title: Frontflip_GFAPCre_Rep1_5; Syn1CreNeg_Rep5_1

status: Public on Mar 30 2020

description:
SRT calling cards
Frontflip_GFAPCre_Rep1_Ctx.ccf; Syn1CreNeg_Rep5_1_Ctx.ccf

data_processing:
filtered for features of true insertion events (presence of piggyBac terminal repeat sequence; intact sequencing adapters, barcodes, and indexes; and a TTAA site)
mapped to build version mm10 of the mouse genome with Novoalign 3 (for SRT) or Bowtie2 (for BrokenHeart)
Reads aligning to the same TTAA with separate barcodes were considered unique insertions, and all analyses in this report considered all unique insertions equally, independent of read depth
Genome_build: mm10
Supplementary_files_format_and_content: .ccf files contain coordinates for each calling card insertion

source_name: Cortex

extract_protocol:
RNA was extracted from lysates with Qiagen RNeasy kit using manufacterer's protocols
SRT libraries were prepared from cortex RNA samples. Prior to library preparation, cortex samples were dissected into 10 separate pieces, from which RNA was independently isolated with the manufacturer’s protocol (Qiagen RNeasy kit, Germantown, MD, USA). This allows for identification of up to 10 independent insertion events into any TTAA site, given that these insertions occur in spatially separate samples. From these RNA samples, transposon sequencing libraries were generated with our bulk SRT protocol (Moudgil et al., in revision). In brief, RNA samples were first reverse transcribed, from which self-reporting transcripts, including flanking genomic sequences, were amplified via PCR. These amplicons were then tagged with universal Illumina sequencing overhangs, with separate indexes for libraries from each dissected piece, allowing for 10 ‘barcodes’ per sample and sequenced on Illumina HiSeq 2500 or NextSeq 500 platforms (Illumina, San Diego, CA, USA).
DNA was extracted from lysates with Qiagen DNeasy kit using manufacterer's protocols
BrokenHeart libraries were prepared from cortical DNA samples, as previously described (Wang et al., Genetics, 2012). A set of 20 individually barcoded BrokenHeart transposons were pooled and packaged into AAV. Thus, independent insertions into the same TTAA can be uniquely identified via barcode, removing the need to dissect and process tissue samples in separate pools as with SRT. Extracted DNA was self-ligated, amplified with inverse PCR, and sequenced with the Illumina NextSeq 500 platform (Illumina, San Diego, CA, USA).

treatment_protocol:
P0-1 AAV injection
P0-1 AAV injection

tag: 5' primer barcode

value: AGTGC; CAGTG


title: Frontflip_GFAPCre_Rep1_3; Syn1CreNeg_Rep4_9; Syn1CreNeg_Rep6_9

type: SRA

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

country: USA

institute: Washington University

description:
SRT calling cards
Frontflip_GFAPCre_Rep1_Ctx.ccf; Syn1CreNeg_Rep4_1_Ctx.ccf; Syn1CreNeg_Rep6_1_Ctx.ccf

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: AGTGC; CAGTG; TGACA


title: Frontflip_GFAPCre_Rep1_2; Syn1CreNeg_Rep4_8; Syn1CreNeg_Rep6_8


title: Frontflip_GFAPCre_Rep1_1; Syn1CreNeg_Rep4_7; Syn1CreNeg_Rep6_7


title: Frontflip_GFAPCre_Rep2_2; Frontflip_GFAPCre_Rep3_7

description:
SRT calling cards
Frontflip_GFAPCre_Rep2_Ctx.ccf; Frontflip_GFAPCre_Rep3_Ctx.ccf

value: GTTAC; AGTGC


title: Frontflip_GFAPCre_Rep2_3; Frontflip_GFAPCre_Rep3_8


title: Frontflip_GFAPCre_Rep1_4; Syn1CreNeg_Rep4_10; Syn1CreNeg_Rep6_10


title: Frontflip_GFAPCre_Rep2_10

description:
SRT calling cards
Frontflip_GFAPCre_Rep2_Ctx.ccf

value: GTTAC


title: Frontflip_GFAPCre_Rep2_1; Frontflip_GFAPCre_Rep3_6


title: Frontflip_GFAPCre_Rep2_5; Frontflip_GFAPCre_Rep3_10


title: Frontflip_GFAPCre_Rep2_6; Frontflip_GFAPCreNeg_Rep3_1

description:
SRT calling cards
Frontflip_GFAPCre_Rep2_Ctx.ccf; Frontflip_GFAPCreNeg_Rep3_Ctx.ccf


title: A375_siCont_GlnF

status: Public on Apr 05 2020

type: RNA

city: Ariake

first: Akihiro

last: Tomida

state: Koto-ku, Tokyo

department: Cancer Chemotherapy Center

country: Japan

institute: Japanese Foundation for Cancer Research (JFCR)

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Normalization of microarray data was carried out by the Robust Multichip Average method using the RMAExpress 1.0.5.

label: biotin

organism: Homo sapiens

source_name: A375_nontargeting siRNA_Glutamine Free medium_18h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were maintained in RPMI1640 (Wako Pure Chemical Industry, Osaka, Japan) supplemented with 10% fetal bovine serum and 100 ug/ml. To analyze the glutamine withdrawal condition, cells were cultured in glutamine-free RPMI1640 (FUJIFILM Wako Pure Chemical Industry) supplemented with 10% fetal bovine serum and 100 ug/ml kanamycin. kanamycin.

extract_protocol: Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).

treatment_protocol: A375 cells were transfected with nontargeting siRNA (siCont) or siRNA specific for BRAF or ATF4. The cells were cultured in normal medium or glutamine-free medium for 18 hours, or  treated with DMSO or vemurafenib (10 uM) for 4 hours.

tag: cell line

tag: treatmant

value: siCont/GlnF


title: A375_siATF4_Normal


title: A375_siBRAF_GlnF

source_name: A375_siBRAF_Glutamine Free medium_18h

value: siBRAF/GlnF


title: A375_siATF4_VEM


title: A375_siCont_Normal

source_name: A375_nontargeting siRNA_Normal

value: siCont/Normal


title: A375_siCont_VEM

value: siCont/VEM


title: Frontflip_GFAPCre_Rep2_7; Frontflip_GFAPCreNeg_Rep3_2


title: A375_VEM+AT_6h

growth_protocol: Cells were maintained in RPMI1640 (Wako Pure Chemical Industry, Osaka, Japan) supplemented with 10% fetal bovine serum and 100 ug/ml kanamycin.

treatment_protocol: A375 cells were treated with DMSO (control), vemurafenib (VEM, 10 uM), AT9283 (100 nM), or in combination with vemurafenib and AT9283 for 6 or 16 hours.

tag: treatment

value: VEM+AT


title: A375_VEM_6h

value: VEM


title: A375_siBRAF_Normal

value: siBRAF/Normal


title: Frontflip_GFAPCre_Rep2_8; Frontflip_GFAPCreNeg_Rep3_3


title: A375_AT_6h

value: AT


title: A375_CONTROL_6h


title: Frontflip_GFAPCreNeg_Rep1_1; Frontflip_GFAPCre_Rep1_6; Syn1CreNeg_Rep5_2

description:
SRT calling cards
Frontflip_GFAPCreNeg_Rep1_Ctx.ccf; Frontflip_GFAPCre_Rep1_Ctx.ccf; Syn1CreNeg_Rep5_1_Ctx.ccf

value: GTTAC; AGTGC; CAGTG


title: A375_siCont_DMSO

source_name: A375_nontargeting siRNA_DMSO

value: siCont/DMSO


title: A375_VEM_16h


title: Frontflip_GFAPCre_Rep2_9; Frontflip_GFAPCreNeg_Rep3_4


title: A375_CONTROL_16h


title: Frontflip_GFAPCre_Rep2_4; Frontflip_GFAPCre_Rep3_9


title: Frontflip_GFAPCreNeg_Rep1_2; Frontflip_GFAPCre_Rep1_7; Syn1CreNeg_Rep5_3


title: Frontflip_GFAPCreNeg_Rep1_3; Frontflip_GFAPCre_Rep1_8; Syn1CreNeg_Rep5_4


title: Frontflip_GFAPCreNeg_Rep1_4; Frontflip_GFAPCre_Rep1_9; Syn1CreNeg_Rep5_5


title: Frontflip_GFAPCreNeg_Rep1_5; Frontflip_GFAPCre_Rep1_10; Syn1CreNeg_Rep5_6


title: Frontflip_GFAPCreNeg_Rep1_7; Frontflip_GFAPCre_Rep3_2; Syn1CreNeg_Rep5_8

description:
SRT calling cards
Frontflip_GFAPCreNeg_Rep1_Ctx.ccf; Frontflip_GFAPCre_Rep3_Ctx.ccf; Syn1CreNeg_Rep5_1_Ctx.ccf


title: Frontflip_GFAPCreNeg_Rep1_6; Frontflip_GFAPCre_Rep3_1; Syn1CreNeg_Rep5_7


title: Frontflip_GFAPCreNeg_Rep1_9; Frontflip_GFAPCre_Rep3_4; Syn1CreNeg_Rep5_10


title: Frontflip_GFAPCreNeg_Rep2_10; Syn1CreNeg_Rep4_6; Syn1CreNeg_Rep6_6

description:
SRT calling cards
Frontflip_GFAPCreNeg_Rep2_Ctx.ccf; Syn1CreNeg_Rep4_1_Ctx.ccf; Syn1CreNeg_Rep6_1_Ctx.ccf


title: Frontflip_GFAPCreNeg_Rep2_1; Frontflip_GFAPCreNeg_Rep3_5

description:
SRT calling cards
Frontflip_GFAPCreNeg_Rep2_Ctx.ccf; Frontflip_GFAPCreNeg_Rep3_Ctx.ccf


title: Frontflip_GFAPCreNeg_Rep2_2; Frontflip_GFAPCreNeg_Rep3_6


title: Frontflip_GFAPCreNeg_Rep2_3; Frontflip_GFAPCreNeg_Rep3_7


title: Frontflip_GFAPCreNeg_Rep2_4

description:
SRT calling cards
Frontflip_GFAPCreNeg_Rep2_Ctx.ccf


title: Frontflip_GFAPCreNeg_Rep2_7; Frontflip_GFAPCreNeg_Rep3_10; Syn1CreNeg_Rep4_3; Syn1CreNeg_Rep6_3

description:
SRT calling cards
Frontflip_GFAPCreNeg_Rep2_Ctx.ccf; Frontflip_GFAPCreNeg_Rep3_Ctx.ccf; Syn1CreNeg_Rep4_1_Ctx.ccf; Syn1CreNeg_Rep6_1_Ctx.ccf

value: AGTGC; TAATT; CAGTG; TGACA


title: Frontflip_GFAPCreNeg_Rep2_9; Syn1CreNeg_Rep4_5; Syn1CreNeg_Rep6_5


title: Syn1Cre_Rep4_1; Syn1Cre_Rep5_6

description:
SRT calling cards
Syn1Cre_Rep4_Ctx.ccf; Syn1Cre_Rep5_Ctx.ccf

value: GTCAT; CGAAA


title: Frontflip_GFAPCreNeg_Rep2_8; Syn1CreNeg_Rep4_4; Syn1CreNeg_Rep6_4


title: Frontflip_GFAPCreNeg_Rep2_6; Frontflip_GFAPCreNeg_Rep3_9; Syn1CreNeg_Rep4_2; Syn1CreNeg_Rep6_2


title: Frontflip_GFAPCreNeg_Rep2_5; Frontflip_GFAPCreNeg_Rep3_8; Syn1CreNeg_Rep4_1; Syn1CreNeg_Rep6_1


title: Syn1Cre_Rep4_3; Syn1Cre_Rep5_8


title: Syn1Cre_Rep4_10; Syn1Cre_Rep6_5

description:
SRT calling cards
Syn1Cre_Rep4_Ctx.ccf; Syn1Cre_Rep6_Ctx.ccf

value: GTCAT; GTTAC


title: Syn1Cre_Rep4_2; Syn1Cre_Rep5_7


title: Syn1Cre_Rep4_5; Syn1Cre_Rep5_10


title: Frontflip_GFAPCreNeg_Rep1_10; Frontflip_GFAPCre_Rep3_5

description:
SRT calling cards
Frontflip_GFAPCreNeg_Rep1_Ctx.ccf; Frontflip_GFAPCre_Rep3_Ctx.ccf


title: Syn1Cre_Rep4_6; Syn1Cre_Rep6_1


title: Syn1Cre_Rep4_8; Syn1Cre_Rep6_3


title: Syn1Cre_Rep4_7; Syn1Cre_Rep6_2


title: Syn1Cre_Rep4_9; Syn1Cre_Rep6_4


title: Syn1Cre_Rep5_1; Syn1Cre_Rep6_6

description:
SRT calling cards
Syn1Cre_Rep5_Ctx.ccf; Syn1Cre_Rep6_Ctx.ccf


title: Syn1Cre_Rep5_2; Syn1Cre_Rep6_7


title: Syn1Cre_Rep5_3; Syn1Cre_Rep6_8

value: CGAAA; GTTAC


title: Frontflip_GFAPCreNeg_Rep1_8; Frontflip_GFAPCre_Rep3_3; Syn1CreNeg_Rep5_9


title: N2a_Exp1_8;N2a_Exp2_11

description:
SRT calling cards
N2a_combined.ccf

data_processing:
Library strategy: SRT calling card
filtered for features of true insertion events (presence of piggyBac terminal repeat sequence; intact sequencing adapters, barcodes, and indexes; and a TTAA site)
mapped to build version mm10 of the mouse genome with Novoalign 3 (for SRT) or Bowtie2 (for BrokenHeart)
Reads aligning to the same TTAA with separate barcodes were considered unique insertions, and all analyses in this report considered all unique insertions equally, independent of read depth
Genome_build: mm10
Supplementary_files_format_and_content: .ccf files contain coordinates for each calling card insertion

extract_protocol:
RNA was extracted from lysates with Qiagen RNeasy kit using manufacterer's protocols
SRT libraries were prepared from cortex RNA samples. Prior to library preparation, cortex samples were dissected into 10 separate pieces, from which RNA was independently isolated with the manufacturer’s protocol (Qiagen RNeasy kit, Germantown, MD, USA). This allows for identification of up to 10 independent insertion events into any TTAA site, given that these insertions occur in spatially separate samples. From these RNA samples, transposon sequencing libraries were generated with our bulk SRT protocol (Moudgil et al., in revision). In brief, RNA samples were first reverse transcribed, from which self-reporting transcripts, including flanking genomic sequences, were amplified via PCR. These amplicons were then tagged with universal Illumina sequencing overhangs, with separate indexes for libraries from each dissected piece, allowing for 10 ‘barcodes’ per sample and sequenced on Illumina HiSeq 2500 or NextSeq 500 platforms (Illumina, San Diego, CA, USA).

