title: BLS354 replicate 2

first: Adam

last: Bogdanove

address: 334 Plant Science Building

department: Plant Pathology and Plant-Microbe Biology

data_processing:
Adapters were trimmed using the Trimmomatic v0.22 ILLUMINACLIP function (Bolger et al., 2014) for single end reads with seedMismatches=2, palindromeClipThreshold=30, and simpleClipThreshold=7
Low quality bases at the ends of reads were trimmed using BRAT trim v2.0.1 (Harris et al., 2010) with the parameters "-q 20 -L 33"
Reads were aligned using Tophat v2.06  with command line options '--num-threads 8 --max-intron-length 10000' and with the -G option specifying that the the MSU Release 7.0 annotation downloaded from the Rice Genome Annotation Project be used to guide transcript assembly
The number of reads aligned to each gene was determined using HTSeq-count (Anders et al., 2014) from the HTSeq framework version 0.5.4p3 with the command line options ‘-i ID -t gene -s no’
Genome_build: The Oryza sativa L. ssp. japonica (cv. Nipponbare) reference genome v.7.0 was downloaded from Phytozyme 10
Supplementary_files_format_and_content: the processed files are text tab-delimited files output by HTSeq-count with locus IDs in the first column and the number of reads aligned to each locus in the second column. The last five lines in each file don't include reads aligned to specific loci, but the number of reads in the following categories: those aligned to no annotated feature (no_feature), those that cannot be unambiguously assigend to a single feature (ambiguous), reads with an alignment quality lower than ten (too_low_aQual), reads that are not aligned (not_aligned), and reads that are aligned to multiple locations (alignment_not_unique)

organism: Oryza sativa Japonica Group

source_name: leaf tissue

growth_protocol: Oryza sativa L. ssp. japonica cv. Nipponbare plants to be inoculated were grown in LC-1 soil mixture (Sungro, Bellevue, WA) in PGC15 growth chambers (Percival Scientific, Perry, IA) in trays approximately 60 cm below a combination of fluorescent and incandescent bulbs providing approximately 1,000 μmoles/m2/s measured at 15 cm, under a cycle of 12 h of light at 28 °C and 12 h of dark at 25 °C.

extract_protocol:
RNA was extracted using a modified hot Trizol protocol (Huang et al., 2005) followed by treatment with RNase-free DNase I (Life Technologies, Carlsbad, CA), then purified using the RNeasy MinElute Cleanup kit (Qiagen, Valencia, CA).
These libraries were prepped with the Illumina TruSeq RNA Sample Prep v2 kit

treatment_protocol: Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaf. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.

tag: cultivar

value: Nipponbare

value: leaf

tag: agent

value: Xanthomonas oryzae pv. oryzicola  strain BLS254


title: BLS354 replicate 3

status: Public on Jul 07 2016

type: SRA

city: Ithaca

state: NY

country: USA

institute: Cornell University

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: 96G4T7

city: Charleston

first: Gary

last: Hardiman

state: SOUTH CAROLINA

address: 135 Cannon Street, Suite 303 MSC835

institute: MUSC

description:
96hrSlick
[raw_counts_HG19.txt column] 96hrSlick: 1253__96G4T7

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: Tab-delimited raw_counts_HG19.txt is a summary file with raw count data extracted from the blastx alignments to HG19.
Supplementary_files_format_and_content: Each tab-delimited *vs*Cntrl.txt file is standard DEseq2 output for a comparison of treated vs control.  The baseMean column reports a mean of the counts for all the treated vs control samples used in that particular comparison.

organism: Coryphaena hippurus

source_name: whole embryo

growth_protocol: Mahi-mahi broodstock were captured off the coast of Miami, FL using hook and line angling techniques and subsequently transferred to the University of Miami Experimental Hatchery (UMEH) where they were acclimated in 80 m3 fiberglass maturation tanks (typically 5-7 per tank).  Tanks were equipped with recirculating aquaculture systems for water quality and temperature control.  All embryos used in experiments were collected <8 h following a volitional (non-induced) spawn using standard UMEH methods (Stieglitz et al 2012).

extract_protocol:
Thirty pooled embryos or larvae per replicate were homogenized with a Kontes Pellet Pestle Cordless Motor (Sigma-Aldrich, St. Louis, Missouri) in RNAzol (Molecular Research Center, Cincinnati, Ohio). 200 ng of total RNA was used to prepare RNA-Seq libraries using the TruSeq RNA Sample Prep kit following the protocol described by the manufacturer (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bulk dilutions were prepared by adding the appropriate volume of slick or source oil HEWAF to 1 µm filtered, UV-sterilized seawater in 5 L glass bottles,  vigorously spinning for several minutes with a stir bar followed by decanting into each of the replicate 1 L glass beakers.   Freshly fertilized embryos were then gently added to each replicate using a glass transfer pipette and each beaker covered with a glass petri dish.  All exposures were static, non-renewal and performed in a temperature controlled environmental chamber at 27°C with a light cycle of 16:8 h light:dark.

value: whole embryo

tag: developmental stage

tag: stress

value: Slick

tag: concentration


title: 96G4T8

description:
96hrSlick
[raw_counts_HG19.txt column] 96hrSlick: 1254__96G4T8


title: A375_shIno80_day2_rep2

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

description: Gene expression 2 days after transfection

data_processing:
Aligned with TopHat2 version 2.0.4 with the following parameters: -g 10
FPKM measurements obtained using CuffLinks version 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: FPKM: 1st column = RefSeq ID, 2nd column = fragments per kilobase of exon per million mapped reads (FPKM value)

organism: Homo sapiens

growth_protocol: A375 cells were maintained in 10% FBS DMEM

extract_protocol:
Cells were harvested and total RNA was extracted by Thermo RNA kit
The sequencing library was generated by Truseq RNA sample preparation kit according to the instruction
Truseq RNA sample preparation kit V2

treatment_protocol: Cells were infected with lenti-viral based shNT or shIno80, cells were harvested 2, 3, and 4 days after infection

tag: cell line

tag: cell type

value: melanoma cell line

tag: transfected with

value: lenti-viral based shIno80

tag: time point

value: 2 days after transfection


title: A375_shIno80_day2_rep1


title: 24G5T11

description:
24hrMass
[raw_counts_HG19.txt column] 24hrMass: 1257__24G5T11

value: Mass


title: A375_shNT_day2_rep2

value: lenti-viral based shNT


title: A375_shNT_day2_rep1


title: 48G4T4

description:
48hrSlick
[raw_counts_HG19.txt column] 48hrSlick: 1250__48G4T4


title: 48G4T5

description:
48hrSlick
[raw_counts_HG19.txt column] 48hrSlick: 1251__48G4T5


title: 24G4T3

description:
24hrSlick
[raw_counts_HG19.txt column] 24hrSlick: 1249__24G4T3


title: Melanocyte_Input

description: ChIP-Seq in wild type cells

library_source: genomic

data_processing:
Aligned with Bowtie version 0.12.8 with the following parameters: -v 2 -m 1 --best --strata
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph: coverage normalized to reads per 10 million aligned reads

molecule: genomic DNA

source_name: Melanocyte

extract_protocol:
Cells were fixed, harvested, and lysed, then submitted to sonication. The sonicated DNA was incubated with specific beads-conjugated antibody overnight. Then the beads were washed, and DNA was eluted, and quantified.
The sequencing library was generated by use of Nextera XT DNA preparation Kit
Nextera XT DNA preparation Kit

treatment_protocol: 80% confluent cells were used for ChIP-Seq analysis, or cells were infected with lenti-viral based shNT or shIno80, cells were harvested 2 days after infection

value: Melanocyte

tag: genotype/variation

value: wild type


title: Melanocyte_Ino80

description: ChIP-Seq in wild type cells

tag: chip antibody

tag: chip antibody vendor

value: proteintech

tag: chip antibody cat. #

tag: chip antibody lot #


title: SKMEL147_Med1

description: ChIP-Seq in wild type cells

value: Bethyl


title: 96C14

description:
96hrControl
[raw_counts_HG19.txt column] 96hrCntrl: 1246__96C14

value: Control


title: BLS354 replicate 1


title: 96C13

description:
96hrControl
[raw_counts_HG19.txt column] 96hrCntrl: 1245__96C13


title: 96C11

description:
96hrControl
[raw_counts_HG19.txt column] 96hrCntrl: 1243__96C11


title: A375_shIno80_Input

description: ChIP-Seq was performed 48 hours after infection

source_name: human A375

value: human A375

tag: infected with

value: 48 hours after infection


title: SKMEL147_Ino80

description: ChIP-Seq in wild type cells


title: 48C9

description:
48hrControl
[raw_counts_HG19.txt column] 48hrCntrl: 1241__48C9


title: 96C10

description:
96hrControl
[raw_counts_HG19.txt column] 96hrCntrl: 1242__96C10


title: A375_shIno80_PolII

value: PolII

value: Santa Cruz


title: A375_shNT_PolII


title: 24G4T2

description:
24hrSlick
[raw_counts_HG19.txt column] 24hrSlick: 1248__24G4T2


title: A375_shNT_Input


title: 48C8

description:
48hrControl
[raw_counts_HG19.txt column] 48hrCntrl: 1240__48C8


title: 48C6

description:
48hrControl
[raw_counts_HG19.txt column] 48hrCntrl: 1238__48C6


title: 96C12

description:
96hrControl
[raw_counts_HG19.txt column] 96hrCntrl: 1244__96C12


title: A375_shNT_Med1


title: 48C4

description:
48hrControl
[raw_counts_HG19.txt column] 48hrCntrl: 1236__48C4


title: A375_H3K27ac

description: ChIP-Seq in wild type cells

value: abcam


title: SKMEL147_Input

description: ChIP-Seq in wild type cells


title: 24G4T1

description:
24hrSlick
[raw_counts_HG19.txt column] 24hrSlick: 1247__24G4T1

value: whole embryo


title: 24C3

description:
24hrControl
[raw_counts_HG19.txt column] 24hrCntrl: 1235__24C3


title: A375_Input

description: ChIP-Seq in wild type cells

data_processing:
Aligned with Bowtie version 0.12.8 with the following parameters: -v 2 -m 1
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph: coverage normalized to reads per 10 million aligned reads

treatment_protocol: 80% confluent cells were used for ChIP-Seq analysis


title: A375_H3K4me1

description: ChIP-Seq in wild type cells


title: 24C2

description:
24hrControl
[raw_counts_HG19.txt column] 24hrCntrl: 1234__24C2


title: A375_Med1

description: ChIP-Seq in wild type cells


title: A375_Ino80

description: ChIP-Seq in wild type cells


title: 48G4T6

description:
48hrSlick
[raw_counts_HG19.txt column] 48hrSlick: 1252__48G4T6

value: Slick


title: 24C1

description:
24hrControl
[raw_counts_HG19.txt column] 24hrCntrl: 1233__24C1


title: A375_shIno80_ATAC

data_processing:
library strategy: ATAC-seq
Aligned with Bowtie version 0.12.8 with the following parameters: -v 2 -m 1 --best --strata
Nucleosome signal was generated from the signal of fragments with insert length between 180 and 247 minus the signal of fragments with insert length less than 100
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph: nucleosome signal normalized to reads per 10 million aligned reads

extract_protocol:
Cells were harvested and counted, and lysed by ATAC-Seq lysis buffer
The sequencing library was generated by nextear DNA preparation kit according to the instruction
Nextera DNA sample preparation kit

treatment_protocol: Cells were infected with lenti-viral based shNT or shIno80, cells were harvested 2 days after infection

