title: small RNA-seq from occipital lobe (ENCLB231ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AFX/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal occipital lobe tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size
experiment encode accession: ENCSR000AFX
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB231ZZZ
size range: <200

source_name: Homo sapiens occipital lobe tissue female fetal (20 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/07ca8271-619b-43b4-9809-54944ecbb0c9/@@download/attachment/SID38500.pdf

value: ENCBS063RNA at ENCODE; https://www.encodeproject.org/ENCBS063RNA/


title: RNAseq-ALL16

status: Public on Mar 18 2016

type: SRA

city: Montreal

first: Daniel

last: Sinnett

state: Quebec

address: 3175 Cote-Sainte-Catherine

country: Canada

institute: CHU Sainte-Justine

library_source: transcriptomic

data_processing:
AB SOLID data:  Primary alignment with Lifescope software version 2.1
ILLUMINA data: Primary alignment with STAR
Mark duplicate with PICARD version 1.107
SplitNCigar with GATK version 3.2-2
Read counts using HTSeq version 0.6.1p1 with Ensembl GRCH37 version 75
Genome_build: hg19
Supplementary_files_format_and_content: counts

molecule: total RNA

organism: Homo sapiens

source_name: Tumoral biospecimen, pre-B ALL patient

growth_protocol: Cells were cultured in RPMI 1640 media supplemented with 10% Fetal Bovine Serum

extract_protocol:
see Baccichet A, Qualman SK, Sinnett D. Allelic loss in childhood acute lymphoblastic leukemia. Leuk Res. 1997;21(9):817-23.
Total RNA was extracted from bone marrow samples at diagnosis for all patients using the mirVana Isolation kit (Ambion) according to the manufacturer’s protocol. The Allprep DNA/RNA Mini kit (Qiagen) was used for all REH samples .Following a DNAse I treatment, total RNA samples were quantified by NanoDrop ND1000 (Thermo-Fisher Scientific) and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent). Ribosomal ribonucleic acid (rRNA) were depleted using the Invitrogen RiboMinus Eukaryote kit (Life Technologies). cDNA libraries were prepared using the SOLiD Total RNA-seq kit (diagnosis samples) and the Illumina TruSeq Stranded Total RNA kit (relapse samples) based on manufacturer’s protocol and sequenced on the Life Technologies SOLiD 5500 System or the Illumina HiSeq 2500 System.

tag: disease state

value: acute lymphoblastic leukemia

tag: tissue

value: Bone marrow

tag: age at diagnosis (years)


title: RNAseq-ALL15


title: RNAseq-ALL14


title: small RNA-seq from metanephros (ENCLB226ZZZ)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR000AFU/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal kidney tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size
experiment encode accession: ENCSR000AFU
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB226ZZZ
size range: <200

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens metanephros tissue female fetal (24 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/8651ccef-4f82-49ae-a749-283c9a4a0794/@@download/attachment/SID38485.pdf

value: metanephros

value: tissue

tag: description

value: Human fetal kidney

tag: biosample encode accession

tag: age

value: 24 week

tag: dev stage

value: fetal

tag: Sex

value: female

tag: lab

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS058RNA at ENCODE; https://www.encodeproject.org/ENCBS058RNA/

value: Derived from ENCODE donor ENCDO067AAA; https://www.encodeproject.org/ENCDO067AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244142-10


title: small RNA-seq from lung (ENCLB230ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AFW/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal lung tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size
experiment encode accession: ENCSR000AFW
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB230ZZZ
size range: <200

source_name: Homo sapiens lung tissue female fetal (24 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c3ab4574-703f-41b9-97e1-ca5af4680404/@@download/attachment/SID38499.pdf

value: lung

value: Human fetal lung

value: ENCBS062RNA at ENCODE; https://www.encodeproject.org/ENCBS062RNA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244152-50


title: RNAseq-ALL-1


title: RNAseq-ALL13


title: small RNA-seq from heart (ENCLB224ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AFT/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal heart tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size
experiment encode accession: ENCSR000AFT
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB224ZZZ
size range: <200

source_name: Homo sapiens heart tissue female fetal (19 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/948872d9-7fef-4a68-8a60-d9b4a7c9981e/@@download/attachment/SID38483.pdf

value: heart

value: Human fetal heart

value: 19 week

value: ENCBS056RNA at ENCODE; https://www.encodeproject.org/ENCBS056RNA/

value: Derived from ENCODE donor ENCDO070AAA; https://www.encodeproject.org/ENCDO070AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244122-50


title: RNAseq-ALL12

value: acute lymphoblastic leukemia

value: Bone marrow


title: Inf2_Lt_8h

city: La Jolla

first: Luke

last: Thompson

address: 9500 Gilman Dr

institute: UC San Diego

data_processing:
Reads from each sample were separated based on their barcodes and aligned to Prochlorococcus MED4 and cyanophage P-HM2 genomes using the Burrows–Wheeler Aligner (BWA).
GenBank annotations (BX548174.1 for MED4 and NC̲015284.1 for P-HM2) were used to generate SAM alignment files using BWA.
SAMtools (Li et al., 2009) and pysam were then used to calculate the number of reads perfectly aligning to the sense and antisense strands of ORFs, rRNAs, tRNAs, and intergenic regions.
Paired reads were mapped separately; paired reads mapping to the same ORF were counted as one transcript for that ORF, whereas paired reads mapping to separate adjacent ORFs were counted once for each ORF.
Genome_build: BX548174.1 for MED4 and NC_015284.1 (GCF_000892475.1)  for P-HM2
Supplementary_files_format_and_content: Tabular format of processed .txt files contains the following fields: 1. Sequential gene number, 2. GenBank identifier, 3. Strand, 4. Start position, 5. End position, 6. Description, 7. Total counts, 8. Sense counts, 9. Antisense counts

organism:
Prochlorococcus marinus subsp. pastoris str. CCMP1986
Prochlorococcus phage P-HM2

source_name: Prochlorococcus culture

growth_protocol: A mid-log-phase mother culture of Prochlorococcus MED4 grown in constant light (90 μE m−2 s−1) in Pro99 medium.

extract_protocol:
Total RNA was extracted using the Ambion mirVana RNA isolation kit, and residual genomic DNA was removed using the Turbo DNA-free kit (Ambion). RNA was then concentrated with the RNA Clean & Concentrator-5 kit (Zymo Research). Total RNA (150 ng) was fragmented to the range of 60–200 nt by magnesium-catalyzed hydrolysis (40 mM Tris-Acetate, pH 8.1, 100 mM potassium acetate, 30 mM magnesium acetate) for 4 min at 83 ∘C, and purified with the RNA Clean & Concentrator-5 kit.
Strand-specific RNA-Seq libraries were prepared using a dUTP second-strand marking protocol as described previously (Levin et al., 2010). Briefly, first-strand cDNA was synthesized from fragmented RNA with random primers (Invitrogen) and Superscript III reverse transcriptase (Invitrogen). Second-strand cDNA was synthesized using dUTP instead of dTTP. Paired-end libraries for Illumina sequencing were prepared from purified double-stranded cDNA (Agencourt AMPure XP beads) as recommended by Illumina. Second strands of cDNA containing dUTP were removed with the Uracil Cleavage System (Enzymatics), and libraries were amplified with the sequencing primers. A duplex-specific nuclease (DSN)-based method (Yi et al., 2011) was used to remove the 16S and 23S rRNAs, which has been successfully used in Prochlorococcus (Giannoukos et al., 2012). Illumina sequencing primers with barcodes were used to amplify the DSN treated libraries. Barcoded libraries (40) were pooled with equal proportion in one lane and paired-end sequencing was done on an Illumina HiSeq 2000 (40 nt for insert + 6 nt for barcode).

treatment_protocol: Infected bottles were inoculated with cyanophage P-HM2 (MOI = 1), and control bottles were given an equal volume of spent medium (late-log phase, no phage). Both spent medium and phage lysate were filtered through 0.2-μm polycarbonate filters (Millipore) prior to addition.

tag: host strain

value: Prochlorococcus marinus MED4

tag: phage strain

value: Cyanophage P-HM2

tag: control or infected

value: infected

tag: light or dark

value: light

tag: timepoint

tag: replicate


title: RNAseq-ALL11


title: small RNA-seq from heart (ENCLB223ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AFT/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal heart tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size
experiment encode accession: ENCSR000AFT
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB223ZZZ
size range: <200

source_name: Homo sapiens heart tissue female fetal (28 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ee618859-2972-4fe4-a7ff-69ceb94c2f9d/@@download/attachment/SID38482.pdf

value: tissue

value: 28 week

value: fetal

value: female

value: Thomas Gingeras, CSHL

value: ENCBS055RNA at ENCODE; https://www.encodeproject.org/ENCBS055RNA/

value: Derived from ENCODE donor ENCDO069AAA; https://www.encodeproject.org/ENCDO069AAA/


title: small RNA-seq from frontal cortex (ENCLB222ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AFS/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal frontal cortex tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size
experiment encode accession: ENCSR000AFS
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB222ZZZ
size range: <200

source_name: Homo sapiens frontal cortex tissue male fetal (22 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2e3011a9-57fc-47b0-8be0-05d8dcdfc326/@@download/attachment/SID38477.pdf

value: frontal cortex

value: Human fetal frontal cortex

value: 22 week

value: male

tag: health state

value: unknown

value: ENCBS054RNA at ENCODE; https://www.encodeproject.org/ENCBS054RNA/

value: Derived from ENCODE donor ENCDO065AAA; https://www.encodeproject.org/ENCDO065AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244051-50


title: Inf2_Lt_4h

value: Prochlorococcus marinus MED4

value: Cyanophage P-HM2

value: infected


title: Inf2_Lt_2h

value: light


title: RNAseq-ALL10

tag: disease state

value: acute lymphoblastic leukemia

value: Bone marrow


title: RNAseq-ALL9

tag: tissue


title: small RNA-seq from frontal cortex (ENCLB221ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AFS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal frontal cortex tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size
experiment encode accession: ENCSR000AFS
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB221ZZZ
size range: <200

source_name: Homo sapiens frontal cortex tissue female fetal (20 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6abb51df-a6fc-43c6-bc49-af5ce63cc9b5/@@download/attachment/SID38476.pdf

