title: DP6_E3

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_C6

status: Public on Apr 18 2017

type: SRA

city: New York

first: Hanseul

last: Yang

state: NY

address: 1230 York Avenue

country: USA

institute: Rockefeller University

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text

library_source: transcriptomic

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
The expression values of each gene were quantified as transcript per million (TPM) using RSEM (v1.2.30)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Mouse back skin

extract_protocol:
Single bulge hair follicle stem cells, hair germ cells and basal hair bulb cells at indicated age were FACS-purified, collected into 96 well plates containing lysis buffer and stored in -80oC
Single cells were lyzed by incubating at 72oC for 3 min. Reverse transcription reaction and whole transcriptome amplification were perforemd according to Smart-seq2 protocol. The amplified cDNA libraries were purified by Ampure XP beads (Beckman Coulter), and tagmentation reaction was perforemd by Illumina Nextera XT DNA Library Prep Kit. The libraries were pooled and sequecned on Illumina Nextseq 500 with mid-output 75cycles paired-end mode.

tag: Sex

value: Male

tag: age

tag: strain

tag: sorting markers

value: GFP, RFP, integrinα9, CD117


title: DP6_C4

description:
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title: DP6_C2

description:
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title: DP6_C5

description:
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title: DP6_C12

description:
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title: DP6_C1

description:
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title: DP6_D5

description:
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title: DP6_B6

description:
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title: DP6_B8

description:
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title: DP6_C11

description:
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title: DP6_B7

description:
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title: DP6_B4

description:
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title: DP6_C10

description:
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title: DP6_B9

description:
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title: DP6_C3

description:
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title: DP6_B10

description:
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title: DP6_B2

description:
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title: DP6_A8

description:
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title: DP6_A6

description:
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title: DP6_A4

description:
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title: DP6_A2

description:
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title: DP6_A3

description:
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title: DP6_A10

description:
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title: DP5_H9

description:
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title: DP5_H7

description:
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title: DP5_H5

description:
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title: DP5_H4

description:
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title: DP5_H6

description:
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title: DP5_H1

description:
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title: DP5_H3

description:
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title: DP5_H10

description:
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title: DP5_G9

description:
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title: DP6_B12

description:
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title: DP5_G7

description:
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title: DP6_B11

description:
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title: DP5_G6

description:
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title: DP5_G5

description:
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title: DP5_G1

description:
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title: DP5_G12

description:
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title: DP5_F8

description:
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title: DP5_F6

description:
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title: DP5_F7

description:
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title: DP5_G10

description:
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title: DP5_G4

description:
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title: DP5_G11

description:
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title: DP5_H8

description:
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title: DP5_F4

description:
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title: DP5_F5

description:
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title: DP5_F2

description:
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title: DP5_F12

description:
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title: DP5_F11

description:
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title: DP5_H11

description:
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title: DP5_E9

description:
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title: DP5_F10

description:
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title: DP5_E8

description:
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title: DP5_E5

description:
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title: DP5_E6

description:
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title: DP5_E4

description:
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title: DP5_E3

description:
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title: DP5_E12

description:
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title: DP5_E2

description:
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title: DP5_E11

description:
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title: DP5_F9

description:
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title: DP5_D12

description:
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title: DP5_D5

description:
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title: DP5_D9

description:
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title: DP5_D8

description:
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title: DP5_D10

description:
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title: DP5_E10

description:
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title: DP5_D4

description:
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title: DP5_D3

description:
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title: DP5_D6

description:
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title: DP5_C9

description:
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title: DP5_D2

description:
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title: DP5_F1

description:
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title: DP5_D7

description:
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title: DP5_D1

description:
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title: DP5_F3

description:
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title: DP5_C6

description:
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title: DP5_C5

description:
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title: DP5_C4

description:
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title: DP5_C3

description:
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title: DP5_C2

description:
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title: DP5_C1

description:
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title: DP5_C8

description:
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title: DP5_C11

description:
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title: DP5_C12

description:
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title: DP5_C10

description:
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title: DP5_B8

description:
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title: DP5_B9

description:
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title: DP5_B7

description:
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title: DP5_B6

description:
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title: DP5_B5

description:
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title: DP5_C7

description:
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title: DP5_B1

description:
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title: DP5_B4

description:
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title: DP5_B2

description:
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title: DP5_A9

description:
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title: DP5_A7

description:
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title: DP5_B11

description:
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title: DP5_A4

description:
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title: DP5_A5

description:
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title: DP5_A11

description:
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title: DP5_A12

description:
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title: DP5_A2

description:
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title: DP5_B12

description:
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title: DP5_B10

description:
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title: DP3_H9

description:
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title: DP5_A8

description:
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title: DP5_A10

description:
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title: DP5_A3

description:
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title: DP3_H5

description:
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title: DP3_H7

description:
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title: DP3_H4

description:
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title: DP5_B3

description:
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title: DP3_H3

description:
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title: DP3_H2

description:
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title: DP3_H1

description:
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title: DP3_H11

description:
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title: DP3_H10

description:
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title: DP3_G8

description:
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title: DP3_G9

description:
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title: DP3_G7

description:
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title: DP3_G5

description:
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title: DP3_G2

description:
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title: DP3_G1

description:
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title: DP3_G3

description:
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title: DP3_G12

description:
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title: DP3_G4

description:
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title: DP3_G10

description:
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title: DP3_F9

description:
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title: DP3_H6

description:
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title: DP3_F5

description:
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title: DP3_F4

description:
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title: DP3_F6

description:
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title: DP3_F2

description:
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title: DP3_H8

description:
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title: DP3_F1

description:
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title: DP3_F8

description:
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title: DP3_F12

description:
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description:
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title: DP3_F10

description:
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title: DP3_E8

description:
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description:
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title: DP3_E9

description:
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title: DP3_E5

description:
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title: DP3_G6

description:
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title: DP3_E1

description:
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title: DP3_E6

description:
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title: DP3_E12

description:
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title: DP3_F7

description:
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title: DP3_E3

description:
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title: DP3_E11

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title: DP3_F3

description:
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title: DP3_D9

description:
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title: DP3_D4

description:
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title: DP3_C7

description:
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title: DP3_D1

description:
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title: DP3_D3

description:
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title: DP3_C9

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title: DP3_D12

description:
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title: DP3_E10

description:
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title: DP3_D10

description:
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title: DP3_C6

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title: DP3_C5

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title: DP3_D2

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title: DP3_C2

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title: DP3_C1

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title: DP2_G2

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Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_G11

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_G10

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_F9

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_F6

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP3_A2

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_F8

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_F7

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_F5

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_F3

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_F1

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_F2

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_F11

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_F12

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_F10

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_F4

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_E8

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_E9

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_E4

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_E6

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_E12

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_E1

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_E2

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_E5

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_E3

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_D9

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_G12

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_D8

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_D7

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_E11

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_D12

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_D1

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_D6

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_C7

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_D10

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_D3

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_C9

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_D5

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_C8

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_C4

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_C1

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_C11

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_C6

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_C2

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_B8

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_B5

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_E10

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_B7

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_C10

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_C3

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_B4

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_B6

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_C5

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_B1

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_B12

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_A9

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_B2

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_B11

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_B3

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_A4

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_A8

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_B10

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_A5

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_A7

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_A1

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_A6

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_A3

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP2_A10

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: P2-1-H4

description:
Ana6_basal_hair_bulb_TPM.txt
mm10
tab-delimited text

extract_protocol:
Single bulge hair follicle stem cells, hair germ cells and basal hair bulb cells at indicated age were FACS-purified, collected into 96 well plates containing lysis buffer and stored in -80oC
Single cells were lyzed by incubating at 72oC for 3 min. Revers transcritpion reaction and whole transcriptome amplification were perforemd according to Smart-seq2 protocol. The amplified cDNA libraries were purified by Ampure XP beads (Beckman Coulter), and tagmentation reaction was perforemd by Illumina Nextera XT DNA Library Prep Kit. The libraries were pooled and sequecned on Illumina Nextseq 500 with mid-output 75cycles paired-end mode.

value: Mixed

value: Lhx2-GFP (CD1)

