title: kidney, aged Tfebfl/fl KAP, scRNAseq

city: Suita

first: Jun

last: Nakamura

state: Osaka

address: Box D11, 2-2 Yamada-oka

department: Nephrology

institute: the University of Osaka Graduate School of Medicine

description: 10x Genomics

data_processing:
The 10× Chromium raw sequencing data were first processed with Cell Ranger (version 6.0.0). SoupX (version 1.6.2) was used to determine ambient RNA contamination and was then applied for background correction. Seurat (version 4.4.0) package was then applied. Initially, genes expressed in more than three cells and cells with at least 200 genes were retained. Cells with less than 1000 feature counts and more than 50% mitochondrial counts were further filtered. Gene expression levels for each cell were normalized by the total expression, multiplied by 10,000, and then log-transformed. The top 2000 highly variable genes (HVGs) were identified using the vst method and were scaled based on their average expression and dispersion. The scaled data were then subjected to principal component (PC) analysis using HVGs and the dimension was reduced. In addition, we identified doublets using DoubletFinder (version 2.0.3) and excluded cells identified as doublets. Then, we used Harmony (version 1.0.3) using RunHarmony function to integrate datasets with batch effect correction. As a result, 30,145 cells were included in downstream analyses.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney

extract_protocol:
All mice were perfused with phosphate-buffered saline (PBS) via the left ventricle to remove blood cells. Afterward, the kidneys were harvested, and the renal cortex was dissected using a razor blade after the renal capsule was removed. Renal cortex samples from two or three mice in each group were combined. These samples were minced with a sterile razor blade and digested in 3.0 ml of Hanks' Balanced Salt Solution (HBSS) containing 250 μg/ml Riberase TH and 100 U/ml DNase I for 30 minutes at 37°C with shaking at 200 rpm. After digestion, the cell suspension was centrifuged at 200  g for 4 minutes. After removing the supernatant, pellets were washed twice with 2.0% bovine serum albumin (BSA) in PBS. Finally, the cell suspension was filtered through a 40 μm cell strainer, and the cells were collected by centrifugation and were resuspended with 2.0% BSA in PBS. Cell viability was investigated by trypan blue staining, and cell concentration was assessed using a hemocytometer.
Libraries of the single cells were prepared using Chromium Next GEM Single Cell 3’ Library and Gel Bead Kit v3.1 according to the manufacturer’s instructions (10x Genomics).

value: Kidney

tag: Sex

value: male

value: Tfebfl/fl KAP

value: 24 months old


title: RNA-Seq of Drosophila melanogaster: larval epidermal bands 7

status: Public on Dec 19 2024

type: SRA

city: Seattle

first: Jay

middle: Z

last: Parrish

state: WA

address: 3747 W Stevens Way NE

country: USA

institute: University of Washington

description: Library name: 38793_7

library_source: transcriptomic

data_processing:
Reads were demultiplexed with CASAVA (Illumina) and read quality was assessed using FastQC and MultiQC. Reads containing adapters were removed using Cutadapt version 2.4 and reads were mapped to the D. melanogaster transcriptome, FlyBase genome release 6.29, using Kallisto version 0.46.0 with default parameters.
Assembly: FlyBase genome release 6.29
Supplementary files format and content: txt file with raw counts

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: epidermal cells

growth_protocol: Larvae were reared at 25 C under 12 h light / dark cycle on standard cornmeal/molassess media and isolated for dissection at 96 h after egg laying.

extract_protocol:
Larvae with cytoplasmic GFP expressed in different epidermal subsets were microdissected and dissociated in collagenase type I (Fisher 17-100-017) into single cell suspensions, largely as previously described, with the addition of 1% BSA to the dissociation mix. After dissociation, cells were transferred to a new 35 mm petri dish with 1 mL 50% Schneider’s media, 50% PBS supplemented with 1% BSA. Under a fluorescent stereoscope, individual fluorescent cells were manually aspirated with a glass pipette into PBS with 0.5% BSA, and then serially transferred until isolated without any additional cellular debris present. Ten cells per sample were aspirated together, transferred to a mini-well containing 3ul lysis solution (0.2 % Triton X-100 in water with 2 U / µL RNAse Inhibitor), lysed by pipetting up and down several times, transferred to a microtube, and stored at -80º C. For the picked cells, 2.3 µL of lysis solution was used as input for library preparation.
RNA-Seq libraries were prepared from the picked cells following the Smart-Seq2 protocol for full length transcriptomes. To minimize batch effects, primers, enzymes, and buffers were all used from the same lots for all libraries. Libraries were multiplexed, pooled, and purified using AMPure XP beads, quality was checked on an Agilent TapeStation, and libraries were sequenced as 51-bp single end reads on a HiSeq4000 at the UCSF Center for Advanced Technology.

treatment_protocol: Epidermal cells were isolated from larvae with different genotypes

tag: cell type

value: epidermal cells

tag: genotype

value: R51F10-GAL4, UAS-GFP


title: kidney, aged Tfebfl/fl, scRNAseq

country: Japan

description: 10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: tissue

value: Tfebfl/fl

tag: age


title: WT45DAP_1

city: Beijing

first: Jinfang

last: Wang

address: No.50 Zhanghua Road, Haidian District

country: China

institute: Beijing Academy of Agricultural and Forestry Sciences

data_processing:
NovaSeq 6000
fastx_toolkit_0.0.14/SeqPrep/Sickle were used for estimating sequencing quality to gain clean reads.
TopHat2 / HISAT2 were used to analysis the mapped data quality.
The mapped reads were spliced using StringTie or Cufflinks software
TPM （Fragments Per Kilobases per Millionreads）values were used to show gene expression level.
Genome_build: http://cucurbitgenomics.org/organism/18
Supplementary_files_format_and_content: text files include TPM values for each Sample

organism: Cucumis melo

source_name: Cucumis melo L.

growth_protocol: The wild type (WT) and cmnac-nor mutant fruits were harveseted at 15 DAP,25 DAP,35 DAP and 45 DAP  (days after pollination)

extract_protocol:
RNA was extracted from WT and cmnac-nor mutant fruits at 15,25,35 and 45 DAP with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed
The 24 libraries were built by TruseqTM RNA sample prep kit (Illumina, USA).

value: fruit flesh

value: 45 days after pollination

value: wild type


title: STRIPE-seq + SLAM-seq mock R1

city: Würzburg

first: Christopher

middle: Sebastian

last: Jürges

state: BY

address: Versbacher Straße 7

department: Institut für Virologie und Immunbiologie

country: Germany

institute: Julius-Maximilians-Universität Würzburg

data_processing:
STAR was used to align all reads to the human genome (Enxembl version 90), ribosomal rRNA, and HCMV genome (KF297339)
Peaks were called by using the tool iTiSS and merged using iTiSS TiSSMerger2
Genome_build: KF297339.1
Supplementary_files_format_and_content: tsv, called TSS

organism: Homo sapiens

source_name: human foreskin fibroblasts (HFF)

growth_protocol: Primary human foreskin fibroblasts were cultured in DMEM supplements with 10% FBS. Cells were infected with HCMV strain TB40 and BAC2 at an MOI of 10.

extract_protocol:
Cells were lyzed using Trizol and total cellular RNA was isolated.
Sequencing libraries were prepared using the dRNA-seq and STRIPE-seq and SLAM-seq inhouse protocols.

treatment_protocol: Cells were infected using an MOI of 10. 4sU labelling at 500uM for 1 hour prior to lysis. GCV and PAA treatment was conducted at 12 hpi using 50 uM and 250 ug/mL, respectively

value: primary fibroblasts

tag: treatment

value: 4sU + IAA

tag: time post infection

value: Mock

tag: replicate

value: Replicate 1


title: RNA-Seq of Drosophila melanogaster: larval epidermal bands 6

description: Library name: 38793_6


title: RNA-Seq of Drosophila melanogaster: larval dorsal epidermal cells 3

description: Library name: ush_3

value: ush-GAL4, UAS-GFP


title: cmnac-nor35DAP_3

value: 35 days after pollination

value: cmnac-nor mutant


title: Ungraft_T_7_5

city: Norwich

first: Hannah

middle: Rae

last: Thomas

address: Norwich Research Park, Colney Lane

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

data_processing:
Fasta files were quality checked using FastQC 0.12.1.
TruSeq3 adaptors trimmed with Trimmomatic v0
39 with a head crop setting of 12, trailing setting of 3, minimum length of 52, and a sliding window of 4:20
The polyA tail was trimmed using Prinseq v0.20.4 with the left and right tail length (i.e. trim_trail_left) of 8 and the minimum length of 40.
Genome indexes were built for tomato and pepper using the ITAG4 and CM334 models respectively. Reads were aligned using STAR 2.7.10b  with two pass mode.
Files were sorted using Samtools 1.18.
Files were assembled using Strintie version 2.2.1.
Assembly: ITAG4.0 4081, Capsicum annuum 4072
Supplementary files format and content: raw reads matrix file for tomato and pepper

organism: Solanum lycopersicum

source_name: Ungrafted stem

growth_protocol: Solanum lycopersicum var. M82 (tomato) and Capsicum annuum var. California Wonder(pepper) seeds were straitified with 50% bleach. Tomato seeds were germinated in moist phytatrays and pepper seeds were germinated on soil on heatmaps. Tomato and pepper seedlings were grown in climate-controlled chambers set to 23 C with 16:8 day/night light cycles. 21 day old pepper and 14 day old tomato seedlings were grafted and allowed to heal in the dark for 3 days.

extract_protocol:
Tissue was flash frozen and hand ground with a mortal and pestle.  Total RNA was purified from Trizol-extracted samples using the Monarch Total RNA Miniprep Kit.
Libraries were built by the Cornell Institute of Biotechnology, Biotechnology Resource Centre using the Lexogen QuantSeq FWD prep kit and Poly(A) RNA Selection Kit V1
5 and subjected to high-throughput sequencing with the Illumina NextSeq 500/550 High-output kit

treatment_protocol: A 0.5 cm of tomato:tomato, pepper:pepper, tomato:pepper, and pepper tomato scion and stock were collected at 7, 14, and 21 days after grafting. Ungrafted tomato and pepper stems of the same age were also collected for tomato and pepper. Each sample had between 3-5 bioreplicates.

tag: time

value: 7 DAG

value: Ungrafted stem


title: STRIPE-seq + SLAM-seq mock no4sU R2

value: IAA

value: Replicate 2


title: kidney, young Tfebfl/fl KAP, scRNAseq

description: 10x Genomics

value: Kidney

value: male

value: Tfebfl/fl KAP

value: 6 weeks old


title: RNA-Seq of Drosophila melanogaster: larval epidermal bands 5

description: Library name: 38793_5

value: epidermal cells

value: R51F10-GAL4, UAS-GFP


title: kidney, young Tfebfl/fl, scRNAseq

description: 10x Genomics

value: Tfebfl/fl


title: STRIPE-seq + SLAM-seq mock no4sU R1

value: primary fibroblasts


title: cmnac-nor35DAP_2

value: fruit flesh


title: RNA-Seq of Drosophila melanogaster: larval epidermal bands 4

description: Library name: 38793_4


title: dRNA-seq + SLAM-seq TB40 72hpi + GCV

value: 4sU + IAA + XRN1 + GCV

value: HCMV 72 h p.i.


title: cmnac-nor35DAP_1

value: 35 days after pollination


title: C57BL/6 B cells, p53-KO, pRetroX_LMP1_IRES_ZsGreen, Day 4 #3

city: Little Rock

first: Mark

last: Manzano

state: AR

address: 4301 W Markham St

department: Microbiology & Immunology

institute: University of Arkansas for Medical Sciences

data_processing:
Raw sequence reads were checked for their quality using FastQC and then trimmed based on quality (PHRED >30). After trimming, reads less than 30 bp were discarded.
Trimmed sequence reads were mapped to reference genome mm10 with STAR aligner with default parameters.
The gene count tables were extracted from the alignment results using bedtool2 software.
The read counts were normalized using voom method.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized expression values for each smple.