value: melanoma cell line

value: 2 days after infection


title: HeLa_CAT9_KD_Rep1

city: Boston

first: Robert

middle: E

last: Kingston

state: Massachusetts

address: 185 Cambridge Street

department: Molbio

institute: MGH/Harvard

description: knockdown of candidate RNA

data_processing:
Basecalls performed using OLB 1.8
RNA-Sequences were aligned to the hg9 transcriptome using tophat 2.4
EdgeR was uset to compute RPKM values
DNA-Sequences were aligned to the hg19 genome using bwa 0.5.9
For one batch of libraries, ("rep2" RNAseq and ChIP samples) high contamination of a single probe made in parallel for another experiment (chr7:15630900-156311000) was observed and the spike was removed in ChIP files
Aligned and filtered sequences were used to compute input normalized read densities using the SPP software (bw files)
Genome_build: hg19

source_name: CAT9 knockdown

growth_protocol: 1x complete dmem with FBS, gentamycin, 37C, 5% CO2, O2

extract_protocol:
Trizol, cleanup/DNAse with Zymo clean and concentrate,  illumina Truseq to make cDNA
from cDNA or sheared DNA: blunt ends, A-tail, ligate illumina sequencing adapters, PCR with full length/indexed illumina primers

treatment_protocol: nucleofection of 20 pmol siRNA

value: HeLa  F-17

tag: ectopic expression construct

value: murine FLAG-Bmi1 overexpression

tag: cell treatment

value: siRNA knockdown by nucleofection + 48hours growth


title: Kelly_500

status: Public on Jul 06 2016

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

description: short RNA

data_processing:
Alignment to small RNA transcriptome + spike in sequences with HISAT 0.1.6.
Transcript quantification using Salmon 0.3.2.
Gene-level summarization.
Natural log transform (plus one pseudocount)
Genome_build: GRCh38

source_name: Kelly

growth_protocol: All cell types were grown in DMEM/F12:MEM media supplemented with 10% IFS. Cells were collected when 70% confluent

extract_protocol:
Standard Trizol extraction protocol
NEBNext Multiplex Small RNA Library Prep Set for Illumina (size selected for miRNA)

treatment_protocol: No treatments applied

value: Kelly

tag: spike-in conc.


title: A375_Input

description: ChIP-Seq in wild type cells

value: wild type


title: SHSY5Y_2

data_processing:
Alignment to transcriptome + spike in sequences with HISAT 0.1.6.
Transcript quantification using Salmon 0.3.2.
Gene-level summarization.
Natural log transform (plus one pseudocount)
Genome_build: GRCh38

molecule: polyA RNA

extract_protocol:
Standard Trizol extraction protocol
NEBNext Ultra DNA Library Prep Kit for Illumina (polyA selected)

tag: mycn status

value: Non-Amplified


title: BE2C_500

description: short RNA


title: Kelly_5

description: short RNA


title: Kelly_50

description: short RNA


title: SHSY5Y_3


title: 48C7

description:
48hrControl
[raw_counts_HG19.txt column] 48hrCntrl: 1239__48C7

tag: tissue

tag: developmental stage


title: REH_Input_ChIPseq

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
mouse and human ChIP-seq reads were aligned to the GRCm38p2/mm10 and  GRCh37/hg19 genome assemblies,respectively.
Alignment done using bowtie version 0.12.7, with the parameters:   --best --all --strata  -n 2 -m1 -l 50
peaks were called using MACS version 1.4.2 with default parameters
Genome_build: GRCm38p2/mm10 for mouse and  GRCh37/hg19 for human
Supplementary_files_format_and_content: wig files were generated using MACS with parameter --space 100, and then normalized to RPM. Scores in the wig files represent the averaged RPM over overlapping 100bp window

source_name: REH

extract_protocol:
For mouse thymocytes RAG1 ChIP-seq, cells were crosslinked with 1% HCHO, quenched with 0.125 M glycine, washed and resuspended in high-salt RIPA buffer (10 mM Tris pH 7.4, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 0.8 M NaCl, 1 mM PMSF, 1 μg/μL pepstatin A)  and sonicated using a water bath sonicator (Diagenode) to obtain DNA of ≈ 100-250 bp.H3K27Ac ChIP-seq in REH cells was performed similarly, with the following modifications.  After crosslinking, cells were resuspended in SDS Lysis Buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS, 1 mM PMSF, 1 μg/μL pepstatin A; 200 μls SDS Lysis Buffer per 10 million cells). For each immunoprecipitation, 300 μls of supernatant (corresponding to 15 million cells) was diluted to 1 mL in ChIP dilution buffer (167 mM NaCl, 16.7 mM Tris pH 8, 1.2mM EDTA, 1.1 % Triton X-100, 0.01% SDS) and pre-cleared with Protein G Dynabeads (Thermo-Fisher).  The Dynabeads were then removed using a Dynal magnetic stand. After preclearing and adding blocking agent, anti-H3K27Ac antibody (5 μg; Abcam) was added, and the samples were incubated overnight at 4°C with rotation.  Protein G Dynabeads were blocked with 2% BSA and 50 ng/μL heparin, and were then added to the samples, incubating for 2 hours at 4°C with rotation.  The Dynabeads were washed (10 min, 4°C, with rotation, for each wash):  2x in Low Salt Wash Buffer (20mM Tris, pH 8, 150mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS and 1 mM DTT), 2x in High Salt Wash Buffer (20mM Tris, pH 8, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS and 1 mM DTT), 2x LiCl Wash Buffer (10mM Tris pH 8, 1mM EDTA, 0.25 M LiCl, 0.5% NP-40, 1% sodium deoxycholate), 1x in TE + 0.2% Triton X-100, and 1x in TE.  Beads were incubated twice with 150 μls of elution buffer (1% SDS, 0.1 M NaHCO3) for 15 minutes at room temperature.  Eluates were pooled and incubated at 65°C overnight followed by treatment with RNase and Proteinase K. DNA was purified by standard phenol:chloroform extraction and ethanol precipitation.
libraries were prepared and sequenced following standard Illumina protocols

value: REH


title: IgG

city: Taipei

first: Meng-Chang

last: Lee

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist.,

country: Taiwan

institute: National Defense Medical Center

data_processing:
SOLiD® Accuracy Enhancement Tool (SAET) was used to enhance color call accuracy
LifeScope™ Genomic Analysis Software was used to map reads to GRCh37/ hg19
CisGenome software v2.0 was used to do peak-calling from mapped reads with the following criteria:  ≧ 30 reads each window,  ≧30% total reads for each single direction, false discovery rate (FDR) < 0.05, and the maximal |log2(fold change)|  for all 100 bp windows within the peak ≧ 5
Genome_build: hg19
Supplementary_files_format_and_content: GFF file with peaks data

source_name: bronchial epithelial cells (BEAS-2B)

growth_protocol: BEAS-2B cells were routinely cultured in 15 cm dish with RPMI1640 under normoxia.

extract_protocol:
Protein-DNA complexes were obtained by using antibody from sheared DNA of cell lysates
DNA libraries were established for sequencing according to SOLiD protocols

tag: cultured condition

value: Normoxia

value: IgG antibody (Millipore, 12-371)


title: BE2C_50

description: short RNA

tag: cell line


title: HIF-2α


title: A375_shNT_ATAC

tag: cell type

value: lenti-viral based shNT


title: VGSC422 dsRNA

city: Caesarea

first: Eyal

last: Maori

address: 17 Alon Hatavor street POB 3164

institute: Forrest Innovations Ltd

description:
dsRNA treatment
small RNA
8152764 uniquely mapped reads

data_processing:
Base-calling and generation of raw, de-multiplexed sequencing data in FASTQ format were performed using BaseSpace (Illumina, USA) platform.
Illumina TruSeq small RNA 3' adapters were trimmed using cutadapt version 1.2.1. Untrimmed reads were discarded from the analysis.
Trimmed reads were aligned to a Broad Institute assembly of Ae. aegypti genome using STAR version 2.4.2a; parameters were set for small RNA's alignment: outFilterMismatchNoverLmax=0.05, outFilterMatchNmin=16, outFilterScoreMinOverLread=0, outFilterMatchNminOverLread=0, alignIntronMax=1. Reads that were uniquely mapped to the sodium channel gene were subjected to further downstream analysis.
The number of reads associated with each position along the silencing region and along the entire sodium channel mRNA were counted using coverageBed (bedtools version 2.17.0). Raw read counts were normalized to one million mapped reads per sample (i.e. RPM).
Genome_build: AaegL2 (GenBank assembly accession: GCA_000004015.2)
Supplementary_files_format_and_content: VGSC422*, random*: Tab-delimited text files include per-position RPM values for each sample.
Supplementary_files_format_and_content: size_dist_VGSC422_dsRNA.txt: Tab-delimited text file includes the sizes of small RNAs matching the VGSC422 transcript in the VGSC422 dsRNA treatment.

organism: Aedes aegypti

source_name: Adult females 10 days after treatment with VGSC422 dsRNA

growth_protocol: Ae. aegypti eggs of the Rio de Janeiro strain (RJ, Nova Iguaçu, 23°S/, 43°W) were obtained from the Laboratório de Fisiologia e Controle de Artrópodes Vetores of the Instituto Oswaldo Cruz (Rio de Janeiro). Adult mosquitoes were maintained as described by Rutledge et al. 1964 [*], with modifications. Briefly, mosquitoes were fed on a 10% sugar solution and were reared at 26-28°C, 70-80% relative humidity and a 12:12 photoperiod. Adult females were fed with artificial feeders, using natural pork gut membrane and defibrinated sheep blood (Laborclin ®). (* Rutledge LC, Ward RA, Gould DJ. Studies on the feeding response of mosquitoes to nutritive solutions in a new membrane feeder. Mosq News. 1964; 24:407-419).

extract_protocol:
Total RNA was extracted from a pool of 5 mosquitoes treated with Random or VGSC422 dsRNAs, using the Direct-zolTM RNA MiniPrep (Zymo Research), following the manufacturer's instructions. RNA quality was verified using Agilent Total RNA Nano chip on Bioanalyzer 2100 instrument, and the quantification of total RNA for small RNA library preparation was performed using Qubit RNA BR Assay fluorimetric method (Invitrogen, USA).
One microgram (µg) RNA was used to generate a small RNA sequencing library using the TruSeq Small RNA Sample Prep Kit 7A (Illumina, USA), according to the manufacturer's instructions. Briefly, T4 RNA ligase and T4 RNA ligase 2 Deletion mutant (Epicentre part #LR2D1132K, USA) were used to ligate RA5 and RA3 oligonucleotides to the 5' and 3' ends of the RNA, respectively. Adapter-ligated RNA was reverse-transcribed using a RTP primer and the resulting cDNA was amplified in an 11-cycle PCR that used RP1 and indexed RP1 primers. PCR products of 140-160 bp were isolated following electrophoresis through a 4% agarose gel (Promega). Quality of the generated small RNA sequencing library was confirmed using Agilent High Sensitivity D1000 Screen Tape on TapeStation 2200 instrument. Sequencing was performed in a HiSeq 2500 (Illumina, USA) instrument, in a 100 bp single-end read run using HiSeq SBS clustering and sequencing kit v3-HS.

