title: fatbody of cricket, group A-1, 1st injection = PBS, 2nd injection = live Bt, rep1

city: Chuncheon-si

first: Saeyoull

last: Cho

address: 1, Kangwondaehak-gil

institute: Kangwon Univ.

description:
2PBSP3
s2PBSP3_rep1

data_processing:
Raw sequencing data was preprocessed using integrated software for adapter and quality trimming, Trim Galore v0.6.5.
Reads with a Phred33 score of less than 20 and a length of less than 20 base pairs were filtered out, and the standard Illumina adapter sequence was trimmed if found.
De novo full-length transcriptome reconstruction was performed by a software to reconstruct full-length transcriptome without a reference genome, Trinity v2.15.1, and ORF (open reading frame) prediction was performed by software to identified candidate coding region from de novo transcriptome assembly, TransDecoder v5.5.0 (25).
Predicted ORFs were assessed using homology search (BLAST), protein domain identification (PFAM), gene ontology assignment, and functional classification (e.g., eggnog) of sequence data using software to annotate de novo transcriptome assembly, Trinotata v4.0.2 (26).
Quantification of gene expression was performed using software to quantify expression of genes and transcripts from transcriptomic data, Salmon v1.10.2 (27).
Assembly: assembled_sequence.fasta
Supplementary files format and content: Normalized count matrix

organism: Gryllus bimaculatus

source_name: fatbody

growth_protocol: We collected 150 crickets from basement of a building or under rocks or log debris in mountain, mated them, and collected eggs. Female laid an average of 90±10 eggs, and hatched young were reared in a sterilized incubator (MIR-553, Sanyo Electric Biomedical, Japan; 25 ± 1 ℃, 40±10%, 16h light:8h dark) maintain a constant environment. We used second- and third-generation adults as experiment insects. We provided sterilized food (Chinese cabbage and wheat husk purchased from Milwormnara Ltd., Korea) and always maintained cleanliness. Healthy crickets consistently exhibit activity through antennae movement, while sick or weak crickets demonstrate diminished antennae mobility and a notable decline in overall activity levels. Therefore, when such crickets are found in a breeding cage, we immediately remove them.

extract_protocol:
To perform RNA sequencing, we extracted fatbodies from group A, B, A-1, and B-1. We selected 10 crickets from each group and prepared them in one tube for each group. Since each group was repeated 3 times, fatbodies were extracted from a total of 30 crickets and prepared in 3 tubes per group (12 tubes in total). Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, USA) (all operations were performed using sterile spaces and tolls to minimize contamination). To briefly summarize the procedures, 100mg of fat bodies were mixed with 1ml of TRIzol reagent (Thermo Fisher Scientific, Waltham, USA). Plastic beads of 0.6 mm, 2 mm, and 7 mm were added to the mixture, and it was homogenized for 10 minutes with a vortex (DAIHAN Ltd., Korea). The sample were centrifuged at 14,000 rpm for 3 min at 4℃ and 1mL of supernatant was extracted. The extracted supernatant was mixed with 200 µL chloroform and reacted at 4℃ for 20 min (Thermo Fisher Scientific, Waltham, USA). The sample were centrifuged at 14,000 rpm for 3 min at 4℃ for 15min and then the supernatant (~600 µL) was loaded into a gDNA elimination column to remove gDNA (Thermo Fisher Scientific, Waltham, USA). The sample was centrifuged at 14,000 rpm for 1 min at 4℃ and then total RNA was precipitated by adding 600 µL of cold isopropanol/70% ethanol (maintained at -20℃, Sigma-Aldrich, USA). The sample was centrifuged at 14,000 rpm for 1min at 4℃ using RNeasy Plus Mini column, mixed with ~700 µL of RW1 buffer (10mM Tris-Hcl, 1mM EDTA, 50mM NaCl, 0.5% Tween-20, pH 8.5, Sigma-Aldrich, USA), and centrifuged at 14,000rpm for 1min. Finally, the sample was mixed with 500 RPE buffer (10mM Tris-Hcl, 80% ethanol, 0.5mM EDTA pH 7.5), centrifuged, and total RNA was extracted by placing ~50 µL RNeasy-free water in a new sterilized tube (Sigma-Aldrich, USA).
The cDNA library was generated from the total RNA, and paired-end sequencing was performed using the Illumina RNA-seq technology (Macrogen Ltd, Korea).

treatment_protocol: All crickets were selected 24 hours after molting from young to adult. Additionally, we removed inactive or unhealthy individuals (less than ~2%) after the first injection and used only healthy individuals that were very active and feeding for the injection of live Bt. In all groups, the crickets were almost identical in age (24 hours after adult molting), health (active movement and no infection), average size (~25±5 mm per cricket), and average weight (~1.1±0.5g per cricket). Immune priming was performed by diluting the OD 1.3 obtained from the LD50 value at a ratio of 1:999, and 2μl was inoculated (2ⅹ103 cfu/insect for Bt and 2.08ⅹ103 cfu/insect for E. coli). The reason for this is similar to preventive vaccination, where we aimed to ensure that there was no impact on survival due to the preventive inoculation. Therefore, we obtained values over the entire observation period of 96 hours where there was no difference between the control group and the survival group. Next, 48 hours after the immune cycle of crickets, all individuals were injected with 10μl of live pathogen at the concentration described in material and method section 2.3. Subsequently, survival analysis and microscopic examinations were conducted at different time intervals. For injection, the crickets were sterilized with 70% alcohol paper, and a finely pulled glass needle was shallowly inserted into the abdomen (Haematocrit capillaries, Sigma-Aldrich) (17, 18). The experiments were repeated three times independently.

value: fatbody


title: Liver_LKO_NASH_5 [A67L]

status: Public on Jun 05 2024

type: SRA

city: Urbana

first: Ye

last: Tian

state: IL

address: 2001 South Lincoln Avenue, room 3612

department: Comparative Biosciences

country: USA

institute: University of Illinois ar Urbana-Champaign

library_source: transcriptomic

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina)
The Fastq files were then mapped to the GRCm39 mouse genome from GENCODE using STAR2.7.10b
The count matrix were generated using Rsubread and the differentially expressed genes were analyzed using DESeq2
Assembly: GRCm39
Supplementary files format and content: tab-delimited txt file (read count table)

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA were extracted from frozen liver samples using TRIzol following manufacturer's instruction. Ribosomal RNA was removed with the FastSelect HMR kit (Qiagen).
The RNAseq libraries were prepared with the Kapa Hyper Stranded mRNAseq Sample Prep kit' (Roche). The libraries were pooled; quantitated by qPCR and sequenced on one SP lane for 101 cycles from one end of the fragments on a NovaSeq 6000.

tag: tissue

value: Liver

tag: strain

tag: Sex

value: male

tag: genotype

value: Lpcat3f/f Albumin-Cre (LKO)

tag: treatment


title: Liver_LKO_NASH_4 [A67R]


title: PMCRC18_N_RNA-seq

city: Daejeon

first: sungghwan

last: park

address: Gwahak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Reference genome sequence data from Homo sapiens were obtained from the NCBI Genome database (assembly ID: GRCh38). The reference genome indexing and read mapping of tissue samples were performed using STAR software (ver. 2.5.4b).
Then, the read counts per million fragments mapped (CPM) of each sample were estimated and were log2-transformed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text format with log2 transformed CPM values of transcripts.

organism: Homo sapiens

source_name: Primary colorectal tumor

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed  by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation  reactions into a single step that greatly increases the efficiency of the library preparation process.  Adapter-ligated fragments are then PCR amplified and gel purified.

tag: subject

value: Primary colorectal tumor

tag: histologic type


title: END-seq, Ctrl, Rep2

city: Bologna

first: Giovanni

last: Capranico

state: BO

address: Via Selmi 3

department: FABIT

country: Italy

institute: University of Bologna

library_source: genomic

data_processing:
library strategy: END-seq
Adaptor sequences of paired-end reads in fastq format were trimmed, using Trim Galore.
Reads were aligned to the GRCh37 (hg19) reference human genome and to GRCm38 (mm10) reference mouse genome, using Bowtie2, default settings. Only properly-paired reads with MAPQ ≥ 30 were kept, including duplicated reads, using Samtools .
Prior peak calling, aligned paired-end reads in BAM format were splitted according to first-in pair orientation, so to potentially discriminate reads aligned on the left side (F2R1- reverse- minus strand) and on the right side (F1R2- forward-plus strand) respect with the DSB.
Peak calling was performed using MACS2 and using control samples as “input”.
Peak calling was performed separately for each replicate and according to first-in-pair reads orientation, using the parameters --nomodel --nolambda -q 0.05 --keep-dup all -f BAMPE as previously described in .
Assembly: hg19
Supplementary files format and content: .bw file contain the normalized genomic level of END-seq signal
Supplementary files format and content: .narrowPeak file contain the output of MACS peak caller in BED format

molecule: genomic DNA

growth_protocol: HCT116 cells were cultured in a humidified incubator at 5% of CO2 and 37°C in McCoy’s 5A medium supplemented with 10% heat-inactivated fetal bovine serum (FBS). Spike in pre-B murine cells: DMEM complemented with 10% FBS, 2mM L-Glutamine, 100 mg/ml Pen/Strep, 1mM Sodium Pyruvate, 1X NEAA, and 55 mM b-mercaptoethanol

extract_protocol:
Cells were embedded in agarose plugs and, after proteinase K and RNase A digestion, DSBs are recovered by ligation of a biotinylated adapter. DNA is then extracted from plug and sheared by sonication. Sheared fragments containing the biotinylated adapter are captured with streptavidin-coated beads. A second adapter is ligated to the other end of the fragments and library amplified with Illumina barcoded p5 and p7.
End-Seq libraries were prepared incorporating Illumina barcoded p5 and p7 with KAPA HiFi HotStart Ready Mix by PCR. All the recovered DNA fragments were used for amplification. Libraries were amplified using 16 cycles on the thermocycler.

treatment_protocol: Cells are treated for 10 or 20 minutes with Camptothecin 10 micromolar

tag: cell line

tag: cell type

value: Human epithelial colorectal carcinoma

value: Ctrl


title: fatbody of cricket, group A-1,1st injection = PBS, 2nd injection = live Bt, rep3

description:
2PBSP3-3
s2PBSP3_rep3


title: Liver_LKO_NASH_3 [A67N]


title: DGM-00413_Tr

type: RNA

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: Trachea

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: S


title: PMCRC17_PT_RNA-seq


title: DGM-00278_Tr


title: DGM-00194 [gene_expr]

source_name: small airway epithelium from healthy nonsmokers or healthy smokers

tag: ethnicity

value: Eur

tag: department of genetic medicine id


title: END-seq, Ctrl, Rep1


title: small airways, LOD-259

source_name: airway epithelial cells obtained by bronchoscopy and brushing

tag: age

tag: sex

value: M

tag: ethnic group

value: black

value: smoker, 53 pack-years


title: qhFB cells, WGBS, DACPano, BR2

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

data_processing:
Raw sequencing reads are trimmed using TrimGalore (v.0.6.1) with "-a AGATCGGAAGAGC".
Bismark (v.0.22.0) was used to prepare bisulfite-converted hg38 reference genome and to align trimmed reads to the prepared genome (-X 2000 --nucleotide_coverage).
Uniquely mapped, deduplicated reads were retained.
hg38
bed (methylC)

molecule: polyA RNA

source_name: skin

extract_protocol:
We extracted genomic DNA with Quick-DNA Miniprep Kit (Zymo, D3024)
We bisulfite converted 200-400 ng of DNA spiked with 0.5% lambda DNA using EZ DNA Methylation-Direct kit (Zymo, D5020). For WGBS, we processed the bisulfite- converted DNA with Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, 30024).

