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

source_name: Hippocampus ventral DG

value: Hippocampus ventral DG


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-30d-5p

status: Public on Jul 29 2022

type: SRA

city: La Jolla

first: Gene

last: Yeo

state: CA

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

country: USA

institute: UCSD

description:
pcr_enriched.hsa-miR-30d-5p_F
chimeric eCLIP

library_source: transcriptomic

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.

molecule: total RNA

organism: Homo sapiens

source_name: HEK293T cells

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.

tag: cell line


title: 1_Covid(6) DSP-1012340008710-C04

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

description:
1_Covid(6)
27
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

tag: tissue

value: Lung


title: Kcnc3 MT Ventral CA, Fear conditioning testing, Replicate 1

city: Dallas

first: Joseph

middle: S.

last: Takahashi

state: TX

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

organism: Mus musculus

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.

tag: strain

value: Hippocampus ventral CA

tag: genotype

value: Kcnc3 MT

tag: treatment

value: Fear conditioning testing

tag: Sex

value: male


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-30e-5p

description:
pcr_enriched.hsa-miR-30e-5p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-B06

description:
1_Covid(6)
17
QC


title: 1_Covid(6) DSP-1012340008710-D03

description:
1_Covid(6)
38
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-30b-5p

description:
pcr_enriched.hsa-miR-30b-5p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-D11

description:
1_Covid(6)
46
QC


title: 1_Covid(6) DSP-1012340008710-A10

description:
1_Covid(6)
9
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-301b-3p

description:
pcr_enriched.hsa-miR-301b-3p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-D07

description:
1_Covid(6)
42
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-30c-5p

description:
pcr_enriched.hsa-miR-30c-5p_F
chimeric eCLIP


title: Kcnc3 MT Ventral DG, Fear conditioning testing, Replicate 2


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-30a-5p

description:
pcr_enriched.hsa-miR-30a-5p_F
chimeric eCLIP


title: 2_H1N1(4) DSP-1012340008710-E01

description:
2_H1N1(4)
1
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-301a-3p

description:
pcr_enriched.hsa-miR-301a-3p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-29c-3p

description:
pcr_enriched.hsa-miR-29c-3p_F
chimeric eCLIP


title: Kcnc3 MT Ventral DG, Fear conditioning testing, Replicate 1


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-29b-3p

description:
pcr_enriched.hsa-miR-29b-3p_F
chimeric eCLIP


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


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

source_name: Hippocampus dorsal CA

value: Hippocampus dorsal CA


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


title: Kcnc3 MT Dorsal CA, Fear conditioning testing, Replicate 2


title: Kcnc3 MT Ventral CA, Fear conditioning testing, Replicate 2


title: 3_Normal(4) DSP-1012340008710-E10

description:
3_Normal(4)
2
QC


title: Kcnc3 MT Dorsal CA, Fear conditioning testing, Replicate 1


title: No Template Control DSP-1012340008710-A01

description:
No Template Control
0
QC


title: 1_Covid(6) DSP-1012340008710-D02

description:
1_Covid(6)
37
QC


title: 1_Covid(6) DSP-1012340008710-B07

description:
1_Covid(6)
18
QC


title: Kcnc3 MT Dorsal DG, Fear conditioning testing, Replicate 4

source_name: Hippocampus dorsal DG

value: Hippocampus dorsal DG


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-26b-5p

description:
pcr_enriched.hsa-miR-26b-5p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-27a-3p

description:
pcr_enriched.hsa-miR-27a-3p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-D12

description:
1_Covid(6)
47
QC


title: Kcnc3 MT Dorsal DG, Fear conditioning testing, Replicate 3


title: 1_Covid(6) DSP-1012340008710-C09

description:
1_Covid(6)
32
QC


title: Kcnc3 MT Dorsal DG, Fear conditioning testing, Replicate 1


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-25-3p

description:
pcr_enriched.hsa-miR-25-3p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-C05

description:
1_Covid(6)
28
QC


title: 1_Covid(6) DSP-1012340008710-C10

description:
1_Covid(6)
33
QC


title: Kcnc3 MT Dorsal DG, Fear conditioning testing, Replicate 2


title: WT Ventral CA, Fear conditioning testing, Replicate 4

value: WT


title: 1_Covid(6) DSP-1012340008710-A05

description:
1_Covid(6)
4
QC


title: 3_Normal(4) DSP-1012340008710-E09

description:
3_Normal(4)
1
QC


title: WT Ventral CA, Fear conditioning testing, Replicate 3


title: WT Ventral CA, Fear conditioning testing, Replicate 2


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-29a-3p

description:
pcr_enriched.hsa-miR-29a-3p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-B02

description:
1_Covid(6)
13
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-218-5p

description:
pcr_enriched.hsa-miR-218-5p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-24-3p

description:
pcr_enriched.hsa-miR-24-3p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-B12

description:
1_Covid(6)
23
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-23a-3p

description:
pcr_enriched.hsa-miR-23a-3p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-221-3p

description:
pcr_enriched.hsa-miR-221-3p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-C01

description:
1_Covid(6)
24
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-210-3p

description:
pcr_enriched.hsa-miR-210-3p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-A04

description:
1_Covid(6)
3
QC


title: WT Ventral DG, Fear conditioning testing, Replicate 2


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-222-3p

description:
pcr_enriched.hsa-miR-222-3p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-20a-5p

description:
pcr_enriched.hsa-miR-20a-5p_F
chimeric eCLIP


title: WT Ventral DG, Fear conditioning testing, Replicate 1


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-19b-3p

description:
pcr_enriched.hsa-miR-19b-3p_F
chimeric eCLIP


title: WT Ventral CA, Fear conditioning testing, Replicate 1


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-21-5p

description:
pcr_enriched.hsa-miR-21-5p_F
chimeric eCLIP


title: WT Dorsal CA, Fear conditioning testing, Replicate 2


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-197-3p

description:
pcr_enriched.hsa-miR-197-3p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-B11

description:
1_Covid(6)
22
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-26a-5p

description:
pcr_enriched.hsa-miR-26a-5p_F
chimeric eCLIP


title: WT Dorsal CA, Fear conditioning testing, Replicate 1


title: 1_Covid(6) DSP-1012340008710-D04

description:
1_Covid(6)
39
QC


title: WT Ventral DG, Fear conditioning testing, Replicate 4


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-19a-3p

description:
pcr_enriched.hsa-miR-19a-3p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-193b-3p

description:
pcr_enriched.hsa-miR-193b-3p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-196a-5p

description:
pcr_enriched.hsa-miR-196a-5p_F
chimeric eCLIP


title: WT Dorsal DG, Fear conditioning testing, Replicate 3


title: 1_Covid(6) DSP-1012340008710-B03

description:
1_Covid(6)
14
QC


title: 1_Covid(6) DSP-1012340008710-C08

description:
1_Covid(6)
31
QC


title: 1_Covid(6) DSP-1012340008710-C06

description:
1_Covid(6)
29
QC


title: WT Ventral DG, Fear conditioning testing, Replicate 3


title: 1_Covid(6) DSP-1012340008710-D05

description:
1_Covid(6)
40
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-191-5p

description:
pcr_enriched.hsa-miR-191-5p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-B04

description:
1_Covid(6)
15
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-196b-5p

description:
pcr_enriched.hsa-miR-196b-5p_F
chimeric eCLIP


title: WT Dorsal DG, Fear conditioning testing, Replicate 4


title: WT Dorsal CA, Fear conditioning testing, Replicate 4


title: 1_Covid(6) DSP-1012340008710-B08

description:
1_Covid(6)
19
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-18a-5p

description:
pcr_enriched.hsa-miR-18a-5p_F
chimeric eCLIP


title: WT Dorsal CA, Fear conditioning testing, Replicate 3


title: WT Dorsal DG, Fear conditioning testing, Replicate 2


title: Kcnc3 MT Ventral CA, Control, Replicate 4

value: Control


title: 1_Covid(6) DSP-1012340008710-C12

description:
1_Covid(6)
35
QC


title: 2_H1N1(4) DSP-1012340008710-E04

description:
2_H1N1(4)
4
QC


title: 1_Covid(6) DSP-1012340008710-C02

description:
1_Covid(6)
25
QC


title: 1_Covid(6) DSP-1012340008710-D01

description:
1_Covid(6)
36
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-186-5p

description:
pcr_enriched.hsa-miR-186-5p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-181b-5p

description:
pcr_enriched.hsa-miR-181b-5p_F
chimeric eCLIP


title: Kcnc3 MT Ventral CA, Control, Replicate 3


title: Kcnc3 MT Ventral CA, Control, Replicate 2


title: 2_H1N1(4) DSP-1012340008710-E03

description:
2_H1N1(4)
3
QC


title: Kcnc3 MT Ventral CA, Control, Replicate 1


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-181a-5p

description:
pcr_enriched.hsa-miR-181a-5p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-C11

