title: SLV51

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV51

value: bi-sulphite converted genomic DNA from SLV51


title: p0-cortex_bedel_14

status: Public on Mar 01 2020

type: SRA

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

country: China

institute: Shanghai JiaoTong University

description: single-cell RNA-seq

library_source: transcriptomic

data_processing:
Single-cell RNA-seq reads were aligned to the mm38_tran genome assembly using hisat2 version 2.1.0 with parameters:-p 8 --mp 7,6 --sp 3,2 --rdg 6,5 --dta-cufflinks -x
File format is  transformed to BAM using samtools version 1.9
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks version 2.2.1
Genome_build: mm38_tran
Supplementary_files_format_and_content: fpkm_tracking files include FPKM values for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: cortex neuron

extract_protocol:
P0 mouse brain was dissected, and the tissue from cerebral cortex was digested with 0.013% of collagenase in Neurobasal Medium (Gibco) at 37℃ for 3 min. The collagenase was neutralized by adding excess amount of Neurobasal Medium. Single-cell suspension was made by gentle pipetting, and then filtered through 100-μm cell strainers.Single cells were then picked under the microscope by using a micro capillary pipette into the thin-walled PCR tube containing 2 µl of cell lysis buffer, 1 µl of oligo-dT primer and 1 µl of dNTP mix.
First,reverse transcription is performed,the cDNA was pre-amplification by PCR. The cDNA library was then purified, tagmented, and ligated with adapters using the Nextera XT DNA Library Preparation kit (Illumina FC-131-1096).. Finally, the adapter-ligated fragments were further amplified by PCR and purified with AMPure XP beads (Beckman).

tag: strain

tag: tissue

value: cortex neuron

tag: age

tag: genotype

value: CBS b-e-/-


title: RC17_after_mesDA_25_B3

city: Uppsala

first: Asa

middle: Kristina

last: Bjorklund

address: Box 596

department: Cell and Molecular Biology

country: Sweden

institute: Uppsala University

data_processing:
All reads were aligned to the human (hg19) genome using STAR v2.3.0e (Dobin et al. 2013)
Non-uniquely mapped reads were removed using Samtools
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in Ensembl ( June 2015)
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression values are provided as rpkms and counts (comma separated text files)

organism: Homo sapiens

source_name: Human graft in rat brain

growth_protocol: Ventral midbrain human embryonic stem cells have been generated following the Nature protocols: Nolbrant et al 2017.

extract_protocol:
Single cells have been extracted from tissue using Papain Dissociation System (Worthington). cDNA was generated from FACS sorted single cells (ventral midbrain human embryonic stem cells before grafting, fetal cells before and after grafting were sorted for size, ventral midbrain human embryonic stem cells after grafting were sorted for GFP expression) using Smart-seq2 protocol (Picelli et al. Nature Methods 2013).  ERCC spike-in RNA was added to the lysis buffer.
Nextera XT DNA sample preparation index kit, 96 indices (Illumina)

tag: cell type

value: B

tag: sortingmethod

value: GFP

tag: plate


title: RC17_after_mesDA_25_B11


title: RC17_after_mesDA_25_B10


title: p0-cortex_bedel_8

description: single-cell RNA-seq


title: VB3_PDX1

city: Cambridge

first: Michael

last: Hemann

state: Massachusetts

address: 500 Main St, Building 76 Room 301

department: Koch Institute

country: USA

institute: Massachusetts Institute of Technology

description:
processed data file:
PDXCells_rawCounts.txt
D16-165012

data_processing:
Read pairs were combined into a single fastq with well/UMI information concatenated with the second read name, reads sharing sequence and UMI information were collapsed into single exemplars and aligned against either a joint human/murine genome (hg19 and mm9) assembly with BWA mem v. 0.7.12-r1039 with flag -t 16 [http://bio-bwa.sourceforge.net/ ].
Subsequently bam files were sorted by read positions and indexed using samtools v 0.1.18 [Li2009].
The UMI is located in read 1, bp 7-16.
Gene expression was estimated based on reads mapping near the 3' end of transcripts using ESAT [Derr2016] with the following parameters -task score3p -alignments $sample_list   -wLen 50 -wExt 5000 -wOlap 0 -sigTest 0.01 -multimap ignore, poiting to a refseq-based gene annotation (hg19 and mm9, as downloaded from the UCSC Genome Browser) and gene-level data were used for downstream analyses
Genome_build: mm9/hg19
Supplementary_files_format_and_content: Tab-delimited txt file with gene-level counts

molecule: total RNA

source_name: Lymphoma PDX cells

growth_protocol: Lymphoma PDX cells are transplanted into NSG mice and harvested along with macrophages from the bone marrow ('B' in sample names) and/or spleen ('S' in sample names) after treatment with single or combination chemotherapy

extract_protocol:
Cell lysis and RNA extraction were performed using the QIAGEN RNeasy Plus Mini kit for human lymphoma PDX cells and the QIAGEN RNeasy Plus Mini kit for mouse macrophages
RNA samples were quantified and quality assessed using an Advanced Analytical Fragment Analyzer. 20ng of totalRNA was used for library preparation with ERCC Spike-in control Mix A (Ambion 10-6 final dilution). All steps were performed on a Tecan EVO150. 3’DGE-custom primers 3V6NEXT-bmc#1-24 are added to a final concentration of 1.2uM. (5'-/5Biosg/ACACTCTTTCCCTACACGACGCTCTTCCGATCT[BC6]N10T30VN-3'  where  5Biosg = 5’  biotin, [BC6] = 6bp barcode specific to each sample/well, N10 = Unique Molecular Identifiers, Integrated DNA technologies).
After addition of the oligonucleotides, samples were denatured at 72C for 2 minutes followed by addition of SMARTScribe RT per manufacturer’s recommendations with Template-Switching oligo5V6NEXT (12uM, [5V6NEXT : 5’-iCiGiCACACTCTTTCCCTACACGACGCrGrGrG-3’  where  iC: iso-dC, iG: iso-dG, rG: RNA G ]) and incubation at 42C for 90’ followed by inactivation at 72C for 10’.
Following the template switching reaction, cDNA from 24 wells containing unique well identifiers were pooled together and cleaned using RNA Ampure beads at 1.0X. cDNA was eluted with 90 ul of water followed by digestion with Exonuclease I at 37C for 45 minutes, inactivation at 80C for 20 minutes.  Single stranded cDNA was then cleaned using RNA Ampure beads at 1.0X and eluted in 50ul of water.
Second strand synthesis and PCR amplification was done using the Advantage 2 Polymerase Mix (Clontech) and the SINGV6 primer (10 pmol, Integrated DNA Technologies 5’-/5Biosg/ACACTCTTTCCCTACACGACGC-3’ ). 12 cycles of PCR was performed followed by clean up using regular SPRI beads at 1.0X, and was eluted with 20ul of EB. Successful amplification of cDNA was confirmed using the Fragment Analyzer. Illumina libraries are then produced using standard Nextera tagmentation substituting P5NEXTPT5-bmc primer (25μM, Integrated DNA Technologies, (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCG*A*T*C*T*-3’  where  * = phosphorothioate bonds. ) in place of the normal N500 primer.
Final libraries were cleaned using SPRI beads at 1X and quantified using the Fragment Analyzer and qPCR before being loaded for paired-end sequencing using the Illumina NextSeq500.

treatment_protocol: Vehicle, doxorubicin, alemtuzumab, cyclophosphamide or a combination of alemtuzumab and cyclophosphamide are intraperitoneally administered into tumor-bearing NSG mice. Tumor-free NSG mice are also treated with vehicle or cyclophosphamide for analysis of cyclophosphamide's effects on bone marrow macrophages.

value: B cell double-hit lymphoma

tag: treatment

value: Vehicle

value: Bone marrow


title: VB1_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165010


title: p0-cortex_bedel_7

description: single-cell RNA-seq


title: RC17_after_mesDA_25_B1


title: CS3_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165009

value: Cyclophosphamide

value: Spleen


title: SLV32

type: genomic

city: London

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

country: United Kingdom

institute: University College London

description: Saliva tissue samples

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Reader using standard recommended Illumina scanner setting

data_processing: idat files processed using minfi 1.22.1, provided beta-value was generated using Illumina definition and default settings

label: Cy5 and Cy3

molecule: genomic DNA

source_name: genomic DNA from saliva sample SLV32

label_protocol: samples were bisulphite converted using the MagPrep 96-well format kit. Overnight conversion was performed using alternative incubation conditions recommended for Infinium arrays (16 cycles of: 95 degrees for 30 seconds, 50 degrees for 60 minutes)

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

tag: molecule subtype

value: bi-sulphite converted genomic DNA from SLV32

tag: gender

value: M


title: SLV33

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV33

value: bi-sulphite converted genomic DNA from SLV33


title: p0-cortex_WT_35

description: single-cell RNA-seq

value: wild type


title: SLV30

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV30

value: bi-sulphite converted genomic DNA from SLV30


title: SLV26

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV26

value: bi-sulphite converted genomic DNA from SLV26


title: CS2_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165008


title: RC17_after_mesDA_25_A8


title: p0-cortex_WT_34

description: single-cell RNA-seq


title: SLV29

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV29

value: bi-sulphite converted genomic DNA from SLV29


title: SLV28

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV28

value: bi-sulphite converted genomic DNA from SLV28


title: CS1_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165007


title: p0-cortex_WT_33

description: single-cell RNA-seq

value: cortex neuron


title: RC17_after_mesDA_25_A9


title: p0-cortex_WT_32

description: single-cell RNA-seq


title: RC17_after_mesDA_25_A6


title: RC17_after_mesDA_25_A7


title: SLV25

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV25

value: bi-sulphite converted genomic DNA from SLV25


title: DS3_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165006

value: Doxorubicin


title: DS2_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165005


title: RC17_after_mesDA_25_A5

value: B

value: GFP


title: SLV23

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV23

value: bi-sulphite converted genomic DNA from SLV23


title: DS1_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165004

value: B cell double-hit lymphoma


title: SLV27

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV27

value: bi-sulphite converted genomic DNA from SLV27


title: VS3_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165003

value: Vehicle

value: Spleen


title: SLV24

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV24

value: bi-sulphite converted genomic DNA from SLV24

value: M


title: p0-cortex_WT_30

description: single-cell RNA-seq

value: wild type


title: p0-cortex_WT_29

description: single-cell RNA-seq


title: VS2_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165002


title: RC17_after_mesDA_25_A3


title: p0-cortex_WT_31

description: single-cell RNA-seq


title: DB1_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165013

value: Bone marrow


title: p0-cortex_WT_28

description: single-cell RNA-seq


title: VS1_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165001


title: p0-cortex_WT_27

description: single-cell RNA-seq


title: RC17_after_mesDA_25_A11


title: RC17_after_mesDA_25_A12


title: SLV22

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV22

value: bi-sulphite converted genomic DNA from SLV22

value: F


title: p0-cortex_WT_26

description: single-cell RNA-seq


title: RC17_after_mesDA_25_A10


title: sample 76

type: RNA

city: Odense C

first: Sambavy

last: Nadaraja

address: Kløvervænget 8, Indgang 109

country: Denmark

institute: Odense University Hospital

hyb_protocol: affymetrix manufactures procedure

scan_protocol: affymetrix manufactures procedure

data_processing: RMA normalization and standard processing available at Qlucore

label: biotin

source_name: tumor biopsy from older ovarian cancer patient

label_protocol: affymetrix manufactures procedure

extract_protocol: Qiagen manufactures procedure automatized on QiaSymphony for FFPE; RNA quality and quantity was controled by BioAnalyzer and Nanodrop.