value: skin

value: HDFa

value: primary dermal fibroblast

value: 1uM DAC 6 days, 100nM Pano 2 days


title: Liver_LKO_NASH_2 [A54L]


title: small airways, LOD-246

value: smoker, 11 pack-years


title: small airways, LOD-244

value: smoker, 19.5 pack-years


title: fatbody of cricket, group A-1,1st injection = PBS, 2nd injection = live Bt, rep2

description:
2PBSP3-2
s2PBSP3_rep2

value: fatbody


title: Ru_Ribo-RTP_2

city: chengdu

first: Yixin

last: Wang

state: sichuan

address: 211 huimin street

department: Institute of Animal Genetics and Breeding, College of Animal Science and Technology

country: China

institute: Sichuan Agricultural University

description: Generated from present study

data_processing:
Five raw RNA-seq data downloaded from GEO (GSE116775) were aggregated into the Ribo group before data processing. Trimmomatic (0.39) was used to remove the adapter sequence and low-quality reads (Q < 20).
The clean reads were aligned to the bovine reference genome (Bos taurus ARS-UCD1.2) using STAR (2.7.9a) with the detection of chimeric (fusion) alignments (--chimSegmentMin 10)
The aligned reads were used for circRNAs identification through CIRCexplorer2 (https://circexplorer2.readthedocs.io/en/latest/)4 with annotating pipeline.
The high-confident circRNAs (BSJ reads ≥ 2, detected in at least all replicates of one method) were maintained to explore the intersection among six methods using TBtools (https://github.com/CJ-Chen/TBtools/releases)
The high confident circRNAs of liver and rumen were integrated, then converted into the human genome position (GRCh38.p13) using UCSC LiftOver with the chain file (bosTau9ToHg38.over.chain.gz)
The genome position of human circRNAs was downloaded from circAtlas database and used to search for overlap regions with cattle circRNAs on human genome position using bedtools (2.30.0)
Assembly: Bos taurus ARS-UCD1.2
Supplementary files format and content: Excel sheet include circRNA information and BSJ read count of each individual sample

organism: Bos taurus

source_name: Rumen

growth_protocol: The three cross-bred (Kinsella Composite) beef steers are managed based on the guidelines established by the Canadian Council on Animal Care (https://ccac.ca/en/standards/guidelines/)

extract_protocol:
Total RNA was extracted using the mirVanaTM miRNA isolation Kit (Ambion, Carlsbad, CA, USA) according to the manufacturer's instructions.
The purified circRNAs were used to build the sequencing libraries following the guidance of TruSeq® Stranded Total RNA cDNA library construction kit

treatment_protocol: The total RNA of each sample was subjected to circRNA enrichment using the following six methods, respectively: The ribosome RNA (rRNA) of total RNA was removed through Ribo-zero (defined as Ribo); the linear RNA of total RNA was removed through RNase R (defined as R); both linear RNA and some lariat RNA were removed through RNase R following polyadenylation and poly (A)+ RNA depletion (defined as RTP); both rRNA and linear RNA were removed through Ribo-zero and following with RNase R (defined as Ribo-R); rRNA, linear RNA and RNA with poly (A) structure were removed through Ribo-zero and following with RNase and poly (A)+ RNA depletion (defined as Ribo-RP); rRNA, linear RNA and lariat RNA were removed through Ribo-zero and following RNase R then polyadenylation and poly (A)+ RNA depletion (defined as Ribo-RTP)

tag: breed

value: Kinsella Composite beef

value: steer

tag: sampling age

value: 15 months old

value: Rumen

value: Ribosomal RNA, linear RNAs and RNAs with structured 3′ ends elimination (Ribo-RTP)


title: small airways, COPD 054

value: white

value: COPDex, GOLD-II, 90 pack-years


title: small airways, LOD-253

value: M

value: smoker, 27 pack-years


title: PMCRC16_PT_RNA-seq

tag: tissue

value: Primary colorectal tumor


title: PMCRC15_PT_RNA-seq


title: Ru_Ribo-RP_3

description: Generated from present study

value: Ribosomal RNA, linear RNAs and RNAs with poly (A) tailing elimination (Ribo-RP)


title: fatbody of cricket, group B-1, 1st injection = heat-killed Bt, 2nd injection = live Bt, rep3

description:
2BTV2-3
s2BTV2_rep3


title: PMCRC13_PT_RNA-seq


title: Ru_Ribo-RP_1

description: Generated from present study


title: Liver_CON_NASH_5 [A55RLL]

value: Liver

tag: strain

value: male

value: Lpcat3f/f (con)


title: PMCRC14_PT_RNA-seq


title: Liver_CON_NASH_4 [A55B]

tag: Sex


title: Liver_CON_NASH_3 [A55L]

tag: genotype


title: fatbody of cricket, group A, 1st injection = PBS, rep1

description:
1PBS
s1PBS-rep1

tag: treatment

value: 1st injection = PBS


title: fatbody of cricket, group B-1,1st injection = heat-killed Bt, 2nd injection = live Bt, rep1

description:
2BTV2
s2BTV2_rep1


title: Liver_LKO_NASH_1 [A54R]

value: Lpcat3f/f Albumin-Cre (LKO)


title: fatbody of cricket, group B-1, 1st injection = heat-killed Bt, 2nd injection = live Bt, rep2

description:
2BTV2-2
s2BTV2_rep2

value: fatbody


title: PMCRC12_PT_RNA-seq

tag: subject


title: Ru_Ribo-R_3

description: Generated from present study

value: Kinsella Composite beef

value: Ribosomal RNAs coupled with linear RNAs (Ribo-R) elimination


title: fatbody of cricket, group A, 1st injection = PBS, rep3

description:
1PBS-3
s1PBS-rep3


title: Liver_CON_NASH_2 [A55R]


title: PMCRC11_PT_RNA-seq

tag: histologic type


title: Ru_Ribo-RP_2

description: Generated from present study

value: steer

value: 15 months old


title: Liver_CON_NASH_1 [A54N]


title: fatbody of cricket, group A, 1st injection = PBS, rep2

description:
1PBS-2
s1PBS-rep2


title: Ru_Ribo-R_1

description: Generated from present study

value: Rumen


title: CKO ILC3, cLPs, infection 4

city: Hangzhou

first: Heping

last: Xu

state: Zhejiang

address: 18 Shilongshan Road

institute: Westlake University

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
LI.CKO4

data_processing:
For bulk RNA-seq: raw fastq files were trimmed with cutadapt v2.10. Alignment to mm10 genome/transcriptome and quantification of gene expression were done using STAR v2.7.5c and RSEM v1.3.3.
For scRNA-seq: 10x Genomics Cellranger v6.1.1 was used to process fastq files and generate the bam file and matrix files. Downstream normalization, filtering and clustering were done using Seurat v4.1.0.
Assembly: mm10
Supplementary files format and content: RSEM extracted TPM matrix filtered by expressed protein-coding genes as one csv file
Supplementary files format and content: Cellranger output expression matrix files and feature barcode setting file packaged in tar.gz

source_name: colon

growth_protocol: All mice were housed in specific-pathogen-free conditions at 22-24℃ with humidity of 40%–70% and a light/dark cycle of 12 hours, and were used and maintained in accordance with the Institutional Animal Care and Use Committee Guidelines of Westlake University

extract_protocol:
RNA were extracted from cells using AMPure XP beads (Backman)
Full-length Smart-seq2 and 10x genomics scRNA-seq

treatment_protocol: For bulk RNA-seq exepriments, a total of 1.5×105 CFU Candida albicans (strain SC5314) or vehicle (PBS) were i.v. injected into the mice. For the scRNA-seq experiment, the mice were at the steady state.

value: colon

value: 8 weeks

value: CCR6+ ILC3s

value: Rorc-cre+Fcer1g f/f (CKO)

value: Candida albicans


title: PMCRC10_PT_RNA-seq

value: Primary colorectal tumor


title: Ru_Ribo-R_2

description: Generated from present study


title: fatbody of cricket, group B, 1st injection = heat-killed Bt, rep1

description:
1BT4
s1BT4_rep1

value: 1st injection = heat-killed Bt


title: CKO ILC3, cLPs, infection 3

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
LI.CKO3

value: male


title: fatbody of cricket, group B, 1st injection = heat-killed Bt, rep3

description:
1BT4-3
s1BT4_rep3


title: Ru_RTP_2

description: Generated from present study

value: Linear RNAs and RNAs with structured 4′ ends degradation (RTP)


title: PMCRC9_PT_RNA-seq


title: CKO ILC3, cLPs, infection 2

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
LI.CKO2


title: Ru_RTP_1

description: Generated from present study

value: Linear RNAs and RNAs with structured 3′ ends degradation (RTP)


title: CKO ILC3, cLPs, infection 1

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
LI.CKO1


title: PMCRC6_MT_RNA-seq

source_name: metastasized tumor into peritoneal

value: metastasized tumor into peritoneal


title: wt Biaux+IAA 3

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

country: Spain

institute: Centro de Biotecnología y Genómica de Plantas

data_processing:
Basecalls performed using CASAVA version 1.4
Clean (FastQC software (Babraham-Bioinformatics, 2014).  Reads are mapped to a reference sequences using HISAT2 with 8 mismatches allowed.
Reads count to a reference  genome  (TAIR 42.gff3) using the htseq-count tool.
Differential expression analysis was calculated with edgeR with the following parameters: pVal<0.05, fold change >1.5 fold  or   < -1.5 fold
Assembly: Asembly was done with Hisat2 using Arabidopsis genome (TAIR42.gff3)
Supplementary files format and content: Difefrential expression analyses were done using edgeR

organism: Arabidopsis thaliana

source_name: root

extract_protocol:
Total  RNA was isolated from Arabidopsis plants using the Trizol reagent and RNeasy columns (Qiagen). Quantity and quality measurements were taken using a NanoDrop spectrophotometer and Bioanalyzer.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 or other sequencer when necessary

treatment_protocol: RNAseq analyses of polyA mRNAs isolated from roots of wild type seedlings grown at 22ºC in half strength MS medium for 4 days and then treated with 5 µM BiAux or 10 nM IAA or 5 µM BiAux plus 10 nM IAA for 3 extra days.