value: tissue

value: 20 week

value: fetal

value: female

value: Thomas Gingeras, CSHL

value: ENCBS053RNA at ENCODE; https://www.encodeproject.org/ENCBS053RNA/

value: Derived from ENCODE donor ENCDO064AAA; https://www.encodeproject.org/ENCDO064AAA/


title: RNAseq-ALL8

tag: age at diagnosis (years)


title: Inf2_Lt_0h


title: Inf2_Dk_8h

value: dark


title: small RNA-seq from liver (ENCLB227ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AFV/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal liver tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size
experiment encode accession: ENCSR000AFV
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-07-07
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB227ZZZ
size range: <200

source_name: Homo sapiens liver tissue female fetal (20 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b3e6e5b1-230b-4b99-9509-ea616fef89e0/@@download/attachment/SID38467.pdf

value: liver

tag: description

value: Human fetal liver

value: ENCBS059RNA at ENCODE; https://www.encodeproject.org/ENCBS059RNA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244149-50


title: Inf2_Lt_1h

value: Prochlorococcus marinus MED4

value: Cyanophage P-HM2


title: Inf2_Dk_4h

value: infected


title: Inf2_Dk_2h


title: RNAseq-ALL7

value: acute lymphoblastic leukemia


title: small RNA-seq from cerebellum (ENCLB217ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal cerebellum tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size
experiment encode accession: ENCSR000AFQ
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB217ZZZ
size range: <200

source_name: Homo sapiens cerebellum tissue female fetal (37 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/db0f54c4-4239-4940-8281-4e99f19d1d22/@@download/attachment/SID38468.pdf

value: cerebellum

value: Human fetal cerebellum

tag: biosample encode accession

value: 37 week

value: ENCBS049RNA at ENCODE; https://www.encodeproject.org/ENCBS049RNA/

value: Derived from ENCODE donor ENCDO063AAA; https://www.encodeproject.org/ENCDO063AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244039-50


title: small RNA-seq from urinary bladder (ENCLB215ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AFP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal urinary bladder tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size
experiment encode accession: ENCSR000AFP
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-07-07
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB215ZZZ
size range: <200

source_name: Homo sapiens urinary bladder tissue female fetal (20 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5a3b5571-566e-4dd0-a4a9-0075de7e3ad6/@@download/attachment/SID38466.pdf

value: urinary bladder

value: tissue

value: Human fetal urinary bladder

tag: age

value: 20 week

value: fetal

value: female

value: Thomas Gingeras, CSHL

value: ENCBS047RNA at ENCODE; https://www.encodeproject.org/ENCBS047RNA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244010-50


title: small RNA-seq from metanephros (ENCLB225ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AFU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal kidney tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size
experiment encode accession: ENCSR000AFU
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB225ZZZ
size range: <200

source_name: Homo sapiens metanephros tissue female fetal (20 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4aa95294-870a-478d-98db-0751963232ee/@@download/attachment/SID38484.pdf

value: metanephros

value: Human fetal kidney

tag: dev stage

value: ENCBS057RNA at ENCODE; https://www.encodeproject.org/ENCBS057RNA/

value: Derived from ENCODE donor ENCDO064AAA; https://www.encodeproject.org/ENCDO064AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244142-10


title: RNAseq-ALL5

value: acute lymphoblastic leukemia

value: Bone marrow


title: RNAseq-ALL6


title: RNAseq-ALL4


title: Inf2_Dk_0h

value: Prochlorococcus marinus MED4

value: Cyanophage P-HM2

value: infected

value: dark


title: small RNA-seq from cerebellum (ENCLB218ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AFQ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal cerebellum tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size
experiment encode accession: ENCSR000AFQ
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB218ZZZ
size range: <200

source_name: Homo sapiens cerebellum tissue female fetal (19 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bf258b06-374d-43f4-9f60-1f883e759bd2/@@download/attachment/SID38469.pdf

value: cerebellum

value: tissue

value: Human fetal cerebellum

value: 19 week

tag: Sex

value: ENCBS050RNA at ENCODE; https://www.encodeproject.org/ENCBS050RNA/

value: Derived from ENCODE donor ENCDO070AAA; https://www.encodeproject.org/ENCDO070AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244039-50


title: Inf2_Dk_1h


title: RNAseq-ALL2


title: Inf1_Lt_8h

value: light


title: RNAseq-ALL3


title: small RNA-seq from GM12878 (ENCLB050ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AEJ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line GM12878.  They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.
experiment encode accession: ENCSR000AEJ
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB050ZZZ
size range: <200

source_name: Homo sapiens GM12878 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c2e1d214-56ae-4a04-9d49-e7c3696b1f8d/@@download/attachment/GM12878_Small_Total_TruSmall_1x101_ENCLB050ZZZ_Ging.pdf

tag: line

value: immortalized cell line

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: unknown

value: adult

value: female

tag: lab

value: Ali Mortazavi, UCI

value: ENCBS090RNA at ENCODE; https://www.encodeproject.org/ENCBS090RNA/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: small RNA-seq from K562 (ENCLB067ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AES/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line K562.  They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.
experiment encode accession: ENCSR000AES
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB067ZZZ
size range: <200

source_name: Homo sapiens K562 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b8462a6d-765a-4e27-a3bc-f4935d78e950/@@download/attachment/K562_Small_Total_TruSmall_1x101_ENCLB067ZZZ_Ging.pdf

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. ENCODE3 RNA-seq evaluation replicate 1.

value: 53 year

tag: passage number

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

tag: link

value: ENCBS087RNA at ENCODE; https://www.encodeproject.org/ENCBS087RNA/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: small RNA-seq from K562 (ENCLB068ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AES/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line K562.  They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.
experiment encode accession: ENCSR000AES
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB068ZZZ
size range: <200

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/1526f7e2-4895-4364-8643-9edf91c00302/@@download/attachment/K562_Small_Total_TruSmall_1x101_ENCLB068ZZZ_Ging.pdf

value: immortalized cell line

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. ENCODE3 RNA-seq evaluation replicate 2.

value: ENCBS088RNA at ENCODE; https://www.encodeproject.org/ENCBS088RNA/


title: Inf1_Lt_4h

tag: host strain

value: Prochlorococcus marinus MED4

tag: phage strain

value: Cyanophage P-HM2

tag: control or infected

value: infected

value: light


title: small RNA-seq from diencephalon (ENCLB219ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AFR/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal diencephalon tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size
experiment encode accession: ENCSR000AFR
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB219ZZZ
size range: <200

source_name: Homo sapiens diencephalon tissue female fetal (20 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bc3f7288-9ccb-44c0-9a12-b2a7524c41a3/@@download/attachment/SID38474.pdf

value: diencephalon

value: tissue

value: Human fetal diencephalon

value: 20 week

value: fetal

value: female

value: Thomas Gingeras, CSHL

value: ENCBS051RNA at ENCODE; https://www.encodeproject.org/ENCBS051RNA/

value: Derived from ENCODE donor ENCDO064AAA; https://www.encodeproject.org/ENCDO064AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244049-10


title: small RNA-seq from diencephalon (ENCLB220ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AFR/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal diencephalon tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size
experiment encode accession: ENCSR000AFR
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB220ZZZ
size range: <200

source_name: Homo sapiens diencephalon tissue male fetal (22 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/df62e59f-319c-4e84-a97b-0cc60fcc81bd/@@download/attachment/SID38475.pdf

value: 22 week

value: male

value: unknown

value: ENCBS052RNA at ENCODE; https://www.encodeproject.org/ENCBS052RNA/

value: Derived from ENCODE donor ENCDO065AAA; https://www.encodeproject.org/ENCDO065AAA/


title: RNAseq-ALL1

source_name: Tumoral biospecimen, pre-B ALL patient

extract_protocol:
see Baccichet A, Qualman SK, Sinnett D. Allelic loss in childhood acute lymphoblastic leukemia. Leuk Res. 1997;21(9):817-23.
Total RNA was extracted from bone marrow samples at diagnosis for all patients using the mirVana Isolation kit (Ambion) according to the manufacturer’s protocol. The Allprep DNA/RNA Mini kit (Qiagen) was used for all REH samples .Following a DNAse I treatment, total RNA samples were quantified by NanoDrop ND1000 (Thermo-Fisher Scientific) and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent). Ribosomal ribonucleic acid (rRNA) were depleted using the Invitrogen RiboMinus Eukaryote kit (Life Technologies). cDNA libraries were prepared using the SOLiD Total RNA-seq kit (diagnosis samples) and the Illumina TruSeq Stranded Total RNA kit (relapse samples) based on manufacturer’s protocol and sequenced on the Life Technologies SOLiD 5500 System or the Illumina HiSeq 2500 System.

value: acute lymphoblastic leukemia

value: Bone marrow


title: RNAseq-ALL0


title: small RNA-seq from GM12878 (ENCLB049ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AEJ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line GM12878.  They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.
experiment encode accession: ENCSR000AEJ
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB049ZZZ
size range: <200

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4226f3a4-8355-48df-bb2e-623a927caa65/@@download/attachment/GM12878_Small_Total_TruSmall_1x101_ENCLB049ZZZ_Ging.pdf

value: immortalized cell line

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: adult

value: Ali Mortazavi, UCI

value: ENCBS089RNA at ENCODE; https://www.encodeproject.org/ENCBS089RNA/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: Inf1_Lt_2h

value: Prochlorococcus marinus MED4

value: Cyanophage P-HM2

value: infected

tag: light or dark

value: light

tag: timepoint

tag: replicate


title: Inf1_Lt_1h


title: Ctr2_Lt_8h

value: control


title: Inf1_Dk_0h

value: dark


title: Inf1_Dk_4h


title: Inf1_Dk_8h


title: Ctr2_Lt_2h


title: Ctr2_Dk_4h


title: Ctr2_Dk_8h


title: Ctr2_Lt_0h


title: Inf1_Dk_2h


title: Ctr2_Lt_1h


title: Ctr2_Dk_1h


title: Ctr2_Dk_2h


title: RIP_GFP_IP_RNaseq

city: Pasadena

first: Maria

last: Ninova

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: Calfironia Institute of Technology

description: GFP-bound RNA

data_processing:
For consistency between different sequencing datasets, 100 bp reads were trimmed to 50 bp before processing.
Standard illumina 3' adaptor sequence was removed using Reaper (Davis et al. 2013)  or Cutadapt tool (Martin et al. 2011).
Data was filtered against Drosophila melanogaster  ribosomal RNA sequences using Bowtie 0.12.7 (Langmead et al., 2009), allowing up to 3 mismatches.
Remaining reads were mapped to D. melanogaster genome (UCSC dm3) allowing 0 mismatches, and only uniquely mapping reads were retained (-m 1).
Genome_build: UCSC dm3
Supplementary_files_format_and_content: Genome coverage histograms for uniquely mapped reads in bigWig format