value: GFP, integrin α6, integrin b1, CD34, Sca-1, Pcadherin


title: P2-1-H7


title: P2-1-H3


title: P2-1-H8


title: P2-1-H9


title: P2-1-H2


title: P2-1-H12


title: P2-1-G8


title: P2-1-G9


title: P2-1-H10


title: P2-1-H6


title: P2-1-G5


title: P2-1-G6


title: P2-1-H11


title: DP2_A2

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: P2-1-H1


title: DP2_A11

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: P2-1-G7


title: P2-1-G2


title: P2-1-G10


title: P2-1-F3


title: P2-1-F4


title: P2-1-H5


title: P2-1-F9


title: P2-1-F12


title: P2-1-E8


title: P2-1-E9


title: P2-1-G4


title: P2-1-F10


title: P2-1-F11


title: P2-1-E3


title: P2-1-E11


title: P2-1-E10


title: P2-1-E4


title: P2-1-D7


title: P2-1-D6


title: P2-1-F7


title: P2-1-E2


title: P2-1-D3


title: P2-1-G3


title: P2-1-E5


title: P2-1-E12


title: P2-1-F8


title: P2-1-E1


title: P2-1-D9


title: P2-1-D1


title: P2-1-D8


title: P2-1-D11


title: P2-1-F2


title: P2-1-C8


title: P2-1-D10


title: P2-1-D2


title: P2-1-D12


title: P2-1-C7


title: P2-1-C3


title: P2-1-C6


title: P2-1-E6


title: P2-1-C5


title: P2-1-C1


title: P2-1-C12


title: P2-1-C11


title: P2-1-B9


title: P2-1-B4


title: P2-1-B2


title: P2-1-B7


title: P2-1-B5


title: P2-1-C10


title: P2-1-B3


title: P2-1-B10


title: P2-1-B6


title: P2-1-A8


title: P2-1-A5


title: P2-1-A10


title: P2-1-A12


title: P2-1-A6


title: P2-1-A4


title: P2-1-A1


title: P2-1-A3


title: P2-1-A9


title: P1-6-H9


title: P2-1-C2


title: P1-6-H3


title: P2-1-B8


title: P1-6-H7


title: P1-6-H6


title: P1-6-H12


title: P1-6-H8


title: P1-6-H11


title: P2-1-B1


title: P1-6-G7


title: P1-6-G6


title: P1-6-G12


title: P1-6-G1


title: P1-6-G5


title: P1-6-G11


title: P1-6-G10


title: P2-1-A2


title: P1-6-G4


title: P1-6-G9


title: P1-6-F9


title: P1-6-F8


title: P1-6-F5


title: P1-6-F1


title: P1-6-F10


title: P1-6-F3


title: P1-6-F2


title: P1-6-E9


title: P1-6-F4


title: P1-6-E7


title: P1-6-E5


title: P1-6-E6


title: P1-6-E3


title: P1-6-E10


title: P1-6-E11


title: P1-6-G8


title: P1-6-D8


title: P1-6-E4


title: P1-6-D7


title: P1-6-D6


title: P1-6-D9


title: P1-6-D4


title: P1-6-C6


title: P1-6-D10


title: P1-6-D2


title: P1-6-D5


title: P1-6-D3


title: P1-6-C8


title: P1-6-D1


title: P1-6-F7


title: P1-6-C4


title: P1-6-C11


title: P1-6-C5


title: P1-6-B7


title: P1-6-C10


title: P1-6-B8


title: P1-6-C3


title: P1-6-B6


title: P1-6-B5


title: P1-6-B4


title: P1-6-B3


title: P1-6-C9


title: P1-6-B12


title: P1-6-B11


title: P1-6-B2


title: P1-6-A9


title: P1-6-B10


title: P1-6-A8


title: P1-6-A5


title: P1-6-C1


title: P1-6-A4


title: P1-6-A1


title: P1-6-A12


title: P1-6-A3


title: P1-5-H6


title: P1-6-A11


title: P1-6-A10


title: P1-5-H1


title: P1-5-H2


title: P1-5-H9


title: P1-5-H5


title: P1-5-H12


title: P1-5-F9


title: P1-5-G10


title: P1-5-G11


title: P1-5-G9


title: P1-5-F8


title: P1-5-G12


title: P1-5-G8


title: P1-6-B1


title: P1-5-G6


title: P1-5-G3


title: P1-5-G5


title: P1-5-H3


title: P1-5-H10


title: P1-5-F11


title: P1-5-F12


title: P1-5-F10


title: P1-5-F5


title: P1-5-E6


title: P1-5-E7


title: P1-5-E12


title: P1-5-E5


title: P1-5-E4


title: P1-5-E8


title: P1-5-G7


title: P1-6-A7


title: P1-5-F7


title: P1-5-E10


title: P1-5-E1


title: P1-5-D8


title: P1-5-D7


title: P1-5-E11


title: P1-5-F2


title: P1-5-E9


title: P1-5-D3


title: P1-5-D4


title: P1-5-C8


title: P1-5-D1


title: P1-5-D10


title: P1-5-D2


title: P1-5-D11


title: P1-5-C7


title: P1-5-C2


title: P1-5-C1


title: P1-5-C6


title: P1-5-C12


title: P1-5-C9


title: P1-5-C11


title: P1-5-C5


title: P1-5-C10


title: P1-5-C3


title: P1-5-B9


title: P1-5-C4


title: P1-5-B5


title: P1-5-D5


title: P1-5-B8


title: P1-5-B7


title: P1-5-B1


title: P1-5-B12


title: P1-5-B11


title: P1-5-B10


title: P1-5-A6


title: P1-5-A5


title: P1-5-A7


title: P1-5-A2


title: P1-5-A12


title: P1-5-A9


title: P1-5-A11


title: P1-5-A3


title: P1-4-H8


title: P1-4-H2


title: P1-4-H1


title: P1-5-A10


title: P1-4-H6


title: P1-4-H12


title: P1-4-H10


title: P1-4-G7


title: P1-4-G8


title: P1-5-B3


title: P1-4-H11


title: P1-4-G5


title: P1-4-G6


title: P1-4-G4


title: P1-4-G2


title: P1-4-G3


title: P1-4-G1


title: P1-4-G10


title: P1-4-F9


title: P1-4-F7


title: P1-4-F5


title: P1-4-F3


title: P1-4-F2


title: P1-4-F8


title: P1-4-H9


title: P1-4-E8


title: P1-4-F1


title: P1-4-G9


title: P1-4-E7


title: P1-4-E9


title: P1-4-F12


title: P1-5-F6


title: P1-4-F11


title: P1-4-E6


title: P1-4-F10


title: P1-4-E5


title: P1-4-E3


title: P1-4-E12


title: P1-4-E4


title: P1-4-D4


title: P1-4-G11


title: P1-4-D8


title: P1-4-D9


title: P1-4-D7


title: P1-4-F4


title: P1-4-E10


title: P1-4-D5


title: P1-4-D3


title: P1-4-D2


title: P1-4-D1


title: P1-4-E2


title: P1-4-D12


title: P1-4-D11


title: P1-4-C9


title: P1-4-C8


title: P1-4-C5


title: P1-4-C4


title: P1-4-C2


title: P1-4-C1


title: P1-4-D10


title: P1-4-B3


title: P1-4-B4


title: P1-4-B8


title: P1-4-B5


title: P1-4-B1


title: P1-4-B2


title: P1-4-C11


title: P1-4-B11


title: P1-4-B10


title: P1-4-A9


title: P1-4-B12


title: P1-4-A5


title: P1-4-A4


title: P1-4-A8


title: P1-4-A2


title: P1-4-A1


title: P1-4-A3


title: P1-4-A12


title: P1-4-A11


title: P1-4-C6


title: P1-3-H9


title: P1-3-H7


title: P1-3-H6


title: P1-3-H5


title: P1-4-C12


title: P1-3-H12


title: P1-3-G4


title: P1-3-G5


title: P1-3-H2


title: P1-3-H4


title: P1-3-G6


title: P1-3-H11


title: P1-3-H10


title: P1-3-H3


title: P1-3-G12


title: P1-3-G1


title: P1-3-G2


title: P1-3-F9


title: P1-3-F8


title: P1-3-F3


title: P1-3-F1


title: P1-3-F11


title: P1-3-F12


title: P1-3-F2


title: P1-3-F10


title: P1-3-E8


title: P1-3-E4


title: P1-3-E5


title: P1-3-G7


title: P1-3-H1


title: P1-3-G3


title: P1-3-E3


title: P1-3-E1


title: P1-3-E10


title: P1-3-E12


title: P1-3-D7


title: P1-3-D3


title: P1-3-D5


title: P1-3-E11


title: P1-3-D10


title: P1-3-C8


title: P1-3-D12


title: P1-3-D8


title: P1-3-F5


title: P1-3-D1


title: P1-3-C7


title: P1-3-C6


title: P1-3-E2


title: P1-3-C2


title: P1-3-C11


title: P1-3-C5


title: P1-3-C1


title: P1-3-B8


title: P1-3-C10


title: P1-3-B6


title: P1-3-B5


title: P1-3-B7


title: P1-3-B4


title: P1-3-D2


title: P1-3-B3


title: P1-3-D9


title: P1-3-B2


title: P1-3-B10


title: P1-3-B12


title: P1-3-A7


title: P1-3-A6


title: P1-3-A4


title: P1-3-A1


title: P1-3-A12


title: P1-3-A8


title: P1-3-A11


title: P1-3-C4


title: P1-3-A2


title: P1-3-A10


title: P1-3-A5


title: 920mat_H6

description:
Tel_Ana1_Ana2_bulge_HG_basal_HB_TPM.txt
mm10
tab-delimited text

value: GFP, tdTomato, integrin α6, integrin b1, CD34, Pcadherin


title: 920mat_H7


title: P1-3-C3


title: 920mat_H3


title: 920mat_H4


title: 920mat_H8


title: 920mat_H11


title: 920mat_G9


title: 920mat_G7


title: 920mat_G8


title: 920mat_G4


title: 920mat_G3


title: 920mat_G2


title: P1-3-A3


title: 920mat_F8


title: 920mat_G1


title: 920mat_F9


title: 920mat_G10


title: 920mat_F7


title: 920mat_F3


title: 920mat_F12


title: 920mat_F2


title: 920mat_F10


title: 920mat_F6


title: 920mat_F4


title: 920mat_E7


title: 920mat_E9


title: 920mat_H5


title: 920mat_E6


title: 920mat_E8


title: 920mat_E2


title: 920mat_E1


title: 920mat_D5


title: 920mat_D6


title: 920mat_D3


title: 920mat_D1


title: 920mat_D7


title: 920mat_D11


title: 920mat_G11


title: 920mat_C9


title: 920mat_D10


title: 920mat_C6


title: 920mat_C7


title: 920mat_D12


title: 920mat_C2


title: 920mat_C4


title: 920mat_C10


title: 920mat_B9


title: 920mat_C8


title: 920mat_B8


title: 920mat_B7


title: 920mat_C5


title: 920mat_E4


title: 920mat_B3


title: 920mat_B1


title: 920mat_E12


title: 920mat_B12


title: 920mat_B5


title: 920mat_B10


title: 920mat_B11


title: 920mat_B4


title: 920mat_A4


title: 920mat_A3


title: 920mat_A1


title: 920mat_A2


title: 920mat_A12


title: 920mat_A11


title: 915mat_H7


title: 915mat_H9


title: 915mat_H5


title: 915mat_H6


title: 915mat_H4


title: 915mat_H11


title: 915mat_G8


title: 915mat_G5


title: 915mat_G7


title: 915mat_G3


title: 915mat_G4


title: 915mat_G11


title: 915mat_H3


title: 915mat_G2


title: 915mat_F9


title: 920mat_A9


title: 915mat_F8


title: 915mat_G10


title: 920mat_A5


title: 915mat_F6


title: 915mat_F5


title: 915mat_F7


title: 915mat_F4


title: 915mat_F2


title: 915mat_F3


title: 915mat_F1


title: 915mat_G9


title: 915mat_F11


title: 915mat_F12


title: 915mat_E9


title: 915mat_E8


title: 915mat_E7


title: 915mat_E1


title: 915mat_D8


title: 915mat_D5


title: 915mat_D2


title: 915mat_E4


title: 915mat_E10


title: 915mat_E12


title: 915mat_D9


title: 915mat_D4


title: 915mat_D7


title: 915mat_D6


title: 915mat_D11


title: 915mat_D12


title: 915mat_D10


title: 920mat_A6


title: 915mat_C5


title: 915mat_C6


title: 915mat_F10


title: 915mat_C4


title: 915mat_C1


title: 915mat_C9


title: 915mat_E2


title: 915mat_E5


title: 915mat_B9


title: 915mat_E11


title: 915mat_E6


title: 915mat_C2


title: 915mat_B8


title: 915mat_D1


title: 915mat_B7


title: 915mat_B1


title: 915mat_B3


title: 915mat_B10


title: 915mat_B11


title: 915mat_B5


title: 915mat_B4


