title: P96_H1b5s_016


title: Group Familiar 5

status: Public on Apr 05 2017

type: SRA

city: Cardiff

first: Hannah

last: Scott

address: Hadyn Ellis Building, Maindy Road

department: UK Dementia Research Institute

country: United Kingdom

institute: Cardiff University

description:
Sample 10
processed data file: Control_v_Familiar.csv, Familiar_v_Novel.csv

library_source: transcriptomic

data_processing:
Base calling and trimming of sequences and adapters was performed using the Torrent Suite Software v4.0.2. . For each sample, the data from both chips were pooled before running the analysis pipeline.
Alignment of the sequencing reads was performed via TopHat using the rat reference genome Rnor_6.0 (GenBank Assembly ID GCA_000001895.4). We used default TopHat parameters except for the range of expected intron lengths, which we set to 12-270,000 based on the current reference gene models. Unmapped reads were then re-aligned using Bowtie2 local alignments and combined with the TopHat alignments.
Reads were mapped to rat genes and the relative abundance of each transcript was quantified using the HTSeq package, counting only uniquely mapped reads and allowing for an alignment quality threshold of 10.
We used RUVSeq to adjust read counts in order to mitigate unwanted variation unrelated to treatment groups. Using these counts as input, differential gene expression analysis was performed using edgeR.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: csv files containing output from edgeR after each RUVSeq normalisation step (fold changes, p values) for each Ensembl gene ID.

molecule: total RNA

organism: Rattus norvegicus

source_name: Familiar_Caudal perirhinal cortex

growth_protocol: All rats were kept on a reversed 12-h light/dark cycle (lights on 20.00-08.00 h) and all behavioural testing. Prior to the start of the behavioural experiments, the animals were placed on food restriction with daily access to food for a period of 2 h. The rats were kept at over 85% of their free-feeding weight. Water was available without restriction.

extract_protocol:
Total RNA was extracted from isolated and snap-frozen caudal perirhinal cortex tissue 1h after completion of the behavoural task using TRIzol (Life Technologies) and the Rneasy Mini kit (Qiagen). Samples were selectively depleted of rRNA using the Low Input Ribominus Eukaryote System v2 (Life Technologies).
cDNA libraries were prepared from 250 ng total RNA using the Ion Total RNA-seq Kit v2 in combination with the Ion Xpress RNA-Seq Barcode 1-16 Kit (both kits from Life Technologies).

treatment_protocol: Rats were trained in the bow-tie maze recognition memory task and on the final day were allowed to explore either completely novel objects (Group Novel) or highly familiar objects (Group Familiar). Group Control consisted of naïve rats that had not undergone any behavioural training.

tag: strain

value: Lister Hooded

tag: Sex

value: male

tag: weight

tag: behavioural task

value: Bow-tie maze

tag: test condition

tag: tissue

value: Caudal perirhinal cortex

tag: molecule subtype

value: rRNA-depleted total RNA


title: MEF_BAtruncM_Input_rep1

city: Stanford

first: Marius

last: Wernig

state: CA

address: 265 Campus Drive, Rm. G3145

department: Institute for Stem Cell Biology & Regenerative Medicine

country: USA

institute: Stanford University

description: ChIP Input

library_source: genomic

data_processing:
Reads were aligned to GRCm38/mm10 using bowtie2 (version 2.2.3) allowing maximum one mismatch per read (Langmead et al., 2012). Peaks for each sample were called using MACS2 (version 2.0.10.20131216 (Zhang et al., 2008) using shift size values from the run_spp.R script of the SPP peak caller (Kharchenko et al., 2008). The IDR pipeline was run to identify high-quality peaks according to https://sites.google.com/site/anshulkundaje/projects/idr using a cutoff value of 0.02.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: narrowPeak files of idr-processed ChIP peaks

molecule: genomic DNA

organism: Mus musculus

source_name: TauEGFP MEFs

growth_protocol: Passage three heterozygous TauEGFP knock-in MEFs were infected with indicated lentivirus in (DMEM; Invitrogen) containing 10% cosmic calf serum (CCS; Hyclone), beta mercaptoethanol (Sigma), non-essential amino acids, sodium pyruvate and penicillin/streptomycin (all from Invitrogen) media containing 8 μg/ml polybrene (Sigma) for 16-20 h. Cells were switched into fresh MEF media containing 2 μg/ml doxycycline (Sigma) to induce transgene expression for 2 days followed by ChIP sequencing.

extract_protocol: ChIP-seq were carried out following the Farnham protocol (O'Geen et al., 2011). Libraries were generated using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina.

treatment_protocol: Lentivirus was produced by transfection of TetO-FUW lentiviral backbones containing the indicated transgenes together with third-generation packaging plasmids into HEK293 cells following the Trono laboratory protocol (Dull et al., 1998). Virus was concentrated from culture supernatant by ultra-centrifugation (23000 rpm, 2 h, 4 °C) and cells were infected with three different viral titers. Infected cell populations that were used for reprogramming and genomic analysis were verified by immunofluorescence to contain approximately 70%-90% transgene-positive cells two days after induction based on immunofluorescence microscopy.

tag: strain background

value: embryonic fibroblasts

tag: overexpressed proteins

value: Brn2, Ascl1, Myt1l(200-623), rtTA


title: MEF_BAflM_Myt1lb_rep2

description:
ChIP
macs2.con.48h_BAflM_Myt1LAB_cat_peaks.narrowPeak

value: Brn2, Ascl1, Myt1l, rtTA

tag: chip antibody

value: Myt1lb (rabbit)


title: P96_H1b5s_014

city: Gainesville

first: Rhonda

last: Bacher

state: FL

address: 2004 Mowry Rd.

institute: University of Florida

description: H1 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequencing reads were mapped to hg19 using bowtie 0.12.8. Single cell samples were mapped to hg19 + ERCC spike-ins.
Gene expected counts were calculated using RSEM 1.2.3
Genome_build: hg19
Supplementary_files_format_and_content: Bacher.RSEM.xlsx: Excel spreadsheet reporting RSEM Expected Counts expression estimation on five tabs, corresponding to different sample types and multiplexing levels.

organism: Homo sapiens

source_name: undifferentiated human embryonic stem cells

growth_protocol: Undifferentiated H1 hESCs were cultured in E8 medium on Matrigel-coated tissue culture plates with daily media feeding at 37 °C. Cells were split every 3-4 days with 0.5 mM EDTA in 1xPBS for standard maintenance

extract_protocol:
Single-cell suspensions were loaded onto a medium size (10-17 μm) C1 Single-Cell Auto Prep IFC (Fluidigm), and cell-loading script was performed according to the manufacturer’s instructions. Full-length single-cell cDNA libraries generated by the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) performed in the C1 system.
Diluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina). The H1 single-cell cDNA libraries were multiplexed at 96 libraries per lane, and single-end reads of 51-bp sequencing was performed on an Illumina HiSeq 2500 system.

tag: cell line

tag: cell type

value: human embryonic stem cells

tag: passage

value: passage 20-30

tag: multiplexing


title: P96_H1b5s_015


title: Group Familiar 4

description:
Sample 09
processed data file: Control_v_Familiar.csv, Familiar_v_Novel.csv

value: highly familiar objects (Group Familiar)


title: Group Familiar 3

description:
Sample 08
processed data file: Control_v_Familiar.csv, Familiar_v_Novel.csv


title: P96_H1b5s_013


title: MEF_BAflM_Input_rep2

description: ChIP Input


title: MEF_BAflM_Myt1lb_rep1


title: P96_H1b5s_006


title: MEF_BAflM_Myt1la_rep1

value: Myt1la (rabbit)


title: Group Familiar 1

description:
Sample 06
processed data file: Control_v_Familiar.csv, Familiar_v_Novel.csv


title: P96_H1b5s_005


title: MEF_BAflM_Input_rep1

description: ChIP Input


title: P96_H1b5s_004


title: E13.5_Mouse Brain_Myt1lb_rep2

description:
ChIP
macs2.con.13-5_Mouse_Brain_Myt1LB_cat_peaks.narrowPeak

source_name: E13.5 Mouse Brain

growth_protocol: untreated

treatment_protocol: untreated

value: E13.5 mouse brain

value: endogenous


title: Group Novel 5

description:
Sample 05
processed data file: Control_v_Novel.csv, Familiar_v_Novel.csv

source_name: Novel_Caudal perirhinal cortex

value: completely novel objects (Group Novel)


title: P96_H1b5s_002


title: P96_H1b5s_003


title: Group Novel 4

description:
Sample 04
processed data file: Control_v_Novel.csv, Familiar_v_Novel.csv


title: E13.5_Mouse Brain_Input_rep2

description: ChIP Input


title: Group Novel 3

description:
Sample 03
processed data file: Control_v_Novel.csv, Familiar_v_Novel.csv


title: P96_H1b5s_001


title: E13.5_Mouse Brain_Input_rep1

description: ChIP Input


title: Group Novel 1

description:
Sample 01
processed data file: Control_v_Novel.csv, Familiar_v_Novel.csv


title: Group Novel 2

description:
Sample 02
processed data file: Control_v_Novel.csv, Familiar_v_Novel.csv


title: Sample_RPE_GFP_PGBD5

status: Public on Apr 04 2017

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human assembly hg19 using bwa mem (v0.7.12) with default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

source_name: retina

growth_protocol: Cells were cultured in 5% CO2 in a humidified atmosphere at 37 ˚C in Dulbecco’s Modified Eagle medium with high glucose (DMEM-HG) supplemented with 10 % FCS and antibiotics (100 U / ml penicillin and 100 µg / ml streptomycin).

extract_protocol: ChIP-seq libraries were constructed with the NEBNext ChIP-seq library prep kit following the manufacturer’s recommended protocol (New England Biolabs, Ipswich, MA, USA).

treatment_protocol: No treatment

tag: tumor type

value: Epithelial cells immortalized with hTERT

value: Mouse anti-GFP, Cell Signaling #2955, lot 4B10

tag: transgene


title: Sample_RPE_GFP

value: GFP


title: Sample_RPE_GFP_PGBD5_TM

value: triple mutant PGBD5-GFP


title: PMD12b

city: Clev

first: Paul

middle: J.

last: Tesar

state: OH

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

institute: Case Western Reserve University School of Medicine

data_processing:
Output FASTQ files were aligned to the GRCh37/hg19 genome using Tophat (Version 2.0.8) with default settings.
Data was normalized and fragments per kilobase per million reads (FPKM) were calculated for known RefSeq genes using Cufflinks (Version 2.0.2).
Genome_build: hg19
Supplementary_files_format_and_content: Standard cufflinks output (genes.fpkm_tracking)

source_name: induced pluripotent stem cells

growth_protocol: iPSC colonies were grown on matrigel in mTeSR media for at minimum 2 passages prior to RNA isolation

extract_protocol:
500,000 cells were pelleted, resuspended in TRIzol, and frozen at -80 degrees Celsius. Total RNA was isolated using the Qiagen Rneasy Mini Kit (ThermoFisher #15596026), beginning with chloroform extraction and separation by PhaseLock gel tubes (5 Prime #2302830).
1ug of each sample was rRNA depleted (Ribo-Zero Gold, Illumina #MRZG12324), fragmented, and indexed using the TruSeq Stranded mRNA Library Preparation Kit (Illumina #RS-122-2103) per the manufacturer’s protocol.

