title: Fenofibrate_rep3

city: 中国

first: hang

last: chen

state: - 请选择 -

address: 北城街道

institute: 昆明医科大学

data_processing:
Sequence reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 by using HISAT (Version 2.0.5).
Read count extraction and normalization were performed using StringTie (Version 1.3.2d) and HTSeq (Version 0.6.0).
Assembly: mm9 (MGSCv37)
Supplementary files format and content: Tab-delimited text files

source_name: liver

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: liver

value: High-fat diet + Fenofibrate


title: ipRGC, P1, rep42

status: Public on May 01 2023

type: SRA

city: Baltimore

first: Alex

last: Kolodkin

state: Maryland

address: 725 N Wolfe St

department: Neuroscience

country: USA

institute: Johns Hopkins University School of Medicine

description:
SmartSeq2
P1_41

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned to the GRCm38.p6 (mm10) mouse reference genome using HISAT2 version 2.1.0.
The resulting SAM files were converted to BAM files using SAMtools version 1.9.
Transcript abundance was estimated using Cuffquant and normalization was performed using Cuffnorm in Cufflinks version 2.2.1.
All analyses were performed using Seurat in R version 3.6.2.
Assembly: mm10
Supplementary files format and content: Cuffnorm matrix containing FPKM values for each gene for each cell
Supplementary files format and content: Cuffnorm matrix containing annotations for each gene
Supplementary files format and content: Cuffnorm matrix containing annotations for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Retina

extract_protocol:
Retinas were dissected in cold Hibernate A medium lacking Ca2+, Mg2+, and phenol red (BrainBits). Retinas were then dissociated in papain (Worthington Biochemical, LS003126), 5.5 mM Cysteine-HCl, and 1.1 mM EDTA dissolved in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red) for seven minutes at 37°C. Cell suspension was passed through a 40 μm cell strainer (Falcon, 352340) and incubated for 30 minutes on ice with Brilliant Violet (BV)-421 anti-mouse CD90.2 antibody (BioLegend, 105341, 1:300), which binds to RGCs and provides an additional selection marker during FACS. The cells were then centrifuged and resuspended in 0.4% bovine serum albumin dissolved in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red). Cells were again centrifuged and resuspended in 2000 U/ml DNase I (New England Biolabs, M0303S) in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red) prior to cell sorting. Individual GFP+, BV-421+ cells were sorted into a lysis solution consisting of 3500 U/ml RNase inhibitor (New England Biolabs, M0314S), 140 U/ml DNase I, and 0.17% v/v Triton X-100 in water using a MoFlo Legacy cell sorter (Beckman Coulter).
Single-cell DNA libraries were prepared according to the Smart-seq2 protocol (Picelli et al., Nature Protocols, 2014) and sequenced using an Illumina NextSeq 500 sequencer (75 bp paired-end reads, 400 million total reads).

value: Retina

tag: cell type

value: ipRGC

tag: genotype

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+

tag: age


title: MP3

city: Tianshui

first: Fang

last: Ma

state: Qinzhou District

address: South Xihe Road

department: College of Bioengineering and Technology

country: China

institute: Tianshui normal university

library_source: transcriptomic

data_processing:
Raw reads were further filtered using fastp(version 0.18.0). After removal of reads containing adapters, containing more than 10% of unknown nucleotides (N) and low quality reads containing more than 50% of low quality (Q-value≤20) bases. The rRNA mapped reads were removed by using Short reads alignment tool Bowtie2
The remaining clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1in a reference-based approach.
The expression abundance and variations of each gene was estimated using abundance and variations by calculated FPKM （fragment per kilobase of transcript per million mapped reads）value. RNAs differential expression analysis was performed by DESeq2 between two different groups
The transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed transcripts.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Gallus gallus

source_name: ileum of Taiping chicken

extract_protocol:
Total RNA of the six libraries  was extracted using the standard TRIzol™. Agarose gel electrophoresis, Nano Photometer® Spectrophotometer and Bioanalyzer 2100 System  were  employed to evaluate the quantity and quality of the total RNAs.
About 3 μg total RNA from each sample was used  to construct small RNA library. Six sequencing libraries were generated using the NEBNext® Multiplex small RNA Library Prep Kit for Illumina®

value: ileum

value: two months

tag: gender

value: male


title: HGSOC001_RNAseq

city: Seongnam-si

first: Je-Gun

last: Joung

address: 335, Pangyo-ro, Bundang-gu

country: South Korea

institute: CHA University

description: RNA-seq S001T

data_processing:
An RNA sequencing library was prepared by cDNA amplification, end-repair, 3’ end adenylation, adapter ligation, and amplification. Library quality and quantity were measured using the Bioanalyzer and Qubit.
Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).
Reads from the FASTQ files were mapped to the hg19 human reference genome, using STAR alignment tool. Raw read counts mapped to genes were measured using the BAM format file by RSEM.
Excel file include TPM (Transcripts Per Million) normalized expression values for samples
An RNA sequencing library was prepared by cDNA amplification, end-repair, 3’ end adenylation, adapter ligation, and amplification. Library quality and quantity were measured using the Bioanalyzer and Qubit.
Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).
Reads from the FASTQ files were mapped to the hg19 human reference genome, using STAR alignment tool. Raw read counts mapped to genes were measured using the BAM format file by RSEM.
Assembly: hg19
Supplementary files format and content: Excel file include TPM (Transcripts Per Million) normalized expression values for samples

organism: Homo sapiens

source_name: ovarian tumor

extract_protocol:
Tumor DNA and 27 RNA were extracted from tumor tissues using ALLPrep DNA/RNA mini kit
Whole transcriptome sequencing was performed using the library constructed with 500 ng genomic RNA from each sample. The library construct was performed using a Truseq RNA sample preparation v2 kit (Illumina, USA). Whole-exome sequencing was carried out using 200 ng genomic DNA per sample, which was sheared using Covaris S220 (Covaris, MA, USA). A paired-end sequencing library was constructed using SureSelect XT Human All Exon v5 and a SureSelect XT reagent kit, HSQ (Agilent Technologies, Santa Clara, CA, USA)

tag: desease state

value: platinum-resistant recurrent ovarian cancer

value: ovarian tumor


title: hTERT-RPE1 p53-/-, treated with nutlin-3a

first: Fred

last: Bunz

address: 1550 Orleans Street

department: Radiation Oncology

institute: Johns Hopkins University

data_processing:
Geneious Prime Version 2020.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BBDuk
Trimmed sequence reads were mapped to Hg38 using the Geneious RNA mapper (parameters-maximum gaps per read 10%, maximum 20% mismatches, minimum overlap identity 80%)
Read count extraction and normalization were performed using Geneious Prime.
Assembly: GRCh38
Supplementary files format and content: tab-delimited excel files include raw read counts, raw transcript counts, RPKM and TPM values for each Sample

growth_protocol: hTERT-RPE1cells were maintained in DMEM/F12 supplemented with 6% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using the Monarch total RNA miniprep kit (NEB). 500 ng of total RNA was used for polyA selection prior to the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were untreated (control) or treated with the p53 activator nutlin-3a (10 µM) for 8 hours prior to harvest..

tag: cell line

value: hTERT-immortalized retinal pigment epithelial cells

tag: treatment

value: 10 microM nutlin-3a

tag: time

value: 8 h


title: ipRGC, P1, rep34

description:
SmartSeq2
P1_33


title: NO25shiguan

city: Guangzhou

first: Yujing

last: He

state: guangdong

address: No.1023-1063 South Shatai Road, Baiyun District, Guangzhou City, Guangdong Province

department: thoracic

institute: nanfang hospital

data_processing:
The original image data file obtained by high-throughput sequencing is converted into the original data of sequencing sequence (Raw) through CASAVA base calling analysis Data), the results are stored in FASTQ (abbreviated as fq) file format, which contains sequence information of sequencing data and its corresponding sequencing quality information
Quality Score or Q-score is obtained based on the Phred mass value formula, an integer mapping is used to determine the probability of base calling errors
AT and GC separation was checked in the distribution of base types
Based on the sequencing characteristics of the Illumina platform, datas from dual end sequencing were used and taken Q30 with an average proportion of over 85%
Sequencing align Clean Reads with the reference genome was used Hisat2 to obtain positional information on the reference genome or gene, as well as sequence characteristic information unique to the sequencing sample
The quality of transcriptome library is assessed by evaluating the randomness of mRNA fragmentation, the dispersion of inserted fragment length, and the adequacy of library capacity and mapped Data
Gene expression quantification was used with network flow algorithms and optional denovo assembly to assemble complex datasets into transcripts. FPKM (Fragments Per Kilobase of script per Million fragments mapped) was an indicator to measure transcript or gene expression levels
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: esophageal squamous carcinoma

extract_protocol:
Total RNA was harvested using Tiangen DP411, CLB+Adlai RN40, CTAB+Adlai RN40, Tiangen DP762-T1C reagent kit/TRIzol reagent. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared following Soexa TruSeq RNA protocols.

value: esophageal squamous carcinoma

value: Cisplatin resistant


title: MP2


title: Fenofibrate_rep4


title: ipRGC, P1, rep33

description:
SmartSeq2
P1_32


title: MP1


title: Fenofibrate_rep2


title: CT2


title: High fat diet_rep4

value: High-fat diet


title: ipRGC, P1, rep30

description:
SmartSeq2
P1_29


title: ipRGC, P1, rep32

description:
SmartSeq2
P1_31


title: ipRGC, P1, rep31

description:
SmartSeq2
P1_30


title: CT3


title: ipRGC, P1, rep36

description:
SmartSeq2
P1_35


title: Serum_DU_6mo_rep4

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

data_processing:
Single-end reads for miRNA were mapped to miRbase version 22 and the Rnor 6.0 Rattus norvegicus genome using sRNAbench and sRNAtoolbox.
Supplementary_files_format_and_content: Tab-delimited matrix table with raw read counts for every miRNA

organism: Rattus norvegicus

source_name: Serum

growth_protocol: Male Sprague–Dawley rats (Rattus norvegicus; age, approximately 30 d; weight, 75 to 100 g) were purchased from Envigo (Barrier 208A, Frederick, MD). Rats were allowed to acclimate in the AFRRI vivarium for at least 2 weeks prior to the start of experiments. The room was maintained at standard temperature (21 ± 2°C) and humidity (30% to 70%), with a 12:12-h light:dark cycle (lights on, 0600) and access to standard rat chow (Teklad Global Rodent Diet 8604, Envigo) and water ad libitum. Rats were pair-housed in plastic microisolation cages (23.8 × 45.4 cm) with filter tops and bedding (Teklad Sani-Chips, Envigo), changed 2 or 3 times weekly. All procedures involving animals were conducted to achieve maximal possible wellbeing of the rats, were IACUC-approved (protocol no. 2016-05-006) prior to the start of the study, and were performed in compliance with the guidelines set forth in the Guide for the Care and Use of Laboratory Animals in an AAALAC-accredited facility.

extract_protocol:
Total RNA was isolated from serum samples and assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Library preparation and sequencing was performed by Norgen Biotek. Briefly, library preparation was done using the Norgen Biotek Small RNA Library Prep Kit (Cat. 63600). Sequencing was performed using the NextSeq 500/550 High Output Kit v2 (51 Cycles using a 75-Cycle Kit) on the Illumina NextSeq 500 platform.

