title: ntj2_mock_rep2

city: Saint Louis

first: Rebecca

last: Bart

state: MO

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were trimmed with Trimmomatic. HISAT2 (version 2.0.6) was used to align the RNA-seq reads against a concatenated genome comprised of the sorghum nuclear genome (version Sorghum bicolor v3.1.1; https://phytozome.jgi.doe.gov), the sorghum chloroplast genome (GenBank: EF115542.1), the sorghum mitochondrial genome (NCBI Reference Sequence: NC_008360.1), and the Xvh genome (https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2757320517) to allow for the best alignment of each read. Default parameters were used except for the inclusion of the '--dta-cufflinks' parameter. The resulting SAM (Sequence Alignment/Map) files (.sam) were sorted and converted to BAM (Binary Alignment/Map) files (.bam) using SAMtools.
Stringtie was used for quantification. The parameter -e was used to limit quantification to alignments matching the reference annotation file (parameter -G). Transcripts were then merged with Stringtie Merge. Both stringtie steps were done with -G parameter using either sorghum or xanh annotation file. This was performed twice, once to quantify the reads mapped to the sorghum genome and again to quantify the reads mapped to the Xvh genome
The Ballgown FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were calculated by Stringtie with the -b parameter, using merged transcripts from stringtie merge as -G parameter.
Genome_build: Sorghum nuclear genome (version Sorghum bicolor v3.1.1; https://phytozome.jgi.doe.gov), the sorghum chloroplast genome (GenBank: EF115542.1), the sorghum mitochondrial genome (NCBI Reference Sequence: NC_008360.1), and the Xanthomonas vasicola pv. holcicola BLS185 genome (https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2757320517)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sorghum bicolor

source_name: mock-inoculated sorghum leaves

growth_protocol: The sroghum plants were grown in a growth chamber set at 28/23°C with 14/10 h (day/night) conditions and 50% relative humidity. 14-day-old plants were used for all experiments. Bacterial strain were grown on plates containing NYGA medium (per liter: 5.0g peptone, 3.0g yeast extract, 20.0g glycerol, and 1% agar) for 48 hours at 30°C.

extract_protocol:
Total RNA was extracted using the TRIzol™ Reagent (Invitrogen). The aqueous phase containing the RNA was mixed with an equal volume of 70% ethanol, and then applied to a column from the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich) following the manufacturer’s instructions, including the On-Column DNase Digestion protocol. RNA quality was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The fourth leaf of sorghum plants was inoculated with 10mM MgCl2 and bacterial suspensions as the mock and Xvh-inoculated treatments, respectively. Bacteria were harvested from the plates containing NYGA medium as “Xvh-culture” samples.

tag: sorghum genotype

tag: treatment

value: sorghum mock inoculation

value: mock-inoculated sorghum leaves

tag: time point

value: 48 hours post inoculation


title: ntj2_xvh_rep2

status: Public on Dec 14 2019

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism:
Sorghum bicolor
Xanthomonas vasicola

source_name: Xvh-inoculated sorghum leaves

value: sorghum Xvh inoculation

tag: tissue

value: Xvh-inoculated sorghum leaves


title: ntj2_xvh_rep3


title: ntj2_mock_rep1


title: grassl_mock_rep3

value: grassl


title: Flower buds, ChIP-seq_date2_2_K4

city: Villenave d'Ornon

first: Benedicte

last: Wenden

address: 71 avenue Edouard Bourlaux

country: France

institute: INRA

description:
Prunus avium L.
date2_2_K4_40218300_count.txt

library_source: genomic

data_processing:
The quality of reads was assessed using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/) and possible adaptor contaminations and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014).
For ChIP-seq data, adaptor-trimmed reads were mapped to the peach (Prunus persica (L) Batsch) reference genome v1.0 (Verde et al., 2013) using Bowtie2 (Langmead et al., 2009).
Possible optical duplicates were removed using Picard tools (https://github.com/broadinstitute/picard).
We used a gene-centric approach to identify genes with significant changes in the strength of H3K4me3 signal between time-points. The DiffBind R package was used for the read counting and differential binding analysis steps (Stark and Brown, 2011; Ross-Innes et al., 2012). Firstly, to quantify H3K4me3 signal at genes, we measured the number of H3K4me3 ChIP reads in a 2000bp window around the TSS of each gene, normalised by H3. Two biological replicates were present for each time point, and DiffBind combines the available information to provide a statistical estimate of the normalised H3K4me4 signal for any particular gene.
Genome_build: Prunus persica (L) Batsch reference genome v1.0 (Verde et al., 2013)
Supplementary_files_format_and_content: ChIP-seq processed data files are txt files that contains the gene_id column that defines the gene name corresponding to the peach locus, locus information (chromosome, position), and the TMM (i.e. counts of H3K4me3 signal normalized by H3 signals at the TSS of each gene) per locus.
Gene list and homology information for Prunus persica genome v1.0 are available at https://www.rosaceae.org/analysis/11

molecule: genomic DNA

organism: Prunus avium

source_name: Sweet cherry flower buds

growth_protocol: Branches and flower buds were collected from the sweet cherry cultivars (Prunus avium L.) 'Burlat'. The trees were grown in an orchard located at the Fruit Experimental Unit of INRA in the South West of France (44° 19′ 56′′ N, 0° 24′ 47′′ E). Sweet cherry flower buds used for the ChIP-seq experiment were collected on October 21st 2014 (Date 1) and December 5th 2014 (Date 2) for dormant buds and January 27th 2015 (Date 3) for non-dormant buds. For each date, buds were harvested from the same branches, flash frozen in liquid nitrogen and stored at -80°C prior to performing RNA-seq and ChIP-seq.

extract_protocol:
For ChIP-seq, ChIP was conducted on 300-500 mg of frozen and pulverized flower buds using the procedure described in Leida et al. (2012) with minor modifications (1% PVP-40was added to the different buffers and DNA extraction and purification was carried out using SPRI beads). For immunoprecipitation , we used anti-trimethyl-histone 3 Lys 4 antibody (Millipore cat#17-614).
For ChIP-seq libraries, library preparation was performed using all the volume for IPs (50µL) and 20 ng in 50µL using the TruSeq ChIP Library Preparation kit (48 samples, 12 indexes, Illumina, cat. no. IP-202-1012). DNA quality from libraries was evaluated using Tapestation 4200. The libraries were sequenced on a NextSeq500, at the Sainsbury Laboratory Cambridge University (SLCU), using paired-end sequencing of 75 bp in length.

tag: cultivar

value: Burlat

value: Flower buds

tag: time-point

tag: chip antibody

tag: lane


title: Dmtr23B-CW

city: jinan

first: Zhang

last: Xiujun

state: shandong province

address: south road of shanda

country: China

institute: shandong university

description: processed data file: all_samples.gene_expression.TPM.txt

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 21-nt long tags. Then low quality tags, one copy tags and tags which are not 21-nt long were removed to generate clean tags. Reference 21-nt tag databases were created from predicted P. decumbens transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed. The copy number of unambiguous tags (tags mapped to one single gene) for each gene was normalized to TPM (number of transcripts per million clean tags) for differential expression analysis.
Genome_build: Whole Genome Shotgun project in GenBank under the accession number AGIH01000000 (pde_v1.0).
Supplementary_files_format_and_content: all_samples.gene_expression.TPM.txt: Tab-delimited text file includes raw counts and TPM values.

organism: Penicillium oxalicum

source_name: Fungal mycelia

growth_protocol: The conidia of Penicillium oxalicum were inoculated in Vogel's medium with 2% glucose as carbon resource for 20 h at 30 °C as the pre-culture, and then mycelia were transferred and grown in the new medium for 24 h. Total RNA was extracted for DGE analysis.

extract_protocol: Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 35bp.