source_name: splenocytes

growth_protocol: Primary B cells were isolated from spleens by AutoMac sorting. B cells were cultured in RPMI +20% FBS, L-glut, pen/strep, BME. Cells were pulsed overnight with 25 uM LPS before retroviral transduction with 5 uM polybrene. Cells were washed and cultured for 4 days.

extract_protocol:
RNA was harvested using trizol.
Library was constructed by BGI Laboratories using DNBSEQ Eukaryotic transcriptome protocol.
Following mRNA isolation, the mRNA was fragmented and first strand synthesis was performed. Double stranded cDNA fragments were subjected to end-repair, and a single 'A' nucleotide was added to the 3' end of the blunt fragment. Following library QC, the single strand cDNAs were circularized and eplicated via rolling cycle amplification. DNA nanoballs were generated and loaded into patterned nanoarrays using high-intesity DNA nanochip technique and sequeced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: Cells were transduced with pRetroX_M2_IRES_ZsGreen, pRetroX_M2.Stop_IRES_ZsGreen, pRetroX_LMP1_IRES_ZsGreen, or pRetroX_M2.Stop_IRES_ZsGreen with 5 uM polybrene by spinoculation. Cells were washed and cultured for 4 days.

value: splenocytes

tag: cell line

value: primary B cells

value: Day 4 post-transduction with pRetroX_LMP1_IRES_ZsGreen


title: C57BL/6 B cells, p53-KO, pRetroX_LMP1_IRES_ZsGreen, Day 4 #2


title: RNA-Seq of Drosophila melanogaster: larval epidermal bands 8

description: Library name: 38793_8


title: WT35DAP_3

value: wild type


title: RNA-Seq of Drosophila melanogaster: larval epidermal bands 3

description: Library name: 38793_3


title: RNA-Seq of Drosophila melanogaster: larval epidermal bands 2

description: Library name: 38793_2


title: WT35DAP_2


title: RNA-Seq of Drosophila melanogaster: larval broad epidermal cells 13

description: Library name: r38_13

value: R38F11-GAL4, UAS-GFP


title: WT35DAP_1


title: dRNA-seq + SLAM-seq TB40 48hpi

value: 4sU + IAA + XRN1

value: HCMV 48 h p.i.


title: C57BL/6 B cells, p53-WT, pRetroX_LMP1_IRES_ZsGreen, Day 4 #3


title: RNA-Seq of Drosophila melanogaster: larval epidermal bands 1

description: Library name: 38793_1


title: C57BL/6 B cells, p53-WT, pRetroX_LMP1_IRES_ZsGreen, Day 4 #2


title: dRNA-seq + SLAM-seq TB40 24hpi R2

value: HCMV 24 h p.i.

value: Replicate 2


title: RNA-Seq of Drosophila melanogaster: larval broad epidermal cells 12

description: Library name: r38_12

value: epidermal cells


title: cmnac-nor25DAP_2

value: 25 days after pollination

value: cmnac-nor mutant


title: RNA-Seq of Drosophila melanogaster: larval broad epidermal cells 11

description: Library name: r38_11


title: C57BL/6 B cells, p53-WT, pRetroX_LMP1_IRES_ZsGreen, Day 4 #1


title: cmnac-nor25DAP_1


title: dRNA-seq + SLAM-seq TB40 6hpi R2

value: primary fibroblasts

value: HCMV 6 h p.i.


title: dRNA-seq + SLAM-seq TB40 12hpi R2

value: HCMV 12 h p.i.


title: C57BL/6 B cells, p53-KO, pRetroX_M2.Stop_IRES_ZsGreen, Day 4 #3

extract_protocol:
RNA was harvested using trizol.
Library was constructed by BGI Laboratories using DNBSEQ Eukaryotic transcriptome protocol.
Following mRNA isolation, the mRNA was fragmented and first strand synthesis was performed. Double stranded cDNA fragments were subjected to end-repair, and a single 'A' nucleotide was added to the 3' end of the blunt fragment. Following library QC, the single strand cDNAs were circularized and eplicated via rolling cycle amplification. DNA nanoballs were generated and loaded into patterned nanoarrays using high-intesity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: Cells were transduced with pRetroX_M2_IRES_ZsGreen or pRetroX_M2.Stop_IRES_ZsGreen with 5 uM polybrene by spinoculation. Cells were washed and cultured for 4 days.

tag: strain

value: Day 4 post-transduction with pRetroX_M2.Stop_IRES_ZsGreen


title: WT25DAP_3

value: fruit flesh


title: C57BL/6 B cells, p53-KO, pRetroX_LMP1_IRES_ZsGreen, Day 4 #1

value: splenocytes


title: dRNA-seq + SLAM-seq TB40 2hpi R2

value: HCMV 2 h p.i.


title: dRNA-seq + SLAM-seq TB40 96hpi

value: HCMV 96 h p.i.


title: C57BL/6 B cells, p53-KO, pRetroX_M2.Stop_IRES_ZsGreen, Day 4 #2

value: primary B cells


title: dRNA-seq + SLAM-seq mock R3

value: Mock

value: Replicate 3


title: C57BL/6 B cells, p53-KO, pRetroX_M2.Stop_IRES_ZsGreen, Day 4 #1


title: RNA-Seq of Drosophila melanogaster: larval broad epidermal cells 10

description: Library name: r38_10

value: R38F11-GAL4, UAS-GFP


title: RNA-Seq of Drosophila melanogaster: larval broad epidermal cells 8

description: Library name: r38_8


title: RNA-Seq of Drosophila melanogaster: larval broad epidermal cells 9

description: Library name: r38_9


title: WT25DAP_2

value: wild type


title: dRNA-seq + SLAM-seq TB40 72hpi R2

value: 4sU + IAA + XRN1

value: HCMV 72 h p.i.

value: Replicate 2


title: C57BL/6 B cells, p53-KO, pRetroX_M2_IRES_ZsGreen, Day 4 #3

value: Day 4 post-transduction with pRetroX_M2_IRES_ZsGreen


title: WT25DAP_1

value: 25 days after pollination


title: dRNA-seq + SLAM-seq mock R2

value: primary fibroblasts


title: cmnac-nor25DAP_3

value: cmnac-nor mutant


title: C57BL/6 B cells, p53-KO, pRetroX_M2_IRES_ZsGreen, Day 4 #2


title: cmnac-nor15DAP_3

value: 15 days after pollination


title: RNA-Seq of Drosophila melanogaster: larval broad epidermal cells 7

description: Library name: r38_7

value: epidermal cells


title: dRNA-seq + SLAM-seq TB40 72hpi R1

value: Replicate 1


title: C57BL/6 B cells, p53-KO, pRetroX_M2_IRES_ZsGreen, Day 4 #1

value: splenocytes


title: RNA-Seq of Drosophila melanogaster: larval broad epidermal cells 5

description: Library name: r38_5


title: dRNA-seq + SLAM-seq TB40 24hpi R1

value: HCMV 24 h p.i.


title: RNA-Seq of Drosophila melanogaster: larval broad epidermal cells 6

description: Library name: r38_6


title: cmnac-nor15DAP_2

value: fruit flesh


title: dRNA-seq + SLAM-seq TB40 12hpi R1

value: HCMV 12 h p.i.


title: C57BL/6 B cells, p53-WT, pRetroX_M2.Stop_IRES_ZsGreen, Day 4 #3

value: primary B cells

value: Day 4 post-transduction with pRetroX_M2.Stop_IRES_ZsGreen


title: cmnac-nor15DAP_1


title: WT15DAP_3

value: wild type


title: C57BL/6 B cells, p53-WT, pRetroX_M2.Stop_IRES_ZsGreen, Day 4 #2


title: dRNA-seq + SLAM-seq TB40 6hpi R1

value: 4sU + IAA + XRN1

value: HCMV 6 h p.i.


title: dRNA-seq + SLAM-seq TB40 2hpi R1

value: HCMV 2 h p.i.


title: C57BL/6 B cells, p53-WT, pRetroX_M2.Stop_IRES_ZsGreen, Day 4 #1


title: WT15DAP_2


title: C57BL/6 B cells, p53-WT, pRetroX_M2_IRES_ZsGreen, Day 4 #2

value: Day 4 post-transduction with pRetroX_M2_IRES_ZsGreen


title: RNA-Seq of Drosophila melanogaster: larval broad epidermal cells 2

description: Library name: r38_2

value: R38F11-GAL4, UAS-GFP


title: RNA-Seq of Drosophila melanogaster: larval broad epidermal cells 1

description: Library name: r38_1


title: WT15DAP_1


title: OC236 EpCAM negative 3

status: Public on Dec 18 2024

city: Herne

first: David

last: Diaz-Carballo

state: NRW

address: Düngelstr. 33

department: Medical clinic of hematology & oncology

institute: Marienhospital Herne, Clinic of Ruhr University Bochum

description: Library name: sample14

data_processing:
sequencing was performed by BGI Genomics (Hong Kong, China)
We used Bowtie2 to align the clean reads to the reference genes.
Assembly: hg38
Supplementary files format and content: excel file with fpkm, tpm, read count and norm read count

source_name: Ovarian

growth_protocol: SKOV3  ovarian carcinomas were cultured in DMEM containing 10 % heat-inactivated FCS supplemented with 6 µg/mL doxycycline. The primary ovarian carcinoma cells OC236  were isolated from ascites from patients and cultured in DMEM/F12 containing 10% FCS and 1% Penicillin/Streptomycin/Amphotericin B (PAN Biotech, Aidenbach Germany). All cell cultures  were incubated at 37°C in a humidified atmosphere of 5 % CO2 and periodically tested for mycoplasma using MycoSPY® kit from Biontex.

extract_protocol:
total RNA was extracted with Trizol® (Life Technologies, California, USA), treated with 7 Kunitz units of DNase I (Qiagen, Hilden, Germany) and further purified on RNeasy mini columns (Qiagen, Hilden, Germany) according to the manufacturer's instructions. RNA integrity was ascertained using the 2100 Bioanalyzer (Agilent, Santa Clara, CA).
1) mRNA enrichment and purification: Oligo dT Selection (mRNA enrichment): Use oligo dT beads to enrich mRNA with poly A tail. 2) RNA fragment and reverse transcription: Fragment the RNA and first-strand cDNA was generated using random N6-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP instead of dTTP. 3) End repair, add A and adaptor ligation: The synthesized cDNA was subjected to end-repair and then was 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments. 4) PCR amplification: Prior to PCR amplification, the dUTP-marked strand is selectively degraded by Uracil-DNA-Glycosylase(UDG). The remaining strand is amplified to generate a cDNA library suitable for sequencing. Many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer. 5) Single strand separation and cyclization: Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6) DNA nanoball synthesis. 7) Sequencing on DNBSEQ (DNBSEQ Technology) platform

treatment_protocol: SKOV3  was subjected to 72h of incubation with 1µg/ml of cisplatine.

value: Ovarian

value: EpCAM negative cells

value: isolated EpCAM negative cells


title: C57BL/6 B cells, p53-WT, pRetroX_M2_IRES_ZsGreen, Day 4 #1


title: OC236 EpCAM negative 2

description: Library name: sample13


title: OC236 EpCAM positive 3

description: Library name: sample11

value: EpCAM positive cells

value: isolated EpCAM positive cells


title: OC236 EpCAM positive 1

description: Library name: sample9


title: SKOV3 cp 3

description: Library name: sample7

value: cisplatine resistent

value: exposure to cisplatine and acquired resistance to cisplatine over time


title: OC236 EpCAM positive 2

description: Library name: sample10


title: SKOV3 cp 4

description: Library name: sample8


title: SKOV3 cp 2

description: Library name: sample6


title: SKOV3 wt 4

description: Library name: sample5

value: wt

value: no treatment


title: SKOV3 wt 3

description: Library name: sample4


title: RNA-Seq of Drosophila melanogaster: larval broad epidermal cells 4

description: Library name: r38_4

value: epidermal cells


title: SKOV3 wt 2

description: Library name: sample3


title: SKOV3 cp 1

data_processing:
HISAT was used to align the clean reads to the reference genome and Bowtie2 to align the clean reads to the reference genes.
Assembly: hg38
Supplementary files format and content: excel file with fpkm, tpm, read count and norm read count

growth_protocol: SKOV3  ovarian carcinomas were cultured in DMEM containing 10 % heat-inactivated FCS supplemented with 6µg/mLdoxycycline and incubated at 37°C in a humidified atmosphere of 5 % CO2. All cell cultures were periodically tested for mycoplasma using MycoSPY® kit from Biontex.