title: 915mat_A3


title: 915mat_A1


title: 915mat_B2


title: 915mat_A7


title: 915mat_A5


title: 915mat_A6


title: 915mat_A8


title: 915mat_A11


title: 915mat_A10


title: 914mat_H8


title: 914mat_H9


title: 914mat_H7


title: 914mat_H4


title: 914mat_H5


title: 914mat_H10


title: 914mat_H11


title: 914mat_H3


title: 915mat_A12


title: 914mat_G8


title: 914mat_H2


title: 914mat_H6


title: 915mat_A9


title: 914mat_G9


title: 914mat_G7


title: 914mat_G2


title: 914mat_G5


title: 914mat_G1


title: 914mat_G3


title: 914mat_F7


title: 914mat_F5


title: 914mat_F4


title: 914mat_G10


title: 914mat_F11


title: 914mat_F1


title: 914mat_G11


title: 914mat_F2


title: 914mat_F10


title: 914mat_E8


title: 914mat_E7


title: 914mat_E5


title: 914mat_E3


title: 914mat_E6


title: 914mat_E4


title: 914mat_E1


title: 914mat_E9


title: 914mat_E11


title: 914mat_E2


title: 914mat_E10


title: 914mat_D6


title: 914mat_D9


title: 914mat_G6


title: 914mat_D5


title: 914mat_E12


title: 914mat_D2


title: 914mat_C9


title: 914mat_C8


title: 914mat_D8


title: 914mat_C6


title: 914mat_C3


title: 914mat_C7


title: 914mat_C2


title: 914mat_D11


title: 914hg_A9


title: 913hg_H4


title: 914hg_A7


title: 913hg_E7


title: 913hg_D6


title: 913hg_C4


title: 913hg_D2


title: 913hg_H2


title: 913hg_E5


title: 914mat_C10


title: 914mat_D7


title: 913hg_C12


title: 913hg_D4


title: 913hg_B3


title: 913hg_B7


title: 913hg_B10


title: 914mat_C5


title: 913hg_A9


title: 902hg_H8


title: 902hg_H5


title: 902hg_H7


title: 902hg_H6


title: 913hg_B11


title: 902hg_H4


title: 902hg_H2


title: 902hg_H1


title: 902hg_H12


title: 902hg_H10


title: 902hg_G4


title: 902hg_G9


title: 914mat_C11


title: 902hg_G2


title: 902hg_G3


title: 902hg_G12


title: 902hg_G10


title: 902hg_G11


title: 902hg_G5


title: 902hg_F8


title: 902hg_F7


title: 902hg_F4


title: 902hg_F3


title: 902hg_F1


title: 902hg_F12


title: 902hg_F11


title: 902hg_H3


title: 902hg_E8


title: 902hg_E7


title: 902hg_E4


title: 902hg_E3


title: 902hg_E5


title: 902hg_D8


title: 902hg_D9


title: 902hg_E10


title: 902hg_E12


title: 902hg_D7


title: 902hg_D6


title: 902hg_D2


title: 902hg_D5


title: 902hg_D4


title: 902hg_D3


title: 902hg_F2


title: 902hg_D1


title: 902hg_C7


title: 902hg_C8


title: 902hg_C6


title: 902hg_C5


title: 902hg_C1


title: 902hg_C4


title: 902hg_C12


title: 902hg_F10


title: 902hg_C10


title: 902hg_B7


title: 902hg_C11


title: 902hg_B5


title: 902hg_B12


title: 902hg_B11


title: 902hg_C3


title: 902hg_A9


title: 902hg_E6


title: 902hg_B10


title: 902hg_B2


title: 902hg_D10


title: 902hg_A8


title: 902hg_A6


title: 902hg_A4


title: 902hg_A2


title: 902hg_A10


title: 902hg_A11


title: 819hg_H9


title: 902hg_A1


title: 819hg_H6


title: 819hg_H4


title: 819hg_H3


title: 819hg_H5


title: 902hg_B4


title: 819hg_H2


title: 819hg_G9


title: 819hg_H1


title: 819hg_G8


title: 819hg_H10


title: 819hg_G4


title: 819hg_G3


title: 819hg_F8


title: 902hg_A5


title: 819hg_F6


title: 819hg_F4


title: 819hg_F3


title: 902hg_D12


title: 819hg_F5


title: 819hg_E6


title: 819hg_F12


title: 819hg_F1


title: 819hg_F11


title: 819hg_E7


title: 819hg_E4


title: 819hg_E2


title: 819hg_E1


title: 819hg_E10


title: 819hg_E12


title: 819hg_G6


title: 819hg_E11


title: 819hg_D9


title: 819hg_D8


title: 819hg_D7


title: 819hg_G12


title: 819hg_G10


title: 819hg_D4


title: 819hg_D2


title: 819hg_F2


title: 819hg_D12


title: 819hg_D10


title: 819hg_D11


title: 819hg_C6


title: 819hg_D1


title: 819hg_C7


title: 819hg_C5


title: 819hg_E3


title: 819hg_C3


title: 819hg_C2


title: 819hg_B9


title: 819hg_C10


title: 819hg_C1


title: Telogen_HG_ATACseq

library_source: genomic

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
Duplicates were removed using Picard. ATAC-seq signal tracks were presented by Integrative Genomics Viewer (IGV) software
Genome_build: mm10
Supplementary_files_format_and_content: bed file containing peaks information

molecule: genomic DNA

extract_protocol:
Bulge hair follicle stem cells (GFP+/CD34+/Itga6+/Itgb1+) and hair germ cells (GFP+/CD34-/Itga6+/Itgb1+) at the second telogen  were FACS-purified and immediately sujected to ATAC-seq library generation.
FACS-sorted cells were pelleted and incubated with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After removing lysis buffer by centrifugation, samples were  subjected to a transposition reaction at 37°C for 30 min with 10μL transposase enzyme (Illumina Nextera DNA Preparation Kit). Transposed DNA was purified using QIAGEN MiniElute PCR purification kit and PCR amplified with 10-15 cycles. Library concentration and quality was assayed by D1000 Tape Station (Agilent) prior to sequencing. The samples were sequenced on Illumina HiSeq 2000 using a 50bp paired-end-reads setting.

value: GFP, CD34, integrin α6, integrin beta1


title: 819hg_B7


title: 819hg_B6


title: 819hg_B5


title: 819hg_B8


title: Telogen_Bulge_ATACseq


title: 819hg_D5


title: Ana-VI_suprabasal_HB_RNAseq_rep1

extract_protocol:
Mouse hair bulb cells were FACS-purified from P30 K14-H2BGFP mice.
FACS-isolated cells were directly lysed into TRIzol LS (Invitrogen). Total RNA was purified using the Direct-zol RNA MiniPrep kit (Zymo Research) per manufacturer’s instructions. Quality of the RNA for sequencing was determined using an Agilent 2100 Bioanalyzer; all samples used had RNA integrity numbers >9. Library preparation using the Illumina TrueSeq mRNA sample preparation kit was performed at the Weill Cornell Medical College Genomic Core facility (New York), and RNAs were paired-end sequenced on Illumina HiSeq 2000 machines.


title: Ana-VI_suprabasal_HB_RNAseq_rep2


title: 819hg_B1


title: 819hg_B11


title: 819hg_B3


title: Ana-VI_basal_HB_RNAseq_rep2


title: 819hg_A7


title: 819hg_A9


title: Ana-VI_basal_HB_RNAseq_rep1


title: 819hg_A6


title: 819hg_A4


title: 819hg_A8


title: Ana-VI_ORS_RNAseq_rep2


title: 819hg_C11


title: Ana-VI_ORS_RNAseq_rep1


title: 819hg_A2


title: 819hg_A3


title: 819hg_B4


title: Ana-VI_HFSC_RNAseq_rep3


title: 819b_D9


title: 819b_D5


title: 819hg_A11


title: 819hg_A12


title: Ana-VI_HFSC_RNAseq_rep1


title: Ana-VI_HFSC_RNAseq_rep2


title: 819b_D6


title: 819b_D8


title: 819hg_A10


title: 819b_D1


title: 819b_D4


title: 819b_D2


title: 819hg_B10


title: 819b_C9


title: 819b_C8


title: T3_NoCyt

city: Bethesda

first: Jennifer

last: Oyler-Yaniv

state: MD

address: 37 Convent Drive, Bldg. 37, Room 4137

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
The output data (FASTQ files) were mapped to the genome using the rnaStar aligner (star/STAR-STAR_2.5.0a) that maps reads genomically and resolves reads across splice junctions. The 2 pass method was used which maps reads twice. The first mapping pass uses a list of known, annotated junctions from Ensemble. Novel junctions found in the first pass are then added to the known junctions and a second mapping pass is done.
After mapping, the output SAM files were processed using the PICARD tools (picard/picard-tools-1.124) to add read groups, which also sorts the file and converts to the compressed BAM format.
The expression count matrix was then computed from the mapped reads using HTSeq (htseq/HTSeq-0.5.3). The raw count matrix is then processed using the R (R/R-3.2.0)/Bioconductor package DESeq. This normalizes the full dataset and analyzes differential expression between sample groups.
Genome_build: UCSC  mm10, Mus_musculus.GRCm38.80
Supplementary_files_format_and_content: Numeric matrix of normalized reads. Each file represents a different timepoint for either IFNg-treated or mock (untreated) conditions.

molecule: polyA RNA

source_name: Clonal, stable cell line - B16 melanoma_T3_NoCyt

growth_protocol: Cells were cultured for no more than 5 passages on tissue-culture treated flasks in RPMI 1640 media supplemented with heat-inactivated 10% fetal calf serum, 2mM L-glutamine, 10mM HEPES, 0.1mM non-essential amino acids, 1mM sodium pyruvate, 100μg/ml of penicillin, 100μg/ml of streptomycin and 50μM β-mercaptoethanol. Where necessary, cells were detached with 0.05% EDTA in PBS with agitation. Cells were maintained at 37◦C with 5% CO2.

extract_protocol:
Total RNA was extracted at the indicated timepoints using the RNAeasy Mini kit (Qiagen).
Standard Illumina library prep

treatment_protocol: Cells were detached and pulsed with 10nM mouse, recombinant IFNγ for 5 hours, or mock pulsed with media alone. After 5 hours, cells were washed 3x in a large volume of warm RPMI then 35000 cells were seeded per well of a 96-well plate in duplicate.

tag: cell line

tag: cell type

value: melanoma

value: C57Bl/6 origin

tag: passages

tag: timepoint (h)


title: T1_NoCyt

source_name: Clonal, stable cell line - B16 melanoma_T1_NoCyt


title: 819b_C3


title: 819b_C7


title: T3_IFNg

source_name: Clonal, stable cell line - B16 melanoma_T3_IFNg


title: 819b_C4


title: 819b_C2


title: 819b_C1


title: T1_IFNg

source_name: Clonal, stable cell line - B16 melanoma_T1_IFNg


title: T0_1

source_name: Clonal, stable cell line - B16 melanoma_T0


title: 819b_C11


title: T2_NoCyt

source_name: Clonal, stable cell line - B16 melanoma_T2_NoCyt


title: 819b_B8


title: 819b_B6


title: 819b_B7


title: 819b_C10


title: MCF7_E2_1280_min_ERalpha

city: Nijmegen

first: H.

middle: G.

