title: Frontal_GreyMatter_C4_6

description: 4_Frontal|6|Full ROI

tag: tissue

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

value: Yes

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210729_11_14903_ROI006_Vessel

status: Public on Sep 23 2024

type: SRA

city: Boston

first: Joseph

last: Franses

state: Massachusetts

department: Cancer Center

country: USA

institute: Massachusetts General Hospital

description: (v1.0) Cancer Transcriptome Atlas

library_source: transcriptomic

data_processing:
Raw sequencing data were processed using the GeoMx NGS Pipeline to generate fastq files followed by dcc files
Sequences were aligned to the Cancer Transcriptome Atlas probe set using default settings
Assembly: hg38
Supplementary files format and content: rawCounts.tsv: gene count matrix file in tsv format
Supplementary files format and content: qnormCounts.tsv: Q3 normalized gene count matrix file in tsv format
Library strategy: GeoMx Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: Liver cancer resection

extract_protocol:
We followed published experimental methods (NanoString) with modifications as noted below. Briefly, slides were baked at 60 °C for one hour, deparaffinized with CitriSolv (DECON), rehydrated, antigen-retrieved in 1x Tris-EDTA/pH 9 in a steamer for 15 min at 100 °C, proteinase K (Thermo Fisher Scientific, AM2548) digested at 0.1 ng/ml for 15 min at 37 °C, and postfixed in neutral-buffered formalin for 10 min, hybridized to UV-photocleavable barcode-conjugated RNA in situ hybridization probe set (CTA with 1,779 gene targets and 32 reference genes) overnight at 37 °C, washed to remove off-target probes and then counterstained with morphology markers for 2 h at room temperature. The morphology markers consisted of: 1:50 CD31 (Abcam, ab47063) and 1:50 Arginase-1 (Cell Signaling Technology, 93668S) in blocking buffer W (NanoString). The anti-CD31 antibody was conjugated using the Alexa Fluor 555 Lightning-Link kit (Abcam, ab269820) and the anti-Arginase-1 antibody with the Alexa Fluor 647 Lightning-Link kit (Abcam, ab269823). These two morphology markers allowed distinction between vessel areas of interest (AOIs) and tumor regions of interest (AOIs) within a microscopic region of interest (ROI). 22 Immunofluorescence images, ROI selection, segmentation into marker-specific AOIs and 23 spatially indexed barcode cleavage and collection were performed on a GeoMx DSP instrument 24 (NanoString). Typical exposure times were 400 ms for CD31 and 300 ms for Arg 1. Approximately 25 4 AOIs on average were collected per specimen (details in Table 1)
Library preparation was performed according to the manufacturer’s instructions and involved PCR amplification to add Illumina adapter sequences and unique dual sample indices. A minimum sequencing depth of 2 150–200 reads per square micron of illumination area was achieved by sequencing all CTA AOIs on a NovaSeq S2 (100 cycles, read 1: 27 nt, read 2: 27 nt, index 1: 8 nt, index 2: 8 nt).

tag: tissue

value: Liver cancer resection

tag: slide name

tag: pool

tag: roi

tag: aoi type

value: Vessel

tag: area


title: Transporter_KO_9days_SIM1_rep3

city: Vienna

first: Giulio

last: Superti-Furga

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: Transporter_KO_9_days_selection_sgRNA_counts.txt

library_source: other

data_processing:
read trimming (transporter-focused KO libraries): tracrRNA sequences flanking the 3’ end of the sgRNA regions were trimmed from the reads using Cutadapt (Galaxy Version 4.8+galaxy1)
read trimming (transporter-focused OE libraries): 5’ flanking primer sequences (ACCCAGCTTTCTTGTACAAAG) were removed from the reads using cutadapt (Galaxy Version 4.8+galaxy1) and the remaining sequence was trimmed after the first 10 bp to receive the cDNA barcodes.
read trimming (genome-wide KO libraries): 5' flanking primer sequences and 3' flanking tracrRNA sequences were trimmed from the reads using Cutadapt (Galaxy Version 4.8+galaxy1) to receive the sgRNA sequences.
read/barcode mapping: MAGeCK count (Galaxy Version 0.5.9.2.4).
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited raw gRNA count tables
Library strategy: Amplicon-Seq

molecule: other

source_name: HAP1 (RRID:CVCL_Y019)

growth_protocol: HAP1 (RRID:CVCL_Y019) cells were cultivated in DMEM (D5796 Sigma) supplemented with 10% Fetal Bovine Serum (10270-106, Lot 42F8381K, Gibco) and Penicillin-Streptomycin (15140-122, Gibco).

extract_protocol:
Genomic DNA was purified using QIAamp DNA Mini columns (Qiagen)
For transporter-focused KO screen samples, gDNA was digested overnight with 20U PacI (NEB) and double size-selected to enrich the sgRNA containing fragments (620 bp). Briefly, 0.6 x vol AmpliClean magnetic beads (Nimagen) were added to the sample to bind large gDNA fragments; the cleared supernatant was added to fresh beads (0.6 x volume of the original gDNA sample) to bind the smaller fragments. After size selection, sgRNA sequences were amplified in  with Q5 Polymerase (NEB) using the program recommended by the manufacturer (28 cycles, 72°C annealing temperature). PCR products were further double size-selected to remove residual large gDNA fragments as described above. For transporter-focused overexpression (OE) screen samples, barcode sequences were amplified from 10-20 µg gDNA per sample using pooled staggered primer containing partial Illumina adapter sequences with Q5 Polymerase (NEB) using the program recommended by the manufacturer (30 cycles, 63°C annealing temperature, 30 seconds extension). PCR products were double size selected using 0.65 x (to bind and remove gDNA) and 0.55 x volumes (to bind PCR products) AmpliClean magnetic beads (Nimagen). 2 µl of the purified PCR products were used in a second PCR with indexing primer with Q5 polymerase (10 cycles, 72°C annealing, 30 seconds extension) to generate Illumina libraries. For genome-wide KO screen samples, libraries were prepared as described previously (doi: 10.1038/nprot.2017.016).

treatment_protocol: Cells were transduced with lentiviral particles containing KO or OE libraries and selected with antibiotics to remove non-transduced cells. After 7-10 days of selection, each replicate was seeded to separate culture dishes and drug treatment was started the next day.

tag: cell line

value: HAP1 (RRID:CVCL_Y019)

tag: cell type

value: Myeloid haploid karyotype cell line

tag: transgene

value: Lentivirally delivered Cas9 gene (Addgene #52962)

tag: screening library

value: Human Transporter Knockout Library with UMIs (Addgene #221409)

tag: treatment

value: 3.15 nM SIM1 for 9 days


title: Frontal_GreyMatter_C4_5

city: Los Angeles

first: Ting

last: Zhang

state: CA

address: 2506 Gonda Bldg, 695 Charles E.Young Dr. South

department: Pathology and laboratory medicine

institute: University of California, Los Angeles

description: 4_Frontal|5|Full ROI

data_processing:
Following sequencing, the processing and normalization of data involves matching the raw probe counts to sequencing results to filter out unused probes and remove outliers, then subjected to third quartile Q3 normalization to the negative probes. The negative probes include probes for whole transcriptomic atlas and SARS-CoV2 (Neg-WTA and SARS-CoV2-Neg).
Processed data includes Q3 normalized counts
Library strategy: Spatial Transcriptomics

source_name: CONTROL

extract_protocol:
The slides were incubated overnight with the GeoMx Human whole transcriptome atlas (WTA) assay probe cocktail, targeting 18,702 genes including 3 SARS-CoV2 targets. Immunofluorescent cell type/morphology markers, anti-NeuN antibody (Millipore) for neurons, anti-GFAP antibody (Invitrogen) for astrocyte, anti-IBA1 antibody (Millipore) for microglia, and Syto83 (Invitrogen) for nuclei were then applied to the slides.
The GeoMx Deep Spatial Platform (DSP) was used to scan the slides, followed by region-of-interest (ROI) selections performed by senior neuropathologists. Probe barcodes were UV cleaved, collected, and sequenced on the Illumina NovaSeq 6000 platform with paired end reads.
5-6 µm were mounted on glass slides and subjected to an overnight baking at 37°C, followed by a 3-hour baking at 65°C. The slides underwent processing on the Leica automation platform, including antigen retrieval for 20 minutes at 100°C and proteinase K treatment.
The slides were incubated overnight with the GeoMx Human whole transcriptome atlas (WTA) assay probe cocktail, targeting 18,702 genes including 3 SARS-CoV2 targets. Immunofluorescent cell type/morphology markers, anti-NeuN antibody (Millipore) for neurons, anti-GFAP antibody (Invitrogen) for astrocyte, anti-IBA1 antibody (Millipore) for microglia, and Syto83 (Invitrogen) for nuclei were then applied to the slides.
The GeoMx Deep Spatial Platform (DSP) was used to scan the slides, followed by region-of-interest (ROI) selections performed by senior neuropathologists. Probe barcodes were UV cleaved, collected, and sequenced on the Illumina NovaSeq 6000 platform with paired end reads.

value: postmortem brain

tag: tissue type

value: FFPE

tag: region

value: Frontal lobe

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

value: Female

tag: immunocompromised status

value: No

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Transporter_KO_9days_SIM1_rep2

tag: cell line

tag: cell type

tag: transgene

tag: screening library

tag: treatment


title: Basal Ganglia_P5

type: RNA

hyb_protocol: A master mix is created containing the hybrid buffer and the reporter probe. 8 ul of master mix is added  to each 12 tubes, and add 5 ul of 20ng/ul of RNA in each tube. Add 2 ul of Capture probeSet to each tube immediately before placing at 65°C.  Briefly spin down and immediately place the tubes in the pre-heated 65°C thermal cycler. Incubate reactions for at least 16 hours. After hybridization, excess probes are washed away using a two-step magnetic bead-based purification on an nCounter instrument. Finally, the purified target-probe complexes are eluted off the beads and are immobilized and aligned for data collection.

scan_protocol: Data collection is performed using epifluorescence microscopy and CCD capture technology on the nCounter analyzer to yield hundreds of thousands of target molecule counts. Digital images are processed within the nCounter instrument and the Reporter probe ounts are tabulated in comma separated value (CSV) format  for data analysis with Nanostring nSolver Analysis Software.

data_processing: The raw data were re-scaled to account for differences in hybridization efficiency using positive control ERCC spike-ins. Internal housekeeping genes were then used to normalize for different input amounts.

source_name: PATIENT

label_protocol: High-plex flourescently labelled DNA oligos annealed to target RNA

extract_protocol: Total RNA was extracted from 3-4 10µm FFPE curls using the Qiagen RNeasy FFPE kit.