extract_protocol:
total RNA was extracted with Trizol® (Life Technologies, California, USA), treated with 7 Kunitz units of DNase I (Qiagen, Hilden, Germany) and further purified on RNeasy mini columns (Qiagen, Hilden, Germany) according to the manufacturer's instructions. RNA integrity was ascertained using the 2100 Bioanalyzer (Agilent, Santa Clara, CA).
In this project, 2 samples were sequenced using DNBSEQ platform, averagely generating about 18.2 Gb bases per sample. The average mapping ratio with reference genome is 98.30%, the average mapping ratio with gene is 70.29%; 18566 genes were identified. sequencing was performed by BGI Genomics (Hong Kong, China)
Sequencing length was PE150. The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads needed to be filtered before the data analysis for reliability analysis results.

value: ovarian carcinomas cells


title: tibia, DEX loading, 5

city: Saitama

first: Nagahiro

last: Ochiai

address: Yoshino-cho 1-403, Kita-ku

institute: Taisho Pharmaceutical, Co., Ltd

data_processing:
Sequenced reads were mapped and quantified using the RSEM v 1.2.28 in conjunction with the STAR aligner v 2.7.10a.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text-file includes read counts for each sample

source_name: tibia

growth_protocol: Three-month-old male C57BL/6J mice were obtained from The Jackson Laboratory for axial tibial loading studies.

extract_protocol:
The frozen bone tissue was pulverized under liquid nitrogen using a Freezer/Mill 6775 (SPEX). For the extraction of RNA, TRIzol reagent was applied to the crushed tissue, followed by chloroform addition for phase separation. The RNA-containing aqueous phase was isolated and purified using the Direct-zol MicroPrep kit.
Total RNA was extracted from mouse tibiae and used for library construction using the SMARTer Stranded Total RNA-Seq Kit v2—Pico Input Mammalian (Takara Bio, 634412).

treatment_protocol: The ElectroForce 5500 system (testing apparatus (TA) instruments) was employed to apply mechanical loading to the left tibia. The loading protocol consisted of 40 cycles per session with a trapezoidal waveform, applying a force of -13 N (approximately 1300 µε) for 0.1 seconds, followed by a 10-second rest interval, two times per week (day 1 and 3).

value: tibia

tag: mechanical loading

value: day 1 and 3

value: injection DEX (1mg/kg) s.c. for 5 days


title: RNA-Seq of Drosophila melanogaster: larval broad epidermal cells 3

description: Library name: r38_3


title: SKOV3 wt 1


title: tibia, DEX loading, 3


title: tibia, DEX loading, 2


title: dRNA-seq + SLAM-seq mock R1

value: primary fibroblasts

value: 4sU + IAA + XRN1

value: Mock

value: Replicate 1


title: tibia, DEX loading, 1


title: tibia, DEX control, 4


title: OC236 EpCAM negative 1

description: Library name: sample12

value: Ovarian

value: EpCAM negative cells


title: tibia, vehicle loading, 5

value: injection water s.c. for 5 days


title: tibia, DEX control, 3


title: tibia, vehicle loading, 1


title: tibia, vehicle loading, 2


title: tibia, vehicle loading, 4


title: tibia, vehicle loading, 3


title: tibia, vehicle control, 5


title: tibia, vehicle control, 3


title: tibia, vehicle control, 2


title: tibia, vehicle control, 1


title: tibia, DEX loading, 4


title: tibia, vehicle control, 4


title: tibia, DEX control, 5


title: tibia, DEX control, 2


title: tibia, DEX control, 1


title: H139-047_S22_L001

city: Rotterdam

first: Paul

last: Hengeveld

address: Dr Molewaterplein 40

department: Immunology

country: Netherlands

institute: Erasmus MC

description: TRBV rearrangements

library_source: genomic

data_processing:
NGS output was uploaded to the ARResT/Interrogate immunoprofiler. Samples  with <20.000 junctioned reads, excluding spiked sequences, were regarded as  QC-failed and discarded. Reads were converted to cell equivalents using the  EuroClonality central in-tube quality control. Clonotypes were defined as  sequences with identical TRBV and TRBJ gene usage, and 100% complementarity  determining region 3 (CDR3) amino acid sequence identity. Unproductive TRB  rearrangements were discarded. Clonotypes associated with <0.5 cell equivalents  were regarded as likely spillover reads and discarded. Shared clonotypes were  cross-referenced against the VDJdb T cell compendium.
Assembly: hg19
Supplementary files format and content: xslx file contained the QC-output of the Arrest/Interrogate immunoprofiler

molecule: genomic DNA

source_name: PBMC

extract_protocol:
DNA was extracted using a QIA-cube
TRB libraries were amplified from genomic DNA, using the EuroClonality two-step TRB assay, developed by the Euroclonality-NGS Working Group (manuscript in preparation), aiming for 1μg of PBMC DNA input per sample. After each PCR step, amplification success was checked using the D1000 DNA ScreenTape assay on a 4200 Agilent TapeStation (Agilent, Santa Clara, CA, USA) and libraries were purified using the AMPure XP kit (Beckman Coulter, Brae, CA, USA.
Pooled PCR products were diluted to 1nM and equimolarly pooled in a single library-pool. Multiplexed libraries sequenced at a final loading concentration of 70pM, with 20% of PhiX (Illumina, San Diego, CA, USA).

treatment_protocol: See methods section of HOVON-139 main publication

value: PBMC

value: Venetoclax/Obinutuzumab


title: H139-046_S21_L001

description: TRBV rearrangements


title: H139-043_S19_L001

description: TRBV rearrangements


title: H139-042_S18_L001

description: TRBV rearrangements


title: H139-041_S17_L001

description: TRBV rearrangements


title: H139-045_S20_L001

description: TRBV rearrangements


title: H139-040_S16_L001

description: TRBV rearrangements


title: H139-039_S15_L001

description: TRBV rearrangements


title: Knockout 3

type: RNA

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from brown adipose tissue of adipose Vegfa knockout.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 1.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package, with R version 2.12.0 and the Brainarray mogene10stmmentrezgcdf R package (version 14.0.0).

label: biotin

source_name: brown adipose tissue

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: aP2-Cre–/– ; Vegfa flox/flox  (littermate control) or aP2-Cre+/– ; Vegfaflox/flox (adipose tissue specific Vegfa knockout) mice were maintained on a standard chow diet (Harlan Teklad global 18% protein rodent diet, #2018). Brown adipose tissue was collected at 14 weeks of age.

extract_protocol: Total RNA was isolated from brown adipose tissue of adipose tissue–specific Vegfa-KO or littermate control mice with RNeasy Lipid Tissue Kit (QIAGEN).

treatment_protocol: Analysis was done at 12 to 14 weeks of age. aP2-Cre (Jackson Laboratories) and Vegfa flox/flox mice (provided by Napoleone Ferrara, Genentech Inc.) on a C57BL/6 background were crossed to create aP2-Cre+/– Vegfaflox/flox adipose tissue–specific Vegfa-KO mice.

value: brown adipose tissue

value: aP2-Cre+/- ; Vegfa flox/flox


title: Control 1

description: Gene expression data from brown adipose tissue of littermate control.

value: aP2-Cre-/- ; Vegfa flox/flox


title: Knockout 4


title: Control 3


title: H139-038_S14_L001

description: TRBV rearrangements


title: Control 2


title: Control 4


title: H139-036_S12_L001

description: TRBV rearrangements


title: Knockout 1


title: H139-035_S11_L001

description: TRBV rearrangements


title: H139-033_S9_L001

description: TRBV rearrangements


title: H139-032_S8_L001

description: TRBV rearrangements


title: H139-031_S7_L001

description: TRBV rearrangements


title: Knockout 2


title: H139-026_S4_L001

description: TRBV rearrangements


title: H139-030_S6_L001

description: TRBV rearrangements


title: H139-029_S5_L001

description: TRBV rearrangements


title: H139-025_S3_L001

description: TRBV rearrangements


title: H139-024_S2_L001

description: TRBV rearrangements


title: H139-022_S9_L001

description: TRBV rearrangements


title: H139-017_S6_L001

description: TRBV rearrangements


title: H139-019_S8_L001

description: TRBV rearrangements


title: H139-018_S7_L001

description: TRBV rearrangements


title: H139-024_S10_L001

description: TRBV rearrangements


title: H139-037_S13_L001

description: TRBV rearrangements


title: H139-016_S5_L001

description: TRBV rearrangements


title: H139-005_S2_L001

description: TRBV rearrangements


title: H139-012_S4_L001

description: TRBV rearrangements


title: H139-034_S10_L001

description: TRBV rearrangements


title: BmE cells, Relact, Biol rep3

city: Chongqing

first: Fei

address: #216 Tiansheng Road, Beibei District

institute: Southwest University

data_processing:
The clean reads, which were obtained after removing reads containing adapter, ploy-N and low-quality reads from raw data, were mapped to NCBI database using HISAT2 v2.0.4.
Differentially expressed genes (DEGs) were identified by DESeq R package (1.18.0). The resulting p-values were adjusted using the Benjamini-Hochberg method to control the false discovery rate. DEGs was defined as p-value < 0.05 and fold change ≥ 2 were.
Structural domain and signal peptide prediction using Smart and SignalP-5.0 programs to find which secreted protein(s) was transcriptionally regulated by BmRelishact.
Assembly: NCBI RefSeq Assembly GCF_014905235.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Bombyx mori

source_name: BmE cells

growth_protocol: BmE cells were maintained at 28°C in Grace medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was extracted from BmRelishact- or EGFP-expressing cells using the Total RNA Kit (Omega Bio-tek, R6934-01, USA) according to the manufacturer's instructions, and then sent to Novogene (China) for transcriptome sequencing.
RNA library were prepared using NEBNext RNA library prep kit by Novagene.

treatment_protocol: BmE cells were transfected with BmRelishact- or EGFP-expressing plasmid (1 μg/1×106 cell) using X-treme GENE transfection reagent (Roche, Switzerland) following the manufacturer's instructions and cultured for 48 hr before RNA extraction.

value: BmE cells

value: transfected with BmRelishact-expressing plamisd pSL1183-Relishact


title: H139-010_S3_L001

description: TRBV rearrangements


title: BmE cells, Relact, Biol rep1


title: BmE cells, EGFP, Biol rep1

value: transfected with EGFP-expressing plamisd pSL1180-EGFP


title: H139-066-T5_S17_L001

description: TRBV rearrangements


title: H139-004_S1_L001

description: TRBV rearrangements


title: BmE cells, EGFP, Biol rep2


title: H139-067-T5_S18_L001

description: TRBV rearrangements


title: H139-069-T5A_S19_L001

description: TRBV rearrangements


title: BmE cells, Relact, Biol rep2


title: BmE cells, EGFP, Biol rep3


title: H139-060-T5_S13_L001

description: TRBV rearrangements


title: H139-061-T5_S14_L001

description: TRBV rearrangements


title: KG-1a cells Overexpression blocking

first: Hui

middle: hui

last: Fu

address: 181 Hanyu Road, Shapingba District, Chongqing

institute: Affiliated Cancer Hospital of Chongqing University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by and the clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: txt，readcount

source_name: Cell line

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
The RNA library construction and subsequent RNA sequencing were performed by BGI-Shenzhen, China. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China)

value: Cell line

value: Leukemic stem cells

value: CX43 Overexpression

value: Co-culture  blocking


title: H139-059-T5_S12_L001

description: TRBV rearrangements


title: KG-1a cells Overexpression

value: Co-culture


title: KG-1a cells Overexpression control

value: CX43 Overexpression control


title: H139-055-T5_S10_L001

description: TRBV rearrangements


title: H139-052-T5_S8_L001

description: TRBV rearrangements


title: H139-053-T5_S9_L001

description: TRBV rearrangements


title: EV-miRNA by Pg-infection

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Human acute monocytic leukemia