treatment_protocol: Pellets were surgically implanted into the gastrocnemius muscle, and each animal received 2 pellets per limb for a total of 4 pellets per rat. Prior to use, pellets were cleaned and chemically sterilized as previously described (https://doi.org/10.1177%2F1091581814565038)

value: Male

tag: strain

value: Sprague-Dawley

tag: metal

value: DU


title: hTERT-RPE1 p53+/A276P, control

value: Control


title: hTERT-RPE1 parental cells, treated with nutlin-3a

value: WT


title: High fat diet_rep1

value: liver


title: ipRGC, P1, rep29

description:
SmartSeq2
P1_28

value: Retina

value: ipRGC

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: High fat diet_rep3


title: hTERT-RPE1 parental cells, control


title: Serum_DU_6mo_rep2


title: Control_rep4


title: Fenofibrate_rep1

value: High-fat diet + Fenofibrate


title: HL-60 circMLLT1e2 tumour (KK75)

city: Adelaide

first: Simon

last: Conn

state: South Australia

address: Sturt Road, Bedford Park

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description:
SCL89
SCL60_SCL94_RawCounts.xlsx

data_processing:
Raw reads were adaptor trimmed and filtered for short sequences using cutadapt v1.8.1 (Martin, 2011), setting minimum-length option to 18, error-rate 0.2 and overlap 5.
The resulting FASTQ files for total RNAseq respectively were analysed and quality checked using the FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were mapped against the human reference genome (hg19) using the STAR spliced alignment algorithm (Dobin et al., 2013) (version 2.5.3a with default parameters and --chimSegmentMin 20).
The resulting STAR produced Chimeric.out.junction file for each sample was parsed and annotated for circRNA prediction and backsplice abundance using CIRCexplorer2 (Zhang et al., 2016).
Alignments were visualised and interrogated using the Integrative Genomics Viewer v2.3.80 (Thorvaldsdóttir et al., 2013).
Assembly: hg19

growth_protocol: K562 and HL-60 cells stably expressing transgenic constructs were cultivated in RPMI1640 medium with 10% FBS at 37oC with 5% carbon dioxide

extract_protocol:
RNA was extracted with TRIzol and purified with Zymo RNA purfiication kit with on-column DNaseI digestion.
NEBNext UltraII Directional RNA sequencing kit

treatment_protocol:
Cells stably transduced with lentivirus were selected on the basis of GFP expression encoded on the pMIG plasmid by flow cytometry. Cell populations with GFP expression >99% were used for experiments.
Cells were xenografted into NSG mice (6-8 per group) in a single-blinded experiment. Mouse welfare was tracked and weekly bleeds were performed to look at prpoportion of human GFP cells in the circulation. Mice were euthanised as a result of tumour cell burden and cells were collected, and following RBC lysis, were sorted by flow cytometry for GFP expression. Cell lines were made and frozen down within 72hrs post-collection.

value: AML

value: Tumour line

value: Transgenic line

tag: passage


title: High fat diet_rep2


title: ipRGC, P1, rep28

description:
SmartSeq2
P1_27


title: Serum_DU_6mo_rep3


title: ipRGC, P1, rep27

description:
SmartSeq2
P1_26


title: HL-60 circMLLT1e2 tumour (KK80)

description:
SCL92
SCL60_SCL94_RawCounts.xlsx


title: HL-60 circMLLe9-10/circMLLT1e2 tumour (KK61)

description:
SCL75
SCL60_SCL94_RawCounts.xlsx


title: HL-60 circMLLe9-10/circMLLT1e2 tumour (KK66)

description:
SCL80
SCL60_SCL94_RawCounts.xlsx


title: Serum_DU_6mo_rep1


title: hTERT-RPE1 p53-/-, control

value: hTERT-immortalized retinal pigment epithelial cells


title: CT1

value: ileum

value: two months

value: male


title: Control_rep3


title: Serum_Pb_6mo_rep4

value: Male

value: Pb


title: Control_rep2


title: HL-60 EV tumour (KK46)

description:
SCL64
SCL60_SCL94_RawCounts.xlsx


title: HL-60 circMLLe9-10 tumour (KK52)

description:
SCL66
SCL60_SCL94_RawCounts.xlsx


title: ipRGC, P1, rep22

description:
SmartSeq2
P1_21


title: ipRGC, P1, rep24

description:
SmartSeq2
P1_23


title: heart tissue, myocardial infarction, Day28, rep1

city: GuangZhou

first: Gang

last: Deng

address: 106 Zhongshan Er Road, Guangzhou, P.R

institute: Guangdong Provincial People's Hospital

description:
cardiac repair
MI_heart1

data_processing:
Illumina Novaseq™ 6000
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of <  research species > was sequenced run with Illumina NovaseqTM 6000 sequence platform. Using the Illumina  paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end  reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases  which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further  filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9).
The mapped reads of each sample were assembled using StringTie  (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes  from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare  software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).  After the final transcriptome was generated, StringTie and ballgown  (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression  levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase  of transcript per million mapped reads) value.  FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)
we aligned reads of all samples to the < research species > reference genome using HISAT2  (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the  reads based on quality information accompanying each read and then maps the reads to the reference genome.  HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping  the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing  the previously unmapped reads against the database of putative junctions. And then by removing  sequence-dependent bias and amplification noise using UMI-tools
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text file includes FPKM and count values for each Sample

source_name: heart

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure.  The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent,  CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing  library. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT)  (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented  into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module  (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create  the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to  synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H  (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the  blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base  overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the  fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB,  cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR  by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec,  annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The  average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end  sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following  the vendor's recommended protocol.
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent,  CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing  library.

value: heart

value: ligation operation

tag: disease state

value: Myocardial infarction


title: ipRGC, P1, rep23

description:
SmartSeq2
P1_22


title: ipRGC, P1, rep26

description:
SmartSeq2
P1_25


title: heart tissue, myocardial infarction, Day28, rep2

description:
cardiac repair
MI_heart2


title: Serum_Pb_6mo_rep2

value: Sprague-Dawley


title: Serum_Pb_6mo_rep3


title: circMLLE9-10/circMLLT1E2_2

description:
SCL46
SCL30-SCL47_RawCounts.xlsx

value: cell line


title: ipRGC, P1, rep20

description:
SmartSeq2
P1_19

value: Retina

value: ipRGC


title: Serum_Pb_6mo_rep1


title: ipRGC, P1, rep21

description:
SmartSeq2
P1_20

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: heart tissue, Sham, Day28, rep1

description:
cardiac repair
S_heart1

value: thoracotomy (no ligation)

value: control


title: circMLLE9-10/circMLLT1E2_3

description:
SCL47
SCL30-SCL47_RawCounts.xlsx

value: AML

value: Transgenic line


title: HL-60 EV tumour (KK42)

description:
SCL60
SCL60_SCL94_RawCounts.xlsx

value: Tumour line


title: Serum_Al_6mo_rep4

value: Al


title: ipRGC, P1, rep18

description:
SmartSeq2
P1_17


title: circMLLE9-10/circMLLT1E2_1

description:
SCL45
SCL30-SCL47_RawCounts.xlsx


title: ipRGC, P1, rep25

description:
SmartSeq2
P1_24


title: heart tissue, Sham, Day28, rep2

description:
cardiac repair
S_heart2


title: ipRGC, P1, rep19

description:
SmartSeq2
P1_18


title: Serum_Al_6mo_rep3


title: Serum_Cu_6mo_rep4

value: Cu


title: Serum_Al_6mo_rep2

value: Male


title: circMLLT2e2-4_3

description:
SCL44
SCL30-SCL47_RawCounts.xlsx


title: Control_rep1

value: liver

value: Control


title: STZ treated, replicate 1, scRNAseq

city: Nanjing

first: Yu

last: Qian

state: Jiangsu

address: 300 Guangzhou Road

department: Department of Endocrinology

institute: the First Affiliated Hospital of Nanjing Medical University

description:
10x Genomics
β cells

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pancreatic islet

extract_protocol:
The mice were anesthetized and the bile duct were injected with 0.5 mg/ml collagenase P dissolved in cold Hanks’ balanced salt solution. The expanded pancreatic tissue was digested at 37°C for 11 min and then stopped using cold Hank's Balanced Salt Solution (HBSS) with 10% fetal bovine serum (FBS). The islets were separated using a density gradient composed of layers of HBSS and Histopaque (11191; Sigma Aldrich). After two rounds of manual selection, the islets were dispersed into single cells with TrypLE (Thermo Scientific) for 15 min in a 37°C water bath and then resuspended in Dulbecco phosphate-buffered saline (containing 2% FBS). GFP+ cells were sorted using flow cytometry and confirmed to have >80% viability using Trypan blue staining.
Single cells were processed to produce gel bead-in-emulsion (GEM) using a Chromium™ Single Cell Platform (10x Genomics) with a Chromium™ Single Cell 3' GEM, Library & Gel Bead Kit v3 and a Chromium™ Chip B Single Cell Kit, following the manufacturer’s protocol. Thereafter, the beads were retrieved into a single tube for reverse transcription, and the cDNAs were tagged at the 5’ ends (that is, the 3’ ends of mRNAs were tagged) with a unique molecular identifier (UMI) and a label indicating each molecule’s cell of origin (CG000206 Rev D). The libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a 2100 Bioanalyzer system (Agilent) with a Qubit High Sensitivity DNA Assay Kit (Thermo Fisher Scientific). The libraries were sequenced (2x150 bp) on a NovaSeq 6000 system (Illumina).

value: beta cells

value: pancreatic islet

value: Ins1-CreERT; Rosa26-mT/mG

value: 20 weeks old


title: Serum_Al_6mo_rep1

value: Sprague-Dawley


title: MIN6, pMx-Bhlhe40, biol_rep_1

city: Kumamoto

first: Tomonori

last: Tsuyama

state: Kumamoto

address: 1-1-1, Honjo Chuo-ku

department: Faculty of Life Sciences

country: Japan

institute: Kumamoto university

data_processing:
Sequence reads were trimmed for universal illumina adaptors using TrimGalore.
Trimmed sequence reads were mapped to GENCODE36 genome sequence (for human) or M25 genome sequence (for mouse) using HISAT2 with default parameters setting. Mapped reads were sorted and converted to a binary alignment/map format using SAMtools.
Gene assembly and quantification were performed using Stringtie.
Assembly: GRCh38, GRCm38
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: MIN6 cells

extract_protocol:
RNA was extracted using RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit (E7765L and E7770, New England Biolabs.) following manufacturer's protocols.

value: MIN6 cells

value: Pancreatic beta cells

value: Bhlhe40 Overexpression

value: Bhlhe40 overexpression


title: MIN6, pMx-Bhlhe40, biol_rep_3


title: circMLLT2e2-4_2

description:
SCL43
SCL30-SCL47_RawCounts.xlsx

value: AML

value: cell line


title: ipRGC, P1, rep13

description:
SmartSeq2
P1_12

value: Retina

value: ipRGC

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: ipRGC, P1, rep14

description:
SmartSeq2
P1_13


title: Serum_Cu_6mo_rep1

value: Male

value: Cu


title: ipRGC, P1, rep17

description:
SmartSeq2
P1_16


title: circMLLT1e2_2

description:
SCL40
SCL30-SCL47_RawCounts.xlsx

value: Transgenic line


title: MIN6, pMx-Bhlhe40, biol_rep_2


title: circMLLT2e2-4_1

description:
SCL42
SCL30-SCL47_RawCounts.xlsx


title: ipRGC, P1, rep16

description:
SmartSeq2
P1_15


title: MIN6, pMx-Ctrl, biol_rep_2

value: WT

value: without Bhlhe40 overexpression


title: Serum_Cu_6mo_rep3


title: Serum_Cu_6mo_rep2


title: circMLLT1e2_3

description:
SCL41
SCL30-SCL47_RawCounts.xlsx


title: MIN6, pMx-Ctrl, biol_rep_1


title: MIN6, pMx-Ctrl, biol_rep_3


title: Serum_Fe_6mo_rep3

value: Fe


title: circMLLe7-8_2

description:
SCL37
SCL30-SCL47_RawCounts.xlsx


title: Serum_Fe_6mo_rep4


title: ipRGC, P1, rep15

description:
SmartSeq2
P1_14


title: circMLLT1e2_1

description:
SCL39
SCL30-SCL47_RawCounts.xlsx


title: ipRGC, P1, rep12

description:
SmartSeq2
P1_11


title: ipRGC, P1, rep10

description:
SmartSeq2
P1_9


title: circMLLe7-8_3

description:
SCL38
SCL30-SCL47_RawCounts.xlsx


title: Serum_Fe_6mo_rep2


title: circMLLe7-8_1

description:
SCL36
SCL30-SCL47_RawCounts.xlsx


title: ipRGC, P1, rep11

description:
SmartSeq2
P1_10


title: Bleomycin induced lung injury control (PBS 48 hr) EpCam+ scRNAseq

city: New York

first: Dana

last: Pe'er

state: NY

address: 417 E 68th St

department: Computational and Systems Biology

institute: Memorial Sloan Kettering Cancer Center

description:
project 10506
Bleomycine_clean_combined_v4.h5ad
Bleomycine_clean_endo.h5ad
Bleomycine_clean_myeloid.h5ad

