title: Expt12_293TC9mix_NoGelChimeCLIP_total_rep1

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description:
R_Chi_As17_S29_L00X_R1_001
chimeric eCLIP

data_processing:
Library strategy: eCLIPseq
Demultiplexing (IPs and inputs): Remove 5' UMIs from the sequencing reads and append to the read name for PCR deduplication further downstream. umi_tools extract –-stdin=R_Chi_2_1g.fastq.gz --bc-pattern=NNNNNNNNNN --log=R_Chi_2_1g.processed.log --stdout R_Chi_2_1g.umi.r1.fq.gz
Fastqc round 1: Run and examine by eye to make sure libraries look alright. fastqc R_Chi_2_1g.umi.r1.fq.gz
Cutadapt: Takes output from demultiplexed files. Run to trim off 3’ adapters. cutadapt --match-read-wildcards --times 3 -e 0.1 -O 1 --quality-cutoff 6 -m 18-a AGATCGGAAG -a GATCGGAAGA -a ATCGGAAGAG -a TCGGAAGAGC -a CGGAAGAGCA -a GGAAGAGCAC -a GAAGAGCACA -a AAGAGCACAC -a AGAGCACACG -a GAGCACACGT -a AGCACACGTC -a GCACACGTCT -a CACACGTCTG -a ACACGTCTGA -a CACGTCTGAA -a ACGTCTGAAC -a CGTCTGAACT -a GTCTGAACTC -a TCTGAACTCC -a CTGAACTCCA -a TGAACTCCAG -a GAACTCCAGT -a AACTCCAGTC -a ACTCCAGTCA -o R_Chi_2_1g.umi.r1.fqTr.gz R_Chi_2_1g.umi.r1.fq.gz > R_Chi_2_1g.umi.r1.fqTr.metrics
Trim 3' UMI: Trim the 9 or 10 nucleotide UMI from the 3' end of the read. cutadapt -u -9 -o R_Chi_2_1g.umi.r1.fqTrTr.fq.gz R_Chi_2_1g.umi.r1.fq.gz > R_Chi_2_1g.umi.r1.fqTrTr.metrics
Sort fastq: fastq-sort --id R_Chi_2_1g.umi.r1.fqTrTr.fq > R_Chi_2_1g.umi.r1.fqTrTr.sorted.fq
Convert fasta. seqtk seq -A R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.fq > R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.fa
Collapse: Collapse unique sequences for reverse Bowtie mapping. fasta2collapse.pl R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.fa R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.collapsed.fa
Map miRNA to collapsed (unique) sequences. bowtie -a -e 35 -f -l 8 -n 1 -p 8 R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.bowtie_index mature.hsa.fa R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.collapsed.tsv 2> R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.collapsed.tsv.log
Select the "best match" positive strand alignments with the least number of mismatches. collapse_bowtie_results.py --bowtie_align R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.collapsed.tsv --out_file R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.collapsed.filtered.tsv
Uncollapse: Takes output from "best match" alignments. For each unique sequence that also maps to a miRNA, recover reads from uncollapsed fasta and identify the mappable mRNA component of these chimeric candidates. find_candidate_chimeric_seqs_from_mir_alignments.py --bowtie_align R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.collapsed.filtered.tsv --fa_file R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.fa --metrics_file R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.collapsed.filtered.tsv.metrics --out_file R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.collapsed.filtered.tsv.chimeric_candidates.fa
Trim miRNA: For pcr-enriched samples only, trim the miRNA primer sequence from the 5' end of the read. cutadapt -g file:0096_miRNA_W_S25.miRNA_seq.fa --match-read-wildcards -O 10 -m 18 -e 0.05 -o 0096_miRNA_W_S25.miRNATrim.fastq.gz 0096_miRNA_W_S25.umi.fqTrTr.fq.gz> 0096_miRNA_W_S25.miRNATrim.metrics
STAR rmRep: Takes output from trimming 3' UMIs (non-chimeric eCLIP), or from chimeric candidate sequences (chimeric eCLIP) or from trimming the miRNA primer for miR-486-enriched samples (pcr-enriched chimeric eCLIP). Maps to a repetitive element database which is used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads STAR --runMode alignReads --runThreadN 8 --genomeDir /path/to/repetitive/elements/genome/ --readFilesIn R_Chi_2_1g.adapterTrim.round2.fastq.gz --outSAMunmapped Within --outFilterMultimapNmax 30 --outFilterMultimapScoreRange 1 --outFileNamePrefix R_Chi_2_1g.adapterTrim.round2.rep.bam --outSAMattributes All --readFilesCommand gunzip -c --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --alignEndsType EndToEnd > R_Chi_2_1g.adapterTrim.round2.rep.bam
Samtools view and count_aligned_from_sam: Takes output from STAR rmRep. Counts the number of reads mapping to each repetitive element samtools view R_Chi_2_1g.adapterTrim.round2.rep.bam | count_aligned_from_sam.py > R_Chi_2_1g.adapterTrim.round2.rmRep.metrics
Fastqc round 2: Takes output from STAR rmRep. Runs a second round of fastqc to verify that after read grooming the data still is usable fastqc R_Chi_2_1g.adapterTrim.round2.rep.bamUnmapped.out.mate1
STAR genome mapping: Takes output from STAR rmRep. Maps unique reads to the appropriate genome STAR --runMode alignReads --runThreadN 8 --genomeDir /path/to/genome/ --readFilesIn R_Chi_2_1g.adapterTrim.round2.rep.bamUnmapped.out.mate1 --outSAMunmapped Within --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFileNamePrefix R_Chi_2_1g.adapterTrim.round2.rmRep.bam --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --alignEndsType EndToEnd > R_Chi_2_1g.adapterTrim.round2.rmRep.bam
Sort bam file: Takes output uniquely mapped genome data and sorts and indexes the results samtools sort R_Chi_2_1g.adapterTrim.round2.rmRep.bam -o R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.bam
Samtools index: Takes output from sort bam, makes bam index for use downstream samtools index R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.bam
Umi_tools dedup: Takes output from STAR genome mapping, performs PCR duplicate removal umi_tools dedup --method=unique -I R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.bam --log= R_Chi_2_1g.dedup.log -S R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.rmDup.bam
Sort bam file: Takes output uniquely mapped human genome data and sorts and indexes the results samtools sort R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.rmDup.bam -o R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.rmDup.sorted.bam
Samtools index: Takes output from sort bam, makes bam index for use downstream samtools index R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.rmDup.sorted.bam
Make_bigwig_files.py: Takes input from samtools view. Makes bw files to be uploaded to the genome browser or for other visualization python make_bigwig_files.py --bam R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.rmDup.sorted.bam --genome /path/to/chrom/sizes/file --bw_pos R_Chi_2_1g.CombinedID.merged.r2.norm.pos.bw --bw_neg R_Chi_2_1g.CombinedID.merged.r2.norm.neg.bw
Clipper: Takes results from sort bam. Calls peaks on those files clipper -b R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.rmDup.sorted.bam -s {species} -o R_Chi_2_1g .adapterTrim.round2.rmRep.sorted.rmDup.sorted.peaks.bed
Fix_scores.py: Takes input from clipper: Fixes p-values to be bed compatible python fix_scores.py --bed R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.rmDup.sorted.peaks.bed --out_file R_Chi_2_1g.CombinedID.merged.r2.peaks.fixed.bed
bedToBigBed: Converts bed file to bigBed file for uploading to the genomeBrowser bedToBigBed R_Chi_2_1g.CombinedID.merged.r2.peaks.fixed.bed /path/to/chrom/sizes/file R_Chi_2_1g.CombinedID.merged.r2.peaks.fixed.bb -type=bed6+4
Peak normalization vs paired SMInput datasets is run as a second processing pipeline (Peak_input_normalization_wrapper.py). Input files for the normalization pipeline include .bam and .peak.bed files (generated through the pipeline above), as well as a manifest file pairing eCLIP datasets with their paired SMInput datasets as follows: uID \t RBP \t Cell line \t CLIP_rep1 \t CLIP_rep2 \t INPUT 001 RBP1 HepG2 /full/path/to/{sample_rep1}.adapterTrim.round2.rmRep.sorted.rmDup.sorted.bam /full/path/to/{sample_rep2}.adapterTrim.round2.rmRep.sorted.rmDup.sorted.bam /full/path/to/{sample_input}.adapterTrim.round2.rmRep.sorted.rmDup.sorted.bam
Assembly: UCSC version GRCh38/hg38 (human) and GRCm38/mm10 (mouse)
Supplementary files format and content: *.umi.r1.fqTrTr.fq.sorted.eclip.genome-mappedSoSo.rmDupSo.norm.pos.bw contains normalized RPM densities for non-chimeric eCLIP reads.
Supplementary files format and content: *.umi.r1.fqTrTr.fq.sorted.genome-mappedSoSo.rmDupSo.norm.*.bw correspond to normalized RPM densities for chimeric reads.
Supplementary files format and content: .normed.compressed.sorted.exclude-regions.bed files contain CLIPper peaks from all eCLIP reads normalized to size-matched input.
Supplementary files format and content: pcr_enriched.*.rmDupSo.peakClusters.bed files contain CLIPper peaks from PCR-enriched chimeric reads.

organism:
Homo sapiens
Rattus norvegicus

source_name: mix of HEK293T and C9 cell lysate

extract_protocol:
For each 10cm plate (~15 million cells), cells were washed once with cold phosphate buffered saline, and then UV crosslinked (254 nm, 400 mJ/cm2) on ice. Cells were then spun down, supernatant removed, and washed with cold phosphate buffered saline. Cell pellets were flash frozen on dry ice and stored at -80°C.
Chimeric eCLIP was based off the previously described seCLIP protocol (Van Nostrand et al., 2016 & 2017) with modifications to enhance chimera formation described below. As in eCLIP, lysis was performed in eCLIP lysis buffer, followed by sonication and digestion with RNase I (Ambion). Immunoprecipitation of AGO2-RNA complexes was achieved with a primary mouse monoclonal Ago2 antibody (eIF2C2 (4F9) Santa Cruz, 4°C overnight) using magnetic beads pre-coupled to the secondary antibody (M-280 Sheep Anti-Mouse IgG Dynabeads, Thermo Fisher 11202D). Initial experiments used standard eCLIP conditions (10 ug of antibody and 125 uL of Dynabeads for 20×10^6 cells), but most experiments used decreased antibody and increased bead amounts based on the trend of decreased cross-species chimeras in those conditions (See Sup. Fig. 2X and Sup. Table X). Where indicated, 2% of each immunoprecipitated (IP) sample was saved as input control. For human/rat mixing experiments, cell pellets were lysed, sonicated, and RNase digested separately, and then mixed during addition of antibody and beads prior to overnight incubation. To phosphorylate the cleaved mRNA 5'-ends, beads were washed and treated with T4 polynucleotide kinase (PNK, 3' -phosphatase minus, NEB) and 1 mM ATP. Chimeric ligation was then performed on-bead at room temperature for one hour with T4 RNA Ligase I (NEB) and 1 mM ATP in a 150 µl total volume. As in seCLIP, samples were then dephosphorylated with alkaline phosphatase (FastAP, Thermo Fisher) and T4 PNK (NEB), and an RNA adapter was ligated to the 3′-ends of the mRNA fragments (T4 RNA Ligase, NEB). With-gel chimeric-eCLIP IP and input samples were then denatured with 1X NuPage buffer (Life Technologies) and DTT, run on 4%–12% Bis-Tris protein gels and transferred to nitrocellulose membranes. The region corresponding to bands at the appropriate Ago2 protein size plus 75 kDa was excised and treated with Proteinase K (NEB) to isolate RNA, which was column purified (Zymo). No-gel chimeric eCLIP samples were treated directly with Proteinase K (NEB) to isolate RNA and column purified (Zymo). For both methods, RNA was then reverse transcribed with SuperScript IV Reverse Transcriptase (Invitrogen), 3 mM manganese chloride (to encourage read-through of crosslink sites), and 0.1 M DTT. Following reverse transcription, samples were treated as in seCLIP, including treatment with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides, hydrolysis with sodium hydroxide (to degrade RNA) and addition of hydrogen chloride (to balance pH). A 5’ Illumina DNA adapter (/5Phos/NNNNNNNNNNAGATCGGAAGAGCGTCGTGT/3SpC3) was then ligated to the 3′-end of cDNA fragments with T4 RNA Ligase (NEB), and after bead purification (Dynabeads MyOne Silane, Thermo Fisher), qPCR was performed on an aliquot of each sample to identify the proper number of PCR cycles. The remainder of the sample was PCR amplified with barcoded Illumina compatible primers (Q5, NEB) based on qPCR quantification and size selected using AMPure XP beads (Beckman). Libraries were quantified using Agilent TapeStation and sequenced on the Illumina HiSeq or NovaSeq platform.

