title: AtRootHair3

description: processed data file: AtRootHair.xlsx

data_processing:
Illumina Casava 1.8.2 was used for base calling.
The first 15bp of each read were trimmed.
Reads were mapped using Tophat v2.0.9. Default settings with --segment length 17 parameter were used to map the reads to the reference annotation (already mentioned in the sample information above).
FPKM values were calculated by Cufflinks2 v2.1.1 with multiread correction (-u -G).
Genome_build: See sample information above.
Supplementary_files_format_and_content: Excel files that contain the FPKM value generated by Cufflinks for the gene expression profiling for each of the six species.

source_name: root hair

extract_protocol:
RNA was extracted using Qiagen RNAeasy Plant Mini Kit.
RNA libraries were prepared for sequencing using SMART-Seq v4 Ultra Low Input RNA kit.

treatment_protocol: Root tissue was stirred in liquid nitrogen and filtered with a 250-mm sieve.

value: Columbia

tag: reference annotation

value: Ensembl Plant Release 19, TAIR10

value: 4-5 days after plating


title: AtRootHair2

status: Public on May 11 2017

type: SRA

city: Ann Arbor

first: John

last: Schiefelbein

state: Michigan

address: 830 North University Avenue

department: Molecular, Cellular, and Developmental Biology

country: USA

institute: University of Michigan

description: processed data file: AtRootHair.xlsx

library_source: transcriptomic

molecule: total RNA

organism: Arabidopsis thaliana

growth_protocol: Seeds were surface sterilized and germinated on agarose-solidified MS media under constant light at 22C.

tag: variety

tag: age


title: BOW3210A94

city: Oxford

first: Eshita

last: Sharma

state: Oxfordshire

address: Roosevelt Drive, Headington

department: Bioinformatics

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics

description: Count_table.txt, CPM_table.txt

data_processing:
Real time Analysis (RTA): HiSeq 2500 - RTA v1.18.64, HCS v2.2.58; HiSeq 4000 - RTA v2.73, HCS v3.3.52
Base-calling: Hiseq 2500 was basecalled with bcl2fastq v1.8.4; HiSeq 4000 was basecalled with bcl2fastq v2.17.1.14
Adapter trimming: RNA-seq reads were trimmed for Nextera and Illumina  adapter sequences using skewer-v0.1.125
Alignment: Reads in gzipped fastq format were aligned using Hisat2 version-2.0.0-beta with default parameters to a modified reference genome comprising the human genome, Homo sapiens GRCh37 - human_g1k_v37, and fasta sequences for ERCC spike-ins
Mark Duplicates: Duplicate reads were marked using MarkDuplicates.jar implemented in Picard tools v1.92
Read counts (abundance measurement): Reads mapping uniquely to genes annotated in ENSEMBL release 75 were counted using featureCounts implemented in subread-v1.5.0
Normalized Counts: Read counts were normalized to counts per million (CPM) by dividing each gene-count by total reads mapped (uniquely mapped to exonic regions) per million
Genome_build: GRCh37
Supplementary_files_format_and_content: Count_table.txt: raw read counts for all 63677 ENSEMBL annotated genes
Supplementary_files_format_and_content: CPM_table.txt:  Counts per million normalized counts all 63677 ENSEMBL annotated genes
Supplementary_files_format_and_content: Metadata_Table.xlsx: Contains two excel sheets with Sheet 1 = cell metadata with information regarding treatment sequencing batch, imaging, and QC metrics
Supplementary_files_format_and_content: Metadata_Table.xlsx: Sheet2= Contains description of column headers of cell metadata in Sheet 1

organism: Homo sapiens

source_name: K562 cell line

growth_protocol: K562 cells were maintained (1–10 × 105 cell/ml) in T75 flasks in RPMI 1640 + 2mM Glutamine + 10% Foetal Bovine Serum (FBS)

extract_protocol:
FluidigmC1 RNAseq protocol: cDNA was generated using SMARTer Ultra Low RNA Kit (Clontech)
Nextera XT DNA Library Preparation Kit (Illumina)

treatment_protocol: CellTracker Orange CMRA "ThermoFisher" (1µM final concentration, 30min at RT), LIVE/DEAD® Fixable Red Dead Cell Stain "ThermoFisher" (per manufacturer protocol)

tag: cell type

value: Human immortalised myelogenous leukemia line

tag: passages

value: 20-22 hours

tag: cell line

tag: treatment

value: treated (3 hour with 10 mM benzene)


title: BOW3210A93

description: Count_table.txt, CPM_table.txt

treatment_protocol: CellTracker Green CMFDA "ThermoFisher" (1µM final concentration, 30min at RT), LIVE/DEAD® Fixable Red Dead Cell Stain "ThermoFisher" (per manufacturer protocol)

value: untreated


title: AtRootHair1

description: processed data file: AtRootHair.xlsx


title: BOW3221A12

description: Count_table.txt, CPM_table.txt

value: treated (1 hour with 1 μM Imatinib)


title: BOW3210A9

description: Count_table.txt, CPM_table.txt


title: BOW3210A8

description: Count_table.txt, CPM_table.txt


title: BOW3210A67

description: Count_table.txt, CPM_table.txt


title: BOW3210A92

description: Count_table.txt, CPM_table.txt


title: BOW3210A70

description: Count_table.txt, CPM_table.txt


title: BOW3210A69

description: Count_table.txt, CPM_table.txt


title: BOW3210A71

description: Count_table.txt, CPM_table.txt


title: BOW3210A7

description: Count_table.txt, CPM_table.txt


title: BOW3210A66

description: Count_table.txt, CPM_table.txt


title: Krt15+ rep 3

city: Philadelphia

first: Veronique

last: Giroux

state: PA

address: 421 Curie Blvd, BRB II/III Room 941

institute: University of Pennsylvania

description: Sample name: s569_GFPplus_rep3

data_processing:
Sequencing was performed using Illumina NextSeq500 and the read lengths were 75 bp.
Paired-end reads were aligned to the mouse genome mm9 using STAR 2.5.
Transcript expression quantification was performed using Cufflinks (v2.2.1).
Differential gene expression analysis was performed using the R package ‘DESeq2’.
Genome_build: mm9
Supplementary_files_format_and_content: csv file with gene expression values from Cufflinks.

organism: Mus musculus

source_name: basal esophageal epithelial cells

extract_protocol:
No RNA extraction, cDNA library establish form cells
SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing from ClonTech

treatment_protocol: Krt15-CrePR1;R26mTomato/mGFP were injected with 1mg RU486 to induce Cre recombination. Twenty-four hours later, Krt15- and Krt15+ basal cells were sorted using CD29 as a basal cell marker and GFP as a Krt15+ marker

tag: cell markers

value: CD29high GFP+

tag: genotype

value: basal esophageal epithelial cells


title: BOW3210A68

description: Count_table.txt, CPM_table.txt


title: Krt15+ rep 1

description: Sample name: s546_GFPplus_rep1


title: Krt15- rep 3

description: Sample name: s569_GFPminus_rep3

value: CD29high GFP-


title: Krt15+ rep 2

description: Sample name: s568_GFPplus_rep2


title: BOW3210A65

description: Count_table.txt, CPM_table.txt


title: BOW3210A63

description: Count_table.txt, CPM_table.txt


title: Krt15- rep 2

description: Sample name: s568_GFPminus_rep2


title: BOW3210A62

description: Count_table.txt, CPM_table.txt


title: BOW3210A61

description: Count_table.txt, CPM_table.txt


title: BOW3210A60

description: Count_table.txt, CPM_table.txt


title: BOW3210A91

description: Count_table.txt, CPM_table.txt


title: Krt15- rep 1

description: Sample name: s546_GFPminus_rep1


title: hetp.Tg.2

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

institute: The Wistar Institute

description: RNA-seq for heterozygous Pten mouse, transgenic Trap1 replicate 2

data_processing:
RNA-Seq data analysis was done with rsem(ver. 1.2.3) and mm10 genome with UCSC known gene set.
Two samples were removed as technical outliers based on Principal Component Analysis.
DESeq2 was used for differential expression was used for differentail expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed file contains raw counts for all genes

source_name: Mouse prostate

growth_protocol: A Pten heterozygous male mouse (http://www.ncbi.nlm.nih.gov/pubmed/9990064) was used in a breeding pair with a TRAP1 transgenic female mouse (line 810). Of the resulting offspring, 25% of the animals were used for further experiments (PTen het-Tg male mice constituted the experimental group, while PTen het-non Tg male mice were used as control group)

extract_protocol:
Total RNA was extracted using Trizol
The sequencing libraries were generated using the Lexogen QuantSeq 3’ mRNA sequencing library preparation kit (SKU:015.24) for Illumina sequencing platform compatible libraries. All 12 libraries were pooled in equal molar amounts and run on the Illumina Nextseq500 using the Mid Output V2 (150 cycles) kit (cat # FC-404-2001)

treatment_protocol: Twelve RNA samples extracted from Tg prostates were first treated with Invitrogen/Ambion DNA-free-kit (cat #AM1906) to remove DNA

tag: tissue type

value: prostate

tag: pten

value: het

value: transgenic

tag: replicate


title: hetp.Tg.3

description: RNA-seq for heterozygous Pten mouse, transgenic Trap1 replicate 3


title: BOW3210A6

description: Count_table.txt, CPM_table.txt


title: hetp.Tg.1

description: RNA-seq for heterozygous Pten mouse, transgenic Trap1 replicate 1


title: BOW3210A59

description: Count_table.txt, CPM_table.txt


title: BOW3210A64

description: Count_table.txt, CPM_table.txt


title: BOW3210A58

description: Count_table.txt, CPM_table.txt


title: hetp.nTg.2

description: RNA-seq for heterozygous Pten mouse, non-transgenic Trap1 replicate 2

value: non-transgenic


title: hetp.nTg.3

description: RNA-seq for heterozygous Pten mouse, non-transgenic Trap1 replicate 3


title: hetp.nTg.1

description: RNA-seq for heterozygous Pten mouse, non-transgenic Trap1 replicate 1


title: BOW3210A55

description: Count_table.txt, CPM_table.txt


title: BOW3210A56

description: Count_table.txt, CPM_table.txt


title: BOW3210A52

description: Count_table.txt, CPM_table.txt


title: BOW3210A54

description: Count_table.txt, CPM_table.txt


title: pten.Tg.2

description: RNA-seq for pten WT mouse, transgenic Trap1 replicate 2

value: WT


title: pten.Tg.3

description: RNA-seq for pten WT mouse, transgenic Trap1 replicate 3


title: pten.Tg.1

description: RNA-seq for pten WT mouse, transgenic Trap1 replicate 1


title: pten.nTg.2

description: RNA-seq for pten WT mouse, non-transgenic Trap1 replicate 2


title: pten.nTg.1

description: RNA-seq for pten WT mouse, non-transgenic Trap1 replicate 1


title: pten.nTg.3

description: RNA-seq for pten WT mouse, non-transgenic Trap1 replicate 3


title: BOW3210A51

description: Count_table.txt, CPM_table.txt


title: BOW3210A50

description: Count_table.txt, CPM_table.txt


title: BOW3210A5

description: Count_table.txt, CPM_table.txt


title: 4189_BD_putamen_CTTGTA

city: Jupiter

first: Courtney

last: MacMullen

state: FL

address: 130 Scripps Way

department: Neuroscience

institute: The Scripps Research Institute

description: Sample 16

data_processing:
Reads were aligned to human genome and transcriptome by Avadis NGS 1.5.1 software
Minimum percent identity was set to 90. reads with average quality scores less than 30 were trimmed at 3' end.  Minimum percent gap was set to 5.  Minimum aligned read length was set to 25.  Number matches to output per read was set to 1.  Kmer size wa set to 11.
Mapped reads with quality score>=30 were quantified based on Ensembl Genes and Transcripts annotation (2013.04.03) in AVADIS NGS 1.5.1 software.  Normalization type was set to Deseq.  Threshold for normalization was set to 1.  The rest of the parameters were set to default.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: text (tab delimited) which includes the log2 normalized counts.

