title: Leydig_exosomestreated_rep2

city: Shanghai

first: Yi

last: Ma

address: 1630, Dongfang road.

institute: Renji hospital

hyb_protocol: One μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: Leydig cells treated with exosomes (5ug/ml) for 24h rep2

label_protocol: The total RNA from each sample was linearly amplified and labeled with Cy3-UTP according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Leydig cells were incubated with F12/DMEM supplemented with 10% fetal bovine serum (10099, Gibco), 50 U/ml penicillin and 50 mg/ml streptomycin (10378, GIBCO). The cells were cultured at 34 degrees Celsius with 5% CO2.

extract_protocol: Total RNA of Leydig cells was isolated using TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer's instruction.

treatment_protocol: Primary rat Sertoli cells released exosomes were isolated and added to the supernatants (5ug/ml) of rat primary Leydig cells for 24h.

value: Sprague-Dawley

value: Leydig cells

value: with Sertoli cell exosomes


title: vector control rep 3

status: Public on May 25 2021

type: SRA

city: Dallas

first: Richard

middle: C

last: Wang

state: TX

address: 5323 Harry Hines Blvd

department: Dermatology

country: USA

institute: UT Southwestern

library_source: transcriptomic

data_processing:
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for quality and adapter trimming. The human reference genome sequence and gene annotation data, hg38, were downloaded from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). The qualities of RNA-sequencing libraries were estimated by mapping the reads onto mouse transcript and ribosomal RNA sequences (Ensembl release 89) using Bowtie (v2.3.4.3)[63]. STAR (v2.7.2b)[64] was employed to align the reads onto the mouse genome, SAMtools (v1.9) [65] was employed to sort the alignments, and HTSeq Python package [66] was employed to count reads per gene. DESeq2 R Bioconductor package [67, 68] was used to normalize read counts and identify differentially expressed (DE) genes.
Genome_build: hg38

molecule: total RNA

organism: Homo sapiens

growth_protocol: 10% FBS DMEM; 5% CO2

extract_protocol:
Qiagen RNA-Easy miniprep
NEBNext Ultra II with Poly-A Selection

tag: time

value: 48hr after transfection

tag: expression

value: WT


title: Leydig_exosomestreated_rep3

type: RNA

country: China

organism: Rattus norvegicus

source_name: Leydig cells treated with exosomes (5ug/ml) for 24h rep3

tag: strain

tag: cell type

tag: treatment


title: BP_Emb_wt_bound_rep2

city: Berkeley

first: Barbara

middle: J.

last: Meyer

state: CA

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

description: Psoralen enriched

library_source: genomic

data_processing:
DNA sequences were first processed with cutadapt (Martin, 2011) to remove readthrough adapter sequences
Reads were mapped to the WS230 C. elegans genome sequence edition using Bowtie (Langmead et al., 2009), retaining only uniquely mapped reads.
Normalized bigwig files were generated using deepTools2 with bamCoverage command.
To generate final BP signal file first log2 of bound singnal over unbound was generated using deepTools2 bigwigCompare command. Then genomic control in the form of log2 genomic bound over genomic unbound was subtracted using deepTools2 bigwigCompare comand.
Genome_build: WS230
Supplementary_files_format_and_content: BigWig files contain reads normalized to the whole genome in 1 bp resolution

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: mixed-stage embryos

growth_protocol: Wild-type C. elegans nematodes (N2 Bristol) were grown to adulthood on NG agar plates with the E. coli strain HB101. Gravid adults were bleached to obtain embryos, and the embryos were hatched in M9 medium without food to obtain developmentally arrest, synchronized L1 larvae (L1s). To obtain mixed-stage embryos for analysis, approximately 1x105 starved, synchronized L1s were cultured on NG agar plates with HB101 for 96 hours, and the resulting gravid adults were bleached to obtain mixed-stage embryos.

extract_protocol:
Nuclei were isolated from frozen embryos or L1s. L1s were first ground in liquid nitrogen to disrupt them. Approximately 3-4 x106 embryos or ground L1s were resuspended in 1 ml of buffer A (15mM Tris ph 7.5, 2mM MgCl2, 340 mM sucrose, 0.2 mM spermine, 0.2 mM spermidine, 0.1% Triton, 0.25% NP-40, 0.5 mM PMSF and a Protease Inhibitor Cocktail Set III from Calbiochem 1:1000 dilution), dounced on ice in a 2 ml glass homogenizer with pestle A and pestle B for 15 times each, and spun at 4°C for 15 min at 100 x g. The nuclei-containing supernatant was saved on ice, the pellet was resuspended in 1 ml of buffer A, and the homogenization procedure above was repeated twice. Nuclei from the three supernatants were pooled together, concentrated to 200 μl by spinning at 1000 x g for 10 minutes at 4°C.
EZ-Link™ Psoralen-PEG3-Biotin (BP) (Thermo Fisher Scientific) was added to the nuclei to a final concentration of 1.38 10-2 mg/ml, nuclei were crosslinked for 30 minutes using a UVL-56 Black-Ray lamp (long wave UV 366 nm), and nuclei were pelleted for 10 min at 4°C at 1000 x g. The supernatant was removed, and the nuclei were resuspended in 200 μl of buffer A and digested with proteinase K (10 μg/ml final) at 55°C for 30 minutes. DNA was extracted once with phenol-chloroform and precipitated once with ethanol. DNA was resuspended in 130 μl of H20, treated with Rnase A (10 μg/ml final) at 37°C for 1 hour, extracted with phenol-chloroform, and precipitated with ethanol. DNA was resuspended in 130 μl of H20 and sonicated to an average size of 150 bp using a Covaris sonicator.
The BP-containing DNA was then trapped on magnetic Dynabeads MyOne Stretavidin T1 (Invitrogen) for further manipulation.  Prior to incubation with BP-containing DNA, 50 μl of Dynabeads were washed with wash buffer WB (10 mM Tris ph 7.5, 1M NaCl, 1mM EDTA), and resuspended in 130 μl of high salt WB (10 mM Tris ph 7.5, 2M NaCl, 1mM EDTA).  The washed Dynabeads were added to 130 μl of DNA (1 M final salt), and incubated for 1 hour while rotating. The DNA-containing beads were collected with a magnet, and the supernatant was saved for BP-depleted DNA samples. DNA-containing beads were washed 3 times with 200 μl of WB and resuspended in 34 μl of EB (10 mM Tris ph 7.5).
Libraries for BP-enriched samples were prepared on the beads.  Libraries for BP-depleted samples were made using approximately 1 μg of the unbound, BP-depleted DNA in the supernatant.  After each step in library preparation, the DNA-containing beads were washed three times with WB followed by one wash with EB.  The BP-depleted DNA samples were cleaned using a Qiagen PCR purification column.
To make libraries, the DNA ends were repaired using the End-it DNA End Repair kit from Epicenter (34 μl of BP-depleted DNA or DNA-containing beads, 5 μl 10XEnd-Repair buffer, 5μl of 2.5 mM dNTP mix, 5 μl of 10 mM ATP, 1 μl End-Repair enzyme mix, and incubated for 45 minutes at room temperature). To add 3'-end A overhangs, 34 μl of BP-depleted DNA or DNA-containing beads were mixed with 5 μl NEB buffer 2, 10 μl of 10 mM dATP, 1 U of Klenow fragment (3-5- exo-), and incubated at 37°C for 30 minutes. Barcoded adapters were ligated using Quick Ligase from NEB (12 μl of Input DNA or beads, 15 μl 2x DNA ligase buffer, 1 μl of 0.125 μM NextFlex adapters, 2 μl DNA ligase, and incubated for 15 minutes at room temperature). Following adapter ligation, DNA-containing beads were cleaned with WB 3 times, once with EB, and resuspended in 37 μl of EB. BP-depleted DNA was cleaned using a Qiagen PCR column and eluted in 20 μl of EB. Unligated adapters were removed from BP-depleted samples using 10 μl of AMPure beads and eluted in 50 μl of EB. Libraries were PCR amplified (37 μl of BP-depleted DNA or DNA-containing beads, 10 μl 5x Phusion HF Buffer, 0.4 μl 25 mM dNTP, 2μl of Netflex primer mix at 12 μM, 1 μl Phusion DNA Polymerase) using the following program (2 min 98°C, [30 sec at 98°C, 30 sec at 65°C, 60 seq at 72°C] for 16 – 30 cycles, 5 min 72°C). Libraries were cleaned using Qiagen PCR purification column. Some samples required an additional AMPure bead clean up to remove unused primers and adapters. Libraries were sequenced using the Illumina HiSeq-4000 platform with 50 bp single end reads.
Control genomic DNA samples were prepared using the same steps outlined above.  However, previously purified genomic DNA was used in place of DNA purified from nuclei.
BP-seq

treatment_protocol: To obtain L1s with inhibited transcription, 4 ml of packed, starved L1s were placed into 10 ml of S-medium containing HB101 bacteria at an OD600 of 2 and α-amanitin at a final concentration of 20 μg/ml.

tag: srain

tag: developmental stage

value: mixed-stage embryos

value: untreated


title: YPW2919_rep2 [114794]

city: Ann Arbor

first: Patricia

middle: J

last: Wittkopp

state: MI

address: 1105 N University Ave

department: Department of Molecular, Cellular, and Developmental Biology

institute: University of Michigan

description:
114794_TCCGGAGA-AGGCGAAG_S2_L007
processed data file: Strain_2919.txt

data_processing:
Raw reads were run through the fastqc (version 0.11.5) read quality software, which indicated high quality reads for all samples sequenced. Reads were then trimmed using cutadapt (version 1.10)
Reads were pseudo-mapped to the a transcriptome index generated using salmon (version 0.9.1) on S. cerevisiae cDNA (Ensemble, release 38)
Read counts from salmon were imported into R using TxDb (version 3.2.2). Read counts for the entire dataset were supplied to DESeq2 to model gene expression levels. The DESeq2 ‘contrast’ wrapper was then used to estimate log2 fold changes for each strain relative to its appropriate reference and identify differentially expressed genes.
Genome_build: S. cerevisiae s288c cDNA (Ensemble, release 38, retrieved from ftp://ftp.ensemblgenomes.org/pub/release-38/fungi/fasta/saccharomyces_cerevisiae/cdna/).
Supplementary_files_format_and_content: three types of processed data files are provided: output of differential expression measures for each strain relative to the appropriate wild type reference as calculated by DESeq2 as tab delimited text files, read count abundance measures as output from salmon for both the endogenous and transgenes present as .sf files, and a raw read count matrix for all samples also as a tab delimited text file.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: haploid yeast culture_YPW2919

growth_protocol: For a total of four replicates, each replicate set of strains, including mutants and controls, were randomly arrayed across the inner wells of a 96 well plate surrounded by an outer row of wells filled with non-inoculated media. Each of the four plate arrays was grown to saturation in YPD, and then glycerol stocked in 80% glycerol and stored at -80C. The glycerol stocks were thawed by transfer using a pin tool onto solid YPG agar plates and strains were grown up for ~3 days at 30C. Strains were then transferred by pin tool again into 500uL liquid YPD in 1mL 96-well plates with glass beads and grown at 30C while shaking at 250rpms for 2 days, until all strains were once again at saturation. 100uL of the saturated culture was then transferred to a Costar 96 well plate and OD measured using a Tecan Sunrise. The OD was then used to calculate cell density. A separate 1mL 96 well plate was then filled with  500uL of YPD in each well, and each well inoculated with a volume of the saturated culture calculated to grow to a cell density of 5x10^6 cell per mL (an OD of about 0.4) after 12.5hr, based on empirical determination of each strain’s growth rate. These cultures were then grown spinning on a wheel at 30C for 12.5hrs, after which 100uL was removed and used to measure OD to ensure all cultures were between an OD of 0.26 to 0.48. Plates were then spun down for 5min at 3000g, and liquid media pipetted off. Remaining cell pellets were frozen by plunging the entire plate containing cell pellets into liquid nitrogen. Plates were sealed with foil and stored at -80C until RNA extractions were performed.

