title: FA_IgG_control

city: Jena

first: Arndt

last: Steube

address: Adolf-Reichwein-Strasse 23

department: Cell and Molecular Biology

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI)

library_source: genomic

data_processing:
Reads were mapped onto the human genome reference (GRCh37/hg19) using Bowtie (-l 50 -3 1 -n 2 -m 1 --best --strata)
Uniquely mapped reads including a maximum of two mismatches were accepted and redundant reads with identical coordinates were filtered out.
Reads were screened against the blacklist regions (collection of signal artifacts) in the human genome (https://sites.google.com/site/anshulkundaje/ projects/blacklists) and overlapping reads were removed.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Read density profiles (signal tracks) were generated as pileup signal files (normalized by fragment pileup in million reads) (q-value 5e-2) and fold enrichment (FE) tracks were generated by normalized ChIP over input DNA pileup signal files using MACS2.

molecule: genomic DNA

organism: Homo sapiens

source_name: germinal center B-cell

growth_protocol: The germinal center B cell like diffuse large B-cell lymphoma (DLBCL) OCI-Ly1 cell line (GCB-DLBCL OCI-Ly1) was maintained in Iscove’s Modified Dulbecco’s Medium (Gibco) supplemented with fetal calf serum (10% v/v, Gibco) at 37°C and 5% CO2.

extract_protocol:
Immediately after irradiation, OCI-Ly1 cell suspensions were added to ice cold PBS (pH 7.4) containing protease inhibitors according to the manufacturer’s recommendations (Complete Protease Inhibitor, Roche Applied Science). All subsequent steps were performed at 4°C. After centrifugation at 1,000 g for 7 min, the pellet was resuspended in 250 µl of ChIP lysis buffer (0.5% NP-40, 150 mM NaCl, 50 mM Tris-HCl pH 8.0, 5 mM EDTA, protease inhibitors). Chromatin was sheared on ice (Microtip sonicator, Labsonic U, Sartorius) into fragments averaging 250 bp and centrifuged at 16,000 g for 10 min. Fragmentation of chromatin was analyzed with purified DNA using agarose gel electrophoresis and a 2100 Bioanalyzer (Agilent Technologies). An aliquot of sheared chromatin was used for UV input DNA sequencing. The supernatant was pre-cleared for 1 h using pre-washed protein A magnetic beads according to the manufacturer’s instructions (Dynabeads Protein A, Invitrogen). A ChIP-grade anti-Bcl6 antibody (Bcl-6 (N-3), sc-858, Lot# A3013, Santa Cruz) was used for ChIP. The specificity and suitability for ChIP was confirmed by immunoblot analysis. For UV IgG control ChIP, normal rabbit IgG (sc-2027, Lot# D1513, Santa Cruz) was used. Clarified chromatin extracts were incubated for 12 h with specific anti-Bcl6 antibody and control IgG antibody, respectively. Nucleoprotein-antibody complexes were precipitated using pre-washed beads for 1 h. The supernatant was removed and beads were sequentially washed twice in low salt (0.1% SDS, 1% Triton-X 100, 150 mM NaCl, 20 mM Tris pH 8.0, 2 mM EDTA), high salt (0.1% SDS, 1% Triton-X 100, 500 mM NaCl, 20 mM Tris-HCl pH 8.0, 2 mM EDTA), LiCl (0.5% NP-40, 0.5% deoxycholic acid (DOC), 250 mM LiCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA) and TE (10 mM Tris pH 8.0, 1 mM EDTA) buffer. For elution of immunoprecipitated nucleoprotein-antibody complexes, beads were resuspended in 0.1 M citrate buffer (pH 2.2) for 2 min at room temperature. The supernatant was removed and transferred into Tris-HCl (pH 8.0) for neutralization. After RNase A treatment (50 µg/ml, Fermentas) for 1 h at 37°C and Proteinase K treatment (100 µg/ml, Fermentas) for 12 h at 50°C, genomic DNA was purified by phenol/chloroform/isoamylalcohol extraction and ethanol precipitation. Formaldehyde (FA) ChIP was performed as described except for the following steps. Cells were harvested, washed twice with ice cold PBS (pH 7.4) and lysed in RIPA buffer (1% NP-40, 0.5% DOC, 0.1% SDS, 150 mM NaCl, 50 mM Tris pH 8.0, 5 mM EDTA, protease inhibitors). For elution of immunocomplexes, beads were resuspended in elution buffer (1% SDS, 0.1 M NaHCO3) and crosslinking was reverted by addition of 0.3 M NaCl and incubation for 5 h at 65°C.
Sequencing libraries were prepared from UV-ChIP, FA ChIP and control DNA fragments according to the manufacturer’s protocol (NEBNext® Ultra™ DNA Library Prep Kit). In brief, DNA fragments were end-repaired and the blunt, phosphorylated ends were treated with Klenow DNA polymerase and dATP to yield a 3’ A base overhang for ligation of adapters. After adapter ligation, DNA was PCR amplified (15 cycles). Libraries were size-selected to achieve ChIP DNA fragment lengths of 200-300 bp. The purified DNA was captured on an Illumina flow cell for cluster generation and libraries were sequenced on a HiSeq 2500 (Illumina) instrument according to manufacturer's protocol.

treatment_protocol: UV laser irradiation of living cells was performed using Quanta-Ray pulsed Nd:YAG laser (Model GCR-150, Spectra Physics) equipped with an HG-2 harmonic generator (Spectra Physics) and dichroic mirrors (DHS-2 Quanta-Ray dichroic harmonic separator) to give monochromatic light at 266 nm. The laser beam was focused by a fused silica lens, deviated by 90° and adjusted to fit the surface of the sample area. The laser energy at the sample position was determined using a Power/Energy Meter (Nova, Ophir Optronics Ltd.) equipped with a Power Thermal Sensor (Model 10A-P-SH, Ophir Optronics Ltd.). The parameters for UV laser irradiation were as follows: pulse duration 5 ns, repetition rate 10 Hz, energy per pulse 50 mJ, diameter of the laser beam 6 mm. Formaldehyde (FA) ChIP was performed as described. OCI-Ly1 cells were fixed with 1% FA for 10 min under rotation at room temperature and the reaction was quenched by addition of 125 mM glycine for 5 min.

tag: cell type

value: B cell lymphoma

tag: cell line

tag: chip antibody


title: c4da3

status: Public on Nov 06 2017

type: SRA

city: Seattle

first: Jay

last: Parrish

state: Washington

department: Department of Biology

country: USA

institute: University of Washington

description: Cells were isolated by FACS on an AriaII and snap frozen in lysis buffer

library_source: transcriptomic

data_processing:
Bases were called and reads were demultiplexed with Illumina CASAVA 1.8.2
Reads were aligned to the transcriptome using STAR version 2.5.2b with the option ‘--quantMode TranscriptomeSAM’
Transcript expression per sample, in transcripts per million (TPM), was calculated with Salmon version 0.7.2 in alignment based mode
Gene expression per sample, in transcripts per million (TPM), was calculated by summing the transcript expression for all transcripts of a given gene
Genome_build: FlyBase genome release 6.10
Supplementary_files_format_and_content: Tab delimited text files showing tpm for all genes for each sample

molecule: total RNA

organism: Drosophila melanogaster

source_name: class IV da sensory neurons

extract_protocol:
Total RNA was isolated with the RNAqueous Micro Kit (Ambion AM1931), converted to cDNA, and pre-amplified as described in the SMARTer Ultra-low input kit (Clontech PN 634833) but with modified procedures for low cell number analysis (Fluidigm)
RNA libraries were prepared for sequencing following Illumina protocols.  cDNA libraries were diluted to 0.25ng/ul, fragmented with the Nextera XT DNA kit (Illumina PN FC-131-1024), multiplexed, and sequenced on a Hi-Seq2500

tag: developmental stage

value: third instar

tag: genotype

value: ppk-Gal4 > UAS-Red Stinger

tag: quantity

value: 100 neurons


title: Salmonella/H.poly Cell 132

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

description: Full-length RNAseq (SMART-Seq2) reads

data_processing:
3' polyA RNA-seq
CellRanger 1.0
PCA (prcomp in R)
kNN-based graph clustering (R code)
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie
RSEM
Genome_build: mm10
Supplementary_files_format_and_content: 3' polyA RNA-seq: UMI count expression values for each gene (rows) in each cell (columns)
Supplementary_files_format_and_content: Full-length RNAseq (SMART-Seq2): Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each cell (columns)

organism: Mus musculus

source_name: WT Mouse intestinal epithelial cells

extract_protocol:
3' polyA RNA seq
10X Genomics Chromium Prep
Full length RNAseq (SMART-Seq2)

tag: stain

value: Wild type

tag: treatment

value: H. polygyrus (Day 10)


title: Salmonella/H.poly Cell 131

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 139

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 130

description: Full-length RNAseq (SMART-Seq2) reads


title: BCL6_FA_ChIP-seq


title: minusUV_control_ChIP


title: FA_input_DNA


title: Salmonella/H.poly Cell 135

description: Full-length RNAseq (SMART-Seq2) reads


title: UV_input_DNA


title: Salmonella/H.poly Cell 133

description: Full-length RNAseq (SMART-Seq2) reads


title: BCL6_UV-ChIP-seq_repl2


title: Salmonella/H.poly Cell 129

description: Full-length RNAseq (SMART-Seq2) reads

value: H. polygyrus (Day 3)


title: UV_IgG_control


title: Salmonella/H.poly Cell 140

description: Full-length RNAseq (SMART-Seq2) reads

value: Salmonella


title: Salmonella/H.poly Cell 128

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 127

description: Full-length RNAseq (SMART-Seq2) reads


title: BCL6_UV-ChIP-seq_repl1

data_processing:
Reads were mapped onto the human genome reference (GRCh37/hg19) using Bowtie (-l 50 -3 1 -n 2 -m 1 --best --strata)
Uniquely mapped reads including a maximum of two mismatches were accepted and redundant reads with identical coordinates were filtered out.
Reads were screened against the blacklist regions (collection of signal artifacts) in the human genome (https://sites.google.com/site/anshulkundaje/projects/blacklists) and overlapping reads were removed.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Read density profiles (signal tracks) were generated as pileup signal files (normalized by fragment pileup in million reads) (q-value 5e-2) and fold enrichment (FE) tracks were generated by normalized ChIP over input DNA pileup signal files using MACS2.


title: Salmonella/H.poly Cell 126

description: Full-length RNAseq (SMART-Seq2) reads


title: Short_15

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

country: China

institute: Tongji Hospital, Tongji University

description: single hESC 121

data_processing:
Clean reads were aligning to hg19 with TopHat2 (Kim et al., 2013). Gene expression levels (TPM) were estimated by RSEM. Genome DNA sequence and gene annotation were download from iGenome (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz).
Genome_build: hg19
Supplementary_files_format_and_content: TPM data

molecule: polyA RNA

source_name: human embryonic stem cell line

growth_protocol: Human embryonic stem cell (WA26) were routinely maintained in undifferentiated state in E8 medium (A1517001, Life technologies) on Matrigel (356230, BD Bioscience) coated tissue culture plates with medium change daily and passaged every 3 days using 0.5 mM EDTA in PBS at 1:20 ratio added with Rocki (sc-281642A, Santa Cruz).

extract_protocol:
Separation of gDNA and mRNA was performed as described previously. Briefly, samples were incubated at 72 °C for 3 min, the Biotin-oligo-dT primer was hybridized to poly (A)+ tail mRNA. Dynabeads in 4 μL (65001, Life technologies) were added to capture poly (A)+ tail mRNA, collected by a magnet, and the gDNA supernatant transferred to a fresh PCR tube. Single-cell cDNA was synthesized in the tubes containing mRNA according to Smart-seq2 protocol.
The libraries were prepared by using TruePrep DNA Library Prep Kit V2 for Illumina® (TD503-02, Vazyme Biotech) according to the instruction manual.