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: Flies were maintained under standard conditions.

extract_protocol:
Total RNA from dissected ovaries was purified using Trizol according to manufacturer's instructions. Chromatin-associated RNAs were isolated as described previously (Khodor et al., 2011), with modifications.  For total RNA-sequencing and input RNA in Thoc5-GFP RIP experiment, ribosomal RNA was depleted using the Ribo-Zero rRNA Removal Kit (human/mouse/rat, Epicenter) with additional Drosophila-specific probes. Thoc5-GFP and GFP-bound RNA (negative control) was isolated from immunopurified protein bound RNA fraction from ovarian lysates using antibodies against GFP. Detailed protocols for chromatin-associated RNAs and protein-bound RNA extraction is available in the accompanying manuscript.
Total and chromatin-associated RNA libraries were generated using the NEBNext library preparation kit (NEB) according to the manufacturer's instructions. For small RNA librarires, 19-29 nt RNAs were isolated from total RNA of dissected ovaries using 12% polyacrylamide gels, and library construction was performed as described in previous studies (Aravin et al., 2008; Brennecke et al., 2007).

treatment_protocol: No treatment (such as fixation) prior to extraction

tag: genotype

value: GFP

tag: antibody

value: DSHB GFP-12A6

value: 1 week old


title: RIP_Thoc5_GFP_IP_RNAseq

description: Thoc5-GFP-bound RNA


title: Input_Thoc5_GFP_RNAseq

description: total RNA


title: Ctr2_Dk_0h

extract_protocol:
Total RNA was extracted using the Ambion mirVana RNA isolation kit, and residual genomic DNA was removed using the Turbo DNA-free kit (Ambion). RNA was then concentrated with the RNA Clean & Concentrator-5 kit (Zymo Research). Total RNA (150 ng) was fragmented to the range of 60–200 nt by magnesium-catalyzed hydrolysis (40 mM Tris-Acetate, pH 8.1, 100 mM potassium acetate, 30 mM magnesium acetate) for 4 min at 83 ∘C, and purified with the RNA Clean & Concentrator-5 kit.
Strand-specific RNA-Seq libraries were prepared using a dUTP second-strand marking protocol as described previously (Levin et al., 2010). Briefly, first-strand cDNA was synthesized from fragmented RNA with random primers (Invitrogen) and Superscript III reverse transcriptase (Invitrogen). Second-strand cDNA was synthesized using dUTP instead of dTTP. Paired-end libraries for Illumina sequencing were prepared from purified double-stranded cDNA (Agencourt AMPure XP beads) as recommended by Illumina. Second strands of cDNA containing dUTP were removed with the Uracil Cleavage System (Enzymatics), and libraries were amplified with the sequencing primers. A duplex-specific nuclease (DSN)-based method (Yi et al., 2011) was used to remove the 16S and 23S rRNAs, which has been successfully used in Prochlorococcus (Giannoukos et al., 2012). Illumina sequencing primers with barcodes were used to amplify the DSN treated libraries. Barcoded libraries (40) were pooled with equal proportion in one lane and paired-end sequencing was done on an Illumina HiSeq 2000 (40 nt for insert + 6 nt for barcode).


title: total_RNAseq_thoc5_mut_ov-2

description: total RNA


title: Ctr1_Lt_2h


title: Ctr1_Lt_4h


title: Inf1_Lt_0h


title: Ctr1_Lt_1h


title: total_RNAseq_thoc5_het_ov-2

description: total RNA


title: Ctr1_Lt_8h


title: chrom_RNAseq_shW

description: Chromatin-associated RNA

molecule: nuclear RNA


title: Inf1_Dk_1h


title: chrom_RNAseq_shCuff

description: Chromatin-associated RNA


title: Ctr1_Dk_8h


title: Ctr2_Lt_4h


title: Ctr1_Dk_2h


title: Ci_invitro_2

status: Public on Mar 17 2016

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Sequenced reads were mapped to the genome of Arabidopsis thaliana (TAIR10) and the genomes of Colletotrichum tofieldiae or Colletotrichum incanum using tophat v2.0.10 with parameters -a 10  -g 10 - r 100  --mate-std-dev 40
Read counts per gene per sample were obtained using the htseq-count script in the HTSeq Python package with options -s reverse -t exon
Genome_build: TAIR10 (Arabidopsis), Ct0861v1 (C. tofieldiae), Ci238704v1 (C. incanum)
Supplementary_files_format_and_content: tab-delimited text files including read counts per gene per sample for each of the analyzed species (Arabidopsis, C. tofieldiae, C. incanum)

molecule: polyA RNA

organism: Colletotrichum incanum

source_name: fungal in vitro hyphae

extract_protocol:
RNA-purification was performed using the NucleoSpin RNA plant (Macherey-Nagel) according to the manufacturer’s protocol.
RNA-seq libraries were prepared by the Max Planck Genome Center Cologne (http://mpgc.mpipz.mpg.de) according to the TruSeq RNA sample preparation v2 guide (Illumina).

tag: tissue

value: fungal in vitro hyphae


title: chrom_RNAseq_thoc5-het

description: Chromatin-associated RNA


title: chrom_RNAseq_thoc5

description: Chromatin-associated RNA


title: Cyp7a1 Transgenic, LPS treated, rep 2

city: Boston

last: Okin

state: MA

address: 55 Fruit St, BUL148

department: Department of Medicine, Division of Pulmonary and Critical Care

institute: Massachusetts General Hospital

description: Sample 8

data_processing:
Illumina Real-Time Analysis v2 was used for basecalling and adapter trimming
Sequenced reads were mapped to mm10 using tophat v2.1.0 with bowtie v2.2.6.
Fragments Per Kilobase of transcript per Million (FPKM) were calculated using Cufflinks and CuffDiff v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files containing FPKM values for all samples

organism: Mus musculus

source_name: Mouse liver

extract_protocol:
Livers were removed, flash frozen on liquid nitrogen, and then pulverized using a mortar and pestle while on liquid nitrogen. RNA was extracted with RNA Bee followed by a clean up and on column DNase digestion using RNeasy Mini Kit from QIAGEN. Illumina TruSeq Stranded mRNA Library Prep Kit (Cat#RS-122-2101) was used with 500ng highly purified RNA for construction of sequencing libraries.
Libraries were prepared using standard Illumina protocols.

tag: strain

value: liver

tag: gender

value: male

value: ApoE-Cyp7a1 transgenic


title: chrom_RNAseq_thoc5-2

description: Chromatin-associated RNA

tag: age


title: chrom_RNAseq_thoc5-het-2

description: Chromatin-associated RNA


title: Ctr1_Lt_0h

source_name: Prochlorococcus culture


title: Ctr1_Dk_0h


title: Ci_invitro_1


title: Cyp7a1 Transgenic, untreated, rep 1

description: Sample 5


title: Wild type, LPS treated, rep 2

description: Sample 4

value: Wild type


title: Cyp7a1 Transgenic, LPS treated, rep 1

description: Sample 7


title: Wild type, untreated, rep 2

description: Sample 2


title: Wild type, LPS treated, rep 1

description: Sample 3


title: Cyp7a1 Transgenic, untreated, rep 2

description: Sample 6


title: Wild type, untreated, rep 1

description: Sample 1


title: minusP10Ci_Exp2_3

description:
independent experiment 2
CountTable_HTSeq_At_raw.txt
CountTable_HTSeq_Ci_raw.txt

organism: Arabidopsis thaliana

source_name: fungal-colonized plant roots

tag: infection

value: Ci-infected

tag: phosphate availability

value: deficient (P-)

tag: time

value: 10 dpi

value: fungal-colonized plant roots


title: Ctr1_Dk_4h

value: Prochlorococcus marinus MED4

value: Cyanophage P-HM2


title: minusP24Ci_Exp2_1

value: 24 dpi


title: LV-shGAS5-mRNA

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

country: China

institute: The Second Military Medical University

description: processed data file: mRNA_All_Counts.xls

data_processing:
RNA-Seq-Ion Proton: Mapping of single-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent ofbases with qualities of <13.
The clean reads were then aligned to hg19 genome using the MapSplice program (v2.1.6). In alignment, preliminary experiments were performed to optimize the alignment parameters (-s 22 -p 15 --ins 6 --del 6 --non-canonical) to provide the largest information on the AS events.
miRNA-Seq: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <20 b) read length < 17bp c) adaptor sequence.
utilizing the BWA software, we mapped the clean data to human miRNA database and human genome.
RNA-Seq-Hiseq: Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent ofbases with qualities of <20.
The clean reads were then aligned to hg19 genome  using the Tophat program (v2.0.11) under following parameter (-a 10 -m 0 -i 31 -I 500000 –G).
Genome_build: hg19
Supplementary_files_format_and_content:
mRNA_All_Counts.xls: processed mRNA counts data for sample LV-GAS5-mRNA, LV-NC-mRNA and LV-shGAS5-mRNA
miRNA_All_Counts.xls: processed miRNA counts data for sample LV-GAS5-miRNA and LV-NC-miRNA
LncRNA_All_RPKM.xlsx: processed lncRNA RPKMs data for sample H1-P67-lncRNA and X01-P58-lncRNA

source_name: human embryonic stem cells

growth_protocol: All hESCs were maintained in feeder-free environment using E8 medium.

extract_protocol:
Total RNAs were harvested using Trizol reagent and small RNAs were harvested using miRcute miRNA extraction reagent (Tian Gen, China).
RNA-seq: The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies).
miRNA-seq: The complementary DNA (cDNA) libraries for single-end sequencing were prepared using TruseqTM Small RNA sample prep Kit (Illumina) according to the manufacturer’s instructions. 1ug small RNA was used to add 3’ adaptor and 5’ adaptor to small RNA and RT-PCR was applied to the small RNA with adaptor to achieve the 1st cDNA; Truseq (Illumina) primer was used for PCR enrichment and introducing index sequence. Size selection was applied to obtain the 145-160bp library sequence. TBS380(Picogreen) was introduced to quantify the library concentration. We applied the cluster formation on flow cell utilizing cBot and sequencing on Hiseq2000 Platform.