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

country: Netherlands

institute: Radboud University

data_processing:
Mapping was done using the GenomatixMapper software (version 3.4) onto the hg19 whole genome for the given time points. No trimming was applied to the reads. Only reads mapping uniquely to the genome with at most 2 mismatches were reported.
Genome_build: NCBI build37
Supplementary_files_format_and_content: tag files in bed format

organism: Homo sapiens

growth_protocol: MCF-7 cells were cultured in DMEM with 10% FCS at 37 °C. Cells were maintained in DMEM w/o phenol red and 5% charcoal stripped FCS for 72 hours before induction.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody using the Transcription factor protocol. Settings: 20 min cross-linking and 20min sonication for H3K4me3 and H2A.Zac, 15min resp. 10min for F3A6 (to ERalpha). 100 µl chromatin and 2.5µl antibody. Pooled 2 samples.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: MCF-7 cells were mock treated or with 10nM 17b-E2 at a series of time points.

tag: tissue

value: mammary gland

tag: chip antibody

value: F3A6 (to ERalpha, Gronemeyer)

tag: treatment


title: 819b_B9


title: 819b_B4


title: 819b_B3


title: 819b_B5


title: T2_IFNg

source_name: Clonal, stable cell line - B16 melanoma_T2_IFNg


title: 819b_C6


title: MCF7_E2_640min_ERalpha


title: 819b_B2


title: 819b_B1


title: MCF7_E2_160min_ERalpha


title: MCF7_E2_320min_ERalpha


title: MCF7_E2_80min_ERalpha


title: 819b_B11


title: 819b_B12


title: 819b_B10


title: 819b_A8


title: MCF7_E2_20min_ERalpha


title: MCF7_E2_40min_ERalpha


title: 819b_A4


title: 819b_A6


title: 819b_A3


title: 819b_A1


title: 819b_A2


title: 819b_A11


title: MCF7_E2_5min_ERalpha


title: 35S:rMYB83_rep-1

city: Knoxville

first: Sarbottam

last: Piya

state: Tennessee

address: 2431 Joe Johnson Dr.

department: Plant Science

institute: University of Tennessee

data_processing:
Quality of the reads were assessed using Fastqc
Low quality reads and adapters were trimmed using Trimmomatic
Reads were mapped to the genome using TopHat v2.0.14
Aligned reads were counted using HTSeq
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each Sample

organism: Arabidopsis thaliana

source_name: Root tissue

growth_protocol: Plants were grown under long day conditions 16 hour light/8 hour dark at 24°C

extract_protocol:
mRNA was isolated using magnetic mRNA isolation kit (NEB)
RNA-seq library was prepared using NEBnext mRNA library prep master mix (NEB)

value: Root

value: 2 weeks

tag: genotype/variation

value: MYB83 overexpression


title: 35S:rMYB83_rep-3


title: 819b_A10


title: 35S:rMYB83_rep-2


title: 35S:miR858_rep-2

value: miR858 overexpression


title: Col-0_rep-3

value: Wild type/Col-0


title: T4004

city: ChiaYi

first: Chin

last: Li

address: 168 University Road, Minhsiung

department: Life Science

country: Taiwan

institute: National Chung Cheng University

data_processing:
Sequencing reads were output from Miseq in fastq files.
The reads were trimmed to 50 bp if 150 cycles were completed using CLC Genomic Workbench v.8.0.
Trimmed reads were uploaded to Illumina cloud service BaseSpace and analyzed using RNA Expression app
The result was downloaded and merged into an Excel file for analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Excel containing read number of preselected 157 targeted genes

source_name: resected gastric tissue

extract_protocol:
Total RNA was extracted using TRIZOL reagent. The quantity and quality of purified samples were determined by dye-based fluorometer (Invitrogen Qbit) and capillary electrophoresis (Agilent TapeStation).
Illumina recommended protol for Truseq targeted RNA expression kit was followed.
Targeted RNA sequencing

tag: noncancer- cancer

value: gastric cancer

tag: cancer stage


title: T3995


title: T3960


title: T3915


title: T3884


title: 35S:miR858_rep-1


title: 819b_A7


title: MCF7_E2_10min_ERalpha


title: Col-0_rep-2


title: 819b_A5


title: Col-0_rep-1


title: T3866


title: MCF7_NoTreat_ERalpha

value: NoTreat


title: T3824


title: T3810


title: T3750


title: CMZ023_NPp53 castrated prostate tumor tissue treated with abiraterone

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

description: Sample name: CMZ023

data_processing:
RNA-seq pipeline description:
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Mouse: UCSC/mm9) using Tophat [1] (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.  We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [2] (version 2.0.2) with default settings. We test for differentially expressed genes under various conditions using DEseq [3]. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Raw RNAseq counts were normalized (variance stabilization) using DESeq2 package in R-studio Version 0.99.484
Genome_build: Mouse: UCSC/mm9
Supplementary_files_format_and_content: Tab-delimited text or xls files include DESeq normalized values for each Sample

source_name: Prostate tissue

extract_protocol:
RNA was extracted using the MagMAX-96 RNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyser 2100
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2500 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.

treatment_protocol: All mice were treated for 4 consecutive days with 100mg/kg/day of tamoxifen by oral gavage at 3 month of age. For NP castrated and NPp53 castrated groups, mice were sergical castrated at 13 and 10 month of age respectively. NPcas and NPp53cas mice were additionally treated with vehicle or abiraterone as indicated between 15 and 16, or 12 and 13 month of age, respectively. The dosage/schedule for abiraterone was 200mg/kg/day daily, 5 days per week for 4 weeks. Corn oil was used as vehicle.

value: hybrid 129/SvImJ and C57Bl/6J strain

value: prostate

value: 13 months

tag: genotype


title: 902hg_B9

value: Mixed


title: CMZ021_NPp53 castrated prostate tumor tissue treated with abiraterone (exp)

description: Sample name: CMZ021


title: CMZ022_NPp53 castrated prostate tumor tissue treated with abiraterone

description: Sample name: CMZ022


title: T3818


title: T3950


title: T3731


title: T3653


title: CMZ014_NPp53 castrated prostate tumor tissue treated with abiraterone

description: Sample name: CMZ014


title: CMZ013_NPp53 castrated prostate tumor tissue treated with abiraterone (exp)

description: Sample name: CMZ013


title: CMZ016_NPp53 castrated prostate tumor tissue treated with abiraterone

description: Sample name: CMZ016


title: T3382


title: T3336


title: CMZ012_NPp53 castrated prostate tumor tissue treated with abiraterone (exp)

description: Sample name: CMZ012


title: CMZ010_NPp53 castrated prostate tumor tissue treated with vehicle

description: Sample name: CMZ010


title: T3416


title: T3201


title: T3260


title: CMZ017_NPp53 castrated prostate tumor tissue treated with vehicle (outlier)

description: Sample name: CMZ017


title: T3173


title: CMZ009_NPp53 castrated prostate tumor tissue treated with vehicle

description: Sample name: CMZ009


title: CMZ011_NPp53 castrated prostate tumor tissue treated with abiraterone

description: Sample name: CMZ011


title: S38_Paget

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapter and HD signatures [Sorefan et al 2012] were trimmed and the files were converted from redundant to non-redundant format
the reads were mapped to the reference genome, allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change on confidence intervals built on replicates, offset = 20
Genome_build: GRCh38
Supplementary_files_format_and_content: csv, raw abundances

source_name: bone

extract_protocol:
Resected tissue was used for RNA extraction before small RNA library construction
Illumina compatible method using HD adapters

tag: disease state

value: Paget disease of the bone

value: bone


title: T3170


title: CMZ008_NPp53 castrated prostate tumor tissue treated with vehicle

description: Sample name: CMZ008


title: S35_Paget


title: S36_Paget


title: NC018_NPp53 intact prostate tumor tissue treated with vehicle

description: Sample name: NC018

value: 12 months


title: NC017_NPp53 intact prostate tumor tissue treated with vehicle

description: Sample name: NC017


title: T2991


title: T4064


title: T3005


title: CMZ007_NP castrated prostate tumor tissue treated with abiraterone

description: Sample name: CMZ007

value: 16 months


title: NC019_NPp53 intact prostate tumor tissue treated with vehicle

description: Sample name: NC019


title: S30_Paget


title: S31_Paget


title: T2973


title: T3371


title: S81_Paget_associated_osteosarcoma

city: Norwich

first: Darrell

last: Green

address: Earlham Road

department: Norwich Medical School

institute: University of East Anglia

description: Small RNA-seq

data_processing:
The original fastq files were converted to fasta format and reads without Ns were kept for further analysis.
The 3' adapter and HD signatures [Sorefan et al. 2012] were trimmed and the files were converted from redundant to non-redundant format.
The reads were mapped to the reference genome, allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al. 2008].
The reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRBase, release 21.
The abundances of the reads were normalized using the RPM method [Mortazavi et al. 2008].
The differential expression was called on offset fold change on confidence intervals built on replicates, offset = 20.
Genome_build: GRCh38
Supplementary_files_format_and_content: *csv: Comma-separated text files include sequences and raw abundances.

source_name: Paget's disease-associated osteosarcoma

extract_protocol:
Resected tissue was used for RNA extraction before small RNA library construction.
Illumina compatible method using HD adapters.