title: c4da2


title: Salmonella/H.poly Cell 125

description: Full-length RNAseq (SMART-Seq2) reads


title: Short_14

description: single hESC 120


title: Short_13

description: single hESC 119


title: c4da1


title: Salmonella/H.poly Cell 121

description: Full-length RNAseq (SMART-Seq2) reads


title: Short_12

description: single hESC 118


title: Salmonella/H.poly Cell 123

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 119

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 117

description: Full-length RNAseq (SMART-Seq2) reads


title: Short_9

description: single hESC 115


title: Short_11

description: single hESC 117


title: Short_8

description: single hESC 114


title: Salmonella/H.poly Cell 115

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 122

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 124

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 114

description: Full-length RNAseq (SMART-Seq2) reads


title: Short_2

description: single hESC 108


title: Salmonella/H.poly Cell 113

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 120

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 118

description: Full-length RNAseq (SMART-Seq2) reads


title: Short_7

description: single hESC 113


title: Short_6

description: single hESC 112


title: Short_5

description: single hESC 111


title: Salmonella/H.poly Cell 116

description: Full-length RNAseq (SMART-Seq2) reads


title: Short_4

description: single hESC 110


title: Salmonella/H.poly Cell 109

description: Full-length RNAseq (SMART-Seq2) reads


title: Medium_22

description: single hESC 103


title: Short_3

description: single hESC 109


title: Salmonella/H.poly Cell 108

description: Full-length RNAseq (SMART-Seq2) reads


title: Short_1

description: single hESC 107


title: Medium_21

description: single hESC 102


title: Medium_25

description: single hESC 106


title: Salmonella/H.poly Cell 112

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 110

description: Full-length RNAseq (SMART-Seq2) reads


title: Short_10

description: single hESC 116


title: Medium_23

description: single hESC 104


title: Salmonella/H.poly Cell 105

description: Full-length RNAseq (SMART-Seq2) reads


title: Medium_18

description: single hESC 99


title: Medium_20

description: single hESC 101


title: Salmonella/H.poly Cell 104

description: Full-length RNAseq (SMART-Seq2) reads


title: Medium_19

description: single hESC 100


title: Salmonella/H.poly Cell 103

description: Full-length RNAseq (SMART-Seq2) reads


title: Medium_17

description: single hESC 98


title: Salmonella/H.poly Cell 102

description: Full-length RNAseq (SMART-Seq2) reads


title: Medium_14

description: single hESC 95


title: Medium_24

description: single hESC 105


title: Medium_15

description: single hESC 96


title: Medium_13

description: single hESC 94


title: Salmonella/H.poly Cell 101

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 111

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 99

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 100

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 107

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 106

description: Full-length RNAseq (SMART-Seq2) reads


title: Medium_11

description: single hESC 92


title: Medium_10

description: single hESC 91


title: Medium_12

description: single hESC 93


title: Salmonella/H.poly Cell 97

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 98

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 96

description: Full-length RNAseq (SMART-Seq2) reads


title: Medium_8

description: single hESC 89


title: Salmonella/H.poly Cell 94

description: Full-length RNAseq (SMART-Seq2) reads


title: Medium_9

description: single hESC 90


title: Medium_16

description: single hESC 97


title: Salmonella/H.poly Cell 93

description: Full-length RNAseq (SMART-Seq2) reads


title: Medium_7

description: single hESC 88


title: Medium_6

description: single hESC 87


title: Salmonella/H.poly Cell 90

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 89

description: Full-length RNAseq (SMART-Seq2) reads


title: Medium_5

description: single hESC 86


title: Salmonella/H.poly Cell 92

description: Full-length RNAseq (SMART-Seq2) reads


title: Medium_2

description: single hESC 83


title: Salmonella/H.poly Cell 87

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_81

description: single hESC 81


title: Salmonella/H.poly Cell 88

description: Full-length RNAseq (SMART-Seq2) reads


title: Medium_1

description: single hESC 82


title: Salmonella/H.poly Cell 86

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 85

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_79

description: single hESC 79


title: Long_78

description: single hESC 78


title: Salmonella/H.poly Cell 95

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 83

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_73

description: single hESC 73


title: Medium_4

description: single hESC 85


title: Long_72

description: single hESC 72


title: Long_75

description: single hESC 75


title: Salmonella/H.poly Cell 80

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 84

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_70

description: single hESC 70


title: Salmonella/H.poly Cell 91

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_71

description: single hESC 71


title: Long_69

description: single hESC 69


title: Long_74

description: single hESC 74


title: Salmonella/H.poly Cell 77

description: Full-length RNAseq (SMART-Seq2) reads


title: Medium_3

description: single hESC 84


title: Salmonella/H.poly Cell 76

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 79

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_76

description: single hESC 76


title: Salmonella/H.poly Cell 74

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 78

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 75

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 81

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_77

description: single hESC 77


title: Long_80

description: single hESC 80


title: Salmonella/H.poly Cell 82

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_67

description: single hESC 67


title: Salmonella/H.poly Cell 73

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 72

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 71

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_66

description: single hESC 66


title: Long_65

description: single hESC 65


title: Long_68

description: single hESC 68


title: Long_64

description: single hESC 64


title: Salmonella/H.poly Cell 69

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 70

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_63

description: single hESC 63


title: Long_62

description: single hESC 62


title: Salmonella/H.poly Cell 68

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_61

description: single hESC 61


title: Salmonella/H.poly Cell 66

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 67

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 65

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_60

description: single hESC 60


title: Salmonella/H.poly Cell 63

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 64

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_57

description: single hESC 57


title: Long_58

description: single hESC 58


title: Salmonella/H.poly Cell 61

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 62

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_56

description: single hESC 56


title: Salmonella/H.poly Cell 59

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 58

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_52

description: single hESC 52


title: Long_54

description: single hESC 54


title: Long_55

description: single hESC 55


title: Salmonella/H.poly Cell 60

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 57

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 56

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_48

description: single hESC 48


title: Salmonella/H.poly Cell 55

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 54

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_59

description: single hESC 59


title: Salmonella/H.poly Cell 53

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 51

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_50

description: single hESC 50


title: Long_47

description: single hESC 47


title: Long_46

description: single hESC 46


title: Long_43

description: single hESC 43


title: Salmonella/H.poly Cell 52

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 48

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 49

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 47

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_51

description: single hESC 51


title: Long_42

description: single hESC 42


title: Long_40

description: single hESC 40


title: Salmonella/H.poly Cell 46

description: Full-length RNAseq (SMART-Seq2) reads


title: monoclonal Flag ChIP-Seq; 8567cells; 60C, minus tetracycline, plus corticosterone, then cort washout; Biological rep 2

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

description: Biological replicate 2

data_processing:
Sequences were aligned to the mouse genome (mm10) using Bowtie2 with default settings.
Duplicate reads were removed using Samtools.
The typical fragment lengths were computed based on strand cross-correlation maxima using the SPP package (Kharchenko et al. 2008) (available at https://github.com/hms-dbmi/spp/). Brg1 reads were extended to a length of 100 bp, and H2A.Z reads were extended to a length of 200 bp.
Genome-wide coverage profiles were computed in MATLAB by stacking all extended reads and counting the number of reads that cover each bp.
IGV tracks (tdf files) were generated using igvtools.
Genome_build: mm10
Supplementary_files_format_and_content: tdf files containing the occupancy profiles, for the IGV genome browser

source_name: 3134 adenocarcinoma cells

growth_protocol: Typical growth protocols with DMEM 10% FBS. Cells were grown 24h on media with 10% charcoal stripped serum before hormone induction. Tet-regulated genes were induced with tet removal for 24h prior to harvest.

extract_protocol:
Cells were fixed in 1% formaldehyde, lysed and sonicated to small DNA fragments. IPs were performed with anti-BRG1 (1 μg, EPNCIR11A, made in collaboration with Epitomics, Burlingame, CA), or anti-Flag (4ug Sigma anti-Flag F1804) antibody.
ChIP-Seq libraries were made by minimal PCR amplification cycles using the Illumina adaptor and PCR primers. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Dexamethasone treatment: 100 nM for 1h. Corticosterone treatment: 600 nM for times indicated in the paper.

tag: antibody

value: anti-Flag (Sigma anti-Flag F1804)


title: monoclonal Flag ChIP-Seq; 8567cells; 90C, minus tetracycline, plus corticosterone; Biological replicate 1

description: Biological replicate 1


title: monoclonal Flag ChIP-Seq; 8567cells; 90C, minus tetracycline, plus corticosterone; Biological replicate 2

description: Biological replicate 2


title: monoclonal Flag ChIP-Seq; 8567cells; 60C, minus tetracycline, plus corticosterone, then cort washout; Biological rep 1

description: Biological replicate 1


title: Long_49

description: single hESC 49


title: Salmonella/H.poly Cell 45

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_39

description: single hESC 39


title: Salmonella/H.poly Cell 44

description: Full-length RNAseq (SMART-Seq2) reads


title: monoclonal Flag ChIP-Seq; 8567cells; 60C, minus tetracycline, plus corticosterone; Biological replicate 2

description: Biological replicate 2


title: Salmonella/H.poly Cell 50

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_45

description: single hESC 45


title: Long_38

description: single hESC 38


title: Salmonella/H.poly Cell 43

description: Full-length RNAseq (SMART-Seq2) reads


title: monoclonal Flag ChIP-Seq; 8567cells; 0C, minus tetracycline; Biological replicate 2

description: Biological replicate 2


title: Long_36

description: single hESC 36


title: Salmonella/H.poly Cell 42

description: Full-length RNAseq (SMART-Seq2) reads


title: monoclonal Flag ChIP-Seq; 8567cells; 0C, minus tetracycline; Biological replicate 1

description: Biological replicate 1


title: Salmonella/H.poly Cell 41

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 40

description: Full-length RNAseq (SMART-Seq2) reads


title: monoclonal Flag ChIP-Seq; 8567cells; 60C, minus tetracycline, plus corticosterone; Biological replicate 1

description: Biological replicate 1


title: Long_41

description: single hESC 41


title: Long_53

description: single hESC 53


title: Long_37

description: single hESC 37


title: Long_44

description: single hESC 44


title: Long_34

description: single hESC 34


title: Salmonella/H.poly Cell 39

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_35

description: single hESC 35


title: monoclonal Flag ChIP-Seq; 8567cells; 0C, plus tetracycline; Biological replicate 1

description: Biological replicate 1


title: Long_33

description: single hESC 33


title: Long_32

description: single hESC 32


title: monoclonal Brg1 ChIP-Seq; Dexamethasone-treated cells; Biological replicate 2

description: Biological replicate 2

value: anti-BRG1 (EPNCIR11A, made in collaboration with Epitomics, Burlingame, CA)


title: Salmonella/H.poly Cell 38

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_31

description: single hESC 31


title: Salmonella/H.poly Cell 37

description: Full-length RNAseq (SMART-Seq2) reads


title: Dexamethasone-treated cells. Biological replicate 2

description: Biological replicate 2

data_processing:
Sequences were aligned to the mouse genome (mm10) using Bowtie2 with default settings.
Mono-nucleosomal reads were size selected, and we kept all reads with the lengths between 120-180 bp.
Genome-wide coverage profiles were computed in MATLAB by stacking all reads and counting the number of reads that cover each bp.
IGV tracks (tdf files) were generated using igvtools.
Genome_build: mm10
Supplementary_files_format_and_content: tdf files containing the occupancy profiles, for the IGV genome browser

growth_protocol: Typical growth protocols with DMEM 10% FBS. Cells were grown 24hrs on media with 10% charcoal stripped serum before hormone induction.

extract_protocol:
Cell nuclei were gently extracted by hypotonic buffer with detergent and then digested with MNase to obtain predominantly mononucleosome. In Experiment 2, the mono-nucleosomal DNA was gel-purified prior to library preparation; in Experiment 1 the mononucleosomal DNA was not gel-purified. The extents of digestion were very similar in both experiments.
MNase-seq libraries were prepared using Illumina paired-end adaptors and primers (Experiment 2) or using the New England Biolabs Illumina kit (E7370) (Experiment 1).

treatment_protocol: Treated cells with 100 nM dexamethasone for 1 hour.