value: Patient-derived induced pluripotent stem cells


title: Sample_G401_H3K27ac

source_name: kidney

value: rhabdoid tumor

value: kidney

value: Rabbit H3K27ac, Abcam #4729, lot GR150367-2


title: Sample_G401_H3K4me3

value: Rabbit H3K4me3, Cell Signaling #9751, lot 7


title: PMD11b


title: Group Familiar 2

description:
Sample 07
processed data file: Control_v_Familiar.csv, Familiar_v_Novel.csv

value: Lister Hooded

value: male

value: Bow-tie maze

value: Caudal perirhinal cortex

value: rRNA-depleted total RNA


title: PMD12a


title: PMD10a


title: PMD11a


title: PMD10b


title: PMD9b


title: E13.5_Mouse Brain_Myt1lb_rep1

value: E13.5 mouse brain

value: Myt1lb (rabbit)


title: PMD8b


title: PMD9a


title: PMD7a


title: PMD7b


title: PMD6b


title: PMD8a


title: PMD3b


title: PMD6a


title: PMD4a


title: PMD2b


title: PMD2a


title: PMD4b


title: PMD1b


title: PMD5b


title: PMD5a


title: NC4


title: NC6


title: NC7


title: PMD1a


title: NC3

source_name: “H9” NIHhESC-10-0062

value: Embryonic stem cells


title: NC2


title: NC1


title: egl-9;vhl-1 mutant 3

city: Medford

first: David

last: Angeles-Albores

state: MA

address: 61 Locust St

institute: Northwestern University

data_processing:
Base-calling was performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4
Pseudo-alignment using Kallisto. All commands were as follow: kallisto quant -i <index-file>  <output-file> --single -s 60 -l 180 -b 200 -t 4 <input files>
Supplementary_files_format_and_content: TPM reads from pseudo-alignment quantification

organism: Caenorhabditis elegans

source_name: egl-9;vhl-1 mutant

growth_protocol: Synchronized populations were grown to the young adult stage (no visible eggs) on NGM plates with ample OP50

extract_protocol:
Pick 30-50 worms per sample. Post-proteinase K digestion (performed in a solution containing 10%SDS and Ambion RNA secure in excess), isolate RNA using a Zymo Microprep RNA Kit
SmartSeq2

tag: genotype


title: egl-9 hif-1 mutant 3

source_name: egl-9 hif-1 mutant


title: PMD3a


title: egl-9;vhl-1 mutant 1


title: NC5


title: egl-9 hif-1 mutant 1


title: hif-1 mutant 1

source_name: hif-1 mutant


title: vhl-1 mutant 3

source_name: vhl-1 mutant


title: vhl-1 mutant 1


title: vhl-1 mutant 2


title: hif-1 mutant 3


title: rhy-1 mutant 3

source_name: rhy-1 mutant


title: rhy-1 mutant 1


title: rhy-1 mutant 2


title: egl-9 mutant 3

source_name: egl-9 mutant


title: egl-9 mutant 2


title: N2 Control 1

source_name: N2 Control


title: egl-9 mutant 1


title: N2 Control 3


title: MA_EVO_DEVO_TP7_R3

city: Haifa

first: Harel

last: Zalts

state: Israel

address: Technion city

country: Israel

institute: Technion

description:
MA_522G_3
Sample name: MA_522G_3

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 10. trimming of read2 to 35 bases - not required).
CEL-Seq (Hashimshony, et a. 2012l) demultiplexing of second mate, using first mate barcode, allowing no mismatches in barcode.
bowtie2, version 2.1.0, against C. elegans genome WS230
Genome_build: WS230
Supplementary_files_format_and_content: tabular Expression matrix. See sample description for sample ID.

molecule: polyA RNA

source_name: pool of 10 whole embryos

growth_protocol: Standard C. elegans techniques were followed to grow worms (Stiernagle 2006).

extract_protocol:
RNA was isolated using TRIzol as previously described (Levin et al., 2012).
The CEL-Seq protocol (Hashimshony, et al. 2012) was used to amplify and sequence. CEL-seq multiplexing barocdes were used.

treatment_protocol: For the embryo collection of all species adult hermaphrodites or females were collected and cut to obtain embryos. Embryos were washed with a bleach solution (70% DDW, 20% bleach, 10% 5M KOH) for 30 seconds and subsequently with a 5% BSA solution for 30 seconds. 4-cell embryos were collected,washed 4 times in clear DDW and incubated at 20°C for the appropriate time for each species to reach stages 1-10. After incubation embryos were frozen in liquid nitrogen and kept at -80°C until RNA extraction.

tag: strain

tag: time after 4-cell embryo (minutes)