value: Paget's disease

value: osteosarcoma


title: epcam mutant 3

city: Freiburg im Breisgau

first: Toma

middle: Antonov

last: Yakulov

address: Hugstetter Str. 55

department: Department of Medicine

country: Germany

institute: University Freiburg Medical Center

description: NG-8710_epcam_mut_3_7_10_lib96996_4194_4

data_processing:
Sequencer: HiSeq2500 or HiSeq4000
Sliding window trimming of low quality base calls with  Trimmomatic 0.36.0
Alignment to GRCz10 with TopHat (2.1.0)
RNA-seq quantification pipeline with SeqMonk (1.37.1)
75th percentile normalization with SeqMonk (1.37.1)
Filter values less than three in any of the datasets (not expressed genes)
Raw count generation with SeqMonk (1.37.1)
Differential gene expression analysis was performed using the DESeq2 statistics in SeqMonk (1.37.1)
Genome_build: GRCz10
Supplementary_files_format_and_content: txt (raw counts), xlsx (differential expression)

organism: Danio rerio

source_name: Distal pronephric tubule of zebrafish

extract_protocol:
50 µl extraction buffer (PicoPure RNA Isolation Kit (Applied, Biosystems, Carlsbad, USA)) was added to the captured LCM material followed by incubation for 45 min at 60 °C to allow de-crosslinking. RNA was extracted with the PicoPure RNA Isolation Kit. 8 µL of the RNA solution was denatured, treated with DNase and reverse transcribed into cDNA using a combination of random and Oligo(dT) primers. The cDNA was amplified with the Qiagen Repli-G WTA (whole transcriptome amplification) Single Cell Kit (Qiagen, Hilden, Germany) using a mix of random and poly-A primers.
unstranded RNA-seq

tag: developmental stage

value: 48 hours post fertilization

value: pronephros


title: 35S:miR858_rep-3

value: Root

value: 2 weeks


title: T2984


title: CMZ018_NPp53 castrated prostate tumor tissue treated with vehicle (outlier)

description: Sample name: CMZ018


title: epcam mutant 2

description: NG-8710_epcam_mut_2_14_9_lib96995_4194_4


title: S86_normal_bone

description: Small RNA-seq

source_name: normal bone

value: normal


title: T2904

value: gastric cancer


title: T2899


title: CMZ005_NP castrated prostate tumor tissue treated with abiraterone

description: Sample name: CMZ005


title: CMZ004_NP castrated prostate tumor tissue treated with vehicle

description: Sample name: CMZ004


title: CMZ003_NP castrated prostate tumor tissue treated with vehicle

description: Sample name: CMZ003


title: S80_Paget_associated_osteosarcoma

description: Small RNA-seq


title: epcam mutant 1

description: NG-8710_epcam_mut_1_13_8_lib96994_4194_4


title: CMZ002_NP castrated prostate tumor tissue treated with vehicle

description: Sample name: CMZ002


title: S84_normal_bone

description: Small RNA-seq


title: control 3

description: NG-8710_cdh17_ctrl_3_14_8_lib96997_4194_4


title: CMZ001_NP castrated prostate tumor tissue treated with vehicle

description: Sample name: CMZ001


title: T2914


title: S85_normal_bone

description: Small RNA-seq


title: CMZ006_NP castrated prostate tumor tissue treated with abiraterone

description: Sample name: CMZ006


title: T2718


title: T2704


title: control 1


title: NC011_NP intact prostate tumor tissue treated with vehicle

description: Sample name: NC011

value: 14 months


title: T2654


title: T2583


title: S82_normal_bone

description: Small RNA-seq


title: NF008_N prostate tissue

description: Sample name: NF008

value: hybrid 129/SvImJ and C57Bl/6J strain

value: 9 months


title: T2494


title: T2414


title: NF007_N prostate tissue

description: Sample name: NF007

value: prostate


title: NC009_NP intact prostate tumor tissue treated with vehicle

description: Sample name: NC009


title: S83_normal_bone

description: Small RNA-seq


title: NC012_NP intact prostate tumor tissue treated with vehicle

description: Sample name: NC012


title: NF005_N prostate tissue

description: Sample name: NF005


title: T2353


title: T2430


title: N4064

value: adjacent normal


title: D8ISPRT4165-1

city: Cincinnati

first: Artem

last: Barski

state: OH

address: 3333 Burnet Av

department: Allergy

institute: Cincinnati Children's Hospital

description: BioWardrobe ID: 1986

data_processing:
RNA-Seq data analysis was performed using the BioWardrobe (PMID: 26248465 )
Briefly, reads were mapped to the hg19 genome and RefSeq-based transcriptome using RNA-STAR (v. 2.4.2a and assigned to the RefSeq genes  using the BioWardrobe algorithm.
STAR PARAMS:
--clip3pNbases 0      --seedSearchStartLmax 15   --alignSJDBoverhangMin 1
--outFilterMultimapNmax 1   --outFilterMismatchNmax 5   --clip5pNbases 0
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes RPKM values for each sample

source_name: Uterine implantation sites (IS) on D8 of pregnancy, PRT4165-treated

growth_protocol: CD-1 female mice (8-10 weeks old) were mated with fertile males to induce pregnancy (D1 = vaginal plug).

extract_protocol:
Total RNAs were isolated using the Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
mRNA-Seq library construction was done at CCHMC using Illumina stranded (dUTP) protocol. Libraries were then sequenced on an Illumina HiSeq 2500 in rapid mode, generating more than 20 million paired-end 75bp reads.
Total RNA (150 to 500 ng) as determined by Qubit 3.0 Fluorometer (Life Technologies) was poly A selected and then reverse transcribed using the TruSeq stranded mRNA library preparation kit (Illumina). Each sample was fitted with one of 24 adapters containing a different 8 base molecular barcode for high level multiplexing. After 15 cycles of PCR amplification, completed libraries were generated.

treatment_protocol: For inhibition of PRC1 in vivo, mice were injected with PRT4165 (Millipore, Billerica, MA) [4 mg/kg in a 0.1 ml solution with sesame oil (Sigma, MO) containing 10% ethanol] or vehicle (0.1 ml sesame oil per mouse containing 10% ethanol, as a control) twice at 0900 and 1800 h on each day during the post-implantation period on D5 through D7, and implantation sites were collected on D8 (0900 h).

value: Uterine implantation sites


title: N4004


title: D8ISCOT-2

description: BioWardrobe ID: 1989

source_name: Uterine implantation sites (IS) on D8 of pregnancy


title: T2755


title: N3995


title: D8ISPRT4165-2

description: BioWardrobe ID: 1987


title: N3960


title: N3915


title: N3884


title: N3866


title: control 2


title: N3950


title: N3653


title: N3416


title: Z3B- Repeat- SEQ 3

city: Richmond

first: Zendra

last: Zehner

state: VA

address: 1101 E Marshall St

department: Department of Biochemistry

institute: Virginia Commonwealth University

description:
Named as "Z3B.2" in processed data
3_batch_raw_reads.txt /  norm_glm_blood.txt

data_processing:
Illumina® TruSeq Small RNA Library Preparation kit and HiSeq 2500 system
The adapter sequence “AGATCGGAAGAGCACACGTCT” (TruSeq Adapter, Index 7) was removed from both 5’ and 3’ end
A second trimming was performed on the data to further eliminate bases at both ends with Phred quality score lower than the 35.
The trimmed data was aligned to human genome (GRCh38) with only 1 seed mismatch allowed.
Three best alignments satisfying such criterion were reported for each read using Bowtie 1.0. The parameters used by Bowtie while performing the alignment were as follows: alignment mode= quality limit, seed mismatch limit =1, seed length = 28 and quality limit =70, both strand alignment, and alignments reported per read = 3
The aligned reads were annotated with miRBase (mature 21, version 2)
The reads were normalized using the default “Trimmed Mean of M values” following a differential expression analysis using Edge R
Genome_build: GRCh 38
Supplementary_files_format_and_content: tab-delimited text files include raw reads  and normalized reads for each sample

source_name: whole blood

extract_protocol:
MiRNA in each sample was extracted using a corresponding PAXgene Blood miRNA kit following the manufacture’s protocol. Samples with small RNA concentration equal to 100 ng/μL were selected for sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole blood

tag: tumor stage

tag: disease stage

value: Patient


title: Z5B-Repeat- SEQ 3

description:
Named as "Z5B.2" in processed data
3_batch_raw_reads.txt /  norm_glm_blood.txt


title: N3810


title: N3731


title: N3336


title: N3750


title: N3382


title: N3260


title: Case8-SEQ 3

description: 3_batch_raw_reads.txt /  norm_glm_blood.txt


title: N3371


title: Case83-SEQ 3


title: N3201


title: Case89-SEQ 3


title: N3170


title: Case 6 SEQ 3


title: Case82-SEQ 3


title: D8ISCOT-1

description: BioWardrobe ID: 1988

tag: strain


title: Case51 SEQ 3


title: Case82 Repeat- SEQ 3

description:
Named as "82JDR.2" in processed data
3_batch_raw_reads.txt /  norm_glm_blood.txt


title: Case36 Repeat- SEQ 3

description:
Named as "36KAB.2" in processed data
3_batch_raw_reads.txt /  norm_glm_blood.txt


title: N3005


title: N3818


title: Z11B SEQ 3

value: Control


title: N3173


title: N2984


title: Case18 Repeat- SEQ 3

description:
Named as "18EHD.2" in processed data
3_batch_raw_reads.txt /  norm_glm_blood.txt


title: Case16-SEQ 3


title: N2914


title: N2973


title: 04062015-SEQ 3


title: 04282015-SEQ 3


title: N2904


title: N2755


title: N2704


title: N2991


title: N3824


title: N2899


title: 03262015-SEQ 3


title: N2718


title: 03242015- SEQ 3


title: Z9B-SEQ 2


title: N2654


title: N2583


title: Case9- SEQ 2


title: N2414


title: N2353


title: N2494


title: Case85-SEQ 2


title: N2430


title: 05202

source_name: gastric epithelial tissue

value: gastritis/IM


title: Case36-SEQ 2


title: Case33-SEQ 2


title: 04242015- SEQ 3


title: Case56-SEQ 2


title: 05201


title: Case40- SEQ 2


title: 05102


title: Z12B- SEQ 3


title: Z10B-SEQ 2


title: Case18-SEQ 2


title: 05101


title: 12192014- SEQ 2


title: 04802


title: Case20- SEQ 2


title: 04801


title: 12172014b-SEQ 2

value: Elevated PSA


title: 04702


title: 04701


title: 12172014a- SEQ 2


title: 04202


title: 091714-SEQ 2


title: 10212014FAM- SEQ 2


title: Z8B- SEQ 1


title: Case100-SEQ 2


title: Z7B- SEQ 1

value: PSA 22


title: Z6B- SEQ 1


title: 04102


title: 04201


title: 03802


title: 03702


title: 04902


title: Z4B- SEQ 1


title: 04101


title: Case31- SEQ 2


title: Case72-SEQ 2


title: 03601


title: Z5B- SEQ 1


title: Z3B-SEQ 1


title: 03402


title: Z1B-SEQ 1


title: 03502


title: MCF_7_E2_640min_H2AZ

value: mammary gland


title: MCF_7_E2_1280min_H2AZ


title: 03501


title: MCF_7_E2_320min_H2AZ


title: 03001


title: 02701


title: 02702


title: MCF_7_E2_160min_H2AZ


title: 03602


title: 02602


title: MCF_7_E2_80min_H2AZ


title: 02301


title: 01602


title: 02302


title: Z2B-SEQ 1


title: 01601


title: MCF_7_E2_20min_H2AZ


title: MCF_7_E2_10min_H2AZ


title: MCF_7_E2_5min_H2AZ


title: 01202


title: 03002


title: MCF7_NoTreat_H3K4me3

value: H3K4me3 (Diagenode, pAb-MEHAHS-024, lot HS-0010)

value: NoTreat


title: MCF_7_noE2_H2AZ


title: 00701


title: 00702


title: MCF7_E2_1280min_H3K4me3


title: 00302


title: MCF7_E2_320min_H3K4me3


title: TB037

data_processing:
Sequencing reads were output from Miseq in fastq files.
The reads were analyzed using CLC Genomic Workbench v.8.0.
Reads were Q20 filtered and the reads shorter than 50 were discarded. The remaining rads were mapped to hg19. The expression level is expressed as FPKM.
The result was downloaded and merged into an Excel file for analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Excel output from CLC Genomic Workbench v.8.0.