value: 100 nM dexamethasone


title: Salmonella/H.poly Cell 36

description: Full-length RNAseq (SMART-Seq2) reads


title: monoclonal Brg1 ChIP-Seq; Dexamethasone-treated cells; Biological replicate 1

description: Biological replicate 1


title: Long_30

description: single hESC 30


title: Dexamethasone-treated cells. Biological replicate 1

description: Biological replicate 1


title: Salmonella/H.poly Cell 35

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 34

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_29

description: single hESC 29


title: Untreated cells. Biological replicate 2

description: Biological replicate 2


title: Long_28

description: single hESC 28


title: Long_27

description: single hESC 27


title: Salmonella/H.poly Cell 33

description: Full-length RNAseq (SMART-Seq2) reads


title: Untreated cells. Biological replicate 1

description: Biological replicate 1


title: Long_26

description: single hESC 26


title: Salmonella/H.poly Cell 32

description: Full-length RNAseq (SMART-Seq2) reads


title: monoclonal Flag ChIP-Seq; 8567cells; 0C, plus tetracycline; Biological replicate 2

description: Biological replicate 2


title: Salmonella/H.poly Cell 31

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 30

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_25

description: single hESC 25


title: Salmonella/H.poly Cell 29

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_23

description: single hESC 23


title: Long_24

description: single hESC 24


title: Salmonella/H.poly Cell 28

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 27

description: Full-length RNAseq (SMART-Seq2) reads


title: GFP3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: bound RNA

data_processing:
Illumina bcl2fastq  v2.17.1.14  was used to perform the basecalling and demultiplexing, Quality check was done using FastQC v0.11.4 ,Babraham Bioinformatics)
Read alignment was performed using STAR v2.5.0.
Data analysis was performed using R (3.3.0) - differential gene expression  was performed using DESeq2, graphs plotting – gplots
Candidate genes were filtered to a minimum of 2-fold  change and FDR-corrected p < 0.05 (p adjusted).
Genome_build: ens84
Supplementary_files_format_and_content: tab delimited files includes RPKM values of each of the samples,Candidates gene list includes list of all genes with respective logFC

source_name: GFP-slam transgene-rep3

growth_protocol: Adult flies were kept on apple juice plates with yeast for egg laying

extract_protocol:
Embryos were dechlorionated with hypochloride, frozen in liquid nitrogen. RNA and protein complexes were isolated by antibody or GFP binder. RNA were further extracted with phenol/chloroform/isoamylalcohol and precipitated. The RNA profile were analyzed by next generation sequencing.
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122-2002) starting from 500 ng of total RNA according to Illumina's instructions. Accurate quantitaion of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000  following the manufacturer's protocols.

tag: tissue

value: embryo

value: GFP-slam transgenic

tag: Stage


title: Long_22

description: single hESC 22


title: GFP1

description: bound RNA

source_name: GFP-slam transgene-rep1


title: Long_21

description: single hESC 21


title: Salmonella/H.poly Cell 26

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_20

description: single hESC 20


title: OrR3

description: bound RNA

source_name: Wild type-rep3


title: Long_19

description: single hESC 19


title: Long_18

description: single hESC 18


title: Salmonella/H.poly Cell 24

description: Full-length RNAseq (SMART-Seq2) reads


title: OrR1

description: bound RNA

source_name: Wild type-rep1


title: OrR2

description: bound RNA

source_name: Wild type-rep2


title: Salmonella/H.poly Cell 25

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 23

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_17

description: single hESC 17


title: Long_16

description: single hESC 16


title: Dia3

description: bound RNA


title: Dia2

description: bound RNA


title: Long_15

description: single hESC 15


title: Salmonella/H.poly Cell 20

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 21

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_14

description: single hESC 14


title: Dia1

description: bound RNA


title: Salmonella/H.poly Cell 19

description: Full-length RNAseq (SMART-Seq2) reads


title: slam3

description: bound RNA


title: Long_12

description: single hESC 12


title: slam2

description: bound RNA


title: Long_11

description: single hESC 11


title: slam1

description: bound RNA


title: Salmonella/H.poly Cell 16

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_10

description: single hESC 10


title: Salmonella/H.poly Cell 17

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 15

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_9

description: single hESC 9


title: Salmonella/H.poly Cell 13

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 14

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 22

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_8

description: single hESC 8


title: Long_7

description: single hESC 7


title: Tor-OE ribosome profiling replicate 3

city: Los Angeles

first: Dion

middle: K

last: Dickman

state: California

address: 3641 Watt Way, HNB 309

department: Neurobiology

institute: University of Southern California

description:
ribosome protected mRNA fragments
Tor-OE ribosome profiling R1_2_3_RPKM.xlsx

data_processing:
Library strategy: Ribo-seq
Base-calling performed using Real Time Analysis (RTA) 2.4.11 (Nextseq 500)
Reads were trimmed to remove low quality-score bases and adaptor sequences using CLC Genomics Workbench 8.0 (QIAGEN)
Trimmed reads were mapped to Drosophila melanogaster genome (NCBI genome release 5_48) using the RNA-seq analysis function of the CLC Genomics Workbench 8.0 (QIAGEN)
The expression value: Reads Per Kilobase of exon per Million mapped reads (RPKM) were generated for all annotated genes as part of the RNA-seq analysis described above
Genome_build: Drosophila melanogaster NCBI genome release 5.48
Supplementary_files_format_and_content: Excel files that include RPKM values

source_name: Tor-OE ribosome profiling

growth_protocol: Drosophila stocks were raised at 25°C on standard molasses food.

extract_protocol:
The frozen tissue was then homogenized in 540 µl lysis solution (10 mM HEPES, PH 7.4, 150 mM KCl, 5 mM MgCl2, 100 µg/ml Cycloheximide) supplemented with 0.5% Triton-X100, 1U/µl ANTI-RNase (ThermoFisher scientific, AM2690) and protease inhibitor (EDTA-free, Sigma, COEDTAF-RO).
240 µl of lysate was incubated with anti-Flag antibody coated magnetic beads and 10000 units of RNase T1 (ThermoFisher scientific, EN0541) to perform digestion of exposed mRNA and ribosome purification simultaneously. 100 µl of Dynabeads protein G coated with 4 µg anti-Flag antibody was used. The lysate-beads-RNase T1 mixture was incubated at 4°C for 6 hours and washed. RNA was extracted from ribosomes bound to the beads by TRIzol Reagent, and the co-precipitant linear acrylamide (ThermoFisher scientific, AM9520) was used to increase the RNA recovery rate. RNA fragments in the range of 30-45 nt was extracted by gel extraction.
Library generation for ribosome profiling was performed using NEBNext Small RNA Library Prep Set for Illumina (NEB, E7330S), additional de-phosphorylation and phosphorylation steps were incorporated in the workflow to ensure compatibility with the kit.

treatment_protocol: third instar larvae were dissected in HL-3 saline, with all internal organs and the central nervous system removed, leaving only the body wall and attached muscle tissue. Following dissection, the tissue was immediately frozen on dry ice. 18 Female larvae body wall were collected for each sample.

value: Third instar larvae

value: body wall muscle


title: Salmonella/H.poly Cell 12

description: Full-length RNAseq (SMART-Seq2) reads


title: Dia4

description: bound RNA


title: Tor-OE transcriptional profiling replicate 2

description:
total RNA
Tor-OE transcriptional profiling R1_2_3_RPKM.xlsx

data_processing:
Base-calling performed using Real Time Analysis (RTA) 2.4.11 (Nextseq 500)
Reads were trimmed to remove low quality-score bases and adaptor sequences using CLC Genomics Workbench 8.0 (QIAGEN)
Trimmed reads were mapped to Drosophila melanogaster genome (NCBI genome release 5_48) using the RNA-seq analysis function of the CLC Genomics Workbench 8.0 (QIAGEN)
The expression value: Reads Per Kilobase of exon per Million mapped reads (RPKM) were generated for all annotated genes as part of the RNA-seq analysis described above
Genome_build: Drosophila melanogaster NCBI genome release 5.48
Supplementary_files_format_and_content: Excel files that include RPKM values

source_name: Tor-OE transcriptional profiling

extract_protocol:
The frozen tissue was then homogenized in 540 µl lysis solution (10 mM HEPES, PH 7.4, 150 mM KCl, 5 mM MgCl2, 100 µg/ml Cycloheximide) supplemented with 0.5% Triton-X100, 1U/µl ANTI-RNase (ThermoFisher scientific, AM2690) and protease inhibitor (EDTA-free, Sigma, COEDTAF-RO).
120 µl of the lysate was used for total RNA extraction by TRIzol LS Reagent (ThermoFisher scientific, 10296010)
2.5 µg of total RNA was used for isolation of mRNA with the Dynabeads mRNA DIRECT Purification Kit (ThermoFisher scientific, 61011). The entire isolated mRNA sample was used for library generation with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina sequencing (NEB, E7420S).


title: Tor-OE transcriptional profiling replicate 3


title: Long_6

description: single hESC 6


title: Salmonella/H.poly Cell 11

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_5

description: single hESC 5


title: Long_13

description: single hESC 13


title: Tor-OE transcriptional profiling replicate 1


title: Salmonella/H.poly Cell 10

description: Full-length RNAseq (SMART-Seq2) reads


title: Tor-OE ribosome profiling replicate 2


title: GluRIIA ribosome profiling replicate 3

description:
ribosome protected mRNA fragments
GluRIIA ribosome profiling R1_2_3_RPKM.xlsx

source_name: GluRIIA ribosome profiling


title: GluRIIA ribosome profiling replicate 2


title: Long_3

description: single hESC 3


title: Salmonella/H.poly Cell 8

description: Full-length RNAseq (SMART-Seq2) reads


title: Tor-OE ribosome profiling replicate 1


title: Long_2

description: single hESC 2


title: GluRIIA ribosome profiling replicate 1


title: Long_1

description: single hESC 1


title: Salmonella/H.poly Cell 7

description: Full-length RNAseq (SMART-Seq2) reads


title: GluRIIA transcriptional profiling replicate 3

description:
total RNA
GluRIIA transcriptional profiling R1_2_3_RPKM.xlsx

source_name: GluRIIA transcriptional profiling


title: GluRIIA transcriptional profiling replicate 2


title: DydcH_stat_3

city: Jouy-en-Josas

first: Cyprien

last: Guérin

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE

data_processing:
Three prime end low quality nucleotides were firstly removed from reads using Trimmomatic (version 0.36; with options -TRAILING:20).
Reads trimmed using Sickle (version 1.33; with options -n -x -q 30 -l 30).
Read mapping against the reference genome of B. subtilis strain 168 (AL009126) was performed using Bowtie 2 (version 2.2.6; with options -N 1 -L 16 -R 4).
Read count was performed on annotated genes of the reference genome using HTSeq count  version 0.6.0 (with default options)
Genome_build: AL009126
Supplementary_files_format_and_content: bam files containing the cleaned reads mapped on the reference genom

organism: Bacillus subtilis

source_name: culture in CH medium

growth_protocol: 200 mL cultures of WT (ABS2005) and ∆ydcH (ASEC56) strains were inoculated at an OD600nm 0.005 from overnight cultures in CH medium, and grown at 37 °C with maximum aeration.

extract_protocol:
RNA were extracted by standard Phenol/Chloroform extraction and precipitated in the presence of isopropanol. RNA pellets were resuspended in 75 µL H2O for 3 h at 4 °C, treated with QIAGen RNase-Free DNase and cleansed with Norgen Concentration Micro Kit as per manufacturer's instructions.
RNA libraries and next generation sequencing were performed and benefits from the expertise of the High-throughput Sequencing Platform of I2BC (CNRS, Gif/Yvette, France). Sequencing was performed using single read 75bases with 30 million stranded reads per sample on a NextSeq 500 Illumina sequencer.

treatment_protocol: At OD600 nm=0.2, 70 mL samples were collected at mid-exponential (OD600nm 1.5) growth and instantly mixed with 30 mL ice-cold killing buffer (20 mM Tris-HCl pH=7.5; 5 mM MgCl2, 20 mM NaN3), centrifuged 10 min at 4700 rpm and 4 °C and pellets were frozen in liquid nitrogen and save at -80 °C until further used. Frozen materials were resuspended in 200 µL ice-cold killing buffer (20 mM Tris-HCl pH = 7.5, 5 mM MgCl2, 20 mM NaN3), 500 µL of small glass beads and 1 mL of lysis buffer (4 M guanidine-thiocyanate, 25 mM sodium acetate pH = 5.2, 0.5% N-lauroylsarcosinate). Cells were disrupted with a Fastprep (MP Biomedicals) at 4 °C for 30 sec at maximum power and centrifuged at maximum speed for 3 min at 4 °C.