value: female

value: ovarian tumor biopsy

tag: diagnosis

value: high-grade serous adenocarcinoma (HGSC)

tag: disease progression

value: early


title: p0-cortex_WT_25

description: single-cell RNA-seq

value: cortex neuron


title: RC17_after_mesDA_25_A2

value: B

value: GFP


title: SLV19

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV19

value: bi-sulphite converted genomic DNA from SLV19


title: RC17_after_mesDA_25_A4


title: p0-cortex_WT_24

description: single-cell RNA-seq


title: VB2_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165011

value: B cell double-hit lymphoma


title: SLV20

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV20

value: bi-sulphite converted genomic DNA from SLV20


title: sample 75

value: late


title: RC17_after_mesDA_18_H11


title: sample 73


title: sample 74


title: RC17_after_mesDA_18_H10


title: RC17_after_mesDA_25_A1


title: SLV17

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV17

value: bi-sulphite converted genomic DNA from SLV17


title: ko retina

city: New York

first: Miruna

middle: Georgiana

last: Ghinia Tegla

state: New York

address: 85 St. Nicholas Terrace

department: Biology

institute: CCNY CUNY

data_processing:
Cell Ranger - demultiplexing, barecode processing, single cell 3' gene counting
BAM files for wt and ko samples
Genome_build: GRCg6a (Gallus gallus6)
Supplementary_files_format_and_content: filtered matrices, barecodes and gene lists for both samples

organism: Gallus gallus

source_name: developing retinal cells

extract_protocol:
not provided
10x Chromium based

value: retina

tag: developmental stage

tag: florescent tag

value: OTX2ECR2::GFP reporter


title: p0-cortex_WT_22

description: single-cell RNA-seq

source_name: cortex neuron

value: wild type


title: SLV21

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV21

value: bi-sulphite converted genomic DNA from SLV21

value: M


title: SLV13

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV13

value: bi-sulphite converted genomic DNA from SLV13

value: F


title: SLV14

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV14

value: bi-sulphite converted genomic DNA from SLV14


title: wt retina


title: p0-cortex_WT_21

description: single-cell RNA-seq


title: sample 70

value: female

value: ovarian tumor biopsy

value: high-grade serous adenocarcinoma (HGSC)


title: G2_S9

city: BEAUCOUZE

first: Adrien

last: PERRIN

address: 42 Rue Georges Morel

country: France

institute: INRA - IRHS

description: Tree versus Graft

library_source: genomic

data_processing:
Bisulfite sequencing reads were mapped on reference genome with Bsmap tool (Xi and Li 2009)
Genome_build: GDDH13_V1.1 reference genome
Supplementary_files_format_and_content: tab-delimited text files methylation_calling
Supplementary_files_format_and_content: Supp_Tab_S3.xlsx

organism: Malus domestica

source_name: Grafted plant

growth_protocol: Malus domestica materials were obtained from ‘GDDH13’ (Lespinasse et al. 1999) line (X9273). Grafted plant materials were obtained by grafting budwood of ‘GDDH13’ orchard tree (2001) on the rootstock ‘MM106’. Seedling materials were obtained by self-fertilization of ‘GDDH13’ tree (2007), apple fruit were then harvested to get seed. Seed dormancy was removed by 3 months of cold stratification before sowing. A clone of the original ‘GDDH13’ from orchard, grafted onto an MM106 rootstock in 2007 and growing in the greenhouse since was used as reference mature adult tree.

extract_protocol:
DNA was extracted using NucleoSpin Plant II kit (Macherey-Nagel, Hoerdt, France). The manufacturer's recommendations were applied with the next modifications: at step 2a PL1 buffer quantity was raised to 800µL and PVP40 was added at 3% of final volume, suspension was then incubated 30min at 65°C under agitation. The lysate solution was centrifuged 2min at 11000g before transferring the supernatant in step 3. At step 4 PC buffer was raised to 900µL. In step 6 the first wash was decreased to 600µL and the third wash was raised to 300µL. An extra-centrifuge step was added after washing to remove ethanol waste from the column. In step 7 DNA was eluted twice in 55µL in total.
Made by sequencing platerform

tag: tissus

value: last and completely opened leave

tag: number sampled plant

tag: biological replicate


title: SLV12

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV12

value: bi-sulphite converted genomic DNA from SLV12


title: RC17_after_mesDA_18_G6

source_name: Human graft in rat brain

value: B

value: GFP


title: p0-cortex_WT_20

description: single-cell RNA-seq

tag: strain

value: cortex neuron


title: RC17_after_mesDA_18_G7


title: sample 71

tag: tissue

value: early


title: RC17_after_mesDA_18_G5


title: SLV15

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV15

value: bi-sulphite converted genomic DNA from SLV15


title: S4_S12

description: Tree versus Seed

source_name: Seedling plant


title: sample 69

value: late


title: RC17_after_mesDA_18_G4


title: SLV10

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV10

value: bi-sulphite converted genomic DNA from SLV10


title: p0-cortex_WT_19

description: single-cell RNA-seq

tag: age

value: wild type


title: S3_S11

description: Tree versus Seed

tag: genotype


title: RC17_after_mesDA_18_G3

tag: cell type


title: p0-cortex_WT_17

description: single-cell RNA-seq


title: S2_S5

description: Tree versus Seed


title: sample 68


title: RC17_after_mesDA_18_G12

tag: sortingmethod


title: SLV11

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV11

value: bi-sulphite converted genomic DNA from SLV11

value: M


title: p0-cortex_WT_16

description: single-cell RNA-seq


title: SLV6

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV6

value: bi-sulphite converted genomic DNA from SLV6


title: SLV18

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV18

value: bi-sulphite converted genomic DNA from SLV18


title: p0-cortex_WT_18

description: single-cell RNA-seq


title: S1_S10

description: Tree versus Seed


title: RC17_after_mesDA_18_G11

tag: plate


title: sample 66

source_name: tumor biopsy from older ovarian cancer patient

value: female


title: p0-cortex_WT_15

description: single-cell RNA-seq


title: T3_S1

description: Tree versus Seed; Tree versus Graft

source_name: Adult mature tree


title: G1_S8

description: Tree versus Graft


title: SLV9

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV9

value: bi-sulphite converted genomic DNA from SLV9


title: p0-cortex_WT_14

description: single-cell RNA-seq


title: RC17_after_mesDA_18_G10


title: sample 67

value: ovarian tumor biopsy

value: high-grade serous adenocarcinoma (HGSC)


title: SLV7

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV7

value: bi-sulphite converted genomic DNA from SLV7


title: sample 64


title: T2_S7

description: Tree versus Seed; Tree versus Graft

value: last and completely opened leave


title: RC17_after_mesDA_18_G1

value: B

value: GFP


title: p0-cortex_WT_13

description: single-cell RNA-seq

source_name: cortex neuron

value: cortex neuron


title: sample 62


title: T1_S4

description: Tree versus Seed; Tree versus Graft


title: SLV3

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV3

value: bi-sulphite converted genomic DNA from SLV3


title: RNA-seq_Folic-acid-treated 3

city: Madison

first: Bermans

middle: J

last: Iskandar

state: WI

address: 600 Highland Ave, K4/832

department: Neurological Surgery

institute: University of Wisconsin

data_processing:
An average of 31.6 million paired-end reads were sequenced per sample. An initial check of quality was assessed for each pair-mate using FastQC.
After reads were assessed for quality, paired-end reads were aligned to the Rattus norvegicus genome (rn6) using RSEM v1.3.1 which utilized STAR v2.7.0.
Gene expression was calculated using RSEM which employed a forward probability of 0.0, followed by differential expression analysis using EBSeq which uses an empirical Bayes method and expectation maximization in the computation of normalized fold changes and to determine differential expression.
To account for multiple comparisons and to reduce false positives, a false discovery rate (FDR) of 0.05 was employed in the determination of differentially expressed genes.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files with counts per gene

organism: Rattus norvegicus

source_name: Spinal cord

extract_protocol:
Approximately 100 ng of total RNA from F3 generation spinal cord tissue was used for sequence library construction following instructions of NuGen mRNA sample prep kit (cat# 0348). In brief, total RNA was copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. These cDNA fragments went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. These products were gel purified and enriched with PCR to create the final cDNA libraries. The library constructs were run on the bioanalyzer to verify the size and concentration before sequencing on the Illumina HiSeq2500 machine where 100-cycle single-end sequencing was performed by the University of Wisconsin Biotechnology Center. In short, libraries from the same mice and combinations that were used to generate the 5hmC data were sequenced for each experimental condition.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague-Dawley

value: Spinal cord

tag: generation

value: F3 of F0-folate lineage


title: RC17_after_mesDA_18_F7


title: RNA-seq_Folic-acid-treated 2


title: SLV16

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV16

tag: molecule subtype

value: bi-sulphite converted genomic DNA from SLV16


title: SLV8

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV8

value: bi-sulphite converted genomic DNA from SLV8

tag: gender

value: M


title: p0-cortex_WT_10

description: single-cell RNA-seq

value: wild type


title: RC17_after_mesDA_18_F4


title: RC17_after_mesDA_18_F2


title: SLV4

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV4

value: bi-sulphite converted genomic DNA from SLV4


title: p0-cortex_WT_9

description: single-cell RNA-seq


title: RNA-seq_Folic-acid-treated 1


title: RC17_after_mesDA_18_F8

source_name: Human graft in rat brain


title: sample 59

value: female

tag: diagnosis

value: early


title: p0-cortex_WT_11

description: single-cell RNA-seq


title: SLV1

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV1

value: bi-sulphite converted genomic DNA from SLV1


title: sample 57

value: ovarian tumor biopsy

value: high-grade serous adenocarcinoma (HGSC)

tag: disease progression

value: late


title: p0-cortex_WT_23

description: single-cell RNA-seq


title: RNA-seq_Control 3

value: F3 of F0-control lineage


title: sample 56


title: sample 53


title: p0-cortex_WT_8

description: single-cell RNA-seq

value: cortex neuron


title: sample 58


title: sample 52


title: SLV5

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV5

value: bi-sulphite converted genomic DNA from SLV5

value: F


title: RC17_after_mesDA_18_F11

value: B

value: GFP


title: RNA-seq_Control 2

value: Sprague-Dawley

value: Spinal cord


title: RC17_after_mesDA_18_F1


title: sample 61


title: p0-cortex_WT_7

description: single-cell RNA-seq


title: RC17_after_mesDA_18_F12


title: RNA-seq_Control 1


title: RC17_after_mesDA_18_E7


title: RC17_after_mesDA_18_E9


title: p0-cortex_bedel_4

description: single-cell RNA-seq

value: CBS b-e-/-


title: p0-cortex_bedel_5

description: single-cell RNA-seq


title: sOB_C

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

country: Netherlands

institute: ErasmusMC

description: miRNA expression in svHFO replicate C

data_processing:
The unprocessed fastq files were generated using the Illumina casava 1.8.3 software allowing
for one mismatch in the barcode. Subsequently alignment of the reads was performed using novoalign
with the inclusion of the adapter trimming option (standard illumina adapter) Special settings that
allow for the alignment of short reads were used. Quantification of counts was done using
feature counts against the human small RNA database. Finally differential expression analysis clustering and
principle component analysis was done in the R enviroment using the DESeq2 package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: svHFO cells

growth_protocol: Simian virus 40-immortalized human osteoblast cells from fetal calvaria, SV-HFO cells (26), were seeded at a density of 1 × 10e4 cells/ cm2 and cultured in α-MEM (GIBCO, Paisley, UK) supplemented with 20 mM HEPES, pH 7.5 (Sigma, St. Louis, MO, USA), streptomycin/ penicillin, 1.8 mM CaCl2 (Sigma), 10 mM β-glycerophosphate (Sigma) and 2% FCS (GIBCO) at 37°C in a humidified atmosphere of 5% CO2 for 12 - 14 days. The culture medium was replaced every 2 - 3 days. Simian virus 40-immortalized human osteoblasts from fetal limb tissue (hFOB 1.19 cells, ATCC® CRL11372™) were seeded at a density of 1.5 × 10e4 cells/ cm2 and cultured in DMEM/F12 (Thermo Fisher Scientific, Waltham, MA, USA), supplemented with 2.5 mM L-glutamine, 0.3 mg/ mL G418, streptomycin/ penicillin and 10% FCS at 34°C in a humidified atmosphere of 5% CO2 for 24 hours. hMSC-TERT cells (27) were seeded at a density of 1.5 × 10e4 cells/ cm2 and cultured in MEM (Thermo Fisher Scientific), supplemented with streptomycin/ penicillin and 10% FCS at 37°C in a humidified atmosphere of 5% CO2 for 24 hours. All cell lines were washed with 1X PBS and refreshed with their respective serum-free culture medium 24 hours prior to EV isolation.

extract_protocol:
Total EV-RNA was isolated using the TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions.
Sequencing of miRNAs was performed by Illumina MiSeq with samples prepared with the NEBNext Small RNA library preparation kit (NEB), according to the manufacturer’s instructions.

treatment_protocol: EVs were isolated from 20 mL conditioned medium by low speed centrifugation (1500 rpm, 5 minutes; 4500 rpm, 10 minutes) followed by ultracentrifugation (20,000g, 30 minutes; 100,000g, 1 hour at 4°C) of the supernatant using the SW32Ti rotor (Beckman Coulter, Fullerton, CA, USA).

tag: cell line

value: Simian virus 40-immortalized human osteoblast cells (SV-HFO cells)

tag: sample type

value: cells


title: sOB_B

description: miRNA expression in svHFO replicate B


title: p0-cortex_bedel_6

description: single-cell RNA-seq


title: p0-cortex_WT_12

description: single-cell RNA-seq

value: wild type


title: SLV2

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV2

value: bi-sulphite converted genomic DNA from SLV2

value: M


title: sOB_A

description: miRNA expression in svHFO replicate A


title: p0-cortex_bedel_3

description: single-cell RNA-seq


title: p0-cortex_bedel_2

description: single-cell RNA-seq


title: RC17_after_mesDA_18_E2


title: sEV_B

description: miRNA expression of extracellular vesicles isolated from svHFO replicate B

source_name: Extracellular vessicles isolated from sEV

value: extracellular vesicles


title: sEV_C

description: miRNA expression of extracellular vesicles isolated from svHFO replicate C


title: RC17_after_mesDA_18_E12


title: p0-cortex_bedel_1

description: single-cell RNA-seq


title: sample 48

value: female

value: ovarian tumor biopsy

value: high-grade serous adenocarcinoma (HGSC)


title: RC17_after_mesDA_18_E11


title: sample 50

value: late


title: sample 43


title: sEV_A

description: miRNA expression of extracellular vesicles isolated from svHFO replicate A


title: p0-cortex_WT_6

description: single-cell RNA-seq

value: cortex neuron


title: RC17_after_mesDA_18_E10


title: sample 45


title: p0-cortex_WT_5

description: single-cell RNA-seq


title: hOB_C

description: miRNA expression in hFOB replicate C

source_name: hFOB cells

value: Simian virus 40-immortalized human osteoblasts from fetal limb tissue (hFOB 1.19 cells, ATCC CRL11372)


title: sample 46

source_name: tumor biopsy from older ovarian cancer patient


title: sample 44


title: hOB_B

description: miRNA expression in hFOB replicate B


title: RC17_after_mesDA_18_E6

value: B


title: RC17_after_mesDA_18_D9

value: GFP


title: sample 42


title: RC17_after_mesDA_18_D7


title: p0-cortex_WT_4

description: single-cell RNA-seq


title: hOB_A

description: miRNA expression in hFOB replicate A


title: p0-cortex_WT_3

description: single-cell RNA-seq


title: RC17_after_mesDA_18_D6


title: hEV_C

description: miRNA expression of extracellular vesicles isolated from hFOB replicate C

source_name: Extracellular vessicles isolated from hFOB


title: p0-cortex_WT_2

description: single-cell RNA-seq


title: sample 41


title: sample 35

value: early


title: sample 38


title: sample 37


title: RC17_after_mesDA_18_D5


title: hEV_B

description: miRNA expression of extracellular vesicles isolated from hFOB replicate B


title: p0-cortex_WT_1

description: single-cell RNA-seq


title: hEV_A

description: miRNA expression of extracellular vesicles isolated from hFOB replicate A


title: RC17_after_mesDA_18_D3


title: CHO_no_metabolic_labeling

city: Cleveland

first: Jeff

last: Coller

state: OH

address: 10900 Euclid Ave

department: Center for RNA Science and Therapeutics

institute: Case Western Reserve University

description:
CHO_FPKM.txt
CHO_Processed_Half_Lives.txt

data_processing:
Supplementary_files_format_and_content: CHO_FPKM.txt - Tab-delimited text, FPKM calculated from CHO metabolic labeling
Supplementary_files_format_and_content: CHO_Processed_Half_Lives.txt - Tab-delimited text, CHO half-lives
Processing: Adapter sequence was clipped from raw reads (CTGTAGGCACCATCAAT) with fastx_clipper ver 0.0.13, and reads smaller than 18 nucleotides were discarded.
Mapping: The reads were then aligned to the Cricetulus griseus genome (GCF_000223135.1_CriGri_1.0) using hisat2 ver 2.1.0.
Downstream analyses: Sam files were converted into bam format and indexed using samtools v.1.7-2. Transcript FPKM values were calculated with Stringtie v.1.3.5 and Ballgown ver 2.16.0 (Pertea et al., Nat Protocol 2016) using default parameters and a gtf file of the CriGri_1 genome downloaded from RefSeq as annotation file. This file was used to create a merged transcripts annotation used in Stringtie to re-estimate the transcripts abundances that were given as input to Ballgown. The raw FPKM numbers at each time-point were normalized to the relative number of reads aligning to the spike-ins (average of reads aligning to Luc and LYSa normalized to the number of total reads) to adjust for the amplification resulting from a smaller pool of transcripts at the later time-points. Transcripts with less than 1 FPKM at time-point 0 and without a corresponding protein-coding sequence were filtered out. Half-lives were calculated as in Presnyak et al. 2015. Briefly, spike-in-normalized FPKM values for each timepoint were further normalized to the 0 hr value. Half-lives were estimated by fitting a least absolute deviations regression model. The decay equation model took into account the estimated doubling time of the cells (15 hr) to correct for the dilution due to cell growth. Resultant half-lives were filtered to exclude genes which had an estimated half-life longer than 18 hr and for which the average absolute residual was more than 20.
Genome_build: GCF_000223135.1, CriGri_1.0

organism: Cricetulus griseus

source_name: Chinese hamster ovary

growth_protocol: Chinese hamster ovary cells (CHO-K1, ATCC CCL-61) were maintained in DMEM, high glucose, pyruvate, glutamine (Thermo Fisher Scientific 11995) supplemented with 10% Fetal Bovine Serum (FBS; Gibco 1992275), 1% Penicillin/Streptomycin, and 20 µg/mL L-proline (VWR  AAA10199-14) and grown at 37°C with 5% CO2 supplementation.

extract_protocol:
Cells were collected by replacing the media by 1 mL Trizol at the following time-points: 0 min, 30 min, 1 hr, 2 hr, 3 hr, 4 hr, 6 hr, 8 hr, 10 hr and 12 hr of chase. RNA was extracted following the Trizol extraction protocol, then re-extracted with phenol-chloroform as in. RNA was precipitated with sodium acetate and 100 % ethanol at -20°C, then spun down at 16,000 g for 20 min at 4°C, washed twice with 70 % EtOH and resuspended in water. DNAse I treatment was performed on duplicate RNA samples (2 x 6 µg) after addition of 5 ng of in vitro-labelled spike-in to each sample. The spike-in mix consisted of partial RNA sequences of B.subtilis LYSa and firefly luciferase transcripts, of which the gene sequences were cloned into pBluescript SK+ plasmid (pJC879 and pJC880, respectively) and transcribed using T7 RNA polymerase and 2 mM of 5-EU.
Samples were depleted of ribosomal RNAs using Illumina Ribo-Zero Gold rRNA removal kit (MRZG12324), then purified using the RNA Clean up and concentrator Kit (R1015, the epigenetics company). The duplicates for each sample were then combined before RNA fragmentation by alkaline treatment at 95°C for 25 min (NaCO3 pH9.2 50 mM final, EDTA 1 mM final). The reaction was immediately stopped on ice by addition of 0.3 M NaOAc pH5.2, 2µL glycoblue and 500µL water. RNA was precipitated with isopropanol, spun at 16,000 g for 30 min at 4°C, washed with 70 % EtOH and resuspended in 15.75 µL of water. Biotinylation of the 5-EU labelled RNA was performed following the Click-iT nascent RNA capture kit protocol and precipitated at -80°C overnight. The fragmented and biotinylated RNA was purified on NuPAGE denaturing polyacrylamide gels (TBE-urea 15 % polyacrylamide, Thermo Fisher Scientific EC62152BOX), excising RNA between 20 and 70 nucleotides. After extraction from the gel with 500 µL of RNA gel extraction buffer (300 mM NaOAc pH5.2, 1 mM EDTA, 0.25% (w/v) SDS) on a rotator at room temperature overnight, samples were precipitated with isopropanol and resuspended in 10 µL of 10 mM Tris-HCL pH8.

treatment_protocol: Cells were seeded into eleven 60mm dishes and pulse-labelled with 0.2 mM of 5-ethynyluridine (5-EU) at 40% confluency, keeping one plate not labelled for a control without 5-EU. 5-EU was chased after 24 hr of incorporation by adding 5 mM of uridine.

value: Chinese hamster ovary

tag: atcc number

tag: passages

tag: treatment

value: no metabolic labeling


title: CHO_12_hr_metabolic_labeling

value: metabolic labeling

tag: time

value: 12 hr


title: CHO_10_hr_metabolic_labeling

value: 10 hr


title: W22 leaf rep 1

city: St Paul

first: Nathan

last: Springer

state: MN

address: 140 Gortner

institute: University of Minnesota

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: B73v4, PH207, W22
Supplementary_files_format_and_content: tab-delimited text files include 100bp window coordinates across the corresponding genome and average methylation levels across samples for CG, CHG, and CHH for each window

organism: Zea mays

source_name: W22 leaf rep 1

extract_protocol:
Tissue was collected and frozen on dry ice then DNA was harvested.
DNA fragments were used to construct whole-genome bisulfite sequencing library using KAPA library preparation kit (KK8232)

tag: cultivar

tag: tissue

value: seedling leaf

tag: developmental stage

value: 14 day old seedling


title: RC17_after_mesDA_18_D10

tag: cell type


title: B73 shoot

source_name: B73 shoot

value: seedling shoot

value: 6 day post germination


title: PH207 shoot

source_name: PH207 shoot


title: RC17_after_mesDA_18_D1

tag: sortingmethod


title: RC17_after_mesDA_18_C9

tag: plate


title: RC17_after_mesDA_18_C8


title: B73 leaf rep 3

source_name: B73 leaf rep 3


title: RC17_after_mesDA_18_C7


title: CHO_6_hr_metabolic_labeling

value: 6 hr


title: sample 33

value: female

value: ovarian tumor biopsy

value: high-grade serous adenocarcinoma (HGSC)


title: RC17_after_mesDA_18_C4


title: CHO_4_hr_metabolic_labeling

value: 4 hr


title: sample 18


title: sample 30


title: sample 28


title: sample 22


title: B73 leaf rep 1

source_name: B73 leaf rep 1


title: sample 17


title: CHO_8_hr_metabolic_labeling

value: 8 hr


title: B73 leaf rep 2

source_name: B73 leaf rep 2


title: sample 15

value: late


title: W22 leaf rep 2

source_name: W22 leaf rep 2


title: RC17_after_mesDA_18_C3

source_name: Human graft in rat brain

value: B

value: GFP


title: B73 root

source_name: B73 root

value: seedling root


title: RC17_after_mesDA_18_C12


title: sample 14


title: CHO_0.5_hr_metabolic_labeling

value: Chinese hamster ovary

value: metabolic labeling


title: CHO_1_hr_metabolic_labeling

value: 1 hr


title: sample 13

value: early


title: CHO_2_hr_metabolic_labeling

value: 2 hr


title: CHO_3_hr_metabolic_labeling

value: 3 hr


title: sample 12


title: Spaceflight, 8 days old, Wassilewskija Rep4

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

description:
FLT 8d WS to GC 8d WS
FLT 4d WS to FLT 8d WS
FLT 8d Sku5 to FLT 8d WS

data_processing:
The data analysis was performed at the ICBR bioinformatics core, University of Florida. Input fastq files were trimmed to remove the adapters and low-quality bases using trimmomatic (version 0.36) with the following parameters: LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:50. Quality control on the trimmed reads was performed using FastQC version 0.11.2. Reads were aligned to the WS genome (Gan et al. Nature. 2011 Aug 28; 477(7365):419-23.) using the STAR aligner (version 2.5.1b), and duplicate reads due to PCR artifacts were removed using the Picard MarkDuplicates tool. In total, 502 million reads were aligned to the transcriptome.
Expression quantification and differential gene expression analysis were performed using cufflinks and cuffdiff respectively (version 2.2.1) with default parameters. The cuffdiff output files were parsed with custom scripts to generate the final annotated tables of differentially expressed genes.

organism: Arabidopsis thaliana

source_name: solid 0.5x MS media plates; grown in spaceflight, 8 days old plant harvested into KFT containing RNAlater fixative

growth_protocol: The laboratory preparations and launch conditions:   Dry, sterilized Arabidopsis seeds were planted aseptically on the surface of 10-cm2 solid media plates comprised of 0.5% Phytagel/0.5× MS media, and then immediately wrapped in light-tight black cloth (Duvetyne, SeattleFabrics.com) and transported to KSC (Kennedy Space Center), FL, USA. The wrapped plates were stored at temperatures between 4 and 10 °C until launch within a cold stowage bag nominally at 4 °C. The seeds remained dormant until removed from cold stowage and exposed to light at the initiation of the experiment on the ISS (International Space Station).   Plant growth on the ISS and ISSES:  The APEX03-2 experiment plates were grown in the Vegetable Production System (VPS/Veggie) hardware on the Columbus Module of the ISS. The 10-cm2 Petri plates were housed perpendicular (“vertical”) to the overhead LED lighting of the VPS. Plants received between 100–135 μmoles/m2/s PAR inside the VPS. Four and eight days after germination was initiated by unwrapping the plates and exposing them to light in the VPS. The ground control plates were grown inside the VPS ground unit within the ISSES (International Space Station Environment Simulator) chamber at KSC with the 48-h delay. The ISSES chamber replicated the temperature, CO2 levels and lighting that had been experienced by the spaceflight plants in the previous 48 h.

extract_protocol:
Sample preparation for transcriptomics:  Seedlings stored in RNAlater were recovered from -80°C freezer. Each tube containing the seedlings was allowed to thaw in the fridge overnight. After completely thawing the samples to room temperature, the seedlings were observed under the microscope. Roots of the preserved seedlings from the spaceflight and ground control harvests were dissected and the rest of the seedlings were saved in RNAlater and stored back to -80°C freezer.  For 4 day old roots 5-8 roots were combined to serve as one biological replica. For 8 day old roots 2-3 roots were used to form one biological replica. In each case the four biological replicas were used for the transcriptomic analysis.   Total RNA extraction: Total RNA was extracted using Qiashredder and RNAeasy™ kits from QIAGEN (QIAGEN Sciences, MD, USA) according to the manufacturer’s instructions. Residual DNA was removed by performing an on-column digestion using an RNase Free DNase (QIAGEN GmbH, Hilden, Germany). Integrity of the RNA was evaluated using the Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA).
Library preparation:  RNASeq Libraries Preparation using SMART-Seq V4 ultra low input RNA kit for sequencing combined with Illumina Nextera DNA Sample Preparation Kit  Ten ng of total RNA was used for cDNA library construction using CloneTech SMART-Seq V4 ultra low input RNA kit for sequencing (Clontech Laboratories, Inc, cat#: 634890) according to manufacturer's protocol. Briefly, 1st strand cDNA was primed by the SMART-Seq v4 oligonucleotide and then base-pairs with these additional nucleotides, creating an extended template. The reverse transcriptase then switches templates and continues transcribing to the end of the oligonucleotide, resulting full-length cDNA that contains an anchor sequence that serves as a universal priming site for second strand synthesis. cDNA was amplified with primer II A for 8 PCR cycles. Then Illumina sequencing libraries were generated with 150 pg of cDNA using Illumina Nextera DNA Sample Preparation Kit (Cat#: FC-131-1024) according to manufacturer’s instructions. Briefly, 150 pg of cDNA was fragmented by tagementation reaction and then adapter sequences added onto template cDNA by PCR amplification. Libraries were quantitated by Bioanalyzer and qPCR (Kapa Biosystems, catalog number: KK4824). Finally, the libraries were pooled equal molar concentration and sequenced by Illumina 2X75 NextSeq 500.
Illumina sequencing:  Sequencing experiments were performed at the Interdisciplinary Center for Biotechnology Research (ICBR) gene expression and sequencing core, University of Florida.  In preparation for sequencing, barcoded libraries were sized on the bioanalyzer, quantitated by QUBIT and qPCR (Kapa Biosystems, catalog number: KK4824). Individual samples were pooled equimolarly at 4 nM. This “working pool” was used as input in the NextSeq500 instrument sample preparation protocol (Illumina, Part # 15048776, Rev A). Typically, a 1.3 pM library concentration resulted in optimum clustering density in our instrument (i.e., ~200,000 clusters per mm2). Samples were sequenced on 5 flowcells (5 NextSeq 500 runs), using a 2x75 cycles (paired-end) configuration. A typical sequencing run in the NextSeq500 produced 750-800 million paired-end read with a Q30>=85%. For RNA seq, around 40 million reads provided sufficient depth for transcriptome analysis.

treatment_protocol: On Orbit Operations and harvest:  At four or for the second experimental set at eight days, seedlings were harvested by an astronaut into KFT (Kennedy Fixation Tube) containing RNAlater solutions. Once the plants were placed in the KFTs, the KFT was actuated with RNAlater to preserve the sample. At 24 hours post-harvest, KFTs were then transferred to MELFI freezer. Following Dragon Capsule splashdown in the Pacific Ocean, the KFTs transferred to the Cold Stowage charter plane at the Long Beach Airport, placed into an insulated shipper with dry ice, and flown to Johnson Space Center (JSC). The KFTs were then transferred via FedEx ground to the Kennedy Space Center. The KFTs were removed from dry ice and transferred to a -80°C freezer. The PIs retrieved the plant samples from the KFTs and transferred the samples back to the University of Florida.  The harvested material was used to compare the transcriptomes of each genotype. The patterns of gene expression was compared between treatments (spaceflight versus ground control) within each genotype of same age or between two ages within same genotype and within same treatment.

value: WS

tag: material type

value: Roots

tag: organism part

value: whole root of the 8 days old seedling

tag: age

value: 8 days old plants, light grown

tag: biosource type

value: RNAlater fixed_sample


title: sample 11

tag: gender

value: female

value: ovarian tumor biopsy

tag: diagnosis

value: high-grade serous adenocarcinoma (HGSC)

tag: disease progression


title: sample 10

value: late


title: RC17_after_mesDA_18_C10

value: B

value: GFP


title: Spaceflight, 8 days old, Wassilewskija Rep3


title: RC17_after_mesDA_18_C11


title: CHO_0_hr_metabolic_labeling

tag: cell line

value: Chinese hamster ovary

tag: atcc number

value: 0 hr


title: Spaceflight, 8 days old, Wassilewskija Rep2


title: RC17_after_mesDA_18_C1


title: RC17_after_mesDA_18_B9


title: RC17_after_mesDA_18_B6


title: RC17_after_mesDA_18_B8


title: sample 9


title: Ground Control, 8 days old, Wassilewskija Rep2

description:
FLT 8d WS to GC 8d WS
GC 4d WS to GC 8d WS
GC 8d Sku5 to GC 8d WS

source_name: solid 0.5x MS media plates; grown on the ground, 8 days old plant harvested into KFT containing RNAlater fixative


title: FFPE_renal_carcinoma_163

city: Madrid

first: Lucia

last: Trilla-Fuertes

state: Madrid

address: Paseo de la Castellana 261

country: Spain

institute: Hospital Universitario La Paz

description:
US22502514_252182714680_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples

hyb_protocol: One hundred ng of Cy3 labeled RNA were hybridized for 20 hours at 55ºC in a hybridization oven (G2545A, Agilent) set to 20 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer

scan_protocol: The scan was done on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) equipped with extended dynamic range (XDR) software.