extract_protocol:
Total RNA was extracted using TRIZOL reagent. The quantity and quality of purified samples were determined by dye-based fluorometer (Invitrogen Qbit) and capillary electrophoresis (Agilent TapeStation).
Agillent  recommended protocol for  SureSelect Strand Specific RNA Library Preparation Kit was followed.


title: MCF7_E2_160min_H3K4me3


title: MCF7_E2_80min_H3K4me3


title: 00301


title: TB029


title: MCF7_E2_20min_H3K4me3


title: MCF7_E2_40min_H3K4me3


title: MCF_7_E2_40min_H2AZ


title: TB033


title: MCF7_E2_10min_H3K4me3


title: TB011


title: TB010


title: TB003


title: 037

value: normal


title: 048


title: Beauveria bassiana at 72 hours post treatment of infection for Galleria mellonella

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

country: China

institute: Anhui Agricultural University

description:
dead
The wild-type strain B. bassiana ARSEF 2860 (stocked in the Chinese Academy of Sciences)

data_processing:
Reads were mapped to the Beauveria bassiana genome from (NCBI, https://www.ncbi.nlm.nih.gov/genome/910)
Differential gene expression levelss were calculated with using the program Cufflinks software (v.2.0.1)
DAnnotations of differentially expressed genes (DEGs) including Pfam, were annotated using including Pfam database were obtained from the reference annotation of available Beauveria bassiana genome database at the NCBI website.
For each differentially expressed peach gene, up-to-datelatest Gene Ontology (GO) annotations were obtained using Blast2GOv.2.3.5 with the default parameters., Theand “GO slim” option was employedset to reduce the number of functional classes.
GO slim annotations results were then used as queries against the AgBase database to perform their classify genesication according into to the three main classes categories (molecular function, biological process and cellular component), and to be further assigned to secondary categories
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Beauveria bassiana

growth_protocol: on PDA and 28ºC

extract_protocol:
Total RNA was isolated separately from Beauveria bassiana with RNA extraction Kit
RNA samples were first treated with RNAse-free DNAse I to remove contaminatinged DNA. Then, the mRNA wais enriched by using the oligo(dT) magnetic beads. After mixed with theadding fragmentation buffer, the mRNA was fragmented into short fragments (about 200 bp). NextThen, the first strand of cDNA was synthesized by using random hexamer-primers. Buffer, dNTPs, RNase H, and DNA polymerase I were added to synthesize the second cDNA strand. The double- stranded cDNA was then purified usingwith magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition was then performed. Finally, sequencing adaptors were ligated to the fragments. The fragments were enriched by PCR amplification. During the QC step, an Agilent 2100 Bioanaylzer (Agilent Technologies, Germany) and ABI StepOnePlus Real-Time PCR System (Applied Biosystems, USA) were used to perform qualitfy-control steps  and to quantify the sample library. The library products wasere then ready for sequencing using anvia Illumina HiSeqTM 2000 (GATC Biotech, Germany), or another sequencer when if necessary


title: Beauveria bassiana at 24 hours post treatment of infection for Galleria mellonella

description:
live
The wild-type strain B. bassiana ARSEF 2860 (stocked in the Chinese Academy of Sciences)


title: Adult wildtype zebrafish pericyte 4

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

data_processing:
adaptor trimming done by bcl2fastq2
Individual fastq files were aligned to the reference genome with Rsubread 1.20.6 with default settings in R version 3.2.2. Counts were then combined across all lanes associated with each biological sample to generate data reflecting the true biological samples.
Yugene-normalised values were calculated using a protocol from Lê Cao et al, 2014, Genomics. This a simple transform (applied to each individual sample) that assigns a modified cumulative proportion value to each measurement, without losing essential underlying information on data distributions or experimental correlates.
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited text files include yugene-normalised data for each sample

source_name: purified pericyte

extract_protocol:
Adult zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate, with 6 brains used per samples.
libraries were prepared for sequencing using standard Illumina protocols

tag: transgene

value: pdgfr beta egfp

value: wildtype

value: muLEC


title: Adult wildtype zebrafish pericyte 3


title: 049


title: MCF7_E2_640min_H3K4me3

tag: cell line


title: Beauveria bassiana grown on potato dextrose agar in the dark at 28 °C for 12 days

description:
mycelial mat reached 8 cm
The wild-type strain B. bassiana ARSEF 2860 (stocked in the Chinese Academy of Sciences)

source_name: control


title: Adult wildtype zebrafish muLECs 1

source_name: purified muLECs

extract_protocol:
Adult zebrafish brains were dissociated using Liberase and lyve1 Dsred postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate, with 6 brains used per samples.
libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: Lyve1 Dsred

tag: cell type


title: Adult wildtype zebrafish muLECs 3


title: Adult wildtype zebrafish pericyte 2


title: Adult wildtype zebrafish pericyte 1


title: 48hpf zebrafish FAC sorted endothelial cell mutant 3

data_processing:
adaptor trimming done by bcl2fastq2
Reads were mapped against the reference genome (danRer7/Zv9) using STAR (Dobin et al. 2013) and read counts for each gene in the Ensembl annotation were generated using htseq-count in the HTSeq python package (Anders et al. 2015).
Genome_build: danRer7/Zv9
Supplementary_files_format_and_content: Tab-delimited text files include yugene-normalised data for each sample

source_name: purified endothelial cell

extract_protocol:
48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate.
libraries were prepared for sequencing using standard Illumina protocols

value: kdrl eGFP

value: mafba uq4bh mutant


title: 48hpf zebrafish FAC sorted endothelial cell mutant 2


title: 48hpf zebrafish FAC sorted endothelial cell mutant 1


title: treated with Chloramphenicol 15ug/mL

city: Vancouver

first: Charles

last: Thompson

state: British Columbia

address: 2350 Health Sciences Mal

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

description: PCR product of transposon junctions

data_processing:
Illumina MiSeq was used for sequencing
Sequencing run was outsourced to a sequencing facility - received FastQ files
Online ESSENTIALS software (http://bamics2.cmbi.ru.nl/websoftware/essentials/essentials_start.php) proccessed the fastQ files
Genome_build: Mycobacterium smegmatis str. MC2 155 (version NC_008596.1)
Supplementary_files_format_and_content: output from Essentials given in ESSENTIALS.xlsx

organism: Mycolicibacterium smegmatis

source_name: M.smegmatis transposon library

extract_protocol:
The Nextera DNA sample preparation kit (Illumina) was used to fragment isolated genomic DNA, with minor modification; 10 ng/mL DNA was used as input for larger fragment generation, and the tagmentation reaction was purified with a Qiagen PCR purification kit with a 57 mL elution. Three 25 mL real-time-qPCR reactions were prepared per primer pair per condition with 9 mL of the eluate. Quanta's PerfeCTa® SYBR® Green SuperMix with a final concentration of 0.8 mM per primer was used for the reactions. A primer targeting the P7 tagmentation (P7tag) was paired with primers targeting either end of the FMycoMarT7 transposon (Accession: AF411123); NX_pMMT7_out1 and NX_pMMT7_out2. Reactions were run in a CFX96 RT-PCR machine (Bio-Rad) with decreasing annealing temperatures: 94 ºC for 30 s, Annealing for 30 s (60 ºC for 5 cycles, 58 ºC for 5 cycles, and then 55 ºC for 35 cycles), 72 ºC for 30 s.  The live readout was monitored, and the PCR was stopped when 6 cycles had passed since the signal increased above background (~23 cycles total). All reactions were then separated on a 2% agarose-TAE gel with the smear between 250-500 bp cut out, the triplicates combined, and the DNA purified with the Qiagen Gel purification kit with a 45 µL elution. Eluates were quantified with the Qubit dsDNA HS assay kit, and the products from the two reactions pooled at equal amounts to a final concentration of ~1.4 ng/µL. Note, if there wasn’t enough DNA from both reactions for an equal pool, the more concentrated partner was added at higher amounts to get the desired final concentration. The Nextera sample preparation kit protocol was then continued. A second PCR was set up with 24 µL of pooled DNA as suggested, but 1 µL of a custom P5 primer (phiP5) at 20 µM was used and the number of cycles increased to 10. The Nextera indexing kit P7 primers were used to barcode the individual conditions. Samples were combined and sequenced using the MiSeq reagent kit v2 (Illumina) with 50 bp reads using the custom P5 primer phiMMT7seq_1. Around 3 million reads were obtained per condition.

More details on the extraction and preparation protocols are available on the series record in the file "Protocol.pdf".

treatment_protocol: Transposon library preparation: phage MycoMarT7 genomic DNA was transformed into M. smegmatis and resulting plaques were replica plated at 30 ºC and 37 ºC to ensure temperature-dependent replication. Thermosensitive plaques were then cut from the agarose, mixed with MP buffer and filter sterilized. Our experience indicated that storing phage at 4 ºC results in a rapid drop of plaque forming units; therefore the phage was diluted by 10-3, 10-4, and 10-5 in buffer and was mixed with M. smegmatis in top agar to generate five plates per dilution. The dilution with a near-confluent plaque lawn was flooded with 3 mL of MP buffer per plate and gently rocked for 3 hours at 4 ºC to prepare the phage stock. 1 L of M. smegmatis was grown in 7H9 to an OD600 of 0.6 – 0.8. The cells were pelleted and washed three times with 30 mL of 7H9 (no tyloxapol) and finally suspended in 50 mL. 4 mL of the suspended M. smegmatis were combined with 1 mL of fresh phage stock and incubated at 37 ºC for 3 hours. The transduction mix was inverted once every 45 minutes. Finally, glycerol was added to 18 % (v/v) and aliquots frozen at -80 ºC. Samples were plated to estimate library quantity for final plating. Roughly 55, 000 colonies obtained from 7H9+kan agar plates were combined in 50 mL 7H9 with 18% (v/v) glycerol to a final OD600 of 100 to generate the transposon library

value: Chloramphenicol 15ug/mL


title: treated with Tetracycline 1ug/mL

description: PCR product of transposon junctions

value: Tetracycline 1ug/mL


title: 48hpf zebrafish FAC sorted endothelial cell wt 1


title: treated with Roxithromycin 2ug/mL

description: PCR product of transposon junctions

value: Roxithromycin 2ug/mL


title: untreated library

description: PCR product of transposon junctions

value: untreated


title: TFIIB ChIP-eeq Rep1

status: Public on Apr 17 2017

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were trimmed to 50 bp and aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were extended to each library's estimated insert size
Genome-wide coverage counts were calculated, normalized to reads per million and saved in BigWig format
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base