description:
1_Covid(6)
34
QC


title: WT Dorsal DG, Fear conditioning testing, Replicate 1


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-17-5p

description:
pcr_enriched.hsa-miR-17-5p_F
chimeric eCLIP


title: Kcnc3 MT Ventral DG, Control, Replicate 4


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-18a-3p

description:
pcr_enriched.hsa-miR-18a-3p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-D10

description:
1_Covid(6)
45
QC


title: 1_Covid(6) DSP-1012340008710-B05

description:
1_Covid(6)
16
QC


title: 1_Covid(6) DSP-1012340008710-D06

description:
1_Covid(6)
41
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-17-3p

description:
pcr_enriched.hsa-miR-17-3p_F
chimeric eCLIP


title: Kcnc3 MT Dorsal CA, Control, Replicate 4


title: Kcnc3 MT Ventral DG, Control, Replicate 3


title: Kcnc3 MT Ventral DG, Control, Replicate 2


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-15b-5p

description:
pcr_enriched.hsa-miR-15b-5p_F
chimeric eCLIP


title: Kcnc3 MT Ventral DG, Control, Replicate 1


title: 2_H1N1(4) DSP-1012340008710-E02

description:
2_H1N1(4)
2
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-15a-5p

description:
pcr_enriched.hsa-miR-15a-5p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-A07

description:
1_Covid(6)
6
QC


title: Kcnc3 MT Dorsal CA, Control, Replicate 3


title: 3_Normal(4) DSP-1012340008710-E12

description:
3_Normal(4)
4
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-151b

description:
pcr_enriched.hsa-miR-151b_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-148b-3p

description:
pcr_enriched.hsa-miR-148b-3p_F
chimeric eCLIP


title: Kcnc3 MT Dorsal CA, Control, Replicate 2


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-148a-3p

description:
pcr_enriched.hsa-miR-148a-3p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-16-5p

description:
pcr_enriched.hsa-miR-16-5p_F
chimeric eCLIP


title: Kcnc3 MT Dorsal DG, Control, Replicate 4


title: 3_Normal(4) DSP-1012340008710-F01

description:
3_Normal(4)
5
QC


title: 1_Covid(6) DSP-1012340008710-B09

description:
1_Covid(6)
20
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-130b-3p

description:
pcr_enriched.hsa-miR-130b-3p_F
chimeric eCLIP


title: Kcnc3 MT Dorsal DG, Control, Replicate 3


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-1307-5p

description:
pcr_enriched.hsa-miR-1307-5p_F
chimeric eCLIP


title: Kcnc3 MT Dorsal DG, Control, Replicate 2


title: 1_Covid(6) DSP-1012340008710-C03

description:
1_Covid(6)
26
QC


title: Kcnc3 MT Dorsal DG, Control, Replicate 1


title: WT Ventral CA, Control, Replicate 4


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-128-3p

description:
pcr_enriched.hsa-miR-128-3p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-1296-5p

description:
pcr_enriched.hsa-miR-1296-5p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-125b-5p

description:
pcr_enriched.hsa-miR-125b-5p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-C07

description:
1_Covid(6)
30
QC


title: WT Ventral CA, Control, Replicate 3


title: Kcnc3 MT Dorsal CA, Control, Replicate 1


title: 2_H1N1(4) DSP-1012340008710-E07

description:
2_H1N1(4)
7
QC


title: WT Ventral CA, Control, Replicate 2


title: 1_Covid(6) DSP-1012340008710-D08

description:
1_Covid(6)
43
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-125a-5p

description:
pcr_enriched.hsa-miR-125a-5p_F
chimeric eCLIP


title: c57BL-6N HTT Δ12 line KO/+ female3 striatum

city: Leiden

first: Pontus

last: Klein

address: Zernikedreef 9

country: Netherlands

institute: ProQR Therapeutics

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline  RTA3.4.4 and Bcl2fastq v2.20
Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic v0.30. Presumed  adapter sequences were removed from the read when the bases matched a sequence in the adapter  sequence set (TruSeq adapters) with 2 or less mismatches and an alignment score of at least 12.
The Mus_musculus.GRCm38.p4.dna.primary_assembly reference was used for alignment. The reads were mapped to the reference sequence using a short read aligner based on Burrows—Wheeler Transform (Tophat v2.0.14) with default settings. The alignment files (BAM files sorted on coordinates and indexed with the samtools v1.3 package)
Read counts per transcript was determined with HTSeq v0.6.1p1
RPKM/FPKM (reads/fragments per kilobase of exon per million reads mapped) values were calculated
Assembly: Mus_musculus.GRCm38.p4
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: striatum

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA was processed with the NEBNext Ultra II Directional RNA Library Prep Kit (NEB) and rRNA depletion kit (NEB #6310)
After cDNA synthesis, clustering and DNA sequencing was perforemed using the NovaSeq6000 (Illumina)

value: striatum

value: HTT KO line KO/+

value: female

tag: time

value: 3 months


title: c57BL-6N HTT KO line KO/+ female2 striatum


title: WT Ventral CA, Control, Replicate 1


title: 3_Normal(4) DSP-1012340008710-E11

description:
3_Normal(4)
3
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-10b-5p

description:
pcr_enriched.hsa-miR-10b-5p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-A11

description:
1_Covid(6)
10
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-10a-5p

description:
pcr_enriched.hsa-miR-10a-5p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-1307-3p

description:
pcr_enriched.hsa-miR-1307-3p_F
chimeric eCLIP


title: c57BL-6N HTT KO line KO/+ female2 cortex

source_name: cortex

value: cortex


title: 2_H1N1(4) DSP-1012340008710-E06

description:
2_H1N1(4)
6
QC


title: 1_Covid(6) DSP-1012340008710-A06

description:
1_Covid(6)
5
QC


title: 1_Covid(6) DSP-1012340008710-D09

description:
1_Covid(6)
44
QC


title: c57BL-6N HTT KO line KO/+ female1 striatum


title: c57BL-6N HTT KO line KO/+ female1 cortex


title: c57BL-6N HTT KO line KO/+ female3 cortex


title: c57BL-6N HTT KO line KO/+ male3 striatum


title: WT Ventral DG, Control, Replicate 4


title: 2_H1N1(4) DSP-1012340008710-E08

description:
2_H1N1(4)
8
QC


title: WT Ventral DG, Control, Replicate 1


title: WT Ventral DG, Control, Replicate 3


title: 1_Covid(6) DSP-1012340008710-B01

description:
1_Covid(6)
12
QC


title: WT Dorsal CA, Control, Replicate 4


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-101-3p

description:
pcr_enriched.hsa-miR-101-3p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-B10

description:
1_Covid(6)
21
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-106b-5p

description:
pcr_enriched.hsa-miR-106b-5p_F
chimeric eCLIP


title: WT Ventral DG, Control, Replicate 2


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-1180-3p

description:
pcr_enriched.hsa-miR-1180-3p_F
chimeric eCLIP


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-106b-3p

description:
pcr_enriched.hsa-miR-106b-3p_F
chimeric eCLIP


title: 1_Covid(6) DSP-1012340008710-A12

description:
1_Covid(6)
11
QC


title: 1_Covid(6) DSP-1012340008710-A02

description:
1_Covid(6)
1
QC


title: c57BL-6N HTT KO line KO/+ male3 cortex


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-miR-103a-3p

description:
pcr_enriched.hsa-miR-103a-3p_F
chimeric eCLIP


title: WT Dorsal CA, Control, Replicate 1


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-let-7g-5p

description:
pcr_enriched.hsa-let-7g-5p_F
chimeric eCLIP


title: WT Dorsal CA, Control, Replicate 3


title: WT Dorsal CA, Control, Replicate 2


title: 1_Covid(6) DSP-1012340008710-A03

description:
1_Covid(6)
2
QC


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-let-7f-5p

description:
pcr_enriched.hsa-let-7f-5p_F
chimeric eCLIP


title: c57BL-6N HTT KO line KO/+ male1 striatum


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-let-7e-5p

description:
pcr_enriched.hsa-let-7e-5p_F
chimeric eCLIP


title: c57BL-6N HTT KO line KO/+ male2 striatum


title: Expt4_293T_PCREnrichedNoGelChimeCLIP_hsa-let-7a-5p

description:
pcr_enriched.hsa-let-7a-5p_F
chimeric eCLIP


title: scHH_LGC_Uninfected_1

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
Uninfected_barcodes.tsv.gz
Uninfected_features.tsv.gz
Uninfected_matrix.mtx.gz
Uninfected_SeuratMetadata.csv

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

tag: cell type

value: LCL

value: mock infection


title: scHH_LGC_Uninfected_2


title: c57BL-6N HTT KO line +/+ female3 striatum

value: HTT KO line +/+


title: c57BL-6N HTT KO line KO/+ male2 cortex


title: WT Dorsal DG, Control, Replicate 4


title: WT Dorsal DG, Control, Replicate 3


title: scHH_LGC_PR8_3

description:
10X Genomics
scHH_combined_NormalizedCountMatrix.xlsx
PR8_barcodes.tsv.gz
PR8_features.tsv.gz
PR8_matrix.mtx.gz
PR8_SeuratMetadata.csv