value: whole embryo


title: MA_EVO_DEVO_TP6_R3

description:
MA_522F_3
Sample name: MA_522F_3


title: N2 Control 2


title: egl-9;vhl-1 mutant 2


title: MA_EVO_DEVO_TP6_R2

description:
MA_522F_2
Sample name: MA_522F_2


title: MA_EVO_DEVO_TP7_R1

description:
MA_522G_1
Sample name: MA_522G_1


title: MA_EVO_DEVO_TP7_R2

description:
MA_522G_2
Sample name: MA_522G_2


title: MA_EVO_DEVO_TP5_R3

description:
MA_522E_3
Sample name: MA_522E_3


title: MA_EVO_DEVO_TP4_R3

description:
MA_522D_3
Sample name: MA_522D_3


title: MA_EVO_DEVO_TP4_R2

description:
MA_522D_2
Sample name: MA_522D_2


title: MA_EVO_DEVO_TP5_R2

description:
MA_522E_2
Sample name: MA_522E_2


title: egl-9 hif-1 mutant 2


title: MA_EVO_DEVO_TP5_R1

description:
MA_522E_1
Sample name: MA_522E_1


title: MA_EVO_DEVO_TP6_R1

description:
MA_522F_1
Sample name: MA_522F_1


title: MA_EVO_DEVO_TP4_R1

description:
MA_522D_1
Sample name: MA_522D_1


title: hif-1 mutant 2


title: MA_EVO_DEVO_TP3_R1

description:
MA_522C_1
Sample name: MA_522C_1


title: MA_EVO_DEVO_TP3_R3

description:
MA_522C_3
Sample name: MA_522C_3


title: MA_EVO_DEVO_TP3_R2

description:
MA_522C_2
Sample name: MA_522C_2


title: MA_EVO_DEVO_TP2_R3

description:
MA_522B_3
Sample name: MA_522B_3


title: MA_EVO_DEVO_TP2_R1

description:
MA_522B_1
Sample name: MA_522B_1


title: MA_EVO_DEVO_TP1_R3

description:
MA_522A_3
Sample name: MA_522A_3


title: MA_EVO_DEVO_139

description:
597F
Sample name: 597F


title: MA_EVO_DEVO_140

description:
597G
Sample name: 597G


title: MA_EVO_DEVO_135

description:
597B
Sample name: 597B


title: MA_EVO_DEVO_138

description:
597E
Sample name: 597E


title: MA_EVO_DEVO_136

description:
597C
Sample name: 597C


title: MA_EVO_DEVO_137

description:
597D
Sample name: 597D


title: MA_EVO_DEVO_134

description:
597A
Sample name: 597A


title: MA_EVO_DEVO_131

description:
566E
Sample name: 566E


title: MA_EVO_DEVO_133

description:
566G
Sample name: 566G


title: MA_EVO_DEVO_132

description:
566F
Sample name: 566F


title: MA_EVO_DEVO_129

description:
566C
Sample name: 566C


title: MA_EVO_DEVO_128

description:
566B
Sample name: 566B


title: MA_EVO_DEVO_127

description:
566A
Sample name: 566A


title: MA_EVO_DEVO_130

description:
566D
Sample name: 566D


title: MA_EVO_DEVO_125

description:
508F
Sample name: 508F


title: MA_EVO_DEVO_121

description:
508B
Sample name: 508B


title: MA_EVO_DEVO_123

description:
508D
Sample name: 508D


title: MA_EVO_DEVO_120

description:
508A
Sample name: 508A


title: MA_EVO_DEVO_126

description:
508G
Sample name: 508G


title: MA_EVO_DEVO_124

description:
508E
Sample name: 508E


title: MA_EVO_DEVO_TP2_R2

description:
MA_522B_2
Sample name: MA_522B_2


title: MA_EVO_DEVO_118

description:
536F
Sample name: 536F


title: MA_EVO_DEVO_TP1_R2

description:
MA_522A_2
Sample name: MA_522A_2


title: MA_EVO_DEVO_117

description:
536E
Sample name: 536E


title: MA_EVO_DEVO_115

description:
536C
Sample name: 536C


title: MA_EVO_DEVO_116

description:
536D
Sample name: 536D


title: MA_EVO_DEVO_TP1_R1

description:
MA_522A_1
Sample name: MA_522A_1


title: MA_EVO_DEVO_110

description:
522E
Sample name: 522E


title: MA_EVO_DEVO_114

description:
536B
Sample name: 536B


title: MA_EVO_DEVO_113

description:
536A
Sample name: 536A


title: MA_EVO_DEVO_111

description:
522F
Sample name: 522F


title: MA_EVO_DEVO_105

description:
552G
Sample name: 552G


title: MA_EVO_DEVO_106

description:
522A
Sample name: 522A


title: MA_EVO_DEVO_107

description:
522B
Sample name: 522B


title: MA_EVO_DEVO_102

description:
552D
Sample name: 552D


title: MA_EVO_DEVO_122

description:
508C
Sample name: 508C


title: MA_EVO_DEVO_119

description:
536G
Sample name: 536G


title: MA_EVO_DEVO_97

description:
516F
Sample name: 516F


title: MA_EVO_DEVO_95

description:
516D
Sample name: 516D


title: MA_EVO_DEVO_104

description:
552F
Sample name: 552F


title: MA_EVO_DEVO_103

description:
552E
Sample name: 552E


title: MA_EVO_DEVO_101

description:
552C
Sample name: 552C


title: MA_EVO_DEVO_109

description:
522D
Sample name: 522D


title: MA_EVO_DEVO_98

description:
516G
Sample name: 516G


title: MA_EVO_DEVO_99

description:
552A
Sample name: 552A


title: MA_EVO_DEVO_94

description:
516C
Sample name: 516C


title: MA_EVO_DEVO_96

description:
516E
Sample name: 516E


title: MA_EVO_DEVO_93

description:
516B
Sample name: 516B


title: MA_EVO_DEVO_92

description:
516A
Sample name: 516A


title: MA_EVO_DEVO_108

description:
522C
Sample name: 522C


title: MA_EVO_DEVO_100

description:
552B
Sample name: 552B


title: MA_EVO_DEVO_91

description:
564G
Sample name: 564G


title: MA_EVO_DEVO_88

description:
564D
Sample name: 564D


title: MA_EVO_DEVO_112

description:
522G
Sample name: 522G


title: MA_EVO_DEVO_87

description:
564C
Sample name: 564C


title: MA_EVO_DEVO_90

description:
564F
Sample name: 564F


title: MA_EVO_DEVO_89

description:
564E
Sample name: 564E


title: MA_EVO_DEVO_86

description:
564B
Sample name: 564B


title: MA_EVO_DEVO_84

description:
573G
Sample name: 573G


title: MA_EVO_DEVO_83

description:
573F
Sample name: 573F


title: MA_EVO_DEVO_80

description:
573C
Sample name: 573C


title: MA_EVO_DEVO_82

description:
573E
Sample name: 573E


title: MA_EVO_DEVO_79

description:
573B
Sample name: 573B


title: MA_EVO_DEVO_77

description:
593G
Sample name: 593G


title: MA_EVO_DEVO_78

description:
573A
Sample name: 573A


title: MA_EVO_DEVO_76

description:
593F
Sample name: 593F


title: MA_EVO_DEVO_74

description:
593D
Sample name: 593D


title: MA_EVO_DEVO_73

description:
593C
Sample name: 593C


title: MA_EVO_DEVO_69

description:
598F
Sample name: 598F


title: MA_EVO_DEVO_68

description:
598E
Sample name: 598E


title: MA_EVO_DEVO_71

description:
593A
Sample name: 593A


title: MA_EVO_DEVO_65

description:
598B
Sample name: 598B


title: MA_EVO_DEVO_63

description:
529G
Sample name: 529G


title: MA_EVO_DEVO_64

description:
598A
Sample name: 598A


title: MA_EVO_DEVO_62

description:
529F
Sample name: 529F


title: MA_EVO_DEVO_66

description:
598C
Sample name: 598C


title: MA_EVO_DEVO_67

description:
598D
Sample name: 598D


title: MA_EVO_DEVO_57

description:
529A
Sample name: 529A


title: MA_EVO_DEVO_60

description:
529D
Sample name: 529D


title: MA_EVO_DEVO_59

description:
529C
Sample name: 529C


title: MA_EVO_DEVO_85

description:
564A
Sample name: 564A


title: MA_EVO_DEVO_56

description:
517G
Sample name: 517G


title: MA_EVO_DEVO_55

description:
517F
Sample name: 517F


title: MA_EVO_DEVO_81

description:
573D
Sample name: 573D


title: MA_EVO_DEVO_54

description:
517E
Sample name: 517E


title: MA_EVO_DEVO_75

description:
593E
Sample name: 593E


title: MA_EVO_DEVO_53

description:
517D
Sample name: 517D


title: MA_EVO_DEVO_70

description:
598G
Sample name: 598G


title: MA_EVO_DEVO_50

description:
517A
Sample name: 517A


title: MA_EVO_DEVO_72

description:
593B
Sample name: 593B


title: MA_EVO_DEVO_51

description:
517B
Sample name: 517B


title: MA_EVO_DEVO_48

description:
530F
Sample name: 530F


title: MA_EVO_DEVO_47

description:
530E
Sample name: 530E


title: MA_EVO_DEVO_46

description:
530D
Sample name: 530D


title: MA_EVO_DEVO_49

description:
530G
Sample name: 530G


title: MA_EVO_DEVO_45

description:
530C
Sample name: 530C


title: MA_EVO_DEVO_43

description:
530A
Sample name: 530A


title: MA_EVO_DEVO_40

description:
575E
Sample name: 575E


title: MA_EVO_DEVO_58

description:
529B
Sample name: 529B


title: MA_EVO_DEVO_42

description:
575G
Sample name: 575G


title: MA_EVO_DEVO_38

description:
575C
Sample name: 575C


title: MA_EVO_DEVO_41

description:
575F
Sample name: 575F


title: MA_EVO_DEVO_39

description:
575D
Sample name: 575D


title: MA_EVO_DEVO_44

description:
530B
Sample name: 530B


title: MA_EVO_DEVO_37

description:
575B
Sample name: 575B


title: MA_EVO_DEVO_36

description:
575A
Sample name: 575A


title: MA_EVO_DEVO_33

description:
N2E
Sample name: N2E


title: MA_EVO_DEVO_32

description:
N2D
Sample name: N2D


title: MA_EVO_DEVO_31

description:
N2C
Sample name: N2C


title: MA_EVO_DEVO_61

description:
529E
Sample name: 529E


title: MA_EVO_DEVO_29

description:
N2A
Sample name: N2A


title: MA_EVO_DEVO_30

description:
N2B
Sample name: N2B


title: MA_EVO_DEVO_34

description:
N2F
Sample name: N2F


title: MA_EVO_DEVO_52

description:
517C
Sample name: 517C


title: MA_EVO_DEVO_23

description:
555B
Sample name: 555B


title: MA_EVO_DEVO_35

description:
N2G
Sample name: N2G


title: MA_EVO_DEVO_25

description:
555D
Sample name: 555D


title: MA_EVO_DEVO_24

description:
555C
Sample name: 555C


title: MA_EVO_DEVO_28

description:
555G
Sample name: 555G


title: MA_EVO_DEVO_26

description:
555E
Sample name: 555E


title: MA_EVO_DEVO_20

description:
502F
Sample name: 502F


title: MA_EVO_DEVO_19

description:
502E
Sample name: 502E


title: MA_EVO_DEVO_21

description:
502G
Sample name: 502G


title: MA_EVO_DEVO_18

description:
502D
Sample name: 502D


title: MA_EVO_DEVO_16

description:
502B
Sample name: 502B


title: MA_EVO_DEVO_14

description:
570G
Sample name: 570G


title: MA_EVO_DEVO_11

description:
570D
Sample name: 570D


title: MA_EVO_DEVO_15

description:
502A
Sample name: 502A


title: MA_EVO_DEVO_13

description:
570F
Sample name: 570F


title: MA_EVO_DEVO_10

description:
570C
Sample name: 570C


title: MA_EVO_DEVO_9

description:
570B
Sample name: 570B


title: MA_EVO_DEVO_5

description:
550E
Sample name: 550E


title: MA_EVO_DEVO_7

description:
550G
Sample name: 550G


title: MA_EVO_DEVO_27

description:
555F
Sample name: 555F


title: MA_EVO_DEVO_4

description:
550D
Sample name: 550D


title: MA_EVO_DEVO_2

description:
550B
Sample name: 550B


title: MA_EVO_DEVO_1

description:
550A
Sample name: 550A


title: MA_EVO_DEVO_22

description:
555A
Sample name: 555A


title: CAD 85

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

description: treatment: Finasteride

data_processing:
RNA-seq pipeline description:
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.
We use RTA (Illumina) for base calling and CASAVA (version 1.8.2) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat [1] (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.  We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [2] (version 2.0.2) with default settings. We test for differentially expressed genes under various conditions using DEseq [3]. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Raw RNAseq counts were normalized (variance stabilization) using DESeq2 package in R-studio Version 0.99.484
Genome_build: Mouse: UCSC/mm9
Supplementary_files_format_and_content: Tab-delimited text or xls files include DESeq normalized values for each Sample

source_name: Nkx3.1 -/- Prostate

extract_protocol:
RNA was extracted using the MagMAX-96 RNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyser 2100
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.

value: hybrid 129/SvImJ and C57Bl/6J

value: prostate

tag: age

value: 12 months


title: CAD 80

description: treatment: Vehicle


title: CAD 84

description: treatment: Finasteride


title: CAD 86

description: treatment: Finasteride


title: CAD 83

description: treatment: Finasteride


title: CAD 82

description: treatment: Finasteride


title: CAD 81

description: treatment: Vehicle


title: CAD 77

description: treatment: Finasteride

source_name: Nkx3.1 +/+ Prostate


title: CAD 78

description: treatment: Finasteride


title: MA_EVO_DEVO_17

description:
502C
Sample name: 502C


title: CAD 76

description: treatment: Finasteride


title: MA_EVO_DEVO_12

description:
570E
Sample name: 570E


title: CAD 75

description: treatment: Finasteride


title: Retinal endothelial cell sample 4

city: Boston

first: Joseph

last: Arboleda-Velasquez

state: Massachusetts

address: 20 Staniford St.

institute: Schepens Eye Research Institute

data_processing:
Sequenced reads were trimmed for adaptor sequence and mapped to hg19 whole genome using Tophat v 2.0.5, creating BAM files.
Partek Flow v3, CuffLinks, EdgeR, DESeq2 were used to analyze BAM files.
Mixed-model ANOVA was used to analyze reads.
Genome_build: hg19
Supplementary_files_format_and_content: .txt files reporting abundance measurements

source_name: Retina

extract_protocol:
Fibrovascular membranes were obtained from patients undergoing a standard pars plana vitrectomy. Retinas was harvested from post-mortem patients. CD31+ cells were isolated using magnetic beads conjugated to CD31 antibodies. RNA was extracted from all FVM and retina samples.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: retinal endothelial cells

tag: disease state

value: non-Diabetic


title: CAD 71

description: treatment: Vehicle


title: CAD 74

description: treatment: Finasteride


title: CAD 72

description: treatment: Vehicle


title: CAD 73

description: treatment: Vehicle


title: MA_EVO_DEVO_8

description:
570A
Sample name: 570A


title: Retinal endothelial cell sample 3


title: MA_EVO_DEVO_6

description:
550F
Sample name: 550F


title: fibrovascular membrane endothelial cells 7

source_name: Fibrovascular Membrane

value: Diabetes Mellitus/proliferative diabetic retinopathy


title: MA_EVO_DEVO_3

description:
550C
Sample name: 550C


title: fibrovascular membrane endothelial cells 6


title: fibrovascular membrane endothelial cells 4


title: fibrovascular membrane endothelial cells 8


title: fibrovascular membrane endothelial cells 5


title: CAD 79

description: treatment: Vehicle


title: fibrovascular membrane endothelial cells 3


title: fibrovascular membrane endothelial cells 1


title: Retinal endothelial cell sample 1


title: fibrovascular membrane endothelial cells 2


title: Retinal endothelial cell sample 2


title: Dam_NC_Rep2

city: Novosibirsk

first: Petr

last: Laktionov

address: Lavrenitev ave 8/2

country: Russia

institute: Institute of molecular and cellular biology SD RAS

description:
Library strategy: DamID-seq
Su(var)3-9 DamID/nurse cells control sample
Su(var)3-9_NC_at_FDR_0.05_probability_track.wig.gz

data_processing:
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.7
The reads obtained were mapped to BDGP R6 Drosophila genome assembly using MOSAIK software with following parameters: -m all -mmp 0.1 -act 20 -a single
For further analysis, only the reads that started with GATC sequence were retained. The number of reads for each genomic fragment between the neighboring GATC sites (GATC fragments) was summed up.
The data were filtered for reproducibility: all GATC fragments were sorted according to the total read count in two biological samples. This list was binned into groups of 200 fragments having similar read counts. For each GATC fragment, a difference in read counts was calculated between the replicates. Those fragments that showed the difference above 2 standard deviations in the particular group were filtered out.
Genome_build: BDGP R6/dm6

organism: Drosophila melanogaster

source_name: adult ovary

growth_protocol: The flies were kept at 18°C

extract_protocol:
For DamID, salivary glands and brain ganglia were isolated from sexed third-instar larvae. Stage 10 egg chambers were isolated from adult females aged for 3 days. Testes were obtained from 3 day old males. Flies were kept at all times at 18С on standard flyfood. Organs were excised and collected in phosphate buffer saline. For each sample 100 salivary glands and brain ganglia, 50 testes and 250 egg chambers were collected.
One microgram of genomic DNA was processed for library preparation using the DNA TruSeq kit. The libraries were sequenced on the Illumina MiSeq (or HiSeq) system.

value: yw

tag: developmental stage

value: 3 days old females


title: Dam_NC_Rep1


title: SuVar_Dam_NC_Rep2

description:
Library strategy: DamID-seq
Su(var)3-9-Dam/nurse cells
Su(var)3-9_NC_at_FDR_0.05_probability_track.wig.gz


title: SuVar_Dam_NC_Rep1


title: fibrovascular membrane endothelial cells 9


title: Dam_can_Rep2

description:
Library strategy: DamID-seq
Su(var)3-9 DamID/can-mut testes control sample
Su(var)3-9_Testes_can_at_FDR_0.05_probability_track.wig.gz

source_name: adult testes

value: 3 days old males

tag: genotype/variation

value: can-mutant


title: pullout_miR-26a_control_replicate_1

city: Copenhagen

first: Francesco

last: Russo

address: Blegdamsvej 3b

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research, University of Copenhagen

data_processing:
NGS data were analysed using the Galaxy platform (https://usegalaxy.org/)
Quality control step: FastQC (version 0.10.1)
Trimming: Cutadapt
Aligner: TopHat 2 (version 2.0.9)
Transcript assembly and FPKM estimation: Cufflinks (version 2.1.1)
Merging of Cufflinks assemblies: Cuffmerge
Finding significant changes in transcript expression: Cuffdiff
Genome_build: Human genome hg38
Supplementary_files_format_and_content: Tab separated files reporting the Cufflinks output (FPKM)

source_name: prostate cancer cell line

growth_protocol: DU-145 cell lines grew in RPMI Medium 1640 (EuroClone). The medium was completed by adding 10% FBS (Fetal Bovine Serum, EuroClone), 1% penicillin (10.000 U/ml) and 1% streptomycin (10.000 mg/ml) (EuroClone) and 1% L-glutamine (200mM, Sigma-Aldrich). The cells were grew at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted adding directly on adherent cells TRIzol reagent (Thermo Fisher) and following the instructions provided by the manufacturer. After DNAse treatment, 15 mg of RNA was incubated for 4 hrs at 4°C with 100 ml of streptavidin-conjugated beads (200 ml of Streptavidin Sepharose high performance, GE Healthcare) previously suspended in PO buffer (1M Tris pH8, 5M NaCl, 1M MgCl2, NP40 50 ml in 100 ml buffer). After 2 washes with PO buffer and 2 washes with DEPC-treated water, the RNA complexed with beads was recovered by adding 1 ml Trizol directly on the beads and then following the TRIzol RNA extraction protocol.
The RNA isolated after the miRNA pullout procedure from both miR-26aCT and miR-26aBIO samples was used for the construction of the cDNA libraries using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina) according to the manufacturer’s suggestions. cDNA libraries were sequenced by HiSeq2000 (Illumina) in single-reads mode (50bp) by IGA Technology Service, Udine, Italy, obtaining about 20 million of reads for each samples.

treatment_protocol: DU-145 cell lines were seeded into the wells of a 6-well at the density of 1.5 x105. After 24 hours from seeding, cells were transfected using lipofectamine (Thermo Fisher) with 60nM of either miR-26a duplex (ds-miR-26aCT) or a mix of 3’ biotin-tagged miR-26a 7tU (nucleotide 7 was a thiouridine) and miR-26a 17tU duplexes (ds-miR-26aBIO). The day after transfection, the cells were washed with PBS and irradiated with UV (365nm, 2J/cm2), using the Bio-Link crosslinking (BLX) (Ambrose Lourmat) with appropriate UV lamps, to induce cross-linking of tU nucleotides to RNA.

tag: tissue

value: prostate cancer

tag: transfection

value: cells were transfected using lipofectamine (Thermo Fisher) with 60nM of miR-26a duplex (ds-miR-26aCT)


title: pullout_miR-26a_bio_replicate_1

value: cells were transfected using lipofectamine (Thermo Fisher) with 60nM of  a mix of 3’ biotin-tagged miR-26a 7tU (nucleotide 7 was a thiouridine) and miR-26a 17tU duplexes (ds-miR-26aBIO)


title: pullout_miR-26a_bio_replicate_2


title: Dam_can_Rep1


title: SuVar_Dam_can_Rep2

description:
Library strategy: DamID-seq
Su(var)3-9-Dam/can-mutant testes
Su(var)3-9_Testes_can_at_FDR_0.05_probability_track.wig.gz


title: SuVar_Dam_can_Rep1


title: Dam_bam_Rep1

description:
Library strategy: DamID-seq
Su(var)3-9 DamID/bam-mut testes control sample
Su(var)3-9_Testes_bam_at_FDR_0.05_probability_track.wig.gz

value: bam-mutatnt


title: Dam_bam_Rep2


title: CM47_control-miR

city: Würzburg

first: Ana

last: Eulalio

address: Josef Schneider Str. 2, D-15

country: Germany

institute: IMIB, University of Würzburg

data_processing:
Demultiplexing
FastQ quality trimming: cut-off value of 20 (FastX)
Fastq to fasta conversion (FastX)
Size filtering: discarding reads shorter than 14 nt (READemption 0.3.3)
Read mapping (READemption 0.3.0 and segemehl version 0.1.7)
Gene-wise quantification and coverage calculation (raw) and normalisation (norm) by total number of aligned reads and multiplied by 1 mio (READemption 0.3.3)
Genome_build: Homo sapiens ensembl build 37
Supplementary_files_format_and_content: Raw and normalized coverage files (wig)

source_name: HeLa-229 cells

growth_protocol: HeLa cells grown in standard conditions  (DMEM 1 g/L glucose (Life Technologies) supplemented with 10% fetal bovine serum (Biochrom), maintained in a 5% CO2, humidified atmosphere, at 37°C)

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.
Library preparation and deep-sequencing was performed by Vertis Biotechnology AG, using standard Illumina protocols

treatment_protocol: MicroRNAs were transfected into HeLa-229 cells using a standard reverse transfection protocol (Lipofectamine RNAiMAX, Life Technologies), at a final miRNA concentration of 50 nM. Cells were collected 72h pos-transfection.

value: transfection with control miR (50nM, 72h)


title: CM48_miR-29b-2-5p

value: transfection with miR-29b-2-5p (50nM, 72h)


title: CM29_Shigella_positive

source_name: Shigella Infected - cells with internalized Shigella

treatment_protocol: Infection with Shigella flexneri M90T strain expressing DsRed (MOI 10), analysed 6hpi; Total population, bystander cells and cells with internalized bacteria were collected.

tag: agent

value: Shigella flexneri 5 str. 8401


title: CM27_total_shigella_infected

source_name: Shigella Infected - total population


title: CM28_Shigella_negative

source_name: Shigella Infected - bystander cells


title: SuVar_Dam_bam_Rep1

description:
Library strategy: DamID-seq
Su(var)3-9-Dam/bam-mutant testes
Su(var)3-9_Testes_bam_at_FDR_0.05_probability_track.wig.gz


title: CM26_control

source_name: mock


title: Neural CS03iCTRmut -T3 biological repeat C

city: Los Angeles

first: Gad

middle: David

last: Vatine

state: California

address: 8700 Beverly blvd

department: RMI

institute: Cedars-Sinai Medical Center

data_processing:
Different adaptors were used for multiplexing samples in one lane.
Sequencing was performed on Illumina NextSeq 500 for a single read 75 run.
Data quality check was done on Illumina SAV.
Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
Genome_build: hg19
Supplementary_files_format_and_content: The processed file is a txt file containing RPKM by gene name (raws) for all of the provided raw files columns

source_name: iPSC-derived mixed neural cutures

growth_protocol:
Generations EZ-spheres from iPSCs. EZ-spheres were generated from iPSC colonies . Briefly, iPSC colonies grown on Matrigel-coated (BD Biosciences) plates (0.5 mg/plate) in mTESR1 (STEMCELL Technologies) media were removed by gentle scraping and placed directly into DMEM:F12 7:3 supplemented with 100 ng/ml basic fibroblast growth factor (bFGF, Chemicon), 100 ng/ml epidermal growth factor (Chemicon), and 5 μg/ml heparin (Sigma) in ultra-low attachment flasks and were passaged weekly using a chopping technique.
Differentiation of EZ-spheres into neural cultures. To induce neural differentiation, spheres were dissociated with Accutase (EMD Millipore) and plated onto poly-ornithine/laminin-coated (Sigma) coverslips or laminin-coated culture or MEA plates in DMEM:F12 with 2% B27, 1% N2 Supplement, 20 ng/ml brain derived neurotrophic factor (BDNF) for 2–6 weeks. For T3-induced gene expression, cells were deprived of T3 for 48 hours, using B27 without T3. Next, T3 was added to the media as needed at 0.1-100 nM for 24-48 hours. For T3 deprivation differentiation assays, cells were grown with B27 without T3, and then supplemented with 100 nM of T3 as needed.

extract_protocol:
Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit.
The workflow consists of mRNA enrichment, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

value: isogenic induced mutation on a control background

tag: protocol

value: Cultured without T3


title: Neural CS03iCTRmut -T3 biological repeat B


title: Dam_aly_Rep1

description:
Library strategy: DamID-seq
Su(var)3-9 DamID/aly-mut testes control sample
Su(var)3-9_Testes_aly_at_FDR_0.05_probability_track.wig.gz

value: aly-mutant


title: Dam_aly_Rep2


title: pullout_miR-26a_control_replicate_2

tag: cell line


title: Neural CS03iCTRmut -T3 biological repeat A


title: SuVar_Dam_aly_Rep2

description:
Library strategy: DamID-seq
Su(var)3-9-Dam/aly-mutant testes
Su(var)3-9_Testes_aly_at_FDR_0.05_probability_track.wig.gz


title: Neural CS03iCTRmut +100 nM T3 biological repeat C

value: Cultured with T3 100nM


title: Dam_WT_Rep2

description:
Library strategy: DamID-seq
Su(var)3-9 DamID in WT control sample
Su(var)3-9_Testes_WT_at_FDR_0.05_probability_track.wig.gz

value: wild type


title: Neural CS03iCTRmut +100 nM T3 biological repeat B


title: SuVar_Dam_aly_Rep1


title: Neural CS03iCTRmut +100 nM T3 biological repeat A


title: Neural CS01iMCT8cor -T3 biological repeat B

value: isogenic corrected MCT8-deficient


title: Neural CS01iMCT8cor -T3 biological repeat C


title: SuVar_Dam_WT_Rep1

description:
Library strategy: DamID-seq
Su(var)3-9-Dam/WT testes
Su(var)3-9_Testes_WT_at_FDR_0.05_probability_track.wig.gz

value: yw


title: Neural CS01iMCT8cor -T3 biological repeat A


title: SuVar_Dam_WT_Rep2


title: Dam_WT_Rep1


title: MethylCapSeq data HK2

city: Ghent

first: Tim

last: De Meyer

address: Coupure Links 653

department: Dept. of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

description:
Keratinocyte Serum Free Medium (K-SFM, GIBCO) supplemented with bovine pituitary extract (BPE) and human recombinant epidermal growth factor (EGF)
MethylCap (Diagenode)

data_processing:
qseq_6_MID9.bowtie; genome build: NCBI 37.3
Paired-end reads were mapped with BOWTIE, and summarized using the Map of the Human Methylome. Significant methylation was assessed by a Poisson model (alpha = 0.01).

source_name: Immortalized proximal tubule epithelial cell line from normal adult human kidney

extract_protocol: After capturing methylated fragments by the respective MBD-capturing kits (see samples, according to manufacturers' instruction, paired-end protocol), the library preparation was performed with a modified ‘multiplexed paired-end ChIP protocol’ (Illumina, San Diego, California, USA). The NEBNext® DNA Sample Prep Master Mix Set 1 (New England BioLabs (NEB) E6040, Ipswich, Massachusetts, USA) was used in combination with the Multiplexing Sample Preparation Oligo Kit (Illumina PE-400-1001). DNA was subsequently subjected to PCR following the Illumina Library Amplification Index Protocol, and PCR products were purified on Qiaquick PCR Purification columns. After concentration of the samples in a rotary evaporator, samples were pooled and each of these pools was used for NaOH denatruation, after which they were used for sequencing on the Illumina GAIIx, following the following protocol: "performing a multiplexed paired-end run".


title: SuVar_Dam_bam_Rep2


title: MethylCapSeq data SKRC59

description:
RPMI 1640 media (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (FBS)
MethylCollector (Active Motif)

data_processing:
qseq_5_MID8.bowtie; genome build: NCBI 37.3
Paired-end reads were mapped with BOWTIE, and summarized using the Map of the Human Methylome. Significant methylation was assessed by a Poisson model (alpha = 0.01).

source_name: Clear cell renal cancer cell line


title: MethylCapSeq data SKRC52

data_processing:
qseq_3_MID3.bowtie; genome build: NCBI 37.3
Paired-end reads were mapped with BOWTIE, and summarized using the Map of the Human Methylome. Significant methylation was assessed by a Poisson model (alpha = 0.01).


title: MethylCapSeq data SKRC10

data_processing:
qseq_3_MID12.bowtie; genome build: NCBI 37.3
Paired-end reads were mapped with BOWTIE, and summarized using the Map of the Human Methylome. Significant methylation was assessed by a Poisson model (alpha = 0.01).


title: Neural CS01iMCT8cor +100 nM T3 biological repeat A


title: Neural CS01iMCT8cor +100 nM T3 biological repeat C


title: Neural CS01iMCT8cor +100 nM T3 biological repeat B


title: Neural CS03iCTR -T3 biological repeat C

value: healthy control


title: Neural CS03iCTR -T3 biological repeat B


title: Neural CS03iCTR -T3 biological repeat A


title: MethylCapSeq data SKRC1

data_processing:
qseq_2_MID7.bowtie; genome build: NCBI 37.3
Paired-end reads were mapped with BOWTIE, and summarized using the Map of the Human Methylome. Significant methylation was assessed by a Poisson model (alpha = 0.01).


title: Mutated strain 3, t20, replicate 2

city: Barcelona

first: Christina

last: Kiel

address: Dr Aiguader 88

department: Systems Biology

country: Spain

institute: CRG

data_processing:
Merging of fastq files from different runs for a same sample (2 files merged for each sample)
Mapping was performed with tophat2
Differential expression analysis (including FPKM calculation) was done with cuffdiff
Genome_build: sacCer3
Supplementary_files_format_and_content: one processed data file for all samples: FPKM per gene per sample, as calculated by cuffdiff

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: Strains used in this study were created from the parent W303-1a sho1::HIS3 leu2::LEU2-pSTL1-qVenus strain by single step gene replacement with cassettes containing a promoter and ORF flanked with selection marker (5’UTR-TRP1-pYPD1-YPD1-HPH-3’UTR, URA3 and KanMX for SLN1). WT and mutant (Mut 1, Mut 2 and Mut 3) strains were confirmed by sequencing. Cells were grown in synthetic complete media (SC).

extract_protocol:
RNA was isolated using the miRNeasy Mini Kit (Qiagen) following the manufactures protocol including the optional DNase digestion step.
Illumina Truseq Stranded mRNA

treatment_protocol: WT, Mut 1, Mut 2, and Mut 3 strains were grown in synthetic complete media (SC) to mid-log phase, treated with 0.4 M NaCl, and samples were taken after  0, 10 and 20 min stimulation.

tag: stimulation time


title: Neural CS03iCTR +100 nM T3 biological repeat C


title: Mutated strain 2, t20, replicate 1


title: Neural CS03iCTR +100 nM T3 biological repeat B


title: Mutated strain 2, t20, replicate 2


title: Mutated strain 3, t20, replicate 1


title: Mutated strain 1, t20, replicate 1


title: wild type strain, t20, replicate 2

value: WT


title: Neural CS01iMCT8 -T3 biological repeat C


title: Neural CS03iCTR +100 nM T3 biological repeat A


title: Mutated strain 3, t10, replicate 2


title: Neural CS01iMCT8 -T3 biological repeat A


title: Mutated strain 3, t10, replicate 1


title: Neural CS01iMCT8 +100 nM T3 biological repeat B


title: Neural CS01iMCT8 -T3 biological repeat B


title: Neural CS01iMCT8 +100 nM T3 biological repeat C


title: wild type strain, t20, replicate 1


title: Neural CS01iMCT8 +100 nM T3 biological repeat A


title: iBMECs CS03iCTRmut biological repeat B

source_name: iPSC-derived brain microvascular endothelial cells

growth_protocol: Differentiation of iPSCs into iBMECs. iPSCs were maintained between passages 15–40 on Matrigel (BD Biosciences) in mTeSR1 medium (STEMCELL Technologies). For differentiation, cells were passaged onto Matrigel in mTeSR1medium for 2–3 days of expansion until reaching a density of 2-3x105 cells/well and then switched to unconditioned medium (UM) lacking bFGF for 6 days. Human endothelial serum-free medium (hESFM; Life Technologies) supplemented with 20 ng/mL bFGF (Chemicon), 10 µM All-trans RA (Sigma) and 1% platelet-poor plasma derived bovine serum (Biomedical Technologies, Inc.) was then added for 2 days. Cells were then gently dissociated with Accutase (EMD Millipore) for 35 minutes and plated onto 1.12 cm2 Transwell-Clear permeable inserts (0.4 µm pore size) coated with a mixture of collagen IV (400 mg/mL; Sigma) and fibronectin (100 mg/mL; Sigma) in H2O. Resultant, purified human iPSC-derived BMECs were then grown in EC medium for 24 h (without bFGF and Retinoic Acid). At 24 hours, iBMEC-plated Transwell inserts were placed on top of 14-28 days EZ-sphere differentiated neural cultures plated on a 12-well plate.


title: iBMECs CS03iCTRmut biological repeat C


title: Mutated strain 2, t10, replicate 1


title: Mutated strain 1, t10, replicate 2


title: Mutated strain 1, t10, replicate 1


title: iBMECs CS03iCTRmut biological repeat A


title: iBMECs CS58iMCT8 biological repeat C


title: Mutated strain 1, t20, replicate 2


title: wild type strain, t10, replicate 2


title: wild type strain, t10, replicate 1


title: FOXA2H-KO+CCl4-1

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

country: China

institute: Changzheng hospital

data_processing:
Basecalls performed using CASAVA version 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk.
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.1.0.
Gene abundance measurements were generationed and normalized  using HTSeq. The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM).
Differential expression were analysed  using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: primary hepatocytes

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany)
Paired-end libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide.

tag: cell

value: primary hepatocytes

tag: gender

value: male


title: FOXA2H-KO+CCl4-2


title: FOXA2H-KO+CCl4-4


title: iBMECs CS58iMCT8 biological repeat B


title: Mutated strain 3, t0, replicate 2


title: FOXA2f/f+CCl4-4


title: iBMECs CS58iMCT8 biological repeat A


title: Mutated strain 3, t0, replicate 1


title: iBMECs CS01iMCT8cor biological repeat C


title: FOXA2f/f+CCl4-2


title: Mutated strain 2, t10, replicate 2


title: FOXA2f/f+CCl4-1


title: Mutated strain 2, t0, replicate 2


title: iBMECs CS01iMCT8cor biological repeat B


title: iBMECs CS01iMCT8cor biological repeat A


title: Mutated strain 1, t0, replicate 2


title: Mutated strain 2, t0, replicate 1


title: 9b_p7m_YFP_pos

city: Davis

first: Mark

middle: O.

last: Huising

address: One Shields Avenue

department: Neurobiology, Physiology and Behavior

institute: University of California, Davis

description: This sample was previously accessioned in GEO as GSM2133089

data_processing:
reads were mapped to GenCode M8 (GRCm38.p4) using STAR v2.5
FeatureCounts was used to create count tables of the sorted bam files using reads aligning to RefSeq defined exons.
EdgeR v3.14.0 was used for statistical comparison.
Genome_build: GenCode M8 (GRCm38.p4)
Supplementary_files_format_and_content: RPKM Expression values for all replicates generated using Gencode defined exons and EdgeR v3.14.0.

source_name: FACS-purified alpha cells

growth_protocol: Isolated were isolated by collagenase injection through the common bile duct per common protocols. Isolated islets were cultured overnight in RPMI supplemented with 5.5 mM glucose and 10% FBS and pen/strep and dissociated the following morning by trypsin (0.25%) EDTA and gentle titturation for FACS purification.

extract_protocol:
Cells were collected in Trizol post FACS purification and isolated by a chloroform extraction, assisted by phase lock tubes. RNA was precipitated by isopropanol and cleaned up over an RNEasy microcolumn per the Qiagen's taking great care to avoid carry over of ethanol following the column washes. Elution volume was 30 microliter.
Indexed sequencing libraries were constructed using the TruSeq RNA sample prep Kit v2 per Illumina instructions.

value: islets

tag: cell type

value: FACS-purified alpha cells

tag: Stage

value: adult


title: 13b_p7f_YFP_pos

description: This sample was previously accessioned in GEO as GSM2133091

value: female


title: iBMECs CS03iCTR biological repeat C


title: 9_p7m_YFP_pos

description: This sample was previously accessioned in GEO as GSM2133087


title: iBMECs CS03iCTR biological repeat B


title: Mutated strain 1, t0, replicate 1


title: wild type strain, t0, replicate 2


title: iBMECs CS03iCTR biological repeat A


title: 8b_p6m_Chy_pos

description: This sample was previously accessioned in GEO as GSM2133082

source_name: FACS-purified beta cells

value: FACS-purified beta cells


title: wild type strain, t0, replicate 1


title: iBMECs CS02iCTR biological repeat C


title: 12b_p6f_Chy_pos

description: This sample was previously accessioned in GEO as GSM2133086


title: Dam_SG_M_Rep2

description:
Library strategy: DamID-seq
Su(var)3-9 DamID/male larval salivary glands control sample
Su(var)3-9_SG_WT_Males_at_FDR_0.05_probability_track.wig.gz

source_name: larval salivary glands

tag: genotype

value: male third-instar larvae


title: 14_p8f_DP

source_name: FACS-purified alpha transdifferentiated cells


title: 12_p6f_Chy_pos

description: This sample was previously accessioned in GEO as GSM2133084


title: iBMECs CS02iCTR biological repeat B


title: Dam_SG_M_Rep1


title: iBMECs CS02iCTR biological repeat A


title: 10_p8m_DP

value: FACS-purified alpha transdifferentiated cells


title: SuVar_Dam_SG_M_Rep2

description:
Library strategy: DamID-seq
Su(var)3-9-Dam/male larval salivary glands
Su(var)3-9_SG_WT_Males_at_FDR_0.05_probability_track.wig.gz


title: iBMECs CS01iMCT8 biological repeat C


title: iBMECs CS01iMCT8 biological repeat B


title: 56_P21

data_processing:
reads were mapped to GenCode M8 (GRCm38.p4) using STAR v2.5
FeatureCounts was used to create count tables of the sorted bam files using reads aligning to Gencode defined exons.
EdgeR v3.14.0 was used for statistical comparison.
Genome_build: GenCode M8 (GRCm38.p4)
Supplementary_files_format_and_content: RPKM Expression values for all replicates generated using Gencode defined exons and EdgeR v3.14.0.


title: 55_P21


title: 54_P21


title: iBMECs CS01iMCT8 biological repeat A


title: Dam_SG_F_Rep2

description:
Library strategy: DamID-seq
Su(var)3-9 DamID/female larval salivary glands control sample
Su(var)3-9_SG_WT_Females_at_FDR_0.05_probability_track.wig.gz

value: female third-instar larvae


title: Dam_SG_F_Rep1


title: Jagged1+DAPT rep3

city: Pathumwan

first: Thanaphum

last: Osathanon

state: Bangkok

address: 34 Henri-dunant Rd. Wongmai

country: Thailand

institute: Chulalongkorn University

data_processing:
Base calling & Q-scoring  (software RTA2)>File convertion & Demultiplexing (software bcl2fastq)
Read quality was checked, trimmed and filtered by FastQC and FastQ Toolkit.
Read mapping with Homo sapiens UCSC hg38 using TopHat2
FPKM estimation of reference genes and transcript using Cufflink2.
Assembly of novel transcripts with Cufflink2.
Variant calling (SNVs and small indels) with the Isaac Variant caller
Differential expression analysis was performed using Cuffdiff2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count gene coverage

source_name: Human dental pulp cells

extract_protocol:
RNA was harvested from cell culture using RNeasy kit using. Illumina TruSeq RNA Sample Prep Kit  was employed for sequencing library construction from total RNA (1 ug).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Dental pulp

tag: treatment

value: Pretreatment with a gamma secretase inhibitor before exposing to recombinant human Jagged1/Fc immobilization


title: Jagged1+DAPT rep2


title: SuVar_Dam_SG_F_Rep2

description:
Library strategy: DamID-seq
Su(var)3-9-Dam/female larval salivary glands
Su(var)3-9_SG_WT_Females_at_FDR_0.05_probability_track.wig.gz


title: 52_P14


title: SuVar_Dam_SG_F_Rep1


title: Jagged1+DAPT rep1


title: Dam_BR_M_Rep2

description:
Library strategy: DamID-seq
Su(var)3-9 DamID/male larval brains control sample
Su(var)3-9_Brain_WT_Males_at_FDR_0.05_probability_track.wig.gz

source_name: larval brains


title: Jagged1 rep3

value: recombinant human Jagged1/Fc immobilization


title: Dam_BR_M_Rep1


title: Jagged1 rep2


title: 50_P14


title: SuVar_Dam_BR_M_Rep2

description:
Library strategy: DamID-seq
Su(var)3-9-Dam/male larval brains
Su(var)3-9_Brain_WT_Males_at_FDR_0.05_probability_track.wig.gz


title: 49_P7


title: Jagged1 rep1


title: 48_P7


title: SuVar_Dam_SG_M_Rep1


title: SuVar_Dam_BR_M_Rep1


title: hFc control rep2

value: human Fc immobilization


title: hFc control rep3


title: 46_P1


title: 47_P7


title: Dam_BR_F_Rep2

description:
Library strategy: DamID-seq
Su(var)3-9 DamID/female larval brains control sample
Su(var)3-9_Brain_WT_Females_at_FDR_0.05_probability_track.wig.gz

value: yw


title: Dam_BR_F_Rep1


title: hFc control rep1


title: 45_P1


title: 44_P1


title: 53_P14


title: SuVar_Dam_BR_F_Rep1

description:
Library strategy: DamID-seq
Su(var)3-9-Dam/female larval brains
Su(var)3-9_Brain_WT_Females_at_FDR_0.05_probability_track.wig.gz


title: SuVar_Dam_BR_F_Rep2


title: 51_P14


title: Male_Spleen

city: Dunedin

last: Hore

address: 270 Great King Street

department: Department of Anatomy

country: New Zealand

institute: University of Otago

data_processing:
Trimming was performed to remove poor-quality calls, adapter sequences and 10bp from the 5' end of reads using TrimGalore v0.4.0  (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with default parameters.
Trimmed reads were aligned using Bismark v0.14.3 (Krueger and Andrews, 2011) with the --pbat option specified. Only genome scaffolds of at least 277kb were used for alignment. Bismark mapping reports were used to determine global methylation levels for low coverage elephant shark data.
Genome_build: Callorhinchus milii 6.1.3
Supplementary_files_format_and_content: Bismark mapping report showing mapped calls, with the respective numbers of methylated and unmethylated calls.