organism: Drosophila melanogaster

source_name: Kc167 cells

growth_protocol: grown at 25C in HyClone SFX-Insect Cell Culture Media

extract_protocol:
cells were cross-linked in 1.0% formaldehyde. Cells were then lysed by lysis buffer. Chromatin was sonicated by bioruptor to an average size of 300~500 bp. ~ 20 million cells was used for one ChIP-nexus
DNA-protein-complexes were isolated with specific antibodies. Sequencing libraries were prepared following Illumina's instructions: DNA was end repaired using NEBNext End repair module. A single 3'-A overhang was added to the blunted ends using NEBNext dA-Tailing module.  Adapters with single 3'-T overhangs were ligated to the adenylated fragments, and after a size-selection step using AmPure beads (200-250 bp) the adapter modified DNA was PCR-amplified. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

value: Kc167 cells

value: anti-TFIIB rabbit polyclonal, Kadonaga lab

tag: illumina multiplex barcode

value: ACAGTG


title: Pol II ChIP-seq Rep1

value: anti-RPB3 rabbit polyclonal, custom (GenScript)

value: ATCACG


title: TFIIA ChIP-seq Rep1

value: anti-TFIIA rabbit polyclonal, Kadonaga lab

value: TGACCA


title: 48hpf zebrafish FAC sorted endothelial cell wt 2


title: Pol II ChIP-nexus with spikein (20 min Triptolide treatment) Rep2

description:
kc167_triptolide_20min_polii_chipnexus_spikein_normalized_2_positive.bw
kc167_triptolide_20min_polii_chipnexus_spikein_normalized_2_negative.bw

data_processing:
Library strategy: ChIP-nexus
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Custom barcode sequences were removed from the first 9bp of each read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3
Remaining reads with length >= 22bp were aligned to the dm3-hg19 combined genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Reads aligned to dm3 genome were separated from reads aligned to hg19 genome
Reads aligned to dm3 genome were separated by strand and reduced to a single base at the 5' end
Genome-wide coverage counts on dm3 genome were calculated and normalized to genome-wide coverage counts on hg19 genome and saved in BigWig format for each strand separately
Genome_build: dm3-hg19 combined genome
Supplementary_files_format_and_content: BigWig files contain genome coordinates and counts of the first base of aligned reads, separated by alignment strand

extract_protocol:
cells were cross-linked in 1.0% formaldehyde. Cells were then lysed by lysis buffer. Chromatin was sonicated by bioruptor to an average size of 300~500 bp. ~ 20 million cells was used for one ChIP-nexus
DNA-protein-complexes were isolated with specific antibodies when still being attached to protein A-dynabeads. A fixed amount of spike-in was added to each ChIP in order to control for the loss of Pol II ChIP signal after Triptolide treatment. Human chromatin extracts from a GM12878 cell line were incubated with Dynabeads coupled to antibodies against human Pol II (N20), the entire mixture of Dynabeads and Pol II ChIP was added into each spike-in sample. DNA was end repaired using NEBNext End repair module (#E6050L). A single 3'-A overhang was added to the blunted ends using NEBNext dA-Tailing module (#E6053L). Adapters with single 3'-T overhangs and 5’ overhangs (barcode composed of 5 random nucleotides) were ligated to the adenylated fragments. Ligated fragments were blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim any possible 3’ overhang. Blunted DNA was subsequently digested by lambda exonuclease first and RecJf afterwards. Digested single strand DNA was then eluted, reverse cross-linked and purified prior to self-circularization by Circligase. An oligonucleotide was mixed with circularized single DNA for subsequent BamHI digestion to linearize the single DNA again. Linearized single strand DNA was then PCR-amplified using adaptor sequences and library was purified on 2% agarose gel to remove adaptor-adaptor ligation products. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

treatment_protocol:
Cells are treated with 500 μM Triptolide (TOCRIS Bioscience Cat. No. 3253 dissolved in DMSO) at room temperature for 20 min.
Cells are treated with 500 μM Triptolide (dissolved in DMSO) at room temperature for 20 min.


title: Pol II ChIP-nexus with spikein (20 min Triptolide treatment) Rep1

description:
kc167_triptolide_20min_polii_chipnexus_spikein_normalized_1_positive.bw
kc167_triptolide_20min_polii_chipnexus_spikein_normalized_1_negative.bw


title: Adult wildtype zebrafish muLECs 2


title: Pol II ChIP-nexus with spikein (10 min Triptolide treatment) Rep2

description:
kc167_triptolide_10min_polii_chipnexus_spikein_normalized_2_positive.bw
kc167_triptolide_10min_polii_chipnexus_spikein_normalized_2_negative.bw

treatment_protocol:
Cells are treated with 500 μM Triptolide (TOCRIS Bioscience Cat. No. 3253 dissolved in DMSO) at room temperature for 10 min.
Cells are treated with 500 μM Triptolide (dissolved in DMSO) at room temperature for 10 min.


title: Pol II ChIP-nexus with spikein (5 min Triptolide treatment) Rep2

description:
kc167_triptolide_5min_polii_chipnexus_spikein_normalized_2_positive.bw
kc167_triptolide_5min_polii_chipnexus_spikein_normalized_2_negative.bw

treatment_protocol:
Cells are treated with 500 μM Triptolide (TOCRIS Bioscience Cat. No. 3253 dissolved in DMSO) at room temperature for 5 min.
Cells are treated with 500 μM Triptolide (dissolved in DMSO) at room temperature for 5 min.

value: TTAGGC


title: Pol II ChIP-nexus with spikein (10 min Triptolide treatment) Rep1

description:
kc167_triptolide_10min_polii_chipnexus_spikein_normalized_1_positive.bw
kc167_triptolide_10min_polii_chipnexus_spikein_normalized_1_negative.bw


title: Pol II ChIP-nexus with spikein (30 min Triptolide treatment) Rep1

description:
kc167_triptolide_30min_polii_chipnexus_spikein_normalized_1_positive.bw
kc167_triptolide_30min_polii_chipnexus_spikein_normalized_1_negative.bw

treatment_protocol:
Cells are treated with 500 μM Triptolide (TOCRIS Bioscience Cat. No. 3253 dissolved in DMSO) at room temperature for 30 min.
Cells are treated with 500 μM Triptolide (dissolved in DMSO) at room temperature for 30 min.

value: CGATGT


title: Pol II ChIP-nexus with spikein (Control condtion) Rep2

description:
kc167_dmso_control_polii_chipnexus_spikein_normalized_2_positive.bw
kc167_dmso_control_polii_chipnexus_spikein_normalized_2_negative.bw

treatment_protocol:
Cells are treated with 2% DMSO at room temperature for 1 h.
Cells are treated with 2% DMSO at room temperature for 1 h.


title: Pol II ChIP-nexus with spikein (5 min Triptolide treatment) Rep1

description:
kc167_triptolide_5min_polii_chipnexus_spikein_normalized_1_positive.bw
kc167_triptolide_5min_polii_chipnexus_spikein_normalized_1_negative.bw


title: Pol II ChIP-nexus with spikein (Control condtion) Rep1

description:
kc167_dmso_control_polii_chipnexus_spikein_normalized_1_positive.bw
kc167_dmso_control_polii_chipnexus_spikein_normalized_1_negative.bw


title: TFIIB ChIP-nexus Rep1

description:
kc167_tfiib_chipnexus_normalized_positive.bw
kc167_tfiib_chipnexus_normalized_negative.bw

data_processing:
Library strategy: ChIP-nexus
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Custom barcode sequences were removed from the first 9bp of each read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3
Remaining reads with length >= 22bp were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were separated by strand and reduced to a single base at the 5' end
Genome-wide coverage counts were calculated for each strand separately and normalized to reads per million
Replicates are merged together and saved as BigWig format
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain genome coordinates and counts of the first base of aligned reads, separated by alignment strand

extract_protocol:
cells were cross-linked in 1.0% formaldehyde. Cells were then lysed by lysis buffer. Chromatin was sonicated by bioruptor to an average size of 300~500 bp. ~ 20 million cells was used for one ChIP-nexus
DNA-protein-complexes were isolated with specific antibodies when still being attached to protein A-dynabeads. DNA was end repaired using NEBNext End repair module (#E6050L). A single 3'-A overhang was added to the blunted ends using NEBNext dA-Tailing module (#E6053L). Adapters with single 3'-T overhangs and 5’ overhangs (barcode composed of 5 random nucleotides) were ligated to the adenylated fragments. Ligated fragments were blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim any possible 3’ overhang. Blunted DNA was subsequently digested by lambda exonuclease first and RecJf afterwards. Digested single strand DNA was then eluted, reverse cross-linked and purified prior to self-circularization by Circligase. An oligonucleotide was mixed with circularized single DNA for subsequent BamHI digestion to linearize the single DNA again. Linearized single strand DNA was then PCR-amplified using adaptor sequences and library was purified on 2% agarose gel to remove adaptor-adaptor ligation products. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

treatment_protocol: no treatment


title: 48hpf zebrafish FAC sorted endothelial cell wt 3

value: wildtype


title: XPB ChIP-nexus (1 h Triptolide treatment) Rep2

description:
kc167_triptolide_xpb_chipnexus_normalized_and_merged_positive.bw
kc167_triptolide_xpb_chipnexus_normalized_and_merged_negative.bw

treatment_protocol: Cells are treated with 500 μM Triptolide (TOCRIS Bioscience Cat. No. 3253 dissolved in DMSO) at room temperature for 1 h.