treatment_protocol: P0-1 AAV injection

value: GTTAC;AGTGC


title: N2a_Exp3_3

description:
SRT calling cards
N2a_combined.ccf


title: N2a_Exp3_11

description:
SRT calling cards
N2a_combined.ccf


title: Syn1Cre_Rep4_4; Syn1Cre_Rep5_9


title: N2a_Exp1_3;N2a_Exp2_6

description:
SRT calling cards
N2a_combined.ccf


title: N2a_Exp2_3

description:
SRT calling cards
N2a_combined.ccf

value: AGTGC


title: N2a_Exp1_9;N2a_Exp2_12

description:
SRT calling cards
N2a_combined.ccf


title: N2a_Exp3_8

description:
SRT calling cards
N2a_combined.ccf

value: GTTAC


title: N2a_Exp3_6

description:
SRT calling cards
N2a_combined.ccf


title: N2a_Exp3_7

description:
SRT calling cards
N2a_combined.ccf


title: N2a_Exp3_9

description:
SRT calling cards
N2a_combined.ccf


title: N2a_Exp1_1;N2a_Exp2_4

description:
SRT calling cards
N2a_combined.ccf


title: N2a_Exp3_12

description:
SRT calling cards
N2a_combined.ccf


title: N2a_Exp1_6;N2a_Exp2_9

description:
SRT calling cards
N2a_combined.ccf


title: N2a_Exp2_1

description:
SRT calling cards
N2a_combined.ccf


title: N2a_Exp3_10

description:
SRT calling cards
N2a_combined.ccf


title: N2a_Exp1_5;N2a_Exp2_8

description:
SRT calling cards
N2a_combined.ccf


title: N2a_Exp2_2

description:
SRT calling cards
N2a_combined.ccf


title: N2a_Exp3_4

description:
SRT calling cards
N2a_combined.ccf


title: N2a_Exp1_2;N2a_Exp2_5

description:
SRT calling cards
N2a_combined.ccf


title: N2a_Exp3_2

description:
SRT calling cards
N2a_combined.ccf


title: BrokenHeart_Rep1,BrokenHeart_Rep2,BrokenHeart_Rep3

description:
DNA calling cards
BrokenHeart_Rep1.ccf,BrokenHeart_Rep2.ccf,BrokenHeart_Rep3.ccf

extract_protocol:
RNA was extracted from lysates with Qiagen RNeasy kit using manufacterer's protocols
SRT libraries were prepared from cortex RNA samples. Prior to library preparation, cortex samples were dissected into 10 separate pieces, from which RNA was independently isolated with the manufacturer’s protocol (Qiagen RNeasy kit, Germantown, MD, USA). This allows for identification of up to 10 independent insertion events into any TTAA site, given that these insertions occur in spatially separate samples. From these RNA samples, transposon sequencing libraries were generated with our bulk SRT protocol (Moudgil et al., in revision). In brief, RNA samples were first reverse transcribed, from which self-reporting transcripts, including flanking genomic sequences, were amplified via PCR. These amplicons were then tagged with universal Illumina sequencing overhangs, with separate indexes for libraries from each dissected piece, allowing for 10 ‘barcodes’ per sample and sequenced on Illumina HiSeq 2500 or NextSeq 500 platforms (Illumina, San Diego, CA, USA).
SRT calling card
DNA was extracted from lysates with Qiagen DNeasy kit using manufacterer's protocols
BrokenHeart libraries were prepared from cortical DNA samples, as previously described (Wang et al., Genetics, 2012). A set of 20 individually barcoded BrokenHeart transposons were pooled and packaged into AAV. Thus, independent insertions into the same TTAA can be uniquely identified via barcode, removing the need to dissect and process tissue samples in separate pools as with SRT. Extracted DNA was self-ligated, amplified with inverse PCR, and sequenced with the Illumina NextSeq 500 platform (Illumina, San Diego, CA, USA).
DNA calling card

tag: transposon barcodes


title: Syn1Cre_Rep5_4; Syn1Cre_Rep6_9


title: N2a_Exp1_7;N2a_Exp2_10

description:
SRT calling cards
N2a_combined.ccf


title: Syn1Cre_SP1_P28_Rep4 - 7,Syn1Cre_SP1_P10_Rep1 - 6,Syn1Cre_SP1_P10_Rep3 - 6

description:
SRT calling cards
Syn1Cre_SP1_P28_Rep4.ccf,Syn1Cre_SP1_P10_Rep1.ccf,Syn1Cre_SP1_P10_Rep3.ccf


title: Syn1Cre_SP1_P28_Rep4 - 6,Syn1Cre_SP1_P10_Rep1 - 5,Syn1Cre_SP1_P10_Rep3 - 5


title: Syn1Cre_SP1_P28_Rep4 - 10,Syn1Cre_SP1_P10_Rep1 - 9,Syn1Cre_SP1_P10_Rep3 - 9


title: Syn1Cre_SP1_P28_Rep4 - 9,Syn1Cre_SP1_P10_Rep1 - 8,Syn1Cre_SP1_P10_Rep3 - 8


title: N2a_Exp3_5

description:
SRT calling cards
N2a_combined.ccf


title: Syn1Cre_SP1_P28_Rep3 - 10,Syn1Cre_SP1_P28_Rep4 - 3,Syn1Cre_SP1_P10_Rep1 - 2,Syn1Cre_SP1_P10_Rep3 - 2

description:
SRT calling cards
Syn1Cre_SP1_P28_Rep3.ccf,Syn1Cre_SP1_P28_Rep4.ccf,Syn1Cre_SP1_P10_Rep1.ccf,Syn1Cre_SP1_P10_Rep3.ccf


title: Syn1Cre_SP1_P28_Rep4 - 5,Syn1Cre_SP1_P10_Rep1 - 4,Syn1Cre_SP1_P10_Rep3 - 4


title: Syn1Cre_SP1_P28_Rep3 - 9,Syn1Cre_SP1_P28_Rep4 - 2,Syn1Cre_SP1_P10_Rep1 - 1,Syn1Cre_SP1_P10_Rep3 - 1


title: Syn1Cre_SP1_P28_Rep4 - 4,Syn1Cre_SP1_P10_Rep1 - 3,Syn1Cre_SP1_P10_Rep3 - 3


title: Syn1Cre_SP1_P28_Rep3 - 8,Syn1Cre_SP1_P28_Rep4 - 1,Syn1Cre_SP1_P10_Rep2 - 10

description:
SRT calling cards
Syn1Cre_SP1_P28_Rep3.ccf,Syn1Cre_SP1_P28_Rep4.ccf,Syn1Cre_SP1_P10_Rep2.ccf


title: Syn1Cre_SP1_P28_Rep3 - 6,Syn1Cre_SP1_P10_Rep2 - 8

description:
SRT calling cards
Syn1Cre_SP1_P28_Rep3.ccf,Syn1Cre_SP1_P10_Rep2.ccf


title: Syn1Cre_SP1_P28_Rep3 - 7,Syn1Cre_SP1_P10_Rep2 - 9


title: N2a_Exp3_1

description:
SRT calling cards
N2a_combined.ccf


title: Syn1Cre_SP1_P28_Rep3 - 4,Syn1Cre_SP1_P10_Rep2 - 6


title: Syn1Cre_SP1_P28_Rep3 - 1,Syn1Cre_SP1_P10_Rep2 - 3


title: Syn1Cre_SP1_P28_Rep2 - 10,Syn1Cre_SP1_P10_Rep2 - 2

description:
SRT calling cards
Syn1Cre_SP1_P28_Rep2.ccf,Syn1Cre_SP1_P10_Rep2.ccf


title: Syn1Cre_SP1_P28_Rep2 - 3

description:
SRT calling cards
Syn1Cre_SP1_P28_Rep2.ccf


title: Syn1Cre_SP1_P28_Rep2 - 8,Syn1Cre_SP1_P10_Rep1 - 10,Syn1Cre_SP1_P10_Rep3 - 10

description:
SRT calling cards
Syn1Cre_SP1_P28_Rep2.ccf,Syn1Cre_SP1_P10_Rep1.ccf,Syn1Cre_SP1_P10_Rep3.ccf


title: Syn1Cre_SP1_P28_Rep1 - 9

description:
SRT calling cards
Syn1Cre_SP1_P28_Rep1.ccf


title: Syn1Cre_SP1_P28_Rep1 - 10


title: Syn1Cre_SP1_P28_Rep2 - 2


title: Syn1Cre_SP1_P28_Rep2 - 1


title: Syn1Cre_SP1_P28_Rep1 - 8


title: Syn1Cre_SP1_P28_Rep1 - 7


title: Syn1Cre_SP1_P28_Rep1 - 4,Syn1Cre_SP1_P28_Rep2 - 7

description:
SRT calling cards
Syn1Cre_SP1_P28_Rep1.ccf,Syn1Cre_SP1_P28_Rep2.ccf


title: Syn1Cre_SP1_P28_Rep1 - 5


title: N2a_Exp1_4;N2a_Exp2_7

description:
SRT calling cards
N2a_combined.ccf


title: Syn1Cre_SP1_P28_Rep1 - 3,Syn1Cre_SP1_P28_Rep2 - 6


title: Syn1Cre_SP1_P28_Rep3 - 5,Syn1Cre_SP1_P10_Rep2 - 7


title: Syn1Cre_SP1_P28_Rep1 - 2,Syn1Cre_SP1_P28_Rep2 - 5


title: Syn1Cre_SP1_P28_Rep1 - 6


title: Syn1Cre_SP1_P28_Rep1 - 1,Syn1Cre_SP1_P28_Rep2 - 4


title: Syn1CreNeg_Rep2_Ctx_7

description:
SRT calling cards
Syn1CreNeg_Rep2_Ctx.ccf


title: Syn1CreNeg_Rep2_Ctx_10


title: Syn1CreNeg_Rep2_Ctx_8


title: Syn1CreNeg_Rep2_Ctx_9


title: Syn1Cre_SP1_P28_Rep3 - 2,Syn1Cre_SP1_P10_Rep2 - 4


title: Syn1CreNeg_Rep1_Ctx_3,Syn1CreNeg_Rep3_Ctx_3

description:
SRT calling cards
Syn1CreNeg_Rep1_Ctx.ccf,Syn1CreNeg_Rep3_Ctx.ccf


title: Syn1CreNeg_Rep1_Ctx_4,Syn1CreNeg_Rep3_Ctx_4


title: Syn1Cre_SP1_P28_Rep3 - 3,Syn1Cre_SP1_P10_Rep2 - 5


title: Syn1Cre_SP1_P28_Rep2 - 9,Syn1Cre_SP1_P10_Rep2 - 1


title: GFAPCreNeg_Rep6_Ctx_2

description:
SRT calling cards
GFAPCreNeg_Rep6_Ctx.ccf


title: GFAPCreNeg_Rep6_Ctx_1


title: GFAPCreNeg_Rep6_Ctx_3


title: Syn1CreNeg_Rep1_Ctx_1,Syn1CreNeg_Rep3_Ctx_1


title: GFAPCreNeg_Rep5_Ctx_9

description:
SRT calling cards
GFAPCreNeg_Rep5_Ctx.ccf


title: GFAPCreNeg_Rep5_Ctx_6


title: GFAPCreNeg_Rep5_Ctx_8


title: GFAPCreNeg_Rep5_Ctx_5


title: GFAPCreNeg_Rep5_Ctx_4


title: GFAPCreNeg_Rep5_Ctx_10


title: GFAPCreNeg_Rep5_Ctx_7


title: GFAPCreNeg_Rep4_Ctx_10,GFAPCre_Rep6_Ctx_9

description:
SRT calling cards
GFAPCreNeg_Rep4_Ctx.ccf,GFAPCre_Rep6_Ctx.ccf


title: GFAPCreNeg_Rep4_Ctx_9,GFAPCre_Rep6_Ctx_8


title: GFAPCre_Rep6_Ctx_10

description:
SRT calling cards
GFAPCre_Rep6_Ctx.ccf


title: GFAPCreNeg_Rep5_Ctx_1


title: Syn1Cre_SP1_P28_Rep4 - 8,Syn1Cre_SP1_P10_Rep1 - 7,Syn1Cre_SP1_P10_Rep3 - 7