organism: Callorhinchus milii

extract_protocol:
Elephant shark tissue samples were provided by commercial fishermen from recently deceased animals. DNA was purified using a modified magnetic bead approach (Deangelis et al., 1995). Briefly, cells were first homogenised in “GITC” lysis buffer (4 M Guanidine thiocyanate, Sigma G6639; 50 mM Tris, Thermo 15568-025; 20 mM EDTA; Thermo 15575-020; 2% Sarkosyl, Sigma L9150-50G; 0.1% Antifoam, Sigma A8311-50ML) and this lysate mixture was then combined with TE-diluted Sera-Mag Magnetic SpeedBeads (GE Healthcare, GEHE45152105050250) and isopropanol in a volumetric ratio of 2:3:4 respectively. Following capture with a neodymium magnet, beads were washed once with isopropanol, twice with 70% ethanol and resuspended in filter-sterile milliQ H2O.
WGBS-seq was undertaken using a post-bisulfite adapter tagging (PBAT) method adapted from Peat et al., 2014. Briefly, 50-100 ng of purified DNA was subjected to bisulfite conversion using the Imprint DNA modification kit (Sigma, MOD50).  Converted DNA underwent first strand synthesis with a biotin labelled adapter sequence possessing seven random nucleotides at its 3’ end (BioP5N7, biotin- ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNN). The product of first strand synthesis was captured using streptavidin-coated Dynabeads (Thermo, 11205D) and magnetic immobilisation. Double stranded DNA was created using the immobilized first-strand as a template and an additional adapter also possessing seven random nucleotides at its 3’ end (P7N7, GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNN). Unique molecular barcodes and sequences necessary for binding to Illumina flow-cells were added to libraries by PCR using 1X HiFi HotStart Uracil+ Mix (KAPA, KK2801 and 10 μM indexed Truseq-type oligos, with thermal cycling as follows: 12*(94°C, 80 sec; 65°C, 30 sec; 72°C, 30 sec).

value: Adult

value: spleen


title: Female_Spleen


title: 42_E18


title: Female_Pancreas

value: pancreas


title: 43_E18


title: 27_p5f2_DN

source_name: FACS-purified double negative non-beta cells

value: FACS-purified double negative cells

tag: Sex


title: Male4_Liver

value: male

value: liver


title: Male3_Liver


title: 23_p5f1_DN

value: islets

value: adult


title: 25_p7f1_DP

source_name: FACS-purified mature beta cells

value: FACS-purified mature beta cells


title: 29_p7f2_DP

value: female


title: 28_p6f2_Chy_pos

source_name: FACS-purified immature beta cells

value: FACS-purified immature beta cells


title: Mature pellicle

city: Guangzhou

first: Pengxia

last: Wang

state: Guangdong

address: 164 Xingang West Rd

department: South China Sea Institute of Oceanology

institute: Chinese Academy of Sciences

description:
processed data file:
11900_Mature_pellicle_vs_planktonic.txt
11900_raw_counts.xls

data_processing:
Sequencing was performed on Illumina HiSeq2000 platform
Dirty raw reads were filtered. Clean reads were mapped to reference genome and genes sequences respectively using SOAP2 (Li, 2009).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated as mentioned (Mortazavi, Williams et al. 2008).
Then, the calculated gene expression can be directly used for comparing the difference of gene expression among samples.
Genome_build: genome sequence of Pseudoalteromonas sp. SCSIO 11900: https://www.ncbi.nlm.nih.gov/nuccore/JEMJ00000000
Supplementary_files_format_and_content: xls files including RPKM values for each sample, and difference of gene expression between initial pellicle and planktonic, and between mature pellicle and planktonic.

organism: Pseudoalteromonas sp. SCSIO_11900

source_name: Mature pellicle Pseudoalteromonas sp. SCSIO 11900

extract_protocol:
Total RNA was isolated using Tiangen RNAprep Pure Cell (Tiangen Biotech, China) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina Hiseq 2000 protocols

value: wild type strain

value: Mature pellicle


title: Initial pellicle

description:
processed data file:
11900_Initial_pellicle_vs_planktonic.txt
11900_raw_counts.xls

source_name: Initial pellicle Pseudoalteromonas sp. SCSIO 11900

value: Initial pellicle


title: 24_p6f1_Chy_pos


title: Planktonic cells

description:
processed data file:
11900_Initial_pellicle_vs_planktonic.txt
11900_Mature_pellicle_vs_planktonic.txt
11900_raw_counts.xls

source_name: Planktonic cells of Pseudoalteromonas sp. SCSIO 11900

value: Planktonic cells


title: Female3_Liver


title: ChIP-Seq_STAT5_input

status: Public on Apr 03 2017

city: Minneapolis

first: Rendong

last: Yang

state: MN

address: 117 Pleasant St. SE

institute: University of Minnesota

data_processing:
ChIP-seq reads  were trimmed for adaptor sequence,aligned to the mm10 genome assembly using BWA 0.7.4
PCR duplicate reads were removed using Picard MarkDuplicate v1.68. Reads with mapping quality less than 1 were discarded.
peaks were called using MACS v2 with pair end mode
Genome_build: mm10
Supplementary_files_format_and_content: BED format, detected peaks by MACS2

extract_protocol:
Lymph nodes from Stat5b-CAxBlnk+/- leukemic mouse were made into single cell suspensions, stimulated with 10 ng/mL murine IL7 for 30 minutes at 37°C, and fixed with 1% formaldyde at room temperature for 10 minutes. Whole cell extracts were sonicated with Diagenode Bioruptor to solubilize and fragment the chromatin to an average size of 200 bp.  The chromatin was then immunoprecipitated with the Santa Cruz sc-835 (C-17)x anti-STAT5 antibody.
Followed the Illumina TruSeq ChIP sample kit

tag: strain background

value: Stat5b-CAxBlnk+/- leukemic mouse

value: Lymph nodes

value: B cell progenitor leukemia

tag: chip antibody

value: none (input)


title: ChIP-Seq_STAT5

value: anti-STAT5 antibody (Santa Cruz, sc-835 (C-17))


title: Male_Pancreas

tag: developmental stage

value: Adult

value: pancreas


title: granulosa cells sample 24

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

institute: Technical University of Denmark

data_processing:
Sequenced reads were trimmed for adaptor sequence, minimum quality threshold of 20. Reads were filtered for average quality lower than 20 and for minimum read length (25 bp).
Pre-processed reads were mapped to Bos taurus (UMD3.1) with STAR 2-pass (setting default parameters and allowing for maximum 5 mismatches).
Reads mapped to each gene (Ensembl Bos taurus 10.2.83) were counted with HTSeq-count
Genome_build: Bos taurus (UMD3.1)
Supplementary_files_format_and_content: Text files (.txt) containing the Ensembl gene IDs and raw counts . One file for each sample (24 samples)

organism: Bos taurus

source_name: granulosa cells

extract_protocol:
RNA was isolated with RNeasy Plus Micro Kit (Qiagen)
Illumina TruSeq-stranded totalRNA RiboZero Gold Prep Kit

treatment_protocol: Granulosa cells were aspirated from all antral follicles of both ovaries in Wash media. Granulosa cells were purified from blood contamination in two steps: i) leukocyte removal by beads covered by antibodies anti-bovine CD45  (pluriSelect S-pluriBead®) and ii) treatment with erythrocytes lysis buffer (Qiagen). Granulosa cells were finally stored at -80 °C.

value: granulosa cells

tag: bull ntm

value: Low

tag: blastocyst rate

tag: morphology

tag: kinetics


title: granulosa cells sample 23

tag: tissue

value: High


title: 1567_Immature IL-10-APCs

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: Sample name: 1567

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using HISAT version 0.1.7-beta  with default parameters.
mRNA quantification according to hg19-RefSeq_Transcripts-2015-11-03.
raw read counts were normalized by DE-Seq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include DE-Seq normailzed expression values for each Sample.

source_name: Human monocyte isolation from buffy coats

growth_protocol: Cells were isolated from peripheral blood by plastic adherence. Adherent monocytes were cultured in RP10 medium supplemented with GM-CSF (100 ng/mL; Leukine, Liquid Sargramostim) and IL-4 (20 ng/ml; R&D Systems) for 7 days. To generate IL-10-APC, IL-10 (10ng/ml; R&D Systems) was added every other day.

extract_protocol:
Cells were lyzed in TRIzol and RNA was extracted with the miRNeasy kit (Qiagen) according to the manufactures’ protocol. mRNA was purified from 100 ng of total RNA using poly-T oligo-attached magnetic beads and the library construction was performed using the Illumina TruSeq RNA Sample Preparation Kit v2.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Maturation was reached after adding LPS (100ng/ml; Sigma) once on day 6 of in vitro differentiation.

value: peripheral blood

tag: donor


title: 1566_LPS-treated moDCs

description: Sample name: 1566

value: moDC

value: LPS


title: granulosa cells sample 22


title: 1565_Immature moDCs

description: Sample name: 1565

value: undiff


title: granulosa cells sample 21


title: sRNA of GC-1spg

city: Beijing

first: lili

last: hao

address: Beichen west road

institute: BIG

description: This line shows characteristics of a stage between type B spermatogonia and primary spermatocytes

data_processing:
eliminating low-quality reads
accurately clipping the adaptor sequences
removing reads whose lengths were smaller than 18 nt
clean reads were mapped to mouse genome mm9
Reads were then screened against the Rfam and NCBI GenBank databases and classified into different types such as small RNAs
Known miRNAs such as small RNAs that perfectly matched the miRBase (version 18.0) mouse miRNA precursor sequences and those identified as known miRNA editing polymorphisms were annotated and calculated to only one category according to priority
Genome_build: mm9, miRBase (version 18.0)
Supplementary_files_format_and_content: expression data matrix: contain miRNA raw and normalized abundance measurements value

source_name: male germ cells

growth_protocol: GC-1spg is a 10 days’ mouse’s type B spermatogonia transformed with pSV3-neo. GC-2spd(ts) is a spermatocyte cell line obtained from 6 weeks’ mouse and then transformed with SV40 large T antigen.

extract_protocol: Total RNA was extracted from GC-1spg and GC-2spd (ts) cell lines by Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. The RNA samples were incubated with 10 U DNaseI (Takara, Dalian, China) for 30 min at 37°C to remove residual genomic DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260/280 nm (A260/A280) using a Nanodrop®ND-1000 spectrophotometer (LabTech, Holliston, MA, USA). The samples had an average RNA integrity number (RIN) value of 8.9, as determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Small RNAs (18–30 nt) were gel-purified from 10 µg total RNA. Adaptors were ligated to eluted RNAs successively with RNA ligase. Libraries were gel-purified after each ligation step. Small RNAs ligated with adaptors were subjected to RT-PCR (15 cycles of amplification) to produce sequencing libraries. PCR products were purified on a non-denaturing acrylamide gel and sequenced for 50 cycles on Illumina HiSeq 2000 Sequencer (BGI, Shenzhen, China).

treatment_protocol: GC-1spg and GC-2spd(ts) were maintained in DMEM medium containing 10% FBS and 1.5 g/L sodium bicarbonate.


title: sRNA of GC-2spd (ts)

description: The cells have lost their differentiation potential, and are currently arrested at a premeiotic stage

value: GC-2spd (ts)

value: premeiotic stage


title: 1560_LPS-treated IL-10-APCs

description: Sample name: 1560


title: Female4_Liver

value: female

value: liver


title: granulosa cells sample 20


title: granulosa cells sample 17


title: Male2_Liver

value: male


title: 1559_Immature IL-10-APCs

description: Sample name: 1559


title: granulosa cells sample 18


title: granulosa cells sample 16


title: granulosa cells sample 15


title: granulosa cells sample 14


title: granulosa cells sample 13


title: 1558_LPS-treated moDCs

description: Sample name: 1558


title: Female2_Liver


title: granulosa cells sample 12


title: 1557_Immature moDCs

description: Sample name: 1557


title: granulosa cells sample 11


title: 1556_LPS-treated IL-10-APCs

description: Sample name: 1556


title: 1568_LPS-treated IL-10-APCs

description: Sample name: 1568


title: granulosa cells sample 10


title: 1555_Immature IL-10-APCs

description: Sample name: 1555


title: granulosa cells sample 9


title: granulosa cells sample 8


title: granulosa cells sample 7


title: granulosa cells sample 19


title: 1554_LPS-treated moDCs

description: Sample name: 1554


title: granulosa cells sample 6


title: 1553_Immature moDCs

description: Sample name: 1553


title: granulosa cells sample 4


title: granulosa cells sample 2


title: granulosa cells sample 1


title: RD42-NI

city: Saint Paul lez Durance

first: Arjan

last: de Groot

address: CEA Cadarache

department: BIAM-SBVME

country: France

institute: CEA

description:
processed data file:
differentialExpression_RD42.txt

data_processing:
In a first step, the RNA-Seq data quality was assessed by including option like reads trimming or merging/split paired-end reads.
In a second step, reads were mapped onto the D. deserti VCD115 genome sequence (GenBank accession numbers CP001114, CP001115, CP001116 and CP001117 for the chromosome and plasmids P1, P2 and P3, respectively) using the SSAHA2 package (Ning et al, 2001) that combines the SSAHA searching algorithm (sequence information is encoded in a perfect hash function) aiming at identifying regions of high similarity, and the cross-match sequence alignment program (Ewing et al, 1998), which aligns these regions using a banded Smith-Waterman-Gotoh algorithm. An alignment score equal to at least half of the read is required for a hit to be retained.
To lower false positives discovery rate, the SAMtools (v.0.1.8) were then used to extract reliable alignments from SAM formatted files.
The number of reads matching each genomic object harbored by the reference genome was subsequently computed with the Bioconductor-GenomicFeatures package.
The Bioconductor-DESeq package with default parameters was used to analyze raw counts data and test for differential expression between conditions.
Genome_build: Deinococcus deserti VCD115
Supplementary_files_format_and_content:
readCountGenes_RD42_RD62.txt: raw number of reads mapped to individual genes for RD42-NI, RD42-IR, RD62-NI and RD62-IR experiments.
differentialExpression_RD42.txt: differential expression analysis from RD42-IR compared to RD42-NI
differentialExpression_RD62.txt: differential expression analysis from RD62-IR compared to RD62-NI