extract_protocol:
Rneasy lipid tissue kit
NEBNext Ultra Directional RNAseq libraries
100bp single read chemistry

tag: subject status

value: Bipolar Disorder individual

tag: tissue

value: Brain

tag: tissue subtype

value: putamen


title: 4185_BD_putamen_TAGCTT

description: Sample 15


title: BOW3210A49

description: Count_table.txt, CPM_table.txt


title: BOW3210A48

description: Count_table.txt, CPM_table.txt


title: 4131_BD_putamen_ACTTGA

description: Sample 14


title: BOW3210A47

description: Count_table.txt, CPM_table.txt


title: 3590_HC_putamen_CAGATC

description: Sample 12

value: healthy control


title: 3003_BD_putamen_CGATGT

description: Sample 13


title: 3589_HC_putamen_GCCAAT

description: Sample 11


title: BOW3210A44

description: Count_table.txt, CPM_table.txt

value: Human immortalised myelogenous leukemia line


title: BOW3210A53

description: Count_table.txt, CPM_table.txt

value: 20-22 hours


title: BOW3210A57

description: Count_table.txt, CPM_table.txt


title: 3529_HC_putamen_TGACCA

description: Sample 9


title: BOW3210A43

description: Count_table.txt, CPM_table.txt

value: treated (3 hour with 10 mM benzene)


title: BOW3210A45

description: Count_table.txt, CPM_table.txt


title: 3543_HC_putamen_ACAGTG

description: Sample 10


title: 4185_BD_c_nucleus_CAGATC

description: Sample 7

value: cuadate nucleus


title: BOW3210A41

description: Count_table.txt, CPM_table.txt


title: BOW3210A42

description: Count_table.txt, CPM_table.txt

value: untreated


title: BOW3210A40

description: Count_table.txt, CPM_table.txt


title: BOW3210A4

description: Count_table.txt, CPM_table.txt


title: 3589_HC_c_nucleus_TTAGGC

description: Sample 3


title: BOW3210A38

description: Count_table.txt, CPM_table.txt


title: BOW3210A39

description: Count_table.txt, CPM_table.txt


title: 3543_HC_c_nucleus_CGATGT

description: Sample 2


title: 3590_HC_c_nucleus_TGACCA

description: Sample 4


title: 4131_BD_c_nucleus_GCCAAT

description: Sample 6


title: 3529_HC_c_nucleus_ATCACG

description: Sample 1


title: BOW3210A37

description: Count_table.txt, CPM_table.txt


title: BOW3210A35

description: Count_table.txt, CPM_table.txt


title: BOW3210A34

description: Count_table.txt, CPM_table.txt


title: BOW3210A46

description: Count_table.txt, CPM_table.txt


title: BOW3210A36

description: Count_table.txt, CPM_table.txt


title: BOW3210A31

description: Count_table.txt, CPM_table.txt


title: BOW3210A32

description: Count_table.txt, CPM_table.txt


title: BOW3210A33

description: Count_table.txt, CPM_table.txt


title: BOW3210A29

description: Count_table.txt, CPM_table.txt


title: 4189_BD_c_nucleus_CTTGTA

description: Sample 8


title: BOW3210A3

description: Count_table.txt, CPM_table.txt


title: BOW3210A28

description: Count_table.txt, CPM_table.txt


title: BOW3210A30

description: Count_table.txt, CPM_table.txt


title: BOW3210A26

description: Count_table.txt, CPM_table.txt


title: BOW3210A25

description: Count_table.txt, CPM_table.txt


title: BOW3210A24

description: Count_table.txt, CPM_table.txt


title: BOW3210A20

description: Count_table.txt, CPM_table.txt


title: BOW3210A22

description: Count_table.txt, CPM_table.txt


title: BOW3210A21

description: Count_table.txt, CPM_table.txt


title: BOW3210A23

description: Count_table.txt, CPM_table.txt


title: BOW3210A2

description: Count_table.txt, CPM_table.txt


title: BOW3210A19

description: Count_table.txt, CPM_table.txt


title: 3003_BD_c_nucleus_ACAGTG

description: Sample 5


title: BOW3210A17

description: Count_table.txt, CPM_table.txt


title: IL-4 rep#2

city: New Haven

first: Lidia

last: Bosurgi

state: Connecticut

address: 300 Cedar street

department: Immunobiology

institute: Yale University

description: Sample 102

data_processing:
The raw reads of RNA-seq experiments were trimmed off sequencing adaptors and low quality regions by btrim
The trimmed reads were mapped to mouse genome (GRCm38) by tophat2
After the counts were collected, the differential expression analysis was done by DEseq2, which calculated the adjusted p-values
Additional analysis: Genes induced in BMDMs at least 1.1-fold by aN, IL-4, or aN+IL-4 compared to BMDMs left untreated were selected
Additional analysis: Among these induced genes, genes which were induced at least 1.25-fold by the combination of aN+IL-4 compared to both aN alone and IL-4 alone were selected
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file includes normalized counts for each Sample

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow cells from C57BL/6 mice were isolated and propagated for 7 days in RPMI containing 20% FCS, 30% L929 conditioned media and 1% Pen/Strep (growth media).

extract_protocol:
BMDMs were lysed using QIAshredder Mini Spin Column (Qiagen, #79656) and RNA was extracted using RNeasy Mini Kit (Qiagen, #74106) following the manufacturer's instruction.
mRNA was purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library was then end-repaired, and A-tailed, adapters were ligated and second-strand digestion was performed by Uricil-DNA-Glycosylase. Indexed libraries that met appropriate cut-offs for both were quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul were used for sequencing.

tag: strain

value: Bone marrow-derived macrophages

value: 8 weeks

value: cultured for 24 hours in growth media containing 10 ng/ml of IL-4


title: aN+IL-4 rep#2

description: Sample 103

value: co-cultured with apoptotic neutrophils for 30 min, washed extensively with PBS and cultured for additional 24 hours in growth media containing 10 ng/ml of IL-4


title: PB-ID2

city: Hefei

first: Mengmeng

last: Guo

address: Anhui University No.111 Jiulong Road  Hefei City Anhui Prov China

country: China

institute: Anhui University

data_processing:
Illumina Hiseq3000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using STAR software
Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by  DESeq
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include the expression values of this transcript  for each Sample

source_name: PB-ID2-transfected 46C mouse embryonic stem cells

growth_protocol: ESCs were routinely maintained on gelatin-coated plates in the conventional mouse ESC medium

extract_protocol:
RNA was harvested using Trizol reagent.TruSeq® RNA LT Sample Prep Kit v2  was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 46C embryonic stem cells

value: Inner cell mass of pre-implantation embryo

tag: genotype/variation


title: Unt. Rep#2

description: Sample 101

value: cultured for 24 hours in growth media


title: BOW3210A16

description: Count_table.txt, CPM_table.txt


title: PB

source_name: PB-transfected 46C mouse embryonic stem cells

value: control


title: BOW3210A15

description: Count_table.txt, CPM_table.txt


title: GmRootHair3

description: processed data file: GmRootHair.xlsx

organism: Glycine max

value: Williams 82

tag: reference annotation

value: Ensembl Release 19, v1

value: 4-5 days after plating


title: aN+IL-4 rep#1

description: Sample 4


title: GmRootHair2

description: processed data file: GmRootHair.xlsx

tag: variety


title: BOW3210A14

description: Count_table.txt, CPM_table.txt


title: aN rep#1

description: Sample 3

tag: age

value: co-cultured with apoptotic neutrophils for 30 min, washed extensively with PBS and cultured for additional 24 hours in growth media


title: BOW3210A27

description: Count_table.txt, CPM_table.txt

tag: cell type

value: Human immortalised myelogenous leukemia line


title: Unt. rep#1

description: Sample 1


title: GmRootHair1

description: processed data file: GmRootHair.xlsx


title: IL-4 rep#1

description: Sample 2


title: BOW3210A11

description: Count_table.txt, CPM_table.txt

tag: passages

value: 20-22 hours


title: BOW3210A13

description: Count_table.txt, CPM_table.txt

tag: cell line


title: CsRootHair3

description: processed data file: CsRootHair.xlsx

organism: Cucumis sativus

tag: cultivar

value: Phytozome Cs122


title: BOW3210A12

description: Count_table.txt, CPM_table.txt

tag: treatment

value: treated (3 hour with 10 mM benzene)


title: Axl-/-Mertk-/- CD45+CD11chiSiglecF+CD11blo Macrophages 7 d.p.i. with N. brasiliensis

description: Sample 8

data_processing:
The raw reads of RNA-seq experiments were trimmed off sequencing adaptors and low quality regions by btrim
The trimmed reads were mapped to mouse genome (GRCm38) by tophat2
After the counts were collected, the differential expression analysis was done by DEseq2, which calculated the adjusted p-values
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file includes normalized counts for each sample

source_name: Lung

extract_protocol:
Cell-sorted lung macrophages were lysed using QIAshredder Mini Spin Column (Qiagen, #79656) and RNA was extracted using RNeasy Mini Kit (Qiagen, #74106) following the manufacturer's instructions.
mRNA was purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library was then end-repaired, and A-tailed, adapters were ligated and second-strand digestion was performed by Uracil-DNA-Glycosylase. Indexed libraries that met appropriate cut-offs for both were quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul were used for sequencing.

treatment_protocol: WT and Axl-/-Mertk-/- mice were individually inoculated subcutaneously with 625 viable third-stage N. brasiliensis larvae. Animals were sacrificed 7 days post infection, and leukocytes from the lung were isolated. FACS sorting of lung macrophages CD45+CD11chiSiglecF+CD11blo was performed.

value: Axl-/-Mertk-/-

tag: infection

value: N. brasiliensis

value: lung resident macrophages


title: BOW3210A1

description: Count_table.txt, CPM_table.txt

value: untreated


title: BOW3210A18

description: Count_table.txt, CPM_table.txt


title: CsRootHair2

description: processed data file: CsRootHair.xlsx


title: CsRootHair1

description: processed data file: CsRootHair.xlsx


title: WT CD45+CD11chiSiglecF+CD11blo Macrophages 7 d.p.i. with N.brasiliensis

description: Sample 6

value: WT

value: 8 weeks


title: OsWT_EXPA30GFP3

description: processed data file: OsWTEXPA30GFP_FPKM.xslx (10020)

data_processing:
Illumina Casava1.7.0 was used for basecalling of Sample 8955 and Casava 1.8.2 was used for all the other samples.
The first 15bp of each read were trimmed.
Reads were mapped using Tophat v2.0.3 for Arabidopsis samples and Tophat v2.0.9 for rice samples. Default settings with --segment length 17 parameter were used to map the reads to the reference annotation (already mentioned in the sample information above).
FPKM values were calculated by Cufflinks2 v2.1.1 with multiread correction (-u -G).
Raw reads were counted by HTSeq v0.6.1 with setting -m intersection-strict -s no -f bam and analyzed by edgeR to identify the differentially expressed genes between Atrhd6_WERGFP and AtWT_WERGFP. For the DE analysis, first, low expressed genes were filtered (counts per million > 1 for at least three out of total six samples were kept). Second, raw counts were normalized using the default timmed mean of M-values and the variation was modeled using a tag-wise dispersion. Last, the raw P values were corrected for multiple testing by Benjamini-Hochberg method and a FDR q-value <= 0.01 and fold-change >=2 was used to find the significantly differentially expressed genes.
Genome_build: See sample information above.
Supplementary_files_format_and_content: Excel file that contains the normalized cpm and DE result for the analysis between Atrhd6_WERGFP and AtWT_WERGFP. Excel files that contain the FPKM value generated by Cufflinks for the gene expression profiling of the AtWT_COLB9GFP and the OsWT_EXPA30GFP.