value: root

tag: cell line

value: wild type

value: grown 4 days and trasnfer to fresh medium with 5 uM BiAux+10 nM IAA_3 days_replicate_14


title: WT ILC3, cLPs, infection 3

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
LI.INF3

tag: cell type

value: Fcer1g f/f (control)


title: fatbody of cricket, group B, 1st injection = heat-killed Bt, rep2

description:
1BT4-2
s1BT4_rep2

value: fatbody


title: PMCRC6_PT_RNA-seq


title: Ru_R_1

description: Generated from present study

value: Kinsella Composite beef

value: steer

value: 15 months old

value: Rumen

value: Linear RNAs degradation (R)


title: Ru_RTP_3

description: Generated from present study

value: Linear RNAs and RNAs with structured 5′ ends degradation (RTP)


title: wt IAA 2

value: grown 4 days and trasnfer to fresh medium with 5 uM BiAux+10 nM IAA_3 days_replicate_6


title: WT ILC3, cLPs, infection 1

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
LI.INF1

value: colon

value: 8 weeks

value: CCR6+ ILC3s

value: Candida albicans


title: Li_Ribo-RTP_3

description: Generated from present study

value: Liver

value: Ribosomal RNA, linear RNAs and RNAs with structured 4′ ends elimination (Ribo-RTP)


title: PMCRC5_MT_RNA-seq

value: metastasized tumor into peritoneal


title: wt IAA 3

value: root

value: wild type

value: grown 4 days and trasnfer to fresh medium with 5 uM BiAux+10 nM IAA_3 days_replicate_8


title: CKO ILC3, siLPs, infection 4

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
SI.CKO4

source_name: small intestine

value: small intestine

value: male

value: Rorc-cre+Fcer1g f/f (CKO)


title: PMCRC5_PT_RNA-seq

value: Primary colorectal tumor


title: Li_Ribo-RTP_1

description: Generated from present study

value: Kinsella Composite beef

value: steer

value: 15 months old

value: Ribosomal RNA, linear RNAs and RNAs with structured 3′ ends elimination (Ribo-RTP)


title: PMCRC8_PT_RNA-seq


title: PMCRC7_PT_RNA-seq


title: Li_Ribo-RP_3

description: Generated from present study

value: Ribosomal RNA, linear RNAs and RNAs with poly (A) tailing elimination (Ribo-RP)


title: naive WT - biol rep 1

city: Bonn

first: Sven

last: Wehner

address: Venusberg-Campus 1

department: Department of Surgery

country: Germany

institute: University Clinics Bonn

data_processing:
Data was analyzed with Partek Flow software and the publicly available Lexogen pipeline (Lexogen12112017)
Partek Flow Software:
Trim adapters - CUTADAPT_1_12 - Version 10.0.21.1116 - Both ends trimmed -Adapter sequences:  AAAAAAAAAAAA,TTTTTTTTTTTT
Pre-alignment QA/QC - Version 10.0.21.1116 - K-mer length 10
Trim adapters - CUTADAPT_1_12 - Version 10.0.21.1116 - 3'-end trimmed -Min overlap length 5 - Min read length 25
Pre-alignment QA/QC - Version 10.0.21.1116 - K-mer length 10
Trim bases - Version 10.0.21.1116 - Trim on quality score Phred 10 - 3'-end timmed - Min read length 20
Pre-alignment QA/QC - Version 10.0.21.1116
Alignment STAR - 2.5.3a - Version 10.0.21.1116
Post-alignment QA/QC - Version 10.0.21.1116
Quantify to annotation model (Partek E/M) - Version 10.0.21.1116
Gene counts were normalized
Gene Set Analysis was performed from normalized reads comparing AOM/DSS treated vs. naive
Gene list was filtered for significance (p<= 0.05)
Assembly: mm10 Ensembl Transcripts release 102
Supplementary files format and content: Excel with differentially expressed genes between naive and AOM/DSS treated samples with p<0.05

source_name: colon tissue

extract_protocol:
RNA was extracted using Rneasy Mini Kit (Qiagen)
RNA libraries for RNA-seq were prepared using QuantSeq 3'-mRNA Library Prep Kit (Lexogen) following the manufacturer's instructions

treatment_protocol: Mice either underwent the AOM/DSS model or kept under naive conditions for the corresponding time span. For AOM/DSS treatment, mice were injected with an intraperitoneal injection of AOM at 10 mg/kg bodyweight on day 0. On day 7, mice received 1.5% dextran-sodium sulfate (DSS) in drinking water for 5 days, followed by 16 days of recovery. Mice underwent 3 DSS cycles in total in the same manner. After the last DSS cycle + recovery phase, mice were sacrificed on day 70.

value: colon tissue

value: female

value: wildtype

value: naive


title: CKO ILC3, siLPs, infection 2

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
SI.CKO2

value: 8 weeks

value: CCR6+ ILC3s

value: Candida albicans


title: CKO ILC3, siLPs, infection 3

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
SI.CKO3


title: wt Biaux+IAA 2

value: root

value: wild type

value: grown 4 days and trasnfer to fresh medium with 5 uM BiAux+10 nM IAA_3 days_replicate_12


title: PMCRC4_MT_RNA-seq

value: metastasized tumor into peritoneal


title: CKO ILC3, siLPs, infection 1

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
SI.CKO1

value: small intestine

value: male

value: Rorc-cre+Fcer1g f/f (CKO)


title: WT ILC3, cLPs, infection 2

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
LI.INF2

value: colon

value: Fcer1g f/f (control)


title: wt IAA 1

value: grown 4 days and trasnfer to fresh medium with 5 uM BiAux+10 nM IAA_3 days_replicate_4


title: wt  Biaux 2

value: grown 4 days and trasnfer to fresh medium with 10 nM IAA_3 days_replicate_3


title: PMCRC4_PT_RNA-seq

value: Primary colorectal tumor


title: Li_Ribo-RP_2

description: Generated from present study

value: Kinsella Composite beef

value: steer

value: 15 months old

value: Liver

value: Ribosomal RNA, linear RNAs and RNAs with poly (A) tailing elimination (Ribo-RP)


title: Ru_R_2

description: Generated from present study

value: Rumen

value: Linear RNAs degradation (R)


title: Ru_R_3

description: Generated from present study


title: wt  Biaux 3

value: root

value: wild type

value: grown 4 days and trasnfer to fresh medium with 5 uM BiAux+10 nM IAA_3 days_replicate_2


title: wt Biaux+IAA 1

value: grown 4 days and trasnfer to fresh medium with 5 uM BiAux+10 nM IAA_3 days_replicate_10


title: WT ILC3, siLPs, infection 3

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
SI.INF3

value: small intestine

value: 8 weeks

value: male

value: CCR6+ ILC3s

value: Candida albicans


title: wt  Biaux 1

value: grown 4 days and trasnfer to fresh medium with 10 nM IAA_3 days_replicate_1


title: PMCRC6_N_RNA-seq

source_name: Normal colorectal mucosae

value: Normal colorectal mucosae


title: PMCRC5_N_RNA-seq


title: PMCRC4_N_RNA-seq


title: Li_Ribo-R_3

description: Generated from present study

value: Kinsella Composite beef

value: steer

value: Ribosomal RNAs coupled with linear RNAs (Ribo-R) elimination


title: wt mock 3

value: grown 4 days and trasnfer to fresh medium with 5 uM BiAux_3 days_replicate_2


title: PMCRC3_MT_RNA-seq

value: metastasized tumor into peritoneal


title: Li_Ribo-RP_1

description: Generated from present study

value: 15 months old

value: Liver

value: Ribosomal RNA, linear RNAs and RNAs with poly (A) tailing elimination (Ribo-RP)


title: WT ILC3, siLPs, infection 1

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
SI.INF1

value: Fcer1g f/f (control)


title: wt mock 2

value: root

value: wild type

value: grown 4 days and trasnfer to fresh medium 3 days_replica_3


title: Li_Ribo-R_1

description: Generated from present study


title: wt mock 1

value: grown 4 days and trasnfer to fresh medium _3 days_replicate_1


title: PMCRC3_PT_RNA-seq

value: Primary colorectal tumor


title: Li_RTP_3

description: Generated from present study

value: Linear RNAs and RNAs with structured 5′ ends degradation (RTP)


title: WT ILC3, siLPs, PBS 3

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
SI.PBS3

value: small intestine

value: 8 weeks

value: male

value: CCR6+ ILC3s

value: PBS


title: PMCRC2_MT_RNA-seq


title: Li_RTP_1

description: Generated from present study

value: Kinsella Composite beef

value: steer

value: Linear RNAs and RNAs with structured 3′ ends degradation (RTP)


title: Li_RTP_2

description: Generated from present study

value: 15 months old

value: Liver

value: Linear RNAs and RNAs with structured 4′ ends degradation (RTP)


title: PMCRC2_PT_RNA-seq


title: PMCRC2_N_RNA-seq

value: Normal colorectal mucosae


title: Arrest-T3-B

city: Stanford

first: Michael

middle: Charles

last: Lanz

state: CA

address: 327 Campus Dr.

department: Biology

institute: Stanford University

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality. The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GCF_000146045.2_R64_genomic

organism: Saccharomyces cerevisiae

extract_protocol: RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer's instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3   ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer's instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.


title: WT ILC3, siLPs, infection 2

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
SI.INF2

value: Fcer1g f/f (control)

value: Candida albicans


title: Arrest-T2-B


title: Arrest-T3-A


title: Li_R_3

description: Generated from present study

value: Linear RNAs degradation (R)


title: PMCRC1_MT_RNA-seq

value: metastasized tumor into peritoneal


title: Arrest-T2-A


title: WT ILC3, siLPs, PBS 4

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
SI.PBS4


title: PMCRC3_N_RNA-seq


title: Li_R_2

description: Generated from present study


title: HCT-116 colorectal adenocarcinoma cell line, single array

type: genomic

city: Catania

first: Daniele

middle: F

last: Condorelli

state: Italy

address: Via S. Sofia 64

department: Biomedical and Biotechnological Sciences

institute: University of Catania

hyb_protocol: Biotin-labeled fragments were hybridized to a Genechip Affymetrix SNP 6.0 arrays at 50°C for 16-18 hours in a GeneChip® Hybridization Oven 640 (Affymetrix, Inc.). Washing and staining with streptavidin-phycoerthrin was performed in a GeneChip® Fluidics Station 450 (Affymetrix, Inc.).

scan_protocol: Arrays were scanned with a GeneChip® Scanner 3000 7G (Affymetrix, Inc.) and raw data processing was performed using the  “GeneChip Operating Software”.

data_processing:
Data processing was performed by the software "Genotyping Console v3.0.1 ". The following algorithms were used: 1) SNP 6.0 Birdseed v2 algorithm for genotyping, 2) BRLMM-P-Plus algorithm and Hidden Markov Model with regional GC correction for copy number analysis, 3) the LOH algorithm.
Intensity Data files (.cel) and Copy Number Data files (.cnchp)  are provided.

source_name: confluent cell cultures

label_protocol: Amplification and labeling were performed according to the protocol supplied by the Affymetrix for  SNP 6.0 arrays. 500 ng of gDNA was digested with NspI and StyI restriction enzymes, ligated to respectively NspI and StyI adaptors, amplified by PCR using a single primer. PCR products were purified and the amplicons were quantified using a NanoDrop spectrophotometer. 40-70 µg of purified amplicons were fragmented and biotin end-labeled.

growth_protocol: CACO-2 and HT-29 cell lines were maintained in Dulbecco’s Modified Eagle Medium (DMEM 1X; GIBCO, Cat. No. 31965-023 containing 4.5 g/L of D-glucose) supplemented with 10-20% fetal bovine serum (Cat. No. 10270-106; Life Technologies) and 1% penicillin-streptomycin (100 unit/ml penicillin and 100 μg/ml streptomycin) (Cat. No. 15140-122; Life Technologies). HCT-116 cell line was maintained in  McCoy's 5a Medium Modified supplemented with 10% fetal bovine serum and 1% of penicillin-streptomycin. The cell cultures were grown in flasks (25 cm2) and incubated at 37 °C in humidified atmosphere with 5% of CO2 and 95% of air.

extract_protocol: Genomic DNA (gDNA) was extracted from Caco-2, HCT-116 and HT-29 colorectal adenocarcinoma cell linse using the QIAamp DNA Mini Kit (COD.51304 QIAGEN Milan, Italy)  according to the manufacturer’s instructions. The concentration and the quality of the DNA were determined using  NanoDrop spectrophotometer.

value: colorectal adenocarcinoma cell line


title: HT-29 colorectal adenocarcinoma cell line, single array

value: female


title: Caco-2 colorectal adenocarcinoma cell line, single array


title: Arrest-T1-A


title: WT ILC3, siLPs, PBS 2

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
SI.PBS2

value: small intestine

value: 8 weeks


title: PMCRC1_PT_RNA-seq

value: Primary colorectal tumor


title: Li_R_1

description: Generated from present study


title: PMCRC1_N_RNA-seq


title: ZYN

status: Public on Jun 04 2024

city: Jinan

first: Yanfeng

last: Liu

address: 107 west wenhua xi road

institute: shandong university

description:
ExVivoBlood
Gene expression after peripheral blood plasma isolation

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Healthy voulenteer peripheral blood 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Peripheral blood from healthy volunteers and DLBCL patients were drawn, and  then isolated the peripheral blood plasma by centrifuge, 1800g, 10 min. The supernant was collected and then centrifuged at 4 °C ,12000rpm for 15 min. The supernant was collected for the gene expression analysis.

value: Peripheral blood plasma

tag: gender


title: ZTH

source_name: DLBCL patient peripheral blood 2


title: ZCL

source_name: Healthy voulenteer peripheral blood 3


title: ZXL

source_name: DLBCL patient peripheral blood 3


title: MLB

source_name: DLBCL patient peripheral blood 1

value: male


title: FFPE archived fetal lung tissue GW18; Visium

city: Toronto

first: Amy

last: Wong

state: Ontario

address: 686 Bay Street, Toronto

department: Developmental & Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

data_processing:
Raw sequencing reads were processed via spaceranger pipeline to generate FASTQ files
Sequences were aligned to GRCh38 using spaceranger
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of genes
Supplementary files format and content: matrix.tsv.gz: gene expression counts
Supplementary files format and content: aligned_fiducials.jpg: aligend fiducials of image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Fetal lung tissue

extract_protocol:
Archived FFPE fetal lung tissues were freshly sectioned (5µm).
Spatial transcriptomic library was done via manufacturer's intruction (10X Genomics FFPE Visium v2 slides and reagent kits)

value: Fetal lung tissue


title: LY

source_name: Healthy voulenteer peripheral blood 1


title: FFPE archived fetal lung tissue GW15; Visium


title: Melanoma murin, 3pRNA, dabrafenib+trametinib, 24h, rep1

first: Thais

middle: Marina

last: Schlee-Guimarães

department: Institute of Clinical Chemistry and Clinical Pharmacology

institute: University Hospital, University of Bonn

data_processing:
Next, sequencing reads were aligned to the human reference genome using STAR (Dobin et al., 2013).
Quantifying  with HTSeq (G Putri, S Anders, PT Pyl, JE Pimanda, F Zanini Analysing high-throughput sequencing data in Python with HTSeq 2.0 ).
Assembly: GRCm39
Supplementary files format and content: counts csv files

growth_protocol: Kept at 37°C 5% CO2, YUMM1.7 cell line was cultured in DMEM/F-12, GlutaMAX™  supplemented with  with 10 % (v/v) fetal calf serum (FCS) and 100 units penicillin and 100µg streptomycin per mL Media (p/s). and non-essential amino acids

extract_protocol:
Qiagen, RNeasy Mini Kit, accodring to manufacturers recomandation
mRNA was purified by poly-A enrichment using NEBNext® Poly(A) mRNA Magnetic Isolation Module. For library preparation NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads with NEBNext® Multiplex Oligos for Illumina® were used.

treatment_protocol: For RIG-I stimulation a chemically synthesized dsRNA with a 3p end was used. CA21 control RNA (5’-CACACACACACACACACACAC-3’) was used als transfection control. For transfection RNA was complexed to Lipofectamine 2000 (Invitrogen) according to the manufactures protocol. Dabrafenib and Trametinib were dissolved in Dimethylsulfoxid (DMSO) and added at indicated concentrations. DMSO at highest used concentration served as vehicle control.

value: melanoma

value: BRAF mut

value: dabrafenib 1000 nM + trametinib 100 nM


title: Melanoma murin, transfection control, dabrafenib+trametinib, 24h, rep1

value: transfection control


title: Melanoma murin, no stimulation, dabrafenib+trametinib, 24h, rep1

value: no stimulation


title: Melanoma murin, 3pRNA, vehicle, 24h, rep1

value: vehicle


title: Arrest-T1-B


title: Melanoma murin, transfection control, vehicle, 24h, rep1


title: Melanoma murin, 3pRNA, trametinib, 24h, rep1

value: trametinib 100 nM


title: Melanoma murin, transfection control, trametinib, 24h, rep1


title: Melanoma murin, 3pRNA, dabrafenib, 24h, rep1

value: dabrafenib 1000 nM


title: Melanoma murin, transfection control, dabrafenib, 24h, rep1


title: Melanoma murin, no stimulation, trametinib, 24h, rep1


title: Melanoma murin, 3pRNA, no inhibitor, 24h, rep1

value: no inhibitor


title: Melanoma murin, transfection control, no inhibitor, 24h, rep1


title: Melanoma murin, no stimulation, no inhibitor, 24h, rep1


title: Bleo-35-days 2

city: Boston

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

institute: BU Single Cell Sequencing Core

library_source: transcriptomic single cell

data_processing:
BaseCalls performed using Illumina
Demultiplexing performed using Cell Ranger v6.1.2 with default settings
Reads aligned to mm10-2020-A reference genome using Cell Ranger v6.1.2 with --expect-cells=8000
Assembly: mm10 version 2020-A
Supplementary files format and content: Tab separated and matrix files

source_name: Lung

extract_protocol:
Lung tissues from uninjured sham (n=3), as well as from those harvested at 14 days (n=2) and 35 days (n=2) after bleomycin challenge, were collected and the lung tissues dissociated into a single-cell suspension. Briefly, mice were anesthetized with FATAL-PLUS solution (Vortech pharmaceuticals, Dearborn, MI, USA). After opening the thoracic cavity of mice, the lungs were perfused with 10 mL of sterile cold PBS through the right ventricle of the heart. The exposed trachea was cannulated with a 20G catheter and injected with 2 mL of digestion solution (PBS containing 80 U/mL collagenase type II (Worthington Biochemical, Lakewood, NJ, USA) and 2 U/mL Dispase II (Sigma-Aldrich)), which was followed by clogging with forceps for 2 min. The lung lobes were dissected from the trachea, finely minced, and incubated with 20 mL digestion solution for 1 h in a 37 °C incubator with shaking followed by passaging through an 18G needle 4–5 times and an additional 15 min incubation at 37 °C. After passing through a 21G needle, the cell suspension was filtered through 70 and 40 μm mesh cell strainers and centrifuged at 400× g for 5 min to collect the isolated cells. Red blood cells were lysed using lysis buffer (Sigma-Aldrich). Hematopoietic (CD45+ve) cells were depleted using magnetic cell separation (MACS). Cells were then centrifuged (500×g, 10 min, 4 °C) and resuspended in 0.2 ml of 1X PBS buffer containing 0.04% BSA.  Cell suspensions were submitted to the Single-Cell Sequencing Core (Boston University) for processing.
scRNA-seq libraries were generated in BU DOM Single Cell sequencing core facility and sequenced by BU Microarray and Sequencing Resource Core Facility according to 10x Genomics protocol

value: Lung

value: CD45-ve whole lung cells

value: 2 months old

value: Bleomycin


title: Bleo-14-days 2


title: Bleo-14-days 1


title: Sham 2

value: Sham


title: Sham 1


title: Sham 3


title: Aged-Bleo 1

data_processing:
BaseCalls performed using Illumina
Demultiplexing performed using Cell Ranger v6.0.1 with default settings
Reads aligned to mm10 v2.1.0 reference genome using Cell Ranger v6.0.1 with --expect-cells=10000
Assembly: mm10 v2.1.0
Supplementary files format and content: Tab separated and matrix files

extract_protocol:
Thirty days pos-bleomycin treatment, mice were anesthetized with ketamine/xylazine solution and perfused via the left ventricle with cold PBS. The lungs were immediately harvested and minced with a razor blade in a 100 mm petri dish in a cold DMEM medium containing 0.2 mg/ml Liberase DL and 100 U/ml DNase I (Roche, Indianapolis, IN, USA). The mixture was transferred into 15 ml tubes and incubated at 37 °C for 35 min in an incubator under continuous rotation to allow enzymatic digestion. Digestion was inactivated with a DMEM medium containing 10% fetal bovine serum, the cell suspension was passed through a 40 µm cell strainer (Fisher, Waltham, MA, USA) to remove debris. Cells were then centrifuged (500×g, 10 min, 4 °C), and suspended in 3 ml red blood cell lysis buffer (Biolegend, San Diego, CA, USA) for 90 s to remove the remaining red blood cells and diluted in 9 mL PBS after incubation. Cells were then centrifuged (500×g, 10 min, 4 °C) and resuspended in 0.2 ml of 1X PBS buffer containing 0.04% BSA.  Cell suspensions were submitted to the Single-Cell Sequencing Core (Boston University) for processing.
scRNA-seq libraries were generated in BU DOM Single Cell sequencing core facility and sequenced by BU Microarray and Sequencing Resource Core Facility according to 10x Genomics protocol

value: Whole cells

value: Wild type

value: 18 months old


title: Aged-Sham 2


title: Aged-Bleo 2


title: Young-Bleo 1


title: Young-Sham 1


title: mRNAseq_KPN_Eto_r3

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

description:
edgeR_KPN_Eto_vs_KPN.tabular
edgeR_normcounts_allreplicates.tabular

data_processing:
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For mRNA-seq, reads were mapped to mm10 withSTAR
Assembly: mm10

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol: RNA was used for library preparation with  NEBNext Poly(A) mRNA Magnetic Isolation Module and  NEBNext Ultra II Directional RNA Library Prep kit. The libraries were amplified with 12-16 PCR cycles depending on the input RNA. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq500 Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform

treatment_protocol: Treatment as indicated

value: KPN

value: Lung cancer cell line

value: KRasG12D, Trp53-/-; NONO knockout

value: 2hr Eto (20µM) with 2hr chase


title: mRNAseq_KPN_Eto_r2


title: mRNAseq_KPN_r3


title: mRNAseq_KPN_r2


title: mRNAseq_KP_Eto_r3

description:
edgeR_KP_Eto_vs_KP.tabular
edgeR_normcounts_allreplicates.tabular

value: KP

value: KRasG12D, Trp53-/-


title: mRNAseq_KP_Eto_r2


title: mRNAseq_KPN_r1


title: mRNAseq_KP_r3


title: mRNAseq_KP_r1


title: Bleo-35-days 1


title: S5 CTD RNAPII Cut&Run_KPN+Eto

data_processing:
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For Cut&Run-seq, reads were mapped to mm10 withBowtie2, then normalized based on read depth.
Assembly: mm10
Library strategy: Cut&Run

extract_protocol: Cut&Run DNA was used for library preparation with NEBNext Ultra II Directional DNA Library Prep kit. The libraries were amplified with 12-16 PCR cycles depending on the input DNA. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq500 Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform

tag: antibody

value: S5 CTD RNAPII


title: mRNAseq_KPN_Eto_r1


title: Melanoma murin, no stimulation, dabrafenib, 24h, rep1

value: melanoma

value: BRAF mut

value: no stimulation

value: dabrafenib 1000 nM


title: Aged-Sham 1

value: Lung


title: S5 CTD RNAPII Cut&Run_KP+Eto


title: S5 CTD RNAPII Cut&Run_KPN


title: IgG_control_all

value: Pooled cells from all conditions

value: IgG


title: mRNAseq_KP_r2


title: Bottom_1

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

data_processing:
Sequencing was performed on an Illumina NextSeq 2000 platform with the paired-end mode.
Illumina RTA version 3.10.30 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by cutadapt v4.1. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.10a with the GENCODE (release 36, GRCh38.p13) gtf file.
The uniquely and properly mapped reads were used for further analysis. Raw read counts were calculated using htseq-count v2.0.2 with the GENCODE gtf file. Gene expression levels were determined as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: Matrix table with TPM for every gene and every sample

source_name: small intesine

growth_protocol: Human iPS cells were seeded on Matrigel Growth Factor Reduced Basement Membrane (Cat# 354230; Corning)-coated cell culture plates and cultured with StemFit AK02N medium containing 10 μM Y-27632 for 1 day. Cells were treated with 100 ng/mL Activin A (Cat# 338-AC; R&D Systems) in RPMI1640 medium (Cat# R8758-500; Sigma-Aldrich) supplemented with 1× B-27 Supplement Minus Vitamin A (Cat# 12587001; Thermo Fisher Scientific), 1× GlutaMAX (Cat# 35050-079; Thermo Fisher Scientific), and 1× penicillin−streptomycin for 3 days. Next, cells were dissociated and resuspended at 5 × 106 cells/mL in the intestinal differentiation medium (Advanced DMEM/F12 (Cat# 12634028; Thermo Fisher Scientific) supplemented with 2% FBS, 1× GlutaMAX, and 1× penicillin−streptomycin) containing 100 ng/mL fibroblast growth factor 2 (FGF2) (Cat# 160-0010-3; Katayama Chemical Industries) and 10 μM Y-27632. Then, a cell suspension (10 µL) was injected into the Matrigel-coated top channel of the PDMS device. After 1 h, the intestinal differentiation medium, containing 100 ng/mL FGF2 and 10 μM Y-27632, was added to the top channel of the PDMS device. During days 5–8, cells were maintained with an intestinal differentiation medium containing 100 ng/mL FGF2. From day 8 to 13, cells were maintained with a 3:1 mixture of the intestinal differentiation medium and Wnt family member 3A (WNT3A), RSPO3, and noggin (NOG)-conditioned medium supplemented with 50 ng/mL epidermal growth factor (EGF) (Cat# AF-100-15; PeproTech) and 20 ng/mL insulin-like growth factor 1 (IGF1) (Cat# AF-100-11; PeproTech). WNT3A, RSPO3, and NOG-conditioned medium was prepared using L-WRN cells (Cat# CRL-3276; American Type Culture Collection (ATCC)). During days 13–24, cells were maintained with 1:1 mixture of the intestinal differentiation medium and Hepatocyte Culture Media BulletKit (Cat# CC-3198; LONZA) supplemented with 10 ng/mL EGF, 15 µM forskolin (Cat# 063-02193; FUJIFILM Wako Pure Chemical), 10 µM PD98059 (Cat# S1177; Selleck), 2.5 µM 5-aza-2'-deoxycytidine (Cat# 018-20941; FUJIFILM Wako Pure Chemical), 0.25 µM A-83-01 (Cat# 035-24113; FUJIFILM Wako Pure Chemical), 2.5 µM (2ʹZ,3ʹE)-6-Bromoindirubin-3ʹ-oxime (BIO) (Cat# 361550; Sigma-Aldrich), and 5 µM (3,5-Difluorophenylacetyl)-Ala-Phg-OBut (DAPT) (Cat# 3219-v; PEPTIDE INSTITUTE). Medium flow was maintained using a peristaltic pump (Programmable motor controller, Cat# RE-C200/C201 and Ring Pump, Cat# RP-TXP5F-P03A-DC3VS, Aqua Tech) at a flow rate of 30 µL/h during days 5 to 24.

extract_protocol:
Total RNA was isolated from micro-small intestine systems using ISOGENE (NIPPON GENE).
The library preparation was performed using a TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: HCoV-229E (0.1 MOI) containing medium was injected into the top or bottom channel of micro-small intestine systems.

value: small intesine

value: human iPS cells

value: micro-small intestine system

value: wild type

value: HCoV-229E infected basolaterally


title: Bottom_3


title: S5 CTD RNAPII Cut&Run_KP

value: Lung cancer cell line


title: Top_1

value: HCoV-229E infected apically


title: Top_2


title: Mock_3

value: mock


title: Mock_2


title: Mock_1


title: mRNAseq_KP_Eto_r1

value: KP

value: KRasG12D, Trp53-/-

value: 2hr Eto (20µM) with 2hr chase


title: pool of embryo, high concentration of P4, rep3

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

data_processing:
Preprocessing of the raw sequencing data was conducted using Trimmomatic. First, the Illumina adapters were removed. The quality threshold of 30 was set and base calls with a score below the threshold were removed from the end or/and start of a read. Trimming was performed with the minimal length set at 32 nt and reads were retained for further processing. Pseudoalignment was carried out using Kallisto and quantification of all transcripts described in release 105 of ENSEMBL cDNA gene annotation was estimated.
Pairwise comparisons in EdgeR was used to identify differential expression of genes between treatment groups. Normalized data were sorted for significance and filtered as per the Transcript Support Level (TSL) used by the Ensembl gene annotation system. Briefly, mRNA and EST alignments were compared to the GENCODE transcripts and transcripts were scored according to how well the alignment matches over its full length. This approach was used to highlight the well supported and poorly supported transcript models. Selected differentially expressed genes were assigned to the evaluated annotation tsl1 and all splice junctions of the transcript were supported by at least one non-suspect mRNA. Due to multiple comparisons, adjusted P-values of differential expression between treatment groups were calculated using the Benjamini-Hochberg correction which controlled for a False Discovery Rate (FDR) of 5%
Assembly: release 105 of ENSEMBL cDNA gene annotation Bos taurus ARS-UCD1.2
Supplementary files format and content: comma-delimited csv file containing ensemble gene id, gene symbol, and raw counts for each sample
Supplementary files format and content: comma-delimited csv file containing ensemble gene id, gene symbol, and normalized count (tpm) for each sample

source_name: pool of embryo

extract_protocol:
Embryo total RNA was extracted from each biological replicate using the PicoPure RNA isolation kit (Thermo Fisher Scientific) with DNAse treatment (Qiagen) as per the manufacturer’s protocol. RNA was eluted in 15 µL of nuclease-free water and kept at -80°C for subsequent library preparation. RNA concentration and integrity were evaluated using an Agilent 4200 TapeStation (Agilent Technologies) with the High Sensitivity RNA ScreenTape Assay (Agilent Technologies). RNA Integrity Number (RIN) ranged from 5.0 to 8.3 RIN with an average of 6.2 ± 1.4 RIN and RNA concentration ranged from 308 to 556 pg/µL with an average of 414 ± 113.6 pg/µL.
Library preparation was performed for each biological replicate. Enrichment of mRNA was conducted using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, New England Biolabs, USA) and libraries were prepared using the NEBNext Ultra II RNA Library kit for Illumina (E7770, E7775, New England Biolabs, USA). The library preparation protocol was followed as recommended by the manufacturer’s guidelines for 10 ng – 1μg of DNA-free total RNA, with 15 cycles for the PCR enrichment of adaptor-ligated DNA and Illumina index primers (Illumina). Purified libraries were eluted in 23 μL of (0.1X) TE buffer and stored at -20°C for future analysis. The quality of the 6 libraries were verified using Agilent bioanalyzer (4200 TapeStation, Agilent Technologies) with the High Sensitivity D1000 ScreenTape Assay (Agilent Technologies) before libraries were pooled in equimolar proportion and sequenced with NovaSeq 6000 using paired-end 100bp protocol.

value: pool of embryo

value: high concentration of P4


title: pool of embryo, high concentration of P4, rep2


title: pool of embryo, high concentration of P4, rep1


title: pool of embryo, low concentration of P4, rep3

value: low concentration of P4


title: pool of embryo, low concentration of P4, rep2


title: pool of embryo, low concentration of P4, rep1


title: Melanoma murin, no stimulation, vehicle, 24h, rep1

value: melanoma

value: BRAF mut

value: no stimulation

value: vehicle


title: Bottom_2

value: small intesine

value: human iPS cells


title: Top_3

value: micro-small intestine system

value: wild type


title: Sample_35_NTBlood_E3APP_E3NTKO

first: Neta

last: Rosenzweig

state: Massachusetts

address: 60 Fenwood Road, 10002K, Brigham and Women’s Hospital

institute: Brigham and Women's Hospital, Harvard Medical School

description: 10X Genomics

data_processing:
Samples were processed according to Smart-Seq2 protocol and sequenced on Illumina sequencers.
Reads in FASTQ were quantified at the transcript level using Salmon (v1.4) against the M. musculus Ensembl gene catalog (May 2020).
Differential expression analysis was conducted using R (v4.1.2) and DESeq2 (v1.34.0). Hypothesis testing was performed by using either DESeq2’s Wald test on appropriate variable contrasts or with a Likelihood Ratio Test (LRT) for models with greater than two variable conditions being tested.
Assembly: mm10
Supplementary files format and content: plain textquantification file (quant.sf)

source_name: Blood

extract_protocol:
Mice were euthanized in a CO2 chamber and transcardially perfused with ice-cold Hanks’ Balanced Salt Solution (HBSS, Thermo Fisher, 14175103). Spleens were mashed with the plunger of a syringe and treated with 1ml of ACK for 10min buffer to remove erythrocytes. Splenic cells were washed, pelleted and stained with the following rat antibodies: BV421 anti-CD45 (1:100, Biolegend, 103133), PE-Cy7 anti-mouse CD11b (1:300, eBioscience, 50-154-54), PerCP/Cy5.5 anti-mouse Ly-6C (1:300, Biolegend, 128012), Alexa Fluor 488 anti-CD115 (1:100, Biolegend, 135512) and Alexa Fluor 700 anti-Ly6g (1:100, Biolegend, 127621) in PBS with 2% FBS. After washing, CD115–CD11b+Ly6cintLy6g+ and CD115–CD11b+Ly6cintLy6g+/Tdt neutrophils were sorted using BD FACSAriaTM II (BD Bioscience). For analysis of Foxp3 and intracellular staining, splenic neutrophils were treated with an eBioscience FoxP3-staining buffer set (cat. no. 00-5523-00) according to manufacturer protocol and stained with PE/Cy7 anti-Foxp3 (1:50, Thermo, 25-5773-82), PE anti-IL-17F (1:50, Biolegend, 517007), APC anti-LAP (TGFb1; 1:50, Biolegend, 141405). FACS data were collected by BD FACS Diva Software. The analysis was done using FlowJoTM 10. For the isolation of brain microglia and neutrophils, brains were extracted removed from the skull and homogenized to form a single cell suspension, then resuspended and centrifuged in a 30% Percoll Plus (GE Healthcare, 17-5445-02) gradient in HBSS at 800 g, 25°C, for 25 min with an acceleration of 4 and a deceleration of 3. Cells were pelleted and stained with rat APC anti-mouse Fcrls (1:400, clone 4G11, Butovsky Lab)51 and all antibodies listed above. After washing, CD115–CD11b+Ly6cintLy6g+ neutrophils and Ly6c–CD11b+Fcrls+ microglia were sorted using BD FACSAriaTM II (BD Bioscience).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Blood

value: Neutrophil

value: APOE3 APP/PS1

value: APOE3 NTKO

value: Female


title: Sample_34_NTBlood_E3APP_E3

description: 10X Genomics


title: Sample_33_NTBlood_E3APP_E3

description: 10X Genomics


title: Sample_38_NTBlood_E3APP_E3NTKO

description: 10X Genomics


title: Sample_32_NTBlood_E3APP_E3

description: 10X Genomics


title: Sample_37_NTBlood_E3APP_E3NTKO

description: 10X Genomics


title: Sample_39_NTBlood_E3APP_E3NTKO

description: 10X Genomics


title: Sample_31_NTBlood_E4APP_E4NTKO

description: 10X Genomics

value: APOE4 APP/PS1

value: APOE4 NTKO


title: Sample_29_NTBlood_E4APP_E4NTKO

description: 10X Genomics


title: Sample_30_NTBlood_E4APP_E4NTKO

description: 10X Genomics


title: Sample_28_NTBlood_E4APP_E4NTKO

description: 10X Genomics


title: Sample_27_NTBlood_E4APP_E4

description: 10X Genomics


title: Sample_25_NTBlood_E4APP_E4

description: 10X Genomics


title: Sample_23_MGNonPhag_Raggc_antiIL17

description: 10X Genomics

source_name: Brain

value: Brain

value: Non-phagocytic microglia

value: Raggc


title: Sample_21_MGNonPhag_Raggc_antiIL17

description: 10X Genomics


title: Sample_22_MGNonPhag_Raggc_antiIL17

description: 10X Genomics


title: Sample_18_MGPhag_Raggc_antiIL17

description: 10X Genomics

value: Phagocytic microglia


title: Sample_17_MGPhag_Raggc_antiIL17

description: 10X Genomics


title: Sample_24_NTBlood_E4APP_E4

description: 10X Genomics


title: Sample_36_NTBlood_E3APP_E3NTKO

description: 10X Genomics


title: Sample_16_MGPhag_Raggc_antiIL17

description: 10X Genomics


title: Sample_26_NTBlood_E4APP_E4

description: 10X Genomics


title: Sample_20_MGNonPhag_Raggc_IgG

description: 10X Genomics

value: IgG


title: Sample_19_MGNonPhag_Raggc_IgG

description: 10X Genomics


title: Sample_15_MGPhag_Raggc_antiIL17

description: 10X Genomics


title: Sample_14_MGPhag_Raggc_IgG

description: 10X Genomics


title: Sample_13_MGPhag_Raggc_IgG

description: 10X Genomics


title: Sample_12_MGPhag_Raggc_IgG

description: 10X Genomics


title: Sample_9_NT_E45FAD_IgG

description: 10X Genomics

source_name: Spleen

value: Spleen

value: APOE4 5FAD


title: Sample_10_NT_E45FAD_IgG

description: 10X Genomics


title: Sample_11_MGPhag_Raggc_IgG

description: 10X Genomics


title: Sample_8_NT_E45FAD_IgG

description: 10X Genomics


title: Sample_7_NT_E45FAD_IgG

description: 10X Genomics


title: Sample_5_NT_E45FAD_IL17

description: 10X Genomics


title: Sample_6_NT_E45FAD_IgG

description: 10X Genomics


title: Sample_3_NT_E45FAD_IL17

description: 10X Genomics


title: Sample_4_NT_E45FAD_IL17

description: 10X Genomics


title: Sample_2_NT_E45FAD_IL17

description: 10X Genomics


title: WT ILC3, siLPs, PBS 1

description:
SMART-seq2
RNAseq_SS2.ILC3_gut.filt_tpm.csv
SI.PBS1

source_name: small intestine

value: small intestine

value: 8 weeks

value: male

value: CCR6+ ILC3s

value: Fcer1g f/f (control)

value: PBS


title: Sample_12_Neutrophils_APOE4_Brain

data_processing:
Count files (fastq) were preprocessed for quality control and adapter trimming using fastp. High quality reads were aligned using Salmon (v1.7).
Technical outliers were removed for further analysis. Downstream differential gene expression analysis was carried out using DESeq2 (v.1.34.00). Biological outliers were determined using PCA and heatmap visualization and removed for final analysis.
Comparisons were run using LRT, and the cutoff for significant genes was either P < 0.01 or P < 0.05.
Assembly: mm10
Supplementary files format and content: zip file of salmon outputs including plain text quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters.

extract_protocol:
Spleens or brain were mashed with the plunger of a syringe and treated with 1ml of ACK for 10min buffer to remove erythrocytes. Splenic cells were washed, pelleted and stained with the following rat antibodies: BV421 anti-CD45 (1:100, Biolegend, 103133), PE-Cy7 anti-mouse CD11b (1:300, eBioscience, 50-154-54), PerCP/Cy5.5 anti-mouse Ly-6C (1:300, Biolegend, 128012), Alexa Fluor 488 anti-CD115 (1:100, Biolegend, 135512) and Alexa Fluor 700 anti-Ly6g (1:100, Biolegend, 127621) in PBS with 2% FBS. After washing, CD115-CD11b+Ly6cintLy6g+ and CD115-CD11b+Ly6cintLy6g+/Tdt neutrophils were sorted using BD FACSAriaTM II (BD Bioscience).
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform. cDNA libraries were generated from sorted cells using the Smart-seq2 protocol. RNA sequencing was performed using Illumina NextSeq500 using a High Output v2 kit to generate 2× 25 bp reads.

value: Neutrophils

value: F


title: Sample_1_NT_E45FAD_IL17

description: 10X Genomics

value: Neutrophil

value: Female


title: Sample_11_Neutrophils_APOE4_Brain

value: Brain


title: Sample_8_Neutrophils_APOE3_Brain


title: Sample_6_Neutrophils_APOE3_Spleen


title: Sample_9_Neutrophils_APOE3_Brain


title: Sample_10_Neutrophils_APOE4_Brain


title: Sample_5_Neutrophils_APOE3_Spleen


title: Sample_7_Neutrophils_APOE3_Spleen


title: Sample_4_Neutrophils_APOE4_Spleen


title: Sample_3_Neutrophils_APOE4_Spleen


title: Sample_1_Neutrophils_APOE4_Spleen


title: Sample_2_Neutrophils_APOE4_Spleen


title: Sample_17_Neutrophils_APOE3_WT

source_name: Neutrophils

extract_protocol:
Spleens were mashed with the plunger of a syringe and treated with 1ml of ACK for 10min buffer to remove erythrocytes. Splenic cells were washed, pelleted and stained with the following rat antibodies: BV421 anti-CD45 (1:100, Biolegend, 103133), PE-Cy7 anti-mouse CD11b (1:300, eBioscience, 50-154-54), PerCP/Cy5.5 anti-mouse Ly-6C (1:300, Biolegend, 128012), Alexa Fluor 488 anti-CD115 (1:100, Biolegend, 135512) and Alexa Fluor 700 anti-Ly6g (1:100, Biolegend, 127621) in PBS with 2% FBS. After washing, CD115-CD11b+Ly6cintLy6g+ and CD115-CD11b+Ly6cintLy6g+/Tdt neutrophils were sorted using BD FACSAriaTM II (BD Bioscience).
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform. cDNA libraries were generated from sorted cells using the Smart-seq2 protocol. RNA sequencing was performed using Illumina NextSeq500 using a High Output v2 kit to generate 2× 25 bp reads.

value: WT


title: Sample_16_Neutrophils_APOE3_WT


title: Sample_18_Neutrophils_APOE3_WT


title: Sample_14_Neutrophils_APOE4_WT


title: Sample_15_Neutrophils_APOE3_WT


title: Sample_11_Neutrophils_APOE4_WT


title: Sample_13_Neutrophils_APOE4_WT


title: Sample_12_Neutrophils_APOE4_WT


title: Sample_13_Neutrophils_APOE4_Brain


title: Sample_10_Neutrophils_APOE4_HOM

value: HOM


title: Sample_6_Neutrophils_APOE4_Het

value: Het


title: Sample_8_Neutrophils_APOE4_HOM


title: Sample_5_Neutrophils_APOE4_Het


title: Sample_4_Neutrophils_APOE3_Het


title: Sample_3_Neutrophils_APOE3_Het


title: Sample_1_Neutrophils_APOE3_Het


title: Sample_2_Neutrophils_APOE3_Het


title: Sample_16_Microglia_APOE3_WT

source_name: Microglia

extract_protocol:
For the isolation of brain microglia, brains were extracted removed from the skull and homogenized to form a single cell suspension, then resuspended and centrifuged in a 30% Percoll Plus (GE Healthcare, 17-5445-02) gradient in HBSS at 800 g, 25°C, for 25 min with an acceleration of 4 and a deceleration of 3. Cells were pelleted and stained with rat APC anti-mouse Fcrls (1:400, clone 4G11, Butovsky Lab). After washing, Ly6c-CD11b+Fcrls+ microglia were sorted using BD FACSAriaTM II (BD Bioscience).
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform. cDNA libraries were generated from sorted cells using the Smart-seq2 protocol. RNA sequencing was performed using Illumina NextSeq500 using a High Output v2 kit to generate 2× 25 bp reads.

value: Microglia


title: Sample_14_Microglia_APOE3_WT


title: Sample_15_Microglia_APOE3_WT


title: Sample_13_Microglia_APOE3_WT


title: Sample_10_Microglia_APOE4_WT


title: Sample_11_Microglia_APOE4_WT


title: Sample_12_Microglia_APOE4_WT


title: Sample_8_Microglia_APOE4_Het


title: Sample_9_Microglia_APOE4_WT


title: Li_Ribo-R_2

description: Generated from present study

data_processing:
Five raw RNA-seq data downloaded from GEO (GSE116775) were aggregated into the Ribo group before data processing. Trimmomatic (0.39) was used to remove the adapter sequence and low-quality reads (Q < 20).
The clean reads were aligned to the bovine reference genome (Bos taurus ARS-UCD1.2) using STAR (2.7.9a) with the detection of chimeric (fusion) alignments (--chimSegmentMin 10)
The aligned reads were used for circRNAs identification through CIRCexplorer2 (https://circexplorer2.readthedocs.io/en/latest/)4 with annotating pipeline.
The high-confident circRNAs (BSJ reads ≥ 2, detected in at least all replicates of one method) were maintained to explore the intersection among six methods using TBtools (https://github.com/CJ-Chen/TBtools/releases)
The high confident circRNAs of liver and rumen were integrated, then converted into the human genome position (GRCh38.p13) using UCSC LiftOver with the chain file (bosTau9ToHg38.over.chain.gz)
The genome position of human circRNAs was downloaded from circAtlas database and used to search for overlap regions with cattle circRNAs on human genome position using bedtools (2.30.0)
Assembly: Bos taurus ARS-UCD1.2
Supplementary files format and content: Excel sheet include circRNA information and BSJ read count of each individual sample

source_name: Liver

extract_protocol:
Total RNA was extracted using the mirVanaTM miRNA isolation Kit (Ambion, Carlsbad, CA, USA) according to the manufacturer's instructions.
The purified circRNAs were used to build the sequencing libraries following the guidance of TruSeq® Stranded Total RNA cDNA library construction kit

value: Kinsella Composite beef

value: steer

value: 15 months old

value: Liver

value: Ribosomal RNAs coupled with linear RNAs (Ribo-R) elimination


title: Sample_6_Microglia_APOE4_Het


title: Sample_9_Neutrophils_APOE4_HOM


title: Sample_5_Microglia_APOE4_Het


title: Sample_4_Microglia_APOE3_Het


title: Sample_7_Neutrophils_APOE4_Het


title: Sample_2_Microglia_APOE3_Het


title: Sample_3_Microglia_APOE3_Het


title: Sample_11_Microglia_CX3_IL17

extract_protocol:
For the isolation of brain microglia, brains were extracted removed from the skull and homogenized to form a single cell suspension, then resuspended and centrifuged in a 30% Percoll Plus (GE Healthcare, 17-5445-02) gradient in HBSS at 800 g, 25°C, for 25 min with an acceleration of 4 and a deceleration of 3. Cells were pelleted and stained with rat APC anti-mouse Fcrls (1:400, clone 4G11, Butovsky Lab) and all antibodies listed above. After washing, Ly6c-CD11b+Fcrls+ microglia were sorted using BD FACSAriaTM II (BD Bioscience).
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform. cDNA libraries were generated from sorted cells using the Smart-seq2 protocol. RNA sequencing was performed using Illumina NextSeq500 using a High Output v2 kit to generate 2× 25 bp reads.

value: M

tag: disease

value: AD


title: Sample_9_Microglia_CX3_IL17


title: Sample_8_Microglia_WT


title: Sample_1_Microglia_APOE3_Het


title: Sample_7_Microglia_WT


title: Sample_10_Microglia_CX3_IL17


title: Sample_12_Microglia_CX3_IL17


title: Sample_4_Microglia_WT


title: Sample_5_Microglia_WT


title: Sample_3_Microglia_WT


title: Sample_2_Microglia_WT


title: MP, CONTROL, M0011764-9

first: Maria

last: Gutierrez-Arcelus

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
Read alignment was performed using STAR (v2.4.2) with the following parameters: -- twopassMode Basic, -- alignIntronMax 1000000, --alignMatesGapMax 1000000, --sjdbScore 2, --quantMode TranscriptomeSAM, --sjdbOverhang 24. RSEM (v1.2.21) was then used for gene quantification with paired-end mode. We used the hg38 reference genome and GENCODE annotation version 24 (Ensembl 83).
Assembly: hg38
Supplementary files format and content: counts.txt.gz is a tab-delimeted file with expected gene counts as calculated by RSEM.
Supplementary files format and content: log2tpm.txt.gz is a tab-delimeted file with the TPM values as calculated by RSEM that were then scaled to log2(tpm+1).
Supplementary files format and content: metadata.txt.gz is a tab-delimeted file with metadata for each sample.

source_name: MP

growth_protocol: Peripheral blood mononuclear cell (PBMC) samples from patients who had been infected with Mtb and either progressed to active TB disease (cases) or remained TB-disease free until sampling (controls) were separated using standard Ficoll density gradient centrifugation from 50mL of venous blood and cryopreserved at 5e6 cells/vial. PBMC samples were thawed, and CD14-expressing monocytes were magnetically sorted using the Miltenyi pan monocyte isolation kit, humans (Miltenyi) following the manufacturer’s instructions in magnetic-associated cell sorting (MACS) buffer: 0.5% bovine serum albumin, 2mM ethylene-diamine-tetra-acetic acid (EDTA) in 1X phosphate-buffered saline (PBS). To generate either monocyte-derived dendritic cells (DC) or macrophages (MP), monocytes were washed and resuspended in supplemented complete RPMI (5% fetal calf serum, 1mM 2-mercaptoethanol, penicillin-streptomycin, L-Glutamine, HEPES buffer, both essential and non-essential amino acids, and sodium hydroxide). The media was either supplemented with 300 Units/mL of granulocyte-macrophage colony stimulating factor (GM-CSF) and 200 Units/mL of interleukin (IL)-4 to generate monocyte-derived dendritic cells (DCs), or 20ng/mL of macrophage colony stimulating factor (M-CSF) to generate monocyte-derived macrophages (MPs). For both cell types, monocytes were differentiated in 6-well tissue culture plates for 6 days, then split between analytical flow cytometry to test viability and differentiation, and cell sorting to generate pure populations for RNA extraction.

extract_protocol:
Cells were lysed with TCL buffer (Qiagen).
RNA-seq library preparation was performed at the Broad Technology Labs (Broad Institute) using a modified Smart-seq protocol for low-input RNA-sequencing, which improves detection of full-length transcripts using template switching and pre-amplification. There were 3 plates of 96 samples each including blank samples. Samples from cases and controls and the two cell-types were randomized across all three plates. Sequencing was performed in an Illumina NextSeq500 as paired-end 2 x 25 bp reads with an additional 8 cycles for each index.

value: MP

tag: tb status

value: CONTROL

tag: age


title: MP, CASE, M0009777-5

value: CASE

value: F


title: Sample_1_Microglia_WT


title: DC, CONTROL, M0006312-4

source_name: DC

value: DC


title: MP, CASE, M0023555-7


title: DC, CONTROL, M0019935-7


title: MP, CONTROL, M0021784-5


title: MP, CONTROL, M0007827-0


title: MP, CONTROL, M0012538-6


title: MP, CONTROL, M0006605-1


title: MP, CONTROL, M0019819-3


title: DC, CASE, M0016843-6


title: DC, CONTROL, M0012019-7


title: DC, CASE, M0018532-3


title: DC, CONTROL, M0015057-4


title: MP, CONTROL, M0006516-0


title: MP, CASE, M0024123-3


title: Sample_6_Microglia_WT

value: Brain


title: DC, CASE, M0020583-2


title: DC, CONTROL, M0007684-5


title: DC, CASE, M0017420-2


title: DC, CONTROL, M0011972-8


title: DC, CONTROL, M0019109-9


title: DC, CASE, M0018551-3


title: MP, CASE, M0019692-4


title: DC, CONTROL, M0020072-6


title: MP, CASE, M0023986-4


title: DC, CONTROL, M0011764-9


title: DC, CONTROL, M0010687-3


title: DC, CONTROL, M0021134-3


title: MP, CONTROL, M0013569-0


title: MP, CASE, M0015236-4


title: MP, CASE, M0007178-8


title: MP, CONTROL, M0015057-4


title: DC, CONTROL, M0010548-7


title: MP, CASE, M0023521-9


title: DC, CASE, M0023521-9


title: DC, CASE, M0024123-3


title: DC, CASE, M0017483-0


title: MP, CASE, M0017461-6


title: DC, CASE, M0012604-6


title: MP, CONTROL, M0012428-0


title: DC, CONTROL, M0019819-3


title: MP, CONTROL, M0011766-4


title: DC, CONTROL, M0008325-4


title: DC, CONTROL, M0022130-0


title: MP, CASE, M0011302-8


title: MP, CONTROL, M0021538-5


title: MP, CASE, M0012411-6


title: DC, CONTROL, M0011248-3


title: DC, CONTROL, M0008353-6


title: MP, CONTROL, M0015573-0


title: DC, CONTROL, M0017902-9


title: DC, CASE, M0008889-9


title: DC, CONTROL, M0022574-9


title: MP, CASE, M0015693-6


title: MP, CASE, M0012987-5


title: DC, CASE, M0011302-8


title: MP, CONTROL, M0019109-9


title: MP, CASE, M0019119-8


title: DC, CASE, M0020202-9


title: DC, CONTROL, M0006516-0


title: DC, CASE, M0021395-0


title: DC, CASE, M0024532-5


title: MP, CASE, M0014149-0


title: MP, CONTROL, M0017830-2


title: DC, CASE, M0015693-6


title: DC, CASE, M0008255-3


title: DC, CASE, M0017461-6


title: DC, CASE, M0015236-4


title: DC, CASE, M0010399-5


title: MP, CONTROL, M0009548-0


title: DC, CASE, M0012131-0


title: DC, CASE, M0012411-6


title: DC, CONTROL, M0008363-5


title: DC, CONTROL, M0019745-0


title: MP, CONTROL, M0022574-9


title: MP, CONTROL, M0013979-1


title: MP, CONTROL, M0021291-1


title: DC, CASE, M0014277-9


title: MP, CASE, M0022752-1


title: MP, CONTROL, M0009034-1


title: MP, CONTROL, M0010548-7


title: MP, CONTROL, M0007683-7


title: MP, CASE, M0022651-5


title: DC, CASE, M0007178-8


title: DC, CONTROL, M0015573-0


title: MP, CASE, M0020154-2


title: MP, CASE, M0025678-5


title: MP, CASE, M0012131-0


title: MP, CONTROL, M0017902-9


title: MP, CONTROL, M0019935-7


title: DC, CASE, M0014546-7


title: DC, CONTROL, M0010508-1


title: DC, CONTROL, M0009885-6


title: DC, CASE, M0023986-4


title: DC, CONTROL, M0021291-1


title: DC, CONTROL, M0008905-3


title: DC, CONTROL, M0006618-4


title: DC, CONTROL, M0019827-6


title: MP, CASE, M0014220-9


title: DC, CASE, M0008723-0


title: DC, CONTROL, M0012428-0


title: DC, CONTROL, M0013418-0


title: DC, CONTROL, M0011702-9


title: DC, CONTROL, M0015874-2


title: MP, CASE, M0018455-7


title: DC, CASE, M0022651-5


title: DC, CONTROL, M0022318-1


title: DC, CASE, M0023555-7


title: DC, CASE, M0014883-4


title: DC, CONTROL, M0022013-8


title: DC, CASE, M0023266-1


title: MP, CASE, M0020583-2


title: MP, CASE, M0013154-1


title: MP, CONTROL, M0007684-5


title: MP, CASE, M0016197-7


title: DC, CASE, M0013713-4


title: MYB2_R_3

city: Qingdao

first: feng

last: zhang

state: Shandong

address: 72 Binhai Road

data_processing:
Raw reads were trimmed by removing low-quality and adaptor sequences, then aligned to the A. thaliana genome using SOAP2 software.
Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the P value and the false discovery rate (FDR) ((Audic and Claverie, 1997).
Assembly: TAIR10_Araport11
Supplementary files format and content: FPKM and differential expression statistics

source_name: seedlings

growth_protocol: The seedlings grew on 1/2 MS in dark  for 8 days, the root of the seedlings were extracted for RNA sequencing.

extract_protocol:
Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

tag: seedling age

value: Roots

value: 35S::MYB2-SRDX dominant negative transgene line


title: MYB2_OE_1

value: MYB2 overexpression line


title: MYB2_OE_2


title: DC, CASE, M0019119-8


title: LBD29_OE_3

value: LBD29 overexpression line


title: MYB2_R_2


title: MYB2_OE_3


title: MP, CASE, M0011249-1


title: LBD29_OE_2


title: DC, CASE, M0021316-6


title: DC, CASE, M0020154-2


title: LBD29_OE_1


title: MP, CASE, M0010368-0


title: Col_2

value: Wild type


title: Col_3


title: MP, CASE, M0018611-5


title: DC, CASE, M0019692-4


title: Col_1


title: DC, CONTROL, M0021538-5


title: MP, CASE, M0025665-2


title: MP, CONTROL, M0008118-3


title: Sample_7_Microglia_APOE4_Het

value: Microglia

value: Het


title: DC, CASE, M0016863-4


title: MYB2_R_1


title: MP, CASE, M0025393-1


title: DC, CASE, M0017691-8


title: MP, CASE, M0018551-3


title: DC, CONTROL, M0021784-5


title: MP, CONTROL, M0015044-2


title: MP, CASE, M0016843-6


title: DC, CONTROL, M0022129-2


title: Sample 000845-001 - CTRL- 4

city: Zacatecas

first: José

middle: Antonio

last: Enciso-Moreno

state: Zacatecas

address: Interior de la Alameda 45

department: Unidad de Investigación Biomédica de Zacatecas

country: Mexico

institute: Instituto Mexicano del Seguro Social

description: L4 refers to slide 4 of 5

hyb_protocol: 1.65 ug of cRNA (specific activity > 9.0 pmol of Cy3 per µg) by sample were hybridized to high-density human GE 4X44K v2 microarrays (Part Number: G4845A, Agilent Technologies, USA) for 17 h at 65°C, according to the manufacturer´s instructions.

scan_protocol: The mean fluorescence intensity (MFI) values of each probe on the chip were obtained using the SureScan Microarray Scanner laser reader (G4900DA, Agilent Technologies, USA) and validated using the Agilent Feature Extraction program (Agilent Technologies, USA).

data_processing:
Statistical processing of the microarray raw data was performed within the R (RRID:SCR_001905) environment (R Foundation for Statistical Computing, 2016) applying the functions from Bioconductor Limma R-packages . The raw data were corrected with the 'norm exp' function. The 'quantile' function was applied to normalize and correct the batch effect among the arrays. The 'aver exp' function was applied to produce the average between the arrays, which was used as input to fit the linear regression models, considering the comparisons at the disease level. Then, the empirical Bayes function (eBayes), which was applied to the resulting linear contrast models, allowed the determination of induced and repressed genes, based on the fold change values extracted from the 'decide test' function (Smyth 2004). This function used a p-value < 0.05 and a logarithm of Fold Change > |1|.
Normalized signal intensity: AverExp of 446 genes having a p-value < 0.05 and a logarithm of Fold Change > |1| for the total of comparisons at the disease level.

source_name: Whole blood

label_protocol: 200 ng of whole RNA samples with 260/280> 2 and RIN> 6 were used to synthesize of complementary Cy3-labeled copy RNA (cRNA) according to the standard low input Quick Amp labelling protocol (Agilent Technologies, USA).

extract_protocol: Whole blood samples were obtained from each participant in vacutainer-EDTA tubes and then mixed with RNAlater (Thermo Fisher Scientific, USA) in a 5:1 proportion and stored at -70°C until use. The Trizol-Chloroform method (Invitrogen) was used, in conjunction with the QIAmp column protocol (Qiagen Inc., USA), to process frozen blood samples. RNA concentration and purity were determined using ND-1000 nanodrop (Thermo Fisher Scientific, USA). The RNA integrity number (RIN) was determined using the RNA 6000 Nano kit (Agilent Technologies, USA) on a Bioanalyzer-2100 equipment (Agilent Technologies Genomics, USA) following the manufacturer's instructions. RNA samples at a concentration of 50 ng/ul were stored at -70°C until use.

value: Whole blood

tag: group

value: CTRL

value: female

tag: glucose (mg/dl)


title: DC, CASE, M0010648-5

value: M


title: Sample 000851-001 - CTRL- 2

description: L2 refers to slide 2 of 5

tag: tissue

value: male


title: DC, CONTROL, M0015044-2

value: CONTROL


title: Sample 000835-001 - CTRL- 3

description: L3 refers to slide 3 of 5


title: MP, CASE, M0016863-4

value: MP

value: CASE


title: MP, CONTROL, M0008353-6


title: Sample 000855-001 - DM2 - 1

description: L1 refers to slide 1 of 5


title: MP, CONTROL, M0022318-1

value: F


title: Sample 000859-001 - DM2 - 4

description: L4 refers to slide 4 of 5


title: Sample 000856-001 - DM2 - 2

description: L2 refers to slide 2 of 5


title: Sample 000860-001 - PDM2 - 4

description: L5 refers to slide 5 of 5


title: DC, CONTROL, M0025675-1

value: DC


title: MP, CASE, M0010399-5


title: Sample DM-026-A - PDM2 - 3

description: L5 refers to slide 5 of 5


title: Sample DM-009-A - PDM2 - 1

description: L5 refers to slide 5 of 5


title: Sample 000858-001 - DM2 - 3

description: L3 refers to slide 3 of 5


title: Sample 000829-001 - CTRL- 1

description: L1 refers to slide 1 of 5


title: Sample 000833-000 - TB - 4

description: L4 refers to slide 4 of 5

value: TB


title: DC, CASE, M0019365-7


title: DC, CONTROL, M0007683-7


title: Sample 000817-000 - TB - 3

description: L3 refers to slide 3 of 5


title: Sample 000798-000 - TB - 2

description: L2 refers to slide 2 of 5


title: Sample DM-012-A - PDM2 - 2

description: L5 refers to slide 5 of 5


title: DC, CASE, M0014220-9


title: DC, CASE, M0025393-1


title: MP, CONTROL, M0006310-8


title: MP, CONTROL, M0006312-4


title: DC, CONTROL, M0025011-9


title: MP, CASE, M0014883-4


title: 8H9 bio_rep_3

city: Memphis

first: Asha Jacob

last: Jannu

state: TN

address: Inspiration4 Advanced Research Center

department: Developmental Neurobiology

institute: St Jude Children's Research Hospital

description: 10x Genomics

data_processing:
Cell ranger
Assembly: hg19
Supplementary files format and content: count, barcode, and matrix files

source_name: retinal organoid

growth_protocol: Retinal organoids derived from hESC line H9 VSX2-GFP/CRX-TdTomato were generated using an established protocol from the Laboratory of Dr David Gamm.

extract_protocol:
Retinal organoid dissociation buffer was prepared by adding 40 U papain to 400 uL of papain buffer and incubating at 37°C with frequent flicking. After 10 minutes 40 uL of DNAse solution was added and incubated at 37°C for an additional 5 min. The cell suspension was filtered through a 40-μm cell strainer with 1.5mL PBS, added to the top of a 4% BSA cushion, spun down at 500g for 10 minutes. The supernatant was removed and the cells were resuspended in REM.
Library was constucted using the 10x genomics Next GEM Single Cell 3’ Kit V3.1

value: retinal organoid

value: R3 knockout


title: 5B2_bio_rep_3

description: 10x Genomics

value: R0 knockout


title: Sample 000822-000 - TBDM2 - 3

description: L3 refers to slide 3 of 5

value: TBDM


title: 5B2_bio_rep_4

description: 10x Genomics


title: Sample 000861-000 - TBDM2 - 4

description: L4 refers to slide 4 of 5


title: Sample 000820-000 - TBDM2 - 2

description: L2 refers to slide 2 of 5


title: 5B2_bio_rep_2

description: 10x Genomics


title: MP, CONTROL, M0013235-8


title: Sample 000790-000 - TBDM2 - 1

description: L1 refers to slide 1 of 5


title: 8H9 bio_rep_2

description: 10x Genomics


title: 5B2_bio_rep_1

description: 10x Genomics


title: Sample 000823-000 - TB - 1

description: L1 refers to slide 1 of 5


title: DC, CONTROL, M0011710-2


title: MP, CONTROL, M0019827-6


title: MP, CONTROL, M0015947-6


title: H9_7mo

description: 10x Genomics

value: wildtype


title: 8H9 bio_rep_1

description: 10x Genomics


title: 8H9 bio_rep_4

description: 10x Genomics


title: H9_8mo

description: 10x Genomics


title: MP, CONTROL, M0025675-1


title: H9_9mo

description: 10x Genomics


title: MP, CASE, M0022181-3


title: U2OS cells G3C2 c

city: London

first: John

middle: J

last: Murphy

state: Greater London

address: School of Life Sciences

country: United Kingdom

institute: University of Westminster, London, UK

data_processing:
Original image data file from high-throughput sequencing platforms is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
Raw reads were filtered to remove reads with adapter contamination or reads with low quality. Only clean reads were used in the downstream analyse
HISAT2 was used to map the filtered sequenced reads to the reference genome
Read counts is proportional to gene expression level, gene length and sequencing depth. FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) was the method used for estimating gene expression levels
Assembly: ensembl_homo_sapiens_grch38_p12_gca_000001405_27
Supplementary files format and content: FPKM files showing read counts for each sample proportional to gene expression level

growth_protocol: U20S cells were grown in DMEM medium supplemented with 10% foetal bovine serum (FBS) and antibiotics at 37C in a humidified 5% CO2 incubator

extract_protocol:
Total RNA was isolated from log growing U2OS cells (65-75% confluency) using RNeasy mini kit (Qiagen #74104) following manufacturer’s guidelines.
Library preparation was done by Novogene - mRNA was enriched from total mRNA using oligo(dT) beads. The mRNA was then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick translation. The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.

treatment_protocol: CRISPR Cas9 targetting of ZFP36L1 in U2OS cells was carried out and ZFP36L1 deficiency was confirmed with NGS sequence analysis and western blotting

value: osteosarcoma cells

value: ZFP36L1 deficient

value: log phase growing


title: MP, CONTROL, M0011702-9


title: DC, CONTROL, M0013235-8


title: DC, CONTROL, M0006605-1


title: U2OS cells G3C2 b


title: U2OS cells WT b

value: WT


title: DC, CASE, M0015230-7

value: M


title: U2OS cells WT

description: genes.FPKM.txt


title: U2OS cells G3C2

description: genes.FPKM.txt


title: DC, CASE, M0025678-5


title: MP, CONTROL, M0022013-8


title: retinal organoid, BM, day 35, clone 2, rep 3

first: Mariya

last: Moosajee

address: 11-43 Bath Street

department: Institute of Ophthalmology

institute: UCL

data_processing:
Adapter sequences and low quality scoring bases were removed using TrimGalore (v3.4). Ribosomal RNA and potential contaminating sequences were removed using SortMeRNA. Low quality sequences with PHRED quality scores below 6 were trimmed from reads using trim galore
Reads passing these quality filters were aligned using HISAT2 (v2.2.1). Alignment output BAM files were sorted by coordinate and indexed using SAMtools.
Alignment statistics including exonic mapping, intronic, intergenic and total reads mapped per sample library were reported. Gene count tables were generated for all samples using featurecounts from the subread package (v2.0.0), and differential expression analysis carried out with DESeq2 v1.34 where WALD analysis, with p-values corrected for multiple testing using the Benjamini-Hochberg method were carried out
Samples were normalised for sequencing library size, and exploratory data analysis carried out, allowing characterisation of samples via principle component analysis, distance to distance correlations and DEGs were subjected to gene ontology (GO) analysis using the Bioconductor R package GOseq (v1.32.0)488 and g:Profiler.
Data was analysed using cofactors of time, condition, clone and replicate. Gene regulatory networks were constructed using literature searches and public databases such as Enrichr and STRING
Assembly: GRCh38, annotation version 102
Supplementary files format and content: Tab-delimited text file including the raw counts of each sample
Supplementary files format and content: Tab-delimited text file including the TPM values of each sample

source_name: in vitro iPSC-derived optic vesicles

growth_protocol: Embryonic bodies (EBs) were formed from iPSC lines by culture in mTeSR1 and 10 μM Y-27632 overnight. 48hours after EB formation, EBs were cultured in Neural Induction Media (NIM), (DMEM/F12, 20% knock-out serum residue (KOSR), 2% B27, 1x Non-Essential Amino Acids (NEAA), 1% P/S, 1xGlutamax and 5 ng/mL IGF-1. Cells were cultured in NIM with decreasing KOSR concentrations, 20% from day 2-7, 15% from day 7-11 and 10% from day 11-18 with all other media components identical. From day 18, cells were cultured in Retinal Differentiation Media (DMEM/F12, 10% FBS, 2% B27, 1×NEAA, 1×Glutamax, 1% P/S, 5 ng/mL IGF-1, 0.1 mM taurine, 40 ng/mL triiodothyronine and 0.5 μM retinoic acid added immediatelybeforeuse.

extract_protocol:
Clontech SMART-seq v4 Ultra Low Input RNA Kit for Sequencing
Clontech SMART-seq v4 Ultra Low Input RNA Kit for Sequencing

value: in vitro iPSC-derived optic vesicles

value: MAC

value: retinal differentiation


title: retinal organoid, BM, day 35, clone 2, rep 4


title: MP, CONTROL, M0013418-0

value: MP

value: CONTROL


title: DC, CASE, M0016197-7

value: DC

value: CASE


title: retinal organoid, BM, day 35, clone 2, rep 2


title: retinal organoid, BM, day 35, clone 2, rep 1


title: DC, CASE, M0015291-9

value: F


title: U2OS cells WT c


title: retinal organoid, BM, day 35, clone 1, rep 3


title: retinal organoid, BM, day 35, clone 1, rep 4


title: DC, CASE, M0018611-5


title: retinal organoid, BM, day 20, clone 2, rep 4


title: DC, CASE, M0018894-7


title: retinal organoid, BM, day 35, clone 1, rep 1


title: retinal organoid, BM, day 35, clone 1, rep 2


title: MP, CASE, M0024532-5


title: MP, CONTROL, M0021134-3


title: DC, CASE, M0017541-5


title: retinal organoid, BM, day 20, clone 2, rep 2


title: DC, CONTROL, M0013979-1