tag: strain

value: DydcH

tag: phase

value: stat

tag: replicate


title: Salmonella/H.poly Cell 5

description: Full-length RNAseq (SMART-Seq2) reads


title: GluRIIA transcriptional profiling replicate 1


title: Salmonella/H.poly Cell 6

description: Full-length RNAseq (SMART-Seq2) reads


title: wild type translational profiling (TRAP) replicate 3

description:
mRNA associated with ribosomes
WT TRAP R1_2_3_RPKM.xlsx

data_processing:
Library strategy: TRAP-Seq
Base-calling performed using Real Time Analysis (RTA) 2.4.11 (Nextseq 500)
Reads were trimmed to remove low quality-score bases and adaptor sequences using CLC Genomics Workbench 8.0 (QIAGEN)
Trimmed reads were mapped to Drosophila melanogaster genome (NCBI genome release 5_48) using the RNA-seq analysis function of the CLC Genomics Workbench 8.0 (QIAGEN)
The expression value: Reads Per Kilobase of exon per Million mapped reads (RPKM) were generated for all annotated genes as part of the RNA-seq analysis described above
Genome_build: Drosophila melanogaster NCBI genome release 5.48
Supplementary_files_format_and_content: Excel files that include RPKM values

extract_protocol:
The frozen tissue was then homogenized in 540 µl lysis solution (10 mM HEPES, PH 7.4, 150 mM KCl, 5 mM MgCl2, 100 µg/ml Cycloheximide) supplemented with 0.5% Triton-X100, 1U/µl ANTI-RNase (ThermoFisher scientific, AM2690) and protease inhibitor (EDTA-free, Sigma, COEDTAF-RO).
180 µl of the lysate was incubated with anti-flag antibody coated magnetic beads to purify ribosomes with associated mRNA. 75 µl of Dynabeads protein G (ThermoFisher scientific, 10004D) was used to coat 3 µg anti-Flag antibody (Sigma, F1804). The lysate-beads mixture was incubated at 4°C with rotation for 2 hours, then washed in buffer (10 mM HEPES, PH 7.4, 150 mM KCl, 5 mM MgCl2, 100 µg/ml Cycloheximide), supplemented with 0.1% Triton-X100 (0.1 U/µl SUPERase in RNase Inhibitor (ThermoFisher scientific, AM2696). RNA was extracted from ribosomes bound to the beads by TRIzol Reagent, and the co-precipitant linear acrylamide (ThermoFisher scientific, AM9520) was used to increase the RNA recovery rate.
2.5 µg of total RNA was used for isolation of mRNA with the Dynabeads mRNA DIRECT Purification Kit (ThermoFisher scientific, 61011). The entire isolated mRNA sample was used for library generation with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina sequencing (NEB, E7420S).


title: DydcH_stat_1


title: Salmonella/H.poly Cell 2

description: Full-length RNAseq (SMART-Seq2) reads


title: Salmonella/H.poly Cell 4

description: Full-length RNAseq (SMART-Seq2) reads


title: Long_4

description: single hESC 4


title: wild type translational profiling (TRAP) replicate 2


title: DydcH_stat_2


title: wild type translational profiling (TRAP) replicate 1


title: WT_stat_2

value: WT


title: WT_stat_3


title: WT_stat_1


title: wild type ribosome profiling replicate 3

description:
ribosome protected mRNA fragments
WT ribosome profiling R1_2_3_RPKM.xlsx

source_name: wild type ribosome profiling


title: Salmonella/H.poly Cell 1

description: Full-length RNAseq (SMART-Seq2) reads


title: DydcH_expo_3

value: expo


title: Salmonella/H.poly Cell 3

description: Full-length RNAseq (SMART-Seq2) reads


title: wild type ribosome profiling replicate 2


title: DydcH_expo_2


title: Salmonella/H.poly Cell 9

description: Full-length RNAseq (SMART-Seq2) reads


title: DydcH_expo_1


title: wild type transcriptional profiling replicate 3

description:
total RNA
WT transcriptional profiling R1_2_3_RPKM.xlsx

source_name: wild type transcriptional profiling


title: wild type ribosome profiling replicate 1


title: WT_expo_3


title: wild type transcriptional profiling replicate 2


title: WT_expo_2


title: WT_expo_1


title: wild type transcriptional profiling replicate 1


title: MT02_128-Rep_2

status: Public on Nov 05 2017

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
FastQ quality trimming: cut-off value of 20 (FastX 0.0.13)
Adaptor trimming (cutadapt 1.10)
Read mapping (READemption 0.4.2 and segemehl version 0.2.0)
Wiggle generation and gene quantification (READemption 0.4.2)
Genome_build: NC_007790.1, NC_007791.1, NC_007792.1, NC_007793.1
Supplementary_files_format_and_content: wiggle

organism: Staphylococcus aureus

source_name: bacterial cells

growth_protocol: Bacterial strains (MT02-sensitive S. aureus JE2 and S. aureus JE2 strain resistant to 80 µM MT02) were cultivated overnight at 37°C in LB medium in a shaking incubator at 200 rpm. The next day, the strains were diluted in 100 mL MH broth (optical density was adjusted at OD600= 0.05) and again incubated until the cells reached the exponential growth phase.

extract_protocol:
RNA was isolated with an RNeasy Mini kit (QIAGEN) according to the instructions of the manufacturer. To remove the DNA template, RNA was treated with RNase-free DNase I (New England, Biolabs® Inc, Frankfurt am Main, Germany).
Total RNA of MT02-resistant and wild-type strain JE2 was extracted with the RNeasy (Qiagen) or the MirVana isolation kit (Thermo Fisher Scientific). Fragmentation of messenger-enriched RNA was performed using zinc. Specific tags were ligated before reverse transcription to conserve strand orientation. Single-stranded ligation of the 3′ Illumina adapter was followed by single-stranded ligation of 5′ bar-coded adapter. Reverse transcription and PCR amplification were performed to generate a cDNA colony template library, and gel purification with selection of fragments of 20 to 300 nt was performed.  For HTS experiments, total RNA was treated with the MICROBExpress kit (Thermo Fisher Scientific) to limit contamination by multicopy structural rRNAs, following manufacturer's instructions with slight modifications. The maximal amount of total RNA per tube was limited to 4–5 µg because previous experiments showed important contamination levels when using 10 µg. Between each purification step, RNA quality and quantity were determined by Bioanalyzer (Agilent) using the RNA Nano chips, and quantified using the ND-8000 (Thermo Fisher Scientific).

treatment_protocol: MT02-resistant S. aureus was incubated in the presence of MT02 (80 µM). RNA was isolated from the cells at OD600= 1. At least 6 mL of the bacterial cultures were harvested by centrifugation for 10 min at 10,000 rpm, and the bacterial pellet was resuspended in 800 µL of RLT buffer (Qiagen, Hilden, Germany) and mechanically disrupted with glass beads (2 mL Lysing Matrix tubes, MP Biochemicals GmbH, Eschwege, Germany) in a Fastprep®-24 (MP Biochemicals). The cell lysate was centrifuged for 2 min at 13,000 rpm, and the supernatant was used for RNA isolation.

tag: background strain

value: LAC USA300 JE2

tag: mt02 sensitivity

value: resistant


title: MT02_128-Rep_1


title: MT02_8-Rep_1

value: sensitive


title: Sample T9_8

city: Bonn

first: Dr. Maren

middle: Julia

last: Proell

address: Endenicher Allee 15

institute: Institute of Animal Science, University of Bonn

data_processing:
Quality control was performed with the tool FastQC: per base sequence quality, sequence quality scores, base sequence content, base GC content, sequence GC content, base N content, sequence length distribution, sequence duplication levels as well as overrepresented sequences and Kmer Content.
Sequenced reads were aligned to the Susscrofa 10.2 genome assembly using Bowtie 2 and TopHat.
Genome_build: Susscrofa 10.2
Supplementary_files_format_and_content: Excel file was generated and provides an expression table with raw reads

organism: Sus scrofa

source_name: PRRSV infected lung DCs (9 hours post infection)

growth_protocol: Lung DCs were isolated from different pieces of lavaged lungs.

extract_protocol:
Total cellular RNA isolation was done with the AllPrep® DNA/RNA/Protein Mini Kit (Qiagen).
The TruSeq RNA Sample Preparation Kit (Illumina) was used to sequence lung DCs RNA samples by GATC Biotech AG company (Konstanz, Germany).

treatment_protocol: Lung DCs were infected with PRRSV at a multiplicity of infection of 0.01. Sample collection was done before the infection at time point 0 (0 h, non-infected samples) and at 3, 6, 9, 12, 24 hours post infection (hpi).

value: lung dendritic cells

tag: infection status

value: PRRSV infected

tag: breed

value: Duroc

tag: gender

value: Female


title: Sample T3_4

source_name: PRRSV infected lung DCs (3 hours post infection)


title: Sample T6_6

source_name: PRRSV infected lung DCs (6 hours post infection)


title: Sample T24_13

source_name: PRRSV infected lung DCs (24 hours post infection)


title: Sample 24_11

value: Pietrain


title: Sample T0_1

source_name: PRRSV non-infected lung DCs (0 hours)

value: non-infected


title: Sample T9_7


title: Sample T12_9

source_name: PRRSV infected lung DCs (12 hours post infection)


title: Sample T6_5


title: Sample T3_3


title: Nmbu-RNA-14

city: Oslo

first: Leonardo

middle: Martin

last: Martin

address: Ullevålsveien 72

department: Basic Sicences and Aquatic medicine

country: Norway

institute: Norwegian University of Life Sciences

description:
8.7 mGy/h 1 yr 3
embryos generation F1
isolated with trizol protocol from where mRNA selected and paired end seq

data_processing:
Adaptor trimming using trim_galore (v0.4.2) with default parameters. Additional, 1 base clipped from 3' end and 12 bases at 5' end in both pair of reads
Quality analysis using FastQC (v0.11.5). Only pair of reads with phred score of 20 or above were retained.
Mapping using STAR aligner (v2.5.2b).
Visualization and mapping quality assessed with seqmonk (v.1.35) using SAM files obtained from the step above.
Gene expression was quantified using in-build mRNA-seq pipeline of seqmonk
Differential expression was assessed using the in-build R filter Deseq2 in seqmonk. Using negative binomial distribution. Genes with expression counts lower than 30 were removed. FDR was set up to p<0.05
Genome_build: GRCz10
Supplementary_files_format_and_content: mapping files in SAM format. Expression files:  Count table matrix for all gene expressed. Count table matrix for  all differentially expressed genes (DEG). Count table matrix for DEG cutoff >1.5 log2FC. All expression files given in comma separate values format (.csv) providing, Chromosome name, genome coordinate, Ensembl transcript ID, Gene symbol and description, gene biotype, per sample expression values as log2 of the normalized read count, FDR.

organism: Danio rerio

source_name: F1 embryos from exposed parents 8.7 mGy/h after 1 year

extract_protocol:
Total RNA was isolated with TRIzol Reagent (Invitrogen) according to manufactures’ instructions. Briefly, 1 ml TRIzol was added to each sample consisting of 100 embryos and homogenized using Magnalyser Beads (Roche Diagnostics). Each sample was eluted in 40 µl RNase-free water and stored at − 80°C until required. RNA purity and yield was determined using NanoDrop-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and RNA integrity number (RIN) was assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) using RNA Nano LabChip Kit (Agilent Technologies), which were all of sufficient quality for sequencing (RIN > 9.0). One sample (control 0 yr) got lost during the RNA extraction and we proceeded with duplicate samples of the controls of 0 yr.
Per sample, a total of 1.5 µg total RNA was used for library preparation. Non-directional libraries were generated using the NEBNExt Ultra mRNA kit (New England Biolabs, USA) according the manufacturers recommendation’s. mRNA was enriched using oligo (dT) beads, followed by fragmentation, followed by first strand cDNA synthesis using random hexamers and M-MuLV reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library is generated after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. PCR products were purified with the AMPure XP system (Beckman, US) and library quality was checked on the Agilent Bioanalyzer 2100 system (Agilent, US). Libraries were analyzed in paired end 150 bp on the Hiseq 4000 (Illumina, US), using 150 bp paired end reads.