treatment_protocol: For each treatment, 100 third instar larvae were placed inside a 50 ml plastic cup with 50 ul of autoclaved food solution (6 g/100 ml - 40% cat food, 40% rabbit food, 10% yeast, 10% fish flakes) and 0.5 ug/ul of VGSC422 dsRNA, in a total of 3 ml autoclaved water. The control group was treated with random dsRNA in 3 ml autoclaved water. Larvae were soaked in dsRNA for 24 h and then transferred to a new tray with 1L of aged water. Larvae were allowed to develop until they became adults. All procedures and larval development were performed at 26-28°C. Adult females were used in the adulticide bioassays or submitted to RNA extraction in order to be used for RNA-seq analysis.

tag: strain/background

value: Rio de Janeiro (RJ)

value: Whole body

tag: Sex

value: Female

value: Adult

tag: dsrna

tag: timepoint

value: 10 days after dsRNA treatment


title: REH_H3K27Ac_ChIPseq

description: control: Input

tag: chip antibody


title: Random dsRNA

description:
dsRNA control
small RNA
8118162 uniquely mapped reads

source_name: Adult females 10 days after treatment with random dsRNA

value: Random


title: BE2C_2

value: Amplified


title: BE2C_3


title: Kelly_3


title: SHSY5Y_1


title: Kelly_2


title: Kelly_1


title: BE2C:MYCN siMYCN/miRCon

treatment_protocol: Cells were harvested 48 hours post transfection


title: BE2C:MYCN siMYCN/let-7a


title: BE2C:MYCN siCon/miRCon


title: BE2C:MYCN siCon/let-7a


title: BE2C_1


title: BE2C_5

description: short RNA


title: Thy_mm_RAG1_ChIPseq_rep1

description: control: Input  and RAG1-/-

organism: Mus musculus

source_name: thymocytes

value: thymocytes

tag: genotype

value: wt

tag: strain

tag: age

value: 5 weeks

value: male


title: Thy_mm_RAG1_ChIPseq_rep2

description: control: Input  and RAG1-/-


title: F3_drought stress_Desiree

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

country: Germany

institute: MPI of Molecular Plant Physiology

data_processing:
Quality of pre-filtered read sequences was tested by FastQC version 0.11.2 (Babraham Institute, http://www.bioinformatics.babraham.ac.uk/projects/fastq). As no overrepresented sequences were detected, an additional 3’-trimming step was skipped.
Mapping was performed  by RSEM v1.2.3 using default parameters and its recommended mapper bowtie v.0.12.9. EnsemblPlants release 17 of Genomic FASTA and cDNA GTF file of S. tuberosum were used to obtain a cDNA fasta file with a 125bp long poly-A tail per transcript generated by RSEM module rsem-prepare-reference.
The RSEM module rsem-calculate-expression outputs transcript abundance measurements as expected counts, Transcripts Per Million reads (TPM) and Fragments Per Kilobase of Exon Per Million reads (FPKM).
Genome_build: EnsemblPlants version 17 of Solanum tuberosum
Supplementary_files_format_and_content: Default RSEM output files (ASCII format). Columns: Gene id, Transcript id, length, effective_length, expected_count, TPM, FPKM

organism: Solanum tuberosum

source_name: terminal leaflet of the first mature source leaf

growth_protocol: Two greenhouse (G) experiments were conducted in a climate-controlled greenhouse cabin at the MPI-MP, Potsdam, Germany (G1, G2) while experiment G3 was conducted in a greenhouse at the JKI Groß Lüsewitz, Germany. Pot experiments were started from axenically grown plants that had been propagated at 22°C and 16 h light at the MPI-MP and at 20°C (light)/17°C (dark) at the JKI. For G1 and G2, plantlets were transferred from in vitro cultivation to pots with pricking substrate and acclimated for a week in a climate chamber at 22°C/70% RH during the 16 h day with a light intensity of 150 µmol m-2s-1 and 18°C/70% RH during the night. Subsequently, plants were transferred to a climate-controlled greenhouse chamber with 20°C/60% RH during the 16 h day and 18°C/50% RH during the night. After another week, plants were transferred to the final 18 cm diameter pots. In G3, in vitro plants were transferred to pots in a greenhouse and irrigated as required. After 14 days, plants were transferred to pots with a volume of 5 l and pots were moved to the rain-out-shelter.   Two field (F) experiments were conducted at the MPI-MP, Potsdam, Germany (F1, F3) while experiment F4 was conducted at the JKI Groß Lüsewitz, Germany. For F1 and F3, tubers were pre-sprouted at 8-10°C and planted into ridges at a depth of approximately 15-20 cm, with a spacing of 30 cm within a row and 75 cm between rows. Plants were sprayed twice with magnesium sulphate solution (25 kg/ha) to compensate for low Mg availability in the soil. Potatoes were sprayed with an insecticide against Colorado beetle larvae when the peak of young larvae was observed. F4 was carried out under a rain-out-shelter and tubers were planted in a split-plot design with two watering regimes. The control plots were cultivated next to the shelter under natural rainfall conditions plus additional irrigation.

extract_protocol:
Homogenized leaf material of two to four replicates per cultivar and treatment was pooled to approximate 100 mg. Total RNA was isolated using a TRIzol protocol based on the “single step” method (Chomczynski and Sacchi 1987). For extraction 1 mL TRIzol reagent (Invitrogen) and 200 µL chloroform were used. The supernatant was precipitated by adding 500 µL isopropanol and 250 µL 2 M NaCl. After washing the pellet twice with 70% ethanol, it was re-suspended in 50 µL RNase-free water.
Samples were transferred to the BGI in China for cDNA library preparation and sequencing. The total RNA samples are first treated with DNase I. Then the mRNA is enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000.

treatment_protocol: Control plants were irrigated optimally during the whole experiment, whereas drought stress was induced by withholding water. Regarding greenhouse (G) experiments, the drought stress experiment started twelve days after transfer to the final pot size by stopping the irrigation of the plants in the drought stress blocks. Plants of the control block were watered by drip-irrigation twice to thrice a week with the amount of water lost by evapotranspiration since the last irrigation event determined by weighing pots. From day 20 onwards, plants in the drought stress blocks received 30% of the amount of water given to the control plants. From day 60 onwards, drought stressed plants received 45% of the amount given to the control plants (G1+2) or furthermore 30% (G3 ). In F1 and F3 plants were drip-irrigated from the top of the ridges with 10mm water during the night when plants in control plots showed signs of decreased turgor at noon. Drought stressed plants were irrigated when they showed signs of water stress 2 h after sunrise. F4 was carried out in a rain-out-shelter where drought stress was applied by stopping watering at the beginning of emergence.

value: leaf

tag: experiment

tag: treatment

value: drought stress

tag: cultivar

value: Desiree


title: Normal_Artery_ATAC_D3

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

data_processing:
Library strategy: ATAC-seq
Alignment
ATAC-seq and ChIP-seq reads in raw fastq files were aligned to hg19 using bowtie2 set to default parameters. RNA-seq reads were aligned to hg19 using the RNA-seq aligner STAR (v2.4.0i).
These ChIPseqs were done on a different machine as paired ends, no replicates, sequences combined in a bam file which was used to create the bed file provided, otherwise handled as noted for the other ChIPseqs.
Peak-calling
ATAC-seq and ChIP-seq peaks were called with MACS1.4 for hg19, set to default parameters using IgG samples as a background control.
Feature counts
ATAC-seq mapped reads were counted using the HOMER annotatePeaks script after normalization of reads. RNA-seq mapped reads were counted using the featurecounts script distributed with the Rsubread package, and differential expression of exons, genes, and transcripts were assayed using the DESeq2 R package from Bioconductor.
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed files standard format
Supplementary_files_format_and_content: RNA-Seq proccesed files (featureCounts): one for gene and one for transcript IDs
Supplementary_files_format_and_content: .csv DESeq output files

source_name: Human coronary artery explant tissue

extract_protocol:
10-20 mg of pulverized fresh frozen tissue was suspended in 1 mL 1x PBS and centrifuged at 2,000 x g for 3 min at 4° C. The pellet was resuspended in 1 mL of a lysis buffer containing 50 mM HEPES, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, and 0.25% Triton X-100 and supplemented with an EDTA-free complete protease inhibitor (Roche). This suspension was incubated at 4° C for 10 minutes and then dounce homogenized. The homogenate was centrifuged at 2,000 x g for 5 min at 4° C, and the resultant pellet was resuspended in 1 mL 1x PBS. Cellular debris was filtered with a cell strainer, and intact nuclei were quantified. 5x10^4 nuclei were subjected to Tn5 mediated transposition for 1 hour and tagmented DNA was purified as previously reported.
Libraries were PCR amplified and purified as described previously and were subjected to an additional electrophoresis step on an E-Gel EX 2% agarose gel (Invitrogen), and gel fragments correlating to 100-1000 bp were excised and purified. The quality of the library preparation was determined by evaluation of the electropherogram traces from an Agilent 2100 Bioanalyzer DNA High Sensitivity, and libraries demonstrating appropriate nucleosomal enrichment were multiplexed. Libraries were quantitated using Qubit high sensitivity DNA reagent, and quantitative PCR (KAPA Biosystems).

treatment_protocol: Normal coronary arteries were dissected from a normal explanted donor heart and media was carefully separated before snap freezing.

tag: tissue state

value: Normal coronary artery (media)


title: Athero_Artery_ATAC_D4

treatment_protocol: Atherosclerotic diseased coronary arteries were dissected from a diseased explanted donor heart and media was carefully separated before snap freezing.

value: Atherosclerotic coronary artery (media)


title: HCASMC_ChIP_IgG_D1

data_processing:
Alignment
ATAC-seq and ChIP-seq reads in raw fastq files were aligned to hg19 using bowtie2 set to default parameters. RNA-seq reads were aligned to hg19 using the RNA-seq aligner STAR (v2.4.0i).
These ChIPseqs were done on a different machine as paired ends, no replicates, sequences combined in a bam file which was used to create the bed file provided, otherwise handled as noted for the other ChIPseqs.
Peak-calling
ATAC-seq and ChIP-seq peaks were called with MACS1.4 for hg19, set to default parameters using IgG samples as a background control.
Feature counts
ATAC-seq mapped reads were counted using the HOMER annotatePeaks script after normalization of reads. RNA-seq mapped reads were counted using the featurecounts script distributed with the Rsubread package, and differential expression of exons, genes, and transcripts were assayed using the DESeq2 R package from Bioconductor.
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed files standard format
Supplementary_files_format_and_content: RNA-Seq proccesed files (featureCounts): one for gene and one for transcript IDs
Supplementary_files_format_and_content: .csv DESeq output files

source_name: HCASMC Cell Applications 2108

growth_protocol: Human coronary artery smooth muscle cells were obtained from Cell Applications, and media was purchased from Lonza. Cells were maintained as suggested in SmGM-2 Smooth Muscle Growth Medium-2 including hEGF, insulin, hFGF-B and 5% FBS, but without antibiotics (Lonza, #CC-3182).

extract_protocol:
1x10^7 HCASMC per condition were crosslinked for 10 min with 1% formaldehyde, followed by quenching with glycine. Cells were lysed for 10 min on ice, and nuclei were then lysed for 10 min on ice. Crosslinked chromatin was sheared to 100-500bp fragments by sonication for 3x5 min using a Bioruptor Pico sonicator (Diagenode). 5 ug IgG or H3K27ac (Abcam ab4729) antibody was incubated with diluted chromatin overnight at 4C, and ChIP DNA was receoved as previously described.
Libraries were generated by ligating ChIP DNA with Illumina TruSeq adapters, followed by PCR amplification and gel electrophoresis. ChIP DNA library fragments around 300bp were selected for PCR amplification and libraries were quantitated using Qubit fluorometric and bioanalyzer analyses.

tag: cell treatment

value: Normal serum


title: HCASMC_RNA_PDGFBB_D2

source_name: HCASMC Cell Applications 1522

extract_protocol:
5x10^5 HCASMC per condition were lysed in Qiazol reagent and total RNA was extracted using the miRNeasy kit (Qiagen). RNA was quantitated using Qubit and bioanalyzer analyses.
Libraries were generated using the Illumina TruSeq library kit.

treatment_protocol: Cells were maintained in normal media until 70% confluence and media was changed to serum-free without supplements for 18h and cells were stimulated with growth factors for 1 or 6 hours in serum-free, supplement-free media.

value: PDGF-BB


title: HCASMC_RNA_Control_D1

source_name: HCASMC Cell Applications 2989

value: Serum-free control


title: HCASMC_ChIP_H3K27ac_D1

value: H3K27ac, Abcam ab4729


title: HCASMC_ChIP_H3K27ac_D3

source_name: HCASMC Cell Applications 2139


title: F3_drought stress_Alegria

tag: tissue

value: Alegria


title: Athero_Artery_ATAC_D6


title: F3_drought stress_Saturna

value: Saturna


title: F3_drought stress_Milva

value: Milva


title: HCASMC_RNA_TGFB_D1


title: Normal_Artery_ATAC_D2


title: HCASMC_ATAC_PDGFDD_D2

source_name: HCASMC Cell Applications 1508

extract_protocol:
5x10^4 fresh HCASMC were collected by centrifugation and and nuclei extracted with cold lysis buffer containting 10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL and nuclei were resuspended in transposition reaction buffer containing Tn5 transposases (Illumina Nextera). Transposition reactions were incubated at 37C for 30 minutes, followed by DNA purification using Zymo DNA Clean-up and Concentration Kit.
Libraries were PCR amplified and purified as described previously. The quality of the library preparation was determined by evaluation of the electropherogram traces from an Agilent 2100 Bioanalyzer DNA High Sensitivity and TBE gel electrophoresis, and libraries demonstrating appropriate nucleosomal enrichment were multiplexed. Libraries were quantitated using Qubit high sensitivity DNA reagent, and quantitative PCR (KAPA Biosystems).

treatment_protocol: Cells were maintained in normal media until 70% confluence and media was changed to serum-free without supplements for 18h and cells were stimulated with growth factors for 6 hours in serum-free, supplement-free media.

value: PDGF-DD


title: F3_control_Saturna

value: control


title: HCASMC_ATAC_PDGFBB_D2


title: HCASMC_ATAC_TGFB_D2


title: F3_control_Milva


title: HCASMC_RNA_TGFB_D2


title: Normal_Artery_ATAC_D1


title: HCASMC_RNA_PDGFBB_D1


title: HCASMC_ChIP_H3K27ac_D2


title: F3_control_Desiree


title: HCASMC_RNA_Control_D2


title: Athero_Artery_ATAC_D5


title: HCASMC_ATAC_Control_D2


title: F3_control_Alegria


title: HCASMC_ATAC_PDGFDD_D1

source_name: HCASMC Cell Applications 020805.2


title: F4_drought stress_Desiree


title: F4_drought stress_Saturna


title: F4_drought stress_Alegria


title: HCASMC_ATAC_TGFB_D1


title: G2_control_Saturna


title: F4_control_Alegria


title: G2_drought stress_Alegria


title: HCASMC_ATAC_PDGFBB_D1


title: G2_drought stress_Milva


title: G2_drought stress_Saturna


title: F4_control_Desiree


title: G2_control_Alegria


title: G2_control_Milva


title: G2_drought stress_Desiree


title: G2_control_Desiree


title: G1_drought stress_Saturna


title: G1_drought stress_Milva


title: G1_control_Saturna


title: G1_control_Milva


title: G1_control_Desiree


title: G1_drought stress_Alegria


title: A375_shIno80_Med1

tag: chip antibody vendor

value: Bethyl

tag: chip antibody cat. #

tag: chip antibody lot #


title: G1_drought stress_Desiree


title: F4_drought stress_Milva


title: G1_control_Alegria


title: F4_control_Milva


title: G3_drought stress_Saturna


title: F4_control_Saturna


title: G3_drought stress_Milva


title: G3_drought stress_Desiree


title: G3_control_Saturna


title: G3_control_Milva


title: G3_control_Alegria


title: F1_drought stress_Saturna


title: G3_control_Desiree


title: HCASMC_ATAC_Control_D1


title: F1_control_Desiree


title: F1_drought stress_Milva


title: F1_control_Milva


title: F1_control_Saturna


title: AAspike-FFss-TT-SS2

status: Public on Jul 05 2016

city: reno

first: Wei

last: Yan

state: NV

address: 1664 N. Virginia Street

department: Physiology

institute: University of Nevada

data_processing:
Illumina Casava1.7 software used for basecalling.
Torrent Suite
The sequence reads were aligned by BWA
Then aligned reads were analyzed though CIRI for circular RNA annotation
Genome_build: mm9
Supplementary_files_format_and_content: The CIRI ananotated all the circular RNAs in the sequencing data. The processed data files contains all the anotate circular RNAs with location and quantity information. The format is txt.

organism: synthetic construct

source_name: ERCC ExFold RNA Spike-In Mixes

extract_protocol:
The library was constructed by SuperScript II
The RNAs was purified by mirvana
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: synthetic RNA


title: AAspike-FFms-TT-SS2

extract_protocol:
The library was constructed by Monster Script
The RNAs was purified by mirvana
RNA libraries were prepared for sequencing using standard Illumina protocols


title: AAspike-FFss-TT-SS1


title: F1_drought stress_Desiree


title: AAspike-FFms-TT-SS1


title: F1_control_Alegria


title: U1-2_0-4

city: Rochester

first: Steven

last: Gill

address: Box 672, Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester School of Medicine and Dentistry

description:
Processed data file: LFR_Gill050615_FPKM.txt
Processed data file: LFR_Gill050615_rawcounts.txt

data_processing:
Sequences were cleaned using Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
Alignment using STAR-2.4.2a "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
All sequences were aligned to MRSA252 (GenBank ID = NC_002952.2).
Raw read counts obtained using HTSeq.
Differential expression using cuffdiff(cufflinks-2.0.2) - "--library-type fr-firststrand --FDR 0.05 -u -b GENOME"
Data normalization and differential expression using DESeq2-1.10.1 p-value 0.05
Genome_build: NC_002952.2
Supplementary_files_format_and_content: "LFR_Gill030116_FPKM.txt" and "LFR_Gill050615_FPKM.txt": Tab-delimited text files include RPKM values for each sample.
Supplementary_files_format_and_content: "LFR_Gill030116_rawCounts.txt" and "LFR_Gill050615_rawCounts.txt": Tab-delimited text files include raw read counts for each sample.

organism: Staphylococcus aureus

source_name: UAMS-1, early exponential phase

growth_protocol: Individual S. aureus colonies for each strain were grown O/N in TSB, diluted to an OD600 ~0.05, incubated with shaking at 37C to an OD600 ~0.4 (early exponential phase), 0.9 (late exponential phase) or 1.2 (early stationary phase) and collected for RNA extraction.

extract_protocol:
Three ml aliquots from each culture were transferred to RNAProtect and then RNA was extracted by acid phenol/mechanical lysis.
Illumina TruSeq library preparation from RiboZero depleted total RNA. 100nt single-end reads.

tag: lineage

tag: strain/background

tag: genotype/variation

value: WT

tag: growth phase

value: early exponential in TSB (OD600=~0.4)


title: 478-1_0-4

description:
UAMS-1 delta SAR2593 (mocR)
Processed data file: LFR_Gill050615_FPKM.txt
Processed data file: LFR_Gill050615_rawcounts.txt

source_name: UAMS-1 delta-mocR, early exponential phase

value: delta SAR2593 (mocR)


title: U1-1_0-4


title: 478-2_0-4


title: 478-2_0-9

source_name: UAMS-1 delta-mocR, late exponential phase

value: late exponential in TSB (OD600=~0.9)


title: U1-2_0-9

source_name: UAMS-1, late exponential phase


title: G3_drought stress_Alegria

value: leaf

value: drought stress


title: F1_drought stress_Alegria


title: 478-1_1-2

description:
UAMS-1 delta SAR2593 (mocR)
Processed data file: LFR_Gill030116_FPKM.txt
Processed data file: LFR_Gill030116_rawcounts.txt

source_name: UAMS-1 delta-mocR, early stationary phase

value: early stationary in TSB (OD600=~1.2)


title: 215-2_1-2

description:
UAMS-1 delta SAR2592 (fad)
Processed data file: LFR_Gill030116_FPKM.txt
Processed data file: LFR_Gill030116_rawcounts.txt

source_name: UAMS-1 delta-fad, early stationary phase

value: delta SAR2592 (fad)


title: 478-2_1-2


title: 215-1_1-2


title: U1-1_1-2

description:
Processed data file: LFR_Gill030116_FPKM.txt
Processed data file: LFR_Gill030116_rawcounts.txt

source_name: UAMS-1, early stationary phase


title: U1-2_1-2


title: ACGI428 29502

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

institute: University of Pennsylvania

data_processing:
Poor quality sequence was trimmed from FASTQ files.
FASTQ files were aligned to human genome hg19 and transcripts using RUM (Grant et al Bioinformatics 2011)
A best representation of each gene was selected using the highest expressing transcript, converted to RPM, and normalized to the average expression of the 10 most deeply sequenced cells.
Differential expression, where reported was performed using EdgeR or DESeq2 on raw read counts.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized expression values for RefSeq transcripts

source_name: pancreas

growth_protocol: islets were cultured in the standand prodo islet media (PIM-S001GMP, PIM-ABS001GMP, PIM-G001GMP) at 37oc with 5% CO2.

extract_protocol:
Islets were dissociated to single cell by 0.05% Trypsin, 9 mins at 37oC. Cells (250-500 cells/μl) were subsequently loaded on Fluidigm C1 IFC with either 5-10 μM or 10-17 μM capture size.
Smarter-seq V2 kit was utilized for library construction per manufacturer's protocol to generate cDNA.  Prepration of Illumina libraries from cDNA was done with the NexteraXT kit per Fluidigm’s instructions.

