title: FUS RIP 3

data_processing:
Base calling: Casava 1.8.2
Mapping: TopHat with default options against GRCh37, aided by Ensembl transcriptome gtf file (GRCh37.75)
Counting: HTSeq -s reverse -a 0 -m union
Genome_build: GRCh37
Supplementary_files_format_and_content: raw counts

source_name: neuroblastoma cell line

extract_protocol:
Total extracts from SH-SY5Y cells were prepared and subjected to FUS-Immunoprecpitation. After subsequent washes of the beads RNA was eluted with TRIreagent.
Subsequently, RNA was isolated, strand specific paired-end RNA libraries were prepared and sequenced on the Illumina HiSeq2000 platform.

value: neuroblastoma cell line


title: osdrm2 Bs-seq

status: Public on Jun 13 2016

type: SRA

city: yichang

first: chao

last: zhou

address: No.8,daxuelu Street

country: China

institute: CTGU

library_source: genomic

data_processing:
Quality Control: fastqc
Remove low quality data:BS-seq raw data, ChIP-seq raw data and RNA-seq raw data's low quality reads were removed from raw data by Trimmomatic. smRNA sequence raw data were cleaned by removing adaptor contamination and low qualityReads by CutAdaptor (Martin, 2011). miRNA (http://www.mirbase.org/ftp.shtml), tRNA(http://rice.plantbiology.msu.edu/analyses_search_tRNA.shtml), rRNA (Rice GenomeAnnotation MSU7.0), snoRNA and snRNA (http://www.arb-silva.de/no_cache/download/archive/release_111/Exports/) were also removed.
Mapping: BS-seq clean data were mapped to MSU7.0 rice reference genome (ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/) by BatMeth (Lim et al., 2012).The RNA-seq clean data were mapped against the MSU7.0 rice genome with corresponding annotation by Tophat2.0(Kim et al., 2013) (http://tophat.cbcb.umd.edu/) using default parameters.And then, the genes’ count were calculated with htseq-count, and the differentially expression’s genes (|log (FC)|>=2 && qvalue < 0.05) were calculated by DESeq2.ChIP-seq Clean reads were aligned to the rice MSU7.0 reference genome by Bowtie (Langmead et al., 2009) allowing 0 mismatches and unique mapping.The ChIP-seq clean reads were mapped to the rice genome (RGAP version 7) by default allowing up to 2 mismatch using Bowtie2 (version 2.1.0).Only uniquely mapped reads were retained for further analysis.
Two types of small RNA abundance was calculated by 21-nt or 24-nt reads number falling into 1 kb windows/regions throughout the whole genomes and windows containing more than 3 reads were tested by EdgeR (Robinson et al., 2010) between samples. Windows with corrected p-value ≤0.01, were defined as differential smRNA regions.
ChIP-seq's peaks calling were used with MACS software with default parameters.
The Differentially Methylated Cytosines (DMCs) between any two genotypes were defined by binomial test (methylSig) (Park et al., 2014). Only cytosine sites whose adjusted q-values ≤ 0.01 and DNA methylation difference of 0.7, 0.5 and 0.1 between any two genotypes were designated for DMCs (Stroud et al., 2013). The Differentially Methylated Regions (DMRs), Differentially Methylated Genes (DMGs) were calculated as DMCs.
Genome_build: MSU7.0:  bulid_all genome.fa
Supplementary_files_format_and_content: wig and peaks' xls files were generated using MACS software;

molecule: genomic DNA

organism: Oryza sativa Japonica Group

source_name: DongJin

growth_protocol: ere germinated and grown on the hormone-free, half-strength Murashige & Skoog (MS) medium under 16/8 hrs light/dark at 30/25°C,Twelve-day-old seedling leaves from each genotype were harvested for chromatin, genomic DNA or total RNA extraction

extract_protocol:
Rice seedling total RNA samples were isolated using TRIzol reagent (Invitrogen).Seedling were crosslinked in 1% formaldehyde under vacuum. Chromatin was extracted and fragmented to 200-750 bp by sonication, and ChIP was performed using the following antibodies: H3K27me3 (a2363, AbclonalABclonal ).The eluted ChIP DNA was used to generate Illumina sequencing libraries following the manufacturer's protocol.
RNA libraries were prepared according to the protocol strictly (http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedmrna/truseq-stranded-mrna-sample-prep-guide-15031047-e.pdf).  Briefly, 1-4 μg of total RNAs were used for mRNA purification and cDNA synthesis. After single ‘A’ nucleotide was added to the 3’ ends of the blunt fragments of the double strand cDNAs, indexing adapters are ligated to the ends of the cDNA. PCR are performed to amplify the DNA fragments. The amplified DNA fragments were purified and sequenced with the Illumina Hiseq-2000 system.The eluted ChIP DNA was used to generate Illumina sequencing libraries following the manufacturer's protocol.
RNA-Seq
ChIP-Seq
Bs-seq

tag: tissue

value: 12 day seedling

tag: mutant


title: H4-48-52h_after_hatching_herma

city: Bronx

first: Byunghyuk

last: Kim

state: NY

address: 1300 Morris Park Ave

department: Genetics

country: USA

institute: Albert Einstein College of Medicine

library_source: transcriptomic

data_processing:
Illumina Casava (version 1.8) software used for basecalling.
Raw FASTQ files were trimmed for adapter sequences using quart.
Alignment to the reference genome was performed using gsnap (version 2012-07-20)
Assignment of reads to genes is performed by htseq-count (version v0.5.3p3)
Genome_build: WS190/ce6
Supplementary_files_format_and_content: Tab-delimited text files include read count data for each gene. These data are not normalized.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: Whole-animal

growth_protocol: Worms were grown at 20C on standard nematode growth media (NGM) plates with OP50 E.coli as a food source until sampling.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen); DNA was removed with TURBO DNA-free (Life Technologies).
For each sample, a total of 1 ug of RNA was used for library preparation according to standard Illumina protocols (detailed protocol available at http://wasp.einstein.yu.edu)

tag: genotype

tag: Sex

value: Hermaphrodite

tag: time

value: young adult:48-52h after hatching


title: Hes1_KO_UT_rep1

city: New York

first: Yingli

last: Shang

address: 535E 70th Street

institute: Hospital for Special Surgery

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie version 1.0.1
Reads have passed Illumina filters, and been trimmed using Sickle using quality threshold >20
Peaks were called using ChIPseeqer with the following setting: p < 10~-15, FDR <0.02)
Annotation and downstream analysis was done using ChIPseeqer
Genome_build: mm10
Supplementary_files_format_and_content: wig

organism: Mus musculus

source_name: Macrophages

growth_protocol: Bone marrows cells from WT and DKO mice were cultured for 5 days in DMEM supplemented with 10% FBS and 10% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor to generate BMDMs

extract_protocol:
Lysates were clarified from sonicated nuclei and Pol II-DNA complexes were isolated with antibody
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and DKO BMDMs were left untreated or exposed to 10 ng/ml cell culture grade LPS (Escherichia coli 0111:B4, Sigma) for 1 hour.

tag: cell type

value: Bone marrow-derived macrophages

tag: strain

tag: chip antibody

value: RNA Pol II


title: osddm1a Bs-seq


title: FUS RIP 2

city: Bern

first: Oliver

last: Muehlemann

address: Freiestrasse 6

country: Switzerland

institute: University of Bern

organism: Homo sapiens

tag: cell line


title: H3-42-46h_after_hatching_herma

value: late L4:42-46h after hatching


title: H2-36-40h_after_hatching_herma

value: early L4:36-40h after hatching


title: FUS RIP 1


title: CSF1R-1_L5.N703

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

institute: F. Hoffmann-La Roche Ltd.

data_processing:
Raw read data was aligned against mouse transcriptome (MouseEnsembl release 61) using Bowtie2 (Langmead and Salzberg, 2012). Splice junctions were defined as available in Ensembl v75. Read mappings were then mapped to genes and transcripts based on the transcript models annotated in Ensembl v75 using in-house tools and, again using in-house software, RPKM values were computed as described previously (Mortazavi et al., 2008).
Genome_build: MouseEnsembl release 61
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each sample

source_name: Dicer_x_LysM.Cre (D–/–)

extract_protocol:
Cells were homogenized in 700 µl Qiazol reagent (Qiagen). 140 ul of chloroform was added to the homogenate and the mixture centrifuged at 16,000 x g for 5 min at 4°C in Phase Lock Tubes (Qiagen). RNA was subsequently extracted from the aqueous phase using the RNeasy Micro kit (Qiagen) according to manufacturer’s instructions. Genomic DNA was removed using the RNase free DNase set (Qiagen) during the extraction. RNA was quality controlled on Agilent RNA 6000 pico chips (Agilent Technologies). High quality RNA (RIN >7) was obtained for all samples. SMARTer ultra low RNA kit for Illumina sequencing (Clontech) was used to prepare and amplify cDNA from two ng of total RNA according to manufacturer’s instructions.
One ng of amplified cDNA was then subjected to Nextera XT library preparation (Illumina) according to manufacturer’s instructions. Sequencing libraries were quantified using the Kapa Library Quantification kit (Kapa Biosystems) and quality controlled by capillary electrophoresis on a Bioanalyzer using High Sensitivity chips (Agilent Technologies). Libraries were sequenced on a HiSeq2500 sequencer (Illumina) for 2 x 50 cycles using version 4 cluster generation kits and version 4 sequencing reagents (Illumina).