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


title: Expt4_293T_WithGelChimeCLIP_rep12lessthan175nt_rep1

description:
4kB_gel_bottom
chimeric eCLIP

tag: sminput


title: WT Dorsal DG, Control, Replicate 2


title: Expt4_293T_NoGelChimeCLIP_rep12lessthan175nt_rep1

description:
4kA_direct_bottom
chimeric eCLIP


title: scHH_LGC_PR8_1


title: c57BL-6N HTT KO line +/+ female2 striatum


title: scHH_LGC_PR8_2


title: WT Dorsal DG, Control, Replicate 1


title: Expt4_293T_WithGelChimeCLIP_total_rep1

description:
4kB_gel
chimeric eCLIP


title: c57BL-6N HTT KO line +/+ female3 cortex


title: c57BL-6N HTT KO line +/+ female1 striatum


title: c57BL-6N HTT KO line +/+ female1 cortex


title: Expt12_293T_NoGelChimeCLIP_total_rep1

description:
R_Chi_As14_S26_L00X_R1_001
chimeric eCLIP


title: Expt12_293T_WithGelChimeCLIP_total_rep1

description:
R_Chi_As2_S14_L00X_R1_001
chimeric eCLIP


title: S833_M_S11

city: Chicago

first: Richard

middle: Thomas

last: D'Aquila

state: IL

address: 303 E Superior St Lurie Research 9-220

department: Medicine (Infectious Diseases)

institute: Northwestern University Feinberg School of Medicine

data_processing:
lllumina HiSeq 4000 NGS Sequencer was used to sequence the libraries with the production of single-end, 50 bp reads
The quality of DNA reads, in FASTQ format, was evaluated using FastQC
Adapters were trimmed and aligned to the human genome using STAR
Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for hg38 obtained from Ensembl (http://useast.ensembl.org/index.html)
Normalization and differential expression were calculated using DESeq2 that employs the Wald test. The cutoff for determining significantly differentially expressed genes was an FDR-adjusted p-value less than 0.05 using the Benjamini-Hochberg method
Genome_build: hg38
Supplementary_files_format_and_content: M_vs_L_Differential_Expression: tab-delimited text document; matrix with differential expression data and normalized read counts for all unstimulated (M) and LPS-stimulated (L) samples
Supplementary_files_format_and_content: M_vs_AL_Differential_Expression: tab-delimited text document; matrix with differential expression data and normalized read counts for all unstimulated (M) and mTORi-pretreated, LPS-stimulated (AL) samples
Supplementary_files_format_and_content: L_vs_AL_Differential_Expression: tab-delimited text document; matrix with differential expression data and normalized read counts for all LPS-stimulated (L) and mTORi-pretreated, LPS-stimulated (AL) samples

source_name: Primary monocyte

growth_protocol: Primary human monocytes were cultured in PTFE-coated well-inserts to prevent contact-induced activation in RPMI with 10% define FBS and pen/strep.

extract_protocol:
RNA was extracted using a Qiagen RNeasy kit according to manufacturer instructions.
Illumina TruSeq Stranded mRNA Library Preparation Kit was used to prepare sequencing libraries from 200 ng of high-quality RNA samples (RIN>7). The kit was used without modification.

treatment_protocol: Using a within-donor design, monocytes from each donor were treated ex vivo in three groups: DMSO-pretreated/unstimulated (M), DMSO-pretreated/stimulated (L), and AZD2014-pretreated/stimulated (AL). AZD2014 was added at 5μM and monocytes were stimulated with LPS isolated from E. coli O111:B4 at 1ng/mL.

value: Peripheral blood monocyte

tag: pretreatment

value: DMSO (vehicle)

tag: stimulation

value: PBS (mock)


title: c57BL-6N HTT KO line KO/+ male1 cortex

value: male


title: Expt4_293T_NoGelChimeCLIP_total_rep1

description:
4kA_direct
chimeric eCLIP


title: FGSC_Rep1 [Hi-C]

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

description: 3. allValidPairs.gz

library_source: genomic

data_processing:
For Hi-C pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16). Then HiCPro (version 2.7) (Servant et al., 2015) was used to map, process and iteratively corrected normalization. Briefly, reads were independently aligned to the mouse reference genome (mm9) with the bowtie2 algorithm (Langmead and Salzberg, 2012). We discarded the uncut DNA reads, re-ligation reads, continuous reads and PCR artifacts. Unique mapped reads (MAPQ>10) were used to build the contact matrix.
Compartment analysis are used R package (HiTC) (Servant et al., 2012) pca.hic function to generate the PC1 eigenvectors using 400kb normalized matrices with following options: (normPerExpected=TRUE, npc=1)
TAD calling is done using Direction Index  method as previously described (Dixon et al., 2012)
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files

molecule: genomic DNA

source_name: Female germline stem cell

growth_protocol: SSCs were cultured on mitotically inactivated STO mouse embryonic fibroblast feeder cells (5 × 104 cells/cm2; ATCC) with culture medium.FGSCs and iGSCs were cultured on mitotically inactivated STO (SIM mouse embryo-derived thioguanine- and ouabain-resistant) cell feeders in minimum essential medium alpha (MEMa; Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Life Technologies), 10 ng/mL mouse leukemia inhibitory factor (Santa Cruz Biotechnology), 20 ng/mL mouse epidermal growth factor (EGF) (PeproTech), 10 ng/mL basic fibroblast growth factor (bFGF) (PeproTech), 10 ng/mL mouse glial cell line-derived neurotrophic factor (GDNF) (PeproTech), 1mM non-essential amino acids (NEAA) (Life Technologies), 2 mM L-glutamine (Sigma), 30 mg/mL pyruvate (Amresco) and 50 mM -mercaptoethanol (Biotech).The primary NSCs was seeded onto poly-l-ornithine (Sigma-Aldrich) and laminin (Invitrogen) coated dishes, cultured as monocultures. Neural basal medium with 20ng/ml EGF (PeproTech), 20ng/ml bFGF(PeproTech), 20ng/ml Hepairn (Sigma-Aldrich) and 2% B27 (Invitrogen) was used as NSC proliferation medium. STOs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) with high-glucose (Life Technologies), 10% FBS (Life Technologies), 1% non-essential amino acids (Life Technologies), 2mM glutamine (Sigma) and Penicillin (100U/ml, Sigma)/streptomycin (0.1mg/ml, Sigma).

extract_protocol:
HiC and library preparation was carried out using the in-situ method as described previously (Rao et. al., 2014)
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: passages

tag: restriction enzyme

value: Mbol


title: FGSC_Rep2 [Hi-C]

description: 3. allValidPairs.gz


title: c57BL-6N HTT KO line +/+ male3 striatum


title: S833_L_S12

value: LPS


title: iGSC_Rep2 [Hi-C]

description: 2. allValidPairs.gz

source_name: Induction of germline stem cell


title: c57BL-6N HTT KO line +/+ male2 striatum


title: iGSC_Rep1 [Hi-C]

description: 2. allValidPairs.gz


title: SSC_Rep2 [Hi-C]

description: 1. allValidPairs.gz

source_name: Spermatogonial stem cell


title: S833_AL_S13

value: mTORi


title: S830_M_S8


title: Expt9_293T_input_total_rep4

description:
Aw38
chimeric eCLIP


title: Expt11_293T_NoGelChimeCLIP_total_rep1

description:
chimericmix_hx
chimeric eCLIP


title: c57BL-6N HTT KO line +/+ female2 cortex


title: S830_L_S9


title: S830_AL_S10


title: c57BL-6N HTT KO line +/+ male3 cortex


title: BCF-Input

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

data_processing:
Illumina HiSeq2500 single end sequencing
Sequenced reads were aligned to the Mus musculus genome assembly mm9 using the bowtie software suite
Bigwig files were generated for merged duplicates with bamCoverage from deepTools suitewith folowing flags: -bs 20 --normalizeTo1x 2150570000 --ignoreForNormalization chrM --smoothLength 40 --ignoreDuplicates
For merged duplicates peak were called with Epic peak caller IgG was use as a control
Genome_build: mm9

source_name: female ES cells

growth_protocol: ES cells were cultured on inactivated MEFs in serum/LIF.