tag: strain

value: Dmtr23B (mtr23B knockout strain)

value: Fungal mycelia

tag: growth media

value: Vogel's medium with 1% wheat bran and 1% cellulose as carbon resource

tag: culture time

value: 24 h after transferring washed mycelia to the new medium


title: Rmtr23B-CW

value: Rmtr23B (mtr23B complemented strain)


title: A14A

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The reads with good quality were firstly aligned to several human reference databases including hg19 human genome, exon, splicing junction segment and contamination database including ribosome and mitochondria sequences using STAR alignment algorithm. After filtering reads mapped to contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 mis-matches for each transcript were then counted as expression level for corresponding transcript.  After filtering out of the transcripts with low read (<100) across all samples, the read counts were log2 transformed and quantile-normalized at an equal global median value in order to compare transcription level across samples.
Genome_build: hg19
Supplementary_files_format_and_content: txt files with normalized log2 transfromed read counts

organism: Homo sapiens

source_name: kidney biopsy

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Fisher Scientific). The RNA quality was evaluated by an Agilent 2100 Bioanalyzer.
The total RNA sample was treated using a Ribo-Zero Magnetic Gold Kit to deplete rRNA, and cDNA libraries were prepared and sequenced at BGI using a HiSeq 4000 system.

tag: group


title: M12-CW

description:
M12 is the uracil auxotrophic mutant (pyrGQ226*) derived from P. oxalicum wild-type strain 114-2.
processed data file: all_samples.gene_expression.TPM.txt

value: M12 (the uracil auxotrophic mutant pyrGQ226*)


title: ntj2_xvh_rep1


title: Flower buds, ChIP-seq_date2_2_H3

value: Anti-Histone H3 antibody (Abcam, ab1791)


title: grassl_mock_rep1


title: Rmtr23B-G

value: Vogel's medium with 2% glucose as carbon resource


title: Flower buds, ChIP-seq_date2_2_INPUT


title: grassl_mock_rep2


title: grassl_xvh_rep3


title: grassl_xvh_rep2


title: Flower buds, ChIP-seq_date1_3_K4

description:
Prunus avium L.
date1_3_K4_40202537_count.txt

value: anti-trimethyl-histone 3 Lys 4 antibody (Millipore cat#17-614)


title: Flower buds, ChIP-seq_date1_3_INPUT


title: Gli2_ChIPSeq_Rep1

city: Toronto

first: Tae-Hee

last: Kim

state: Ontario

address: 686 Bay Street. Room 16.9709

department: Developmental & Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

data_processing:
Adaptor sequences were trimmed using Trimmomatic 0.36 with adaptor sequence file TruSeq3-PE-2.fa
Reads were aligned to the mm9 reference genome using default parameters of BWA MEM
Aligned reads were filtered using bamtools to exclude unmappped reads, mapping quality < 5, and not proper pairs.
ENCODE blacklist regions in mm9 were filtered out using bedtools
Peaks were called using MACS2 with q = 0.05. --broad option was used for histone marks
Genome_build: mm9
Supplementary_files_format_and_content: peaks called from MACS2

organism: Mus musculus

source_name: E17.5 stomach

extract_protocol:
E17.5 stomachs were dissected, cut into small pieces, and crosslinked in solution A (1% formaldehyde, 50mM Hepes-KOH, 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA) for 20 minutes at room temperature. 1/20 volume of 2.5 M glycine was added to quench formaldehyde. Tissues were rinsed in ice-cold PBS and dounced in Wheaton tissue grinder. Cell suspensions were passed through a 100μm cell strainer to remove connective tissues, then centrifuged at 4 °C at 2500 × rcf for 3 min, followed by a wash in PBS. Gli2, H27K27ac, or H3K36me3 antibodies were incubated with pre-blocked magnetic beads in 250μL total volume for 8 hours at 4 °C, then washed and resuspended in 100μL 0.5% BSA (w/v) solution. Cell pellets were lysed by sequentially resuspending and centrifuging in LB1 (50 mM Hepes-KOH, pH 7.5; 140 mM NaCl; 1mM EDTA; 10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100), and LB2 (10 mM Tris-HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA). Pellet was resuspended in LB3 (10 mM Tris-HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine) and sonicated into 200-400bp fragments. Sonicated lysates were diluted with LB3. After saving 50μL for input control, they were split into tubes containing 10% v/v Triton X-100 with Gli2 (homemade), H3K27ac (Millipore 05-1334 lot 2489078), or H3K36me3 (Abcam ab9050 lot GR204353-1) antibody, and incubated overnight. Beads were washed 6 times in RIPA buffer (50 mM Hepes-KOH, pH 7.5; 500 mM LiCl; 1mM EDTA; 1% NP-40 or Igepal CA-630; 0.7% Na-Deoxycholate), and once in TBS (20 mM Tris-HCl, pH 7.6; 150 mM NaCl). Protein-DNA complexes were eluted and crosslink reversed with 200 μL of elution buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA; 1% SDS). The 50μL input lysate was also included in this step. Eluted DNA was diluted with 200 μL of TE, and treated with RNaseA for 30 min at 37°C, and subsequently with proteinase K for 2 hours at 55°C. Phenol:chloroform:isoamyl alcohol was used to extract DNA.
Libraries were prepared according to manfacturer's instructions for the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® kit.

tag: developmental stage

value: stomach


title: Dmtr23B-G


title: bs_mock_rep3

value: bs

value: sorghum mock inoculation

value: mock-inoculated sorghum leaves


title: ntj2_mock_rep3

value: 48 hours post inoculation


title: grassl_xvh_rep1

value: grassl

value: sorghum Xvh inoculation

value: Xvh-inoculated sorghum leaves


title: M12-G


title: bs_xvh_rep3


title: Flower buds, ChIP-seq_date1_2_K4

description:
Prunus avium L.
date1_2_K4_40192924_count.txt

value: Burlat

value: Flower buds


title: xvh_culture_rep3

organism: Xanthomonas vasicola

source_name: bacterial cell

value: bacterial in culture

value: bacterial cell

value: 48 hours post growth in NYGA medium


title: bs_xvh_rep2


title: Flower buds, ChIP-seq_date1_2_INPUT


title: bs_mock_rep1


title: MSAJ-05

city: Nanjing

first: Yuting

last: Shou

state: Jiangsu

address: 159 Longpan Rd

institute: Nanjing Forestry University

data_processing:
illumina software was used for basecalling
pre-treatment:Each pair of reads were firstly merged together into a single read if they shared a sequence with a length longer than 30bp and an identity higher than 0.9. Each not-merged read was pruned to preserve the high-quality 50bp part from its terminal.
map the reads, tophat-v2.0.8b was applied with the parameter -g 1 to ensure a unique map result for every read
cufflinks-v2.2.1 was next used to offer a hybrid annotation based on the information from both the previously published bamboo genome annotation and our own mapping results
Genome_build: Peng et al., 2013  The draft genome of the fast-growing non-timber forest species moso bamboo (phyllostachys heterocycla)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Phyllostachys edulis

source_name: rhizome lateral buds

extract_protocol:
samples frozen by liquid nitrogen were grinded and total RNA were extracted using EASYSPIN RNA extraction kit (Yuanpinghao Biotech Co.,Ltd) and treated with RNase-free DNase I for 30min at 37℃ to remove residual DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: early shoot

tag: genotype

value: wild type


title: xvh_culture_rep2


title: MSAJ-01

value: germination


title: bs_xvh_rep1


title: Flower buds, ChIP-seq_date1_2_H3

value: Anti-Histone H3 antibody (Abcam, ab1791)


title: bs_mock_rep2


title: xvh_culture_rep1


title: 2M-127B-262A_DEX

status: Public on Dec 13 2019

city: San Francisco

first: Benjamin

last: Huang

state: CA

address: 1450 3rd Street

institute: University of California San Francisco

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using Bowtie v2.
Transcript quantification was performed with RNA-seq by Expectation Maximization (RSEM) protocol.
Differential gene expression analysis was performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated values files including FPKM values for each sample.