data_processing:
Cell by gene count matrices were constructed using the Sequence Quality Control (SEQC) package (Azizi Cell 2018).
The cell barcodes are contained in the dense.csv files. It is the      first column (which is followed by CLUSTER and then genes). The      cell barcodes are stored as numerals instead of basepair sequence for      legacy and memory issues, and is hard-wired in the pre-processing software      we use (SEQC: https://github.com/dpeerlab/seqc). However, to make the cell      barcodes accessible in basepair sequence format, we have provided a Python      code that converts the cell barcodes from numerals to basepair sequences.
Assembly: GRCm38
Supplementary files format and content: csv files

source_name: lung

extract_protocol:
For isolation of immune and stromal cells, lungs were perfused, placed into 5 ml Eppendorf tubes containing 400ml of cold serum-free RPMI and chopped with scissors (1-2 mm). Lung fragments were placed in 2-3 ml of pre-warmed digestion medium (RPMI 1640, 10 mM HEPES buffer, 1% penicillin–streptomycin, 1% L-glutamine, liberase (Sigma-Aldrich #05401020001) and 1 U/ml DNase I (Sigma-Aldrich #10104159001)) (2-3 ml) and incubated for 30 min at 37°C. After digestion supernatant was collected and cells were resuspended in ice-cold RPMI1640 containing 5% FCS (ThermoFisher #35010CV), 1mM HEPES (Corning #MT25060CI), 1% penicillin–streptomycin (Corning #MT30002CI) and 200mM L-glutamine (Corning #MT25005CI). After additional digestion for 1 hr of the remaining tissue, both digested cell fractions passed through a 100um strainer (Corning #07-201-432), washed and FACS sorted.
Bulk RNA seq - Cell populations were sorted straight into Trizol (ThermoFisher #15596018), RNA was precipitated with isopropanol and linear acrylamide, washed with 75% ethanol, and resuspended in RNase-free water. After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.4-2.0ng total RNA with RNA integrity numbers ranging from 1.0 to 9.9 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech #63488), with 12 cycles of amplification. Subsequently, 1.5-10ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems #KK8504) using 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 or HiSeq 2500 in Rapid Mode in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit or HiSeq Rapid SBS Kit v2 (Illumina).  An average of 32 million paired reads were generated per sample and the percent of mRNA bases per sample ranged from 62% to 88%. scRNAseq- Single-cell RNA-Seq was performed on FACS sorted mouse lung KP cells or patient LuAd samples, on the Chromium instrument (10X genomics) following the user guide manual (CG00052 Rev E) for 3′ v2 and v3 as previously described46.  Briefly, sorted cells were washed once with PBS containing 0.04% bovine serum albumin (BSA) and resuspended in PBS containing 0.04% BSA to a final concentration of 700–1,200 cells per μl. Viability of cells was confirmed to be above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). Then samples were encapsulated in microfluidic droplets at a dilution of ∼70 cells/μl (doublet rate ∼3.9%.). Encapsulated cells were subjected to reverse transcription (RT) reaction at 53°C for 60 min. After RT, the emulsion droplets were broken and barcoded-cDNA was purified with DynaBeads MyOne SILANE, followed by 14-cycles of PCR-amplification (98°C for 180 s; [98°C for 15 s, 67°C for 20 s, 72°C for 60 s] x 12-cycles; 72°C for 60 s). 50 ng of PCR-amplified barcoded-cDNA was fragmented with the reagents provided in the kit and purified with SPRI beads to obtain an average fragment size of 600 bp. Next, the DNA library was ligated to the sequencing adaptor followed by indexing PCR (98°C for 45 s; [98°C for 20 s, 54°C for 30 s, 72°C for 20 s] x 10 cycles; 72°C for 60 s). An average of 5,000 cells were targeted for each tumor sample. The resulting DNA library was double-size purified (0.6-0.8X) with SPRI beads and sequenced on an Illumina NovaSeq platform (R1 – 26 cycles (KP) 28 cycles (LuAd), i7 – 8 cycles, R2 – 96 cycles (KP), 90 cycles (LuAd)) resulting in 184.5-186.1 million reads per sample (average reads per single-cell being 42,000 and average reads per transcript 4.40-7.14) (KP)
Bulk RNA seq, scRNA-seq

value: EpCam+

value: lung

value: 21-25 weeks


title: circMLLe9-10_3

description:
SCL35
SCL30-SCL47_RawCounts.xlsx


title: ipRGC, P1, rep9

description:
SmartSeq2
P1_8


title: Serum_Co_6mo_rep4

value: Sprague-Dawley

value: Co


title: Bleomycin induced lung injury control (PBS 48 hr) CD45+ scRNAseq


title: circMLLe9-10_2

description:
SCL34
SCL30-SCL47_RawCounts.xlsx


title: Bleomycin induced lung injury DT (Diphtheria Toxin 48 hr) CD45+ scRNAseq


title: ipRGC, P1, rep8

description:
SmartSeq2
P1_7


title: Serum_Co_6mo_rep2


title: Bleomycin induced lung injury DT (Diphtheria Toxin 48 hr) EpCam+ scRNAseq


title: circMLLe9-10_1

description:
SCL33
SCL30-SCL47_RawCounts.xlsx


title: pMIG(EV)_3

description:
SCL32
SCL30-SCL47_RawCounts.xlsx


title: ipRGC, P1, rep7

description:
SmartSeq2
P1_6


title: Serum_Co_6mo_rep1


title: ipRGC, P1, rep6

description:
SmartSeq2
P1_5


title: Bleomycin induced lung injury DT (Diphtheria Toxin 48 hr) CD45- scRNAseq


title: Lung KP control (PBS 48 hr) sample #3, CD45- scRNAseq

description:
project 7734
clean_combined.h5ad
clean_endo.h5ad
clean_myeloid.h5ad
clean_fib.h5ad


title: pMIG(EV)_2

description:
SCL31
SCL30-SCL47_RawCounts.xlsx


title: ipRGC, P1, rep5

description:
SmartSeq2
P1_4


title: Serum_Ni_6mo_rep4

value: Ni


title: pMIG(EV)_1

description:
SCL30
SCL30-SCL47_RawCounts.xlsx

value: AML


title: Serum_Fe_6mo_rep1


title: ipRGC, P1, rep4

description:
SmartSeq2
P1_3


title: Lung KP DT (Diphtheria Toxin 48hr) sample #3, CD45+ scRNAseq


title: K562 circMLLe9-10 tumour (KK37)

description:
SC44
SC1_SC46_RawCounts.xlsx

value: CML

value: tumour line


title: Bleomycin induced lung injury control (PBS 48 hr) CD45- scRNAseq


title: ipRGC, P1, rep3

description:
SmartSeq2
P1_2

value: Retina

value: ipRGC


title: Serum_Ni_6mo_rep3

value: Male


title: Lung KP DT (Diphtheria Toxin 48hr) sample #3, CD45- scRNAseq


title: Serum_Co_6mo_rep3


title: Serum_Ni_6mo_rep2


title: ipRGC, P1, rep1

description:
SmartSeq2
P1_0

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: ipRGC, P1, rep2

description:
SmartSeq2
P1_1


title: Serum_W_6mo_rep3

value: W


title: Lung KP DT (Diphtheria Toxin 48hr) sample #2, CD45+ scRNAseq


title: Serum_W_6mo_rep2


title: ipRGC, P5, rep47

description:
SmartSeq2
P5_46


title: Serum_W_6mo_rep1


title: ipRGC, P5, rep48

description:
SmartSeq2
P5_47


title: K562 circMLLT1e2 tumour (KK18)

description:
SC31
SC1_SC46_RawCounts.xlsx

value: Transgenic line


title: Serum_Ni_6mo_rep1


title: K562 circMLLe9-10/circMLLT1e2 2

description:
SC15
SC1_SC46_RawCounts.xlsx

value: cell line


title: Lung KP DT (Diphtheria Toxin 48hr) sample #1, CD45+ scRNAseq


title: Lung KP DT (Diphtheria Toxin 48hr) sample #1, CD45- scRNAseq


title: Lung KP control (PBS 48 hr) sample #3, CD45+ scRNAseq


title: K562 circMLLe9-10/circMLLT1e2 1

description:
SC14
SC1_SC46_RawCounts.xlsx


title: ipRGC, P5, rep44

description:
SmartSeq2
P5_43


title: K562 circMLLe9-10/circMLLT1e2 tumour (KK9)

description:
SC23
SC1_SC46_RawCounts.xlsx


title: ipRGC, P5, rep46

description:
SmartSeq2
P5_45


title: K562 EV tumour (KK2)

description:
SC19
SC1_SC46_RawCounts.xlsx


title: Serum_Ta_6mo_rep1

value: Ta


title: Serum_Ta_6mo_rep3


title: Lung KP control (PBS 48 hr) sample #1, CD45+ scRNAseq


title: Lung KP control (PBS 48 hr) sample #2, CD45+ scRNAseq


title: Serum_DU_1mo_rep4

value: DU


title: ipRGC, P5, rep42

description:
SmartSeq2
P5_41


title: Serum_Ta_6mo_rep2


title: K562 circMLLe9-10/circMLLT1e2

description:
SC13
SC1_SC46_RawCounts.xlsx


title: K562 circMLLT1e2

description:
SC7
SC1_SC46_RawCounts.xlsx


title: K562 circMLLT1e2 2

description:
SC9
SC1_SC46_RawCounts.xlsx


title: Lung KP control (PBS 48 hr) sample #1, CD45- scRNAseq

value: lung


title: ipRGC, P5, rep41

description:
SmartSeq2
P5_40


title: Lung KP control (PBS 48 hr) sample #2, CD45- scRNAseq

value: 21-25 weeks


title: Serum_DU_1mo_rep3

value: Sprague-Dawley


title: K562 circMLLe9-10 2

description:
SC6
SC1_SC46_RawCounts.xlsx


title: ipRGC, P5, rep43

description:
SmartSeq2
P5_42


title: Lung KP DT (Diphtheria Toxin 48hr) sample #2, CD45- scRNAseq


title: NDT2

first: Binghua

last: Li

address: Zhongshan road 321, Nanjing, Jiangsu, China

department: Department of Hepatobiliary Surgery

institute: the Affiliated Drum Tower Hospital, Medical School of Nanjing University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
The sequence quality was verified using FastQC. The cleaned sequence data were aligned to the mouse reference genome (mm10) by HISAT2. SAMtools was used to convert between the formats, sort and index the alignment output. The read count program called featureCounts was used to quantify reads to genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Tumor tissue