treatment_protocol: To generate stable colonies, lentiviruses were initially added to the hESCs on the second day of passage at multiplicity of infection (MOI) 10, and continued for three days. Puromycin was added on the fifth day at the concentration of 100ng/ml for selection, and hESCs colonies that survived were passaged and analyzed by either qRT-PCR or fluorescence microscopy.

tag: cell line

tag: cell type

value: hESC cell line

tag: passage

tag: genotype/variation

value: stable knockdown of GAS5 by short hairpin RNA


title: LV-GAS5-mRNA

value: stable GAS5 overexpressed


title: LV-NC-mRNA

value: stable control RNA overexpressed


title: minusP10Ci_Exp2_1


title: minusP24Ci_Exp2_3


title: minusP10Ci_Exp1_3

description:
independent experiment 1
CountTable_HTSeq_At_raw.txt


title: Ctr1_Dk_1h

tag: host strain

tag: phage strain

tag: control or infected

value: control

value: dark


title: minusP10Ci_Exp1_2


title: minusP10Ci_Exp1_1


title: Ci_invitro_3

value: fungal in vitro hyphae


title: minusP16Ct_3

description:
CountTable_HTSeq_At_raw.txt
CountTable_HTSeq_Ct_raw.txt

value: Ct-infected

value: 16 dpi


title: minusP24Ct_1


title: minusP16Ct_1


title: minusP10Ct_3


title: minusP16Ct_2


title: minusP10Ct_2


title: minusP10Ct_1


title: minusP06Ct_2

value: 6 dpi


title: minusP06Ct_3


title: minusP06Ct_1


title: minusP10Ci_Exp2_2

value: Ci-infected


title: minusP24mock_1

source_name: plant roots

value: mock

value: deficient (P-)

value: plant roots


title: minusP16mock_3


title: minusP24mock_2


title: minusP16mock_2


title: minusP06mock_3


title: minusP16mock_1


title: minusP10mock_1

value: 10 dpi


title: minusP10mock_2


title: minusP06mock_2


title: plusP24Ct_2

value: sufficient (P+)

value: fungal-colonized plant roots


title: minusP06mock_1


title: minusP24Ct_3

value: 24 dpi


title: plusP24Ct_3


title: minusP24Ct_2


title: minusP24Ci_Exp2_2


title: plusP24Ct_1


title: plusP16Ct_2


title: plusP16Ct_1


title: plusP10Ct_3


title: minusP24mock_3


title: plusP06Ct_3


title: plusP10Ct_2


title: plusP06Ct_2


title: plusP24mock_2


title: plusP24mock_1


title: minusP10mock_3


title: plusP10mock_3


title: plusP06mock_2


title: plusP06mock_3


title: plusP16mock_1


title: plusP16mock_2


title: plusP10mock_2


title: plusP24mock_3


title: plusP16mock_3


title: plusP10mock_1


title: hCMEC.D3.Replicate.2 [miRNA]

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using FASTQC and Cutadapt was used to trim the FASTQ files
The paired end reads were aligned by Bowtie 0.12.7
microRNA counts were generated using MirDeep 2.0.0.5
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file including the raw read counts and RPM values for each microRNA

source_name: Blood Brain Barrier

extract_protocol:
RNA was extracted from tissue using the Qiagen miRNEasy kit following the manufacturer's protocol.
Small RNA libraries were prepared according to manufacturer’s instructions for the NEBNext Multiplex Small RNA Kit (New England Biolabs; Ipswich, MA).  Briefly, adaptors were ligated to the 3’ and 5’ ends of the miRNAs as part of total RNA samples.  A complementary primer was annealed to 3’ adaptor sequences followed by reverse transcriptase (Superscript III; Invitrogen; Carlsbad, CA) to generate a cDNA library of small RNAs.  The library was enriched by 12-15 cycles of PCR employing a common 5’ primer and up to 24 unique Index primers (3’ adaptor complement; equivalent to Illumina TruSeq Small RNA sequences).  PCR products were assessed for miRNA products by Agilent Bioanalyzer DNA 1000 (Santa Clara, CA) analysis.  The 130-155bp fraction was quantitated by region analysis to determine equimolar amounts of libraries to pool.  Pooled PCR reactions were purified and concentrated using a Qiagen MinElute protocol and eluted in 30L nuclease-free dH2O. Small RNA libraries were fractionated to extract an miRNA-enriched sample via 3% Pippin Prep gel cassettes (Sage Science, Beverly, MA).  The 125-160bp recovered fraction was purified by Qiagen MinElute and recovered in 10L nuclease-free dH2O. Individual or pooled miRNA fractions were assessed by a second Agilent DNA 1000 assay. A predominant peak at 140-150bp is evidence that the miRNA-modification molecular biology and size selection steps have performed as expected. The final concentration of each library or pool was determined by Qubit fluorometry using the Broad Range or High Sensitivity reagents (Invitrogen). Libraries were then loaded onto paired end flow cells at concentrations of 8-10 pM to generate cluster densities of 700,000/mm2 following Illumina’s standard protocol using the Illumina cBot and cBot Paired end cluster kit version 3.

value: Blood Brain Barrier cell line

tag: molecule subtype

value: small RNA


title: hCMEC.D3.Replicate.8

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file including the raw read counts and RPKM values for each gene

extract_protocol:
RNA libraries from hCMEC/D3 cells were prepared according  to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego CA).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: hCMEC.D3.Replicate.8 [miRNA]


title: plusP06mock_1


title: hCMEC.D3.Replicate.7


title: plusP16Ct_3


title: hCMEC.D3.Replicate.5


title: plusP10Ct_1


title: plusP06Ct_1


title: hCMEC.D3.Replicate.4


title: hCMEC.D3.Replicate.6


title: hCMEC.D3.Replicate.1


title: hCMEC.D3.Replicate.2


title: hCMEC.D3.Replicate.3


title: CTR1

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

data_processing: After adapter removal reads without adapter and/or with N were discarded, only reads between  15 and 26 nt with base quality of at least 30 and with less than 2 nt with base quality lower than 20 were considered. Reads were mapped using bowtie (only exact matches) to hairpins sequences from miRBase v21 and to human genome sequence (GRCh38). Reads belonging to unique sequences mapping to more than 5 genomic loci out of miRNA hairpins were discarded. A subsequent phase of accurate mapping of reads to extended hairpins (30 nt before and after hairpin precursor) was performed with bowtie with -best -y -strata options. Reads alignment results were integrated with known miRNA positions to classify reads according to number of mismatches and relative position to known mature miRNA. The raw read count were corrected considering the number of reference sequences showing equally good alignments with the read. Known miRNA quantification and isomiRs characterization is based on exact alignments and on alignments with at most 1 mismatch. New miRNA and moRNA discovery is based only on exact alignments.

source_name: bone marrow CD34+ cells normal controls

extract_protocol: Total RNA was extracted using Trizol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany, http://www.home.agilent.com) were used to determine concentration and purity/integrity of RNA with Agilent 2100 Bioanalyzer. For each sample, a small RNA library was prepared starting from 1 ug total RNA, using the TruSeq Small RNA Sample Preparation Kits and protocols (Illumina, San Diego, CA, USA, http://www.illumina.com). Library quality was checked using High Sensitivity DNA chip (Agilent Technologies, Waldbrunn, Germany, http://www.home.agilent.com).

value: Bone Marrow

tag: disease state

value: normal


title: MF3

source_name: peripheral blood CD34+ cells PMF patient

value: M

value: Peripheral Blood

value: Primary myelofibrosis


title: CTR3


title: MF1

source_name: peripheral blood CD34+ cells PMF patients

value: 4 (2 Males + 2 Females)

value: mixed


title: RN319J

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

description: processed data file: data2.txt.gz

library_source: genomic

data_processing:
Data were mapped using BOWTIE
For each nucleotide, the amount of mapped fragments was considered (= coverage)
Data files were compressed by merging neighbouring nucleotides with equal coverages into single rows, with indication of start and end position of nucleotides with that specific coverage
Genome_build: HG19
Supplementary_files_format_and_content: txt files with columns containing resp. line number, chromosome, start and end position (nucleotide) and amount of mapped fragments

molecule: genomic DNA

source_name: Kidney sample

extract_protocol:
DNA extracted using Qiagen Blood and Tissue Kit according to manufacturers Instuctions
Libraries were prepared using standard multiplexed paired-end Chip-seq protocol (Illumina). In summary, 500 ng of DNA per sample was fragmented by ultrasound mediated DNA shearing (Covaris S2, Covaris, Woburn, Massachusetts, USA) set to obtain fragments with an average length of 200bp. We employed the MethylCap kit (Diagenode AF-100-0048, Liège, Belgium) to obtain methylated DNA fragments using the highest salt concentration single elution step option. This was followed by the library preparation for the enriched DNA, which was performed with a modified 'multiplexed paired-end ChIP protocol' (Illumina, San Diego, California, USA). Therefore, the NEBNext® DNA Sample Prep Master Mix Set 1 (New England BioLabs (NEB) E6040, Ipswich, Massachusetts, USA) was combined with the Multiplexing Sample Preparation Oligo Kit (Illumina PE-400-1001). Per sample, 22µl of the prepared sample was subjected to PCR (21 cycles) following the Illumina Library Amplification Index Protocol. After purification (Qiaquick PCR Purification columns, Qiagen), elution and concentration (evaporation), the libraries were pooled and denaturated (NaOH), followed by Illumina HiSeq 2000 sequencing ('multiplexed paired-end run, 2 times 45 cycles) of 10pM/pool.

