title: H3K4me3 ChIP-seq in NCIH810 cells

data_processing:
Reads were aligned to GRCh37 using bwa (version 0.6.2) After removal of PCR duplicates using Picard(http://broadinstitute.github.io/picard), read counts were normalized for sequencing depth and scaled to 10 million reads to generate bigwig files.
Genome_build: hg19

extract_protocol:
Chromatin from formaldehyde-fixed cells (2-5 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with AMP Pure beads(Beckman Coulter) after crosslink reversal, RNAse A and Proteinase K treatment.
ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

tag: chip antibody


title: it33 warm rep1

status: Public on Jul 30 2018

type: SRA

city: Beltsville

first: Sunchung

last: Park

state: MD

address: 10300 Baltimore ave, Bldg001

department: ARS-NEA

country: USA

institute: USDA -ARS

description: Plants grown at 22⁰C on soil under a photoperiod of 12 h for 23 days, sampled at ZT4

library_source: transcriptomic

data_processing:
Illumina Real Time Analysis (RTA) v1.18.64  software used for basecalling.
Reads were mapped to the Arabidopsis reference genome (TAIR10) using Tophat version 2.1.0 in default mode with minimum and maxmum intron lengths being set to 10 and 15,000 bp, respectively. The transcript abundance (FPKM) was estimated using Cufflinks (version 2.1.1). Cuffdiff was run using default parameters with inputs of the TAIR10 genome and transcript annotations.
Genome_build: TAIR v10
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: aerial part

growth_protocol: Plants were grown on soil at 22⁰C under a 12 h photoperiod with 100-120 μmol m-2 s-1 light intensity

extract_protocol:
RNA was extracted using the RNeasy plant mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Cold treatment was for 24 hour or 2 weeks at 4⁰C under a 12 h photoperiod of ~35 µmol m-2 sec-1
Cold treated and control samples (all samples) were collected at ZT4

tag: tissue

value: entire aerial part

tag: age

value: 23 days after germination

tag: genotype

value: Italian ecotype


title: IT warm rep1


title: H3K9me3 ChIP-seq in A673.2 cells with dCAS9 targeting enhancer of SOX2 (gRNA 2)

city: Boston

first: Sowmya

last: Iyer

state: MA

department: Pathology

institute: Massachusetts General Hospital

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: cell line

tag: cell line


title: NRO-seq in SKNMC cell line

description:
nascent RNA
SKNMC.NRO

data_processing:
Library strategy: NRO-seq
Reads were aligned to GRCh37(hg19) using bwa mem. PCR duplicates were removed using Picard(http://broadinstitute.github.io/picard). Genome-wide smoothed signals were generated by counting reads in 150-bp sliding windows with 20 bp overlap using bedtools coverage. All signals were normalized for sequencing depth and scaled to 10 million reads.
Genome_build: hg19

extract_protocol:
Freshly extracted nuclei were incubated 30 minutes at 30°C in presence of BrUTP (Roche). Nuclear RNA was extracted using the NucleoSpin miRNA kit (Clontech) and nascent RNA was immunoprecipitated with an anti-BrdU monoclonal antibody (Santa Cruz). Following washes, purified RNA was isolated using the NucleoZOL extraction kit (Clontech).
Nascent RNA samples were treated with RiboGone oligonucleotides to remove ribosomal RNA (Clontech). Illumina compatible sequencing libraries were constructed using SMARTer Stranded Total RNA sample Prep Kit (Clontech) according to the manufacturer’s instructions

value: SKNMC

tag: infection

value: uninfected


title: it8 24hr-cold rep2


title: H3K27ac ChIP-seq in A673.2 cells with dCAS9 targeting enhancer of SOX2 (gRNA 1)


title: INPUT library in NCIH810 cells

value: INPUT


title: H3K27ac ChIP-seq in NCIH810 cells


title: H3K27ac ChIP-seq in A673.2 cells with dCAS9 targeting enhancer of SOX2 (gRNA 2)


title: H3K27ac ChIP-seq in A673.2 cells with dCAS9 targeting control


title: H3K9me3 ChIP-seq in A673.2 cells with dCAS9 targeting enhancer of SOX2 (gRNA 1)


title: IT 24hr-cold rep1


title: H3K27ac ChIP-seq in A673.1 cells with dCAS9 targeting enhancer of NKX2-2 (gRNA 2)


title: FLI1 ChIP-seq in A673.2 cells with dCAS9 targeting enhancer of SOX2 (gRNA 1)


title: H3K9me3 ChIP-seq in A673.2 cells with dCAS9 targeting control


title: FLI1 ChIP-seq in A673.2 cells with dCAS9 targeting enhancer of SOX2 (gRNA 2)


title: H3K9me3 ChIP-seq in A673.1 cells with dCAS9 targeting enhancer of NKX2-2 (gRNA 1)


title: H3K27ac ChIP-seq in A673.1 cells with dCAS9 targeting enhancer of NKX2-2 (gRNA 1)


title: FLI1 ChIP-seq in A673.2 cells with dCAS9 targeting control


title: H3K9me3 ChIP-seq in A673.1 cells with dCAS9 targeting enhancer of NKX2-2 (gRNA 2)


title: FLI1 ChIP-seq in A673.1 cells with dCAS9 targeting enhancer of NKX2-2 (gRNA 1)


title: H3K9me3 ChIP-seq in A673.1 cells with dCAS9 targeting control


title: FLI1 ChIP-seq in A673.1 cells with dCAS9 targeting control


title: BCG W10 8343

city: Oxford

first: Julius

last: Muller

state: Oxfordshire

address: ORCRB, Roosevelt Drive

department: Nuffield Department of Medicine

country: United Kingdom

institute: The Jenner Institute, University of Oxford

description:
featureCounts.tsv
featureCounts_voom.tsv

data_processing:
Illumina Casava v1.8 was used for basecalling.
Reads were adapter removed, quality filtered and trimmed to 80Bp using trimmomatic 0.35 with parameters ILLUMINACLIP:/TOOLS/trimmomatic-0.35/adapters/TruSeq3-PE-2.fa:2:30:10 HEADCROP:15 CROP:80 SLIDINGWINDOW:5:6 MINLEN:80
Sequences were mapped to bosTau8 using STAR aligner v2.5.0b with parameter --outSAMmultNmax 20
Genome_build: bosTau8
Supplementary_files_format_and_content: tab-delimited text files include per gene read counts. Counts were calculated using featureCounts v1.5.0 with parameters: -M --donotsort -s 0 and the reference gtf file containing refGene definitions was downloaded from UCSC on 10.12.2015; voom transformed log2 CPM values were calculated as follows: only genes with cpm values greater 1 in at least 20 samples were kept for the analysis;  To scale raw library sizes, the calcNormFactors method of the edgeR package was used in R with default parameters. voomWithQualityWeights and duplicateCorrelation from the limma package was used to combine observational-level with sample-specific quality weights while accounting for inter-animal correlation.
Supplementary_files_format_and_content: /TOOLS/subread-1.5.0-Linux-x86_64/bin/featureCounts -a /data/GENOMES/bosTau8/UCSC/UCSC_refGene_bosTau8_20151210.gtf -M --donotsort -s 0

organism: Bos taurus

source_name: Tempus tubes (Whole Blood)

extract_protocol:
After stimulation blood was stored in Tempus tubes and RNA extracted using 5 Prime's Perfect Pure RNA blood kit for RNA extraction following the manufacturer's instructions.
Libraries were contstructed using Illumina's kit's and standard protocols

treatment_protocol: Whole blood was cultured overnight with 10 µg/ml PPD-B or with105 cfu/ ml BCG Tokyo or with medium only.

tag: animal

value: Whole Blood

value: 6 months

tag: week post challenge

tag: stimulus

value: BCG

tag: strain

value: Holstein X Friesian

tag: group

value: protected


title: Unstim W10 8343

value: Unstim


title: BCG W10 8341


title: BCG W10 8340


title: PPDB W10 8341

value: PPDB


title: Unstim W10 8341


title: BCG W10 8336

value: unprotected


title: Unstim W10 8344


title: BCG W10 8346


title: Unstim W10 8340


title: Unstim W10 8336


title: PPDB W10 8333


title: BCG W10 8333


title: PPDB W10 8343


title: FLI1 ChIP-seq in A673.1 cells with dCAS9 targeting enhancer of NKX2-2 (gRNA 2)