value: pancreatic islets

value: adult

tag: health

tag: curated-cell-type

value: dropped


title: ACGI428 29491

tag: age

value: duct


title: ACGI428 29493


title: ACGI428 29498


title: ACGI428 29499


title: ACGI428 29500


title: ACGI428 29495


title: 478-1_0-9


title: ACGI428 29503

value: beta


title: ACGI428 29494

value: mesenchyme


title: ACGI428 29497


title: ACGI428 29489


title: ACGI428 29501


title: ACGI428 29490


title: ACGI428 29488


title: ACGI428 29486


title: ACGI428 29487


title: ACGI428 29484


title: U1-1_0-9


title: ACGI428 29483


title: ACGI428 29482


title: ACGI428 29479


title: ACGI428 29481


title: ACGI428 29480


title: ACGI428 29477


title: ACGI428 29492


title: ACGI428 29476


title: ACGI428 29478


title: ACGI428 29485


title: ACGI428 29471


title: ACGI428 29475


title: ACGI428 29470


title: ACGI428 29466


title: ACGI428 29463

value: acinar


title: ACGI428 29474


title: ACGI428 29462


title: ACGI428 29461


title: ACGI428 29457


title: ACGI428 29473


title: ACGI428 29458


title: ACGI428 29467


title: ACGI428 29456


title: ACGI428 29465


title: ACGI428 29460


title: ACGI428 29459


title: ACGI428 29464


title: ACGI428 29455


title: ACGI428 29454


title: ACGI428 29452


title: ACGI428 29453


title: ACGI428 29451


title: ACGI428 29449


title: ACGI428 29450


title: ACGI428 29472


title: ACGI428 29447


title: ACGI428 29469


title: ACGI428 29446


title: ACGI428 29443


title: ACGI428 29444


title: ACGI428 29441


title: ACGI428 29440


title: ACGI428 29442


title: ACGI428 29435


title: ACGI428 29445


title: ACGI428 29438


title: ACGI428 29436


title: ACGI428 29431


title: ACGI428 29434


title: ACGI428 29437


title: ACGI428 29433


title: ACGI428 29439


title: ACGI428 29432


title: ACGI428 29428


title: ACGI428 29429


title: ACGI428 29427


title: ACGI428 29425


title: ACGI428 29430


title: ACGI428 29426


title: ACGI428 29448


title: ACGI428 29423


title: ACGI428 29421


title: ACGI428 29420


title: ACGI428 29422


title: 48C5

description:
48hrControl
[raw_counts_HG19.txt column] 48hrCntrl: 1237__48C5

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: Tab-delimited raw_counts_HG19.txt is a summary file with raw count data extracted from the blastx alignments to HG19.
Supplementary_files_format_and_content: Each tab-delimited *vs*Cntrl.txt file is standard DEseq2 output for a comparison of treated vs control.  The baseMean column reports a mean of the counts for all the treated vs control samples used in that particular comparison.

source_name: whole embryo

extract_protocol:
Thirty pooled embryos or larvae per replicate were homogenized with a Kontes Pellet Pestle Cordless Motor (Sigma-Aldrich, St. Louis, Missouri) in RNAzol (Molecular Research Center, Cincinnati, Ohio). 200 ng of total RNA was used to prepare RNA-Seq libraries using the TruSeq RNA Sample Prep kit following the protocol described by the manufacturer (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole embryo

tag: developmental stage

tag: stress

value: Control

tag: concentration


title: ACGI428 29419


title: ACGI428 29418


title: ACGI428 29414


title: ACGI428 29412

value: alpha


title: ACGI428 29408


title: ACGI428 29415


title: ACGI428 29410


title: RC-mixtures

city: chengdu

first: Mingzhou

last: Li

state: Sichuan

address: No.211 Huimin Road, Wenjiang District

country: China

institute: Sichuan Agricultural University

data_processing:
Illumina Casava1.82 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to itself assembly genome using Tophat.
Cufflinks version 2.2.1 were applied to quantify gene expression and obtain FPKM expression values (denoted as the fragments per Kb of transcript per Mb mapped reads).
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Sus scrofa

source_name: mixture of multiple tissues

extract_protocol:
The total RNA was extracted using the TrIzol reagent (Life Technologies, Beijing, China) according to the manufacturer’s protocols. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 60 days old

value: mixture of multiple tissues

tag: breed name

value: Rongchang


title: RC-subcutaneous adipose

source_name: subcutaneous adipose

value: subcutaneous adipose


title: TP-spleen

source_name: spleen

value: spleen

value: Tibetan wild boar


title: RC-longissimus dorsi muscle

source_name: longissimus dorsi muscle

value: longissimus dorsi muscle


title: ACGI428 29424

value: pancreatic islets


title: TP-psoas major muscle

source_name: psoas major muscle

value: psoas major muscle


title: TP-longissimus dorsi muscle


title: RC-spleen


title: RC-kidney

source_name: kidney

value: kidney


title: RC-ovary

source_name: ovary

value: ovary


title: RC-heart

source_name: heart

value: heart


title: MS-ovary

value: Meishan


title: RC-psoas major muscle


title: MS-mixtures


title: MS-longissimus dorsi muscle


title: RC-liver

source_name: liver

value: liver


title: MS-subcutaneous adipose


title: MS-psoas major muscle


title: MS-kidney


title: MS-lung

source_name: lung

value: lung


title: ACGI428 29416

value: adult

value: duct


title: ACGI428 29417

value: mesenchyme


title: MS-spleen

value: 60 days old


title: JH-mixtures

value: mixture of multiple tissues

value: Jinhua


title: MS-heart


title: JH-longissimus dorsi muscle


title: MS-liver


title: JH-psoas major muscle


title: JH-lung


title: JH-spleen

value: spleen


title: BM-ovary

value: Bamei


title: JH-kidney


title: BM-mixtures


title: JH-liver


title: BM-psoas major muscle


title: BM-lung


title: JH-heart


title: BM-longissimus dorsi muscle

value: longissimus dorsi muscle


title: PI-mixtures

value: Piétrain


title: BM-spleen


title: BM-heart


title: BM-liver


title: PI-ovary


title: PI-subcutaneous adipose

value: subcutaneous adipose


title: PI-kidney

value: kidney


title: PI-psoas major muscle

value: psoas major muscle


title: PI-spleen


title: PI-heart

value: heart


title: LW-mixtures

value: Large White


title: JH-subcutaneous adipose


title: JH-ovary

value: ovary


title: BM-subcutaneous adipose


title: PI-lung

value: lung


title: LW-subcutaneous adipose


title: LW-ovary


title: LW-psoas major muscle


title: PI-liver

value: liver


title: LW-liver


title: BM-kidney


title: LW-heart


title: LW-kidney


title: LA-subcutaneous adipose

value: Landrace


title: PI-longissimus dorsi muscle


title: LA-longissimus dorsi muscle


title: LA-ovary


title: LA-lung


title: LA-psoas major muscle


title: LA-spleen


title: LW-longissimus dorsi muscle


title: LW-lung


title: LA-liver


title: LA-heart


title: HA-subcutaneous adipose

value: Hampshire


title: HA-ovary

value: 60 days old


title: LA-kidney


title: HA-psoas major muscle


title: HA-spleen


title: HA-longissimus dorsi muscle


title: HA-kidney


title: BK-mixtures

value: mixture of multiple tissues

value: Berkshire


title: HA-lung


title: HA-heart


title: BK-longissimus dorsi


title: BK-kidney


title: HA-liver


title: BK-lung


title: BK-ovary


title: BK-subcutaneous adipose


title: BK-psoas major muscle


title: LW-spleen

value: spleen


title: HA-mixtures


title: BK-heart


title: BK-liver


title: Nalm6 H3K4me3 [ChIP-Seq]

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

country: Finland

institute: university of eastern finland

description: Immunoprecipitated DNA

data_processing:
Libraries were single-end sequenced on a Hi-Seq 2000 (Illumina) for 51 cycles, according to the manufacturer’s instructions.
Sequence reads were quality filtered with the FASTX software (-q 10 -p 97) and read stacks were collapsed.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.9 (-v 2 -k 3 -m 1 --best)
Bedgraphs were generated using the HOMER software. The Pol2 bedgraphs were generated at 50bp resolution for change point analysis. Data analysis was performed using HOMER and custom scripts http://biowhat.ucsd.edu/homer/
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph ChIP-seq signal files

source_name: Nalm6 cell line

growth_protocol: Cells were cultured in RPMI (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) suppelemented with 2 mM L-glut, 100 U penicillin, 100 ug/ml streptomycin and 10% Tet System Approved FBS (Clontech, Mountain View, CA, USA).

extract_protocol:
40 million cells were crosslinked with 1% formaldehyde for 10-15 mins.  The reactions were quenched by adding glycine to a final concentration of 125 mM, and the cells were centrifuged and washed twice with ice-cold PBS. For each ChIP 5 million cells was used. Nuclei was extracted by washing cell pellet twice with 1 ml of MNase buffer (10mM Tris ph 7,4, 10mM NaCl, 5mM MgCl2, 0,5% IGEPAL CA-630 [Sigma], 1x protease inhibitor cocktail [PIC, Roche], 1 mM PMSF [Thermofisher]). Nuclei were spun down (1500 x g, +4 °C, 5 min) and suspended into 90µl of MNase buffer supplemented with 5mM CaCl2 and 0.1% Triton-X. Different amounts of MNase (0.5-20U; #88216, Thermofisher) was added to the nuclei in 10 µl volume and incubated at 37°C for 10 mins.  To stop the reaction, 100 µl of 2xLysis buffer was added to the reaction (1% SDS, 40mM EDTA, 100mM Tris-HCl pH 8.1) and samples were sonicated using Bioruptor (Diagenode) for 5 cycles (30 s – 30 s) to break the nuclei.  The lysate was cleared by centrifugation and supernatant was diluted 5 x with dilution buffer (for H3K4me3; 20mM Trix-HCl pH 7.4, 100mM NaCl, 2mM EDTA, 0.5% TritonX, PIC). The diluted lysate was pre-cleared by rotating for 2 h at 4°C with 60 µl 80% CL-4B sepharose slurry (GE Healthcare; Before use, sepharose was washed twice with TE buffer, blocked for 1h min at room temperature with 0.5% BSA and 20 µg/ml glycogen in 1 ml TE buffer, washed twice with TE and brought up to the original volume with TE). The beads were discarded, and 1% of the supernatant were kept as ChIP input. The protein of interest was immunoprecipitated by rotating the supernatant with 3-5 µg antibody overnight at 4°C. Antibody H3K4me3 (ab8580) was purchased from Abcam. The Ab was captured using 25 µl blocked Protein G Sepharose® 4 Fast Flow (GE Healthcare, sepharose was blocked rorating overnight at 4°C) and rotating the sample for 2 h at 4°C. The beads were pelleted (1 min, 1000× g, 4°C), the supernatant discarded, and were washed three times with wash buffer I (20 mM Tris/HCl pH 7.4@20°C, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA), twice with buffer II (20 mM Tris/HCl pH 7.4@20°C, 500 mM NaCl, 1% Triton X-100, 2 mM EDTA) and buffer III (10 mM Tris/HCl pH 7.4@20°C, 250 mM LiCl, 1% IGEPAL CA-630, 1% Na-deoxycholate, 1 mM EDTA), once with TE+0.2% TritonX and twice with TE.
Immunoprecipitated chromatin was eluted twice with 100 µl elution buffer (TE, 1% SDS). The NaCl concentration was adjusted to 300 mM with 5 M NaCl and crosslinks were reversed overnight at 65°C. The samples were sequentially incubated at 37°C for 2 h each with 0.33 mg/ml RNase A and 0.5 mg/ml proteinase K. The DNA was isolated using the ChIP DNA Clean & Concentrator (Zymo Research) according to the manufacturer’s instructions. Sequencing libraries were prepared from collected DNA by blunting, A-tailing, adaptor ligation as previously described (Heinz 2010; MolCell) using barcoded adapters (NextFlex, Bioo Scientific). Between the reactions, the DNA was purified using Sera-Mag SpeedBeads (Thermo Scientific). Libraries were PCR-amplified for 15-16 cycles and size selected for 230-350bp fragments by gel extraction.