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analyzed by NanoPhotometer spectrophotometer. RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Tumor tissue

value: hepatocellular carcinoma

value: Normal diet


title: ipRGC, P5, rep39

description:
SmartSeq2
P5_38


title: Serum_DU_1mo_rep2


title: K562 circMLLT1e2 1

description:
SC8
SC1_SC46_RawCounts.xlsx

value: CML


title: ipRGC, P5, rep40

description:
SmartSeq2
P5_39


title: NDT3


title: K562 circMLLe9-10 1

description:
SC5
SC1_SC46_RawCounts.xlsx


title: K562 MIG EV 1

description:
SC2
SC1_SC46_RawCounts.xlsx


title: NDT4


title: Serum_DU_1mo_rep1


title: Serum_Pb_1mo_rep4

value: Pb


title: NDN1

source_name: Nontumor tissue

value: Nontumor tissue

value: liver


title: K562 circMLLe9-10

description:
SC4
SC1_SC46_RawCounts.xlsx


title: ipRGC, P5, rep38

description:
SmartSeq2
P5_37

value: Retina

value: ipRGC


title: KDT4

value: Ketogenic diet


title: Serum_Pb_1mo_rep3

value: Male


title: K562 MIG EV 2

description:
SC3
SC1_SC46_RawCounts.xlsx

value: cell line

value: Transgenic line


title: ipRGC, P5, rep36

description:
SmartSeq2
P5_35

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: ipRGC, P5, rep32

description:
SmartSeq2
P5_31


title: KDT3


title: ipRGC, P5, rep37

description:
SmartSeq2
P5_36


title: ipRGC, P5, rep45

description:
SmartSeq2
P5_44


title: Serum_Al_1mo_rep3

value: Al


title: UNC rep2 RNA

city: Duarte

first: Dustin

middle: E.

last: Schones

state: CA

address: 1500 E Duarte, 2131B North Gonda

institute: Beckman Research Institute of the City of Hope

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FastQC v0.11.8 and trimgalore v0.4.5 at default settings
Trimmed sequence reads were mapped to the hg19 reference genome using TopHat v2.1.1 (parameter: --bowtie1)
Read count extraction was performed using HTSeq-0.6.1 and normalization were performed using DESeq2
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: blood

extract_protocol:
Total RNA was collected from cells using Trizol (ThermoFisher Scientific: 15596018) followed by an ethanol precipitation according to the manufacturerÕs protocol (Invitrogen). Extracted RNA was further purified by treatment with DNase (ThermoFisher Scientific: TURBO DNase, AM2238) to remove any trace DNA contaminants. Purity of RNA was analyzed by NanoDrop
RNA-seq libraries were prepared (Roche: KAPA RNA HyperPrep Kit with RiboErase) according to manufacturer's protocol

value: blood

value: CD34+ hematopoietic stem and progenitor cells

tag: condition

value: H3K9me2 inhibition


title: NDN4


title: Serum_Pb_1mo_rep2

value: Sprague-Dawley


title: NDN3

value: Normal diet


title: K562 MIG EV

description:
SC1
SC1_SC46_RawCounts.xlsx

value: CML


title: Serum_Pb_1mo_rep1

value: Pb


title: KDT2

value: Tumor tissue

value: hepatocellular carcinoma


title: ipRGC, P5, rep34

description:
SmartSeq2
P5_33

value: Retina


title: ipRGC, P5, rep35

description:
SmartSeq2
P5_34

value: ipRGC


title: Serum_Cu_1mo_rep4

value: Cu


title: ipRGC, P5, rep30

description:
SmartSeq2
P5_29


title: Serum_Al_1mo_rep4

value: Male


title: Control rep2 RNA

value: WT

value: DMSO


title: UNC rep1 RNA


title: ipRGC, P5, rep29

description:
SmartSeq2
P5_28

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: NDT1


title: ipRGC, P5, rep33

description:
SmartSeq2
P5_32


title: KDN4

value: Nontumor tissue

value: liver

value: Ketogenic diet


title: DAC rep1 RNA

value: blood

value: CD34+ hematopoietic stem and progenitor cells

value: DNA methylation inhibition

value: Decitabine


title: Serum_Al_1mo_rep2

value: Sprague-Dawley

value: Al


title: Serum_Al_1mo_rep1


title: Serum_Cu_1mo_rep2


title: KDT1

value: Tumor tissue

value: hepatocellular carcinoma


title: Serum_Cu_1mo_rep1


title: NDN2

value: Normal diet


title: ipRGC, P5, rep28

description:
SmartSeq2
P5_27

value: Retina

value: ipRGC


title: ipRGC, P5, rep27

description:
SmartSeq2
P5_26


title: ipRGC, P5, rep31

description:
SmartSeq2
P5_30


title: DAC rep2 RNA


title: ipRGC, P5, rep25

description:
SmartSeq2
P5_24


title: KDN3


title: Control rep1 RNA

value: WT


title: ipRGC, P5, rep24

description:
SmartSeq2
P5_23


title: KDN2


title: Serum_Fe_1mo_rep4

value: Male

value: Fe


title: Serum_Fe_1mo_rep2


title: U251TR rep2

city: Beijing

first: hanjie

last: liu

address: Nansihuanxi street，NO.119

institute: 1. Beijing Neurosurgical Institute and Beijing Tiantan Hospital

description:
Central Nervous System
U251TR-8_FRAS192011613-1a

data_processing:
RNA-seq mapping and quantification were processed by using STAR (v2.5.2b, Dobin et al., 2012) and RSEM (v1.2.31, Li et al., 2011) software. Briefly, the reads were aligned to the human genome reference (GENCODE v19, hg19) with STAR, and then sequencing read counts for each GENCODE gene were calculated using RSEM. The expression levels of different samples were merged into a FPKM (fragments per kilobase transcriptome per million fragments) matrix. We define a expressed gene only if its expressed level is larger than 0 at half of samples. Finally, we only retain the expressed genes in mRNA expression profile. The details describes as below:
The mRNA Analysis pipeline begins with the alignment workflow by using STAR (v2.5.2b). For each RNA-seq sample, STAR aligns each read group to human reference genome (GENCODE v19, hg19) separately and then merges the resulting alignments into one.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with RPKM value for every gene and every sample

source_name: glioblastoma cells

growth_protocol: Cells were cultured in DMEM culture medium supplemented with 10% FBS with a standard humidified incubator under 5% CO2 at 37°C.

extract_protocol:
Total RNA from U251MG, U87MG, U251TR and U87TR cell lines were extracted and quantified. A total amount of 3 μg RNA per sample was used as input material for library preparation. The library preparations went through standard Illumina Hiseq platform and 150 bp paired-end reads from transcriptome sequencing were generated.
Total RNA was isolated using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Pestle and QIAshredder (Qiagen) were used to disrupt and homogenize frozen tissue. The RNA intensity was checked using a 2,100 Bioanalyzer (Agilent Technologies) and only high quality samples with an RNA Integrity Number (RIN) value greater than or equal to 6.8 were used to construct the sequencing library. Typically,3 μg of total RNA was used with the TruSeq RNA library preparation kit (Illumina) in accordance with low-throughput protocol, except that SuperScript III reverse transcriptase (Invitrogen) was used to synthesize first strand cDNA. After PCR enrichment and purification of adapter-ligated fragments, the concentration of DNA with adapters was determined with quantitative PCR (Applied Biosystems 7,500) using primers QP1 5′-AATGATACGGCGACCACCGA-3′ and QP2 5′-CAAGCAGAAGACGGCATACGAGA-3′. The length of the DNA fragment was measured using a 2,100 Bioanalyzer, with median insert sizes of 200 nucleotides. Then, RNA-seq libraries were sequenced using the Illumina HiSeq 2500 Sequencing System. The libraries were prepared using the paired-end strategy with the read length of 150 bp. Base-calling was performed by the Illumina CASAVA v1.8.2 pipeline.

treatment_protocol: Temozolomide (TMZ) resistant U87MG cells (U87TR) and TMZ resistant U251MG cells (U251TR) of glioblastoma (GBM) sub-cell lines, were established through repetitive exposure to increasing TMZ concentrations in vitro in our laboratory.

value: glioblastoma

tag: phenotype

value: temozolomide resistant cells


title: U87TR rep2

description:
Central Nervous System
U87TR-3-17_FRAS192013741-1a


title: Serum_Cu_1mo_rep3

value: Cu


title: Triplet-157

city: Shanghai

first: Dawei

last: Wang

address: 197 Ruijin Road II

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Low quality reads, such as only adaptor, unknown nucleotides>5%, or Q20 <20% (percentage of sequences with sequencing error rates <1%), were removed by perl script. The clean reads that were filtered from the raw reads were mapped to honeybee (Apis mellifera) genome (OGSv3.2) using Tophat2 (Kim, Pertea et al. 2013) software. The aligned records from the aligners in BAM/SAM format were further examined to remove potential duplicate molecules. Gene expression levels were estimated using FPKM values (fragments per kilobase of exon per million fragments mapped) by the Cufflinks software (Trapnell, Williams et al. 2010).
DESeq (Anders and Huber 2010) and Q-value were employed and used to evaluate differential gene expression between queen and worker honeybee. After that, gene abundance differences between those samples were calculated based on the ratio of the FPKM values. The false discovery rate (FDR) control method was used to identify the threshold of the P-value in multiple tests in order to compute the significance of the differences.
Genes were compared against various protein database by BLASTX, including the National Center for Biotechnology Information (NCBI) non-redundant protein (Nr) database, Swiss-Prot database with a cut-off E-value of 10-5. Furthermore, genes were searched against the NCBI non-redundant nucleotide sequence (Nt) database using BLASTn by a cut-off E-value of 10-5. Genes were retrieved based on the best BLAST hit (highest score) along with their protein functional annotation.
To annotate the gene with gene ontology (GO) terms, the Nr BLAST results were imported into the Blast2 GO program (Conesa, Gotz et al. 2005). GO annotations for the genes were obtained by Blast2GO. This analysis mapped all of the annotated genes to GO terms in the database and counted the number of genes associated with each term. Perl script was then used to plot GO functional classification for the unigenes with a GO term hit to view the distribution of gene functions. The obtained annotation was enriched and refined using TopGo (R package). The gene sequences were also aligned to the Clusters of Orthologous Group (COG) database to predict and classify functions (Tatusov, Galperin et al. 2000). KEGG pathways were assigned to the assembled sequences by perl script.
Assembly: GRCm38
Supplementary files format and content: counts, fpkm, and different expression genes between Control group and Dual group, or Control group and Triplet group.

source_name: Breast tumor

extract_protocol:
Total RNA of each sample was extracted from the honeybee larvae according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA). RNA integrity and concentration were checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). The mRNA was isolated by NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB, E7490).
The cDNA library was constructed following the manufacturer’s instructions of NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530) and NEBNext Multiplex Oligos for Illumina (NEB, E7500).

treatment_protocol: Control group: Intratumoral and intraperitoneal injection of PBS. Ab group: Intraperitoneal injection of PD-1 antibody. Dual group: Intratumoral injection of oHSV and intraperitoneal injection of OLA. Triplet group: Intratumoral injection of oHSV and intraperitoneal injection of OLA and PD-1 antibody.