extract_protocol:
Cross-linked cells were sonicated, chromatin was purified and histone-DNA complexes were isolated by immunoprecipitation with the corresponding antibodies.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: passage

value: C57BL/6 x CAST/EiJ F16

value: ES cells


title: c57BL-6N HTT KO line +/+ male2 cortex


title: Expt9_293T_input_total_rep3

description:
Aw37
chimeric eCLIP


title: BCM-Input

source_name: male ES cells

value: C57BL/6 x CAST/EiJ F15


title: SSC_Rep1 [Hi-C]

description: 1. allValidPairs.gz


title: Expt10_293T_NoGelChimeCLIP_total_rep1

description:
EV269
chimeric eCLIP


title: S829_L_S18


title: Expt9_293T_input_total_rep2

description:
Aw34
chimeric eCLIP


title: S829_AL_S19


title: c57BL-6N HTT Δ12 line  Δ12/Δ12 female3 striatum

value: striatum

value: HTT delta12 line delta12/ delta12

value: female


title: Expt9_293T_NoGelChimeCLIP_total_rep2

description:
Aw30
chimeric eCLIP


title: BCM1-IgG

value: C57BL/6 x CAST/EiJ F13


title: S198_L_S15


title: c57BL-6N HTT KO line +/+ male1 cortex

value: cortex

value: 3 months


title: c57BL-6N HTT KO line +/+ male1 striatum

value: HTT KO line +/+


title: c57BL-6N HTT Δ12 line  Δ12/Δ12 female2 striatum


title: Expt9_293T_WithGelChimeCLIP_total_rep1

description:
Aw10
chimeric eCLIP


title: c57BL-6N HTT Δ12 line  Δ12/Δ12 female1 striatum


title: S829_M_S17

value: Peripheral blood monocyte


title: Expt4_Expt9_293T_input_total_rep1

description:
Aw33
chimeric eCLIP


title: BCF4-IgG

value: C57BL/6 x CAST/EiJ F14


title: S198_M_S14

value: DMSO (vehicle)

value: PBS (mock)


title: Expt9_293T_WithGelChimeCLIP_total_rep2

description:
Aw14
chimeric eCLIP


title: BCF4-H3K4M1

value: C57BL/6 x CAST/EiJ F12


title: c57BL-6N HTT Δ12 line  Δ12/Δ12 female2 cortex


title: BCF3-H3K4M1

value: C57BL/6 x CAST/EiJ F9


title: Expt9_293T_NoGelChimeCLIP_total_rep1

description:
Aw26
chimeric eCLIP


title: c57BL-6N HTT Δ12 line  Δ12/Δ12 female3 cortex


title: BCF3-H3K27Me3

value: C57BL/6 x CAST/EiJ F8


title: Expt8_293TmiR124oe_input_total_rep2

description:
At26
chimeric eCLIP


title: BCF4-H3K27Me3

value: C57BL/6 x CAST/EiJ F11


title: Expt8_293TmiR1oe_input_total_rep2

description:
At24
chimeric eCLIP


title: Expt8_293TmiR124oe_input_total_rep1

description:
At25
chimeric eCLIP


title: BCF4-H3K27Ac

value: C57BL/6 x CAST/EiJ F10

value: ES cells


title: c57BL-6N HTT Δ12 line  Δ12/Δ12 female1 cortex


title: S176_L_S24

value: LPS


title: S002_M_S20


title: S176_M_S23


title: S176_AL_S25

value: mTORi


title: c57BL-6N HTT Δ12 line  Δ12/Δ12 male3 striatum

value: striatum

value: HTT delta12 line delta12/ delta12

value: male


title: Expt8_293TmiR124oe_ProbeEnrichedNoGelChimeCLIP_miR124_rep1

description:
At15
chimeric eCLIP


title: c57BL-6N HTT Δ12 line  Δ12/Δ12 male3 cortex

value: cortex

value: 3 months


title: c57BL-6N HTT Δ12 line  Δ12/Δ12 male2 striatum


title: Expt8_293TmiR124oe_ProbeEnrichedNoGelChimeCLIP_miR124_rep2

description:
At16
chimeric eCLIP


title: S198_AL_S16

value: Peripheral blood monocyte


title: BCF3-H3K27Ac

value: C57BL/6 x CAST/EiJ F7

value: female


title: BCM2-H3K4M1

value: C57BL/6 x CAST/EiJ F6


title: c57BL-6N HTT Δ12 line  Δ12/Δ12 male1 striatum


title: Expt8_293TmiR1oe_input_total_rep1

description:
At23
chimeric eCLIP


title: BCM1-H3K27Me3

value: C57BL/6 x CAST/EiJ F2


title: Expt8_293TmiR124oe_WithGelChimeCLIP_total_rep2

description:
At4
chimeric eCLIP


title: c57BL-6N HTT Δ12 line  Δ12/+ female3 striatum

value: delta12 line delta12/+


title: BCM2-H3K27Me3

value: C57BL/6 x CAST/EiJ F5


title: S002_AL_S22


title: BCM2-H3K27Ac

value: C57BL/6 x CAST/EiJ F4


title: Expt11_C9_NoGelChimeCLIP_total_rep1

description:
chimericmix_Rx
chimeric eCLIP

organism: Rattus norvegicus

source_name: C9 cells


title: S002_L_S21

value: DMSO (vehicle)


title: c57BL-6N HTT Δ12 line  Δ12/Δ12 male2 cortex


title: Expt8_293TmiR1oe_ProbeEnrichedNoGelChimeCLIP_miR1_rep2

description:
At14
chimeric eCLIP


title: Expt8_293TmiR1oe_WithGelChimeCLIP_total_rep2

description:
At2
chimeric eCLIP


title: Expt8_293TmiR1oe_ProbeEnrichedNoGelChimeCLIP_miR1_rep1

description:
At13
chimeric eCLIP


title: c57BL-6N HTT Δ12 line Δ12/Δ12 male1 cortex


title: BCM1-H3K27Ac

value: C57BL/6 x CAST/EiJ F1

value: ES cells


title: c57BL-6N HTT Δ12 line  Δ12/+ female3 cortex


title: Expt12_C9_WithGelChimeCLIP_total_rep1

description:
R_Chi_As11_S23_L00X_R1_001
chimeric eCLIP


title: BCM1-H3K4M1

value: C57BL/6 x CAST/EiJ F3


title: Expt12_C9_NoGelChimeCLIP_total_rep1

description:
R_Chi_As23_S35_L00X_R1_001
chimeric eCLIP


title: c57BL-6N HTT Δ12 line  Δ12/+ female1 striatum

value: striatum


title: Expt8_293TmiR124oe_WithGelChimeCLIP_total_rep1

description:
At3
chimeric eCLIP


title: Expt7_293T_input_total_rep1

description:
Ah9_S78_L008_R1_001
chimeric eCLIP


title: Expt10_C9_NoGelChimeCLIP_total_rep1

description:
EV272
chimeric eCLIP


title: Expt7_293T_GeneEnrichedNoGelChimeCLIP_ULK1_rep2

description:
Catch2_26c_S30
chimeric eCLIP


title: c57BL-6N HTT Δ12 line  Δ12/+ female2 cortex


title: Expt9_C9_WithGelChimeCLIP_total_rep2

description:
Aw16
chimeric eCLIP


title: Expt8_293TmiR1oe_WithGelChimeCLIP_total_rep1

description:
At1
chimeric eCLIP


title: Expt9_C9_NoGelChimeCLIP_total_rep2

description:
Aw32
chimeric eCLIP


title: c57BL-6N HTT Δ12 line  Δ12/+ female2 striatum


title: Expt9_C9_NoGelChimeCLIP_total_rep1

description:
Aw28
chimeric eCLIP


title: Expt9_C9_WithGelChimeCLIP_total_rep1

description:
Aw12
chimeric eCLIP


title: Expt7_293T_GeneEnrichedNoGelChimeCLIP_ULK1_rep1

description:
Catch2_24c_S28
chimeric eCLIP


title: Expt7_293T_GeneEnrichedNoGelChimeCLIP_APP_rep2

description:
Catch2_25c_S29
chimeric eCLIP


title: c57BL-6N HTT Δ12 line  Δ12/+ male3 striatum


title: c57BL-6N HTT Δ12 line  Δ12/+ male2 striatum


title: c57BL-6N HTT Δ12 line  Δ12/+ male1 striatum


title: Expt9_C9_input_total_rep3

description:
Aw39
chimeric eCLIP


title: Expt5_293T_input_total_rep2

description:
input_p_cap_B_R1
chimeric eCLIP


title: Healthy_control_2

city: Bengaluru

first: Kalpana

last: SR

state: Karnataka

address: Jayanagar 9th block, Bannerghatta Road

department: Department of Pathology

country: India

institute: Sri Jayadeva Institute of Cardiovascular Sciences & Research

data_processing:
Quality of reads was checked using FastQC
Reads were trimmed using TrimGalore
Salmon was used for aligning and quantifying reads
tximport was used to import the transcript-level abundance, estimated counts and transcript lengths
Deseq2 was used for downstream analysis
Assembly: GRCh38
Supplementary files format and content: Raw_counts_matrix.txt - contains raw counts of all genes for each sample. Each row represents a gene while each column represents a sample

source_name: Whole blood

extract_protocol:
QIAamp RNA Blood Mini Kit (Catalog no. 52304)  was used to extract RNA from human whole blood samples. Extraction was performed according to manufacturer's instructions
A modified NEBNext RNA Ultra protocol was used to prepare the libraries for mRNA sequencing. The poly-A containing mRNA molecules was purified using oligo-dTattached magnetic beads. Following purification, the mRNA was fragmented using divalent cations under elevated temperature. Next, the cDNA was synthesized using Reverse transcriptase and random hexamers in a first strand synthesis reaction. Subsequently, the cDNA was converted to doublestranded cDNA in a DNA polymerase based reaction. These DNA molecules were then subjected to a series of enzymatic steps for end repair, A-Tailing and ligation with NEB adapters. Finally, these adapter ligated molecules were enriched in a limited cycle PCR with indexed primers and purified using AMPure beads to create final cDNA library for sequencing.