value: kidney

tag: tissue type

value: Biopsy

tag: agent

value: no sunitinib


title: MF4

tag: tissue


title: RN319I

description: processed data file: data2.txt.gz


title: CTR2

tag: gender


title: RN319H

description: processed data file: data2.txt.gz


title: RN319A

description: processed data file: data2.txt.gz

value: Nephrectomy

value: sunitinib


title: RN319B

description: processed data file: data2.txt.gz


title: RN318G

description: processed data file: data2.txt.gz


title: RN319C

description: processed data file: data2.txt.gz


title: RN318H

description: processed data file: data2.txt.gz


title: RN318F

description: processed data file: data2.txt.gz


title: RN318C

description: processed data file: data2.txt.gz


title: RN318A

description: processed data file: data2.txt.gz


title: RN318B

description: processed data file: data2.txt.gz


title: SU16A 3/41

description: processed data file: data.txt.gz


title: SU06A 8/12

description: processed data file: data.txt.gz


title: SU09A 2/5

description: processed data file: data.txt.gz


title: SU13B 1/3

description: processed data file: data.txt.gz


title: SU54 A2

description:
processed data file: data.txt.gz
SU54 A2 corresponds to X43.SU54.A2 in data.txt.gz


title: SU46 A2

description: processed data file: data.txt.gz


title: SU05H 1/4

description: processed data file: data.txt.gz


title: SU04 7/8

description: processed data file: data.txt.gz


title: SU48 A2

description: processed data file: data.txt.gz


title: SU36 A1

description: processed data file: data.txt.gz


title: SU32 A2

description: processed data file: data.txt.gz


title: SU23 A6

description: processed data file: data.txt.gz


title: SU46A 5/8

description: processed data file: data.txt.gz


title: SU16 A4

description: processed data file: data.txt.gz


title: SU48A 3/4

description: processed data file: data.txt.gz


title: SU13 B2

description: processed data file: data.txt.gz


title: D10 regenerating ear tissue Acomys cahirinus

city: Lexington

first: Ashley

last: Seifert

state: Kentucky

address: 675 Rose St.

department: Biology

institute: University of Kentucky

description:
D10 regenerating ear tissue
haib14AWS2783

data_processing:
Normalize raw data using Trinity
Build references for each species using RSEM
Calculate raw transcript expression for each time point in each species using RSEM
Calculate expression fold change and probability of differential expression using Ebseq
Genome_build: de novo-assembled transcriptome for Acomys, mm10 for Mus
Supplementary_files_format_and_content: .result files were generated for each species comparing all time points versus D0.  Probability of differential expression and fold change are reported.  Due to the method the data was processed in, fold changes reported in this list are D0/DX.  To get DX/D0, the inverse of the reported fold change is used.

organism: Acomys cahirinus

source_name: Ear Tissue

extract_protocol:
tissue was frozen in liquid nitrogen, homgenized with ceramic beads in TriZol and extracted following TriZol protocol
HudsonAlpha directional RNAseq with ribosomal RNA reduction

tag: healing mechanism

value: ear tissue

value: D10 regenerating ear tissue


title: D15 regenerating ear tissue Acomys cahirinus

description:
D15 regenerating ear tissue
haib14AWS2783

value: D15 regenerating ear tissue


title: D5 regenerating ear tissue Acomys cahirinus

description:
D5 regenerating ear tissue
haib14AWS2783

value: D5 regenerating ear tissue


title: D20 regenerating ear tissue Acomys cahirinus

description:
D20 regenerating ear tissue
haib14AWS2783

value: D20 regenerating ear tissue


title: PiAgo1-input_rep1

city: Uppsala

first: Anna

last: Åsman

address: PO Box 7080

department: Molecular Sciences

country: Sweden

institute: Swedish University of Agricultural Sciences (SLU)

data_processing:
Read length filtration, 18-30 nt. Custom Perl script
tRNA/rRNA filtration (RFAM v10), bowtie v1.0.0 -v 0
Map to P. Infestans genome (http://www.broadinstitute.org) using bowtie v1.0.0, -v 0 -a
Count reads mapping to features (genes/repeats) using featureCount v1.4.6 (-M --fraction -s 1/2). Gene annotation was taken from http://www.broadinstitute.org, repeat annotation was made by mapping repeats from Haas et al. (2009) to the P. infestans genome (RepeatMasker v4.0.3)
Genome_build: P. infestans strain T30-4, http://www.broadinstitute.org
Supplementary_files_format_and_content: For each sample, there are four data files, containing the number of sense|antisense reads mapping to genes|repeats. Each file consists of tab-separated values with the following columns:Geneid, Chr, Start, End, Strand, Length, Number of reads

organism: Phytophthora infestans

source_name: Total RNA

extract_protocol:
Mycelium from the different strains were harvested and flash frozen in liquid nitrogen. PiAgo and control GFP immunoprecipitations were performed with anti-GFP antibody (Chromotek, gtm-100). PiAgo1_input RNA samples enriched for the low molecular weight fraction were prepared using the mirVana™ miRNA Isolation Kit (Ambion).
Barcoded sequencing libraries were constructed using the Ion Total RNA-Seq Kit v2 and Ion Xpress barcode primers. Sequencing was performed on the Ion Proton platform using the Ion PI Sequencing 200 kit v3 (Life Technologies).

tag: gfp-tagged protein

tag: wild-type background

tag: transformed construct

value: Mycelium

tag: ip antibody


title: D0 uninjured ear tissue Acomys cahirinus

description:
D0 uninjured ear tissue
haib14AWS2783

value: D0 uninjured ear tissue


title: SU09 A2

description: processed data file: data.txt.gz


title: PiAgo1-input_rep2


title: Sample 13 Necrotrophic phase

first: Lisa

last: Vaillancourt

address: 201F Plant Science Building

department: Plant Pathology

description: Necrotrophic hyphae, wild-type, biological replicate 3

data_processing:
Illumina software CASAVA-1.7.0 used for base calling and de-multiplexing
Fungal reads were stored as individual files for each sample in FASTQ format
The sequencing raw reads were mapped to the 12,006 annotated genes of C. graminicola strain M1.001 (ACOD01000001) using the CLC Genomics Workbench (GWB) RNA-Seq analysis tool
Aligned against Colletotrichum graminicola genome annotated genes (available via http://www.broadinstitute.org/annotation/genome/colletotrichum_group/MultiHome.html) using CLC Genomics Workbench RNA-seq analysis tool.
Supplementary_files_format_and_content: Tab-delimited text file include raw reads for each gene of C.graminicola in the biological replicates of the colonization stages of wild-type and mutant strains

organism: Colletotrichum graminicola

source_name: fungus +  plant (samples that mapped to fungus only)

growth_protocol: Samples were produced as described in Mosquera et al. (The Plant Cell 21: 1273 (2009) with modifications.

extract_protocol:
Two µg of PolyA-enriched RNA per sample was processed, including chemical fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end-repair, 3’end adenylation, adapter ligation (including different barcoding indices) and PCR amplification. After quality control analysis, libraries were pooled (3 libraries per pool) followed by single-read sequencing (1-4 lanes/pool) with a read length of 76 bp (including 7 bp for the barcode adaptor) using the Illumina Genome Analyzer IIx, according to standard Illumina protocols.
Illumina TruSeqTM RNA Sample Preparation Kit

tag: strain

value: wild-type

tag: Stage

value: Necrotrophic phase, 60h


title: GFP-IP_rep2

source_name: Immunoprecipitation of control GFP

value: GFP

value: GFP (Chromotek, gtm-100)


title: Sample 12 Necrotrophic phase

description: Necrotrophic hyphae, wild-type, biological replicate 2


title: SU05 G3

description: processed data file: data.txt.gz


title: SU39 A3

description: processed data file: data.txt.gz


title: SU06 A2

description: processed data file: data.txt.gz


title: SU04 A3

description:
processed data file: data.txt.gz
SU04 A3 corresponds to X30.SU04.A3 in data.txt.gz


title: GFP-IP_rep1


title: Sample 11 Necrotrophic phase

description: Necrotrophic hyphae, wild-type, biological replicate 1


title: SU54A2

description:
processed data file: data.txt.gz
SU54A2 corresponds to X29.SU54A2 in data.txt.gz


title: Sample 10 Biotrophic phase

description: Biotrophic hyphae, mutant, biological replicate 1

value: mutant

value: Biotrophic phase, 36h


title: Sample 9 Biotrophic phase

description: Biotrophic hyphae, wild-type, biological replicate 3


title: SU25 A6

description: processed data file: data.txt.gz

value: kidney


title: PiAgo4-IP_rep2

source_name: Ago-RNA co-immunoprecipitation


title: SU48A1

description: processed data file: data.txt.gz


title: PiAgo5-IP_rep1


title: Sample 8 Biotrophic phase

description: Biotrophic hyphae, wild-type, biological replicate 2


title: Sample 7 Biotrophic phase

description: Biotrophic hyphae, wild-type, biological replicate 1


title: PiAgo3-IP_rep1


title: PiAgo4-IP_rep1


title: Sample 6 Pre-penetration appressoria

description: Penetrating appressoria, mutant, biological replicate 3

value: Pre-penetration appressoria, 24h


title: Sample 3 Pre-penetration appressoria

description: Penetrating appressoria, wild-type, biological replicate 3


title: Sample 2 Pre-penetration appressoria

description: Penetrating appressoria, wild-type, biological replicate 2


title: Sample 4 Pre-penetration appressoria

description: Penetrating appressoria, mutant, biological replicate 1


title: SU39A2

description: processed data file: data.txt.gz

value: Nephrectomy


title: SU39A 3/3

description: processed data file: data.txt.gz

value: sunitinib


title: PiAgo1-IP_rep3


title: Ct_invitro_2

organism: Colletotrichum tofieldiae

value: fungal in vitro hyphae


title: Sample 11 Biotrophic phase

description: Biotrophic hyphae, mutant, biological replicate 2


title: SU32A1

description: processed data file: data.txt.gz


title: Ct_invitro_1


title: SU36A1

description: processed data file: data.txt.gz


title: 6hpf_amanitin

city: Kita-ku

first: Yuichiro

last: Mishima

state: Kyoto

address: Motoyama, Kamigamo,

department: Department of Frontier Life Sciences

country: Japan

institute: Kyoto Sangyo University

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were filtered with the quality cut-off 20 and minimum percentage 90.
Qualified reads were mapped to the zebrafish genome (Zv9/danRer7) using TopHat v1.4.0. with the gene model annotation Zv9.72.
Reads overlapping with UCSC RepeatMasker annotations (Zv9/danRer7) were discarded.
Differential expression levels between conditions were calculated using Cuffdiff v2.1.1. with the gene model annotation Zv9.72.
Genome_build: Zv9/danRer7
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample, differential expression between condotions in log2 scale and statistical significance.

organism: Danio rerio

source_name: whole embryo

growth_protocol: fertilized eggs were obtained by natural breadings

extract_protocol:
Total RNA was extracted from 40–50 embryos using TRI Reagent (Molecular Research Center), treated with DNaseI (TAKARA) and purified with RNeasy Mini Kit (QIAGEN).
Libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero (Illumina).