treatment_protocol: To explore the role of DICER in the development, activation and immunological functions of TAMs, we crossed homozygous LysM-Cre (Clausen et al., 1999) with Dicerlox/lox (Harfe et al., 2005) mice to obtain mice with myeloid-cell-specific Dicer1 gene deletion (LysM-Cre;Dicer–/–, referred to as D–/–). These mice were then backcrossed to LysM-Cre to obtain the control LysM-Cre mice; Dicer+/+ mice (referred to as D+/+). Both LysM-Cre and Dicerlox/lox mutations were always homozygous in our experiment. We then inoculated Lewis lung carcinoma (LLC) cells subcutaneously (s.c.) in D–/– and control D+/+ mice. Once the tumors were established, we isolated by fluorescence-activated cell sorting (FACS) tumor-associated macrophages (F4/80+ cells).

tag: genotype/variation

tag: protocol

value: inoculated Lewis lung carcinoma (LLC) cells subcutaneously in mice


title: M1-30-34h_after_hatching_male

value: Male

value: late L3:30-34h after hatching


title: WT_UT_rep1


title: Input RNA


title: Cr-DJ Bs-seq

value: DJ


title: osddm1a/1b Bs-seq


title: H1-30-34h_after_hatching_herma


title: 20,000 R Day 10, Rep 1

status: Public on Jun 12 2016

city: Providence

first: Michael

last: Antosh

state: RI

address: Brown University Box 1843

institute: Michael Antosh

data_processing:
Sequences were aligned using Tophat version 2.0
Gene counts were calculated using bioconductor package easyRNASeq, with annotation coming from the bioconductor package biomaRt
Differentially expressed genes were determined using the bioconductor package DESeq
Genome_build: dm3
Supplementary_files_format_and_content: text file with normalized gene expression

organism: Drosophila melanogaster

extract_protocol:
Flies were aged 2, 10 and 20 days after irradiation, then collected using light anesthesia and frozen using liquid nitrogen. mRNA was extracted from whole flies.
Illumina TruSeq kit

value: whole body

tag: radiation dose

value: 20,000 Roentgen

tag: time post-irradiation (days)


title: 20,000 R Day 20, Rep 3


title: 20,000 R Day 10, Rep 3


title: 20,000 R Day 20, Rep 2


title: 20,000 R Day 2, Rep 3


title: 10,000 R Day 20, Rep 3

value: 10,000 Roentgen


title: 20,000 R Day 20, Rep 1


title: WT_LPS_rep1


title: 10,000 R Day 10, Rep 1


title: 10,000 R Day 2, Rep 2


title: 10,000 R Day 2, Rep 3


title: 5,000 R Day 20, Rep 3

value: 5,000 Roentgen


title: 10,000 R Day 2, Rep 1


title: 5,000 R Day 20, Rep 1


title: SGC_H4K5ac_ChIP

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were aligned to the human genome (G1k V37) using bwa 0.6.2-r126
Peak-calling was performed using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: bed files from MACS2 for each sample

source_name: MV4;11 cell line

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with 20% fetal calf serum, penicillin (100 units/mL) and streptomycin (100 ug/mL)

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin, then immunoprecipitated with antibody
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics)

treatment_protocol: Cell lines were grown in 0.1% DMSO or 5uM of SGC0946

value: peripheral blood

tag: treatment


title: 5,000 R Day 10, Rep 2


title: 5,000 R Day 10, Rep 3


title: 20,000 R Day 10, Rep 2


title: 5,000 R Day 10, Rep 1


title: SGCwashout_Pol2_ChIP

treatment_protocol: Cell lines were grown in 0.1% DMSO, 500nM of I-BET151 and/or 5uM of SGC0946

value: Mixed lineage leukemia (MLL) fusion protein (FP) leukemia cell line

value: 5uM SGC0946 for 8 hrs and washout

value: anti-RNA Pol II (CTD4H8, Millipore, lot 2491218)


title: 20,000 R Day 2, Rep 1


title: 20,000 R Day 2, Rep 2


title: DMSO_H4K5ac_ChIP

value: DMSO


title: SGCwashout_BRD4_ChIP

value: anti-BRD4 (E2A7X, cell signalling, lot 1)


title: SGCwashout_H3K79me2_ChIP


title: SGC8h_Pol2_ChIP

value: 5uM SGC0946 for 8hrs


title: 10,000 R Day 10, Rep 2


title: 5,000 R Day 2, Rep 2


title: SGC8h_H3K79me2_ChIP


title: 10,000 R Day 20, Rep 1


title: 1,000 R Day 20, Rep 3

value: 1,000 Roentgen


title: 5,000 R Day 2, Rep 1


title: SGC8h_BRD4_ChIP


title: 1,000 R Day 20, Rep 2


title: 10,000 R Day 10, Rep 3


title: 5,000 R Day 20, Rep 2


title: 1,000 R Day 20, Rep 1


title: 1,000 R Day 10, Rep 3


title: 5,000 R Day 2, Rep 3


title: DMSO_BRD4_ChIP2

value: 0.1% DMSO


title: DMSO_H3K79me2_ChIP2


title: I-BET + SGC0946 Rep 2

description: Replicate 2

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were aligned to the human genome (G1k V37) using tophat2 and bowtie2
Reads were assigned to genes using htseq-count. Differential expression was calculated using edgeR.
Genes with a false discovery rate below 0.05 and a fold‐change greater than 2 were considered significantly differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file of normalised expression values for all Samples

molecule: polyA RNA

extract_protocol:
RNA was prepared using the Qiagnen RNeasy kit
TruSeq RNA Sample Preparation protocol (Illumina)

tag: tissue source

tag: treated with

value: 500nM I-BET151 and 5uM SGC0946


title: 1,000 R Day 2, Rep 3


title: 1,000 R Day 10, Rep 1


title: SGC0946 treated Rep 2

description: Replicate 2

source_name: MV4;11_SGC0946 treated

value: 5uM SGC0946


title: 1,000 R Day 2, Rep 2


title: 10,000 R Day 20, Rep 2


title: 1,000 R Day 2, Rep 1


title: I-BET + SGC0946 Rep 1

description: Replicate 1


title: I-BET treated Rep 2

description: Replicate 2

source_name: MV4;11_I-BET treated


title: DMSO Rep 2

description: Replicate 2


title: DMSO Rep 1

description: Replicate 1


title: 10 R Day 20, Rep 2

source_name: 10 R Day 20

value: 10 Roentgen


title: DMSO_Pol2_ChIP2


title: I-BET treated Rep 1

description: Replicate 1


title: 10 R Day 20, Rep 1


title: input DNA

source_name: MV4;11_input DNA


title: 10 R Day 10, Rep 1

source_name: 10 R Day 10


title: IBET+SGC_Pol2_ChIP


title: 10 R Day 10, Rep 3


title: 10 R Day 10, Rep 2


title: 10 R Day 2, Rep 3

source_name: 10 R Day 2


title: 10 R Day 2, Rep 1


title: IBET+SGC_H3K79me2_ChIP


title: IBET+SGC_BRD4_ChIP


title: 10 R Day 2, Rep 2


title: SGC_H3K79me2_ChIP


title: SGC_BRD4_ChIP


title: SGC_Pol2_ChIP


title: SGC0946 treated Rep 1

description: Replicate 1


title: Control Day 20, Rep 1

source_name: Control Day 20

value: Control (background)


title: IBET_H3K79me2_ChIP


title: Control Day 10, Rep 2

source_name: Control Day 10

value: whole body


title: Control Day 10, Rep 3


title: Control Day 20, Rep 2


title: DMSO_Pol2_ChIP


title: IBET_BRD4_ChIP


title: Control Day 10, Rep 1


title: DMSO_H3K79me2_ChIP


title: Control Day 2, Rep 3

source_name: Control Day 2


title: Control Day 2, Rep 2


title: DMSO_H3K27ac_ChIP

value: anti-H3K27ac (ab4729, abcam, lot GR85490-1)


title: Control Day 2, Rep 1


title: DMSO_BRD4_ChIP


title: Patient5_N

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

data_processing:
Base calling with CASAVA 1.8.2
Alignment was performed with TopHat2
For quantification and variant calling Avadis NGS (Strand) was used.
Genome_build: hg19

source_name: Peripheral blood mononuclear cells

extract_protocol:
Peripheral blood mononuclear were stained with anti CD8 PE and CD57 FITC antibodies and sorted by FACS. RNA was extracted with TRIzol and purified with the RNeasy Mini Kit
Libraries were prepared using the NuGEN Encore platform according to manufacturer´s giudelines

value: sorted CD8 neg CD57 neg T cells

tag: sample type

value: normal


title: Patient3_T

value: sorted CD8 pos CD57 pos T cells

value: tumour (T-cell large granular lymphocytic leukemia)


title: Patient4_T


title: IBET_Pol2_ChIP

value: peripheral blood

value: Mixed lineage leukemia (MLL) fusion protein (FP) leukemia cell line


title: Hlf/Hlf forced dimer lentivirus transduced GMLPs cultured on OP9 stroma, Replicate 1

city: Lund

first: Martin

last: Wahlestedt

address: Klinikgatan 26

department: Divison of Molecular Hematology

country: Sweden

institute: Lund University

description:
hlf_hlf_2_rna_2
Control_virus_vs_HlfHlf_virus_edgeR.txt

data_processing:
Libraries were prepared and sequenced on the Illumina HiSeq 2500 platform at the Genome Access Technology Center (GTAC, Washington University School of Medicine, St. Louis, MO). The data was processed by the GTAC standard pipeline.
In brief, this included converting the raw image data to basecalls with Casava 1.8+. The fastQ files were then aligned to the transcriptome and the whole-genome (Ensembl_R72) with TopHat version 2.0.8 using Bowtie2 version 2.1.0.
Differentially expressed genes were determined using EdgeR.
Genome_build: Ensembl_R72
Supplementary_files_format_and_content: Text files with differentially expressed genes as determined by EdgeR.