value: mix of HEK293T and C9 cell lysate


title: prostate_cancer_primary_64

status: Public on Jul 29 2022

type: RNA

city: Tampa

first: Kosj

last: Yamoah

state: Florida

address: 12902 Magnolia Drive

country: USA

institute: Moffitt Cancer Center

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.

tag: tissue

value: prostate cancer

tag: primary gleason

tag: secondary gleason

tag: pre-treatment psa (ng/ml)

tag: age

tag: race

value: AAM


title: Expt12_293TC9mix_WithGelChimeCLIP_total_rep1

type: SRA

state: CA

description:
R_Chi_As5_S17_L00X_R1_001
chimeric eCLIP

library_source: transcriptomic

tag: cell line


title: prostate_cancer_primary_57


title: prostate_cancer_primary_61

value: NAAM


title: prostate_cancer_primary_56


title: prostate_cancer_primary_52


title: prostate_cancer_primary_58


title: prostate_cancer_primary_54


title: prostate_cancer_primary_53


title: prostate_cancer_primary_51


title: Expt11_293TC9mix_NoGelChimeCLIP_total_rep1

description:
chimericmix_Hx_Rx_S33_L008_R1_001
chimeric eCLIP


title: Expt10_293TC9mix_NoGelChimeCLIP_total_rep2

description:
EV266
chimeric eCLIP


title: Expt10_293TC9mix_NoGelChimeCLIP_total_rep3

description:
EV267
chimeric eCLIP


title: Expt10_293TC9mix_NoGelChimeCLIP_total_rep4

description:
EV268
chimeric eCLIP


title: Expt10_293TC9mix_NoGelChimeCLIP_total_rep1

description:
EV265
chimeric eCLIP


title: prostate_cancer_primary_55


title: prostate_cancer_primary_50


title: Expt10_293TC9mix_WithGelChimeCLIP_total_rep4

description:
EV260
chimeric eCLIP


title: Expt10_293TC9mix_WithGelChimeCLIP_total_rep1

description:
EV257
chimeric eCLIP


title: prostate_cancer_primary_49


title: prostate_cancer_primary_43


title: prostate_cancer_primary_46


title: prostate_cancer_primary_44


title: prostate_cancer_primary_45


title: Expt9_293TC9mix_WithGelChimeCLIP_total_rep4

description:
Aw8
chimeric eCLIP


title: Expt10_293TC9mix_WithGelChimeCLIP_total_rep3

description:
EV259
chimeric eCLIP


title: Expt9_293TC9mix_WithGelChimeCLIP_total_rep2

description:
Aw4
chimeric eCLIP


title: Expt9_293TC9mix_WithGelChimeCLIP_total_rep1

description:
Aw2
chimeric eCLIP


title: Expt9_293TC9mix_NoGelChimeCLIP_total_rep4

description:
Aw24
chimeric eCLIP


title: prostate_cancer_primary_48


title: Expt9_293TC9mix_NoGelChimeCLIP_total_rep2

description:
Aw20
chimeric eCLIP


title: prostate_cancer_primary_47


title: prostate_cancer_primary_42


title: Expt9_293TC9mix_WithGelChimeCLIP_total_rep3

description:
Aw6
chimeric eCLIP


title: Expt9_293TC9mix_NoGelChimeCLIP_total_rep1

description:
Aw18
chimeric eCLIP


title: prostate_cancer_primary_38


title: Expt9_293TC9mix_NoGelChimeCLIP_total_rep3

description:
Aw22
chimeric eCLIP


title: prostate_cancer_primary_40


title: prostate_cancer_primary_41


title: ARP1-LPA-3_S6_L004

city: Houston

first: Pan

last: Su

state: TX

address: 6550 FANNIN STREET

institute: Houston Methodist Research Institute

data_processing:
Firstly, we removed the reads mapped to rRNAs and get rawdata.
Then we filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads.
Then we map those clean reads onto reference genome(mm10).
Finally, we identify gene expression in samples.
Genome_build: mm 10
Supplementary_files_format_and_content: excel with Fragments Per Kilobase of transcript per Million mapped reads (fpkm) for every gene and every sample

source_name: Human MM cell line

extract_protocol:
After 24 hours culture with vehicle (PBS) or LPA (4 mg/mL ), the cells were collected. Total RNA of these collected cells was extracted with the RNeasy Mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard DNB protocols

treatment_protocol: Human ARP1 multiple myeloma cells were cultured with vehicle (PBS) or LPA (4 mg/mL) for 24 hours, then the cells were washed with ice-cold PBS and total RNA was isolated for the gene expression detection.

value: Multiple Myeloma

tag: cell type

value: In vitro cultured tumor cells

tag: treatement

value: cultured with LPA for 24 hours


title: prostate_cancer_primary_35


title: ARP1-LPA-3_S6_L001


title: prostate_cancer_primary_39


title: prostate_cancer_primary_36


title: prostate_cancer_primary_37


title: ARP1-LPA-3_S6_L002


title: prostate_cancer_primary_33


title: ARP1-LPA-2_S5_L004


title: prostate_cancer_primary_30


title: ARP1-LPA-2_S5_L002


title: ARP1-LPA-2_S5_L003


title: ARP1-LPA-1_S4_L004


title: ARP1-LPA-3_S6_L003


title: ARP1-LPA-2_S5_L001


title: prostate_cancer_primary_32


title: prostate_cancer_primary_34


title: prostate_cancer_primary_28


title: ARP1-3_S3_L004

value: cultured with PBS as vehicle control


title: ARP1-LPA-1_S4_L002


title: prostate_cancer_primary_29


title: prostate_cancer_primary_27


title: prostate_cancer_primary_25


title: prostate_cancer_primary_31


title: prostate_cancer_primary_23


title: ARP1-2_S2_L004


title: ARP1-LPA-1_S4_L003


title: prostate_cancer_primary_24


title: Expt10_293TC9mix_WithGelChimeCLIP_total_rep2

description:
EV258
chimeric eCLIP


title: ARP1-LPA-1_S4_L001


title: prostate_cancer_primary_19


title: ARP1-3_S3_L001


title: ARP1-2_S2_L001


title: ARP1-3_S3_L003


title: ARP1-3_S3_L002


title: prostate_cancer_primary_16


title: prostate_cancer_primary_17


title: ARP1-2_S2_L003


title: ARP1-2_S2_L002


title: ARP1-1_S1_L003


title: prostate_cancer_primary_22


title: ARP1-1_S1_L004


title: prostate_cancer_primary_21


title: ARP1-1_S1_L002


title: prostate_cancer_primary_20


title: prostate_cancer_primary_26


title: prostate_cancer_primary_13


title: R2960 (retrospective study)

type: genomic

city: FuZhou

first: Haiwei

last: Wang

state: FuJian

address: Daoshan road 180

country: China

institute: Fujian Maternity and Child Health Hospital

description:
R2960
Single nucleotide polymorphism array

hyb_protocol: DNA was digested, amplified, purified, fragmented, labeled and hybridized according to the standard Affymetrix protocol.

scan_protocol: SNP arrays were scanned with GeneChip Scanner 3000 7G System.

data_processing: Raw CEL data was annotated using GRCh37 (hg19) genome version and was converted into CYCHP form through the ChAS. SNP array was further analyzed using ChAS.

molecule: genomic DNA

source_name: Amniotic fluid

extract_protocol: Fetal DNA samples were extracted from chorionic villi, amniotic fluid or skin tissues using the QIAGEN DNA Mini Kit (Qiagen, Valencia, CA, USA).

tag: maternal age

tag: gender of fetus

value: Male

tag: chromosome

value: X chromosome

tag: chromosomal abnormality

value: Klinefelter syndrome


title: P9074 (retrospective study)

description:
P9074
Single nucleotide polymorphism array

label_protocol: DNA was digested, amplified, purified, fragmented, labeled and hybridized according to the standard Affymetrix protocol.

value: Female

value: Deletions/duplications


title: C2052 (retrospective study)

description:
C2052
Single nucleotide polymorphism array

source_name: Chorionic villi

value: Mosaic Turner syndrome


title: P9189 (retrospective study)

description:
P9189
Single nucleotide polymorphism array


title: ARP1-1_S1_L001


title: prostate_cancer_primary_11


title: P9186 (retrospective study)

description:
P9186
Single nucleotide polymorphism array

value: Y chromosome

value: XYY syndrome


title: prostate_cancer_primary_15


title: prostate_cancer_primary_14


title: prostate_cancer_primary_12


title: P8874 (retrospective study)

description:
P8874
Single nucleotide polymorphism array


title: prostate_cancer_primary_18


title: E3456 (retrospective study)

description:
E3456
Single nucleotide polymorphism array

source_name: Cord blood


title: E1960 (retrospective study)

description:
E1960
Single nucleotide polymorphism array

value: Turner syndrome


title: P86 (retrospective study)

description:
P86
Single nucleotide polymorphism array


title: prostate_cancer_primary_10


title: prostate_cancer_primary_9


title: P5575 (retrospective study)

description:
P5575
Single nucleotide polymorphism array


title: prostate_cancer_primary_8


title: prostate_cancer_primary_7


title: prostate_cancer_primary_6


title: prostate_cancer_primary_4


title: P4637 (retrospective study)

description:
P4637
Single nucleotide polymorphism array


title: prostate_cancer_primary_1


title: prostate_cancer_primary_3


title: P8733 (retrospective study)

description:
P8733
Single nucleotide polymorphism array

value: Mosaic XYY syndrome


title: prostate_cancer_primary_5

value: prostate cancer


title: P8373 (retrospective study)

description:
P8373
Single nucleotide polymorphism array

value: Triple X syndrome


title: P8276 (retrospective study)

description:
P8276
Single nucleotide polymorphism array


title: P8439 (retrospective study)

description:
P8439
Single nucleotide polymorphism array


title: P7977 (retrospective study)

description:
P7977
Single nucleotide polymorphism array


title: C1993 (retrospective study)

description:
C1993
Single nucleotide polymorphism array


title: C1963 (retrospective study)

description:
C1963
Single nucleotide polymorphism array


title: GBM_anti-ANXA2 siRNA, 3

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from primary GBM cells treated with sirna antiANAXA2 for 48h

hyb_protocol: 15 ug were fragmented; following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array (GPL570 Platform). 5.5ug of sscDNA were fragmentated and 5.2 uf were hybridized for 16 hr at 45°C on GeneChip Human Clariom S Array (GPL23159 Platform). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA

source_name: primary GBM cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol starting  from 100ng of Total RNA using the Affymetrix 3' IVT Plus Kit

growth_protocol: Primary GBM cells were cultured DMEM/F12 supplemented with 10% BIT9500 , 20 ng/ml basic Fibroblast Growth Factor (bFGF) and 20 ng/ml Epidermal Growth Factor (EGF) and maintained in an atmosphere of 2% oxygen, 5% carbon dioxide and balanced nitrogen in a H35 hypoxic cabinet.