title: Syn1CreNeg_Rep1_Ctx_2,Syn1CreNeg_Rep3_Ctx_2


title: GFAPCreNeg_Rep5_Ctx_3


title: GFAPCreNeg_Rep4_Ctx_5,GFAPCre_Rep6_Ctx_4


title: GFAPCreNeg_Rep4_Ctx_7,GFAPCre_Rep6_Ctx_6


title: GFAPCreNeg_Rep4_Ctx_8,GFAPCre_Rep6_Ctx_7


title: GFAPCreNeg_Rep5_Ctx_2


title: GFAPCreNeg_Rep4_Ctx_6,GFAPCre_Rep6_Ctx_5


title: GFAPCreNeg_Rep4_Ctx_1

description:
SRT calling cards
GFAPCreNeg_Rep4_Ctx.ccf


title: GFAPCreNeg_Rep4_Ctx_3,GFAPCre_Rep6_Ctx_2


title: GFAPCreNeg_Rep4_Ctx_4,GFAPCre_Rep6_Ctx_3


title: GFAPCreNeg_Rep4_Ctx_2,GFAPCre_Rep6_Ctx_1


title: GFAPCreNeg_Rep3_Ctx_10,GFAPCre_Rep5_Ctx_10

description:
SRT calling cards
GFAPCreNeg_Rep3_Ctx.ccf,GFAPCre_Rep5_Ctx.ccf


title: GFAPCreNeg_Rep3_Ctx_8,GFAPCre_Rep5_Ctx_8


title: GFAPCreNeg_Rep3_Ctx_9,GFAPCre_Rep5_Ctx_9


title: GFAPCreNeg_Rep3_Ctx_5,GFAPCre_Rep5_Ctx_5


title: GFAPCreNeg_Rep3_Ctx_3,GFAPCre_Rep5_Ctx_3,GFAPCreNeg_Rep6_Ctx_6,GFAPCreNeg_Rep6_Ctx_10

description:
SRT calling cards
GFAPCreNeg_Rep3_Ctx.ccf,GFAPCre_Rep5_Ctx.ccf,GFAPCreNeg_Rep6_Ctx.ccf,GFAPCreNeg_Rep6_Ctx.ccf


title: GFAPCreNeg_Rep3_Ctx_4,GFAPCre_Rep5_Ctx_4,GFAPCreNeg_Rep6_Ctx_7

description:
SRT calling cards
GFAPCreNeg_Rep3_Ctx.ccf,GFAPCre_Rep5_Ctx.ccf,GFAPCreNeg_Rep6_Ctx.ccf


title: GFAPCreNeg_Rep3_Ctx_2,GFAPCre_Rep5_Ctx_2,GFAPCreNeg_Rep6_Ctx_5,GFAPCreNeg_Rep6_Ctx_9


title: GFAPCreNeg_Rep2_Ctx_5,GFAPCreNeg_Rep2_Ctx_6,GFAPCreNeg_Rep2_Ctx_7,GFAPCreNeg_Rep2_Ctx_8

description:
SRT calling cards
GFAPCreNeg_Rep2_Ctx.ccf


title: GFAPCreNeg_Rep2_Ctx_1,GFAPCreNeg_Rep2_Ctx_2,GFAPCreNeg_Rep2_Ctx_3,GFAPCreNeg_Rep2_Ctx_4


title: GFAPCreNeg_Rep2_Ctx_9,GFAPCreNeg_Rep2_Ctx_10


title: GFAPCreNeg_Rep3_Ctx_1,GFAPCre_Rep5_Ctx_1,GFAPCreNeg_Rep6_Ctx_4,GFAPCreNeg_Rep6_Ctx_8


title: GFAPCreNeg_Rep1_Ctx_1,GFAPCreNeg_Rep1_Ctx_2,GFAPCreNeg_Rep1_Ctx_3,GFAPCreNeg_Rep1_Ctx_4

description:
SRT calling cards
GFAPCreNeg_Rep1_Ctx.ccf


title: GFAPCre_Rep2_Ctx_2,GFAPCre_Rep3_Ctx_4,Syn1CreNeg_Rep2_Ctx_6

description:
SRT calling cards
GFAPCre_Rep2_Ctx.ccf,GFAPCre_Rep3_Ctx.ccf,Syn1CreNeg_Rep2_Ctx.ccf


title: GFAPCre_Rep2_Ctx_1,GFAPCre_Rep3_Ctx_3,Syn1CreNeg_Rep2_Ctx_5


title: GFAPCreNeg_Rep1_Ctx_9,GFAPCreNeg_Rep1_Ctx_10,GFAPCre_Rep4_Ctx_1,GFAPCre_Rep4_Ctx_2

description:
SRT calling cards
GFAPCreNeg_Rep1_Ctx.ccf,GFAPCreNeg_Rep1_Ctx.ccf,GFAPCre_Rep4_Ctx.ccf,GFAPCre_Rep4_Ctx.ccf


title: GFAPCre_Rep1_Ctx_8,GFAPCre_Rep2_Ctx_10,Syn1CreNeg_Rep2_Ctx_2

description:
SRT calling cards
GFAPCre_Rep1_Ctx.ccf,GFAPCre_Rep2_Ctx.ccf,Syn1CreNeg_Rep2_Ctx.ccf


title: GFAPCre_Rep1_Ctx_3,GFAPCre_Rep2_Ctx_5,GFAPCre_Rep3_Ctx_7,Syn1CreNeg_Rep1_Ctx_7,Syn1CreNeg_Rep3_Ctx_7

description:
SRT calling cards
GFAPCre_Rep1_Ctx.ccf,GFAPCre_Rep2_Ctx.ccf,GFAPCre_Rep3_Ctx.ccf,Syn1CreNeg_Rep1_Ctx.ccf,Syn1CreNeg_Rep3_Ctx.ccf


title: GFAPCre_Rep1_Ctx_7,GFAPCre_Rep2_Ctx_9,Syn1CreNeg_Rep2_Ctx_1


title: GFAPCreNeg_Rep3_Ctx_6,GFAPCre_Rep5_Ctx_6


title: GFAPCreNeg_Rep3_Ctx_7,GFAPCre_Rep5_Ctx_7


title: GFAPCre_Rep1_Ctx_4,GFAPCre_Rep2_Ctx_6,GFAPCre_Rep3_Ctx_8,Syn1CreNeg_Rep1_Ctx_8,Syn1CreNeg_Rep3_Ctx_8


title: GFAPCre_Rep1_Ctx_2,GFAPCre_Rep2_Ctx_4,GFAPCre_Rep3_Ctx_6,Syn1CreNeg_Rep1_Ctx_6,Syn1CreNeg_Rep3_Ctx_6


title: GFAPCre_Rep1_Ctx_6,GFAPCre_Rep2_Ctx_8,GFAPCre_Rep3_Ctx_10,Syn1CreNeg_Rep1_Ctx_10,Syn1CreNeg_Rep3_Ctx_10


title: GFAPCre_Rep1_Ctx_1,GFAPCre_Rep2_Ctx_3,GFAPCre_Rep3_Ctx_5,Syn1CreNeg_Rep1_Ctx_5,Syn1CreNeg_Rep3_Ctx_5


title: Syn1Cre_Rep2_Ctx_2,Syn1Cre_Rep3_Ctx_4

description:
SRT calling cards
Syn1Cre_Rep2_Ctx.ccf,Syn1Cre_Rep3_Ctx.ccf


title: Syn1Cre_Rep2_Ctx_1,Syn1Cre_Rep3_Ctx_3


title: Syn1Cre_Rep1_Ctx_10,Syn1Cre_Rep3_Ctx_2

description:
SRT calling cards
Syn1Cre_Rep1_Ctx.ccf,Syn1Cre_Rep3_Ctx.ccf


title: Syn1Cre_Rep1_Ctx_9,Syn1Cre_Rep3_Ctx_1


title: Syn1Cre_Rep1_Ctx_8,Syn1Cre_Rep2_Ctx_10

description:
SRT calling cards
Syn1Cre_Rep1_Ctx.ccf,Syn1Cre_Rep2_Ctx.ccf


title: Syn1Cre_Rep1_Ctx_6,Syn1Cre_Rep2_Ctx_8,Syn1Cre_Rep3_Ctx_10

description:
SRT calling cards
Syn1Cre_Rep1_Ctx.ccf,Syn1Cre_Rep2_Ctx.ccf,Syn1Cre_Rep3_Ctx.ccf


title: Syn1Cre_Rep1_Ctx_7,Syn1Cre_Rep2_Ctx_9


title: Syn1Cre_Rep1_Ctx_5,Syn1Cre_Rep2_Ctx_7,Syn1Cre_Rep3_Ctx_9


title: Syn1Cre_Rep1_Ctx_4,Syn1Cre_Rep2_Ctx_6,Syn1Cre_Rep3_Ctx_8


title: GFAPCre_Rep1_Ctx_10,GFAPCre_Rep3_Ctx_2,Syn1CreNeg_Rep2_Ctx_4

description:
SRT calling cards
GFAPCre_Rep1_Ctx.ccf,GFAPCre_Rep3_Ctx.ccf,Syn1CreNeg_Rep2_Ctx.ccf


title: GFAPCre_Rep4_Ctx_3,GFAPCre_Rep4_Ctx_4,GFAPCre_Rep4_Ctx_5,GFAPCre_Rep4_Ctx_6

description:
SRT calling cards
GFAPCre_Rep4_Ctx.ccf


title: GFAPCre_Rep1_Ctx_5,GFAPCre_Rep2_Ctx_7,GFAPCre_Rep3_Ctx_9,Syn1CreNeg_Rep1_Ctx_9,Syn1CreNeg_Rep3_Ctx_9


title: GFAPCre_Rep1_Ctx_9,GFAPCre_Rep3_Ctx_1,Syn1CreNeg_Rep2_Ctx_3


title: Syn1Cre_Rep1_Ctx_1,Syn1Cre_Rep2_Ctx_3,Syn1Cre_Rep3_Ctx_5


title: GFAPCre_Rep4_Ctx_7,GFAPCre_Rep4_Ctx_8,GFAPCre_Rep4_Ctx_9,GFAPCre_Rep4_Ctx_10

description:
SRT calling cards
GFAPCre_Rep4_Ctx.ccf


title: C57bl6J_Rep2_Ctx_9,C57bl6J_Rep2_Ctx_10

description:
SRT calling cards
C57bl6J_Rep2_Ctx.ccf


title: Syn1Cre_Rep1_Ctx_2,Syn1Cre_Rep2_Ctx_4,Syn1Cre_Rep3_Ctx_6


title: Syn1Cre_Rep1_Ctx_3,Syn1Cre_Rep2_Ctx_5,Syn1Cre_Rep3_Ctx_7


title: GFAPCreNeg_Rep1_Ctx_5,GFAPCreNeg_Rep1_Ctx_6,GFAPCreNeg_Rep1_Ctx_7,GFAPCreNeg_Rep1_Ctx_8


title: C57_Rep2_Ctx_1,C57_Rep2_Ctx_2,C57_Rep2_Ctx_3,C57_Rep2_Ctx_4,C57_Rep2_Ctx_5,C57_Rep2_Ctx_6,C57_Rep2_Ctx_7,C57_Rep2_Ctx_8

description:
SRT calling cards
C57bl6J_Rep2_Ctx.ccf


title: C57bl6J_Rep1_Ctx_9,C57bl6J_Rep1_Ctx_10

description:
SRT calling cards
C57bl6J_Rep1_Ctx.ccf


title: C57_Rep1_Ctx_1,C57_Rep1_Ctx_2,C57_Rep1_Ctx_3,C57_Rep1_Ctx_4,C57_Rep1_Ctx_5,C57_Rep1_Ctx_6,C57_Rep1_Ctx_7,C57_Rep1_Ctx_8

description:
SRT calling cards
C57bl6J_Rep1_Ctx.ccf


title: Rbp4Cre_Rep3_TRAP - 2

description:
SRT calling cards
Rbp4Cre_Rep3_TRAP.ccf

source_name: Whole forebrain; Rbp4 TRAP


title: Rbp4Cre_Rep3_TRAP - 1

description:
SRT calling cards
Rbp4Cre_Rep3_TRAP.ccf


title: Rbp4Cre_Rep2_TRAP - 2

description:
SRT calling cards
Rbp4Cre_Rep2_TRAP.ccf


title: Rbp4Cre_Rep4_TRAP - 2

description:
SRT calling cards
Rbp4Cre_Rep4_TRAP.ccf


title: Rbp4Cre_Rep4_TRAP - 1

description:
SRT calling cards
Rbp4Cre_Rep4_TRAP.ccf


title: Rbp4Cre_Rep1_TRAP - 1

description:
SRT calling cards
Rbp4Cre_Rep1_TRAP.ccf


title: -N_control_Rep3

status: Public on Feb 27 2020

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

country: Italy

institute: University of Bologna

data_processing:
base-calling and demultiplexing with Illumina CASAVA 1.8
adapter clipping and quality filtering with Trimmomatic 0.33
mapping with tophat-2.0.13; parameters: -N 3 --read-gap-length 3 --read-edit-dist 3 --b2-very-sensitive -i 5 -I 60000 --coverage-search --min-coverage-intron 5 --max-coverage-intron 60000 --min-segment-intron 5 --max-segment-intron 60000 --library-type fr-firststrand
Differential expression analysis usign Cufflinks version 2.2.1 --multi-read-correct, --compatible-hits-norm, --dispersion-method per-condition and --library-norm-method quartile
Genome_build: RefGen ZmB73 Assembly AGPv4
Supplementary_files_format_and_content: tab-delimited matrix with normalized RPKM values for all the samples

molecule: polyA RNA

organism: Zea mays

source_name: primary root apexes

growth_protocol: Maize seeds were germinated on wet filter paper at 25°C in the dark; after three days, seedlings were moved to a controlled environmental chamber in 500 ml tanks containing a nutrient medium (Quaggiotti et al. 2003).