source_name: Bone marrow

growth_protocol: Duplicate cultures of WT GMLPs, transduced overnight on retronectin coated plates with pHAGE2-Hlf/Hlf or a pHAGE2 control virus, and Hlf inducible GMLPs maintained in the presence or absence of DOX (1 ug/ml), were cultured on OP9 stroma in NK cell permissive conditions (OptiMEM, FCS, IL7, Flt3L, SCF, IL2, IL15) for 4 days.

extract_protocol:
After 4 days of coculture, ZsGreen+/CD45+ cells were sorted directly into RLT lysis buffer (1000 – 50,000 cells). Total RNA was extracted from the samples using the Qiagen RNeasy Micro Kit.
Library preparation was conducted using the SMARTer Ultra Low Input RNA Kit for Sequencing (Clontech). Barcode sequence for each sample is included in the fastq file name.

tag: age

value: 8-10 weeks

value: GMLPs


title: Control lentivirus transduced GMLPs cultured on OP9 stroma, Replicate 2

description:
control_3_rna_12
Control_virus_vs_HlfHlf_virus_edgeR.txt

value: Control lentivirus transduced


title: Patient5_T


title: Hlf/Hlf forced dimer lentivirus transduced GMLPs cultured on OP9 stroma, Replicate 2

description:
hlf_hlf_3_rna_3
Control_virus_vs_HlfHlf_virus_edgeR.txt


title: Control lentivirus transduced GMLPs cultured on OP9 stroma, Replicate 1

description:
control_1_rna_10
Control_virus_vs_HlfHlf_virus_edgeR.txt


title: Hlf inducible GMLPs cultured on OP9 stroma with doxycycline, Replicate 2

description:
plus_dox_2_16_rna
no_dox_vs_DOX_edgeR.txt

value: Hlf-inducible GMLPs

value: with doxycycline


title: Patient4_N


title: Patient3_N


title: Patient2_T


title: Hlf inducible GMLPs cultured on OP9 stroma without doxycycline, Replicate 1

description:
no_dox_1_13_rna
no_dox_vs_DOX_edgeR.txt

value: without doxycycline


title: Hlf inducible GMLPs cultured on OP9 stroma without doxycycline, Replicate 2

description:
no_dox_2_14_rna
no_dox_vs_DOX_edgeR.txt


title: Patient2_N


title: Patient1_N


title: HPAF_2_SL23297

status: Public on Jun 11 2016

city: Huntsville

first: Marie

middle: K

last: Kirby

state: AL

address: 601 Genome Way NE

institute: HudsonAlpha Institute for Biotechnology

data_processing:
RNA-seq paired-end FASTQ files were aligned to hg19 using Tophat and Cufflinks
Sequence counts for each transcript were compiled across all experiments for each time point
Genome_build: hg19
Supplementary_files_format_and_content: Gene transcript sequence counts for all genes across all cell lines using GENCODE v. 9

source_name: Pancreatic cancer cell line

growth_protocol: Cells were grown in standard conditions as described by ATCC.

extract_protocol:
RNA was extracted from the pancreatic tissue using the Norgen Animal RNA isolation kit.
RNA-seq was performed as previously outlned (Gertz et al. 2012)

value: HPAF-II

tag: gemcitabine sensitivity

value: Resistant


title: Capan_1_SL23294


title: Degradome short-time

city: Anyang

first: Zujun

last: Yin

state: Henan

address: 38 Huanghe Dadao, Anyang 455000, Henan, China

department: Cotton Research Institute

institute: Chinese Academy of Agricultural Sciences

data_processing:
The very basic figure from sequencing is converted into sequence data by the base calling step.As there are some adaptor sequences and/or low quality reads present in the raw reads, data filtering is carried out to obtain high quality reads as the clean reads
We summarize the length distribution of these clean reads. Normally, length distribution peak of degradom fragment is between 20nt and 21nt. Summarize the common and specific tags, including the summary of unique tags and total tags.
Annotate the Degradome tags with rRNA, scRNA, snoRNA, snRNA and tRNA from Rfam and get rid of matched tags from unannotated tags. Annotate the Degradome tags with rRNA, scRNA, snoRNA, snRNA and tRNA from Genbank and get rid of matched tags from unannotated tags.
Identify degraded sequences with single base over 70% in the clean reads as polyN.
To map every unique Degradome to only one annotation, we follow the priority rule: Rfam > Genbank > Poly N, and map unannotated tags to reference genes (cDNA). The tags mapped to cDNA_sense were used to predict cleavage sites.
Genome_build: Cotton Unigenes database (obtained by transcriptome sequencing ) Rfam and Genbank database
Supplementary_files_format_and_content: Total_cleave_site.txt    This file contains cleavage information of total cleaved genes

organism: Gossypium hirsutum

source_name: Cotton leaves

growth_protocol: The upland cotton cultivar SN-011 was used in this study. Seeds were sterilized and germinated in vermiculite. Growth conditions were 30/22 day/night temperature, 55–70% relative humidity, and a 14 h/10 h light/dark cycle under 450 μmol m−2⋅s−1 light intensity. At the two-leaf stage, healthy seedlings were grown in pots containing aerated nutrient solution. Plants were cultured under non-saline conditions for 10 d to ensure full establishment before starting the salinity treatments. The pH was maintained close to 6.9 by adding H2SO4 or KOH as required.

extract_protocol:
Total RNA was isolated using a modified CTAB method and purified using Qiagen RNeasy columns (Qiagen, Hilden, Germany).By using the Oligotex kit (Qiagen, location), 200 μg of total RNA was used for extracting poly (A) RNA, which were ligated with an RNA adapter consisting of a MmeI recognition site in its 3′end.
The extracted PloyA RNAs  were ligated with an RNA adapter consisting of a MmeI recognition site in its 3′end. After ligation, first-strand cDNA was generated using oligod (T) and the PCR product was amplified using five PCR cycles. The PCR product was purified and digested with MmeI. The digested PCR product was then ligated to a double-stranded DNA oligonucleotide with degenerate nucleotides at the 5′-or 3′-ends. The ligation product was further gel purified and amplified using 10 PCR cycles. The final PCR product was purified and sequenced using Illumina’s sequencing by synthesis (SBS) sequencing technology.

treatment_protocol: For short-term salt treatment samples, seedlings were treated with 150 mM solution of NaCl. After exposing the seedlings to salt stress for 4 h, cotton leaves of the short-term salt treatment samples were harvested. For long-term salt treatment samples, seedlings were exposed to salinity by adding NaCl to the growth medium in 50 mM increments every 12 h, until a final concentration of 150 mM was reached. After exposing the seedlings to salt stress for 5 d, leaves were harvested directly into liquid nitrogen and stored at −80 °C for subsequent use.

tag: tissue

value: Cotton leaves

value: under saline conditions for 4h

tag: cultivar


title: Degradome CK

value: under non-saline conditions

tag: time


title: Capan_2_SL23295


title: AsPC_1_SL23292


title: Panc_6_03_SL23302

value: PANC 6.03


title: L3_6pl_SL23298

value: Sensitive


title: PANC_1_SL23300


title: S2_LM7_AA_SL23305


title: S2013_SL23307


title: T_11_06_A104a_SL13102

data_processing:
RNA-seq paired-end FASTQ files were aligned to hg19 using Tophat and Cufflinks
Sequence counts for each transcript were compiled across all experiments for each time point
Genome_build: hg19
Supplementary_files_format_and_content: Gene transcript sequence counts for all genes across all tissues using GENCODE v. 9

source_name: pancreatic adenocarcinoma cancer tissue

tag: patient survival status

value: Dead

tag: survival time (days)

tag: patient race

value: white

tag: patient gender

value: male

tag: t (tnm score)

tag: n (tnm score)

tag: m (tnm score)

tag: diabetes status

value: no


title: S2_LM7_YB_SL23306

tag: cell line


title: S2_VP10_SL23308


title: T_11_02_A148a_SL13037

value: yes


title: Suit_2_SL23304


title: Hlf inducible GMLPs cultured on OP9 stroma with doxycycline, Replicate 1

description:
plus_dox_1_15_rna
no_dox_vs_DOX_edgeR.txt

tag: strain

value: 8-10 weeks

tag: cell type

tag: protocol


title: T_11_05_A018b_SL13062

tag: age


title: T_11_04_A026b_SL13061

value: Alive

value: female


title: Patient1_T

value: sorted CD8 pos CD57 pos T cells

tag: sample type

value: tumour (T-cell large granular lymphocytic leukemia)