organism: Oryza sativa

extract_protocol:
RNA was extracted using Qiagen RNAeasy Plant Micro Kit.
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols

treatment_protocol: Root tips of seedlings plated 4-5 days were pooled and digested using cell wall degrading enzymes. Fluorescence-activated cell sorting was used to specifically collect the cells that expressed GFP.

value: Japonica

value: Ensembl Release 19, MSU6


title: OsWT_EXPA30GFP1

description: processed data file: OsWTEXPA30GFP_FPKM.xslx (9487)


title: OsWT_EXPA30GFP2

description: processed data file: OsWTEXPA30GFP_FPKM.xslx (9523)


title: Q111 DOP rep3

city: Cambridge

first: Brook

last: Wassie

state: MA

address: 77 Massachusetts Ave.

institute: Massachusetts Institute of Technology

description:
Q111SST_vs_Q111DOP_DEGs_with_fpkm.diff
Q7SST_vs_Q111DOP_DEGs_with_fpkm.diff

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads for each sample were aligned to mm9 genome using TopHat (v2.0.10) with parameters  -p 8 -G genes.gtf --b2-very-sensitive --library-type fr-firststrand -r 80
Differential gene expression was performed using CuffDiff (version 2.1.1) for Q7 SST replicates against Q111 DOP replicates, Q7 SST replicates against Q111 SST replicates, and Q111 SST replicates against Q111 DOP replicates with paramters -p 8 --library-type fr-firststrand
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files containing genes (official gene symbol) with mean FPKM values for each condition (Q7 SST, Q111 SST, or Q111 DOP), log2 fold change against other conditions (specified in file name), p values, and q values for significance of change in expression

molecule: polyA RNA

source_name: Striatal Progenitor Cells

growth_protocol: Cells were maintained at permissive temperature (33°C) in a humidified incubator with 5% CO2 and cultured in Dulbecco’s modified Eagle’s medium (DMEM, Corning, 10-013), supplemented with 10% fetal bovine serum (FBS, Gemini Bio-Products, 100-106), 1% penicillin/streptomycin (Gemini Bio-Products, 400-109) and 400 μg/ml G418 (Gemini Bio-Products, 400-113)

extract_protocol:
Cells were washed three times with ice-cold DPBS, scraped on ice and centrifuged. The pellets were flash-frozen with liquid nitrogen and stored at -80°C until needed.  RNA from striatal cell lines was extracted with the RNA/DNA/Protein Purification Kit (Norgen Biotek Corp., 23500), treated with DNase I and quantified with Nanodrop 2000 (Thermo Scientific). RNA quality and integrity were evaluated using the Fragment Analyzer™ (Advanced Analytical). All samples had an RNA Quality Number (RQN) higher than 9.8. 1 µg of total RNA was used for library preparation.
Libraries were generated using the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101), according to the manufacturer’s instructions.

treatment_protocol: For cell treatment experiments, the medium was removed 24 h after seeding and cells were washed once with Dulbecco's Phosphate-Buffered Saline (DPBS) solution. Serum-free medium containing either vehicle (DPBS) or 4mM 4-deoxypyridoxine hydrochloride (DOP - Sigma Aldrich, D0501) was subsequently added for 24 h

tag: genotype

value: mutant (STHdhQ111/Q111)

value: 4mM 4-deoxypyridoxine hydrochloride in serum-free medium


title: Sample 3 16-month

city: Worcester

first: Filiz

last: Korkmaz

address: 364 Plantation St.

institute: UMass Chan Medical School

description: old

library_source: genomic

data_processing:
Illumina Casava software was used for basecalling.
A propriety pipeline by Zymo Research Inc. was used for bioinformatic analysis which assesses quality with FastQC (v0.11.1) and TrimGalore (v0.3.7) Illumina adaptors and bases with a Phred score less than 20 were trimmed along with the first 2 bases from the 3’ end of the sequence to avoid the final filled in cytosine being used to make a methylation call.
Alignment and methylation calling were performed with the Babraham Bismark software (v0.13.1). Bismark is designed for aligning bisulfite sequencing data while simultaneously making methylation calls. The result of bisulfite sequencing is four sets of potential sequences at any given locus. To determine which of these four potential sequences is correct, Bismark creates two bisulfite converted reference genomes, one that is a C to T conversion and one that is a G to A conversion to account for conversion on the reverse strand. Each sequence read is also bisulfite converted in silico and is aligned to the pre-converted version of the reference genome. The best alignment is then identified and used to make a methylation call. Alignments that are uniquely mapped were kept for analysis. Alignments that mapped to multiple regions were discarded.
Genome_build: BosTau8
Supplementary_files_format_and_content: bigbed
Supplementary_files_format_and_content: CpG_result_table.txt: text, all results coverage >5X
Supplementary_files_format_and_content: CpG_p_less_than_0.05.csv: Excel, all significant results, P<0.05, >5X coverage

molecule: genomic DNA

organism: Bos taurus

source_name: dermal fibroblast cells

growth_protocol: Primary dermal fibroblasts were revived from cryo-preservation simultaneously and cultured in DMEM, 1X ITS, 1X Pen/Strep antibiotic, 5% FBS into a T-75 until confluency

extract_protocol:
Genomic DNA was extracted from cell lysate using 5 Prime PerfectPure DNA Kit per manufacturer's instructions.
Libraries were generated at Zymo Research with 2 ug of genomic DNA. Briefly, DNA was treated with MSPI, end-repaired, A-tailed and purified with Zymo's DNA clean and concentrator kit. Illumina adaptors were added per Illumina protocols. DNA was then bisulfite converted, PCR amplified and purified. Size selection was performed with a 4% NuSieve 3:1 agarose gel and libraries extracted with the Zymoclean Gel DNA Recovery Kit.  DNA libraries were sequenced on the Illumina HiSeq2000 generating 50 bp paired end reads.

treatment_protocol: No treatment

value: primary dermal fibroblasts

tag: passage

tag: breed

value: Holstein


title: Sample 2 16-month

description: old


title: Q111 DOP rep2


title: Sample 1 16-month

description: old


title: Sample 4 16-month

description: old


title: Q111 DOP rep1


title: Q111 SST rep3

description:
Q111SST_vs_Q111DOP_DEGs_with_fpkm.diff
Q7SST_vs_Q111SST_DEGs_with_fpkm.diff

value: serum starvation


title: Sample 5 5-month

description: young


title: Sample 4 5-month

description: young


title: Sample 6 5-month

description: young


title: Q7 SST rep3

description:
Q7SST_vs_Q111SST_DEGs_with_fpkm.diff
Q7SST_vs_Q111DOP_DEGs_with_fpkm.diff

value: wild type (STHdhQ7/Q7)


title: Q111 SST rep2


title: BOW3210A10

description: Count_table.txt, CPM_table.txt

value: Human immortalised myelogenous leukemia line

value: 20-22 hours


title: Sample 1 5-month

description: young


title: Q111 SST rep1


title: Sample 2 5-month

description: young


title: SlRootHair3

description: processed data file: SlRootHair.xlsx

organism: Solanum lycopersicum

value: Heinz 1706

value: Ensembl Release 19, SL2.4

value: 4-5 days after plating


title: Q7 SST rep1


title: ZmRootHair3

description: processed data file: ZmRootHair.xlsx

organism: Zea mays

value: Ensembl Release 19, AGPv3


title: Sample 3 5-month

description: young


title: Sample 5 16-month

description: old


title: Q111 DOP rep2 ChIP-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome using BWA v 0.7.10 with the option --samse
SAM files were merged and converted to BED. Peak calling was performed on BED files using GPS (version 2.6) and mm9 genome using the following paramters: -f BED --k_min 6 --k_max 13
Genome_build: mm9
Supplementary_files_format_and_content: bed files generated from peak calling with GPS. Each row contains chromosome number, start and end coordinates, peak identifier (chromosome number and peak summit), and an integer score used for visualization of peak in genome track browsers

extract_protocol:
Cells were washed once with 1X DPBS and then cross-linked. The cross-linked material was then rinsed, pelleted, and frozen in liquid nitrogen for later use. Frozen cell pellets were resuspended in lysis buffer and sonicated to shear DNA. Sheared DNA was immunopercipitated with anti-Histone H3 (acetyl K9) antibody. A negative control ChIP reaction was performed using normal rabbit IgG. The immunopercipitate was washed on protein G beads and reverse crosslinked with Proteinase K at 62 o C for 4 hours.
Libraries were prepared with NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB) according to manufacturer instructions.

tag: chip-antibody

value: H3K9ac (Abcam, ab4441)


title: Q111 IgG

value: Normal rabbit IgG (Santa Cruz Biotechnology, sc-2027)


title: Q111 DOP rep1 ChIP-seq


title: ZmRootHair2

description: processed data file: ZmRootHair.xlsx


title: SlRootHair1

description: processed data file: SlRootHair.xlsx


title: SlRootHair2

description: processed data file: SlRootHair.xlsx


title: Sample 6 16-month

description: old


title: ZmRootHair1

description: processed data file: ZmRootHair.xlsx


title: Q111 SST rep2 ChIP-seq


title: DLBB14-09

city: Johns Island

first: Jeanine

last: Morey

state: SC

address: 3419 Maybank Hwy, Ste B

department: Conservation Medicine

institute: National Marine Mammal Foundation

data_processing:
The Illumina BCL output files were converted to fastq-sanger file format and sequence quality triming was performed using Trimmomatic on iPlant Collaborative's Discovery Environment using the High-Performance Computing applications.  The following Trimmomatic parameters were used: ILLUMINACLIP:TruSeq3-SE.fa 2:30:10; LEADING:10; TRAILING:10; SLIDINGWINDOW:4:20; HEADCROP:6; MINLEN:36.
The read files from one male (DLBB13-02) and one female (DLBB13-07) animal were concatenated into a single fastq file for assembly in Trinity v2.0.4 using a minimum K-mer coverage of 3, a minimum overlap value of 25 and a minimum contig length of 400 nucleotides on the CyVerse Atmosphere cloud computing platform.
Annotation of the de novo assembly was obtained by BLASTx searches of the human subset of the uniprot_swissprot database augmented with conserved domian mapping and gene ontology assignment using Blast2GO.
Reads were mapped to the de novo Trinity assembly, using RSEM v 1.2.21 with bowtie2 as the alignment engine and read counts were generated as TPM (transcripts per million) at the gene level on the CyVerse Atmosphere cloud computing platform.
Supplementary_files_format_and_content: Processed data is supplied in a single file.  The first column "Gene ID" contains the gene ID from the de novo Trinity assembly.  The second column "Accession Number" contains the accession number of the top hit from BLASTx searches of the human subset of the UniProt-SwissProt database.  The third column "Entrez Gene ID" contains the Entrez Gene ID, if assigned, following BLASTx searches and Blast2GO annotation. The remaining columns contain the TPM values for each sample as generated by RSEM.  A TPM > 0 in at least half the samples and an average TPM ≥ 1 across all samples was required for all further data analysis.  Only genes meeting these requirements are included in the processed data table.