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: The human monocytic cell line THP-1 was seeded at a concentration of 30,000 cells/mL and cultured in 10% FBS/RPMI 1640 medium at 37°C under a humidified atmosphere of 5% CO2.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

treatment_protocol: THP-1 cells were seeded in 10% FBS/RPMI 1640 medium. After 24 hours, they were differentiated into macrophages by treating them with 100 nM phorbol myristate acetate (PMA) for 48 hours. Subsequently, the medium was replaced with 2% FBS/RPMI 1640, and the cells were infected with Pg (MOI=100).

value: Pg-infection


title: KG-1a cells Monoculture

value: WT

value: Monoculture


title: H139-065-T5_S16_L001

description: TRBV rearrangements

value: PBMC


title: H139-051-T5_S7_L001

description: TRBV rearrangements

value: Venetoclax/Obinutuzumab


title: H139-050-T5_S6_L001

description: TRBV rearrangements


title: H139-062-T5_S15_L001

description: TRBV rearrangements


title: H139-049-T5_S5_L001

description: TRBV rearrangements


title: H139-047-T5_S4_L001

description: TRBV rearrangements


title: H139-045-T5_S3_L001

description: TRBV rearrangements


title: H139-040-T5_S18_L001

description: TRBV rearrangements


title: H139-042-T5A_S2_L001

description: TRBV rearrangements


title: EV-miRNA by non-infection

value: non-infection


title: H139-041-T5_S19_L001

description: TRBV rearrangements


title: H139-057-T5_S11_L001

description: TRBV rearrangements


title: H139-037-T5_S17_L001

description: TRBV rearrangements


title: H139-036-T5_S16_L001

description: TRBV rearrangements


title: H139-035-T5_S15_L001

description: TRBV rearrangements


title: H139-034-T5_S14_L001

description: TRBV rearrangements


title: DAP-CDF1_rep1

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

description: Protein-DNA interaction

data_processing:
2*75 bp pair-  ended reads
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with Bowtie2
BAM files are used for peak calling with GEMv3.4, using input files as control
Assembly: ENSEMBLE Solanum tuberosum, DM 1-3-516-R44v4.03 reference genome
Supplementary files format and content: Significant peaks of protein-DNA interactions in narrowpeak fromat generated by GEMv3.4
Library strategy: DAP-seq

organism: Solanum tuberosum

source_name: stolon

extract_protocol:
Genomic DNA extraacted with the CTAB method and RNase A treated
gDNA fragmented to 200 bp fragments in average and ligated a a truncated Illumina TruSeq adapter (Y adapter). gDNA library is incubated with recombinant protein expressed in E.coli, previously immobilized with Amylose beads. After binding and washing, DNA is eluted and PCR-amplified with Truseq primers, including a single index.

value: stolon

tag: protein

value: E.coli expressed


title: H139-030-T5_S13_L001

description: TRBV rearrangements


title: Input Stub

description: Input DNA for samples 2-4

value: input


title: RNAi StCDF1.2 rep 1

data_processing:
2*150 bp pair  -  ended reads with a total of at least 6GB of data per replicate
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with HISAT2
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) based on transcript abundance by HTSeq-count
Statistical analysis of differential gene expression between overexpressed StCDF1 and knockdown StCDF1 was conducted with DESeq2
Assembly: ENSEMBLE Solanum tuberosum, DM 1-3-516-R44v4.03 reference genome
Supplementary files format and content: Text format with seven  columns: gene_ID and FPKM of genes per sample

source_name: Thrid leaf

growth_protocol: Plants were initially grown in tissue culture and  further transplanted into soil and grown in climate cha  mbers under short days. After 4 weeks,  the third leaf from the apex was sampled at  ZT

extract_protocol:
Total RNA was extracted with RNeasy Plus Mini Kit (Qiagen, the Netherlands). RNA qualit  y  and quantity were evaluated by NanoDrop 1000 V.3.7
The RNA-seq library was prepared by Novogene, using standard Illumina protocols.

value: Thrid leaf

value: diploid potato CE3027

value: RNAi StCDF1.2


title: Overexpression StCDF1.2 rep 2

value: Overexpression StCDF1.2


title: siNCOA7+IL1B_12

city: Pittsburgh

last: Okawa

state: PA

address: 200 Lothrop Street

institute: University of Pittsburgh

hyb_protocol: Following fragmentation and end labeling, ss-cDNA was hybridized on the Human Clariom D GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner with 7G upgrade.

data_processing: Microarray data were obtained using the Affymetrix Clariom D Human Array at the Genomics Research Core at the University of Pittsburgh. The microarray chip was performed on four groups in triplicate for a total of 12 samples. PAECs were subjected to either knockdown control or of the gene NCOA7. Additionally, groups were then either left in control conditions or further challenged with the proinflammatory cytokine IL-1β for 24 hours. Raw data were processed using Bioconductor packages in the language R to produce a list of differentially expressed genes that were selected using a Benjamini-Hochberg corrected p-value less than 0.05 in order to minimize the false discovery rate (FDR). The following add-on packages were utilized: oligo, limma, affycore tools, gplots, pd.clariom.d.human for the analysis of this microarray data. Very broadly, the flow of this program serves to take raw microarray data in .CEL format into a list of differentially expressed genes. The workflow included loading the raw data into R, filtering and normalizing the raw data, plotting to demonstrate uniformity among the samples, adding annotations, setting up a comparison matrix to run statistical analyses among the groups, generating a list of differentially expressed genes, filtering said list, and constructing a heat map to depict generalized trends.

label: Biotin

source_name: siNCOA7+IL1B human PAECs

label_protocol: Biotinylate ss-cDNA were prepared according to Affymetrix Clariom D protocol.

growth_protocol: Human PAECs (Lonza; CC-2530) were grown in Endothelial Growth Media-2 (EGM-2; Lonza; CC-3162).

extract_protocol: Cells were lysed in QIAzol Lysis Reagent (Qiagen; 79306), and RNA was extracted using the Rnaeasy Kit (Qiagen; 74004).

treatment_protocol: Human PAECs were transfected at approximately 70 to 80% confluency using negative control (siNC) or NCOA7 (siNCOA7) silencing RNA (siRNA) at 20 nM. Lipofectamine® 2000 (ThermoFisher; 11668019) was mixed with siRNA per manufacturer’s protocol. Lipofectamine®:siRNA mixture was incubated with human PAECs in Opti-MEMTM reduced serum media for 4 to 6 hours (ThermoFisher; 31985062). After incubation, transfection media was removed and replaced with full serum, cell-specific growth media. Experiments were performed 48 hours post-transfection.

value: Human pulmonary artery endothelial cells


title: H139-024-T5_S10_L001

description: TRBV rearrangements


title: siNCOA7+IL1B_11


title: siNCOA7+IL1B_10


title: Overexpression StCDF1.2 rep 1


title: siNCOA7_7

source_name: siNCOA7 human PAECs


title: H139-022-T5_S9_L001

description: TRBV rearrangements


title: WT control plants rep 2

value: WT control plants


title: siNCOA7_8


title: siNC_3

source_name: siNC human PAECs

value: siNC


title: H139-018-T5_S8_L001

description: TRBV rearrangements


title: H139-017-T5_S7_L001

description: TRBV rearrangements


title: siNCOA7_9


title: WT control plants rep 1


title: H139-016-T5_S6_L001

description: TRBV rearrangements


title: HCC day 16 OE rep 2

city: Heidelberg

first: Moritz

last: Mall

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

description:
Library name: HCC_d16_Prox1_108
Prox1 OE d16

data_processing:
Raw reads were mapped to the reference genome mm10 using STAR.
Differential expression was determined using DESeq2 (R package version 1.28.1) with size factor normalization and Wald significance tests.
Assembly: mm10
Supplementary files format and content: tsv file with deseq2 statistics (vs EV control as baseline)
Supplementary files format and content: tsv file with normalised counts

source_name: Liver tumour

extract_protocol:
At day 16 following HDTVI, primary mouse liver tumor samples were dissected and placed into TRIzol (Invitrogen). Samples were crushed and then homogenized using QIAshredder (Qiagen).
For bulk RNA sequencing, libraries were prepared according to the dUTP protocol and paired-end sequencing (2x100bp) was performed on the NovaSeq 6000 platform (Illumina).

treatment_protocol: For hydrodynamic tail vein injection (HDTVI), 2 mL of sterile 0.9% NaCl solution, corresponding to 10% of body weight, containing the plasmids of interest was injected into the tail vein of 8-week-old female C57BL/6N mice within 5 to 7 s. Each mouse was injected with 20 µg of pX330-sgRNA-Tp53 (p53 KO) and 4 µg of CMV-Sleeping Beauty transposase plus 10 µg of pT3-EF1a-MYC-IRES-rtTA (Myc OE), together with 10 µg of pT3-Tre-FLAG-mmProx1-IRES-GFP (late Prox1 overexpression) or pT3-Tre-IRES-GFP (EV control). A doxycycline-containing diet (6.25% doxycycline hyclate, Envigo Teklad, Indianapolis) was given at day 14 to induce Prox1 overexpression and livers were harvested on day 16.

value: Liver tumour

value: Hepatocytes (transformed)

value: Myc OE, p53 KO, late Prox1 overexpression


title: siNC+IL1B_4

source_name: siNC+IL1B human PAECs


title: H139-012-T5_S5_L001

description: TRBV rearrangements


title: HCC day 16 OE rep 1

description:
Library name: HCC_d16_Prox1_106
Prox1 OE d16


title: RNAi StCDF1.2 rep 2


title: H139-027-T5_S11_L001

description: TRBV rearrangements


title: H139-028-T5_S12_L001

description: TRBV rearrangements


title: siNC_2


title: HCC day 16 OE rep 3

description:
Library name: HCC_d16_Prox1_109
Prox1 OE d16


title: siNC+IL1B_6


title: H139-010-T5_S4_L001

description: TRBV rearrangements


title: HCC day 16 EV rep 3

description:
Library name: HCC_d16_EV_103
Control d16

value: Myc OE, p53 KO, control overexpression


title: H139-004-T5_S3_L001

description: TRBV rearrangements

value: PBMC


title: H139-001-T5_S2_L001

description: TRBV rearrangements

value: Venetoclax/Obinutuzumab


title: siNC+IL1B_5


title: siNC_1


title: HCC day 16 EV rep 2

description:
Library name: HCC_d16_EV_102
Control d16


title: H139-069_S21_L001

description: TRBV rearrangements


title: HCC day 16 EV rep 1

description:
Library name: HCC_d16_EV_101
Control d16


title: H139-070_S22_L001

description: TRBV rearrangements


title: Akt_Notch OE rep 1

description:
Library name: Akt_Notch_OE_rep1
Prox1 OE

data_processing:
Raw reads were mapped to the reference genome mm10 using STAR.
Differential expression was determined using DESeq2 (R package version 1.28.1) with size factor normalization and Wald significance tests.
Assembly: mm10
Supplementary files format and content: tsv file with deseq2 statistics (vs control as baseline)
Supplementary files format and content: tsv file with normalised counts

extract_protocol:
After one week of overexpression or at humane endpoint, primary mouse liver tumor samples were dissected and placed into TRIzol (Invitrogen). Samples were crushed and then homogenized using QIAshredder (Qiagen).
For bulk RNA sequencing, libraries were prepared according to the dUTP protocol and paired-end sequencing (2x100bp) was performed on the NovaSeq 6000 platform (Illumina).