treatment_protocol: AB wild type adults zebrafish were exposed to 8.7 and 53 mGy/h during gametogenesis, F1 offspring was collected one month after exposure from control and exposed parents. After one year, exposed (only 8.7 mGy/h) and control parents were bred again and F1 generation was collected. In both cases total RNA was extracted and mRNA sequenced.

value: AB wild type

value: 5.5 hpf


title: Nmbu-RNA-13

description:
8.7 mGy/h 1 yr 2
embryos generation F1
isolated with trizol protocol from where mRNA selected and paired end seq


title: Nmbu-RNA-7

description:
Control 0 yr 1
embryos generation F1
isolated with trizol protocol from where mRNA selected and paired end seq

source_name: F1 embryos from non-exposed parents


title: Nmbu-RNA-12

description:
8.7 mGy/h 1 yr 1
embryos generation F1
isolated with trizol protocol from where mRNA selected and paired end seq


title: Nmbu-RNA-10

description:
Control 1 yr 2
embryos generation F1
isolated with trizol protocol from where mRNA selected and paired end seq

source_name: F1 embryos from non-exposed parents 1 year later


title: Nmbu-RNA-9

description:
Control 1 yr 1
embryos generation F1
isolated with trizol protocol from where mRNA selected and paired end seq


title: Nmbu-RNA-5

description:
53 mGy/h 0 yr 2
embryos generation F1
isolated with trizol protocol from where mRNA selected and paired end seq

source_name: F1 embryos from exposed parents 53 mGy/h


title: Nmbu-RNA-8

description:
Control 0 yr 2
embryos generation F1
isolated with trizol protocol from where mRNA selected and paired end seq


title: Nmbu-RNA-6

description:
53 mGy/h 0 yr 3
embryos generation F1
isolated with trizol protocol from where mRNA selected and paired end seq


title: MT02_8-Rep_2


title: Nmbu-RNA-2

description:
8.7 mGy/h 0 yr 2
embryos generation F1
isolated with trizol protocol from where mRNA selected and paired end seq

source_name: F1 embryos from exposed parents 8.7 mGy/h


title: Nmbu-RNA-4

description:
53 mGy/h 0 yr 1
embryos generation F1
isolated with trizol protocol from where mRNA selected and paired end seq


title: Nmbu-RNA-11

description:
Control 1 yr 3
embryos generation F1
isolated with trizol protocol from where mRNA selected and paired end seq

source_name: F1 embryos from non-exposed parents after 1 year


title: Nmbu-RNA-1

description:
8.7 mGy/h 0 yr 1
embryos generation F1
isolated with trizol protocol from where mRNA selected and paired end seq


title: Sample T12_10


title: Sample T0_2


title: KD shNega SOX17 locus

status: Public on Nov 04 2017

city: Kyoto

first: Takuya

last: Yamamoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: CiRA

country: Japan

institute: Kyoto University

data_processing:
Library strategy: ms4C-seq
Illumina adapter sequences were removed by cutadapt-1.4.2. Reads that contained the HindIII recognition sequence (AAGCTT) were used for the following analysis. Reads were separated into 47 baits by mapping the sequence from 1st bp to HindIII sites of read 1 to the 47 baits sequences using BWA (bwa-0.6.2). The processed read pairs excluding bait sequences were mapped to the hg19 reference genome by BWA (bwa-0.6.2). After removing self-ligation and undigested read pairs, PCR duplicates were removed by Picard (Picard-tools-1.97). The reads numbers mapped within 1,000 bp from each HindIII were counted, and the counted numbers in each HindIII site were given as wiggle format files. HindIII sites in repeat regions were ignored.
Genome_build: hg19
Supplementary_files_format_and_content: The wiggle (WIG) format files were generated for read counts in all HindIII positions outside of the repeated regions.

source_name: 428C2 iPSC

growth_protocol: iPSC (428C2) was cultured in DMEM/F12 supplemented with 20% KSR, L-glutamine, non-essential amino acid, 2-mercaptoethanol, penicillin/streptomycin and hbFGF on mitomycin-C-treated SNL feeder cells. HDFs (1388) was cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Chromosome conformation capture (3C) was performed as described previously (Lieberman-Aiden et al., 2009) in HDF and iPSC. The restriction enzyme HindIII was used for digesting DNA in the crosslinked nuclear. 3C library was purified by phenol chloroform extraction and PureLink® Genomic DNA Mini Kit (Invitrogen).
3C libraries were sonicated into 300 to 700 bp by covaris E210 system. Ends of the sonicated 3C library were repaired and A-tailed by NEBNext® Ultra™ End Repair/dA-Tailing Module (NEB E7442S) according to manufacturer's instructions. Splinkerette adapters were ligated to the dA-tailed 3C libraries by Ligation high Ver.2 (TOYOBO LGK-201). Adaptor ligated 3C libraries were purified with 1.8 x AMPureXP beads. Target (bait) loci were enriched by nested PCR using universal primers and bait primers. The amplified 3C libraries were resolved on 2% agalose gel, and the libraries between 350 bp and 700 bp were excised and purified with QIAquick Gel Extraction Kit (QIAGEN 28704). Quantification of the ms4C-Seq libraries was performed by Library Quantification Kits (KAPA KK4824)

treatment_protocol: SNL feeder cells were removed with CTK solution prior to 3C library preparation. In KD experiments, shRNAs for EED, RING1B and WDR5 were transfected into iPSC (428C2) and cultured in the mTeSR1 medium on matrigel coated dishes without feeder cells. Puromycin selection was performed from 2 days after transfection and those cells were harvested 4 days after transfection for preparation of ms4C-seq libraries.

tag: cell type

value: induced pluripotent stem cells

tag: bait


title: Nmbu-RNA-3

description:
8.7 mGy/h 0 yr 3
embryos generation F1
isolated with trizol protocol from where mRNA selected and paired end seq

tag: developmental stage


title: KD shNega PAX6 locus


title: KD shNega NEUROG2 locus


title: KD shNega NKX2-5 locus


title: KD WDR5-sh2 TWIST1 locus


title: KD shNega GSC locus

value: GSC


title: KD shNega NEUROD1 locus


title: KD WDR5-sh2 NEUROG2 locus


title: KD WDR5-sh2 NKX2-5 locus


title: KD WDR5-sh2 SOX17 locus


title: KD WDR5-sh2 PAX6 locus


title: KD WDR5-sh1 NEUROG2 locus


title: KD WDR5-sh1 SOX17 locus


title: KD WDR5-sh2 HOXA13 locus


title: KD WDR5-sh1 NKX2-5 locus


title: KD WDR5-sh2 NEUROD1 locus


title: KD WDR5-sh1 PAX6 locus


title: KD RING1B-sh2 TWIST1 locus


title: KD WDR5-sh1 HOXA13 locus


title: KD WDR5-sh1 NEUROD1 locus


title: KD shNega TWIST1 locus


title: KD shNega HOXA13 locus


title: KD RING1B-sh2 NEUROG2 locus


title: KD RING1B-sh2 PAX6 locus


title: KD RING1B-sh2 NKX2-5 locus


title: KD RING1B-sh2 NEUROD1 locus


title: KD RING1B-sh2 HOXA13 locus


title: KD RING1B-sh1 TWIST1 locus


title: KD WDR5-sh2 GSC locus


title: KD RING1B-sh2 GSC locus


title: KD WDR5-sh1 TWIST1 locus


title: KD WDR5-sh1 GSC locus


title: KD RING1B-sh1 PAX6 locus


title: KD RING1B-sh1 SOX17 locus


title: KD RING1B-sh1 GSC locus


title: KD RING1B-sh1 NKX2-5 locus


title: KD RING1B-sh1 NEUROG2 locus


title: KD RING1B-sh1 NEUROD1 locus


title: KD RING1B-sh2 SOX17 locus


title: KD RING1B-sh1 HOXA13 locus


title: KD EED-sh2 TWIST1 locus


title: KD EED-sh1 TWIST1 locus


title: KD EED-sh2 GSC locus


title: KD EED-sh2 PAX6 locus


title: KD EED-sh2 NEUROG2 locus


title: KD EED-sh2 NEUROD1 locus


title: KD EED-sh2 HOXA13 locus


title: Salmonella/H.poly Cell 18

description: Full-length RNAseq (SMART-Seq2) reads

source_name: WT Mouse intestinal epithelial cells

tag: genotype

value: Wild type

value: H. polygyrus (Day 3)


title: KD EED-sh1 PAX6 locus


title: KD EED-sh2 SOX17 locus


title: KD EED-sh1 NEUROG2 locus


title: KD EED-sh1 SOX17 locus


title: KD EED-sh1 NEUROD1 locus


title: KD EED-sh1 HOXA13 locus


title: Ex.2 hiPS VPREB1 locus


title: KD EED-sh2 NKX2-5 locus


title: Ex.2 hiPS TNFSF8 locus


title: Ex.2 hiPS STX5 locus


title: Ex.2 hiPS YTHDF2 locus


title: Ex.2 hiPS ZFP42 locus


title: Ex.2 hiPS YBX1 locus


title: Ex.2 hiPS PTPRZ1 locus


title: Ex.2 hiPS ZZZ3 locus


title: Ex.2 hiPS SLC34A1 locus


title: KD EED-sh1 NKX2-5 locus


title: Ex.2 hiPS PRSS3 locus


title: Ex.2 hiPS NCL locus

value: NCL


title: Ex.2 hiPS OBP2B locus


title: Ex.2 hiPS PRAME locus

value: PRAME


title: Ex.2 hiPS PODXL locus

value: PODXL


title: KD EED-sh1 GSC locus


title: Ex.2 hiPS LIG1 locus


title: Ex.2 hiPS KRTAP5-11 locus


title: Ex.2 hiPS KIF2A locus


title: Ex.2 hiPS KDM2B locus


title: Ex.2 hiPS TAF2 locus


title: Ex.2 hiPS SALL4 locus


title: Ex.2 hiPS TREM1 locus


title: Ex.2 hiPS MC3R locus


title: Ex.2 hiPS HEMGN locus

value: HEMGN


title: Ex.2 hiPS GIMAP1 locus


title: Ex.2 hiPS IGLL5 locus


title: Ex.2 hiPS GAST locus

value: GAST


title: Ex.2 hiPS FLRT1 locus


title: Ex.2 hiPS MYCN locus

value: MYCN


title: Ex.2 hiPS MITD1 locus


title: Ex.2 hiPS METAP2 locus


title: Ex.2 hiPS DNMT3B locus


title: Ex.2 hiPS DPH3 locus


title: Ex.2 hiPS DEFB132 locus


title: Ex.2 hiPS FGFR2 locus


title: Ex.2 hiPS COLQ locus

value: COLQ


title: Ex.2 hiPS CBLN2 locus


title: Ex.2 hiPS LIN28B locus


title: Ex.2 hiPS ACO2 locus


title: Ex.2 hiPS ANKRD1 locus


title: Ex.2 hiPS BCAT1 locus


title: Ex.1 hiPS ZZZ3 locus


title: Ex.1 hiPS ZFP42 locus


title: Ex.1 hiPS YTHDF2 locus


title: Ex.1 hiPS YBX1 locus


title: Ex.1 hiPS VPREB1 locus


title: Ex.1 hiPS TAF2 locus


title: Ex.1 hiPS TNFSF8 locus


title: Ex.1 hiPS SALL4 locus


title: Ex.1 hiPS SOX6 locus


title: Ex.1 hiPS STX5 locus


title: Ex.1 hiPS SLC34A1 locus


title: Ex.1 hiPS PRAME locus


title: Ex.1 hiPS PRSS3 locus


title: Ex.1 hiPS PODXL locus


title: Ex.1 hiPS MC3R locus


title: Ex.1 hiPS OBP2B locus


title: Ex.1 hiPS METAP2 locus


title: Ex.1 hiPS PTPRZ1 locus


title: Ex.1 hiPS NCL locus


title: Ex.2 hiPS ARHGEF38 locus


title: Ex.1 hiPS MYCN locus

treatment_protocol: SNL feeder cells were removed with CTK solution prior to 3C library preparation. In KD experiments, shRNAs for EED, RING1B and WDR5 were transfected into iPSC (428C2) and cultured in the mTeSR1 medium on matrigel coated dishes without feeder cells. Puromycin selection was performed from 2 days after transfection and those cells were harvested 4 days after transfection for preparation of ms3C-seq libraries.