organism: Delphinapterus leucas

source_name: blood

extract_protocol:
Whole blood RNA was extracted using a PAXgene Blood RNA kit (Qiagen).
Libraries were constructed using a NEBNext ultra Directional RNA Library Prep kit for Illumina and indexed with the NEBNextMultiplex Oligos for Illumina

tag: date

tag: Sex

value: Female

tag: latitude

tag: longitude


title: FCS 5d 4

city: South San Francisco

first: Christopher

middle: John

last: Bohlen

state: CA

address: Room 15-2006, Genentech Building 15

institute: Genentech

data_processing:
Sequencing reads were mapped to the UCSC rat reference genome rn6 using HISAT version 2.0.3 via the Galaxy platform (http://usegalaxy.org), resulting in concordant pair alignment rates of >75% for each sample. Transcript FPKM (fragments per kilobase of transcript sequence per million mapped fragments) scores were obtained using Cufflinks version 2.2.1 with the iGenomes rn6 gtf file as a reference annotation.
Genome_build: rn6
Supplementary_files_format_and_content: processed_FPKM.xlsx contains a table with Cufflinks-output FPKM values for each sample after mappind to the iGenomes rn6 annotation gtf file

organism: Rattus norvegicus

source_name: P21 rat microglia_FCS 5d

growth_protocol: Rat cell isolation: All procedures involving rodents conformed to Stanford University guidelines, which comply to national and state laws and policies. Sprague-Dawley rats were obtained from Charles River. Animals less than fourteen days old were euthanized with a lethal dose of ketamine/xylazine (100 mL of 24 mg/mL ketamine, 2.4 mg/mL xylazine); older animals were euthanized by carbon dioxide asphyxiation. Animal unresponsiveness to toe pinch was confirmed before transcardial perfusion with ice-cold dPBS containing 50 mg/mL heparin (Sigma). Immediately after perfusion, brains were rapidly isolated and placed into ice-cold dPBS. Cerebella and spinal cords were discarded and the remaining brains were chopped to ~1 mm3 with a scalpel blade and transferred to an ice-cold dounce homogenizer (Wheaton #357424) with ice-cold dPBS containing 100 mL of 0.4% DNaseI (Worthington) per 50 mL of dPBS. Tissue chunks were subjected to three successive rounds of 3 to 10 gentle strokes of the homogenizer piston and centrifuged. For animals less than 12 days old, tissue was centrifuged at 300g for 7 minutes at 4°C. For animals greater than 12 days old, Percoll was added during centrifugation to separate myelin from cells. The cell suspension volume was adjusted to 33.4 mL and 10 mL of 100% isotonic Percoll (9 mL Percoll PLUS from GE Healthcare, 1 mL 10x dPBS, 9 mL 1 M CaCl2, 5 mL 1 M MgCl2) was added and thoroughly mixed (23% isotonic Percoll final). Suspensions were centrifuged (15 min, 500g, 4°C) and the supernatant and top layer of myelin were discarded. Cell pellets were resuspended in 15 mL of dPBS containing 2 mg/mL peptone from milk solids (Sigma), passed through a 40 mm cell strainer (BD Biosciences), and applied directly to positive-selection immunopanning dishes coated with mouse anti-rat CD11b monoclonal antibodies (OX42 clone, MCA275R from Bio-Rad). Immunopanning dishes were prepared the day before as follows. First, a sterile petri dish was incubated in a solution of 50 mM Tris adjusted to pH 9.5 with HCl that contained 6 mg/mL goat-anti-mouse IgG secondary antibody (Jackson ImmunoResearch) at 37°C for 1-2 hours. Dishes were rinsed three times with dPBS and transferred to a solution of dPBS containing 1 mg/mL OX42 antibody (Bio-Rad) and 2 mg/mL of peptone from milk solids as a blocking agent. Dishes were coated overnight at room temperature and rinsed three times with dPBS immediately before addition of cell suspensions for immunopanning. Cell suspensions were allowed to interact with the immunopanning dish for 20 min at room temperature. Unbound cells and debris were removed by washing the dish with dPBS ten consecutive times. For freshly isolated cell lysates used in RNAseq and QPCR experiments, cells were lysed directly from the panning dish in RLT buffer. Otherwise, immunopanned cells were trypsinized (12 min at 37°C) in 12 mL dPBS without calcium and magnesium containing 200 mL of a 30,000 units/mL stock solution of trypsin (#T9935, Sigma). Microglia were still strongly adherent, and so the trypsin solution was discarded and replaced with MGM unless otherwise noted. Panning dishes were placed on ice for one minute to weaken cell interaction with the surface, and the cells were recovered by repeated pipetting. Recovered cells were centrifuged (300g, 7 min, room temperature) and gently resuspended in 500 mL of MGM. For experiments testing gene expression changes after two hours, cells were resuspended in alternative medium instead. Rat microglia culture: Base microglial growth medium (MGM) was sterile-filtered and stored at 4°C for up to one month and was comprised of: DMEM/F12 containing 100 units/mL penicillin, 100 mg/mL streptomycin, 2mM glutamine, 5 mg/ml N-acetyl cysteine, 5 mg/ml insulin, 100 mg/mL apo-transferrin, and 100 ng/mL sodium selenite, all from Gibco or Sigma. ACM, 10% heat-inactivated fetal calf serum (FCS), growth factors, or drugs were added after filtering. For preparation of cholesterol-containing medium, MGM and a 1.5 mg/mL ethanolic stock solution of cholesterol were warmed to 37°C and an appropriate volume of cholesterol stock was added and rapidly mixed to avoid precipitation. For experiments involving methyl-b-cyclodextrin (MbC), MbC (Sigma) was dissolved to 5 mM in MGM and passed through a 20 mm syringe filter before addition of other factors. For cholesterol-saturated MbC, 1 mg of cholesterol powder was added to 10 mL of 5 mM MbC in MGM and the mixture was incubated at 37°C for one hour before being passed through a 20 mm syringe filter and addition of other factors. TIC medium was comprised of MGM containing human TGF-b2 (2 ng/mL, 100-35B, Peprotech), murine IL-34 (100 ng/mL, 5195-ML/CF, R&D Systems), and ovine wool cholesterol (1.5 mg/mL, 700000P, Avanti Polar Lipids) unless otherwise noted. Microglia isolated from animals older than 12 days old, heparan sulfate (1 mg/mL, Galen Laboratory Supplies) was included to maximize cell adhesion and process extension. Cells were plated either directly onto tissue culture plastic for animals less than 12 days old, or onto plastic coated for 1 hour at 37°C with collagen IV (2 mg/mL, Corning) for animals over 12 days old and aspirated off immediately before plating cells. Different coatings (poly-D-lysine, poly-L-ornithine, laminin, matrigel, or collagen VI) had minimal impact on the findings described, although the most extensive ramification of cells was observed with collagen IV or laminin coating and inclusion of heparan sulfate in the culture medium. For microglia cultures from P21 rats, monounsaturated fatty acids (0.1 mg/mL oleic acid, 0.001 mg/mL gondoic acid) were included in the growth medium unless otherwise stated.Cells were plated at various densities depending on the experiment. For survival or immunohistochemical assays, cells were cultured at low density to minimize the influence of neighboring cells. 3,500 cells were pre-plated in 24-well plates in 10 mL, cells were allowed 10 minutes at room temperature to lightly adhere to the plate, and 500 mL of culture medium was gently added to each well before transfer to the incubator. For phagocytosis assays, 10,000 cells were added per 96-well well or 3,500 cells were added per 384-well well. Cells were briefly centrifuged (30 s, 100g, room temperature) to promote adhesion and plates were transferred to the incubator. For gene expression analysis, 20,000 to 40,000 cells were seeded in 24-well plates and allowed to settle for 10 minutes at room temperature before transfer to the incubator. Cells were grown in a humidified incubator held at 37°C and 10% CO2. 50% medium changes were performed every 2 to 3 days.

extract_protocol:
RNA was isolated using the RNeasy Micro Kit (Qiagen) with on-column DNase treatment.
For each replicate, 10 ng of total RNA (RIN > 9.7) was used to prepare a poly-A enriched cDNA library using the SmartSeq2 protocol. Libraries were modified for sequencing using the Nextera XT DNA Sample Preparation Kit (Illumina) with 150 pg of cDNA as input material. Libraries were sequenced using an Illumina MiSeq to obtain 75 bp paired-end reads. Data were collected in two batches of library preparation and sequencing, with samples from each experimental condition included in each batch.

treatment_protocol: 10% fetal calf serum was added to FCS  wells and mixed rapidly 1, 3, or 5 days prior to harvesting RNA.

tag: strain

value: Sprague-Dawley

value: P21 brain CD11b-immunopanned microglia

tag: time in culture

value: 8 days

tag: serum exposure

value: 10% fetal calf serum for the last 5 days in culture


title: Q7 SST rep2


title: DLBB14-07

value: Male


title: DLBB14-10


title: FCS 5d 3

tag: cell type


title: DLBB14-08


title: FCS 5d 1


title: Msx1-/- upper molar

city: Salt Lake City

first: Shihai

last: Jia

state: ut

address: 20 South 2030 East, Room 320 BPRB

department: Department of Neurobiology

institute: University of Utah

description: run0161_lane8_index702=Msx1MTupperE14~mouse

data_processing:
Illumina offline basecaller v1.9.0.
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.7
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.Implanted in tophat 1.4.1 using parameters:tophat -G mm9.gtf -o tophat -p 4 -r 0 mm9 reads.fastq. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: molar mesenchyme

extract_protocol: E14 mouse embryo heads were frozen in OCT in liquid nitrogen, micro-dissect the molar mesenchyme by LCM after frozen section. Micro-dissected tissues were frozen at -80℃, total RNA was extracted by using RNeasy micro kit from Qiagen.cDNA was made by the NuGEN Ovation RNA-Seq v2 Assay.

value: mixed background

tag: genotype/variation

value: mutant Msx1-/-

tag: age

value: embryonic day 14

tag: tissue

value: maxillary (upper) molar

tag: tissue subtype

value: molar mesechyme


title: Msx1-/- lower molar

description: run0161_lane8_index703=Msx1MTlowerE14~mouse

value: mandibular(lower) molar


title: DLBB14-06


title: FCS 3d 3

source_name: P21 rat microglia_FCS 3d

value: 10% fetal calf serum for the last 3 days in culture


title: Msx1+/- lower molar

description: run0161_lane8_index701=Msx1WTlowerE14~mouse

value: Control Msx1+/-


title: FCS 5d 2


title: DLBB14-01


title: Msx1+/- upper molar

description: run0161_lane8_index712=Msx1WTupperE14~mouse


title: FCS 3d 2


title: DLBB13-10


title: DLBB13-09


title: DLBB14-03


title: Q111 SST rep1 ChIP-seq

value: mutant (STHdhQ111/Q111)

tag: treatment

value: serum starvation


title: FCS 3d 1


title: FCS 1d 4

source_name: P21 rat microglia_FCS 1d

value: 10% fetal calf serum for the last 1 day in culture


title: FCS 1d 5


title: DLBB13-08


title: FCS 1d 2


title: DLBB14-05


title: DLBB13-07

value: Female


title: FCS 1d 1

value: Sprague-Dawley


title: FCS 1d 3

value: P21 brain CD11b-immunopanned microglia


title: FCS 3d 4

value: 8 days


title: DLBB13-03


title: DLBB13-02


title: TIC 5

source_name: P21 rat microglia_TIC


title: DLBB13-01


title: TIC 6


title: TIC 4


title: DLBB12-09


title: TIC 3


title: DLBB12-06


title: DLBB12-04


title: DLBB12-05


title: TIC 2


title: Acute 3

source_name: P21 rat microglia_Acute

value: 0 hr


title: DLBB12-01

value: Male


title: OsRootHair2

description: processed data file: OsRootHair.xlsx

source_name: root hair

tag: variety

value: Japonica

tag: reference annotation

value: Ensembl Plant Release 19, MSU6

value: 4-5 days after plating


title: DLBB13-04


title: OsRootHair1

description: processed data file: OsRootHair.xlsx


title: TIC 1


title: DLBB12-07


title: PB

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

data_processing:
Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from BGI company. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library of BGI.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: HES2 human embryonic stem cells

extract_protocol:
Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. BGISEQ-500 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryo

tag: expression

value: PB


title: ChIP-Seq_Pol-II_ET_NegativeControl

status: Public on May 10 2017

city: Riverside

first: Xueqing

middle: Maggie

last: Lu

address: 3401 Watkins Drive, Genomics, Room 2126

institute: University of California, Riverside

description:
ET_NegativeControl_cell400_GGCTAC
ChIP-Seq data measuring background noise for parasite at early trophozoite stage. Negative control sample correponding to ChIP-Seq_Pol-II_ET sample using ChIP-Seq protocol with no Pol II antibody
Processed data file(s):
ChIPSeq_GeneExpressionProfile.xlsx