source_name: Primary murine TALL_DEX_4hrs

extract_protocol:
Bone marrow cells were collected, subjected to RBC lysis, homogenized in Trizol. RNA was extracted using standard Trizol based techniques.
Libraries were prepared using the TruSeq Stranded Total RNA kit. Libraries were sequenced on a Illumina HiSeq 2500 using 100 bp paired-end chemistry.

treatment_protocol: Mice were transplanted with primary leukemias and observed daily. Moribund mice were treated with vehicle or dexamethasone 4 hours prior to euthanization.

tag: strain background

value: C57BL/6 x 129Sv/Jae F1

tag: cell type

value: primary murine T lineage acute lymphoblastic leukemias (T-ALLs)

tag: treatment condition

value: DEX

tag: drug exposure time

value: 4 hours


title: JW-81-59B-202A_DEX


title: 78A-143B-190A_DEX


title: JW-81-59B-200A_VEH

source_name: Primary murine TALL_VEH_4hrs

value: VEH


title: 20M-116B-226A_DEX


title: 73M-19A-249A_DEX


title: 73M-19A-243A_VEH


title: 73A-46B-184A_DEX


title: H37Rv 3

city: St Louis

first: Jennifer

middle: A

last: Philips

state: Missouri

address: 660 S. Euclid Ave

department: Dept of Medicine

institute: Washington University School of Medicine

description: wt mtb infected

data_processing:
convert fastq files to unaligned .bam files (Samtools:FastqToSam)
adapter trimming (Trimmomatic)
genome indexing and read mapping (HiSat2)
genewise read counts (featureCounts)
Genome_build: GRCm38.97
Supplementary_files_format_and_content: genomic features read count matrix (tab delimited)

molecule: polyA RNA

source_name: bone marrow derived macrophage

growth_protocol: BMDMs were seeded at 1.6E6 cells per well in a six-well plate 1 d before infection

extract_protocol:
At 4 hpi, RNA was prepared using the Direct-Zol RNA Mini-Prep Kit (Zymo Research).
RNA-seq by poly-A selection

treatment_protocol: Cells were uninfected or infectedwith H37Rv orΔcpsAusing a MOI of 4

tag: mouse strain

tag: mtb strain

tag: replicate


title: Flower buds, ChIP-seq_date1_3_H3

tag: cultivar

tag: tissue

tag: time-point


title: 2M-127B-259A_VEH


title: 73A-46B-183A_VEH


title: 20M-116B-225A_VEH


title: H37Rv 2

description: wt mtb infected


title: cpsA 2

description: cpsA mtb infected

value: ∆cpsA


title: cpsA 1

description: cpsA mtb infected


title: Control 3

description: uninfected


title: Control 1

description: uninfected


title: 78A-143B-191A_VEH


title: Control 2

description: uninfected


title: Htr4-EGFP/Rpl10a (ES1299) cerebral cortex IP Rep3 [1166]

first: Laura

last: Kus

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

description:
Ribosomal-bound RNA
1166_Htr4_TRAP_ES1299_cerebral_cortex_IP_Rep3_GCCAAT_L003

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

source_name: Cerebral cortex

growth_protocol: Not applicable

extract_protocol:
The cerebral cortex was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: No treatment

value: Cerebral cortex

tag: animal line

value: Htr4-TRAP ES1299

tag: application

value: RNA-seq

tag: sample type

value: Immunopurified (IP)


title: Htr4-EGFP/Rpl10a (ES1299) cerebral cortex IP Rep2 [1165]

description:
Ribosomal-bound RNA
1165_Htr4_TRAP_ES1299_cerebral_cortex_IP_Rep2_GCCAAT_L002


title: Htr4-EGFP/Rpl10a (ES1299) cerebral cortex input Rep3 [1163]

description: 1163_Htr4_TRAP_ES1299_cerebral_cortex_input_Rep3_CTTGTA_L003

value: Input


title: Htr4-EGFP/Rpl10a (ES1299) cerebral cortex IP Rep1 [1164]

description:
Ribosomal-bound RNA
1164_Htr4_TRAP_ES1299_cerebral_cortex_IP_Rep1_GCCAAT_L001


title: Htr4-EGFP/Rpl10a (ES1299) cerebral cortex input Rep2 [1162]

description: 1162_Htr4_TRAP_ES1299_cerebral_cortex_input_Rep2_CTTGTA_L002


title: H37Rv 1

description: wt mtb infected


title: Htr4-EGFP/Rpl10a (ES1299) cerebral cortex input Rep1  [1161]

description: 1161_Htr4_TRAP_ES1299_cerebral_cortex_input_Rep1_CTTGTA_L001


title: cpsA 3

description: cpsA mtb infected


title: Prk_Nu

city: West Haven

first: Sidi

last: Chen

state: CT

address: ISTC 320, 850 West Campus Dr

department: Genetics, Systems Biology

institute: Yale University

description:
SeqWell, DropSeq
PolyA RNA
Prkar1a-knockout
The R1 fastqs have a cell barcode at bases 1-12 and a UMI at bases 13-20; The R2 fastqs have the cDNA sequence.

data_processing:
SeqWell scRNA-seq data: Drop-seq tools (version 1.12) (Macosko et al., 2015) were used to process all Seq-Well (Gierahn et al., 2017) single-cell RNA-seq data unless stated otherwise. First the paired-end read fastq files were merged and converted to Bam files by Picard-FastqToSam (Picard version 2.9.0). From the Bam files, cellular and unique molecular identifier barcodes were extracted, and reads were filtered to exclude those with single-base quality scores below 10. The sequences were then trimmed to remove adapters and polyA tails, and the files were converted back to fastq format by Picard-SamToFastq. The sequences were then mapped by STAR aligner (version 2.5.3a) (Dobin et al., 2013) to the mm10 mouse reference genome, provided by the McCarroll lab (GEO dataset: GSE63472) (Macosko et al., 2015). The aligned data were sorted by Picard-SortSam, and the cell and UMI barcode metadata were attached using Picard-MergeBamAlignment. Gencode annotations were added to the aligned reads, and digital gene expression (DGE) files were prepared for the 1000 most frequently occurring cell barcodes.
10x Chromium scRNA-seq data: Processing was performed using the Cell Ranger software count-pipeline (10X Genomics), aligning to the mm10 mouse genome reference with default settings.
All processed data were analyzed using the Seurat package (Satija et al., 2015) for the R programming language (version 3.4.4), and the data were filtered to include genes detected in >5 cells, and cells with >200 detected genes and <5% mitochondrial genes. The data were then normalized to 10,000 transcripts/cell and log-transformed, using a pseudo-count of 1 (ln[x + 1]).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_top1000.dge.txt.gz: Tab-delimited txt files containing transcript counts.
Supplementary_files_format_and_content: Prk_PrkB6_barcodes.tsv: Tab-delimited txt file containing cell barcodes.
Supplementary_files_format_and_content: Prk_PrkB6_genes.tsv: Tab-delimited txt file containing gene identifiers.
Supplementary_files_format_and_content: Prk_PrkB6_matrix.mtx: Matrix file containing transcript counts.