treatment_protocol: For hydrodynamic tail vein injection (HDTVI), 2 mL of sterile 0.9% NaCl solution, corresponding to 10% of body weight, containing the plasmids of interest was injected into the tail vein of 8-week-old female C57BL/6N mice within 5 to 7 s. Each mouse was injected with 4 µg of CMV-Sleeping Beauty transposase and 10 µg pT3-EF1a-based plasmid for transposon-mediated stable overexpression of Akt (pT3-EF1a-AKT) and NICD (pT3-EF1a-NICD-IRES-rtTA), together with 10 µg of pT3-Tre-FLAG-mmProx1-IRES-GFP (late Prox1 overexpression) or pT3-Tre-IRES-GFP (EV control). A doxycycline-containing diet (6.25% doxycycline hyclate, Envigo Teklad, Indianapolis) was given at day 21 to induce Prox1 overexpression from week 3 to 4.

value: AKT/NICD, late Prox1 overexpression


title: Akt_Notch OE rep 2

description:
Library name: Akt_Notch_OE_rep2
Prox1 OE


title: Akt_Notch OE rep 3

description:
Library name: Akt_Notch_OE_rep3
Prox1 OE


title: H139-067_S19_L001

description: TRBV rearrangements


title: H139-068_S20_L001

description: TRBV rearrangements


title: Akt_Notch Control rep 1

description:
Library name: Akt_Notch_EV_rep1
Control

value: AKT/NICD, GFP control overexpression


title: Akt_Notch Control rep 2

description:
Library name: Akt_Notch_EV_rep2
Control


title: H139-066_S18_L001

description: TRBV rearrangements


title: H139-065_S17_L001

description: TRBV rearrangements


title: H139-064_S16_L001

description: TRBV rearrangements


title: H139-062_S15_L001

description: TRBV rearrangements


title: BUMPT cells,tRF-Val-2

city: Changsha

first: Ni

last: Yin

state: Hunan

address: Yin Penling Street

institute: The Third Xiangya Hospital, Central South University

description: Library name: Sample 5

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0)software
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.10.0)
Assembly: GRCh38
Supplementary files format and content: The xlsx format file contains the FPKM value of gene in every sample

source_name: BUMPT cells

extract_protocol:
he joint capsule tissues were washed by phosphate buffer saline, and then synovium tissues were removed from joint capsules. The isolated joint capsule tissues were used in following study，RNA was harvested using Trizol reagent.RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Libraries were prepared by using KAPA Stranded RNA-Seq Library Prep Kit(Illumina). Briefly,Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

value: BUMPT cells

value: Renal tubular epithelial cells


title: BUMPT cells, tRF-Val-1

description: Library name: Sample 4


title: H139-060_S13_L001

description: TRBV rearrangements


title: H139-061_S14_L001

description: TRBV rearrangements


title: BUMPT cells, NC-2

description: Library name: Sample 2


title: BUMPT cells, tRF-Val-3

description: Library name: Sample 6


title: BUMPT cells, NC-3

description: Library name: Sample 3


title: H139-059_S12_L001

description: TRBV rearrangements


title: H139-057_S11_L001

description: TRBV rearrangements


title: H139-056_S10_L001

description: TRBV rearrangements


title: V28z/αNGF, scRNA-seq

city: Nanjing

first: peiwei

last: yang

state: Jiangsu

address: 639 Longmian Avenue

institute: China pharmaceutical university

data_processing:
FASTQ files were quantified using CellRanger, referencing the mm10 genome
Assembly: mm10
Supplementary files format and content: tab-saperated value files and matrix

source_name: tumor

extract_protocol:
Freshly collected tumor tissues were pooled (3 tumors per group). The tissues were minced and digested using the Tumor Dissociation Kit. The digested cell suspension was filtered through a 70 μm filter. Dead cells were removed using the Dead Cell Removal Kit.
Single viable cells were collected, and the library was prepared using the 10x Genomics 3′ V3 kit, following the standard protocol of 10x Genomics. The prepared library was sequenced on the Novaseq 6000 platform using the PE150 mode.

value: tumor

value: mix cell

value: distal tumor


title: H139-055_S9_L001

description: TRBV rearrangements


title: V28z, scRNA-seq


title: H139-054_S8_L001

description: TRBV rearrangements


title: T_V28z/αNGF replicate 3, RNA-seq

data_processing:
Paired FASTQ data were quantified for transcripts by aligning to the mm39 reference genome using Salmon
Assembly: mm39
Supplementary files format and content: comma-saperated value files and matrix

source_name: spleen

extract_protocol:
For tumor RNA-seq, total RNA is extracted from tumor tissues. For T cell RNA-seq, T cells are isolated from activated splenocytes using the above method, and total RNA is extracted from the T cells.
Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit

value: spleen

value: T cell


title: H139-053_S7_L001

description: TRBV rearrangements


title: H139-052_S6_L001

description: TRBV rearrangements


title: T_V28z/αNGF replicate 2, RNA-seq


title: T_V28z/αNGF replicate 1, RNA-seq


title: H139-050_S4_L001

description: TRBV rearrangements


title: T_V28z replicate 3, RNA-seq


title: T_V28z replicate 1, RNA-seq


title: H139-048_S2_L001

description: TRBV rearrangements


title: H139-051_S5_L001

description: TRBV rearrangements


title: H139-069-T6-4_S24_L001

description: TRBV rearrangements


title: T_V28z replicate 2, RNA-seq


title: V28z/αNGF replicate 3, RNA-seq


title: H139-065-T6-4_S21_L001

description: TRBV rearrangements


title: BUMPT cells, NC-1

description: Library name: Sample 1


title: H139-066-T6-4_S22_L001

description: TRBV rearrangements


title: H139-067-T6-4_S23_L001

description: TRBV rearrangements


title: V28z/αNGF replicate 2, RNA-seq


title: V28z/αNGF replicate 1, RNA-seq


title: UT, scRNA-seq


title: V28z replicate 2, RNA-seq


title: H139-062-T6-4_S20_L001

description: TRBV rearrangements


title: H139-061-T6-4_S19_L001

description: TRBV rearrangements


title: V28z replicate 3, RNA-seq


title: H139-060-T6-4_S18_L001

description: TRBV rearrangements


title: H139-059-T6-4_S17_L001

description: TRBV rearrangements


title: V28z replicate 1, RNA-seq


title: UT replicate 3, RNA-seq


title: H139-057-A-T6-4_S16_L001

description: TRBV rearrangements


title: H139-049_S3_L001

description: TRBV rearrangements


title: T_UT replicate 2, RNA-seq


title: UT replicate 1, RNA-seq


title: H139-055-T6-4_S15_L001

description: TRBV rearrangements


title: H139-052-T6-4_S13_L001

description: TRBV rearrangements


title: H139-051-T6-4_S12_L001

description: TRBV rearrangements


title: DTA+ rep 1

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

data_processing:
Raw sequencing data was processed by cellranger v4.0.0 'count' with default settings.
Assembly: mm10
Supplementary files format and content: CellRanger output files in tab-delimited text or matrix formats.

source_name: Male Genitalia

extract_protocol:
10x genomics
Libraries were generated by using 10x 3' mRNA single cell kit

value: Male

value: Genitalia

value: DTA+


title: T_UT replicate 1, RNA-seq


title: DTA+ rep 2


title: UT replicate 2, RNA-seq


title: H139-053-T6-4_S14_L001

description: TRBV rearrangements


title: H139-050-T6-4_S11_L001

description: TRBV rearrangements


title: DTA- rep 2

value: WT


title: H139-047-T6-4_S9_L001

description: TRBV rearrangements


title: H139-046-T6-4_S8_L001

description: TRBV rearrangements


title: Tex-2

city: shang hai

first: yin

middle: shen

last: hui

address: xiangyin road 800

institute: Second military medical university

data_processing:
Hisat2 (version:2.0.4)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM counts for each sample

extract_protocol:
RNA was harvest with trizol kit; 0.6 μg RNA was used for the construction of sequencing libraries.
RNA library for RNA-sequencing were prepared using Illumina standard instruction (VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® )

value: t cell


title: H139-049-T6-4_S10_L001

description: TRBV rearrangements


title: DTA- rep 1


title: Teff-3


title: H139-045-T6-4_S7_L001

description: TRBV rearrangements


title: Tex-3


title: H139-042-T6-4_S6_L001

description: TRBV rearrangements


title: Tex-1


title: Teff-1


title: H139-041-T6-4_S5_L001

description: TRBV rearrangements


title: Teff-2


title: H139-040-T6-4_S4_L001

description: TRBV rearrangements


title: SPF2

city: Jerusalem

first: Yasmin

last: Jaber

address: Hadassah Ein-Kerem

country: Israel

institute: Hebrew University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using spacernager
Assembly: mm10
Supplementary files format and content: 10x counts: zipped folder of tab-separated values files and matrix files from cellranger
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in jason format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Gingival mucosa

growth_protocol: SPF mice were kept in Specific-pathogen-free facilities while GF nice were kept in Germ-free facilities in the IACUC of the Weizmann Institute of Science. Housing conditions were 21-24°C, 30-70% humidity, with lights in the room for 12 hours, between 7:00-19:00, and dark for 12 hours from 19:00-7:00.

extract_protocol:
Mice were euthanized and gingival tissues were extracted. OCT coated freshly obtained tissues were placed in OCT filled cryomold, which was lowered into metal beaker with isopanteneplaced in a liquid nitrogen dewar. Samples were stored in sealed containers in -80 conditions.
Library was prepared using Visium Spatial Gene Expression Reagent Kit

value: SPF

value: Gingival mucosa


title: H139-037-T6-4_S3_L001

description: TRBV rearrangements

source_name: PBMC

value: PBMC

value: Venetoclax/Obinutuzumab


title: SPF1

description: 10x Genomics


title: GF2

description: 10x Genomics

value: GF


title: H139-036-T6-4_S2_L001

description: TRBV rearrangements


title: H139-034-T6-4_S24_L001

description: TRBV rearrangements


title: Yasmin_10x_010123_GF

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using cellranger
Assembly: mm10
Supplementary files format and content: 10x counts: zipped folder of tab-separated values files and matrix files from cellranger

source_name: gingival mucosa

extract_protocol:
The gingival tissues were excised. Tissues were then minced and treated with a Collagenase type II (2 mg/mL; Worthington Biochemicals) and DNase I (1 mg/mL; Sigma) solution in PBS plus 2% FCS for 25 min at 37 °C in a shaker bath. A total of 20 μL of 0.5 M EDTA per 2 mL sample was added to the digested tissues and incubated for an additional 10 min. The cells were then washed and filtered with 70-μM filter.
Library was prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index)

value: gingival mucosa


title: H139-030-T6-4_S22_L001

description: TRBV rearrangements

data_processing:
NGS output was uploaded to the ARResT/Interrogate immunoprofiler. Samples  with <20.000 junctioned reads, excluding spiked sequences, were regarded as  QC-failed and discarded. Reads were converted to cell equivalents using the  EuroClonality central in-tube quality control. Clonotypes were defined as  sequences with identical TRBV and TRBJ gene usage, and 100% complementarity  determining region 3 (CDR3) amino acid sequence identity. Unproductive TRB  rearrangements were discarded. Clonotypes associated with <0.5 cell equivalents  were regarded as likely spillover reads and discarded. Shared clonotypes were  cross-referenced against the VDJdb T cell compendium.
Assembly: hg19
Supplementary files format and content: xslx file contained the QC-output of the Arrest/Interrogate immunoprofiler

extract_protocol:
DNA was extracted using a QIA-cube
TRB libraries were amplified from genomic DNA, using the EuroClonality two-step TRB assay, developed by the Euroclonality-NGS Working Group (manuscript in preparation), aiming for 1μg of PBMC DNA input per sample. After each PCR step, amplification success was checked using the D1000 DNA ScreenTape assay on a 4200 Agilent TapeStation (Agilent, Santa Clara, CA, USA) and libraries were purified using the AMPure XP kit (Beckman Coulter, Brae, CA, USA.
Pooled PCR products were diluted to 1nM and equimolarly pooled in a single library-pool. Multiplexed libraries sequenced at a final loading concentration of 70pM, with 20% of PhiX (Illumina, San Diego, CA, USA).