title: BCG W9 8345


title: H3K27ac ChIP-seq in A673.1 cells with dCAS9 targeting control


title: BCG W9 8336


title: Unstim W9 8336


title: PPDB W9 8342


title: Unstim W10 8333


title: PPDB W9 8347


title: BCG W9 8346


title: Unstim W9 8347


title: PPDB W9 8346


title: PPDB W8 8345


title: BCG W9 8344


title: BCG W9 8347


title: Unstim W9 8346


title: PPDB W9 8344


title: Unstim W9 8344


title: Unstim W9 8343


title: PPDB W9 8341


title: BCG W9 8341


title: BCG W9 8343


title: PPDB W9 8340


title: Unstim W9 8340


title: PPDB W8 8336


title: Unstim W8 8347


title: PPDB W8 8347


title: BCG W8 8347


title: Unstim W8 8346


title: BCG W8 8346


title: PPDB W8 8346


title: BCG W8 8343


title: BCG W8 8344


title: Unstim W8 8343


title: Unstim W8 8344


title: BCG W8 8341


title: PPDB W8 8343


title: PPDB W8 8341


title: PPDB W8 8340


title: Unstim W8 8341


title: Unstim W8 8340


title: PPDB W10 8344


title: PPDB W9 8343


title: Unstim W9 8341


title: PPDB W8 8344


title: BCG W0 8347


title: Unstim W0 8347


title: PPDB W0 8347


title: PPDB W0 8346


title: BCG W0 8344


title: PPDB W0 8344


title: Unstim W0 8344


title: Unstim W0 8346


title: BCG W0 8343


title: PPDB W10 8340


title: PPDB W0 8343


title: BCG W0 8340


title: PPDB W0 8341


title: BCG W8 8340


title: Unstim W0 8341


title: Unstim W0 8340


title: PPDB W0 8340


title: Unstim W10 8345


title: Unstim W0 8343


title: BCG W9 8340


title: BCG W10 8342


title: BCG W10 8338


title: Unstim W10 8342


title: PPDB W10 8338


title: BCG W10 8337


title: PPDB W10 8336


title: Unstim W10 8338


title: Unstim W9 8342


title: PPDB W9 8345


title: Unstim W9 8338


title: PPDB W9 8338


title: BCG W9 8338


title: PPDB W10 8345


title: BCG W9 8337


title: PPDB W9 8336


title: Unstim W9 8345


title: Unstim W9 8333


title: PPDB W10 8337


title: BCG W10 8345


title: PPDB W9 8333


title: Unstim W9 8337


title: BCG W9 8333


title: PPDB W9 8337


title: PPDB W8 8338


title: Unstim W8 8342


title: PPDB W8 8342


title: Unstim W8 8345


title: BCG W8 8345


title: BCG W8 8342


title: BCG W8 8338


title: PPDB W8 8337


title: BCG W8 8337


title: Unstim W8 8337


title: BCG W9 8342


title: Unstim W8 8336


title: BCG W8 8336


title: BCG W8 8333


title: Unstim W8 8333


title: BCG W0 8345


title: Unstim W0 8345


title: PPDB W0 8345


title: BCG W0 8337


title: PPDB W0 8337


title: BCG W0 8338


title: PPDB W0 8342


title: Unstim W0 8342


title: Unstim W8 8338


title: PPDB W0 8338


title: Unstim W0 8338


title: Unstim W10 8346


title: Unstim W0 8337


title: BCG W0 8336


title: BCG W10 8347


title: PPDB W0 8336


title: Unstim W10 8347


title: BCG W10 8344


title: PPDB W8 8333


title: BCG W10 8365

value: naive


title: Unstim W0 8336


title: BCG W0 8342


title: Unstim W10 8365


title: Unstim W10 8361


title: PPDB W10 8347


title: PPDB W10 8361


title: PPDB W10 8363


title: BCG W10 8361


title: Unstim W10 8359


title: PPDB W10 8342


title: PPDB W10 8358


title: BCG W10 8355


title: BCG W10 8363


title: PPDB W10 8359


title: BCG W10 8358


title: PPDB W10 8346


title: Unstim W10 8358


title: BCG W9 8358


title: Unstim W0 8333


title: Unstim W9 8355


title: Unstim W9 8358


title: PPDB W9 8355


title: PPDB W10 8365


title: BCG W8 8359


title: Unstim W10 8363


title: PPDB W9 8358


title: BCG W10 8359


title: PPDB W8 8359


title: BCG W8 8358


title: Unstim W8 8358


title: BCG W8 8365


title: PPDB W8 8355


title: PPDB W8 8358


title: BCG W8 8355


title: Unstim W8 8355


title: PPDB W8 8365


title: BCG W8 8363


title: PPDB W10 8355


title: BCG W8 8361


title: Unstim W8 8363


title: Unstim W8 8365


title: PPDB W8 8363


title: BCG W9 8355


title: BCG W0 8365


title: Unstim W8 8361


title: PPDB W0 8363


title: PPDB W0 8365


title: PPDB W0 8361


title: Unstim W8 8359


title: BCG W0 8361


title: Unstim W0 8363


title: BCG W9 8359


title: PPDB W9 8359


title: Unstim W9 8359


title: PPDB W9 8365


title: Unstim W9 8365


title: BCG W9 8365


title: Unstim W10 8355


title: PPDB W8 8361


title: Unstim W9 8363


title: PPDB W9 8361


title: PPDB W9 8363


title: Unstim W9 8361


title: BCG W9 8361


title: BCG W0 8333


title: BCG W9 8363


title: BCG W0 8359


title: Unstim W0 8365


title: BCG W0 8363


title: Unstim W0 8361


title: PPDB W0 8359


title: Unstim W0 8359


title: JWCB005delta_rex - late log phase - 2

city: Oak Ridge

first: Kyle

last: Sander

state: TN

address: 1 Bethel Valley Road, MS 6038

department: Biosciences

institute: University of Tennessee/Oak Ridge National Laboratory

data_processing:
Reads obtained were scored for quality, trimmed, mapped, and the mapped reads counted using the corresponding functions in the CLC Genomics Workbench version 8 using default settings for genome analysis of prokaryotes.
Raw read counts for each coding sequence were used as input for differential expression analysis using the DEseq2 package as part of the Bioconductor Suite in R
Genome_build: NC_012034
Supplementary_files_format_and_content: DESeq2_Output, .xlsx format - Microsoft Excel spreadsheet version 2016.  Spreadsheet contains five tabs.  The first three tabs are differential expression output from the DEseq2 package of strain JWCB005delta_rex strain vs. JWCB005 strain for early, mid, and late log phase, respectively.   The fourth and fifth tab contain DEseq2 output differential expression analysis for late vs. early phase for strain JWCB005 and strain JWCB005delta_rex, respectively.  Also included are DESeq2_input with count data and DESeq2_input_column_data with sample index information.

organism: Caldicellulosiruptor bescii

source_name: Caldicellulosiruptor bescii strain JWCB005 with the rex gene knocked out

growth_protocol: Cells were cultured in 3L fermenters in a working/culture volume of 1.5 L at a growth temperature of 75oC.  Maltose, resazurin and an appropriate volume of water were added to assembled fermenters and autoclaved.  Fermenters were allowed to cool while sparging with N2 gas.  Upon cooling, the other media components were added as pre-sterilized stock solutions.  The media was again heated and sparged with N2 gas.  Upon reaching temperature, the pH was adjusted to 7.1 by sparging 80%/20% N2/CO2.  The pH was then aseptically checked using a second probe which had been calibrated with fresh pH buffers maintained at 75oC.  Any adjustments differences were inputted as the pH probe offset.  Fermenters were inoculated to equivalent OD680’s of 0.01-0.05 using batch grown cultures grown to mid-log phase.  Stirring was maintained at 200 rpm, and no gas was sparged during growth, though the outlet line was kept open to allow fermentation off-gasses to vent through a sterilized water trap.

extract_protocol:
Total RNA was extracted by first incubating cell pellets in 250 µL of 20 mg/mL Lysozyme (Sigma Aldrich part number L-7651, St. Louis, MO) resuspended in SET buffer (50 mM Tris-HCl pH 8.0 50 mM EDTA, 20% w/v Sucrose) and incubated in a dry stationary bath at 37oC for eight minutes, vortexing briefly every two minutes.  900 µL of buffer RLT from a Qiagen RNeasy Kit (Qiagen, Hilden, Germany) was added and the sample was split into two equal aliquots of ~575 µL each.  325 µL of 100% ethanol was added to each aliquot and the contents were mixed by pipetting.  Contents from both tubes were spun through an RNeasy spin column (Qiagen, Hilden, Germany).  Spin columns were washed once with buffer RW1 (Qiagen, Hilden, Germany).  10 µL of DNAse stock I (Qiagen, Hilden, Germany) and 70 uL of buffer RDD (Qiagen, Hilden, Germany) were combined, pipetted onto the spin column and allowed to incubate for 15 minutes at room temperature to digest residual DNA.  The columns were washed once more with buffer RW1 (Qiagen, Hilden, Germany), followed by two washes of 500 µL buffer RDE (Qiagen, Hilden, Germany) and eluted in 35 µL RNAse free H20 (Qiagen, Hilden, Germany).  RNA concentration was quantified using a Nanodrop 1000 instrument (ThermoScientific, Waltham, MA) and RNA quality was verified by obtaining RNA Integrity Numbers (RIN) using an Agilent 2100 Bioanalyzer and corresponding RNAchip (Agilent Technologies, Santa Clara, CA).
Depleted RNA was used as the starting material for the Epicentre ScriptSeq™ v2 RNA-Seq Library preparation kit (Illumina compatible) utilising Epicentres Fail Safe PCR Enzyme mix (Epicentre, WI) and following the manufacturer’s protocol. cDNA, tagged with ScriptSeq adaptors (1-12), was purified with Agencourt AMPure XP magnetic beads (Beckman Coulter, IN ) and  eluted in water according to the ScriptSeq™ v2 RNA -Seq Library preparation kit protocol.  Twelve PCR cycles were used during library amplification and samples were purified with Agencourt AmPureXP magnetic beads and eluted with 20 µl of water. The final mRNA Seq library was quantified with a Qubit Fluorometer (Invitrogen, CA) and library quality was assessed with an Agilent Bioanalyzer DNA Chip (Agilent, CA). Samples were pooled and the concentration determined.  Pools of barcoded samples were sent to Hudson Alpha for SR50 sequencing run on an Illumina Hiseq 2500 platform.

treatment_protocol: Strain JWCB005 was the genetic parent strain to strain JWCB005delta_rex.   JWCB005delta_rex was the treatment while JWCB005 was the control.  JWCB005delta_rex contains a markerless deletion of the rex gene (ATHE_RS03255).

tag: stage of log phase

value: late

value: delta_pyrF delta_rex

tag: background strain


title: JWCB005delta_rex - late log phase - 1


title: JWCB005delta_rex - late log phase - 3


title: JWCB005delta_rex - mid log phase - 2

value: mid


title: Unstim W0 8358


title: PPDB W0 8358


title: JWCB005delta_rex - mid log phase - 1


title: BCG W0 8358


title: JWCB005delta_rex - early log phase - 3

value: early


title: BCG W0 8355


title: PPDB W0 8333


title: JWCB005delta_rex - early log phase - 2


title: JWCB005delta_rex - early log phase - 1


title: JWCB005 - late log phase - 2

source_name: Caldicellulosiruptor bescii strain JWCB005


title: JWCB005 - late log phase - 1


title: JWCB005 - late log phase - 3


title: JWCB005 - mid log phase - 2


title: PPDB W0 8355


title: JWCB005 - mid log phase - 3


title: JWCB005delta_rex - mid log phase - 3


title: islet preparation from long duration type 1 diabetes

city: Indianapolis

first: Teresa

middle: L.

last: Mastracci

institute: Indiana Biosciences Research Institute

data_processing:
Sequencing reads were mapped to the human genome (version GRCh37/hg19) using the program Tophat.
GTF files: Mapped reads were used to quantify transcripts from the RefSeq reference database, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: The processed data files are in standard transcript GTF format (for the full format description see http://www.ensembl.org/info/website/upload/gff.html). The attributes column contains informations on the transcript length, transcript abundance quantification RPKM (reads per kilobase per million mapped reads) and the number of read that mapped to it.

molecule: polyA RNA

source_name: islets of Langerhans

growth_protocol: Human islets were obtained from the pancreata of deceased organ donors for research purposes. Islets were permitted to recover in culture standard human islet media (PRODO; islet media, PIM-S001GMP; human AB serum supplement, PIM-ABS001GMP; glutamine and glutathione supplement, PIM-G001GMP; Ciprofloxacin, 10 mg/mL) and then were hand-picked to separate islets from any remaining non-islet material.

extract_protocol:
RNA was isolated using the RNeasy Mini Extraction kit (Qiagen). Purified total RNA was eluted from the column with RNase-free water and immediately snap frozen. RNA concentration and quality was measured using a Bioanalyzer (Agilent) prior to RNA sample processing; concentrations ranged from 160 to 900 ng/uL.
paired-end RNA-seq library

value: pancreas

tag: tissue compartment

value: islets of Langerhans

tag: disease state

value: long duration type 1 diabetes


title: JWCB005 - early log phase - 2


title: JWCB005 - early log phase - 3


title: islet preparation from short duration type 1 diabetes

value: short duration type 1


title: JWCB005 - early log phase - 1


title: islet preparation from normo-glycemic individual 2

value: normo-glycemic


title: islet preparation from normo-glycemic individual 3


title: JWCB005 - mid log phase - 1


title: FLI1 ChIP-seq in MSC infected with EWSFLI1

source_name: primary tissue

tag: cell type

value: MSC


title: INPUT library in MSC infected with EWSFLI1

value: INPUT


title: islet preparation from normo-glycemic individual 1


title: H3K9ac ChIP-seq in MSC infected with EWSFLI1


title: INPUT library in MSC infected with control

description: MSC.control.INPUT


title: H3K27me3 ChIP-seq in MSC infected with EWSFLI1


title: Unstim W0 8355

value: Whole Blood

value: 6 months

value: Holstein X Friesian


title: FLI1 ChIP-seq in MSC


title: H3K27me3 ChIP-seq in MSC


title: H3K4me3 ChIP-seq in MSC


title: H3K27ac ChIP-seq in MSC infected with EWSFLI1


title: H3K27ac ChIP-seq in MSC


title: H3K4me1 ChIP-seq in MSC


title: hag1-SIM 2 weeks

status: Public on Jul 29 2018

city: Düsseldorf

first: Jiyun

last: Kim

address: Universitätsstr. 1

department: Biology

country: Germany

institute: HHU

data_processing:
After total RNA extraction, mRNA  was enriched by using the oligo(dT) magnetic beads. Adding the fragmentation buffer, the mRNA was interrupted to short fragments (about 200 bp), then the first strand cDNA was synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythesize the second strand. The double strand cDNA was purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors were ligated to the fragments. The required fragments were purified by agrose gel electrophoresis and enriched by PCR amplification. The library products were then sequenced via Illumina HiSeq™ 2000.
Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level was calculated by using RPKM method (Reads per kb per million reads)
Genome_build: Arabidopsis Thaliana (TAIR10)
Supplementary_files_format_and_content: Excel files include RPKM values for each sample

source_name: root explants incubated on CIM for 4 days and further incubated on SIM (S) for 2 weeks

growth_protocol: Seeds were germinated on Murashige and Skoog (MS) medium supplemented with 1% sucrose and buffered to pH 5.7 with 0.05% MES. Plants were grown under 100 μmol m-2 s-1 cool white fluorescent lights at 22°C in long days (LD) with a 16 hr light and 8 hr dark photoperiod.