source_name: subcutaneous hepatocellular tumor

extract_protocol:
Tumors were harvested from mice, then immediately placed in PBS containing 2% FBS to maintain cell viability. Tumor tissue was then manually cut into small pieces using a razor in a 10cm dish containing 5ml PBS containing 2% FBS. Tumor tissue was then suspended into 15-20ml PBS and loaded into gentleMACs tubes. Collagenase IV was added in a 1:100 dilution to each sample, prior to loading into the gentleMACs tissue dissociation machine. Tissue was then dissociated for 30’ at 37 C. After dissociation, samples were passed through a 100uM filter and re-suspended into 40mL of PBS. Samples were then spun down at 400g for 5 min, and supernatant was discarded. Cell pellets then were washed with 40mL PBS, and spun down again at 400g for 5 min and supernatant was discarded. 3mL ACK lysis buffer was added to each cell pellet, gently pipetting to mix, then incubated for 3-5 min. After incubation, samples were re-suspended in 40mL PBS and passed through a 40uM filter to remove debris. Cells were then washed again, and stained with anti-CD45.2 antibody for 30’ using a 1:100 dilution (1e6 cells per mL). Prior to FACS, cells were washed 2x in PBS. Cells were then sorted based on CD45.2 (pan-immune cells) and GFP (cancer cells), and mixed as 90%:10% for single cell transcriptomics analysis. Unique molecular identifier (UMI) and single cell barcoded library preparation and sequencing were done using a slightly modified approach based on previously established methods (Gierahn et al., 2017; Macosko et al., 2015).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: Nu/Nu

tag: sg

value: subcutaneous hepatocellular tumor


title: Ntc_Rag

description:
SeqWell, DropSeq
PolyA RNA
Negative control
The R1 fastqs have a cell barcode at bases 1-12 and a UMI at bases 13-20; The R2 fastqs have the cDNA sequence.

value: sgNTC


title: Prk_B6

description:
Chromium, 10x Genomics
PolyA RNA
Prkar1a-knockout
The I1 fastqs have the i7-sample barcoding for multiplexing; The R1 fastqs have a cell barcode at bases 1-16 and a UMI at bases 17-26; The R2 fastqs have the cDNA sequence.


title: Prk_Rag


title: NKT.19-8-TCRb+CD1daGalCerTet+.Th#2_RNA-seq

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description:
iNKT Cell
SK-3N77_F7

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Thymus

growth_protocol: 6 week old C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME) housed in facility at least one week before harvesting cells

extract_protocol:
Extractions follow ImmGen standard operating protocol (available on https://www.immgen.org/). Briefly, organs are harvested at 9am on day of sort, perterbed as little as possible during preparation, and 1000 cells are double sorted into TCL buffer (Qiagen, Hilden, Germany) containing 1% BME.
Libraries are constructed according to the standard protocol for Smart-seq2 (Picelli et al, 2013) at the Broad Techology Labs in Cambridge, MA

tag: strain

tag: age

value: 6 weeks old

value: Thymus

tag: sorting markers

value: ab T Cell


title: SAM24287386 EXC

city: South San Francisco

first: Brad

last: Friedman

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database based on RefSeq. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from sorted neuronal subtypes

extract_protocol: Isolation of pure populations of neurons from adult mouse cortex using fluorescence activated cell sorting (FACS) was performed following published protocols 56 with the following modifications:  After enzymatic digestion with papain and trituration to obtain a homogenous cell suspension, cells were washed with 5ml of Hibernate A- LF twice at 1800 x g and resuspended in 5 ml of Hibernate A with 2.5ul of DAPI (1 ug/ml stock) added for FACS sorting. Neurons were sorted as DAPI(-):GFP(+) or DAPI(-):tdTomato(+) (depending on the transgenic reporter line) using a 100 micron filter in the ARIA sorter. Sorted cells (collected live) in Hibernate A medium were spun at 2000 x g at 4deg C for 5 min and cell pellets were processed for RNA extraction using a Qiagen RNeasy Plus Micro kit. RNA quality was checked using BioAnalzyer and cell type purity was checked using multiple TaqMan markers specific to the cell type of interest using BioMark Fluidigm chips. 500 ng RNA was submitted for sequencing after the samples passed these quality checks.

tag: gender

value: Male

tag: subtype

value: EXC

tag: poolid

value: adult mouse cortex


title: SAM24306368 VIP

value: Female

value: VIP


title: SAM24306365 SST

value: SST


title: SAM24287399 PV

value: PV


title: SAM24306367 SST


title: SAM24287400 PV


title: SAM24306363 SST


title: SAM24287389 EXC


title: SAM24306366 SST


title: SAM24306362 SST


title: SAM24306372 VIP


title: SAM24287390 EXC


title: SAM24287401 PV


title: SAM24306374 EXC


title: SAM24306364 SST


title: SAM24306373 VIP


title: SAM24306369 VIP


title: SAM24287403 PV


title: SAM24287402 PV


title: SAM24306370 VIP


title: SAM24287391 EXC


title: SAM24287398 PV


title: SAM24306371 VIP


title: SAM24287387 EXC


title: 12_Pre-Deferasirox

type: RNA

city: Salamanca

first: Jesus

middle: Maria

last: Hernandez Sanchez

state: España

address: Av Coimbra S/N

country: Spain

institute: Cancer Research of Salamanca

hyb_protocol: GeneChip® Hybridization Oven 645, Affymetrix : Incubate with rotation at 60 rpm for 16 hr at 47ºC.

scan_protocol: The scanner (GeneChip® Scanner 30000Dx 7G, Affymetrix) is controlled by GeneChip Operating Software (GCOS). The probe array is scanned after the wash protocols are complete in GeneChip® Fluidics Station 450, Affymetrix.

data_processing: The RMA function provided by the package oligo from R/Bioconductor was applied to the raw expression data.

label: Biotin

label_protocol: The fragmented cDNA is labelled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Not cultured

extract_protocol: Total RNA extraction was performed with the RNeasy Kit (Qiagen) as suggested by the manufacturer.

treatment_protocol: Not treated

tag: diagnosis

value: Low-grade myelodysplastic syndromes (MDS)

value: Peripheral blood

tag: treatment

value: Untreated

tag: patient


title: 15_Post-Deferasirox

value: Treated


title: 8_Post-Deferasirox


title: 11_Post-Deferasirox


title: 10_Post-Deferasirox


title: 13_Post-Deferasirox


title: 4_Pre-Deferasirox


title: 15_Pre-Deferasirox


title: 4_Post-Deferasirox


title: 7_Pre-Deferasirox


title: 12_Post-Deferasirox


title: 3_Post-Deferasirox


title: 5_Post-Deferasirox


title: 10_Pre-Deferasirox


title: 14_Post-Deferasirox


title: 16_Post-Deferasirox


title: 2_Post-Deferasirox


title: 11_Pre-Deferasirox


title: 2_Pre-Deferasirox


title: 8_Pre-Deferasirox


title: 7_Post-Deferasirox


title: 6_Pre-Deferasirox


title: 13_Pre-Deferasirox


title: 16_Pre-Deferasirox


title: 5_Pre-Deferasirox


title: 1_Post-Deferasirox


title: 6_Post-Deferasirox


title: 14_Pre-Deferasirox


title: 3_Pre-Deferasirox


title: 2MPA

city: Charlottesville

first: Alexander

last: Mathew

state: VA

address: 415 Lane Road

institute: University of Virginia

data_processing:
Base calling software: RTA v2
An average of 1531 cells per condition were sequenced on a NextSeq 500 (Illumina) at an average depth of 87,184 reads per cell. The CellRanger v3.0.2 pipeline was implemented to first convert bcl2 reads to FASTQ files (see https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq) followed by alignment to the mm10 (Ensembl 84) mouse reference genome and filtering (see https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count).
All further single cell analysis was performed in R using Seurat v3.0.2 with default parameters unless otherwise specified.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are in h5 matrix format after feature filtering and counting and include UMI counts for each barcoded cell. See https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices for more details.

source_name: mRuby+ cells from striatum

growth_protocol: Male C57BL/6 mice were purchased from Charles River and maintained on a 12/12 hour light/dark cycle. Mice used in the experiments weighed between 22 and 28 g and were given food and water ad libitum. All animal experiments were approved by the Animal Care and Use Committee at the University of Virginia and conformed to the National Institutes of Health regulations for the use of animals in research.