data_processing:
Images provided by the scanner were analyzed using Agilent´s software Feature Extraction version 10.7.3.1.
Only miRNAs with an average intensity over the 20th percentile of the overall intensities and a detectable signal in at least 10 percent of the hybridized samples considered for further analysis.

source_name: renal carcinoma

label_protocol: 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3´ end of each RNA molecule by using T4 RNA ligase.

extract_protocol: FFPE tumor specimens were cut into serial sections with a thickness of 10 µm. Total RNA was then isolated using the miRNEasy Kit (Quiagen). Purified RNA quality control for quantity and purity was assessed using an ND-1000 NanoDrop spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: Paraffin samples with at least 50% of tumor cells were selected by a pathologist.

value: renal carcinoma


title: FFPE_renal_carcinoma_162

description:
US22502514_252182714680_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_164

description:
US22502514_252182714680_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: Ground Control, 8 days old, Wassilewskija Rep3


title: RC17_after_mesDA_18_B4


title: FFPE_renal_carcinoma_161

description:
US22502514_252182714680_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_18_B2


title: Spaceflight, 8 days old, Wassilewskija Rep1


title: Spaceflight, 8 days old, Sku5 Rep4

description:
FLT 8d Sku5 to GC 8d Sku5
FLT 4d Sku5 to FLT 8d Sku5
FLT 8d Sku5 to FLT 8d WS


title: Ground Control, 8 days old, Wassilewskija Rep1


title: FFPE_renal_carcinoma_160

description:
US22502514_252182714680_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_18_B12


title: Ground Control, 8 days old, Wassilewskija Rep4


title: FFPE_renal_carcinoma_159

description:
US22502514_252182714680_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: Treatment B_3

city: Wako-shi

first: Kazuko

last: Yoshida

state: Saitama

address: 2-1, Hirosawa

country: Japan

institute: RIKEN

data_processing:
Sequencing software: HiSeq Control Software 2.2.58
Image analysis and base calling: Real-Time Analysis (RTA) 1.18.64
fastq-file generation: BCL2FASTQ Conversion Software 1.8.3
Reads were trimmed for quality (limit=0.05, max of 2 amibiguous bases) and aligned to Arabidopsis genome assembly in CLC Genomics Workbench version 11.0 (Qiagen) using paired read parameters.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: seedling

growth_protocol: Six to eight Arabidopsis seeds (Col-0) were sown on 1/2 MS medium (1.5% sucrose and 0.5% Agar) in a 96-well plate. After stratification at 4°C for at least 2 days, the seedlings were grown for 8 days at 22°C.

extract_protocol:
Total RNA from plants treated with chemical was isolated using the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s protocol and treated with RNase-Free DNase Set (Qiagen), followed by column purification using Rneasy MiElute Cleanup kit (Qiagen).
Library construction and sequencing for the Illumina HiSeq 2500 was provided as a custom service of Eurofins Genomics K. K. (Tokyo, Japan). The polyA fraction (mRNA) was isolated from total RNA, followed by its fragmentation.Then double-stranded (ds) cDNA was reverse transcribed from fragmented mRNA. The ds cDNA fragments were processed for adaptor ligation, size selection (for 200 bp inserts) and amplification to generate strand-specific cDNA libraries.Prepared libraries were subjected to paired-end 2 x 100 bp sequencing on the HiSeq 2500 platform with v4 chemistry.

treatment_protocol: Seedlings were treated with liquid 1/2 MS solution (with 1.5% sucrose) containing 10 µM of each chemical (DMSO, ABA, 3'-propyl ABA, and 3'-butyl ABA) and incubated at 22°C under cotinuous light for 6 h before collecting the samples.

tag: treatment

value: 3'-butyl ABA

tag: ecotype

value: seedling

value: 8 day


title: sample 8

value: early


title: Spaceflight, 8 days old, Sku5 Rep3

tag: cultivar

value: Roots


title: RC17_after_mesDA_18_B11


title: Spaceflight, 8 days old, Sku5 Rep2

value: whole root of the 8 days old seedling


title: sample 4

tag: tissue


title: sample 6


title: FFPE_renal_carcinoma_158

description:
US22502514_252182714680_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_18_B10


title: Treatment B_2


title: sample 3


title: sample 7


title: sample 2


title: sample 1


title: RC17_after_mesDA_18_A9


title: Spaceflight, 8 days old, Sku5 Rep1

value: 8 days old plants, light grown


title: Ground Control, 8 days old, Sku5 Rep4

description:
FLT 8d Sku5 to GC 8d Sku5
GC 4d Sku5 to GC 8d Sku5
GC 8d Sku5 to GC 8d WS

value: RNAlater fixed_sample


title: Treatment B_1


title: Treatment P_3

value: 3'-propyl ABA


title: Treatment P_2


title: Treatment P_1


title: FFPE_renal_carcinoma_157

description:
US22502514_252182714680_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_18_A7


title: RC17_after_mesDA_18_A3


title: RC17_after_mesDA_18_A6


title: FFPE_renal_carcinoma_156

description:
US22502514_252182714679_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: Treatment A_3

value: ABA


title: Ground Control, 8 days old, Sku5 Rep3


title: Ground Control, 8 days old, Sku5 Rep2


title: Ground Control, 8 days old, Sku5 Rep1


title: FFPE_renal_carcinoma_153

description:
US22502514_252182714679_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_152

description:
US22502514_252182713772_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_154

description:
US22502514_252182714679_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_155

description:
US22502514_252182714679_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_18_A2


title: RC17_after_mesDA_18_A12


title: RC17_after_mesDA_18_A11


title: Spaceflight, 4 days old, Wassilewskija Rep4

description:
FLT 4d WS to GC 4d WS
FLT 4d WS to FLT 8d WS

source_name: solid 0.5x MS media plates; grown in spaceflight, 4 days old plant harvested into KFT containing RNAlater fixative

value: WS

value: whole root of the 4 days old seedling

value: 4 days old plants, light grown


title: Treatment A_2


title: Spaceflight, 4 days old, Wassilewskija Rep3


title: Treatment A_1


title: FFPE_renal_carcinoma_151

description:
US22502514_252182714679_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_150

description:
US22502514_252182714679_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: Control_3

value: DMSO


title: FFPE_renal_carcinoma_149

description:
US22502514_252182714679_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_H11

value: B

value: GFP


title: RC17_after_mesDA_18_A1


title: Control_2


title: RC17_after_mesDA_17_G8


title: Spaceflight, 4 days old, Wassilewskija Rep2


title: RC17_after_mesDA_18_A10


title: Ground Control, 4 days old, Wassilewskija Rep4

description:
FLT 4d WS to GC 4d WS
GC 4d WS to GC 8d WS
GC 4d Sku5 to GC 4d WS

source_name: solid 0.5x MS media plates; grown on the ground, 4 days old plant harvested into KFT containing RNAlater fixative


title: Spaceflight, 4 days old, Wassilewskija Rep1


title: Control_1


title: HeLa_tRNA_3

description:
HeLa_tRNA_gene_summary_cyto_RPM.csv
HeLa_tRNA_anticodon_summary_RPM.csv

data_processing:
Supplementary_files_format_and_content: HeLa_tRNA_gene_summary_cyto_RPM.csv - CSV, Reads per million (RPM) from HeLa tRNA-seq per unique tRNA gene sequence
Supplementary_files_format_and_content: HeLa_tRNA_anticodon_summary_RPM.csv - CSV, Reads per million (RPM) from HeLa tRNA-seq per anticodon group
Processing: cutadapt ver 1.12 was used twice in succession with the following parameters first to remove potential 5' adapter (-g ^ACTGGATACTGG) and then to remove the 3' CCA + adapter (-a CCAGTATCCAGTTGGAATT).
Mapping: bowtie2 ver 2.3.5 was used to map processed reads to a reference generated from high confidence tRNAs (unique sequences collapsed) defined in GtRNAdb (hg38) using the following parameters: --quiet --min-score L,1,0 --local -D 20 -R 3 -N 1 -L 10 -i S,1,0.5.
Downstream analyses: Mapped sam files were converted to bam files using samtools ver 1.9 (samtools view). Further analyses were carried out in Rstudio ver 1.1.463 (R ver 3.5.2 (2018-12-20) -- "Eggshell Igloo"). Read count tables over tRNA genes were generated by using featureCounts from the Rsubread package using the following parameters: strandSpecific = 1,useMetaFeatures=F,minMQS = 10.
Genome_build: hg38

source_name: Human cervical adenocarcinoma

growth_protocol: HeLa cells were grown in complete DMEM to 80% confluency.

extract_protocol:
Media was aspirated and Trizol was added immediately to culture dishes. Total RNA was isolated using Trizol manufacturer's instructions (ThermoFisher) followed by treatment with Turbo Dnase (ThermoFisher).
tRNA-sequencing: 1 micrograms of total RNA was ligated to annealed adapters under conditions as in (Shigematsu et al., 2017; PMID: 28108659) using 10-fold more RNA ligase. cDNA was synthesized using SuperScript IV Reverse Transcriptase (ThermoFisher 18090010) using manufacturer’s recommended conditions and gel purified with denaturing polyacrylamide gel electorphoresis. Gel purified cDNA was then ligated using CircLigase (Lucigen CL4111K) with manufacturer’s recommended conditions and libraries were amplified using Q5 DNA polymerase (New England Biolabs M0491) for 7-8 cycles then purified from a 2% agarose gel. Libraries were sequenced as single-end reads on an Illumina NextSeq 550.

value: HeLa

value: Human cervical adenocarcinoma cells

tag: passages


title: HeLa_tRNA_2

tag: cell type


title: Ground Control, 4 days old, Wassilewskija Rep3


title: FFPE_renal_carcinoma_147

description:
US22502514_252182713986_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples

value: renal carcinoma


title: FFPE_renal_carcinoma_148

description:
US22502514_252182714679_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_145

description:
US22502514_252182713986_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: HeLa_tRNA_1


title: RC17_after_mesDA_17_G7

tag: sortingmethod


title: FFPE_renal_carcinoma_146

description:
US22502514_252182713986_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_G4

tag: plate


title: Ground Control, 4 days old, Wassilewskija Rep1

tag: material type


title: Ground Control, 4 days old, Wassilewskija Rep2

tag: organism part


title: Spaceflight, 4 days old, Sku5 Rep4

description:
FLT 4d Sku5 to GC 4d Sku5
FLT 4d Sku5 to FLT 8d Sku5

tag: age


title: RC17_after_mesDA_17_G10


title: FFPE_renal_carcinoma_142

description:
US22502514_252182713985_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_144

description:
US22502514_252182713986_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_143

description:
US22502514_252182713986_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: 16046X41

city: Salt Lake City

first: Katherine

last: Beebe

state: UT

address: 15 North 2030 East

department: Molecular Medicine

institute: University of Utah

data_processing:
Optical duplicates were removed with clumpify, adapter trimming was performed with cutadapt (version 1.16), and alignment was done using STAR (version 2.7.0f). Transcript expression was quantified with RSEM v1.3.1 (Li and Dewey 2011) following alignment to the dm6 genome (Ensembl release 96) with STAR v2.7.0f (Dobin et al. 2013).
Genome_build: dm6
Supplementary_files_format_and_content: excel file, has raw counts, normalized counts, vsd log counts (DESeq2 version 1.22.2), fpkm values, and sample IDs.

organism: Drosophila melanogaster

source_name: ERR mutant

growth_protocol: Animals were staged as WPP for timecourse collection

extract_protocol:
Zymo Direct-zol RNA miniprep kit (with DNase treatment)
Illumina TruSeq Stranded mRNA Library Prep (RIN 8-10) with UDI. Intact poly(A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Prep kit (20020595) and TruSeq RNA UD Indexes (20022371) .  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis.

treatment_protocol: All animals were subjected to heat-treatment on days 4 and 5 AEL. Experimental and control animals differed in their genotype (presence or absence of hsFLP transgene)

tag: genotype

value: ERR mutant

value: whole fly

tag: time point


title: 16046X42


title: Spaceflight, 4 days old, Sku5 Rep2

value: Roots

tag: biosource type


title: 16046X40


title: Spaceflight, 4 days old, Sku5 Rep1


title: 16046X38

source_name: Control

value: Control


title: FFPE_renal_carcinoma_141

description:
US22502514_252182713985_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: 16046X37


title: RC17_after_mesDA_17_F7


title: Ground Control, 4 days old, Sku5 Rep3

description:
FLT 4d Sku5 to GC 4d Sku5
GC 4d Sku5 to GC 8d Sku5
GC 4d Sku5 to GC 4d WS


title: RC17_after_mesDA_17_G3


title: Ground Control, 4 days old, Sku5 Rep2


title: Spaceflight, 4 days old, Sku5 Rep3


title: FFPE_renal_carcinoma_140

description:
US22502514_252182713985_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_139

description:
US22502514_252182713985_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_F5


title: FFPE_renal_carcinoma_138

description:
US22502514_252182713985_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: 16046X36


title: RC17_after_mesDA_17_G2


title: FFPE_renal_carcinoma_137

description:
US22502514_252182713985_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: 16046X39


title: RC17_after_mesDA_17_G1


title: 16046X35


title: Ground Control, 4 days old, Sku5 Rep4


title: RC17_after_mesDA_17_F4


title: RC17_after_mesDA_17_F9


title: 16046X34


title: RC17_after_mesDA_17_F3


title: RC17_after_mesDA_17_F2


title: 16046X33


title: Ground Control, 4 days old, Sku5 Rep1


title: 16046X32


title: FFPE_renal_carcinoma_135

description:
US22502514_252182713773_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_F12


title: 16046X31


title: FFPE_renal_carcinoma_136

description:
US22502514_252182713985_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_F11


title: 16046X29


title: FFPE_renal_carcinoma_133

description:
US22502514_252182713773_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_132

description:
US22502514_252182713773_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_F1


title: 16046X28


title: FFPE_renal_carcinoma_130

description:
US22502514_252182713772_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_134

description:
US22502514_252182713773_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: 16046X27


title: RC17_after_mesDA_17_E9


title: RC17_after_mesDA_17_F10


title: 16046X30


title: 16046X26


title: RC17_after_mesDA_17_E8


title: FFPE_renal_carcinoma_128

description:
US22502514_252182713771_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_E7


title: FFPE_renal_carcinoma_131

description:
US22502514_252182713773_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_129

description:
US22502514_252182713772_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_127

description:
US22502514_252182713771_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: HT 27

city: Bangalore

first: Ruchi

last: Jain

state: Karnataka

address: C V Raman Road

department: Molecular Reproduction Development and Genetics

country: India

institute: Indian Institute of Science

description:
HT 27
9631032052_K

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization in R

label: Biotin

source_name: Human Testis

label_protocol: Biotinylated cRNA were prepared with  TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: gender

value: Male

tag: developmental stage

value: Adult

tag: disease state

value: Non obstructive azoospermia with meiotic arrest

value: Testis


title: 16046X25


title: RC17_after_mesDA_17_E5


title: HT 20

description:
HT 20
9631032052_J


title: 16046X24


title: HT 12

description:
HT 12
9631032052_G


title: HT 14

description:
HT 14
9631032052_H

value: Obstructive azoospermia


title: HT 16

description:
HT 16
9631032052_I


title: HT 8

description:
HT 8
9631032052_E

value: Non obstructive azoospermia with pre-meiotic arrest


title: HT 7

description:
HT 7
9631032052_D


title: FFPE_renal_carcinoma_126

description:
US22502514_252182713771_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_125

description:
US22502514_252182713771_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_E4


title: 16046X23


title: HT 29

description:
HT 29
9631032052_L


title: HT 11

description:
HT 11
9631032052_F


title: RC17_after_mesDA_17_E12


title: RC17_after_mesDA_17_E2


title: FFPE_renal_carcinoma_124

description:
125_3990_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: 16046X22


title: 16046X20


title: RC17_after_mesDA_17_E3


title: HT 5

description:
HT 5
9631032052_C


title: FFPE_renal_carcinoma_122

description:
US22502514_252182713771_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_121

description:
US22502514_252182713771_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: HT 3

description:
HT 3
9631032052_B


title: FFPE_renal_carcinoma_123

description:
US22502514_252182713771_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_E11


title: 16046X21


title: RC17_after_mesDA_17_E10


title: 16046X19


title: SMMHC1520

city: Halle (Saale)

first: Barbara

last: Schreier

address: Magdeburgerstr. 6

country: Germany

institute: Martin Luther University Halle-Wittenberg

description: processed data file: Kidney-EGFRko-VSMC__HFD-SFD.txt

data_processing:
Adaptor removal (Cutadapt - v1.8.1)
Alignment (tophat - 2.0.14)
Counting (featureCounts - 1.4.6)
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing raw counts obtained after Counting with featureCounts

source_name: VSMC-EGFR knockout_high fat diet_kidney

growth_protocol: Mice were kept at constant temperature of 22±2°C, relative humidity of 30–60%, under a 12/12 h light-dark cycle with ad libitum access to water and standard chow. Recently, we generated and described an inducible knock out for EGFR in VSMC via the Cre/loxP system by mating EGFRflox/flox C57BL/6 mice (originally provided by Maria Sibilia, Vienna, Austria) with SMMHC-Cre+/- C57BL/6N mice (originally provided by Stefan Offermanns, Bad Nauheim, Germany)

extract_protocol:
Total RNA was isolated with TriZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
rRNA were removed using RiboMinus (Life Technologies) according to the manufacturer's instructions. RNA was fragmented (w/ Tris-acetate, Potassium acetate and Magnesium acetate) and precipitated (w/ 100% Ethanol, Ammonium acetate and glycogen).
Resulting RNAs were used to generate cDNA libraries using Illumina index adapters.  10nM of pools of up to 10 libraries were used for cluster generation (Illumina cBot). Paired end sequencing (2x100bp) was performed on Illumina HiScanHQ and HiSeq2000.

treatment_protocol: All animals received intraperitoneal injection of tamoxifen (1mg/ 50µl Miglyol 812/mouse/day for 5 consecutive days). HFD was started 7 days after tamoxifen application in mice, 6 weeks of age, and lasted for 18 weeks. Afterwards mice were anaesthetized with isofluran, sacrificed in deep narcosis by cervical dislocation. Aortas were freed of adjacent fat and connective tissue, both organs were snap frozen in liquid nitrogen.

tag: strain background

tag: genotype/variation

value: VSMC-EGFR knockout

tag: treatment

value: high fat diet for 18 weeks

value: kidney


title: SMMHC1558

tag: tissue


title: SMMHC1504


title: SMMHC1437


title: SMMHC1451

source_name: VSMC-EGFR knockout_standard fat diet_kidney

value: standard fat diet for 18 weeks


title: RC17_after_mesDA_17_E1

data_processing:
All reads were aligned to the human (hg19) genome using STAR v2.3.0e (Dobin et al. 2013)
Non-uniquely mapped reads were removed using Samtools
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in Ensembl ( June 2015)
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression values are provided as rpkms and counts (comma separated text files)

extract_protocol:
Single cells have been extracted from tissue using Papain Dissociation System (Worthington). cDNA was generated from FACS sorted single cells (ventral midbrain human embryonic stem cells before grafting, fetal cells before and after grafting were sorted for size, ventral midbrain human embryonic stem cells after grafting were sorted for GFP expression) using Smart-seq2 protocol (Picelli et al. Nature Methods 2013).  ERCC spike-in RNA was added to the lysis buffer.
Nextera XT DNA sample preparation index kit, 96 indices (Illumina)

value: B

value: GFP


title: FFPE_renal_carcinoma_119

description:
US22502514_252182713757_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples

value: renal carcinoma


title: FFPE_renal_carcinoma_120

description:
US22502514_252182713771_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: 16046X17

value: ERR mutant


title: SMMHC1319


title: SMMHC1318


title: RC17_after_mesDA_17_D9


title: RC17_after_mesDA_17_D8


title: 16046X16

value: whole fly


title: CT HT Pool

description:
CT HT Pool
9631032052_A

value: pooled control


title: RC17_after_mesDA_17_D7


title: SMMHC1642

source_name: WT_high fat diet_kidney

value: wild type


title: 16046X15

value: Control


title: FFPE_renal_carcinoma_117

description:
US22502514_252182713757_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: 16046X14


title: 16046X18


title: FFPE_renal_carcinoma_115

description:
US22502514_252182713757_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_116

description:
US22502514_252182713757_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: 16046X13


title: RC17_after_mesDA_17_D3


title: RC17_after_mesDA_17_D2


title: FFPE_renal_carcinoma_114

description:
US22502514_252182713757_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: 16046X11


title: SMMHC1613


title: FFPE_renal_carcinoma_113

description:
US22502514_252182713757_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: SMMHC1535


title: FFPE_renal_carcinoma_118

description:
US22502514_252182713757_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_D12


title: 16046X10


title: FFPE_renal_carcinoma_112

description:
US22502514_252182713757_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_111

description:
US22502514_252182713755_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: SMMHC1695

source_name: WT_standard fat diet_kidney


title: 16046X9


title: SMMHC1694


title: FFPE_renal_carcinoma_110

description:
US22502514_252182713755_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_D1


title: SMMHC1446


title: SMMHC1641


title: 16046X7


title: 16046X8


title: FFPE_renal_carcinoma_109

description:
US22502514_252182713755_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_108

description:
US22502514_252182713755_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: 16046X6

value: WPP


title: RC17_after_mesDA_17_D11


title: BS_1505

description: processed data file: Aorta-EGFRko-VSMC__HFD-SFD.txt

source_name: VSMC-EGFR knockout_high fat diet_aorta

value: aorta


title: SMMHC1309


title: 16046X5


title: RC17_after_mesDA_17_C5

source_name: Human graft in rat brain


title: BS_1504


title: RC17_after_mesDA_17_C4


title: 16046X12


title: RC17_after_mesDA_17_D10


title: 16046X4


title: FFPE_renal_carcinoma_107

description:
US22502514_252182713755_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_C3


title: BS_1503


title: FFPE_renal_carcinoma_106

description:
US22502514_252182713755_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: 16046X3


title: FFPE_renal_carcinoma_105

description:
US22502514_252182713755_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: BS_1454


title: RC17_after_mesDA_17_C9


title: SMMHC1303

description: processed data file: Kidney-EGFRko-VSMC__HFD-SFD.txt


title: RC17_after_mesDA_17_C7


title: RC17_after_mesDA_17_C2


title: FFPE_renal_carcinoma_104

description:
US22502514_252182713755_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_C12


title: BS_1507

source_name: VSMC-EGFR knockout_standard fat diet_aorta


title: 16046X1


title: BS_1452


title: FFPE_renal_carcinoma_103

description:
US22502514_252182713754_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_C11


title: LG2_r2: TFLG2 Zm00001d042777 ChIP-Seq

city: Hong Hong

first: Silin

last: Zhong

address: Shatin, N.T.

department: School of Life Sciences

institute: CUHK

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR

data_processing:
For mapping, we aligned the raw reads to the unmasked maize genome (B73 RefGen_v4) using Bowtie 2 (version 2.2.5) under the default parameters with the 3’  100 bp trimming option. Reads with mapping quality >= 10 were kept and PCR duplicates are removed using SAMTools (version 1.3). Deeptools bamcoverage was used to convert the BAM to bigwig files for viewing.
For peak calling, BAM files of biological replicates were used to call peaks with the SPP peak caller using relaxed parameters “-i = <INPUT BAM file>”, “-npeak = 300,000”, with input as control. Peaks in the transformed TF genebody itself are removed. Reproducible peaks were obtained with the IDR (Irreproducible discovery rate) statistical framework (version 2.0.3), as implemented in the PhantomPeakQualTools package, using 1% IDR as the threshold (cut-off).
To identify the high confident target genes of each TF, we used the probabilistic model TIP (Cheng et al., Bioinformatics, 2011, 3221–3227) with FDR 0.05 as cutoff.
Genome_build: B73 RefGen_v4
Supplementary_files_format_and_content: peak and bigwig files
Supplementary_files_format_and_content: TF_target_TIP.txt: High cofident TF target genes called by TIP

source_name: Leaf protoplast

growth_protocol: Leaf protoplast from 1-2 weeks old maize seedlings

extract_protocol:
Lysates were clarified from sonicated nuclei and TF-DNA complexes were isolated with streptavidin dynabeads.
Libraries were prepared according to Illumina's instructions using purified HS-Tn5 transposase, Tn5-MEA/B adapter as well as N5xx and N7xx PCR primers.

treatment_protocol: PEG mediated protoplast transformation

tag: cultivar

value: Leaf protoplast

tag: transcription factor


title: BS_1319


title: RC17_after_mesDA_17_C10

city: Uppsala

first: Asa

last: Bjorklund

address: Box 596

institute: Uppsala University

tag: cell type

tag: sortingmethod


title: RC17_after_mesDA_17_C1

tag: plate


title: BS_1448

source_name: WT_high fat diet_aorta


title: FFPE_renal_carcinoma_102

description:
US22502514_252182713754_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples

source_name: renal carcinoma


title: LG2_r1: TFLG2 Zm00001d042777 ChIP-Seq


title: 9_r2: TF9 Zm00001d033719 ChIP-Seq


title: FFPE_renal_carcinoma_101

description:
US22502514_252182713754_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_B8


title: FFPE_renal_carcinoma_99

description:
US22502514_252182713754_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: BS_1447


title: RC17_after_mesDA_17_B9


title: FFPE_renal_carcinoma_100

description:
US22502514_252182713754_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: 16046X2


title: 9_r1: TF9 Zm00001d033719 ChIP-Seq


title: 98_r2: TF98 Zm00001d006551 ChIP-Seq


title: RC17_after_mesDA_17_B7


title: BS_1443


title: 98_r1: TF98 Zm00001d006551 ChIP-Seq


title: BS_1442


title: BS_1445

source_name: WT_standard fat diet_aorta


title: FFPE_renal_carcinoma_98

description:
US22502514_252182713754_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_B6


title: FFPE_renal_carcinoma_97

description:
US22502514_252182713754_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: BS_1310


title: 97_r2: TF97 Zm00001d002762 ChIP-Seq


title: FFPE_renal_carcinoma_95

description:
US22502514_252182713899_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_96

description:
US22502514_252182713754_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_B5


title: RC17_after_mesDA_17_B4


title: 97_r1: TF97 Zm00001d002762 ChIP-Seq


title: FFPE_renal_carcinoma_94

description:
US22502514_252182713899_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: BS_1309

description: processed data file: Aorta-EGFRko-VSMC__HFD-SFD.txt


title: RC17_after_mesDA_17_B2


title: RNA_EpiLSCs_Rep2

city: Nijmegen

first: Hendrik

middle: G

last: Stunnenberg

address: Geert Grooteplein 30

institute: Radboud University

data_processing:
FASTQ files against mouse rRNA, tRNA, snRNA, snoRNA, mtRNA sequences using Bowtie (Ref) to deplete these small RNA contamination in sequenced libraries. We then mapped the cleaned files against mouse genome (mm9) using GSNAP (Ref) and by applying the following parameters:  -B 5 -t 15 -N 1 -E 100 -w 100000 -n 10 -s mm9refGene_splice.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig tracks, data are not normalized for sequencing depth.

growth_protocol: E14Tg2a ESCs were cultured in standard culture medium without feeder and on gelatin coated-dishes. Serum supplemented medium contains Dulbecco's Modified Eagle's Medium (DMEM, Gibco) supplemented with 10% fetal calf serum (FCS, Gibco), L-glutamine (2 nM, Gibco), Na-Pyruvate (1 mM, Gibco), non-essential amino acids (0.1 mM each, Gibco), Penicillin Streptomycin (Gibco), 2-mercaptoethanol (55 µM, Gibco) and LIF (1000 U/ml, Milipore). For serum free culture, cells were maintained in NDiff 227 (StemCells, Inc.) supplemented with MEK inhibitor PD0325901 (1 μM) and GSK3 inhibitor CHIR99021 (3 μM) and LIF (1000 U/ml, Milipore). For EpiLSC-differentiation, 2i-ESCs were seeded in ~15,000 cells per cm2 density on Fibronectin (10 μg/ml) coated dishes and in NDiff 227 (StemCells, Inc.) supplemented with Penicillin Streptomycin (Gibco), 20 ng/ml ActivinA (R&D systems), 12 ng/ml bFGF (R&D systems) and 1% knock out serum replacement (Gibco) and cells were maintained for 72h in this culture.

extract_protocol:
Illumina RNA-seq strand specific
RNA isolation was performed using 8 time points: Day1, Day3 and Day7 of serum-2i and 2i-serum transitions and both steady-states (serum and 2i) samples. RNA isolation was performed using Qiagen RNeasy protocol and 4 microgram RNA was employed for generating the RNA-seq libraries. Total RNA was subjected to rRNA depletion using the Ribo-ZeroTM Gold kit (Epicentre) according to manufacture instruction. rRNA-depleted samples were employed in first and second strand cDNA synthesis and by using dUTP for strand-specificity. Sequencing libraries were then prepared using Kapa-Hifi (KAPA Biosystems) according to manufactory’s instruction and the final libraries were sequenced on HiSeq 2000 Illumina sequencer.
Illumina library preparation was done using the Kapa Hyper Prep Kit. For end repair and A-tailing double stranded DNA was incubated with end repair and A-tailing buffer and enzyme and incubated first for 30 minutes at 20°C and then for 30 minutes at 65°C.Subsequently adapters were  ligated  by adding 30µl ligation buffer, 10 Kapa l DNA  ligase, 5µl diluted adaptor  in a total volume of 110µl and incubated for 15 minutes at 15°C.Post-ligation cleanup was performed using Agencourt AMPure XP reagent and products were eluted in 20µl elution buffer. Libraries were amplified by adding 25µl 2x KAPA HiFi Hotstart ReadyMix and 5µl 10x Library Amplification Primer Mix and PCR, 10 cycles. Samples were purified using the QIAquick MinElute PCR purification kit and 300bp fragments selected using E-gel. Correct size selection was confirmed by BioAnalyzer analysis.   Sequencing was performed using Illumina HiSeq 2000 machines and generated 43bp single end reads.

tag: background strain

value: Mouse Embryonic Stem Cells

value: 2i/LIF to EpiLSCs transfer for 72h

tag: cell line


title: FFPE_renal_carcinoma_92

description:
US22502514_252182713899_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: 91_r1: TF91 Zm00001d015468 ChIP-Seq


title: RC17_after_mesDA_17_B12


title: RNA_EpiLSCs_Rep1


title: FFPE_renal_carcinoma_93

description:
US22502514_252182713899_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_91

description:
US22502514_252182713899_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: RNA_SL_d7_Rep2

value: 2i/LIF to serum/LIF transfer for 7days


title: RC17_after_mesDA_17_B11


title: 90_r1: TF90 Zm00001d039077 ChIP-Seq


title: RNA_SL_d7_Rep1


title: RC17_after_mesDA_17_B1


title: FFPE_renal_carcinoma_90

description:
US22502514_252182713899_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_89

description:
90_3990_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_88

description:
US22502514_252182713899_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: RNA_SL_d3_Rep2

value: 2i/LIF to serum/LIF transfer for 3days


title: RNA_SL_d3_Rep1


title: 91_r2: TF91 Zm00001d015468 ChIP-Seq

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR


title: RC17_after_mesDA_17_A9


title: 87_r2: TF87 Zm00001d034298 ChIP-Seq


title: RC17_after_mesDA_17_A7


title: 87_r1: TF87 Zm00001d034298 ChIP-Seq


title: FFPE_renal_carcinoma_87

description:
US22502514_252182713899_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: RNA_SL_d1_Rep1

value: 2i/LIF to serum/LIF transfer for 1day


title: RC17_after_mesDA_17_A6


title: RNA_SL_d1_Rep2


title: 90_r2: TF90 Zm00001d039077 ChIP-Seq


title: RC17_after_mesDA_17_B10


title: RNA_SL_Rep2

value: serum/LIF culture


title: 85_r2: TF85 Zm00001d043205 ChIP-Seq


title: 89_r2: TF89 Zm00001d025770 ChIP-Seq


title: 85_r1: TF85 Zm00001d043205 ChIP-Seq


title: RNA_SL_Rep1


title: RC17_after_mesDA_17_A4

value: B


title: RC17_after_mesDA_17_A5

value: GFP


title: 89_r1: TF89 Zm00001d025770 ChIP-Seq


title: FFPE_renal_carcinoma_85

description:
US22502514_252182713989_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples

value: renal carcinoma


title: RNA_2iL_d7_Rep2

value: serum/LIF to 2i/LIF transfer for 7days


title: FFPE_renal_carcinoma_83

description:
US22502514_252182713989_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_A2


title: RNA_2iL_d7_Rep1


title: RNA_2iL_d3_Rep2

value: serum/LIF to 2i/LIF transfer for 3days


title: FFPE_renal_carcinoma_82

description:
US22502514_252182713989_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_86

description:
US22502514_252182713989_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: 80_r2: TF80 Zm00001d049364 ChIP-Seq


title: RC17_after_mesDA_17_A12


title: 80_r1: TF80 Zm00001d049364 ChIP-Seq


title: RNA_2iL_d3_Rep1


title: FFPE_renal_carcinoma_81

description:
US22502514_252182713989_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_17_A11


title: FFPE_renal_carcinoma_80

description:
US22502514_252182713989_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: 79_r2: TF79 Zm00001d020409 ChIP-Seq


title: RNA_2iL_d1_Rep2

value: serum/LIF to 2i/LIF transfer for 1day


title: RC17_after_mesDA_17_A10


title: FFPE_renal_carcinoma_79

description:
US22502514_252182713989_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: 84_r2: TF84 Zm00001d033049 ChIP-Seq


title: FFPE_renal_carcinoma_78

description:
US22502514_252182713988_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_H9


title: 79_r1: TF79 Zm00001d020409 ChIP-Seq


title: RNA_2iL_d1_Rep1


title: 84_r1: TF84 Zm00001d033049 ChIP-Seq


title: 72_r2: TF72 Zm00001d002364 ChIP-Seq


title: RNA_2iL_Rep2

value: 2i/LIF culture


title: RC17_after_mesDA_16_H8


title: 72_r1: TF72 Zm00001d002364 ChIP-Seq


title: FFPE_renal_carcinoma_77

description:
US22502514_252182713988_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_H6


title: RNA_2iL_Rep1


title: FFPE_renal_carcinoma_84

description:
US22502514_252182713989_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: 70_r2: TF70 Zm00001d013777 ChIP-Seq


title: FFPE_renal_carcinoma_76

description:
US22502514_252182713988_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: RFP_EpiLSCs_Rep2

data_processing:
Library strategy: Ribosome-profiling
To analyze the ribosome profiling data, FASTQ reads were processed s previously described (Ingolia et al., 2012). Briefly, adaptor sequences were removed using fastx_clipper (fastx_toolkit-0.0.14) (http://hannonlab.cshl.edu/fastx_toolkit/index.html) and by employing the following parameters clipper -Q33 -a CTGTAGGCACCATCAAT -l 25 -c -n –v. Reads were then trimmed using fastx_trimmer (fastx_toolkit-0.0.14) and  -Q33 -f 2 parameters.  Both RNA-seq reads and the trimmed ribosome profiling reads were then aligned against mouse rRNA, tRNA, snRNA, snoRNA, mtRNA sequences using Bowtie (Langmead et al., 2009) and --seedlen=23 to deplete these small RNA contamination. Unmapped reads (cleaned) were then mapped against mouse genome (mm9) using GSNAP (Wu and Watanabe, 2005) and by employing the following parameters:  -B 5 -t 15 -N 1 -E 100 -w 100000 -n 10 -s mm9refGene_splice. Mapped reads were counted in the coding sequence using HTseq-count (Anders et al., 2015) with the settings: -m union -s reverse -t CDS.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig tracks, data are not normalized for sequencing depth.

growth_protocol: E14Tg2a ESCs were cultured in standard culture medium without feeder and on gelatin coated-dishes. Serum supplemented medium contains Dulbecco's Modified Eagle's Medium (DMEM, Gibco) supplemented with 10% fetal calf serum (FCS, Gibco), L-glutamine (2 nM, Gibco), Na-Pyruvate (1 mM, Gibco), non-essential amino acids (0.1 mM each, Gibco), Penicillin Streptomycin (Gibco), 2-mercaptoethanol (55 µM, Gibco) and LIF (1000 U/ml, Milipore). For serum free culture, cells were maintained in NDiff 227 (StemCells, Inc.) supplemented with MEK inhibitor PD0325901 (1 μM) and GSK3 inhibitor CHIR99021 (3 μM) and LIF (1000 U/ml, Milipore). To test the genome wide binding of Esrrb, Nr5a2 and Klf4, we generated BAC lines expressing the GFP-tagged proteins as described previously by Poser et al (poser I et al Nat. Methods 5, 409–415 (2008). For Nr5a2-null ESCs, cre-recombination was induced by treating with 4-hydroxy tamoxifen (0.5 μM) for 2 days. Cells were confirmed for the correct deletion using PCR. All siRNA experiments were performed for 72h and by using 25pmol stealth siRNAs per well of 6-well plates.

extract_protocol:
Illumina RNA-seq strand specific
Briefly, 500 µg of the ribonucleoproteins (2 biological replicates per sample) were treated with 1000U RNase I (Ambion Cat# AM2295) at 4oC for 50 min with gentle end-over-end rotation followed by incubation with SuperaseIn (Ambion, Cat# AM2696). Monosomes were pelleted by ultracentrifugation in a 34% sucrose cushion at 70,000 rpm in TLA-120.2 rotor (Beckman Coulter) at 4oC for 3h. RNA fragments were extracted with acid phenol (2x), once with chloroform, and precipitated with isopropanol at -20oC in the presence of NaOAc and GlycoBlue (Invitrogen). Purified RNA samples were resolved on a denaturing 15% polyacrylamide-urea gel and the sections corresponding to 28-32 nucleotides containing the ribosome footprints (RFPs) were excised, eluted, and precipitated by isopropanol.
Purified RFPs were dephosphorylated using T4 polynucleotide kinase (New England Biolabs) for 1 h at 37°C. Denatured fragments were resuspended in 10 mM Tris (pH 7) and quantified using the Bio-Analyzer Small RNA assay (Agilent). A sample of 10 pmol of RNA was ligated to the 3′-adaptor with T4 RNA ligase 1 (New England Biolabs) for 2 h at 37°C. Reverse transcription was carried out using oNTI223 adapter (Illumina) and SuperScript III reverse transcriptase (Invitrogen) according to the manufacturer’s instructions. Products were separated from the empty adaptor on a 10% polyacrylamide Tris/Borate/EDTA-urea (TBE-urea) gel and circularized by CircLigase (Epicentre). Ribosomal RNA amounts were reduced by subtractive hybridization using biotinylated rDNA complementary oligos (Ingolia et al., 2012). The RFP libraries were amplified by PCR (11 cycles) using indexed primers and quantified using the Agilent BioAnalyzer High-Sensitivity assay. DNA was then sequenced on the HiSeq-2000 platform with read length of 50 nucleotides (SR50) according to the manufacturer’s instructions, with sequencing primer oNTI202 (5CGACAGGTTCAGAGTTCTACAGTCCGACGATC).


title: 70_r1: TF70 Zm00001d013777 ChIP-Seq


title: FFPE_renal_carcinoma_75

description:
US22502514_252182713988_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: RFP_EpiLSCs_Rep1


title: FFPE_renal_carcinoma_74

description:
US22502514_252182713988_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: 6_r2: TF6 Zm00001d038357 ChIP-Seq


title: RC17_after_mesDA_16_H3


title: RC17_after_mesDA_16_H4


title: 6_r1: TF6 Zm00001d038357 ChIP-Seq


title: RC17_after_mesDA_16_H11


title: FFPE_renal_carcinoma_73

description:
US22502514_252182713988_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: RFP_SL_d7_Rep1


title: RC17_after_mesDA_17_A3


title: FFPE_renal_carcinoma_72

description:
US22502514_252182713988_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_G9


title: RC17_after_mesDA_16_H10


title: RFP_SL_d7_Rep2


title: 69_r3: TF69 Zm00001d033050 ChIP-Seq

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR


title: 69_r2: TF69 Zm00001d033050 ChIP-Seq


title: RFP_SL_d3_Rep1


title: FFPE_renal_carcinoma_71

description:
US22502514_252182713988_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_G8


title: RC17_after_mesDA_16_G7


title: RFP_SL_d3_Rep2


title: FFPE_renal_carcinoma_70

description:
US22502514_252182713905_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: RFP_SL_d1_Rep2


title: 66_r2: TF66 Zm00001d020492 ChIP-Seq


title: RC17_after_mesDA_16_G6


title: RFP_SL_d1_Rep1


title: FFPE_renal_carcinoma_69

description:
US22502514_252182713905_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_68

description:
US22502514_252182713905_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_G5


title: RC17_after_mesDA_16_G4


title: 64_r2: TF64 Zm00001d031796 ChIP-Seq


title: 66_r1: TF66 Zm00001d020492 ChIP-Seq


title: RFP_SL_Rep1


title: RFP_SL_Rep2


title: 64_r1: TF64 Zm00001d031796 ChIP-Seq


title: RC17_after_mesDA_16_G2


title: FFPE_renal_carcinoma_66

description:
US22502514_252182713905_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_65

description:
US22502514_252182713905_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: RFP_2iL_d7_Rep2


title: RFP_2iL_d7_Rep1


title: 69_r1: TF69 Zm00001d033050 ChIP-Seq


title: 61_r2: TF61 Zm00001d046925 ChIP-Seq


title: RC17_after_mesDA_16_G11


title: FFPE_renal_carcinoma_64

description:
65_3990_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: 61_r1: TF61 Zm00001d046925 ChIP-Seq


title: FFPE_renal_carcinoma_63

description:
US22502514_252182713905_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: RFP_2iL_d3_Rep2


title: RFP_2iL_d3_Rep1


title: RC17_after_mesDA_16_F9


title: RC17_after_mesDA_16_G1


title: RFP_2iL_d1_Rep2


title: FFPE_renal_carcinoma_62

description:
US22502514_252182713905_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_67

description:
US22502514_252182713905_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_F8


title: FFPE_renal_carcinoma_61

description:
US22502514_252182713904_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: 5_r1: TF5 Zm00001d044785 ChIP-Seq


title: FFPE_renal_carcinoma_60

description:
US22502514_252182713904_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: 59_r2: TF59 Zm00001d027901 ChIP-Seq


title: RFP_2iL_d1_Rep1


title: RC17_after_mesDA_16_F5


title: RFP_2iL_Rep2


title: 59_r1: TF59 Zm00001d027901 ChIP-Seq


title: 58_r4: TF58 Zm00001d015407 ChIP-Seq


title: RC17_after_mesDA_16_F3


title: FFPE_renal_carcinoma_58

description:
US22502514_252182713904_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_F4


title: 58_r3: TF58 Zm00001d015407 ChIP-Seq