extract_protocol:
Total RNA was isolated by using Tri Reagent (MRC) and purified with RNeasy Mini Kit (QIAGEN) (OD260/280 ratio of 1.8 to 2.2).
RNA libraries were prepared by Beijing Genomics Institute (BGI) using standard Illumina protocols

treatment_protocol: WT and hag1 roots (R), 4 d CIM-incubated root explants (C), 4 d CIM-incubated + 2 d SIM (S)- and 2 w SIM (S2W)-incubated root explants were collected for the assay.

value: hag1 mutant


title: hag1-CIM

source_name: root explants incubated on CIM for 4 days


title: Col_H3Ac

data_processing:
Basecalls were performed by Beijing Genomics Institute (Hong Kong).
ChIP-seq reads were aligned to the Col-0 genome using SOAP2 aligner.
BWA was used for genome alignment after evaluating the performance.
MACS (Model-based analysis for ChIP-seq) was used for peak calling. Dynamic Possion Distribution was used to calculate the p value of the specific region based on the unique mapped reads, and the region was defined as a peak when p-value < le-05.
Genome_build: Col-0
Supplementary_files_format_and_content: The whole genome peak scanning was performed using MACS. The results include peak location, peak length, etc. Results are stored in wiggle (wig) files.

source_name: Col root explants incubated on CIM for 7 d

extract_protocol:
Chromatin was digested by sonication and immunoprecipitated with anti-H3Ac antibody (Millipore 06-599). Input and ChIPed DNAs were eluted using MinElute PCR Purification Kit (QIAGEN).12 ng of ChIPed DNA and input DNA were pooled from 7 independent experiments, and their quality was assessed with 2100 (Agilent) and Lab ChIP GX (Caliper).
Libraries were prepared and performed by Beijing Genomics Institute (Hong Kong).

treatment_protocol: Root-derived explants from 2 w- to 20 d-old seedlings were excised, transferred onto callus induction media (CIM), and cultured in the dark. The composition of CIM is as follows: Gamborg’s B5 medium with minimal organics (Sigma-Aldrich), 3% sucrose buffered to pH 5.7 with 0.05% MES, and 0.8% phytoagar supplemented with 0.5 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D) and 0.1 mg kinetin. Explants were incubated on CIM for 7 days.

value: anti-H3Ac (Millipore 06-599)


title: Col-CIM

value: wild type

value: root explants incubated on CIM for 4 days


title: Col-root

source_name: Roots

value: Roots


title: H3K4me1 ChIP-seq in MSC infected with EWSFLI1


title: H3K9ac ChIP-seq in MSC


title: hag1-root


title: Col-SIM 2 weeks

value: root explants incubated on CIM for 4 days and further incubated on SIM (S) for 2 weeks


title: hag1_Input

source_name: hag1 root explants incubated on CIM for 7 d


title: hag1_H3Ac

value: hag1 root explants incubated on CIM for 7 d


title: hag1-SIM

source_name: root explants incubated on CIM for 4 days and further incubated on SIM (S) for 2 days


title: Staphylococcus aureus subsp. aureus ST398 (W-604)

city: Shanghai

first: Min

last: Li

state: China

address: Department  of  Laboratory  Medicine,  Renji  Hospital,  School  of  Medicine,  8 Shanghai Jiao Tong University, Shanghai, China

department: Department  of  Laboratory  Medicine

country: China

institute: Renji  Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then respectively aligned to S. aureus subsp. aureus ST398 (RefSeq accession number AM990992) and S. aureus subsp. aureus TW20 (RefSeq accession number NC _017331) using BWA. Based on the above standard, the QC of alignment was produced.
The commonly used fragments per kilobase of transcript per million mapped fragments (RPKM) incorporate normalization steps to ensure that expression levels for different genes and transcripts can be compared across runs.
Based on RPKM normalization, we performed analyses of differentially expressed genes. Genes with an adjusted P value < 0.05, FDR < 0.001 and fold change > 2 were identified as being differentially expressed.
The type of G1/G2>2 was selected for further analyses.
Genome_build: ASM958v1 [S. aureus subsp. aureus ST398 (RefSeq accession number AM990992)] and ASM2704v1 [S. aureus subsp. aureus TW20 (RefSeq accession number NC_017331)]
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each 2 Samples

growth_protocol: Overnight cultures were diluted 1:100 into 50 ml of TSB and incubated at 37°C with shaking at 200 rpm until grown to an OD600 nm of 1.5-2.0 (mid-logarithmic growth phase).

extract_protocol:
Total RNA was isolated using an RNeasy Mini Kit (Qiagen) as recommended in a standard protocol as described before. A total of 10 μg of each RNA sample was subjected to further purification to enrich the mRNA using a MICROBExpress Kit (Ambion) according to the manufacturer's instructions.
An Illumina Paired End Sample Prep kit was used to prepare RNA-seq library according to the manufacturer's instructions.

treatment_protocol: The same bacterial CFU cultures were then collected, the cells were washed twice in 10 mM sodium phosphate buffer (pH 6.5).

tag: growth phase

value: mid-logarithmic (4h incubation time)


title: Staphylococcus aureus subsp. aureus ST398 (R-1089)


title: Staphylococcus aureus subsp. aureus ST398 (R-1025)


title: Staphylococcus aureus subsp. aureus ST398 (J-92)


title: Col_Input

source_name: Col root explants incubated on callus-induction media (CIM) for 7 days (d)

tag: chip antibody


title: 13571X13 MSN-PEG500-1

status: Public on Jul 28 2018

city: Salt Lake City

first: Philip

middle: J

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

description: processed data column: MSN-PEG5000

data_processing:
RNA-seq reads were mapped to the GRCm38 transcriptome reference using Novoalign (v2.08.03).
A transcriptome reference was created by combining GRCm38 (mouse) chromosome sequences with Ensembl build 84 splice junction sequences generated with USeq (v8.8.8) MakeTranscriptome. Splice junction alignments were converted back to genomic space using USeq SamTranscriptomeParser.
USeq DefinedRegionDifferentialSeq was used to generate per gene read counts, which were used in DESeq2 to determine differential expression.
FPKM data was used as input for limma (3.28.21) comparing the mesoporous samples to all the other samples
BinReg2 - based on the limma result a metagene analysis was performed between the FPKM data for the mesoporous and all other samples with 618 gene set for the metagene, no additional normalizations were performed.
Genome_build: mm10
Supplementary_files_format_and_content: excel with tabs for data in counts, rlog, FPKM, flagged genes, etc.

organism: Mus musculus

source_name: RAW264.7_mesoporous 500 nm pegylated nanosilica

growth_protocol: Cells were cultured at 37 °C in 5% CO2 in RPMI with 10% fetal bovine serum (FBS) in T75 flask (typically 2 × 106 cells) up to 90% confluency.

extract_protocol:
Total RNA was extracted and purified following 4 h of incubation with SNPs using Qiagen RNeasy minikit protocol. The samples were kept at −80 °C until further use. RNA was quantified by Nanodrop spectrophotometer ND-1000 and the RNA samples were assessed for quality using an Agilent 2200 TapeStation prior to expression analysis. All RNA samples had RNA Integrity Numbers (RIN) ranging from 8 to 10.
Libraries were prepared using Illumina TruSeq RNA Library Prep Kits.  HiSeq2000 50 Cycle Single Read Sequencing was performed with a maximum of 8 multiplexed samples per lane to ensure sufficient depth of sequencing.

treatment_protocol: For the treatment, cells were seeded onto 6-well plates and allowed to grow for 24 h. After 24 h the media was replaced and the cells were washed with PBS. Fresh media was then added without (control) and with silica nanoparticles in the presence of 10% fetal bovine serum. The cells were then incubated for 24 h, after which the media was aspirated and the cells were washed twice with PBS.

value: macrophage; Abelson murine leukemia virus transformed

tag: passages

tag: treated with

value: mesoporous 500 nm pegylated nanosilica

tag: dosage

value: half LC50 dose of 84 microg/ml


title: 13571X12 MSN500-3

description: processed data column: MSN5002

source_name: RAW264.7_mesoporous 500 nm nanosilica

tag: cell line

value: mesoporous 500 nm nanosilica

value: half LC50 dose of 111.8 microg/ml


title: H3K4me3 ChIP-seq in MSC infected with EWSFLI1

value: MSC


title: 13571X11 MSN500-2

description: processed data column: MSN5001


title: 13571X8 Control-2

description: processed data column: Control1

source_name: RAW264.7_untreated control

value: none (untreated control)


title: 13571X10 MSN500-1

description: processed data column: MSN5000


title: 13571X9 Control-3

description: processed data column: Control2


title: Staphylococcus aureus subsp. aureus ST239 (J-99)

organism: Staphylococcus aureus CN79

tag: genotype


title: Staphylococcus aureus subsp. aureus ST239 (J-95)


title: 13571X6 Stober500-3

description: processed data column: Stober5002

source_name: RAW264.7_Stober 500 nm nanosilica

value: Stober 500 nm nanosilica

value: half LC50 dose of 16.8 microg/ml


title: 13571X7 Control-1

description: processed data column: Control0


title: 13571X15 MSN-PEG500-3

description: processed data column: MSN-PEG5002


title: 13571X5 Stober500-2

description: processed data column: Stober5001


title: 13571X3 Stober50-3

description: processed data column: Stober502

source_name: RAW264.7_Stober 50 nm nanosilica

value: Stober 50 nm nanosilica

value: half LC50 dose of 13.1 microg/ml


title: 13571X2 Stober50-2

description: processed data column: Stober501


title: 13571X14 MSN-PEG500-2

description: processed data column: MSN-PEG5001


title: BMS-21 6h rep 4

city: Brisbane

first: Justin

middle: Mark

last: Mitchell

state: Queensland

address: 306 Carmody Road, Queensland Bioscience Precinct (Building 80), The University of Queensland

country: Australia

institute: Institute for molecular Bioscience

description:
Sample name: 20
Barcode: GTTTCG

data_processing:
De-multiplexing and FASTQ sequence data was generated using the Illumina CASAVA1.8.2 pipeline.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the illumina rat iGenome (build 75 - Rnor_5.0 (GCA_000001895.3)) using TopHat (2.0.12) + Bowtie (2.2.3.0).
Aligned RNAseq BAM files were indexed using SAMtools (0.1.19.0)
Reads were summarized using R package Subread-feature counts (1.4.6).
Differential gene analysis was performed using the DESeq() function within DESeq2 (1.6.3) within Rstudio (0.98.945).
GLP-1 or BMS-21 treatments were compared to Control at 1h or 6h. Genes were considered significant if raw reads were >10 and Benjamini–Hochberg adjusted p-value representing the False Discovery Rate (p-adj) was < 0.05.
Gene Ontology (GO) analysis, visualization and clustering of GO terms was performed using Cytoscape (3.2.0) software with BiNGO (3.0.2), EnrichmentMap (2.0.1).
Basic KEGG pathway analysis was performed in R using GAGE (2.14.4) and Pathview (1.5.2) packages following native gage workflow(http:// www.bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNAseqWorkflow.pdf). Gene clustering and pathway perturbation was deemed significant at q-value < 0.05.
Genome_build: illumina rat iGenome (build 75 - Rnor_5.0 (GCA_000001895.3))
Supplementary_files_format_and_content: DESeq2 output (differential expression results + raw counts): .csv file that contains the differental gene expression results from DESeq analysis. For in depth description of each colum see Deseq2 manual (https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf).  The last 8 columns are the raw gene counts from each indiviual sample within the comparison. These numbers correspond to the sample number as per raw Files uploaded. Briefly they are as follows: samples #1,7,13,19  are GLP-1 @ 6h. #2,8,14,20 are BMS-21 @ 6h. #3,9,15,21 are Control @ 6h. #4, 10, 16, 22 are GLP-1 @ 1h. #5,11,17,23 are BMS-21 @ 1h. #6,12,18,24 are Control @ 1h).