tag: tissue

tag: tissue preparation

tag: region

value: Basal Ganglia

tag: age

tag: gender

value: Male

tag: postmortem interval (day)

tag: immunocompromised status


title: Transporter_KO_9days_SIM1_rep1


title: Frontal_GreyMatter_C4_4

description: 4_Frontal|4|Full ROI

tag: tissue type

tag: area

tag: lotid

tag: roi

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Frontal_GreyMatter_C4_3

description: 4_Frontal|3|Full ROI

tag: tissue

tag: tissue type

tag: area

tag: region

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Frontal_GreyMatter_C4_2

description: 4_Frontal|2|Full ROI

tag: lotid

tag: roi

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: scanwidth


title: Transporter_KO_9days_DAT5519_rep3

tag: cell line

tag: cell type

tag: transgene

tag: screening library

tag: treatment

value: 500 nM DAT551 for 9 days


title: Basal Ganglia_P4

tag: tissue

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: HCC_TMA_20210729_06_67338_ROI003_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

value: Tumor

tag: area


title: Basal Ganglia_P2


title: HCC_TMA_20210729_15_78424_ROI002_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210729_15_78424_ROI002_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210729_06_67338_ROI003_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Basal Ganglia_P3

value: Yes


title: Frontal_GreyMatter_C4_1

description: 4_Frontal|1|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Basal Ganglia_P13

tag: tissue

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: HCC_TMA_20210729_06_67338_ROI004_Tumor

description: (v1.0) Cancer Transcriptome Atlas

value: Liver cancer resection

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_GreyMatter_C3_6

description: 3_Frontal|11|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: Frontal_GreyMatter_C3_5

description: 3_Frontal|10|Full ROI

tag: tissue

tag: area

tag: region

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210729_15_78424_ROI001_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: aoi type


title: HCC_TMA_20210729_15_78424_ROI001_Vessel

description: (v1.0) Cancer Transcriptome Atlas

value: Vessel


title: Transporter_KO_9days_MZ1_rep3

tag: cell line

value: HAP1 (RRID:CVCL_Y019)

tag: cell type

tag: transgene

tag: screening library

tag: treatment

value: 180 nM MZ1 for 9 days


title: Basal Ganglia_P11

tag: tissue

tag: tissue preparation

tag: region


title: HCC_TMA_20210729_NA_ROINA_NA

description: (v1.0) Cancer Transcriptome Atlas

source_name: Control

value: Control

value: No Template Control

tag: roi

tag: area


title: Frontal_GreyMatter_C3_4

description: 3_Frontal|9|Full ROI

tag: tissue type

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Frontal_GreyMatter_C3_3

description: 3_Frontal|8|Full ROI

tag: tissue

tag: tissue type

tag: area

tag: region

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Transporter_KO_9days_DAT5519_rep2

tag: cell line

tag: cell type

value: Myeloid haploid karyotype cell line

tag: transgene

value: Lentivirally delivered Cas9 gene (Addgene #52962)

tag: screening library

value: Human Transporter Knockout Library with UMIs (Addgene #221409)

tag: treatment


title: HCC_TMA_20210616_NA_ROI8_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: aoi type


title: Transporter_KO_9days_MZ1_rep1


title: Transporter_KO_9days_MZ1_rep2


title: Transporter_KO_9days_DMSO_rep3


title: Basal Ganglia_C5

value: postmortem brain

tag: tissue preparation

value: FFPE

tag: region

tag: immunocompromised status


title: Basal Ganglia_P1

tag: age

tag: postmortem interval (day)

value: No


title: Frontal_GreyMatter_C3_1

description: 3_Frontal|6|Full ROI

tag: tissue type

tag: area

value: Frontal lobe

tag: lotid

tag: roi

tag: gender

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx


title: HCC_TMA_20210616_NA_ROI7_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Transporter_KO_9days_DAT5519_rep1

tag: cell line

tag: cell type

tag: transgene

tag: screening library

tag: treatment


title: Frontal_GreyMatter_C3_2

description: 3_Frontal|7|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

value: Male

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: scanoffsety

tag: loq


title: Transporter_KO_9days_DMSO_rep2

tag: cell line

tag: cell type

tag: transgene

tag: screening library


title: Transporter_KO_9days_DMSO_rep1


title: HCC_TMA_20210616_NA_ROI6_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_GreyMatter_C2_6

description: 2_Frontal|6|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

value: Female

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx


title: HCC_TMA_20210616_NA_ROI5_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

value: Tumor

tag: area


title: Basal Ganglia_C2

tag: tissue preparation

tag: region

value: Basal Ganglia

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Basal Ganglia_C4

value: Yes


title: Basal Ganglia_C3


title: Arabidopsis,atx3-1/4/5, H3K4me3, rep2

city: Davis

first: Satoyo

last: Oya

address: 1 Shields Ave, Plant_ Enviro Sci, RM 1210, 387 N Quad (MS11665)

department: Plant Sciences

institute: UC Davis

library_source: genomic

data_processing:
The exact codes for trimming and mapping are provided at https://github.com/Satoyo08/seven_ATXRs. For ChIP-seq against 3xFLAG-tagged H3K4-ATX(R)s, pair-end files were trimmed by trimmomatic with the following option; ILLUMINACLIP:$adaptor:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36. Trimmed reads were mapped to TAIR10 genome by bowtie2 without option. The browser track files were generated by deeptools bamCoverage -b [bamfile] -o [outputfilename] --normalizeUsing RPKM --outFileFormat bedgraph then by converted to bw file by ucsctools/bedGraphToBigWig. For ChIP-seq against histone, read 1 file was mapped to TAIR10 genome by bowtie with the following options; -M 1 -3 80 --best --chunkmbs 200. The bam files were converted to bw by deeptools bamCoverage without option.
Assembly: TAIR10
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 15 dai seedling

growth_protocol: seedling grown on MS media under 22°C Long day condition

extract_protocol:
ChIP-seq targeting histone modifications and epitope-tagged proteins were carried out based on Inagaki, S. et al., Nat Plants (2021)  with some modifications. Briefly, approximately 1.5 g frozen seedlings were ground into a fine powder in liquid nitrogen and suspended in 25 ml of nuclei isolation buffer. The buffer for histone modifications was 10mM HEPES pH7.6, 1M sucrose, 5mM KCl, 5mM MgCl2, 5mM EDTA, 1 % formaldehyde, 0.1 % β-mercaptoethanol, 0.6 % Triton X-100, supplemented with 1 tablet/50 ml cOmplete proteinase inhibitor and 1 mM Pefabloc SC (Roche)). The buffer for epitope-tagged proteins additionally contains 0.1 mM spermine, 0.5 mM spermidine and 1.5 mM ethylene glycol bis(succinimidyl succcinate) (EGS; ThermoFisher) and 0.3 % IGEPAL CA-630 was used instead of 0.6 % Triton X-100. The suspension was incubated for 10 minutes in RT to crosslink, quenched by adding glycine to 130 mM, filtered through a 40 µm nylon cell strainer, and pelleted by centrifugation at 3,000 rpm at 4°C for 10 min. The pellet was resuspended in 300 µl of nuclei isolation buffer and layered on top of 500 µl of nuclei separation buffer (10 mM HEPES pH 7.6, 1 M sucrose, 5 mM KCl, 5 mM MgCl2, 5 mM EDTA pH 8.0, 15 % Percoll) and pelleted by centrifugation at 3,000 × g for 5 min at 4 °C. The pellet was directly resuspended in 950 µl RIPA buffer without Triton-X (50mM Tris-HCl pH7.8, 150 mM NaCl, -1mM EDTA, 0.1% SDS, 0.1% Sodium deoxycholate and cOmplete proteinase inhibitor). The suspension was sonicated using picoruptor (Diagenode) with the following settings: water bath; 4 °C, 30 sec ON and 30 sec OFF, 7 cycles for histone modifications, and 5 cycles for epitope-tagged protein. The sonicated chromatin was then supplemented with Triton-X to 1.0 %, then centrifuged at 13,000 g for 3 min, and the supernatant was diluted with RIPA buffer and aliquoted. The chromatin solution was incubated with 1-2 μg of antibodies overnight at 4 °C. Antibodies used are : H3 antibody (ab1791; Abcam) and others with H3K4 methylation-specific antibodies (H3K4me1 (ab8895; Abcam), H3K4me2 (ab32356; Abcam), H3K4me3 (ab8580; Abcam) and FLAG (F1804; SIGMA). Then the antibody-chromatin mix was incubated for 2 h at 4 °C with Dynabeads Protein G magnetic beads. For histone modifications, the incubated beads were washed once with 1 ml of RIPA buffer, twice with 1 ml of High-salt RIPA buffer (RIPA buffer with 500 mM NaCl), once with 1 ml of LiCl buffer (10 mM Tris–HCl, pH 7.8, 1 mM EDTA, 0.25 M LiCl, 1% IGEPAL CA-630, 1% sodium deoxycholate) and once with 1 ml of TE buffer (10 mM Tris–HCl, pH 7.8, 1 mM EDTA), each time rotating for 10 min in 4 °C. For epitope-tagged proteins, beads were washed once with RIPA buffer, medium salt RIPA buffer (RIPA buffer with 300 mM NaCl), high salt RIPA buffer, and TE buffer. DNA was eluted from the beads and reverse-crosslinked by adding 100 μl of elution buffer (10 mM Tris–HCl, pH 7.8, 0.3 M NaCl, 5 mM EDTA, 0.5% SDS) and incubating overnight at 65 °C. The DNA samples were then treated with RNase A (Nippon Gene) for 30 min and with Proteinase K (ThermoFisher) for 2 h at 37 °C, and purified using the Monarch PCR & DNA Cleanup Kit (NEB).
ChIP-seq libraries were made with a ThruPlex kit as directed in manufacture’s protocol  and dual size-selected using SPRI select beads to enrich 200 – 500 bp fragments.

value: 15 dai seedling

tag: genotype

value: atx3-1/atx4/atx5 triple mutant


title: Frontal_GreyMatter_C2_5

description: 2_Frontal|5|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanoffsety

tag: loq


title: Transporter_KO_3days_Input_rep2

description: Transporter_KO_3_days_selection_sgRNA_counts.txt

tag: cell line

value: HAP1 (RRID:CVCL_Y019)

tag: cell type

tag: transgene

tag: screening library


title: Arabidopsis,atx4/5, H3K4me3, rep2

tag: tissue

tag: genotype

value: atx4/atx5 double mutant


title: HCC_TMA_20210616_NA_ROI6_Vessel

description: (v1.0) Cancer Transcriptome Atlas

value: Liver cancer resection

tag: slide name

tag: pool

tag: roi

tag: aoi type

value: Vessel

tag: area


title: HCC_TMA_20210616_NA_ROI3_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_GreyMatter_C2_4

description: 2_Frontal|4|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanwidth

tag: scanheight

tag: scanoffsetx


title: Basal Ganglia_C1

tag: tissue

tag: tissue preparation

tag: region

tag: age


title: HCC_TMA_20210616_NA_ROI2_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_GreyMatter_C2_1

description: 2_Frontal|1|Full ROI

tag: tissue type

tag: lotid

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanoffsety

tag: loq


title: Arabidopsis,atx3-1, H3K4me3, rep2

tag: tissue

tag: genotype


title: HCC_TMA_20210616_NA_ROI1_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_GreyMatter_C2_3

description: 2_Frontal|3|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanwidth

tag: scanheight

tag: scanoffsetx


title: Arabidopsis,WT, H3K4me3, rep2

tag: tissue

tag: genotype

value: WT


title: Transporter_KO_3days_SIM1_rep1

tag: cell line

tag: cell type

value: Myeloid haploid karyotype cell line

tag: transgene

value: Lentivirally delivered Cas9 gene (Addgene #52962)

tag: screening library

value: Human Transporter Knockout Library with UMIs (Addgene #221409)

tag: treatment

value: 5.3 nM SIM1 for 3 days


title: Frontal_GreyMatter_C2_2

description: 2_Frontal|2|Full ROI

value: postmortem brain

tag: tissue type

value: FFPE

tag: area

tag: region

value: Frontal lobe

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

value: No

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanoffsety

tag: loq


title: Frontal_GreyMatter_C1_6

description: 1_Frontal|6|Full ROI

tag: tissue

tag: tissue type

tag: area

value: Male

tag: duration

tag: ventilation

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanwidth

tag: scanheight

tag: scanoffsetx


title: Transporter_KO_3days_DAT551_rep3

tag: cell line

tag: cell type

tag: transgene

tag: screening library

tag: treatment

value: 245 nM DAT551 for 3 days


title: Transporter_KO_3days_SIM1_rep3


title: Arabidopsis,atx4/5, H3K4me2, rep2

source_name: 14 dai seedling

tag: tissue

value: 14 dai seedling

tag: genotype


title: HCC_TMA_20210616_07_49554_ROI33_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210616_07_49554_ROI33_Tumor

description: (v1.0) Cancer Transcriptome Atlas

value: Tumor


title: Transporter_KO_3days_SIM1_rep2

value: HAP1 (RRID:CVCL_Y019)


title: Transporter_KO_3days_Input_rep1


title: HCC_TMA_20210616_NA_ROI4_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_GreyMatter_C1_5

description: 1_Frontal|5|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

value: Yes

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanoffsety

tag: loq


title: Arabidopsis,atx3-1, H3K4me2, rep2

tag: tissue

tag: genotype


title: Transporter_KO_3days_DAT551_rep1

tag: cell line

tag: cell type

tag: transgene

tag: screening library

tag: treatment


title: HCC_TMA_20210616_07_49554_ROI32_Vessel

description: (v1.0) Cancer Transcriptome Atlas

value: Liver cancer resection

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Transporter_KO_3days_DAT551_rep2


title: Arabidopsis,WT, H3K4me2, rep2


title: Arabidopsis,atx3-1/4/5, H3, rep2

value: atx3-1/atx4/atx5 triple mutant


title: Arabidopsis,atx3-1/4/5, H3K4me2, rep2


title: HCC_TMA_20210616_07_49554_ROI32_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_GreyMatter_C1_2

description: 1_Frontal|2|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: scanwidth

tag: scanheight

tag: scanoffsetx


title: Frontal_GreyMatter_C1_3

description: 1_Frontal|3|Full ROI

tag: tissue

tag: tissue type

tag: area

tag: region

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: stitchedreads

tag: sequencingsaturation

tag: scanoffsety

tag: loq


title: HCC_TMA_20210616_07_43970_ROI29_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: aoi type


title: Transporter_KO_3days_DMSO_rep3

tag: cell line

tag: cell type

tag: transgene

tag: screening library


title: HCC_TMA_20210616_07_43970_ROI31_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

value: Vessel

tag: area


title: Frontal_GreyMatter_C1_1

description: 1_Frontal|1|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: scanwidth

tag: scanheight

tag: scanoffsetx


title: Transporter_KO_3days_MZ1_rep2

tag: cell line

tag: cell type

value: Myeloid haploid karyotype cell line

tag: transgene

tag: screening library

tag: treatment

value: 100 nM MZ1 for 3 days


title: Arabidopsis,atx4/5, H3, rep2

tag: tissue

tag: genotype

value: atx4/atx5 double mutant


title: Arabidopsis,WT, H3, rep2

value: WT


title: Transporter_KO_3days_MZ1_rep3

value: Lentivirally delivered Cas9 gene (Addgene #52962)

value: Human Transporter Knockout Library with UMIs (Addgene #221409)


title: HCC_TMA_20210616_07_43970_ROI29_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Transporter_KO_3days_DMSO_rep2


title: HCT116, TET2-ChIP, rep3

city: Shanghai

first: Yu

last: Yuanyuan

address: No. 1239, Siping Road, Shanghai

country: China

institute: Tongji University

data_processing:
ChIP-seq data were checked with FASTQC (v0.11.8) and trimmed using TrimGalore (v0.6.4)
ChIP-seq reads were aligned to hg38 using Bowtie2 (v2.3.5.1) with parameters: --no-unal --no-mixed --no-discordant, and were further filtered with mapping quality of at least 20
PCR duplicates were removed using Sambamba (v0.7.0)
Peaks were called using  MACS2 (v2.1.2) to call peaks with parameter -p 0.001
bigWig files were generated by bamCoverage in deepTools (v3.3.0) with 25 bp bin size and normalized as FPKM
Assembly: hg38
Supplementary files format and content: narrowPeak

extract_protocol:
HCT116 cells were crosslinked with 1 % formaldehyde for 10 min at room temperature and quenched with 125 mM glycine. The fragmented chromatin fragments were precleared and then immunoprecipitated with Protein A + G Magnetic beads coupled with anti-TET2 antibodies. After reverse crosslinking, ChIPed and input DNA fragments were end-repaired and A-tailed using the NEBNext End Repair/dA-Tailing Module (E7442, NEB) followed by adapter ligation with the NEBNext Ultra Ligation Module (E7445, NEB).
Sequencing libraries were generated by Genefund Biotech (Shanghai, China). The DNA libraries were amplified for 15 cycles and sequenced using Illumina Hi-Seq with 150 bp paired-end protocol.

value: NC

value: control


title: HCT116, TET2-ChIP, rep2


title: Arabidopsis,atx4/5, H3K4me3, rep1


title: HCC_TMA_20210616_07_36686_ROI27_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210616_07_36686_ROI28_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_GreyMatter_C1_4

description: 1_Frontal|4|Full ROI

value: postmortem brain

tag: tissue type

value: FFPE

tag: region

value: Frontal lobe

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

value: Male

tag: immunocompromised status

value: No

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanoffsety

tag: loq


title: PHHs, scRNAseq

city: luzhou

last: Jiang

address: Zhong Shan Road

institute: SWMU

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: hg38
Supplementary files format and content: tab-separated values files and matrix files

source_name: Primary human hepatocytes

growth_protocol: PHHs were freshly isolated from liver donors.

extract_protocol:
Fresh uncultured PHHs were lysed and the released RNA was barcoded through reverse transcription in individual gel beads in emulsion (GEMs). Reverse transcription was performed on a S1000 Touch Thermal Cycler (Bio-Rad) at 53 °C for 45 min, followed by 85 °C for 5 min, and then held at 4 °C. The cDNA was generated and then amplified, and quality-assessed using the Agilent 4200 system.
According to the manufacturer’s instructions, scRNA-seq libraries were constructed using the Single Cell 3′ Library and Gel Bead Kit V3.1.

tag: cell type

value: Primary human hepatocytes

tag: treatment

value: freshly-isolated


title: HCT116, TET2-ChIP, rep1

tag: cell line

tag: genotype


title: Arabidopsis,WT, H3K4me3, rep1

tag: tissue

value: 14 dai seedling


title: HCT116, Valine deprivation, TET2-ChIP, rep3

value: Valine deprivation


title: Arabidopsis,atx3-1, H3K4me3, rep1


title: Arabidopsis,atx3-1, H3, rep2


title: Transporter_KO_3days_MZ1_rep1

value: HAP1 (RRID:CVCL_Y019)

value: Myeloid haploid karyotype cell line

tag: transgene

tag: screening library


title: BHEM, replicate6, RNAseq

data_processing:
RNAseqv1
Adapter of sequence reads were trimmed and poor quality reads  were removed by TrimGalore(quality <20 or length <30),
Paired-end RNA-seq reads were trimmed and then mapped to hg38 genome by STAR (v.2.7.4a)
Raw count tables of genes were computed using featureCounts (v2.0.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: PHHs

extract_protocol:
Total RNA was isolated using the RNeasyMini kit (QIAGEN) or Direct-zol RNA Miniprep (ZYMO RESEARCH).
RNA sequencing libraries were prepared using the NEBNext UltraTM RNA Library Prep kit for Illumina (NEB, USA) or VAHTS Universal V8 RNA-seq Library Prep Kit for NovaSeq (Vazyme, China) following the manufacturer’s recommendations.

value: PHHs

value: HPLCs

value: BHEM


title: Arabidopsis,atx3-1/4/5, H3K4me3, rep1

value: atx3-1/atx4/atx5 triple mutant


title: HCC_TMA_20210616_07_43970_ROI31_Tumor

description: (v1.0) Cancer Transcriptome Atlas

value: Liver cancer resection

tag: slide name

tag: pool

tag: roi

tag: aoi type

value: Tumor

tag: area


title: Transporter_KO_3days_DMSO_rep1

value: Lentivirally delivered Cas9 gene (Addgene #52962)

value: Human Transporter Knockout Library with UMIs (Addgene #221409)


title: HCC_TMA_20210616_07_36686_ROI28_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210616_07_36686_ROI26_Vessel

description: (v1.0) Cancer Transcriptome Atlas

value: Vessel


title: Arabidopsis,atx3-1/4/5, H3K4me2, rep1


title: BHEM, replicate5, RNAseq


title: HCT116, Valine deprivation, TET2-ChIP, rep2

value: NC


title: HCT116, Valine deprivation, TET2-ChIP, rep1


title: HCT116, HDAC6-KD, TET2-ChIP, rep2

value: control


title: HCC_TMA_20210616_07_36686_ROI25_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210616_07_36686_ROI27_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Arabidopsis,atx4/5, H3K4me2, rep1

value: atx4/atx5 double mutant


title: BHEM, replicate3, RNAseq


title: Arabidopsis,atx3-1, H3K4me2, rep1


title: BHEM, replicate2, RNAseq


title: HCT116, HDAC6-KD, TET2-ChIP, rep1


title: HCC_TMA_20210616_07_36686_ROI25_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCT116, HDAC6-KD, Valine deprivation, TET2-ChIP, rep3


title: Arabidopsis,WT, H3K4me2, rep1

value: WT


title: BHEM, replicate1, RNAseq


title: HCC_TMA_20210616_07_24083_ROI23_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Arabidopsis,atx3-1/4/5, H3, rep1

value: 14 dai seedling


title: BHEM, replicate4, RNAseq


title: Arabidopsis,atx3-1, H3, rep1


title: HCC_TMA_20210616_07_24083_ROI23_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Arabidopsis,atx4/5, H3, rep1


title: HCC_TMA_20210616_07_36686_ROI26_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCT116, HDAC6-KD, TET2-ChIP, rep3


title: fresh, replicate1, RNAseq

value: fresh


title: 6C, replicate2, RNAseq


title: HCT116, HDAC6-KD, Valine deprivation, TET2-ChIP, rep2

value: Valine deprivation


title: HCT116, HDAC6-KD, Valine deprivation, TET2-ChIP, rep1


title: ACICU after 1-week desiccation (third biological replicate)

city: Rome

first: Massimiliano

last: Lucidi

state: Rome

address: Viale Guglielmo Marconi 446

department: Sciences

country: Italy

institute: University of Roma Tre

description: ACICU desiccated cells (#3)

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 Acinetobacter_baumannii_ATCC 19606 reference genome available on ENSEMBL using the Bowtie2 aligner v.2.2.6. BAM files were generated because of this step. Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within gene regions were counted. After the extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were defined as differentially expressed genes for each comparison.
Assembly: A. baumannii ATCC 19606T [NZ_CP058289.1]
Assembly: A. baumannii ACICU [NZ_CP031380.1]
Supplementary files format and content: Processed data: tab-delimited text files including raw counts for each sample
Supplementary files format and content: Raw data files: tab-delimited text files including RPKM values for each sample

organism: Acinetobacter baumannii ACICU

source_name: A. baumannii [NZ_CP031380.1]

growth_protocol: ATCC 19606T and ACICU were grown in LB and incubated at 37°C under shaking for 18 h. Bacterial cultures were sub-cultured (1:100 dilution) in a flask and incubated at 37°C under shaking for 6 h.

extract_protocol:
RNA was purified with RNeasy MiniElute Cleanup Kit (Qiagen) and RNA samples were treated with TURBO DNase (Invitrogen) to remove genomic DNA.
The RNA-seq analysis, RNA quality assessment, library preparation, sequencing, and statistical analysis of the data were performed at the GENEWIZ Biotechnology Facility (GENEWIZ, Azenta Life Sciences Company, Leipzig, Germany), as previously described [doi: 10.1128/spectrum.00961-22].

treatment_protocol: ATCC 19606T and ACICU were washed, diluted in ultrapure distilled water to an OD600 of 1.0, and desiccated on glass Petri plates for 1 week. Before and after desiccation, samples were collected and mixed with 2 mL of RNA Protect Bacteria Reagent (Qiagen). Total RNA isolation was performed by using miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

value: wild-type

value: Total RNA extraction from cells harvested after 1-week desiccation (desiccated sample)


title: HCC_TMA_20210616_07_24083_ROI22_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: 6C, replicate1, RNAseq

value: PHHs


title: HCC_TMA_20210616_07_24083_ROI22_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: REH_CSF_2

city: Minneapolis

first: Peter

middle: M

last: Gordon

state: MN

address: 420 Delaware S. SE, MMC 366

institute: University of Minnesota

data_processing:
Quality control of raw sequencing data was performed using FastQC and trimmed using Trimmomatic (v 0.33) enabled with the “-q” option. Read mapping was performed with Hisat2 (v2.1.0) using the human genome (Homo sapiens GRCH38) as a reference. Gene quantification was done with FeatureCounts using raw read counts. Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood City, CA) using raw read counts.
Assembly: Homo sapiens GRCH38
Supplementary files format and content: CPM values for each sample

source_name: lymphoid

growth_protocol: Media (RPMI/FCS 10%) or cerebrospinal fluid

extract_protocol:
RNA was extraced using a RNAeasy mini plus kit (Qiagen)
Dual-indexed (UDI) TruSeq stranded mRNA libraries

treatment_protocol: 48 hours

value: lymphoid

value: REH

value: B-cell lymphoblastic leukemia

value: Cerebrospinal fluid


title: HCC_TMA_20210616_07_24083_ROI21_Vessel

description: (v1.0) Cancer Transcriptome Atlas

value: Liver cancer resection


title: REH_CSF_3


title: 5C, replicate1, RNAseq


title: REH_CSF_1


title: 5C, replicate2, RNAseq


title: HCC_TMA_20210616_07_24083_ROI21_Tumor

description: (v1.0) Cancer Transcriptome Atlas

value: Tumor


title: ACICU after 1-week desiccation (second biological replicate)

description: ACICU desiccated cells(#2)


title: NHEM, replicate6, RNAseq

value: HPLCs

value: NHEM


title: ACICU before desiccation (third biological replicate)

description: ACICU before desiccation (#3)

value: Total RNA extraction from cells harvested immediately after resuspension in ultrapure distilled water (before desiccation)


title: HCC_TMA_20210616_07_19660_ROI20_Vessel

description: (v1.0) Cancer Transcriptome Atlas

value: Vessel


title: ACICU after 1-week desiccation (first biological replicate)

description: ACICU desiccated cells (#1)


title: REH_RPMI_3

value: RPMI


title: NHEM, replicate5, RNAseq


title: HCC_TMA_20210616_07_19660_ROI20_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: REH_RPMI_2


title: ACICU before desiccation (second biological replicate)

description: ACICU before desiccation (#2)


title: NHEM, replicate3, RNAseq


title: HCC_TMA_20210616_07_19660_ROI19_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: NHEM, replicate4, RNAseq


title: ACICU before desiccation (first biological replicate)

description: ACICU before desiccation (#1)


title: NALM6_CSF_3


title: HCC_TMA_20210616_07_19660_ROI19_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: BMDMs, DCA-1

city: tianjin

first: Yunhuan

last: Gao

address: Wei Jin Road No. 94

department: School of Medicine

institute: Nankai University

data_processing:
All the reads were mapped to the mouse reference genome (GRCm38/mm10) using STAR aligner (v2.5.0c).
Alignments were guided by a Gene Transfer File (Ensembl GTF version GRCm38.74) and the mean read insert sizes and their standard deviations were calculated using Picard tools (v.1.126) (http://broadinstitute.github.io/picard/).
The Read Per Million (RPM) normalized BigWig files were generated using BEDTools (v2.17.0) and bedGraphToBigWig tool (v4).
Read count tables were generated using HTSeq (v0.6.0) normalized based on their geometric library size factors using DESeq2 (v3.0) and Deferential Expression (DE) analyses were performed.
Assembly: mm10
Supplementary files format and content: tab-demilited text files includs raw counts for each sample
Supplementary files format and content: tab-demilited text files includ FPKM values for each sample

organism: Mus musculus

source_name: bone marrow

extract_protocol:
BMDMs were treatment with 100 µM DCA for 24h. One days later, all cells with or without DCA treatment were collected for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

value: Bone marrow-derived macrophages

value: macrophage

value: DCA


title: NALM6_CSF_2


title: NHEM, replicate2, RNAseq


title: BMDMs NC-1

value: NC


title: NALM6_CSF_1


title: Cortical neurons, Bicuculline CHX

city: New Haven

first: Paul

last: Lee

state: CT

address: 100 College St Room 225

department: Neuroscience

institute: Yale University

data_processing:
After clipping both 5' and 3' adaptors, reads were deduplicated using FASTX-Toolkit. The 10 nt UMIs were then removed using Cutadapt. Reads were first mapped to a mammalian rRNA and tRNA reference using Bowtie. The remaining unmapped reads were reversed by fastx_reverse_complement then mapped to mouse reference genome GRCm39 and transcriptome by STAR. 28-31 nt footprints were used for subsequent analysis, with the P site offset for each footprint length being determined by using RiboMiner. For each read, P site was inferred by adding the P site offset to the 5' coordinate.
Assembly: GRCm39
Supplementary files format and content: Comma-separated values (csv) file of footprint counts mapped to each codon of Nptxr mRNA

molecule: cytoplasmic RNA

source_name: primary cortical neurons

growth_protocol: Neurobasal medium supplemented with B27 Plus, L-Glutamax, 33 mM glucose, and 37.5 mM NaCl.

extract_protocol: Neurons were washed twice briefly with ice-cold PBS supplemented with 100 μg/ml cycloheximide. 400 μl cold cell lysis buffer (20 mM HEPES, pH 7.4, 100 mM KCl, 5 mM, MgCl2, 500U/ml RNasin-Plus (Promega), 1x protease inhibitor cocktail (200X, Millipore), 100 μg/ml cycloheximide) was added directly to the cells, which were then scraped off of the dishes and transferred to 2 ml microcentrifuge tube containing Lysing Matrix-D (MP Biomedicals). Cells were lysed by vortexing 6 times (20 seconds each) with 40 s intervals on ice. After centrifugation for 10 min at 13,000 g at 4 °C, the supernatant was transferred into a new microcentrifuge tube and RNA concentrations of the cell lysates were measured using Qubit RNA High Sensitivity Assay Kit (Thermo Fisher, Q32855). 10U RNase I (Thermo Fisher, EN0601) was added into cell lysate for every 100 μg RNA, and digestion was carried out at 4°C overnight with gentle rotation. The next day, RNase I digestion was stopped by adding Superase-In RNase inhibitor (Thermo Fisher, AM2696) at 1 U/μl. Digested cell lysate was loaded on top of 0.8 ml sucrose cushion (1 M sucrose, 20 mM HEPES, pH 7.4, 100 mM KCl, 5 mM, MgCl2, 100 μg/ml cycloheximide) in a 1.5 ml ultracentrifuge tube (Beckman Coulter, 343778) and centrifuged for 1.5 h at 75,000 rpm at 4°C using a TLA-120.2 rotor (Beckman Coulter). After carefully removing the supernatant, the ribosome pellet was solubilized in TRIzol (ThermoFisher) for RNA extraction. The extracted RNA was separated in a 15% Urea-TBE gel, and RNA fragments of 25 - 35 nt in length were excised for subsequent library construction.

treatment_protocol: Day 12 primary neurons were treated with either DMSO or bicuculline (40 μM) for 10 hours.

value: primary cortical neurons

value: WT

value: Bicuculline


title: Cortical neurons, Bicuculline

data_processing:
After clipping both 5' and 3' adaptors, reads were deduplicated using FASTX-Toolkit. The 10 nt UMIs were then removed using Cutadapt. Reads were first mapped to a mammalian rRNA and tRNA reference using Bowtie. The remaining unmapped reads were then mapped to mouse reference genome GRCm39 and transcriptome by STAR. 28-31 nt footprints were used for subsequent analysis, with the P site offset for each footprint length being determined by using RiboMiner. For each read, P site was inferred by adding the P site offset to the 5' coordinate.
Assembly: GRCm39
Supplementary files format and content: Comma-separated values (csv) file of codon usage of highest P sites
Library strategy: Ribosome profiling