title: T_10_11_A128a_SL13032


title: T_10_11_A130b_SL13034


title: Degradome long-time

tag: tissue

tag: treatment

value: seedlings were treated with 150 mM solution of NaCl

value: under saline conditions for 5d


title: T_11_02_A171a_2_SL13039


title: T_10_10_A222aa_SL13029


title: T_10_12_A057a_SL13036


title: T_08_03_A203a_SL13024

value: black


title: Normal [B5]

city: Chongqing

first: Hangxing

last: Ren

address: Rongchang District, Changlong Street 51#

institute: Chongqing Academy of Animal Sciences

data_processing:
The libraries were sequenced on an Illumina Hiseq 2000 platform and 100 bp paired-end reads were generated. Raw data were processed through in-house perl script.In this step, clean data were abtained by removeing adapter and low quality reads from raw data.
Index of the reference genome was built using Bowtie (v2.0.6) and paired-end clean reads were aligned to the reference genome using TopHat(v2.0.9)
The reads were classified into two clusters by mapping to the reference genome, the mRNAs and lncRNAs. For mRNAs, alternative splicing , InDel, SNP, and DEU analysis were performed using Asprofile 1.0,GATK2,and Cuffdiff 2.2.2 respectively .For identification of the lncRNAs,the prelimilary scanning was conducted  by both Scripture (beta2)and Cufflinks (v2.1.1) in a reference-based approach, follwed by coding poteintial analysis using CNCI (v2), CPC (0.9-r2), Pfam Scan (v1.3), and PhyloCSF (v20121028).
Gene differential expression analysis was  conducted using Cuffdiff (2.1.1), and the targets for lncRNAs were also predicted in cis and trans action.
Functional enrichment analyses of differential genes and lncRNA targets were conducted by DAVID platform. RNA-seq results were validated by quantitative PCR.
genome build: CHIR_1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values, gene type,chromosome, and strand information for each Sample.

organism: Capra hircus

source_name: White skin

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA, USA),according to the manufacturer’s instructions.
Sequencing libraries were generated using the rRNA-depleted RNA by NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations.

tag: developmental stage

value: 100-day fetus

tag: breed

value: Yudong white goat


title: Normal [B6]


title: T_08_06_A060a_SL13027

tag: patient survival status

tag: survival time (days)


title: T_08_01_A194a_SL13021

tag: patient race

tag: patient gender


title: Hyperpigmented [Y3]

source_name: Dark skin

value: Youzhou dark-skin goat


title: T_07_10_A215a_SL13017

tag: t (tnm score)

tag: n (tnm score)


title: T_11_06_A011a_SL13100

tag: m (tnm score)

tag: diabetes status


title: Normal [B4]


title: T_08_05_A123a_SL13026


title: T_07_10_A153a_1_SL12835


title: T_07_10_A314a_SL13019


title: Hyperpigmented [Y2]


title: T_07_06_A323a_1_SL12833


title: Hyperpigmented [Y1]


title: T_07_02_A216a_SL12830


title: T_07_06_A104a_SL12831


title: T_07_03_A187a_SL12838


title: T_06_09_A196a_2_SL12825


title: T_06_11_A299b_SL12826


title: T_06_05_A309a_3_SL12836

value: MX


title: T_08_02_A333a_SL13022

value: Dead


title: T_06_02_A026a_SL12822

value: white


title: T_05_08_A230b_SL12821

value: male


title: T_05_06_A121b_SL12820

value: no


title: T_05_03_A215c_SL12819

value: yes


title: wt_3

description: WT RNA from SH-SY5Y cells

data_processing:
Mapping: TopHat v2.0.9
Counting: HTSeq-count, –r name –s reverse –a 0 –m union
Genome_build: GRCh38.81
Supplementary_files_format_and_content: Counts: Ensembl gene id, reads count

source_name: WT RNA from SH-SY5Y cells

extract_protocol:
Total RNA was extracted from biological replicates.
PolyA transcripts were selected. Stranded Illumina library kit was employed.

treatment_protocol: Three wells of a six well plate containing 80 % confluent SH-SY5Y neuroblastoma cells were each transfected with 2.7 μg FUS knockout ZeoR matrix (GeneArt, Life Technologies) and 1.3 μg of plasmid coding for the Cas9 endonuclease and the guide RNAs which target the first intron of FUS

value: neuroblastoma cell line

tag: cell line


title: T_05_01_A082b_SL12818


title: T_04_04_A207b_SL12815


title: T_04_06_A027c_SL12816


title: T_04_12_A158b_SL12817

value: Alive


title: T_07_08_A346a_SL11236


title: T_06_11_A455b_SL11223


title: T_07_02_A073a_SL12837

value: female


title: T_11_03_A060a_SL11234


title: T_07_02_A181a_SL12828


title: T_10_12_A046a_SL11232


title: T_04_02_A274c_SL11240


title: T_10_11_A059a_SL11238


title: T_07_09_A064a_SL11235


title: T_03_11_A244a_SL11221


title: T_11_03_A138a_SL11227


title: T_06_04_A296a_T_SL9581


title: T_10_11_A100a_SL13030


title: T_06_01_A033a_T_SL9583


title: Naive 1

city: Tucson

first: Deepta

last: Bhattacharya

state: Arizona

address: 1656 E. Mabel Street, MRB 217

department: Department of Immunobiology

institute: University of Arizona

description: peripheral blood B cells were purified by fluorescence activated cell sorting

data_processing:
FastQ Groomer
TopHat for gapped read mapping
Partek Genomics Suite v6.6 for generation of RPKM values
Genome_build: Ensembl_R72 reference human genome
Supplementary_files_format_and_content: Excel file of RPKM values for each sample

source_name: Peripheral blood naïve B cells

growth_protocol: primary ex vivo

extract_protocol:
Qiagen Rneasy Micro Kit
Clontech Smart Seq; barcodes: TCCCAGC:CD19+ BMPC1; TGTTTGT:CD19+ BMPC2; ATGACAG:CD19+ BMPC3; CTCCCGA:CD19+ BMPC4; CGGTGGC:plasmablast; TGAGGTT:IgG memory 1; TTTAACT:IgM memory 1; ACGTCTG:naïve

value: peripheral blood

tag: markers

tag: cell type

value: Peripheral blood naive B cells


title: T_07_11_A090a_SL11231

tag: age


title: T_07_07_A082a_SL11228


title: Plasmablast 1

source_name: Peripheral blood plasmablasts

value: CD19+ CD27-high CD38-high CD20- CD2-

value: Peripheral blood plasmablasts


title: CD19+ BMPC4

description: CD19+ CD138+ plasma cells were purified by fluorescence activated cell sorting from bone marrow apsirates

source_name: bone marrow plasma cells

value: bone marrow

value: bone marrow plasma cells


title: T_06_06_A349a_SL11225


title: CD19+ BMPC3


title: 3h-con-gfp2.20nt_S23_L001_R1_001_AF_SOL_672_OUTPUT.fasta

status: Public on Jun 10 2016

city: Stanford

first: Andrew

last: Fire

state: California

address: 300 Pasteur Drive Lane building L302

institute: Stanford

data_processing:
No processing. There is just a calculation of retention scores for each sequence with n>=50 counts in the control samples.
Computational Methods: Calculation of retention and normalization:
We use the log2 of retention in the PCR pool as a measure of target cleavage by Cas9, with a retention score calculated for each sequence in each experiment.
For each sequence 'X':
Retention[X]= log2(RepresentationX[Cleaved Library]/RepresentationX[Uncleaved Library])
Representationx in a library gives the ratio between:
[Instances of sequence X in the library]/[Instances of a reference population in the library]
As reference populations we used either an aggregate of all sequences with 4-7 mismatches to the original trigger, or (for the unc-22A library) an "internal control" population comprising a subset of plasmids from the protospacer 4 library.  Comparable results were obtained with these two references for normalization.
Supplementary_files_format_and_content: Raw data is in fastq format. Data used to calculate retention is in fasta format. Refer to PMID: 25399416 for how to calcuate retention. This analysis step should be performed by further processing depending on user parameters.

organism: synthetic construct

source_name: type II RVL

extract_protocol:
Cas9 in vitro cleavage specificity assay
In vitro Cas9 cleavage assays and gRNA transcription (17, 18, and 20 nt of complementarity) were performed as described in PMID: 25399416.
Cas9 in vivo cleavage specificity assays
Yeast culturing and sample collection was performed using a cell-screening platform that integrates temperature-controlled absorbance plate readers, plate coolers, and a liquid handling robot. Briefly, 700 ul yeast cultures were grown in 48 well plates at 30oC with orbital shaking in Infinite plate readers (Tecan). To maintain cultures in log phase over 10 doublings, 80 uls of the culture was removed when it reached an OD of 0.76, added to a well containing 620 ul of media, and then allowed to grow further. After two such dilutions, 600 uls of the culture was collected and saved to a 4oC cooling station (Torrey Pines) when it reached an OD of 0.76. This amounted to approximately 10 culture doublings from the beginning of the experiment. Pipetting events were triggered automatically by Pegasus Software and performed by a Freedom EVO workstation (Tecan). After sample collection, yeast plasmids were purified using the Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research).