organism: Deinococcus deserti

source_name: upper sand layers of the Sahara

growth_protocol: D. deserti strains are routinely grown at 30°C with aeration in tenfold diluted tryptic soy broth supplemented with trace elements

extract_protocol:
RNAprotect-treated cells were centrifuged and cell pellets stored at -80°C. Cell pellets were pretreated with lysozyme and proteinase K. Total RNAs were isolated using the mirVana RNA isolation kit (Ambion) including DNase treatment.
From each RNA preparation (i.e. non-irradiated and irradiated cells), one cDNA synthesis was carried out. RNA was directly poly(A)-tailed using poly(A) polymerase, followed by TAP treatment. An RNA adapter was then ligated to the 5'P of the total RNA samples. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and M-MLV H- reverse transcriptase. The resulting cDNAs were PCR-amplified to about 60-90 ng/μl using a high fidelity DNA polymerase. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina, with the 3’-sequencing adapter containing a barcode specific for each library. For Illumina sequencing, the samples were pooled at approximately equimolar amounts and size fractionated in the range between 250 – 500 bp on Agarose Gel. The pools were sequenced on a Illumina HiSeq 2000 machine (read length: 100 bp).

treatment_protocol: For RNAseq, a 100 ml culture of RD42 or RD62 was grown to exponential phase (OD600 0.5), and then divided in two. One part (45 ml) was exposed to 1 kGy gamma irradiation at room temperature (23 Gy/min, 60Co source; CEA/Cadarache, France), and then recovered for 30 min. The other part (45 ml) was not irradiated but otherwise treated in the same manner. After recovery, 15 ml of each culture was added to RNAprotect Bacteria Reagent (Qiagen) to stabilize RNA, following the instructions of the manufacturer.

tag: strain

tag: genotype/variation

value: irrE mutant

tag: exposed to

value: none (non-irradiated)


title: RD62-NI

description:
processed data file:
differentialExpression_RD62.txt

data_processing:
In a first step, the RNA-Seq data quality was assessed by including option like reads trimming or merging/split paired-end reads.
In a second step, reads were mapped onto the D. deserti VCD115 genome sequence (GenBank accession numbers CP001114, CP001115, CP001116 and CP001117 for the chromosome and plasmids P1, P2 and P3, respectively) using the SSAHA2 package (Ning et al, 2001) that combines the SSAHA searching algorithm (sequence information is encoded in a perfect hash function) aiming at identifying regions of high similarity, and the cross-match sequence alignment program (Ewing et al, 1998), which aligns these regions using a banded Smith-Waterman-Gotoh algorithm. An alignment score equal to at least half of the read is required for a hit to be retained.
To lower false positives discovery rate, the SAMtools (v.0.1.8) were then used to extract reliable alignments from SAM formatted files.
The number of reads matching each genomic object harbored by the reference genome was subsequently computed with the Bioconductor-GenomicFeatures package.
The Bioconductor-DESeq package with default parameters was used to analyze raw counts data and test for differential expression between conditions.
Genome_build: Deinococcus deserti VCD115
Supplementary_files_format_and_content:
readCountGenes_RD42_RD62.txt:  raw number of reads mapped to individual genes for RD42-NI, RD42-IR, RD62-NI and RD62-IR experiments.
differentialExpression_RD42.txt: differential expression analysis from RD42-IR compared to RD42-NI
differentialExpression_RD62.txt: differential expression analysis from RD62-IR compared to RD62-NI

value: ddrOc mutant


title: RD62-IR

value: 1 kGy gamma irradiation (23 Gy/min)


title: N_CP_sc11

city: Shenyang

first: Wensu

last: Liu

state: Liaoning

address: 77 Puhe Road, Shenyang North New Area

institute: China Medical University

description: single cell sequencing

data_processing:
Adaptor contamination and low-quality reads were removed from the raw data
TopHat (version 2.0.10) was used for sequence alignment, and FPKM values were generated by Cufflinks (version 2.1.1)
Remove genes with average FPKM<1

source_name: human embroynic neuron cells (N)

extract_protocol:
The single cells were lysed. The released mRNAs were reverse translated into cDNAs and were amplified. The amplified cDNAs were fragmented to about 200bp, and were constructed into the cDNA library.
manual of NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, E7370L)
cDNA libraries were sequenced on Illumina HiSeq 2500 instruments

value: embryo

value: prenatal human brain

tag: cell subtype

value: human embroynic neuron cells (N)

tag: sequence type

value: single cell sequencing


title: N_CP_sc12

description: single cell sequencing

tag: Stage


title: p53NULL_shPFKFB4_rep3

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
Fastq files were generated using Illumina's CASAVA software.
Fastq files were mapped to the human genome assembly hg19 using TopHat v2.0.7 with default parameters and subsequently normalized to the number of mapped reads in the smallest sample.
Reads per gene were counted using the countOverlaps function from the R package (Genomic Ranges).
Weakly expressed genes were removed (threshold: mean read count over all samples <1) and differentially expressed genes were called using EdgeR.
Genome_build: hg19
Supplementary_files_format_and_content: txt files containing Ensembl gene ID, gene symbol, gene description, log2FC, p-value and q-value for each comparison described in RNAseq_README.txt

source_name: HCT116 p53-/- cells

growth_protocol: Cells were infected with pBabe-Luciferase retroviral vector. After selection, cells were transduced with lentiviral vectors expressing (pLKO-TETON) containing shRNA sequnces targeting PFKFB4 (Ros et al. Cancer Discovery 2013). 1x10e6 cells were subcutaneously injected into the dorsal flank of male nude mice (ICRF nude). Animals were randomly assigned to two cohorts. Mice were sacrificed and tumours were excised at day 21 post injection. All animal experiments were performed according to UK Home Office guidelines.

extract_protocol:
Total RNA from 3 tumours in each treatment group was extracted using RNeasy mini columns (Qiagen) with on column DNase I digestion.
PolyA+ RNA was extracted using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, Ipswich, MA, USA). For library preparation, the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) was used. Quantification and quality control was performed using the Experion Automated Electrophoresis System (BioRad, Hercules, CA, USA). Sequencing was performed using an Illumina NextSeq500 System (Illumina, San Diego, CA, USA).

treatment_protocol: For induction of shRNA expression, animals  received doxycycline (Doxycycline diet, 0.2 g/kg food pellet, Harlan D.98186) starting 1 day after implantation.

tag: cell line

tag: p53 genotype

value: xenograft tumor

tag: host mouse genotype

value: nude mice (ICRF nude)

tag: treatment 1 (luciferase)

value: constitutive expression of luciferase

tag: treatment 2 (shrna)

value: shPFKFB4 seq#70

tag: treatment 3 (doxycycline)

value: Doxycycline in mouse food to induce shRNA expression


title: N_CP_sc22

description: single cell sequencing

tag: developmental stage


title: p53NULL_shPFKFB4_rep2

value: shPFKFB4 seq#69


title: granulosa cells sample 5

value: granulosa cells

tag: bull ntm

value: Low

tag: blastocyst rate

tag: morphology


title: IPC_OSVZ_sc5

description: single cell sequencing

source_name: human embroynic intermediate progenitor cell (IPC)

tag: tissue


title: p53NULL_shPFKFB4_rep1

value: shPFKFB4 seq#68


title: spt6-1004_rRNA-depl_exp2_rep1

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description:
RNA strand specific, rRNA-depleted
Biological replicate 1 of 2. RNA profiling in spt6-1004 cells treated 80 minutes at 37°C.

data_processing:
Reads were mapped to the sacCer3 assembly of the S. cerevisiae genome using Tophat2 (Kim et al., 2013). Intron length range was set at 50 to 1000 bp and a reference annotation file was provided to guide the assembly.
The reads in the BAM files were separated into two files corresponding to the reads on the plus and minus strands. This was done using samtools with the options -f 99 and -f 147 for the minus strand and -f 83 and -f 163 for the plus strands.
For each strand, BAM files were converted into BEDPE records using bamtobed sub-command of the BEDTools suite. BEDPE records were use to create fragments by merging paired-end reads.
Fragments were then used to calculate the coverage using the genomecov sub-command of the BEDTools suite. A scaling factors was provided in order to normalize reads per million of mapped fragments
the resulting bedgraph files were converted to bigwig files using the bedGraphToBigWig program from the UCSC binary utilities
Genome_build: SacCer3

source_name: Frozen yeast cells

growth_protocol: Cells from spt16-1004 and its respective WT strain were grown to an OD600 of 0.5 at 30°C and shifted to 37°C for 80 min before RNA extraction.

extract_protocol:
Total RNA was extracted using the hot phenol method. Prior to library preparation, total RNA was either depleted for ribosomal RNA using the Ribo-zero Gold yeast kit (Epicentre-Illumina) or enriched for polyadenylated RNA using  the NEBnext Poly(A) kit (New England Biolabs).
Strand specific RNA-seq libraries were prepared using the KAPA stranded RNA-Seq library preparation kit prior to paired-end sequencing on an Illumina Hi-Seq2000.

treatment_protocol: 80 min at 37°C

tag: strain

tag: genotype

value: MATalpha his3delta200 leu2delta1 lys2-128d  ura3-52 spt6-1004-FLAG


title: SPT6 WT_rRNA-depl_exp2_rep2

description:
RNA strand specific, rRNA-depleted
Biological replicate 2 of 2. RNA profiling in SPT6 cells treated 80 minutes at 37°C.

value: MATa leu2delta1 lys2-128d  trp1delta63 ura3-52


title: spt6-1004_polyA_exp2_rep2

description:
RNA strand specific, polyA-enriched
Biological replicate 2 of 2. RNA profiling in spt6-1004 cells treated 80 minutes at 37°C.


title: IPC_OSVZ_sc8

description: single cell sequencing

value: human embroynic intermediate progenitor cell (IPC)


title: granulosa cells sample 3

value: High

tag: kinetics


title: RG_VZ_sc108

description: single cell sequencing

source_name: human embroynic radial glial cell (RG)

value: embryo

tag: cell subtype

value: human embroynic radial glial cell (RG)


title: 07_R103_DRG

city: Glostrup

first: Lisette

last: Kogelman

address: Nordre Ringvej 67

department: Danish Headache Centre

institute: Rigshospital Glostrup

description: PolyA RNA

data_processing:
Filtering using NGSQC toolkit, default settings.
Alignment using STAR.
Quantification of reads using HTSeq.
Genome_build: Rattus norvegicus 6.0.83 (Rnor_6.0)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include raw count data (output from HTSeq).

source_name: Dorsal root ganglia

growth_protocol: Reversed night/day conditions, food and water ad lib.

extract_protocol:
TG and DRG were dissected and frozen in isopentane on dry ice.
RNA extracted using NucleoSpin RNA kit in combination with QIAzol. mRNA isolated using poly(A) selection.
Sequencing on Illumina HiSeq 2500 platform.

treatment_protocol: Anaesthetized with intraperitoneal injection of pentobarbital with lidocaine, perfused with cold saline to remove blood from tissue.

tag: strain/background

value: Wistar Han

value: Dorsal root ganglia

tag: age

value: 10 weeks

tag: Sex

value: male

tag: rat identifier


title: spt6-1004_polyA_exp2_rep1

description:
RNA strand specific, polyA-enriched
Biological replicate 1 of 2. RNA profiling in spt6-1004 cells treated 80 minutes at 37°C.