value: AB

value: whole embryo

tag: treatment

value: a-amanitin injected

tag: stages

value: 6 hpf


title: Ct_invitro_3

source_name: fungal in vitro hyphae


title: 6hpf_controlB

value: control (for amanitin experiment)


title: Sample 1 Pre-penetration appressoria

description: Penetrating appressoria, wild-type, biological replicate 1


title: 6hpf_CNOT7DN

value: CNOT7-DN injected


title: SU25A2

description: processed data file: data.txt.gz


title: 2hpf_control

value: control

value: 2 hpf


title: SU46A3

description: processed data file: data.txt.gz


title: 6hpf_control


title: Sample 5 Pre-penetration appressoria

description: Penetrating appressoria, mutant, biological replicate 2


title: SU23A2

description: processed data file: data.txt.gz


title: SU16A4

description: processed data file: data.txt.gz


title: DICER KO #43 (set 2)

city: Hwasun, Jeollanam-do

first: Young-Kook

last: Kim

address: 264, Seoyang-ro

department: Department of Biochemistry

country: South Korea

institute: Chonnam National University Medical School

description: small RNA (17-30nt)

data_processing:
FASTQ sequences produced from the sequencer were aligned to the human reference genome (GRCh38) by Bowtie2.
By comparing with genomic coordinates of miRNAs (obtained from mirbase.org), miRNA reads were chosen. Only the reads that matched perfectly with miRNA sequences were selected for further analyses.
To normalize miRNA reads, the read of miR-320a-3p was used for DROSHA and XPO5 knockouts. In the case of DICER knockout, the combined reads from rRNAs and tRNAs were used for the normalization.
Genome_build: GRCh38
Supplementary_files_format_and_content: Read numbers for each miRNA was calculated.

source_name: HCT116 cell line

extract_protocol:
10 µg of total RNA from parental and knockout cells was extracted with TRIzol reagent (Life Technologies).
TruSeq Small RNA Sample Prep Kit (Illumina) was used for the preparation of the small RNA sequencing library. Total RNA was size-separated on a 15% urea-polyacrylamide gel. The region of the gel containing RNA with the size from 17 to 30 nucleotides was excised and eluted for adaptor ligation at both 5' and 3' ends. The ligated RNAs were reverse-transcribed with SuperScript III (Life Technologies) reverse transcriptase and amplified using Phusion High-Fidelity DNA polymerase (Thermo Scientific). The final products were sequenced by MiSeq system (Illumina).

tag: genotype/variation

value: DICER knockout

tag: cell line

tag: experimental set

value: set 2


title: Parental cells (set 2)

description: small RNA (17-30nt)

value: wild type


title: XPO5 KO #19-1 (set 2)

description: small RNA (17-30nt)

value: XPO5 knockout


title: DROSHA KO #40 (set 1) replicate 2

description: small RNA (17-30nt)

value: DROSHA knockout

value: set 1


title: PiAgo1-IP_rep2

value: Mycelium

value: GFP (Chromotek, gtm-100)


title: SU13B1

description: processed data file: data.txt.gz

value: kidney

value: Nephrectomy

value: sunitinib


title: PiAgo1-IP_rep1


title: DROSHA KO #40 (set 1) replicate 1

description: small RNA (17-30nt)


title: SU09A2

description: processed data file: data.txt.gz


title: Parental cells (set 1) replicate 1

description: small RNA (17-30nt)


title: Parental cells (set 1) replicate 2

description: small RNA (17-30nt)


title: SU4A3

description:
processed data file: data.txt.gz
SU4A3 corresponds to X16.SU04A3 in data.txt.gz


title: SU05G2

description: processed data file: data.txt.gz


title: input DNA

city: Nagasaki

first: Masamichi

last: Doiguchi

address: Sakamoto 1-12-4

institute: University of Nagasaki

data_processing:
Basecalls performed using Illumina Miseq/Real Time Analysis.
ChIP-seq reads were aligned to the dm6 genome assembly using Burrows-Wheeler Alignment v0.7.5 (BWA) program, with default "aln" and "sames" parameters.
ChIP peaks were called using Model-based Alignment of ChIP-Seq (MACS) program with the following setting: macs, t, treatment_bamfile; c, control_bamfile; bdg; P=0.05
Genome_build: dm6
Supplementary_files_format_and_content: xls files were generated using MACS program and csv files were generated using R-package ChippeakAnno.

source_name: S2 cell

growth_protocol: S2 cells were grown at 26 °C in Schneider’s Drosophila media (Gibco), supplemented with 10% FBS.

extract_protocol:
Lysates were clarified from Mnase digested nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared using TruSeq ChIP Sample Prep Kit (Illumina) according to the manufacture’s instruction.

treatment_protocol: S2 cells (2 x 107) were plated in 5 ml of 1x Schneider’s Drosophila medium without FBS in 10-cm dishes. dsRNA of EGFP was added at 26 °C for 6 h, followed by 5 ml of 1x Schneider’s Drosophila medium with 10% FBS. The cells were then incubated for an additional 72 h to allow for turnover of the target mRNA.

tag: chip antibody


title: CBP ChIP

value: anti-CBP, custom-made antibodies


title: SMARCAD1 (ASNA) ChIP

value: anti-SMARCAD1 (ASNA), custom-made antibodies


title: SU54 D

description: processed data file: data.txt.gz

tag: tissue type

value: Biopsy

value: no sunitinib


title: SU36A 2/4

description: processed data file: data.txt.gz

tag: agent


title: DICER KO #45 (set 2)

description: small RNA (17-30nt)


title: SU48 D

description: processed data file: data.txt.gz

tag: tissue


title: SU46 D

description: processed data file: data.txt.gz


title: SU25 C

description: processed data file: data.txt.gz


title: SU36 C

description: processed data file: data.txt.gz


title: SU32 D

description: processed data file: data.txt.gz


title: XPO5 KO #19 (set 2)

description: small RNA (17-30nt)


title: SU04 E

description: processed data file: data.txt.gz


title: SU06A1

description: processed data file: data.txt.gz


title: SU23 C

description: processed data file: data.txt.gz


title: 6hpf_430MO

value: AB

value: whole embryo

value: miR-430 MO injected

value: 6 hpf


title: SU13 F

description: processed data file: data.txt.gz


title: SU09 C

description: processed data file: data.txt.gz


title: SU05 L

description: processed data file: data.txt.gz


title: SU16 E

description: processed data file: data.txt.gz


title: SU32A 1/2

description: processed data file: data.txt.gz


title: SU21 C

description: processed data file: data.txt.gz


title: SU16 F

description: processed data file: data.txt.gz


title: SU09 E

description: processed data file: data.txt.gz


title: SU25A 7/8

description: processed data file: data.txt.gz


title: LV-NC-miRNA

description: processed data file: miRNA_All_Counts.xls

tag: cell type

value: hESC cell line

tag: passage

value: stable control RNA overexpressed


title: SU23A 3/7

description: processed data file: data.txt.gz


title: X01-P58-lncRNA

description: processed data file: LncRNA_All_RPKM.xlsx


title: H1-P67-lncRNA


title: SU39 D

description: processed data file: data.txt.gz


title: Standard-housed VIP-Cre rep 3

first: Ivo

last: Spiegel

address: 220 Longwood Ave

department: Department of Neurobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mm9 genome using TopHat (v2.0.13) and Bowtie (2.1.0.0)42. On average, ~70% of mapped IP reads were uniquely mapped to the mm9 genome allowing for 0 mismatches and were therefore assignable to genic features. Values from all IP libraries were normalized using Cufform (v2.2.1), and values from the Cuffnorm output file 'genes-Count_Table' (normalized reads) were taken as a proxy for gene expression. P-values were generated for each Cre-line for each Dark-Light conditions using Cuffdiff (v2.2.1) using the timeseries (-T) flag based on 3 biological replicates.
Genome_build: mm9
Supplementary_files_format_and_content: Standard bigWig-formatted files (.bw) represent bwa-aligned reads piled up with single-base-pair resolution and then averaged over tiles of width 20bp.
Supplementary_files_format_and_content: Values from all IP libraries were normalized using Cufform (v2.2.1), and values from the Cuffnorm output file 'genes-Count_Table' (normalized reads) were taken as a proxy for gene expression and are shown in the .xlsx file.  The first set of 25 columns represent the mean of 3 bioreplicates for each Cre line and each stimulation condition; each subsequent set of 25 reports one of 3 bioreplicates.

source_name: Mouse brain

extract_protocol:
RiboTag-purification accoriding to Spiegel et al (Cell, 2014) and Sanz et al (PNAS 2009)
All samples had RIN numbers above 8.0. 5-10 ng of RNA were SPIA-amplified with the Ovation RNA Amplification System V2, yielding 5-8 μg of cDNA per sample. SPIA-amplified samples from RiboTag-IP fractions were processed in triplicate. For preparing Seq-libraries, 2 mg of each amplified cDNA were fragmented to 200-400 bp using a Covaris S2 sonicator (Acoustic wave instruments) using the following parameters: duty cycle = 10%, intensity = 5, cycles per burst = 200, time: = 60 seconds, total time = 5 minutes. After validating the fragment length of the sonicated cDNA using a 2100 BioAnalyzer, 2 mg of the fragmented cDNA were used for Seq library preparation using the PrepX DNA kit on an Apollo 324 robot (IntegenX). Quality of completed Seq-libraries was assessed using a 2100 BioAnalyzer (Agilent, Palo Alto, CA) and the completed libraries were sequenced on an Illumina HiSeq 2000 instrument per the manufacturer's standard protocols for single-end 50-bp sequencing with single-index reads.
SPIA amplification of 5-10 ng ribosome bound RNA

tag: age

value: 8 week

value: Visual cortex

tag: cre line

value: VIP

tag: housing

value: Standard

tag: light exposure

tag: replicate


title: Standard-housed VIP-Cre rep 2

tag: strain


title: Dark-housed VIP-Cre 3hr light rep 3

value: Dark


title: Dark-housed VIP-Cre 7.5hr light rep 2


title: Standard-housed VIP-Cre rep 1


title: Dark-housed VIP-Cre 7.5hr light rep 3


title: Dark-housed VIP-Cre 3hr light rep 1


title: Dark-housed VIP-Cre 1hr light rep 3


title: Dark-housed VIP-Cre 7.5hr light rep 1


title: 416b_IgGR

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description: Chromatin Immunoprecipitated DNA