title: P5

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

institute: HUJI

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10 (ref 1). The processed reads were aligned to the mouse transcriptome and genome version GRCm39 with annotations from Ensembl release 106 using TopHat v2.1.1. Counts per gene quantification was done with htseq-count v2.01. Normalization and differential expression analysis were done with the DESeq2 package v 1.36.0.
Assembly: GRCm39 with annotations from Ensembl release 106
Supplementary files format and content: raw_and_norm_counts.txt
Supplementary files format and content: Each row in the file contains a certain ensembl Gene ID, Symbol, name, raw counts and DESEq2 normalized counts per sample. Missing values are denoted by “?” are for genes with a too low expression that were filtered out prior to normalization (sum of counts in all samples lower than 10).

source_name: Palatal gingival epithelium

growth_protocol: Housing conditions were 21-24°C, 30-70% humidity, with lights in the room for 12 hours, between 7:00-19:00, and dark for 12 hours from 19:00-7:00.

extract_protocol:
gingival tissues were incubated in 1 mL of 4 mg/ml Dispase in PBS + 2% FCS until fully distended for 30 min and epithelium was carefully separated using forceps and binocular microscope. Buccal and palatal sides were seperated and RNA was extracted using QIAGEN RNeasy Micro Kit according to the manufacturer's instructions.
PolyA-selection, mRNA libraries were prepared using KAPA Stranded mRNA kit with mRNA Capture Beads (KAPA Biosystems, KK8421). In brief, 1µg was used for the library construction; library was eluted in 20µl of elution buffer. All DNA samples libraries were pooled to 10nM sample. Multiplex samples Pool were loaded on NovaSeq 6000 (Illumina), using NovaSeq 6000 SP Reagent Kit v1.5 100 cycles (cat# 20028401), with 122 cycles
Single End 122bp length

value: Palatal gingival epithelium


title: GF1

description: 10x Genomics


title: H139-033-T6-4_S23_L001

description: TRBV rearrangements


title: P4


title: H139-025-T6-4_S20_L001

description: TRBV rearrangements


title: H139-027-T6-4_S21_L001

description: TRBV rearrangements


title: H139-022-T6-4_S19_L001

description: TRBV rearrangements


title: P2


title: P1


title: P3


title: H139-019-T6-4_S16_L001

description: TRBV rearrangements


title: H139-018-T6-4_S15_L001

description: TRBV rearrangements


title: H139-020-T6-4_S17_L001

description: TRBV rearrangements


title: H139-015-T6-4_S14_L001

description: TRBV rearrangements


title: B3

source_name: buccal gingival epithelium

value: buccal gingival epithelium


title: B5


title: H139-013-T6-4_S13_L001

description: TRBV rearrangements


title: B1


title: H139-012-T6-4_S12_L001

description: TRBV rearrangements


title: H139-035-T6-4_S25_L001

description: TRBV rearrangements


title: Yasmin_10x_010123_SPF

description: 10x Genomics


title: H139-011-T6-4_S11_L001

description: TRBV rearrangements


title: HepDKO ZT22,Nodose, biol rep 2

city: Philadelphia

first: Mohit

middle: K.

last: Midha

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
RNA-sequencing reads were assessed for quality using FASTQC (0.11.7) and Trim Galore (0.6.10) was used for trimming adapters. High-quality processed reads were mapped to mouse genome (UCSC mm10) using STAR (V2.7.10b)with “--quantMode GeneCounts” to obtain gene-based counts.
Assembly: mm10
Supplementary files format and content: Tab-limited text file for raw-counts for each sample

source_name: Nodose ganglion

growth_protocol: Male Rev-erba/b flox/flox mice on a C57Bl6/J background were maintained in 12:12 light:dark conditions at 27C with ad libitum access to food and normal chow diet. 6-10 week old mice underwent tail vein injection of AAV8-TBG-EGFP to create the control group or AAV8-TBG-Cre to create the HepDKO group. Animals were under these envirionmental conditions for 2-4 weeks before euthanasia and tissue collection.

extract_protocol:
For arcuate samples, the tissue was homogenized with 1mL of QIAzol Lysis Reagent  (Qiagen, 79306) using Pellet-Pestel (Kimble, 749540). After homogenization, total RNA was purified and collected using RNeasy Mini Kits (Qiagen, 74004). RNA quality and quantity was determined by NanoDrop (Thermo Scientific, ND-ONE-W). Arcuate library preparation and sequencing were performed by Novogene, Inc. For nodose samples, the tissue was homogenized with 1mL of QIAzol Lysis Reagent  (Qiagen, 79306) using Pellet-Pestel (Kimble, 749540). After homogenization, total RNA was purified and collected using RNeasy Mini Kits (Qiagen, 74004). RNA quality and quantity was determined by NanoDrop (Thermo Scientific, ND-ONE-W). 500ng of total purified RNA was used for library preparation with the KAPA RNA HyperPrep Kit with RiboErase (HMR) for Illumina Platforms (KAPA Biosystems KK8561) according to the manufacturers protocol.
Total Arc RNA was sent to Novogene, Inc. for library preparation and sequencing. For nodose samples, 500ng of total purified RNA was used for library preparation with the KAPA RNA HyperPrep Kit with RiboErase (HMR) for Illumina Platforms (KAPA Biosystems, KK8561) according to the manufacturers protocol.

treatment_protocol: Arcuate micropunches were collected from three mice per group per time point and pooled for each biological replicate. Left nodose ganglia were collected from four mice per group per time point and pooled for each biological replicate. Tissue pools were snap frozen in liquid nitrogen and stored at -80C until RNA extraction.

value: Nodose ganglion

tag: time(zt)

value: Reverb a/b fl/fl

value: 10-12 weeks

tag: diet

value: Chow

value: AAV8-TBG-Cre tail vein injection


title: H139-009-T6-4_S9_L001

description: TRBV rearrangements


title: HepDKO ZT16,Nodose, biol rep 3

value: Male


title: HepDKO ZT22,Nodose, biol rep 1


title: H139-021-T6-4_S18_L001

description: TRBV rearrangements


title: H139-010-T6-4_S10_L001

description: TRBV rearrangements


title: H139-008-A-T6-4_S8_L001

description: TRBV rearrangements


title: HepDKO ZT16,Nodose, biol rep 1


title: H139-007-T6-4_S7_L001

description: TRBV rearrangements


title: HepDKO ZT16,Nodose, biol rep 2


title: H139-006-T6-4_S6_L001

description: TRBV rearrangements


title: B4


title: H139-005-T6-4_S5_L001

description: TRBV rearrangements


title: HepDKO ZT10,Nodose, biol rep 3


title: H139-004-T6-4_S4_L001

description: TRBV rearrangements


title: B2


title: HepDKO ZT10,Nodose, biol rep 1


title: HepDKO ZT10,Nodose, biol rep 2


title: HepDKO ZT4,Nodose, biol rep 3


title: H139-003-T6-4_S3_L001

description: TRBV rearrangements


title: H139-001-T6-4_S2_L001

description: TRBV rearrangements


title: HepDKO ZT22,Nodose, biol rep 3


title: Control ZT22,Nodose, biol rep 3

value: AAV8-TBG-EGFP tail vein injection


title: Control ZT22,Nodose, biol rep 2


title: HepDKO ZT4,Nodose, biol rep 2


title: HepDKO ZT4,Nodose, biol rep 1


title: Control ZT22,Nodose, biol rep 1


title: Control ZT16,Nodose, biol rep 1


title: Control ZT16,Nodose, biol rep 2


title: Heat stress rep3 (HS3)

city: Nakhon Ratchasima

first: Yongcai

last: Zhu

address: School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand

country: Thailand

institute: Suranaree University of Technology

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument，image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB + GAPipeline-1.6 (Illumina) on the NovaSeq instrument，image analysis and base calling were conducted by the Zebeacall on the MGI2000 instrument.
Low-quality and technical sequences were removed from the raw sequencing reads using Cutadapt version 1.9.1
Hisat2 version 2.0.1 was used to align the clean reads against the chicken reference genome, GRCg6a (GenBank Assembly ID: GCF_000002315.6).
Gene expression levels were estimated based on fragments per kilobase of transcript per million fragments mapped (FPKM) using HTSeq version 0.6.1. The DESeq2 Bioconductor package was used for differential expression analysis between control and heat stress groups.
Assembly: GCF_000002315.6_GRCg6a
Supplementary files format and content: Column 1, st_gene_id; Column 2, gene_id; Column 3, gene_symbol; Column 4 - 9,   Sample_FPKM: FPKM of each gene; Column 10-115, Sample: read_count, count of each gene.

organism: Gallus gallus

source_name: Jejunal mucosa

extract_protocol:
Total RNA was harvested using  an RNeasy Mini Kit (Qiagen, Hilden, Germany). Three RNA pools were generated for each treatment from 12 hens, with each pool consisting of four individual jejunal mucosa samples. The pooled samples were utilized to create an RNA-seq library.
The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, and fragments of ~400 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR andP5/ P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: Jejunal mucosa

tag: breed

value: SUT breeder hen

value: Acute heat stress


title: Heat stress rep2 (HS2)


title: Heat stress rep1 (HS1)


title: Control ZT10,Nodose, biol rep 2


title: Control ZT10,Nodose, biol rep 1


title: Control rep3 (CS3)

value: No heat stress


title: Sham group-4

city: Jiaxing

first: Huadong

last: Ni

address: zhonghuan nan road 1882

institute: Department of Anesthesiology and Pain Research Center, The Affiliated Hospital of Jiaxing University

hyb_protocol: Labeled cRNA (1 μg) for each sample was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, followed by heating at 60°C for 30 min. Finally, 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. Hybridization solution (50 μl) was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hrs at 65°C in an Agilent hybridization oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using a DNA Microarray Scanner (part No. G2505C, Agilent, Santa Clara, CA, USA).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). Differentially expressed lncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering.

organism: Rattus norvegicus

source_name: DRG, Sham group-4

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNA samples were then purified using RNeasy Mini Kit (Qiagen, Hilden, Germany). Concentration and specific activity of labeled cRNA samples (pmol Cy3/μg cRNA) were subsequently measured using a NanoDrop ND-1000.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: DRG tissues from bone cancer pain and sham group rats and promptly frozen in liquid nitrogen.

value: DRG

tag: gender

value: female


title: Control ZT4,Nodose, biol rep 3

tag: Sex


title: Control rep2 (CS2)


title: Control ZT4,Nodose, biol rep 2


title: Control rep1 (CS1)


title: BCP group-4

source_name: DRG, BCP group-4


title: Control ZT4,Nodose, biol rep 1


title: Sham group-1

source_name: DRG, Sham group-1


title: Sham group-3

source_name: DRG, Sham group-3


title: P6497-24hpi-RNA-seq_rep2

first: Haidong

last: Shu

address: Weigang NO.1

department: Department of Plant Pathology

institute: Nanjing Agricultural University

data_processing:
Clean reads were aligned to Phytophthora sojae whole genome using hisat2 v2.1.0 with default parameters
TPM was calculated using stringtie v1.3.3b with default parameters
Assembly: Phytophthora sojae V1.1
Supplementary files format and content: Excel file with gene expression matrix (TPM value of all genes)
Supplementary files format and content: gtf files include FPKM,TPM,and coverage values for each Sample

organism: Phytophthora sojae

source_name: 24hpi Phytophthora sojae infected soybean

extract_protocol:
Total RNA was extracted using the E.Z.N.A.® Total RNA Kit I (Omega BIO-TEK) according to the product manual.
RNA libraries were prepared for sequencing using standard Illumina protocols. RNA-seq library preparation and construction services were  provided by BGI.

tag: Stage

value: WT


title: BCP group-2

source_name: DRG, BCP group-2


title: HepDKO, ZT22, Arcuate Nucleus, biol rep 2

source_name: Arcuate Nucleus

value: Arcuate Nucleus

tag: genotype


title: P6497-24hpi-RNA-seq_rep1

tag: tissue

value: 24hpi Phytophthora sojae infected soybean


title: P6497-12hpi-RNA-seq_rep2

source_name: 12hpi Phytophthora sojae infected soybean


title: HepDKO, ZT22, Arcuate Nucleus, biol rep 1

tag: age


title: Control ZT16,Nodose, biol rep 3

tag: treatment


title: Sham group-2

source_name: DRG, Sham group-2


title: BCP group-3

source_name: DRG, BCP group-3


title: Control ZT10,Nodose, biol rep 3


title: P6497-12hpi-RNA-seq_rep1

value: 12hpi Phytophthora sojae infected soybean


title: HepDKO, ZT16, Arcuate Nucleus, biol rep 3


title: HepDKO, ZT16, Arcuate Nucleus, biol rep 2


title: P6497-MY-ChIP-seq_H3K4me3_rep2

data_processing:
Clean reads were aligned to P. sojae or P. infestans genome using bowtie2 v2.3.3.1 with parameter -N 1
Bigwig files were generated by DeepTools "bamCompare" using --normalizeUsing RPKM --scaleFactorsMethod None or "bamCoverage"
Assembly: Psojae v1.1 and P. infestans(T30-4)
Supplementary files format and content: Bigwig files, scores represent enriched value(log2(fold-change))

source_name: Phytophthora sojae mycelium

extract_protocol:
After antibody Immunoprecipitation, target DNA was eluted from Dynabeads and precipitated using ethanol followed by twice washes, finally the samples was dried and dissolved in 33 μl ddH2O
Qualified library for sequencing was prepared using the QIAquick PCR Purification Kit(Qiagen). Briefly, 10-300ng DNA was taken to do DNA-end repair(3'-dA overhang and ligation of methylated sequencing adaptors) followed by PCR amplication and size selection (usually 100-300bp, including adaptor sequencing).

value: Phytophthora sojae mycelium

value: mycelium

tag: chip antibody

value: H3K4me3(abcam, ab8580)


title: HepDKO, ZT16, Arcuate Nucleus, biol rep 1

value: Reverb a/b fl/fl

value: 10-12 weeks

value: Chow


title: P6497-24hpi-ChIP-seq_input_rep2


title: HepDKO, ZT10, Arcuate Nucleus, biol rep 3

value: Male

value: AAV8-TBG-Cre tail vein injection


title: HepDKO, ZT10, Arcuate Nucleus, biol rep 2


title: P6497-24hpi-ChIP-seq_input_rep1


title: HepDKO, ZT10, Arcuate Nucleus, biol rep 1


title: P6497-24hpi-ChIP-seq_H3K36me3_rep1

value: H3K36me3(abcam, ab9050)


title: P6497-24hpi-ChIP-seq_H3K27me3_rep2

value: H3K27me3(millipore, 07-449)


title: P6497-24hpi-ChIP-seq_H3K36me3_rep2


title: HepDKO, ZT22, Arcuate Nucleus, biol rep 3


title: HepDKO, ZT4, Arcuate Nucleus, biol rep 2


title: Control, ZT22, Arcuate Nucleus, biol rep 3

value: AAV8-TBG-EGFP tail vein injection


title: P6497-24hpi-ChIP-seq_H3K4me3_rep2


title: P6497-24hpi-ChIP-seq_H3K4me3_rep1


title: Control, ZT22, Arcuate Nucleus, biol rep 1


title: P6497-24hpi-ChIP-seq_H3K27me3_rep1


title: P6497-12hpi-ChIP-seq_input_rep1


title: P6497-12hpi-ChIP-seq_input_rep2


title: Control, ZT16, Arcuate Nucleus, biol rep 3


title: P6497-12hpi-ChIP-seq_H3K36me3_rep1


title: HepDKO, ZT4, Arcuate Nucleus, biol rep 3


title: Control, ZT16, Arcuate Nucleus, biol rep 1


title: P6497-12hpi-ChIP-seq_H3K36me3_rep2


title: Control, ZT10, Arcuate Nucleus, biol rep 3


title: P6497-MY-ChIP-seq_H3K4me3_rep1


title: P6497-12hpi-ChIP-seq_H3K27me3_rep2


title: P6497-12hpi-ChIP-seq_H3K27me3_rep1


title: P6497-12hpi-ChIP-seq_H3K4me3_rep2


title: Control, ZT10, Arcuate Nucleus, biol rep 1


title: Control, ZT10, Arcuate Nucleus, biol rep 2


title: Control, ZT4, Arcuate Nucleus, biol rep 3


title: Hep3B cell line Day7 Prox1 OE rep 3

description:
Library name: Hep3B_day7_Prox1_rep3
Prox1 OE

data_processing:
Raw reads were mapped to the reference genome hg38 using STAR.
Differential expression was determined using DESeq2 (R package version 1.28.1) with size factor normalization and Wald significance tests.
Assembly: hg38
Supplementary files format and content: tsv file with deseq2 statistics (vs control as baseline)
Supplementary files format and content: tsv file with normalised counts

growth_protocol: Hep3B grown in DMEM (Invitrogen) containing 10% foetal bovine serum (Sigma), non-essential amino acids, sodium pyruvate, L-glutamine, and penicillin/streptomycin (all from Invitrogen) were transduced with pLIX-Puro-hsPROX1 (PROX1 overexpression) lentivirus. Puromycin (2 μg/ml) selection was performed for 2 days to generate stable cell lines.

extract_protocol:
Hep3B cells were harvested from culture plates by the addition of TRIzol. RNA harvested in TRIzol was isolated using the RNA Miniprep kit (Zymo Research).
For bulk RNA sequencing, libraries were prepared according to the dUTP protocol and paired-end sequencing (2x100bp) was performed on the NovaSeq 6000 platform (Illumina).

treatment_protocol: 2 μg/ml doxycycline (Sigma) was used to induce Prox1 overexpression (PROX1 OE) in growth media for7 days and compared to no doxycycline treated cells (Control).

value: Prox1 OE


title: Control, ZT22, Arcuate Nucleus, biol rep 2


title: HepDKO, ZT4, Arcuate Nucleus, biol rep 1


title: Hep3B cell line Day7 Prox1 OE rep 1

description:
Library name: Hep3B_day7_Prox1_rep1
Prox1 OE


title: Control, ZT4, Arcuate Nucleus, biol rep 2


title: Hep3B cell line Day7 Prox1 OE rep 2

description:
Library name: Hep3B_day7_Prox1_rep2
Prox1 OE


title: Eif2s2 cKO mouse ovaries polled

city: Guangzhou

first: Wenjun

last: Zhou

state: Guangdong

address: Waihuan East Road, Mega center city

department: School of Medicine

institute: South China University of Technology

description: 6 ovaries from 3 mice, polled single cell sample

data_processing:
Raw BCL files obtained from the 10x GENOMICS snRNA-seq platform were converted to FASTQ files.
We used the Cell Ranger package (10x GENOMICS) to demultiplex and map the files to the mm10 transcriptome.
For quality control, we used the R software (v.4.1.0) package Seurat (v.4.0.6)132 (http://satijalab.org/seurat) to term cells as outliers of a number of the genes, UMIs, and the percentage of mitochondrial genes and excluded them from further analysis.
We clustered the cells by the FindCluster function on K-nearest neighbor (KNN) graph model with the granularity. The Seurat’s FindAllMarkers was used to find the marker genes of each significant cluster. Cell types were determined by marker genes using a combination of previous literatures and the CellMarker (http://bio-bigdata.hrbmu.edu.cn/CellMarker/).
Assembly: mm10
Supplementary files format and content: Tab-seperated and matrix files

source_name: Ovary

extract_protocol:
6 ovaries from 3 eif2s2 floxed or cKO mice were digested into single cells. Then, cells were sorted into PBS containing 0.04% BSA and then quantified. Their integrity was assessed using trypan blue by Countess II automated counter (Thermo Fisher Scientific).
Nuclei were loaded on a 10x GENOMICS GemCode single-nucleus instrument to generate single-nucleus Gel Bead-In-EMlusion (GEM). Reverse transcription and library preparation were performed using the Chromium Next GEM Single nucleus 30 Reagent Kits v3.1 (10x GENOMICS, CG000204) based on the instructions from the manufacturer.

value: Ovary

value: not applicalble

tag: cell type

value: cKO


title: WT, single haplotype, spleen, replicate 5

city: Memphis

first: Mitchell

last: Weiss

state: Tennessee

address: 262 Danny Thomas Place

department: Hematology

institute: St. Jude Children's Research Hospital

data_processing:
Reads were aligned with STAR (v2.7.9a) to the mouse mm10 genome with the following parameters: --readFilesCommand unpigz -c -p 4 --limitBAMsortRAM 67108864000 --outReadsUnmapped None --outSAMtype BAM SortedByCoordinate --outSAM strandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --outSAMmapqUnique 60 --outSAMmultNmax 1 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM --outFilterType BySJout --outFi lterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 10 0000 --alignMatesGapMax 100000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 10 --alignSJstitchMismatchNmax 5 -1 5 5 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimOutType Junctions With inBAM SoftClip --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic
Sequencing reads overlapping the mm10 Hbb-bt and Hbb-bs genes, including 1000 bases upsteam and downstream of the genes, and the intergenic region between the genes (chr7:103811548-103828825), were extracted using samtools view command.  Paired end reads were reconstituted by matching sequencing IDs. A reference genome consisting of the Hbb-bt and Hbb-bs genes from mm10 genome (C57BL6/J) and the Hbb-b1 and Hbb-b2 from the BALB/C globin locus region (Genbank record X14061.1) was generated (including 1000 bases upstream and downstream plus intronic sequence).
STAR (2.5.3a) was used to generate an indexed genome from the four globin reference sequence (following non-default parameters used: genomeSAindexNbases=9, sjdbOverhang=99). STAR was then used to align b-globin RNA-SEQ reads to this reference genome. (Non default parameters used : outFilterMismatchNmax 100 , alignIntronMax 500000 , sjdbFileChrStartEnd -, chimSegmentMin 20, chimJunctionOverhangMin 20, outSAMstrandField intronMotif, outBAMcompression -1, outSAMtype BAM Unsorted, outReadsUnmapped Fastx, --outFilterScoreMinOverLread .33 --outFilterMatchNminOverLread .33). For reads mapping to multiple b-globin genes equally well, only one mapping per read pair was retained.
For RNA-SEQ data from the single strain, if the reads mapped equally to Hbb-bs and Hbb-bt, it was classified as ambiguous. If only one of the single globin genes was a top match, but a diffuse gene (Hbb-b1 and/or Hbb-b2) was the top match, then the mapping to the single gene (Hbb-bs or Hbb-bt) was retained. The same decision was applied for diffuse strain data, but genes were switched. HTSEQ-Count was used to identify genes mapping to the four Hbb genes (gene annotation includes entire coordinates from transcriptional start to transcriptin end site).
An annotation file of introns was also created with the first/last 10 bases of the intron not included in the annotation. Running HTSEQ-Count with the introns file was performed to get intron counts. Exon counts for each sample and gene combination was calculated by substracting the intron count from total gene count.
Assembly: mm10
Supplementary files format and content: ec3751bf9ea548ebd1d7018304b2f413  is an xlsx file containing intron and exon counts of the different Hbb and Hba alleles from each samples.