extract_protocol:
Immediately following euthanasia, the mouse brains treated with 0 MPa, 0.1 MPa, 0.2 MPa, or 0.4 MPa (n = 3 per group) were harvested. The front right quadrants of each brain were excised and made into single cell suspensions using the Adult Brain Dissociation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany). Suspensions were pooled by treatment group and incubated briefly with SYTOX Green Nucleic Acid Stain (1:500,000; Thermo Scientific) to identify live and dead cells. mRuby+ cells were isolated from 0.1 MPa, 0.2 MPa, and 0.4 MPa cell suspensions using a BD Influx Cell Sorter (BD Biosciences, San Jose, California) with the 100 µm nozzle at 20 psi. The sort gate was established using the 0 MPa cells as a reference. Live singlet mRuby+ cells were collected for single cell RNA-sequencing. FACS data were analyzed using FCS Express 6 software.
After FACS, 0 MPa (unsorted), 0.1 MPa (mRuby+), 0.2 MPa (mRuby+), and 0.4 MPa (mRuby+) single cell libraries were generated using the Chromium Controller (10X Genomics, Pleasanton, CA) with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X Genomics) and Chromium Single Cell B Chip Kit (10X Genomics).

treatment_protocol: Male C57BL/6 mice were anesthetized with an intraperitoneal injection of 120 mg/kg ketamine, 12 mg/kg xylazine, and 0.08 mg/kg atropine in sterilized 0.9% saline. A tail vein catheter was inserted to permit intravenous injections of MBs, plasmid, and the MRI contrast agent. The heads of the mice were shaved and depilated, and the animals were then placed in a supine position over a degassed water bath coupled to an MR-compatible small animal FUS system (RK-100; FUS Instruments, Toronto, Canada). The entire system was then placed in a 3T MR scanner (Magnetom Trio; Siemens Medical Solutions, Malvern, Pennsylvania). A 2 inch cylindrical transmit-receive RF coil, designed and built in-house, was placed around the mouse’s head to maximize imaging SNR. Baseline T1-weighted MR images were acquired and used to select 4 FUS target locations in and around the right striatum.

tag: Sex

value: male

value: 0.2 MPa, mRUBY FACS


title: 4MPA

value: 0.4 MPa, mRUBY FACS


title: 1MPA

value: 0.1 MPa, mRUBY FACS


title: C

source_name: Unsorted cells from striatum

value: Sham, unsorted


title: 1_Pre-Deferasirox

tag: tissue


title: Cocaine self-administration, escalating group IP Rep2 [2076] copy of 1795

description:
Ribosomal-bound RNA
2076_Drd2_TRAP_CP101_cocaine_escalating_IP_Rep2_S10

source_name: Dorsal striatum

extract_protocol:
The dorsal striatum was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: Saline self-administration. Cocaine self-administration.

value: FVB/N-Swiss Webster x 9 generations C57BL/6 minimum

value: Drd2-TRAP CP101

value: RNA-seq

value: Immunopurified (IP)

value: cocaine


title: Cocaine self-administration, escalating group IP Rep1 [2075] copy of 1794

description:
Ribosomal-bound RNA
2075_Drd2_TRAP_CP101_cocaine_escalating_IP_Rep1_S9


title: Cocaine self-administration, nonescalating group withdrawl IP Rep3 [2081] copy of 1800

description:
Ribosomal-bound RNA
2081_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep3_S15


title: Cocaine self-administration, nonescalating group IP Rep1 [2071] copy of 1790

description:
Ribosomal-bound RNA
2071_Drd2_TRAP_CP101_cocaine_nonescalating_IP_Rep1_S5


title: Cocaine self-administration, nonescalating group input Rep1 [2084] copy of 1803

description:
Total RNA
2084_Drd2_TRAP_CP101_cocaine_nonescalating_input_S18

value: Input


title: Cocaine self-administration, nonescalating group IP Rep3 [2073] copy of 1792

description:
Ribosomal-bound RNA
2073_Drd2_TRAP_CP101_cocaine_nonescalating_IP_Rep3_S7


title: Cocaine self-administration, nonescalating group IP Rep4 [2074] copy of 1793

description:
Ribosomal-bound RNA
2074_Drd2_TRAP_CP101_cocaine_nonescalating_IP_Rep4_S8


title: Cocaine self-administration, nonescalating group withdrawl IP Rep4 [2082] copy of 1801

description:
Ribosomal-bound RNA
2082_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep4_S16


title: Cocaine self-administration, nonescalating group IP Rep2 [2072] copy of 1791

description:
Ribosomal-bound RNA
2072_Drd2_TRAP_CP101_cocaine_nonescalating_IP_Rep2_S6


title: Saline self-administration withdrawl IP Rep1 [2077] copy of 1796

description:
Ribosomal-bound RNA
2077_Drd2_TRAP_CP101_saline_withdrawl_IP_Rep1_S11

value: saline


title: Saline self-administration IP Rep4 [2070] copy of 1789

description:
Ribosomal-bound RNA
2070_Drd2_TRAP_CP101_saline_IP_Rep4_S4


title: Saline self-administration IP Rep3 [2069] copy of 1788

description:
Ribosomal-bound RNA
2069_Drd2_TRAP_CP101_saline_IP_Rep3_S3


title: Saline self-administration IP Rep1 [2067] copy of 1786

description:
Ribosomal-bound RNA
2067_Drd2_TRAP_CP101_saline_IP_Rep1_S1


title: Cocaine self-administration, nonescalating group withdrawl IP Rep5 [1833]

description:
Ribosomal-bound RNA
1833_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep5_S8


title: Cocaine self-administration, nonescalating group withdrawl IP Rep3 [1831]

description:
Ribosomal-bound RNA
1831_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep3_S6


title: Saline self-administration withdrawl IP Rep2 [1827]

description:
Ribosomal-bound RNA
1827_Drd2_TRAP_CP101_saline_withdrawl_IP_Rep2_S2


title: Saline self-administration withdrawl IP Rep3 [1828]

description:
Ribosomal-bound RNA
1828_Drd2_TRAP_CP101_saline_withdrawl_IP_Rep3_S3


title: Cocaine self-administration, nonescalating group withdrawl IP Rep1 [1829]

description:
Ribosomal-bound RNA
1829_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep1_S4


title: Saline self-administration input Rep1 [2083] copy of 1802

description:
Total RNA
2083_Drd2_TRAP_CP101_saline_input_S17


title: Saline self-administration withdrawl IP Rep2 [1797]

description:
Ribosomal-bound RNA
1797_Drd2_TRAP_CP101_saline_withdrawl_IP_Rep2_S12


title: Cocaine self-administration, nonescalating group withdrawl IP Rep2 [2080] copy of 1799

description:
Ribosomal-bound RNA
2080_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep2_S14


title: Lypd1-EGFP/Rpl10a (OI82) dentate gyrus IP Rep1 [1295]

description:
Ribosomal-bound RNA
1295_Lypd1_TRAP_OI82_dentate_gyrus_IP_Rep1_S9

source_name: Dentate gyrus

extract_protocol:
The dentate gyrus was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

value: Dentate gyrus

value: Lypd1-TRAP OI82


title: Saline self-administration withdrawl IP Rep1 [1826]

description:
Ribosomal-bound RNA
1826_Drd2_TRAP_CP101_saline_withdrawl_IP_Rep1_S1


title: Cocaine self-administration, nonescalating group withdrawl IP Rep1 [2079] copy of 1798

description:
Ribosomal-bound RNA
2079_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep1_S13


title: Cocaine self-administration, nonescalating group withdrawl IP Rep2 [1830]

description:
Ribosomal-bound RNA
1830_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep2_S5


title: Cocaine self-administration, nonescalating group withdrawl IP Rep4 [1832]

description:
Ribosomal-bound RNA
1832_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep4_S7


title: Kcnip2-EGFP/Rpl10a (NIDA115) cerebral cortex IP Rep2

description:
Ribosomal-bound RNA
1486_Kcnip2_TRAP_NIDA115_cerebral cortex_IP_Rep2_S14

value: Kcnip2-TRAP NIDA115


title: Saline self-administration withdrawl input Rep1 [1834]

description:
Total RNA
1834_Drd2_TRAP_CP101_saline_withdrawl_input_S9


title: Kcnip2-EGFP/Rpl10a (NIDA115) cerebral cortex IP Rep1

description:
Ribosomal-bound RNA
1485_Kcnip2_TRAP_NIDA115_cerebral cortex_IP_Rep1_S13


title: 20_S18_R1_001

city: Munich

first: Bärbel

last: Stecher

address: Pettenkoferstr. 9a

department: Max von Pettenkofer Institute

country: Germany

institute: Ludwig Maximilian University of Munich

description: Since these samples do not contain the tested organisms but are negative controls, there is no processed data available for them.

data_processing:
Illumina NextSeq500 reads were trimmed and clipped for quality control in Trimmomatic v0.39
Contamination (mouse RNA and ribosomal RNA) were removed using kneaddata and the provided reference databases
Read quality was checked using FastQC
Bowtie2 v2.3.5. was used to map the reads with the flag --very-sensitive
htseq-count v0.11.2. was used to count mapped reads (-m union)
Genome_build: NZ_CP028714.1, NC_016810.1
Supplementary_files_format_and_content: tab delimited files with raw counts

source_name: Mouse cecum

extract_protocol:
cecal content was flash frozen on dry ice, total RNA was extracted "protocol name"
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: microbiota

value: ASF

tag: condition

value: ASF negative control


title: 19_S17_R1_001

value: ASF + Salmonella M2702

value: ASF Salmonella M2702


title: 13_S12_R1_001

value: ASF + E. coli Mt1B1

value: ASF E. coli Mt1B1


title: 24_S16_R1_001


title: 23_S21_R1_001


title: 15_S13_R1_001


title: 9_S1_R1_001

value: OMM + Salmonella M2702

value: OMM Salmonella M2702


title: 8_S2_R1_001

value: OMM + E. coli Mt1B1

value: OMM E. coli Mt1B1


title: 18_S16_R1_001


title: 22_S20_R1_001


title: 10_S2_R1_001


title: 7_S1_R1_001


title: 21_S19_R1_001


title: Kcnip2-EGFP/Rpl10a (NIDA115) cerebral cortex IP Rep3

description:
Ribosomal-bound RNA
1487_Kcnip2_TRAP_NIDA115_cerebral cortex_IP_Rep3_S15

tag: animal line

tag: application

value: RNA-seq

value: Immunopurified (IP)


title: 11_S2_R1_001


title: 5_S4_R1_001


title: 12_S2_R1_001


title: 6_S5_R1_001


title: 3_S2_R1_001

value: OMM

value: OMM negative control


title: 2_S1_R1_001


title: Htr6-Trap (NIDA113) deep cerebellar nuclei IP Rep3 [1475]

description:
Ribosomal-bound RNA
1475_Htr6_TRAP_NIDA113_deep_cerebellar_nuclei_IP_Rep3_S3

source_name: Deep nuclei of the cerebellum

extract_protocol:
The deep cerebellar nuclei were homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

value: Htr6-TRAP NIDA113

tag: sample type


title: 1_S15_R1_001


title: Htr6-Trap (NIDA113) deep cerebellar nuclei IP Rep2 [1474]

description:
Ribosomal-bound RNA
1474_Htr6_TRAP_NIDA113_deep_cerebellar_nuclei_IP_Rep2_S2


title: 4_S3_R1_001


title: 25_S17_R1_001


title: 17_S15_R1_001


title: 16_S14_R1_001


title: Htr6-Trap (NIDA113) deep cerebellar nuclei IP Rep1 [1473]

description:
Ribosomal-bound RNA
1473_Htr6_TRAP_NIDA113_deep_cerebellar_nuclei_IP_Rep1_S1


title: 95H3_S312

city: Leuven

first: Araks

last: Martirosyan

address: Herestraat 49

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

data_processing:
abundance measurement: NextSeq Control Software 1.4.1.2
quality check: FASTQC 0.11.4
alignment: STAR 2.5.2b
HtseqCount version 0.6.1p1
Genome_build: Gencode GRCm38.p5 Release M12
ERCC sequences: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/cms_095047.txt
Supplementary_files_format_and_content: Processed data files contein htseq counts of genes and ERCC control RNAs

source_name: Brain

growth_protocol: Animals were kept in a specific pathogen free (SPF) facility with controlled humidity, temperature and light conditions; water and food was provided ad libitum.

extract_protocol:
The protocol used adult mice (post-natal day 56). Astrocytes were isolated from hippocampus and cortex and FACS purified using staining against pan-astrocytic marker Atp1b2 protein.
Sorted cells were prepared using an optimized SMART-seq2 library preparation protocol with the addition of ERCC (External RNA Controls Consortium) control RNAs (ThermoFisher Scientific, 4456740). The protocol was defined to detect poly-adenylated RNAs (which encode protein coding genes). Libraries were paired-end sequenced with Illumina NextSeq 500 system. On average read depth is 1.5 million reads per cell, sequenced fragments have 74-76 bp length.

treatment_protocol: Not Applicable

tag: plate name

tag: brain area

value: Cortex

tag: sample name

tag: reverse transcription date

tag: reverse transcription termal block

tag: tso freeze/thaw cycles

tag: pre-pcr delay days

tag: cdna ampure beads purification date

tag: cdna concentration measurement date

tag: library prep date

tag: library pcr thermal block

tag: index kit used

value: C

tag: pool name

value: G


title: 95H6_S336


title: 95H8_S352


title: 95H11_S376


title: 95G9_S359


title: 95G4_S319


title: 95G10_S367


title: 95F7_S342


title: 95G11_S375


title: 95G8_S351


title: 95H4_S320


title: 95F11_S374


title: 95G5_S327


title: 95F10_S366


title: 95G1_S295


title: 95F5_S326


title: 95F3_S310


title: 95G6_S335


title: 95E8_S349


title: 95F2_S302


title: 95F4_S318


title: 95E9_S357


title: 95E6_S333


title: 95H9_S360


title: 95E3_S309


title: 95E5_S325


title: 95E2_S301


title: 95G7_S343


title: 95F6_S334


title: 95E1_S293


title: 95D5_S324


title: 95E12_S381


title: 95E11_S373


title: 95D6_S332


title: 95D9_S356


title: 95D7_S340


title: 95C5_S323


title: 95D1_S292


title: 95D2_S300


title: 95C3_S307


title: 95D3_S308


title: 95C4_S315


title: 95B8_S346


title: 95D10_S364


title: 95C10_S363


title: 95C8_S347


title: 95C6_S331


title: 95D4_S316


title: 95C1_S291


title: 95D11_S372


title: 95C7_S339


title: 95C2_S299


title: 95B5_S322


title: 95B6_S330


title: 95B3_S306


title: 95B4_S314


title: 95B7_S338


title: 95E10_S365


title: 95B2_S298


title: 95B1_S290


title: 95B12_S378


title: 95A3_S305


title: 95A2_S297


title: 95B11_S370


title: 95A11_S369


title: 95A10_S361


title: 95A9_S353


title: 95A8_S345


title: 95A1_S289


title: 88H9_S360

value: Hippocampus

value: D


title: 88H3_S312


title: 88G8_S351


title: 88G7_S343


title: 95A4_S313


title: 88H6_S336


title: 88H2_S304


title: 88G6_S335


title: 88G1_S295


title: 88G10_S367


title: 88G5_S327


title: 88G3_S311


title: 88G2_S303


title: 88H11_S376


title: 95A5_S321


title: 88F8_S350


title: 88F7_S342


title: Lypd1-EGFP/Rpl10a (OI82) dentate gyrus IP Rep2 [1296]

description:
Ribosomal-bound RNA
1296_Lypd1_TRAP_OI82_dentate_gyrus_IP_Rep2_S10

tag: tissue

value: Dentate gyrus

value: Lypd1-TRAP OI82


title: 88F3_S310


title: 88F10_S366


title: 88H8_S352


title: 88F11_S374


title: 88E8_S349


title: 88E1_S293


title: 88E7_S341


title: 88E5_S325


title: 88D9_S356


title: 88D8_S348


title: 88E2_S301


title: 88E12_S381


title: 88E11_S373


title: 88D5_S324


title: 88D6_S332


title: 88D4_S316


title: 88F6_S334


title: 88D2_S300


title: 88C9_S355


title: 88D7_S340


title: 88E6_S333


title: 88C7_S339


title: 88C6_S331


title: 88F1_S294


title: 88C5_S323


title: 88C2_S299


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title: 118H8_S160


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title: 118H3_S120


title: 118H5_S136


title: 118H2_S112


title: 118G9_S167


title: 118H1_S104


title: 118H10_S176


title: 118G8_S159


title: 118G11_S183


title: 118G1_S103


title: 118G3_S119


title: 118G10_S175


title: 118G7_S151


title: 118F9_S166


title: 118F7_S150


title: 118F8_S158


title: 118F6_S142


title: 118F3_S118


title: 118F2_S110


title: 118F1_S102


title: 118E7_S149


title: P01635

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Fastq files were align to the hg19 reference genome using STAR and default parameters
Ensembl v67 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using SVA and the 'LIMMA-Voom' method
Genome_build: hg19
Supplementary_files_format_and_content: Voom transformed abundance measurements

source_name: Left Ventricle

extract_protocol:
Total RNA was extracted using the miRNeasy Kit (Qiagen) including DNAse treatment. RNA concentration and quality was determined using the NanoVue Plus™ spectrophotometer (GE Healthcare) and the Agilent 2100 RNA Nano Chip (Agilent)
RNA sequencing libraries were prepared using the Illumina TruSeq stranded mRNA kit followed by the Nugen Ovation amplification kit.

treatment_protocol: Explanted myocardium snap frozen in liquid nitrogen.

tag: etiology

value: Non-Failing Donor

tag: Sex

value: Female

tag: race

value: African American

tag: age


title: 118E5_S133

tag: plate name

tag: brain area


title: P01640

value: Dilated cardiomyopathy (DCM)


title: P01630

value: Hypertrophic cardiomyopathy (HCM)

value: Male

value: Caucasian


title: P01628


title: P01631


title: P01639


title: P01634


title: 118E4_S125

tag: sample name

tag: reverse transcription date

value: C


title: 118E1_S101

value: Hippocampus

tag: reverse transcription termal block

tag: tso freeze/thaw cycles


title: P01629


title: P01623


title: P01626


title: P01627


title: P01622


title: 118E2_S109

tag: pre-pcr delay days

tag: cdna ampure beads purification date

value: D


title: 118D8_S156

tag: cdna concentration measurement date

tag: library prep date


title: 118D9_S164

tag: library pcr thermal block

tag: index kit used


title: P01621


title: 118E12_S189

tag: pool name


title: P01618

tag: etiology


title: 118D7_S148


title: 118D6_S140


title: P01616

tag: Sex


title: P01615

tag: race


title: 118E6_S141


title: P01611

tag: age


title: 118D3_S116

tag: plate name


title: 118D2_S108

tag: brain area


title: P01610


title: 118C9_S163

tag: sample name


title: P01608


title: 118D10_S172

tag: reverse transcription date


title: P01606


title: P01605


title: 118C8_S155

tag: reverse transcription termal block


title: 118C7_S147

tag: tso freeze/thaw cycles


title: P01603


title: P01602


title: 118C3_S115

tag: pre-pcr delay days


title: P01597


title: P01600


title: 118C11_S179

tag: cdna ampure beads purification date


title: 118C6_S139

tag: cdna concentration measurement date


title: 118C4_S123

tag: library prep date


title: P01596


title: P01617


title: 118B7_S146

tag: library pcr thermal block


title: P01595


title: 118B6_S138

tag: index kit used


title: 118E3_S117

tag: pool name


title: 118B5_S130


title: 118D5_S132


title: P01593

tag: etiology


title: 118D4_S124


title: P01592

tag: Sex


title: 118B2_S106


title: P01609

tag: race


title: P01591

tag: age


title: 118B1_S98

tag: plate name


title: P01590


title: 118A9_S161

tag: brain area


title: P01588


title: P01585


title: 118A7_S145

tag: sample name


title: 118A8_S153

tag: reverse transcription date


title: 118A4_S121

tag: reverse transcription termal block


title: P01581


title: P01582


title: 118A5_S129

tag: tso freeze/thaw cycles


title: 118A3_S113

tag: pre-pcr delay days


title: P01578


title: 118A1_S97

tag: cdna ampure beads purification date


title: 118A11_S177

tag: cdna concentration measurement date


title: P01568


title: P01563


title: 118A10_S169

tag: library prep date


title: P01573


title: P01567


title: 115H9_S264

value: Cortex

tag: library pcr thermal block


title: 115H8_S256

tag: index kit used


title: 115H5_S232

tag: pool name


title: P01561

tag: etiology


title: P01562

tag: Sex


title: 115H3_S216


title: 115H4_S224


title: 115H2_S208


title: P01556

tag: race


title: P01584

tag: age


title: P01559


title: 115H1_S200

tag: plate name


title: 118A6_S137

tag: brain area


title: P01549


title: P01580


title: 115H11_S280

tag: sample name


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tag: reverse transcription termal block


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title: P01547


title: 115G8_S255

tag: tso freeze/thaw cycles


title: P01539


title: 115G3_S215

tag: pre-pcr delay days


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tag: cdna ampure beads purification date


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tag: cdna concentration measurement date


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tag: library prep date


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title: P01540


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title: 115F9_S262

tag: library pcr thermal block


title: P01535


title: 115F8_S254

tag: index kit used


title: P01528


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tag: pool name


title: 115F6_S238


title: 115F5_S230


title: 115F4_S222


title: P01516

tag: etiology


title: 115F3_S214


title: P01515

tag: Sex


title: P01513

tag: race


title: P01510

tag: age


title: P01543


title: 115F2_S206

tag: plate name


title: 115F1_S198

tag: brain area


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tag: sample name


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tag: reverse transcription termal block


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tag: tso freeze/thaw cycles


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tag: cdna ampure beads purification date


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title: 115D7_S244

tag: pool name


title: P01485

tag: etiology


title: 115F11_S278


title: 115D6_S236


title: P01473

tag: Sex


title: P01472

tag: race


title: P01471

tag: age


title: 115D5_S228

tag: plate name


title: 115D4_S220

tag: brain area


title: 115D2_S204

tag: sample name


title: P01469


title: 115D3_S212

tag: reverse transcription date


title: P01466


title: 115D1_S196

tag: reverse transcription termal block


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title: P01465


title: 115D12_S284

tag: tso freeze/thaw cycles


title: 115D11_S276

tag: pre-pcr delay days


title: 115C9_S259

tag: cdna ampure beads purification date


title: P01462


title: P01457


title: 115E11_S277

tag: cdna concentration measurement date


title: P01452


title: 115C8_S251

tag: library prep date


title: P01447


title: 115C7_S243

tag: library pcr thermal block


title: 115C5_S227

tag: index kit used


title: 115C4_S219

tag: pool name


title: P01437

tag: etiology


title: P01436

tag: Sex


title: 115C1_S195


title: 115C12_S283


title: P01430

tag: race


title: P01425

tag: age


title: 115C11_S275

tag: plate name


title: P01422


title: P01454


title: 115C10_S267

tag: brain area


title: 115B9_S258

tag: sample name


title: P01413


title: P01414


title: 115C6_S235

tag: reverse transcription date


title: P01420


title: 115B7_S242

tag: reverse transcription termal block


title: P01444


title: 115B4_S218

tag: tso freeze/thaw cycles


title: P01412


title: 115C2_S203

tag: pre-pcr delay days


title: P01404


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title: P01440


title: P01433


title: 115B12_S282

tag: cdna ampure beads purification date


title: 115B1_S194

tag: cdna concentration measurement date


title: 115B3_S210

tag: library prep date


title: P01400


title: 115B10_S266

tag: library pcr thermal block


title: 115B11_S274

tag: index kit used


title: 115B8_S250

tag: pool name


title: P01397

tag: etiology


title: 115A8_S249


title: 115A7_S241


title: P01421

tag: Sex


title: P01388

tag: race


title: 115B5_S226


title: 115A6_S233


title: P01387

tag: age


title: P01396


title: 115A5_S225

tag: plate name


title: P01385


title: 115A3_S209

tag: brain area


title: P01381


title: P01383


title: 115A4_S217

tag: sample name


title: 115A2_S201

tag: reverse transcription date


title: P01380


title: P01375


title: P01374


title: 105H7_S152

tag: reverse transcription termal block


title: P01379


title: 105H8_S160

tag: tso freeze/thaw cycles


title: P01377


title: 115A10_S265

tag: pre-pcr delay days


title: 105H9_S168

tag: cdna ampure beads purification date


title: 115A12_S281

tag: cdna concentration measurement date


title: 115A11_S273

tag: library prep date


title: P01360


title: P01362


title: 115A1_S193

tag: library pcr thermal block


title: P01365


title: P01367


title: 105H2_S112

tag: index kit used


title: 105H11_S184

tag: pool name


title: 105H10_S176


title: P01358

tag: etiology


title: 105G6_S143


title: 105G8_S159


title: 105G5_S135


title: 105G9_S167


title: P01354

tag: Sex


title: P01356

tag: race


title: P01357

tag: age


title: P01371


title: P01369


title: 105H6_S144

tag: plate name


title: 105G4_S127

tag: brain area


title: 105G2_S111

tag: sample name


title: P01352


title: P01350


title: 105G11_S183

tag: reverse transcription date


title: 105G3_S119

tag: reverse transcription termal block


title: P01348


title: P01359


title: P01340


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title: P01339


title: 105F7_S150

tag: tso freeze/thaw cycles


title: P01337


title: 105F9_S166

tag: pre-pcr delay days


title: P01334


title: P01330


title: 105F1_S102

tag: cdna ampure beads purification date


title: 105F8_S158

tag: cdna concentration measurement date


title: P01329


title: P01325


title: 105F10_S174

tag: library prep date


title: 105F4_S126

tag: library pcr thermal block


title: 105E9_S165

tag: index kit used


title: P01323


title: 105E8_S157

tag: pool name


title: P01320

tag: etiology


title: P01322

tag: Sex


title: 105E7_S149


title: 105E5_S133


title: P01310

tag: race


title: P01318

tag: age


title: 105E1_S101

tag: plate name


title: 105E12_S189

tag: brain area


title: P01309


title: 105G10_S175

tag: sample name


title: P01305


title: 105F11_S182

tag: reverse transcription date


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title: P01307


title: 105D7_S148

tag: reverse transcription termal block


title: 105E3_S117

tag: tso freeze/thaw cycles


title: 105D6_S140

tag: pre-pcr delay days


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title: 105D3_S116

tag: cdna ampure beads purification date


title: P01300


title: 105D1_S100

tag: cdna concentration measurement date


title: P01298


title: P01294


title: P01293

value: Peripartum cardiomyopathy (PPCM)


title: P01292


title: 105D4_S124

tag: library prep date


title: 105D12_S188

tag: library pcr thermal block


title: 105D2_S108

tag: index kit used


title: P01290


title: 105D11_S180

tag: pool name


title: P01289

tag: etiology


title: P01288

tag: Sex


title: 105D10_S172


title: P01287

tag: race


title: 105C9_S163


title: 105D8_S156


title: 105C8_S155


title: 105C7_S147


title: P01282

tag: age


title: P01279


title: 105C4_S123

tag: plate name


title: P01264


title: P01266


title: 105C5_S131

tag: brain area


title: 105C2_S107

tag: sample name


title: P01262


title: P01254


title: P01259


title: P01275


title: 105C12_S187

tag: reverse transcription date


title: 105C10_S171

tag: reverse transcription termal block


title: 105B9_S162

tag: tso freeze/thaw cycles


title: 105C11_S179

tag: pre-pcr delay days


title: 105B3_S114

tag: cdna ampure beads purification date


title: P01247


title: P01252


title: P01248


title: 105B2_S106

tag: cdna concentration measurement date


title: P01246


title: P01245


title: P01241


title: 105B12_S186

tag: library prep date


title: 105C1_S99

tag: library pcr thermal block


title: 105B1_S98

tag: index kit used


title: 105B11_S178

tag: pool name


title: P01238

tag: etiology


title: 105A6_S137


title: P01233

tag: Sex


title: P01226

tag: race


title: 105A5_S129


title: P01228

tag: age


title: 105A4_S121

tag: plate name


title: 105A9_S161

tag: brain area


title: P01217


title: 105A11_S177

tag: sample name


title: 105A12_S185

tag: reverse transcription date


title: 105A10_S169

tag: reverse transcription termal block


title: 105A1_S97

tag: tso freeze/thaw cycles


title: P01215


title: P01224


title: P01211


title: 105A2_S105

tag: pre-pcr delay days


title: P01208


title: 659-RNF43-3

city: Santa Cruz

first: Alexis

middle: Marie

last: Thornton

address: 1156 High Street

department: Biomolecular Engineering

institute: UC Santa Cruz

data_processing:
kallisto, version 0.45.1
Genome_build: Ensembl release 94 GRCh38 cDNA transcriptome
Supplementary_files_format_and_content: *_abundance.tsv: kallisto transcript abundance estimates.

source_name: RNF43 G659fs overexpression replicate 3

extract_protocol:
Qiagen RNeasy protocol, including DNase I treatment.
NEBNext protocol for Illumina.

tag: cell line

tag: overexpression

value: RNF43 frameshift mutant G659fs


title: 659-RNF43-2

source_name: RNF43 G659fs overexpression replicate 2


title: P01207


title: P01206


title: 659-RNF43-1

source_name: RNF43 G659fs overexpression replicate 1


title: P01205


title: 117-RNF43-3

source_name: RNF43 R117fs overexpression replicate 3

value: RNF43 frameshift mutant R117fs


title: P01204


title: P01202


title: 117-RNF43-4

source_name: RNF43 R117fs overexpression replicate 4


title: 105A3_S113

tag: cdna ampure beads purification date

tag: cdna concentration measurement date

tag: library prep date


title: P01222


title: 117-RNF43-2

source_name: RNF43 R117fs overexpression replicate 2


title: P01209


title: P01199


title: P01185


title: 659-RNF43-4

source_name: RNF43 G659fs overexpression replicate 4


title: P01197


title: WT-RNF43-1

source_name: WT RNF43 overexpression replicate 1

value: Wild-type RNF43


title: P01184


title: WT-RNF43-2

source_name: WT RNF43 overexpression replicate 2


title: WT-RNF43-4

source_name: WT RNF43 overexpression replicate 4


title: P01173


title: P01183


title: GFP-3

source_name: GFP overexpression replicate 3

value: GFP control


title: 117-RNF43-1

source_name: RNF43 R117fs overexpression replicate 1


title: WT-RNF43-3

source_name: WT RNF43 overexpression replicate 3


title: P01171


title: P01179


title: GFP-1

source_name: GFP overexpression replicate 1


title: P01168


title: P01167


title: GFP-2

source_name: GFP overexpression replicate 2


title: P01221


title: P01165


title: P01155