extract_protocol:
Neurons were washed twice briefly with ice-cold PBS supplemented with 5 μM harringtonine. 400 μl cold cell lysis buffer (20 mM HEPES, pH 7.4, 100 mM KCl, 5 mM, MgCl2, 500U/ml RNasin-Plus (Promega), 1x protease inhibitor cocktail (200X, Millipore), 5 μM harringtonine) was added directly to the cells, which were then scraped off of the dishes and transferred to 2 ml microcentrifuge tube containing Lysing Matrix-D (MP Biomedicals). Cells were lysed by vortexing 6 times (20 seconds each) with 40 s intervals on ice. After centrifugation for 10 min at 13,000 g at 4 °C. The supernatant was transferred into a new microcentrifuge tube and supplemented with 10 mM creatine phosphate, 0.1 mM spermidine, 40 μg/mL creatine phosphokinase, 0.8 mM ATP, and 25 μM puromycin, before incubation at 35 °C for 15 min. After incubation, RNA concentrations of the cell lysates were measured using Qubit RNA High Sensitivity Assay Kit (Thermo Fisher, Q32855). 10U RNase I (Thermo Fisher, EN0601) was added into cell lysate for every 100 μg RNA, and digestion was carried out at 4°C overnight with gentle rotation. The next day, RNase I digestion was stopped by adding Superase-In RNase inhibitor (Thermo Fisher, AM2696) at 1 U/μl. Digested cell lysate was loaded on top of 0.8 ml sucrose cushion (1 M sucrose, 20 mM HEPES, pH 7.4, 100 mM KCl, 5 mM, MgCl2, 5 μM harringtonine, 25 μM of puromycin) in a 1.5 ml ultracentrifuge tube (Beckman Coulter, 343778) and centrifuged for 1.5 h at 75,000 rpm at 4°C using a TLA-120.2 rotor (Beckman Coulter). After carefully removing the supernatant, the ribosome pellet was solubilized in TRIzol (ThermoFisher) for RNA extraction. The extracted RNA was separated in a 15% Urea-TBE gel, and RNA fragments of 25 - 35 nt in length were excised for subsequent library construction.
Extracted RNA fragments were first treated with T4 Polynucleotide Kinase (T4 PNK, NEB, M0201L) without adding ATP to remove the 3' end phosphates. A 5ʹ pre-adenylated and 3' blocked adaptor (/5rApp/NNNNNNNNNNCACGGCGATCTTGCCGCC/3ddC/) was ligated to the 3' ends of RNA fragments by using T4 RNA Ligase 2, truncated KQ (NEB, M0373L). The 5' ends of RNA fragments were phosphorylated by T4 PNK and ligated to 5' adaptor (CGATCTCCAATTCCCACTCCTTTCAAGACCTrC) using T4 RNA Ligase 1 (NEB, M0437M). Ribosomal RNA (rRNA) was depleted using RiboPOOL probes against human/mouse/rat rRNAs (siTOOLs BIOTECH). Reverse transcription (RT) was conducted using SuperScript IV Reverse Transcriptase (Thermo Fisher, 18090050) with RT primer GGGCGGCAAGATCGCCGTG. Libraries were amplified by PCR using Q5 Hot Start High-Fidelity DNA Polymerase (NEB, M0493L) with P5 primer (AATGATACGGCGACCACCGAGATCT ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNAGGGCGGCAAGATCGCCGTG) and P7 primers (DMSO sample: CAAGCAGAAGACGGCATACGAGATCGGTTCAAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCCAATTCCCACTCCTTTCAAGACCT; Bicuculline sample: CAAGCAGAAGACGGCATACGAGATGCTGGATTGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCCAATTCCCACTCCTTTCAAGACCT).


title: HCC_TMA_20210616_07_19307_ROI18_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210616_07_19307_ROI16_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: NALM6_RPMI_2

value: lymphoid

value: B-cell lymphoblastic leukemia


title: NALM6_RPMI_3


title: REH_RPMI_1

value: REH


title: control E4 quail NTs

city: Jerusalem

first: Chaya

last: Kalcheim

address: Hadassah Medical School

department: Medical Neurobiology

country: Israel

institute: The Hebrew University in Jerusalem

data_processing:
Demultiplexing, alignment, filtering, barcode counting and Unique Molecular Identifier (UMI) counting were made using the Cell Ranger pipeline (v6.0.1)
Assembly: NCBI (RefSeq assembly GCF_001577835.2)
Supplementary files format and content: zipped folder of tab-separated values files and matrix files from cellranger (filtered)

organism: Coturnix japonica

source_name: embryonic (E4) neural tubes with associated mesoderm

extract_protocol:
At E4, ten NTs per group (with associated mesoderm) were mechanically microdissected in Phosphate-buffered saline (PBS) supplemented with Ca2+/ Mg2+ and 5% fetal calf serum (FCS). NTs were incubated for 15 min at 37oC in 1.5 ml Accutase (Sigma Israel, A6964) containing 30 ul Papain (Sigma Israel, P3125) and 300 ng DNaseI (Sigma Israel, DN25) and dissociated mechanically using sequentially 1000 and 200 ul pipettes. Cells were filtered through a 40-micron filter and resuspended in PBS containing 2% FCS. Samples were sorted using a BD FACSAria III sorter (BD Biosciences UK). Single cells were isolated by sequentially gating cells according to their SSC-A vs. FSC-A and FSC-H vs FSC-W profiles, following standard flow cytometry practices. Dead or damaged cells were excluded following Propidium Iodide uptake. Citrine fluorescence was detected using a 488 nm laser;  age-matched NT cells from untransfected embryos served as negative control to determine the fluorescence gate.
Sorted fluorescent cells were loaded into the 10X Genomics Chromium Next controller.  Libraries were prepared following manufacturer’s instructions (GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1, 10× Genomics, CA, USA). Approximately 10.000 cells were loaded per sample. Sequencing was performed using the Illumina Nextseq500 platform (Illumina Inc, San Diego, CA,USA) with the following sequencing conditions: 28 bp (Read1) and 54 bp (Read2).

treatment_protocol: Embryos were electroporated at E2.5 with either control or RARa403 vectors, together with a Msx1-Citrine plasmid

value: control


title: HCC_TMA_20210616_07_19307_ROI16_Tumor

description: (v1.0) Cancer Transcriptome Atlas

value: Liver cancer resection

value: Tumor


title: RARa403 E4 quail NTs

value: embryonic (E4) neural tubes with associated mesoderm


title: Cortical neurons, DMSO

value: DMSO


title: NALM6_RPMI_1

value: RPMI


title: overlap-brain-sample3

city: Suzhou

first: Li

last: Yong-Chang

address: Renai road 199

institute: Soochow university

description: biol rep 3 overlap

data_processing:
Trim_galore, Adapter and PolyA cut-off
STAR, align reads to gex-mm10-2020-A
umi_homopolymer.py(UMI extraction)/umi_tools (Deduplication) provided by Foley, J.W., et al., Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ. Genome research, 2019. 29(11): p. 1816-1825.
FeatureCounts, Align reads preferentially to 3'end and calculate the strand-specific reads counts
RSeQC, Show reads distribution on the gene bodies
Assembly: gex-mm10-2020-A
Supplementary files format and content: one excell files include raw count values for each sample

molecule: polyA RNA

source_name: brain

extract_protocol:
RNA was released directly in PCR tube during lysis from LCM isolated samples.
Each library was prepared using Smart-3SEQ protocol (Foley, J.W., et al., Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ. Genome research, 2019. 29(11): p. 1816-1825.)

value: brain

value: neuron


title: HCC_TMA_20210616_07_19307_ROI18_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210616_07_19307_ROI15_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCT116, Tet2KD, Valine deprivation, ACE-seq

data_processing:
ACE-seq data were checked with FASTQC (v0.11.8) and trimmed using TrimGalore (v0.6.4)
ACE-seq reads were aligned to hg38 using Bismark (v0.22.1) in paired-end mode. Duplicates were removed using deduplicate_bismark.
5hmC in the CpG contexts were extracted by MethPipe software package (v3.4.3)
Cytosines sites covered by at least 3 reads were retained.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: ACE-seq

extract_protocol:
For the ACE-seq libraries construction, 200 ng of the genomic DNA was firstly fragmented into 300 bp by the Covaris M220. Then, the T4 Phage β-glucosyltransferase (NEB) and uridine diphosphoglucose were used to convert 5hmC into 5ghmC at 37 °C for 2 h. After that, 0.1 M NaOH (5×) was added to the modified fragments for denaturation at 50 °C for 10 min. Then, the DEA enzyme mix (Vazyme) was used to deaminate dC or 5mC to U or T, respectively, at 37 °C for 3 h.
After deamination, DNA fragments were purified and subjected to library construction with Scale Methyl-DNA Lib Prep Kit according to the instruction manual (Illumina). Briefly, the single-stranded heat-denatured DNA fragments were ligated to T7 truncated adapter and dA-tailed. Next, the ligated DNA was extended to the second strand synthesis and the methylated adapters were ligated. The DNA was ampliﬁed for 10 cycles using Illumina 8-bp dual index primers. Finally, the ACE-seq libraries were analyzed by Agilent 2100 Bioanalyzer and sequenced on an Illumina NovaSeq 6000 platform by 150 bp paired-end sequencing.

value: Valine deprivation


title: HCT116, Tet2KD, ACE-seq


title: overlap-brain-sample1

description: biol rep 1 overlap


title: Cortical neurons, DMSO CHX


title: HCC_TMA_20210616_07_14746_ROI14_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: cfos-brain-sample3

description: biol rep 3 cfos


title: HCC_TMA_20210616_07_19307_ROI15_Vessel

description: (v1.0) Cancer Transcriptome Atlas

value: Vessel


title: HCC_TMA_20210616_07_14746_ROI14_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: MSC_NSC_4_24 h (transcriptome)

city: Saarbrücken

first: Annika

last: Engel

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

hyb_protocol: The labeled cRNA samples were hybridized to Human SurePrint G3 Gene Expression Microarrays (V3, G4851C) from Agilent Technologies following the inctructions from the Gene Expression Hybridization Kit (Agilent Technologies)

scan_protocol: The microarray slides were scanned with a resolution of 3 μm.

data_processing: Raw data was extracted using Feature Extraction software (Agilent Technologies, Santa Clara, CA, USA). Raw microarray data were extracted and concatenated into one matrix using python (v 3.7) with numpy (v 1.16.4).

source_name: human bone marrow-derived MSCs , 24h

label_protocol: Cyanine-3 (Cy3) labeling of cRNA was performed following the instructions from Low Input Quick Amp Labeling Kit (One-Color) (Agilent Technologies, Santa Clara, CA, USA). The cRNA samples were using RNeasy Mini Kit (Qiagen, Hilden, Germany). Resulting cRNA concentrations were determined using a NanoDrop™ 2000c Spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA).

growth_protocol: Cells were seeded at a density of 100.000 per 25 cm2 flask (coated with fibronectin), grown with Mesenchymal Stem cell Growth Medium (PromoCell) and expanded for 1-2 passages before induction of the trans-differentiation.

extract_protocol: Total RNA was prepared using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations.

treatment_protocol: Time-course cell samples were collected at 0, 3, 6, 9, 12, 24 and 48 h after addition of a standard commercial neurogenic differentiation medium (C-28015, PromoCell).

value: human bone marrow-derived MSCs

tag: timepoint

tag: replicate

value: neurogenic differentiation medium


title: MSC_NSC_4_48 h (transcriptome)

source_name: human bone marrow-derived MSCs , 48h


title: cfos-brain-sample2

description: biol rep 2 cfos


title: HCC_TMA_20210616_07_14746_ROI13_Vessel

description: (v1.0) Cancer Transcriptome Atlas

data_processing:
Raw sequencing data were processed using the GeoMx NGS Pipeline to generate fastq files followed by dcc files
Sequences were aligned to the Cancer Transcriptome Atlas probe set using default settings
Assembly: hg38
Supplementary files format and content: rawCounts.tsv: gene count matrix file in tsv format
Supplementary files format and content: qnormCounts.tsv: Q3 normalized gene count matrix file in tsv format
Library strategy: GeoMx Spatial Transcriptomics

source_name: Liver cancer resection

extract_protocol:
We followed published experimental methods (NanoString) with modifications as noted below. Briefly, slides were baked at 60 °C for one hour, deparaffinized with CitriSolv (DECON), rehydrated, antigen-retrieved in 1x Tris-EDTA/pH 9 in a steamer for 15 min at 100 °C, proteinase K (Thermo Fisher Scientific, AM2548) digested at 0.1 ng/ml for 15 min at 37 °C, and postfixed in neutral-buffered formalin for 10 min, hybridized to UV-photocleavable barcode-conjugated RNA in situ hybridization probe set (CTA with 1,779 gene targets and 32 reference genes) overnight at 37 °C, washed to remove off-target probes and then counterstained with morphology markers for 2 h at room temperature. The morphology markers consisted of: 1:50 CD31 (Abcam, ab47063) and 1:50 Arginase-1 (Cell Signaling Technology, 93668S) in blocking buffer W (NanoString). The anti-CD31 antibody was conjugated using the Alexa Fluor 555 Lightning-Link kit (Abcam, ab269820) and the anti-Arginase-1 antibody with the Alexa Fluor 647 Lightning-Link kit (Abcam, ab269823). These two morphology markers allowed distinction between vessel areas of interest (AOIs) and tumor regions of interest (AOIs) within a microscopic region of interest (ROI). 22 Immunofluorescence images, ROI selection, segmentation into marker-specific AOIs and 23 spatially indexed barcode cleavage and collection were performed on a GeoMx DSP instrument 24 (NanoString). Typical exposure times were 400 ms for CD31 and 300 ms for Arg 1. Approximately 25 4 AOIs on average were collected per specimen (details in Table 1)
Library preparation was performed according to the manufacturer’s instructions and involved PCR amplification to add Illumina adapter sequences and unique dual sample indices. A minimum sequencing depth of 2 150–200 reads per square micron of illumination area was achieved by sequencing all CTA AOIs on a NovaSeq S2 (100 cycles, read 1: 27 nt, read 2: 27 nt, index 1: 8 nt, index 2: 8 nt).


title: HCT116, Valine deprivation, ACE-seq

value: wildtype


title: HCT116, Hdac6KD, ACE-seq


title: HCC_TMA_20210616_07_14746_ROI13_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: cfos-brain-sample1

description: biol rep 1 cfos


title: MSC_NSC_4_9 h (transcriptome)

source_name: human bone marrow-derived MSCs , 9h


title: HCC_TMA_20210616_07_14746_ROI11_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCT116, ACE-seq


title: mCherry-brain-sample3

description: biol rep 3 mCherry


title: overlap-brain-sample2

description: biol rep 2 overlap


title: MSC_NSC_4_6 h (transcriptome)

source_name: human bone marrow-derived MSCs , 6h


title: mCherry-brain-sample2

description: biol rep 2 mCherry


title: HCT116, Tet2KD, Valine deprivation, WGBS, rep2

data_processing:
WGBS data were checked with FASTQC (v0.11.8) and trimmed using TrimGalore (v0.6.4)
WGBS reads were aligned to hg38 using Bismark (v0.22.1) in paired-end mode. Duplicates were removed using deduplicate_bismark.
Cytosine not converted by bisulfite in the CpG contexts were extracted by MethPipe software package (v3.4.3)
Cytosines sites covered by at least 3 reads were retained.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
The genomic DNA of each sample was purified by Wizard Genomic DNA Purification Kit (Promega). 1 μg of the genomic DNA was firstly fragmented into 300 bp by the Covaris LE220R. The methylated adapters were ligated to the fragmented DNA. Bisulfite treatment was performed with EZ DNA Methylation-Gold Kit (Zymo Research) according to the instruction manual. The resulting single-stranded DNA were amplificated using KAPA HiFi HotStart Uracil+ ReadyMix (2×) (Roche). The concentration of purified libraries was measured with the Qubit fluorometer dsDNA HS Assay (Thermo Fisher Scientific). Size distribution of the sequencing libraries was analyzed using Agilent 2100 Bioanalyzer.
WGBS was performed using an Illumina NovaSeq 6000 platform for 150 bp paired-end sequencing


title: HCT116, Tet2KD, Valine deprivation, WGBS, rep1


title: HCC_TMA_20210616_06_67338_ROI10_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: MSC_NSC_4_12 h (transcriptome)

source_name: human bone marrow-derived MSCs , 12h


title: MSC_NSC_4_0 h (transcriptome)

source_name: human bone marrow-derived MSCs , 0h


title: HCC_TMA_20210616_07_14746_ROI11_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCT116, Hdac6KD, Valine deprivation, ACE-seq


title: mCherry-brain-sample1

description: biol rep 1 mCherry


title: HCC_TMA_20210616_06_67338_ROI10_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Th2.WT.STIM.5

city: Toulouse

first: Isabelle

last: Lamsoul

address: CHU Purpan

country: France

institute: Inserm

data_processing:
nf-core RNA-seq pipeline
Sequence reads were trimmed for adapters and low-quality sequences using Cutadapt v.3.4
Trimmed reads were mapped to the GRCm39 assembly and annotation v.107 using STAR v.2.7.9a
Read count extraction wase performed using Salmon v.1.10.1
Assembly: GRCm39
Supplementary files format and content: Tab-separated text file includes raw counts for each sample
Supplementary files format and content: Tab-separated text file includes TPM values for each sample

source_name: Th2 lymphocytes

growth_protocol: Ctrl and ASB2 cKO mouse naive CD4+ cells were isolated from spleen of female Asb2fl/fl and VE-cadherin (VEC) -Cre;Asb2fl/fl transgenic mice (Metais et al., Circulation Research, 2018; Lamsoul et al., Blood, 2013), respectively, using a CD4+ T-cell Isolation Kit (BioLegend) and cultured for 3 days with plate-bound anti-CD3ε (5 µg/ml) in the presence of Th2 polarizing cytokines and antibody cocktails (10 ng/ml IL-2, 40 ng/ml IL-4, 1 µg/ml anti-CD28, and 10 µg/ml anti-IFNγ) in RPMI containing 10% FCS, 1% glutamine, 0.1% β-mercaptoethanol, and 1% penicillin/streptomycin in 24-well plates. Cells were then split across five noncoated plates and cultured for 3 additional days in fresh differentiating medium without antibodies (20 ng/ml IL-2 and 20 ng/ml IL-4).

extract_protocol:
RNA isolation was performed using the Nuclespin RNA kit (Macherey-Nagel).
RNA librairies for RNA-seq were  prepared using the Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Kit following manufacturer's protocol.

treatment_protocol: Th2 lymphocytes were stimulated at day 5 with 3µg/ml coated anti-CD3ε and 2µg/ml soluble anti-CD28 for 24h.

value: Th2 lymphocytes

value: anti-CD3ε/anti-CD28 for 24h


title: HCT116, Tet2KD, WGBS, rep2


title: HCT116, Tet2KD, WGBS, rep1


title: MSC_NSC_3_24 h (transcriptome)


title: Th2.WT.NS.3


title: Th2.WT.STIM.4


title: HCC_TMA_20210616_06_67338_ROI9_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210616_06_61783_ROI8_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCT116, Hdac6KD, Valine deprivation, WGBS, rep2


title: HCT116, Hdac6KD, Valine deprivation, WGBS, rep1


title: MSC_NSC_4_3 h (transcriptome)

source_name: human bone marrow-derived MSCs , 3h


title: Th2.WT.NS.2


title: MSC_NSC_3_12 h (transcriptome)


title: MSC_NSC_3_48 h (transcriptome)


title: HCT116, Hdac6KD, WGBS, rep2


title: MSC_NSC_3_9 h (transcriptome)


title: Th2.WT.STIM.3


title: MSC_NSC_3_6 h (transcriptome)


title: HCT116, Hdac6KD, WGBS, rep1


title: HCC_TMA_20210616_06_61783_ROI7_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Th2.WT.NS.1


title: MSC_NSC_3_3 h (transcriptome)


title: Th2.WT.STIM.2


title: HCC_TMA_20210616_06_67338_ROI9_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210616_06_61783_ROI7_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCT116, Valine deprivation, WGBS, rep2


title: HCC_TMA_20210616_06_61783_ROI6_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCT116, Valine deprivation, WGBS, rep1


title: MSC_NSC_2_48 h (transcriptome)


title: Th2.WT.STIM.1


title: HCC_TMA_20210616_06_61783_ROI8_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210616_06_61783_ROI6_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCT116, WGBS, rep2


title: MSC_NSC_2_12 h (transcriptome)


title: HCT116, WGBS, rep1


title: HCC_TMA_20210616_06_60911_ROI5_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Th2.ASB2KO.NS.3


title: Th2.ASB2KO.STIM.4


title: HCT116, RNAseq, rep3

description:
NC_gene_count.txt
NC_3

data_processing:
RNA-seq data were checked with FASTQC (v0.11.8) and trimmed using TrimGalore (v0.6.4)
RNA-seq reads were aligned to GRCh38/hg38 using HISAT2 (v2.1.0)
Gene expression levels were quantified to fragments per kilobase of exon model per million mapped fragments (FPKM) by StringTie (v2.2.1) and counts by prepDE.py based on hg38 annotations
Assembly: hg38
Supplementary files format and content: Tab-delimited tex files include raw count for each sample

extract_protocol:
RNAs were extracted from HCT116 cells using the RNA isolater Total RNA Extraction Reagent (Vazyme, R401-01). RNA sequencing libraries were prepared from 2 μg of RNA per sample as input material for the RNA sample preparations
Sequencing libraries were generated by Annoroad Gene Technology (Beijing, PR China) Co., Ltd. The sequencing was conducted on an Illumina NovaSeq 6000.


title: HCC_TMA_20210616_06_60911_ROI5_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Th2.ASB2KO.STIM.3


title: HCT116, RNAseq, rep2

description:
NC_gene_count.txt
NC_2


title: HCC_TMA_20210616_06_60911_ROI4_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: MSC_NSC_3_0 h (transcriptome)


title: MSC_NSC_2_24 h (transcriptome)


title: MSC_NSC_2_6 h (transcriptome)


title: Th2.ASB2KO.NS.2


title: MSC_NSC_2_9 h (transcriptome)


title: MSC_NSC_2_3 h (transcriptome)


title: HCT116, RNAseq, rep1

description:
NC_gene_count.txt
NC_1


title: HCC_TMA_20210616_06_60911_ROI4_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Th2.ASB2KO.STIM.2


title: HCT116, Valine deprivation, RNAseq, rep3

description:
NC_gene_count.txt
NC_V_3


title: MSC_NSC_2_0 h (transcriptome)


title: MSC_NSC_1_48 h (transcriptome)


title: HCC_TMA_20210616_06_60911_ROI3_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCT116, Valine deprivation, RNAseq, rep2

description:
NC_gene_count.txt
NC_V_2


title: Th2.ASB2KO.NS.1


title: Th2.ASB2KO.STIM.1


title: HCT116, Valine deprivation, RNAseq, rep1

description:
NC_gene_count.txt
NC_V_1


title: BMSCs，PCL-SE，Day7

city: 南充市

first: Cai-Ping

last: Yan

state: sichuan

address: No. 1 The South of Maoyuan Road

department: orthopedics

institute: North sichuan medical college

data_processing:
NanoDrop 2000 spectrophotometer: Detects RNA purity and concentration；Agient2100/LabChip GX detection: Accurate detection of RNA integrity.
The Qubit 3.0 fluorometric quantifier was used for preliminary quantification, and the concentration should reach more than 1ng/ul. Then, the Qsep400 high-throughput analysis system was used to detect the inserted fragments of the library. After the inserted fragments met the expectations, the effective concentration of the library (the effective concentration of the library was > 2nM) was accurately quantified by Q-PCR method
After the library was qualified, PE150 mode sequencing was performed using Illumina NovaSeq6000 sequencing platform.
After the sequencing data was unloaded, the bioinformatics analysis process provided by BMKCloud(www.biocloud.net) was used for data analysis.
FPKM=cDNAFragments/MappedFragments(Millions)∗TranscriptLength(kb).In the formula, cDNA Fragments represent the number of fragments that are compared to a transcript, that is, the number of double-ended Reads. Mapped Fragments (Millions) indicates the total number of fragments aligned to the transcript, in 10^6; Transcript Length(kb) : Length of the transcript, in units of 10^3 bases.
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw counts for each Sample
Supplementary files format and content: tab-delimited file includes FPKM values for each Sample

source_name: BMSCs cell line

growth_protocol: 5% CO2 medium was added at 37 °C, incubated for complete DMEM medium containing 10% FBS was used as the medium of extraction

extract_protocol:
The cells were lysed with 1ml TRIzol to extract the RNA samples (n=3), and the specimens were subsequently analyzed
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols

treatment_protocol: The complete DMEM medium containing 10% FBS was used as the medium of extraction, and the PCL scaffolds were added to it at an area/volume ratio of 1.25 cm2/ml and immersed for 72 h at 37 °C to prepare the solution for material extraction.