data_processing:
For both GRO-Seq and ChIP-Seq datasets, the first ten bases and the last base or last 20 bases were systematically trimmed from 50 bp and 75 bp reads using FASTX-Toolkit. Poly A/T and adaptor comtaiminated reads were removed. Reads containing bases with a quality score below 25 and Ns, reads that were unpaired, and reads shorter than 18 bases were also filtered using Sickle. High quality single reads that lost their mate pair during read processing were kept and mapped as single-end reads in parallel with paired-end reads.High quality single reads that lost their mate pair during read processing were kept and mapped as single-end reads in parallel with paired-end reads. reads that mapped to multiple locations in the genome, reads that were PCR duplicates, pair-end reads that were not properly paired, and reads that mapped to ribosomal RNA or transfer RNA were discarded from the final working reads. High quality single-end reads were combined with pair-end reads by merging mapped bam files.
For each stage, bam files from mapped reads for both high quality single-ended mapping and paired-end mapping were combined. In addition, bam files from each biological replicate were merged using Samtools. Genome-wide coverage profiles were generated using BEDtools.
For GRO-Seq data sets, genome-wide coverage profiles were normlaized to the amount of RNA yield per parasite by dividing the gene counts by a stage-specific scaling factor as described in the original manualscript. For ChIP-Seq data set, coverage profiles were normalized per million number of reads for each library, and then signals obtained from the negative controls were subtracted from the ChIP-Seq sample of the same stage. ChIP-Seq input data was normalized per million number of reads only.
Genome_build: PlasmoDB_v13
Supplementary_files_format_and_content: GROSeq_GeneExpressionProfile.xlsx (Gene Expression Counts for GRO-Seq dataset)
Supplementary_files_format_and_content: ChIPSeq_GeneExpressionProfile.xlsx (Gene Expression Counts for ChIP-Seq dataset)
Supplementary_files_format_and_content: .bed files report normalized genome wide coverage profiles

organism: Plasmodium falciparum

source_name: Erythrocytic stage

growth_protocol: P. falciparum strain 3D7 was maintained in human O+ erythrocytes in 5% haematocrit according to a previously described protocol (Trager et al., Science 1976). Gametocyte stage parasite were obtained from P. falciparum strain NF54 as described in protocol (Ifediba et al., Nature 1981)

extract_protocol:
Nuclear RNA was purified sing Trizol LS Reagent (Life Technologies). Base hydrolysis was performed as described in (Core at el., Science, 2008). Finally, nascent RNA was purified using Click-iT Nascent RNA Capture Kit (Thermo Fisher) according to the manufacturer’s instructions.
Libraries were prepared using the KAPA Biosystems Library Preparation Kit (KAPA Biosystems, Woburn, MA) according to the manufacturer’s instructions with the following modifications for the high AT-content of the P. falciparum genome: the libraries were amplified for 15 PCR cycles (45s at 98°C followed by 15 cycles of [15s at 98°C, 30s at 55°C, 30s at 62°C], 5 min 62°C). Libraries were sequenced on the Illumina HiSeq2500 (Illumina, San Diego, CA) generating 50 bp paired-end sequence reads or the NextSeq500 generating 75 bp paired-end sequence reads.

treatment_protocol: For GRO-Seq data set, nuclear isolation was performed as described in (Bunnik at el., Genome Biology, 2014), and nuclei (100 μl) were incubated with 600 μl of nuclear run-on reaction buffer (10 mM Tris-Cl pH 8.0, 5 mM MgCl2 , 1 mM DTT, 300 mM KCl, and 200 units of SUPERaseIn, 1% sarkosyl, 4 mM ATP, 1 mM CTP, 1 mM GTP, 200 mM Ethylene uridine (EU) (Click-it Nascent RNA Capture Kit, Thermo Fisher), 400 mM creatine phosphate, and 0.2 mg/mL creatine kinases) adopted and modified from {Core, 2008 #81;Sims, 2009 #354}. Reaction mixtures were incubated for 30 min at 37°C followed by nuclear RNA isolation. Experimental noise was measured by performing the nuclear run-on reaction in the presence of unmodified uridine (Negative control samples).  For ChIP-Seq data set, synchronized parasite cultures were collected and subsequently lysed by incubating in 0.15% saponin for 10 min on ice. Parasites were centrifuged at 3,234 x g for 10 min at 4°C, and washed three times with PBS. For each wash, parasites were resuspended in cold PBS and centrifuged for 10 min at 3,234 x g at 4°C. Subsequently, parasites were crosslinked for 10 min with 1% formaldehyde in PBS at 37°C. Glycine was added to a final concentration of 0.125 M to quench the crosslinking reaction, and incubated for 5 min at 37°C. Parasites were centrifuged for 5 min at 2,500 x g at 4°C, washed twice with cold PBS and stored at -80°C. For chromatin immunoprecipitation, parasites were first incubated on ice in nuclear extraction buffer (10 mM HEPES, 10 mM KCl, 0.1 mM EDTA, 0.1 mM EGTA, 1 mM DTT, 0.5 mM 4-(2-aminoethyl)benzenesulfonyl fluoride hydrochloride (AEBSF), EDTA-free protease inhibitor cocktail (Roche) and phosphatase inhibitor cocktail (Roche)). After 30 min, Igepal CA-360 (Sigma-Aldrich) was added to a final concentration of 0.25% and the parasites were lysed by passing the suspension through a 26 G ½ inch needle seven times. Parasite nuclei were centrifuged at 4°C for 20 min at 2,500 x g. Parasite nuclei were resuspended in shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris HCl pH 7.5, EDTA-free protease inhibitor cocktail, and phosphatase inhibitor cocktail). Chromatin was fragmented using the Covaris Ultra Sonicator (S220) for 10 min with the following settings; 5% duty cycle, 140 intensity peak incident power, 200 cycles per burst). To remove insoluble material, samples were centrifuged for 10 min at 17,000 x g at 4°C.Fragmented chromatin was diluted 1:1 in ChIP dilution buffer (30 mM Tris-HCl pH 8, 3 mM EDTA, 0.1% SDS, 300 mM NaCl, 1.8% Triton X-100, EDTA-free protease inhibitor cocktail and phosphatase inhibitor cocktail). Samples were precleared with Protein A Agarose beads to reduce non-specific background and incubated overnight at 4°C with 2 μg of anti-RNA pol II antibody (ab5095, Abcam). A sample with no antibody was also incubated overnight at 4°C to be used as the negative control. Antibody-protein complexes were recovered using Protein A Agarose beads, followed by extensive washes with low salt immune complex wash buffer, high salt immune complex was buffer, LiCl immune complex wash buffer and TE buffer. Chromatin was eluted from the beads by incubating twice with freshly prepared elution buffer (1% SDS, 0.1 M NaHCO3) for 15 min at RT. Samples were reverse crosslinked overnight at 45°C by adding NaCl to a final concentration of 0.5 M. RNase A (Life Technologies) was added to the samples and incubated for 30 min at 37°C followed by a 2 h incubation at 45°C with the addition of EDTA (final concentration 8 mM), Tris-HCl pH 7 (final concentration 33 mM) and proteinase K (final concentration 66 μg/mL; New England Biolabs). DNA was extracted by phenol:chloroform:isoamylalcohol and ethanol precipitation. Extracted DNA was purified using 1.8X Agencourt AMPure XP Beads (Beckman Coulter).

tag: Stage

value: Early Trophozoite


title: Acute 2


title: ChIP-Seq_Pol-II_LS_NegativeControl

description:
LS_NegativeControl_cell430_ACAGTG
ChIP-Seq data measuring background noise for parasite at late schizont stage. Negative control sample correponding to ChIP-Seq_Pol-II_LS sample using ChIP-Seq protocol with no Pol II antibody
Processed data file(s):
ChIPSeq_GeneExpressionProfile.xlsx

value: Late Schizont


title: ChIP-Seq_Pol-II_input

description:
input_cell430_CAGATC
cross-linked, sonicated, but not immunoprecipated genomic DNA sample for parasite at late schizont stage
Processed data file(s):
ChIPSeq_GeneExpressionProfile.xlsx, ChIPSeq_input_normalized.bed

tag: chip antibody

value: none (input)


title: ChIP-Seq_Pol-II_ET

description:
ET_PolII_cell400_CAGATC
ChIP-Seq data capturing Pol II occupancy for parasite at early trophozoite stage
Processed data file(s):
ChIPSeq_GeneExpressionProfile.xlsx, ChIPSeq_ET_normalized.bed

value: anti-RNA pol II antibody (Abcam, catalog# ab5095, lot#  GR-124547-2)


title: PB-Tcf1


title: ChIP-Seq_Pol-II_ER

description:
ER_PolII_cell430_ATCACG
ChIP-Seq data capturing Pol II occupancy for parasite at early ring stage
Processed data file(s):
ChIPSeq_GeneExpressionProfile.xlsx, ChIPSeq_ER_normalized.bed

value: Early Ring


title: ChIP-Seq_Pol-II_ER_NegativeControl

description:
ER_NegativeControl_cell430_CGATGT
ChIP-Seq data measuring background noise for parasite at early ring stage. Negative control sample correponding to ChIP-Seq_Pol-II_ER sample using ChIP-Seq protocol with no Pol II antibody
Processed data file(s):
ChIPSeq_GeneExpressionProfile.xlsx


title: ChIP-Seq_Pol-II_LS

description:
LS_PolII_cell430_TGACCA
ChIP-Seq data capturing Pol II occupancy for parasite at late schizont stage
Processed data file(s):
ChIPSeq_GeneExpressionProfile.xlsx, ChIPSeq_LS_normalized.bed


title: GROSeq_G.III

description:
GametocyteIII_CTTGTA_2016-4-20
nascent RNA
GROseq sample capturing nascent RNA for parasite at gametocyte stage III
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx, GametocyteIII_scaleFactor-0.034.bed

data_processing:
Library strategy: GRO-Seq
For both GRO-Seq and ChIP-Seq datasets, the first ten bases and the last base or last 20 bases were systematically trimmed from 50 bp and 75 bp reads using FASTX-Toolkit. Poly A/T and adaptor comtaiminated reads were removed. Reads containing bases with a quality score below 25 and Ns, reads that were unpaired, and reads shorter than 18 bases were also filtered using Sickle. High quality single reads that lost their mate pair during read processing were kept and mapped as single-end reads in parallel with paired-end reads.High quality single reads that lost their mate pair during read processing were kept and mapped as single-end reads in parallel with paired-end reads. reads that mapped to multiple locations in the genome, reads that were PCR duplicates, pair-end reads that were not properly paired, and reads that mapped to ribosomal RNA or transfer RNA were discarded from the final working reads. High quality single-end reads were combined with pair-end reads by merging mapped bam files.
For each stage, bam files from mapped reads for both high quality single-ended mapping and paired-end mapping were combined. In addition, bam files from each biological replicate were merged using Samtools. Genome-wide coverage profiles were generated using BEDtools.
For GRO-Seq data sets, genome-wide coverage profiles were normlaized to the amount of RNA yield per parasite by dividing the gene counts by a stage-specific scaling factor as described in the original manualscript. For ChIP-Seq data set, coverage profiles were normalized per million number of reads for each library, and then signals obtained from the negative controls were subtracted from the ChIP-Seq sample of the same stage. ChIP-Seq input data was normalized per million number of reads only.
Genome_build: PlasmoDB_v13
Supplementary_files_format_and_content: GROSeq_GeneExpressionProfile.xlsx (Gene Expression Counts for GRO-Seq dataset)
Supplementary_files_format_and_content: ChIPSeq_GeneExpressionProfile.xlsx (Gene Expression Counts for ChIP-Seq dataset)
Supplementary_files_format_and_content: .bed files report normalized genome wide coverage profiles

value: Gametoyte Stage III


title: GROSeq_G.V

description:
GametocyteV_cell356_CAGATC
nascent RNA
GROseq sample capturing nascent RNA for parasite at gametocyte stage V
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx, GametocyteV_scaleFactor-0.201.bed

value: Gametocyte Stage V


title: GROSeq_LS_rep2

description:
LS_rep2_cell400_TTAGGC
nascent RNA
GROseq sample (Biological replicate 2) capturing nascent RNA for parasite at late schizont stage
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx, GROSeq_LS_scaleFactor-0.27.bed


title: OsRootHair3

description: processed data file: OsRootHair.xlsx

data_processing:
Illumina Casava 1.8.2 was used for base calling.
The first 15bp of each read were trimmed.
Reads were mapped using Tophat v2.0.9. Default settings with --segment length 17 parameter were used to map the reads to the reference annotation (already mentioned in the sample information above).
FPKM values were calculated by Cufflinks2 v2.1.1 with multiread correction (-u -G).
Genome_build: See sample information above.
Supplementary_files_format_and_content: Excel files that contain the FPKM value generated by Cufflinks for the gene expression profiling for each of the six species.

extract_protocol:
RNA was extracted using Qiagen RNAeasy Plant Mini Kit.
RNA libraries were prepared for sequencing using SMART-Seq v4 Ultra Low Input RNA kit.


title: GROSeq_ES_rep2

description:
ES_rep2_cell356_GGCTAC
nascent RNA
GROseq sample (Biological replicate 2) capturing nascent RNA for parasite at early schizont stage
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx, GROSeq_ES_scaleFactor-0.18.bed

value: Early Schizont


title: GROSeq_LT_rep2

description:
LT_rep2_cell400_ACTTGA
nascent RNA
GROseq sample (Biological replicate 2) capturing nascent RNA for parasite at late trophozoite stage
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx, GROSeq_LT_scaleFactor-0.202.bed

value: Late Trophozoite


title: DLBB12-03

tag: date

tag: Sex

value: Female


title: DLBB12-02

tag: latitude

tag: longitude


title: GROSeq_ET_rep2

description:
ET_rep2_cell355_ATCACG
nascent RNA
GROseq sample (Biological replicate 2) capturing nascent RNA for parasite at early trophozoite stage
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx, GROSeq_ET_scaleFactor-0.193.bed

tag: strain


title: GROSeq_LR_rep1

description:
LR_rep1_cell356_GCCAAT
nascent RNA
GROseq sample (Biological replicate 1) capturing nascent RNA for parasite at late ring stage
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx, GROSeq_LR_scaleFactor-1.403.bed

value: Late Ring


title: GROSeq_LR_rep2

description:
LR_rep2_cell356_CTTGTA
nascent RNA
GROseq sample (Biological replicate 2) capturing nascent RNA for parasite at late ring stage
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx, GROSeq_LR_scaleFactor-1.403.bed


title: GROSeq_ER

description:
ER_rep1_cell355_TGACCA
nascent RNA
GROseq sample capturing nascent RNA for parasite at early ring stage
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx, GROSeq_ER_scaleFactor-1.bed


title: E2348_DMEM_0.5_BR2_2

city: Baltimore

first: Sean

last: Daugherty

state: Maryland

address: 801 W. Baltimore St.

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

data_processing:
Illumina reads were mapped to the EPEC genomes using Bowtie
The mapped reads were counted using HTSeq and normalized and then the differential expression of each gene for one sample compared to another was determined using DESeq v. 1.5.24, and statistical analyses were performed using R-2.15.2, and was represented as the log2 of the fold-change values.
Genome_build: E2348/69, B171, C581-05, E110019, 401140, 402290, 401588, 302053, 100329, 103385 TEPEC, 300059 TEPEC

organism: Escherichia coli O127:H6 str. E2348/69

source_name: Escherichia coli cells

growth_protocol: The EPEC strains were grown overnight in Luria-Bertani (LB) media and were inoculated 1:100 into 250 ml of fresh LB or DMEM and were incubated with shaking (225 rpm) at 37˚C to a final optical density (OD600) of approximately 0.5.

extract_protocol:
RNA was isolated from cells grown in LB or DMEM using the Ribopure Bacteria kit (Ambion) and contaminating DNA was removed using the Ribopure Dnase I and also the Turbo DNA-free kit (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: E2348_LB_0.5_BR1_2


title: E2348_LB_0.5_BR2_2


title: 401588_DMEM_0.5_BR2

organism: Escherichia coli


title: 401588_DMEM_0.5_BR1


title: 401588_LB_0.5_BR2


title: 401588_LB_0.5_BR1


title: CTCF.sample2.unbound

city: Palo Alto

first: Zheng

last: Zuo

address: Stanford

department: Genetics

institute: Stanford university

data_processing:
Library strategy: Methyl-Spec-seq
Methylation property identification: For any particular DNA variant inside library, it carries particular barcode to indicate its methylation property, i.e., unmethylated, top hemimethylated, bottom hemimethylated, duplex methylated. Thus acording to the unique methylation barcode information, each read was identified and sorted to its methylation type.
Variant reads counting and sorting: For each randomized binding site, its number in Bound and Unbound portions were counted separately. The Bound/Unbound ratio was supposedly porportional to its relative binding affinity, and the negative logarithm of this ratio indicates the relative binding energy in kT unit.
Energy logo visualization: Based on the binding energy for particular reference and all its single variants, an energy logo can be generated to indicate the specificity of particular protein-DNA interactions. Futhermore, besides conventional G-T-A-C bases, we used two extra “M" and ”W" to represent methylated cytosine on upper and lower strand of DNA respectively, in which the height of M or W indicate the extra binding energy contribution between methylated and unmethylated base.
Supplementary_files_format_and_content: All processed data were saved in .excel files, including the methylation property, bound reads, unbound reads, Bound/Unbound ratio, relative binding energy for each variant.

source_name: In vitro protein-DNA binding reactions

extract_protocol:
After EMSA, DNA fragments were cut and extracted by gel extraction buffer at 50C for 30mins.
For each portion of DNA fragment, PE1 and PE2 PCR primers were used to PCR amplify extracted DNA by at least 8 cycles (95C 15s, 52C 15s, 72C 30s)
For each particular sample, there are two raw data files, i.e., bound reads and unbound reads with different Illumina Index. The processed data file was based on analysis of Bound and Unbound data together.

treatment_protocol: All EMSA reactions were done in 9% Tris-glycine gel, 200V, 30mins

tag: dna library composition

value: Compared to CTCF sample1, the barcodes labeling unmethylated and M.sssI treated dsDNA were swapped to each other.

tag: recombinant protein used

value: mouse CTCF (Finger 1 to Finger 9)


title: CTCF.sample1.bound

value: Including unmethylated dsDNA library CTCF-R1-R5, and M.sssI methylated dsDNA library CTCF-R1-R5-M.sssI


title: CTCF.sample1.unbound


title: ZFP57.unbound

value: Including unmethylated dsDNA library ZFP57-R2, R4N; top hemimethylated libarary ZFP57-R2; bottom hemimethylated library R2; duplex methylated library R2; M.sssI methylated library R1, R2, R3, R5

value: mouse ZFP57 (Finger 1 to Finger 3)


title: ZFP57.bound

value: Including unmethylated dsDNA library ZFP57-R2, R4N; top hemimethylated libarary ZFP57-R2; bottom hemimethylated library R2; duplex methylated library R2; M.sssI methylated library R1, R2, R3, R4


title: CTCF.sample2.bound


title: TRF2 F/F exp3

city: Milan

first: Fabrizio

last: d'Adda di Fagagna

state: Mi

address: Via Adamello 16

country: Italy

institute: IFOM - The FIRC Institute of Molecular Oncology

description: RNA products generated in TRF2 F/F mouse embryonic fibroblasts

data_processing:
Illumina adapters and linkers used in the targeted sequencing of small RNA were trimmed using Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) discarding reads that became shorter than 10 nucleotides of length after trimming.
Reads were mapped to a telomeric contig made of 15 consecutive TTAGGG repeats and in parallel to the mouse genome (GRCm38/mm10) using Bowtie2 with a very sensitive local option (-D 20 -R 3 -N 0 -L 20 -i S,1,0.50).
Strand information was preserved in order to divide the aligned reads according to the original strand.
Reads were parsed using SAMtools and ad hoc bash and perl scripts.
In order to avoid spurious reads contamination, telomeric reads with mismatches or soft clipped portions were removed with ad hoc R scripts.
Genome_build: telomere.fa (telomeric contig made of 15 consecutive TTAGGG repeats)
Supplementary_files_format_and_content: bedgraph files showing the coverage of each position as calculated by samtools mpileup.
Supplementary_files_format_and_content: Briefly, we aligned the raw fastq files to a telomeric contig (supplementary file telomere.fa) and to the mouse genome (GRCm38/mm10 assembly), in order to split the telomeric reads and the reads aligning to the mouse genome in particular to the mir29b1 locus on mouse genome.
Supplementary_files_format_and_content: Please find below the steps of the pipeline, that differ only for the reference file used for the alignment.
Supplementary_files_format_and_content: 1) Files indC*.bedgraph, indG*.bedgraph, unindC*.bedgraph, unindG*.bedgraph were generated with the following procedure:
Supplementary_files_format_and_content: - Reads were mapped to a telomeric contig made of 15 consecutive TTAGGG repeats (supplementary file telomere.fa) using Bowtie2 with a very sensitive local option (-D 20 -R 3 -N 0 -L 20 -i S,1,0.50).
Supplementary_files_format_and_content: - Strand information was preserved in order to divide the aligned reads according to the original strand (G strand or C strand, as telomere sequence is composed of TTAGGG reapeats on one strand and CCCTAA reapeats on the other strand).
Supplementary_files_format_and_content: - The resulting bedgraph files (indC*.bedgraph, indG*.bedgraph, unindC*.bedgraph, unindG*.bedgraph) were obtained from the reads aligned on each separate strand.
Supplementary_files_format_and_content: 2) *.mir29b1.bedgraph files were generated with the following procedure:
Supplementary_files_format_and_content: - Reads were mapped to the mouse genome (GRCm38/mm10) using Bowtie2 with a very sensitive local option (-D 20 -R 3 -N 0 -L 20 -i S,1,0.50).
Supplementary_files_format_and_content: - Strand information was preserved in order to divide the aligned reads according to the original strand.
Supplementary_files_format_and_content: - The resulting bedgraph files (*.mir29b1.bedgraph) were obtained from the reads aligned to mir29b1 locus on mouse genome.

source_name: MEFs TRF2 F/F +4OHT

growth_protocol: DMEM + 10% serum + glutamine

extract_protocol:
small RNA was extracted with mirVana isolation kit
libraries were constructed using the ScriptSeq RNA-Seq Library Preparation Kit (Illumina, RSBC10948)

treatment_protocol: Cells were treated with 4-hydroxytamoxifen 0.6 uM for 48 hours.

tag: genotype

value: TRF2 F/F

tag: cell type

value: mouse embryonic fibroblasts


title: TRF2 F/+ exp2

description: RNA products generated in TRF2 F/+ mouse embryonic fibroblasts

source_name: MEFs TRF2 F/+ +4OHT

value: TRF2 F/+


title: TRF2 F/+ exp1


title: TRF2 F/F exp2


title: IW2982_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis

city: Menlo Park

middle: Dennis

last: McFarland

address: 2647 Alpine RD

department: Cancer Systems Biology

institute: Stanford University

description: A KTC mouse transduced with lentivirus carrying only the sgSetd2 guide RNA (not the multiplexed-pool)

data_processing:
Data was processed using the Tuba-seq analysis pipeline developed for the novel method detailed in this publication
See https://github.com/petrov-lab/tuba-seq
Fastq files were filtered & trimmed using preprocess.py
Barcode pileups were clustered using DADA2_clustering.R, trained via DADA2_error_training.R, and merged with postprocess.py
Bias of sizes by GC-content of barcode was corrected using a 4th-order polynomial, as described in manuscript
Tumors were called using a minimum cell size of 500 cells (unless otherwise specified in the manuscript) and a clustering proclivity of OMEGA_A = 1e-10
Genome_build: Custom Lentiviral Amplicon
Supplementary_files_format_and_content: Estimated size of every tumor in the study

source_name: KTC-Setd2_whole Lung Extract

growth_protocol: Tumors were transduced in mice via Cre & Cas9-mediated genome editing via intratracheal intubation of lentivirus

extract_protocol:
Mice were humanely sacrificed, then barcodes were PCR-amplified from DNA extract derived from whole lungs harboring multiplexed tumors
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit and multiplexed by mouse sample.