treatment_protocol: Cells in basal conditions

tag: cell line

value: ALL leukemia cell line Nalm6

tag: antibody

value: H3K4me3 (Abcam, catalog# 8580)

tag: replicate


title: REH ser5pol2 [ChIP-Seq]

description: Immunoprecipitated DNA

source_name: REH cell line

extract_protocol:
40 million cells were crosslinked with 1% formaldehyde for 10-15 mins.  The reactions were quenched by adding glycine to a final concentration of 125 mM, and the cells were centrifuged and washed twice with ice-cold PBS. For each ChIP 10 million cells was used. Nuclei was extracted by washing cell pellet twice with 1 ml of MNase buffer (10mM Tris ph 7,4, 10mM NaCl, 5mM MgCl2, 0,5% IGEPAL CA-630 [Sigma], 1x protease inhibitor cocktail [PIC, Roche], 1 mM PMSF [Thermofisher]). Nuclei were spun down (1500 x g, +4 °C, 5 min) and suspended into 90µl of MNase buffer supplemented with 5mM CaCl2 and 0.1% Triton-X. Different amounts of MNase (0.5-20U; #88216, Thermofisher) was added to the nuclei in 10 µl volume and incubated at 37°C for 10 mins.  To stop the reaction, 100 µl of 2xLysis buffer was added to the reaction (1% SDS, 40mM EDTA, 100mM Tris-HCl pH 8.1) and samples were sonicated using Bioruptor (Diagenode) for 5 cycles (30 s – 30 s) to break the nuclei.  The lysate was cleared by centrifugation and supernatant was diluted 5 x with RIPA buffer (1X PBS, 1% NP-40, 0.5% Sodium deoxycholate, 0.1% SDS, PIC). The diluted lysate was pre-cleared by rotating for 2 h at 4°C with 60 µl 80% CL-4B sepharose slurry (GE Healthcare; Before use, sepharose was washed twice with TE buffer, blocked for 1h min at room temperature with 0.5% BSA and 20 µg/ml glycogen in 1 ml TE buffer, washed twice with TE and brought up to the original volume with TE). The beads were discarded, and 1% of the supernatant were kept as ChIP input. The protein of interest was immunoprecipitated by rotating the supernatant with 3-5 µg antibody overnight at 4°C. Antibodies against Pol2 Ser2P (ab5095) and Pol2 Ser5P (ab5131) were from Abcam. The Ab was captured using 25 µl blocked Protein G Sepharose® 4 Fast Flow (GE Healthcare, sepharose was blocked rorating overnight at 4°C) and rotating the sample for 2 h at 4°C. The beads were pelleted (1 min, 1000× g, 4°C), the supernatant discarded, and the beads used to bind Ser2P/5P Ab were washed five times with 5X LiCl IP wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% Sodium deoxycholate) and twice with TE in 0.45 µm filter cartridges (Ultrafree MC, Millipore).
Immunoprecipitated chromatin was eluted twice with 100 µl elution buffer (TE, 1% SDS). The NaCl concentration was adjusted to 300 mM with 5 M NaCl and crosslinks were reversed overnight at 65°C. The samples were sequentially incubated at 37°C for 2 h each with 0.33 mg/ml RNase A and 0.5 mg/ml proteinase K. The DNA was isolated using the ChIP DNA Clean & Concentrator (Zymo Research) according to the manufacturer’s instructions. Sequencing libraries were prepared from collected DNA by blunting, A-tailing, adaptor ligation as previously described (Heinz 2010; MolCell) using barcoded adapters (NextFlex, Bioo Scientific). Between the reactions, the DNA was purified using Sera-Mag SpeedBeads (Thermo Scientific). Libraries were PCR-amplified for 15-16 cycles and size selected for 230-350bp fragments by gel extraction.

value: ALL leukemia cell line REH

tag: chip antibody

value: Pol2 Ser5P (Abcam, catalog# ab5131)


title: REH ser2pol2 [ChIP-Seq]

description: Immunoprecipitated DNA

value: Pol2 Ser2P (Abcam, catalog# ab5095)


title: whole-limb(1)

city: New Orleans

first: Yiping

last: Chen

state: LA

address: 6400 Freret

department: CMB

institute: Tulane University

description: Whole limb

data_processing:
Initial demutilexing and filtering of reads were performed at BGI
Mapping by Tophat using default setting
Cufflink-cuffdiff-CummRbund pipline were perfomed seperately on each litter to obtain DEGs
Subsequently DEGs were cross analyzed with Shox2 binding peaks using BETA(http://cistrome.org/BETA/)
Putative Shox2 targets in each litter obtained by BETA analysis were intersected
Genome_build: mm9

source_name: embryonic limb

growth_protocol: fresh dissected tissue

extract_protocol:
Rneasy Micro Kit(Qiagen)
Extracted RNA were submitted to BGI(Hongkong) for library construction and subsequent sequencing

treatment_protocol: digetion and subsequently sorting based on GFP expression

value: WT


title: L3Mutant-GFP+(2)

description: FACS-Sorted Shox2+ (Shox2 mutant) cells (Litter3)


title: L1Mutant-GFP+(2)

description: FACS-Sorted Shox2+ (Shox2 mutant) cells (Litter1)


title: L2Mutant-GFP+(2)

description: FACS-Sorted Shox2+ (Shox2 mutant) cells (Litter2)


title: REH input [ChIP-Seq]

description: Mnase digested input


title: whole-limb(2)

description: Whole limb


title: L3Control-GFP+(1)

description: FACS-Sorted Shox2+ cells (Litter3)


title: L1Mutant-GFP+(1)


title: BK-spleen

tag: tissue


title: L1Control-GFP+(1)

description: FACS-Sorted Shox2+ cells (Litter1)


title: Nalm6 ser5pol2 2 [ChIP-Seq]

description: Immunoprecipitated DNA


title: L2Control-GFP+(1)

description: FACS-Sorted Shox2+ cells (Litter2)


title: Nalm6 ser2pol2 2 [ChIP-Seq]

description: Immunoprecipitated DNA


title: Nalm6 ser5pol2 1 [ChIP-Seq]

description: Immunoprecipitated DNA


title: Nalm6 ser2pol2 1 [ChIP-Seq]

description: Immunoprecipitated DNA


title: REH H3K4me3 [ChIP-Seq]

description: Immunoprecipitated DNA


title: Nalm6 input 1 [ChIP-Seq]

description: Mnase digested input


title: control-input

data_processing:
Standard mapping using bowtie for illumina
Peaks calling using MACS/MACS2 with default setting in Galaxy main/Cistrome instance
mm9
bedgraph files are generated by MACS
Bedgraph was converted to bigwig using Bedgraph to bigwig tool in Galaxy main instance
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-signal filtered against Non tagged control by MACS2

extract_protocol:
ChIP, following manufracture protocol provided by Active Motif ChIP-IT high sensitivity protocol
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced


title: Shox2-palate E12.5

source_name: embryonic palate

tag: sample type

value: anti-HA(Abcam, Cat.Ab9110, Lot.  GR146572-6)


title: Pbx-limb E12.5

value: Pbx

value: Anti-Pbx(Santa Cruz H-260 SC-25411, lot D1806)


title: Control-nontagged

source_name: embryonic limb/Palate mix


title: Case5_rep2_60min_160312_SNc_dopamine neuron

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

data_processing:
Illumina Casava1.7 software used for basecalling
RNA-seq reads of mouse and human samples were separately mapped to the mouse reference genome (mm10) and human reference genome (hg38) using STAR (version 2.4.1) with parameter --outSAMstrandField intronMotif.
Expression  of genes for each sample was quantified and normalized using Cufflinks and Cuffnorm (version 2.2.1) with parameter -library-norm-method geometric.
Genome_build: mm10 for mouse samples, hg38 for human samples
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: neurons

extract_protocol:
For RNA extraction from LCM dissected motor neurons, the Arcturus PicoPure RNA Isolation Kit was used. For other samples, cells are diectly picked after dissociation and deposited into lyssis buffer. No RNA extraction is conducted.The cell lysis is proceed directly to library preparation.
Libraries for RNA-seq were prepared by using SMART-seq2 combined with Tn5 tagementation

value: dopamine neurons

tag: cell number


title: Case6_rep2_60min_160311_SNc_dopamine neuron


title: Case7_rep2_60min_160310_SNc_dopamine neuron


title: Shox2-limb/palate E12.5


title: Case7_rep1_60min_160310_SNc_dopamine neuron


title: Shox2-limb E13.5


title: Case6_rep2_20min_160312_SNc_dopamine neuron


title: Case6_rep1_20min_160312_SNc_dopamine neuron


title: Shox2-limb E12.5


title: Case5_rep1_20min_160312_SNc_dopamine neuron


title: Hb9_MN_168

source_name: Hb9 neurons

value: motor neurons


title: Case5_rep2_20min_160312_SNc_dopamine neuron


title: Hb9_MN_164


title: Hb9_MN_163


title: Case7_rep2_20min_160310_SNc_dopamine neuron


title: Case7_rep1_20min_160310_SNc_dopamine neuron


title: Hb9_MN_162


title: Case6_rep1_4min_160312_SNc_dopamine neuron


title: Case5_rep2_4min_160311_SNc_dopamine neuron


title: Hb9_MN_154


title: Nalm6 input 2 [ChIP-Seq]

description: Mnase digested input


title: Hb9_MN_151


title: 63


title: Hb9_MN_153


title: Hb9_MN_155


title: Hb9_MN_150


title: Hb9_MN_149


title: 60


title: Case6_rep2_4min_160312_SNc_dopamine neuron


title: 61


title: Hb9_MN_166


title: Case7_rep1_4min_160310_SNc_dopamine neuron


title: 59


title: Hb9_MN_148


title: 57


title: Hb9_MN_146


title: 43


title: Hb9_MN_161


title: Hb9_MN_157


title: Hb9_MN_145


title: 232_mouse_5

source_name: small neurons


title: 56


title: Case5_rep1_4min_160311_SNc_dopamine neuron


title: 28


title: 29


title: 217_mouse_5


title: Case7_rep2_4min_160310_SNc_dopamine neuron


title: 205_mouse_5


title: 218_mouse_1


title: 27


title: 214_mouse_1


title: 26


title: 62


title: 25


title: 204_mouse_1


title: 45


title: Hb9_MN_147


title: 211_mouse_1


title: 8


title: 50


title: HTT Control Rep 2

city: La Jolla

first: Gene

last: Yeo

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

institute: UCSD

data_processing:
Sequencing reads from RNA-seq libraries were first trimmed of polyA tails, adapters, and low quality ends using cutadapt with parameters --match-read-wildcards --times 2 -e 0 -O 5 --quality-cutoff' 6 -m 18 -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b TGGAATTCTCGGGTGCCAAGG -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT.
Reads were then mapped against a database of repetitive elements derived from RepBase18.05. Bowtie version 1.0.0 with parameters -S -q -p 16 -e 100 -l 20 was used to align reads against an index generated from Repbase sequences (Langmead et al., 2009).
Reads not mapped to Repbase sequences were aligned to the mm9 human genome (UCSC assembly) using STAR (Dobin et al., 2013) version 2.3.0e with parameters --outSAMunmapped Within –outFilterMultimapNmax 1 –outFilterMultimapScoreRange 1.
counts of reads for each gene annotated in gencode vM1 were calculated from featureCounts
Genome_build: mm9
Supplementary_files_format_and_content: count file, contains counts of reads for each sample

source_name: HTT Control

growth_protocol: eight-week old female C57Bl/b mice were grown under normal conditions

extract_protocol:
tissues were harvested and frozen in TRIzol (Invitrogen).
TruSeq Stranded mRNA and Total RNA Sample Preparation Kit

treatment_protocol: Sterotactic injections of ASO complementary to TAF15 were performed in eight-week old female C57Bl/b mice to deplete TAF15. ASOs were delivered specifically to the striatum by intrastriatal (12.5 mg)  injection (300 mg). Mice were regularly monitored for 14 days until sacrificed.