value: Whole blood

tag: age

tag: gender

value: F


title: CHD_4


title: Healthy_control_1

value: M


title: CHD_2


title: CHD_5


title: CHD_3


title: Expt9_C9_input_total_rep2

description:
Aw36
chimeric eCLIP


title: ARF_4


title: Expt5_293T_input_total_rep1

description:
input_p_cap_A_R1
chimeric eCLIP


title: CHD_1


title: ARF_3


title: Expt9_C9_input_total_rep1

description:
Aw35
chimeric eCLIP


title: D2125-18: Charles Rivers Randomized

city: Ann Arbor

first: Stephen

middle: J.

last: Gurczynski

state: MI

address: 109 Zina Pitcher Pl, Room 4062

department: Internal Medicine

institute: University Of Michigan

data_processing:
sequence trimming and alignment was performed by genewiz
raw counts were provided by genewiz
normalized counts were calculated using DeSEQ2 in R v3.6

source_name: Whole Lung Homogenate

extract_protocol:
Lungs were extracted and homogenzed in trizol regeant following the manufacturers instructions
libraries and downstream sequencing was performed by genewiz

treatment_protocol: Mice from various vendors were cage randomized or left non-randomized for 2 weeks.  Mice were subsequently treated o.n. with .75 / kg units of bleomycin for 14 days to induce pulmonary fibrosis.

tag: condition

value: pulmonary fibrosis

value: Whole Lung Homogenate

value: Bleomycin 14-days


title: Expt7_293T_GeneEnrichedNoGelChimeCLIP_APP_rep1

description:
Catch2_23c_S27
chimeric eCLIP

source_name: HEK293T cells

tag: cell line


title: c57BL-6N HTT Δ12 line  Δ12/+ male2 cortex

tag: tissue

value: cortex

value: male

value: 3 months


title: ARF_2


title: Expt9_C9_input_total_rep4

description:
Aw40
chimeric eCLIP


title: ARF_5


title: c57BL-6N HTT Δ12 line  Δ12/+ female1 cortex

tag: strain

value: delta12 line delta12/+

value: female


title: c57BL-6N HTT Δ12 line +/+ female1 striatum

tag: genotype

value: HTT delta12 line +/+


title: c57BL-6N HTT Δ12 line +/+ female3 cortex


title: c57BL-6N HTT Δ12 line +/+ female2 striatum


title: Expt5_293T_ProbeEnrichedNoGelChimeCLIP_5mir_rep2

description:
R_CC_A5
chimeric eCLIP


title: c57BL-6N HTT Δ12 line Δ12/+ male1 cortex


title: Expt5_293T_ProbeEnrichedNoGelChimeCLIP_mir17_rep2

description:
R_CC_B4
chimeric eCLIP


title: D2125-13: Jax Randomized

tag: treatment


title: D2125-15: Charles Rivers Randomized


title: RHD_4


title: RHD_2


title: Expt3_293T_NoGelChimeCLIP_total_rep2

description:
2_S15
chimeric eCLIP


title: c57BL-6N HTT Δ12 line  Δ12/+ male3 cortex

tag: Sex


title: Expt5_293T_ProbeEnrichedNoGelChimeCLIP_5mir_rep1

description:
R_CC_B5
chimeric eCLIP


title: c57BL-6N HTT Δ12 line +/+ male3 striatum

tag: time


title: D2125-16: Charles Rivers Randomized


title: c57BL-6N HTT Δ12 line +/+ female3 striatum


title: ARF_1


title: RHD_5


title: Expt5_293T_ProbeEnrichedNoGelChimeCLIP_let7_rep2

description:
R_CC_B3
chimeric eCLIP


title: Expt5_293T_ProbeEnrichedNoGelChimeCLIP_let7_rep1

description:
R_CC_A3
chimeric eCLIP


title: c57BL-6N HTT Δ12 line +/+ male2 striatum


title: D2125-14: Charles Rivers Randomized


title: D2125-10: Jax Randomized


title: RHD_3


title: Expt5_293T_ProbeEnrichedNoGelChimeCLIP_mir17_rep1

description:
R_CC_A4
chimeric eCLIP


title: D2125-17: Charles Rivers Randomized


title: Expt1_293T_input_total_rep2

description:
R_Chi_i9_inp2_R1
chimeric eCLIP


title: RHD_1


title: c57BL-6N HTT Δ12 line +/+ male3 cortex


title: c57BL-6N HTT Δ12 line +/+ female1 cortex


title: Expt3_293T_NoGelChimeCLIP_total_rep1

description:
1_S14
chimeric eCLIP


title: D2125-7: Charles Rivers Non-Randomized


title: D2125-11: Jax Randomized


title: D2125-12: Jax Randomized


title: c57BL-6N HTT Δ12 line +/+ female2 cortex


title: Expt2_293T_NoGelChimeCLIP_total_rep1

description:
Catch2_6_S18
chimeric eCLIP


title: c57BL-6N HTT Δ12 line +/+ male1 striatum


title: NASH_HFD_rep1

type: RNA

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

description: Gene expression in the fetal livers from HFD-fed dams or CD-fed dams

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/ug cRNA) was fragmented at 60 °C for 30 min in a reaction volume of 25 µl containing 1x fragmentation buffer (Agilent) and 2x blocking agent (Agilent) following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 µl of 2x GE Hybridization Buffer HI-RPM (Agilent) was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray 8x60K Ver. 2.0 (G4858A #74809, Agilent Technologies) for 17 h at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 1 min at room temperature with GE Wash Buffer 1 (Agilent) and for 1 min with 37 °C GE Wash buffer 2 (Agilent) and then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters  (protocol AgilentG3_GX_1Color and Grid: 074809_D_F_20150624)  to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered wtih three filters with GeneSpring software 13 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than  20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was exluded. In the last filter, when the value (log scale) of CV was over 50 percent in both conditions, the probe was exluded. After flitering, control probes were excluded, and log scale values were transformed into normal scale.

source_name: fetal liver, HFD-fed dam, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: The female C57BL/6J mice were fed either a control diet (CD; 4.3% kcal fat, 19.2% kcal protein, 67.3% kcal carbohydrate, Research Diets Inc., New Brunswick, NJ) or a high-fat diet (HFD; 60% kcal fat, 20% kcal protein, 20% kcal carbohydrate; Research Diets Inc.) during gestation.

tag: cell type

value: fetal liver

value: high-fat diet


title: NASH_CD_rep2

source_name: fetal liver, CD-fed dam, replicate 2

value: control diet


title: D2125-6: Charles Rivers Non-Randomized


title: D2125-9: Jax Randomized


title: Expt2_293T_NoGelChimeCLIP_total_rep2

description:
Catch2_7_S19
chimeric eCLIP

tag: sminput


title: D2125-8: Charles Rivers Non-Randomized


title: NASH_HFD_rep2

source_name: fetal liver, HFD-fed dam, replicate 2


title: Expt1_293T_NoGelChimeCLIP_total_rep1

description:
R_Chi_6_1dir
chimeric eCLIP


title: Expt1_293T_WithGelChimeCLIP_total_rep2

description:
R_Chi_10_2g
chimeric eCLIP
R_Chi_2_1g.vs.R_Chi_10_2g.bed


title: c57BL-6N HTT Δ12 line +/+ male2 cortex


title: D2125-5: Charles Rivers Non-Randomized


title: Expt1_293T_WithGelChimeCLIP_total_rep1

description:
R_Chi_2_1g
chimeric eCLIP
R_Chi_2_1g.vs.R_Chi_10_2g.bed


title: B16 tumour

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

data_processing:
Raw data bcl files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
Assembly: mm10
Supplementary files format and content: comma-delimited text files including raw UMI counts and metadata with information per cell

source_name: tumour

extract_protocol: All methods listed in Murgaski et al. Efficacy of CD40 agonists is mediated by distinct cDC subsets and subverted by suppressive macrophages. 2022.

value: B16 tumour

tag: platform

value: 10x Genomics


title: c57BL-6N HTT Δ12 line +/+ male1 cortex


title: mDCT15 wild type_bio rep2

city: Nijmegen

first: Valentina

last: Carotti

address: Geert Grooteplein Zuid 10

institute: Radboudumc

data_processing:
Low-quality ﬁltering and adapter trimming were performed using Trim Galore! v0.4.5
Reads were mapped to a mouse reference genome (GRCm39.105, Ensembl) with Star v2.7.5a, resulting in BAM ﬁles
BAM ﬁles were counted (number of reads mapped to a feature, e.g., a gene) with HTSeq [HTSeq-count tool v0.11.0] with default parameters using a complementary gtf ﬁle, containing annotation for GRCm39.105 (Ensembl)
Counts were normalized using gene length and Transcripts Per Million (TPMs) were produced
MultiQC (quality control) was used to combine results and quality checks of all the samples.
Diﬀerential gene expression analysis was carried out with DESeq2 v1.22.0 in R v3.5.3 (25), with internal statistical and normalization method (i.e., correction for multiple testing with Benjamini–Hochberg) using a cutoﬀ value of at least 5 counts per sample per gene
Assembly: GRCm39.105
Supplementary files format and content: tab-delimited csv files

growth_protocol: Wild type and Pkd1-/- mDCT15 cells were cultured in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F12 Ham (DMEM/F12; Life Technologies, Carlsbad, USA) supplemented with 5% (v/v) fetal bovine serum (FBS) and 1% (v/v) penicillin-streptomycin. All cell lines were cultured at 37 °C in an incubator with 5% (v/v) CO2 and humidified atmosphere, trypsinized and passaged every 3-4 days.