data_processing:
Reads aligned to mm10 using Bowtie
bedGraphs created using bedtools
bigWigs created using UCSC utilities
Peaks called using MACS
Genome_build: mm10
Supplementary_files_format_and_content: fastq (unmapped reads), bigWig (density profile of mapped reads) and bed (peaks)

source_name: myeloid progenitor cell line

growth_protocol: Grown in RPMI 1640 plus 10% fetal calf serum plus penicillin and streptomycin

extract_protocol:
As described in Wilson et al., Cell Stem Cell. 2010 Oct 8;7(4):532-44
According to Illumina TruSeq DNA Sample Prep Kit

value: myeloid progenitor cell line

value: IgG

tag: chip antibody vendor

value: Sigma


title: 416b_Scl

description: Chromatin Immunoprecipitated DNA

value: Santa Cruz

tag: chip antibody cat. #

tag: chip antibody lot#


title: Dark-housed VIP-Cre 3hr light rep 2


title: SU06 D

description: processed data file: data.txt.gz

value: kidney

value: Biopsy


title: 416b_PU.1

description: Chromatin Immunoprecipitated DNA

tag: cell line


title: Dark-housed VIP-Cre 1hr light rep 2


title: 416b_Lyl1

description: Chromatin Immunoprecipitated DNA

value: Abcam


title: Dark-housed VIP-Cre rep 3


title: 416b_Runx1

description: Chromatin Immunoprecipitated DNA


title: Standard-housed SST-Cre rep 1

value: SST


title: Dark-housed VIP-Cre rep 2


title: Dark-housed VIP-Cre 1hr light rep 1


title: Dark-housed VIP-Cre rep 1


title: Standard-housed SST-Cre rep 3


title: 416b_Meis1

description: Chromatin Immunoprecipitated DNA


title: Dark-housed SST-Cre 7.5hr light rep 1


title: 416b_Gfi1b

description: Chromatin Immunoprecipitated DNA


title: Dark-housed SST-Cre 3hr light rep 3


title: 416b_Gata2

description: Chromatin Immunoprecipitated DNA


title: 416b_Fli-1

description: Chromatin Immunoprecipitated DNA


title: 416b_Erg

description: Chromatin Immunoprecipitated DNA

value: Erg


title: Testis_RNAseq_Control_24hr_R2

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description:
replicate 2
EC106
G Control24 R2

data_processing:
Reads passing the Illumina chastity filter were mapped to the D. melanogaster genome and assigned to gene models using Tophat 1.4.1 (Trapnell et al., 2009) and default settings except for the following; -G=true, minimum intron length was set to 42bp (-i 42), the maximum multihits was set to 1 (-g 1).
Transcript abundance was determined using HT-seq.
Genome_build: dm3, Flybase release 5 with no Uextra
Supplementary_files_format_and_content: Text files with raw counts; output from HT-seq.

source_name: testis

growth_protocol: 15 males and 30 virgin females were used to set up  6-8 crosses in bottles. Parent flies were flipped to new bottles after 5 days. All flies were raised and maintained at 18°C. Experimental and control flies were collected within 24 hours of eclosion and aged 5 days.

extract_protocol:
Ovary and testis were dissected from age-matched adult flies of the genotypes w1118; tra2ts2/tra2ts1 (experimental) or w1118 (control for dsxF->dsxM experiments); for dsxM->dsxF experiments the genotypes were: y1 w*; P{w+mc=UAS-Tra.F}20J7; P{w+mc=tubP-GAL80ts}7/P{w+mc=tubP-GAL4}LL7 (experimental) or P{w+mc=tubP-GAL80ts}7/P{w+mc=tubP-GAL4}LL7 (control). All samples were raised at 18°C until 5 days after eclosion when adults were shifted to either 29°C (for tra2ts) or 30°C (for UAS-TraF) for 0, 12, or 24 hours.  Total RNA was extracted from ovary and testis dissected at room temperature (placed on ice after 30 minutes) using TRIzol Reagent following manufacturer’s protocol (Ambion Life Technologies, Carlsbad, CA, USA).  Egg chambers stage 10 and older were removed and discarded to enrich for younger-staged egg chambers in the ovaries. Purified RNA was treated with DNAse I following manufacturer's protocol (New England Biolabs, Ipswich, MA, USA) and purified again using phenol:chloroform extraction followed by ethanol precipitation.  Duplicate RNA-seq libraries were constructed from 200 ng total RNA from independent dissection of each sample using the TruSeq RNA Sample Preparation v2 high-throughput (HT) protocol (Illumina, San Diego, CA, USA, 2011).  Libraries were sequenced on the HiSeq 2000 machine following a 76 bp single-end protocol (Illumina, San Diego, CA, USA).
True-Seq v2 protocol starting with 200 ng of total RNA.

treatment_protocol: On the 5th day, 15-20 time matched flies were separated into 3 vials designated as t=0, t=12, and t=24hrs. Flies were maintained at 29°C for 0, 12, and 24hrs and dissected at 25°C.

tag: Stage

value: adult

value: testis

tag: genotype

value: XY; tub-Gal4/tub-Gal80[ts]

tag: hours at restrictive temperature


title: Dark-housed SST-Cre 7.5hr light rep 2

value: 8 week


title: Dark-housed SST-Cre 1hr light rep 1

value: Visual cortex


title: Dark-housed SST-Cre 1hr light rep 3


title: Dark-housed SST-Cre 3hr light rep 2


title: Dark-housed SST-Cre 7.5hr light rep 3


title: Testis_RNAseq_Control_12hr_R2

description:
replicate 2
EC105
G Control12 R2


title: Dark-housed SST-Cre 3hr light rep 1


title: Dark-housed SST-Cre 1hr light rep 2


title: Dark-housed SST-Cre rep 3


title: 416b_H3K27Ac

description: Chromatin Immunoprecipitated DNA

tag: chip antibody


title: Standard-housed PV-Cre rep 1

tag: tissue

value: PV


title: Standard-housed SST-Cre rep 2

value: Standard


title: Standard-housed PV-Cre rep 3


title: Dark-housed SST-Cre rep 2

value: Dark


title: Standard-housed PV-Cre rep 2


title: Dark-housed PV-Cre 7.5hr light rep 3


title: Dark-housed PV-Cre 7.5hr light rep 2


title: miGh3e rep1

city: Chongqing

first: quan

last: sun

address: Chongwen road 2#

department: College of Bioinformation

institute: Chongqing University of Posts and Telecommunications

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to cotton genome no more than 5 mismatches using the SOAP aligner/SOAP2 software after low-quality reads (reads with unknown sequences ‘N’), adaptor sequence fragments, and empty reads were removed
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
The GeneIDs in the processed data files represent (e.g. CotAD_22466, CotAD_64340, etc.), The cotton genome and cds sequences we download form http://cgp.genomics.org.cn (Free to register to use). The reference :(Li F, Fan G, Lu C, Xiao G, Zou C, Kohel RJ, Ma Z, Shang H, Ma X, Wu J et al: Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution.
Genome_build: ASM98774v1; NCBI WGS Project: LBLM01 (Gossypium hirsutum)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Gossypium hirsutum

source_name: stem tip

extract_protocol:
RNA was harvested using Plant RNA EASYspin Plus Kit(Aidlab, Peking, China).
RNA and miRNA libraries were prepared for sequencing using standard Illumina protocols

value: shoot apical

value: the budding stage,twelve pieces of leaf

value: nulliplex-branch


title: miGh3e rep3


title: miGh3e rep2


title: miGh3c rep3

value: Huazhong 94-3130

value: the budding stage,eight pieces of leaf

value: normal branch


title: Dark-housed PV-Cre 3hr light rep 2


title: Dark-housed PV-Cre 1hr light rep 3


title: Dark-housed PV-Cre 3hr light rep 3


title: miGh3c rep1


title: Dark-housed PV-Cre 7.5hr light rep 1


title: Testis_RNAseq_TraF_0hr_R2

description:
replicate 2
EC101
G TraF0 R2

value: XY; UAS-tra[F]; tub-Gal4/tub-Gal80[ts]


title: miGh2e rep3

value: the pre-budding stage, five pieces of leaf


title: Testis_RNAseq_Control_12hr_R1

description:
replicate 1
EC99
G Control12 R1


title: Dark-housed SST-Cre rep 1

value: SST


title: miGh3c rep2


title: Testis_RNAseq_Control_24hr_R1

description:
replicate 1
EC100
G Control24 R1

value: adult


title: Dark-housed PV-Cre 1hr light rep 2


title: Testis_RNAseq_Control_0hr_R2

description:
replicate 2
EC104
G Control0 R2

value: testis


title: Testis_RNAseq_TraF_24hr_R2

description:
replicate 2
EC103
G TraF24 R2


title: Testis_RNAseq_TraF_12hr_R2

description:
replicate 2
EC102
G TraF12 R2


title: miGh2e rep2


title: Dark-housed PV-Cre 3hr light rep 1


title: Dark-housed PV-Cre 1hr light rep 1


title: Dark-housed PV-Cre rep 3


title: Testis_RNAseq_Control_0hr_R1

description:
replicate 1
EC98
G Control0 R1

value: XY; tub-Gal4/tub-Gal80[ts]


title: Testis_RNAseq_TraF_24hr_R1

description:
replicate 1
EC97
G TraF24 R1


title: miGh2e rep1


title: miGh2c rep3

value: the pre-budding stage, six pieces of leaf


title: miGh2c rep2


title: Testis_RNAseq_TraF_12hr_R1

description:
replicate 1
EC96
G TraF12 R1


title: Standard-housed Gad2-Cre rep 3

value: 8 week

value: Visual cortex


title: miGh2c rep1


title: Standard-housed Gad2-Cre rep 2

value: Standard


title: miGh1e rep 3

value: seedling stage, have two pieces of leaf


title: Ovary_RNAseq_w1118_12hr_R2

description:
replicate 2
EC81
G Wt12 R2

source_name: ovary

value: ovary


title: Standard-housed Gad2-Cre rep 1


title: Ovary_RNAseq_w1118_0hr_R2

description:
replicate 2
EC80
G Wt0 R2


title: miGh1e rep 1

value: shoot apical


title: Dark-housed Gad2-Cre 7.5hr light rep 3

value: Dark


title: Ovary_RNAseq_tra2ts_24hr_R2

description:
replicate 2
EC79
G tra2ts24 R2

value: XX; tra2[ts1]/tra2[ts2]


title: miGh1e rep 2

value: nulliplex-branch


title: Dark-housed Gad2-Cre 7.5hr light rep 2


title: Dark-housed Gad2-Cre 7.5hr light rep 1


title: miGh1c rep3

value: Huazhong 94-3130

value: normal branch


title: Ovary_RNAseq_tra2ts_12hr_R2

description:
replicate 2
EC78
G tra2ts12 R2


title: Dark-housed Gad2-Cre 3hr light rep 3


title: Sample_AH-9 Glioblastoma

city: Houston

first: Amy

middle: B

last: Heimberger

state: TX

address: 1400 Holcombe Blvd., FC7.2000

department: Neurosurgery

institute: The University of Texas MD Anderson Cancer Center

description: Glioblastoma tissue sample corresponding to Sample_AH-9

data_processing:
Reads were aligned with BWA 0.5.7 to both refseq Ensembl64 transcriptome and hg19 genome.
Genome Analysis Toolkit (GATK) 2.8.1 was used to do base recalibration.
RNA-SeQC v1.1.7 was used to evaluate and report the sequencing quality and produce the fpkm gene expression values per sample.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression profiles (fpkm) for 32 individual samples were assembled into one plain tex file separated by tab in which rows for genes and columns for samples.