tag: strain

value: striatum

value: ctrl


title: HTT Control Rep 1

tag: genotype/variation


title: 7


title: TAF15 Rep 2

value: TAF15 knockdown


title: TAF15 Rep 1


title: TAF15 KD 4hr

data_processing:
RNA-seq libraries were first trimmed of polyA tails, adapters, and low quality ends using cutadapt with parameters --match-read-wildcards --times 2 -e 0 -O 5 --quality-cutoff' 6 -m 18 -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b TGGAATTCTCGGGTGCCAAGG -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT.
Reads were then mapped against a database of repetitive elements derived from RepBase18.05. Bowtie version 1.0.0 with parameters -S -q -p 16 -e 100 -l 20 was used to align reads against an index generated from Repbase sequences (Langmead et al., 2009).
Reads not mapped to Repbase sequences were aligned to the hg19 human genome (UCSC assembly) using STAR (Dobin et al., 2013) version 2.3.0e with parameters --outSAMunmapped Within –outFilterMultimapNmax 1 –outFilterMultimapScoreRange 1.
counts of reads for each gene annotated in gencode v17 were calculated from featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: count file, contains counts of reads for each sample

source_name: TAF15 KD 4hr

growth_protocol: Lentiviral shRNA constructs (Open Biosystems) complementary to human TAF-15 (TRCN0000020140, TRCN0000020141 or TRCN0000020143,), human FUS/TLS (TRCN0000010450, TRCN0000039824, or TRCN0000039825), and human TDP-43 (TRCN0000016038) in the pLKO.1 vector system were used to produce lentivirus as previously described53. Virus produced from a pLKO.1 construct containing a control sequence was used as the control. At 60-70% confluency, NPCs were infected with virus (MOI=3) for 24 hours, followed by a complete media change and further incubation for 72 hours.

extract_protocol:
Total RNA was extracted from human cells using TRIzol (Invitrogen) according to manufacturer’s instructions. 1 ug of total RNA was DNase treated and subjected to poly(A) selection.
TruSeq Stranded mRNA and Total RNA Sample Preparation Kit

treatment_protocol: 96 hours post infection, cells were treated with Actinomycin D (10 μg/mL) for the indicated times. Cells were washed with cold PBS and harvested for RNA extraction using TRIzol (Life Technologies) or protein for Western blot analysis.

tag: cell type

value: NPC

tag: knockdown

tag: agent

value: Actinomycin D

tag: time


title: Ctrl 4hr

source_name: Ctrl 4hr


title: 1_5e

value: cervical spinal cord


title: 2


title: 215_mouse_1


title: TAF15_1

description: library strategy: CLIP-seq

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 or hg18 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
wig files are strand specific read densities generated using custom scripts from duplicate removed bam files.
bed files represent CLIP-seq peaks and were generated using an in-house peak finding algorithm.
Genome_build: mm9
Supplementary_files_format_and_content: bed files of peaks called and wiggle files of read densities across the genome

source_name: brain, Anti-TAF15 IP

extract_protocol:
Brains from 8-week-old female C57Bl/6 mice were rapidly dissociated by forcing the tissue through a cell strainer with a pore size of 100 mm (BD Falcon) before ultraviolet crosslinking.
CLIP-seq libraries were constructed using 10 mg of a polyclonal antibody against TAF15 (300A 308, Bethyl Laboratories).

value: brain

tag: antibody manufacturer

value: Bethyl

tag: antibody catalog#


title: 1_5b


title: TAF15 KD 30min

source_name: TAF15 KD 30min


title: FUS KD 30min

source_name: FUS KD 30min

value: FUS


title: 1_5c


title: TAF15 KD 2hr

source_name: TAF15 KD 2hr


title: 1_3


title: FUS KD 2hr

source_name: FUS KD 2hr


title: TAF15 KD 1hr

source_name: TAF15 KD 1hr


title: Ctrl 2hr

source_name: Ctrl 2hr


title: 1_1l


title: FUS KD 1hr

source_name: FUS KD 1hr


title: 1_1k


title: 1_1h


title: Ctrl 1hr

source_name: Ctrl 1hr


title: 1_2


title: 1_1g


title: TAF15 KD 15m

source_name: TAF15 KD 15m


title: FUS KD 4hr

source_name: FUS KD 4hr


title: 1_1e

source_name: neurons


title: FUS KD 15m

source_name: FUS KD 15m


title: 1_1c


title: TAF15 KD 0m

source_name: TAF15 KD 0m


title: Ctrl 15m

source_name: Ctrl 15m


title: 1_5a


title: Ctrl 30min

source_name: Ctrl 30min


title: 2_5c


title: 2_5b


title: 1_4a


title: Ctrl 0m

source_name: Ctrl 0m


title: 2_5d


title: 2_4a


title: FUS KD 0m

source_name: FUS KD 0m


title: WT Sibling Control Rep 2 scramble shRNA treated

source_name: WT Sibling Control, scramble shRNA treated

growth_protocol: iPSCs were grown on Matrigel-coated plates (BD) in mTeSR1 growth media (Stem Cell Technologies). Stem cell colonies were grown on ultra low-attachment plates in DMEM/F12 + GlutaMAX supplemented with N2 and FGF-2 (20 ng/ml). After one week, neural rosettes were manually picked, replated, and maintained in DMEM/F12 + GlutaMAX supplemented with N2, B27, and FGF-2 (20 ng/ml). Human motor neurons were differentiated from iPSCs (CVB) using a protocol modified from Chambers et al.39. Briefly, human iPSCs were maintained in hEB Media (Knockout D-MEM + 10% Knockout Serum Replacement (Life Technologies) + 10% Plasmanate (Biocare) + GlutaMAX + NEAA (Life Technologies) and supplemented with 10 mM SB431542 and 10 mM Dorsomorphin dihydrochloride (Tocris) on feeder-free dishes. Cells were maintained in SB431542 and Dorsomorphin until day 18 of differentiation. On days 4, 5, and 6 of differentiation, hEB media was mixed with N2 Base media (D-MEM/F12 + GlutaMAX, 1% N2 Supplement + 4.5 mM D-Glucose, 0.05 mM Ascorbic Acid (Sigma)) at a ratio of 70:30, 50:50, and 50:50, respectively. On days 7 and 8 of differentiation, cells were maintained in 50:50 combination of hEB media and maturation media (D-MEM/F12 + GlutaMAX, 2% N2 Supplement, 4% B27 Serum-Free Supplement (Invitrogen), 9.0 mM D-Glucose, 0.1 mM Ascorbic Acid (Sigma)) supplemented with 2 ng/mL each of Ciliary Neurotrophic Factor (CNTF), Brain-Derived Neurotrophic Factor (BDNF), and Glial Cell-Derived Neurotrophic Factor (GDNF) (Peprotech). From day 7 to day 22 of differentiation, cells were treated with 200 nM Smoothened Agonist (SAG; EMD Biosciences) and 1.5 mM Retinoic Acid (RA; Sigma). On day 18 of differentiation, cells were dissociated using Accutase, and transferred to dishes coated with Poly-D-Lysine (Sigma) + Laminin (Life Technologies) and maintained in maturation media supplemented with RA and SAG. On day 22, cells were maintained in maturation media containing 2 mM DAPT (Tocris). On day 26, cells were maintained in maturation media only. Throughout the differentiation protocol media was changed daily. The identity and purity of motor neurons were analyzed by immunofluorescence for markers of stem cell, motor neurons, astrocytes, and glial cells.

extract_protocol:
Total RNA was extractedcells using TRIzol (Invitrogen) according to manufacturer’s instructions. 0.5-3 mg of total RNA was DNase treated and subjected to Ribo-Zero treatment
TruSeq Stranded mRNA and Total RNA Sample Preparation Kit

treatment_protocol: Lentiviral shRNA constructs (Open Biosystems) complementary to human TAF-15 (TRCN0000020140, TRCN0000020141 or TRCN0000020143,), human FUS/TLS (TRCN0000010450, TRCN0000039824, or TRCN0000039825), and human TDP-43 (TRCN0000016038) in the pLKO.1 vector system were used to produce lentivirus as previously described53. Virus produced from a pLKO.1 construct containing a control sequence was used as the control. For lentiviral infection of motor neurons, media containing virus (MOI=5) was added to cells on day 28 of the motor neuron differentiation protocol. After 24 hours, a complete media change was performed and cells incubated for an additional 48 hours. A second round of infection, similar to the first, began on day 31. On day 34 of MN differentiation, corresponding to a six-day exposure period to shRNA expression, cells were either collected and frozen in TRIzol (Invitrogen) or pelleted and frozen in liquid nitrogen for RNA and protein analysis, respectively.

value: Motor Neuron

tag: shRNA

value: scramble


title: 2_4b


title: 2_2f


title: WT Sibling Control Rep 1

source_name: WT Sibling Control

value: WT


title: 2_2c


title: 2_2g


title: FUS R521G Rep 2

source_name: FUS R521G

value: FUS R521G


title: 2_2a


title: LA-mixtures

source_name: mixture of multiple tissues

tag: age

value: 60 days old

value: mixture of multiple tissues

tag: breed name

value: Landrace


title: FUS R521G Rep 3


title: TDP43 Knockdown Rep2

source_name: TDP43 Knockdown

value: TDP43 Knockdown


title: FUS R521G Rep 1


title: TDP43 Knockdown Rep1


title: TAF15 Knockdown Rep2

source_name: TAF15 Knockdown

value: TAF15 Knockdown


title: 2_1b


title: 2_1a


title: Scramble Knockdown Rep2

source_name: Scramble Knockdown

value: Scramble

value: Scramble Knockdown


title: WT Sibling Control Rep 2


title: 5_4b


title: TAF15 Knockdown Rep1


title: 5_4a


title: FUS and TAF15 Knockdown Rep1

source_name: FUS and TAF15 Knockdown

value: FUS and TAF15

value: FUS and TAF15 Knockdown


title: 5_5a

value: cervical spinal cord


title: FUS Knockdown Rep2

source_name: FUS Knockdown

value: FUS Knockdown


title: Scramble Knockdown Rep1


title: FUS and TAF15 Knockdown Rep2


title: 5_3


title: FUS Knockdown Rep1


title: 5_2


title: 2_2d


title: 2_1d


title: Case6_VTA_dopamine_neuron_LCM93

value: ventral tegmental area


title: Case5_VTA_dopamine_neuron_LCM104


title: 5_1a


title: 2_1c


title: 5_1c


title: 5_1b


title: Case7_VTA_dopamine_neuron_LCM4


title: Case6_VTA_dopamine_neuron_LCM89


title: Case7_SNc_dopamine_neuron_LCM3

value: substantia nigra pars compacta


title: Case5_VTA_dopamine_neuron_LCM91


title: 10_4c


title: 10_4b


title: Case7_SNc_dopamine_neuron_LCM99


title: 10_4


title: Case7_SNc_dopamine_neuron_LCM101


title: Case6_SNc_dopamine_neuron_LCM102


title: 10_2


title: 10_2b


title: Case6_SNc_dopamine_neuron_LCM103


title: Case5_SNc_dopamine_neuron_LCM94


title: Case5_SNc_dopamine_neuron_LCM100


title: 10_1b


title: Case4_spinal_motor_neuron_LCM92

value: spinal motor


title: Case1_spinal_motor_neuron_LCM96


title: 30_5c


title: 10_1a


title: 10_5


title: Case3_spinal_motor_neuron_LCM90


title: 30_5b


title: Case2_spinal_motor_neuron_LCM44


title: Case4_spinal_motor_neuron_LCM105


title: 30_4


title: 30_4b


title: 10_3


title: 30_5


title: 30_2


title: REH cell line co-cultured with differentiated (A) stromal cells [Gro-Seq]

description:
Sample name: REH_d1
REH coculture
nascent RNA
REHs_minus_1e7_fs1e50_res50.bedGraph.gz, REHs_plus_1e7_fs1e50_res50.bedGraph.gz
GRO-seq

data_processing:
Libraries were sequenced for 51 cycles (single-end) on an Illumina HiSeq 2000, according to the manufacturer’s instructions.
GRO-Seq reads were trimmed to remove A-stretches originating from the library preparation using the Homer software (homerTools trim) and from resulting sequences those shorter than 25 bp were discarded.  Sequence reads were further quality filtered with the FASTX software (-q 10 -p 97)
GRO-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.9 (-v 2 -k 3 -m 1 --best)
Bedgraphs were generated using the HOMER software from combined tagDirectories (per cell line). Data analysis was performed using HOMER and custom scripts http://biowhat.ucsd.edu/homer/
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph GRO-seq signal files, separately for plus and minus strand

growth_protocol: Cells were cultured in RPMI (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) suppelemented with 2 mM L-glut, 100 U penicillin, 100 ug/ml streptomycin and 10% Tet System Approved FBS (Clontech, Mountain View, CA, USA). Co-cultured cells were grown separated by membrane with human primary stromal cells isolated from bone marrow.