value: Primary tumor tissue

value: BALB/C

value: 6-8 weeks

tag: sample group

value: Triplet group


title: U251TR rep3

description:
Central Nervous System
U251TR-9_FRAS192011614-1a


title: U87TR rep3

description:
Central Nervous System
U87TR-3-18_FRAS192013742-1a


title: U87TR rep1

description:
Central Nervous System
U87TR-3-16_FRAS192013740-1a


title: ipRGC, P5, rep26

description:
SmartSeq2
P5_25

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: Triplet-163


title: Serum_Co_1mo_rep3

value: Sprague-Dawley

value: Co


title: U251TR rep1

description:
Central Nervous System
U251TR-7_FRAS192011612-1a


title: Serum_Fe_1mo_rep1


title: Serum_Co_1mo_rep4


title: KDN1

value: Nontumor tissue

value: liver

value: Ketogenic diet


title: Triplet-155


title: Triplet-179


title: ipRGC, P5, rep23

description:
SmartSeq2
P5_22

value: Retina

value: ipRGC


title: Serum_Fe_1mo_rep3

value: Male


title: U87MG rep2

description:
Central Nervous System
U87MG-2_FRAS192011607-1a

value: Malignant Glioma cells


title: ipRGC, P5, rep21

description:
SmartSeq2
P5_20


title: Dual-174

value: Dual group


title: ipRGC, P5, rep22

description:
SmartSeq2
P5_21


title: U87MG rep1

description:
Central Nervous System
U87MG-1_FRAS192011606-1a

value: glioblastoma


title: ipRGC, P5, rep19

description:
SmartSeq2
P5_18


title: U251MG rep2

description:
Central Nervous System
U251MG-5_FRAS192011610-1a


title: Serum_Co_1mo_rep1


title: Serum_Co_1mo_rep2


title: U251MG rep3

description:
Central Nervous System
U251MG-6_FRAS192011611-1a


title: U87MG rep3

description:
Central Nervous System
U87MG-3_FRAS192011608-1a


title: Dual-173


title: Dual-154


title: ipRGC, P5, rep20

description:
SmartSeq2
P5_19


title: Serum_Ni_1mo_rep4

value: Ni


title: Serum_Ni_1mo_rep3


title: ipRGC, P5, rep17

description:
SmartSeq2
P5_16


title: U251MG rep1

description:
Central Nervous System
U251MG-4_FRAS192011609-1a


title: Dual-166

value: Primary tumor tissue


title: Ab-192

value: BALB/C

value: Ab group


title: Serum_Ni_1mo_rep2


title: Ab-187

value: 6-8 weeks


title: ipRGC, P5, rep16

description:
SmartSeq2
P5_15

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: ipRGC, P5, rep15

description:
SmartSeq2
P5_14


title: Serum_Ni_1mo_rep1

value: Sprague-Dawley


title: Ab-185


title: Serum_W_1mo_rep4

value: W


title: Ab-159


title: PCS_1_1_B_R1.fastq.gz

city: Jerusalem

first: Yosef

last: Buganim

address: Jerusalem, IMRIC-Hadassah Medical School

department: Developmental Biology and Cancer Research

country: Israel

institute: HUJI

library_source: genomic

data_processing:
Raw reads were quality-trimmed and adapters removed.
BSMAP V 2.9 was used to align the paired-end reads to the human genome (hg19)
The methylation ratio of CpGs with sequencing depth of at least 10 reads were computed based on 100bp tiles.

molecule: genomic DNA

growth_protocol: hiTSC and hbdTSC cells were grown on a layer of Mitomycin C-treated mouse embryonic fibroblast (MEF) feeder cells and cultured in human TSC medium (Okae et al, 2018). HFFs were grown in DMEM containing 10%FBS, 1% L-glutamine and 1% penicillin-streptomycin. hiTSC and hbdTSC cells were passaged twice on matrigel in order to minimize the presence of MEF feeder cells. hESCs and hiPSCs were grown in human embryonic stem cell (hES) medium comprised of Knockout DMEM containing 15% KnockOut serum replacement, 0.1 mM 2-mercaptoethanol, 1% L-glutamine, 1% non-essential amino acids and 1% Penicillin-Streptomycin, supplemented with freshly added 4ng/ml bFGF.

extract_protocol:
DNA was isolated from samples and incubated in lysis buffer (25mM Tris-HCl at pH8, 2mM EDTA, 0.2%SDS, 200mM NaCl) supplemented with 300μg/mL proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation. hiTSC colonies and hbdTSC colonies were passaged twice on matrigel in order to eliminate the presence of MEF feeder cells.
Libraries were prepared as previously described in Boyle et al., 2012.

value: Human induced trophoblast stem cells - line #11


title: ipRGC, P5, rep14

description:
SmartSeq2
P5_13


title: PCS_1_1_A_R1.fastq.gz


title: ipRGC, P5, rep18

description:
SmartSeq2
P5_17


title: PCS_1_1_C_R1.fastq.gz


title: Control-189

value: Control group


title: Serum_W_1mo_rep2


title: hES_B_R1.fastq.gz

source_name: hESC

value: Human embryonic stem cell line


title: hES_A_R1.fastq.gz


title: Serum_W_1mo_rep1


title: Control-180


title: GMOK_25col3_F2_R1.fastq.gz

value: Human induced trophoblast stem cells - line #3


title: Control-188


title: GMOK_25col3_E2_R1.fastq.gz


title: ipRGC, P5, rep11

description:
SmartSeq2
P5_10

value: Retina

value: ipRGC


title: Control-167


title: ipRGC, P5, rep10

description:
SmartSeq2
P5_9


title: Serum_Ta_1mo_rep3

value: Male

value: Ta


title: GMOK_25col3_A1_R1.fastq.gz


title: WT, wildtype, untreated, 12-month-old, rep3

first: Siying

address: No.25, Lane 2200 Xie-Tu Road.

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (http://github.com/OpenGene/fastp) with parameters -q 20-lenghth_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
The clean reads were separately aligned to reference genome with orientation mode using hisat software.
The expression level of each transcript was calculated according to the fragments per Transcripts Per Million Reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Livers from WT or Ftcd LKO mice were removed, visible tumors (>0.5 mm) were counted and measured. Livers and indicated tumors were dissected into different sections, part of them were immediately frozen in liquid nitrogen and stored in -80℃ subsequently used for RNA Seq.

extract_protocol:
Total RNA was harvested using TRIzol® Reagent(Invitrogen) according to the manufacturer's instructions. RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280 =1.8~2.2, OD260/230>=2.0, RIN>= 6.5, 28S:18S >=1.0, >10μg) was used to construct sequencing library.
RNA-sequencing transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.

treatment_protocol:
For chemical induction of hepatocarcinogenesis, WT and Ftcd LKO mice at postnatal day 14 were injected intraperitoneally with DEN (20 mg/kg, N0258-1G; Sigma-Aldrich), and then weaned and maintained on regular chow food. Livers and tumors were harvested for analysis at 12 month after the initial injection.
For spontaneous hepatocarcinogenesis, wild-type (WT) and liver-specific Ftcd knockout (LKO) mice at postnatal day 14 were monitored, and then weaned and maintained on regular chow food. Livers and tumors were harvested for analysis at the age of 12 month.

value: liver

value: liver tissues

value: WT

value: untreated

value: Month 12


title: Serum_Ta_1mo_rep2


title: Serum_Ta_1mo_rep4


title: hES_C_R1.fastq.gz


title: GMOK_25_1_C_R1.fastq.gz

value: Human induced trophoblast stem cells - line #2


title: ipRGC, P5, rep13

first: Alex

address: 725 N Wolfe St

description:
SmartSeq2
P5_12

data_processing:
FASTQ files were aligned to the GRCm38.p6 (mm10) mouse reference genome using HISAT2 version 2.1.0.
The resulting SAM files were converted to BAM files using SAMtools version 1.9.
Transcript abundance was estimated using Cuffquant and normalization was performed using Cuffnorm in Cufflinks version 2.2.1.
All analyses were performed using Seurat in R version 3.6.2.
Assembly: mm10
Supplementary files format and content: Cuffnorm matrix containing FPKM values for each gene for each cell
Supplementary files format and content: Cuffnorm matrix containing annotations for each gene
Supplementary files format and content: Cuffnorm matrix containing annotations for each sample

extract_protocol:
Retinas were dissected in cold Hibernate A medium lacking Ca2+, Mg2+, and phenol red (BrainBits). Retinas were then dissociated in papain (Worthington Biochemical, LS003126), 5.5 mM Cysteine-HCl, and 1.1 mM EDTA dissolved in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red) for seven minutes at 37°C. Cell suspension was passed through a 40 μm cell strainer (Falcon, 352340) and incubated for 30 minutes on ice with Brilliant Violet (BV)-421 anti-mouse CD90.2 antibody (BioLegend, 105341, 1:300), which binds to RGCs and provides an additional selection marker during FACS. The cells were then centrifuged and resuspended in 0.4% bovine serum albumin dissolved in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red). Cells were again centrifuged and resuspended in 2000 U/ml DNase I (New England Biolabs, M0303S) in Hibernate A medium (lacking Ca2+, Mg2+, and phenol red) prior to cell sorting. Individual GFP+, BV-421+ cells were sorted into a lysis solution consisting of 3500 U/ml RNase inhibitor (New England Biolabs, M0314S), 140 U/ml DNase I, and 0.17% v/v Triton X-100 in water using a MoFlo Legacy cell sorter (Beckman Coulter).
Single-cell DNA libraries were prepared according to the Smart-seq2 protocol (Picelli et al., Nature Protocols, 2014) and sequenced using an Illumina NextSeq 500 sequencer (75 bp paired-end reads, 400 million total reads).

value: Opn4Cre/+; Brn3bzDta/+; Rosa26fsTRAP/+


title: Serum_Ta_1mo_rep1

value: Sprague-Dawley


title: GMOK_25_1_B_R1.fastq.gz


title: ipRGC, P5, rep12

description:
SmartSeq2
P5_11


title: ipRGC, P5, rep7

description:
SmartSeq2
P5_6


title: Serum_DU_12mo_rep4

value: DU


title: LKO, liver-specific Ftcd knockout, untreated, 12-month-old, rep3

value: liver-specific Ftcd knockout


title: WT, wildtype, untreated, 12-month-old, rep2


title: WT, wildtype, untreated, 12-month-old, rep1


title: GMOK_25_1_A_R1.fastq.gz


title: Serum_W_1mo_rep3

value: W


title: Serum_DU_12mo_rep3


title: LKO, liver-specific Ftcd knockout, untreated, 12-month-old, rep2


title: ipRGC, P5, rep6

description:
SmartSeq2
P5_5


title: GMOK_2233_3_C_R1.fastq.gz

value: Human induced trophoblast stem cells - line #4


title: Serum_DU_12mo_rep2


title: ipRGC, P5, rep5

description:
SmartSeq2
P5_4


title: ipRGC, P5, rep4

description:
SmartSeq2
P5_3


title: ipRGC, P5, rep9

description:
SmartSeq2
P5_8


title: GMOK_2233_3_B_R1.fastq.gz


title: ipRGC, P5, rep2

description:
SmartSeq2
P5_1


title: LKO, liver-specific Ftcd knockout, untreated, 12-month-old, rep1


title: ipRGC, P5, rep8

description:
SmartSeq2
P5_7


title: DEN12WT, wildtype, DEN12, rep5

value: nontumourous liver tissues

value: DEN


title: GMOK_2233_3_A_R1.fastq.gz


title: DEN12WT, wildtype, DEN12, rep6


title: Serum_Pb_12mo_rep4

value: Pb


title: Serum_Pb_12mo_rep3

value: Male


title: E9_C_R1.fastq.gz

value: Human bastocyst-derived trophoblast stem cells - line #9


title: DEN12WT, wildtype, DEN12, rep4

value: liver


title: E9_B_R1.fastq.gz


title: ipRGC, P5, rep1

description:
SmartSeq2
P5_0

value: Retina

value: ipRGC


title: DEN12WT, wildtype, DEN12, rep3

value: WT


title: Serum_Pb_12mo_rep2


title: E9_A_R1.fastq.gz


title: DEN12WT, wildtype, DEN12, rep2

value: Month 12


title: ipRGC, P5, rep3

description:
SmartSeq2
P5_2


title: E2_c_R1.fastq.gz

value: Human bastocyst-derived trophoblast stem cells - line #2


title: Serum_DU_12mo_rep1


title: Serum_Pb_12mo_rep1


title: E2_b1_R1.fastq.gz


title: Serum_Al_12mo_rep4

value: Al


title: Serum_Al_12mo_rep3

value: Sprague-Dawley


title: VEA 12.5 mg/kg treatment, 68

city: jeongeup

first: seonghoon

last: yoon

address: baekhak 1 gil 30

institute: Korea Institute of Toxicology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: lung