organism: Rattus norvegicus

source_name: BMS-21 6h, INS-1 cells

growth_protocol: Rat INS-1 insulinoma insulin secreting cells were cultured at 37°C, 5% CO2 in 11mM glucose RPMI1640 media (Gibco, Thermo Fisher Scientific) containing additional 1% Sodium pyruvate (Gibco, Thermo Fisher Scientific), 1% HEPES (1M, pH 7.4) (Gibco, Thermo Fisher Scientific), 1% GlutaMAX™ (Gibco, Thermo Fisher Scientific), 1% Pen Strep (Gibco, Thermo Fisher Scientific), 10% FBS and 50μM β-Mercaptoethanol (Sigma-Aldrich). During cell culture passage, TrypLE™ (Gibco, Thermo Fisher Scientific) was used to dissociate INS-1 cells from the surface of culture flask

extract_protocol:
Following incubation with treatments, cells were washed (PBS) and, following RNA isolation Kit 2 (Bioline) manufacturers instructions, RNA was isolated. RNA quality was assessed via examination of nucleic acid concentration and purity using a Nanodrop spectrophotometer. RNA sample quality was further analysed using a bioanalyser and had RIN > 8.
mRNA libraries were constructed from total RNA using TruSeq RNA Library Prep Kit v2 for sequencing using standard Illumina protocols

treatment_protocol: INS-1 cells were seeded in 12-well tissue culture plates (5 × 10^5 cells per well) and incubated for 3 days at 37°C in a humidified atmosphere (95% air, 5% CO2) to allow adherence. Media was replaced on day 3. Experiments were performed on day 4. Prior to treatment, cells were washed (PBS), pre-incubated in RPMI1640 (3mM glucose) INS-1 culture medium for 90 minutes, and then supplied with fresh RPMI1640 (11mM glucose) INS-1 culture medium.  Next cells were treated with GLP-1 (100 nM), BMS-21 (1uM) or vehicle DMSO (concentration equivalent) and incubated for 1 h or 6 h. Each treatment condition was replicated n=4.

value: Insulinoma cell line INS-1

tag: agent

tag: time


title: BMS-21 6h rep 3

description:
Sample name: 14
Barcode: AGTTCC


title: 13571X1 Stober50-1

description: processed data column: Stober500


title: Control 6h rep 4

description:
Sample name: 21
Barcode: CGTACG

source_name: Control 6h, INS-1 cells

value: Control


title: Control 6h rep 3

description:
Sample name: 15
Barcode: ATGTCA


title: GLP-1 6h rep 2

description:
Sample name: 7
Barcode: CAGATC

source_name: GLP-1 6h, INS-1 cells


title: Control 6h rep 2

description:
Sample name: 9
Barcode: GATCAG


title: GLP-1 6h rep 4

description:
Sample name: 19
Barcode: GTGGCC


title: BMS-21 1h rep 4

description:
Sample name: 23
Barcode: ACTGAT

source_name: BMS-21 1h, INS-1 cells


title: Col-SIM

value: wild type

tag: tissue

value: root explants incubated on CIM for 4 days and further incubated on SIM (S) for 2 days


title: Control 6h rep 1

description:
Sample name: 3
Barcode: TTAGGC


title: BMS-21 6h rep 1

description:
Sample name: 2
Barcode: CGATGT


title: GLP-1 6h rep 3

description:
Sample name: 13
Barcode: AGTCAA


title: BMS-21 1h rep 2

description:
Sample name: 11
Barcode: GGCTAC


title: GLP-1 6h rep 1

description:
Sample name: 1
Barcode: ATCACG


title: Control 1h rep 3

description:
Sample name: 18
Barcode: GTGAAA

source_name: Control 1h, INS-1 cells


title: BMS-21 1h rep 1

description:
Sample name: 5
Barcode: ACAGTG


title: Control 1h rep 1

description:
Sample name: 6
Barcode: GCCAAT


title: GLP-1 1h rep 3

description:
Sample name: 16
Barcode: CCGTCC

source_name: GLP-1 1h, INS-1 cells


title: 13571X4 Stober500-1

description: processed data column: Stober5000


title: BMS-21 6h rep 2

description:
Sample name: 8
Barcode: ACTTGA


title: Control 1h rep 4

description:
Sample name: 24
Barcode: ATTCCT


title: Control 1h rep 2

description:
Sample name: 12
Barcode: CTTGTA


title: GLP-1 1h rep 4

description:
Sample name: 22
Barcode: GAGTGG


title: GLP-1 1h rep 2

description:
Sample name: 10
Barcode: TAGCTT


title: GLP-1 1h rep 1

description:
Sample name: 4
Barcode: TGACCA


title: 3/4 iPSC, replicate1, RNA-seq

status: Public on Jul 27 2018

first: Benjamin

middle: A

last: Schwarz

address: 185 Cambridge St.

department: Molecular Biology

institute: MGH

description: iPSC 1

data_processing:
Quality control: PICARD, Version: 1.100
Alignment: STAR, version 2.3.0
Allelic assignment:  Reads were aligned separately to parental genomes. Unambiguous reads were then assigned to parent-specific alleles according to the method in Engström PG, et al. (2013) Nature Methods.
Rad counts per gene: HTSeq, version 0.6.0 (unstranded) using Ensembl release 67 transcript annotations
Genome_build: mm9
Supplementary_files_format_and_content: text files with Htseq raw counts

source_name: mouse iPSCs

growth_protocol: MEFs were grown in MEF media, reprogramming was done in ES media supplemented with dox and AA, iPSCs were grown in ES media.

extract_protocol:
RNA was islolated and extracted using the Rneasy Micro Kit (Qiagen).
cDNA libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit (NEB) based on poly-A selection. RNA and libraries were validated using a bioanalyzer (Agilent).

treatment_protocol: Cells were harvested following trypsin treatment, stained with antibodies for flow cytometry, and sorted by FACS.

tag: strain

value: iPSC


title: iPS SSEA1+, replicate3, RNA-seq

description: iPS SSEA1+ 3

data_processing:
Quality control: PICARD, Version: 1.100
Alignment: STAR, version 2.3.0
Allelic assignment: Reads were aligned separately to parental genomes. Unambiguous reads were then assigned to parent-specific alleles according to the Read counts per gene: method in Engström PG, et al. (2013) Nature Methods.
HTSeq, version 0.6.0 (unstranded) using Ensembl release 67 transcript annotations
Genome_build: mm9
Supplementary_files_format_and_content: text files contain Htseq raw counts

source_name: sorted reprogramming intermediates

growth_protocol: MEFs were grown in MEF media, reprogramming was done in ES media supplemented with dox and AA.

value: Reprogramming intermediate


title: d6 SSEA1+EpCAM-Sca1+, replicate2, RNA-seq

description: d6 Ineff 2


title: iPS SSEA1+, replicate2, RNA-seq

description: iPS SSEA1+ 2


title: d6 SSEA1+EpCAM+Sca1-, replicate2, RNA-seq

description: d6 Eff 2


title: d6 SSEA1+EpCAM-Sca1+, replicate1, RNA-seq

description: d6 Ineff 1


title: d6 SSEA1+EpCAM+Sca1-, replicate1, RNA-seq

description: d6 Eff 1


title: d3 SSEA1+CD73-Sca1+, replicate1, RNA-seq

description: d3 Ineff 1


title: iPS SSEA1+, replicate1, RNA-seq

description: iPS SSEA1+ 1


title: d12 SSEA1+, replicate3, RNA-seq

description: d12 SSEA1+ 3


title: 3/4 MEF, replicate1, RNA-seq

description: MEF 1

source_name: mouse embryonic fibroblasts

value: MEF


title: BMS-21 1h rep 3

description:
Sample name: 17
Barcode: GTCCGC


title: d12 SSEA1+, replicate1, RNA-seq

description: d12 SSEA1+ 1


title: d3 SSEA1+CD73-Sca1+, replicate2, RNA-seq

description: d3 Ineff 2


title: d3 SSEA1+CD73+Sca1-, replicate2, RNA-seq

description: d3 Eff 2


title: d9 SSEA1+, replicate2, RNA-seq

description: d9 SSEA1+ 2


title: d9 SSEA1+, replicate3, RNA-seq

description: d9 SSEA1+ 3


title: 3/4 MEF, replicate2, RNA-seq

description: MEF 2


title: d6 SSEA1+, replicate3, RNA-seq

description: d6 SSEA1+ 3


title: d9 SSEA1+, replicate1, RNA-seq

description: d9 SSEA1+ 1


title: d6 SSEA1+, replicate1, RNA-seq

description: d6 SSEA1+ 1


title: d6 SSEA1+, replicate2, RNA-seq

description: d6 SSEA1+ 2


title: d3 SSEA1+, replicate3, RNA-seq

description: d3 SSEA1+ 3


title: d12 SSEA1+, replicate2, RNA-seq

description: d12 SSEA1+ 2


title: iPS SSEA1-, replicate3, RNA-seq

description: iPS SSEA1- 3


title: d3 SSEA1+, replicate2, RNA-seq

description: d3 SSEA1+ 2


title: 3/4 iPSC, replicate2, RNA-seq

description: iPSC 2


title: d3 SSEA1+, replicate1, RNA-seq

description: d3 SSEA1+ 1


title: iPS SSEA1-, replicate2, RNA-seq

description: iPS SSEA1- 2


title: d3 SSEA1+CD73+Sca1-, replicate1, RNA-seq

description: d3 Eff 1


title: d6 SSEA1-, replicate3, RNA-seq

description: d6 SSEA1- 3


title: d6 SSEA1-, replicate2, RNA-seq

description: d6 SSEA1- 2


title: d3 SSEA1-, replicate2, RNA-seq

description: d3 SSEA1- 2


title: d9 SSEA1-, replicate3, RNA-seq

description: d9 SSEA1- 3


title: d12 SSEA1-, replicate3, RNA-seq

description: d12 SSEA1- 3


title: d6 SSEA1-, replicate1, RNA-seq

description: d6 SSEA1- 1


title: d3 SSEA1-, replicate1, RNA-seq

description: d3 SSEA1- 1


title: d9 SSEA1-, replicate2, RNA-seq

description: d9 SSEA1- 2


title: d12 SSEA1-, replicate1, RNA-seq

description: d12 SSEA1- 1


title: d12 SSEA1-, replicate2, RNA-seq

description: d12 SSEA1- 2


title: d9 SSEA1-, replicate1, RNA-seq

description: d9 SSEA1- 1


title: MEF, replicate3, RNA-seq

description: MEF 3


title: d3 SSEA1-, replicate3, RNA-seq

description: d3 SSEA1- 3


title: 3/4 iPSC, replicate2, ATAC-seq

description: iPSC 2

data_processing:
Sequencing reads were mapped to the mouse genome (mm9 build) by using the BWA aligner
Genome_build: mm9
Supplementary_files_format_and_content: Coverage files (bigwig)are generated by using Deeptools v. 2.4.3

extract_protocol:
50,000 sorted cells were resuspended in nuclear isolation buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL). Nuclei were then treated with Tn5 transposase (Illumina).
DNA was isolate using the MinElute Kit (Qiagen) and PCR-amplified using barcoded Nextera primers (Illumina). The DNA libraries were validated using a bioanalyzer (Agilent).


