title: 21-2454_1082/1157_072821-ROI 003-Segment 3

value: thymoma 1082 B cells


title: 21-2454_1082/1157_072821-ROI 002-Segment 3

status: Public on Jan 25 2023

type: SRA

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

country: USA

institute: NIH/NCI

library_source: transcriptomic

data_processing:
Raw basecall files were demultiplexed into individual fastqs corresponding to each ROI using bclconvert software (v3.7.5)
Fastqs were converted to Digital Count Conversion files (DCC files) using NanoString’s GeoMx NGS Pipeline v.2.0.0 using default parameters.
DCC files were processed using the GeoMX tools workflow.  ROIs with less than 1000 raw reads, 65% trimmed/stitched/aligned reads, or 50% sequencing saturation were removed, along with samples containing fewer than 20 cells per region of interest. Probe data was filtered using a minProbeRatio value of 0.1 and a percentFailGrubbs value of 20. The background noise within the study is defined as the expression signal from negative control probes. ROIs with 2 geometric standard deviations above the background were kept along with those containing > 15% gene detection rate (82 ROIs).  Genes detected in 30% of ROIs were kept.  Q3 normalization was then performed on the filtered data.
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx .pkc file.
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode).

molecule: total RNA

organism: Mus musculus

source_name: Thymoma

extract_protocol:
The FFPE tissue blocks were cut at 5um, and the slides were subjected for in-situ mRNA hybridization. The slides were incubated at 60C for 35m and moved into Leica BOND RX for RNA antigen retrieval, using proteinase K (1ug/ml) for 5 minutes and HIER2 for 20m. RNA probes (NanoString GeoMx Mouse Whole Transcriptome Atlas) were added for hybridization at 37 C for 16h. The stringent washes were performed according to the manufacturer's instructions. The slides were blocked with W buffer for 1h and then incubated with primary antibody cocktail for 1h at room temperature. The cocktail contains CD3 (1:100 dilution, Ab135372) and B220 (1:60 dilution, BD #550286) antibodies. The slides were washed with SSC buffer two times and subjected to incubation with secondary antibodies, AF594 Goat anti Rat at 1:100 dilution and AF647 Goat anti Rabbit at 1:100 dilution, for 45 minutes at RT. The slides were washed with SCC buffer twice and incubated with morphology markers cocktail, which contains Pancytokeratin-AF532 (1:40 dilution) and Syto13 (1:10 dilution), for at RT for 1h.  After washing with ASSC buffer twice, the slides were immediately loaded on to the GeoMX DSP and scanned for selection of regions of interest (ROIs). Upon ROI selection, segmentation was performed by masking for desired markers.  ROIs within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform.
Each collection of oligo tags from one well representing an ROI was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR. After PCR, indexed ROIs were pooled and purified in two rounds of AMPure XP PCR purification and sequenced on the NextSeq 2000 using a P3 flow cell kit (27 x 27 and index 8 x 8).

tag: tissue

value: Thymoma

tag: cell type

tag: genotype

value: Gtf2ifl/wt Foxn1-Cre/wt

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: roi

tag: segment

value: Segment 3

tag: aoi

value: Segment 3-aoi-001

tag: ab positivity

tag: number of_cells

tag: area (um^2)


title: GBM, Primary, Patient 2

city: Cleveland

first: Andrew

last: Dhawan

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

data_processing:
Raw reads from Fastq files from the sequencing runs underwent adapter trimming using the TrimGalore package (Barbraham Informatics), version 0.6.2.
Fastq files were then checked for quality using FastQC version 2.
Reads were aligned using Salmon version 0.8.2 to the ENSEMBL reference human transcriptome, version 37.75, hg1910. Reads were aligned using the --gcbias filter. Default settings were used otherwise.
The txImport package, version 1.16.1 was used to import the reads into an R script from which further analyses were carried out
Assembly: GrCh 37.75
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Glioblastoma

extract_protocol:
Library preparation was performed with 1-50 ng of total RNA
cDNA was prepared using the SeqPlex RNA Amplification Kit (Sigma-Aldrich, St. Louis, MO, USA) per manufacturer's protocol, and Illumina sequencing adapters were ligated to the ends of cDNA fragments. These were amplified for 12 cycles using primers incorporating unique index tags.

value: Glioblastoma

tag: disease state

value: Primary

tag: patient


title: GBM, Recurrent, Patient 4

value: Recurrent


title: 21-2454_1082/1157_072821-ROI 001-Segment 3


title: 21-2454_1042/1044_072821-ROI 013-Segment 3

value: thymoma 1044 epithelial

value: PanCK


title: 21-2454_1042/1044_072821-ROI 013-Segment 1

value: thymoma 1044 T cells

value: Segment 1

value: Segment 1-aoi-001


title: THP-1 cells, Exp2, BATF2-/-#2, 9.2s RNA, rep1

city: Bonn

first: Gabor

last: Zsurka

address: Venusberg-Campus 1

department: IEECR

country: Germany

institute: University of Bonn

data_processing:
Sequence reads were mapped to GRCh38 using the STAR algorithm on the Galaxy platform (Galaxy Version 2.7.2b)
Read count extraction were performed using STAR algorithm on the Galaxy platform (Galaxy Version 2.7.2b)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw gene counts for each Sample

growth_protocol: THP-1 leukemia monocytic cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuantSeq 3´-mRNA Library Prep (Lexogen, Vienna, Austria) following manufacturer's protocols.

treatment_protocol: untreated OR 9.2s RNA complexed with poly-L-Arginin OR R848

tag: exp

tag: cell line

value: leukemia monocytic cells

tag: treatment

value: 9.2s RNA


title: 21-2454_1042/1044_072821-ROI 012-Segment 3


title: 21-2454_1042/1044_072821-ROI 012-Segment 1


title: THP-1 cells, Exp2, BATF2-/-#2, untreated, rep2

value: untreated


title: THP-1 cells, Exp2, wild-type, 9.2s RNA, rep1

value: wild-type


title: THP-1 cells, Exp2, BATF2-/-#2, 9.2s RNA, rep2


title: THP-1 cells, Exp2, BATF2-/-#1, untreated, rep2


title: THP-1 cells, Exp2, BATF2-/-#1, untreated, rep1


title: 21-2454_1042/1044_072821-ROI 011-Segment 1

value: Thymoma


title: THP-1 cells, Exp2, BATF2-/-#2, untreated, rep1


title: THP-1 cells, Exp2, BATF2-/-#1, 9.2s RNA, rep2


title: 21-2454_1042/1044_072821-ROI 010-Segment 2

value: thymoma 1044 B cells

value: Gtf2ifl/wt Foxn1-Cre/wt

value: Segment 2

value: Segment 2-aoi-001


title: THP-1 cells, Exp2, wild-type, 9.2s RNA, rep2


title: 21-2454_1042/1044_072821-ROI 011-Segment 3

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

value: Segment 3

value: Segment 3-aoi-001


title: THP-1 cells, Exp2, wild-type, untreated, rep1


title: 21-2454_1042/1044_072821-ROI 007-Segment 2

value: thymoma 1042 B cells


title: THP-1 cells, Exp2, BATF2-/-#1, 9.2s RNA, rep1


title: 21-2454_1042/1044_072821-ROI 008-Segment 2


title: THP-1 cells, Exp3, BATF2-/-#1, R848, rep2


title: 21-2454_1042/1044_072821-ROI 009-Segment 2


title: 21-2454_1042/1044_072821-ROI 004-Segment 1

value: thymoma 1042 T cells


title: THP-1 cells, Exp3, BATF2-/-#2, R848, rep2


title: 21-2454_1042/1044_072821-ROI 006-Segment 2


title: THP-1 cells, Exp3, BATF2-/-#1, R848, rep3


title: THP-1 cells, Exp3, BATF2-/-#2, R848, rep3


title: THP-1 cells, Exp2, wild-type, untreated, rep2


title: THP-1 cells, Exp3, BATF2-/-#2, R848, rep1


title: 21-2454_1042/1044_072821-ROI 003-Segment 3

value: thymoma 1042 epithelial

value: PanCK


title: 21-2454_1042/1044_072821-ROI 005-Segment 2


title: 21-2454_1042/1044_072821-ROI 004-Segment 3


title: 21-2454_1042/1044_072821-ROI 003-Segment 1

value: Segment 1

value: Segment 1-aoi-001


title: 21-2454_1172/1143_072821-ROI 018-Segment 1

source_name: Thymus

value: Thymus

value: thymus 1143 cortical T cells


title: 21-2454_1042/1044_072821-ROI 002-Segment 3


title: 21-2454_1172/1143_072821-ROI 017-Segment 3

value: thymus 1143 cortical epithelial


title: THP-1 cells, Exp3, BATF2-/-#2, untreated, rep2

value: leukemia monocytic cells

value: untreated


title: 21-2454_1042/1044_072821-ROI 002-Segment 1

value: Thymoma

value: Gtf2ifl/wt Foxn1-Cre/wt


title: THP-1 cells, Exp3, BATF2-/-#2, untreated, rep1


title: THP-1 cells, Exp3, BATF2-/-#1, R848, rep1


title: THP-1 cells, Exp3, wild-type, R848, rep3

value: wild-type


title: THP-1 cells, Exp3, BATF2-/-#1, untreated, rep3


title: THP-1 cells, Exp3, wild-type, R848, rep1


title: THP-1 cells, Exp3, BATF2-/-#2, untreated, rep3


title: THP-1 cells, Exp3, BATF2-/-#1, untreated, rep2


title: THP-1 cells, Exp3, BATF2-/-#1, untreated, rep1


title: THP-1 cells, Exp3, wild-type, untreated, rep3


title: 21-2454_1172/1143_072821-ROI 016-Segment 1

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: THP-1 cells, Exp3, wild-type, untreated, rep2


title: 21-2454_1172/1143_072821-ROI 015-Segment 2

value: thymus 1143 B cells

value: Segment 2

value: Segment 2-aoi-001


title: 21-2454_1172/1143_072821-ROI 016-Segment 3

value: Segment 3

value: Segment 3-aoi-001


title: THP-1 cells, Exp3, wild-type, R848, rep2


title: 21-2454_1042/1044_072821-ROI 001-Segment 3

value: thymoma 1042 epithelial

value: PanCK


title: 21-2454_1172/1143_072821-ROI 013-Segment 2


title: 21-2454_1172/1143_072821-ROI 014-Segment 2


title: THP-1 cells, Exp3, wild-type, untreated, rep1


title: 21-2454_1172/1143_072821-ROI 018-Segment 3


title: 21-2454_1172/1143_072821-ROI 012-Segment 3

value: thymus 1143 medullar epithelial


title: THP-1 cells, Exp1, wild-type, untreated, rep3


title: 21-2454_1172/1143_072821-ROI 012-Segment 1

value: Thymus

value: thymus 1143 medullar T cells

value: Segment 1

value: Segment 1-aoi-001


title: THP-1 cells, Exp1, wild-type, 9.2s RNA, rep3

value: leukemia monocytic cells

value: 9.2s RNA


title: THP-1 cells, Exp1, wild-type, untreated, rep2

value: untreated


title: 21-2454_1172/1143_072821-ROI 017-Segment 1

value: thymus 1143 cortical T cells


title: 21-2454_1172/1143_072821-ROI 011-Segment 1

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: 21-2454_1172/1143_072821-ROI 010-Segment 3


title: THP-1 cells, Exp1, wild-type, untreated, rep1

value: wild-type


title: 21-2454_1172/1143_072821-ROI 011-Segment 3


title: THP-1 cells, Exp1, wild-type, 9.2s RNA, rep1


title: 21-2454_1172/1143_072821-ROI 009-Segment 3

value: thymus 1172 cortical epithelial


title: THP-1 cells, Exp1, BATF2-/-#1, untreated, rep3


title: THP-1 cells, Exp1, BATF2-/-#1, 9.2s RNA, rep3


title: THP-1 cells, Exp1, BATF2-/-#1, untreated, rep2


title: 21-2454_1172/1143_072821-ROI 009-Segment 1

value: thymus 1172 cortical T cells


title: THP-1 cells, Exp1, BATF2-/-#1, 9.2s RNA, rep2


title: 21-2454_1172/1143_072821-ROI 008-Segment 3

value: Segment 3


title: THP-1 cells, Exp1, BATF2-/-#1, untreated, rep1


title: 21-2454_1172/1143_072821-ROI 008-Segment 1


title: 21-2454_1172/1143_072821-ROI 007-Segment 3

value: Segment 3-aoi-001


title: THP-1 cells, Exp1, wild-type, 9.2s RNA, rep2


title: THP-1 cells, Exp1, BATF2-/-#1, 9.2s RNA, rep1


title: 21-2454_1172/1143_072821-ROI 010-Segment 1


title: 21-2454_1172/1143_072821-ROI 006-Segment 3

value: thymus 1172 medullar epithelial


title: 21-2454_1172/1143_072821-ROI 007-Segment 1


title: 21-2454_1172/1143_072821-ROI 005-Segment 3

value: PanCK


title: #88, tumor Treg

city: Daejeon

first: Seung Hyuck

last: Jeon

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
FASTQ files were mapped to the human genomic DNA reference (GRCh37/hg19) using Hisat2
StringTie was used to quantify gene expression based on the aligned reads.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes TPM expression for each Sample

source_name: Tumor infiltrating lymphocytes

extract_protocol:
Total RNA was extracted from the sorted cells using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara).
Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara).

value: Tumor infiltrating lymphocytes

value: primary

value: regulatory T cell

tag: individual


title: #88, peripheral Treg

source_name: Peripheral blood

value: Peripheral blood


title: 21-2454_1172/1143_072821-ROI 005-Segment 1

value: Thymus

value: thymus 1172 medullar T cells

value: Segment 1

value: Segment 1-aoi-001


title: #198, tumor Treg


title: #200, tumor Treg


title: #198, peripheral Treg


title: #173, tumor Treg


title: 21-2454_1172/1143_072821-ROI 006-Segment 1


title: 21-2454_1172/1143_072821-ROI 004-Segment 3


title: 21-2454_1172/1143_072821-ROI 003-Segment 2

value: thymus 1172 B cells

value: Segment 2

value: Segment 2-aoi-001


title: 21-2454_1172/1143_072821-ROI 004-Segment 1

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: #140, tumor Treg


title: #173, peripheral Treg


title: #200, peripheral Treg


title: 21-2454_1172/1143_072821-ROI 002-Segment 2


title: 21-2454_1172/1143_072821-ROI 001-Segment 2


title: #135, tumor Treg


title: #135, peripheral Treg


title: 21-2454_1057/1059_072821-ROI 017-Segment 2

value: thymus 1057 medullar T cells


title: #140, peripheral Treg


title: 21-2454_1057/1059_072821-ROI 017-Segment 1

value: thymus 1057 medullar epithelial


title: #193, CEACAM1- Treg

data_processing:
FASTQ files were mapped to the human genomic DNA reference (GRCh37/hg19) using Hisat2
StringTie was used to quantify gene expression based on the aligned reads.
Supplementary files format and content: hg19
Supplementary files format and content: tab-delimited text files include TPM expression for each Sample

tag: cell subtype

value: CEACAM1- Treg


title: #193, CEACAM1+ Treg

tag: tissue

value: CEACAM1+ Treg


title: 21-2454_1057/1059_072821-ROI 015-Segment 2

tag: cell type

value: thymus 1059 cortical T cells


title: 21-2454_1057/1059_072821-ROI 014-Segment 2

tag: genotype


title: 21-2454_1057/1059_072821-ROI 014-Segment 1

value: thymus 1059 cortical epithelial

tag: panel

value: PanCK


title: 21-2454_1057/1059_072821-ROI 015-Segment 1

tag: roi


title: #190, CEACAM1- Treg

value: Tumor infiltrating lymphocytes

value: primary

value: regulatory T cell


title: #189, CEACAM1- Treg


title: #122, CEACAM1+ Treg


title: #122, CEACAM1- Treg


title: #190, CEACAM1+ Treg


title: 21-2454_1057/1059_072821-ROI 013-Segment 1

value: Thymus

tag: segment


title: 21-2454_1057/1059_072821-ROI 013-Segment 2

tag: aoi


title: 21-2454_1057/1059_072821-ROI 012-Segment 3

value: thymus 1059 B cells

value: Segment 3

value: Segment 3-aoi-001

tag: ab positivity


title: 21-2454_1057/1059_072821-ROI 011-Segment 3

tag: number of_cells


title: #115, CEACAM1- Treg


title: #115, CEACAM1+ Treg


title: 21-2454_1057/1059_072821-ROI 010-Segment 3

tag: area (um^2)


title: 21-2454_1057/1059_072821-ROI 009-Segment 2

value: thymus 1057 cortical T cells

value: Segment 2


title: 21-2454_1057/1059_072821-ROI 007-Segment 2

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

value: Segment 2-aoi-001


title: mRNA_RectalCancer_rep297

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

country: Japan

institute: Japanese Foundation Cancer Research

data_processing:
Read count extraction and calculation of TPM and FPKM were performed by RSEM 1.3.0.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM, FPKM and expected count values for each Sample

source_name: Rectal Cancer

extract_protocol:
Total RNA from fresh-frozen tumor samples was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instructions.
mRNA libraries were constructed using the TruSeq RNA Access Library Prep Kit (Illumina), with the starting amount of RNA determined as per the manufacturer’s instructions.

value: Rectal Cancer

tag: age

tag: Sex

value: male


title: 21-2454_1057/1059_072821-ROI 008-Segment 1

value: thymus 1057 cortical epithelial

value: Segment 1

value: Segment 1-aoi-001


title: mRNA_RectalCancer_rep296


title: #86, CEACAM1+ Treg

value: CEACAM1+ Treg


title: 21-2454_1057/1059_072821-ROI 009-Segment 1

value: PanCK


title: 21-2454_1057/1059_072821-ROI 008-Segment 2


title: mRNA_RectalCancer_rep295


title: #189, CEACAM1+ Treg

value: Tumor infiltrating lymphocytes

value: primary


title: 21-2454_1057/1059_072821-ROI 006-Segment 2

value: Thymus


title: 21-2454_1057/1059_072821-ROI 007-Segment 1


title: #86, CEACAM1- Treg

value: regulatory T cell

value: CEACAM1- Treg


title: mRNA_RectalCancer_rep289


title: mRNA_RectalCancer_rep292


title: mRNA_RectalCancer_rep298

value: female


title: mRNA_RectalCancer_rep290


title: mRNA_RectalCancer_rep293


title: 21-2454_1057/1059_072821-ROI 006-Segment 1


title: mRNA_RectalCancer_rep288


title: 21-2454_1057/1059_072821-ROI 005-Segment 2

value: thymus 1057 medullar T cells


title: 21-2454_1057/1059_072821-ROI 004-Segment 2

value: Segment 2


title: mRNA_RectalCancer_rep286


title: mRNA_RectalCancer_rep284


title: 21-2454_1057/1059_072821-ROI 001-Segment 3

value: thymus 1057 B cells

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

value: Segment 3

value: Segment 3-aoi-001


title: mRNA_RectalCancer_rep285

value: Rectal Cancer

value: male


title: 21-2454_1057/1059_072821-ROI 002-Segment 2

value: Segment 2-aoi-001


title: mRNA_RectalCancer_rep283


title: mRNA_RectalCancer_rep294


title: 21-2454_1057/1059_072821-ROI 002-Segment 1

value: thymus 1057 medullar epithelial

value: Segment 1

value: Segment 1-aoi-001


title: 21-2454_1057/1059_072821-ROI 005-Segment 1

value: PanCK


title: 21-2454_1057/1059_072821-ROI 003-Segment 2

value: Thymus


title: mRNA_RectalCancer_rep291


title: mRNA_RectalCancer_rep280


title: 21-2454_1057/1059_072821-ROI 003-Segment1


title: mRNA_RectalCancer_rep282


title: 21-2454_1057/1059_072821-ROI 004-Segment 1


title: mRNA_RectalCancer_rep276


title: mRNA_RectalCancer_rep278


title: mRNA_RectalCancer_rep279


title: mRNA_RectalCancer_rep275


title: mRNA_RectalCancer_rep281


title: mRNA_RectalCancer_rep272


title: mRNA_RectalCancer_rep287


title: mRNA_RectalCancer_rep277


title: mRNA_RectalCancer_rep271


title: PC-12 60min Control (Cy5) x PACAP (Cy3)

type: RNA

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing: Software: Feature Extraction ver 11.0.1.1

organism: Rattus norvegicus

source_name: PC12 PACAP Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: PC12 cells (RCB0009) were obtained from the Riken Cell Bank (Japan). Cells were cultivated in RPMI medium 1640 (ATCC Modification, Thermo Fisher) in a CO2 incubator (37ºC, 5%) with 5% fetal bovine serum (FBS, 16140063, Gibco), 10% horse serum (HS, H1138, SIGMA) and antibiotics (Penicillin-Streptomycin, P4458, Sigma). Cellmatrix Type IV (Nitta Gelatin Inc.) was used to coat the culture dish. Institutional ethical approval was not required for this study.

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: PC12 cells were adjusted to 1×103 to 5×103 cells/well in a 96-well plate, and after about 6 hours, PACAP (PACAP38, (10⁻⁷ M), 052-05 Phoenix Pharmaceuticals, Inc.) was added to the cell culture medium at concentrations of 10-7M, after confirming complete adhesion to the plate. Samples were taken at 5, 10, 15, 30, 60, and 120 min after PACAP treatment.

value: PACAP-differentiated

tag: timepoint

source_name: PC12 Cont Cy5

value: Control


title: PC-12 120min Control (Cy3) x PACAP (Cy5)

source_name: PC12 Cont Cy3

tag: cell line

source_name: PC12 PACAP Cy5


title: PC-12 30min Control (Cy3) x PACAP (Cy5)

tag: treatment


title: mRNA_RectalCancer_rep273


title: mRNA_RectalCancer_rep269


title: mRNA_RectalCancer_rep274

value: female


title: PC-12 10min Control (Cy5) x PACAP (Cy3)


title: PC-12 15min Control (Cy5) x PACAP (Cy3)


title: mRNA_RectalCancer_rep270


title: WT_4

city: Pamplona

first: Ana

last: Garcia Osta

state: Navarra

address: Juslarrocha 10, 3H

department: neuroscience

country: Spain

institute: Cima

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCm38 mouse assembly using STAR v2.6.1c with default parameters.
featureCounts v1.6.0 software and Gencode vM25 release were used to obtain read counts at gene level considering only those reads aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: hippocampus

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

treatment_protocol: Mice were treated day for five weeks with vehicle (sesame oil) or DHA (450 mg/kg)

value: hippocampus

value: vehicle


title: PC-12 15min Control (Cy3) x PACAP (Cy5)


title: mRNA_RectalCancer_rep267


title: PC-12 60min Control (Cy3) x PACAP (Cy5)


title: mRNA_RectalCancer_rep268


title: PC-12 10min Control (Cy3) x PACAP (Cy5)


title: Rg5_rep2

city: Gwangju

first: YouMin

last: KIM

address: 123, Cheomdangwagi-ro, Buk-gu

department: DEPARTMENT OF BIOMEDICAL SCIENCE AND ENGINEERING

institute: Gwangju Institute of Science and Technology

description: Gene expression data from Rg5-treated following PMA induced NCI-H292 cell

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the GeneChip® Mouse Gene 2.0 ST arrays for 17 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: Quantile-normalization was performed on the log2-intensities from gMedianSignal

label: biotin

source_name: NCI-H292, Rg5-treatment following Rg5-treatment

label_protocol: The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: NCI-H292 cells were culture at 37 °C in a 5% CO2 atmosphere using DMEM/High Glucose culture medium enriched with 10% fetal bovine serum (FBS) and 1% penicillin and streptomycin (P/S).

extract_protocol: Total RNA was isolated using RNeasy Mini Kit columns as described by the manufacturer (Qiagen, Hilden, Germany).

treatment_protocol: NCI-H292 cells were treated with Rg5 or vehicle following treatment with PMA(10ng/ml) for 24H.

value: NCI-H292 cells


title: PC-12 30min Control (Cy5) x PACAP (Cy3)


title: PC-12 120min Control (Cy5) x PACAP (Cy3)


title: mRNA_RectalCancer_rep265


title: veh_rep1

description: Gene expression data from PMA induced NCI-H292 cell

source_name: NCI-H292, PMA-treatment

value: PMA treatment


title: PC-12 5min Control (Cy5) x PACAP (Cy3)


title: mRNA_RectalCancer_rep266


title: WT_1


title: veh_rep2


title: Brain endothelial cell, Brd4 WT

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software was used for basecalling.
Using Perl scripts to process the Raw Data to ensure the quality of the data for further analysis.The filtering standards are as follows:1) Delete reads contaminated by the adapter. (Reads containing more than 5 adapter-polluted bases were considered as adapter contamination readings and would be filtered out;2) Eliminate low-quality reading. Low-quality Reads (phred quality value less than 19) accounted for more than 15% of the total base number.3) Remove reads with more than 5% of the number of N bases.
The genome index was built with Bowtie2 v2.2.3 and the Clean Data was mapped to the reference genome using TopHat v2.0.12.
Using the Integrative Genomics Viewer (IGV) to view mapping results through a Heatmap, histogram, scatter plot, or other stytles.
The Reads Count of each gene in each sample were calculated by HTSeq v0.6.0, and then FPKM (Fragments per Kilobase per Million Mapped Fragments) was calculated to estimate the expression level of genes in each sample.
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes counts and normalized counts for each Sample

source_name: Brain endothelial cell

extract_protocol:
Total RNA was collected with the RNA microextraction kit. A sequencing library was constructed with 2ug total RNA.
RNA libraries sequencing  were performed with standard Illumina protocols.

value: Brain

value: endothelial cell

tag: strain

value: WT


title: Brain endothelial cell, Brd4 KO

value: KO


title: WT_3


title: WT_DHA_4

value: DHA


title: mRNA_RectalCancer_rep260

value: Rectal Cancer

value: male


title: mRNA_RectalCancer_rep264


title: WT_2


title: PC-12 5min Control (Cy3) x PACAP (Cy5)


title: mRNA_RectalCancer_rep263


title: mRNA_RectalCancer_rep259


title: mRNA_RectalCancer_rep262


title: WT_DHA_3


title: WT_DHA_2


title: mRNA_RectalCancer_rep257


title: T_3


title: Rg5_rep1


title: mRNA_RectalCancer_rep255


title: T_2


title: mRNA_RectalCancer_rep254


title: T_DHA_3


title: mRNA_RectalCancer_rep252


title: mRNA_RectalCancer_rep251


title: T_1


title: T_DHA_2


title: T_DHA_1


title: mRNA_RectalCancer_rep258


title: Astrocytes, shControl, TNF-alpha treatment rep2

city: Birmingham

first: Shinichi

last: Kano

state: AL

address: 1720 7th Ave South

department: Psychiatry

institute: University of Alabama at Birmingham

data_processing:
Sequence reads were mapped to GRCm38/mm10 using STAR (v.2.5.4b) and transcript levels were quantified using RSEM (v.1.3.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files ("RSEM genes.results" file, including gene_id, TPM, and FPKM values for each sample)

source_name: Neonatal brains

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEB Next® Ultra™ Directional RNA Library Prep Kit (New England BioLabs).

value: Neonatal brains

value: Primary cells

value: Astrocytes

value: Control knockdown

value: TNF-alpha


title: Astrocytes, shGstm1, TNF-alpha treatment rep1

value: Gstm1 knockdown


title: mRNA_RectalCancer_rep250

value: female


title: mRNA_RectalCancer_rep261


title: WT_DHA_1

value: hippocampus


title: Astrocytes, shGstm1, TNF-alpha treatment rep2


title: mRNA_RectalCancer_rep249


title: mRNA_RectalCancer_rep248


title: mRNA_RectalCancer_rep246


title: T_4

value: vehicle


title: mRNA_RectalCancer_rep247


title: Astrocytes, shGstm1, no-stimulation rep2


title: Astrocytes, shControl, TNF-alpha treatment rep1


title: Astrocytes, shGstm1, no-stimulation rep1


title: mRNA_RectalCancer_rep245


title: mRNA_RectalCancer_rep256


title: Astrocytes, shControl, no-stimulation rep2


title: mRNA_RectalCancer_rep253


title: mRNA_RectalCancer_rep244


title: Astrocytes, shControl, no-stimulation rep1


title: mRNA_RectalCancer_rep243


title: mRNA_RectalCancer_rep241


title: mRNA_RectalCancer_rep242


title: pooled oocyte null-2

city: Houston

first: Ying-Wooi

last: Wan

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
10 bp were removed from the 5’ end of the raw reads. trimmed reads were aligned to the Mus musculus genome (GRcm38, p6.VM24) using TopHat v2.0.9. HTSeq was used to obtain read counts.
Differential expression analysis between Nlrp2-null and WT superovulated oocytes was carried out based on the read counts using the DESeq package in the R environment.
to determine transcript abundance compared to a recently published oocyte reference transcriptome, raw reads were mapped to the oocyte-specific transcriptome reported by Veselovska et al.using STAR (version 2.5.0a) with default parameters. Next, featureCounts (version 1.5.0-p1) was used to quantify the reads for oocyte-specific transcripts based on the annotation Gene Transfer Format (GTF) file provided by Veselovska et al. Based on the read counts, differential transcript analysis between Nlrp2-null and WT superovulated oocytes was performed using DESeq2 (version 1.22.2) in R. We annotated the transcripts to their closest genes using HOMER. and a gene is considered for following analyses if the transcript is within 10 kb upstream of the gene’s transcription start site.
Assembly: mm10
Supplementary files format and content: normalized read counts per gene
Supplementary files format and content: normalized read counts per oocyte specific transcript

source_name: denuded oocytes from COCs

extract_protocol:
COCs were collected from the ampulla of the oviduct. Denuded oocytes were prepared by treating COCs with 3 mg/ml hyaluronidase for 2 minutes at room temperature. Oocytes from 3-4 mice of the same genotype were pooled to obtain pools of approximately 150 oocytes in each sequenced RNA sample. RNA was isolated from four Nlrp2-null and three WT oocyte pools using the Qiagen miRNeasy kit (QIAGEN, US) and used for the preparation of RNA-Seq libraries.
Libraries were prepared with the NuGEN RNA-Seq library preparation protocol. Briefly, purified double-stranded cDNA was generated from approximately 20 ng of total RNA and amplified using both oligo d(T) and random primers. Five hundred nanograms of each sample’s ds-cDNA were sheared using the Covaris S2 focused-ultrasonicator to a target size of 400 bp. A double-stranded DNA library was then generated from 1 g of sheared, double-stranded cDNA, preparing the fragments for hybridization to the flowcell. Using the concentration from the ViiA7TM qPCR machine, 14 pM of the equimolarly pooled library is loaded onto an Illumina HiSeq 2500 sequencing instrument (Illumina, USA).

value: denuded oocytes

value: 4 weeks


title: pooled oocyte null-3


title: pooled oocyte null-4


title: mRNA_RectalCancer_rep240


title: pooled oocyte null-1


title: pooled oocyte WT-1

value: Wild type


title: mRNA_RectalCancer_rep239


title: mRNA_RectalCancer_rep236


title: mRNA_RectalCancer_rep238


title: Hp1α/β DKO clone2 rep1

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

data_processing:
Sequence reads were mapped to mm10 using STAR (v2.5.0a) with parameters --outFilterMultimapNmax 300 --outSAMmultNmax 1 --outMultimapperOrder Random
Read count extraction was performed using QuasR.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Hp1ab_genes_readcounts.csv: Semicolon-separated text file.

source_name: mouse embryonic stem cells

growth_protocol: mESCs were cultured in DMEM medium with 4.5 g/L glucose (Gibco) containing knockout serum replacement (Invitrogen), LIF, penicillin, streptomycin, 2 mM L-glutamine, 0.1 mM b-mercaptoethanol, non-essential amino acids, 1 mM sodium pyruvate (Gibco), in the presence of GSK3b and MEK1 inhibitors (2i) (3 µM CHIR99021, 0.8 µM PD184352, Axon Medchem) at 37°C 5% CO2.

extract_protocol:
RNA was isolated with the RNeasy mini kit (Qiagen) according to the manufacturer's protocol. RNA was further treated with Turbo DNase (AMbion) to remove residual DNA.
Sequencing libraries were prepared with ScriptSeq v2 RNA-Seq Library Prep Kit (Illumina).

treatment_protocol: No treatment.

value: mouse embryonic stem cells

value: Hp1alpha and Hp1beta double knockout


title: mRNA_RectalCancer_rep234


title: Hp1α/β DKO clone2 rep2


title: pooled oocyte WT-3


title: Hp1α/β DKO clone1 rep2


title: mRNA_RectalCancer_rep231


title: mRNA_RectalCancer_rep237


title: mRNA_RectalCancer_rep235


title: pooled oocyte WT-2


title: mRNA_RectalCancer_rep233


title: mRNA_RectalCancer_rep232


title: Hp1α/β DKO clone1 rep1


title: mRNA_RectalCancer_rep229


title: Hp1α/β F/F rep2

value: WT


title: D3_WT_OXA

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

data_processing:
Library quality control: FASTQC version 0.11.5
Quality and adapter trimming: trim_galore (uses cutadapt version 1.10)
Mapping: Tophat2 version 2.1.0 (uses Bowtie2 version 2.2.6)
Gene counting: HTseq-count version 0.11.2
Normalization and differential expression analysis: DESeq2 R package version 1.18.1
Genome_build: GRCm38
Supplementary_files_format_and_content: normalized_counts.csv

source_name: esophagus

extract_protocol:
RNA extraction using TRIZOL (Ambion)
The CEL-Seq library was ran on anIllumina HiSeq 2500 sequencer

treatment_protocol: Mice underwent a murine experimental EoE model using the chemical Allergan 4-Ethoxymethylene-2-phenyl-2-oxazolin-5-one (OXA) or control (Vehicle ) treatment.

value: esophagus

value: OXA


title: D4_WT_OXA


title: Hp1α/β F/F rep1


title: D1_WT_OXA


title: C1_WT_OXA


title: mRNA_RectalCancer_rep230

value: Rectal Cancer

value: male


title: mRNA_RectalCancer_rep227


title: D2_WT_OXA


title: mRNA_RectalCancer_rep224


title: A5_WT_Vehicle


title: mRNA_RectalCancer_rep226


title: mRNA_RectalCancer_rep222


title: A3_WT_Vehicle


title: mRNA_RectalCancer_rep223


title: mRNA_RectalCancer_rep220


title: mRNA_RectalCancer_rep228


title: A1_WT_Vehicle


title: mRNA_RectalCancer_rep225


title: mRNA_RectalCancer_rep219


title: mRNA_RectalCancer_rep218


title: A2_WT_Vehicle


title: mRNA_RectalCancer_rep221


title: PGCLCd5_KOB1 (RNAseq)

city: Pozzuoli

first: Margherita

last: Mutarelli

address: Via Campi Flegrei 34

department: ISASI

country: Italy

institute: CNR

data_processing:
Sequence reads were trimmed using TrimGalore (0.4.3.1) to remove adapter sequences using default settings
Alignment was performed with RNAstar (2.6.0b-2) on mm10 reference assembly (GRCm38.p4) using a minimum aligment score of 0.66
Quantification analysis was performed with Seqmonk (1.47.1)
Genome_build: GRCm38.p4/mm10
Supplementary_files_format_and_content: normalized counts matrix

source_name: Primordial Germ cells

growth_protocol: Esrrb KO and WT SGET mES cells were routinely maintained and regularly passaged on gelatin in 2i/L culture media. Epiblast-like cells (EpiLC) were induced by seeding 3x104 naïve ESC per cm2 on fibronectin-coated plates and maintained in EpiLC media by addiction of ActivinA (20 ng/ml) and bFGF (12.5 ng/ml). PGC were induced by seeding 1.5x106 EpiLC using PGCLC culture media by addiction of BMP4 (500 ng/ml), LIF (1000 U/ml), SCF (100 ng/ml), BMP8a (500 ng/ml), EGF (50 ng/ml).

extract_protocol:
RNA was extracted using PicoPure RNA isolation kit (Applied Biosystems KIT0204)
Library was constructed using the NEB next Ultra II Directional RNA protocol for Poly(A) mRNA magnetic Isolation Module (NEB #E7490), following manifacturer instructions

treatment_protocol: PGCLC SG+ETlow were sorted at FACS after 3 or 5 days form differentiation

value: ESC-derived Primordial Germ cells

tag: time (pgc days of differentiation)

value: 5 days

tag: facs sort

value: SG+ETlow

value: EsrrbKO


title: PGCLCd5_KOA5 (RNAseq)

tag: cell type


title: PGCLCd5_WT_3 (RNAseq)

tag: genotype


title: mRNA_RectalCancer_rep217

tag: tissue


title: PGCLCd5_WT_1 (RNAseq)


title: A4_WT_Vehicle


title: mRNA_RectalCancer_rep216


title: PGCLCd5_KO2 (RNAseq)


title: mRNA_RectalCancer_rep215

value: female


title: PGCLCd5_WT_2 (RNAseq)


title: mRNA_RectalCancer_rep212


title: mRNA_RectalCancer_rep214


title: PGCLCd3_KOB1 (RNAseq)

value: 3 days


title: PGCLCd3_KO2 (RNAseq)


title: mRNA_RectalCancer_rep213


title: PGCLCd3_WT_2 (RNAseq)


title: mRNA_RectalCancer_rep209


title: mRNA_RectalCancer_rep208


title: mRNA_RectalCancer_rep211


title: PGCLCd3_WT_1 (RNAseq)


title: mRNA_RectalCancer_rep205


title: PGCLCd3_WT_3 (RNAseq)


title: EpiLC_KO2 (RNAseq)

source_name: Epiblast like cells

value: ESC-derived Epiblast-Like cells

value: unsorted


title: mRNA_RectalCancer_rep210


title: mRNA_RectalCancer_rep206


title: EpiLC_KOA5 (RNAseq)


title: mRNA_RectalCancer_rep207


title: mRNA_RectalCancer_rep202


title: EpiLC_KOB1 (RNAseq)


title: EpiLC_WT_1 (RNAseq)


title: EpiLC_WT_2 (RNAseq)


title: mRNA_RectalCancer_rep203


title: cnmc842t

city: Stanford

first: Michelle

last: Monje

state: CA

address: 265 Campus Drive, SIM1 G3035

institute: Stanford University

description: Due to patient privacy concerns, we are witholding raw sequencing files at this time.

data_processing:
Reads were mapped to hg19 annotation using Tophat2 (Kim et al 2013) (version 2.0.13). Transcript expression was quantified against RefSeq gene annotations using featureCounts (Liao et al, 2014). Attached files indicate transcript expression via tpm values.
Assembly: hg19
Supplementary files format and content: Raw tpm counts of gene expression abundance for cnmc842t and pons02 (in csv format)

source_name: Primary human patient cnmc842t tumor tissue

extract_protocol:
Total RNA was extracted using chloroform extraction followed by ethanol precipitation and quantified using Qubit, as described in Nagaraja 2017. After extraction, RNA-seq samples were poly(A) selected using Dynabeads mRNA Purification Kit (Life Tech) before fragmentation using Fragmentation Buffer (Ambion, #AM8740) and Second Strand Synthesis using DNA Pol I (Invitrogen #18010-025). Libraries were sequenced at 1x75 on an Illumina NextSeq 500.
RNA-seq samples were poly(A) selected using Dynabeads mRNA Purification Kit (Life Tech) before fragmentation using Fragmentation Buffer (Ambion, #AM8740) and Second Strand Synthesis using DNA Pol I (Invitrogen #18010-025). Libraries were sequenced at 1x75 on an Illumina NextSeq 500.

value: Pons DIPG tumor

value: Primary DIPG cells


title: mRNA_RectalCancer_rep201


title: EpiLC_WT_3 (RNAseq)


title: mRNA_RectalCancer_rep199


title: mRNA_RectalCancer_rep204


title: mRNA_RectalCancer_rep197


title: PGCLCd3_KOA5 (RNAseq)


title: mRNA_RectalCancer_rep200


title: pons02

source_name: Primary human patient pons02 non-tumor tissue

value: Pons non-tumor

value: Primary pontine cells


title: mRNA_RectalCancer_rep194

source_name: Rectal Cancer


title: mRNA_RectalCancer_rep192


title: mRNA_RectalCancer_rep193


title: mRNA_RectalCancer_rep196


title: mRNA_HCT116_WT_Nutlin_BRep1

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

data_processing:
nanoCAGE-seq libraries were sequenced on the Illumina NextSeq platform and aligned to the hg38 reference genome with STAR v2.5.4b. All browser tracks are visualized on the WashU Epigenome Browser70.
Assembly: hg38
Supplementary files format and content: reads are aligned to hg38

source_name: HCT116 cancer cell line with WT P53

growth_protocol: All cell lines were grown under the optimal condition according to ATCC handling guidelines for each cell line.

extract_protocol:
To profile gene expression, we generated mRNA-seq libraries following published methods. In brief, we extracted mRNA from cancer cell lines using PolyA pull down kit (Universal Plus mRNA-seq, NuGEN, PART NO. 0508, 9133, 9134). Afterwards, we processed 500ng of mRNA following standard mRNA-seq library prep protocol following the used kit (Ultra II Directional RNA library Prep Kit, NEB #E7760S).
mRNA-seq
To profile gene expression, we generated mRNA-seq libraries following published methods. In brief, we extracted mRNA from cancer cell lines using PolyA pull down kit (Universal Plus mRNA-seq, NuGEN, PART NO. 0508, 9133, 9134). Afterwards, we processed 500ng of mRNA following standard mRNA-seq library prep protocol following the used kit (Ultra II Directional RNA library Prep Kit, NEB #E7760S).

treatment_protocol: Cells were treated with 10µM Nutlin-3 for 48hrs before being collected for RNA extraction.

tag: cancer type

value: Colon cancer


title: mRNA_HCT116_WT_Dox_BRep2

treatment_protocol: Cells were treated with 0.6µg/ml Doxorubicin hydrochloride for 48hrs before being collected for RNA extraction.


title: mRNA_HCT116_WT_DMSO_BRep2

treatment_protocol: Cells were treated with DMSO for 48hrs before being collected for RNA extraction.


title: mRNA_HCT116_p53KO_Dox_BRep2

source_name: HCT116 cancer cell line with KO P53


title: mRNA_HCT116_p53KO_Nutlin_BRep1


title: mRNA_HCT116_WT_DMSO_BRep1


title: mRNA_RectalCancer_rep189


title: mRNA_RectalCancer_rep198


title: mRNA_HCT116_WT_Nutlin_BRep2


title: mRNA_HCT116_p53KO_DMSO_BRep1


title: mRNA_HCT116_WT_Dox_BRep1


title: mRNA_RectalCancer_rep187


title: mRNA_RectalCancer_rep195


title: mRNA_HCT116_p53KO_Nutlin_BRep2


title: mRNA_RectalCancer_rep191


title: mRNA_RectalCancer_rep186


title: mRNA_RectalCancer_rep190


title: T180261

city: Taipei

first: Yu-Hung

last: Wang

address: N0 7, Chung-Shan South Rd

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Reads were aligned to the human genome (GRCh38 GENCODE release 25) and gene annotated with their corresponding GTF file (GENCODE GRCh38 release 25) using STAR version 2.4.2a with the settings --outFilterMultimapNmax 20 ,--outFilterType BySJout, --alignSJoverhangMin 8, --quantMode GeneCounts (Dobin A, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21). DEseq2 was used to perform differential gene expression analysis and calculate FPKM (fragments per kilobase of transcript per million mapped reads) values for each gene (Love et al., 2014).
Assembly: GRCh38
Supplementary files format and content: read_counts

source_name: human BM Mononuclear cells

growth_protocol: not applicable

extract_protocol:
RNA was extracted from cells using the RNeasy Kit (Qiagen) following the instructions of the manufacturer. The purified RNA was used to prepare the sequencing library using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA) following the manufacturer’s recommendations. Briefly, mRNA was purified from total RNA (1 mg) using oligo(dT)-coupled magnetic beads and fragmented into small pieces at elevated temperatures. First-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of doublestrand cDNA and adenylation on the 39 ends of DNA fragments, the adaptors were ligated and purified with the AMPure XP system (Beckman Coulter, Beverly, MA). The quality of the libraries was assessed using an Agilent Bioanalyzer 2100 system and a real-time polymerase chain reaction system.
The quality of the libraries was assessed using an Agilent Bioanalyzer 2100 system and a real-time polymerase chain reaction system. The qualified libraries were then sequenced on an Illumina NovaSeq 6000 platform with 150-bp paired-end reads generated by Genomics, BioSci & Tech Co. (New Taipei City, Taiwan).

treatment_protocol: not applicable

tag: disease state

value: MDS

value: M

value: BM

value: Mononuclear cells


title: mRNA_RectalCancer_rep185

value: Rectal Cancer

value: male


title: T180176


title: mRNA_RectalCancer_rep182


title: mRNA_HCT116_p53KO_Dox_BRep1


title: mRNA_RectalCancer_rep181


title: mRNA_RectalCancer_rep188


title: mRNA_HCT116_p53KO_DMSO_BRep2


title: S180197


title: T180172

value: F


title: T180169


title: mRNA_RectalCancer_rep176


title: T180231


title: mRNA_RectalCancer_rep183


title: mRNA_RectalCancer_rep175


title: mRNA_RectalCancer_rep184


title: S180190


title: mRNA_RectalCancer_rep173


title: S180189


title: mRNA_RectalCancer_rep180


title: mRNA_RectalCancer_rep179


title: T180103


title: T170135


title: T180165


title: mRNA_RectalCancer_rep178


title: S180194


title: mRNA_RectalCancer_rep177


title: T170120


title: S180199


title: S180192


title: mRNA_RectalCancer_rep168


title: R170130


title: R170111


title: mRNA_RectalCancer_rep174


title: mRNA_RectalCancer_rep172


title: S180185


title: S180184


title: mRNA_RectalCancer_rep169


title: mRNA_RectalCancer_rep171


title: mRNA_RectalCancer_rep167


title: R160145


title: mRNA_RectalCancer_rep166


title: mRNA_RectalCancer_rep165


title: mRNA_RectalCancer_rep170


title: R160146


title: S180183


title: mRNA_RectalCancer_rep163


title: R160144


title: mRNA_RectalCancer_rep164


title: R170126


title: mRNA_RectalCancer_rep162


title: mRNA_RectalCancer_rep160


title: mRNA_RectalCancer_rep161


title: R160143


title: mRNA_RectalCancer_rep158


title: R170101


title: R160122


title: mRNA_RectalCancer_rep159


title: MDS993


title: Myeloid090


title: Myeloid068


title: mRNA_RectalCancer_rep157


title: mRNA_RectalCancer_rep156


title: MDS985


title: MDS980


title: mRNA_RectalCancer_rep155


title: mRNA_RectalCancer_rep154


title: MDS957


title: mRNA_RectalCancer_rep153


title: MDS976


title: R160126


title: MDS969


title: mRNA_RectalCancer_rep151


title: mRNA_RectalCancer_rep152


title: MDS953


title: mRNA_RectalCancer_rep150


title: MDS954


title: MDS952


title: mRNA_RectalCancer_rep149


title: MDS947


title: mRNA_RectalCancer_rep148


title: MDS902


title: MDS911


title: mRNA_RectalCancer_rep147


title: mRNA_RectalCancer_rep143


title: mRNA_RectalCancer_rep144


title: MDS884


title: MDS879


title: MDS868


title: MDS873


title: mRNA_RectalCancer_rep145


title: mRNA_RectalCancer_rep140


title: MDS870


title: mRNA_RectalCancer_rep141


title: AEG-1-WT-replicate 2

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

data_processing:
Illumina adapters were trimmed using TrimGalore! V.0.6.6, replicates were merged and aligned with their reference genome (UCSC mouse genome build mm10) using STAR v.2.7.9a. The BAM files from alignment were processed using STAR v.2.7.9a to obtain the counts per gene in all samples. Mus_musculus.GRCm38.100.gtf gene definition file was used.
The differential expression analysis was performed using edgeR v3.36.0. Genes having counts per million less than 2 in all samples were excluded. Differentially expressed genes were defined using false discovery rate (FDR) cut-off value of 0.05. All bioinformatics analyses were conducted in R/Bioconductor computing environment v4.0.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read count values for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted using the QIAGEN miRNAeasy Mini Kit (QIAGEN, Valencia, CA). cDNA preparation was done using ABI cDNA synthesis kit (Applied Biosystems, Foster City, CA). Q-RT-PCR was performed using an ABI ViiA7 fast real-time PCR system and Taqman gene expression assays according to the manufacturer’s protocol (Applied Biosystems, Foster City, CA).
RNA-Seq library was prepared using Illumina TruSeq RNA sample preparation kit and subjected to sequencing on Illumina HiSeq3000 platform.

value: liver

value: hepatocytes

value: WT

value: Control


title: mRNA_RectalCancer_rep139

value: female


title: MDS864


title: mRNA_RectalCancer_rep146


title: mRNA_RectalCancer_rep137


title: AEG-1-WT-replicate 1


title: AEG-1-C75S-replicate 3

value: AEG-1 mutant (AEG-1-C75S)


title: mRNA_RectalCancer_rep142


title: MDS844


title: mRNA_RectalCancer_rep136


title: AEG-1-C75S-replicate 2


title: mRNA_RectalCancer_rep138


title: MDS829


title: MDS824


title: mRNA_RectalCancer_rep135


title: Mll3KOMll4KI_D4_H3K27ac

city: Bethesda

first: Kai

last: Ge

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

library_source: genomic

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration - For ChIP-Seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3); for ChIP-Seq of MLL4: Windows (50), Gaps (50), FDR (1e-10)
Single-end reads of RNA-seq are aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilo base per million (RPKM) on exonic regions as expression measurements for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include FPKM values for each gene.

molecule: genomic DNA

source_name: Embryoid bodies (EBs)

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min and quenched by 125 mM glycine for 10 min. 30 million fixed cells were swelled in cold buffer containing 5mM PIPES (pH 8.0), 85mM KCl, 1% NP-40 and protease inhibitors for 20 min, and centrifuged at 2,000 g for 5 min at 4°C. Nuclei were resuspended with 3 mL TE buffer (pH 8.0), and subjected to sonication. Sheared chromatin was clarified by centrifugation at 4,000 g for 10 min at 4°C. The supernatant was transferred to a new tube and further supplemented with 150mM NaCl, 0.1% SDS, 1% Triton-X100 and protease inhibitors. 2% of the total material was set aside as input and 20 ng of spike-in chromatin (Active Motif, #53083) was added to each ChIP material. For each ChIP material, 2 - 8 µg of target antibodies and 1.5 μg of spike-in antibody (anti-H2Av, Active Motif, #61686) pre-bound with protein A Dynabeads (ThermoFisher) were added and incubated on a rotator at 4°C overnight. Beads were then collected on a magnetic rack and washed twice with 1 mL cold RIPA buffer, once with 1 mL cold RIPA buffer containing 500mM NaCl, twice with 1 mL cold LiCl buffer and once with 1 mL TE buffer. Finally, beads were eluted with 100 μL buffer containing 0.1M NaHCO3, 1% SDS, and 100 μg Proteinase K at 65°C overnight. Samples were then purified using QIAquick PCR purification kit (Qiagen) and eluted in 50 μL 10mM Tris-HCl.
Libraries were prepared according to NEB (Illumina kit) instructions. DNA were used to construct libraries using NEBNext® Ultra™ II DNA Library Prep kit with AMPure XP magnetic beads (Beckman Coulter).

value: ES-derived EBs

tag: stage of differentiation

tag: antibodies

value: H3K27ac (Abcam, ab4729)


title: AEG-1-C75S-replicate 1


title: mRNA_RectalCancer_rep134


title: Mll3KOMll4flox_D4_H3K27ac


title: Mll3KOMll4flox_D0_H3K27ac

source_name: Embryonic stem cells (ESCs)

value: ESC


title: Mll3KOMll4KI_D4_H3K4me1

value: H3K4me1 (EpiCypher, 13-0040)


title: MDS846

value: MDS


title: Mll3KOMll4flox_D4_H3K4me1


title: MDS817

value: M


title: AEG-1-WT-replicate 3


title: MDS816

value: BM


title: mRNA_RectalCancer_rep133


title: Mll3KOMll4KI_D4_MLL4

value: MLL4 (homemade, #3)


title: mRNA_RectalCancer_rep132

value: Rectal Cancer


title: MDS823

value: Mononuclear cells


title: Mll3KOMll4KI_D0_H3K27ac


title: Mll3KOMll4KI_D0_MLL4


title: Mll3KOMll4flox_D0_H3K4me1


title: MDS792


title: MDS858


title: mRNA_RectalCancer_rep131

value: male


title: Mll3KOMll4flox_D0_MLL4


title: Mll3KOMll4KI_D0_H3K4me1


title: Mll3KOMll4KI_D4_input


title: Mll3KOMll4flox_D4_MLL4


title: MDS788

value: F


title: Mll3KOMll4KI_D0_input


title: MDS786


title: mRNA_RectalCancer_rep128


title: mRNA_RectalCancer_rep130


title: mRNA_RectalCancer_rep129


title: MDS765


title: mRNA_RectalCancer_rep126


title: Mll3KOMll4flox_D0_input


title: Mll3KOMll4flox_D4_input


title: BETA 10- REPLICATE 5

city: Dunedin

first: Alexandra

middle: Boix

last: De Jesus

address: 56 Hanover Street, Central Dunedin, Dunedin 9016

country: New Zealand

institute: University of Otago

data_processing:
FASTQ aligned with HiSAT2
Differential gene expression performed using Limma ®
Reads counted using featurecounts ®
Assembly: hg38
Supplementary files format and content: Aligned Reads (feature counts output)

source_name: CELL

extract_protocol:
RNA  was extracted from cell lines using the Pure LinkTM RNA Mini Kit (ThermoFisher, USA) and Trizol (ThermoFisher, USA)
1. Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail;  2. mRNA molecules were fragmented into small pieces;  3. The fragmented mRNA was synthesized into first strand cDNA using random primers;  4. The second strand cDNA was synthesized with dUTP instead of dTTP;  5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments;  6. Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) and perform PCR amplification;

value: CELL

value: non-small cell lung cancer

value: plasmid


title: mRNA_RectalCancer_rep127

value: female


title: NULL 1- REPLICATE 3

value: (p53 deficient)

value: vector only


title: BETA 10- REPLICATE 4


title: MDS703


title: mRNA_RectalCancer_rep125


title: MDS683


title: BETA 10- REPLICATE 2


title: NULL 1- REPLICATE 2


title: BETA 10- REPLICATE 1


title: mRNA_RectalCancer_rep124


title: NULL 1- REPLICATE 4


title: MDS665


title: BETA 10- REPLICATE 3


title: BETA 5- REPLICATE 1


title: BETA 5- REPLICATE 2


title: mRNA_RectalCancer_rep123


title: NULL 1- REPLICATE 1


title: mRNA_RectalCancer_rep122


title: BETA 5- REPLICATE 3


title: MDS637


title: MDS766


title: ALPHA 8- REPLICATE 3


title: mRNA_RectalCancer_rep121


title: MDS570


title: ALPHA 8- REPLICATE 4


title: ALPHA 2- REPLICATE 4


title: ALPHA 8- REPLICATE 2


title: mRNA_RectalCancer_rep120


title: MDS1714


title: ALPHA 2- REPLICATE 2


title: MDS740


title: mRNA_RectalCancer_rep119


title: ALPHA 2- REPLICATE 1


title: ALPHA 1 - REPLICATE 4


title: ALPHA 1 - REPLICATE 1


title: ALPHA 8- REPLICATE 1


title: ALPHA 2- REPLICATE 3


title: MDS1713


title: MDS1709


title: 30 Days Training 3

city: Gainesville

first: Mark

middle: Robert

last: Viggars

state: Alachua

address: University of Florida, M531

department: Physiology & Aging

institute: University of Florida

data_processing:
Partek Flow Software
Sequenced reads were trimmed for adaptor sequence, quality score (Phred score >20) from 3-prime end.
Aligned using STAR - 2.7.3a to rn6. Annotated to rn6, Ensembl transcript release 99.
Partek Deseq2 normalization and Deseq2 differential gene set analysis
Genome_build: rn6
Supplementary_files_format_and_content: .txt deseqcounts
Supplementary_files_format_and_content: .txt rawcounts
Supplementary_files_format_and_content: .txt gsaresult

source_name: Tibialis Anterior Skeletal Muscle Tissue

extract_protocol:
Muscles removed, flash frozen in liquid nitrogen. Homogenized with TRIzol and Qiagen ceramic beads to extract RNA (Qiagen, Tissue Lyser II).
Library prepped using Poly-A tail enrichment of mRNA using NEBNext® Ultra™ II Directional RNA Library kit. Sequenced on Illumina NextSeq550, 150bp paired end reads.

value: Wistar

tag: condition

value: 30 Days Training


title: ALPHA 1 - REPLICATE 3


title: mRNA_RectalCancer_rep115

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

institute: Japanese Foundation Cancer Research

data_processing:
Read count extraction and calculation of TPM and FPKM were performed by RSEM 1.3.0.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM, FPKM and expected count values for each Sample

extract_protocol:
Total RNA from fresh-frozen tumor samples was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instructions.
mRNA libraries were constructed using the TruSeq RNA Access Library Prep Kit (Illumina), with the starting amount of RNA determined as per the manufacturer’s instructions.


title: 30 Days Training 3 (Contralateral Control)

value: Tibialis Anterior Skeletal Muscle Tissue

value: 30 Days Training  (Contralateral Control)


title: MDS1702

value: MDS

value: M


title: 30 Days Training 1


title: MDS2101

value: BM


title: mRNA_RectalCancer_rep117

value: Rectal Cancer


title: MDS1707

value: Mononuclear cells


title: 20 Days Training 2 (Contralateral Control)

value: 20 Days Training  (Contralateral Control)


title: ALPHA 1 - REPLICATE 2


title: 20 Days Training 3

value: 20 Days Training


title: MDS1698


title: mRNA_RectalCancer_rep111

value: male


title: 30 Days Training 1 (Contralateral Control)


title: 30 Days Training 2


title: 20 Days Training 3 (Contralateral Control)


title: mRNA_RectalCancer_rep116


title: 10 Days Training 3 (Contralateral Control)

value: 10 Days Training  (Contralateral Control)


title: mRNA_RectalCancer_rep118


title: MDS1699


title: MDS1704

value: F


title: mRNA_RectalCancer_rep114


title: mRNA_RectalCancer_rep112


title: MDS1694


title: wildtype retina rep 2 [R56-WT02]

city: London

first: Mariya

last: Moosajee

address: 11-43 Bath Street

department: Institute of Ophthalmology

country: United Kingdom

institute: UCL

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimgalore
Reads were aligned to the genome and transcriptome using HISAT2 v2.2.1 using using standard paired end based parameters.
Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates
Count files were created using featurecounts (v2) and modelled using DESeq2 (v1.30.1)
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

organism: Danio rerio

source_name: wildtype retina

growth_protocol: zebrafish were harvested at appropriate time points (hpf), retinal regions dissected

extract_protocol:
RNA was extracted using Qiagen Rneasy FFPE kit and quantified
RNA-seq libraries were constructed using the SMARTer low input  kit using standard protocols

value: wildtype A/B

tag: hpf

value: dorsal retina


title: MDS1689

tag: age


title: mRNA_RectalCancer_rep113

tag: Sex


title: MDS1693


title: 20 Days Training 2


title: mRNA_RectalCancer_rep107


title: 30 Days Training 2 (Contralateral Control)


title: 20 Days Training 1 (Contralateral Control)


title: 10 Days Training 2 (Contralateral Control)


title: wildtype retina rep 5 [R56-WT05]


title: mRNA_RectalCancer_rep110


title: 20 Days Training 1


title: wildtype retina rep 4 [R56-WT04]


title: MDS1692


title: 10 Days Training 2

value: 10 Days Training


title: wildtype retina rep 3 [R56-WT03]


title: MDS1690


title: mRNA_RectalCancer_rep108

value: female


title: crb2a m289/m289 retina rep 5 [R56-crb05]

source_name: crb2a m289/m289 retina


title: wildtype retina rep 1 [R56-WT01]


title: mRNA_RectalCancer_rep106


title: mRNA_RectalCancer_rep105


title: MDS1684


title: MDS1687


title: crb2a m289/m289 retina rep 6 [R56-crb06]


title: 10 Days Training 3

value: Wistar


title: 10 Days Training 1 (Contralateral Control)

value: Tibialis Anterior Skeletal Muscle Tissue


title: 10 Days Training 1


title: MDS1683


title: 2 Days Training 3 (Contralateral Control)

value: 2 Days Training  (Contralateral Control)


title: 2 Days Training 3

value: 2 Days Training


title: MDS1679

value: MDS

value: M


title: mRNA_RectalCancer_rep104

value: Rectal Cancer


title: MDS1682

value: BM

value: Mononuclear cells


title: mRNA_RectalCancer_rep102


title: mRNA_RectalCancer_rep103


title: mRNA_RectalCancer_rep101


title: crb2a m289/m289 retina rep 1 [R56-crb01]


title: 2 Days Training 2 (Contralateral Control)


title: mRNA_RectalCancer_rep100


title: MDS1677


title: crb2a m289/m289 retina rep 4 [R56-crb04]


title: crb2a m289/m289 retina rep 2 [R56-crb02]


title: MDS1676


title: MDS1672


title: mRNA_RectalCancer_rep099


title: MDS1669


title: mRNA_RectalCancer_rep098


title: crb2a m289/m289 retina rep 3 [R56-crb03]


title: 2 Days Training 2


title: MDS1668


title: 2 Days Training 1


title: 2 Days Training 1 (Contralateral Control)


title: XJD_NOR

first: Yixun

last: Lu

state: Haidian

address: Fuxing Road

department: Department of General Surgery

institute: Chinese PLA General Hospital

description: Fresh  tissues collected from resected specimens of gastric cancer patients

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: The scanned images were imported into Agilent Feature Extraction software for raw data extraction.

source_name: Stomach, normal tissue

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from tissues using the TRIzol reagent (Invitrogen) according to manufacturer's instructions. Then, RNA concentration was determined by NanoDrop ND-1000 spectrophotometer (ThermoFisher, USA). Then, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

treatment_protocol: Fresh gastric cancer and adjacent normal tissues were collected immediately after tumor resection and kept in liquid nitrogen and then transferred to −80 °C refrigerator for preservation.

tag: gender

value: Female

tag: tumor stage

value: TNM IIIB

tag: differentiation

value: poor


title: X29_C94, scRNA-seq

city: Bunkyo-ku

first: Yuka

last: Haneda

state: Tokyo

address: 7-3-1 Hongo

department: Graduate School of Medicine

institute: The University of Tokyo

description: Fluidigm C1

library_source: transcriptomic single cell

data_processing:
Sequence reads from fastq files were mapped by HISAT2 version 2.1.0. Gene expression counts were calculated with the featureCounts function from the Rsubread version 1.34.7 package using R
Assembly: Gallus_gallus.GRCg6a.96
Supplementary files format and content: Tab-separated matrix files

organism: Gallus gallus

source_name: amniogenic somatopleure

extract_protocol:
For ASCs single-cell preparation, AS grafts including ectodermal and mesodermal layers were collected from more than 15 chick embryos at E1.5 (st10). The grafts were treated with 0.25 w/v% trypsin / EDTA (0.2g/L) at 37 ℃, 15 min to dissociate into single cells. Enzymes were neutralized with equal volume of DMEM with 10% fetal bovine serum (FBS). Cell suspensions were filtered through 35 μm nylon mesh cell strainer (FALCON, 352235) to exclude dirt, doublet or triplet cells.
Prepared cells were captured on the Fluidigm C1 Single-Cell Auto Prep Array integrated fluidic circuit (IFC) for small cells (5-10 μm in diameter). Cells were loaded on the IFC chips at concentration of 500 cells per μL. All captured cells were photographed to check if they were truly dissociated for single cells by using KEYENCE BZ-X710. cDNAs of captured single cells were prepared by using SMARTer v4 Ultra Input Low RNA kit for the Fluidigm C1 System as manufacture provided (Clontech). Then cDNAs were quality checked by using the Agilent 2200 TapeStation system and quantified by Qubit (Thermo Fisher). High quality cDNAs were further constructed sequencing libraries by using Nextera XT DNA Sample Preparation Kit (Illumina). Each single cell cDNAs were sequenced 50 pair-end on the Illumina Hiseq 2500.

value: amniogenic somatopleure

tag: cell line

value: wild type

tag: treatment


title: mRNA_RectalCancer_rep097

value: male


title: X29_C93, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep094


title: MDS1663

value: F


title: LXF_NOR


title: MDS1667


title: X29_C89, scRNA-seq

description: Fluidigm C1


title: MDS1662


title: mRNA_RectalCancer_rep095


title: CXR_NOR

value: Male

value: TNM IIIA

value: moderate


title: X29_C88, scRNA-seq

description: Fluidigm C1


title: X29_C90, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep096


title: XJD_GC

source_name: Stomach, gastric cancer tissue


title: MDS1658


title: X29_C84, scRNA-seq

description: Fluidigm C1


title: X29_C79, scRNA-seq

description: Fluidigm C1


title: CXR_GC


title: LXF_GC


title: mRNA_RectalCancer_rep093


title: mRNA_RectalCancer_rep090


title: MDS1655


title: MDS1624


title: X29_C69, scRNA-seq

description: Fluidigm C1


title: MDS1656


title: mRNA_RectalCancer_rep091


title: MDS1619


title: mRNA_RectalCancer_rep088

value: female


title: mRNA_RectalCancer_rep089


title: X29_C75, scRNA-seq

description: Fluidigm C1


title: MDS1628


title: mRNA_RectalCancer_rep087


title: mRNA_RectalCancer_rep086


title: X29_C58, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep092


title: X29_C55, scRNA-seq

description: Fluidigm C1


title: X29_C64, scRNA-seq

description: Fluidigm C1


title: MDS1618


title: X29_C60, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep109


title: mRNA_RectalCancer_rep084


title: mRNA_RectalCancer_rep085


title: MDS1611


title: mRNA_RectalCancer_rep083


title: X29_C53, scRNA-seq

description: Fluidigm C1


title: X29_C54, scRNA-seq

description: Fluidigm C1


title: X29_C51, scRNA-seq

description: Fluidigm C1


title: MDS1612


title: mRNA_RectalCancer_rep081


title: MDS1614


title: MDS1607


title: MDS1609


title: mRNA_RectalCancer_rep082


title: CC53-2

type: genomic

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

country: Canada

institute: McGill University

hyb_protocol: Briefly, ~500ng of DNA was bisulfite converted using an EZ DNA methylation Kit, followed by whole genome amplification, enzymatic fragmentation and hybridized to the Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged on the Illumina iScan BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Preprocessing of the raw data files (IDAT), quality control (QC) assessment and normalization was performed using the R package minfi (version 1.36.0).  The function preprocessFunnorm was used for the functional normalization of the data using internal control probes on the array to infer between-array technical vairaion.  This function applies preprocessNoob function first, for background substraction and dye-bias normalization.  The annotation of the array to determine the genomic location of probes was determined with IlluminaHumanMethylation450kanno.ilmn12.hg19 (version 0.6.0)

label: Cy5 and Cy3

source_name: Sperm

label_protocol: Standard Illumina Protocol

extract_protocol: Frozen sperm was thawed on ice and genomic DNA isolation was performed using Qiagen DNeasy Blood & Tissue Kits (Qiagen, Canada) according to the manufacturer’s guide, with modifications. For sample  were incubated overnight at 37oC in a buffer containing EDTA, Tris , sarkosyl , dithiothreitol (DTT) and proteinase K (Invitrogen, Canada). The following day, Buffer AL was added to the buffer, and incubated at 70oC for 10min and the manufacturer’s guide was continued.

tag: group

value: CC

value: Sperm


title: MDS1606

value: MDS

tag: cell type


title: CC65-0


title: MDS1616


title: mRNA_RectalCancer_rep080

value: Rectal Cancer


title: X29_C46, scRNA-seq

description: Fluidigm C1

tag: genotype


title: CC65-2

tag: tissue


title: CC33-0


title: CC53-1


title: mRNA_RectalCancer_rep079


title: MDS1602

value: M

value: BM


title: CC33-2


title: CC65-1


title: X29_C32, scRNA-seq

description: Fluidigm C1


title: MDS1603

value: Mononuclear cells


title: mRNA_RectalCancer_rep077


title: X29_C41, scRNA-seq

description: Fluidigm C1


title: X29_C29, scRNA-seq

description: Fluidigm C1


title: CC33-1


title: mRNA_RectalCancer_rep075


title: MDS1596


title: mRNA_RectalCancer_rep078


title: HD205-0

value: HD


title: HD202-0


title: MDS1595


title: X29_C18, scRNA-seq

description: Fluidigm C1


title: MDS1594


title: CC52-2


title: CC52-0


title: MDS1601


title: X29_C30, scRNA-seq

description: Fluidigm C1


title: TC206-0

value: TC


title: TC63-6


title: MDS1599


title: TC63-2


title: HD210-1


title: mRNA_RectalCancer_rep071


title: X29_C21, scRNA-seq

description: Fluidigm C1

value: amniogenic somatopleure


title: MDS1597


title: mRNA_RectalCancer_rep070


title: mRNA_RectalCancer_rep069


title: X29_C26, scRNA-seq

description: Fluidigm C1

value: wild type


title: X29_C10, scRNA-seq

description: Fluidigm C1


title: MDS1586


title: mRNA_RectalCancer_rep072

value: male


title: MDS1590


title: mRNA_RectalCancer_rep073


title: X29_C17, scRNA-seq

description: Fluidigm C1


title: TC29-7


title: mRNA_RectalCancer_rep074


title: mRNA_RectalCancer_rep068


title: X29_C34, scRNA-seq

description: Fluidigm C1


title: MDS1583


title: mRNA_RectalCancer_rep067


title: X09_C95, scRNA-seq

description: Fluidigm C1


title: MDS1587


title: X09_C92, scRNA-seq

description: Fluidigm C1


title: CC76-1


title: TC201-0


title: X09_C91, scRNA-seq

description: Fluidigm C1


title: MDS1585


title: X29_C11, scRNA-seq

description: Fluidigm C1


title: X29_C13, scRNA-seq

description: Fluidigm C1


title: MDS1579

value: F


title: MDS1577


title: X29_C09, scRNA-seq

description: Fluidigm C1


title: TC63-5


title: HD210-0


title: TC63-0


title: CC51-1


title: X09_C88, scRNA-seq

description: Fluidigm C1


title: MDS1582


title: HD15-3


title: mRNA_RectalCancer_rep066


title: CC51-2


title: CC51-0


title: X29_C06, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep065


title: mRNA_RectalCancer_rep061


title: MDS1581


title: X09_C82, scRNA-seq

description: Fluidigm C1


title: MDS1571


title: HD15-1


title: mRNA_RectalCancer_rep063


title: mRNA_RectalCancer_rep064


title: HD15-0


title: TC29-2


title: mRNA_RectalCancer_rep058


title: X09_C75, scRNA-seq

description: Fluidigm C1


title: MDS1569


title: X09_C87, scRNA-seq

description: Fluidigm C1


title: TC29-0


title: X09_C74, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep062


title: TC29-3


title: MDS1565


title: mRNA_RectalCancer_rep076


title: mRNA_RectalCancer_rep055


title: MDS1563


title: TC29-1


title: CC41-1


title: X09_C85, scRNA-seq

description: Fluidigm C1


title: MDS1568


title: MDS1562


title: X09_C67, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep060


title: MDS1574


title: HD12-1


title: mRNA_RectalCancer_rep057


title: mRNA_RectalCancer_rep054


title: MDS1576


title: X09_C80, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep059


title: X09_C61, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep052


title: mRNA_RectalCancer_rep050


title: X09_C71, scRNA-seq

description: Fluidigm C1


title: X09_C68, scRNA-seq

description: Fluidigm C1


title: X09_C58, scRNA-seq

description: Fluidigm C1


title: MDS1566


title: MDS1580


title: mRNA_RectalCancer_rep056


title: X09_C76, scRNA-seq

description: Fluidigm C1


title: X09_C56, scRNA-seq

description: Fluidigm C1


title: MDS1549


title: mRNA_RectalCancer_rep048


title: HD12-2


title: CC41-2


title: TC207-0


title: HD12-0


title: X09_C54, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep047


title: MDS1546


title: mRNA_RectalCancer_rep046


title: MDS1561


title: mRNA_RectalCancer_rep053


title: X09_C65, scRNA-seq

description: Fluidigm C1


title: MDS1544


title: X09_C59, scRNA-seq

description: Fluidigm C1


title: MDS1560


title: mRNA_RectalCancer_rep045


title: MDS1550


title: MDS1551


title: TC208-0


title: mRNA_RectalCancer_rep051


title: TC207-3


title: mRNA_RectalCancer_rep049


title: mRNA_RectalCancer_rep043


title: X09_C50, scRNA-seq

description: Fluidigm C1


title: TC63-1


title: MDS1543


title: CC76-0


title: X09_C44, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep042


title: HD12-4


title: X09_C48, scRNA-seq

description: Fluidigm C1


title: MDS1538


title: MDS1537


title: HD211-0


title: X09_C49, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep041


title: X09_C53, scRNA-seq

description: Fluidigm C1


title: CC41-0


title: CC36-1


title: mRNA_RectalCancer_rep038


title: HD5-0


title: X09_C42, scRNA-seq

description: Fluidigm C1


title: MDS1548


title: X09_C41, scRNA-seq

description: Fluidigm C1


title: X09_C38, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep036


title: CC36-0


title: MDS1536


title: MDS1539


title: MDS1535


title: CC36-2


title: mRNA_RectalCancer_rep044


title: mRNA_RectalCancer_rep039


title: mRNA_RectalCancer_rep040


title: MDS1534


title: X09_C40, scRNA-seq

description: Fluidigm C1


title: X09_C39, scRNA-seq

description: Fluidigm C1


title: MDS1531


title: X09_C36, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep037


title: TC8-6


title: HD5-1


title: X09_C34, scRNA-seq

description: Fluidigm C1


title: MDS1532


title: MDS1530


title: TC8-1


title: crb2a m289/m289 retina rep 3

data_processing:
Illumina Casava1.7 software used for basecalling.
Basecalls were processed to FASTQ reads using NuGENs custom python scripts for RRBS analysis that can be found at [NuGEN company provided pipeline](https://github.com/nugentechnologies/NuMetRRBS).
Reads were trimmed using Trimgalore further processed using  NuGEN Diversity Triming
Reads were aligned using Bismark (v0.22.3) using the parameter --bowtie2
Resulting BAM files were sorted by coodinates and duplicates were processed with NuDUP from NuGEN
Methylation was assessed using Methykit (Bioconductor)
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text files include CpG tables from Methylkit analysis  (processBismarkAln).

source_name: retina

extract_protocol:
High quality genomic DNA was isolated using standard protocols.
RRBS libraries were constructed using the Ovation® RRBS Methyl-Seq (Nugen) kit using standard protocols

value: retina


title: X09_C32, scRNA-seq

description: Fluidigm C1


title: MDS1533


title: crb2a m289/m289 retina rep 2


title: HD5-5


title: X09_C35, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep034


title: wildtype retina rep 2

value: wildtype A/B


title: X09_C31, scRNA-seq

description: Fluidigm C1


title: MDS1528


title: mRNA_RectalCancer_rep035


title: mRNA_RectalCancer_rep032


title: crb2a m289/m289 retina rep 1


title: TC8-0


title: mRNA_RectalCancer_rep033


title: wildtype retina rep 1


title: wildtype retina rep 3


title: HD5-4


title: mRNA_RectalCancer_rep031


title: CC53-0


title: X09_C29, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep028


title: MDS1521


title: X09_C25, scRNA-seq

description: Fluidigm C1


title: MDS1522


title: X09_C30, scRNA-seq

description: Fluidigm C1


title: KO3, 24h, replicate 3 (RNA-seq)_2

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include digital counts values for each Sample and normalized count matrix

source_name: E14 mouse Embryonic Stem cells

growth_protocol: E14 mouse Embryonic Stem cells, wild-type or Esrrb KO,  were routinely cultured on 0.2% gelatin coated multiwell plates in N2B27 medium (DMEM-F12 Neurobasal at 1:1 ratio (Life Technologies), 1X N2 Supplement (Life Technologies), 1X B27 Supplement (Life Technologies), 2mM L-Glutamine (Life Technologies), 0.1mM 2-mercaptoethanol with the addition of 2iL (3uM CHIR99021 (Axon), 1uM PD0325901 (Axon), 1uM LIF (Qkine)).

extract_protocol:
Cells were harvested at the appropriate time point and RNA was purified by using "Total RNA extraction kit, Norgen".
NEGEDIA Digital mRNAseq - research grade.

treatment_protocol: Cells were plated at single cell density on 0.2% Gelatin coated plates in N2B27 medium with 2iL. The next day 2iL was removed and replaced with N2B27 medium. Cells were collected after 24, 48 or 72 hours.

value: E14 mouse Embryonic Stem cells

value: Mouse Embryonic Stem cells blastocyst derived

value: ESRRB KO

value: 2iL withdrawal for 24 hours


title: MDS1520

value: MDS


title: X09_C28, scRNA-seq

description: Fluidigm C1


title: KO3, 48h, replicate 4 (RNA-seq)

value: 2iL withdrawal for 48 hours


title: KO1, 2iL, replicate 3 (RNA-seq)

value: untreated (2iL)


title: KO3, 24h, replicate 3 (RNA-seq)


title: mRNA_RectalCancer_rep030

source_name: Rectal Cancer

value: Rectal Cancer


title: CC36-3

value: CC

value: Sperm


title: X09_C23, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep029


title: X09_C21, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep025


title: mRNA_RectalCancer_rep027

value: female


title: MDS1523

value: BM

value: Mononuclear cells


title: X09_C20, scRNA-seq

description: Fluidigm C1

value: amniogenic somatopleure

value: wild type


title: KO3, 48h, replicate 3 (RNA-seq)


title: MDS1526

value: M


title: X09_C19, scRNA-seq

description: Fluidigm C1


title: MDS1524

value: F


title: WT, 48h, replicate 2 (RNA-seq)

value: E14 mouse Embryonic Stem cells

value: WT


title: mRNA_RectalCancer_rep023

value: male


title: MDS1514


title: MDS1519


title: KO2, 48h, replicate 4 (RNA-seq)

value: Mouse Embryonic Stem cells blastocyst derived

value: ESRRB KO


title: mRNA_RectalCancer_rep020


title: X09_C22, scRNA-seq

description: Fluidigm C1


title: MDS1515

value: MDS


title: mRNA_RectalCancer_rep024


title: MDS1500


title: mRNA_RectalCancer_rep021


title: MDS1493


title: MDS1518


title: mRNA_RectalCancer_rep018


title: X09_C14, scRNA-seq

description: Fluidigm C1


title: KO2, 48h, replicate 3 (RNA-seq)

value: 2iL withdrawal for 48 hours


title: MDS1508


title: KO3, 2iL, replicate 1 (RNA-seq)

value: untreated (2iL)


title: KO3, 24h, replicate 2 (RNA-seq)

value: 2iL withdrawal for 24 hours


title: X09_C18, scRNA-seq

description: Fluidigm C1


title: MDS1511


title: KO3, 48h, replicate 1 (RNA-seq)


title: X09_C12, scRNA-seq

description: Fluidigm C1


title: X09_C17, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep017

value: Rectal Cancer


title: KO2, 72h, replicate 2 (RNA-seq)

value: 2iL withdrawal for 72 hours


title: MDS1488

value: BM


title: mRNA_RectalCancer_rep022


title: MDS1542

value: Mononuclear cells


title: X09_C15, scRNA-seq

description: Fluidigm C1

value: amniogenic somatopleure


title: mRNA_RectalCancer_rep026


title: X09_C16, scRNA-seq

description: Fluidigm C1

value: wild type


title: mRNA_RectalCancer_rep019


title: KO3, 2iL, replicate 2 (RNA-seq)


title: KO3, 24h, replicate 1 (RNA-seq)


title: MDS1477


title: mRNA_RectalCancer_rep015

value: female


title: KO2, 48h, replicate 2 (RNA-seq)


title: mRNA_RectalCancer_rep013


title: X09_C11, scRNA-seq

description: Fluidigm C1


title: MDS1492

value: F


title: KO1, 2iL, replicate 1 (RNA-seq)

value: E14 mouse Embryonic Stem cells


title: mRNA_RectalCancer_rep012


title: mRNA_RectalCancer_rep011


title: KO2, 72h, replicate 1 (RNA-seq)


title: MDS1466

value: M


title: X09_C04, scRNA-seq

description: Fluidigm C1


title: X09_C06, scRNA-seq

description: Fluidigm C1


title: MDS1456


title: MDS1463


title: MDS1468


title: KO2, 2iL, replicate 1 (RNA-seq)


title: mRNA_RectalCancer_rep014


title: X09_C09, scRNA-seq

description: Fluidigm C1


title: X09_C01, scRNA-seq

description: Fluidigm C1


title: mRNA_RectalCancer_rep016

value: male


title: KO2, 24h, replicate 2 (RNA-seq)

value: Mouse Embryonic Stem cells blastocyst derived


title: X09_C10, scRNA-seq

description: Fluidigm C1


title: MDS1427


title: MDS1424


title: KO1, 72h, replicate 1 (RNA-seq)

value: ESRRB KO


title: KO2, 2iL, replicate 2 (RNA-seq)


title: KO2, 24h, replicate 1 (RNA-seq)


title: X09_C03, scRNA-seq

description: Fluidigm C1


title: MDS1461

value: MDS


title: MDS1470


title: MDS1339


title: mRNA_RectalCancer_rep006


title: KO1, 48h, replicate 2 (RNA-seq)

value: 2iL withdrawal for 48 hours


title: KO1, 72h, replicate 2 (RNA-seq)


title: mRNA_RectalCancer_rep010


title: MDS1310


title: mRNA_RectalCancer_rep005


title: KO2, 48h, replicate 1 (RNA-seq)


title: X09_C02, scRNA-seq

description: Fluidigm C1


title: A3_S16

city: Oxford

first: James

middle: Oliver Joshua

last: Davies

state: Oxon

address: Weatherall Institute of Molecular Medicine, John Radcliffe Hospital

department: Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine, Oxford University

description:
PCR and sequencing of base editing site
Base_Editing_Frequencies.txt

data_processing:
Base editing data were analysed with CRISPRESSO
RNA-seq data was aligned using STAR (2.7.3a) to hg19. Aberrant splicing of Poly-A negative RNA was detected using PySam (https://github.com/pysam-developers/pysam) find_introns method, considering position 5,248,159 of chromosome 11 (hg19) as the canonical splice site for exon 1 of the HBB gene. An RNA variant calling pipeline was established using GATK best practices. In keeping with the Broad Institutes recommendation for this tool, these data were realigned to hg38 using STAR two-pass alignment, followed by PCR duplicate removal and base score recalibration. GATK Haplotype Caller (4.0.11.0) was then used to call variants.
Assembly: Hg19
Supplementary files format and content: Base_Editing_Frequencies.txt
Supplementary files format and content: RNAseq_splicing.txt

source_name: Patient edited material

growth_protocol: CD34+ cells were resuspended in Phase I medium for a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 3x10^5 cells were resuspended on day 0 in Phase I media at 2x10^5 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 105 cells ml-1. On day 7, cells were counted and pelleted (300 rcf, 5 min, RT) and resuspended in Phase II media at 2x10^5 cells ml-1. Cells were counted on day 9 and diluted to 2x10^5 cells ml-1 Phase II media. HUDEP-2 cells were cultured in expansion phase as previously described Canver, M. C. et al.,2015.

extract_protocol:
DNA was extracted using the PureLink Genomic DNA Mini Kit (Thermofisher) following the manufacturer's protocol with no modifications
For sequencing of base edited sites, modified 2-PCR version of the NEBnext Ultra (NEB) library preparation protocol was followed. In the first PCR primer pairs with NEB adaptor sequences 5’ to the HBB exon 1-specific primer sequence were used for amplification using the Herculase II PCR kit (Agilent) in a 50μl reaction, ensuring the products had the adaptor sequences added by the end of the PCR. 5μl of this was used directly without clean-up for the indexing PCR. This added either single or dual end indices taken from a NEBNext Multiplex Oligos for Illumina kit (NEB).

value: Blood cells

value: Differentiated erythroid cells

value: HbE/beta thalassaemia

value: Control


title: C4_S26

value: HbE gRNA


title: KO1, 24h, replicate 1 (RNA-seq)

value: 2iL withdrawal for 24 hours


title: B3_S17


title: B4_S25


title: E3_S20


title: MDS1304

value: BM

value: Mononuclear cells


title: MDS1301


title: mRNA_RectalCancer_rep003

value: Rectal Cancer


title: mRNA_RectalCancer_rep008

value: female


title: G3_S22


title: KO1, 2iL, replicate 2 (RNA-seq)

value: E14 mouse Embryonic Stem cells

value: untreated (2iL)


title: mRNA_RectalCancer_rep004

value: male


title: mRNA_RectalCancer_rep001


title: MDS1295

value: F


title: MDS1291


title: WT, 72h, replicate 1 (RNA-seq)

value: Mouse Embryonic Stem cells blastocyst derived

value: WT

value: 2iL withdrawal for 72 hours


title: UCB5HBE01_S73

description:
Pre_xenotransplant_S4_edited
PCR and sequencing of base editing site

data_processing:
CIRCLE-seq data were analysed using the standard pipeling (https://github.com/tsailabSJ/circleseq)
Targetted capture NGS data were analysed with bowtie2 and samtools mpileup followed by custom scripts
Base editing data were analysed with CRISPRESSO
Assembly: Hg19
Supplementary files format and content: Processed data files are included in the manuscript

source_name: Blood cells

growth_protocol: CD34+ cells were resuspended in Phase I medium for a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 3x105 cells were resuspended on day 0 in Phase I media at 2x105 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 105 cells ml-1. On day 7, cells were counted and pelleted (300 rcf, 5 min, RT) and resuspended in Phase II media at 2x105 cells ml-1. Cells were counted on day 9 and diluted to 2x105 cells ml-1 Phase II media. HUDEP-2 cells were cultured in expansion phase as previously described Canver, M. C. et al.,2015.

value: Blood cells

value: Umbilical cord blood

value: HbE_WT_ gRNA


title: WT, 48h, replicate 1 (RNA-seq)

value: 2iL withdrawal for 48 hours


title: MDS1290

source_name: human BM Mononuclear cells

value: MDS

value: M


title: N2 12 days after return to ground Rep2

city: Newark

first: Irem

last: Celen

state: DE

address: 15 Innovation Way

institute: University of Delaware

data_processing:
Quality control was implemented on the raw sequence data with FASTQC software (version 0.11.2).
The raw reads were mapped to the reference genome (WBCel235), obtained from Ensembl along with the annotation file, by using TopHat.
The Tuxedo pipeline was employed to find differential gene expressions with default parameters.
Genome_build: WBCel235
Supplementary_files_format_and_content: format: cuffdiff; output: fold changes for the gene expressions among the conditions

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: After bleaching the adult worms, L1 worms were cultured in ground conditions in CeHR medium for three weeks. Then, the worms were exposed to clinostat-simulated microgravity for four days and the maintained impacts were observed at four, eight, and twelve days after placing the worms back to ground conditions All animals were grown at room temperature.

extract_protocol:
Total RNA from mixed stage C. elegans  were isolated with a modified TRIzol protocol and recovered by alcohol precipitation. Total RNA was further purified by PureLink ™ RNA Mini Kit (Life Technologies).
Two micrograms of total RNA were used for library preparations using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina).

value: 12 days after return to ground

value: whole organism

tag: strain

tag: developmental stage

value: Mixed stage


title: N2 12 days after return to ground Rep3


title: KO1, 24h, replicate 2 (RNA-seq)

value: ESRRB KO

value: 2iL withdrawal for 24 hours


title: mRNA_RectalCancer_rep007

value: Rectal Cancer


title: UCB4HBE01_S72

description:
Pre_xenotransplant_S3_edited
PCR and sequencing of base editing site


title: UCB3HBE01_S71

description:
Pre_xenotransplant_S2_edited
PCR and sequencing of base editing site


title: KO1, 48h, replicate 1 (RNA-seq)

value: E14 mouse Embryonic Stem cells


title: N2 8 days after return to ground Rep3

value: 8 days after return to ground


title: N2 12 days after return to ground Rep1


title: mRNA_RectalCancer_rep002

value: male


title: MDS1300

tag: disease state

value: BM

value: Mononuclear cells


title: WT, 2iL, replicate 1 (RNA-seq)

value: Mouse Embryonic Stem cells blastocyst derived

value: WT

value: untreated (2iL)


title: MDS1270


title: KO3, 72h, replicate 2 (RNA-seq)

value: 2iL withdrawal for 72 hours


title: MDS1285

value: MDS


title: UCB5NTC_S69

description:
Pre_xenotransplant_S4_control
PCR and sequencing of base editing site

value: Blood cells

value: Umbilical cord blood

value: Control


title: NSG2nd2_S10

description:
Xenotransplant2_S2
PCR and sequencing of base editing site

value: Murine xenograft bone marrow


title: UCB3NTC_S67

description:
Pre_xenotransplant_S2_control
PCR and sequencing of base editing site


title: UCB4NTC_S68

description:
Pre_xenotransplant_S3_control
PCR and sequencing of base editing site


title: WT, 24h, replicate 2 (RNA-seq)


title: WT, 72h, replicate 2 (RNA-seq)


title: WT, 2iL, replicate 2 (RNA-seq)


title: WT, 24h, replicate 1 (RNA-seq)


title: N2 8 days after return to ground Rep1

value: whole organism

value: Mixed stage


title: NSG2nd3_S11

description:
Xenotransplant2_S3
PCR and sequencing of base editing site


title: MDS1266

value: F


title: N2 4 days after return to ground Rep3

value: 4 days after return to ground


title: UCB2HBE01_S70

description:
Pre_xenotransplant_S1_edited
PCR and sequencing of base editing site

value: HbE_WT_ gRNA


title: N2 4 days after return to ground Rep2


title: MDS1277

value: M


title: MDS1264

value: BM


title: UCB2NTC_S66

description:
Pre_xenotransplant_S1_control
PCR and sequencing of base editing site


title: N2 8 days after return to ground Rep2

value: 8 days after return to ground


title: mRNA_RectalCancer_rep009

value: Rectal Cancer

value: female


title: MDS1286

value: Mononuclear cells


title: N2 4 days after return to ground Rep1


title: KO3, 48h, replicate 2 (RNA-seq)

value: E14 mouse Embryonic Stem cells

value: Mouse Embryonic Stem cells blastocyst derived

value: ESRRB KO

value: 2iL withdrawal for 48 hours


title: MDS1280

value: MDS


title: KO3, 72h, replicate 1 (RNA-seq)

value: 2iL withdrawal for 72 hours


title: MDS1263


title: N2 Simulated Microgravity Rep2

description: MG

value: Simulated Microgravity

value: whole organism


title: NSG1st2_S4

description:
Xenotransplant1_S2
PCR and sequencing of base editing site

value: Blood cells

value: Murine xenograft bone marrow

value: WT


title: NSG1st3_S6

description:
Xenotransplant1_S3
PCR and sequencing of base editing site


title: MDS1268

value: M


title: ICH2_input

city: Hangzhou

first: Hao

last: Liu

address: 234 Gucui Road, Xihu District, Hangzhou City

institute: Tongde Hospital of Zhejiang Province

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Homo sapiens (Version: GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak2 (https://bioconductor.org/packages/exomePeak2), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).  HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using Annovar (https://bioconductor.org/packages/Annovar).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: GRCh38（hg38）
Supplementary files format and content: text files include FPKM values and annotation for each Sample
Supplementary files format and content: text files include peak  information for each group

source_name: brain tissue

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average  size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: brain tissue

value: autologous blood


title: Acupuncture2_input

value: acupuncture


title: NSG2nd1_S7

description:
Xenotransplant2_S1
PCR and sequencing of base editing site


title: N2 Ground Control Rep 1

description: GC

value: Ground Control

value: Mixed stage


title: Sham2_input

value: sham-operation


title: NSG1st1_S3

description:
Xenotransplant1_S1
PCR and sequencing of base editing site


title: MDS1083

value: BM

value: Mononuclear cells


title: MDS1087


title: Sham3_input


title: N2 Simulated Microgravity Rep1

description: MG


title: Acupuncture1_IP


title: N2 Ground Control Rep 2

description: GC


title: Sri-6-2_S21

description:
Patient edited material
PCR and sequencing of base editing site

value: Differentiated erythroid cells

value: HbE/beta thalassaemia

value: HbE gRNA


title: MDS1246

value: MDS


title: MDS1070


title: Duplo_29ºC_3

city: Pozuelo de Alarcón

first: Isabel

last: Díaz

state: Madrid

address: Campus Montegarcedo

department: Interacción de las Plantas con el Medio

institute: CBGP-INIA-UPM

description:
275_29_3
DUP29r3

data_processing:
Reads were mapped to rapeseed genome (AST_PRJEB5043_v1 (Chalhoub et al., 2014)) using HISAT2 (Kim et al., 2015).
Differential expression analysis of raw count data was performed using DESEQ2 (Love et al., 2014) in R.
Genome_build: AST_PRJEB5043_v1 (Chalhoub et al., 2014)
Supplementary_files_format_and_content: DESEQ2 output and raw counts

organism: Brassica napus

source_name: Duplo_29ºC_root tips

growth_protocol: Seeds were germinated in ¼ MS agar plates for 3 days and transferred to a pouch-and-wick system in nutrient solution (1/4MS) (Adapted from (Adu et al., 2014; Atkinson et al., 2015; Thomas et al., 2016)). Six seedlings per pouch were grown in a growth chamber set at constant temperature (21ºC/29ºC), 16h daylight and 40% RH.

extract_protocol:
Total RNA was extracted from 7 days’ root tips from pouch-and-wick grown seedlings using TRIzol reagent (Invitrogen) and total DNA free RNA was cleaned using RNeasy Plant Mini Kit purification columns (Qiagen).
Library preparation was performed using 1 μg of high-integrity total RNA (RIN>8) using the TruSeq Stranded mRNA library preparation kit.

treatment_protocol: optimal temperature (21ºC) vs warm temperature (29ºC)

value: Duplo

value: 7 days at 29ºC

value: root tips (1 cm)


title: N2 Simulated Microgravity Rep3

description: MG

value: Simulated Microgravity

value: whole organism


title: K-4_S14

value: Blood cells


title: MDS1259

data_processing:
Reads were aligned to the human genome (GRCh38 GENCODE release 25) and gene annotated with their corresponding GTF file (GENCODE GRCh38 release 25) using STAR version 2.4.2a with the settings --outFilterMultimapNmax 20 ,--outFilterType BySJout, --alignSJoverhangMin 8, --quantMode GeneCounts (Dobin A, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21). DEseq2 was used to perform differential gene expression analysis and calculate FPKM (fragments per kilobase of transcript per million mapped reads) values for each gene (Love et al., 2014).
Assembly: GRCh38
Supplementary files format and content: read_counts

value: M


title: MDS1255

value: F


title: K-5_S15