extract_protocol:
Total RNA was extracted using TRIzol reagent, followed by DNAse treatment
TruSeq RNA Library Prep Kit

treatment_protocol: 24h of growth in nutrient solution supplemented with 1mM KNO3 or 1mM NH4Cl

tag: inbred

value: control


title: +NO3_Rep3


title: +NO3_Rep1


title: -N_control_Rep1


title: Rbp4Cre_Rep1_TRAP - 2

description:
SRT calling cards
Rbp4Cre_Rep1_TRAP.ccf


title: Spo11KOZ_3_combined

status: Public on Feb 12 2020

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

country: China

institute: Fudan University

library_source: genomic

data_processing:
Library strategy: COOL-seq
Raw COOL-seq sequencing reads were firstly trimmed 9-bp random primer, removed adaptors and low-quality bases using trim_galore (version: 0.1.3) with parameters ‘--quality 20 --stringency 3 --length 50 --clip_R1 9 --clip_R2 9 --paired --trim1 --phred33’. Clean reads were mapped against human reference genome hg19 (UCSC) using Bismark (version: 0.7.6) with a paired-end and non-directional mode (parameters ‘--fastq --non_directional –unmapped --phred33-quals’)1. For improving the number of mapped reads, the unmapped reads were realigned again the same reference genome in a single-end aligned mode. After alignment, PCR duplicated reads were removed using SAMtools (version: 0.1.18). We defined the methylation level of each detected cytosine site as the methylated reads ‘C’ dividing by the all detected reads (methylated and unmethylated reads, ‘C+T’). We used WCG (ACG/TCG) for DNA methylation analysis and GCH (GCA/GCC/GCT) for chromatin accessibility analysis.
Genome_build: Mus musculus (mm10)
Supplementary_files_format_and_content: For either 'DNA_methylation' or 'chromatin accessibility' data, each column indicates 'chr, start, end, unmethylated C reads, methylated C reads'.

molecule: genomic DNA

source_name: Germ cells

extract_protocol: About 1,000 cells were transferred into a 0.2 μL PCR tube containing 7 μL of ice-cold lysate buffer (50 mM Tris-HCl (pH7.4), 50 mM NaCl, 0.25 mM EDTA, 10 mM DTT, 0.25 mM PMSF and 0.5% NP-40, plus 2 pg λDNA). After gently vortex, the cell lysate was kept on ice for 10 min. The GpC methyltransferase M. CviPI and SAM were then added to the lysate to a final volume of 10 μL containing 1 U/μL M. CviPI and 160 μM SAM. The in vitro methylation of nuclei was performed by incubating the mixture in a thermocycler at 37℃ for 45 min followed by heating at 65℃ for 25 min to inactive the enzyme activity. After in vitro methylation, 1 μL of 20 mg/mL protease (Qiagen) was added and the mixture was incubated for 3 hrs at 50℃ to release genomic DNA. The released genomic DNA was then bisulfite converted using the EZ-96 DNA Methylation-Direct MagPrep (Zymo) according the manufacturer’s instructions. Afterwards, the purified DNAs were annealed using random nonamer primers with a 5’-biotin tag (5′-Biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3′) in the presence of Klenow fragments (3’-5’ exo-, NEB). Then, the primers were digested by exonuclease I (NEB) and the DNA was purified using Agencourt Ampure XP beads (Beckman Coulter). Dynabeads M-280 Streptavidin (Invitrogen) were then used to immobilize the newly synthesized biotin-tagged DNA strands, and the original bisulfite-converted DNA templates were removed. Second DNA strands were synthesized using Klenow fragment with random nonamer primers (5′-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3′). After washing, the beads were used to amplify libraries using 15 cycles of PCR with the universal primer and index primer (NEB). The amplified libraries were purified with Agencourt Ampure XP beads twice. Fragment from 300 bp to 800 bp were selected by argarose gel electrophoresis and purified by Zymoclean Gel DNA Recovery Kit (Zymo). Finally, libraries were pooled and sequenced on the Illumina HiSeq 2500 sequencer for 150-bp paired-end sequencing.

tag: cell type

value: Germ cells

tag: development stage

value: Zygotene spermatocytes (Z)

tag: biology replication

value: Replication 3

tag: genotype/variation

value: Knock out Spo11


title: Spo11KOZ_2_combined

value: Replication 2


title: Spo11KOZ_1_combined

value: Replication 1


title: Prdm9KOZ_2_combined

value: Knock out Prdm9


title: Prdm9KOZ_3_combined


title: Rbp4Cre_Rep2_TRAP - 1

description:
SRT calling cards
Rbp4Cre_Rep2_TRAP.ccf


title: -N_control_Rep2


title: D_2_combined

value: Diplotene spermatocytes (D)

value: Wild type


title: Dmc1KOZ_3_combined

value: Knock out Dmc1


title: Prdm9KOZ_1_combined


title: Dmc1KOZ_2_combined


title: Dmc1KOZ_1_combined


title: D_3_combined


title: P_1_combined

value: Pachytene spermatocytes (P)


title: D_1_combined


title: P_2_combined


title: +NO3_Rep2


title: Z_1_combined


title: Z_2_combined


title: L_2_combined

value: Leptotene spermatocytes (L)


title: L_1_combined


title: Cg_GABA_urea_K2SO4_vs_glucose_urea_K2SO4_4

status: Public on Mar 24 2020

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

hyb_protocol: Purified cDNA samples to be compared were pooled and the prepared two-color samples were hybridized at 65°C while rotating for 16 hours using Agilent’s Gene Expression Hybridization Kit, hybridization oven and hybridization chamber. After hybridization the arrays were washed using Agilent’s Wash Buffer Kit according to the manufacturer’s instructions.

scan_protocol: Fluorescence of hybridized DNA microarrays was determined at 532 nm (Cy3) and 635 nm (Cy5) at 5 μm resolution with a GenePix 4000B laser scanner and GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA). Fluorescence images were saved to raw data files in TIFF format (GenePix Pro 6.0). Quantitative TIFF image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0).

data_processing: For ratio calculation and ratio normalization, GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

organism: Corynebacterium glutamicum

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532 and in Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott. 2004. Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol. Microbiol. 54: 420-438.

growth_protocol: For precultivation of C. glutamicum, brain heart infusion (BHI) medium (Becton Dickinson and Company, New Jersey, USA) with 90 g L-1 sorbitol was used. The cells of these precultures were harvested by centrifugation (5,000×g, 4°C, 10 min), and washed twice with PBS (pH 7.0). The main cultures were inoculated to an OD600 of 1 in CGXII minimal medium with with K2SO4 (20 mM) instead of (NH4)2SO4, with urea (151mM) and glucose or GABA as carbon source (250 mM carbon each). At an OD of 5 the cells were harvested by centrifugation (4120 x g, 10 min and 4 °C). The cell pellet was subsequently frozen in liquid nitrogen and stored at -70°C. Four biological replicates were performed.

extract_protocol: The preparation of total RNA was performed as described previously with the RNeasy Kit from Qiagen (Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott, (2004) Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol Microbiol 54: 420-438.)

treatment_protocol: see growth protocol

tag: agent

value: GABA

value: glucose


title: pL_2_combined

value: Preleptotene spermatocytes (pL)


title: pL_1_combined


title: Cg_GABA_urea_K2SO4_vs_glucose_urea_K2SO4_2


title: A1_1_combined

value: Type A1 spermatogonia (A1)


title: WT_1uM_Fe_vs_36uM_Fe_III

status: Public on Feb 24 2020

hyb_protocol: Purified cDNA samples to be compared were pooled and the prepared two-color samples were hybridized at 65°C while rotating for 17 hours using Agilent’s Gene Expression Hybridization Kit, hybridization oven and hybridization chamber. After hybridization the arrays were washed using Agilent’s Wash Buffer Kit according to the manufacturer’s instructions.

data_processing: For calculation and normalization of ratios reflecting the relative mRNA levels (Ratio of Medians, GenePix Pro), GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

organism: Corynebacterium glutamicum ATCC 13032

source_name: wild type

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm (2003) Appl. Environm. Microbiol. 69:2521-2532 and in Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott. (2004) Mol. Microbiol. 54: 420-438.

growth_protocol: Corynebacterium glutamicum ATCC13032 strain served as the wild type in the present study. Cultivation was performed in CGXII minimal medium containing 4% or 2% (wt/vol) glucose as main carbon and energy source (Keilhauer et al.) and 195 uM protocatechuic acid (PCA, Frunzke et al., 2008). To create iron limitation conditions in C. glutamicum, the amount of ferrous iron in the medium was reduced to 1 uM (compared to a standard concentration of 36 uM), similar as published by us previously (Küberl et al., 2016). Briefly, a growth experiment was started with a first pre-culture (5 ml Brain-Heart-Infusion medium) shaken for 8 h at 170 rpm. The second pre-culture (20 ml CGXII minimal medium) was inoculated using 500 ul of the first pre-culture and shaken overnight (16 h). The second pre-culture was used to inoculate the main culture (50 ml CGXII medium) to an OD600 of 1 and growth was monitored using a spectrophotometer. For cultivation under iron limitation, the cells were washed in 0.9% (wt/vol) NaCl solution before inoculating the next cultures.

extract_protocol: The preparation of total RNA was performed as described previously with the RNeasy Kit from Qiagen (Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott, (2004)  Mol Microbiol 54: 420-438.)

value: wild type


title: Undiff_2_combined

value: Germ cells

value: Undifferentiated spermatogonia (Undiff)


title: Cg_GABA_urea_K2SO4_vs_glucose_urea_K2SO4_3


title: B_1_combined

value: Type B spermatogonia (B)


title: Undiff_1_combined


title: A1_2_combined


title: WT_1uM_Fe_vs_36uM_Fe_I


title: Cg_GABA_urea_K2SO4_vs_glucose_urea_K2SO4_1


title: B_2_combined


title: WT_36uM_Fe_vs_1uM_Fe_II_CSW


title: WT_1uM_Fe_vs_36uM_Fe_I

value: 1 uM Fe, OD 4-5

value: 36 uM Fe, OD 4-5


title: WT_36uM_Fe_vs_1uM_Fe_III_CSW


title: 24 hour replicate 3

status: Public on Jan 01 2020

city: Ottawa

first: Vern

last: Lewis

state: Ontario

address: 1125 Colonel By Drive

department: Neuroscience

country: Canada

institute: Carleton University

description:
24hour_vs_control.DESeq2.csv
eXpress_output
Annotation_File_Trinotate

data_processing:
RNA-seq was performed on RNA extracted from Brain tissue.
Quality trimming and de novo transcriptome assembly was performed using the Trinity assembly suite.
Read alignment was performed using Bowtie2 integrated in to the Trinity suite.
Differential expression analysis was performed using eXpress and DESeq2
Annotation was done using the Trinnotate annotation platform which uses the ref-seq NCBI, and Uniprot databases to run homology searches.
Gene ontology enrichment analysis and co-expression clustering was performed using the David Bioinformatics Resources website, and the MeV: MultiExperiment Viewer data analysis tool.
Supplementary_files_format_and_content: DESeq2 files for each treatment comparison (2h vs. con, 4h vs. con, 24 vs. con). Files are comma delimited and the output consists of log2 fold changes, p-values, and p-adjusted values (FDR).
Supplementary_files_format_and_content: eXpress output is a tab delimited file consisting of fpkm and tpm values for each transcript.
Supplementary_files_format_and_content: Full processed dataset is a tab delimited file which includes output from the trinotate annotation tool, abundance measure from the eXpress tool, and differential expression output from DSeq2. Trinotate output consists of homology search results from both NCBI's refseq database and Uniprots protein database. Also included are pfam, signalP, eggnog, KEGG, and gene ontology annotations, as well as the associated nucleotide and protein sequences. TPM and FPKM are included for all transcripts, as well as , the log2 Fold-change and FDR for all differentially expressed transcripts.

organism: Bombina orientalis

source_name: Whole brain

extract_protocol:
Trizol extraction + isolation with a Qiagen RNease kit
RNA libraries were prepared for sequencing using standard Illumina protocols by The Center for Advanced Genomic (TCAG) at The Hospital for Sick Children's.

tag: tissue

value: Brain

tag: post-training sacrifice timings

value: 24 hours post


title: 24 hour replicate 1


title: Set2_WT_AmyE_ind_vs_unind_III

status: Public on Feb 03 2020

hyb_protocol: Custom-made whole-genome DNA microarrays for C. glutamicum ATCC 13032 printed with 70-mer oligonucleotides were obtained from Operon (Cologne, Germany) and are based on the genome sequence entry NC_006958. Hybridisation and stringent washing of the microarrays were performed according to the instructions of the supplier. Hybridisation was carried out for 16 - 18 h at 42°C using a MAUI hybridization system (BioMicro Systems, Salt Lake City, USA).

scan_protocol: After washing the microarrays were dried by centrifugation (5 min, 1600 g) and fluorescence was determined at 532 nm (Cy3-dUTP) and 635 nm (Cy5-dUTP) with 10 µm resolution using an Axon GenePix 6000 laser scanner (Axon Instruments, Sunnyvale, U.S.A).

data_processing: Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0, Axon Instruments). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (www.bioconductor.org). Processed and normalized data as well as experimental details (according to MIAME) were stored in the in-house microarray database for further analysis.

source_name: WT AmyE

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532

growth_protocol: Precultures of the respective C. glutamicum strains in CgXII medium containing 4% glucose were grown to an OD600 of 5-6 and used to inoculate the main cultures in the same medium to an OD600 of 0.5, which subsequently were grown to the mid-exponential growth phase. The main cultures were then split into two cultures and IPTG was added to a final concentration of 1 mM to one of the cultures (induced samples). The cells were harvested 30 min after IPTG addition by pouring the cultures into ice-containing tubes precooled to -20°C followed by centifugation (3 min, 4200 x g, 4°C). Control cultures (uninduced) did not contain IPTG. The cell pellets were quickly frozen in liquid nitrogen and stored at -80°C until use for RNA isolation.