value: VEA 12.5 mg/kg


title: DEN12LKO_T, liver-specific Ftcd knockout, DEN12, rep3

value: tumorous tissues

value: liver-specific Ftcd knockout


title: Serum_Al_12mo_rep2


title: E2_a_R1.fastq.gz


title: VEA 12.5 mg/kg treatment, 66


title: DEN12LKO_N, liver-specific Ftcd knockout, DEN12, rep3

value: nontumourous liver tissues


title: Cov3_A

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

data_processing:
Sequencing in 75 cycles produced 20 bp Read 1 (bases 6-11 sample barcode, bases 13-20 UMI) and 55 bp Read 2 (sequence derived from the mRNA).
Raw sequence data was filtered to remove reads shorter than 20 bp.
The original pipeline suggested in (Macosko EZ et al. Cell 2015; https://github.com/broadinstitute/Drop-seq) for processing of drop-seq data was used. Briefly, reads were additionally filtered to remove polyA tails of length 6 or greater, then aligned to the mouse (mm10) genome using STAR aligner, with default settings. Uniquely mapped reads were grouped according to the 1-12 barcode, and gene transcripts were counted by their Unique Molecular Identifiers (UMIs) to reduce bias emerging from the PCR amplification. Digital expression matrices (DGE) reported the number of transcripts per gene in a given sample (according to the distinct UMI sequences counted).
Differentially expressed genes were identified using edgeR
Supplementary files format and content: Digital Gene Expression (DGE): tab-delimited text file containing UMI read counts for each sample

source_name: BALB/c mice

growth_protocol: Spleen cells from individual mice were seeded in 48 well plates at 5x106 cells/ml in RPMI 1640 medium (750 μl volume) containing heat-inactivated fetal calf serum (10%), penicillin/ streptomycin, glutamine and HEPES (25 mM), at 37°C and 5% CO2. Cells were stimulated for 3 days with recombinant spike RBD protein, produced in HEK-293 cells (10 μg/ml). After 3 days, cells were harvested, and bulk RNA was isolated.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) and following manufacturer’s guidelines. Cells were homogenized with QIAshredder colums (Qiagen). RNA samples were stored at -70°C.
RNA sequencing method was designed based on the Drop-seq protocol described in (Macosko EZ et al. Cell 2015). Briefly, 10 ng of RNA was mixed with Indexing Oligonucleotides. After 5 minutes of incubation the RNA was combined with RT mix (1 x Maxima RT buffer, 1 mM dNTPs, 10 U/µl Maxima H- RTase, 1 U/µl RNase inhibitor and 2.5 µM Template Switch Oligo). Samples were incubated for 30 minutes at 22°C and 90 minutes at 52°C. The constructed cDNA was amplified by PCR. The PCR products were pooled together in sets of 12 samples containing different Indexing Oligos and purified with Agencourt AMPure XP Beads according to the manufacturer’s instructions. The 3’-end cDNA fragments for sequencing were prepared using the Nextera XT (Illumina) tagmentation reaction. The reaction was performed according to manufacturer’s instruction, with the exception of the P5 SMART primer that was used instead of S5xx Nextera primer. Each set of 12-18 samples that was pooled after the PCR reaction was tagmented with a different Nextera N7xx index. Subsequently, the samples were PCR amplified and purified twice using Agencourt AMPure Beads. The libraries were sequenced on a Illumina NextSeq 500, with a custom primer producing read 1 of 20 bp and read 2 (paired end) of 50 bp. Sequencing was performed at the Functional Genomics Unit of the University of Helsinki, Finland.
scRNA-seq (Drop-seq-like)

treatment_protocol: HLA-DQ6, huCD4 transgenic Ab0 NOD mice were originally purchased from The Jackson Laboratory (Bar Harbor, ME, USA), and bred at the University of Helsinki Laboratory Animal Centre. Mice were maintained under specific pathogen–free conditions, on normal chow.  For vaccination, mice were sedated with isoflurane, and placed in supine position for intranasal inoculation during normal inhalation using a pipette, or onto the left side, for intramuscular injection into the right thigh using a 27G needle. Mice were vaccinated once with different doses of Ad5-RBD, administered in 30 µL of PBS (dose range 106-1010 vp), and were allowed to recover naturally. After 25 days, mice were anesthesized with ketamine/xylazine intraperitoneally, and exsanguinated by retroorbital bleeding. After cervical dislocation, spleens were removed from the abdomen aseptically.

value: BALB/c mice


title: DEN12LKO_T, liver-specific Ftcd knockout, DEN12, rep2

source_name: liver

value: DEN


title: KEN_d1_R1.fastq.gz

source_name: HFF (KEN)

value: Human foreskin fibroblasts - KEN line


title: KEN_b2_R1.fastq.gz


title: VEA 6.25 mg/kg treatment, 65

value: VEA 6.25 mg/kg


title: Cov3_B

source_name: DQ6 mice

value: DQ6 mice


title: VEA 6.25 mg/kg treatment, 64


title: KEN_a2_R1.fastq.gz


title: DEN12LKO_N, liver-specific Ftcd knockout, DEN12, rep2

value: liver


title: VEA 12.5 mg/kg treatment, 70


title: DEN12WT, wildtype, DEN12, rep1


title: Serum_Cu_12mo_rep3

value: Male

value: Cu


title: DEN12LKO_T, liver-specific Ftcd knockout, DEN12, rep1

value: Month 12


title: Serum_Cu_12mo_rep4


title: Serum_Cu_12mo_rep2


title: VEA 3.12 mg/kg treatment, 59

value: VEA 3.12 mg/kg


title: Serum_Cu_12mo_rep1


title: TET1 homozygous loss of function mutant replicate 2

city: Toronto

first: Fiona

middle: J

last: Coutinho

state: ON

address: 686 Bay Street, PGCRL 16-9801

department: Developmental and Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

data_processing:
FASTQ files were aligned to the hg19 genome and sorted using STAR v2.4.2a in two-pass mode with the following redefined parameters: --sjdbOverhang 47,  --genomeChrBinNbits 18, --genomeSAsparseD 2
Read groups were added to the aligned and coordinate-sorted BAM files using picard v1.9.1
QC of BAM files were checked using RNA-SeQC v1.1.8
Read counts were generated from the bam files using HTSeq v0.6.1 with the following redefined parameters: --stranded=reverse, --type=exon, --idattr=gene_id, --mode=union
Annotation file was based on the Gencode v19 GTF file
Genome_build: hg19
Supplementary_files_format_and_content: Read counts by clone_EnsemblID.txt file contains log2 normalized read counts by gene

source_name: TET1 homozygous loss of function mutant, primary human glioblastoma culture

growth_protocol: Cells were grown adherently on laminin-coated tissue culture plates in neural stem cell media containing EGF and FGF

extract_protocol:
Cells were lysed on the plate using RLT buffer (Qiagen) and total RNA was extracted using the Qiagen Rneasy kit with on-column Dnase digestion
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untreated

value: adult brain

tag: tumor

value: Glioblastoma (Grade IV)

tag: derived culture

tag: genotype/variation

value: TET1 homozygous loss of function mutant


title: TET1 homozygous loss of function mutant replicate 3

tag: tissue


title: VEA 3.12 mg/kg treatment, 57

value: lung


title: Serum_Al_12mo_rep1

value: Sprague-Dawley

value: Al


title: DEN12LKO_N, liver-specific Ftcd knockout, DEN12, rep1

tag: cell type

value: nontumourous liver tissues

tag: genotype

value: liver-specific Ftcd knockout


title: Serum_Fe_12mo_rep4

tag: gender

value: Fe


title: TET1 heterozygous loss of function mutant replicate 3

source_name: TET1 heterozygous loss of function mutant, primary human glioblastoma culture


title: Serum_Fe_12mo_rep3

source_name: Serum


title: VEA 3.12 mg/kg treatment, 56


title: VEA 6.25 mg/kg treatment, 63


title: Serum_Fe_12mo_rep2


title: PG 1,100 mg/kg treatment, 30

value: PG 1,100 mg/kg


title: TET1 heterozygous loss of function mutant replicate 2


title: TET1 heterozygous loss of function mutant replicate 1


title: PG 1,100 mg/kg treatment, 28


title: Microglia,DRNAb+ with Captopril,rep1

city: Cambridge

first: Joshua

last: Levin

state: MA

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description: 10X Genomics v3.1

data_processing:
Sequenced data is processed to make fastq files with CellRanger mkfastq command.
Fastq files are fed into CellRanger count v6.1.2 with standard parameters except with the number of expected cells set based on the number of expected cells per sample.
Data was loaded into R with emptyDroplets using emptyDropsCellRanger, downsampling so all samples had the same average number of reads per cell, and processed with the standard Seurat v4.0.0 pipeline.
Clusters were annotated with known markers and non-microglia were removed.
Assembly: mm10
Supplementary files format and content: h5 matrix with molcular count data produced by CellRanger, used downstream to produce UMI count matrices

source_name: Hippocampus

extract_protocol:
Mice were anesthetized with Euthasol and perfused with pre-perfusion buffer containing 0.5% sodium nitrite, 0.9% sodium chloride, and 0.1% heparin. The hippocampus was extracted and dissociated using Miltenyi Neural Tissue Dissociation Kit. Microglia were isolated according to manufacturer’s instructions using Myelin Removal Beads II followed by FACS sorting based on Live/Dead Fixable Violet, CD45, and CD11b signal.
Library preparation was performed according to the manufacturer’s instructions (Next GEM Single Cell 3’GEM v3.1 protocol, 10x Genomics). Briefly, microglia were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Female B6.H2d mice 6-8 weeks old were immunized with DWEYS peptide on a polylysine backbone (DNRAb+) or with polylysine backbone alone (DNRAb-) emulsified with CFA and boosted with IFA emulsions at two and four weeks following initial injection. Mice were administered two doses of 5 mg/kg LPS i.p. 48 hours apart two weeks after completion of immunization to induce blood brain barrier permeability. Captopril (5 mg/kg) or saline was administered daily for two weeks at five weeks post-LPS. Mice were sacrificed at 8 weeks post-LPS.

value: Hippocampus

tag: age

value: 22-26 weeks

value: Microglia

value: DRNAb+ with Captopril


title: Microglia,DRNAb+ with Captopril,rep2

description: 10X Genomics v3.1

tag: treatment


title: Microglia,DRNAb+,rep3

description: 10X Genomics v3.1

value: DRNAb+


title: Microglia,DRNAb+,rep2

description: 10X Genomics v3.1


title: Microglia,DRNAb+ with Captopril,rep3

description: 10X Genomics v3.1


title: TET1 homozygous loss of function mutant replicate 1


title: Microglia,DRNAb+,rep1

description: 10X Genomics v3.1


title: WT control replicate 3

source_name: WT control, primary human glioblastoma culture

value: WT


title: Serum_Fe_12mo_rep1

first: Yuan

address: 760 Press Ave

data_processing:
Single-end reads for miRNA were mapped to miRbase version 22 and the Rnor 6.0 Rattus norvegicus genome using sRNAbench and sRNAtoolbox.
Supplementary_files_format_and_content: Tab-delimited matrix table with raw read counts for every miRNA

extract_protocol:
Total RNA was isolated from serum samples and assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Library preparation and sequencing was performed by Norgen Biotek. Briefly, library preparation was done using the Norgen Biotek Small RNA Library Prep Kit (Cat. 63600). Sequencing was performed using the NextSeq 500/550 High Output Kit v2 (51 Cycles using a 75-Cycle Kit) on the Illumina NextSeq 500 platform.