extract_protocol:
GRO-Seq: Nuclei were extracted from 5-16 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads and precipitated overnight. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified. The recovered cDNA was circularized, linearized, amplified for 11-14 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina HiSeq 2000.
Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified. The recovered cDNA was circularized, linearized, amplified for 11-14 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina HiSeq 2000.

tag: cell line

value: ALL leukemia cell line REH

tag: culture

value: with differentiated (A) stromal cells


title: REH cell line co-cultured with stromal cells_3 [Gro-Seq]

description:
Sample name: REH_c3
REH coculture
nascent RNA
REHs_minus_1e7_fs1e50_res50.bedGraph.gz, REHs_plus_1e7_fs1e50_res50.bedGraph.gz
GRO-seq

value: with stromal cells

tag: replicate


title: REH cell line co-cultured with differentiated (O) stromal cells [Gro-Seq]

description:
Sample name: REH_d2
REH coculture
nascent RNA
REHs_minus_1e7_fs1e50_res50.bedGraph.gz, REHs_plus_1e7_fs1e50_res50.bedGraph.gz
GRO-seq

value: with differentiated (O) stromal cells


title: 30_1

tag: tissue


title: 50_4b


title: REH cell line_3 [Gro-Seq]

description:
Sample name: REH_3
REH basal
nascent RNA
REHs_minus_1e7_fs1e50_res50.bedGraph.gz, REHs_plus_1e7_fs1e50_res50.bedGraph.gz
GRO-seq

source_name: REH cell line

value: alone

value: 0 h


title: REH cell line co-cultured with stromal cells_2 [Gro-Seq]

description:
Sample name: REH_c2
REH coculture
nascent RNA
REHs_minus_1e7_fs1e50_res50.bedGraph.gz, REHs_plus_1e7_fs1e50_res50.bedGraph.gz
GRO-seq


title: REH cell line co-cultured with stromal cells_1 [Gro-Seq]

description:
Sample name: REH_c1
REH coculture
nascent RNA
REHs_minus_1e7_fs1e50_res50.bedGraph.gz, REHs_plus_1e7_fs1e50_res50.bedGraph.gz
GRO-seq


title: 50_4

source_name: neurons


title: 10_5b


title: REH cell line_2 [Gro-Seq]

description:
Sample name: REH_2
REH basal
nascent RNA
REHs_minus_1e7_fs1e50_res50.bedGraph.gz, REHs_plus_1e7_fs1e50_res50.bedGraph.gz
GRO-seq


title: 50_3


title: 50_5


title: 50_2b


title: 50_2


title: Nalm6 cell line co-cultured with stromal cells [Gro-Seq]

description:
Sample name: Nalm6_c
Nalm6 coculture
nascent RNA
Nalms_minus_1e7_fs1e50_res50.bedGraph.gz, Nalms_plus_1e7_fs1e50_res50.bedGraph.gz
GRO-seq

value: ALL leukemia cell line Nalm6


title: 30_3


title: Nalm6 cell line [Gro-Seq]

description:
Sample name: Nalm6_a
Nalm6 basal
nascent RNA
Nalms_minus_1e7_fs1e50_res50.bedGraph.gz, Nalms_plus_1e7_fs1e50_res50.bedGraph.gz
GRO-seq

source_name: Nalm6 cell line


title: REH cell line_1 [Gro-Seq]

description:
Sample name: REH_1
REH basal
nascent RNA
REHs_minus_1e7_fs1e50_res50.bedGraph.gz, REHs_plus_1e7_fs1e50_res50.bedGraph.gz
GRO-seq


title: Case3_spinal_motor_neuron_LCM57


title: 50_1


title: 50_1b


title: 120_5


title: AAold-FFms-TTtestis-SS2

source_name: testis

value: wild type

value: testis


title: AAnew-FFssii-TTtestis-SS2


title: AAold-FFssii-TTtestis-SS2


title: 100_1


title: AAold-FFms-TTtestis-SS1


title: 120_4


title: AAnew-FFms-TTtestis-SS2


title: 4X


title: 5X


title: AAnew-FFssii-TTtestis-SS1


title: AAnew-FFms-TTtestis-SS1


title: 7X


title: 6X


title: 3X


title: 100_2


title: 125

value: lumbar spinal cord


title: CD56+ natural killer cell

city: Athens

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: TAB-seq

data_processing:
Data were mapped to the H. sapiens GRCh38 reference genome
TAB-seq analysis were performed as described in Yu, M.; Hon, G.C.; Szulwach, K.E.; Song, C.X.; Zhang, L.; Kim, A.; Li, X.K.; Dai, Q.; Shen, Y.; Park, B.; Min, J.H.; Jin, P.*; Ren, B.*; He, C.* Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell.2012, 149, 1368-1380.
Genome_build: H. sapiens GRCh38
Supplementary_files_format_and_content: tab delimited text file
Supplementary_files_format_and_content: Column1: chromosome
Supplementary_files_format_and_content: Column2: cytosine position
Supplementary_files_format_and_content: Column3: strand
Supplementary_files_format_and_content: Column4: CNN (N = A, T, C, G)
Supplementary_files_format_and_content: Column5: methylated cytosines in this site
Supplementary_files_format_and_content: Column6: totally detected cytosines in this site

source_name: CD56+ natural killer cell

growth_protocol: Peripheral blood was collected from a healthy male and the seven leukocyte types were isolated reiterativly using antibodies to cell type specific surface antigens bound to magnetic Dynabeads.

extract_protocol: Genomic DNA (gDNA) was purified from seven isolated cell types using DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA cat# 69506), according to the manufacturer’s instructions. TAB-seq libraries were constructed according to Yu, M.; Hon, G.C.; Szulwach, K.E.; Song, C.X.; Zhang, L.; Kim, A.; Li, X.K.; Dai, Q.; Shen, Y.; Park, B.; Min, J.H.; Jin, P.*; Ren, B.*; He, C.* Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell. 2012, 149, 1368-1380.

value: CD56+ natural killer cell


title: CD16+ neutrophil

description: TAB-seq

source_name: CD16+ neutrophil

value: CD16+ neutrophil


title: CD8+ T cell

description: TAB-seq

source_name: CD8+ T cell

value: CD8+ T cell


title: CD4+ T cell

description: TAB-seq

source_name: CD4+ T cell

value: CD4+ T cell


title: AAold-FFssii-TTtestis-SS1

extract_protocol:
The library was constructed by SuperScript II
The RNAs was purified by mirvana
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 123


title: 127


title: Siglec8+ eosinophil

description: TAB-seq

source_name: Siglec8+ eosinophil

value: Siglec8+ eosinophil


title: 119


title: HUES14

status: Public on Jul 04 2016

city: Pardess hana

first: Uri

last: Weissbein

state: Please Select

address: Haalon 4

institute: Hebrew University of Jerusalem

data_processing:
Reads were mapped to the human reference genome (GRCh38/hg38) using TopHat (version 2.0.8b)
Reads per kilobase of transcript per million mapped reads (FPKM) values were calculated using Cufflinks (version 2.1.1)
Genome_build: USCS/GRCh38/hg38
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each sample

source_name: HUES14 Human embryonic stem cells

extract_protocol:
Total RNA was extracted using NucleoSpin RNA Plus kit (Marcherey-Nagel). mRNA was enriched by Poly-A selection.
Sequencing libraries were prepared using TruSeq RNA Library Prep Kit v2 (Illumina).

tag: differentiation status

value: Undifferentiated

tag: karyotype


title: CSES21

source_name: CSES21 Human embryonic stem cells

value: Trisomy 21


title: 128

tag: cell number


title: CSES22

source_name: CSES22 Human embryonic stem cells

value: Trisomy 12


title: CSES9

source_name: CSES9 Human embryonic stem cells

value: Diploid


title: CSES7

source_name: CSES7 Human embryonic stem cells


title: Haematopoietic progenitor cell Prog_Rep_852

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

country: United Kingdom

institute: University of Cambridge

description: single cell RNA-Seq

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts / gene counts (.txt)

source_name: Bone Marrow

extract_protocol:
Bone marrow cells were isolated from the femurs, tibiae and iliac crest of 20 8-12 week old C57BL/6 mice.
The cells were lineage depleted and stained with antibodies to separate individual populations by FACS.
Single-cell sorting was done using a FACS Influx5 (BD Biosciences) using unstained cells and single-stained cells are gate-settng controls.
Cells were sorted directly into individual wells of a 96-well PCR plate containing lysis buffer.
Single-cell RNA-seq analysis was performed as described previously (Picelli et al., 2014).
Pooled libraries were run on the Illumina Hi-Seq 2500.
RNA libraries were prepared for sequencing using the Illumina Nextera XT DNA preparation kit

value: Haematopoietic progenitor cell

tag: strain

value: 8-12 weeks


title: Haematopoietic progenitor cell Prog_Rep_851

description: single cell RNA-Seq

tag: cell type


title: CD14+ monocyte

first: Robert

description: TAB-seq

source_name: CD14+ monocyte

value: CD14+ monocyte


title: Haematopoietic progenitor cell Prog_Rep_846

description: single cell RNA-Seq


title: CD19+ B cell

description: TAB-seq

source_name: CD19+ B cell

value: CD19+ B cell


title: Haematopoietic progenitor cell Prog_Rep_848

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_847

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_849

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_845

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_843

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_844

description: single cell RNA-Seq


title: 30_2b

value: cervical spinal cord


title: Haematopoietic progenitor cell Prog_Rep_841

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_842

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_839

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_837

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_835

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_836

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_832

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_831

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_833

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_850

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_838

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_834

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_828

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_829

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_830

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_826

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_824

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_821

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_816

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_827

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_820

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_815

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_819

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_823

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_840

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_818

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_813

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_822

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_817

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_812

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_809

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_810

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_814

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_808

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_807

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_806

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_803

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_804

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_825

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_802

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_805

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_800

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_801

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_799

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_797

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_798

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_811

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_793

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_790

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_791

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_789

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_794

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_795

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_783

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_784

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_787

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_781

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_786

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_785

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_782

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_780

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_779

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_788

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_778

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_776

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_777

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_775

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_773

description: single cell RNA-Seq


title: Haematopoietic progenitor cell Prog_Rep_774

description: single cell RNA-Seq