value: BMSCs cell line

value: bone marrow mesenchymal stem cells

value: WT

value: osteogenic differentiation


title: HCT116, HDAC6-KD, RNAseq, rep3

description:
Hdac6KD_gene_count.txt
H6_3


title: HCC_TMA_20210610_08_75502_ROI39_Vessel

description: (v1.0) Cancer Transcriptome Atlas

value: Liver cancer resection


title: BMSCs，PCL-E，Day7


title: HCC_TMA_20210616_NA_ROINA_NA

description: (v1.0) Cancer Transcriptome Atlas

source_name: Control

value: Control

value: No Template Control


title: HCC_TMA_20210610_08_75502_ROI39_Tumor

description: (v1.0) Cancer Transcriptome Atlas

value: Tumor


title: MSC_NSC_1_24 h (transcriptome)


title: HCT116, HDAC6-KD, RNAseq, rep2

description:
Hdac6KD_gene_count.txt
H6_2


title: MSC_NSC_1_9 h (transcriptome)


title: MSC_NSC_1_12 h (transcriptome)


title: BMSCs，PCL-S，Day7


title: HCC_TMA_20210610_08_75502_ROI38_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: MSC_NSC_1_3 h (transcriptome)


title: HCC_TMA_20210616_06_60911_ROI3_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: BMSCs，PCL@SS31@E7，Day7


title: BMSCs，PCL-O，Day7


title: HCT116, HDAC6-KD, RNAseq, rep1

description:
Hdac6KD_gene_count.txt
H6_1


title: BMSCs，PCL-SE，Day3


title: HCT116, HDAC6-KD, Valine deprivation, RNAseq, rep3

description:
Hdac6KD_gene_count.txt
H6_V_3


title: MSC_NSC_1_0 h (transcriptome)


title: HCC_TMA_20210610_08_75502_ROI37_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: BMSCs，PCL@E7，Day7


title: HCC_TMA_20210610_08_75502_ROI37_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: BMSCs，PCL@SS31，Day7


title: HCT116, HDAC6-KD, Valine deprivation, RNAseq, rep2

description:
Hdac6KD_gene_count.txt
H6_V_2


title: BMSCs，PCL-S，Day3


title: HCT116, HDAC6-KD, Valine deprivation, RNAseq, rep1

description:
Hdac6KD_gene_count.txt
H6_V_1


title: HCC_TMA_20210610_08_75502_ROI38_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: BMSCs，PCL，Day7


title: HCC_TMA_20210610_08_69696_ROI36_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: NHEM, replicate1, RNAseq

source_name: PHHs

value: PHHs

value: HPLCs

value: NHEM


title: HCT116, TET2-KD, RNAseq, rep3

description:
Tet2KD_gene_count.txt
T2_3


title: BMSCs，PCL-O，Day3


title: HCT116, TET2-KD, RNAseq, rep2

description:
Tet2KD_gene_count.txt
T2_2


title: BMSCs，PCL-E，Day3


title: HCC_TMA_20210610_08_69696_ROI35_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: MSC_NSC_1_6 h (transcriptome)


title: BMSCs，PCL@E7，Day3


title: BMSCs，PCL@SS31@E7，Day3


title: KO-DOX

city: Beijing

first: Haidong

last: Tang

address: Shuangqing Road

institute: Tsinghua University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the SeekOne tools software v1.2.0 (https://www.seekgene.com/fxrj).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Lymph node

extract_protocol:
Single cell suspensions were prepared from draining lymph nodes of tumor-bearing mice. Live total T cells were sorted by flow cytometry.
Library was performed according to the manufacturer’s instructions (SeekOne® DD Single Cell 5’ library preparation kit, SeekOne).

value: Lymph node

value: T cells

value: PD-L1 knockout

tag: condition

value: Tumor bearing (inoculated with MC38-OVA tumor cells)

value: Doxorubicin


title: HCT116, TET2-KD, RNAseq, rep1

description:
Tet2KD_gene_count.txt
T2_1


title: HCC_TMA_20210610_08_61452_ROI34_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: KO-CTRL


title: BMSCs，PCL@SS31，Day3


title: WT-DOX


title: HCC_TMA_20210610_08_61452_ROI33_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: BMSCs，PCL，Day3


title: HCT116, TET2-KD, Valine deprivation, RNAseq, rep2

description:
Tet2KD_gene_count.txt
T2_V_2

value: Valine deprivation


title: HCC_TMA_20210610_08_54387_ROI29_Vessel

description: (v1.0) Cancer Transcriptome Atlas

value: Vessel


title: CCM3KONormoxia2

city: La Jolla

first: Miguel

middle: Alejandro

last: Lopez-Ramirez

state: Ca

address: 9500 Gilman Dr

department: Medicine

institute: University of California, San Diego

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Library strategy: Spatial Transcriptomics

source_name: Brain

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufacturer's construction

treatment_protocol: Animals were subjected to 12% oxygen for two days.

value: Brain

value: Hypoxia


title: WT-CTRL


title: DC2.4 PD-L1 KO rep3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.39).
Trimmed sequence reads were mapped to mm10 using STAR (2.7.5c).
Read count extraction was performed using StringTie (v2.1.7).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

extract_protocol:
RNA was harvested using TRIzol. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Hyper Prep Kits following manufacturer's protocols.


title: CCM3KONormoxia1


title: HCC_TMA_20210610_08_54387_ROI29_Tumor

city: Boston

last: Franses

institute: Massachusetts General Hospital

description: (v1.0) Cancer Transcriptome Atlas


title: CCM3FloxNormoxia2

value: Normoxia


title: K562 TASOR2 KO, TASOR2, ChIP

city: Madison

last: Lewis

state: Wisconsin

address: 440 Henry Mall

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

data_processing:
ChIP-seq reads were aligned to hg38 human genome using Bowtie2-2.3.5.1 (--no-mixed --no-discordant --maxins 500 --end-to-end) to allow for capture of multi-mapped repetitive elements.
Reads were normalized to mm9 genome from spike-in (1000000/number of reads aligned to the exogenous refernce genome(mm9))
Peaks were called using MACS2
Deeptools was used to generate bigwig files for visuallization
Assembly: Assembly: hg38
Supplementary files format and content: Supplementary files format and content: bigwig (genome wide enrichment)

growth_protocol: RPMI-1640, 10% fetal bocine serum, 1x Glutamax, 1x penicillin-streptomycin, grown at 37C at 5% CO2

extract_protocol:
Cells were fixed with 1% formaldehyde at 37C for 10 minutes. After quenching and cell lysis, chromatin was treated with MNAse and sonication with Covaris S220, 80ug of human chromatin, with 1:40 mouse chromatin spike-in was used for ChIP.
ChIP-seq libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina and amplified with NEBNext Multiplex Oligos, Unique Dual Index Primer Pairs with 13 cycles. Post amplification libraries were purified using size selection Agencourt Ampure XP beads

treatment_protocol: K-562 cells were transfected with px458 GFP CRISPR/Cas9 sgRNA plasmids and sorted for GFP expressing cells as single colonies. Resulting clonal populations were verified for targeted knockout using gDNA sequencing and western blot analysis. Cells were transduced with lentivirus containing empty puromycin resistance vectors (negative control) or FLAG tagged transgenes of interest.

tag: chip antibody

value: TASOR2 in house

value: Human Lymphoblast

value: TASOR2 KO


title: K562, TASOR2, ChIP

value: WT


title: DC2.4 PD-L1 KO rep2


title: DC2.4 PD-L1 KO rep1


title: HCC_TMA_20210610_08_54387_ROI28_Tumor

description: (v1.0) Cancer Transcriptome Atlas

value: Liver cancer resection

value: Tumor


title: HCC_TMA_20210610_08_54387_ROI27_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HEM, replicate2, RNAseq

data_processing:
RNAseqv1
Adapter of sequence reads were trimmed and poor quality reads  were removed by TrimGalore(quality <20 or length <30),
Paired-end RNA-seq reads were trimmed and then mapped to hg38 genome by STAR (v.2.7.4a)
Raw count tables of genes were computed using featureCounts (v2.0.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was isolated using the RNeasyMini kit (QIAGEN) or Direct-zol RNA Miniprep (ZYMO RESEARCH).
RNA sequencing libraries were prepared using the NEBNext UltraTM RNA Library Prep kit for Illumina (NEB, USA) or VAHTS Universal V8 RNA-seq Library Prep Kit for NovaSeq (Vazyme, China) following the manufacturer’s recommendations.

value: PHHs

value: HPLCs

value: HEM


title: CCM3FloxNormoxia1


title: DC2.4 Control rep3

value: Control


title: HEM, replicate1, RNAseq


title: DC2.4 Control rep2


title: HCC_TMA_20210610_08_54387_ROI23_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCT116, TET2-KD, Valine deprivation, RNAseq, rep3

description:
Tet2KD_gene_count.txt
T2_V_3


title: CCM3KOHypoxia3

data_processing:
Data was processed using the systempipeR workflow.
RNA reads were aligned to the GRCm39 genome assembly using hisat2.
Differential gene expression was calculated using EdgeR.
Assembly: GRCm39 release 104

extract_protocol:
Brain tissue was harvested from animals and homogenized in TRIzol solution for RNAseq analysis according to the manufacturer’s instructions.
Following isolation, RNA quality was assessed using an Agilent Tapestation 4200. Only samples with with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries using the Illumina Stranded mRNA Prep according to the manufacturer’s insturctions.

treatment_protocol: Hypoxic conditions consisted of 12% O2,  for seven days and normoxic conditions consisted of 21% O2.