extract_protocol:
Total RNA was obtained using the RNeasy Mini Kit (Qiagen, Hilden, Germany)
RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems, Wilmington, MA, USA)

value: distal convoluted tubule cells

value: wild type


title: mDCT15 wild type_bio rep1


title: mDCT15 wild type_bio rep3


title: Expt1_293T_NoGelChimeCLIP_total_rep2

description:
R_Chi_15_2dir
chimeric eCLIP


title: Non-transfected RNA-seq rep2

description:
mRNAseq_non_tfxd_2_R1
Expt8_293Tuntfx_RNAseq_total_rep2
polyA RNA-seq

data_processing:
Reads in the RNA-seq libraries contain a 10 nucleotide UMI at the 5' end of each read. UMIs were pruned from 5' ends of R1 read sequences using umi_tools (v1.0.1). Next, 3'-adapters were trimmed from reads using cutadapt (v2.7). Remaining reads shorter than 18 nucleotides in length were discarded. Reads were mapped to a database of human repetitive elements and rRNA sequences compiled from Dfam and Genbank. Reads that did not align to the repeats database were then mapped to the human genome (hg38) using STAR (v2.6.0c). PCR duplicates were removed using umi_tools (v1.0.1) by utilizing UMI sequences from the read names and mapping positions. Gene counts per sample were obtained using a custom perl script as well as transcript information from GENCODE (V29). Differential expression analysis was performed using the R package DESeq2 (v 1.34.0).
Genome_build: UCSC version GRCh38/hg38
Supplementary_files_format_and_content: bigWig (+) and bigWig (-) files.

growth_protocol: Human HEK293xT cells were acquired from Takara Bio and cultured in DMEM media (GIBCO) with 10% FBS 1% penicillin/streptomycin at 37°C in 5% CO2.

extract_protocol:
15 million HEK293xT cells were spun down, supernatant removed, and washed with cold PBS. Cell pellets were flash frozen on dry ice and stored at -80°C. Total RNA was isolated using the miRNeasy Mini Kit (Qiagen). Poly(A) RNA was isolated using Dynabeads Oligo (dT)25 (Thermo Fisher). RNA integrity and purity was measured using the Agilent 4200 TapeStation.
To prepare RNA-sequencing libraries, 50 ng of poly(A) selected RNA was heat fragmented in 2X FastAP buffer and then treated with alkaline phosphatase (FastAP, Thermo Fisher) and T4 PNK (NEB). An RNA adapter was then ligated to the 3′-ends of the mRNA fragments (T4 RNA Ligase, NEB), after which RNA was column purified (Zymo) and reverse transcribed with SuperScript III Reverse Transcriptase (Invitrogen), then treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A 5’ Illumina DNA adapter (/5Phos/NNNNNNNNNNAGATCGGAAGAGCGTCGTGT/3SpC3) was ligated to the 3′-end of cDNA fragments with T4 RNA Ligase (NEB) and after on-bead cleanup (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) and size selected using AMPure XP beads (Beckman). Libraries were quantified using Agilent4200 TapeStation and sequenced on the Illumina NovaSeq platform.

treatment_protocol: Human HEK293xT cells grown to ~70% confluency in antibiotic-free media were transfected with a final concentration of 100 nM of miR-1 or miR-124 miRNA mimics (IDT) or no mimic (mock) with Lipofectamine™ RNAiMAX (Invitrogen). Cells were incubated with mimics for 16 hours with 70-80% viability. To harvest, cells were washed with cold 1X PBS, and flash frozen without crosslinking.

tag: transfection


title: Non-transfected RNA-seq rep1

description:
mRNAseq_non_tfxd_1_R1
Expt8_293Tuntfx_RNAseq_total_rep1
polyA RNA-seq


title: miR-124 transfected RNA-seq rep2

description:
mRNAseq_miR124_2_R1
Expt8_293TmiR124oe_RNAseq_total_rep2
polyA RNA-seq


title: mDCT15 Pkd1-/- _bio rep 1

value: PKD1 knockdown


title: mDCT15 Pkd1-/-_bio rep 3


title: LLC_tumour Citeseq_DL16_CDNA

value: LLC tumour


title: Tsc1 RPE KO, scRNAseq

city: Oklahoma city

first: Yan

last: Chen

state: Oklahoma

address: 608 Stanton L Young Blvd

institute: The University of Oklahoma Health Sciences Center/DMEI

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: RPE/choroid

extract_protocol:
After removal of the neuroretina, the posterior eye cups were digested with the mixture of collagenase and dispase in the presence of LIVE/DEAD fixable near-IR dead cell dye for 15 min at 37°C.  After washing, the cells were digested with 0.05% Trypsin for 5 min at 37°C.  The cell suspension was pelleted, and washed with resuspension buffer (PBS containing 0.04% BSA).  After removing the cell clumps with a 40 m cell strainer, the single-cell suspension was sorted via FACS with gates set to include live cells.  Collected cells were used to prepare barcoded, next-generation sequencing libraries of single cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: RPE/choroid

value: Tsc1 RPE KO

value: 10 weeks old


title: miR-124 transfected RNA-seq rep1

description:
mRNAseq_miR124_1_R1
Expt8_293TmiR124oe_RNAseq_total_rep1
polyA RNA-seq


title: H3K27me3_dbKO_2

city: Boston

first: Dong Feng

state: Massachusetts

address: 20 Staniford St

institute: Schepens Eye Research Institute

data_processing:
ChIP-seq reads were aligned to mm10 mouse genome.
Qualitz control was done with fastqc, for alignment Bowtie2 was applied.
Samtools and macs2 were used for data processing.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage

source_name: retinal ganglion cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries werer prepared according to manufacturer's protocol (Rubicon Genomics Thruplex DNAseq Kit)

treatment_protocol: Retinas were removed and enzymatically dissociated. Dissociated retinal cells were incubated with a magnetic bead conjugated anti-Thy-1 antibody to isolate retinal ganglion cells. Chromatin Immunoprecipitation was performed following manufacturer’s protocols (EZ-Chip 17-371, Merck Millipore).

value: retinal ganglion cells

tag: developmental stage

tag: chip antibodies

value: H3K27me3 (07-449, Merck Millipore)


title: mDCT15 Pkd1-/-_bio rep 2


title: NASH_CD_rep1

source_name: fetal liver, CD-fed dam, replicate 1


title: D2125-3: Jax Non-Randomized

value: pulmonary fibrosis

value: Whole Lung Homogenate

value: Bleomycin 14-days


title: LZX5

city: Tianjin

first: Hideo

last: Ema

state: Tianjin

address: 288#, Nanjing Road

department: State key laboratory of experimental hematolog

institute: Inatitute of Hematology & Blood Disease Hospital, Chinese Academy of Sciences.

data_processing:
Raw sequencing reads were demultiplexed and assigned to each single cell according to the unique barcode sequences pooled in sequencing libraries.
We next trimmed polyA tails, artificial sequences introduced during sequencing library construction, including TSO and UMI, and low quality bases from the 5’ prime or 3’ prime of each paired reads
Sequencing reads that passed quality control were aligned to the mouse reference genome (genome version: mm10) by using Tophat with default settings (version 2.0.12).
HTSeq package was used to summarize the uniquely aligned reads for each gene and duplicated transcripts were removed referring to UMI sequences.The number of transcripts for each gene was calculated as the number of different UMIs aligned.
Low quality cells were further removed based on the number of genes and transcripts detected in each cell referring to Scater R package.
We also removed genes with low expression abundance across all cells as described in Scater package.
Gene expression level was normalized as log2 (TPM/10 + 1), in which TPM is short for Transcripts per million and adding one is to avoid negative expression values.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each single cells.

source_name: CD48+HSC2, MPP4

extract_protocol:
Single cells were sorted or transferred directly into cell lysis buffer. The reverse transcription and template switch steps were then performed following the modified Smart-seq2* protocol. Amplified cDNA was sonicated to ~300-base-pair (bp) fragments by the Covaris S2 system. The 3' ends of the transcripts are enriched by Dynabeads Myone streptavidin C1 beads (invitrogen) after biotin-primer PCR.
The cDNA libraries were generated using a KAPA Hyper Prep Kit for Illumina (KAPA). Finally, the samples were ready for sequencing on an Illumina Hiseq platform (Novogene).