extract_protocol:
Frozen cell pellets were resuspended in 700uL of a lysis buffer containing beta-mercaptoethanol and transferred to a plate containing ~250uL of acid-washed 425-600um beads. Beaded plates were beaten 10x for 1min each with 1min on ice in between. Plates were spun down at 3000rpm at 4C for 4min, and 400uL of lysis supernatant were removed and transferred into a new 96 well plate containing oligodT magnetic beads (Dynabeads mRNA DIRECT Kit, Ambion, cat# 61011). Beads and lysate were incubated at room temperature with agitation for 5 minutes, and then placed on a magnetic stand. Beads were then washed according to the Dynabeads mRNA direct kit user guide. After extraction, several representative samples were run on Agilent Bioanalyzer to check RNA quality and concentration before moving on to library preparation. In addition, selected wells were tested for the presence of NAT or KAN resistance markers present in distinct strains and controls by RT-PCR and visualized on a gel to ensure well-cross contamination had not taken place at any step previous to library prep.
RNA sequencing libraries were prepared using a modified, ⅓ volume reaction TruSeq RNA Sample Preparation v2 Guide, and using multiplexable adapters from the TruSeq RNA CD Index Plate (cat# 20019792).

value: alpha

tag: genotype/variation

value: trans-regulatory mutant to TDH3


title: Leydig_noexosomestreated_rep3

source_name: Leydig cells reference rep3

value: no exosomes


title: Leydig_exosomestreated_rep1

source_name: Leydig cells treated with exosomes (5ug/ml) for 24h rep1


title: Leydig_noexosomestreated_rep1

source_name: Leydig cells reference rep1


title: MEFs_Con_Magoh_rep2

city: San Francisco

first: Duygu

last: Kuzuoglu Ozturk

state: California

address: 1450 3rd Street, Helen Diller Cancer Building

institute: UCSF

data_processing:
RNA-seq reads were aligned to mouse GRCm38 genome by using HISAT v2.0.5 (Kim et al., 2015)with default settings.
Gene read counts and expression values (measured by Transcripts Per Kilobase Million, TPM) were further calculated by RSEM v1.3.0 (Li and Dewey, 2011) with default settings.
Differential expression analyses were conducted with DESeq2 (Love et al., 2014) R package, where only genes with an average TPM over 0.5 were involved.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 fold change for each gene

organism: Mus musculus

source_name: Mouse embryonic fibroblasts (MEFs)

extract_protocol:
eIF4E+/+ and eIF4E+/- MEFs expressing scramble, Magoh, eIF4A3 and Rbm8a sgRNAs were induced with Dox for 48 hours in triplicates, total RNA was isolated by Trizol and ribosomal RNA was removed by Ribo-Zero (Illumina).
RNA seq libraries were prepared by ScriptSeq v2 RNA-seq library preparation kit (Epicenter) following the manufacturer’s protocol and sequenced as paired-end 100 bp on HiSeq 4000

treatment_protocol: All cells were treated with 0.4ug/ml doxycycline to induce dCas9-Krab expression

tag: cell line

value: Immortalized, Myc and Ras expressed WT MEFs

tag: induction

value: 48h DOX induction


title: Leydig_noexosomestreated_rep2

source_name: Leydig cells reference rep2


title: MEFs_Con_Magoh_rep1


title: BP_Emb_y93_unbound_rep1

description: Psoralen depleted

value: RNAi


title: BP_Emb_wt_unbound_rep1

description: Psoralen depleted


title: YPW2798_rep2 [114793]

description:
114793_ATTACTCG-AGGCGAAG_S1_L007
processed data file: Strain_2798.txt

source_name: haploid yeast culture_YPW2798


title: MEFs_Con_4A3_rep3


title: vector control rep 1


title: BP_Emb_wt_bound_rep1

description: Psoralen enriched


title: MEFs_Con_4A3_rep2


title: YPW3016r4_rep1 [105246]

source_name: haploid yeast culture_YPW3016r4

value: alpha wild type control


title: MEFs_Con_4A3_rep1


title: MEFs_Con_Scr_rep3


title: TBRS_P307

type: genomic

city: Paris

first: Guillaume

last: Velasco

address: 35 rue Hélène Brion

department: UMR7216 Epigenetics and Cell Fate

country: France

institute: Université Paris Cité

hyb_protocol: Infinium MethylationEPIC BeadChip (850K) array were carried out following Infinium HD Methylation Assay Protocol by the Infinium MethylationEPIC Array Service (Diagenode Cat# G02090000)

data_processing: Raw IDAT files were loaded and and pre-processed using the ChAMP R package. Probes with a detection p-value > 0.01, a bead count <3 in 5% of samples, non-CpG content, SNP-related, multi-hits and probes located on sex chromosomes were filtered out. Data were normalized using beta-mixture quantile normalization (BMIQ) with the function champ.norm(norm =’’BMIQ’’), and then corrected for batch effects using champ.runCombat function. Because samples were assayed using two different platforms (HM450k and EPIC), only the probes shared between the two types of arrays were considered before normalization and correction of batch effects. The methylation levels for each probe were measured as a beta value (β).

label: Cy5 and Cy3

source_name: genomic DNA from whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from whole blood samples using Qiagen Gentra Puregene DNA Extraction kit  according to standard instructions

tag: gender

value: Male

tag: sample type

value: Blood

tag: disease state

value: TBRS


title: MEFs_Con_Scr_rep2


title: GP2A

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: Patient-derived cell line

data_processing:
FASTQ files were aligned to Gencode v25 gene annotations and hg38 genome build using the STAR short-read aligner (v2.6.1a)
Gene expression estimates (FPKM) were computed using cufflinks (v.2.2.1) using the Gencode v25 gene annotations and default parameters.
Gene expression files (genes.fpkm_tracking) generated by cufflinks were merged with gene annotations in R
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text; FPKM values from cufflinks

source_name: Pancreatic ductal adenocarcinoma cell line

growth_protocol: Cells were cultured in appropriate media supplemented with FBS and 1% Penicillin/Streptomycin for 48 hours.  Specific FBS concentrations and other media components noted under "growth media".

extract_protocol:
Trizol protocol
1000 ng RNA per sample was processed using the NuGEN Encore Complete strand-specific RNA Library Prep Kits.  Sequencing was performed on an Illumina HiSeq 2000 sequencer.

treatment_protocol: No treatment was performed

tag: library prep kit

value: EncoreMR

tag: growth media

value: DMEM+F12 + 10% FBS


title: GP13A

description: Patient-derived cell line


title: TBRS_P595

scan_protocol: Infinium MethylationEPIC BeadChip (850K) array were carried out following Infinium HD Methylation Assay Protocol by the Infinium MethylationEPIC Array Service (Diagenode Cat# G02090000)


title: YPW3288_rep1 [105245]

description:
105245_TCCGCGAA-GGCTCTGA_S45_L007
processed data file: Strain_3288.txt

source_name: haploid yeast culture_YPW3288


title: YPW3275_rep1 [105243]

description:
105243_TAATGCGC-GGCTCTGA_S43_L007
processed data file: Strain_3275.txt

source_name: haploid yeast culture_YPW3275


title: YPW3282_rep1 [105244]

description:
105244_CGGCTATG-GGCTCTGA_S44_L007
processed data file: Strain_3282.txt

source_name: haploid yeast culture_YPW3282


title: YPW3092_rep1 [105242]

description:
105242_CTGAAGCT-GGCTCTGA_S42_L007
processed data file: Strain_3092.txt

source_name: haploid yeast culture_YPW3092


title: vector control rep 2


title: Sotos_like_P2452

value: Sotos-like


title: Sotos_like_P1815


title: GP3A

description: Patient-derived cell line


title: BP_Emb_y93_bound_rep1

description: Psoralen enriched


title: MEFs_Con_Scr_rep1


title: P0_GFP_Low

city: Philadelphia

first: Eric

last: Larson

state: PA

address: 240 S 40th St

institute: University of Pennsylvania

data_processing:
Basecalling by Illumina Real-Time Analysis v2.7.3
Trimming/filtering with Trimmomatic v0.36
Mapping to mm10 with GMAP/GSNAP v20141217
FPKM generated with Cufflinks v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain all protein coding genes and FPKM values for each sample

source_name: lingual epithelium

extract_protocol:
Digestion by 1.25% pancreatin and 0.125% Trypsin EDTA followed by Collagenase II/Elastase (both 1 m/mL) digestion.  Cells were passed through a 30 um mesh filter prior to FACS where GFP-high and GFP-low cells were collected.  ~100,000 cells per population were collected. RNA was extracted using Arcturus PicoPure RNA Isolation kit.
Stranded libraries were constructed using Illumina Truseq mRNA kit and sequenced using an Illumina HiSEQ4000 (1x50bp) to a depth of ~75M reads/sample.

tag: genotype

tag: population


title: GP5B

description: Patient-derived cell line


title: YPW3059_rep1 [105241]

description:
105241_GAATTCGT-GGCTCTGA_S41_L007
processed data file: Strain_3059.txt

source_name: haploid yeast culture_YPW3059

value: A

value: overexpression of TDH3


title: GP7B

description: Patient-derived cell line


title: YPW2798_rep1 [105240]

description:
105240_ATTCAGAA-GGCTCTGA_S40_L007
processed data file: Strain_2798.txt


title: P0_GFP_High


title: LATE LEFT COLON-3

city: Portland

first: Sudarshan

last: Anand

state: OR

address: 2720 S Moody Ave

institute: Oregon Health & Science University

hyb_protocol: Per Nanostring SOPs

scan_protocol: Per Nanostring SOPs

data_processing:
Early and late onset patient cohorts were compared using a two-tailed unpaired T-test for continuous variables and chi-squared test was used for categorical data. Raw NanoString immune gene expression counts were normalized to the best 10 housekeeping genes. The nSolver Advanced Analysis module was used to derive differential expression signatures according to NanoString recommendations. Adjusted P-values were obtained with a Benjamini-Hochberg post-hoc correction. The genes with an adjusted p value of less than 0.2 in the entire colorectal cancer cohort and at least one location specific cohort (right colon, left colon, or rectum) were designated genes of interest.
nSOLVER default settings and Advanced Analysis Module were used to generate normalized counts.

source_name: FFPE (CRC sample)

label_protocol: Per Nanostring SOPs

growth_protocol: Formalin-fixed paraffin-embedded (FFPE) slides were reviewed by pathology and only used if at least 70% of the tissue was tumor. The FFPE blocks were sectioned into 5µm-thick slides of tissue for use. Hematoxylin and Eosin stained slides were prepared for each sample to identify the tumor and were used as guides to sharply dissect the tumor from the unstained slides to be used for RNA extraction. RNA was isolated using the RNeasy FFPE kit (Qiagen). RNA concentration and purity was confirmed with the NanoDrop spectrophotometer

extract_protocol: 100ng of RNA extracted from the FFPE tissue was used per the manufacturer’s instructions.