value: Male


title: HEM_LS, replicate2, RNAseq


title: HCC_TMA_20210610_08_61452_ROI32_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210610_08_54387_ROI23_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCT116, TET2-KD, Valine deprivation, RNAseq, rep1

description:
Tet2KD_gene_count.txt
T2_V_1


title: CCM3KOHypoxia2


title: DC2.4 Control rep1


title: HEM_LS, replicate1, RNAseq


title: HCC_TMA_20210610_08_54387_ROI22_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: CCM3KOHypoxia1


title: NHEM, replicate9, RNAseq

value: NHEM


title: GPR40-KO, replicate 3, RNAseq

city: Huzhou

first: Yunliang

last: Yao

state: Zhejiang

address: 759 East Second Ring Road

department: Medical School

institute: Huzhou University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (v3.2.5)  were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5)  was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.3.1) .
Assembly: mm10
Supplementary files format and content: table-delimited text include gene expression for each sample
Supplementary files format and content: table-delimited text include RNA expression for each sample

source_name: Spleen

extract_protocol:
Mice splenic B lymphocytes were enriched by negative selection using MACS B-lymphocyte isolation kit (130-090-862, Miltenyi Biotec).
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 pair end 100 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: Spleen

value: B Lymphcytes

value: Lymphcytes


title: GPR40-KO, replicate 2, RNAseq


title: HCC_TMA_20210610_08_54387_ROI21_Vessel

first: Joseph

description: (v1.0) Cancer Transcriptome Atlas

value: Vessel


title: CCM3KOHypoxia4

value: Brain

value: Hypoxia


title: CCM3FloxHypoxia3


title: CCM3FloxHypoxia2


title: NHEM, replicate8, RNAseq


title: NHEM, replicate7, RNAseq


title: CCM3FloxHypoxia1


title: HCC_TMA_20210610_08_54387_ROI21_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: GPR40-WT, replicate 2, RNAseq


title: CCM3KONormoxia3

value: Normoxia


title: HCC_TMA_20210610_08_42516_ROI17_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210610_08_42516_ROI16_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: SW1990_ATACseq

first: Boshi

last: Wang

address: No.800 Dongchuan Road

institute: Shanghai Cancer Institute

data_processing:
The sequencing reads obtained from the Illumina platform were subjected to quality control using FastQC (v0.11.9) to assess the quality of the reads.
Adapter trimming and read filtering were performed using Trim-galore (0.6.5-1) with the following parameters: --phred33 --length 35 --stringency 3.
The filtered reads were then aligned to the human genome (UCSC hg38) using Bowtie2 version 2.2.6 with parameters: --local --very-sensitive -X 2000 --no-mixed --no-discordant --phred33.
The aligned reads were processed by MACS2 (v2.2.7.1) to call peaks and transformed to bigwig formatted files by bedGraphToBigWig (v4) program.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: pancreas

extract_protocol:
The ATAC experiments were performed using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme Biotech Co., Ltd., TD711) according to the manufacturer’s instructions.
The library was constructed by TruePrep® Index Kit V4 for Illumina kit and PCR amplification

value: pancreas

tag: phenotype

value: Parental


title: SW1990R_ATACseq

value: Gemcitabine-resistant


title: GPR40-WT, replicate 1, RNAseq

tag: cell type


title: CCM3KONormoxia2

tag: treatment


title: HCC_TMA_20210610_08_42516_ROI16_Tumor

description: (v1.0) Cancer Transcriptome Atlas

value: Liver cancer resection

value: Tumor


title: CCM3KONormoxia1

tag: cell line


title: Mouse14, ITS1-2, After Stress

first: Xiaofei

last: Yu

address: 2005 Songhu Rd

institute: Fudan University

description:
F_A_14
its_asv_table.tsv

data_processing:
Raw fastq files were imported into QIIME2 and trimmed by cutadapt
QIIME2 DADA2 were used to denoise and generate representative sequences. Pre-built QIIME2 classifier was used to classify the representitave sequences.
Shannon diversity and PCoA using unweighted Unifrac distance were calculated by QIIME2 and visualized using R package phyloseq (v1.36.0) and ggplot2 (v3.3.5).
Assembly: SILVA v138(NR99) for 16s v3v4 and UNITE v9 for ITS1-2
Supplementary files format and content: OTU count tables (tsv format)

organism: feces metagenome

source_name: Fecal pellets

extract_protocol:
Fecal microbial DNA were extracted using the QIAamp PowerFecal Pro DNA Kit (Cat. 51804).
DNA sequencing library were constructed by KAPA High Throughput Library Preparation Kit (KK8234) per the manufacturer's guide.
DNA amplicon sequencing

treatment_protocol: Fecal pellets were collected from mice before and after 30-min restraint stress.

tag: animal id

tag: strain

value: After Stress

tag: region


title: HCC_TMA_20210610_08_42516_ROI15_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue


title: FNC231W MSCs  sample 3

city: Montreal

first: Neha

last: Dinesh

state: Quebec

address: 3640 Rue University

department: Anatomy and Cell Biology

country: Canada

institute: McGill University

description: Raw sequence reads

data_processing:
Adaptor sequences and low-quality score containing bases (Phred score < 30) were trimmed from reads using Trimmomatic (Bolger, Lohse, and Usadel 2014). The resulting reads were aligned to the genome, using STAR (Dobin et al 2012). Read counts are obtained using HTSeq (Anders et al 2015). The R package DESeq2 (Love et al. 2014) was used to identify differences in expression levels between the groups using negative Binomial GLM fitting and Wald statistics
Differential Expression at the gene level - Using STAR for mapping, HTseq for gene quantification and DESeq2 for the differential expression.
Assembly: GRCh38.p13 (Genome Reference Consortium Human Build 38), INSDC Assembly GCA_000001405.28,
Supplementary files format and content: CSV file contains processed differential gene rlong counts
Supplementary files format and content: FASTAq conatins raw data sequence reads

source_name: mesenchymal stem cells

growth_protocol: IPSCs were differentiated into MSCs using the STEMdiff Mesenchymal Progenitor Kit (Stem Cell Technologies; Catalogue #05240;). The differentiation protocol involved treatment of IPSCs with STEMdiff Animal Component-Free (ACF) Mesenchymal Induction Medium for 4 d, followed by expansion and further culturing with MesenCult ACF medium (Stem Cell Technologies; Catalogue #05445), supplemented with 2mM L-Glutamine (Stem Cell Technologies; Catalogue #07100) for 21 d. MSCs were differentiated into chondrocytes using the MesenCult-ACF Chondrogenic Differentiation Kit (Stem Cell Technologies; Catalogue #05426) comprising of MesenCult-ACF Chondrogenic Differentiation Basal Medium (Stem Cell Technologies; Catalogue #05456) and MesenCult-ACF 20× Chondrogenic Differentiation Supplement (Stem Cell Technologies; Catalogue #05457) culturing for 22 d (5×105 cells per micromass) in 15mL conical tubes (Corning; Catalogue #352096). All cells were cultured at 37°C, 5% CO2, 5%O2 and 90% humidity.

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen; Catalogue #74104) as per the manufacturer’s instructions. 1 µg RNA per sample. Bulk RNA sequencing was performed with the Illumina NovaSeq6000 system.
Truseq RNA stranded protocol

value: mesenchymal stem cells

tag: genotype


title: FNC231W Chondrocytes sample 3

description: Raw sequence reads

source_name: Chondrocytes

value: Chondrocytes


title: HCC_TMA_20210610_08_54387_ROI22_Tumor

description: (v1.0) Cancer Transcriptome Atlas

source_name: Liver cancer resection

tag: slide name

tag: pool


title: Mouse13, ITS1-2, After Stress

city: Shanghai

description:
F_A_13
its_asv_table.tsv


title: GPR40-KO, replicate 1, RNAseq


title: GPR40-WT, replicate 3, RNAseq


title: Mouse12, ITS1-2, After Stress

description:
F_A_12
its_asv_table.tsv


title: FNC231W MSCs  sample 2

description: Raw sequence reads


title: HCC_TMA_20210610_08_42516_ROI14_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: roi

tag: aoi type


title: CCM3FloxNormoxia2

value: Male


title: HCC_TMA_20210610_08_42516_ROI13_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: area


title: CCM3FloxNormoxia1


title: FNC231W Chondrocytes sample 1

description: Raw sequence reads


title: FNC231W MSCs  sample1

description: Raw sequence reads


title: HCC_TMA_20210610_08_42516_ROI12_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: FloxHypoxia5

value: Pdcd10fl/fl; Aldh1l1-EGFP/Rpl10a


title: HCC_TMA_20210610_08_42516_ROI12_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Mouse8, ITS1-2, After Stress

description:
F_A_8
its_asv_table.tsv


title: FloxHypoxa6


title: Mouse9, ITS1-2, After Stress

description:
F_A_9
its_asv_table.tsv


title: FNC123R Chondrocytes sample 3

description: Raw sequence reads


title: CCM3FloxNormoxia3


title: FloxHypoxia4


title: FNC123R MSCs  sample 3

description: Raw sequence reads


title: FloxHypoxia3


title: FNC231W Chondrocytes sample 2

description: Raw sequence reads


title: FNC123R Chondrocytes sample 2

description: Raw sequence reads


title: HCC_TMA_20210610_08_39798_ROI11_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Mouse13, ITS1-2, Before Stress

description:
F_B_13
its_asv_table.tsv

value: Before Stress


title: HCC_TMA_20210610_08_39798_ROI11_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: FloxHypoxia2


title: Mouse10, ITS1-2, After Stress

description:
F_A_10
its_asv_table.tsv


title: FNC123R MSCs  sample 2

description: Raw sequence reads


title: HCC_TMA_20210610_08_39798_ROI10_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210610_08_42516_ROI14_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: FNC123R Chondrocytes sample 1

description: Raw sequence reads


title: HCC_TMA_20210610_08_39798_ROI10_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Mouse12, ITS1-2, Before Stress

description:
F_B_12
its_asv_table.tsv


title: Mouse11, ITS1-2, After Stress

description:
F_A_11
its_asv_table.tsv


title: KOHypoxia7


title: FNC123R MSCs  sample1

description: Raw sequence reads


title: Mouse10, ITS1-2, Before Stress

description:
F_B_10
its_asv_table.tsv


title: HCC_TMA_20210610_08_39798_ROI9_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Mouse14, ITS1-2, Before Stress

description:
F_B_14
its_asv_table.tsv


title: HCC_TMA_20210610_08_39798_ROI9_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Mouse9, ITS1-2, Before Stress

description:
F_B_9
its_asv_table.tsv


title: HCC_TMA_20210610_08_39798_ROI8_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Control MSCs  sample 3

description: Raw sequence reads

value: Control


title: Control Chondrocytes sample 2

description: Raw sequence reads


title: Mouse8, ITS1-2, Before Stress

description:
F_B_8
its_asv_table.tsv


title: Mouse14, 16s v3v4, After Stress

description:
F-A-14
16s_asv_table.tsv


title: HCC_TMA_20210610_08_39798_ROI8_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: FloxHypoxia1


title: KOHypoxia3


title: Mouse11, ITS1-2, Before Stress

description:
F_B_11
its_asv_table.tsv


title: HCC_TMA_20210610_08_39798_ROI7_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: KOHypoxia2


title: Mouse13, 16s v3v4, After Stress

description:
F-A-13
16s_asv_table.tsv


title: Control MSCs  sample 2

description: Raw sequence reads


title: Control Chondrocytes sample 1

description: Raw sequence reads


title: HCC_TMA_20210610_08_39798_ROI7_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: KOHypoxia6


title: KOHypoxia1


title: Mouse11, 16s v3v4, After Stress

description:
F-A-11
16s_asv_table.tsv


title: FloxNormoxia4


title: Control MSCs  sample1

description: Raw sequence reads


title: Mouse12, 16s v3v4, After Stress

description:
F-A-12
16s_asv_table.tsv


title: HCC_TMA_20210610_08_39798_ROI6_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Control Chondrocytes sample 3

description: Raw sequence reads


title: HCC_TMA_20210610_08_39798_ROI6_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: FloxNormoxia3


title: KOHypoxia5


title: Mouse10, 16s v3v4, After Stress

description:
F-A-10
16s_asv_table.tsv