extract_protocol: Preparation of total RNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532

tag: genotype

value: WT

value: induced

value: uninduced


title: Set3_WT_NprECut_ind_vs_unind_I


title: 2 hour replicate 3

description:
2hour_vs_control.DESeq2.csv
eXpress_output
Annotation_File_Trinotate

value: 2 hours post


title: Set3_WT_NprECut_ind_vs_unind_III


title: Set3_WT_NprECut_ind_vs_unind_II


title: 2 hour replicate 2


title: 2 hour replicate 1


title: Set1_WT_AmyE_noSP_ind_vs_unind_I

source_name: WT AmyE_noSP


title: unstimulated CD8-positive dendritic cells_Rep1 (ATAC-seq)

status: Public on Jul 31 2019

city: Debrecen

first: Lajos

last: Széles

address: Egyetem tér 1.

country: Hungary

institute: University of Debrecen

data_processing:
read trimming with Trimmomatic using SE and -phread33 parameters, TruSeq3-SE.fa:2:30:10 adapter and LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 values
alignment with bwa v0.7.17 using default parameters
bam generation with Picard tools v2.8.1 using SortSam, AddOrReplaceReadGroups, CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, MarkDuplicates with default parameters
tag directory generation with homer v4.9.1 makeTagDirectory using -checkGC and -single parameter
peak calling with MACS2 using -B, -q 0.001, --call-summits parameters
mm10 ENCODE blacklist were subtracted from the peak list
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph, bed (chr, start, end, name, score, strand, signalValue, pValue, qValue, peak)

source_name: dendritic cells from the spleen

growth_protocol: CD8-positive dendritic cells were cultured in IMDM-glutamax medium supplemented with 10% FCS, 1% penicillin + streptomycin and 0,1% β-mercaptoethanol

extract_protocol:
Cells were double cross-linked with DSG (40 min) and  formaldehyde (10 min). Nuclei were isolated using lysis buffer containing 150 mM NaCl, 1 nM EDTA pH 8, 20 mM Tris-HCl pH 8, 1% Triton x-100, 1% SDS with EDTA-free protease inhibitor (Roche). Chromtain was sheared with sonication and immunoprecipitated overnight using antibodies against IRF3 (D83B9, Cell Signaling), IRF5 (ab21689, Abcam), IRF9 (AF5629, R&D Systems). Chromatin-antibody complexes were washed and eluted after pull-down by superparamagnetic beads (ThermoFisher Scientific). Eluted complexes were decrosslinked overnight and purified by NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel). ChIP-DNA was quantified by Qubit fluorometer. In case of unstimulated cells for ATAC-seq after lysis, nuclei were subjected to tagmentation.
Indexed cDNA libraries were prepared from 1-10 ng ChIP-DNA using TruSeq ChIP Library Preparation Kit (Illumina) according to manufacturer’s instructions. Libraries were sequenced on NextSeq 500. Nextera DNA Library Prep Kit was used for library generation according to manufacturer's protocol (Illumina) for ATAC-seq.

treatment_protocol: Cells were left stimulated with 5 μg/ml poly(I:C) HMW or 1 mM class B CpG oligonucleotide 1826 (CpG)  or 10U IFN-beta for 90 min. Unstimulated CD8-positive dendritic cells were used for ATAC-seq experiments.

value: CD8-positive dendritic cell line

tag: treatment (stimulation)


title: Set1_WT_AmyE_noSP_ind_vs_unind_II


title: IFNB-stimulated dendritic cell_90 min_Rep2 (ChIP-seq)

value: 90 min; 10U IFN-beta

tag: chip antibody

value: IRF9 (AF5629, R&D Systems)


title: unstimulated CD8-positive dendritic cells_Rep2 (ATAC-seq)


title: BGI EC109 plenti ADAR1

status: Public on Dec 22 2019

city: Singapore

first: Polly Leilei

last: Chen

address: #12-01, MD6, 14 Medical Drive

department: Department of Anatomy

country: Singapore

institute: Cancer Science Institute of Singapore NUS

description: strand-specific RNA-Seq

data_processing:
Reads with adapters, unknown bases more than 10% and low quality bases (<=5) more than 50% were removed using SOAPnuke software.
Read mapping was performed by using STAR (v2.5) with the reference human genome version 19 (hg19) as the annotation library.
For the splicing analysis, mapped reads were filtered and classified into the following three groups based on their distance and location around the annotated splice sites: 1) reads mapped to exon-exon junctions, 2) reads bridging exon-intron junctions, and 3) reads mapped completely to introns.
The reads in Group 3 were used for intron retention coverage and depth calculations. The reads in Groups 1 and 2 were used for the calculation of splicing index (SI) for each splice site for the selection of potential differential splicing candidates.
To identify the various types of splicing events including exon skipping, intron retention and alternative splice sites, the SI calculation was adjusted for each type of splicing events.
All potential splicing candidates were classified into either known/annotated alternative splicing or novel splicing events that are not represented in the annotation library, and were assessed by Fisher’s exact test and SI change.
For this study, only candidates with total junction reads≥15, |ΔSI| ≥ 10% with a FDR<0.2 in the opposite direction of change for KD and OE samples were selected.
Genome_build: hg19
Supplementary_files_format_and_content: spreadsheet file include ADAR1 or ADAR2 knockdown or overexpression specific high confidence alternative splicing events (intron retention, casette exon and alternative splice site)

source_name: human esophageal squamous carcinoma cells

extract_protocol:
Total RNA samples were extracted using Qiagen Rneasy Mini Kit.
Strand-specific cDNA library according to Illumina's TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Human ESCC cells were treated with specific shRNAs for silecing ADAR1/2 or transfected with expression construct for overexpressing ADAR1/2.

value: ADAR1 over expression


title: Set2_WT_AmyE_ind_vs_unind_I


title: IFNB-stimulated dendritic cell_90 min_Rep1 (ChIP-seq)


title: DcyaB_vs_WT_Glc-Ac_rep1

status: Public on Jan 09 2020

source_name: Glucose-Acetate

growth_protocol: Bacterial strains, media and growth conditions. The C. glutamicum type strain ATCC 13032 was used as wild type (WT) and C. glutamicum Δcg0375 as the ΔcyaB mutant. For growth experiments, cells from a fresh LB agar plate were inoculated into 5 ml BHI medium and cultivated for 9 hour at 30 °C and 120 rpm. The second culture was inoculated in 60 ml CGXII minimal medium with glucose in a 500 ml baffled shake flask and was incubated over night at 30°C and 120 rpm. The main culture was inoculated to an OD600 of 1 in 60 ml CGXII with glucose and acetate as carbon sources (each 100 mM) and cultivated at 30° and 120 rpm until they reached the exponential phase.

value: wild type (WT)


title: Set1_WT_AmyE_noSP_ind_vs_unind_III


title: Set2_WT_AmyE_ind_vs_unind_II


title: DcyaB_vs_WT_Glc-Ac_rep2


title: pIC-stimulated dendritic cell_90 min_Rep2 (ChIP-seq)

value: 90 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)

value: IRF3 (D83B9, Cell Signaling)


title: CpG-stimulated dendritic cell_90 min_Rep1 (ChIP-seq)

value: 90 min; 1 mM class B CpG oligonucleotide (1826)

value: IRF5 (ab21689, Abcam)


title: CpG-stimulated dendritic cell_90 min_Rep2 (ChIP-seq)


title: pIC-stimulated dendritic cell_90 min_Rep1 (ChIP-seq)


title: 24 hour replicate 2


title: DcyaB_vs_WT_Glc-Ac_rep3


title: B134T64

status: Public on Jun 18 2019

city: Paris

first: Olivier

last: KOSMIDER

address: 27 Rue du faubourg Saint Jacques

country: France

institute: Institut Cochin

data_processing:
Reads were mapped to the human reference genome Hg19, using TopHat (v2.0.6).
Read count normalizations, differential gene expression analysis and differential junction read counts were performed using DESeq2.
Assuming that a maximum of 80% of genes are expressed, we selected the 20% lowest counts for each sample as background. A threshold was fixed at two standard deviations over the mean of the background. All transcripts for which normalized counts were lower than the computed threshold were designated as background for each array. When comparing normalized counts between two groups, a transcript was included in the analysis if its counts exceeded the background in at least 80% of the sample from at least 1 group.
To identify differentially expressed transcripts, we used empirical Bayes estimation. For the differential expression study, the results obtained after DESeq2 comparison were selected for further analysis and filtered at P ≤ 0.05 and fold-changes of 1.2, 1.5, or 2.
Read counts for splicing junctions from junctions.bed TopHat output were considered. Differential analysis of junctions was performed using DESeq2 (13). Only alternative acceptor splice sites (two or more 30ss with junctions to the same 50ss) and alternative donor splice sites (two or more 50ss with junctions to the same 30ss) were considered for this analysis. Predictions and analysis of branch point sequences were done with the online tools SVM-BPfinder (http://regulatorygenomics.upf.edu/ Software/SVM_BP/) and the Human Splicing Finder (http://www.umd.be/HSF/). The SVM_BP code was altered to allow for BP six base pairs from the 3′ss by setting minidist3ss=6 in svm_getfeat.py.
Genome_build: Human reference genome Hg19 RefSeq (RNA sequences, GRCh37), UCSC
Supplementary_files_format_and_content: Fastq and mapped.bam files.

source_name: Bone marrow mononuclear cells

extract_protocol:
Bone marrow mononuclear cells were purified on Ficoll gradient and processed for nucleic acid extraction using the DNA/RNA Kit (Qiagen). cDNA synthesis was conducted with MuLV Reverse Transcriptase (Invitrogen), with quality controls conducted on an Agilent 2100 Bioanalyzer (Agilent).
Libraries were constructed using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) and sequenced on an Illumina HiSeq 2500 platform using a 100-bp paired-end sequencing strategy.

tag: sample type

value: Control

value: Bone marrow mononuclear cells


title: B134T56


title: Cglu_DaceE_Dpyc_vs_Dpyc_II

description:
ch1: ATCC 13032 ΔaceE Δpyc
ch2: ATCC 13032 ΔaceE

source_name: C. glutamicum culture

label_protocol: Synthesis of fluorescently labelled cDNA was performed as described previously (Baumgart M, Luder K, Grover S, Gätgens C, Besra GS, Frunzke J. 2013. IpsA, a novel LacI-type regulator, is required for inositol-derived lipid formation in Corynebacteria and Mycobacteria. BMC Biology 11).

growth_protocol: For analysis of the transcriptome, C. glutamicum ΔaceE and ΔaceE Δpyc were cultivated in triplicates as described in 2.1 in 50 ml CGXII containing 154 mM acetate and 222 mM glucose in shake flasks. After reaching exponential phase at an OD600 of around 12-15, the cell suspension was harvested by centrifugation (4256 g, 10 min, 4°C). The resulting pellet was directly frozen in liquid nitrogen and stored at -80°C. RNA preparation.

extract_protocol: The preparation of total RNA samples was performed as described previously (Baumgart M, Luder K, Grover S, Gätgens C, Besra GS, Frunzke J. 2013. IpsA, a novel LacI-type regulator, is required for inositol-derived lipid formation in Corynebacteria and Mycobacteria. BMC Biology 11).

value: <delta>aceE <delta>pyc

tag: media

value: CGXII glucose+acetate

value: <delta>aceE


title: CUT&RUN-CTCF_iPSC-induced lower motor neurons_rep1

status: Public on Jun 15 2019

city: SAN FRANCISCO

first: Yin

last: Shen

state: CALIFORNIA

address: 513 Parnassus Ave

department: Department of Neurology

institute: UCSF

description:
MN.CTCF.merged.0.05_peaks.narrowPeak
MN.CTCF.merged.hg19.bw

data_processing:
library strategy: CUT&RUN
All reads were trimmed to 50 bp with fastp.
Alignment was performed using bowtie2 with the following options: -local -very-sensitive-local -nomixed -no-discordant -phred33 -I 10 -X 700. Picard Tools was used to remove duplicate reads.
Narrow peaks called using MACS2 with a q-value threshold of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Narrow peaks called using MACS2 and signal tracks in bigwig format

source_name: iPSC-induced lower motor neurons

extract_protocol:
Cells were washed with PBS and nuclei were extracted prior to library construction.
CUT&RUN libraries were prepared according to the published protocol (Skene and Henikoff 2017).

value: iPSC-induced excitatory neurons

tag: cut&run antibody

value: CTCF (Millipore, cat# 07-729, lot# 305960)


title: CUT&RUN-CTCF_iPSC-induced lower motor neurons_rep2

value: iPSC-induced lower motor neurons


title: CUT&RUN-H3K27ac_iPSC-induced lower motor neurons_rep2

description:
MN.H3K27ac.merged.0.05_peaks.narrowPeak
MN.H3K27ac.merged.hg19.bw


title: CUT&RUN-CTCF_iPSC-induced excitatory neurons_rep1

description:
IJ196.hg19.nuc.nodups.0.05_peaks.narrowPeak
IJ196.hg19.bowtie2.bw

source_name: iPSC-induced excitatory neurons


title: B133-B136T40


title: B132T32


title: B131T8


title: CUT&RUN-H3K27ac_iPSC-induced excitatory neurons_rep1

description:
IJ195.hg19.nuc.nodups.0.05_peaks.narrowPeak
IJ195.hg19.bowtie2.bw


title: CUT&RUN-H3K27ac_iPSC-induced lower motor neurons_rep1


title: SLE.665.T3 [RNA-seq]

status: Public on May 17 2019

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the hg19 version of the mouse genome using Tophat2 and the UCSC hg19 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique RefSeq gene using the summarizeOverlaps function of GenomicRanges 1.28.6 R package.
Genes were filtered for detection based on having greater than 3 reads per million (rpm) in at least 1 cell type and resulted in the expression of 11284 genes.
Genome_build: hg19
Supplementary_files_format_and_content: Annotation file containing FPKM normalized read counts for each sample.