treatment_protocol: NanoString immune profiling was performed using the human PanCancer Immune panel (cat#115000132)

tag: age (early = <50, late >65)

value: late

tag: anatomical location

value: Left Colon

tag: left or right

value: left


title: YPW3284_rep1 [105239]

description:
105239_GAGATTCC-GGCTCTGA_S39_L007
processed data file: Strain_3284.txt

source_name: haploid yeast culture_YPW3284

tag: cell type

value: alpha

value: trans-regulatory mutant to TDH3


title: YPW2728_rep1 [105238]

description:
105238_CGCTCATT-GGCTCTGA_S38_L007
processed data file: Strain_2728.txt

source_name: haploid yeast culture_YPW2728


title: KO-N3

city: Kaohsiung

first: Wei

middle: Shiung

last: Lian

address: No.123, Dapi Rd., Niaosong Dist.,

department: Department of Medic al Research

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

data_processing:
Quality assurance and base-calling performed with CLC Genomic Workbench v10.1
The sequence reads were trimmed to adapter, quality and length for data assembly and mapping.
The number of reads were mapped with mm10 by CLC Genomic Workbench v10.1
ChIP-seq results for peak finding reports contains chromosome location, the position of peak, peak shape score, p-value and gene names.
Comparison between WT and KO reads, the differential expression value measured in RPM and RPKM.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated and contain

source_name: articular cartilage

growth_protocol: Mice primary chondrocyte isolated from 7 day pup's knee joints and following the previously culture protocol (Nature Protocols, 2008. 3:1253).

extract_protocol: Primary chondrocytes were cultured for harvested 5x106 cells for immunoprecipitation with anti-H3K27me3 antibody and subjected to ChIP-sequencing.

tag: tissue

value: articular cartilage

tag: strain

value: Chondrocyte

tag: age

value: post natal day 7

value: Col2alpha1-UTX KO

tag: antibody

value: input


title: Hs766T

description: Established cell line

source_name: Carcinoma

value: DMEM+10% FBS


title: LATE RIGHT COLON-9

value: Right Colon

value: right


title: LATE RECTOSIGMOID-4

value: Rectosigmoid


title: KO-N2


title: YPW3272_rep1 [105237]

description:
105237_TCCGGAGA-GGCTCTGA_S37_L007
processed data file: Strain_3272.txt

source_name: haploid yeast culture_YPW3272

tag: genotype/variation


title: CAPAN-1

description: Established cell line

value: EncoreMR

value: Iscove's Modified Dulbecco's Medium+20% FBS


title: KO3

value: pulldown with H3K27me3 (Cell Signaling, #9733 )


title: ICF1_P282

value: Male

value: Blood


title: Panc 05.04

description: Established cell line

value: RPMI 1640 (high glucose+pyruvate)+15% FBS+10U/ml human insulin


title: KO-N1


title: AS-PC-1

description: Established cell line

value: RPMI 1640 (high glucose+pyruvate)+10% FBS


title: LATE RIGHT COLON -8

value: late

value: right colon


title: Pa-Tu-8988S

description: Established cell line


title: YPW2800_rep1 [105236]

description:
105236_ATTACTCG-GGCTCTGA_S36_L007
processed data file: Strain_2800.txt

source_name: haploid yeast culture_YPW2800

value: alpha

value: trans-regulatory mutant to TDH3


title: Panc 02.03

description: Established cell line


title: LATE RECTUM -16

value: rectum

value: left


title: YPW1200_rep1 [105235]

description:
105235_AGCGATAG-CCTATCCT_S35_L007
processed data file: Strain_1200.txt

source_name: haploid yeast culture_YPW1200

value: A

value: cis-regulatory mutant to TDH3


title: YPW3202_rep1 [105233]

description:
105233_TCCGCGAA-CCTATCCT_S33_L007
processed data file: Strain_3202.txt

source_name: haploid yeast culture_YPW3202


title: YPW3296_rep1 [105234]

description:
105234_TCTCGCGC-CCTATCCT_S34_L007
processed data file: Strain_3296.txt

source_name: haploid yeast culture_YPW3296

value: TDH2 deletion


title: EARLY RIGHT COLON -5

value: early

value: right


title: YPW3283_rep1 [105232]

description:
105232_CGGCTATG-CCTATCCT_S32_L007
processed data file: Strain_3283.txt

source_name: haploid yeast culture_YPW3283


title: EARLY RIGHT COLON-4


title: KO1

value: articular cartilage

value: Chondrocyte

value: post natal day 7

value: Col2alpha1-UTX KO


title: EARLY RECTOSIGMOID-9

value: Rectosigmoid


title: WT-N3

value: wild type

value: input


title: IMIM-PC-1

description: Established cell line

source_name: Pancreatic ductal adenocarcinoma cell line

value: EncoreMR

value: DMEM+10% FBS


title: WT-N2


title: KP-2

description: Established cell line


title: YPW3286_rep1 [105231]

description:
105231_TAATGCGC-CCTATCCT_S31_L007
processed data file: Strain_3286.txt

source_name: haploid yeast culture_YPW3286

value: alpha

value: trans-regulatory mutant to TDH3


title: KO2

value: pulldown with H3K27me3 (Cell Signaling, #9733 )


title: EARLY SIGMOID-8

value: sigmoid

value: left


title: YPW2682_rep1 [105230]

source_name: haploid yeast culture_YPW2682

value: A

value: duplication control


title: HPAF II

description: Established cell line


title: WT-N1


title: EARLY RECTOSIGMOID-8

value: early


title: PANC-1

description: Established cell line

source_name: Epithelioid carcinoma


title: YPW3203_rep1 [105229]

description:
105229_GAATTCGT-CCTATCCT_S29_L007
processed data file: Strain_3203.txt

source_name: haploid yeast culture_YPW3203


title: WT2

value: articular cartilage


title: YPW2525_rep1 [105228]

description:
105228_ATTCAGAA-CCTATCCT_S28_L007
processed data file: Strain_2525.txt

source_name: haploid yeast culture_YPW2525


title: YPW3247_rep1 [105227]

description:
105227_GAGATTCC-CCTATCCT_S27_L007
processed data file: Strain_3247.txt

source_name: haploid yeast culture_YPW3247


title: EARLY CECUM-3

source_name: FFPE (CRC sample)

value: Cecum

value: right


title: CAPAN-2

description: Established cell line

value: McCoy's 5a medium+10% FBS


title: WT1

value: Chondrocyte

value: post natal day 7


title: WT3

value: wild type


title: LATE SIGMOID-3

value: late

value: Sigmoid


title: SK-PC-1

description: Established cell line

value: EncoreMR

value: DMEM+10% FBS


title: LATE RECTOSIGMOID-3

value: Rectosigmoid


title: YPW3290_rep1 [105225]

description:
105225_TCCGGAGA-CCTATCCT_S25_L007
processed data file: Strain_3290.txt

source_name: haploid yeast culture_YPW3290

value: alpha

value: trans-regulatory mutant to TDH3


title: YPW2504_rep1 [105226]

description:
105226_CGCTCATT-CCTATCCT_S26_L007
processed data file: Strain_2504.txt

source_name: haploid yeast culture_YPW2504


title: IMIM-PC-2

description: Established cell line


title: LATE RECTUM-15

value: rectum

value: left


title: LATE RECTOSIGMOID -2

value: rectosigmoid


title: YPW3285_rep1 [105224]

description:
105224_ATTACTCG-CCTATCCT_S24_L007
processed data file: Strain_3285.txt

source_name: haploid yeast culture_YPW3285


title: SW-1990

description: Established cell line

value: Iscove's Modified Dulbecco's Medium+20% FBS


title: YPW3256_rep1 [105223]

description:
105223_AGCGATAG-ATAGAGGC_S23_L007
processed data file: Strain_3256.txt

source_name: haploid yeast culture_YPW3256


title: BxPC3

description: Established cell line

value: RPMI 1640 (high glucose+pyruvate)+10% FBS


title: KP-3

description: Established cell line

source_name: Adenosquamous carcinoma


title: AT4_ATM_VEH9

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray hybridization intensity data were filtered to remove undetected and array control probes before computing a log z-score for each sample to identify and exclude possible outlying samples via clustering, scatter plots, and principal components analysis. After removal of the outlying samples, a sample-specific quantile normalization of the filtered raw average signal was employed to yield quantile normalized log scale z-scores. These quantile z-scores were used to ensure a standard normal distribution in further statistical analysis, including ANOVA, t- and z-testing. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a combination of thresholds, including p<value 0.05, 30% false discovery rate (FDR), and average signal intensity of comparison >0. The gene expression change z-ratio values were then used as input to perform Parametric Analysis of Gene Set Enrichment (PAGE) testing. For each gene set change, an aggregate z-score, and p-value with false discovery change was calculated and reported for statistical significance.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: Human fibroblasts were obtained from Coriell Institute (Camden, NJ). Healthy controls (HT1-5): GM05757, GM07532, GM00316, GM08398, AG01522. A-T cells (AT1-5): GM07481, GM03487, GM02052, GM03395. AG03058. Cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin (10,000 U/ml; Thermo Fisher Scientific).

extract_protocol: Cell pellets (4 X 105 cells) were homogenized and RNA extracted with PureLinkTM RNA isolation kit following manufacturer's protocol (Thermo). RNA concentration and quality was assayed using RNA6000 Bioanalyzer chips (Agilent).

tag: coriell id

value: Fibroblast

value: Male

tag: age at biopsy

value: 13 years

tag: ethnicity

value: AA

tag: treatment

value: Vehicle


title: AT5_ATM_VEH10

tag: gender

value: Female

value: 14 years


title: LATE RIGHT COLON -7

value: late

value: right colon

value: right


title: Panc 03.27

description: Established cell line

tag: library prep kit

value: EncoreMR

tag: growth media

value: RPMI 1640 (high glucose+pyruvate)+15% FBS+10U/ml human insulin


title: YPW2794_rep1 [105222]

description:
105222_TCTCGCGC-ATAGAGGC_S22_L007
processed data file: Strain_2794.txt

source_name: haploid yeast culture_YPW2794

value: alpha

value: trans-regulatory mutant to TDH3


title: LATE TRANSVERSE COLON -2

value: transverse colon


title: MIA-PACA-2

description: Established cell line

value: DMEM+10% FBS


title: Panc 08.13

description: Established cell line


title: LATE-SIGMOID-2

value: Sigmoid

value: left


title: LATE RECTUM-14

value: rectum


title: Panc 04.03

description: Established cell line


title: YPW2911_rep1 [105221]

description:
105221_TCCGCGAA-ATAGAGGC_S21_L007
processed data file: Strain_2911.txt

source_name: haploid yeast culture_YPW2911


title: YPW3287_rep1 [105219]

description:
105219_TAATGCGC-ATAGAGGC_S19_L007
processed data file: Strain_3287.txt

source_name: haploid yeast culture_YPW3287


title: YPW3198_rep1 [105220]

description:
105220_CGGCTATG-ATAGAGGC_S20_L007
processed data file: Strain_3198.txt

source_name: haploid yeast culture_YPW3198


title: EARLY RECTOSIGMOID -7

value: early

value: rectosigmoid


title: AT2_ATM_VEH6

value: Fibroblast

value: Male

value: 8 years

value: CAUC

value: Vehicle


title: EARLY SIGMOID COLON-7

value: sigmoid colon


title: Panc 10.05

description: Established cell line

source_name: Pancreatic ductal adenocarcinoma cell line

value: EncoreMR


title: EARLY RECTUM-11


title: SU-86.86

description: Established cell line


title: 8024 MAEL KO

city: Hong Kong SAR

first: Xinyuan

last: Guan

address: No. 21 SASSOON Road Rm10-56 Laboratory Block

department: Clinical Oncology

institute: The University of Hong Kong

description: knockout MAEL verified by western blot and T7E1 assay

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl  scripts. In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data.  At the same time, Q20, Q30 and GC content the clean data were calculated. All  the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using Hisat2 v2.0.5 and  paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.  We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of  splice junctions based on the gene model annotation file and thus a better mapping  result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.  And then FPKM of each gene was calculated based on the length of the gene and  reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and  is currently the most commonly used method for estimating gene expression levels.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for each genes and each Sample
Supplementary_files_format_and_content: Matrix table with  FPKM values for each genes and each Sample

source_name: HCC

extract_protocol:
Culture medium was removed, cell line flash frozen on -80℃ freeezer with Trizol reagent. Total RNA was extracted and qualtified.  And 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MAEL knockout with sgRNA, knockout efficiency verified by western blot and T7E1 assay

value: liver

value: Alexander cells

tag: morphology

value: epithelial

tag: cell line

tag: genotype

value: MAEL KO


title: YPW3016r3_rep1 [105217]

source_name: haploid yeast culture_YPW3016r3

value: alpha

value: alpha wild type control


title: YPW3191_rep1 [105218]

description:
105218_CTGAAGCT-ATAGAGGC_S18_L007
processed data file: Strain_3191.txt

source_name: haploid yeast culture_YPW3191

value: trans-regulatory mutant to TDH3


title: EARLY SIGMOID COLON-6

tag: age (early = <50, late >65)

tag: anatomical location

tag: left or right

value: left


title: AT3_ATM_VEH7

tag: cell type

value: Female

value: 15 years


title: AT1_ATM_VEH5

value: Fibroblast

value: 5 years


title: YPW2690_rep1 [105216]

description:
105216_ATTCAGAA-ATAGAGGC_S16_L007
processed data file: Strain_2690.txt

source_name: haploid yeast culture_YPW2690


title: HPAC

description: Established cell line

value: DMEM+10% FBS


title: LATE RECTUM-13

value: late

value: rectum


title: SK-PC-3

description: Established cell line


title: LATE RECTUM-12


title: EF1_15_MOCK_HRV

city: New Haven

first: Ellen

middle: F

last: Foxman

state: Connecticut

address: 333 Cedar Street

department: Department of Laboratory Medicine

institute: Yale University

data_processing:
Sequencing reads were aligned to human and rhinovirus 1A genome and processed to generate cell-feature matrix using 10x Genomics Cell Ranger
Genome_build: hg19 (human), KC894166.1 (Rhinovirus 1A)
Supplementary_files_format_and_content: Matrix of gene counts in each cell specified by a barcode

source_name: differentiated culture

growth_protocol: Primary human bronchial epithelial cells from healthy adult donors were obtained commercially (Lonza, Walkersville, MD, USA) and cultured at air-liquid interface according to manufacturer’s instructions using reduced hydrocortisone (Stem Cell Technologies, Vancouver, Canada).

extract_protocol:
Single cell suspension was generated using trypisin/EDTA . Single cell droplets were achieved through 10x Genomics Chronium System. Tag primers weremixed with cell lysate allowing barcoding of mRNA.
Library was prepared using 10x Genomics Chromium Single Cell 3' Reagent Kits according to the manufactorer's instructions. Quality control is also included in the manufactorer's instructions.
Droplet-based 3' end single cell RNA sequencing

treatment_protocol: HRV-01A infection at MOI = 0.1 and mock infection were performed on differentiated culture . At day 5 post infection, the samples disassociated into single cell suspension and sequenced.

tag: tissue source

value: airway epithelium

tag: cell status

value: differentiated culture

value: Mock


title: EARLY RECTUM-10

value: early


title: YPW3016r2_rep1 [105213]

source_name: haploid yeast culture_YPW3016r2

tag: genotype/variation


title: YPW1188_rep1 [105214]

description:
105214_CGCTCATT-ATAGAGGC_S14_L007
processed data file: Strain_1188.txt

source_name: haploid yeast culture_YPW1188

value: A

value: cis-regulatory mutant to TDH3


title: EARLY RECTOSIGMOID -6

source_name: FFPE (CRC sample)

value: rectosigmoid


title: DMSO Treatment 72h, rep3

city: Boston

first: Sizun

last: Jiang

state: MA

address: 3 Blackfan Circle

institute: BIDMC/Harvard

description:
DMSO 72h
72hrDMSO-3
PolyA mRNA
processed data file: exon_intron_counts.txt

data_processing:
Sequencing library quality was checked using FASTQC v0.11.8 at the default settings.
Trim Galore v0.6.0 was used to trim out adapter and poor-quality sequences at default settings.
Reads were aligned against the human genome (GRCh38 build), using HISAT2 v2.1.0. Gene annotation was retrieved from Ensembl (Homo_sapiens.GRCh38.98.chr.gtf).
Exon/Intron fragment counting was performed as described (https://github.com/csglab/CRIES). In short, individual GTF files were constructed for Exons and Introns. Subsequently, HTSeq-count was used to count the fragments mapping to Exons or Introns for each individual gene. A ‘-m intersection-strict’ flag was used during Exon counting, and a ‘-m union’ flag was used during Intron counting.
Genome_build: GRCh38
Supplementary_files_format_and_content: exon_intron_counts.txt: HTSeq count file.

source_name: TYK-Nu

growth_protocol: TYK-nu cells were grown in Eagle’s minimal essential medium (American Tissue Culture Collection). Media were supplemented with 10% heat-inactivated fetal bovine serum, 100 U/mL penicillin (Gibco, Invitrogen), and 100 mg/mL streptomycin (Gibco, Invitrogen). Cells were cultured in a humidified cell incubator at 37 °C with 5% CO2 conditions and split with TrypLE Express (Gibco, Invitrogen) every 2-3 days.

extract_protocol:
RNA was extracted using the PureLink RNA Mini Kit (ThermoFisher, USA), following the manufacturer protocol for monolayer cells. The NEBNext Poly(A) mRNA magnetic Isolation Module (E7490, New England Biolabs, USA) was used for mRNA isolation.
The sequencing library was prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760) and NEBNext Multiplex Oligos for Illumina (E7500). Library quality was verified on a Bioanalyzer 2100 (Agilent Technologies, USA) and the library sequenced on a single lane of Hi-Seq 4000 (2x100bp) at the Stanford Center for Genomics and Personalized Medicine sequencing Center.

treatment_protocol: Triplicates of TYK-nu cells were grown with 15uM of Cisplatin or DMSO control added for 24 or 72 hours.

value: TYK-Nu

value: High grade ovarian serous adenocarcinoma cell line

value: DMSO

tag: treatment duration


title: CFPAC

description: Established cell line

source_name: Ductal adenocarcinoma; cystic fibrosis

value: EncoreMR

value: Iscove's Modified Dulbecco's Medium+20% FBS


title: HPDE

description: Established cell line

value: Keratinocyte Serum-Free (KSF)


title: YPW2506_rep1 [105215]

description:
105215_GAGATTCC-ATAGAGGC_S15_L007
processed data file: Strain_2506.txt

source_name: haploid yeast culture_YPW2506

value: alpha

value: trans-regulatory mutant to TDH3


title: EARLY RECTUM-9

value: left


title: YPW3245_rep1 [105211]

description:
105211_AGCGATAG-TATAGCCT_S11_L007
processed data file: Strain_3245.txt

source_name: haploid yeast culture_YPW3245


title: EF2_21_RV_HRV

value: Primary human bronchial epithelial cells

value: HRV-01A, MOI 0.1, day 5


title: HT1_WT_VEH1

tag: coriell id

value: Fibroblast

value: Male

tag: age at biopsy

value: 7 years

value: AA

value: Vehicle


title: PL-45

description: Established cell line

value: DMEM+10% FBS


title: GP5A

description: Patient-derived cell line

value: DMEM+F12 + 10% FBS


title: HT2_WT_VEH4

value: Female

value: 16 years

tag: ethnicity

value: CAUC/A

tag: treatment


title: HT4_WT_VEH9

tag: gender

value: 8 years

value: CAUC


title: YPW3016r1_rep1 [105212]

source_name: haploid yeast culture_YPW3016r1

value: alpha

value: alpha wild type control


title: YPW3298_rep1 [105210]

description:
105210_TCTCGCGC-TATAGCCT_S10_L007
processed data file: Strain_3298.txt

source_name: haploid yeast culture_YPW3298

value: A

value: TDH2/3 double deletion


title: YPW3068_rep1 [105209]

description:
105209_TCCGCGAA-TATAGCCT_S9_L007
processed data file: Strain_3068.txt

source_name: haploid yeast culture_YPW3068

value: trans-regulatory mutant to TDH3


title: HT5_WT_VEH10

value: Fibroblast

value: 3 days


title: HT3_WT_VEH5

value: Male

value: 12 years


title: DMSO Treatment 24h, rep2

description:
DMSO 24h
24hrDMSO-2
PolyA mRNA
processed data file: exon_intron_counts.txt

value: TYK-Nu

value: High grade ovarian serous adenocarcinoma cell line

value: DMSO


title: Pa-Tu-8988T

description: Established cell line

tag: library prep kit

value: EncoreMR

tag: growth media

value: DMEM+10% FBS


title: LATE RECTUM-11

value: late

value: rectum

value: left


title: DMSO Treatment 72h, rep2

description:
DMSO 72h
72hrDMSO-2
PolyA mRNA
processed data file: exon_intron_counts.txt

tag: cell line


title: DMSO Treatment 24h, rep1

description:
DMSO 24h
24hrDMSO-1
PolyA mRNA
processed data file: exon_intron_counts.txt


title: EARLY RECTOSIGMOID-5

value: early

value: rectosigmoid


title: YPW3228_rep1 [105208]

description:
105208_CGGCTATG-TATAGCCT_S8_L007
processed data file: Strain_3228.txt

source_name: haploid yeast culture_YPW3228

value: alpha


title: LATE RECTUM -10


title: YPW3161_rep1 [105207]

description:
105207_TAATGCGC-TATAGCCT_S7_L007
processed data file: Strain_3161.txt

source_name: haploid yeast culture_YPW3161


title: DMSO Treatment 72h, rep1

description:
DMSO 72h
72hrDMSO-1
PolyA mRNA
processed data file: exon_intron_counts.txt


title: Panc1_bruChaseseq_rep1

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

description:
Panc1 bruChaseseq replicate 1
bru-labeled RNA

data_processing:
Library strategy: BruChase-seq
Illumina Casava v1.8.2 software used for basecalling.
Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2 (2.3.3)
Reads that did not align with rRNA, mitochondrial and EBV genomes were subsequently mapped to human genome build hg38/GRCh38 using STAR (v 2.5.3a) and a STAR index created from GENCODE annotation version 27
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Genome_build: hg38
Supplementary_files_format_and_content: Please refer to Supplementary Table 1 for information on cell lines. The columns of the genes.bed indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) strand; (6) gene length (7) read count (8) RPKM

growth_protocol: HCT116 were grown in RPMI (RPMI 1640, 10% FBS, 100U/ml penicillin and 100U/ml streptomycin). HeLa, MiaPaCa and Panc1 were grown in DMEM (DMEM, 10% FBS, 100 U/ml penicillin and 100 U/ml streptomycin). MEM growth media (Minimal Essential Medium, 10% FBS, 1× MEM amino acids, 1× non-essential amino acids, 2 mM L-glutamine, 1× antibiotic–antimycotic, 1× MEM vitamin mixture and 0.15% (w/v) sodium bicarbonate) was used for HF1. K562 were grown in IMDM with 10% FBS and antibiotics

extract_protocol:
For bruseq and BruChaseseq, total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013
Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then  synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.

tag: bru labeling time

value: 0.5 hours

tag: time between end of bru labeling and rna extraction

value: 6 hours

tag: labeling agent

value: Bromouridine (Bru)


title: K562_bruChaseseq_rep4

description:
K562 bruChaseseq replicate 4
bru-labeled RNA


title: DMSO Treatment 24h, rep3

description:
DMSO 24h
24hrDMSO-3
PolyA mRNA
processed data file: exon_intron_counts.txt


title: RWP-1

description: Established cell line

source_name: Pancreatic ductal adenocarcinoma cell line


title: Cisplatin Treatment 72h, rep3

description:
Cis 72h
72hrCisplatin-3
PolyA mRNA
processed data file: exon_intron_counts.txt

value: Cisplatin


title: K562_bruChaseseq_rep3

description:
K562 bruChaseseq replicate 3
bru-labeled RNA


title: Cisplatin Treatment 72h, rep2

description:
Cis 72h
72hrCisplatin-2
PolyA mRNA
processed data file: exon_intron_counts.txt


title: Cisplatin Treatment 24h, rep3

description:
Cis 24h
24hrCisplatin-3
PolyA mRNA
processed data file: exon_intron_counts.txt


title: LATE RECTUM -8

tag: age (early = <50, late >65)

tag: anatomical location

tag: left or right


title: LATE RECTUM -7


title: MiaPaCa_bruChaseseq_rep1

description:
MiaPaCa bruChaseseq replicate 1
bru-labeled RNA

source_name: MiaPaCa

value: MiaPaCa


title: K562_bruChaseseq_rep2

description:
K562 bruChaseseq replicate 2
bru-labeled RNA


title: YPW3088_rep1 [105203]

description:
105203_CGCTCATT-TATAGCCT_S3_L007
processed data file: Strain_3088.txt

source_name: haploid yeast culture_YPW3088

tag: cell type

value: trans-regulatory mutant to TDH3


title: YPW3241_rep1 [105206]

description:
105206_CTGAAGCT-TATAGCCT_S6_L007
processed data file: Strain_3241.txt

source_name: haploid yeast culture_YPW3241

tag: genotype/variation


title: YPW3291_rep1 [105205]

description:
105205_GAATTCGT-TATAGCCT_S5_L007
processed data file: Strain_3291.txt

source_name: haploid yeast culture_YPW3291

value: TDH1 deletion


title: YPW1177_rep1 [105202]

description:
105202_TCCGGAGA-TATAGCCT_S2_L007
processed data file: Strain_1177.txt

source_name: haploid yeast culture_YPW1177

value: A

value: TDH3 deletion


title: EARLY RECTUM-8


title: K562_bruChaseseq_rep1

description:
K562 bruChaseseq replicate 1
bru-labeled RNA


title: YPW3254_rep1 [105204]

description:
105204_GAGATTCC-TATAGCCT_S4_L007
processed data file: Strain_3254.txt

source_name: haploid yeast culture_YPW3254


title: EARLY RECTUM-6

source_name: FFPE (CRC sample)


title: Cisplatin Treatment 24h, rep1

description:
Cis 24h
24hrCisplatin-1
PolyA mRNA
processed data file: exon_intron_counts.txt

source_name: TYK-Nu

value: TYK-Nu

value: High grade ovarian serous adenocarcinoma cell line

tag: treatment duration


title: Cisplatin Treatment 24h, rep2

description:
Cis 24h
24hrCisplatin-2
PolyA mRNA
processed data file: exon_intron_counts.txt


title: YPW1156_rep1 [105201]

description:
105201_ATTACTCG-TATAGCCT_S1_L007
processed data file: Strain_1156.txt

source_name: haploid yeast culture_YPW1156

value: cis-regulatory mutant to TDH3


title: LATE RIGHT COLON-6

value: late

value: right colon

value: right


title: HF1_bruChaseseq_rep3

description:
HF1 bruChaseseq replicate 3
bru-labeled RNA


title: Cisplatin Treatment 72h, rep1

description:
Cis 72h
72hrCisplatin-1
PolyA mRNA
processed data file: exon_intron_counts.txt


title: LATE RECTUM-9

value: rectum

value: left


title: EARLY RECTUM-7

value: early


title: HF1_bruChaseseq_rep2

description:
HF1 bruChaseseq replicate 2
bru-labeled RNA

value: 0.5 hours

value: 6 hours


title: telithromycin-treated yeast, biol rep2

city: chicago

first: Maxim

last: Svetlov

state: ILLINOIS

address: 900 south ashland ave

department: Department of Medicinal Chemistry and Pharmacognosy

institute: University of Illinois at Chicago

data_processing:
Library strategy: Ribo-Seq (Ribosome profiling)
Fastq files were first trimmed to remove linkers and, when necessary, demultiplexed (for samples None2 and Teli2) to obtain individual samples from pooled data using CUTADAPT
To remove tRNA and rRNA reads, the files were aligned to an index of noncoding RNAs with BOWTIE
The fastq files after noncoding RNA removal step (for high TEL samples) were then aligned to coding regions and splice junctions using BOWTIE (version 1.1.2)
with the following parameters: -v 2-y-a-m 1--best--strata (2 mismatches allowed and multiple alignments suppressed) and using the R64-1-1 S288C reference genome assembly (SacCer3, Saccharomyces Genome Database Project)
Only 25-34 nt footprints were included in the analysis.
The primary alignments were mapped to the 3' end position of the read to create initial .wig files for visualization and gene-level quantification. After visual inspection an offset of 18 nt was applied to align Ribo-seq data to ribosomal P-sites. RPKM for each CDS was calculated for each Ribo-seq data from these .wig mappings.
Genome_build: reference genome: R64-1-1 S288C (SacCer3)
Supplementary_files_format_and_content: wig

source_name: strain NOY891 with pJD694_G2400A plasmid

growth_protocol: The culture of G2400A mutant yeast was grown at 30C in YPD medium supplemented with ampicillin (100 μg/mL)

extract_protocol:
The non-treated and telithromycin treated cells were collected by rapid filtration through membrane filter (Millipore), frozen in liquid nitrogen and processed for ribosome profiling as described in Becker et al., 2013 (for samples None1 and Teli1) or McGlincy and Ingolia, 2017 (for samples None2 and Teli2)
The library for next-generation sequencing was prepared using RNA fragments ranging in size from 20 to 35 nt. Analysis of ribosome profiling was carried out using the GALAXY pipeline. The first position of the P site codon was assigned at the 3’ end of the read.

treatment_protocol: When the culture density reached A600=0.6, telithromycin was added to the final concentration 1.5 mg/mL (x8 MIC) and the culture was incubated with shaking for 10 minutes

tag: strain

tag: genotype

value: G2400A mutant

value: telithromycin


title: LATE SIGMOID -1

value: sigmoid


title: KP-4

description: Established cell line

source_name: Pancreatic ductal cell carcinoma

value: EncoreMR


title: pBMH_F_ICFX

source_name: genomic DNA from whole blood

value: Female

tag: sample type

value: Blood

tag: disease state

value: ICFX


title: HF1_bruChaseseq_rep1

description:
HF1 bruChaseseq replicate 1
bru-labeled RNA

value: Bromouridine (Bru)


title: non-treated yeast, biol rep2

tag: treatment

value: control


title: EARLY SIGMOID -5


title: EARLY RIGHT COLON-3


title: telithromycin-treated yeast, biol rep1


title: HeLa_bruChaseseq_rep2

description:
HeLa bruChaseseq replicate 2
bru-labeled RNA

source_name: HeLa

value: HeLa


title: LATE CECUM-1

value: late

value: cecum


title: HeLa_bruChaseseq_rep3

description:
HeLa bruChaseseq replicate 3
bru-labeled RNA


title: Panc1_bruseq_rep4

description:
Panc1 bruseq replicate 4
bru-labeled RNA

data_processing:
Library strategy: Bru-Seq
Illumina Casava v1.8.2 software used for basecalling.
Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2 (2.3.3)
Reads that did not align with rRNA, mitochondrial and EBV genomes were subsequently mapped to human genome build hg38/GRCh38 using STAR (v 2.5.3a) and a STAR index created from GENCODE annotation version 27
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Genome_build: hg38
Supplementary_files_format_and_content: Please refer to Supplementary Table 1 for information on cell lines. The columns of the genes.bed indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) strand; (6) gene length (7) read count (8) RPKM

value: 0 hours


title: LATE RECTOSIGMOID-1

value: rectosigmoid

value: left


title: HCT116_bruChaseseq_rep1

description:
HCT116 bruChaseseq replicate 1
bru-labeled RNA

value: 0.5 hours


title: HeLa_bruChaseseq_rep1

description:
HeLa bruChaseseq replicate 1
bru-labeled RNA

value: 6 hours


title: EARLY RECTUM-5

value: early

value: Rectum


title: LATE LEFT COLON -2

value: left colon


title: non-treated yeast, biol rep1

value: G2400A mutant


title: CD34+_control_day2

city: Fukuoka

first: Daisuke

last: Sugiyama

state: Fukioka

address: 3-1-1, Maidashi, Higasi-ku

department: Incubation Center for Advanced Medical Science (ICAMS)

country: Japan

institute: Kyushu university

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: cord blood CD34+ cells

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: Human cord blood CD34+ cells from healthy donors was cultured for 2 days with or without SL-13R.

tag: tissue

value: cord blood

value: PBS


title: pN_F_ICFX

tag: gender

value: Female

value: Blood

value: ICFX


title: LATE TRANSVERSE COLON -1

value: transverse colon

value: right


title: Panc1_bruseq_rep3

description:
Panc1 bruseq replicate 3
bru-labeled RNA

value: Bromouridine (Bru)

tag: cell line


title: LATE RIGHT COLON-5

value: late

value: right colon


title: CCR2 KO normal_10

first: Walter

last: Eckalbar

address: 513 Parnassus Ave MSB-813

institute: University of California, San Francisco

description: Ly6G- CD45+ FACS sorted cells

data_processing:
Alignment of raw FASTQ files to the Mouse Genome (GRCm38) and Ensembl Annotation Build 96 with STAR version 2.7.5c
Star Parameters: --outSAMtype BAM   SortedByCoordinate      --outFilterType BySJout   --outFilterMultimapNmax 1   --outFilterMismatchNmax 999   --outFilterMismatchNoverLmax 0.04   --clip3pAdapterSeq GATCGGAAGAGCACACGTCTGAACTCCAGTCAC        --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJDBoverhangMin 1   --soloType Droplet   --soloUMIlen 12   --soloBarcodeReadLength 30   --soloCBwhitelist 3M-february-201  8.txt
Supplementary_files_format_and_content: STARsolo outputs containing Gene.stats, barcodes.tsv, matrix.mtx and genes.tsv

source_name: originally from The Jackson Laboratory, colony bred at San Francisco VA Animal Facility

extract_protocol:
Four days post-injury animals were euthanized and perfused with ice cold GKN buffer (8 g/L NaCl, 0.4 g/L KCl, 1.41 g/L Na2HPO4, 0.6 g/L NaH2PO4, and 2 g/L D(+) glucose, pH 7.4) through the heart to eliminate circulating blood.  Brains were harvested and ipsilateral hemispheres were dissected for further study.  Ipsilateral brain hemispheres were harvested and the olfactory bulbs removed. Tissues were minced and washed in cold GKN buffer.  Tissue chunks were resuspended in 2.5 mL of digestion buffer (NOSE buffer (4 g/L MgCl2, 2.55 g/L CaCl2, 3.73 g/L KCl, 8.95 g/L NaCL, pH 6-7) with 200 U/ml DNase I (Sigma-Aldrich) and 0.2 mg/mL Collagenase I (Worthington Biochemical)) and incubated at 37C in a dry incubator for 1h with shaking every 15 min. All samples were placed on ice to halt enzymatic activity.  Tissues were crushed through a 100 micron nylon filter cup (BD Biosciences) and the cell suspension was washed with GKN buffer. An isotonic Percoll solution (90% Percoll (GE Biosciences), 10% 1.5M NaCl) was made and brought to room temperature.  Cells were resuspended in 20 mL of a 1.03 g/mL isotonic Percoll solution in GKN buffer and underlayed with 10 mL of a 1.095 g/L isotonic Percoll solution in PBS.  Cells were spun at ~850g at room temperature for 20 min. Buffy layers were isolated.    Cells were blocked with 10% rat serum for 10 min on ice and then stained with the following antibodies: anti-CD45 PE-Cy5.5 (Clone 30-F11, Invitrogen), anti-Ly6G PE-eFluor610 (Clone 1A8, Invitrogen), anti-CD11b PE (Clone M1/70, BD Biosciences), anti-Ly6C PE-Cy7 (Clone AL-21, BD Biosciences), and anti-CD3 FITC (Clone 17A2, BD Biosciences).  DAPI (Invitrogen) was used at 1 uM to gate out dead cells.   Cells were sorted on a FACS AriaIIu (BD Biosciences) at the San Francisco VA Medical Center Flow Cytometry Core Facility.
Single cell RNA seq was performed at the Genomics Core Facility at the Institute for Human Genetics (University of California, San Francisco) using the 10X Genomics platform with gel emulsion bead technology.   Chromium Single Cell 3’ Reagent Kits v3 were used according to manufacturer protocols and each sample was run on separate lanes.   Libraries were sequenced on a NovaSeq6000 at the UCSF Center for Advanced Technologies with an average of 2967 average UMI per cell.

treatment_protocol: For the TBI groups, adult male C57BL/6 wild type mice and Ccr2-/- mice were given traumatic brain injury (TBI)  using a controlled cortical impact model to induce a focal TBI injury with a pneumatic piston with the parameters of 1.5mm deep, 150 ms dwell time, and 3m/s piston speed.

tag: animal age

value: 12 weeks old

tag: Sex

value: male

value: CCR2 KO

value: brain


title: Panc1_bruseq_rep2

description:
Panc1 bruseq replicate 2
bru-labeled RNA

tag: bru labeling time

value: 0.5 hours

tag: time between end of bru labeling and rna extraction

value: 0 hours

tag: labeling agent


title: LATE RECTUM -6

tag: age (early = <50, late >65)

tag: anatomical location

value: rectum

tag: left or right

value: left


title: CCR2 KO normal_11

description: Ly6G- CD45+ FACS sorted cells

tag: genotype/variation


title: Panc1_bruseq_rep1

description:
Panc1 bruseq replicate 1
bru-labeled RNA


title: WT normal_9

description: Ly6G- CD45+ FACS sorted cells

source_name: The Jackson Laboratory

tag: strain

value: WT


title: CD34+_SL-13R_day2

value: cord blood


title: MiaPaCa_bruseq_rep8

description:
MiaPaCa bruseq replicate 8
bru-labeled RNA

value: MiaPaCa


title: WT normal_8

description: Ly6G- CD45+ FACS sorted cells


title: EARLY RECTUM-4

value: Early


title: MiaPaCa_bruseq_rep7

description:
MiaPaCa bruseq replicate 7
bru-labeled RNA


title: EARLY RECTUM-3

value: early

value: Rectum


title: MiaPaCa_bruseq_rep6

description:
MiaPaCa bruseq replicate 6
bru-labeled RNA

value: Bromouridine (Bru)


title: WT normal_7

description: Ly6G- CD45+ FACS sorted cells


title: EARLY RIGHT COLON-2

value: Right Colon

value: right


title: EARLY TRANSVERSE COLON-2

value: Transverse Colon


title: CCR2 KO TBI d4_6

description: Ly6G- CD45+ FACS sorted cells

value: 12 weeks old

value: male

value: ipsilateral brain hemisphere


title: MiaPaCa_bruseq_rep5

description:
MiaPaCa bruseq replicate 5
bru-labeled RNA

value: 0.5 hours


title: Cerebellum_Atm--_NR4

growth_protocol: Atm heterozygous strain (B6;129S4-Atmtm1Bal/J) was purchased from Jacksons Laboratory. Atm homozygous (Atm-/-) mice and their wild type (WT) littermates were used forexperiments. All mice were maintained in the in a constant-temperature facility with a 12 h light/12 h dark cycle and given food and water ad libitum. Animal phenotyping experiments were carried out according to standard operational procedures (SOPs) established and validated by Transnetyx. For genotyping, primers for WT included forward primer (F): TCAAGGCATGCCATTATCTGTCTT, reverse primer (R): CTGACTGGAAACTGATCGCTACTTT; primers for mutant allele were F: GGGCGCCCGGTTCTT, and R: CCTCGTCCTGCAGTTCATTCA. The Atm-/- mice and their age- and sex-matched littermates were used for behavioral studies. All animal experiments were performed and approved by NIA Animal Care and Use Committee.

extract_protocol: Twenty milligrams of cerebellar cortex from each mouse was homogenized and RNA extracted purified with PureLinkTM RNA isolation kit following manufacturer's protocol (Thermo). RNA concentration and quality was assayed on an RNA6000 Bioanalyzer chip (Agilent).

treatment_protocol: Six week old male mice from either wild-type (WT) or Atm homozygous (Atm-/-, ATM) were given 3.5 mg/ml (12 mM)  nicotinamide riboside (NR) at in their drinking water while the control groups  received only water (Veh) for 2 months.

tag: genotype

value: Cerebellum

value: Male

tag: age

value: 3.5 months

value: 2 months NR


title: Cerebellum_Atm--_NR2


title: Cerebellum_Atm--_NR3


title: Cerebellum_Atm--_NR1


title: Cerebellum_Atm--_Veh4

value: Vehicle


title: Cerebellum_Atm--_Veh3


title: Cerebellum_Atm--_Veh2


title: Cerebellum_Atm--_Veh1


title: CCR2 KO TBI d4_4

description: Ly6G- CD45+ FACS sorted cells

value: CCR2 KO


title: Cerebellum_WT_NR4


title: MiaPaCa_bruseq_rep2

description:
MiaPaCa bruseq replicate 2
bru-labeled RNA

value: 0 hours

value: MiaPaCa


title: EARLY TRANSVERSE COLON-1

value: early

value: transverse colon


title: EARLY RECTUM-2

value: rectum

value: left


title: MiaPaCa_bruseq_rep4

description:
MiaPaCa bruseq replicate 4
bru-labeled RNA

value: Bromouridine (Bru)


title: MiaPaCa_bruseq_rep3

description:
MiaPaCa bruseq replicate 3
bru-labeled RNA


title: WT TBI d4_2

description: Ly6G- CD45+ FACS sorted cells

value: 12 weeks old

value: WT


title: WT TBI d4_3

description: Ly6G- CD45+ FACS sorted cells

value: male

value: ipsilateral brain hemisphere


title: LATE LEFT COLON -1

value: late

value: left colon


title: LATE RIGHT COLON -4

value: right colon

value: right


title: CCR2 KO TBI d4_5

description: Ly6G- CD45+ FACS sorted cells


title: MiaPaCa_bruseq_rep1

description:
MiaPaCa bruseq replicate 1
bru-labeled RNA

value: 0.5 hours


title: LATE RECTUM -5


title: Cerebellum_WT_NR3

value: Cerebellum

value: Male

value: 3.5 months

value: 2 months NR


title: Cerebellum_WT_NR2


title: WT TBI d4_1

description: Ly6G- CD45+ FACS sorted cells


title: K562_bruseq_rep5

description:
K562 bruseq replicate 5
bru-labeled RNA

value: 0 hours


title: K562_bruseq_rep4

description:
K562 bruseq replicate 4
bru-labeled RNA


title: 50-IP_db/db-5

city: Beijing

first: wenhao

last: ju

address: chaoyang

institute: pumc

data_processing:
library strategy: meRIP-seq
FastQC (v0.11.7) was used for quality inspection of raw sequence data
original sequence filtered using Trimmomatic (V0.32)
Filtered high-quality data were compared with the reference genome (HISAT2 v2.1.0) in the Ensembl database
exomePeak (v2.13.2) used to identify peaks in each sample and differentially methylated peaks in compared samples.
Genome_build: mm9
Supplementary_files_format_and_content: excel format

extract_protocol:
Hearts collected in 1.5 ml RNase-free centrifuge tubes, immediately immersed in liquid nitrogen to prevent RNA degradation, and finally stored at -80°C.RNA was harvested using Trizol reagent.Complete mRNA was obtained by purification  using Arraystar Seq-StarTM ploy(A) mRNA Isolation Kit
A KAPA Stranded mRNA-seq Kit (Illumina) was used to construct sequencing libraries of post-enrichment m6A mRNA.

value: db/db

value: heart

tag: antibody

value: Affinity purified anti-m6A rabbit (Synaptic Systems, 202003, 2-108)


title: Cerebellum_WT_Veh4

tag: treatment

value: Vehicle


title: Cerebellum_WT_Veh3

tag: tissue


title: LATE RECTUM -4

value: rectum

value: left


title: 49-IP_db/db-4


title: LATE RECTUM-3


title: 48-IP_db/db-3


title: K562_bruseq_rep3

description:
K562 bruseq replicate 3
bru-labeled RNA

value: Bromouridine (Bru)


title: K562_bruseq_rep1

description:
K562 bruseq replicate 1
bru-labeled RNA


title: K562_bruseq_rep2

description:
K562 bruseq replicate 2
bru-labeled RNA


title: Cerebellum_WT_NR1


title: 47-IP_db/db-2


title: Cerebellum_WT_Veh1


title: LATE RECTUM -2

value: late


title: Cerebellum_WT_Veh2


title: EARLY CECUM-2

value: early

value: cecum


title: Panc1_bruChaseseq_rep2

description:
Panc1 bruChaseseq replicate 2
bru-labeled RNA

value: 6 hours


title: T84 colonic epithelial cells #4 postlarazotide rep 2

first: Oscar

middle: Colin

last: Stine

address: 660 W. Redwood St.

department: Epidemiology and Public Health

institute: University of Maryland Baltimore

description: Followed standard Affymetrix protocols

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: rma

label: Standard Affymetrix label

source_name: Differentiated T84 colonic epithelial cells treated with larazotide

label_protocol: Affymetrix protocol

growth_protocol: The colonic epithelial cell line was grow to a differentiated monolayer on collagen membranes.  Differebtiation was determined by an increased transepithelial electronic resistance. The growth medium was DMEM with fetal calf sera

extract_protocol: RNAlater and RNA was extracted following manufacturer’s instructions

treatment_protocol: RNA was isolated from T84 cells prior to and five hours after treatment with 10 mM larazotide

value: larazotide

tag: cell type

value: Colonic epithelial cell line from ATCC


title: EARLY LEFT COLON-2

value: Left Colon


title: T84 colonic epithelial cells #5 postlarazotide rep 3

description: Followed standard Affymetrix protocols


title: HF1_bruseq_rep3

description:
HF1 bruseq replicate 3
bru-labeled RNA

value: 0.5 hours

tag: cell line


title: EARLY LEFT COLON-1


title: 44-IP_db/+-4

value: wild type


title: HF1_bruseq_rep2

description:
HF1 bruseq replicate 2
bru-labeled RNA

value: 0 hours


title: T84 colonic epithelial cells #5 prelarazotide rep 3

description: Followed standard Affymetrix protocols

source_name: Differentiated T84 colonic epithelial cells untreated

value: untreated


title: 43-IP_db/+-3

value: heart


title: T84 colonic epithelial cells #3 prelarazotide rep 2

description: Followed standard Affymetrix protocols


title: EARLY RIGHT COLON-1

value: Right Colon

value: right


title: EARLY SIGMOID-4

value: Sigmoid


title: HF1_bruseq_rep4

description:
HF1 bruseq replicate 4
bru-labeled RNA


title: ino80_SD_H3K4me3_repeat2

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Basecalls performed using bcl2fastq version 2.16.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
The SICER was used to identify ChIP-enriched peaks between wild type and mutant.
Genome_build: TAIR10
Supplementary_files_format_and_content: Wig files were generated using bamCoverage.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a long-day (LD) photoperiod (23℃, 16 h light/ 22℃, 8 h darkness) or short-day (SD) photoperiod (23℃, 8h light/ 22℃, 16 h darkness).

extract_protocol:
Chromatin isolated from 11-day-old seedlings in LD or 14-day-old seedlings in SD were subjected to sonication and immunoprecipitation with the anti-H3K4me3 antibody.
Libraries were built for ChIP-seq (Illumina HiSeq X Ten; 150-bp pair-end sequencing).

value: Seedlings

value: 14 days

tag: growth conditions

value: short day (8 h light, 16 h dark)

tag: chip antibody

value: anti-H3K4me3 (Millipore, 07-473)


title: T84 colonic epithelial cells #1 prelarazotide rep 1

description: Followed standard Affymetrix protocols


title: HF1_bruseq_rep1

institute: University of Michigan

description:
HF1 bruseq replicate 1
bru-labeled RNA

tag: bru labeling time

value: Bromouridine (Bru)


title: ino80_SD_H3K4me3_repeat1


title: 45-IP_db/+-5

value: Affinity purified anti-m6A rabbit (Synaptic Systems, 202003, 2-108)


title: HeLa_bruseq_rep7

description:
HeLa bruseq replicate 7
bru-labeled RNA

tag: time between end of bru labeling and rna extraction

value: HeLa


title: HeLa_bruseq_rep6

description:
HeLa bruseq replicate 6
bru-labeled RNA

tag: labeling agent


title: EARLY RECTOSIGMOID-4

tag: age (early = <50, late >65)

value: early

value: Rectosigmoid

value: left


title: 41-IP_db/+-1

value: wild type


title: 42-IP_db/+-2


title: Col-0_SD_H3K4me3_repeat2


title: LATE RECTUM -1

value: late

tag: anatomical location

value: rectum


title: 50_db/db-5

data_processing:
FastQC (v0.11.7) was used for quality inspection of raw sequence data
original sequence filtered using Trimmomatic (V0.32)
Filtered high-quality data were compared with the reference genome (HISAT2 v2.1.0) in the Ensembl database
exomePeak (v2.13.2) used to identify peaks in each sample and differentially methylated peaks in compared samples.
Genome_build: mm9
Supplementary_files_format_and_content: excel format

value: db/db

value: heart


title: Col-0_SD_H3K4me3_repeat1


title: 49_db/db-4


title: LATE RIGHT COLON -3

value: right colon

tag: left or right

value: right


title: 48_db/db-3


title: LATE RIGHT COLON -2


title: HeLa_bruseq_rep4

description:
HeLa bruseq replicate 4
bru-labeled RNA

value: 0.5 hours

value: 0 hours


title: atx4/5;jmj24_SD_H3K4me3_repeat2

value: Seedlings

value: 14 days

value: short day (8 h light, 16 h dark)


title: HeLa_bruseq_rep3

description:
HeLa bruseq replicate 3
bru-labeled RNA

value: Bromouridine (Bru)


title: LATE RIGHT COLON-1


title: T84 colonic epithelial cells #2 postlarazotide rep 1

description: Followed standard Affymetrix protocols

value: larazotide

value: Colonic epithelial cell line from ATCC


title: atx4/5;jmj24_SD_H3K4me3_repeat1

value: anti-H3K4me3 (Millipore, 07-473)


title: 47_db/db-2


title: ino80_LD_H3K4me3_repeat2

value: 11 days

value: long day (16 h light, 8 h dark)


title: HeLa_bruseq_rep2

description:
HeLa bruseq replicate 2
bru-labeled RNA

value: HeLa


title: EARLY RECTOSIGMOID-3

value: early

value: Rectosigmoid

value: left


title: ino80_LD_H3K4me3_repeat1


title: HeLa_bruseq_rep1

description:
HeLa bruseq replicate 1
bru-labeled RNA


title: 45_db/+-5

value: wild type

value: heart


title: 40_db/db-1

value: db/db


title: HCT116_bruseq_rep5

description:
HCT116 bruseq replicate 5
bru-labeled RNA

value: 0.5 hours

value: 0 hours


title: EARLY SIGMOID-3

value: sigmoid


title: EARLY RECTOSIGMOID-2


title: Col-0_LD_H3K4me3_repeat3

value: Seedlings


title: HeLa_bruseq_rep5

description:
HeLa bruseq replicate 5
bru-labeled RNA

value: Bromouridine (Bru)


title: 44_db/+-4


title: EARLY CECUM-1

value: Cecum

value: right


title: Col-0_LD_H3K4me3_repeat2

value: anti-H3K4me3 (Millipore, 07-473)


title: 43_db/+-3


title: EARLY SIGMOID-2

value: Sigmoid


title: HCT116_bruseq_rep3

description:
HCT116 bruseq replicate 3
bru-labeled RNA


title: 42_db/+-2


title: HCT116_bruseq_rep2

description:
HCT116 bruseq replicate 2
bru-labeled RNA


title: Col-0_LD_H3K4me3_repeat1

value: 11 days

value: long day (16 h light, 8 h dark)


title: atx4/5;jmj24_LD_H3K4me3_repeat2


title: EARLY SIGMOID -1

value: early


title: 41_db/+-1


title: EARLY RECTOSIGMOID-1

value: Rectosigmoid


title: HCT116_bruseq_rep1

description:
HCT116 bruseq replicate 1
bru-labeled RNA


title: atx4/5;jmj24_LD_H3K4me3_repeat1


title: EARLY RECTUM-1

value: Rectum

value: left


title: HLE-Drew-input

status: Public on May 24 2021

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

data_processing:
DATA PROCESSING STEPS TO GENERATE THE *summary.txt FILES:
Raw reads were trimmed using Trimmomatic [11] to remove adaptor sequences, as well as low quality and short reads (2:30:10:26:true SLIDINGWINDOW:4:20 TRAILING:20 LEADING:20 MINLEN:50).
We used seqtk to randomly select 2.5 million trimmed read pairs from each ChIP sample. The random subsets of reads were converted to fasta format using manual bash scripts.
Repeats in the pre-processed ChIP-seq libraries were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation.
We used a custom script to group repeats in each library based on repeat class and family in each of the read pair files, and to calculate the %count and %length (of total repeats) they constituted
Genome_build: Not applicable
Supplementary_files_format_and_content: Text files summarizing the %count and %length of each repeat, repeat family and repeat class among randomly subsampled reads from each ChIP library.
DATA PROCESSING STEPS TO GENERATE THE *contigs.fa FILES:
We used the K-mer Analysis Toolkit (KAT) to determine the optimal k-mer size and predicted genome coverage for each library.
We used RepARK for de novo assembly of reads from each ChIP-seq library.
Genome_build: not applicable
Supplementary_files_format_and_content: Fasta files representing assembled contigs obtained from each ChIP-seq library.

organism: Hoolock leuconedys

source_name: Eastern hoolock gibbon (Hoolock leuconedys)

extract_protocol:
We performed ChIP-seq using the Magnify ChIP kit (Thermo Fisher Scientific) according to manufacturer’s instructions with minor modifications. Briefly, per ChIP assay we fixed 3x105 EBV transformed gibbon LCLs with 1% formaldehyde at room temperature for 10 min. Fixation was quenched with glycine, and cells were washed three times with cold 1XPBS. Cells were lysed for 10 min on ice using the Magnify Lysis buffer, in presence of Proteinase inhibitor cocktail. Lysed cells were then sonicated using the Bioruptor Pico sonicator (Diagenode) for 12 cycles (30 sec on/off) and spun down to remove cell debris. A 1% aliquot was taken from the chromatin as input, and the rest was incubated with the appropriate antibody [CENP-A (ab13939): 2ug, CENP-B (ab25734): 4ug, CENP-C (ab50974): 2ug] at 4℃, with rotation overnight. The next day we incubated samples with Dynabead protein A/G rotating at 4℃ for 2 hours, followed by bead washes, reverse-crosslink and DNA purification according to Magnify ChIP kit protocol.
All sequencing libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) for 1-5ng of starting material and without size selection. The Qubit dsDNA High Sensitivity kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100 were used to QC the libraries.

value: EBV-tranformed lymphocyte cell line


title: HMO-Lionel-input

data_processing:
DATA PROCESSING STEPS TO GENERATE THE *summary.txt FILES:
Raw reads were trimmed using Trimmomatic [11] to remove adaptor sequences, as well as low quality and short reads (2:30:10:26:true SLIDINGWINDOW:4:20 TRAILING:20 LEADING:20 MINLEN:50).
We used seqtk to randomly select 2.5 million trimmed read pairs from each ChIP sample. The random subsets of reads were converted to fasta format using manual bash scripts.
Repeats in the pre-processed ChIP-seq libraries were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation.
We used a custom script to group repeats in each library based on repeat class and family in each of the read pair files, and to calculate the %count and %length (of total repeats) they constituted
Genome_build: Not applicable
Supplementary_files_format_and_content: Text files summarizing the %count and %length of each repeat, repeat family and repeat class among randomly subsampled reads from each ChIP library.
DATA PROCESSING STEPS TO GENERATE THE *contigs.fa FILES:
We used the K-mer Analysis Toolkit (KAT) to determine the optimal k-mer size and predicted genome coverage for each library.
We used RepARK for de novo assembly of reads from each ChIP-seq library.
Genome_build: not applicable
Supplementary_files_format_and_content: Fasta files representing assembled contigs obtained from each ChIP-seq library.
DATA PROCESSING STEPS TO GENERATE THE CENP_BroadPeaks_sortedbyFE.xlsx FILE:
Raw reads were trimmed using Trimmomatic to remove adaptor sequences, as well as low quality and short reads (2:30:10:26:true SLIDINGWINDOW:4:20 TRAILING:20 LEADING:20 MINLEN:50).
Trimmed reads were aligned to the gibbon genome (Nleu3.0) using Bowtie2, with "very sensitive" paired-end settings.
Significant (q<0.01) broad peaks were identified using MACS2,while allowing maximum fof two read duplcates. Peaks were sorted based on fold enrichment.
Genome_build: Nleu3.0
Supplementary_files_format_and_content.xlsx spreadsheet containing the coordinates of all broad peaks across CENP libraries. Peaks are sorted from high fold-enrichment (FE) to low FE.

organism: Hylobates moloch

source_name: silvery gibbon (Hylobates moloch)


title: HLE-ChanThar-input


title: LATE CECUM -2

data_processing:
Early and late onset patient cohorts were compared using a two-tailed unpaired T-test for continuous variables and chi-squared test was used for categorical data. Raw NanoString immune gene expression counts were normalized to the best 10 housekeeping genes. The nSolver Advanced Analysis module was used to derive differential expression signatures according to NanoString recommendations. Adjusted P-values were obtained with a Benjamini-Hochberg post-hoc correction. The genes with an adjusted p value of less than 0.2 in the entire colorectal cancer cohort and at least one location specific cohort (right colon, left colon, or rectum) were designated genes of interest.
nSOLVER default settings and Advanced Analysis Module were used to generate normalized counts.

value: late

value: cecum


title: HMO-Lionel-RNA

data_processing:
DATA PROCESSING STEPS TO GENERATE THE '*_summary.txt' FILES:
Raw reads were trimmed using Trimmomatic to remove adaptor sequences, as well as low quality and short reads (2:30:10:26:true SLIDINGWINDOW:4:20 TRAILING:20 LEADING:20 MINLEN:50).
Trimmed RNA-seq libraries were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation.
We used a custom script to group repeats in each library based on repeat class and family, and to calculate the %count and %length (of total repeats) they constituted.
Supplementary_files_format_and_content: Text files (*_summary.txt) summarizing the %count and %length of each repeat, repeat family and repeat class of the annotated RNA-seq reads.

DATA PROCESSING STEPS TO GENERATE THE '*_mapped.fasta.out_summary.txt' FILES:
The Burrow's Wheeler Aligner bwa-mem algorithm was used to map RNA-seq reads to de novo assembled contigs generated from CENP-A, CENP-B, and CENP-C ChIP-sequencing data.
Reads that successfully aligned to the de novo assemblies were extracted using SAMtools and converted to FASTA format using Bedtools and Seqtk.
Repeats in the subsequent processed FASTA files were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation.
We used a custom script to group repeats in each library based on repeat class and family, and to calculate the %count and %length (of total repeats) they constituted.
Supplementary_files_format_and_content: Text files (*_mapped.fasta.out_summary.txt) summarizing the %count and %length of each repeat, repeat family and repeat class of the annotated RNA-seq reads.

DATA PROCESSING STEPS TO GENERATE THE '*-RM-summary.txt' FILES:
RNA-seq library reads were mapped to the Nleu3.0 genome using the Burrows-Wheeler Aligner bwa-mem algorithm.
Unaligned reads, assumed to contain centromere-derived reads, were separated using SAMtools and converted to FASTA format using Bedtools and Seqtk.
Next, we used the Burrow's Wheeler Aligner bwa-mem algorithm to map the unaligned reads to de novo assembled contigs generated from CENP-A, CENP-B, and CENP-C ChIP-sequencing data.
Reads that successfully aligned to the de novo assemblies, assumed to be enriched for centromere-derived reads, were extracted using SAMtools and converted to FASTA format using Bedtools and Seqtk.
Repeats in the subsequent processed FASTA files were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation.
We used a custom script to group repeats in each library based on repeat class and family, and to calculate the %count and %length (of total repeats) they constituted.
Genome_build: Nleu3.0
Supplementary_files_format_and_content: Text files (*-RM-summary.txt) summarizing the %count and %length of each repeat, repeat family and repeat class of the annotated RNA-seq reads.

extract_protocol:
Total RNA was extracted using the mirVana™ Total RNA Isolation kit (ThermoFisher Scientific) following the manufacturer's instructions on each EBV-transformed lymphocyte cell line.
High-quality RNA was subjected to llumina Tru-seq stranded total RNA library preparation, including Ribo-depletion. The Qubit dsDNA High Sensitivity kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100 were used to QC the libraries.

value: EBV-transformed lymphocyte cell line


title: Py1065sexual-3

city: University Park

first: Scott

middle: E.

last: Lindner

state: Pennsylvania

address: W224 Millennium Science Complex

department: Biochemistry and Molecular Biology

institute: Penn State University

description: NotIg Sexual DEseq2.xlsx

data_processing:
Hisat2: Samples were mapped to the reference genome (P. yoelii 17XNL strain, plasmodb.org v50)
FeatureCounts: Raw read counts for the annotated genes were obtained from the alignments using featureCounts (Version2.0.0)
DESeq2: Reads counts were normalized and differentially expressed genes between WT and NOT1-G knockout samples were obtained separately in different life stages using DESeq2.
Genome_build: All data sets were aligned to the P. yoelii 17XNL strain obtained from PlasmoDB version 50.

organism: Plasmodium yoelii

source_name: Purified Gametocytes

growth_protocol: Plasmodium yoelii (17XNL strain) parasites were used to infect swiss webster mice. Gametocyte samples were produced by treatment of mice with sulfadiazine. Schizont samples with gametocytes depleted were produced by counter-selecting against magnetic parasites (trophozoites, schizonts, gametocytes) and collecting ring stage parasites. These ring stage parasites were allowed to grow and develop to schizonts ex vivo.

extract_protocol:
Parasite pellets were immediately subjected to the QIAgen Rneasy Kit with an additional on-column DNasI digestion step. RNA quality was assessed by Bioanalyzer.
A barcorded library was made with the Illumina TruSeq stranded mRNA library prep kit according to manufacturer's protocol.

treatment_protocol: Parasites were purified by Accudenz discontinuous density gradient, treated with 0.1% w/v saponin (final) to lyse erythrocyte membranes, and then washed in 1xPBS.

value: pynot1-g null

tag: Stage

value: gametocyte


title: HMO-Lionel-CENPC


title: HMO-Lionel-CENPB


title: Py1065sexual-1

description: NotIg Sexual DEseq2.xlsx

tag: strain


title: PyWTsexual-GFP-2

description: NotIg Sexual DEseq2.xlsx

tag: genotype

value: wild type


title: HMO-Lionel-CENPA


title: Py1065asexual-2

description: Not1g vs WT Asexual RNA-seq.xlsx

source_name: Asexual blood stage sans gametocytes

value: schizont


title: Py1065sexual-2

description: NotIg Sexual DEseq2.xlsx


title: PyWTsexual-GFP-3

description: NotIg Sexual DEseq2.xlsx


title: HCT116_bruseq_rep4

description:
HCT116 bruseq replicate 4
bru-labeled RNA

value: 0.5 hours

value: 0 hours

value: Bromouridine (Bru)


title: Py1065asexual-1

description: Not1g vs WT Asexual RNA-seq.xlsx


title: Py1065asexual-3

description: Not1g vs WT Asexual RNA-seq.xlsx


title: PyWTasexual-2

description: Not1g vs WT Asexual RNA-seq.xlsx


title: PyWTasexual-3

description: Not1g vs WT Asexual RNA-seq.xlsx


title: PyWTasexual-1

description: Not1g vs WT Asexual RNA-seq.xlsx


title: SB2_16S

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description:
Adult flies, 3 to 4 days after eclosion.
16S rRNA
16S_OTU_counts.txt

data_processing:
Library strategy: 16S rRNA sequencing
All raw sequencing data were quality controlled by fastq (version 0.18.0). Adapters, reads with more than 10% unknown nucleotide (N) content, and reads with more than half low quality (Q-value <20) bases were removed.
For RNA-seq data:
The sequencing data after quality control was firstly mapped to ribosome RNA (rRNA) database using Bowtie2 (version 2.2.8) to remove rRNA reads and get the clean sequencing data.
The clean sequencing data were mapped to the Drosophila melanogaster reference genome (dm6) using HISAT2 (version 2.2.4) with "-rna-strandness RF" and other default parameters after index building of the transcriptome.
The mapped reads of each sample were assembled and quantified by StringTie (version 1.3.1) in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated.
RNA differential expression analyses among groups were performed by DESeq2 (version 1.30.1), and RNA differential expression analyses between two samples were performed by edgeR (version 3.32.1). The genes/transcripts with a false discovery rate (FDR) < 0.05 and absolute fold change >2 were considered as differentially expressed genes/transcripts and used for downstream analyses.
For 16S-seq clean data:
Paired-end clean reads were merged as raw tags using FLASH (version 1.2.11) with a minimum overlap of 10 bp and a mismatch error rate of 2%.
Noisy sequences of the raw tags were filtered by QIIME (version 1.9.1) pipeline under specific filtering conditions to obtain the high-quality clean tags.
Clean tags were searched against the reference database (version r20110519, http://drive5.com/uchime/uchime_download.html) to perform reference-based chimera checking using UCHIME algorithm. All chimeric tags were removed to obtain the effective tags for downstream analyses.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: Sterile_RNA_counts.txt: Tab-delimited text file includes raw read counts for the RNA-seq data of sterile samples.
Supplementary_files_format_and_content: RNA_counts.txt: Tab-delimited text file includes raw read counts for RNA-seq samples.
Supplementary_files_format_and_content: 16S_OTU_counts.txt: Tab-delimited text file includes raw OTU counts for the 16S rRNA sequencing samples.

organism: insect gut metagenome

source_name: Midgut

growth_protocol: The Drosophila melanogaster w1118 samples were reared on yeast-glucose medium (1L water, 100 g yeast, 100 g glucose, 1.2% agar, and 0.1% potassium sorbate) stocks at 25°C under 12 hours light/12 hours dark cycles in an artificial climate box.

extract_protocol:
Total RNA of RNA-seq samples were homogenized in 1 ml TRIzol (Accurate Biotechnology) and precipitated by isopropyl alcohol. Total DNA of 16S-seq samples were extracted from Drosophila midgut using TIANamp genomic DNA kit (Tiangen, DP304) following the manufacturer's protocol.
After total RNAs of each sample were extracted, the mRNAs enriched by Oligo(dT) beads were fragmented using fragmentation buffer and reverse transcribed into cDNAs with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP, and buffer. The cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen), and were end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeq2500 by Genedenovo Biotechnology Co, Ltd.

treatment_protocol: For treatment group, 100mM sodium butyrate (Sigma) was added to Drosophila medium.

value: Midgut of Drosophila

tag: age

value: Adult

tag: culture environment

value: Bacteria

value: Sodium butyrate feeding

tag: replicate


title: C1_16S

tag: tissue

tag: treatment

value: Untreated


title: C2_16S


title: C3_16S


title: 88529_Xen_Transplant

city: Heidelberg

first: Tobias

last: Gerber

address: Meyerhofstr. 1

department: Developmental Biology

country: Germany

institute: EMBL Heidelberg

data_processing:
Cell Ranger (10x Genomics) was used to align sequencing reads originating from Xenopus samples using default parameters. Reads originating from axolotl libraries were mapped using STARsolo (STAR 2.7.5a, Dobin et al., 2013) with parameters mimicking Cell Ranger’s (10x Genomics) transcript counting strategy.
Cellranger and STARsolo generated transcript count matrix files readable by the R package Seurat.
Seurat (v3.1) was used to normalize and scale raw counts which were used for all analyses.
Genome_build: Xenbase v9.2 (Xenopus laevis) (www.xenbase.org, Karimi et al., 2018)
Genome_build: AmexG (Ambystoma mexicanum) (www.axolotl-omics.org, Nowoshilow and Tanaka, 2020)
Supplementary_files_format_and_content: tab-delimited text files include either cellular barcodes or gene features and matrix files contain raw transcript counts for each gene across all cells

organism: Xenopus laevis

source_name: hindlimb

extract_protocol:
Single-cell suspensions were obtained by chopping the tissues into <1mm cubes and immediately transferring the cubes to a tube of digesting solution (0.13WU/mL Liberase in 0.7x PBS). The enzymatic digestion was placed on a rotating wheel at room temperature for 45 minutes and then the cells were mechanically dissociated by pipetting 10-15 times with a P1000 pipet tip. Enzymatic reactions were stopped by adding high-serum culture medium (HS-AMEM, 125ml MEM, 20ml heat inactivated A1 FCS, 2ml insulin, 2mL glutamine, 2mL Pen/Strep, 50mL ddH2O), and samples were filtered sequentially through 70 μm and 30 μm MACS® SmartStrainers (Miltenyi Biotec, 130-098-458 and 130-098-462). Dissociated cells were pelleted using 300x rcf centrifugation for 5 minutes at room temperature, then washed twice with 0.7x PBS before resuspension in serum-free medium (114.3ml F12:DMEM+Glutmax, 1.5ml Sodium pyruvate, 1.5ml B27 supplement, 1.5ml MEM NEAA, 1.5ml insulin, 1.5ml Pen/Strep, 28.2mL ddH2O) on ice.
Single-cell cDNA and sequencing libraries were generated following the manufacturer recommendations (10X Genomics, 3’ library kit, v3 chemistry). The quality of the cDNA and resulting sequencing libraries were checked by either bioanalyzer or fragment analyzer.

value: limb bud

value: mCherry


title: 88528_Xen_Pool_LBst54_BL0dpa

source_name: upper hindlimb

value: limb bud/intact limb

value: TFP/mCherry


title: 131285_Axo_LBst54

organism: Ambystoma mexicanum

value: GFP


title: 107606_Xen_Pool_BL7_10_14dpa

value: blastema

value: Venus/mCherry/TFP


title: PyWTsexual-GFP-1

description: NotIg Sexual DEseq2.xlsx

value: wild type

value: gametocyte


title: 107606_Xen_LBst51


title: 131284_Axo_LBst52


title: GER047_Axo_BL11dpa

source_name: upper forelimb


title: 107606_Xen_FACS_BL0dpa

source_name: upper hindlimb CT enriched

value: intact limb


title: GER046_Axo_BL11dpa


title: 107606_Xen_FACS_BL3dpa


title: SB1_16S