title: d3 SSEA1+CD73+Sca1-, replicate2, ATAC-seq

description: d3 Eff 2


title: d6 SSEA1+EpCAM+Sca1-, replicate2, ATAC-seq

description: d6 Eff 2


title: MEF, replicate1, RNA-seq

description: MEF 1


title: 3/4 iPSC, replicate1, ATAC-seq

description: iPSC 1


title: d3 SSEA1+CD73-Sca1+, replicate2, ATAC-seq

description: d3 Ineff 2


title: d6 SSEA1+EpCAM+Sca1-, replicate1, ATAC-seq

description: d6 Eff 1


title: d6 SSEA1+EpCAM-Sca1+, replicate1, ATAC-seq

description: d6 Ineff 1


title: 3/4 iPSC, WGBS

description: iPSC

data_processing:
Preprocessing: 10bp were trimmed from the beginning of each read to remove possible adapter contamination.
Alignment: Reads were aligned using Bsmap with the following flags: -v 0.05 -s 16 -w 100 -S 1 -p 8 -.
Methylation calling: CpGs in the reference sequence were compared to the sequence in the aligned read. If bisulfite conversion (signifying an unmethylated cytosine) was detected, the read was added to the unmethylated count for that CpG, otherwise, it was added to the methylated count.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *bed: Bed files contain the number of methylated and total reads for CpGs covered by RRBS with the columns: chromosome, start, end, number of reads methylated divided by number of reads seen, methylation percent*1000.

extract_protocol:
Genomic DNA was purified from sorted cells.
Libraries were created using the Nugen Ovation bisulfite kit.

tag: strain/background


title: d6 SSEA1+EpCAM-Sca1+, replicate2, ATAC-seq

description: d6 Ineff 2


title: d6 SSEA1+EpCAM+Sca1-, WGBS

description: d6 Eff


title: d3 SSEA1+CD73+Sca1-, replicate1, ATAC-seq

description: d3 Eff 1


title: 3/4 MEF, replicate2, ATAC-seq

description: MEF 2


title: MEF, replicate2, RNA-seq

description: MEF 2


title: d6 SSEA1+EpCAM-Sca1+, WGBS

description: d6 Ineff


title: 3/4 MEF, WGBS

description: MEF


title: d3 SSEA1+CD73-Sca1+, WGBS

description: d3 Ineff


title: 360_1hr_F_CA1

city: La Jolla

first: Fred

middle: H

last: Gage

state: CA

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

data_processing:
Reads trimmed with Solexa-QA++ dynamic trim
Trimmed reads aligned to mm10 with Ensembl annotation using RSEM (bowtie)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files contain either raw counts or tpm normalized counts

extract_protocol:
The nuclei dissociation protocol is similar to the previously described protocol with some modifications. Hippocampus was carefully excised and immediately placed into a nuclei isolation medium (sucrose 0.25 M, KCl 25 mM, MgCl2 5 mM, TrisCl 10 mM, dithiothreitol, 0.1 % Triton, protease inhibitors). Tissue was Dounce homogenized, allowing for mechanical separation of nuclei from cells. The nucleic acid stain Hoechst 33342 (5 µM, Life Technologies) was included in the media to facilitate visualization of the nuclei for quantification, but excluded for sorting. Samples were washed, resuspended in nuclei storage buffer (sucrose, MgCl2 5 mM, and TrisCl 10 mM) and filtered. Solutions and samples were kept cold throughout the protocol. For RNA-seq experiments, tools and solutions were made RNAse-free and RNAse inhibitors were used.
Library preparation followed the Smart-seq2 protocol. The Nextera XT kit was used for sample preparation following all transcriptome amplifications. Single-nuclei and amplified bulk samples were measured by Picogreen (LifeTech) and normalized so that samples were at a concentration of 0.3 ng/µl. Samples were first subjected to a tagmentation reaction, indexed, and PCR amplified. Libraries were then mixed in 48-sample pools and purified with magnetic beads (AMPure). Quality control checks for the library preparations included electrophoresis (Agilent Technologies 2100 Bioanalyzer). Samples were sequenced in the Salk Institute Next Generation Sequencing Core on an Illumina HiSeq 2500 high-throughput sequencing system with single-end 50bp reads.

treatment_protocol: Mice either remained in the homecage (exposure = HC) of were exposed to a novel environment (NE) for 15 min and returned to the homecage for 1 hr (exposure = 1hr). Dimensions of the novel environment (NE) cage were 54" x 34" base, 12" height. The NE included huts and tunnels that the animal was not previously exposed to. NE exposures were performed between 7:00 am and 11:00 am during light cycle. Animals did not undergo any special treatment prior to NE exposure.

tag: gender

value: Female

tag: age, weeks

tag: exposure

tag: mouse number

value: hippocampus

value: N

value: F

tag: unalignable

tag: alignable

tag: multimap

tag: total reads

tag: predicted cell type


title: 359_1hr_F_CA3


title: 358_1hr_F_Sub

value: Sub


title: 357_1hr_F_CA3


title: iPS SSEA1-, replicate1, RNA-seq

description: iPS SSEA1- 1

tag: cell type


title: 345_1hr_F_CA1


title: 355_1hr_F_Sub


title: 3/4 MEF, replicate1, ATAC-seq

description: MEF 1


title: 347_1hr_F_CA3


title: 350_1hr_F_CA1


title: 353_1hr_F_CA1


title: 356_1hr_F_Sub


title: 352_1hr_F_Sub


title: 343_1hr_N_CA3


title: 351_1hr_F_CA3


title: 348_1hr_F_CA3


title: 341_1hr_N_Sub


title: 346_1hr_F_Pvalb

value: Pvalb


title: 339_1hr_N_CA1


title: 342_1hr_N_CA1


title: 344_1hr_N_CA3


title: 340_1hr_N_Sub


title: d3 SSEA1+CD73+Sca1-, WGBS

description: d3 Eff


title: 338_1hr_N_Sub


title: 354_1hr_F_CA1


title: d3 SSEA1+CD73-Sca1+, replicate1, ATAC-seq

description: d3 Ineff 1


title: 336_1hr_N_CA1


title: 349_1hr_F_Pvalb


title: 337_1hr_N_Sub


title: 335_1hr_N_Pvalb


title: 332_1hr_N_CA3


title: 333_1hr_N_CA1


title: 331_1hr_N_CA1


title: 329_1hr_N_CA3


title: 330_1hr_N_CA1


title: 326_HC_N_CA3

value: HC


title: 328_HC_N_Sub


title: 327_HC_N_CA3


title: 324_HC_N_CA1


title: 325_HC_N_CA1


title: 319_HC_N_CA1


title: 317_HC_N_Sub


title: 315_HC_N_CA3


title: 320_HC_N_Sub


title: 334_1hr_N_CA3


title: 323_HC_N_Sub


title: 321_HC_N_Sub


title: 322_HC_N_Sub


title: 318_HC_N_Pvalb


title: 314_HC_N_CA1


title: 313_HC_N_VIP

value: VIP


title: 316_HC_N_Ivy

value: Ivy


title: 310_HC_N_DG

value: P

value: C

value: DG


title: 311_HC_N_DG


title: 312_HC_N_DG


title: 309_HC_N_DG


title: 308_HC_N_DG


title: 307_HC_N_DG


title: 306_HC_N_DG


title: 305_HC_N_DG


title: 296_HC_N_DG


title: 286_1hr_F_VIP


title: 290_HC_N_DG


title: 283_1hr_F_Ivy


title: 293_HC_N_DG


title: 299_HC_N_DG


title: 302_HC_N_DG


title: 303_HC_N_DG


title: 282_1hr_F_VIP


title: 297_HC_N_DG


title: 292_HC_N_DG


title: 281_1hr_F_VIP


title: 294_HC_N_DG


title: 284_1hr_F_VIP


title: 295_HC_N_DG


title: 301_HC_N_DG


title: 304_HC_N_DG


title: 300_HC_N_DG


title: 276_1hr_F_Th

value: Th


title: 279_1hr_F_VIP


title: 278_1hr_F_VIP


title: 280_1hr_F_VIP


title: 277_1hr_F_VIP


title: 288_1hr_F_VIP


title: 275_1hr_F_VIP


title: 298_HC_N_DG


title: 289_HC_N_DG


title: 291_HC_N_DG


title: 287_1hr_F_VIP


title: 272_1hr_N_VIP


title: 285_1hr_F_VIP


title: 271_1hr_N_VIP


title: 273_1hr_F_VIP


title: 268_1hr_N_Ivy


title: 270_1hr_N_VIP


title: 266_1hr_N_Th


title: 265_1hr_N_VIP


title: 264_1hr_N_VIP


title: 259_1hr_N_Sub


title: 262_1hr_N_VIP


title: 258_1hr_N_Ivy


title: 257_1hr_N_VIP


title: 263_1hr_N_VIP


title: 255_HC_N_Ivy


title: 254_HC_N_VIP


title: 253_HC_N_DG


title: 250_HC_N_Th


title: 251_HC_N_VIP


title: 252_HC_N_VIP


title: 274_1hr_F_VIP


title: 269_1hr_N_VIP


title: 247_HC_N_VIP


title: 248_HC_N_Th


title: 260_1hr_N_Ivy


title: 244_HC_N_Th


title: 267_1hr_N_VIP


title: 261_1hr_N_VIP


title: 243_HC_N_VIP


title: 245_HC_N_VIP


title: 239_1hr_F_Ivy


title: 237_1hr_F_VIP


title: 242_HC_N_Th


title: 234_1hr_F_VIP


title: 240_1hr_F_VIP


title: 246_HC_N_VIP


title: 236_1hr_F_VIP


title: 235_1hr_F_VIP


title: 232_1hr_F_VIP


title: 238_1hr_F_VIP


title: 230_1hr_F_VIP


title: 231_1hr_F_VIP


title: 241_HC_N_Th


title: 229_1hr_F_VIP


title: 249_HC_N_VIP


title: 226_1hr_N_Ivy


title: 225_1hr_N_VIP


title: 227_1hr_F_VIP


title: 233_1hr_F_VIP


title: 228_1hr_F_VIP


title: 224_1hr_N_VIP


title: 220_1hr_N_VIP


title: 218_1hr_N_VIP


title: 219_1hr_N_VIP


title: 221_1hr_N_VIP


title: 222_1hr_N_VIP


title: 217_1hr_N_VIP


title: 216_1hr_N_Ivy


title: 256_HC_N_CA1


title: 214_1hr_N_VIP


title: 212_1hr_N_Ivy


title: 215_1hr_N_VIP


title: 211_1hr_N_VIP


title: 213_1hr_N_VIP


title: 209_HC_N_VIP


title: 210_1hr_N_VIP


title: 204_HC_N_VIP


title: 205_HC_N_VIP


title: 223_1hr_N_VIP


title: 207_HC_N_VIP


title: 202_HC_N_VIP


title: 203_HC_N_VIP


title: 200_HC_N_DG


title: 199_HC_N_VIP


title: 206_HC_N_VIP


title: 201_HC_N_VIP


title: 196_HC_N_Ivy


title: 195_HC_N_VIP


title: 192_1hr_F_CA3


title: 194_HC_N_VIP


title: 191_1hr_F_CA1


title: 190_1hr_F_CA3


title: 198_HC_N_VIP


title: 189_1hr_F_CA3


title: 193_HC_N_VIP


title: 186_1hr_F_CA1


title: 187_1hr_F_CA3


title: 188_1hr_F_CA1


title: 208_HC_N_VIP


title: 183_1hr_F_CA3


title: 182_1hr_F_CA3


title: 181_1hr_F_CA1


title: 184_1hr_F_Sub


title: 197_HC_N_VIP


title: 177_1hr_F_CA3


title: 178_1hr_F_Pvalb


title: 175_1hr_N_Sub


title: 179_1hr_F_Pvalb


title: 169_1hr_N_CA1


title: 171_1hr_N_CA3


title: 176_1hr_N_Sub


title: 180_1hr_F_Sub


title: 167_1hr_N_CA1


title: 174_1hr_N_CA1


title: 172_1hr_N_Ivy


title: 162_1hr_N_Sub


title: 173_1hr_N_CA3


title: 168_1hr_N_Sub


title: 164_1hr_N_CA3


title: 170_1hr_N_CA3


title: 166_1hr_N_Ivy


title: 160_HC_N_CA1


title: 165_1hr_N_CA3


title: 185_1hr_F_CA3


title: 155_HC_N_Sub


title: 163_1hr_N_CA1


title: 161_1hr_N_CA1


title: 159_HC_N_VIP


title: 157_HC_N_CA3


title: 153_HC_N_Sub


title: 151_HC_N_Sub


title: 152_HC_N_Sub


title: 141_1hr_N_DG


title: 143_1hr_N_DG


title: 148_HC_N_CA1


title: 149_HC_N_Sub


title: 158_HC_N_Pvalb


title: 156_HC_N_Pvalb


title: 137_1hr_N_DG


title: 140_1hr_F_DG


title: 146_HC_N_CA1


title: 145_HC_N_CA1


title: 147_HC_N_Sub


title: 133_1hr_N_DG


title: 131_1hr_F_DG


title: 132_1hr_F_DG


title: 139_1hr_F_DG


title: 138_1hr_F_DG


title: 144_1hr_F_DG


title: 135_1hr_N_DG


title: 154_HC_N_VIP


title: 136_1hr_F_DG


title: 126_1hr_N_DG


title: 127_1hr_N_DG


title: 130_1hr_F_DG


title: 150_HC_N_Sub


title: 125_1hr_F_DG


title: 123_1hr_N_DG


title: 124_1hr_F_DG


title: 142_1hr_N_DG


title: 129_1hr_N_DG


title: 122_1hr_F_DG


title: 128_1hr_N_DG


title: 119_1hr_N_DG


title: 134_1hr_N_DG


title: 118_1hr_F_DG


title: 120_1hr_N_DG


title: 115_1hr_F_DG


title: 117_1hr_F_DG


title: 114_1hr_N_DG


title: 110_1hr_F_DG


title: 112_1hr_N_DG


title: 109_1hr_F_DG


title: 108_1hr_N_DG


title: 105_1hr_N_DG


title: 96_1hr_N_DG


title: 102_1hr_F_DG


title: 97_1hr_N_DG


title: 107_1hr_F_DG


title: 99_1hr_F_DG


title: 121_1hr_N_DG


title: 113_1hr_N_DG


title: 104_1hr_N_DG


title: Mock CLIP-seq exp1

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

data_processing:
library strategy: CLIP-seq
novoindex
Remove 3’adapter using flexbar
collapse data and remove PCR duplicates using pyCRAC
align using novalign
Readcounter using pyCRAC
calculate FDR using Mock sample using pyCRAC
intersect fdr with reads using bedtools intersect
Cluster reads using pyCRAC
Genome_build: hg38; Homo_sapiens-ensembl-release_83 genome annotation
Supplementary_files_format_and_content: GTF representing clusters of hits

source_name: Mock CLIP-seq

growth_protocol: Two P100 dishes per sample were transfected with plasmid expressing T7-tagged TRIM25 or Mock transfected.

extract_protocol:
Cells were lysed with passive lysis buffer.
The protocol was adapted from Moore et al., 2014
Anti-T7 antibody was coupled to 50 μl Dynabeads per sample. Following immunoprecipitation, the RNA was dephosphorylated, the 3’ linker was ligated and radiolabeled and the 5’ linker was ligated on the beads. The 3’ linker reaction was performed in a total of 80 μl, with 1x PNK buffer, 1 μM 3’ adapter, 800 U T4 RNA ligase 2 truncated K227Q, 80 U RNase out, and 10% PEG 8000. The 5’ linker reaction occurred in a total of 80 μl, with 1x PNK buffer, 1 mM ATP, 12.5 nM 5’ linker, 80 U RNase OUT and 40 U T4 RNA ligase. The RNA was reverse transcribed and amplified by PCR using LA Takara Taq.

treatment_protocol: Transfected cells were UV cross-linked.

tag: cell line

value: HeLa

tag: genotype/variation

value: mock-transfected

tag: 5' adapters

value: NNNAGAGCN

tag: 3' adapter

value: NAGATCGGAAGAGCACACGTCTG


title: 101_1hr_F_DG

value: Female

tag: tissue


title: 116_1hr_N_DG

tag: strain

value: hippocampus


title: 103_1hr_F_DG


title: 98_1hr_N_DG

value: N


title: 100_1hr_N_DG


title: 92_1hr_F_DG

value: F


title: Mock CLIP-seq exp3

value: NNNCACTAGCN


title: Mock CLIP-seq exp2


title: 95_1hr_F_DG


title: 93_1hr_F_DG


title: 90_1hr_N_DG


title: 111_1hr_F_DG


title: 94_1hr_F_DG


title: Trim25 CLIP-seq exp2

source_name: Trim25 CLIP-seq

value: transiently expressing T7-tagged TRIM25

value: NNNGTGAGCN


title: 106_1hr_N_DG


title: Trim25 CLIP-seq exp3

value: NNNTCTCTAGCN


title: 87_1hr_N_CA1


title: 88_1hr_N_CA1


title: 85_HC_N_CA1

value: HC


title: 84_HC_N_CA1


title: 91_1hr_N_DG

value: P


title: 89_1hr_F_DG

value: C


title: 86_1hr_N_CA1


title: MCM6rtt105d_16dC_ChIP_rep2

city: Beijing

first: Qing

address: No.5 Yiheyuan Road Haidian District

department: School of Life Science

institute: Peking University

data_processing:
After quality control, samples were mapped by bowtie2 with parameters -k 1 -N 1 --very-sensitive --no-mixed
Reads coverage were calculated and normalized to total reads.
Signal enriched regions were called by MACS2 with parameters -t ChIP_file -c input_file -g 12000000 -B
Genome_build: sacCer3
Supplementary_files_format_and_content: bigWig format

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: Yeast cells were grown on YPD at 25°C and were arrested at G1 phase with alpha-factor, and then released into fresh YPD media containing 0.2 M Hydroxyurea for 45min at 25°C, or released into fresh YPD media for 72min at 16°C.

extract_protocol:
The HA-tagged protein-DNA were isolated with anti-HA antibody (12CA5, Roche, Cat. No. 11 583 816 001).
Libraries were prepared according to NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (E7370).

treatment_protocol: Cells were crosslinked with PFA at 25°C 180rpm for 20min, and PFA was quenched by Glycine.

tag: cell cycle stage

value: S phase

tag: release condition

value: YPD, 16 degree C

tag: chip protein


title: Trim25 CLIP-seq exp1

value: HeLa


title: 82_1hr_F_CA1

tag: gender

tag: age, weeks

tag: exposure


title: MCM6_G1_ChIP_rep2

value: WT

value: G1 phase


title: 83_1hr_F_CA1

tag: mouse number

tag: unalignable

tag: alignable


title: MCM6_16dC_ChIP_rep2


title: 81_1hr_F_CA1

tag: multimap

tag: total reads

tag: predicted cell type


title: 79_1hr_F_CA1


title: 80_HC_N_CA1


title: CDC45rtt105d_16dC_ChIP_rep2

tag: genotype/variation


title: CDC45_G1_ChIP_rep2


title: CDC45_16dC_ChIP_rep2


title: CDC45rtt105d_G1_ChIP_rep2


title: 77_1hr_N_VIP

value: VIP


title: MCM6rtt105d_G1_Input_rep2


title: 78_1hr_N_CA1

value: Female


title: MCM6rtt105d_G1_ChIP_rep2


title: MCM6rtt105d_16dC_Input_rep2


title: 76_1hr_N_CA1

value: hippocampus


title: 75_HC_N_CA1

value: N


title: MCM6_G1_Input_rep2


title: 73_HC_N_CA1


title: 72_1hr_F_CA1

value: F


title: 71_1hr_F_CA1


title: 70_1hr_F_CA1


title: 74_HC_N_DG

value: DG


title: CDC45_16dC_Input_rep2


title: CDC45rtt105d_G1_Input_rep2


title: CDC45rtt105d_16dC_Input_rep2


title: MCM6rtt105d_16dC_ChIP_rep1


title: 69_HC_N_CA1


title: CDC45_G1_Input_rep2


title: 68_1hr_F_Sub

value: Sub


title: MCM6_16dC_ChIP_rep1


title: MCM6rtt105d_G1_ChIP_rep1


title: MCM6_16dC_Input_rep2


title: 67_1hr_N_CA1


title: 66_1hr_N_Sub


title: MCM6_G1_ChIP_rep1


title: 64_HC_N_CA1


title: CDC45rtt105d_G1_ChIP_rep1


title: 61_1hr_F_Sub


title: 60_1hr_F_CA1


title: 62_HC_N_CA1


title: 59_1hr_F_CA1


title: CDC45rtt105d_16dC_ChIP_rep1


title: CDC45_16dC_ChIP_rep1


title: 58_HC_N_CA1


title: 56_1hr_N_Ivy

value: Ivy


title: CDC45_G1_ChIP_rep1


title: 55_1hr_N_Sub


title: MCM6rtt105d_16dC_Input_rep1


title: MCM6rtt105d_G1_Input_rep1


title: 54_1hr_N_VIP


title: 51_HC_N_CA1


title: 65_1hr_N_CA1


title: MCM6_G1_Input_rep1


title: 50_HC_N_CA1


title: 49_1hr_F_CA1


title: MCM6_16dC_Input_rep1


title: 63_HC_N_CA1


title: 48_1hr_F_Sub


title: 46_HC_N_CA1


title: 45_1hr_F_CA1


title: CDC45rtt105d_16dC_Input_rep1


title: 47_1hr_F_CA1


title: 43_1hr_N_CA1


title: 57_1hr_F_CA1


title: 41_1hr_N_CA1


title: 52_HC_N_CA1


title: 53_1hr_N_Sub


title: CDC45_16dC_Input_rep1


title: 44_1hr_N_CA1


title: CDC45rtt105d_G1_Input_rep1


title: CDC45_G1_Input_rep1


title: 40_HC_N_CA1


title: 38_HC_N_Sub


title: 39_HC_N_CA1


title: 37_1hr_F_CA1


title: 35_1hr_F_CA1


title: 36_1hr_F_CA1


title: 34_HC_N_CA1


title: 42_1hr_N_CA1


title: 32_1hr_N_CA1


title: 31_1hr_N_CA1


title: 33_1hr_F_CA1


title: 29_1hr_N_CA1


title: 28_HC_N_CA1


title: 24_1hr_F_CA1


title: 23_1hr_F_CA1


title: 26_HC_N_CA1


title: 30_1hr_N_Sub


title: 25_1hr_F_CA1


title: 21_1hr_F_CA1


title: 27_HC_N_CA1


title: 20_1hr_N_CA1


title: 22_HC_N_CA1


title: 19_1hr_N_CA1


title: 16_HC_N_CA1


title: 15_1hr_F_CA1


title: 12_HC_N_CA1


title: 18_1hr_N_CA1


title: 11_1hr_F_CA1


title: 14_1hr_F_Sub


title: 9_1hr_N_CA1


title: 10_1hr_N_CA1


title: 13_1hr_F_CA1


title: 7_HC_N_CA1


title: 8_1hr_N_CA1


title: 17_1hr_N_CA1


title: 3_1hr_F_CA1


title: 4_1hr_F_CA1


title: 1_HC_N_CA1


title: 2_1hr_F_Sub


title: RNA from mutant grown at 42 °C Replicate 3

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Read trimming and adapter clipping with cutadapt 1.13
Read mapping with READemption 0.4.3 and segemehl 0.2.0
Coverage calculation (full read and first base only) using READemption 0.4.3
Genome_build: NC_007493.2, NC_007494.2, NC_009007.1, NC_007488.2, NC_007489.1, NC_007490.2, NC_009008.1
Supplementary_files_format_and_content: wiggle format

organism: Cereibacter sphaeroides

source_name: mutant grown at 42 °C

growth_protocol: Cells were cultivated in minimal malate medium under microaerobic conditions to exponential phase (Remes et al., 2017, J. Bacteriol. 199, doi: 10.1128/JB.00249-17)

extract_protocol:
RNA was isolated and processed as published  (Remes et al., 2017, J. Bacteriol. 199, doi: 10.1128/JB.00249-17)
NEBNext Multiplex Small RNA Library Prep Set

value: RNase E mutant

tag: growth temperature

value: 42 °C


title: RNA from mutant grown at 42 °C Replicate 2


title: T31-5, 75 mM NaCl

city: Leiden

first: Christiaan

last: Henkel

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: University Leiden

description: Expressing 3F-VP16 fusion inducing salinity tolerance

data_processing:
Illumina software used for basecalling.
tophat 2.0.5
htsec count
Genome_build: TAIR10_GFF3_genes.gff
Supplementary_files_format_and_content: htsec count tab delimited .htseq files

source_name: Whole plant

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

value: Whole plant

tag: expression


title: Col-0, 75 mM NaCl

description: Wild type

tag: tissue

value: Wild type


title: T31-5, 0 mM NaCl

value: Expressing 3F-VP16 fusion inducing salinity tolerance


title: T43-11, 0 mM NaCl


title: T43-11, 75 mM NaCl


title: RNA from mutant grown at 32 °C Replicate 3

source_name: mutant grown at 32 °C

tag: strain

value: 32 °C


title: Empty vector control, 75 mM NaCl

description: Expressing VP16 only

value: Expressing VP16 only


title: Col-0, 0 mM NaCl

description: Wild type


title: RNA from mutant grown at 42 °C Replicate 1


title: Col-0 A

source_name: Shoot

value: Shoot

tag: genotype


title: Col-0 C


title: Col-0 B


title: VP16 pool 5 background B


title: VP16 pool 5 background A


title: RNA from wild type grown at 42 °C Replicate 2

source_name: wild type grown at 42 °C

value: wild type


title: RNA from wild type grown at 42 °C Replicate 3


title: RNA from wild type grown at 42 °C Replicate 1


title: Empty vector control, 0 mM NaCl

description: Expressing VP16 only


title: VP16 pool 2 background C


title: RNA from mutant grown at 32 °C Replicate 1


title: VP16 pool 2 background B


title: 5_HC_N_CA1

value: HC

value: C


title: VP16 pool 2 background A


title: RNA from wild type grown at 32 °C Replicate 2

source_name: wild type grown at 32 °C


title: RNA from wild type grown at 32 °C Replicate 3


title: 6_HC_N_CA1

value: Female

value: hippocampus


title: RNA from wild type grown at 32 °C Replicate 1


title: RNA from mutant grown at 32 °C Replicate 2


title: VP16-05-014 A


title: VP16 pool 5 background C


title: VP16-02-003 C


title: VP16-05-014 B


title: VP16-02-003 A


title: VP16-02-003 B


title: EAR pool 15 background A

value: EAR


title: EAR pool 15 background C


title: EAR pool 15 background B


title: EAR pool 13 background C


title: EAR pool 13 background B


title: EAR-15-053 C


title: EAR-15-053 B


title: EAR pool 13 background A


title: EAR-15-053 A


title: EAR-15-025 B


title: EAR-15-025 C


title: EAR-15-025 A


title: EAR-13-068 C


title: EAR-13-068 A


title: VP16-05-014 C


title: PDX1-GFPneg spermatogonia rep 3 [RNA-seq]

status: Public on Jul 26 2018

city: CLAYTON

first: Robin

last: Hobbs

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

institute: Hudson Institute of Medical Research

data_processing:
Used RNAsik pipeline to bam, counts and gather different metrics on RNAseq data https://github.com/MonashBioinformaticsPlatform/RNAsik-pipe
Used Degust  to analysis table of counts, output form RNAsik. Degust is a webapp that uses either edgeR or limma-voom for differential gene analysis http://degust.erc.monash.edu
Genome_build: Mus_musculus.GRCm38.dna_sm.primary_assembly.fa
Supplementary_files_format_and_content: raw counts file was generated by featureCounts, which than was uploaded to Degust

source_name: GFP-

growth_protocol: Adult transgenic mice (6-8 weeks old) containing both PDX1-GFP and Plzf-mCherry/CreER reporters were maintained under standard conditions.

extract_protocol:
Sorted cells were lysed in TRIzol LS reagent (Thermo Fisher Scientific) then RNA was purified and DNase treated using a Direct-zol RNA Microprep kit (Zymo Research).
SPIA libraries: - Nugen Ovation RNA-Seq system V2 (for SPIA amplifications and cDNA generation) using Nugen protocol M01206v5, 2013; followed by Ovation Ultralow System V2 (for rest of library preparation) using Nugen protocol M01379v1, 2014.

treatment_protocol: Testis cell suspensions were prepared by a standard two step digestion protocol with collagenase and trypsin. Cells were sorted on a BD Influx Cell Sorter (BD Biosciences). The undifferentiated population was gated according to expression of the Plzf-mCherry/CreER reporter plus surface markers c-Kit and CD9. Plzf is a well-established marker of undifferentiated spermatogonia plus cells at early differentiation stages. c-Kit marks differentiating spermatogonia and CD9 is enriched on functional stem cells. Undifferentiated cells were then isolated according to whether they were positive or negative for PDX1-GFP expression.

tag: strain background

value: mixed C57BL/6 x CBA

value: transgenic containing both PDX1-GFP and Plzf-mCherry/CreER reporters

tag: age

value: adult; 6-8 weeks

value: Testis

tag: sorted fraction

value: PDX1-GFPneg spermatogonia


title: PDX1-GFPpos spermatogonia rep 3 [RNA-seq]

source_name: GFP+

value: PDX1-GFPpos spermatogonia


title: PDX1-GFPpos spermatogonia rep 2 [RNA-seq]


title: PDX1-GFPpos spermatogonia rep 1 [RNA-seq]


title: G1_PEG_Human

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

institute: Ludwig-Maximilians University Munich

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB PEG CGTCCG
processed data file: Species_mixing_counts.txt

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned to the Human Genome (hg38) or Mouse genome (mm10) with STAR 2.5.3
Quantification was done with ENSEMBL gene models (GRCh38.84/GRCm38.75)
Genome_build: Human: hg38, Ensembl 84; Mouse: mm10, Ensembl 75
Supplementary_files_format_and_content: cell (columns) and gene (rows) -wise UMI expression table

source_name: human induced pluripotent stem cell

extract_protocol:
Cells were FACS sorted into lysis buffer
Libraries were constructed using various developments of the SCRB-seq protocol, see sample description for more details

tag: protocol

value: mcSCRB-seq

value: human induced pluripotent stem cell


title: F12_noPEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB noPEG CGGGGA
processed data file: Species_mixing_counts.txt

value: mcSCRB-seq without PEG


title: F2_PEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB PEG CCCCTG
processed data file: Species_mixing_counts.txt


title: PDX1-GFPneg spermatogonia rep 1 [RNA-seq]


title: E11_noPEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB noPEG CAGCCG
processed data file: Species_mixing_counts.txt


title: E10_noPEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB noPEG CACCCC
processed data file: Species_mixing_counts.txt


title: F1_PEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB PEG CCCAGC
processed data file: Species_mixing_counts.txt


title: G8_noPEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB noPEG GCCGAC
processed data file: Species_mixing_counts.txt


title: E7_noPEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB noPEG ACGCCG
processed data file: Species_mixing_counts.txt


title: G10_noPEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB noPEG GCGCAC
processed data file: Species_mixing_counts.txt


title: PDX1-GFPneg spermatogonia rep 4 [RNA-seq]


title: E9_noPEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB noPEG AGGCCC
processed data file: Species_mixing_counts.txt


title: D11_noPEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB noPEG CCGATT
processed data file: Species_mixing_counts.txt


title: C7_noPEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB noPEG TATATC
processed data file: Species_mixing_counts.txt


title: PDX1-GFPpos spermatogonia rep 4 [RNA-seq]


title: EAR-13-068 B


title: B7_noPEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB noPEG CAATAA
processed data file: Species_mixing_counts.txt


title: C3_PEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB PEG TAAGTA
processed data file: Species_mixing_counts.txt


title: B2_PEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB PEG ATCATT
processed data file: Species_mixing_counts.txt


title: PDX1-GFPneg spermatogonia rep 2 [RNA-seq]


title: A11_noPEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB noPEG ATAACA
processed data file: Species_mixing_counts.txt


title: A7_noPEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB noPEG AATTGA
processed data file: Species_mixing_counts.txt


title: UHRR_TCCAAC

description:
Libraries were constructed using the original SCRB-seq protocol using Advantage2 Polymerase (see Soumillon et al., 2014)
barcode: TCCAAC
processed data file:
UHRR_UMIcounts.txt

source_name: universal human reference RNA

extract_protocol:
Cells were FACS sorted into lysis buffer
The Universal Human Reference RNA was obtained from Agilent (catalog number 740000).
Libraries were constructed using various developments of the SCRB-seq protocol, see sample description for more details

value: SCRB-seq (Soumillon et al., 2014)

tag: cell type/rna source

value: universal human reference RNA


title: UHRR_TTAACT

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase and SmartScribe reverse transcriptase
barcode: TTAACT
processed data file:
UHRR_UMIcounts.txt

value: SCRB-seq (Smartscribe/KAPA)


title: UHRR_TTATCA

description:
Libraries were constructed using the original SCRB-seq protocol using Advantage2 Polymerase (see Soumillon et al., 2014)
barcode: TTATCA
processed data file:
UHRR_UMIcounts.txt


title: UHRR_TTGTTA

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: TTGTTA
processed data file:
UHRR_UMIcounts.txt

value: SCRB-seq (Ziegenhain et al., 2017)


title: UHRR_TAGAAT

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: TAGAAT
processed data file:
UHRR_UMIcounts.txt


title: UHRR_GGACAT

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase and SmartScribe reverse transcriptase
barcode: GGACAT
processed data file:
UHRR_UMIcounts.txt


title: UHRR_GGTCCC

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGTCCC
processed data file:
UHRR_UMIcounts.txt


title: UHRR_TTTTAG

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: TTTTAG
processed data file:
UHRR_UMIcounts.txt


title: UHRR_GGGCGA

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GGGCGA
processed data file:
UHRR_UMIcounts.txt


title: UHRR_GCCCCT

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GCCCCT
processed data file:
UHRR_UMIcounts.txt


title: UHRR_TATCAT

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: TATCAT
processed data file:
UHRR_UMIcounts.txt


title: C10_noPEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB noPEG TCATTA
processed data file: Species_mixing_counts.txt


title: UHRR_GGCGCT

description:
Libraries were constructed using the original SCRB-seq protocol using Advantage2 Polymerase (see Soumillon et al., 2014)
barcode: GGCGCT
processed data file:
UHRR_UMIcounts.txt


title: UHRR_TAAAAC

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase and SmartScribe reverse transcriptase
barcode: TAAAAC
processed data file:
UHRR_UMIcounts.txt


title: D2_PEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB PEG TTACAT
processed data file: Species_mixing_counts.txt


title: B10_noPEG_Human

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Human mcSCRB noPEG GAAATT
processed data file: Species_mixing_counts.txt


title: UHRR_CTCTCC

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: CTCTCC
processed data file:
UHRR_UMIcounts.txt


title: UHRR_CGTCGC

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase and SmartScribe reverse transcriptase
barcode: CGTCGC
processed data file:
UHRR_UMIcounts.txt


title: UHRR_GCTGGG

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase and SmartScribe reverse transcriptase
barcode: GCTGGG
processed data file:
UHRR_UMIcounts.txt


title: UHRR_GAGGGC

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GAGGGC
processed data file:
UHRR_UMIcounts.txt


title: UHRR_CGCAGG

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGCAGG
processed data file:
UHRR_UMIcounts.txt


title: UHRR_CCGCAG

description:
Libraries were constructed using the original SCRB-seq protocol using Advantage2 Polymerase (see Soumillon et al., 2014)
barcode: CCGCAG
processed data file:
UHRR_UMIcounts.txt


title: UHRR_CCTCGG

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: CCTCGG
processed data file:
UHRR_UMIcounts.txt


title: UHRR_CCCCAC

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase and SmartScribe reverse transcriptase
barcode: CCCCAC
processed data file:
UHRR_UMIcounts.txt


title: UHRR_CTGGGC

description:
Libraries were constructed using the original SCRB-seq protocol using Advantage2 Polymerase (see Soumillon et al., 2014)
barcode: CTGGGC
processed data file:
UHRR_UMIcounts.txt


title: UHRR_ATTGTT

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ATTGTT
processed data file:
UHRR_UMIcounts.txt


title: UHRR_ATGTAA

description:
Libraries were constructed using the original SCRB-seq protocol using Advantage2 Polymerase (see Soumillon et al., 2014)
barcode: ATGTAA
processed data file:
UHRR_UMIcounts.txt


title: UHRR_TAATAG

description:
Libraries were constructed using the original SCRB-seq protocol using Advantage2 Polymerase (see Soumillon et al., 2014)
barcode: TAATAG
processed data file:
UHRR_UMIcounts.txt


title: UHRR_AATATG

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: AATATG
processed data file:
UHRR_UMIcounts.txt


title: H8_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG GTCCCC
processed data file: Species_mixing_counts.txt

source_name: JM8 embryonic stem cell

value: JM8 embryonic stem cell


title: UHRR_AATTTC

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: AATTTC
processed data file:
UHRR_UMIcounts.txt


title: UHRR_AACATA

description:
Libraries were constructed using the original SCRB-seq protocol using Advantage2 Polymerase (see Soumillon et al., 2014)
barcode: AACATA
processed data file:
UHRR_UMIcounts.txt


title: UHRR_ACGCGC

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: ACGCGC
processed data file:
UHRR_UMIcounts.txt


title: H11_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG TGCCCC
processed data file: Species_mixing_counts.txt


title: UHRR_AAACAT

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase and SmartScribe reverse transcriptase
barcode: AAACAT
processed data file:
UHRR_UMIcounts.txt


title: H10_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG TCCGGG
processed data file: Species_mixing_counts.txt


title: H3_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG GGCGAG
processed data file: Species_mixing_counts.txt


title: H5_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG GGGCCT
processed data file: Species_mixing_counts.txt


title: H6_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG GGGGCA
processed data file: Species_mixing_counts.txt


title: H1_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG GCTGCC
processed data file: Species_mixing_counts.txt


title: H7_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG GGGTGC
processed data file: Species_mixing_counts.txt


title: G5_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG GAGGCG
processed data file: Species_mixing_counts.txt


title: G11_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG GCGGAG
processed data file: Species_mixing_counts.txt


title: G7_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG GCCCAG
processed data file: Species_mixing_counts.txt


title: G9_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG GCCTCG
processed data file: Species_mixing_counts.txt


title: UHRR_CATAAA

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CATAAA
processed data file:
UHRR_UMIcounts.txt


title: G3_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG CTGGCG
processed data file: Species_mixing_counts.txt


title: UHRR_ATATGA

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase and SmartScribe reverse transcriptase
barcode: ATATGA
processed data file:
UHRR_UMIcounts.txt


title: F8_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG CGCCGA
processed data file: Species_mixing_counts.txt


title: F10_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG CGGACG
processed data file: Species_mixing_counts.txt


title: F9_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG CGCGGT
processed data file: Species_mixing_counts.txt


title: G6_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG GCAGCG
processed data file: Species_mixing_counts.txt


title: F4_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG CCGGCA
processed data file: Species_mixing_counts.txt


title: F3_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG CCGAGG
processed data file: Species_mixing_counts.txt


title: E8_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG AGCCCG
processed data file: Species_mixing_counts.txt


title: F6_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG CGACCC
processed data file: Species_mixing_counts.txt


title: F5_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG CCGTGC
processed data file: Species_mixing_counts.txt


title: H4_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG GGCTCC
processed data file: Species_mixing_counts.txt


title: F7_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG CGCACC
processed data file: Species_mixing_counts.txt


title: H9_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG GTGGCC
processed data file: Species_mixing_counts.txt


title: E12_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG CCACCG
processed data file: Species_mixing_counts.txt


title: G4_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG GACGCC
processed data file: Species_mixing_counts.txt


title: E3_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG TAGTGG
processed data file: Species_mixing_counts.txt


title: H2_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG GGAGGG
processed data file: Species_mixing_counts.txt


title: E1_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG GCTTAC
processed data file: Species_mixing_counts.txt


title: E4_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG TTCCTC
processed data file: Species_mixing_counts.txt


title: D12_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG CTTCTG
processed data file: Species_mixing_counts.txt


title: E2_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG GTACAC
processed data file: Species_mixing_counts.txt


title: D7_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG TTTGTA
processed data file: Species_mixing_counts.txt


title: D6_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG TTTAGT
processed data file: Species_mixing_counts.txt


title: D10_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG CAGTCA
processed data file: Species_mixing_counts.txt


title: D9_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG AGGGAT
processed data file: Species_mixing_counts.txt


title: F11_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG CGGCGT
processed data file: Species_mixing_counts.txt


title: E5_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG CCTTCC
processed data file: Species_mixing_counts.txt


title: D3_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG TTATAC
processed data file: Species_mixing_counts.txt


title: C8_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG TATGTT
processed data file: Species_mixing_counts.txt


title: D4_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG TTCAAT
processed data file: Species_mixing_counts.txt


title: D1_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG TTAAAG
processed data file: Species_mixing_counts.txt


title: C12_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG TGTAAA
processed data file: Species_mixing_counts.txt


title: C6_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG TAGTTT
processed data file: Species_mixing_counts.txt


title: C9_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG TATTTG
processed data file: Species_mixing_counts.txt


title: C5_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG TACTTA
processed data file: Species_mixing_counts.txt


title: C11_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG TGAAAT
processed data file: Species_mixing_counts.txt


title: C2_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG TAAATG
processed data file: Species_mixing_counts.txt


title: B9_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG CTATTA
processed data file: Species_mixing_counts.txt


title: D8_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG TCTTTC
processed data file: Species_mixing_counts.txt


title: C1_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG GTTTTA
processed data file: Species_mixing_counts.txt


title: C4_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG TAATTC
processed data file: Species_mixing_counts.txt


title: B5_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG ATTGAA
processed data file: Species_mixing_counts.txt


title: B11_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG GATATA
processed data file: Species_mixing_counts.txt


title: B12_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG GTATAA
processed data file: Species_mixing_counts.txt


title: A6_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG AATGAT
processed data file: Species_mixing_counts.txt


title: D5_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG TTGATT
processed data file: Species_mixing_counts.txt


title: A5_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG AATAGT
processed data file: Species_mixing_counts.txt


title: A8_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG ACATAA
processed data file: Species_mixing_counts.txt


title: A2_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG AAATAC
processed data file: Species_mixing_counts.txt


title: A10_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG AGTAAT
processed data file: Species_mixing_counts.txt


title: A4_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG AAGTAT
processed data file: Species_mixing_counts.txt


title: A12_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG ATACTT
processed data file: Species_mixing_counts.txt


title: J1 mcSCRB/KAPAHiFi TGTTTA

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: TGTTTA
processed data file:
J1.KAPA_UMIcounts.txt

source_name: J1 embryonic stem cell

value: mcSCRB-seq (KAPA HiFi)

value: J1 embryonic stem cell


title: J1 mcSCRB/KAPAHiFi GTTTAT

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: GTTTAT
processed data file:
J1.KAPA_UMIcounts.txt


title: B6_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG ATTTGT
processed data file: Species_mixing_counts.txt


title: J1 mcSCRB/KAPAHiFi TAAGAT

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: TAAGAT
processed data file:
J1.KAPA_UMIcounts.txt


title: A1_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG AAAATC
processed data file: Species_mixing_counts.txt


title: A3_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG AACAAT
processed data file: Species_mixing_counts.txt


title: J1 mcSCRB/KAPAHiFi TTATTG

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: TTATTG
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi GGAGCC

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: GGAGCC
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi TTAGTT

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: TTAGTT
processed data file:
J1.KAPA_UMIcounts.txt


title: B3_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG ATGATA
processed data file: Species_mixing_counts.txt


title: J1 mcSCRB/KAPAHiFi TTAATC

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: TTAATC
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi GCTCGC

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: GCTCGC
processed data file:
J1.KAPA_UMIcounts.txt


title: B4_PEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB PEG ATTAGA
processed data file: Species_mixing_counts.txt


title: J1 mcSCRB/KAPAHiFi GCTAGA

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: GCTAGA
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi TCTGCA

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: TCTGCA
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi TAATGA

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: TAATGA
processed data file:
J1.KAPA_UMIcounts.txt


title: B8_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG CATTTA
processed data file: Species_mixing_counts.txt


title: J1 mcSCRB/KAPAHiFi TAAAGT

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: TAAAGT
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi CGTGGG

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: CGTGGG
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi CCGGAC

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: CCGGAC
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi GACCGC

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: GACCGC
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi GGCCAC

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: GGCCAC
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi CTGCGG

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: CTGCGG
processed data file:
J1.KAPA_UMIcounts.txt