA_CD8_AZ8709_300nM_D2_KT_10

description:
AA_CD8_AZ8709_300nM_D2_KT_10_S6
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

value: healthy

value: CD8+ T-cells


title: Mtb from infected collagen gels, D14 [Dual_Mtb1]


title: Normal_1

description:
N-1_FRAS202431940-1r
processed data file:
AML_VS_Normal_count_and_DESeq2Normalised_anno.csv,AML_VS_Normal_rMATS_results.csv

value: normal


title: AA_CD8_AZ8709_300nM_D3_KT_11

description:
AA_CD8_AZ8709_300nM_D3_KT_11_S10
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: AA_CD8_AZ8709_300nM_D1_KT_09

description:
AA_CD8_AZ8709_300nM_D1_KT_09_S2
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: cosmetic reduction mammoplasty 1

value: breast


title: INS-1E cells, 20 mM glucose + drugs, rep, 18

status: Public on Jan 29 2023

city: Waurn Ponds

first: Kathryn

last: Aston-Mourney

state: VIC

address: 75 Pigdons Rd

country: Australia

institute: Deakin University

data_processing:
Quality control (QC) of the raw sequence data was performed using the BaseSpace app FastQC Version 1.0.0, where the minimum quality value for all samples was well above Q30 (highest quality range)
The sequences were trimmed to remove adapter sequence using FASTQ Toolkit Version: 2.0.0 by BaseSpace Labs
Sequences were then aligned against reference genome (Rattus norvegicus UCSC rn5 (RefSeq gene annotations)) using TopHat Alignment app by Illumina, Inc (using Bowtie 1)
Using Cufflinks 2, the expression values were calculated for each transcripts, based on the number of FPKM (Fragments Per Kilobase of exon model per Million mapped reads).
Assembly: Rattus norvegicus UCSC rn5 (RefSeq gene annotations)
Supplementary files format and content: The processed file contains genes in rows  and samples in columns. Column A contains the tracking id of each gene as identified from the TopHat Alignment. Column B contains the Gene ID and column C the length in bases. Columns D through to BJ contain the data for each sample (identified from the sample ID in row 1).

organism: Rattus norvegicus

extract_protocol:
Treated INS-1E cells were washed twice with phosphate buffered saline (PBS) and  then collected in TRIzol reagent (Invitrogen, Carlsbad, USA). RNA was extracted by  first adding chloroform followed by centrifugation, to separate the organic and  aqueous components, and collection of the supernatant. An equal volume of ethanol  was added followed by centrifugation and collection of the supernatant. The aqueous  supernatant was then further purified using RNeasy Mini columns (Qiagen, Hilden,  Germany). Purified total RNA was eluted in RNase-free water.
Total RNA samples were quantified and tested for quality using Agilent RNA 6000 Nano Kit. mRNA from the total RNA (0.1 ug) were converted into a library of template molecules suitable for subsequent cluster generation and sequencing using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA) using TruSeq RNA Sample Preparation v2 LS protocol and 12 indexed adapters.

value: beta-cell

value: 20 mM glucose + drugs


title: INS-1E cells, 11.1 mM glucose, rep, 19

value: 11.1 mM glucose


title: INS-1E cells, 20 mM glucose + drugs, rep, 19


title: INS-1E cells, 20 mM glucose + drugs, rep, 20


title: INS-1E cells, 11.1 mM glucose, rep, 18


title: 10X_Bone_Marrow_Patients

description:
human_AML_S1_L001_R1_001.fastq.gz
processed data file:
hsa_10X_scRNA_Landscape_of_leukemogenesis_all_counts.csv
hsa_10X_scRNA_Landscape_of_leukemogenesis_all.rds

data_processing:
ScRNA-seq alignment process was completed by cellranger(version 2.1.0)
Seurat V3 workflow
Genome_build: mm10 mouse genome references for mouse and hg19 human genome references
Supplementary_files_format_and_content: txt files with gene counts, rds files with annotation and umap information