title: Ex.1 hiPS MITD1 locus


title: Ex.1 hiPS LIN28B locus


title: Ex.1 hiPS LIG1 locus


title: Ex.1 hiPS KDM2B locus


title: Ex.1 hiPS GAST locus


title: Ex.1 hiPS KRTAP5-11 locus


title: Ex.1 hiPS HEMGN locus


title: Ex.1 hiPS TREM1 locus


title: Ex.1 hiPS GIMAP1 locus


title: Ex.1 hiPS FLRT1 locus


title: Ex.1 hiPS KIF2A locus


title: Ex.1 hiPS FGFR2 locus


title: Ex.1 hiPS DNMT3B locus


title: Ex.1 hiPS DPH3 locus


title: Ex.1 hiPS DEFB132 locus


title: Ex.1 hiPS CBLN2 locus


title: Ex.1 hiPS BCAT1 locus


title: Ex.1 hiPS COLQ locus


title: Ex.1 hiPS ACO2 locus


title: Ex.1 hiPS ANKRD1 locus


title: Ex.2 HDF TCF21 locus

source_name: TIG120 HDF

value: Human dermal fibroblasts


title: Ex.2 HDF SST locus

value: SST


title: Ex.1 hiPS IGLL5 locus


title: Ex.2 hiPS SOX6 locus


title: Ex.2 HDF TBX6 locus


title: Ex.2 HDF TWIST1 locus


title: Ex.2 HDF ZIC1 locus


title: Ex.1 hiPS ARHGEF38 locus


title: Ex.2 HDF SOX2 locus


title: Ex.2 HDF SOX7 locus


title: Ex.2 HDF SOX1 locus


title: Ex.2 HDF SNAI1 locus


title: Ex.2 HDF POU5F1 locus


title: Ex.2 HDF PAX6 locus


title: Ex.2 HDF PAX3 locus


title: Ex.2 HDF NKX2-5 locus


title: Ex.2 HDF NEUROD4 locus


title: Ex.2 HDF NEUROD1 locus


title: Ex.2 HDF NEUROG2 locus


title: Ex.2 HDF NR2F2 locus


title: Ex.2 HDF NANOG P locus


title: Ex.2 HDF NANOG locus

value: NANOG


title: Ex.2 HDF T locus

value: T


title: Ex.2 HDF KLF4 locus


title: Ex.2 HDF LHX1 locus


title: Ex.2 HDF MESP1 locus


title: Ex.2 HDF intergenic4 locus


title: Ex.2 HDF intergenic2 locus


title: Ex.2 HDF intergenic3 locus


title: Ex.2 HDF intergenic5 locus


title: Ex.2 HDF SOX17 locus


title: Ex.2 HDF HNF4A locus


title: Ex.2 HDF GATA4 locus


title: Ex.2 HDF GSC locus


title: Ex.2 HDF GATA6 locus


title: Ex.2 HDF HOXA13 locus


title: Ex.2 HDF intergenic1 locus


title: Ex.2 HDF GATA5 locus


title: Ex.2 HDF FOXA2 locus


title: Ex.2 HDF ETS2 locus


title: Ex.2 HDF FOXF1 locus


title: Ex.2 HDF GAPDH locus

value: GAPDH


title: Ex.2 HDF EOMES locus

value: EOMES


title: Ex.2 HDF EVX1 locus


title: Ex.2 HDF COL2A1 locus


title: Ex.2 HDF ASCL2 locus


title: Ex.2 HDF ERCC3 locus


title: Ex.2 HDF DPPA4 locus


title: Ex.2 HDF ASCL1 locus


title: Ex.2 HDF MIXL1 locus


title: Ex.2 hiPS ZIC1 locus

value: induced pluripotent stem cells


title: Ex.2 hiPS T locus


title: Ex.2 hiPS TWIST1 locus


title: Ex.2 hiPS TCF21 locus


title: Ex.2 hiPS TBX6 locus


title: Ex.2 hiPS SST locus


title: Ex.2 hiPS SOX7 locus


title: Ex.2 hiPS SOX17 locus


title: Ex.2 hiPS SOX1 locus


title: Ex.2 hiPS SNAI1 locus


title: Ex.2 hiPS PAX3 locus


title: Ex.2 hiPS POU5F1 locus


title: Ex.2 hiPS NR2F2 locus


title: Ex.2 hiPS NEUROD4 locus


title: Ex.2 hiPS NKX2-5 locus


title: Ex.2 hiPS NEUROD1 locus


title: Ex.2 hiPS NANOG locus


title: Ex.2 hiPS PAX6 locus


title: Ex.2 hiPS NANOG P locus


title: Ex.2 hiPS NEUROG2 locus


title: Ex.2 hiPS MIXL1 locus


title: Ex.2 hiPS MESP1 locus


title: Ex.2 hiPS intergenic5 locus


title: Ex.2 hiPS KLF4 locus


title: Ex.2 hiPS intergenic2 locus


title: Ex.2 hiPS intergenic3 locus


title: Ex.2 hiPS LHX1 locus


title: Ex.2 hiPS HOXA13 locus


title: Ex.2 hiPS HNF4A locus


title: Ex.2 hiPS intergenic1 locus


title: Ex.2 hiPS GSC locus

value: GSC


title: Ex.2 hiPS GATA6 locus

extract_protocol:
Chromosome conformation capture (3C) was performed as described previously (Lieberman-Aiden et al., 2009) in HDF and iPSC. The restriction enzyme HindIII was used for digesting DNA in the crosslinked nuclear. 3C library was purified by phenol chloroform extraction and PureLink® Genomic DNA Mini Kit (Invitrogen).
3C libraries were sonicated into 300 to 700 bp by covaris E210 system. Ends of the sonicated 3C library were repaired and A-tailed by NEBNext® Ultra™ End Repair/dA-Tailing Module (NEB E7442S) according to manufacturer's instructions. Splinkerette adapters were ligated to the dA-tailed 3C libraries by Ligation high Ver.2 (TOYOBO LGK-201). Adaptor ligated 3C libraries were purified with 1.8 x AMPureXP beads. Target (bait) loci were enriched by nested PCR using universal primers and bait primers. The amplified 3C libraries were resolved on 2% agalose gel, and the libraries between 350 bp and 700 bp were excised and purified with QIAquick Gel Extraction Kit (QIAGEN 28704). Quantification of the ms34C-Seq libraries was performed by Library Quantification Kits (KAPA KK4824)


title: Ex.2 hiPS GATA5 locus


title: Ex.2 hiPS GATA4 locus


title: Ex.2 hiPS FOXA2 locus


title: Ex.2 hiPS EVX1 locus


title: Ex.2 hiPS FOXF1 locus


title: Ex.2 hiPS ERCC3 locus


title: Ex.2 hiPS ETS2 locus


title: Ex.2 hiPS intergenic4 locus


title: Ex.2 hiPS EOMES locus


title: Ex.1 HDF ZIC1 locus


title: Ex.2 hiPS COL2A1 locus


title: Ex.1 HDF TWIST1 locus


title: Ex.1 HDF T locus


title: Ex.1 HDF TBX6 locus


title: Ex.1 HDF SOX17 locus


title: Ex.2 hiPS ASCL1 locus


title: Ex.1 HDF SST locus


title: Ex.1 HDF SOX1 locus


title: Ex.1 HDF SOX7 locus


title: Ex.2 hiPS DPPA4 locus


title: Ex.1 HDF SOX2 locus


title: Ex.2 hiPS SOX2 locus


title: Ex.2 hiPS GAPDH locus


title: Ex.1 HDF SNAI1 locus


title: Ex.1 HDF PAX3 locus


title: Ex.1 HDF POU5F1 locus


title: Ex.1 HDF NR2F2 locus


title: Ex.1 HDF PAX6 locus


title: Ex.1 HDF NEUROG2 locus


title: Ex.1 HDF NKX2-5 locus


title: Ex.1 HDF TCF21 locus


title: Ex.2 hiPS ASCL2 locus


title: Ex.1 HDF NEUROD1 locus


title: Ex.1 HDF NEUROD4 locus


title: Ex.1 HDF NANOG P locus


title: Ex.1 HDF MIXL1 locus


title: Ex.1 HDF NANOG locus


title: Ex.1 HDF KLF4 locus


title: Ex.1 HDF intergenic4 locus


title: Ex.1 HDF intergenic5 locus


title: Ex.1 HDF MESP1 locus


title: Ex.1 HDF LHX1 locus


title: Ex.1 HDF intergenic3 locus


title: Ex.1 HDF GATA6 locus


title: Ex.1 HDF HNF4A locus


title: Ex.1 HDF intergenic2 locus


title: Ex.1 HDF intergenic1 locus


title: Ex.1 HDF GSC locus


title: Ex.1 HDF HOXA13 locus


title: Ex.1 HDF GAPDH locus


title: Ex.1 HDF GATA4 locus


title: Ex.1 HDF FOXF1 locus


title: Ex.1 HDF EVX1 locus


title: Ex.1 HDF FOXA2 locus


title: Ex.1 HDF EOMES locus

extract_protocol:
Chromosome conformation capture (3C) was performed as described previously (Lieberman-Aiden et al., 2009) in HDF and iPSC. The restriction enzyme HindIII was used for digesting DNA in the crosslinked nuclear. 3C library was purified by phenol chloroform extraction and PureLink® Genomic DNA Mini Kit (Invitrogen).
3C libraries were sonicated into 300 to 700 bp by covaris E210 system. Ends of the sonicated 3C library were repaired and A-tailed by NEBNext® Ultra™ End Repair/dA-Tailing Module (NEB E7442S) according to manufacturer's instructions. Splinkerette adapters were ligated to the dA-tailed 3C libraries by Ligation high Ver.2 (TOYOBO LGK-201). Adaptor ligated 3C libraries were purified with 1.8 x AMPureXP beads. Target (bait) loci were enriched by nested PCR using universal primers and bait primers. The amplified 3C libraries were resolved on 2% agalose gel, and the libraries between 350 bp and 700 bp were excised and purified with QIAquick Gel Extraction Kit (QIAGEN 28704). Quantification of the ms3C-Seq libraries was performed by Library Quantification Kits (KAPA KK4824)


title: Ex.1 HDF COL2A1 locus


title: Ex.1 HDF DPPA4 locus


title: Ex.1 HDF ETS2 locus


title: Ex.1 HDF ASCL1 locus


title: Ex.1 HDF ERCC3 locus


title: Ex.1 HDF ASCL2 locus


title: Ex.1 hiPS TBX6 locus


title: Ex.1 HDF GATA5 locus


title: Ex.1 hiPS TCF21 locus


title: Ex.1 hiPS T locus


title: Ex.1 hiPS ZIC1 locus


title: Ex.1 hiPS SNAI1 locus


title: Ex.1 hiPS TWIST1 locus


title: Ex.1 hiPS SOX7 locus


title: Ex.1 hiPS PAX6 locus


title: Ex.1 hiPS PAX3 locus


title: Ex.1 hiPS SOX17 locus


title: Ex.1 hiPS SOX2 locus


title: Ex.1 hiPS NEUROG2 locus


title: Ex.1 hiPS NEUROD4 locus

data_processing:
Library strategy: ms43C-seq
Illumina adapter sequences were removed by cutadapt-1.4.2. Reads that contained the HindIII recognition sequence (AAGCTT) were used for the following analysis. Reads were separated into 47 baits by mapping the sequence from 1st bp to HindIII sites of read 1 to the 47 baits sequences using BWA (bwa-0.6.2). The processed read pairs excluding bait sequences were mapped to the hg19 reference genome by BWA (bwa-0.6.2). After removing self-ligation and undigested read pairs, PCR duplicates were removed by Picard (Picard-tools-1.97). The reads numbers mapped within 1,000 bp from each HindIII were counted, and the counted numbers in each HindIII site were given as wiggle format files. HindIII sites in repeat regions were ignored.
Genome_build: hg19
Supplementary_files_format_and_content: The wiggle (WIG) format files were generated for read counts in all HindIII positions outside of the repeated regions.