value: Male

tag: time


title: Serum_Co_12mo_rep4

tag: strain

value: Co


title: PG 1,100 mg/kg treatment, 27


title: Serum_Co_12mo_rep3

tag: metal


title: PG 826 mg/kg treatment, 23

value: PG 826 mg/kg


title: WT control replicate 2

value: adult brain

value: Glioblastoma (Grade IV)


title: Microglia,DRNAb-,rep3

description: 10X Genomics v3.1

value: DRNAb-


title: WT control replicate 1


title: Serum_Co_12mo_rep2

value: Sprague-Dawley


title: Microglia,DRNAb-,rep2

description: 10X Genomics v3.1


title: PG 826 mg/kg treatment, 22

value: lung


title: EWY55 YPX Rep F

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

description:
Gasch-1272
20510_AHLNF3DSX3-HTSeq-counts.txt

data_processing:
Reads trimmed with Trimmomatic version 0.3
reads mapped to Y22-3 genome usign Bowtie 2 version 2.2.2 with default settings
Read counts were calculated using HTSeq version 0.6.0
Assembly: Y22-3
Supplementary files format and content: All processed data files contain raw read counts from HTSeq. Each column is a different sample, each row is a different gene

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: Cells were first grown in aerobic YPD >16 hours to saturation. Cells from these saturated cultures were used to inoculate anaerobic YPD medium at an OD of 0.05. Once cells reached early/mid-log phase, 50 mL of YPD culture was collected, washed with anaerobic YPX, then used to inoculate an anaerobic YPX flask. 5% phenol 95% ethanol was added to the remaining YPD culture, which was subsequently spun down, flash frozen iin liquid nitrogen, and stored at -80C. The YPX cultures were grown for 3.5 hours, then 5% phenol 95% ethanol was added to culture, which was subsequently spun down, flash frozen iin liquid nitrogen, and stored at -80C.

extract_protocol:
Hot phenol lysis followed by DNA digestion with Turbo-Dnase.
rRNA was depleted with EPiCenter Ribo-Zero Magnetic Gold Kit (Yeast) RevA kit (Illumina Inc, San Diego, CA), and the remaining RNA was purified using Agencourt RNACleanXP (Beckman Coulter, Indianapolis, IN) by following the manufacturers’ protocols. RNA-seq libraries were created with the Illumnia TruSeq stranded total RNA kit (Illumina) following the preparation guide (revision C), AMPure XP beads were used for PCR purification (Beckman Coulter, Indianapolis, IN), and cDNA generated with SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA) as described in the Illumina kit.

value: Y184 bcy1::KanMX (G418-R) opi1-T715G tpk1-G829C toa1-T354A rim8-C1591T chr. I dup.

tag: growth medium

value: YP 2% xylose, anaerobic

tag: growth phase

value: early/mid-log phase

value: yeast cell


title: Microglia,DRNAb-,rep1

description: 10X Genomics v3.1

value: Hippocampus

value: 22-26 weeks


title: 10% Ethanol treatment (VEA control), 14

source_name: lung

value: 10% Ethanol (VEA control)


title: 10% Ethanol treatment (VEA control), 13


title: Y184 bcy1∆ YPX Rep F

description:
Gasch-1271
20510_AHLNF3DSX3-HTSeq-counts.txt

value: Y184 bcy1::KanMX


title: EWY55 YPX Rep E

description:
Gasch-1268
20510_AHLNF3DSX3-HTSeq-counts.txt


title: PG 826 mg/kg treatment, 25


title: 10% Ethanol treatment (VEA control), 12


title: N5-H3K9me3

city: Wuhan

first: Chen-Yu

state: Hubei

address: 299 Bayi Road, Wuchang District

institute: Wuhan University

data_processing:
Sequenced reads were trimmed for adaptor sequence using Trimgalore version 0.6.7 , and masked for low-complexity or low-quality sequence.
ChIP-seq reads were aligned to the mm10 genome assembly using  with bowtie2-align-s version 2.3.5.1
peaks were called using macs2 2.1.1.20160309 with the following setting -p 1E-10 --nomodel --keep-dup all --SPMR --extsize 147 --broad --broad-cutoff 1E-10
bigWig files were generated using the deeptools 3.1.3 bamCoverage with the following setting -p 10 --normalizeUsing RPKM
Assembly: mm10
Supplementary files format and content: bigWig, bam

source_name: Liver tissue

growth_protocol: Male C57BL/6 mice at 6 weeks of age were obtained from Gempharmatech Co., Ltd.  All the mice were maintained under pathogen-free condition 20~24℃ with a humidity of 40~70% and a 12/12-hours dark/light cycle (lights on at 7:00 AM, lights off at 7:00 PM), with free access of water and food (Animal Center of College of Life Sciences, Wuhan University).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed by VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND606). Briefly, 50 μL of purified ChIP DNA (8–10 ng) was end-repaired for dA tailing, followed by adaptor ligation. Each adaptor was marked with a barcode of 6 bp which can be recognized after mixing different samples together. Adaptor-ligated ChIP DNA was purified by AMPure XP beads (1:1) and then amplified by PCR of 11–13 cycles with the primer matching with adaptor universal part. Amplified ChIP DNA was purified again using AMPure XP beads (1:1) in 35-μL EB elution buffer. For multiplexing, libraries with different barcode were mixed together with equal molar quantities by considering appropriate sequencing depth (30–40 million reads per library). Libraries were sequenced by Illumina Hi-seq X Ten platform with pair-end reads of 150 bp.

treatment_protocol: Mice were allowed to acclimate in the facility for 1 week before being randomly assigned to a Normal diet or an HF diet (60% calories from fat, D12452, Research Diets，USA) for 16 weeks (n=5/group). Body weight was recorded weekly. Livers were collected for subsequent study, and plasma samples were collected and stored at −80°C for analyses of biochemical parameters.

value: Liver tissue

value: Regular chow diet

tag: chip antibody


title: Serum_W_12mo_rep3

institute: University of Kentucky

value: Male

value: W


title: Serum_W_12mo_rep4


title: Saline treatment (PG control), 10

value: Saline (PG control)


title: Saline treatment (PG control), 8


title: EWY55 YPX Rep D

description:
Gasch-1264
20510_AHLNF3DSX3-HTSeq-counts.txt


title: Y184 bcy1∆ YPX Rep D

description:
Gasch-1263
20510_AHLNF3DSX3-HTSeq-counts.txt


title: N5-H3K27ac


title: N4-Input


title: Serum_Ta_12mo_rep3

value: Ta


title: N5-Input


title: Serum_Co_12mo_rep1

value: Co


title: Serum_Ta_12mo_rep4

value: Sprague-Dawley


title: Saline treatment (PG control), 6

value: lung


title: Serum_Ta_12mo_rep2


title: Serum_W_12mo_rep1


title: N4-H3K9me3


title: N4-H3K27ac


title: CD90neg IFNg A (nxid3616)

city: Lausanne

first: Laurent

last: Beziaud

address: Route Cantonale

country: Switzerland

institute: EPFL

data_processing:
Mapping was done with STAR (assembly mm10). Only reads uniquely mapped were conserved
Counts were obtained with HTSeq-counts
Assembly: GRCm38/mm10
Supplementary files format and content: Table S1_allgenes_normExpr_logFC_fromHTS.xlsm

source_name: mammary

growth_protocol: PyMT cells were maintained in DMEMF12 supplemented with 2% fetal bovine serum (FBS), 10ug/ml insuline, 20ng/ml EGF, and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA from CD90pos and CD90neg FACS-sorted cell populations were extracted using the RNeasy Micro kit (Qiagen)
The samples were subjected to library preparation by the TruSeq mRNA stranded method (Illumina).

treatment_protocol: IFNg 10 IU/ml 24h

value: primary mammary tumor

tag: cell line

value: PyMT

value: WT

value: IFNg


title: Y184 ira2∆bcy1∆ YPX Rep B

description:
A-2-4-2_S25_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt

value: Y184 ira2::MR bcy1::KanMX

value: YP 2% xylose, anaerobic

value: early/mid-log phase

value: yeast cell


title: Y184 ira2∆bcy1∆ YPX Rep C

description:
A-2-4-3_S26_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt


title: Y184 ira2∆bcy1∆ YPX Rep A

description:
A-2-4-1_S24_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt


title: CD90pos IFNg A (nxid3615)


title: Serum_Ta_12mo_rep1

city: Lexington

last: Wen


title: N3-Input

value: Liver tissue


title: N3-H3K9me3

value: Regular chow diet


title: CD90neg control A (nxid3614)

value: Control


title: Y184 bcy1∆ YPX Rep C

description:
A-2-3-3_S23_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt

value: Y184 bcy1::KanMX


title: CD90pos control A (nxid3613)


title: Y184 bcy1∆ YPX Rep B

description:
A-2-3-2_S22_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt


title: N3-H3K27ac


title: H4-Input

value: High fat diet


title: Y184 bcy1∆ YPX Rep A

description:
A-2-3-1_S21_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt


title: Serum_DU_3mo_rep3

value: Male

value: DU


title: Serum_DU_3mo_rep2

value: Sprague-Dawley


title: CD90pos IFNg B (nxid3612)


title: CD90neg IFNg B (nxid3611)


title: H4-H3K9me3


title: Serum_DU_3mo_rep1


title: CD90neg control B (nxid3610)


title: Y184 ira2Δ YPX Rep B

description:
A-2-2-2_S19_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt

value: Y184 ira2::MR


title: Y184 ira2Δ YPX Rep C

description:
A-2-2-3_S20_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt


title: Serum_Pb_3mo_rep4

value: Pb


title: Y184 ira2Δ YPX Rep A

description:
A-2-2-1_S18_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt


title: H3-Input


title: Serum_DU_3mo_rep4


title: H4-H3K27ac


title: CD90pos control B (nxid3609)

value: primary mammary tumor

value: PyMT


title: Serum_Pb_3mo_rep3


title: Serum_Pb_3mo_rep2


title: Y184 YPX Rep C

description:
A-2-1-3_S17_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt

value: CRB strain with xylose utilization genes (G418-R), gre3::MR isu1::loxP-Hyg (Hyg-R)


title: mm DRG culture 11j rep3 [BDLP3]

first: Zachary

middle: T

last: Campbell

address: 1111 Highland Avenue

department: Anesthesiology

institute: University of Wisconsin - Madison

data_processing:
FastQ file generation was followed by quality check via FastQC 0.11.5
Adaptor sequences were trimmed and read mapping was performed using TopHat 2.1.1
Reads were mapped to reference genome and transcriptome.
Gene abundance quantification was performed using Cufflinks 2.2.1 with option --no-length-correction
FPKM values were converted first to TPM values
Assembly: mm10
Supplementary files format and content: xlsx workbook with TPM values, fold changes, and p-values for all samples

source_name: dorsal root ganglion (DRG)

growth_protocol: Cells were cultured in DRG culture media supplemented with NGF and FRDU. Media was exchanged on alternating days. Cultures were incubated at 37°C in a humidified chamber maintained with 5% CO2.

extract_protocol:
Mouse DRGs were excised. Tissue samples were homogenized. Cultures were generated. RNA was harvested using Trizol reagent. Lexogen QuantSeq 3'mRNA-seq library kit and RiboCop rRNA depletion kit were used with 50ng-1ug total RNA.
RNA libraries were prepared for sequencing using maufacturer's protocols

treatment_protocol: On day in vitro six, cells were treated with the selective SMG1 kinase inhibitor, compound 11j (1 µM) or vehicle for 4 hours.