source_name: AML patient_BM__10X genomics

extract_protocol:
Preparation: Whole Bone Marrow (WBM) are isolated from mouse tibiae, femora and ilia leg bones by crushing in 2%FBS(PBS) buffer, add 1:1000 DNase1 and then translate into 15mL BD tube, centrifuge at 1200rpm, RT for 3min. Then discard the supernatant and add 3mL 1XACK lysis buffer to resuspend bone marrow pellet on ice for 3~5 min, and then add PBS (more than lysis buffer) to terminate lysis reaction, centrifuge at 1200rpm, RT for 3min. Discard the supernatant and then add 0.04% PBS-BSA buffer to resuspend cell pellet and then filtered through a 40μm cell strainer. More than 80% of the living cells in the sample and the density of living cells ranged from 600 to 1200 cells/μl was preferable. Sample quality is measured using Bio-rad TC20 automated cell counter.
Follwed by v2 protocol of chemistry of the 3’ scRNA-seq 10X genomics platform and modified SMART-seq2 protocol based on published previously (Fuchou Tang, 2010).

value: AML patient

value: BM

value: 10X genomics


title: INS-1E cells, 20 mM glucose + drugs, rep, 17


title: INS-1E cells, 11.1 mM glucose, rep, 20


title: INS-1E cells, 20 mM glucose, rep, 17

value: 20 mM glucose


title: breast - morphological changes 2

value: fibrocystic and columnar cell change with flat epitheliaal atypia; no malignancy


title: INS-1E cells, 20 mM glucose, rep, 15


title: INS-1E cells, 11.1 mM glucose, rep, 15


title: INS-1E cells, 20 mM glucose + drugs, rep, 14


title: INS-1E cells, 20 mM glucose, rep, 13


title: Invasive ductal carcinoma 2

value: Breast cancer

value: Invasive ductal carcinoma

value: IHC showed homogeneous IDC


title: INS-1E cells, 11.1 mM glucose, rep, 13


title: INS-1E cells, 20 mM glucose, rep, 20


title: INS-1E cells, 11.1 mM glucose, rep, 17


title: INS-1E cells, 20 mM glucose, rep, 19


title: INS-1E cells, 11.1 mM glucose, rep, 16


title: INS-1E cells, 20 mM glucose + drugs, rep, 12


title: INS-1E cells, 20 mM glucose, rep, 16


title: INS-1E cells, 20 mM glucose + drugs, rep, 11


title: INS-1E cells, 11.1 mM glucose, rep, 10


title: INS-1E cells, 20 mM glucose, rep, 10


title: INS-1E cells, 20 mM glucose, rep, 9


title: INS-1E cells, 20 mM glucose + drugs, rep, 9


title: INS-1E cells, 20 mM glucose + drugs, rep, 8


title: INS-1E cells, 11.1 mM glucose, rep, 11


title: INS-1E cells, 11.1 mM glucose, rep, 14


title: INS-1E cells, 20 mM glucose + drugs, rep, 13


title: INS-1E cells, 20 mM glucose + drugs, rep, 15


title: INS-1E cells, 20 mM glucose, rep, 8


title: INS-1E cells, 20 mM glucose, rep, 18


title: INS-1E cells, 11.1 mM glucose, rep, 8


title: INS-1E cells, 20 mM glucose + drugs, rep, 6


title: INS-1E cells, 20 mM glucose, rep, 7


title: INS-1E cells, 20 mM glucose + drugs, rep, 7


title: INS-1E cells, 20 mM glucose, rep, 12


title: INS-1E cells, 20 mM glucose, rep, 5


title: INS-1E cells, 11.1 mM glucose, rep, 5


title: breast - morphological changes 1

value: Normal

value: duct etasia, periductal chronic infammation; no malignancy


title: INS-1E cells, 20 mM glucose + drugs, rep, 4


title: INS-1E cells, 20 mM glucose, rep, 14


title: INS-1E cells, 20 mM glucose, rep, 4


title: INS-1E cells, 20 mM glucose, rep, 11


title: INS-1E cells, 11.1 mM glucose, rep, 3


title: INS-1E cells, 11.1 mM glucose, rep, 12


title: INS-1E cells, 20 mM glucose + drugs, rep, 2


title: INS-1E cells, 20 mM glucose + drugs, rep, 10


title: INS-1E cells, 20 mM glucose, rep, 2


title: INS-1E cells, 20 mM glucose, rep, 6


title: INS-1E cells, 20 mM glucose + drugs, rep, 5


title: INS-1E cells, 11.1 mM glucose, rep, 6


title: INS-1E cells, 11.1 mM glucose, rep, 7


title: INS-1E cells, 11.1 mM glucose, rep, 9


title: INS-1E cells, 20 mM glucose + drugs, rep, 3


title: INS-1E cells, 11.1 mM glucose, rep, 4


title: INS-1E cells, 20 mM glucose, rep, 3


title: Patient 83

city: Braga

first: Rui

middle: Pedro

last: Ferreira Marques

address: Campus de Gualtar

department: Life and Health Sciences Institute

country: Portugal

institute: School of Medicine, University of Minho

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
CTR2

hyb_protocol: All washing steps and the probe-mRNA complexes fixation into the cartridge were performed automatically in the prep station of the nCounter® PrepStation (NanoString). No post-process actions are needed since all the probes were already marked with specific color sequences.

scan_protocol: The cartridges containing immobilized reporter complexes were transferred to nCounter® Digital Analyzer (NanoString) and analyzed using the PanCancer Immune Profiling Panel (NanoString Technologies, Inc., Seattle, WA)

data_processing: ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library

label: Capture and reporter probes

source_name: non-tumoral brain metastasis surrounfing tissue

label_protocol: Capture and reporter probes were used for 21 hours to label the mRNA.

extract_protocol: RNA isolation and quantification were performed using the RNeasy Mini Kit (Qiagen, Venlo, The Netherlands) and NanoDroPVR 2000 (Thermo Scientific, Waltham).

tag: age years

tag: dead status

tag: metastasis

tag: subgroup


title: Patient 78

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
e18-5882

source_name: Medulloblastoma

value: No

tag: gender

value: F

value: SHH


title: INS-1E cells, 11.1 mM glucose, rep, 2


title: INS-1E cells, 20 mM glucose, rep, 1


title: INS-1E cells, 20 mM glucose + drugs, rep, 1


title: Patient 77

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
e15-15489-GRP4

value: Yes

value: M

value: Group 4


title: Patient 82

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
CTR1


title: Patient 71

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
e18-35718-WNT

value: WNT


title: Patient 73

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
82-GRP4


title: Patient 74

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
e18-21168-GRP4


title: Patient 80

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
157-GRP4


title: Patient 79

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
e18-12670-SHH


title: Patient 81

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
CTR3


title: Patient 75

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
e15-7461-WNT


title: Patient 76

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
e15-20129-GRP4


title: Patient 65

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
134-SHH


title: Patient 67

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
136-SHH


title: Patient 69

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
150-GRP4


title: Patient 66

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
135-GRP4


title: Patient 70

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
159-GRP4


title: INS-1E cells, 11.1 mM glucose, rep, 1

value: beta-cell

value: 11.1 mM glucose


title: Patient 72

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
e18-30329-SHH


title: Patient 62

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
106-SHH


title: Patient 68

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
146-SHH


title: Patient 63

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
128-SHH


title: Patient 64

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
132-SHH


title: Patient 61

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
104-SHH


title: Patient 59

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
102-WNT


title: Patient 52

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
79-GRP3

value: Group 3


title: Patient 51

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
78-WNT


title: Patient 55

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
97-SHH


title: Patient 58

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
100-SHH


title: IP

city: Kunming

last: Bai

address: No. 2, Cuihu North Road

institute: Yunnan University

data_processing:
The DNA libraries were sequenced on the Illumina sequencing platform and anaylzed by Genedenovo Biotechnology Co., Ltd (Guangzhou, China).
Assembly: ADOT00000000.1
Library strategy: DAP-seq

organism: Orbilia oligospora

source_name: Fungal hyphae cells  ADOT00000000.1

growth_protocol: The cDNA sequence encoding protein AoSte12 is constructed in Halo Tag plasmid, the construct vector pAoSte12-halo was identified by sequencing,and for protein expression

extract_protocol: The DNA libraries were sequenced on the Illumina sequencing platform by Genedenovo Biotechnology Co., Ltd (Guangzhou, China).

treatment_protocol: Through the combination with high-throughput sequencing technology, DNA products after DAP were sequenced and analyzed, DNA binding sites of target proteins were searched from the whole genome, and high-throughput data results were obtained by efficient sequencing methods.

value: Fungal hyphae

tag: chip target


title: Patient 54

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
86-SHH

value: Lost of follow up


title: Input


title: Patient 47

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
87-SHH


title: Patient 45

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
148SHH


title: Patient 49

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
85-GRP4


title: Patient 46

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
83-SHH


title: Patient 56

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
96-SHH


title: Patient 53

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
75-WNT


title: Patient 41

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
109SHH


title: B_5_3

data_processing:
Data analysis carried out at Shanghai Meiji Biological Company.
Assembly: ADOT00000000.1

growth_protocol: WT and ΔAoste12 strains grown on cellophane-overlaid CMY plates at 28°C for 5 and 7 days.

extract_protocol: After collecting the samples, RNA was extracted with the AxyPrep Multisource RNA Miniprep Kit (Axygen, Jiangsu, China)

treatment_protocol: Three replicates were used for each sample.

value: delta Aoste12

value: 5 days


title: Patient 43

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
125GRP4


title: Patient 42

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
121SHH


title: Patient 50

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
80-SHH


title: Patient 44

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
145GRP4


title: Patient 60

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
103-WNT


title: Patient 57

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
98-SHH


title: B_5_1


title: B_7_3

value: 7 days


title: Patient 39

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
23SHH


title: A_7_3

value: WT


title: Patient 48

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
76-GRP3


title: Patient 40

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
39SHH


title: B_7_2


title: A_5_2


title: B_7_1


title: Patient 29

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
39-GRP4


title: Liver, WT/WT, male, rep2

city: Chengdu

first: Haoran

last: Tai

address: #783 Xindu Avenue

department: Department of Histology and Embryology

institute: Chengdu Medical College

data_processing:
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads need to be filtered before the data analysis for reliability analysis results.
HISAT was used to align the clean reads to the reference genome.
Bowtie2 was used to align the clean reads to the reference genes.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes FPKM, TPM and read count values for each Sample

organism: Mus musculus

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China)

tag: Sex

value: male

value: Liver

tag: strain

value: WT/WT


title: Patient 26

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
122-WNT

value: No


title: A_5_1

tag: tissue


title: A_5_3


title: Patient 36

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
46-SHH

value: Yes

value: F

value: SHH


title: A_7_1


title: Liver, WT/WT, male, rep3


title: Patient 34

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
44-SHH


title: Patient 37

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
47-SHH


title: Patient 28

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
38-GRP4

value: M

value: Group 4


title: Patient 32

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
42-SHH


title: A_7_2


title: Patient 33

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
43-SHH


title: Liver, S400D/S400D, male, rep3


title: Patient 38

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
2SHH


title: Patient 20

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
25-SHH


title: Patient 24

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
31-GRP3


title: Patient 35

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
45-SHH


title: Patient 30

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
40-SHH


title: Patient 27

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
12-GRP4


title: Patient 19

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
11-SHH


title: cancercell_treatment-naïve_macophage-depleted_replicate5

city: Edinburgh

first: Cigdem

last: Selli

address: Little France Crescent

department: Centre for Reproductive Health

institute: Queen's Medical Research Institute

description:
Vec_MDT_FPKM.csv
BC.0226_FPKM

data_processing:
Quality controlled reads were aligned to the mouse reference genome using Bowtie2 and visualised using IGV tool.
FPKM normalisation was performed
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with FPKM value for every gene and every sample

source_name: MycCaP Bo prostate cancer bone metastasis cancer cells

growth_protocol: Mice (4-6 weeks old) received intracardiac injection of prostate cancer cells MycCaP-Bo (4*10^5 cells/mouse) at day -7 to develop bone metastasis. Mice with bone metastasis detected by bioluminescence images (BLI) at day 0 were administered with different treatments. The growth of bone metastasis was monitored by bioluminescence twice a week.

extract_protocol:
Cancer cells (CD45-iRFP+ cells) from prostate cancer bone metastasis with different treatments were sorted by flow cytometry. Cancer cells from 3 mice were pooled together for total RNA extraction using RNAeasy micro plus kit (Qiagen, Catalog # 74034) following the manufacturer’s instructions. The quality control of samples was performed using bioanalyser picokit (Agilent Technologies).
mRNAs were enriched using oligo dT magnetic beads, fragmented, and converted into a library of cDNA fragments. The cDNAs were then purified and amplified by PCR using ABI StepOnePlus Real-Time PCR System. The constructed cDNA library was quality checked by Agilent 2100 Bioanalyzer. 2 x 150 bp paired end sequencing was performed using BGISEQ-500 following the manufacturer’s instructions.

treatment_protocol: Vehicle and Enzalutamide (30mg kg-1 body weight) was given via daily oral gavage. Liposome-clodronate in PBS (1mg/mouse, twice a week) was administered by i.v. injection.

tag: source

value: prostate cancer cells from tretment-naïve macrophage-depleted bone metastasis

tag: disease state

value: prostate cancer bone metastasis

tag: batch


title: Patient 18

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
6-SHH


title: Patient 31

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
41-SHH


title: cancercell_treatment-naïve_macophage-depleted_replicate3

description:
Vec_MDT_FPKM.csv
AB.0220_FPKM


title: Patient 17

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
124-GRP3

value: Group 3


title: Patient 21

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
28-GRP4


title: cancercell_treatment-naïve_macophage-depleted_replicate2

description:
Vec_MDT_FPKM.csv
A.0302_FPKM


title: Liver, S400D/WT, male, rep2

source_name: Liver


title: Liver, WT/WT, male, rep1


title: Patient 15

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
19-GRP3


title: Liver, S400D/WT, male, rep3


title: B_5_2

value: Fungal hyphae


title: cancercell_treatment-naïve_macophage-depleted_replicate1

description:
Vec_MDT_FPKM.csv
A.0219_FPKM


title: Patient 23

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
149-GRP3


title: Patient 22

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
147-GRP3


title: Liver, S400D/S400D, male, rep1


title: Patient 13

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
113-WNT

value: WNT


title: Liver, S400D/S400D, male, rep2


title: Patient 25

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
110-WNT


title: Patient 10

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
5-GRP4


title: Liver, S400D/WT, male, rep1


title: Liver, S400D/S400D, female

value: female


title: cancercell_treatment-naïve_macophage-depleted_replicate4

description:
Vec_MDT_FPKM.csv
B.0219_FPKM


title: Patient 12

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
47-WNT


title: Patient 8

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
17-SHH


title: Patient 16

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
35R-GRP3


title: cancercell_treatment-resistant_replicate2

description:
tumour_FPKM.csv
X18dD_T_FPKM

value: prostate cancer cells from treatment-resistant bone metastasis


title: cancercell_treatment-resistant_replicate3

description:
tumour_FPKM.csv
X18dF_T_FPKM


title: Patient 6

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
9-GRP4


title: Patient 4

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
50-GRP3


title: cancercell_treatment-resistant macrophage-depleted_replicate5

description:
tumour_MDT_FPKM.csv
X0604A10B_FPKM

value: prostate cancer cells from treatment-resistant and macrophage-depleted bone metastasis


title: Patient 14

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
111-WNT


title: cancercell_treatment-naïve_replicate5

description:
tumour_FPKM.csv
VF_T_FPKM

value: prostate cancer cells from treatment-naive bone metastasis


title: Patient 11

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
34-GRP4


title: Patient 9

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
18-SHH


title: cancercell_treatment-naïve_replicate3

description:
tumour_FPKM.csv
VC_T_FPKM


title: Patient 2

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
26-WNT


title: cancercell_treatment-resistant macrophage-depleted_replicate4

description:
tumour_MDT_FPKM.csv
X0604A0B1_FPKM


title: Patient 7

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
1R-SHH


title: Patient 5

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
51-GRP3


title: cancercell_treatment-naïve_replicate1

description:
tumour_FPKM.csv
VA_T_FPKM


title: cancercell_treatment-resistant macrophage-depleted_replicate3

description:
tumour_MDT_FPKM.csv
X0510BB_FPKM


title: cancercell_treatment-resistant_replicate5

description:
tumour_FPKM.csv
X18dI_T_FPKM


title: cancercell_treatment-resistant macrophage-depleted_replicate2

description:
tumour_MDT_FPKM.csv
X0510ABC_FPKM


title: DMSO-2

city: Shanghai

first: Feifei

last: Mao

address: 301 Yanchang Middle Road

institute: Shanghai Tenth People’s Hospital

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2(v2.0.4)mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

growth_protocol: L02 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: L02 cells were treated with 20 μmol Resinacein S or DMSO for 48 hours.

tag: cell type

value: normal human hepatic cells

value: WT

value: DMSO


title: DMSO-3

tag: cell line


title: Res S-3

tag: treatment

value: Resinacein S


title: cancercell_treatment-naïve_replicate4

description:
tumour_FPKM.csv
VD_T_FPKM


title: Res S-2


title: cancercell_treatment-resistant macrophage-depleted_replicate1

description:
tumour_MDT_FPKM.csv
A0A10_FPKM


title: cancercell_treatment-naïve_replicate2

description:
tumour_FPKM.csv
VB_T_FPKM


title: cancercell_treatment-resistant_replicate4

description:
tumour_FPKM.csv
X18dG_T_FPKM


title: DMSO-1


title: Res S-1


title: cancercell_treatment-resistant_replicate1

description:
tumour_FPKM.csv
X18dA_T_FPKM


title: Patient 3

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
44-WNT

value: No

value: F


title: Patient 1

description:
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
8-SHH

value: M

value: SHH


title: LX-2 cells, siCTL, 48h, replicate 1

city: Rennes

first: Vincent

last: Legagneux

address: 2 avenue du Professeur Léon Bernard, Bâtiment 5

country: France

institute: Inserm

description:
SiCTL_1
FA_05_S7
LX-2_6_samples_norm_counts.csv

data_processing:
FASTQ reads were aligned on the reference genome (GRCh38) using the STAR software and read counts per genes were computed using htseq-count. Read counts were normalized using the R-package DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized read count values for each Sample

growth_protocol: LX-2 cells were cultured in DMEM containing 4.5 g/l Glucose, Pyruvate, Glutamine, penicillin (100 IU/ml)-streptomycin (100 mg/ml) and supplemented with 10% fetal calf serum (Eurobio).

extract_protocol:
total RNA was extracted using TRIzol (Invitrogen) reagent according to the manufacturer’s instructions. RNA samples from siRNA-transfected or control LX-2 cells, and from mouse liver samples (see above) were quality controlled by RNA integrity number (RIN) measurement on a Bioanalyzer with RNA 6000 Nano assays (Agilent). RINs were comprised between 9.2 and 9.9.
RNA-sequencing libraries were prepared from 500ng total RNA and quality-controlled on TapesStation (fragment sizes of approximately 260 bp) by the GenoBiRD facility (Nantes, France) using the TruSeq® Stranded mRNA Library Prep (96 samples) from Illumina. Multiplexed (bar-coded) libraries were randomized and sequenced on a NovaSeq 6000.

treatment_protocol:
LX-2 cells were transfected with ADAMTS12 or control siRNAs for 48h using Lipofectamine® RNAiMAX Reagent according to the manufacturer’s instructions. Small interfering RNAs were provided by Eurogentec.
siADAMTS12 sequence (sense): GCCAAAGUUUGGAGGGAAAdTdT - siCTRL (negative control): Eurogentec reference SR-CL000-005.

value: Activated Hepatic Stellate Cells

value: siCTL

tag: time


title: Peripheral Blood, VDJ

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

library_source: transcriptomic single cell

data_processing:
The raw data was processed using cellranger multi. Read counts for genes and proteins are saved in data_RNA.zip and data_ADT.zip
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting,and csv files of TCR clonality were performed using the cellranger analysis pipeline.
Metadata for hashed samples and HTO oligo sequence are available in the file "HTO.csv"
Paired-end reads were mapped to the hg19 genome with cellranger for gene-level read counts
Data normalization, dimension reduction, and differential expression analysis were performed using R and the Seurat R package. Cells were clustered with PhenoGraph.
T cell receptor VDJ analysis: Cellranger vdj
VDJ of Tcells were infered with cellranger vdj pipeline to get TCR contig annotations.
Assembly: hg19
Supplementary files format and content: contig_annotations
Supplementary files format and content: counts
Supplementary files format and content: HTO.csv
Supplementary files format and content: metaData_GEO.csv

source_name: Peripheral Blood

extract_protocol:
Cells from pre- and post-treatment of one patient were loaded into the 10XChromium Controller using the Single Cell 5' Library and Gel BeadKit (10X Genomics). The Chromium Single Cell V(D)J protocol was used to profile  gene expression and T cell receptor.
scRNA-seq + TCR +cell surface proteins

tag: library type

value: VDJ

tag: antibody


title: LX-2 cells, siCTL, 48h, replicate 2

description:
SiCTL_2
FA_08_S93
LX-2_6_samples_norm_counts.csv

tag: genotype


title: BC10_PBMC_TIL_CITESEQ.tar.gz

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

description: CITEseq feature barcode matrix

data_processing:
For demuliplexing of samples, bcl2fastq (v2.20.0) was used with the following settings for 3' v2 samples: --use-bases-mask=Y26,I8,Y98 \ --create-fastq-for-index-reads \ --minimum-trimmed-read-length=8 \ --mask-short-adapter-reads=8 \ --ignore-missing-positions \ --ignore-missing-controls \ --ignore-missing-filter \ --ignore-missing-bcls \ -barcode-mismatches=0. The following settings were used for 5' v1 samples: --use-bases-mask=Y28,I8,Y91 \ --create-fastq-for-index-reads \ --minimum-trimmed-read-length=8 \ --mask-short-adapter-reads=8 \ --ignore-missing-positions \ --ignore-missing-controls \ --ignore-missing-filter \ --ignore-missing-bcls \ -barcode-mismatches=0.
CellRanger (v3.1.0; 10X Genomics) was used to align gene expression data to the GRCh38 reference and generate feature barcode expression matrices using the default settings. CITEseqCount was used to align oligonucleotide tags to TotalSeqC (Biolegend) sequences to create citeseq feature barcode expression matrices using the following custom settings: -cbf 1 -cbl 16 -umif 17 -umil 26 \ -trim 10.
Genome_build: GRCh38
Supplementary_files_format_and_content: Each processed data file consists of a gzipped tar file containing either gene expression feature barcode matrices (GEX) or CITEseq feature barcode matrices (CITEseq).

molecule: other

source_name: Peripheral blood, tumor infiltrating leukocytes

extract_protocol:
Blood and tumors were obtained from patients undergoing surgical resection as treatment for breast cancer. Blood specimens were collected by venipuncture into EDTA collection tubes.  Peripheral blood mononuclear cells were isolated from whole blood by Ficoll-Hyapque density gradient centrifugation. Surgical specimens were collected in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin. Single cell suspensions were generated from tissues by manually micing tissues and incubating the resulting tissue fragments in serum-free RPMI 1640 with 50 ug/ml of Liberase DL and 1 mg/ml DNase I for 30 minutes. Live CD45+ cells (i.e. all immune cells) were then sorted using a MoFlo Astrios High Speed Sorter (Beckman Coulter). Cell hashing using oligonucleotide conjugated antibodies was performed to multiplex peripheral blood and tumor specimens from the same patients as indiciated in the sample records. Samples were run using either 3'- or 5'-based single-cell RNAseq as described in the samples records.
Libraries were prepared as per the manufacturer's protocol for 3'- and 5'-based single-cell RNAseq. For cell hashed samples, CITEseq libraries were generated as descibed by Stoeckius et al (Nature Biotechnology, 2017).

value: Live CD45+ cells

tag: cancer type

value: Breast cancer

tag: cancer subtype

value: ILC


title: LX-2 cells, siADAMTS12, 48h, replicate 3

description:
SiTS12_3
FA_12_S85
LX-2_6_samples_norm_counts.csv


title: MouseBrain_20um_100barcodes_rep2 ATAC

city: New Haven

first: Di

state: CT

address: 55 Prospect St

department: Biomedical Engineering

institute: Yale University

data_processing:
Two constant linker sequences (linker 1 and linker 2) were used to filter Read 2, and the sequences were converted to Cell Ranger ATAC format (10x Genomics). The genome sequences were in the newly formed Read 1, barcodes A and barcodes B were included in newly formed Read 2. Human reference (GRCh38) or mouse reference (mm10) were used to align the fastq files. The achieved BED like fragments were used to conduct downstream analysis. The fragments file includes fragments information on spatial locations (barcode A x barcode B) and genome.
Assembly: mm10
Supplementary files format and content: BED like fragments file for downstream analysis. The fragments file contains fragments information on the genome and tissue location (barcode A x barcode B).

source_name: Mouse brain P22

extract_protocol: The fresh frozen tissue section was fixed with formaldehyde. The adapters loaded Tn5 transposition containing a ligation linker was inserted into transposase accessible genomic DNA loci. The biotin decorated poly-T primer with a ligation linker was added to capture the mRNA for reverse transcription. In situ ligation was conducted by introducing distinct spatial barcode Ai (i = 1-50/100) to the adapters through an array of lateral microchannels. Then, distinct spatial barcode Bj (j = 1-50/100) were introduced through the longitudinal microchannels. Barcodes A and B with linkers were ligated to the 5’ end of the Tn5 oligo separately during each ligation. The tissue can be spatially barcoded with a distinct combination of barcodes Ai and Bj (i = 1-50/100, j = 1-50/100, n of barcoded pixels = 2,500/10,000). To correlate the spatially chromatin accessibility, transcriptome, and tissue morphology, the tissue was imaged after each ligation. Reverse crosslinking was then performed to collect barcoded cDNA and DNA fragments. The streptavidin beads were used to separate DNA and cDNA fragments. The cDNA fragments can be enriched with streptavidin beads and the DNA fragment was left in the supernatant. After separation, the DNA and cDNA libraries were constructed separately during PCR amplification. NGS sequencing was then performed using a NovaSeq 6000 sequencer with pair-end 150 bp mode.

value: Mouse brain

tag: spatial resolution

value: 20 um


title: LX-2 cells, siCTL, 48h, replicate 3

description:
SiCTL_3
FA_11_S36
LX-2_6_samples_norm_counts.csv


title: BC6_PBMC_TIL_CITESEQ.tar.gz

description: CITEseq feature barcode matrix

value: IDC


title: LX-2 cells, siADAMTS12, 48h, replicate 2

description:
SiTS12_2
FA_09_S37
LX-2_6_samples_norm_counts.csv