treatment_protocol:
Cas9 in vitro cleavage specificity assay
Cas9 in vitro cleavage assays and gRNA transcription (17, 18, and 20 nt complementarity) were performed as described in Fu et al. 2014 (doi: 10.1093/nar/gku1102). Over 4000 unique species were assayed in vitro.
Cas9 in vivo cleavage specificity assays
Starting cultures were grown overnight at 30oC in synthetic complete media –Ura. This culture was then used to inoculate experimental cultures to OD 0.1 in YP Galactose media with 250ng/ml anhydrotetracycline (ATC). To control for possible effects of non-homologous end joining (NHEJ) events, we did our initial experiments in both wild BY4741 strain and a KU70 null NHEJ deficient strain.  17, 18, 20 and 20+G nt complementarity gRNA strains were grown for 12 hours in inducing conditions.  No detectible difference in the cleavage pattern was observed. Wild type BY4741 was used for all further experiments. Approximately 3000-4500 unique species were assayed in vivo.
Further experiments were done with 18 and 20 nt complementarity versions of the gRNAs in BY4741.  Yeast culturing and sample collection was performed using a cell-screening platform that integrates temperature-controlled absorbance plate readers, plate coolers, and a liquid handling robot. Briefly, 700 ul yeast cultures were grown in 48 well plates at 30oC with orbital shaking in Infinite plate readers (Tecan). To maintain cultures in log phase over 10 doublings, 80 uls of the culture was removed when it reached an OD of 0.76, added to a well containing 620 ul of media, and then allowed to grow further. After two such dilutions, 600 uls of the culture was collected and saved to a 4oC cooling station (Torrey Pines) when it reached an OD of 0.76. This amounted to approximately 10 culture doublings from the beginning of the experiment. Pipetting events were triggered automatically by Pegasus Software and performed by a Freedom EVO workstation (Tecan). After sample collection, yeast plasmids were purified using the Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research).

tag: target random variant library (rvl)

value: type II RVL

tag: molecule subtype

value: library DNA


title: CD19+ BMPC2

tag: tissue


title: 3f-lo-10-gfp2.20nt_S21_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 3g-lo-10-gfp2.20nt_S22_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 3b-lo-10-rol6.17nt_S17_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 3e-lo-10-gfp2.20nt_S20_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 3c-lo-10-rol6.17nt_S18_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 3a-lo-10-rol6.17nt_S16_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 3d-con-rol6.17nt_S19_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 2h-con-unc22.17nt_S16_L001_R1_001_AF_SOL_676_OUTPUT.fasta


title: 2g-lo-10-unc22.17nt_S15_L001_R1_001_AF_SOL_676_OUTPUT.fasta


title: 2h-con-rol6.18nt_S15_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: T_06_11_A168a_SL11229


title: 2g-lo-10-rol6.18nt_S14_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 2f-lo-10-unc22.17nt_S14_L001_R1_001_AF_SOL_676_OUTPUT.fasta


title: 2e-lo-10-rol6.18nt_S12_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 2d-con-unc22.18nt_S11_L001_R1_001_AF_SOL_676_OUTPUT.fasta


title: 2f-lo-10-rol6.18nt_S13_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 2e-lo-10-unc22.17nt_S13_L001_R1_001_AF_SOL_676_OUTPUT.fasta


title: CD19+ BMPC1


title: IgG memory 1

source_name: Peripheral blood IgG memory B cells

value: Peripheral blood IgG memory B cells


title: 2d-con-rol6.20nt_S11_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 2c-lo-10-unc22.18nt_S10_L001_R1_001_AF_SOL_676_OUTPUT.fasta


title: 2c-lo-10-rol6.20nt_S10_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 2b-lo-10-rol6.20nt_S9_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 2b-lo-10-unc22.18nt_S9_L001_R1_001_AF_SOL_676_OUTPUT.fasta


title: 2a-lo-10-unc22.18nt_S8_L001_R1_001_AF_SOL_676_OUTPUT.fasta


title: 2a-lo-10-rol6.20nt_S8_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 1h-con-gfp2.17nt_S7_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 10 R Day 20, Rep 3

source_name: 10 R Day 20

value: whole body

tag: radiation dose

value: 10 Roentgen

tag: time post-irradiation (days)


title: 1h-con-unc22.20nt_S7_L001_R1_001_AF_SOL_676_OUTPUT.fasta


title: 1g-lo-10-gfp2.17nt_S6_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 1f-lo-10-unc22.20nt_S5_L001_R1_001_AF_SOL_676_OUTPUT.fasta


title: 1d-con-gfp2.18nt_S3_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 1g-lo-10-unc22.20nt_S6_L001_R1_001_AF_SOL_676_OUTPUT.fasta


title: 1e-lo-10-unc22.20nt_S4_L001_R1_001_AF_SOL_676_OUTPUT.fasta


title: 1f-lo-10-gfp2.17nt_S5_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 1e-lo-10-gfp2.17nt_S4_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 1c-lo-10-gfp2.18nt_S2_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 1b-lo-10-gfp2.18nt_S1_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 1d-con-gfp1r18nt_S3_L001_R1_001_AF_SOL_676_OUTPUT.fasta


title: 1a-lo-10-gfp1r18nt_S12_L001_R1_001_AF_SOL_676_OUTPUT.fasta


title: IgM memory 1

source_name: Peripheral blood IgM memory B cells

value: Peripheral blood IgM memory B cells


title: 1h-con-gfp1-os17_S7_L001_R1_001_AF_SOL_675_OUTPUT.fasta


title: 1c-lo-10-gfp1r18nt_S2_L001_R1_001_AF_SOL_676_OUTPUT.fasta


title: 1b-lo-10-gfp1r18nt_S1_L001_R1_001_AF_SOL_676_OUTPUT.fasta


title: 1,000 R Day 10, Rep 2

value: 1,000 Roentgen


title: 1f-lo-10-gfp1os17_S5_L001_R1_001_AF_SOL_675_OUTPUT.fasta


title: 1g-lo-10-gfp1os17_S6_L001_R1_001_AF_SOL_675_OUTPUT.fasta


title: 1c-lo-10-gfp1os18_S2_L001_R1_001_AF_SOL_675_OUTPUT.fasta


title: 1b-lo-10-gfp1os18_S1_L001_R1_001_AF_SOL_675_OUTPUT.fasta


title: 1d-con-gfp1-os18_S3_L001_R1_001_AF_SOL_675_OUTPUT.fasta


title: 3h-con-gfp1-os_S23_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 1a-lo-10-gfp1os18_S12_L001_R1_001_AF_SOL_675_OUTPUT.fasta


title: CFPac_1_SL23296

tag: gemcitabine sensitivity

value: Sensitive


title: 1e-lo-10-gfp1os17_S4_L001_R1_001_AF_SOL_675_OUTPUT.fasta


title: 3g-lo-10-gfp1os20_S22_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 3f-lo-10-gfp1os20_S21_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 3d-con-gfp1r17nt_S19_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 3c-lo-10-gfp1r17nt_S18_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 3b-lo-10-gfp1r17nt_S17_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 2g-lo-10-gfp1r17nt_S14_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 2e-lo-10-gfp1r20nt_S12_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 3a-lo-10-gfp1r17nt_S16_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 1a-lo-10-gfp2.18nt_S24_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 2h-con-gfp1r20nt_S15_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 2f-lo-10-gfp1r20nt_S13_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 2d-con-gfp1-f17nt_S11_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 2b-lo-10-gfp1-f17nt_S9_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 2c-lo-10-gfp1-f17nt_S10_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 1g-con-gfp1-f18nt_S7_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 1a-lo-3-20nt-unc22_S1_L001_R1_001_OUTPUT_AF_SOL_664.fasta


title: 1f-lo-10-gfp1-f18nt_S5_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 1f-lo-10-gfp1-f18nt_S6_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 1c-lo-3-18nt-unc22_S3_L001_R1_001_OUTPUT_AF_SOL_664.fasta


title: 1e-lo-3-17nt-unc22_S5_L001_R1_001_OUTPUT_AF_SOL_664.fasta


title: 2a-con_S9_L001_R1_001_OUTPUT_AF_SOL_664.fasta


title: 1e-lo-10-gfp1-f18nt_S4_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 3e-lo-10-gfp1os20_S20_L001_R1_001_AF_SOL_673_OUTPUT.fasta


title: 1h-lo-180-17nt-rol6_S8_L001_R1_001_OUTPUT_AF_SOL_664.fasta


title: 4a-lo-3-20nt-rol6_S23_L001_R1_001_OUTPUT_AF_SOL_637.fasta


title: 1b-lo-180-20nt-unc22_S2_L001_R1_001_OUTPUT_AF_SOL_664.fasta


title: 4e-lo-180-20nt-rol6_S27_L001_R1_001_OUTPUT_AF_SOL_637.fasta


title: 1g-lo-3-17nt-rol6_S7_L001_R1_001_OUTPUT_AF_SOL_664.fasta


title: 1b-lo-10-gfp1-f20nt_S1_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 1c-lo-10-gfp1-f20nt_S2_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 2g-lo-3-17nt-rol6_S15_L001_R1_001_OUTPUT_AF_SOL_643.fasta


title: 2a-lo-10-gfp1-f17nt_S8_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 3a-con_S17_L001_R1_001_OUTPUT_AF_SOL_637.fasta