source_name: Spleen

extract_protocol:
Bone marrow and spleens were harvested from mice of the following genotypes: WT sing, WT diff, HbbTh3/+ sing, HbbTh3/+ diff. For each sample Ter119+ cells were isolated from 3 x 107 live bone marrow or spleen cells respectively with Anti-Ter-119 MicroBeads, mouse (Miltenyi, 130-049-901) on MS Columns (Miltenyi Biotec, 130-042-201). Total RNA was purified from Ter119+ cells with the RNeasy Plus Mini Kit (Qiagen, 74134) following the manufacturer’s instructions.
Libraries were prepared with the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, 20020599) according to the manufacturer’s instructions.

value: Spleen

tag: replicate

value: WT single


title: Hep3B cell line Day7 control rep 2

description:
Library name: Hep3B_day7_ctr_rep2
Control

tag: cell line

value: Control


title: TFEB KO (clone #c20) 48hr Torin1 biol rep 1

city: Berkeley

first: Meagan

middle: Nicole

last: Esbin

state: California

address: 475 Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California Berkeley

description:
Library name: Sample 32
RNASeq batch 2

data_processing:
Raw data were assessed using FastQC
FASTQ files were pseudoaligned to the hg38 transcriptome using Salmon to quantify transcripts in mapping-based mode (salmon quant -i) using decoy-aware mapping with gencode.v39. transcripts.fa.
Differential gene expression analysis was performed with EdgeR in Jupyter Notebook. Raw counts were filtered to remove genes with fewer than 10 reads per sample or fewer than 15 reads summed across all samples. Counts per million reads (CPM) was calculated for the filtered count data using the EdgeR function cpm. Statistical comparisons between individual sample conditions were made using EdgeR makeContrasts and then glmQLFit. The reported P-values and FDR values were corrected with adjust.method = “BH,” and differentially expressed genes are reported with an adjusted FDR of <0.05.
To create bigwig files for visualization with IGV, mapping of FASTQ files was performed using STAR (with settings --quantMode GeneCounts --outSJfilterReads Unique --outFilterMultimapNmax 1)
Bam files (STAR outputs) were converted to bigwig files using deeptools bamcoverage (with settings --binSize 50 --normalizeTo1x 3049315783 --ignoreDuplicates)
Assembly: hg38
Supplementary files format and content: Comma separated values file contains CPM-normalized count data for each Sample by NCBI Gene ID
Supplementary files format and content: Bigwig file to be used for Genome track visualization (i.e. IGV viewer) of binned reads mapped across the human genome for each Sample
Supplementary files format and content: Comma separated values file containing differential gene expression analysis output from EdgeR with the Log2 Fold-Change (FC), p-value (PVAL) and Benjamini-Hochberg (BH) corrected False Discovery Rate (FDR) for each gene across different comparisons between Samples. Comparisons are noted as (Sample X - Sample Y) where positive FC values indicates higher gene expression in Sample X.

source_name: BeWo

growth_protocol: BeWo cells (ATCC CCL-98) were cultured at 37°C and 5% CO2 in F-12K medium (Corning or ATCC) supplemented with 10% fetal bovine serum and 10 U/mL penicillin–streptomycin. Cells were passaged by trypsinization every 2–4 days and split at a ratio of 1:3–1:5. Media was changed completely every 24–36 h.

extract_protocol:
RNA was extracted from each well using 500 µL of Trizol followed by two sequential chloroform extractions followed by ethanol precipitation per the Trizol user guide (Thermo Fisher MAN0001271).
500ng total RNA was used as starting material for each sample and then depleted of rRNA using the Illumina rRNA depletion kit (NEB E6310). For Batch 1 samples, 1uL of 1:100 diluted ERCC RNA Spike-In Mix (Thermo #4456740) was first added to the 500ng starting total RNA before rRNA depletion and libraries were prepared for Illumina sequencing using the NEBNext Ultra II directional RNA library preparation kit for Illumina (E7760) per the manufacturer’s protocol. For Batch 2 samples, libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770L) per the manufacturer’s protocol.

treatment_protocol: BeWo cells were plated at 300,000 cells per well into a 6 well plate and allowed to settle 6 h to overnight. Cells were then treated with 0.1% DMSO, 20 μM Forskolin, or 250nM Torin1 for 48 h or left untreated. For 2 hour Torin1 treatment, cells were treated with 0.1% DMSO for 46 h and then switched to 250 nM Torin1 media for 2 h before harvesting. Media for all treatments was changed at 24 h.

value: BeWo

value: choriocarcinoma

value: TFEB KO (clone #c20)

value: 250nM Torin1 for 48hrs


title: Hep3B cell line Day7 control rep 3

description:
Library name: Hep3B_day7_ctr_rep3
Control


title: Control, ZT16, Arcuate Nucleus, biol rep 2

value: Arcuate Nucleus

value: Reverb a/b fl/fl

value: 10-12 weeks

value: Chow

tag: strain


title: WT, single haplotype, spleen, replicate 3


title: Control, ZT4, Arcuate Nucleus, biol rep 1

value: Male


title: WT, single haplotype, spleen, replicate 2


title: WT, single haplotype, spleen, replicate 4


title: Hep3B cell line Day7 control rep 1

description:
Library name: Hep3B_day7_ctr_rep1
Control


title: TFEB KO (clone #c13) 48hr Torin1 biol rep 1

description:
Library name: Sample 29
RNASeq batch 2

value: TFEB KO (clone #c13)


title: WT, single haplotype, spleen, replicate 1


title: TFEB KO (clone #c20) DMSO biol rep 1

description:
Library name: Sample 30
RNASeq batch 2

value: 0.1% DMSO for 48hrs


title: β-Thalassemia (Hbb[th3/+]), single haplotype, spleen, replicate 4

value: Hbb[th3/+] single


title: β-Thalassemia (Hbb[th3/+]), single haplotype, spleen, replicate 5


title: P6497-12hpi-ChIP-seq_H3K4me3_rep1

value: 12hpi Phytophthora sojae infected soybean

value: WT

value: H3K4me3(abcam, ab8580)


title: TFEB KO (clone #c13) 48hr FSK biol rep 1

description:
Library name: Sample 28
RNASeq batch 2

value: 20uM Forskolin for 48hrs


title: TFEB KO (clone #c13) DMSO biol rep 1

description:
Library name: Sample 27
RNASeq batch 2


title: β-Thalassemia (Hbb[th3/+]), single haplotype, spleen, replicate 3

value: Spleen


title: TFEB/3 DKO (#C2) BeWo 48hr Torin1 biol rep 1

description:
Library name: Sample 26
RNASeq batch 2

value: BeWo

value: TFEB/TFE3 double KO (clone #C2)


title: β-Thalassemia (Hbb[th3/+]), single haplotype, spleen, replicate 1


title: TFEB/3 DKO (#C2) BeWo DMSO biol rep 1

description:
Library name: Sample 24
RNASeq batch 2

value: choriocarcinoma


title: WT BeWo 48hr Torin1 biol rep 3

description:
Library name: Sample 23
RNASeq batch 2

value: wild-type

value: 250nM Torin1 for 48hrs


title: TFEB/3 DKO (#C2) BeWo 48hr FSK biol rep 4

description:
Library name: Sample 25
RNASeq batch 2


title: WT, diffuse haplotype, spleen, replicate 4

value: WT diffuse


title: WT, diffuse haplotype, spleen, replicate 5


title: WT BeWo 48hr Torin1 biol rep 2

description:
Library name: Sample 22
RNASeq batch 2


title: WT, diffuse haplotype, spleen, replicate 2


title: WT BeWo 48hr Torin1 biol rep 1

description:
Library name: Sample 21
RNASeq batch 2


title: TFEB KO (clone #c20) 48hr FSK biol rep 1

description:
Library name: Sample 31
RNASeq batch 2

value: TFEB KO (clone #c20)


title: β-Thalassemia (Hbb[th3/+]), diffuse haplotype, spleen, replicate 4

value: Hbb[th3/+] diffuse


title: WT, diffuse haplotype, spleen, replicate 1


title: TFEB/3 DKO (#C2) BeWo 48hr FSK biol rep 3

description:
Library name: Sample 18
RNASeq batch 1


title: Eif2s2 floxed mouse ovaries polled

value: Ovary

value: not applicalble

value: Eif2s2 fl/fl


title: WT, diffuse haplotype, spleen, replicate 3


title: WT BeWo 48hr FSK biol rep 4

description:
Library name: Sample 20
RNASeq batch 2


title: WT BeWo DMSO biol rep 1

description:
Library name: Sample 19
RNASeq batch 2

value: 0.1% DMSO for 48hrs


title: β-Thalassemia (Hbb[th3/+]), diffuse haplotype, spleen, replicate 5


title: β-Thalassemia (Hbb[th3/+]), diffuse haplotype, spleen, replicate 3


title: β-Thalassemia (Hbb[th3/+]), diffuse haplotype, spleen, replicate 1


title: TFEB/3 DKO (#C2) BeWo Untreated biol rep 3

description:
Library name: Sample 16
RNASeq batch 1

value: Untreated


title: β-Thalassemia (Hbb[th3/+]), single haplotype, spleen, replicate 2

value: Hbb[th3/+] single


title: WT BeWo 2hr Torin1 biol rep 3

description:
Library name: Sample 14
RNASeq batch 1

value: 250nM Torin1 for 2hrs


title: WT, single haplotype, bone marrow, replicate 5

source_name: Bone marrow

value: Bone marrow

value: WT single


title: WT BeWo Untreated biol rep 3

description:
Library name: Sample 13
RNASeq batch 1

value: BeWo


title: WT, single haplotype, bone marrow, replicate 2


title: WT, single haplotype, bone marrow, replicate 3


title: TFEB/3 DKO (#C2) BeWo Untreated biol rep 2

description:
Library name: Sample 10
RNASeq batch 1

value: TFEB/TFE3 double KO (clone #C2)


title: TFEB/3 DKO (#C2) BeWo 2hr Torin1 biol rep 2

description:
Library name: Sample 11
RNASeq batch 1

value: choriocarcinoma


title: WT, single haplotype, bone marrow, replicate 1


title: WT BeWo 48hr FSK biol rep 2

description:
Library name: Sample 9
RNASeq batch 1

value: wild-type

value: 20uM Forskolin for 48hrs


title: WT BeWo 2hr Torin1 biol rep 2

description:
Library name: Sample 8
RNASeq batch 1


title: TFEB/3 DKO (#C2) BeWo 2hr Torin1 biol rep 3

description:
Library name: Sample 17
RNASeq batch 1


title: WT BeWo Untreated biol rep 2

description:
Library name: Sample 7
RNASeq batch 1


title: β-Thalassemia (Hbb[th3/+]), single haplotype, bone marrow, replicate 5


title: β-Thalassemia (Hbb[th3/+]), diffuse haplotype, spleen, replicate 2

value: Spleen


title: TFEB/3 DKO (#C2) BeWo 48hr FSK biol rep 1

description:
Library name: Sample 6
RNASeq batch 1


title: β-Thalassemia (Hbb[th3/+]), single haplotype, bone marrow, replicate 4


title: β-Thalassemia (Hbb[th3/+]), single haplotype, bone marrow, replicate 1


title: TFEB/3 DKO (#C2) BeWo Untreated biol rep 1

description:
Library name: Sample 4
RNASeq batch 1


title: TFEB/3 DKO (#C2) BeWo 2hr Torin1 biol rep 1

description:
Library name: Sample 5
RNASeq batch 1


title: β-Thalassemia (Hbb[th3/+]), single haplotype, bone marrow, replicate 3


title: WT BeWo 48hr FSK biol rep 3

description:
Library name: Sample 15
RNASeq batch 1


title: β-Thalassemia (Hbb[th3/+]), single haplotype, bone marrow, replicate 2


title: WT, diffuse haplotype, bone marrow, replicate 5

value: WT diffuse


title: WT, diffuse haplotype, bone marrow, replicate 4


title: WT, single haplotype, bone marrow, replicate 4


title: TFEB/3 DKO (#C2) BeWo 48hr FSK biol rep 2

description:
Library name: Sample 12
RNASeq batch 1