source_name: SLE_Circulating B cells

extract_protocol:
RNA was extracted from FACS isolated cell populations using the AllPrep DNA/RNA Mini Kit (Qiagen).
50 pg of total RNA was used as input for the SMART-seq v3 cDNA synthesis kit (Takara).  1 ng of cDNA was used as input for the NexteraXT kit (Illumina).

tag: subject status

value: Systemic lupus erythematosus (SLE)

value: Circulating B cells

tag: cell subtype

value: Transitional 3 B cells (T3)

tag: sorting markers


title: SLE.665.SM [RNA-seq]

value: Switched Memory B cells (SM)


title: old_yw_Input_rep2

status: Public on Apr 25 2019

city: Ames

first: Allison

last: Birnbaum

email: abirnba1@iastate.edu, abirnba1@uab.edu

state: AL

address: 3247 Pammel Dr

institute: Iowa State University

description: input

data_processing:
Base calls performed by Illumina HiSeq 3000 Real-Time Analysis software RTA2
Homer Suite-mergePeaks: Collate biological replicates
Galaxy-FastQC: Check for quality
Galaxy-FASTQ Groomer: readability control
Galaxy-Bowtie2: Alignment against dm6 genome
Galaxy-MACS2: Peak calling from alignment reads
BedTools intersect: assign genes to peaks
Genome_build: Aug. 2014 (BDGP R6 + ISO1 MT/dm6)
Supplementary_files_format_and_content: Fold Enrichment values, each group contains two replicates

organism: Drosophila melanogaster

source_name: Whole Body

growth_protocol: Flies were maintained at 25°C, 40% relative humidity and 12-hour light/dark. Adults were reared on agar-based diet with 0.8% cornmeal, 10% sugar, and 2.5% yeast

extract_protocol:
~200 female flies were anesthetized with Flynap (Carolina, Burlington, NC) and ground into a powder in liquid nitrogen. Crosslinking was allowed for 20 minutes in 1X PBS with 1% paraformaldehyde before quenched with glycine. Chromatin was washed several times with 1X PBS supplemented with protease inhibitor. Pellets were washed once with cold cell lysis buffer (5mM HEPES pH7.6, 100mM NaCl, 1M EDTA,0.5% NP-40, ddH2O, 0.1% PIC). Buffer was removed and samples were snap frozen in liquid nitrogen and stored at -80°C to synchronize experiments. Samples were thawed and treated with nuclear lysis buffer (50mM HEPES pH7.6, 10mM EDTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, ddH2O, 0.1% PIC) and incubated at 4°C for 10 minutes. Chromatin was sheared for 500bp using Branson digital sonifier 250, using 30%, with 30 seconds on 30 seconds 0ff for 5 cycles. Supernatant was snap frozen and stored at -80°C. Immunoprecipitation was carried out using Protein-G SureBeads (BioRad Hurcules, CA, USA). Beads were washed once with 1X PBS prior to blocking with 1X PBS and 0.5% BSA for 20 minutes at 4°C. Samples were precipitated with affinity purified anti-dFOXO antibody (Tatar Lab). Samples were reverse crosslinked at 65°C for 12 hours.
DNA size selection and library prep were done using NEBNext Ultra II DNA library prep kit for Illumina an indexed using NEBNext multiplex oligos for Illumina (Primer set 1) (New England BioLabs, Ipwsich MA). DNA from either ChIP or input samples was mixed with AMPure XP beads (**) to select for a final library size of 320bp. Samples were diluted to a final concentration of 2nM for Illumina sequencing on Illumina 3000 (Illumina, San Diego CA) with single-end 50 bp reads format

treatment_protocol: Larvae were reared on normal food. Eclosed flies were collected over the course of 2 days and allowed to mate before separation. 25-30 females were collected per food vial and aged under standard conditions. Flies were transferred to new food every 3-4 days until reaching the age for extraction.

value: Whole Body

tag: developmental

value: 35 days after eclosion

tag: condition

value: old

tag: Sex

value: Female


title: Cglu_DaceE_Dpyc_vs_Dpyc_III


title: old_yw_Input_rep1

description: input


title: Cglu_DaceE_Dpyc_vs_Dpyc_I


title: Dcg2460_vs_WT_I

status: Public on Jul 11 2019

source_name: wild type ATCC 13032 [delta]cg2460

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. (2003)

extract_protocol: The preparation of total RNA was performed as described previously with the RNeasy Kit from Qiagen (Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott, (2004)

tag: growth medium

value: CGXII glucose

source_name: wild type ATCC 13032

value: WT


title: old_yw_ChIP_rep2

description: dFOXO antibody (Tatar Lab)


title: Dcg2460_vs_WT_III

tag: genotype/variation


title: young_yw_Input_rep2

description: input

value: 14 days after eclosion

value: young


title: Dcg2460_vs_WT_II


title: old_yw_ChIP_rep1

description: dFOXO antibody (Tatar Lab)


title: Dcg2460_vs_WT_IIII_csw


title: young_yw_ChIP_rep1

description: dFOXO antibody (Tatar Lab)


title: young_yw_Input_rep1

description: input


title: young_yw_ChIP_rep2

description: dFOXO antibody (Tatar Lab)


title: Cglutamicum_ pEKEx2-malR_vs_pEKEx2_C

status: Public on May 10 2019

hyb_protocol: RNA sample preparation, labelling, hybridization and comparative transcriptome analysis was performed as described previously (Vogt et al., 2014).

source_name: ATCC13032 pEKEx2-malR CGXII glucose

growth_protocol: For transcriptome analysis, C. glutamicum ATCC1303 pEKEx2-malR and ATCC13032 pEKEx2 cells were grown in 4.5 ml BHI (Brain Heart Infusion, Difco) with 25 µg/ml Kanamycin for about 8 hours at 30°C. A second precultivation was performed in CGXII minimal medium containing 2% (w/v) glucose as carbon source with 25 µg/ml Kanamycin. The main cultures were inoculated to an OD600 of 1 in CGXII minimal medium with 2% (w/v) glucose, 25 µg/ml Kanamycin and 100 µM IPTG. After 4 hours of incubation, the cells were centrifuged and harvested on ice and the cell pellet was subsequently frozen in liquid nitrogen and stored at -70°C.

tag: vector

source_name: ATCC13032 pEKEx2 CGXII glucose

value: empty vector control


title: Cglutamicum_delta-cg1631_vs_WT_II

status: Public on Jul 12 2019

description: ratio Δcg1631 / WT

source_name: ATCC13032ΔftsR CGXII glucose

label_protocol: RNA sample preparation, labelling, hybridization and comparative transcriptome analysis was performed as described previously (Vogt et al., 2014).

growth_protocol: For transcriptome analysis, C. glutamicum ATCC13032ΔftsR and ATCC13032 cells were grown in 5 ml BHI (Brain Heart Infusion, Difco) for about 6 hours at 30°C. A second precultivation was performed in CGXII minimal medium containing 2% (w/v) glucose as carbon source. The main cultures were inoculated to an OD600 of 1 in CGXII minimal medium with 2% (w/v) glucose. At an OD of 6, the cells were centrifuged and harvested on ice and the cell pellet was subsequently frozen in liquid nitrogen and stored at -70°C.

value: {delta}ftsR

source_name: ATCC13032 CGXII glucose

value: wild-type strain


title: Cglutamicum_ pEKEx2-malR_vs_pEKEx2_B

extract_protocol: RNA sample preparation, labelling, hybridization and comparative transcriptome analysis was performed as described previously (Vogt et al., 2014).


title: Cglutamicum_ pEKEx2-malR_vs_pEKEx2_A_csw


title: Cglutamicum_delta-cg1631_vs_WT_I_csw

description: ratio Δcg1631 / WT


title: TTseq_TX1072_WT_4h_Dox_Rep2

status: Public on Jan 01 2019

first: Aurélie

last: Bousard

address: 26, rue d'Ulm

institute: Institut Curie

data_processing:
library strategy: TT-seq
Reads were first mapped on rRNA with Tophat (2.1.0) (Trapnell et al., 2009), with options [-g 1 --no-coverage-search --library-type fr-secondstrand]. Paired unmapped reads were then used to reconstruct fastq files with bedTools bamToFastq (2.25.0) (Quinlan and Hall, 2010). Those files were then mapped with Tophat (2.1.0) (Trapnell et al., 2009), with options [-p 8 -g 1 -x 1 -N 3 --read-edit-dist 3 --no-coverage-search --library-type fr-secondstrand], with refFlat annotation.
Reads covering exons of each gene were then counted with featureCounts (1.5.1) with options [-C -p -s 1 -T 8] (Liao et al., 2014).
D-scores were then calculated for genes with minimum 10 allelic reads.
Genome_build: mm10
Supplementary_files_format_and_content: Count table per gene including : BL6 counts, CAST counts, dscore, total counts

growth_protocol: TX1072 (mouse, female, [Mus musculus castaneus X C57BL/6] embryonic stem cells) cells have been previously derived in the lab (Schulz et al, 2014). Cells were cultured on gelatin-coated plates in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% foetal bovine serum, 2-mercaptoethanol (0.1mM), LIF(1000u/mL) and 2i (PD0325901 [0.4 mM], CHIR99021 [3 mM]) (Ying et al., 2008).

extract_protocol:
The TTseq protocol was performed as previously described with modifications {Schwalb, 2016 #1988}. The spike-in mix, containing three 4sU-labeled and three unlabeled RNAs, was synthesized in vitrowith MEGAscript T7 Transcription Kit (Thermo Fisher), where 1/10 UTP in the transcription reactions was replaced with 4sU for the 4sU-labeled spike-ins. RNA lysates were thawed on ice and 24 ng of spike-in mix was added per 10 million cells. The RNA was then purified according to the manufacturer’s protocol. 4sU-labeled RNA was isolated from 300 µg total RNA, for this two aliquots of 150 µg were sheared in Covaris MicroTube with the Covaris S220 System (Thermo Fisher) for 10 s with settings 100 W and 1% duty cycle. These were then pooled and 2 µg of sonicated total RNA was taken for total RNA fraction. The RNA was biotinylated with EZ-Link HPDP-Biotin (Thermo Fisher) in two biotinylation reactions per sample (150 µg RNA in 10 mM Tris pH 7.5; 1 mM EDTA, 40 % DMSO; and 200 ng/ml HPDP-biotin) were incubated 1.5 h at 24 ºC. The biotinylated RNA was extracted with chloroform and precipitated with isopropanol. 4sU-labeled RNA was isolated by incubating the biotinylated RNA with paramagnetic streptavidin µMACS MicroBeads (Miltenyi) for 15 min at room temperature and binding to MACS columns. The columns were washed three times with wash buffer (100 mM Tris pH 7.5; 10 mM EDTA; 100 mM NaCl; and 0.1% Tween 20) at 65 ºC and three times with wash buffer at room temperature. The RNA was eluted from the columns with 100 mM DTT. The eluted 4sU-labeled RNA and reserved total RNA were purified with the miRNeasy Micro kit (Qiagen) according to the manufacturer’s protocol with on-column DNAse I treatment.
200 µg of isolated newly synthesized RNA were used to prepare NGS libraries with the TruSeq Stranded Total RNA Library Prep Kit (Illumina). The sample libraries were pooled and sequenced as a single run on the Nextseq550 (Illumina) using PE150 mode.

treatment_protocol: TX1072 based ESC lines were plated at a density of 1.8mln/T75 flask. After 24hrs of culture in DMEM/15%FCS+LIF+2i cell the medium was supplemented with doxycycline (1ug/ml). After 0, 4h, 8, 12 and 24hrs RNA was labelled by the addition of 0.5 mM 4-thiouridine (4sU) for 5 min. Medium was quickly removed and cells were lysed with 10 mL of TRI reagent (Sigma-Aldrich). Lysates were stored at -80 deg.

tag: strain

value: CAST / C57BL/6

tag: cell line

value: 4h Dox

tag: replicate


title: TTseq_TX1072_WT_0h_Dox_Rep1

tag: genotype

value: 0h Dox


title: TTseq_TX1072_WT_8h_Dox_Rep1

value: 8h Dox


title: TTseq_TX1072_WT_4h_Dox_Rep1


title: TTseq_TX1072_WT_8h_Dox_Rep2


title: TTseq_TX1072_WT_0h_Dox_Rep2


title: TTseq_TX1072_WT_24h_Dox_Rep2

value: 24h Dox


title: TTseq_TX1072_WT_12h_Dox_Rep2

value: 12h Dox


title: TTseq_TX1072_WT_12h_Dox_Rep1


title: TTseq_TX1072_WT_24h_Dox_Rep1


title: Cglutamicum_delta-cg1631_vs_WT_III

description: ratio Δcg1631 / WT


title: 13-101K3_LN

status: Public on Oct 19 2018

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: 13-104AA2 CRPC lymph node (LN) metastasis

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.X software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Reads were mapped to the hg19 human genome build using TopHat v2.X and bowtie2 v2.2.X.
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.1
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package v1.12.2 using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.

source_name: CRPC lymph node (LN) metastasis

extract_protocol:
Total RNA was isolated from sections of frozen tissue using RNA STAT-60 (Tel-Test) while incorporating Phase Lock Gel Heavy tubes (5 Prime) into the protocol to better facilitate phase separation.   RNA yield and purity was obtained on a NanoDrop 2000 (Thermo Fisher Scientific).  RNA Integrity was evaluated on a 2100 Bioanalyzer (Agilent Technologies).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced six per lane on the Illumina HiSeq 2500 generating 50 bp paired end reads.