title: 2g-lo-180-17nt-gfp2_S15_L001_R1_001_OUTPUT_AF_SOL_637.fasta


title: 1d-lo-180-18nt-unc22_S4_L001_R1_001_OUTPUT_AF_SOL_664.fasta


title: 2h-con_S16_L001_R1_001_OUTPUT_AF_SOL_637.fasta


title: 1a-lo-3-20nt-gfp2_S1_L001_R1_001_OUTPUT_AF_SOL_637.fasta


title: 2c-lo-3-17nt-gfp2_S11_L001_R1_001_OUTPUT_AF_SOL_637.fasta


title: 2h-lo-3-17nt-gfp1_S16_L001_R1_001_OUTPUT_AF_SOL_636.fasta


title: 1d-con-gfp1_S3_L001_R1_001_AF_SOL_672_OUTPUT.fasta


title: 3d-lo-180-17nt-gfp1_S20_L001_R1_001_OUTPUT_AF_SOL_636.fasta


title: 2b-lo-180-20nt-gfp1_S10_L001_R1_001_OUTPUT_AF_SOL_636.fasta


title: Panc_2_03_SL23301

value: Resistant


title: 2b-con_S10_L001_R1_001_OUTPUT_AF_SOL_664.fasta


title: 1e-lo-180-18nt-rol6_S5_L001_R1_001_OUTPUT_AF_SOL_636.fasta


title: 1e-lo-180-20nt-gfp2_S5_L001_R1_001_OUTPUT_AF_SOL_637.fasta


title: 1f-lo-3-18nt-gfp2_S6_L001_R1_001_OUTPUT_AF_SOL_637.fasta


title: 3f-con_S22_L001_R1_001_OUTPUT_AF_SOL_636.fasta


title: 3e-con_S21_L001_R1_001_OUTPUT_AF_SOL_636.fasta


title: 1f-lo-3-20nt-gfp1_S6_L001_R1_001_OUTPUT_AF_SOL_636.fasta


title: 2a-lo-3-18bp_S8_L001_R1_001_OUTPUT_AF_SOL_596.fasta

source_name: type I unc-22 RVL library

value: type I unc-22 RVL library


title: 2g-lo-180-18nt-gfp1_S15_L001_R1_001_OUTPUT_AF_SOL_636.fasta


title: 1c-lo-30-18bp_S3_L001_R1_001_OUTPUT_AF_SOL_596.fasta


title: 1a-lo-3-18nt-rol6_S1_L001_R1_001_OUTPUT_AF_SOL_636.fasta


title: 3f-con-20bp_S20_L001_R1_001_OUTPUT_AF_SOL_594.fasta


title: 4a-lo-180-17nt-rol6_S25_L001_R1_001_OUTPUT_AF_SOL_635.fasta


title: 3d-lo-90-20bp_S18_L001_R1_001_OUTPUT_AF_SOL_594.fasta


title: 2b-lo-180-18nt-gfp2_S10_L001_R1_001_OUTPUT_AF_SOL_637.fasta


title: 2e-lo-180-18bp_S12_L001_R1_001_OUTPUT_AF_SOL_596.fasta


title: 2d-lo-90-18bp_S11_L001_R1_001_OUTPUT_AF_SOL_596.fasta


title: 1e-lo-180-17bp_S5_L001_R1_001_OUTPUT_AF_SOL_594.fasta


title: 1d-lo-90-18bp_S4_L001_R1_001_OUTPUT_AF_SOL_596.fasta


title: 2b-lo-10-18bp_S9_L001_R1_001_OUTPUT_AF_SOL_596.fasta


title: 2c-lo-30-18bp_S10_L001_R1_001_OUTPUT_AF_SOL_596.fasta


title: 1a-lo-3-18bp_S1_L001_R1_001_OUTPUT_AF_SOL_596.fasta


title: 1b-lo-10-18bp_S2_L001_R1_001_OUTPUT_AF_SOL_596.fasta


title: 3g-con-20bp_S21_L001_R1_001_OUTPUT_AF_SOL_594.fasta


title: 1e-lo-180-18bp_S5_L001_R1_001_OUTPUT_AF_SOL_596.fasta


title: 3c-lo-30-20bp_S17_L001_R1_001_OUTPUT_AF_SOL_594.fasta


title: 3e-lo-180-20bp_S19_L001_R1_001_OUTPUT_AF_SOL_594.fasta


title: 3a-lo-3-20bp_S15_L001_R1_001_OUTPUT_AF_SOL_594.fasta


title: 3a-con-20bpNEB30deg_S17_L001_R1_001_OUTPUT_AF_SOL_591.fasta


title: 2c-lo-3-18nt-gfp1_S11_L001_R1_001_OUTPUT_AF_SOL_636.fasta


title: 2g-lo-180-20bpNEB30deg_S15_L001_R1_001_OUTPUT_AF_SOL_591.fasta


title: 1c-lo-30-17bp_S3_L001_R1_001_OUTPUT_AF_SOL_594.fasta


title: 3h-lo-10-P90LA_S24_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 1g-con-18bp_S7_L001_R1_001_OUTPUT_AF_SOL_596.fasta


title: 1f-con-17bp_S6_L001_R1_001_OUTPUT_AF_SOL_594.fasta


title: 3f-lo-10-P90LA_S22_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 1b-lo-10-17bp_S2_L001_R1_001_OUTPUT_AF_SOL_594.fasta


title: 3b-con-20bpNEB30deg_S18_L001_R1_001_OUTPUT_AF_SOL_591.fasta


title: 1f-con-18bp_S6_L001_R1_001_OUTPUT_AF_SOL_596.fasta


title: 1g-con-17bp_S7_L001_R1_001_OUTPUT_AF_SOL_594.fasta


title: 3b-lo-10-20bp_S16_L001_R1_001_OUTPUT_AF_SOL_594.fasta


title: 3b-lo-10-P90L1_S18_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 3g-lo-10-P90LA_S23_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 3e-lo-10-P89LA_S21_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 3d-lo-10-P89LA_S20_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 3c-lo-10-P89LA_S19_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 3a-lo-10-P90L1_S17_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 2h-lo-10-P90L1_S16_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 1e-con-P90LA_S5_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 1c-con-P89LA_S3_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 1a-con-P89LA_S1_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 1a-lo-3-17bp_S1_L001_R1_001_OUTPUT_AF_SOL_594.fasta


title: 2f-lo-10-P89L1_S14_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 2e-lo-10-P89L1_S13_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 2e-con-20bp_S13_L001_R1_001_OUTPUT_AF_SOL_585.fasta


title: 2d-con-P90L1_S12_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 2a-con-P89L1_S9_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 1g-con-P89L1_S7_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 1h-con-P89L1_S8_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 2b-con-P90L1_S10_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 2c-con-P90L1_S11_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 1d-con-P90LA_S4_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 1c-lo-10-20bp_S3_L001_R1_001_OUTPUT_AF_SOL_585.fasta


title: 1a-lo-3-20bp_S1_L001_R1_001_OUTPUT_AF_SOL_585.fasta


title: 3b-con-P92_S18_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 1b-con-P89LA_S2_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 2g-lo-10-P89L1_S15_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 1g-lo-90-20bp_S7_L001_R1_001_OUTPUT_AF_SOL_585.fasta


title: 1f-con-P90LA_S6_L001_R1_001_OUTPUT_AF_SOL_588.fasta


title: 3a-con-P90_S17_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 1e-lo-30-20bp_S5_L001_R1_001_OUTPUT_AF_SOL_585.fasta


title: 2f-lo-10-P92_S14_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 2d-lo-5-P92_S12_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 2h-con-P90_S16_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 2f-con-20bp_S14_L001_R1_001_OUTPUT_AF_SOL_585.fasta


title: 2g-lo-10-P92_S15_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 3c-con-P92_S19_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 2b-lo-5-P92_S10_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 2c-lo-5-P92_S11_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 1g-lo-20-P90_S7_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 1h-lo-20-P90_S8_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 2e-lo-10-P92_S13_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 1e-lo-10-P90_S5_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 1d-lo-10-P90_S4_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 1b-lo-5-P90_S2_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 4a-con-P89-BY_S25_L001_R1_001_OUTPUT_AF_SOL_579.fasta


title: 1a-lo-5-P90_S1_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 3h-con-P89-BY_S24_L001_R1_001_OUTPUT_AF_SOL_579.fasta


title: 1c-lo-5-P90_S3_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 1f-lo-10-P90_S6_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 1f-lo-10-P89-BY_S6_L001_R1_001_OUTPUT_AF_SOL_579.fasta


title: 1h-lo-20-P89-BY_S8_L001_R1_001_OUTPUT_AF_SOL_579.fasta


title: 2a-lo-20-P89-BY_S9_L001_R1_001_OUTPUT_AF_SOL_579.fasta


title: 1e-lo-10-P89-BY_S5_L001_R1_001_OUTPUT_AF_SOL_579.fasta


title: 2a-lo-20-P90_S9_L001_R1_001_OUTPUT_AF_SOL_580.fasta


title: 2a-lo-180-20bp_S9_L001_R1_001_OUTPUT_AF_SOL_585.fasta


title: 1d-lo-10-P89-BY_S4_L001_R1_001_OUTPUT_AF_SOL_579.fasta


title: 1a-lo-5-P89-BY_S1_L001_R1_001_OUTPUT_AF_SOL_579.fasta


title: 1c-con-12-Cas9-7_S3_L001_R1_001_OUTPUT_AF_SOL_574.fasta


title: 1c-lo-5-P89-BY_S3_L001_R1_001_OUTPUT_AF_SOL_579.fasta


title: 1g-lo-20-P89-BY_S7_L001_R1_001_OUTPUT_AF_SOL_579.fasta


title: 3b-lo-12-Cas9-4_S18_L001_R1_001_OUTPUT_AF_SOL_572.fasta


title: 1d-con-12-Cas9-7_S4_L001_R1_001_OUTPUT_AF_SOL_574.fasta


title: 2f-lo-12-Cas9-7_S14_L001_R1_001_OUTPUT_AF_SOL_574.fasta


title: 2e-lo-12-Cas9-7_S13_L001_R1_001_OUTPUT_AF_SOL_574.fasta


title: 2d-lo-12-Cas9-1_S12_L001_R1_001_OUTPUT_AF_SOL_572.fasta


title: 2f-lo-12-Cas9-2_S14_L001_R1_001_OUTPUT_AF_SOL_572.fasta


title: 3a-lo-12-Cas9-4_S17_L001_R1_001_OUTPUT_AF_SOL_572.fasta


title: 1b-lo-5-P89-BY_S2_L001_R1_001_OUTPUT_AF_SOL_579.fasta


title: 2e-lo-12-Cas9-2_S13_L001_R1_001_OUTPUT_AF_SOL_572.fasta


title: 1f-lo-180-17nt-unc22_S6_L001_R1_001_OUTPUT_AF_SOL_664.fasta


title: 1h-con-Cas9-4_S8_L001_R1_001_OUTPUT_AF_SOL_572.fasta


title: 1g-con-Cas9-4_S7_L001_R1_001_OUTPUT_AF_SOL_572.fasta


title: 1c-con-Cas9-2_S3_L001_R1_001_OUTPUT_AF_SOL_572.fasta


title: 1d-con-Cas9-2_S4_L001_R1_001_OUTPUT_AF_SOL_572.fasta


title: 2c-lo-12-Cas9-1_S11_L001_R1_001_OUTPUT_AF_SOL_572.fasta


title: 1a-con-Cas9-1_S1_L001_R1_001_OUTPUT_AF_SOL_572.fasta


title: cat2-2 High CO2 rep2

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University

description:
cat2-2 High CO2
c-0h-II_S2.fastq.gz

data_processing:
Adapter sequences and low quality base-pairs (Q < 20) were trimmed using Trim Galore (v0.3.3, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), retaining high-quality reads of at least 50 bp length.
Quality-filtered reads were aligned to the TAIR10 Arabidopsis reference genome using the spliced aligner TopHat2 (v2.1.0)
The number of reads per gene was quantified using featureCounts function as implemented in the Subread package v1.4.6
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Table containing gene counts for all 6 samples as delivered by featureCounts

organism: Arabidopsis thaliana

source_name: Three-week-old seedlings (shoot tissue)

growth_protocol: cat2-2 mutant plants were grown under elevated CO2 concentrations (3,000 ppm) to impair photorespiration. Individual plants were organized according to a completely randomized block design in a controlled climate chamber (Votsch Industrietechnik) in a 16:8 day/night regime (relative humidity of 75%, 21°C and an irradiance of 120 umol m-2 s-1).

extract_protocol:
RNA was extracted using a combination of TRIzol and RNeasy Kit (Qiagen) according to the manufacturers’ instructions.
Library preparation and sequencing was performed at the VIB Nucleomics Core (www.nucleomics.be). Sequencing libraries were constructed with using the TruSeq Stranded mRNA Library Preparation Kit (Illumina).

treatment_protocol: For high light treatments, 3-week-old plants were transferred to a Sanyo Fitotron plant growth chamber in ambient air conditions (400 ppm CO2, relative humidity of 55%, 21°C) and irradiation of 1,200 umol m-1 s-1 for  three hours. Middle aged leaves of 15 individual plants per line were sampled, pooled and frozen in liquid nitrogen. This entire set-up was repeated to obtain three biological repeats.

value: leaf

tag: ecotype

tag: genotype


title: cat2-2 High CO2 rep1

description:
cat2-2 High CO2
c-0h-I_S1.fastq.gz


title: cat2-2 High light rep2

description:
cat2-2 High light
c-3h-II_S5.fastq.gz


title: cat2-2 High light rep3

description:
cat2-2 High light
c-3h-III_S6.fastq.gz


title: cat2-2 gox2 High light rep3

description:
cat2-2 gox2 High light
cg2-3h-III_S18.fastq.gz

data_processing:
Adapter sequences and low quality base-pairs (Q < 20) were trimmed using Trim Galore (v0.3.3, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), retaining high-quality reads of at least 50 bp length.
Quality-filtered reads were aligned to the TAIR10 Arabidopsis reference genome using the spliced aligner TopHat2 (v2.1.0)
The number of reads per gene was quantified using featureCounts function as implemented in the Subread package v1.4.6
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Table containing gene counts for all 12 samples as delivered by featureCounts

growth_protocol: cat2 gox1 and cat2 gox2 mutant plants were grown under elevated CO2 concentrations (3,000 ppm) to impair photorespiration. Individual plants were organized according to a completely randomized block design in a controlled climate chamber (Votsch Industrietechnik) in a 16:8 day/night regime (relative humidity of 75%, 21°C and an irradiance of 120 umol m-2 s-1).

value: cat2-2, gox2


title: cat2-2 gox2 High light rep2

description:
cat2-2 gox2 High light
cg2-3h-II_S17.fastq.gz


title: WP3

city: Shanghai

first: Xinwei

last: Yang

address: #800, Dongchuan Road

institute: SJTU

description: wild type

data_processing:
Illumina HCS (1.5.15.1) software and RTA (1.13.48.0) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to WP3 whole genome using SOAPaligner/soap2 (Release 2.21)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Audic, S. et al., Genome Res  Research, 1997.
Genome_build: ASM1488v1
Supplementary_files_format_and_content: Matrix table: the final, normalized values that are comparable across samples,and processed as described in "The regulatory role of ferric uptake regulator (Fur) during anaerobic respiration of Shewanella piezotolerans WP3".

organism: Shewanella piezotolerans WP3

growth_protocol: mid-log phase under anaerobic conditions using 20 mM fumarate as the EA

extract_protocol:
RNA was harvested  in triplicate using Trizol reagent, then mixed together. Illumina TruSeq SBS KIT-HS v3 and TruSeq PE Cluster Kit v3 –cBot - HS (Cat#FC-401-3001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

tag: strain


title: Fur

description: fur mutant

source_name: Fur

value: fur mutant


title: cat2-2 gox2 High light rep1

description:
cat2-2 gox2 High light
cg2-3h-I_S16.fastq.gz


title: 1b-con-Cas9-1_S2_L001_R1_001_OUTPUT_AF_SOL_572.fasta


title: cat2-2 gox2 High CO2 rep3

description:
cat2-2 gox2 High CO2
cg2-0h-III_S15.fastq.gz


title: cat2-2 gox2 High CO2 rep1

description:
cat2-2 gox2 High CO2
cg2-0h-I_S13.fastq.gz


title: cat2-2 gox1 High light rep3

description:
cat2-2 gox1 High light
cg1-3h-III_S12.fastq.gz

value: cat2-2, gox1


title: cat2-2 gox2 High CO2 rep2

description:
cat2-2 gox2 High CO2
cg2-0h-II_S14.fastq.gz


title: cat2-2 gox1 High light rep2

description:
cat2-2 gox1 High light
cg1-3h-II_S11.fastq.gz


title: cat2-2 gox1 High CO2 rep3

description:
cat2-2 gox1 High CO2
cg1-0h-III_S9.fastq.gz


title: cat2-2 gox1 High CO2 rep2

description:
cat2-2 gox1 High CO2
cg1-0h-II_S8.fastq.gz


title: cat2-2 High light rep1

description:
cat2-2 High light
c-3h-I_S4.fastq.gz


title: cat2-2 gox1 High CO2 rep1

description:
cat2-2 gox1 High CO2
cg1-0h-I_S7.fastq.gz


title: cat2-2 High CO2 rep3

description:
cat2-2 High CO2
c-0h-III_S3.fastq.gz


title: cat2-2 gox1 High light rep1

description:
cat2-2 gox1 High light
cg1-3h-I_S10.fastq.gz


title: C1-1772117-035-C07

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

institute: Karolinska Institutet

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited table of total number of detected mRNA molecules from each gene in each cell

source_name: cortex S1

growth_protocol: Wild-type (CD1 or C57BL6) and transgenic mice (5Pdgfratm11(EGFP) Sor/J, Lhx6 Cre RFP and PDGFR-GFP) between post-natal day 21 and 31 of both sexes were used. In the PDGFRa-GFP knock-in mice, H2B-eGFP fusion gene is expressed under the promoter of the oligodendrocyte precursor marker PDGFRa. The Lhx6–Cre transgenic mouse is a BAC transgenic mouse that expresses Cre under transcriptional control of Lhx6. This mouse line was crossed with the Cre-reporter line where tandem-dimer red fluorescent protein (tdRFP) is ubiquitously expressed under the ROSA26 locus. In the BAC transgenic mouse 5HT3aEGFP, EGFP is expressed under control of the Htr3a promoter.

extract_protocol:
Selected CNS regions were dissected in 300µm thick vibratome sections and cut out with scalpel. Tissue was then dissociated into a single cell suspension (described in Zeisel & Munoz-Manchado, Science 2015 Mar 6;347(6226):1138). For the spinal cord, an extra gradient step was used after the strainer and final centrifugation step. The pellet was ressuspended in 2ml Neurobasal-A medium including supplements and transferred onto an Optiprep Density Gradient, which consisted of 3 phases (Bottom phase: 160µl Optiprep + 340µl Neurobasal-A; middle phase: 220µl Optiprep + 1780µl Neurobasal-A; top phase: 75µl Optiprep + 925µl Neurobasal-A). The gradient was then centrifuged at 300g for 10min at 8°C and cells were located between the bottom and the middle phase. Cell suspension in a concentration of 600-1000 cells/μL was used. C1 Suspension Reagent was added in a ratio of 4 μL to every 7 μL cell suspension. 11 μL of the cell suspension mix was loaded on a C1 Single-Cell AutoPrep IFC  microfluidic chip designed for 10- to 17-μm cells, and the chip was then processed on a Fluidigm C1 instrument using the 'mRNA Seq: Cell Load (1772x/1773x)' script (30 min at 4°C).
Lysis mix, RT mix and PCR mix (described in Islam et al., Nat Methods. 2014 Feb;11(2):163-6) were added to the chip. The plate was placed in the Fluidigm C1 instrument and the 'mRNA Seq: RT + Amp (1772x/1773x)' script was executed, and included lysis, reverse transcription and 21 cycles of PCR. The amplified cDNA was harvested in a total of 13 μL C1 Harvesting Reagent. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation using Tn5 DNA transposase to transfer adaptors to the target DNA as described (Ibid.). 100 µl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were washed in 2× BWT (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) and resuspended in 2 ml 2× BWT. Twenty microliters of beads were added to each well and incubated at room temperature for 15 min. All fractions were pooled, the beads were immobilized and the supernatant removed. The beads were resuspended in 100 μL TNT (20 mM Tris, pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 μL Qiagen Qiaquick PB, and twice in 100 μL TNT. The beads were resuspended in 100 μL restriction mix (1× NEB CutSmart, 0.4 U/μL PvuI-HF enzyme), designed to cleave 3′ fragments carrying a PvuI recognition site. The mix was incubated for 1 h at 37 °C, then washed three times in TNT. Finally, to elute DNA, beads were resuspend in 30 µL ddH2O and incubated 10 minutes at 70°C. Beads were then immediately bound to magnet and the supernatant was collected. To remove short fragments,  Ampure beads (Beckman Coulter) were used at 1.8× volume and eluted in 30 µL.

treatment_protocol: In the stress treatment mice, acute stress was induced injection of 4% PFA into the left paw.

value: PDGFRa-Cre

tag: Sex

value: M

tag: treatment

value: No

tag: inferred cell type


title: C1-1772117-035-D07


title: C1-1772117-035-F01


title: C1-1772117-035-D04


title: C1-1772117-035-G02


title: C1-1772117-035-F10


title: C1-1772117-035-D02


title: C1-1772117-035-F09


title: C1-1772117-035-G10


title: C1-1772117-035-D10


title: C1-1772117-035-C12


title: C1-1772117-035-D12


title: C1-1772117-035-G05

value: PPR


title: C1-1772117-035-G09


title: C1-1772117-035-D05


title: C1-1772117-035-E06


title: C1-1772117-035-G04


title: C1-1772117-035-F06


title: C1-1772117-035-F11


title: C1-1772117-035-C01


title: C1-1772117-035-B11


title: C1-1772117-035-C02


title: C1-1772117-035-B10


title: C1-1772117-035-B09


title: C1-1772117-035-B05


title: C1-1772117-035-B03


title: C1-1772117-035-D03


title: C1-1772117-035-B01


title: C1-1772117-035-C03


title: C1-1772117-034-H10


title: C1-1772117-035-A06


title: C1-1772117-034-F12


title: C1-1772117-034-G04


title: C1-1772117-034-G01


title: C1-1772117-034-F09


title: C1-1772117-035-A07


title: C1-1772117-034-F06


title: C1-1772117-034-H11


title: C1-1772117-034-G07


title: C1-1772117-034-G10


title: C1-1772117-034-H12


title: C1-1772117-035-A02


title: C1-1772117-034-E06


title: C1-1772117-034-E09


title: C1-1772117-034-E05


title: C1-1772117-034-H07


title: C1-1772117-034-E03


title: C1-1772117-035-A03


title: C1-1772117-034-D06


title: C1-1772117-034-G03


title: C1-1772117-034-D07


title: C1-1772117-034-D03


title: C1-1772117-035-C05


title: C1-1772117-035-A10


title: C1-1772117-035-A04


title: C1-1772117-034-F08


title: C1-1772117-034-E07


title: C1-1772117-034-G05


title: C1-1772117-034-C10


title: C1-1772117-034-C08


title: C1-1772117-034-C05


title: C1-1772117-034-C04


title: C1-1772117-034-B01


title: C1-1772117-034-B06


title: C1-1772117-034-B04


title: C1-1772117-034-C02


title: C1-1772117-034-A12


title: C1-1772117-034-B12


title: C1-1772117-034-C03


title: C1-1772117-034-C06


title: C1-1772117-034-A06


title: C1-1772117-034-A07


title: C1-1772117-034-A11


title: C1-1772117-034-A03


title: C1-1772117-031-H10

source_name: corpus callosum


title: C1-1772117-034-B02


title: C1-1772117-031-G12


title: C1-1772117-031-H06


title: C1-1772117-031-G10


title: C1-1772117-031-G11


title: C1-1772117-031-G05


title: C1-1772117-031-G06


title: C1-1772117-031-G02


title: C1-1772117-031-F09


title: C1-1772117-034-B05


title: C1-1772117-031-F10


title: C1-1772117-034-A09


title: C1-1772117-031-F06


title: C1-1772117-031-E10


title: C1-1772117-031-E11


title: C1-1772117-031-F02


title: C1-1772117-031-F12


title: C1-1772117-031-E12


title: C1-1772117-031-E02


title: C1-1772117-031-E08


title: C1-1772117-031-F04


title: C1-1772117-031-E03


title: C1-1772117-031-D11


title: C1-1772117-031-D09


title: C1-1772117-031-D04


title: C1-1772117-031-D03


title: C1-1772117-031-F05


title: C1-1772117-031-D10


title: C1-1772117-031-C04


title: C1-1772117-031-C12


title: C1-1772117-031-E07


title: C1-1772117-031-B07


title: C1-1772117-031-C03


title: C1-1772117-031-B02


title: C1-1772117-031-A11


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title: C1-1772099-092-A05


title: C1-1772099-092-A09


title: C1-1772099-091-F01


title: C1-1772099-091-H06


title: C1-1772099-091-H12


title: C1-1772099-091-F02


title: C1-1772099-091-F08


title: C1-1772099-091-E10


title: C1-1772099-091-F07


title: C1-1772099-091-G02


title: C1-1772099-091-E08


title: C1-1772099-091-H05


title: C1-1772099-091-F06


title: C1-1772099-091-E05


title: C1-1772099-092-A02


title: C1-1772099-091-E06


title: C1-1772099-091-D12


title: C1-1772099-091-D10


title: C1-1772099-091-F12


title: C1-1772099-091-D08


title: C1-1772099-091-B11


title: C1-1772099-091-A10


title: C1-1772099-091-E12


title: C1-1772099-090-H05


title: C1-1772099-090-H12


title: C1-1772099-090-H10


title: C1-1772099-091-A05


title: C1-1772099-090-G04


title: C1-1772099-090-H09


title: C1-1772099-091-E03


title: C1-1772099-090-F10


title: C1-1772099-090-F06


title: C1-1772099-090-F12


title: C1-1772099-090-F02


title: C1-1772099-090-D12


title: C1-1772099-090-C07


title: C1-1772099-090-C03


title: C1-1772099-090-B12


title: C1-1772099-090-E04


title: C1-1772099-090-B09


title: C1-1772099-090-C11


title: C1-1772099-090-D04


title: C1-1772099-090-A06


title: C1-1772099-091-C06


title: C1-1772099-090-A01


title: C1-1772099-090-A08


title: C1-1772099-087-H02

source_name: zona incerta


title: C1-1772099-090-E06


title: C1-1772099-090-E01


title: C1-1772099-087-D09


title: C1-1772099-090-D02


title: C1-1772099-090-D05


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title: C1-1772099-086-D12


title: C1-1772099-086-F06


title: C1-1772099-087-A09


title: C1-1772099-090-B06


title: C1-1772099-090-A11


title: C1-1772099-086-E01


title: C1-1772099-086-H05


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title: C1-1772099-086-D09


title: C1-1772099-086-C12


title: C1-1772099-086-B03


title: C1-1772099-086-B01


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title: C1-1772099-085-H05


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title: C1-1772099-087-A06


title: C1-1772099-085-D03


title: C1-1772099-085-G03


title: C1-1772099-085-A06


title: C1-1772099-084-H01

value: pooled male and female


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title: C1-1772099-086-C11


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title: C1-1772099-084-C06


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title: C1-1772099-070-B11


title: C1-1772099-070-C06


title: C1-1772099-070-B01


title: C1-1772099-058-A11

source_name: Amygdala


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title: C1-1772099-055-H06


title: C1-1772099-057-A04


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title: C1-1772099-048-G03


title: C1-1772099-048-A04


title: C1-1772099-047-F12

source_name: SN-VTA


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title: C1-1772099-055-F12


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title: C1-1772099-031-B02


title: C1-1772099-033-B11


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title: C1-1772099-030-B07


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title: C1-1772099-010-G01