extract_protocol: RNA was extracted using Trizol

treatment_protocol: Transfection with 200pmol of siNEG and siANXA2 or cells treated with 50nM HHT or matched DMSO concentration.

tag: treatment


title: P7953 (retrospective study)

description:
P7953
Single nucleotide polymorphism array

value: Mosaic Triple X syndrome


title: C1943 (retrospective study)

description:
C1943
Single nucleotide polymorphism array


title: G361-shCYGB RSL3 replicate 1

city: Antwerpen

first: Joey

last: De Backer

state: Antwerpen

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCh38/hg38
Supplementary files format and content: Comma separated values file containing unique hit counts for each sample

growth_protocol: G361 cells were maintained in DMEM medium supplemented with 10% fetal bovine serum and antibiotics in a humidified atmosphere with 5% CO2 at 37 degrees celcius

extract_protocol:
RNA extraction and purification was performed using a PureLink RNA Mini Kit (Invitrogen)
mRNA sequencing via polyA selection

treatment_protocol: G361 cells were treated with 7.5 uM RSL3 and incubated for 6h at 37C before total RNA was collected for RNA sequencing

value: melanoma

tag: genotype

value: CYGB-knockdown

value: RSL3 treatment 6h


title: G361-shCYGB RSL3 replicate 2


title: G361-shCTR RSL3 replicate 3

value: WT


title: G361-shCYGB RSL3 replicate 3


title: G361-shCTR RSL3 replicate 2


title: prostate_cancer_primary_2

value: AAM


title: GBM siNEG, 4

description: Gene expression data from primary GBM cells treated with sirna neg for 48h

value: siNEG


title: G361-shCTR RSL3 replicate 1


title: GBM_anti-ANXA2 siRNA, 1


title: GBM siNEG, 1


title: GBM_anti-ANXA2 siRNA, 2


title: GBM siNEG, 2


title: G361-shCYGB replicate 2

value: Untreated


title: GBM siNEG, 3


title: G361-shCYGB replicate 3


title: GBM_anti-ANXA2 siRNA, 4


title: C1793 (retrospective study)

description:
C1793
Single nucleotide polymorphism array

value: Female

value: X chromosome


title: E3064 (retrospective study)

description:
E3064
Single nucleotide polymorphism array

value: Male

value: Klinefelter syndrome


title: P7965 (retrospective study)

description:
P7965
Single nucleotide polymorphism array

value: Deletions/duplications


title: G361-shCTR UT replicate 2


title: P6052 (retrospective study)

description:
P6052
Single nucleotide polymorphism array

value: Mosaic Klinefelter syndrome


title: P6009 (retrospective study)

description:
P6009
Single nucleotide polymorphism array


title: C1804 (retrospective study)

description:
C1804
Single nucleotide polymorphism array

value: Turner syndrome


title: G361-shCTR UT replicate 3


title: C1784 (retrospective study)

description:
C1784
Single nucleotide polymorphism array


title: G361-shCTR UT replicate 1


title: C1760 (retrospective study)

description:
C1760
Single nucleotide polymorphism array


title: E2969 (retrospective study)

description:
E2969
Single nucleotide polymorphism array

value: Mosaic Turner syndrome


title: C1717 (retrospective study)

description:
C1717
Single nucleotide polymorphism array


title: C1746 (retrospective study)

description:
C1746
Single nucleotide polymorphism array


title: E3049 (retrospective study)

description:
E3049
Single nucleotide polymorphism array

value: Triple X syndrome


title: C1737 (retrospective study)

description:
C1737
Single nucleotide polymorphism array


title: G361-shCYGB replicate 1


title: C1716 (retrospective study)

description:
C1716
Single nucleotide polymorphism array


title: C1697 (retrospective study)

description:
C1697
Single nucleotide polymorphism array


title: C1741 (retrospective study)

description:
C1741
Single nucleotide polymorphism array


title: P5539 (retrospective study)

description:
P5539
Single nucleotide polymorphism array


title: C1678 (retrospective study)

description:
C1678
Single nucleotide polymorphism array


title: P4074 (retrospective study)

description:
P4074
Single nucleotide polymorphism array


title: C1683 (retrospective study)

description:
C1683
Single nucleotide polymorphism array


title: R4877 (retrospective study)

description:
R4877
Single nucleotide polymorphism array


title: P981 (retrospective study)

description:
P981
Single nucleotide polymorphism array

value: Y chromosome

value: XYY syndrome


title: R4933 (retrospective study)

description:
R4933
Single nucleotide polymorphism array


title: P4517 (retrospective study)

description:
P4517
Single nucleotide polymorphism array


title: R4823 (retrospective study)

description:
R4823
Single nucleotide polymorphism array


title: R4760 (retrospective study)

description:
R4760
Single nucleotide polymorphism array


title: R5037 (retrospective study)

description:
R5037
Single nucleotide polymorphism array


title: R4979 (retrospective study)

description:
R4979
Single nucleotide polymorphism array


title: R4616 (retrospective study)

description:
R4616
Single nucleotide polymorphism array


title: R4675 (retrospective study)

description:
R4675
Single nucleotide polymorphism array


title: R4959 (retrospective study)

description:
R4959
Single nucleotide polymorphism array


title: R4956 (retrospective study)

description:
R4956
Single nucleotide polymorphism array


title: R3948 (retrospective study)

description:
R3948
Single nucleotide polymorphism array


title: R3954 (retrospective study)

description:
R3954
Single nucleotide polymorphism array

value: Mosaic Triple X syndrome


title: R5329 (retrospective study)

description:
R5329
Single nucleotide polymorphism array


title: R4794 (retrospective study)

description:
R4794
Single nucleotide polymorphism array


title: R4475 (retrospective study)

description:
R4475
Single nucleotide polymorphism array


title: PureLink Kidney PBS sample #2

city: Seattle

first: Karol

last: Bomsztyk

state: WA

address: 850 Republican St

department: UW Medicine South Lake Union

institute: University of Washington

description: 2mg sample from frozen organ in CryoTray

data_processing:
Illumina RTA version 3.9.25
Index for alignment was built using the 'buildindex'  function from the Bioconductor 'Rsubread' (version 2.3.2) package. Index was assembled from the NCBI Genome Reference Consortium Mouse Build 39 (GRCm39) RefSeq assembly
Reads were aligned and counted in RStudio using the Bioconductor ‘RSubread’ (version 2.8.2) package. Alignment was done with the ‘align’ function on the paired gzFASTQ files creating sorted BAM files. Align commands:  type = "rna", input_format = "gzFASTQ", output_format = "BAM", sortReadsByCoordinates = TRUE, PE_orientation = "fr"
‘featureCounts’ function was used with the NCBI GRCm39 RefSeq Annotation and the commands: isGTFAnnotationFile=TRUE, countMultiMappingReads = FALSE, strandSpecific = 2, isPairedEnd=TRUE.
Assembly: mm39
Supplementary files format and content: tab deliminted text files include raw gene counts and gene annotation for each sample.
Supplementary files format and content: .csv table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Kidney

extract_protocol:
1-2mg samples of frozen tissue were sampled with the CryoCore and put into separate wells of a 96 well plates.  100ul of either PIXUL PK Buffer, PureLink Lysis Buffer, or TRIZOL buffer was added to the wells and then all samples were sonicated in PIXUL sonicator (Matchstick Technologies, Inc Kirkland WA and Active Motif Carlsbad, CA). Samples are processed for 30 seconds in PIXUL with settings: Pulse=50, PRF=1.0 Burst=20.  TRIZOL samples then received additional 100ul of TRIZOL and followed manufacturers protocol for RNA isolation. PureLink samples then follow manufacturers protocol at step 1 of the ‘Binding, Washing, and Elution’ section of ‘Purifying RNA from Animal Tissues’ using on-column DNase digestion and a final elution volume of 20ul. PIXUL PK Buffer samples are immediately incubated (After sonication) in the same PIXUL plate at 95C for 20 minutes, and then put on ice for 5 minutes. Cooled samples are centrifuged in a plate centrifuge for 10 minutes at 4,200g and 4C and then put back on ice. 60ul of clear supernatant (without any floating residue) from each well is carefully transferred via pipette to a new semi-skirted 96 well PCR plate on ice. Isolation of nucleic acids with 1.8x SPRI beads is done as per the Omega Bio-tek protocol (Norcross, GA) with a two-minute final SPRI bead drying time and final elution to 50ul of ultrapure ddH2O and then put samples on ice. Finally, DNase I and RNAse Out are added to the eluted RNA samples and DNase I digestion is done as per the manufacturer’s protocol.
Sequencing libraries were prepared using Zymo-Seq RiboFree Total RNA Library Kit with starting RNA between 205-480ng and libraries amplified between 13-14 cycles of PCR as per manufacturers protocol. Libraries were diluted as per Illumina NextSeq2000 Sequencing System Guide to a final pooled loading concentration of 650pM in resuspension buffer (RSB) plus Tween 20 with a 10% PhiX spike-in and sequenced in Illumina P2 cartridges on NextSeq 2000 that employed a dual-index, paired-end, 75 base read length (PE75).

treatment_protocol: Female 8–12-week-old C57bl/6 mice were injected intraperitoneally (IP) with 5mg/kg lipopolysaccharide (LPS) in 200ml PBS or with 200ml PBS as control. The specific protocol was approved by Institutional Animal Care and Use Committee (IACUC) at the University of Washington. After 12 hours mice were euthanized by isoflurane overdose and confirmatory cervical dislocation. Brains, hearts, kidneys, and livers were harvested, immediately placed on ice, and then frozen in CryoTrays

tag: tissue treatment

value: Phosphate Buffered Saline (PBS) treated

tag: rna isolation buffer

value: PureLink RNA Micro Kit Column

tag: mouse number

tag: gender

value: female

tag: characteristcs

value: age:8-12 week old

tag: strain


title: PureLink Liver LPS sample #1

source_name: Liver

value: Lipopolysaccharide (LPS) treated


title: PureLink Liver LPS sample #2


title: PureLink Liver PBS sample #1


title: R4175 (retrospective study)

description:
R4175
Single nucleotide polymorphism array

value: Female


title: R4523 (retrospective study)

description:
R4523
Single nucleotide polymorphism array

value: X chromosome


title: R4824 (retrospective study)

description:
R4824
Single nucleotide polymorphism array

value: Male


title: PureLink Liver PBS sample #2


title: E2029 (retrospective study)

description:
E2029
Single nucleotide polymorphism array


title: R3704 (retrospective study)

description:
R3704
Single nucleotide polymorphism array


title: R3808 (retrospective study)

description:
R3808
Single nucleotide polymorphism array

value: Klinefelter syndrome


title: R3732 (retrospective study)

description:
R3732
Single nucleotide polymorphism array

value: Deletions/duplications


title: R4919 (retrospective study)

description:
R4919
Single nucleotide polymorphism array


title: PureLink Kidney PBS sample #1


title: R3227 (retrospective study)

description:
R3227
Single nucleotide polymorphism array


title: PureLink Heart PBS sample #2

source_name: Heart


title: R3546 (retrospective study)

description:
R3546
Single nucleotide polymorphism array


title: PureLink Kidney LPS sample #1


title: R3566 (retrospective study)

description:
R3566
Single nucleotide polymorphism array


title: R3421 (retrospective study)

description:
R3421
Single nucleotide polymorphism array


title: R3198 (retrospective study)

description:
R3198
Single nucleotide polymorphism array


title: R3510 (retrospective study)