title: Ex.1 hiPS SST locus

treatment_protocol: SNL feeder cells were removed with CTK solution prior to 4C library preparation. In KD experiments, shRNAs for EED, RING1B and WDR5 were transfected into iPSC (428C2) and cultured in the mTeSR1 medium on matrigel coated dishes without feeder cells. Puromycin selection was performed from 2 days after transfection and those cells were harvested 4 days after transfection for preparation of ms3C-seq libraries.


title: Ex.1 hiPS NANOG P locus


title: Ex.1 hiPS SOX1 locus


title: Ex.1 hiPS NEUROD1 locus


title: Ex.1 hiPS MIXL1 locus


title: Ex.1 hiPS POU5F1 locus


title: Ex.1 hiPS LHX1 locus


title: Ex.1 hiPS MESP1 locus


title: Ex.1 hiPS intergenic5 locus


title: Ex.1 hiPS NANOG locus


title: Ex.1 hiPS NR2F2 locus


title: Ex.1 hiPS intergenic2 locus


title: Ex.1 hiPS intergenic1 locus


title: Ex.1 hiPS KLF4 locus


title: Ex.1 hiPS GATA6 locus


title: Ex.1 hiPS GATA5 locus


title: Ex.1 hiPS intergenic3 locus


title: Ex.1 hiPS GSC locus


title: Ex.1 hiPS HOXA13 locus


title: Ex.1 hiPS NKX2-5 locus


title: Ex.1 hiPS HNF4A locus


title: Normal rep3

city: Chengdu

first: Linyuan

last: Shen

state: Sichuan

address: 211# Huiming Road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

data_processing:
Clean data were obtained by removing reads containing adapters, reads containing over 10% of poly(N), and lowquality reads (> 50% of the bases had Phred quality scores ≤ 10) from the raw data.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.14.
The mapped reads from each library were assembled with Cufflinks v2.2.1. We used the reference annotation based transcript (RABT) assembly method in Cufflinks v2.2.1 to construct and identify mRNA transcripts from the TopHat2 alignment results.
Cuffdiff v2.1.1 was used to calculate FPKM (fragment per kilobase of exon model per million mapped reads) scores for transcripts in each library.
Differentially exprssed genes (DEGs) were identified by edgeR (release 3.2). The statistical significance of gene expression differences was evaluated using an adjusted P value (Q value) < 0.01 and an |log2(fold change)| ≥ 2 as the threshold.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: liver

growth_protocol: A total of 8 pairs of normal brith weight (~1.49 kg ) and IUGR (~0.97 kg) PIC breeding piglets chosen from 8 sows were used in this study. Live in same environment at 150 days old.

extract_protocol:
Total RNA was extracted from liver using TRIzol (Invitrogen, CA, USA) and further  purified with RNeasy column (Qiagen, USA) according to the manufacturer’s protocol. RNA integrity and concentration were analysis with the Bioanalyzer 2100 (Agilent Technologies) and NanoDrop (Thermo Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PIC

value: liver

tag: age

value: 150 days


title: IUGR rep3


title: IUGR rep2


title: Ex.1 hiPS intergenic4 locus


title: Ex.1 hiPS GAPDH locus


title: IUGR rep1


title: Ex.1 hiPS FOXF1 locus


title: Normal rep2


title: Normal rep1


title: Ex.1 hiPS FOXA2 locus


title: small RNA Control rep3

data_processing:
Sequence  reads  that  fit  any  of  the  following  parameters  were  removed  with  following   standard quality control criteria: 1) The reads with N; more than 4 bases whose quality score   is lower  than  10 or more  than  6 bases whose quality  score is lower  than 13. 2) The  reads   with 5’ primer contaminants or without 3’ primer. 3) The reads without the insert tag. 4) The   reads with ploy A. 5) The reads shorter than 18nt. The clean reads were obtained after data   filtration.
Mapping to genome: Small RNA tags were mapped to rat genome (Rnor_5.0) by SOAP to analyze their distribution and expression on the genome.
Small RNA Annotation: Small RNA tags were annotated with miRNA, tRNA, rRNA and other  small  noncoding  RNA  from  miRBase19,  Genbank  and  Rfam  databases  using  blastn  with  standard parameters: ‐F F ‐e 0.01. rRNA reads were removed for length distribution analysis.
Differentially expressed TRFs were generated by DEGseq
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: Read abundance and tRFs sequence for each Sample

organism: Rattus norvegicus

source_name: heart

extract_protocol:
Total RNAs are extracted by Trizol (Invitrogen). 1-2 μg total RNAs were separated by denatured 15% PAGE with 7M urea. The gel was stained with SYBR Green I solution (Invitrogen). Small RNAs sized at 15-40 nt were excised from the gel were uesd to construct small RNA-sequencing library and sequenced on an Illumina Hi-Seq 2000 apparatus.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 6 week old male Sprague Dawley (SD) rats were randomly divided into two groups: Control (Con: saline administration through subcutaneous,14 days, n=8) and Hypertrophy (Hyp: isoproterenol administration through subcutaneous,14 days,5 mg/kg/day, n= 8).

value: Sprague Dawley

value: heart

value: 8 weeks

tag: Sex

value: male


title: Ex.1 hiPS EVX1 locus


title: small RNA Control rep2


title: Ex.1 hiPS ETS2 locus


title: Ex.1 hiPS ERCC3 locus


title: Ex.1 hiPS EOMES locus


title: small RNA Control rep1


title: small RNA ISO rep3


title: Ex.1 hiPS GATA4 locus


title: Ex.1 hiPS DPPA4 locus


title: small RNA ISO rep2


title: Ex.1 hiPS ASCL1 locus


title: small RNA ISO rep1


title: Ex.1 hiPS ASCL2 locus


title: Ex.1 hiPS COL2A1 locus


title: Nalm6_BCL11A_ChIPSeq

status: Public on Nov 03 2017

city: Austin

first: Bum-Kyu

last: Lee

state: TX

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

description: Chromatin IP against BCL11A

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mouse hg18 genome using BWA version 0.5.9-r16.
Peaks were called using  a Parzen window based algorithm (LEE et al, 2011. Nucleic Acis Res. 39(9):3558-73).
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak

source_name: peripheral blood pre-B cell leukemia

growth_protocol: Cells were grown in DMEM supplemented L-glutamine, 10% FBS, and 1% PenStrep

extract_protocol:
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNA was applied for generation of sequencing libraries using the NEB ChIP-seq library prep. kit (E6200L ) following by manufacturer’s instructions.

value: peripheral blood pre-B cell leukemia

tag: chip antibody

value: Anti-BCL11a polyclonal (Bethyl Labs BL1797)


title: Raji_BCL11A_ChIPSeq

description: Chromatin IP against BCL11A

source_name: Burkitt lymphoma

value: Burkitt lymphoma


title: At_mesophyll.cell.ATAC_rep3

city: Atlanta

first: Roger

middle: B

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

data_processing:
Raw reads were aligned to the Arabidopsis TAIR10 genome using Bowtie2 with default parameters
Mapped reads were filtered to remove those mapping to organelle genomes, and reads with a mapping quality score of q>2 were retained for further analysis.
Peaks (transposase hypersensitive sites; THSs) were identified using the Findpeaks function of the Homer package, with the parameters "-region" "-minDist 150" and "-regionRes 1". Bed files of the THS regions are included for each dataset.
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: .bed files containing ATAC-seq transposase hypersensitive site locations as defined using the findPeaks function of the Homer software package.

organism: Arabidopsis thaliana

source_name: Leaves 5 and 6 from 21 day old plants

growth_protocol: All plants were grown under 16hr light/8 hr dark cycles on 1/2 MS plates for seedling collection (for stem cell) and on soil for leaf tissue collection (for mesophyll cells)

extract_protocol:
Tn5 Transposase treatment (Using the Illumina Nextera kit) was performed on 25,000 nuclei from each sample, followed by isolation of fragmented genomic DNA using the Qiagen PCR purification kit.
Purified transposase-fragmented DNAs were converted to sequencing libraries through a limited number of PCR cycles using indexed primers, followed by purification of library fragments using SPRI beads.

treatment_protocol: Entire shoot systems were collected from seedlings for purification of stem cell nuclei. Leaves number 5 and 6 were collected for purification of mesophyll cell nuclei. Niclei from each tissue were purified by INTACT.

value: mesophyll cell

tag: nuclei purification method

value: INTACT streptavidin affinity purification

tag: ecotype


title: At_stem.cell.ATAC_rep1

source_name: 6 day old seedling

value: CLV3-expressing stem cell


title: At_mesophyll.cell.ATAC_rep2


title: At_stem.cell.ATAC_rep2


title: At_stem.cell.ATAC_rep3


title: At_mesophyll.cell.ATAC_rep1


title: CO_WT_180_23

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

data_processing:
Color-space base calling
Mapping, alignment with Lifescope
Lifescope transcriptome workflow
Genome_build: hg19
Supplementary_files_format_and_content: counts data

source_name: skin

growth_protocol: samples from the skin

extract_protocol:
After local anesthesia and under standard aseptic conditions, 4 mm punch biopsies were taken. After subcutaneous fat tissue removal, the skin biopsies were directly snap frozen in liquid nitrogen. To further minimize potential RNA degradation by skin RNAses, biopsies were not stored at -80° C, but directly processed for RNA extraction. Skin biopsies were homogenized in TRIZOL (Ambion, Austin, TX) and thereafter centrifuged to eliminate contaminating fat prior extraction with chloroform. After precipitation using isopropanol at -20°C, RNA was washed twice with ethanol and then re-suspended in Tris-EDTA buffer (Ambion, Austin, TX). Then, samples were incubated at 57°C for 10 min and RNA concentration was determined by using a NanoDrop (Thermoscientific, Waltham, MA). RNA quality was assessed by using a Bioanalyzer chip assay (Agilent technologies, Santa Clara, CA). Samples were stored at -80°C until RNA sequencing.
50 ng of total RNA were amplified by applying Ovation RNA-Seq System V2 (NuGen, Emeryville, CA). The resulting cDNAs were pooled in equal amount and used to prepare the DNA fragment library with SOLiD System chemistry (Life Technologies Corp., Carlsbad, CA). Sequencing was performed using SOLiD 5500W platform and DNA sequencing chemistry (Life Technologies Corp., Carlsbad, CA). Raw reads (75 bp) were color-space mapped to the human genome hg19 reference using Maxmapper algorithm implemented in the Lifescope software (Life Technologies Corp., Carlsbad, CA). Mapping to multiple locations was permitted. Reads with score less than 10 were excluded. Average mapping quality was 30. Analysis of the RNA content and gene-based annotation was done with whole-transcriptome work- flow of Lifescope.

treatment_protocol: mutation or wild-type

tag: disease

value: control (CO)

tag: mutation

value: WT


title: CO_WT_179_22


title: CO_WT_177_21


title: CO_WT_176_20


title: CO_WT_175_19


title: CO_WT_170_18


title: CO_WT_165_16


title: CO_WT_164_15


title: IV_r501x2447x_155_13

value: ichthyosis vulgaris (IV)

value: FLG mutation


title: IV_r2447x2282del4_150_12


title: Nalm6_Input

description: Input

value: preimmune rabbit IgG (Bethyl Labs P120-101)


title: AD_r501x_153_9

value: atopic dermatitis (AD)


title: EE3447

source_name: bone paraffin section FFPE

growth_protocol: samples from the FFPE bone

extract_protocol:
For each FFPE sample, 6 pieces of 10 μm thick sections were used. RNA was extracted with PureLink FFPE Total RNA Isolation Kit from Invitrogen (Invitrogen Corporation, Carlsbad, CA, USA). For all samples (fresh and FFPE) osteosarcoma was confirmed samples by two independent pathologists
50 ng of total RNA was amplified by applying Ovation RNA-Seq System V2 (NuGen, Emeryville, CA, USA) after which the resulting cDNAs were pooled in equal amount and the pool was used to prepare the DNA fragment library with SOLiD System chemistry (Life Technologies Corp., Carlsbad, CA, USA). Sequencing was performed using SOLiD 5500W platform and DNA sequencing chemistry (Life Technologies Corp., Carlsbad, CA, USA). Raw reads (75 bp) were color-space mapped to the human genome hg19 reference using Maxmapper algorithm implemented in the Lifescope software (Life Technologies, Ltd). Mapping to multiple locations was permitted. The quality threshold was set to 10 giving the mapping confidence more than 90. Reads with score less than 10 were filtered out. Average mapping quality was 30. Analysis of the RNA content and gene-based annotation was done within whole transcriptome workflow implemented in Lifescope.