tag: gender

value: male

tag: tissue

value: Castration Resistant Prostate Cancer (CRPC)

tag: tumor type

value: CRPC metastasis

tag: tumor site

value: lymph node

tag: patient


title: 14-091E1_LUNG

description: 15-023L2 CRPC lung metastasis

source_name: CRPC lung metastasis

value: lung


title: B6

status: Public on Sep 25 2018

city: Lausanne

first: Joern

last: Pezoldt

address: Station 19, SV 3818.A

department: SV

country: Switzerland

institute: EPFL

data_processing:
library strategy: Drop-Seq
Data were analyzed using Cell Ranger™ v2.0 pipelines and were visualized by Loupe™ Cell Browser v1.0. Both are available in 10xGenomics website.
Genome_build: mm10
Supplementary_files_format_and_content: It includes mean UMI counts, log2 fold changes and adjusted p-values for the differentially expressed genes among the intentified cell clusters.

source_name: mLN-SPF

extract_protocol:
For stromal cell isolation, skin-draining pLNs (inguinal and axillary) or mLNs (small intestinal and colon/caecum-draining) were resected and digested in RPMI 1640 medium (Gibco) containing 0.2 mg/ml collagenase P (Roche), 0.15 U/ml dispase (Roche) and 0.2 mg/ml DNase I (Roche) as described previously (Fletcher et al., 2011, https://doi.org/10.3389/fimmu.2011.00035). After digestion, cells were kept at 4°C in PBS containing 0.2 % BSA and 5 mM EDTA (Roth). CD45- cells were enriched by MACS separation after direct magnetic labeling of CD45+ cells using  anti-CD45 Nanobeads (Biolegend). Subsequently, the CD45- fraction was stained using fluorescence-coupled antibodies and used to sort CD45‑CD24‑ cells by FACS (Aria II)) for single-cell mRNA‑seq analysis.
Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs) and Single Cell 3’ reagent kit v2 for reverse transcription, cDNA amplification and library construction (10xGenomics). The detailed protocol was provided by 10xGenomics.

tag: cell type

tag: antibody

tag: index id

tag: index seq

value: CGTTAATC,GCCACGCT,TTACTCAG,AAGGGTGA


title: L1700567

data_processing:
Library strategy: Drop-Seq
Data were analyzed using Cell Ranger™ v2.0 pipelines and were visualized by Loupe™ Cell Browser v1.0. Both are available in 10xGenomics website.
Genome_build: mm10
Supplementary_files_format_and_content: .csv files include mean UMI counts, log2 fold changes and adjusted p-values for the differentially expressed genes among the intentified cell clusters.

value: mLNs (small intestinal and colon/caecum-draining)

value: CTAGGTGA,TCGTTCAG,AGCCAATT,GATACGCC


title: MYC-OE_4_130d (techn. Rep. 2)

status: Public on May 30 2018

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

description:
56548_4
barcode: 703:AGGCAGAA /505:GTAAGGAG

data_processing:
Bascalling performed using RTA 1.18.64.0
The strand specific reads were screened for ribosomal RNA by aligning with BWA (v0.7.12) against known rRNA sequences (RefSeq).
Transcripts are derived from Homo sapiens genome (hg38) by using a RefSeq annotation derived as GTF (UCSC, 2015_01, hg38).
The rRNA subtracted reads were subjected to abundance estimation with kallisto (0.43.0; parameter: -b 100 --single -l 200 -s 20 ).
Genome_build: hg38
Supplementary_files_format_and_content: TAB-separated files (tsv) containing the TPMs (standard Kallisto output)

source_name: human embryonic stem cells

growth_protocol: Human ESCs were differentiated to 3D brain tissue according to the original cerebral organoid protocol (Lancaster et al. Nature 2013)

extract_protocol:
RNA was isolated from individual organoids using RNeasy Micro Kit (QIAGEN, cat. #74004) according to the manufacturers instructions.
RNA concentration and integrity was analysed using RNA 6000 Nano Chip (Agilent techReplicatenologies, cat. #5067-1511). RNA was enriched for mRNA using SMART-Seq v4 Ultra Low Input RNA Kit  (Clontech, cat. # 634891). Libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, cat. # E7420L). Barcoded samples were multiplexed and sequenced 50bp SE on a HighSeq2500 (Illumina). Sample preparation and sequencing was performed at the VBCF NGS Unit (www.vbcf.ac.at). Samples were sequenced twice each.

treatment_protocol: Embryoid bodies were introduced gene aberrations via genome-editing techniques Sleeping Beauty transposon and CRISPR-Cas9 system

value: cerebral organoids

tag: gene aberrations

value: MYC-OE

tag: days in culture

value: 130 days


title: MYC-OE_2_130d (techn. Rep. 2)

description:
56546_4
barcode: 703:AGGCAGAA /502:CTCTCTAT


title: GBM-3_3_130d (techn. Rep. 2)

description:
56544_4
barcode: 702:CGTACTAG /510:CGTCTAAT


title: MYC-OE_1_130d (techn. Rep. 2)

description:
56545_4
barcode: 702:CGTACTAG /511:TCTCTCCG


title: MYC-OE_3_130d (techn. Rep. 2)

description:
56547_4
barcode: 703:AGGCAGAA /503:TATCCTCT


title: GBM-3_2_130d (techn. Rep. 2)

description:
56542_4
barcode: 702:CGTACTAG /507:AAGGAGTA


title: GBM-2_3_130d (techn. Rep. 2)

description:
56539_4
barcode: 702:CGTACTAG /503:TATCCTCT


title: GBM-3_1_130d (techn. Rep. 2)

description:
56541_4
barcode: 702:CGTACTAG /506:ACTGCATA


title: GBM-1_4_130d (techn. Rep. 2)

description:
56536_4
barcode: 701:TAAGGCGA /510:CGTCTAAT


title: GBM-2_4_130d (techn. Rep. 2)

description:
56540_4
barcode: 702:CGTACTAG /505:GTAAGGAG


title: GBM-1_3_130d (techn. Rep. 2)

description:
56535_4
barcode: 701:TAAGGCGA /508:CTAAGCCT


title: GBM-2_1_130d (techn. Rep. 2)

description:
56537_4
barcode: 701:TAAGGCGA /511:TCTCTCCG


title: CTRL_2_130d (techn. Rep. 2)

description:
56531_4
barcode: 701:TAAGGCGA /503:TATCCTCT


title: GBM-1_1_130d (techn. Rep. 2)

description:
56533_4
barcode: 701:TAAGGCGA /506:ACTGCATA


title: CTRL_1_130d (techn. Rep. 2)

description:
56530_4
barcode: 701:TAAGGCGA /502:CTCTCTAT


title: CTRL_3_130d (techn. Rep. 2)

description:
56532_4
barcode: 701:TAAGGCGA /505:GTAAGGAG


title: GBM-1_2_130d (techn. Rep. 2)

description:
56534_4
barcode: 701:TAAGGCGA /507:AAGGAGTA


title: MYC-OE_3_130d (techn. Rep. 1)

description:
56547_3
barcode: 703:AGGCAGAA /503:TATCCTCT


title: WT_no_Cu_vs_WT_Cu_1

status: Public on Aug 28 2018

hyb_protocol: Custom-made whole-genome DNA microarrays for C. glutamicum ATCC 13032 printed with 70-mer oligonucleotides were obtained from Operon (Cologne, Germany) and are based on the genome sequence entry NC_006958. Hybridisation and stringent washing of the microarrays were performed according to the instructions of the supplier. Hybridisation was carried out for 16 - 18 h with Nexterion Oligo Hyb buffer (Shott, Jena, Germany) covered with a 25 mm x 60 mm LifterSlip (Implen, Munich, Germany) in a humid camber.

scan_protocol: After washing the microarrays were dried by centrifugation (5 min, 1600 g) and fluorescence was determined at 532 nm (Cy3-dUTP) and 635 nm (Cy5-dUTP) with 10 µm resolution using an Axon GenePix 4000B laser scanner (Axon Instruments, Sunnyvale, U.S.A).

data_processing: Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6, Axon Instruments). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (www.bioconductor.org). Processed and normalized data as well as experimental details (according to MIAME) were stored in the in-house microarray database for further analysis. For determination of differentially expressed genes data were quality filtered as decribed (Polen et al., 2007) using Signal/Noise >=3 for Cy5 or Cy3 channel.

source_name: Cu starvation

tag: genotype/variation

value: wild type ATCC 13032

source_name: Cu sufficiency


title: WT_no_Cu_vs_WT_Cu_3_csw


title: WT_no_Cu_vs_WT_Cu_2


title: MYC-OE_2_130d (techn. Rep. 1)

description:
56546_3
barcode: 703:AGGCAGAA /502:CTCTCTAT


title: MYC-OE_1_130d (techn. Rep. 1)

description:
56545_3
barcode: 702:CGTACTAG /511:TCTCTCCG


title: GBM-2_2_130d (techn. Rep. 2)

description:
56538_4
barcode: 702:CGTACTAG /502:CTCTCTAT


title: Dcg2699_vs_WT_I

source_name: Δcg2699 CGXII glucose

value: wild type ATCC 13032 Δcg2699

source_name: wt CGXII glucose


title: Dcg2699_vs_WT_II


title: GBM-3_3_130d (techn. Rep. 1)

description:
56544_3
barcode: 702:CGTACTAG /510:CGTCTAAT


title: Dcg2699_vs_WT_III_csw

source_name: CGXII glucose

source_name: Δcg2699 wt CGXII glucose


title: GBM-3_2_130d (techn. Rep. 1)

description:
56542_3
barcode: 702:CGTACTAG /507:AAGGAGTA


title: GBM-2_4_130d (techn. Rep. 1)

description:
56540_3
barcode: 702:CGTACTAG /505:GTAAGGAG


title: GBM-3_1_130d (techn. Rep. 1)

description:
56541_3
barcode: 702:CGTACTAG /506:ACTGCATA


title: GBM-1_4_130d (techn. Rep. 1)

description:
56536_3
barcode: 701:TAAGGCGA /510:CGTCTAAT


title: CTRL_3_130d (techn. Rep. 1)

description:
56532_3
barcode: 701:TAAGGCGA /505:GTAAGGAG


title: GBM-1_2_130d (techn. Rep. 1)

description:
56534_3
barcode: 701:TAAGGCGA /507:AAGGAGTA


title: GBM-2_2_130d (techn. Rep. 1)

description:
56538_3
barcode: 702:CGTACTAG /502:CTCTCTAT


title: GBM-1_1_130d (techn. Rep. 1)

description:
56533_3
barcode: 701:TAAGGCGA /506:ACTGCATA


title: GBM-2_1_130d (techn. Rep. 1)

description:
56537_3
barcode: 701:TAAGGCGA /511:TCTCTCCG


title: GBM-1_3_130d (techn. Rep. 1)

description:
56535_3
barcode: 701:TAAGGCGA /508:CTAAGCCT


title: CTRL_2_130d (techn. Rep. 1)

description:
56531_3
barcode: 701:TAAGGCGA /503:TATCCTCT


title: CTRL_1_130d (techn. Rep. 1)

description:
56530_3
barcode: 701:TAAGGCGA /502:CTCTCTAT


title: MYC-OE_4_130d (techn. Rep. 1)

description:
56548_3
barcode: 703:AGGCAGAA /505:GTAAGGAG


title: GBM-2_3_130d (techn. Rep. 1)

description:
56539_3
barcode: 702:CGTACTAG /503:TATCCTCT


title: GBM-2_1_45d (techn. Rep. 2)

description: barcode: GAGTGG

data_processing:
Bascalling performed using RTA 1.18.64.0
The strand specific reads were screened for ribosomal RNA by aligning with BWA (v0.7.12) against known rRNA sequences (RefSeq).
The rRNA subtracted reads were aligned with TopHat (v2.1.1) against the Homo sapiens genome (hg38). Microexon-search was enabled. Additionally, a gene model was provided as GTF (UCSC, 2015_01, hg38).
The aligned reads were counted with HTSeq (0.6.1p1) and counts of technical replicates were summed for each gene. The genes were subjected to differential expression analysis with DESeq2 (v1.12.4).
Genome_build: hg38
Supplementary_files_format_and_content: Excel files (xlsx) containing the differential expression analysis (standard DESeq2 output)

value: 45 days


title: MYC-OE_3_45d (techn. Rep. 2)

description: barcode: CAGATC


title: GBM-3_3_45d (techn. Rep. 2)

description: barcode: GTTTCG


title: MYC-OE_2_45d (techn. Rep. 2)

description: barcode: ATCACG


title: GBM-1_1_45d (techn. Rep. 2)

description: barcode: CTTGTA


title: CTRL_2_45d (techn. Rep. 2)

description: barcode: CCGTCC


title: GBM-3_1_45d (techn. Rep. 2)

description: barcode: GTCCGC


title: GBM-3_2_45d (techn. Rep. 2)

description: barcode: AGTCAA


title: MYC-OE_1_45d (techn. Rep. 2)

description: barcode: TAGCTT


title: CTRL_1_45d (techn. Rep. 2)

description: barcode: AGTTCC


title: GBM-2_3_45d (techn. Rep. 2)

description: barcode: ACTGAT


title: CTRL_3_45d (techn. Rep. 2)

description: barcode: GCCAAT


title: GBM-2_2_45d (techn. Rep. 2)

description: barcode: TGACCA


title: GBM-3_3_45d (techn. Rep. 1)

description: barcode: GTTTCG


title: MYC-OE_1_45d (techn. Rep. 1)

description: barcode: TAGCTT


title: MYC-OE_2_45d (techn. Rep. 1)

description: barcode: ATCACG


title: MYC-OE_3_45d (techn. Rep. 1)

description: barcode: CAGATC


title: GBM-2_1_45d (techn. Rep. 1)

description: barcode: GAGTGG


title: GBM-2_2_45d (techn. Rep. 1)

description: barcode: TGACCA


title: GBM-3_2_45d (techn. Rep. 1)

description: barcode: AGTCAA


title: CTRL_3_45d (techn. Rep. 1)

description: barcode: GCCAAT


title: CTRL_1_45d (techn. Rep. 1)

description: barcode: AGTTCC


title: GBM-1_1_45d (techn. Rep. 1)

description: barcode: CTTGTA


title: CTRL_2_45d (techn. Rep. 1)

description: barcode: CCGTCC


title: GBM-3_1_45d (techn. Rep. 1)

description: barcode: GTCCGC


title: shRNA-NC [C3]

status: Public on May 12 2018

first: Ming

middle: zhe

last: Ma

state: Shanghai

address: 270 DongAn Road

department: Department of Gastric Surgery

institute: Fudan University Shanghai Cancer Center

description:
C3
processed data file: Expression_Gene.xlsx
processed data file: Expression_Transcript.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome.
Fragments per kilobase Million (FPKM) were calculated using the formula: (total exon reads)/[mapped reads(million)*exon length (kb)]
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *xlsx: Excel files include FPKM values for each Sample.