value: anti-XPB rabbit polyclonal, Santa Cruz (sc-293)

value: GCCAAT


title: Pol II ChIP-nexus Rep1

description:
kc167_polii_chipnexus_normalized_positive.bw
kc167_polii_chipnexus_normalized_negative.bw


title: TFIIF ChIP-nexus (1 h Triptolide treatment) Rep2

description:
kc167_triptolide_tfiif_chipnexus_normalized_and_merged_positive.bw
kc167_triptolide_tfiif_chipnexus_normalized_and_merged_negative.bw

value: anti-TFIIF rabbit polyclonal, Kadonaga lab


title: XPB ChIP-nexus (1 h Triptolide treatment) Rep1

value: CAGATC


title: TFIIB ChIP-nexus (1 h Triptolide treatment) Rep2

description:
kc167_triptolide_tfiib_chipnexus_normalized_and_merged_positive.bw
kc167_triptolide_tfiib_chipnexus_normalized_and_merged_negative.bw


title: TFIIA ChIP-nexus (1 h Triptolide treatment) Rep2

description:
kc167_triptolide_tfiia_chipnexus_normalized_and_merged_positive.bw
kc167_triptolide_tfiia_chipnexus_normalized_and_merged_negative.bw


title: TFIIB ChIP-nexus (1 h Triptolide treatment) Rep1

value: ACTTGA


title: TFIIF ChIP-nexus (1 h Triptolide treatment) Rep1


title: TBP ChIP-nexus (1 h Triptolide treatment) Rep2

description:
kc167_triptolide_tbp_chipnexus_normalized_and_merged_positive.bw
kc167_triptolide_tbp_chipnexus_normalized_and_merged_negative.bw

value: anti-TBP rabbit polyclonal, Kadonaga lab


title: Pol II ChIP-nexus with spikein (30 min Triptolide treatment) Rep2

description:
kc167_triptolide_30min_polii_chipnexus_spikein_normalized_2_positive.bw
kc167_triptolide_30min_polii_chipnexus_spikein_normalized_2_negative.bw


title: TFIIA ChIP-nexus (1 h Triptolide treatment) Rep1


title: TBP ChIP-nexus (1 h Triptolide treatment) Rep1


title: TAF2 ChIP-nexus (1 h Triptolide treatment) Rep2

description:
kc167_triptolide_taf2_chipnexus_normalized_and_merged_positive.bw
kc167_triptolide_taf2_chipnexus_normalized_and_merged_negative.bw

value: anti-TAF2 guinea pig polyclonal, Verrijzer lab


title: Pol II ChIP-nexus (1 h Triptolide treatment) Rep2

description:
kc167_triptolide_polii_chipnexus_normalized_and_merged_positive.bw
kc167_triptolide_polii_chipnexus_normalized_and_merged_negative.bw

value: Kc167 cells

value: anti-RPB3 rabbit polyclonal, GenScript (custom antibody)


title: TAF2 ChIP-nexus (1 h Triptolide treatment) Rep1


title: XPB ChIP-nexus (Control condtion) Rep1

description:
kc167_dmso_xpb_chipnexus_normalized_and_merged_positive.bw
kc167_dmso_xpb_chipnexus_normalized_and_merged_negative.bw

treatment_protocol: Cells are treated with 2% DMSO at room temperature for 1 h.


title: Pol II ChIP-nexus (1 h Triptolide treatment) Rep1


title: XPB ChIP-nexus (Control condtion) Rep2

value: ACAGTG


title: TFIIB ChIP-nexus (Control condtion) Rep1

description:
kc167_dmso_tfiib_chipnexus_normalized_and_merged_positive.bw
kc167_dmso_tfiib_chipnexus_normalized_and_merged_negative.bw

value: anti-TFIIB rabbit polyclonal, Kadonaga lab


title: TFIIB ChIP-nexus (Control condtion) Rep2


title: TFIIA ChIP-nexus (Control condtion) Rep2

description:
kc167_dmso_tfiia_chipnexus_normalized_and_merged_positive.bw
kc167_dmso_tfiia_chipnexus_normalized_and_merged_negative.bw


title: TFIIA ChIP-nexus (Control condtion) Rep1

value: ATCACG


title: TFIIA ChIP-nexus Rep1

description:
kc167_tfiia_chipnexus_normalized_positive.bw
kc167_tfiia_chipnexus_normalized_negative.bw

value: anti-TFIIA rabbit polyclonal, Kadonaga lab


title: TBP ChIP-nexus (Control condtion) Rep1

description:
kc167_dmso_tbp_chipnexus_normalized_and_merged_positive.bw
kc167_dmso_tbp_chipnexus_normalized_and_merged_negative.bw


title: TAF2 ChIP-nexus (Control condtion) Rep1

description:
kc167_dmso_taf2_chipnexus_normalized_and_merged_positive.bw
kc167_dmso_taf2_chipnexus_normalized_and_merged_negative.bw


title: TAF2 ChIP-nexus (Control condtion) Rep2


title: P20_1

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

description:
ATAC-seq using WT and mutant POU5F1-eGFP reporter hESC.
Mutant clones with PRRC2A core promoter deletion derived from POU5F1-eGFP H1 hESC reporter cells purchased from WiWell Institute.

data_processing:
Library strategy: ATAC-seq
We processed our ATAC-seq data in the following steps: 1) ATAC-seq sequencing reads were mapped to hg19 reference genome using Bowtie(61) in pair-end mode; 2) poorly mapped,  improperly paired and mitochondrial reads were filtered; 3) PCR duplications were further removed using Picards MarkDuplicates (http://broadinstitute.github.io/picard.); 4) Mapping  positions of reads were adjusted accounting for Tn5 insertion; 6) Reads were next shifted for 75bp followed by peak calling using MACS2(71) with following parameters “-q 0.01 --nomodel --shift 175 –B --SPMR --keep-dup all --call-summits”; 7) ATAC-seq signal was normalized into RPKM using deeptools(72) for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: .bw

source_name: H1 POU5F1-IRES-eGFP

growth_protocol: Cells were cultured at 37 celsius degree in 5% CO2, in Essential 8 media (Stemcell Technologies).

extract_protocol:
ATAC-seq was performed by following the protocol described earlier (Buenrostro et al, Nature Method, 2013).
Briefly, each library starts with 100k cells which were permeabilized with NPB (0.2% NP-40, 5%BSA, 1Mm DTT in PBS with one complete proteinase inhibitor) at 4 degree for 10min, followed by spin down at 500g for 5min. The resulting nuclei were resuspended in 20ul 1xDMF (33mM Tris-acetate (pH=7.8), 166mM K-Acetate, 10mM Mg-Acetate, 16 % DMF). The chromatin tagmentation was done by adding 0.5ul Tn5 into 10ul solution for 30min at 37 degrees, followed by standar Illumina Tru-seq library prep protocol.

treatment_protocol:
Regular hESC culture without any special treatment.
The core promoter of MSH5 and PRRC2A was deleted by a pair of CRISPR/Cas9 targeting- 150bp to +100bp region near TSS. After picking single clones and Sanger sequencing verification of the genotype, the mutant cells and wild-type control cells were subjected to ATAC-seq analysis.

value: H1 POU5F7-eGFP reporter cells


title: P17_1

value: H1 POU5F5-eGFP reporter cells


title: H1_1

description:
ATAC-seq using WT and mutant POU5F1-eGFP reporter hESC.
POU5F1-eGFP H1 hESC reporter cells purchased from WiWell Institute.

value: H1 POU5F1-eGFP reporter cells


title: P20_2

value: H1 POU5F8-eGFP reporter cells


title: H1_2

value: H1 POU5F2-eGFP reporter cells


title: TL32

description: eGFP-/POU5F+ cells, sorted from H1 POU5F1-eGFP reporter cells after CREST-seq screen, replicate 5

data_processing:
Library strategy: 4C-Seq
4C-Seq data were mapped using 4Cseqpipe (van de Werken et al., 2012) with the first cutter set as DpnII and the second cutter set as NlaIII.
Genome_build: hg18

extract_protocol:
4C-Seq library was prepared following the protocol described in van de Werken et al. 2012 (PMID: 22961246). DpnII and NlaIII were used as the 4 base cutter in 4C-Seq.
Libraries were prepared according to Illumina's instructions, using TruSeq DNA Sample Preparation Kits v2, Set A (Cat# FC-121-2001). 4-12 library preps were mixed for multiplexed single-read sequencing using Illumina Hi-seq 2000 (Illumina).

treatment_protocol: Regular hESC culture without any special treatment.

value: H1 POU5F4-eGFP reporter cells


title: M3_1

description:
ATAC-seq using WT and mutant POU5F1-eGFP reporter hESC.
Mutant clones with MSH5 core promoter deletion derived from POU5F1-eGFP H1 hESC reporter cells purchased from WiWell Institute.

value: H1 POU5F3-eGFP reporter cells


title: TL28

description: eGFP-/POU5F+ cells, sorted from H1 POU5F1-eGFP reporter cells after CREST-seq screen, replicate 2


title: TL29

description: eGFP-/POU5F+ cells, sorted from H1 POU5F1-eGFP reporter cells after CREST-seq screen, replicate 4


title: TFIIF ChIP-nexus (Control condtion) Rep2

description:
kc167_dmso_tfiif_chipnexus_normalized_and_merged_positive.bw
kc167_dmso_tfiif_chipnexus_normalized_and_merged_negative.bw

value: anti-TFIIF rabbit polyclonal, Kadonaga lab

value: TGACCA


title: TFIIF ChIP-nexus (Control condtion) Rep1

value: CGATGT


title: MCF10A_-gf_R3

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

description:
growth factor-
MCF10A_without_growth_factors_RNA-Seq_R3

data_processing:
Remove adapter reads (Cutadapt v1.6). Trim low quality base calls from both ends,  Min score >= 20, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0).
The reads were aligned to hg38 transciptome with Tophat2 (v0.6)
Reads were quantified using HTSeq-count (v0.6) with gencode annotation (v22). Genes with very low expression (<3  counts) were removed from the analysis.
Differential gene expression was calculated by using the Deseq2 version 1.8.1 package in R 3.2.0.
Genome_build: hg38
Supplementary_files_format_and_content: Tables showing the counts from the HTSeq-count quantification.

source_name: mammary gland/breast epithelial cell

growth_protocol: MCF10a cells were grown in DMEM: F12 (Hyclone-SH30271), 5% (v/v) horse serum (Gibco #16050 lot #1075876) + 10ug/ml human insulin (Sigma I-1882)+ 20ng/ml recombinant hEGF (Peprotech AF-100-15) + 100ng/ml Cholera toxin (Sigma C-8052) + 0.5 ug/ml Hydrocortisone (Sigma H-0888) Pen/Strep (Life Technologies) and Glutamine (Life Technologies). MCF10A cells without growth factors were grown in DMEM: F12 (Hyclone-SH30271), 5% (v/v) horse serum (Gibco #16050 lot #1075876) + Pen/Strep (Life Technologies) and Glutamine (Life Technologies).

extract_protocol:
Total RNA was isolated from Trizol using Direct-zol RNA mini-prep kit (Zymo Research #R2050) with DNaseI digestion.
RNA libraries were prepared for sequencing with the TruSeq Stranded Total RNA with Ribo-Zero Gold kit using standard Illumina protocols with the exception that library amplifcation was performed using KAPA HiFi™ Real-Time PCR Library Amplification Kit (Kapa Biosystems #KK2701).
Barcoded libraries (Illumina TruSeq) were then loaded onto an Illumina HiSeq 1500 and single-end 100-base (SE100) sequencing was performed at the Advanced Genome Technologies Core Massively Parallel Sequencing Facility at UVM.

treatment_protocol: Cells were seeded at 1.5x106 cells per 100 mm dish and grown to 80% confluence. Cells were washed twice with phosphate buffered saline (PBS) and stored at -80C in TRIzol.

tag: tissue

value: breast

value: luminal ductal cells

tag: neoplasia type

value: fibrocystic disease

tag: atcc id

value: ATCC CRL-10317


title: MCF10A_-gf_R2

description:
growth factor-
MCF10A_without_growth_factors_RNA-Seq_R2


title: MCF10A_-gf_R1

description:
growth factor-
MCF10A_without_growth_factors_RNA-Seq_R1