source_name: brain

extract_protocol:
Extract RNA using Qiagen Allprep DNA/RNA mini kit.
Tru-Seq RNA sample prep kit

treatment_protocol: PolyA selection

tag: tumor type

value: glioblastoma (Grade IV)


title: miGh1c rep2


title: miGh1c rep1


title: Dark-housed PV-Cre rep 2

value: PV


title: Ovary_RNAseq_tra2ts_0hr_R2

description:
replicate 2
EC77
G tra2ts0 R2

value: adult


title: Ovary_RNAseq_w1118_12hr_R1

description:
replicate 1
EC75
G Wt12 R1


title: Sample_AH-8 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-8


title: Dark-housed PV-Cre rep 1


title: Sample_AH-7 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-7


title: Ovary_RNAseq_w1118_24hr_R2

description:
replicate 2
EC82
G Wt24 R2


title: Sample_AH-6 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-6


title: Dark-housed Gad2-Cre 3hr light rep 2


title: Ovary_RNAseq_w1118_24hr_R1

description:
replicate 1
EC76
G Wt24 R1


title: Testis_RNAseq_TraF_0hr_R1

description:
replicate 1
EC95
G TraF0 R1

value: testis

value: XY; UAS-tra[F]; tub-Gal4/tub-Gal80[ts]


title: Dark-housed Gad2-Cre 3hr light rep 1


title: Ovary_RNAseq_w1118_0hr_R1

description:
replicate 1
EC74
G Wt0 R1


title: Gh3e rep3

value: the budding stage,twelve pieces of leaf


title: Sample_AH-4 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-4


title: Dark-housed Gad2-Cre 1hr light rep 3

value: 8 week


title: Dark-housed Gad2-Cre 1hr light rep 2

value: Visual cortex


title: Gh3e rep2


title: Gh3e rep1


title: Ovary_RNAseq_tra2ts_24hr_R1

description:
replicate 1
EC73
G tra2ts24 R1


title: Sample_AH-3 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-3


title: Dark-housed Gad2-Cre 1hr light rep 1


title: LV-GAS5-miRNA

source_name: human embryonic stem cells

tag: cell type

value: hESC cell line

tag: passage

tag: genotype/variation

value: stable GAS5 overexpressed


title: Gh3c rep3

tag: age

value: the budding stage,eight pieces of leaf


title: Ovary_RNAseq_tra2ts_0hr_R1

description:
replicate 1
EC71
G tra2ts0 R1

value: ovary


title: Dark-housed Gad2-Cre rep 3

tag: cre line

tag: housing

value: Dark

tag: light exposure


title: Sample_AH-32 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-32


title: Gh3c rep2

tag: strain

value: shoot apical


title: Dark-housed Gad2-Cre rep 2

tag: replicate


title: Sample_AH-5 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-5


title: FB.4ht_RNASeq_rep2

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description:
For each replicate, fat bodies were dissected from 3 larvae of each indicated genotype.
processed data file: RNA-seq_Counts.txt, DESeq-processed_FB.control_vs_FB.25mkM.4HT.txt
FB.25mkM.4HT.2

data_processing:
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2000.
For each sample, reads were mapped against the Drosophila reference genome (dm3) using TopHat (Trapnell, C. et al. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 25(9), 1105-11, 2009), which was supplied with a known set of gene models. In order to get per sample absolute counts for every gene, HTSeq (Anders, S. et al. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 31(2), 166-9, 2015) was used.
Differentially expressed genes were identified by using the R package DESeq (Anders, S. and Huber, W. Differential expression analysis for sequence count data. Genome Biol 11(10), R106, 2010; Anders, S. et al. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat Protoc 8(9), 1765-86, 2013).
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files

source_name: larval fat bodies

growth_protocol: Flies were raised at 25°C on standard cornmeal/molasses/agar medium supplemented with 4-hydroxytamoxifen (Sigma-Aldrich, H7904) at a final concentration of 25 µM.

extract_protocol:
Tissue was homogenized in TRIzol reagent in a 15ml tube using a polytron DI 18 disperser (IKA). Total RNA extraction was performed according to the TRIzol reagent manufacturer’s instructions. Briefly, 0.2× volumes of chloroform (st. amylene) (Biosolve, 030810) was added to the homogenate and the tube was shaken vigorously. The tube was incubated for 3 minutes at room temperature and spun for 1 hour at 4120×g at 4°C. Approximately 70% of the upper aqueous phase was transferred into a new 15ml tube and 0.5× volume of isopropanol (Sigma-Aldrich, 33539) was added and mixed. The tube was incubated for 10 minutes at room temperature and spun for 30 minutes at 4120×g at 4°C. The supernatant was removed and the pellet was washed twice with 80% ethanol (Sigma-Aldrich, 32221). The total RNA pellet was air-dried for 8 minutes, dissolved in an appropriate volume of nuclease free water (Ambion, AM9938) and quantified using a NanoDrop spectrophotometer. The total RNA was further purified using the RNeasy MinElute Cleanup Kit (QIAGEN, 74204) according to the manufacturer’s instructions. Quality (RIN>8) and quantity of the total RNA was assessed by using an Agilent BioAnalyzer 2100 Nano chip (Agilent, 5067-1511).
Illumina TruSeq mRNA libraries were generated using the TruSeq RNA Library Preparation Kit v2 (Illumina, RS-122-2001/2) according to the manufacturer’s instructions. Briefly, polyadenylated RNA from intact total RNA was purified using oligo-dT beads. Following purification, the RNA was fragmented, random primed and reverse transcribed using SuperScript II Reverse Transcriptase (Invitrogen, 18064-014). Second strand synthesis was accomplished by using Polymerase I and RNase H. The generated cDNA fragments were 3′ end adenylated and ligated to Illumina paired-end sequencing adapters and subsequently amplified by 15 cycles of PCR. The libraries were analyzed using an Agilent BioAnalyzer 2100 DNA 7500 chip (Agilent, 5067-1506), diluted and pooled equimolar into a 10nM sequencing pool.

treatment_protocol: Fat bodies were dissected from 18 larvae in 1×PBS [140 mM NaCl, 10 mM PO4 Buffer, 3 mM KCl; Invitrogen cat. no. 18912-014] using forceps and dissection needles and collected in TRIzol reagent (Invitrogen, 15596-018) on ice.

tag: gender

value: male

value: equal mix of the following 6 lines: [1] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]}ZH51C  [2] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]-PC}ZH51C  [3] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]-H1}ZH51C  [4] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]-HP1}ZH51C  [5] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]-MRG15}ZH51C  [6] y,w; M{FL.hsp70P-Dam[4-HT-intein@L127C]-BRM}ZH51C

tag: developmental stage

value: wandering third instar larvae

value: fat bodies


title: Sample_AH-30 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-30

value: glioblastoma (Grade IV)


title: FB.4ht_RNASeq_rep1

description:
For each replicate, fat bodies were dissected from 3 larvae of each indicated genotype.
processed data file: RNA-seq_Counts.txt, DESeq-processed_FB.control_vs_FB.25mkM.4HT.txt
FB.25mkM.4HT.1


title: Gh2e rep3

value: the pre-budding stage, five pieces of leaf

value: nulliplex-branch


title: Dark-housed Gad2-Cre rep 1


title: Sample_AH-2 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-2


title: Gh3c rep1

value: Huazhong 94-3130

value: normal branch


title: Sample_AH-31 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-31


title: FB.wt_RNASeq_rep2

description:
For each replicate, fat bodies were dissected from 3 larvae of each indicated genotype.
processed data file: RNA-seq_Counts.txt, DESeq-processed_FB.control_vs_BR.txt, DESeq-processed_FB.control_vs_FB.25mkM.4HT.txt
FB.control.2

growth_protocol: Flies were raised at 25°C on standard cornmeal/molasses/agar medium.


title: Gh2e rep2


title: Sample_AH-29 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-29


title: FB.wt_RNASeq_rep1

description:
For each replicate, fat bodies were dissected from 3 larvae of each indicated genotype.
processed data file: RNA-seq_Counts.txt, DESeq-processed_FB.control_vs_BR.txt, DESeq-processed_FB.control_vs_FB.25mkM.4HT.txt
FB.control.1


title: Ovary_RNAseq_tra2ts_12hr_R1

description:
replicate 1
EC72
G tra2ts12 R1

tag: Stage

value: adult

value: XX; tra2[ts1]/tra2[ts2]


title: Standard-housed Emx-Cre rep 2

value: 8 week

value: Visual cortex

value: Emx

value: Standard


title: Standard-housed Emx-Cre rep 1


title: Gh2e rep1

tag: genotype


title: Sample_AH-27 Glioblastoma

description: Glioblastoma tissue sample corresponding to Sample_AH-27


title: Gh2c rep3

value: the pre-budding stage, six pieces of leaf


title: Dark-housed Emx-Cre 7.5hr light rep 3

value: Dark


title: Gh2c rep2

value: shoot apical