title: p53NULL_shCtrl_rep2

tag: cell line

tag: p53 genotype

value: xenograft tumor

tag: host mouse genotype

value: nude mice (ICRF nude)

value: constitutive expression of luciferase

value: shControl


title: spt6-1004_rRNA-depl_exp2_rep2

description:
RNA strand specific, rRNA-depleted
Biological replicate 2 of 2. RNA profiling in spt6-1004 cells treated 80 minutes at 37°C.


title: 07_R103_TG

description: PolyA RNA

source_name: Trigeminal ganglia

value: Trigeminal ganglia


title: p53WT_shPFKFB4_rep3

source_name: HCT116 p53+/+ cells

tag: treatment 1 (luciferase)

tag: treatment 2 (shrna)

value: shPFKFB4 seq#70

tag: treatment 3 (doxycycline)

value: Doxycycline in mouse food to induce shRNA expression


title: RG_VZ_sc55

description: single cell sequencing

tag: developmental stage

tag: Stage

value: prenatal human brain

tag: sequence type

value: single cell sequencing


title: SPT6 WT_polyA_exp2_rep2

description:
RNA strand specific, polyA-enriched
Biological replicate 2 of 2. RNA profiling in SPT6 cells treated 80 minutes at 37°C.

tag: strain

value: MATa leu2delta1 lys2-128d  trp1delta63 ura3-52


title: SPT6 WT_polyA_exp2_rep1

description:
RNA strand specific, polyA-enriched
Biological replicate 1 of 2. RNA profiling in SPT6 cells treated 80 minutes at 37°C.

tag: genotype


title: RG_VZ_sc57

description: single cell sequencing

tag: tissue


title: p53WT_shPFKFB4_rep2

value: shPFKFB4 seq#69


title: spt6-1004_polyA_exp1_rep2

value: MATalpha his3delta200 leu2delta1 lys2-128d  ura3-52 spt6-1004-FLAG


title: N_CP_sc48

description: single cell sequencing

value: embryo

tag: cell subtype

value: human embroynic neuron cells (N)


title: RG_VZ_sc58

description: single cell sequencing

value: human embroynic radial glial cell (RG)


title: SPT6 WT_rRNA-depl_exp2_rep1

description:
RNA strand specific, rRNA-depleted
Biological replicate 1 of 2. RNA profiling in SPT6 cells treated 80 minutes at 37°C.


title: 07_R104_TG

description: PolyA RNA

tag: strain/background

value: Wistar Han

value: 10 weeks


title: p53WT_shPFKFB4_rep1

value: xenograft tumor

value: shPFKFB4 seq#68


title: RD42-IR

tag: genotype/variation

value: irrE mutant

tag: exposed to

value: 1 kGy gamma irradiation (23 Gy/min)


title: spt6-1004_polyA_exp1_rep1


title: oRG_OSVZ_sc155

description: single cell sequencing

source_name: human embroynic outer radial glial cell (oRG)


title: p53NULL_shCtrl_rep3

value: nude mice (ICRF nude)

value: constitutive expression of luciferase

value: shControl


title: SPT6 WT_polyA_exp1_rep2


title: p53WT_shCtrl_rep3

value: Doxycycline in mouse food to induce shRNA expression


title: 07_R105_TG

description: PolyA RNA

value: Trigeminal ganglia

tag: age

tag: Sex

value: male

tag: rat identifier


title: p53NULL_shCtrl_rep1

tag: cell line

tag: p53 genotype

tag: host mouse genotype


title: RG_VZ_sc60

description: single cell sequencing

value: prenatal human brain

value: single cell sequencing


title: RG_VZ_sc85

description: single cell sequencing

value: embryo


title: p53WT_shCtrl_rep2

tag: treatment 1 (luciferase)

tag: treatment 2 (shrna)

tag: treatment 3 (doxycycline)


title: SPT6 WT_polyA_exp1_rep1

value: MATa leu2delta1 lys2-128d  trp1delta63 ura3-52


title: p53WT_shCtrl_rep1


title: 07_R104_DRG

description: PolyA RNA

value: Dorsal root ganglia


title: oRG_OSVZ_sc188

description: single cell sequencing

tag: developmental stage

tag: Stage

value: human embroynic outer radial glial cell (oRG)

tag: sequence type


title: RG_VZ_sc194

description: single cell sequencing

tag: tissue

value: human embroynic radial glial cell (RG)


title: 07_R101_DRG

description: PolyA RNA

value: Wistar Han

value: 10 weeks


title: 07_R106_TG

description: PolyA RNA


title: RG_VZ_sc198

description: single cell sequencing

tag: cell subtype


title: 07_R106_DRG

description: PolyA RNA

tag: strain/background


title: RG_VZ_sc84

description: single cell sequencing


title: IPC_VZ_sc57

description: single cell sequencing

value: human embroynic intermediate progenitor cell (IPC)


title: 07_R105_DRG

description: PolyA RNA


title: RG_VZ_sc98

description: single cell sequencing


title: IPC_VZ_sc85

description: single cell sequencing


title: 07_R102_TG

description: PolyA RNA


title: oRG_OSVZ_sc76

description: single cell sequencing


title: oRG_OSVZ_sc130

description: single cell sequencing


title: oRG_OSVZ_sc131

description: single cell sequencing


title: oRG_OSVZ_sc187

description: single cell sequencing


title: oRG_OSVZ_sc95

description: single cell sequencing


title: IM_D14_Rep2

city: denver

first: steve

middle: C

last: pugliese

state: CO

address: 12700 East 19th Avenue

department: Medicine

institute: University of Colorado

data_processing:
Derived sequences were analyzed by applying a custom computational pipeline consisting of the open-source gSNAP, Cufflinks, and R for sequence alignment and ascertainment of differential gene expression (CITES). In short, reads generated were mapped to the mouse genome (mm10) by gSNAP, expression (FPKM) derived by Cufflinks, and differential expression analyzed with ANOVA in R.
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing average FKPM data (3 samples) for control sea level macrophage and hypoxic macrophage counterpart (IM D4 or D14, AM D4 or D14).  Fold change, P value, q value and individual FKPM values for each sample also listed

source_name: interstitial macrophage hypoxia day 14

extract_protocol:
Mice lung was digested, macrophages were facs sorted and RNA was isolated using trizol extraction and qiagen Rneasy MinElute kit
RNA libraries were prepared for sequencing using standard Illumina protocols with Nugen ovation amplication kit

treatment_protocol: mice remained at sea level or were exposed to simulated altitude of 18,000 feet

tag: strain

value: lung

tag: tissue compartment

value: interstitial

tag: cell type

value: macrophage


title: IM_D14_Rep3


title: IM_D14_Rep1


title: N_CP_sc97

description: single cell sequencing

value: human embroynic neuron cells (N)


title: IM_D4_Rep3

source_name: interstitial macrophage hypoxia day 4


title: 07_R101_TG

description: PolyA RNA

tag: age

tag: Sex


title: vir-1_1

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

institute: University of Nottingham

description:
RNA later treated
E1

data_processing:
Each transcriptome was loaded to occupy 1/4 of the lane capacity in a flow cell. C-Bot (TruSeq PE Cluster Kit v3, Illumina) was used for cluster generation and Illumina HiSeq2000 platform (TruSeq SBS Kit v3 reagent kit) for paired end sequencing
100M reads obtained for wild type and control respectively
100bp paired-end reads were then quality trimmed to a length of 93bp
For differential gene expression, sequences were aligned against the TAIR10 genome using TopHat (v2.0.8b) with the options --bowtie1 and --no-discordant in two runs and a mean inner distance between mate pairs of 112 to 133 (std dev 50). Transcript counts werecalculated with HTSeq with features marked in the Ensembl v72 TAIR10 Gene Transfer Format annotation. Differential gene expression was assessed with the DEseq package.
For splicing analysis, quality filtered reads in FASTQ format were trimmed to 80 nucleotide using the rMATS trimFastq python script. The trimmed reads were then aligned to the TAIR10 genome build using STAR.
Supplementary_files_format_and_content: DEseq_DifferentialGeneExpression.txt: differential gene expression in tab delimited text file
Supplementary_files_format_and_content: rMATs_A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt: Alternative 5' splicing in tab delimited text format
Supplementary_files_format_and_content: rMATs_MXE.MATS.ReadsOnTargetAndJunctionCounts.txt: Alternative splicing, mutually exclusive exons in tab delimited text format
Supplementary_files_format_and_content: rMATs_RI.MATS.ReadsOnTargetAndJunctionCounts.txt: Alternative splicing, retained introns in tab delimited text format
Supplementary_files_format_and_content: rMATs_SE.MATS.ReadsOnTargetAndJunctionCounts.txt: Alternative splicing, skipped exons in tab delimited text format
Supplementary_files_format_and_content: rMATs_A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt: Alternative 3' splicing in tab delimited text format

organism: Arabidopsis thaliana

source_name: root tips

growth_protocol: 5-days old seedlings

extract_protocol:
seedlings treated with RNA later, RNA extracted with Ambion RNA kit (AM1919)
The poly(A)+ RNA was reverse transcribed to cDNA (SuperScript Double-Stranded cDNA Synthesis Kit, Life Technologies). Random hexamers (New England BioLabs) were used for priming the first strand synthesis reaction and SPRI beads (Agencourt AMPure XP, Beckman Coulter) for purification of cDNA. Illumina compatible Nextera Technology (Illumina) was used for preparation of RNA-seq libraries, employing DNA fragmentation and tagging by in vitro cut-and-paste transposition. 60 ng of cDNA was used instead of DNA. After the tagmentation reaction, the fragmented cDNA was purified with SPRI beads. In order to add the Illumina specific bridge PCR compatible sites and enrich the library, limited-cycle PCR (5 cycles) was performed according to the instructions for the Nextera system with minor modifications. For bar coded libraries, 50 X Nextera Adaptor 2 was replaced with a bar coded Illumina-compatible Adaptors from the Nextera Bar Codes kit (Illumina) in PCR setup. SPRI beads were used for purification of the PCR-products and the library QC was evaluated by Agilent Bioanalyzer (Agilent).

treatment_protocol: MS medium

tag: genotype/variation

tag: ecotype

tag: tissue source

value: 2mm root tips


title: WT_3

description:
RNA later treated
W3

value: WT


title: IM_D4_Rep1


title: vir-1_3

description:
RNA later treated
E3


title: WT_1

description:
RNA later treated
W1


title: vir-1_2

description:
RNA later treated
E2


title: IM_SL_Rep1

source_name: interstitial macrophage sea level


title: IM_SL_Rep2


title: oRG_OSVZ_sc74

description: single cell sequencing


title: ChIP-Seq Apicidin H3K4me3 rep2

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

country: South Korea

institute: Yonsei University

data_processing:
Reads were quality trimmed and filtered using the NGS QC toolkit v2.3 to remove reads containing low-quality bases.
After preprocessing, the RNA sequenced reads were mapped to T.vaginalis genome using RSEM with bowtie2 v2.0.0-beta7.
ChIP sequence reads were mapped to T.vaginalis genome using bowtie2 v2.0.0-beta7.
FPKM (fragments per kilobase of exon per million fragments mapped) for RNA-Seq were calculated using RSEM.
ChIP-Seq read counts were calculated for each gene using HTSeq v0.6.1 and were converted log2 CPM (count per million) values using Bioconductor package edgeR v3.6.8
Peaks for ChIP-seq data were called using HOMER with the options: -gsize 176000000 -F 2, -fdr 0.05 -size 150 -minDist 150.
Genome_build: ASM282v1
Supplementary_files_format_and_content: RNA-Seq bigwig files were generated using RSEM and ChIP-Seq bigwig files were generated using Galaxy tools.

organism: Trichomonas vaginalis

source_name: Trichomonas vaginalis_ChIP-Seq Apicidin H3K4me3

growth_protocol: The T016 strain of Trichomonas vaginalis was axenically subcultivated at 37°C in Diamond’s trypticase–yeast extract–maltose (TYM) medium with 10% heat-inactivated horse serum and 0.5% penicillin/streptomycin.

extract_protocol:
Genomic DNA extraction protocol not provided.
ChIP-seq library construction protocol not provided.

treatment_protocol: HDAC inhibitor, apicidin (70nM) and TSA (1μM) were treated for 4hrs.

tag: treatment

value: Apicidin

tag: chip antibody

value: H3K4me3 (Abcam, ab8580)


title: ChIP-Seq DMSO H3K4me3 rep1

source_name: Trichomonas vaginalis_ChIP-Seq DMSO H3K4me3

value: DMSO