value: dorsal root ganglion (DRG)

value: Swiss Webster

value: compound 11j

tag: condition

value: inhibition of SMG1


title: Y184 YPX Rep B

description:
A-2-1-2-twolib5-86_S16_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt

value: YP 2% xylose, anaerobic

value: early/mid-log phase

value: yeast cell


title: mm DRG culture 11j rep2 [BDLP2]


title: H3-H3K27ac

value: Liver tissue


title: Serum_Pb_3mo_rep1


title: H2-Input

value: High fat diet


title: Serum_Al_3mo_rep4

value: Male

value: Al


title: Y184 YPX Rep A

description:
A-2-1-1_S14_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt

value: YP 2% glucose, anaerobic


title: mm DRG culture 11j rep1 [BDLP1]


title: H2-H3K9me3


title: Y184 ira2∆bcy1∆ YPD Rep C

description:
A-1-4-3-twolib21-87_S13_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt

value: Y184 ira2::MR bcy1::KanMX


title: Serum_Al_3mo_rep3

value: Sprague-Dawley


title: H2-H3K27ac


title: mm DRG culture CON rep3 [SWnegQT2]

value: vehicle

value: control


title: Serum_Al_3mo_rep1


title: H3-H3K9me3


title: mm DRG culture CON rep2 [SWnegQT1]


title: Y184 ira2∆bcy1∆ YPD Rep A

description:
A-1-4-1_S10_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt


title: mm DRG culture CON rep1 [B6negQT1]


title: mm DRG culture 11j rep4 [BDLP4]


title: Serum_W_12mo_rep2

value: W


title: Skin scivMSC3

city: Hangzhou

first: Chunting

last: Hua

state: Zhejiang

address: 3 East Qingchun Road

institute: Sir Run Run Shaw Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Dorsal skin

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Dorsal skin


title: Y184 bcy1∆ YPD Rep C

description:
A-1-3-3_S9_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt

value: Y184 bcy1::KanMX


title: Serum_Cu_3mo_rep3

value: Cu


title: Serum_Al_3mo_rep2


title: Y184 bcy1∆ YPX Rep E

description:
Gasch-1267
20510_AHLNF3DSX3-HTSeq-counts.txt


title: Skin scivMSC2


title: Y184 bcy1∆ YPD Rep B

description:
A-1-3-2_S8_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt


title: Serum_Cu_3mo_rep2


title: repo>Ras bratdsRNA-L6-CloneF9_rep2

city: Boston

first: Yanhui

last: Hu

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

data_processing:
FastQC was used for sequencing data quality control and MultiQC was used to aggregate the results.
Raw data processing was performed using STAR sequence aligner, the reads from 3 runs are added.
featureCounts were used to get gene counts from all samples into a single counts' matrix
Differential gene expression testing was performed by DESeq2
Assembly: Drosophila, FlyBase release r6.48
Supplementary files format and content: text file including read counts of each sample

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: Cell cultures were grown and expanded in their respective media. All cell lines were cultured in Schneiders Drosophila Medium (Gibco Cat # 21720001), supplemented with 10% Fetal Bovine Serum (Cytiva Hyclone Cat SH30070.03). For Act5C-GS>Ras attP-GFP-LI-Clone 2, Act5C-GS>Ras attP-GFP-LI-Clone 3 and Act5C-GS>Ras attP-GFP-LB-Clone 6 cultures were grown in the same basal media supplemented with 10 nM of Mifepristone (Thermofisher Cat# H11001).

extract_protocol:
Total RNA was isolated from the pellets using the TRIzolTM reagent (Life technologies (Ambion), Cat#:15596018) as per manufacturer’s instructions. The isolated total RNA was subjected to a cleanup using the RNeasy Mini Kit (Qiagen, Cat#74104) and the RNA post-cleanup was eluted in RNase-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: repo>Ras bratdsRNA-L6-CloneF9

tag: tissue specificity

value: glial


title: repo>Ras bratdsRNA-L6-CloneF9_rep3


title: Skin scivMSC1


title: Y184 ira2Δ YPD Rep C

description:
A-1-2-3_S6_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt

value: Y184 ira2::MR

value: early/mid-log phase


title: repo>Ras bratdsRNA-L6-CloneF9_rep1


title: Single cells of thymic total Double negative cells, sorted for live/dead

first: CBDM

last: Lab

department: Microbiology and Immunobiology

description: resection of fresh thymus tissue, sorted on  CD3-/Cd8-/CD19-/CD11b-/NK1.1- /GR1-/Ter119-/TCRb-/CD4-/TCRd-

data_processing:
Sequenced reads were demultiplexed, aligned, assigned to cells, and output as transcript-by-cell matrices using Cell Ranger (10X Genomics).
Assembly: mm10
Supplementary files format and content: tsv files for barcodes, features and counts for gene expression

source_name: Thymus

extract_protocol:
thymic resection
Purified cells were sent to the Broad Institute's Regev lab, which performed 10x 3' scRNA-seq)

value: Thymus

value: DN

value: WT


title: Single cells of thymic Double negative 1 cells, sorted for live/dead

description: resection of fresh thymus tissue, sorted on  CD3-/Cd8-/CD19-/CD11b-/NK1.1- /GR1-/Ter119-/TCRb-/CD4-/TCRd-/CD44+/CD25-


title: Serum_Fe_3mo_rep4

value: Male

value: Fe


title: Skin scMSC3


title: Y184 ira2∆bcy1∆ YPD Rep B

description:
A-1-4-2_S11_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt

value: Y184 ira2::MR bcy1::KanMX

value: YP 2% glucose, anaerobic

value: yeast cell


title: Y184 ira2Δ YPD Rep A

description:
A-1-2-1_S4_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt


title: Serum_Cu_3mo_rep4

value: Sprague-Dawley


title: Serum_Fe_3mo_rep3


title: repo>Ras bratdsRNA-L6-Clone4_rep1

value: repo>Ras bratdsRNA-L6-Clone4


title: repo>Ras bratdsRNA-L6-Clone4_rep2


title: Skin scMSC1

value: Dorsal skin


title: repo>Ras bratdsRNA-L6-Clone4_rep3


title: Serum_Fe_3mo_rep2


title: Skin DNCB3


title: Y184 YPD Rep B

description:
A-1-1-2_S2_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt

value: CRB strain with xylose utilization genes (G418-R), gre3::MR isu1::loxP-Hyg (Hyg-R)


title: Serum_Fe_3mo_rep1


title: Y184 YPD Rep C

description:
A-1-1-3-85_S3_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt


title: Skin DNCB2


title: repo>Ras bratdsRNA-L6-Clone2_rep2

value: repo>Ras bratdsRNA-L6-Clone2


title: Serum_Cu_3mo_rep1

value: Cu


title: Serum_Co_3mo_rep4

value: Co


title: repo>Ras bratdsRNA-L6-Clone2_rep1

value: glial


title: Y184 YPD Rep A

description:
A-1-1-1_S1_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt

value: early/mid-log phase


title: Skin DNCB1


title: Serum_Co_3mo_rep3


title: Y184 ira2Δ YPD Rep B

description:
A-1-2-2_S5_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt

value: Y184 ira2::MR


title: iKD AP2XII-1 +IAA 24h, biological repeat 3

first: Bang

last: Shen

address: No. 1 SHizishan St

institute: Huazhong Agricultural University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome of Toxoplasma gondii type I strain GT1
Read count extraction and normalization were performed using Salmon (version 1.9) and edgeR
Assembly: ToxoDB (https://toxodb.org/common/downloads/Current_Release/TgondiiGT1/fasta/data/)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Toxoplasma gondii

source_name: merozoites

growth_protocol: All Toxoplasma gondii used in this study were maintained in human foreskin fibroblasts cultured at 37 ℃ in 5% CO2 in complete Dulbecco’s Modified Eagle Medium supplemented with 10% heat-inactivated fetal bovine serum, 100 unit/mL penicillin, and 100 μg/mL streptomycin

extract_protocol:
RNA was harvested using Trizol reagent, and 1 ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

value: merozoites

value: AP2 XII-1 knock down 24h

value: add IAA 24h


title: Skin Solvent3


title: btl>Ras attP-p35-L8_rep3

value: btl>Ras attP-p35-L8

value: tracheal


title: Skin scMSC2


title: iKD AP2XII-1 +IAA 24h, biological repeat 2


title: Serum_Co_3mo_rep1

value: Male


title: Skin Solvent2


title: btl>Ras attP-p35-L8_rep2


title: repo>Ras bratdsRNA-L6-Clone2_rep3


title: iKD AP2XII-1 +IAA 12h, biological repeat 3

value: AP2 XII-1 knock down 12h

value: add IAA 12h


title: Serum_Ni_3mo_rep4

value: Sprague-Dawley

value: Ni


title: btl>Ras attP-p35-L8_rep1


title: iKD AP2XII-1 +IAA 24h, biological repeat 1


title: Serum_Ni_3mo_rep3


title: btl>Ras attP-p35-L7_rep2

value: btl>Ras attP-p35-L7


title: iKD AP2XII-1 +IAA 12h, biological repeat 2


title: Skin Solvent1

value: Dorsal skin


title: btl>Ras attP-p35-L7_rep3


title: MIN6, 5% oxygen, biol_rep_2

first: Tomonori

last: Tsuyama

address: 1-1-1, Honjo Chuo-ku

institute: Kumamoto university

data_processing:
Sequence reads were trimmed for universal illumina adaptors using TrimGalore.
Trimmed sequence reads were mapped to GENCODE36 genome sequence (for human) or M25 genome sequence (for mouse) using HISAT2 with default parameters setting. Mapped reads were sorted and converted to a binary alignment/map format using SAMtools.
Gene assembly and quantification were performed using Stringtie.
Assembly: GRCh38, GRCm38
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: MIN6 cells

extract_protocol:
RNA was extracted using RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit (E7765L and E7770, New England Biolabs.) following manufacturer's protocols.

value: MIN6 cells

value: Pancreatic beta cells

value: WT

value: 5percent_oxygen (6h)


title: MIN6, 5% oxygen, biol_rep_3


title: iKD AP2XII-1 +IAA 12h, biological repeat 1


title: Serum_Ni_3mo_rep2


title: MIN6, 5% oxygen, biol_rep_1


title: Serum_Ni_3mo_rep1


title: iKD AP2XII-1 +IAA 0h, biological repeat 3

value: add IAA 0h


title: btl>Ras attP-p35-L7_rep1


title: btl>Ras-p35-L3_rep3


title: Serum_Co_3mo_rep2

value: Co


title: Y184 bcy1∆ YPD Rep A

description:
A-1-3-1_S7_L001_R1_001
200102_BHJCGYDRXX-HTSeq-counts.txt

value: Y184 bcy1::KanMX

value: YP 2% glucose, anaerobic

value: early/mid-log phase

value: yeast cell


title: MIN6, 20% oxygen, biol_rep_2

value: 20percent_oxygen (6h)


title: Serum_W_3mo_rep4

value: Male

value: W


title: MIN6, 20% oxygen, biol_rep_3


title: btl>Ras-p35-L3_rep2

value: tracheal


title: MIN6, 20% oxygen, biol_rep_1


title: Serum_W_3mo_rep3

value: Sprague-Dawley


title: Serum_W_3mo_rep2


title: btl>Ras-p35-L3_rep1


title: Act5C-GS>Ras attP-GFP-LB-Clone6_rep3

value: Act5C-GS>Ras attP-GFP-LB-Clone6

value: neuronal-like


title: Mouse islets, 5% oxygen, biol_rep_3

source_name: Primary islets cells

value: Primary islets cells

value: Pancreatic endocrine cells

value: 5percent_oxygen (24h)


title: Mouse islets, 5% oxygen, biol_rep_2

value: WT


title: Serum_Ta_3mo_rep4

value: Ta


title: Serum_W_3mo_rep1


title: Mouse islets, 5% oxygen, biol_rep_1


title: Serum_Ta_3mo_rep3


title: iKD AP2XII-1 +IAA 0h, biological repeat 2

value: merozoites

value: add IAA 0h


title: Mouse islets, 20% oxygen, biol_rep_2

value: 20percent_oxygen (24h)


title: iKD AP2XII-1 +IAA 0h, biological repeat 1


title: Serum_Ta_3mo_rep2