tag: mouse genotype

tag: genotype/variation

tag: tissue

value: Whole Lung Extract

value: Lung Epithelium, heterogenous progression to adenocarcinoma

tag: weeks of tumor growth

tag: molecule subtype

value: DNA amplicon


title: IW2903_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis

value: A KTC mouse transduced with lentivirus carrying only the sgSetd2 guide RNA (not the multiplexed-pool)


title: E2348_DMEM_0.5_BR1_2


title: IW2856_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis

description: A KTC mouse transduced with lentivirus carrying only the sgNeo2 guide RNA (not the multiplexed-pool)

source_name: KTC-Neo_whole Lung Extract

value: KTC-Neo


title: IW2956_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: IW2880_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis

value: A KTC mouse transduced with lentivirus carrying only the sgNeo2 guide RNA (not the multiplexed-pool)


title: IW2899_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: TRF2 F/+ exp3


title: IW2079_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis

description: Tranduced with multiplexed-pannel of Cas9-mediated Tumor Suppressors knockouts

source_name: KTC_whole Lung Extract

value: KTC

value: tranduced with multiplexed-pannel of Cas9-mediated Tumor Suppressors knockouts


title: TRF2 F/F exp1


title: Acute 1

value: Sprague-Dawley

value: P21 brain CD11b-immunopanned microglia

tag: time in culture

value: 0 hr

tag: serum exposure


title: IW2851_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: IW2047_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: MW1649_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: MW1648_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: MW1646_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: MW1606_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: DC971 _unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis

source_name: KT_whole Lung Extract

value: KT


title: MW1634_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: IW2022_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: DC966 _unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: DC968 _unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: IW2953_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: DC954_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: IW1261_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis

description: Tranduced with mBC Cre-mediated lentiviral library, sequenced in triplicate to test reproducibility of Tuba-seq

value: tranduced with mBC Cre-mediated lentiviral library


title: IW1257_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: JB1159_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis

source_name: KPT_whole Lung Extract

value: KPT


title: IW1258_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: JB1154_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: JB1353_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis

source_name: KLT_whole Lung Extract

value: KLT


title: JB1158_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: JB1357_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: JB1349_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: JB1347_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: JB1351_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: IW2060_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: MW1658_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: IW2042_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: Mutant Labyrinth RNA-seq at E13.5 (3)

city: Toronto

first: Paul

last: Delgado-Olguin

state: Ontario

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
Trimmomatic with ILLUMINACLIP, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
STAR: default settings
htseq to generate counts files: Strandedness=not standed -i gene_name
DESEQ2 for normalization of counts
Gene set enrichment analysis using pre-ranked data based on fold change
Genome_build: mm10
Supplementary_files_format_and_content: "*.counts" files were generated by htseq-counts and were used as input for DESEQ2, these counts are not normalized! "*.rnk" files are the ranked files used as input for GSEA

source_name: Labyrinth

extract_protocol:
Bead homogonization in trizol, Direct-zolTM RNA MiniPrep Plus Kit (Zymo Research) for extraction of RNA
mRNA was enriched by pull-down using the NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs). Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs), skipped actinomyosin, libraries not stranded

value: placenta


title: Mutant Labyrinth RNA-seq at E13.5 (4)


title: Mutant Labyrinth RNA-seq at E13.5 (2)


title: Wildtype Labyrinth RNA-seq at E13.5 (3)


title: Wildtype Labyrinth RNA-seq at E13.5 (1)


title: IW1262_unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: Mutant Labyrinth RNA-seq at E12.5 (4)


title: Mutant Labyrinth RNA-seq at E12.5 (1)


title: Mutant Labyrinth RNA-seq at E12.5 (2)


title: DC957 _unique mouse tranduced with multiplexed lentiviral library for Tuba-seq analysis


title: Mutant Labyrinth RNA-seq at E12.5 (3)


title: Wildtype Labyrinth RNA-seq at E13.5 (2)


title: Wildtype Labyrinth RNA-seq at E12.5 (3)


title: Wildtype Labyrinth RNA-seq at E12.5 (4)


title: Wildtype Labyrinth RNA-seq at E12.5 (1)


title: 20 week biological replicate 4

city: Rochester

first: Anna

middle: Kathleen

last: Bird

state: New York

address: 601 Elmwood Ave, Box 695

institute: University of Rochester

data_processing:
DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - htseq-count v0.6.1 "-q -f bam -s no -r pos -i gene_name"
DIFFERENTIAL EXP. - DESeq2_1.12.3
Genome_build: GRCm38.p4; Gencode M6
Supplementary_files_format_and_content: text files include deseq normalized expression counts

source_name: neutrophils

growth_protocol: Neutrophils isolated from total splenocytes ex vivo, sort-purified by FACS as DAPI-Ly6b+Ly6CintCD11b+Ly6G+ singlet cells, and frozen in Qiagen RLTPlus lysis buffer.

extract_protocol:
Neutrophil total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen)
Illumina compatible sequencing libraries were generated using 1ng of cDNA with the NexteraXT (Illumina) library preparation kit. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina) at a concentration of 10pM per lane. Single end reads of 100nt were generated for each sample and aligned to the organism specific reference genome.

treatment_protocol: No treatment [isolated ex vivo]

value: female

value: spleen


title: 26 week biological replicate 1


title: 20 week biological replicate 5


title: 26 week biological replicate 3


title: 26 week biological replicate 6


title: 26 week biological replicate 2


title: 26 week biological replicate 5


title: 20 week biological replicate 3


title: Mutant Labyrinth RNA-seq at E13.5 (1)


title: Wildtype Labyrinth RNA-seq at E13.5 (4)


title: 20 week biological replicate 2


title: 14 week biological replicate 5


title: 20 week biological replicate 1


title: 14 week biological replicate 6


title: 14 week biological replicate 4


title: 26 week biological replicate 4


title: 14 week biological replicate 3


title: 14 week biological replicate 2


title: 14 week biological replicate 1


title: Wildtype Labyrinth RNA-seq at E12.5 (2)


title: small H9p38 siRNA3

city: Turku

first: Riikka

last: Lund

address: Tykistökatu 6

country: Finland

institute: Turku Centre for Biotechnology, University of Turku

data_processing:
SmallRNA reads were trimmed using trim_galore to remove primer sequences, low-quality bases from read ends, and to discard trimmed reads < 18bp. The reads were then mapped to hg19 reference transcriptome (with tRNAs) using tophat2 (v2.0.13) with default parameters. PolyA+ reads were mapped to hg19 transcriptome using tophat2 (v2.0.13) with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by using the total exon length of the isoform with the longest total exon length and normalizing by this length and sequencing depth (according to the number of uniquely mapped reads obtained from htseq). For smallRNA-seq, genes with length > 250bp were excluded.
ChIP-seq data: reads with average quality below 20 were removed and reads with length 20-50 bp were retained with Trimmomatic 0.32, the reads were mapped to hg19 genome with Bowtie2 2.2.6 and non-unique reads were discarded, the ChIP peaks were called with MACS 1.0.1. with default parameters, except arbitrary shift size of 100 bp was used instead of shifting model and p-value cut off was 1.00E-04 for POL peak detection.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample in RNA-seq data or RPM in smallRNA-seq data, in ChIP-seq data the bigwig files contain the enrichment intensities and bed files the peaks with p-value =<0.0001.

source_name: Embryonic stem cells

growth_protocol: hESC (S1-13): mTeSR1+matrigel, NT2D1 (S14-16): DMEM+15%FCS

extract_protocol:
Qiagen all prep for smallRNA (S7-13) and mRNA (S1-6), ChIP-DNA (S14-18): Qiagen MinElute PCR Purification Kit
smallRNA-seq (S7-13): Illumina TruSeq smallRNA, mRNA-seq (S1-6): Illumina TruSeq mRNA, ChIP-seq (S14-18): Diagenode Microplex Library Preparation kit v2

tag: passages

value: 46 XX, POLR3G siRNA knockdown


title: small H9p38 siRNA2


title: small H360p66 SCR

value: 46 XY, wild type


title: small H9p38 SCR

value: 46 XX, wild type


title: small H360p62 SiRNA1

value: 46 XY, POLR3G siRNA knockdown


title: 20 week biological replicate 6


title: small H360p62 SCR


title: H9p38 SCR


title: H9p38 siRNA


title: H360p66 siRNA


title: H360p62 SCR


title: H360p66 SCR


title: H360p62 SiRNA


title: small H360p62 SiRNA2


title: PC9 Brain metastatic derivative, replicate 1

city: Hangzhou

first: Yilong

last: Zou

state: Zhejiang

address: Shilongshan Road #18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake University

data_processing:
Sequencing data quality control: Paired end reads in FASTQ format (50bp/50bp or 75bp/75bp) were quality assessed by FastQC v0.11.3 for sequencing integrity and completeness.
Sequencing read mapping: RNA-Seq reads were mapped to human genome hg19 (GRCh37, February 2009) or mouse genome mm10 (GRCm38, December 2011) with STAR2.3.0e using standard settings for paired-end reads. 75-90% (avergae 80%) of raw reads were uniquely mapped.
RNA-Seq read counting to genes: Uniquely mapped reads were counted to each gene with HTSeq v0.5.4 with default settings.
Read count normalization: Read counts from technical replicates of each biological sample were colllapsed into one sample in "DESeq2" package deposited in Bioconductor. Overall read counts within each cancer cell line model were normalized by library size through the “DESeq2” package.
Genome_build: hg19 (GRCh37) for human cell lines (HCC1954, MDA-MB-231 and PC9); mm10 (GRCm38) for mouse cell lines (LLC)
Supplementary_files_format_and_content: Text files contain normalized read counts of each gene in each sample from RNA-Seq experiments of four cancer cell line models. Read counts were normalized by library size.

growth_protocol: Parental cell lines (MDA-MB-231, HCC1954, PC9 and LLC) all stably express GFP. Mice harboring leptomeningeal metastases from MDAMB231, HCC1954, PC9 or LLC cell lines were euthanized. The leptomeningeal space was rinsed repeatedly with PBS. Cells dislodged from this space were collected and grown in culture on bare, tissue-culture treated plastic plates, in DMEM with 10% FBS, with supplemental L-glutamine and Pen-Strep (MDA, LLC cell lines and their derivatives); PC9 and HCC1954 were cultured in RPMI1640 wtih 10% FBS, L-glutamine and Pen-Strep. Derivative cells were grown in culture until a homogenous population of GFP-expressing cells was obtained. These cells were maintained in culture in media described above, and passaged three times prior to analysis.

extract_protocol:
Total RNA was extracted from cells using PrepEase RNA isolation kits (Affymetrix) according to the manufacturer's instructions.
Extracted total RNA samples were quantified by Ribogreen and quality assessed by Agilent BioAnalyzer 2000. 500ng RNA with integrity number (RIN) > 9.5 from each sample was used for library construction with TruSeq RNA Sample Prep Kit v2 (Illumina) according to manufacturer’s instructions.
Libraries were constructed for RNA-Seq analysis on Hi-Seq 2000 platform.
HCC1954, PC9 and LLC: 50/50bp paired-end RNA-Seq; MDA-MB-231: 75/75bp paired-end RNA-Seq. 25-65 million (average 40 million) raw read pairs were generated for each sample.

tag: cell line source

value: cell line PC9

tag: cancer type

value: Human non-small cell lung adenocarcinoma with elevated EGFR expression


title: PC9 Parental cell line, replicate 1


title: MDA-MB-231 Intermediate stage derivative, replicate 2

value: cell line MDA-MB-231

value: Grade IV invasive ductal breast carcinoma, ER-, PR-,  HER2-


title: MDA-MB-231 Brain metastatic derivative, replicate 2


title: PC9 Brain metastatic derivative, replicate 3


title: PC9 Intermediate stage derivative, replicate 2


title: PC9 Intermediate stage derivative, replicate 1


title: MDA-MB-231 Leptomeningeal metastatic derivative, replicate 2


title: PC9 Brain metastatic derivative, replicate 2


title: MDA-MB-231 Brain metastatic derivative, replicate 3


title: MDA-MB-231 Intermediate stage derivative, replicate 1


title: PC9 Leptomeningeal metastatic derivative, replicate 2


title: PC9 Leptomeningeal metastatic derivative, replicate 1


title: MDA-MB-231 Parental cell line, replicate 3


title: MDA-MB-231 Parental cell line, replicate 2


title: MDA-MB-231 Parental cell line, replicate 1


title: HCC1954 Leptomeningeal metastatic derivative, replicate 2

value: cell line HCC1954

value: Grade III invasive ductal breast carcinoma with elevated HER2/Neu expression


title: HCC1954 Leptomeningeal metastatic derivative, replicate 3


title: HCC1954 Intermediate stage derivative, replicate 2


title: PC9 Parental cell line, replicate 2


title: HCC1954 Intermediate stage derivative, replicate 1


title: HCC1954 Leptomeningeal metastatic derivative, replicate 1


title: PC9 Parental cell line, replicate 3


title: MDA-MB-231 Brain metastatic derivative, replicate 1


title: MDA-MB-231 Leptomeningeal metastatic derivative, replicate 1


title: HCC1954 Brain metastatic derivative, replicate 2


title: HCC1954 Brain metastatic derivative, replicate 1


title: HCC1954 Parental cell line, replicate 2


title: HCC1954 Parental cell line, replicate 1


title: MNase-seq_Nucleosomes_CondensingSpermatid_H2AL2-less

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

data_processing:
Base calling was performed using RTA v2.
MNase-seq fragments were aligned to the mm9 genome assembly using bowtie version 2.2.9 with default arguments.
Read coverage was computed using deepTools bamCoverage version 2.2.4 (https://github.com/fidelram/deepTools; (Ramirez et al., 2016)), considering only reads with mapping quality higher than 30, using one nucleotide bin size and normalizing using RPKM.
Nucleosome positions were called using DANPOS version 2.2.2 (https://sites.google.com/site/danposdoc/; (Chen et al., 2012)) with default arguments.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files correspond to read coverage computed with deepTools. Xls files correspond to positions called by DANPOS.

source_name: Spermatogenic cells (condensing spermatids)

extract_protocol:
Nucleosomal and sub-nucleosomal particles were generated and fractionated on a sucrose gradient as previously published (Govin et al., 2007, PMID: 17261847; Montellier et al., 2013, PMID: 23884607).
Libraries were prepared for sequencing using standard Illumina protocols for ChIP-Seq.

treatment_protocol: Spermatogenic cell fractions enriched in different cell types were enriched as recently described (Buchou et al., 2016, PMID: 27761820).

tag: developmental stage

value: condensing spermatids

value: testis


title: MNase-seq_Nucleosomes_CondensingSpermatid_WT


title: MNase-seq_Small_structures_CondensingSpermatid_WT


title: MNase-seq_Small_structures_CondensingSpermatid_H2AL2-less


title: MNase-seq_Nucleosomes_RoundSpermatid_WT

source_name: Spermatogenic cells (round spermatids)

value: round spermatids


title: MNase-seq_Nucleosomes_RoundSpermatid_H2AL2-less

source_name: Spermatogenic cells(round spermatids)


title: CKO.E12.4

city: Farmington

first: James

middle: YH

last: Li

state: CT

address: 263 Farmington Ave

department: Genetics and Genome Sciences

institute: UCHC

data_processing:
RNA-seq reads were mapped to the mouse genome with STAR.
Resulted BAM files were used to generate gene counts with featureCount using the uniq-counting mode.
Genome_build: For reading mapping and counting, we obtained the mouse and human reference genome sequences (GRCm38 and GRCh38) from Ensembl, and gene annotation files (vM5 and V22) from GENCODE. The reference genome was indexed using the genomeGenerate command of STAR.
Supplementary_files_format_and_content: Raw gene count table in the Comma Separated Values format

source_name: Cerebellum

extract_protocol:
The cerebellar anlage was micro-dissected from brains at E12.5, E13.5, or brain slices produced with a vibratome (Leica) from E14.5 brains. Total RNA was isolated with TRIzol (Life Technologies) or Maxwell® 16 LEV RNA FFPE Kit for automated RNA isolation (Promega). RNA integrity was determined with an Agilent Bioanalyzer 2100 (Agilent Technologies).
Approximately 500ng of total RNA was used for library preparation with a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s protocol. The E13.5 cDNA libraries were prepared by Stranded specific Kit.
The libraries were sequenced with HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 50 bp. Sequencing chemistry v2 (Illumina) was used, and samples were multiplexed in four samples per lane. For the E13.5, 21 samples will be pooled and run on a NextSeq500 (Illumina) using 75-base single end sequencing chemistry.

value: cerebellum

tag: age

value: CKO


title: CTRL.7

tag: strain


title: MEK.2


title: CTRL.8


title: CTRL.6


title: CTRL.9


title: CKO.E14.1


title: MEK.1


title: CKO.E12.3


title: MNase-seq_Nucleosomes_Spermatocyte_H2AL2-less

source_name: Spermatogenic cells (spermatocytes)

value: spermatocytes


title: CTRL.5


title: CTRL.3


title: CKO.E12.2


title: CTRL.4


title: CKO.E12.1


title: MNase-seq_Nucleosomes_Spermatocyte_WT


title: CTRL.E14.1

value: CTR


title: HCC1954 Parental cell line, replicate 3


title: CTRL.E12.2


title: CTRL.E12.1


title: CKO.MEK.5


title: Lewis lung carcinoma (LLC) Leptomeningeal metastatic derivative, replicate 3

source_name: LLC

value: cell line LLC

value: spontaneous non-small cell lung carcinoma from C57/B6 mouse


title: Lewis lung carcinoma (LLC) Leptomeningeal metastatic derivative, replicate 2


title: CKO.MEK.4


title: CTRL.2


title: CKO.MEK.2


title: Lewis lung carcinoma (LLC) Intermediate stage derivative, replicate 2


title: Lewis lung carcinoma (LLC) Leptomeningeal metastatic derivative, replicate 1


title: Lewis lung carcinoma (LLC) Brain metastatic derivative, replicate 1


title: Lewis lung carcinoma (LLC) Brain metastatic derivative, replicate 3


title: 103385_TEPEC_DMEM_0.5_BR2

organism: Escherichia coli 103385

source_name: Escherichia coli cells


title: CKO.1


title: CKO.3


title: CKO.2


title: 302053_LB_0.5_BR2

organism: Escherichia coli 302053


title: Lewis lung carcinoma (LLC) Parental cell line, replicate 3


title: 302053_DMEM_0.5_BR1


title: 103385_TEPEC_DMEM_0.5_BR1


title: CKO.MEK.1


title: Lewis lung carcinoma (LLC) Brain metastatic derivative, replicate 2


title: 103385_TEPEC_LB_0.5_BR2


title: Lewis lung carcinoma (LLC) Parental cell line, replicate 2


title: CKO.4


title: 302053_DMEM_0.5_BR2


title: Lewis lung carcinoma (LLC) Parental cell line, replicate 1


title: CTRL.1


title: 302053_LB_0.5_BR1


title: B171_DMEM_0.5_BR1_2

organism: Escherichia coli B171


title: 103385_TEPEC_LB_0.5_BR1


title: CKO.MEK.3


title: B171_LB_0.5_BR2_2


title: Lewis lung carcinoma (LLC) Intermediate stage derivative, replicate 1


title: B171_LB_0.5_BR1_2


title: GROSeq_LS_rep1_NegativeControl

description:
LS_rep1_NegativeControl_cell290_CAGATC
nascent RNA
GROseq control sample (nuclear run-on reaction with no labeled uridine) measuring background noise generated by GROseq methodology for parasite at late schizont stage. Negative control sample corresponding to GROSeq_LS_rep1 sample
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx

source_name: Erythrocytic stage

tag: Stage

value: Late Schizont


title: GROSeq_ES_rep1_NegativeControl

description:
ES_rep1_cell290_NegativeControl_CTTGTA
nascent RNA
GROseq control sample (nuclear run-on reaction with no labeled uridine) measuring background noise generated by GROseq methodology for parasite at early schizont stage. Negative control sample corresponding to GROSeq_ES_rep1 sample
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx

value: Early Schizont


title: GROSeq_LS_rep1

description:
LS_rep1_cell290_ACAGTG
nascent RNA
GROseq sample (Biological replicate 1) capturing nascent RNA for parasite at late schizont stage
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx, GROSeq_LS_scaleFactor-0.27.bed


title: GROSeq_ES_rep1

description:
ES_rep1_cell290_GGCTAC
nascent RNA
GROseq sample (Biological replicate 1) capturing nascent RNA for parasite at early schizont stage
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx, GROSeq_ES_scaleFactor-0.18.bed


title: GROSeq_LT_rep1_NegativeControl

description:
LT_rep1_NegativeControl_cell290_GCCAAT
nascent RNA
GROseq control sample (nuclear run-on reaction with no labeled uridine) measuring background noise generated by GROseq methodology for parasite at late trophozoite stage. Negative control sample corresponding to GROSeq_LT_rep1 sample
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx

value: Late Trophozoite


title: B171_DMEM_0.5_BR2_2


title: GROSeq_LT_rep1

description:
LT_rep1_cell290_TGACCA
nascent RNA
GROseq sample (Biological replicate 1) capturing nascent RNA for parasite at late trophozoite stage
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx, GROSeq_LT_scaleFactor-0.202.bed


title: GROSeq_ET_rep1

description:
ET_rep1_cell245_GATCAG
nascent RNA
GROseq sample (Biological replicate 1) capturing nascent RNA for parasite at early trophozoite stage
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx, GROSeq_ET_scaleFactor-0.193.bed

value: Early Trophozoite


title: NT2D1p39 Input rep 2

source_name: Embryonal carcinoma stem cells

value: 46 XY +complex


title: NT2D1p37 POLR3G ChIP rep1

tag: chip antibody

value: anti-POLR3G (SZ3070, Prof. Nouria Hernandez)


title: 401140_DMEM_0.5_BR2

organism: Escherichia coli 401140


title: NT2D1p37 Input rep1

organism: Homo sapiens

tag: genotype


title: GROSeq_ET_rep1_NegativeControl

description:
ET_rep1_NegativeControl_cell245_ACTTGA
nascent RNA
GROseq control sample (nuclear run-on reaction with no labeled uridine) measuring background noise generated by GROseq methodology for parasite at early trophozoite stage. Negative control sample corresponding to GROSeq_ET_rep1 sample
Processed data file(s):
GROSeq_GeneExpressionProfile.xlsx


title: 401140_LB_0.5_BR1


title: 401140_LB_0.5_BR2


title: 401140_DMEM_0.5_BR1


title: NT2D1p37 H3K4me3 ChIP rep1

tag: cell type

value: anti-H3K4me3 (C15410003, Diagenode)


title: E110019_DMEM_0.5_BR2_2

organism: Escherichia coli E110019