value: Bone marrow

value: 8 weeks

tag: cell markers

value: CD48+HSC2, MPP4


title: D2125-2: Jax Non-Randomized


title: D2125-1: Jax Non-Randomized


title: Expt6_MusLiver_input_total_rep3

description:
Ay21_S8_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.

source_name: Liver tissue

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: Liver


title: LZX4

description: 3' ends mRNA

data_processing:
Raw sequencing reads were demultiplexed and assigned to each single cell according to the unique barcode sequences pooled in sequencing libraries.
We next trimmed polyA tails, artificial sequences introduced during sequencing library construction, including TSO and UMI, and low quality bases from the 5’ prime or 3’ prime of each paired reads
Sequencing reads that passed quality control were aligned to the mouse reference genome (genome version: mm10) by using Tophat with default settings (version 2.0.12).
HTSeq package was used to summarize the uniquely aligned reads for each gene and duplicated transcripts were removed referring to UMI sequences.The number of transcripts for each gene was calculated as the number of different UMIs aligned.
Low quality cells were further removed based on the number of genes and transcripts detected in each cell referring to Scater R package.
We also removed genes with low expression abundance across all cells as described in Scater package.
Gene expression level was normalized as log2 (TPM/10 + 1), in which TPM is short for Transcripts per million and adding one is to avoid negative expression values.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each single cell.

molecule: polyA RNA

source_name: CD201-CD48-HPC1, MPP2, CD48+HSC1, CD48+HPC1

tag: age

value: 8-10 weeks


title: LZX6


title: LZX3

description: 3' ends mRNA

value: Spleen


title: Tsc1 Flox, scRNAseq

description: 10x Genomics

value: Tsc1 flox


title: Expt6_MusLiver_input_total_rep1

description:
RD_Ay19_S60_L004_R1_001
chimeric eCLIP


title: miR-1 transfected RNA-seq rep2

description:
mRNAseq_miR1_2_R1
Expt8_293TmiR1oe_RNAseq_total_rep2
polyA RNA-seq


title: Mock transfected RNA-seq rep1

description:
mRNAseq_mock_1_R1
Expt8_293Tmocktfx_RNAseq_total_rep1
polyA RNA-seq

value: Mock


title: LLC_tumour Citeseq_DL16_ADT

value: LLC tumour

value: 10x Genomics


title: H3K27me3_WT_2

value: WT


title: H3K27me3_dbKO_1


title: LZX2

description: 3' ends mRNA


title: miR-124 transfected small RNA-seq rep1

description:
miR124_1_S7
Expt8_293TmiR124oe_smRNAseq_total_rep1
small RNA-seq

data_processing:
Reads in sRNA-seq libraries contain the sequence “AACTGTAGGCACCATCAAT” followed by a 12 nucleotide UMI at the 3' end of each read. The “AACTGTAGGCACCATCAAT” sequence was identified within each read using cutadapt (v2.7) and reads that did not contain this sequence were discarded. Next, the UMIs were appended to the read names, and the “AACTGTAGGCACCATCAAT” sequence as well as following 3' sequence (this includes the UMI and sequencing adapter) using a custom python script. Reads were mapped to a database of human repetitive elements and rRNA sequences compiled from Dfam [Ref: PMID: 26612867] and Genbank [Ref: PMID: 23193287]. Reads that did not align to the repeats database were then mapped uniquely to the human genome (hg38) using STAR (v2.6.0c) [Ref: PMID: 23104886]. PCR duplicates were removed using umi_tools (v1.0.1) by considering both UMI sequences and mapping positions. miRNA counts were obtained using a custom python script and miRNA annotations from miRBase (v22). In order to allow relative comparison of abundances of miRNAs that are transcribed from multiple genomic locations, reads that failed to map uniquely were re-mapped allowing multimapping and selecting primary alignment like described above for miRNA quantification with non-chimeric reads.
Genome_build: UCSC version GRCh38/hg38
Supplementary_files_format_and_content: bigWig (+) and bigWig (-) files.

extract_protocol:
15 million HEK293xT cells were spun down, supernatant removed, and washed with cold PBS. Cell pellets were flash frozen on dry ice and stored at -80°C. Total RNA was isolated using the miRNeasy Mini Kit (Qiagen).
Small RNA-sequencing libraries were prepared using the QIAseq miRNA Library Kit (Qiagen). Briefly, a pre-adenylated DNA adapter was ligated to the 3' ends of the RNA followed by ligation of an RNA adapter to the 5' ends of the RNA. The adapter-ligated RNA was then reverse transcribed, and on-bead cleanup of cDNA was performed. Library amplification and barcoding were achieved using a universal forward primer and indexing 8-base reverse primers (HT Plate Indices 331565). Libraries were quantified using Agilent TapeStation and sequenced on the Illumina NovaSeq platform.


title: miR-124 transfected small RNA-seq rep2

description:
miR124_2_S8
Expt8_293TmiR124oe_smRNAseq_total_rep2
small RNA-seq


title: Mock transfected RNA-seq rep2

description:
mRNAseq_mock_2_R1
Expt8_293Tmocktfx_RNAseq_total_rep2
polyA RNA-seq


title: D2125-4: Jax Non-Randomized


title: miR-1 transfected small RNA-seq rep2

description:
miR1_2_S6
Expt8_293TmiR1oe_smRNAseq_total_rep2
small RNA-seq


title: input WT 1

value: none (input)


title: input dbKO 2

value: retinal ganglion cells


title: input dbKO 1


title: miR-1 transfected small RNA-seq rep1

description:
miR1_1_S5
Expt8_293TmiR1oe_smRNAseq_total_rep1
small RNA-seq


title: LZX1

description: 3' ends mRNA


title: Expt1_293T_input_total_rep1

description:
R_Chi_i1_inp1_R1
chimeric eCLIP


title: Expt6_MusLiver_input_total_rep2

description:
RD_Ay20_S61_L004_R1_001
chimeric eCLIP


title: Expt6_MusLiver_ProbeEnrichedNoGelChimeCLIP_mir122_rep2

description:
RD_Ay14_S55_L004
chimeric eCLIP


title: input singleKO2

value: Math5Cre;Ezh2-/- (single knockout)


title: Non-transfected small RNA-seq rep2

description:
non_tfxd 2_S4
Expt8_293Tuntfx_smRNAseq_total_rep2
small RNA-seq


title: Expt6_MusLiver_NoGelChimeCLIP_total_rep3

description:
RD_Ay18_S59_L004
chimeric eCLIP


title: Expt6_MusLiver_ProbeEnrichedNoGelChimeCLIP_let7_rep3

description:
RD_Ay13_S54_L004
chimeric eCLIP


title: H3K27me3_WT_1

value: H3K27me3 (07-449, Merck Millipore)


title: Non-transfected small RNA-seq rep1

description:
non_tfxd 1_S3
Expt8_293Tuntfx_smRNAseq_total_rep1
small RNA-seq


title: Expt6_MusLiver_NoGelChimeCLIP_total_rep2

description:
RD_Ay17_S58_L004
chimeric eCLIP


title: H3K27me3_singleKO2


title: Mock transfected small RNA-seq rep2

description:
Mock2_S2
Expt8_293Tmocktfx_smRNAseq_total_rep2
small RNA-seq


title: Expt6_MusLiver_ProbeEnrichedNoGelChimeCLIP_let7_rep2

description:
RD_Ay12_S53_L004
chimeric eCLIP


title: H3K27me3_singleKO1


title: miR-1 transfected RNA-seq rep1

description:
mRNAseq_miR1_1_R1
Expt8_293TmiR1oe_RNAseq_total_rep1
polyA RNA-seq


title: Expt6_MusLiver_NoGelChimeCLIP_total_rep1

description:
RD_Ay16_S57_L004
chimeric eCLIP


title: input WT 2


title: Expt6_MusLiver_ProbeEnrichedNoGelChimeCLIP_mir122_rep3

description:
RD_Ay15_S56_L004
chimeric eCLIP


title: Expt6_MusLiver_ProbeEnrichedNoGelChimeCLIP_let7_rep1

description:
RD_Ay10_S51_L004
chimeric eCLIP


title: GBM_HHT, 2

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 HHT(50nM) after 16h

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

label: biotin

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.


title: GBM_DMSO, 4

description: Gene expression data from primary GBM cells treated with DMSO after 16h

value: DMSO


title: GBM_HHT, 4


title: Expt6_MusLiver_ProbeEnrichedNoGelChimeCLIP_mir122_rep1

city: La Jolla

first: Gene

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

institute: UCSD

description:
RD_Ay11_S52_L004
chimeric eCLIP


title: GBM_HHT, 3


title: GBM_DMSO, 3


title: Mock transfected small RNA-seq rep1

description:
Mock1_S1
Expt8_293Tmocktfx_smRNAseq_total_rep1
small RNA-seq


title: input singleKO1


title: Scramble cKit Sample 2

status: Public on Jul 28 2022

city: Tampa

first: Paulo

last: Rodriguez

state: Florida

address: 3011 W. Holly Drive, MRC, 2067

institute: H. Lee Moffitt Cancer Center

data_processing:
bcl2fastq2 is used for base-calling and demultiplexing
STAR-2.5.3a is used to align reads to reference genome
HTSeq-0.6.1 is used to count reads for gene expression
DESeq2 ver1.30.1 is used for normalization and differential expression analyses
Assembly: mm10
Supplementary files format and content: text (raw read count as expression value)
Supplementary files format and content: text (normalized read count as expression value)

source_name: cKit+ precursors from B16F10 scramble tumor #2

growth_protocol: Wildtype C57BL6 age and sex matched mice 6 weeks of age were injected with 150,000 B16F10 tumor cells (either Scramble B16F10 or PERK KO B16F10) as subcutaneous tumors; tumors were permitted to grow until day 17

extract_protocol:
RNA was isolated from cKit precursors via Qiagen RNEasy with the inline Qiagen DNase digestion
RNA extracted from tumor tissue was quantitated with the Qubit Fluorometer (ThermoFisher Scientific, Waltham, MA) and screened for quality on the Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA).  The samples were then processed for RNA-sequencing using the NuGEN Universal Mouse RNA-Seq Library Preparation Kit with NuQuant (Tecan Genomics, Redwood City, CA).  Briefly, 100 ng of RNA was used to generate cDNA and a strand-specific library following the manufacturer’s protocol.  Quality control steps were performed, including TapeStation size assessment and quantification using the Kapa Library Quantification Kit (Roche, Wilmington, MA).  The final libraries were normalized, denatured, and sequenced on the Illumina NextSeq 2000 sequencer with the 2-200 cycle reagent kit in order to generate approximately 50M million 105-base read pairs per sample (Illumina, Inc., San Diego, CA)

treatment_protocol: On day 17 of tumor growth, mice were humanely euthanized and tumors dissected into compelte RPMI media; after manually tissue disaggregation, tumors were treated with liberase and DNAse for 1 hour at 37C to enable generation of a single cell suspension (tumor processing); after tumor processing, red blood cells were lysed with red blood cell lysis buffer (ACK bufer) and total viable cells counted followed by magnetic bead based enrichment of ckit positive tumor infilrtating precursors- this method was chosed as it enables isolation of viable, fresh precursors which do not survive well when processed via flow sorting

value: cKit+ precursors infiltrating tumor

tag: injected tumor cells

value: Scramble B16F10 melanoma


title: Scramble cKit Sample 3

source_name: cKit+ precursors from B16F10 scramble tumor #3


title: Hippocampus_mutant_GD_biological_rep4

city: Cologne

first: Andrea

last: Merseburg

state: North Rhine-Westphalia

address: Kerpener Str. 62

department: Institute for Molecular and Behavioral Neuroscience

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE), Bonn, and University of Cologne, Cologne, Germany

description:
HPC_650_GD
Gene expression data from hippocampus of heterozygous mutant Hcn1GD/+ mouse.

hyb_protocol: Labeled cDNA samples were hybridized to Affymetrix Clariom™ S Mouse arrays (ThermoFisher Scientific, USA, Cat# 902931) and incubated in Genechip Hybridization Oven-645 (Affymetrix, ThermoFisher Scientific, USA) rotating at 60 rpm at 45°C for 16 h. Subsequently, arrays were washed on a Genechip Fluidics Station-450 (Affymetrix, ThermoFisher Scientific, USA) and stained with the Affymetrix HWS kit according to the manufacturer’s protocol.

scan_protocol: Chips were scanned with an Affymetrix Gene-Chip Scanner-3000-7G and the Affymetrix GCOS software was used for the generation of .dat and .cel files.

data_processing: Data processing was performed with the Transcriptome Analysis Console software (TAC4.0, ThermoFisher Scientific, USA), using SST-RMA for summarization and a LIMMA Bioconductor package for differential gene expression evaluation with empirical Bayesian (eBayes) analysis and Benjamini-Hochberg method for FDR adjusted P-value calculations. All samples passed each of the QC criteria.

source_name: Hippocampus from heterozygous male Hcn1GD/+ mouse

label_protocol: 100 ng total RNA were used for reverse transcription and the resulting cDNA was fragmented and labeled via the GeneChip® WT PLUS Reagent Kit as per the manufacturer’s instructions (Affymetrix, ThermoFisher Scientific, USA).

growth_protocol: Animals were kept in type II long plastic cages under standard housing conditions (21±2°C, 50% relative humidity) with food (ssniff Spezialitäten GmbH, Soest, Germany) and water ad libitum.

extract_protocol: Total RNA was prepared from hippocampus (using material from both hemispheres) from 6-month-old male mice. Tissue from hippocampus (~40µg) was submerged in RNAprotect Tissue Reagent (Qiagen, Germany), and subsequent RNA isolation was performed with RNeasy Mini Kit (Qiagen, Germany) and RNase-free DNase Set (Qiagen, Germany).

treatment_protocol: Animals did not receive any treatment.

tag: gender

value: male

value: heterozygous mutant (Hcn1GD/+)

value: 6 months

value: hippocampus from both hemispheres


title: Hippocampus_mutant_MI_biological_rep1

description:
HPC_353_MI
Gene expression data from hippocampus of heterozygous mutant Hcn1MI/+ mouse.

source_name: Hippocampus from heterozygous male Hcn1MI/+ mouse

value: heterozygous mutant (Hcn1MI/+)


title: Hippocampus_control_WT_biological_rep1

description:
HPC_609_WT
Gene expression data from hippocampus of wildtype control mouse of the Hcn1GD line.

source_name: Hippocampus from WT male mouse

value: wildtype control


title: Hippocampus_mutant_MI_biological_rep4

description:
HPC_361_MI
Gene expression data from hippocampus of heterozygous mutant Hcn1MI/+ mouse.


title: Hippocampus_control_WT_biological_rep4

description:
HPC_358_WT
Gene expression data from hippocampus of wildtype control mouse of the Hcn1MI line.


title: GBM_DMSO, 2

tag: cell line


title: GBM_DMSO, 1


title: GBM_HHT, 1


title: Muscle LPS Treated Rep 1

city: Piscataway

first: Sohaib

last: Hassan

address: 145 Bevier Road

department: Department of Genetics and Human Genetics Institute of New Jersey

institute: Rutgers University

description:
LPS treated (10 mg/kg b.w., i.p.)
FPKM_Muscle.txt
Results_Muscle_CtrlvsMuscle_LPS.txt
Results_Muscle_LPSvsMuscle_LPS_MIC.txt

data_processing:
Alignment: RNA-seq: Kallisto v0.46.11
RNA-seq Transcript Import: tximport 1.18.02
DESeq2 1.30.13
Assembly: RefSeq mm9
Supplementary files format and content: RNA-Seq: FPKM table outputted by DESeq2 for fragment counts normalized per kilobase of feature length per million mapped fragments and Results table outputted by DESeq2 that extracts Log2FC values, p values, adjusted p values, baseMean values, and test statistic values.

organism: Mus

source_name: Gastrocnemius

extract_protocol:
C57BL/6 mice were purchased from Charles River Laboratories (Malvern, PA). C57BL/6 male mice were randomly put into vehicle control, LPS-treated, or LPS-MIC-1-treated group as previously described in GEO (accession no. GSE155738). MIC-1 (80 mg/kg b.w.) was given by gavage daily for 3 days before LPS treatment, which was administered intraperitoneally. Gastrocnemius muscles were collected from euthanized mice after 16 h of LPS treatment. Fat and connective tissue were trimmed from muscle tissues before freezing in liquid nitrogen for further analyses. The handling and care of animals used in this study followed the standard procedures recommended by the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health, and the Rutgers University Institutional Animal Care and Use Committee approved the protocol (ID999900474)
RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

value: wild type


title: Hippocampus_mutant_GD_biological_rep1

description:
HPC_604_GD
Gene expression data from hippocampus of heterozygous mutant Hcn1GD/+ mouse.

tag: tissue


title: PERK KO cKit Sample 3

source_name: cKit+ precursors from B16F10 PERK KO tumor #3

tag: strain

value: PERK KO B16F10 melanoma


title: Muscle LPS Treated Rep 3

tag: genotype


title: PERK KO cKit Sample 4

source_name: cKit+ precursors from B16F10 PERK KO tumor #4


title: Muscle LPS + MIC-1 Treated Rep 1

description:
MIC-1 (80mg/kg b.w.) gavaged group injected with LPS. Mice were pretreated (3 days) with MIC-1 in 10% DMSO (Sigma-Aldrich) via oral gavage before a LPS (10 mg/kg b.w.) intraperitoneal injection
FPKM_Muscle.txt
Results_Muscle_CtrlvsMuscle_LPS_MIC.txt
Results_Muscle_LPSvsMuscle_LPS_MIC.txt


title: PERK KO cKit Sample 1

source_name: cKit+ precursors from B16F10 PERK KO tumor #1