treatment_protocol: paraffin sections

tag: subject status

value: osteosarcoma patient

tag: chemotherapy

value: yes

tag: tissue

value: osteosarcoma bone; tumor

tag: sample type

value: paraffin section FFPE


title: AD_r501x2282del4_172_10


title: IV_wt2282del4_148_11


title: AD_WT_149_1


title: AD_WT_152_2


title: EE6065

value: female


title: EE6762

value: male


title: EE9244

value: no


title: EE4878


title: AD_WT_168_7


title: Raji_Input

description: Input

value: Burkitt lymphoma


title: EE13536


title: AD_WT_154_3


title: AD_WT_161_5


title: EE1480


title: AD_r501x_151_8


title: AD_WT_162_6


title: EE6921


title: AD_WT_157_4


title: VN25065


title: CO_WT_166_17


title: EE8076


title: IV_2282del42282del4_159_14


title: VN21890


title: VN26391


title: EE648


title: EE6311


title: OSHN016L_BC10

source_name: bone

growth_protocol: samples from the bone

extract_protocol:
Bone samples (40-50 mg) were grinded with nitrogen by pestle and mortar into powder and pretreated with trizol. Total RNA was extracted with RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia CA, USA) according to the manufacturer’s protocol.
50 ng of total RNA was amplified by applying Ovation RNA-Seq System V2 (NuGen, Emeryville, CA, USA) after which the resulting cDNAs were pooled in equal amount and the pool was used to prepare the DNA fragment library with SOLiD System chemistry (Life Technologies Corp., Carlsbad, CA, USA). Sequencing was performed using SOLiD 5500W platform and DNA sequencing chemistry (Life Technologies Corp., Carlsbad, CA, USA). Raw reads (75 bp) were color-space mapped to the human genome hg19 reference using Maxmapper algorithm implemented in the Lifescope software (Life Technologies, Ltd). Mapping to multiple locations was permitted. The quality threshold was set to 10 giving the mapping confidence more than 90. Reads with score less than 10 were filtered out. Average mapping quality was 30. Analysis of the RNA content and gene-based annotation was done within whole transcriptome workflow implemented in Lifescope.

treatment_protocol: opaired tumor and normal bone samples

tag: tumor

value: NORMAL

tag: barcode


title: OSHN017B_BC12

value: TUMOR


title: OSHN014L_BC4


title: OSVN015B_BC5


title: OSHN016B_BC9


title: OSVN015M_BC6


title: OSHN017L_BC11


title: VN23611


title: WT_pre-B_VkJk-seq_rep1

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq1000 platforms using the default RTA analysis software.
Sequences were trimmed for adaptors and low quality (Phred < 20) using TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and demultiplexed based on Truseq barcodes. Due to the similarity of the J primers, the sequencing quality can drop at positions 3-4 for the J reads (read 2). The first four bases were therefore trimmed off all J read sequences. Chimaeric J reads produced through mis-priming of a Jκ gene with the incorrect Jκ-PE2 PCR primer were identified by examining the sequence immediately downstream of the primer binding sites, and a find-and-replace step was used to replace the incorrect Jκ primer sequences within commonly occurring chimaeras with the correct primer sequence. Thereafter, the Jκ primer (‘bait’) sequences were used to assign each read to the corresponding Jκ gene. Any sequence without a bait was discarded. Sequences were further filtered to exclude any that had less than 20 bases downstream of the bait in read 2, or that did not include one of the two anchor sequences following the molecular identifier in read 1. The V end reads (read 1), excluding the first 15 bases which comprise the molecular identifier and anchor sequence, were aligned to the NCBIM37/mm9 mouse genome assembly using Bowtie, discarding multimapping hits (-m 1 --strata --best). The data was deduplicated based on the sequence of the molecular identifier (6N), the sequence downstream of the bait in read 2, which includes the Vκ-Jκ junctions, and the start position of the V read alignment. Any paired reads identical for all criteria were considered PCR duplicates, and only one was retained. Finally, aligned read 1 sequences were output as Bowtie mapped BAM files.
Genome_build: NCBIM37/mm9
Quantitated VkJk-seq datafile is tab delimited and contains the following columns: (1) Igk V gene name; (2) Chromosome; (3) Start; (4) End; (5) Strand; (6-21) Count of unique sense-oriented (relative to V gene) reads that are associated with each Jk gene over the 750bp proximal to the V RSS encompassing the V exon, intron, leader exon and ~200bp of proximal sequence.

growth_protocol: All cells were depleted of non-B lineage cells by magnetic cell sorting, and then flow sorted for pre-B cells, directly from bone marrow single cell suspensions

extract_protocol:
Genomic DNA was isolated using a Qiagen Dneasy blood and tissue kit
For each sample 10 µg genomic DNA was sonicated to 400 bp using a Covaris E220 sonicator. Except where AMPure XP beads were used, all following reactions were cleaned up by column purification (Qiagen QIAquick PCR purification kit). Fragmented DNA was end-repaired and A-tailed using standard protocols. Samples were divided in half and short asymmetric adaptors, including a molecular identifier and one of two different anchor sequences, were ligated to both ends of all fragments (T4 DNA ligase, NEB); the two ligations were then pooled. Primer extension (8 x 50 µl; 2 units NEB Vent Exo- polymerase per reaction) using biotinylated primers annealing downstream of all functional Jk genes (Jk1, 2, 4 and 5) allowed enrichment of fragments containing a Jk gene using streptavidin beads (My-one C1; Invitrogen), following the manufacturer’s protocol with incubation overnight, rotating at room temperature (20 μl beads per sample). After washing the beads, 4 cycles of PCR amplification off the beads were performed, using an Illumina PE1 primer corresponding to the long strand of the asymmetric adaptors, in combination with Jk-specific PE2 primers (4 x 25 μl; Pwo master mix, Roche). A second primer extension reaction (4 x 50 μl) using biotinylated primers that anneal within intergenic regions upstream of each functional Jk gene (ie present only when unrecombined) was then performed. Unrecombined sequences were removed using streptavidin beads, with a 4 hour incubation at room temperature. The remaining DNA fragments, containing the Vk-Jk recombined sequences, were further enriched, with 11 additional PCR cycles using the same primers as above. PCR products were cleaned up, and small products removed, using AMPure XP beads (1 x; Beckman Coulter). A final PCR amplification of 5 cycles was performed to add the flowcell-binding portions of the PE1 and PE2 adaptors, including Truseq bar codes within PE2. Final libraries were purified and size-selected by double-sided AMPure XP bead purification (0.5 x followed by 1 x), before quality control using a high sensitivity DNA assay on the Agilent Bioanalyzer, and KAPA qPCR.

value: bone marrow

tag: cell type

value: ex vivo flow sorted pre-B cells

tag: markers


title: OSHN012L_BC12


title: OSHN013B_BC1


title: OSHN012B_BC11


title: WT_pre-B_VkJk-seq_rep2


title: OSHN011N_BC10


title: hF9_Exp5_Arm2_H4_M

city: Carlsbad

first: Sagar

middle: S

last: Damle

state: CA

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

data_processing:
demultiplexing and base-calling was performed by Illumina bcl2fastq2 software (version 2.17.1.14)
reads were associated to transcripts using a quasi-mapping based mode of Salmon  (version 0.7.2)
gene-level TPM was computed by normalizing number of reads mapped per transcript by number of mapped reads, using gene models from mouse ensembl build 81.  Salmon TPM column was disregarded
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited files containing standard salmon output (ensembl transcript id, Number mapped reads per transcript, and salmon-computed TPM)

growth_protocol: Mice grown under standard husbandry protocol that is approved by the institutional Animal Care and Use Committee at Ionis Pharmaceuticals

extract_protocol:
Animal tissues were homogenized in guanidine isothiocyanate solution (Invitrogen) supplemented with 8% 2-mercaptoethanol (Sigma-Aldrich). Total RNA was prepared using the RNeasy Mini Kit (Qiagen).
Illumina TruSeq Single Index Library Prep Kit

treatment_protocol: hFIX-R29X mice 8-14 weeks of age (n=3-4/group) were treated every 5 days with 6 total doses of DPBS, Control-GalNAc-ASO (15mg/kg), Upf1-GalNAc-ASO (10 mg/kg) and Upf3b-GalNAc-ASO (10 mg/kg). Animals were sacrificed 48 hours after the last dose.

tag: treatment

tag: weekly dosing

value: 10 mg/kg

value: M

tag: strain

value: liver


title: OSHN014B_BC3

tag: Sex


title: OSHN010N_BC8


title: hF9_Exp5_Arm2_H1_F

value: F


title: OSHN011B_BC9


title: OSHN010B_BC7


title: hF9_Exp5_Arm2_C4_M


title: hF9_Exp5_Arm2_C3_M


title: OSHN009L_BC6


title: hF9_Exp5_Arm2_C2_F


title: OSHN015B_BC7


title: OSHN015L_BC8


title: OSHN013L_BC2


title: WT_pre-B_VkJk-seq_rep3

tag: genotype


title: OSHN009B_BC5


title: OSVN008M_BC2


title: OSHN008L_BC4


title: hF9_Exp5_Arm2_H2_M


title: hF9_Exp5_Arm2_C1_F


title: hF9_Exp5_Arm2_B3_M

value: Control-GalNAc-ASO

value: 15 mg/kg


title: OSHN008B_BC3


title: OSVN006L_BC12


title: OSVN006B_BC11


title: hF9_Exp5_Arm2_B1_F


title: OSVN008B_BC1


title: hF9_Exp5_Arm2_B4_M


title: hF9_Exp5_Arm2_A4_M

value: DBPS


title: Rag1-/-_VH81X_pre-B_VkJk-seq

value: Rag1-/- VH81X


title: hF9_Exp5_Arm2_A3_M


title: hF9_Exp5_Arm2_A2_F


title: hF9_Exp5_Arm2_B2_F


title: OSVN005N_BC10


title: hF9_Exp5_Arm2_A1_F


title: OSVN004L_BC8


title: OSVN004B_BC7


title: OSVN003M_BC6


title: OSVN003L_BC5


title: WT mice transplanted with WT bone marrow 2

city: Kitakyushu

first: Takaaki

last: Ogoshi

state: Fukuoka

address: 1-1 Iseigaoka, Yahatanishi-ku

department: Department of Respiratory Medicine

institute: University of Occupational and Environmental Health,  Japan

description:
wild type transplanted with wild type bone marrow after 3 days under the hypoxia
Lung6

data_processing:
CASAVA software (v1.8.2, Illumina, San Diego, CA) was used for basecalling.
The trimmed reads were mapped onto the reference mouse genome mm10 using TopHat program (v2.0.13) in combination with Bowtie2 (v2.2.3) and SAMtools (v0.1.19).
Gene expression was quantified with the Cufflinks program (v2.2.1).  We detected raw mapped reads and the fragments per kilobase of exon per million mapped fragments (FPKM)
Genome_build: mm10
Supplementary_files_format_and_content: Files containing normalized abundance measurements and raw counts of sequencing reads

source_name: Lung

extract_protocol:
Total RNA concentrations were determined by a spectrophotometer (NanoDrop 2000, Thermo Scientific, Wilmington, DE), and the quality of the total RNA samples was assessed by an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).  RNA integrity number (RIN) was ranging from 7.8 to 8.2 in the 8 samples.  mRNA was extracted using a Dynabeads mRNA Purfication Kit (Thermo,Waltham, MA), and cDNA was generated from 500 ng of mRNA using a PrimeScript Double Strand cDNA Synthesis Kit (Takara Bio, Otsu, Japan).  Fifty ng of each cDNA sample was sheared in 200-500 bp using the Covaris S220 (Covaris, Woburn, MA) and 75 bp single-end reads were prepared using KAPA Library Preparation Kits (Kapa Biosystems, Wilmington, MA).  The cDNA libraries were indexed for multiplexing, and were sequenced on the Illumina HiSeq 2500 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung