title: ccRCC tumor Spatial RNA-seq P_18

description: Corresponds to bulk sample 13c2


title: ccRCC tumor Spatial RNA-seq P_17

status: Public on Jul 08 2026

type: SRA

city: PARIS

first: Isaias

last: Hernandez-Verdin

state: Ile-de-France

address: GH PITIE SALPETRIERE ICM IHU A, 47 Boulevard DE L'HOPITAL

department: Genetics and Development of Nervous System Tumors

country: France

institute: Institut du cerveau

description: Corresponds to bulk sample 0a58

library_source: transcriptomic

data_processing:
Raw fastqs were processed with SpaceRanger (v1.3.0)
Assembly: Genome build: hg38
Supplementary files format and content: TLS_annotation.csv: A comma-separated values file containing the spatial barcodes and indicating whether or not they are associated with TLS presence which was determined by chromogenic staining using CD3 and CD20.
Supplementary files format and content: TumoralZone_annotation.csv: comma-separated values file containing the spatial barcodes and indicating the tumoral area which was detected by a trained pathologist.
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image.
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots.
Supplementary files format and content: scalefactors_json.json: scalefactors in json format.
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue.
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue.
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots.
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 file containing only tissue-associated barcodes (columns) and number of UMIs associated with a feature (rows).
Supplementary files format and content: raw_feature_bc_matrix.h5: HDF5 file containing all barcodes (columns) and number of UMIs associated with a feature (rows).
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: Kidney

extract_protocol:
Spatial transcriptomics: RNA extraction with the 10X Visium protocol
Libraries were prepared with Truseq Illumina libraries and sequenced on a NovaSeq (Illumina)

tag: tissue

value: Kidney

tag: disease state

value: renal cell cancer

tag: cancer type

value: Clear cell renal cell carcinoma


title: Male, GFP-RNAi, Thorax, replicate 3

city: Wageningen

first: Julien

last: Rougeot

address: Droevendaalsesteeg 1

department: Plant Science Group

country: Netherlands

institute: Wageningen University and Research (Netherlands)

data_processing:
Raw data filtering was performed to remove reads with adaptor contamination, uncertain nucleotides on more than 10% of the sequence (N>10%) and reads with low-quality nucleotides (<20) on more than 50% of the sequence.
Clean paired-end reads were mapped on the Nasonia vitripennis genome Nvit_psr_1.1 (GCA_009193385.2 Nvit_psr_1.1) using HISAT2 (v2.0.5) and default parameters.
Gene counts were obtained using HTSeq (v0.6.1) and the union method on the annotation GCF_009193385.1_Nvit_psr_1.
Assembly: Nvit_psr_1.1
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

organism: Nasonia vitripennis

source_name: thorax

growth_protocol: Nasonia vitripennis lab strain AsymCX was reared on Calliphora sp. under a 16 hours light / 8 hours dark cycle at 25°C.

extract_protocol:
After 3 days post-injection, five samples with three individuals were collected for each time point and sex and flash-frozen in liquid nitrogen. For adult parts, seven adults were collected one day after emergence, between 7 and 8 days after pupae injection. Adults were flash-frozen in liquid nitrogen, then immediately dissected apart on ice into head, thorax, and abdomen, and finally flash-frozen back in liquid nitrogen. All samples were stored at −80 °C until RNA extraction. For 1 day-old embryo (parental RNAi), F0 female pupae 8 days after oviposition were injected as described above, kept until emergence, and then crossed with uninjected AsymCX males or kept virgin. Every female was then set up individually with one host, changed every 4 hours. Virgin females produce only male progeny while mated females produce between 90-95% females. Batches of 100 embryos were collected  24 hours later by dissecting the host, transfer into a microcentrifugation tube on ice without buffer, flash-frozen in liquid nitrogen, and stored at −80 °C until RNA extraction. Total RNA was extracted with Quick-RNA Tissue/Insect Kit coupled with on column DNase treatment (ZymoResearch - R2030) according to manufacturer's protocol.
Library preparation was performed at the Novogene (HK) Company Limited. Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Sequencing libraries were paired-end sequenced (150 bp read-length) on an Illumina NovaSeq platform.

treatment_protocol: Larval RNAi knockdown was induced in AsymCX males or females at 4, 6, and 8 days after oviposition. Larvae at 4 and 6 days were injected on PBS-1%agar plates. After injection, the 4 day-old larvae were transferred back to host (6-8 per host) and sealed with the host shell, while 6 day-old larvae were kept on the PBS-agar plate. Pupae at 8 days were fixed on microscopy slides with double-sided tape, inject, and kept until emergence. Larvae and pupae were injected in the posterior part with 4 μg/μl dsx or GFP dsRNA diluted in milliQ water mixed with red food dye in the ratio 9:1. Injections were performed using custom made capillary needles and a Femtojet (Eppendorf).

value: thorax

tag: strain

value: AsymCX

tag: Sex

value: Male

tag: developmental stage

value: adult

tag: treatment

value: GFP-RNAi


title: F_84_2

city: Tsu

first: Yuhei

last: Nishimura

state: Mie

address: 2-174 Edobashi

department: Integrative Pharmacology

country: Japan

institute: Mie University Graduate School of Medicine

description: Library name: F_84_2

data_processing:
Sequencing of 150-bp paired-end reads was conducted using a HiSeq X Ten system (Illumina).
Assembly: Quantification of gene expression was conducted using Danio_rerio.GRCz11.cdna.all.fa as described previously (Kashima et al., 2022).
Supplementary files format and content: csv (count.csv and metadata.csv)

organism: Danio rerio

source_name: whole body

extract_protocol:
total RNA was extracted from each larva using Direct-TRI, and RNA concentrations were determined using a QuantiFluor RNA System Kit with a Quantus Fluorometer.
a library was prepared for RNA-Seq as described previously (Kamitani et al., 2019, Taya et al., 2025).

value: whole body

tag: hpf

tag: idents


title: FX_84_2

description: Library name: FX_84_2


title: FX_60_2

description: Library name: FX_60_2


title: ccRCC tumor Spatial RNA-seq P_16

description: Corresponds to bulk sample afd5


title: Male, GFP-RNAi, Thorax, replicate 2


title: Male, GFP-RNAi, Thorax, replicate 1


title: F_60_2

description: Library name: F_60_2


title: ccRCC tumor Spatial RNA-seq P_15

description: Corresponds to bulk sample 001a


title: F_37_2

description: Library name: F_37_2


title: FX_36_2

description: Library name: FX_36_2


title: Male, GFP-RNAi, Head, replicate 4

source_name: head

value: head


title: FX_37_2

description: Library name: FX_37_2


title: ccRCC tumor Spatial RNA-seq P_14

description: Corresponds to bulk sample f544


title: Male, GFP-RNAi, Head, replicate 5


title: ccRCC tumor Spatial RNA-seq P_13

description: Corresponds to bulk sample 0d2e


title: F_36_2

description: Library name: F_36_2


title: Male, GFP-RNAi, Head, replicate 3


title: HemECs, sh-NC, independent run 3

status: Public on Jul 09 2026

city: Jinan

first: Zheren

last: Su

address: No. 324, Jingwu Road

department: Plastic and Cosmetic Surgery

country: China

institute: Shandong Provincial Hospital

description:
Library name: Sample 3
L1EIJ1000723-sh_nc_3

data_processing:
Sequencing was performed on the Illumina NovaSeq X Plus platform using paired-end 150 bp reads (PE150) with the NovaSeq Reagent Kit.
The raw paired end reads were trimmed and quality controlled by fastp (Version 0.23.4) with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (Version 2.2.1) software.
The mapped reads of each sample were assembled by StringTie (Version 2.2.1) in a reference-based approach.
Gene-level expression was quantified using RSEM (Version 1.3.3) to calculate TPM (transcripts per million) values.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes TPM values for all samples

source_name: infantile hemangioma endothelial cells (HemECs)

growth_protocol: HemECs were cultured in complete Endothelial Cell Medium (ECM; ScienCell, 1001), supplemented with 5% fetal bovine serum (FBS), 1% endothelial cell growth supplement (ECGS), and 1% penicillin-streptomycin (P/S). Cells were cultured under normoxic (21% O₂, 5% CO₂) conditions in CO₂ incubators (Thermo Fisher).

extract_protocol:
Total RNA was extracted from cultured HemECs using TRIzol® Reagent according the manufacturer’s instructions.
RNA-seq transcriptome library was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA).

treatment_protocol: EPAS1 knockdown lentiviruses were constructed using the GV493 vector by Shanghai GeneChem (China), with the target sequence CAGTACCCAGACGGATTTCAA for sh-EPAS1. The negative control lentivirus (sh-NC) contained a non-targeting shRNA sequence (TTCTCCGAACGTGTCACGT). HemECs were infected with sh-NC or sh-EPAS1 lentivirus, followed by puromycin selection.

tag: cell type

tag: genotype

value: sh-NC


title: FX_60_1

description: Library name: FX_60_1


title: ccRCC tumor Spatial RNA-seq P_12

description: Corresponds to bulk sample 43eb


title: Male, GFP-RNAi, Head, replicate 2


title: F_60_1

description: Library name: F_60_1


title: F_84_1

description: Library name: F_84_1


title: FX_37_1

description: Library name: FX_37_1


title: Male, GFP-RNAi, Head, replicate 1


title: F_37_1

description: Library name: F_37_1


title: FX_36_1

description: Library name: FX_36_1


title: ccRCC tumor Spatial RNA-seq P_11

description: Corresponds to bulk sample bc24


title: ccRCC tumor Spatial RNA-seq P_10

description: Corresponds to bulk sample 764b


title: F_36_1

description: Library name: F_36_1


title: ccRCC tumor Spatial RNA-seq P_9

description: Corresponds to bulk sample fa13


title: Male, GFP-RNAi, F1 embryo, replicate 4

source_name: embryo

value: embryo

value: 1 day


title: C_84_6

description: Library name: C_84_6


title: RNA-seq in BACH1-overexpressing (BACH1 cDNA vector) wild-type BMDMs treated with LPS (4h) (rep1)

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

description: Library name: mm_BMDM_RNA_WT_BACH1_VECTOR_DOX_LPS4h_rep1.fastq.gz

data_processing:
[mm_RNA_Lung_*.bw, mm_BMDM_RNA_*.bw]
alignment to mm10 reference genome with HISAT2 (v2.1.0) using default parameters
transcript assembly with StringTie (v1.3.4d)
BAM file indexing with SAMtools (v1.7)
coverage (bigwig) file generation with bamCoverage program of deepTools (v3.0.2)
[mm_ATAC_AM_*.bedgraph.gz]
alignment to mm10 reference genome with BWA v0.7.10 using default parameters
bam generation with SAMtools v1.7 using default parameters
tag directory generation with HOMER's makeTagDirectory using -checkGC parameter
generation of coverage (bedgraph) files with HOMER's makeUCSCfile using -fsize 1e50 -norm parameters
peak prediction with callpeak function of MACS2
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: bedgraph
[mm_BMDM_C57_ATAC_*.bw]
alignment to mm10 reference genome with BWA v0.7.10 using default parameters
bam generation with SAMtools v1.7 using default parameters
tag directory generation with HOMER's makeTagDirectory using -checkGC parameter
generation of coverage (bedgraph) files with HOMER's makeUCSCfile followed by conversation to bigwig using UCSC bedGraphToBigWig
peak prediction with callpeak function of MACS2

organism: Mus musculus

source_name: bone marrow-derived macrophage

growth_protocol:
For the alveolar macrophages (AMs) profiling experiment, tissue-derived CD45.1⁺ WT and CD45.2⁺ Bach1 fl/flLyz2-Cre alveolar macrophages (AMs) were FAC-Sorted from Bone Marrow chimeric mice (lethally irradiated recipients ≥8 weeks after transfer of a 1:1 mixture of donor BM cells).
For the alveolar macrophages (AMs) profiling experiment, WT and Bach1 fl/flLyz2-Cre alveolar macrophages (AMs) were FAC-Sorted and were lysed with the following lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL). After lysis, nuclei were subjected to tagmentation. Nextera DNA Library Prep Kit was used for library generation according to manufacturer's protocol.
For the Lentiviral transduction of BMDMs, a high titer (>1x108 TU/ml) lentiviral vector containing the full-length cDNA of mouse BACH1 was designed and ordered as packaged virus from VectorBuilder (pLV[Exp]-Neo-CMV>3xFLAG/mBach1). Transduction efficiency was tested with control virus: pLV[Exp]-EGFP/Puro-EF1A>mCherry. 5x105 BMDMs were transduced at Day 3 of differentiation at MOI:5 and used for RNA-seq after 48-72 hours in the presence of 10ug/ml doxycycline.
For the Lentiviral transduction of BMDMs, a high titer (>1x108 TU/ml) lentiviral vector containing the full-length cDNA of mouse BACH1 was designed and ordered as packaged virus from VectorBuilder (pLV[Exp]-Neo-CMV>3xFLAG/mBach1). Transduction efficiency was tested with control virus: pLV[Exp]-EGFP/Puro-EF1A>mCherry. 5x105 BMDMs were transduced at Day 3 of differentiation at MOI:5 and used for ATAC-seq after 48-72 hours in the presence of 10ug/ml doxycycline.

extract_protocol:
AMs were sorted directly to 500μl Tri Reagent (MRC) and total RNA was isolated according to the manufacturer’s protocol.
Indexed cDNA libraries were prepared following the TruSeq™ RNA Sample Preparation Kit (Illumina, Inc.) protocol.
WT and Bach1 fl/flLyz2-Cre alveolar macrophages (AMs) were FAC-Sorted and were lysed with the following lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL).
Nextera DNA Library Prep Kit was used for library generation according to manufacturer's protocol.
Total RNA was extracted from transduced BMDMs 48–72 hours post-transduction.
Indexed cDNA libraries were prepared following the TruSeq™ RNA Sample Preparation Kit (Illumina, Inc.) protocol.

value: bone marrow-derived macrophage

value: wild-type

value: doxycycline, LPS (4h)


title: C_60_6

description: Library name: C_60_6


title: X_60_6

description: Library name: X_60_6


title: ccRCC tumor Spatial RNA-seq P_7

description: Corresponds to bulk sample eebb


title: ccRCC tumor Spatial RNA-seq P_8

description: Corresponds to bulk sample 9f6a


title: X_84_6

description: Library name: X_84_6


title: Male, GFP-RNAi, F1 embryo, replicate 3


title: Male, GFP-RNAi, F1 embryo, replicate 2


title: TRA_F14_3N_FH_A53

city: Nanjing

first: Xuan

last: Li

address: No. 666, Binjiang Avenue, Jiangbei New Area

institute: Nanjing Agricultural University

description:
Library name: A53
TRA_F14_3N_FH_A53

data_processing:
Alignment was performed with STAR (v2.7.11a) against the reference genome using a pre-built STAR genome index. STAR was run with “--outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts” to generate sorted alignment files and gene-level count profiles. Gene-level expression quantification was carried out using RSEM (v1.3.1) with STAR-generated transcriptome BAM files as input (--paired-end --no-bam-output --alignments).
Assembly: Nasonia vitripennis reference genome (RefSeq No. GCF_009193385.2, NCBI GenBank)
Supplementary files format and content: Tab-delimited text file includes raw counts and tpm value for each sample

molecule: polyA RNA

source_name: Head

extract_protocol:
RNA extraction was performed using Quick-RNATM Tissue/Insect Microprep (Catalogue No. R2030 Zymo Research, Germany) (without DNase treatment). For sequencing, RNA was resuspended in 10 µL DNase/RNase-free water and the RNA concentration and purity was measured using a fluorometer (Qubit 2.0, Life Technologies); poor quality samples judged by A260/A280 and A260/A230 ratios were discarded. The extracted RNA was sent to Novogene (UK) Company Limited for sequencing. Novogene Hongkong prepared the sample library.
Unique index codes were added to each sample using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, USA). mRNA was purified from total RNA using poly-T magnetic beads, and libraries were prepared according to the manufacturer's instructions (Illumina).

value: Head

value: female

tag: age

value: 1 day after emergence

value: TRA


title: Male, GFP-RNAi, F1 embryo, replicate 1


title: X_36_6

description: Library name: X_36_6


title: C_36_6

description: Library name: C_36_6


title: C_37_6

description: Library name: C_37_6


title: X_84_5

description: Library name: X_84_5


title: ccRCC tumor Spatial RNA-seq P_5

description: Corresponds to bulk sample 8bbc

value: Kidney

value: renal cell cancer

value: Clear cell renal cell carcinoma


title: C_84_5

description: Library name: C_84_5


title: Male, GFP-RNAi, Abdomen, replicate 5

source_name: abdomen

value: abdomen

value: AsymCX

value: Male

value: adult


title: Male, GFP-RNAi, Abdomen, replicate 4

value: GFP-RNAi


title: X_60_5

description: Library name: X_60_5

value: whole body


title: C_60_5

description: Library name: C_60_5


title: ccRCC tumor Spatial RNA-seq P_3

description: Corresponds to bulk sample e38f


title: X_36_5

description: Library name: X_36_5


title: Male, GFP-RNAi, Abdomen, replicate 2


title: X_84_4

description: Library name: X_84_4


title: ccRCC tumor Spatial RNA-seq P_1


title: Male, GFP-RNAi, 9  day, replicate 5

source_name: larvae

value: larvae

value: 9 day


title: ccRCC tumor bulk RNA-seq f1a2

description:
f1a2
processed data file column header:
f1a2

data_processing:
RNA fastq files were aligned to the human reference genome using  kallisto (version 0.46.2)
Assembly: Genome build: GRCh38, release 97
Supplementary files format and content: tab-delimited text files include read counts for each Sample

extract_protocol:
Total RNA was extracted from formalin-fixed paraffin embedded (FFPE) tumours using the Allprep DNA/RNA FFPE Kits according to the manufacturer’s instructions (Qiagen, #80234). The sizing, quantitation, integrity and purity of all samples were measured using the 2100 Bioanalyzer instrument (Agilent).
Sequencing libraries were prepared by IntegraGen as described in Foley et al (Genome Research, 2019) and sequenced with the Illumina NovaSeq.


title: X_37_4

description: Library name: X_37_4


title: Male, GFP-RNAi, 9  day, replicate 4


title: C_37_4

description: Library name: C_37_4


title: X_36_4

description: Library name: X_36_4


title: Male, GFP-RNAi, 9  day, replicate 3


title: ccRCC tumor bulk RNA-seq fa13

description:
fa13
processed data file column header:
fa13


title: C_36_4

description: Library name: C_36_4


title: Male, GFP-RNAi, 9  day, replicate 2


title: X_60_3

description: Library name: X_60_3


title: Male, GFP-RNAi, 9  day, replicate 1


title: ccRCC tumor bulk RNA-seq e907

description:
e907
processed data file column header:
e907


title: X_37_3

description: Library name: X_37_3


title: Male, GFP-RNAi, 7 day, replicate 5

value: 7 day


title: ccRCC tumor bulk RNA-seq cdbf

description:
cdbf
processed data file column header:
cdbf


title: FX_84_1

description: Library name: FX_84_1


title: ccRCC tumor bulk RNA-seq 5306

description:
5306
processed data file column header:
5306


title: C_36_3

description: Library name: C_36_3


title: X_84_2

description: Library name: X_84_2


title: Male, GFP-RNAi, 7 day, replicate 3


title: Male, GFP-RNAi, F1 embryo, replicate 5

value: embryo

value: 1 day


title: C_84_2

description: Library name: C_84_2


title: ccRCC tumor bulk RNA-seq 4a14

description:
4a14
processed data file column header:
4a14


title: X_37_6

description: Library name: X_37_6


title: Male, GFP-RNAi, 7 day, replicate 2


title: ccRCC tumor Spatial RNA-seq P_6

description: Corresponds to bulk sample 39c4


title: C_60_2

description: Library name: C_60_2


title: RNA-seq in wild-type alveolar macrophages from bone marrow-chimeric mice (rep3)

description: Library name: mm_RNA_Lung_AM_WT_CD45_1_rep3

source_name: alveolar macrophage

value: alveolar macrophage

value: wild-type

value: untreated


title: ccRCC tumor bulk RNA-seq 0c10

description:
0c10
processed data file column header:
0c10

value: Kidney


title: ccRCC tumor Spatial RNA-seq P_4

description: Corresponds to bulk sample 40ba

value: renal cell cancer


title: X_37_5

description: Library name: X_37_5


title: Male, GFP-RNAi, 7 day, replicate 1


title: C_36_5

description: Library name: C_36_5


title: C_37_5

description: Library name: C_37_5


title: X_37_2

description: Library name: X_37_2


title: ccRCC tumor Spatial RNA-seq P_2

description: Corresponds to bulk sample 547f

value: Clear cell renal cell carcinoma


title: Male, GFP-RNAi, Abdomen, replicate 1

value: abdomen


title: C_37_2

description: Library name: C_37_2


title: X_60_4

description: Library name: X_60_4


title: C_84_4

description: Library name: C_84_4


title: X_36_2

description: Library name: X_36_2


title: Male, GFP-RNAi, 11 day, replicate 5

source_name: pupae

value: pupae

value: AsymCX

value: 11 day


title: ccRCC tumor bulk RNA-seq f839

description:
f839
processed data file column header:
f839


title: C_36_2

description: Library name: C_36_2


title: C_60_4

description: Library name: C_60_4


title: ccRCC tumor bulk RNA-seq 1ec1

description:
1ec1
processed data file column header:
1ec1


title: ccRCC tumor bulk RNA-seq 5b96

description:
5b96
processed data file column header:
5b96


title: X_84_1

description: Library name: X_84_1


title: Male, GFP-RNAi, 11 day, replicate 4

value: Male

value: GFP-RNAi


title: C_84_1

description: Library name: C_84_1

value: whole body


title: X_60_1

description: Library name: X_60_1


title: ccRCC tumor bulk RNA-seq 13c2

description:
13c2
processed data file column header:
13c2


title: Male, GFP-RNAi, 11 day, replicate 3


title: X_84_3

description: Library name: X_84_3


title: C_60_1

description: Library name: C_60_1


title: brain, 699_Hip, hippocampus

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

country: USA

institute: University of Wisconsin Madison

description:
Library name: 699_Hip
699_Hip

data_processing:
Alignment (STAR)
Read counts (Rsubread)
Differential expression analysis (DEseq2 R package)
Annotation
Assembly: ARS-UI_Ramb_v3.0
Supplementary files format and content: read counts

organism: Ovis aries

source_name: Brain

extract_protocol:
RNA were extracted with either TRIzol reagent  (for sheep samples) or  Zymo Quick-RNA miniprep plus extraction kit (rat samples) followed by DNase I treatment before RNA sequencing.
RNA sequencing was performed for all samples using the NovaSeq X Plus platform with two 25B lanes, using V1.0 sequencing kits, and as 150 bp paired-end reads. Sheep RNA-Seq libraries were prepared with the Kapa Hyper Stranded mRNA library kit. Rat RNA-Seq libraries were prepared with the Watchmaker Stranded mRNA library kit. The libraries were pooled, quantified by qPCR, and sequenced on one 25B lane for 151 cycles from both ends of the fragments.

treatment_protocol: No specific treatment was applied.

value: Brain


title: ccRCC tumor bulk RNA-seq 0a58

description:
0a58
processed data file column header:
0a58


title: X_37_1

description: Library name: X_37_1


title: Male, GFP-RNAi, 11 day, replicate 2


title: C_37_1

description: Library name: C_37_1


title: ccRCC tumor bulk RNA-seq e846

description:
e846
processed data file column header:
e846


title: X_36_1

description: Library name: X_36_1


title: Male, GFP-RNAi, 11 day, replicate 1


title: C_84_3

description: Library name: C_84_3


title: C_36_1

description: Library name: C_36_1


title: ccRCC tumor bulk RNA-seq bcf3

description:
bcf3
processed data file column header:
bcf3


title: Des 1383 P4

type: RNA

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

institute: University of Pittsburgh

hyb_protocol: 15-μg of purified, amplified, biotin-labeled cRNA was fragmented and hybridized to an Affymetrix Mouse ClariomTM S array (ThermoFisher Scientific 902930) for 18 hours.

scan_protocol: Washing, staining, and scanning of arrays were performed on an Affymetrix Fluidics Station 450 and Scanner 3000 immediately after hybridization according to manufacturer’s instructions (ThermoFisher Scientific 00-0079, 00-0210).

data_processing:
Scanned microchips (in .Cel format) were imported in Transcription Analysis Software (TAC software, ThermoFisher Scientific version 2.0) and compared statistically.
The data were analyzed with Microarray Suite version 2.0  using Affymetrix default analysis settings and global scaling as normalization method. T

label: biotin

source_name: primary fibroblasts

label_protocol: In-vitro transcription was performed with 100 ng of purified total RNA using the MessageAmp Premier Enhanced assay protocol (Fisher Scientific).

growth_protocol: Primary fetal mouse lung fibroblasts were prepared from E18.5 fetal mice, plated in 10cm culture plates and maintained in Waymouth media supplemented with 10% fetal bovine serum.

extract_protocol: Total cellular RNA was isolated from mouse fetal lung fibroblasts following the TRIzol (Ambion, USA) extraction protocol. The concentration and purity (RIN No.) of RNA were determined using a NanoDrop spectrophotometer and the Bioanalyzer.

treatment_protocol: Prepared primary fetal mouse lung fibroblasts were cultured in 6 well plates and treated for 6 hours with 10-6M DES-Cic, dexamethasone and control media.

value: lung E18.5 fetal mouse


title: ccRCC tumor bulk RNA-seq b0a3

description:
b0a3
processed data file column header:
b0a3


title: Des 1368 P3


title: Male, dsx-RNAi, Thorax, replicate 5

value: thorax

value: adult

value: dsx-RNAi


title: Des 1360 P5


title: ccRCC tumor bulk RNA-seq 5f15

description:
5f15
processed data file column header:
5f15


title: Male, dsx-RNAi, Thorax, replicate 4


title: Des 1335 P4


title: ccRCC tumor bulk RNA-seq ad26

description:
ad26
processed data file column header:
ad26


title: C_37_3

description: Library name: C_37_3


title: Cil 1383 P7


title: C_60_3

description: Library name: C_60_3


title: Male, dsx-RNAi, Thorax, replicate 3


title: Cil 1368 P4


title: Male, dsx-RNAi, Thorax, replicate 2


title: ccRCC tumor bulk RNA-seq 9589

description:
9589
processed data file column header:
9589


title: Cil 1360 P8


title: Dex 1383 P2


title: Male, dsx-RNAi, Thorax, replicate 1


title: Dex 1335 P3


title: Dex 1360 P4


title: ccRCC tumor bulk RNA-seq 0c25

description:
0c25
processed data file column header:
0c25


title: Dex 1368 P1


title: Veh 1383 P5


title: ccRCC tumor bulk RNA-seq 9347

description:
9347
processed data file column header:
9347


title: Male, dsx-RNAi, Head, replicate 4

value: head


title: Veh 1383 P6


title: Veh 1360 P2


title: Male, dsx-RNAi, Head, replicate 3


title: ccRCC tumor bulk RNA-seq 42a1

description:
42a1
processed data file column header:
42a1


title: ccRCC tumor bulk RNA-seq a667

description:
a667
processed data file column header:
a667


title: ccRCC tumor bulk RNA-seq 9fe7

description:
9fe7
processed data file column header:
9fe7


title: Male, dsx-RNAi, Head, replicate 2


title: Mixture of MCF10A and HCT116, 10Gy radiation, day 2, bio rep 1

city: Toronto

first: Gregory

last: Schwartz

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

description: Library name: Sample 16

data_processing:
fastp was used for QC and adaptor trimming, reads were aligned with STAR, featureCounts was used to obtain gene counts
Assembly: GRCh38
Supplementary files format and content: tsv files outlining the counts per gene

source_name: HCT116 + MCF10A

extract_protocol:
TriZol reagent (Life Technologies, 15596018)
Illumina Stranded mRNA Prep

tag: cell line

value: HCT116 + MCF10A


title: Mixture of MCF10A and HCT116, non-treated, day 2, bio rep 3

description: Library name: Sample 15


title: Mixture of MCF10A and HCT116, 10Gy radiation, day 2, bio rep 3

description: Library name: Sample 18


title: Mixture of MCF10A and HCT116, 10Gy radiation, day 2, bio rep 2

description: Library name: Sample 17


title: Male, dsx-RNAi, Head, replicate 5


title: ccRCC tumor bulk RNA-seq afd5

description:
afd5
processed data file column header:
afd5

value: Kidney


title: HCT116, 10Gy radiation, day 2, bio rep 1

description: Library name: Sample 10


title: HCT116, non-treated, day 2, bio rep 3

description: Library name: Sample 9


title: Male, dsx-RNAi, F1 embryo, replicate 2

value: embryo

value: 1 day


title: HCT116, non-treated, day 2, bio rep 2

description: Library name: Sample 8


title: Male, dsx-RNAi, F1 embryo, replicate 1


title: X_36_3

description: Library name: X_36_3


title: ccRCC tumor bulk RNA-seq 001a

description:
001a
processed data file column header:
001a

value: renal cell cancer

value: Clear cell renal cell carcinoma


title: M14KD, rep4

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
Reads were aligned to the mouse transcriptome (Ensembl version 111) using kallisto and transcript counts were converted to gene counts using tximport.
Assembly: Mouse ensembl version 111
Supplementary files format and content: CSV of gene counts

growth_protocol: Normal aTC6 growth media. Cells reverse transfected at 70% confluency

extract_protocol:
Trizol with Qiagen columns
Stranded mRNA Library

treatment_protocol: collected 72h post-KD

value: METTL14 KD


title: MCF10A, 10Gy radiation, day 2, bio rep 2

description: Library name: Sample 5


title: F_36_5

description: Library name: F_36_5


title: M14KD, rep2


title: MCF10A, 10Gy radiation, day 2, bio rep 1

description: Library name: Sample 4


title: ccRCC tumor bulk RNA-seq 1aeb

description:
1aeb
processed data file column header:
1aeb


title: Male, dsx-RNAi, F1 embryo, replicate 5

value: AsymCX


title: ccRCC tumor bulk RNA-seq 4341

description:
4341
processed data file column header:
4341


title: Mixture of MCF10A and HCT116, non-treated, day 2, bio rep 2

description: Library name: Sample 14


title: HCT116, 10Gy radiation, day 2, bio rep 3

description: Library name: Sample 12


title: ccRCC tumor bulk RNA-seq aac3

description:
aac3
processed data file column header:
aac3


title: Male, GFP-RNAi, 7 day, replicate 4

value: larvae

value: Male

value: 7 day


title: Male, dsx-RNAi, F1 embryo, replicate 3


title: ccRCC tumor bulk RNA-seq 9f6a

description:
9f6a
processed data file column header:
9f6a


title: ccRCC tumor bulk RNA-seq 5a8f

description:
5a8f
processed data file column header:
5a8f


title: M14KD, rep1


title: CLRN1 knockout rabbit retina pool, 10 months, 3 biological replicates

city: Ann Arbor

first: Dongshan

last: Yang

address: 2800 Plymouth Rd

institute: University of Michigan

description:
Library name: Pool2_KO
Pooled nuclei from 3 CLRN1 knockout rabbits at 10 months. Tissue: 5mm retinal visual streak punch (2-3mm ventral to medullary rays). SNP-based demultiplexing with Vireo assigned nuclei to individual animals.

data_processing:
Raw sequencing reads were processed using Cell Ranger v7.0 aligned to rabbit reference genome OryCun2.0. SNP-based demultiplexing performed with cellsnp-lite and Vireo to assign nuclei to individual animals. Quality control filtering retained nuclei with >500 genes, <5% mitochondrial reads, and 500-50,000 total UMI counts. Data integration and cell type annotation performed using Seurat v4.3.0. Differential expression analysis using DESeq2 v1.38.0 with pseudobulk aggregation.
Assembly: OryCun2.0
Supplementary files format and content: Tab-delimited text files. GSE_raw_counts.txt.gz: gene expression matrix with genes as rows and cells as columns (raw UMI counts).
Supplementary files format and content: GSE_umap_coordinates.txt: UMAP dimensional reduction coordinates for visualization.
Supplementary files format and content: GSE_cell_metadata.txt.gz: cell-level metadata including sample ID, genotype, QC metrics(nCount_RNA, nFeature_RNA, percent_mt), cell type annotation, and cluster assignment.

organism: Oryctolagus cuniculus

source_name: retina

extract_protocol:
5mm retinal punch from visual streak region (2-3mm ventral to medullary rays) was collected from each animal and snap-frozen in liquid nitrogen. Nuclei were isolated using 10x Genomics Chromium Nuclei Isolation Kit according to manufacturer's protocol. Nuclei from 3 biological replicates were pooled at equal concentration (target 10,000 nuclei total) prior to library preparation.
10x Genomics Chromium Single Cell 3' v3.1 following manufacturer's protocol.

value: retina

value: retinal nuclei

value: CLRN1 knockout

value: 10 Months


title: Male, dsx-RNAi, Abdomen, replicate 2

value: abdomen

value: adult

value: dsx-RNAi


title: ccRCC tumor bulk RNA-seq 3d43

description:
3d43
processed data file column header:
3d43

value: Kidney


title: HCT116, non-treated, day 2, bio rep 1

description: Library name: Sample 7


title: M3KD, rep4

value: METTL3 KD


title: Male, dsx-RNAi, Abdomen, replicate 1


title: MCF10A, non-treated, day 2, bio rep 2

description: Library name: Sample 2


title: Male, dsx-RNAi, Abdomen, replicate 5


title: ccRCC tumor bulk RNA-seq 5445

description:
5445
processed data file column header:
5445


title: MCF10A, 10Gy radiation, day 2, bio rep 3

description: Library name: Sample 6


title: M3KD, rep3


title: MCF10A, non-treated, day 2, bio rep 1

description: Library name: Sample 1


title: M3KD, rep2


title: Male, dsx-RNAi, 9  day, replicate 4

value: 9 day


title: ccRCC tumor bulk RNA-seq b1b9

description:
b1b9
processed data file column header:
b1b9

value: renal cell cancer


title: M14KD, rep3


title: oeCD300A-3

city: Taiyuan

first: Fengjing

last: Wang

address: 56 Xinjian South Road, Yingze District, Taiyuan, Shanxi, 030001, China

institute: 山西医科大学

description: Library name: Sample6

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean  reads were separately aligned to reference genome with orientation mode using HISAT2 software.
Assembly: GRCh38/hg38
Supplementary files format and content: gene.TPM.matrix.annotation

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions . The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA.

value: Human acute monocytic leukemia cell line


title: M3KD, rep1


title: Male, dsx-RNAi, 9  day, replicate 3


title: ccRCC tumor bulk RNA-seq f544

description:
f544
processed data file column header:
f544

value: Clear cell renal cell carcinoma


title: Male, dsx-RNAi, Abdomen, replicate 4

value: AsymCX


title: ccRCC tumor bulk RNA-seq fc18

description:
fc18
processed data file column header:
fc18


title: vector-3

description: Library name: Sample5

value: WT


title: Male, dsx-RNAi, 9  day, replicate 2

value: larvae

value: Male


title: oeCD300A-2

description: Library name: Sample4


title: SCR, rep3

value: scramble control


title: SCR, rep2


title: vector-2

description: Library name: Sample3


title: ccRCC tumor bulk RNA-seq 54f9

description:
54f9
processed data file column header:
54f9


title: Male, dsx-RNAi, 9  day, replicate 1


title: SCR, rep1


title: ccRCC tumor bulk RNA-seq 0387

description:
0387
processed data file column header:
0387


title: Male, dsx-RNAi, 7 day, replicate 5

value: 7 day


title: Male, dsx-RNAi, 7 day, replicate 4


title: mouse-DRG-cKO-rep4

city: Shenzhen

first: Jian

last: Zhang

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

description: Library name: sample8

data_processing:
The raw data was filtered with SOAPnuke (v1.6.5) , afterwards clean reads were obtained and stored in FASTQ format.
The clean data were mapped to the reference genome GRCm38/mm10 by HISAT (v2.2.1)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5). The expression level of genes was calculated by RSEM (v1.3.1).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: dorsal root ganglia

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen,15596026)
Optimal Dual-mode mRNA Library Prep Kit

value: dorsal root ganglia


title: vector-1

description: Library name: Sample1


title: mouse-DRG-cKO-rep3

description: Library name: sample7


title: Male, dsx-RNAi, 7 day, replicate 3


title: Male, dsx-RNAi, Abdomen, replicate 3


title: ccRCC tumor bulk RNA-seq 15ab

description:
15ab
processed data file column header:
15ab

source_name: Kidney


title: KO_D7_rep4

first: Shigeki

last: Iwase

state: MI

address: 1241 E. Catherine St., 5815 Medical Science II

department: Department of Human Genetics

institute: University of Michigan Medical School

description:
Library name: 11876-BZ-36
RAI1 knockout mutant iNeuron Day 7 biological replicate 4

data_processing:
Adapter trimming and quality filtering were performed using Cutadapt v4.8.
Sequencing quality was assessed using FastQC v0.11.8 and summarized with MultiQC v1.20.
Trimmed reads were aligned to the human reference genome using STAR v2.7.8a.
Gene-level expression estimates were generated using RSEM v1.3.3.
Differential expression and downstream analyses were performed using count matrices generated from the RNA-seq workflow.
Assembly: GRCh38 (Ensembl release 109)
Supplementary files format and content: Gene-level raw read count matrix generated from RNA-seq data. Rows correspond to genes and columns correspond to individual biological samples.
Supplementary files format and content: Raw count values were generated using RSEM following alignment to the GRCh38 (Ensembl release 109) reference genome and are provided as tab-delimited text files.

source_name: hESC (H9)

growth_protocol: H9 hESC lines (WT and RAI1 mutant) were maintained on Geltrex-coated plates in mTeSR Plus medium and dissociated using Accutase. Cells were supplemented with 10 μM ROCK inhibitor (Y-27632) during plating/recovery.

extract_protocol:
Total RNA was isolated using TRIzol reagent followed by purification with the RNeasy Mini Kit according to the manufacturers’ instructions.
RNA-seq libraries were prepared using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) v2 and the NEBNext UltraExpress RNA Library Prep Kit, and sequenced on an Illumina NovaSeq X Plus platform (151 bp paired-end).

treatment_protocol: Neuronal differentiation was induced by doxycycline-dependent NGN2 expression. Cells were harvested at days 0, 3, and 7 of differentiation. Cultures were maintained in Neurobasal-A medium supplemented with GlutaMAX, B27, GDNF, NT3, and CultureOne (with doxycycline as indicated during induction).

value: hESC (H9)

value: iNeuron

value: RAI1 Knockout

value: NGN2-induced neuronal differentiation

tag: time

tag: batch


title: mouse-DRG-cKO-rep2

description: Library name: sample6


title: ccRCC tumor bulk RNA-seq d5f0

description:
d5f0
processed data file column header:
d5f0

value: Kidney


title: KO_D7_rep3

description:
Library name: 11876-BZ-35
RAI1 knockout mutant iNeuron Day 7 biological replicate 3


title: ccRCC tumor bulk RNA-seq 4c26

description:
4c26
processed data file column header:
4c26


title: mouse-DRG-cKO-rep1

description: Library name: sample5


title: Male, dsx-RNAi, 7 day, replicate 1

value: dsx-RNAi


title: KO_D7_rep2

description:
Library name: 11876-BZ-34
RAI1 knockout mutant iNeuron Day 7 biological replicate 2


title: ccRCC tumor bulk RNA-seq 0d2e

description:
0d2e
processed data file column header:
0d2e


title: Male, dsx-RNAi, 11 day, replicate 5

value: pupae

value: 11 day


title: mouse-DRG-WT-rep4

description: Library name: sample4


title: KO_D7_rep1

description:
Library name: 11876-BZ-33
RAI1 knockout mutant iNeuron Day 7 biological replicate 1


title: ccRCC tumor bulk RNA-seq 726d

description:
726d
processed data file column header:
726d

value: renal cell cancer


title: mouse-DRG-WT-rep3

description: Library name: sample3


title: Male, dsx-RNAi, 11 day, replicate 4


title: HET_D7_rep4

description:
Library name: 11876-BZ-32
RAI1 heterozygous mutant iNeuron Day 7 biological replicate 4

value: RAI1 Het


title: ccRCC tumor bulk RNA-seq dcbf

description:
dcbf
processed data file column header:
dcbf

value: Clear cell renal cell carcinoma


title: X_60_2

description: Library name: X_60_2

source_name: whole body

value: whole body


title: Male, dsx-RNAi, 11 day, replicate 3

value: AsymCX


title: mouse-DRG-WT-rep2

description: Library name: sample2


title: HET_D7_rep3

description:
Library name: 11876-BZ-31
RAI1 heterozygous mutant iNeuron Day 7 biological replicate 3


title: MCF10A, non-treated, day 2, bio rep 3

description: Library name: Sample 3


title: HET_D7_rep2

description:
Library name: 11876-BZ-30
RAI1 heterozygous mutant iNeuron Day 7 biological replicate 2


title: Male, dsx-RNAi, 11 day, replicate 2

value: Male


title: ccRCC tumor bulk RNA-seq b45e

description:
b45e
processed data file column header:
b45e


title: IFN gamma Treated 4

city: Chicago

first: Aiyu

last: Gong

state: IL

address: 1735 W. Harrison St

department: MPI

institute: Rush University

description: Gene expression

data_processing:
Base-calling sofeware, version, parameters;
BGI SOAPnuke v1.5.2 software used for basecalling.
Sequencing data filtering:this project uses the filtering software SOAPnuke developed by BGI independently for filtering. Software Information:  SOAPnuke:Version v1.5.2; Parameters -l 15 -q 0.2 -n 0.05
Data filtering steps; 1) Remove the reads containing the adaptor (adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" are saved in FASTQ format.
Read alignment: Align to the reference genome: After getting clean reads, used HISAT to align the clean reads to the reference genome. Software Information: HISAT2;  Version：v2.0.4; Parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF
Assembly: mm10; Reference species: Species：Mus_musculus; Source：NCBI;  Reference Genome Version：GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include gene expression RPKM values level for each Sample

source_name: IEC 4.1

extract_protocol:
IEC 4.1 cells were harvested, and RNA were extract using Rneasy Mini Kit (QIAGEN Cat. No. 74104).  Agilent 2100 or Fragment Analyzer was used to detect thequality of RNA. 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using DNBSEQ platform

value: IEC 4.1

value: Intestinal Epithelium

value: Interferon Gamma Treatment


title: mouse-DRG-WT-rep1

description: Library name: sample1

value: dorsal root ganglia


title: ccRCC tumor bulk RNA-seq 43eb

description:
43eb
processed data file column header:
43eb


title: Male, dsx-RNAi, 11 day, replicate 1


title: HET_D7_rep1

description:
Library name: 11876-BZ-29
RAI1 heterozygous mutant iNeuron Day 7 biological replicate 1

value: hESC (H9)

value: iNeuron


title: ccRCC tumor bulk RNA-seq 5c4e

description:
5c4e
processed data file column header:
5c4e


title: Female, GFP-RNAi, Thorax, replicate 5

source_name: thorax

value: thorax

value: Female

value: adult

value: GFP-RNAi


title: WT_D7_rep4

description:
Library name: 11876-BZ-28
WT iNeuron Day 7 biological replicate 4

value: WT

value: NGN2-induced neuronal differentiation


title: IFN gamma Treated 2

description: Gene expression


title: ccRCC tumor bulk RNA-seq dee4

description:
dee4
processed data file column header:
dee4

value: Kidney

value: renal cell cancer


title: ccRCC tumor bulk RNA-seq b580

description:
b580
processed data file column header:
b580

value: Clear cell renal cell carcinoma


title: Male, dsx-RNAi, 9  day, replicate 5

value: larvae

value: AsymCX

value: 9 day

value: dsx-RNAi


title: IFN gamma Treated 1

description: Gene expression

value: IEC 4.1

value: Intestinal Epithelium

value: Interferon Gamma Treatment


title: Female, GFP-RNAi, Thorax, replicate 4


title: WT_D7_rep3

description:
Library name: 11876-BZ-27
WT iNeuron Day 7 biological replicate 3

value: hESC (H9)

value: iNeuron


title: ccRCC tumor bulk RNA-seq 5f65

description:
5f65
processed data file column header:
5f65


title: Female, GFP-RNAi, Thorax, replicate 3

value: thorax

value: Female


title: ccRCC tumor bulk RNA-seq 2af0

description:
2af0
processed data file column header:
2af0


title: Ctrl 4

description: Gene expression

value: Control


title: WT_D7_rep2

description:
Library name: 11876-BZ-26
WT iNeuron Day 7 biological replicate 2

value: WT


title: ccRCC tumor bulk RNA-seq eebb

description:
eebb
processed data file column header:
eebb


title: Ctrl 3

description: Gene expression


title: Female, GFP-RNAi, Thorax, replicate 2

value: adult

value: GFP-RNAi


title: WT_D7_rep1

description:
Library name: 11876-BZ-25
WT iNeuron Day 7 biological replicate 1

value: NGN2-induced neuronal differentiation


title: ccRCC tumor bulk RNA-seq cff1

description:
cff1
processed data file column header:
cff1

value: Kidney

value: renal cell cancer

value: Clear cell renal cell carcinoma


title: Ctrl 2

description: Gene expression


title: KO_D3_rep4

description:
Library name: 11876-BZ-24
RAI1 knockout mutant iNeuron Day 3 biological replicate 4

value: RAI1 Knockout


title: ccRCC tumor bulk RNA-seq 3e11

description:
3e11
processed data file column header:
3e11


title: Female, GFP-RNAi, Head, replicate 5

source_name: head

value: head

value: AsymCX


title: Female, GFP-RNAi, Thorax, replicate 1


title: KO_D3_rep3

description:
Library name: 11876-BZ-23
RAI1 knockout mutant iNeuron Day 3 biological replicate 3


title: WT-C90-R3

city: Qingdao

first: zhaoxia

state: Shandong

address: 700, Changcheng Road, Changyang

department: Agronomy College

institute: Qingdao Agricultural University

description: heat stress plus NMD inhibitor cycloheximide (CHX, 10 μg/L) treatment

data_processing:
Barcode adapters were randomized to reduce any systemic errors associated with the adaptors. Raw reads were aligned to the Arabidopsis genome (Araport10 genome release).
Kallisto(http://pachterlab.github.io/kallisto/starting.html) and Sleuth (http://pachterlab.github.io/sleuth/download) were used to identify the differentially expressed isoforms (DEIs). In brief, first, built a kallisto index of Arabidopsis_thaliana.TAIR10.cdna file downloaded from https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-56/plants/fasta/arabidopsis_thaliana/cdna/, and then quantified transcripts using kallisto quant to generate count files. Used Sleuth to perform the differential expression analysis. The threshold for differential expression is the absolute log2 (fold value) more than one and adjusted p value less than 0.05.
Assembly: Arabidopsis_thaliana.TAIR10.cdna
Supplementary files format and content: Normalized_counts are provided for each technical replicate, each represented by a unique SRR
Supplementary files format and content: DE_file1_treatment.xlsx: Differentally expressed isoforms (heat/control)
Supplementary files format and content: DE_file1a_genotype.xlsx: Differentally expressed isoforms (upf/WT and WT CHX/WT)

organism: Arabidopsis thaliana

source_name: WT (10-day-old seedlings, 44°C,  heat and CHX treatment 90 min), replicate 3

growth_protocol: Wild-type (WT) Arabidopsis Columbia-0 (Col-0) and the NMD-compromised mutants upf1-5upf3-1 and upf3-1upf1-5 (kindly provided by Dr. Sang Hyon Kim’s lab) were used in this study. Seeds were sterilized in 70% ethanol for 2 min and then with 50% (v:v) bleach with 0.1% (v:v) Triton X-100 (Fisher Scientific, BP151) for 8 min, followed by washing with sterile water at least 5 times. Sterilized seeds were plated on ½ strength MS solid medium (Murashige & Skoog vitamin and salt mixture [Caisson Laboratories, MSP01], 0.5% [w:v] sucrose [Sigma-Aldrich, S0389], 2.4 mM MES [Sigma-Aldrich, M3671], pH 5.7, and 0.6% [w:v] phytoagar [Caisson Laboratories, PTP01]). After stratifying in the dark at 4°C for at least 48 hr, the seeds were germinated and grown at 23°C day/18°C night in long-day conditions (16 hr light/8 hr dark) for 10 days.

extract_protocol:
RNA was extracted from samples (~0.1 g) of seedlings before and during heat stress. The samples were ground to a powder in liquid nitrogen, and RNA was isolated using a Plant RNeasy Mini Kit and treated with DNase (Qiagen, www.qiagen.com/us/) according to the manufacturer’s instructions. RNA quality and quantity were determined by UV absorbance, gel electrophoresis and Agilent 2000 BioAnalyzer (http://www.agilent.com).
For transcriptome analysis, library preparations (stranded mRNA-Seq library) and the 150-cycle paired end NovaSeq 6000 SP flow cell sequencing were performed by the Iowa State University DNA Facility. Barcode adapters were randomized to reduce any systemic errors associated with the adaptors.

treatment_protocol: 10-day-old seedlings (3 hr after start of the light) were transferred to liquid ½ MS medium or liquid ½ MS medium plus cycloheximide (CHX, 10 μg/L). The plants were then subjected to heat stress conditions (44°C) in the light for various periods of time and sampled with three biological repeats before heat stress (0) and 15, 30, 45, 90 min during heat stress (Figure 1) . Samples were flash frozen and stored at -80°C for RNA extraction and used for RT-PCR and transcriptome analysis.

tag: background ecotype

value: Columbia-0 (Col-0)

value: seedlings

tag: group

value: WT (Col-0)

value: heat and CHX treatment 90 min


title: WT-C90-R2

source_name: WT (10-day-old seedlings, 44°C,  heat and CHX treatment 90 min), replicate 2

tag: tissue


title: ccRCC tumor bulk RNA-seq 4a7b

description:
4a7b
processed data file column header:
4a7b

tag: disease state


title: Female, GFP-RNAi, Head, replicate 4


title: KO_D3_rep2

description:
Library name: 11876-BZ-22
RAI1 knockout mutant iNeuron Day 3 biological replicate 2

value: hESC (H9)

value: iNeuron


title: WT-C90-R1

source_name: WT (10-day-old seedlings, 44°C,  heat and CHX treatment 90 min), replicate 1


title: Female, GFP-RNAi, Head, replicate 3

value: Female


title: KO_D3_rep1

description:
Library name: 11876-BZ-21
RAI1 knockout mutant iNeuron Day 3 biological replicate 1


title: WT-C45-R3

source_name: WT (10-day-old seedlings, 44°C,  heat and CHX treatment 45 min), replicate 3

value: WT

value: heat and CHX treatment 45 min


title: ccRCC tumor bulk RNA-seq 763a

description:
763a
processed data file column header:
763a

tag: cancer type


title: oeCD300A-1

description: Library name: Sample2

value: Human acute monocytic leukemia cell line


title: HET_D3_rep4

description:
Library name: 11876-BZ-20
RAI1 heterozygous mutant iNeuron Day 3 biological replicate 4

value: RAI1 Het

value: NGN2-induced neuronal differentiation


title: ccRCC tumor bulk RNA-seq e0c7

description:
e0c7
processed data file column header:
e0c7

value: Kidney

value: renal cell cancer


title: ccRCC tumor bulk RNA-seq 39c4

description:
39c4
processed data file column header:
39c4

value: Clear cell renal cell carcinoma


title: WT-C45-R2

source_name: WT (10-day-old seedlings, 44°C,  heat and CHX treatment 45 min), replicate 2


title: Female, GFP-RNAi, Head, replicate 1

value: head

tag: strain

value: adult

value: GFP-RNAi


title: HET_D3_rep3

description:
Library name: 11876-BZ-19
RAI1 heterozygous mutant iNeuron Day 3 biological replicate 3


title: ccRCC tumor bulk RNA-seq f158

description:
f158
processed data file column header:
f158


title: WT-C45-R1

source_name: WT (10-day-old seedlings, 44°C,  heat and CHX treatment 45 min), replicate 1

value: Columbia-0 (Col-0)

value: seedlings


title: Female, GFP-RNAi, F1 embryo, replicate 5

source_name: embryo

value: embryo

value: AsymCX

tag: Sex

value: 1 day


title: HET_D3_rep2

description:
Library name: 11876-BZ-18
RAI1 heterozygous mutant iNeuron Day 3 biological replicate 2

value: hESC (H9)

value: iNeuron


title: ccRCC tumor bulk RNA-seq 4f16

description:
4f16
processed data file column header:
4f16


title: Female, GFP-RNAi, F1 embryo, replicate 4

value: Female

tag: developmental stage


title: HET_D3_rep1

description:
Library name: 11876-BZ-17
RAI1 heterozygous mutant iNeuron Day 3 biological replicate 1

tag: treatment


title: ccRCC tumor bulk RNA-seq ccbb

description:
ccbb
processed data file column header:
ccbb


title: WT_D3_rep4

description:
Library name: 11876-BZ-16
WT iNeuron Day 3 biological replicate 4

value: WT


title: ccRCC tumor bulk RNA-seq 579d

description:
579d
processed data file column header:
579d


title: WT_D3_rep3

description:
Library name: 11876-BZ-15
WT iNeuron Day 3 biological replicate 3


title: Female, GFP-RNAi, F1 embryo, replicate 2


title: WT-C15-R3

description: heat stress plus NMD inhibitor cycloheximide (CHX, 10 μg/L) treatment

source_name: WT (10-day-old seedlings, 44°C,  heat and CHX treatment 15 min), replicate 3

value: WT (Col-0)

value: heat and CHX treatment 15 min


title: Female, GFP-RNAi, F1 embryo, replicate 1


title: WT_D3_rep2

description:
Library name: 11876-BZ-14
WT iNeuron Day 3 biological replicate 2

value: NGN2-induced neuronal differentiation


title: ccRCC tumor bulk RNA-seq 19c0

description:
19c0
processed data file column header:
19c0

value: Kidney

value: renal cell cancer


title: Female, GFP-RNAi, Abdomen, replicate 5

source_name: abdomen

value: abdomen


title: WT-C15-R2

source_name: WT (10-day-old seedlings, 44°C,  heat and CHX treatment 15 min), replicate 2


title: ccRCC tumor bulk RNA-seq 61e8

description:
61e8
processed data file column header:
61e8

value: Clear cell renal cell carcinoma


title: WT_D3_rep1

description:
Library name: 11876-BZ-13
WT iNeuron Day 3 biological replicate 1


title: WT-C15-R1

source_name: WT (10-day-old seedlings, 44°C, heat and CHX treatment 15 min), replicate 1


title: KO_D0_rep4

description:
Library name: 11876-BZ-12
RAI1 knockout mutant iNeuron Day 0 biological replicate 4

value: RAI1 Knockout


title: ccRCC tumor bulk RNA-seq 4b33

description:
4b33
processed data file column header:
4b33

source_name: Kidney


title: KO_D0_rep3

description:
Library name: 11876-BZ-11
RAI1 knockout mutant iNeuron Day 0 biological replicate 3

source_name: hESC (H9)


title: WT-90-R3

source_name: WT (10-day-old seedlings, 44°C, heat stress 90 min), replicate 3

value: Columbia-0 (Col-0)

value: heat stress 90 min


title: Female, GFP-RNAi, Abdomen, replicate 3

value: adult

value: GFP-RNAi


title: ccRCC tumor bulk RNA-seq 8831

description:
8831
processed data file column header:
8831


title: WT-90-R2

source_name: WT (10-day-old seedlings, 44°C, heat stress 90 min), replicate 2

value: seedlings


title: Female, GFP-RNAi, Abdomen, replicate 2

value: AsymCX


title: ccRCC tumor bulk RNA-seq 65f1

description:
65f1
processed data file column header:
65f1


title: WT-90-R1

source_name: WT (10-day-old seedlings, 44°C, heat stress 90 min), replicate 1


title: KO_D0_rep1

description:
Library name: 11876-BZ-9
RAI1 knockout mutant iNeuron Day 0 biological replicate 1

value: hESC (H9)

value: iNeuron


title: Female, GFP-RNAi, Abdomen, replicate 1

value: Female


title: ccRCC tumor bulk RNA-seq 0787

description:
0787
processed data file column header:
0787


title: Female, GFP-RNAi, 9  day, replicate 5

source_name: larvae

value: larvae

value: 9 day


title: WT-45-R3

source_name: WT (10-day-old seedlings, 44°C, heat stress 45 min), replicate 3

value: WT

value: WT (Col-0)

value: heat stress 45 min


title: HET_D0_rep4

description:
Library name: 11876-BZ-8
RAI1 heterozygous mutant iNeuron Day 0 biological replicate 4

value: RAI1 Het

value: NGN2-induced neuronal differentiation


title: WT-45-R2

source_name: WT (10-day-old seedlings, 44°C, heat stress 45 min), replicate 2


title: Female, GFP-RNAi, 9  day, replicate 4


title: HET_D0_rep3

description:
Library name: 11876-BZ-7
RAI1 heterozygous mutant iNeuron Day 0 biological replicate 3


title: WT-45-R1

source_name: WT (10-day-old seedlings, 44°C, heat stress 45 min), replicate 1


title: HET_D0_rep2

description:
Library name: 11876-BZ-6
RAI1 heterozygous mutant iNeuron Day 0 biological replicate 2


title: Female, GFP-RNAi, 9  day, replicate 3


title: ccRCC tumor bulk RNA-seq caa3

description:
caa3
processed data file column header:
caa3

value: Kidney

value: renal cell cancer

value: Clear cell renal cell carcinoma


title: ccRCC tumor bulk RNA-seq 3bea

description:
3bea
processed data file column header:
3bea


title: WT-30-R3

source_name: WT (10-day-old seedlings, 44°C, heat stress 30 min), replicate 3

value: Columbia-0 (Col-0)

value: heat stress 30 min


title: Female, GFP-RNAi, 9  day, replicate 2

value: GFP-RNAi


title: HET_D0_rep1

description:
Library name: 11876-BZ-5
RAI1 heterozygous mutant iNeuron Day 0 biological replicate 1


title: ccRCC tumor bulk RNA-seq bc24

description:
bc24
processed data file column header:
bc24


title: Female, GFP-RNAi, 9  day, replicate 1

value: AsymCX


title: WT_D0_rep4

description:
Library name: 11876-BZ-4
WT iNeuron Day 0 biological replicate 4

value: hESC (H9)


title: WT-30-R2

source_name: WT (10-day-old seedlings, 44°C, heat stress 30 min), replicate 2

value: seedlings


title: WT-30-R1

source_name: WT (10-day-old seedlings, 44°C, heat stress 30 min), replicate 1


title: Female, GFP-RNAi, 7 day, replicate 5

value: Female

value: 7 day


title: WT_D0_rep3

description:
Library name: 11876-BZ-3
WT iNeuron Day 0 biological replicate 3

value: iNeuron


title: Female, GFP-RNAi, 7 day, replicate 4

value: larvae


title: WT_D0_rep2

description:
Library name: 11876-BZ-2
WT iNeuron Day 0 biological replicate 2

value: WT


title: WT-15-R2

source_name: WT (10-day-old seedlings, 44°C, heat stress 15 min), replicate 2

value: WT (Col-0)

value: heat stress 15 min


title: WT_D0_rep1

description:
Library name: 11876-BZ-1
WT iNeuron Day 0 biological replicate 1

value: NGN2-induced neuronal differentiation


title: Female, GFP-RNAi, 7 day, replicate 3


title: ccRCC tumor bulk RNA-seq 0d38

description:
0d38
processed data file column header:
0d38

value: Kidney


title: WT-15-R1

source_name: WT (10-day-old seedlings, 44°C, heat stress 15 min), replicate 1


title: Female, GFP-RNAi, 7 day, replicate 2


title: ccRCC tumor bulk RNA-seq 40de

description:
40de
processed data file column header:
40de

value: renal cell cancer


title: Female, GFP-RNAi, 7 day, replicate 1


title: LNCaP AR ChIP (Whole media)

city: Maywood

first: Steven

last: Kregel

address: 2160 S. First Avenue

department: Cancer Biology

institute: Loyola University Chicago

description:
Library name: LNCaP AR ChIP (Whole media)
bigWig and BED files

library_source: genomic

data_processing:
Peaks were called using MACS2 and aligned to the human genome assembly GRCh38.p14. ChIP-seq data quality was assessed using FastQC (v0.12.1).
Assembly: GRCh38.p14
Supplementary files format and content: bigWig, BED (for all except inputs)

molecule: genomic DNA

source_name: cell line

extract_protocol:
Following fixation and quenching, we performed chromatin immunoprecipitation, size selection, and purification using the Diagenode iDeal ChIP kit for Transcription Factors (Diagenode, Cat: C01010055) according to manufacturer’s protocol.
Library preparation and sequencing was performed at the University of Illinois Urbana-Champaign (UIUC) Roy J. Carver Biotechnology Center using the Ovation® Ultralow System V2 DNA-Seq Library Preparation Kit (Tecan, Cat: 402666). The libraries were pooled; quantitated by qPCR and sequenced on one 25B lane for 151 cycles from both ends of the fragments on a NovaSeq X Plus with V1.0 sequencing kits (reads were 150bp in length). Fastq files were generated and demultiplexed with the bcl-convert v4.1.7 Conversion Software (Illumina).

value: cell line

value: LNCaP shMETTL3-26

value: prostate adenocarcinoma


title: ccRCC tumor bulk RNA-seq 40ba

first: Isaias

address: GH PITIE SALPETRIERE ICM IHU A, 47 Boulevard DE L'HOPITAL

institute: Institut du cerveau

description:
40ba
processed data file column header:
40ba

value: Clear cell renal cell carcinoma


title: WT-0-R2

source_name: WT (10-day-old seedlings, before heat treatment), replicate 2

value: Columbia-0 (Col-0)


title: Female, GFP-RNAi, 11 day, replicate 5

first: Julien

address: Droevendaalsesteeg 1

institute: Wageningen University and Research (Netherlands)

data_processing:
Raw data filtering was performed to remove reads with adaptor contamination, uncertain nucleotides on more than 10% of the sequence (N>10%) and reads with low-quality nucleotides (<20) on more than 50% of the sequence.
Clean paired-end reads were mapped on the Nasonia vitripennis genome Nvit_psr_1.1 (GCA_009193385.2 Nvit_psr_1.1) using HISAT2 (v2.0.5) and default parameters.
Gene counts were obtained using HTSeq (v0.6.1) and the union method on the annotation GCF_009193385.1_Nvit_psr_1.
Assembly: Nvit_psr_1.1
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

source_name: pupae

extract_protocol:
After 3 days post-injection, five samples with three individuals were collected for each time point and sex and flash-frozen in liquid nitrogen. For adult parts, seven adults were collected one day after emergence, between 7 and 8 days after pupae injection. Adults were flash-frozen in liquid nitrogen, then immediately dissected apart on ice into head, thorax, and abdomen, and finally flash-frozen back in liquid nitrogen. All samples were stored at −80 °C until RNA extraction. For 1 day-old embryo (parental RNAi), F0 female pupae 8 days after oviposition were injected as described above, kept until emergence, and then crossed with uninjected AsymCX males or kept virgin. Every female was then set up individually with one host, changed every 4 hours. Virgin females produce only male progeny while mated females produce between 90-95% females. Batches of 100 embryos were collected  24 hours later by dissecting the host, transfer into a microcentrifugation tube on ice without buffer, flash-frozen in liquid nitrogen, and stored at −80 °C until RNA extraction. Total RNA was extracted with Quick-RNA Tissue/Insect Kit coupled with on column DNase treatment (ZymoResearch - R2030) according to manufacturer's protocol.
Library preparation was performed at the Novogene (HK) Company Limited. Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Sequencing libraries were paired-end sequenced (150 bp read-length) on an Illumina NovaSeq platform.

value: pupae

value: AsymCX

value: 11 day

value: GFP-RNAi


title: ccRCC tumor bulk RNA-seq 743e

description:
743e
processed data file column header:
743e

source_name: Kidney


title: LNCaP Input (Whole media)

description:
Library name: LNCaP Input (Whole media)
bigWig file

value: LNCaP shMETTL3-25


title: WT-0-R1

source_name: WT (10-day-old seedlings, before heat treatment), replicate 1

value: seedlings


title: Female, GFP-RNAi, 11 day, replicate 4

value: Female


title: 22Rv1 METTL3 ChIP (Whole media)

description:
Library name: 22Rv1 METTL3 ChIP (Whole media)
bigWig and BED files

value: LNCaP shMETTL3-24


title: ccRCC tumor bulk RNA-seq 8523

description:
8523
processed data file column header:
8523


title: ccRCC tumor bulk RNA-seq 8bbc

description:
8bbc
processed data file column header:
8bbc


title: ccRCC tumor bulk RNA-seq 8c0e

description:
8c0e
processed data file column header:
8c0e


title: Female, GFP-RNAi, 11 day, replicate 3


title: upf-90-R3

description: NMD-compromised mutants upf3-1upf1-5, short name upf used

source_name: upf3-1upf1-5 (10-day-old seedlings, 44°C, heat stress 90 min), replicate 3

value: NMD-compromised mutant upf

value: heat stress 90 min


title: LNCaP METTL3 ChIP (Whole media)

description:
Library name: LNCaP METTL3 ChIP (Whole media)
bigWig and BED files

value: LNCaP shMETTL3-27


title: 22Rv1 AR ChIP (Whole media)

description:
Library name: 22Rv1 AR ChIP (Whole media)
bigWig and BED files

value: LNCaP shMETTL3-23


title: ccRCC tumor bulk RNA-seq 764b

description:
764b
processed data file column header:
764b

value: Kidney

value: renal cell cancer


title: ccRCC tumor bulk RNA-seq bdd0

description:
bdd0
processed data file column header:
bdd0


title: WT-0-R3

source_name: WT (10-day-old seedlings, before heat treatment), replicate 3

value: WT

value: WT (Col-0)


title: Female, GFP-RNAi, 11 day, replicate 2


title: upf-90-R2

source_name: upf3-1upf1-5 (10-day-old seedlings, 44°C, heat stress 90 min), replicate 2

value: Columbia-0 (Col-0)


title: 22Rv1 Input (Whole media)

description:
Library name: 22Rv1 Input (Whole media)
bigWig file

value: cell line

value: LNCaP shMETTL3-22

value: prostate adenocarcinoma


title: upf-90-R1

source_name: upf3-1upf1-5 (10-day-old seedlings, 44°C, heat stress 90 min), replicate 1


title: ccRCC tumor bulk RNA-seq 7216

description:
7216
processed data file column header:
7216

value: Clear cell renal cell carcinoma


title: Female, GFP-RNAi, 11 day, replicate 1

value: pupae

value: AsymCX

value: 11 day

value: GFP-RNAi


title: ccRCC tumor bulk RNA-seq 816a

description:
816a
processed data file column header:
816a


title: Female, dsx-RNAi, Thorax, replicate 5

source_name: thorax

value: thorax

value: Female

value: adult

value: dsx-RNAi


title: upf-45-R3

source_name: upf3-1upf1-5 (10-day-old seedlings, 44°C, heat stress 45 min), replicate 3

value: seedlings

value: NMD-compromised mutant upf

value: heat stress 45 min


title: LNCaP-Clone21 METTL3 ChIP (DOX/EtOH)

description:
Library name: LNCaP-Clone21 METTL3 ChIP (DOX/EtOH)
bigWig and BED files

value: LNCaP shMETTL3-21


title: LNCaP-Clone21 METTL3 ChIP (DOX/R1881)

description:
Library name: LNCaP-Clone21 METTL3 ChIP (DOX/R1881)
bigWig and BED files


title: Female, dsx-RNAi, Thorax, replicate 4


title: upf-45-R2

source_name: upf3-1upf1-5 (10-day-old seedlings, 44°C, heat stress 45 min), replicate 2

value: Columbia-0 (Col-0)


title: ccRCC tumor bulk RNA-seq e38f

description:
e38f
processed data file column header:
e38f

value: Kidney

value: renal cell cancer


title: ccRCC tumor bulk RNA-seq d022

description:
d022
processed data file column header:
d022


title: Female, GFP-RNAi, Head, replicate 2

source_name: head

value: head


title: LNCaP-Clone21 METTL3 ChIP (DMSO/R1881)

description:
Library name: LNCaP-Clone21 METTL3 ChIP (DMSO/R1881)
bigWig and BED files

value: cell line

value: prostate adenocarcinoma


title: ccRCC tumor bulk RNA-seq eba5

description:
eba5
processed data file column header:
eba5

value: Clear cell renal cell carcinoma


title: Female, dsx-RNAi, Thorax, replicate 3

value: AsymCX


title: upf-45-R1

source_name: upf3-1upf1-5 (10-day-old seedlings, 44°C, heat stress 45 min), replicate 1


title: LNCaP-Clone21 METTL3 ChIP (DMSO/EtOH)

description:
Library name: LNCaP-Clone21 METTL3 ChIP (DMSO/EtOH)
bigWig and BED files


title: upf-30-R3

source_name: upf3-1upf1-5 (10-day-old seedlings, 44°C, heat stress 30 min), replicate 3

value: heat stress 30 min


title: Female, dsx-RNAi, Thorax, replicate 2

value: thorax


title: WT-C30-R3

description: heat stress plus NMD inhibitor cycloheximide (CHX, 10 μg/L) treatment

source_name: WT (10-day-old seedlings, 44°C,  heat and CHX treatment 30 min), replicate 3

value: WT

value: WT (Col-0)

value: heat and CHX treatment 30 min


title: ccRCC tumor bulk RNA-seq 547f

description:
547f
processed data file column header:
547f


title: LNCaP-Clone78 METTL3 ChIP (DOX/R1881)

description:
Library name: LNCaP-Clone78 METTL3 ChIP (DOX/R1881)
bigWig and BED files

value: LNCaP shMETTL3-78


title: WT-C30-R2

source_name: WT (10-day-old seedlings, 44°C,  heat and CHX treatment 30 min), replicate 2

value: seedlings


title: ccRCC tumor bulk RNA-seq f469

description:
f469
processed data file column header:
f469


title: Female, GFP-RNAi, F1 embryo, replicate 3

source_name: embryo

value: embryo

value: Female

value: 1 day

value: GFP-RNAi


title: upf-30-R2

description: NMD-compromised mutants upf3-1upf1-5, short name upf used

source_name: upf3-1upf1-5 (10-day-old seedlings, 44°C, heat stress 30 min), replicate 2

value: Columbia-0 (Col-0)

value: NMD-compromised mutant upf


title: Female, dsx-RNAi, Thorax, replicate 1

value: adult

value: dsx-RNAi


title: WT-C30-R1

source_name: WT (10-day-old seedlings, 44°C,  heat and CHX treatment 30 min), replicate 1


title: ccRCC tumor bulk RNA-seq ccaf

description:
ccaf
processed data file column header:
ccaf

source_name: Kidney

value: Kidney

value: renal cell cancer

value: Clear cell renal cell carcinoma


title: ccRCC tumor bulk RNA-seq 919f

description:
919f
processed data file column header:
919f


title: LNCaP-Clone78 METTL3 ChIP (DOX/EtOH)

description:
Library name: LNCaP-Clone78 METTL3 ChIP (DOX/EtOH)
bigWig and BED files

source_name: cell line

value: cell line

value: prostate adenocarcinoma


title: upf-30-R1

source_name: upf3-1upf1-5 (10-day-old seedlings, 44°C, heat stress 30 min), replicate 1

value: heat stress 30 min


title: Female, dsx-RNAi, Head, replicate 5

value: head

value: AsymCX


title: LNCaP-Clone78 METTL3 ChIP (DMSO/R1881)

description:
Library name: LNCaP-Clone78 METTL3 ChIP (DMSO/R1881)
bigWig and BED files

value: LNCaP shMETTL3-78


title: ccRCC tumor bulk RNA-seq b48c

description:
b48c
processed data file column header:
b48c


title: upf-15-R3

source_name: upf3-1upf1-5 (10-day-old seedlings, 44°C, heat stress 15 min), replicate 3

value: seedlings

value: heat stress 15 min


title: Female, dsx-RNAi, Head, replicate 4

value: Female


title: LNCaP-Clone78 METTL3 ChIP (DMSO/EtOH)

description:
Library name: LNCaP-Clone78 METTL3 ChIP (DMSO/EtOH)
bigWig and BED files


title: 15672_Mtb_LDA_Day_56

city: Aurora

first: Jo

last: Hendrix

state: CO

department: Pulmonology

institute: University of Colorado

description: Library name: NW_527

data_processing:
After sequencing, bacterial reads were trimmed by Skewer v0.2.2 using an adapter sequence of 5’- CTGTCTCTTATACACATCT-3’, a length of 50-175 bases, and an end quality of 20. Individual reads were reunited with their mate pair using PairFQ lite v0.17.0. Paired-end reads were then aligned to the 2016 Mtb Erdman reference assembly using Bowtie2 v2.5.0 with default parameters. Mapped sequences were counted using HtSeq v1.0 with the default parameters. The SEARCH-TB panel amplifies Mtb 3,568 genes. Genes with high incidences of 0 expression values were excluded.
Sequenced mouse reads were processed using Trimmomatic v0.39 to remove TruSeq3-PE-2 adapter sequences, trim leading and trailing bases with a quality score below 3, and filter for reads longer than 36 bases after trimming. Reads were aligned to the mm39 genome assembly (GCA_000001635.9) and using Star v2.7.10b with default parameters. The genome assembly and associated annotation file were acquired from the University of California Santa Cruz Genomics Institute. Additional alignment metrics were collected using Picard v2.27.5. Genes with excessive number of zero values (>90%) or low variance across samples were removed from analysis, resulting in a final dataset of 29,579 host genes.
Assembly: 2016 Mtb Erdman reference assembly for Mtb sequencing reads. mm39 genome assembly (GCA_000001635.9) for murine sequencing reads.
Supplementary files format and content: Read counts per organism gene are provided in .txt format

organism: Mycobacterium tuberculosis str. Erdman = ATCC 35801

growth_protocol: All animal procedures were conducted according to relevant national and international guidelines and approved by the Colorado State University Animal Care and Use Committee as described in the Supplemental Information. For the chronic infection model, 30 BALB/c female mice (7-9 weeks old) were infected with a low dose aerosol (LDA) of Mtb Erdman using the Glas-Col Inhalation Exposure System. This resulted in the deposition of 2.40 ± 0.07 (SEM) log10 CFU in lungs one day post-infection. Five mice were sacrificed on days 1, 7, 11, 19, 28, and 56 post-infection for lung specimen collection, respectively. Following sacrifice, the lungs were aseptically harvested and sectioned into the left lobe, upper right lob, and lower right robes for subsequent analysis.

extract_protocol:
Murine tissue samples were snap frozen in 7 mL Precellys tubes (Bertin) under liquid nitrogen. To each tissue sample, 1.5 mL GTC-TCEP buffer was added and samples were homogenized at 7,200 rpm for 16s using a Precellys Evolution (Bertin). Homogenates were incubated at room temperature for 5 minutes while protected from light. Unlysed mycobacterial cells were pelleted at 10,000g for 3 minutes, then resuspended in 0.8 mL RLT+ BME buffer (Qiagen, TCEP concentration 0.75 mM). Mycobacterial cells were lysed on a Precellys Evolution (Bertin) at 6,500 rpm for 30s three times, resting on ice for 5 minutes each time, and stored at -80C. After storage at -80C, murine lysates were thawed, and RNA was purified using the Maxwell simplyRNA tissue kit (murine samples) using the Maxwell RSC instrument following the manufacturer’s instructions with the following modifications. Additional kit DNase was added at twice the manufacturer’s recommended amount. Purified RNA was quantified using the Quantifluor RNA system (Promega).
Murine RNA was purified with Maxwell simplyRNA tissue kit while bacterial RNA was prepared for SEARCH-TB using Illumina’s AmpliSeq for Illumina Custom and Community RNA Panels kit.

treatment_protocol: no treatment was given.

value: Erdman


title: upf-15-R2

source_name: upf3-1upf1-5 (10-day-old seedlings, 44°C, heat stress 15 min), replicate 2

value: Columbia-0 (Col-0)


title: Female, dsx-RNAi, Head, replicate 3


title: LNCaP-Clone21 AR ChIP (DOX/R1881)

description:
Library name: LNCaP-Clone21 AR ChIP (DOX/R1881)
bigWig and BED files

value: LNCaP shMETTL3-21


title: Female, dsx-RNAi, Head, replicate 2

value: adult


title: 15671_Mtb_LDA_Day_56

description: Library name: NW_526

source_name: Mycobacterium tuberculosis str. Erdman = ATCC 35801


title: upf-15-R1

source_name: upf3-1upf1-5 (10-day-old seedlings, 44°C, heat stress 15 min), replicate 1

value: NMD-compromised mutant upf


title: Female, GFP-RNAi, Abdomen, replicate 4

source_name: abdomen

value: abdomen

value: GFP-RNAi


title: LNCaP-Clone21 AR ChIP (DOX/EtOH)

description:
Library name: LNCaP-Clone21 AR ChIP (DOX/EtOH)
bigWig and BED files


title: upf-0-R3

source_name: upf3-1upf1-5 (10-day-old seedlings, before heat treatment), replicate 3


title: 15669_Mtb_LDA_Day_56

description: Library name: NW_524

value: Mycobacterium tuberculosis str. Erdman = ATCC 35801


title: Female, dsx-RNAi, Head, replicate 1

source_name: head

value: dsx-RNAi


title: 15668_Mtb_LDA_Day_56

description: Library name: NW_523


title: upf-0-R2

source_name: upf3-1upf1-5 (10-day-old seedlings, before heat treatment), replicate 2


title: LNCaP-Clone21 AR ChIP (DMSO/R1881)

description:
Library name: LNCaP-Clone21 AR ChIP (DMSO/R1881)
bigWig and BED files

value: cell line

value: prostate adenocarcinoma


title: KO_D0_rep2

description:
Library name: 11876-BZ-10
RAI1 knockout mutant iNeuron Day 0 biological replicate 2

source_name: hESC (H9)

value: hESC (H9)

value: iNeuron

value: RAI1 Knockout

value: NGN2-induced neuronal differentiation


title: Female, dsx-RNAi, F1 embryo, replicate 5

value: embryo

value: AsymCX

value: 1 day


title: LNCaP-Clone21 AR ChIP (DMSO/EtOH)

description:
Library name: LNCaP-Clone21 AR ChIP (DMSO/EtOH)
bigWig and BED files


title: 15667_Mtb_LDA_Day_28

description: Library name: NW_522

value: Erdman


title: upf-0-R1

source_name: upf3-1upf1-5 (10-day-old seedlings, before heat treatment), replicate 1

value: Columbia-0 (Col-0)

value: seedlings


title: Female, dsx-RNAi, F1 embryo, replicate 4

value: Female


title: bui1, 48h, rep3

city: Shanghai

first: yangxuan

last: liu

address: 300 Fenglin Road

institute: CAS Center for Excellence in Molecular Plant Science (CEMPS), Chinese Academy of Sciences

description: Library name: bui1_48h_3

data_processing:
The raw reads were trimmed with Trimmomatic v.0.39 with parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:8:true SLIDINGWINDOW:4:20 LEADING:20 TRAILING:20 MINLEN:50.
Clean reads were then aligned to the TAIR10 transcriptome using Hisat2 v2.2.1.
Expression levels were extracted for each gene using TPMCalculator v0.0.3 and featureCounts v2.0.6.
Assembly: Oryza_sativa.IRGSP-1.0
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

organism: Oryza sativa

source_name: leaf

extract_protocol:
Around  5-6 leaves were pooled as one replicate. Total RNAs were extracted with the RNAprep Pure Plant Plus Kit Kit (TIANGEN) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using TransNGS Fast RNA-Seq Library Prep Kit for Illumina  following the manufacturer’s instructions.

treatment_protocol: The leaves of ZJ22 and bui1 plants following Xoo inoculation were sampled at 0h, 6h, 12h, 24h and 48h for transcriptome analysis.

value: leaf

value: Xoo inoculation

tag: time point


title: LNCaP-Clone78 AR ChIP (DOX/R1881)

description:
Library name: LNCaP-Clone78 AR ChIP (DOX/R1881)
bigWig and BED files

value: LNCaP shMETTL3-78


title: Female, dsx-RNAi, F1 embryo, replicate 3

city: Wageningen

last: Rougeot

source_name: embryo

value: dsx-RNAi


title: 15666_Mtb_LDA_Day_28

description: Library name: NW_521

value: Mycobacterium tuberculosis str. Erdman = ATCC 35801


title: LNCaP-Clone78 AR ChIP (DOX/EtOH)

description:
Library name: LNCaP-Clone78 AR ChIP (DOX/EtOH)
bigWig and BED files

value: cell line

value: prostate adenocarcinoma


title: 15665_Mtb_LDA_Day_28

description: Library name: NW_520


title: Female, dsx-RNAi, F1 embryo, replicate 2


title: bui1, 48h, rep2

description: Library name: bui1_48h_2


title: LNCaP-Clone78 AR ChIP (DMSO/R1881)

description:
Library name: LNCaP-Clone78 AR ChIP (DMSO/R1881)
bigWig and BED files


title: bui1, 48h, rep1

description: Library name: bui1_48h_1


title: ccRCC tumor bulk RNA-seq 44b3

city: PARIS

last: Hernandez-Verdin

description:
44b3
processed data file column header:
44b3

value: Kidney

value: renal cell cancer

value: Clear cell renal cell carcinoma


title: Female, dsx-RNAi, F1 embryo, replicate 1

value: embryo


title: LNCaP-Clone78 AR ChIP (DMSO/EtOH)

description:
Library name: LNCaP-Clone78 AR ChIP (DMSO/EtOH)
bigWig and BED files


title: 15664_Mtb_LDA_Day_28

description: Library name: NW_519


title: bui1, 24h, rep3

description: Library name: bui1_24h_3


title: 15663_Mtb_LDA_Day_28

description: Library name: NW_518


title: Female, dsx-RNAi, Abdomen, replicate 5

value: abdomen

value: AsymCX

value: adult


title: 15662_Mtb_LDA_Day_19

description: Library name: NW_517

value: Erdman


title: LNCaP-Clone21 Input (DOX/R1881)

description:
Library name: LNCaP-Clone21 Input (DOX/R1881)
bigWig file

value: LNCaP shMETTL3-21


title: bui1, 24h, rep2

description: Library name: bui1_24h_2


title: Female, dsx-RNAi, Abdomen, replicate 4

value: Female


title: LNCaP-Clone21 Input (DOX/EtOH)

description:
Library name: LNCaP-Clone21 Input (DOX/EtOH)
bigWig file


title: 15661_Mtb_LDA_Day_19

description: Library name: NW_516


title: bui1, 24h, rep1

description: Library name: bui1_24h_1

value: leaf


title: Female, dsx-RNAi, Abdomen, replicate 3


title: LNCaP-Clone21 Input  (DMSO/R1881)

description:
Library name: LNCaP-Clone21 Input  (DMSO/R1881)
bigWig file


title: 15660_Mtb_LDA_Day_19

description: Library name: NW_515


title: bui1, 12h, rep3

description: Library name: bui1_12h_3

value: Xoo inoculation


title: Female, dsx-RNAi, Abdomen, replicate 2


title: LNCaP-Clone21 Input (DMSO/EtOH)

description:
Library name: LNCaP-Clone21 Input (DMSO/EtOH)
bigWig file


title: 15659_Mtb_LDA_Day_19

description: Library name: NW_514


title: bui1, 12h, rep2

description: Library name: bui1_12h_2


title: Female, dsx-RNAi, Abdomen, replicate 1


title: LNCaP-Clone78 Input (DOX/R1881)

description:
Library name: LNCaP-Clone78 Input (DOX/R1881)
bigWig file

value: LNCaP shMETTL3-78


title: 15658_Mtb_LDA_Day_19

description: Library name: NW_513


title: LNCaP-Clone78 Input (DOX/EtOH)

description:
Library name: LNCaP-Clone78 Input (DOX/EtOH)
bigWig file


title: Female, dsx-RNAi, 9  day, replicate 5

source_name: larvae

value: larvae

value: 9 day

value: dsx-RNAi


title: 15657_Mtb_LDA_Day_11

description: Library name: NW_512

value: Mycobacterium tuberculosis str. Erdman = ATCC 35801


title: bui1, 6h, rep3

description: Library name: bui1_6h_3


title: bui1, 12h, rep1

description: Library name: bui1_12h_1


title: Female, dsx-RNAi, 9  day, replicate 4


title: LNCaP-Clone78 Input  (DMSO/R1881)

description:
Library name: LNCaP-Clone78 Input  (DMSO/R1881)
bigWig file

value: cell line

value: prostate adenocarcinoma


title: 15656_Mtb_LDA_Day_11

description: Library name: NW_511


title: Veh 1335 P6

source_name: primary fibroblasts

value: lung E18.5 fetal mouse


title: bui1, 6h, rep2

description: Library name: bui1_6h_2


title: Female, dsx-RNAi, 9  day, replicate 3


title: LNCaP-Clone78 Input (DMSO/EtOH)

description:
Library name: LNCaP-Clone78 Input (DMSO/EtOH)
bigWig file


title: 15655_Mtb_LDA_Day_11

description: Library name: NW_510


title: bui1, 6h, rep1

description: Library name: bui1_6h_1


title: Female, dsx-RNAi, 9  day, replicate 2


title: WT-15-R3

source_name: WT (10-day-old seedlings, 44°C, heat stress 15 min), replicate 3

value: Columbia-0 (Col-0)

value: WT

value: seedlings

value: WT (Col-0)

value: heat stress 15 min


title: V1_ki67-myc-_ROI14_S4_Vehicle

city: Umeå

first: Lixiao

state: Sverige

address: Medicinsk biovetenskap, M21, Försörjningsvägen 1

department: Department of Medical Biosciences

country: Sweden

institute: Umeå University

description:
Library name: DSP-1001660037306-B-H07
Tumor V1, Slide S4, ROI 14, Segment ki67-myc-, Replicate V1_ki67-myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

data_processing:
FASTQ files were converted to DCC count files via NanoString GeoMx NGS Pipeline. DCC files loaded into R using GeomxTools (Bioconductor). Segment QC: min 1,000 reads, 75% alignment, 50% saturation, 20 nuclei, 1,000 um2 area. Probe QC: ratio >0.1, Grubbs outlier removal. Aggregated to gene-level by geometric mean.
Counts imported into standR (Bioconductor) as SpatialExperiment. Low-expression genes filtered (sample_fraction=0.9, min_count=5). TMM normalization (edgeR). Batch effects assessed by PCA.
DE analysis: limma-voom with duplicateCorrelation (tumor as block). Treatment comparisons per cell population. Gene set analysis: limma::camera for MYC targets, ribosomal, cell cycle, apoptosis pathways. Significance: BH-adjusted P < 0.05 and |log2FC| > 0.5.
R (v4.4.2), GeomxTools, standR, limma, edgeR, SpatialExperiment (Bioconductor).
Assembly: hg38 (GRCh38)
Supplementary files format and content: DCC files: per-AOI probe-level count files from NanoString GeoMx NGS Pipeline, containing raw/trimmed/stitched/aligned read counts and per-probe expression values
Supplementary files format and content: standR_counts.txt: tab-delimited gene-level raw count matrix (genes x 92 AOIs)
Library strategy: Spatial Transcriptomics

source_name: Raji Burkitt lymphoma xenograft

growth_protocol: Raji Burkitt lymphoma cells (ATCC CCL-86, p53 R213Q) were harvested during logarithmic growth, washed, and resuspended in serum-free media. A total of 5x10^6 cells in 200 uL of a 1:1 mixture of Matrigel and medium were injected subcutaneously into the right flank of 6-8-week-old NSG mice (Charles River). Tumors grew to approximately 100-150 mm3 before randomization.

extract_protocol:
FFPE tumor sections were processed on the NanoString GeoMx Digital Spatial Profiler (DSP) at the Genomic Medicine Sweden Center North / Clinical Genomics Umea. Sections were stained with fluorescent antibodies against Ki67 and c-Myc. Within each ROI, cells were segmented into four populations: Ki67+MYC+, Ki67-MYC+, Ki67-MYC-, and Ki67+MYC-. UV-cleavable oligonucleotide tags from each segment (AOI) were collected for library preparation.
Libraries were prepared using the NanoString GeoMx NGS Library Preparation Kit per manufacturer protocol. Human NGS Whole Transcriptome Atlas (WTA v1.0) panel (~18,000 genes). Each AOI received a unique indexing barcode. 92 AOIs across 10 tumors on four slides (S1-S4), each slide containing both conditions.

treatment_protocol: Mice were randomized into milademetan-treated (n=5) and vehicle control (n=5) groups. Milademetan (20 mg/kg) or vehicle was administered daily by oral gavage for 15 days. Tumors were harvested, formalin-fixed, and paraffin-embedded (FFPE).

value: Raji Burkitt lymphoma xenograft

value: Raji (ATCC CCL-86)

value: Vehicle


title: 15654_Mtb_LDA_Day_11

description: Library name: NW_509

value: Erdman


title: bui1, 0h, rep3

description: Library name: bui1_0h_3

value: leaf

value: Xoo inoculation


title: V1_ki67+myc+_ROI14_S4_Vehicle

description:
Library name: DSP-1001660037306-B-H06
Tumor V1, Slide S4, ROI 14, Segment ki67+myc+, Replicate V1_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Female, dsx-RNAi, 9  day, replicate 1

value: larvae

value: AsymCX

value: Female

value: 9 day


title: bui1, 0h, rep2

description: Library name: bui1_0h_2


title: V1_ki67+myc+_ROI13_S4_Vehicle

description:
Library name: DSP-1001660037306-B-H05
Tumor V1, Slide S4, ROI 13, Segment ki67+myc+, Replicate V1_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: 15653_Mtb_LDA_Day_11

description: Library name: NW_508

value: Mycobacterium tuberculosis str. Erdman = ATCC 35801


title: Tn M2 D3 r3

first: Ruiqing

last: Ma

address: 2901 Caolang Rd., Jinshan District

institute: Shanghai Public Health Clinical Center

description:
Library name: M2-2 rep3
M2 rep 3

data_processing:
Basecalling: Illumina GA Pipeline v1.8
Transit v3.0, Transit Pre-Processor (TPP) step for read aligment, Resampling -a for pairwise comparison
Assembly: NC_000962, Mycobacterium tuberculosis H37Rv, complete genome
Supplementary files format and content: *.xlsx files generated by Transit contain log2FoldChange and p-value of the comparison results between two conditions

organism: Mycobacterium tuberculosis

extract_protocol:
CTAB genome extraction method
Tn-seq

tag: sample group

value: Tn M2 D3


title: Female, dsx-RNAi, 7 day, replicate 5

value: 7 day

value: dsx-RNAi


title: Female, dsx-RNAi, 7 day, replicate 4


title: V1_ki67-myc-_ROI8_S4_Vehicle

description:
Library name: DSP-1001660037306-B-G12
Tumor V1, Slide S4, ROI 8, Segment ki67-myc-, Replicate V1_ki67-myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

tag: cell type


title: ZJ22, 48h, rep3

description: Library name: ZJ22_48h_3

tag: genotype


title: V1_ki67+myc+_ROI8_S4_Vehicle

description:
Library name: DSP-1001660037306-B-G11
Tumor V1, Slide S4, ROI 8, Segment ki67+myc+, Replicate V1_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Female, dsx-RNAi, 7 day, replicate 2


title: Tn M2 D3 r1

description:
Library name: M2-2 rep1
M2 rep 1


title: V1_ki67+myc+_ROI7_S4_Vehicle

description:
Library name: DSP-1001660037306-B-G10
Tumor V1, Slide S4, ROI 7, Segment ki67+myc+, Replicate V1_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: ZJ22, 48h, rep2

description: Library name: ZJ22_48h_2


title: Tn M1 D3 r3

description:
Library name: M1-2 rep3
M1 rep 3

value: Tn M1 D3


title: ZJ22, 48h, rep1

description: Library name: ZJ22_48h_1


title: V1_ki67+myc+_ROI6_S4_Vehicle

description:
Library name: DSP-1001660037306-B-G09
Tumor V1, Slide S4, ROI 6, Segment ki67+myc+, Replicate V1_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Female, dsx-RNAi, 7 day, replicate 1


title: Tn M1 D3 r2

description:
Library name: M1-2 rep2
M1 rep 2


title: Tn M1 D3 r1

description:
Library name: M1-2 rep1
M1 rep 1


title: ZJ22, 24h, rep3

description: Library name: ZJ22_24h_3


title: V1_ki67-myc-_ROI5_S4_Vehicle

description:
Library name: DSP-1001660037306-B-G08
Tumor V1, Slide S4, ROI 5, Segment ki67-myc-, Replicate V1_ki67-myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Female, dsx-RNAi, 11 day, replicate 4

source_name: pupae

value: pupae

value: 11 day


title: Tn M0 D3 r2

description:
Library name: M0-2 rep2
M0 rep 2

value: Tn M0 D3


title: ZJ22, 24h, rep1

description: Library name: ZJ22_24h_1


title: Tn M0 D3 r1

description:
Library name: M0-2 rep1
M0 rep 1


title: Female, dsx-RNAi, 11 day, replicate 3


title: ZJ22, 12h, rep3

description: Library name: ZJ22_12h_3


title: Female, dsx-RNAi, 11 day, replicate 2


title: D2_ki67+myc+_ROI16_S4_Milademetan

description:
Library name: DSP-1001660037306-B-H09
Tumor D2, Slide S4, ROI 16, Segment ki67+myc+, Replicate D2_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji Burkitt lymphoma xenograft

value: Raji (ATCC CCL-86)

value: Milademetan 20mg/kg


title: D2_ki67+myc+_ROI15_S4_Milademetan

description:
Library name: DSP-1001660037306-B-H08
Tumor D2, Slide S4, ROI 15, Segment ki67+myc+, Replicate D2_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: ZJ22, 12h, rep2

description: Library name: ZJ22_12h_2

value: leaf


title: D2_ki67+myc+_ROI4_S4_Milademetan

description:
Library name: DSP-1001660037306-B-G06
Tumor D2, Slide S4, ROI 4, Segment ki67+myc+, Replicate D2_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Tn M1 D0 r1

description:
Library name: M1-1 rep1
input

value: Tn M1 D0


title: ZJ22, 12h, rep1

description: Library name: ZJ22_12h_1

value: Xoo inoculation


title: D2_ki67-myc+_ROI3_S4_Milademetan

description:
Library name: DSP-1001660037306-B-G05
Tumor D2, Slide S4, ROI 3, Segment ki67-myc+, Replicate D2_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Stool-20w-Apc-5-775

city: Taipei

first: Linda

last: Yu

address: 1 Jen-Ai Rd. Sec. 1

country: Taiwan

institute: National Taiwan University

data_processing:
The library was loaded onto the instrument with Sequel Sequencing Kit 2.1 (4 rxn) (Part Number PB 101-310-500) and a Sequel™ SMRT® Cell 1M v2 Tray (4 cells) (Part Number PB101-008-000) for sequencing.
Assembly: The training method of the QIIME2 classifier follows these steps: - Extract all the read datafrom a reference database, in our report, SILVA version 138 with 99% similarity was used.
Supplementary files format and content: File name = abs-abund-table-7 (all 90 samples); Format = excel (.xlsx); Content = raw counts of sequencing reads for the bacteria strain
Supplementary files format and content: File name = rel-table-7 (all 90 samples); Format = excel (.xlsx); Content=relative abundance of sequencing reads for the bacteria strain

source_name: Feces

extract_protocol:
Fecalpellets werecollected asepticallyand placed in sterile eppendorf. Immediately freezing stool in liquid nitrogen (LN) and store at -80°C. Extract stool bacterial DNA followed by QIAamp Fast DNA Stool Kit protocol.
For the PacBio library construction and sequencing, 16S rRNA was amplified by using primer set 27F: AGRGTTYGATYMTGGCTCAG and 1492R: RGYTACCTTGTTACGACTT followed by purification via binding to pre-washed AMPure PB beads (Part Number PB100-265-900)
16S ribosomal RNA (rRNA) gene sequencing

value: Feces

value: ApcMin

value: Untreated

value: 20 weeks old


title: ZJ22, 6h, rep3

description: Library name: ZJ22_6h_3


title: D2_ki67-myc+_ROI2_S4_Milademetan

description:
Library name: DSP-1001660037306-B-G04
Tumor D2, Slide S4, ROI 2, Segment ki67-myc+, Replicate D2_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Tn 7H9 r2

description:
Library name: pro-rep 2
input

value: Tn 7H9


title: ZJ22, 6h, rep2

description: Library name: ZJ22_6h_2


title: Stool-20w-Apc-3-743


title: ZJ22, 6h, rep1

description: Library name: ZJ22_6h_1


title: D2_ki67-myc+_ROI1_S4_Milademetan

description:
Library name: DSP-1001660037306-B-G03
Tumor D2, Slide S4, ROI 1, Segment ki67-myc+, Replicate D2_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Stool-20w-Apc-2-731


title: D1_ki67+myc+_ROI12_S4_Milademetan

description:
Library name: DSP-1001660037306-B-H04
Tumor D1, Slide S4, ROI 12, Segment ki67+myc+, Replicate D1_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Stool-20w-Apc-1-727


title: Proliferation Late time point, Replicate 2

city: Solna

first: Bernhard

last: Schmierer

state: (optional)

address: Biomedicum 9B, Solnavagen 9

department: Medical Biochemistry and Biophysics

institute: Karolinska Institutet

description:
Library name: Prol_LTP_Rep2
Custom Read1 primer, 20 cycles

data_processing:
MAGeCK v. 0.5.6 read counting
Assembly: hg38
Supplementary files format and content: .txt file containing read counts per guide for all samples
Library strategy: CRISPR Screen

source_name: Blood

extract_protocol:
QIAamp DNA Blood Maxi kit (Qiagen)
PCR

value: Blood

value: Adult acute monocytic leukemia

value: Replicate 2


title: D1_ki67+myc+_ROI11_S4_Milademetan

description:
Library name: DSP-1001660037306-B-H03
Tumor D1, Slide S4, ROI 11, Segment ki67+myc+, Replicate D1_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Proliferation Early time point, Replicate 2

description:
Library name: Prol_ETP_Rep2
Custom Read1 primer, 20 cycles


title: ZJ22, 0h, rep2

description: Library name: ZJ22_0h_2


title: Stool-20w-WT-5-777


title: D1_ki67+myc+_ROI10_S4_Milademetan

description:
Library name: DSP-1001660037306-B-H02
Tumor D1, Slide S4, ROI 10, Segment ki67+myc+, Replicate D1_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Proliferation Late time point, Replicate 1

description:
Library name: Prol_LTP_Rep1
Custom Read1 primer, 20 cycles

value: Replicate 1


title: ZJ22, 0h, rep1

description: Library name: ZJ22_0h_1


title: Stool-20w-WT-4-776


title: D1_ki67+myc+_ROI9_S4_Milademetan

description:
Library name: DSP-1001660037306-B-H01
Tumor D1, Slide S4, ROI 9, Segment ki67+myc+, Replicate D1_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Proliferation Early time point, Replicate 1

description:
Library name: Prol_ETP_Rep1
Custom Read1 primer, 20 cycles


title: Female, dsx-RNAi, 7 day, replicate 3

value: larvae

value: AsymCX

value: Female

value: 7 day

value: dsx-RNAi


title: bui1, 0h, rep1

description: Library name: bui1_0h_1

value: leaf


title: Tn M2 D3 r2

description:
Library name: M2-2 rep2
M2 rep 2

value: Tn M2 D3


title: Region_21dpn_2

city: Callaghan

first: M. Fairuz

last: B. Jamaluddin

state: NSW

address: University drive

country: Australia

institute: University of Newcastle

hyb_protocol: A custom Xenium gene expression probe panel (10x Genomics) was hybridized to FFPE tissue sections following the Xenium In Situ Gene Expression FFPE user guide. Hybridization, washing, and signal amplification steps were performed according to the manufacturer’s protocol.

scan_protocol: Slides were imaged on the Xenium Analyzer (10x Genomics) using default acquisition settings for FFPE samples as specified by the Xenium In Situ Gene Expression workflow. Fluorescence imaging was performed across multiple channels to detect hybridized transcripts and morphology.

data_processing: Raw imaging data were processed using the Xenium analysis pipeline (10x Genomics). Transcript detection, cell segmentation, and transcript assignment to cells were performed using default parameters unless otherwise stated. Gene by cell count matrices and spatial coordinate files were generated for downstream analysis.

source_name: Uterus

extract_protocol: FFPE tissue blocks were sectioned and mounted onto Xenium slides according to the Xenium In Situ Gene Expression FFPE protocol (10x Genomics). Sections were baked, deparaffinized, rehydrated, and subjected to target retrieval and protease treatment following the manufacturer’s instructions prior to probe hybridization.

value: Uterus

tag: tissue preservation method

value: 4% PFA


title: Stool-20w-WT-3-774

value: Feces


title: V4_ki67+myc+_ROI16_S3_Vehicle

description:
Library name: DSP-1001660037306-B-G02
Tumor V4, Slide S3, ROI 16, Segment ki67+myc+, Replicate V4_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji Burkitt lymphoma xenograft

tag: cell line

value: Raji (ATCC CCL-86)

value: Vehicle


title: ATRA, sorted for CD11b, Replicate 2

description:
Library name: ATRA_Rep2
Custom Read1 primer, 20 cycles

value: Blood


title: Stool-20w-WT-2-747

value: Untreated

tag: time

value: 20 weeks old


title: Region_21dpn_1


title: V4_ki67+myc+_ROI15_S3_Vehicle

description:
Library name: DSP-1001660037306-B-G01
Tumor V4, Slide S3, ROI 15, Segment ki67+myc+, Replicate V4_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

tag: batch


title: DMSO control for ATRA, sorted for CD11b, Replicate 2

description:
Library name: DMSO_ATRA_Rep2
Custom Read1 primer, 20 cycles

value: Adult acute monocytic leukemia

value: Replicate 2


title: ZJ22, 24h, rep2

description: Library name: ZJ22_24h_2

value: Xoo inoculation


title: Stool-20w-WT-1-730


title: Region_12dpn_2


title: ATRA, sorted for CD11b, Replicate 1

description:
Library name: ATRA_Rep1
Custom Read1 primer, 20 cycles

value: Replicate 1