source_name: gastric cancer cell line MKN45

growth_protocol: MKN45 cells were routinely generated by re-plating d 4 in DMEM supplemented with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: MKN45 cells were transfected with shRNA or shRNA-NC.

value: gastric cancer cell line

tag: shRNA

value: control


title: shRNA-NC [C1]

description:
C1
processed data file: Expression_Gene.xlsx
processed data file: Expression_Transcript.xlsx


title: shRNA [T2]

description:
T2
processed data file: Expression_Gene.xlsx
processed data file: Expression_Transcript.xlsx


title: GBM-2_3_45d (techn. Rep. 1)

description: barcode: ACTGAT


title: shRNA-NC [C2]

description:
C2
processed data file: Expression_Gene.xlsx
processed data file: Expression_Transcript.xlsx


title: shRNA [T1]

description:
T1
processed data file: Expression_Gene.xlsx
processed data file: Expression_Transcript.xlsx


title: MNCs at diagnosis. Patient p07

status: Public on Aug 21 2017

first: Fikret

last: Rifatbegovic

address: Zimmermannplatz 10

department: Tumor biology

institute: Children's Cancer Research Institute

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M07d

data_processing:
RNA-seq reads were mapped with GSNAP v2014-12- 28 [20147302] (“-- maxsearch=100 -- npaths=1 -- max-mismatches=1 --novelsplicing=0 “) to human reference genome build GRCh37. Known SNPs and splice sites were extracted from dbSNP build 138 and Ensembl GRCh37 build 75, respectively.
DESeq2-normalized fragments per million (FPM), log2 scale
Genome_build: hg19
Supplementary_files_format_and_content: DESeq expression matrix (log2)

source_name: Non-tumor mononuclear cells (MNCs)

extract_protocol:
miRNeasy Micro Kit
30 ng of total RNA was used for cDNA synthesis following the NEBNext® UltraT RNA Library Prep Kit for Illumina® protocol (New England BioLabs). From the point when cDNA was synthesized, the library was completed in an automated way at the EMBL Genomics Core Facility (Heidelberg, Germany) following the manufacture's protocol.

value: DTCs-depleted bone marrow (MNCs)


title: MNCs at diagnosis. Patient p30

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M30d


title: MNCs at diagnosis. Patient p59

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M59d


title: MNCs at diagnosis. Patient p28

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M28d


title: MNCs at diagnosis. Patient p27

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M27d


title: MNCs at diagnosis. Patient p31

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M31d


title: shRNA [T3]

description:
T3
processed data file: Expression_Gene.xlsx
processed data file: Expression_Transcript.xlsx


title: MNCs at diagnosis. Patient p33

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M33d


title: MNCs at diagnosis. Patient p06

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M06d


title: delta_esrI_II

status: Public on Nov 21 2017

data_processing: Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 7.0, Axon Instruments). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (www.bioconductor.org).

source_name: Cg wild type

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Frunzke, J., V. Engels, S. Hasenbein, C. Gätgens & M. Bott, (2008) Co-ordinated regulation of gluconate catabolism and glucose uptake in Corynebacterium glutamicum by two functionally equivalent transcriptional regulators, GntR1 and GntR2. Mol Microbiol 67: 305-322.

growth_protocol: For the transcriptome analyses, pre-cultures of the respective C. glutamicum strains grown to an OD600 of 5-6 were used to inoculate the main cultures to an OD600 of 0.5 which subsequently were grown to the mid-exponential phase. For the comparison of the esrSR deletion mutant expressing EsrR from plasmid with the wild-type strain carrying the corresponding empty vector, BHIS medium was used and 1 mM IPTG was added at this stage. The cultures were harvested after an additional hour at 30°C. For the analysis of the bacitracin influence, the main culture was split into two cultures and bacitracin was added to a final concentration of 1 µg ml-1 to one of the cultures. The cells were harvested 30 min after bacitracin addition. For the comparison of the wild-type strain and the esrI (cg0706) deletion mutant, the main cultures were used to inoculate second main cultures to an optical density of 0.5 and the cells were harvested when the cultures had reached an OD600 of 5. For the latter two experiments, CGXII medium with 4 % glucose was used.

extract_protocol: The preparation of total RNA was performed as described previously with the RNeasy Kit from Qiagen (Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott, (2004) Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol Microbiol 54: 420-438.)

tag: strain

tag: growth phase

value: exponential

source_name: Cg delta cg0706

value: ATCC 13032 delta cg0706


title: MNCs at diagnosis. Patient p03

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M03d


title: MNCs at diagnosis. Patient p02

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M02d


title: MNCs at diagnosis. Patient p04

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M04d


title: cgtR7_overexpression_II

source_name: Cg /pEKEx3

source_name: Cg delta cgtSR7 /pEKEx3_R7

value: ATCC 13032 delta cgtSR7


title: delta_esrI_I


title: bacitracin_III

source_name: Cg +bacitracin

tag: treatment

value: bacitracin

source_name: Cg control


title: delta_esrI_III


title: MNCs at diagnosis. Patient p10

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M10d


title: bacitracin_I


title: MNCs at diagnosis. Patient p01

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
M01d


title: cgtR7_overexpression_III


title: bacitracin_II


title: MB001_vs_C1_ExpA

status: Public on Aug 23 2017

data_processing: For ratio calculation and ratio normalization, GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

source_name: MB001 CGXII glucose

growth_protocol: For transcriptome analysis C. glutamicum MB001 and C1 cells were grown in 5 ml BHI (Brain Heart Infusion, Difco) for about 6 hours at 30°C. A second precultivation was performed in CGXII minimal medium containing 2% (w/v) glucose as carbon source. The main cultures were inoculated to an OD of 1 in CGXII minimal medium with 2% (w/v) glucose. At an OD of 5 the cells were harvested by centrifugation (4120 x g, 10 min and 4 °C). The cell pellet was subsequently frozen in liquid nitrogen and stored at -70°C.

tag: sample type

value: prophage free wild type

source_name: C1 CGXII glucose

value: genome reduced chassis C1


title: WT_1uM_Fe_vs_36uM_Fe_II

status: Public on Feb 24 2020

data_processing: For calculation and normalization of ratios reflecting the relative mRNA levels (Ratio of Medians, GenePix Pro), GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

source_name: wild type

extract_protocol: The preparation of total RNA was performed as described previously with the RNeasy Kit from Qiagen (Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott, (2004)  Mol Microbiol 54: 420-438.)

value: wild type

value: 1 uM Fe, OD 4-5

value: 36 uM Fe, OD 4-5


title: MB001_vs_C1_ExpB


title: MB001_vs_C1_ExpC


title: MB001_vs_C1_ExpD


title: cgtR7_overexpression_I


title: HY6

status: Public on Nov 10 2016

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: Heart

extract_protocol:
Human hypertrophic heart tissue samples were obtained from patients previously diagnosed with HCM, undergoing septal myectomy surgery (n=5). Control samples were obtained from normal heart donor left ventricles (n=4)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart


title: NH6

description: Control samples were obtained from normal heart donor left ventricles (n=4)


title: HY1

description: Human hypertrophic heart tissue samples were obtained from patients previously diagnosed with HCM, undergoing septal myectomy surgery (n=5)


title: HY5


title: HY4


title: NH2


title: NH4


title: NH1


title: HY2


title: WT ESC D0_2

status: Public on Jun 13 2017

city: Heraklion, Crete

first: Christiana

last: Hadjimichael

address: Nikolaou Plastira 100

department: Institute of Molecular Biology and Biotechnology (IMBB)

country: Greece

institute: Foundation for Research and Technology - Hellas (FORTH)

description: Gene exppression data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse ST1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000.

data_processing: The data were analyzed using Transcriptome Analysis Console Software according to Affymetrix' instructions.

source_name: Embryonic Stem Cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2005-2009, Affymetrix).Breifly, double-stranded cDNA is synthesized from 10 μg total RNA isolated from ESC cells. An in vitro transcription (IVT) reaction is then done to produce biotin-labeled cRNA from the cDNA. The cRNA is fragmented before hybridization.

growth_protocol: The murine feeder-independent ESC line CGR8 was cultured in gelatin-coated flasks in Dulbecco’s modified eagle medium (DMEM; Gibco) supplemented with 100U/ml LIF (ESGRO-Millipore), 2mM L-Glutamine (Gibco), 2mM non-essential amino acids (Gibco), 0,1mM beta-mercaptoethanol (Gibco) and 15% heat-inactivated HyClone fetal bovine serum (FBS; GE Healthcare Life Sciences).The generation of stably expressing PML-shRNA ESC lines was achieved using PML shRNA-pLKO.1 lentiviral vector. Briefly, CGR8 cells were grown to 80% confluency and infected with the lenti-viruses produced either by the empty shRNA or PML shRNA vector, for 72h. Selection of shRNA infected cells was achieved with puromycin (2μg/ml).

extract_protocol: Total RNA was extracted from PML KD and WT ESC cell lines at D0 and D4 of EBs differentiation using RNeasy Microarray Tissue Mini Kit (Qiagen).

treatment_protocol: For Embryoid Bodies (EB) formation, cells were trypsinised and diluted in Iscove's Modified Dulbecco's Medium (IMDM; Gibco) supplemented with 2mM L-Glutamine (Gibco), 2mM non-essential amino acids (Gibco), 0,1mM beta-mercaptoethanol (Gibco) and 20% heat-inactivated HyClone FBS (GE Healthcare Life Sciences), to a final concentration of 1000 cells/20μl. EB were cultured without LIF as hanging drops for 2 days and subsequently collected and cultured in suspension for 6 additional days.

tag: background strain

value: WT

tag: donor strain

tag: passages


title: PML KD EBs D4_2

description: Gene exppression data

value: PML KD


title: CpdAover_vs_empty_ExpC_CS

status: Public on Nov 15 2016

scan_protocol: After washing the microarrays the fluorescence was determined at 532 nm (Cy3-dUTP) and 635 nm (Cy5-dUTP) with 5 µm resolution using an Axon GenePix 4000B laser scanner (Axon Instruments, Sunnyvale, U.S.A).

data_processing: Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 7.0, Axon Instruments). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (www.bioconductor.org). Processed and normalized data as well as experimental details (according to MIAME) were stored in the in-house microarray database for further analysis. For determination of differentially expressed genes data were quality filtered as decribed (Polen et al., 2007) using Signal/Noise >=3 for Cy5 or Cy3 channel.

source_name: C. glutamicum pEKEx2

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Polen T, Schluesener D, Poetsch A, Bott M, Wendisch VF (2007) Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol Lett. 273(1):109-19.

growth_protocol: Strains C. glutamicum ATCC13032 (WT) pEKEx2, C. glutamicum ∆cpdA pEKEx2 and C. glutamicum WT pEKEx2-cpdA were grown in the defined minimal medium CGXII + 100 mM glucose as sole carbon and cultivated at 30°C. Cells were harvested at an OD600 of 5 in pre-cooled ice-filled tubes via centrifugation (4,500 x g, 10 min, and 4 °C) and subsequently frozen in liquid nitrogen as well as stored at -70°C until preparation of RNA.

extract_protocol: The preparation of total RNA was performed as described elsewhere with the RNeasy Kit from Qiagen (Polen T, Schluesener D, Poetsch A, Bott M, Wendisch VF (2007) Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol Lett. 273(1):109-19).

treatment_protocol: CGXII medium 100 mM glucose, 250 µM IPTG, 30°C

source_name: C. glutamicum pEKEx2-cpdA


title: PML KD ESC D0_2

description: Gene exppression data


title: WT EBs D4_2

description: Gene exppression data


title: CpdAover_vs_empty_ExpB


title: WT EBs D4_1

description: Gene exppression data


title: PML KD ESC D0_1

description: Gene exppression data


title: WT ESC D0_1

description: Gene exppression data


title: CpdAover_vs_empty_ExpA


title: CpdAdel_vs_WT_ExpC_CS

source_name: C. glutamicum ∆cpdA pEKEx2


title: PML KD EBs D4_1

description: Gene exppression data


title: CpdAdel_vs_WT_ExpB


title: CpdAdel_vs_WT_ExpA


title: Sample_3_Wt_vs_dpup_1uMFe_III_csw

status: Public on Apr 04 2016

description: Sample 3

growth_protocol: DNA microarray analyses were performed to compare the mRNA levels of the C. glutamicum Δpup mutant and its parent wild type under iron-limited conditions. The two strains precultivated in CGXII medium with 4% (w/v) glucose and 1 µM FeSO4 were inoculated into fresh medium to an OD600 of 1, cultured for 2 h, and harvested on ice by centrifugation (5 min at 4,000 g and 4°C).

value: Δpup mutant


title: Sample_1_Wt_vs_dpup_1uMFe_I

description: Sample 1