description:
R3510
Single nucleotide polymorphism array


title: R3394 (retrospective study)

description:
R3394
Single nucleotide polymorphism array


title: R3068 (retrospective study)

description:
R3068
Single nucleotide polymorphism array


title: R2890 (retrospective study)

description:
R2890
Single nucleotide polymorphism array


title: R2969 (retrospective study)

description:
R2969
Single nucleotide polymorphism array


title: PureLink Heart LPS sample #2

description: 2mg sample from frozen organ in CryoTray


title: R2734 (retrospective study)

description:
R2734
Single nucleotide polymorphism array


title: R2742 (retrospective study)

description:
R2742
Single nucleotide polymorphism array


title: R3835 (retrospective study)

description:
R3835
Single nucleotide polymorphism array


title: PureLink Brain PBS sample #2

source_name: Brain


title: R2676 (retrospective study)

description:
R2676
Single nucleotide polymorphism array


title: R2859 (retrospective study)

description:
R2859
Single nucleotide polymorphism array


title: E3732 (retrospective study)

description:
E3732
Single nucleotide polymorphism array


title: R2951 (retrospective study)

description:
R2951
Single nucleotide polymorphism array


title: PureLink Brain LPS sample #2


title: PureLink Kidney LPS sample #2


title: C2564 (retrospective study)

description:
C2564
Single nucleotide polymorphism array


title: PureLink Brain PBS sample #1


title: C2536 (retrospective study)

description:
C2536
Single nucleotide polymorphism array

source_name: Skin tissue


title: C2491 (retrospective study)

description:
C2491
Single nucleotide polymorphism array


title: C2487 (retrospective study)

description:
C2487
Single nucleotide polymorphism array


title: C2486 (retrospective study)

description:
C2486
Single nucleotide polymorphism array


title: PureLink Heart PBS sample #1


title: C2435 (retrospective study)

description:
C2435
Single nucleotide polymorphism array


title: C2416 (retrospective study)

description:
C2416
Single nucleotide polymorphism array


title: R4-500

city: Columbus

first: Dawei

last: Zhou

state: OH

address: 400 W 12th Ave, Wiseman Hall 351C

department: Pathology

institute: The Ohio State University Wexner Medical Center

description: Independent replicate 4, CBL0137, 500 nM

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison. Below are the results of the number of significantly differentially expressed genes for all comparisons provided.
A gene ontology analysis was performed on the statistically significant set of genes by implementing the software GeneSCF v.1.1-p2. The goa_human GO list was used to cluster the set of genes based on their biological processes and determine their statistical significance. A list of genes clustered based on their gene ontologies was generated.
To estimate the expression levels of alternatively spliced transcripts, the splice variant hit counts were extracted from the RNA-seq reads mapped to the genome. Differentially spliced genes were identified for groups with more than one sample by testing for significant differences in read counts on exons (and junctions) of the genes using DEXSeq. For groups with only one sample, the exon hit count tables were provided. The results of the splice variant expression analysis are included in separate reports.
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: peripheral blood

growth_protocol: Cryopreserved NK-92 cells were culture for at least two weeks before performing experiments. Cells were cultured and handled according to ATCC guideline.

extract_protocol:
Total RNA samples from four independent repeats were extracted by using the NucleoSpin RNA isolation kit (MACHEREY-NAGEL) following manufacturer’s manual.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cell number was determined with Trypan Blue staining. Viable cells with the density of 2.5 × 10^5 cells/ml were treated with either DMSO or 500 nM of CBL0137 for 24 h.

value: natural killer cell

tag: morphology

value: lymphoblast

tag: disease

value: malignant Non-Hodgkins Lymphoma


title: CQ10 (retrospective study)

description:
CQ10
Single nucleotide polymorphism array

value: Turner syndrome


title: C2433 (retrospective study)

description:
C2433
Single nucleotide polymorphism array


title: C2414 (retrospective study)

description:
C2414
Single nucleotide polymorphism array


title: C2396 (retrospective study)

description:
C2396
Single nucleotide polymorphism array

value: Mosaic Turner syndrome


title: R4-Ctrl

description: Independent replicate 4, DMSO control


title: C2347 (retrospective study)

description:
C2347
Single nucleotide polymorphism array


title: C2365 (retrospective study)

description:
C2365
Single nucleotide polymorphism array


title: C2339 (retrospective study)

description:
C2339
Single nucleotide polymorphism array


title: C2323 (retrospective study)

description:
C2323
Single nucleotide polymorphism array


title: C2329 (retrospective study)

description:
C2329
Single nucleotide polymorphism array


title: R2-500

description: Independent replicate 2, CBL0137, 500 nM


title: R3-Ctrl

description: Independent replicate 3, DMSO control


title: C2313 (retrospective study)

description:
C2313
Single nucleotide polymorphism array


title: PureLink Brain LPS sample #1

description: 2mg sample from frozen organ in CryoTray


title: C2307 (retrospective study)

description:
C2307
Single nucleotide polymorphism array


title: R2642 (retrospective study)

description:
R2642
Single nucleotide polymorphism array


title: C2285 (retrospective study)

description:
C2285
Single nucleotide polymorphism array


title: 4T1 parental cells

city: Taipei

first: Min-Ying

last: Lin

address: No. 155, Sec. 2, Linong St. Beitou District,

country: Taiwan

institute: National Yang Ming Chao Tung University

description: Gene expression data from 4T1 parental cells

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Mouse Genome 430 2.0 Array.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Mammary carcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 4T1-3R_L cells were isolated from in vivo experiment of liver metastatic cells.

value: 4T1 parental cells


title: R2-Ctrl

description: Independent replicate 2, DMSO control


title: R1-500

description: Independent replicate 1, CBL0137, 500 nM


title: C2280 (retrospective study)

description:
C2280
Single nucleotide polymorphism array


title: 4T1-3R liver metastatic cells

description: Gene expression data from 4T1-3R liver metastatic cells

value: 4T1-3R liver metastatic cells


title: R1-Ctrl

description: Independent replicate 1, DMSO control


title: R2452 (retrospective study)

description:
R2452
Single nucleotide polymorphism array


title: R2237 (retrospective study)

description:
R2237
Single nucleotide polymorphism array

value: Y chromosome

value: XYY syndrome


title: R2563 (retrospective study)

description:
R2563
Single nucleotide polymorphism array


title: NC_3

city: Beijing

first: Yabing Nan

last: Yabing Nan

address: 17 Panjiayuan Nanli, Chaoyang Diistrict

institute: Cancer Hospital Chinese Academy of Medical Sciences

library_source: genomic

data_processing:
Raw data were filtered using Trimmomatic (version 0.36) and deduplicated with FastUniq (version 1.1).
Clean reads were mapped to the reference genome by using bowtie2 software (version 2.2.6) with default parameters. RSeQC software (version 2.6) was used for read distribution analysis, and the insert length was counted using Collect Insert Size Metrics tools from Picard software (version 2.8.2).
Peak calling was conducted using MACS2 software (Version 2.1.1), and peak annotation and distribution analysis were performed using BEDTools (Version 2.25.0).
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: peak text files

source_name: Lung squamous cell carcinoma

extract_protocol:
10 000–50 000 cells were treated with cell lysis buffer, and nuclei were collected by centrifugation for 5 min at 500 g.
Transposition was performed and high-throughput DNA sequencing library was obtained using TruePrep DNA Library Prep Kit V2 for Illumina kit (TD501; Vazyme Biotech). The library products were then enriched, quantified, and sequenced on a Novaseq 6000 sequencer (Illumina) by using the PE150 model.

tag: tissue

value: LUSC

tag: cell line

value: control


title: R3-500

description: Independent replicate 3, CBL0137, 500 nM

tag: cell type


title: C2357 (retrospective study)

description:
C2357
Single nucleotide polymorphism array

tag: maternal age


title: PureLink Heart LPS sample #1

value: Lipopolysaccharide (LPS) treated

value: PureLink RNA Micro Kit Column

value: female

value: age:8-12 week old


title: R2105 (retrospective study)

description:
R2105
Single nucleotide polymorphism array

tag: gender of fetus

value: Male

value: X chromosome

value: Klinefelter syndrome


title: C2257 (retrospective study)

description:
C2257
Single nucleotide polymorphism array

value: Female

tag: chromosome


title: R2065 (retrospective study)

description:
R2065
Single nucleotide polymorphism array

tag: chromosomal abnormality


title: NC_2

tag: treatment


title: NC_1


title: R2174 (retrospective study)

description:
R2174
Single nucleotide polymorphism array

value: Triple X syndrome


title: R1978 (retrospective study)

description:
R1978
Single nucleotide polymorphism array


title: R2019 (retrospective study)

description:
R2019
Single nucleotide polymorphism array


title: R1912 (retrospective study)

description:
R1912
Single nucleotide polymorphism array


title: ASO_3

value: silenced DLGAP1-AS2


title: R1641 (retrospective study)

description:
R1641
Single nucleotide polymorphism array

value: Mosaic Turner syndrome


title: R2450 (retrospective study)

description:
R2450
Single nucleotide polymorphism array

value: Turner syndrome


title: ASO_1


title: R1778 (retrospective study)

description:
R1778
Single nucleotide polymorphism array


title: C2237 (retrospective study)

description:
C2237
Single nucleotide polymorphism array


title: R1711 (retrospective study)

description:
R1711
Single nucleotide polymorphism array


title: C2278 (retrospective study)

description:
C2278
Single nucleotide polymorphism array


title: R1472 (retrospective study)

description:
R1472
Single nucleotide polymorphism array


title: R1469 (retrospective study)

description:
R1469
Single nucleotide polymorphism array


title: R1331 (retrospective study)

description:
R1331
Single nucleotide polymorphism array


title: R1245 (retrospective study)

description:
R1245
Single nucleotide polymorphism array

value: Deletions/duplications


title: ASO_2


title: C2217 (retrospective study)

description:
C2217
Single nucleotide polymorphism array


title: PCR69_KO_2wpi_Fah-sg1

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

data_processing:
Basecalling and demultiplexing were performed using bcl2fastq.
Sequencing adapters were trimmed using BBDuk from bbtools (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/).
Combined samples were demultiplexed using a custom Python script by treating  the first 6 bp of the forward and reverse reads respectively as inline barcodes.
Paired-end reads were merged using FLASH merger (https://ccb.jhu.edu/software/FLASH/) with parameters “-m 10 -r 250 -f 420 -s 40 -p 33” which ensures a minimum overlap of 10 bp.
The reads were analyzed with respect to their expected CRISPR cleavage site(s) with a custom Python script.
For a single cut site, each read is aligned independently to the sequence directly preceding the cut site and to the sequence directly proceeding the cut site using Blastn (Altschul, S.F. et al. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.) with a word size of 28. The extent of net insertions and deletions is calculated accordingly, and the extent of microhomology is inferred based on the overlap of the alignments.
For sequences with two cut sites, a perfect joining of the two cut ends is considered to have zero indels, and sequences containing the excised region (not cleaved) are discarded
Downstream analysis of the tabulated data for each sequence was performed in Excel and R v4.2.1.
Assembly: mm10
Supplementary files format and content: Excel files (.xlsx) are the final outputs of the indel analysis.
Supplementary files format and content: The bigwig files (.bw) are generated by aligning the sequence tags to mm10 by bowtie2 with default parameters and converting the bam files to bigwig using bamCoverage.

extract_protocol:
Genomic DNA was extracted using DNeasy Blood and Tissue Kit (Qiagen).
Genomic regions flanking cut sites of sgRNAs were individually amplified by PCR using Phusion Flash High Fidelity PCR Master Mix (Thermo). Amplicons derived from the same samples were then pooled at equimolar, and then subjected to library preparation using NEBNext® Ultra™ II DNA Library Prep Kit (NEB) using Index primers.
Amplicon sequencing

treatment_protocol: AAV packaged with empty sgRNA (AAV-EV) or sgRNAs were retro-orbitally injected to Rosa-LSL-Cas9-EGFP mice.

value: Liver

value: Hepatocyte

tag: genotype


title: PCR72_KO_3wpi_Fah-sg2


title: PCR68_PTG_6wpi_Lats2-sg2


title: PCR71_KO_3wpi_Fah-sg1


title: PCR67_PTG_6wpi_Lats2-sg1


title: R1329 (retrospective study)

description:
R1329
Single nucleotide polymorphism array


title: R1180 (retrospective study)

description:
R1180
Single nucleotide polymorphism array


title: C2216 (retrospective study)

description:
C2216
Single nucleotide polymorphism array


title: PCR70_KO_2wpi_Fah-sg2


title: R1105 (retrospective study)

description:
R1105
Single nucleotide polymorphism array


title: R1684 (retrospective study)

description:
R1684
Single nucleotide polymorphism array


title: R1044 (retrospective study)

description:
R1044
Single nucleotide polymorphism array

value: Y chromosome


title: PCR65_PTG_6wpi_Lats1-sg1


title: PCR66_PTG_6wpi_Lats1-sg2


title: R789 (retrospective study)

description:
R789
Single nucleotide polymorphism array


title: C2195 (retrospective study)

description:
C2195
Single nucleotide polymorphism array


title: R1059 (retrospective study)

description:
R1059
Single nucleotide polymorphism array


title: C2200 (retrospective study)

description:
C2200
Single nucleotide polymorphism array


title: PCR63_PTG_3wpi_Lats2-sg1


title: R637 (retrospective study)

description:
R637
Single nucleotide polymorphism array


title: R1559 (retrospective study)

description:
R1559
Single nucleotide polymorphism array


title: PCR64_PTG_3wpi_Lats2-sg2


title: R603 (retrospective study)

description:
R603
Single nucleotide polymorphism array


title: PCR62_PTG_3wpi_Lats1-sg2


title: R565 (retrospective study)

description:
R565
Single nucleotide polymorphism array

value: XYY syndrome


title: R517 (retrospective study)

description:
R517
Single nucleotide polymorphism array


title: R439 (retrospective study)

description:
R439
Single nucleotide polymorphism array


title: PCR61_PTG_3wpi_Lats1-sg1


title: E3602 (retrospective study)

description:
E3602
Single nucleotide polymorphism array


title: R487 (retrospective study)

description:
R487
Single nucleotide polymorphism array


title: R188 (retrospective study)

description:
R188
Single nucleotide polymorphism array


title: C2171 (retrospective study)

description:
C2171
Single nucleotide polymorphism array


title: R66 (retrospective study)

description:
R66
Single nucleotide polymorphism array


title: R395 (retrospective study)

description:
R395
Single nucleotide polymorphism array


title: R424 (retrospective study)

description:
R424
Single nucleotide polymorphism array


title: P9935 (retrospective study)

description:
P9935
Single nucleotide polymorphism array


title: PCR57_PTG_2wpi_Lats1-sg1


title: C2116 (retrospective study)

description:
C2116
Single nucleotide polymorphism array


title: PCR56_coinjection_3wpi_Lats2-sg2


title: P9894 (retrospective study)

description:
P9894
Single nucleotide polymorphism array


title: PCR59_PTG_2wpi_Lats2-sg1


title: R314 (retrospective study)

description:
R314
Single nucleotide polymorphism array


title: PCR58_PTG_2wpi_Lats1-sg2


title: P9866 (retrospective study)

description:
P9866
Single nucleotide polymorphism array


title: P9852 (retrospective study)

description:
P9852
Single nucleotide polymorphism array


title: C2122 (retrospective study)

description:
C2122
Single nucleotide polymorphism array


title: PCR55_coinjection_3wpi_Lats2-sg1


title: R144 (retrospective study)

description:
R144
Single nucleotide polymorphism array


title: P9548 (retrospective study)

description:
P9548
Single nucleotide polymorphism array


title: E3548 (retrospective study)

description:
E3548
Single nucleotide polymorphism array


title: PCR54_coinjection_3wpi_Lats1-sg2


title: PCR52_coinjection_2wpi_Lats2-sg2


title: PCR53_coinjection_3wpi_Lats1-sg1


title: C2083 (retrospective study)

description:
C2083
Single nucleotide polymorphism array


title: PCR60_PTG_2wpi_Lats2-sg2


title: P9419 (retrospective study)

description:
P9419
Single nucleotide polymorphism array


title: C2093 (retrospective study)

description:
C2093
Single nucleotide polymorphism array


title: PCR49_coinjection_2wpi_Lats1-sg1


title: PCR50_coinjection_2wpi_Lats1-sg2


title: P9443 (retrospective study)

description:
P9443
Single nucleotide polymorphism array


title: P9749 (retrospective study)

description:
P9749
Single nucleotide polymorphism array


title: C2062 (retrospective study)

description:
C2062
Single nucleotide polymorphism array


title: C2078 (retrospective study)

description:
C2078
Single nucleotide polymorphism array


title: PCR46_KO_2wpi_Tfam-sg2-3


title: P9735 (retrospective study)

description:
P9735
Single nucleotide polymorphism array


title: PCR51_coinjection_2wpi_Lats2-sg1


title: P7813 (retrospective study)

description:
P7813
Single nucleotide polymorphism array


title: P7647 (retrospective study)

description:
P7647
Single nucleotide polymorphism array


title: PCR43_KO_Polg2-sg3


title: P7909 (retrospective study)

description:
P7909
Single nucleotide polymorphism array


title: P8955 (retrospective study)

description:
P8955
Single nucleotide polymorphism array


title: E3299 (retrospective study)

description:
E3299
Single nucleotide polymorphism array


title: P7592 (retrospective study)

description:
P7592
Single nucleotide polymorphism array


title: C1882 (retrospective study)

description:
C1882
Single nucleotide polymorphism array


title: PCR42_KO_Polg2-sg2


title: PCR41_KO_Polg2-sg1


title: PCR40_KO_Polg-sg3


title: P7191 (retrospective study)

description:
P7191
Single nucleotide polymorphism array


title: P7357 (retrospective study)

description:
P7357
Single nucleotide polymorphism array


title: E3215 (retrospective study)

description:
E3215
Single nucleotide polymorphism array


title: P6966 (retrospective study)

description:
P6966
Single nucleotide polymorphism array


title: PCR45_KO_2wpi_Tfam-sg1


title: E3164 (retrospective study)

description:
E3164
Single nucleotide polymorphism array


title: PCR39_KO_Polg-sg2


title: E3275 (retrospective study)

description:
E3275
Single nucleotide polymorphism array


title: PCR37_KO_8wpi_Kif11-sg3


title: P6557 (retrospective study)

description:
P6557
Single nucleotide polymorphism array


title: P6571 (retrospective study)

description:
P6571
Single nucleotide polymorphism array


title: PCR38_KO_Polg-sg1


title: C1830 (retrospective study)

description:
C1830
Single nucleotide polymorphism array


title: P7119 (retrospective study)

description:
P7119
Single nucleotide polymorphism array


title: PCR36_KO_8wpi_Kif11-sg2


title: P6967 (retrospective study)

description:
P6967
Single nucleotide polymorphism array


title: ID:P780 Tis:Ileum Group:LD

city: Little Rock

first: Brian

last: Piccolo

state: AR

address: 15 Children's Way

institute: Arkanssa Children's Nutrition Center

data_processing:
Sequencing was performed using Nextseq 500 (1 X 75 bp). Reads were demultiplexed using Illumina Basespace. Reads were trimmed for adapters and filtered for quality using FASTX  toolkit. Filtered reads were aligned to the rat genome (rn6) using STAR with default settings. Bam files were imported into SeqMonk and gene level read count quantitation was performed.
Supplementary_files_format_and_content: comma delimited matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: comma delimited matrix table with counts per million values for every gene and every sample

organism: Rattus norvegicus

source_name: Ileum Tissue

extract_protocol:
Ileum and colon tissues were removed, flash frozen in liquid nitrogen. Total RNA was isolated using TRI reagent and Rneasy mini columns. Illumina TruSeq mRNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Directional mRNA-Seq

tag: rat

tag: litterdateofbirth

tag: age

tag: Sex

tag: diabetic

value: Y

tag: diabetesonsetage

tag: diabetesdays

tag: bodyweight

tag: group

tag: colonlength

tag: fastingglucose

tag: flowcell


title: ID:K3961 Tis:Ileum Group:LD


title: ID:K3977 Tis:Ileum Group:LD


title: PCR30_KO_2wpi_Kif11-sg2

tag: tissue

tag: cell type


title: ID:K3959 Tis:Ileum Group:LD


title: ID:K3980 Tis:Ileum Group:LD


title: ID:P762 Tis:Ileum Group:LD


title: ID:K3990 Tis:Ileum Group:RD

value: RD


title: PCR31_KO_2wpi_Kif11-sg3


title: PCR29_KO_2wpi_Kif11-sg1


title: PCR28_KO_Hnf4a-sg3


title: ID:K3988 Tis:Ileum Group:RD


title: S52 (retrospective study)

description:
S52
Single nucleotide polymorphism array

tag: maternal age

tag: gender of fetus

tag: chromosome

tag: chromosomal abnormality


title: PCR27_KO_Hnf4a-sg2

tag: genotype

tag: treatment


title: PCR35_KO_8wpi_Kif11-sg1


title: ID:K3987 Tis:Ileum Group:RD

tag: rat

tag: litterdateofbirth

tag: age

tag: Sex


title: ID:K3986 Tis:Ileum Group:RD

tag: diabetic

tag: diabetesonsetage

tag: diabetesdays

tag: bodyweight


title: PCR26_KO_Hnf4a-sg1


title: PCR25_KO_EGFP-sg1_21dpi


title: ID:K3978 Tis:Ileum Group:RD

tag: group

tag: colonlength

tag: fastingglucose

tag: flowcell


title: PCR24_KO_EGFP-sg1_14dpi

tag: tissue

tag: cell type


title: ID:K3989 Tis:Ileum Group:RD


title: ID:K4048 Tis:Ileum Group:ND

value: N

value: PD


title: ID:K4047 Tis:Ileum Group:ND

value: Male


title: PCR22_EV_Fah-sg2


title: PCR23_KO_EGFP-sg1_7dpi


title: PCR20_EV_Lats2-sg2


title: PCR21_EV_Fah-sg1


title: ID:K4038 Tis:Ileum Group:ND


title: PCR19_EV_Lats2-sg1


title: ID:K4037 Tis:Ileum Group:ND


title: ID:K4028 Tis:Ileum Group:ND


title: PCR18_EV_Lats1-sg2


title: ID:P762 Tis:Colon Group:LD

source_name: Proximal Colon Tissue


title: PCR17_EV_Lats1-sg1


title: ID:P780 Tis:Colon Group:LD


title: ID:K3980 Tis:Colon Group:LD


title: ID:K4040 Tis:Ileum Group:ND


title: ID:K3977 Tis:Colon Group:LD


title: PCR16_EV_Tfam-sg2-3


title: B3colorectal cancer tissues

city: Jinan

first: Ya'nan

last: Zhen

state: Shandong

address: No.38 Wuyinshan Road

department: Department of Gastrointestinal Surgery

institute: The Third Affiliated Hospital of Shandong First Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G

data_processing: The data was analyzed using GeneChip GCOS 1.4 software (Affymetrix, USA)

label: total RNA

source_name: colorectal cancer tissues

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Six pairs of fresh tumors and their adjacent (at least 5 cm away) normal tissues were collected from CRC patients underwent surgical resection

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

treatment_protocol: After grinded under the ice,colorectal cancer and normal  tissue were collected for further total RNA extraction

value: colorectal cancer tissues

tag: grade/stage


title: B3normal tissues

source_name: normal tissues

value: normal tissues


title: PCR15_EV_Tfam-sg1

tag: genotype


title: NO3_ΔnarP rep2

city: Wuhan

first: Qiuhong

last: Zhang

address: No. 1, Shizishan Street

institute: Huazhong Agricultural University

data_processing:
Data filtering and quality control were performed by Cutadapt and FastQC to remove reads with an average quality score below Q20.
High-quality clean reads were aligned to the A. pleuropneumoniae 4074 genome (NZ_CP029003.1) by Bowtie2.
The raw expression levels of the genes were counted using HTSeq 0.6.1p2 (union protocol), and the expression levels were normalized using FPKM. Analysis of sequencing RPKM saturation using RSeQC.
Assembly: Actinobacillus pleuropneumoniae serovar 1 str. 4074 (NZ_CP029003.1)/ASM17849v2
Supplementary files format and content: Bam files contain the sequence alignment information of the filtered reads and the reference genome
Supplementary files format and content: Microsoft Excel file  contains reads count and FPKM for all samples

source_name: Bacteria

growth_protocol: Strains WT, ΔnarQ, and ΔnarP were cultured to mid-log phase (4 h) at 37°C in TSB-NAD (10 μg/mL) medium in an anaerobic condition.

extract_protocol:
Total RNA was isolated from strains WT, ΔnarQ, and ΔnarP cultured to mid-log phase supplemented with or without NaNO3 (5 mM) in anaerobic conditions. Total RNA was extracted using Trizol lysis according to the protocol recommended by the manufacturer (Total RNA Extraction Kit, Tianmo Biotech, Beijing, China), with three replicates per condition group.
RNA libraries for RNA-seq were prepared using IlluminaTruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

treatment_protocol: Supplemented with or without NaNO3 (5 mM)

value: Bacteria

tag: strain

value: narP deletion mutant

tag: treatment

value: anaerobic culture, supplemented with 5mM nitrate


title: NO3_ΔnarP rep3

organism: Actinobacillus pleuropneumoniae serovar 1 str. 4074


title: NO3_ΔnarP rep1


title: NO3_ΔnarQ rep3

value: narQ deletion mutant


title: A1colorectal cancer tissues


title: scHH_EIK_Uninfected

city: Durham

first: Benjamin

middle: Huston

last: Schott

state: North Carolina

address: 0048B CARL, Box 3053 DUMC

department: MGM

institute: Duke University

description:
10X Genomics
scHH_combined_NormalizedCountMatrix.xlsx

library_source: transcriptomic single cell

data_processing:
Raw sequencing results were processed using the 10X Genomics CellRanger 4.0 pipeline
For scHH_EIK, since the library was single-indexed, we used 10X Genomics Index-hopping-filter to remove index-hopped reads (https://github.com/10XGenomics/index_hopping_filter)
Assembly: GRCh37
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Excel-formatted pseudo bulk expresion data

source_name: LCL

extract_protocol:
Cell samples were counted and checked for viability on a Guava EasyCyte HT system by 7-AAD staining before they were diluted to 1 million cells/mL with an intended capture of 10,000 cells/sample.
10x Chromium Single Cell 3’ platform version 3.1

value: LCL

value: Mock infection

tag: time


title: scHH_EIK_PR8

value: Infected with A/Puerto Rico/8/1934


title: A1normal tissues


title: B1normal tissues


title: A2colorectal cancer tissues


title: ID:K3959 Tis:Colon Group:LD

tag: rat

tag: litterdateofbirth

tag: age


title: NO3_ΔnarQ rep1


title: PCR13_EV_Polg2-sg3

value: Liver

value: Hepatocyte


title: PCR12_EV_Polg2-sg2


title: NO3_ΔnarQ rep2


title: A3colorectal cancer tissues


title: ID:K3961 Tis:Colon Group:LD

tag: Sex

tag: diabetic

tag: diabetesonsetage


title: B2colorectal cancer tissues


title: A3normal tissues


title: PCR11_EV_Polg2-sg1


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-99b-5p

description:
pcr_enriched.hsa-miR-99b-5p_F
chimeric eCLIP

source_name: HEK293T cells

tag: cell line


title: B1colorectal cancer tissues


title: ID:K3990 Tis:Colon Group:RD

tag: diabetesdays

tag: bodyweight

tag: group

tag: colonlength


title: NO3_WT rep3

tag: tissue

value: wild type


title: NO3_WT rep2


title: B2normal tissues

tag: grade/stage


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-9-5p

description:
pcr_enriched.hsa-miR-9-5p_F
chimeric eCLIP


title: A2normal tissues


title: NO3_WT rep1

tag: genotype


title: ID:K3988 Tis:Colon Group:RD

value: Y

tag: fastingglucose

tag: flowcell


title: PCR10_EV_Polg-sg3

tag: cell type

tag: treatment


title: PCR9_EV_Polg-sg2


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-99a-5p

description:
pcr_enriched.hsa-miR-99a-5p_F
chimeric eCLIP


title: ID:K3989 Tis:Colon Group:RD

tag: rat

tag: litterdateofbirth

value: RD


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-93-5p

description:
pcr_enriched.hsa-miR-93-5p_F
chimeric eCLIP


title: PCR8_EV_Polg-sg1


title: PCR7_EV_Kif11-sg3


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-92b-3p

description:
pcr_enriched.hsa-miR-92b-3p_F
chimeric eCLIP


title: ID:K3987 Tis:Colon Group:RD

tag: age

tag: Sex


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-92a-3p

description:
pcr_enriched.hsa-miR-92a-3p_F
chimeric eCLIP


title: ΔnarP rep3

tag: strain

value: anaerobic culture


title: PCR6_EV_Kif11-sg2


title: ID:K3978 Tis:Colon Group:RD

tag: diabetic

tag: diabetesonsetage


title: ΔnarP rep2


title: ΔnarP rep1


title: PCR5_EV_Kif11-sg1


title: ID:K4048 Tis:Colon Group:ND

value: N

tag: bodyweight

value: PD


title: ΔnarQ rep3


title: PCR4_EV_Hnf4a-sg3


title: ID:K4047 Tis:Colon Group:ND

value: Male

tag: group


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-671-5p

description:
pcr_enriched.hsa-miR-671-5p_F
chimeric eCLIP

tag: cell line


title: ΔnarQ rep2

tag: tissue


title: ΔnarQ rep1


title: PCR3_EV_Hnf4a-sg2


title: ID:K4038 Tis:Colon Group:ND

tag: colonlength


title: WT rep3

tag: genotype


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-652-3p

description:
pcr_enriched.hsa-miR-652-3p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-615-3p

description:
pcr_enriched.hsa-miR-615-3p_F
chimeric eCLIP


title: ID:K4037 Tis:Colon Group:ND

tag: fastingglucose


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-744-5p

description:
pcr_enriched.hsa-miR-744-5p_F
chimeric eCLIP


title: ID:K3986 Tis:Colon Group:RD

tag: diabetesdays

tag: flowcell


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-503-5p

description:
pcr_enriched.hsa-miR-503-5p_F
chimeric eCLIP


title: PCR1_EV_EGFP-sg1

tag: cell type

tag: treatment


title: ID:K4028 Tis:Colon Group:ND

tag: rat

tag: litterdateofbirth


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-7-5p

description:
pcr_enriched.hsa-miR-7-5p_F
chimeric eCLIP


title: WT rep1


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-484

description:
pcr_enriched.hsa-miR-484_F
chimeric eCLIP


title: miRNA-seq sgMtdh-2-2

city: New York

first: Adam

last: Schmitt

state: New York

address: 417 E 68th St

institute: MSKCC

data_processing:
basepair
Sequence reads were trimmed for adaptor sequence/low-quality sequence using basepair QC, Trim
Trimmed sequence reads were mapped to GRCm38/mm10 using basepair STAR
Read count extraction and normalization were performed using basepair
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample

source_name: cerebellum

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using small RNA-Seq Library Prep Kit following manufacturer's protocols.

value: cerebellum

value: stem-like medulloblastoma cells

value: Mtdh knockdown

value: Math1-Cre; SmoM2


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-455-3p

description:
pcr_enriched.hsa-miR-455-3p_F
chimeric eCLIP


title: PCR2_EV_Hnf4a-sg1


title: miRNA-seq sgMtdh-2-1


title: ID:K4040 Tis:Colon Group:ND

tag: age

tag: Sex


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-454-3p

description:
pcr_enriched.hsa-miR-454-3p_F
chimeric eCLIP


title: Rassf531_PBS

city: Xiamen

first: Bo

last: Liu

address: Xiang'an South Rd 4221-120

institute: Xiamen University

data_processing:
Demultiplexing performed with bcl2fastq
Quality control assessed by FastQC
Sequencing reads mapped using STAR
Count data generated using featureCounts
EdgeR used for differential expression analysis
Genome_build: dm6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: whole fly

growth_protocol: Drosophila strains were raised under normal condition.

extract_protocol:
Total RNA from mouse livers was isolated using TRIzol™ Plus RNA Purification Kit (Cat# 12183555, Thermo Fisher) and DNA was removed by treatment with TURBO DNA-free™ Kit (Cat# AM1907, Thermo Fisher).
The quality of samples was determined on the Agilent Tapestation 4200, and only high quality RNA is used (RIN Score 8 or higher). The Qubit® 4.0 Fluorimeter from ThermoFisher was used to determine the concentration prior to staring library preparation. One microgram of total DNAse treated RNA was then prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina. Total RNA was depleted of its rRNA and fragmented before strand specific cDNA synthesis. cDNAs were then a-tailed and indexed adapters were ligated. After adapter ligation, samples were PCR amplified and purified with AmpureXP beads, then validated again on the Agilent Tapestation 4200.

treatment_protocol: Flies were infected by intrathoracic injection (Nanoject III apparatus; Drummond Scientific) of a FHV suspension.

tag: strain

value: dRassf-/-

tag: developmental stage

value: adult

value: 3- to 6-days-old

value: PBS


title: Rassf531_FHV

value: Flock House Virus infection


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-425-5p

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description:
pcr_enriched.hsa-miR-425-5p_F
chimeric eCLIP

data_processing:
Library strategy: eCLIPseq
Demultiplexing (IPs and inputs): Remove 5' UMIs from the sequencing reads and append to the read name for PCR deduplication further downstream. umi_tools extract –-stdin=R_Chi_2_1g.fastq.gz --bc-pattern=NNNNNNNNNN --log=R_Chi_2_1g.processed.log --stdout R_Chi_2_1g.umi.r1.fq.gz
Fastqc round 1: Run and examine by eye to make sure libraries look alright. fastqc R_Chi_2_1g.umi.r1.fq.gz
Cutadapt: Takes output from demultiplexed files. Run to trim off 3’ adapters. cutadapt --match-read-wildcards --times 3 -e 0.1 -O 1 --quality-cutoff 6 -m 18-a AGATCGGAAG -a GATCGGAAGA -a ATCGGAAGAG -a TCGGAAGAGC -a CGGAAGAGCA -a GGAAGAGCAC -a GAAGAGCACA -a AAGAGCACAC -a AGAGCACACG -a GAGCACACGT -a AGCACACGTC -a GCACACGTCT -a CACACGTCTG -a ACACGTCTGA -a CACGTCTGAA -a ACGTCTGAAC -a CGTCTGAACT -a GTCTGAACTC -a TCTGAACTCC -a CTGAACTCCA -a TGAACTCCAG -a GAACTCCAGT -a AACTCCAGTC -a ACTCCAGTCA -o R_Chi_2_1g.umi.r1.fqTr.gz R_Chi_2_1g.umi.r1.fq.gz > R_Chi_2_1g.umi.r1.fqTr.metrics
Trim 3' UMI: Trim the 9 or 10 nucleotide UMI from the 3' end of the read. cutadapt -u -9 -o R_Chi_2_1g.umi.r1.fqTrTr.fq.gz R_Chi_2_1g.umi.r1.fq.gz > R_Chi_2_1g.umi.r1.fqTrTr.metrics
Sort fastq: fastq-sort --id R_Chi_2_1g.umi.r1.fqTrTr.fq > R_Chi_2_1g.umi.r1.fqTrTr.sorted.fq
Convert fasta. seqtk seq -A R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.fq > R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.fa
Collapse: Collapse unique sequences for reverse Bowtie mapping. fasta2collapse.pl R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.fa R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.collapsed.fa
Map miRNA to collapsed (unique) sequences. bowtie -a -e 35 -f -l 8 -n 1 -p 8 R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.bowtie_index mature.hsa.fa R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.collapsed.tsv 2> R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.collapsed.tsv.log
Select the "best match" positive strand alignments with the least number of mismatches. collapse_bowtie_results.py --bowtie_align R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.collapsed.tsv --out_file R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.collapsed.filtered.tsv
Uncollapse: Takes output from "best match" alignments. For each unique sequence that also maps to a miRNA, recover reads from uncollapsed fasta and identify the mappable mRNA component of these chimeric candidates. find_candidate_chimeric_seqs_from_mir_alignments.py --bowtie_align R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.collapsed.filtered.tsv --fa_file R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.fa --metrics_file R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.collapsed.filtered.tsv.metrics --out_file R_Chi_2_1g.umi.r1.fqTrTr.fq.sorted.collapsed.filtered.tsv.chimeric_candidates.fa
Trim miRNA: For pcr-enriched samples only, trim the miRNA primer sequence from the 5' end of the read. cutadapt -g file:0096_miRNA_W_S25.miRNA_seq.fa --match-read-wildcards -O 10 -m 18 -e 0.05 -o 0096_miRNA_W_S25.miRNATrim.fastq.gz 0096_miRNA_W_S25.umi.fqTrTr.fq.gz> 0096_miRNA_W_S25.miRNATrim.metrics
STAR rmRep: Takes output from trimming 3' UMIs (non-chimeric eCLIP), or from chimeric candidate sequences (chimeric eCLIP) or from trimming the miRNA primer for miR-486-enriched samples (pcr-enriched chimeric eCLIP). Maps to a repetitive element database which is used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads STAR --runMode alignReads --runThreadN 8 --genomeDir /path/to/repetitive/elements/genome/ --readFilesIn R_Chi_2_1g.adapterTrim.round2.fastq.gz --outSAMunmapped Within --outFilterMultimapNmax 30 --outFilterMultimapScoreRange 1 --outFileNamePrefix R_Chi_2_1g.adapterTrim.round2.rep.bam --outSAMattributes All --readFilesCommand gunzip -c --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --alignEndsType EndToEnd > R_Chi_2_1g.adapterTrim.round2.rep.bam
Samtools view and count_aligned_from_sam: Takes output from STAR rmRep. Counts the number of reads mapping to each repetitive element samtools view R_Chi_2_1g.adapterTrim.round2.rep.bam | count_aligned_from_sam.py > R_Chi_2_1g.adapterTrim.round2.rmRep.metrics
Fastqc round 2: Takes output from STAR rmRep. Runs a second round of fastqc to verify that after read grooming the data still is usable fastqc R_Chi_2_1g.adapterTrim.round2.rep.bamUnmapped.out.mate1
STAR genome mapping: Takes output from STAR rmRep. Maps unique reads to the appropriate genome STAR --runMode alignReads --runThreadN 8 --genomeDir /path/to/genome/ --readFilesIn R_Chi_2_1g.adapterTrim.round2.rep.bamUnmapped.out.mate1 --outSAMunmapped Within --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFileNamePrefix R_Chi_2_1g.adapterTrim.round2.rmRep.bam --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --alignEndsType EndToEnd > R_Chi_2_1g.adapterTrim.round2.rmRep.bam
Sort bam file: Takes output uniquely mapped genome data and sorts and indexes the results samtools sort R_Chi_2_1g.adapterTrim.round2.rmRep.bam -o R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.bam
Samtools index: Takes output from sort bam, makes bam index for use downstream samtools index R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.bam
Umi_tools dedup: Takes output from STAR genome mapping, performs PCR duplicate removal umi_tools dedup --method=unique -I R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.bam --log= R_Chi_2_1g.dedup.log -S R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.rmDup.bam
Sort bam file: Takes output uniquely mapped human genome data and sorts and indexes the results samtools sort R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.rmDup.bam -o R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.rmDup.sorted.bam
Samtools index: Takes output from sort bam, makes bam index for use downstream samtools index R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.rmDup.sorted.bam
Make_bigwig_files.py: Takes input from samtools view. Makes bw files to be uploaded to the genome browser or for other visualization python make_bigwig_files.py --bam R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.rmDup.sorted.bam --genome /path/to/chrom/sizes/file --bw_pos R_Chi_2_1g.CombinedID.merged.r2.norm.pos.bw --bw_neg R_Chi_2_1g.CombinedID.merged.r2.norm.neg.bw
Clipper: Takes results from sort bam. Calls peaks on those files clipper -b R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.rmDup.sorted.bam -s {species} -o R_Chi_2_1g .adapterTrim.round2.rmRep.sorted.rmDup.sorted.peaks.bed
Fix_scores.py: Takes input from clipper: Fixes p-values to be bed compatible python fix_scores.py --bed R_Chi_2_1g.adapterTrim.round2.rmRep.sorted.rmDup.sorted.peaks.bed --out_file R_Chi_2_1g.CombinedID.merged.r2.peaks.fixed.bed
bedToBigBed: Converts bed file to bigBed file for uploading to the genomeBrowser bedToBigBed R_Chi_2_1g.CombinedID.merged.r2.peaks.fixed.bed /path/to/chrom/sizes/file R_Chi_2_1g.CombinedID.merged.r2.peaks.fixed.bb -type=bed6+4
Peak normalization vs paired SMInput datasets is run as a second processing pipeline (Peak_input_normalization_wrapper.py). Input files for the normalization pipeline include .bam and .peak.bed files (generated through the pipeline above), as well as a manifest file pairing eCLIP datasets with their paired SMInput datasets as follows: uID \t RBP \t Cell line \t CLIP_rep1 \t CLIP_rep2 \t INPUT 001 RBP1 HepG2 /full/path/to/{sample_rep1}.adapterTrim.round2.rmRep.sorted.rmDup.sorted.bam /full/path/to/{sample_rep2}.adapterTrim.round2.rmRep.sorted.rmDup.sorted.bam /full/path/to/{sample_input}.adapterTrim.round2.rmRep.sorted.rmDup.sorted.bam
Assembly: UCSC version GRCh38/hg38 (human) and GRCm38/mm10 (mouse)
Supplementary files format and content: *.umi.r1.fqTrTr.fq.sorted.eclip.genome-mappedSoSo.rmDupSo.norm.pos.bw contains normalized RPM densities for non-chimeric eCLIP reads.
Supplementary files format and content: *.umi.r1.fqTrTr.fq.sorted.genome-mappedSoSo.rmDupSo.norm.*.bw correspond to normalized RPM densities for chimeric reads.
Supplementary files format and content: .normed.compressed.sorted.exclude-regions.bed files contain CLIPper peaks from all eCLIP reads normalized to size-matched input.
Supplementary files format and content: pcr_enriched.*.rmDupSo.peakClusters.bed files contain CLIPper peaks from PCR-enriched chimeric reads.

extract_protocol:
For each 10cm plate (~15 million cells), cells were washed once with cold phosphate buffered saline, and then UV crosslinked (254 nm, 400 mJ/cm2) on ice. Cells were then spun down, supernatant removed, and washed with cold phosphate buffered saline. Cell pellets were flash frozen on dry ice and stored at -80°C.
Chimeric eCLIP was based off the previously described seCLIP protocol (Van Nostrand et al., 2016 & 2017) with modifications to enhance chimera formation described below. As in eCLIP, lysis was performed in eCLIP lysis buffer, followed by sonication and digestion with RNase I (Ambion). Immunoprecipitation of AGO2-RNA complexes was achieved with a primary mouse monoclonal Ago2 antibody (eIF2C2 (4F9) Santa Cruz, 4°C overnight) using magnetic beads pre-coupled to the secondary antibody (M-280 Sheep Anti-Mouse IgG Dynabeads, Thermo Fisher 11202D). Initial experiments used standard eCLIP conditions (10 ug of antibody and 125 uL of Dynabeads for 20×10^6 cells), but most experiments used decreased antibody and increased bead amounts based on the trend of decreased cross-species chimeras in those conditions (See Sup. Fig. 2X and Sup. Table X). Where indicated, 2% of each immunoprecipitated (IP) sample was saved as input control. For human/rat mixing experiments, cell pellets were lysed, sonicated, and RNase digested separately, and then mixed during addition of antibody and beads prior to overnight incubation. To phosphorylate the cleaved mRNA 5'-ends, beads were washed and treated with T4 polynucleotide kinase (PNK, 3' -phosphatase minus, NEB) and 1 mM ATP. Chimeric ligation was then performed on-bead at room temperature for one hour with T4 RNA Ligase I (NEB) and 1 mM ATP in a 150 µl total volume. As in seCLIP, samples were then dephosphorylated with alkaline phosphatase (FastAP, Thermo Fisher) and T4 PNK (NEB), and an RNA adapter was ligated to the 3′-ends of the mRNA fragments (T4 RNA Ligase, NEB). With-gel chimeric-eCLIP IP and input samples were then denatured with 1X NuPage buffer (Life Technologies) and DTT, run on 4%–12% Bis-Tris protein gels and transferred to nitrocellulose membranes. The region corresponding to bands at the appropriate Ago2 protein size plus 75 kDa was excised and treated with Proteinase K (NEB) to isolate RNA, which was column purified (Zymo). No-gel chimeric eCLIP samples were treated directly with Proteinase K (NEB) to isolate RNA and column purified (Zymo). For both methods, RNA was then reverse transcribed with SuperScript IV Reverse Transcriptase (Invitrogen), 3 mM manganese chloride (to encourage read-through of crosslink sites), and 0.1 M DTT. Following reverse transcription, samples were treated as in seCLIP, including treatment with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides, hydrolysis with sodium hydroxide (to degrade RNA) and addition of hydrogen chloride (to balance pH). A 5’ Illumina DNA adapter (/5Phos/NNNNNNNNNNAGATCGGAAGAGCGTCGTGT/3SpC3) was then ligated to the 3′-end of cDNA fragments with T4 RNA Ligase (NEB), and after bead purification (Dynabeads MyOne Silane, Thermo Fisher), qPCR was performed on an aliquot of each sample to identify the proper number of PCR cycles. The remainder of the sample was PCR amplified with barcoded Illumina compatible primers (Q5, NEB) based on qPCR quantification and size selected using AMPure XP beads (Beckman). Libraries were quantified using Agilent TapeStation and sequenced on the Illumina HiSeq or NovaSeq platform.


title: Rassf35_FHV


title: RNA samples from spleens of GF uninfected mice 3

city: Chicago

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

institute: University of Chicago

description: TG-L

data_processing:
RNA-Seq reads were aligned to the Mus musculus reference by Kallisto (v0.44.0; default settings) for transcript quantification.
mRNA expression was quantified at transcript level (transcript per million; TPM) and then summarized into gene level (TPMs summed over all gene transcripts) measurements.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each gene and sample

source_name: spleen

extract_protocol:
RNA extraction was performed using PureLink RNA mini kit (Invitrogen, USA) according to the manufacturer’s instructions.
RNASeq libraries were prepared using Illumina TotalRNA TruSEQ kits (RiboZero 753 depletion).

value: spleen

tag: microbiome

value: SPF

tag: viral status

value: uninfected

value: male

value: BALB/cJ


title: RNA samples from spleens of GF uninfected mice 1

description: TG-J


title: RNA samples from spleens of SPF uninfected mice 1

description: TG-G

value: GF


title: RNA samples from spleens of SPF uninfected mice 3

description: TG-I


title: miRNA-seq sgMtdh-1-1


title: miRNA-seq sgMtdh-1-2


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-424-5p

description:
pcr_enriched.hsa-miR-424-5p_F
chimeric eCLIP

tag: cell line


title: miRNA-seq sgMiat-96-2

tag: tissue

value: Miat knockdown


title: RNA samples from spleens of GF uninfected mice 2

description: TG-K


title: WT rep2

value: Bacteria

value: wild type

value: anaerobic culture


title: RNA samples from spleens of SPF uninfected mice 2

description: TG-H


title: WT_FHV

value: Wild type


title: RNA samples from spleens of SPF virus-infected mice 3

description: TG-F

value: virus-infected


title: miRNA-seq sgMiat-96-1

value: cerebellum

value: stem-like medulloblastoma cells

value: Math1-Cre; SmoM2


title: WT_PBS

value: adult

value: 3- to 6-days-old

value: PBS


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-421

description:
pcr_enriched.hsa-miR-421_F
chimeric eCLIP


title: AS2_6

data_processing:
Clean reads were obtained after the removal of reads containing adapter and ploy-N and having low quality.
HISAT2 was used to align the clean reads to the reference genome.
Differential expression was assessed using DESeq by using read counts as input.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: Text file for counts and RPKM values of each gene

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

value: Human ESCC cell lines

value: overexpressed DLGAP1-AS2


title: RNA samples from spleens of SPF virus-infected mice 1

description: TG-D

value: spleen

value: SPF

value: male


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-378a-3p

description:
pcr_enriched.hsa-miR-378a-3p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-423-3p

description:
pcr_enriched.hsa-miR-423-3p_F
chimeric eCLIP


title: Rassf35_PBS

value: dRassf-/-


title: miRNA-seq sgMiat-6-1

value: Miat knockdown


title: AS2_5


title: AS2_4


title: RNA samples from spleens of GF virus-infected mice 3

description: TG-C

value: GF

value: BALB/cJ


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-423-5p

description:
pcr_enriched.hsa-miR-423-5p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-361-5p

description:
pcr_enriched.hsa-miR-361-5p_F
chimeric eCLIP


title: RNA samples from spleens of GF virus-infected mice 2

description: TG-B


title: miRNA-seq sgGal4-4-4

value: WT


title: AS2_3


title: miRNA-seq sgGal4-4-3


title: AS2_2


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-34a-5p

description:
pcr_enriched.hsa-miR-34a-5p_F
chimeric eCLIP


title: RNA samples from spleens of SPF virus-infected mice 2

description: TG-E

value: virus-infected


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-374b-5p

description:
pcr_enriched.hsa-miR-374b-5p_F
chimeric eCLIP


title: miRNA-seq sgMiat-6-2

value: cerebellum


title: RNA samples from spleens of GF virus-infected mice 1

description: TG-A


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-374a-5p

description:
pcr_enriched.hsa-miR-374a-5p_F
chimeric eCLIP


title: miRNA-seq sgGal4-4-2

value: stem-like medulloblastoma cells


title: miRNA-seq sgGal4-4-1

value: Math1-Cre; SmoM2


title: mouse islets 35mM glucose 3

city: Jerusalem

first: Dana

last: Tzfati

address: Jerusalem

country: Israel

institute: hebrew university

data_processing:
A modified version of the CELSeq2 pipeline was applied. Raw reads were processed with cutadapt, removing from the 3' end low quality bases, adapter sequences and poly-A stretches. Processed reads were aligned to the mouse genome with TopHat. The genome version was GRCm38, with gene annotations from the Ensembl database, supplemented with the spike-in ERCC data. Alignment allowed up to 2 mismatches per read. Raw counts were calculated with htseq-count, ignoring the UMI information.
Raw counts were normalized and differential expression was calculated with DESeq2, after removing genes with a mean normalized expression less than 2. Default parameters were used except for disabling the search for outlier genes (setting cooksCutoff=FALSE). Significance level was taken as padj<0.1 (default).
cutadapt -e 0 -q 10 -a "A\{100\}" -a "A\{15\}N\{100\}" -a GATCGTCGGACT -n 3 -m 28 -o $outFile $infile
Alignment:
tophat -N 2 --read-edit-dist 2 -o $outFile -G GRCm38.p4.pc_ERCC.genes.gtf -p 4 genome_ERCC92 $infile
Counting:
Via the CELSeq2 pipeline, with the following config parameters -
pipe_input_files = *.sam
gff_file = GRCm38.p4.pc_ERCC.genes.gtf
output_dir= mouse_expression/
umi= false
extra_params = -q
count_filename = mouse_transcript_counts.tab
Assembly: GRCm38
Supplementary files format and content: 'mouse_transcript_counts.tab' - raw counts at the barcode level
Supplementary files format and content: 'mouse_gene_counts_combined.tab' raw counts at the sample level
Supplementary files format and content: 'mouse_mix.txt'  -  information about which barcode belongs to which mix and the meaning of the mix numbers in "normal" sample names.
Supplementary files format and content: 'mouse_sample_condition.txt' - condition assignment for each sample.
Supplementary files format and content: DESeq2_normc.txt' -normalized counts.

source_name: pancreatic islets

growth_protocol: mouse islets were cultured in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: RNA concentration was measured using Qubit 3 Fluorometer (ThermoFisher Scientific) and RNA quality was measured using Agilent 2200 TapeStation (Agilent).  RNA sequencing libraries were prepared using the CEL-Seq2 protocol, as published by Hashimshony et al. [Hashimshony et al. Genome Biology (2016) 17:77], with one modification- instead of single-cells as input, 3 ng purified RNA was taken as input for library preparation. The CEL-Seq2 libraries were analyzed for average fragment size using Agilent 2200 TapeStation (Agilent) and concentration was measured using Qubit 3 Fluorometer (Thermo Fisher Scientific). The libraries were sequenced on the Illumina Hiseq 2500 sequencer (Illumina) rapid mode, 15 bases for read 1 and 52 bases for read 2. Demultiplexing was performed in two steps. First, Illumina demultiplexing was performed using bcl2fastq Illumina software with the following parameters: barcode-mismatches =1, minimum-trimmed-read-length = 0, and mask-short-adapter-reads = 0. Second, Cell-seq demultiplexing using the pipeline described in Hashimshony et al. (https://github.com/yanailab/CEL-Seq-pipeline) was executed with the following parameters: min_bc_quality = 15, bc_length = 6, umi_length = 6, and cut_length = 50. RNA measurements, library preparation and sequencing were performed by the Technion Genomics Center, Technion, Israel.

treatment_protocol: islets isolated from 9 mice were indubated with normal RPMI (11.8mM glucose) or with 20mM or 25mM glucose for 3 days, n=3 per condition.

value: pancreatic islets

value: ICR

value: 35mM glucose 3 days


title: mouse islets 35mM glucose 2


title: AS2_1

value: Human ESCC cell lines


title: EV_6

value: control


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-342-3p

description:
pcr_enriched.hsa-miR-342-3p_F
chimeric eCLIP


title: UE7T9 SHC4-OE bio rep 2

city: Tokyo

first: Anri

last: Koyanagi

state: Bunkyo, Yushima

department: Comprehensive pathology

country: Japan

institute: Tokyo medical and dental university

data_processing:
Mapping: Hisat2 v2.0.5.
Remove reads with adapter contamination. Remove reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%). Remove reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read.
Reference genome version:Homo_sapiens_Ensemble_94
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
DEseq2 for differential analysis
Supplementary files format and content: b37
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: UE7T-9 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, FUJIFILM Wako Pure Chemical Co., Osaka, Japan).

extract_protocol:
Total RNA was extracted  by RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol including DNase I treatment.
NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: Targeted genes, SHC4 were overexpressed by infection with lentivirus


title: mouse islets 20mM glucose 3

value: 20mM glucose 3 days


title: UE7T9 SHC4-OE bio rep 1


title: UE7T9 SHC4-OE bio rep 3


title: EV_4


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-33b-5p

description:
pcr_enriched.hsa-miR-33b-5p_F
chimeric eCLIP


title: mouse islets 20mM glucose 2


title: UE7T9 Nontarget bio rep 3


title: EV_5


title: UE7T9 Nontarget bio rep 2


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-32-5p

description:
pcr_enriched.hsa-miR-32-5p_F
chimeric eCLIP


title: EV_3


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-339-5p

description:
pcr_enriched.hsa-miR-339-5p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-331-3p

description:
pcr_enriched.hsa-miR-331-3p_F
chimeric eCLIP


title: EV_1


title: mouse islets 11.8mM glucose control 1

value: 11.8mM glucose control 3 days


title: mouse islets 11.8mM glucose control 3


title: mouse islets 11.8mM glucose control 2


title: mouse islets 20mM glucose 1


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-324-5p

description:
pcr_enriched.hsa-miR-324-5p_F
chimeric eCLIP


title: Kcnc3 MT Ventral CA, Fear conditioning testing, Replicate 4

city: Dallas

first: Joseph

middle: S.

last: Takahashi

address: 5323 Harry Hines Blvd., NA4.118

institute: University of Texas Southwestern Medical Center

data_processing:
Sequence reads were trimmed for low-quality score and N calling. Using cutadapt, the reads are further trimmed for adptor sequences, and poly A signal.
Trimmed reads were mapped with STAR (version 2.5.3a) only considering chromosomes without contigs.
From uniquely mapped reads, reads from genes containing transcripts (≧ 200bp) were considered aligned reads. They are counted as considering thier directions using featureCounts (version 1.6.0).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include count values for each sample

source_name: Hippocampus ventral CA

extract_protocol:
DynabeadTM mRNA DIRECTTM Micro kit (Ambion) according to the manufacturer’s instructions.
TruSeq Stranded mRNA Sample preparation guide (Illumina)

treatment_protocol: One hour after contextual fear conditioning training, tissues were collected.

value: Hippocampus ventral CA

value: Kcnc3 MT

value: Fear conditioning testing

value: male


title: 1_Covid(6) DSP-1012340008710-A08

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

description:
1_Covid(6)
7
QC

data_processing:
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27”
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1“
Assembly: sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx COVID19 Immune Response Atlas v1 Platform file & GeoMx_COVID19_v1.0.pkc file
Supplementary files format and content: Processed data files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Initial: uncollapsed probe counts, QC: collapsed probe counts, Q3: third quartile normalised data

source_name: Lung

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.
other: GeoMx Seq

value: Lung


title: UE7T9 Nontarget bio rep 1

value: WT


title: mouse islets 35mM glucose 1


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-31-5p

description:
pcr_enriched.hsa-miR-31-5p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-320a-3p

description:
pcr_enriched.hsa-miR-320a-3p_F
chimeric eCLIP


title: EV_2


title: 1_Covid(6) DSP-1012340008710-A09

description:
1_Covid(6)
8
QC


title: Kcnc3 MT Ventral CA, Fear conditioning testing, Replicate 3


title: 2_H1N1(4) DSP-1012340008710-E05

description:
2_H1N1(4)
5
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-33a-5p

description:
pcr_enriched.hsa-miR-33a-5p_F
chimeric eCLIP